diff --git a/addons/Pfam-A.clans.tsv b/addons/Pfam-A.clans.tsv
index d5215a0a3d54277318aaca72c91f2121621f4d11..1c34ff92a7c0e9c7588c1dc436fd7e434e2303e1 100644
--- a/addons/Pfam-A.clans.tsv
+++ b/addons/Pfam-A.clans.tsv
@@ -110,7 +110,7 @@ PF00111 CL0486 Fer2 Fer2 2Fe-2S iron-sulfur cluster binding domain
PF00112 CL0125 Peptidase_CA Peptidase_C1 Papain family cysteine protease
PF00113 CL0256 Enolase_TIM Enolase_C Enolase, C-terminal TIM barrel domain
PF00114 CL0327 Pilus Pilin Pilin (bacterial filament)
-PF00115 COX1 Cytochrome C and Quinol oxidase polypeptide I
+PF00115 CL0714 COX1-like COX1 Cytochrome C and Quinol oxidase polypeptide I
PF00116 CL0026 CU_oxidase COX2 Cytochrome C oxidase subunit II, periplasmic domain
PF00117 CL0014 Glutaminase_I GATase Glutamine amidotransferase class-I
PF00118 Cpn60_TCP1 TCP-1/cpn60 chaperonin family
@@ -222,7 +222,7 @@ PF00226 CL0392 Chaperone-J DnaJ DnaJ domain
PF00227 CL0052 NTN Proteasome Proteasome subunit
PF00228 Bowman-Birk_leg Bowman-Birk serine protease inhibitor family
PF00229 CL0100 C1q_TNF TNF TNF(Tumour Necrosis Factor) family
-PF00230 MIP Major intrinsic protein
+PF00230 CL0716 Aquaporin-like MIP Major intrinsic protein
PF00231 ATP-synt ATP synthase
PF00232 CL0058 Glyco_hydro_tim Glyco_hydro_1 Glycosyl hydrolase family 1
PF00233 CL0237 HD_PDEase PDEase_I 3'5'-cyclic nucleotide phosphodiesterase
@@ -236,7 +236,7 @@ PF00240 CL0072 Ubiquitin ubiquitin Ubiquitin family
PF00241 CL0092 ADF Cofilin_ADF Cofilin/tropomyosin-type actin-binding protein
PF00242 DNA_pol_viral_N DNA polymerase (viral) N-terminal domain
PF00243 CL0079 Cystine-knot NGF Nerve growth factor family
-PF00244 14-3-3 14-3-3 protein
+PF00244 CL0020 TPR 14-3-3 14-3-3 protein
PF00245 CL0088 Alk_phosphatase Alk_phosphatase Alkaline phosphatase
PF00246 CL0035 Peptidase_MH Peptidase_M14 Zinc carboxypeptidase
PF00248 Aldo_ket_red Aldo/keto reductase family
@@ -466,7 +466,7 @@ PF00483 CL0110 GT-A NTP_transferase Nucleotidyl transferase
PF00484 Pro_CA Carbonic anhydrase
PF00485 CL0023 P-loop_NTPase PRK Phosphoribulokinase / Uridine kinase family
PF00486 CL0123 HTH Trans_reg_C Transcriptional regulatory protein, C terminal
-PF00487 FA_desaturase Fatty acid desaturase
+PF00487 CL0713 Acyl-CoA_desat FA_desaturase Fatty acid desaturase
PF00488 CL0023 P-loop_NTPase MutS_V MutS domain V
PF00489 CL0053 4H_Cytokine IL6 Interleukin-6/G-CSF/MGF family
PF00490 CL0036 TIM_barrel ALAD Delta-aminolevulinic acid dehydratase
@@ -632,7 +632,7 @@ PF00654 Voltage_CLC Voltage gated chloride channel
PF00656 CL0093 Peptidase_CD Peptidase_C14 Caspase domain
PF00657 CL0264 SGNH_hydrolase Lipase_GDSL GDSL-like Lipase/Acylhydrolase
PF00658 PABP Poly-adenylate binding protein, unique domain
-PF00659 POLO_box POLO box duplicated region
+PF00659 CL0708 Polo-box POLO_box POLO box duplicated region
PF00660 SRP1_TIP1 Seripauperin and TIP1 family
PF00661 Matrix Viral matrix protein
PF00662 Proton_antipo_N NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
@@ -738,7 +738,7 @@ PF00765 CL0257 Acetyltrans Autoind_synth Autoinducer synthase
PF00766 CL0085 FAD_DHS ETF_alpha Electron transfer flavoprotein FAD-binding domain
PF00767 Poty_coat Potyvirus coat protein
PF00768 CL0013 Beta-lactamase Peptidase_S11 D-alanyl-D-alanine carboxypeptidase
-PF00769 ERM Ezrin/radixin/moesin family
+PF00769 CL0719 Moesin_tail ERM_C Ezrin/radixin/moesin family C terminal
PF00770 CL0125 Peptidase_CA Peptidase_C5 Adenovirus endoprotease
PF00771 FHIPEP FHIPEP family
PF00772 DnaB DnaB-like helicase N terminal domain
@@ -851,7 +851,7 @@ PF00884 CL0088 Alk_phosphatase Sulfatase Sulfatase
PF00885 DMRL_synthase 6,7-dimethyl-8-ribityllumazine synthase
PF00886 Ribosomal_S16 Ribosomal protein S16
PF00887 CL0632 FERM_M ACBP Acyl CoA binding protein
-PF00888 Cullin Cullin family
+PF00888 CL0020 TPR Cullin Cullin family
PF00889 EF_TS Elongation factor TS
PF00890 CL0063 NADP_Rossmann FAD_binding_2 FAD binding domain
PF00891 CL0063 NADP_Rossmann Methyltransf_2 O-methyltransferase domain
@@ -930,7 +930,7 @@ PF00967 CL0199 DPBB Barwin Barwin family
PF00969 CL0343 MHC MHC_II_beta Class II histocompatibility antigen, beta domain
PF00970 CL0076 FAD_Lum_binding FAD_binding_6 Oxidoreductase FAD-binding domain
PF00971 EIAV_GP90 EIAV coat protein, gp90
-PF00972 CL0027 RdRP Flavi_NS5 Flavivirus RNA-directed RNA polymerase
+PF00972 CL0027 RdRP Flavi_NS5 Flavivirus RNA-directed RNA polymerase, fingers and palm domains
PF00973 CL0156 Nucleocapsid Paramyxo_ncap Paramyxovirus nucleocapsid protein
PF00974 Rhabdo_glycop Rhabdovirus spike glycoprotein
PF00975 CL0028 AB_hydrolase Thioesterase Thioesterase domain
@@ -989,7 +989,7 @@ PF01031 Dynamin_M Dynamin central region
PF01032 CL0142 Membrane_trans FecCD FecCD transport family
PF01033 Somatomedin_B Somatomedin B domain
PF01034 Syndecan Syndecan domain
-PF01035 DNA_binding_1 6-O-methylguanine DNA methyltransferase, DNA binding domain
+PF01035 CL0123 HTH DNA_binding_1 6-O-methylguanine DNA methyltransferase, DNA binding domain
PF01036 CL0192 GPCR_A Bac_rhodopsin Bacteriorhodopsin-like protein
PF01037 CL0032 Dim_A_B_barrel AsnC_trans_reg Lrp/AsnC ligand binding domain
PF01039 CL0127 ClpP_crotonase Carboxyl_trans Carboxyl transferase domain
@@ -1000,7 +1000,7 @@ PF01043 SecA_PP_bind SecA preprotein cross-linking domain
PF01044 CL0705 VBS-like Vinculin Vinculin family
PF01047 CL0123 HTH MarR MarR family
PF01048 CL0408 PUP PNP_UDP_1 Phosphorylase superfamily
-PF01049 Cadherin_C Cadherin cytoplasmic region
+PF01049 CADH_Y-type_LIR Cadherin, Y-type LIR-motif
PF01050 CL0029 Cupin MannoseP_isomer Mannose-6-phosphate isomerase
PF01051 CL0123 HTH Rep_3 Initiator Replication protein
PF01052 FliMN_C Type III flagellar switch regulator (C-ring) FliN C-term
@@ -1143,7 +1143,7 @@ PF01199 Ribosomal_L34e Ribosomal protein L34e
PF01200 CL0021 OB Ribosomal_S28e Ribosomal protein S28e
PF01201 Ribosomal_S8e Ribosomal protein S8e
PF01202 CL0023 P-loop_NTPase SKI Shikimate kinase
-PF01203 T2SSN Type II secretion system (T2SS), protein N
+PF01203 CL0401 AsmA-like T2SSN Type II secretion system (T2SS), protein N
PF01204 CL0059 6_Hairpin Trehalase Trehalase
PF01205 CL0329 S5 UPF0029 Uncharacterized protein family UPF0029
PF01206 CL0397 TusA-like TusA Sulfurtransferase TusA
@@ -1164,7 +1164,7 @@ PF01221 Dynein_light Dynein light chain type 1
PF01222 CL0115 Steroid_dh ERG4_ERG24 Ergosterol biosynthesis ERG4/ERG24 family
PF01223 CL0263 His-Me_finger Endonuclease_NS DNA/RNA non-specific endonuclease
PF01225 CL0063 NADP_Rossmann Mur_ligase Mur ligase family, catalytic domain
-PF01226 Form_Nir_trans Formate/nitrite transporter
+PF01226 CL0716 Aquaporin-like Form_Nir_trans Formate/nitrite transporter
PF01227 CL0334 THBO-biosyn GTP_cyclohydroI GTP cyclohydrolase I
PF01228 CL0339 PFL-like Gly_radical Glycine radical
PF01229 CL0058 Glyco_hydro_tim Glyco_hydro_39 Glycosyl hydrolases family 39
@@ -1175,7 +1175,7 @@ PF01233 CL0257 Acetyltrans NMT Myristoyl-CoA:protein N-myristoyltransferase, N-t
PF01234 CL0063 NADP_Rossmann NNMT_PNMT_TEMT NNMT/PNMT/TEMT family
PF01235 CL0062 APC Na_Ala_symp Sodium:alanine symporter family
PF01237 Oxysterol_BP Oxysterol-binding protein
-PF01238 CL0029 Cupin PMI_typeI Phosphomannose isomerase type I
+PF01238 CL0029 Cupin PMI_typeI_C Phosphomannose isomerase type I C-terminal
PF01239 CL0020 TPR PPTA Protein prenyltransferase alpha subunit repeat
PF01241 PSI_PSAK Photosystem I psaG / psaK
PF01242 CL0334 THBO-biosyn PTPS 6-pyruvoyl tetrahydropterin synthase
@@ -1234,7 +1234,7 @@ PF01295 Adenylate_cycl Adenylate cyclase, class-I
PF01296 Galanin Galanin
PF01297 CL0043 Chelatase ZnuA Zinc-uptake complex component A periplasmic
PF01298 CL0193 MBB TbpB_B_D C-lobe and N-lobe beta barrels of Tf-binding protein B
-PF01299 Lamp Lysosome-associated membrane glycoprotein (Lamp)
+PF01299 CL0721 LAMP Lamp Lysosome-associated membrane glycoprotein (Lamp)
PF01300 Sua5_yciO_yrdC Telomere recombination
PF01301 CL0058 Glyco_hydro_tim Glyco_hydro_35 Glycosyl hydrolases family 35
PF01302 CL0010 SH3 CAP_GLY CAP-Gly domain
@@ -1292,7 +1292,7 @@ PF01359 CL0219 RNase_H Transposase_1 Transposase (partial DDE domain)
PF01361 CL0082 MIF Tautomerase Tautomerase enzyme
PF01363 CL0390 zf-FYVE-PHD FYVE FYVE zinc finger
PF01364 CL0093 Peptidase_CD Peptidase_C25 Peptidase family C25
-PF01365 RYDR_ITPR RIH domain
+PF01365 CL0020 TPR RYDR_ITPR RIH domain
PF01366 PRTP Herpesvirus processing and transport protein
PF01367 CL0464 5_3_exonuc_C 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold
PF01368 CL0137 HAD DHH DHH family
@@ -1323,13 +1323,13 @@ PF01393 CL0049 Tudor Chromo_shadow Chromo shadow domain
PF01394 CL0020 TPR Clathrin_propel Clathrin propeller repeat
PF01395 PBP_GOBP PBP/GOBP family
PF01396 CL0167 Zn_Beta_Ribbon zf-C4_Topoisom Topoisomerase DNA binding C4 zinc finger
-PF01397 Terpene_synth Terpene synthase, N-terminal domain
+PF01397 CL0059 6_Hairpin Terpene_synth Terpene synthase, N-terminal domain
PF01398 CL0366 JAB JAB JAB1/Mov34/MPN/PAD-1 ubiquitin protease
PF01399 CL0123 HTH PCI PCI domain
PF01400 CL0126 Peptidase_MA Astacin Astacin (Peptidase family M12A)
PF01401 CL0126 Peptidase_MA Peptidase_M2 Angiotensin-converting enzyme
PF01402 CL0057 Met_repress RHH_1 Ribbon-helix-helix protein, copG family
-PF01403 Sema Sema domain
+PF01403 CL0186 Beta_propeller Sema Sema domain
PF01404 CL0202 GBD Ephrin_lbd Ephrin receptor ligand binding domain
PF01405 PsbT Photosystem II reaction centre T protein
PF01406 CL0039 HUP tRNA-synt_1e tRNA synthetases class I (C) catalytic domain
@@ -1377,7 +1377,7 @@ PF01450 CL0106 6PGD_C IlvC Acetohydroxy acid isomeroreductase, catalytic domain
PF01451 CL0031 Phosphatase LMWPc Low molecular weight phosphotyrosine protein phosphatase
PF01452 Rota_NSP4 Rotavirus non structural protein
PF01453 CL0186 Beta_propeller B_lectin D-mannose binding lectin
-PF01454 CL0123 HTH MAGE MAGE family
+PF01454 CL0123 HTH MAGE MAGE homology domain
PF01455 HupF_HypC HupF/HypC family
PF01456 Mucin Mucin-like glycoprotein
PF01457 CL0126 Peptidase_MA Peptidase_M8 Leishmanolysin
@@ -1443,12 +1443,12 @@ PF01522 CL0158 GH_CE Polysacc_deac_1 Polysaccharide deacetylase
PF01523 PmbA_TldD PmbA/TldA metallopeptidase domain 1
PF01524 Gemini_V2 Geminivirus V2 protein
PF01525 Rota_NS26 Rotavirus NS26
-PF01526 DDE_Tnp_Tn3 Tn3 transposase DDE domain
+PF01526 CL0219 RNase_H DDE_Tnp_Tn3 Tn3 transposase DDE domain
PF01527 CL0123 HTH HTH_Tnp_1 Transposase
PF01528 Herpes_glycop Herpesvirus glycoprotein M
PF01529 DHHC DHHC palmitoyltransferase
PF01530 zf-C2HC Zinc finger, C2HC type
-PF01531 Glyco_transf_11 Glycosyl transferase family 11
+PF01531 CL0113 GT-B Glyco_transf_11 Glycosyl transferase family 11
PF01532 CL0059 6_Hairpin Glyco_hydro_47 Glycosyl hydrolase family 47
PF01533 Tospo_nucleocap Tospovirus nucleocapsid protein
PF01534 CL0192 GPCR_A Frizzled Frizzled/Smoothened family membrane region
@@ -1508,7 +1508,7 @@ PF01591 CL0023 P-loop_NTPase 6PF2K 6-phosphofructo-2-kinase
PF01592 CL0233 SufE_NifU NifU_N NifU-like N terminal domain
PF01593 CL0063 NADP_Rossmann Amino_oxidase Flavin containing amine oxidoreductase
PF01594 AI-2E_transport AI-2E family transporter
-PF01595 DUF21 Cyclin M transmembrane N-terminal domain
+PF01595 CNNM Cyclin M transmembrane N-terminal domain
PF01596 CL0063 NADP_Rossmann Methyltransf_3 O-methyltransferase
PF01597 CL0105 Hybrid GCV_H Glycine cleavage H-protein
PF01599 CL0167 Zn_Beta_Ribbon Ribosomal_S27 Ribosomal protein S27a
@@ -1627,7 +1627,7 @@ PF01728 CL0063 NADP_Rossmann FtsJ FtsJ-like methyltransferase
PF01729 CL0036 TIM_barrel QRPTase_C Quinolinate phosphoribosyl transferase, C-terminal domain
PF01730 UreF UreF
PF01731 CL0186 Beta_propeller Arylesterase Arylesterase
-PF01732 CL0124 Peptidase_PA DUF31 Putative peptidase (DUF31)
+PF01732 CL0124 Peptidase_PA Mycop_pep_DUF31 Mycoplasma peptidase (DUF31)
PF01733 CL0015 MFS Nucleoside_tran Nucleoside transporter
PF01734 CL0323 Patatin Patatin Patatin-like phospholipase
PF01735 CL0323 Patatin PLA2_B Lysophospholipase catalytic domain
@@ -1745,9 +1745,9 @@ PF01855 CL0254 THDP-binding POR_N Pyruvate flavodoxin/ferredoxin oxidoreductase,
PF01856 CL0193 MBB HP_OMP Helicobacter outer membrane protein
PF01857 CL0065 Cyclin RB_B Retinoblastoma-associated protein B domain
PF01858 CL0065 Cyclin RB_A Retinoblastoma-associated protein A domain
-PF01861 CL0063 NADP_Rossmann DUF43 Branched-chain polyamine synthase A C-terminal domain
+PF01861 CL0063 NADP_Rossmann BpsA_C Branched-chain polyamine synthase A C-terminal domain
PF01862 PvlArgDC Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
-PF01863 CL0126 Peptidase_MA DUF45 Protein of unknown function DUF45
+PF01863 CL0126 Peptidase_MA YgjP-like YgjP-like, metallopeptidase domain
PF01864 CL0234 CTPT CarS-like CDP-archaeol synthase
PF01865 CL0297 PhoU PhoU_div Protein of unknown function DUF47
PF01866 Diphthamide_syn Putative diphthamide synthesis protein
@@ -1764,13 +1764,13 @@ PF01876 CL0034 Amidohydrolase RNase_P_p30 RNase P subunit p30
PF01877 RNA_binding RNA binding
PF01878 CL0178 PUA EVE EVE domain
PF01880 CL0503 SOR Desulfoferrodox Desulfoferrodoxin
-PF01881 CL0362 RAMPS-Cas5-like Cas_Cas6 CRISPR associated protein Cas6
+PF01881 CL0362 RAMPS-Cas5-like Cas_Cas6_C CRISPR associated protein Cas6, C-terminal
PF01882 CL0128 vWA-like DUF58 Protein of unknown function DUF58
PF01883 CL0232 NifU FeS_assembly_P Iron-sulfur cluster assembly protein
PF01884 CL0036 TIM_barrel PcrB PcrB family
PF01885 CL0084 ADP-ribosyl PTS_2-RNA RNA 2'-phosphotransferase, Tpt1 / KptA family
PF01886 DUF61 Protein of unknown function DUF61
-PF01887 SAM_adeno_trans S-adenosyl-l-methionine hydroxide adenosyltransferase
+PF01887 SAM_HAT_N SAM hydroxide adenosyltransferase N-terminal domain
PF01888 CbiD CbiD
PF01889 DUF63 Membrane protein of unknown function DUF63
PF01890 CbiG_C Cobalamin synthesis G C-terminus
@@ -1795,7 +1795,7 @@ PF01913 FTR Formylmethanofuran-tetrahydromethanopterin formyltransferase
PF01914 CL0292 LysE MarC MarC family integral membrane protein
PF01915 Glyco_hydro_3_C Glycosyl hydrolase family 3 C-terminal domain
PF01916 CL0085 FAD_DHS DS Deoxyhypusine synthase
-PF01917 CL0159 E-set Arch_flagellin Archaebacterial flagellin
+PF01917 CL0327 Pilus Arch_flagellin Archaebacterial flagellin
PF01918 CL0441 AlbA Alba Alba
PF01920 CL0200 Prefoldin Prefoldin_2 Prefoldin subunit
PF01921 CL0039 HUP tRNA-synt_1f tRNA synthetases class I (K)
@@ -1810,7 +1810,7 @@ PF01929 CL0107 KOW Ribosomal_L14e Ribosomal protein L14
PF01930 CL0236 PDDEXK Cas_Cas4 Domain of unknown function DUF83
PF01931 CL0269 Maf NTPase_I-T Protein of unknown function DUF84
PF01933 CofD 2-phospho-L-lactate transferase CofD
-PF01934 CL0291 KNTase_C DUF86 Protein of unknown function DUF86
+PF01934 CL0291 KNTase_C HepT-like Ribonuclease HepT-like
PF01935 CL0023 P-loop_NTPase DUF87 Helicase HerA, central domain
PF01936 CL0280 PIN NYN NYN domain
PF01937 ARMT1-like_dom Damage-control phosphatase ARMT1-like domain
@@ -1821,16 +1821,16 @@ PF01941 AdoMet_Synthase S-adenosylmethionine synthetase (AdoMet synthetase)
PF01943 CL0222 MviN_MATE Polysacc_synt Polysaccharide biosynthesis protein
PF01944 SpoIIM Stage II sporulation protein M
PF01946 CL0063 NADP_Rossmann Thi4 Thi4 family
-PF01947 CL0122 UTRA DUF98 p-hydroxybenzoic acid synthase
+PF01947 CL0122 UTRA Rv2949c-like Chorismate pyruvate-lyase Rv2949c-like
PF01948 PyrI Aspartate carbamoyltransferase regulatory chain, allosteric domain
PF01949 CL0219 RNase_H DUF99 Protein of unknown function DUF99
PF01950 FBPase_3 Fructose-1,6-bisphosphatase
PF01951 CL0319 SHS2 Archease Archease protein family (MTH1598/TM1083)
-PF01954 DUF104 Protein of unknown function DUF104
+PF01954 AF2212-like AF2212-like
PF01955 CbiZ Adenosylcobinamide amidohydrolase
PF01956 CL0376 Oxa1 EMC3_TMCO1 Integral membrane protein EMC3/TMCO1-like
PF01957 CL0021 OB NfeD NfeD-like C-terminal, partner-binding
-PF01958 CL0139 GADPH_aa-bio_dh DUF108 Domain of unknown function DUF108
+PF01958 CL0139 GADPH_aa-bio_dh Asp_DH_C Aspartate dehydrogenase, C-terminal
PF01959 DHQS 3-dehydroquinate synthase II
PF01960 CL0635 DmpA_ArgJ ArgJ ArgJ family
PF01963 CL0572 TIKI TraB_PrgY_gumN TraB/PrgY/gumN family
@@ -1839,10 +1839,10 @@ PF01965 CL0014 Glutaminase_I DJ-1_PfpI DJ-1/PfpI family
PF01966 CL0237 HD_PDEase HD HD domain
PF01967 MoaC MoaC family
PF01968 CL0108 Actin_ATPase Hydantoinase_A Hydantoinase/oxoprolinase
-PF01969 DUF111 Protein of unknown function DUF111
+PF01969 Ni_insertion Nickel insertion protein
PF01970 TctA Tripartite tricarboxylate transporter TctA family
PF01972 CL0127 ClpP_crotonase SDH_sah Serine dehydrogenase proteinase
-PF01973 MAF_flag10 Protein of unknown function DUF115
+PF01973 MptE-like 6-hydroxymethylpterin diphosphokinase MptE-like
PF01974 CL0236 PDDEXK tRNA_int_endo tRNA intron endonuclease, catalytic C-terminal domain
PF01975 SurE Survival protein SurE
PF01976 DUF116 Protein of unknown function DUF116
@@ -1858,7 +1858,7 @@ PF01985 CRS1_YhbY CRS1 / YhbY (CRM) domain
PF01986 CL0418 GIY-YIG DUF123 Domain of unknown function DUF123
PF01987 CL0029 Cupin AIM24 Mitochondrial biogenesis AIM24
PF01988 VIT1 VIT family
-PF01989 CL0364 Leu-IlvD DUF126 Aconitase X swivel domain
+PF01989 CL0364 Leu-IlvD AcnX_swivel_put Aconitase X swivel domain
PF01990 ATP-synt_F ATP synthase (F/14-kDa) subunit
PF01991 CL0255 ATP_synthase vATP-synt_E ATP synthase (E/31 kDa) subunit
PF01992 vATP-synt_AC39 ATP synthase (C/AC39) subunit
@@ -1934,7 +1934,7 @@ PF02072 Orexin Prepro-orexin
PF02073 Peptidase_M29 Thermophilic metalloprotease (M29)
PF02074 CL0126 Peptidase_MA Peptidase_M32 Carboxypeptidase Taq (M32) metallopeptidase
PF02075 CL0219 RNase_H RuvC Crossover junction endodeoxyribonuclease RuvC
-PF02076 STE3 Pheromone A receptor
+PF02076 CL0192 GPCR_A STE3 Pheromone A receptor
PF02077 CL0131 DoxD-like SURF4 SURF4 family
PF02078 CL0483 PreATP-grasp Synapsin Synapsin, N-terminal domain
PF02079 TP1 Nuclear transition protein 1
@@ -2001,7 +2001,7 @@ PF02149 CL0573 KA1-like KA1 Kinase associated domain 1
PF02150 CL0167 Zn_Beta_Ribbon RNA_POL_M_15KD RNA polymerases M/15 Kd subunit
PF02151 CL0671 AAA_lid UVR UvrB/uvrC motif
PF02152 CL0334 THBO-biosyn FolB Dihydroneopterin aldolase
-PF02153 CL0063 NADP_Rossmann PDH Prephenate dehydrogenase
+PF02153 CL0063 NADP_Rossmann PDH_N Prephenate dehydrogenase, nucleotide-binding domain
PF02154 CL0355 CheC-like FliM Flagellar motor switch protein FliM
PF02155 GCR Glucocorticoid receptor
PF02156 CL0058 Glyco_hydro_tim Glyco_hydro_26 Glycosyl hydrolase family 26
@@ -2040,7 +2040,7 @@ PF02190 CL0178 PUA LON_substr_bdg ATP-dependent protease La (LON) substrate-bind
PF02191 CL0434 Sialidase OLF Olfactomedin-like domain
PF02192 CL0072 Ubiquitin PI3K_p85B PI3-kinase family, p85-binding domain
PF02194 PXA PXA domain
-PF02195 CL0248 ParBc ParBc ParB-like nuclease domain
+PF02195 CL0248 ParBc ParBc ParB/Sulfiredoxin domain
PF02196 CL0072 Ubiquitin RBD Raf-like Ras-binding domain
PF02197 CL0068 RIIa RIIa Regulatory subunit of type II PKA R-subunit
PF02198 CL0003 SAM SAM_PNT Sterile alpha motif (SAM)/Pointed domain
@@ -2216,7 +2216,7 @@ PF02388 CL0257 Acetyltrans FemAB FemAB family
PF02389 Cornifin Cornifin (SPRR) family
PF02390 CL0063 NADP_Rossmann Methyltransf_4 Putative methyltransferase
PF02391 MoaE MoaE protein
-PF02392 Ycf4 Ycf4
+PF02392 CL0266 PH Ycf4 Ycf4
PF02393 CL0526 SUKH US22 US22 like
PF02394 IL1_propep Interleukin-1 propeptide
PF02395 CL0124 Peptidase_PA Peptidase_S6 Immunoglobulin A1 protease
@@ -2301,11 +2301,11 @@ PF02478 Pneumo_phosprot Pneumovirus phosphoprotein
PF02479 Herpes_IE68 Herpesvirus immediate early protein
PF02480 CL0011 Ig Herpes_gE Alphaherpesvirus glycoprotein E
PF02481 CL0349 SLOG DNA_processg_A DNA recombination-mediator protein A
-PF02482 Ribosomal_S30AE Sigma 54 modulation protein / S30EA ribosomal protein
+PF02482 CL0219 RNase_H Ribosomal_S30AE Sigma 54 modulation protein / S30EA ribosomal protein
PF02484 Rhabdo_NV Rhabdovirus Non-virion protein
PF02485 CL0110 GT-A Branch Core-2/I-Branching enzyme
PF02486 CL0407 TBP-like Rep_trans Replication initiation factor
-PF02487 CLN3 CLN3 protein
+PF02487 CL0015 MFS CLN3 CLN3 protein
PF02488 EMA Merozoite Antigen
PF02489 Herpes_glycop_H Herpesvirus glycoprotein H main domain
PF02491 CL0319 SHS2 SHS2_FTSA SHS2 domain inserted in FTSA
@@ -2336,7 +2336,7 @@ PF02516 CL0111 GT-C STT3 Oligosaccharyl transferase STT3 subunit
PF02517 CL0472 Peptidase_U Rce1-like Type II CAAX prenyl endopeptidase Rce1-like
PF02518 CL0025 His_Kinase_A HATPase_c Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
PF02519 Auxin_inducible Auxin responsive protein
-PF02520 DUF148 Domain of unknown function DUF148
+PF02520 ANIS5_cation-bd SXP/RAL-2 family protein Ani s 5-like, metal-binding domain
PF02521 CL0193 MBB HP_OMP_2 Putative outer membrane protein
PF02522 CL0627 Antibiotic_NAT Antibiotic_NAT Aminoglycoside 3-N-acetyltransferase
PF02524 KID KID repeat
@@ -2383,14 +2383,14 @@ PF02570 CbiC Precorrin-8X methylmutase
PF02571 CL0063 NADP_Rossmann CbiJ Precorrin-6x reductase CbiJ/CobK
PF02572 CL0023 P-loop_NTPase CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
PF02574 S-methyl_trans Homocysteine S-methyltransferase
-PF02575 YbaB_DNA_bd YbaB/EbfC DNA-binding family
-PF02576 DUF150 RimP N-terminal domain
-PF02577 DUF151 Domain of unknown function (DUF151)
+PF02575 CL0717 YbaB YbaB_DNA_bd YbaB/EbfC DNA-binding family
+PF02576 RimP_N RimP N-terminal domain
+PF02577 BFN_dom Bifunctional nuclease domain
PF02578 CL0663 CNF1_YfiH Cu-oxidase_4 Multi-copper polyphenol oxidoreductase laccase
PF02579 Nitro_FeMo-Co Dinitrogenase iron-molybdenum cofactor
PF02580 Tyr_Deacylase D-Tyr-tRNA(Tyr) deacylase
PF02581 CL0036 TIM_barrel TMP-TENI Thiamine monophosphate synthase
-PF02582 DUF155 Uncharacterised ACR, YagE family COG1723
+PF02582 DUF155 RMND1/Sif2-Sif3/Mrx10, DUF155
PF02583 Trns_repr_metal Metal-sensitive transcriptional repressor
PF02585 PIG-L GlcNAc-PI de-N-acetylase
PF02586 SRAP SOS response associated peptidase (SRAP)
@@ -2398,7 +2398,7 @@ PF02588 CL0181 ABC-2 YitT_membrane Uncharacterised 5xTM membrane BCR, YitT famil
PF02589 CL0246 ISOCOT_Fold LUD_dom LUD domain
PF02590 CL0098 SPOUT SPOUT_MTase Predicted SPOUT methyltransferase
PF02591 CL0167 Zn_Beta_Ribbon zf-RING_7 C4-type zinc ribbon domain
-PF02592 Vut_1 Putative vitamin uptake transporter
+PF02592 CL0315 Gx_transp Vut_1 Putative vitamin uptake transporter
PF02593 CL0063 NADP_Rossmann DUF166 Domain of unknown function
PF02594 DUF167 Uncharacterised ACR, YggU family COG1872
PF02595 Gly_kinase Glycerate kinase family
@@ -2474,7 +2474,7 @@ PF02673 CL0292 LysE BacA Bacitracin resistance protein BacA
PF02674 CL0292 LysE Colicin_V Colicin V production protein
PF02675 CL0407 TBP-like AdoMet_dc S-adenosylmethionine decarboxylase
PF02676 TYW3 Methyltransferase TYW3
-PF02677 QueH Epoxyqueuosine reductase QueH
+PF02677 CL0039 HUP QueH Epoxyqueuosine reductase QueH
PF02678 CL0029 Cupin Pirin Pirin
PF02679 CL0036 TIM_barrel ComA (2R)-phospho-3-sulfolactate synthase (ComA)
PF02680 DUF211 Uncharacterized ArCR, COG1888
@@ -2504,7 +2504,7 @@ PF02707 MOSP_N Major Outer Sheath Protein N-terminal region
PF02709 CL0110 GT-A Glyco_transf_7C N-terminal domain of galactosyltransferase
PF02710 Hema_HEFG Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein
PF02711 Pap_E4 E4 protein
-PF02713 DUF220 Domain of unknown function DUF220
+PF02713 CL0209 Bet_v_1_like DUF220 Domain of unknown function DUF220
PF02714 CL0416 Anoctamin-like RSN1_7TM Calcium-dependent channel, 7TM region, putative phosphate
PF02718 Herpes_UL31 Herpesvirus UL31-like protein
PF02719 CL0063 NADP_Rossmann Polysacc_synt_2 Polysaccharide biosynthesis protein
@@ -2525,7 +2525,7 @@ PF02734 Dak2 DAK2 domain
PF02735 CL0616 SPOC Ku Ku70/Ku80 beta-barrel domain
PF02736 CL0010 SH3 Myosin_N Myosin N-terminal SH3-like domain
PF02737 CL0063 NADP_Rossmann 3HCDH_N 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
-PF02738 Ald_Xan_dh_C2 Molybdopterin-binding domain of aldehyde dehydrogenase
+PF02738 CL0635 DmpA_ArgJ MoCoBD_1 Molybdopterin cofactor-binding domain
PF02739 CL0280 PIN 5_3_exonuc_N 5'-3' exonuclease, N-terminal resolvase-like domain
PF02740 CL0621 Colipase Colipase_C Colipase, C-terminal domain
PF02741 FTR_C FTR, proximal lobe
@@ -2637,12 +2637,12 @@ PF02865 STAT_int STAT protein, protein interaction domain
PF02866 CL0341 LDH_C Ldh_1_C lactate/malate dehydrogenase, alpha/beta C-terminal domain
PF02867 CL0339 PFL-like Ribonuc_red_lgC Ribonucleotide reductase, barrel domain
PF02868 CL0126 Peptidase_MA Peptidase_M4_C Thermolysin metallopeptidase, alpha-helical domain
-PF02870 Methyltransf_1N 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
+PF02870 CL0219 RNase_H Methyltransf_1N 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
PF02872 5_nucleotid_C 5'-nucleotidase, C-terminal domain
PF02873 MurB_C UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain
PF02874 CL0275 HAS-barrel ATP-synt_ab_N ATP synthase alpha/beta family, beta-barrel domain
PF02875 Mur_ligase_C Mur ligase family, glutamate ligase domain
-PF02876 CL0386 Ant-toxin_C Stap_Strp_tox_C Staphylococcal/Streptococcal toxin, beta-grasp domain
+PF02876 CL0072 Ubiquitin Stap_Strp_tox_C Staphylococcal/Streptococcal toxin, beta-grasp domain
PF02877 PARP_reg Poly(ADP-ribose) polymerase, regulatory domain
PF02878 PGM_PMM_I Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
PF02879 PGM_PMM_II Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
@@ -2741,8 +2741,8 @@ PF02976 CL0236 PDDEXK MutH DNA mismatch repair enzyme MutH
PF02977 CL0096 Pept_Inhib_IE CarbpepA_inh Carboxypeptidase A inhibitor
PF02978 CL0123 HTH SRP_SPB Signal peptide binding domain
PF02979 NHase_alpha Nitrile hydratase, alpha chain
-PF02980 CL0123 HTH FokI_C Restriction endonuclease FokI, catalytic domain
-PF02981 CL0123 HTH FokI_N Restriction endonuclease FokI, recognition domain
+PF02980 CL0123 HTH FokI_dom_2 FokI, recognition domain, subdomain 2
+PF02981 CL0123 HTH FokI_D1 FokI, recognition domain, subdomain 1
PF02982 CL0051 NTF2 Scytalone_dh Scytalone dehydratase
PF02983 Pro_Al_protease Alpha-lytic protease prodomain
PF02984 CL0065 Cyclin Cyclin_C Cyclin, C-terminal domain
@@ -2792,7 +2792,7 @@ PF03032 FSAP_sig_propep Frog skin active peptide family signal and propeptide
PF03033 CL0113 GT-B Glyco_transf_28 Glycosyltransferase family 28 N-terminal domain
PF03034 PSS Phosphatidyl serine synthase
PF03035 RNA_capsid Calicivirus putative RNA polymerase/capsid protein
-PF03036 Perilipin Perilipin family
+PF03036 CL0718 Perilipin_sf Perilipin Perilipin family
PF03037 KMP11 Kinetoplastid membrane protein 11
PF03038 Herpes_UL95 UL95 family
PF03039 CL0053 4H_Cytokine IL12 Interleukin-12 alpha subunit
@@ -2809,8 +2809,8 @@ PF03050 CL0219 RNase_H DDE_Tnp_IS66 Transposase IS66 family
PF03051 CL0125 Peptidase_CA Peptidase_C1_2 Peptidase C1-like family
PF03052 Adeno_52K Adenoviral protein L1 52/55-kDa
PF03053 Corona_NS3b ORF3b coronavirus protein
-PF03054 CL0039 HUP tRNA_Me_trans tRNA methyl transferase
-PF03055 RPE65 Retinal pigment epithelial membrane protein
+PF03054 CL0039 HUP tRNA_Me_trans tRNA methyl transferase HUP domain
+PF03055 CL0186 Beta_propeller RPE65 Retinal pigment epithelial membrane protein
PF03057 DUF236 DUF236 repeat
PF03058 Sar8_2 Sar8.2 family
PF03059 CL0063 NADP_Rossmann NAS Nicotianamine synthase protein
@@ -2840,7 +2840,7 @@ PF03083 CL0141 MtN3-like MtN3_slv Sugar efflux transporter for intercellular exc
PF03084 Sigma_1_2 Reoviral Sigma1/Sigma2 family
PF03085 RAP-1 Rhoptry-associated protein 1 (RAP-1)
PF03086 DUF240 Domain of unknown function (DUF240)
-PF03087 CL0133 AT14A-like DUF241 Arabidopsis protein of unknown function
+PF03087 CL0133 AT14A-like BPS1 Protein BPS1
PF03088 CL0186 Beta_propeller Str_synth Strictosidine synthase
PF03089 CL0186 Beta_propeller RAG2 Recombination activating protein 2
PF03090 CL0243 AEP Replicase Replicase family
@@ -2849,7 +2849,7 @@ PF03092 CL0015 MFS BT1 BT1 family
PF03094 Mlo Mlo family
PF03095 PTPA Phosphotyrosyl phosphate activator (PTPA) protein
PF03096 CL0028 AB_hydrolase Ndr Ndr family
-PF03097 BRO1 BRO1-like domain
+PF03097 CL0020 TPR BRO1 BRO1-like domain
PF03098 CL0617 Peroxidase An_peroxidase Animal haem peroxidase
PF03099 CL0040 tRNA_synt_II BPL_LplA_LipB Biotin/lipoate A/B protein ligase family
PF03100 CL0021 OB CcmE CcmE
@@ -2927,7 +2927,6 @@ PF03178 CL0186 Beta_propeller CPSF_A CPSF A subunit region
PF03179 CL0255 ATP_synthase V-ATPase_G Vacuolar (H+)-ATPase G subunit
PF03180 CL0177 PBP Lipoprotein_9 NlpA lipoprotein
PF03181 BURP BURP domain
-PF03183 Borrelia_rep Borrelia repeat protein
PF03184 CL0219 RNase_H DDE_1 DDE superfamily endonuclease
PF03185 CaKB Calcium-activated potassium channel, beta subunit
PF03186 CL0685 AmpE_CobD-like CobD_Cbib CobD/Cbib protein
@@ -2996,7 +2995,7 @@ PF03253 UT Urea transporter
PF03254 XG_FTase Xyloglucan fucosyltransferase
PF03255 CL0127 ClpP_crotonase ACCA Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
PF03256 CL0202 GBD ANAPC10 Anaphase-promoting complex, subunit 10 (APC10)
-PF03257 Adhesin_P1 Mycoplasma adhesin P1
+PF03257 Adhesin_P1_C Mycoplasma adhesin P1, C-terminal
PF03258 Baculo_FP Baculovirus FP protein
PF03259 CL0431 PF Robl_LC7 Roadblock/LC7 domain
PF03260 CL0066 Trefoil Lipoprotein_11 Lepidopteran low molecular weight (30 kD) lipoprotein
@@ -3019,7 +3018,7 @@ PF03277 Herpes_UL4 Herpesvirus UL4 family
PF03278 IpaB_EvcA IpaB/EvcA family
PF03279 CL0228 Acyltransferase Lip_A_acyltrans Bacterial lipid A biosynthesis acyltransferase
PF03280 Lipase_chap Proteobacterial lipase chaperone protein
-PF03281 Mab-21 Mab-21 protein
+PF03281 CL0260 NTP_transf Mab-21 Mab-21 protein nucleotidyltransferase domain
PF03283 CL0028 AB_hydrolase PAE Pectinacetylesterase
PF03284 CL0051 NTF2 PHZA_PHZB Phenazine biosynthesis protein A/B
PF03285 Paralemmin Paralemmin
@@ -3047,7 +3046,7 @@ PF03306 CL0615 ALDC AAL_decarboxy Alpha-acetolactate decarboxylase
PF03307 Adeno_E3_15_3 Adenovirus 15.3kD protein in E3 region
PF03308 CL0023 P-loop_NTPase MeaB Methylmalonyl Co-A mutase-associated GTPase MeaB
PF03309 CL0108 Actin_ATPase Pan_kinase Type III pantothenate kinase
-PF03310 Cauli_DNA-bind Caulimovirus DNA-binding protein
+PF03310 CL0720 Lag3_N Cauli_DNA-bind Caulimovirus DNA-binding protein
PF03311 Cornichon Cornichon protein
PF03312 DUF272 Protein of unknown function (DUF272)
PF03313 SDH_alpha Serine dehydratase alpha chain
@@ -3087,7 +3086,7 @@ PF03350 UPF0114 Uncharacterized protein family, UPF0114
PF03351 CL0559 CBD9-like DOMON DOMON domain
PF03352 Adenine_glyco Methyladenine glycosylase
PF03353 Lin-8 Ras-mediated vulval-induction antagonist
-PF03354 CL0023 P-loop_NTPase Terminase_1 Phage Terminase
+PF03354 CL0023 P-loop_NTPase TerL_ATPase Terminase large subunit, ATPase domain
PF03355 Pox_TAP Viral Trans-Activator Protein
PF03356 Pox_LP_H2 Viral late protein H2
PF03357 CL0235 PspA Snf7 Snf7
@@ -3129,7 +3128,7 @@ PF03394 Pox_E8 Poxvirus E8 protein
PF03395 Pox_P4A Poxvirus P4A protein
PF03396 Pox_RNA_pol_35 Poxvirus DNA-directed RNA polymerase, 35 kD subunit
PF03397 Rhabdo_matrix Rhabdovirus matrix protein
-PF03398 Ist1 Regulator of Vps4 activity in the MVB pathway
+PF03398 CL0235 PspA Ist1 Regulator of Vps4 activity in the MVB pathway
PF03399 CL0123 HTH SAC3_GANP SAC3/GANP family
PF03400 CL0219 RNase_H DDE_Tnp_IS1 IS1 transposase
PF03401 CL0177 PBP TctC Tripartite tricarboxylate transporter family receptor
@@ -3212,7 +3211,7 @@ PF03477 ATP-cone ATP cone domain
PF03478 DUF295 Protein of unknown function (DUF295)
PF03479 CL0615 ALDC PCC Plants and Prokaryotes Conserved (PCC) domain
PF03480 CL0177 PBP DctP Bacterial extracellular solute-binding protein, family 7
-PF03481 CL0113 GT-B SUA5 Putative GTP-binding controlling metal-binding
+PF03481 CL0113 GT-B Sua5_C Threonylcarbamoyl-AMP synthase, C-terminal domain
PF03482 SIC sic protein repeat
PF03483 CL0383 PheT-TilS B3_4 B3/4 domain
PF03484 CL0123 HTH B5 tRNA synthetase B5 domain
@@ -3253,7 +3252,7 @@ PF03521 Kv2channel Kv2 voltage-gated K+ channel
PF03522 SLC12 Solute carrier family 12
PF03523 Macscav_rec Macrophage scavenger receptor
PF03524 CL0159 E-set CagX Conjugal transfer protein
-PF03525 Meiotic_rec114 Meiotic recombination protein rec114
+PF03525 CL0266 PH Meiotic_rec114 Meiotic recombination protein Rec7 N-terminal domain
PF03526 Microcin Colicin E1 (microcin) immunity protein
PF03527 RHS RHS protein
PF03528 Rabaptin Rabaptin
@@ -3341,7 +3340,7 @@ PF03615 CL0274 WRKY-GCM1 GCM GCM motif protein
PF03616 CL0064 CPA_AT Glt_symporter Sodium/glutamate symporter
PF03617 IBV_3A IBV 3A protein
PF03618 CL0023 P-loop_NTPase Kinase-PPPase Kinase/pyrophosphorylase
-PF03619 Solute_trans_a Organic solute transporter Ostalpha
+PF03619 CL0192 GPCR_A Solute_trans_a Organic solute transporter Ostalpha
PF03620 IBV_3C IBV 3C protein
PF03621 MbtH MbtH-like protein
PF03622 IBV_3B IBV 3B protein
@@ -3356,14 +3355,14 @@ PF03631 Virul_fac_BrkB Virulence factor BrkB
PF03632 CL0059 6_Hairpin Glyco_hydro_65m Glycosyl hydrolase family 65 central catalytic domain
PF03633 Glyco_hydro_65C Glycosyl hydrolase family 65, C-terminal domain
PF03634 TCP TCP family transcription factor
-PF03635 Vps35 Vacuolar protein sorting-associated protein 35
+PF03635 CL0020 TPR Vps35 Vacuolar protein sorting-associated protein 35
PF03636 CL0103 Gal_mutarotase Glyco_hydro_65N Glycosyl hydrolase family 65, N-terminal domain
PF03637 Mob1_phocein Mob1/phocein family
PF03638 TCR Tesmin/TSO1-like CXC domain, cysteine-rich domain
PF03639 CL0103 Gal_mutarotase Glyco_hydro_81 Glycosyl hydrolase family 81 N-terminal domain
PF03640 Lipoprotein_15 Secreted repeat of unknown function
PF03641 CL0349 SLOG Lysine_decarbox Possible lysine decarboxylase
-PF03642 CL0386 Ant-toxin_C MAP MAP domain
+PF03642 MAP MAP domain
PF03643 CL0135 Arrestin_N-like Vps26 Vacuolar protein sorting-associated protein 26
PF03644 CL0058 Glyco_hydro_tim Glyco_hydro_85 Glycosyl hydrolase family 85
PF03645 Tctex-1 Tctex-1 family
@@ -3386,12 +3385,12 @@ PF03664 CL0143 B_Fructosidase Glyco_hydro_62 Glycosyl hydrolase family 62
PF03665 CL0366 JAB UPF0172 Uncharacterised protein family (UPF0172)
PF03666 CL0435 NPR NPR3 Nitrogen Permease regulator of amino acid transport activity 3
PF03668 CL0023 P-loop_NTPase ATP_bind_2 P-loop ATPase protein family
-PF03669 UPF0139 Uncharacterised protein family (UPF0139)
+PF03669 ASTER PAT complex subunit Asterix
PF03670 UPF0184 Uncharacterised protein family (UPF0184)
PF03671 CL0072 Ubiquitin Ufm1 Ubiquitin fold modifier 1 protein
PF03672 UPF0154 Uncharacterised protein family (UPF0154)
PF03673 UPF0128 Uncharacterised protein family (UPF0128)
-PF03676 UPF0183 Uncharacterised protein family (UPF0183)
+PF03676 PHAF1 Phagosome assembly factor 1
PF03677 UPF0137 Uncharacterised protein family (UPF0137)
PF03678 CL0055 Nucleoplasmin Adeno_hexon_C Hexon, adenovirus major coat protein, C-terminal domain
PF03682 UPF0158 Uncharacterised protein family (UPF0158)
@@ -3463,7 +3462,7 @@ PF03749 CL0236 PDDEXK SfsA Sugar fermentation stimulation protein RE domain
PF03750 Csm2_III-A Csm2 Type III-A
PF03752 ALF Short repeats of unknown function
PF03753 HHV6-IE Human herpesvirus 6 immediate early protein
-PF03754 CL0405 DNA_b-psBarrel DUF313 Domain of unknown function (DUF313)
+PF03754 CL0405 DNA_b-psBarrel At2g31720-like B3 domain-containing protein At2g31720-like
PF03755 YicC_N YicC-like family, N-terminal region
PF03756 CL0050 HotDog AfsA A-factor biosynthesis hotdog domain
PF03759 PRONE PRONE (Plant-specific Rop nucleotide exchanger)
@@ -3475,13 +3474,13 @@ PF03764 CL0329 S5 EFG_IV Elongation factor G, domain IV
PF03765 CL0214 UBA CRAL_TRIO_N CRAL/TRIO, N-terminal domain
PF03766 Remorin_N Remorin, N-terminal region
PF03767 CL0137 HAD Acid_phosphat_B HAD superfamily, subfamily IIIB (Acid phosphatase)
-PF03768 Attacin_N Attacin, N-terminal region
-PF03769 Attacin_C Attacin, C-terminal region
+PF03768 CL0193 MBB Attacin_N Attacin, N-terminal region
+PF03769 CL0193 MBB Attacin_C Attacin, C-terminal region
PF03770 CL0016 PKinase IPK Inositol polyphosphate kinase
PF03771 SPDY Domain of unknown function (DUF317)
PF03772 Competence Competence protein
-PF03773 ArsP_1 Predicted permease
-PF03775 MinC_C Septum formation inhibitor MinC, C-terminal domain
+PF03773 CL0182 IT ArsP_1 Predicted permease
+PF03775 CL0268 Pec_lyase-like MinC_C Septum formation inhibitor MinC, C-terminal domain
PF03776 MinE Septum formation topological specificity factor MinE
PF03777 ChpA-C ChpA-C
PF03778 DUF321 Protein of unknown function (DUF321)
@@ -3504,9 +3503,9 @@ PF03795 CL0032 Dim_A_B_barrel YCII YCII-related domain
PF03796 CL0023 P-loop_NTPase DnaB_C DnaB-like helicase C terminal domain
PF03797 CL0193 MBB Autotransporter Autotransporter beta-domain
PF03798 TRAM_LAG1_CLN8 TLC domain
-PF03799 FtsQ Cell division protein FtsQ
-PF03800 Nuf2 Nuf2 family
-PF03801 Ndc80_HEC HEC/Ndc80p family
+PF03799 FtsQ_DivIB_C Cell division protein FtsQ/DivIB, C-terminal
+PF03800 CL0188 CH Nuf2 Nuf2 family
+PF03801 CL0188 CH Ndc80_HEC HEC/Ndc80p family
PF03802 CitX Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase
PF03803 CL0395 Tubby_C Scramblase Scramblase
PF03804 DUF325 Viral proteins of unknown function
@@ -3627,7 +3626,7 @@ PF03923 Lipoprotein_16 Uncharacterized lipoprotein
PF03924 CL0165 Cache CHASE CHASE domain
PF03925 SeqA SeqA protein C-terminal domain
PF03927 CL0032 Dim_A_B_barrel NapD NapD protein
-PF03928 CL0161 GAF Haem_degrading Haem-degrading
+PF03928 CL0161 GAF HbpS-like Haem degrading protein HbpS-like
PF03929 CL0490 PepSY_TM-like PepSY_TM PepSY-associated TM region
PF03930 CL0469 l-integrase_N Flp_N Recombinase Flp protein N-terminus
PF03931 CL0033 POZ Skp1_POZ Skp1 family, tetramerisation domain
@@ -3659,7 +3658,7 @@ PF03957 Jun Jun-like transcription factor
PF03958 Secretin_N Bacterial type II/III secretion system short domain
PF03959 CL0028 AB_hydrolase FSH1 Serine hydrolase (FSH1)
PF03960 CL0172 Thioredoxin ArsC ArsC family
-PF03961 CL0268 Pec_lyase-like FapA Flagellar Assembly Protein A
+PF03961 CL0268 Pec_lyase-like FapA Flagellar Assembly Protein A beta solenoid domain
PF03962 CL0123 HTH Mnd1 Mnd1 HTH domain
PF03963 FlgD Flagellar hook capping protein - N-terminal region
PF03964 Chorion_2 Chorion family 2
@@ -3682,7 +3681,7 @@ PF03980 Nnf1 Nnf1
PF03981 Ubiq_cyt_C_chap Ubiquinol-cytochrome C chaperone
PF03982 CL0228 Acyltransferase DAGAT Diacylglycerol acyltransferase
PF03983 SHD1 SLA1 homology domain 1, SHD1
-PF03984 DUF346 Repeat of unknown function (DUF346)
+PF03984 CL0186 Beta_propeller DUF346 Repeat of unknown function (DUF346)
PF03985 Paf1 Paf1
PF03987 CL0097 TypeIII_Chap Autophagy_act_C Autophagocytosis associated protein, active-site domain
PF03988 DUF347 Repeat of Unknown Function (DUF347)
@@ -3746,7 +3745,7 @@ PF04050 CL0020 TPR Upf2 Up-frameshift suppressor 2
PF04051 CL0210 HNOX-like TRAPP Transport protein particle (TRAPP) component
PF04052 CL0342 TolB_N TolB_N TolB amino-terminal domain
PF04053 CL0186 Beta_propeller Coatomer_WDAD Coatomer WD associated region
-PF04054 Not1 CCR4-Not complex component, Not1
+PF04054 CL0020 TPR Not1 CCR4-Not complex component, Not1
PF04055 CL0036 TIM_barrel Radical_SAM Radical SAM superfamily
PF04056 CL0128 vWA-like Ssl1 Ssl1-like
PF04057 CL0021 OB Rep-A_N Replication factor-A protein 1, N-terminal domain
@@ -3768,7 +3767,7 @@ PF04074 CL0029 Cupin DUF386 YhcH/YjgK/YiaL
PF04075 CL0336 FMN-binding F420H2_quin_red F420H(2)-dependent quinone reductase
PF04076 CL0021 OB BOF Bacterial OB fold (BOF) protein
PF04077 CL0394 DsrEFH-like DsrH DsrH like protein
-PF04078 Rcd1 Cell differentiation family, Rcd1-like
+PF04078 CL0020 TPR Rcd1 Cell differentiation family, Rcd1-like
PF04079 CL0123 HTH SMC_ScpB Segregation and condensation complex subunit ScpB
PF04080 CL0192 GPCR_A Per1 Per1-like family
PF04081 DNA_pol_delta_4 DNA polymerase delta, subunit 4
@@ -3786,7 +3785,7 @@ PF04092 SAG SRS domain
PF04093 CL0315 Gx_transp MreD rod shape-determining protein MreD
PF04095 CL0036 TIM_barrel NAPRTase Nicotinate phosphoribosyltransferase (NAPRTase) family
PF04096 CL0661 Gain Nucleoporin2 Nucleoporin autopeptidase
-PF04097 Nic96 Nup93/Nic96
+PF04097 CL0020 TPR Nic96 Nup93/Nic96
PF04098 CL0196 DSRM Rad52_Rad22 Rad52/22 family double-strand break repair protein
PF04099 CL0431 PF Sybindin Sybindin-like family
PF04100 CL0295 Vps51 Vps53_N Vps53-like, N-terminal
@@ -3804,7 +3803,7 @@ PF04112 Mak10 Mak10 subunit, NatC N(alpha)-terminal acetyltransferase
PF04113 Gpi16 Gpi16 subunit, GPI transamidase component
PF04114 Gaa1 Gaa1-like, GPI transamidase component
PF04115 CL0029 Cupin Ureidogly_lyase Ureidoglycolate lyase
-PF04116 FA_hydroxylase Fatty acid hydroxylase superfamily
+PF04116 CL0713 Acyl-CoA_desat FA_hydroxylase Fatty acid hydroxylase
PF04117 Mpv17_PMP22 Mpv17 / PMP22 family
PF04118 CL0020 TPR Dopey_N Dopey, N-terminal
PF04119 HSP9_HSP12 Heat shock protein 9/12
@@ -3827,7 +3826,7 @@ PF04138 GtrA GtrA-like protein
PF04139 CL0060 DNA_clamp Rad9 Rad9
PF04140 CL0115 Steroid_dh ICMT Isoprenylcysteine carboxyl methyltransferase (ICMT) family
PF04142 CL0184 DMT Nuc_sug_transp Nucleotide-sugar transporter
-PF04143 Sulf_transp Sulphur transport
+PF04143 CL0710 YeeE Sulf_transp Sulphur transport
PF04144 SCAMP SCAMP family
PF04145 Ctr Ctr copper transporter family
PF04146 CL0178 PUA YTH YT521-B-like domain
@@ -3850,12 +3849,12 @@ PF04166 CL0270 Iso_DH PdxA Pyridoxal phosphate biosynthetic protein PdxA
PF04167 DUF402 Protein of unknown function (DUF402)
PF04168 Alpha-E A predicted alpha-helical domain with a conserved ER motif.
PF04170 CL0116 Calycin NlpE NlpE N-terminal domain
-PF04172 LrgB LrgB-like family
+PF04172 CL0064 CPA_AT LrgB LrgB-like family
PF04173 CL0131 DoxD-like DoxD TQO small subunit DoxD
PF04174 CL0179 ATP-grasp CP_ATPgrasp_1 A circularly permuted ATPgrasp
PF04175 DUF406 Protein of unknown function (DUF406)
PF04176 TIP41 TIP41-like family
-PF04177 TAP42 TAP42-like family
+PF04177 CL0020 TPR TAP42 TAP42-like family
PF04178 Got1 Got1/Sft2-like family
PF04179 CL0031 Phosphatase Init_tRNA_PT Rit1 DUSP-like domain
PF04180 LTV Low temperature viability protein
@@ -3868,14 +3867,14 @@ PF04186 FxsA FxsA cytoplasmic membrane protein
PF04187 CL0572 TIKI Cofac_haem_bdg Haem-binding uptake, Tiki superfamily, ChaN
PF04188 CL0111 GT-C Mannosyl_trans2 Mannosyltransferase (PIG-V)
PF04189 Gcd10p Gcd10p family
-PF04190 GET4 Golgi to ER traffic protein 4
+PF04190 CL0020 TPR GET4 Golgi to ER traffic protein 4
PF04191 CL0115 Steroid_dh PEMT Phospholipid methyltransferase
PF04192 Utp21 Utp21 specific WD40 associated putative domain
PF04193 CL0141 MtN3-like PQ-loop PQ loop repeat
PF04194 PDCD2_C Programmed cell death protein 2, C-terminal putative domain
PF04195 Transposase_28 Putative gypsy type transposon
PF04196 Bunya_RdRp Bunyavirus RNA dependent RNA polymerase
-PF04197 CL0027 RdRP Birna_RdRp Birnavirus RNA dependent RNA polymerase (VP1)
+PF04197 CL0027 RdRP Birna_RdRp_palm Birnavirus RNA dependent RNA polymerase (VP1), palm domain
PF04198 CL0246 ISOCOT_Fold Sugar-bind Putative sugar-binding domain
PF04199 CL0364 Leu-IlvD Cyclase Putative cyclase
PF04200 Lipoprotein_17 Lipoprotein associated domain
@@ -3887,7 +3886,7 @@ PF04205 FMN_bind FMN-binding domain
PF04206 MtrE Tetrahydromethanopterin S-methyltransferase, subunit E
PF04207 MtrD Tetrahydromethanopterin S-methyltransferase, subunit D
PF04208 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A
-PF04209 CL0029 Cupin HgmA homogentisate 1,2-dioxygenase
+PF04209 CL0029 Cupin HgmA_C Homogentisate 1,2-dioxygenase C-terminal
PF04210 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G
PF04211 MtrC Tetrahydromethanopterin S-methyltransferase, subunit C
PF04212 MIT MIT (microtubule interacting and transport) domain
@@ -3930,7 +3929,7 @@ PF04252 CL0098 SPOUT RNA_Me_trans Predicted SAM-dependent RNA methyltransferase
PF04253 TFR_dimer Transferrin receptor-like dimerisation domain
PF04254 DUF432 Protein of unknown function (DUF432)
PF04255 CL0123 HTH DUF433 Protein of unknown function (DUF433)
-PF04256 DUF434 Protein of unknown function (DUF434)
+PF04256 CL0123 HTH DUF434 Protein of unknown function (DUF434)
PF04257 CL0023 P-loop_NTPase Exonuc_V_gamma Exodeoxyribonuclease V, gamma subunit
PF04258 CL0130 Peptidase_AD Peptidase_A22B Signal peptide peptidase
PF04259 SASP_gamma Small, acid-soluble spore protein, gamma-type
@@ -3946,7 +3945,7 @@ PF04268 CL0289 FBD SoxG Sarcosine oxidase, gamma subunit family
PF04269 DUF440 Protein of unknown function, DUF440
PF04270 Strep_his_triad Streptococcal histidine triad protein
PF04272 Phospholamban Phospholamban
-PF04273 CL0031 Phosphatase DUF442 Putative phosphatase (DUF442)
+PF04273 CL0031 Phosphatase BLH_phosphatase Beta-lactamase hydrolase-like protein, phosphatase-like domain
PF04275 P-mevalo_kinase Phosphomevalonate kinase
PF04276 DUF443 Protein of unknown function (DUF443)
PF04277 OAD_gamma Oxaloacetate decarboxylase, gamma chain
@@ -3988,7 +3987,7 @@ PF04315 EpmC Elongation factor P hydroxylase
PF04316 FlgM Anti-sigma-28 factor, FlgM
PF04317 CL0023 P-loop_NTPase DUF463 YcjX-like family, DUF463
PF04318 DUF468 Protein of unknown function (DUF468)
-PF04319 NifZ NifZ domain
+PF04319 CL0010 SH3 NifZ NifZ domain
PF04320 YggL_50S_bp YggL 50S ribosome-binding protein
PF04321 CL0063 NADP_Rossmann RmlD_sub_bind RmlD substrate binding domain
PF04322 DUF473 Protein of unknown function (DUF473)
@@ -4011,7 +4010,7 @@ PF04342 CL0184 DMT DMT_6 Putative member of DMT superfamily (DUF486)
PF04343 DUF488 Protein of unknown function, DUF488
PF04344 CheZ Chemotaxis phosphatase, CheZ
PF04345 CL0122 UTRA Chor_lyase Chorismate lyase
-PF04346 EutH Ethanolamine utilisation protein, EutH
+PF04346 CL0182 IT EutH Ethanolamine utilisation protein, EutH
PF04347 FliO Flagellar biosynthesis protein, FliO
PF04348 CL0144 Periplas_BP LppC LppC putative lipoprotein
PF04349 CL0103 Gal_mutarotase MdoG Periplasmic glucan biosynthesis protein, MdoG
@@ -4067,7 +4066,7 @@ PF04403 PqiA Paraquat-inducible protein A
PF04404 ERF ERF superfamily
PF04405 ScdA_N Domain of Unknown function (DUF542)
PF04406 TP6A_N Type IIB DNA topoisomerase
-PF04407 DUF531 Protein of unknown function (DUF531)
+PF04407 CL0098 SPOUT DUF531 Protein of unknown function (DUF531)
PF04408 HA2 Helicase associated domain (HA2)
PF04409 DUF530 Protein of unknown function (DUF530)
PF04410 CL0575 EFTPs Gar1 Gar1/Naf1 RNA binding region
@@ -4094,7 +4093,7 @@ PF04432 FrhB_FdhB_C Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C te
PF04433 CL0123 HTH SWIRM SWIRM domain
PF04434 SWIM SWIM zinc finger
PF04435 SPK Domain of unknown function (DUF545)
-PF04437 RINT1_TIP1 RINT-1 / TIP-1 family
+PF04437 CL0020 TPR RINT1_TIP1 RINT-1 / TIP-1 family
PF04438 CL0175 TRASH zf-HIT HIT zinc finger
PF04439 CL0260 NTP_transf Adenyl_transf Streptomycin adenylyltransferase
PF04440 Dysbindin Dysbindin (Dystrobrevin binding protein 1)
@@ -4104,12 +4103,12 @@ PF04443 CL0378 ANL LuxE Acyl-protein synthetase, LuxE
PF04444 Dioxygenase_N Catechol dioxygenase N terminus
PF04445 CL0063 NADP_Rossmann SAM_MT Putative SAM-dependent methyltransferase
PF04446 Thg1 tRNAHis guanylyltransferase
-PF04447 CL0231 MazG DUF550 Protein of unknown function (DUF550)
+PF04447 CL0231 MazG dATP-dGTP_PPHyd dATP/dGTP pyrophosphohydrolase
PF04448 DUF551 Protein of unknown function (DUF551)
PF04449 Fimbrial_CS1 CS1 type fimbrial major subunit
PF04450 CL0126 Peptidase_MA BSP Peptidase of plants and bacteria
PF04451 CL0611 Hexon Capsid_NCLDV Large eukaryotic DNA virus major capsid protein
-PF04452 CL0098 SPOUT Methyltrans_RNA RNA methyltransferase
+PF04452 CL0098 SPOUT Methyltrans_RNA RNA methyltransferase domain
PF04453 CL0193 MBB LptD LPS transport system D
PF04454 CL0373 Phage-coat Linocin_M18 Encapsulating protein for peroxidase
PF04455 Saccharop_dh_N LOR/SDH bifunctional enzyme conserved region
@@ -4173,7 +4172,7 @@ PF04518 Effector_1 Effector from type III secretion system
PF04519 CL0268 Pec_lyase-like Bactofilin Polymer-forming cytoskeletal
PF04520 Senescence_reg Senescence regulator
PF04521 Viral_P18 ssRNA positive strand viral 18kD cysteine rich protein
-PF04522 DUF585 Protein of unknown function (DUF585)
+PF04522 BBMV_Gp1_N Broad bean mottle virus, Gp1, N-terminal
PF04523 Herpes_U30 Herpes virus tegument protein U30
PF04525 CL0395 Tubby_C LOR LURP-one-related
PF04526 DUF568 Protein of unknown function (DUF568)
@@ -4185,7 +4184,7 @@ PF04531 Phage_holin_1 Bacteriophage holin
PF04532 DUF587 Protein of unknown function (DUF587)
PF04533 Herpes_U44 Herpes virus U44 protein
PF04534 Herpes_UL56 Herpesvirus UL56 protein
-PF04535 CL0396 Marvel-like DUF588 Domain of unknown function (DUF588)
+PF04535 CL0396 Marvel-like CASP_dom Casparian strip membrane protein domain
PF04536 CL0063 NADP_Rossmann TPM_phosphatase TPM domain
PF04537 Herpes_UL55 Herpesvirus UL55 protein
PF04538 BEX Brain expressed X-linked like family
@@ -4207,7 +4206,7 @@ PF04554 Extensin_2 Extensin-like region
PF04555 CL0236 PDDEXK XhoI Restriction endonuclease XhoI
PF04556 CL0236 PDDEXK DpnII DpnII restriction endonuclease
PF04557 tRNA_synt_1c_R2 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2
-PF04558 tRNA_synt_1c_R1 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1
+PF04558 CL0279 GatB_YqeY tRNA_synt_1c_R1 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1
PF04559 Herpes_UL17 Herpesvirus UL17 protein
PF04560 RNA_pol_Rpb2_7 RNA polymerase Rpb2, domain 7
PF04561 RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2
@@ -4374,7 +4373,7 @@ PF04730 Agro_virD5 Agrobacterium VirD5 protein
PF04731 Caudal_act Caudal like protein activation region
PF04732 Filament_head Intermediate filament head (DNA binding) region
PF04733 CL0020 TPR Coatomer_E Coatomer epsilon subunit
-PF04734 Ceramidase_alk Neutral/alkaline non-lysosomal ceramidase, N-terminal
+PF04734 CL0635 DmpA_ArgJ Ceramidase_alk Neutral/alkaline non-lysosomal ceramidase, N-terminal
PF04735 Baculo_helicase Baculovirus DNA helicase
PF04736 Eclosion Eclosion hormone
PF04738 Lant_dehydr_N Lantibiotic dehydratase, N terminus
@@ -4424,7 +4423,7 @@ PF04784 DUF547 Protein of unknown function, DUF547
PF04785 Rhabdo_M2 Rhabdovirus matrix protein M2
PF04786 Baculo_DNA_bind ssDNA binding protein
PF04787 Pox_H7 Late protein H7
-PF04788 DUF620 Protein of unknown function (DUF620)
+PF04788 CL0048 LolA_LolB DUF620 Protein of unknown function (DUF620)
PF04789 CL0192 GPCR_A DUF621 Protein of unknown function (DUF621)
PF04790 Sarcoglycan_1 Sarcoglycan complex subunit protein
PF04791 LMBR1 LMBR1-like membrane protein
@@ -4436,9 +4435,9 @@ PF04796 CL0123 HTH RepA_C Plasmid encoded RepA protein
PF04797 CL0153 dUTPase Herpes_ORF11 Herpesvirus dUTPase protein
PF04798 Baculo_19 Baculovirus 19 kDa protein conserved region
PF04799 Fzo_mitofusin fzo-like conserved region
-PF04800 ETC_C1_NDUFA4 ETC complex I subunit conserved region
+PF04800 NDUS4 NADH dehydrogenase ubiquinone Fe-S protein 4
PF04801 CL0662 Triple_barrel RPC5 RPC5 protein
-PF04802 SMK-1 Component of IIS longevity pathway SMK-1
+PF04802 PP4R3 Phosphatase 4 regulatory subunit 3
PF04803 Cor1 Cor1/Xlr/Xmr conserved region
PF04805 Pox_E10 E10-like protein conserved region
PF04806 EspF EspF protein repeat
@@ -4475,8 +4474,8 @@ PF04836 IFRD_C Interferon-related protein conserved region
PF04837 MbeB_N MbeB-like, N-term conserved region
PF04838 Baculo_LEF5 Baculoviridae late expression factor 5
PF04839 PSRP-3_Ycf65 Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65)
-PF04840 Vps16_C Vps16, C-terminal region
-PF04841 Vps16_N Vps16, N-terminal region
+PF04840 CL0020 TPR Vps16_C Vps16, C-terminal region
+PF04841 CL0186 Beta_propeller Vps16_N Vps16, N-terminal region
PF04842 CL0484 Peroxisome DUF639 Plant protein of unknown function (DUF639)
PF04843 CL0125 Peptidase_CA Herpes_teg_N Herpesvirus tegument protein, N-terminal conserved region
PF04844 Ovate Transcriptional repressor, ovate
@@ -4487,7 +4486,7 @@ PF04848 CL0219 RNase_H Pox_A22 Poxvirus A22 protein
PF04849 HAP1_N HAP1 N-terminal conserved region
PF04850 CL0372 Hy-ly_N Baculo_E66 Baculovirus E66 occlusion-derived virus envelope protein
PF04851 CL0023 P-loop_NTPase ResIII Type III restriction enzyme, res subunit
-PF04852 DUF640 Protein of unknown function (DUF640)
+PF04852 ALOG_dom ALOG domain
PF04854 DUF624 Protein of unknown function, DUF624
PF04855 SNF5 SNF5 / SMARCB1 / INI1
PF04856 Securin Securin sister-chromatid separation inhibitor
@@ -4502,7 +4501,7 @@ PF04865 Baseplate_J Baseplate J-like protein
PF04866 Rota_NS6 Rotavirus non-structural protein 6
PF04867 DUF643 Protein of unknown function (DUF643)
PF04868 PDE6_gamma Retinal cGMP phosphodiesterase, gamma subunit
-PF04869 Uso1_p115_head Uso1 / p115 like vesicle tethering protein, head region
+PF04869 CL0020 TPR Uso1_p115_head Uso1 / p115 like vesicle tethering protein, head region
PF04870 Moulting_cycle Moulting cycle
PF04871 Uso1_p115_C Uso1 / p115 like vesicle tethering protein, C terminal region
PF04872 Pox_L5 Poxvirus L5 protein family
@@ -4517,7 +4516,7 @@ PF04880 NUDE_C NUDE protein, C-terminal conserved region
PF04881 CL0159 E-set Adeno_GP19K Adenovirus GP19K
PF04882 Peroxin-3 Peroxin-3
PF04883 CL0348 Phage_tail HK97-gp10_like Bacteriophage HK97-gp10, putative tail-component
-PF04884 UVB_sens_prot Vitamin B6 photo-protection and homoeostasis
+PF04884 CL0015 MFS UVB_sens_prot Vitamin B6 photo-protection and homoeostasis
PF04885 Stig1 Stigma-specific protein, Stig1
PF04886 PT PT repeat
PF04887 Pox_M2 Poxvirus M2 protein
@@ -4548,7 +4547,7 @@ PF04914 CL0264 SGNH_hydrolase DltD DltD protein
PF04916 CL0052 NTN Phospholip_B Phospholipase B
PF04917 Shufflon_N Bacterial shufflon protein, N-terminal constant region
PF04919 CL0198 HHH DUF655 Protein of unknown function (DUF655)
-PF04920 DUF656 Family of unknown function (DUF656)
+PF04920 BNYVV_p31 Beet necrotic yellow vein virus, p31
PF04921 XAP5 XAP5, circadian clock regulator
PF04922 CL0111 GT-C DIE2_ALG10 DIE2/ALG10 family
PF04923 Ninjurin Ninjurin
@@ -4638,7 +4637,7 @@ PF05014 CL0498 Nribosyltransf Nuc_deoxyrib_tr Nucleoside 2-deoxyribosyltransfera
PF05015 CL0136 Plasmid-antitox HigB-like_toxin RelE-like toxin of type II toxin-antitoxin system HigB
PF05016 CL0136 Plasmid-antitox ParE_toxin ParE toxin of type II toxin-antitoxin system, parDE
PF05017 TMP TMP repeat
-PF05018 DUF667 Protein of unknown function (DUF667)
+PF05018 CFA20_dom CFA20 domain
PF05019 Coq4 Coenzyme Q (ubiquinone) biosynthesis protein Coq4
PF05020 zf-NPL4 NPL4 family, putative zinc binding region
PF05021 CL0366 JAB NPL4 NPL4 family
@@ -4697,7 +4696,7 @@ PF05077 DUF678 Protein of unknown function (DUF678)
PF05078 DUF679 Protein of unknown function (DUF679)
PF05079 DUF680 Protein of unknown function (DUF680)
PF05080 DUF681 Protein of unknown function (DUF681)
-PF05081 DUF682 Protein of unknown function (DUF682)
+PF05081 AcMNPV_P18 Autographa californica nuclear polyhedrosis virus (AcMNPV), P18
PF05082 Rop-like Rop-like
PF05083 LST1 LST-1 protein
PF05084 GRA6 Granule antigen protein (GRA6)
@@ -4758,7 +4757,7 @@ PF05139 CL0572 TIKI Erythro_esteras Erythromycin esterase
PF05140 ResB ResB-like family
PF05141 DIT1_PvcA Pyoverdine/dityrosine biosynthesis protein
PF05142 DUF702 Domain of unknown function (DUF702)
-PF05144 Phage_CRI Phage replication protein CRI
+PF05144 CL0407 TBP-like Phage_CRI Phage replication protein CRI
PF05145 CL0142 Membrane_trans AbrB Transition state regulatory protein AbrB
PF05147 CL0059 6_Hairpin LANC_like Lanthionine synthetase C-like protein
PF05148 CL0063 NADP_Rossmann Methyltransf_8 Hypothetical methyltransferase
@@ -4791,7 +4790,7 @@ PF05177 RCSD RCSD region
PF05178 Kri1 KRI1-like family
PF05179 CL0023 P-loop_NTPase CDC73_C RNA pol II accessory factor, Cdc73 family, C-terminal
PF05180 zf-DNL DNL zinc finger
-PF05181 XPA_C XPA protein C-terminus
+PF05181 CL0123 HTH XPA_C XPA protein C-terminus
PF05182 Fip1 Fip1 motif
PF05183 RdRP RNA dependent RNA polymerase
PF05184 CL0707 Saposin_like SapB_1 Saposin-like type B, region 1
@@ -4824,7 +4823,7 @@ PF05211 CL0342 TolB_N NLBH Neuraminyllactose-binding hemagglutinin precursor (NL
PF05212 DUF707 Protein of unknown function (DUF707)
PF05213 CL0247 2H Corona_NS2A Coronavirus NS2A protein
PF05214 Baculo_p33 Baculovirus P33
-PF05215 Spiralin Spiralin
+PF05215 Spiralin Spiralin domain
PF05216 UNC-50 UNC-50 family
PF05217 STOP STOP protein
PF05218 DUF713 Protein of unknown function (DUF713)
@@ -4885,7 +4884,7 @@ PF05278 PEARLI-4 Arabidopsis phospholipase-like protein (PEARLI 4)
PF05279 Asp-B-Hydro_N Aspartyl beta-hydroxylase N-terminal region
PF05280 FlhC Flagellar transcriptional activator (FlhC)
PF05281 Secretogranin_V Neuroendocrine protein 7B2 precursor (Secretogranin V)
-PF05282 AAR2 AAR2 protein
+PF05282 CL0020 TPR AAR2 AAR2 protein
PF05283 MGC-24 Multi-glycosylated core protein 24 (MGC-24), sialomucin
PF05284 DUF736 Protein of unknown function (DUF736)
PF05285 SDA1 SDA1
@@ -4905,7 +4904,7 @@ PF05299 CL0126 Peptidase_MA Peptidase_M61 M61 glycyl aminopeptidase
PF05300 MIC19_MIC25 MICOS complex subunit MIC19/MIC25
PF05301 CL0257 Acetyltrans Acetyltransf_16 GNAT acetyltransferase, Mec-17
PF05302 DUF720 Protein of unknown function (DUF720)
-PF05303 DUF727 Protein of unknown function (DUF727)
+PF05303 GSKIP_dom GSKIP domain
PF05304 DUF728 Protein of unknown function (DUF728)
PF05305 DUF732 Protein of unknown function (DUF732)
PF05306 DUF733 Protein of unknown function (DUF733)
@@ -4930,7 +4929,7 @@ PF05326 CL0159 E-set SVA Seminal vesicle autoantigen (SVA)
PF05327 RRN3 RNA polymerase I specific transcription initiation factor RRN3
PF05328 CL0335 FumRed-TM CybS CybS, succinate dehydrogenase cytochrome B small subunit
PF05331 CL0123 HTH DUF742 Protein of unknown function (DUF742)
-PF05332 DUF743 Protein of unknown function (DUF743)
+PF05332 Vesi_VP2 Vesivirus VP2 protein
PF05334 DUF719 Protein of unknown function (DUF719)
PF05335 DUF745 Protein of unknown function (DUF745)
PF05336 CL0032 Dim_A_B_barrel rhaM L-rhamnose mutarotase
@@ -4985,7 +4984,7 @@ PF05386 TEP1_N TEP1 N-terminal domain
PF05387 Chorion_3 Chorion family 3
PF05388 Carbpep_Y_N Carboxypeptidase Y pro-peptide
PF05389 MecA Negative regulator of genetic competence (MecA)
-PF05390 KRE9 Yeast cell wall synthesis protein KRE9/KNH1
+PF05390 Kre9_KNH1_C Yeast cell wall synthesis protein KRE9/KNH1 C-terminal
PF05391 Lsm_interact Lsm interaction motif
PF05392 COX7B Cytochrome C oxidase chain VIIB
PF05393 Hum_adeno_E3A Human adenovirus early E3A glycoprotein
@@ -5057,7 +5056,7 @@ PF05464 Phi-29_GP4 Phi-29-like late genes activator (early protein GP4)
PF05465 Halo_GVPC Halobacterial gas vesicle protein C (GVPC) repeat
PF05466 BASP1 Brain acid soluble protein 1 (BASP1 protein)
PF05467 Herpes_U47 Herpesvirus glycoprotein U47
-PF05470 eIF-3c_N Eukaryotic translation initiation factor 3 subunit 8 N-terminus
+PF05470 CL0020 TPR eIF-3c_N Eukaryotic translation initiation factor 3 subunit 8 N-terminus
PF05472 Ter DNA replication terminus site-binding protein (Ter protein)
PF05473 CL0056 C_Lectin UL45 UL45 protein, carbohydrate-binding C-type lectin-like
PF05474 Semenogelin Semenogelin
@@ -5068,7 +5067,7 @@ PF05478 Prominin Prominin
PF05479 PsaN Photosystem I reaction centre subunit N (PSAN or PSI-N)
PF05480 PSMbeta Phenol-soluble modulin beta protein
PF05481 Myco_19_kDa Mycobacterium 19 kDa lipoprotein antigen
-PF05482 Serendipity_A Serendipity locus alpha protein (SRY-A)
+PF05482 CL0705 VBS-like Serendipity_A Serendipity locus alpha protein (SRY-A)
PF05483 SCP-1 Synaptonemal complex protein 1 (SCP-1)
PF05484 CL0020 TPR LRV_FeS LRV protein FeS4 cluster
PF05485 THAP THAP domain
@@ -5088,7 +5087,7 @@ PF05502 Dynactin_p62 Dynactin p62 family
PF05503 Pox_G7 Poxvirus G7-like
PF05504 Spore_GerAC Spore germination B3/ GerAC like, C-terminal
PF05505 CL0156 Nucleocapsid Ebola_NP Ebola nucleoprotein
-PF05506 DUF756 Domain of unknown function (DUF756)
+PF05506 PLipase_C_C Bacterial phospholipase C, C-terminal domain
PF05507 MAGP Microfibril-associated glycoprotein (MAGP)
PF05508 Ran-binding RanGTP-binding protein
PF05509 CL0057 Met_repress TraY TraY domain
@@ -5108,7 +5107,7 @@ PF05524 PEP-utilisers_N PEP-utilising enzyme, N-terminal
PF05525 CL0062 APC Branch_AA_trans Branched-chain amino acid transport protein
PF05526 R_equi_Vir Rhodococcus equi virulence-associated protein
PF05527 DUF758 Domain of unknown function (DUF758)
-PF05528 Coronavirus_5 Coronavirus gene 5 protein
+PF05528 Acc5b_avian_CoV Accessory protein 5b, avian coronavirus
PF05529 Bap31 Bap31/Bap29 transmembrane region
PF05531 NPV_P10 Nucleopolyhedrovirus P10 protein
PF05532 CL0406 YjbJ-CsbD-like CsbD CsbD-like
@@ -5119,7 +5118,7 @@ PF05536 CL0020 TPR Neurochondrin Neurochondrin
PF05537 DUF759 Borrelia burgdorferi protein of unknown function (DUF759)
PF05538 CL0193 MBB Campylo_MOMP Campylobacter major outer membrane protein
PF05539 Pneumo_att_G Pneumovirinae attachment membrane glycoprotein G
-PF05540 Serpulina_VSP Serpulina hyodysenteriae variable surface protein
+PF05540 CL0193 MBB Serpulina_VSP Serpulina hyodysenteriae variable surface protein
PF05541 Spheroidin Entomopoxvirus spheroidin protein
PF05542 DUF760 Protein of unknown function (DUF760)
PF05543 CL0125 Peptidase_CA Peptidase_C47 Staphopain peptidase C47
@@ -5170,25 +5169,25 @@ PF05590 DUF769 Xylella fastidiosa protein of unknown function (DUF769)
PF05591 T6SS_VipA Type VI secretion system, VipA, VC_A0107 or Hcp2
PF05592 CL0004 Concanavalin Bac_rhamnosid Bacterial alpha-L-rhamnosidase concanavalin-like domain
PF05593 RHS_repeat RHS Repeat
-PF05594 CL0268 Pec_lyase-like Fil_haemagg Haemagluttinin repeat
+PF05594 CL0268 Pec_lyase-like Fil_haemagg Haemagglutinin repeat
PF05595 DUF771 Domain of unknown function (DUF771)
PF05596 Taeniidae_ag Taeniidae antigen
PF05597 Phasin Poly(hydroxyalcanoate) granule associated protein (phasin)
PF05598 DUF772 Transposase domain (DUF772)
PF05599 Deltaretro_Tax Deltaretrovirus Tax protein
-PF05600 DUF773 CDK5 regulatory subunit-associated protein 3
+PF05600 CDK5RAP3 CDK5 regulatory subunit-associated protein 3
PF05602 CLPTM1 Cleft lip and palate transmembrane protein 1 (CLPTM1)
PF05603 DUF775 Protein of unknown function (DUF775)
PF05604 DUF776 Protein of unknown function (DUF776)
PF05605 CL0361 C2H2-zf zf-Di19 Drought induced 19 protein (Di19), zinc-binding
PF05606 DUF777 Borrelia burgdorferi protein of unknown function (DUF777)
PF05608 DUF778 Protein of unknown function (DUF778)
-PF05609 CL0023 P-loop_NTPase LAP1C Lamina-associated polypeptide 1C (LAP1C)
+PF05609 CL0023 P-loop_NTPase LAP1_C Lamina-associated polypeptide 1, AAA+ activator domain
PF05610 DUF779 Protein of unknown function (DUF779)
PF05611 DUF780 Caenorhabditis elegans protein of unknown function (DUF780)
PF05612 Leg1 Leg1
PF05613 Herpes_U15 Human herpesvirus U15 protein
-PF05614 DUF782 Circovirus protein of unknown function (DUF782)
+PF05614 Circovir_ORF3 Circovirus ORF3
PF05615 THOC7 Tho complex subunit 7
PF05616 Neisseria_TspB Neisseria meningitidis TspB protein
PF05617 CL0482 Prolamin Prolamin_like Prolamin-like
@@ -5207,7 +5206,7 @@ PF05629 Nanovirus_C8 Nanovirus component 8 (C8) protein
PF05630 NPP1 Necrosis inducing protein (NPP1)
PF05631 CL0015 MFS MFS_5 Sugar-tranasporters, 12 TM
PF05632 DUF792 Borrelia burgdorferi protein of unknown function (DUF792)
-PF05633 CL0133 AT14A-like BPS1 Protein BYPASS1-related
+PF05633 CL0133 AT14A-like ROH1-like Protein ROH1-like
PF05634 APO_RNA-bind APO RNA-binding
PF05635 23S_rRNA_IVP 23S rRNA-intervening sequence protein
PF05636 CL0039 HUP HIGH_NTase1 HIGH Nucleotidyl Transferase
@@ -5230,14 +5229,14 @@ PF05653 CL0184 DMT Mg_trans_NIPA Magnesium transporter NIPA
PF05655 AvrD Pseudomonas avirulence D protein (AvrD)
PF05656 DUF805 Protein of unknown function (DUF805)
PF05657 DUF806 Protein of unknown function (DUF806)
-PF05658 YadA_head Head domain of trimeric autotransporter adhesin
+PF05658 YadA_head YadA head domain repeat (2 copies)
PF05659 RPW8 Arabidopsis broad-spectrum mildew resistance protein RPW8
PF05660 DUF807 Coxiella burnetii protein of unknown function (DUF807)
PF05661 DUF808 Protein of unknown function (DUF808)
PF05662 YadA_stalk Coiled stalk of trimeric autotransporter adhesin
PF05663 DUF809 Protein of unknown function (DUF809)
PF05666 Fels1 Fels-1 Prophage Protein-like
-PF05667 DUF812 Protein of unknown function (DUF812)
+PF05667 CCDC22 Coiled-coil domain-containing protein 22
PF05669 Med31 SOH1
PF05670 CL0684 NFACT_RNA-bind NFACT-R_1 NFACT protein RNA binding domain
PF05671 GETHR GETHR pentapeptide repeat (5 copies)
@@ -5308,7 +5307,7 @@ PF05737 CL0204 Adhesin Collagen_bind Collagen binding domain
PF05738 CL0287 Transthyretin Cna_B Cna protein B-type domain
PF05739 SNARE SNARE domain
PF05741 zf-nanos Nanos RNA binding domain
-PF05742 TANGO2 Transport and Golgi organisation 2
+PF05742 CL0052 NTN TANGO2 Transport and Golgi organisation 2
PF05743 CL0208 UBC UEV UEV domain
PF05744 Benyvirus_P25 Benyvirus P25/P26 protein
PF05745 CRPA Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA)
@@ -5327,7 +5326,7 @@ PF05758 Ycf1 Ycf1
PF05760 IER Immediate early response protein (IER)
PF05761 CL0137 HAD 5_nucleotid 5' nucleotidase family
PF05762 CL0128 vWA-like VWA_CoxE VWA domain containing CoxE-like protein
-PF05763 DUF835 Protein of unknown function (DUF835)
+PF05763 CL0023 P-loop_NTPase DUF835 Protein of unknown function (DUF835)
PF05764 YL1 YL1 nuclear protein
PF05766 CL0263 His-Me_finger NinG Bacteriophage Lambda NinG protein
PF05767 Pox_A14 Poxvirus virion envelope protein A14
@@ -5373,7 +5372,7 @@ PF05811 DUF842 Eukaryotic protein of unknown function (DUF842)
PF05812 Herpes_BLRF2 Herpesvirus BLRF2 protein
PF05813 Orthopox_F7 Orthopoxvirus F7 protein
PF05814 Ac76 Orf76 (Ac76)
-PF05815 DUF844 Baculovirus protein of unknown function (DUF844)
+PF05815 AcMNPV_Orf101 Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101
PF05816 TelA Toxic anion resistance protein (TelA)
PF05817 Ribophorin_II Oligosaccharyltransferase subunit Ribophorin II
PF05818 TraT Enterobacterial TraT complement resistance protein
@@ -5385,7 +5384,7 @@ PF05823 Gp-FAR-1 Nematode fatty acid retinoid binding protein (Gp-FAR-1)
PF05824 Pro-MCH Pro-melanin-concentrating hormone (Pro-MCH)
PF05825 CL0451 FnI-like PSP94 Beta-microseminoprotein (PSP-94)
PF05826 CL0629 PLA2 Phospholip_A2_2 Phospholipase A2
-PF05827 ATP-synt_S1 Vacuolar ATP synthase subunit S1 (ATP6S1)
+PF05827 CL0721 LAMP VAS1_LD V-type proton ATPase subunit S1, luminal domain
PF05829 Adeno_PX Adenovirus late L2 mu core protein (Protein X)
PF05830 CL0113 GT-B NodZ Nodulation protein Z (NodZ)
PF05831 GAGE GAGE protein
@@ -5415,7 +5414,7 @@ PF05856 ARPC4 ARP2/3 complex 20 kDa subunit (ARPC4)
PF05857 CL0316 Acyl_transf_3 TraX TraX protein
PF05858 BIV_Env Bovine immunodeficiency virus surface protein (SU)
PF05859 Mis12 Mis12 protein
-PF05860 CL0268 Pec_lyase-like Haemagg_act haemagglutination activity domain
+PF05860 CL0268 Pec_lyase-like TPS TPS secretion domain
PF05861 PhnI Bacterial phosphonate metabolism protein (PhnI)
PF05862 IceA2 Helicobacter pylori IceA2 protein
PF05864 Chordopox_RPO7 Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
@@ -5426,13 +5425,13 @@ PF05868 CL0217 Rotavirus_VP7 Rotavirus_VP7 Rotavirus major outer capsid protein
PF05869 Dam DNA N-6-adenine-methyltransferase (Dam)
PF05870 CL0116 Calycin PA_decarbox Phenolic acid decarboxylase (PAD)
PF05871 CL0123 HTH ESCRT-II ESCRT-II complex subunit
-PF05872 CL0023 P-loop_NTPase DUF853 Bacterial protein of unknown function (DUF853)
+PF05872 CL0023 P-loop_NTPase HerA_C Helicase HerA-like C-terminal
PF05873 Mt_ATP-synt_D ATP synthase D chain, mitochondrial (ATP5H)
PF05874 PBAN Pheromone biosynthesis activating neuropeptide (PBAN)
PF05875 CL0192 GPCR_A Ceramidase Ceramidase
-PF05876 CL0023 P-loop_NTPase Terminase_GpA Phage terminase large subunit (GpA)
+PF05876 CL0023 P-loop_NTPase GpA_ATPase Phage terminase large subunit gpA, ATPase domain
PF05878 Phyto_Pns9_10 Phytoreovirus nonstructural protein Pns9/Pns10
-PF05879 CL0023 P-loop_NTPase RHD3 Root hair defective 3 GTP-binding protein (RHD3)
+PF05879 CL0023 P-loop_NTPase RHD3_GTPase Root hair defective 3 GTP-binding protein (RHD3) GTPase domain
PF05880 Fiji_64_capsid Fijivirus 64 kDa capsid protein
PF05881 CL0247 2H CNPase 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase)
PF05883 CL0229 RING Baculo_RING Baculovirus U-box/Ring-like domain
@@ -5453,12 +5452,12 @@ PF05902 4_1_CTD 4.1 protein C-terminal domain (CTD)
PF05903 CL0125 Peptidase_CA Peptidase_C97 PPPDE putative peptidase domain
PF05904 DUF863 Plant protein of unknown function (DUF863)
PF05906 DUF865 Herpesvirus-7 repeat of unknown function (DUF865)
-PF05907 DUF866 Eukaryotic protein of unknown function (DUF866)
+PF05907 CXXC_Zn-b_euk CXXC motif containing zinc binding protein, eukaryotic
PF05908 CL0035 Peptidase_MH Gamma_PGA_hydro Poly-gamma-glutamate hydrolase
PF05910 DUF868 Plant protein of unknown function (DUF868)
PF05911 FPP Filament-like plant protein, long coiled-coil
PF05912 DUF870 Caenorhabditis elegans protein of unknown function (DUF870)
-PF05913 CL0475 Cyclophil-like DUF871 DUF871 C-terminal domain
+PF05913 CL0475 Cyclophil-like MupG_C 6-phospho-N-acetylmuramidase, C-terminal
PF05914 RIB43A RIB43A
PF05915 TMEM_230_134 Transmembrane proteins 230/134
PF05916 Sld5 GINS complex protein
@@ -5484,7 +5483,7 @@ PF05936 T6SS_VasE Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE
PF05937 EB1_binding EB-1 Binding Domain
PF05938 Self-incomp_S1 Plant self-incompatibility protein S1
PF05939 Phage_min_tail Phage minor tail protein
-PF05940 NnrS NnrS protein
+PF05940 CL0714 COX1-like NnrS NnrS protein
PF05941 Chordopox_A20R Chordopoxvirus A20R protein
PF05942 CL0291 KNTase_C PaREP1 Archaeal PaREP1/PaREP8 family
PF05943 VipB EvpB/VC_A0108, tail sheath N-terminal domain
@@ -5526,7 +5525,7 @@ PF05982 CL0064 CPA_AT Sbt_1 Na+-dependent bicarbonate transporter superfamily
PF05983 Med7 MED7 protein
PF05984 Cytomega_UL20A Cytomegalovirus UL20A protein
PF05985 EutC Ethanolamine ammonia-lyase light chain (EutC)
-PF05986 ADAM_spacer1 ADAM-TS Spacer 1
+PF05986 ADAMTS_spacer1 ADAM-TS Spacer 1
PF05987 DUF898 Bacterial protein of unknown function (DUF898)
PF05988 CL0172 Thioredoxin DUF899 Bacterial protein of unknown function (DUF899)
PF05989 Chordopox_A35R Chordopoxvirus A35R protein
@@ -5534,12 +5533,12 @@ PF05990 CL0028 AB_hydrolase DUF900 Alpha/beta hydrolase of unknown function (DUF
PF05991 CL0280 PIN NYN_YacP YacP-like NYN domain
PF05992 CL0241 ABC_membrane SbmA_BacA SbmA/BacA-like family
PF05993 Reovirus_M2 Reovirus major virion structural protein Mu-1/Mu-1C (M2)
-PF05994 FragX_IP Cytoplasmic Fragile-X interacting family
+PF05994 CL0715 Nckap1_CYFIP1-2 FragX_IP Cytoplasmic Fragile-X interacting family
PF05995 CL0029 Cupin CDO_I Cysteine dioxygenase type I
PF05996 Fe_bilin_red Ferredoxin-dependent bilin reductase
PF05997 Nop52 Nucleolar protein,Nop52
PF05999 Herpes_U5 Herpesvirus U5-like family
-PF06001 DUF902 Domain of Unknown Function (DUF902)
+PF06001 RING_CBP-p300 CREB-binding protein/p300, atypical RING domain
PF06002 CST-I Alpha-2,3-sialyltransferase (CST-I)
PF06003 CL0049 Tudor SMN Survival motor neuron protein (SMN)
PF06004 CL0527 Sm-like DUF903 Bacterial protein of unknown function (DUF903)
@@ -5588,7 +5587,7 @@ PF06049 LSPR Coagulation Factor V LSPD Repeat
PF06050 CL0108 Actin_ATPase HGD-D 2-hydroxyglutaryl-CoA dehydratase, D-component
PF06051 DUF928 Domain of Unknown Function (DUF928)
PF06052 CL0029 Cupin 3-HAO 3-hydroxyanthranilic acid dioxygenase
-PF06053 DUF929 Domain of unknown function (DUF929)
+PF06053 CL0172 Thioredoxin DUF929 Domain of unknown function (DUF929)
PF06054 CL0236 PDDEXK CoiA Competence protein CoiA-like family
PF06055 ExoD Exopolysaccharide synthesis, ExoD
PF06056 CL0123 HTH Terminase_5 Putative ATPase subunit of terminase (gpP-like)
@@ -5610,7 +5609,7 @@ PF06073 DUF934 Bacterial protein of unknown function (DUF934)
PF06074 DUF935 Protein of unknown function (DUF935)
PF06075 DUF936 Plant protein of unknown function (DUF936)
PF06076 Orthopox_F14 Orthopoxvirus F14 protein
-PF06078 DUF937 Bacterial protein of unknown function (DUF937)
+PF06078 CL0123 HTH DUF937 Bacterial protein of unknown function (DUF937)
PF06079 CL0143 B_Fructosidase Apyrase Apyrase
PF06080 CL0063 NADP_Rossmann DUF938 Protein of unknown function (DUF938)
PF06081 CL0307 FUSC ArAE_1 Aromatic acid exporter family member 1
@@ -5636,14 +5635,14 @@ PF06102 RRP36 rRNA biogenesis protein RRP36
PF06103 DUF948 Bacterial protein of unknown function (DUF948)
PF06105 CL0472 Peptidase_U Aph-1 Aph-1 protein
PF06106 SAUGI S. aureus uracil DNA glycosylase inhibitor
-PF06107 DUF951 Bacterial protein of unknown function (DUF951)
+PF06107 CL0010 SH3 DUF951 Bacterial protein of unknown function (DUF951)
PF06108 CL0084 ADP-ribosyl DUF952 Protein of unknown function (DUF952)
PF06109 HlyE Haemolysin E (HlyE)
PF06110 CL0172 Thioredoxin DUF953 Eukaryotic protein of unknown function (DUF953)
PF06112 Herpes_capsid Gammaherpesvirus capsid protein
PF06113 BRE Brain and reproductive organ-expressed protein (BRE)
PF06114 CL0126 Peptidase_MA Peptidase_M78 IrrE N-terminal-like domain
-PF06115 DUF956 Domain of unknown function (DUF956)
+PF06115 CL0266 PH DUF956 Domain of unknown function (DUF956)
PF06116 RinB Transcriptional activator RinB
PF06119 NIDO Nidogen-like
PF06120 Phage_HK97_TLTM Tail length tape measure protein
@@ -5653,7 +5652,7 @@ PF06123 CreD Inner membrane protein CreD
PF06124 DUF960 Staphylococcal protein of unknown function (DUF960)
PF06125 CL0021 OB DUF961 Bacterial protein of unknown function (DUF961)
PF06126 Herpes_LAMP2 Herpesvirus Latent membrane protein 2
-PF06127 DUF962 Protein of unknown function (DUF962)
+PF06127 Mpo1-like 2-hydroxy-palmitic acid dioxygenase Mpo1-like
PF06128 Shigella_OspC Shigella flexneri OspC protein
PF06129 Chordopox_G3 Chordopoxvirus G3 protein
PF06130 PTAC Phosphate propanoyltransferase
@@ -5661,7 +5660,7 @@ PF06131 DUF963 Schizosaccharomyces pombe repeat of unknown function (DUF963)
PF06133 Com_YlbF Control of competence regulator ComK, YlbF/YmcA
PF06134 CL0036 TIM_barrel RhaA L-rhamnose isomerase (RhaA)
PF06135 IreB IreB regulatory phosphoprotein
-PF06136 SOK2_plant Protein SOSEKI 2, plant
+PF06136 SOK Protein SOSEKI, plant
PF06138 Chordopox_E11 Chordopoxvirus E11 protein
PF06139 BphX BphX-like
PF06140 Ifi-6-16 Interferon-induced 6-16 family
@@ -5693,7 +5692,7 @@ PF06168 DUF981 Protein of unknown function (DUF981)
PF06169 DUF982 Protein of unknown function (DUF982)
PF06170 DUF983 Protein of unknown function (DUF983)
PF06172 CL0029 Cupin Cupin_5 Cupin superfamily (DUF985)
-PF06173 DUF986 Protein of unknown function (DUF986)
+PF06173 CL0266 PH DUF986 Protein of unknown function (DUF986)
PF06174 DUF987 Protein of unknown function (DUF987)
PF06175 CL0044 Ferritin MiaE tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
PF06176 CL0016 PKinase WaaY Lipopolysaccharide core biosynthesis protein (WaaY)
@@ -5742,7 +5741,7 @@ PF06222 CL0567 Phage_TACs Phage_TAC_1 Phage tail assembly chaperone
PF06223 Phage_tail_T Minor tail protein T
PF06224 CL0123 HTH HTH_42 Winged helix DNA-binding domain
PF06226 DUF1007 Protein of unknown function (DUF1007)
-PF06227 Poxvirus dsDNA Poxvirus
+PF06227 CL0551 BCLiA Poxv_Bcl-2-like Poxvirus Bcl-2-like proteins
PF06228 CL0312 HemS_ChuX ChuX_HutX Haem utilisation ChuX/HutX
PF06229 CL0066 Trefoil FRG1 FRG1-like domain
PF06230 CL0109 CDA LpxI_C LpxI C-terminal domain
@@ -5756,7 +5755,7 @@ PF06237 DUF1011 Protein of unknown function (DUF1011)
PF06239 ECSIT Evolutionarily conserved signalling intermediate in Toll pathway
PF06240 CL0209 Bet_v_1_like COXG Carbon monoxide dehydrogenase subunit G (CoxG)
PF06241 CL0582 TrkA_C Castor_Poll_mid Castor and Pollux, part of voltage-gated ion channel
-PF06242 DUF1013 Protein of unknown function (DUF1013)
+PF06242 TrcR Transcriptional cell cycle regulator TrcR
PF06243 PaaB Phenylacetic acid degradation B
PF06244 CL0114 HMG-box Ccdc124 Coiled-coil domain-containing protein 124 /Oxs1
PF06245 DUF1015 Protein of unknown function (DUF1015)
@@ -5765,8 +5764,8 @@ PF06247 CL0001 EGF Plasmod_Pvs28 Pvs28 EGF domain
PF06248 CL0295 Vps51 Zw10 Centromere/kinetochore Zw10
PF06249 CL0029 Cupin EutQ Ethanolamine utilisation protein EutQ
PF06250 CL0236 PDDEXK YhcG_C YhcG PDDEXK nuclease domain
-PF06251 CL0072 Ubiquitin Caps_synth_GfcC Capsule biosynthesis GfcC
-PF06252 DUF1018 Protein of unknown function (DUF1018)
+PF06251 CL0072 Ubiquitin Caps_syn_GfcC_C Capsule biosynthesis GfcC C-terminal
+PF06252 GemA Bacteriophage Mu, GemA protein
PF06253 MTTB Trimethylamine methyltransferase (MTTB)
PF06254 YdaT_toxin Putative bacterial toxin ydaT
PF06255 MafB Neisseria toxin MafB
@@ -5777,7 +5776,7 @@ PF06259 CL0028 AB_hydrolase Abhydrolase_8 Alpha/beta hydrolase
PF06260 DUF1024 Protein of unknown function (DUF1024)
PF06261 LktC Actinobacillus actinomycetemcomitans leukotoxin activator LktC
PF06262 CL0126 Peptidase_MA Zincin_1 Zincin-like metallopeptidase
-PF06265 DUF1027 Protein of unknown function (DUF1027)
+PF06265 YutD-like Putative antitoxin YutD-like
PF06266 HrpF HrpF protein
PF06267 DUF1028 Family of unknown function (DUF1028)
PF06268 CL0066 Trefoil Fascin Fascin domain
@@ -5801,7 +5800,7 @@ PF06288 DUF1040 Protein of unknown function (DUF1040)
PF06289 FlbD Flagellar and Swarming motility proteins
PF06290 PsiB Plasmid SOS inhibition protein (PsiB)
PF06291 Lambda_Bor Bor protein
-PF06292 MUN MUN domain
+PF06292 CL0020 TPR MUN MUN domain
PF06293 CL0016 PKinase Kdo Lipopolysaccharide kinase (Kdo/WaaP) family
PF06294 CL0188 CH CH_2 CH-like domain in sperm protein
PF06295 DUF1043 Protein of unknown function (DUF1043)
@@ -5822,7 +5821,7 @@ PF06311 NumbF NUMB domain
PF06312 CL0159 E-set Neurexophilin Neurexophilin
PF06313 ACP53EA Drosophila ACP53EA protein
PF06314 CL0403 ADC-like ADC Acetoacetate decarboxylase (ADC)
-PF06315 CL0016 PKinase AceK Isocitrate dehydrogenase kinase/phosphatase (AceK)
+PF06315 CL0016 PKinase AceK_kinase Isocitrate dehydrogenase kinase/phosphatase (AceK) kinase domain
PF06316 CL0193 MBB Ail_Lom Enterobacterial Ail/Lom protein
PF06317 Arena_RNA_pol Arenavirus RNA polymerase
PF06319 CL0236 PDDEXK MmcB-like DNA repair protein MmcB-like
@@ -5833,7 +5832,7 @@ PF06323 Phage_antiter_Q Phage antitermination protein Q
PF06324 Pigment_DH Pigment-dispersing hormone (PDH)
PF06325 CL0063 NADP_Rossmann PrmA Ribosomal protein L11 methyltransferase (PrmA)
PF06326 Vesiculo_matrix Vesiculovirus matrix protein
-PF06327 CL0276 Nucleot_cyclase DUF1053 Domain of Unknown Function (DUF1053)
+PF06327 CL0276 Nucleot_cyclase Adcy_cons_dom Adenylate cyclase, conserved domain
PF06328 CL0159 E-set Lep_receptor_Ig Ig-like C2-type domain
PF06330 CL0613 Terp_synthase TRI5 Trichodiene synthase (TRI5)
PF06331 Tfb5 Transcription factor TFIIH complex subunit Tfb5
@@ -5858,7 +5857,7 @@ PF06353 DUF1062 Protein of unknown function (DUF1062)
PF06355 CL0293 CDC Aegerolysin Aegerolysin
PF06356 DUF1064 Protein of unknown function (DUF1064)
PF06357 CL0083 Omega_toxin Omega-toxin Omega-atracotoxin
-PF06358 DUF1065 Protein of unknown function (DUF1065)
+PF06358 BNYVV_TGB3 Beet necrotic yellow vein virus, movement protein TGB3
PF06360 E_raikovi_mat Euplotes raikovi mating pheromone
PF06361 RTBV_P12 Rice tungro bacilliform virus P12 protein
PF06362 DUF1067 Protein of unknown function (DUF1067)
@@ -5871,7 +5870,7 @@ PF06368 Met_asp_mut_E Methylaspartate mutase E chain (MutE)
PF06369 CL0293 CDC Anemone_cytotox Sea anemone cytotoxic protein
PF06370 DUF1069 Protein of unknown function (DUF1069)
PF06371 CL0020 TPR Drf_GBD Diaphanous GTPase-binding Domain
-PF06372 CL0010 SH3 Gemin6 Gemin6 protein
+PF06372 CL0527 Sm-like Gemin6 Gemin6 Sm-like domain
PF06373 CL0083 Omega_toxin CART Cocaine and amphetamine regulated transcript protein (CART)
PF06374 NDUF_C2 NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2)
PF06375 AP3D1 AP-3 complex subunit delta-1
@@ -5933,7 +5932,7 @@ PF06435 DUF1079 Repeat of unknown function (DUF1079)
PF06436 Pneumovirus_M2 Pneumovirus matrix protein 2 (M2)
PF06437 ISN1 IMP-specific 5'-nucleotidase
PF06438 HasA Heme-binding protein A (HasA)
-PF06439 CL0004 Concanavalin DUF1080 Domain of Unknown Function (DUF1080)
+PF06439 CL0004 Concanavalin 3keto-disac_hyd 3-keto-disaccharide hydrolase
PF06440 DNA_pol3_theta DNA polymerase III, theta subunit
PF06441 CL0028 AB_hydrolase EHN Epoxide hydrolase N terminus
PF06442 CL0610 ETAP DHFR_2 R67 dihydrofolate reductase
@@ -5942,27 +5941,27 @@ PF06444 NADH_dehy_S2_C NADH dehydrogenase subunit 2 C-terminus
PF06445 CL0319 SHS2 GyrI-like GyrI-like small molecule binding domain
PF06446 Hepcidin Hepcidin
PF06448 DUF1081 Domain of Unknown Function (DUF1081)
-PF06449 DUF1082 Mitochondrial domain of unknown function (DUF1082)
+PF06449 YMF19_C ATP synthase YMF19, C-terminal
PF06450 CL0182 IT NhaB Bacterial Na+/H+ antiporter B (NhaB)
PF06451 Moricin Moricin
PF06452 CL0559 CBD9-like CBM9_1 Carbohydrate family 9 binding domain-like
PF06453 LT-IIB Type II heat-labile enterotoxin , B subunit (LT-IIB)
-PF06454 DUF1084 Protein of unknown function (DUF1084)
+PF06454 CL0192 GPCR_A THH1_TOM1-3_dom THH1/TOM1/TOM3 domain
PF06455 NADH5_C NADH dehydrogenase subunit 5 C-terminus
PF06456 CL0145 Golgi-transport Arfaptin Arfaptin-like domain
PF06457 Ectatomin Ectatomin
PF06458 CL0072 Ubiquitin MucBP MucBP domain
PF06459 RR_TM4-6 Ryanodine Receptor TM 4-6
PF06460 CL0063 NADP_Rossmann CoV_Methyltr_2 Coronavirus 2'-O-methyltransferase
-PF06461 DUF1086 Domain of Unknown Function (DUF1086)
+PF06461 CHDII_SANT-like CHD subfamily II, SANT-like domain
PF06462 CL0186 Beta_propeller Hyd_WA Propeller
PF06463 Mob_synth_C Molybdenum Cofactor Synthesis C
PF06464 CL0660 SHOCT DMAP_binding DMAP1-binding Domain
-PF06465 DUF1087 Domain of Unknown Function (DUF1087)
+PF06465 DUF1087 CHD subfamily II, DUF1087
PF06466 PCAF_N PCAF (P300/CBP-associated factor) N-terminal domain
PF06467 CL0175 TRASH zf-FCS MYM-type Zinc finger with FCS sequence motif
PF06468 CL0154 C2 Spond_N Spondin_N
-PF06469 DUF1088 Domain of Unknown Function (DUF1088)
+PF06469 DUF1088 Neurobeachin-like, DUF1088
PF06470 SMC_hinge SMC proteins Flexible Hinge Domain
PF06471 CL0063 NADP_Rossmann CoV_ExoN Coronavirus proofreading exoribonuclease
PF06472 CL0241 ABC_membrane ABC_membrane_2 ABC transporter transmembrane region 2
@@ -5978,7 +5977,7 @@ PF06481 CL0026 CU_oxidase COX_ARM COX Aromatic Rich Motif
PF06482 CL0056 C_Lectin Endostatin Collagenase NC10 and Endostatin
PF06483 ChiC Chitinase C
PF06484 Ten_N Teneurin Intracellular Region
-PF06485 Tab2_like RNA-binding protein Tab2/Atab2
+PF06485 Tab2-like_N RNA-binding protein Tab2/Atab2 N terminal
PF06486 DUF1093 Protein of unknown function (DUF1093)
PF06487 CL0072 Ubiquitin SAP18 Sin3 associated polypeptide p18 (SAP18)
PF06488 CL0569 Phage_TTPs L_lac_phage_MSP Phage tail tube protein
@@ -5988,7 +5987,7 @@ PF06491 Disulph_isomer Disulphide isomerase
PF06493 DUF1096 Protein of unknown function (DUF1096)
PF06495 Transformer Fruit fly transformer protein
PF06496 DUF1097 Protein of unknown function (DUF1097)
-PF06497 DUF1098 Protein of unknown function (DUF1098)
+PF06497 Baculo_Ac102 Baculovirus Ac102
PF06500 CL0028 AB_hydrolase FrsA-like Esterase FrsA-like
PF06501 CL0153 dUTPase Herpes_U55 Human herpesvirus U55 protein
PF06502 Equine_IAV_S2 Equine infectious anaemia virus S2 protein
@@ -6046,7 +6045,7 @@ PF06559 CL0153 dUTPase DCD 2'-deoxycytidine 5'-triphosphate deaminase (DCD)
PF06560 CL0029 Cupin GPI Glucose-6-phosphate isomerase (GPI)
PF06563 DUF1125 Protein of unknown function (DUF1125)
PF06564 CL0023 P-loop_NTPase CBP_BcsQ Cellulose biosynthesis protein BcsQ
-PF06565 CL0266 PH DUF1126 DUF1126 PH-like domain
+PF06565 CL0266 PH DM10_dom DM10 domain
PF06566 Chon_Sulph_att Chondroitin sulphate attachment domain
PF06567 Neural_ProG_Cyt Neural chondroitin sulphate proteoglycan cytoplasmic domain
PF06568 DUF1127 Domain of unknown function (DUF1127)
@@ -6092,7 +6091,7 @@ PF06611 DUF1145 Protein of unknown function (DUF1145)
PF06612 DUF1146 Protein of unknown function (DUF1146)
PF06613 CL0206 TRB KorB_C KorB C-terminal beta-barrel domain
PF06614 Neuromodulin Neuromodulin
-PF06615 DUF1147 Protein of unknown function (DUF1147)
+PF06615 Circovir2_Orf1 Circovirus 2, Orf1
PF06616 CL0236 PDDEXK BsuBI_PstI_RE BsuBI/PstI restriction endonuclease domain
PF06617 M-inducer_phosp M-phase inducer phosphatase
PF06618 DUF1148 Protein of unknown function (DUF1148)
@@ -6112,7 +6111,7 @@ PF06631 DUF1154 Protein of unknown function (DUF1154)
PF06632 XRCC4 DNA double-strand break repair and V(D)J recombination protein XRCC4
PF06633 DUF1155 Protein of unknown function (DUF1155)
PF06634 DUF1156 Protein of unknown function (DUF1156)
-PF06635 CL0255 ATP_synthase NolV Nodulation protein NolV
+PF06635 CL0255 ATP_synthase T3SS_SCTL Type 3 secretion system stator protein
PF06636 DUF1157 Protein of unknown function (DUF1157)
PF06637 PV-1 PV-1 protein (PLVAP)
PF06638 Strabismus Strabismus protein
@@ -6121,8 +6120,8 @@ PF06640 P_C P protein C-terminus
PF06643 DUF1158 Protein of unknown function (DUF1158)
PF06644 ATP11 ATP11 protein
PF06645 SPC12 Microsomal signal peptidase 12 kDa subunit (SPC12)
-PF06646 CL0177 PBP Mycoplasma_p37 High affinity transport system protein p37
-PF06648 DUF1160 Protein of unknown function (DUF1160)
+PF06646 CL0177 PBP CypI Extracytoplasmic thiamine-binding lipoprotein
+PF06648 AcMNPV_Ac75 Autographa californica nuclear polyhedrosis virus (AcMNPV), Ac75
PF06649 DUF1161 Protein of unknown function (DUF1161)
PF06650 SHR-BD SHR-binding domain of vacuolar-sorting associated protein 13
PF06651 DUF1163 Protein of unknown function (DUF1163)
@@ -6133,7 +6132,7 @@ PF06657 Cep57_MT_bd Centrosome microtubule-binding domain of Cep57
PF06658 DUF1168 Protein of unknown function (DUF1168)
PF06661 VirE3 VirE3
PF06662 CL0059 6_Hairpin C5-epim_C D-glucuronyl C5-epimerase C-terminus
-PF06663 DUF1170 Protein of unknown function (DUF1170)
+PF06663 CNK2_3_dom Connector enhancer of kinase suppressor of ras 2/3 domain
PF06664 MIG-14_Wnt-bd Wnt-binding factor required for Wnt secretion
PF06666 DUF1173 Protein of unknown function (DUF1173)
PF06667 PspB Phage shock protein B
@@ -6191,7 +6190,7 @@ PF06723 CL0108 Actin_ATPase MreB_Mbl MreB/Mbl protein
PF06724 DUF1206 Domain of Unknown Function (DUF1206)
PF06725 CL0199 DPBB 3D 3D domain
PF06726 BC10 Bladder cancer-related protein BC10
-PF06727 DUF1207 Protein of unknown function (DUF1207)
+PF06727 CL0193 MBB DUF1207 Protein of unknown function (DUF1207)
PF06728 CL0111 GT-C PIG-U GPI transamidase subunit PIG-U
PF06729 CENP-R Kinetochore component, CENP-R
PF06730 CL0145 Golgi-transport FAM92 FAM92 protein
@@ -6200,7 +6199,7 @@ PF06733 CL0023 P-loop_NTPase DEAD_2 DEAD_2
PF06734 CL0016 PKinase UL97 UL97
PF06736 TMEM175 Endosomal/lysosomal potassium channel TMEM175
PF06737 CL0037 Lysozyme Transglycosylas Transglycosylase-like domain
-PF06738 CL0470 UMP_1 ThrE Putative threonine/serine exporter
+PF06738 CL0470 ThrE ThrE Putative threonine/serine exporter
PF06739 CL0186 Beta_propeller SBBP Beta-propeller repeat
PF06740 DUF1213 Protein of unknown function (DUF1213)
PF06741 LsmAD LsmAD domain
@@ -6218,7 +6217,6 @@ PF06752 E_Pc_C Enhancer of Polycomb C-terminus
PF06753 Bradykinin Bradykinin
PF06754 PhnG Phosphonate metabolism protein PhnG
PF06755 CbtA_toxin CbtA_toxin of type IV toxin-antitoxin system
-PF06756 S19 Chorion protein S19 C-terminal
PF06757 Ins_allergen_rp Insect allergen related repeat, nitrile-specifier detoxification
PF06758 Olduvai Olduvai domain
PF06760 DUF1221 Protein of unknown function (DUF1221)
@@ -6234,7 +6232,7 @@ PF06771 Desmo_N Viral Desmoplakin N-terminus
PF06772 LtrA Bacterial low temperature requirement A protein (LtrA)
PF06773 Bim_N Bim protein N-terminus
PF06775 Seipin Putative adipose-regulatory protein (Seipin)
-PF06776 IalB Invasion associated locus B (IalB) protein
+PF06776 CL0159 E-set IalB Invasion associated locus B (IalB) protein
PF06777 HBB Helical and beta-bridge domain
PF06778 CL0032 Dim_A_B_barrel Chlor_dismutase Chlorite dismutase
PF06779 CL0015 MFS MFS_4 Uncharacterised MFS-type transporter YbfB
@@ -6246,7 +6244,7 @@ PF06784 UPF0240 Uncharacterised protein family (UPF0240)
PF06785 UPF0242 Uncharacterised protein family (UPF0242) N-terminus
PF06786 UPF0253 Uncharacterised protein family (UPF0253)
PF06787 HcgF FeGP cofactor biosynthesis protein HcgF
-PF06788 UPF0257 Uncharacterised protein family (UPF0257)
+PF06788 CL0193 MBB UPF0257 Uncharacterised protein family (UPF0257)
PF06789 MINAR1_C MINAR1 C-terminal domain
PF06790 UPF0259 Uncharacterised protein family (UPF0259)
PF06791 TMP_2 Prophage tail length tape measure protein
@@ -6257,7 +6255,7 @@ PF06795 Erythrovirus_X Erythrovirus X protein
PF06796 NapE Periplasmic nitrate reductase protein NapE
PF06797 DUF1229 Protein of unknown function (DUF1229)
PF06798 PrkA PrkA serine protein kinase C-terminal domain
-PF06799 DUF1230 Conserved in the green lineage and diatoms 27
+PF06799 CGLD27-like Conserved in the green lineage and diatoms 27
PF06800 CL0184 DMT Sugar_transport Sugar transport protein
PF06802 DUF1231 Protein of unknown function (DUF1231)
PF06803 DUF1232 Protein of unknown function (DUF1232)
@@ -6307,7 +6305,7 @@ PF06852 CL0257 Acetyltrans DUF1248 Protein of unknown function (DUF1248)
PF06853 DUF1249 Protein of unknown function (DUF1249)
PF06854 Phage_Gp15 Bacteriophage Gp15 protein
PF06855 YozE_SAM_like YozE SAM-like fold
-PF06856 DUF1251 Protein of unknown function (DUF1251)
+PF06856 AcMNPV_Orf17 Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf17
PF06857 ACP Malonate decarboxylase delta subunit (MdcD)
PF06858 CL0023 P-loop_NTPase NOG1 Nucleolar GTP-binding protein 1 (NOG1)
PF06859 CL0063 NADP_Rossmann Bin3 Bicoid-interacting protein 3 (Bin3)
@@ -6338,7 +6336,7 @@ PF06887 DUF1265 Protein of unknown function (DUF1265)
PF06888 CL0137 HAD Put_Phosphatase Putative Phosphatase
PF06889 DUF1266 Protein of unknown function (DUF1266)
PF06890 Phage_Mu_Gp45 Bacteriophage Mu Gp45 spike protein
-PF06891 P2_Phage_GpR P2 phage tail completion protein R (GpR)
+PF06891 CL0691 Phage_tail_2 P2_Phage_GpR P2 phage tail completion protein R (GpR)
PF06892 Phage_CP76 Phage regulatory protein CII (CP76)
PF06894 CL0567 Phage_TACs Phage_TAC_2 Bacteriophage lambda tail assembly chaperone, TAC, protein G
PF06896 CL0567 Phage_TACs Phage_TAC_3 Phage tail assembly chaperone proteins, TAC
@@ -6355,13 +6353,13 @@ PF06906 DUF1272 Protein of unknown function (DUF1272)
PF06907 CL0121 Cystatin Latexin Latexin
PF06908 CL0349 SLOG YpsA YspA SLOG family
PF06910 MEA1 Male enhanced antigen 1 (MEA1)
-PF06911 Senescence Senescence-associated protein
+PF06911 CL0023 P-loop_NTPase Senescence Senescence domain
PF06912 CL0142 Membrane_trans DUF1275 Protein of unknown function (DUF1275)
-PF06916 DUF1279 Protein of unknown function (DUF1279)
+PF06916 FAM210A-B_dom FAM210A/B-like domain
PF06917 Pectate_lyase_2 Periplasmic pectate lyase
PF06918 DUF1280 Protein of unknown function (DUF1280)
PF06919 Phage_T4_Gp30_7 Phage Gp30.7 protein
-PF06920 CL0020 TPR DHR-2 Dock homology region 2
+PF06920 CL0020 TPR DHR-2_Lobe_A DHR-2, Lobe A
PF06922 CTV_P13 Citrus tristeza virus P13 protein
PF06923 GutM Glucitol operon activator protein (GutM)
PF06924 DUF1281 Protein of unknown function (DUF1281)
@@ -6413,7 +6411,7 @@ PF06975 DUF1299 Protein of unknown function (DUF1299)
PF06977 CL0186 Beta_propeller SdiA-regulated SdiA-regulated
PF06978 POP1 Ribonucleases P/MRP protein subunit POP1
PF06979 TMEM70 TMEM70/TMEM186/TMEM223 protein family
-PF06980 DUF1302 Protein of unknown function (DUF1302)
+PF06980 CL0193 MBB DUF1302 Protein of unknown function (DUF1302)
PF06983 CL0104 Glyoxalase 3-dmu-9_3-mt 3-demethylubiquinone-9 3-methyltransferase
PF06984 CL0346 Ribo_L29 MRP-L47 Mitochondrial 39-S ribosomal protein L47 (MRP-L47)
PF06985 HET Heterokaryon incompatibility protein (HET)
@@ -6455,13 +6453,13 @@ PF07026 DUF1317 Protein of unknown function (DUF1317)
PF07027 DUF1318 Protein of unknown function (DUF1318)
PF07028 DUF1319 Protein of unknown function (DUF1319)
PF07029 CryBP1 CryBP1 protein
-PF07030 DUF1320 Protein of unknown function (DUF1320)
+PF07030 Phage_Mu_Gp36 Bacteriophage Mu, Gp36
PF07032 DUF1322 Protein of unknown function (DUF1322)
PF07033 Orthopox_B11R Orthopoxvirus B11R protein
PF07034 CL0023 P-loop_NTPase ORC3_N Origin recognition complex (ORC) subunit 3 N-terminus
PF07035 Mic1 Colon cancer-associated protein Mic1-like
PF07037 CL0123 HTH DUF1323 Putative transcription regulator (DUF1323)
-PF07038 DUF1324 Protein of unknown function (DUF1324)
+PF07038 Circovir2_Orf4 Circovirus 2, anti-apoptotic ORF4
PF07039 CL0049 Tudor DUF1325 SGF29 tudor-like domain
PF07040 DUF1326 Protein of unknown function (DUF1326)
PF07041 DUF1327 Protein of unknown function (DUF1327)
@@ -6507,7 +6505,7 @@ PF07084 Spot_14 Thyroid hormone-inducible hepatic protein Spot 14
PF07085 CL0365 MurF-HprK_N DRTGG DRTGG domain
PF07086 Jagunal Jagunal, ER re-organisation during oogenesis
PF07087 DUF1353 Protein of unknown function (DUF1353)
-PF07088 CL0023 P-loop_NTPase GvpD GvpD gas vesicle protein
+PF07088 CL0023 P-loop_NTPase GvpD_P-loop GvpD gas vesicle protein, P-loop domain
PF07090 CL0014 Glutaminase_I GATase1_like Putative glutamine amidotransferase
PF07091 CL0063 NADP_Rossmann FmrO Ribosomal RNA methyltransferase (FmrO)
PF07092 DUF1356 Protein of unknown function (DUF1356)
@@ -6520,7 +6518,7 @@ PF07098 DUF1360 Protein of unknown function (DUF1360)
PF07099 DUF1361 Protein of unknown function (DUF1361)
PF07100 ASRT Anabaena sensory rhodopsin transducer
PF07101 DUF1363 Protein of unknown function (DUF1363)
-PF07102 DUF1364 Protein of unknown function (DUF1364)
+PF07102 YbcO Putative nuclease YbcO
PF07103 DUF1365 Protein of unknown function (DUF1365)
PF07104 DUF1366 Protein of unknown function (DUF1366)
PF07105 DUF1367 Protein of unknown function (DUF1367)
@@ -6536,7 +6534,7 @@ PF07116 DUF1372 Protein of unknown function (DUF1372)
PF07117 DUF1373 Protein of unknown function (DUF1373)
PF07118 DUF1374 Protein of unknown function (DUF1374)
PF07119 DUF1375 Protein of unknown function (DUF1375)
-PF07120 DUF1376 Protein of unknown function (DUF1376)
+PF07120 CL0123 HTH DUF1376 Protein of unknown function (DUF1376)
PF07122 VLPT Variable length PCR target protein (VLPT)
PF07123 PsbW Photosystem II reaction centre W protein (PsbW)
PF07124 Phytoreo_P8 Phytoreovirus outer capsid protein P8
@@ -6548,10 +6546,10 @@ PF07129 DUF1381 Protein of unknown function (DUF1381)
PF07130 YebG YebG protein
PF07131 DUF1382 Protein of unknown function (DUF1382)
PF07133 Merozoite_SPAM Merozoite surface protein (SPAM)
-PF07134 DUF1383 Protein of unknown function (DUF1383)
+PF07134 AcMNPV_Orf18 Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf18
PF07136 DUF1385 Protein of unknown function (DUF1385)
PF07137 CL0116 Calycin VDE VDE lipocalin domain
-PF07138 DUF1386 Protein of unknown function (DUF1386)
+PF07138 AcMNPV_AC11 Baculovirus protein AC11
PF07139 DUF1387 Protein of unknown function (DUF1387)
PF07140 CL0159 E-set IFNGR1 Interferon gamma receptor (IFNGR1)
PF07141 Phage_term_sma Putative bacteriophage terminase small subunit
@@ -6571,8 +6569,8 @@ PF07155 CL0315 Gx_transp ECF-ribofla_trS ECF-type riboflavin transporter, S comp
PF07156 CL0063 NADP_Rossmann Prenylcys_lyase Prenylcysteine lyase
PF07157 DNA_circ_N DNA circularisation protein N-terminus
PF07158 CL0182 IT MatC_N Dicarboxylate carrier protein MatC N-terminus
-PF07159 DUF1394 CYRIA/CYRIB Rac1 binding domain
-PF07160 SKA1 Spindle and kinetochore-associated protein 1
+PF07159 CYRIA-B_Rac1-bd CYRIA/CYRIB Rac1 binding domain
+PF07160 CL0123 HTH SKA1 Spindle and kinetochore-associated protein 1
PF07161 CL0048 LolA_LolB LppX_LprAFG LppX_LprAFG lipoprotein
PF07162 CL0154 C2 B9-C2 Ciliary basal body-associated, B9 protein
PF07163 Pex26 Pex26 protein
@@ -6656,7 +6654,7 @@ PF07246 Phlebovirus_NSM Phlebovirus nonstructural protein NS-M
PF07247 CL0149 CoA-acyltrans AATase Alcohol acetyltransferase
PF07248 DUF1431 Protein of unknown function (DUF1431)
PF07249 CL0199 DPBB Cerato-platanin Cerato-platanin
-PF07250 Glyoxal_oxid_N Glyoxal oxidase N-terminus
+PF07250 CL0186 Beta_propeller Glyoxal_oxid_N Glyoxal oxidase N-terminus
PF07252 DUF1433 Protein of unknown function (DUF1433)
PF07253 Gypsy Gypsy protein
PF07254 Cpta_toxin Membrane-bound toxin component of toxin-antitoxin system
@@ -6688,7 +6686,7 @@ PF07282 CL0167 Zn_Beta_Ribbon OrfB_Zn_ribbon Putative transposase DNA-binding do
PF07283 TrbH Conjugal transfer protein TrbH
PF07284 BCHF 2-vinyl bacteriochlorophyllide hydratase (BCHF)
PF07285 DUF1444 Protein of unknown function (DUF1444)
-PF07286 DUF1445 Protein of unknown function (DUF1445)
+PF07286 D-Glu_cyclase D-glutamate cyclase
PF07287 AtuA Acyclic terpene utilisation family protein AtuA
PF07288 RpoY RNA polymerase epsilon subunit
PF07289 CL0266 PH BBL5 Bardet-Biedl syndrome 5 protein
@@ -6702,7 +6700,7 @@ PF07296 TraP TraP protein
PF07297 DPM2 Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2)
PF07298 CL0115 Steroid_dh NnrU NnrU protein
PF07299 EF-G-binding_N Elongation factor G-binding protein, N-terminal
-PF07301 DUF1453 Protein of unknown function (DUF1453)
+PF07301 DUF1453 CcdC protein
PF07302 CL0399 Asp-glut_race AroM AroM protein
PF07303 Occludin_ELL Occludin homology domain
PF07304 SRA1 Steroid receptor RNA activator (SRA1)
@@ -6718,7 +6716,7 @@ PF07313 CL0125 Peptidase_CA DUF1460 Protein of unknown function (DUF1460)
PF07314 DUF1461 Protein of unknown function (DUF1461)
PF07315 CL0172 Thioredoxin DUF1462 Protein of unknown function (DUF1462)
PF07316 DUF1463 Protein of unknown function (DUF1463)
-PF07317 YcgR Flagellar regulator YcgR
+PF07317 PilZN Flagellar regulator YcgR, PilZN domain
PF07318 CL0108 Actin_ATPase DUF1464 Protein of unknown function (DUF1464)
PF07319 DnaI_N Primosomal protein DnaI N-terminus
PF07321 CL0419 T3SS-Chaperone YscO Type III secretion protein YscO
@@ -6737,7 +6735,7 @@ PF07334 IFP_35_N Interferon-induced 35 kDa protein (IFP 35) N-terminus
PF07335 Glyco_hydro_75 Fungal chitosanase of glycosyl hydrolase group 75
PF07336 ABATE Putative stress-induced transcription regulator
PF07337 CagY_M DC-EC Repeat
-PF07338 DUF1471 Protein of unknown function (DUF1471)
+PF07338 YdgH_BhsA-like YdgH/BhsA/McbA-like domain
PF07340 Herpes_IE1 Cytomegalovirus IE1 protein
PF07341 DUF1473 Protein of unknown function (DUF1473)
PF07342 DUF1474 Protein of unknown function (DUF1474)
@@ -6782,10 +6780,10 @@ PF07382 HC2 Histone H1-like nucleoprotein HC2
PF07383 DUF1496 Protein of unknown function (DUF1496)
PF07384 DUF1497 Protein of unknown function (DUF1497)
PF07385 CL0029 Cupin Lyx_isomer D-lyxose isomerase
-PF07386 DUF1499 Protein of unknown function (DUF1499)
+PF07386 CL0545 APCOP-app_sub DUF1499 Protein of unknown function (DUF1499)
PF07387 CL0016 PKinase Seadorna_VP7 Seadornavirus VP7
PF07388 CL0113 GT-B A-2_8-polyST Alpha-2,8-polysialyltransferase (POLYST)
-PF07389 DUF1500 Protein of unknown function (DUF1500)
+PF07389 Pox_B6 Vaccinia B6 protein
PF07390 P30 Mycoplasma P30 protein
PF07391 NPR NPR nonapeptide repeat (2 copies)
PF07392 P19Arf_N Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus
@@ -6862,7 +6860,7 @@ PF07465 PsaM Photosystem I protein M (PsaM)
PF07466 DUF1517 Protein of unknown function (DUF1517)
PF07467 CL0320 PepSY BLIP Beta-lactamase inhibitor (BLIP)
PF07468 CL0066 Trefoil Agglutinin Agglutinin domain
-PF07469 DUF1518 Domain of unknown function (DUF1518)
+PF07469 DUF1518 Nuclear receptor coactivator, DUF1518
PF07470 CL0059 6_Hairpin Glyco_hydro_88 Glycosyl Hydrolase Family 88
PF07471 CL0123 HTH Phage_Nu1 Phage DNA packaging protein Nu1
PF07472 PA-IIL Fucose-binding lectin II (PA-IIL)
@@ -6897,7 +6895,7 @@ PF07502 CL0168 PAN MANEC MANEC domain
PF07503 zf-HYPF HypF finger
PF07504 CL0121 Cystatin FTP Fungalysin/Thermolysin Propeptide Motif
PF07505 DUF5131 Protein of unknown function (DUF5131)
-PF07506 RepB RepB plasmid partitioning protein
+PF07506 CL0123 HTH RepB RepB plasmid partitioning protein
PF07507 WavE WavE lipopolysaccharide synthesis
PF07508 Recombinase Recombinase
PF07509 DUF1523 Protein of unknown function (DUF1523)
@@ -6917,7 +6915,7 @@ PF07525 CL0642 SOCS_box SOCS_box SOCS box
PF07526 POX Associated with HOX
PF07527 Hairy_orange Hairy Orange
PF07528 CL0260 NTP_transf DZF DZF domain
-PF07529 CL0023 P-loop_NTPase HSA HSA
+PF07529 HSA HSA domain
PF07530 PRE_C2HC Associated with zinc fingers
PF07531 TAFH NHR1 homology to TAF
PF07532 CL0159 E-set Big_4 Bacterial Ig-like domain (group 4)
@@ -6994,11 +6992,11 @@ PF07611 CL0264 SGNH_hydrolase DUF1574 Protein of unknown function (DUF1574)
PF07613 DUF1576 Protein of unknown function (DUF1576)
PF07614 DUF1577 Protein of unknown function (DUF1577)
PF07615 CL0360 MTH1187-YkoF Ykof YKOF-related Family
-PF07617 DUF1579 Protein of unknown function (DUF1579)
+PF07617 CL0116 Calycin DUF1579 Protein of unknown function (DUF1579)
PF07618 DUF1580 Protein of unknown function (DUF1580)
PF07619 DUF1581 Protein of unknown function (DUF1581)
PF07621 DUF1582 Protein of unknown function (DUF1582)
-PF07622 CL0004 Concanavalin DUF1583 Protein of unknown function (DUF1583)
+PF07622 CL0004 Concanavalin DUF1583 Protein of unknown function (DUF1583) C domain
PF07624 PSD2 Protein of unknown function (DUF1585)
PF07626 PSD3 Protein of unknown function (DUF1587)
PF07627 PSCyt3 Protein of unknown function (DUF1588)
@@ -7023,7 +7021,7 @@ PF07652 CL0023 P-loop_NTPase Flavi_DEAD Flavivirus DEAD domain
PF07653 CL0010 SH3 SH3_2 Variant SH3 domain
PF07654 CL0011 Ig C1-set Immunoglobulin C1-set domain
PF07655 Secretin_N_2 Secretin N-terminal domain
-PF07657 CL0154 C2 MNNL N terminus of Notch ligand
+PF07657 CL0154 C2 MNNL N terminus of Notch ligand C2-like domain
PF07659 DUF1599 Nucleotide modification associated domain 1
PF07660 STN Secretin and TonB N terminus short domain
PF07661 CL0251 MORN MORN_2 MORN repeat variant
@@ -7063,7 +7061,7 @@ PF07697 7TMR-HDED 7TM-HD extracellular
PF07698 CL0192 GPCR_A 7TM-7TMR_HD 7TM receptor with intracellular HD hydrolase
PF07699 CL0001 EGF Ephrin_rec_like Tyrosine-protein kinase ephrin type A/B receptor-like
PF07700 CL0210 HNOX-like HNOB Haem-NO-binding
-PF07701 HNOBA Heme NO binding associated
+PF07701 CL0161 GAF HNOBA Heme NO binding associated
PF07702 CL0122 UTRA UTRA UTRA domain
PF07703 CL0159 E-set A2M_BRD Alpha-2-macroglobulin bait region domain
PF07704 CL0057 Met_repress PSK_trans_fac Rv0623-like transcription factor
@@ -7128,12 +7126,12 @@ PF07762 DUF1618 Protein of unknown function (DUF1618)
PF07763 FEZ FEZ-like protein
PF07764 CL0057 Met_repress Omega_Repress Omega Transcriptional Repressor
PF07765 KIP1 KIP1-like protein
-PF07766 LETM1 LETM1-like protein
+PF07766 CL0306 HeH LETM1_RBD LETM1-like, RBD
PF07767 Nop53 Nop53 (60S ribosomal biogenesis)
PF07768 PVL_ORF50 PVL ORF-50-like family
PF07769 PsiF_repeat psiF repeat
PF07771 TSGP1 Tick salivary peptide group 1
-PF07773 DUF1619 Protein of unknown function (DUF1619)
+PF07773 TCTN_DUF1619 Tectonic domain DUF1619
PF07774 EMC1_C ER membrane protein complex subunit 1, C-terminal
PF07775 PaRep2b PaRep2b protein
PF07776 CL0361 C2H2-zf zf-AD Zinc-finger associated domain (zf-AD)
@@ -7157,7 +7155,7 @@ PF07794 DUF1633 Protein of unknown function (DUF1633)
PF07795 DUF1635 Protein of unknown function (DUF1635)
PF07796 DUF1638 Protein of unknown function (DUF1638)
PF07797 DUF1639 Protein of unknown function (DUF1639)
-PF07798 DUF1640 Protein of unknown function (DUF1640)
+PF07798 CCDC90-like Coiled-coil domain-containing protein 90-like
PF07799 DUF1643 Protein of unknown function (DUF1643)
PF07800 CL0229 RING DUF1644 Protein of unknown function (DUF1644)
PF07801 DUF1647 Protein of unknown function (DUF1647)
@@ -7175,7 +7173,7 @@ PF07813 CL0515 LTXXQ-like LTXXQ LTXXQ motif family protein
PF07814 WAPL Wings apart-like protein regulation of heterochromatin
PF07815 Abi_HHR Abl-interactor HHR
PF07816 DUF1645 Protein of unknown function (DUF1645)
-PF07817 GLE1 GLE1-like protein
+PF07817 CL0020 TPR GLE1 GLE1-like protein
PF07818 HCNGP HCNGP-like protein
PF07819 CL0028 AB_hydrolase PGAP1 PGAP1-like protein
PF07820 TraC TraC-like protein
@@ -7209,7 +7207,7 @@ PF07849 DUF1641 Protein of unknown function (DUF1641)
PF07850 Renin_r Renin receptor-like protein
PF07851 TMPIT TMPIT-like protein
PF07852 DUF1642 Protein of unknown function (DUF1642)
-PF07853 DUF1648 Protein of unknown function (DUF1648)
+PF07853 DUF1648 Domain of unknown function (DUF1648)
PF07854 CL0182 IT DUF1646 Protein of unknown function (DUF1646)
PF07855 CL0651 Mad2 ATG101 Autophagy-related protein 101
PF07856 Orai-1 Mediator of CRAC channel activity
@@ -7242,7 +7240,7 @@ PF07883 CL0029 Cupin Cupin_2 Cupin domain
PF07884 VKOR Vitamin K epoxide reductase family
PF07885 CL0030 Ion_channel Ion_trans_2 Ion channel
PF07886 BA14K BA14K-like protein
-PF07887 Calmodulin_bind Calmodulin binding protein-like
+PF07887 CL0073 P53-like Calmodulin_bind Calmodulin binding protein-like N-terminal domain
PF07888 CALCOCO1 Calcium binding and coiled-coil domain (CALCOCO1) like
PF07889 DUF1664 Protein of unknown function (DUF1664)
PF07890 Rrp15p Rrp15p
@@ -7268,7 +7266,7 @@ PF07910 CL0125 Peptidase_CA Peptidase_C78 Peptidase family C78
PF07911 DUF1677 Protein of unknown function (DUF1677)
PF07912 CL0172 Thioredoxin ERp29_N ERp29, N-terminal domain
PF07913 DUF1678 Protein of unknown function (DUF1678)
-PF07914 CL0016 PKinase DUF1679 Protein of unknown function (DUF1679)
+PF07914 CL0016 PKinase DUF1679 Uncharacterized oxidoreductase dhs-27
PF07915 CL0226 M6PR PRKCSH Glucosidase II beta subunit-like protein
PF07916 TraG_N TraG-like protein, N-terminal region
PF07918 CAP160 CAP160 repeat
@@ -7294,15 +7292,15 @@ PF07938 CL0434 Sialidase Fungal_lectin Fungal fucose-specific lectin
PF07939 DUF1685 Protein of unknown function (DUF1685)
PF07940 CL0103 Gal_mutarotase Hepar_II_III Heparinase II/III-like protein
PF07941 K_channel_TID Potassium channel Kv1.4 tandem inactivation domain
-PF07942 CL0063 NADP_Rossmann N2227 N2227-like protein
+PF07942 CL0063 NADP_Rossmann CARME Carnosine N-methyltransferase
PF07943 PBP5_C Penicillin-binding protein 5, C-terminal domain
PF07944 CL0059 6_Hairpin Glyco_hydro_127 Beta-L-arabinofuranosidase, GH127
PF07945 CL0083 Omega_toxin Toxin_16 Janus-atracotoxin
-PF07946 DUF1682 Protein of unknown function (DUF1682)
+PF07946 CCDC47 PAT complex subunit CCDC47
PF07947 YhhN YhhN family
PF07948 CL0361 C2H2-zf Nairovirus_M Nairovirus M polyprotein-like
PF07949 YbbR YbbR-like protein
-PF07950 CL0335 FumRed-TM DUF1691 Protein of unknown function (DUF1691)
+PF07950 CL0335 FumRed-TM MCP1_TM MDM10-complementing protein 1, transmembrane domain
PF07951 CL0066 Trefoil Toxin_R_bind_C Clostridium neurotoxin, C-terminal receptor binding
PF07952 Toxin_trans Clostridium neurotoxin, Translocation domain
PF07953 CL0004 Concanavalin Toxin_R_bind_N Clostridium neurotoxin, N-terminal receptor binding
@@ -7337,7 +7335,7 @@ PF07981 Plasmod_MYXSPDY Plasmodium repeat_MYXSPDY
PF07982 Herpes_UL74 Herpes UL74 glycoproteins
PF07983 X8 X8 domain
PF07984 CL0260 NTP_transf NTP_transf_7 Nucleotidyltransferase
-PF07985 SRR1 SRR1
+PF07985 CL0063 NADP_Rossmann SRR1 SRR1 domain
PF07986 CL0391 CAP_C-like TBCC Tubulin binding cofactor C
PF07987 DUF1775 Domain of unkown function (DUF1775)
PF07988 LMSTEN LMSTEN motif
@@ -7351,7 +7349,7 @@ PF07995 CL0186 Beta_propeller GSDH Glucose / Sorbosone dehydrogenase
PF07996 T4SS Type IV secretion system proteins
PF07997 DUF1694 Protein of unknown function (DUF1694)
PF07998 CL0126 Peptidase_MA Peptidase_M54 Peptidase family M54
-PF07999 CL0023 P-loop_NTPase RHSP Retrotransposon hot spot protein
+PF07999 CL0023 P-loop_NTPase RHSP Retrotransposon hot spot protein, P-loop domain
PF08000 CL0266 PH bPH_1 Bacterial PH domain
PF08001 CMV_US CMV US
PF08002 DUF1697 Protein of unknown function (DUF1697)
@@ -7359,7 +7357,7 @@ PF08003 CL0063 NADP_Rossmann Methyltransf_9 Protein of unknown function (DUF1698
PF08004 DUF1699 Protein of unknown function (DUF1699)
PF08005 PHR PHR domain
PF08006 CL0112 Yip1 DUF1700 Protein of unknown function (DUF1700)
-PF08007 CL0029 Cupin Cupin_4 Cupin superfamily protein
+PF08007 CL0029 Cupin JmjC_2 JmjC domain
PF08008 CL0083 Omega_toxin Viral_cys_rich Viral cysteine rich
PF08009 CDP-OH_P_tran_2 CDP-alcohol phosphatidyltransferase 2
PF08010 Phage_30_3 Bacteriophage protein GP30.3
@@ -7452,7 +7450,7 @@ PF08097 Toxin_26 Conotoxin T-superfamily
PF08098 ATX_III Anemonia sulcata toxin III family
PF08099 CL0083 Omega_toxin Toxin_27 Scorpion calcine family
PF08100 CL0123 HTH Dimerisation Dimerisation domain
-PF08101 CL0409 GAP DUF1708 Domain of unknown function (DUF1708)
+PF08101 CL0409 GAP Msb1-Mug8_dom Meiotically up-regulated protein Msb1/Mug8 domain
PF08102 Antimicrobial_7 Scorpion antimicrobial peptide
PF08103 Antimicrobial_8 Uperin family
PF08104 Antimicrobial_9 Ponericin L family
@@ -7511,7 +7509,7 @@ PF08157 NUC129 NUC129 domain
PF08158 NUC130_3NT NUC130/3NT domain
PF08159 NUC153 NUC153 domain
PF08161 NUC173 NUC173 domain
-PF08163 NUC194 NUC194 domain
+PF08163 CL0020 TPR DNAPKcs_CC3 DNA-dependent protein kinase catalytic subunit, CC3
PF08164 TRAUB Apoptosis-antagonizing transcription factor, C-terminal
PF08165 FerA FerA (NUC095) domain
PF08166 NUC202 NUC202 domain
@@ -7560,9 +7558,9 @@ PF08209 CL0361 C2H2-zf Sgf11 Sgf11 (transcriptional regulation protein)
PF08210 CL0109 CDA APOBEC_N APOBEC-like N-terminal domain
PF08211 CL0109 CDA dCMP_cyt_deam_2 Cytidine and deoxycytidylate deaminase zinc-binding region
PF08212 CL0116 Calycin Lipocalin_2 Lipocalin-like domain
-PF08213 DUF1713 Mitochondrial domain of unknown function (DUF1713)
+PF08213 COX24_C Mitochondrial mRNA-processing protein COX24, C-terminal
PF08214 CL0257 Acetyltrans HAT_KAT11 Histone acetylation protein
-PF08216 CTNNBL Catenin-beta-like, Arm-motif containing nuclear
+PF08216 CL0020 TPR CTNNBL Catenin-beta-like, Arm-motif containing nuclear
PF08218 CL0039 HUP Citrate_ly_lig Citrate lyase ligase C-terminal domain
PF08219 TOM13 Outer membrane protein TOM13
PF08220 CL0123 HTH HTH_DeoR DeoR-like helix-turn-helix domain
@@ -7638,7 +7636,7 @@ PF08290 Hep_core_N Hepatitis core protein, putative zinc finger
PF08291 CL0170 Peptidase_MD Peptidase_M15_3 Peptidase M15
PF08292 CL0021 OB RNA_pol_Rbc25 RNA polymerase III subunit Rpc25
PF08293 MRP-S33 Mitochondrial ribosomal subunit S27
-PF08294 CL0455 MIM-OM_import TIM21 TIM21
+PF08294 CL0051 NTF2 TIM21 TIM21
PF08295 Sin3_corepress Sin3 family co-repressor
PF08297 U3_snoRNA_assoc U3 snoRNA associated
PF08298 CL0023 P-loop_NTPase AAA_PrkA PrkA AAA domain
@@ -7653,7 +7651,7 @@ PF08307 Glyco_hydro_98C Glycosyl hydrolase family 98 C-terminal domain
PF08308 CL0287 Transthyretin PEGA PEGA domain
PF08309 CL0186 Beta_propeller LVIVD LVIVD repeat
PF08310 CL0186 Beta_propeller LGFP LGFP repeat
-PF08311 Mad3_BUB1_I Mad3/BUB1 homology region 1
+PF08311 CL0020 TPR Mad3_BUB1_I Mad3/BUB1 homology region 1
PF08312 cwf21 cwf21 domain
PF08313 SCA7 SCA7, zinc-binding domain
PF08314 Sec39 Secretory pathway protein Sec39
@@ -7664,13 +7662,13 @@ PF08318 CL0294 Sec10 COG4 COG4 transport protein
PF08320 PIG-X PIG-X / PBN1
PF08321 CL0020 TPR PPP5 PPP5 TPR repeat region
PF08323 CL0113 GT-B Glyco_transf_5 Starch synthase catalytic domain
-PF08324 PUL PUL domain
+PF08324 CL0020 TPR PUL PUL domain
PF08325 CL0126 Peptidase_MA WLM WLM domain
PF08326 ACC_central Acetyl-CoA carboxylase, central region
PF08327 CL0209 Bet_v_1_like AHSA1 Activator of Hsp90 ATPase homolog 1-like protein
PF08328 ASL_C Adenylosuccinate lyase C-terminal
PF08329 CL0159 E-set ChitinaseA_N Chitinase A, N-terminal domain
-PF08331 DUF1730 Domain of unknown function (DUF1730)
+PF08331 QueG_DUF1730 Epoxyqueuosine reductase QueG, DUF1730
PF08332 CL0051 NTF2 CaMKII_AD Calcium/calmodulin dependent protein kinase II association domain
PF08333 DUF1725 Protein of unknown function (DUF1725)
PF08334 CL0327 Pilus T2SSG Type II secretion system (T2SS), protein G
@@ -7688,8 +7686,8 @@ PF08346 AntA AntA/AntB antirepressor
PF08347 CTNNB1_binding N-terminal CTNNB1 binding
PF08348 CL0183 PAS_Fold PAS_6 YheO-like PAS domain
PF08349 DUF1722 Protein of unknown function (DUF1722)
-PF08350 DUF1724 Domain of unknown function (DUF1724)
-PF08351 CL0023 P-loop_NTPase DUF1726 Domain of unknown function (DUF1726)
+PF08350 FilR1_middle Methanogenesis regulatory protein FilR1, middle domain
+PF08351 CL0023 P-loop_NTPase TmcA_N tRNA(Met) cytidine acetyltransferase TmcA, N-terminal
PF08352 oligo_HPY Oligopeptide/dipeptide transporter, C-terminal region
PF08353 MurT_C MurT ligase C-terminal
PF08354 DUF1729 Domain of unknown function (DUF1729)
@@ -7744,7 +7742,7 @@ PF08405 Calici_PP_N Viral polyprotein N-terminal
PF08406 CL0671 AAA_lid CbbQ_C CbbQ/NirQ/NorQ C-terminal
PF08407 Chitin_synth_1N Chitin synthase N-terminal
PF08408 DNA_pol_B_3 DNA polymerase family B viral insert
-PF08409 DUF1736 Domain of unknown function (DUF1736)
+PF08409 TMTC_DUF1736 Protein O-mannosyl-transferase TMTC, DUF1736
PF08410 DUF1737 Domain of unknown function (DUF1737)
PF08411 Exonuc_X-T_C Exonuclease C-terminal
PF08412 Ion_trans_N Ion transport protein N-terminal
@@ -7756,7 +7754,7 @@ PF08421 CL0045 Rubredoxin Methyltransf_13 Putative zinc binding domain
PF08423 CL0023 P-loop_NTPase Rad51 Rad51
PF08424 NRDE-2 NRDE-2, necessary for RNA interference
PF08426 ICE2 ICE2
-PF08427 DUF1741 Domain of unknown function (DUF1741)
+PF08427 ARMH3_C Armadillo-like helical domain-containing protein 3, C-terminal
PF08428 CL0159 E-set Rib Rib domain
PF08429 PLU-1 PLU-1-like protein
PF08430 Forkhead_N Forkhead N-terminal region
@@ -7781,13 +7779,13 @@ PF08449 CL0184 DMT UAA UAA transporter family
PF08450 CL0186 Beta_propeller SGL SMP-30/Gluconolactonase/LRE-like region
PF08451 A_deaminase_N Adenosine/AMP deaminase N-terminal
PF08452 DNAP_B_exo_N DNA polymerase family B exonuclease domain, N-terminal
-PF08453 Peptidase_M9_N Peptidase family M9 N-terminal
-PF08454 RIH_assoc RyR and IP3R Homology associated
+PF08453 CL0020 TPR Peptidase_M9_N Peptidase family M9 N-terminal
+PF08454 CL0020 TPR RIH_assoc RyR and IP3R Homology associated
PF08455 SNF2_assoc Bacterial SNF2 helicase associated
PF08456 Vmethyltransf_C Viral methyltransferase C-terminal
PF08457 Sfi1 Sfi1 spindle body protein
PF08458 CL0266 PH PH_2 Plant pleckstrin homology-like region
-PF08459 CL0219 RNase_H UvrC_HhH_N UvrC RIbonuclease H-like domain
+PF08459 CL0219 RNase_H UvrC_RNaseH_dom UvrC RNAse H endonuclease domain
PF08460 CL0010 SH3 SH3_5 Bacterial SH3 domain
PF08461 CL0123 HTH HTH_12 Ribonuclease R winged-helix domain
PF08462 CL0055 Nucleoplasmin Carmo_coat_C Carmovirus coat protein
@@ -7838,10 +7836,10 @@ PF08507 COPI_assoc COPI associated protein
PF08508 DUF1746 Fungal domain of unknown function (DUF1746)
PF08509 Ad_cyc_g-alpha Adenylate cyclase G-alpha binding domain
PF08510 PIG-P PIG-P
-PF08511 COQ9 COQ9
+PF08511 CL0174 TetR_C COQ9 COQ9
PF08512 CL0266 PH Rtt106 Histone chaperone Rttp106-like
PF08513 CL0561 LisH LisH LisH
-PF08514 STAG STAG domain
+PF08514 CL0020 TPR STAG STAG domain
PF08515 TGF_beta_GS Transforming growth factor beta type I GS-motif
PF08516 ADAM_CR ADAM cysteine-rich
PF08517 CL0363 H-int AXH Ataxin-1 and HBP1 module (AXH)
@@ -7876,14 +7874,14 @@ PF08545 CL0046 Thiolase ACP_syn_III 3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
PF08546 CL0106 6PGD_C ApbA_C Ketopantoate reductase PanE/ApbA C terminal
PF08547 CL0202 GBD CIA30 Complex I intermediate-associated protein 30 (CIA30)
PF08548 CL0592 beta_Roll Peptidase_M10_C Peptidase M10 serralysin C terminal
-PF08549 SWI-SNF_Ssr4 Fungal domain of unknown function (DUF1750)
+PF08549 SWI-SNF_Ssr4_N SWI/SNF and RSC complexes subunit Ssr4 N-terminal
PF08550 DUF1752 Fungal protein of unknown function (DUF1752)
PF08551 CL0207 Rhomboid-like DUF1751 Eukaryotic integral membrane protein (DUF1751)
PF08552 Kei1 Inositolphosphorylceramide synthase subunit Kei1
PF08553 CL0186 Beta_propeller VID27 VID27 C-terminal WD40-like domain
PF08555 FAM32A FAM32A
PF08557 Lipid_DES Sphingolipid Delta4-desaturase (DES)
-PF08558 TRF Telomere repeat binding factor (TRF)
+PF08558 CL0020 TPR TRF Telomere repeat binding factor (TRF)
PF08559 Cut8 Cut8, nuclear proteasome tether protein
PF08560 DUF1757 Protein of unknown function (DUF1757)
PF08561 Ribosomal_L37 Mitochondrial ribosomal protein L37
@@ -7893,12 +7891,12 @@ PF08564 CDC37_C Cdc37 C terminal domain
PF08565 CDC37_M Cdc37 Hsp90 binding domain
PF08566 CL0142 Membrane_trans Pam17 Mitochondrial import protein Pam17
PF08567 CL0266 PH PH_TFIIH TFIIH p62 subunit, N-terminal domain
-PF08568 Kinetochor_Ybp2 Uncharacterised protein family, YAP/Alf4/glomulin
+PF08568 CL0020 TPR Kinetochor_Ybp2 Uncharacterised protein family, YAP/Alf4/glomulin
PF08569 CL0020 TPR Mo25 Mo25-like
PF08570 DUF1761 Protein of unknown function (DUF1761)
PF08571 Yos1 Yos1-like
PF08572 PRP3 pre-mRNA processing factor 3 (PRP3)
-PF08573 SAE2 DNA repair protein endonuclease SAE2/CtIP C-terminus
+PF08573 SAE2 DNA endonuclease activator SAE2/CtIP C-terminus
PF08574 Iwr1 Transcription factor Iwr1
PF08576 DUF1764 Eukaryotic protein of unknown function (DUF1764)
PF08577 PI31_Prot_C PI31 proteasome regulator
@@ -7915,7 +7913,7 @@ PF08588 DUF1769 Protein of unknown function (DUF1769)
PF08589 ATG43 Autophagy receptor ATG43
PF08590 DUF1771 Domain of unknown function (DUF1771)
PF08591 RNR_inhib Ribonucleotide reductase inhibitor
-PF08592 DUF1772 Domain of unknown function (DUF1772)
+PF08592 Anthrone_oxy Anthrone oxygenase
PF08593 DUF1773 Domain of unknown function
PF08594 UPF0300 Uncharacterised protein family (UPF0300)
PF08595 RXT2_N RXT2-like, N-terminal
@@ -7931,7 +7929,7 @@ PF08604 Nup153 Nucleoporin Nup153-like
PF08605 CL0049 Tudor Rad9_Rad53_bind Fungal Rad9-like Rad53-binding
PF08606 Prp19 Prp19/Pso4-like
PF08608 Wyosine_form Wyosine base formation
-PF08609 Fes1 Nucleotide exchange factor Fes1
+PF08609 CL0020 TPR Fes1 Nucleotide exchange factor Fes1
PF08610 Pex16 Peroxisomal membrane protein (Pex16)
PF08611 DUF1774 Fungal protein of unknown function (DUF1774)
PF08612 CL0273 CYTH Med20 TATA-binding related factor (TRF) of subunit 20 of Mediator complex
@@ -8015,9 +8013,9 @@ PF08689 Med5 Mediator complex subunit Med5
PF08690 CL0706 EMC6 GET2 GET complex subunit GET2
PF08691 Nse5 DNA repair proteins Nse5 and Nse6
PF08692 Pet20 Mitochondrial protein Pet20
-PF08693 SKG6 Transmembrane alpha-helix domain
+PF08693 SKG6 SKG6 family
PF08694 CL0208 UBC UFC1 Ubiquitin-fold modifier-conjugating enzyme 1
-PF08695 CL0455 MIM-OM_import Coa1 Cytochrome oxidase complex assembly protein 1
+PF08695 CL0051 NTF2 Coa1 Cytochrome oxidase complex assembly protein 1
PF08696 CL0236 PDDEXK Dna2 DNA replication factor Dna2
PF08698 Fcf2 Fcf2 pre-rRNA processing
PF08699 ArgoL1 Argonaute linker 1 domain
@@ -8043,7 +8041,7 @@ PF08718 GLTP Glycolipid transfer protein (GLTP)
PF08719 NADAR NADAR domain
PF08720 Hema_stalk Influenza C hemagglutinin stalk
PF08721 CL0123 HTH Tn7_Tnp_TnsA_C TnsA endonuclease C terminal
-PF08722 CL0236 PDDEXK Tn7_Tnp_TnsA_N TnsA endonuclease N terminal
+PF08722 CL0236 PDDEXK Tn7_TnsA-like_N TnsA-like endonuclease N terminal
PF08723 CL0074 Matrix Gag_p15 Gag protein p15
PF08724 CL0169 Rep Rep_N Rep protein catalytic domain like
PF08725 Integrin_b_cyt Integrin beta cytoplasmic domain
@@ -8067,7 +8065,7 @@ PF08743 Nse4_C Nse4 C-terminal
PF08744 NOZZLE Plant transcription factor NOZZLE
PF08745 CL0280 PIN PIN_5 PINc domain ribonuclease
PF08746 CL0229 RING zf-RING-like RING-like domain
-PF08747 DUF1788 Domain of unknown function (DUF1788)
+PF08747 BrxB BREX protein BrxB
PF08748 CL0567 Phage_TACs Phage_TAC_4 Phage tail assembly chaperone
PF08750 CNP1 CNP1-like family
PF08751 CL0169 Rep TrwC TrwC relaxase
@@ -8116,7 +8114,7 @@ PF08795 DUF1796 Putative papain-like cysteine peptidase (DUF1796)
PF08796 DUF1797 Protein of unknown function (DUF1797)
PF08797 HIRAN HIRAN domain
PF08798 CL0362 RAMPS-Cas5-like CRISPR_assoc CRISPR associated protein
-PF08799 PRP4 pre-mRNA processing factor 4 (PRP4) like
+PF08799 CL0306 HeH PRP4 pre-mRNA processing factor 4 (PRP4) like
PF08800 VirE_N VirE N-terminal domain
PF08801 CL0186 Beta_propeller Nucleoporin_N Nup133 N terminal like
PF08803 CL0032 Dim_A_B_barrel ydhR Putative mono-oxygenase ydhR
@@ -8162,7 +8160,7 @@ PF08845 SymE_toxin Toxin SymE, type I toxin-antitoxin system
PF08846 DUF1816 Domain of unknown function (DUF1816)
PF08847 Crr6 Chlororespiratory reduction 6
PF08848 CL0609 sPC4_like DUF1818 Domain of unknown function (DUF1818)
-PF08849 CL0123 HTH DUF1819 Putative inner membrane protein (DUF1819)
+PF08849 CL0123 HTH BrxA BrxA
PF08850 DUF1820 Domain of unknown function (DUF1820)
PF08852 CL0020 TPR DUF1822 Protein of unknown function (DUF1822)
PF08853 DUF1823 Domain of unknown function (DUF1823)
@@ -8174,7 +8172,7 @@ PF08858 IDEAL IDEAL domain
PF08859 DGC DGC domain
PF08860 DUF1827 Domain of unknown function (DUF1827)
PF08861 DUF1828 Domain of unknown function DUF1828
-PF08862 DUF1829 Domain of unknown function DUF1829
+PF08862 CL0236 PDDEXK DUF1829 Domain of unknown function DUF1829
PF08863 CL0654 WYL YolD YolD-like protein
PF08864 UPF0302 UPF0302 domain
PF08865 DUF1830 Domain of unknown function (DUF1830)
@@ -8184,12 +8182,12 @@ PF08868 YugN YugN-like family
PF08869 XisI XisI protein
PF08870 CL0057 Met_repress DndE DNA sulphur modification protein DndE
PF08872 KGK KGK domain
-PF08873 DUF1834 Domain of unknown function (DUF1834)
+PF08873 CL0691 Phage_tail_2 Phage_Mu_Gp37 Bacteriophage Mu, Gp37
PF08874 DUF1835 Domain of unknown function (DUF1835)
PF08875 CL0249 Phage_tail_L DUF1833 Domain of unknown function (DUF1833)
PF08876 CL0123 HTH DUF1836 Domain of unknown function (DUF1836)
-PF08877 CL0236 PDDEXK MepB MepB protein
-PF08878 Cap4_SAVED Cap4 SAVED domain
+PF08877 CL0236 PDDEXK MepB-like MepB-like
+PF08878 HamA HamA
PF08879 WRC WRC
PF08880 QLQ QLQ
PF08881 CVNH CVNH domain
@@ -8207,7 +8205,7 @@ PF08892 YqcI_YcgG YqcI/YcgG family
PF08893 DUF1839 Domain of unknown function (DUF1839)
PF08894 DUF1838 Protein of unknown function (DUF1838)
PF08895 DUF1840 Domain of unknown function (DUF1840)
-PF08896 DUF1842 Domain of unknown function (DUF1842)
+PF08896 CL0193 MBB DUF1842 Domain of unknown function (DUF1842)
PF08897 DUF1841 Domain of unknown function (DUF1841)
PF08898 DUF1843 Domain of unknown function (DUF1843)
PF08899 DUF1844 Domain of unknown function (DUF1844)
@@ -8219,7 +8217,7 @@ PF08904 EipB_like EipB-like
PF08905 DUF1850 Domain of unknown function (DUF1850)
PF08906 DUF1851 Domain of unknown function (DUF1851)
PF08907 DUF1853 Domain of unknown function (DUF1853)
-PF08908 DUF1852 Domain of unknown function (DUF1852)
+PF08908 MesX Putative oxygenase MesX
PF08909 DUF1854 Domain of unknown function (DUF1854)
PF08910 Aida_N Aida N-terminus
PF08911 NUP50 NUP50 (Nucleoporin 50 kDa)
@@ -8257,8 +8255,8 @@ PF08944 p47_phox_C NADPH oxidase subunit p47Phox, C terminal domain
PF08945 Bclx_interact Bcl-x interacting, BH3 domain
PF08946 Osmo_CC Osmosensory transporter coiled coil
PF08947 BPS BPS (Between PH and SH2)
-PF08948 DUF1859 Domain of unknown function (DUF1859)
-PF08949 CL0100 C1q_TNF DUF1860 Domain of unknown function (DUF1860)
+PF08948 PRD1_P5_spike_N Bacteriophage PRD1, P5, spike N-terminal
+PF08949 CL0100 C1q_TNF PRD1_P5_C Bacteriophage PRD1, spike protein P5, C-terminal
PF08950 CL0143 B_Fructosidase DUF1861 Protein of unknown function (DUF1861)
PF08951 EntA_Immun Enterocin A Immunity
PF08952 CL0221 RRM DUF1866 Domain of unknown function (DUF1866)
@@ -8267,9 +8265,9 @@ PF08954 Trimer_CC Trimerisation motif
PF08955 BofC_C BofC C-terminal domain
PF08956 DUF1869 Domain of unknown function (DUF1869)
PF08958 DUF1871 Domain of unknown function (DUF1871)
-PF08960 DUF1874 Domain of unknown function (DUF1874)
+PF08960 STIV_B116-like STIV B116-like
PF08961 NRBF2 Nuclear receptor-binding factor 2, autophagy regulator
-PF08962 DUF1876 Domain of unknown function (DUF1876)
+PF08962 Rv2632c-like Rv2632c-like
PF08963 DUF1878 Protein of unknown function (DUF1878)
PF08964 CL0333 gCrystallin Crystall_3 Beta/Gamma crystallin
PF08965 CL0123 HTH DUF1870 Domain of unknown function (DUF1870)
@@ -8287,9 +8285,9 @@ PF08976 CL0220 EF_hand EF-hand_11 EF-hand domain
PF08977 BOFC_N Bypass of Forespore C, N terminal
PF08978 CL0004 Concanavalin Reoviridae_Vp9 Reoviridae VP9
PF08979 DUF1894 Domain of unknown function (DUF1894)
-PF08980 DUF1883 Domain of unknown function (DUF1883)
-PF08982 CL0209 Bet_v_1_like DUF1857 Domain of unknown function (DUF1857)
-PF08983 DUF1856 Domain of unknown function (DUF1856)
+PF08980 CL0202 GBD DUF1883 Domain of unknown function (DUF1883)
+PF08982 CL0209 Bet_v_1_like AtaL Acetylaranotin biosynthesis cluster protein L
+PF08983 V1R_C Vasopressin V1 receptor, C-terminal
PF08984 DUF1858 Domain of unknown function (DUF1858)
PF08985 CL0026 CU_oxidase DP-EP DP-EP family
PF08986 DUF1889 Domain of unknown function (DUF1889)
@@ -8310,7 +8308,7 @@ PF09000 Cytotoxic Cytotoxic
PF09001 DUF1890 Domain of unknown function (DUF1890)
PF09002 CL0236 PDDEXK DUF1887 Domain of unknown function (DUF1887)
PF09003 CL0081 MBD-like Arm-DNA-bind_1 Bacteriophage lambda integrase, Arm DNA-binding domain
-PF09004 DUF1891 Domain of unknown function (DUF1891)
+PF09004 ALKBH8_N Alkylated DNA repair protein alkB homolog 8, N-terminal
PF09005 DUF1897 Domain of unknown function (DUF1897)
PF09006 Surfac_D-trimer Lung surfactant protein D coiled-coil trimerisation
PF09007 CL0466 PDZ-like EBP50_C EBP50, C-terminal
@@ -8384,7 +8382,7 @@ PF09077 Phage-MuB_C Mu B transposition protein, C terminal
PF09078 CL0634 CheY-binding CheY-binding CheY binding
PF09079 CL0123 HTH Cdc6_C CDC6, C terminal winged helix domain
PF09080 CL0065 Cyclin K-cyclin_vir_C K cyclin, C terminal
-PF09081 CL0369 GHD DUF1921 Domain of unknown function (DUF1921)
+PF09081 CL0369 GHD AMT4_dom_C Glucan 1,4-alpha-maltotetraohydrolase, domain C
PF09082 DUF1922 Domain of unknown function (DUF1922)
PF09083 CL0369 GHD DUF1923 Domain of unknown function (DUF1923)
PF09084 CL0177 PBP NMT1 NMT1/THI5 like
@@ -8396,13 +8394,13 @@ PF09089 CL0606 Phage_fibre gp12-short_mid Phage short tail fibre protein gp12, m
PF09090 CL0020 TPR MIF4G_like_2 MIF4G like
PF09092 CL0202 GBD Lyase_N Lyase, N terminal
PF09093 CL0372 Hy-ly_N Lyase_catalyt Lyase, catalytic
-PF09094 CL0599 GH57_38_middle DUF1925 Domain of unknown function (DUF1925)
-PF09095 CL0103 Gal_mutarotase DUF1926 Domain of unknown function (DUF1926)
+PF09094 CL0599 GH57_38_middle AmyA-A_glucT_m Alpha-amylase/4-alpha-glucanotransferase, middle domain
+PF09095 CL0103 Gal_mutarotase AmyA-gluTrfs_C Alpha-amylase/4-alpha-glucanotransferase, C-terminal
PF09096 CL0504 Phage_barrel Phage-tail_2 Baseplate structural protein, domain 2
PF09097 CL0504 Phage_barrel Phage-tail_1 Baseplate structural protein, domain 1
PF09098 CL0318 Cytochrome-c Dehyd-heme_bind Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding
PF09099 CL0159 E-set Qn_am_d_aIII Quinohemoprotein amine dehydrogenase, alpha subunit domain III
-PF09100 Qn_am_d_aIV Quinohemoprotein amine dehydrogenase, alpha subunit domain IV
+PF09100 CL0159 E-set Qn_am_d_aIV Quinohemoprotein amine dehydrogenase, alpha subunit domain IV
PF09101 CL0004 Concanavalin Exotox-A_bind Exotoxin A binding
PF09102 Exotox-A_target Exotoxin A, targeting
PF09103 CL0021 OB BRCA-2_OB1 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1
@@ -8420,7 +8418,7 @@ PF09114 CL0123 HTH MotA_activ Transcription factor MotA, activation domain
PF09115 CL0604 post-AAA DNApol3-delta_C DNA polymerase III, delta subunit, C terminal
PF09116 CL0060 DNA_clamp gp45-slide_C gp45 sliding clamp, C terminal
PF09117 CL0333 gCrystallin MiAMP1 MiAMP1
-PF09118 CL0159 E-set DUF1929 Domain of unknown function (DUF1929)
+PF09118 CL0159 E-set GO-like_E_set Galactose oxidase-like, Early set domain
PF09119 SicP-binding SicP binding
PF09121 Tower Tower
PF09122 CL0487 FKBP DUF1930 Domain of unknown function (DUF1930)
@@ -8447,14 +8445,14 @@ PF09142 CL0178 PUA TruB_C tRNA Pseudouridine synthase II, C terminal
PF09143 CL0084 ADP-ribosyl AvrPphF-ORF-2 AvrPphF-ORF-2
PF09144 CL0202 GBD YpM Yersinia pseudo-tuberculosis mitogen
PF09145 CL0214 UBA Ubiq-assoc Ubiquitin-associated
-PF09147 CL0052 NTN DUF1933 Domain of unknown function (DUF1933)
+PF09147 CL0052 NTN CarA_N Carbapenam-3-carboxylate synthase, N-terminal
PF09148 CL0116 Calycin DUF1934 Domain of unknown function (DUF1934)
PF09149 DUF1935 Domain of unknown function (DUF1935)
PF09150 Carot_N Orange carotenoid protein, N-terminal
PF09151 CL0167 Zn_Beta_Ribbon DUF1936 Domain of unknown function (DUF1936)
PF09152 CL0498 Nribosyltransf DUF1937 Domain of unknown function (DUF1937)
-PF09153 DUF1938 Domain of unknown function (DUF1938)
-PF09154 CL0369 GHD DUF1939 Domain of unknown function (DUF1939)
+PF09153 CL0219 RNase_H MGMT_N Methylated DNA-protein cysteine methyltransferase, N-terminal
+PF09154 CL0369 GHD Alpha-amy_C_pro Alpha-amylase C-terminal
PF09155 CL0601 Cob_adeno_trans DUF1940 Domain of unknown function (DUF1940)
PF09156 CL0084 ADP-ribosyl Anthrax-tox_M Anthrax toxin lethal factor, middle domain
PF09157 CL0178 PUA TruB-C_2 Pseudouridine synthase II TruB, C-terminal
@@ -8469,15 +8467,15 @@ PF09166 CL0139 GADPH_aa-bio_dh Biliv-reduc_cat Biliverdin reductase, catalytic
PF09167 CL0524 MPT63-MPB63 DUF1942 Domain of unknown function (DUF1942)
PF09168 PepX_N X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal
PF09169 BRCA-2_helical BRCA2, helical
-PF09170 CL0123 HTH STN1_2 CST, Suppressor of cdc thirteen homolog, complex subunit STN1
+PF09170 CL0123 HTH STN1_2 CST, complex subunit STN1, C terminal
PF09171 AGOG N-glycosylase/DNA lyase
-PF09172 DUF1943 Domain of unknown function (DUF1943)
+PF09172 Vit_open_b-sht Vitellinogen, open beta-sheet
PF09173 eIF2_C Initiation factor eIF2 gamma, C terminal
PF09174 Maf1 Maf1 regulator
-PF09175 DUF1944 Domain of unknown function (DUF1944)
+PF09175 Vit_b-sht_shell Vitellinogen, beta-sheet shell
PF09176 CL0603 AA_dh_N Mpt_N Methylene-tetrahydromethanopterin dehydrogenase, N-terminal
PF09177 Syntaxin-6_N Syntaxin 6, N-terminal
-PF09178 CL0369 GHD DUF1945 Domain of unknown function (DUF1945)
+PF09178 CL0369 GHD MGTA_C 4-alpha-glucanotransferase, C-terminal
PF09179 TilS TilS substrate binding domain
PF09180 ProRS-C_1 Prolyl-tRNA synthetase, C-terminal
PF09181 ProRS-C_2 Prolyl-tRNA synthetase, C-terminal
@@ -8509,7 +8507,7 @@ PF09206 CL0004 Concanavalin ArabFuran-catal Alpha-L-arabinofuranosidase B, catal
PF09207 CL0333 gCrystallin Yeast-kill-tox Yeast killer toxin
PF09208 CL0236 PDDEXK Endonuc-MspI Restriction endonuclease MspI
PF09209 CL0174 TetR_C CecR_C HTH-type transcriptional dual regulator CecR, C-terminal domain
-PF09210 CL0599 GH57_38_middle DUF1957 Domain of unknown function (DUF1957)
+PF09210 CL0599 GH57_38_middle BE_C 1,4-alpha-glucan branching enzyme, C-terminal
PF09211 DUF1958 Domain of unknown function (DUF1958)
PF09212 CL0202 GBD CBM27 Carbohydrate binding module 27
PF09213 M3 M3
@@ -8525,7 +8523,7 @@ PF09223 CL0116 Calycin ZinT ZinT (YodA) periplasmic lipocalin-like zinc-recruitm
PF09224 CL0004 Concanavalin DUF1961 Domain of unknown function (DUF1961)
PF09225 CL0236 PDDEXK Endonuc-PvuII Restriction endonuclease PvuII
PF09226 CL0236 PDDEXK Endonuc-HincII Restriction endonuclease HincII
-PF09227 DUF1962 Domain of unknown function (DUF1962)
+PF09227 Bubble Bubble protein
PF09228 Prok-TraM Prokaryotic Transcriptional repressor TraM
PF09229 CL0648 Aha1_BPI Aha1_N Activator of Hsp90 ATPase, N-terminal
PF09230 CL0263 His-Me_finger DFF40 DNA fragmentation factor 40 kDa
@@ -8552,13 +8550,13 @@ PF09250 Prim-Pol Bifunctional DNA primase/polymerase, N-terminal
PF09251 CL0268 Pec_lyase-like PhageP22-tail Salmonella phage P22 tail-spike
PF09252 CL0370 Uteroglobin Feld-I_B Allergen Fel d I-B chain
PF09253 Ole_e_6 Pollen allergen Ole e 6
-PF09254 CL0236 PDDEXK Endonuc-FokI_C Restriction endonuclease FokI, C terminal
+PF09254 CL0236 PDDEXK FokI_cleav_dom FokI, cleavage domain
PF09255 CL0204 Adhesin Antig_Caf1 Caf1 Capsule antigen
PF09256 CL0607 TNF_receptor BaffR-Tall_bind BAFF-R, TALL-1 binding
PF09257 CL0607 TNF_receptor BCMA-Tall_bind BCMA, TALL-1 binding
PF09258 CL0110 GT-A Glyco_transf_64 Glycosyl transferase family 64 domain
PF09259 Fve Fungal immunomodulatory protein Fve
-PF09260 CL0369 GHD DUF1966 Domain of unknown function (DUF1966)
+PF09260 CL0369 GHD A_amylase_dom_C Alpha-amylase, domain C
PF09261 CL0599 GH57_38_middle Alpha-mann_mid Alpha mannosidase middle domain
PF09262 CL0402 Cdc48_2-like PEX-1N Peroxisome biogenesis factor 1, N-terminal
PF09263 CL0332 AcetylDC-like PEX-2N Peroxisome biogenesis factor 1, N-terminal
@@ -8613,7 +8611,7 @@ PF09312 CL0262 Trigger_C SurA_N SurA N-terminal domain
PF09313 CL0029 Cupin DUF1971 Domain of unknown function (DUF1971)
PF09314 CL0113 GT-B DUF1972 Domain of unknown function (DUF1972)
PF09316 Cmyb_C C-myb, C-terminal
-PF09317 DUF1974 Domain of unknown function (DUF1974)
+PF09317 ACDH_C Acyl-CoA dehydrogenase, C-terminal, bacterial type
PF09318 Glyco_trans_A_1 Glycosyl transferase 1 domain A
PF09320 DUF1977 Domain of unknown function (DUF1977)
PF09321 DUF1978 Domain of unknown function (DUF1978)
@@ -8645,7 +8643,7 @@ PF09346 CL0526 SUKH SMI1_KNR4 SMI1 / KNR4 family (SUKH-1)
PF09347 DUF1989 Domain of unknown function (DUF1989)
PF09348 DUF1990 Domain of unknown function (DUF1990)
PF09349 OHCU_decarbox OHCU decarboxylase
-PF09350 DUF1992 Domain of unknown function (DUF1992)
+PF09350 DJC28_CD DnaJ homologue, subfamily C, member 28, conserved domain
PF09351 CL0310 DinB DUF1993 Domain of unknown function (DUF1993)
PF09353 DUF1995 Domain of unknown function (DUF1995)
PF09354 HNF_C HNF3 C-terminal domain
@@ -8663,7 +8661,7 @@ PF09365 DUF2461 Conserved hypothetical protein (DUF2461)
PF09366 DUF1997 Protein of unknown function (DUF1997)
PF09367 CL0116 Calycin CpeS CpeS-like protein
PF09368 Sas10 Sas10 C-terminal domain
-PF09369 DUF1998 Domain of unknown function (DUF1998)
+PF09369 MZB MrfA Zn-binding domain
PF09370 CL0151 PK_TIM PEP_hydrolase Phosphoenolpyruvate hydrolase-like
PF09371 Tex_N Tex-like protein N-terminal domain
PF09372 CL0271 F-box PRANC PRANC domain
@@ -8671,7 +8669,7 @@ PF09373 PMBR Pseudomurein-binding repeat
PF09374 CL0244 PGBD PG_binding_3 Predicted Peptidoglycan domain
PF09375 Peptidase_M75 Imelysin
PF09376 CL0219 RNase_H NurA NurA domain
-PF09377 CL0437 EF-G_C SBDS_C SBDS protein C-terminal domain
+PF09377 CL0437 EF-G_C SBDS_domain_II SBDS protein, domain II
PF09378 CL0275 HAS-barrel HAS-barrel HAS barrel domain
PF09379 CL0072 Ubiquitin FERM_N FERM N-terminal domain
PF09380 CL0266 PH FERM_C FERM C-terminal PH-like domain
@@ -8716,12 +8714,12 @@ PF09422 WTX WTX protein
PF09423 CL0163 Calcineurin PhoD PhoD-like phosphatase
PF09424 CL0279 GatB_YqeY YqeY Yqey-like protein
PF09425 CL0281 CCT Jas_motif Jas motif
-PF09426 CL0431 PF Nyv1_N Vacuolar R-SNARE Nyv1 N terminal
+PF09426 CL0431 PF Nyv1_longin Vacuolar R-SNARE Nyv1, longin domain
PF09427 DUF2014 Domain of unknown function (DUF2014)
PF09428 DUF2011 Fungal protein of unknown function (DUF2011)
PF09429 Wbp11 WW domain binding protein 11
-PF09430 CL0287 Transthyretin DUF2012 Protein of unknown function (DUF2012)
-PF09431 DUF2013 Protein of unknown function (DUF2013)
+PF09430 CL0287 Transthyretin EMC7_beta-sandw ER membrane protein complex subunit 7, beta-sandwich domain
+PF09431 SPIN90_LRD SPIN90/Ldb17, leucine-rich domain
PF09432 THP2 Tho complex subunit THP2
PF09435 DUF2015 Fungal protein of unknown function (DUF2015)
PF09436 DUF2016 Domain of unknown function (DUF2016)
@@ -8763,7 +8761,7 @@ PF09472 MtrF Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF)
PF09474 Type_III_YscX Type III secretion system YscX (type_III_YscX)
PF09475 CL0084 ADP-ribosyl Dot_icm_IcmQ Dot/Icm secretion system protein (dot_icm_IcmQ)
PF09476 Pilus_CpaD Pilus biogenesis CpaD protein (pilus_cpaD)
-PF09477 Type_III_YscG Bacterial type II secretion system chaperone protein (type_III_yscG)
+PF09477 CL0020 TPR Type_III_YscG Bacterial type II secretion system chaperone protein (type_III_yscG)
PF09478 CL0203 CBD CBM49 Carbohydrate binding domain CBM49
PF09479 CL0072 Ubiquitin Flg_new Listeria-Bacteroides repeat domain (List_Bact_rpt)
PF09480 CL0357 SMAD-FHA PrgH Type III secretion system protein PrgH-EprH (PrgH)
@@ -8826,7 +8824,7 @@ PF09543 DUF2379 Protein of unknown function (DUF2379)
PF09544 DUF2381 Protein of unknown function (DUF2381)
PF09545 RE_AccI AccI restriction endonuclease
PF09546 Spore_III_AE Stage III sporulation protein AE (spore_III_AE)
-PF09547 CL0023 P-loop_NTPase Spore_IV_A Stage IV sporulation protein A (spore_IV_A)
+PF09547 CL0023 P-loop_NTPase SpoIVA_ATPase Stage IV sporulation protein A, ATPase domain
PF09548 Spore_III_AB Stage III sporulation protein AB (spore_III_AB)
PF09549 CL0236 PDDEXK RE_Bpu10I Bpu10I restriction endonuclease
PF09550 CL0567 Phage_TACs Phage_TAC_6 Phage tail assembly chaperone protein, TAC
@@ -8873,7 +8871,7 @@ PF09592 DUF2031 Protein of unknown function (DUF2031)
PF09593 Pathogen_betaC1 Beta-satellite pathogenicity beta C1 protein
PF09594 CL0111 GT-C GT87 Glycosyltransferase family 87
PF09595 Metaviral_G Metaviral_G glycoprotein
-PF09596 MamL-1 MamL-1 domain
+PF09596 CL0720 Lag3_N MamL-1 MamL-1 domain
PF09597 CL0003 SAM IGR IGR protein motif
PF09598 Stm1_N Stm1
PF09599 IpaC_SipC Salmonella-Shigella invasin protein C (IpaC_SipC)
@@ -8895,7 +8893,7 @@ PF09614 Cas_Csy2 CRISPR-associated protein (Cas_Csy2)
PF09615 Cas_Csy3 CRISPR-associated protein (Cas_Csy3)
PF09617 Cas_GSU0053 CRISPR-associated protein GSU0053 (Cas_GSU0053)
PF09618 CL0362 RAMPS-Cas5-like Cas_Csy4 CRISPR-associated protein (Cas_Csy4)
-PF09619 YscW Type III secretion system lipoprotein chaperone (YscW)
+PF09619 CL0159 E-set YscW Type III secretion system lipoprotein chaperone (YscW)
PF09620 Cas_csx3 CRISPR-associated protein (Cas_csx3)
PF09621 LcrR Type III secretion system regulator (LcrR)
PF09622 DUF2391 Putative integral membrane protein (DUF2391)
@@ -8923,9 +8921,9 @@ PF09643 YopX YopX protein
PF09644 Mg296 Mg296 protein
PF09645 CL0123 HTH F-112 F-112 protein
PF09646 CL0691 Phage_tail_2 Gp37 Gp37 protein
-PF09648 CL0285 YycI_YycH YycI YycH protein
+PF09648 CL0285 YycI_YycH YycI YycI protein
PF09649 CHZ Histone chaperone domain CHZ
-PF09650 PHA_gran_rgn Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)
+PF09650 CL0545 APCOP-app_sub PHA_gran_rgn Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)
PF09651 CL0236 PDDEXK Cas_APE2256 CRISPR-associated protein (Cas_APE2256)
PF09652 Cas_VVA1548 Putative CRISPR-associated protein (Cas_VVA1548)
PF09654 DUF2396 Protein of unknown function (DUF2396)
@@ -8945,7 +8943,7 @@ PF09667 DUF2028 Domain of unknown function (DUF2028)
PF09668 CL0129 Peptidase_AA Asp_protease Aspartyl protease
PF09669 Phage_pRha Phage regulatory protein Rha (Phage_pRha)
PF09670 CL0236 PDDEXK Cas_Cas02710 CRISPR-associated protein (Cas_Cas02710)
-PF09671 Spore_GerQ Spore coat protein (Spore_GerQ)
+PF09671 CL0010 SH3 Spore_GerQ Spore coat protein (Spore_GerQ)
PF09673 TrbC_Ftype Type-F conjugative transfer system pilin assembly protein
PF09674 DUF2400 Protein of unknown function (DUF2400)
PF09675 Chlamy_scaf Chlamydia-phage Chp2 scaffold (Chlamy_scaf)
@@ -8992,7 +8990,7 @@ PF09718 Tape_meas_lam_C Lambda phage tail tape-measure protein (Tape_meas_lam_
PF09719 CL0317 Multiheme_cytos C_GCAxxG_C_C Putative redox-active protein (C_GCAxxG_C_C)
PF09720 Unstab_antitox Putative addiction module component
PF09721 Exosortase_EpsH Transmembrane exosortase (Exosortase_EpsH)
-PF09722 DUF2384 Protein of unknown function (DUF2384)
+PF09722 Xre_MbcA_ParS_C Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain
PF09723 CL0167 Zn_Beta_Ribbon Zn-ribbon_8 Zinc ribbon domain
PF09724 Dcc1 Sister chromatid cohesion protein Dcc1
PF09725 Fra10Ac1 Folate-sensitive fragile site protein Fra10Ac1
@@ -9005,7 +9003,7 @@ PF09731 Mitofilin Mitochondrial inner membrane protein
PF09732 CactinC_cactus Cactus-binding C-terminus of cactin protein
PF09733 VEFS-Box VEFS-Box of polycomb protein
PF09734 CL0123 HTH Tau95 RNA polymerase III transcription factor (TF)IIIC subunit HTH domain
-PF09735 Nckap1 Membrane-associated apoptosis protein
+PF09735 CL0715 Nckap1_CYFIP1-2 Nckap1 Nck-associated protein 1
PF09736 Bud13 Pre-mRNA-splicing factor of RES complex
PF09737 Det1 De-etiolated protein 1 Det1
PF09738 LRRFIP LRRFIP family
@@ -9015,14 +9013,14 @@ PF09741 DUF2045 Uncharacterized conserved protein (DUF2045)
PF09742 CL0456 Golgi_traff Dymeclin Dyggve-Melchior-Clausen syndrome protein
PF09743 E3_UFM1_ligase E3 UFM1-protein ligase 1
PF09744 Jnk-SapK_ap_N JNK_SAPK-associated protein-1
-PF09745 DUF2040 Coiled-coil domain-containing protein 55 (DUF2040)
+PF09745 NSRP1_N Nuclear speckle splicing regulatory protein 1, N-terminal
PF09746 Membralin Tumour-associated protein
-PF09747 DUF2052 Coiled-coil domain containing protein (DUF2052)
+PF09747 CCD97-like_C Coiled-coil domain containing protein 97-like, C-terminal
PF09748 Med10 Transcription factor subunit Med10 of Mediator complex
PF09749 CL0247 2H HVSL Uncharacterised conserved protein
PF09750 DRY_EERY Alternative splicing regulator
PF09751 Es2 Nuclear protein Es2
-PF09752 CL0028 AB_hydrolase DUF2048 Alpha/beta hydrolase domain containing 18
+PF09752 CL0028 AB_hydrolase ABHD18 Alpha/beta hydrolase domain containing 18
PF09753 Use1 Membrane fusion protein Use1
PF09754 CL0408 PUP PAC2 PAC2 family
PF09755 DUF2046 Uncharacterized conserved protein H4 (DUF2046)
@@ -9038,11 +9036,11 @@ PF09766 FmiP_Thoc5 Fms-interacting protein/Thoc5
PF09767 DUF2053 Predicted membrane protein (DUF2053)
PF09768 CL0126 Peptidase_MA Peptidase_M76 Peptidase M76 family
PF09769 ApoO Apolipoprotein O
-PF09770 PAT1 Topoisomerase II-associated protein PAT1
+PF09770 CL0020 TPR PAT1 Topoisomerase II-associated protein PAT1
PF09771 Tmemb_18A Transmembrane protein 188
PF09772 Tmem26 Transmembrane protein 26
PF09773 Meckelin Meckelin (Transmembrane protein 67)
-PF09774 Cid2 Caffeine-induced death protein 2
+PF09774 MIX23 Intermembrane space protein MIX23
PF09775 Keratin_assoc Keratinocyte-associated protein 2
PF09776 Mitoc_L55 Mitochondrial ribosomal protein L55
PF09777 OSTMP1 Osteopetrosis-associated transmembrane protein 1 precursor
@@ -9056,8 +9054,8 @@ PF09785 Prp31_C Prp31 C terminal domain
PF09786 CytochromB561_N Cytochrome B561, N terminal
PF09787 Golgin_A5 Golgin subfamily A member 5
PF09788 Tmemb_55A Transmembrane protein 55A
-PF09789 DUF2353 Uncharacterized coiled-coil protein (DUF2353)
-PF09790 Hyccin Hyccin
+PF09789 CC149 Coiled-coil domain-containing protein 149-A
+PF09790 CL0020 TPR Hyccin Hyccin
PF09791 Oxidored-like Oxidoreductase-like protein, N-terminal
PF09792 But2 Ubiquitin 3 binding protein But2 C-terminal domain
PF09793 AD Anticodon-binding domain
@@ -9079,12 +9077,12 @@ PF09809 MRP-L27 Mitochondrial ribosomal protein L27
PF09810 CL0236 PDDEXK Exo5 Exonuclease V - a 5' deoxyribonuclease
PF09811 CL0255 ATP_synthase Yae1_N Essential protein Yae1, N terminal
PF09812 MRP-L28 Mitochondrial ribosomal protein L28
-PF09813 Coiled-coil_56 Coiled-coil domain-containing protein 56
+PF09813 Coa3_cc Cytochrome c oxidase assembly factor 3
PF09814 CL0552 Hect HECT_2 HECT-like Ubiquitin-conjugating enzyme (E2)-binding
PF09815 XK-related XK-related protein
PF09816 EAF RNA polymerase II transcription elongation factor
PF09817 CL0273 CYTH Zwilch RZZ complex, subunit zwilch
-PF09818 CL0023 P-loop_NTPase ABC_ATPase Predicted ATPase of the ABC class
+PF09818 CL0023 P-loop_NTPase ABC_ATPase ATPase of the ABC class
PF09819 ABC_cobalt ABC-type cobalt transport system, permease component
PF09820 CL0023 P-loop_NTPase AAA-ATPase_like Predicted AAA-ATPase
PF09821 AAA_assoc_C C-terminal AAA-associated domain
@@ -9112,7 +9110,7 @@ PF09844 CL0403 ADC-like DUF2071 Uncharacterized conserved protein (COG2071)
PF09845 CL0167 Zn_Beta_Ribbon DUF2072 Zn-ribbon containing protein
PF09846 DUF2073 Uncharacterized protein conserved in archaea (DUF2073)
PF09847 CL0181 ABC-2 12TM_1 Membrane protein of 12 TMs
-PF09848 CL0023 P-loop_NTPase DUF2075 Uncharacterized conserved protein (DUF2075)
+PF09848 CL0023 P-loop_NTPase DUF2075 Schlafen group 3, DNA/RNA helicase domain
PF09849 DUF2076 Uncharacterized protein conserved in bacteria (DUF2076)
PF09850 DotU Type VI secretion system protein DotU
PF09851 CL0660 SHOCT SHOCT Short C-terminal domain
@@ -9140,7 +9138,7 @@ PF09873 DUF2100 Uncharacterized protein conserved in archaea (DUF2100)
PF09874 DUF2101 Predicted membrane protein (DUF2101)
PF09875 DUF2102 Uncharacterized protein conserved in archaea (DUF2102)
PF09876 DUF2103 Predicted metal-binding protein (DUF2103)
-PF09877 DUF2104 Predicted membrane protein (DUF2104)
+PF09877 EhaL Energy-converting hydrogenase subunit EhaL
PF09878 DUF2105 Predicted membrane protein (DUF2105)
PF09879 DUF2106 Predicted membrane protein (DUF2106)
PF09880 DUF2107 Predicted membrane protein (DUF2107)
@@ -9174,7 +9172,7 @@ PF09910 DUF2139 Uncharacterized protein conserved in archaea (DUF2139)
PF09911 DUF2140 Uncharacterized protein conserved in bacteria (DUF2140)
PF09912 DUF2141 Uncharacterized protein conserved in bacteria (DUF2141)
PF09913 CL0111 GT-C DUF2142 Predicted membrane protein (DUF2142)
-PF09916 DUF2145 Uncharacterized protein conserved in bacteria (DUF2145)
+PF09916 CL0125 Peptidase_CA DUF2145 Uncharacterized protein conserved in bacteria (DUF2145)
PF09917 CL0116 Calycin DUF2147 Uncharacterized protein conserved in bacteria (DUF2147)
PF09918 DUF2148 Uncharacterized protein containing a ferredoxin domain (DUF2148)
PF09919 DUF2149 Uncharacterized conserved protein (DUF2149)
@@ -9203,7 +9201,7 @@ PF09945 DUF2177 Predicted membrane protein (DUF2177)
PF09946 DUF2178 Predicted membrane protein (DUF2178)
PF09947 CL0167 Zn_Beta_Ribbon DUF2180 Uncharacterized protein conserved in archaea (DUF2180)
PF09948 DUF2182 Predicted metal-binding integral membrane protein (DUF2182)
-PF09949 DUF2183 Uncharacterized conserved protein (DUF2183)
+PF09949 CL0137 HAD APP1_cat Phosphatidate phosphatase APP1, catalytic domain
PF09950 CL0373 Phage-coat DUF2184 Uncharacterized protein conserved in bacteria (DUF2184)
PF09951 DUF2185 Protein of unknown function (DUF2185)
PF09952 CL0578 AbiEI AbiEi_2 Transcriptional regulator, AbiEi antitoxin, Type IV TA system
@@ -9231,7 +9229,7 @@ PF09973 DUF2208 Predicted membrane protein (DUF2208)
PF09974 DUF2209 Uncharacterized protein conserved in archaea (DUF2209)
PF09976 CL0020 TPR TPR_21 Tetratricopeptide repeat-like domain
PF09977 CL0496 Tad-like Tad_C Putative Tad-like Flp pilus-assembly
-PF09979 DUF2213 Uncharacterized protein conserved in bacteria (DUF2213)
+PF09979 CL0201 Peptidase_SH DUF2213 Uncharacterized protein conserved in bacteria (DUF2213)
PF09980 DUF2214 Predicted membrane protein (DUF2214)
PF09981 DUF2218 Uncharacterized protein conserved in bacteria (DUF2218)
PF09982 CL0193 MBB DUF2219 Uncharacterized protein conserved in bacteria (DUF2219)
@@ -9242,7 +9240,7 @@ PF09986 CL0020 TPR DUF2225 Uncharacterized protein conserved in bacteria (DUF222
PF09987 DUF2226 Uncharacterized protein conserved in archaea (DUF2226)
PF09988 CL0368 PhosC-NucP1 DUF2227 Uncharacterized metal-binding protein (DUF2227)
PF09989 CL0108 Actin_ATPase DUF2229 CoA enzyme activase uncharacterised domain (DUF2229)
-PF09990 DUF2231 Predicted membrane protein (DUF2231)
+PF09990 CL0328 2heme_cytochrom DUF2231 Predicted membrane protein (DUF2231)
PF09991 DUF2232 Predicted membrane protein (DUF2232)
PF09992 NAGPA Phosphodiester glycosidase
PF09994 CL0028 AB_hydrolase DUF2235 Uncharacterized alpha/beta hydrolase domain (DUF2235)
@@ -9254,7 +9252,7 @@ PF09999 DUF2240 Uncharacterized protein conserved in archaea (DUF2240)
PF10000 CL0070 ACT ACT_3 ACT domain
PF10001 DUF2242 Uncharacterized protein conserved in bacteria (DUF2242)
PF10002 DUF2243 Predicted membrane protein (DUF2243)
-PF10003 DUF2244 Integral membrane protein (DUF2244)
+PF10003 CL0266 PH DUF2244 Integral membrane protein (DUF2244)
PF10004 DUF2247 Uncharacterized protein conserved in bacteria (DUF2247)
PF10005 CL0167 Zn_Beta_Ribbon zinc-ribbon_6 zinc-ribbon domain
PF10006 CL0397 TusA-like DUF2249 Uncharacterized conserved protein (DUF2249)
@@ -9282,7 +9280,7 @@ PF10030 CL0125 Peptidase_CA DUF2272 Uncharacterized protein conserved in bacteri
PF10031 DUF2273 Small integral membrane protein (DUF2273)
PF10032 Pho88 Phosphate transport (Pho88)
PF10033 CL0651 Mad2 ATG13 Autophagy-related protein 13
-PF10034 Dpy19 Q-cell neuroblast polarisation
+PF10034 CL0111 GT-C Dpy19 Q-cell neuroblast polarisation
PF10035 CL0089 GlnB-like DUF2179 Uncharacterized protein conserved in bacteria (DUF2179)
PF10036 RLL RNA transcription, translation and transport factor protein
PF10037 CL0020 TPR MRP-S27 Mitochondrial 28S ribosomal protein S27
@@ -9307,7 +9305,7 @@ PF10055 DUF2292 Uncharacterized small protein (DUF2292)
PF10056 DUF2293 Uncharacterized conserved protein (DUF2293)
PF10057 MpsC Na+-translocating membrane potential-generating system (MpsC)
PF10058 CL0167 Zn_Beta_Ribbon zinc_ribbon_10 Predicted integral membrane zinc-ribbon metal-binding protein
-PF10060 DUF2298 Uncharacterized membrane protein (DUF2298)
+PF10060 CL0111 GT-C DUF2298 Uncharacterized membrane protein (DUF2298)
PF10061 CL0097 TypeIII_Chap DUF2299 Uncharacterized conserved protein (DUF2299)
PF10062 DUF2300 Predicted secreted protein (DUF2300)
PF10063 DUF2301 Uncharacterized integral membrane protein (DUF2301)
@@ -9315,12 +9313,12 @@ PF10065 DUF2303 Uncharacterized conserved protein (DUF2303)
PF10066 DUF2304 Uncharacterized conserved protein (DUF2304)
PF10067 DUF2306 Predicted membrane protein (DUF2306)
PF10069 DICT Sensory domain in DIguanylate Cyclases and Two-component system
-PF10070 MpsB Na+-translocating membrane potential-generating system (MpsB)
+PF10070 DabA Probable inorganic carbon transporter subunit DabA
PF10071 DUF2310 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310)
PF10073 DUF2312 Uncharacterized protein conserved in bacteria (DUF2312)
PF10074 DUF2285 Uncharacterized conserved protein (DUF2285)
PF10075 CL0123 HTH CSN8_PSD8_EIF3K CSN8/PSMD8/EIF3K family
-PF10076 DUF2313 Uncharacterised protein conserved in bacteria (DUF2313)
+PF10076 Phage_Mu_Gp48 Bacteriophage Mu-like, Gp48
PF10077 DUF2314 Uncharacterized protein conserved in bacteria (DUF2314)
PF10078 CL0123 HTH DUF2316 Uncharacterized protein conserved in bacteria (DUF2316)
PF10079 CL0039 HUP BshC Bacillithiol biosynthesis BshC
@@ -9369,14 +9367,14 @@ PF10124 Mu-like_gpT Mu-like prophage major head subunit gpT
PF10125 CL0425 ComplexI-N NADHdeh_related NADH dehydrogenase I, subunit N related protein
PF10126 CL0089 GlnB-like Nit_Regul_Hom Uncharacterized protein, homolog of nitrogen regulatory protein PII
PF10127 CL0260 NTP_transf RlaP RNA repair pathway DNA polymerase beta family
-PF10128 OpcA_G6PD_assem Glucose-6-phosphate dehydrogenase subunit
+PF10128 CL0063 NADP_Rossmann OpcA_G6PD_assem Glucose-6-phosphate dehydrogenase subunit N-terminal domain
PF10129 CL0316 Acyl_transf_3 OpgC_C OpgC protein
PF10130 CL0280 PIN PIN_2 PIN domain
PF10131 CL0111 GT-C PTPS_related 6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein
PF10133 CooT CO dehydrogenase accessory protein CooT
PF10134 CL0123 HTH RPA Replication initiator protein A
PF10135 Rod-binding Rod binding protein
-PF10136 SpecificRecomb Site-specific recombinase
+PF10136 CL0716 Aquaporin-like SpecificRecomb Site-specific recombinase
PF10137 CL0173 STIR TIR-like Predicted nucleotide-binding protein containing TIR-like domain
PF10138 CL0128 vWA-like vWA-TerF-like vWA found in TerF C terminus
PF10139 Virul_Fac Putative bacterial virulence factor
@@ -9397,18 +9395,18 @@ PF10153 Efg1 rRNA-processing protein Efg1
PF10154 CL0223 MACRO DUF2362 Uncharacterised conserved protein (DUF2362)
PF10155 CNOT11 CCR4-NOT transcription complex subunit 11
PF10156 Med17 Subunit 17 of Mediator complex
-PF10157 BORCS6 BLOC-1-related complex sub-unit 6
+PF10157 BORCS6 BLOC-1-related complex sub-unit 6 C-terminal helix
PF10158 LOH1CR12 Tumour suppressor protein
PF10159 MMtag Multiple myeloma tumor-associated
-PF10160 Tmemb_40 Predicted membrane protein
+PF10160 CL0192 GPCR_A Tmemb_40 Predicted membrane protein
PF10161 DDDD Putative mitochondrial precursor protein
PF10162 G8 G8 domain
PF10163 EnY2 Transcription factor e(y)2
-PF10164 DUF2367 Uncharacterized conserved protein (DUF2367)
+PF10164 BRI3 Brain protein I3
PF10165 Ric8 Guanine nucleotide exchange factor synembryn
PF10166 DUF2368 Uncharacterised conserved protein (DUF2368)
PF10167 BORCS8 BLOC-1-related complex sub-unit 8
-PF10168 Nup88 Nuclear pore component
+PF10168 CL0186 Beta_propeller Nup88 Nuclear pore component
PF10169 Laps Learning-associated protein
PF10170 C6_DPF Cysteine-rich domain
PF10171 Tim29 Translocase of the Inner Mitochondrial membrane 29
@@ -9419,7 +9417,7 @@ PF10175 MPP6 M-phase phosphoprotein 6
PF10176 DUF2370 Protein of unknown function (DUF2370)
PF10177 DUF2371 Uncharacterised conserved protein (DUF2371)
PF10178 PAC3 Proteasome assembly chaperone 3
-PF10179 NDNF Neuron-derived neurotrophic factor
+PF10179 CL0159 E-set NDNF Neuron-derived neurotrophic factor, first Fn(III) domain
PF10180 WKF WKF domain
PF10181 PIG-H GPI-GlcNAc transferase complex, PIG-H component
PF10182 CL0321 PLAT Flo11 Flo11 domain
@@ -9429,7 +9427,7 @@ PF10185 Mesd Chaperone for wingless signalling and trafficking of LDL receptor
PF10186 CL0551 BCLiA ATG14 Vacuolar sorting 38 and autophagy-related subunit 14
PF10187 FAM192A_Fyv6_N FAM192A/Fyv6, N-terminal domain
PF10188 Oscp1 Organic solute transport protein 1
-PF10189 Ints3_N Integrator complex subunit 3 N-terminal
+PF10189 CL0020 TPR Ints3_N Integrator complex subunit 3 N-terminal
PF10190 Tmemb_170 Putative transmembrane protein 170
PF10191 CL0294 Sec10 COG7 Golgi complex component 7 (COG7)
PF10192 CL0192 GPCR_A GpcrRhopsn4 Rhodopsin-like GPCR transmembrane domain
@@ -9455,7 +9453,7 @@ PF10216 ChpXY CO2 hydration protein (ChpXY)
PF10217 DUF2039 Uncharacterized conserved protein (DUF2039)
PF10218 SPRING1 SREBP regulating gene protein
PF10220 Smg8_Smg9 Smg8_Smg9
-PF10221 DUF2151 Cell cycle and development regulator
+PF10221 Mat89Bb Cell cycle and development regulator Mat89Bb
PF10222 DUF2152 Uncharacterized conserved protein (DUF2152)
PF10223 DUF2181 Uncharacterized conserved protein (DUF2181)
PF10224 DUF2205 Short coiled-coil protein
@@ -9464,7 +9462,7 @@ PF10226 CCDC85 CCDC85 family
PF10228 DUF2228 Uncharacterised conserved protein (DUF2228)
PF10229 CL0529 FMN-dep-NRtase MMADHC Methylmalonic aciduria and homocystinuria type D protein
PF10230 CL0028 AB_hydrolase LIDHydrolase Lipid-droplet associated hydrolase
-PF10231 DUF2315 Apoptogenic protein 1
+PF10231 COA8 Cytochrome c oxidase assembly factor 8
PF10232 Med8 Mediator of RNA polymerase II transcription complex subunit 8
PF10233 Cg6151-P Uncharacterized conserved protein CG6151-P
PF10234 Cluap1 Clusterin-associated protein-1
@@ -9490,14 +9488,14 @@ PF10253 PRCC Mitotic checkpoint regulator, MAD2B-interacting
PF10254 Pacs-1 PACS-1 cytosolic sorting protein
PF10255 CL0020 TPR Paf67 RNA polymerase I-associated factor PAF67
PF10256 Erf4 Golgin subfamily A member 7/ERF4 family
-PF10257 RAI16-like Retinoic acid induced 16-like protein
-PF10258 RNA_GG_bind PHAX RNA-binding domain
+PF10257 CL0020 TPR RAI16-like Retinoic acid induced 16-like protein
+PF10258 PHAX_RNA-bd Phosphorylated adapter RNA export protein, RNA-binding domain
PF10259 Rogdi_lz Rogdi leucine zipper containing protein
PF10260 SAYSvFN Uncharacterized conserved domain (SAYSvFN)
PF10261 CL0525 pap2 Scs3p Inositol phospholipid synthesis and fat-storage-inducing TM
PF10262 CL0172 Thioredoxin Rdx Rdx family
PF10263 CL0126 Peptidase_MA SprT-like SprT-like family
-PF10264 Stork_head Winged helix Storkhead-box1 domain
+PF10264 CL0123 HTH Stork_head Winged helix Storkhead-box1 domain
PF10265 Miga Mitoguardin
PF10266 Strumpellin Hereditary spastic paraplegia protein strumpellin
PF10267 Tmemb_cc2 Predicted transmembrane and coiled-coil 2 protein
@@ -9519,9 +9517,9 @@ PF10282 CL0186 Beta_propeller Lactonase Lactonase, 7-bladed beta-propeller
PF10283 zf-CCHH PBZ domain
PF10284 Luciferase_3H Luciferase helical bundle domain
PF10285 CL0116 Calycin Luciferase_cat Luciferase catalytic domain
-PF10287 CL0004 Concanavalin DUF2401 Putative TOS1-like glycosyl hydrolase (DUF2401)
+PF10287 CL0004 Concanavalin YJL171C_Tos1_C Cell wall protein YJL171C/Tos1, C-terminal
PF10288 CTU2 Cytoplasmic tRNA 2-thiolation protein 2
-PF10290 DUF2403 Glycine-rich protein domain (DUF2403)
+PF10290 YJL171C_Tos1_N Cell wall protein YJL171C/Tos1, N-terminal
PF10291 CL0448 Cargo_bd_muHD muHD Muniscin C-terminal mu homology domain
PF10292 CL0192 GPCR_A 7TM_GPCR_Srab Serpentine type 7TM GPCR receptor class ab chemoreceptor
PF10293 DUF2405 Domain of unknown function (DUF2405)
@@ -9530,8 +9528,8 @@ PF10295 DUF2406 Uncharacterised protein (DUF2406)
PF10296 MMM1 Maintenance of mitochondrial morphology protein 1
PF10297 Hap4_Hap_bind Minimal binding motif of Hap4 for binding to Hap2/3/5
PF10298 CL0324 Homing_endonuc WhiA_N WhiA N-terminal LAGLIDADG-like domain
-PF10300 CL0020 TPR DUF3808 Protein of unknown function (DUF3808)
-PF10302 CL0072 Ubiquitin DUF2407 DUF2407 ubiquitin-like domain
+PF10300 CL0020 TPR Iml2-TPR_39 Iml2/Tetratricopeptide repeat protein 39
+PF10302 CL0072 Ubiquitin Dsc3_N DSC E3 ubiquitin ligase complex subunit 3, ubiquitin-like domain
PF10303 DUF2408 Protein of unknown function (DUF2408)
PF10304 RTP1_C2 Required for nuclear transport of RNA pol II C-terminus 2
PF10305 Fmp27_SW RNA pol II promoter Fmp27 protein domain
@@ -9568,17 +9566,17 @@ PF10338 DUF2423 Protein of unknown function (DUF2423)
PF10339 Vel1p Yeast-specific zinc responsive
PF10340 CL0028 AB_hydrolase Say1_Mug180 Steryl acetyl hydrolase
PF10341 CL0021 OB TPP1 Shelterin complex subunit, TPP1/ACD
-PF10342 CL0159 E-set GPI-anchored Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family
+PF10342 CL0159 E-set Kre9_KNH Kre9/KNH-like N-terminal Ig-like domain
PF10343 Q_salvage Potential Queuosine, Q, salvage protein family
PF10344 Fmp27 Mitochondrial protein from FMP27
PF10345 CL0020 TPR Cohesin_load Cohesin loading factor
PF10346 Con-6 Conidiation protein 6
PF10347 Fmp27_GFWDK RNA pol II promoter Fmp27 protein domain
PF10348 CL0328 2heme_cytochrom DUF2427 Domain of unknown function (DUF2427)
-PF10350 DUF2428 Putative death-receptor fusion protein (DUF2428)
+PF10350 DUF2428 THADA/TRM732, DUF2428
PF10351 Apt1 Golgi-body localisation protein domain
PF10353 DUF2430 Protein of unknown function (DUF2430)
-PF10354 CL0063 NADP_Rossmann DUF2431 Domain of unknown function (DUF2431)
+PF10354 CL0063 NADP_Rossmann BMT5-like rRNA (uridine-N3-)-methyltransferase BTM5-like
PF10355 Ytp1 Protein of unknown function (Ytp1)
PF10356 CL0236 PDDEXK DUF2034 Protein of unknown function (DUF2034)
PF10357 CL0123 HTH Kin17_mid Domain of Kin17 curved DNA-binding protein
@@ -9692,7 +9690,7 @@ PF10470 AKAP7_RIRII_bdg PKA-RI-RII subunit binding domain of A-kinase anchor p
PF10471 ANAPC_CDC26 Anaphase-promoting complex APC subunit CDC26
PF10472 CReP_N eIF2-alpha phosphatase phosphorylation constitutive repressor
PF10473 CENP-F_leu_zip Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
-PF10474 DUF2451 Protein of unknown function C-terminus (DUF2451)
+PF10474 CL0294 Sec10 DUF2451 Protein of unknown function C-terminus (DUF2451)
PF10475 CL0295 Vps51 Vps54_N Vacuolar-sorting protein 54, of GARP complex
PF10476 DUF2448 Protein of unknown function C-terminus (DUF2448)
PF10477 EIF4E-T Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E
@@ -9733,7 +9731,7 @@ PF10515 APP_amyloid Beta-amyloid precursor protein C-terminus
PF10516 CL0020 TPR SHNi-TPR SHNi-TPR
PF10517 DM13 Electron transfer DM13
PF10518 CL0300 TAT TAT_signal TAT (twin-arginine translocation) pathway signal sequence
-PF10520 Lipid_desat Lipid desaturase domain
+PF10520 CL0713 Acyl-CoA_desat Lipid_desat Lipid desaturase domain
PF10521 Tti2 Tti2 family
PF10522 RII_binding_1 RII binding domain
PF10523 BEN BEN domain
@@ -9768,7 +9766,7 @@ PF10555 MraY_sig1 Phospho-N-acetylmuramoyl-pentapeptide-transferase signature
PF10557 CL0123 HTH Cullin_Nedd8 Cullin protein neddylation domain
PF10558 MTP18 Mitochondrial 18 KDa protein (MTP18)
PF10559 Plug_translocon Plug domain of Sec61p
-PF10561 UPF0565 Uncharacterised protein family UPF0565
+PF10561 C2orf69 C2orf69
PF10562 CaM_bdg_C0 Calmodulin-binding domain C0 of NMDA receptor NR1 subunit
PF10563 CA_like Delta carbonic anhydrase
PF10564 MAR_sialic_bdg Sialic-acid binding micronemal adhesive repeat
@@ -9789,7 +9787,7 @@ PF10580 Neuromodulin_N Gap junction protein N-terminal region
PF10581 Synapsin_N Synapsin N-terminal
PF10583 Involucrin_N Involucrin of squamous epithelia N-terminus
PF10584 CL0052 NTN Proteasome_A_N Proteasome subunit A N-terminal signature
-PF10585 UBA_e1_thiolCys Ubiquitin-activating enzyme active site
+PF10585 UBA_E1_SCCH Ubiquitin-activating enzyme, SCCH domain
PF10587 EF-1_beta_acid Eukaryotic elongation factor 1 beta central acidic region
PF10588 NADH-G_4Fe-4S_3 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
PF10589 NADH_4Fe-4S NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
@@ -9808,7 +9806,7 @@ PF10602 CL0020 TPR RPN7 26S proteasome subunit RPN7
PF10604 CL0209 Bet_v_1_like Polyketide_cyc2 Polyketide cyclase / dehydrase and lipid transport
PF10605 CL0028 AB_hydrolase 3HBOH 3HB-oligomer hydrolase (3HBOH)
PF10606 GluR_Homer-bdg Homer-binding domain of metabotropic glutamate receptor
-PF10607 CLTH CTLH/CRA C-terminal to LisH motif domain
+PF10607 CTLH CTLH/CRA C-terminal to LisH motif domain
PF10608 MAGUK_N_PEST Polyubiquitination (PEST) N-terminal domain of MAGUK
PF10609 CL0023 P-loop_NTPase ParA NUBPL iron-transfer P-loop NTPase
PF10610 CL0159 E-set Tafi-CsgC Thin aggregative fimbriae synthesis protein
@@ -9816,7 +9814,7 @@ PF10611 DUF2469 Protein of unknown function (DUF2469)
PF10612 Spore-coat_CotZ Spore coat protein Z
PF10613 CL0177 PBP Lig_chan-Glu_bd Ligated ion channel L-glutamate- and glycine-binding site
PF10614 CsgF Type VIII secretion system (T8SS), CsgF protein
-PF10615 DUF2470 Protein of unknown function (DUF2470)
+PF10615 DUF2470 Domain of unknown function (DUF2470)
PF10616 DUF2471 Protein of unknown function (DUF2471)
PF10617 DUF2474 Protein of unknown function (DUF2474)
PF10618 Tail_tube Phage tail tube protein
@@ -9826,7 +9824,7 @@ PF10622 Ehbp Energy-converting hydrogenase B subunit P (EhbP)
PF10623 PilI Plasmid conjugative transfer protein PilI
PF10624 TraS Plasmid conjugative transfer entry exclusion protein TraS
PF10625 UspB Universal stress protein B (UspB)
-PF10626 TraO Conjugative transposon protein TraO
+PF10626 CL0193 MBB TraO Conjugative transposon protein TraO
PF10627 CsgE Curli assembly protein CsgE
PF10628 CotE Outer spore coat protein E (CotE)
PF10629 DUF2475 Protein of unknown function (DUF2475)
@@ -9932,7 +9930,7 @@ PF10735 DUF2526 Protein of unknown function (DUF2526)
PF10736 DUF2527 Protein of unknown function (DUF2627)
PF10737 GerPC Spore germination protein GerPC
PF10738 CL0619 Mog1p_PsbP Lpp-LpqN Probable lipoprotein LpqN
-PF10739 DUF2550 Protein of unknown function (DUF2550)
+PF10739 CL0266 PH DUF2550 Protein of unknown function (DUF2550)
PF10740 CL0067 SIS DUF2529 Domain of unknown function (DUF2529)
PF10741 CL0331 EpsM T2SSM_b Type II secretion system (T2SS), protein M subtype b
PF10742 DUF2555 Protein of unknown function (DUF2555)
@@ -9952,18 +9950,18 @@ PF10755 DUF2585 Protein of unknown function (DUF2585)
PF10756 CL0266 PH bPH_6 Bacterial PH domain
PF10757 YbaJ Biofilm formation regulator YbaJ
PF10758 DUF2586 Protein of unknown function (DUF2586)
-PF10759 DUF2587 Protein of unknown function (DUF2587)
+PF10759 BPA Bacterial proteasome activator
PF10761 DUF2590 Protein of unknown function (DUF2590)
PF10762 DUF2583 Protein of unknown function (DUF2583)
PF10763 CL0178 PUA DUF2584 Protein of unknown function (DUF2584)
PF10764 Gin Inhibitor of sigma-G Gin
-PF10765 DUF2591 Protein of unknown function (DUF2591)
+PF10765 Phage_P22_NinX Bacteriophage P22, NinX
PF10766 AcrZ Multidrug efflux pump-associated protein AcrZ
PF10767 DUF2593 Protein of unknown function (DUF2593)
PF10768 FliX Class II flagellar assembly regulator
PF10769 DUF2594 Protein of unknown function (DUF2594)
PF10771 CL0123 HTH DUF2582 Winged helix-turn-helix domain (DUF2582)
-PF10772 DUF2597 Protein of unknown function (DUF2597)
+PF10772 Phage_HP1_Orf24 Bacteriophage HP1, Orf24
PF10774 CL0352 EsxAB DUF4226 Domain of unknown function (DUF4226)
PF10775 ATP_sub_h ATP synthase complex subunit h
PF10776 DUF2600 Protein of unknown function (DUF2600)
@@ -10003,19 +10001,19 @@ PF10809 DUF2732 Protein of unknown function (DUF2732)
PF10810 DUF2545 Protein of unknown function (DUF2545)
PF10811 DUF2532 Protein of unknown function (DUF2532)
PF10812 DUF2561 Protein of unknown function (DUF2561)
-PF10813 DUF2733 Protein of unknown function (DUF2733)
+PF10813 Herpesvir_UL11 Herpesvirus UL11 homologue
PF10814 CwsA Cell wall synthesis protein CwsA
PF10815 ComZ ComZ
PF10816 DUF2760 Domain of unknown function (DUF2760)
PF10817 CL0352 EsxAB DUF2563 Protein of unknown function (DUF2563)
-PF10818 DUF2547 Protein of unknown function (DUF2547)
+PF10818 SecM_small secA translation cis-regulator SecM, small type
PF10819 DUF2564 Protein of unknown function (DUF2564)
PF10820 DUF2543 Protein of unknown function (DUF2543)
PF10821 DUF2567 Protein of unknown function (DUF2567)
PF10823 DUF2568 Protein of unknown function (DUF2568)
PF10824 CL0352 EsxAB T7SS_ESX_EspC Excreted virulence factor EspC, type VII ESX diderm
PF10825 DUF2752 Protein of unknown function (DUF2752)
-PF10826 DUF2551 Protein of unknown function (DUF2551)
+PF10826 CL0123 HTH DUF2551 Protein of unknown function (DUF2551)
PF10827 DUF2552 Protein of unknown function (DUF2552)
PF10828 DUF2570 Protein of unknown function (DUF2570)
PF10829 DUF2554 Protein of unknown function (DUF2554)
@@ -10030,7 +10028,7 @@ PF10838 DUF2677 Protein of unknown function (DUF2677)
PF10839 DUF2647 Protein of unknown function (DUF2647)
PF10840 DUF2645 Protein of unknown function (DUF2645)
PF10841 DUF2644 Protein of unknown function (DUF2644)
-PF10842 DUF2642 Protein of unknown function (DUF2642)
+PF10842 CL0010 SH3 DUF2642 Protein of unknown function (DUF2642)
PF10843 RGI1 Respiratory growth induced protein 1
PF10844 DUF2577 Protein of unknown function (DUF2577)
PF10845 DUF2576 Protein of unknown function (DUF2576)
@@ -10077,7 +10075,7 @@ PF10888 DUF2742 Protein of unknown function (DUF2742)
PF10890 CL0429 UcrQ-like Cyt_b-c1_8 Cytochrome b-c1 complex subunit 8
PF10891 DUF2719 Protein of unknown function (DUF2719)
PF10892 DUF2688 Protein of unknown function (DUF2688)
-PF10893 DUF2724 Protein of unknown function (DUF2724)
+PF10893 Phage_186_Fil Bacteriophage 186, Fil
PF10894 DUF2689 Protein of unknown function (DUF2689)
PF10895 CL0193 MBB DUF2715 Domain of unknown function (DUF2715)
PF10896 DUF2714 Protein of unknown function (DUF2714)
@@ -10094,7 +10092,7 @@ PF10907 DUF2749 Protein of unknown function (DUF2749)
PF10908 DUF2778 Protein of unknown function (DUF2778)
PF10909 DUF2682 Protein of unknown function (DUF2682)
PF10910 DUF2744 Protein of unknown function (DUF2744)
-PF10911 DUF2717 Protein of unknown function (DUF2717)
+PF10911 T7-like_Y65 Bacteriophage T7-like gene 6.5
PF10912 DUF2700 Protein of unknown function (DUF2700)
PF10913 DUF2706 Protein of unknown function (DUF2706)
PF10915 DUF2709 Protein of unknown function (DUF2709)
@@ -10102,9 +10100,9 @@ PF10916 DUF2712 Protein of unknown function (DUF2712)
PF10917 Fungus-induced Fungus-induced protein
PF10918 DUF2718 Protein of unknown function (DUF2718)
PF10920 CL0181 ABC-2 DUF2705 Protein of unknown function (DUF2705)
-PF10921 DUF2710 Protein of unknown function (DUF2710)
-PF10922 DUF2745 Protein of unknown function (DUF2745)
-PF10923 CL0023 P-loop_NTPase DUF2791 P-loop Domain of unknown function (DUF2791)
+PF10921 CL0717 YbaB DUF2710 Protein of unknown function (DUF2710)
+PF10922 T7-like_gp12 Bacteriophage T7-like, gene 1.2
+PF10923 CL0023 P-loop_NTPase BrxC_BrxD BREX system ATP-binding protein BrxC/D
PF10924 DUF2711 Protein of unknown function (DUF2711)
PF10925 DUF2680 Protein of unknown function (DUF2680)
PF10926 CL0236 PDDEXK DUF2800 Protein of unknown function (DUF2800)
@@ -10114,14 +10112,14 @@ PF10929 DUF2811 Protein of unknown function (DUF2811)
PF10930 DUF2737 Protein of unknown function (DUF2737)
PF10931 DUF2735 Protein of unknown function (DUF2735)
PF10932 DUF2783 Protein of unknown function (DUF2783)
-PF10933 DUF2827 Protein of unknown function (DUF2827)
+PF10933 CL0113 GT-B DUF2827 Protein of unknown function (DUF2827)
PF10934 DUF2634 Protein of unknown function (DUF2634)
PF10935 DUF2637 Protein of unknown function (DUF2637)
PF10936 DUF2617 Protein of unknown function DUF2617
PF10937 S36_mt Ribosomal protein S36, mitochondrial
PF10938 YfdX YfdX protein
PF10939 DUF2631 Protein of unknown function (DUF2631)
-PF10940 DUF2618 Protein of unknown function (DUF2618)
+PF10940 SpeFL Leader peptide SpeFL
PF10941 DUF2620 Protein of unknown function DUF2620
PF10942 DUF2619 Protein of unknown function (DUF2619)
PF10943 DUF2632 Protein of unknown function (DUF2632)
@@ -10136,7 +10134,7 @@ PF10951 DUF2776 Protein of unknown function (DUF2776)
PF10952 DUF2753 Protein of unknown function (DUF2753)
PF10953 DUF2754 Protein of unknown function (DUF2754)
PF10954 DUF2755 Protein of unknown function (DUF2755)
-PF10955 DUF2757 Protein of unknown function (DUF2757)
+PF10955 Fin Anti-sigma-F factor Fin
PF10956 DUF2756 Protein of unknown function (DUF2756)
PF10957 Spore_Cse60 Sporulation protein Cse60
PF10958 DUF2759 Protein of unknown function (DUF2759)
@@ -10189,7 +10187,7 @@ PF11004 Kdo_hydroxy 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase
PF11005 DUF2844 Protein of unknown function (DUF2844)
PF11006 DUF2845 Protein of unknown function (DUF2845)
PF11007 CotJA Spore coat associated protein JA (CotJA)
-PF11008 DUF2846 Protein of unknown function (DUF2846)
+PF11008 CL0287 Transthyretin DUF2846 Protein of unknown function (DUF2846)
PF11009 CL0172 Thioredoxin DUF2847 Protein of unknown function (DUF2847)
PF11010 CL0377 FAH DUF2848 Protein of unknown function (DUF2848)
PF11011 DUF2849 Protein of unknown function (DUF2849)
@@ -10224,7 +10222,7 @@ PF11039 DUF2824 Protein of unknown function (DUF2824)
PF11040 DGF-1_C Dispersed gene family protein 1 of Trypanosoma cruzi C-terminus
PF11041 DUF2612 Protein of unknown function (DUF2612)
PF11042 DUF2750 Protein of unknown function (DUF2750)
-PF11043 DUF2856 Protein of unknown function (DUF2856)
+PF11043 Anti-RecBCD_p2 Bacteriophage P22, anti-RecBCD protein 2
PF11044 TMEMspv1-c74-12 Plectrovirus spv1-c74 ORF 12 transmembrane protein
PF11045 YbjM Putative inner membrane protein of Enterobacteriaceae
PF11046 HycA_repressor Transcriptional repressor of hyc and hyp operons
@@ -10260,7 +10258,7 @@ PF11077 DUF2616 Protein of unknown function (DUF2616)
PF11078 Optomotor-blind Optomotor-blind protein N-terminal region
PF11079 YqhG Bacterial protein YqhG of unknown function
PF11080 GhoS Endoribonuclease GhoS
-PF11081 DUF2890 Protein of unknown function (DUF2890)
+PF11081 Adeno_L433K_22K Adenovirus L4-33K/L4-22K
PF11082 DUF2880 Protein of unknown function (DUF2880)
PF11083 Streptin-Immun Lantibiotic streptin immunity protein
PF11084 DUF2621 Protein of unknown function (DUF2621)
@@ -10269,7 +10267,7 @@ PF11086 DUF2878 Protein of unknown function (DUF2878)
PF11087 PRD1_DD PRD1 phage membrane DNA delivery
PF11088 RL11D Glycoprotein encoding membrane proteins RL5A and RL6
PF11089 SyrA Exopolysaccharide production repressor
-PF11090 DUF2833 Protein of unknown function (DUF2833)
+PF11090 CL0257 Acetyltrans Phage_T7_Gp13 Bacteriophage T7, probable scaffold protein Gp13
PF11091 T4_tail_cap Tail-tube assembly protein
PF11092 Alveol-reg_P311 Neuronal protein 3.1 (p311)
PF11093 Mitochondr_Som1 Mitochondrial export protein Som1
@@ -10285,7 +10283,7 @@ PF11103 CL0236 PDDEXK DUF2887 Protein of unknown function (DUF2887)
PF11104 CL0108 Actin_ATPase PilM_2 Type IV pilus assembly protein PilM;
PF11105 CCAP Arthropod cardioacceleratory peptide 2a
PF11106 YjbE Exopolysaccharide production protein YjbE
-PF11107 FANCF Fanconi anemia group F protein (FANCF)
+PF11107 CL0020 TPR FANCF Fanconi anemia group F protein (FANCF)
PF11108 Phage_glycop_gL Viral glycoprotein L
PF11109 RFamide_26RFa Orexigenic neuropeptide Qrfp/P518
PF11110 Phage_hub_GP28 Baseplate hub distal subunit
@@ -10302,8 +10300,8 @@ PF11120 CBP_BcsF Cellulose biosynthesis protein BcsF
PF11121 DUF2639 Protein of unknown function (DUF2639)
PF11122 Spore-coat_CotD Inner spore coat protein D
PF11123 DNA_Packaging_2 DNA packaging protein
-PF11124 Pho86 Inorganic phosphate transporter Pho86
-PF11125 DUF2830 Protein of unknown function (DUF2830)
+PF11124 CL0257 Acetyltrans Pho86 Inorganic phosphate transporter chaperone Pho86
+PF11125 Phage_MS2_lysis Bacteriophage MS2, lysis protein
PF11126 Phage_DsbA Transcriptional regulator DsbA
PF11127 DUF2892 Protein of unknown function (DUF2892)
PF11128 Nucleocap_ssRNA Plant viral coat protein nucleocapsid
@@ -10357,13 +10355,13 @@ PF11177 DUF2964 Protein of unknown function (DUF2964)
PF11178 DUF2963 Protein of unknown function (DUF2963)
PF11179 DUF2967 Protein of unknown function (DUF2967)
PF11180 DUF2968 Protein of unknown function (DUF2968)
-PF11181 YflT Heat induced stress protein YflT
+PF11181 YflT Heat induced stress protein YflT domain
PF11182 AlgF Alginate O-acetyl transferase AlgF
PF11183 PmrD Polymyxin resistance protein PmrD
PF11184 DUF2969 Protein of unknown function (DUF2969)
PF11185 DUF2971 Protein of unknown function (DUF2971)
PF11186 DUF2972 Protein of unknown function (DUF2972)
-PF11187 CL0028 AB_hydrolase DUF2974 Protein of unknown function (DUF2974)
+PF11187 CL0028 AB_hydrolase Mbeg1-like Mbeg1-like
PF11188 DUF2975 Protein of unknown function (DUF2975)
PF11189 DUF2973 Protein of unknown function (DUF2973)
PF11190 DUF2976 Protein of unknown function (DUF2976)
@@ -10371,7 +10369,7 @@ PF11191 DUF2782 Protein of unknown function (DUF2782)
PF11192 DUF2977 Protein of unknown function (DUF2977)
PF11193 DUF2812 Protein of unknown function (DUF2812)
PF11195 DUF2829 Protein of unknown function (DUF2829)
-PF11196 DEP1 Terpene cyclase DEP1
+PF11196 DUF2834 Protein of unknown function DUF2834
PF11197 DUF2835 Protein of unknown function (DUF2835)
PF11198 DUF2857 Protein of unknown function (DUF2857)
PF11199 DUF2891 Protein of unknown function (DUF2891)
@@ -10397,15 +10395,15 @@ PF11219 DUF3014 Protein of unknown function (DUF3014)
PF11220 DUF3015 Protein of unknown function (DUF3015)
PF11221 Med21 Subunit 21 of Mediator complex
PF11222 DUF3017 Protein of unknown function (DUF3017)
-PF11223 DUF3020 Protein of unknown function (DUF3020)
+PF11223 DUF3020 SPP41, DUF3020
PF11224 DUF3023 Protein of unknown function (DUF3023)
PF11225 DUF3024 Protein of unknown function (DUF3024)
PF11226 DUF3022 Protein of unknown function (DUF3022)
PF11227 DUF3025 Protein of unknown function (DUF3025)
PF11228 DUF3027 Protein of unknown function (DUF3027)
-PF11229 Focadhesin Focadhesin
+PF11229 CL0020 TPR Focadhesin Focadhesin
PF11230 CL0339 PFL-like DUF3029 Protein of unknown function (DUF3029)
-PF11231 DUF3034 Protein of unknown function (DUF3034)
+PF11231 CL0193 MBB DUF3034 Protein of unknown function (DUF3034)
PF11232 CL0616 SPOC Med25 Mediator complex subunit 25 PTOV activation and synapsin 2
PF11233 DUF3035 Protein of unknown function (DUF3035)
PF11235 Med25_SD1 Mediator complex subunit 25 synapsin 1
@@ -10420,7 +10418,7 @@ PF11243 DUF3045 Protein of unknown function (DUF3045)
PF11244 Med25_NR-box Mediator complex subunit 25 C-terminal NR box-containing
PF11245 DUF2544 Protein of unknown function (DUF2544)
PF11246 CL0187 LysM Phage_gp53 Base plate wedge protein 53
-PF11247 DUF2675 Protein of unknown function (DUF2675)
+PF11247 Phage_T7_55 Bacteriophage T7, gene 5.5
PF11248 DUF3046 Protein of unknown function (DUF3046)
PF11249 DUF3047 Protein of unknown function (DUF3047)
PF11250 FAF Fantastic Four meristem regulator
@@ -10442,7 +10440,6 @@ PF11266 CL0044 Ferritin Ald_deCOase Long-chain fatty aldehyde decarbonylase
PF11267 DUF3067 Domain of unknown function (DUF3067)
PF11268 DUF3071 Protein of unknown function (DUF3071)
PF11269 DUF3069 Protein of unknown function (DUF3069)
-PF11270 DUF3070 Protein of unknown function (DUF3070)
PF11271 PorA Porin PorA
PF11272 DUF3072 Protein of unknown function (DUF3072)
PF11273 DUF3073 Protein of unknown function (DUF3073)
@@ -10464,14 +10461,14 @@ PF11288 CL0028 AB_hydrolase DUF3089 Protein of unknown function (DUF3089)
PF11289 bCoV_viroporin Betacoronavirus viroporin
PF11290 DUF3090 Protein of unknown function (DUF3090)
PF11291 DUF3091 Protein of unknown function (DUF3091)
-PF11292 DUF3093 Protein of unknown function (DUF3093)
+PF11292 CL0266 PH DUF3093 Protein of unknown function (DUF3093)
PF11293 DUF3094 Protein of unknown function (DUF3094)
PF11294 DUF3095 Protein of unknown function (DUF3095)
PF11295 DUF3096 Protein of unknown function (DUF3096)
PF11296 DUF3097 Protein of unknown function (DUF3097)
PF11297 DUF3098 Protein of unknown function (DUF3098)
PF11298 DUF3099 Protein of unknown function (DUF3099)
-PF11299 DUF3100 Protein of unknown function (DUF3100)
+PF11299 CL0064 CPA_AT DUF3100 Protein of unknown function (DUF3100)
PF11300 DUF3102 Protein of unknown function (DUF3102)
PF11301 DUF3103 Protein of unknown function (DUF3103)
PF11302 CL0010 SH3 DUF3104 Protein of unknown function (DUF3104)
@@ -10490,7 +10487,7 @@ PF11314 DUF3117 Protein of unknown function (DUF3117)
PF11315 Med30 Mediator complex subunit 30
PF11316 CL0110 GT-A Rhamno_transf Putative rhamnosyl transferase
PF11317 DUF3119 Protein of unknown function (DUF3119)
-PF11318 DUF3120 Protein of unknown function (DUF3120)
+PF11318 CL0316 Acyl_transf_3 DUF3120 Protein of unknown function (DUF3120)
PF11319 VasI Type VI secretion system VasI, EvfG, VC_A0118
PF11320 DUF3122 Protein of unknown function (DUF3122)
PF11321 DUF3123 Protein of unknown function (DUF3123)
@@ -10518,7 +10515,7 @@ PF11343 DUF3145 Protein of unknown function (DUF3145)
PF11344 DUF3146 Protein of unknown function (DUF3146)
PF11345 CL0420 GlpM-like DUF3147 Protein of unknown function (DUF3147)
PF11346 DUF3149 Protein of unknown function (DUF3149)
-PF11347 DUF3148 Protein of unknown function (DUF3148)
+PF11347 CL0010 SH3 DUF3148 Protein of unknown function (DUF3148)
PF11348 DUF3150 Protein of unknown function (DUF3150)
PF11349 DUF3151 Protein of unknown function (DUF3151)
PF11350 CL0126 Peptidase_MA DUF3152 Protein of unknown function (DUF3152)
@@ -10533,7 +10530,7 @@ PF11358 DUF3158 Protein of unknown function (DUF3158)
PF11359 gpUL132 Glycoprotein UL132
PF11360 DUF3110 Protein of unknown function (DUF3110)
PF11361 DUF3159 Protein of unknown function (DUF3159)
-PF11362 DUF3161 Protein of unknown function (DUF3161)
+PF11362 CL0123 HTH DUF3161 Protein of unknown function (DUF3161)
PF11363 DUF3164 Protein of unknown function (DUF3164)
PF11364 DUF3165 Protein of unknown function (DUF3165)
PF11365 SOGA Protein SOGA
@@ -10616,12 +10613,12 @@ PF11445 DUF2894 Protein of unknown function (DUF2894)
PF11446 DUF2897 Protein of unknown function (DUF2897)
PF11447 DUF3201 Protein of unknown function (DUF3201)
PF11448 DUF3005 Protein of unknown function (DUF3005)
-PF11449 ArsP_2 Putative, 10TM heavy-metal exporter
+PF11449 CL0182 IT ArsP_2 Putative, 10TM heavy-metal exporter
PF11450 DUF3008 Protein of unknwon function (DUF3008)
PF11452 DUF3000 Protein of unknown function (DUF3000)
PF11453 DUF2950 Protein of unknown function (DUF2950)
PF11454 DUF3016 Protein of unknown function (DUF3016)
-PF11455 DUF3018 Protein of unknown function (DUF3018)
+PF11455 MazE-like Antitoxin MazE-like
PF11456 DUF3019 Protein of unknown function (DUF3019)
PF11457 DUF3021 Protein of unknown function (DUF3021)
PF11458 Mistic Membrane-integrating protein Mistic
@@ -10662,7 +10659,7 @@ PF11494 Ta0938 Ta0938
PF11495 CL0479 PLD Regulator_TrmB Archaeal transcriptional regulator TrmB
PF11496 CL0023 P-loop_NTPase HDA2-3 Class II histone deacetylase complex subunits 2 and 3
PF11497 NADH_Oxid_Nqo15 NADH-quinone oxidoreductase chain 15
-PF11498 Activator_LAG-3 Transcriptional activator LAG-3
+PF11498 CL0720 Lag3_N Activator_LAG-3 Transcriptional activator LAG-3
PF11500 Cut12 Cut12 conserved domain
PF11501 bCoV_NSP1 Betacoronavirus replicase NSP1
PF11502 BCL9 B-cell lymphoma 9 protein
@@ -10672,7 +10669,7 @@ PF11505 DUF3216 Protein of unknown function (DUF3216)
PF11506 CL0021 OB DUF3217 Protein of unknown function (DUF3217)
PF11507 Transcript_VP30 Ebola virus-specific transcription factor VP30
PF11508 CL0037 Lysozyme DUF3218 Protein of unknown function (DUF3218)
-PF11510 FA_FANCE Fanconi Anaemia group E protein FANCE
+PF11510 CL0020 TPR FA_FANCE Fanconi Anaemia group E protein FANCE
PF11511 RhodobacterPufX Intrinsic membrane protein PufX
PF11512 Atu4866 Agrobacterium tumefaciens protein Atu4866
PF11513 TA0956 Thermoplasma acidophilum protein TA0956
@@ -10712,7 +10709,7 @@ PF11547 CL0214 UBA E3_UbLigase_EDD E3 ubiquitin ligase EDD
PF11548 Receptor_IA-2 Protein-tyrosine phosphatase receptor IA-2
PF11549 Sec31 Protein transport protein SEC31
PF11550 IglC Intracellular growth locus C protein
-PF11551 Omp28 Outer membrane protein Omp28
+PF11551 CL0159 E-set Omp28 Outer membrane protein Omp28
PF11553 CL0044 Ferritin DUF3231 Protein of unknown function (DUF3231)
PF11554 DUF3232 Protein of unknown function (DUF3232)
PF11555 Inhibitor_Mig-6 EGFR receptor inhibitor Mig-6
@@ -10733,7 +10730,7 @@ PF11570 E2R135 Coiled-coil receptor-binding R-domain of colicin E2
PF11571 Med27 Mediator complex subunit 27
PF11572 DUF3234 Protein of unknown function (DUF3234)
PF11573 Med23 Mediator complex subunit 23
-PF11574 DUF3235 Protein of unknown function (DUF3235)
+PF11574 Rpf1_C Resuscitation-promoting factor Rpf1, C-terminal
PF11575 FhuF_C FhuF 2Fe-2S C-terminal domain
PF11576 CL0269 Maf HcgB FeGP cofactor biosynthesis protein HcgB, guanylyltransferase
PF11577 NEMO NF-kappa-B essential modulator NEMO
@@ -10767,7 +10764,7 @@ PF11604 CL0021 OB CusF_Ec Copper binding periplasmic protein CusF
PF11605 CL0266 PH Vps36_ESCRT-II Vacuolar protein sorting protein 36 Vps36
PF11606 CL0159 E-set AlcCBM31 Family 31 carbohydrate binding protein
PF11607 CL0010 SH3 DUF3247 Protein of unknown function (DUF3247)
-PF11608 CL0221 RRM Limkain-b1 Limkain b1
+PF11608 CL0221 RRM MARF1_RRM1 MARF1, RNA recognition motif 1
PF11609 DUF3248 Protein of unknown function (DUF3248)
PF11610 Ste5 Scaffold protein Ste5, Fus3-binding region
PF11611 CL0524 MPT63-MPB63 DUF4352 Domain of unknown function (DUF4352)
@@ -10788,7 +10785,7 @@ PF11626 Rap1_C TRF2-interacting telomeric protein/Rap1 - C terminal domain
PF11627 HnRNPA1 Nuclear factor hnRNPA1
PF11628 TCR_zetazeta T-cell surface glycoprotein CD3 zeta chain
PF11629 Mst1_SARAH C terminal SARAH domain of Mst1
-PF11630 DUF3254 Protein of unknown function (DUF3254)
+PF11630 Anti-LPS-SCYG Anti-lipopolysaccharide factor/Scygonadin
PF11631 CL0116 Calycin DUF3255 Protein of unknown function (DUF3255)
PF11632 LcnG-beta Lactococcin G-beta
PF11633 CL0223 MACRO bCoV_SUD_M Betacoronavirus single-stranded poly(A) binding domain
@@ -10837,7 +10834,7 @@ PF11677 DUF3273 Protein of unknown function (DUF3273)
PF11678 DUF3274 Protein of unknown function (DUF3274)
PF11679 DUF3275 Protein of unknown function (DUF3275)
PF11680 CL0609 sPC4_like DUF3276 Protein of unknown function (DUF3276)
-PF11681 DUF3277 Protein of unknown function (DUF3277)
+PF11681 KPP10_Orf10 Bacteriophage KPP10, Structural protein ORF10
PF11682 CL0167 Zn_Beta_Ribbon zinc_ribbon_11 Probable zinc-ribbon
PF11683 DUF3278 Protein of unknown function (DUF3278)
PF11684 CL0342 TolB_N DUF3280 Protein of unknown function (DUF2380)
@@ -10901,7 +10898,7 @@ PF11742 DUF3302 Protein of unknown function (DUF3302)
PF11743 DUF3301 Protein of unknown function (DUF3301)
PF11744 CL0307 FUSC ALMT Aluminium activated malate transporter
PF11745 DUF3304 Protein of unknown function (DUF3304)
-PF11746 DUF3303 Protein of unknown function (DUF3303)
+PF11746 CL0032 Dim_A_B_barrel DUF3303 Domain of unknown function (DUF3303)
PF11747 RebB Killing trait
PF11748 DUF3306 Protein of unknown function (DUF3306)
PF11749 DUF3305 Protein of unknown function (DUF3305)
@@ -10946,7 +10943,7 @@ PF11787 Aft1_HRR Aft1 HRR domain
PF11788 CL0261 NUDIX MRP-L46 39S mitochondrial ribosomal protein L46
PF11789 CL0229 RING zf-Nse Zinc-finger of the MIZ type in Nse subunit
PF11790 CL0058 Glyco_hydro_tim Glyco_hydro_cc Glycosyl hydrolase catalytic core
-PF11791 Aconitase_B_N Aconitate B N-terminal domain
+PF11791 CL0020 TPR Aconitase_B_N Aconitate B N-terminal domain
PF11792 CL0167 Zn_Beta_Ribbon Baculo_LEF5_C Baculoviridae late expression factor 5 C-terminal domain
PF11793 CL0229 RING FANCL_C FANCL C-terminal domain
PF11794 HpaB_N 4-hydroxyphenylacetate 3-hydroxylase N terminal
@@ -10961,7 +10958,7 @@ PF11802 CENP-K Centromere-associated protein K
PF11803 UXS1_N UDP-glucuronate decarboxylase N-terminal
PF11804 DUF3325 Protein of unknown function (DUF3325)
PF11805 DUF3326 Protein of unknown function (DUF3326)
-PF11806 CL0159 E-set DUF3327 Domain of unknown function (DUF3327)
+PF11806 CL0159 E-set Enterochelin_N Enterochelin esterase, N-terminal
PF11807 UstYa Mycotoxin biosynthesis protein UstYa
PF11808 PhoR Phosphate regulon sensor protein PhoR
PF11809 DUF3330 Domain of unknown function (DUF3330)
@@ -10976,9 +10973,9 @@ PF11817 CL0020 TPR Foie-gras_1 Foie gras liver health family 1
PF11818 DUF3340 C-terminal domain of tail specific protease (DUF3340)
PF11819 CUPID Cytohesin Ubiquitin Protein Inducing Domain
PF11820 DUF3339 Protein of unknown function (DUF3339)
-PF11821 DUF3341 Protein of unknown function (DUF3341)
-PF11822 CL0033 POZ DUF3342 Domain of unknown function (DUF3342)
-PF11823 DUF3343 Protein of unknown function (DUF3343)
+PF11821 ActD Alternative complex III, ActD subunit
+PF11822 CL0033 POZ SANBR_BTB SANT and BTB domain regulator of CSR, BTB domain
+PF11823 Se_S_carrier Putative Se/S carrier protein-like
PF11824 DUF3344 Protein of unknown function (DUF3344)
PF11825 Nuc_recep-AF1 Nuclear/hormone receptor activator site AF-1
PF11826 DUF3346 Protein of unknown function (DUF3346)
@@ -10992,22 +10989,22 @@ PF11833 CPP1-like Protein CHAPERONE-LIKE PROTEIN OF POR1-like
PF11834 KHA KHA, dimerisation domain of potassium ion channel
PF11835 CL0221 RRM RRM_8 RRM-like domain
PF11836 CL0567 Phage_TACs Phage_TAC_11 Phage tail tube protein, GTA-gp10
-PF11837 DUF3357 Domain of unknown function (DUF3357)
+PF11837 INV_N Beta-fructofuranosidase, N-terminal domain
PF11838 CL0159 E-set ERAP1_C ERAP1-like C-terminal domain
PF11839 CL0590 OML_zippers Alanine_zipper Alanine-zipper, major outer membrane lipoprotein
-PF11840 DUF3360 Protein of unknown function (DUF3360)
-PF11841 DUF3361 Domain of unknown function (DUF3361)
+PF11840 CL0062 APC DUF3360 Protein of unknown function (DUF3360)
+PF11841 CL0020 TPR ELMO_ARM ELMO, armadillo-like helical domain
PF11842 DUF3362 Domain of unknown function (DUF3362)
PF11843 DUF3363 Protein of unknown function (DUF3363)
PF11844 CL0043 Chelatase DUF3364 Domain of unknown function (DUF3364)
PF11845 DUF3365 Protein of unknown function (DUF3365)
PF11846 CL0020 TPR Wzy_C_2 Virulence factor membrane-bound polymerase, C-terminal
-PF11847 DUF3367 Alpha-(1->3)-arabinofuranosyltransferase
+PF11847 CL0111 GT-C DUF3367 Alpha-(1->3)-arabinofuranosyltransferase
PF11848 DUF3368 Domain of unknown function (DUF3368)
PF11849 CL0161 GAF DUF3369 Domain of unknown function (DUF3369)
PF11850 DUF3370 Protein of unknown function (DUF3370)
PF11851 DUF3371 Domain of unknown function (DUF3371)
-PF11852 CL0369 GHD DUF3372 Domain of unknown function (DUF3372)
+PF11852 CL0369 GHD Pullul_strch_C Alpha-1,6-glucosidases, pullulanase-type, C-terminal
PF11853 CL0193 MBB DUF3373 Protein of unknown function (DUF3373)
PF11854 CL0193 MBB MtrB_PioB Putative outer membrane beta-barrel porin, MtrB/PioB
PF11855 DUF3375 Protein of unknown function (DUF3375)
@@ -11024,16 +11021,16 @@ PF11865 CL0020 TPR DUF3385 Domain of unknown function (DUF3385)
PF11866 DUF3386 Protein of unknown function (DUF3386)
PF11867 DUF3387 Domain of unknown function (DUF3387)
PF11868 DUF3388 Protein of unknown function (DUF3388)
-PF11869 DUF3389 Protein of unknown function (DUF3389)
-PF11870 DUF3390 Domain of unknown function (DUF3390)
+PF11869 CL0266 PH DUF3389 Protein of unknown function (DUF3389)
+PF11870 LutB_C Lactate utilisation protein B, C-terminal
PF11871 DUF3391 Domain of unknown function (DUF3391)
PF11872 DUF3392 Protein of unknown function (DUF3392)
PF11873 Mltc_N Membrane-bound lytic murein transglycosylase C, N-terminal domain
PF11874 DUF3394 Domain of unknown function (DUF3394)
-PF11875 DUF3395 Domain of unknown function (DUF3395)
+PF11875 DnaJ-like_C11_C DnaJ-like protein C11, C-terminal
PF11876 DUF3396 Protein of unknown function (DUF3396)
PF11877 DUF3397 Protein of unknown function (DUF3397)
-PF11878 DUF3398 Domain of unknown function (DUF3398)
+PF11878 DOCK_C-D_N Dedicator of cytokinesis C/D, N terminal
PF11879 DUF3399 Domain of unknown function (DUF3399)
PF11880 DUF3400 Domain of unknown function (DUF3400)
PF11881 SPAR_C C-terminal domain of SPAR protein
@@ -11044,14 +11041,14 @@ PF11885 DUF3405 Protein of unknown function (DUF3405)
PF11886 TOC159_MAD Translocase of chloroplast 159/132, membrane anchor domain
PF11887 Mce4_CUP1 Cholesterol uptake porter CUP1 of Mce4, putative
PF11888 DUF3408 Protein of unknown function (DUF3408)
-PF11889 DUF3409 Domain of unknown function (DUF3409)
+PF11889 Capsid_pestivir Capsid protein C, pestivirus
PF11890 CL0063 NADP_Rossmann DUF3410 Domain of unknown function (DUF3410)
PF11891 RETICULATA-like Protein RETICULATA-related
PF11892 CL0349 SLOG DUF3412 Domain of unknown function (DUF3412)
PF11893 DUF3413 Domain of unknown function (DUF3413)
PF11894 CL0585 Nucleoporin_A Nup192 Nuclear pore complex scaffold, nucleoporins 186/192/205
PF11895 CL0617 Peroxidase Peroxidase_ext Fungal peroxidase extension region
-PF11896 CL0159 E-set DUF3416 Domain of unknown function (DUF3416)
+PF11896 CL0159 E-set GlgE_dom_N_S Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S
PF11897 DUF3417 Protein of unknown function (DUF3417)
PF11898 DUF3418 Domain of unknown function (DUF3418)
PF11899 DUF3419 Protein of unknown function (DUF3419)
@@ -11066,7 +11063,7 @@ PF11907 DUF3427 Domain of unknown function (DUF3427)
PF11909 NdhN NADH-quinone oxidoreductase cyanobacterial subunit N
PF11910 NdhO Cyanobacterial and plant NDH-1 subunit O
PF11911 DUF3429 Protein of unknown function (DUF3429)
-PF11912 DUF3430 Protein of unknown function (DUF3430)
+PF11912 CfaA_B_C Counting factor-associated protein A/B/C
PF11913 DUF3431 Protein of unknown function (DUF3431)
PF11914 DUF3432 Domain of unknown function (DUF3432)
PF11915 DUF3433 Protein of unknown function (DUF3433)
@@ -11088,7 +11085,7 @@ PF11931 CL0361 C2H2-zf SF3a60_Prp9_C SF3a60/Prp9 C-terminal
PF11932 DUF3450 Protein of unknown function (DUF3450)
PF11933 Na_trans_cytopl Cytoplasmic domain of voltage-gated Na+ ion channel
PF11934 CL0065 Cyclin DUF3452 Domain of unknown function (DUF3452)
-PF11935 SYMPK_PTA1_N Symplekin/PTA1 N-terminal
+PF11935 CL0020 TPR SYMPK_PTA1_N Symplekin/PTA1 N-terminal
PF11937 DUF3455 Protein of unknown function (DUF3455)
PF11938 DUF3456 TLR4 regulator and MIR-interacting MSAP
PF11939 NiFe-hyd_HybE [NiFe]-hydrogenase assembly, chaperone, HybE
@@ -11101,7 +11098,7 @@ PF11945 WASH_WAHD WAHD domain of WASH complex
PF11946 DUF3463 Domain of unknown function (DUF3463)
PF11947 DUF3464 Photosynthesis affected mutant 68
PF11948 DUF3465 Protein of unknown function (DUF3465)
-PF11949 DUF3466 Protein of unknown function (DUF3466)
+PF11949 CL0186 Beta_propeller DUF3466 Protein of unknown function (DUF3466)
PF11950 DUF3467 Protein of unknown function (DUF3467)
PF11951 CL0507 Fungal_trans Fungal_trans_2 Fungal specific transcription factor domain
PF11952 XTBD XRN-Two Binding Domain, XTBD
@@ -11115,7 +11112,7 @@ PF11959 DUF3473 Domain of unknown function (DUF3473)
PF11960 DUF3474 Domain of unknown function (DUF3474)
PF11961 DUF3475 Domain of unknown function (DUF3475)
PF11962 Peptidase_G2 Peptidase_G2, IMC autoproteolytic cleavage domain
-PF11963 DUF3477 Protein of unknown function (DUF3477)
+PF11963 B-CoV_A_NSP1 Betacoronavirus, lineage A, NSP1
PF11964 CL0502 STAS SpoIIAA-like SpoIIAA-like
PF11965 DUF3479 Domain of unknown function (DUF3479)
PF11966 SSURE SSURE domain
@@ -11135,9 +11132,9 @@ PF11979 DUF3480 Domain of unknown function (DUF3480)
PF11980 DUF3481 C-terminal domain of neuropilin glycoprotein
PF11981 CL0500 Glycine-zipper DUF3482 Domain of unknown function (DUF3482)
PF11982 DUF3483 Domain of unknown function (DUF3483)
-PF11983 DUF3484 Membrane-attachment and polymerisation-promoting switch
+PF11983 FtsA_C Cell division protein FtsA, C-terminal
PF11984 DUF3485 Protein of unknown function (DUF3485)
-PF11985 DUF3486 Protein of unknown function (DUF3486)
+PF11985 Phage_Mu_Gp27 Bacteriophage Mu, Gp27
PF11986 PB1-F2 Influenza A Proapoptotic protein
PF11987 IF-2 Translation-initiation factor 2
PF11988 CL0295 Vps51 Dsl1_N Retrograde transport protein Dsl1 N terminal
@@ -11146,7 +11143,7 @@ PF11990 DUF3487 Protein of unknown function (DUF3487)
PF11991 Trp_DMAT Tryptophan dimethylallyltransferase
PF11992 TgpA_N TgpA N-terminal domain
PF11993 Ribosomal_S4Pg Ribosomal S4P (gammaproteobacterial)
-PF11994 DUF3489 Protein of unknown function (DUF3489)
+PF11994 CL0123 HTH DUF3489 Protein of unknown function (DUF3489)
PF11995 DUF3490 Domain of unknown function (DUF3490)
PF11996 DUF3491 Protein of unknown function (DUF3491)
PF11997 CL0113 GT-B DUF3492 Domain of unknown function (DUF3492)
@@ -11166,14 +11163,14 @@ PF12011 NPH-II RNA helicase NPH-II
PF12012 CL0382 DNA-mend DUF3504 Domain of unknown function (DUF3504)
PF12013 OrsD Orsellinic acid/F9775 biosynthesis cluster protein D
PF12014 Cyclin_D1_bind Cyclin D1 binding domain
-PF12015 DUF3507 Domain of unknown function (DUF3507)
+PF12015 Bud3_N Bud3, N-terminal
PF12016 Stonin2_N Stonin 2
PF12017 Tnp_P_element Transposase protein
PF12018 FAP206 Domain of unknown function
PF12019 CL0327 Pilus GspH Type II transport protein GspH
PF12020 TAFA TAFA family
PF12021 DUF3509 Protein of unknown function (DUF3509)
-PF12022 DUF3510 Domain of unknown function (DUF3510)
+PF12022 COG2_C COG complex component, COG2, C-terminal
PF12023 DUF3511 Domain of unknown function (DUF3511)
PF12024 DUF3512 Domain of unknown function (DUF3512)
PF12025 Phage_C Phage protein C
@@ -11187,7 +11184,7 @@ PF12032 CL0678 CLIP CLIP Regulatory CLIP domain of proteinases
PF12033 CL0688 BECR DUF3519 Protein of unknown function (DUF3519)
PF12034 DUF3520 Domain of unknown function (DUF3520)
PF12036 CL0192 GPCR_A DUF3522 Protein of unknown function (DUF3522)
-PF12037 DUF3523 Domain of unknown function (DUF3523)
+PF12037 ATAD3_N ATPase family AAA domain-containing protein 3, N-terminal
PF12038 DUF3524 Domain of unknown function (DUF3524)
PF12039 DUF3525 Protein of unknown function (DUF3525)
PF12040 CL0181 ABC-2 DUF3526 Domain of unknown function (DUF3526)
@@ -11242,7 +11239,7 @@ PF12090 Spt20 Spt20 family
PF12091 DUF3567 Protein of unknown function (DUF3567)
PF12092 DUF3568 Protein of unknown function (DUF3568)
PF12093 CL0011 Ig bCoV_NS8 Betacoronavirus NS8 protein
-PF12094 DUF3570 Protein of unknown function (DUF3570)
+PF12094 CL0193 MBB DUF3570 Protein of unknown function (DUF3570)
PF12095 CRR7 Protein CHLORORESPIRATORY REDUCTION 7
PF12096 DUF3572 Protein of unknown function (DUF3572)
PF12097 CL0193 MBB DUF3573 Protein of unknown function (DUF3573)
@@ -11275,10 +11272,10 @@ PF12123 CL0089 GlnB-like CBD_PlyG PlyG Cell wall binding domain
PF12124 bCoV_SUD_C Betacoronavirus SUD-C domain
PF12125 Beta-TrCP_D D domain of beta-TrCP
PF12126 DUF3583 Protein of unknown function (DUF3583)
-PF12127 YdfA_immunity SigmaW regulon antibacterial
+PF12127 FloA Flotillin-like protein FloA
PF12128 CL0023 P-loop_NTPase DUF3584 Protein of unknown function (DUF3584)
-PF12129 Phtf-FEM1B_bdg Male germ-cell putative homeodomain transcription factor
-PF12130 DUF3585 Bivalent Mical/EHBP Rab binding domain
+PF12129 PHTF1-2_N Homeodomain containing protein PHTF1/2, N-terminal
+PF12130 bMERB_dom Bivalent Mical/EHBP Rab binding domain
PF12131 DUF3586 Protein of unknown function (DUF3586)
PF12132 DUF3587 Protein of unknown function (DUF3587)
PF12133 bCoV_NS6 Betacoronavirus NS6 protein
@@ -11289,7 +11286,7 @@ PF12137 RapA_C RNA polymerase recycling family C-terminal
PF12138 Spherulin4 Spherulation-specific family 4
PF12139 APS-reductase_C Adenosine-5'-phosphosulfate reductase beta subunit
PF12140 SLED SLED domain
-PF12141 DUF3589 Beta-mannosyltransferases
+PF12141 BMT Beta-mannosyltransferases
PF12142 PPO1_DWL Polyphenol oxidase middle domain
PF12143 CL0122 UTRA PPO1_KFDV Protein of unknown function (DUF_B2219)
PF12144 Med12-PQL Eukaryotic Mediator 12 catenin-binding domain
@@ -11359,7 +11356,7 @@ PF12208 CL0010 SH3 DUF3601 Domain of unknown function (DUF3601)
PF12209 SAC3 Leucine permease transcriptional regulator helical domain
PF12210 Hrs_helical Hepatocyte growth factor-regulated tyrosine kinase substrate
PF12211 LMWSLP_N Low molecular weight S layer protein N terminal
-PF12212 CL0638 PAZ PAZ_siRNAbind PAZ domain
+PF12212 CL0638 PAZ PAZ_2 PAZ domain
PF12213 CL0671 AAA_lid Dpoe2NT DNA polymerases epsilon N terminal
PF12214 TPX2_importin Cell cycle regulated microtubule associated protein
PF12215 CL0103 Gal_mutarotase Glyco_hydr_116N beta-glucosidase 2, glycosyl-hydrolase family 116 N-term
@@ -11387,7 +11384,7 @@ PF12236 Head-tail_con Bacteriophage head to tail connecting protein
PF12237 PCIF1_WW Phosphorylated CTD interacting factor 1 WW domain
PF12238 MSA-2c Merozoite surface antigen 2c
PF12239 DUF3605 Protein of unknown function (DUF3605)
-PF12240 Angiomotin_C Angiomotin C terminal
+PF12240 CL0145 Golgi-transport Angiomotin_C Angiomotin C terminal
PF12241 CL0063 NADP_Rossmann Enoyl_reductase Trans-2-enoyl-CoA reductase catalytic region
PF12242 CL0063 NADP_Rossmann Eno-Rase_NADH_b NAD(P)H binding domain of trans-2-enoyl-CoA reductase
PF12243 CL0020 TPR CTK3 CTD kinase subunit gamma CTK3
@@ -11397,7 +11394,7 @@ PF12246 MKT1_C Temperature dependent protein affecting M2 dsRNA replication
PF12247 MKT1_N Temperature dependent protein affecting M2 dsRNA replication
PF12248 CL0004 Concanavalin Methyltransf_FA Farnesoic acid 0-methyl transferase
PF12249 AftA_C Arabinofuranosyltransferase A C terminal
-PF12250 AftA_N Arabinofuranosyltransferase N terminal
+PF12250 CL0111 GT-C AftA_N Arabinofuranosyltransferase N terminal
PF12251 SNAPC3 snRNA-activating protein complex (SNAPc), subunit 3
PF12252 CL0237 HD_PDEase SidE_PDE SidE phosphodiesterase (PDE) domain
PF12253 CAF1A Chromatin assembly factor 1 subunit A
@@ -11408,7 +11405,7 @@ PF12257 IML1 Vacuolar membrane-associated protein Iml1
PF12258 Microcephalin Microcephalin protein
PF12259 CL0595 Fusion_gly Baculo_F Baculovirus F protein
PF12260 CL0016 PKinase PIP49_C Protein-kinase domain of FAM69
-PF12261 T_hemolysin Thermostable hemolysin
+PF12261 CL0257 Acetyltrans T_hemolysin Thermostable hemolysin
PF12262 CL0159 E-set Lipase_bact_N Bacterial virulence factor lipase N-terminal
PF12263 DUF3611 Protein of unknown function (DUF3611)
PF12264 CL0055 Nucleoplasmin Waikav_capsid_1 Waikavirus capsid protein 1
@@ -11418,26 +11415,26 @@ PF12267 DUF3614 Protein of unknown function (DUF3614)
PF12268 DUF3612 Protein of unknown function (DUF3612)
PF12269 CpG_bind_C CpG binding protein C-terminal domain
PF12270 Cyt_c_ox_IV Cytochrome c oxidase subunit IV
-PF12271 Chs7 Chitin synthase export chaperone
+PF12271 CL0192 GPCR_A Chs7 Chitin synthase export chaperone
PF12273 RCR Chitin synthesis regulation, resistance to Congo red
PF12274 DUF3615 Protein of unknown function (DUF3615)
-PF12275 DUF3616 Protein of unknown function (DUF3616)
+PF12275 CL0186 Beta_propeller DUF3616 Protein of unknown function (DUF3616)
PF12276 DUF3617 Protein of unknown function (DUF3617)
PF12277 DUF3618 Protein of unknown function (DUF3618)
PF12278 SDP_N Sex determination protein N terminal
PF12279 DUF3619 Protein of unknown function (DUF3619)
PF12280 BSMAP Brain specific membrane anchored protein
PF12281 CL0260 NTP_transf NTP_transf_8 Nucleotidyltransferase
-PF12282 H_kinase_N Signal transduction histidine kinase
+PF12282 CL0161 GAF PdtaS_GAF Histidine kinase PdtaS, GAF domain
PF12283 Protein_K Bacteriophage protein K
PF12284 HoxA13_N Hox protein A13 N terminal
-PF12285 DUF3621 Mamastrovirus p20 protein
+PF12285 Astrovir_pp_1 Astroviridae polyprotein 1
PF12286 DUF3622 Protein of unknown function (DUF3622)
PF12287 Caprin-1_C Cytoplasmic activation/proliferation-associated protein-1 C term
PF12288 CsoS2_M Carboxysome shell peptide mid-region
PF12289 Rotavirus_VP1 Rotavirus VP1 C-terminal domain
PF12290 DUF3802 Protein of unknown function (DUF3802)
-PF12291 DUF3623 Protein of unknown function (DUF3623)
+PF12291 CL0316 Acyl_transf_3 DUF3623 Protein of unknown function (DUF3623)
PF12292 DUF3624 Protein of unknown function (DUF3624)
PF12293 T4BSS_DotH_IcmK Putative outer membrane core complex of type IVb secretion
PF12294 DUF3626 Protein of unknown function (DUF3626)
@@ -11450,7 +11447,7 @@ PF12300 RhlB ATP-dependent RNA helicase RhlB
PF12301 CD99L2 CD99 antigen like protein 2
PF12302 DUF3629 Protein of unknown function (DUF3629)
PF12304 BCLP Beta-casein like protein
-PF12305 DUF3630 Protein of unknown function (DUF3630)
+PF12305 CL0545 APCOP-app_sub DUF3630 Protein of unknown function (DUF3630)
PF12306 CL0026 CU_oxidase PixA Inclusion body protein
PF12307 DUF3631 Protein of unknown function (DUF3631)
PF12308 Noelin-1 Neurogenesis glycoprotein
@@ -11521,7 +11518,7 @@ PF12374 Dmrt1 Double-sex mab3 related transcription factor 1
PF12375 DUF3653 Phage protein
PF12376 DUF3654 Protein of unknown function (DUF3654)
PF12377 DuffyBP_N Duffy binding protein N terminal
-PF12378 CytadhesinP1 Trypsin-sensitive surface-exposed protein
+PF12378 CL0186 Beta_propeller P1_N Mycoplasma adhesin P1, N-terminal
PF12379 bCoV_NSP3_N Betacoronavirus replicase NSP3, N-terminal
PF12380 CL0124 Peptidase_PA Peptidase_C62 Gill-associated viral 3C-like peptidase
PF12381 CL0124 Peptidase_PA Peptidase_C3G Tungro spherical virus-type peptidase
@@ -11544,7 +11541,7 @@ PF12397 U3snoRNP10 U3 small nucleolar RNA-associated protein 10
PF12398 DUF3660 Receptor serine/threonine kinase
PF12399 CL0023 P-loop_NTPase BCA_ABC_TP_C Branched-chain amino acid ATP-binding cassette transporter
PF12400 STIMATE STIMATE family
-PF12401 DUF3662 Protein of unknown function (DUF3662)
+PF12401 FhaA_N FhaA, N-terminal domain
PF12402 nlz1 NocA-like zinc-finger protein 1
PF12403 Pax2_C Paired-box protein 2 C terminal
PF12404 DUF3663 Peptidase
@@ -11610,7 +11607,7 @@ PF12465 Pr_beta_C Proteasome beta subunits C terminal
PF12466 GDH_N Glutamate dehydrogenase N terminal
PF12467 CMV_1a Cucumber mosaic virus 1a protein family
PF12468 CL0022 LRR TTSSLRR Type III secretion system leucine rich repeat protein
-PF12469 CL0276 Nucleot_cyclase DUF3692 CRISPR-associated protein
+PF12469 CL0276 Nucleot_cyclase Cmr2_N CRISPR-associated protein Cmr2, N-terminal
PF12470 SUFU_C Suppressor of Fused Gli/Ci N terminal binding domain
PF12471 GTP_CH_N GTP cyclohydrolase N terminal
PF12472 DUF3693 Phage related protein
@@ -11669,7 +11666,7 @@ PF12526 DUF3729 Protein of unknown function (DUF3729)
PF12527 DUF3727 Protein of unknown function (DUF3727)
PF12528 T2SSppdC Type II secretion prepilin peptidase dependent protein C
PF12529 Xylo_C Xylosyltransferase C terminal
-PF12530 DUF3730 Protein of unknown function (DUF3730)
+PF12530 CL0020 TPR DUF3730 Focadhesin/RST1, DUF3730
PF12531 DUF3731 DNA-K related protein
PF12532 DUF3732 Protein of unknown function (DUF3732)
PF12533 Neuro_bHLH Neuronal helix-loop-helix transcription factor
@@ -11708,7 +11705,7 @@ PF12565 DUF3747 Protein of unknown function (DUF3747)
PF12566 CL0186 Beta_propeller DUF3748 Protein of unknown function (DUF3748)
PF12567 CL0159 E-set CD45 Leukocyte receptor CD45
PF12568 CL0257 Acetyltrans PanZ Acetyltransferase (GNAT) domain, PanZ
-PF12569 CL0020 TPR NARP1 NMDA receptor-regulated protein 1
+PF12569 CL0020 TPR NatA_aux_su N-terminal acetyltransferase A, auxiliary subunit
PF12570 DUF3750 Protein of unknown function (DUF3750)
PF12571 DUF3751 Phage tail-collar fibre protein
PF12572 DUF3752 Protein of unknown function (DUF3752)
@@ -11719,7 +11716,7 @@ PF12576 DUF3754 Protein of unknown function (DUF3754)
PF12577 PPARgamma_N PPAR gamma N-terminal region
PF12578 3-PAP Myotubularin-associated protein
PF12579 DUF3755 Protein of unknown function (DUF3755)
-PF12580 TPPII Tripeptidyl peptidase II
+PF12580 CL0159 E-set TPPII Tripeptidyl peptidase II
PF12581 DUF3756 Protein of unknown function (DUF3756)
PF12582 DUF3757 Protein of unknown function (DUF3757)
PF12583 TPPII_N Tripeptidyl peptidase II N terminal
@@ -11731,15 +11728,15 @@ PF12588 PSDC Phophatidylserine decarboxylase
PF12589 WBS_methylT Methyltransferase involved in Williams-Beuren syndrome
PF12590 Acyl-thio_N Acyl-ATP thioesterase
PF12591 DUF3762 Protein of unknown function (DUF3762)
-PF12592 DUF3763 Protein of unknown function (DUF3763)
+PF12592 ATPase_RavA_C ATPase, RavA, C-terminal
PF12593 McyA_C Microcystin synthetase C terminal
PF12594 DUF3764 Protein of unknown function (DUF3764)
PF12595 Rhomboid_SP Rhomboid serine protease
PF12596 Tnp_P_element_C 87kDa Transposase
-PF12597 DUF3767 Protein of unknown function (DUF3767)
+PF12597 Cox20 Cytochrome c oxidase assembly protein COX20
PF12598 TBX T-box transcription factor
PF12599 DUF3768 Protein of unknown function (DUF3768)
-PF12600 DUF3769 Protein of unknown function (DUF3769)
+PF12600 CL0193 MBB DUF3769 Protein of unknown function (DUF3769)
PF12601 Rubi_NSP_C Rubivirus non-structural protein
PF12602 FinO_N Fertility inhibition protein N terminal
PF12603 DUF3770 Protein of unknown function (DUF3770)
@@ -11773,7 +11770,7 @@ PF12630 Pox_polyA_pol_N Poxvirus poly(A) polymerase N-terminal domain
PF12631 MnmE_helical MnmE helical domain
PF12632 Vezatin Mysoin-binding motif of peroxisomes
PF12633 CL0260 NTP_transf Adenyl_cycl_N Adenylate cyclase NT domain
-PF12634 Inp1 Inheritance of peroxisomes protein 1
+PF12634 CL0266 PH Inp1 Inheritance of peroxisomes protein 1
PF12635 DUF3780 Protein of unknown function (DUF3780)
PF12636 DUF3781 Protein of unknown function (DUF3781)
PF12637 TSCPD TSCPD domain
@@ -11797,7 +11794,7 @@ PF12655 DUF3787 Domain of unknown function (DUF3787)
PF12656 CL0449 G-PATCH G-patch_2 G-patch domain
PF12657 TFIIIC_delta Transcription factor IIIC subunit delta N-term
PF12658 CL0021 OB Ten1 Telomere capping, CST complex subunit
-PF12659 Stn1_C Telomere capping C-terminal wHTH
+PF12659 CL0123 HTH Stn1_C Telomere capping C-terminal wHTH
PF12660 zf-TFIIIC Putative zinc-finger of transcription factor IIIC complex
PF12661 CL0001 EGF hEGF Human growth factor-like EGF
PF12662 CL0001 EGF cEGF Complement Clr-like EGF-like
@@ -11885,7 +11882,7 @@ PF12745 CL0458 IIaaRS-ABD HGTP_anticodon2 Anticodon binding domain of tRNAs
PF12746 CL0257 Acetyltrans GNAT_acetyltran GNAT acetyltransferase
PF12747 DdrB DdrB-like protein
PF12749 CL0461 Metallothionein Metallothio_Euk Eukaryotic metallothionein
-PF12750 Maff2 Maff2 family
+PF12750 CL0690 TrbC_VirB2 Maff2 Maff2 family
PF12751 Vac7 Vacuolar segregation subunit 7
PF12752 SUZ SUZ domain
PF12753 CL0020 TPR Nro1 Nuclear pore complex subunit Nro1
@@ -11917,7 +11914,6 @@ PF12778 PXPV PXPV repeat (3 copies)
PF12779 WXXGXW WXXGXW repeat (2 copies)
PF12780 CL0023 P-loop_NTPase AAA_8 P-loop containing dynein motor region D4
PF12781 CL0023 P-loop_NTPase AAA_9 ATP-binding dynein motor region
-PF12782 Innate_immun Invertebrate innate immunity transcript family
PF12783 Sec7_N Guanine nucleotide exchange factor in Golgi transport N-terminal
PF12784 CL0236 PDDEXK PDDEXK_2 PD-(D/E)XK nuclease family transposase
PF12785 VESA1_N Variant erythrocyte surface antigen-1
@@ -11955,7 +11951,7 @@ PF12816 Vps8 Golgi CORVET complex core vacuolar protein 8
PF12818 Tegument_dsDNA dsDNA viral tegument protein
PF12819 CL0202 GBD Malectin_like Malectin-like domain
PF12820 BRCT_assoc Serine-rich domain associated with BRCT
-PF12821 CL0470 UMP_1 ThrE_2 Threonine/Serine exporter, ThrE
+PF12821 CL0470 ThrE ThrE_2 Threonine/Serine exporter, ThrE
PF12822 CL0315 Gx_transp ECF_trnsprt ECF transporter, substrate-specific component
PF12823 DUF3817 Domain of unknown function (DUF3817)
PF12824 CL0123 HTH MRP-L20 Mitochondrial ribosomal protein subunit L20
@@ -11975,7 +11971,7 @@ PF12837 CL0344 4Fe-4S Fer4_6 4Fe-4S binding domain
PF12838 CL0344 4Fe-4S Fer4_7 4Fe-4S dicluster domain
PF12840 CL0123 HTH HTH_20 Helix-turn-helix domain
PF12841 YvrJ YvrJ protein family
-PF12842 DUF3819 Domain of unknown function (DUF3819)
+PF12842 DUF3819 CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819
PF12843 QSregVF_b Putative quorum-sensing-regulated virulence factor
PF12844 CL0123 HTH HTH_19 Helix-turn-helix domain
PF12845 TBD TBD domain
@@ -11991,7 +11987,7 @@ PF12854 CL0020 TPR PPR_1 PPR repeat
PF12855 Ecl1 ECL1/2/3 zinc binding proteins
PF12856 ANAPC9 Anaphase-promoting complex subunit 9
PF12857 CL0021 OB TOBE_3 TOBE-like domain
-PF12859 ANAPC1 Anaphase-promoting complex subunit 1
+PF12859 CL0186 Beta_propeller ANAPC1 Anaphase-promoting complex subunit 1 WD40 beta-propeller domain
PF12860 CL0183 PAS_Fold PAS_7 PAS fold
PF12861 CL0229 RING zf-ANAPC11 Anaphase-promoting complex subunit 11 RING-H2 finger
PF12862 CL0020 TPR ANAPC5 Anaphase-promoting complex subunit 5
@@ -12042,14 +12038,14 @@ PF12911 OppC_N N-terminal TM domain of oligopeptide transport permease C
PF12912 N_NLPC_P60 NLPC_P60 stabilising domain, N term
PF12913 CL0010 SH3 SH3_6 SH3 domain (SH3b1 type)
PF12914 SH3_7 SH3 domain of SH3b2 type
-PF12915 DUF3833 Protein of unknown function (DUF3833)
+PF12915 CL0116 Calycin DUF3833 Protein of unknown function (DUF3833)
PF12916 CL0177 PBP DUF3834 Protein of unknown function (DUF3834)
-PF12917 CL0237 HD_PDEase HD_2 HD containing hydrolase-like enzyme
+PF12917 CL0237 HD_PDEase YfbR-like 5'-deoxynucleotidase YfbR-like
PF12918 TcdB_N TcdB toxin N-terminal helical domain
PF12919 CL0110 GT-A TcdA_TcdB TcdA/TcdB catalytic glycosyltransferase domain
PF12920 TcdA_TcdB_pore TcdA/TcdB pore forming domain
PF12921 ATP13 Mitochondrial ATPase expression
-PF12922 Cnd1_N non-SMC mitotic condensation complex subunit 1, N-term
+PF12922 CL0020 TPR Cnd1_N non-SMC mitotic condensation complex subunit 1, N-term
PF12923 RRP7 Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain
PF12924 APP_Cu_bd Copper-binding of amyloid precursor, CuBD
PF12925 APP_E2 E2 domain of amyloid precursor protein
@@ -12072,7 +12068,7 @@ PF12941 HCV_NS5a_C HCV NS5a protein C-terminal region
PF12942 Archaeal_AmoA Archaeal ammonia monooxygenase subunit A (AmoA)
PF12943 DUF3839 Protein of unknown function (DUF3839)
PF12944 CL0055 Nucleoplasmin HAV_VP Hepatitis A virus viral protein VP
-PF12945 YcgR_2 Flagellar protein YcgR
+PF12945 PilZNR Flagellar protein YcgR
PF12946 CL0001 EGF EGF_MSP1_1 MSP1 EGF domain 1
PF12947 CL0001 EGF EGF_3 EGF domain
PF12948 MSP7_C MSP7-like protein C-terminal domain
@@ -12135,7 +12131,7 @@ PF13005 zf-IS66 zinc-finger binding domain of transposase IS66
PF13006 Nterm_IS4 Insertion element 4 transposase N-terminal
PF13007 LZ_Tnp_IS66 Transposase C of IS166 homeodomain
PF13008 zf-Paramyx-P Zinc-binding domain of Paramyxoviridae V protein
-PF13009 CL0382 DNA-mend Phage_Integr_2 Putative phage integrase
+PF13009 CL0382 DNA-mend Integrase_2 Putative integrase
PF13010 pRN1_helical Primase helical domain
PF13011 CL0123 HTH LZ_Tnp_IS481 leucine-zipper of insertion element IS481
PF13012 MitMem_reg Maintenance of mitochondrial structure and function
@@ -12145,7 +12141,7 @@ PF13016 CL0482 Prolamin Gliadin Cys-rich Gliadin N-terminal
PF13017 CL0219 RNase_H Maelstrom piRNA pathway germ-plasm component
PF13018 ESPR Extended Signal Peptide of Type V secretion system
PF13019 CL0072 Ubiquitin Sde2_N_Ubi Silencing defective 2 N-terminal ubiquitin domain
-PF13020 CL0236 PDDEXK DUF3883 Domain of unknown function (DUF3883)
+PF13020 CL0236 PDDEXK NOV_C Protein NO VEIN, C-terminal
PF13021 DUF3885 Domain of unknown function (DUF3885)
PF13022 CL0123 HTH HTH_Tnp_1_2 Helix-turn-helix of insertion element transposase
PF13023 CL0237 HD_PDEase HD_3 HD domain
@@ -12156,10 +12152,10 @@ PF13027 DUF3888 Protein of unknown function (DUF3888)
PF13028 CL0121 Cystatin DUF3889 Protein of unknown function (DUF3889)
PF13029 DUF3890 Domain of unknown function (DUF3890)
PF13030 DUF3891 Protein of unknown function (DUF3891)
-PF13031 DUF3892 Protein of unknown function (DUF3892)
+PF13031 CL0219 RNase_H DUF3892 Protein of unknown function (DUF3892)
PF13032 RNaseH_pPIWI_RE RNaseH domain of pPIWI_RE
PF13033 DUF3894 Protein of unknown function (DUF3894)
-PF13034 DUF3895 Protein of unknown function (DUF3895)
+PF13034 CL0123 HTH DUF3895 Protein of unknown function (DUF3895)
PF13035 DUF3896 Protein of unknown function (DUF3896)
PF13036 CL0342 TolB_N LpoB Peptidoglycan-synthase activator LpoB
PF13037 DUF3898 Domain of unknown function (DUF3898)
@@ -12281,11 +12277,11 @@ PF13153 DUF3985 Protein of unknown function (DUF3985)
PF13154 DUF3991 Protein of unknown function (DUF3991)
PF13155 CL0413 Toprim-like Toprim_2 Toprim-like
PF13156 CL0236 PDDEXK Mrr_cat_2 Restriction endonuclease
-PF13157 DUF3992 Protein of unknown function (DUF3992)
+PF13157 Enas Endospore appendages
PF13158 DUF3993 Protein of unknown function (DUF3993)
PF13159 DUF3994 Domain of unknown function (DUF3994)
PF13160 DUF3995 Protein of unknown function (DUF3995)
-PF13161 DUF3996 Protein of unknown function (DUF3996)
+PF13161 CL0193 MBB DUF3996 Protein of unknown function (DUF3996)
PF13162 DUF3997 Protein of unknown function (DUF3997)
PF13163 DUF3999 Protein of unknown function (DUF3999)
PF13164 Diedel Diedel
@@ -12334,7 +12330,7 @@ PF13207 CL0023 P-loop_NTPase AAA_17 AAA domain
PF13208 TerB_N TerB N-terminal domain
PF13209 DUF4017 Protein of unknown function (DUF4017)
PF13210 DUF4018 Domain of unknown function (DUF4018)
-PF13211 DUF4019 Protein of unknown function (DUF4019)
+PF13211 CL0051 NTF2 DUF4019 Protein of unknown function (DUF4019)
PF13212 DUF4020 Domain of unknown function (DUF4020)
PF13213 DUF4021 Protein of unknown function (DUF4021)
PF13214 DUF4022 Protein of unknown function (DUF4022)
@@ -12366,7 +12362,7 @@ PF13240 CL0167 Zn_Beta_Ribbon zinc_ribbon_2 zinc-ribbon domain
PF13241 CL0063 NADP_Rossmann NAD_binding_7 Putative NAD(P)-binding
PF13242 CL0137 HAD Hydrolase_like HAD-hyrolase-like
PF13243 CL0059 6_Hairpin SQHop_cyclase_C Squalene-hopene cyclase C-terminal domain
-PF13244 DUF4040 Domain of unknown function (DUF4040)
+PF13244 MbhD MBH, subunit D
PF13245 CL0023 P-loop_NTPase AAA_19 AAA domain
PF13246 CL0137 HAD Cation_ATPase Cation transport ATPase (P-type)
PF13247 CL0344 4Fe-4S Fer4_11 4Fe-4S dicluster domain
@@ -12391,7 +12387,7 @@ PF13266 DUF4057 Protein of unknown function (DUF4057)
PF13267 DUF4058 Protein of unknown function (DUF4058)
PF13268 DUF4059 Protein of unknown function (DUF4059)
PF13269 DUF4060 Protein of unknown function (DUF4060)
-PF13270 DUF4061 Domain of unknown function (DUF4061)
+PF13270 CCDC28 Coiled-coil domain-containing protein 28
PF13271 DUF4062 Domain of unknown function (DUF4062)
PF13272 Holin_2-3 Putative 2/3 transmembrane domain holin
PF13273 CL0347 Tetraspannin DUF4064 Protein of unknown function (DUF4064)
@@ -12401,9 +12397,9 @@ PF13276 CL0123 HTH HTH_21 HTH-like domain
PF13277 CL0163 Calcineurin YmdB YmdB-like protein
PF13279 CL0050 HotDog 4HBT_2 Thioesterase-like superfamily
PF13280 CL0654 WYL WYL WYL domain
-PF13281 MAP3K_TRAF_bd MAP3K TRAFs-binding domain
+PF13281 CL0020 TPR MAP3K_TRAF_bd MAP3K TRAFs-binding domain
PF13282 DUF4070 Domain of unknown function (DUF4070)
-PF13283 NfrA_C Bacteriophage N adsorption protein A C-term
+PF13283 CL0193 MBB NfrA_C Bacteriophage N adsorption protein A C-term
PF13284 DUF4072 Domain of unknown function (DUF4072)
PF13285 DUF4073 Domain of unknown function (DUF4073)
PF13286 HD_assoc Phosphohydrolase-associated domain
@@ -12438,7 +12434,7 @@ PF13314 DUF4083 Domain of unknown function (DUF4083)
PF13315 DUF4085 Protein of unknown function (DUF4085)
PF13316 DUF4087 Protein of unknown function (DUF4087)
PF13317 DUF4088 Protein of unknown function (DUF4088)
-PF13318 DUF4089 Protein of unknown function (DUF4089)
+PF13318 AtzG-like 1-carboxybiuret hydrolase subunit AtzG-like
PF13319 DUF4090 Protein of unknown function (DUF4090)
PF13320 DUF4091 Domain of unknown function (DUF4091)
PF13321 DUF4084 Domain of unknown function (DUF4084)
@@ -12457,7 +12453,7 @@ PF13333 CL0219 RNase_H rve_2 Integrase core domain
PF13334 DUF4094 Domain of unknown function (DUF4094)
PF13335 CL0671 AAA_lid Mg_chelatase_C Magnesium chelatase, subunit ChlI C-terminal
PF13336 CL0246 ISOCOT_Fold AcetylCoA_hyd_C Acetyl-CoA hydrolase/transferase C-terminal domain
-PF13337 CL0023 P-loop_NTPase Lon_2 Putative ATP-dependent Lon protease
+PF13337 CL0023 P-loop_NTPase BrxL_ATPase Lon-like protease BrxL-like, ATPase domain
PF13338 CL0123 HTH AbiEi_4 Transcriptional regulator, AbiEi antitoxin
PF13339 AATF-Che1 Apoptosis antagonizing transcription factor
PF13340 DUF4096 Putative transposase of IS4/5 family (DUF4096)
@@ -12473,7 +12469,7 @@ PF13351 DUF4099 Protein of unknown function (DUF4099)
PF13352 DUF4100 Protein of unknown function (DUF4100)
PF13353 CL0344 4Fe-4S Fer4_12 4Fe-4S single cluster domain
PF13354 CL0013 Beta-lactamase Beta-lactamase2 Beta-lactamase enzyme family
-PF13355 ARC6-like_IMS ARC6-like, IMS domain
+PF13355 CL0051 NTF2 ARC6-like_IMS ARC6-like, IMS domain
PF13356 CL0081 MBD-like Arm-DNA-bind_3 Arm DNA-binding domain
PF13358 CL0219 RNase_H DDE_3 DDE superfamily endonuclease
PF13359 CL0219 RNase_H DDE_Tnp_4 DDE superfamily endonuclease
@@ -12490,7 +12486,7 @@ PF13369 CL0125 Peptidase_CA Transglut_core2 Transglutaminase-like superfamily
PF13370 CL0344 4Fe-4S Fer4_13 4Fe-4S single cluster domain of Ferredoxin I
PF13371 CL0020 TPR TPR_9 Tetratricopeptide repeat
PF13372 CL0193 MBB Alginate_exp Alginate export
-PF13373 DUF2407_C DUF2407 C-terminal domain
+PF13373 Dsc3_C DSC E3 ubiquitin ligase complex subunit 3, C-terminal domain
PF13374 CL0020 TPR TPR_10 Tetratricopeptide repeat
PF13375 CL0105 Hybrid RnfC_N RnfC Barrel sandwich hybrid domain
PF13376 OmdA Bacteriocin-protection, YdeI or OmpD-Associated
@@ -12550,7 +12546,7 @@ PF13430 DUF4112 Domain of unknown function (DUF4112)
PF13431 CL0020 TPR TPR_17 Tetratricopeptide repeat
PF13432 CL0020 TPR TPR_16 Tetratricopeptide repeat
PF13433 CL0144 Periplas_BP Peripla_BP_5 Periplasmic binding protein domain
-PF13434 CL0063 NADP_Rossmann K_oxygenase L-lysine 6-monooxygenase (NADPH-requiring)
+PF13434 CL0063 NADP_Rossmann Lys_Orn_oxgnase L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase
PF13435 CL0317 Multiheme_cytos Cytochrome_C554 Cytochrome c554 and c-prime
PF13436 CL0500 Glycine-zipper Gly-zipper_OmpA Glycine-zipper domain
PF13437 CL0105 Hybrid HlyD_3 HlyD family secretion protein
@@ -12671,7 +12667,7 @@ PF13554 CL0691 Phage_tail_2 DUF4128 Bacteriophage related domain of unknown func
PF13555 CL0023 P-loop_NTPase AAA_29 P-loop containing region of AAA domain
PF13556 CL0123 HTH HTH_30 PucR C-terminal helix-turn-helix domain
PF13557 CL0193 MBB Phenol_MetA_deg Putative MetA-pathway of phenol degradation
-PF13558 CL0023 P-loop_NTPase SbcCD_C Putative exonuclease SbcCD, C subunit
+PF13558 CL0023 P-loop_NTPase SbcC_Walker_B SbcC/RAD50-like, Walker B motif
PF13559 DUF4129 Domain of unknown function (DUF4129)
PF13560 CL0123 HTH HTH_31 Helix-turn-helix domain
PF13561 CL0063 NADP_Rossmann adh_short_C2 Enoyl-(Acyl carrier protein) reductase
@@ -12762,7 +12758,7 @@ PF13650 CL0129 Peptidase_AA Asp_protease_2 Aspartyl protease
PF13651 EcoRI_methylase Adenine-specific methyltransferase EcoRI
PF13652 QSregVF Putative quorum-sensing-regulated virulence factor
PF13653 CL0384 PLC GDPD_2 Glycerophosphoryl diester phosphodiesterase family
-PF13654 CL0023 P-loop_NTPase AAA_32 AAA domain
+PF13654 CL0023 P-loop_NTPase AAA_32 LonB-like, AAA domain
PF13655 RVT_N N-terminal domain of reverse transcriptase
PF13656 CL0509 RBP11-like RNA_pol_L_2 RNA polymerase Rpb3/Rpb11 dimerisation domain
PF13657 Couple_hipA HipA N-terminal domain
@@ -12771,7 +12767,7 @@ PF13661 CL0029 Cupin 2OG-FeII_Oxy_4 2OG-Fe(II) oxygenase superfamily
PF13662 CL0413 Toprim-like Toprim_4 Toprim domain
PF13663 DUF4148 Domain of unknown function (DUF4148)
PF13664 CL0430 CopD_like DUF4149 Domain of unknown function (DUF4149)
-PF13665 DUF4150 Domain of unknown function (DUF4150)
+PF13665 Tox-PAAR-like Toxin PAAR-like domain
PF13667 ThiC-associated ThiC-associated domain
PF13668 CL0044 Ferritin Ferritin_2 Ferritin-like domain
PF13669 CL0104 Glyoxalase Glyoxalase_4 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
@@ -12791,7 +12787,7 @@ PF13683 CL0219 RNase_H rve_3 Integrase core domain
PF13684 CL0245 EDD Dak1_2 Dihydroxyacetone kinase family
PF13685 CL0224 DHQS Fe-ADH_2 Iron-containing alcohol dehydrogenase
PF13686 CL0394 DsrEFH-like DrsE_2 DsrE/DsrF/DrsH-like family
-PF13687 CL0165 Cache DUF4153 Domain of unknown function (DUF4153)
+PF13687 DUF4153 Domain of unknown function (DUF4153)
PF13688 CL0126 Peptidase_MA Reprolysin_5 Metallo-peptidase family M12
PF13689 DUF4154 YfiR/HmsC-like
PF13690 CL0355 CheC-like CheX Chemotaxis phosphatase CheX
@@ -12859,7 +12855,7 @@ PF13756 CL0165 Cache Stimulus_sens_1 Stimulus-sensing domain
PF13757 CL0029 Cupin VIT_2 Vault protein inter-alpha-trypsin domain
PF13758 CL0200 Prefoldin Prefoldin_3 Prefoldin subunit
PF13759 CL0029 Cupin 2OG-FeII_Oxy_5 Putative 2OG-Fe(II) oxygenase
-PF13761 DUF4166 Domain of unknown function (DUF4166)
+PF13761 CL0116 Calycin DUF4166 Domain of unknown function (DUF4166)
PF13762 MNE1 Mitochondrial splicing apparatus component
PF13763 DUF4167 Domain of unknown function (DUF4167)
PF13764 E3_UbLigase_R4 E3 ubiquitin-protein ligase UBR4
@@ -12874,7 +12870,6 @@ PF13773 DUF4170 Domain of unknown function (DUF4170)
PF13774 CL0431 PF Longin Regulated-SNARE-like domain
PF13775 DUF4171 Domain of unknown function (DUF4171)
PF13776 DUF4172 Domain of unknown function (DUF4172)
-PF13777 CL0165 Cache DUF4173 Domain of unknown function (DUF4173)
PF13778 CL0172 Thioredoxin DUF4174 Domain of unknown function (DUF4174)
PF13779 DUF4175 Domain of unknown function (DUF4175)
PF13780 DUF4176 Domain of unknown function (DUF4176)
@@ -12901,12 +12896,12 @@ PF13801 CL0515 LTXXQ-like Metal_resist Heavy-metal resistance
PF13802 CL0103 Gal_mutarotase Gal_mutarotas_2 Galactose mutarotase-like
PF13803 CL0368 PhosC-NucP1 DUF4184 Domain of unknown function (DUF4184)
PF13804 HERV-K_env_2 Retro-transcribing viruses envelope glycoprotein
-PF13805 Pil1 Eisosome component PIL1
+PF13805 CL0145 Golgi-transport Pil1 Eisosome component PIL1
PF13806 CL0516 ISP-domain Rieske_2 Rieske-like [2Fe-2S] domain
PF13807 GNVR G-rich domain on putative tyrosine kinase
PF13808 DDE_Tnp_1_assoc DDE_Tnp_1-associated
PF13809 CL0566 Tubulin Tubulin_2 Tubulin like
-PF13810 DUF4185 Domain of unknown function (DUF4185)
+PF13810 CL0143 B_Fructosidase DUF4185 Domain of unknown function (DUF4185)
PF13811 DUF4186 Domain of unknown function (DUF4186)
PF13812 CL0020 TPR PPR_3 Pentatricopeptide repeat domain
PF13813 CL0517 MBOAT-like MBOAT_2 Membrane bound O-acyl transferase family
@@ -12985,18 +12980,18 @@ PF13888 MRF_C2 Myelin gene regulatory factor C-terminal domain 2
PF13889 Chromosome_seg Chromosome segregation during meiosis
PF13890 Rab3-GTPase_cat Rab3 GTPase-activating protein catalytic subunit
PF13891 zf-C3Hc3H Potential DNA-binding domain
-PF13892 CL0023 P-loop_NTPase DBINO DNA-binding domain
+PF13892 DBINO DNA-binding domain
PF13893 CL0221 RRM RRM_5 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13894 CL0361 C2H2-zf zf-C2H2_4 C2H2-type zinc finger
PF13895 CL0011 Ig Ig_2 Immunoglobulin domain
PF13896 CL0110 GT-A Glyco_transf_49 Glycosyl-transferase for dystroglycan
PF13897 CL0521 GOLD-like GOLD_2 Golgi-dynamics membrane-trafficking
-PF13898 DUF4205 Domain of unknown function (DUF4205)
+PF13898 MINDY-3_4_CD Deubiquitinating enzyme MINDY-3/4, conserved domain
PF13899 CL0172 Thioredoxin Thioredoxin_7 Thioredoxin-like
PF13901 CL0229 RING zf-RING_9 Putative zinc-RING and/or ribbon
PF13902 R3H-assoc R3H-associated N-terminal domain
PF13903 CL0375 Transporter Claudin_2 PMP-22/EMP/MP20/Claudin tight junction
-PF13904 DUF4207 Domain of unknown function (DUF4207)
+PF13904 CCDC34 Coiled-coil domain-containing protein 3
PF13905 CL0172 Thioredoxin Thioredoxin_8 Thioredoxin-like
PF13906 CL0062 APC AA_permease_C C-terminus of AA_permease
PF13907 DUF4208 Domain of unknown function (DUF4208)
@@ -13062,8 +13057,8 @@ PF13968 DUF4220 Domain of unknown function (DUF4220)
PF13969 Pab87_oct Pab87 octamerisation domain
PF13970 CL0186 Beta_propeller DUF4221 Domain of unknown function (DUF4221)
PF13971 Mei4 Meiosis-specific protein Mei4
-PF13972 TetR Bacterial transcriptional repressor
-PF13973 DUF4222 Domain of unknown function (DUF4222)
+PF13972 CL0174 TetR_C TetR Bacterial transcriptional repressor
+PF13973 CL0010 SH3 DUF4222 Domain of unknown function (DUF4222)
PF13974 YebO YebO-like protein
PF13975 CL0129 Peptidase_AA gag-asp_proteas gag-polyprotein putative aspartyl protease
PF13976 gag_pre-integrs GAG-pre-integrase domain
@@ -13141,7 +13136,7 @@ PF14047 DCR Dppa2/4 conserved region
PF14048 MBD_C C-terminal domain of methyl-CpG binding protein 2 and 3
PF14049 Dppa2_A Dppa2/4 conserved region in higher vertebrates
PF14050 Nudc_N N-terminal conserved domain of Nudc.
-PF14051 Requiem_N N-terminal domain of DPF2/REQ.
+PF14051 DPF1-3_N DPF1-3, N-terminal
PF14052 CL0193 MBB Caps_assemb_Wzi Capsule assembly protein Wzi
PF14053 DUF4248 Domain of unknown function (DUF4248)
PF14054 DUF4249 Domain of unknown function (DUF4249)
@@ -13166,7 +13161,7 @@ PF14072 DndB DNA-sulfur modification-associated
PF14073 Cep57_CLD Centrosome localisation domain of Cep57
PF14074 DUF4257 Protein of unknown function (DUF4257)
PF14075 UBN_AB Ubinuclein conserved middle domain
-PF14076 DUF4258 Domain of unknown function (DUF4258)
+PF14076 CL0136 Plasmid-antitox DUF4258 Domain of unknown function (DUF4258)
PF14077 WD40_alt Alternative WD40 repeat motif
PF14078 DUF4259 Domain of unknown function (DUF4259)
PF14079 DUF4260 Domain of unknown function (DUF4260)
@@ -13189,7 +13184,7 @@ PF14096 DUF4274 Domain of unknown function (DUF4274)
PF14097 SpoVAE Stage V sporulation protein AE1
PF14098 SSPI Small, acid-soluble spore protein I
PF14099 CL0004 Concanavalin Polysacc_lyase Polysaccharide lyase
-PF14100 PmoA Methane oxygenase PmoA
+PF14100 DUF6807 Family of unknown function (DUF6807)
PF14101 DUF4275 Domain of unknown function (DUF4275)
PF14102 Caps_synth_CapC Capsule biosynthesis CapC
PF14103 DUF4276 Domain of unknown function (DUF4276)
@@ -13197,13 +13192,13 @@ PF14104 DUF4277 Domain of unknown function (DUF4277)
PF14105 DUF4278 Domain of unknown function (DUF4278)
PF14106 DUF4279 Domain of unknown function (DUF4279)
PF14107 DUF4280 Domain of unknown function (DUF4280)
-PF14108 DUF4281 Domain of unknown function (DUF4281)
+PF14108 ABA4-like ABA DEFICIENT 4-like
PF14109 GldH_lipo GldH lipoprotein
PF14110 DUF4282 Domain of unknown function (DUF4282)
PF14111 DUF4283 Domain of unknown function (DUF4283)
PF14112 DUF4284 Immunity protein 22
PF14113 CL0125 Peptidase_CA Tae4 Type VI secretion system (T6SS), amidase effector protein 4
-PF14114 DUF4286 Domain of unknown function (DUF4286)
+PF14114 CL0032 Dim_A_B_barrel DUF4286 Domain of unknown function (DUF4286)
PF14115 YuzL YuzL-like protein
PF14116 YyzF YyzF-like protein
PF14117 DUF4287 Domain of unknown function (DUF4287)
@@ -13246,7 +13241,7 @@ PF14153 Spore_coat_CotO Spore coat protein CotO
PF14154 DUF4306 Domain of unknown function (DUF4306)
PF14155 DUF4307 Domain of unknown function (DUF4307)
PF14156 AbbA_antirepres Antirepressor AbbA
-PF14157 YmzC YmzC-like protein
+PF14157 CL0186 Beta_propeller YmzC YmzC-like protein
PF14158 YndJ YndJ-like protein
PF14159 CAAD CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
PF14160 FAM110_C Centrosome-associated C terminus
@@ -13273,13 +13268,13 @@ PF14182 YgaB YgaB-like protein
PF14183 YwpF YwpF-like protein
PF14184 YrvL Regulatory protein YrvL
PF14185 SpoIISB_antitox Antitoxin SpoIISB, type II toxin-antitoxin system
-PF14186 CL0154 C2 Aida_C2 Cytoskeletal adhesion
+PF14186 CL0154 C2 Aida_C2 Axin interactor dorsalisation-associated protein, C-terminal
PF14187 DUF4310 Domain of unknown function (DUF4310)
PF14188 DUF4311 Domain of unknown function (DUF4311)
PF14189 DUF4312 Domain of unknown function (DUF4312)
PF14190 DUF4313 Domain of unknown function (DUF4313)
PF14191 YodL YodL-like
-PF14192 DUF4314 Domain of unknown function (DUF4314)
+PF14192 CL0010 SH3 DUF4314 Domain of unknown function (DUF4314)
PF14193 DUF4315 Domain of unknown function (DUF4315)
PF14194 Cys_rich_VLP Cysteine-rich VLP
PF14195 DUF4316 Domain of unknown function (DUF4316)
@@ -13341,12 +13336,12 @@ PF14254 CL0051 NTF2 DUF4348 Domain of unknown function (DUF4348)
PF14255 Cys_rich_CPXG Cysteine-rich CPXCG
PF14256 YwiC YwiC-like protein
PF14257 DUF4349 Domain of unknown function (DUF4349)
-PF14258 DUF4350 Domain of unknown function (DUF4350)
+PF14258 CL0014 Glutaminase_I DUF4350 Domain of unknown function (DUF4350)
PF14260 zf-C4pol C4-type zinc-finger of DNA polymerase delta
PF14261 DUF4351 Domain of unknown function (DUF4351)
PF14262 CL0268 Pec_lyase-like Cthe_2159 Carbohydrate-binding domain-containing protein Cthe_2159
PF14263 CL0524 MPT63-MPB63 DUF4354 Domain of unknown function (DUF4354)
-PF14264 Glucos_trans_II Glucosyl transferase GtrII
+PF14264 CL0111 GT-C Glucos_trans_II Glucosyl transferase GtrII
PF14265 DUF4355 Domain of unknown function (DUF4355)
PF14266 YceG_bac Putative component of 'biosynthetic module'
PF14267 DUF4357 Domain of unknown function (DUF4357)
@@ -13372,15 +13367,15 @@ PF14286 CL0264 SGNH_hydrolase DHHW DHHW protein
PF14287 DUF4368 Domain of unknown function (DUF4368)
PF14288 FKS1_dom1 1,3-beta-glucan synthase subunit FKS1, domain-1
PF14289 DUF4369 Domain of unknown function (DUF4369)
-PF14290 DUF4370 Domain of unknown function (DUF4370)
+PF14290 SDH5_plant Succinate dehydrogenase subunit 5, mitochondrial
PF14291 DUF4371 Domain of unknown function (DUF4371)
PF14292 CL0159 E-set SusE SusE outer membrane protein
PF14293 YWFCY YWFCY protein
PF14294 DUF4372 Domain of unknown function (DUF4372)
PF14295 CL0168 PAN PAN_4 PAN domain
PF14296 CL0499 O-anti_assembly O-ag_pol_Wzy O-antigen polysaccharide polymerase Wzy
-PF14297 DUF4373 Domain of unknown function (DUF4373)
-PF14298 DUF4374 Domain of unknown function (DUF4374)
+PF14297 CL0123 HTH DUF4373 Domain of unknown function (DUF4373)
+PF14298 CL0186 Beta_propeller DUF4374 Domain of unknown function (DUF4374)
PF14299 PP2 Phloem protein 2
PF14300 DUF4375 Domain of unknown function (DUF4375)
PF14301 DUF4376 Domain of unknown function (DUF4376)
@@ -13420,8 +13415,8 @@ PF14334 DUF4390 Domain of unknown function (DUF4390)
PF14335 DUF4391 Domain of unknown function (DUF4391)
PF14336 DUF4392 Domain of unknown function (DUF4392)
PF14337 Abi_alpha Abortive infection alpha
-PF14338 Mrr_N Mrr N-terminal domain
-PF14339 DUF4394 Domain of unknown function (DUF4394)
+PF14338 CL0123 HTH Mrr_N Mrr N-terminal domain
+PF14339 CL0186 Beta_propeller DUF4394 Domain of unknown function (DUF4394)
PF14340 DUF4395 Domain of unknown function (DUF4395)
PF14341 PilX_N PilX N-terminal
PF14342 DUF4396 Domain of unknown function (DUF4396)
@@ -13508,7 +13503,7 @@ PF14424 CL0109 CDA Toxin-deaminase The BURPS668_1122 family of deaminases
PF14425 Imm3 Immunity protein Imm3
PF14426 Imm2 Immunity protein Imm2
PF14427 CL0109 CDA Pput2613-deam Pput_2613-like deaminase
-PF14428 CL0109 CDA SCP1201-deam SCP1.201-like deaminase
+PF14428 CL0109 CDA DddA-like Double-stranded DNA deaminase toxin A
PF14429 CL0154 C2 DOCK-C2 C2 domain in Dock180 and Zizimin proteins
PF14430 Imm1 Immunity protein Imm1
PF14431 CL0109 CDA YwqJ-deaminase YwqJ-like deaminase
@@ -13622,7 +13617,7 @@ PF14541 CL0129 Peptidase_AA TAXi_C Xylanase inhibitor C-terminal
PF14542 CL0257 Acetyltrans Acetyltransf_CG GCN5-related N-acetyl-transferase
PF14543 CL0129 Peptidase_AA TAXi_N Xylanase inhibitor N-terminal
PF14544 CL0250 GAD DUF4443 Domain of unknown function (DUF4443)
-PF14545 DBB Dof, BCAP, and BANK (DBB) motif,
+PF14545 CL0159 E-set DBB Dof, BCAP, and BANK (DBB) motif,
PF14547 CL0482 Prolamin Hydrophob_seed Hydrophobic seed protein
PF14549 CL0123 HTH P22_Cro DNA-binding transcriptional regulator Cro
PF14550 CL0201 Peptidase_SH Peptidase_S78_2 Putative phage serine protease XkdF
@@ -13691,7 +13686,7 @@ PF14612 Ino80_Iec3 IEC3 subunit of the Ino80 complex, chromatin re-modelling
PF14613 DUF4449 Protein of unknown function (DUF4449)
PF14614 CL0103 Gal_mutarotase DUF4450 Domain of unknown function (DUF4450)
PF14615 Rsa3 Ribosome-assembly protein 3
-PF14616 DUF4451 Domain of unknown function (DUF4451)
+PF14616 Rua1_C Transcription regulator Rua1, C-terminal
PF14617 CL0023 P-loop_NTPase CMS1 U3-containing 90S pre-ribosomal complex subunit
PF14618 DUF4452 Domain of unknown function (DUF4452)
PF14619 SnAC Snf2-ATP coupling, chromatin remodelling complex
@@ -13729,7 +13724,7 @@ PF14651 CL0116 Calycin Lipocalin_7 Lipocalin / cytosolic fatty-acid binding prot
PF14652 DUF4457 Domain of unknown function (DUF4457)
PF14653 IGFL Insulin growth factor-like family
PF14654 Epiglycanin_C Mucin, catalytic, TM and cytoplasmic tail region
-PF14655 RAB3GAP2_N Rab3 GTPase-activating protein regulatory subunit N-terminus
+PF14655 CL0186 Beta_propeller RAB3GAP2_N Rab3 GTPase-activating protein regulatory subunit N-terminus
PF14656 RAB3GAP2_C Rab3 GTPase-activating protein regulatory subunit C-terminus
PF14657 CL0081 MBD-like Arm-DNA-bind_4 Arm DNA-binding domain
PF14658 CL0220 EF_hand EF-hand_9 EF-hand domain
@@ -13748,13 +13743,13 @@ PF14670 CL0001 EGF FXa_inhibition Coagulation Factor Xa inhibitory site
PF14671 CL0031 Phosphatase DSPn Dual specificity protein phosphatase, N-terminal half
PF14672 LCE Late cornified envelope
PF14673 DUF4459 Domain of unknown function (DUF4459)
-PF14674 FANCI_S1-cap FANCI solenoid 1 cap
-PF14675 FANCI_S1 FANCI solenoid 1
-PF14676 FANCI_S2 FANCI solenoid 2
-PF14677 FANCI_S3 FANCI solenoid 3
-PF14678 FANCI_S4 FANCI solenoid 4
-PF14679 FANCI_HD1 FANCI helical domain 1
-PF14680 FANCI_HD2 FANCI helical domain 2
+PF14674 CL0020 TPR FANCI_S1-cap FANCI solenoid 1 cap
+PF14675 CL0020 TPR FANCI_S1 FANCI solenoid 1
+PF14676 CL0020 TPR FANCI_S2 FANCI solenoid 2
+PF14677 CL0020 TPR FANCI_S3 FANCI solenoid 3
+PF14678 CL0020 TPR FANCI_S4 FANCI solenoid 4
+PF14679 CL0020 TPR FANCI_HD1 FANCI helical domain 1
+PF14680 CL0020 TPR FANCI_HD2 FANCI helical domain 2
PF14681 CL0533 PRTase-like UPRTase Uracil phosphoribosyltransferase
PF14682 SPOB_ab Sporulation initiation phospho-transferase B, C-terminal
PF14683 CL0202 GBD CBM-like Polysaccharide lyase family 4, domain III
@@ -13791,7 +13786,7 @@ PF14714 KH_dom-like KH-domain-like of EngA bacterial GTPase enzymes, C-termina
PF14715 FixP_N N-terminal domain of cytochrome oxidase-cbb3, FixP
PF14716 CL0198 HHH HHH_8 Helix-hairpin-helix domain
PF14717 CL0202 GBD DUF4465 Domain of unknown function (DUF4465)
-PF14718 SLT_L Soluble lytic murein transglycosylase L domain
+PF14718 CL0020 TPR SLT_L Soluble lytic murein transglycosylase L domain
PF14719 CL0266 PH PID_2 Phosphotyrosine interaction domain (PTB/PID)
PF14720 NiFe_hyd_SSU_C NiFe/NiFeSe hydrogenase small subunit C-terminal
PF14721 CL0608 Reductase_C AIF_C Apoptosis-inducing factor, mitochondrion-associated, C-term
@@ -13818,7 +13813,7 @@ PF14741 GH114_assoc N-terminal glycosyl-hydrolase-114-associated domain
PF14742 GDE_N_bis N-terminal domain of (some) glycogen debranching enzymes
PF14743 CL0021 OB DNA_ligase_OB_2 DNA ligase OB-like domain
PF14744 WASH-7_mid WASH complex subunit 7
-PF14745 WASH-7_N WASH complex subunit 7, N-terminal
+PF14745 CL0715 Nckap1_CYFIP1-2 WASH-4_N WASH complex subunit 4, N-terminal
PF14746 WASH-7_C WASH complex subunit 7, C-terminal
PF14747 DUF4473 Domain of unknown function (DUF4473)
PF14748 CL0106 6PGD_C P5CR_dimer Pyrroline-5-carboxylate reductase dimerisation
@@ -13834,7 +13829,7 @@ PF14757 NSP2-B_epitope Immunogenic region of nsp2 protein of arterivirus polyp
PF14758 CL0575 EFTPs NSP2_assoc Non-essential region of nsp2 of arterivirus polyprotein
PF14759 CL0608 Reductase_C Reductase_C Reductase C-terminal
PF14760 Rnk_N Rnk N-terminus
-PF14761 HPS3_N Hermansky-Pudlak syndrome 3
+PF14761 CL0186 Beta_propeller HPS3_N Hermansky-Pudlak syndrome 3
PF14762 HPS3_Mid Hermansky-Pudlak syndrome 3, middle region
PF14763 HPS3_C Hermansky-Pudlak syndrome 3, C-terminal
PF14764 SPG48 AP-5 complex subunit, vesicle trafficking
@@ -13854,7 +13849,7 @@ PF14777 BBIP10 Cilia BBSome complex subunit 10
PF14778 ODR4-like Odorant response abnormal 4-like
PF14779 BBS1 Ciliary BBSome complex subunit 1
PF14780 DUF4477 Domain of unknown function (DUF4477)
-PF14781 BBS2_N Ciliary BBSome complex subunit 2, N-terminal
+PF14781 CL0186 Beta_propeller BBS2_N Ciliary BBSome complex subunit 2, N-terminal
PF14782 BBS2_C Ciliary BBSome complex subunit 2, C-terminal
PF14783 CL0186 Beta_propeller BBS2_Mid Ciliary BBSome complex subunit 2, middle region
PF14784 ECSIT_C C-terminal domain of the ECSIT protein
@@ -13883,7 +13878,7 @@ PF14806 CL0545 APCOP-app_sub Coatomer_b_Cpla Coatomer beta subunit appendage pla
PF14807 CL0545 APCOP-app_sub AP4E_app_platf Adaptin AP4 complex epsilon appendage platform
PF14808 TMEM164 TMEM164 family
PF14809 TGT_C1 C1 domain of tRNA-guanine transglycosylase dimerisation
-PF14810 TGT_C2 Patch-forming domain C2 of tRNA-guanine transglycosylase
+PF14810 CL0668 Pre-PUA TGT_C2 Patch-forming domain C2 of tRNA-guanine transglycosylase
PF14811 TPD Protein of unknown function TPD sequence-motif
PF14812 PBP1_TM Transmembrane domain of transglycosylase PBP1 at N-terminal
PF14813 NADH_B2 NADH dehydrogenase 1 beta subcomplex subunit 2
@@ -13898,7 +13893,7 @@ PF14821 Thr_synth_N Threonine synthase N terminus
PF14822 CL0125 Peptidase_CA Vasohibin Vasohibin
PF14823 Sirohm_synth_C Sirohaem biosynthesis protein C-terminal
PF14824 Sirohm_synth_M Sirohaem biosynthesis protein central
-PF14825 DUF4483 Domain of unknown function (DUF4483)
+PF14825 CFAP77 Cilia- and flagella-associated protein 77
PF14826 CL0356 AMP_N-like FACT-Spt16_Nlob FACT complex subunit SPT16 N-terminal lobe domain
PF14827 CL0165 Cache dCache_3 Double sensory domain of two-component sensor kinase
PF14828 Amnionless Amnionless
@@ -13954,7 +13949,7 @@ PF14877 mIF3 Mitochondrial translation initiation factor
PF14879 DUF4489 Domain of unknown function (DUF4489)
PF14880 COX14 Cytochrome oxidase c assembly
PF14881 CL0566 Tubulin Tubulin_3 Tubulin domain
-PF14882 PHINT_rpt Phage-integrase repeat unit
+PF14882 INT_rpt Integrase repeat unit
PF14883 CL0058 Glyco_hydro_tim GHL13 Hypothetical glycosyl hydrolase family 13
PF14884 CL0543 Viral_gly_cn_dm EFF-AFF Type I membrane glycoproteins cell-cell fusogen
PF14885 CL0058 Glyco_hydro_tim GHL15 Hypothetical glycosyl hydrolase family 15
@@ -13978,10 +13973,10 @@ PF14902 DUF4494 Domain of unknown function (DUF4494)
PF14903 WG_beta_rep WG containing repeat
PF14904 FAM86 Family of unknown function
PF14905 CL0193 MBB OMP_b-brl_3 Outer membrane protein beta-barrel family
-PF14906 DUF4495 Domain of unknown function (DUF4495)
+PF14906 CL0294 Sec10 DUF4495 Domain of unknown function (DUF4495)
PF14907 CL0260 NTP_transf NTP_transf_5 Uncharacterised nucleotidyltransferase
PF14908 CL0548 IHF-likeDNA-bdg HU-CCDC81_euk_1 CCDC81 eukaryotic HU domain 1
-PF14909 SPATA6 Spermatogenesis-assoc protein 6
+PF14909 CL0154 C2 SPATA6 Spermatogenesis-assoc protein 6
PF14910 MMS22L_N S-phase genomic integrity recombination mediator, N-terminal
PF14911 MMS22L_C S-phase genomic integrity recombination mediator, C-terminal
PF14912 THEG Testicular haploid expressed repeat
@@ -13998,15 +13993,15 @@ PF14922 FWWh Protein of unknown function
PF14923 CCDC142 Coiled-coil protein 142
PF14924 DUF4497 Protein of unknown function (DUF4497)
PF14925 HPHLAWLY Domain of unknown function
-PF14926 DUF4498 Domain of unknown function (DUF4498)
+PF14926 CFAP300 Cilia- and flagella-associated protein 300
PF14927 Neurensin Neurensin
PF14928 S_tail_recep_bd Short tail fibre protein receptor-binding domain
-PF14929 TAF1_subA TAF RNA Polymerase I subunit A
-PF14930 CL0159 E-set Qn_am_d_aII Quinohemoprotein amine dehydrogenase, alpha subunit domain II
+PF14929 CL0020 TPR TAF1_subA TAF RNA Polymerase I subunit A
+PF14930 Qn_am_d_aII Quinohemoprotein amine dehydrogenase, alpha subunit domain II
PF14931 IFT20 Intraflagellar transport complex B, subunit 20
PF14932 HAUS-augmin3 HAUS augmin-like complex subunit 3
PF14933 CEP19 CEP19-like protein
-PF14934 DUF4499 Domain of unknown function (DUF4499)
+PF14934 TMEM254 Transmembrane protein 254
PF14935 TMEM138 Transmembrane protein 138
PF14936 p53-inducible11 Tumour protein p53-inducible protein 11
PF14937 DUF4500 Domain of unknown function (DUF4500)
@@ -14030,7 +14025,7 @@ PF14954 CL0196 DSRM LIX1 Limb expression 1
PF14955 CL0007 KH MRP-S24 Mitochondrial ribosome subunit S24
PF14956 DUF4505 Domain of unknown function (DUF4505)
PF14957 BORG_CEP Cdc42 effector
-PF14958 DUF4506 Domain of unknown function (DUF4506)
+PF14958 PAAT-like ATPase PAAT-like
PF14959 GSAP-16 gamma-Secretase-activating protein C-term
PF14960 ATP_synth_reg ATP synthase regulation
PF14961 BROMI Broad-minded protein
@@ -14080,7 +14075,7 @@ PF15005 IZUMO Izumo sperm-egg fusion, Ig domain-associated
PF15006 DUF4517 Domain of unknown function (DUF4517)
PF15007 CEP44 Centrosomal spindle body, CEP44
PF15008 CL0051 NTF2 DUF4518 Domain of unknown function (DUF4518)
-PF15009 TMEM173 Transmembrane protein 173
+PF15009 CL0709 STING TMEM173 Transmembrane protein 173
PF15010 FAM131 Putative cell signalling
PF15011 CK2S Casein Kinase 2 substrate
PF15012 DUF4519 Domain of unknown function (DUF4519)
@@ -14170,7 +14165,7 @@ PF15096 G6B G6B family
PF15097 Ig_J_chain Immunoglobulin J chain
PF15098 TMEM89 TMEM89 protein family
PF15099 PIRT Phosphoinositide-interacting protein family
-PF15100 TMEM187 TMEM187 protein family
+PF15100 CL0192 GPCR_A TMEM187 TMEM187 protein family
PF15101 TERB2 Telomere-associated protein TERB2
PF15102 TMEM154 TMEM154 protein family
PF15103 G0-G1_switch_2 G0/G1 switch protein 2
@@ -14236,7 +14231,7 @@ PF15164 WBS28 Williams-Beuren syndrome chromosomal region 28 protein homologue
PF15165 REC114-like Meiotic recombination protein REC114-like
PF15167 DUF4581 Domain of unknown function (DUF4581)
PF15168 TRIQK Triple QxxK/R motif-containing protein family
-PF15169 Cybc1_Eros Cytochrome b-245 chaperone 1 / Eros
+PF15169 CL0266 PH Cybc1_Eros Cytochrome b-245 chaperone 1 / Eros
PF15170 CaM-KIIN Calcium/calmodulin-dependent protein kinase II inhibitor
PF15171 Spexin Neuropeptide secretory protein family, NPQ, spexin
PF15172 Prolactin_RP Prolactin-releasing peptide
@@ -14432,7 +14427,7 @@ PF15366 DUF4597 Domain of unknown function (DUF4597)
PF15367 CABS1 Calcium-binding and spermatid-specific protein 1
PF15368 BioT2 Spermatogenesis family BioT2
PF15369 KIAA1328 Uncharacterised protein KIAA1328
-PF15370 DUF4598 Domain of unknown function (DUF4598)
+PF15370 NOPCHAP1 NOP protein chaperone 1
PF15371 DUF4599 Domain of unknown function (DUF4599)
PF15372 DUF4600 Domain of unknown function (DUF4600)
PF15373 DUF4601 Domain of unknown function (DUF4601)
@@ -14451,7 +14446,7 @@ PF15386 Tantalus Drosophila Tantalus-like
PF15387 DUF4611 Domain of unknown function (DUF4611)
PF15388 FAM117 Protein Family FAM117
PF15389 DUF4612 Domain of unknown function (DUF4612)
-PF15390 WDCP WD repeat and coiled-coil-containing protein family
+PF15390 CL0186 Beta_propeller WDCP WD repeat and coiled-coil-containing protein family
PF15391 DUF4614 Domain of unknown function (DUF4614)
PF15392 Joubert Joubert syndrome-associated
PF15393 DUF4615 Domain of unknown function (DUF4615)
@@ -14476,7 +14471,7 @@ PF15412 Nse4-Nse3_bdg Binding domain of Nse4/EID3 to Nse3-MAGE
PF15413 CL0266 PH PH_11 Pleckstrin homology domain
PF15414 CL0055 Nucleoplasmin DUF4621 Protein of unknown function (DUF4621)
PF15415 CL0450 FimbA Mfa_like_2 Fimbrillin-like
-PF15416 DUF4623 Domain of unknown function (DUF4623)
+PF15416 CL0186 Beta_propeller DUF4623 Domain of unknown function (DUF4623)
PF15417 DUF4624 Domain of unknown function (DUF4624)
PF15418 CL0159 E-set DUF4625 Domain of unknown function (DUF4625)
PF15419 LNP1 Leukemia NUP98 fusion partner 1
@@ -14563,7 +14558,7 @@ PF15501 MDM1 Nuclear protein MDM1
PF15502 MPLKIP M-phase-specific PLK1-interacting protein
PF15503 PPP1R35_C Protein phosphatase 1 regulatory subunit 35 C-terminus
PF15504 DUF4647 Domain of unknown function (DUF4647)
-PF15505 CL0010 SH3 DUF4648 Domain of unknown function (DUF4648)
+PF15505 CL0010 SH3 Vexin Vexin domain
PF15506 OCC1 OCC1 family
PF15507 DUF4649 Domain of unknown function (DUF4649)
PF15508 NAAA-beta beta subunit of N-acylethanolamine-hydrolyzing acid amidase
@@ -14698,8 +14693,8 @@ PF15639 Tox-MPTase3 Metallopeptidase toxin 3
PF15640 Tox-MPTase4 Metallopeptidase toxin 4
PF15641 Tox-MPTase5 Metallopeptidase toxin 5
PF15642 Tox-ODYAM1 Toxin in Odyssella and Amoebophilus
-PF15643 Tox-PL-2 Papain fold toxin 2
-PF15644 Gln_amidase Papain fold toxin 1, glutamine deamidase
+PF15643 CL0125 Peptidase_CA Tox-PL-2 Papain fold toxin 2
+PF15644 CL0125 Peptidase_CA Gln_amidase Papain fold toxin 1, glutamine deamidase
PF15645 CL0125 Peptidase_CA Tox-PLDMTX Dermonecrotoxin of the Papain-like fold
PF15646 CL0236 PDDEXK Tox-REase-2 Restriction endonuclease fold toxin 2
PF15647 CL0236 PDDEXK Tox-REase-3 Restriction endonuclease fold toxin 3
@@ -14757,7 +14752,7 @@ PF15698 CL0067 SIS Phosphatase Phosphatase
PF15699 NPR1_interact NPR1 interacting
PF15700 DUF4667 Domain of unknown function (DUF4667)
PF15701 DUF4668 Domain of unknown function (DUF4668)
-PF15702 HPS6 Hermansky-Pudlak syndrome 6 protein
+PF15702 CL0186 Beta_propeller HPS6 Hermansky-Pudlak syndrome 6 protein N-terminal domain
PF15703 LAT2 Linker for activation of T-cells family member 2
PF15704 Mt_ATP_synt Mitochondrial ATP synthase subunit
PF15705 TMEM132D_N Mature oligodendrocyte transmembrane protein, TMEM132D, N-term
@@ -14822,13 +14817,13 @@ PF15763 DUF4692 Regulator of human erythroid cell expansion (RHEX)
PF15764 DUF4693 Domain of unknown function (DUF4693)
PF15765 DUF4694 Domain of unknown function (DUF4694)
PF15766 DUF4695 Domain of unknown function (DUF4695)
-PF15767 DUF4696 Domain of unknown function (DUF4696)
+PF15767 ARMH4 Armadillo-like helical domain-containing protein 4
PF15768 CC190 Coiled-coil domain-containing protein 190
PF15769 DUF4698 Domain of unknown function (DUF4698)
PF15770 DUF4699 Domain of unknown function (DUF4699)
PF15771 IHO1 Interactor of HORMAD1 protein 1
PF15772 UPF0688 UPF0688 family
-PF15773 DUF4701 Domain of unknown function (DUF4701)
+PF15773 DAAP1 Dynein axonemal-associated protein 1
PF15774 DUF4702 Domain of unknown function (DUF4702)
PF15775 DUF4703 Domain of unknown function (DUF4703)
PF15776 PRR22 Proline-rich protein family 22
@@ -14837,12 +14832,12 @@ PF15778 UNC80_N UNC80 N-terminal
PF15779 LRRC37 Leucine-rich repeat-containing protein 37 family
PF15780 CL0556 PapD-like ASH Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
PF15781 CL0136 Plasmid-antitox ParE-like_toxin ParE-like toxin of type II bacterial toxin-antitoxin system
-PF15782 GREB1 Gene regulated by oestrogen in breast cancer
+PF15782 GREB1 GREB1 N-terminal region
PF15783 FSIP2 Fibrous sheath-interacting protein 2
PF15784 GPS2_interact G-protein pathway suppressor 2-interacting domain
PF15785 SMG1 Serine/threonine-protein kinase smg-1
PF15786 PET117 PET assembly of cytochrome c oxidase, mitochondrial
-PF15787 DUF4704 Domain of unknown function (DUF4704)
+PF15787 CL0020 TPR DUF4704 Neurobeachin/BDCP, DUF4704 alpha solenoid region
PF15788 DUF4705 Domain of unknown function (DUF4705)
PF15789 Hyr1 Hyphally regulated cell wall GPI-anchored protein 1
PF15790 EP400_N E1A-binding protein p400, N-terminal
@@ -14857,7 +14852,7 @@ PF15798 PRAS Proline-rich AKT1 substrate 1
PF15799 CCD48 Coiled-coil domain-containing protein 48
PF15800 CiPC Clock interacting protein circadian
PF15801 CL0175 TRASH zf-C6H2 zf-MYND-like zinc finger, mRNA-binding
-PF15802 DCAF17 DDB1- and CUL4-associated factor 17
+PF15802 CL0186 Beta_propeller DCAF17 DDB1- and CUL4-associated factor 17
PF15803 zf-SCNM1 Zinc-finger of sodium channel modifier 1
PF15804 CCDC168_N Coiled-coil domain-containing protein 168
PF15805 SCNM1_acidic Acidic C-terminal region of sodium channel modifier 1 SCNM1
@@ -15051,7 +15046,7 @@ PF16003 DUF4776 Domain of unknown function (DUF4776)
PF16004 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
PF16005 CL0007 KH MOEP19 KH-like RNA-binding domain
PF16006 NUSAP Nucleolar and spindle-associated protein
-PF16007 DUF4777 Domain of unknown function (DUF4777)
+PF16007 CL0123 HTH DUF4777 Domain of unknown function (DUF4777)
PF16008 DUF4778 Domain of unknown function (DUF4778)
PF16009 DUF4779 Domain of unknown function (DUF4779)
PF16010 CL0559 CBD9-like CDH-cyt Cytochrome domain of cellobiose dehydrogenase
@@ -15067,7 +15062,7 @@ PF16019 CSRNP_N Cysteine/serine-rich nuclear protein N-terminus
PF16020 Deltameth_res Deltamethrin resistance
PF16021 PDCD7 Programmed cell death protein 7
PF16022 CL0051 NTF2 DUF4783 Domain of unknown function (DUF4783)
-PF16023 DUF4784 Domain of unknown function (DUF4784)
+PF16023 CL0186 Beta_propeller DUF4784 DUF4784 WD40-like domain
PF16024 DUF4785 Domain of unknown function (DUF4785)
PF16025 CaM_bind Calcium-dependent calmodulin binding
PF16026 MIEAP Mitochondria-eating protein
@@ -15102,7 +15097,7 @@ PF16055 DUF4798 Domain of unknown function (DUF4798)
PF16056 DUF4799 Domain of unknown function (DUF4799)
PF16057 DUF4800 Domain of unknown function (DUF4800)
PF16058 Mucin-like Mucin-like
-PF16059 DUF4801 Domain of unknown function (DUF4801)
+PF16059 MGA_dom MGA, conserved domain
PF16060 DUF4802 Domain of unknown function (DUF4802)
PF16061 DUF4803 Domain of unknown function (DUF4803)
PF16062 DUF4804 Domain of unknown function (DUF4804)
@@ -15135,7 +15130,7 @@ PF16088 BORCS7 BLOC-1-related complex sub-unit 7
PF16089 DUF4818 Domain of unknown function (DUF4818)
PF16090 CL0049 Tudor DUF4819 Domain of unknown function (DUF4819)
PF16091 DUF4820 Domain of unknown function (DUF4820)
-PF16092 DUF4821 Domain of unknown function (DUF4821)
+PF16092 CL0257 Acetyltrans CFAP61_N Cilia- and flagella-associated protein 61, N-terminal domain
PF16093 PAC4 Proteasome assembly chaperone 4
PF16094 PAC1 Proteasome assembly chaperone 4
PF16095 COR C-terminal of Roc, COR, domain
@@ -15171,7 +15166,7 @@ PF16124 RecQ_Zn_bind RecQ zinc-binding
PF16125 DUF4837 Domain of unknown function (DUF4837)
PF16126 CL0058 Glyco_hydro_tim DUF4838 Domain of unknown function (DUF4838)
PF16127 DUF4839 Domain of unknown function (DUF4839)
-PF16128 DUF4840 Domain of unknown function (DUF4840)
+PF16128 CL0193 MBB DUF4840 Domain of unknown function (DUF4840)
PF16129 DUF4841 Domain of unknown function (DUF4841)
PF16130 DUF4842 Domain of unknown function (DUF4842)
PF16131 CL0537 CCCH_zf Torus Torus domain
@@ -15292,7 +15287,7 @@ PF16247 CL0051 NTF2 DUF4904 Domain of unknown function (DUF4904)
PF16248 DUF4905 Domain of unknown function (DUF4905)
PF16249 CL0450 FimbA DUF4906 Domain of unknown function (DUF4906)
PF16250 DUF4907 Domain of unknown function (DUF4907)
-PF16251 bCoV_NAR Betacoronavirus nucleic acid-binding (NAR)
+PF16251 bCoV_NAB Betacoronavirus nucleic acid-binding (NAB)
PF16252 DUF4908 Domain of unknown function (DUF4908)
PF16253 DUF4909 Domain of unknown function (DUF4909)
PF16254 CL0035 Peptidase_MH DUF4910 Domain of unknown function (DUF4910)
@@ -15301,8 +15296,8 @@ PF16256 DUF4911 Domain of unknown function (DUF4911)
PF16257 UxaE tagaturonate epimerase
PF16258 DUF4912 Domain of unknown function (DUF4912)
PF16259 DUF4913 Domain of unknown function (DUF4913)
-PF16260 DUF4914 Domain of unknown function (DUF4914)
-PF16261 DUF4915 Domain of unknown function (DUF4915)
+PF16260 CL0023 P-loop_NTPase DUF4914 Domain of unknown function (DUF4914)
+PF16261 CL0186 Beta_propeller DUF4915 Domain of unknown function (DUF4915)
PF16262 CL0261 NUDIX DUF4916 Domain of unknown function (DUF4916)
PF16263 CL0085 FAD_DHS DUF4917 Domain of unknown function (DUF4917)
PF16264 CL0123 HTH SatD SatD family (SatD)
@@ -15318,7 +15313,7 @@ PF16273 NuDC Nuclear distribution C domain
PF16274 Qua1 Qua1 domain
PF16275 SF1-HH Splicing factor 1 helix-hairpin domain
PF16276 NPM1-C Nucleophosmin C-terminal domain
-PF16277 DUF4926 Domain of unknown function (DUF4926)
+PF16277 CL0010 SH3 DUF4926 Domain of unknown function (DUF4926)
PF16278 CL0361 C2H2-zf zf-C2HE C2HE / C2H2 / C2HC zinc-binding finger
PF16279 DUF4927 Domain of unknown function (DUF4927)
PF16280 DUF4928 Domain of unknown function (DUF4928)
@@ -15375,7 +15370,7 @@ PF16331 TolA_bind_tri TolA binding protein trimerisation
PF16332 DUF4962 Domain of unknown function (DUF4962)
PF16334 DUF4964 Domain of unknown function (DUF4964)
PF16335 DUF4965 Domain of unknown function (DUF4965)
-PF16338 CL0103 Gal_mutarotase DUF4968 Domain of unknown function (DUF4968)
+PF16338 CL0103 Gal_mutarotase AGL_N Alpha-glucosidase, N-terminal
PF16339 DUF4969 Domain of unknown function (DUF4969)
PF16341 DUF4971 Domain of unknown function (DUF4971)
PF16342 DUF4972 Domain of unknown function (DUF4972)
@@ -15388,7 +15383,7 @@ PF16349 DUF4978 Domain of unknown function (DUF4978)
PF16350 FAO_M FAD dependent oxidoreductase central domain
PF16351 DUF4979 Domain of unknown function (DUF4979)
PF16352 DUF4980 Domain of unknown function (DUF4980)
-PF16353 CL0159 E-set DUF4981 Domain of unknown function (DUF4981)
+PF16353 CL0159 E-set LacZ_4 Beta-galactosidase, domain 4
PF16355 CL0159 E-set DUF4982 Domain of unknown function (DUF4982)
PF16356 DUF4983 Domain of unknown function (DUF4983)
PF16357 CL0490 PepSY_TM-like PepSY_TM_like_2 Putative PepSY_TM-like
@@ -15398,7 +15393,7 @@ PF16360 GTP-bdg_M GTP-binding GTPase Middle Region
PF16361 Peptidase_S8_N N-terminal of Subtilase family
PF16362 YaiA YaiA protein
PF16363 CL0063 NADP_Rossmann GDP_Man_Dehyd GDP-mannose 4,6 dehydratase
-PF16364 Antigen_C Cell surface antigen C-terminus
+PF16364 CL0204 Adhesin Antigen_C Cell surface antigen C-terminus
PF16365 CL0123 HTH EutK_C Ethanolamine utilization protein EutK C-terminus
PF16366 CEBP_ZZ Cytoplasmic polyadenylation element-binding protein ZZ domain
PF16367 CL0221 RRM RRM_7 RNA recognition motif
@@ -15417,7 +15412,6 @@ PF16379 CL0594 DUF1735 DUF4989 Domain of unknown function (DUF4989)
PF16380 DUF4990 Domain of unknown function
PF16381 CL0545 APCOP-app_sub Coatomer_g_Cpla Coatomer subunit gamma-1 C-terminal appendage platform
PF16383 DUF4992 Domain of unknown function
-PF16384 DUF4993 Domain of unknown function
PF16385 DUF4994 Domain of unknown function
PF16386 DUF4995 Domain of unknown function
PF16387 DUF4996 Domain of unknown function
@@ -15430,7 +15424,7 @@ PF16395 CL0116 Calycin DUF5004 Domain of unknown function (DUF5004)
PF16396 CL0143 B_Fructosidase DUF5005 Domain of unknown function (DUF5005)
PF16397 DUF5006 Domain of unknown function (DUF5006)
PF16398 DUF5007 Domain of unknown function (DUF5007)
-PF16399 Aquarius_N Intron-binding protein aquarius N-terminus
+PF16399 CL0020 TPR Aquarius_N Intron-binding protein aquarius N-terminus
PF16400 CL0159 E-set DUF5008 Domain of unknown function (DUF5008)
PF16401 CL0316 Acyl_transf_3 DUF5009 Domain of unknown function (DUF5009)
PF16402 CL0058 Glyco_hydro_tim DUF5010 Domain of unknown function (DUF5010)
@@ -15446,11 +15440,11 @@ PF16411 SusF_SusE Outer membrane protein SusF_SusE
PF16412 CL0193 MBB DUF5020 Domain of unknown function (DUF5020)
PF16413 Mlh1_C DNA mismatch repair protein Mlh1 C-terminus
PF16414 CL0644 Fz NPC1_N Niemann-Pick C1 N terminus
-PF16415 CNOT1_CAF1_bind CCR4-NOT transcription complex subunit 1 CAF1-binding domain
+PF16415 CL0020 TPR CNOT1_CAF1_bind CCR4-NOT transcription complex subunit 1 CAF1-binding domain
PF16416 CL0020 TPR GUN4_N ARM-like repeat domain, GUN4-N terminal
-PF16417 CNOT1_TTP_bind CCR4-NOT transcription complex subunit 1 TTP binding domain
+PF16417 CL0020 TPR CNOT1_TTP_bind CCR4-NOT transcription complex subunit 1 TTP binding domain
PF16418 CNOT1_HEAT CCR4-NOT transcription complex subunit 1 HEAT repeat
-PF16419 CNOT1_HEAT_N CCR4-NOT transcription complex subunit 1 HEAT repeat
+PF16419 CL0020 TPR CNOT1_HEAT_N CCR4-NOT transcription complex subunit 1 HEAT repeat
PF16420 ATG7_N Ubiquitin-like modifier-activating enzyme ATG7 N-terminus
PF16421 E2F_CC-MB E2F transcription factor CC-MB domain
PF16422 COE1_DBD Transcription factor COE1 DNA-binding domain
@@ -15504,7 +15498,7 @@ PF16469 NPA Nematode polyprotein allergen ABA-1
PF16470 CL0570 PPP-I S8_pro-domain Peptidase S8 pro-domain
PF16471 JIP_LZII JNK-interacting protein leucine zipper II
PF16472 CL0186 Beta_propeller DUF5050 Domain of unknown function (DUF5050)
-PF16473 CL0219 RNase_H DUF5051 3' exoribonuclease, RNase T-like
+PF16473 CL0219 RNase_H Rv2179c-like 3'-5' exoribonuclease Rv2179c-like domain
PF16474 CL0016 PKinase KIND Kinase non-catalytic C-lobe domain
PF16475 DUF5052 Domain of unknown function (DUF5052)
PF16476 DUF5053 Domain of unknown function (DUF5053)
@@ -15548,7 +15542,7 @@ PF16514 CL0397 TusA-like NADH-UOR_E putative NADH-ubiquinone oxidoreductase chai
PF16515 CL0705 VBS-like HIP1_clath_bdg Clathrin-binding domain of Huntingtin-interacting protein 1
PF16516 CC2-LZ Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
PF16517 Nore1-SARAH Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain
-PF16518 GrlR T3SS negative regulator,GrlR
+PF16518 CL0193 MBB GrlR T3SS negative regulator,GrlR
PF16519 TRPM_tetra Tetramerisation domain of TRPM
PF16520 BDV_M ssRNA-binding matrix protein of Bornaviridae
PF16521 Myosin-VI_CBD Myosin VI cargo binding domain
@@ -15599,7 +15593,7 @@ PF16565 CL0479 PLD MIT_C Phospholipase D-like domain at C-terminus of MIT
PF16566 CREPT Cell-cycle alteration and expression-elevated protein in tumour
PF16567 CagD Pathogenicity island component CagD
PF16568 Sam68-YY Tyrosine-rich domain of Sam68
-PF16569 GramPos_pilinBB Gram-positive pilin backbone subunit 2, Cna-B-like domain
+PF16569 CL0204 Adhesin GramPos_pilinBB Gram-positive pilin backbone subunit 2, Cna-B-like domain
PF16570 CL0287 Transthyretin GramPos_pilinD3 Gram-positive pilin backbone subunit 3, Cna-B-like domain
PF16571 FBP_C FBP C-terminal treble-clef zinc-finger
PF16572 CL0105 Hybrid HlyD_D4 Long alpha hairpin domain of cation efflux system protein, CusB
@@ -15616,7 +15610,7 @@ PF16582 CL0085 FAD_DHS TPP_enzyme_M_2 Middle domain of thiamine pyrophosphate
PF16583 CL0159 E-set ZirS_C Zinc-regulated secreted antivirulence protein C-terminal domain
PF16584 CL0048 LolA_LolB LolA_2 Outer membrane lipoprotein carrier protein LolA
PF16585 CL0116 Calycin Lipocalin_8 Lipocalin-like domain
-PF16586 DUF5060 Domain of unknown function (DUF5060)
+PF16586 CL0159 E-set DUF5060 Domain of unknown function (DUF5060)
PF16587 CL0500 Glycine-zipper DUF5061 17 kDa common-antigen outer membrane protein
PF16588 CL0361 C2H2-zf zf-C2H2_10 C2H2 zinc-finger
PF16589 CL0459 BRCT-like BRCT_2 BRCT domain, a BRCA1 C-terminus domain
@@ -15770,7 +15764,7 @@ PF16740 SKA2 Spindle and kinetochore-associated protein 2
PF16741 mRNA_decap_C mRNA-decapping enzyme C-terminus
PF16742 IL17R_D_N N-terminus of interleukin 17 receptor D
PF16743 PliI Periplasmic lysozyme inhibitor of I-type lysozyme
-PF16744 Zf_RING KIAA1045 RING finger
+PF16744 CL0229 RING zf-RING_15 KIAA1045 RING finger
PF16745 CL0021 OB RsgA_N RsgA N-terminal domain
PF16746 CL0145 Golgi-transport BAR_3 BAR domain of APPL family
PF16747 Adhesin_E Surface-adhesin protein E
@@ -15808,7 +15802,7 @@ PF16778 CL0348 Phage_tail Phage_tail_APC Phage tail assembly chaperone protein
PF16779 DMP12 DNA-mimic protein
PF16780 AIMP2_LysRS_bd AIMP2 lysyl-tRNA synthetase binding domain
PF16781 DUF5068 Domain of unknown function (DUF5068)
-PF16782 SIL1 Nucleotide exchange factor SIL1
+PF16782 CL0020 TPR SIL1 Nucleotide exchange factor SIL1
PF16783 FANCM-MHF_bd FANCM to MHF binding domain
PF16784 CL0263 His-Me_finger HNHc_6 Putative HNHc nuclease
PF16785 SMBP Small metal-binding protein
@@ -15830,7 +15824,7 @@ PF16800 CL0051 NTF2 Endopep_inhib IseA DL-endopeptidase inhibitor
PF16801 MSL1_dimer Dimerisation domain of Male-specific-Lethal 1
PF16802 CL0029 Cupin DUF5070 Domain of unknown function (DUF5070)
PF16803 CL0063 NADP_Rossmann DRE2_N Fe-S cluster assembly protein DRE2 N-terminus
-PF16804 DUF5071 Domain of unknown function (DUF5071)
+PF16804 CL0020 TPR DUF5071 Domain of unknown function (DUF5071)
PF16805 Trans_coact Phage late-transcription coactivator
PF16806 ExsD Antiactivator protein ExsD
PF16807 CL0691 Phage_tail_2 DUF5072 Domain of unknown function (DUF5072)
@@ -15849,7 +15843,7 @@ PF16819 DUF5074 Domain of unknown function (DUF5074)
PF16820 CL0159 E-set PKD_3 PKD-like domain
PF16821 CL0577 Paramyxovirin_C C_Hendra C protein from hendra and measles viruses
PF16822 CL0264 SGNH_hydrolase ALGX SGNH hydrolase-like domain, acetyltransferase AlgX
-PF16823 PilZ_2 Atypical PilZ domain, cyclic di-GMP receptor
+PF16823 tPilZ Atypical PilZ domain, cyclic di-GMP receptor
PF16824 CL0202 GBD CBM_26 C-terminal carbohydrate-binding module
PF16825 CL0056 C_Lectin DUF5075 IGP family C-type lectin domain
PF16826 DUF5076 Domain of unknown function (DUF5076)
@@ -15880,7 +15874,7 @@ PF16850 CL0066 Trefoil Inhibitor_I66 Peptidase inhibitor I66
PF16851 Stomagen Stomagen
PF16852 HHV-1_VABD Herpes viral adaptor-to-host cellular mRNA binding domain
PF16853 CL0021 OB CDC13_N Cell division control protein 13 N-terminus
-PF16854 VPS53_C Vacuolar protein sorting-associated protein 53 C-terminus
+PF16854 CL0020 TPR VPS53_C Vacuolar protein sorting-associated protein 53 C-terminus
PF16855 Soc Small outer capsid protein
PF16856 CDC4_D Cell division control protein 4 dimerisation domain
PF16857 RNA_pol_inhib RNA polymerase inhibitor
@@ -15928,7 +15922,7 @@ PF16898 TOPRIM_C C-terminal associated domain of TOPRIM
PF16899 CL0065 Cyclin Cyclin_C_2 Cyclin C-terminal domain
PF16900 CL0021 OB REPA_OB_2 Replication protein A OB domain
PF16901 CL0667 Fer2_BFD DAO_C C-terminal domain of alpha-glycerophosphate oxidase
-PF16902 Type2_restr_D3 Type-2 restriction enzyme D3 domain
+PF16902 FokI_D3 FokI, D3 domain
PF16903 CL0055 Nucleoplasmin Capsid_N Major capsid protein N-terminus
PF16904 PurL_C Phosphoribosylformylglycinamidine synthase II C-terminus
PF16905 GPHH Voltage-dependent L-type calcium channel, IQ-associated
@@ -15940,7 +15934,7 @@ PF16910 VPS13_mid_rpt Repeating coiled region of VPS13
PF16911 CL0149 CoA-acyltrans PapA_C Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus
PF16912 CL0063 NADP_Rossmann Glu_dehyd_C Glucose dehydrogenase C-terminus
PF16913 CL0184 DMT PUNUT Purine nucleobase transmembrane transport
-PF16914 TetR_C_12 Bacterial transcriptional repressor C-terminal
+PF16914 CL0174 TetR_C TetR_C_12 Bacterial transcriptional repressor C-terminal
PF16915 Eryth_link_C Annelid erythrocruorin linker subunit C-terminus
PF16916 ZT_dimer Dimerisation domain of Zinc Transporter
PF16917 CL0040 tRNA_synt_II BPL_LplA_LipB_2 Biotin/lipoate A/B protein ligase family
@@ -15959,7 +15953,7 @@ PF16929 CL0028 AB_hydrolase Asp2 Accessory Sec system GspB-transporter
PF16930 CL0193 MBB Porin_5 Putative porin
PF16931 Phage_holin_8 Putative phage holin
PF16932 T4SS_TraI Type IV secretory system, conjugal DNA-protein transfer
-PF16933 PelG Putative exopolysaccharide Exporter (EPS-E)
+PF16933 CL0222 MviN_MATE PelG Putative exopolysaccharide Exporter (EPS-E)
PF16934 Mersacidin Two-component Enterococcus faecalis cytolysin (EFC)
PF16935 Hol_Tox Putative Holin-like Toxin (Hol-Tox)
PF16936 Holin_9 Putative holin
@@ -15998,7 +15992,7 @@ PF16970 CL0204 Adhesin FimA Type-1 fimbrial protein, A
PF16971 RcpB Rough colony protein B, tight adherence - tad - subunit
PF16972 TipE Na+ channel auxiliary subunit TipE
PF16973 FliN_N Flagellar motor switch protein FliN N-terminal
-PF16974 NAR2 High-affinity nitrate transporter accessory
+PF16974 CL0159 E-set NAR2 High-affinity nitrate transporter accessory, Ig-like domain
PF16975 CL0117 uPAR_Ly6_toxin UPAR_LY6_2 Ly6/PLAUR domain-containing protein 6, Lypd6
PF16976 CL0489 SAF RcpC Flp pilus assembly protein RcpC/CpaB
PF16977 ApeC C-terminal domain of apextrin
@@ -16021,7 +16015,7 @@ PF16993 CL0113 GT-B Asp1 Accessory Sec system protein Asp1
PF16994 CL0113 GT-B Glyco_trans_4_5 Glycosyl-transferase family 4
PF16995 tRNA-synt_2_TM Transmembrane region of lysyl-tRNA synthetase
PF16996 Asp4 Accessory secretory protein Sec Asp4
-PF16997 Wap1 Wap1 domain
+PF16997 CL0020 TPR Wap1 Wap1 domain
PF16998 CL0500 Glycine-zipper 17kDa_Anti_2 17 kDa outer membrane surface antigen
PF16999 CL0255 ATP_synthase V-ATPase_G_2 Vacuolar (H+)-ATPase G subunit
PF17000 Asp5 Accessory secretory protein Sec, Asp5
@@ -16060,7 +16054,7 @@ PF17032 CL0167 Zn_Beta_Ribbon zinc_ribbon_15 zinc-ribbon family
PF17033 CL0035 Peptidase_MH Peptidase_M99 Carboxypeptidase controlling helical cell shape catalytic
PF17034 CL0229 RING zinc_ribbon_16 Zinc-ribbon like family
PF17035 CL0665 BET BET Bromodomain extra-terminal - transcription regulation
-PF17036 CBP_BcsS Cellulose biosynthesis protein BcsS
+PF17036 CL0193 MBB CBP_BcsS Cellulose biosynthesis protein BcsS
PF17037 CBP_BcsO Cellulose biosynthesis protein BcsO
PF17038 CBP_BcsN Cellulose biosynthesis protein BcsN
PF17039 Glyco_tran_10_N Fucosyltransferase, N-terminal
@@ -16140,18 +16134,18 @@ PF17112 Tom6 Mitochondrial import receptor subunit Tom6, fungal
PF17113 CL0685 AmpE_CobD-like AmpE Regulatory signalling modulator protein AmpE
PF17114 Nod1 Gef2-related medial cortical node protein Nod1
PF17115 CL0268 Pec_lyase-like Toast_rack_N N-terminal domain of toast_rack, DUF2154
-PF17116 DUF5103 Domain of unknown function (DUF5103)
+PF17116 CL0159 E-set DUF5103 Domain of unknown function (DUF5103)
PF17117 CL0051 NTF2 DUF5104 Domain of unknown function (DUF5104)
PF17118 CL0051 NTF2 DUF5105 Domain of unknown function (DUF5105)
PF17119 MMU163 Mitochondrial protein up-regulated during meiosis
-PF17120 CL0229 RING Zn_ribbon_17 Zinc-ribbon, C4HC2 type
+PF17120 CL0229 RING zf-RING_16 RING/Ubox like zinc-binding domain
PF17121 CL0229 RING zf-C3HC4_5 Zinc finger, C3HC4 type (RING finger)
PF17122 CL0229 RING zf-C3H2C3 Zinc-finger
PF17123 CL0229 RING zf-RING_11 RING-like zinc finger
PF17124 CL0014 Glutaminase_I ThiJ_like ThiJ/PfpI family-like
PF17125 CL0063 NADP_Rossmann Methyltr_RsmF_N N-terminal domain of 16S rRNA methyltransferase RsmF
-PF17126 RsmF_methylt_CI RsmF rRNA methyltransferase first C-terminal domain
-PF17127 DUF5106 Domain of unknown function (DUF5106)
+PF17126 CL0668 Pre-PUA RsmF_methylt_CI RsmF rRNA methyltransferase first C-terminal domain
+PF17127 CL0020 TPR DUF5106 Domain of unknown function (DUF5106)
PF17128 CL0103 Gal_mutarotase DUF5107 Domain of unknown function (DUF5107)
PF17129 Peptidase_M99_C C-terminal domain of metallo-carboxypeptidase
PF17130 Peptidase_M99_m beta-barrel domain of carboxypeptidase M99
@@ -16181,8 +16175,8 @@ PF17154 GAPES3 Gammaproteobacterial periplasmic sensor domain
PF17155 CL0165 Cache GAPES1 Gammaproteobacterial periplasmic sensor domain
PF17156 GAPES2 Gammaproteobacterial periplasmic sensor domain
PF17157 GAPES4 Gammaproteobacterial periplasmic sensor domain
-PF17158 MASE4 Membrane-associated sensor, integral membrane domain
-PF17159 MASE3 Membrane-associated sensor domain
+PF17158 CL0192 GPCR_A MASE4 Membrane-associated sensor, integral membrane domain
+PF17159 CL0192 GPCR_A MASE3 Membrane-associated sensor domain
PF17160 DUF5124 Domain of unknown function (DUF5124)
PF17161 DUF5123 Domain of unknown function (DUF5123)
PF17162 DUF5118 Domain of unknown function (DUF5118)
@@ -16259,8 +16253,8 @@ PF17232 Pep1_7 Elicitor peptide 1-7
PF17233 DUF5308 Family of unknown function (DUF5308)
PF17234 MPM1 Mitochondrial peculiar membrane protein 1
PF17235 STD1 STD1/MTH1
-PF17236 DUF5309 Family of unknown function (DUF5309)
-PF17237 DUF5310 Family of unknown function (DUF5310)
+PF17236 CL0373 Phage-coat DUF5309 Family of unknown function (DUF5309)
+PF17237 Emr1 ERMES regulator 1
PF17238 DUF5311 Family of unknown function (DUF5311)
PF17239 DUF5312 Family of unknown function (DUF5312)
PF17240 DUF5313 Family of unknown function (DUF5313)
@@ -16335,11 +16329,11 @@ PF17308 Corazonin Pro-corazonin
PF17309 DUF5356 Family of unknown function (DUF5356)
PF17310 DUF5357 Family of unknown function (DUF5357)
PF17311 DUF5358 Family of unknown function (DUF5358)
-PF17312 Helveticin_J Bacteriocin helveticin-J
+PF17312 CL0186 Beta_propeller Helveticin_J Bacteriocin helveticin-J
PF17313 DUF5359 Family of unknown function (DUF5359)
PF17314 DUF5360 Family of unknown function (DUF5360)
PF17315 FMP23 Found in mitochondrial proteome
-PF17316 Perilipin_2 Perilipin protein
+PF17316 CL0718 Perilipin_sf Perilipin_2 Perilipin protein
PF17317 MFA1_2 Mating hormone A-factor 1&2
PF17318 DUF5361 Family of unknown function (DUF5361)
PF17319 DUF5362 Family of unknown function (DUF5362)
@@ -16396,7 +16390,7 @@ PF17371 DUF5393 Family of unknown function (DUF5393)
PF17372 DUF5394 Family of unknown function (DUF5394)
PF17373 DUF5395 Family of unknown function (DUF5395)
PF17374 DUF5396 Family of unknown function (DUF5396)
-PF17375 DUF5397 Family of unknown function (DUF5397)
+PF17375 CL0010 SH3 DUF5397 Family of unknown function (DUF5397)
PF17376 DUF5398 Family of unknown function (DUF5398)
PF17377 DUF5399 Family of unknown function (DUF5399)
PF17378 REC104 Meiotic recombination protein REC104
@@ -16490,7 +16484,7 @@ PF17465 U83 Chemokine-like protein, HHV-6 U83 gene product
PF17466 NinD Family of unknown function
PF17467 E7R Viral Protein E7
PF17468 GP52 Phage gene product 52
-PF17469 GP68 Phage protein Gp68
+PF17469 GP68 Gp68-like predicted RNA polymerase component
PF17470 Gp45_2 Phage gene product 45.2
PF17471 GP63 Gene product 63
PF17472 DUF5425 Family of unknown function (DUF5425)
@@ -16504,7 +16498,7 @@ PF17479 DUF3048_C Protein of unknown function (DUF3048) C-terminal domain
PF17480 AlphaC_N2 AlphaC N-terminal domain 2
PF17481 Phage_sheath_1N Phage tail sheath protein beta-sandwich domain
PF17482 Phage_sheath_1C Phage tail sheath C-terminal domain
-PF17483 CL0193 MBB TbpB_C C-lobe handle domain of Tf-binding protein B
+PF17483 TbpB_C C-lobe handle domain of Tf-binding protein B
PF17484 TbpB_A N-Lobe handle Tf-binding protein B
PF17485 SatRNA_48 Satellite RNA 48 kDa protein
PF17486 CL0079 Cystine-knot Cys_Knot_tox Cystine knot toxins
@@ -16522,7 +16516,6 @@ PF17497 DUF5432 Family of unknown function (DUF5432)
PF17498 DUF5433 Family of unknown function (DUF5433)
PF17499 Pilosulin Ant venom peptides
PF17500 CKI Colicin-K immunity
-PF17501 CL0027 RdRP Viral_RdRp_C Viral RNA-directed RNA polymerase C-terminal
PF17502 DUF5434 Family of unknown function (DUF5434)
PF17503 DUF5435 Family of unknown function (DUF5435)
PF17504 DUF5436 Family of unknown function (DUF5436)
@@ -16549,10 +16542,10 @@ PF17524 CnrY Anti-sigma factor CnrY
PF17525 DUF5447 Family of unknown function (DUF5447)
PF17526 DUF5448 Family of unknown function (DUF5448)
PF17527 ALC Phage ALC protein
-PF17528 DUF5449 Family of unknown function (DUF5449)
+PF17528 HdcB Histidine decarboxylase maturation protein HdcB
PF17529 DUF5450 Family of unknown function (DUF5450)
PF17530 NS3 Non-structural protein NS3
-PF17531 O_Spanin_T7 outer-membrane spanin sub-unit
+PF17531 O_Spanin_T7 Spanin, outer lipoprotein subunit T7-like virus
PF17532 DUF5451 Family of unknown function (DUF5451)
PF17533 DUF5452 Family of unknown function (DUF5452)
PF17534 DUF5453 Family of unknown function (DUF5453)
@@ -16589,7 +16582,7 @@ PF17566 DUF5472 Family of unknown function (DUF5472)
PF17567 DUF5473 Family of unknown function (DUF5473)
PF17568 DUF5474 Family of unknown function (DUF5474)
PF17569 DUF5475 Family of unknown function (DUF5475)
-PF17570 DUF5476 Family of unknown function (DUF5476)
+PF17570 T7-like_gp67 Bacteriophage T7-like, protein 6.7
PF17571 DUF5477 Family of unknown function (DUF5477)
PF17572 DUF5478 Family of unknown function (DUF5478)
PF17573 CL0598 B_GA GA-like GA-like domain
@@ -16767,7 +16760,7 @@ PF17744 DUF5581 Family of unknown function (DUF5581)
PF17745 CL0662 Triple_barrel Ydr279_N Ydr279p protein triple barrel domain
PF17746 CL0021 OB SfsA_N SfsA N-terminal OB domain
PF17747 CL0266 PH VID27_PH VID27 PH-like domain
-PF17748 VID27_N VID27 N-terminal region
+PF17748 CL0266 PH VID27_N VID27 N-terminal region
PF17749 MIP-T3_C Microtubule-binding protein MIP-T3 C-terminal region
PF17750 Reo_sigmaC_M Reovirus sigma C capsid protein triple beta spiral
PF17751 CL0159 E-set SKICH SKICH domain
@@ -16790,7 +16783,7 @@ PF17767 CL0105 Hybrid NAPRTase_N Nicotinate phosphoribosyltransferase (NAPRTase)
PF17768 CL0021 OB RecJ_OB RecJ OB domain
PF17769 CL0105 Hybrid PurK_C Phosphoribosylaminoimidazole carboxylase C-terminal domain
PF17770 RNase_J_C Ribonuclease J C-terminal domain
-PF17771 ADAM_CR_2 ADAM cysteine-rich domain
+PF17771 ADAMTS_CR_2 ADAMTS cysteine-rich domain 2
PF17772 CL0361 C2H2-zf zf-MYST MYST family zinc finger domain
PF17773 CL0622 Acylphosphatase UPF0176_N UPF0176 acylphosphatase like domain
PF17774 CL0221 RRM YlmH_RBD Putative RNA-binding domain in YlmH
@@ -16841,7 +16834,7 @@ PF17818 KCT2 Keratinocyte-associated gene product
PF17819 DUF5582 Family of unknown function (DUF5582)
PF17820 CL0466 PDZ-like PDZ_6 PDZ domain
PF17821 DUF5583 Family of unknown function (DUF5583)
-PF17822 DUF5584 Family of unknown function (DUF5584)
+PF17822 ARMH2 Armadillo-like helical domain-containing protein 2
PF17823 DUF5585 Family of unknown function (DUF5585)
PF17824 DUF5586 Family of unknown function (DUF5586)
PF17825 DUF5587 Family of unknown function (DUF5587)
@@ -16900,7 +16893,7 @@ PF17877 Dis3l2_C_term DIS3-like exonuclease 2 C terminal
PF17878 CL0021 OB ssDBP Single-stranded DNA-binding protein
PF17879 CL0021 OB DNA_ligase_C DNA ligase C-terminal domain
PF17880 Yos9_DD Yos9 dimerzation domain
-PF17881 DUF5590 Domain of unknown function (DUF5590)
+PF17881 CL0121 Cystatin DUF5590 Domain of unknown function (DUF5590)
PF17882 SBD OAA-family lectin sugar binding domain
PF17883 CL0682 MBG MBG MBG domain
PF17884 DUF5591 Domain of unknown function (DUF5591)
@@ -16916,7 +16909,7 @@ PF17893 Cas9_b_hairpin CRISPR-associated endonuclease Cas9 beta-hairpin domain
PF17894 Cas9_Topo Topo homolgy domain in CRISPR-associated endonuclease Cas9
PF17895 CL0196 DSRM Dicer_N Giardia Dicer N-terminal domain
PF17896 NSP2_gammaCoV Non-structural protein 2, gammacoronavirus
-PF17897 VCPO_N Vanadium chloroperoxidase N-terminal domain
+PF17897 CL0525 pap2 VCPO_N Vanadium chloroperoxidase N-terminal domain
PF17898 GerD Spore germination GerD central core domain
PF17899 CL0672 p35 Peptidase_M61_N Peptidase M61 N-terminal domain
PF17900 CL0672 p35 Peptidase_M1_N Peptidase M1 N-terminal domain
@@ -16986,11 +16979,11 @@ PF17963 CL0159 E-set Big_9 Bacterial Ig domain
PF17964 CL0159 E-set Big_10 Bacterial Ig domain
PF17965 CL0072 Ubiquitin MucBP_2 Mucin binding domain
PF17966 CL0072 Ubiquitin Muc_B2 Muc B2-like domain
-PF17967 Pullulanase_N2 Pullulanase N2 domain
+PF17967 CL0159 E-set Pullulanase_N2 Pullulanase N2 domain
PF17968 Tlr3_TMD Toll-like receptor 3 trans-membrane domain
PF17969 Ldt_C L,D-transpeptidase C-terminal domain
PF17970 CL0159 E-set bMG1 Bacterial Alpha-2-macroglobulin MG1 domain
-PF17971 LIFR_D2 Leukemia inhibitory factor receptor D2 domain
+PF17971 CL0159 E-set LIFR_D2 Leukemia inhibitory factor receptor D2 domain
PF17972 CL0159 E-set bMG5 Bacterial Alpha-2-macroglobulin MG5 domain
PF17973 CL0159 E-set bMG10 Bacterial Alpha-2-macroglobulin MG10 domain
PF17974 CL0004 Concanavalin GalBD_like Galactose-binding domain-like
@@ -17009,7 +17002,7 @@ PF17986 EKAL EMP3-KAHRP-like N-terminal domain
PF17987 PMT2_N Phosphoethanolamine N-methyltransferase 2 N-terminal
PF17988 VEGFR-2_TMD VEGFR-2 Transmembrane domain
PF17989 CL0108 Actin_ATPase ALP_N Actin like proteins N terminal domain
-PF17990 LodA_N L-Lysine epsilon oxidase N-terminal
+PF17990 CL0159 E-set LodA_N L-Lysine epsilon oxidase N-terminal
PF17991 CL0202 GBD Thioredoxin_10 Thioredoxin like C-terminal domain
PF17992 CL0202 GBD Agarase_CBM Agarase CBM like domain
PF17993 CL0202 GBD HA70_C Haemagglutinin 70 C-terminal domain
@@ -17017,7 +17010,7 @@ PF17994 CL0202 GBD Glft2_N Galactofuranosyltransferase 2 N-terminal
PF17995 CL0202 GBD GH101_N Endo-alpha-N-acetylgalactosaminidase N-terminal
PF17996 CL0202 GBD CE2_N Carbohydrate esterase 2 N-terminal
PF17997 CL0202 GBD Cry1Ac_D5 Insecticidal delta-endotoxin CryIA(c) domain 5
-PF17998 AgI_II_C2 Cell surface antigen I/II C2 terminal domain
+PF17998 CL0204 Adhesin AgI_II_C2 Cell surface antigen I/II C2 terminal domain
PF17999 CL0202 GBD PulA_N1 Pullulanase N1-terminal domain
PF18000 CL0159 E-set Top6b_C Type 2 DNA topoisomerase 6 subunit B C-terminal domain
PF18001 CL0159 E-set Il13Ra_Ig Interleukin-13 receptor subunit alpha Ig-like domain
@@ -17074,7 +17067,7 @@ PF18051 RPN1_C 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal
PF18052 Rx_N Rx N-terminal domain
PF18053 GyrB_insert DNA gyrase B subunit insert domain
PF18054 CEL_III_C CEL-III C-terminal
-PF18055 RPN6_N 26S proteasome regulatory subunit RPN6 N-terminal domain
+PF18055 CL0020 TPR RPN6_N 26S proteasome regulatory subunit RPN6 N-terminal domain
PF18056 PBP3 Penicillin Binding Protein 3 Domain
PF18057 DUF5594 Domain of unknown function (DUF5594)
PF18058 SbsC_C SbsC C-terminal domain
@@ -17090,7 +17083,7 @@ PF18067 CL0287 Transthyretin Lipase_C Lipase C-terminal domain
PF18068 Npun_R1517 Npun R1517
PF18069 DR2241 DR2241 stabilising domain
PF18070 Cas9_PI2 CRISPR-Cas9 PI domain
-PF18071 HMW1C_N HMW1C N-terminal
+PF18071 CL0020 TPR HMW1C_N HMW1C N-terminal
PF18072 FGAR-AT_linker Formylglycinamide ribonucleotide amidotransferase linker domain
PF18073 CL0167 Zn_Beta_Ribbon Rubredoxin_2 Rubredoxin metal binding domain
PF18074 PriA_C Primosomal protein N C-terminal domain
@@ -17111,8 +17104,8 @@ PF18088 Glyco_H_20C_C Glycoside Hydrolase 20C C-terminal domain
PF18089 CL0209 Bet_v_1_like DAPG_hydrolase DAPG hydrolase PhiG domain
PF18090 CL0123 HTH SoPB_HTH Centromere-binding protein HTH domain
PF18091 CL0214 UBA E3_UbLigase_RBR E3 Ubiquitin Ligase RBR C-terminal domain
-PF18092 DraK_HK_N DraK Histidine Kinase N-terminal domain
-PF18093 Trm5_N tRNA methyltransferase 5 N-terminal domain
+PF18092 CL0161 GAF DraK_HK_N DraK Histidine Kinase N-terminal domain
+PF18093 CL0437 EF-G_C Trm5_N tRNA methyltransferase 5 N-terminal domain
PF18094 CL0198 HHH DNA_pol_B_N DNA polymerase beta N-terminal domain
PF18095 CL0183 PAS_Fold PAS_12 UPF0242 C-terminal PAS-like domain
PF18096 Thump_like THUMP domain-like
@@ -17124,7 +17117,7 @@ PF18101 CL0016 PKinase Pan3_PK Pan3 Pseudokinase domain
PF18102 DTC Deltex C-terminal domain
PF18103 CL0010 SH3 SH3_11 Retroviral integrase C-terminal SH3 domain
PF18104 CL0049 Tudor Tudor_2 Jumonji domain-containing protein 2A Tudor domain
-PF18105 PGM1_C PGM1 C-terminal domain
+PF18105 CL0105 Hybrid PGM1_C PGM1 C-terminal domain
PF18106 CL0407 TBP-like Rol_Rep_N Rolling Circle replication initiation protein N-terminal domain
PF18107 CL0123 HTH HTH_ABP1_N Fission yeast centromere protein N-terminal domain
PF18108 CL0172 Thioredoxin QSOX_Trx1 QSOX Trx-like domain
@@ -17139,7 +17132,7 @@ PF18116 CL0266 PH SNX17_FERM_C Sorting Nexin 17 FERM C-terminal domain
PF18117 EDS1_EP Enhanced disease susceptibility 1 protein EP domain
PF18118 CL0123 HTH PRC2_HTH_1 Polycomb repressive complex 2 tri-helical domain
PF18119 RIG-I_C RIG-I receptor C-terminal domain
-PF18120 DUF5597 Domain of unknown function (DUF5597)
+PF18120 CL0369 GHD DUF5597 Domain of unknown function (DUF5597)
PF18121 CL0123 HTH TFA2_Winged_2 TFA2 Winged helix domain 2
PF18122 APC1_C Anaphase-promoting complex sub unit 1 C-terminal domain
PF18124 CL0072 Ubiquitin Kindlin_2_N Kindlin-2 N-terminal domain
@@ -17207,7 +17200,7 @@ PF18186 CL0676 SLATT SLATT_4 SMODS and SLOG-associating 2TM effector domain fami
PF18187 RIF5_SNase_1 TbRIF5 SNase domain 1
PF18188 CL0243 AEP PPL4 Prim-pol 4
PF18189 RIF5_SNase_2 TbRIF5 SNase domain 2
-PF18190 Plk4_PB1 Polo-like Kinase 4 Polo Box 1
+PF18190 CL0708 Polo-box Plk4_PB1 Polo-like Kinase 4 Polo Box 1
PF18191 PnpCD_PnpD_N Hydroquinone 1,2-dioxygenase large subunit N-terminal
PF18192 DNTTIP1_dimer DNTTIP1 dimerisation domain
PF18193 CL0001 EGF Fibrillin_U_N Fibrillin 1 unique N-terminal domain
@@ -17219,7 +17212,7 @@ PF18198 CL0671 AAA_lid AAA_lid_11 Dynein heavy chain AAA lid domain
PF18199 Dynein_C Dynein heavy chain C-terminal domain
PF18200 CL0159 E-set Big_11 Bacterial Ig-like domain
PF18201 CL0190 HSP20 PIH1_CS PIH1 CS-like domain
-PF18202 TQ T-Q ester bond containing domain
+PF18202 CL0159 E-set TQ T-Q ester bond containing domain
PF18203 IPTL-CTERM IPTL-CTERM motif
PF18204 PGF-CTERM PGF-CTERM motif
PF18205 VPDSG-CTERM VPDSG-CTERM motif
@@ -17245,7 +17238,7 @@ PF18224 ToxB_N ToxB N-terminal domain
PF18225 CL0183 PAS_Fold AbfS_sensor Sensor histidine kinase (AbfS) sensor domain
PF18226 QslA_E LasR-specific antiactivator QslA chain E
PF18227 LepB_GAP_C LepB GAP domain C-terminal subdomain
-PF18228 CdiI_N CdiI N-terminal domain
+PF18228 CL0609 sPC4_like CdiI_N CdiI N-terminal domain
PF18229 CL0546 Hexosaminidase GcnA_N N-acetyl-beta-D-glucosaminidase N-terminal domain
PF18230 CL0369 GHD Glyc_hyd_38C_2 Glycosyl hydrolases family 38 C-terminal sub-domain
PF18231 DUF5603 Domain of unknown function (DUF5603)
@@ -17255,7 +17248,7 @@ PF18234 CL0048 LolA_LolB VioE Violacein biosynthetic enzyme VioE
PF18235 OST_P2 Oligosaccharyltransferase Peripheral 2 domain
PF18236 AGO_N Argonaute N domain
PF18237 CL0570 PPP-I Tk-SP_N-pro Tk-SP N-propeptide domain
-PF18238 LnmK_N_HDF LnmK N-terminal Hot Dog Fold domain
+PF18238 CL0050 HotDog LnmK_N_HDF LnmK N-terminal Hot Dog Fold domain
PF18239 CL0004 Concanavalin HA1 Hemagglutinin I
PF18240 PSII_Pbs31 Photosystem II Psb31 protein
PF18241 AvrM-A Flax-rust effector AvrM-A
@@ -17279,7 +17272,7 @@ PF18258 CL0333 gCrystallin IL4_i_Ig Interleukin-4 inducing immunoglobulin-bindin
PF18259 CL0202 GBD CBM65_1 Carbohydrate binding module 65 domain 1
PF18260 CL0537 CCCH_zf Nab2p_Zf1 Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1
PF18261 Rpn9_C Rpn9 C-terminal helix
-PF18262 PhetRS_B1 Phe-tRNA synthetase beta subunit B1 domain
+PF18262 CL0123 HTH PhetRS_B1 Phe-tRNA synthetase beta subunit B1 domain
PF18263 MCM6_C MCM6 C-terminal winged-helix domain
PF18264 preSET_CXC CXC domain
PF18265 Nas2_N Nas2 N_terminal domain
@@ -17302,12 +17295,12 @@ PF18281 CL0072 Ubiquitin BILBO1_N BILBO1 N-terminal domain
PF18282 CL0702 UIM RAP80_UIM RAP80 N-terminal ubiquitin interaction motif
PF18283 CBM77 Carbohydrate binding module 77
PF18284 CL0123 HTH DNA_meth_N DNA methylase N-terminal domain
-PF18285 LuxT_C Tetracycline repressor LuxT C-terminal domain
+PF18285 CL0174 TetR_C LuxT_C Tetracycline repressor LuxT C-terminal domain
PF18286 T3SS_ExsE Type III secretion system ExsE
PF18287 Hfx_Cass5 Integron Cassette Protein Hfx_Cass5
PF18288 FAA_hydro_N_2 Fumarylacetoacetase N-terminal domain 2
PF18289 CL0548 IHF-likeDNA-bdg HU-CCDC81_euk_2 CCDC81 eukaryotic HU domain 2
-PF18290 Nudix_hydro Nudix hydrolase domain
+PF18290 CL0261 NUDIX Nudix_hydro Nudix hydrolase domain
PF18291 CL0548 IHF-likeDNA-bdg HU-HIG HU domain fused to wHTH, Ig, or Glycine-rich motif
PF18292 ZIP4_domain Zinc transporter ZIP4 domain
PF18293 Caprin-1_dimer Caprin-1 dimerization domain
@@ -17325,11 +17318,11 @@ PF18305 CL0426 HRDC-like DNA_pol_A_exoN 3' to 5' exonuclease C-terminal domain
PF18306 CL0349 SLOG LDcluster4 SLOG cluster4 family
PF18307 Tfb2_C Transcription factor Tfb2 (p52) C-terminal domain
PF18308 GGA_N-GAT N-terminal extension of GAT domain
-PF18309 CL0638 PAZ Ago_PAZ Argonaute PAZ domain
+PF18309 CL0638 PAZ PAZ_3 Argonaute PAZ domain
PF18310 DUF5605 Domain of unknown function (DUF5605)
PF18311 Rrp40_N Exosome complex exonuclease Rrp40 N-terminal domain
PF18312 ScsC_N Copper resistance protein ScsC N-terminal domain
-PF18313 TLP1_add_C Thiolase-like protein type 1 additional C-terminal domain
+PF18313 CL0021 OB TLP1_add_C Thiolase-like protein type 1 additional C-terminal domain
PF18314 FAS_I_H Fatty acid synthase type I helical domain
PF18315 VCH_CASS14 Integron cassette protein VCH_CASS1 chain
PF18316 S-l_SbsC_C S-layer protein SbsC C-terminal domain
@@ -17341,7 +17334,7 @@ PF18321 CL0063 NADP_Rossmann 3HCDH_RFF 3-hydroxybutyryl-CoA dehydrogenase reduce
PF18322 CL0678 CLIP CLIP_1 Serine protease Clip domain PPAF-2
PF18323 CSN5_C Cop9 signalosome subunit 5 C-terminal domain
PF18324 TT1725 Hypothetical protein TT1725
-PF18325 Fas_alpha_ACP Fatty acid synthase subunit alpha Acyl carrier domain
+PF18325 CL0314 PP-binding Fas_alpha_ACP Fatty acid synthase subunit alpha Acyl carrier domain
PF18326 RFX5_N RFX5 N-terminal domain
PF18327 PRODH Proline utilization A proline dehydrogenase N-terminal domain
PF18328 PfaD_N Fatty acid synthase subunit PfaD N-terminal domain
@@ -17365,7 +17358,7 @@ PF18345 CL0537 CCCH_zf zf_CCCH_4 Zinc finger domain
PF18346 CL0010 SH3 SH3_15 Mind bomb SH3 repeat domain
PF18347 DUF5606 Domain of unknown function (DUF5606)
PF18348 CL0010 SH3 SH3_16 Bacterial dipeptidyl-peptidase Sh3 domain
-PF18349 CL0638 PAZ Paz_1 PAZ domain
+PF18349 CL0638 PAZ PAZ_4 PAZ domain
PF18350 CL0010 SH3 SH3_17 Restriction endonuclease SH3 domain
PF18351 Ago_N_1 Fungal Argonaute N-terminal domain
PF18352 CL0021 OB Gp138_N Phage protein Gp138 N-terminal domain
@@ -17423,10 +17416,10 @@ PF18403 CL0172 Thioredoxin Thioredoxin_15 Thioredoxin-like domain
PF18404 CL0110 GT-A Glyco_transf_24 Glucosyltransferase 24
PF18405 SLC25_like Mitochondrial SLC25 homolog
PF18406 DUF1281_C Ferredoxin-like domain in Api92-like protein
-PF18407 GNAT_like GCN5-related N-acetyltransferase like domain
+PF18407 CL0257 Acetyltrans GNAT_like GCN5-related N-acetyltransferase like domain
PF18408 CL0361 C2H2-zf zf_Hakai C2H2 Hakai zinc finger domain
-PF18409 Plk4_PB2 Polo-like Kinase 4 Polo Box 2
-PF18410 BTHB Basic tilted helix bundle domain
+PF18409 CL0708 Polo-box Plk4_PB2 Polo-like Kinase 4 Polo Box 2
+PF18410 CL0306 HeH BTHB Basic tilted helix bundle domain
PF18411 Annexin_like Annexin-like domain
PF18412 Wza_C Outer-membrane lipoprotein Wza C-terminal domain
PF18413 CL0434 Sialidase Neuraminidase Neuraminidase-like domain
@@ -17506,20 +17499,20 @@ PF18486 PUB_1 PNGase/UBA- or UBX-containing domain
PF18487 TSR Thrombospondin type 1 repeat
PF18488 CL0654 WYL WYL_3 WYL domain
PF18489 Alpha_Helical Alpha helical domain
-PF18490 tRNA_bind_4 tRNA-binding domain
+PF18490 CL0094 Peptidase_ME tRNA_bind_4 tRNA-binding domain
PF18491 CL0178 PUA SRA SET and RING associated domain
-PF18492 ORF_2_N Open reading frame 2 N-terminal domain
+PF18492 CL0570 PPP-I ORF_2_N Open reading frame 2 N-terminal domain
PF18493 DUF5617 Domain of unknown function (DUF5617)
PF18494 Pullulanase_Ins Pullulanase Ins domain
PF18495 CL0660 SHOCT VbhA Antitoxin VbhA
PF18496 ColG_sub Collagenase G catalytic helper subdomain
PF18497 RNase_3_N Ribonuclease III N-terminal domain
-PF18498 DUF5618 Domain of unknown function (DUF5618)
+PF18498 CL0291 KNTase_C DUF5618 Domain of unknown function (DUF5618)
PF18499 Cue1_U7BR Ubc7p-binding region of Cue1
PF18500 CL0342 TolB_N CadC_C1 CadC C-terminal domain 1
PF18501 REC1 Alpha helical recognition lobe domain
PF18502 Mrpl_C 54S ribosomal protein L8 C-terminal domain
-PF18503 RPN6_C_helix 26S proteasome subunit RPN6 C-terminal helix domain
+PF18503 CL0123 HTH RPN6_C_helix 26S proteasome subunit RPN6 C-terminal helix domain
PF18504 Csm1_N Csm1 N-terminal domain
PF18505 DUF5619 Domain of unknown function (DUF5619)
PF18506 RelB_N RelB Antitoxin alpha helical domain
@@ -17544,10 +17537,10 @@ PF18524 HPIP_like High potential iron-sulfur protein like
PF18525 Cas9_C Cas9 C-terminal domain
PF18526 DB_JBP1 Thymine dioxygenase JBP1 DNA-binding domain
PF18527 STT3_PglB_C STT3/PglB C-terminal beta-barrel domain
-PF18528 Ret2_MD RNA editing 3' terminal uridylyl transferase 2 middle domain
-PF18529 MIX Mitochondrial membrane-anchored proteins
+PF18528 CL0221 RRM Ret2_MD RNA editing 3' terminal uridylyl transferase 2 middle domain
+PF18529 CL0020 TPR MIX Mitochondrial membrane-anchored proteins
PF18530 CL0123 HTH Swi6_N Swi6 N-terminal domain
-PF18531 Polo_box_2 Polo box domain
+PF18531 CL0708 Polo-box Polo_box_2 Polo box domain
PF18532 DUF5621 Domain of unknown function (DUF5621)
PF18533 DUF5622 Domain of unknown function (DUF5622)
PF18534 HBD Helical bundle domain
@@ -17560,7 +17553,7 @@ PF18540 DUF5626 Domain of unknown function (DUF5626)
PF18541 RuvC_III RuvC endonuclease subdomain 3
PF18542 CL0065 Cyclin TFIIB_C_1 Transcription factor IIB C-terminal module 1
PF18543 CL0021 OB ID Intracellular delivery domain
-PF18544 Polo_box_3 Polo box domain
+PF18544 CL0708 Polo-box Polo_box_3 Polo box domain
PF18545 HalOD1 Halobacterial output domain 1
PF18546 CL0210 HNOX-like MetOD1 Methanogen output domain 1
PF18547 HalOD2 Halobacterial output domain 2
@@ -17611,7 +17604,7 @@ PF18591 IMP2_C Immune Mapped Protein 2 (IMP2) C-terminal domain
PF18592 Tho1_MOS11_C Tho1/MOS11 C-terminal domain
PF18593 CdiI_2 CdiI immunity protein
PF18594 Sas6_CC Sas6/XLF/XRCC4 coiled-coil domain
-PF18595 CL0231 MazG DHR10 Designed helical repeat protein 10 domain
+PF18595 CL0231 MazG Nuf2_DHR10-like Nuf2, DHR10-like domain
PF18596 Sld7_C Sld7 C-terminal domain
PF18597 CL0010 SH3 SH3_19 Myosin X N-terminal SH3 domain
PF18598 CL0174 TetR_C TetR_C_36 Tetracyclin repressor-like, C-terminal domain
@@ -17636,15 +17629,15 @@ PF18617 Nup214_FG Nucleoporin Nup214 phenylalanine-glycine (FG) domain
PF18618 HP0268 HP0268
PF18619 GAIN_A GPCR-Autoproteolysis-INducing (GAIN) subdomain A
PF18620 DUF5627 Family of unknown function (DUF5627)
-PF18621 DUF5628 Family of unknown function (DUF5628)
+PF18621 CL0161 GAF DUF5628 Family of unknown function (DUF5628)
PF18622 CL0123 HTH HTH_55 RctB helix turn helix domain
PF18623 TnsE_C TnsE C-terminal domain
PF18624 CdiI_4 CDI immunity protein
-PF18625 EspB_PE ESX-1 secreted protein B PE domain
+PF18625 CL0352 EsxAB EspB_PE ESX-1 secreted protein B PE domain
PF18626 CL0125 Peptidase_CA Gln_deamidase_2 Glutaminase
PF18627 PgdA_N Peptidoglycan GlcNAc deacetylase N-terminal domain
PF18628 P2_N Viral coat protein P2 N-terminal domain
-PF18629 DUF5629 Family of unknown function (DUF5629)
+PF18629 CL0266 PH DUF5629 Family of unknown function (DUF5629)
PF18630 CL0556 PapD-like Peptidase_M60_C Peptidase M60 C-terminal domain
PF18631 Cucumopine_C Cucumopine synthase C-terminal helical bundle domain
PF18632 DUF5630 Family of unknown function (DUF5630)
@@ -17687,7 +17680,7 @@ PF18668 Tail_spike_N Tail spike TSP1/Gp66 receptor binding N-terminal domain
PF18669 Trp_ring Trimeric autotransporter adhesin Trp ring domain
PF18670 V_ATPase_I_N V-type ATPase subunit I, N-terminal domain
PF18671 4HPAD_g_N 4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal
-PF18672 DUF5634_N Family of unknown function (DUF5634) N-terminal domain
+PF18672 PilZN1 N-terminal PilZ-like domain PilZN1
PF18673 CL0159 E-set IrmA interleukin receptor mimic protein A
PF18674 CL0159 E-set TarS_C1 TarS beta-glycosyltransferase C-terminal domain 1
PF18675 CL0369 GHD HepII_C Heparinase II C-terminal domain
@@ -17697,7 +17690,7 @@ PF18678 CL0650 AOC_barrel AOC_like Allene oxide cyclase barrel like domain
PF18679 CL0123 HTH HTH_57 ThcOx helix turn helix domain
PF18680 SPECT1 Plasmodium host cell traversal SPECT1
PF18681 DUF5634 Family of unknown function (DUF5634)
-PF18682 PilA4 Pilin A4
+PF18682 CL0327 Pilus PilA4 Pilin A4
PF18683 CL0159 E-set ChiW_Ig_like Chitinase W immunoglobulin-like domain
PF18684 PlyB_C Pleurotolysin B C-terminal domain
PF18685 CL0123 HTH DUF5635 Family of unknown function (DUF5635)
@@ -17705,7 +17698,7 @@ PF18686 DUF5636 Family of unknown function (DUF5636)
PF18687 CL0083 Omega_toxin DUF5637 Family of unknown function (DUF5637)
PF18688 DUF5638 Family of unknown function (DUF5638)
PF18689 PriX Primase X
-PF18690 DUF5639 Family of unknown function (DUF5639)
+PF18690 CL0277 FAD-oxidase_C DUF5639 Family of unknown function (DUF5639)
PF18691 CL0021 OB Cdc13_OB2 Cell division control protein 13, OB2 domain
PF18692 CL0116 Calycin DUF5640 Family of unknown function (DUF5640)
PF18693 CL0021 OB TRAM_2 TRAM domain
@@ -17718,7 +17711,7 @@ PF18699 MRPL52 Mitoribosomal protein mL52
PF18700 Castor1_N Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain
PF18701 DUF5641 Family of unknown function (DUF5641)
PF18702 CL0619 Mog1p_PsbP DUF5642 Domain of unknown function (DUF5642)
-PF18703 MALT1_Ig MALT1 Ig-like domain
+PF18703 CL0159 E-set MALT1_Ig MALT1 Ig-like domain
PF18704 CL0049 Tudor Chromo_2 Chromatin organization modifier domain 2
PF18705 CL0159 E-set DUF5643 Family of unknown function (DUF5643)
PF18706 CL0063 NADP_Rossmann ISPD_C D-ribitol-5-phosphate cytidylyltransferase C-terminal domain
@@ -17796,7 +17789,7 @@ PF18777 CL0020 TPR CRM1_repeat Chromosome region maintenance or exportin repeat
PF18778 CL0109 CDA NAD1 Novel AID APOBEC clade 1
PF18779 CL0022 LRR LRR_RI_capping Capping Ribonuclease inhibitor Leucine Rich Repeat
PF18780 HNH_repeat Homing endonuclease associated repeat
-PF18781 Phage_spike_2 Phage spike trimer
+PF18781 CL0268 Pec_lyase-like Phage_spike_2 Phage spike trimer
PF18782 CL0109 CDA NAD2 Novel AID APOBEC clade 2
PF18783 CL0268 Pec_lyase-like IPU_b_solenoid Isopullulanase beta-solenoid repeat
PF18784 CRM1_repeat_2 CRM1 / Exportin repeat 2
@@ -17806,7 +17799,7 @@ PF18787 CL0020 TPR CRM1_repeat_3 CRM1 / Exportin repeat 3
PF18788 DarA_N Defence against restriction A N-terminal
PF18789 DarA_C Defence against restriction A C-terminal
PF18790 KfrB KfrB protein
-PF18791 Transp_inhibit Transport inhibitor response 1 protein domain
+PF18791 CL0022 LRR Transp_inhibit Transport inhibitor response 1 protein domain
PF18792 UspA1_rep Ubiquitous surface protein adhesin repeat
PF18793 CL0186 Beta_propeller nos_propeller_2 Nitrous oxide reductase propeller repeat 2
PF18794 CL0020 TPR HSM3_C DNA mismatch repair protein HSM3, C terminal domain
@@ -17924,7 +17917,7 @@ PF18905 DUF5661 Protein of unknown function (DUF5661)
PF18906 Phage_tube_2 Phage tail tube protein
PF18907 DUF5662 Family of unknown function (DUF5662)
PF18908 DUF5663 Protein of unknown function (DUF5663)
-PF18909 DUF5664 Domain of unknown function (DUF5664)
+PF18909 dGTP_diPhyd_N dATP/dGTP diphosphohydrolase, N-terminal
PF18910 DUF5665 Domain of unknown function (DUF5665)
PF18911 CL0159 E-set PKD_4 PKD domain
PF18912 CL0167 Zn_Beta_Ribbon DZR_2 Double zinc ribbon domain
@@ -17938,7 +17931,7 @@ PF18919 DUF5670 Family of unknown function (DUF5670)
PF18920 DUF5671 Domain of unknown function (DUF5671)
PF18921 Cyanophycin_syn Cyanophycin synthase-like N-terminal domain
PF18922 DUF5672 Protein of unknown function (DUF5672)
-PF18923 DUF5673 Domain of unknown function (DUF5673)
+PF18923 CL0266 PH DUF5673 Domain of unknown function (DUF5673)
PF18924 DUF5674 Protein of unknown function (DUF5674)
PF18925 DUF5675 Family of unknown function (DUF5675)
PF18926 DUF5676 2TM family of unknown function (DUF5676)
@@ -17954,11 +17947,11 @@ PF18935 DUF5683 Family of unknown function (DUF5683)
PF18936 DUF5684 Family of unknown function (DUF5684)
PF18937 DUF5685 Family of unknown function (DUF5685)
PF18938 CL0159 E-set aRib Atypical Rib domain
-PF18939 DUF5686 Family of unknown function (DUF5686)
+PF18939 CL0193 MBB DUF5686 Family of unknown function (DUF5686)
PF18940 DUF5687 Family of unknown function (DUF5687)
PF18941 DUF5688 Family of unknown function (DUF5688)
PF18942 DUF5689 Family of unknown function (DUF5689)
-PF18943 DUF5690 Family of unknown function (DUF5690)
+PF18943 CL0015 MFS DUF5690 Family of unknown function (DUF5690)
PF18944 CL0020 TPR DUF5691 Family of unknown function (DUF5691)
PF18945 VipB_2 EvpB/VC_A0108, tail sheath gpW/gp25-like domain
PF18946 Apex GpV Apex motif
@@ -17980,7 +17973,7 @@ PF18961 CL0103 Gal_mutarotase DUF5703_N Domain of unknown function (DUF5703)
PF18962 CL0159 E-set Por_Secre_tail Secretion system C-terminal sorting domain
PF18963 DUF5703 Family of unknown function (DUF5703)
PF18964 DUF5704 Family of unknown function (DUF5704)
-PF18965 DUF5705 Family of unknown function (DUF5705)
+PF18965 VP3-like Outer capsid protein VP3-like
PF18966 Lipoprotein_23 Uncharacterised lipoprotein
PF18967 DUF5706 Family of unknown function (DUF5706)
PF18968 DUF5707 Family of unknown function (DUF5707)
@@ -18005,7 +17998,7 @@ PF18986 DUF5719 Family of unknown function (DUF5719)
PF18987 DUF5720 Family of unknown function (DUF5720)
PF18988 DUF5721 Family of unknown function (DUF5721)
PF18989 DUF5722 Family of unknown function (DUF5722)
-PF18990 DUF5723 Family of unknown function (DUF5723)
+PF18990 CL0193 MBB DUF5723 Family of unknown function (DUF5723)
PF18991 DUF5724 Family of unknown function (DUF5724)
PF18992 DUF5725 Family of unknown function (DUF5725)
PF18993 Rv0078B Rv0078B-related antitoxin
@@ -18102,7 +18095,7 @@ PF19083 DUF5774 Family of unknown function (DUF5774)
PF19084 DUF5775 Family of unknown function (DUF5775)
PF19085 CL0694 Choline_binding Choline_bind_2 Choline-binding repeat
PF19086 CL0613 Terp_synthase Terpene_syn_C_2 Terpene synthase family 2, C-terminal metal binding
-PF19087 DUF5776 Domain of unknown function (DUF5776)
+PF19087 CL0010 SH3 DUF5776 Domain of unknown function (DUF5776)
PF19088 CL0260 NTP_transf TUTase TUTase nucleotidyltransferase domain
PF19089 CL0193 MBB DUF5777 Membrane bound beta barrel domain (DUF5777)
PF19090 DUF5778 Family of unknown function (DUF5778)
@@ -18136,7 +18129,7 @@ PF19117 Mim2 Mitochondrial import 2
PF19118 DUF5802 Family of unknown function (DUF5802)
PF19119 DUF5803 Family of unknown function (DUF5803)
PF19120 DUF5804 Family of unknown function (DUF5804)
-PF19121 DUF5805 Family of unknown function (DUF5805)
+PF19121 CL0123 HTH DUF5805 Family of unknown function (DUF5805)
PF19122 DUF5806 Family of unknown function (DUF5806)
PF19123 DUF5807 Family of unknown function (DUF5807)
PF19124 DUF5808 Family of unknown function (DUF5808)
@@ -18194,7 +18187,7 @@ PF19175 DUF5857 Family of unknown function (DUF5857)
PF19176 DUF5858 Family of unknown function (DUF5858)
PF19177 DUF5859 Family of unknown function (DUF5859)
PF19178 DUF5860 Family of unknown function (DUF5860)
-PF19179 DUF5861 Domain of unknown function (DUF5861)
+PF19179 TTC3_DZIP3_dom E3 ubiquitin-protein ligase TTC3/DZIP3 domain
PF19180 DUF5862 Family of unknown function (DUF5862)
PF19181 DUF5863 Family of unknown function (DUF5863)
PF19182 DUF5864 Family of unknown function (DUF5864)
@@ -18215,7 +18208,7 @@ PF19196 DUF5871 Family of unknown function (DUF5871)
PF19197 DUF5872 Family of unknown function (DUF5872)
PF19198 RsaA_NTD RsaA N-terminal domain
PF19199 CL0371 Inovirus-Coat Phage_coatGP8 Phage major coat protein, Gp8
-PF19200 DUF871_N DUF871 N-terminal domain
+PF19200 MupG_N 6-phospho-N-acetylmuramidase, N-terminal
PF19201 DUF5873 Family of unknown function (DUF5873)
PF19202 DUF5874 Family of unknown function (DUF5874)
PF19203 DUF5875 Family of unknown function (DUF5875)
@@ -18250,7 +18243,7 @@ PF19232 DUF5885 Family of unknown function (DUF5885)
PF19233 DUF5886 Family of unknown function (DUF5886)
PF19234 DUF5887 Family of unknown function (DUF5887)
PF19235 DUF5888 Family of unknown function (DUF5888)
-PF19236 ADAM_CR_3 ADAM cysteine-rich domain
+PF19236 ADAMTS_CR_3 ADAMTS cysteine-rich domain
PF19237 DUF5889 Family of unknown function (DUF5889)
PF19238 CL0036 TIM_barrel Radical_SAM_2 Radical SAM-like domain
PF19239 CL0418 GIY-YIG GIY_YIG_domain GIY-YIG domain-containing protein
@@ -18305,12 +18298,12 @@ PF19287 DUF5910 Family of unknown function (DUF5910)
PF19288 CofH_C CofH/MqnC C-terminal region
PF19289 PmbA_TldD_C PmbA/TldA metallopeptidase C-terminal domain
PF19290 PmbA_TldD_M PmbA/TldA metallopeptidase central domain
-PF19291 DUF5911 Domain of unknown function (DUF5911)
+PF19291 TREH_N Trehalase-like, N-terminal
PF19292 KPBB_C Phosphorylase b kinase C-terminal domain
PF19293 CdaA_N CdaA N-terminal transmembrane domain
-PF19294 DUF5912 Domain of unknown function (DUF5912)
+PF19294 DACZ_N Diadenylate cyclase, N-terminal
PF19295 SufBD_N SufBD protein N-terminal region
-PF19296 DUF5913 Domain of unknown function (DUF5913)
+PF19296 RelA_AH_RIS RelA/SpoT, AH and RIS domains
PF19297 QcrA_N QcrA subunit N-terminal region
PF19298 CL0209 Bet_v_1_like KshA_C 3-Ketosteroid 9alpha-hydroxylase C-terminal domain
PF19299 DUF5914 Domain of unknown function (DUF5914)
@@ -18353,7 +18346,7 @@ PF19335 CL0105 Hybrid HMBD Heavy metal binding domain
PF19336 DUF5921 Domain of unknown function (DUF5921)
PF19337 BAMBI_C BMP and activin membrane-bound inhibitor homolog C-terminus
PF19338 NTF3_N Neutrophin-3 N-terminus
-PF19339 DUF5922 Domain of unknown function (DUF5922)
+PF19339 ANGEL2_N Protein angel homolog 2 N-terminal
PF19340 GCP6_N Gamma-tubulin complex component 6 N-terminus
PF19341 B3GALT2_N Beta-1,3-galactosyltransferase 2 N-terminus
PF19342 MGP3_C MGP3 C-terminal domain
@@ -18437,19 +18430,19 @@ PF19419 DUF5983 Family of unknown function (DUF5983)
PF19420 CL0197 GME DDAH_eukar N,N dimethylarginine dimethylhydrolase, eukaryotic
PF19421 Fry_C Furry protein C-terminal
PF19422 Ariadne Ariadne domain
-PF19423 E3_UBR4_N E3 ubiquitin-protein ligases UBR4 N-terminal
-PF19424 UNC80 Protein UNC80
+PF19423 E3_UBR4_N E3 ubiquitin-protein ligase UBR4 N-terminal
+PF19424 UNC80 Protein UNC80 central region
PF19425 Csd3_N2 Csd3 second domain
-PF19426 MIER1_beta_C Mesoderm induction early response protein 1 beta C-terminal
+PF19426 MIER1_3_C Mesoderm induction early response protein 1/3 C-terminal
PF19427 CL0020 TPR Insc_C Protein inscuteable C-terminal
PF19428 Sema4F_C Semaphorin 4F C-terminal
PF19429 EVA_Class_A Evasins Class A
PF19430 TBC1D23_C TBC1 domain family member 23 C-terminal
PF19431 MEKK4_N MEKK4 N-terminal
PF19432 RME-8_N DNAJ protein RME-8 N-terminal
-PF19433 NDNF_C Neuron-derived Neurotrophic Factor C-terminal
-PF19434 CL0023 P-loop_NTPase OPA1_C Dynamin-like GTPase OPA1 C-terminal
-PF19435 IntS14 Integrator complex subunit 14
+PF19433 CL0159 E-set NDNF_C Neuron-derived Neurotrophic Factor C-terminal
+PF19434 OPA1_C Dynamin-like GTPase OPA1 C-terminal
+PF19435 IntS14_b-barrel Integrator complex subunit 14, beta-barrel domain
PF19436 ACS_CODH_B_C ACS/CODH beta subunit C-terminal
PF19437 VCIP135_N VCIP135 N-terminal
PF19438 LIN9_C LIN9 C-terminal
@@ -18596,7 +18589,7 @@ PF19578 DUF6090 Family of unknown function (DUF6090)
PF19579 CL0225 FtsL FtsL_2 Bacteriodetes cell division protein (FtsL-like)
PF19580 CL0530 DNase_I-like Exo_endo_phos_3 Endonuclease/Exonuclease/phosphatase family
PF19581 CL0104 Glyoxalase Glyoxalase_7 Glyoxalase superfamily protein
-PF19582 DUF6091 Family of unknown function (DUF6091)
+PF19582 AdeT1_2 Solute-binding protein AdeT 1/2
PF19583 CL0381 Metallo-HOrase ODP ODP family beta lactamase
PF19584 MCAfunc MCAfunc domain
PF19585 DUF6092 Family of unknown function (DUF6092)
@@ -18644,7 +18637,7 @@ PF19626 DUF6131 Family of unknown function (DUF6131)
PF19627 ADNP_N Activity-dependent neuroprotector homeobox protein N-terminal
PF19628 DUF6132 Family of unknown function (DUF6132)
PF19629 DUF6133 Family of unknown function (DUF6133)
-PF19630 DUF6134 Family of unknown function (DUF6134)
+PF19630 CL0048 LolA_LolB DUF6134 Domain of unknown function (DUF6134)
PF19631 Trypco2 Trypsin-co-occurring domain 2
PF19632 DUF6136 Family of unknown function (DUF6136)
PF19633 SDG2_C Protein SET DOMAIN GROUP 2 C-terminal
@@ -18718,7 +18711,7 @@ PF19700 CL0181 ABC-2 DUF6198 Family of unknown function (DUF6198)
PF19701 DUF6199 Family of unknown function (DUF6199)
PF19702 DUF6200 Family of unknown function (DUF6200)
PF19703 DUF6201 Family of unknown function (DUF6201)
-PF19704 DNAPKcs_CC5 DNA-PKcs, CC5
+PF19704 CL0020 TPR DNAPKcs_CC5 DNA-PKcs, CC5
PF19705 DUF6202 Family of unknown function (DUF6202)
PF19706 DUF6203 Family of unknown function (DUF6203)
PF19707 DUF6204 Family of unknown function (DUF6204)
@@ -18743,7 +18736,7 @@ PF19725 RPC5_C DNA-directed RNA polymerase III subunit RPC5 C-terminal
PF19726 DUF6218 Family of unknown function (DUF6218)
PF19727 DUF6219 Family of unknown function (DUF6219)
PF19728 DUF6220 Family of unknown function (DUF6220)
-PF19729 CL0022 LRR FBXL18_C F-box/LRR-repeat protein 18 C-terminal
+PF19729 CL0022 LRR FBXL18_LRR F-box/LRR-repeat protein 18, LRR
PF19730 DUF6221 Family of unknown function (DUF6221)
PF19731 DUF6222 Family of unknown function (DUF6222)
PF19732 SpoIIE_N Stage II sporulation protein E N-terminal
@@ -18847,7 +18840,7 @@ PF19829 DUF6310 Family of unknown function (DUF6310)
PF19830 DUF6311 Family of unknown function (DUF6311)
PF19831 DUF6312 Family of unknown function (DUF6312)
PF19832 DUF6313 Family of unknown function (DUF6313)
-PF19833 RecG_C ATP-dependent DNA helicase RecG C-terminal
+PF19833 RecG_dom3_C ATP-dependent DNA helicase RecG, domain 3, C-terminal
PF19834 DUF6314 Family of unknown function (DUF6314)
PF19835 CL0418 GIY-YIG SegE_GIY-YIG Putative endonuclease segE, GIY-YIG domain
PF19836 DUF6315 Family of unknown function (DUF6315)
@@ -19075,13 +19068,13 @@ PF20057 DUF6456 Domain of unknown function (DUF6456)
PF20058 DUF6457 Domain of unknown function (DUF6457)
PF20059 DUF6458 Domain of unknown function (DUF6458)
PF20060 DUF6459 Family of unknown function (DUF6459)
-PF20061 DUF6460 Family of unknown function (DUF6460)
+PF20061 DUF6460 Domain of unknown function (DUF6460)
PF20062 DUF6461 Family of unknown function (DUF6461)
PF20063 CL0123 HTH DUF6462 Family of unknown function (DUF6462)
PF20064 DUF6463 Family of unknown function (DUF6463)
PF20065 DUF6464 Family of unknown function (DUF6464)
PF20066 CL0104 Glyoxalase Glyoxalase_8 Glyoxalase superfamily protein
-PF20067 CL0186 Beta_propeller APMAP_N Adipocyte plasma membrane-associated protein-like, N-terminal
+PF20067 CL0186 Beta_propeller SSL_N Strictosidine synthase-like, N-terminal
PF20068 Amphi-Trp Amphi-Trp domain
PF20069 DUF6465 Family of unknown function (DUF6465)
PF20070 DUF6466 Family of unknown function (DUF6466)
@@ -19145,9 +19138,9 @@ PF20127 DUF6517 Family of unknown function (DUF6517)
PF20128 DUF6518 Family of unknown function (DUF6518)
PF20129 DUF6519 Family of unknown function (DUF6519)
PF20130 DUF6520 Family of unknown function (DUF6520)
-PF20131 DUF6521 Family of unknown function (DUF6521)
+PF20131 MC3 ABC-three component (ABC-3C) system Middle Component 3
PF20132 DUF6522 Family of unknown function (DUF6522)
-PF20133 DUF6523 Family of unknown function (DUF6523)
+PF20133 HHL1-like Protein HHL1-like
PF20134 DUF6524 Family of unknown function (DUF6524)
PF20135 DUF6525 Family of unknown function (DUF6525)
PF20136 DUF6526 Family of unknown function (DUF6526)
@@ -19173,7 +19166,467 @@ PF20155 TMP_3 Tape measure protein
PF20156 Maf_C Flagellin glycosyltransferase Maf helical bundle domain
PF20157 Maf_flag10_N Glycosyltransferase Maf N-terminal domain
PF20158 Cas5fv_helical Cas5fv helical domain
-PF20159 YidB YidB-like protein
+PF20159 CL0123 HTH YidB YidB-like protein
PF20160 C-JID C-JID domain
PF20161 CL0304 CheY VpsR VpsR domain
PF20162 Etd1 Septation protein etd1
+PF20163 DUF6536 Family of unknown function (DUF6536)
+PF20164 CL0159 E-set GspA_SrpA_N GspA/SrpA SigLec-like domain
+PF20165 KBTB_W-LIR KBTB, W-type LIR motif
+PF20166 ATG4_LIR ATG4, F-type LIR motif
+PF20167 Transposase_32 Putative plant transposon protein
+PF20168 CL0020 TPR PDS5 Sister chromatid cohesion protein PDS5 protein
+PF20169 DUF6537 Family of unknown function (DUF6537)
+PF20170 CL0072 Ubiquitin Plexin_RBD Plexin cytoplasmic RhoGTPase-binding domain
+PF20171 CL0139 GADPH_aa-bio_dh OpcA_G6PD_C Glucose-6-phosphate dehydrogenase subunit C-terminal domain
+PF20172 DUF6538 Domain of unknown function (DUF6538)
+PF20173 DUF6539 Family of unknown function (DUF6539)
+PF20174 DUF6540 Family of unknown function (DUF6540)
+PF20175 Tra1_central Tra1 HEAT repeat central region
+PF20176 DUF6541 Family of unknown function (DUF6541)
+PF20177 DUF6542 Domain of unknown function (DUF6542)
+PF20178 DUF6543 Family of unknown function (DUF6543)
+PF20179 MSS51_C MSS51 C-terminal domain
+PF20180 CL0491 LYR-like UQCC2_CBP6 Complex III assembly factor UQCC2/CBP6
+PF20181 DUF6544 Family of unknown function (DUF6544)
+PF20182 DUF6545 Family of unknown function (DUF6545)
+PF20183 DUF6546 Family of unknown function (DUF6546)
+PF20184 DUF6547 Family of unknown function (DUF6547)
+PF20185 DUF6548 Family of unknown function (DUF6548)
+PF20186 DUF6549 Family of unknown function (DUF6549)
+PF20187 DUF6550 Family of unknown function (DUF6550)
+PF20188 CL0248 ParBc DUF6551 Family of unknown function (DUF6551)
+PF20189 DUF6552 Family of unknown function (DUF6552)
+PF20190 DUF6553 Family of unknown function (DUF6553)
+PF20191 DUF6554 Family of unknown function (DUF6554)
+PF20192 DUF6555 Family of unknown function (DUF6555)
+PF20193 DUF6556 Family of unknown function (DUF6556)
+PF20194 DUF6557 Family of unknown function (DUF6557)
+PF20195 CL0504 Phage_barrel DUF6558 Family of unknown function (DUF6558)
+PF20196 DUF6559 Family of unknown function (DUF6559)
+PF20197 DUF6560 Family of unknown function (DUF6560)
+PF20198 DUF6561 Family of unknown function (DUF6561)
+PF20199 RepSA Replication initiator protein, pSAM2
+PF20200 CL0450 FimbA DUF6562 Family of unknown function (DUF6562)
+PF20201 DUF6563 Family of unknown function (DUF6563)
+PF20202 CL0110 GT-A DUF6564 Domain of unknown function (DUF6564)
+PF20203 DUF6565 Domain of unknown function (DUF6565)
+PF20204 DUF6566 Domain of unknown function (DUF6566)
+PF20205 DUF6567 Family of unknown function (DUF6567)
+PF20206 CL0020 TPR Tra1_ring Tra1 HEAT repeat ring region
+PF20207 CL0172 Thioredoxin DUF6568 Family of unknown function (DUF6568)
+PF20208 DUF6569 Family of unknown function (DUF6569)
+PF20209 DUF6570 Domain of unknown function (DUF6570)
+PF20210 CL0020 TPR Laa1_Sip1_HTR5 Laa1/Sip1/HEATR5 HEAT repeat region
+PF20211 DUF6571 Family of unknown function (DUF6571)
+PF20212 DUF6572 Family of unknown function (DUF6572)
+PF20213 DUF6573 Family of unknown function (DUF6573)
+PF20214 CL0167 Zn_Beta_Ribbon DUF6574 Family of unknown function (DUF6574)
+PF20215 DUF6575 Family of unknown function (DUF6575)
+PF20216 DUF6576 Family of unknown function (DUF6576)
+PF20217 DUF6577 Family of unknown function (DUF6577)
+PF20218 DUF6578 Family of unknown function (DUF6578)
+PF20219 DUF6579 Family of unknown function (DUF6579)
+PF20220 ABC_toxin_N ABC toxin N-terminal region
+PF20221 CL0315 Gx_transp DUF6580 Family of unknown function (DUF6580)
+PF20222 DUF6581 Family of unknown function (DUF6581)
+PF20223 DUF6582 Family of unknown function (DUF6582)
+PF20224 DUF6583 Family of unknown function (DUF6583)
+PF20225 CL0020 TPR DUF6584 Family of unknown function (DUF6584)
+PF20226 DUF6585 Family of unknown function (DUF6585)
+PF20227 DUF6586 Family of unknown function (DUF6586)
+PF20228 DUF6587 Family of unknown function (DUF6587)
+PF20229 ChrB_N Protein ChrB, N-terminal
+PF20230 DUF6588 Family of unknown function (DUF6588)
+PF20231 DUF6589 Family of unknown function (DUF6589)
+PF20232 T6SS_FHA_C C-terminal domain of Type VI secretion system FHA protein
+PF20233 DUF6590 Family of unknown function (DUF6590)
+PF20234 DUF6591 Family of unknown function (DUF6591)
+PF20235 DUF6592 Family of unknown function (DUF6592)
+PF20236 DUF6593 Family of unknown function (DUF6593)
+PF20237 DUF6594 Family of unknown function (DUF6594)
+PF20238 CL0159 E-set DUF6595 Family of unknown function (DUF6595)
+PF20239 DUF6596 Family of unknown function (DUF6596)
+PF20240 DUF6597 Domain of unknown function (DUF6597)
+PF20241 DUF6598 Domain of unknown function (DUF6598)
+PF20242 Emfourin Emfourin
+PF20243 MbnP MbnP
+PF20244 DUF6599 Family of unknown function (DUF6599)
+PF20245 DUF6600 Family of unknown function (DUF6600)
+PF20246 DUF6601 Family of unknown function (DUF6601)
+PF20247 DUF6602 Domain of unknown function (DUF6602)
+PF20248 DUF6603 Family of unknown function (DUF6603)
+PF20249 VasX_N VasX toxin N-terminal region
+PF20250 FapA_N Flagellar Assembly Protein A N-terminal region
+PF20251 CL0159 E-set Big_14 Bacterial Ig-like domain
+PF20252 BIG2_C BIG2 C-terminal domain
+PF20253 DUF6604 Family of unknown function (DUF6604)
+PF20254 DUF6605 Domain of unknown function (DUF6605)
+PF20255 DUF6606 Family of unknown function (DUF6606)
+PF20256 CL0635 DmpA_ArgJ MoCoBD_2 Molybdopterin cofactor-binding domain
+PF20257 SAM_HAT_C SAM hydroxide adenosyltransferase C-terminal domain
+PF20258 tRNA_Me_trans_C Aminomethyltransferase beta-barrel domain
+PF20259 CL0350 PRC-barrel tRNA_Me_trans_M tRNA methyl transferase PRC-barrel domain
+PF20260 CL0178 PUA PUA_4 RNA methyltransferase PUA domain
+PF20262 UNC80_C Protein UNC80 C-terminal region
+PF20263 CL0491 LYR-like LYRM2-like LYR motif-containing protein 2-like
+PF20264 CL0159 E-set DUF4784_N DUF4784 N-terminal Ig-like domain
+PF20265 LARA_dom ATPase, RavA, LARA domain
+PF20266 Mab-21_C Mab-21 protein HhH/H2TH-like domain
+PF20267 GREB1_C GREB1 C-terminal region
+PF20268 CL0437 EF-G_C SBDS_C SBDS protein, C-terminal domain
+PF20269 CATRA-N CASPASE and TPR Repeat-Associated N-terminal domain
+PF20270 CATRA-C CASPASE and TPR Repeat-Associated C-terminal domain
+PF20271 CATASP CATRA-Associated Small Protein
+PF20272 E2-Crich Cysteine-rich domain, C-terminal to E2 domain
+PF20273 E2-E1mid Domain observed between E2 and E1 domains
+PF20274 CL0304 CheY cREC_REC Cyclic-phosphate processing Receiver domain
+PF20275 CTD10 C-terminal domain 10 of the ABC-three component (ABC-3C) systems
+PF20276 CTD1 C-terminal domain 1 of the ABC-three component (ABC-3C) systems
+PF20277 CTD11 C-terminal domain 11 of the ABC-three component (ABC-3C) systems
+PF20278 CTD2 C-terminal domain 2 of the ABC-three component (ABC-3C) systems
+PF20279 CTD12 C-terminal domain 12 of the ABC-three component (ABC-3C) systems
+PF20280 CTD4 C-terminal domain 4 of the ABC-three component (ABC-3C) systems
+PF20281 CTD5 C-terminal domain 5 of the ABC-three component (ABC-3C) systems
+PF20282 CTD6 C-terminal domain 6 of the ABC-three component (ABC-3C) systems
+PF20283 CTD7 C-terminal domain 7 of the ABC-three component (ABC-3C) systems
+PF20284 CTD8 C-terminal domain 8 of the ABC-three component (ABC-3C) systems
+PF20285 CTD9 C-terminal domain 9 of the ABC-three component (ABC-3C) systems
+PF20286 CL0194 DNA_pol_B-like divDNApol Divergent Family B DNA polymerase
+PF20287 SH3DP SH3 fold domain associated with phage DNA polymerases
+PF20288 MC2 ABC-three component (ABC-3C) system Middle Component 2
+PF20289 MComp1 ABC-three component (ABC-3C) system Middle Component 1
+PF20290 MC4 ABC-three component (ABC-3C) system Middle Component 4
+PF20291 MC5 ABC-three component (ABC-3C) system Middle Component 5
+PF20292 CL0123 HTH MC7 ABC-three component (ABC-3C) system Middle Component 7
+PF20293 CL0123 HTH MC6 ABC-three component (ABC-3C) system Middle Component 6
+PF20294 KMPT-N KTSC and Metallopeptidase N-terminal fusion domain
+PF20295 CL0123 HTH MC8 ABC-three component (ABC-3C) system Middle Component 8
+PF20296 MTaX1 Methylase-associated X1
+PF20297 CL0010 SH3 MSSS MutS2 and Smr-associated SH3 domain
+PF20298 CL0208 UBC E2-ntca Prokaryotic E2 domain
+PF20299 CL0304 CheY NARF Nucleotidyltransferase-Associated Rossmannoid Fold
+PF20300 CL0709 STING prok_STING Prokaryotic STING domain
+PF20301 pNTSase1 Predicted novel nucleotide synthetase
+PF20302 CL0090 Globin HisK-N-like HisK-N-like globin domain of the ASK signalosome
+PF20303 YLATT YEATS-Like-Associating Three TM
+PF20304 Sp-CxC Small protein from certain CxC ATPase-based DNA modification systems
+PF20305 CL0154 C2 pYEATS prokaryotic YEATS domain
+PF20306 Sp-DndD Small protein found in certain Dnd DNA modification systems
+PF20307 CL0023 P-loop_NTPase divDNAB Divergent DnaB-like ATPase
+PF20308 CL0020 TPR TPR-S Tetratricopeptide Repeats-Sensor
+PF20309 CL0498 Nribosyltransf DRHyd-ASK Deoxyribohydrolase (DRHyd) domain of the ASK signalosome
+PF20310 CL0123 HTH HTH_Tnp_2 Transposon related HTH domain protein
+PF20311 DUF6607 Family of unknown function (DUF6607)
+PF20312 DUF6608 Family of unknown function (DUF6608)
+PF20313 DUF6609 Family of unknown function (DUF6609)
+PF20314 DUF6610 Family of unknown function (DUF6610)
+PF20315 DUF6611 Family of unknown function (DUF6611)
+PF20316 CL0048 LolA_LolB DUF6612 Family of unknown function (DUF6612)
+PF20317 CL0123 HTH HTH_60 Helix-turn-helix domain
+PF20318 DUF6613 Family of unknown function (DUF6613)
+PF20319 DUF6614 Family of unknown function (DUF6614)
+PF20320 DUF6615 Family of unknown function (DUF6615)
+PF20321 DUF6616 Family of unknown function (DUF6616)
+PF20322 DUF6617 Family of unknown function (DUF6617)
+PF20323 DUF6618 Family of unknown function (DUF6618)
+PF20324 DUF6619 Family of unknown function (DUF6619)
+PF20325 DUF6620 Family of unknown function (DUF6620)
+PF20326 DUF6621 Family of unknown function (DUF6621)
+PF20327 DUF6622 Family of unknown function (DUF6622)
+PF20328 DUF6623 Family of unknown function (DUF6623)
+PF20329 DUF6624 Family of unknown function (DUF6624)
+PF20330 DUF6625 Family of unknown function (DUF6625)
+PF20331 DUF6626 Family of unknown function (DUF6626)
+PF20332 DUF6627 Family of unknown function (DUF6627)
+PF20333 DUF6628 Family of unknown function (DUF6628)
+PF20334 DUF6629 Family of unknown function (DUF6629)
+PF20335 DUF6630 Family of unknown function (DUF6630)
+PF20336 DUF6631 Family of unknown function (DUF6631)
+PF20337 DUF6632 Family of unknown function (DUF6632)
+PF20338 DUF6633 Family of unknown function (DUF6633)
+PF20339 DUF6634 Family of unknown function (DUF6634)
+PF20340 DUF6635 Family of unknown function (DUF6635)
+PF20341 DUF6636 Family of unknown function (DUF6636)
+PF20342 DUF6637 Family of unknown function (DUF6637)
+PF20343 DUF6638 Family of unknown function (DUF6638)
+PF20344 DUF6639 Family of unknown function (DUF6639)
+PF20345 DUF6640 Family of unknown function (DUF6640)
+PF20346 DUF6641 Family of unknown function (DUF6641)
+PF20347 DUF6642 Family of unknown function (DUF6642)
+PF20348 DUF6643 Family of unknown function (DUF6643)
+PF20349 DUF6644 Family of unknown function (DUF6644)
+PF20350 DUF6645 Family of unknown function (DUF6645)
+PF20351 DUF6646 Family of unknown function (DUF6646)
+PF20352 DUF6647 Family of unknown function (DUF6647)
+PF20353 DUF6648 Family of unknown function (DUF6648)
+PF20354 DUF6649 Family of unknown function (DUF6649)
+PF20355 DUF6650 Family of unknown function (DUF6650)
+PF20356 DUF6651 Family of unknown function (DUF6651)
+PF20357 DUF6652 Family of unknown function (DUF6652)
+PF20358 DUF6653 Family of unknown function (DUF6653)
+PF20360 DUF6655 Family of unknown function (DUF6655)
+PF20361 DUF6656 Family of unknown function (DUF6656)
+PF20362 DUF6657 Family of unknown function (DUF6657)
+PF20363 DUF6658 Family of unknown function (DUF6658)
+PF20364 DUF6659 Family of unknown function (DUF6659)
+PF20365 DUF6660 Family of unknown function (DUF6660)
+PF20366 DUF6661 Family of unknown function (DUF6661)
+PF20367 DUF6662 Family of unknown function (DUF6662)
+PF20368 DUF6663 Family of unknown function (DUF6663)
+PF20369 DUF6664 Family of unknown function (DUF6664)
+PF20370 DUF6665 Family of unknown function (DUF6665)
+PF20371 DUF6666 Family of unknown function (DUF6666)
+PF20372 DUF6667 Family of unknown function (DUF6667)
+PF20373 DUF6668 Family of unknown function (DUF6668)
+PF20374 DUF6669 Family of unknown function (DUF6669)
+PF20375 DUF6670 Family of unknown function (DUF6670)
+PF20376 CL0236 PDDEXK DUF6671 Domain of unknown function (DUF6671)
+PF20377 DUF6672 Family of unknown function (DUF6672)
+PF20378 DUF6673 Family of unknown function (DUF6673)
+PF20379 DUF6674 Family of unknown function (DUF6674)
+PF20380 DUF6675 Family of unknown function (DUF6675)
+PF20381 DUF6676 Family of unknown function (DUF6676)
+PF20382 DUF6677 Family of unknown function (DUF6677)
+PF20383 DUF6678 Family of unknown function (DUF6678)
+PF20384 DUF6679 Family of unknown function (DUF6679)
+PF20385 DUF6680 Family of unknown function (DUF6680)
+PF20386 DUF6681 Family of unknown function (DUF6681)
+PF20387 DUF6682 Family of unknown function (DUF6682)
+PF20388 DUF6683 Family of unknown function (DUF6683)
+PF20389 DUF6684 Family of unknown function (DUF6684)
+PF20390 DUF6685 Family of unknown function (DUF6685)
+PF20391 DUF6686 Family of unknown function (DUF6686)
+PF20392 DUF6687 Family of unknown function (DUF6687)
+PF20393 Pro_CA_2 Putative carbonic anhydrase
+PF20394 DUF6688 Family of unknown function (DUF6688)
+PF20395 CTD3 C-terminal domain 3 of the ABC-three component (ABC-3C) systems
+PF20396 DUF6689 Family of unknown function (DUF6689)
+PF20397 DUF6690 Family of unknown function (DUF6690)
+PF20398 CL0710 YeeE DUF6691 Family of unknown function (DUF6691)
+PF20399 CL0266 PH PH_20 PH domain
+PF20400 CL0145 Golgi-transport BAR_4 BAR-like domain
+PF20401 CL0207 Rhomboid-like Rhomboid_2 Rhomboid-like protein
+PF20402 CL0044 Ferritin DUF6692 Domain of unknown function (DUF6692)
+PF20403 DUF6693 Family of unknown function (DUF6693)
+PF20404 DUF6694 Family of unknown function (DUF6694)
+PF20405 DUF6695 Family of unknown function (DUF6695)
+PF20406 SAM_KSR1_N Kinase suppressor RAS 1 N-terminal helical hairpin
+PF20407 CL0004 Concanavalin DUF1583_N Domain of unknown function (DUF1583_N)
+PF20408 CL0028 AB_hydrolase Abhydrolase_11 Alpha/beta hydrolase domain
+PF20409 CL0051 NTF2 SnoaL_5 SnoaL-like domain
+PF20410 DUF6696 Domain of unknown function (DUF6696)
+PF20411 DUF6697 Domain of unknown function (DUF6697)
+PF20412 RALGAPB_N RALGAPB N-terminal domain
+PF20413 Kiaa1109_N Kiaa1109 N-terminal region
+PF20414 DUF6698 Family of unknown function (DUF6698)
+PF20415 DUF6699 Family of unknown function (DUF6699)
+PF20416 DUF6700 Domain of unknown function (DUF6700)
+PF20417 Gemin6_C Gemin6 C-terminal domain
+PF20418 Herpes_gE_N Alphaherpesvirus glycoprotein E N-terminal
+PF20419 DUF6701 Family of unknown function (DUF6701)
+PF20420 DUF6702 Domain of unknown function (DUF6702)
+PF20421 CL0020 TPR DHR-2_Lobe_C DHR-2, Lobe C
+PF20422 DHR-2_Lobe_B DHR-2, Lobe B
+PF20423 AceK_regulatory Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain
+PF20424 PilZN3 PilZN3 domain
+PF20425 CL0020 TPR Neurobeachin Neurobeachin alpha solenoid region
+PF20426 CL0186 Beta_propeller NBCH_WD40 Neurobeachin beta propeller domain
+PF20427 NRP1_C Nuclear speckle splicing regulatory protein 1, RS-like domain
+PF20428 Sey1_3HB Sey1 three-helix bundle domain
+PF20429 Tab2-like_C RNA-binding protein Tab2/Atab2, C terminal
+PF20430 Eplus_motif E+ motif
+PF20431 CL0020 TPR E_motif E motif
+PF20432 CL0123 HTH Xre-like-HTH Antitoxin Xre-like helix-turn-helix domain
+PF20433 PKAT_KLD PKAT, KLD domain
+PF20434 CL0028 AB_hydrolase BD-FAE BD-FAE
+PF20435 ASY3-like Meiosis-specific protein ASY3-like
+PF20436 CL0671 AAA_lid LonB_AAA-LID Archaeal LonB, AAA+ ATPase LID domain
+PF20437 LonC_helical Lon-like LonC helical domain
+PF20438 SpoIVA_middle Stage IV sporulation protein A, middle domain
+PF20439 SpoIVA_C Sporulation stage IV protein A, C-terminal
+PF20440 GvpD_bR2 GvpD basic region 2
+PF20441 CL0219 RNase_H TerL_nuclease Terminase large subunit, endonuclease domain
+PF20442 BrxL_N BREX system Lon protease-like protein BrxL N-terminal
+PF20443 LAP1_N Lamina-associated polypeptide 1, N-terminal
+PF20444 DUF6703 Family of unknown function (DUF6703)
+PF20445 RHS_N Retrotransposon hot spot proteins N-terminal
+PF20446 ABC_N ATPase of the ABC class N-terminal
+PF20447 DUF6704 Family of unknown function (DUF6704)
+PF20448 DUF6705 Family of unknown function (DUF6705)
+PF20449 DUF6706 Family of unknown function (DUF6706)
+PF20450 CL0169 Rep PPV_E1_DBD Papillomavirus E1, DNA-binding domain
+PF20451 Calmod_bind_M Calmodulin binding protein central domain
+PF20452 Calmod_bind_C Calmodulin binding protein C-terminal domain
+PF20453 DUF6707 Family of unknown function (DUF6707)
+PF20454 CL0023 P-loop_NTPase GpA_nuclease Terminase large subunit gpA, endonuclease domain
+PF20455 DUF6708 Family of unknown function (DUF6708)
+PF20456 DUF6709 Family of unknown function (DUF6709)
+PF20457 DUF6710 Family of unknown function (DUF6710)
+PF20458 DUF6711 Family of unknown function (DUF6711)
+PF20459 DUF6712 Family of unknown function (DUF6712)
+PF20460 DUF6713 Family of unknown function (DUF6713)
+PF20461 DUF6714 Family of unknown function (DUF6714)
+PF20462 CL0051 NTF2 DUF6715 Domain of unknown function (DUF6715)
+PF20463 CL0106 6PGD_C PDH_C Prephenate dehydrogenase, dimerization domain
+PF20464 MmeI_N MmeI, N-terminal domain
+PF20465 MmeI_hel MmeI, helicase spacer domain
+PF20466 MmeI_TRD MmeI, target recognition domain
+PF20467 MmeI_C MmeI, C-terminal domain
+PF20468 CL0020 TPR HPS6_C Hermansky-Pudlak syndrome 6 protein C-terminal domain
+PF20469 CL0413 Toprim-like OLD-like_TOPRIM Overcoming lysogenization defect protein-like, TOPRIM domain
+PF20470 CL0123 HTH HTH_61 Helix-turn-helix domain
+PF20471 CL0113 GT-B DUF6716 Putative glycosyltransferase (DUF6716)
+PF20472 CL0236 PDDEXK PDDEXK_11 PD-(D/E)XK nuclease superfamily domain
+PF20473 CL0063 NADP_Rossmann MmeI_Mtase MmeI, DNA-methyltransferase domain
+PF20474 PHL PHL domain
+PF20475 DUF6717 Family of unknown function (DUF6717)
+PF20476 DUF6718 Family of unknown function (DUF6718)
+PF20477 DUF6719 Family of unknown function (DUF6719)
+PF20478 P2RX7_C P2X purinoreceptor 7 intracellular domain
+PF20479 TMEM128 TMEM128 protein
+PF20480 DUF6720 Family of unknown function (DUF6720)
+PF20481 DUF6721 Domain of unknown function (DUF6721)
+PF20482 DUF6722 Family of unknown function (DUF6722)
+PF20483 CL0027 RdRP Flavi_NS5_thumb Flavivirus RNA-directed RNA polymerase, thumb domain
+PF20484 DUF6723 Family of unknown function (DUF6723)
+PF20485 DUF6724 Family of unknown function (DUF6724)
+PF20486 DUF6725 Family of unknown function (DUF6725)
+PF20487 DUF6726 Family of unknown function (DUF6726)
+PF20488 CL0027 RdRP Birna_VP1_thumb Birnavirus RNA dependent RNA polymerase (VP1), thumb domain
+PF20489 Birna_RdRp_C Birnavirus RNA dependent RNA polymerase (VP1), C-terminal
+PF20490 CL0370 Uteroglobin SCGB3A Secretoglobin 3A
+PF20491 CL0719 Moesin_tail Ermin Ermin
+PF20492 ERM_helical Ezrin/radixin/moesin, alpha-helical domain
+PF20493 WD-like_fungi Fungal WD-like
+PF20494 YfjS_YafY Lipoprotein YfjS/YafY domain
+PF20495 DUF6727 Family of unknown function (DUF6727)
+PF20496 Dbl7 Double strand break localizing Dbl7
+PF20497 SWI-SNF_Ssr4_C SWI/SNF and RSC complexes subunit Ssr4 C-terminal
+PF20498 DUF6728 Family of unknown function (DUF6728)
+PF20499 DUF6729 Domain of unknown function (DUF6729)
+PF20500 CL0020 TPR DNA-PKcs_N DNA-PKcs, N-terminal
+PF20501 MbhE MBH, subunit E
+PF20502 CL0020 TPR DNAPKcs_CC1-2 DNA-dependent protein kinase catalytic subunit, CC1/2
+PF20503 DUF6730 Family of unknown function (DUF6730)
+PF20504 IntS14_C Integrator complex subunit 14, alpha-helical domain
+PF20505 DUF6731 Family of unknown function (DUF6731)
+PF20506 DUF6732 Family of unknown function (DUF6732)
+PF20507 DUF6733 Family of unknown function (DUF6733)
+PF20508 DUF6734 Family of unknown function (DUF6734)
+PF20509 DUF6735 Family of unknown function (DUF6735)
+PF20510 CL0029 Cupin HgmA_N Homogentisate 1,2-dioxygenase N-terminal
+PF20511 CL0029 Cupin PMI_typeI_cat Phosphomannose isomerase type I, catalytic domain
+PF20512 PMI_typeI_hel Phosphomannose isomerase type I, helical insertion domain
+PF20513 UBact Prokaryotic ubiquitin-like protein UBact
+PF20514 CL0123 HTH ROXA-like_wH ROXA-like winged helix
+PF20515 CL0029 Cupin 2OG-FeII_Oxy_6 Tet-like 2OG-Fe(II) oxygenase superfamily
+PF20516 CL0236 PDDEXK PDDEXK_12 PD-(D/E)XK nuclease superfamily
+PF20517 CL0375 Transporter TMEM127 Transmembrane protein 127
+PF20518 CL0020 TPR Apc1_MidN Anaphase-promoting complex subunit 1 middle domain
+PF20519 CL0030 Ion_channel Polycystin_dom Polycystin domain
+PF20520 Ac45-VOA1_TM V0 complex accessory subunit Ac45/VOA1 transmembrane domain
+PF20521 DUF6736 Family of unknown function (DUF6736)
+PF20522 DUF6737 Domain of unknown function (DUF6737)
+PF20523 DUF6738 Domain of unknown function (DUF6738)
+PF20524 DUF6739 Family of unknown function (DUF6739)
+PF20525 DUF6740 Family of unknown function (DUF6740)
+PF20526 DUF6741 Domain of unknown function (DUF6741)
+PF20527 DUF6742 Domain of unknown function (DUF6742)
+PF20528 DUF6743 Domain of unknown function (DUF6743)
+PF20529 DUF6744 Family of unknown function (DUF6744)
+PF20530 DUF6745 Domain of unknown function (DUF6745)
+PF20531 DUF6746 Family of unknown function (DUF6746)
+PF20532 DUF6747 Family of unknown function (DUF6747)
+PF20533 DUF6748 Domain of unknown function (DUF6748)
+PF20534 DUF6749 Domain of unknown function (DUF6749)
+PF20535 DUF6750 Family of unknown function (DUF6750)
+PF20536 DUF6751 Family of unknown function (DUF6751)
+PF20537 DUF6752 Domain of unknown function (DUF6752)
+PF20538 DUF6753 Family of unknown function (DUF6753)
+PF20539 DUF6754 Domain of unknown function (DUF6754)
+PF20540 DUF6755 Family of unknown function (DUF6755)
+PF20541 DUF6756 Family of unknown function (DUF6756)
+PF20542 DUF6757 Family of unknown function (DUF6757)
+PF20543 CowN N2-fixation sustaining protein CowN
+PF20544 DUF6758 Family of unknown function (DUF6758)
+PF20545 DUF6759 Domain of unknown function (DUF6759)
+PF20546 DUF6760 Family of unknown function (DUF6760)
+PF20547 DUF6761 Family of unknown function (DUF6761)
+PF20548 DUF6762 Family of unknown function (DUF6762)
+PF20549 DUF6763 Family of unknown function (DUF6763)
+PF20550 DUF6764 Family of unknown function (DUF6764)
+PF20551 DUF6765 Family of unknown function (DUF6765)
+PF20552 HTH_62 Recombinase-like helix-turn-helix domain
+PF20553 Methyltransf_35 Putative O-methyltransferase
+PF20554 DUF6766 Domain of unknown function (DUF6766)
+PF20555 DUF6767 Domain of unknown function (DUF6767)
+PF20556 DUF6768 Family of unknown function (DUF6768)
+PF20557 DnaT_2 Putative DnaT-like ssDNA binding protein
+PF20558 DUF6769 Family of unknown function (DUF6769)
+PF20559 DUF6770 Family of unknown function (DUF6770)
+PF20560 MotA_N Motility protein A N-terminal
+PF20561 DUF6771 Domain of unknown function (DUF6771)
+PF20562 DUF6772 Domain of unknown function (DUF6772)
+PF20563 DUF6773 Family of unknown function (DUF6773)
+PF20564 DUF6774 Family of unknown function (DUF6774)
+PF20565 DUF6775 Probable metallopeptidase family (DUF6775)
+PF20566 Eap1 eIF4E-associated protein
+PF20567 DUF6776 Family of unknown function (DUF6776)
+PF20568 DUF6777 Domain of unknown function (DUF6777)
+PF20569 DUF6778 Family of unknown function (DUF6778)
+PF20570 DUF6779 Domain of unknown function (DUF6779)
+PF20571 DUF6780 Domain of unknown function (DUF6780)
+PF20572 DUF6781 Family of unknown function (DUF6781)
+PF20573 DUF6782 Putative metallopeptidase family (DUF6782)
+PF20574 DUF6783 Family of unknown function (DUF6783)
+PF20575 HTH_63 Helix-turn-helix domain
+PF20576 HEWD HEWD domain
+PF20577 Phage_ORF5 Phage ORF5 protein
+PF20578 aBig_2 Atrophied bacterial Ig domain
+PF20579 LapA LapA domain
+PF20580 DUF6784 Domain of unknown function (DUF6784)
+PF20581 DUF6785 Family of unknown function (DUF6785)
+PF20582 UPF0758_N UPF0758 N-terminal
+PF20583 DUF6786 Family of unknown function (DUF6786)
+PF20584 DUF6787 Family of unknown function (DUF6787)
+PF20585 Pectate_lyase_5 Putative pectate lyase-like adhesive domain
+PF20586 DUF6788 Family of unknown function (DUF6788)
+PF20587 DUF6789 Family of unknown function (DUF6789)
+PF20588 DMTF1_N Cyclin-D-binding Myb-like transcription factor 1 N-terminal
+PF20589 DUF6790 Family of unknown function (DUF6790)
+PF20590 DUF6791 Domain of unknown function (DUF6791)
+PF20591 DUF6792 Domain of unknown function (DUF6792)
+PF20592 pAdhesive_10 Putative adhesin domain (group 10)
+PF20593 DUF6793 Family of unknown function (DUF6793)
+PF20594 DUF6794 Domain of unknown function (DUF6794)
+PF20595 pAdhesive_6 Putative adhesive domain (group 6)
+PF20596 pAdhesive_11 Putative adhesive domain (group 11)
+PF20597 pAdhesive_15 Putative Ice-binding-like adhesive domain
+PF20598 DUF6795 Domain of unknown function (DUF6795)
+PF20599 DUF6796 Family of unknown function (DUF6796)
+PF20600 ExoX-like_C Exodeoxyribonuclease X-like C-terminal
+PF20601 DUF6797 Domain of unknown function (DUF6797)
+PF20602 pAdhesive_8 Putative adhesive domain (group 8)
+PF20603 Bact_hydrolase Bacterial hydrolase
+PF20604 DUF6798 Domain of unknown function (DUF6798)
+PF20605 Antitox_RHH Antitoxin-like ribbon-helix-helix
+PF20606 DUF6799 Domain of unknown function (DUF6799)
+PF20607 DUF6800 Family of unknown function (DUF6800)
+PF20608 Phage_tube_C Phage tail tube protein C-terminal domain
+PF20609 pAdhesive_17 Putative adhesive domain (group 17)
+PF20610 TED_2 Thioester domain
+PF20611 DUF6801 Family of unknown function (DUF6801)
+PF20612 SHOCT_2 SHOCT domain
+PF20613 HipA_2 HipA-like kinase
+PF20614 Mycovirus_RNAse Homologues of viral RNAse III, found in viruses infecting fungi
+PF20615 DUF6802 Family of unknown function (DUF6802)
+PF20616 Caps_syn_GfcC_N Capsule biosynthesis GfcC, N-terminal
+PF20617 DUF6803 Family of unknown function (DUF6803)
+PF20618 GPD_NAD_C_bact Bacterial GPD, NAD-dependent C-terminal
+PF20619 DUF6804 Family of unknown function (DUF6804)
+PF20620 DUF6805 Family of unknown function (DUF6805)
+PF20621 DUF6806 Family of unknown function (DUF6806)
+PF20622 CL0159 E-set Big_15 Bacterial Ig domain (Big_16)
+PF20623 CL0204 Adhesin Sgo0707_N2 Sgo0707 N2 domain
+PF20624 DMRT5_DMB DMRT5, DMB domain
diff --git a/addons/gene_ontology.txt b/addons/gene_ontology.txt
index 91693b12600de487ef7e15bd7fc973250b89a5fb..d5623e328c69150acbb925dc1f8bc5b60b3bf3b1 100644
--- a/addons/gene_ontology.txt
+++ b/addons/gene_ontology.txt
@@ -30,7 +30,6 @@ PF01198 GO:0005840 ribosome component
PF01198 GO:0006412 translation process
PF01198 GO:0003735 structural constituent of ribosome function
PF01420 GO:0003677 DNA binding function
-PF01420 GO:0006304 DNA modification process
PF00834 GO:0005975 carbohydrate metabolic process process
PF00834 GO:0016857 racemase and epimerase activity, acting on carbohydrates and derivatives function
PF01428 GO:0008270 zinc ion binding function
@@ -46,7 +45,6 @@ PF00556 GO:0019684 photosynthesis, light reaction process
PF00556 GO:0030077 plasma membrane light-harvesting complex component
PF00556 GO:0016021 integral component of membrane component
PF00556 GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity function
-PF01004 GO:0019031 viral envelope component
PF01004 GO:0019058 viral life cycle process
PF01095 GO:0030599 pectinesterase activity function
PF01095 GO:0042545 cell wall modification process
@@ -67,7 +65,6 @@ PF00947 GO:0006508 proteolysis process
PF00947 GO:0008233 peptidase activity function
PF00947 GO:0016032 viral process process
PF00039 GO:0005576 extracellular region component
-PF00293 GO:0016787 hydrolase activity function
PF00348 GO:0008299 isoprenoid biosynthetic process process
PF00277 GO:0005576 extracellular region component
PF00825 GO:0000049 tRNA binding function
@@ -105,17 +102,16 @@ PF01110 GO:0005127 ciliary neurotrophic factor receptor binding function
PF00979 GO:0005198 structural molecule activity function
PF00979 GO:0019058 viral life cycle process
PF00638 GO:0046907 intracellular transport process
+PF01582 GO:0003953 NAD+ nucleosidase activity function
PF01582 GO:0007165 signal transduction process
-PF01582 GO:0005515 protein binding function
+PF13676 GO:0003953 NAD+ nucleosidase activity function
PF13676 GO:0007165 signal transduction process
-PF13676 GO:0005515 protein binding function
PF00788 GO:0007165 signal transduction process
PF00257 GO:0009415 response to water process
PF01355 GO:0009055 electron transfer activity function
PF01355 GO:0019646 aerobic electron transport chain process
PF00732 GO:0016614 oxidoreductase activity, acting on CH-OH group of donors function
PF00732 GO:0050660 flavin adenine dinucleotide binding function
-PF00732 GO:0055114 oxidation-reduction process process
PF00209 GO:0016021 integral component of membrane component
PF00583 GO:0008080 N-acetyltransferase activity function
PF13302 GO:0008080 N-acetyltransferase activity function
@@ -133,11 +129,6 @@ PF00006 GO:0005524 ATP binding function
PF01280 GO:0005840 ribosome component
PF01280 GO:0006412 translation process
PF01280 GO:0003735 structural constituent of ribosome function
-PF02135 GO:0042025 host cell nucleus component
-PF02135 GO:0006355 regulation of transcription, DNA-templated process
-PF02135 GO:0004402 histone acetyltransferase activity function
-PF02135 GO:0008270 zinc ion binding function
-PF02135 GO:0003712 transcription coregulator activity function
PF00620 GO:0007165 signal transduction process
PF00548 GO:0006508 proteolysis process
PF00548 GO:0004197 cysteine-type endopeptidase activity function
@@ -148,8 +139,8 @@ PF00242 GO:0003677 DNA binding function
PF00242 GO:0006260 DNA replication process
PF00972 GO:0005524 ATP binding function
PF00972 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
-PF00082 GO:0004252 serine-type endopeptidase activity function
PF00082 GO:0006508 proteolysis process
+PF00082 GO:0008236 serine-type peptidase activity function
PF00651 GO:0005515 protein binding function
PF00845 GO:0003677 DNA binding function
PF00845 GO:0033644 host cell membrane component
@@ -163,7 +154,6 @@ PF00260 GO:0003677 DNA binding function
PF00260 GO:0007283 spermatogenesis process
PF00260 GO:0000786 nucleosome component
PF00514 GO:0005515 protein binding function
-PF00447 GO:0042025 host cell nucleus component
PF00447 GO:0006355 regulation of transcription, DNA-templated process
PF00447 GO:0043565 sequence-specific DNA binding function
PF00447 GO:0003700 DNA-binding transcription factor activity function
@@ -174,6 +164,7 @@ PF02033 GO:0006364 rRNA processing process
PF00102 GO:0006470 protein dephosphorylation process
PF00102 GO:0004725 protein tyrosine phosphatase activity function
PF01112 GO:0016787 hydrolase activity function
+PF00936 GO:0031469 polyhedral organelle component
PF01828 GO:0006508 proteolysis process
PF01828 GO:0004190 aspartic-type endopeptidase activity function
PF00498 GO:0005515 protein binding function
@@ -186,8 +177,6 @@ PF01208 GO:0006779 porphyrin-containing compound biosynthetic process process
PF00818 GO:0009279 cell outer membrane component
PF00419 GO:0009289 pilus component
PF00419 GO:0007155 cell adhesion process
-PF01059 GO:0006120 mitochondrial electron transport, NADH to ubiquinone process
-PF01059 GO:0055114 oxidation-reduction process process
PF12763 GO:0005515 protein binding function
PF01070 GO:0016491 oxidoreductase activity function
PF00844 GO:0019028 viral capsid component
@@ -233,13 +222,13 @@ PF00594 GO:0005576 extracellular region component
PF00639 GO:0003755 peptidyl-prolyl cis-trans isomerase activity function
PF13145 GO:0003755 peptidyl-prolyl cis-trans isomerase activity function
PF00510 GO:0016020 membrane component
-PF00510 GO:0015002 heme-copper terminal oxidase activity function
+PF00510 GO:0004129 cytochrome-c oxidase activity function
PF01363 GO:0046872 metal ion binding function
PF00886 GO:0005840 ribosome component
PF00886 GO:0006412 translation process
PF00886 GO:0003735 structural constituent of ribosome function
PF01276 GO:0003824 catalytic activity function
-PF00591 GO:0016757 transferase activity, transferring glycosyl groups function
+PF00591 GO:0016757 glycosyltransferase activity function
PF00643 GO:0008270 zinc ion binding function
PF02068 GO:0008270 zinc ion binding function
PF03510 GO:0006508 proteolysis process
@@ -249,7 +238,6 @@ PF01055 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF01055 GO:0005975 carbohydrate metabolic process process
PF01082 GO:0005507 copper ion binding function
PF01082 GO:0004497 monooxygenase activity function
-PF01082 GO:0055114 oxidation-reduction process process
PF01082 GO:0016715 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen function
PF00157 GO:0006355 regulation of transcription, DNA-templated process
PF00157 GO:0003700 DNA-binding transcription factor activity function
@@ -284,16 +272,14 @@ PF00862 GO:0005985 sucrose metabolic process process
PF02060 GO:0016020 membrane component
PF02060 GO:0005249 voltage-gated potassium channel activity function
PF02060 GO:0006811 ion transport process
-PF01031 GO:0005525 GTP binding function
PF02122 GO:0004252 serine-type endopeptidase activity function
PF02122 GO:0016021 integral component of membrane component
PF02122 GO:0016032 viral process process
PF02129 GO:0016787 hydrolase activity function
PF00893 GO:0016021 integral component of membrane component
+PF00893 GO:0022857 transmembrane transporter activity function
PF00866 GO:0006725 cellular aromatic compound metabolic process process
-PF00866 GO:0055114 oxidation-reduction process process
PF00142 GO:0005524 ATP binding function
-PF00142 GO:0055114 oxidation-reduction process process
PF00142 GO:0016491 oxidoreductase activity function
PF00309 GO:0001216 DNA-binding transcription activator activity function
PF00309 GO:0016987 sigma factor activity function
@@ -313,8 +299,8 @@ PF00287 GO:0005890 sodium:potassium-exchanging ATPase complex component
PF00287 GO:0006813 potassium ion transport process
PF00287 GO:0006814 sodium ion transport process
PF01350 GO:0016070 RNA metabolic process process
+PF01350 GO:0044423 virion component component
PF01350 GO:0016032 viral process process
-PF01350 GO:0019012 virion component
PF02115 GO:0005094 Rho GDP-dissociation inhibitor activity function
PF02115 GO:0005737 cytoplasm component
PF01150 GO:0016787 hydrolase activity function
@@ -333,7 +319,6 @@ PF00436 GO:0003697 single-stranded DNA binding function
PF00230 GO:0016020 membrane component
PF00230 GO:0055085 transmembrane transport process
PF00230 GO:0015267 channel activity function
-PF10584 GO:0004175 endopeptidase activity function
PF10584 GO:0019773 proteasome core complex, alpha-subunit complex component
PF10584 GO:0006511 ubiquitin-dependent protein catabolic process process
PF00511 GO:0042025 host cell nucleus component
@@ -349,7 +334,6 @@ PF00569 GO:0008270 zinc ion binding function
PF00827 GO:0005840 ribosome component
PF00827 GO:0006412 translation process
PF00827 GO:0003735 structural constituent of ribosome function
-PF00507 GO:0055114 oxidation-reduction process process
PF00507 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
PF00633 GO:0003677 DNA binding function
PF01264 GO:0009073 aromatic amino acid family biosynthetic process process
@@ -374,14 +358,13 @@ PF00236 GO:0005576 extracellular region component
PF00236 GO:0005179 hormone activity function
PF00878 GO:0007041 lysosomal transport process
PF00878 GO:0038023 signaling receptor activity function
-PF00878 GO:0005520 insulin-like growth factor binding function
PF00878 GO:0005537 mannose binding function
PF00124 GO:0009772 photosynthetic electron transport in photosystem II process
PF00124 GO:0019684 photosynthesis, light reaction process
PF00124 GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity function
PF13404 GO:0043565 sequence-specific DNA binding function
PF01002 GO:0004252 serine-type endopeptidase activity function
-PF01002 GO:0019012 virion component
+PF01002 GO:0044423 virion component component
PF00531 GO:0007165 signal transduction process
PF00531 GO:0005515 protein binding function
PF00809 GO:0042558 pteridine-containing compound metabolic process process
@@ -396,12 +379,10 @@ PF01366 GO:0019073 viral DNA genome packaging process
PF00076 GO:0003676 nucleic acid binding function
PF16367 GO:0003676 nucleic acid binding function
PF01450 GO:0004455 ketol-acid reductoisomerase activity function
-PF01450 GO:0055114 oxidation-reduction process process
PF01450 GO:0009082 branched-chain amino acid biosynthetic process process
PF01158 GO:0005840 ribosome component
PF01158 GO:0006412 translation process
PF01158 GO:0003735 structural constituent of ribosome function
-PF00148 GO:0055114 oxidation-reduction process process
PF00148 GO:0016491 oxidoreductase activity function
PF01265 GO:0005739 mitochondrion component
PF01265 GO:0004408 holocytochrome-c synthase activity function
@@ -412,6 +393,7 @@ PF00528 GO:0055085 transmembrane transport process
PF02069 GO:0046872 metal ion binding function
PF01032 GO:0016020 membrane component
PF01032 GO:0022857 transmembrane transporter activity function
+PF01078 GO:0005524 ATP binding function
PF00392 GO:0006355 regulation of transcription, DNA-templated process
PF00392 GO:0003700 DNA-binding transcription factor activity function
PF01051 GO:0003887 DNA-directed DNA polymerase activity function
@@ -428,7 +410,6 @@ PF00123 GO:0005576 extracellular region component
PF00123 GO:0005179 hormone activity function
PF01118 GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor function
PF01118 GO:0051287 NAD binding function
-PF01118 GO:0055114 oxidation-reduction process process
PF01040 GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups function
PF01040 GO:0016021 integral component of membrane component
PF00193 GO:0007155 cell adhesion process
@@ -453,7 +434,9 @@ PF00935 GO:0003735 structural constituent of ribosome function
PF01251 GO:0005840 ribosome component
PF01251 GO:0006412 translation process
PF01251 GO:0003735 structural constituent of ribosome function
+PF01398 GO:0008237 metallopeptidase activity function
PF01398 GO:0005515 protein binding function
+PF01398 GO:0070122 isopeptidase activity function
PF02011 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF02011 GO:0030245 cellulose catabolic process process
PF02011 GO:0008810 cellulase activity function
@@ -464,14 +447,12 @@ PF00119 GO:0045263 proton-transporting ATP synthase complex, coupling factor F(o
PF00119 GO:0015078 proton transmembrane transporter activity function
PF00632 GO:0004842 ubiquitin-protein transferase activity function
PF00642 GO:0046872 metal ion binding function
-PF00174 GO:0042128 nitrate assimilation process
PF00983 GO:0019028 viral capsid component
PF00983 GO:0005198 structural molecule activity function
PF01306 GO:0016020 membrane component
PF01306 GO:0008643 carbohydrate transport process
PF01306 GO:0005351 carbohydrate:proton symporter activity function
-PF01166 GO:0006355 regulation of transcription, DNA-templated process
-PF01166 GO:0003700 DNA-binding transcription factor activity function
+PF01166 GO:0006357 regulation of transcription by RNA polymerase II process
PF00920 GO:0003824 catalytic activity function
PF00887 GO:0000062 fatty-acyl-CoA binding function
PF12052 GO:0070588 calcium ion transmembrane transport process
@@ -488,7 +469,6 @@ PF01667 GO:0005840 ribosome component
PF01667 GO:0006412 translation process
PF01667 GO:0003735 structural constituent of ribosome function
PF03836 GO:0005515 protein binding function
-PF00899 GO:0008641 ubiquitin-like modifier activating enzyme activity function
PF00297 GO:0005840 ribosome component
PF00297 GO:0006412 translation process
PF00297 GO:0003735 structural constituent of ribosome function
@@ -503,7 +483,6 @@ PF02118 GO:0016020 membrane component
PF02118 GO:0004888 transmembrane signaling receptor activity function
PF02118 GO:0007606 sensory perception of chemical stimulus process
PF01679 GO:0016021 integral component of membrane component
-PF00379 GO:0042302 structural constituent of cuticle function
PF00892 GO:0016020 membrane component
PF00892 GO:0016021 integral component of membrane component
PF00424 GO:0042025 host cell nucleus component
@@ -514,7 +493,6 @@ PF14560 GO:0005515 protein binding function
PF00775 GO:0006725 cellular aromatic compound metabolic process process
PF00775 GO:0008199 ferric iron binding function
PF00775 GO:0003824 catalytic activity function
-PF00775 GO:0055114 oxidation-reduction process process
PF00410 GO:0005840 ribosome component
PF00410 GO:0006412 translation process
PF00410 GO:0003735 structural constituent of ribosome function
@@ -527,13 +505,14 @@ PF00741 GO:0005198 structural molecule activity function
PF01434 GO:0006508 proteolysis process
PF01434 GO:0005524 ATP binding function
PF01434 GO:0004222 metalloendopeptidase activity function
+PF01434 GO:0004176 ATP-dependent peptidase activity function
PF00837 GO:0004800 thyroxine 5'-deiodinase activity function
-PF00837 GO:0055114 oxidation-reduction process process
PF01310 GO:0031423 hexon binding function
PF01310 GO:0019028 viral capsid component
PF00859 GO:0005634 nucleus component
PF00859 GO:0006355 regulation of transcription, DNA-templated process
PF00859 GO:0003700 DNA-binding transcription factor activity function
+PF01237 GO:0008289 lipid binding function
PF01008 GO:0044237 cellular metabolic process process
PF00121 GO:0004807 triose-phosphate isomerase activity function
PF09048 GO:0003677 DNA binding function
@@ -566,8 +545,7 @@ PF00320 GO:0006355 regulation of transcription, DNA-templated process
PF00320 GO:0043565 sequence-specific DNA binding function
PF00320 GO:0008270 zinc ion binding function
PF00921 GO:0016020 membrane component
-PF01408 GO:0016491 oxidoreductase activity function
-PF05001 GO:0005665 RNA polymerase II, core complex component
+PF01408 GO:0000166 nucleotide binding function
PF05001 GO:0003677 DNA binding function
PF05001 GO:0006366 transcription by RNA polymerase II process
PF00016 GO:0000287 magnesium ion binding function
@@ -621,8 +599,8 @@ PF00274 GO:0004332 fructose-bisphosphate aldolase activity function
PF00274 GO:0006096 glycolytic process process
PF00295 GO:0005975 carbohydrate metabolic process process
PF00295 GO:0004650 polygalacturonase activity function
+PF01006 GO:0044423 virion component component
PF01006 GO:0016032 viral process process
-PF01006 GO:0019012 virion component
PF06617 GO:1902751 positive regulation of cell cycle G2/M phase transition process
PF06617 GO:0006470 protein dephosphorylation process
PF06617 GO:0004725 protein tyrosine phosphatase activity function
@@ -665,7 +643,6 @@ PF00513 GO:0005198 structural molecule activity function
PF02073 GO:0006508 proteolysis process
PF02073 GO:0004177 aminopeptidase activity function
PF02867 GO:0006260 DNA replication process
-PF02867 GO:0055114 oxidation-reduction process process
PF01111 GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity function
PF01184 GO:0016021 integral component of membrane component
PF00196 GO:0006355 regulation of transcription, DNA-templated process
@@ -685,7 +662,7 @@ PF00352 GO:0006352 DNA-templated transcription, initiation process
PF01285 GO:0006355 regulation of transcription, DNA-templated process
PF01285 GO:0003700 DNA-binding transcription factor activity function
PF00883 GO:0006508 proteolysis process
-PF00883 GO:0004177 aminopeptidase activity function
+PF00883 GO:0070006 metalloaminopeptidase activity function
PF01458 GO:0016226 iron-sulfur cluster assembly process
PF01219 GO:0016020 membrane component
PF01219 GO:0008654 phospholipid biosynthetic process process
@@ -711,7 +688,6 @@ PF00356 GO:0006355 regulation of transcription, DNA-templated process
PF01048 GO:0009116 nucleoside metabolic process process
PF01048 GO:0003824 catalytic activity function
PF01113 GO:0009089 lysine biosynthetic process via diaminopimelate process
-PF01113 GO:0055114 oxidation-reduction process process
PF01113 GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase function
PF00126 GO:0006355 regulation of transcription, DNA-templated process
PF00126 GO:0003700 DNA-binding transcription factor activity function
@@ -725,13 +701,10 @@ PF00685 GO:0008146 sulfotransferase activity function
PF00280 GO:0009611 response to wounding process
PF00280 GO:0004867 serine-type endopeptidase inhibitor activity function
PF00578 GO:0016209 antioxidant activity function
-PF00578 GO:0055114 oxidation-reduction process process
PF00578 GO:0016491 oxidoreductase activity function
PF00219 GO:0005520 insulin-like growth factor binding function
PF00219 GO:0005576 extracellular region component
-PF00857 GO:0003824 catalytic activity function
PF02066 GO:0005507 copper ion binding function
-PF00501 GO:0003824 catalytic activity function
PF02044 GO:0007218 neuropeptide signaling pathway process
PF00272 GO:0005576 extracellular region component
PF00272 GO:0019731 antibacterial humoral response process
@@ -744,14 +717,12 @@ PF00819 GO:0044564 envenomation resulting in occlusion of the pore of voltage-ga
PF00115 GO:0020037 heme binding function
PF00115 GO:0004129 cytochrome-c oxidase activity function
PF00115 GO:0016021 integral component of membrane component
-PF00115 GO:0055114 oxidation-reduction process process
PF00115 GO:0009060 aerobic respiration process
PF01410 GO:0005201 extracellular matrix structural constituent function
PF01081 GO:0016829 lyase activity function
PF00908 GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity function
PF00255 GO:0006979 response to oxidative stress process
PF00255 GO:0004602 glutathione peroxidase activity function
-PF00255 GO:0055114 oxidation-reduction process process
PF00871 GO:0016774 phosphotransferase activity, carboxyl group as acceptor function
PF00871 GO:0016310 phosphorylation process
PF00871 GO:0016301 kinase activity function
@@ -763,7 +734,7 @@ PF00448 GO:0006614 SRP-dependent cotranslational protein targeting to membrane p
PF00448 GO:0005525 GTP binding function
PF01231 GO:0020037 heme binding function
PF01369 GO:0032012 regulation of ARF protein signal transduction process
-PF01369 GO:0005086 ARF guanyl-nucleotide exchange factor activity function
+PF01369 GO:0005085 guanyl-nucleotide exchange factor activity function
PF03122 GO:0019028 viral capsid component
PF03122 GO:0005198 structural molecule activity function
PF01159 GO:0005840 ribosome component
@@ -797,11 +768,8 @@ PF00659 GO:0005515 protein binding function
PF01258 GO:0008270 zinc ion binding function
PF02067 GO:0046872 metal ion binding function
PF01422 GO:0005634 nucleus component
-PF01422 GO:0006355 regulation of transcription, DNA-templated process
PF01422 GO:0008270 zinc ion binding function
-PF01422 GO:0003700 DNA-binding transcription factor activity function
-PF00601 GO:0042025 host cell nucleus component
-PF00601 GO:0006405 RNA export from nucleus process
+PF00601 GO:0039675 exit of virus from host cell nucleus through nuclear pore process
PF00042 GO:0020037 heme binding function
PF00340 GO:0005615 extracellular space component
PF00340 GO:0005125 cytokine activity function
@@ -848,12 +816,9 @@ PF00503 GO:0019001 guanyl nucleotide binding function
PF00503 GO:0003924 GTPase activity function
PF01477 GO:0005515 protein binding function
PF01426 GO:0003682 chromatin binding function
-PF00669 GO:0071973 bacterial-type flagellum-dependent cell motility process
PF00669 GO:0005198 structural molecule activity function
-PF00700 GO:0071973 bacterial-type flagellum-dependent cell motility process
PF00700 GO:0005198 structural molecule activity function
PF00975 GO:0009058 biosynthetic process process
-PF00975 GO:0016788 hydrolase activity, acting on ester bonds function
PF08220 GO:0006355 regulation of transcription, DNA-templated process
PF08220 GO:0003700 DNA-binding transcription factor activity function
PF00873 GO:0016020 membrane component
@@ -863,7 +828,6 @@ PF00552 GO:0003676 nucleic acid binding function
PF01652 GO:0006413 translational initiation process
PF01652 GO:0003743 translation initiation factor activity function
PF01652 GO:0003723 RNA binding function
-PF00111 GO:0009055 electron transfer activity function
PF00111 GO:0051536 iron-sulfur cluster binding function
PF01566 GO:0016020 membrane component
PF01566 GO:0046873 metal ion transmembrane transporter activity function
@@ -886,11 +850,10 @@ PF01106 GO:0016226 iron-sulfur cluster assembly process
PF01106 GO:0005506 iron ion binding function
PF01106 GO:0051536 iron-sulfur cluster binding function
PF00891 GO:0008171 O-methyltransferase activity function
-PF00198 GO:0016746 transferase activity, transferring acyl groups function
+PF00198 GO:0016746 acyltransferase activity function
PF00337 GO:0030246 carbohydrate binding function
PF00114 GO:0009289 pilus component
PF00114 GO:0007155 cell adhesion process
-PF00649 GO:0042025 host cell nucleus component
PF00649 GO:0003677 DNA binding function
PF00649 GO:0006355 regulation of transcription, DNA-templated process
PF00649 GO:0005507 copper ion binding function
@@ -903,7 +866,6 @@ PF02056 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF02056 GO:0005975 carbohydrate metabolic process process
PF01404 GO:0005515 protein binding function
PF00478 GO:0003824 catalytic activity function
-PF00478 GO:0055114 oxidation-reduction process process
PF03255 GO:0003989 acetyl-CoA carboxylase activity function
PF03255 GO:0009317 acetyl-CoA carboxylase complex component
PF03255 GO:0006633 fatty acid biosynthetic process process
@@ -928,7 +890,6 @@ PF01080 GO:0004190 aspartic-type endopeptidase activity function
PF00709 GO:0006164 purine nucleotide biosynthetic process process
PF00709 GO:0005525 GTP binding function
PF00709 GO:0004019 adenylosuccinate synthase activity function
-PF00394 GO:0055114 oxidation-reduction process process
PF01003 GO:0019028 viral capsid component
PF01003 GO:0005198 structural molecule activity function
PF01810 GO:0016020 membrane component
@@ -939,15 +900,13 @@ PF00358 GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system
PF00067 GO:0020037 heme binding function
PF00067 GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen function
PF00067 GO:0005506 iron ion binding function
-PF00067 GO:0055114 oxidation-reduction process process
+PF00067 GO:0004497 monooxygenase activity function
PF01026 GO:0016788 hydrolase activity, acting on ester bonds function
PF03166 GO:0006355 regulation of transcription, DNA-templated process
PF00346 GO:0016651 oxidoreductase activity, acting on NAD(P)H function
PF00346 GO:0051287 NAD binding function
PF00346 GO:0048038 quinone binding function
-PF00346 GO:0055114 oxidation-reduction process process
PF00985 GO:0007155 cell adhesion process
-PF00172 GO:0005634 nucleus component
PF00172 GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific function
PF00172 GO:0006355 regulation of transcription, DNA-templated process
PF00172 GO:0008270 zinc ion binding function
@@ -955,7 +914,6 @@ PF01777 GO:0005840 ribosome component
PF01777 GO:0006412 translation process
PF01777 GO:0003735 structural constituent of ribosome function
PF01375 GO:0005615 extracellular space component
-PF01375 GO:0009405 pathogenesis process
PF01375 GO:0090729 toxin activity function
PF01157 GO:0005840 ribosome component
PF01157 GO:0006412 translation process
@@ -966,7 +924,6 @@ PF01290 GO:0003785 actin monomer binding function
PF00967 GO:0050832 defense response to fungus process
PF00967 GO:0042742 defense response to bacterium process
PF00724 GO:0010181 FMN binding function
-PF00724 GO:0055114 oxidation-reduction process process
PF00724 GO:0016491 oxidoreductase activity function
PF01412 GO:0005096 GTPase activator activity function
PF01222 GO:0016020 membrane component
@@ -977,8 +934,11 @@ PF00519 GO:0005524 ATP binding function
PF00519 GO:0006260 DNA replication process
PF00519 GO:0003678 DNA helicase activity function
PF00555 GO:0005102 signaling receptor binding function
-PF00555 GO:0009405 pathogenesis process
PF00254 GO:0003755 peptidyl-prolyl cis-trans isomerase activity function
+PF01415 GO:0008083 growth factor activity function
+PF01415 GO:0005576 extracellular region component
+PF01415 GO:0006955 immune response process
+PF01415 GO:0005139 interleukin-7 receptor binding function
PF01098 GO:0051301 cell division process
PF01098 GO:0016021 integral component of membrane component
PF00530 GO:0016020 membrane component
@@ -987,7 +947,6 @@ PF00397 GO:0005515 protein binding function
PF18507 GO:0005515 protein binding function
PF01314 GO:0009055 electron transfer activity function
PF01314 GO:0016625 oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor function
-PF01314 GO:0055114 oxidation-reduction process process
PF01314 GO:0051536 iron-sulfur cluster binding function
PF01314 GO:0016491 oxidoreductase activity function
PF01384 GO:0016020 membrane component
@@ -1002,7 +961,7 @@ PF00872 GO:0004803 transposase activity function
PF00872 GO:0006313 transposition, DNA-mediated process
PF00493 GO:0003677 DNA binding function
PF00493 GO:0005524 ATP binding function
-PF00493 GO:0006270 DNA replication initiation process
+PF00493 GO:0032508 DNA duplex unwinding process
PF00253 GO:0005840 ribosome component
PF00253 GO:0006412 translation process
PF00253 GO:0003735 structural constituent of ribosome function
@@ -1010,6 +969,7 @@ PF00833 GO:0005840 ribosome component
PF00833 GO:0006412 translation process
PF00833 GO:0003735 structural constituent of ribosome function
PF00856 GO:0005515 protein binding function
+PF00937 GO:0003723 RNA binding function
PF00937 GO:0019013 viral nucleocapsid component
PF00139 GO:0030246 carbohydrate binding function
PF01096 GO:0008270 zinc ion binding function
@@ -1018,10 +978,10 @@ PF01096 GO:0003676 nucleic acid binding function
PF00704 GO:0005975 carbohydrate metabolic process process
PF01139 GO:0006396 RNA processing process
PF01139 GO:0008452 RNA ligase activity function
-PF00056 GO:0055114 oxidation-reduction process process
PF00056 GO:0016491 oxidoreductase activity function
PF00697 GO:0004640 phosphoribosylanthranilate isomerase activity function
PF00697 GO:0006568 tryptophan metabolic process process
+PF00668 GO:0003824 catalytic activity function
PF07714 GO:0004672 protein kinase activity function
PF07714 GO:0006468 protein phosphorylation process
PF02133 GO:0016020 membrane component
@@ -1035,19 +995,13 @@ PF00089 GO:0006508 proteolysis process
PF01057 GO:0019079 viral genome replication process
PF01436 GO:0005515 protein binding function
PF01218 GO:0004109 coproporphyrinogen oxidase activity function
-PF01218 GO:0055114 oxidation-reduction process process
PF01218 GO:0006779 porphyrin-containing compound biosynthetic process process
PF01090 GO:0005840 ribosome component
PF01090 GO:0006412 translation process
PF01090 GO:0003735 structural constituent of ribosome function
PF00265 GO:0005524 ATP binding function
PF00265 GO:0004797 thymidine kinase activity function
-PF00329 GO:0055114 oxidation-reduction process process
PF00329 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
-PF01207 GO:0017150 tRNA dihydrouridine synthase activity function
-PF01207 GO:0050660 flavin adenine dinucleotide binding function
-PF01207 GO:0055114 oxidation-reduction process process
-PF01207 GO:0008033 tRNA processing process
PF01293 GO:0005524 ATP binding function
PF01293 GO:0006094 gluconeogenesis process
PF01293 GO:0004612 phosphoenolpyruvate carboxykinase (ATP) activity function
@@ -1068,6 +1022,7 @@ PF02159 GO:0043401 steroid hormone mediated signaling pathway process
PF02159 GO:0005496 steroid binding function
PF02176 GO:0008270 zinc ion binding function
PF15965 GO:0008270 zinc ion binding function
+PF00534 GO:0016757 glycosyltransferase activity function
PF00427 GO:0030089 phycobilisome component
PF00427 GO:0015979 photosynthesis process
PF00811 GO:0007160 cell-matrix adhesion process
@@ -1094,17 +1049,16 @@ PF00432 GO:0003824 catalytic activity function
PF00951 GO:0019031 viral envelope component
PF02074 GO:0006508 proteolysis process
PF02074 GO:0004181 metallocarboxypeptidase activity function
-PF00518 GO:0042025 host cell nucleus component
PF00721 GO:0019028 viral capsid component
PF00721 GO:0005198 structural molecule activity function
PF01185 GO:0009277 fungal-type cell wall component
PF01185 GO:0005199 structural constituent of cell wall function
+PF01331 GO:0005524 ATP binding function
PF01331 GO:0006370 7-methylguanosine mRNA capping process
PF01331 GO:0004484 mRNA guanylyltransferase activity function
PF00742 GO:0006520 cellular amino acid metabolic process process
-PF00742 GO:0055114 oxidation-reduction process process
PF00353 GO:0005509 calcium ion binding function
-PF00605 GO:0044212 transcription regulatory region DNA binding function
+PF00605 GO:0000976 transcription cis-regulatory region binding function
PF01380 GO:1901135 carbohydrate derivative metabolic process process
PF01380 GO:0097367 carbohydrate derivative binding function
PF13580 GO:1901135 carbohydrate derivative metabolic process process
@@ -1115,7 +1069,6 @@ PF02046 GO:0005751 mitochondrial respiratory chain complex IV component
PF00189 GO:0006412 translation process
PF00189 GO:0003735 structural constituent of ribosome function
PF00227 GO:0051603 proteolysis involved in cellular protein catabolic process process
-PF00227 GO:0004298 threonine-type endopeptidase activity function
PF00227 GO:0005839 proteasome core complex component
PF00046 GO:0003677 DNA binding function
PF00232 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
@@ -1155,8 +1108,8 @@ PF00957 GO:0016021 integral component of membrane component
PF00957 GO:0016192 vesicle-mediated transport process
PF00624 GO:0000128 flocculation process
PF01216 GO:0005509 calcium ion binding function
+PF00443 GO:0004843 thiol-dependent deubiquitinase function
PF00443 GO:0016579 protein deubiquitination process
-PF00443 GO:0036459 thiol-dependent ubiquitinyl hydrolase activity function
PF01516 GO:0019028 viral capsid component
PF01516 GO:0005198 structural molecule activity function
PF00103 GO:0005576 extracellular region component
@@ -1166,6 +1119,7 @@ PF00740 GO:0005198 structural molecule activity function
PF00183 GO:0006457 protein folding process
PF00183 GO:0005524 ATP binding function
PF00183 GO:0051082 unfolded protein binding function
+PF00183 GO:0016887 ATPase function
PF00602 GO:0003723 RNA binding function
PF00602 GO:0039694 viral RNA genome replication process
PF00602 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
@@ -1193,7 +1147,6 @@ PF00080 GO:0046872 metal ion binding function
PF01036 GO:0016020 membrane component
PF01036 GO:0005216 ion channel activity function
PF01036 GO:0006811 ion transport process
-PF00175 GO:0055114 oxidation-reduction process process
PF00175 GO:0016491 oxidoreductase activity function
PF01272 GO:0032784 regulation of DNA-templated transcription, elongation process
PF01272 GO:0003677 DNA binding function
@@ -1201,7 +1154,6 @@ PF00515 GO:0005515 protein binding function
PF01255 GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups function
PF01413 GO:0005201 extracellular matrix structural constituent function
PF01413 GO:0005581 collagen trimer component
-PF00460 GO:0071973 bacterial-type flagellum-dependent cell motility process
PF00797 GO:0016407 acetyltransferase activity function
PF00269 GO:0006265 DNA topological change process
PF00269 GO:0003690 double-stranded DNA binding function
@@ -1210,7 +1162,6 @@ PF07653 GO:0005515 protein binding function
PF14604 GO:0005515 protein binding function
PF00851 GO:0006508 proteolysis process
PF00851 GO:0004197 cysteine-type endopeptidase activity function
-PF00499 GO:0055114 oxidation-reduction process process
PF00499 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
PF00905 GO:0008658 penicillin binding function
PF00336 GO:0004523 RNA-DNA hybrid ribonuclease activity function
@@ -1225,21 +1176,20 @@ PF00847 GO:0006355 regulation of transcription, DNA-templated process
PF00847 GO:0003700 DNA-binding transcription factor activity function
PF00595 GO:0005515 protein binding function
PF13180 GO:0005515 protein binding function
-PF02083 GO:0097746 regulation of blood vessel diameter process
+PF02083 GO:0097746 blood vessel diameter maintenance process
PF02083 GO:0008217 regulation of blood pressure process
PF02083 GO:0005576 extracellular region component
PF02083 GO:0005179 hormone activity function
PF01152 GO:0019825 oxygen binding function
PF00439 GO:0005515 protein binding function
PF02048 GO:0005615 extracellular space component
-PF02048 GO:0009405 pathogenesis process
PF02048 GO:0090729 toxin activity function
PF01001 GO:0004252 serine-type endopeptidase activity function
PF01001 GO:0004197 cysteine-type endopeptidase activity function
PF01001 GO:0017111 nucleoside-triphosphatase activity function
PF01001 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF03810 GO:0006886 intracellular protein transport process
-PF03810 GO:0008536 Ran GTPase binding function
+PF03810 GO:0031267 small GTPase binding function
PF02076 GO:0007186 G protein-coupled receptor signaling pathway process
PF02076 GO:0016021 integral component of membrane component
PF02076 GO:0004932 mating-type factor pheromone receptor activity function
@@ -1250,7 +1200,6 @@ PF00852 GO:0008417 fucosyltransferase activity function
PF01400 GO:0006508 proteolysis process
PF01400 GO:0004222 metalloendopeptidase activity function
PF01370 GO:0003824 catalytic activity function
-PF01370 GO:0050662 coenzyme binding function
PF00645 GO:0003677 DNA binding function
PF00645 GO:0008270 zinc ion binding function
PF01655 GO:0005840 ribosome component
@@ -1267,19 +1216,17 @@ PF00145 GO:0008168 methyltransferase activity function
PF02150 GO:0006351 transcription, DNA-templated process
PF01329 GO:0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity function
PF01329 GO:0006729 tetrahydrobiopterin biosynthetic process process
-PF01060 GO:0005615 extracellular space component
+PF01060 GO:0009986 cell surface component
PF00798 GO:0019031 viral envelope component
PF00588 GO:0006396 RNA processing process
PF00588 GO:0003723 RNA binding function
PF00588 GO:0008173 RNA methyltransferase activity function
PF01050 GO:0016779 nucleotidyltransferase activity function
PF01050 GO:0005976 polysaccharide metabolic process process
-PF01136 GO:0006508 proteolysis process
-PF01136 GO:0008233 peptidase activity function
PF01097 GO:0006952 defense response process
PF01063 GO:0003824 catalytic activity function
PF00150 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
-PF00150 GO:0005975 carbohydrate metabolic process process
+PF00150 GO:0071704 organic substance metabolic process process
PF01401 GO:0016020 membrane component
PF01401 GO:0008241 peptidyl-dipeptidase activity function
PF01401 GO:0006508 proteolysis process
@@ -1302,8 +1249,7 @@ PF01907 GO:0005840 ribosome component
PF01907 GO:0006412 translation process
PF01907 GO:0003735 structural constituent of ribosome function
PF02868 GO:0004222 metalloendopeptidase activity function
-PF03832 GO:0006605 protein targeting process
-PF03832 GO:0007165 signal transduction process
+PF03832 GO:0005516 calmodulin binding function
PF00161 GO:0017148 negative regulation of translation process
PF00161 GO:0030598 rRNA N-glycosylase activity function
PF00162 GO:0006096 glycolytic process process
@@ -1312,7 +1258,7 @@ PF01457 GO:0016020 membrane component
PF01457 GO:0007155 cell adhesion process
PF01457 GO:0006508 proteolysis process
PF01457 GO:0004222 metalloendopeptidase activity function
-PF01088 GO:0004843 thiol-dependent ubiquitin-specific protease activity function
+PF01088 GO:0004843 thiol-dependent deubiquitinase function
PF01088 GO:0006511 ubiquitin-dependent protein catabolic process process
PF00262 GO:0006457 protein folding process
PF00262 GO:0005783 endoplasmic reticulum component
@@ -1352,8 +1298,6 @@ PF13855 GO:0005515 protein binding function
PF01146 GO:0070836 caveola assembly process
PF01275 GO:0016021 integral component of membrane component
PF01338 GO:0005576 extracellular region component
-PF01338 GO:0009405 pathogenesis process
-PF00995 GO:0006904 vesicle docking involved in exocytosis process
PF00995 GO:0016192 vesicle-mediated transport process
PF02049 GO:0003774 motor activity function
PF02049 GO:0009288 bacterial-type flagellum component
@@ -1364,7 +1308,6 @@ PF00950 GO:0005887 integral component of plasma membrane component
PF00950 GO:0042626 ATPase-coupled transmembrane transporter activity function
PF00950 GO:0043190 ATP-binding cassette (ABC) transporter complex component
PF01403 GO:0005515 protein binding function
-PF00105 GO:0042025 host cell nucleus component
PF00105 GO:0006355 regulation of transcription, DNA-templated process
PF00105 GO:0043565 sequence-specific DNA binding function
PF00105 GO:0008270 zinc ion binding function
@@ -1399,7 +1342,6 @@ PF02121 GO:0005548 phospholipid transporter activity function
PF01076 GO:0003677 DNA binding function
PF01076 GO:0006310 DNA recombination process
PF00465 GO:0046872 metal ion binding function
-PF00465 GO:0055114 oxidation-reduction process process
PF00465 GO:0016491 oxidoreductase activity function
PF00342 GO:0004347 glucose-6-phosphate isomerase activity function
PF00342 GO:0006094 gluconeogenesis process
@@ -1410,7 +1352,6 @@ PF00958 GO:0006177 GMP biosynthetic process process
PF00958 GO:0006164 purine nucleotide biosynthetic process process
PF00777 GO:0006486 protein glycosylation process
PF00777 GO:0008373 sialyltransferase activity function
-PF00073 GO:0019028 viral capsid component
PF00073 GO:0005198 structural molecule activity function
PF01189 GO:0008168 methyltransferase activity function
PF00400 GO:0005515 protein binding function
@@ -1423,13 +1364,10 @@ PF02154 GO:0003774 motor activity function
PF02154 GO:0071973 bacterial-type flagellum-dependent cell motility process
PF00765 GO:0016740 transferase activity function
PF00146 GO:0016020 membrane component
-PF00146 GO:0055114 oxidation-reduction process process
PF01186 GO:0016641 oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor function
PF01186 GO:0005507 copper ion binding function
-PF01186 GO:0055114 oxidation-reduction process process
PF01115 GO:0051016 barbed-end actin filament capping process
PF01115 GO:0008290 F-actin capping protein complex component
-PF00907 GO:0005634 nucleus component
PF00907 GO:0006355 regulation of transcription, DNA-templated process
PF00907 GO:0003700 DNA-binding transcription factor activity function
PF00759 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
@@ -1462,12 +1400,10 @@ PF00490 GO:0033014 tetrapyrrole biosynthetic process process
PF00490 GO:0004655 porphobilinogen synthase activity function
PF03721 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
PF03721 GO:0051287 NAD binding function
-PF03721 GO:0055114 oxidation-reduction process process
PF00474 GO:0016020 membrane component
PF00474 GO:0055085 transmembrane transport process
PF00474 GO:0022857 transmembrane transporter activity function
PF00614 GO:0003824 catalytic activity function
-PF01429 GO:0042025 host cell nucleus component
PF01429 GO:0003677 DNA binding function
PF00898 GO:0005198 structural molecule activity function
PF01405 GO:0016020 membrane component
@@ -1480,7 +1416,6 @@ PF01347 GO:0006869 lipid transport process
PF01125 GO:0005634 nucleus component
PF00225 GO:0007018 microtubule-based movement process
PF00225 GO:0005524 ATP binding function
-PF00225 GO:0003777 microtubule motor activity function
PF00225 GO:0008017 microtubule binding function
PF00378 GO:0003824 catalytic activity function
PF00215 GO:0004590 orotidine-5'-phosphate decarboxylase activity function
@@ -1509,12 +1444,10 @@ PF00978 GO:0003723 RNA binding function
PF00978 GO:0006351 transcription, DNA-templated process
PF00978 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF00072 GO:0000160 phosphorelay signal transduction system process
-PF00466 GO:0042254 ribosome biogenesis process
PF02123 GO:0003723 RNA binding function
PF02123 GO:0006351 transcription, DNA-templated process
PF02123 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF00186 GO:0046654 tetrahydrofolate biosynthetic process process
-PF00186 GO:0055114 oxidation-reduction process process
PF00186 GO:0004146 dihydrofolate reductase activity function
PF00812 GO:0016020 membrane component
PF01441 GO:0009279 cell outer membrane component
@@ -1536,7 +1469,7 @@ PF15966 GO:0005515 protein binding function
PF00048 GO:0005576 extracellular region component
PF00048 GO:0006955 immune response process
PF00048 GO:0008009 chemokine activity function
-PF00913 GO:0020012 evasion or tolerance of host immune response process
+PF00913 GO:0042783 evasion of host immune response process
PF00413 GO:0031012 extracellular matrix component
PF00413 GO:0006508 proteolysis process
PF00413 GO:0004222 metalloendopeptidase activity function
@@ -1548,7 +1481,6 @@ PF00539 GO:0042025 host cell nucleus component
PF00539 GO:0050434 positive regulation of viral transcription process
PF00539 GO:0001070 RNA-binding transcription regulator activity function
PF01376 GO:0005576 extracellular region component
-PF01376 GO:0009405 pathogenesis process
PF00019 GO:0008083 growth factor activity function
PF02128 GO:0005615 extracellular space component
PF02128 GO:0004222 metalloendopeptidase activity function
@@ -1563,7 +1495,7 @@ PF00949 GO:0003724 RNA helicase activity function
PF02653 GO:0055085 transmembrane transport process
PF02653 GO:0016021 integral component of membrane component
PF02653 GO:0022857 transmembrane transporter activity function
-PF01323 GO:0015035 protein disulfide oxidoreductase activity function
+PF01323 GO:0016491 oxidoreductase activity function
PF00831 GO:0005840 ribosome component
PF00831 GO:0006412 translation process
PF00831 GO:0003735 structural constituent of ribosome function
@@ -1590,7 +1522,6 @@ PF00486 GO:0003677 DNA binding function
PF00486 GO:0000160 phosphorelay signal transduction system process
PF00486 GO:0006355 regulation of transcription, DNA-templated process
PF01289 GO:0015485 cholesterol binding function
-PF01289 GO:0009405 pathogenesis process
PF01252 GO:0016020 membrane component
PF01252 GO:0006508 proteolysis process
PF01252 GO:0004190 aspartic-type endopeptidase activity function
@@ -1628,7 +1559,6 @@ PF00974 GO:0019031 viral envelope component
PF01397 GO:0016829 lyase activity function
PF01397 GO:0010333 terpene synthase activity function
PF01352 GO:0006355 regulation of transcription, DNA-templated process
-PF01352 GO:0003676 nucleic acid binding function
PF01165 GO:0005840 ribosome component
PF01165 GO:0006412 translation process
PF01165 GO:0003735 structural constituent of ribosome function
@@ -1644,13 +1574,12 @@ PF00322 GO:0005576 extracellular region component
PF01249 GO:0005840 ribosome component
PF01249 GO:0006412 translation process
PF01249 GO:0003735 structural constituent of ribosome function
-PF00481 GO:0003824 catalytic activity function
-PF07228 GO:0003824 catalytic activity function
+PF00481 GO:0016791 phosphatase activity function
+PF07228 GO:0016791 phosphatase activity function
PF00616 GO:0043087 regulation of GTPase activity process
PF02151 GO:0005515 protein binding function
PF00451 GO:0008200 ion channel inhibitor activity function
PF00451 GO:0005576 extracellular region component
-PF00451 GO:0009405 pathogenesis process
PF02127 GO:0006508 proteolysis process
PF02127 GO:0004177 aminopeptidase activity function
PF02127 GO:0008270 zinc ion binding function
@@ -1695,7 +1624,6 @@ PF01304 GO:0031412 gas vesicle organization process
PF01304 GO:0031411 gas vesicle component
PF00658 GO:0003723 RNA binding function
PF00906 GO:0005198 structural molecule activity function
-PF00906 GO:0009405 pathogenesis process
PF01318 GO:0019028 viral capsid component
PF01318 GO:0005198 structural molecule activity function
PF01311 GO:0016020 membrane component
@@ -1703,14 +1631,16 @@ PF01311 GO:0006605 protein targeting process
PF00446 GO:0007275 multicellular organism development process
PF00446 GO:0005576 extracellular region component
PF00446 GO:0005179 hormone activity function
-PF02383 GO:0042578 phosphoric ester hydrolase activity function
-PF00790 GO:0006886 intracellular protein transport process
+PF02383 GO:0016791 phosphatase activity function
+PF00790 GO:0043130 ubiquitin binding function
+PF00790 GO:0035091 phosphatidylinositol binding function
PF00141 GO:0006979 response to oxidative stress process
PF00141 GO:0020037 heme binding function
PF00141 GO:0004601 peroxidase activity function
-PF00141 GO:0055114 oxidation-reduction process process
PF00435 GO:0005515 protein binding function
-PF00285 GO:0046912 transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer function
+PF00699 GO:0035550 urease complex component
+PF00699 GO:0043419 urea catabolic process process
+PF00285 GO:0046912 acyltransferase, acyl groups converted into alkyl on transfer function
PF00973 GO:0005198 structural molecule activity function
PF00973 GO:0019013 viral nucleocapsid component
PF00547 GO:0043419 urea catabolic process process
@@ -1729,6 +1659,7 @@ PF00036 GO:0005509 calcium ion binding function
PF13202 GO:0005509 calcium ion binding function
PF13405 GO:0005509 calcium ion binding function
PF13499 GO:0005509 calcium ion binding function
+PF13833 GO:0005509 calcium ion binding function
PF01183 GO:0003796 lysozyme activity function
PF01183 GO:0016998 cell wall macromolecule catabolic process process
PF01183 GO:0009253 peptidoglycan catabolic process process
@@ -1736,9 +1667,11 @@ PF02064 GO:0006886 intracellular protein transport process
PF02064 GO:0006605 protein targeting process
PF02064 GO:0005742 mitochondrial outer membrane translocase complex component
PF00313 GO:0003676 nucleic acid binding function
+PF00494 GO:0009058 biosynthetic process process
+PF00494 GO:0016740 transferase activity function
+PF00537 GO:0044063 modulation by symbiont of host nervous system process process
PF00537 GO:0008200 ion channel inhibitor activity function
PF00537 GO:0005576 extracellular region component
-PF00537 GO:0009405 pathogenesis process
PF00537 GO:0019871 sodium channel inhibitor activity function
PF00714 GO:0005576 extracellular region component
PF00714 GO:0006955 immune response process
@@ -1746,6 +1679,7 @@ PF00714 GO:0005133 interferon-gamma receptor binding function
PF00243 GO:0005102 signaling receptor binding function
PF00233 GO:0007165 signal transduction process
PF00233 GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity function
+PF01151 GO:0009922 fatty acid elongase activity function
PF01151 GO:0016021 integral component of membrane component
PF00158 GO:0005524 ATP binding function
PF00158 GO:0006355 regulation of transcription, DNA-templated process
@@ -1753,7 +1687,6 @@ PF00158 GO:0008134 transcription factor binding function
PF14532 GO:0005524 ATP binding function
PF14532 GO:0006355 regulation of transcription, DNA-templated process
PF14532 GO:0008134 transcription factor binding function
-PF01141 GO:0019028 viral capsid component
PF00917 GO:0005515 protein binding function
PF01340 GO:0006555 methionine metabolic process process
PF01340 GO:0006355 regulation of transcription, DNA-templated process
@@ -1778,23 +1711,22 @@ PF00589 GO:0006310 DNA recombination process
PF00404 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF00404 GO:0000272 polysaccharide catabolic process process
PF00241 GO:0003779 actin binding function
-PF00462 GO:0015035 protein disulfide oxidoreductase activity function
-PF00462 GO:0009055 electron transfer activity function
-PF00462 GO:0045454 cell redox homeostasis process
+PF00462 GO:0097573 glutathione oxidoreductase activity function
PF00023 GO:0005515 protein binding function
PF13606 GO:0005515 protein binding function
PF01372 GO:0004860 protein kinase inhibitor activity function
PF01372 GO:0005576 extracellular region component
PF00570 GO:0003676 nucleic acid binding function
-PF01553 GO:0016746 transferase activity, transferring acyl groups function
+PF01553 GO:0016746 acyltransferase activity function
PF01215 GO:0005740 mitochondrial envelope component
-PF01215 GO:0004129 cytochrome-c oxidase activity function
+PF01215 GO:0006123 mitochondrial electron transport, cytochrome c to oxygen process
+PF01215 GO:0005751 mitochondrial respiratory chain complex IV component
PF00028 GO:0016020 membrane component
PF00028 GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules process
PF00028 GO:0005509 calcium ion binding function
PF00282 GO:0019752 carboxylic acid metabolic process process
-PF00282 GO:0016831 carboxy-lyase activity function
PF00282 GO:0030170 pyridoxal phosphate binding function
+PF00282 GO:0016830 carbon-carbon lyase activity function
PF00160 GO:0003755 peptidyl-prolyl cis-trans isomerase activity function
PF00160 GO:0000413 protein peptidyl-prolyl isomerization process
PF00573 GO:0005840 ribosome component
@@ -1861,12 +1793,9 @@ PF00959 GO:0016998 cell wall macromolecule catabolic process process
PF00959 GO:0009253 peptidoglycan catabolic process process
PF02954 GO:0043565 sequence-specific DNA binding function
PF00964 GO:0005576 extracellular region component
-PF00964 GO:0009405 pathogenesis process
-PF01075 GO:0016757 transferase activity, transferring glycosyl groups function
+PF01075 GO:0016757 glycosyltransferase activity function
PF00368 GO:0015936 coenzyme A metabolic process process
PF00368 GO:0004420 hydroxymethylglutaryl-CoA reductase (NADPH) activity function
-PF00368 GO:0055114 oxidation-reduction process process
-PF00368 GO:0050662 coenzyme binding function
PF00521 GO:0003677 DNA binding function
PF00521 GO:0005524 ATP binding function
PF00521 GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity function
@@ -1876,7 +1805,7 @@ PF00344 GO:0015031 protein transport process
PF00167 GO:0008083 growth factor activity function
PF00500 GO:0019028 viral capsid component
PF00500 GO:0005198 structural molecule activity function
-PF00201 GO:0016758 transferase activity, transferring hexosyl groups function
+PF00201 GO:0008194 UDP-glycosyltransferase activity function
PF00846 GO:0019013 viral nucleocapsid component
PF00130 GO:0035556 intracellular signal transduction process
PF00701 GO:0016829 lyase activity function
@@ -1887,7 +1816,6 @@ PF00014 GO:0004867 serine-type endopeptidase inhibitor activity function
PF01073 GO:0006694 steroid biosynthetic process process
PF01073 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
PF01073 GO:0003854 3-beta-hydroxy-delta5-steroid dehydrogenase activity function
-PF01073 GO:0055114 oxidation-reduction process process
PF00264 GO:0016491 oxidoreductase activity function
PF16499 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF16499 GO:0005975 carbohydrate metabolic process process
@@ -1934,8 +1862,8 @@ PF01333 GO:0005506 iron ion binding function
PF01333 GO:0015979 photosynthesis process
PF02167 GO:0009055 electron transfer activity function
PF02167 GO:0020037 heme binding function
-PF00941 GO:0055114 oxidation-reduction process process
PF00941 GO:0016491 oxidoreductase activity function
+PF00106 GO:0016491 oxidoreductase activity function
PF00050 GO:0005515 protein binding function
PF07648 GO:0005515 protein binding function
PF02087 GO:0070026 nitric oxide binding function
@@ -1951,6 +1879,7 @@ PF00137 GO:1902600 proton transmembrane transport process
PF00137 GO:0033177 proton-transporting two-sector ATPase complex, proton-transporting domain component
PF00137 GO:0015078 proton transmembrane transporter activity function
PF00118 GO:0005524 ATP binding function
+PF00118 GO:0016887 ATPase function
PF00116 GO:0016020 membrane component
PF00116 GO:0005507 copper ion binding function
PF00116 GO:0004129 cytochrome-c oxidase activity function
@@ -1961,7 +1890,6 @@ PF02137 GO:0006396 RNA processing process
PF02137 GO:0003723 RNA binding function
PF02137 GO:0004000 adenosine deaminase activity function
PF00930 GO:0006508 proteolysis process
-PF02089 GO:0098599 palmitoyl hydrolase activity function
PF01472 GO:0003723 RNA binding function
PF01474 GO:0003849 3-deoxy-7-phosphoheptulonate synthase activity function
PF01474 GO:0009073 aromatic amino acid family biosynthetic process process
@@ -1973,7 +1901,6 @@ PF01484 GO:0042302 structural constituent of cuticle function
PF01486 GO:0005634 nucleus component
PF01486 GO:0006355 regulation of transcription, DNA-templated process
PF01486 GO:0003700 DNA-binding transcription factor activity function
-PF01493 GO:0055114 oxidation-reduction process process
PF01493 GO:0016491 oxidoreductase activity function
PF01496 GO:0033179 proton-transporting V-type ATPase, V0 domain component
PF01496 GO:1902600 proton transmembrane transport process
@@ -1981,11 +1908,11 @@ PF01496 GO:0015078 proton transmembrane transporter activity function
PF01498 GO:0015074 DNA integration process
PF01498 GO:0003677 DNA binding function
PF01498 GO:0006313 transposition, DNA-mediated process
-PF01499 GO:0042025 host cell nucleus component
+PF01499 GO:0019028 viral capsid component
PF01499 GO:0019072 viral genome packaging process
PF01500 GO:0045095 keratin filament component
PF13885 GO:0045095 keratin filament component
-PF01501 GO:0016757 transferase activity, transferring glycosyl groups function
+PF01501 GO:0016757 glycosyltransferase activity function
PF01502 GO:0000105 histidine biosynthetic process process
PF01502 GO:0004635 phosphoribosyl-AMP cyclohydrolase activity function
PF01504 GO:0016307 phosphatidylinositol phosphate kinase activity function
@@ -1996,9 +1923,9 @@ PF01510 GO:0008745 N-acetylmuramoyl-L-alanine amidase activity function
PF01510 GO:0009253 peptidoglycan catabolic process process
PF01513 GO:0003951 NAD+ kinase activity function
PF01513 GO:0006741 NADP biosynthetic process process
-PF01515 GO:0016746 transferase activity, transferring acyl groups function
-PF01517 GO:0042025 host cell nucleus component
+PF01515 GO:0016746 acyltransferase activity function
PF01517 GO:0003723 RNA binding function
+PF01517 GO:0046718 viral entry into host cell process
PF01518 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF01518 GO:0003727 single-stranded RNA binding function
PF01520 GO:0008745 N-acetylmuramoyl-L-alanine amidase activity function
@@ -2009,11 +1936,11 @@ PF01523 GO:0006508 proteolysis process
PF01523 GO:0008237 metallopeptidase activity function
PF01524 GO:0060967 negative regulation of gene silencing by RNA process
PF01524 GO:0030430 host cell cytoplasm component
-PF01524 GO:0019048 modulation by virus of host morphology or physiology process
+PF01524 GO:0019048 modulation by virus of host process process
PF01525 GO:0000287 magnesium ion binding function
PF01525 GO:0030430 host cell cytoplasm component
PF01525 GO:0019079 viral genome replication process
-PF01525 GO:0016887 ATPase activity function
+PF01525 GO:0016887 ATPase function
PF01526 GO:0004803 transposase activity function
PF01526 GO:0006313 transposition, DNA-mediated process
PF01527 GO:0003677 DNA binding function
@@ -2022,7 +1949,6 @@ PF01527 GO:0006313 transposition, DNA-mediated process
PF01530 GO:0005634 nucleus component
PF01530 GO:0006355 regulation of transcription, DNA-templated process
PF01530 GO:0008270 zinc ion binding function
-PF01530 GO:0003700 DNA-binding transcription factor activity function
PF01531 GO:0016020 membrane component
PF01531 GO:0008107 galactoside 2-alpha-L-fucosyltransferase activity function
PF01531 GO:0005975 carbohydrate metabolic process process
@@ -2048,13 +1974,13 @@ PF01554 GO:0055085 transmembrane transport process
PF01554 GO:0015297 antiporter activity function
PF01554 GO:0042910 xenobiotic transmembrane transporter activity function
PF01559 GO:0045735 nutrient reservoir activity function
-PF01561 GO:0030683 evasion or tolerance by virus of host immune response process
-PF01561 GO:0019012 virion component
+PF01561 GO:0044423 virion component component
+PF01561 GO:0030683 mitigation of host immune response by virus process
PF01563 GO:0004252 serine-type endopeptidase activity function
PF01563 GO:0055036 virion membrane component
PF01563 GO:0019028 viral capsid component
-PF01567 GO:0030683 evasion or tolerance by virus of host immune response process
-PF01567 GO:0019012 virion component
+PF01567 GO:0044423 virion component component
+PF01567 GO:0030683 mitigation of host immune response by virus process
PF01573 GO:0044156 host cell junction component
PF01573 GO:0046740 transport of virus in host, cell to cell process
PF01577 GO:0006508 proteolysis process
@@ -2067,18 +1993,17 @@ PF01580 GO:0000166 nucleotide binding function
PF01581 GO:0007218 neuropeptide signaling pathway process
PF01584 GO:0007165 signal transduction process
PF01584 GO:0006935 chemotaxis process
-PF01586 GO:0005634 nucleus component
-PF01586 GO:0003677 DNA binding function
-PF01586 GO:0006355 regulation of transcription, DNA-templated process
-PF01586 GO:0007517 muscle organ development process
PF01588 GO:0000049 tRNA binding function
PF01589 GO:0004252 serine-type endopeptidase activity function
PF01589 GO:0055036 virion membrane component
PF01589 GO:0019028 viral capsid component
PF01600 GO:0019064 fusion of virus membrane with host plasma membrane process
-PF01601 GO:0061025 membrane fusion process
+PF01601 GO:0019064 fusion of virus membrane with host plasma membrane process
+PF01601 GO:0055036 virion membrane component
PF01601 GO:0019031 viral envelope component
+PF01601 GO:0075509 endocytosis involved in viral entry into host cell process
PF01601 GO:0016021 integral component of membrane component
+PF01601 GO:0039654 fusion of virus membrane with host endosome membrane process
PF01601 GO:0046813 receptor-mediated virion attachment to host cell process
PF01602 GO:0006886 intracellular protein transport process
PF01602 GO:0030117 membrane coat component
@@ -2087,7 +2012,6 @@ PF01603 GO:0007165 signal transduction process
PF01603 GO:0000159 protein phosphatase type 2A complex component
PF01603 GO:0019888 protein phosphatase regulator activity function
PF01607 GO:0008061 chitin binding function
-PF01607 GO:0006030 chitin metabolic process process
PF01607 GO:0005576 extracellular region component
PF01608 GO:0003779 actin binding function
PF01609 GO:0003677 DNA binding function
@@ -2101,10 +2025,10 @@ PF01621 GO:0016020 membrane component
PF01623 GO:0006355 regulation of transcription, DNA-templated process
PF01623 GO:0003676 nucleic acid binding function
PF01625 GO:0008113 peptide-methionine (S)-S-oxide reductase activity function
-PF01625 GO:0055114 oxidation-reduction process process
-PF01635 GO:0019058 viral life cycle process
+PF01635 GO:0055036 virion membrane component
+PF01635 GO:0039660 structural constituent of virion function
+PF01635 GO:0016021 integral component of membrane component
PF01641 GO:0033743 peptide-methionine (R)-S-oxide reductase activity function
-PF01641 GO:0055114 oxidation-reduction process process
PF01649 GO:0005840 ribosome component
PF01649 GO:0003723 RNA binding function
PF01649 GO:0006412 translation process
@@ -2128,12 +2052,12 @@ PF01671 GO:0042330 taxis process
PF01673 GO:0019031 viral envelope component
PF01686 GO:0075509 endocytosis involved in viral entry into host cell process
PF01686 GO:0039623 T=25 icosahedral viral capsid component
-PF01692 GO:0030683 evasion or tolerance by virus of host immune response process
+PF01692 GO:0030683 mitigation of host immune response by virus process
PF01695 GO:0005524 ATP binding function
PF01700 GO:0005198 structural molecule activity function
PF01701 GO:0009522 photosystem I component
PF01701 GO:0015979 photosynthesis process
-PF01702 GO:0016763 transferase activity, transferring pentosyl groups function
+PF01702 GO:0016763 pentosyltransferase activity function
PF01702 GO:0006400 tRNA modification process
PF01704 GO:0070569 uridylyltransferase activity function
PF01708 GO:0016021 integral component of membrane component
@@ -2152,9 +2076,9 @@ PF01719 GO:0003916 DNA topoisomerase activity function
PF01721 GO:0005576 extracellular region component
PF01721 GO:0042742 defense response to bacterium process
PF01723 GO:0007304 chorion-containing eggshell formation process
-PF01723 GO:0005213 structural constituent of chorion function
+PF01723 GO:0005213 structural constituent of egg chorion function
PF01723 GO:0007275 multicellular organism development process
-PF01723 GO:0042600 chorion component
+PF01723 GO:0042600 egg chorion component
PF01725 GO:0009143 nucleoside triphosphate catabolic process process
PF01725 GO:0047429 nucleoside-triphosphate diphosphatase activity function
PF01729 GO:0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity function
@@ -2180,11 +2104,11 @@ PF01754 GO:0008270 zinc ion binding function
PF01756 GO:0006635 fatty acid beta-oxidation process
PF01756 GO:0003997 acyl-CoA oxidase activity function
PF01756 GO:0005777 peroxisome component
-PF01757 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF01757 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF01758 GO:0016020 membrane component
PF01762 GO:0016020 membrane component
PF01762 GO:0006486 protein glycosylation process
-PF01762 GO:0008378 galactosyltransferase activity function
+PF01762 GO:0016758 hexosyltransferase activity function
PF01763 GO:0006323 DNA packaging process
PF01766 GO:0005198 structural molecule activity function
PF01767 GO:0005198 structural molecule activity function
@@ -2209,12 +2133,11 @@ PF01782 GO:0006364 rRNA processing process
PF01783 GO:0015934 large ribosomal subunit component
PF01783 GO:0006412 translation process
PF01783 GO:0003735 structural constituent of ribosome function
-PF01785 GO:0019012 virion component
-PF01786 GO:0055114 oxidation-reduction process process
+PF01785 GO:0044423 virion component component
PF01786 GO:0009916 alternative oxidase activity function
PF01787 GO:0006413 translational initiation process
PF01787 GO:0003723 RNA binding function
-PF01787 GO:0019012 virion component
+PF01787 GO:0044423 virion component component
PF01788 GO:0016020 membrane component
PF01788 GO:0009539 photosystem II reaction center component
PF01788 GO:0009523 photosystem II component
@@ -2281,22 +2204,18 @@ PF01867 GO:0003676 nucleic acid binding function
PF01868 GO:0006396 RNA processing process
PF01868 GO:0003723 RNA binding function
PF01868 GO:0030677 ribonuclease P complex component
-PF01868 GO:0004540 ribonuclease activity function
+PF01868 GO:0001682 tRNA 5'-leader removal process
PF01872 GO:0009231 riboflavin biosynthetic process process
PF01872 GO:0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity function
-PF01872 GO:0055114 oxidation-reduction process process
PF01873 GO:0006413 translational initiation process
PF01873 GO:0003743 translation initiation factor activity function
PF01874 GO:0016310 phosphorylation process
PF01874 GO:0046917 triphosphoribosyl-dephospho-CoA synthase activity function
PF01874 GO:0005524 ATP binding function
-PF01876 GO:0004526 ribonuclease P activity function
PF01876 GO:0008033 tRNA processing process
PF01880 GO:0005506 iron ion binding function
-PF01880 GO:0055114 oxidation-reduction process process
PF01880 GO:0016491 oxidoreductase activity function
-PF01885 GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation process
-PF01885 GO:0016772 transferase activity, transferring phosphorus-containing groups function
+PF01885 GO:0016740 transferase activity function
PF01888 GO:0008168 methyltransferase activity function
PF01888 GO:0009236 cobalamin biosynthetic process process
PF01890 GO:0009236 cobalamin biosynthetic process process
@@ -2307,10 +2226,9 @@ PF01896 GO:0003896 DNA primase activity function
PF01899 GO:0016021 integral component of membrane component
PF01899 GO:0006812 cation transport process
PF01899 GO:0008324 cation transmembrane transporter activity function
-PF01900 GO:0004540 ribonuclease activity function
-PF01900 GO:0008033 tRNA processing process
-PF01903 GO:0009236 cobalamin biosynthetic process process
-PF01903 GO:0016852 sirohydrochlorin cobaltochelatase activity function
+PF01900 GO:0030677 ribonuclease P complex component
+PF01900 GO:0001682 tRNA 5'-leader removal process
+PF01903 GO:0016829 lyase activity function
PF01912 GO:0043022 ribosome binding function
PF01912 GO:0042256 mature ribosome assembly process
PF02741 GO:0006730 one-carbon metabolic process process
@@ -2341,7 +2259,6 @@ PF01958 GO:0033735 aspartate dehydrogenase activity function
PF01958 GO:0009435 NAD biosynthetic process process
PF01959 GO:0009073 aromatic amino acid family biosynthetic process process
PF01959 GO:0003856 3-dehydroquinate synthase activity function
-PF01959 GO:0055114 oxidation-reduction process process
PF01959 GO:0016491 oxidoreductase activity function
PF01960 GO:0004358 glutamate N-acetyltransferase activity function
PF01960 GO:0006526 arginine biosynthetic process process
@@ -2353,14 +2270,13 @@ PF01972 GO:0016021 integral component of membrane component
PF01975 GO:0016787 hydrolase activity function
PF01977 GO:0016831 carboxy-lyase activity function
PF01981 GO:0004045 aminoacyl-tRNA hydrolase activity function
-PF01983 GO:0016779 nucleotidyltransferase activity function
+PF01983 GO:0043814 phospholactate guanylyltransferase activity function
PF01984 GO:0003677 DNA binding function
PF01991 GO:0033178 proton-transporting two-sector ATPase complex, catalytic domain component
PF01991 GO:1902600 proton transmembrane transport process
PF01991 GO:0046961 proton-transporting ATPase activity, rotational mechanism function
PF01993 GO:0008901 ferredoxin hydrogenase activity function
PF01993 GO:0015948 methanogenesis process
-PF01993 GO:0055114 oxidation-reduction process process
PF01994 GO:0002128 tRNA nucleoside ribose methylation process
PF01994 GO:0008175 tRNA methyltransferase activity function
PF01994 GO:0005737 cytoplasm component
@@ -2380,12 +2296,11 @@ PF01665 GO:0003723 RNA binding function
PF01688 GO:0043657 host cell component
PF01728 GO:0008168 methyltransferase activity function
PF01728 GO:0032259 methylation process
-PF01855 GO:0055114 oxidation-reduction process process
PF01855 GO:0016491 oxidoreductase activity function
+PF01933 GO:0043743 LPPG:FO 2-phospho-L-lactate transferase activity function
PF01483 GO:0004252 serine-type endopeptidase activity function
PF01483 GO:0006508 proteolysis process
PF01799 GO:0046872 metal ion binding function
-PF01799 GO:0055114 oxidation-reduction process process
PF01799 GO:0016491 oxidoreductase activity function
PF01835 GO:0004866 endopeptidase inhibitor activity function
PF01537 GO:0016021 integral component of membrane component
@@ -2406,61 +2321,54 @@ PF01491 GO:0016226 iron-sulfur cluster assembly process
PF01491 GO:0008199 ferric iron binding function
PF01852 GO:0008289 lipid binding function
PF01791 GO:0016829 lyase activity function
+PF01674 GO:0016042 lipid catabolic process process
PF01674 GO:0016787 hydrolase activity function
PF01764 GO:0006629 lipid metabolic process process
PF01691 GO:0019050 suppression by virus of host apoptotic process process
PF01738 GO:0016787 hydrolase activity function
PF01576 GO:0016459 myosin complex component
-PF01576 GO:0003774 motor activity function
PF01690 GO:0019028 viral capsid component
PF01645 GO:0015930 glutamate synthase activity function
PF01645 GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors function
PF01645 GO:0006537 glutamate biosynthetic process process
-PF01645 GO:0055114 oxidation-reduction process process
PF01546 GO:0016787 hydrolase activity function
PF01909 GO:0016779 nucleotidyltransferase activity function
PF01596 GO:0008171 O-methyltransferase activity function
-PF01593 GO:0055114 oxidation-reduction process process
PF01593 GO:0016491 oxidoreductase activity function
PF01494 GO:0071949 FAD binding function
PF01555 GO:0003677 DNA binding function
PF01555 GO:0008170 N-methyltransferase activity function
PF01555 GO:0006306 DNA methylation process
PF01479 GO:0003723 RNA binding function
-PF02098 GO:0030682 evasion or tolerance of host defenses process
+PF02098 GO:0030682 mitigation of host defenses by symbiont process
PF02098 GO:0043176 amine binding function
-PF01468 GO:0009405 pathogenesis process
PF02100 GO:0008073 ornithine decarboxylase inhibitor activity function
PF02104 GO:0016020 membrane component
PF02077 GO:0016021 integral component of membrane component
PF02146 GO:0070403 NAD+ binding function
+PF00091 GO:0005525 GTP binding function
PF00091 GO:0003924 GTPase activity function
PF00795 GO:0006807 nitrogen compound metabolic process process
PF01590 GO:0005515 protein binding function
PF13185 GO:0005515 protein binding function
PF13492 GO:0005515 protein binding function
PF00131 GO:0046872 metal ion binding function
-PF02144 GO:0042025 host cell nucleus component
-PF02144 GO:0000077 DNA damage checkpoint process
+PF02144 GO:0000077 DNA damage checkpoint signaling process
PF00575 GO:0003676 nucleic acid binding function
PF02093 GO:0019068 virion assembly process
PF02109 GO:0008250 oligosaccharyltransferase complex component
-PF02109 GO:0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity function
PF02109 GO:0016021 integral component of membrane component
PF02402 GO:0019867 outer membrane component
PF02402 GO:0019835 cytolysis process
-PF02402 GO:0009405 pathogenesis process
PF03526 GO:0015643 toxic substance binding function
PF03526 GO:0030153 bacteriocin immunity process
PF03513 GO:0015643 toxic substance binding function
PF03513 GO:0030153 bacteriocin immunity process
PF00525 GO:0005212 structural constituent of eye lens function
PF02180 GO:0042981 regulation of apoptotic process process
-PF00667 GO:0055114 oxidation-reduction process process
PF00667 GO:0016491 oxidoreductase activity function
PF02153 GO:0006571 tyrosine biosynthetic process process
PF02153 GO:0008977 prephenate dehydrogenase (NAD+) activity function
-PF02153 GO:0055114 oxidation-reduction process process
PF02153 GO:0004665 prephenate dehydrogenase (NADP+) activity function
PF02170 GO:0005515 protein binding function
PF02172 GO:0006355 regulation of transcription, DNA-templated process
@@ -2470,7 +2378,6 @@ PF02173 GO:0006355 regulation of transcription, DNA-templated process
PF02179 GO:0051087 chaperone binding function
PF02183 GO:0006355 regulation of transcription, DNA-templated process
PF02183 GO:0043565 sequence-specific DNA binding function
-PF02183 GO:0003700 DNA-binding transcription factor activity function
PF02184 GO:0006396 RNA processing process
PF02187 GO:0008017 microtubule binding function
PF02188 GO:0030695 GTPase regulator activity function
@@ -2478,12 +2385,10 @@ PF02189 GO:0016020 membrane component
PF02189 GO:0004888 transmembrane signaling receptor activity function
PF02189 GO:0007166 cell surface receptor signaling pathway process
PF02196 GO:0007165 signal transduction process
-PF02198 GO:0042025 host cell nucleus component
PF02198 GO:0043565 sequence-specific DNA binding function
PF02200 GO:0005634 nucleus component
PF02200 GO:0006355 regulation of transcription, DNA-templated process
PF02200 GO:0003700 DNA-binding transcription factor activity function
-PF02201 GO:0005515 protein binding function
PF02203 GO:0007165 signal transduction process
PF02203 GO:0006935 chemotaxis process
PF02205 GO:0003779 actin binding function
@@ -2494,7 +2399,6 @@ PF02212 GO:0005525 GTP binding function
PF02212 GO:0003924 GTPase activity function
PF02214 GO:0051260 protein homooligomerization process
PF02216 GO:0019865 immunoglobulin binding function
-PF02216 GO:0009405 pathogenesis process
PF02217 GO:0003688 DNA replication origin binding function
PF02217 GO:0006260 DNA replication process
PF02226 GO:0019028 viral capsid component
@@ -2503,8 +2407,6 @@ PF02228 GO:0005198 structural molecule activity function
PF02228 GO:0019013 viral nucleocapsid component
PF02230 GO:0016787 hydrolase activity function
PF02237 GO:0006464 cellular protein modification process process
-PF02244 GO:0004180 carboxypeptidase activity function
-PF02244 GO:0006508 proteolysis process
PF02254 GO:0006813 potassium ion transport process
PF02257 GO:0003677 DNA binding function
PF02257 GO:0006355 regulation of transcription, DNA-templated process
@@ -2515,7 +2417,7 @@ PF02265 GO:0006308 DNA catabolic process process
PF02265 GO:0004519 endonuclease activity function
PF02265 GO:0003676 nucleic acid binding function
PF02272 GO:0003676 nucleic acid binding function
-PF02273 GO:0016746 transferase activity, transferring acyl groups function
+PF02273 GO:0016746 acyltransferase activity function
PF02273 GO:0006631 fatty acid metabolic process process
PF02276 GO:0009055 electron transfer activity function
PF02276 GO:0020037 heme binding function
@@ -2533,14 +2435,13 @@ PF02186 GO:0006367 transcription initiation from RNA polymerase II promoter proc
PF02213 GO:0005515 protein binding function
PF02219 GO:0006555 methionine metabolic process process
PF02219 GO:0004489 methylenetetrahydrofolate reductase (NAD(P)H) activity function
-PF02219 GO:0055114 oxidation-reduction process process
PF02229 GO:0003677 DNA binding function
PF02229 GO:0006355 regulation of transcription, DNA-templated process
PF02232 GO:0003677 DNA binding function
PF02232 GO:0006355 regulation of transcription, DNA-templated process
PF02234 GO:0005634 nucleus component
PF02234 GO:0004861 cyclin-dependent protein serine/threonine kinase inhibitor activity function
-PF02234 GO:0007050 cell cycle arrest process
+PF02234 GO:0051726 regulation of cell cycle process
PF02236 GO:0003677 DNA binding function
PF02236 GO:0006268 DNA unwinding involved in DNA replication process
PF02240 GO:0015948 methanogenesis process
@@ -2574,17 +2475,17 @@ PF02267 GO:0003953 NAD+ nucleosidase activity function
PF02269 GO:0006366 transcription by RNA polymerase II process
PF02271 GO:0005750 mitochondrial respiratory chain complex III component
PF02271 GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c process
-PF02277 GO:0009236 cobalamin biosynthetic process process
PF02277 GO:0008939 nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity function
PF02282 GO:0003677 DNA binding function
PF02282 GO:0006260 DNA replication process
-PF02283 GO:0051188 cofactor biosynthetic process process
PF02283 GO:0000166 nucleotide binding function
PF02283 GO:0043752 adenosylcobinamide kinase activity function
PF02283 GO:0009236 cobalamin biosynthetic process process
-PF02284 GO:0004129 cytochrome-c oxidase activity function
+PF02284 GO:0006123 mitochondrial electron transport, cytochrome c to oxygen process
PF02284 GO:0005743 mitochondrial inner membrane component
-PF02285 GO:0004129 cytochrome-c oxidase activity function
+PF02284 GO:0005751 mitochondrial respiratory chain complex IV component
+PF02285 GO:0006123 mitochondrial electron transport, cytochrome c to oxygen process
+PF02285 GO:0005751 mitochondrial respiratory chain complex IV component
PF02286 GO:0031419 cobalamin binding function
PF02286 GO:0016836 hydro-lyase activity function
PF02289 GO:0006730 one-carbon metabolic process process
@@ -2596,6 +2497,7 @@ PF02290 GO:0008312 7S RNA binding function
PF02293 GO:0016020 membrane component
PF02294 GO:0004521 endoribonuclease activity function
PF02294 GO:0003677 DNA binding function
+PF02297 GO:0045277 respiratory chain complex IV component
PF02297 GO:0005739 mitochondrion component
PF03811 GO:0006313 transposition, DNA-mediated process
PF03589 GO:0003677 DNA binding function
@@ -2610,7 +2512,6 @@ PF03488 GO:0005576 extracellular region component
PF03488 GO:0005179 hormone activity function
PF02298 GO:0009055 electron transfer activity function
PF02915 GO:0046872 metal ion binding function
-PF02915 GO:0055114 oxidation-reduction process process
PF02915 GO:0016491 oxidoreductase activity function
PF17136 GO:0005840 ribosome component
PF17136 GO:0006412 translation process
@@ -2618,28 +2519,21 @@ PF17136 GO:0003735 structural constituent of ribosome function
PF00730 GO:0006284 base-excision repair process
PF03534 GO:0005737 cytoplasm component
PF02430 GO:0016020 membrane component
-PF02430 GO:0009405 pathogenesis process
PF03516 GO:0005198 structural molecule activity function
PF02018 GO:0016798 hydrolase activity, acting on glycosyl bonds function
PF02020 GO:0005515 protein binding function
PF02022 GO:0008270 zinc ion binding function
-PF02023 GO:0006355 regulation of transcription, DNA-templated process
-PF02023 GO:0003700 DNA-binding transcription factor activity function
PF02311 GO:0006355 regulation of transcription, DNA-templated process
PF02316 GO:0003677 DNA binding function
-PF02319 GO:0005667 transcription factor complex component
+PF02319 GO:0005667 transcription regulator complex component
PF02319 GO:0006355 regulation of transcription, DNA-templated process
-PF02319 GO:0003700 DNA-binding transcription factor activity function
PF02322 GO:0016020 membrane component
-PF02322 GO:0055114 oxidation-reduction process process
PF02324 GO:0046527 glucosyltransferase activity function
PF02324 GO:0009250 glucan biosynthetic process process
PF02335 GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity function
PF02335 GO:0006807 nitrogen compound metabolic process process
-PF02335 GO:0055114 oxidation-reduction process process
PF02335 GO:0042597 periplasmic space component
PF02337 GO:0005198 structural molecule activity function
-PF02344 GO:0042025 host cell nucleus component
PF02344 GO:0006355 regulation of transcription, DNA-templated process
PF02344 GO:0003700 DNA-binding transcription factor activity function
PF02354 GO:0016020 membrane component
@@ -2690,12 +2584,11 @@ PF02429 GO:0030076 light-harvesting complex component
PF02429 GO:0018298 protein-chromophore linkage process
PF03311 GO:0016192 vesicle-mediated transport process
PF02434 GO:0016020 membrane component
-PF02434 GO:0016757 transferase activity, transferring glycosyl groups function
+PF02434 GO:0016757 glycosyltransferase activity function
PF02438 GO:0003723 RNA binding function
PF02438 GO:0039657 suppression by virus of host gene expression process
PF02438 GO:0039704 viral translational shunt process
PF02441 GO:0003824 catalytic activity function
-PF02443 GO:0042025 host cell nucleus component
PF02443 GO:0019069 viral capsid assembly process
PF02444 GO:0030430 host cell cytoplasm component
PF02446 GO:0005975 carbohydrate metabolic process process
@@ -2709,13 +2602,12 @@ PF02460 GO:0016021 integral component of membrane component
PF02462 GO:0016020 membrane component
PF02462 GO:0015288 porin activity function
PF02468 GO:0016020 membrane component
-PF02468 GO:0009539 photosystem II reaction center component
-PF02468 GO:0009523 photosystem II component
PF02468 GO:0015979 photosynthesis process
PF02472 GO:0055085 transmembrane transport process
PF02472 GO:0022857 transmembrane transporter activity function
+PF02479 GO:0010468 regulation of gene expression process
PF02485 GO:0016020 membrane component
-PF02485 GO:0008375 acetylglucosaminyltransferase activity function
+PF02485 GO:0016757 glycosyltransferase activity function
PF02497 GO:0019031 viral envelope component
PF02501 GO:0015628 protein secretion by the type II secretion system process
PF02501 GO:0015627 type II protein secretion system complex component
@@ -2726,9 +2618,6 @@ PF02313 GO:0016020 membrane component
PF02313 GO:0006106 fumarate metabolic process process
PF02315 GO:0004022 alcohol dehydrogenase (NAD+) activity function
PF02315 GO:0015946 methanol oxidation process
-PF02315 GO:0055114 oxidation-reduction process process
-PF02317 GO:0055114 oxidation-reduction process process
-PF02317 GO:0050662 coenzyme binding function
PF02317 GO:0016491 oxidoreductase activity function
PF02321 GO:0055085 transmembrane transport process
PF02321 GO:0015562 efflux transmembrane transporter activity function
@@ -2743,16 +2632,15 @@ PF02330 GO:0005759 mitochondrial matrix component
PF02331 GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process function
PF02331 GO:0043066 negative regulation of apoptotic process process
PF02332 GO:0006725 cellular aromatic compound metabolic process process
-PF02332 GO:0055114 oxidation-reduction process process
PF02333 GO:0016158 3-phytase activity function
PF02334 GO:0003677 DNA binding function
PF02334 GO:0006274 DNA replication termination process
-PF02336 GO:0019028 viral capsid component
PF02336 GO:0005198 structural molecule activity function
+PF02341 GO:0110102 ribulose bisphosphate carboxylase complex assembly process
+PF02341 GO:0044183 protein folding chaperone function
PF02346 GO:0019064 fusion of virus membrane with host plasma membrane process
PF02346 GO:0019031 viral envelope component
PF00005 GO:0005524 ATP binding function
-PF00005 GO:0016887 ATPase activity function
PF02364 GO:0016020 membrane component
PF02364 GO:0006075 (1->3)-beta-D-glucan biosynthetic process process
PF02364 GO:0003843 1,3-beta-D-glucan synthase activity function
@@ -2768,7 +2656,7 @@ PF02386 GO:0006812 cation transport process
PF02386 GO:0008324 cation transmembrane transporter activity function
PF02387 GO:0006276 plasmid maintenance process
PF02388 GO:0044038 cell wall macromolecule biosynthetic process process
-PF02388 GO:0016755 transferase activity, transferring amino-acyl groups function
+PF02388 GO:0016755 aminoacyltransferase activity function
PF02391 GO:0006777 Mo-molybdopterin cofactor biosynthetic process process
PF02399 GO:0003688 DNA replication origin binding function
PF02399 GO:0005524 ATP binding function
@@ -2799,12 +2687,11 @@ PF02447 GO:0016020 membrane component
PF02447 GO:0035429 gluconate transmembrane transport process
PF02447 GO:0015128 gluconate transmembrane transporter activity function
PF02452 GO:0003677 DNA binding function
-PF02454 GO:0019048 modulation by virus of host morphology or physiology process
+PF02454 GO:0019048 modulation by virus of host process process
PF02455 GO:0019028 viral capsid component
-PF02458 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF02458 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF02465 GO:0009424 bacterial-type flagellum hook component
-PF02474 GO:0009877 nodulation process
-PF02474 GO:0016746 transferase activity, transferring acyl groups function
+PF02474 GO:0016746 acyltransferase activity function
PF02474 GO:0005829 cytosol component
PF02477 GO:0019013 viral nucleocapsid component
PF02478 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
@@ -2831,9 +2718,8 @@ PF02300 GO:0016020 membrane component
PF02303 GO:0003697 single-stranded DNA binding function
PF02303 GO:0006260 DNA replication process
PF02304 GO:0019069 viral capsid assembly process
-PF02304 GO:0046729 viral procapsid component
PF02305 GO:0005198 structural molecule activity function
-PF02306 GO:0019048 modulation by virus of host morphology or physiology process
+PF02306 GO:0019048 modulation by virus of host process process
PF03511 GO:0043240 Fanconi anaemia nuclear complex component
PF03511 GO:0036297 interstrand cross-link repair process
PF03503 GO:0005201 extracellular matrix structural constituent function
@@ -2842,15 +2728,13 @@ PF02542 GO:0016114 terpenoid biosynthetic process process
PF03607 GO:0035556 intracellular signal transduction process
PF03549 GO:0005515 protein binding function
PF03496 GO:0005576 extracellular region component
-PF03496 GO:0009405 pathogenesis process
PF03523 GO:0016020 membrane component
PF03523 GO:0005044 scavenger receptor activity function
PF03523 GO:0006898 receptor-mediated endocytosis process
PF03379 GO:0016020 membrane component
-PF03379 GO:0015232 heme transporter activity function
+PF03379 GO:0015232 heme transmembrane transporter activity function
PF03379 GO:0017004 cytochrome complex assembly process
PF03379 GO:0015886 heme transport process
-PF03498 GO:0009405 pathogenesis process
PF00489 GO:0072540 T-helper 17 cell lineage commitment process
PF00489 GO:0005615 extracellular space component
PF00489 GO:0005138 interleukin-6 receptor binding function
@@ -2883,10 +2767,12 @@ PF03106 GO:0043565 sequence-specific DNA binding function
PF03106 GO:0003700 DNA-binding transcription factor activity function
PF00672 GO:0007165 signal transduction process
PF00672 GO:0016021 integral component of membrane component
+PF18947 GO:0007165 signal transduction process
+PF18947 GO:0016021 integral component of membrane component
PF00512 GO:0000155 phosphorelay sensor kinase activity function
PF00512 GO:0007165 signal transduction process
PF02504 GO:0006633 fatty acid biosynthetic process process
-PF02504 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF02504 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF02504 GO:0003824 catalytic activity function
PF02507 GO:0009538 photosystem I reaction center component
PF02507 GO:0009522 photosystem I component
@@ -2899,12 +2785,12 @@ PF02511 GO:0050797 thymidylate synthase (FAD) activity function
PF02511 GO:0050660 flavin adenine dinucleotide binding function
PF02513 GO:0007276 gamete generation process
PF02514 GO:0009058 biosynthetic process process
-PF02515 GO:0008410 CoA-transferase activity function
+PF02515 GO:0003824 catalytic activity function
PF02516 GO:0016020 membrane component
PF02516 GO:0006486 protein glycosylation process
PF02516 GO:0004576 oligosaccharyl transferase activity function
PF02517 GO:0016020 membrane component
-PF02517 GO:0004197 cysteine-type endopeptidase activity function
+PF02517 GO:0004222 metalloendopeptidase activity function
PF02517 GO:0071586 CAAX-box protein processing process
PF02519 GO:0009733 response to auxin process
PF02522 GO:0046677 response to antibiotic process
@@ -2927,7 +2813,6 @@ PF02533 GO:0009539 photosystem II reaction center component
PF02533 GO:0009523 photosystem II component
PF02533 GO:0015979 photosynthesis process
PF02534 GO:0016020 membrane component
-PF02534 GO:0009291 unidirectional conjugation process
PF02535 GO:0016020 membrane component
PF02535 GO:0055085 transmembrane transport process
PF02535 GO:0046873 metal ion transmembrane transporter activity function
@@ -2939,7 +2824,6 @@ PF02538 GO:0003824 catalytic activity function
PF02543 GO:0009058 biosynthetic process process
PF02543 GO:0003824 catalytic activity function
PF02545 GO:0047429 nucleoside-triphosphate diphosphatase activity function
-PF02547 GO:0008616 queuosine biosynthetic process process
PF02547 GO:0016853 isomerase activity function
PF02547 GO:0016740 transferase activity function
PF02548 GO:0015940 pantothenate biosynthetic process process
@@ -2976,7 +2860,6 @@ PF02570 GO:0016993 precorrin-8X methylmutase activity function
PF02570 GO:0009236 cobalamin biosynthetic process process
PF02571 GO:0016994 precorrin-6A reductase activity function
PF02571 GO:0009236 cobalamin biosynthetic process process
-PF02571 GO:0055114 oxidation-reduction process process
PF02572 GO:0005524 ATP binding function
PF02572 GO:0009236 cobalamin biosynthetic process process
PF02572 GO:0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity function
@@ -2987,6 +2870,9 @@ PF02580 GO:0051499 D-aminoacyl-tRNA deacylase activity function
PF02583 GO:0046872 metal ion binding function
PF02583 GO:0003677 DNA binding function
PF02583 GO:0006355 regulation of transcription, DNA-templated process
+PF02586 GO:0003697 single-stranded DNA binding function
+PF02586 GO:0006974 cellular response to DNA damage stimulus process
+PF02586 GO:0018142 protein-DNA covalent cross-linking process
PF02590 GO:0008168 methyltransferase activity function
PF02590 GO:0006364 rRNA processing process
PF02592 GO:1990397 queuosine salvage process
@@ -2994,7 +2880,7 @@ PF02599 GO:0003723 RNA binding function
PF02599 GO:0006109 regulation of carbohydrate metabolic process process
PF02599 GO:0006402 mRNA catabolic process process
PF02600 GO:0006457 protein folding process
-PF02600 GO:0015035 protein disulfide oxidoreductase activity function
+PF02600 GO:0015035 protein-disulfide reductase activity function
PF02600 GO:0016021 integral component of membrane component
PF02602 GO:0033014 tetrapyrrole biosynthetic process process
PF02602 GO:0004852 uroporphyrinogen-III synthase activity function
@@ -3014,18 +2900,13 @@ PF02611 GO:0008654 phospholipid biosynthetic process process
PF02611 GO:0008715 CDP-diacylglycerol diphosphatase activity function
PF02614 GO:0006064 glucuronate catabolic process process
PF02614 GO:0008880 glucuronate isomerase activity function
-PF02615 GO:0055114 oxidation-reduction process process
PF02615 GO:0016491 oxidoreductase activity function
PF02617 GO:0030163 protein catabolic process process
PF02623 GO:0044780 bacterial-type flagellum assembly process
-PF02627 GO:0055114 oxidation-reduction process process
PF02627 GO:0051920 peroxiredoxin activity function
-PF02628 GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors function
-PF02628 GO:0006784 heme a biosynthetic process process
+PF02628 GO:0006784 heme A biosynthetic process process
PF02628 GO:0016021 integral component of membrane component
-PF02628 GO:0055114 oxidation-reduction process process
-PF02629 GO:0048037 cofactor binding function
-PF13380 GO:0048037 cofactor binding function
+PF02628 GO:0016653 oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor function
PF02631 GO:0006282 regulation of DNA repair process
PF02632 GO:0015878 biotin transport process
PF02632 GO:0015225 biotin transmembrane transporter activity function
@@ -3036,24 +2917,21 @@ PF02652 GO:0005887 integral component of plasma membrane component
PF02652 GO:0015129 lactate transmembrane transporter activity function
PF02652 GO:0015727 lactate transport process
PF02654 GO:0008818 cobalamin 5'-phosphate synthase activity function
-PF02654 GO:0009236 cobalamin biosynthetic process process
PF02654 GO:0051073 adenosylcobinamide-GDP ribazoletransferase activity function
PF02655 GO:0046872 metal ion binding function
PF02655 GO:0005524 ATP binding function
PF02660 GO:0008654 phospholipid biosynthetic process process
PF02660 GO:0043772 acyl-phosphate glycerol-3-phosphate acyltransferase activity function
PF02660 GO:0005886 plasma membrane component
-PF02662 GO:0055114 oxidation-reduction process process
PF02664 GO:0043768 S-ribosylhomocysteine lyase activity function
PF02664 GO:0005506 iron ion binding function
PF02664 GO:0009372 quorum sensing process
PF02666 GO:0008654 phospholipid biosynthetic process process
PF02666 GO:0004609 phosphatidylserine decarboxylase activity function
-PF02668 GO:0055114 oxidation-reduction process process
PF02668 GO:0016491 oxidoreductase activity function
PF02669 GO:0006813 potassium ion transport process
PF02669 GO:0016021 integral component of membrane component
-PF02669 GO:0008556 potassium transmembrane transporter activity, phosphorylative mechanism function
+PF02669 GO:0008556 P-type potassium transmembrane transporter activity function
PF02671 GO:0006355 regulation of transcription, DNA-templated process
PF02673 GO:0016020 membrane component
PF02673 GO:0050380 undecaprenyl-diphosphatase activity function
@@ -3064,7 +2942,6 @@ PF02675 GO:0004014 adenosylmethionine decarboxylase activity function
PF02675 GO:0008295 spermidine biosynthetic process process
PF02683 GO:0016020 membrane component
PF02683 GO:0017004 cytochrome complex assembly process
-PF02683 GO:0055114 oxidation-reduction process process
PF02684 GO:0008915 lipid-A-disaccharide synthase activity function
PF02684 GO:0009245 lipid A biosynthetic process process
PF02685 GO:0051156 glucose 6-phosphate metabolic process process
@@ -3078,9 +2955,8 @@ PF02689 GO:0005524 ATP binding function
PF02689 GO:0004386 helicase activity function
PF02690 GO:0016020 membrane component
PF02690 GO:0044341 sodium-dependent phosphate transport process
-PF02690 GO:0015321 sodium-dependent phosphate transmembrane transporter activity function
+PF02690 GO:0005436 sodium:phosphate symporter activity function
PF02691 GO:0005576 extracellular region component
-PF02691 GO:0009405 pathogenesis process
PF02694 GO:0016020 membrane component
PF02701 GO:0003677 DNA binding function
PF02701 GO:0006355 regulation of transcription, DNA-templated process
@@ -3098,6 +2974,10 @@ PF02710 GO:0046789 host cell surface receptor binding function
PF02710 GO:0019031 viral envelope component
PF02710 GO:0016788 hydrolase activity, acting on ester bonds function
PF02714 GO:0016020 membrane component
+PF02723 GO:0046760 viral budding from Golgi membrane process
+PF02723 GO:0039707 pore formation by virus in membrane of host cell process
+PF02723 GO:0016021 integral component of membrane component
+PF02723 GO:0019068 virion assembly process
PF02724 GO:0006270 DNA replication initiation process
PF00622 GO:0005515 protein binding function
PF02095 GO:0005199 structural constituent of cell wall function
@@ -3106,14 +2986,11 @@ PF05964 GO:0005634 nucleus component
PF05965 GO:0005634 nucleus component
PF02854 GO:0003723 RNA binding function
PF02854 GO:0005515 protein binding function
-PF02845 GO:0005515 protein binding function
-PF07531 GO:0006355 regulation of transcription, DNA-templated process
-PF07531 GO:0003700 DNA-binding transcription factor activity function
+PF02845 GO:0043130 ubiquitin binding function
+PF07531 GO:0006351 transcription, DNA-templated process
PF03505 GO:0005576 extracellular region component
-PF03505 GO:0009405 pathogenesis process
PF02917 GO:0005576 extracellular region component
PF02917 GO:0003950 NAD+ ADP-ribosyltransferase activity function
-PF02917 GO:0009405 pathogenesis process
PF02505 GO:0015948 methanogenesis process
PF03615 GO:0003677 DNA binding function
PF03615 GO:0006355 regulation of transcription, DNA-templated process
@@ -3125,15 +3002,18 @@ PF03185 GO:0016020 membrane component
PF03185 GO:0006813 potassium ion transport process
PF03185 GO:0015269 calcium-activated potassium channel activity function
PF00004 GO:0005524 ATP binding function
+PF00004 GO:0016887 ATPase function
PF07724 GO:0005524 ATP binding function
+PF07724 GO:0016887 ATPase function
PF13304 GO:0005524 ATP binding function
+PF13304 GO:0016887 ATPase function
PF00041 GO:0005515 protein binding function
PF01108 GO:0005515 protein binding function
PF16794 GO:0005515 protein binding function
PF03521 GO:0006813 potassium ion transport process
PF03521 GO:0005249 voltage-gated potassium channel activity function
PF03521 GO:0008076 voltage-gated potassium channel complex component
-PF02794 GO:0016746 transferase activity, transferring acyl groups function
+PF02794 GO:0016746 acyltransferase activity function
PF02794 GO:0009404 toxin metabolic process process
PF02794 GO:0005737 cytoplasm component
PF02733 GO:0006071 glycerol metabolic process process
@@ -3154,15 +3034,17 @@ PF02805 GO:0006355 regulation of transcription, DNA-templated process
PF02805 GO:0008168 methyltransferase activity function
PF02805 GO:0008270 zinc ion binding function
PF02898 GO:0004517 nitric-oxide synthase activity function
-PF02898 GO:0055114 oxidation-reduction process process
PF02898 GO:0006809 nitric oxide biosynthetic process process
PF00822 GO:0016021 integral component of membrane component
PF13903 GO:0016021 integral component of membrane component
PF01209 GO:0008168 methyltransferase activity function
PF03822 GO:0007165 signal transduction process
PF07650 GO:0003723 RNA binding function
+PF02798 GO:0006749 glutathione metabolic process process
PF02798 GO:0005515 protein binding function
+PF13409 GO:0006749 glutathione metabolic process process
PF13409 GO:0005515 protein binding function
+PF13417 GO:0006749 glutathione metabolic process process
PF13417 GO:0005515 protein binding function
PF03827 GO:0007186 G protein-coupled receptor signaling pathway process
PF03827 GO:0016499 orexin receptor activity function
@@ -3181,14 +3063,12 @@ PF00015 GO:0007165 signal transduction process
PF02820 GO:0005634 nucleus component
PF02820 GO:0006355 regulation of transcription, DNA-templated process
PF02821 GO:0005576 extracellular region component
-PF02821 GO:0009405 pathogenesis process
PF02821 GO:0031639 plasminogen activation process
PF02822 GO:0004867 serine-type endopeptidase inhibitor activity function
PF02833 GO:0016462 pyrophosphatase activity function
PF02833 GO:0005737 cytoplasm component
PF02840 GO:0005681 spliceosomal complex component
PF02840 GO:0008380 RNA splicing process
-PF02852 GO:0055114 oxidation-reduction process process
PF02852 GO:0045454 cell redox homeostasis process
PF02874 GO:0046034 ATP metabolic process process
PF02874 GO:1902600 proton transmembrane transport process
@@ -3199,8 +3079,6 @@ PF02877 GO:0003950 NAD+ ADP-ribosyltransferase activity function
PF02877 GO:0006471 protein ADP-ribosylation process
PF02884 GO:0016829 lyase activity function
PF02884 GO:0005576 extracellular region component
-PF02894 GO:0055114 oxidation-reduction process process
-PF02894 GO:0016491 oxidoreductase activity function
PF02895 GO:0000155 phosphorelay sensor kinase activity function
PF02895 GO:0000160 phosphorelay signal transduction system process
PF02895 GO:0006935 chemotaxis process
@@ -3219,8 +3097,6 @@ PF02909 GO:0045892 negative regulation of transcription, DNA-templated process
PF02913 GO:0050660 flavin adenine dinucleotide binding function
PF02913 GO:0003824 catalytic activity function
PF02926 GO:0003723 RNA binding function
-PF02948 GO:0062023 collagen-containing extracellular matrix component
-PF02948 GO:0007275 multicellular organism development process
PF02949 GO:0016020 membrane component
PF02949 GO:0007608 sensory perception of smell process
PF02949 GO:0005549 odorant binding function
@@ -3243,10 +3119,8 @@ PF03030 GO:0009678 pyrophosphate hydrolysis-driven proton transmembrane transpor
PF03037 GO:0006952 defense response process
PF03037 GO:0008284 positive regulation of cell population proliferation process
PF03051 GO:0006508 proteolysis process
-PF03051 GO:0004197 cysteine-type endopeptidase activity function
-PF03060 GO:0055114 oxidation-reduction process process
+PF03051 GO:0008234 cysteine-type peptidase activity function
PF03060 GO:0018580 nitronate monooxygenase activity function
-PF03063 GO:0055114 oxidation-reduction process process
PF03063 GO:0016491 oxidoreductase activity function
PF03071 GO:0008375 acetylglucosaminyltransferase activity function
PF03071 GO:0006486 protein glycosylation process
@@ -3264,7 +3138,8 @@ PF03120 GO:0006260 DNA replication process
PF03120 GO:0003911 DNA ligase (NAD+) activity function
PF03125 GO:0016021 integral component of membrane component
PF03125 GO:0007606 sensory perception of chemical stimulus process
-PF03127 GO:0006886 intracellular protein transport process
+PF03127 GO:0043130 ubiquitin binding function
+PF03127 GO:0035091 phosphatidylinositol binding function
PF03137 GO:0016020 membrane component
PF03137 GO:0055085 transmembrane transport process
PF03141 GO:0008168 methyltransferase activity function
@@ -3273,10 +3148,9 @@ PF01144 GO:0008410 CoA-transferase activity function
PF02816 GO:0005524 ATP binding function
PF02816 GO:0004674 protein serine/threonine kinase activity function
PF02816 GO:0006468 protein phosphorylation process
-PF02817 GO:0016746 transferase activity, transferring acyl groups function
+PF02817 GO:0016746 acyltransferase activity function
PF02819 GO:0008200 ion channel inhibitor activity function
PF02819 GO:0005576 extracellular region component
-PF02819 GO:0009405 pathogenesis process
PF02827 GO:0006469 negative regulation of protein kinase activity process
PF02827 GO:0004862 cAMP-dependent protein kinase inhibitor activity function
PF02829 GO:0036094 small molecule binding function
@@ -3312,7 +3186,6 @@ PF02920 GO:0015074 DNA integration process
PF02920 GO:0008907 integrase activity function
PF02920 GO:0003677 DNA binding function
PF02921 GO:0008121 ubiquinol-cytochrome-c reductase activity function
-PF02921 GO:0055114 oxidation-reduction process process
PF02922 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF02922 GO:0005975 carbohydrate metabolic process process
PF02925 GO:0046797 viral procapsid maturation process
@@ -3321,19 +3194,20 @@ PF02927 GO:0008810 cellulase activity function
PF02929 GO:0009341 beta-galactosidase complex component
PF02929 GO:0004565 beta-galactosidase activity function
PF02929 GO:0005975 carbohydrate metabolic process process
-PF02935 GO:0004129 cytochrome-c oxidase activity function
-PF02936 GO:0004129 cytochrome-c oxidase activity function
-PF02939 GO:0008121 ubiquinol-cytochrome-c reductase activity function
+PF02935 GO:0006123 mitochondrial electron transport, cytochrome c to oxygen process
+PF02935 GO:0005751 mitochondrial respiratory chain complex IV component
+PF02936 GO:0006123 mitochondrial electron transport, cytochrome c to oxygen process
+PF02936 GO:0005751 mitochondrial respiratory chain complex IV component
+PF02939 GO:0005750 mitochondrial respiratory chain complex III component
+PF02939 GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c process
PF02940 GO:0004651 polynucleotide 5'-phosphatase activity function
PF02941 GO:0015979 photosynthesis process
PF02943 GO:0016730 oxidoreductase activity, acting on iron-sulfur proteins as donors function
-PF02943 GO:0055114 oxidation-reduction process process
PF02944 GO:0003677 DNA binding function
PF02947 GO:0016020 membrane component
PF02947 GO:0005125 cytokine activity function
PF02950 GO:0008200 ion channel inhibitor activity function
PF02950 GO:0005576 extracellular region component
-PF02950 GO:0009405 pathogenesis process
PF02951 GO:0004363 glutathione synthase activity function
PF02951 GO:0006750 glutathione biosynthetic process process
PF02955 GO:0005524 ATP binding function
@@ -3358,10 +3232,8 @@ PF02979 GO:0046914 transition metal ion binding function
PF02979 GO:0003824 catalytic activity function
PF02980 GO:0003677 DNA binding function
PF02980 GO:0009307 DNA restriction-modification system process
-PF02980 GO:0009036 type II site-specific deoxyribonuclease activity function
PF02981 GO:0003677 DNA binding function
PF02981 GO:0009307 DNA restriction-modification system process
-PF02981 GO:0009036 type II site-specific deoxyribonuclease activity function
PF02982 GO:0006582 melanin metabolic process process
PF02982 GO:0030411 scytalone dehydratase activity function
PF02983 GO:0006508 proteolysis process
@@ -3380,10 +3252,11 @@ PF03014 GO:0005198 structural molecule activity function
PF03026 GO:0019028 viral capsid component
PF03028 GO:0007018 microtubule-based movement process
PF03028 GO:0030286 dynein complex component
-PF03028 GO:0003777 microtubule motor activity function
+PF03028 GO:0008569 ATP-dependent microtubule motor activity, minus-end-directed function
PF03033 GO:0030259 lipid glycosylation process
PF03033 GO:0005975 carbohydrate metabolic process process
-PF03033 GO:0016758 transferase activity, transferring hexosyl groups function
+PF03033 GO:0016758 hexosyltransferase activity function
+PF03034 GO:0106245 L-serine-phosphatidylethanolamine phosphatidyltransferase activity function
PF03034 GO:0006659 phosphatidylserine biosynthetic process process
PF03039 GO:0008083 growth factor activity function
PF03039 GO:0005576 extracellular region component
@@ -3393,7 +3266,6 @@ PF03040 GO:0016021 integral component of membrane component
PF03041 GO:0019083 viral transcription process
PF03047 GO:0005186 pheromone activity function
PF03055 GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen function
-PF03055 GO:0055114 oxidation-reduction process process
PF03059 GO:0030410 nicotianamine synthase activity function
PF03059 GO:0030418 nicotianamine biosynthetic process process
PF03065 GO:0005975 carbohydrate metabolic process process
@@ -3403,7 +3275,6 @@ PF03073 GO:0016021 integral component of membrane component
PF03074 GO:0004357 glutamate-cysteine ligase activity function
PF03074 GO:0006750 glutathione biosynthetic process process
PF03079 GO:0010309 acireductone dioxygenase [iron(II)-requiring] activity function
-PF03079 GO:0055114 oxidation-reduction process process
PF03082 GO:0005576 extracellular region component
PF03082 GO:0007618 mating process
PF03083 GO:0016021 integral component of membrane component
@@ -3417,7 +3288,6 @@ PF03095 GO:0019211 phosphatase activator activity function
PF03100 GO:0017003 protein-heme linkage process
PF03100 GO:0020037 heme binding function
PF03100 GO:0017004 cytochrome complex assembly process
-PF03110 GO:0005634 nucleus component
PF03110 GO:0003677 DNA binding function
PF03116 GO:0016020 membrane component
PF03116 GO:0055085 transmembrane transport process
@@ -3431,7 +3301,6 @@ PF03136 GO:0019941 modification-dependent protein catabolic process process
PF03136 GO:0010498 proteasomal protein catabolic process process
PF03139 GO:0009399 nitrogen fixation process
PF03139 GO:0016163 nitrogenase activity function
-PF03139 GO:0055114 oxidation-reduction process process
PF03525 GO:0007131 reciprocal meiotic recombination process
PF03333 GO:0006355 regulation of transcription, DNA-templated process
PF00152 GO:0005524 ATP binding function
@@ -3439,18 +3308,16 @@ PF00152 GO:0006418 tRNA aminoacylation for protein translation process
PF00152 GO:0000166 nucleotide binding function
PF00152 GO:0004812 aminoacyl-tRNA ligase activity function
PF01336 GO:0003676 nucleic acid binding function
-PF02984 GO:0042025 host cell nucleus component
PF01361 GO:0016853 isomerase activity function
PF01361 GO:0006725 cellular aromatic compound metabolic process process
-PF04075 GO:0055114 oxidation-reduction process process
PF04075 GO:0016491 oxidoreductase activity function
PF02595 GO:0031388 organic acid phosphorylation process
PF02595 GO:0008887 glycerate kinase activity function
+PF02575 GO:0003677 DNA binding function
PF03205 GO:0006777 Mo-molybdopterin cofactor biosynthetic process process
PF03205 GO:0005525 GTP binding function
PF03971 GO:0006099 tricarboxylic acid cycle process
PF03971 GO:0004450 isocitrate dehydrogenase (NADP+) activity function
-PF03971 GO:0055114 oxidation-reduction process process
PF03616 GO:0016021 integral component of membrane component
PF03616 GO:0015813 L-glutamate transmembrane transport process
PF03616 GO:0015501 glutamate:sodium symporter activity function
@@ -3481,10 +3348,8 @@ PF03740 GO:0005737 cytoplasm component
PF03834 GO:0005634 nucleus component
PF03834 GO:0006281 DNA repair process
PF03834 GO:0003684 damaged DNA binding function
-PF03834 GO:0004519 endonuclease activity function
PF04551 GO:0016114 terpenoid biosynthetic process process
PF04551 GO:0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity function
-PF04551 GO:0055114 oxidation-reduction process process
PF07975 GO:0006281 DNA repair process
PF07975 GO:0008270 zinc ion binding function
PF03846 GO:0051782 negative regulation of cell division process
@@ -3511,10 +3376,11 @@ PF03590 GO:0006529 asparagine biosynthetic process process
PF03590 GO:0005737 cytoplasm component
PF03309 GO:0004594 pantothenate kinase activity function
PF03814 GO:0006813 potassium ion transport process
-PF03814 GO:0008556 potassium transmembrane transporter activity, phosphorylative mechanism function
+PF03814 GO:0008556 P-type potassium transmembrane transporter activity function
PF03786 GO:0006064 glucuronate catabolic process process
PF03786 GO:0008927 mannonate dehydratase activity function
PF03808 GO:0009058 biosynthetic process process
+PF03808 GO:0016740 transferase activity function
PF05681 GO:0016829 lyase activity function
PF05683 GO:0016836 hydro-lyase activity function
PF03843 GO:0019867 outer membrane component
@@ -3553,7 +3419,7 @@ PF03821 GO:0016021 integral component of membrane component
PF03817 GO:0016020 membrane component
PF03840 GO:0009306 protein secretion process
PF03840 GO:0016021 integral component of membrane component
-PF03840 GO:0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity function
+PF03840 GO:0015450 protein-transporting ATPase activity function
PF03842 GO:0015708 silicic acid import across plasma membrane process
PF03595 GO:0055085 transmembrane transport process
PF03595 GO:0016021 integral component of membrane component
@@ -3589,11 +3455,10 @@ PF03547 GO:0055085 transmembrane transport process
PF03547 GO:0016021 integral component of membrane component
PF06026 GO:0009052 pentose-phosphate shunt, non-oxidative branch process
PF06026 GO:0004751 ribose-5-phosphate isomerase activity function
-PF03169 GO:0055085 transmembrane transport process
+PF03169 GO:0035673 oligopeptide transmembrane transporter activity function
PF01467 GO:0009058 biosynthetic process process
PF01467 GO:0003824 catalytic activity function
PF02969 GO:0006352 DNA-templated transcription, initiation process
-PF03131 GO:0005634 nucleus component
PF03131 GO:0003677 DNA binding function
PF03131 GO:0006355 regulation of transcription, DNA-templated process
PF00170 GO:0006355 regulation of transcription, DNA-templated process
@@ -3614,13 +3479,11 @@ PF00263 GO:0009306 protein secretion process
PF03146 GO:0043113 receptor clustering process
PF03146 GO:0007213 G protein-coupled acetylcholine receptor signaling pathway process
PF03146 GO:0043236 laminin binding function
-PF03150 GO:0055114 oxidation-reduction process process
PF03150 GO:0016491 oxidoreductase activity function
PF03152 GO:0006511 ubiquitin-dependent protein catabolic process process
PF03153 GO:0005672 transcription factor TFIIA complex component
PF03153 GO:0006367 transcription initiation from RNA polymerase II promoter process
-PF03155 GO:0016758 transferase activity, transferring hexosyl groups function
-PF03155 GO:0005789 endoplasmic reticulum membrane component
+PF03155 GO:0016758 hexosyltransferase activity function
PF03159 GO:0004527 exonuclease activity function
PF03159 GO:0003676 nucleic acid binding function
PF00961 GO:0004519 endonuclease activity function
@@ -3648,16 +3511,16 @@ PF03206 GO:0009399 nitrogen fixation process
PF03211 GO:0005576 extracellular region component
PF03211 GO:0030570 pectate lyase activity function
PF03213 GO:0019031 viral envelope component
-PF03220 GO:0019012 virion component
+PF03220 GO:0044423 virion component component
PF03223 GO:1902600 proton transmembrane transport process
PF03223 GO:0015078 proton transmembrane transporter activity function
PF03223 GO:0033180 proton-transporting V-type ATPase, V1 domain component
PF03224 GO:1902600 proton transmembrane transport process
PF03224 GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain component
PF03224 GO:0046961 proton-transporting ATPase activity, rotational mechanism function
+PF03227 GO:0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor function
PF03228 GO:0019028 viral capsid component
PF03229 GO:0019050 suppression by virus of host apoptotic process process
-PF03233 GO:0019089 transmission of virus process
PF03239 GO:0016020 membrane component
PF03239 GO:0033573 high-affinity iron permease complex component
PF03239 GO:0034755 iron ion transmembrane transport process
@@ -3686,10 +3549,10 @@ PF03261 GO:0016533 protein kinase 5 complex component
PF03261 GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity function
PF03265 GO:0004531 deoxyribonuclease II activity function
PF03265 GO:0006259 DNA metabolic process process
-PF03266 GO:0098519 nucleotide phosphatase activity, acting on free nucleotides function
+PF03266 GO:0017111 nucleoside-triphosphatase activity function
PF03271 GO:0008017 microtubule binding function
PF03273 GO:0019031 viral envelope component
-PF03273 GO:0019048 modulation by virus of host morphology or physiology process
+PF03273 GO:0019048 modulation by virus of host process process
PF03274 GO:0016032 viral process process
PF03274 GO:0045893 positive regulation of transcription, DNA-templated process
PF03276 GO:0042025 host cell nucleus component
@@ -3699,7 +3562,6 @@ PF03276 GO:0019028 viral capsid component
PF03276 GO:0075521 microtubule-dependent intracellular transport of viral material towards nucleus process
PF03276 GO:0044163 host cytoskeleton component
PF03276 GO:0046718 viral entry into host cell process
-PF03278 GO:0009405 pathogenesis process
PF03279 GO:0016021 integral component of membrane component
PF03279 GO:0016740 transferase activity function
PF03280 GO:0016020 membrane component
@@ -3721,8 +3583,10 @@ PF03300 GO:0046740 transport of virus in host, cell to cell process
PF03301 GO:0020037 heme binding function
PF03301 GO:0019441 tryptophan catabolic process to kynurenine process
PF03301 GO:0004833 tryptophan 2,3-dioxygenase activity function
-PF03307 GO:0019049 evasion or tolerance of host defenses by virus process
+PF03303 GO:0110134 meiotic drive process
+PF03307 GO:0019049 mitigation of host defenses by virus process
PF03310 GO:0003677 DNA binding function
+PF03319 GO:0031469 polyhedral organelle component
PF03323 GO:0016021 integral component of membrane component
PF03323 GO:0009847 spore germination process
PF03324 GO:0019079 viral genome replication process
@@ -3758,12 +3622,11 @@ PF03360 GO:0015018 galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransfe
PF03361 GO:0006355 regulation of transcription, DNA-templated process
PF03362 GO:0006355 regulation of transcription, DNA-templated process
PF03366 GO:0006355 regulation of transcription, DNA-templated process
-PF03368 GO:0016891 endoribonuclease activity, producing 5'-phosphomonoesters function
PF03370 GO:0005515 protein binding function
PF03373 GO:0019865 immunoglobulin binding function
PF03374 GO:0003677 DNA binding function
PF03376 GO:0016020 membrane component
-PF03378 GO:0008536 Ran GTPase binding function
+PF03378 GO:0031267 small GTPase binding function
PF03378 GO:0005515 protein binding function
PF03381 GO:0016020 membrane component
PF03387 GO:0006355 regulation of transcription, DNA-templated process
@@ -3772,8 +3635,8 @@ PF03391 GO:0019028 viral capsid component
PF03391 GO:0005198 structural molecule activity function
PF03393 GO:0019031 viral envelope component
PF03393 GO:0019068 virion assembly process
+PF03395 GO:0044423 virion component component
PF03395 GO:0005198 structural molecule activity function
-PF03395 GO:0019012 virion component
PF03396 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF03396 GO:0003677 DNA binding function
PF03396 GO:0019083 viral transcription process
@@ -3784,11 +3647,9 @@ PF03400 GO:0006313 transposition, DNA-mediated process
PF03403 GO:0016042 lipid catabolic process process
PF03403 GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity function
PF03404 GO:0030151 molybdenum ion binding function
-PF03404 GO:0055114 oxidation-reduction process process
PF03404 GO:0016491 oxidoreductase activity function
PF03405 GO:0045300 acyl-[acyl-carrier-protein] desaturase activity function
PF03405 GO:0006631 fatty acid metabolic process process
-PF03405 GO:0055114 oxidation-reduction process process
PF03408 GO:0019031 viral envelope component
PF03410 GO:0004222 metalloendopeptidase activity function
PF03410 GO:0008270 zinc ion binding function
@@ -3802,7 +3663,7 @@ PF03412 GO:0005524 ATP binding function
PF03412 GO:0016021 integral component of membrane component
PF03414 GO:0016020 membrane component
PF03414 GO:0005975 carbohydrate metabolic process process
-PF03414 GO:0016758 transferase activity, transferring hexosyl groups function
+PF03414 GO:0016758 hexosyltransferase activity function
PF03418 GO:0006508 proteolysis process
PF03418 GO:0008233 peptidase activity function
PF03418 GO:0009847 spore germination process
@@ -3821,23 +3682,16 @@ PF03427 GO:0006032 chitin catabolic process process
PF03427 GO:0008061 chitin binding function
PF03431 GO:0039694 viral RNA genome replication process
PF03431 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
-PF03435 GO:0055114 oxidation-reduction process process
PF03435 GO:0016491 oxidoreductase activity function
PF03444 GO:0003677 DNA binding function
PF03444 GO:0006355 regulation of transcription, DNA-templated process
PF03445 GO:0008773 [protein-PII] uridylyltransferase activity function
PF03447 GO:0050661 NADP binding function
-PF03447 GO:0055114 oxidation-reduction process process
PF03447 GO:0016491 oxidoreductase activity function
PF03453 GO:0032324 molybdopterin cofactor biosynthetic process process
PF03454 GO:0032324 molybdopterin cofactor biosynthetic process process
-PF03460 GO:0055114 oxidation-reduction process process
PF03460 GO:0016491 oxidoreductase activity function
PF03461 GO:0006281 DNA repair process
-PF03171 GO:0055114 oxidation-reduction process process
-PF03171 GO:0016491 oxidoreductase activity function
-PF13640 GO:0055114 oxidation-reduction process process
-PF13640 GO:0016491 oxidoreductase activity function
PF03179 GO:1902600 proton transmembrane transport process
PF03179 GO:0042626 ATPase-coupled transmembrane transporter activity function
PF03179 GO:0016471 vacuolar proton-transporting V-type ATPase complex component
@@ -3847,8 +3701,9 @@ PF03315 GO:0003941 L-serine ammonia-lyase activity function
PF03315 GO:0006094 gluconeogenesis process
PF03315 GO:0051539 4 iron, 4 sulfur cluster binding function
PF03334 GO:0005451 monovalent cation:proton antiporter activity function
-PF03334 GO:1902600 proton transmembrane transport process
-PF03334 GO:0015672 monovalent inorganic cation transport process
+PF03334 GO:0098662 inorganic cation transmembrane transport process
+PF03372 GO:0003824 catalytic activity function
+PF14529 GO:0003824 catalytic activity function
PF03462 GO:0006415 translational termination process
PF03483 GO:0004826 phenylalanine-tRNA ligase activity function
PF03483 GO:0003723 RNA binding function
@@ -3875,8 +3730,7 @@ PF03730 GO:0006303 double-strand break repair via nonhomologous end joining proc
PF03730 GO:0003678 DNA helicase activity function
PF03497 GO:0005576 extracellular region component
PF03497 GO:0008294 calcium- and calmodulin-responsive adenylate cyclase activity function
-PF03497 GO:0009405 pathogenesis process
-PF03557 GO:0019048 modulation by virus of host morphology or physiology process
+PF03557 GO:0019048 modulation by virus of host process process
PF03626 GO:0016021 integral component of membrane component
PF03618 GO:0005524 ATP binding function
PF03618 GO:0016772 transferase activity, transferring phosphorus-containing groups function
@@ -3891,30 +3745,29 @@ PF03632 GO:0005975 carbohydrate metabolic process process
PF03632 GO:0003824 catalytic activity function
PF03636 GO:0005975 carbohydrate metabolic process process
PF03636 GO:0003824 catalytic activity function
-PF03659 GO:0016787 hydrolase activity function
+PF03659 GO:0051118 glucan endo-1,3-alpha-glucosidase activity function
PF03662 GO:0016020 membrane component
PF03662 GO:0016798 hydrolase activity, acting on glycosyl bonds function
PF03644 GO:0033925 mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity function
PF03644 GO:0005737 cytoplasm component
-PF03585 GO:0042025 host cell nucleus component
PF03585 GO:0045893 positive regulation of transcription, DNA-templated process
-PF03584 GO:0042025 host cell nucleus component
PF03584 GO:0045893 positive regulation of transcription, DNA-templated process
PF03581 GO:0019073 viral DNA genome packaging process
PF03586 GO:0019784 NEDD8-specific protease activity function
PF03586 GO:0039693 viral DNA genome replication process
+PF03559 GO:0016829 lyase activity function
PF03652 GO:0006364 rRNA processing process
PF04079 GO:0051304 chromosome separation process
PF04029 GO:0050532 2-phosphosulfolactate phosphatase activity function
PF04029 GO:0000287 magnesium ion binding function
PF04166 GO:0051287 NAD binding function
-PF04166 GO:0055114 oxidation-reduction process process
PF03492 GO:0008168 methyltransferase activity function
PF03562 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF03473 GO:0030151 molybdenum ion binding function
PF03473 GO:0003824 catalytic activity function
PF03473 GO:0030170 pyridoxal phosphate binding function
-PF03587 GO:0008168 methyltransferase activity function
+PF03587 GO:0070037 rRNA (pseudouridine) methyltransferase activity function
+PF03587 GO:0070475 rRNA base methylation process
PF03688 GO:0019028 viral capsid component
PF03689 GO:0019028 viral capsid component
PF03709 GO:0016831 carboxy-lyase activity function
@@ -3928,6 +3781,7 @@ PF03574 GO:0043158 heterocyst differentiation process
PF03575 GO:0006508 proteolysis process
PF03575 GO:0008236 serine-type peptidase activity function
PF03577 GO:0006508 proteolysis process
+PF03577 GO:0070004 cysteine-type exopeptidase activity function
PF03577 GO:0016805 dipeptidase activity function
PF03714 GO:0030246 carbohydrate binding function
PF03714 GO:0005975 carbohydrate metabolic process process
@@ -3949,10 +3803,13 @@ PF03702 GO:0009254 peptidoglycan turnover process
PF03661 GO:0016021 integral component of membrane component
PF03660 GO:0000398 mRNA splicing, via spliceosome process
PF03647 GO:0016020 membrane component
+PF03669 GO:0030176 integral component of endoplasmic reticulum membrane component
+PF03669 GO:0045048 protein insertion into ER membrane process
+PF03669 GO:0044183 protein folding chaperone function
PF03694 GO:0016021 integral component of membrane component
PF03666 GO:0034198 cellular response to amino acid starvation process
PF03666 GO:0032007 negative regulation of TOR signaling process
-PF03665 GO:0072546 ER membrane protein complex component
+PF03665 GO:0072546 EMC complex component
PF03699 GO:0016021 integral component of membrane component
PF03671 GO:0071569 protein ufmylation process
PF03728 GO:0003677 DNA binding function
@@ -3964,8 +3821,7 @@ PF03635 GO:0015031 protein transport process
PF03468 GO:0031047 gene silencing by RNA process
PF03470 GO:0031047 gene silencing by RNA process
PF04792 GO:0005576 extracellular region component
-PF04792 GO:0009405 pathogenesis process
-PF09599 GO:0009405 pathogenesis process
+PF00235 GO:0003779 actin binding function
PF05824 GO:0007268 chemical synaptic transmission process
PF05824 GO:0030354 melanin-concentrating hormone activity function
PF01382 GO:0009374 biotin binding function
@@ -3993,7 +3849,8 @@ PF03744 GO:0009102 biotin biosynthetic process process
PF03748 GO:0009425 bacterial-type flagellum basal body component
PF03748 GO:0071973 bacterial-type flagellum-dependent cell motility process
PF03748 GO:0006935 chemotaxis process
-PF03759 GO:0005089 Rho guanyl-nucleotide exchange factor activity function
+PF03754 GO:0003677 DNA binding function
+PF03759 GO:0005085 guanyl-nucleotide exchange factor activity function
PF03760 GO:0009793 embryo development ending in seed dormancy process
PF03764 GO:0005525 GTP binding function
PF03768 GO:0005576 extracellular region component
@@ -4035,7 +3892,6 @@ PF03868 GO:0006412 translation process
PF03868 GO:0003735 structural constituent of ribosome function
PF03869 GO:0003677 DNA binding function
PF03870 GO:0006351 transcription, DNA-templated process
-PF03871 GO:0042025 host cell nucleus component
PF03871 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF03871 GO:0003677 DNA binding function
PF03871 GO:0006351 transcription, DNA-templated process
@@ -4046,7 +3902,6 @@ PF03875 GO:0046848 hydroxyapatite binding function
PF03875 GO:0030500 regulation of bone mineralization process
PF03875 GO:0005576 extracellular region component
PF03875 GO:0042742 defense response to bacterium process
-PF03876 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF03876 GO:0006351 transcription, DNA-templated process
PF03878 GO:0005789 endoplasmic reticulum membrane component
PF03878 GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport process
@@ -4057,12 +3912,12 @@ PF03893 GO:0016042 lipid catabolic process process
PF03894 GO:0005975 carbohydrate metabolic process process
PF03894 GO:0016832 aldehyde-lyase activity function
PF03896 GO:0005789 endoplasmic reticulum membrane component
-PF03901 GO:0016757 transferase activity, transferring glycosyl groups function
+PF03901 GO:0016757 glycosyltransferase activity function
PF03907 GO:0019888 protein phosphatase regulator activity function
PF03908 GO:0005484 SNAP receptor activity function
PF03908 GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum process
PF03910 GO:0003677 DNA binding function
-PF03910 GO:0019012 virion component
+PF03910 GO:0044423 virion component component
PF03912 GO:0016020 membrane component
PF03912 GO:0009523 photosystem II component
PF03912 GO:0009654 photosystem II oxygen evolving complex component
@@ -4074,7 +3929,6 @@ PF03920 GO:0005515 protein binding function
PF03922 GO:0019867 outer membrane component
PF03934 GO:0009306 protein secretion process
PF03934 GO:0016021 integral component of membrane component
-PF03935 GO:0006078 (1->6)-beta-D-glucan biosynthetic process process
PF03936 GO:0000287 magnesium ion binding function
PF03936 GO:0016829 lyase activity function
PF03936 GO:0010333 terpene synthase activity function
@@ -4082,20 +3936,20 @@ PF03938 GO:0051082 unfolded protein binding function
PF03943 GO:0005634 nucleus component
PF03943 GO:0051028 mRNA transport process
PF03944 GO:0090729 toxin activity function
-PF03945 GO:0009405 pathogenesis process
+PF03945 GO:0001897 cytolysis by symbiont of host cells process
PF03945 GO:0090729 toxin activity function
PF03955 GO:0031423 hexon binding function
PF03955 GO:0019028 viral capsid component
PF03956 GO:1903401 L-lysine transmembrane transport process
PF03956 GO:0015661 L-lysine efflux transmembrane transporter activity function
PF03964 GO:0007275 multicellular organism development process
-PF03964 GO:0042600 chorion component
+PF03964 GO:0042600 egg chorion component
PF03965 GO:0045892 negative regulation of transcription, DNA-templated process
PF03965 GO:0003677 DNA binding function
PF03969 GO:0005524 ATP binding function
PF03970 GO:0019068 virion assembly process
PF03972 GO:0016829 lyase activity function
-PF03973 GO:0030682 evasion or tolerance of host defenses process
+PF03973 GO:0030682 mitigation of host defenses by symbiont process
PF03974 GO:0004867 serine-type endopeptidase inhibitor activity function
PF03975 GO:0050568 protein-glutamine glutaminase activity function
PF03975 GO:0006935 chemotaxis process
@@ -4104,12 +3958,10 @@ PF03977 GO:0006814 sodium ion transport process
PF04281 GO:0006886 intracellular protein transport process
PF04281 GO:0005741 mitochondrial outer membrane component
PF04209 GO:0004411 homogentisate 1,2-dioxygenase activity function
-PF04209 GO:0055114 oxidation-reduction process process
PF04209 GO:0006570 tyrosine metabolic process process
PF04209 GO:0006559 L-phenylalanine catabolic process process
PF01180 GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors function
PF01180 GO:0005737 cytoplasm component
-PF01180 GO:0055114 oxidation-reduction process process
PF16906 GO:0015934 large ribosomal subunit component
PF16906 GO:0006412 translation process
PF16906 GO:0003735 structural constituent of ribosome function
@@ -4145,7 +3997,6 @@ PF00110 GO:0007275 multicellular organism development process
PF00110 GO:0005576 extracellular region component
PF00110 GO:0016055 Wnt signaling pathway process
PF00110 GO:0005102 signaling receptor binding function
-PF00538 GO:0042025 host cell nucleus component
PF00538 GO:0003677 DNA binding function
PF00538 GO:0006334 nucleosome assembly process
PF00538 GO:0000786 nucleosome component
@@ -4160,7 +4011,6 @@ PF00083 GO:0055085 transmembrane transport process
PF00083 GO:0016021 integral component of membrane component
PF00083 GO:0022857 transmembrane transporter activity function
PF01117 GO:0005576 extracellular region component
-PF01117 GO:0009405 pathogenesis process
PF00483 GO:0009058 biosynthetic process process
PF00483 GO:0016779 nucleotidyltransferase activity function
PF00813 GO:0016020 membrane component
@@ -4182,13 +4032,11 @@ PF04211 GO:0016021 integral component of membrane component
PF04210 GO:0015948 methanogenesis process
PF04210 GO:0030269 tetrahydromethanopterin S-methyltransferase activity function
PF04210 GO:0016021 integral component of membrane component
-PF04650 GO:0016020 membrane component
PF04277 GO:0016020 membrane component
PF04277 GO:0008948 oxaloacetate decarboxylase activity function
PF04277 GO:0036376 sodium ion export across plasma membrane process
PF04277 GO:0015081 sodium ion transmembrane transporter activity function
PF10550 GO:0035792 host cell postsynaptic membrane component
-PF10550 GO:0009405 pathogenesis process
PF04275 GO:0006695 cholesterol biosynthetic process process
PF04275 GO:0005737 cytoplasm component
PF04275 GO:0004631 phosphomevalonate kinase activity function
@@ -4198,13 +4046,10 @@ PF14572 GO:0004749 ribose phosphate diphosphokinase activity function
PF14572 GO:0009165 nucleotide biosynthetic process process
PF04272 GO:0016020 membrane component
PF04272 GO:0042030 ATPase inhibitor activity function
-PF04272 GO:0005246 calcium channel regulator activity function
-PF04272 GO:0006816 calcium ion transport process
+PF04272 GO:1901894 regulation of ATPase-coupled calcium transmembrane transporter activity process
PF04279 GO:0016021 integral component of membrane component
PF00804 GO:0016020 membrane component
PF14523 GO:0016020 membrane component
-PF00640 GO:0005515 protein binding function
-PF14719 GO:0005515 protein binding function
PF01160 GO:0007218 neuropeptide signaling pathway process
PF01029 GO:0003723 RNA binding function
PF01029 GO:0006355 regulation of transcription, DNA-templated process
@@ -4219,7 +4064,6 @@ PF02080 GO:0008324 cation transmembrane transporter activity function
PF00860 GO:0016020 membrane component
PF00860 GO:0055085 transmembrane transport process
PF00860 GO:0022857 transmembrane transporter activity function
-PF00190 GO:0045735 nutrient reservoir activity function
PF00128 GO:0005975 carbohydrate metabolic process process
PF00128 GO:0003824 catalytic activity function
PF02806 GO:0043169 cation binding function
@@ -4230,13 +4074,11 @@ PF00229 GO:0005164 tumor necrosis factor receptor binding function
PF00229 GO:0006955 immune response process
PF00977 GO:0000105 histidine biosynthetic process process
PF01077 GO:0020037 heme binding function
-PF01077 GO:0055114 oxidation-reduction process process
PF01077 GO:0051536 iron-sulfur cluster binding function
PF01077 GO:0016491 oxidoreductase activity function
PF01300 GO:0003725 double-stranded RNA binding function
PF01926 GO:0005525 GTP binding function
PF02934 GO:0016874 ligase activity function
-PF01266 GO:0055114 oxidation-reduction process process
PF01266 GO:0016491 oxidoreductase activity function
PF01044 GO:0051015 actin filament binding function
PF01044 GO:0007155 cell adhesion process
@@ -4246,19 +4088,14 @@ PF00323 GO:0006952 defense response process
PF00323 GO:0005576 extracellular region component
PF00485 GO:0005524 ATP binding function
PF00485 GO:0016301 kinase activity function
-PF00752 GO:0006281 DNA repair process
PF00752 GO:0004518 nuclease activity function
PF00867 GO:0004518 nuclease activity function
PF02770 GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors function
-PF02770 GO:0055114 oxidation-reduction process process
PF01565 GO:0050660 flavin adenine dinucleotide binding function
-PF01565 GO:0055114 oxidation-reduction process process
PF01565 GO:0016491 oxidoreductase activity function
PF00208 GO:0006520 cellular amino acid metabolic process process
-PF00208 GO:0055114 oxidation-reduction process process
PF00208 GO:0016491 oxidoreductase activity function
PF02812 GO:0006520 cellular amino acid metabolic process process
-PF02812 GO:0055114 oxidation-reduction process process
PF02812 GO:0016491 oxidoreductase activity function
PF01642 GO:0031419 cobalamin binding function
PF01642 GO:0016866 intramolecular transferase activity function
@@ -4268,30 +4105,25 @@ PF02836 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF02836 GO:0005975 carbohydrate metabolic process process
PF02837 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF02837 GO:0005975 carbohydrate metabolic process process
+PF00725 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
PF00725 GO:0006631 fatty acid metabolic process process
-PF00725 GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity function
-PF00725 GO:0055114 oxidation-reduction process process
PF00725 GO:0016491 oxidoreductase activity function
PF07479 GO:0005975 carbohydrate metabolic process process
-PF07479 GO:0055114 oxidation-reduction process process
PF07479 GO:0004367 glycerol-3-phosphate dehydrogenase [NAD+] activity function
PF01192 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF01192 GO:0003677 DNA binding function
PF01192 GO:0006351 transcription, DNA-templated process
PF00393 GO:0006098 pentose-phosphate shunt process
PF00393 GO:0004616 phosphogluconate dehydrogenase (decarboxylating) activity function
-PF00393 GO:0055114 oxidation-reduction process process
PF03446 GO:0050661 NADP binding function
PF00239 GO:0003677 DNA binding function
-PF00239 GO:0000150 recombinase activity function
+PF00239 GO:0000150 DNA strand exchange activity function
PF00239 GO:0006310 DNA recombination process
PF02796 GO:0003677 DNA binding function
-PF02796 GO:0000150 recombinase activity function
+PF02796 GO:0000150 DNA strand exchange activity function
PF02796 GO:0006310 DNA recombination process
PF00403 GO:0046872 metal ion binding function
-PF00403 GO:0030001 metal ion transport process
PF02876 GO:0005576 extracellular region component
-PF02876 GO:0009405 pathogenesis process
PF01676 GO:0046872 metal ion binding function
PF01676 GO:0003824 catalytic activity function
PF01297 GO:0046872 metal ion binding function
@@ -4305,16 +4137,10 @@ PF00136 GO:0003677 DNA binding function
PF00136 GO:0000166 nucleotide binding function
PF01312 GO:0016020 membrane component
PF01312 GO:0009306 protein secretion process
-PF01058 GO:0055114 oxidation-reduction process process
PF01058 GO:0051536 iron-sulfur cluster binding function
PF00389 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
PF00389 GO:0051287 NAD binding function
-PF00389 GO:0055114 oxidation-reduction process process
PF02826 GO:0051287 NAD binding function
-PF02826 GO:0055114 oxidation-reduction process process
-PF00529 GO:0016020 membrane component
-PF00529 GO:0055085 transmembrane transport process
-PF00529 GO:0022857 transmembrane transporter activity function
PF00849 GO:0003723 RNA binding function
PF00849 GO:0009451 RNA modification process
PF00849 GO:0001522 pseudouridine synthesis process
@@ -4324,7 +4150,7 @@ PF00999 GO:0055085 transmembrane transport process
PF00999 GO:0016021 integral component of membrane component
PF00999 GO:0006812 cation transport process
PF00999 GO:0015299 solute:proton antiporter activity function
-PF02099 GO:0004843 thiol-dependent ubiquitin-specific protease activity function
+PF02099 GO:0004843 thiol-dependent deubiquitinase function
PF02099 GO:0016579 protein deubiquitination process
PF02152 GO:0004150 dihydroneopterin aldolase activity function
PF02152 GO:0006760 folic acid-containing compound metabolic process process
@@ -4335,11 +4161,9 @@ PF02735 GO:0006303 double-strand break repair via nonhomologous end joining proc
PF02732 GO:0003677 DNA binding function
PF02732 GO:0004518 nuclease activity function
PF01395 GO:0005549 odorant binding function
-PF01123 GO:0009405 pathogenesis process
+PF01123 GO:0090729 toxin activity function
+PF02737 GO:0070403 NAD+ binding function
PF02737 GO:0006631 fatty acid metabolic process process
-PF02737 GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity function
-PF02737 GO:0055114 oxidation-reduction process process
-PF02737 GO:0016491 oxidoreductase activity function
PF01176 GO:0006413 translational initiation process
PF01176 GO:0003743 translation initiation factor activity function
PF01176 GO:0003723 RNA binding function
@@ -4349,11 +4173,6 @@ PF02931 GO:0005230 extracellular ligand-gated ion channel activity function
PF02931 GO:0016021 integral component of membrane component
PF02931 GO:0006811 ion transport process
PF00288 GO:0005524 ATP binding function
-PF00757 GO:0016020 membrane component
-PF00757 GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway process
-PF00757 GO:0005524 ATP binding function
-PF00757 GO:0006468 protein phosphorylation process
-PF00757 GO:0004714 transmembrane receptor protein tyrosine kinase activity function
PF00793 GO:0009058 biosynthetic process process
PF06039 GO:0006099 tricarboxylic acid cycle process
PF06039 GO:0008924 malate dehydrogenase (quinone) activity function
@@ -4363,7 +4182,6 @@ PF04267 GO:0008115 sarcosine oxidase activity function
PF04267 GO:0046653 tetrahydrofolate metabolic process process
PF04261 GO:0020037 heme binding function
PF04261 GO:0004601 peroxidase activity function
-PF04261 GO:0055114 oxidation-reduction process process
PF04107 GO:0042398 cellular modified amino acid biosynthetic process process
PF04107 GO:0004357 glutamate-cysteine ligase activity function
PF04259 GO:0030435 sporulation resulting in formation of a cellular spore process
@@ -4381,17 +4199,16 @@ PF04216 GO:0005737 cytoplasm component
PF04759 GO:0010274 hydrotropism process
PF04223 GO:0006084 acetyl-CoA metabolic process process
PF04223 GO:0008814 citrate CoA-transferase activity function
-PF04223 GO:0009346 citrate lyase complex component
+PF04223 GO:0009346 ATP-independent citrate lyase complex component
PF04223 GO:0005737 cytoplasm component
PF03543 GO:0004197 cysteine-type endopeptidase activity function
-PF03543 GO:0009405 pathogenesis process
PF05107 GO:0043571 maintenance of CRISPR repeat elements process
PF04492 GO:0006260 DNA replication process
PF04043 GO:0004857 enzyme inhibitor activity function
PF06213 GO:0009236 cobalamin biosynthetic process process
+PF12409 GO:0019829 ATPase-coupled cation transmembrane transporter activity function
PF12409 GO:0016021 integral component of membrane component
PF12409 GO:0006812 cation transport process
-PF12409 GO:0016887 ATPase activity function
PF13307 GO:0005524 ATP binding function
PF13307 GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides function
PF13307 GO:0006139 nucleobase-containing compound metabolic process process
@@ -4402,7 +4219,6 @@ PF17907 GO:0018024 histone-lysine N-methyltransferase activity function
PF07535 GO:0008270 zinc ion binding function
PF07535 GO:0003676 nucleic acid binding function
PF05773 GO:0005515 protein binding function
-PF07533 GO:0016817 hydrolase activity, acting on acid anhydrides function
PF07533 GO:0005515 protein binding function
PF04721 GO:0006516 glycoprotein catabolic process process
PF04721 GO:0005737 cytoplasm component
@@ -4412,17 +4228,14 @@ PF03604 GO:0006351 transcription, DNA-templated process
PF08513 GO:0005515 protein binding function
PF16045 GO:0005515 protein binding function
PF07289 GO:0034464 BBSome component
-PF05485 GO:0003676 nucleic acid binding function
-PF06337 GO:0004843 thiol-dependent ubiquitin-specific protease activity function
-PF04845 GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding function
+PF06337 GO:0004843 thiol-dependent deubiquitinase function
+PF04845 GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding function
PF04845 GO:0032422 purine-rich negative regulatory element binding function
PF03798 GO:0016021 integral component of membrane component
PF02357 GO:0006355 regulation of transcription, DNA-templated process
PF01344 GO:0005515 protein binding function
-PF00384 GO:0055114 oxidation-reduction process process
PF00384 GO:0016491 oxidoreductase activity function
PF01568 GO:0043546 molybdopterin cofactor binding function
-PF01568 GO:0055114 oxidation-reduction process process
PF01568 GO:0016491 oxidoreductase activity function
PF01769 GO:0006812 cation transport process
PF01769 GO:0008324 cation transmembrane transporter activity function
@@ -4435,6 +4248,7 @@ PF04909 GO:0016787 hydrolase activity function
PF00924 GO:0016020 membrane component
PF00924 GO:0055085 transmembrane transport process
PF00025 GO:0005525 GTP binding function
+PF00025 GO:0003924 GTPase activity function
PF03989 GO:0003677 DNA binding function
PF03989 GO:0005524 ATP binding function
PF03989 GO:0006265 DNA topological change process
@@ -4445,7 +4259,6 @@ PF04053 GO:0005198 structural molecule activity function
PF04053 GO:0016192 vesicle-mediated transport process
PF04083 GO:0006629 lipid metabolic process process
PF04116 GO:0005506 iron ion binding function
-PF04116 GO:0055114 oxidation-reduction process process
PF04116 GO:0008610 lipid biosynthetic process process
PF04116 GO:0016491 oxidoreductase activity function
PF04309 GO:0006071 glycerol metabolic process process
@@ -4467,19 +4280,19 @@ PF04621 GO:0005634 nucleus component
PF04621 GO:0006355 regulation of transcription, DNA-templated process
PF04621 GO:0003700 DNA-binding transcription factor activity function
PF04624 GO:0007304 chorion-containing eggshell formation process
-PF04624 GO:0005213 structural constituent of chorion function
+PF04624 GO:0005213 structural constituent of egg chorion function
PF04624 GO:0005576 extracellular region component
-PF04624 GO:0042600 chorion component
+PF04624 GO:0042600 egg chorion component
PF04625 GO:0007304 chorion-containing eggshell formation process
-PF04625 GO:0005213 structural constituent of chorion function
+PF04625 GO:0005213 structural constituent of egg chorion function
PF04625 GO:0005576 extracellular region component
-PF04625 GO:0042600 chorion component
+PF04625 GO:0042600 egg chorion component
PF04626 GO:0007304 chorion-containing eggshell formation process
-PF04626 GO:0005213 structural constituent of chorion function
+PF04626 GO:0005213 structural constituent of egg chorion function
PF04626 GO:0005576 extracellular region component
-PF04626 GO:0042600 chorion component
+PF04626 GO:0042600 egg chorion component
PF04627 GO:0015986 ATP synthesis coupled proton transport process
-PF04627 GO:0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) component
+PF04627 GO:0000275 mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) component
PF04627 GO:0046933 proton-transporting ATP synthase activity, rotational mechanism function
PF04628 GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport process
PF04632 GO:0055085 transmembrane transport process
@@ -4495,7 +4308,6 @@ PF04644 GO:0005179 hormone activity function
PF04647 GO:0008233 peptidase activity function
PF04647 GO:0016021 integral component of membrane component
PF04647 GO:0009372 quorum sensing process
-PF04647 GO:0009405 pathogenesis process
PF04648 GO:0019953 sexual reproduction process
PF04648 GO:0000772 mating pheromone activity function
PF04648 GO:0005576 extracellular region component
@@ -4512,8 +4324,6 @@ PF04664 GO:0016020 membrane component
PF04664 GO:0038023 signaling receptor activity function
PF04670 GO:0005525 GTP binding function
PF04673 GO:0030639 polyketide biosynthetic process process
-PF04683 GO:0005634 nucleus component
-PF04683 GO:0005737 cytoplasm component
PF04684 GO:0005634 nucleus component
PF04684 GO:0003677 DNA binding function
PF04684 GO:0006338 chromatin remodeling process
@@ -4532,9 +4342,8 @@ PF04699 GO:0030833 regulation of actin filament polymerization process
PF04699 GO:0005885 Arp2/3 protein complex component
PF04699 GO:0034314 Arp2/3 complex-mediated actin nucleation process
PF04699 GO:0015629 actin cytoskeleton component
+PF04700 GO:0044423 virion component component
PF04700 GO:0005198 structural molecule activity function
-PF04700 GO:0019012 virion component
-PF04703 GO:0009289 pilus component
PF04703 GO:0006355 regulation of transcription, DNA-templated process
PF04704 GO:0005634 nucleus component
PF04704 GO:0046872 metal ion binding function
@@ -4569,7 +4378,6 @@ PF04722 GO:0005634 nucleus component
PF04722 GO:0004721 phosphoprotein phosphatase activity function
PF04723 GO:0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor function
PF04723 GO:0030699 glycine reductase activity function
-PF04723 GO:0055114 oxidation-reduction process process
PF04723 GO:0030700 glycine reductase complex component
PF04724 GO:0016020 membrane component
PF04724 GO:0003830 beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity function
@@ -4592,7 +4400,6 @@ PF04736 GO:0007218 neuropeptide signaling pathway process
PF04736 GO:0008255 ecdysis-triggering hormone activity function
PF04736 GO:0018990 ecdysis, chitin-based cuticle process
PF04739 GO:0005515 protein binding function
-PF04741 GO:0009405 pathogenesis process
PF04750 GO:0016021 integral component of membrane component
PF04752 GO:0003839 gamma-glutamylcyclotransferase activity function
PF04752 GO:0006751 glutathione catabolic process process
@@ -4600,14 +4407,14 @@ PF04758 GO:0005840 ribosome component
PF04758 GO:0006412 translation process
PF04758 GO:0003735 structural constituent of ribosome function
PF04762 GO:0002098 tRNA wobble uridine modification process
-PF04762 GO:0033588 Elongator holoenzyme complex component
+PF04762 GO:0033588 elongator holoenzyme complex component
+PF04766 GO:0004518 nuclease activity function
PF04767 GO:0019082 viral protein processing process
PF04767 GO:0003677 DNA binding function
PF04769 GO:0045895 positive regulation of mating-type specific transcription, DNA-templated process
PF04769 GO:0005634 nucleus component
PF04769 GO:0007531 mating type determination process
PF04769 GO:0008301 DNA binding, bending function
-PF04771 GO:0042025 host cell nucleus component
PF04771 GO:0019051 induction by virus of host apoptotic process process
PF04772 GO:1902600 proton transmembrane transport process
PF04772 GO:0016021 integral component of membrane component
@@ -4624,7 +4431,6 @@ PF04800 GO:0022900 electron transport chain process
PF04800 GO:0016651 oxidoreductase activity, acting on NAD(P)H function
PF04801 GO:0005634 nucleus component
PF04801 GO:0006351 transcription, DNA-templated process
-PF04805 GO:0055114 oxidation-reduction process process
PF04805 GO:0016972 thiol oxidase activity function
PF04810 GO:0006886 intracellular protein transport process
PF04810 GO:0030127 COPII vesicle coat component
@@ -4686,13 +4492,11 @@ PF04869 GO:0000139 Golgi membrane component
PF04871 GO:0006886 intracellular protein transport process
PF04871 GO:0016192 vesicle-mediated transport process
PF04873 GO:0005634 nucleus component
-PF04879 GO:0055114 oxidation-reduction process process
PF04879 GO:0016491 oxidoreductase activity function
PF04881 GO:0050690 regulation of defense response to virus by virus process
PF04881 GO:0005537 mannose binding function
PF04882 GO:0005779 integral component of peroxisomal membrane component
PF04882 GO:0007031 peroxisome organization process
-PF04888 GO:0009405 pathogenesis process
PF04889 GO:0005681 spliceosomal complex component
PF04889 GO:0000398 mRNA splicing, via spliceosome process
PF04891 GO:0009399 nitrogen fixation process
@@ -4700,7 +4504,6 @@ PF04891 GO:0030151 molybdenum ion binding function
PF04893 GO:0016020 membrane component
PF04898 GO:0006807 nitrogen compound metabolic process process
PF04898 GO:0015930 glutamate synthase activity function
-PF04898 GO:0055114 oxidation-reduction process process
PF04900 GO:0032040 small-subunit processome component
PF04901 GO:0006886 intracellular protein transport process
PF04901 GO:0008277 regulation of G protein-coupled receptor signaling pathway process
@@ -4790,22 +4593,24 @@ PF05000 GO:0003677 DNA binding function
PF05000 GO:0006351 transcription, DNA-templated process
PF04197 GO:0019079 viral genome replication process
PF04197 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
+PF04427 GO:0006364 rRNA processing process
+PF04427 GO:0019843 rRNA binding function
PF00562 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF00562 GO:0003677 DNA binding function
PF00562 GO:0006351 transcription, DNA-templated process
PF00125 GO:0003677 DNA binding function
-PF00125 GO:0000786 nucleosome component
PF03979 GO:0003677 DNA binding function
PF03979 GO:0006355 regulation of transcription, DNA-templated process
PF03980 GO:0000818 nuclear MIS12/MIND complex component
-PF03982 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF03982 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF03983 GO:0043130 ubiquitin binding function
PF03983 GO:0042802 identical protein binding function
-PF03983 GO:0030674 protein binding, bridging function
+PF03983 GO:0030674 protein-macromolecule adaptor activity function
PF03983 GO:0008092 cytoskeletal protein binding function
PF03985 GO:0006368 transcription elongation from RNA polymerase II promoter process
PF03985 GO:0016593 Cdc73/Paf1 complex component
PF03985 GO:0016570 histone modification process
+PF03987 GO:0019787 ubiquitin-like protein transferase activity function
PF03996 GO:0019064 fusion of virus membrane with host plasma membrane process
PF03996 GO:0046789 host cell surface receptor binding function
PF03996 GO:0019031 viral envelope component
@@ -4817,20 +4622,21 @@ PF03998 GO:0006364 rRNA processing process
PF04004 GO:0006368 transcription elongation from RNA polymerase II promoter process
PF04004 GO:0016593 Cdc73/Paf1 complex component
PF04004 GO:0016570 histone modification process
-PF04005 GO:0000077 DNA damage checkpoint process
+PF04005 GO:0000077 DNA damage checkpoint signaling process
PF04005 GO:0030896 checkpoint clamp complex component
PF04013 GO:0008175 tRNA methyltransferase activity function
PF04014 GO:0003677 DNA binding function
+PF04019 GO:0016301 kinase activity function
+PF04019 GO:0015937 coenzyme A biosynthetic process process
PF04023 GO:0046914 transition metal ion binding function
PF04026 GO:0030435 sporulation resulting in formation of a cellular spore process
PF04030 GO:0016020 membrane component
PF04030 GO:0003885 D-arabinono-1,4-lactone oxidase activity function
-PF04030 GO:0055114 oxidation-reduction process process
PF04031 GO:0006364 rRNA processing process
PF04031 GO:0004519 endonuclease activity function
PF04031 GO:0090730 Las1 complex component
+PF04032 GO:0006396 RNA processing process
PF04037 GO:0005634 nucleus component
-PF04042 GO:0003887 DNA-directed DNA polymerase activity function
PF04042 GO:0003677 DNA binding function
PF04042 GO:0006260 DNA replication process
PF04045 GO:0030833 regulation of actin filament polymerization process
@@ -4869,9 +4675,8 @@ PF04073 GO:0002161 aminoacyl-tRNA editing activity function
PF04077 GO:0002143 tRNA wobble position uridine thiolation process
PF04077 GO:0005737 cytoplasm component
PF04080 GO:0006506 GPI anchor biosynthetic process process
-PF04081 GO:0042025 host cell nucleus component
+PF04081 GO:0000731 DNA synthesis involved in DNA repair process
PF04081 GO:0006260 DNA replication process
-PF04082 GO:0005634 nucleus component
PF04082 GO:0003677 DNA binding function
PF04082 GO:0008270 zinc ion binding function
PF04082 GO:0006351 transcription, DNA-templated process
@@ -4890,8 +4695,8 @@ PF04088 GO:0005777 peroxisome component
PF04090 GO:0001164 RNA polymerase I core promoter sequence-specific DNA binding function
PF04090 GO:0006361 transcription initiation from RNA polymerase I promoter process
PF04090 GO:0001181 RNA polymerase I general transcription initiation factor activity function
-PF04091 GO:0000145 exocyst component
-PF04091 GO:0006904 vesicle docking involved in exocytosis process
+PF04091 GO:0006886 intracellular protein transport process
+PF04091 GO:0090522 vesicle tethering involved in exocytosis process
PF04092 GO:0016020 membrane component
PF04093 GO:0016021 integral component of membrane component
PF04093 GO:0008360 regulation of cell shape process
@@ -4902,7 +4707,7 @@ PF04097 GO:0005643 nuclear pore component
PF04097 GO:0017056 structural constituent of nuclear pore function
PF04099 GO:0030008 TRAPP complex component
PF04099 GO:0016192 vesicle-mediated transport process
-PF04101 GO:0016758 transferase activity, transferring hexosyl groups function
+PF04101 GO:0016758 hexosyltransferase activity function
PF04103 GO:0016021 integral component of membrane component
PF04104 GO:0006269 DNA replication, synthesis of RNA primer process
PF04106 GO:0006914 autophagy process
@@ -4926,19 +4731,21 @@ PF04121 GO:0017056 structural constituent of nuclear pore function
PF04124 GO:0017119 Golgi transport complex component
PF04131 GO:0006051 N-acetylmannosamine metabolic process process
PF04131 GO:0047465 N-acylglucosamine-6-phosphate 2-epimerase activity function
+PF04134 GO:0015035 protein-disulfide reductase activity function
PF04135 GO:0030515 snoRNA binding function
PF04135 GO:0042254 ribosome biogenesis process
PF04135 GO:0001522 pseudouridine synthesis process
PF04136 GO:0016020 membrane component
PF04136 GO:0006886 intracellular protein transport process
PF04136 GO:0005801 cis-Golgi network component
+PF04137 GO:0015035 protein-disulfide reductase activity function
PF04137 GO:0005783 endoplasmic reticulum component
-PF04137 GO:0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor function
-PF04137 GO:0003756 protein disulfide isomerase activity function
-PF04137 GO:0055114 oxidation-reduction process process
+PF04137 GO:0034975 protein folding in endoplasmic reticulum process
+PF04137 GO:0016972 thiol oxidase activity function
+PF04137 GO:0071949 FAD binding function
PF04138 GO:0016021 integral component of membrane component
PF04138 GO:0000271 polysaccharide biosynthetic process process
-PF04139 GO:0000077 DNA damage checkpoint process
+PF04139 GO:0000077 DNA damage checkpoint signaling process
PF04139 GO:0030896 checkpoint clamp complex component
PF04140 GO:0016021 integral component of membrane component
PF04140 GO:0006481 C-terminal protein methylation process
@@ -4954,14 +4761,13 @@ PF04145 GO:0016021 integral component of membrane component
PF04145 GO:0005375 copper ion transmembrane transporter activity function
PF04146 GO:0003723 RNA binding function
PF04147 GO:0032040 small-subunit processome component
-PF04148 GO:0097020 COPII adaptor activity function
+PF04148 GO:0097020 COPII receptor activity function
PF04148 GO:0016021 integral component of membrane component
PF04148 GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport process
PF04152 GO:0006302 double-strand break repair process
PF04152 GO:0005634 nucleus component
PF04152 GO:0004519 endonuclease activity function
PF04152 GO:0030145 manganese ion binding function
-PF04153 GO:0042025 host cell nucleus component
PF04153 GO:0006355 regulation of transcription, DNA-templated process
PF04159 GO:0016021 integral component of membrane component
PF04161 GO:0032366 intracellular sterol transport process
@@ -4976,7 +4782,8 @@ PF04183 GO:0019290 siderophore biosynthetic process process
PF04185 GO:0016788 hydrolase activity, acting on ester bonds function
PF04186 GO:0016020 membrane component
PF04188 GO:0006506 GPI anchor biosynthetic process process
-PF04188 GO:0004584 dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity function
+PF04188 GO:0000009 alpha-1,6-mannosyltransferase activity function
+PF04188 GO:0004376 glycolipid mannosyltransferase activity function
PF04190 GO:0045048 protein insertion into ER membrane process
PF04192 GO:0032040 small-subunit processome component
PF04192 GO:0006364 rRNA processing process
@@ -4990,8 +4797,9 @@ PF04199 GO:0019441 tryptophan catabolic process to kynurenine process
PF04205 GO:0016020 membrane component
PF04205 GO:0010181 FMN binding function
PF04220 GO:0005096 GTPase activator activity function
+PF04225 GO:0042834 peptidoglycan binding function
PF04226 GO:0016021 integral component of membrane component
-PF04227 GO:0016798 hydrolase activity, acting on glycosyl bonds function
+PF04227 GO:0004730 pseudouridylate synthase activity function
PF04231 GO:0004518 nuclease activity function
PF04234 GO:0005507 copper ion binding function
PF04234 GO:0046688 response to copper ion process
@@ -5036,6 +4844,8 @@ PF04346 GO:0034229 ethanolamine transport process
PF04346 GO:0034228 ethanolamine transmembrane transporter activity function
PF04349 GO:0016051 carbohydrate biosynthetic process process
PF04349 GO:0042597 periplasmic space component
+PF04350 GO:0043683 type IV pilus assembly process
+PF04350 GO:0043107 type IV pilus-dependent motility process
PF04353 GO:0006355 regulation of transcription, DNA-templated process
PF04354 GO:0090529 cell septum assembly process
PF04355 GO:0019867 outer membrane component
@@ -5060,6 +4870,7 @@ PF04382 GO:0005856 cytoskeleton component
PF04382 GO:0008092 cytoskeletal protein binding function
PF04382 GO:0030866 cortical actin cytoskeleton organization process
PF04384 GO:0016226 iron-sulfur cluster assembly process
+PF04389 GO:0008235 metalloexopeptidase activity function
PF04390 GO:0019867 outer membrane component
PF04390 GO:0043165 Gram-negative-bacterium-type cell outer membrane assembly process
PF04397 GO:0003677 DNA binding function
@@ -5076,8 +4887,9 @@ PF04428 GO:0016773 phosphotransferase activity, alcohol group as acceptor functi
PF04431 GO:0030570 pectate lyase activity function
PF04433 GO:0005515 protein binding function
PF04434 GO:0008270 zinc ion binding function
-PF04437 GO:0005783 endoplasmic reticulum component
-PF04437 GO:0048193 Golgi vesicle transport process
+PF04437 GO:0070939 Dsl1/NZR complex component
+PF04437 GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum process
+PF04437 GO:0060628 regulation of ER to Golgi vesicle-mediated transport process
PF04440 GO:0005737 cytoplasm component
PF04441 GO:0045893 positive regulation of transcription, DNA-templated process
PF04442 GO:0005507 copper ion binding function
@@ -5086,7 +4898,6 @@ PF04443 GO:0047474 long-chain fatty acid luciferin component ligase activity fun
PF04444 GO:0009712 catechol-containing compound metabolic process process
PF04444 GO:0018576 catechol 1,2-dioxygenase activity function
PF04444 GO:0005506 iron ion binding function
-PF04444 GO:0055114 oxidation-reduction process process
PF04445 GO:0031167 rRNA methylation process
PF04445 GO:0008990 rRNA (guanine-N2-)-methyltransferase activity function
PF04449 GO:0009289 pilus component
@@ -5119,9 +4930,8 @@ PF04501 GO:0019028 viral capsid component
PF04501 GO:0005198 structural molecule activity function
PF04504 GO:0006355 regulation of transcription, DNA-templated process
PF04505 GO:0016021 integral component of membrane component
-PF04506 GO:0005319 lipid transporter activity function
-PF04506 GO:0006869 lipid transport process
PF04506 GO:0016021 integral component of membrane component
+PF04506 GO:0006488 dolichol-linked oligosaccharide biosynthetic process process
PF04508 GO:0016032 viral process process
PF04509 GO:0016787 hydrolase activity function
PF04512 GO:0019031 viral envelope component
@@ -5131,6 +4941,8 @@ PF04513 GO:0019031 viral envelope component
PF04513 GO:0019028 viral capsid component
PF04513 GO:0005198 structural molecule activity function
PF04514 GO:0003723 RNA binding function
+PF04515 GO:0055085 transmembrane transport process
+PF04515 GO:0022857 transmembrane transporter activity function
PF04517 GO:0019054 modulation by virus of host cellular process process
PF04517 GO:0004857 enzyme inhibitor activity function
PF04522 GO:0003723 RNA binding function
@@ -5153,6 +4965,7 @@ PF04546 GO:0006355 regulation of transcription, DNA-templated process
PF04546 GO:0016987 sigma factor activity function
PF04546 GO:0003700 DNA-binding transcription factor activity function
PF04546 GO:0006352 DNA-templated transcription, initiation process
+PF04552 GO:0001216 DNA-binding transcription activator activity function
PF04555 GO:0003677 DNA binding function
PF04555 GO:0009307 DNA restriction-modification system process
PF04555 GO:0009036 type II site-specific deoxyribonuclease activity function
@@ -5170,7 +4983,7 @@ PF04558 GO:0000166 nucleotide binding function
PF04558 GO:0004812 aminoacyl-tRNA ligase activity function
PF04558 GO:0005737 cytoplasm component
PF04559 GO:0006323 DNA packaging process
-PF04559 GO:0019012 virion component
+PF04559 GO:0044423 virion component component
PF04560 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF04560 GO:0003677 DNA binding function
PF04560 GO:0006351 transcription, DNA-templated process
@@ -5190,11 +5003,11 @@ PF04567 GO:0006351 transcription, DNA-templated process
PF04568 GO:0032780 negative regulation of ATPase activity process
PF04568 GO:0042030 ATPase inhibitor activity function
PF04568 GO:0005739 mitochondrion component
-PF04573 GO:0008233 peptidase activity function
PF04573 GO:0016021 integral component of membrane component
PF04573 GO:0005787 signal peptidase complex component
PF04573 GO:0006465 signal peptide processing process
-PF04577 GO:0016757 transferase activity, transferring glycosyl groups function
+PF04575 GO:0009279 cell outer membrane component
+PF04577 GO:0016757 glycosyltransferase activity function
PF04579 GO:0045095 keratin filament component
PF04579 GO:0005198 structural molecule activity function
PF04583 GO:0019058 viral life cycle process
@@ -5206,9 +5019,7 @@ PF04589 GO:0005634 nucleus component
PF04589 GO:0003677 DNA binding function
PF04589 GO:0006355 regulation of transcription, DNA-templated process
PF04595 GO:0016032 viral process process
-PF04597 GO:0005783 endoplasmic reticulum component
PF04597 GO:0006486 protein glycosylation process
-PF04597 GO:0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity function
PF04597 GO:0016021 integral component of membrane component
PF04602 GO:0071766 Actinobacterium-type cell wall biogenesis process
PF04602 GO:0052636 arabinosyltransferase activity function
@@ -5220,7 +5031,8 @@ PF04608 GO:0006629 lipid metabolic process process
PF04610 GO:0030255 protein secretion by the type IV secretion system process
PF04611 GO:0019953 sexual reproduction process
PF04611 GO:0006355 regulation of transcription, DNA-templated process
-PF04612 GO:0009306 protein secretion process
+PF04612 GO:0015628 protein secretion by the type II secretion system process
+PF04612 GO:0015627 type II protein secretion system complex component
PF00772 GO:0005524 ATP binding function
PF00772 GO:0006260 DNA replication process
PF00772 GO:0003678 DNA helicase activity function
@@ -5233,12 +5045,13 @@ PF01624 GO:0030983 mismatched DNA binding function
PF05192 GO:0005524 ATP binding function
PF05192 GO:0006298 mismatch repair process
PF05192 GO:0030983 mismatched DNA binding function
+PF05003 GO:0045927 positive regulation of growth process
PF05007 GO:0006506 GPI anchor biosynthetic process process
+PF05007 GO:0004376 glycolipid mannosyltransferase activity function
PF05007 GO:0016021 integral component of membrane component
-PF05007 GO:0016758 transferase activity, transferring hexosyl groups function
+PF05007 GO:0051751 alpha-1,4-mannosyltransferase activity function
PF05008 GO:0016020 membrane component
PF05008 GO:0006886 intracellular protein transport process
-PF05009 GO:0042025 host cell nucleus component
PF05009 GO:0016032 viral process process
PF05011 GO:0006397 mRNA processing process
PF05011 GO:0016788 hydrolase activity, acting on ester bonds function
@@ -5254,11 +5067,8 @@ PF05025 GO:0005996 monosaccharide metabolic process process
PF05025 GO:0048029 monosaccharide binding function
PF05025 GO:0016853 isomerase activity function
PF05026 GO:0003723 RNA binding function
-PF05026 GO:0016787 hydrolase activity function
-PF05026 GO:0030145 manganese ion binding function
PF05028 GO:0004649 poly(ADP-ribose) glycohydrolase activity function
PF05028 GO:0005975 carbohydrate metabolic process process
-PF05030 GO:0003713 transcription coactivator activity function
PF05033 GO:0005634 nucleus component
PF05033 GO:0008270 zinc ion binding function
PF05033 GO:0034968 histone lysine methylation process
@@ -5278,22 +5088,18 @@ PF05049 GO:0005525 GTP binding function
PF05051 GO:0005507 copper ion binding function
PF05051 GO:0005758 mitochondrial intermembrane space component
PF05051 GO:0016531 copper chaperone activity function
-PF05051 GO:0006825 copper ion transport process
PF05052 GO:0016020 membrane component
PF05052 GO:0015694 mercury ion transport process
PF05052 GO:0015097 mercury ion transmembrane transporter activity function
PF05053 GO:0005634 nucleus component
-PF05058 GO:0009405 pathogenesis process
PF05059 GO:0019028 viral capsid component
PF05060 GO:0005795 Golgi stack component
PF05060 GO:0008455 alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity function
PF05060 GO:0016021 integral component of membrane component
PF05060 GO:0009312 oligosaccharide biosynthetic process process
PF05066 GO:0006355 regulation of transcription, DNA-templated process
-PF05066 GO:0006351 transcription, DNA-templated process
PF05071 GO:0016020 membrane component
-PF05071 GO:0009055 electron transfer activity function
-PF05071 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
+PF05071 GO:0032981 mitochondrial respiratory chain complex I assembly process
PF05072 GO:0016020 membrane component
PF05072 GO:0019033 viral tegument component
PF05073 GO:0019028 viral capsid component
@@ -5332,7 +5138,6 @@ PF05138 GO:0010124 phenylacetate catabolic process process
PF05139 GO:0046677 response to antibiotic process
PF05145 GO:0010468 regulation of gene expression process
PF05145 GO:0016021 integral component of membrane component
-PF05148 GO:0005730 nucleolus component
PF05148 GO:0008168 methyltransferase activity function
PF05149 GO:0031514 motile cilium component
PF05149 GO:0005516 calmodulin binding function
@@ -5343,7 +5148,6 @@ PF05151 GO:0015979 photosynthesis process
PF05153 GO:0019310 inositol catabolic process process
PF05153 GO:0005506 iron ion binding function
PF05153 GO:0005737 cytoplasm component
-PF05153 GO:0055114 oxidation-reduction process process
PF05153 GO:0050113 inositol oxygenase activity function
PF05158 GO:0005666 RNA polymerase III complex component
PF05158 GO:0006383 transcription by RNA polymerase III process
@@ -5372,20 +5176,19 @@ PF05191 GO:0004017 adenylate kinase activity function
PF05194 GO:0019627 urea metabolic process process
PF05194 GO:0065003 protein-containing complex assembly process
PF05194 GO:0016151 nickel cation binding function
-PF05195 GO:0004177 aminopeptidase activity function
+PF05195 GO:0070006 metalloaminopeptidase activity function
PF05195 GO:0030145 manganese ion binding function
PF05197 GO:0016020 membrane component
-PF05197 GO:0015672 monovalent inorganic cation transport process
-PF05197 GO:0005261 cation channel activity function
+PF05197 GO:0042802 identical protein binding function
+PF05197 GO:0005267 potassium channel activity function
+PF05197 GO:0071805 potassium ion transmembrane transport process
PF05199 GO:0016614 oxidoreductase activity, acting on CH-OH group of donors function
-PF05199 GO:0055114 oxidation-reduction process process
PF05203 GO:0030908 protein splicing process
PF05204 GO:0003677 DNA binding function
PF05204 GO:0030908 protein splicing process
PF05204 GO:0004519 endonuclease activity function
PF05206 GO:0008168 methyltransferase activity function
PF05206 GO:0008033 tRNA processing process
-PF05208 GO:0030176 integral component of endoplasmic reticulum membrane component
PF05208 GO:0000030 mannosyltransferase activity function
PF05209 GO:0051302 regulation of cell division process
PF05210 GO:0016020 membrane component
@@ -5393,6 +5196,7 @@ PF05210 GO:0007275 multicellular organism development process
PF05210 GO:0009966 regulation of signal transduction process
PF05211 GO:0009279 cell outer membrane component
PF05215 GO:0016020 membrane component
+PF05219 GO:0106370 protein-L-histidine N-pros-methyltransferase activity function
PF05223 GO:0046677 response to antibiotic process
PF04218 GO:0003677 DNA binding function
PF05225 GO:0003677 DNA binding function
@@ -5400,9 +5204,6 @@ PF05236 GO:0005669 transcription factor TFIID complex component
PF05236 GO:0006352 DNA-templated transcription, initiation process
PF05238 GO:0007059 chromosome segregation process
PF05238 GO:0051382 kinetochore assembly process
-PF05241 GO:0047750 cholestenol delta-isomerase activity function
-PF05241 GO:0016021 integral component of membrane component
-PF05241 GO:0016125 sterol metabolic process process
PF05251 GO:0006487 protein N-linked glycosylation process
PF05251 GO:0034998 oligosaccharyltransferase I complex component
PF05261 GO:0003677 DNA binding function
@@ -5411,11 +5212,9 @@ PF05269 GO:0003677 DNA binding function
PF05269 GO:0006355 regulation of transcription, DNA-templated process
PF05270 GO:0046556 alpha-L-arabinofuranosidase activity function
PF05270 GO:0046373 L-arabinose metabolic process process
-PF05271 GO:0019089 transmission of virus process
PF05273 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF05273 GO:0003677 DNA binding function
PF05273 GO:0019083 viral transcription process
-PF05274 GO:0042025 host cell nucleus component
PF05274 GO:0019031 viral envelope component
PF05275 GO:0009279 cell outer membrane component
PF05275 GO:0006878 cellular copper ion homeostasis process
@@ -5430,7 +5229,6 @@ PF05281 GO:0007218 neuropeptide signaling pathway process
PF05292 GO:0006633 fatty acid biosynthetic process process
PF05292 GO:0050080 malonyl-CoA decarboxylase activity function
PF05294 GO:0005576 extracellular region component
-PF05294 GO:0009405 pathogenesis process
PF05296 GO:0050909 sensory perception of taste process
PF05296 GO:0007186 G protein-coupled receptor signaling pathway process
PF05296 GO:0016021 integral component of membrane component
@@ -5439,8 +5237,6 @@ PF05297 GO:0019087 transformation of host cell by virus process
PF05297 GO:0016021 integral component of membrane component
PF05298 GO:0005576 extracellular region component
PF05298 GO:0042742 defense response to bacterium process
-PF05300 GO:0005739 mitochondrion component
-PF05300 GO:0061617 MICOS complex component
PF05301 GO:0005874 microtubule component
PF05301 GO:0019799 tubulin N-acetyltransferase activity function
PF05301 GO:0071929 alpha-tubulin acetylation process
@@ -5451,7 +5247,6 @@ PF05314 GO:0019031 viral envelope component
PF05316 GO:0005761 mitochondrial ribosome component
PF05316 GO:0006412 translation process
PF05316 GO:0003735 structural constituent of ribosome function
-PF05318 GO:0019089 transmission of virus process
PF05320 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF05320 GO:0003677 DNA binding function
PF05320 GO:0006351 transcription, DNA-templated process
@@ -5470,7 +5265,6 @@ PF05349 GO:0003677 DNA binding function
PF05349 GO:0008270 zinc ion binding function
PF05349 GO:0045893 positive regulation of transcription, DNA-templated process
PF05353 GO:0005576 extracellular region component
-PF05353 GO:0009405 pathogenesis process
PF05353 GO:0019871 sodium channel inhibitor activity function
PF05354 GO:0019068 virion assembly process
PF05355 GO:0042627 chylomicron component
@@ -5479,9 +5273,8 @@ PF05355 GO:0008047 enzyme activator activity function
PF05355 GO:0006629 lipid metabolic process process
PF05361 GO:0042325 regulation of phosphorylation process
PF05361 GO:0005737 cytoplasm component
-PF05363 GO:0019049 evasion or tolerance of host defenses by virus process
+PF05363 GO:0019049 mitigation of host defenses by virus process
PF05365 GO:0005750 mitochondrial respiratory chain complex III component
-PF05365 GO:0005743 mitochondrial inner membrane component
PF05365 GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c process
PF05366 GO:0016020 membrane component
PF05366 GO:0030234 enzyme regulator activity function
@@ -5493,9 +5286,7 @@ PF05369 GO:0032259 methylation process
PF05372 GO:0005576 extracellular region component
PF05372 GO:0019836 hemolysis by symbiont of host erythrocytes process
PF05373 GO:0016706 2-oxoglutarate-dependent dioxygenase activity function
-PF05373 GO:0055114 oxidation-reduction process process
PF05374 GO:0005576 extracellular region component
-PF05374 GO:0009405 pathogenesis process
PF05374 GO:0019871 sodium channel inhibitor activity function
PF05375 GO:0030414 peptidase inhibitor activity function
PF05379 GO:0016817 hydrolase activity, acting on acid anhydrides function
@@ -5512,7 +5303,8 @@ PF07421 GO:0005576 extracellular region component
PF07421 GO:0005184 neuropeptide hormone activity function
PF15085 GO:0005102 signaling receptor binding function
PF15085 GO:0005184 neuropeptide hormone activity function
-PF05925 GO:0009405 pathogenesis process
+PF05994 GO:0030833 regulation of actin filament polymerization process
+PF05994 GO:0031267 small GTPase binding function
PF05925 GO:0016791 phosphatase activity function
PF04834 GO:0016021 integral component of membrane component
PF04834 GO:0009966 regulation of signal transduction process
@@ -5544,6 +5336,8 @@ PF01199 GO:0003735 structural constituent of ribosome function
PF00095 GO:0005576 extracellular region component
PF00095 GO:0030414 peptidase inhibitor activity function
PF02070 GO:0006940 regulation of smooth muscle contraction process
+PF01934 GO:0110001 toxin-antitoxin complex component
+PF01934 GO:0004540 ribonuclease activity function
PF01884 GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups function
PF01627 GO:0000160 phosphorelay signal transduction system process
PF01383 GO:0030089 phycobilisome component
@@ -5556,27 +5350,24 @@ PF01284 GO:0016020 membrane component
PF00258 GO:0010181 FMN binding function
PF12641 GO:0010181 FMN binding function
PF12682 GO:0010181 FMN binding function
+PF01244 GO:0070573 metallodipeptidase activity function
PF01244 GO:0006508 proteolysis process
-PF01244 GO:0016805 dipeptidase activity function
PF05362 GO:0004252 serine-type endopeptidase activity function
PF05362 GO:0006508 proteolysis process
PF05362 GO:0004176 ATP-dependent peptidase activity function
-PF02738 GO:0055114 oxidation-reduction process process
PF02738 GO:0016491 oxidoreductase activity function
PF01648 GO:0000287 magnesium ion binding function
PF01648 GO:0008897 holo-[acyl-carrier-protein] synthase activity function
PF00391 GO:0016310 phosphorylation process
PF00391 GO:0016772 transferase activity, transferring phosphorus-containing groups function
PF02789 GO:0006508 proteolysis process
-PF02789 GO:0004177 aminopeptidase activity function
+PF02789 GO:0070006 metalloaminopeptidase activity function
PF03711 GO:0003824 catalytic activity function
-PF06130 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF06130 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF12404 GO:0006508 proteolysis process
-PF12404 GO:0004177 aminopeptidase activity function
PF12404 GO:0005737 cytoplasm component
+PF12404 GO:0070006 metalloaminopeptidase activity function
PF12404 GO:0030145 manganese ion binding function
-PF12404 GO:0008235 metalloexopeptidase activity function
-PF00210 GO:0006879 cellular iron ion homeostasis process
PF00210 GO:0008199 ferric iron binding function
PF02870 GO:0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity function
PF02870 GO:0006281 DNA repair process
@@ -5605,8 +5396,6 @@ PF05511 GO:0000276 mitochondrial proton-transporting ATP synthase complex, coupl
PF05511 GO:0015078 proton transmembrane transporter activity function
PF05827 GO:1902600 proton transmembrane transport process
PF05827 GO:0033180 proton-transporting V-type ATPase, V1 domain component
-PF05827 GO:0046961 proton-transporting ATPase activity, rotational mechanism function
-PF05827 GO:0046933 proton-transporting ATP synthase activity, rotational mechanism function
PF05493 GO:0033179 proton-transporting V-type ATPase, V0 domain component
PF05493 GO:1902600 proton transmembrane transport process
PF05493 GO:0015078 proton transmembrane transporter activity function
@@ -5642,7 +5431,6 @@ PF05432 GO:0007155 cell adhesion process
PF05432 GO:0005576 extracellular region component
PF05432 GO:0001503 ossification process
PF05791 GO:0016020 membrane component
-PF05791 GO:0009405 pathogenesis process
PF05847 GO:0003677 DNA binding function
PF05847 GO:0006355 regulation of transcription, DNA-templated process
PF05920 GO:0003677 DNA binding function
@@ -5661,6 +5449,7 @@ PF05392 GO:0004129 cytochrome-c oxidase activity function
PF05392 GO:0005746 mitochondrial respirasome component
PF05428 GO:0051424 corticotropin-releasing hormone binding function
PF05745 GO:0019867 outer membrane component
+PF05556 GO:0030018 Z disc component
PF05792 GO:0007155 cell adhesion process
PF05388 GO:0004185 serine-type carboxypeptidase activity function
PF05388 GO:0005773 vacuole component
@@ -5668,11 +5457,10 @@ PF05864 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF05864 GO:0003677 DNA binding function
PF05864 GO:0006351 transcription, DNA-templated process
PF05836 GO:0007275 multicellular organism development process
-PF05836 GO:0042600 chorion component
+PF05836 GO:0042600 egg chorion component
PF05452 GO:0005576 extracellular region component
PF05737 GO:0005518 collagen binding function
PF05425 GO:0016021 integral component of membrane component
-PF05454 GO:0007016 cytoskeletal anchoring at plasma membrane process
PF05454 GO:0016010 dystrophin-associated glycoprotein complex component
PF05395 GO:0004864 protein phosphatase inhibitor activity function
PF05395 GO:0007165 signal transduction process
@@ -5680,7 +5468,6 @@ PF05499 GO:0045892 negative regulation of transcription, DNA-templated process
PF05499 GO:0005634 nucleus component
PF05558 GO:0046658 anchored component of plasma membrane component
PF05430 GO:0016645 oxidoreductase activity, acting on the CH-NH group of donors function
-PF05430 GO:0055114 oxidation-reduction process process
PF05506 GO:0016042 lipid catabolic process process
PF05506 GO:0004629 phospholipase C activity function
PF05527 GO:0042981 regulation of apoptotic process process
@@ -5695,8 +5482,6 @@ PF05653 GO:0015693 magnesium ion transport process
PF05653 GO:0016021 integral component of membrane component
PF05653 GO:0015095 magnesium ion transmembrane transporter activity function
PF05656 GO:0016021 integral component of membrane component
-PF05695 GO:0005524 ATP binding function
-PF05695 GO:0009507 chloroplast component
PF05832 GO:0016021 integral component of membrane component
PF05853 GO:0019475 L-lysine catabolic process to acetate process
PF05853 GO:0016740 transferase activity function
@@ -5704,6 +5489,7 @@ PF05871 GO:0071985 multivesicular body sorting pathway process
PF05871 GO:0000814 ESCRT II complex component
PF05891 GO:0006480 N-terminal protein amino acid methylation process
PF05891 GO:0008168 methyltransferase activity function
+PF05903 GO:0008233 peptidase activity function
PF05869 GO:0003677 DNA binding function
PF05869 GO:0032775 DNA methylation on adenine process
PF05869 GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity function
@@ -5715,7 +5501,6 @@ PF05497 GO:0003796 lysozyme activity function
PF05720 GO:0007155 cell adhesion process
PF05424 GO:0046789 host cell surface receptor binding function
PF05424 GO:0016021 integral component of membrane component
-PF05424 GO:0009405 pathogenesis process
PF05502 GO:0005869 dynactin complex component
PF05672 GO:0000226 microtubule cytoskeleton organization process
PF05672 GO:0015630 microtubule cytoskeleton component
@@ -5729,25 +5514,23 @@ PF05505 GO:0019013 viral nucleocapsid component
PF05842 GO:0005186 pheromone activity function
PF05842 GO:0005576 extracellular region component
PF05842 GO:0007154 cell communication process
-PF05427 GO:0017134 fibroblast growth factor binding function
PF05397 GO:0006357 regulation of transcription by RNA polymerase II process
PF05397 GO:0016592 mediator complex component
PF05397 GO:0003712 transcription coregulator activity function
PF05719 GO:0070273 phosphatidylinositol-4-phosphate binding function
-PF05637 GO:0016757 transferase activity, transferring glycosyl groups function
+PF05637 GO:0016757 glycosyltransferase activity function
PF05637 GO:0016021 integral component of membrane component
PF05693 GO:0005978 glycogen biosynthetic process process
PF05693 GO:0004373 glycogen (starch) synthase activity function
PF05823 GO:0008289 lipid binding function
PF05800 GO:0031412 gas vesicle organization process
PF05662 GO:0019867 outer membrane component
-PF05662 GO:0009405 pathogenesis process
+PF05622 GO:0008017 microtubule binding function
+PF05622 GO:0031122 cytoplasmic microtubule organization process
PF05465 GO:0031412 gas vesicle organization process
PF05465 GO:0031411 gas vesicle component
PF05658 GO:0019867 outer membrane component
-PF05658 GO:0009405 pathogenesis process
PF05459 GO:0006355 regulation of transcription, DNA-templated process
-PF05784 GO:0009405 pathogenesis process
PF05393 GO:0016021 integral component of membrane component
PF05439 GO:0016021 integral component of membrane component
PF05390 GO:0042546 cell wall biogenesis process
@@ -5757,8 +5540,7 @@ PF05805 GO:0016021 integral component of membrane component
PF05851 GO:0019058 viral life cycle process
PF05893 GO:0008218 bioluminescence process
PF05893 GO:0003995 acyl-CoA dehydrogenase activity function
-PF05893 GO:0055114 oxidation-reduction process process
-PF05557 GO:0007094 mitotic spindle assembly checkpoint process
+PF05557 GO:0007094 mitotic spindle assembly checkpoint signaling process
PF05507 GO:0001527 microfibril component
PF05854 GO:0042262 DNA protection process
PF05436 GO:0005576 extracellular region component
@@ -5776,23 +5558,15 @@ PF05440 GO:0015948 methanogenesis process
PF05440 GO:0030269 tetrahydromethanopterin S-methyltransferase activity function
PF05440 GO:0016021 integral component of membrane component
PF05481 GO:0016020 membrane component
-PF05676 GO:0003954 NADH dehydrogenase activity function
PF05676 GO:0005739 mitochondrion component
-PF05676 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
-PF05821 GO:0003954 NADH dehydrogenase activity function
PF05821 GO:0005739 mitochondrion component
-PF05821 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
-PF05531 GO:0019028 viral capsid component
-PF05896 GO:0055114 oxidation-reduction process process
+PF05531 GO:0039679 viral occlusion body component
PF05896 GO:0006814 sodium ion transport process
PF05896 GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor function
PF05401 GO:0008757 S-adenosylmethionine-dependent methyltransferase activity function
-PF05401 GO:0009877 nodulation process
PF05401 GO:0009312 oligosaccharide biosynthetic process process
-PF05830 GO:0009877 nodulation process
PF05830 GO:0009312 oligosaccharide biosynthetic process process
-PF05830 GO:0016758 transferase activity, transferring hexosyl groups function
-PF05819 GO:0009877 nodulation process
+PF05830 GO:0016758 hexosyltransferase activity function
PF05460 GO:0003677 DNA binding function
PF05460 GO:0005664 nuclear origin of replication recognition complex component
PF05460 GO:0006260 DNA replication process
@@ -5800,7 +5574,7 @@ PF05788 GO:0003723 RNA binding function
PF05788 GO:0006351 transcription, DNA-templated process
PF05788 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF05625 GO:0002098 tRNA wobble uridine modification process
-PF05625 GO:0033588 Elongator holoenzyme complex component
+PF05625 GO:0033588 elongator holoenzyme complex component
PF05870 GO:0016831 carboxy-lyase activity function
PF05874 GO:0042811 pheromone biosynthetic process process
PF05874 GO:0007218 neuropeptide signaling pathway process
@@ -5812,12 +5586,11 @@ PF05476 GO:0070131 positive regulation of mitochondrial translation process
PF05648 GO:0005779 integral component of peroxisomal membrane component
PF05648 GO:0016559 peroxisome fission process
PF05407 GO:0004197 cysteine-type endopeptidase activity function
-PF05407 GO:0017111 nucleoside-triphosphatase activity function
-PF05407 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF05408 GO:0019082 viral protein processing process
PF05408 GO:0004197 cysteine-type endopeptidase activity function
PF05408 GO:0016032 viral process process
PF05409 GO:0019082 viral protein processing process
+PF05409 GO:0008233 peptidase activity function
PF05410 GO:0004197 cysteine-type endopeptidase activity function
PF05412 GO:0019082 viral protein processing process
PF05412 GO:0016032 viral process process
@@ -5859,7 +5632,6 @@ PF05757 GO:0019898 extrinsic component of membrane component
PF05757 GO:0005509 calcium ion binding function
PF05757 GO:0009654 photosystem II oxygen evolving complex component
PF05757 GO:0015979 photosynthesis process
-PF05394 GO:0009405 pathogenesis process
PF05398 GO:0030494 bacteriochlorophyll biosynthetic process process
PF05398 GO:0015979 photosynthesis process
PF05645 GO:0003677 DNA binding function
@@ -5874,7 +5646,7 @@ PF05817 GO:0016021 integral component of membrane component
PF05817 GO:0006487 protein N-linked glycosylation process
PF05433 GO:0019867 outer membrane component
PF05868 GO:0016021 integral component of membrane component
-PF05868 GO:0019012 virion component
+PF05868 GO:0044423 virion component component
PF05750 GO:0016021 integral component of membrane component
PF05750 GO:0019013 viral nucleocapsid component
PF05748 GO:0016021 integral component of membrane component
@@ -5898,7 +5670,6 @@ PF05889 GO:0016740 transferase activity function
PF05669 GO:0016592 mediator complex component
PF05669 GO:0006355 regulation of transcription, DNA-templated process
PF05669 GO:0003712 transcription coregulator activity function
-PF05563 GO:0009405 pathogenesis process
PF05463 GO:0005615 extracellular space component
PF05474 GO:0050817 coagulation process
PF05474 GO:0005576 extracellular region component
@@ -5908,7 +5679,6 @@ PF05482 GO:0007349 cellularization process
PF05482 GO:0005737 cytoplasm component
PF05504 GO:0016020 membrane component
PF05504 GO:0009847 spore germination process
-PF05480 GO:0009405 pathogenesis process
PF05843 GO:0006397 mRNA processing process
PF05843 GO:0005634 nucleus component
PF05835 GO:0019905 syntaxin binding function
@@ -5917,7 +5687,7 @@ PF05793 GO:0005634 nucleus component
PF05793 GO:0003677 DNA binding function
PF05793 GO:0032968 positive regulation of transcription elongation from RNA polymerase II promoter process
PF05793 GO:0006367 transcription initiation from RNA polymerase II promoter process
-PF05434 GO:0016021 integral component of membrane component
+PF05434 GO:0005765 lysosomal membrane component
PF05724 GO:0008757 S-adenosylmethionine-dependent methyltransferase activity function
PF05404 GO:0005783 endoplasmic reticulum component
PF05404 GO:0016021 integral component of membrane component
@@ -5931,7 +5701,10 @@ PF05735 GO:0005576 extracellular region component
PF05472 GO:0003677 DNA binding function
PF05472 GO:0006274 DNA replication termination process
PF05472 GO:0005737 cytoplasm component
-PF05431 GO:0009405 pathogenesis process
+PF05876 GO:0005524 ATP binding function
+PF05876 GO:0004519 endonuclease activity function
+PF05876 GO:0016887 ATPase function
+PF05431 GO:0090729 toxin activity function
PF05513 GO:0005576 extracellular region component
PF05513 GO:0000746 conjugation process
PF05818 GO:0046999 regulation of conjugation process
@@ -5971,7 +5744,6 @@ PF05746 GO:0005524 ATP binding function
PF05746 GO:0006420 arginyl-tRNA aminoacylation process
PF05453 GO:0008200 ion channel inhibitor activity function
PF05453 GO:0005576 extracellular region component
-PF05453 GO:0009405 pathogenesis process
PF05495 GO:0008270 zinc ion binding function
PF02163 GO:0006508 proteolysis process
PF02163 GO:0004222 metalloendopeptidase activity function
@@ -6000,13 +5772,11 @@ PF13442 GO:0009055 electron transfer activity function
PF13442 GO:0020037 heme binding function
PF07743 GO:0051259 protein complex oligomerization process
PF00441 GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors function
-PF00441 GO:0055114 oxidation-reduction process process
PF08771 GO:0044877 protein-containing complex binding function
PF09077 GO:0003677 DNA binding function
PF09077 GO:0006313 transposition, DNA-mediated process
PF07711 GO:0008270 zinc ion binding function
PF07711 GO:0004663 Rab geranylgeranyltransferase activity function
-PF09008 GO:0009405 pathogenesis process
PF09034 GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling process
PF09034 GO:0005515 protein binding function
PF06554 GO:0007608 sensory perception of smell process
@@ -6018,20 +5788,18 @@ PF06369 GO:0006812 cation transport process
PF06369 GO:0015267 channel activity function
PF09000 GO:0043022 ribosome binding function
PF09000 GO:0003723 RNA binding function
-PF09000 GO:0009405 pathogenesis process
PF09000 GO:0016788 hydrolase activity, acting on ester bonds function
PF06373 GO:0007186 G protein-coupled receptor signaling pathway process
PF06373 GO:0005615 extracellular space component
PF06373 GO:0009267 cellular response to starvation process
PF06373 GO:0008343 adult feeding behavior process
+PF06373 GO:0043410 positive regulation of MAPK cascade process
PF06373 GO:0032099 negative regulation of appetite process
-PF06373 GO:0000186 activation of MAPKK activity process
PF07834 GO:0007165 signal transduction process
PF07834 GO:0005096 GTPase activator activity function
PF06399 GO:0009890 negative regulation of biosynthetic process process
PF05993 GO:0046812 host cell surface binding function
PF05993 GO:0039624 viral outer capsid component
-PF05993 GO:0009405 pathogenesis process
PF05993 GO:0046718 viral entry into host cell process
PF14960 GO:0005753 mitochondrial proton-transporting ATP synthase complex component
PF07361 GO:0009055 electron transfer activity function
@@ -6039,8 +5807,6 @@ PF07361 GO:0022900 electron transport chain process
PF07361 GO:0020037 heme binding function
PF07361 GO:0005506 iron ion binding function
PF07361 GO:0042597 periplasmic space component
-PF06442 GO:0042493 response to drug process
-PF06442 GO:0055114 oxidation-reduction process process
PF06442 GO:0004146 dihydrofolate reductase activity function
PF06874 GO:0006094 gluconeogenesis process
PF06874 GO:0042132 fructose 1,6-bisphosphate 1-phosphatase activity function
@@ -6053,7 +5819,7 @@ PF05927 GO:0008061 chitin binding function
PF05927 GO:0005737 cytoplasm component
PF05929 GO:0019069 viral capsid assembly process
PF05933 GO:0015986 ATP synthesis coupled proton transport process
-PF05933 GO:0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) component
+PF05933 GO:0045263 proton-transporting ATP synthase complex, coupling factor F(o) component
PF05933 GO:0015078 proton transmembrane transporter activity function
PF05937 GO:0016055 Wnt signaling pathway process
PF05937 GO:0008013 beta-catenin binding function
@@ -6071,7 +5837,6 @@ PF05992 GO:1904680 peptide transmembrane transporter activity function
PF05992 GO:0015833 peptide transport process
PF05996 GO:0010024 phytochromobilin biosynthetic process process
PF05996 GO:0016636 oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor function
-PF05996 GO:0055114 oxidation-reduction process process
PF05996 GO:0050897 cobalt ion binding function
PF06005 GO:0090529 cell septum assembly process
PF06005 GO:0005737 cytoplasm component
@@ -6138,7 +5903,7 @@ PF06326 GO:0005198 structural molecule activity function
PF06327 GO:0004016 adenylate cyclase activity function
PF06327 GO:0005886 plasma membrane component
PF06327 GO:0006171 cAMP biosynthetic process process
-PF06331 GO:0006355 regulation of transcription, DNA-templated process
+PF06331 GO:0006367 transcription initiation from RNA polymerase II promoter process
PF06331 GO:0000439 transcription factor TFIIH core complex component
PF06331 GO:0006289 nucleotide-excision repair process
PF06333 GO:0006357 regulation of transcription by RNA polymerase II process
@@ -6149,13 +5914,11 @@ PF06355 GO:0019836 hemolysis by symbiont of host erythrocytes process
PF06357 GO:0019855 calcium channel inhibitor activity function
PF06357 GO:0006952 defense response process
PF06357 GO:0005576 extracellular region component
-PF06357 GO:0009405 pathogenesis process
-PF06363 GO:0019012 virion component
+PF06363 GO:0044423 virion component component
PF06372 GO:0005634 nucleus component
PF06372 GO:0000245 spliceosomal complex assembly process
PF06374 GO:0006120 mitochondrial electron transport, NADH to ubiquinone process
PF06374 GO:0005743 mitochondrial inner membrane component
-PF06374 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
PF06384 GO:0008013 beta-catenin binding function
PF06385 GO:0006355 regulation of transcription, DNA-templated process
PF06385 GO:0019058 viral life cycle process
@@ -6184,19 +5947,17 @@ PF06420 GO:0003697 single-stranded DNA binding function
PF06420 GO:0006281 DNA repair process
PF06420 GO:0000002 mitochondrial genome maintenance process
PF06423 GO:0006506 GPI anchor biosynthetic process process
-PF06423 GO:0016746 transferase activity, transferring acyl groups function
+PF06423 GO:0016746 acyltransferase activity function
PF06423 GO:0016021 integral component of membrane component
PF06427 GO:0006486 protein glycosylation process
PF06427 GO:0003980 UDP-glucose:glycoprotein glucosyltransferase activity function
PF06432 GO:0006506 GPI anchor biosynthetic process process
-PF06432 GO:0017176 phosphatidylinositol N-acetylglucosaminyltransferase activity function
PF06432 GO:0016021 integral component of membrane component
PF06433 GO:0030058 amine dehydrogenase activity function
-PF06433 GO:0055114 oxidation-reduction process process
PF06433 GO:0042597 periplasmic space component
PF06436 GO:0046782 regulation of viral transcription process
+PF06436 GO:0044423 virion component component
PF06436 GO:0005198 structural molecule activity function
-PF06436 GO:0019012 virion component
PF06437 GO:0000287 magnesium ion binding function
PF06437 GO:0050483 IMP 5'-nucleotidase activity function
PF06437 GO:0006190 inosine salvage process
@@ -6209,17 +5970,14 @@ PF06451 GO:0005576 extracellular region component
PF06451 GO:0042742 defense response to bacterium process
PF06457 GO:0005216 ion channel activity function
PF06457 GO:0005576 extracellular region component
-PF06457 GO:0009405 pathogenesis process
PF06459 GO:0005219 ryanodine-sensitive calcium-release channel activity function
PF06459 GO:0016021 integral component of membrane component
PF06459 GO:0006874 cellular calcium ion homeostasis process
PF06466 GO:0005634 nucleus component
PF06466 GO:0006355 regulation of transcription, DNA-templated process
PF06466 GO:0004402 histone acetyltransferase activity function
-PF06471 GO:0016896 exoribonuclease activity, producing 5'-phosphomonoesters function
PF06471 GO:0008168 methyltransferase activity function
-PF06471 GO:0004197 cysteine-type endopeptidase activity function
-PF06471 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
+PF06471 GO:0004532 exoribonuclease activity function
PF06478 GO:0003723 RNA binding function
PF06478 GO:0005524 ATP binding function
PF06478 GO:0006351 transcription, DNA-templated process
@@ -6227,20 +5985,17 @@ PF06478 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF06484 GO:0007165 signal transduction process
PF06484 GO:0016021 integral component of membrane component
PF06485 GO:0003723 RNA binding function
-PF06511 GO:0009405 pathogenesis process
PF06516 GO:0055085 transmembrane transport process
PF06558 GO:0045182 translation regulator activity function
PF06573 GO:0007275 multicellular organism development process
PF06573 GO:0008270 zinc ion binding function
PF06573 GO:0045893 positive regulation of transcription, DNA-templated process
-PF06578 GO:0009405 pathogenesis process
PF06581 GO:0005634 nucleus component
PF06581 GO:0007096 regulation of exit from mitosis process
PF06596 GO:0016020 membrane component
PF06596 GO:0009523 photosystem II component
PF06596 GO:0015979 photosynthesis process
PF05733 GO:0003723 RNA binding function
-PF05733 GO:0019013 viral nucleocapsid component
PF06608 GO:0005634 nucleus component
PF06616 GO:0000287 magnesium ion binding function
PF06616 GO:0003677 DNA binding function
@@ -6248,7 +6003,6 @@ PF06616 GO:0009307 DNA restriction-modification system process
PF06616 GO:0009036 type II site-specific deoxyribonuclease activity function
PF06638 GO:0007275 multicellular organism development process
PF06638 GO:0016021 integral component of membrane component
-PF06645 GO:0008233 peptidase activity function
PF06645 GO:0016021 integral component of membrane component
PF06645 GO:0005787 signal peptidase complex component
PF06645 GO:0006465 signal peptide processing process
@@ -6260,16 +6014,12 @@ PF06682 GO:0030176 integral component of endoplasmic reticulum membrane componen
PF06687 GO:0005886 plasma membrane component
PF06699 GO:0006506 GPI anchor biosynthetic process process
PF06699 GO:0005789 endoplasmic reticulum membrane component
-PF06703 GO:0008233 peptidase activity function
PF06703 GO:0016021 integral component of membrane component
PF06703 GO:0005787 signal peptidase complex component
PF06703 GO:0006465 signal peptide processing process
PF06713 GO:0030153 bacteriocin immunity process
PF06714 GO:0005515 protein binding function
PF06720 GO:0039693 viral DNA genome replication process
-PF06728 GO:0042765 GPI-anchor transamidase complex component
-PF06728 GO:0016021 integral component of membrane component
-PF06728 GO:0016255 attachment of GPI anchor to protein process
PF06729 GO:0006355 regulation of transcription, DNA-templated process
PF06729 GO:0034080 CENP-A containing nucleosome assembly process
PF06740 GO:0000226 microtubule cytoskeleton organization process
@@ -6277,8 +6027,6 @@ PF06753 GO:0005576 extracellular region component
PF06753 GO:0005179 hormone activity function
PF06754 GO:0019634 organic phosphonate metabolic process process
PF06754 GO:0015716 organic phosphonate transport process
-PF06756 GO:0007275 multicellular organism development process
-PF06756 GO:0042600 chorion component
PF06769 GO:0006401 RNA catabolic process process
PF06769 GO:0004519 endonuclease activity function
PF06775 GO:0019915 lipid storage process
@@ -6288,16 +6036,14 @@ PF06809 GO:0016021 integral component of membrane component
PF06810 GO:0019069 viral capsid assembly process
PF06814 GO:0016021 integral component of membrane component
PF06825 GO:0003714 transcription corepressor activity function
-PF06870 GO:0042025 host cell nucleus component
PF06870 GO:0003677 DNA binding function
PF06870 GO:0006351 transcription, DNA-templated process
PF06872 GO:0004197 cysteine-type endopeptidase activity function
-PF06872 GO:0009405 pathogenesis process
PF06883 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF06883 GO:0005634 nucleus component
PF06883 GO:0006351 transcription, DNA-templated process
PF06925 GO:0009247 glycolipid biosynthetic process process
-PF06925 GO:0016758 transferase activity, transferring hexosyl groups function
+PF06925 GO:0016758 hexosyltransferase activity function
PF06936 GO:0006886 intracellular protein transport process
PF06936 GO:0030176 integral component of endoplasmic reticulum membrane component
PF06954 GO:0005576 extracellular region component
@@ -6315,7 +6061,6 @@ PF06974 GO:0004144 diacylglycerol O-acyltransferase activity function
PF06988 GO:0009399 nitrogen fixation process
PF06989 GO:0005737 cytoplasm component
PF06990 GO:0009247 glycolipid biosynthetic process process
-PF06990 GO:0005794 Golgi apparatus component
PF06990 GO:0016021 integral component of membrane component
PF06990 GO:0001733 galactosylceramide sulfotransferase activity function
PF06992 GO:0006270 DNA replication initiation process
@@ -6323,6 +6068,7 @@ PF06994 GO:0001533 cornified envelope component
PF06994 GO:0030216 keratinocyte differentiation process
PF07012 GO:0009289 pilus component
PF07012 GO:0007155 cell adhesion process
+PF07038 GO:0039526 modulation by virus of host apoptotic process process
PF07043 GO:0005886 plasma membrane component
PF07057 GO:0003677 DNA binding function
PF07057 GO:0005524 ATP binding function
@@ -6336,6 +6082,7 @@ PF07074 GO:0016021 integral component of membrane component
PF07086 GO:0005789 endoplasmic reticulum membrane component
PF07086 GO:0007029 endoplasmic reticulum organization process
PF07088 GO:0005524 ATP binding function
+PF07110 GO:0016491 oxidoreductase activity function
PF07111 GO:0030154 cell differentiation process
PF07123 GO:0009523 photosystem II component
PF07123 GO:0009507 chloroplast component
@@ -6343,12 +6090,13 @@ PF07123 GO:0015979 photosynthesis process
PF07124 GO:0019028 viral capsid component
PF07124 GO:0005198 structural molecule activity function
PF07127 GO:0046872 metal ion binding function
-PF07127 GO:0009878 nodule morphogenesis process
PF07155 GO:0016020 membrane component
+PF07159 GO:0031267 small GTPase binding function
PF07160 GO:0007059 chromosome segregation process
PF07160 GO:0051301 cell division process
PF07160 GO:0008017 microtubule binding function
PF07168 GO:0071705 nitrogen compound transport process
+PF07175 GO:0031214 biomineral tissue development process
PF07178 GO:0019867 outer membrane component
PF07178 GO:0000746 conjugation process
PF07207 GO:0009507 chloroplast component
@@ -6360,7 +6108,6 @@ PF07213 GO:0014068 positive regulation of phosphatidylinositol 3-kinase signalin
PF07213 GO:0005102 signaling receptor binding function
PF07213 GO:0050776 regulation of immune response process
PF07225 GO:0005739 mitochondrion component
-PF07225 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
PF07229 GO:0003677 DNA binding function
PF07231 GO:0006952 defense response process
PF07238 GO:0035438 cyclic-di-GMP binding function
@@ -6371,8 +6118,7 @@ PF07263 GO:0030198 extracellular matrix organization process
PF07263 GO:0001503 ossification process
PF07267 GO:0019028 viral capsid component
PF07271 GO:0016021 integral component of membrane component
-PF07271 GO:0009405 pathogenesis process
-PF07271 GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules process
+PF07271 GO:0044650 adhesion of symbiont to host cell process
PF07284 GO:0016836 hydro-lyase activity function
PF07284 GO:0030494 bacteriochlorophyll biosynthetic process process
PF07284 GO:0019685 photosynthesis, dark reaction process
@@ -6388,7 +6134,6 @@ PF07328 GO:0004519 endonuclease activity function
PF07335 GO:0016977 chitosanase activity function
PF07347 GO:0005743 mitochondrial inner membrane component
PF07347 GO:0042773 ATP synthesis coupled electron transport process
-PF07347 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
PF07348 GO:0009898 cytoplasmic side of plasma membrane component
PF07352 GO:0042262 DNA protection process
PF07352 GO:0003690 double-stranded DNA binding function
@@ -6397,14 +6142,12 @@ PF07357 GO:0030701 NAD+-dinitrogen-reductase ADP-D-ribosyltransferase activity f
PF07359 GO:0042742 defense response to bacterium process
PF07365 GO:0030550 acetylcholine receptor inhibitor activity function
PF07365 GO:0005576 extracellular region component
-PF07365 GO:0009405 pathogenesis process
PF07366 GO:0030638 polyketide metabolic process process
PF07378 GO:1902209 negative regulation of bacterial-type flagellum assembly process
PF07378 GO:0048027 mRNA 5'-UTR binding function
PF07378 GO:0006402 mRNA catabolic process process
PF07382 GO:0030261 chromosome condensation process
PF07382 GO:0003677 DNA binding function
-PF07393 GO:0048278 vesicle docking process
PF07393 GO:0005737 cytoplasm component
PF07393 GO:0006887 exocytosis process
PF07402 GO:0016021 integral component of membrane component
@@ -6425,7 +6168,6 @@ PF07464 GO:0005576 extracellular region component
PF07465 GO:0015979 photosynthesis process
PF07469 GO:0005634 nucleus component
PF07473 GO:0005576 extracellular region component
-PF07473 GO:0009405 pathogenesis process
PF12689 GO:0016791 phosphatase activity function
PF11612 GO:0015628 protein secretion by the type II secretion system process
PF11612 GO:0015627 type II protein secretion system complex component
@@ -6433,20 +6175,16 @@ PF10503 GO:0016787 hydrolase activity function
PF10503 GO:0005576 extracellular region component
PF01881 GO:0016788 hydrolase activity, acting on ester bonds function
PF07355 GO:0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor function
-PF07355 GO:0055114 oxidation-reduction process process
-PF05932 GO:0050708 regulation of protein secretion process
-PF05932 GO:0005737 cytoplasm component
+PF05932 GO:0030254 protein secretion by the type III secretion system process
PF05935 GO:0004062 aryl sulfotransferase activity function
PF05944 GO:0019069 viral capsid assembly process
PF05944 GO:0003677 DNA binding function
PF05944 GO:0004519 endonuclease activity function
PF05946 GO:0009289 pilus component
PF05946 GO:0043230 extracellular organelle component
-PF05946 GO:0009405 pathogenesis process
PF05953 GO:0005184 neuropeptide hormone activity function
PF05955 GO:0016021 integral component of membrane component
PF05955 GO:0016032 viral process process
-PF05957 GO:0043022 ribosome binding function
PF05958 GO:0006396 RNA processing process
PF05958 GO:0008173 RNA methyltransferase activity function
PF05969 GO:0009523 photosystem II component
@@ -6459,7 +6197,6 @@ PF05971 GO:0008168 methyltransferase activity function
PF05975 GO:0016021 integral component of membrane component
PF05995 GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen function
PF05995 GO:0005506 iron ion binding function
-PF05995 GO:0055114 oxidation-reduction process process
PF05997 GO:0030688 preribosome, small subunit precursor component
PF05997 GO:0006364 rRNA processing process
PF06003 GO:0006397 mRNA processing process
@@ -6481,7 +6218,6 @@ PF06046 GO:0000145 exocyst component
PF06046 GO:0006887 exocytosis process
PF06052 GO:0000334 3-hydroxyanthranilate 3,4-dioxygenase activity function
PF06052 GO:0005506 iron ion binding function
-PF06052 GO:0055114 oxidation-reduction process process
PF06056 GO:0019069 viral capsid assembly process
PF06056 GO:0005524 ATP binding function
PF06058 GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA process
@@ -6560,9 +6296,11 @@ PF06350 GO:0008203 cholesterol metabolic process process
PF06350 GO:0016298 lipase activity function
PF06367 GO:0003779 actin binding function
PF06367 GO:0016043 cellular component organization process
+PF06371 GO:0031267 small GTPase binding function
PF06371 GO:0003779 actin binding function
-PF06371 GO:0017048 Rho GTPase binding function
PF06371 GO:0030036 actin cytoskeleton organization process
+PF06375 GO:0030123 AP-3 adaptor complex component
+PF06375 GO:0015031 protein transport process
PF06377 GO:0005179 hormone activity function
PF06393 GO:0043065 positive regulation of apoptotic process process
PF06393 GO:0005737 cytoplasm component
@@ -6571,7 +6309,7 @@ PF06401 GO:0008201 heparin binding function
PF06401 GO:0050750 low-density lipoprotein particle receptor binding function
PF06414 GO:0005524 ATP binding function
PF06414 GO:0016301 kinase activity function
-PF06416 GO:0044403 symbiotic process process
+PF06416 GO:0044403 biological process involved in symbiotic interaction process
PF06416 GO:0004842 ubiquitin-protein transferase activity function
PF06419 GO:0017119 Golgi transport complex component
PF06419 GO:0006891 intra-Golgi vesicle-mediated transport process
@@ -6579,6 +6317,7 @@ PF06424 GO:0000398 mRNA splicing, via spliceosome process
PF06426 GO:0006535 cysteine biosynthetic process from serine process
PF06426 GO:0009001 serine O-acetyltransferase activity function
PF06426 GO:0005737 cytoplasm component
+PF06439 GO:0016787 hydrolase activity function
PF06446 GO:0006879 cellular iron ion homeostasis process
PF06446 GO:0005576 extracellular region component
PF06452 GO:0030246 carbohydrate binding function
@@ -6588,7 +6327,6 @@ PF16011 GO:0030246 carbohydrate binding function
PF16011 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF16011 GO:0016052 carbohydrate catabolic process process
PF06453 GO:0005576 extracellular region component
-PF06453 GO:0009405 pathogenesis process
PF06456 GO:0019904 protein domain specific binding function
PF06463 GO:0006777 Mo-molybdopterin cofactor biosynthetic process process
PF06463 GO:0051539 4 iron, 4 sulfur cluster binding function
@@ -6597,10 +6335,8 @@ PF06467 GO:0008270 zinc ion binding function
PF06479 GO:0006397 mRNA processing process
PF06479 GO:0004540 ribonuclease activity function
PF06481 GO:0022900 electron transport chain process
-PF06481 GO:0008827 cytochrome o ubiquinol oxidase activity function
+PF06481 GO:0009486 cytochrome bo3 ubiquinol oxidase activity function
PF06481 GO:0016021 integral component of membrane component
-PF06481 GO:0055114 oxidation-reduction process process
-PF06495 GO:0042025 host cell nucleus component
PF06495 GO:0006397 mRNA processing process
PF06495 GO:0046660 female sex differentiation process
PF06506 GO:0003677 DNA binding function
@@ -6661,7 +6397,6 @@ PF06632 GO:0006302 double-strand break repair process
PF06632 GO:0005634 nucleus component
PF06632 GO:0003677 DNA binding function
PF06632 GO:0006310 DNA recombination process
-PF06635 GO:0009877 nodulation process
PF06644 GO:0005739 mitochondrion component
PF06644 GO:0065003 protein-containing complex assembly process
PF06652 GO:0004930 G protein-coupled receptor activity function
@@ -6688,10 +6423,13 @@ PF06734 GO:0005524 ATP binding function
PF06734 GO:0004672 protein kinase activity function
PF06734 GO:0016032 viral process process
PF06736 GO:0005267 potassium channel activity function
-PF06743 GO:0004672 protein kinase activity function
+PF06737 GO:0016787 hydrolase activity function
+PF06743 GO:0044528 regulation of mitochondrial mRNA stability process
PF06751 GO:0006520 cellular amino acid metabolic process process
PF06751 GO:0008851 ethanolamine ammonia-lyase activity function
PF06766 GO:0005576 extracellular region component
+PF06778 GO:0020037 heme binding function
+PF06778 GO:0016491 oxidoreductase activity function
PF06788 GO:0005886 plasma membrane component
PF06800 GO:0034219 carbohydrate transmembrane transport process
PF06800 GO:0015144 carbohydrate transmembrane transporter activity function
@@ -6712,10 +6450,12 @@ PF06849 GO:0006188 IMP biosynthetic process process
PF06849 GO:0005524 ATP binding function
PF06858 GO:0005525 GTP binding function
PF06859 GO:0008168 methyltransferase activity function
-PF06862 GO:0005634 nucleus component
+PF06862 GO:0034511 U3 snoRNA binding function
+PF06862 GO:0005730 nucleolus component
+PF06862 GO:0006364 rRNA processing process
PF06876 GO:0007165 signal transduction process
+PF06881 GO:0006368 transcription elongation from RNA polymerase II promoter process
PF06881 GO:0005634 nucleus component
-PF06881 GO:0006357 regulation of transcription by RNA polymerase II process
PF06881 GO:0070449 elongin complex component
PF06899 GO:0016021 integral component of membrane component
PF06899 GO:0009246 enterobacterial common antigen biosynthetic process process
@@ -6748,14 +6488,10 @@ PF06984 GO:0006412 translation process
PF06984 GO:0003735 structural constituent of ribosome function
PF07022 GO:0045892 negative regulation of transcription, DNA-templated process
PF07022 GO:0003677 DNA binding function
-PF12242 GO:0055114 oxidation-reduction process process
PF12242 GO:0016491 oxidoreductase activity function
PF07062 GO:0016021 integral component of membrane component
-PF07095 GO:0009276 Gram-negative-bacterium-type cell wall component
PF07095 GO:0016021 integral component of membrane component
PF07137 GO:0046422 violaxanthin de-epoxidase activity function
-PF07137 GO:0055114 oxidation-reduction process process
-PF07137 GO:0009507 chloroplast component
PF07147 GO:0005840 ribosome component
PF07147 GO:0006412 translation process
PF07147 GO:0005739 mitochondrion component
@@ -6763,7 +6499,6 @@ PF07147 GO:0003735 structural constituent of ribosome function
PF07148 GO:0008643 carbohydrate transport process
PF07148 GO:0042597 periplasmic space component
PF07156 GO:0030328 prenylcysteine catabolic process process
-PF07156 GO:0055114 oxidation-reduction process process
PF07156 GO:0016670 oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor function
PF07163 GO:0005779 integral component of peroxisomal membrane component
PF07163 GO:0045046 protein import into peroxisome membrane process
@@ -6776,10 +6511,10 @@ PF07194 GO:0004673 protein histidine kinase activity function
PF07195 GO:0007155 cell adhesion process
PF07195 GO:0009288 bacterial-type flagellum component
PF07201 GO:0019867 outer membrane component
-PF07201 GO:0009405 pathogenesis process
PF07201 GO:0046903 secretion process
+PF07240 GO:0002376 immune system process process
PF07243 GO:0016021 integral component of membrane component
-PF07243 GO:0019012 virion component
+PF07243 GO:0044423 virion component component
PF07244 GO:0019867 outer membrane component
PF16649 GO:0005125 cytokine activity function
PF16649 GO:0005576 extracellular region component
@@ -6787,11 +6522,10 @@ PF16649 GO:0006955 immune response process
PF07259 GO:0010951 negative regulation of endopeptidase activity process
PF07259 GO:0004866 endopeptidase inhibitor activity function
PF07309 GO:0044781 bacterial-type flagellum organization process
-PF07340 GO:0042025 host cell nucleus component
-PF07340 GO:0050792 regulation of viral process process
+PF07340 GO:0039695 DNA-templated viral transcription process
PF07354 GO:0005576 extracellular region component
PF07354 GO:0007339 binding of sperm to zona pellucida process
-PF07392 GO:0007050 cell cycle arrest process
+PF07392 GO:0051726 regulation of cell cycle process
PF07392 GO:0008285 negative regulation of cell population proliferation process
PF07392 GO:0006915 apoptotic process process
PF07404 GO:0000781 chromosome, telomeric region component
@@ -6802,9 +6536,7 @@ PF07432 GO:0003677 DNA binding function
PF07448 GO:0005576 extracellular region component
PF07448 GO:0046849 bone remodeling process
PF07462 GO:0016020 membrane component
-PF07462 GO:0009405 pathogenesis process
PF07463 GO:0016788 hydrolase activity, acting on ester bonds function
-PF08686 GO:0008233 peptidase activity function
PF03193 GO:0005525 GTP binding function
PF03193 GO:0003924 GTPase activity function
PF06017 GO:0016459 myosin complex component
@@ -6819,10 +6551,8 @@ PF06431 GO:0003677 DNA binding function
PF06431 GO:0005524 ATP binding function
PF06431 GO:0006260 DNA replication process
PF06444 GO:0006120 mitochondrial electron transport, NADH to ubiquinone process
-PF06444 GO:0055114 oxidation-reduction process process
PF06444 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
PF06455 GO:0042773 ATP synthesis coupled electron transport process
-PF06455 GO:0055114 oxidation-reduction process process
PF06455 GO:0008137 NADH dehydrogenase (ubiquinone) activity function
PF06470 GO:0005524 ATP binding function
PF06470 GO:0005515 protein binding function
@@ -6853,7 +6583,7 @@ PF07486 GO:0016787 hydrolase activity function
PF07491 GO:0032515 negative regulation of phosphoprotein phosphatase activity process
PF07491 GO:0004865 protein serine/threonine phosphatase inhibitor activity function
PF07508 GO:0003677 DNA binding function
-PF07508 GO:0000150 recombinase activity function
+PF07508 GO:0000150 DNA strand exchange activity function
PF07498 GO:0006353 DNA-templated transcription, termination process
PF07497 GO:0006353 DNA-templated transcription, termination process
PF07497 GO:0003723 RNA binding function
@@ -6881,16 +6611,15 @@ PF02603 GO:0006109 regulation of carbohydrate metabolic process process
PF01210 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
PF01210 GO:0046168 glycerol-3-phosphate catabolic process process
PF01210 GO:0051287 NAD binding function
-PF01210 GO:0055114 oxidation-reduction process process
PF01043 GO:0016020 membrane component
PF01043 GO:0017038 protein import process
PF12924 GO:0046914 transition metal ion binding function
+PF06929 GO:0004482 mRNA (guanine-N7-)-methyltransferase activity function
PF06929 GO:0005525 GTP binding function
PF06929 GO:0019013 viral nucleocapsid component
PF06929 GO:0016032 viral process process
PF01557 GO:0003824 catalytic activity function
PF00296 GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen function
-PF00296 GO:0055114 oxidation-reduction process process
PF06415 GO:0006007 glucose catabolic process process
PF06415 GO:0004619 phosphoglycerate mutase activity function
PF06415 GO:0005737 cytoplasm component
@@ -6946,17 +6675,17 @@ PF07545 GO:0005634 nucleus component
PF07545 GO:0006355 regulation of transcription, DNA-templated process
PF16517 GO:0007165 signal transduction process
PF00664 GO:0055085 transmembrane transport process
+PF00664 GO:0140359 ABC-type transporter activity function
PF00664 GO:0005524 ATP binding function
PF00664 GO:0016021 integral component of membrane component
-PF00664 GO:0042626 ATPase-coupled transmembrane transporter activity function
PF06472 GO:0055085 transmembrane transport process
+PF06472 GO:0140359 ABC-type transporter activity function
PF06472 GO:0005524 ATP binding function
PF06472 GO:0016021 integral component of membrane component
-PF06472 GO:0042626 ATPase-coupled transmembrane transporter activity function
PF13748 GO:0055085 transmembrane transport process
+PF13748 GO:0140359 ABC-type transporter activity function
PF13748 GO:0005524 ATP binding function
PF13748 GO:0016021 integral component of membrane component
-PF13748 GO:0042626 ATPase-coupled transmembrane transporter activity function
PF00955 GO:0006820 anion transport process
PF00955 GO:0016021 integral component of membrane component
PF00554 GO:0003677 DNA binding function
@@ -6971,26 +6700,25 @@ PF06480 GO:0005524 ATP binding function
PF06480 GO:0004222 metalloendopeptidase activity function
PF06480 GO:0016021 integral component of membrane component
PF06480 GO:0008270 zinc ion binding function
+PF06480 GO:0004176 ATP-dependent peptidase activity function
PF00916 GO:0008272 sulfate transport process
PF00916 GO:0015116 sulfate transmembrane transporter activity function
PF00916 GO:0016021 integral component of membrane component
-PF02765 GO:0000784 nuclear chromosome, telomeric region component
+PF02765 GO:0000781 chromosome, telomeric region component
PF02765 GO:0003677 DNA binding function
PF02765 GO:0000723 telomere maintenance process
PF03232 GO:0006744 ubiquinone biosynthetic process process
-PF03232 GO:0055114 oxidation-reduction process process
+PF03232 GO:0004497 monooxygenase activity function
PF01292 GO:0009055 electron transfer activity function
PF01292 GO:0016021 integral component of membrane component
PF01637 GO:0005524 ATP binding function
PF01353 GO:0008218 bioluminescence process
PF00010 GO:0046983 protein dimerization activity function
PF02873 GO:0008762 UDP-N-acetylmuramate dehydrogenase activity function
-PF02873 GO:0055114 oxidation-reduction process process
PF00874 GO:0006355 regulation of transcription, DNA-templated process
PF00199 GO:0020037 heme binding function
PF00199 GO:0004096 catalase activity function
-PF00199 GO:0055114 oxidation-reduction process process
-PF00870 GO:0044212 transcription regulatory region DNA binding function
+PF00870 GO:0000976 transcription cis-regulatory region binding function
PF03612 GO:0016021 integral component of membrane component
PF03612 GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system process
PF03612 GO:0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity function
@@ -7033,17 +6761,15 @@ PF07745 GO:0015926 glucosidase activity function
PF07765 GO:0003779 actin binding function
PF07740 GO:0008200 ion channel inhibitor activity function
PF07740 GO:0005576 extracellular region component
-PF07740 GO:0009405 pathogenesis process
PF07722 GO:0016787 hydrolase activity function
-PF07685 GO:0009236 cobalamin biosynthetic process process
PF07685 GO:0003824 catalytic activity function
PF07690 GO:0055085 transmembrane transport process
+PF07690 GO:0022857 transmembrane transporter activity function
PF07726 GO:0005524 ATP binding function
-PF07726 GO:0016887 ATPase activity function
+PF07726 GO:0016887 ATPase function
PF07728 GO:0005524 ATP binding function
-PF07728 GO:0016887 ATPase activity function
+PF07728 GO:0016887 ATPase function
PF07731 GO:0005507 copper ion binding function
-PF07731 GO:0055114 oxidation-reduction process process
PF07731 GO:0016491 oxidoreductase activity function
PF07732 GO:0005507 copper ion binding function
PF07733 GO:0008408 3'-5' exonuclease activity function
@@ -7065,7 +6791,7 @@ PF08254 GO:0009088 threonine biosynthetic process process
PF08254 GO:0031554 regulation of DNA-templated transcription, termination process
PF08755 GO:0003677 DNA binding function
PF08042 GO:0018189 pyrroloquinoline quinone biosynthetic process process
-PF09604 GO:0008556 potassium transmembrane transporter activity, phosphorylative mechanism function
+PF09604 GO:0008556 P-type potassium transmembrane transporter activity function
PF09604 GO:0043462 regulation of ATPase activity process
PF09604 GO:0005886 plasma membrane component
PF02790 GO:0022900 electron transport chain process
@@ -7092,13 +6818,11 @@ PF10032 GO:0045047 protein targeting to ER process
PF00502 GO:0030089 phycobilisome component
PF00502 GO:0015979 photosynthesis process
PF00815 GO:0046872 metal ion binding function
-PF00815 GO:0000105 histidine biosynthetic process process
+PF00815 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
PF00815 GO:0051287 NAD binding function
-PF00815 GO:0004399 histidinol dehydrogenase activity function
-PF00815 GO:0055114 oxidation-reduction process process
PF04006 GO:0005634 nucleus component
PF04006 GO:0034457 Mpp10 complex component
-PF04006 GO:0005732 small nucleolar ribonucleoprotein complex component
+PF04006 GO:0005732 sno(s)RNA-containing ribonucleoprotein complex component
PF04006 GO:0006364 rRNA processing process
PF02774 GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor function
PF02774 GO:0008652 cellular amino acid biosynthetic process process
@@ -7110,7 +6834,6 @@ PF08702 GO:0005577 fibrinogen complex component
PF08702 GO:0030168 platelet activation process
PF08702 GO:0005102 signaling receptor binding function
PF00390 GO:0004471 malate dehydrogenase (decarboxylating) (NAD+) activity function
-PF00390 GO:0055114 oxidation-reduction process process
PF03949 GO:0051287 NAD binding function
PF04675 GO:0003677 DNA binding function
PF04675 GO:0006281 DNA repair process
@@ -7134,22 +6857,18 @@ PF13545 GO:0003677 DNA binding function
PF13545 GO:0006355 regulation of transcription, DNA-templated process
PF01149 GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity function
PF01149 GO:0006284 base-excision repair process
-PF01149 GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds function
-PF01149 GO:0003684 damaged DNA binding function
+PF01149 GO:0019104 DNA N-glycosylase activity function
PF01149 GO:0008270 zinc ion binding function
PF08117 GO:0019855 calcium channel inhibitor activity function
PF08117 GO:0005576 extracellular region component
-PF08117 GO:0009405 pathogenesis process
PF02086 GO:0032775 DNA methylation on adenine process
PF02086 GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity function
PF08804 GO:0003697 single-stranded DNA binding function
PF10662 GO:0005524 ATP binding function
PF10662 GO:0006576 cellular biogenic amine metabolic process process
PF07823 GO:0004112 cyclic-nucleotide phosphodiesterase activity function
-PF07886 GO:0009405 pathogenesis process
PF07936 GO:0008200 ion channel inhibitor activity function
PF07936 GO:0042151 nematocyst component
-PF07936 GO:0009405 pathogenesis process
PF07936 GO:0090729 toxin activity function
PF07887 GO:0005516 calmodulin binding function
PF07839 GO:0005516 calmodulin binding function
@@ -7178,29 +6897,25 @@ PF07781 GO:0019028 viral capsid component
PF07781 GO:0005198 structural molecule activity function
PF07810 GO:0016021 integral component of membrane component
PF07822 GO:0005576 extracellular region component
-PF07822 GO:0009405 pathogenesis process
PF07822 GO:0019871 sodium channel inhibitor activity function
PF07829 GO:0030550 acetylcholine receptor inhibitor activity function
PF07829 GO:0005576 extracellular region component
-PF07829 GO:0009405 pathogenesis process
PF07945 GO:0005576 extracellular region component
-PF07945 GO:0009405 pathogenesis process
PF07952 GO:0008320 protein transmembrane transporter activity function
PF07952 GO:0046929 negative regulation of neurotransmitter secretion process
-PF07952 GO:0009405 pathogenesis process
PF07928 GO:0042147 retrograde transport, endosome to Golgi process
PF07947 GO:0016021 integral component of membrane component
PF08112 GO:0015986 ATP synthesis coupled proton transport process
PF08112 GO:0033178 proton-transporting two-sector ATPase complex, catalytic domain component
PF08112 GO:0042626 ATPase-coupled transmembrane transporter activity function
PF08098 GO:0042151 nematocyst component
-PF08098 GO:0009405 pathogenesis process
PF08098 GO:0019871 sodium channel inhibitor activity function
PF08043 GO:0003779 actin binding function
PF08043 GO:0030036 actin cytoskeleton organization process
PF08043 GO:0030054 cell junction component
PF08027 GO:0045735 nutrient reservoir activity function
-PF08027 GO:0009405 pathogenesis process
+PF08105 GO:0019732 antifungal humoral response process
+PF08105 GO:0019731 antibacterial humoral response process
PF08106 GO:0042742 defense response to bacterium process
PF08106 GO:0042381 hemolymph coagulation process
PF08107 GO:0042742 defense response to bacterium process
@@ -7212,8 +6927,8 @@ PF08023 GO:0006952 defense response process
PF08023 GO:0005576 extracellular region component
PF08025 GO:0005576 extracellular region component
PF08025 GO:0019836 hemolysis by symbiont of host erythrocytes process
+PF08024 GO:0098542 defense response to other organism process
PF08024 GO:0005576 extracellular region component
-PF08024 GO:0019836 hemolysis by symbiont of host erythrocytes process
PF08026 GO:0005576 extracellular region component
PF08026 GO:0042381 hemolymph coagulation process
PF08102 GO:0005576 extracellular region component
@@ -7230,9 +6945,8 @@ PF08072 GO:0006260 DNA replication process
PF08072 GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides function
PF08096 GO:0043303 mast cell degranulation process
PF08096 GO:0005576 extracellular region component
-PF08096 GO:0009405 pathogenesis process
PF08001 GO:0044386 integral to host endoplasmic reticulum membrane component
-PF08001 GO:0030683 evasion or tolerance by virus of host immune response process
+PF08001 GO:0030683 mitigation of host immune response by virus process
PF08140 GO:0042302 structural constituent of cuticle function
PF08184 GO:0042302 structural constituent of cuticle function
PF08147 GO:0005634 nucleus component
@@ -7240,15 +6954,14 @@ PF08147 GO:0003723 RNA binding function
PF08147 GO:0005524 ATP binding function
PF08147 GO:0003724 RNA helicase activity function
PF08019 GO:0016021 integral component of membrane component
+PF08137 GO:0008285 negative regulation of cell population proliferation process
PF08131 GO:0005576 extracellular region component
-PF08131 GO:0009405 pathogenesis process
PF08181 GO:1900192 positive regulation of single-species biofilm formation process
PF08085 GO:0016020 membrane component
PF08085 GO:0009636 response to toxic substance process
PF08057 GO:0046677 response to antibiotic process
PF08165 GO:0016021 integral component of membrane component
PF08150 GO:0016021 integral component of membrane component
-PF08152 GO:0005634 nucleus component
PF08152 GO:0003723 RNA binding function
PF08152 GO:0005524 ATP binding function
PF08152 GO:0004386 helicase activity function
@@ -7259,7 +6972,6 @@ PF08118 GO:0000001 mitochondrion inheritance process
PF08118 GO:0005743 mitochondrial inner membrane component
PF08118 GO:0007005 mitochondrion organization process
PF08039 GO:0005739 mitochondrion component
-PF08040 GO:0003954 NADH dehydrogenase activity function
PF08040 GO:0005739 mitochondrion component
PF08122 GO:0022900 electron transport chain process
PF08122 GO:0005739 mitochondrion component
@@ -7319,36 +7031,25 @@ PF08038 GO:0005742 mitochondrial outer membrane translocase complex component
PF08038 GO:0030150 protein import into mitochondrial matrix process
PF08086 GO:0019870 potassium channel inhibitor activity function
PF08086 GO:0005576 extracellular region component
-PF08086 GO:0009405 pathogenesis process
PF08089 GO:0005576 extracellular region component
-PF08089 GO:0009405 pathogenesis process
PF08089 GO:0090729 toxin activity function
PF08091 GO:0005576 extracellular region component
-PF08091 GO:0009405 pathogenesis process
PF08092 GO:0005576 extracellular region component
PF08092 GO:0019871 sodium channel inhibitor activity function
PF08093 GO:0005576 extracellular region component
-PF08093 GO:0009405 pathogenesis process
PF08093 GO:0019871 sodium channel inhibitor activity function
PF08094 GO:0005576 extracellular region component
-PF08094 GO:0009405 pathogenesis process
PF08094 GO:0019871 sodium channel inhibitor activity function
PF08095 GO:0005576 extracellular region component
-PF08095 GO:0009405 pathogenesis process
PF08097 GO:0005576 extracellular region component
PF08099 GO:0019855 calcium channel inhibitor activity function
PF08099 GO:0005576 extracellular region component
-PF08099 GO:0009405 pathogenesis process
PF08115 GO:0005576 extracellular region component
-PF08115 GO:0009405 pathogenesis process
PF08116 GO:0005576 extracellular region component
-PF08116 GO:0009405 pathogenesis process
PF08119 GO:0019870 potassium channel inhibitor activity function
PF08119 GO:0005576 extracellular region component
-PF08119 GO:0009405 pathogenesis process
PF08120 GO:0019870 potassium channel inhibitor activity function
PF08120 GO:0005576 extracellular region component
-PF08120 GO:0009405 pathogenesis process
PF08120 GO:0090729 toxin activity function
PF08121 GO:0030550 acetylcholine receptor inhibitor activity function
PF08121 GO:0005576 extracellular region component
@@ -7358,12 +7059,10 @@ PF09515 GO:0005886 plasma membrane component
PF09515 GO:0015234 thiamine transmembrane transporter activity function
PF09505 GO:0015948 methanogenesis process
PF09505 GO:0008168 methyltransferase activity function
-PF17001 GO:0009306 protein secretion process
-PF08988 GO:0009405 pathogenesis process
+PF17001 GO:0030254 protein secretion by the type III secretion system process
PF01056 GO:0006355 regulation of transcription, DNA-templated process
PF01056 GO:0003700 DNA-binding transcription factor activity function
PF13806 GO:0008942 nitrite reductase [NAD(P)H] activity function
-PF13806 GO:0055114 oxidation-reduction process process
PF09506 GO:0050530 glucosylglycerol 3-phosphatase activity function
PF11734 GO:0016879 ligase activity, forming carbon-nitrogen bonds function
PF11734 GO:0005524 ATP binding function
@@ -7377,21 +7076,20 @@ PF02050 GO:0009288 bacterial-type flagellum component
PF02050 GO:0071973 bacterial-type flagellum-dependent cell motility process
PF13597 GO:0006260 DNA replication process
PF13597 GO:0008998 ribonucleoside-triphosphate reductase activity function
-PF13597 GO:0055114 oxidation-reduction process process
PF13597 GO:0016491 oxidoreductase activity function
PF07966 GO:0006508 proteolysis process
PF07966 GO:0004190 aspartic-type endopeptidase activity function
PF07821 GO:0004556 alpha-amylase activity function
PF07821 GO:0005509 calcium ion binding function
PF07821 GO:0005975 carbohydrate metabolic process process
-PF07931 GO:0005524 ATP binding function
-PF07931 GO:0016740 transferase activity function
PF07930 GO:0004177 aminopeptidase activity function
PF07782 GO:0016021 integral component of membrane component
PF07847 GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen function
-PF07847 GO:0055114 oxidation-reduction process process
+PF07946 GO:0005783 endoplasmic reticulum component
+PF07946 GO:0036503 ERAD pathway process
+PF07946 GO:0032469 endoplasmic reticulum calcium ion homeostasis process
+PF07946 GO:0005509 calcium ion binding function
PF07955 GO:0005739 mitochondrion component
-PF07955 GO:0055114 oxidation-reduction process process
PF07955 GO:0016491 oxidoreductase activity function
PF07912 GO:0005788 endoplasmic reticulum lumen component
PF07912 GO:0009306 protein secretion process
@@ -7424,7 +7122,6 @@ PF07925 GO:0003723 RNA binding function
PF07925 GO:0032774 RNA biosynthetic process process
PF07925 GO:0019013 viral nucleocapsid component
PF07925 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
-PF07808 GO:0005634 nucleus component
PF07809 GO:0009968 negative regulation of signal transduction process
PF07809 GO:0005737 cytoplasm component
PF07780 GO:0005634 nucleus component
@@ -7436,13 +7133,11 @@ PF07962 GO:0006974 cellular response to DNA damage stimulus process
PF07851 GO:0016021 integral component of membrane component
PF07953 GO:0005576 extracellular region component
PF07953 GO:0046929 negative regulation of neurotransmitter secretion process
-PF07953 GO:0009405 pathogenesis process
PF07926 GO:0006606 protein import into nucleus process
PF07820 GO:0000746 conjugation process
PF07927 GO:0003729 mRNA binding function
PF07776 GO:0005634 nucleus component
PF07776 GO:0008270 zinc ion binding function
-PF07967 GO:0042025 host cell nucleus component
PF07967 GO:0008270 zinc ion binding function
PF07984 GO:1990817 RNA adenylyltransferase activity function
PF07989 GO:0005815 microtubule organizing center component
@@ -7452,7 +7147,6 @@ PF07973 GO:0004812 aminoacyl-tRNA ligase activity function
PF08142 GO:0005634 nucleus component
PF08142 GO:0042254 ribosome biogenesis process
PF08031 GO:0050660 flavin adenine dinucleotide binding function
-PF08031 GO:0055114 oxidation-reduction process process
PF08031 GO:0016491 oxidoreductase activity function
PF08145 GO:0006364 rRNA processing process
PF08172 GO:0030173 integral component of Golgi membrane component
@@ -7462,6 +7156,8 @@ PF07998 GO:0006508 proteolysis process
PF07998 GO:0008233 peptidase activity function
PF08100 GO:0046983 protein dimerization activity function
PF08064 GO:0004674 protein serine/threonine kinase activity function
+PF08715 GO:0006508 proteolysis process
+PF08715 GO:0008234 cysteine-type peptidase activity function
PF00276 GO:0005840 ribosome component
PF00276 GO:0006412 translation process
PF00276 GO:0003735 structural constituent of ribosome function
@@ -7486,30 +7182,24 @@ PF06220 GO:0008270 zinc ion binding function
PF03491 GO:0005335 serotonin:sodium symporter activity function
PF03491 GO:0005887 integral component of plasma membrane component
PF03491 GO:0006836 neurotransmitter transport process
-PF00096 GO:0003676 nucleic acid binding function
PF07859 GO:0016787 hydrolase activity function
-PF07831 GO:0016763 transferase activity, transferring pentosyl groups function
+PF07831 GO:0016763 pentosyltransferase activity function
PF07831 GO:0006213 pyrimidine nucleoside metabolic process process
PF07951 GO:0046929 negative regulation of neurotransmitter secretion process
-PF08022 GO:0055114 oxidation-reduction process process
PF08022 GO:0016491 oxidoreductase activity function
PF08029 GO:0000287 magnesium ion binding function
PF08029 GO:0000105 histidine biosynthetic process process
PF08029 GO:0003879 ATP phosphoribosyltransferase activity function
PF08029 GO:0005737 cytoplasm component
-PF08125 GO:0055114 oxidation-reduction process process
-PF08125 GO:0050662 coenzyme binding function
PF08125 GO:0016491 oxidoreductase activity function
-PF08030 GO:0055114 oxidation-reduction process process
PF08030 GO:0016491 oxidoreductase activity function
PF08032 GO:0008168 methyltransferase activity function
-PF01232 GO:0055114 oxidation-reduction process process
+PF00012 GO:0005524 ATP binding function
+PF00012 GO:0016887 ATPase function
PF01232 GO:0016491 oxidoreductase activity function
PF03102 GO:0016051 carbohydrate biosynthetic process process
PF08198 GO:0003677 DNA binding function
-PF00107 GO:0055114 oxidation-reduction process process
PF00382 GO:0017025 TBP-class protein binding function
-PF08240 GO:0055114 oxidation-reduction process process
PF08264 GO:0006418 tRNA aminoacylation for protein translation process
PF08264 GO:0004812 aminoacyl-tRNA ligase activity function
PF08225 GO:0006952 defense response process
@@ -7524,6 +7214,7 @@ PF08218 GO:0008771 [citrate (pro-3S)-lyase] ligase activity function
PF08211 GO:0009972 cytidine deamination process
PF08211 GO:0004126 cytidine deaminase activity function
PF08211 GO:0008270 zinc ion binding function
+PF08194 GO:0006952 defense response process
PF08278 GO:0006269 DNA replication, synthesis of RNA primer process
PF08278 GO:0003896 DNA primase activity function
PF08285 GO:0006486 protein glycosylation process
@@ -7536,7 +7227,6 @@ PF08289 GO:0003723 RNA binding function
PF08289 GO:0005198 structural molecule activity function
PF08300 GO:0008270 zinc ion binding function
PF08290 GO:0005198 structural molecule activity function
-PF08290 GO:0009405 pathogenesis process
PF08267 GO:0008652 cellular amino acid biosynthetic process process
PF08267 GO:0008270 zinc ion binding function
PF08267 GO:0003871 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity function
@@ -7564,6 +7254,8 @@ PF08281 GO:0006352 DNA-templated transcription, initiation process
PF08287 GO:0042729 DASH complex component
PF08287 GO:0005876 spindle microtubule component
PF08287 GO:0008608 attachment of spindle microtubules to kinetochore process
+PF08234 GO:0007059 chromosome segregation process
+PF08234 GO:0031262 Ndc80 complex component
PF08236 GO:0006355 regulation of transcription, DNA-templated process
PF08236 GO:0005694 chromosome component
PF08236 GO:0034968 histone lysine methylation process
@@ -7580,11 +7272,8 @@ PF15180 GO:0001664 G protein-coupled receptor binding function
PF09472 GO:0016020 membrane component
PF09472 GO:0015948 methanogenesis process
PF09472 GO:0030269 tetrahydromethanopterin S-methyltransferase activity function
-PF09477 GO:0009405 pathogenesis process
PF09025 GO:0030257 type III protein secretion system complex component
PF09025 GO:0030254 protein secretion by the type III secretion system process
-PF09025 GO:0009405 pathogenesis process
-PF09482 GO:0009405 pathogenesis process
PF09618 GO:0043571 maintenance of CRISPR repeat elements process
PF09618 GO:0004519 endonuclease activity function
PF01131 GO:0003677 DNA binding function
@@ -7598,7 +7287,6 @@ PF01028 GO:0003677 DNA binding function
PF01028 GO:0003917 DNA topoisomerase type I (single strand cut, ATP-independent) activity function
PF01028 GO:0006265 DNA topological change process
PF02975 GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors function
-PF02975 GO:0055114 oxidation-reduction process process
PF02975 GO:0009308 amine metabolic process process
PF02975 GO:0042597 periplasmic space component
PF00204 GO:0003677 DNA binding function
@@ -7611,8 +7299,6 @@ PF01119 GO:0030983 mismatched DNA binding function
PF00317 GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor function
PF00317 GO:0005524 ATP binding function
PF00317 GO:0006260 DNA replication process
-PF00317 GO:0055114 oxidation-reduction process process
-PF02670 GO:0055114 oxidation-reduction process process
PF02670 GO:0070402 NADPH binding function
PF00360 GO:0006355 regulation of transcription, DNA-templated process
PF00360 GO:0009584 detection of visible light process
@@ -7621,8 +7307,6 @@ PF00853 GO:0003677 DNA binding function
PF00853 GO:0006355 regulation of transcription, DNA-templated process
PF00853 GO:0003700 DNA-binding transcription factor activity function
PF01061 GO:0016020 membrane component
-PF01154 GO:0008299 isoprenoid biosynthetic process process
-PF01154 GO:0004421 hydroxymethylglutaryl-CoA synthase activity function
PF02449 GO:0009341 beta-galactosidase complex component
PF02449 GO:0004565 beta-galactosidase activity function
PF02449 GO:0005975 carbohydrate metabolic process process
@@ -7640,21 +7324,17 @@ PF08332 GO:0004683 calmodulin-dependent protein kinase activity function
PF08332 GO:0006468 protein phosphorylation process
PF08332 GO:0005516 calmodulin binding function
PF08335 GO:0016779 nucleotidyltransferase activity function
-PF08336 GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen function
PF08336 GO:0005783 endoplasmic reticulum component
PF08336 GO:0004656 procollagen-proline 4-dioxygenase activity function
-PF08336 GO:0055114 oxidation-reduction process process
PF08352 GO:0005524 ATP binding function
PF08352 GO:0000166 nucleotide binding function
PF08352 GO:0015833 peptide transport process
PF08354 GO:0004318 enoyl-[acyl-carrier-protein] reductase (NADH) activity function
-PF08354 GO:0055114 oxidation-reduction process process
PF08360 GO:0045892 negative regulation of transcription, DNA-templated process
PF08360 GO:0003700 DNA-binding transcription factor activity function
PF08361 GO:0003677 DNA binding function
PF08362 GO:0045892 negative regulation of transcription, DNA-templated process
PF08367 GO:0006508 proteolysis process
-PF08369 GO:0055114 oxidation-reduction process process
PF08369 GO:0015995 chlorophyll biosynthetic process process
PF08369 GO:0015979 photosynthesis process
PF08369 GO:0016491 oxidoreductase activity function
@@ -7663,19 +7343,19 @@ PF08375 GO:0042176 regulation of protein catabolic process process
PF08375 GO:0030234 enzyme regulator activity function
PF08392 GO:0016020 membrane component
PF08392 GO:0006633 fatty acid biosynthetic process process
-PF08392 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF08392 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF08395 GO:0050909 sensory perception of taste process
PF08395 GO:0016021 integral component of membrane component
-PF08396 GO:0009405 pathogenesis process
PF08396 GO:0090729 toxin activity function
PF08397 GO:0007009 plasma membrane organization process
PF08398 GO:0005198 structural molecule activity function
+PF08401 GO:0003697 single-stranded DNA binding function
PF08402 GO:0055085 transmembrane transport process
PF08402 GO:0005524 ATP binding function
PF08402 GO:0043190 ATP-binding cassette (ABC) transporter complex component
PF08402 GO:0022857 transmembrane transporter activity function
PF08405 GO:0004197 cysteine-type endopeptidase activity function
-PF08405 GO:0044419 interspecies interaction between organisms process
+PF08405 GO:0044419 biological process involved in interspecies interaction between organisms process
PF08405 GO:0017111 nucleoside-triphosphatase activity function
PF08405 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF08407 GO:0004100 chitin synthase activity function
@@ -7684,10 +7364,8 @@ PF08411 GO:0006281 DNA repair process
PF08411 GO:0008852 exodeoxyribonuclease I activity function
PF08414 GO:0050664 oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor function
PF08414 GO:0004601 peroxidase activity function
-PF08414 GO:0055114 oxidation-reduction process process
PF08416 GO:0005515 protein binding function
PF08417 GO:0010277 chlorophyllide a oxygenase [overall] activity function
-PF08417 GO:0055114 oxidation-reduction process process
PF08430 GO:0019904 protein domain specific binding function
PF08430 GO:0008134 transcription factor binding function
PF08436 GO:0005515 protein binding function
@@ -7697,7 +7375,7 @@ PF08440 GO:0018144 RNA-protein covalent cross-linking process
PF08440 GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides function
PF08440 GO:0005198 structural molecule activity function
PF08440 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
-PF08445 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF08445 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF08446 GO:0006355 regulation of transcription, DNA-templated process
PF08447 GO:0005515 protein binding function
PF08449 GO:0055085 transmembrane transport process
@@ -7715,7 +7393,6 @@ PF08469 GO:0005524 ATP binding function
PF08469 GO:0017111 nucleoside-triphosphatase activity function
PF08469 GO:0006351 transcription, DNA-templated process
PF08471 GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor function
-PF08471 GO:0055114 oxidation-reduction process process
PF08471 GO:0050897 cobalt ion binding function
PF08472 GO:0005986 sucrose biosynthetic process process
PF08472 GO:0050307 sucrose-phosphate phosphatase activity function
@@ -7731,7 +7408,6 @@ PF08490 GO:0008270 zinc ion binding function
PF08491 GO:0016021 integral component of membrane component
PF08491 GO:0050660 flavin adenine dinucleotide binding function
PF08491 GO:0004506 squalene monooxygenase activity function
-PF08491 GO:0055114 oxidation-reduction process process
PF08492 GO:0006614 SRP-dependent cotranslational protein targeting to membrane process
PF08492 GO:0048500 signal recognition particle component
PF08492 GO:0008312 7S RNA binding function
@@ -7747,7 +7423,6 @@ PF08498 GO:0006694 steroid biosynthetic process process
PF08498 GO:0008168 methyltransferase activity function
PF08499 GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity function
PF08500 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
-PF08501 GO:0055114 oxidation-reduction process process
PF08501 GO:0004764 shikimate 3-dehydrogenase (NADP+) activity function
PF08502 GO:0009098 leucine biosynthetic process process
PF08502 GO:0003852 2-isopropylmalate synthase activity function
@@ -7778,21 +7453,20 @@ PF08534 GO:0016491 oxidoreductase activity function
PF08536 GO:0003697 single-stranded DNA binding function
PF08536 GO:0006952 defense response process
PF08536 GO:0006355 regulation of transcription, DNA-templated process
-PF08540 GO:0008299 isoprenoid biosynthetic process process
+PF08540 GO:0010142 farnesyl diphosphate biosynthetic process, mevalonate pathway process
PF08540 GO:0004421 hydroxymethylglutaryl-CoA synthase activity function
+PF08540 GO:0006084 acetyl-CoA metabolic process process
PF08545 GO:0004315 3-oxoacyl-[acyl-carrier-protein] synthase activity function
PF08545 GO:0006633 fatty acid biosynthetic process process
PF00154 GO:0003697 single-stranded DNA binding function
PF00154 GO:0006281 DNA repair process
PF00154 GO:0005524 ATP binding function
-PF00085 GO:0045454 cell redox homeostasis process
PF00989 GO:0006355 regulation of transcription, DNA-templated process
PF07565 GO:0006820 anion transport process
PF07565 GO:0016021 integral component of membrane component
PF07565 GO:0008509 anion transmembrane transporter activity function
PF02771 GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors function
PF02771 GO:0050660 flavin adenine dinucleotide binding function
-PF02771 GO:0055114 oxidation-reduction process process
PF00218 GO:0004425 indole-3-glycerol-phosphate synthase activity function
PF02865 GO:0007165 signal transduction process
PF02865 GO:0006355 regulation of transcription, DNA-templated process
@@ -7806,9 +7480,9 @@ PF00333 GO:0005840 ribosome component
PF00333 GO:0003723 RNA binding function
PF00333 GO:0006412 translation process
PF00333 GO:0003735 structural constituent of ribosome function
+PF00151 GO:0004806 triglyceride lipase activity function
PF00305 GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen function
PF00305 GO:0046872 metal ion binding function
-PF00305 GO:0055114 oxidation-reduction process process
PF01634 GO:0000105 histidine biosynthetic process process
PF01634 GO:0003879 ATP phosphoribosyltransferase activity function
PF01634 GO:0005737 cytoplasm component
@@ -7843,9 +7517,12 @@ PF08563 GO:0005515 protein binding function
PF08566 GO:0001405 PAM complex, Tim23 associated import motor component
PF08573 GO:0006281 DNA repair process
PF08573 GO:0004519 endonuclease activity function
+PF08584 GO:0030677 ribonuclease P complex component
+PF08584 GO:0001682 tRNA 5'-leader removal process
PF08586 GO:0016586 RSC-type complex component
-PF08586 GO:0043044 ATP-dependent chromatin remodeling process
PF08587 GO:0004674 protein serine/threonine kinase activity function
+PF08589 GO:0140580 mitochondrion autophagosome adaptor activity function
+PF08589 GO:0000423 mitophagy process
PF08597 GO:0003743 translation initiation factor activity function
PF08597 GO:0005852 eukaryotic translation initiation factor 3 complex component
PF08597 GO:0005737 cytoplasm component
@@ -7913,12 +7590,12 @@ PF08661 GO:0006281 DNA repair process
PF08661 GO:0006260 DNA replication process
PF08661 GO:0006310 DNA recombination process
PF02730 GO:0016625 oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor function
-PF02730 GO:0055114 oxidation-reduction process process
PF02730 GO:0051536 iron-sulfur cluster binding function
PF02730 GO:0016491 oxidoreductase activity function
PF01213 GO:0003779 actin binding function
PF01213 GO:0007010 cytoskeleton organization process
PF00524 GO:0016817 hydrolase activity, acting on acid anhydrides function
+PF00580 GO:0005524 ATP binding function
PF13361 GO:0016787 hydrolase activity function
PF13361 GO:0005524 ATP binding function
PF00946 GO:0005524 ATP binding function
@@ -7927,10 +7604,8 @@ PF00946 GO:0004482 mRNA (guanine-N7-)-methyltransferase activity function
PF00946 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF00984 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
PF00984 GO:0051287 NAD binding function
-PF00984 GO:0055114 oxidation-reduction process process
PF03720 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
PF03720 GO:0051287 NAD binding function
-PF03720 GO:0055114 oxidation-reduction process process
PF00736 GO:0003746 translation elongation factor activity function
PF00736 GO:0006414 translational elongation process
PF00889 GO:0003746 translation elongation factor activity function
@@ -7946,16 +7621,19 @@ PF06519 GO:0019534 toxin transmembrane transporter activity function
PF06519 GO:0016021 integral component of membrane component
PF09547 GO:0005524 ATP binding function
PF09547 GO:0043934 sporulation process
-PF09547 GO:0016887 ATPase activity function
+PF09547 GO:0016887 ATPase function
PF14620 GO:0009847 spore germination process
PF17366 GO:0009277 fungal-type cell wall component
PF17366 GO:0050839 cell adhesion molecule binding function
PF17366 GO:0000752 agglutination involved in conjugation with cellular fusion process
PF02703 GO:0006355 regulation of transcription, DNA-templated process
-PF02703 GO:0019048 modulation by virus of host morphology or physiology process
-PF12328 GO:0005634 nucleus component
-PF12328 GO:0004526 ribonuclease P activity function
-PF12328 GO:0008033 tRNA processing process
+PF02703 GO:0019048 modulation by virus of host process process
+PF11507 GO:0003723 RNA binding function
+PF11507 GO:0008270 zinc ion binding function
+PF12328 GO:0000172 ribonuclease MRP complex component
+PF12328 GO:0006396 RNA processing process
+PF12328 GO:0005655 nucleolar ribonuclease P complex component
+PF12328 GO:0001682 tRNA 5'-leader removal process
PF11504 GO:0050829 defense response to Gram-negative bacterium process
PF11504 GO:0019835 cytolysis process
PF11504 GO:0016021 integral component of membrane component
@@ -7983,6 +7661,8 @@ PF08689 GO:0006357 regulation of transcription by RNA polymerase II process
PF08689 GO:0016592 mediator complex component
PF08689 GO:0003712 transcription coregulator activity function
PF08692 GO:0005739 mitochondrion component
+PF08694 GO:0071569 protein ufmylation process
+PF08694 GO:0061657 UFM1 conjugating enzyme activity function
PF08703 GO:0016042 lipid catabolic process process
PF08703 GO:0004435 phosphatidylinositol phospholipase C activity function
PF08703 GO:0005509 calcium ion binding function
@@ -7994,12 +7674,6 @@ PF08710 GO:0003723 RNA binding function
PF08710 GO:0019079 viral genome replication process
PF08714 GO:0016840 carbon-nitrogen lyase activity function
PF08714 GO:0016051 carbohydrate biosynthetic process process
-PF08715 GO:0004197 cysteine-type endopeptidase activity function
-PF08715 GO:0016740 transferase activity function
-PF08715 GO:0008242 omega peptidase activity function
-PF08716 GO:0004197 cysteine-type endopeptidase activity function
-PF08716 GO:0016740 transferase activity function
-PF08716 GO:0008242 omega peptidase activity function
PF08717 GO:0004197 cysteine-type endopeptidase activity function
PF08717 GO:0016740 transferase activity function
PF08717 GO:0008242 omega peptidase activity function
@@ -8012,10 +7686,8 @@ PF08720 GO:0019031 viral envelope component
PF08727 GO:0004197 cysteine-type endopeptidase activity function
PF08727 GO:0017111 nucleoside-triphosphatase activity function
PF08727 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
-PF08728 GO:0006357 regulation of transcription by RNA polymerase II process
PF08731 GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific function
PF08731 GO:0036086 positive regulation of transcription from RNA polymerase II promoter in response to iron ion starvation process
-PF08740 GO:0034551 mitochondrial respiratory chain complex III assembly process
PF08744 GO:0003700 DNA-binding transcription factor activity function
PF08767 GO:0005049 nuclear export signal receptor activity function
PF08769 GO:0006355 regulation of transcription, DNA-templated process
@@ -8027,14 +7699,13 @@ PF08774 GO:0016788 hydrolase activity, acting on ester bonds function
PF08777 GO:0003723 RNA binding function
PF08782 GO:0046332 SMAD binding function
PF08783 GO:0008270 zinc ion binding function
-PF08785 GO:0016817 hydrolase activity, acting on acid anhydrides function
PF08797 GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides function
PF08797 GO:0008270 zinc ion binding function
PF08797 GO:0003676 nucleic acid binding function
-PF08815 GO:0035257 nuclear hormone receptor binding function
PF08815 GO:0005634 nucleus component
PF08815 GO:0003713 transcription coactivator activity function
PF08815 GO:0006355 regulation of transcription, DNA-templated process
+PF08815 GO:0016922 nuclear receptor binding function
PF08825 GO:0045116 protein neddylation process
PF08825 GO:0019781 NEDD8 activating enzyme activity function
PF08826 GO:0005524 ATP binding function
@@ -8048,7 +7719,7 @@ PF08880 GO:0005634 nucleus component
PF08880 GO:0005524 ATP binding function
PF08880 GO:0006355 regulation of transcription, DNA-templated process
PF08911 GO:0005643 nuclear pore component
-PF08912 GO:0017048 Rho GTPase binding function
+PF08912 GO:0031267 small GTPase binding function
PF08915 GO:0005524 ATP binding function
PF08915 GO:0004829 threonine-tRNA ligase activity function
PF08915 GO:0008270 zinc ion binding function
@@ -8081,14 +7752,12 @@ PF08943 GO:0005506 iron ion binding function
PF08961 GO:0006914 autophagy process
PF08964 GO:0016020 membrane component
PF08964 GO:0098609 cell-cell adhesion process
-PF08990 GO:0048037 cofactor binding function
PF08990 GO:0016740 transferase activity function
PF08992 GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors function
-PF08992 GO:0055114 oxidation-reduction process process
PF08996 GO:0003887 DNA-directed DNA polymerase activity function
PF08996 GO:0006260 DNA replication process
-PF08997 GO:0009055 electron transfer activity function
-PF08997 GO:0008121 ubiquinol-cytochrome-c reductase activity function
+PF08997 GO:0005750 mitochondrial respiratory chain complex III component
+PF08997 GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c process
PF08998 GO:0031342 negative regulation of cell killing process
PF08998 GO:0015643 toxic substance binding function
PF08998 GO:0009636 response to toxic substance process
@@ -8097,14 +7766,12 @@ PF09003 GO:0008907 integrase activity function
PF09003 GO:0003677 DNA binding function
PF09004 GO:0016706 2-oxoglutarate-dependent dioxygenase activity function
PF09004 GO:0008168 methyltransferase activity function
-PF09004 GO:0055114 oxidation-reduction process process
PF09005 GO:0006355 regulation of transcription, DNA-templated process
PF09005 GO:0003676 nucleic acid binding function
PF09009 GO:0047286 NAD+-diphthamide ADP-ribosyltransferase activity function
PF09010 GO:0006355 regulation of transcription, DNA-templated process
PF09013 GO:0006470 protein dephosphorylation process
PF09013 GO:0004725 protein tyrosine phosphatase activity function
-PF09013 GO:0009405 pathogenesis process
PF09015 GO:0009307 DNA restriction-modification system process
PF09015 GO:0009036 type II site-specific deoxyribonuclease activity function
PF09017 GO:0003810 protein-glutamine gamma-glutamyltransferase activity function
@@ -8112,7 +7779,6 @@ PF09019 GO:0003677 DNA binding function
PF09019 GO:0009307 DNA restriction-modification system process
PF09019 GO:0009036 type II site-specific deoxyribonuclease activity function
PF09020 GO:0050765 negative regulation of phagocytosis process
-PF09026 GO:0005634 nucleus component
PF09026 GO:0003677 DNA binding function
PF09026 GO:0003682 chromatin binding function
PF09026 GO:0000775 chromosome, centromeric region component
@@ -8128,10 +7794,9 @@ PF09036 GO:0005096 GTPase activator activity function
PF09040 GO:0016020 membrane component
PF09040 GO:0000287 magnesium ion binding function
PF09040 GO:1902600 proton transmembrane transport process
-PF09040 GO:0008900 potassium:proton exchanging ATPase activity function
+PF09040 GO:0008900 P-type potassium:proton transporter activity function
PF09040 GO:0005524 ATP binding function
PF09044 GO:0005576 extracellular region component
-PF09044 GO:0009405 pathogenesis process
PF09057 GO:0005739 mitochondrion component
PF09057 GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process process
PF09057 GO:0006915 apoptotic process process
@@ -8164,12 +7829,9 @@ PF09107 GO:0001514 selenocysteine incorporation process
PF09107 GO:0005525 GTP binding function
PF09107 GO:0005737 cytoplasm component
PF09110 GO:0031491 nucleosome binding function
-PF09110 GO:0043044 ATP-dependent chromatin remodeling process
+PF09110 GO:0003677 DNA binding function
PF09111 GO:0005634 nucleus component
-PF09111 GO:0006338 chromatin remodeling process
-PF09111 GO:0005524 ATP binding function
-PF09111 GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides function
-PF09111 GO:0003676 nucleic acid binding function
+PF09111 GO:0003677 DNA binding function
PF09115 GO:0003887 DNA-directed DNA polymerase activity function
PF09115 GO:0003677 DNA binding function
PF09115 GO:0009360 DNA polymerase III complex component
@@ -8182,15 +7844,14 @@ PF09126 GO:0009307 DNA restriction-modification system process
PF09126 GO:0009036 type II site-specific deoxyribonuclease activity function
PF09127 GO:0008237 metallopeptidase activity function
PF09127 GO:0008270 zinc ion binding function
+PF09128 GO:0005085 guanyl-nucleotide exchange factor activity function
PF09128 GO:0005737 cytoplasm component
-PF09128 GO:0005089 Rho guanyl-nucleotide exchange factor activity function
PF09138 GO:0034227 tRNA thio-modification process
PF09138 GO:0005737 cytoplasm component
PF09139 GO:0032049 cardiolipin biosynthetic process process
PF09139 GO:0004605 phosphatidate cytidylyltransferase activity function
PF09141 GO:0001726 ruffle component
PF09141 GO:0005925 focal adhesion component
-PF09141 GO:0007016 cytoskeletal anchoring at plasma membrane process
PF09141 GO:0005200 structural constituent of cytoskeleton function
PF09142 GO:0003723 RNA binding function
PF09142 GO:0009451 RNA modification process
@@ -8205,16 +7866,13 @@ PF09157 GO:0003723 RNA binding function
PF09157 GO:0009451 RNA modification process
PF09157 GO:0001522 pseudouridine synthesis process
PF09157 GO:0009982 pseudouridine synthase activity function
-PF09162 GO:0042025 host cell nucleus component
PF09162 GO:0006406 mRNA export from nucleus process
PF09162 GO:0003723 RNA binding function
PF09162 GO:0005737 cytoplasm component
PF09165 GO:0008121 ubiquinol-cytochrome-c reductase activity function
-PF09165 GO:0055114 oxidation-reduction process process
PF09166 GO:0042167 heme catabolic process process
PF09166 GO:0008270 zinc ion binding function
-PF09166 GO:0055114 oxidation-reduction process process
-PF09166 GO:0004074 biliverdin reductase activity function
+PF09166 GO:0004074 biliverdin reductase (NAD(P)+) activity function
PF09167 GO:0005615 extracellular space component
PF09168 GO:0006508 proteolysis process
PF09168 GO:0008239 dipeptidyl-peptidase activity function
@@ -8266,7 +7924,6 @@ PF09206 GO:0031221 arabinan metabolic process process
PF09206 GO:0046556 alpha-L-arabinofuranosidase activity function
PF09207 GO:0005576 extracellular region component
PF09207 GO:0008219 cell death process
-PF09207 GO:0009405 pathogenesis process
PF09208 GO:0003677 DNA binding function
PF09208 GO:0009307 DNA restriction-modification system process
PF09208 GO:0009036 type II site-specific deoxyribonuclease activity function
@@ -8296,7 +7953,6 @@ PF09239 GO:0003677 DNA binding function
PF09239 GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity function
PF09239 GO:0006265 DNA topological change process
PF09242 GO:0050660 flavin adenine dinucleotide binding function
-PF09242 GO:0055114 oxidation-reduction process process
PF09242 GO:0016491 oxidoreductase activity function
PF09243 GO:0008168 methyltransferase activity function
PF09243 GO:0006412 translation process
@@ -8305,10 +7961,9 @@ PF09246 GO:0006355 regulation of transcription, DNA-templated process
PF09249 GO:0016437 tRNA cytidylyltransferase activity function
PF09249 GO:0004810 tRNA adenylyltransferase activity function
PF09252 GO:0005615 extracellular space component
-PF09254 GO:0003677 DNA binding function
PF09254 GO:0009307 DNA restriction-modification system process
PF09254 GO:0009036 type II site-specific deoxyribonuclease activity function
-PF09258 GO:0016757 transferase activity, transferring glycosyl groups function
+PF09258 GO:0016757 glycosyltransferase activity function
PF09258 GO:0016021 integral component of membrane component
PF09259 GO:0030246 carbohydrate binding function
PF09259 GO:0002682 regulation of immune system process process
@@ -8324,7 +7979,6 @@ PF09264 GO:0033691 sialic acid binding function
PF09265 GO:0019139 cytokinin dehydrogenase activity function
PF09265 GO:0009690 cytokinin metabolic process process
PF09265 GO:0050660 flavin adenine dinucleotide binding function
-PF09265 GO:0055114 oxidation-reduction process process
PF09266 GO:0003677 DNA binding function
PF09266 GO:0006265 DNA topological change process
PF09266 GO:0003916 DNA topoisomerase activity function
@@ -8373,9 +8027,7 @@ PF09308 GO:0016791 phosphatase activity function
PF09308 GO:0004673 protein histidine kinase activity function
PF09317 GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase process
PF09317 GO:0003995 acyl-CoA dehydrogenase activity function
-PF09317 GO:0055114 oxidation-reduction process process
PF09326 GO:0016651 oxidoreductase activity, acting on NAD(P)H function
-PF09326 GO:0055114 oxidation-reduction process process
PF09326 GO:0051536 iron-sulfur cluster binding function
PF09328 GO:0046872 metal ion binding function
PF09328 GO:0046938 phytochelatin biosynthetic process process
@@ -8390,16 +8042,13 @@ PF09334 GO:0006418 tRNA aminoacylation for protein translation process
PF09334 GO:0000166 nucleotide binding function
PF09334 GO:0004812 aminoacyl-tRNA ligase activity function
PF09338 GO:0050485 oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond, with a disulfide as acceptor function
-PF09338 GO:0055114 oxidation-reduction process process
PF09340 GO:0000123 histone acetyltransferase complex component
PF09340 GO:0016573 histone acetylation process
PF09290 GO:0019439 aromatic compound catabolic process process
-PF09290 GO:0055114 oxidation-reduction process process
PF09290 GO:0008774 acetaldehyde dehydrogenase (acetylating) activity function
PF03530 GO:0006813 potassium ion transport process
PF03530 GO:0016021 integral component of membrane component
PF03530 GO:0016286 small conductance calcium-activated potassium channel activity function
-PF00171 GO:0055114 oxidation-reduction process process
PF00171 GO:0016491 oxidoreductase activity function
PF00224 GO:0030955 potassium ion binding function
PF00224 GO:0000287 magnesium ion binding function
@@ -8408,17 +8057,14 @@ PF00224 GO:0006096 glycolytic process process
PF01179 GO:0008131 primary amine oxidase activity function
PF01179 GO:0005507 copper ion binding function
PF01179 GO:0048038 quinone binding function
-PF01179 GO:0055114 oxidation-reduction process process
PF01179 GO:0009308 amine metabolic process process
PF02727 GO:0008131 primary amine oxidase activity function
PF02727 GO:0005507 copper ion binding function
PF02727 GO:0048038 quinone binding function
-PF02727 GO:0055114 oxidation-reduction process process
PF02727 GO:0009308 amine metabolic process process
PF02728 GO:0008131 primary amine oxidase activity function
PF02728 GO:0005507 copper ion binding function
PF02728 GO:0048038 quinone binding function
-PF02728 GO:0055114 oxidation-reduction process process
PF02728 GO:0009308 amine metabolic process process
PF03967 GO:0019684 photosynthesis, light reaction process
PF03967 GO:0030077 plasma membrane light-harvesting complex component
@@ -8441,14 +8087,13 @@ PF02268 GO:0006367 transcription initiation from RNA polymerase II promoter proc
PF00848 GO:0051537 2 iron, 2 sulfur cluster binding function
PF00848 GO:0005506 iron ion binding function
PF00848 GO:0044237 cellular metabolic process process
-PF00848 GO:0055114 oxidation-reduction process process
PF00728 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF00728 GO:0005975 carbohydrate metabolic process process
PF06831 GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity function
+PF06831 GO:0006284 base-excision repair process
PF06831 GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds function
PF06831 GO:0003684 damaged DNA binding function
PF06831 GO:0008270 zinc ion binding function
-PF06831 GO:0006289 nucleotide-excision repair process
PF02952 GO:0006004 fucose metabolic process process
PF02952 GO:0005737 cytoplasm component
PF02952 GO:0008736 L-fucose isomerase activity function
@@ -8457,11 +8102,9 @@ PF02263 GO:0003924 GTPase activity function
PF05201 GO:0050661 NADP binding function
PF05201 GO:0008883 glutamyl-tRNA reductase activity function
PF05201 GO:0033014 tetrapyrrole biosynthetic process process
-PF05201 GO:0055114 oxidation-reduction process process
PF00745 GO:0050661 NADP binding function
PF00745 GO:0008883 glutamyl-tRNA reductase activity function
PF00745 GO:0033014 tetrapyrrole biosynthetic process process
-PF00745 GO:0055114 oxidation-reduction process process
PF00631 GO:0007186 G protein-coupled receptor signaling pathway process
PF03275 GO:0008767 UDP-galactopyranose mutase activity function
PF03561 GO:0000256 allantoin catabolic process process
@@ -8474,7 +8117,6 @@ PF11791 GO:0006099 tricarboxylic acid cycle process
PF11791 GO:0003994 aconitate hydratase activity function
PF06021 GO:0005739 mitochondrion component
PF06021 GO:0047961 glycine N-acyltransferase activity function
-PF02910 GO:0055114 oxidation-reduction process process
PF02910 GO:0016491 oxidoreductase activity function
PF01177 GO:0006807 nitrogen compound metabolic process process
PF01177 GO:0036361 racemase activity, acting on amino acids and derivatives function
@@ -8492,10 +8134,8 @@ PF08303 GO:0003972 RNA ligase (ATP) activity function
PF07487 GO:0090630 activation of GTPase activity process
PF07487 GO:0031532 actin cytoskeleton reorganization process
PF07487 GO:0005085 guanyl-nucleotide exchange factor activity function
-PF07487 GO:0009405 pathogenesis process
PF01126 GO:0006788 heme oxidation process
PF01126 GO:0004392 heme oxygenase (decyclizing) activity function
-PF01126 GO:0055114 oxidation-reduction process process
PF09180 GO:0006433 prolyl-tRNA aminoacylation process
PF09180 GO:0005524 ATP binding function
PF09180 GO:0000166 nucleotide binding function
@@ -8512,11 +8152,8 @@ PF00068 GO:0004623 phospholipase A2 activity function
PF05826 GO:0050482 arachidonic acid secretion process
PF05826 GO:0006644 phospholipid metabolic process process
PF05826 GO:0004623 phospholipase A2 activity function
-PF02815 GO:0016020 membrane component
PF01065 GO:0019028 viral capsid component
PF03678 GO:0019028 viral capsid component
-PF03515 GO:0009405 pathogenesis process
-PF06958 GO:0009405 pathogenesis process
PF00345 GO:0030288 outer membrane-bounded periplasmic space component
PF00345 GO:0071555 cell wall organization process
PF00049 GO:0005576 extracellular region component
@@ -8539,10 +8176,11 @@ PF10605 GO:0005615 extracellular space component
PF10605 GO:0047989 hydroxybutyrate-dimer hydrolase activity function
PF16974 GO:0010167 response to nitrate process
PF16974 GO:0015706 nitrate transport process
+PF10093 GO:0106361 protein-arginine rhamnosyltransferase activity function
PF13869 GO:0003729 mRNA binding function
PF13869 GO:0005849 mRNA cleavage factor complex component
PF13869 GO:0006378 mRNA polyadenylation process
-PF04922 GO:0004583 dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity function
+PF04922 GO:0106073 dolichyl pyrophosphate Glc2Man9GlcNAc2 alpha-1,2-glucosyltransferase activity function
PF04922 GO:0006488 dolichol-linked oligosaccharide biosynthetic process process
PF13741 GO:0005763 mitochondrial small ribosomal subunit component
PF13741 GO:0003735 structural constituent of ribosome function
@@ -8566,13 +8204,13 @@ PF10620 GO:0016779 nucleotidyltransferase activity function
PF10995 GO:0035438 cyclic-di-GMP binding function
PF11991 GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups function
PF11991 GO:0009820 alkaloid metabolic process process
+PF18916 GO:0016872 intramolecular lyase activity function
PF04987 GO:0006506 GPI anchor biosynthetic process process
PF04987 GO:0005789 endoplasmic reticulum membrane component
PF04987 GO:0016740 transferase activity function
PF00433 GO:0005524 ATP binding function
PF00433 GO:0004674 protein serine/threonine kinase activity function
PF00433 GO:0006468 protein phosphorylation process
-PF04777 GO:0055114 oxidation-reduction process process
PF04777 GO:0016972 thiol oxidase activity function
PF01114 GO:0016042 lipid catabolic process process
PF01114 GO:0007586 digestion process
@@ -8584,8 +8222,6 @@ PF02740 GO:0005576 extracellular region component
PF02740 GO:0008047 enzyme activator activity function
PF08711 GO:0005634 nucleus component
PF00355 GO:0051537 2 iron, 2 sulfur cluster binding function
-PF00355 GO:0055114 oxidation-reduction process process
-PF00355 GO:0016491 oxidoreductase activity function
PF01273 GO:0008289 lipid binding function
PF02178 GO:0003677 DNA binding function
PF11799 GO:0006281 DNA repair process
@@ -8594,7 +8230,6 @@ PF00003 GO:0007186 G protein-coupled receptor signaling pathway process
PF00003 GO:0016021 integral component of membrane component
PF00003 GO:0004930 G protein-coupled receptor activity function
PF03502 GO:0009279 cell outer membrane component
-PF01715 GO:0008033 tRNA processing process
PF02637 GO:0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor function
PF00165 GO:0006355 regulation of transcription, DNA-templated process
PF00165 GO:0043565 sequence-specific DNA binding function
@@ -8605,9 +8240,9 @@ PF12833 GO:0003700 DNA-binding transcription factor activity function
PF00367 GO:0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity function
PF03088 GO:0016844 strictosidine synthase activity function
PF03088 GO:0009058 biosynthetic process process
-PF03145 GO:0042025 host cell nucleus component
PF03145 GO:0006511 ubiquitin-dependent protein catabolic process process
PF03145 GO:0007275 multicellular organism development process
+PF03145 GO:0005737 cytoplasm component
PF03002 GO:0005576 extracellular region component
PF03002 GO:0005179 hormone activity function
PF03135 GO:0005524 ATP binding function
@@ -8621,7 +8256,6 @@ PF00996 GO:0007264 small GTPase mediated signal transduction process
PF00996 GO:0005092 GDP-dissociation inhibitor activity function
PF03222 GO:0003333 amino acid transmembrane transport process
PF10297 GO:0005634 nucleus component
-PF10297 GO:0003677 DNA binding function
PF10297 GO:0006355 regulation of transcription, DNA-templated process
PF09510 GO:0005634 nucleus component
PF09510 GO:0016586 RSC-type complex component
@@ -8633,6 +8267,7 @@ PF10404 GO:0003677 DNA binding function
PF10405 GO:0003677 DNA binding function
PF03837 GO:0003677 DNA binding function
PF03837 GO:0006259 DNA metabolic process process
+PF10523 GO:0003677 DNA binding function
PF03601 GO:0016021 integral component of membrane component
PF03606 GO:0016021 integral component of membrane component
PF03480 GO:0055085 transmembrane transport process
@@ -8646,7 +8281,7 @@ PF10204 GO:0005789 endoplasmic reticulum membrane component
PF10204 GO:0015031 protein transport process
PF10147 GO:0005634 nucleus component
PF09730 GO:0070840 dynein complex binding function
-PF09730 GO:0008093 cytoskeletal adaptor activity function
+PF09730 GO:0008093 cytoskeletal anchor activity function
PF00370 GO:0005975 carbohydrate metabolic process process
PF00370 GO:0016773 phosphotransferase activity, alcohol group as acceptor function
PF02782 GO:0005975 carbohydrate metabolic process process
@@ -8661,7 +8296,6 @@ PF00191 GO:0005544 calcium-dependent phospholipid binding function
PF00191 GO:0005509 calcium ion binding function
PF02382 GO:0005509 calcium ion binding function
PF02382 GO:0005576 extracellular region component
-PF02382 GO:0009405 pathogenesis process
PF03170 GO:0016020 membrane component
PF03170 GO:0006011 UDP-glucose metabolic process process
PF03528 GO:0008083 growth factor activity function
@@ -8670,6 +8304,9 @@ PF03542 GO:0043547 positive regulation of GTPase activity process
PF03542 GO:0005096 GTPase activator activity function
PF09367 GO:0017009 protein-phycocyanobilin linkage process
PF09388 GO:0043937 regulation of sporulation process
+PF09405 GO:0006397 mRNA processing process
+PF09405 GO:0003729 mRNA binding function
+PF09405 GO:0035145 exon-exon junction complex component
PF09415 GO:0006281 DNA repair process
PF09415 GO:0051382 kinetochore assembly process
PF09421 GO:0007623 circadian rhythm process
@@ -8684,33 +8321,34 @@ PF09494 GO:0005634 nucleus component
PF09494 GO:0006281 DNA repair process
PF09494 GO:0033557 Slx1-Slx4 complex component
PF09494 GO:0006260 DNA replication process
-PF09494 GO:0017108 5'-flap endonuclease activity function
PF09589 GO:0005615 extracellular space component
-PF09589 GO:0009405 pathogenesis process
-PF09594 GO:0016758 transferase activity, transferring hexosyl groups function
+PF09594 GO:0016758 hexosyltransferase activity function
PF09648 GO:0016021 integral component of membrane component
PF09692 GO:0033167 ARC complex component
PF09692 GO:0031047 gene silencing by RNA process
PF09696 GO:0031390 Ctf18 RFC-like complex component
PF09696 GO:0007064 mitotic sister chromatid cohesion process
PF09740 GO:0009411 response to UV process
+PF09743 GO:0061666 UFM1 ligase activity function
+PF09743 GO:0071569 protein ufmylation process
PF09776 GO:0005762 mitochondrial large ribosomal subunit component
PF09776 GO:0003735 structural constituent of ribosome function
PF09795 GO:0000407 phagophore assembly site component
PF09795 GO:0006914 autophagy process
-PF09798 GO:0000077 DNA damage checkpoint process
+PF09798 GO:0000077 DNA damage checkpoint signaling process
PF09802 GO:0031207 Sec62/Sec63 complex component
PF09802 GO:0031204 posttranslational protein targeting to membrane, translocation process
-PF09803 GO:0033617 mitochondrial respiratory chain complex IV assembly process
+PF09803 GO:0033617 mitochondrial cytochrome c oxidase assembly process
PF09803 GO:0005739 mitochondrion component
PF09807 GO:0002098 tRNA wobble uridine modification process
-PF09807 GO:0033588 Elongator holoenzyme complex component
+PF09807 GO:0033588 elongator holoenzyme complex component
PF09815 GO:0016021 integral component of membrane component
-PF09817 GO:0007093 mitotic cell cycle checkpoint process
+PF09817 GO:0007093 mitotic cell cycle checkpoint signaling process
PF09817 GO:1990423 RZZ complex component
PF09861 GO:0050043 lactate racemase activity function
PF09905 GO:0003677 DNA binding function
PF09907 GO:0016788 hydrolase activity, acting on ester bonds function
+PF09995 GO:0016491 oxidoreductase activity function
PF10033 GO:1990316 Atg1/ULK1 kinase complex component
PF10033 GO:0006914 autophagy process
PF10034 GO:0016021 integral component of membrane component
@@ -8729,6 +8367,7 @@ PF10163 GO:0006406 mRNA export from nucleus process
PF10163 GO:0005643 nuclear pore component
PF10163 GO:0003713 transcription coactivator activity function
PF10163 GO:0045893 positive regulation of transcription, DNA-templated process
+PF10178 GO:0043248 proteasome assembly process
PF10231 GO:0097193 intrinsic apoptotic signaling pathway process
PF10240 GO:0000813 ESCRT I complex component
PF10272 GO:0061630 ubiquitin protein ligase activity function
@@ -8748,7 +8387,6 @@ PF10487 GO:0017056 structural constituent of nuclear pore function
PF10514 GO:0006915 apoptotic process process
PF10574 GO:0051126 negative regulation of actin nucleation process
PF10645 GO:0030246 carbohydrate binding function
-PF10664 GO:0055114 oxidation-reduction process process
PF10664 GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor function
PF10430 GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway process
PF10430 GO:0005887 integral component of plasma membrane component
@@ -8780,11 +8418,11 @@ PF09401 GO:0003723 RNA binding function
PF09401 GO:0019079 viral genome replication process
PF09401 GO:0008270 zinc ion binding function
PF09412 GO:0004521 endoribonuclease activity function
-PF09416 GO:0003677 DNA binding function
+PF09416 GO:0003723 RNA binding function
PF09416 GO:0005524 ATP binding function
+PF09416 GO:0003724 RNA helicase activity function
PF09416 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay process
PF09416 GO:0008270 zinc ion binding function
-PF09416 GO:0004386 helicase activity function
PF09416 GO:0005737 cytoplasm component
PF09427 GO:0045944 positive regulation of transcription by RNA polymerase II process
PF09427 GO:0032933 SREBP signaling pathway process
@@ -8816,7 +8454,6 @@ PF09497 GO:0006357 regulation of transcription by RNA polymerase II process
PF09497 GO:0016592 mediator complex component
PF09497 GO:0003712 transcription coregulator activity function
PF09507 GO:0005634 nucleus component
-PF09507 GO:0003887 DNA-directed DNA polymerase activity function
PF09507 GO:0043625 delta DNA polymerase complex component
PF09507 GO:0006260 DNA replication process
PF09514 GO:0005634 nucleus component
@@ -8883,13 +8520,15 @@ PF09769 GO:0061617 MICOS complex component
PF09771 GO:0035307 positive regulation of protein dephosphorylation process
PF09771 GO:0071595 Nem1-Spo7 phosphatase complex component
PF09773 GO:0060271 cilium assembly process
-PF09773 GO:0010826 negative regulation of centrosome duplication process
PF09773 GO:0036038 MKS complex component
+PF09774 GO:0005758 mitochondrial intermembrane space component
PF09782 GO:0005747 mitochondrial respiratory chain complex I component
PF09782 GO:0006120 mitochondrial electron transport, NADH to ubiquinone process
PF09787 GO:0007030 Golgi organization process
PF09788 GO:0034597 phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity function
PF09788 GO:0046856 phosphatidylinositol dephosphorylation process
+PF09796 GO:0005750 mitochondrial respiratory chain complex III component
+PF09796 GO:0006122 mitochondrial electron transport, ubiquinol to cytochrome c process
PF09810 GO:0045145 single-stranded DNA 5'-3' exodeoxyribonuclease activity function
PF09830 GO:0003877 ATP adenylyltransferase activity function
PF10018 GO:0006357 regulation of transcription by RNA polymerase II process
@@ -8914,8 +8553,12 @@ PF10191 GO:0006886 intracellular protein transport process
PF10191 GO:0017119 Golgi transport complex component
PF10192 GO:0007186 G protein-coupled receptor signaling pathway process
PF10192 GO:0019236 response to pheromone process
+PF10218 GO:2000640 positive regulation of SREBP signaling pathway process
PF10220 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay process
PF10229 GO:0009235 cobalamin metabolic process process
+PF10230 GO:0019915 lipid storage process
+PF10230 GO:0005811 lipid droplet component
+PF10230 GO:0016298 lipase activity function
PF10232 GO:0006357 regulation of transcription by RNA polymerase II process
PF10232 GO:0016592 mediator complex component
PF10232 GO:0003712 transcription coregulator activity function
@@ -8940,8 +8583,12 @@ PF10288 GO:0000049 tRNA binding function
PF10309 GO:0003729 mRNA binding function
PF10309 GO:0000340 RNA 7-methylguanosine cap binding function
PF10324 GO:0008528 G protein-coupled peptide receptor activity function
+PF10341 GO:0000781 chromosome, telomeric region component
+PF10341 GO:0042162 telomeric DNA binding function
+PF10341 GO:0005697 telomerase holoenzyme complex component
+PF10341 GO:0007004 telomere maintenance via telomerase process
+PF10341 GO:0051973 positive regulation of telomerase activity process
PF10345 GO:0007064 mitotic sister chromatid cohesion process
-PF10371 GO:0055114 oxidation-reduction process process
PF10371 GO:0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors function
PF10385 GO:0003899 DNA-directed 5'-3' RNA polymerase activity function
PF10385 GO:0006351 transcription, DNA-templated process
@@ -8951,7 +8598,6 @@ PF10392 GO:0017119 Golgi transport complex component
PF10392 GO:0006891 intra-Golgi vesicle-mediated transport process
PF10394 GO:0006325 chromatin organization process
PF10399 GO:0008121 ubiquinol-cytochrome-c reductase activity function
-PF10399 GO:0055114 oxidation-reduction process process
PF10401 GO:0006355 regulation of transcription, DNA-templated process
PF10401 GO:0003700 DNA-binding transcription factor activity function
PF10408 GO:0034450 ubiquitin-ubiquitin ligase activity function
@@ -8959,9 +8605,7 @@ PF10408 GO:0006511 ubiquitin-dependent protein catabolic process process
PF10408 GO:0000151 ubiquitin ligase complex component
PF10408 GO:0016567 protein ubiquitination process
PF10410 GO:0016779 nucleotidyltransferase activity function
-PF10414 GO:0055114 oxidation-reduction process process
PF10414 GO:0006779 porphyrin-containing compound biosynthetic process process
-PF10417 GO:0055114 oxidation-reduction process process
PF10417 GO:0051920 peroxiredoxin activity function
PF10432 GO:0004347 glucose-6-phosphate isomerase activity function
PF10432 GO:0005975 carbohydrate metabolic process process
@@ -8988,19 +8632,20 @@ PF10473 GO:0070840 dynein complex binding function
PF10473 GO:0042803 protein homodimerization activity function
PF10473 GO:0008134 transcription factor binding function
PF10483 GO:0002098 tRNA wobble uridine modification process
-PF10483 GO:0033588 Elongator holoenzyme complex component
+PF10483 GO:0033588 elongator holoenzyme complex component
PF10486 GO:0005944 phosphatidylinositol 3-kinase complex, class IB component
PF10486 GO:0046935 1-phosphatidylinositol-3-kinase regulator activity function
+PF10502 GO:0004252 serine-type endopeptidase activity function
+PF10502 GO:0006465 signal peptide processing process
PF10505 GO:0008023 transcription elongation factor complex component
PF10508 GO:0043248 proteasome assembly process
-PF10509 GO:0005534 galactose binding function
PF10510 GO:0042765 GPI-anchor transamidase complex component
PF10510 GO:0016255 attachment of GPI anchor to protein process
+PF10530 GO:0090729 toxin activity function
PF10568 GO:0001401 SAM complex component
-PF10579 GO:0043495 protein membrane anchor function
+PF10579 GO:0043495 protein-membrane adaptor activity function
PF10579 GO:0033130 acetylcholine receptor binding function
PF10579 GO:0007268 chemical synaptic transmission process
-PF10588 GO:0055114 oxidation-reduction process process
PF10588 GO:0016491 oxidoreductase activity function
PF10589 GO:0051539 4 iron, 4 sulfur cluster binding function
PF10591 GO:0005509 calcium ion binding function
@@ -9011,7 +8656,6 @@ PF10613 GO:0016020 membrane component
PF10613 GO:0004970 ionotropic glutamate receptor activity function
PF10637 GO:0016706 2-oxoglutarate-dependent dioxygenase activity function
PF10637 GO:0005506 iron ion binding function
-PF10637 GO:0055114 oxidation-reduction process process
PF10637 GO:0031418 L-ascorbic acid binding function
PF10640 GO:0004651 polynucleotide 5'-phosphatase activity function
PF10640 GO:0004484 mRNA guanylyltransferase activity function
@@ -9020,7 +8664,6 @@ PF10660 GO:0051537 2 iron, 2 sulfur cluster binding function
PF10672 GO:0008168 methyltransferase activity function
PF10681 GO:0005783 endoplasmic reticulum component
PF10681 GO:0006458 'de novo' protein folding process
-PF10716 GO:0055114 oxidation-reduction process process
PF10716 GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor function
PF10717 GO:0019031 viral envelope component
PF10723 GO:0006276 plasmid maintenance process
@@ -9046,21 +8689,17 @@ PF10796 GO:0005737 cytoplasm component
PF13174 GO:0005515 protein binding function
PF13176 GO:0005515 protein binding function
PF13181 GO:0005515 protein binding function
-PF01558 GO:0055114 oxidation-reduction process process
PF01558 GO:0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors function
PF00351 GO:0016714 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced pteridine as one donor, and incorporation of one atom of oxygen function
-PF00351 GO:0055114 oxidation-reduction process process
PF05198 GO:0006413 translational initiation process
PF05198 GO:0003743 translation initiation factor activity function
PF00707 GO:0006413 translational initiation process
PF00081 GO:0006801 superoxide metabolic process process
PF00081 GO:0004784 superoxide dismutase activity function
PF00081 GO:0046872 metal ion binding function
-PF00081 GO:0055114 oxidation-reduction process process
PF02777 GO:0006801 superoxide metabolic process process
PF02777 GO:0004784 superoxide dismutase activity function
PF02777 GO:0046872 metal ion binding function
-PF02777 GO:0055114 oxidation-reduction process process
PF00347 GO:0005840 ribosome component
PF00347 GO:0006412 translation process
PF00347 GO:0003735 structural constituent of ribosome function
@@ -9077,7 +8716,6 @@ PF03950 GO:0000166 nucleotide binding function
PF03950 GO:0004812 aminoacyl-tRNA ligase activity function
PF03950 GO:0005737 cytoplasm component
PF02918 GO:0005576 extracellular region component
-PF02918 GO:0009405 pathogenesis process
PF01392 GO:0005515 protein binding function
PF11087 GO:0039641 viral inner membrane component
PF05196 GO:0008083 growth factor activity function
@@ -9086,8 +8724,7 @@ PF01416 GO:0003723 RNA binding function
PF01416 GO:0009451 RNA modification process
PF01416 GO:0001522 pseudouridine synthesis process
PF01416 GO:0009982 pseudouridine synthase activity function
-PF10890 GO:0022900 electron transport chain process
-PF10890 GO:0005743 mitochondrial inner membrane component
+PF10890 GO:0005750 mitochondrial respiratory chain complex III component
PF10890 GO:0070469 respirasome component
PF10955 GO:0010468 regulation of gene expression process
PF11480 GO:0030153 bacteriocin immunity process
@@ -9100,15 +8737,13 @@ PF11108 GO:0019064 fusion of virus membrane with host plasma membrane process
PF15163 GO:0005634 nucleus component
PF01287 GO:0043022 ribosome binding function
PF01287 GO:0003723 RNA binding function
-PF01287 GO:0006452 translational frameshifting process
PF01287 GO:0003746 translation elongation factor activity function
PF01287 GO:0045905 positive regulation of translational termination process
PF01287 GO:0045901 positive regulation of translational elongation process
PF17308 GO:0071858 corazonin receptor binding function
PF17308 GO:0045823 positive regulation of heart contraction process
-PF16818 GO:0034448 EGO complex component
-PF16818 GO:0016237 lysosomal microautophagy process
PF16818 GO:0007165 signal transduction process
+PF16818 GO:0071986 Ragulator complex component
PF17112 GO:0005742 mitochondrial outer membrane translocase complex component
PF17112 GO:0030150 protein import into mitochondrial matrix process
PF11095 GO:0034719 SMN-Sm protein complex component
@@ -9135,19 +8770,17 @@ PF02843 GO:0009113 purine nucleobase biosynthetic process process
PF02843 GO:0004637 phosphoribosylamine-glycine ligase activity function
PF02844 GO:0009113 purine nucleobase biosynthetic process process
PF02844 GO:0004637 phosphoribosylamine-glycine ligase activity function
-PF04613 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF04613 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF04613 GO:0009245 lipid A biosynthetic process process
PF02601 GO:0008855 exodeoxyribonuclease VII activity function
PF02347 GO:0006546 glycine catabolic process process
-PF02347 GO:0055114 oxidation-reduction process process
PF02347 GO:0004375 glycine dehydrogenase (decarboxylating) activity function
PF07826 GO:0006188 IMP biosynthetic process process
PF07826 GO:0006164 purine nucleotide biosynthetic process process
PF07826 GO:0003937 IMP cyclohydrolase activity function
-PF00108 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
-PF02803 GO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups function
+PF00108 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
+PF02803 GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups function
PF00763 GO:0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity function
-PF00763 GO:0055114 oxidation-reduction process process
PF02882 GO:0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity function
PF00298 GO:0005840 ribosome component
PF00298 GO:0006412 translation process
@@ -9159,15 +8792,14 @@ PF14630 GO:0005634 nucleus component
PF14630 GO:0000808 origin recognition complex component
PF14630 GO:0006260 DNA replication process
PF00166 GO:0006457 protein folding process
-PF00044 GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor function
-PF00044 GO:0055114 oxidation-reduction process process
+PF00166 GO:0005524 ATP binding function
+PF00166 GO:0016887 ATPase function
+PF00044 GO:0051287 NAD binding function
PF02800 GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor function
-PF02800 GO:0055114 oxidation-reduction process process
PF13892 GO:0003677 DNA binding function
PF07688 GO:0007623 circadian rhythm process
PF07688 GO:0006468 protein phosphorylation process
PF11909 GO:0016020 membrane component
-PF11909 GO:0055114 oxidation-reduction process process
PF11909 GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor function
PF02863 GO:0034618 arginine binding function
PF02863 GO:0051259 protein complex oligomerization process
@@ -9175,7 +8807,6 @@ PF01316 GO:0006525 arginine metabolic process process
PF01316 GO:0006355 regulation of transcription, DNA-templated process
PF01316 GO:0003700 DNA-binding transcription factor activity function
PF11910 GO:0005886 plasma membrane component
-PF11910 GO:0055114 oxidation-reduction process process
PF11910 GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor function
PF11520 GO:0005737 cytoplasm component
PF11520 GO:0003690 double-stranded DNA binding function
@@ -9184,13 +8815,12 @@ PF02085 GO:0020037 heme binding function
PF00743 GO:0050661 NADP binding function
PF00743 GO:0050660 flavin adenine dinucleotide binding function
PF00743 GO:0004499 N,N-dimethylaniline monooxygenase activity function
-PF00743 GO:0055114 oxidation-reduction process process
PF12249 GO:0044038 cell wall macromolecule biosynthetic process process
-PF12249 GO:0016757 transferase activity, transferring glycosyl groups function
+PF12249 GO:0016757 glycosyltransferase activity function
PF12249 GO:0016021 integral component of membrane component
PF12249 GO:0005886 plasma membrane component
PF12250 GO:0044038 cell wall macromolecule biosynthetic process process
-PF12250 GO:0016757 transferase activity, transferring glycosyl groups function
+PF12250 GO:0016757 glycosyltransferase activity function
PF12250 GO:0016021 integral component of membrane component
PF12250 GO:0005886 plasma membrane component
PF11468 GO:0016740 transferase activity function
@@ -9199,11 +8829,11 @@ PF11956 GO:0016020 membrane component
PF11956 GO:0005267 potassium channel activity function
PF11421 GO:0006754 ATP biosynthetic process process
PF11421 GO:0005524 ATP binding function
-PF11421 GO:0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) component
-PF11421 GO:0016887 ATPase activity function
+PF11421 GO:0000275 mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) component
+PF11421 GO:0016887 ATPase function
PF11602 GO:0019072 viral genome packaging process
PF12539 GO:0005515 protein binding function
-PF11031 GO:0044659 cytolysis by virus of host cell process
+PF11031 GO:0044659 viral release from host cell by cytolysis process
PF11545 GO:0020037 heme binding function
PF11802 GO:0005634 nucleus component
PF11802 GO:0051382 kinetochore assembly process
@@ -9224,11 +8854,11 @@ PF12199 GO:0005615 extracellular space component
PF12343 GO:0016817 hydrolase activity, acting on acid anhydrides function
PF12270 GO:0004129 cytochrome-c oxidase activity function
PF12270 GO:0016021 integral component of membrane component
-PF12270 GO:0055114 oxidation-reduction process process
PF11389 GO:0055085 transmembrane transport process
PF11389 GO:0015288 porin activity function
PF11389 GO:0005886 plasma membrane component
PF11770 GO:0016021 integral component of membrane component
+PF11955 GO:0003723 RNA binding function
PF12326 GO:0034599 cellular response to oxidative stress process
PF12326 GO:0005789 endoplasmic reticulum membrane component
PF12590 GO:0016790 thiolester hydrolase activity function
@@ -9237,10 +8867,10 @@ PF00214 GO:0005179 hormone activity function
PF11099 GO:0019050 suppression by virus of host apoptotic process process
PF04962 GO:0016861 intramolecular oxidoreductase activity, interconverting aldoses and ketoses function
PF09392 GO:0015031 protein transport process
-PF09392 GO:0009405 pathogenesis process
PF09704 GO:0043571 maintenance of CRISPR repeat elements process
PF07140 GO:0016020 membrane component
PF07140 GO:0019955 cytokine binding function
+PF01062 GO:0005254 chloride channel activity function
PF00311 GO:0006099 tricarboxylic acid cycle process
PF00311 GO:0015977 carbon fixation process
PF00311 GO:0008964 phosphoenolpyruvate carboxylase activity function
@@ -9252,13 +8882,13 @@ PF02718 GO:0046765 viral budding from nuclear membrane process
PF01628 GO:0003677 DNA binding function
PF01628 GO:0006355 regulation of transcription, DNA-templated process
PF12549 GO:0004511 tyrosine 3-monooxygenase activity function
-PF12549 GO:0055114 oxidation-reduction process process
PF11069 GO:0003352 regulation of cilium movement process
PF11081 GO:0019073 viral DNA genome packaging process
PF11277 GO:0016592 mediator complex component
PF11380 GO:0016772 transferase activity, transferring phosphorus-containing groups function
PF11382 GO:0016020 membrane component
PF11382 GO:0055070 copper ion homeostasis process
+PF11395 GO:0016021 integral component of membrane component
PF11411 GO:0003910 DNA ligase (ATP) activity function
PF11461 GO:0046983 protein dimerization activity function
PF11522 GO:0016773 phosphotransferase activity, alcohol group as acceptor function
@@ -9309,8 +8939,8 @@ PF11889 GO:0017111 nucleoside-triphosphatase activity function
PF11889 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF11894 GO:0005643 nuclear pore component
PF11896 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
-PF11960 GO:0055114 oxidation-reduction process process
PF11960 GO:0016717 oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water function
+PF11961 GO:0045927 positive regulation of growth process
PF12009 GO:0003964 RNA-directed DNA polymerase activity function
PF12011 GO:0017111 nucleoside-triphosphatase activity function
PF12017 GO:0004803 transposase activity function
@@ -9347,11 +8977,8 @@ PF12387 GO:0070008 serine-type exopeptidase activity function
PF12387 GO:0017111 nucleoside-triphosphatase activity function
PF12387 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF12398 GO:0004674 protein serine/threonine kinase activity function
-PF12424 GO:0005388 calcium transmembrane transporter activity, phosphorylative mechanism function
+PF12424 GO:0005388 P-type calcium transporter activity function
PF12437 GO:0004356 glutamate-ammonia ligase activity function
-PF12443 GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific function
-PF12443 GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding function
-PF12443 GO:0001837 epithelial to mesenchymal transition process
PF12463 GO:0031464 Cul4A-RING E3 ubiquitin ligase complex component
PF12463 GO:0006511 ubiquitin-dependent protein catabolic process process
PF12474 GO:0004674 protein serine/threonine kinase activity function
@@ -9362,7 +8989,7 @@ PF12501 GO:0006817 phosphate ion transport process
PF12503 GO:0016817 hydrolase activity, acting on acid anhydrides function
PF12503 GO:0008168 methyltransferase activity function
PF12513 GO:0016817 hydrolase activity, acting on acid anhydrides function
-PF12554 GO:0008274 gamma-tubulin ring complex component
+PF12554 GO:0000931 gamma-tubulin large complex component
PF12554 GO:0033566 gamma-tubulin complex localization process
PF12581 GO:0004252 serine-type endopeptidase activity function
PF12581 GO:0016817 hydrolase activity, acting on acid anhydrides function
@@ -9371,15 +8998,11 @@ PF12581 GO:0070008 serine-type exopeptidase activity function
PF12581 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF12589 GO:0016435 rRNA (guanine) methyltransferase activity function
PF12589 GO:0070476 rRNA (guanine-N7)-methylation process
-PF12601 GO:0016817 hydrolase activity, acting on acid anhydrides function
PF12601 GO:0004197 cysteine-type endopeptidase activity function
-PF12601 GO:0017111 nucleoside-triphosphatase activity function
-PF12601 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
PF12605 GO:0004674 protein serine/threonine kinase activity function
PF15432 GO:0015031 protein transport process
PF16929 GO:0015031 protein transport process
PF15461 GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen function
-PF15461 GO:0055114 oxidation-reduction process process
PF12191 GO:0043065 positive regulation of apoptotic process process
PF12191 GO:0005515 protein binding function
PF12191 GO:0005886 plasma membrane component
@@ -9387,8 +9010,7 @@ PF12019 GO:0015628 protein secretion by the type II secretion system process
PF12019 GO:0015627 type II protein secretion system complex component
PF16993 GO:0015031 protein transport process
PF02866 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
-PF02866 GO:0055114 oxidation-reduction process process
-PF02749 GO:0016763 transferase activity, transferring pentosyl groups function
+PF02749 GO:0016763 pentosyltransferase activity function
PF02807 GO:0016301 kinase activity function
PF02807 GO:0016772 transferase activity, transferring phosphorus-containing groups function
PF00217 GO:0016301 kinase activity function
@@ -9402,18 +9024,16 @@ PF03900 GO:0004418 hydroxymethylbilane synthase activity function
PF00220 GO:0005576 extracellular region component
PF00220 GO:0005185 neurohypophyseal hormone activity function
PF12603 GO:0003968 RNA-directed 5'-3' RNA polymerase activity function
-PF12597 GO:0033617 mitochondrial respiratory chain complex IV assembly process
+PF12597 GO:0033617 mitochondrial cytochrome c oxidase assembly process
PF12597 GO:0005743 mitochondrial inner membrane component
PF12537 GO:0016020 membrane component
PF10824 GO:0009306 protein secretion process
-PF12592 GO:0042626 ATPase-coupled transmembrane transporter activity function
PF10843 GO:0006112 energy reserve metabolic process process
PF11965 GO:0016851 magnesium chelatase activity function
PF10863 GO:0030686 90S preribosome component
PF10863 GO:0042274 ribosomal small subunit biogenesis process
PF11080 GO:0004521 endoribonuclease activity function
PF11266 GO:0071771 aldehyde decarbonylase activity function
-PF11973 GO:0055114 oxidation-reduction process process
PF11973 GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor function
PF11975 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF10868 GO:0050832 defense response to fungus process
@@ -9446,7 +9066,6 @@ PF00705 GO:0006275 regulation of DNA replication process
PF02747 GO:0003677 DNA binding function
PF02747 GO:0006275 regulation of DNA replication process
PF05173 GO:0009089 lysine biosynthetic process via diaminopimelate process
-PF05173 GO:0055114 oxidation-reduction process process
PF05173 GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase function
PF00181 GO:0005840 ribosome component
PF00181 GO:0006412 translation process
@@ -9465,10 +9084,8 @@ PF03727 GO:0016773 phosphotransferase activity, alcohol group as acceptor functi
PF00479 GO:0006006 glucose metabolic process process
PF00479 GO:0050661 NADP binding function
PF00479 GO:0016614 oxidoreductase activity, acting on CH-OH group of donors function
-PF00479 GO:0055114 oxidation-reduction process process
PF02781 GO:0006006 glucose metabolic process process
PF02781 GO:0050661 NADP binding function
-PF02781 GO:0055114 oxidation-reduction process process
PF02781 GO:0004345 glucose-6-phosphate dehydrogenase activity function
PF01233 GO:0004379 glycylpeptide N-tetradecanoyltransferase activity function
PF02799 GO:0004379 glycylpeptide N-tetradecanoyltransferase activity function
@@ -9492,17 +9109,14 @@ PF12105 GO:0009020 tRNA (guanosine-2'-O-)-methyltransferase activity function
PF12109 GO:0019955 cytokine binding function
PF12122 GO:0004252 serine-type endopeptidase activity function
PF12122 GO:0016021 integral component of membrane component
-PF12124 GO:0004197 cysteine-type endopeptidase activity function
+PF12133 GO:0044165 host cell endoplasmic reticulum component
PF12137 GO:0016817 hydrolase activity, acting on acid anhydrides function
-PF12142 GO:0055114 oxidation-reduction process process
PF12142 GO:0004097 catechol oxidase activity function
-PF12143 GO:0055114 oxidation-reduction process process
PF12143 GO:0004097 catechol oxidase activity function
PF12153 GO:0042742 defense response to bacterium process
PF11047 GO:0033644 host cell membrane component
-PF11047 GO:0009405 pathogenesis process
PF11051 GO:0006486 protein glycosylation process
-PF11051 GO:0016757 transferase activity, transferring glycosyl groups function
+PF11051 GO:0016757 glycosyltransferase activity function
PF12162 GO:0003700 DNA-binding transcription factor activity function
PF12169 GO:0003887 DNA-directed DNA polymerase activity function
PF11408 GO:0043138 3'-5' DNA helicase activity function
@@ -9510,21 +9124,23 @@ PF11408 GO:0003676 nucleic acid binding function
PF01694 GO:0004252 serine-type endopeptidase activity function
PF01694 GO:0016021 integral component of membrane component
PF06268 GO:0051015 actin filament binding function
-PF06268 GO:0030674 protein binding, bridging function
+PF06268 GO:0030674 protein-macromolecule adaptor activity function
PF05706 GO:0004721 phosphoprotein phosphatase activity function
PF05706 GO:0004725 protein tyrosine phosphatase activity function
PF04347 GO:0016021 integral component of membrane component
PF04347 GO:0044781 bacterial-type flagellum organization process
PF07412 GO:0006275 regulation of DNA replication process
PF02156 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
+PF01203 GO:0015628 protein secretion by the type II secretion system process
+PF01203 GO:0015627 type II protein secretion system complex component
PF05234 GO:0006360 transcription by RNA polymerase I process
PF05786 GO:0000796 condensin complex component
PF05786 GO:0007076 mitotic chromosome condensation process
PF05044 GO:0003677 DNA binding function
PF14829 GO:0004366 glycerol-3-phosphate O-acyltransferase activity function
+PF00248 GO:0047834 D-threo-aldose 1-dehydrogenase activity function
PF17433 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF02897 GO:0004252 serine-type endopeptidase activity function
-PF02897 GO:0070008 serine-type exopeptidase activity function
PF05634 GO:0003723 RNA binding function
PF02007 GO:0008168 methyltransferase activity function
PF02007 GO:0006730 one-carbon metabolic process process
@@ -9538,22 +9154,19 @@ PF01982 GO:0016773 phosphotransferase activity, alcohol group as acceptor functi
PF10484 GO:0005840 ribosome component
PF10484 GO:0006412 translation process
PF10484 GO:0003735 structural constituent of ribosome function
+PF01327 GO:0042586 peptide deformylase activity function
PF03932 GO:0055070 copper ion homeostasis process
PF03932 GO:0005507 copper ion binding function
-PF07992 GO:0055114 oxidation-reduction process process
PF07992 GO:0016491 oxidoreductase activity function
PF13994 GO:0043709 cell adhesion involved in single-species biofilm formation process
PF00909 GO:0016020 membrane component
PF00909 GO:0008519 ammonium transmembrane transporter activity function
PF00909 GO:0015696 ammonium transport process
PF05224 GO:0003677 DNA binding function
-PF14850 GO:0055114 oxidation-reduction process process
PF14850 GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity function
PF00180 GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor function
-PF00180 GO:0055114 oxidation-reduction process process
PF14724 GO:0050290 sphingomyelin phosphodiesterase D activity function
PF16672 GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process process
-PF16672 GO:0019079 viral genome replication process
PF16672 GO:0043066 negative regulation of apoptotic process process
PF16672 GO:0071986 Ragulator complex component
PF16672 GO:0005737 cytoplasm component
@@ -9568,7 +9181,6 @@ PF12658 GO:1990879 CST complex component
PF12658 GO:0043047 single-stranded telomeric DNA binding function
PF12189 GO:0006457 protein folding process
PF12189 GO:0005515 protein binding function
-PF12189 GO:0009405 pathogenesis process
PF11654 GO:0009306 protein secretion process
PF11435 GO:0003723 RNA binding function
PF12659 GO:0016233 telomere capping process
@@ -9585,15 +9197,22 @@ PF13000 GO:0008521 acetyl-CoA transmembrane transporter activity function
PF13000 GO:0016021 integral component of membrane component
PF13001 GO:0043248 proteasome assembly process
PF13001 GO:0060090 molecular adaptor activity function
+PF11633 GO:0002151 G-quadruplex RNA binding function
+PF11289 GO:0005216 ion channel activity function
+PF11289 GO:0039707 pore formation by virus in membrane of host cell process
+PF11774 GO:0003677 DNA binding function
+PF12217 GO:0016996 endo-alpha-(2,8)-sialidase activity function
PF11429 GO:0004540 ribonuclease activity function
-PF12529 GO:0030158 protein xylosyltransferase activity function
-PF12529 GO:0006024 glycosaminoglycan biosynthetic process process
PF06382 GO:0035092 sperm chromatin condensation process
PF06382 GO:0007283 spermatogenesis process
PF12822 GO:0022857 transmembrane transporter activity function
PF11890 GO:0046983 protein dimerization activity function
+PF12897 GO:0004069 L-aspartate:2-oxoglutarate aminotransferase activity function
PF11109 GO:0031854 orexigenic neuropeptide QRFP receptor binding function
PF12201 GO:0006915 apoptotic process process
+PF11931 GO:0003723 RNA binding function
+PF11931 GO:0005681 spliceosomal complex component
+PF11931 GO:0000398 mRNA splicing, via spliceosome process
PF07961 GO:0032979 protein insertion into mitochondrial inner membrane from matrix process
PF07961 GO:0005743 mitochondrial inner membrane component
PF12766 GO:0010181 FMN binding function
@@ -9601,6 +9220,10 @@ PF12940 GO:0061630 ubiquitin protein ligase activity function
PF12940 GO:0033151 V(D)J recombination process
PF12940 GO:0043565 sequence-specific DNA binding function
PF12940 GO:0004519 endonuclease activity function
+PF12829 GO:0003697 single-stranded DNA binding function
+PF12829 GO:0000150 DNA strand exchange activity function
+PF12829 GO:0000002 mitochondrial genome maintenance process
+PF12829 GO:0006310 DNA recombination process
PF11093 GO:0042720 mitochondrial inner membrane peptidase complex component
PF06330 GO:0016838 carbon-oxygen lyase activity, acting on phosphates function
PF11705 GO:0006383 transcription by RNA polymerase III process
@@ -9621,16 +9244,14 @@ PF10798 GO:0071468 cellular response to acidic pH process
PF12634 GO:0045033 peroxisome inheritance process
PF12634 GO:0005780 extrinsic component of intraperoxisomal membrane component
PF12678 GO:0008270 zinc ion binding function
-PF12920 GO:0009405 pathogenesis process
-PF12919 GO:0016757 transferase activity, transferring glycosyl groups function
+PF12919 GO:0016757 glycosyltransferase activity function
PF12814 GO:0005938 cell cortex component
-PF12814 GO:0032065 cortical protein anchoring process
+PF12814 GO:0032065 maintenance of protein location in cell cortex process
PF12814 GO:0005515 protein binding function
PF12814 GO:0005543 phospholipid binding function
PF12884 GO:0008140 cAMP response element binding protein binding function
PF12884 GO:0051289 protein homotetramerization process
PF15168 GO:0005789 endoplasmic reticulum membrane component
-PF15070 GO:0005794 Golgi apparatus component
PF15313 GO:0000122 negative regulation of transcription by RNA polymerase II process
PF15313 GO:0005634 nucleus component
PF15313 GO:0004861 cyclin-dependent protein serine/threonine kinase inhibitor activity function
@@ -9649,8 +9270,12 @@ PF04446 GO:0006400 tRNA modification process
PF06657 GO:0008017 microtubule binding function
PF13017 GO:0060964 regulation of gene silencing by miRNA process
PF12859 GO:0005680 anaphase-promoting complex component
+PF12861 GO:0061630 ubiquitin protein ligase activity function
+PF12861 GO:0031145 anaphase-promoting complex-dependent catabolic process process
+PF12861 GO:0008270 zinc ion binding function
+PF12861 GO:0097602 cullin family protein binding function
PF12861 GO:0005680 anaphase-promoting complex component
-PF12861 GO:0004842 ubiquitin-protein transferase activity function
+PF13225 GO:0005506 iron ion binding function
PF13397 GO:0045893 positive regulation of transcription, DNA-templated process
PF13397 GO:0001000 bacterial-type RNA polymerase core enzyme binding function
PF13085 GO:0009055 electron transfer activity function
@@ -9665,9 +9290,14 @@ PF13184 GO:0003723 RNA binding function
PF13947 GO:0030247 polysaccharide binding function
PF13949 GO:0005515 protein binding function
PF14027 GO:0016491 oxidoreductase activity function
+PF14130 GO:0004518 nuclease activity function
+PF14290 GO:0006099 tricarboxylic acid cycle process
+PF14290 GO:0045273 respiratory chain complex II component
PF14144 GO:0043565 sequence-specific DNA binding function
PF14144 GO:0006351 transcription, DNA-templated process
PF14372 GO:0003677 DNA binding function
+PF13326 GO:0010206 photosystem II repair process
+PF13326 GO:0009523 photosystem II component
PF13326 GO:0010207 photosystem II assembly process
PF13851 GO:0031514 motile cilium component
PF13851 GO:0048870 cell motility process
@@ -9700,15 +9330,12 @@ PF14073 GO:0042802 identical protein binding function
PF13841 GO:0005576 extracellular region component
PF13841 GO:0045087 innate immune response process
PF14171 GO:0016021 integral component of membrane component
-PF14171 GO:0009405 pathogenesis process
PF11540 GO:0007018 microtubule-based movement process
PF11540 GO:0005868 cytoplasmic dynein complex component
PF13965 GO:0016021 integral component of membrane component
-PF13965 GO:0051033 RNA transmembrane transporter activity function
-PF13965 GO:0033227 dsRNA transport process
PF12643 GO:0009143 nucleoside triphosphate catabolic process process
PF12643 GO:0047429 nucleoside-triphosphate diphosphatase activity function
-PF13506 GO:0016757 transferase activity, transferring glycosyl groups function
+PF13506 GO:0016757 glycosyltransferase activity function
PF16317 GO:0016798 hydrolase activity, acting on glycosyl bonds function
PF15332 GO:0050853 B cell receptor signaling pathway process
PF15332 GO:0050852 T cell receptor signaling pathway process
@@ -9744,7 +9371,7 @@ PF15880 GO:0005747 mitochondrial respiratory chain complex I component
PF15880 GO:0005739 mitochondrion component
PF15172 GO:0005179 hormone activity function
PF15328 GO:0016591 RNA polymerase II, holoenzyme component
-PF16954 GO:0015232 heme transporter activity function
+PF16954 GO:0015232 heme transmembrane transporter activity function
PF16954 GO:0015886 heme transport process
PF16969 GO:0006614 SRP-dependent cotranslational protein targeting to membrane process
PF16969 GO:0005786 signal recognition particle, endoplasmic reticulum targeting component
@@ -9781,11 +9408,12 @@ PF16006 GO:0040001 establishment of mitotic spindle localization process
PF16006 GO:0005819 spindle component
PF15170 GO:0004860 protein kinase inhibitor activity function
PF12632 GO:0017022 myosin binding function
+PF13350 GO:0004721 phosphoprotein phosphatase activity function
PF14304 GO:0031124 mRNA 3'-end processing process
PF13367 GO:0008233 peptidase activity function
PF13922 GO:0003677 DNA binding function
+PF13887 GO:0016540 protein autoprocessing process
PF06109 GO:0044179 hemolysis in other organism process
-PF06109 GO:0009405 pathogenesis process
PF12257 GO:0005096 GTPase activator activity function
PF01459 GO:0055085 transmembrane transport process
PF01459 GO:0005741 mitochondrial outer membrane component
@@ -9797,19 +9425,24 @@ PF09749 GO:0004518 nuclease activity function
PF12519 GO:0032865 ERMES complex component
PF12519 GO:0007005 mitochondrion organization process
PF16934 GO:0050830 defense response to Gram-positive bacterium process
+PF09419 GO:0008962 phosphatidylglycerophosphatase activity function
PF13691 GO:0008033 tRNA processing process
PF13096 GO:0034080 CENP-A containing nucleosome assembly process
PF13096 GO:0000775 chromosome, centromeric region component
PF15077 GO:0003677 DNA binding function
PF15019 GO:0005085 guanyl-nucleotide exchange factor activity function
PF15021 GO:2001032 regulation of double-strand break repair via nonhomologous end joining process
+PF15162 GO:0007130 synaptonemal complex assembly process
+PF14990 GO:0034551 mitochondrial respiratory chain complex III assembly process
+PF15133 GO:0034121 regulation of toll-like receptor signaling pathway process
PF15384 GO:0006303 double-strand break repair via nonhomologous end joining process
PF11365 GO:0005615 extracellular space component
PF11365 GO:0010506 regulation of autophagy process
PF15387 GO:0000408 EKC/KEOPS complex component
PF15141 GO:0034551 mitochondrial respiratory chain complex III assembly process
-PF15061 GO:0033617 mitochondrial respiratory chain complex IV assembly process
+PF15061 GO:0033617 mitochondrial cytochrome c oxidase assembly process
PF15061 GO:0016021 integral component of membrane component
+PF15370 GO:0000492 box C/D snoRNP assembly process
PF14554 GO:0008201 heparin binding function
PF15199 GO:1900758 negative regulation of D-amino-acid oxidase activity process
PF15201 GO:0042622 photoreceptor outer segment membrane component
@@ -9821,18 +9454,21 @@ PF15127 GO:0034237 protein kinase A regulatory subunit binding function
PF15333 GO:0005634 nucleus component
PF15333 GO:0006355 regulation of transcription, DNA-templated process
PF15333 GO:0005668 RNA polymerase transcription factor SL1 complex component
+PF15203 GO:0097524 sperm plasma membrane component
+PF15203 GO:0007342 fusion of sperm to egg plasma membrane involved in single fertilization process
PF15208 GO:0001881 receptor recycling process
PF14876 GO:0005634 nucleus component
PF14876 GO:0005739 mitochondrion component
PF14876 GO:0045333 cellular respiration process
PF15551 GO:0003334 keratinocyte development process
+PF13925 GO:0008017 microtubule binding function
PF14984 GO:0007155 cell adhesion process
PF15091 GO:0042138 meiotic DNA double-strand break formation process
+PF15072 GO:0000725 recombinational repair process
PF14859 GO:0042742 defense response to bacterium process
+PF14860 GO:0031267 small GTPase binding function
PF14860 GO:0044161 host cell cytoplasmic vesicle component
PF14860 GO:0043087 regulation of GTPase activity process
-PF14860 GO:0009405 pathogenesis process
-PF14860 GO:0017137 Rab GTPase binding function
PF14862 GO:0050829 defense response to Gram-negative bacterium process
PF14862 GO:0050830 defense response to Gram-positive bacterium process
PF15225 GO:0006955 immune response process
@@ -9840,8 +9476,9 @@ PF15096 GO:0016021 integral component of membrane component
PF14641 GO:0003677 DNA binding function
PF15171 GO:0005184 neuropeptide hormone activity function
PF15337 GO:0005634 nucleus component
+PF15337 GO:0003723 RNA binding function
+PF15337 GO:0003677 DNA binding function
PF15337 GO:0006351 transcription, DNA-templated process
-PF15337 GO:0003700 DNA-binding transcription factor activity function
PF15337 GO:0045893 positive regulation of transcription, DNA-templated process
PF15281 GO:0042998 positive regulation of Golgi to plasma membrane protein transport process
PF15281 GO:0005802 trans-Golgi network component
@@ -9865,7 +9502,6 @@ PF15341 GO:0030686 90S preribosome component
PF15341 GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) process
PF15341 GO:0005730 nucleolus component
PF15341 GO:0030688 preribosome, small subunit precursor component
-PF15453 GO:0005923 bicellular tight junction component
PF15050 GO:0097197 tetraspanin-enriched microdomain component
PF15050 GO:0016021 integral component of membrane component
PF15050 GO:0001772 immunological synapse component
@@ -9891,7 +9527,7 @@ PF15068 GO:0061572 actin filament bundle organization process
PF15351 GO:0005911 cell-cell junction component
PF14764 GO:0044599 AP-5 adaptor complex component
PF15182 GO:0007605 sensory perception of sound process
-PF15306 GO:0017053 transcriptional repressor complex component
+PF15306 GO:0017053 transcription repressor complex component
PF14777 GO:0060271 cilium assembly process
PF14777 GO:0034464 BBSome component
PF15064 GO:0097228 sperm principal piece component
@@ -9926,7 +9562,8 @@ PF05088 GO:0004352 glutamate dehydrogenase (NAD+) activity function
PF05088 GO:0019551 glutamate catabolic process to 2-oxoglutarate process
PF16554 GO:0046983 protein dimerization activity function
PF15630 GO:0071821 FANCM-MHF complex component
-PF15556 GO:0007093 mitotic cell cycle checkpoint process
+PF12695 GO:0016787 hydrolase activity function
+PF15556 GO:0007093 mitotic cell cycle checkpoint signaling process
PF15556 GO:0000776 kinetochore component
PF15550 GO:0005576 extracellular region component
PF15550 GO:0016055 Wnt signaling pathway process
@@ -9938,7 +9575,6 @@ PF15501 GO:0046600 negative regulation of centriole replication process
PF15501 GO:0008017 microtubule binding function
PF15497 GO:0005634 nucleus component
PF15497 GO:0006384 transcription initiation from RNA polymerase III promoter process
-PF15497 GO:0003700 DNA-binding transcription factor activity function
PF15497 GO:0006366 transcription by RNA polymerase II process
PF14820 GO:0001533 cornified envelope component
PF15490 GO:1990879 CST complex component
@@ -9981,7 +9617,7 @@ PF15340 GO:0005634 nucleus component
PF15340 GO:0043985 histone H4-R3 methylation process
PF15319 GO:0005634 nucleus component
PF15319 GO:0071479 cellular response to ionizing radiation process
-PF15319 GO:0000077 DNA damage checkpoint process
+PF15319 GO:0000077 DNA damage checkpoint signaling process
PF14619 GO:0042393 histone binding function
PF15310 GO:0007283 spermatogenesis process
PF15307 GO:0001669 acrosomal vesicle component
@@ -9999,7 +9635,7 @@ PF15129 GO:0030298 receptor signaling protein tyrosine kinase activator activity
PF15108 GO:0005244 voltage-gated ion channel activity function
PF15108 GO:0016021 integral component of membrane component
PF15108 GO:0005262 calcium channel activity function
-PF15457 GO:0044419 interspecies interaction between organisms process
+PF15457 GO:0044419 biological process involved in interspecies interaction between organisms process
PF15048 GO:0046982 protein heterodimerization activity function
PF15048 GO:0015721 bile acid and bile salt transport process
PF15048 GO:0005886 plasma membrane component
@@ -10009,7 +9645,6 @@ PF15001 GO:0030119 AP-type membrane coat adaptor complex component
PF15001 GO:0000724 double-strand break repair via homologous recombination process
PF14980 GO:0005576 extracellular region component
PF14980 GO:0007218 neuropeptide signaling pathway process
-PF14811 GO:0030218 erythrocyte differentiation process
PF14631 GO:0006281 DNA repair process
PF14521 GO:0004222 metalloendopeptidase activity function
PF14496 GO:0016567 protein ubiquitination process
@@ -10037,7 +9672,7 @@ PF17067 GO:0005840 ribosome component
PF18024 GO:0003677 DNA binding function
PF16358 GO:0009279 cell outer membrane component
PF16358 GO:0035556 intracellular signal transduction process
-PF16715 GO:0016755 transferase activity, transferring amino-acyl groups function
+PF16715 GO:0016755 aminoacyltransferase activity function
PF15953 GO:0005198 structural molecule activity function
PF17097 GO:0000775 chromosome, centromeric region component
PF15666 GO:2000401 regulation of lymphocyte migration process
@@ -10048,7 +9683,7 @@ PF17095 GO:0031175 neuron projection development process
PF17095 GO:0005516 calmodulin binding function
PF17095 GO:0030507 spectrin binding function
PF15673 GO:0032922 circadian regulation of gene expression process
-PF15673 GO:0000976 transcription regulatory region sequence-specific DNA binding function
+PF15673 GO:0000976 transcription cis-regulatory region binding function
PF17085 GO:0045667 regulation of osteoblast differentiation process
PF15678 GO:0090307 mitotic spindle assembly process
PF15679 GO:0042254 ribosome biogenesis process
@@ -10085,10 +9720,10 @@ PF17064 GO:1903818 positive regulation of voltage-gated potassium channel activi
PF15699 GO:0010112 regulation of systemic acquired resistance process
PF15703 GO:0002764 immune response-regulating signaling pathway process
PF15703 GO:0042113 B cell activation process
-PF17063 GO:0009405 pathogenesis process
PF15704 GO:0009555 pollen development process
PF17060 GO:0030474 spindle pole body duplication process
PF17060 GO:0071988 protein localization to spindle pole body process
+PF15710 GO:1990918 double-strand break repair involved in meiotic recombination process
PF15718 GO:0007099 centriole replication process
PF15721 GO:0038023 signaling receptor activity function
PF15723 GO:0017148 negative regulation of translation process
@@ -10100,7 +9735,7 @@ PF17053 GO:0000002 mitochondrial genome maintenance process
PF17052 GO:0006413 translational initiation process
PF17052 GO:0005845 mRNA cap binding complex component
PF17052 GO:0017148 negative regulation of translation process
-PF17051 GO:0033617 mitochondrial respiratory chain complex IV assembly process
+PF17051 GO:0033617 mitochondrial cytochrome c oxidase assembly process
PF17050 GO:0042407 cristae formation process
PF17050 GO:0044284 mitochondrial crista junction component
PF17050 GO:0061617 MICOS complex component
@@ -10119,6 +9754,7 @@ PF15757 GO:0070175 positive regulation of enamel mineralization process
PF15757 GO:0042475 odontogenesis of dentin-containing tooth process
PF15771 GO:0042138 meiotic DNA double-strand break formation process
PF15771 GO:0006310 DNA recombination process
+PF15773 GO:0070840 dynein complex binding function
PF15785 GO:0016310 phosphorylation process
PF15785 GO:0004674 protein serine/threonine kinase activity function
PF15785 GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay process
@@ -10133,8 +9769,9 @@ PF16944 GO:0005887 integral component of plasma membrane component
PF16944 GO:0071805 potassium ion transmembrane transport process
PF16944 GO:0015079 potassium ion transmembrane transporter activity function
PF16941 GO:0098657 import into cell process
-PF16940 GO:0009507 chloroplast component
PF15802 GO:0016567 protein ubiquitination process
+PF15806 GO:0060271 cilium assembly process
+PF15806 GO:0043014 alpha-tubulin binding function
PF15812 GO:0032402 melanosome transport process
PF15812 GO:0042470 melanosome component
PF15826 GO:0043065 positive regulation of apoptotic process process
@@ -10143,12 +9780,12 @@ PF15826 GO:0005739 mitochondrion component
PF15826 GO:0097193 intrinsic apoptotic signaling pathway process
PF16892 GO:0046983 protein dimerization activity function
PF15836 GO:0051087 chaperone binding function
+PF15838 GO:0007342 fusion of sperm to egg plasma membrane involved in single fertilization process
PF15847 GO:0030280 structural constituent of skin epidermis function
PF15847 GO:0001533 cornified envelope component
PF15854 GO:0001664 G protein-coupled receptor binding function
PF16867 GO:0047869 dimethylpropiothetin dethiomethylase activity function
PF16855 GO:0019028 viral capsid component
-PF16851 GO:2000123 positive regulation of stomatal complex development process
PF16850 GO:0004867 serine-type endopeptidase inhibitor activity function
PF15886 GO:0030246 carbohydrate binding function
PF15894 GO:0046325 negative regulation of glucose import process
@@ -10170,6 +9807,7 @@ PF15937 GO:0003700 DNA-binding transcription factor activity function
PF16796 GO:0008017 microtubule binding function
PF16790 GO:0003677 DNA binding function
PF16790 GO:0006260 DNA replication process
+PF16787 GO:0003677 DNA binding function
PF16785 GO:0046872 metal ion binding function
PF15957 GO:0007411 axon guidance process
PF16782 GO:0005783 endoplasmic reticulum component
@@ -10181,6 +9819,7 @@ PF15971 GO:0004169 dolichyl-phosphate-mannose-protein mannosyltransferase activi
PF15972 GO:0007259 receptor signaling pathway via JAK-STAT process
PF15972 GO:0001700 embryonic development via the syncytial blastoderm process
PF16752 GO:0015631 tubulin binding function
+PF16732 GO:0043683 type IV pilus assembly process
PF16719 GO:0003682 chromatin binding function
PF16714 GO:0003723 RNA binding function
PF16711 GO:0003779 actin binding function
@@ -10188,15 +9827,14 @@ PF16048 GO:0006952 defense response process
PF16048 GO:0005576 extracellular region component
PF16049 GO:0006952 defense response process
PF16049 GO:0005576 extracellular region component
-PF16692 GO:0005085 guanyl-nucleotide exchange factor activity function
PF16686 GO:0043047 single-stranded telomeric DNA binding function
PF16685 GO:0061630 ubiquitin protein ligase activity function
-PF16683 GO:0016755 transferase activity, transferring amino-acyl groups function
+PF16683 GO:0016755 aminoacyltransferase activity function
PF16053 GO:0005739 mitochondrion component
PF16053 GO:0003735 structural constituent of ribosome function
PF16671 GO:0090527 actin filament reorganization process
PF16668 GO:0007155 cell adhesion process
-PF16074 GO:0043683 type IV pilus biogenesis process
+PF16074 GO:0043683 type IV pilus assembly process
PF16093 GO:0043248 proteasome assembly process
PF16411 GO:2001070 starch binding function
PF16411 GO:0019867 outer membrane component
@@ -10205,8 +9843,8 @@ PF16099 GO:0000166 nucleotide binding function
PF16422 GO:0003677 DNA binding function
PF16590 GO:0005615 extracellular space component
PF16590 GO:0005186 pheromone activity function
-PF16113 GO:0003860 3-hydroxyisobutyryl-CoA hydrolase activity function
PF16557 GO:0003677 DNA binding function
+PF16537 GO:0015627 type II protein secretion system complex component
PF16178 GO:0046983 protein dimerization activity function
PF16525 GO:0020037 heme binding function
PF16519 GO:0051262 protein tetramerization process
@@ -10214,8 +9852,12 @@ PF16452 GO:0051259 protein complex oligomerization process
PF16331 GO:0070206 protein trimerization process
PF16326 GO:0003677 DNA binding function
PF16276 GO:0003676 nucleic acid binding function
+PF16257 GO:0016853 isomerase activity function
PF16251 GO:0003676 nucleic acid binding function
PF12679 GO:0055085 transmembrane transport process
+PF12679 GO:0140359 ABC-type transporter activity function
+PF13822 GO:0003989 acetyl-CoA carboxylase activity function
+PF13822 GO:0004658 propionyl-CoA carboxylase activity function
PF14611 GO:0005743 mitochondrial inner membrane component
PF14612 GO:0005634 nucleus component
PF14612 GO:0006338 chromatin remodeling process
@@ -10227,8 +9869,9 @@ PF15347 GO:0035556 intracellular signal transduction process
PF15347 GO:0005886 plasma membrane component
PF16047 GO:0042742 defense response to bacterium process
PF15270 GO:0008191 metalloendopeptidase inhibitor activity function
-PF13911 GO:0055114 oxidation-reduction process process
PF14432 GO:0008270 zinc ion binding function
+PF19052 GO:0045930 negative regulation of mitotic cell cycle process
+PF19052 GO:0045666 positive regulation of neuron differentiation process
PF17175 GO:0005892 acetylcholine-gated channel complex component
PF12351 GO:0016020 membrane component
PF12351 GO:0032220 plasma membrane fusion involved in cytogamy process
@@ -10241,14 +9884,13 @@ PF18361 GO:0003697 single-stranded DNA binding function
PF17752 GO:0051097 negative regulation of helicase activity process
PF13609 GO:0016020 membrane component
PF13609 GO:0015288 porin activity function
-PF04424 GO:0004843 thiol-dependent ubiquitin-specific protease activity function
+PF04424 GO:0004843 thiol-dependent deubiquitinase function
PF04424 GO:1990380 Lys48-specific deubiquitinase activity function
PF18699 GO:0005762 mitochondrial large ribosomal subunit component
PF18699 GO:0032543 mitochondrial translation process
PF18699 GO:0003735 structural constituent of ribosome function
PF18253 GO:0046983 protein dimerization activity function
PF01128 GO:0070567 cytidylyltransferase activity function
-PF00580 GO:0005524 ATP binding function
PF15348 GO:0032797 SMN complex component
PF15348 GO:0000387 spliceosomal snRNP assembly process
PF00821 GO:0006094 gluconeogenesis process
@@ -10262,7 +9904,7 @@ PF17548 GO:0003677 DNA binding function
PF17538 GO:0003677 DNA binding function
PF17312 GO:0042742 defense response to bacterium process
PF17323 GO:0016021 integral component of membrane component
-PF17321 GO:0043495 protein membrane anchor function
+PF17321 GO:0043495 protein-membrane adaptor activity function
PF17321 GO:0000011 vacuole inheritance process
PF17317 GO:0000772 mating pheromone activity function
PF17317 GO:0000750 pheromone-dependent signal transduction involved in conjugation with cellular fusion process
@@ -10275,21 +9917,34 @@ PF17378 GO:0042138 meiotic DNA double-strand break formation process
PF11182 GO:0042121 alginic acid biosynthetic process process
PF11107 GO:0043240 Fanconi anaemia nuclear complex component
PF11107 GO:0036297 interstrand cross-link repair process
+PF17541 GO:0033104 type VI protein secretion system complex component
+PF17541 GO:0033103 protein secretion by the type VI secretion system process
PF12774 GO:0005524 ATP binding function
+PF11704 GO:0005085 guanyl-nucleotide exchange factor activity function
+PF19117 GO:0045040 protein insertion into mitochondrial outer membrane process
+PF19117 GO:0070096 mitochondrial outer membrane translocase complex assembly process
PF03544 GO:0055085 transmembrane transport process
+PF17672 GO:0007342 fusion of sperm to egg plasma membrane involved in single fertilization process
PF15335 GO:0042981 regulation of apoptotic process process
PF14587 GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds function
PF14369 GO:0061630 ubiquitin protein ligase activity function
PF13539 GO:0008233 peptidase activity function
PF17825 GO:0000712 resolution of meiotic recombination intermediates process
PF17825 GO:0000794 condensed nuclear chromosome component
-PF17825 GO:0016887 ATPase activity function
+PF17825 GO:0016887 ATPase function
PF16647 GO:0005125 cytokine activity function
PF16647 GO:0045639 positive regulation of myeloid cell differentiation process
PF04130 GO:0043015 gamma-tubulin binding function
PF18329 GO:0030247 polysaccharide binding function
+PF17980 GO:0010468 regulation of gene expression process
+PF17980 GO:0006306 DNA methylation process
+PF17664 GO:0060271 cilium assembly process
+PF17951 GO:0004317 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity function
PF17659 GO:0003697 single-stranded DNA binding function
+PF18325 GO:0008897 holo-[acyl-carrier-protein] synthase activity function
PF17649 GO:0034272 phosphatidylinositol 3-kinase complex, class III, type II component
+PF18678 GO:0016853 isomerase activity function
+PF18678 GO:0017000 antibiotic biosynthetic process process
PF17764 GO:0003677 DNA binding function
PF18652 GO:0005618 cell wall component
PF10237 GO:0008168 methyltransferase activity function
@@ -10298,6 +9953,55 @@ PF17642 GO:1901998 toxin transport process
PF17642 GO:0033104 type VI protein secretion system complex component
PF18392 GO:0008180 COP9 signalosome component
PF18392 GO:0010387 COP9 signalosome assembly process
+PF18089 GO:0016787 hydrolase activity function
PF17879 GO:0003690 double-stranded DNA binding function
PF18032 GO:0042651 thylakoid membrane component
PF18209 GO:0010098 suspensor development process
+PF13086 GO:0004386 helicase activity function
+PF02295 GO:0003723 RNA binding function
+PF02295 GO:0003726 double-stranded RNA adenosine deaminase activity function
+PF00529 GO:0055085 transmembrane transport process
+PF18872 GO:0005515 protein binding function
+PF19225 GO:0007130 synaptonemal complex assembly process
+PF19225 GO:0000217 DNA secondary structure binding function
+PF19225 GO:0010520 regulation of reciprocal meiotic recombination process
+PF18876 GO:0005634 nucleus component
+PF19221 GO:0051301 cell division process
+PF19189 GO:0005739 mitochondrion component
+PF19188 GO:0005887 integral component of plasma membrane component
+PF19188 GO:0004930 G protein-coupled receptor activity function
+PF19055 GO:0140359 ABC-type transporter activity function
+PF19060 GO:0003677 DNA binding function
+PF19060 GO:0006323 DNA packaging process
+PF19049 GO:0016579 protein deubiquitination process
+PF19048 GO:0003956 NAD(P)+-protein-arginine ADP-ribosyltransferase activity function
+PF19047 GO:0030705 cytoskeleton-dependent intracellular transport process
+PF19046 GO:0005515 protein binding function
+PF19046 GO:0005794 Golgi apparatus component
+PF19046 GO:0005801 cis-Golgi network component
+PF19045 GO:0043758 acetate-CoA ligase (ADP-forming) activity function
+PF19097 GO:0003729 mRNA binding function
+PF19097 GO:0000398 mRNA splicing, via spliceosome process
+PF19021 GO:0051607 defense response to virus process
+PF19021 GO:0099048 CRISPR-cas system process
+PF19043 GO:0005846 nuclear cap binding complex component
+PF19042 GO:0005846 nuclear cap binding complex component
+PF19041 GO:0005846 nuclear cap binding complex component
+PF19039 GO:0000165 MAPK cascade process
+PF19038 GO:0016192 vesicle-mediated transport process
+PF19037 GO:0016192 vesicle-mediated transport process
+PF19036 GO:0016192 vesicle-mediated transport process
+PF19035 GO:0007165 signal transduction process
+PF19031 GO:0016192 vesicle-mediated transport process
+PF19032 GO:0016192 vesicle-mediated transport process
+PF19033 GO:0016192 vesicle-mediated transport process
+PF19034 GO:0004521 endoribonuclease activity function
+PF18927 GO:0016746 acyltransferase activity function
+PF19112 GO:0016491 oxidoreductase activity function
+PF18972 GO:0051879 Hsp90 protein binding function
+PF11563 GO:0020037 heme binding function
+PF11563 GO:0019825 oxygen binding function
+PF19088 GO:0016779 nucleotidyltransferase activity function
+PF13354 GO:0030655 beta-lactam antibiotic catabolic process process
+PF13354 GO:0017001 antibiotic catabolic process process
+PF13354 GO:0008800 beta-lactamase activity function
diff --git a/addons/go-basic.obo b/addons/go-basic.obo
index 1cb3660660a57e980d92f8006649085bb6ca0905..ba052768870783be62466e0bc4a07ed7e5a3fecf 100644
--- a/addons/go-basic.obo
+++ b/addons/go-basic.obo
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: releases/2021-05-01
+data-version: releases/2021-12-15
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
@@ -48,7 +48,6 @@ def: "The production of new individuals that contain some portion of genetic mat
subset: goslim_agr
subset: goslim_chembl
subset: goslim_flybase_ribbon
-subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "reproductive physiological process" EXACT []
@@ -341,7 +340,7 @@ is_a: GO:0019239 ! deaminase activity
id: GO:0000035
name: acyl binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid." [GOC:curators, ISBN:0198506732]
+def: "Binding to an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid." [GOC:curators, ISBN:0198506732]
synonym: "acyl-CoA or acyl binding" BROAD []
is_a: GO:0005488 ! binding
@@ -381,7 +380,7 @@ name: transition metal ion transport
namespace: biological_process
def: "The directed movement of transition metal ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [ISBN:0198506732]
synonym: "transition metal transport" EXACT []
-is_a: GO:0006812 ! cation transport
+is_a: GO:0030001 ! metal ion transport
[Term]
id: GO:0000044
@@ -421,8 +420,8 @@ consider: GO:0009055
id: GO:0000048
name: peptidyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: peptidyl-tRNA(1) + aminoacyl-tRNA(2) = tRNA(1) + peptidylaminoacyl-tRNA(2)." [EC:2.3.2.12, PMID:11433365, PMID:9242921]
-synonym: "peptidyl-tRNA:aminoacyl-tRNA N-peptidyltransferase activity" RELATED [EC:2.3.2.12]
+def: "Catalysis of the reaction: peptidyl-tRNA(1) + aminoacyl-tRNA(2) = tRNA(1) + peptidylaminoacyl-tRNA(2)." [PMID:11433365, PMID:9242921]
+synonym: "peptidyl-tRNA:aminoacyl-tRNA N-peptidyltransferase activity" RELATED []
xref: EC:2.3.2.12
xref: MetaCyc:PEPTIDYLTRANSFERASE-RXN
xref: Reactome:R-HSA-156912 "Peptide transfer from P-site tRNA to the A-site tRNA"
@@ -433,7 +432,7 @@ id: GO:0000049
name: tRNA binding
namespace: molecular_function
alt_id: GO:0000946
-def: "Interacting selectively and non-covalently with transfer RNA." [GOC:ai]
+def: "Binding to a transfer RNA." [GOC:ai]
synonym: "base pairing with tRNA" NARROW []
is_a: GO:0003723 ! RNA binding
@@ -491,9 +490,10 @@ synonym: "ribosomal subunit export out of nucleus" EXACT [GOC:mah]
synonym: "ribosomal subunit transport from nucleus to cytoplasm" EXACT [GOC:mah]
synonym: "ribosomal subunit-nucleus export" EXACT [GOC:mah]
synonym: "ribosome export from nucleus" RELATED [GOC:mah, GOC:rb]
+is_a: GO:0031503 ! protein-containing complex localization
is_a: GO:0033750 ! ribosome localization
+is_a: GO:0051168 ! nuclear export
is_a: GO:0051656 ! establishment of organelle localization
-is_a: GO:0071428 ! rRNA-containing ribonucleoprotein complex export from nucleus
relationship: part_of GO:0042254 ! ribosome biogenesis
[Term]
@@ -569,7 +569,7 @@ is_obsolete: true
id: GO:0000062
name: fatty-acyl-CoA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a fatty-acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group." [GOC:jl, GOC:krc, ISBN:0198506732]
+def: "Binding to a fatty-acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group." [GOC:jl, GOC:krc, ISBN:0198506732]
synonym: "fatty-acyl binding" BROAD []
synonym: "fatty-acyl-coenzyme A binding" EXACT []
is_a: GO:0120227 ! acyl-CoA binding
@@ -994,13 +994,13 @@ is_a: GO:0008652 ! cellular amino acid biosynthetic process
id: GO:0000107
name: imidazoleglycerol-phosphate synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphoribulosylformimino-AICAR-P + L-glutamine = D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide + L-glutamate + 2 H(+)." [RHEA:24795]
+def: "Catalysis of the reaction: phosphoribulosylformimino-AICAR-P + L-glutamine = D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide + L-glutamate + 2 H(+)." [RHEA:24793]
synonym: "glutamine amidotransferase:cyclase activity" BROAD []
synonym: "imidazole glycerol phosphate synthase activity" EXACT []
synonym: "imidazole-glycerol-phosphate synthase activity" RELATED []
synonym: "imidazoleglycerol phosphate synthase activity" EXACT []
xref: MetaCyc:GLUTAMIDOTRANS-RXN
-xref: RHEA:24795
+xref: RHEA:24793
is_a: GO:0016763 ! pentosyltransferase activity
[Term]
@@ -1190,21 +1190,19 @@ relationship: part_of GO:0005654 ! nucleoplasm
id: GO:0000124
name: SAGA complex
namespace: cellular_component
-def: "A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8." [PMID:10637607, PMID:17337012, PMID:19056896, PMID:20838651]
+alt_id: GO:0000125
+alt_id: GO:0030914
+def: "A SAGA-type histone acetyltransferase complex that deubiquitinates H2A and/or H2B. This complex is organized into several functional submodules: a structural core including the activator binding module and consisting of ADA1 or a homolog, members of the SPT and TAF protein families as well as promotor recruitment factor TRRAP/TRA1, a histone acetyltransferase (HAT) module consisting of GCN5/KAT2A or PCAF/KAT2B, ADA2, ADA3/NGG1, and SGF29 or homologues thereof, a histone deubiquitinase (DUB) module consisting of ATXN7/SGF73, ATXN7L3/SGF11, ENY2/SUS1 and USP22/UBP8 or homologues thereof, and in some taxa a splicing module consisting of SF3B3 and SF3B5 or homologues thereof (not in fungi). In budding yeast also contains Spt8 which distinguishes it from SAGA-like (SLIK) complex (GO:0046695)." [PMID:10637607, PMID:17337012, PMID:19056896, PMID:20838651, PMID:33004486]
+synonym: "PCAF complex" NARROW []
+synonym: "PCAF histone acetylase-associated complex" NARROW []
synonym: "Spt-Ada-Gcn5-acetyltransferase complex" EXACT []
+synonym: "SPT3-TAF9-GCN5 acetylase complex" RELATED [GOC:rl, PMID:18838386]
+synonym: "SPT3-TAF9-PCAF acetylase complex" NARROW [PMID:18838386]
+synonym: "STAGA coactivator complex" RELATED []
+synonym: "STAGA complex" RELATED [PMID:32616828, PMID:33004486, PMID:34112237]
is_a: GO:0070461 ! SAGA-type complex
is_a: GO:1905368 ! peptidase complex
-[Term]
-id: GO:0000125
-name: PCAF complex
-namespace: cellular_component
-def: "A large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs." [PMID:10637607]
-comment: See also the cellular component term 'SAGA complex ; GO:0000124'.
-synonym: "PCAF histone acetylase-associated complex" EXACT []
-synonym: "SPT3-TAF9-PCAF acetylase complex" EXACT [GOC:rl, PMID:18838386]
-is_a: GO:0070461 ! SAGA-type complex
-
[Term]
id: GO:0000126
name: transcription factor TFIIIB complex
@@ -1307,7 +1305,7 @@ name: Golgi membrane
namespace: cellular_component
def: "The lipid bilayer surrounding any of the compartments of the Golgi apparatus." [GOC:mah]
is_a: GO:0098588 ! bounding membrane of organelle
-relationship: part_of GO:0098791 ! Golgi apparatus subcompartment
+relationship: part_of GO:0005794 ! Golgi apparatus
[Term]
id: GO:0000140
@@ -1360,7 +1358,7 @@ id: GO:0000146
name: microfilament motor activity
namespace: molecular_function
alt_id: GO:0030898
-def: "Generation of movement along a microfilament, driven by ATP hydrolysis." [PMID:29716949]
+def: "A motor activity that generates movement along a microfilament, driven by ATP hydrolysis." [PMID:29716949]
synonym: "actin filament motor activity" EXACT [GOC:dph]
synonym: "actin-activated ATPase activity" EXACT []
synonym: "actin-dependent ATPase activity" EXACT []
@@ -1371,8 +1369,8 @@ xref: EC:5.6.1.8
xref: Reactome:R-HSA-2316352 "SLC2A4 (GLUT4) vesicle translocates and docks at the plasma membrane"
xref: Reactome:R-HSA-432237 "Translocation of Aquaporin-2 from intracellular vesicles to the apical plasma membrane"
xref: Reactome:R-HSA-9023171 "Insulin secretory granule translocates across the cortical actin network"
-is_a: GO:0003774 ! motor activity
-is_a: GO:0016887 ! ATPase
+is_a: GO:0003774 ! cytoskeletal motor activity
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0000147
@@ -1397,7 +1395,7 @@ is_a: GO:1990234 ! transferase complex
id: GO:0000149
name: SNARE binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein." [PMID:12642621]
+def: "Binding to a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein." [PMID:12642621]
subset: goslim_chembl
synonym: "SNAP receptor binding" EXACT []
xref: Reactome:R-HSA-210426 "Glutamate synaptic vesicle docking and priming"
@@ -1507,7 +1505,6 @@ namespace: biological_process
def: "A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins." [PMID:9191038]
subset: goslim_metagenomics
synonym: "histidyl-aspartyl phosphorelay" EXACT []
-synonym: "phosphorelay signal transduction system" NARROW []
is_a: GO:0035556 ! intracellular signal transduction
[Term]
@@ -1557,7 +1554,6 @@ synonym: "tryptophan formation" EXACT []
synonym: "tryptophan synthesis" EXACT []
xref: MetaCyc:TRPSYN-PWY
is_a: GO:0006568 ! tryptophan metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009073 ! aromatic amino acid family biosynthetic process
is_a: GO:0046219 ! indolalkylamine biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -1574,6 +1570,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0000165
name: MAPK cascade
namespace: biological_process
+alt_id: GO:0007255
def: "An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain an additional tiers: the upstream MAP4K. The kinases in each tier phosphorylate and activate the kinase in the downstream tier to transmit a signal within a cell." [GOC:bf, GOC:mtg_signaling_feb11, PMID:20811974, PMID:9561267]
comment: MAPK cascades lie downstream of many cell surface receptors and cooperate in transmitting various extracellular signals to the nucleus. One way by which the specificity of each cascade is regulated is through the existence of several distinct components in each tier of the different cascades. The cascades are typically named according to the component in the MAPK tier.
synonym: "ERK/MAPK cascade" NARROW []
@@ -1593,7 +1590,7 @@ is_a: GO:0035556 ! intracellular signal transduction
id: GO:0000166
name: nucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC:mah, ISBN:0198547684]
+def: "Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC:mah, ISBN:0198547684]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
@@ -1616,7 +1613,7 @@ namespace: molecular_function
def: "Catalysis of the site-specific cleavage of RNA by a catalytic RNA-mediated mechanism; substrates include the A3 site in the ITS1 of pre-rRNA." [PMID:17881380]
synonym: "RNase MRP" EXACT []
xref: Wikipedia:RNase_MRP
-is_a: GO:0004540 ! ribonuclease activity
+is_a: GO:0004521 ! endoribonuclease activity
[Term]
id: GO:0000172
@@ -1626,7 +1623,7 @@ def: "A ribonucleoprotein complex that contains an RNA molecule of the snoRNA fa
synonym: "ribonuclease mitochondrial RNA processing complex" EXACT []
synonym: "RNase MRP complex" EXACT []
is_a: GO:0005732 ! sno(s)RNA-containing ribonucleoprotein complex
-is_a: GO:1902494 ! catalytic complex
+is_a: GO:1902555 ! endoribonuclease complex
[Term]
id: GO:0000174
@@ -1726,7 +1723,7 @@ consider: GO:0022627
id: GO:0000182
name: rDNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA." [GOC:mah]
+def: "Binding to a DNA sequence encoding a ribosomal RNA." [GOC:mah]
synonym: "ribosomal DNA binding" EXACT []
is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
@@ -1739,7 +1736,8 @@ synonym: "chromatin silencing at rDNA" RELATED []
synonym: "chromatin silencing at ribosomal DNA" BROAD []
synonym: "heterochromatic silencing at rDNA" BROAD []
synonym: "rDNA chromatin silencing" BROAD [GOC:mah]
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0140718 ! facultative heterochromatin assembly
+relationship: part_of GO:1990700 ! nucleolar chromatin organization
[Term]
id: GO:0000184
@@ -1758,49 +1756,58 @@ is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process
[Term]
id: GO:0000185
-name: activation of MAPKKK activity
+name: obsolete activation of MAPKKK activity
namespace: biological_process
-def: "Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase (MAPKKK)." [PMID:9561267]
+def: "OBSOLETE. Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase (MAPKKK)." [PMID:9561267]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of MAP kinase kinase kinase" EXACT []
synonym: "activation of MAP3K activity" EXACT [GOC:bf]
synonym: "activation of MAPKKK activity during sporulation" NARROW []
synonym: "positive regulation of MAP kinase kinase kinase activity" BROAD []
synonym: "positive regulation of MAPKKK activity" BROAD []
-is_a: GO:0032147 ! activation of protein kinase activity
-is_a: GO:0043406 ! positive regulation of MAP kinase activity
+is_obsolete: true
+consider: GO:0000165
+consider: GO:0043539
[Term]
id: GO:0000186
-name: activation of MAPKK activity
+name: obsolete activation of MAPKK activity
namespace: biological_process
-alt_id: GO:0007255
-def: "The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK)." [PMID:9561267]
+def: "OBSOLETE. The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK)." [PMID:9561267]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of MAP kinase kinase activity" EXACT []
synonym: "activation of MAP/ERK kinase kinase" EXACT []
synonym: "activation of MAP2K activity" EXACT [GOC:bf]
synonym: "activation of MAPKK activity during sporulation" NARROW []
synonym: "positive regulation of MAPKK activity" BROAD []
-is_a: GO:0032147 ! activation of protein kinase activity
+is_obsolete: true
+consider: GO:0000165
+consider: GO:0043539
[Term]
id: GO:0000187
-name: activation of MAPK activity
+name: obsolete activation of MAPK activity
namespace: biological_process
-def: "The initiation of the activity of the inactive enzyme MAP kinase (MAPK)." [PMID:9561267]
+def: "OBSOLETE. The initiation of the activity of the inactive enzyme MAP kinase (MAPK)." [PMID:9561267]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of MAP kinase" EXACT []
synonym: "activation of MAPK activity during sporulation" NARROW []
synonym: "MAPK activation" EXACT []
-is_a: GO:0032147 ! activation of protein kinase activity
-is_a: GO:0043406 ! positive regulation of MAP kinase activity
+is_obsolete: true
+consider: GO:0000165
+consider: GO:0043539
[Term]
id: GO:0000188
-name: inactivation of MAPK activity
+name: obsolete inactivation of MAPK activity
namespace: biological_process
-def: "Any process that terminates the activity of the active enzyme MAP kinase." [PMID:9561267]
+def: "OBSOLETE. Any process that terminates the activity of the active enzyme MAP kinase." [PMID:9561267]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "inactivation of MAPK during sporulation" NARROW []
synonym: "termination of MAPK activity" EXACT []
-is_a: GO:0043407 ! negative regulation of MAP kinase activity
+is_obsolete: true
+consider: GO:0000165
+consider: GO:0043539
[Term]
id: GO:0000189
@@ -1896,6 +1903,8 @@ synonym: "activation of MAPKKK activity involved in cell wall integrity" EXACT [
synonym: "cell wall biogenesis, activation of MAP kinase kinase kinase activity" EXACT []
synonym: "cell wall biogenesis, activation of MAPKKK activity" EXACT []
is_obsolete: true
+consider: GO:0000165
+consider: GO:0043539
[Term]
id: GO:0000198
@@ -2130,7 +2139,7 @@ is_obsolete: true
id: GO:0000217
name: DNA secondary structure binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA containing secondary structure elements such as four-way junctions, bubbles, loops, Y-form DNA, or double-strand/single-strand junctions." [GOC:krc]
+def: "Binding to a DNA secondary structure element such as a four-way junction, a bubble, a loop, Y-form DNA, or a double-strand/single-strand junction." [GOC:krc]
is_a: GO:0003677 ! DNA binding
[Term]
@@ -2152,7 +2161,7 @@ def: "The V0 domain of a proton-transporting V-type ATPase found in the vacuolar
comment: Note that this domain often consists of five subunits, although in some mammalian tissues it may have an additional subunit.
synonym: "vacuolar hydrogen ion-transporting ATPase V0 domain" EXACT []
is_a: GO:0033179 ! proton-transporting V-type ATPase, V0 domain
-relationship: part_of GO:0005773 ! vacuole
+relationship: part_of GO:0016471 ! vacuolar proton-transporting V-type ATPase complex
[Term]
id: GO:0000221
@@ -2230,7 +2239,6 @@ id: GO:0000226
name: microtubule cytoskeleton organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah]
-subset: goslim_drosophila
subset: goslim_pombe
synonym: "microtubule cytoskeleton organisation" EXACT [GOC:mah]
synonym: "microtubule cytoskeleton organization and biogenesis" RELATED [GOC:mah]
@@ -2261,14 +2269,13 @@ relationship: part_of GO:0031981 ! nuclear lumen
[Term]
id: GO:0000229
-name: cytoplasmic chromosome
+name: obsolete cytoplasmic chromosome
namespace: cellular_component
-def: "A chromosome found in the cytoplasm." [GOC:mah]
-subset: goslim_chembl
-subset: goslim_generic
+def: "OBSOLETE. A chromosome found in the cytoplasm." [GOC:mah]
+comment: This term was obsoleted because it is an unnecessary grouping class.
synonym: "cytoplasmic interphase chromosome" NARROW []
-is_a: GO:0005694 ! chromosome
-relationship: part_of GO:0005737 ! cytoplasm
+is_obsolete: true
+replaced_by: GO:0005694
[Term]
id: GO:0000230
@@ -2308,7 +2315,7 @@ def: "OBSOLETE. A chromosome found in the cytoplasm during interphase." [GOC:mah
comment: This term was made obsolete because it is based on a temporal division of the cell cycle.
synonym: "cytoplasmic interphase chromosome" EXACT []
is_obsolete: true
-consider: GO:0000229
+consider: GO:0005694
[Term]
id: GO:0000234
@@ -2671,7 +2678,7 @@ synonym: "mitochondrial DNA" NARROW []
synonym: "mitochondrial genome" RELATED []
synonym: "mtDNA" NARROW []
xref: NIF_Subcellular:sao1186327184
-is_a: GO:0000229 ! cytoplasmic chromosome
+is_a: GO:0005694 ! chromosome
relationship: part_of GO:0042645 ! mitochondrial nucleoid
[Term]
@@ -2732,7 +2739,7 @@ id: GO:0000268
name: peroxisome targeting sequence binding
namespace: molecular_function
alt_id: GO:0005051
-def: "Interacting selectively and non-covalently with a peroxisomal targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome." [GOC:mah, ISBN:0879693568]
+def: "Binding to a peroxisomal targeting sequence, a sequence of amino acids within a protein that acts as a signal for the localization of a protein into the peroxisome." [GOC:mah, ISBN:0879693568]
synonym: "peroxisome targeting signal receptor" NARROW []
synonym: "PTS binding" EXACT []
synonym: "PTS receptor" NARROW []
@@ -2941,8 +2948,9 @@ is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0000287
name: magnesium ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC:ai]
+def: "Binding to a magnesium (Mg) ion." [GOC:ai]
synonym: "magnesium binding" EXACT []
+synonym: "Mg binding" EXACT []
is_a: GO:0046872 ! metal ion binding
[Term]
@@ -3454,7 +3462,7 @@ is_a: GO:0070646 ! protein modification by small protein removal
id: GO:0000339
name: RNA cap binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 7-methylguanosine (m7G) group or derivative located at the 5' end of an RNA molecule." [GOC:krc]
+def: "Binding to a 7-methylguanosine (m7G) group or derivative located at the 5' end of an RNA molecule." [GOC:krc]
synonym: "binding to mRNA cap" NARROW []
synonym: "mRNA cap binding" NARROW []
synonym: "snRNA cap binding" NARROW []
@@ -3464,7 +3472,7 @@ is_a: GO:0003723 ! RNA binding
id: GO:0000340
name: RNA 7-methylguanosine cap binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II." [GOC:krc]
+def: "Binding to a 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II." [GOC:krc]
synonym: "RNA m7G cap binding" EXACT []
is_a: GO:0000339 ! RNA cap binding
@@ -3472,7 +3480,7 @@ is_a: GO:0000339 ! RNA cap binding
id: GO:0000341
name: RNA trimethylguanosine cap binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the trimethylguanosine (m(3)(2,2,7)-GTP) group located at the 5' end of some RNA molecules. Such trimethylated cap structures, generally produced by posttranscriptional modification of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by RNA polymerase II, but have also be found on snRNAs transcribed by RNA polymerase III. They have also been found on a subset of the mRNA population in some species, e.g. C. elegans." [GOC:krc]
+def: "Binding to the trimethylguanosine (m(3)(2,2,7)-GTP) group located at the 5' end of some RNA molecules. Such trimethylated cap structures, generally produced by posttranscriptional modification of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by RNA polymerase II, but have also be found on snRNAs transcribed by RNA polymerase III. They have also been found on a subset of the mRNA population in some species, e.g. C. elegans." [GOC:krc]
synonym: "RNA m2,2,7G cap binding" EXACT []
is_a: GO:0000339 ! RNA cap binding
@@ -3480,7 +3488,7 @@ is_a: GO:0000339 ! RNA cap binding
id: GO:0000342
name: RNA cap 4 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a hypermethylated cap structure consisting of 7-methylguanosine (m(7)G) followed by four methylated nucleotides (cap 4): 7-methylguanosine-ppp-N6, N6, 2'-O-trimethyladenosine-p-2'-O-methyladenosine-p-2'-O-methylcytosine-p-N3, 2'-O-dimethyluridine Such caps are known to be found at the 5' ends of SL RNAs of trypanosomatid protozoa." [GOC:krc, PMID:10880518, PMID:12121975]
+def: "Binding to a hypermethylated cap structure consisting of 7-methylguanosine (m(7)G) followed by four methylated nucleotides (cap 4): 7-methylguanosine-ppp-N6, N6, 2'-O-trimethyladenosine-p-2'-O-methyladenosine-p-2'-O-methylcytosine-p-N3, 2'-O-dimethyluridine Such caps are known to be found at the 5' ends of SL RNAs of trypanosomatid protozoa." [GOC:krc, PMID:10880518, PMID:12121975]
is_a: GO:0000339 ! RNA cap binding
[Term]
@@ -3920,7 +3928,7 @@ relationship: part_of GO:0032153 ! cell division site
id: GO:0000400
name: four-way junction DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC:krc, ISBN:0815332181, PMID:15563464]
+def: "Binding to a DNA segment containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC:krc, ISBN:0815332181, PMID:15563464]
synonym: "forked DNA binding" BROAD []
synonym: "Holliday junction binding" EXACT []
is_a: GO:0000217 ! DNA secondary structure binding
@@ -3929,7 +3937,7 @@ is_a: GO:0000217 ! DNA secondary structure binding
id: GO:0000401
name: open form four-way junction DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA containing the open form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The open form of a four-way junction can be diagrammed without any of the strands crossing over." [GOC:krc, ISBN:0815332181, PMID:15563464]
+def: "Binding to a DNA segment containing the open form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The open form of a four-way junction can be diagrammed without any of the strands crossing over." [GOC:krc, ISBN:0815332181, PMID:15563464]
synonym: "open form Holliday junction binding" EXACT []
is_a: GO:0000400 ! four-way junction DNA binding
@@ -3937,7 +3945,7 @@ is_a: GO:0000400 ! four-way junction DNA binding
id: GO:0000402
name: crossed form four-way junction DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA containing the crossed form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The crossed form of a four-way junction cannot be diagrammed without any of the strands crossing over, and instead contains a single crossover between two of the strands." [GOC:krc, ISBN:0815332181, PMID:15563464]
+def: "Binding to a DNA segment containing the crossed form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The crossed form of a four-way junction cannot be diagrammed without any of the strands crossing over, and instead contains a single crossover between two of the strands." [GOC:krc, ISBN:0815332181, PMID:15563464]
synonym: "crossed form Holliday junction binding" EXACT []
is_a: GO:0000400 ! four-way junction DNA binding
@@ -3945,7 +3953,7 @@ is_a: GO:0000400 ! four-way junction DNA binding
id: GO:0000403
name: Y-form DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with segment of DNA shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end." [GOC:elh, PMID:16781730]
+def: "Binding to a DNA segment shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end." [GOC:elh, PMID:16781730]
synonym: "forked DNA binding" BROAD []
synonym: "splayed Y-form DNA binding" EXACT []
is_a: GO:0000217 ! DNA secondary structure binding
@@ -3954,7 +3962,7 @@ is_a: GO:0000217 ! DNA secondary structure binding
id: GO:0000404
name: heteroduplex DNA loop binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration." [GOC:elh, PMID:16781730]
+def: "Binding to a DNA segment containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration." [GOC:elh, PMID:16781730]
synonym: "loop DNA binding" RELATED [GOC:jh]
is_a: GO:0000217 ! DNA secondary structure binding
is_a: GO:0032135 ! DNA insertion or deletion binding
@@ -3963,14 +3971,14 @@ is_a: GO:0032135 ! DNA insertion or deletion binding
id: GO:0000405
name: bubble DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA." [GOC:elh, GOC:vw, PMID:16781730]
+def: "Binding to DNA segment that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA." [GOC:elh, GOC:vw, PMID:16781730]
is_a: GO:0000217 ! DNA secondary structure binding
[Term]
id: GO:0000406
name: double-strand/single-strand DNA junction binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a region of DNA that contains double-stranded DNA flanked by a region of single-stranded DNA." [GOC:elh, PMID:16781730]
+def: "Binding to a DNA segment that contains double-stranded DNA flanked by a region of single-stranded DNA." [GOC:elh, PMID:16781730]
is_a: GO:0000217 ! DNA secondary structure binding
[Term]
@@ -4737,7 +4745,7 @@ is_a: GO:0034964 ! box H/ACA RNA processing
id: GO:0000497
name: DNA template activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with nucleic acid via hydrogen bonds between the bases of a gene product molecule and the bases of a target DNA molecule." [GOC:krc]
+def: "Binding to nucleic acid via hydrogen bonds between the bases of a gene product molecule and the bases of a target DNA molecule." [GOC:krc]
comment: Note that with respect to annotation, "base pairing" and its child terms are intended to be used to annotate the activity of gene products composed of nucleic acid, presumably RNA, to interact with DNA molecules via base pairing. Internal base pairing with itself is considered part of the secondary structure of the molecule and is not within the scope of GO function.
synonym: "base pairing with DNA" RELATED []
is_a: GO:0003677 ! DNA binding
@@ -4809,7 +4817,7 @@ name: purine-specific mismatch base pair DNA N-glycosylase activity
namespace: molecular_function
def: "Catalysis of the removal of purines present in mismatches, especially opposite oxidized purines, by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic (AP) site." [GOC:elh, PMID:9224623]
synonym: "A/G-specific adenine DNA glycosylase activity" NARROW []
-xref: EC:3.2.2.-
+xref: EC:3.2.2.31
is_a: GO:0000700 ! mismatch base pair DNA N-glycosylase activity
[Term]
@@ -5028,7 +5036,6 @@ def: "Any process that contributes to the maintenance of proper telomeric length
synonym: "regulation of telomere length" RELATED [GOC:dph, GOC:tb]
is_a: GO:0006259 ! DNA metabolic process
is_a: GO:0032200 ! telomere organization
-is_a: GO:0060249 ! anatomical structure homeostasis
[Term]
id: GO:0000724
@@ -5049,7 +5056,7 @@ is_a: GO:0006302 ! double-strand break repair
id: GO:0000725
name: recombinational repair
namespace: biological_process
-def: "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC:elh]
+def: "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region." [GOC:elh]
xref: Wikipedia:Recombinational_repair
is_a: GO:0006281 ! DNA repair
is_a: GO:0006310 ! DNA recombination
@@ -5058,7 +5065,7 @@ is_a: GO:0006310 ! DNA recombination
id: GO:0000726
name: obsolete non-recombinational repair
namespace: biological_process
-def: "OBSOLETE. A DNA repair process in which that does not require the exchange of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC:elh]
+def: "OBSOLETE. A DNA repair process in which that does not require the exchange of genetic material between the broken DNA molecule and a homologous DNA region." [GOC:elh]
comment: This term was obsoleted because it was defined negatively, and it represents an unnecessary grouping class.
is_obsolete: true
@@ -5614,7 +5621,7 @@ alt_id: GO:0000789
alt_id: GO:0000790
alt_id: GO:0005717
def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130]
-comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
+comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
synonym: "chromosome scaffold" RELATED []
synonym: "cytoplasmic chromatin" NARROW []
synonym: "nuclear chromatin" NARROW []
@@ -5643,8 +5650,10 @@ id: GO:0000791
name: euchromatin
namespace: cellular_component
alt_id: GO:0005719
-def: "A dispersed and relatively uncompacted form of chromatin." [GOC:elh]
+alt_id: GO:0035327
+def: "A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation." [PMID:32017156]
synonym: "nuclear euchromatin" RELATED []
+synonym: "transcriptionally active chromatin" EXACT []
xref: NIF_Subcellular:sao445485807
xref: Wikipedia:Euchromatin
is_a: GO:0000785 ! chromatin
@@ -5654,8 +5663,11 @@ id: GO:0000792
name: heterochromatin
namespace: cellular_component
alt_id: GO:0005720
-def: "A compact and highly condensed form of chromatin." [GOC:elh]
+alt_id: GO:0035328
+def: "A compact and highly condensed form of chromatin that is refractory to transcription." [PMID:32017156]
synonym: "nuclear heterochromatin" NARROW []
+synonym: "transcriptionally inactive chromatin" EXACT []
+synonym: "transcriptionally silent chromatin" EXACT []
xref: NIF_Subcellular:sao581845896
xref: Wikipedia:Heterochromatin
is_a: GO:0000785 ! chromatin
@@ -5808,7 +5820,7 @@ def: "A multisubunit complex that is located at the replication origins of a chr
synonym: "cytoplasmic ORC" EXACT []
synonym: "prokaryotic ORC" RELATED []
is_a: GO:0000808 ! origin recognition complex
-relationship: part_of GO:0000229 ! cytoplasmic chromosome
+relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0000810
@@ -5866,7 +5878,7 @@ relationship: part_of GO:0010008 ! endosome membrane
id: GO:0000815
name: ESCRT III complex
namespace: cellular_component
-def: "An endosomal sorting complex required for transport. Consists of two soluble subcomplexes of highly charged coiled-coil proteins and is required for sorting and/or concentration of multivesicular body (MVB) cargoes." [GOC:rb, PMID:12892785, PMID:12900393]
+def: "A complex with membrane scission activity that plays a major role in many processes where membranes are remodelled - including endosomal transport (vesicle budding), nuclear envelope organisation (membrane closure, mitotic bridge cleavage), and cytokinesis (abscission)." [PMID:17556548, PMID:22361144, PMID:28242692, PMID:31132588, PMID:32243490, PMID:34449766]
synonym: "endosomal sorting complex required for transport" BROAD []
is_a: GO:0036452 ! ESCRT complex
is_a: GO:0098796 ! membrane protein complex
@@ -5922,7 +5934,7 @@ relationship: regulates GO:0006525 ! arginine metabolic process
id: GO:0000822
name: inositol hexakisphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with inositol hexakisphosphate." [GOC:go_curators]
+def: "Binding to inositol hexakisphosphate." [GOC:go_curators]
synonym: "InsP6 binding" EXACT []
synonym: "IP6 binding" EXACT []
is_a: GO:0043168 ! anion binding
@@ -6120,7 +6132,6 @@ alt_id: GO:0045791
def: "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_yeast
synonym: "cellular morphogenesis" EXACT []
is_a: GO:0009653 ! anatomical structure morphogenesis
@@ -6217,6 +6228,7 @@ comment: Note that this term should not be used for direct annotation. When anno
subset: gocheck_do_not_manually_annotate
subset: goslim_aspergillus
subset: goslim_candida
+subset: goslim_generic
subset: goslim_yeast
synonym: "cell cycle cytokinesis" EXACT []
synonym: "cytokinesis involved in cell cycle" EXACT [GOC:dph, GOC:tb]
@@ -6283,7 +6295,7 @@ id: GO:0000916
name: actomyosin contractile ring contraction
namespace: biological_process
def: "The process of an actomyosin ring getting smaller in diameter, in the context of cytokinesis that takes place as part of a cell cycle." [GOC:clt, GOC:dph, GOC:mah, GOC:tb]
-synonym: "contractile ring constriction" BROAD [GOC:ascb_2009, GOC:dph, GOC:tb]
+synonym: "actomyosin contractile ring constriction" EXACT [GOC:vw]
synonym: "contractile ring contraction involved in cell cycle cytokinesis" EXACT [GOC:mah, GOC:vw]
synonym: "cytokinesis, actomyosin ring contraction" EXACT []
synonym: "cytokinesis, contractile ring contraction" BROAD [GOC:dph, GOC:tb]
@@ -6361,8 +6373,8 @@ def: "The aggregation, arrangement and bonding together of septins and associate
synonym: "septin assembly and septum biosynthesis" BROAD []
synonym: "septin assembly and septum formation" BROAD []
is_a: GO:0031106 ! septin ring organization
-is_a: GO:0034622 ! cellular protein-containing complex assembly
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0065003 ! protein-containing complex assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:0000922
@@ -6764,9 +6776,15 @@ id: GO:0000976
name: transcription cis-regulatory region binding
namespace: molecular_function
alt_id: GO:0000975
+alt_id: GO:0000984
+alt_id: GO:0001017
alt_id: GO:0044212
-def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH]
+def: "Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH]
comment: Note that this term is meant to also capture non-specific binding to regulatory regions. Also, to minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription.
+synonym: "bacterial-type RNA polymerase regulatory region DNA binding" NARROW []
+synonym: "bacterial-type RNA polymerase transcription regulatory region sequence-specific DNA binding" NARROW []
+synonym: "eubacterial-type RNA polymerase regulatory region DNA binding" NARROW []
+synonym: "eubacterial-type RNA polymerase regulatory region sequence-specific DNA binding" NARROW []
synonym: "regulatory region DNA binding" BROAD []
synonym: "transcription regulatory region DNA binding" RELATED []
synonym: "transcription regulatory region sequence-specific DNA binding" EXACT []
@@ -6778,7 +6796,7 @@ id: GO:0000977
name: RNA polymerase II transcription regulatory region sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0001012
-def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II." [GOC:txnOH]
+def: "Binding to a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II." [GOC:txnOH]
comment: To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription.
synonym: "RNA polymerase II regulatory region DNA binding" RELATED []
is_a: GO:0000976 ! transcription cis-regulatory region binding
@@ -6788,7 +6806,7 @@ id: GO:0000978
name: RNA polymerase II cis-regulatory region sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0000980
-def: "Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase II." [GOC:txnOH-2018]
+def: "Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase II." [GOC:txnOH-2018]
comment: Note that the phrase "upstream activating sequence", or UAS is often used in S. cerevisiae literature to refer to cis-regulatory sequences. In bacteria such as E. coli, the phrase "upstream activating sequence", or UAS is usually a synonym for "enhancer".
synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding" RELATED []
synonym: "RNA polymerase II distal enhancer sequence-specific DNA binding" RELATED []
@@ -6802,7 +6820,7 @@ is_a: GO:0000987 ! cis-regulatory region sequence-specific DNA binding
id: GO:0000979
name: RNA polymerase II core promoter sequence-specific DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DNA sequence that is part of the core promoter of a RNA polymerase II-transcribed gene." [GOC:pg, GOC:txnOH, PMID:12381658]
+def: "Binding to a DNA sequence that is part of the core promoter of a RNA polymerase II-transcribed gene." [GOC:pg, GOC:txnOH, PMID:12381658]
is_a: GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding
is_a: GO:0001046 ! core promoter sequence-specific DNA binding
@@ -6843,54 +6861,27 @@ synonym: "transcription factor activity, RNA polymerase II proximal promoter seq
synonym: "zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity" NARROW []
is_a: GO:0003700 ! DNA-binding transcription factor activity
-[Term]
-id: GO:0000984
-name: bacterial-type RNA polymerase transcription regulatory region sequence-specific DNA binding
-namespace: molecular_function
-alt_id: GO:0001017
-def: "Interacting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase." [GOC:txnOH]
-comment: To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription.
-synonym: "bacterial-type RNA polymerase regulatory region DNA binding" RELATED []
-synonym: "eubacterial-type RNA polymerase regulatory region DNA binding" EXACT []
-synonym: "eubacterial-type RNA polymerase regulatory region sequence-specific DNA binding" RELATED []
-is_a: GO:0000976 ! transcription cis-regulatory region binding
-
-[Term]
-id: GO:0000985
-name: bacterial-type RNA polymerase core promoter sequence-specific DNA binding
-namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DNA sequence that is part of the core promoter of a bacterial gene." [GOC:pg, GOC:txnOH]
-synonym: "eubacterial-type RNA polymerase core promoter sequence-specific DNA binding" EXACT []
-is_a: GO:0000984 ! bacterial-type RNA polymerase transcription regulatory region sequence-specific DNA binding
-is_a: GO:0001046 ! core promoter sequence-specific DNA binding
-
-[Term]
-id: GO:0000986
-name: bacterial-type cis-regulatory region sequence-specific DNA binding
-namespace: molecular_function
-alt_id: GO:0001150
-def: "Interacting selectively and non-covalently with a specific upstream cis-regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the promoter of a bacterial gene (or cistron, or operon)." [GOC:txnOH-2018]
-synonym: "bacterial-type proximal promoter sequence-specific DNA binding" NARROW []
-synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding" EXACT []
-synonym: "bacterial-type RNA polymerase enhancer sequence-specific DNA binding" NARROW []
-synonym: "bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding" NARROW []
-synonym: "eubacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding" EXACT []
-is_a: GO:0000984 ! bacterial-type RNA polymerase transcription regulatory region sequence-specific DNA binding
-is_a: GO:0000987 ! cis-regulatory region sequence-specific DNA binding
-
[Term]
id: GO:0000987
name: cis-regulatory region sequence-specific DNA binding
namespace: molecular_function
+alt_id: GO:0000986
+alt_id: GO:0001150
alt_id: GO:0001158
alt_id: GO:0001159
alt_id: GO:0035326
-def: "Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. The proximal promoter is in cis with and relatively close to the core promoter." [GOC:txnOH-2018]
+def: "Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. The proximal promoter is in cis with and relatively close to the core promoter." [GOC:txnOH-2018]
+synonym: "bacterial-type cis-regulatory region sequence-specific DNA binding" NARROW []
+synonym: "bacterial-type proximal promoter sequence-specific DNA binding" NARROW []
+synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding" NARROW []
+synonym: "bacterial-type RNA polymerase enhancer sequence-specific DNA binding" NARROW []
+synonym: "bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding" NARROW []
synonym: "cis-regulatory region binding" RELATED []
synonym: "core promoter proximal region DNA binding" NARROW []
synonym: "core promoter proximal region sequence-specific DNA binding" NARROW []
synonym: "enhancer binding" RELATED []
synonym: "enhancer sequence-specific DNA binding" RELATED []
+synonym: "eubacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding" NARROW []
synonym: "promoter proximal region sequence-specific DNA binding" NARROW []
synonym: "proximal promoter sequence-specific DNA binding" NARROW []
is_a: GO:0000976 ! transcription cis-regulatory region binding
@@ -6899,7 +6890,7 @@ is_a: GO:0000976 ! transcription cis-regulatory region binding
id: GO:0000988
name: obsolete transcription factor activity, protein binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a protein or protein complex, to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "protein binding transcription factor activity" EXACT []
synonym: "transcription factor activity" BROAD []
@@ -6911,7 +6902,7 @@ consider: GO:0140110
id: GO:0000989
name: obsolete transcription factor activity, transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "transcription factor binding transcription factor activity" EXACT []
is_obsolete: true
@@ -6922,7 +6913,7 @@ consider: GO:0140110
id: GO:0000990
name: obsolete transcription factor activity, core RNA polymerase binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to an RNA polymerase in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "core RNA polymerase binding transcription factor activity" EXACT []
is_obsolete: true
@@ -6933,7 +6924,7 @@ consider: GO:0140110
id: GO:0000991
name: obsolete transcription factor activity, core RNA polymerase II binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "core RNA polymerase II binding transcription factor activity" EXACT []
is_obsolete: true
@@ -6944,7 +6935,7 @@ consider: GO:0140110
id: GO:0000992
name: RNA polymerase III cis-regulatory region sequence-specific DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase III. The transcribed region might be contain a single gene or a cistron containing multiple genes." [GOC:txnOH, PMID:12381659]
+def: "Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase III. The transcribed region might be contain a single gene or a cistron containing multiple genes." [GOC:txnOH, PMID:12381659]
is_a: GO:0000987 ! cis-regulatory region sequence-specific DNA binding
is_a: GO:0001016 ! RNA polymerase III transcription regulatory region sequence-specific DNA binding
@@ -6952,7 +6943,7 @@ is_a: GO:0001016 ! RNA polymerase III transcription regulatory region sequence-s
id: GO:0000993
name: RNA polymerase II complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits." [GOC:txnOH]
+def: "Binding to an RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits." [GOC:txnOH]
synonym: "RNA polymerase II core binding" EXACT []
synonym: "RNAP II core binding" EXACT []
is_a: GO:0001099 ! basal RNA polymerase II transcription machinery binding
@@ -6962,7 +6953,7 @@ is_a: GO:0043175 ! RNA polymerase core enzyme binding
id: GO:0000994
name: RNA polymerase III core binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with RNA polymerase III core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits." [GOC:txnOH]
+def: "Binding to an RNA polymerase III core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits." [GOC:txnOH]
is_a: GO:0043175 ! RNA polymerase core enzyme binding
[Term]
@@ -6982,7 +6973,7 @@ is_a: GO:0140223 ! general transcription initiation factor activity
id: GO:0001000
name: bacterial-type RNA polymerase core enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit." [GOC:txnOH]
+def: "Binding to a bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit." [GOC:txnOH]
comment: Should omega be included here?
synonym: "eubacterial-type RNA polymerase core enzyme binding" EXACT []
is_a: GO:0043175 ! RNA polymerase core enzyme binding
@@ -6991,7 +6982,7 @@ is_a: GO:0043175 ! RNA polymerase core enzyme binding
id: GO:0001001
name: mitochondrial single-subunit type RNA polymerase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a single subunit mitochondrial RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995, PMID:2088182]
+def: "Binding to a single subunit mitochondrial RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995, PMID:2088182]
is_a: GO:0001050 ! single-subunit type RNA polymerase binding
[Term]
@@ -6999,7 +6990,7 @@ id: GO:0001002
name: RNA polymerase III type 1 promoter sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0001030
-def: "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition." [GOC:txnOH, PMID:12381659]
+def: "Binding to a sequence of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition." [GOC:txnOH, PMID:12381659]
synonym: "RNA polymerase III type 1 promoter DNA binding" RELATED []
is_a: GO:0000992 ! RNA polymerase III cis-regulatory region sequence-specific DNA binding
is_a: GO:0080084 ! 5S rDNA binding
@@ -7009,7 +7000,7 @@ id: GO:0001003
name: RNA polymerase III type 2 promoter sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0001031
-def: "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659]
+def: "Binding to a sequence of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659]
synonym: "RNA polymerase III type 2 promoter DNA binding" RELATED []
is_a: GO:0000992 ! RNA polymerase III cis-regulatory region sequence-specific DNA binding
@@ -7049,7 +7040,7 @@ id: GO:0001006
name: RNA polymerase III type 3 promoter sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0001032
-def: "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III (Pol III). A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659]
+def: "Binding to a sequence of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III (Pol III). A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659]
synonym: "RNA polymerase III type 3 promoter DNA binding" RELATED []
is_a: GO:0000992 ! RNA polymerase III cis-regulatory region sequence-specific DNA binding
@@ -7057,7 +7048,7 @@ is_a: GO:0000992 ! RNA polymerase III cis-regulatory region sequence-specific DN
id: GO:0001007
name: obsolete transcription factor activity, RNA polymerase III transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "RNA polymerase III transcription factor binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7076,7 +7067,7 @@ is_a: GO:0030674 ! protein-macromolecule adaptor activity
id: GO:0001011
name: obsolete transcription factor activity, sequence-specific DNA binding, RNA polymerase recruiting
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a specific DNA sequence and recruiting RNA polymerase to the DNA in order to form the preinitiation complex (PIC)." [GOC:txnOH]
+def: "OBSOLETE. Binding to a specific DNA sequence and recruiting RNA polymerase to the DNA in order to form the preinitiation complex (PIC)." [GOC:txnOH]
comment: This term was obsoleted because it was not clearly defined and usage has been inconsistent.
synonym: "sequence-specific DNA binding RNA polymerase recruiting transcription factor activity" EXACT []
is_obsolete: true
@@ -7104,7 +7095,7 @@ is_a: GO:0009302 ! sno(s)RNA transcription
id: GO:0001016
name: RNA polymerase III transcription regulatory region sequence-specific DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw, PMID:12381659]
+def: "Binding to a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw, PMID:12381659]
synonym: "RNA polymerase III regulatory region DNA binding" RELATED []
is_a: GO:0000976 ! transcription cis-regulatory region binding
@@ -7119,7 +7110,7 @@ alt_id: GO:0070361
alt_id: GO:0070362
alt_id: GO:0070363
alt_id: GO:0070364
-def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of the mitochondrial DNA." [GOC:txnOH, GOC:vw, PMID:20056105]
+def: "Binding to a DNA region that controls the transcription of the mitochondrial DNA." [GOC:txnOH, GOC:vw, PMID:20056105]
synonym: "HSP coding strand binding" NARROW [PMID:9485316]
synonym: "HSP non-coding strand binding" NARROW [PMID:9485316]
synonym: "HSPas binding" NARROW [PMID:9485316]
@@ -7143,7 +7134,7 @@ is_a: GO:0000976 ! transcription cis-regulatory region binding
id: GO:0001019
name: plastid promoter transcription regulatory region sequence-specific DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by a plastid RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw]
+def: "Binding to a DNA region that controls transcription by a plastid RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw]
comment: plastid promoter regulatory region sequence-specific DNA binding
is_a: GO:0000976 ! transcription cis-regulatory region binding
@@ -7151,7 +7142,7 @@ is_a: GO:0000976 ! transcription cis-regulatory region binding
id: GO:0001025
name: RNA polymerase III general transcription initiation factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA polymerase III transcription factor, any protein required to initiate or regulate transcription by RNA polymerase III." [GOC:txnOH]
+def: "Binding to an RNA polymerase III transcription factor, a protein required to initiate or regulate transcription by RNA polymerase III." [GOC:txnOH]
synonym: "RNA polymerase III transcription factor binding" BROAD []
is_a: GO:0140296 ! general transcription initiation factor binding
@@ -7159,7 +7150,7 @@ is_a: GO:0140296 ! general transcription initiation factor binding
id: GO:0001026
name: obsolete TFIIIB-type transcription factor activity
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, Once recruited to an RNA polymerase III promoter by one or more other transcription factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH]
+def: "OBSOLETE. Binding to an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, Once recruited to an RNA polymerase III promoter by one or more other transcription factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH]
comment: This term was obsoleted because it represents a gene product.
synonym: "RNA polymerase III recruiting transcription factor activity" EXACT []
is_obsolete: true
@@ -7168,7 +7159,7 @@ is_obsolete: true
id: GO:0001027
name: obsolete RNA polymerase III type 1 promoter TFIIIB-type transcription factor activity
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 1 promoter by TFIIIA-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH-2018, PMID:12381659]
+def: "OBSOLETE. Binding to an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 1 promoter by TFIIIA-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH-2018, PMID:12381659]
comment: The reason for obsoletion is that there is a single TFIIIB activity; this is not dependent on the promoter.
synonym: "RNA polymerase III type 1 promoter polymerase recruiting transcription factor activity" RELATED []
is_obsolete: true
@@ -7177,7 +7168,7 @@ is_obsolete: true
id: GO:0001028
name: obsolete RNA polymerase III type 2 promoter TFIIIB-type transcription factor activity
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 2 promoter by a TFIIIC-type factor, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH-2018, PMID:12381659]
+def: "OBSOLETE. Binding to an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 2 promoter by a TFIIIC-type factor, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH-2018, PMID:12381659]
comment: The reason for obsoletion is that there is a single TFIIIB activity; this is not dependent on the promoter.
synonym: "RNA polymerase III type 2 promoter polymerase recruiting transcription factor activity" RELATED []
is_obsolete: true
@@ -7186,7 +7177,7 @@ is_obsolete: true
id: GO:0001029
name: obsolete RNA polymerase III type 3 promoter TFIIIB-type transcription factor activity
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 3 promoter by SNAP-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH-2018, PMID:12381659]
+def: "OBSOLETE. Binding to an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 3 promoter by SNAP-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH-2018, PMID:12381659]
synonym: "RNA polymerase III type 3 promoter polymerase recruiting transcription factor activity" RELATED []
is_obsolete: true
@@ -7195,7 +7186,7 @@ id: GO:0001039
name: RNA polymerase III hybrid type promoter sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0001037
-def: "Interacting selectively and non-covalently with a sequence of DNA that is a part of a hybrid type promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659]
+def: "Binding to a sequence of DNA that is a part of a hybrid type promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659]
synonym: "RNA polymerase III hybrid type promoter DNA binding" RELATED []
is_a: GO:0000992 ! RNA polymerase III cis-regulatory region sequence-specific DNA binding
@@ -7203,7 +7194,7 @@ is_a: GO:0000992 ! RNA polymerase III cis-regulatory region sequence-specific DN
id: GO:0001040
name: obsolete RNA polymerase III hybrid type promoter TFIIIB-type transcription factor activity
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III hybrid type promoter, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH-2018, PMID:12381659]
+def: "OBSOLETE. Binding to an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III hybrid type promoter, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH-2018, PMID:12381659]
comment: The reason for obsoletion is that there is a single TFIIIB activity; this is not dependent on the promoter.
is_obsolete: true
@@ -7211,37 +7202,40 @@ is_obsolete: true
id: GO:0001042
name: RNA polymerase I core binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with RNA polymerase I core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits." [GOC:txnOH]
+def: "Binding to a RNA polymerase I core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits." [GOC:txnOH]
is_a: GO:0043175 ! RNA polymerase core enzyme binding
[Term]
id: GO:0001046
name: core promoter sequence-specific DNA binding
namespace: molecular_function
+alt_id: GO:0000985
alt_id: GO:0001047
-def: "Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon." [GOC:pg, GOC:txnOH]
+def: "Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon." [GOC:pg, GOC:txnOH]
+synonym: "bacterial-type RNA polymerase core promoter sequence-specific DNA binding" NARROW []
synonym: "core promoter binding" RELATED []
+synonym: "eubacterial-type RNA polymerase core promoter sequence-specific DNA binding" NARROW []
is_a: GO:0000976 ! transcription cis-regulatory region binding
[Term]
id: GO:0001048
name: RNA polymerase IV core binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with RNA polymerase IV core enzyme, a multisubunit eukaryotic nuclear RNA polymerase found in plants and involved in siRNA production." [GOC:txnOH, PMID:19110459]
+def: "Binding to RNA polymerase IV core enzyme, a multisubunit eukaryotic nuclear RNA polymerase found in plants and involved in siRNA production." [GOC:txnOH, PMID:19110459]
is_a: GO:0043175 ! RNA polymerase core enzyme binding
[Term]
id: GO:0001049
name: RNA polymerase V core binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with RNA polymerase V core enzyme, a multisubunit eukaryotic nuclear RNA polymerase found in plants and involved in production of noncoding transcripts at target loci for silencing." [GOC:txnOH, PMID:19110459]
+def: "Binding to RNA polymerase V core enzyme, a multisubunit eukaryotic nuclear RNA polymerase found in plants and involved in production of noncoding transcripts at target loci for silencing." [GOC:txnOH, PMID:19110459]
is_a: GO:0043175 ! RNA polymerase core enzyme binding
[Term]
id: GO:0001050
name: single-subunit type RNA polymerase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a single subunit RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995]
+def: "Binding to a single subunit RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995]
synonym: "SP6-type RNA polymerase binding" EXACT []
synonym: "T3-type RNA polymerase binding" EXACT []
synonym: "T3/T7 type RNA polymerase binding" EXACT []
@@ -7252,14 +7246,14 @@ is_a: GO:0070063 ! RNA polymerase binding
id: GO:0001051
name: plastid single-subunit type RNA polymerase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a single subunit plastid RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995]
+def: "Binding to a single subunit plastid RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995]
is_a: GO:0001050 ! single-subunit type RNA polymerase binding
[Term]
id: GO:0001052
name: plastid PEP RNA polymerase core enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the bacterial-type plastid PEP RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one double prime subunit." [GOC:txnOH, PMID:20701995]
+def: "Binding to a bacterial-type plastid PEP RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one double prime subunit." [GOC:txnOH, PMID:20701995]
is_a: GO:0001000 ! bacterial-type RNA polymerase core enzyme binding
[Term]
@@ -7376,7 +7370,7 @@ is_a: GO:0001064 ! single subunit type RNA polymerase activity
id: GO:0001067
name: transcription regulatory region nucleic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH]
+def: "Binding to a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH]
synonym: "regulatory region nucleic acid binding" RELATED []
is_a: GO:0003676 ! nucleic acid binding
@@ -7384,14 +7378,14 @@ is_a: GO:0003676 ! nucleic acid binding
id: GO:0001068
name: transcription regulatory region RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a RNA region within the transcript that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon." [GOC:txnOH]
+def: "Binding to a RNA region within the transcript that regulates the transcription of a gene, cistron, or operon." [GOC:txnOH]
is_a: GO:0001069 ! regulatory region RNA binding
[Term]
id: GO:0001069
name: regulatory region RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a RNA region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH]
+def: "Binding to a RNA region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH]
is_a: GO:0001067 ! transcription regulatory region nucleic acid binding
is_a: GO:0003723 ! RNA binding
@@ -7424,7 +7418,7 @@ is_a: GO:0140110 ! transcription regulator activity
id: GO:0001074
name: obsolete transcription factor activity, RNA polymerase II proximal promoter sequence-specific DNA binding involved in preinitiation complex assembly
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter." [GOC:txnOH]
+def: "OBSOLETE. Binding to a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter." [GOC:txnOH]
comment: This term has been obsoleted because it represents a GO-CAM model.
synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly" EXACT []
synonym: "transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding involved in preinitiation complex assembly" EXACT []
@@ -7434,7 +7428,7 @@ is_obsolete: true
id: GO:0001076
name: obsolete transcription factor activity, RNA polymerase II transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "RNA polymerase II transcription factor binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7472,7 +7466,7 @@ is_a: GO:0090295 ! nitrogen catabolite repression of transcription
id: GO:0001082
name: obsolete transcription factor activity, RNA polymerase I transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase I transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to an RNA polymerase I transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "RNA polymerase I transcription factor binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7481,7 +7475,7 @@ is_obsolete: true
id: GO:0001083
name: obsolete transcription factor activity, RNA polymerase II basal transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a basal RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "RNA polymerase II basal transcription factor binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7490,7 +7484,7 @@ is_obsolete: true
id: GO:0001084
name: obsolete transcription factor activity, TFIID-class binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "TFIID-class binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7500,7 +7494,7 @@ consider: GO:0001094
id: GO:0001086
name: obsolete transcription factor activity, TFIIA-class binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIA class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIA class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "TFIIA-class binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7510,7 +7504,7 @@ consider: GO:0001092
id: GO:0001087
name: obsolete transcription factor activity, TFIIB-class binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIB class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIB class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "TFIIB-class binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7520,7 +7514,7 @@ consider: GO:0001093
id: GO:0001088
name: obsolete transcription factor activity, TFIIE-class binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIE class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIE class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "TFIIE-class binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7530,7 +7524,7 @@ consider: GO:0001095
id: GO:0001089
name: obsolete transcription factor activity, TFIIF-class transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIF class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIF class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "TFIIF-class binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7540,7 +7534,7 @@ consider: GO:0001096
id: GO:0001090
name: obsolete transcription factor activity, TFIIH-class binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIH class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to a basal RNA polymerase II transcription factor of the TFIIH class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "TFIIH-class binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7549,7 +7543,7 @@ is_obsolete: true
id: GO:0001091
name: RNA polymerase II general transcription initiation factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, any of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:txnOH, PMID:16858867]
+def: "Binding to a basal RNA polymerase II transcription factor, any of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:txnOH, PMID:16858867]
synonym: "RNA polymerase II basal transcription factor binding" EXACT []
is_a: GO:0001099 ! basal RNA polymerase II transcription machinery binding
is_a: GO:0140296 ! general transcription initiation factor binding
@@ -7558,7 +7552,7 @@ is_a: GO:0140296 ! general transcription initiation factor binding
id: GO:0001092
name: TFIIA-class transcription factor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIA complex, one of the complexes involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867]
+def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIIA complex, one of the complexes involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867]
synonym: "TFIIA-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -7567,14 +7561,14 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0001093
name: TFIIB-class transcription factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general RNA polymerase II transcription factor of the TFIIB class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
+def: "Binding to a general RNA polymerase II transcription factor of the TFIIB class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
[Term]
id: GO:0001094
name: TFIID-class transcription factor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIID complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
+def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIID complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
synonym: "TFIID-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -7583,7 +7577,7 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0001095
name: TFIIE-class transcription factor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIE complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
+def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIIE complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
synonym: "TFIIE-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -7592,7 +7586,7 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0001096
name: TFIIF-class transcription factor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIF complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
+def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIIF complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
synonym: "TFIIF-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -7601,7 +7595,7 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0001097
name: TFIIH-class transcription factor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general RNA polymerase II transcription factor belonging to the TFIIH complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
+def: "Binding to a general RNA polymerase II transcription factor belonging to the TFIIH complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II." [GOC:krc, PMID:16858867]
synonym: "TFIIH-class transcription factor binding" EXACT []
is_a: GO:0001091 ! RNA polymerase II general transcription initiation factor binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -7610,7 +7604,7 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0001098
name: basal transcription machinery binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH]
+def: "Binding to a component of the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH]
comment: Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors.
is_a: GO:0005515 ! protein binding
@@ -7618,7 +7612,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0001099
name: basal RNA polymerase II transcription machinery binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH]
+def: "Binding to a component of the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH]
comment: Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors.
synonym: "basal RNAP II transcription machinery binding" EXACT []
is_a: GO:0001098 ! basal transcription machinery binding
@@ -7652,7 +7646,7 @@ is_a: GO:0042221 ! response to chemical
id: GO:0001108
name: bacterial-type RNA polymerase holo enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase." [GOC:txnOH]
+def: "Binding to a component of the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase." [GOC:txnOH]
synonym: "basal bacterial-type RNA polymerase transcription machinery binding" EXACT []
is_a: GO:0001098 ! basal transcription machinery binding
@@ -7660,8 +7654,10 @@ is_a: GO:0001098 ! basal transcription machinery binding
id: GO:0001109
name: promoter clearance during DNA-templated transcription
namespace: biological_process
+alt_id: GO:0001122
def: "Any process involved in the transition from the initiation to the elongation phases of transcription by a DNA-dependent RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH, PMID:15020047, PMID:18280161]
synonym: "promoter clearance during DNA-dependent transcription" EXACT [GOC:txnOH]
+synonym: "promoter clearance from bacterial-type RNA polymerase promoter" NARROW []
synonym: "promoter escape" BROAD []
is_a: GO:0032774 ! RNA biosynthetic process
relationship: part_of GO:0006351 ! transcription, DNA-templated
@@ -7687,10 +7683,13 @@ relationship: part_of GO:0006366 ! transcription by RNA polymerase II
id: GO:0001112
name: DNA-templated transcription open complex formation
namespace: biological_process
+alt_id: GO:0001127
def: "Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH, PMID:15020047, PMID:18280161]
synonym: "DNA-dependent transcriptional open complex formation" EXACT [GOC:txnOH]
synonym: "DNA-templated transcriptional open complex formation" EXACT []
synonym: "promoter melting" BROAD []
+synonym: "transcription open complex formation at bacterial-type RNA polymerase promoter" NARROW []
+synonym: "transcriptional open complex formation at bacterial-type RNA polymerase promoter" NARROW []
is_a: GO:0001120 ! protein-DNA complex remodeling
relationship: part_of GO:0006352 ! DNA-templated transcription, initiation
@@ -7717,7 +7716,7 @@ name: protein-DNA-RNA complex subunit organization
namespace: biological_process
def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA-RNA complex." [GOC:txnOH]
synonym: "protein-DNA-RNA complex subunit organisation" EXACT [GOC:mah]
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0001116
@@ -7725,7 +7724,7 @@ name: protein-DNA-RNA complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins, DNA, and RNA molecules to form a protein-DNA-RNA complex." [GOC:txnOH]
is_a: GO:0001115 ! protein-DNA-RNA complex subunit organization
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0001117
@@ -7760,72 +7759,11 @@ def: "The acquisition, loss, or modification of macromolecules within a protein-
is_a: GO:0034367 ! protein-containing complex remodeling
is_a: GO:0071824 ! protein-DNA complex subunit organization
-[Term]
-id: GO:0001121
-name: bacterial transcription
-namespace: biological_process
-def: "The synthesis of RNA from a DNA template by a bacterial-type RNA polymerase, originating at a bacterial-type promoter." [GOC:txnOH]
-synonym: "transcription from bacterial-type RNA polymerase promoter" EXACT []
-is_a: GO:0006351 ! transcription, DNA-templated
-
-[Term]
-id: GO:0001122
-name: promoter clearance from bacterial-type RNA polymerase promoter
-namespace: biological_process
-def: "Any process involved in the transition from the initiation to the elongation phase of transcription by a bacterial-type RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance generally involves dissociation of the sigma initiation factor." [GOC:txnOH, PMID:18280161]
-is_a: GO:0001109 ! promoter clearance during DNA-templated transcription
-relationship: part_of GO:0001121 ! bacterial transcription
-
-[Term]
-id: GO:0001123
-name: transcription initiation from bacterial-type RNA polymerase promoter
-namespace: biological_process
-def: "Any process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription." [GOC:txnOH, PMID:18280161]
-is_a: GO:0006352 ! DNA-templated transcription, initiation
-relationship: part_of GO:0001121 ! bacterial transcription
-
-[Term]
-id: GO:0001124
-name: transcription elongation from bacterial-type RNA polymerase promoter
-namespace: biological_process
-def: "The extension of an RNA molecule after transcription initiation and promoter clearance at a bacterial-type RNA polymerase promoter by the addition of ribonucleotides catalyzed by a bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161]
-synonym: "RNA elongation from bacterial-type RNA polymerase promoter" EXACT []
-is_a: GO:0006354 ! DNA-templated transcription, elongation
-relationship: part_of GO:0001121 ! bacterial transcription
-
-[Term]
-id: GO:0001125
-name: transcription termination from bacterial-type RNA polymerase promoter
-namespace: biological_process
-def: "The process in which the synthesis of an RNA molecule by a bacterial-type RNA polymerase using a DNA template is completed." [GOC:txnOH, PMID:18280161]
-is_a: GO:0006353 ! DNA-templated transcription, termination
-relationship: part_of GO:0001121 ! bacterial transcription
-
-[Term]
-id: GO:0001126
-name: bacterial-type RNA polymerase preinitiation complex assembly
-namespace: biological_process
-def: "The aggregation, arrangement and bonding together of proteins on a bacterial-type RNA polymerase promoter DNA to form the transcriptional preinitiation complex (PIC), required for transcription." [GOC:txnOH, PMID:18280161]
-synonym: "bacterial-type RNA polymerase transcription PIC biosynthesis" EXACT []
-synonym: "bacterial-type RNA polymerase transcription PIC formation" EXACT []
-synonym: "bacterial-type RNA polymerase transcriptional preinitiation complex formation" EXACT []
-is_a: GO:0070897 ! transcription preinitiation complex assembly
-relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter
-
-[Term]
-id: GO:0001127
-name: transcription open complex formation at bacterial-type RNA polymerase promoter
-namespace: biological_process
-def: "Any process involved in the melting of the DNA hybrid of the core promoter region within a bacterial-type RNA polymerase promoter to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH, PMID:18280161]
-synonym: "transcriptional open complex formation at bacterial-type RNA polymerase promoter" EXACT []
-is_a: GO:0001112 ! DNA-templated transcription open complex formation
-relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter
-
[Term]
id: GO:0001128
name: obsolete RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or stability of the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC). Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:16858867]
+def: "OBSOLETE. Binding to an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or stability of the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC). Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:16858867]
comment: This term was obsoleted because it represented a mix of function and process and is not annotated consistently
synonym: "RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly" EXACT []
is_obsolete: true
@@ -7834,7 +7772,7 @@ is_obsolete: true
id: GO:0001129
name: obsolete RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), to facilitate the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867]
+def: "OBSOLETE. Binding to a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), to facilitate the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "TATA-binding protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" NARROW []
synonym: "TBP-class protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" EXACT []
@@ -7844,7 +7782,7 @@ is_obsolete: true
id: GO:0001132
name: obsolete RNA polymerase II transcription factor activity, TBP-class protein binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH, PMID:16858867]
+def: "OBSOLETE. Binding to a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH, PMID:16858867]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "TATA-binding protein binding RNA polymerase II transcription factor activity" NARROW []
synonym: "TBP-class protein binding RNA polymerase II transcription factor activity" EXACT []
@@ -7888,7 +7826,7 @@ replaced_by: GO:0003712
id: GO:0001139
name: RNA polymerase II complex recruiting activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867]
+def: "Binding to an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867]
synonym: "core RNA polymerase II recruiting transcription factor activity" EXACT []
synonym: "transcription factor activity, core RNA polymerase II recruiting" RELATED []
is_a: GO:0000993 ! RNA polymerase II complex binding
@@ -7901,7 +7839,7 @@ alt_id: GO:0001145
alt_id: GO:0001146
alt_id: GO:0001148
alt_id: GO:0001160
-def: "Interacting selectively and non-covalently with a sequence of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH, PMID:18280161, PMID:18391175]
+def: "Binding to a sequence of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH, PMID:18280161, PMID:18391175]
comment: Transcription termination sites can be recognized by the RNA polymerase (RNAP) itself or by another protein which interacts with the RNAP to promote transcription termination. Note that not all genes have a DNA specific sequence that functions as a termination site; for most mRNAs transcribed by RNAP II termination is not mediated by a specific termination sequence, but is coupled to polyadenylation.
synonym: "bacterial-type RNA polymerase termination site sequence-specific DNA binding" NARROW []
synonym: "mitochondrial RNA polymerase termination site sequence-specific DNA binding" NARROW []
@@ -7914,7 +7852,7 @@ is_a: GO:0000976 ! transcription cis-regulatory region binding
id: GO:0001149
name: obsolete transcription factor activity, bacterial-type RNA polymerase termination site sequence-specific binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a sequence of DNA that is a termination site for bacterial-type RNA polymerase in order to promote transcription termination by bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161]
+def: "OBSOLETE. Binding to a sequence of DNA that is a termination site for bacterial-type RNA polymerase in order to promote transcription termination by bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161]
synonym: "bacterial-type RNA polymerase termination site sequence-specific DNA binding transcription factor activity" EXACT []
is_obsolete: true
@@ -7942,7 +7880,7 @@ is_obsolete: true
id: GO:0001154
name: TFIIIB-class transcription factor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general RNA polymerase III transcription factor belonging to the TFIIB complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III." [GOC:txnOH, PMID:12381659]
+def: "Binding to a general RNA polymerase III transcription factor belonging to the TFIIB complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III." [GOC:txnOH, PMID:12381659]
synonym: "TFIIIB-class transcription factor binding" EXACT []
is_a: GO:0001025 ! RNA polymerase III general transcription initiation factor binding
@@ -7950,14 +7888,14 @@ is_a: GO:0001025 ! RNA polymerase III general transcription initiation factor bi
id: GO:0001155
name: TFIIIA-class transcription factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA polymerase III transcription factor of the TFIIIA class, one of the factors involved in formation of the preinitiation complex (PIC) at RNA polymerase III promoters." [GOC:txnOH, PMID:12381659]
+def: "Binding to an RNA polymerase III transcription factor of the TFIIIA class, one of the factors involved in formation of the preinitiation complex (PIC) at RNA polymerase III promoters." [GOC:txnOH, PMID:12381659]
is_a: GO:0001025 ! RNA polymerase III general transcription initiation factor binding
[Term]
id: GO:0001156
name: TFIIIC-class transcription factor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general RNA polymerase III transcription factor belonging to the TFIIC complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III." [GOC:txnOH, PMID:12381659]
+def: "Binding to a general RNA polymerase III transcription factor belonging to the TFIIC complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III." [GOC:txnOH, PMID:12381659]
synonym: "TFIIIC-class transcription factor binding" EXACT []
is_a: GO:0001025 ! RNA polymerase III general transcription initiation factor binding
@@ -7966,7 +7904,7 @@ id: GO:0001161
name: intronic transcription regulatory region sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0044213
-def: "Interacting selectively and non-covalently with an intronic DNA sequence that regulates the transcription of the transcript it is contained within." [GOC:txnOH]
+def: "Binding to an intronic DNA sequence that regulates the transcription of the transcript it is contained within." [GOC:txnOH]
comment: To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription.
synonym: "intronic transcription regulatory region DNA binding" RELATED []
is_a: GO:0000976 ! transcription cis-regulatory region binding
@@ -7975,7 +7913,7 @@ is_a: GO:0000976 ! transcription cis-regulatory region binding
id: GO:0001162
name: RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within." [GOC:txnOH]
+def: "Binding to an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within." [GOC:txnOH]
comment: To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription.
is_a: GO:0000977 ! RNA polymerase II transcription regulatory region sequence-specific DNA binding
is_a: GO:0001161 ! intronic transcription regulatory region sequence-specific DNA binding
@@ -7985,7 +7923,7 @@ id: GO:0001163
name: RNA polymerase I transcription regulatory region sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0001013
-def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase I." [GOC:txnOH]
+def: "Binding to a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase I." [GOC:txnOH]
synonym: "RNA polymerase I regulatory region DNA binding" RELATED []
is_a: GO:0000976 ! transcription cis-regulatory region binding
@@ -7994,11 +7932,9 @@ id: GO:0001164
name: RNA polymerase I core promoter sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0001187
-def: "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
+def: "Binding to a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
synonym: "RNA polymerase I CORE element sequence-specific DNA binding" EXACT []
-synonym: "RNA polymerase I core element sequence-specific DNA binding" EXACT []
synonym: "RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity" RELATED []
-synonym: "RNA polymerase I core promoter sequence-specific DNA binding" EXACT []
synonym: "transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting" RELATED []
is_a: GO:0001046 ! core promoter sequence-specific DNA binding
is_a: GO:0001163 ! RNA polymerase I transcription regulatory region sequence-specific DNA binding
@@ -8008,7 +7944,7 @@ id: GO:0001165
name: RNA polymerase I cis-regulatory region sequence-specific DNA binding
namespace: molecular_function
alt_id: GO:0001166
-def: "Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase I. RNA polymerase I elements are referred to either enhancers or upstream control element (UCE, or alternately referred to as the upstream element)." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
+def: "Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase I. RNA polymerase I elements are referred to either enhancers or upstream control element (UCE, or alternately referred to as the upstream element)." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
synonym: "RNA polymerase I enhancer sequence-specific DNA binding" RELATED []
synonym: "RNA polymerase I upstream control element sequence-specific DNA binding" RELATED []
synonym: "RNA polymerase I upstream element sequence-specific DNA binding" RELATED []
@@ -8018,7 +7954,7 @@ is_a: GO:0001163 ! RNA polymerase I transcription regulatory region sequence-spe
id: GO:0001167
name: obsolete RNA polymerase I transcription factor activity, sequence-specific DNA binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase I. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH]
+def: "OBSOLETE. Binding to a specific DNA sequence in order to modulate transcription by RNA polymerase I. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "sequence-specific DNA binding RNA polymerase I transcription factor activity" EXACT []
is_obsolete: true
@@ -8027,7 +7963,7 @@ is_obsolete: true
id: GO:0001168
name: obsolete transcription factor activity, RNA polymerase I upstream control element sequence-specific binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with the upstream control element (UCE, or alternately referred to as the upstream element, UE), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
+def: "OBSOLETE. Binding to a upstream control element (UCE, or alternately referred to as the upstream element, UE), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "RNA polymerase I upstream control element sequence-specific DNA binding transcription factor activity" EXACT []
is_obsolete: true
@@ -8036,7 +7972,7 @@ is_obsolete: true
id: GO:0001169
name: obsolete transcription factor activity, RNA polymerase I CORE element sequence-specific binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with CORE element, a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
+def: "OBSOLETE. Binding to CORE element, a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "RNA polymerase I CORE element sequence-specific DNA binding transcription factor activity" EXACT []
synonym: "RNA polymerase I core promoter sequence-specific DNA binding transcription factor" EXACT []
@@ -8046,7 +7982,7 @@ is_obsolete: true
id: GO:0001170
name: obsolete transcription factor activity, RNA polymerase I enhancer sequence-specific binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a RNA polymerase I (Pol I) enhancer in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
+def: "OBSOLETE. Binding to a RNA polymerase I (Pol I) enhancer in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832]
comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
synonym: "RNA polymerase I enhancer sequence-specific DNA binding transcription factor activity" EXACT []
is_obsolete: true
@@ -8071,8 +8007,10 @@ is_a: GO:0097659 ! nucleic acid-templated transcription
id: GO:0001173
name: DNA-templated transcriptional start site selection
namespace: biological_process
+alt_id: GO:0001176
def: "Any process involved in the selection of the specific location within the template strand of a DNA-dependent RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH, PMID:16826228, PMID:18846104]
synonym: "DNA-dependent transcriptional start site selection" EXACT [GOC:txnOH]
+synonym: "transcriptional start site selection at bacterial-type RNA polymerase promoter" NARROW []
is_a: GO:0032774 ! RNA biosynthetic process
relationship: part_of GO:0006352 ! DNA-templated transcription, initiation
@@ -8092,14 +8030,6 @@ def: "Any process involved in the selection of the specific location within the
is_a: GO:0001173 ! DNA-templated transcriptional start site selection
relationship: part_of GO:0006384 ! transcription initiation from RNA polymerase III promoter
-[Term]
-id: GO:0001176
-name: transcriptional start site selection at bacterial-type RNA polymerase promoter
-namespace: biological_process
-def: "Any process involved in the selection of the specific location within the template strand of a bacterial-type RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH]
-is_a: GO:0001173 ! DNA-templated transcriptional start site selection
-relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter
-
[Term]
id: GO:0001177
name: regulation of transcription open complex formation at RNA polymerase II promoter
@@ -8115,7 +8045,6 @@ name: regulation of transcriptional start site selection at RNA polymerase II pr
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of a process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH]
synonym: "regulation of transcription start site selection at RNA polymerase II promoter" EXACT []
-synonym: "regulation of transcriptional start site selection at RNA polymerase II promoter" EXACT []
is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter
relationship: regulates GO:0001174 ! transcriptional start site selection at RNA polymerase II promoter
@@ -8123,7 +8052,7 @@ relationship: regulates GO:0001174 ! transcriptional start site selection at RNA
id: GO:0001179
name: RNA polymerase I general transcription initiation factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA polymerase I transcription factor, any protein required to initiate or regulate transcription by RNA polymerase I." [GOC:txnOH]
+def: "Binding to an RNA polymerase I transcription factor, a protein required to initiate or regulate transcription by RNA polymerase I." [GOC:txnOH]
synonym: "RNA polymerase I transcription factor binding" BROAD []
is_a: GO:0140296 ! general transcription initiation factor binding
@@ -8190,7 +8119,7 @@ relationship: part_of GO:0006361 ! transcription initiation from RNA polymerase
id: GO:0001190
name: obsolete transcriptional activator activity, RNA polymerase II transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
+def: "OBSOLETE. Binding to an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "RNA polymerase II transcription factor binding transcription activator activity" EXACT []
synonym: "RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription" EXACT []
@@ -8202,7 +8131,7 @@ consider: GO:0061629
id: GO:0001191
name: obsolete transcriptional repressor activity, RNA polymerase II transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH, PMID:9811836]
+def: "OBSOLETE. Binding to an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH, PMID:9811836]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription" EXACT []
synonym: "RNA polymerase II transcription factor binding transcription repressor activity" EXACT []
@@ -8215,8 +8144,11 @@ consider: GO:0061629
id: GO:0001192
name: maintenance of transcriptional fidelity during DNA-templated transcription elongation
namespace: biological_process
+alt_id: GO:0001194
def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation on a DNA template." [GOC:txnOH]
synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation" EXACT [GOC:txnOH]
+synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation from bacterial-type RNA polymerase promoter" EXACT [GOC:txnOH]
+synonym: "maintenance of transcriptional fidelity during DNA-templated transcription elongation from bacterial-type RNA polymerase promoter" NARROW []
is_a: GO:0032774 ! RNA biosynthetic process
relationship: part_of GO:0006354 ! DNA-templated transcription, elongation
@@ -8229,15 +8161,6 @@ synonym: "maintenance of transcriptional fidelity during DNA-dependent transcrip
is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-templated transcription elongation
relationship: part_of GO:0006368 ! transcription elongation from RNA polymerase II promoter
-[Term]
-id: GO:0001194
-name: maintenance of transcriptional fidelity during DNA-templated transcription elongation from bacterial-type RNA polymerase promoter
-namespace: biological_process
-def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a bacterial-type RNA polymerase promoter." [GOC:txnOH]
-synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation from bacterial-type RNA polymerase promoter" EXACT [GOC:txnOH]
-is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-templated transcription elongation
-relationship: part_of GO:0001124 ! transcription elongation from bacterial-type RNA polymerase promoter
-
[Term]
id: GO:0001195
name: maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter
@@ -8282,17 +8205,21 @@ is_a: GO:0045894 ! negative regulation of mating-type specific transcription, DN
[Term]
id: GO:0001207
-name: histone displacement
+name: obsolete histone displacement
namespace: biological_process
-def: "The removal of histones, including histone dimers, from nucleosomes within chromatin." [GOC:krc, PMID:15525516, PMID:17496903, PMID:21807128]
-is_a: GO:0034728 ! nucleosome organization
+def: "OBSOLETE. The removal of histones, including histone dimers, from nucleosomes within chromatin." [GOC:krc, PMID:15525516, PMID:17496903, PMID:21807128]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0140713
[Term]
id: GO:0001208
-name: histone H2A-H2B dimer displacement
+name: obsolete histone H2A-H2B dimer displacement
namespace: biological_process
-def: "The removal of a H2A-H2B histone dimer from a nucleosome within chromatin." [GOC:krc, PMID:15525516, PMID:17496903, PMID:21807128]
-is_a: GO:0001207 ! histone displacement
+def: "OBSOLETE. The removal of a H2A-H2B histone dimer from a nucleosome within chromatin." [GOC:krc, PMID:15525516, PMID:17496903, PMID:21807128]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0140713
[Term]
id: GO:0001216
@@ -8340,7 +8267,7 @@ id: GO:0001221
name: transcription coregulator binding
namespace: molecular_function
alt_id: GO:0001224
-def: "Interacting selectively and non-covalently with a transcription coregulator, any protein involved in regulation of transcription via protein-protein interactions with transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery." [GOC:krc]
+def: "Binding to a transcription coregulator, a protein involved in regulation of transcription via protein-protein interactions with transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery." [GOC:krc]
synonym: "RNA polymerase II transcription cofactor binding" RELATED []
synonym: "RNA polymerase II transcription coregulator binding" RELATED []
synonym: "transcription cofactor binding" RELATED []
@@ -8351,7 +8278,7 @@ id: GO:0001222
name: transcription corepressor binding
namespace: molecular_function
alt_id: GO:0001226
-def: "Interacting selectively and non-covalently with a transcription corepressor, any protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery." [GOC:krc]
+def: "Binding to a transcription corepressor, a protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery." [GOC:krc]
synonym: "RNA polymerase II transcription corepressor binding" RELATED []
is_a: GO:0001221 ! transcription coregulator binding
@@ -8360,7 +8287,7 @@ id: GO:0001223
name: transcription coactivator binding
namespace: molecular_function
alt_id: GO:0001225
-def: "Interacting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery." [GOC:krc]
+def: "Binding to a transcription coactivator, a protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery." [GOC:krc]
synonym: "RNA polymerase II transcription coactivator binding" RELATED []
is_a: GO:0001221 ! transcription coregulator binding
@@ -8958,23 +8885,20 @@ consider: GO:0005509
id: GO:0001512
name: dihydronicotinamide riboside quinone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone = 1-(beta-D-ribofuranosyl)nicotinamide + a hydroquinone." [EC:1.10.99.2]
-synonym: "1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide:quinone oxidoreductase activity" RELATED [EC:1.10.99.2]
-synonym: "N-ribosyldihydronicotinamide dehydrogenase (quinone) activity" RELATED [EC:1.10.99.2]
-synonym: "NAD(P)H:quinone oxidoreductase 2 activity" RELATED [EC:1.10.99.2]
-synonym: "NAD(P)H:quinone oxidoreductase-2" RELATED [EC:1.10.99.2]
-synonym: "NAD(P)H:quinone oxidoreductase2" RELATED [EC:1.10.99.2]
-synonym: "NQO(2) activity" RELATED [EC:1.10.99.2]
-synonym: "NQO2" RELATED [EC:1.10.99.2]
-synonym: "NRH:quinone oxidoreductase 2 activity" NARROW [EC:1.10.99.2]
-synonym: "QR2 activity" RELATED [EC:1.10.99.2]
-synonym: "quinone reductase 2 activity" RELATED [EC:1.10.99.2]
+def: "Catalysis of the reaction: 1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone = 1-(beta-D-ribofuranosyl)nicotinamide + a hydroquinone." [RHEA:12364]
+comment: Formerly EC:1.10.99.2.
+synonym: "N-ribosyldihydronicotinamide dehydrogenase (quinone) activity" RELATED [EC:1.10.5.1]
+synonym: "NQO(2) activity" RELATED [EC:1.10.5.1]
+synonym: "NQO2" RELATED [EC:1.10.5.1]
+synonym: "NRH:quinone oxidoreductase 2 activity" NARROW [EC:1.10.5.1]
+synonym: "QR2 activity" RELATED [EC:1.10.5.1]
+synonym: "quinone reductase 2 activity" RELATED [EC:1.10.5.1]
synonym: "ribosyldihydronicotinamide dehydrogenase (quinone) activity" EXACT []
-xref: EC:1.10.99.2
+xref: EC:1.10.5.1
xref: MetaCyc:1.10.99.2-RXN
xref: Reactome:R-HSA-8936519 "NQO2:FAD dimer reduces quinones to hydroquinones"
xref: RHEA:12364
-is_a: GO:0016491 ! oxidoreductase activity
+is_a: GO:0016679 ! oxidoreductase activity, acting on diphenols and related substances as donors
[Term]
id: GO:0001514
@@ -9130,7 +9054,7 @@ replaced_by: GO:0030023
id: GO:0001530
name: lipopolysaccharide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lipopolysaccharide." [PMID:11079463]
+def: "Binding to a lipopolysaccharide." [PMID:11079463]
synonym: "endotoxin binding" BROAD []
synonym: "LPS binding" EXACT []
is_a: GO:0008289 ! lipid binding
@@ -9140,7 +9064,7 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:0001531
name: interleukin-21 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-21 receptor." [GOC:ai]
+def: "Binding to an interleukin-21 receptor." [GOC:ai]
synonym: "IL-21" NARROW []
synonym: "interleukin-21 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -9214,7 +9138,7 @@ is_a: GO:0048870 ! cell motility
id: GO:0001540
name: amyloid-beta binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with amyloid-beta peptide/protein." [GOC:hjd]
+def: "Binding to an amyloid-beta peptide/protein." [GOC:hjd]
subset: goslim_chembl
synonym: "beta-amyloid binding" EXACT []
is_a: GO:0042277 ! peptide binding
@@ -10030,7 +9954,6 @@ synonym: "PACAP receptor" EXACT []
synonym: "pituitary adenylate cyclase activating polypeptide receptor" EXACT []
synonym: "pituitary adenylate cyclase activating protein receptor activity" EXACT [GOC:dph, GOC:tb]
synonym: "pituitary adenylate cyclase-activating peptide receptor activity" RELATED []
-synonym: "pituitary adenylate cyclase-activating polypeptide receptor activity" RELATED []
synonym: "pituitary adenylyl cyclase activating protein receptor activity" EXACT []
is_a: GO:0004930 ! G protein-coupled receptor activity
@@ -10260,7 +10183,7 @@ is_a: GO:0042596 ! fear response
id: GO:0001664
name: G protein-coupled receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a G protein-coupled receptor." [GOC:ceb, GOC:dph]
+def: "Binding to a G protein-coupled receptor." [GOC:ceb, GOC:dph]
synonym: "G protein coupled receptor binding" EXACT []
synonym: "G protein coupled receptor ligand" NARROW []
synonym: "G-protein coupled receptor binding" EXACT [GOC:bf]
@@ -10324,8 +10247,7 @@ def: "Binds to and increases the activity of an ATP hydrolysis activity." [GOC:a
synonym: "ATPase stimulator activity" EXACT []
xref: Reactome:R-HSA-5251955 "HSP40s activate intrinsic ATPase activity of HSP70s in the nucleoplasm"
xref: Reactome:R-HSA-5251959 "HSP40s activate intrinsic ATPase activity of HSP70s in the cytosol"
-is_a: GO:0008047 ! enzyme activator activity
-is_a: GO:0060590 ! ATPase regulator activity
+is_a: GO:0140677 ! molecular function activator activity
[Term]
id: GO:0001672
@@ -10987,20 +10909,23 @@ is_a: GO:0030154 ! cell differentiation
[Term]
id: GO:0001743
-name: optic placode formation
+name: lens placode formation
namespace: biological_process
def: "The initial developmental process that will lead to the formation of an eye." [GOC:dph]
+synonym: "optic placode formation" RELATED []
is_a: GO:0060788 ! ectodermal placode formation
relationship: part_of GO:0048598 ! embryonic morphogenesis
[Term]
id: GO:0001744
-name: optic lobe placode formation
+name: insect visual primordium formation
namespace: biological_process
alt_id: GO:0007457
-def: "Establishment of the optic placode, a thickened area of densely packed ectoderm cells directly overlying the optic vesicle in the early embryo. In Drosophila, for example, the placode appears in the dorsolateral region of the head in late stage 11 embryos and is the precursor to the larval visual system." [GOC:mtg_sensu, PMID:8402833]
+def: "Establishment of the optic lobe placode. In Drosophila, for example, the placode appears in the dorsolateral region of the head in late stage 11 embryos and is the precursor to the larval visual system." [GOC:mtg_sensu, PMID:8402833]
synonym: "optic lobe and Bolwig's organ precursor formation" EXACT []
+synonym: "optic lobe placode formation" EXACT []
is_a: GO:0060788 ! ectodermal placode formation
+relationship: part_of GO:0001748 ! insect visual primordium development
[Term]
id: GO:0001745
@@ -11021,11 +10946,12 @@ relationship: part_of GO:0055034 ! Bolwig's organ development
[Term]
id: GO:0001748
-name: optic lobe placode development
+name: insect visual primordium development
namespace: biological_process
alt_id: GO:0048049
def: "The process whose specific outcome is the progression of the optic placode over time, from its formation to the mature structure. During embryonic stage 12 the placode starts to invaginate, forming a pouch. Cells that will form Bolwig's organ segregate from the ventral lip of this pouch, remaining in the head epidermis. The remainder of the invagination loses contact with the outer surface and becomes the optic lobe. An example of this process is found in Drosophila melanogaster." [GOC:mtg_sensu, PMID:8402833]
synonym: "optic lobe and Bolwig's organ precursor development" EXACT []
+synonym: "optic lobe placode development" EXACT []
synonym: "optic placode development" BROAD []
is_a: GO:0048856 ! anatomical structure development
@@ -11405,7 +11331,7 @@ is_a: GO:0070227 ! lymphocyte apoptotic process
id: GO:0001784
name: phosphotyrosine residue binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein." [PMID:14636584]
+def: "Binding to a phosphorylated tyrosine residue within a protein." [PMID:14636584]
synonym: "phosphotyrosine binding" RELATED []
is_a: GO:0045309 ! protein phosphorylated amino acid binding
@@ -11422,7 +11348,7 @@ is_a: GO:0004955 ! prostaglandin receptor activity
id: GO:0001786
name: phosphatidylserine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine." [ISBN:0198506732, PMID:12000961]
+def: "Binding to phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine." [ISBN:0198506732, PMID:12000961]
is_a: GO:0005543 ! phospholipid binding
is_a: GO:0072341 ! modified amino acid binding
@@ -11455,14 +11381,14 @@ is_a: GO:0001909 ! leukocyte mediated cytotoxicity
id: GO:0001790
name: polymeric immunoglobulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a J-chain-containing polymeric immunoglobulin of the IgA or IgM isotypes." [GOC:add, ISBN:0781735149]
+def: "Binding to a J-chain-containing polymeric immunoglobulin of the IgA or IgM isotypes." [GOC:add, ISBN:0781735149]
is_a: GO:0019865 ! immunoglobulin binding
[Term]
id: GO:0001791
name: IgM binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an immunoglobulin of the IgM isotype." [GOC:add, ISBN:0781735149]
+def: "Binding to an immunoglobulin of the IgM isotype." [GOC:add, ISBN:0781735149]
is_a: GO:0019865 ! immunoglobulin binding
[Term]
@@ -11765,7 +11691,7 @@ alt_id: GO:0042089
alt_id: GO:0042107
alt_id: GO:0050663
def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149]
-comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules.
+comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "cytokine biosynthetic process" NARROW []
@@ -12096,7 +12022,7 @@ relationship: part_of GO:0090382 ! phagosome maturation
id: GO:0001846
name: opsonin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an opsonin, such as a complement component or antibody, deposited on the surface of a bacteria, virus, immune complex, or other particulate material." [GOC:add, ISBN:0781735149]
+def: "Binding to an opsonin, such as a complement component or antibody, deposited on the surface of a bacteria, virus, immune complex, or other particulate material." [GOC:add, ISBN:0781735149]
comment: Note that an opsonin is a blood serum protein or fragment which when deposited on the surface of a bacteria, virus, immune complex, or other particulate material acts a signal for phagocytosis to cells bearing the appropriate receptors. Not all complement components or fragments and not all antibodies have opsonic properties.
is_a: GO:0005515 ! protein binding
@@ -12111,7 +12037,7 @@ is_a: GO:0004888 ! transmembrane signaling receptor activity
id: GO:0001848
name: complement binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any component or product of the complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a component or product of the complement cascade." [GOC:add, ISBN:0781735149]
comment: Note that the complement cascade includes all of the components involved in the classical complement pathway, the alternative complement pathway, and the lectin complement pathway, as well as the common components of all three pathways.
is_a: GO:0005515 ! protein binding
@@ -12119,7 +12045,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0001849
name: complement component C1q complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C1q complex, a component of the classical complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a C1q complex, a component of the classical complement cascade." [GOC:add, ISBN:0781735149]
is_a: GO:0001846 ! opsonin binding
is_a: GO:0001848 ! complement binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -12128,14 +12054,14 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0001850
name: complement component C3a binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C3a product of the complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a C3a product of the complement cascade." [GOC:add, ISBN:0781735149]
is_a: GO:0001848 ! complement binding
[Term]
id: GO:0001851
name: complement component C3b binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C3b product of the complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a C3b product of the complement cascade." [GOC:add, ISBN:0781735149]
is_a: GO:0001846 ! opsonin binding
is_a: GO:0001848 ! complement binding
@@ -12143,7 +12069,7 @@ is_a: GO:0001848 ! complement binding
id: GO:0001852
name: complement component iC3b binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the iC3b product of the complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a iC3b product of the complement cascade." [GOC:add, ISBN:0781735149]
is_a: GO:0001846 ! opsonin binding
is_a: GO:0001848 ! complement binding
@@ -12151,21 +12077,21 @@ is_a: GO:0001848 ! complement binding
id: GO:0001853
name: complement component C3dg binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C3dg product of the complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a C3dg product of the complement cascade." [GOC:add, ISBN:0781735149]
is_a: GO:0001848 ! complement binding
[Term]
id: GO:0001854
name: complement component C3d binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C3d product of the complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a C3d product of the complement cascade." [GOC:add, ISBN:0781735149]
is_a: GO:0001848 ! complement binding
[Term]
id: GO:0001855
name: complement component C4b binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C4b product of the classical complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a C4b product of the classical complement cascade." [GOC:add, ISBN:0781735149]
is_a: GO:0001846 ! opsonin binding
is_a: GO:0001848 ! complement binding
@@ -12173,7 +12099,7 @@ is_a: GO:0001848 ! complement binding
id: GO:0001856
name: complement component C5a binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C5a product of the complement cascade." [GOC:add, ISBN:0781735149]
+def: "Binding to a C5a product of the complement cascade." [GOC:add, ISBN:0781735149]
is_a: GO:0001848 ! complement binding
[Term]
@@ -12218,7 +12144,7 @@ is_a: GO:0004875 ! complement receptor activity
id: GO:0001862
name: collectin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a collectin, a member of a group of structurally related pattern recognition molecules characterized by having a carbohydrate recognition domain of the C-type lectin family at the C-terminus and a collagenous domain at the N-terminus." [GOC:add, ISBN:0781735149]
+def: "Binding to a collectin, a member of a group of structurally related pattern recognition molecules characterized by having a carbohydrate recognition domain of the C-type lectin family at the C-terminus and a collagenous domain at the N-terminus." [GOC:add, ISBN:0781735149]
comment: Note that collectins include such proteins as mannose-binding lectins (MBL) and surfactant proteins A and D (SP-A and SP-D).
is_a: GO:0001846 ! opsonin binding
@@ -12234,7 +12160,7 @@ is_a: GO:0001847 ! opsonin receptor activity
id: GO:0001864
name: pentraxin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pentraxin, a member of a family of inflammatory proteins with a radially symmetric arrangement of five identical, noncovalently linked chains in a pentagonal array." [GOC:add, ISBN:0781735149]
+def: "Binding to a pentraxin, a member of a family of inflammatory proteins with a radially symmetric arrangement of five identical, noncovalently linked chains in a pentagonal array." [GOC:add, ISBN:0781735149]
comment: Note that pentraxins include such proteins as serum amyloid P component (SAP) and C-reactive protein (CRP).
is_a: GO:0001846 ! opsonin binding
@@ -12325,7 +12251,7 @@ relationship: positively_regulates GO:0001867 ! complement activation, lectin pa
id: GO:0001871
name: obsolete pattern binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a repeating or polymeric structure, such as a polysaccharide or peptidoglycan." [PMID:12072369, PMID:12225919, PMID:12507420, PMID:12925128, PMID:14523544]
+def: "OBSOLETE. Binding to a repeating or polymeric structure, such as a polysaccharide or peptidoglycan." [PMID:12072369, PMID:12225919, PMID:12507420, PMID:12925128, PMID:14523544]
comment: This term was obsoleted because it was an unnecessary grouping term.
synonym: "pattern recognition activity" BROAD []
is_obsolete: true
@@ -12335,7 +12261,7 @@ id: GO:0001872
name: (1->3)-beta-D-glucan binding
namespace: molecular_function
alt_id: GO:0080087
-def: "Interacting selectively and non-covalently with (1->3)-beta-D-glucans." [PMID:14707091]
+def: "Binding to a (1->3)-beta-D-glucan." [PMID:14707091]
synonym: "1,3-beta-D-glucan binding" EXACT []
synonym: "callose binding" NARROW []
synonym: "zymosan binding" NARROW [GOC:tb]
@@ -12375,7 +12301,7 @@ is_a: GO:0038187 ! pattern recognition receptor activity
id: GO:0001876
name: lipoarabinomannan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lipoarabinomannan." [PMID:10586073]
+def: "Binding to lipoarabinomannan." [PMID:10586073]
synonym: "LAM binding" EXACT []
is_a: GO:0034235 ! GPI anchor binding
@@ -12393,7 +12319,7 @@ id: GO:0001878
name: response to yeast
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a yeast species." [PMID:14707091]
-comment: defined as response to Saccharomycotina (true yeasts). This excludes fission yeast.
+comment: defined as response to Saccharomycotina (true yeasts). This excludes fission yeast.
is_a: GO:0009620 ! response to fungus
[Term]
@@ -12424,7 +12350,7 @@ is_a: GO:0043112 ! receptor metabolic process
id: GO:0001882
name: nucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose." [GOC:hjd]
+def: "Binding to a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose." [GOC:hjd]
subset: goslim_pir
is_a: GO:0036094 ! small molecule binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -12435,14 +12361,14 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0001883
name: purine nucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a purine nucleoside, a compound consisting of a purine base linked either to ribose or deoxyribose." [GOC:hjd]
+def: "Binding to a purine nucleoside, a compound consisting of a purine base linked either to ribose or deoxyribose." [GOC:hjd]
is_a: GO:0001882 ! nucleoside binding
[Term]
id: GO:0001884
name: pyrimidine nucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pyrimidine nucleoside, a compound consisting of a pyrimidine base linked either to ribose or deoxyribose." [GOC:hjd]
+def: "Binding to a pyrimidine nucleoside, a compound consisting of a pyrimidine base linked either to ribose or deoxyribose." [GOC:hjd]
is_a: GO:0001882 ! nucleoside binding
[Term]
@@ -12565,9 +12491,8 @@ name: cytolysis by symbiont of host cells
namespace: biological_process
def: "The killing by an organism of a cell in its host organism by means of the rupture of cell membranes and the loss of cytoplasm. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add]
synonym: "cytolysis by organism of host cells" EXACT []
-synonym: "pathogenesis" NARROW []
+synonym: "pathogenesis" RELATED []
is_a: GO:0001907 ! killing by symbiont of host cells
-is_a: GO:0051801 ! cytolysis in other organism involved in symbiotic interaction
[Term]
id: GO:0001898
@@ -12575,7 +12500,7 @@ name: regulation of cytolysis by symbiont of host cells
namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of the cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb]
synonym: "regulation by symbiont of cytolysis of host cells" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0051802 ! regulation of cytolysis in other organism involved in symbiotic interaction
+is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
relationship: regulates GO:0001897 ! cytolysis by symbiont of host cells
[Term]
@@ -12589,7 +12514,7 @@ synonym: "downregulation by symbiont of cytolysis of host cells" EXACT []
synonym: "inhibition by symbiont of cytolysis of host cells" NARROW []
synonym: "negative regulation by symbiont of cytolysis of host cells" EXACT [GOC:dph, GOC:tb]
is_a: GO:0001898 ! regulation of cytolysis by symbiont of host cells
-is_a: GO:0051803 ! negative regulation of cytolysis in other organism involved in symbiotic interaction
+is_a: GO:0048519 ! negative regulation of biological process
relationship: negatively_regulates GO:0001897 ! cytolysis by symbiont of host cells
[Term]
@@ -12604,7 +12529,7 @@ synonym: "up regulation by symbiont of cytolysis of host cells" EXACT []
synonym: "up-regulation by symbiont of cytolysis of host cells" EXACT []
synonym: "upregulation by symbiont of cytolysis of host cells" EXACT []
is_a: GO:0001898 ! regulation of cytolysis by symbiont of host cells
-is_a: GO:0051804 ! positive regulation of cytolysis in other organism involved in symbiotic interaction
+is_a: GO:0048518 ! positive regulation of biological process
relationship: positively_regulates GO:0001897 ! cytolysis by symbiont of host cells
[Term]
@@ -12636,9 +12561,8 @@ id: GO:0001907
name: killing by symbiont of host cells
namespace: biological_process
def: "Any process mediated by an organism that results in the death of cells in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add]
-synonym: "pathogenesis" NARROW []
+synonym: "pathogenesis" RELATED []
is_a: GO:0051701 ! biological process involved in interaction with host
-is_a: GO:0051883 ! killing of cells in other organism involved in symbiotic interaction
[Term]
id: GO:0001909
@@ -12801,7 +12725,7 @@ is_a: GO:0110165 ! cellular anatomical entity
id: GO:0001918
name: farnesylated protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a farnesylated protein." [GOC:add, PMID:14555765]
+def: "Binding to a farnesylated protein." [GOC:add, PMID:14555765]
is_a: GO:0005515 ! protein binding
[Term]
@@ -12922,7 +12846,7 @@ id: GO:0001927
name: exocyst assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of various polypeptides into the exocyst complex." [GOC:hjd, PMID:9700152, Wikipedia:Exocyst]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
is_a: GO:0140029 ! exocytic process
relationship: part_of GO:0006904 ! vesicle docking involved in exocytosis
@@ -13294,7 +13218,7 @@ is_a: GO:0008378 ! galactosyltransferase activity
id: GO:0001963
name: synaptic transmission, dopaminergic
namespace: biological_process
-def: "The vesicular release of dopamine. from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." [GOC:dos, GOC:dph]
+def: "The vesicular release of dopamine. from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." [GOC:dos, GOC:dph]
synonym: "dopaminergic synaptic transmission" EXACT []
is_a: GO:0007268 ! chemical synaptic transmission
@@ -13311,7 +13235,7 @@ is_a: GO:0050905 ! neuromuscular process
id: GO:0001965
name: G-protein alpha-subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a G-protein alpha subunit. The alpha subunit binds a guanine nucleotide." [GOC:hjd]
+def: "Binding to a G-protein alpha subunit. The alpha subunit binds a guanine nucleotide." [GOC:hjd]
synonym: "G-alpha protein subunit binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -13337,7 +13261,7 @@ is_a: GO:0007631 ! feeding behavior
id: GO:0001968
name: fibronectin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids." [GOC:hjd]
+def: "Binding to a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids." [GOC:hjd]
subset: goslim_chembl
is_a: GO:0005515 ! protein binding
@@ -13404,7 +13328,7 @@ relationship: negatively_regulates GO:0001905 ! activation of membrane attack co
id: GO:0001972
name: retinoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with retinoic acid, 3,7-dimethyl-9-(2,6,-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid." [GOC:hjd]
+def: "Binding to retinoic acid, 3,7-dimethyl-9-(2,6,-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid." [GOC:hjd]
is_a: GO:0005501 ! retinoid binding
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0043177 ! organic acid binding
@@ -13885,7 +13809,7 @@ is_a: GO:0002016 ! regulation of blood volume by renin-angiotensin
id: GO:0002020
name: protease binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protease or peptidase." [GOC:hjd]
+def: "Binding to a protease or a peptidase." [GOC:hjd]
xref: Reactome:R-HSA-1297354 "Acrosin Cleavage"
is_a: GO:0019899 ! enzyme binding
@@ -13961,7 +13885,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph]
synonym: "regulation of Na+ transport" EXACT []
synonym: "regulation of sodium transport" EXACT []
-is_a: GO:0043269 ! regulation of ion transport
+is_a: GO:0010959 ! regulation of metal ion transport
relationship: regulates GO:0006814 ! sodium ion transport
[Term]
@@ -14072,7 +13996,6 @@ synonym: "regulation of L-glutamate import" BROAD []
is_a: GO:0002036 ! regulation of L-glutamate import across plasma membrane
is_a: GO:0051956 ! negative regulation of amino acid transport
is_a: GO:1903960 ! negative regulation of anion transmembrane transport
-is_a: GO:2001024 ! negative regulation of response to drug
relationship: negatively_regulates GO:0098712 ! L-glutamate import across plasma membrane
[Term]
@@ -14106,7 +14029,7 @@ relationship: positively_regulates GO:0098712 ! L-glutamate import across plasma
id: GO:0002039
name: p53 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with one of the p53 family of proteins." [GOC:hjd]
+def: "Binding to one of the p53 family of proteins." [GOC:hjd]
is_a: GO:0005515 ! protein binding
[Term]
@@ -14161,7 +14084,7 @@ id: GO:0002046
name: opsin binding
namespace: molecular_function
alt_id: GO:0016030
-def: "Interacting selectively and non-covalently with an opsin, any of a group of hydrophobic, integral membrane glycoproteins located primarily in the disc membrane of rods or cones, involved in photoreception." [GOC:hjd]
+def: "Binding to an opsin, any of a group of hydrophobic, integral membrane glycoproteins located primarily in the disc membrane of rods or cones, involved in photoreception." [GOC:hjd]
synonym: "metarhodopsin binding" NARROW []
is_a: GO:0005515 ! protein binding
@@ -14250,7 +14173,7 @@ relationship: positively_regulates GO:0010463 ! mesenchymal cell proliferation
id: GO:0002054
name: nucleobase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases." [GOC:hjd]
+def: "Binding to a nucleobase, any of a class of pyrmidines or purines, organic nitrogenous bases." [GOC:hjd]
subset: goslim_pir
is_a: GO:0036094 ! small molecule binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -14260,7 +14183,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0002055
name: adenine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with adenine, a purine base." [GOC:hjd]
+def: "Binding to adenine, a purine base." [GOC:hjd]
synonym: "6-aminopurine binding" EXACT []
is_a: GO:0002060 ! purine nucleobase binding
@@ -14268,35 +14191,35 @@ is_a: GO:0002060 ! purine nucleobase binding
id: GO:0002056
name: cytosine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cytosine." [GOC:hjd, GOC:vw]
+def: "Binding to cytosine." [GOC:hjd, GOC:vw]
is_a: GO:0002061 ! pyrimidine nucleobase binding
[Term]
id: GO:0002057
name: guanine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with guanine." [GOC:hjd]
+def: "Binding to guanine." [GOC:hjd]
is_a: GO:0002060 ! purine nucleobase binding
[Term]
id: GO:0002058
name: uracil binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with uracil." [GOC:hjd]
+def: "Binding to uracil." [GOC:hjd]
is_a: GO:0002061 ! pyrimidine nucleobase binding
[Term]
id: GO:0002059
name: thymine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with thymine." [GOC:hjd]
+def: "Binding to thymine." [GOC:hjd]
is_a: GO:0002061 ! pyrimidine nucleobase binding
[Term]
id: GO:0002060
name: purine nucleobase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a purine nucleobase, an organic nitrogenous base with a purine skeleton." [GOC:hjd]
+def: "Binding to a purine nucleobase, an organic nitrogenous base with a purine skeleton." [GOC:hjd]
synonym: "purine base binding" EXACT [GOC:go_curators]
synonym: "purine binding" RELATED []
is_a: GO:0002054 ! nucleobase binding
@@ -14305,7 +14228,7 @@ is_a: GO:0002054 ! nucleobase binding
id: GO:0002061
name: pyrimidine nucleobase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pyrimidine nucleobase, an organic nitrogenous base with a pyrimidine skeleton." [GOC:hjd]
+def: "Binding to a pyrimidine nucleobase, an organic nitrogenous base with a pyrimidine skeleton." [GOC:hjd]
synonym: "1,3-diazine binding" NARROW []
synonym: "pyrimidine base binding" EXACT [GOC:go_curators]
synonym: "pyrimidine binding" RELATED []
@@ -14447,7 +14370,7 @@ name: inner acrosomal membrane
namespace: cellular_component
def: "The acrosomal membrane region that underlies the acrosomal vesicle and is located toward the sperm nucleus. This region is responsible for molecular interactions allowing the sperm to penetrate the zona pellucida and fuses with the egg plasma membrane." [GOC:dph, PMID:3899643, PMID:8936405]
comment: Note that this term is not a descendant of 'organelle inner membrane ; GO:0019866' because the outer acrosomal membrane is a portion of the acrosomal membrane; the latter is a single lipid bilayer.
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
relationship: part_of GO:0002080 ! acrosomal membrane
[Term]
@@ -14464,7 +14387,7 @@ name: outer acrosomal membrane
namespace: cellular_component
def: "The acrosomal membrane region that underlies the plasma membrane of the sperm. This membrane fuses with the sperm plasma membrane as part of the acrosome reaction." [GOC:dph, PMID:8936405]
comment: Note that this term is not a descendant of 'organelle outer membrane ; GO:0031968' because the outer acrosomal membrane is a portion of the acrosomal membrane; the latter is a single lipid bilayer.
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
relationship: part_of GO:0002080 ! acrosomal membrane
[Term]
@@ -14741,7 +14664,7 @@ is_a: GO:0140513 ! nuclear protein-containing complex
id: GO:0002112
name: interleukin-33 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-33 receptor." [GOC:hjd]
+def: "Binding to an interleukin-33 receptor." [GOC:hjd]
synonym: "IL-33" NARROW [GOC:mah]
synonym: "interleukin-33 receptor ligand" NARROW [GOC:mah]
is_a: GO:0005126 ! cytokine receptor binding
@@ -14750,7 +14673,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0002113
name: interleukin-33 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-33." [GOC:hjd]
+def: "Binding to interleukin-33." [GOC:hjd]
synonym: "IL-33 binding" EXACT [GOC:mah]
is_a: GO:0019955 ! cytokine binding
@@ -14922,7 +14845,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0002134
name: UTP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with UTP, uridine 5'-triphosphate." [GOC:hjd, ISBN:0198506732]
+def: "Binding to UTP, uridine 5'-triphosphate." [GOC:hjd, ISBN:0198506732]
is_a: GO:0032557 ! pyrimidine ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -14930,7 +14853,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0002135
name: CTP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with CTP, cytidine 5'-triphosphate." [GOC:hjd, ISBN:0124020607]
+def: "Binding to CTP, cytidine 5'-triphosphate." [GOC:hjd, ISBN:0124020607]
is_a: GO:0032557 ! pyrimidine ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -15077,7 +15000,7 @@ is_a: GO:0044282 ! small molecule catabolic process
id: GO:0002151
name: G-quadruplex RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with G-quadruplex RNA structures, in which groups of four guanines adopt a flat, cyclic hydrogen-bonding arrangement known as a guanine tetrad." [PMID:18294969, PMID:18568163, PMID:19330720]
+def: "Binding to a G-quadruplex RNA structure, in which groups of four guanines adopt a flat, cyclic hydrogen-bonding arrangement known as a guanine tetrad." [PMID:18294969, PMID:18568163, PMID:19330720]
comment: The structures of RNA and DNA G quartets differ regarding sugar conformation so that a protein binding to the RNA structure might not bind to the DNA structure.
synonym: "G quadruplex binding" EXACT [GOC:mah]
synonym: "G quartet binding" BROAD [GOC:hjd]
@@ -15097,7 +15020,7 @@ is_a: GO:0008206 ! bile acid metabolic process
id: GO:0002153
name: steroid receptor RNA activator RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the steroid receptor RNA activator RNA (SRA). SRA enhances steroid hormone receptor transcriptional activity as an RNA transcript by an indirect mechanism that does not involve SRA-steroid receptor binding." [GOC:vw, PMID:10199399, PMID:15180993]
+def: "Binding to a steroid receptor RNA activator RNA (SRA). SRA enhances steroid hormone receptor transcriptional activity as an RNA transcript by an indirect mechanism that does not involve SRA-steroid receptor binding." [GOC:vw, PMID:10199399, PMID:15180993]
comment: Note: there is also evidence that the RNA itself may code a protein (solution structure of mouse steroid receptor RNA activator 1 (SRA1) protein submitted to PDB by Riken).
synonym: "SRA binding" EXACT []
is_a: GO:0003727 ! single-stranded RNA binding
@@ -15181,7 +15104,7 @@ name: dystroglycan binding
namespace: molecular_function
alt_id: GO:0002163
alt_id: GO:0002166
-def: "Interacting selectively and non-covalently with dystroglycan. Dystroglycan is glycoprotein found in non-muscle tissues as well as in muscle tissues, often in association with dystrophin. The native dystroglycan cleaved into two non-covalently associated subunits, alpha (N-terminal) and beta (C-terminal)." [GOC:hjd]
+def: "Binding to dystroglycan, a glycoprotein found in non-muscle tissues as well as in muscle tissues, often in association with dystrophin. The native dystroglycan cleaved into two non-covalently associated subunits, alpha (N-terminal) and beta (C-terminal)." [GOC:hjd]
synonym: "alpha-dystroglycan binding" NARROW []
synonym: "beta-dystroglycan binding" NARROW []
is_a: GO:0005515 ! protein binding
@@ -15323,7 +15246,7 @@ name: cytoplasmic translation
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein." [GOC:hjd]
comment: Note that this term applies to translation performed by cytoplasmic ribosomes, which is distinct from translation performed by organellar ribosomes. For mitochondrial translation, consider GO:0032543 'mitochondrial translation' or its child terms.
-subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
is_a: GO:0006412 ! translation
@@ -15635,7 +15558,7 @@ synonym: "PAMP receptor signaling pathway" EXACT [ISBN:0781735149, PMID:15199967
synonym: "pathogen receptor signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447]
synonym: "pathogen receptor signalling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447]
synonym: "PRR signaling pathway" EXACT [ISBN:0781735149, PMID:15199967, PMID:15728447]
-is_a: GO:0007165 ! signal transduction
+is_a: GO:0002764 ! immune response-regulating signaling pathway
[Term]
id: GO:0002222
@@ -16731,7 +16654,7 @@ is_a: GO:0002327 ! immature B cell differentiation
id: GO:0002330
name: pre-B cell receptor expression
namespace: biological_process
-def: "The process leading up to expression of the pre-B cell receptor on the surface of pre-B cells, starting with the recombination of an immunuglobulin heavy chain locus, including expression of the surrogate light chain, the association of the surrogate light chain with the heavy chain, and expression of the complete pre-B cell receptor on the cell surface. pre-B cell receptor expression is a key checkpoint in the transition of pro-B cell to pre-B cell." [GOC:add, GOC:jal, ISBN:0781735149]
+def: "The process leading up to expression of the pre-B cell receptor on the surface of pre-B cells, starting with the recombination of an immunuglobulin heavy chain locus, including expression of the surrogate light chain, the association of the surrogate light chain with the heavy chain, and expression of the complete pre-B cell receptor on the cell surface. pre-B cell receptor expression is a key checkpoint in the transition of pro-B cell to pre-B cell." [GOC:add, GOC:jal, PMID:15263090, PMID:22949502, PMID:9834086]
is_a: GO:0048869 ! cellular developmental process
relationship: part_of GO:0002329 ! pre-B cell differentiation
@@ -17356,7 +17279,7 @@ id: GO:0002396
name: MHC protein complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form an MHC protein complex." [GOC:add, ISBN:0781735149, PMID:15771591, PMID:15928678]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0002397
@@ -18289,7 +18212,7 @@ id: GO:0002501
name: peptide antigen assembly with MHC protein complex
namespace: biological_process
def: "The binding of a peptide to the antigen binding groove of an MHC protein complex." [GOC:add, ISBN:0781735149, PMID:15771591]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0002396 ! MHC protein complex assembly
relationship: part_of GO:0048002 ! antigen processing and presentation of peptide antigen
@@ -23532,7 +23455,7 @@ relationship: part_of GO:0048163 ! scattered antral spaces stage
id: GO:0003006
name: developmental process involved in reproduction
namespace: biological_process
-def: "A developmental process in which a progressive change in the state of some part of an organism specifically contributes to its ability to form offspring." [GOC:dph, GOC:isa_complete]
+def: "A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring." [GOC:dph, GOC:isa_complete]
synonym: "puberty" NARROW [GOC:dph]
synonym: "reproductive developmental process" RELATED [GOC:dph, GOC:tb]
is_a: GO:0022414 ! reproductive process
@@ -23582,6 +23505,8 @@ id: GO:0003012
name: muscle system process
namespace: biological_process
def: "A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers." [GOC:mtg_cardio]
+subset: goslim_drosophila
+subset: goslim_generic
synonym: "muscle physiological process" RELATED []
is_a: GO:0003008 ! system process
@@ -23600,6 +23525,7 @@ id: GO:0003014
name: renal system process
namespace: biological_process
def: "A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila)." [GOC:cjm, GOC:mtg_cardio, GOC:mtg_kidney_jan10]
+subset: goslim_generic
synonym: "excretory system process" EXACT []
synonym: "kidney system process" RELATED []
is_a: GO:0003008 ! system process
@@ -23618,6 +23544,7 @@ name: respiratory system process
namespace: biological_process
alt_id: GO:0010802
def: "A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange." [GOC:dph, GOC:mtg_cardio, GOC:tb]
+subset: goslim_generic
synonym: "respiratory gaseous exchange" EXACT []
is_a: GO:0003008 ! system process
relationship: part_of GO:0007585 ! respiratory gaseous exchange by respiratory system
@@ -27264,7 +27191,6 @@ comment: Note that, in addition to forming the root of the molecular function on
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
@@ -27285,7 +27211,7 @@ id: GO:0003676
name: nucleic acid binding
namespace: molecular_function
alt_id: GO:0000496
-def: "Interacting selectively and non-covalently with any nucleic acid." [GOC:jl]
+def: "Binding to a nucleic acid." [GOC:jl]
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
@@ -27322,17 +27248,18 @@ name: DNA helicase activity
namespace: molecular_function
alt_id: GO:0003679
alt_id: GO:0004003
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix." [EC:3.6.4.12, GOC:jl]
+def: "Unwinding of a DNA helix, driven by ATP hydrolysis." [EC:3.6.4.12, GOC:jl]
synonym: "ATP-dependent DNA helicase activity" EXACT []
xref: EC:3.6.4.12
xref: Reactome:R-HSA-5693589 "D-loop dissociation and strand annealing"
is_a: GO:0004386 ! helicase activity
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
[Term]
id: GO:0003680
name: minor groove of adenine-thymine-rich DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the structure formed by the minor groove of adenine-thymine-rich DNA regions. Examples of proteins having this function are AT-rich interaction domain (ARID)-containing proteins." [GOC:jl, PMID:10545119, PMID:15802641, PMID:26223912, PMID:2670564]
+def: "Binding to a DNA structure formed by the minor groove of adenine-thymine-rich DNA regions. Examples of proteins having this function are AT-rich interaction domain (ARID)-containing proteins." [GOC:jl, PMID:10545119, PMID:15802641, PMID:26223912, PMID:2670564]
synonym: "AT binding" EXACT []
synonym: "AT DNA binding" EXACT []
synonym: "AT-rich DNA binding" EXACT []
@@ -27342,14 +27269,14 @@ is_a: GO:0000217 ! DNA secondary structure binding
id: GO:0003681
name: bent DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA in a bent conformation." [GOC:jl, PMID:12627977]
+def: "Binding to DNA in a bent conformation." [GOC:jl, PMID:12627977]
is_a: GO:0003677 ! DNA binding
[Term]
id: GO:0003682
name: chromatin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732, PMID:20404130]
+def: "Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." [GOC:jl, ISBN:0198506732, PMID:20404130]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_pir
@@ -27375,7 +27302,7 @@ consider: GO:0005521
id: GO:0003684
name: damaged DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with damaged DNA." [GOC:jl]
+def: "Binding to damaged DNA." [GOC:jl]
synonym: "DNA repair enzyme" RELATED []
synonym: "DNA repair protein" RELATED []
is_a: GO:0003677 ! DNA binding
@@ -27414,7 +27341,7 @@ consider: GO:0006260
id: GO:0003688
name: DNA replication origin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally." [GOC:curators]
+def: "Binding to a DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally." [GOC:curators]
synonym: "ARS binding" NARROW []
is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
@@ -27423,7 +27350,7 @@ id: GO:0003689
name: DNA clamp loader activity
namespace: molecular_function
alt_id: GO:0033170
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex." [GOC:mah, GOC:vw, PMID:16082778]
+def: "Facilitating the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their closing around the DNA duplex, driven by ATP hydrolysis." [GOC:mah, GOC:vw, PMID:16082778]
synonym: "DNA clamp loading ATPase activity" EXACT []
synonym: "DNA-protein loading ATPase activity" RELATED [GOC:mah]
synonym: "PCNA loading activity" NARROW []
@@ -27431,13 +27358,13 @@ synonym: "PCNA loading complex activity" NARROW []
synonym: "protein-DNA loading ATPase activity" RELATED []
xref: Reactome:R-HSA-174439 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere"
xref: Reactome:R-HSA-176264 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA"
-is_a: GO:0008094 ! ATPase, acting on DNA
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
[Term]
id: GO:0003690
name: double-stranded DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA." [GOC:elh, GOC:vw]
+def: "Binding to double-stranded DNA." [GOC:elh, GOC:vw]
synonym: "dsDNA binding" EXACT [GOC:elh]
is_a: GO:0003677 ! DNA binding
@@ -27445,7 +27372,7 @@ is_a: GO:0003677 ! DNA binding
id: GO:0003691
name: double-stranded telomeric DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded telomere-associated DNA." [GOC:jl, ISBN:0321000382]
+def: "Binding to double-stranded telomere-associated DNA." [GOC:jl, ISBN:0321000382]
is_a: GO:0003690 ! double-stranded DNA binding
is_a: GO:0042162 ! telomeric DNA binding
@@ -27453,14 +27380,14 @@ is_a: GO:0042162 ! telomeric DNA binding
id: GO:0003692
name: left-handed Z-DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA in the Z form, i.e. a left-handed helix in which the phosphate backbone zigzags." [ISBN:0716720094]
+def: "Binding to DNA in the Z form, i.e. a left-handed helix in which the phosphate backbone zigzags." [ISBN:0716720094]
is_a: GO:0003690 ! double-stranded DNA binding
[Term]
id: GO:0003693
name: P-element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any P-element, a class of Drosophila transposon responsible for hybrid dysgenesis." [GOC:jl, PMID:9440262]
+def: "Binding to a P-element, a class of Drosophila transposon responsible for hybrid dysgenesis." [GOC:jl, PMID:9440262]
is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
[Term]
@@ -27480,7 +27407,7 @@ id: GO:0003695
name: obsolete random coil DNA binding
namespace: molecular_function
alt_id: GO:0016017
-def: "OBSOLETE. Interacting selectively and non-covalently with DNA in a random coil configuration." [GOC:mah]
+def: "OBSOLETE. Binding to DNA in a random coil configuration." [GOC:mah]
comment: This term was obsoleted because the definition was not clear enough as to what is directing specificity of the binding to the DNA.
synonym: "random coil binding" EXACT []
is_obsolete: true
@@ -27489,7 +27416,7 @@ is_obsolete: true
id: GO:0003696
name: satellite DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [GOC:jl, SO:0000005]
+def: "Binding to satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [GOC:jl, SO:0000005]
is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
[Term]
@@ -27498,7 +27425,7 @@ name: single-stranded DNA binding
namespace: molecular_function
alt_id: GO:0003698
alt_id: GO:0003699
-def: "Interacting selectively and non-covalently with single-stranded DNA." [GOC:elh, GOC:vw, PMID:22976174]
+def: "Binding to single-stranded DNA." [GOC:elh, GOC:vw, PMID:22976174]
comment: Note that this term is restricted to those cases where the binding is to a single-stranded DNA molecule, not to one of the stands of double-stranded DNA.
synonym: "ssDNA binding" EXACT [GOC:mah]
is_a: GO:0003677 ! DNA binding
@@ -27521,7 +27448,6 @@ subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_plant
@@ -27615,7 +27541,6 @@ namespace: molecular_function
def: "A molecular function that regulates transcriptional elongation by enabling the transition from transcription initiation to elongation or by altering the elongation properties of the enzyme during the elongation phase of transcription." [GOC:txnOH-2018, PMID:23878398, PMID:28892040]
comment: Restored term from obsolete.
synonym: "transcription elongation factor activity" EXACT []
-synonym: "transcription elongation regulator activity" EXACT []
synonym: "transcriptional elongation regulator activity" EXACT []
is_a: GO:0140110 ! transcription regulator activity
@@ -27644,7 +27569,6 @@ synonym: "RNA polymerase II transcription co-activator activity" RELATED []
synonym: "RNA polymerase II transcription coactivator activity" RELATED []
synonym: "RNA polymerase II transcription mediator activity" RELATED []
synonym: "transcription co-activator activity" EXACT []
-synonym: "transcription coactivator activity" EXACT []
is_a: GO:0003712 ! transcription coregulator activity
[Term]
@@ -27657,7 +27581,6 @@ comment: For usage guidance, see comment in GO:0003712 ; transcription coregulat
synonym: "RNA polymerase II transcription co-repressor activity" RELATED []
synonym: "RNA polymerase II transcription corepressor activity" RELATED []
synonym: "transcription co-repressor activity" EXACT []
-synonym: "transcription corepressor activity" EXACT []
is_a: GO:0003712 ! transcription coregulator activity
[Term]
@@ -27738,7 +27661,7 @@ name: RNA binding
namespace: molecular_function
alt_id: GO:0000498
alt_id: GO:0044822
-def: "Interacting selectively and non-covalently with an RNA molecule or a portion thereof." [GOC:jl, GOC:mah]
+def: "Binding to an RNA molecule or a portion thereof." [GOC:jl, GOC:mah]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
@@ -27761,18 +27684,20 @@ id: GO:0003724
name: RNA helicase activity
namespace: molecular_function
alt_id: GO:0004004
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix." [EC:3.6.4.13, GOC:jl]
+def: "Unwinding of an RNA helix, driven by ATP hydrolysis." [GOC:jl, PMID:19158098]
synonym: "ATP-dependent RNA helicase activity" EXACT []
xref: EC:3.6.4.13
+xref: MetaCyc:ADENOSINETRIPHOSPHATASE-RXN
xref: Reactome:R-HSA-72647 "Cap-bound mRNA is activated by helicases"
is_a: GO:0004386 ! helicase activity
+is_a: GO:0008186 ! ATP-dependent activity, acting on RNA
is_a: GO:0140098 ! catalytic activity, acting on RNA
[Term]
id: GO:0003725
name: double-stranded RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded RNA." [GOC:jl]
+def: "Binding to double-stranded RNA." [GOC:jl]
synonym: "dsRNA binding" EXACT [GOC:ecd]
is_a: GO:0003723 ! RNA binding
@@ -27792,7 +27717,7 @@ id: GO:0003727
name: single-stranded RNA binding
namespace: molecular_function
alt_id: GO:0003728
-def: "Interacting selectively and non-covalently with single-stranded RNA." [GOC:jl]
+def: "Binding to single-stranded RNA." [GOC:jl]
synonym: "ssRNA binding" EXACT [GOC:mah]
is_a: GO:0003723 ! RNA binding
@@ -27801,9 +27726,8 @@ id: GO:0003729
name: mRNA binding
namespace: molecular_function
alt_id: GO:0000499
-def: "Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns." [GOC:kmv, GOC:pr, SO:0000234]
+def: "Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns." [GOC:kmv, GOC:pr, SO:0000234]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_yeast
synonym: "base pairing with mRNA" NARROW []
is_a: GO:0003723 ! RNA binding
@@ -27812,7 +27736,7 @@ is_a: GO:0003723 ! RNA binding
id: GO:0003730
name: mRNA 3'-UTR binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule." [GOC:mah]
+def: "Binding to a 3' untranslated region of an mRNA molecule." [GOC:mah]
synonym: "mRNA 3' UTR binding" EXACT []
is_a: GO:0003729 ! mRNA binding
@@ -27872,7 +27796,6 @@ def: "The action of a molecule that contributes to the structural integrity of t
comment: Note that this term may be used to annotate ribosomal RNAs as well as ribosomal proteins.
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_yeast
synonym: "ribosomal protein" BROAD []
@@ -28075,15 +27998,17 @@ consider: GO:0042026
[Term]
id: GO:0003774
-name: motor activity
+name: cytoskeletal motor activity
namespace: molecular_function
def: "Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force)." [GOC:mah, GOC:vw, PMID:11242086, PMID:29716949]
subset: goslim_aspergillus
subset: goslim_candida
+subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
+synonym: "motor activity" BROAD []
xref: Reactome:R-HSA-1861595 "Extension of pseudopodia by myosin-X in a PI3K dependent manner"
-is_a: GO:0017111 ! nucleoside-triphosphatase activity
+is_a: GO:0003674 ! molecular_function
[Term]
id: GO:0003775
@@ -28112,8 +28037,10 @@ consider: GO:0043292
id: GO:0003777
name: microtubule motor activity
namespace: molecular_function
-def: "Generation of movement along a microtubule, driven by ATP hydrolysis." [PMID:32684327]
+alt_id: GO:1990939
+def: "A motor activity that generates movement along a microtubule, driven by ATP hydrolysis." [PMID:19686686, PMID:32684327, PMID:32842864]
comment: Consider also annotating to the molecular function term 'microtubule binding ; GO:0008017'.
+synonym: "ATP-dependent microtubule motor activity" EXACT []
synonym: "axonemal motor activity" NARROW []
synonym: "dynein" BROAD []
synonym: "dynein ATPase activity" NARROW []
@@ -28122,7 +28049,9 @@ synonym: "kinesin motor activity" NARROW []
synonym: "kinetochore motor activity" NARROW []
xref: Reactome:R-HSA-177479 "Axonal transport of NGF:Trk complexes"
xref: Reactome:R-HSA-265160 "Insulin secretory granule translocates to cell cortex"
-is_a: GO:0003774 ! motor activity
+xref: Reactome:R-HSA-9610627 "KIF17 transports GluN1:GluN2B (GRIN1:GRIN2B) NMDA receptors to the plasma membrane"
+is_a: GO:0003774 ! cytoskeletal motor activity
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0003778
@@ -28137,7 +28066,7 @@ is_obsolete: true
id: GO:0003779
name: actin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments." [GOC:clt]
+def: "Binding to monomeric or multimeric forms of actin, including actin filaments." [GOC:clt]
synonym: "membrane associated actin binding" NARROW []
is_a: GO:0008092 ! cytoskeletal protein binding
@@ -28197,7 +28126,7 @@ consider: GO:0051016
id: GO:0003785
name: actin monomer binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with monomeric actin, also known as G-actin." [GOC:ai]
+def: "Binding to monomeric actin, also known as G-actin." [GOC:ai]
synonym: "G actin binding" EXACT []
is_a: GO:0003779 ! actin binding
@@ -28205,7 +28134,7 @@ is_a: GO:0003779 ! actin binding
id: GO:0003786
name: actin lateral binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an actin filament along its length." [GOC:mah]
+def: "Binding to an actin filament along its length." [GOC:mah]
is_a: GO:0051015 ! actin filament binding
[Term]
@@ -28714,7 +28643,7 @@ is_obsolete: true
id: GO:0003823
name: antigen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen." [GOC:jl, ISBN:0198506732, ISBN:0721662544]
+def: "Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen." [GOC:jl, ISBN:0198506732, ISBN:0721662544]
subset: goslim_chembl
subset: goslim_pir
synonym: "antibody" RELATED []
@@ -28821,12 +28750,12 @@ namespace: molecular_function
def: "Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + beta-D-galactosyl-(1->3)-N-acetyl-D-galactosaminyl-R = UDP + beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-D-galactosaminyl-R." [EC:2.4.1.102]
synonym: "beta(6)-N-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.102]
synonym: "beta6-N-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.102]
-synonym: "core 2 acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.102]
-synonym: "core 6-beta-GlcNAc-transferase A" RELATED [EC:2.4.1.102]
+synonym: "core 2 acetylglucosaminyltransferase activity" RELATED []
+synonym: "core 6-beta-GlcNAc-transferase A" RELATED []
synonym: "O-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase I activity" RELATED [EC:2.4.1.102]
-synonym: "UDP-N-acetyl-D-glucosamine:O-glycosyl-glycoprotein (N-acetyl-D-glucosamine to N-acetyl-D-galactosamine of beta-D-galactosyl-1,3-N-acetyl-D-galactosaminyl-R) beta-1,6-N-acetyl-D-glucosaminyltransferase activity" RELATED [EC:2.4.1.102]
-synonym: "uridine diphosphoacetylglucosamine-mucin beta-(1,6)-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.102]
-synonym: "uridine diphosphoacetylglucosamine-mucin beta-(1->6)-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.102]
+synonym: "UDP-N-acetyl-D-glucosamine:O-glycosyl-glycoprotein (N-acetyl-D-glucosamine to N-acetyl-D-galactosamine of beta-D-galactosyl-1,3-N-acetyl-D-galactosaminyl-R) beta-1,6-N-acetyl-D-glucosaminyltransferase activity" RELATED []
+synonym: "uridine diphosphoacetylglucosamine-mucin beta-(1,6)-acetylglucosaminyltransferase activity" RELATED []
+synonym: "uridine diphosphoacetylglucosamine-mucin beta-(1->6)-acetylglucosaminyltransferase activity" RELATED []
xref: EC:2.4.1.102
xref: MetaCyc:2.4.1.102-RXN
xref: Reactome:R-HSA-914012 "GCNTs transfer GlcNAc from UDP-GlcNAc to Core 1 mucins"
@@ -28898,24 +28827,24 @@ is_a: GO:0016787 ! hydrolase activity
[Term]
id: GO:0003833
-name: beta-alanyl-dopamine synthase activity
+name: beta-alanyl amine synthase activity
namespace: molecular_function
-def: "Catalysis of the synthesis of beta-alanyl-dopamine from the precursor dopamine (3,4-dihydroxyphenylethylamine)." [GOC:bf, ISBN:0198506732, PMID:12957543]
+def: "Catalysis of the synthesis of beta-alanyl amine conjugate from a precursor biogenetic amine, such as dopamine or histamine." [GOC:bf, ISBN:0198506732, PMID:12900414, PMID:12957543, PMID:25229196]
+synonym: "beta-alanyl-dopamine synthase activity" RELATED []
synonym: "N-beta-alanyl dopamine synthetase activity" EXACT []
synonym: "NBAD transferase activity" EXACT []
-is_a: GO:0016874 ! ligase activity
+is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
[Term]
id: GO:0003834
-name: beta-carotene 15,15'-monooxygenase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: beta-carotene + O(2) = 2 retinal." [EC:1.14.99.36, RHEA:32887]
-comment: Note that this function was formerly EC:1.13.11.21.
-synonym: "beta-carotene 15,15'-dioxygenase activity" EXACT []
-synonym: "beta-carotene:oxygen 15,15'-oxidoreductase (bond-cleaving)" RELATED [EC:1.14.99.36]
-synonym: "carotene 15,15'-dioxygenase activity" RELATED [EC:1.14.99.36]
-synonym: "carotene dioxygenase activity" RELATED [EC:1.14.99.36]
-xref: EC:1.14.99.36
+name: beta-carotene 15,15'-dioxygenase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: all-trans-beta-carotene + O2 = 2 all-trans-retinal." [RHEA:32887]
+comment: Formerly EC:1.13.11.n2, EC:1.13.11.21 and then EC 1.14.99.36.
+synonym: "beta-carotene 15,15'-monooxygenase activity" RELATED []
+synonym: "carotene 15,15'-dioxygenase activity" RELATED [EC:1.13.11.63]
+synonym: "carotene dioxygenase activity" RELATED [EC:1.13.11.63]
+xref: EC:1.13.11.63
xref: KEGG_REACTION:R00032
xref: MetaCyc:BETA-CAROTENE-1515-DIOXYGENASE-RXN
xref: Reactome:R-HSA-975635 "BCMO1:Fe2+ cleaves betaC to atRAL"
@@ -29151,13 +29080,13 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0003845
name: 11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity
namespace: molecular_function
-def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NAD(P)+ = an 11-oxosteroid + NAD(P)H + H(+)." [EC:1.1.1.146, PMID:15761036]
-synonym: "11beta-hydroxy steroid dehydrogenase" RELATED [EC:1.1.1.146]
-synonym: "11beta-hydroxysteroid dehydrogenase" RELATED [EC:1.1.1.146]
-synonym: "beta-hydroxysteroid dehydrogenase" BROAD [EC:1.1.1.146]
-synonym: "corticosteroid 11-reductase" RELATED [EC:1.1.1.146]
-synonym: "corticosteroid 11beta-dehydrogenase" RELATED [EC:1.1.1.146]
-synonym: "dehydrogenase, 11beta-hydroxy steroid" RELATED [EC:1.1.1.146]
+def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NAD(P)+ = an 11-oxosteroid + NAD(P)H + H(+)." [PMID:15761036]
+subset: gocheck_do_not_annotate
+synonym: "11beta-hydroxy steroid dehydrogenase" RELATED []
+synonym: "11beta-hydroxysteroid dehydrogenase" RELATED []
+synonym: "beta-hydroxysteroid dehydrogenase" BROAD []
+synonym: "corticosteroid 11-reductase" RELATED []
+synonym: "corticosteroid 11beta-dehydrogenase" RELATED []
xref: MetaCyc:11-BETA-HYDROXYSTEROID-DEHYDROGENASE-RXN
xref: Reactome:R-HSA-194023 "HSD11B2,HSD11B1 dimer oxidise CORT to COR"
xref: Wikipedia:11beta-hydroxysteroid_dehydrogenase
@@ -29167,7 +29096,7 @@ is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of
id: GO:0003846
name: 2-acylglycerol O-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + 2-acylglycerol = CoA + diacylglycerol." [EC:2.3.1.22]
+def: "Catalysis of the reaction: acyl-CoA + 2-acylglycerol = CoA + diacylglycerol." [PMID:4016575]
synonym: "acyl coenzyme A-monoglyceride acyltransferase activity" RELATED [EC:2.3.1.22]
synonym: "acyl-CoA:2-acylglycerol O-acyltransferase activity" RELATED [EC:2.3.1.22]
synonym: "acylglycerol palmitoyltransferase activity" RELATED [EC:2.3.1.22]
@@ -29828,7 +29757,7 @@ name: ATP citrate synthase activity
namespace: molecular_function
alt_id: GO:0046913
def: "Catalysis of the reaction: acetyl-CoA + ADP + H(+) + oxaloacetate + phosphate = ATP + citrate + CoA." [RHEA:21160]
-comment: Note that this function was formerly EC:4.1.3.8.
+comment: Note that this function was formerly EC:4.1.3.8. Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "acetyl-CoA:oxaloacetate acetyltransferase (isomerizing; ADP- phosphorylating) activity" RELATED [EC:2.3.3.8]
synonym: "acetyl-CoA:oxaloacetate acetyltransferase (isomerizing; ADP-phosphorylating)" RELATED [EC:2.3.3.8]
synonym: "acetyl-CoA:oxaloacetate C-acetyltransferase [(pro-S)-carboxymethyl-forming, ADP-phosphorylating]" RELATED [EC:2.3.3.8]
@@ -30233,6 +30162,7 @@ id: GO:0003906
name: DNA-(apurinic or apyrimidinic site) endonuclease activity
namespace: molecular_function
def: "Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER)." [Wikipedia:AP_endonuclease]
+comment: Note that this term is does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. Class II AP endonuclease is a nuclease, but not Class I, III and IV.
synonym: "abasic deoxyendoribonuclease activity" EXACT []
synonym: "AP deoxyendoribonuclease activity" EXACT []
synonym: "apurinic deoxyendoribonuclease activity" EXACT []
@@ -30415,7 +30345,7 @@ id: GO:0003918
name: DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
namespace: molecular_function
alt_id: GO:0061505
-def: "Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2." [PMID:8811192]
+def: "Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined, driven by ATP hydrolysis. The enzyme changes the linking number in multiples of 2." [PMID:8811192]
synonym: "deoxyribonucleate topoisomerase" BROAD [GOC:krc]
synonym: "deoxyribonucleic topoisomerase activity" BROAD [EC:5.6.2.2, GOC:krc]
synonym: "DNA topoisomerase (ATP-hydrolysing)" RELATED [EC:5.6.2.2, GOC:krc]
@@ -30430,7 +30360,7 @@ xref: EC:5.6.2.2
xref: MetaCyc:5.99.1.3-RXN
xref: Wikipedia:Type_II_topoisomerase
is_a: GO:0003916 ! DNA topoisomerase activity
-is_a: GO:0008094 ! ATPase, acting on DNA
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
[Term]
id: GO:0003919
@@ -31111,8 +31041,7 @@ synonym: "NAD(P)H: menadione oxidoreductase activity" BROAD [EC:1.6.5.2]
synonym: "NAD(P)H:(quinone-acceptor)oxidoreductase activity" RELATED [EC:1.6.5.2]
synonym: "NAD(P)H:quinone oxidoreductase activity" RELATED [EC:1.6.5.2]
synonym: "NADH-menadione reductase activity" NARROW [EC:1.6.5.2]
-synonym: "Naphthoquinone reductase activity" NARROW [EC:1.6.5.2]
-synonym: "naphthoquinone reductase activity" NARROW []
+synonym: "naphthoquinone reductase activity" NARROW [EC:1.6.5.2]
synonym: "NQO1" RELATED []
synonym: "p-benzoquinone reductase activity" NARROW [EC:1.6.5.2]
synonym: "phylloquinone reductase activity" NARROW [EC:1.6.5.2]
@@ -31445,16 +31374,25 @@ is_a: GO:0008452 ! RNA ligase activity
id: GO:0003973
name: (S)-2-hydroxy-acid oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-2-hydroxy-acid + O2 = 2-oxo acid + hydrogen peroxide." [EC:1.1.3.15]
-synonym: "(S)-2-hydroxy-acid:oxygen 2-oxidoreductase" RELATED [EC:1.1.3.15]
+alt_id: GO:0008891
+alt_id: GO:0052852
+alt_id: GO:0052853
+alt_id: GO:0052854
+def: "Catalysis of the reaction: (S)-2-hydroxy-acid + O2 = 2-oxo acid + hydrogen peroxide." [RHEA:16789]
+synonym: "glycolate oxidase activity" RELATED []
synonym: "hydroxy-acid oxidase A activity" NARROW [EC:1.1.3.15]
synonym: "hydroxy-acid oxidase B activity" NARROW [EC:1.1.3.15]
-synonym: "hydroxyacid oxidase A" RELATED [EC:1.1.3.15]
-synonym: "L-2-hydroxy acid oxidase" RELATED [EC:1.1.3.15]
-synonym: "L-alpha-hydroxy acid oxidase" RELATED [EC:1.1.3.15]
-synonym: "oxidase, L-2-hydroxy acid" RELATED [EC:1.1.3.15]
+synonym: "hydroxyacid oxidase A" RELATED []
+synonym: "L-2-hydroxy acid oxidase" RELATED []
+synonym: "L-alpha-hydroxy acid oxidase" RELATED []
+synonym: "long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity" NARROW []
+synonym: "medium-chain-(S)-2-hydroxy-acid oxidase activity" NARROW []
+synonym: "very-long-chain-(S)-2-hydroxy-acid oxidase activity" NARROW []
xref: EC:1.1.3.15
+xref: MetaCyc:RXN-969
xref: MetaCyc:S-2-HYDROXY-ACID-OXIDASE-RXN
+xref: Reactome:R-HSA-389842 "HAO1 tetramer oxidizes glycolate to glyoxylate"
+xref: Reactome:R-HSA-6787811 "HAO2 tetramer oxidises 2OH-PALM"
xref: RHEA:16789
is_a: GO:0016899 ! oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor
@@ -33046,6 +32984,7 @@ id: GO:0004068
name: aspartate 1-decarboxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-aspartate = beta-alanine + CO2." [EC:4.1.1.11]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "aspartate alpha-decarboxylase activity" RELATED [EC:4.1.1.11]
synonym: "aspartic alpha-decarboxylase" BROAD [EC:4.1.1.11]
synonym: "L-aspartate 1-carboxy-lyase (beta-alanine-forming)" RELATED [EC:4.1.1.11]
@@ -33589,22 +33528,27 @@ is_a: GO:0004601 ! peroxidase activity
id: GO:0004097
name: catechol oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 catechol + O2 = 2 1,2-benzoquinone + 2 H2O." [EC:1.10.3.1]
+alt_id: GO:0036263
+alt_id: GO:0036264
+alt_id: GO:0102316
+def: "Catalysis of the reaction: 2 L-dopa + O2 = 2 H2O + 2 L-dopaquinone. This reaction catalyzes exclusively the oxidation of catechols (i.e., o-diphenols) to the corresponding o-quinones." [EC:1.10.3.1, PMID:22120533]
comment: GO:0004097 describes oxidation of catechols (i.e., o-diphenols) to the corresponding o-quinones. For monooxygenation of monophenols, consider instead the term 'monophenol monooxygenase activity ; GO:0004503'.
-synonym: "1,2-benzenediol:oxygen oxidoreductase activity" RELATED [EC:1.10.3.1]
-synonym: "catecholase" BROAD [EC:1.10.3.1]
-synonym: "diphenol oxidase activity" RELATED [EC:1.10.3.1]
-synonym: "dopa oxidase" BROAD [EC:1.10.3.1]
-synonym: "o-diphenol oxidoreductase" BROAD [EC:1.10.3.1]
-synonym: "o-diphenol:oxygen oxidoreductase" BROAD [EC:1.10.3.1]
-synonym: "o-diphenolase activity" RELATED [EC:1.10.3.1]
+synonym: "catecholase" EXACT [EC:1.10.3.1]
+synonym: "diphenol oxidase activity" EXACT [EC:1.10.3.1]
+synonym: "dopamine monooxygenase activity" NARROW []
+synonym: "L-DOPA monooxygenase activity" NARROW []
+synonym: "L-dopa oxidase activity" NARROW []
+synonym: "o-diphenol oxidoreductase" EXACT []
+synonym: "o-diphenolase activity" EXACT [EC:1.10.3.1]
synonym: "phenolase activity" BROAD [EC:1.10.3.1]
synonym: "polyphenol oxidase activity" RELATED [EC:1.10.3.1]
-synonym: "pyrocatechol oxidase" BROAD [EC:1.10.3.1]
+synonym: "pyrocatechol oxidase" BROAD []
synonym: "tyrosinase activity" BROAD [EC:1.10.3.1]
xref: EC:1.10.3.1
xref: MetaCyc:CATECHOL-OXIDASE-RXN
+xref: MetaCyc:RXN-13061
xref: RHEA:21632
+is_a: GO:0004497 ! monooxygenase activity
is_a: GO:0016682 ! oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
[Term]
@@ -34125,7 +34069,9 @@ xref: Reactome:R-HSA-163214 "Electron transfer from reduced cytochrome c to mole
xref: RHEA:11436
is_a: GO:0009055 ! electron transfer activity
is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity
is_a: GO:0016675 ! oxidoreductase activity, acting on a heme group of donors
+is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0004130
@@ -34638,17 +34584,17 @@ is_a: GO:0016634 ! oxidoreductase activity, acting on the CH-CH group of donors,
[Term]
id: GO:0004159
-name: dihydrouracil dehydrogenase (NAD+) activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 5,6-dihydrouracil + NAD+ = uracil + NADH + H+." [EC:1.3.1.1]
-synonym: "5,6-dihydrouracil:NAD+ oxidoreductase activity" RELATED [EC:1.3.1.1]
-synonym: "dehydrogenase, dihydrouracil" RELATED [EC:1.3.1.1]
-synonym: "pyrimidine reductase activity" RELATED [EC:1.3.1.1]
-synonym: "thymine reductase activity" RELATED [EC:1.3.1.1]
-synonym: "uracil reductase activity" RELATED [EC:1.3.1.1]
+name: dihydropyrimidine dehydrogenase (NAD+) activity
+namespace: molecular_function
+def: "Catalysis of the reaction: a 5,6-dihydropyrimidine (5,6-dihydrouracil or 5,6-dihydrothymine) + NAD+ = a pyrimidine (uracil or thymine) + NADH + H+." [PMID:23150645]
+synonym: "5,6-dihydrouracil:NAD+ oxidoreductase activity" RELATED []
+synonym: "dihydrothymine dehydrogenase (NAD+) activity" NARROW []
+synonym: "dihydrouracil dehydrogenase (NAD+) activity" NARROW []
+synonym: "pyrimidine reductase activity" RELATED []
+synonym: "thymine reductase activity" NARROW []
+synonym: "uracil reductase activity" NARROW []
xref: EC:1.3.1.1
xref: MetaCyc:DIHYDROURACIL-DEHYDROGENASE-NAD+-RXN
-xref: RHEA:20189
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
[Term]
@@ -34724,14 +34670,14 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0004164
name: diphthine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-adenosyl-L-methionine + 2-(3-carboxy-3-aminopropyl)-L-histidine = S-adenosyl-L-homocysteine + 2-(3-carboxy-3-(methylammonio)propyl)-L-histidine." [EC:2.1.1.98]
+def: "Catalysis of the reaction: S-adenosyl-L-methionine + 2-(3-carboxy-3-aminopropyl)-L-histidine = S-adenosyl-L-homocysteine + 2-(3-carboxy-3-(methylammonio)propyl)-L-histidine." [PMID:15485916, PMID:20873788, PMID:3042777]
synonym: "diphthine methyltransferase activity" RELATED [EC:2.1.1.98]
synonym: "S-adenosyl-L-methionine:2-(3-carboxy-3-aminopropyl)-L-histidine methyltransferase activity" RELATED [EC:2.1.1.98]
synonym: "S-adenosyl-L-methionine:elongation factor 2 methyltransferase activity" RELATED [EC:2.1.1.98]
xref: EC:2.1.1.98
xref: MetaCyc:RXN-11370
xref: Reactome:R-HSA-5358484 "DPH5 transfers four methyl groups from AdoMet to aminocarboxypropyl EEF2"
-xref: RHEA:20145
+xref: RHEA:36415
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
@@ -34748,7 +34694,6 @@ synonym: "delta3,Delta2-enoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
synonym: "delta3-cis-delta2-trans-enoyl-CoA isomerase" BROAD [EC:5.3.3.8]
synonym: "dodecenoyl-CoA (3Z)-(2E)-isomerase activity" RELATED [EC:5.3.3.8]
synonym: "dodecenoyl-CoA D-isomerase activity" EXACT []
-synonym: "dodecenoyl-CoA Delta-isomerase activity" RELATED [EC:5.3.3.8]
synonym: "dodecenoyl-CoA delta3-cis-delta2-trans-isomerase activity" RELATED [EC:5.3.3.8]
synonym: "dodecenoyl-CoA isomerase activity" RELATED [EC:5.3.3.8]
xref: EC:5.3.3.8
@@ -35012,11 +34957,11 @@ id: GO:0004176
name: ATP-dependent peptidase activity
namespace: molecular_function
alt_id: GO:0004280
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the hydrolysis of peptide bonds." [GOC:mah]
+def: "Catalysis of the hydrolysis of peptide bonds, driven by ATP hydrolysis." [GOC:mah]
synonym: "ATP-dependent proteolysis" RELATED [GOC:mah]
xref: Reactome:R-HSA-9698929 "pPR-AP:pAP cleaves the MCP:pPR-AP:pAP Complex"
is_a: GO:0008233 ! peptidase activity
-is_a: GO:0016887 ! ATPase
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0004177
@@ -37212,32 +37157,37 @@ is_a: GO:0016419 ! S-malonyltransferase activity
id: GO:0004315
name: 3-oxoacyl-[acyl-carrier-protein] synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]." [EC:2.3.1.41]
+alt_id: GO:0033817
+def: "Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]." [RHEA:22836]
synonym: "3-ketoacyl-acyl carrier protein synthase activity" RELATED [EC:2.3.1.41]
synonym: "3-oxoacyl-[acyl-carrier protein] synthase activity" EXACT []
synonym: "3-oxoacyl-ACP synthase activity" EXACT []
+synonym: "3-oxoacyl-acyl carrier protein synthase I activity" NARROW [EC:2.3.1.179]
synonym: "3-oxoacyl-acyl-carrier-protein synthase activity" RELATED [EC:2.3.1.41]
-synonym: "3-oxoacyl:ACP synthase I" RELATED [EC:2.3.1.41]
+synonym: "3-oxoacyl:ACP synthase I" NARROW [EC:2.3.1.41]
synonym: "acyl-acyl-carrier-protein:malonyl-acyl-carrier-protein C-acyltransferase (decarboxylating)" RELATED [EC:2.3.1.41]
synonym: "acyl-malonyl acyl carrier protein-condensing enzyme activity" RELATED [EC:2.3.1.41]
synonym: "acyl-malonyl(acyl-carrier-protein)-condensing enzyme activity" RELATED [EC:2.3.1.41]
synonym: "beta-ketoacyl acyl carrier protein synthase activity" RELATED [EC:2.3.1.41]
synonym: "beta-ketoacyl synthetase activity" RELATED [EC:2.3.1.41]
synonym: "beta-ketoacyl-[acyl carrier protein] synthase activity" RELATED [EC:2.3.1.41]
-synonym: "beta-ketoacyl-ACP synthase I activity" RELATED [EC:2.3.1.41]
+synonym: "beta-ketoacyl-ACP synthase I activity" NARROW [EC:2.3.1.41]
+synonym: "beta-ketoacyl-ACP synthase II activity" NARROW [EC:2.3.1.179]
synonym: "beta-ketoacyl-ACP synthetase activity" RELATED [EC:2.3.1.41]
synonym: "beta-ketoacyl-acyl carrier protein synthase activity" RELATED [EC:2.3.1.41]
synonym: "beta-ketoacyl-acyl carrier protein synthetase activity" RELATED [EC:2.3.1.41]
-synonym: "beta-ketoacyl-acyl-carrier-protein synthase I" RELATED [EC:2.3.1.41]
+synonym: "beta-ketoacyl-acyl-carrier-protein synthase I" NARROW [EC:2.3.1.41]
+synonym: "beta-ketoacyl-acyl-carrier-protein synthase II activity" NARROW []
synonym: "beta-ketoacylsynthase activity" RELATED [EC:2.3.1.41]
synonym: "condensing enzyme activity" BROAD [EC:2.3.1.41]
-synonym: "FabB" RELATED [EC:2.3.1.41]
-synonym: "FabF1" RELATED [EC:2.3.1.41]
synonym: "fatty acid condensing enzyme activity" BROAD [EC:2.3.1.41]
synonym: "KAS I activity" NARROW [EC:2.3.1.41]
-synonym: "KASI" RELATED [EC:2.3.1.41]
+synonym: "KAS II" NARROW [EC:2.3.1.179]
+synonym: "KASI" NARROW [EC:2.3.1.41]
+synonym: "KASII" NARROW [EC:2.3.1.179]
synonym: "ketoacyl-ACP synthase activity" EXACT []
xref: EC:2.3.1.41
+xref: MetaCyc:2.3.1.179-RXN
xref: MetaCyc:3-OXOACYL-ACP-SYNTH-RXN
xref: RHEA:22836
is_a: GO:0004312 ! fatty acid synthase activity
@@ -37246,7 +37196,7 @@ is_a: GO:0004312 ! fatty acid synthase activity
id: GO:0004316
name: 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ = 3-oxoacyl-[acyl-carrier protein] + NADPH + H+." [EC:1.1.1.100]
+def: "Catalysis of the reaction: (3R)-3-hydroxyacyl-[acyl-carrier protein] + NADP+ = 3-oxoacyl-[acyl-carrier protein] + NADPH + H+." [RHEA:17397]
synonym: "(3R)-3-hydroxyacyl-acyl-carrier-protein:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.100]
synonym: "3-ketoacyl acyl carrier protein reductase activity" RELATED [EC:1.1.1.100]
synonym: "3-oxoacyl-[acyl-carrier protein] reductase activity" EXACT []
@@ -37329,6 +37279,7 @@ id: GO:0004320
name: oleoyl-[acyl-carrier-protein] hydrolase activity
namespace: molecular_function
def: "Catalysis of the reaction: oleoyl-[acyl-carrier protein] + H2O = [acyl-carrier protein] + oleate." [EC:3.1.2.14]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "oleoyl-[acyl-carrier protein] hydrolase activity" EXACT []
synonym: "oleoyl-ACP hydrolase activity" EXACT []
synonym: "oleoyl-ACP thioesterase activity" RELATED [EC:3.1.2.14]
@@ -37357,7 +37308,7 @@ is_a: GO:0016408 ! C-acyltransferase activity
id: GO:0004322
name: ferroxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O." [RHEA:11149]
+def: "Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O." [RHEA:11148]
synonym: "caeruloplasmin" NARROW []
synonym: "ceruloplasmin" NARROW [EC:1.16.3.1]
synonym: "Fe(II):oxygen oxidoreductase activity" RELATED []
@@ -37377,7 +37328,7 @@ xref: Reactome:R-HSA-5621402 "Defective CP does not oxidise Fe2+ to Fe3+"
xref: Reactome:R-HSA-5691107 "FTMT 24mer oxidises 4Fe2+ to 4Fe(3+)O(OH)"
xref: Reactome:R-HSA-917891 "SLC40A1:CP:6Cu2+ oxidises Fe2+ to Fe3+"
xref: Reactome:R-HSA-917933 "SLC40A1:HEPH:6Cu2+ oxidises 4Fe2+ to 4Fe3+"
-xref: RHEA:11149
+xref: RHEA:11148
is_a: GO:0016724 ! oxidoreductase activity, acting on metal ions, oxygen as acceptor
[Term]
@@ -37794,8 +37745,7 @@ synonym: "glucose 6-phosphate dehydrogenase (NADP) activity" EXACT []
synonym: "glucose-6-phosphate 1-dehydrogenase activity" EXACT []
synonym: "NADP-dependent glucose 6-phosphate dehydrogenase activity" EXACT []
synonym: "NADP-glucose-6-phosphate dehydrogenase activity" EXACT []
-synonym: "Zwischenferment" RELATED []
-synonym: "zwischenferment" RELATED [EC:1.1.1.49]
+synonym: "Zwischenferment" RELATED [EC:1.1.1.49]
xref: EC:1.1.1.49
xref: MetaCyc:GLU6PDEHYDROG-RXN
xref: Reactome:R-HSA-70377 "alpha-D-glucose 6-phosphate + NADP+ => D-glucono-1,5-lactone 6-phosphate + NADPH + H+"
@@ -37978,6 +37928,7 @@ id: GO:0004354
name: glutamate dehydrogenase (NADP+) activity
namespace: molecular_function
def: "Catalysis of the reaction: L-glutamate + H2O + NADP+ = 2-oxoglutarate + NH3 + NADPH + H+." [EC:1.4.1.4]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "dehydrogenase, glutamate (nicotinamide adenine dinucleotide (phosphate))" RELATED [EC:1.4.1.4]
synonym: "glutamic acid dehydrogenase" BROAD [EC:1.4.1.4]
synonym: "glutamic dehydrogenase activity" BROAD [EC:1.4.1.4]
@@ -38617,7 +38568,6 @@ comment: Note that most helicases catalyze processive duplex unwinding.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
subset: goslim_yeast
synonym: "ATP-dependent helicase activity" EXACT []
@@ -38625,13 +38575,14 @@ xref: Reactome:R-HSA-169461 "MCM8 mediated fork unwinding"
xref: Reactome:R-HSA-169468 "MCM2-7 mediated fork unwinding"
xref: Reactome:R-HSA-5686410 "BLM mediates dissolution of double Holliday junction"
xref: Reactome:R-HSA-5690996 "ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA"
-is_a: GO:0008094 ! ATPase, acting on DNA
+is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0004392
name: heme oxygenase (decyclizing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: heme + 3 donor-H2 + 3 O2 = biliverdin + Fe2+ + CO + 3 acceptor + 3 H2O." [EC:1.14.14.18]
+def: "Catalysis of the reaction: heme b + 3 O2 + 3 reduced [NADPH-hemoprotein reductase] = biliverdin + CO + Fe2+ + H+ + 3 H2O + 3 oxidized [NADPH-hemoprotein reductase]." [RHEA:21764]
synonym: "haem oxidase activity" RELATED [EC:1.14.14.18]
synonym: "haem oxygenase (decyclizing) activity" EXACT []
synonym: "haem oxygenase activity" RELATED [EC:1.14.14.18]
@@ -38643,7 +38594,7 @@ xref: EC:1.14.14.18
xref: MetaCyc:HEME-OXYGENASE-DECYCLIZING-RXN
xref: Reactome:R-HSA-189398 "HMOX1 dimer, HMOX2 cleave heme"
xref: RHEA:21764
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0004394
@@ -38819,7 +38770,7 @@ is_a: GO:0061733 ! peptide-lysine-N-acetyltransferase activity
id: GO:0004407
name: histone deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes." [EC:3.5.1.98, PMID:9893272]
+def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes." [PMID:9893272, RHEA:58196]
xref: EC:3.5.1.98
xref: MetaCyc:3.5.1.98-RXN
xref: Reactome:R-HSA-2545203 "Deacetylation of cleaved cohesin"
@@ -39050,9 +39001,11 @@ is_a: GO:0016833 ! oxo-acid-lyase activity
id: GO:0004420
name: hydroxymethylglutaryl-CoA reductase (NADPH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-mevalonate + CoA + 2 NADP(+) = (S)-3-hydroxy-3-methylglutaryl-CoA + 2 H(+) + 2 NADPH." [EC:1.1.1.34, RHEA:15989]
+alt_id: GO:0042282
+def: "Catalysis of the reaction: (R)-mevalonate + CoA + 2 NADP(+) = (S)-3-hydroxy-3-methylglutaryl-CoA + 2 H(+) + 2 NADPH." [PMID:29224355, RHEA:15989]
synonym: "3-hydroxy-3-methylglutaryl-coenzyme A reductase activity" BROAD [EC:1.1.1.34]
synonym: "HMG-CoA reductase activity" BROAD [EC:1.1.1.34]
+synonym: "hydroxymethylglutaryl-CoA reductase activity" RELATED []
xref: EC:1.1.1.34
xref: KEGG_REACTION:R02082
xref: MetaCyc:1.1.1.34-RXN
@@ -39646,13 +39599,13 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0004458
name: D-lactate dehydrogenase (cytochrome) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c." [EC:1.1.2.4]
-synonym: "(R)-lactate:ferricytochrome-c 2-oxidoreductase activity" RELATED [EC:1.1.2.4]
-synonym: "cytochrome-dependent D-(-)-lactate dehydrogenase activity" RELATED [EC:1.1.2.4]
+def: "Catalysis of the reaction: (R)-lactate + 2 [Fe(III)cytochrome c] = 2 [Fe(II)cytochrome c] + 2 H+ + pyruvate." [RHEA:13521]
+synonym: "(R)-lactate:ferricytochrome-c 2-oxidoreductase activity" EXACT []
+synonym: "cytochrome-dependent D-(-)-lactate dehydrogenase activity" RELATED []
synonym: "D-(-)-lactic cytochrome c reductase activity" RELATED [EC:1.1.2.4]
synonym: "D-lactate (cytochrome) dehydrogenase activity" RELATED [EC:1.1.2.4]
synonym: "D-lactate ferricytochrome c oxidoreductase activity" RELATED [EC:1.1.2.4]
-synonym: "D-lactate-cytochrome c reductase activity" RELATED [EC:1.1.2.4]
+synonym: "D-lactate-cytochrome c reductase activity" RELATED []
synonym: "lactic acid dehydrogenase activity" BROAD [EC:1.1.2.4]
xref: EC:1.1.2.4
xref: MetaCyc:D-LACTATE-DEHYDROGENASE-CYTOCHROME-RXN
@@ -39680,7 +39633,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0004460
name: L-lactate dehydrogenase (cytochrome) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c." [EC:1.1.2.3]
+def: "Catalysis of the reaction: (S)-lactate + 2 [Fe(III)cytochrome c] = 2 [Fe(II)cytochrome c] + 2 H+ + pyruvate." [RHEA:19909]
synonym: "(S)-lactate:ferricytochrome-c 2-oxidoreductase activity" RELATED [EC:1.1.2.3]
synonym: "cytochrome b2" RELATED []
synonym: "cytochrome b2 (flavin-free derivative of flavocytochrome b2)" RELATED [EC:1.1.2.3]
@@ -39821,6 +39774,7 @@ name: long-chain fatty acid-CoA ligase activity
namespace: molecular_function
alt_id: GO:0003996
def: "Catalysis of the reaction: ATP + a long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; a long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [RHEA:15421]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "acyl-activating enzyme activity" BROAD []
synonym: "acyl-CoA ligase activity" RELATED []
synonym: "acyl-CoA synthetase activity" RELATED [EC:6.2.1.3]
@@ -40534,40 +40488,33 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
[Term]
id: GO:0004503
-name: monophenol monooxygenase activity
+name: tyrosinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tyrosine + L-DOPA + O2 = L-DOPA + DOPAquinone + H2O." [EC:1.14.18.1, GOC:bf, GOC:sart, PMID:4965136]
+def: "Catalysis of the reaction: L-tyrosine + O2 = L-DOPAquinone + H2O. This reaction can use both monophenols (such as tyrosine) and catechols (o-diphenols) as substrates." [PMID:4965136, RHEA:18117]
comment: In mammals, L-DOPA can act as a cofactor for the catalyzed reaction; therefore in some resources L-DOPA is shown on both sides of the reaction. GO:0004503 describes the monooxygenation of the monophenol, L-tyrosine. For oxidation of diphenols (including L-DOPA and dopamine), consider instead the term 'catechol oxidase activity ; GO:0004097' and its children.
-synonym: "catecholase" RELATED [EC:1.14.18.1]
-synonym: "chlorogenic acid oxidase activity" RELATED [EC:1.14.18.1]
-synonym: "chlorogenic oxidase activity" RELATED [EC:1.14.18.1]
+synonym: "catecholase" RELATED []
+synonym: "chlorogenic acid oxidase activity" RELATED []
+synonym: "chlorogenic oxidase activity" RELATED []
synonym: "cresolase activity" RELATED [EC:1.14.18.1]
-synonym: "dopa oxidase" RELATED [EC:1.14.18.1]
+synonym: "dopa oxidase" RELATED []
synonym: "L-tyrosine monooxygenase activity" EXACT [GOC:bf]
-synonym: "monophenol dihydroxyphenylalanine:oxygen oxidoreductase activity" RELATED [EC:1.14.18.1]
-synonym: "monophenol monooxidase activity" RELATED [EC:1.14.18.1]
+synonym: "monophenol monooxidase activity" RELATED []
+synonym: "monophenol monooxygenase activity" EXACT [EC:1.14.18.1]
synonym: "monophenol oxidase activity" RELATED [EC:1.14.18.1]
-synonym: "monophenol oxygenase" EXACT [PMID:2494997]
-synonym: "monophenol, dihydroxy-L-phenylalanine oxygen oxidoreductase activity" RELATED [EC:1.14.18.1]
-synonym: "monophenol,L-dopa:oxygen oxidoreductase activity" RELATED [EC:1.14.18.1]
-synonym: "monophenolase activity" RELATED [EC:1.14.18.1]
+synonym: "monophenol oxygenase" EXACT [EC:1.14.18.1, PMID:2494997]
+synonym: "monophenolase activity" RELATED []
synonym: "N-acetyl-6-hydroxytryptophan oxidase activity" RELATED [EC:1.14.18.1]
-synonym: "o-diphenol oxidase activity" RELATED [EC:1.14.18.1]
-synonym: "o-diphenol oxidoreductase" RELATED [EC:1.14.18.1]
+synonym: "o-diphenol oxidase activity" RELATED []
+synonym: "o-diphenol oxidoreductase" RELATED []
synonym: "o-diphenol:O2 oxidoreductase activity" RELATED [EC:1.14.18.1]
-synonym: "o-diphenol:oxygen oxidoreductase" RELATED [EC:1.14.18.1]
synonym: "phenol oxidase activity" BROAD []
synonym: "phenolase activity" BROAD [EC:1.14.18.1]
-synonym: "polyaromatic oxidase activity" RELATED [EC:1.14.18.1]
-synonym: "polyphenolase activity" RELATED [EC:1.14.18.1]
synonym: "prophenol oxidase activity" RELATED [GOC:sart]
synonym: "prophenoloxidase activity" RELATED []
-synonym: "pyrocatechol oxidase" BROAD [EC:1.14.18.1]
-synonym: "tyrosinase activity" RELATED [EC:1.14.18.1]
+synonym: "pyrocatechol oxidase" BROAD []
synonym: "tyrosine-dopa oxidase activity" RELATED [EC:1.14.18.1]
xref: EC:1.14.18.1
xref: MetaCyc:MONOPHENOL-MONOOXYGENASE-RXN
-xref: RHEA:18117
is_a: GO:0016716 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen
[Term]
@@ -40811,7 +40758,7 @@ is_a: GO:0070566 ! adenylyltransferase activity
id: GO:0004516
name: nicotinate phosphoribosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H(+) + nicotinate." [EC:6.3.4.21, RHEA:13393]
+def: "Catalysis of the reaction: diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H(+) + nicotinate." [PMID:7503993]
synonym: "niacin ribonucleotidase activity" RELATED [EC:6.3.4.21]
synonym: "nicotinate-nucleotide:diphosphate phospho-alpha-D-ribosyltransferase activity" RELATED [EC:6.3.4.21]
synonym: "nicotinic acid mononucleotide glycohydrolase activity" RELATED [EC:6.3.4.21]
@@ -40821,7 +40768,7 @@ xref: EC:6.3.4.21
xref: KEGG_REACTION:R01724
xref: MetaCyc:NICOTINATEPRIBOSYLTRANS-RXN
xref: Reactome:R-HSA-197186 "NAPRT1 dimer transfers PRIB to NCA to form NAMN"
-xref: RHEA:13393
+xref: RHEA:36163
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
[Term]
@@ -40852,7 +40799,6 @@ def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN
comment: Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', and 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906' do not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis.
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
is_a: GO:0016788 ! hydrolase activity, acting on ester bonds
@@ -41230,12 +41176,12 @@ is_a: GO:0016798 ! hydrolase activity, acting on glycosyl bonds
id: GO:0004555
name: alpha,alpha-trehalase activity
namespace: molecular_function
-def: "Catalysis of the reaction: alpha,alpha-trehalose + H2O = 2 D-glucose." [EC:3.2.1.28]
+def: "Catalysis of the reaction: alpha,alpha-trehalose + H2O = 2 D-glucose." [PMID:19897915, RHEA:32675]
synonym: "alpha,alpha-trehalose glucohydrolase activity" RELATED [EC:3.2.1.28]
xref: EC:3.2.1.28
xref: MetaCyc:TREHALA-RXN
xref: Reactome:R-HSA-188985 "trehalose + H2O => 2 D-glucose"
-xref: RHEA:20868
+xref: RHEA:32675
is_a: GO:0015927 ! trehalase activity
[Term]
@@ -41280,7 +41226,6 @@ alt_id: GO:0004562
alt_id: GO:0016982
def: "Catalysis of the hydrolysis of terminal, non-reducing alpha-(1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose." [EC:3.2.1.20]
synonym: "acid maltase activity" RELATED [EC:3.2.1.20]
-synonym: "alpha-1,4-glucosidase activity" RELATED [EC:3.2.1.20]
synonym: "alpha-D-glucosidase activity" RELATED [EC:3.2.1.20]
synonym: "alpha-D-glucoside glucohydrolase activity" RELATED [EC:3.2.1.20]
synonym: "alpha-glucopyranosidase activity" RELATED [EC:3.2.1.20]
@@ -41416,19 +41361,12 @@ name: beta-galactosidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides." [EC:3.2.1.23]
comment: Note that the inclusion of 'MetaCyc:BGALACT-PWY' is exceptional: normally MetaCyc pathway entries are database references for biological process terms, not molecular function terms. An exception was made in this case because the MetaCyc entry 'BGALACT-PWY' describes only one reaction, that catalyzed by beta-galactosidase.
-synonym: "beta-D-galactanase activity" RELATED [EC:3.2.1.23]
-synonym: "beta-D-galactoside galactohydrolase activity" RELATED [EC:3.2.1.23]
-synonym: "beta-D-lactosidase activity" RELATED [EC:3.2.1.23]
-synonym: "beta-lactosidase activity" RELATED [EC:3.2.1.23]
+synonym: "beta-D-galactanase activity" RELATED []
+synonym: "beta-D-galactoside galactohydrolase activity" RELATED []
+synonym: "beta-D-lactosidase activity" RELATED []
+synonym: "beta-lactosidase activity" RELATED []
synonym: "exo-(1->4)-beta-D-galactanase activity" RELATED [EC:3.2.1.23]
-synonym: "hydrolact" RELATED [EC:3.2.1.23]
-synonym: "lactose hydrolysis" RELATED []
-synonym: "lactozym" RELATED [EC:3.2.1.23]
-synonym: "maxilact" RELATED [EC:3.2.1.23]
-synonym: "oryzatym" RELATED [EC:3.2.1.23]
-synonym: "S 2107" RELATED [EC:3.2.1.23]
-synonym: "sumiklat" RELATED [EC:3.2.1.23]
-synonym: "trilactase activity" RELATED [EC:3.2.1.23]
+synonym: "hydrolact" RELATED []
xref: EC:3.2.1.23
xref: MetaCyc:3.2.1.23-RXN
xref: MetaCyc:BGALACT-PWY
@@ -41519,7 +41457,6 @@ synonym: "1,2-alpha-mannosyl-oligosaccharide alpha-D-mannohydrolase activity" RE
synonym: "exo-alpha-1,2-mannanase activity" RELATED [EC:3.2.1.113]
synonym: "glycoprotein processing mannosidase I" RELATED [EC:3.2.1.113]
synonym: "Man9-mannosidase activity" NARROW [EC:3.2.1.113]
-synonym: "man9-mannosidase activity" NARROW [EC:3.2.1.113]
synonym: "ManI activity" NARROW [EC:3.2.1.113]
synonym: "mannose-9 processing alpha-mannosidase activity" NARROW [EC:3.2.1.113]
synonym: "mannosidase 1A activity" NARROW [EC:3.2.1.113]
@@ -41569,14 +41506,14 @@ is_a: GO:0015924 ! mannosyl-oligosaccharide mannosidase activity
[Term]
id: GO:0004573
-name: mannosyl-oligosaccharide glucosidase activity
+name: Glc3Man9GlcNAc2 oligosaccharide glucosidase activity
namespace: molecular_function
def: "Catalysis of the exohydrolysis of the non-reducing terminal glucose residue in the mannosyl-oligosaccharide Glc(3)Man(9)GlcNAc(2)." [EC:3.2.1.106]
-synonym: "Glc3Man9NAc2 oligosaccharide glucosidase activity" RELATED [EC:3.2.1.106]
synonym: "mannosyl-oligosaccharide glucohydrolase activity" RELATED [EC:3.2.1.106]
synonym: "mannosyl-oligosaccharide glucosidase (processing A-glucosidase I) activity" EXACT []
+synonym: "mannosyl-oligosaccharide glucosidase activity" RELATED [EC:3.2.1.106]
synonym: "processing A-glucosidase I activity" RELATED [EC:3.2.1.106]
-synonym: "trimming glucosidase I" RELATED [EC:3.2.1.106]
+synonym: "trimming glucosidase I" EXACT [EC:3.2.1.106]
xref: EC:3.2.1.106
xref: MetaCyc:3.2.1.106-RXN
xref: Reactome:R-HSA-4793947 "Defective MOGS does not cleave glucose from an N-glycosylated protein"
@@ -42512,17 +42449,21 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0004623
name: phospholipase A2 activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate." [EC:3.1.1.4]
+alt_id: GO:0102567
+alt_id: GO:0102568
+def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycero-3-phospholipid + H2O = 1-acyl-sn-glycero-3-phospholipid + a fatty acid. This reaction removes the fatty acid attached to the sn2-position. Substrates include phosphatidylcholine, phosphatidylethanolamine, choline plasmalogen and phosphatides." [RHEA:15801]
subset: goslim_chembl
synonym: "cytosolic phospholipase A2 activity" NARROW []
synonym: "lecithinase A activity" RELATED [EC:3.1.1.4]
synonym: "phosphatidase activity" RELATED [EC:3.1.1.4]
synonym: "phosphatidolipase activity" RELATED [EC:3.1.1.4]
synonym: "phosphatidylcholine 2-acylhydrolase activity" RELATED [EC:3.1.1.4]
-synonym: "phospholipase A" RELATED [EC:3.1.1.4]
+synonym: "phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine)" NARROW []
+synonym: "phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)" NARROW []
synonym: "secreted phospholipase A2 activity" NARROW []
xref: EC:3.1.1.4
xref: MetaCyc:PHOSPHOLIPASE-A2-RXN
+xref: MetaCyc:RXN-15067
xref: Reactome:R-HSA-1482604 "PA is hydrolyzed to 1-acyl LPA by PLA2[1] (OM)"
xref: Reactome:R-HSA-1482656 "PA is hydrolysed to 1-acyl LPA by PLA2[1]"
xref: Reactome:R-HSA-1482679 "PA is hydrolysed to 1-acyl LPA by PLA2G2A"
@@ -42937,18 +42878,6 @@ xref: EC:2.4.1.1
xref: MetaCyc:RXN-1826
is_a: GO:0016758 ! hexosyltransferase activity
-[Term]
-id: GO:0004647
-name: phosphoserine phosphatase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: L(or D)-O-phosphoserine + H2O = L(or D)-serine + phosphate, on a free amino acid." [PMID:9188776]
-comment: Do not confuse with protein phosphatases. For protein phosphatases, consider GO:0004722 ; protein serine/threonine phosphatase activity or GO:0008138 ; protein tyrosine/serine/threonine phosphatase activity.
-synonym: "O-phosphoserine phosphohydrolase activity" RELATED [EC:3.1.3.3]
-xref: EC:3.1.3.3
-xref: MetaCyc:PSERPHOSPHA-RXN
-xref: Reactome:R-HSA-977324 "PSPH:Mg2+ dimer dephosphorylates O-P-Ser"
-is_a: GO:0016791 ! phosphatase activity
-
[Term]
id: GO:0004648
name: O-phospho-L-serine:2-oxoglutarate aminotransferase activity
@@ -43405,11 +43334,13 @@ namespace: molecular_function
alt_id: GO:0004695
alt_id: GO:0004696
alt_id: GO:0004700
+alt_id: GO:0106311
def: "Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [GOC:bf, PMID:2956925]
synonym: "protein kinase (phosphorylating) activity" NARROW [EC:2.7.11.1]
synonym: "protein phosphokinase activity" NARROW [EC:2.7.11.1]
synonym: "protein serine kinase activity" NARROW [EC:2.7.11.1]
synonym: "protein serine-threonine kinase activity" RELATED [EC:2.7.11.1]
+synonym: "protein threonine kinase activity" NARROW []
synonym: "protein-serine kinase activity" NARROW [EC:2.7.11.1]
synonym: "serine kinase activity" NARROW [EC:2.7.11.1]
synonym: "serine protein kinase activity" NARROW [EC:2.7.11.1]
@@ -43889,14 +43820,8 @@ id: GO:0004675
name: transmembrane receptor protein serine/threonine kinase activity
namespace: molecular_function
def: "Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate." [EC:2.7.11.30]
-synonym: "activin receptor kinase activity" NARROW [EC:2.7.11.30]
-synonym: "ATP:receptor-protein phosphotransferase activity" RELATED [EC:2.7.11.30]
synonym: "receptor protein serine/threonine kinase activity" RELATED [EC:2.7.11.30]
synonym: "receptor serine/threonine protein kinase activity" RELATED [EC:2.7.11.30]
-synonym: "receptor type I serine/threonine protein kinase activity" NARROW [EC:2.7.11.30]
-synonym: "receptor type II serine/threonine protein kinase activity" NARROW [EC:2.7.11.30]
-synonym: "STK13" RELATED [EC:2.7.11.30]
-synonym: "TGF-beta kinase activity" NARROW [EC:2.7.11.30]
xref: EC:2.7.11.30
xref: MetaCyc:2.7.11.30-RXN
xref: Reactome:R-HSA-170868 "Activated type I receptor phosphorylates SMAD2/3 directly"
@@ -44350,7 +44275,6 @@ alt_id: GO:0004678
def: "Catalysis of the reaction: ATP + G protein-coupled receptor = ADP + G protein-coupled receptor phosphate." [GOC:dph]
synonym: "ATP:G-protein-coupled receptor phosphotransferase activity" RELATED [EC:2.7.11.16]
synonym: "G protein coupled receptor phosphorylating protein kinase activity" EXACT []
-synonym: "G protein-coupled receptor kinase activity" RELATED [EC:2.7.11.16]
synonym: "G-protein coupled receptor kinase activity" RELATED [EC:2.7.11.16]
synonym: "G-protein-coupled receptor phosphorylating protein kinase activity" EXACT []
synonym: "GPCR kinase activity" RELATED [EC:2.7.11.16]
@@ -44522,14 +44446,8 @@ id: GO:0004712
name: protein serine/threonine/tyrosine kinase activity
namespace: molecular_function
def: "Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate." [GOC:mah]
-synonym: "ADK1" RELATED [EC:2.7.12.1]
-synonym: "Arabidopsis dual specificity kinase 1 activity" NARROW [EC:2.7.12.1]
-synonym: "ATP:protein phosphotransferase (Ser/Thr- and Tyr-phosphorylating) activity" RELATED [EC:2.7.12.1]
-synonym: "CLK1" RELATED [EC:2.7.12.1]
-synonym: "dDYRK2" RELATED [EC:2.7.12.1]
-synonym: "dual-specificity kinase activity" BROAD [EC:2.7.12.1]
-synonym: "dual-specificity protein kinase" BROAD []
-synonym: "Mps1p" RELATED [EC:2.7.12.1]
+synonym: "dual-specificity kinase activity" EXACT [EC:2.7.12.1]
+synonym: "dual-specificity protein kinase" EXACT []
synonym: "protein threonine/tyrosine kinase activity" NARROW []
xref: EC:2.7.12.1
xref: Reactome:R-HSA-5672969 "Phosphorylation of RAF"
@@ -44550,11 +44468,8 @@ id: GO:0004713
name: protein tyrosine kinase activity
namespace: molecular_function
alt_id: GO:0004718
-def: "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate." [EC:2.7.10.-]
-synonym: "JAK" NARROW []
-synonym: "Janus kinase activity" NARROW []
+def: "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate." [RHEA:10596]
synonym: "protein-tyrosine kinase activity" EXACT []
-xref: EC:2.7.10.-
xref: Reactome:R-HSA-112333 "SRC autophosphorylation is positively regulated by InlA-bound CDH1"
xref: Reactome:R-HSA-114600 "Fyn/Lyn-mediated phosphorylation of FcR1 gamma"
xref: Reactome:R-HSA-1168394 "STAT5 tyrosine phosphorylation"
@@ -44908,6 +44823,7 @@ xref: Reactome:R-HSA-982807 "JAK2 phosphorylation of GHR"
xref: Reactome:R-HSA-983703 "p-6Y-SYK phosphorylates BLNK (SLP65)"
xref: Reactome:R-HSA-983707 "SYK autophosphorylates at the activated BCR"
xref: Reactome:R-HSA-983709 "LYN, FYN, BLK phosphorylate ITAMs of Ig-alpha (CD79A) and Ig-beta (CD79B)"
+xref: RHEA:10596
is_a: GO:0004672 ! protein kinase activity
[Term]
@@ -44915,21 +44831,8 @@ id: GO:0004714
name: transmembrane receptor protein tyrosine kinase activity
namespace: molecular_function
def: "Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate." [EC:2.7.10.1, GOC:mah]
-synonym: "anaplastic lymphoma kinase activity" NARROW [EC:2.7.10.1]
-synonym: "ATP:protein-L-tyrosine O-phosphotransferase (receptor-type) activity" RELATED [EC:2.7.10.1]
-synonym: "ATP:protein-tyrosine O-phosphotransferase activity" BROAD [EC:2.7.10.1]
-synonym: "Drosophila Eph kinase activity" NARROW [EC:2.7.10.1]
-synonym: "ephrin-B3 receptor tyrosine kinase activity" NARROW [EC:2.7.10.1]
-synonym: "insulin receptor protein-tyrosine kinase activity" NARROW [EC:2.7.10.1]
-synonym: "neurite outgrowth regulating kinase activity" NARROW [EC:2.7.10.1]
-synonym: "neurotrophin TRK receptor activity" RELATED []
-synonym: "neurotrophin TRKA receptor activity" RELATED []
-synonym: "neurotrophin TRKB receptor activity" RELATED []
-synonym: "neurotrophin TRKC receptor activity" RELATED []
-synonym: "novel oncogene with kinase-domain activity" NARROW [EC:2.7.10.1]
synonym: "receptor protein tyrosine kinase activity" RELATED [EC:2.7.10.1]
synonym: "receptor protein-tyrosine kinase activity" RELATED [EC:2.7.10.1]
-synonym: "sevenless receptor activity" RELATED []
xref: EC:2.7.10.1
xref: MetaCyc:2.7.10.1-RXN
xref: Reactome:R-HSA-166544 "TrkA receptor autophosphorylates"
@@ -44975,7 +44878,6 @@ xref: Reactome:R-HSA-8987150 "IL24:IL20RA:p-JAK1:IL20RB:STAT1,STAT3 phosphorylat
xref: Reactome:R-HSA-8987179 "IL20:IL20RA:JAK1:IL20RB:JAK2,JAK3 phosphorylates JAK2,JAK3"
xref: Reactome:R-HSA-8987202 "IFNL1:IFNLR1:JAK1:IL10RB:TYK2 phosphorylates JAK1,TYK2"
xref: Reactome:R-HSA-8987255 "IL26:IL10RB:p-TYK2:IL20RA:p-JAK1:STAT1,STAT3 phosphorylates STAT1,STAT3"
-xref: RHEA:10596
is_a: GO:0004713 ! protein tyrosine kinase activity
is_a: GO:0019199 ! transmembrane receptor protein kinase activity
@@ -45121,39 +45023,23 @@ alt_id: GO:0030357
alt_id: GO:0030358
alt_id: GO:0030360
alt_id: GO:0030361
+alt_id: GO:0106306
+alt_id: GO:0106307
def: "Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate." [GOC:bf]
-synonym: "3-hydroxy 3-methylglutaryl coenzymeA reductase phosphatase" NARROW [EC:3.1.3.16]
-synonym: "Aspergillus awamori acid protein phosphatase" NARROW [EC:3.1.3.16]
-synonym: "BCKDH phosphatase" NARROW [EC:3.1.3.16]
-synonym: "branched-chain alpha-keto acid dehydrogenase phosphatase" NARROW [EC:3.1.3.16]
-synonym: "calcineurin" NARROW []
-synonym: "casein phosphatase" NARROW [EC:3.1.3.16]
-synonym: "HMG-CoA reductase phosphatase" NARROW [EC:3.1.3.16]
synonym: "magnesium-dependent protein serine/threonine phosphatase activity" RELATED []
-synonym: "phosphatase 2A" NARROW [EC:3.1.3.16]
-synonym: "phosphatase 2B" NARROW [EC:3.1.3.16]
-synonym: "phosphatase C-II" NARROW [EC:3.1.3.16]
-synonym: "phosphatase H-II" NARROW [EC:3.1.3.16]
-synonym: "phosphatase I" NARROW [EC:3.1.3.16]
-synonym: "phosphatase IB" NARROW [EC:3.1.3.16]
-synonym: "phosphatase II" NARROW [EC:3.1.3.16]
-synonym: "phosphatase III" NARROW [EC:3.1.3.16]
-synonym: "phosphatase IV" NARROW [EC:3.1.3.16]
-synonym: "phosphatase SP" NARROW [EC:3.1.3.16]
-synonym: "phosphopyruvate dehydrogenase phosphatase" NARROW [EC:3.1.3.16]
-synonym: "phosphospectrin phosphatase" NARROW [EC:3.1.3.16]
-synonym: "polycation modulated (PCM-) phosphatase" NARROW [EC:3.1.3.16]
-synonym: "protein D phosphatase" NARROW [EC:3.1.3.16]
+synonym: "phosphatase I" NARROW []
+synonym: "phosphatase II" NARROW []
+synonym: "phosphatase III" NARROW []
synonym: "protein phosphatase type 1 activity" NARROW []
-synonym: "protein phosphatase type 1, intrinsic catalyst activity" NARROW []
synonym: "protein phosphatase type 2A activity" NARROW []
-synonym: "protein phosphatase type 2A, intrinsic catalyst activity" NARROW []
synonym: "protein phosphatase type 2B activity" NARROW []
-synonym: "protein phosphatase type 2B, intrinsic catalyst activity" NARROW []
synonym: "protein phosphatase type 2C activity" NARROW []
-synonym: "protein phosphatase type 4 activity" NARROW []
-synonym: "protein phosphatase type 4, intrinsic catalyst activity" NARROW []
-synonym: "protein phosphatase X" NARROW []
+synonym: "protein phosphatase-1" NARROW [EC:3.1.3.16]
+synonym: "protein phosphatase-2A" NARROW [EC:3.1.3.16]
+synonym: "protein phosphatase-2B" NARROW [EC:3.1.3.16]
+synonym: "protein phosphatase-2C" NARROW [EC:3.1.3.16]
+synonym: "protein serine phosphatase activity" NARROW []
+synonym: "protein threonine phosphatase activity" NARROW []
synonym: "serine/threonine specific protein phosphatase activity" EXACT []
xref: EC:3.1.3.16
xref: Reactome:R-HSA-1295632 "PPA2A dephosphorylates SPRY2"
@@ -45481,20 +45367,11 @@ id: GO:0004740
name: pyruvate dehydrogenase (acetyl-transferring) kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + pyruvate dehydrogenase (acetyl-transferring) = ADP + pyruvate dehydrogenase (acetyl-transferring) phosphate." [EC:2.7.11.2]
-synonym: "[pyruvate dehydrogenase (lipoamide)] kinase activity" EXACT []
-synonym: "ATP:pyruvate dehydrogenase (acetyl-transferring) phosphotransferase activity" RELATED [EC:2.7.11.2]
synonym: "PDH kinase activity" RELATED [EC:2.7.11.2]
synonym: "PDHK" RELATED [EC:2.7.11.2]
synonym: "PDK" RELATED [EC:2.7.11.2]
-synonym: "PDK1" RELATED [EC:2.7.11.2]
-synonym: "PDK2" RELATED [EC:2.7.11.2]
-synonym: "PDK3" RELATED [EC:2.7.11.2]
-synonym: "PDK4" RELATED [EC:2.7.11.2]
-synonym: "pyruvate dehydrogenase (lipoamide) kinase activity" EXACT []
synonym: "pyruvate dehydrogenase kinase (phosphorylating) activity" RELATED [EC:2.7.11.2]
-synonym: "pyruvate dehydrogenase kinase activator protein activity" NARROW [EC:2.7.11.2]
synonym: "pyruvate dehydrogenase kinase activity" RELATED [EC:2.7.11.2]
-synonym: "STK1" RELATED [EC:2.7.11.2]
xref: EC:2.7.11.2
xref: MetaCyc:2.7.11.2-RXN
xref: Reactome:R-HSA-203946 "PDK isoforms phosphorylate lipo-PDH"
@@ -45650,6 +45527,7 @@ id: GO:0004749
name: ribose phosphate diphosphokinase activity
namespace: molecular_function
def: "Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H(+)." [EC:2.7.6.1, RHEA:15609]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "5-phosphoribose pyrophosphorylase activity" RELATED [EC:2.7.6.1]
synonym: "5-phosphoribosyl-1-pyrophosphate synthetase activity" RELATED [EC:2.7.6.1]
synonym: "5-phosphoribosyl-alpha-1-pyrophosphate synthetase activity" RELATED [EC:2.7.6.1]
@@ -45678,7 +45556,7 @@ is_a: GO:0016778 ! diphosphotransferase activity
[Term]
id: GO:0004750
-name: ribulose-phosphate 3-epimerase activity
+name: D-ribulose-phosphate 3-epimerase activity
namespace: molecular_function
def: "Catalysis of the reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate." [EC:5.1.3.1, RHEA:13677]
synonym: "D-ribulose 5-phosphate epimerase activity" RELATED [EC:5.1.3.1]
@@ -45689,11 +45567,13 @@ synonym: "D-ribulose-5-phosphate epimerase activity" RELATED [EC:5.1.3.1]
synonym: "D-xylulose-5-phosphate 3-epimerase activity" RELATED [EC:5.1.3.1]
synonym: "erythrose-4-phosphate epimerase activity" RELATED [EC:5.1.3.1]
synonym: "erythrose-4-phosphate isomerase activity" RELATED [EC:5.1.3.1]
+synonym: "pentose phosphate epimerase (PPE)" RELATED [PMID:9872416]
synonym: "pentose-5-phosphate 3-epimerase activity" RELATED [EC:5.1.3.1]
synonym: "phosphoketopentose 3-epimerase activity" RELATED [EC:5.1.3.1]
synonym: "phosphoketopentose epimerase activity" RELATED [EC:5.1.3.1]
synonym: "phosphoribulose epimerase activity" RELATED [EC:5.1.3.1]
synonym: "ribulose 5-phosphate 3-epimerase activity" RELATED [EC:5.1.3.1]
+synonym: "ribulose-phosphate 3-epimerase activity" RELATED []
synonym: "xylulose phosphate 3-epimerase activity" RELATED [EC:5.1.3.1]
xref: EC:5.1.3.1
xref: KEGG_REACTION:R01529
@@ -45708,15 +45588,16 @@ id: GO:0004751
name: ribose-5-phosphate isomerase activity
namespace: molecular_function
def: "Catalysis of the reaction: D-ribose 5-phosphate = D-ribulose 5-phosphate." [EC:5.3.1.6, RHEA:14657]
-synonym: "5-phosphoribose isomerase activity" RELATED [EC:5.3.1.6]
-synonym: "D-ribose 5-phosphate isomerase activity" RELATED [EC:5.3.1.6]
-synonym: "D-ribose-5-phosphate aldose-ketose-isomerase activity" RELATED [EC:5.3.1.6]
-synonym: "D-ribose-5-phosphate ketol-isomerase activity" RELATED [EC:5.3.1.6]
-synonym: "phosphopentoseisomerase activity" RELATED [EC:5.3.1.6]
-synonym: "phosphopentosisomerase activity" RELATED [EC:5.3.1.6]
-synonym: "phosphoriboisomerase activity" RELATED [EC:5.3.1.6]
-synonym: "ribose 5-phosphate epimerase activity" RELATED [EC:5.3.1.6]
-synonym: "ribose phosphate isomerase activity" RELATED [EC:5.3.1.6]
+synonym: "5-phosphoribose isomerase activity" EXACT [EC:5.3.1.6]
+synonym: "D-ribose 5-phosphate isomerase activity" EXACT [EC:5.3.1.6]
+synonym: "D-ribose-5-phosphate aldose-ketose-isomerase activity" EXACT [EC:5.3.1.6]
+synonym: "D-ribose-5-phosphate ketol-isomerase activity" EXACT [EC:5.3.1.6]
+synonym: "pentose phosphate isomerase (PPI)" EXACT []
+synonym: "phosphopentoseisomerase activity" EXACT [EC:5.3.1.6]
+synonym: "phosphopentosisomerase activity" EXACT [EC:5.3.1.6]
+synonym: "phosphoriboisomerase activity" EXACT [EC:5.3.1.6]
+synonym: "ribose 5-phosphate epimerase activity" EXACT [EC:5.3.1.6]
+synonym: "ribose phosphate isomerase activity" EXACT [EC:5.3.1.6]
xref: EC:5.3.1.6
xref: KEGG_REACTION:R01056
xref: MetaCyc:RIB5PISOM-RXN
@@ -45732,8 +45613,8 @@ id: GO:0004753
name: saccharopine dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the cleavage of N6-(L-1,3-dicarboxypropyl)-L-lysine to release an amino acid (lysine or glutamate), with the concomitant reduction of an electron acceptor." [GOC:mah]
-synonym: "lysine-2-oxoglutarate reductase activity" RELATED [EC:1.5.1.-]
-synonym: "lysine-ketoglutarate reductase activity" RELATED [EC:1.5.1.-]
+synonym: "lysine-2-oxoglutarate reductase activity" RELATED []
+synonym: "lysine-ketoglutarate reductase activity" RELATED []
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
[Term]
@@ -46034,16 +45915,13 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0004775
name: succinate-CoA ligase (ADP-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + succinate + CoA = ADP + succinyl-CoA + phosphate." [EC:6.2.1.5]
-synonym: "A-SCS" RELATED [EC:6.2.1.5]
-synonym: "A-STK (adenin nucleotide-linked succinate thiokinase)" RELATED [EC:6.2.1.5]
+def: "Catalysis of the reaction: ATP + succinate + CoA = ADP + succinyl-CoA + phosphate." [PMID:9874242, RHEA:17661]
synonym: "succinate thiokinase activity" RELATED [EC:6.2.1.5]
-synonym: "succinate:CoA ligase (ADP-forming) activity" RELATED [EC:6.2.1.5]
-synonym: "succinic thiokinase" BROAD [EC:6.2.1.5]
-synonym: "succinyl coenzyme A synthetase" BROAD [EC:6.2.1.5]
-synonym: "succinyl coenzyme A synthetase (adenosine diphosphate-forming) activity" RELATED [EC:6.2.1.5]
+synonym: "succinic thiokinase" BROAD []
+synonym: "succinyl coenzyme A synthetase" BROAD []
+synonym: "succinyl coenzyme A synthetase (adenosine diphosphate-forming) activity" RELATED []
synonym: "succinyl-CoA synthetase (ADP-forming) activity" RELATED [EC:6.2.1.5]
-synonym: "succinyl-CoA synthetase activity" RELATED [EC:6.2.1.5]
+synonym: "succinyl-CoA synthetase activity" RELATED []
xref: EC:6.2.1.5
xref: KEGG_REACTION:R00405
xref: MetaCyc:SUCCCOASYN-RXN
@@ -46055,18 +45933,13 @@ is_a: GO:0004774 ! succinate-CoA ligase activity
id: GO:0004776
name: succinate-CoA ligase (GDP-forming) activity
namespace: molecular_function
-def: "Catalysis of the reaction: GTP + succinate + CoA = GDP + succinyl-CoA + phosphate." [EC:6.2.1.4]
-synonym: "G-STK" RELATED [EC:6.2.1.4]
-synonym: "P-enzyme" RELATED [EC:6.2.1.4]
-synonym: "SCS" RELATED [EC:6.2.1.4]
-synonym: "succinate-phosphorylating enzyme" RELATED [EC:6.2.1.4]
+def: "Catalysis of the reaction: GTP + succinate + CoA = GDP + succinyl-CoA + phosphate." [RHEA:22120]
synonym: "succinate:CoA ligase (GDP-forming) activity" RELATED [EC:6.2.1.4]
-synonym: "succinic thiokinase" BROAD [EC:6.2.1.4]
-synonym: "succinyl CoA synthetase activity" RELATED [EC:6.2.1.4]
-synonym: "succinyl coenzyme A synthetase" BROAD [EC:6.2.1.4]
-synonym: "succinyl coenzyme A synthetase (GDP-forming) activity" RELATED [EC:6.2.1.4]
-synonym: "succinyl coenzyme A synthetase (guanosine diphosphate-forming) activity" RELATED [EC:6.2.1.4]
-synonym: "succinyl-CoA synthetase (GDP-forming) activity" RELATED [EC:6.2.1.4]
+synonym: "succinyl CoA synthetase activity" RELATED []
+synonym: "succinyl coenzyme A synthetase" BROAD []
+synonym: "succinyl coenzyme A synthetase (GDP-forming) activity" RELATED []
+synonym: "succinyl coenzyme A synthetase (guanosine diphosphate-forming) activity" RELATED []
+synonym: "succinyl-CoA synthetase (GDP-forming) activity" RELATED []
xref: EC:6.2.1.4
xref: KEGG_REACTION:R00432
xref: MetaCyc:SUCCINATE--COA-LIGASE-GDP-FORMING-RXN
@@ -47702,8 +47575,9 @@ name: enzyme inhibitor activity
namespace: molecular_function
alt_id: GO:0048551
def: "Binds to and stops, prevents or reduces the activity of an enzyme." [GOC:ai, GOC:ebc]
+comment: This term should only be used in cases when the regulator directly interacts with the enzyme.
synonym: "metalloenzyme inhibitor activity" NARROW []
-is_a: GO:0003674 ! molecular_function
+is_a: GO:0030234 ! enzyme regulator activity
[Term]
id: GO:0004858
@@ -47913,7 +47787,6 @@ synonym: "ligand-activated sequence-specific DNA binding RNA polymerase II trans
synonym: "ligand-dependent nuclear receptor activity" RELATED [GOC:bf]
synonym: "ligand-dependent transcription factor activity" RELATED [GOC:bf]
synonym: "nuclear hormone receptor" NARROW []
-synonym: "nuclear receptor activity" RELATED [GOC:bf]
synonym: "retinoic acid receptor activity" NARROW []
synonym: "retinoid-X receptor activity" NARROW [GOC:bf]
synonym: "RNA polymerase II transcription factor activity, estrogen-activated sequence-specific DNA binding" NARROW []
@@ -49300,7 +49173,7 @@ consider: GO:0038024
id: GO:0005046
name: KDEL sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a KDEL sequence, the C terminus tetrapeptide sequence Lys-Asp-Glu-Leu found in proteins that are to be retained in the endoplasmic reticulum." [GOC:ai]
+def: "Binding to a KDEL sequence, the C terminus tetrapeptide sequence Lys-Asp-Glu-Leu found in proteins that are to be retained in the endoplasmic reticulum." [GOC:ai]
synonym: "KDEL receptor activity" NARROW []
is_a: GO:0046923 ! ER retention sequence binding
@@ -49308,7 +49181,7 @@ is_a: GO:0046923 ! ER retention sequence binding
id: GO:0005047
name: signal recognition particle binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the signal recognition particle." [ISBN:0198506732]
+def: "Binding to a signal recognition particle." [ISBN:0198506732]
comment: See also the cellular component term 'signal recognition particle, endoplasmic reticulum targeting ; GO:0005786'.
synonym: "docking protein" BROAD []
synonym: "signal recognition particle receptor" NARROW []
@@ -49319,7 +49192,7 @@ id: GO:0005048
name: signal sequence binding
namespace: molecular_function
alt_id: GO:0008249
-def: "Interacting selectively and non-covalently with a signal sequence, a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized." [GOC:ai]
+def: "Binding to a signal sequence, a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized." [GOC:ai]
synonym: "leader sequence binding" NARROW []
synonym: "protein signal sequence binding" NARROW []
synonym: "signal sequence receptor" NARROW []
@@ -49352,7 +49225,7 @@ consider: GO:0038023
id: GO:0005052
name: peroxisome matrix targeting signal-1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 peroxisome targeting signal, a tripeptide with the consensus sequence (S/A/C)-(K/R/H)-L." [GOC:mah, PMID:11687502]
+def: "Binding to a type 1 peroxisome targeting signal, a tripeptide with the consensus sequence (S/A/C)-(K/R/H)-L." [GOC:mah, PMID:11687502]
synonym: "peroxisomal targeting signal 1 (PTS1) binding" EXACT [PMID:14709540]
synonym: "peroxisome targeting signal-1 binding" EXACT []
synonym: "peroxisome targeting signal-1 receptor" NARROW []
@@ -49365,7 +49238,7 @@ is_a: GO:0000268 ! peroxisome targeting sequence binding
id: GO:0005053
name: peroxisome matrix targeting signal-2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 peroxisome targeting signal, a nonapeptide with a broad consensus sequence of (R/K)-(L/V/I)-(XXXXX)-(H/Q)-(L/A/F)." [GOC:mah, PMID:11687502]
+def: "Binding to a type 2 peroxisome targeting signal, a nonapeptide with a broad consensus sequence of (R/K)-(L/V/I)-(XXXXX)-(H/Q)-(L/A/F)." [GOC:mah, PMID:11687502]
synonym: "peroxisomal targeting signal 2 (PTS2) binding" EXACT [PMID:14709540]
synonym: "peroxisome targeting signal-2 binding" EXACT []
synonym: "peroxisome targeting signal-2 receptor" NARROW []
@@ -49563,7 +49436,7 @@ namespace: molecular_function
alt_id: GO:0072568
alt_id: GO:0072569
alt_id: GO:0097024
-def: "Interacting selectively and non-covalently with protein kinase C." [GOC:jl]
+def: "Binding to protein kinase C." [GOC:jl]
synonym: "PKC alpha binding" EXACT []
synonym: "PKC binding" EXACT []
synonym: "PKC delta binding" EXACT [GOC:BHF, GOC:pr]
@@ -49791,7 +49664,7 @@ xref: Reactome:R-HSA-9672163 "SOS-mediated nucleotide exchange on RAS downstream
xref: Reactome:R-HSA-9672170 "SOS-mediated nucleotide exchange of RAS downstream of mutant PDGFR receptors"
xref: Reactome:R-HSA-9695853 "FLT3 mutants:GRB2:SOS1-mediated nucleotide exchange on RAS"
xref: Reactome:R-HSA-9703441 "SOS1-mediated nucleotide exchange of RAS downstream of FLT3 fusion mutants"
-is_a: GO:0005096 ! GTPase activator activity
+is_a: GO:0030695 ! GTPase regulator activity
[Term]
id: GO:0005091
@@ -49885,7 +49758,7 @@ is_a: GO:0030695 ! GTPase regulator activity
id: GO:0005102
name: signaling receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732]
+def: "Binding to one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:bf, GOC:ceb, ISBN:0198506732]
comment: Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'.
subset: goslim_agr
subset: goslim_chembl
@@ -49904,7 +49777,7 @@ name: fibroblast growth factor receptor binding
namespace: molecular_function
alt_id: GO:0001521
alt_id: GO:0005162
-def: "Interacting selectively and non-covalently with the fibroblast growth factor receptor (FGFR)." [GOC:ceb]
+def: "Binding to a fibroblast growth factor receptor (FGFR)." [GOC:ceb]
comment: Note that branchless is the Drosophila gene encoding fibroblast growth factor.
synonym: "FGF receptor binding" EXACT []
synonym: "FGFR binding" EXACT []
@@ -49917,7 +49790,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005105
name: type 1 fibroblast growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the type 1 fibroblast growth factor receptor (FGFR1)." [GOC:ceb, GOC:fb_curators]
+def: "Binding to a type 1 fibroblast growth factor receptor (FGFR1)." [GOC:ceb, GOC:fb_curators]
comment: Note that breathless is the Drosophila gene encoding the type 1 fibroblast growth factor receptor (FGFR1).
synonym: "breathless binding" NARROW []
synonym: "breathless ligand" NARROW []
@@ -49963,7 +49836,7 @@ id: GO:0005109
name: frizzled binding
namespace: molecular_function
alt_id: GO:0005110
-def: "Interacting selectively and non-covalently with a frizzled (fz) receptor." [GOC:ceb]
+def: "Binding to a frizzled (fz) receptor." [GOC:ceb]
subset: goslim_chembl
synonym: "frizzled ligand" NARROW []
synonym: "frizzled-2 binding" NARROW []
@@ -49978,7 +49851,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0005111
name: type 2 fibroblast growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the type 2 fibroblast growth factor receptor (FGFR2)." [GOC:fb_curators]
+def: "Binding to a type 2 fibroblast growth factor receptor (FGFR2)." [GOC:fb_curators]
comment: Note that heartless is the Drosophila gene encoding the type 2 fibroblast growth factor receptor (FGFR2).
synonym: "FGFR2 binding" EXACT []
synonym: "FGFR2 ligand" NARROW []
@@ -49991,7 +49864,7 @@ is_a: GO:0005104 ! fibroblast growth factor receptor binding
id: GO:0005112
name: Notch binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor." [GOC:ceb]
+def: "Binding to a Notch (N) protein, a surface receptor." [GOC:ceb]
synonym: "N binding" EXACT []
synonym: "N ligand" NARROW []
synonym: "Notch ligand" NARROW []
@@ -50002,7 +49875,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005113
name: patched binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the patched (ptc) protein, a receptor for hedgehog proteins." [GOC:ceb, PMID:11731473]
+def: "Binding to a patched (ptc) protein, a receptor for hedgehog proteins." [GOC:ceb, PMID:11731473]
synonym: "patched ligand" NARROW []
synonym: "ptc binding" EXACT []
synonym: "ptc ligand" NARROW []
@@ -50012,7 +49885,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005114
name: type II transforming growth factor beta receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type II transforming growth factor beta receptor." [GOC:ceb, GOC:mah, PMID:11252892]
+def: "Binding to a type II transforming growth factor beta receptor." [GOC:ceb, GOC:mah, PMID:11252892]
synonym: "punt binding" NARROW []
synonym: "punt ligand" NARROW []
synonym: "TGF-beta type II binding" EXACT []
@@ -50025,7 +49898,7 @@ is_a: GO:0005160 ! transforming growth factor beta receptor binding
id: GO:0005115
name: receptor tyrosine kinase-like orphan receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the receptor tyrosine kinase-like orphan receptor (Ror)." [GOC:ceb, GOC:vw]
+def: "Binding to a receptor tyrosine kinase-like orphan receptor (Ror)." [GOC:ceb, GOC:vw]
synonym: "receptor tyrosine kinase-like orphan receptor ligand" NARROW []
synonym: "Ror binding" BROAD []
synonym: "Ror ligand" RELATED []
@@ -50035,7 +49908,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005117
name: wishful thinking binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with wishful thinking (Wit), a type II bone morphogenic protein receptor." [GOC:ceb, PMID:11856529]
+def: "Binding to wishful thinking (Wit), a type II bone morphogenic protein receptor." [GOC:ceb, PMID:11856529]
synonym: "SE20 receptor binding" NARROW []
synonym: "wishful thinking ligand" NARROW []
synonym: "Wit binding" EXACT []
@@ -50046,7 +49919,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005118
name: sevenless binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the sevenless (sev) protein, a receptor tyrosine kinase." [GOC:ceb, PMID:3151175]
+def: "Binding to a sevenless (sev) protein, a receptor tyrosine kinase." [GOC:ceb, PMID:3151175]
synonym: "sev binding" EXACT []
synonym: "sev ligand" NARROW []
synonym: "sevenless ligand" NARROW []
@@ -50056,7 +49929,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005119
name: smoothened binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the smoothened (smo) protein, which interacts with patched to transmit hedgehog signals." [GOC:ceb, PMID:11731473]
+def: "Binding to a smoothened (smo) protein, which interacts with patched to transmit hedgehog signals." [GOC:ceb, PMID:11731473]
synonym: "smo binding" EXACT []
synonym: "smo ligand" NARROW []
synonym: "smoothened ligand" NARROW []
@@ -50066,7 +49939,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0005121
name: Toll binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the Toll protein, a transmembrane receptor." [GOC:ceb]
+def: "Binding to a Toll protein, a transmembrane receptor." [GOC:ceb]
synonym: "Tl binding" EXACT []
synonym: "Toll ligand" NARROW []
synonym: "Toll receptor binding" EXACT []
@@ -50076,7 +49949,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005122
name: torso binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the torso (tor) protein, a receptor tyrosine kinase." [GOC:ceb, PMID:2927509]
+def: "Binding to a torso (tor) protein, a receptor tyrosine kinase." [GOC:ceb, PMID:2927509]
synonym: "tor binding" EXACT []
synonym: "tor ligand" NARROW []
synonym: "torso ligand" NARROW []
@@ -50086,7 +49959,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005123
name: death receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the death receptor (DR) family. The DR family falls within the tumor necrosis factor receptor superfamily and is characterized by a cytoplasmic region of ~80 residues termed the death domain (DD)." [GOC:ceb, GOC:rl, PMID:15654015]
+def: "Binding to a member of the death receptor (DR) family. The DR family falls within the tumor necrosis factor receptor superfamily and is characterized by a cytoplasmic region of ~80 residues termed the death domain (DD)." [GOC:ceb, GOC:rl, PMID:15654015]
subset: goslim_chembl
synonym: "APO binding" NARROW [GOC:rl]
synonym: "death receptor adaptor protein activity" RELATED []
@@ -50106,7 +49979,7 @@ is_a: GO:0032813 ! tumor necrosis factor receptor superfamily binding
id: GO:0005124
name: scavenger receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with scavenger receptors, a family of proteins that are expressed on myeloid cells and are involved in the uptake of effete cellular components and foreign particles." [GOC:ceb]
+def: "Binding to scavenger receptors, a family of proteins that are expressed on myeloid cells and are involved in the uptake of effete cellular components and foreign particles." [GOC:ceb]
synonym: "scavenger receptor ligand" NARROW []
is_a: GO:0005102 ! signaling receptor binding
@@ -50124,7 +49997,7 @@ is_a: GO:0048018 ! receptor ligand activity
id: GO:0005126
name: cytokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cytokine receptor." [GOC:mah, GOC:vw]
+def: "Binding to a cytokine receptor." [GOC:mah, GOC:vw]
synonym: "hematopoietin/interferon-class (D200-domain) cytokine receptor binding" EXACT [GOC:add, GOC:mah]
synonym: "hematopoietin/interferon-class (D200-domain) cytokine receptor ligand" NARROW []
is_a: GO:0005102 ! signaling receptor binding
@@ -50133,7 +50006,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005127
name: ciliary neurotrophic factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the ciliary neurotrophic factor receptor." [GOC:ai]
+def: "Binding to a ciliary neurotrophic factor receptor." [GOC:ai]
synonym: "ciliary neurotrophic factor" NARROW []
synonym: "ciliary neurotrophic factor receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50142,7 +50015,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005128
name: erythropoietin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the erythropoietin receptor." [GOC:ai]
+def: "Binding to an erythropoietin receptor." [GOC:ai]
synonym: "erythropoietin" NARROW []
synonym: "erythropoietin receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50151,7 +50024,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005129
name: granulocyte macrophage colony-stimulating factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the granulocyte macrophage colony-stimulating factor receptor." [GOC:ai]
+def: "Binding to a granulocyte macrophage colony-stimulating factor receptor." [GOC:ai]
synonym: "GM-CSF receptor binding" EXACT [GOC:vk]
synonym: "GM-CSF receptor ligand" NARROW []
synonym: "GMC-SF receptor ligand" NARROW []
@@ -50165,7 +50038,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005130
name: granulocyte colony-stimulating factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the granulocyte colony-stimulating factor receptor." [GOC:ai]
+def: "Binding to a granulocyte colony-stimulating factor receptor." [GOC:ai]
synonym: "G-CSF receptor ligand" EXACT []
synonym: "GC-SF receptor ligand" EXACT []
synonym: "granulocyte colony stimulating factor receptor binding" EXACT []
@@ -50178,7 +50051,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005131
name: growth hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the growth hormone receptor." [GOC:ai]
+def: "Binding to a growth hormone receptor." [GOC:ai]
synonym: "growth hormone" NARROW []
synonym: "growth hormone receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50188,7 +50061,7 @@ is_a: GO:0051427 ! hormone receptor binding
id: GO:0005132
name: type I interferon receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an interferon-type I receptor, a heterodimeric complex composed of an alpha subunit (IFNAR1) and a beta subunit (IFNAR2)." [GOC:ai, GOC:signaling, PMID:17502368]
+def: "Binding to an interferon-type I receptor, a heterodimeric complex composed of an alpha subunit (IFNAR1) and a beta subunit (IFNAR2)." [GOC:ai, GOC:signaling, PMID:17502368]
synonym: "IFNAR binding" RELATED [PMID:17502368]
synonym: "IFNAR1 binding" NARROW [PR:000008922]
synonym: "IFNAR2 binding" NARROW [PR:000008923]
@@ -50202,7 +50075,7 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0005133
name: interferon-gamma receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interferon-gamma receptor." [GOC:ai]
+def: "Binding to an interferon-gamma receptor." [GOC:ai]
synonym: "interferon-gamma" NARROW []
synonym: "interferon-gamma receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50211,7 +50084,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005134
name: interleukin-2 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-2 receptor." [GOC:ai]
+def: "Binding to an interleukin-2 receptor." [GOC:ai]
synonym: "IL-2" NARROW []
synonym: "interleukin-2 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50221,7 +50094,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005135
name: interleukin-3 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-3 receptor." [GOC:ai]
+def: "Binding to an interleukin-3 receptor." [GOC:ai]
synonym: "IL-3" NARROW []
synonym: "interleukin-3 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50231,7 +50104,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005136
name: interleukin-4 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-4 receptor." [GOC:ai]
+def: "Binding to an interleukin-4 receptor." [GOC:ai]
synonym: "IL-4" NARROW []
synonym: "interleukin-4 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50241,7 +50114,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005137
name: interleukin-5 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-5 receptor." [GOC:ai]
+def: "Binding to an interleukin-5 receptor." [GOC:ai]
subset: goslim_chembl
synonym: "IL-5" NARROW []
synonym: "interleukin-5 receptor ligand" NARROW []
@@ -50252,7 +50125,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005138
name: interleukin-6 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-6 receptor." [GOC:ai]
+def: "Binding to an interleukin-6 receptor." [GOC:ai]
subset: goslim_chembl
synonym: "IL-6" NARROW []
synonym: "interleukin-6 receptor ligand" NARROW []
@@ -50263,7 +50136,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005139
name: interleukin-7 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-7 receptor." [GOC:ai]
+def: "Binding to an interleukin-7 receptor." [GOC:ai]
synonym: "IL-7" NARROW []
synonym: "interleukin-7 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50273,7 +50146,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005140
name: interleukin-9 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-9 receptor." [GOC:ai]
+def: "Binding to an interleukin-9 receptor." [GOC:ai]
synonym: "IL-9" NARROW []
synonym: "interleukin-9 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50283,7 +50156,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005141
name: interleukin-10 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-10 receptor." [GOC:ai]
+def: "Binding to an interleukin-10 receptor." [GOC:ai]
synonym: "IL-10" NARROW []
synonym: "interleukin-10 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50293,7 +50166,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005142
name: interleukin-11 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-11 receptor." [GOC:ai]
+def: "Binding to an interleukin-11 receptor." [GOC:ai]
synonym: "IL-11" NARROW []
synonym: "interleukin-11 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50303,7 +50176,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005143
name: interleukin-12 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-12 receptor." [GOC:ai]
+def: "Binding to an interleukin-12 receptor." [GOC:ai]
synonym: "IL-12" NARROW []
synonym: "interleukin-12 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50313,25 +50186,26 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005144
name: interleukin-13 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-13 receptor." [GOC:ai]
+def: "Binding to an interleukin-13 receptor." [GOC:ai]
synonym: "IL-13" NARROW []
synonym: "interleukin-13 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
[Term]
id: GO:0005145
-name: interleukin-14 receptor binding
+name: obsolete interleukin-14 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-14 receptor." [GOC:ai]
+def: "OBSOLETE. Binding to an interleukin-14 receptor." [GOC:ai]
+comment: This term was obsoleted because the gene was shown not to exist, see PMID:8755619.
synonym: "IL-14" NARROW []
synonym: "interleukin-14 receptor ligand" NARROW []
-is_a: GO:0005126 ! cytokine receptor binding
+is_obsolete: true
[Term]
id: GO:0005146
name: leukemia inhibitory factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the leukemia inhibitory factor receptor." [GOC:ai]
+def: "Binding to an leukemia inhibitory factor receptor." [GOC:ai]
synonym: "leukemia inhibitory factor" NARROW []
synonym: "leukemia inhibitory factor receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50340,7 +50214,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005147
name: oncostatin-M receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the oncostatin-M receptor." [GOC:ai]
+def: "Binding to an oncostatin-M receptor." [GOC:ai]
synonym: "oncostatin-M" NARROW []
synonym: "oncostatin-M receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50349,7 +50223,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005148
name: prolactin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the prolactin receptor." [GOC:ai]
+def: "Binding to a prolactin receptor." [GOC:ai]
synonym: "prolactin" NARROW []
synonym: "prolactin receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50358,7 +50232,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005149
name: interleukin-1 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-1 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-1 receptor." [GOC:go_curators]
synonym: "IL-1" NARROW []
synonym: "interleukin-1 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50368,7 +50242,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005150
name: interleukin-1, type I receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Type I interleukin-1 receptor." [GOC:ai]
+def: "Binding to a Type I interleukin-1 receptor." [GOC:ai]
synonym: "IL-1 type I" NARROW []
synonym: "interleukin-1, type I receptor ligand" NARROW []
is_a: GO:0005149 ! interleukin-1 receptor binding
@@ -50377,7 +50251,7 @@ is_a: GO:0005149 ! interleukin-1 receptor binding
id: GO:0005151
name: interleukin-1, type II receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Type II interleukin-1 receptor." [GOC:ai]
+def: "Binding to a Type II interleukin-1 receptor." [GOC:ai]
synonym: "IL-1 type II" NARROW []
synonym: "interleukin-1, type II receptor ligand" NARROW []
is_a: GO:0005149 ! interleukin-1 receptor binding
@@ -50396,7 +50270,7 @@ is_a: GO:0048019 ! receptor antagonist activity
id: GO:0005153
name: interleukin-8 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-8 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-8 receptor." [GOC:go_curators]
subset: goslim_chembl
synonym: "IL-8" NARROW []
synonym: "interleukin-8 receptor ligand" NARROW []
@@ -50407,7 +50281,7 @@ id: GO:0005154
name: epidermal growth factor receptor binding
namespace: molecular_function
alt_id: GO:0008185
-def: "Interacting selectively and non-covalently with the epidermal growth factor receptor." [GOC:ai]
+def: "Binding to an epidermal growth factor receptor." [GOC:ai]
subset: goslim_chembl
synonym: "EGF" NARROW []
synonym: "EGF receptor binding" EXACT []
@@ -50454,7 +50328,7 @@ consider: GO:0030293
id: GO:0005157
name: macrophage colony-stimulating factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the macrophage colony-stimulating factor receptor." [GOC:ai]
+def: "Binding to a macrophage colony-stimulating factor receptor." [GOC:ai]
synonym: "M-CSF receptor binding" EXACT [GOC:vk]
synonym: "macrophage colony stimulating factor receptor binding" EXACT []
synonym: "macrophage colony-stimulating factor receptor ligand" NARROW []
@@ -50464,7 +50338,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005158
name: insulin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the insulin receptor." [GOC:ai]
+def: "Binding to an insulin receptor." [GOC:ai]
synonym: "insulin receptor ligand" NARROW []
is_a: GO:0005102 ! signaling receptor binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -50474,7 +50348,7 @@ id: GO:0005159
name: insulin-like growth factor receptor binding
namespace: molecular_function
alt_id: GO:0005067
-def: "Interacting selectively and non-covalently with the insulin-like growth factor receptor." [GOC:jl]
+def: "Binding to an insulin-like growth factor receptor." [GOC:jl]
synonym: "IGF receptor binding" EXACT []
synonym: "insulin-like growth factor" NARROW []
synonym: "insulin-like growth factor receptor ligand" NARROW []
@@ -50484,7 +50358,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0005160
name: transforming growth factor beta receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the transforming growth factor beta receptor." [GOC:ai]
+def: "Binding to a transforming growth factor beta receptor." [GOC:ai]
synonym: "activin" RELATED []
synonym: "inhibin" RELATED []
synonym: "TGF-beta receptor binding" EXACT []
@@ -50500,7 +50374,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005161
name: platelet-derived growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the platelet-derived growth factor receptor." [GOC:ai]
+def: "Binding to a platelet-derived growth factor receptor." [GOC:ai]
synonym: "PDGF" NARROW []
synonym: "PDGF receptor binding" EXACT []
synonym: "PDGFR binding" EXACT []
@@ -50512,7 +50386,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005163
name: nerve growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the nerve growth factor receptor." [GOC:ai, PMID:15654015]
+def: "Binding to a nerve growth factor receptor." [GOC:ai, PMID:15654015]
synonym: "nerve growth factor receptor ligand" NARROW []
synonym: "neurotrophin" NARROW []
synonym: "NGF receptor binding" EXACT []
@@ -50523,7 +50397,7 @@ is_a: GO:0005165 ! neurotrophin receptor binding
id: GO:0005164
name: tumor necrosis factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the tumor necrosis factor receptor." [GOC:ai]
+def: "Binding to a tumor necrosis factor receptor." [GOC:ai]
subset: goslim_chembl
synonym: "TNF receptor binding" EXACT []
synonym: "tumor necrosis factor" NARROW []
@@ -50534,7 +50408,7 @@ is_a: GO:0032813 ! tumor necrosis factor receptor superfamily binding
id: GO:0005165
name: neurotrophin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neurotrophin receptor." [GOC:ai]
+def: "Binding to a neurotrophin receptor." [GOC:ai]
synonym: "neurotrophin" NARROW []
synonym: "neurotrophin receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -50543,7 +50417,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005166
name: neurotrophin p75 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the neurotrophin p75 receptor." [GOC:ai]
+def: "Binding to a neurotrophin p75 receptor." [GOC:ai]
synonym: "neurotrophin p75 receptor ligand" NARROW []
is_a: GO:0005165 ! neurotrophin receptor binding
@@ -50551,7 +50425,7 @@ is_a: GO:0005165 ! neurotrophin receptor binding
id: GO:0005167
name: neurotrophin TRK receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neurotrophin TRK receptor." [GOC:ai]
+def: "Binding to a neurotrophin TRK receptor." [GOC:ai]
synonym: "neurotrophin TRK receptor ligand" NARROW []
is_a: GO:0005165 ! neurotrophin receptor binding
@@ -50559,7 +50433,7 @@ is_a: GO:0005165 ! neurotrophin receptor binding
id: GO:0005168
name: neurotrophin TRKA receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the neurotrophin TRKA receptor." [GOC:ai]
+def: "Binding to a neurotrophin TRKA receptor." [GOC:ai]
synonym: "neurotrophin TRKA receptor ligand" NARROW []
is_a: GO:0005167 ! neurotrophin TRK receptor binding
@@ -50567,7 +50441,7 @@ is_a: GO:0005167 ! neurotrophin TRK receptor binding
id: GO:0005169
name: neurotrophin TRKB receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the neurotrophin TRKB receptor." [GOC:ai]
+def: "Binding to a neurotrophin TRKB receptor." [GOC:ai]
synonym: "neurotrophin TRKB receptor ligand" NARROW []
is_a: GO:0005167 ! neurotrophin TRK receptor binding
@@ -50575,7 +50449,7 @@ is_a: GO:0005167 ! neurotrophin TRK receptor binding
id: GO:0005170
name: neurotrophin TRKC receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the neurotrophin TRKC receptor." [GOC:ai]
+def: "Binding to a neurotrophin TRKC receptor." [GOC:ai]
synonym: "neurotrophin TRKC receptor ligand" NARROW []
is_a: GO:0005167 ! neurotrophin TRK receptor binding
@@ -50583,7 +50457,7 @@ is_a: GO:0005167 ! neurotrophin TRK receptor binding
id: GO:0005171
name: hepatocyte growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the hepatocyte growth factor receptor." [GOC:ai]
+def: "Binding to an hepatocyte growth factor receptor." [GOC:ai]
synonym: "hepatocyte growth factor" NARROW []
synonym: "hepatocyte growth factor receptor ligand" NARROW []
synonym: "HGF receptor binding" EXACT []
@@ -50593,7 +50467,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005172
name: vascular endothelial growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any vascular endothelial growth factor receptor." [GOC:ai]
+def: "Binding to a vascular endothelial growth factor receptor." [GOC:ai]
synonym: "vascular endothelial growth factor" NARROW []
synonym: "vascular endothelial growth factor receptor ligand" NARROW []
synonym: "VEGF receptor binding" EXACT []
@@ -50605,7 +50479,7 @@ is_a: GO:0070851 ! growth factor receptor binding
id: GO:0005173
name: stem cell factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the stem cell factor receptor (SCFR), a type III transmembrane kinase receptor." [GOC:jl, PMID:10698217]
+def: "Binding to a stem cell factor receptor (SCFR), a type III transmembrane kinase receptor." [GOC:jl, PMID:10698217]
synonym: "KIT binding" NARROW []
synonym: "SCF" NARROW []
synonym: "SCFR binding" EXACT []
@@ -50617,21 +50491,21 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0005174
name: CD40 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with CD40, a receptor found on the surface of all B-lymphocytes." [GOC:jl, ISBN:0120781859]
+def: "Binding to CD40, a receptor found on the surface of all B-lymphocytes." [GOC:jl, ISBN:0120781859]
is_a: GO:0032813 ! tumor necrosis factor receptor superfamily binding
[Term]
id: GO:0005175
name: CD27 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CD27, a receptor found on the surface of T cells and some B cells and NK cells." [GOC:jl, ISBN:0120781859]
+def: "Binding to a CD27, a receptor found on the surface of T cells and some B cells and NK cells." [GOC:jl, ISBN:0120781859]
is_a: GO:0032813 ! tumor necrosis factor receptor superfamily binding
[Term]
id: GO:0005176
name: ErbB-2 class receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the protein-tyrosine kinase receptor Neu/ErbB-2/HER2." [GOC:jl]
+def: "Binding to a protein-tyrosine kinase receptor Neu/ErbB-2/HER2." [GOC:jl]
synonym: "ErbB-2 class receptor ligand" NARROW []
synonym: "HER2 receptor binding" EXACT []
synonym: "HER2 receptor ligand" NARROW []
@@ -50652,7 +50526,7 @@ consider: GO:0042043
id: GO:0005178
name: integrin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an integrin." [GOC:ceb]
+def: "Binding to an integrin." [GOC:ceb]
subset: goslim_chembl
synonym: "integrin ligand" NARROW []
is_a: GO:0005102 ! signaling receptor binding
@@ -50988,6 +50862,7 @@ subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
+subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
@@ -51501,13 +51376,14 @@ is_a: GO:0015174 ! basic amino acid transmembrane transporter activity
[Term]
id: GO:0005289
-name: high-affinity arginine transmembrane transporter activity
+name: high-affinity L-arginine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of arginine from one side of a membrane to the other. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations." [GOC:mtg_transport]
synonym: "high affinity arginine transmembrane transporter activity" EXACT []
+synonym: "high-affinity arginine transmembrane transporter activity" EXACT []
synonym: "high-affinity arginine transporter activity" BROAD []
is_a: GO:0005287 ! high-affinity basic amino acid transmembrane transporter activity
-is_a: GO:0015181 ! arginine transmembrane transporter activity
+is_a: GO:0061459 ! L-arginine transmembrane transporter activity
[Term]
id: GO:0005290
@@ -51828,7 +51704,6 @@ id: GO:0005326
name: neurotransmitter transmembrane transporter activity
namespace: molecular_function
def: "Enables the directed movement of a neurotransmitter into, out of or within a cell, or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [GOC:ai, ISBN:0198506732]
-synonym: "neurotransmitter transmembrane transporter activity" EXACT [GOC:mah]
synonym: "neurotransmitter transporter activity" RELATED []
xref: Reactome:R-HSA-374896 "Uptake of Noradrenaline"
xref: Reactome:R-HSA-374919 "Noradrenaline clearance from the synaptic cleft"
@@ -51881,7 +51756,6 @@ def: "Enables the transfer of a solute or solutes from one side of a membrane to
synonym: "levarterenol transporter activity" EXACT []
synonym: "noradrenaline transporter activity" EXACT []
synonym: "norepinephrine transmembrane transporter activity" EXACT []
-synonym: "norepinephrine:sodium symporter activity" EXACT []
synonym: "norepinephrine:sodium:chloride symporter activity" EXACT []
synonym: "sodium/norepinephrine symporter activity" EXACT []
xref: Reactome:R-HSA-443997 "SLC6A2 cotransports NAd, Na+ from extracellular region to cytosol"
@@ -51922,7 +51796,6 @@ xref: Reactome:R-HSA-727740 "Equilibrative transport (import) of adenosine and b
xref: Reactome:R-HSA-727749 "SLC29A3 transports nucleosides from lysosomal lumen to cytosol"
xref: Reactome:R-HSA-727767 "SLC29A3 transports nucleosides from cytosol to lysosomal lumen"
xref: Reactome:R-HSA-727768 "Equilibrative transport (export) of adenosine and biogenic amines by solute carrier family 29 (nucleoside transporters), member 4"
-xref: RHEA:27318
is_a: GO:0015932 ! nucleobase-containing compound transmembrane transporter activity
is_a: GO:1901505 ! carbohydrate derivative transmembrane transporter activity
@@ -52200,7 +52073,6 @@ id: GO:0005368
name: taurine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of taurine from one side of a membrane to the other. Taurine (2-aminoethanesulfonic acid) is a sulphur-containing amino acid derivative which is important in the metabolism of fats." [GOC:ai]
-xref: RHEA:14613
is_a: GO:0005342 ! organic acid transmembrane transporter activity
is_a: GO:0042959 ! alkanesulfonate transmembrane transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
@@ -52304,7 +52176,6 @@ xref: Reactome:R-HSA-5623558 "Defective SLC11A2 does not cotransport Fe2+, H+ fr
xref: Reactome:R-HSA-5655733 "Defective SLC40A1 does not transport Fe2+ from cytosol to extracellular region"
xref: Reactome:R-HSA-904830 "SLC40A1:CP:6Cu2+ transports Fe2+ from cytosol to extracellular region"
xref: Reactome:R-HSA-917936 "MCOLN1 transports Fe2+ from endosome lumen to cytosol"
-xref: RHEA:29579
is_a: GO:0046915 ! transition metal ion transmembrane transporter activity
[Term]
@@ -52748,7 +52619,7 @@ consider: GO:0016080
id: GO:0005483
name: soluble NSF attachment protein activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with both N-ethylmaleimide-sensitive fusion protein (NSF) and a cis-SNARE complex (i.e. a SNARE complex in which all proteins are associated with the same membrane) and increasing the ATPase activity of NSF, thereby allowing ATP hydrolysis by NSF to disassemble the cis-SNARE complex." [GOC:mah, PMID:14570579, PMID:15556857]
+def: "Binding to both N-ethylmaleimide-sensitive fusion protein (NSF) and a cis-SNARE complex (i.e. a SNARE complex in which all proteins are associated with the same membrane) and increasing the ATPase activity of NSF, thereby allowing ATP hydrolysis by NSF to disassemble the cis-SNARE complex." [GOC:mah, PMID:14570579, PMID:15556857]
synonym: "SNAP" EXACT []
is_a: GO:0030674 ! protein-macromolecule adaptor activity
@@ -52825,7 +52696,7 @@ is_obsolete: true
id: GO:0005496
name: steroid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene." [GOC:jl, ISBN:0198506732]
+def: "Binding to a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene." [GOC:jl, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0008289 ! lipid binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -52834,14 +52705,14 @@ is_a: GO:0097159 ! organic cyclic compound binding
id: GO:0005497
name: androgen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any androgen, male sex hormones." [GOC:jl]
+def: "Binding to an androgen, a male sex hormone." [GOC:jl]
is_a: GO:0042562 ! hormone binding
[Term]
id: GO:0005499
name: vitamin D binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3)." [GOC:mah, ISBN:0471331309]
+def: "Binding to vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3)." [GOC:mah, ISBN:0471331309]
synonym: "calciferol binding" NARROW []
synonym: "cholecalciferol binding" NARROW []
synonym: "ergocalciferol binding" NARROW []
@@ -52852,7 +52723,7 @@ is_a: GO:0019842 ! vitamin binding
id: GO:0005500
name: juvenile hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with juvenile hormone, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:jl, ISBN:0198506732]
+def: "Binding to a juvenile hormone, a sesquiterpenoid derivative that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." [GOC:jl, ISBN:0198506732]
is_a: GO:0019840 ! isoprenoid binding
is_a: GO:0042562 ! hormone binding
@@ -52860,7 +52731,7 @@ is_a: GO:0042562 ! hormone binding
id: GO:0005501
name: retinoid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity." [GOC:jl, ISBN:0198506732]
+def: "Binding to a retinoid, a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity." [GOC:jl, ISBN:0198506732]
xref: Reactome:R-HSA-2454113 "RBP3 transports 11cRAL to rod photoreceptor outer segment"
xref: Reactome:R-HSA-2464809 "RBP3 regulates the transport of atROL from ROS to RPE"
xref: Reactome:R-HSA-2465934 "11cROL translocates from Muller cells to cone photoreceptor cells"
@@ -52871,7 +52742,7 @@ is_a: GO:0019840 ! isoprenoid binding
id: GO:0005502
name: 11-cis retinal binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 11-cis retinal, an isomer of retinal that plays an important role in the visual process in most vertebrates. 11-cis retinal combines with opsin in the rods (scotopsin) to form rhodopsin or visual purple. Retinal is one of the three compounds that makes up vitamin A." [PMID:24403072]
+def: "Binding to 11-cis retinal, an isomer of retinal that plays an important role in the visual process in most vertebrates. 11-cis retinal combines with opsin in the rods (scotopsin) to form rhodopsin or visual purple. Retinal is one of the three compounds that makes up vitamin A." [PMID:24403072]
synonym: "11-cis retinaldehyde binding" EXACT []
synonym: "11-cis-retinal binding" NARROW []
synonym: "vitamin A binding" BROAD []
@@ -52881,7 +52752,7 @@ is_a: GO:0016918 ! retinal binding
id: GO:0005503
name: all-trans retinal binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with all-trans retinal, a compound that plays an important role in the visual process in most vertebrates. All-trans retinal (trans r., visual yellow) results from the bleaching of rhodopsin by light, in which the 11-cis form is converted to the all-trans form. Retinal is one of the forms of vitamin A." [GOC:curators]
+def: "Binding to all-trans retinal, a compound that plays an important role in the visual process in most vertebrates. All-trans retinal (trans r., visual yellow) results from the bleaching of rhodopsin by light, in which the 11-cis form is converted to the all-trans form. Retinal is one of the forms of vitamin A." [GOC:curators]
synonym: "all-trans retinaldehyde binding" EXACT []
synonym: "trans retinal binding" EXACT []
synonym: "visual yellow binding" EXACT []
@@ -52893,7 +52764,7 @@ is_a: GO:0016918 ! retinal binding
id: GO:0005504
name: fatty acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN:0198506732]
+def: "Binding to a fatty acid, an aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [ISBN:0198506732]
is_a: GO:0008289 ! lipid binding
is_a: GO:0033293 ! monocarboxylic acid binding
@@ -52911,7 +52782,7 @@ consider: GO:0046872
id: GO:0005506
name: iron ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with iron (Fe) ions." [GOC:ai]
+def: "Binding to an iron (Fe) ion." [GOC:ai]
synonym: "iron binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
@@ -52919,7 +52790,7 @@ is_a: GO:0046914 ! transition metal ion binding
id: GO:0005507
name: copper ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with copper (Cu) ions." [GOC:ai]
+def: "Binding to a copper (Cu) ion." [GOC:ai]
synonym: "copper binding" EXACT []
synonym: "copper/cadmium binding" BROAD []
is_a: GO:0046914 ! transition metal ion binding
@@ -52939,7 +52810,7 @@ consider: GO:0046870
id: GO:0005509
name: calcium ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with calcium ions (Ca2+)." [GOC:ai]
+def: "Binding to a calcium ion (Ca2+)." [GOC:ai]
synonym: "calcium ion storage activity" RELATED []
is_a: GO:0046872 ! metal ion binding
@@ -52972,7 +52843,7 @@ name: protein binding
namespace: molecular_function
alt_id: GO:0001948
alt_id: GO:0045308
-def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)." [GOC:go_curators]
+def: "Binding to a protein." [GOC:go_curators]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
@@ -52987,7 +52858,7 @@ is_a: GO:0005488 ! binding
id: GO:0005516
name: calmodulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states." [GOC:krc]
+def: "Binding to calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states." [GOC:krc]
subset: goslim_chembl
is_a: GO:0005515 ! protein binding
@@ -53005,21 +52876,21 @@ consider: GO:0005516
id: GO:0005518
name: collagen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%)." [GOC:ai, ISBN:0198506732]
+def: "Binding to collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%)." [GOC:ai, ISBN:0198506732]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0005519
name: cytoskeletal regulatory protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein involved in modulating the reorganization of the cytoskeleton." [GOC:go_curators, PMID:15163540]
+def: "Binding to a protein involved in modulating the reorganization of the cytoskeleton." [GOC:go_curators, PMID:15163540]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
id: GO:0005520
name: insulin-like growth factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it." [ISBN:0198506732]
+def: "Binding to an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it." [ISBN:0198506732]
subset: goslim_chembl
synonym: "IGF binding" EXACT []
is_a: GO:0019838 ! growth factor binding
@@ -53028,7 +52899,7 @@ is_a: GO:0019838 ! growth factor binding
id: GO:0005521
name: lamin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lamin; any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope." [GOC:jl, ISBN:0198506732]
+def: "Binding to lamin; any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope." [GOC:jl, ISBN:0198506732]
synonym: "lamin/chromatin binding" BROAD []
is_a: GO:0005515 ! protein binding
@@ -53036,21 +52907,21 @@ is_a: GO:0005515 ! protein binding
id: GO:0005522
name: profilin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with profilin, an actin-binding protein that forms a complex with G-actin and prevents it from polymerizing to form F-actin." [ISBN:0721662544]
+def: "Binding to profilin, an actin-binding protein that forms a complex with G-actin and prevents it from polymerizing to form F-actin." [ISBN:0721662544]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0005523
name: tropomyosin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with tropomyosin, a protein associated with actin filaments both in cytoplasm and, in association with troponin, in the thin filament of striated muscle." [GOC:curators, ISBN:0815316194]
+def: "Binding to tropomyosin, a protein associated with actin filaments both in cytoplasm and, in association with troponin, in the thin filament of striated muscle." [GOC:curators, ISBN:0815316194]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
id: GO:0005524
name: ATP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN:0198506732]
+def: "Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." [ISBN:0198506732]
xref: Reactome:R-HSA-265682 "KCNJ11 tetramer:ABCC8 tetramer binds 4xATP, closing the channel"
is_a: GO:0032559 ! adenyl ribonucleotide binding
is_a: GO:0035639 ! purine ribonucleoside triphosphate binding
@@ -53059,7 +52930,7 @@ is_a: GO:0035639 ! purine ribonucleoside triphosphate binding
id: GO:0005525
name: GTP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with GTP, guanosine triphosphate." [GOC:ai]
+def: "Binding to GTP, guanosine triphosphate." [GOC:ai]
xref: Reactome:R-HSA-167429 "The receptor:G-protein complex binds GTP"
is_a: GO:0032561 ! guanyl ribonucleotide binding
is_a: GO:0035639 ! purine ribonucleoside triphosphate binding
@@ -53068,8 +52939,7 @@ is_a: GO:0035639 ! purine ribonucleoside triphosphate binding
id: GO:0005527
name: macrolide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a macrolide, any of a large group of structurally related antibiotics produced by Streptomyces species." [GOC:jl, ISBN:0198506732]
-is_a: GO:0008144 ! drug binding
+def: "Binding to a macrolide, any of a large group of structurally related antibiotics produced by Streptomyces species." [GOC:jl, ISBN:0198506732]
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -53077,7 +52947,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0005528
name: FK506 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506." [GOC:jl]
+def: "Binding to a 23-membered macrolide lactone FK506." [GOC:jl]
synonym: "FK506-sensitive peptidyl-prolyl cis-trans isomerase" RELATED []
is_a: GO:0005527 ! macrolide binding
is_a: GO:0033218 ! amide binding
@@ -53131,7 +53001,7 @@ consider: GO:0046871
id: GO:0005534
name: galactose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the aldohexose galactose (galacto-hexose), a common constituent of many oligo- and polysaccharides." [GOC:jl, ISBN:0198506732]
+def: "Binding to aldohexose galactose (galacto-hexose), a common constituent of many oligo- and polysaccharides." [GOC:jl, ISBN:0198506732]
synonym: "galactose binding lectin" RELATED []
is_a: GO:0048029 ! monosaccharide binding
@@ -53139,14 +53009,14 @@ is_a: GO:0048029 ! monosaccharide binding
id: GO:0005536
name: glucose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the D- or L-enantiomer of glucose." [GOC:jl]
+def: "Binding to D- or L-enantiomers of glucose." [GOC:jl]
is_a: GO:0048029 ! monosaccharide binding
[Term]
id: GO:0005537
name: mannose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans." [GOC:jl, ISBN:0192800981]
+def: "Binding to mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans." [GOC:jl, ISBN:0192800981]
subset: goslim_chembl
synonym: "mannose binding lectin" RELATED []
xref: Reactome:R-HSA-947991 "Transport of glycoproteins with Man8 (or Man9) N-glycans to the Golgi"
@@ -53156,7 +53026,7 @@ is_a: GO:0048029 ! monosaccharide binding
id: GO:0005539
name: glycosaminoglycan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues." [GOC:jl, ISBN:0198506732]
+def: "Binding to a glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues." [GOC:jl, ISBN:0198506732]
subset: goslim_chembl
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -53164,7 +53034,7 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:0005540
name: hyaluronic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with hyaluronic acid, a polymer composed of repeating dimeric units of glucuronic acid and N-acetyl glucosamine." [GOC:jl]
+def: "Binding to hyaluronic acid, a polymer composed of repeating dimeric units of glucuronic acid and N-acetyl glucosamine." [GOC:jl]
synonym: "hyaluronan binding" EXACT []
is_a: GO:0005539 ! glycosaminoglycan binding
@@ -53183,7 +53053,7 @@ consider: GO:0000062
id: GO:0005542
name: folic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines." [GOC:jl, ISBN:0198506732]
+def: "Binding to folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines." [GOC:jl, ISBN:0198506732]
synonym: "folate binding" EXACT []
synonym: "vitamin B9 binding" EXACT []
synonym: "vitamin M binding" EXACT []
@@ -53199,28 +53069,28 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0005543
name: phospholipid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester." [ISBN:0198506732]
+def: "Binding to a phospholipid, a class of lipids containing phosphoric acid as a mono- or diester." [ISBN:0198506732]
is_a: GO:0008289 ! lipid binding
[Term]
id: GO:0005544
name: calcium-dependent phospholipid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium." [GOC:jl]
+def: "Binding to a phospholipid, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium." [GOC:jl]
is_a: GO:0005543 ! phospholipid binding
[Term]
id: GO:0005545
name: 1-phosphatidylinositol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol." [ISBN:0198506732]
+def: "Binding to a phosphatidylinositol, a glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol." [ISBN:0198506732]
is_a: GO:0035091 ! phosphatidylinositol binding
[Term]
id: GO:0005546
name: phosphatidylinositol-4,5-bisphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions." [GOC:bf, GOC:jl]
+def: "Binding to phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions." [GOC:bf, GOC:jl]
synonym: "1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate binding" EXACT []
synonym: "phosphatidylinositol 4,5-bisphosphate binding" EXACT [GOC:ebc]
synonym: "PIP2 binding" BROAD []
@@ -53232,7 +53102,7 @@ is_a: GO:1902936 ! phosphatidylinositol bisphosphate binding
id: GO:0005547
name: phosphatidylinositol-3,4,5-trisphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions." [GOC:bf, GOC:jl]
+def: "Binding to phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions." [GOC:bf, GOC:jl]
synonym: "PIP3 binding" EXACT [GOC:bf]
is_a: GO:0043168 ! anion binding
is_a: GO:1901981 ! phosphatidylinositol phosphate binding
@@ -53256,7 +53126,7 @@ is_a: GO:0005319 ! lipid transporter activity
id: GO:0005549
name: odorant binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell." [GOC:jl, ISBN:0721662544]
+def: "Binding to an odorant, any substance capable of stimulating the sense of smell." [GOC:jl, ISBN:0721662544]
subset: goslim_pir
is_a: GO:0005488 ! binding
@@ -53264,7 +53134,7 @@ is_a: GO:0005488 ! binding
id: GO:0005550
name: pheromone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pheromone, a substance, or characteristic mixture of substances, that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process." [GOC:ai]
+def: "Binding to a pheromone, a substance, or characteristic mixture of substances, that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process." [GOC:ai]
is_a: GO:0005549 ! odorant binding
[Term]
@@ -53475,7 +53345,6 @@ comment: Note that, in addition to forming the root of the cellular component on
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
@@ -53853,6 +53722,8 @@ id: GO:0005618
name: cell wall
namespace: cellular_component
def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins." [GOC:giardia, ISBN:0198547684, PMID:15134259, Wikipedia:Microbial_cyst]
+comment: Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for \nplants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
+subset: gocheck_do_not_annotate
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
@@ -54375,15 +54246,15 @@ replaced_by: GO:0005669
[Term]
id: GO:0005671
-name: Ada2/Gcn5/Ada3 transcription activator complex
+name: obsolete Ada2/Gcn5/Ada3 transcription activator complex
namespace: cellular_component
alt_id: GO:0002928
-def: "A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues." [PMID:10637607]
-comment: In human, this complex is composed of GCN5 or PCAF, ADA2a, ADA3, ZZZ3, ATAC2, SGF29, HCF1, WDR5,YEATS2, NC2-beta, and MBIP.
-synonym: "Ada Two-A containing complex" EXACT [GOC:rl, PMID:18838386]
-synonym: "Ada-Two-A-containing complex" EXACT []
-synonym: "ATAC complex" EXACT [GOC:rl, PMID:18838386]
-is_a: GO:1902562 ! H4 histone acetyltransferase complex
+def: "OBSOLETE. A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues." [PMID:10637607]
+comment: This term was obsoleted because it was incorrectly annotated. Consider ADA complex ; GO:0140671 or ATAC complex; GO:0140672.
+synonym: "ATAC complex" RELATED [GOC:rl, PMID:18838386]
+is_obsolete: true
+consider: GO:0140671
+consider: GO:0140672
[Term]
id: GO:0005672
@@ -54779,7 +54650,7 @@ name: pericentric heterochromatin
namespace: cellular_component
alt_id: GO:0002137
alt_id: GO:0031618
-def: "Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3." [PMID:12019236, PMID:20206496, PMID:22729156, PMID:9413993]
+def: "Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3)." [PMID:12019236, PMID:20206496, PMID:22729156, PMID:9413993]
synonym: "centric heterochromatin" EXACT []
synonym: "centromeric heterochromatin" EXACT [GOC:dph]
synonym: "nuclear centric heterochromatin" NARROW []
@@ -54938,7 +54809,7 @@ relationship: part_of GO:0005730 ! nucleolus
id: GO:0005737
name: cytoplasm
namespace: cellular_component
-def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
+def: "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [ISBN:0198547684]
subset: goslim_candida
subset: goslim_chembl
subset: goslim_generic
@@ -55047,7 +54918,6 @@ namespace: cellular_component
alt_id: GO:0097249
def: "The protein complexes that form the mitochondrial electron transport system (the respiratory chain), associated with the inner mitochondrial membrane. The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient." [GOC:curators, GOC:ecd, ISBN:0198547684]
synonym: "mitochondrial electron transport chain" EXACT []
-synonym: "mitochondrial respirasome" RELATED []
synonym: "mitochondrial respiratory chain" EXACT []
synonym: "mitochondrial respiratory chain supercomplex" EXACT []
synonym: "mitochondrial respiratory supercomplex" EXACT []
@@ -55226,7 +55096,7 @@ relationship: part_of GO:0005761 ! mitochondrial ribosome
id: GO:0005764
name: lysosome
namespace: cellular_component
-def: "A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC:mah, ISBN:0198506732]
+def: "A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." [GOC:mah, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_plant
@@ -55446,7 +55316,7 @@ relationship: part_of GO:0012505 ! endomembrane system
id: GO:0005784
name: Sec61 translocon complex
namespace: cellular_component
-def: "A translocon complex that contains a core heterotrimer of conserved alpha, beta and gamma subunits, and may contain additional proteins (translocon-associated proteins or TRAPs); in budding yeast the core proteins are Sec61p, Sbh1p, and Sss1p. The Sec61 translocon complex functions in cotranslational and posttranslational translocation events." [GOC:mah, PMID:18166647]
+def: "A translocon complex that contains a core heterotrimer of conserved alpha, beta and gamma subunits, and may contain additional proteins (translocon-associated proteins or TRAPs); in budding yeast the core proteins are Sec61p, Sbh1p, and Sss1p. The Sec61 translocon complex functions in cotranslational and posttranslational translocation events." [GOC:mah, PMID:18166647, PMID:32820719, PMID:33960686]
synonym: "Sec61p-Sbh1p-Sss1p complex" NARROW [GOC:mah]
is_a: GO:0071256 ! translocon complex
@@ -56623,7 +56493,9 @@ consider: GO:0030122
id: GO:0005911
name: cell-cell junction
namespace: cellular_component
-def: "A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects." [GOC:aruk, GOC:bc, GOC:dgh, GOC:hb, GOC:mah, PMID:21422226, PMID:28096264]
+def: "A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects." [GOC:aruk, GOC:bc, GOC:dgh, GOC:hb, GOC:mah, PMID:21422226, PMID:28096264]
+synonym: "cell-cell contact region" BROAD []
+synonym: "cell-cell contact zone" BROAD []
synonym: "intercellular junction" EXACT [NIF_Subcellular:sao1395777368]
xref: NIF_Subcellular:sao1922892319
is_a: GO:0070161 ! anchoring junction
@@ -57120,7 +56992,7 @@ is_a: GO:0045242 ! isocitrate dehydrogenase complex (NAD+)
id: GO:0005963
name: magnesium-dependent protein serine/threonine phosphatase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the removal of serine- or threonine-bound phosphate groups from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase." [EC:3.1.3.16]
+def: "An enzyme complex that catalyzes the removal of serine- or threonine-bound phosphate groups from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase." [PMID:17517611, PMID:22343722]
is_a: GO:0008287 ! protein serine/threonine phosphatase complex
is_a: GO:0140535 ! intracellular protein-containing complex
@@ -57166,7 +57038,6 @@ namespace: cellular_component
def: "An protein-containing complex which catalyzes of the transfer of a geranyl-geranyl group from geranylgeranyl pyrophosphate to a Rab protein. In mammals it is composed of an alpha and a beta subunit, and associates with an accessory protein Rep (Rab escort protein)." [GOC:jl, PMID:11886217]
synonym: "GGTase-II complex" EXACT []
synonym: "Rab geranylgeranyltransferase complex" EXACT []
-synonym: "RAB-protein geranylgeranyltransferase complex" EXACT []
synonym: "RabGGTase complex" EXACT []
is_a: GO:1990234 ! transferase complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -58130,7 +58001,7 @@ is_a: GO:0046381 ! CMP-N-acetylneuraminate metabolic process
id: GO:0006056
name: mannoprotein metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving mannoproteins, any protein that contains covalently bound mannose residues." [ISBN:0198506732]
+def: "The chemical reactions and pathways involving a mannoprotein, a protein that contains covalently bound mannose residues." [ISBN:0198506732]
synonym: "mannoprotein metabolism" EXACT []
is_a: GO:0009100 ! glycoprotein metabolic process
@@ -58138,7 +58009,7 @@ is_a: GO:0009100 ! glycoprotein metabolic process
id: GO:0006057
name: mannoprotein biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of mannoproteins, any protein that contains covalently bound mannose residues." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a mannoprotein, a protein that contains covalently bound mannose residues." [ISBN:0198506732]
synonym: "mannoprotein anabolism" EXACT []
synonym: "mannoprotein biosynthesis" EXACT []
synonym: "mannoprotein formation" EXACT []
@@ -58150,7 +58021,7 @@ is_a: GO:0009101 ! glycoprotein biosynthetic process
id: GO:0006058
name: mannoprotein catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of mannoproteins, any protein that contains covalently bound mannose residues." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a mannoprotein, a protein that contains covalently bound mannose residues." [ISBN:0198506732]
synonym: "mannoprotein breakdown" EXACT []
synonym: "mannoprotein catabolism" EXACT []
synonym: "mannoprotein degradation" EXACT []
@@ -58502,6 +58373,7 @@ name: pyruvate metabolic process
namespace: biological_process
alt_id: GO:0006087
def: "The chemical reactions and pathways involving pyruvate, 2-oxopropanoate." [GOC:go_curators]
+subset: goslim_drosophila
synonym: "pyruvate dehydrogenase bypass" RELATED []
synonym: "pyruvate metabolism" EXACT []
xref: MetaCyc:P41-PWY
@@ -59679,8 +59551,8 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of guanosine monophosphate into other compounds, including inosine monophosphate." [ISBN:0198506732]
synonym: "GMP breakdown to IMP" EXACT []
synonym: "GMP degradation to IMP" EXACT []
-is_a: GO:0006188 ! IMP biosynthetic process
is_a: GO:0046038 ! GMP catabolic process
+is_a: GO:0046040 ! IMP metabolic process
[Term]
id: GO:0006202
@@ -59690,7 +59562,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of guanosin
synonym: "GMP breakdown to guanine" EXACT []
synonym: "GMP degradation to guanine" EXACT []
is_a: GO:0046038 ! GMP catabolic process
-is_a: GO:0046099 ! guanine biosynthetic process
+is_a: GO:0046098 ! guanine metabolic process
[Term]
id: GO:0006203
@@ -60336,7 +60208,6 @@ subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
@@ -60353,6 +60224,7 @@ alt_id: GO:0055133
def: "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [GOC:mah]
comment: DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'.
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
@@ -60426,7 +60298,6 @@ name: DNA replication, synthesis of RNA primer
namespace: biological_process
def: "The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis." [PMID:11395402]
synonym: "replication priming" RELATED []
-is_a: GO:0006259 ! DNA metabolic process
is_a: GO:0032774 ! RNA biosynthetic process
relationship: part_of GO:0006261 ! DNA-dependent DNA replication
@@ -60539,6 +60410,7 @@ name: DNA repair
namespace: biological_process
def: "The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway." [PMID:11563486]
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
@@ -60778,7 +60650,6 @@ id: GO:0006308
name: DNA catabolic process
namespace: biological_process
def: "The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:go_curators, ISBN:0198506732]
-subset: goslim_drosophila
synonym: "DNA breakdown" EXACT []
synonym: "DNA catabolism" EXACT []
synonym: "DNA degradation" EXACT []
@@ -60808,6 +60679,7 @@ name: DNA recombination
namespace: biological_process
def: "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." [ISBN:0198506732]
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
is_a: GO:0006259 ! DNA metabolic process
@@ -60825,7 +60697,7 @@ is_a: GO:0061982 ! meiosis I cell cycle process
id: GO:0006312
name: mitotic recombination
namespace: biological_process
-def: "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous region of DNA that occurs during mitotic cell cycles." [GOC:elh]
+def: "The exchange, reciprocal or nonreciprocal, of genetic material between one DNA molecule and a homologous DNA region that occurs during mitotic cell cycles." [GOC:elh]
xref: Wikipedia:Mitotic_crossover
is_a: GO:0006310 ! DNA recombination
@@ -60894,6 +60766,7 @@ name: chromatin organization
namespace: biological_process
alt_id: GO:0016568
def: "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin." [GOC:mah, GOC:vw, PMID:20404130]
+subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
synonym: "chromatin modification" RELATED []
@@ -60974,20 +60847,22 @@ relationship: part_of GO:0031497 ! chromatin assembly
[Term]
id: GO:0006335
-name: DNA replication-dependent nucleosome assembly
+name: DNA replication-dependent chromatin assembly
namespace: biological_process
def: "The formation of nucleosomes on newly replicated DNA, coupled to strand elongation." [GOC:mah]
-is_a: GO:0006334 ! nucleosome assembly
-is_a: GO:0034723 ! DNA replication-dependent nucleosome organization
+synonym: "DNA replication-dependent nucleosome assembly" EXACT []
+is_a: GO:0031497 ! chromatin assembly
+is_a: GO:0034723 ! DNA replication-dependent chromatin organization
[Term]
id: GO:0006336
-name: DNA replication-independent nucleosome assembly
+name: DNA replication-independent chromatin assembly
namespace: biological_process
-def: "The formation of nucleosomes outside the context of DNA replication." [GOC:mah]
+def: "The formation of chromatin outside the context of DNA replication." [GOC:mah]
+synonym: "DNA replication-independent nucleosome assembly" EXACT []
synonym: "transcription-coupled nucleosome assembly" EXACT []
-is_a: GO:0006334 ! nucleosome assembly
-is_a: GO:0034724 ! DNA replication-independent nucleosome organization
+is_a: GO:0031497 ! chromatin assembly
+is_a: GO:0034724 ! DNA replication-independent chromatin organization
[Term]
id: GO:0006337
@@ -61002,7 +60877,10 @@ relationship: part_of GO:0031498 ! chromatin disassembly
id: GO:0006338
name: chromatin remodeling
namespace: biological_process
-def: "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [GOC:jid, GOC:vw, PMID:12697820]
+alt_id: GO:0043044
+def: "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [GOC:jid, GOC:vw, PMID:12042764, PMID:12697820]
+synonym: "ATP-dependent chromatin remodeling" NARROW []
+synonym: "ATP-dependent chromatin remodelling" NARROW []
synonym: "chromatin modeling" EXACT []
synonym: "chromatin modelling" EXACT []
synonym: "chromatin remodelling" EXACT []
@@ -61016,9 +60894,9 @@ def: "OBSOLETE. Any process that activates or increases the frequency, rate or e
comment: This term was made obsolete because it relates to a specific gene family rather than a process.
synonym: "positive regulation of transcription of homeotic gene (trithorax group)" EXACT []
is_obsolete: true
-consider: GO:0006342
+consider: GO:0031507
+consider: GO:0045815
consider: GO:0045944
-consider: GO:0048096
[Term]
id: GO:0006340
@@ -61029,8 +60907,8 @@ comment: This term was made obsolete because it relates to a specific gene famil
synonym: "negative regulation of transcription of homeotic gene (Polycomb group)" EXACT []
is_obsolete: true
consider: GO:0000122
-consider: GO:0006342
-consider: GO:0048096
+consider: GO:0031507
+consider: GO:0045815
[Term]
id: GO:0006341
@@ -61042,23 +60920,6 @@ synonym: "chromatin insulator sequence binding" EXACT []
is_obsolete: true
replaced_by: GO:0043035
-[Term]
-id: GO:0006342
-name: chromatin silencing
-namespace: biological_process
-alt_id: GO:0016440
-def: "Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin." [GOC:mah, PMID:10219245]
-comment: Note that this process is the opposite of chromatin-mediated maintenance of transcription. This regulation is exemplified by members of the Polycomb group, which maintain the inactive state of homeotic gene transcription.
-synonym: "chromatin-mediated maintenance of transcriptional inactivation" EXACT []
-synonym: "chromatin-mediated silencing" EXACT []
-synonym: "heterochromatic silencing" RELATED []
-synonym: "TGS" EXACT []
-synonym: "transcriptional gene silencing" EXACT []
-is_a: GO:0016458 ! gene silencing
-is_a: GO:0045814 ! negative regulation of gene expression, epigenetic
-is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
-is_a: GO:0097549 ! chromatin organization involved in negative regulation of transcription
-
[Term]
id: GO:0006346
name: DNA methylation-dependent heterochromatin assembly
@@ -61066,58 +60927,47 @@ namespace: biological_process
def: "Repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:mah]
synonym: "methylation-dependent chromatin silencing" BROAD []
synonym: "methylation-dependent heterochromatic silencing" BROAD []
-is_a: GO:0016569 ! covalent chromatin modification
-is_a: GO:0031507 ! heterochromatin assembly
-
-[Term]
-id: GO:0006348
-name: chromatin silencing at telomere
-namespace: biological_process
-def: "Repression of transcription of telomeric DNA by altering the structure of chromatin." [PMID:10219245]
-synonym: "heterochromatic silencing at telomere" EXACT []
-synonym: "telomere chromatin silencing" EXACT [GOC:mah]
-synonym: "Telomere Position Effect" EXACT [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:21847107]
-synonym: "telomeric silencing" EXACT [GOC:bf]
-is_a: GO:0006342 ! chromatin silencing
+is_a: GO:0140718 ! facultative heterochromatin assembly
[Term]
id: GO:0006349
-name: regulation of gene expression by genetic imprinting
+name: regulation of gene expression by genomic imprinting
namespace: biological_process
-def: "Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself." [GOC:ems, ISBN:0198506732, PMID:11498578]
+def: "An epigenetic mechanism of regulation of gene expression in which epigenetic modifications (imprints) are established during gametogenesis. For a given gene to show parentally biased expression, the imprint are established exclusively in one of the two parental genomes, thus generating an asymmetry between the maternal and paternal alleles." [PMID:11498578, PMID:31896690, PMID:7502071]
synonym: "regulation of gene expression by DNA imprinting" EXACT [GOC:mah]
+synonym: "regulation of gene expression by genetic imprinting" RELATED []
xref: Wikipedia:Genomic_imprinting
is_a: GO:0040029 ! regulation of gene expression, epigenetic
-is_a: GO:0071514 ! genetic imprinting
[Term]
id: GO:0006351
name: transcription, DNA-templated
namespace: biological_process
+alt_id: GO:0001121
alt_id: GO:0006350
alt_id: GO:0061018
alt_id: GO:0061022
def: "The cellular synthesis of RNA on a template of DNA." [GOC:jl, GOC:txnOH]
subset: goslim_aspergillus
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
+synonym: "bacterial transcription" NARROW []
synonym: "cellular transcription" BROAD []
-synonym: "cellular transcription, DNA-dependent" EXACT []
synonym: "DNA-dependent transcription" EXACT []
synonym: "transcription" BROAD []
-synonym: "transcription regulator activity" RELATED []
+synonym: "transcription from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH]
xref: Wikipedia:Transcription_(genetics)
-is_a: GO:0034645 ! cellular macromolecule biosynthetic process
is_a: GO:0097659 ! nucleic acid-templated transcription
-relationship: part_of GO:0010467 ! gene expression
[Term]
id: GO:0006352
name: DNA-templated transcription, initiation
namespace: biological_process
+alt_id: GO:0001123
def: "Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription." [GOC:jid, GOC:txnOH, PMID:18280161]
comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
subset: goslim_yeast
@@ -61126,6 +60976,7 @@ synonym: "DNA-dependent transcription, initiation" EXACT [GOC:txnOH]
synonym: "initiation of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "initiation of transcription, DNA-dependent" EXACT [GOC:mah]
synonym: "transcription initiation factor activity" RELATED []
+synonym: "transcription initiation from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription initiation, DNA-dependent" RELATED [GOC:jh2]
is_a: GO:0032774 ! RNA biosynthetic process
relationship: part_of GO:0006351 ! transcription, DNA-templated
@@ -61134,12 +60985,14 @@ relationship: part_of GO:0006351 ! transcription, DNA-templated
id: GO:0006353
name: DNA-templated transcription, termination
namespace: biological_process
+alt_id: GO:0001125
def: "The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA." [GOC:txnOH, ISBN:0716720094, PMID:15020047, PMID:18280161]
subset: goslim_yeast
synonym: "DNA-dependent transcription, termination" EXACT [GOC:txnOH]
synonym: "termination of DNA-dependent transcription" EXACT [GOC:jh2]
synonym: "termination of transcription, DNA-dependent" EXACT [GOC:mah]
synonym: "transcription termination factor activity" RELATED []
+synonym: "transcription termination from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription termination, DNA-dependent" RELATED [GOC:jh2]
synonym: "transcriptional complex disassembly" BROAD []
is_a: GO:0032774 ! RNA biosynthetic process
@@ -61149,11 +61002,14 @@ relationship: part_of GO:0006351 ! transcription, DNA-templated
id: GO:0006354
name: DNA-templated transcription, elongation
namespace: biological_process
+alt_id: GO:0001124
def: "The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase." [GOC:mah, GOC:txnOH, PMID:15020047, PMID:18280161]
subset: goslim_pir
subset: goslim_yeast
synonym: "DNA-dependent transcription, elongation" EXACT [GOC:txnOH]
synonym: "RNA elongation" BROAD []
+synonym: "RNA elongation from bacterial-type RNA polymerase promoter" NARROW []
+synonym: "transcription elongation from bacterial-type RNA polymerase promoter" NARROW []
synonym: "transcription elongation, DNA-dependent" EXACT [GOC:jh2]
synonym: "transcriptional elongation, DNA-dependent" EXACT []
is_a: GO:0032774 ! RNA biosynthetic process
@@ -61167,13 +61023,14 @@ alt_id: GO:0032583
alt_id: GO:0045449
alt_id: GO:0061019
def: "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH]
+subset: goslim_drosophila
+subset: goslim_generic
synonym: "regulation of cellular transcription, DNA-dependent" EXACT []
synonym: "regulation of gene-specific transcription" RELATED []
synonym: "regulation of transcription, DNA-dependent" EXACT [GOC:txnOH]
synonym: "transcriptional control" BROAD []
is_a: GO:0010468 ! regulation of gene expression
is_a: GO:1903506 ! regulation of nucleic acid-templated transcription
-is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0006351 ! transcription, DNA-templated
[Term]
@@ -61566,6 +61423,7 @@ name: RNA processing
namespace: biological_process
alt_id: GO:0006394
def: "Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules." [GOC:mah]
+subset: goslim_drosophila
subset: goslim_pir
xref: Wikipedia:Post-transcriptional_modification
is_a: GO:0016070 ! RNA metabolic process
@@ -61577,7 +61435,6 @@ name: mRNA processing
namespace: biological_process
def: "Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide." [GOC:mah]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_yeast
synonym: "mRNA maturation" RELATED []
is_a: GO:0006396 ! RNA processing
@@ -61620,7 +61477,6 @@ id: GO:0006401
name: RNA catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732]
-subset: goslim_drosophila
subset: goslim_yeast
synonym: "RNA breakdown" EXACT []
synonym: "RNA catabolism" EXACT []
@@ -61687,7 +61543,6 @@ synonym: "mRNA-nucleus export" EXACT []
is_a: GO:0006405 ! RNA export from nucleus
is_a: GO:0051028 ! mRNA transport
relationship: part_of GO:0010467 ! gene expression
-relationship: part_of GO:0071427 ! mRNA-containing ribonucleoprotein complex export from nucleus
[Term]
id: GO:0006407
@@ -61701,7 +61556,6 @@ synonym: "rRNA-nucleus export" EXACT []
is_a: GO:0051029 ! rRNA transport
is_a: GO:0097064 ! ncRNA export from nucleus
relationship: part_of GO:0042254 ! ribosome biogenesis
-relationship: part_of GO:0071428 ! rRNA-containing ribonucleoprotein complex export from nucleus
[Term]
id: GO:0006408
@@ -61726,7 +61580,6 @@ synonym: "tRNA transport from nucleus to cytoplasm" EXACT []
synonym: "tRNA-nucleus export" EXACT []
is_a: GO:0051031 ! tRNA transport
is_a: GO:0097064 ! ncRNA export from nucleus
-relationship: part_of GO:0071431 ! tRNA-containing ribonucleoprotein complex export from nucleus
[Term]
id: GO:0006410
@@ -61748,7 +61601,7 @@ def: "The cellular metabolic process in which a protein is formed, using the seq
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
+subset: goslim_drosophila
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
@@ -61802,7 +61655,7 @@ def: "The process resulting in the release of a polypeptide chain from the ribos
synonym: "protein synthesis termination" BROAD []
synonym: "translation termination" EXACT []
synonym: "translational complex disassembly" EXACT []
-is_a: GO:0043624 ! cellular protein complex disassembly
+is_a: GO:0032984 ! protein-containing complex disassembly
relationship: part_of GO:0006412 ! translation
[Term]
@@ -62126,7 +61979,7 @@ id: GO:0006463
name: steroid hormone receptor complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a steroid hormone receptor complex, an intracellular receptor that binds steroid hormones. The complex is often a dimer, and forms after the steroid has bound the receptor." [GOC:jl, Wikipedia:Steroid_hormone_receptor]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0006464
@@ -62136,7 +61989,6 @@ def: "The covalent alteration of one or more amino acids occurring in proteins,
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "process resulting in protein modification" RELATED []
@@ -62329,6 +62181,7 @@ name: protein glycosylation
namespace: biological_process
alt_id: GO:0065006
def: "A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins." [GOC:curators, GOC:pr]
+subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
synonym: "protein amino acid glycosylation" EXACT [GOC:bf]
@@ -62384,7 +62237,6 @@ name: oligosaccharide-lipid intermediate biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of an oligosaccharide-lipid intermediate, such as a molecule of dolichol-P-man or dolicol-P-Glc used in N-linked glycosylation." [GOC:dph, GOC:hjd, GOC:isa_complete, GOC:pr, GOC:rb]
synonym: "oligosaccharide-lipid intermediate assembly" NARROW [GOC:pr]
-synonym: "oligosaccharide-lipid intermediate biosynthetic process" NARROW [GOC:pr]
is_a: GO:0044255 ! cellular lipid metabolic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
@@ -62683,7 +62535,7 @@ is_a: GO:0051603 ! proteolysis involved in cellular protein catabolic process
id: GO:0006516
name: glycoprotein catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732]
synonym: "glycoprotein breakdown" EXACT []
synonym: "glycoprotein catabolism" EXACT []
synonym: "glycoprotein degradation" EXACT []
@@ -62761,7 +62613,6 @@ synonym: "alanine biosynthesis" EXACT []
synonym: "alanine formation" EXACT []
synonym: "alanine synthesis" EXACT []
is_a: GO:0006522 ! alanine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009079 ! pyruvate family amino acid biosynthetic process
[Term]
@@ -62798,7 +62649,6 @@ xref: MetaCyc:ARGININE-SYN4-PWY
xref: MetaCyc:ARGSYN-PWY
xref: MetaCyc:ARGSYNBSUB-PWY
is_a: GO:0006525 ! arginine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009084 ! glutamine family amino acid biosynthetic process
[Term]
@@ -62832,7 +62682,6 @@ synonym: "asparagine biosynthesis" EXACT []
synonym: "asparagine formation" EXACT []
synonym: "asparagine synthesis" EXACT []
is_a: GO:0006528 ! asparagine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
[Term]
@@ -62867,7 +62716,6 @@ synonym: "aspartate biosynthesis" EXACT []
synonym: "aspartate formation" EXACT []
synonym: "aspartate synthesis" EXACT []
is_a: GO:0006531 ! aspartate metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
@@ -62934,7 +62782,6 @@ synonym: "glutamate synthesis" EXACT []
synonym: "glutamic acid biosynthesis" EXACT []
synonym: "glutamic acid biosynthetic process" EXACT []
is_a: GO:0006536 ! glutamate metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009084 ! glutamine family amino acid biosynthetic process
is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
@@ -63008,7 +62855,6 @@ synonym: "glutamine formation" EXACT []
synonym: "glutamine synthesis" EXACT []
xref: MetaCyc:GLNSYN-PWY
is_a: GO:0006541 ! glutamine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009084 ! glutamine family amino acid biosynthetic process
[Term]
@@ -63042,7 +62888,6 @@ synonym: "glycine formation" EXACT []
synonym: "glycine synthesis" EXACT []
xref: MetaCyc:GLYCINE-SYN2-PWY
is_a: GO:0006544 ! glycine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009070 ! serine family amino acid biosynthetic process
[Term]
@@ -63105,7 +62950,8 @@ name: leucine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving leucine, 2-amino-4-methylpentanoic acid." [GOC:ai]
synonym: "leucine metabolism" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0009081 ! branched-chain amino acid metabolic process
+is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
id: GO:0006552
@@ -63117,7 +62963,8 @@ synonym: "leucine catabolism" EXACT []
synonym: "leucine degradation" EXACT []
xref: MetaCyc:LEU-DEG2-PWY
is_a: GO:0006551 ! leucine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009083 ! branched-chain amino acid catabolic process
+is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
id: GO:0006553
@@ -63229,7 +63076,6 @@ synonym: "proline synthesis" EXACT []
xref: MetaCyc:PROSYN-PWY
xref: MetaCyc:PWY-3341
is_a: GO:0006560 ! proline metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009084 ! glutamine family amino acid biosynthetic process
[Term]
@@ -63263,7 +63109,6 @@ synonym: "L-serine formation" EXACT []
synonym: "L-serine synthesis" EXACT []
xref: MetaCyc:SERSYN-PWY
is_a: GO:0006563 ! L-serine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009070 ! serine family amino acid biosynthetic process
[Term]
@@ -63373,7 +63218,8 @@ name: valine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid." [GOC:ai]
synonym: "valine metabolism" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
+is_a: GO:0009081 ! branched-chain amino acid metabolic process
+is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
id: GO:0006574
@@ -63385,13 +63231,16 @@ synonym: "valine catabolism" EXACT []
synonym: "valine degradation" EXACT []
xref: MetaCyc:VALDEG-PWY
is_a: GO:0006573 ! valine metabolic process
-is_a: GO:0009063 ! cellular amino acid catabolic process
+is_a: GO:0009083 ! branched-chain amino acid catabolic process
+is_a: GO:1901606 ! alpha-amino acid catabolic process
[Term]
id: GO:0006575
name: cellular modified amino acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents." [GOC:ai]
+subset: goslim_drosophila
+subset: goslim_generic
synonym: "amino acid derivative metabolic process" EXACT []
synonym: "cellular amino acid derivative metabolic process" EXACT []
synonym: "cellular amino acid derivative metabolism" EXACT []
@@ -63582,7 +63431,6 @@ synonym: "ornithine biosynthesis" EXACT []
synonym: "ornithine formation" EXACT []
synonym: "ornithine synthesis" EXACT []
is_a: GO:0006591 ! ornithine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
[Term]
@@ -63602,6 +63450,7 @@ id: GO:0006595
name: polyamine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups." [ISBN:0198506732]
+subset: goslim_drosophila
synonym: "polyamine metabolism" EXACT []
is_a: GO:0006576 ! cellular biogenic amine metabolic process
@@ -63710,8 +63559,6 @@ namespace: biological_process
def: "The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif." [GOC:ma]
comment: Note that protein targeting encompasses the transport of the protein to the specified location, and may also include additional steps such as protein processing.
subset: goslim_chembl
-subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
synonym: "nascent polypeptide association" RELATED []
@@ -63856,7 +63703,7 @@ def: "The process in which SRP binds to the signal peptide in a nascent protein,
synonym: "signal sequence recognition during SRP-dependent cotranslational protein targeting to membrane" EXACT []
synonym: "SRP-dependent cotranslational membrane targeting, signal sequence recognition" EXACT []
synonym: "SRP-dependent cotranslational protein-membrane targeting, signal sequence recognition" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0006614 ! SRP-dependent cotranslational protein targeting to membrane
[Term]
@@ -65305,6 +65152,7 @@ id: GO:0006744
name: ubiquinone biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme." [GOC:mah]
+subset: goslim_drosophila
subset: goslim_pombe
synonym: "coenzyme Q biosynthesis" EXACT []
synonym: "coenzyme Q biosynthetic process" EXACT []
@@ -65507,6 +65355,8 @@ namespace: biological_process
def: "The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems." [GOC:ai]
subset: goslim_aspergillus
subset: goslim_candida
+subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
@@ -65581,6 +65431,7 @@ synonym: "thiamine metabolism" EXACT []
synonym: "vitamin B1 metabolic process" EXACT []
synonym: "vitamin B1 metabolism" EXACT []
xref: Wikipedia:Thiamine
+is_a: GO:0034308 ! primary alcohol metabolic process
is_a: GO:0042723 ! thiamine-containing compound metabolic process
[Term]
@@ -65944,10 +65795,14 @@ replaced_by: GO:0004601
id: GO:0006805
name: xenobiotic metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide." [GOC:cab2]
+alt_id: GO:0017144
+def: "The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:cab2, GOC:krc]
subset: goslim_chembl
subset: goslim_pir
+synonym: "drug metabolic process" RELATED []
+synonym: "drug metabolism" RELATED []
synonym: "xenobiotic metabolism" EXACT []
+xref: Wikipedia:Drug_metabolism
xref: Wikipedia:Xenobiotic_metabolism
is_a: GO:0044237 ! cellular metabolic process
relationship: part_of GO:0071466 ! cellular response to xenobiotic stimulus
@@ -66006,7 +65861,6 @@ subset: gocheck_do_not_annotate
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
@@ -66052,7 +65906,7 @@ synonym: "potassium conductance" NARROW []
synonym: "potassium ion conductance" NARROW []
synonym: "potassium transport" RELATED []
synonym: "sodium/potassium transport" BROAD []
-is_a: GO:0006812 ! cation transport
+is_a: GO:0030001 ! metal ion transport
[Term]
id: GO:0006814
@@ -66067,7 +65921,7 @@ synonym: "sodium transport" EXACT []
synonym: "sodium/potassium transport" BROAD []
synonym: "sodium:calcium exchange" NARROW []
synonym: "sodium:solute transport" NARROW []
-is_a: GO:0006812 ! cation transport
+is_a: GO:0030001 ! metal ion transport
[Term]
id: GO:0006815
@@ -66175,7 +66029,6 @@ def: "The directed movement of zinc (Zn II) ions into, out of or within a cell,
synonym: "zinc II ion transport" EXACT []
synonym: "zinc transport" EXACT [GOC:mah]
is_a: GO:0000041 ! transition metal ion transport
-is_a: GO:0030001 ! metal ion transport
[Term]
id: GO:0006832
@@ -66238,10 +66091,7 @@ name: mitochondrial transport
namespace: biological_process
def: "Transport of substances into, out of or within a mitochondrion." [GOC:ai]
subset: goslim_drosophila
-synonym: "mitochondrial alpha-ketoglutarate/malate transport" NARROW []
-synonym: "mitochondrial aspartate/glutamate transport" NARROW []
-synonym: "mitochondrial sodium/calcium ion exchange" NARROW []
-is_a: GO:0006810 ! transport
+is_a: GO:0046907 ! intracellular transport
[Term]
id: GO:0006840
@@ -66345,6 +66195,7 @@ namespace: biological_process
def: "The process in which a calcium ion (Ca2+) is transported across a mitochondrial membrane, into or out of the mitochondrion." [GOC:ai]
synonym: "mitochondrial calcium transport" EXACT []
is_a: GO:0070588 ! calcium ion transmembrane transport
+is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0006852
@@ -66367,6 +66218,7 @@ namespace: biological_process
def: "The transfer of acyl groups to and from acyl-CoA molecules to form O-acylcarnitine, which can exchange across the mitochondrial inner membrane with unacylated carnitine." [ISBN:0198547684]
comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'.
xref: Wikipedia:Carnitine#Role_in_fatty_acid_metabolism
+is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0015909 ! long-chain fatty acid transport
is_a: GO:0032365 ! intracellular lipid transport
is_a: GO:1902001 ! fatty acid transmembrane transport
@@ -66384,13 +66236,14 @@ replaced_by: GO:0005471
[Term]
id: GO:0006855
-name: drug transmembrane transport
+name: xenobiotic transmembrane transport
namespace: biological_process
-def: "The process in which a drug is transported across a membrane." [GOC:ai, GOC:bf]
+def: "The process in which a xenobiotic, a compound foreign to the organim exposed to it, is transported across a membrane. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:ai, GOC:bf, GOC:krc]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "drug membrane transport" EXACT []
+synonym: "drug transmembrane transport" RELATED []
synonym: "multidrug transport" RELATED []
-is_a: GO:0015893 ! drug transport
+is_a: GO:0042908 ! xenobiotic transport
is_a: GO:0055085 ! transmembrane transport
[Term]
@@ -66634,6 +66487,7 @@ name: intracellular protein transport
namespace: biological_process
alt_id: GO:0032779
def: "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." [GOC:mah]
+subset: goslim_generic
synonym: "copper-induced intracellular protein transport" RELATED [GOC:al]
is_a: GO:0015031 ! protein transport
is_a: GO:0046907 ! intracellular transport
@@ -66665,7 +66519,6 @@ synonym: "anterograde transport, ER to Golgi" EXACT []
synonym: "anterograde vesicle-mediated transport, endoplasmic reticulum to Golgi" EXACT []
synonym: "anterograde vesicle-mediated transport, ER to Golgi" EXACT []
synonym: "endoplasmic reticulum to Golgi transport" EXACT []
-synonym: "endoplasmic reticulum to Golgi vesicle-mediated transport" EXACT []
synonym: "ER to Golgi transport" EXACT []
synonym: "ER to Golgi vesicle-mediated transport" EXACT []
synonym: "rough endoplasmic reticulum to cis-Golgi transport" EXACT []
@@ -66699,7 +66552,6 @@ synonym: "cis-Golgi to rough ER vesicle-mediated transport" EXACT []
synonym: "retrograde (Golgi to ER) transport" EXACT []
synonym: "retrograde transport, Golgi to endoplasmic reticulum" EXACT []
synonym: "retrograde transport, Golgi to ER" EXACT []
-synonym: "retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum" RELATED []
synonym: "retrograde vesicle-mediated transport, Golgi to ER" EXACT []
is_a: GO:0048193 ! Golgi vesicle transport
@@ -66760,7 +66612,6 @@ def: "The directed movement of substances from the Golgi to the vacuole." [GOC:a
synonym: "Golgi to vacuole vesicle-mediated transport" EXACT []
is_a: GO:0006892 ! post-Golgi vesicle-mediated transport
is_a: GO:0007034 ! vacuolar transport
-is_a: GO:0046907 ! intracellular transport
[Term]
id: GO:0006897
@@ -67260,7 +67111,6 @@ subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_plant
synonym: "response to abiotic stress" RELATED []
@@ -67292,6 +67142,7 @@ id: GO:0006954
name: inflammatory response
namespace: biological_process
def: "The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages." [GO_REF:0000022, ISBN:0198506732]
+subset: goslim_generic
synonym: "inflammation" BROAD []
xref: Wikipedia:Inflammation
is_a: GO:0006952 ! defense response
@@ -67696,7 +67547,7 @@ synonym: "nuclear pore complex organization and biogenesis" RELATED [GOC:mah]
synonym: "nuclear pore organisation" EXACT []
synonym: "nuclear pore organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0006997 ! nucleus organization
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0007000
@@ -67789,7 +67640,6 @@ name: plasma membrane organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." [GOC:dph, GOC:jl, GOC:mah]
subset: goslim_chembl
-subset: goslim_generic
synonym: "plasma membrane organisation" EXACT []
synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0061024 ! membrane organization
@@ -67803,6 +67653,7 @@ def: "A process that is carried out at the cellular level which results in the a
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
+subset: goslim_drosophila
subset: goslim_generic
subset: goslim_yeast
synonym: "cytoskeletal organization and biogenesis" RELATED [GOC:mah]
@@ -67864,6 +67715,8 @@ id: GO:0007018
name: microtubule-based movement
namespace: biological_process
def: "A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." [GOC:cjm, ISBN:0815316194]
+subset: goslim_drosophila
+subset: goslim_generic
is_a: GO:0006928 ! movement of cell or subcellular component
is_a: GO:0007017 ! microtubule-based process
@@ -67897,7 +67750,7 @@ def: "The aggregation and bonding together of alpha- and beta-tubulin to form a
synonym: "tubulin assembly" EXACT []
synonym: "tubulin folding" RELATED []
synonym: "tubulin-specific chaperone activity" RELATED []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0007023
@@ -67978,6 +67831,8 @@ id: GO:0007031
name: peroxisome organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules." [GOC:mah]
+subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pir
subset: goslim_pombe
subset: goslim_yeast
@@ -68003,6 +67858,7 @@ name: vacuole organization
namespace: biological_process
alt_id: GO:0044086
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole." [GOC:mah]
+subset: goslim_drosophila
subset: goslim_pir
subset: goslim_yeast
synonym: "vacuolar assembly" NARROW [GOC:mah]
@@ -68017,9 +67873,7 @@ name: vacuolar transport
namespace: biological_process
def: "The directed movement of substances into, out of or within a vacuole." [GOC:ai]
subset: goslim_chembl
-subset: goslim_generic
-is_a: GO:0006810 ! transport
-is_a: GO:0009987 ! cellular process
+is_a: GO:0046907 ! intracellular transport
[Term]
id: GO:0007035
@@ -68042,8 +67896,8 @@ namespace: biological_process
def: "The directed movement of proteins imported into a cell by endocytosis to the vacuole." [GOC:ai]
comment: See also the biological process term 'endocytosis ; GO:0006897'.
synonym: "delivery of endocytosed proteins to the vacuole" EXACT []
+is_a: GO:0006886 ! intracellular protein transport
is_a: GO:0007034 ! vacuolar transport
-is_a: GO:0015031 ! protein transport
[Term]
id: GO:0007039
@@ -68061,6 +67915,7 @@ id: GO:0007040
name: lysosome organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases." [GOC:mah]
+subset: goslim_generic
synonym: "lysosome organisation" EXACT []
synonym: "lysosome organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0080171 ! lytic vacuole organization
@@ -68121,7 +67976,6 @@ subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
-subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "cell-division cycle" EXACT []
@@ -68167,7 +68021,7 @@ name: spindle assembly involved in male meiosis
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the spindle during a meiotic cell cycle in males. An example of this is found in Drosophila melanogaster." [GOC:mah]
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-is_a: GO:0090306 ! spindle assembly involved in meiosis
+is_a: GO:0090306 ! meiotic spindle assembly
relationship: part_of GO:0007140 ! male meiotic nuclear division
[Term]
@@ -68195,7 +68049,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the spindle during a meiotic cell cycle in females. An example of this is found in Drosophila melanogaster." [GOC:mah]
synonym: "female meiotic spindle assembly" RELATED []
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
-is_a: GO:0090306 ! spindle assembly involved in meiosis
+is_a: GO:0090306 ! meiotic spindle assembly
relationship: part_of GO:0007143 ! female meiotic nuclear division
[Term]
@@ -68222,6 +68076,7 @@ name: chromosome segregation
namespace: biological_process
def: "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." [GOC:jl, GOC:mah, GOC:mtg_cell_cycle, GOC:vw]
subset: goslim_chembl
+subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pir
subset: goslim_yeast
@@ -68582,7 +68437,6 @@ synonym: "Mad2-dependent checkpoint" NARROW []
synonym: "mitotic cell cycle spindle assembly checkpoint" EXACT []
synonym: "mitotic checkpoint" EXACT []
synonym: "mitotic spindle assembly checkpoint" EXACT []
-synonym: "mitotic spindle assembly checkpoint signaling" EXACT []
synonym: "mitotic spindle assembly checkpoint signalling" EXACT []
synonym: "SAC-independent checkpoint" NARROW []
synonym: "signal transduction involved in Dma1-dependent checkpoint" NARROW []
@@ -68941,7 +68795,6 @@ namespace: biological_process
def: "The meiotic cell cycle process where side by side pairing and physical juxtaposition of homologous chromosomes is created during meiotic prophase. Homologous chromosome pairing begins when the chromosome arms begin to pair from the clustered telomeres and ends when synaptonemal complex or linear element assembly is complete." [GOC:mtg_cell_cycle, PMID:22582262, PMID:23117617, PMID:31811152]
synonym: "chromosomal pairing" RELATED [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "chromosomal synapsis" NARROW [GOC:ascb_2009, GOC:dph, GOC:tb]
-synonym: "homologous chromosome pairing at meiosis" EXACT []
synonym: "synapsis" NARROW []
xref: Wikipedia:Synapsis
is_a: GO:0070192 ! chromosome organization involved in meiotic cell cycle
@@ -69235,6 +69088,8 @@ namespace: biological_process
alt_id: GO:0030012
alt_id: GO:0030467
def: "Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns." [GOC:mah]
+subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pombe
synonym: "cell polarity" RELATED [GOC:mah, GOC:vw]
synonym: "establishment and/or maintenance of cell polarity" RELATED []
@@ -69262,7 +69117,6 @@ comment: Note that signal transduction is defined broadly to include a ligand in
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_plant
synonym: "signal transduction by cis-phosphorylation" NARROW []
@@ -69333,7 +69187,7 @@ def: "Any process that initiates the activity of the inactive transmembrane rece
synonym: "transmembrane receptor protein tyrosine kinase activation" RELATED [GOC:dph, GOC:tb]
synonym: "transmembrane receptor protein tyrosine kinase dimerization" RELATED [GOC:dph, GOC:mtg_lung]
is_a: GO:0032147 ! activation of protein kinase activity
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway
[Term]
@@ -69343,7 +69197,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a complex capable of relaying a signal within a cell." [GOC:bf, GOC:signaling, PMID:9646862]
synonym: "signal complex formation" EXACT []
is_a: GO:0009966 ! regulation of signal transduction
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0007173
@@ -69448,7 +69302,7 @@ def: "The aggregation, arrangement and bonding together of a ligand-bound type I
synonym: "TGF-beta receptor complex assembly" EXACT []
synonym: "TGF-beta:type II receptor:type I receptor complex assembly" EXACT []
synonym: "TGFbeta receptor complex assembly" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0007179 ! transforming growth factor beta receptor signaling pathway
[Term]
@@ -69469,7 +69323,7 @@ name: SMAD protein complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins." [GOC:isa_complete]
synonym: "SMAD protein heteromerization" NARROW [GOC:mah, PMID:9670020]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway
[Term]
@@ -70230,24 +70084,25 @@ is_a: GO:0051403 ! stress-activated MAPK cascade
[Term]
id: GO:0007256
-name: activation of JNKK activity
+name: obsolete activation of JNKK activity
namespace: biological_process
-def: "The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress." [GOC:bf, PMID:11790549]
+def: "OBSOLETE. The initiation of the activity of the inactive enzyme JUN kinase kinase (JNKK) activity. JNKKs are involved in a signaling pathway that is primarily activated by cytokines and exposure to environmental stress." [GOC:bf, PMID:11790549]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of JUN kinase kinase activity" EXACT []
synonym: "positive regulation of JUNKK activity" BROAD []
-is_a: GO:0000186 ! activation of MAPKK activity
-is_a: GO:0043507 ! positive regulation of JUN kinase activity
-relationship: part_of GO:0007254 ! JNK cascade
+is_obsolete: true
+consider: GO:0043539
+consider: GO:0046328
[Term]
id: GO:0007257
-name: activation of JUN kinase activity
+name: obsolete activation of JUN kinase activity
namespace: biological_process
-def: "The initiation of the activity of the inactive enzyme JUN kinase (JNK)." [GOC:bf]
+def: "OBSOLETE. The initiation of the activity of the inactive enzyme JUN kinase (JNK)." [GOC:bf]
synonym: "activation of SAPK activity" BROAD []
-is_a: GO:0000187 ! activation of MAPK activity
-is_a: GO:0043507 ! positive regulation of JUN kinase activity
-relationship: part_of GO:0007254 ! JNK cascade
+is_obsolete: true
+consider: GO:0007254
+consider: GO:0043539
[Term]
id: GO:0007258
@@ -70341,7 +70196,6 @@ name: cell-cell signaling
namespace: biological_process
def: "Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions." [GOC:dos, GOC:mah]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_plant
synonym: "cell-cell signalling" EXACT []
is_a: GO:0007154 ! cell communication
@@ -70423,6 +70277,7 @@ name: multicellular organism development
namespace: biological_process
def: "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:dph, GOC:ems, GOC:isa_complete, GOC:tb]
comment: Note that this term was 'developmental process'.
+subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_plant
is_a: GO:0032501 ! multicellular organismal process
@@ -70544,9 +70399,8 @@ relationship: part_of GO:0048515 ! spermatid differentiation
id: GO:0007287
name: Nebenkern assembly
namespace: biological_process
-def: "Fusion of mitochondria during insect spermatid differentiation to form two masses, which wrap around each other to form a densely packed sphere called the Nebenkern." [GOC:bf, ISBN:0879694238]
+def: "Fusion of mitochondria during insect spermatid differentiation to form two masses, which wrap around each other to form a densely packed sphere called the Nebenkern." [GOC:bf, ISBN:0879694238, PMID:9550716]
comment: See also the cellular component term 'Nebenkern ; GO:0016006', and the fly_anatomy.ontology term 'Nebenkern ; FBbt:00004943'.
-synonym: "Nebenkern assembly" EXACT [PMID:9550716]
synonym: "Nebenkern formation" RELATED [GOC:dph]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
@@ -71003,7 +70857,6 @@ id: GO:0007341
name: penetration of zona pellucida
namespace: biological_process
def: "The infiltration by sperm of the zona pellucida to reach the oocyte. The process involves digestive enzymes from a modified lysosome called the acrosome, situated at the head of the sperm." [GOC:jl, http://arbl.cvmbs.colostate.edu/hbooks/pathphys/reprod/fert/fert.html]
-is_a: GO:0044703 ! multi-organism reproductive process
is_a: GO:0044706 ! multi-multicellular organism process
is_a: GO:0048609 ! multicellular organismal reproductive process
relationship: part_of GO:0007338 ! single fertilization
@@ -71177,11 +71030,11 @@ is_obsolete: true
[Term]
id: GO:0007358
-name: establishment of central gap gene boundaries
+name: obsolete establishment of central gap gene boundaries
namespace: biological_process
-def: "Specification of the borders of central gap gene expression mediated largely by the effects of other gap genes; in insects this is exemplified by knirps repression of Kruppel." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
-is_a: GO:0048859 ! formation of anatomical boundary
-relationship: part_of GO:0007356 ! thorax and anterior abdomen determination
+def: "OBSOLETE. Specification of the borders of central gap gene expression mediated largely by the effects of other gap genes; in insects this is exemplified by knirps repression of Kruppel." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+comment: This term has been obsoleted because it represents a transcriptional feedback loop covered by other processes.
+is_obsolete: true
[Term]
id: GO:0007359
@@ -71209,11 +71062,11 @@ is_obsolete: true
[Term]
id: GO:0007361
-name: establishment of posterior gap gene boundaries
+name: obsolete establishment of posterior gap gene boundaries
namespace: biological_process
-def: "Specification of the borders of posterior gap gene expression mediated largely by the effects of other gap genes; in insects this is exemplified by hunchback and tailless repression of knirps." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
-is_a: GO:0048859 ! formation of anatomical boundary
-relationship: part_of GO:0007359 ! posterior abdomen determination
+def: "OBSOLETE. Specification of the borders of posterior gap gene expression mediated largely by the effects of other gap genes; in insects this is exemplified by hunchback and tailless repression of knirps." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+comment: This term has been obsoleted because it represents a transcriptional feedback loop covered by other processes.
+is_obsolete: true
[Term]
id: GO:0007362
@@ -71239,11 +71092,11 @@ is_obsolete: true
[Term]
id: GO:0007364
-name: establishment of terminal gap gene boundary
+name: obsolete establishment of terminal gap gene boundary
namespace: biological_process
-def: "Specification of the borders of terminal gap gene expression mediated largely by the effects of other gap genes." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
-is_a: GO:0048859 ! formation of anatomical boundary
-relationship: part_of GO:0007362 ! terminal region determination
+def: "OBSOLETE. Specification of the borders of terminal gap gene expression mediated largely by the effects of other gap genes." [http://fly.ebi.ac.uk/allied-data/lk/interactive-fly/aimain/1aahome.htm, ISBN:0879694238]
+comment: This term has been obsoleted because it represents a transcriptional feedback loop covered by other processes.
+is_obsolete: true
[Term]
id: GO:0007365
@@ -71729,6 +71582,7 @@ id: GO:0007423
name: sensory organ development
namespace: biological_process
def: "The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure." [GOC:go_curators]
+subset: goslim_drosophila
synonym: "sense organ development" EXACT [GOC:dph]
is_a: GO:0048513 ! animal organ development
@@ -71799,6 +71653,7 @@ id: GO:0007431
name: salivary gland development
namespace: biological_process
def: "The process whose specific outcome is the progression of the salivary gland over time, from its formation to the mature structure. Salivary glands include any of the saliva-secreting exocrine glands of the oral cavity." [GOC:jid, UBERON:0001044]
+subset: goslim_drosophila
is_a: GO:0048732 ! gland development
relationship: part_of GO:0035272 ! exocrine system development
@@ -72317,6 +72172,7 @@ id: GO:0007498
name: mesoderm development
namespace: biological_process
def: "The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue." [GOC:dph, GOC:tb]
+subset: goslim_drosophila
is_a: GO:0009888 ! tissue development
[Term]
@@ -72932,6 +72788,7 @@ namespace: biological_process
alt_id: GO:0016280
def: "A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators]
subset: goslim_chembl
+subset: goslim_drosophila
subset: goslim_generic
synonym: "ageing" EXACT []
xref: Wikipedia:Aging
@@ -73113,6 +72970,7 @@ id: GO:0007588
name: excretion
namespace: biological_process
def: "The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds." [ISBN:0192801023]
+subset: gocheck_do_not_annotate
subset: goslim_pir
xref: Wikipedia:Excretion
is_a: GO:0003008 ! system process
@@ -73705,7 +73563,7 @@ is_a: GO:0005214 ! structural constituent of chitin-based cuticle
id: GO:0008013
name: beta-catenin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the beta subunit of the catenin complex." [GOC:bf]
+def: "Binding to a catenin beta subunit." [GOC:bf]
is_a: GO:0005515 ! protein binding
[Term]
@@ -73745,7 +73603,7 @@ relationship: regulates GO:0060047 ! heart contraction
id: GO:0008017
name: microtubule binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers." [GOC:krc]
+def: "Binding to a microtubule, a filament composed of tubulin monomers." [GOC:krc]
synonym: "microtubule severing activity" RELATED []
synonym: "microtubule/chromatin interaction" RELATED []
xref: Reactome:R-HSA-9614343 "Viral UL47:UL48 Proteins Bind HCMV Tegumented Virion to Host Microtuble and Dynein complexs"
@@ -73801,7 +73659,7 @@ relationship: part_of GO:0098793 ! presynapse
id: GO:0008022
name: protein C-terminus binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxyl function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732]
+def: "Binding to a protein C-terminus, the end of a peptide chain at which the 1-carboxyl function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732]
subset: goslim_chembl
synonym: "C-terminal binding" EXACT []
synonym: "C-terminal end binding" EXACT [GOC:sl]
@@ -73905,7 +73763,7 @@ is_a: GO:0034470 ! ncRNA processing
id: GO:0008034
name: obsolete lipoprotein binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." [GOC:jl, ISBN:0198506732]
+def: "OBSOLETE. Binding to a conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." [GOC:jl, ISBN:0198506732]
comment: This term was made obsolete because its text definition and implicit ontology-structure definition disagreed, and as a result the term had been used in annotations with more than one meaning.
synonym: "lipoprotein binding" EXACT []
is_obsolete: true
@@ -73916,7 +73774,7 @@ consider: GO:0071813
id: GO:0008035
name: high-density lipoprotein particle binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with high-density lipoprotein particle, a lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE." [GOC:mah]
+def: "Binding to high-density lipoprotein particle, a lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE." [GOC:mah]
synonym: "HDL binding" EXACT [GOC:mah]
is_a: GO:0071813 ! lipoprotein particle binding
@@ -74018,8 +73876,9 @@ name: enzyme activator activity
namespace: molecular_function
alt_id: GO:0010577
def: "Binds to and increases the activity of an enzyme." [GOC:dph, GOC:mah, GOC:tb]
+comment: This term should only be used in cases when the regulator directly interacts with the enzyme.
synonym: "metalloenzyme activator activity" NARROW []
-is_a: GO:0003674 ! molecular_function
+is_a: GO:0030234 ! enzyme regulator activity
[Term]
id: GO:0008048
@@ -74078,7 +73937,7 @@ is_a: GO:0048284 ! organelle fusion
id: GO:0008055
name: ocellus pigment biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ocellus pigments, any general or particular coloring matter in living organisms, found or utilized in the ocellus, a minute simple eye found in many invertebrates." [GOC:ai, PMID:15176085, PMID:18421706]
+def: "The chemical reactions and pathways resulting in the formation of ocellus pigments, general or particular coloring matter in living organisms, found or utilized in the ocellus, a minute simple eye found in many invertebrates." [GOC:ai, PMID:15176085, PMID:18421706]
synonym: "ocellus pigment anabolism" EXACT []
synonym: "ocellus pigment biosynthesis" EXACT []
synonym: "ocellus pigment formation" EXACT []
@@ -74120,7 +73979,7 @@ is_a: GO:0048753 ! pigment granule organization
id: GO:0008061
name: chitin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues." [GOC:jl, ISBN:0198506732]
+def: "Binding to chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues." [GOC:jl, ISBN:0198506732]
subset: goslim_drosophila
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -74332,7 +74191,7 @@ is_a: GO:0048018 ! receptor ligand activity
id: GO:0008084
name: imaginal disc growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an imaginal disc growth factor receptor." [GOC:mah]
+def: "Binding to an imaginal disc growth factor receptor." [GOC:mah]
synonym: "imaginal disc growth factor" NARROW []
is_a: GO:0070851 ! growth factor receptor binding
@@ -74410,7 +74269,7 @@ relationship: part_of GO:0030864 ! cortical actin cytoskeleton
id: GO:0008092
name: cytoskeletal protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." [GOC:mah]
+def: "Binding to a protein component of a cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." [GOC:mah]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
@@ -74430,17 +74289,18 @@ is_a: GO:0030674 ! protein-macromolecule adaptor activity
[Term]
id: GO:0008094
-name: ATPase, acting on DNA
+name: ATP-dependent activity, acting on DNA
namespace: molecular_function
alt_id: GO:0004011
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction." [GOC:jl]
+def: "Catalytic activity that acts to modify DNA, driven by ATP hydrolysis." [GOC:pdt]
synonym: "adenosinetriphosphatase (DNA-dependent)" EXACT []
-synonym: "ATPase activity, acting on DNA" RELATED []
+synonym: "ATPase activity, acting on DNA" EXACT []
+synonym: "ATPase, acting on DNA" EXACT []
synonym: "DNA dependent ATPase activity" EXACT []
synonym: "DNA-dependent adenosinetriphosphatase activity" EXACT []
-synonym: "DNA-dependent ATPase activity" RELATED []
-is_a: GO:0016887 ! ATPase
+synonym: "DNA-dependent ATPase activity" EXACT []
is_a: GO:0140097 ! catalytic activity, acting on DNA
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0008096
@@ -74454,14 +74314,14 @@ is_a: GO:0004301 ! epoxide hydrolase activity
id: GO:0008097
name: 5S rRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 5S ribosomal RNA, the smallest RNA constituent of a ribosome." [GOC:jl, ISBN:0321000382]
+def: "Binding to a 5S ribosomal RNA, the smallest RNA constituent of a ribosome." [GOC:jl, ISBN:0321000382]
is_a: GO:0019843 ! rRNA binding
[Term]
id: GO:0008098
name: 5S rRNA primary transcript binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the unprocessed 5S ribosomal RNA transcript." [GOC:jl]
+def: "Binding to an unprocessed 5S ribosomal RNA transcript." [GOC:jl]
is_a: GO:0008097 ! 5S rRNA binding
[Term]
@@ -74491,6 +74351,7 @@ name: protein localization
namespace: biological_process
alt_id: GO:0008105
def: "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai]
+subset: goslim_drosophila
synonym: "asymmetric protein localisation" RELATED [GOC:mah]
synonym: "asymmetric protein localization" RELATED []
synonym: "establishment and maintenance of asymmetric protein localization" RELATED []
@@ -74516,7 +74377,7 @@ is_a: GO:0004033 ! aldo-keto reductase (NADP) activity
id: GO:0008107
name: galactoside 2-alpha-L-fucosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-L-fucose + beta-D-galactosyl-R = GDP + alpha-L-fucosyl-(1,2)-beta-D-galactosyl-R." [EC:2.4.1.69, RHEA:50667]
+def: "Catalysis of the reaction: GDP-L-fucose + beta-D-galactosyl-R = GDP + alpha-L-fucosyl-(1,2)-beta-D-galactosyl-R." [EC:2.4.1.69, RHEA:50664]
synonym: "alpha(1,2)-L-fucosyltransferase activity" EXACT []
synonym: "alpha-(1->2)-L-fucosyltransferase activity" RELATED [EC:2.4.1.69]
synonym: "alpha-2-fucosyltransferase activity" RELATED [EC:2.4.1.69]
@@ -74546,7 +74407,7 @@ xref: MetaCyc:GALACTOSIDE-2-L-FUCOSYLTRANSFERASE-RXN
xref: Reactome:R-HSA-9036987 "FUT2 transfers Fuc to Type 1 chains to form H antigen-sec"
xref: Reactome:R-HSA-9603982 "FUT2 transfers Fuc to LeA to form LeB"
xref: Reactome:R-HSA-9603983 "FUT2 transfers Fuc to LeX to form LeY"
-xref: RHEA:50667
+xref: RHEA:50664
is_a: GO:0031127 ! alpha-(1,2)-fucosyltransferase activity
[Term]
@@ -74811,7 +74672,10 @@ xref: MetaCyc:1.10.2.2-RXN
xref: Reactome:R-HSA-164651 "Electron transfer from ubiquinol to cytochrome c of complex III"
xref: RHEA:11484
is_a: GO:0009055 ! electron transfer activity
+is_a: GO:0015078 ! proton transmembrane transporter activity
+is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity
is_a: GO:0016679 ! oxidoreductase activity, acting on diphenols and related substances as donors
+is_a: GO:0022853 ! active ion transmembrane transporter activity
[Term]
id: GO:0008123
@@ -74929,7 +74793,7 @@ name: primary amine oxidase activity
namespace: molecular_function
alt_id: GO:0004041
alt_id: GO:0008122
-def: "Catalysis of the reaction: a primary amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide." [EC:1.4.3.21, EC:1.4.3.22, EC:1.4.3.4, MetaCyc:RXN-9597]
+def: "Catalysis of the reaction: a primary amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide." [EC:1.4.3.21]
synonym: "amine oxidase (copper-containing) activity" NARROW []
synonym: "amine oxidase activity" BROAD [EC:1.4.3.21]
synonym: "primary-amine:oxygen oxidoreductase (deaminating) activity" EXACT systematic_synonym [EC:1.4.3.21]
@@ -74971,13 +74835,12 @@ replaced_by: GO:0004222
id: GO:0008134
name: transcription factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a transcription factor, a protein required to initiate or regulate transcription." [ISBN:0198506732]
+def: "Binding to a transcription factor, a protein required to initiate or regulate transcription." [ISBN:0198506732]
comment: Note that this term should not be used for direct annotation. Please consier one of the more specific descendants, GO:0140297 ; DNA-binding transcription factor binding, GO:0140296 ; general transcription initiation factor binding or GO:0001221 ; transcription coregulator binding.
subset: gocheck_do_not_annotate
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_yeast
synonym: "TF binding" EXACT []
@@ -74987,9 +74850,8 @@ is_a: GO:0005515 ! protein binding
id: GO:0008135
name: translation factor activity, RNA binding
namespace: molecular_function
-def: "Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome." [GOC:ai, GOC:vw]
+def: "Functions during translation by binding to RNA during polypeptide synthesis at the ribosome." [GOC:ai, GOC:vw]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_plant
subset: goslim_yeast
synonym: "translation factor activity, nucleic acid binding" BROAD [GOC:mah]
@@ -75032,6 +74894,7 @@ xref: MetaCyc:RXN0-5330
xref: Reactome:R-HSA-163217 "Complex I oxidises NADH to NAD+, reduces CoQ to QH2"
xref: RHEA:29091
is_a: GO:0009055 ! electron transfer activity
+is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity
is_a: GO:0050136 ! NADH dehydrogenase (quinone) activity
[Term]
@@ -75050,7 +74913,7 @@ is_a: GO:0004721 ! phosphoprotein phosphatase activity
id: GO:0008139
name: nuclear localization sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus." [GOC:ai]
+def: "Binding to a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus." [GOC:ai]
synonym: "NLS binding" EXACT []
synonym: "nuclear localisation sequence binding" EXACT [GOC:mah]
synonym: "nuclear localization signal binding" EXACT []
@@ -75060,7 +74923,7 @@ is_a: GO:0005048 ! signal sequence binding
id: GO:0008140
name: cAMP response element binding protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cAMP response element binding protein (a CREB protein)." [GOC:mah]
+def: "Binding to a cAMP response element binding protein (a CREB protein)." [GOC:mah]
synonym: "3',5' cAMP response element binding protein binding" EXACT []
synonym: "3',5'-cAMP response element binding protein binding" EXACT []
synonym: "adenosine 3',5'-cyclophosphate response element binding protein binding" EXACT []
@@ -75084,14 +74947,14 @@ consider: GO:0007594
id: GO:0008142
name: oxysterol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with oxysterol, an oxidized form of cholesterol." [GOC:curators]
+def: "Binding to oxysterol, an oxidized form of cholesterol." [GOC:curators]
is_a: GO:0032934 ! sterol binding
[Term]
id: GO:0008143
name: poly(A) binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA." [GOC:jl]
+def: "Binding to a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA." [GOC:jl]
synonym: "poly(A) binding, within an RNA molecule" EXACT []
synonym: "poly(rA) binding" EXACT [GOC:mah]
synonym: "poly-A binding" EXACT [GOC:mah]
@@ -75100,18 +74963,17 @@ is_a: GO:0070717 ! poly-purine tract binding
[Term]
id: GO:0008144
-name: drug binding
+name: obsolete drug binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease." [GOC:jl, ISBN:0198506732]
-subset: goslim_pir
-is_a: GO:0005488 ! binding
+def: "OBSOLETE. Binding to a drug, a naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism;typically used in the diagnosis, prevention, or treatment of disease." [GOC:jl, ISBN:0198506732]
+comment: It is not meaningful to describe a molecular function by what role a compound may be used for at some times.
+is_obsolete: true
[Term]
id: GO:0008145
name: phenylalkylamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phenylalkylamine or any of its derivatives." [GOC:jl]
-is_a: GO:0008144 ! drug binding
+def: "Binding to phenylalkylamine or one of its derivatives." [GOC:jl]
is_a: GO:0043176 ! amine binding
[Term]
@@ -75168,7 +75030,6 @@ comment: Note that, in addition to forming the root of the biological process on
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_plant
@@ -75258,7 +75119,7 @@ relationship: negatively_regulates GO:0006260 ! DNA replication
id: GO:0008157
name: protein phosphatase 1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme protein phosphatase 1." [GOC:jl]
+def: "Binding to a protein phosphatase 1." [GOC:jl]
is_a: GO:0019903 ! protein phosphatase binding
[Term]
@@ -75363,7 +75224,6 @@ alt_id: GO:0004480
def: "Catalysis of the transfer of a methyl group to an acceptor molecule." [ISBN:0198506732]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_yeast
synonym: "methylase" BROAD []
xref: EC:2.1.1.-
@@ -75487,7 +75347,7 @@ is_a: GO:0016635 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0008179
name: adenylate cyclase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme adenylate cyclase." [GOC:jl]
+def: "Binding to an adenylate cyclase." [GOC:jl]
synonym: "adenylyl cyclase binding" EXACT []
xref: Reactome:R-HSA-170672 "Galpha-olf:GTP binds to adenylate cyclase and activates it"
is_a: GO:0019899 ! enzyme binding
@@ -75526,20 +75386,21 @@ is_a: GO:0004645 ! 1,4-alpha-oligoglucan phosphorylase activity
[Term]
id: GO:0008186
-name: ATPase, acting on RNA
+name: ATP-dependent activity, acting on RNA
namespace: molecular_function
alt_id: GO:0004010
def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of RNA, and it drives another reaction." [GOC:jl]
-synonym: "ATPase activity, acting on RNA" RELATED []
+synonym: "ATPase activity, acting on RNA" EXACT []
+synonym: "ATPase, acting on RNA" EXACT []
synonym: "RNA-dependent adenosinetriphosphatase activity" EXACT []
-synonym: "RNA-dependent ATPase activity" RELATED []
-is_a: GO:0016887 ! ATPase
+synonym: "RNA-dependent ATPase activity" EXACT []
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0008187
name: poly-pyrimidine tract binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any stretch of pyrimidines (cytosine or uracil) in an RNA molecule." [GOC:jl]
+def: "Binding to a stretch of pyrimidines (cytosine or uracil) in an RNA molecule." [GOC:jl]
is_a: GO:0003727 ! single-stranded RNA binding
[Term]
@@ -75563,7 +75424,7 @@ replaced_by: GO:0043066
id: GO:0008190
name: eukaryotic initiation factor 4E binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with eukaryotic initiation factor 4E, a polypeptide factor involved in the initiation of ribosome-mediated translation." [ISBN:0198506732]
+def: "Binding to eukaryotic initiation factor 4E, a polypeptide factor involved in the initiation of ribosome-mediated translation." [ISBN:0198506732]
synonym: "eIF4E binding" EXACT []
is_a: GO:0031369 ! translation initiation factor binding
@@ -75649,14 +75510,14 @@ consider: GO:0045735
id: GO:0008198
name: ferrous iron binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ferrous iron, Fe(II)." [GOC:ai]
+def: "Binding to a ferrous iron ion, Fe(II)." [GOC:ai]
is_a: GO:0005506 ! iron ion binding
[Term]
id: GO:0008199
name: ferric iron binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ferric iron, Fe(III)." [GOC:ai]
+def: "Binding to a ferric iron ion, Fe(III)." [GOC:ai]
is_a: GO:0005506 ! iron ion binding
[Term]
@@ -75671,7 +75532,7 @@ is_a: GO:0099106 ! ion channel regulator activity
id: GO:0008201
name: heparin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." [GOC:jl, ISBN:0198506732]
+def: "Binding to heparin, a member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." [GOC:jl, ISBN:0198506732]
synonym: "heparan sulfate binding" RELATED []
is_a: GO:0005539 ! glycosaminoglycan binding
is_a: GO:1901681 ! sulfur compound binding
@@ -75721,7 +75582,7 @@ is_a: GO:1902652 ! secondary alcohol metabolic process
id: GO:0008206
name: bile acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [GOC:go_curators]
+def: "The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [GOC:go_curators]
synonym: "bile acid metabolism" EXACT []
is_a: GO:0008202 ! steroid metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
@@ -75791,7 +75652,7 @@ is_a: GO:0034754 ! cellular hormone metabolic process
id: GO:0008213
name: protein alkylation
namespace: biological_process
-def: "The addition of an alkyl group to a protein amino acid. An alkyl group is any group derived from an alkane by removal of one hydrogen atom." [GOC:ma]
+def: "The addition of an alkyl group to a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom." [GOC:ma]
subset: goslim_yeast
synonym: "protein amino acid alkylation" EXACT [GOC:bf]
is_a: GO:0006464 ! cellular protein modification process
@@ -75800,7 +75661,7 @@ is_a: GO:0006464 ! cellular protein modification process
id: GO:0008214
name: protein dealkylation
namespace: biological_process
-def: "The removal of an alkyl group from a protein amino acid. An alkyl group is any group derived from an alkane by removal of one hydrogen atom." [GOC:ai]
+def: "The removal of an alkyl group from a protein amino acid. Alkyl groups are derived from alkanes by removal of one hydrogen atom." [GOC:ai]
synonym: "protein amino acid dealkylation" EXACT [GOC:bf]
is_a: GO:0006464 ! cellular protein modification process
@@ -75851,7 +75712,6 @@ comment: This term should not be used for direct annotation. The only exception
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_mouse
subset: goslim_plant
synonym: "accidental cell death" RELATED []
@@ -75971,7 +75831,6 @@ subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
@@ -76384,7 +76243,7 @@ is_a: GO:0016783 ! sulfurtransferase activity
id: GO:0008266
name: poly(U) RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule." [GOC:mah]
+def: "Binding to a sequence of uracil residues in an RNA molecule." [GOC:mah]
synonym: "poly(U) binding" EXACT [GOC:mah]
is_a: GO:0008187 ! poly-pyrimidine tract binding
@@ -76392,7 +76251,7 @@ is_a: GO:0008187 ! poly-pyrimidine tract binding
id: GO:0008267
name: poly-glutamine tract binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a polyglutamine tract, i.e. a series of consecutive glutamine residues, in a protein." [GOC:mah]
+def: "Binding to a polyglutamine tract, i.e. a series of consecutive glutamine residues, in a protein." [GOC:mah]
is_a: GO:0005515 ! protein binding
[Term]
@@ -76417,8 +76276,9 @@ is_a: GO:0035591 ! signaling adaptor activity
id: GO:0008270
name: zinc ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with zinc (Zn) ions." [GOC:ai]
+def: "Binding to a zinc ion (Zn)." [GOC:ai]
synonym: "zinc binding" EXACT []
+synonym: "Zn binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
[Term]
@@ -76556,7 +76416,6 @@ subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_flybase_ribbon
-subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
synonym: "cell proliferation" RELATED []
@@ -76621,7 +76480,7 @@ is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity
id: GO:0008289
name: lipid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lipid." [GOC:ai]
+def: "Binding to a lipid." [GOC:ai]
subset: goslim_agr
subset: goslim_candida
subset: goslim_chembl
@@ -76736,7 +76595,7 @@ id: GO:0008299
name: isoprenoid biosynthetic process
namespace: biological_process
alt_id: GO:0009241
-def: "The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [ISBN:0198506732]
synonym: "isoprenoid anabolism" EXACT []
synonym: "isoprenoid biosynthesis" EXACT []
synonym: "isoprenoid formation" EXACT []
@@ -76758,7 +76617,7 @@ id: GO:0008300
name: isoprenoid catabolic process
namespace: biological_process
alt_id: GO:0016097
-def: "The chemical reactions and pathways resulting in the breakdown of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [ISBN:0198506732]
synonym: "isoprenoid breakdown" EXACT []
synonym: "isoprenoid catabolism" EXACT []
synonym: "isoprenoid degradation" EXACT []
@@ -76884,7 +76743,7 @@ is_a: GO:0008309 ! double-stranded DNA exodeoxyribonuclease activity
id: GO:0008312
name: 7S RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 7S RNA, the RNA component of the signal recognition particle (SRP)." [GOC:jl, PMID:6181418]
+def: "Binding to a 7S RNA, the RNA component of the signal recognition particle (SRP)." [GOC:jl, PMID:6181418]
is_a: GO:0003723 ! RNA binding
[Term]
@@ -76899,7 +76758,7 @@ is_a: GO:0005006 ! epidermal growth factor-activated receptor activity
id: GO:0008314
name: gurken signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to the ligand Gurken." [GOC:bf, PMID:23972992]
+def: "The series of molecular signals generated as a consequence of an epidermal growth factor receptor binding to a ligand Gurken." [GOC:bf, PMID:23972992]
synonym: "gurken receptor signaling pathway" EXACT []
synonym: "gurken receptor signalling pathway" EXACT []
synonym: "gurken-activated signaling pathway" RELATED [GOC:signaling]
@@ -76929,7 +76788,7 @@ is_a: GO:0005198 ! structural molecule activity
id: GO:0008317
name: gurken receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the gurken growth factor receptor." [GOC:ai]
+def: "Binding to a gurken growth factor receptor." [GOC:ai]
synonym: "gurken receptor ligand" NARROW []
is_a: GO:0005154 ! epidermal growth factor receptor binding
@@ -77005,7 +76864,7 @@ is_a: GO:0015075 ! ion transmembrane transporter activity
id: GO:0008327
name: methyl-CpG binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide." [GOC:jl, PMID:11746232]
+def: "Binding to a methylated cytosine/guanine dinucleotide." [GOC:jl, PMID:11746232]
is_a: GO:0000166 ! nucleotide binding
is_a: GO:0043565 ! sequence-specific DNA binding
@@ -77055,7 +76914,6 @@ namespace: biological_process
def: "The directed movement of substances from endosomes to lysosomes." [GOC:ai, ISBN:0716731363]
is_a: GO:0007041 ! lysosomal transport
is_a: GO:0016192 ! vesicle-mediated transport
-is_a: GO:0046907 ! intracellular transport
[Term]
id: GO:0008334
@@ -77542,7 +77400,6 @@ def: "Catalysis of the reaction: ATP + IkappaB protein = ADP + IkappaB phosphopr
comment: Note that phosphorylation of IkappaB targets it for proteasomal degradation and allows the nuclear translocation of kB.
synonym: "ATP:IkappaB protein phosphotransferase activity" RELATED [EC:2.7.11.10]
synonym: "CHUK" RELATED [EC:2.7.11.10]
-synonym: "ikappaB kinase activity" RELATED [EC:2.7.11.10]
synonym: "IKBKA" RELATED [EC:2.7.11.10]
synonym: "IKBKB" RELATED [EC:2.7.11.10]
synonym: "IKK" RELATED [EC:2.7.11.10]
@@ -77723,20 +77580,19 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0008398
name: sterol 14-demethylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: obtusifoliol + 3 O2 + 3 NADPH + 3 H+ = 4-alpha-methyl-5-alpha-ergosta-8,14,24(28)-trien-3-beta-ol + formate + 3 NADP+ + 3 H2O." [EC:1.14.13.70]
-synonym: "cytochrome P450 51 activity" NARROW [EC:1.14.13.70]
+def: "Catalysis of the reaction: a 14alpha-methyl steroid + 3 O2 + 3 reduced [NADPH-hemoprotein reductase] = a delta14 steroid + formate + 4 H+ + 4 H2O + 3 oxidized [NADPH-hemoprotein reductase]." [RHEA:54028]
+synonym: "cytochrome P450 51 activity" NARROW [EC:1.14.14.154]
synonym: "cytochrome P450 CYP51" NARROW []
-synonym: "lanosterol 14-alpha-demethylase activity" NARROW [EC:1.14.13.70]
-synonym: "lanosterol 14-demethylase activity" NARROW [EC:1.14.13.70]
-synonym: "lanosterol 14alpha-demethylase activity" RELATED [EC:1.14.13.70]
-synonym: "obtusufoliol 14-demethylase activity" NARROW [EC:1.14.13.70]
-synonym: "sterol 14-alpha-demethylase activity" RELATED [EC:1.14.13.70]
-synonym: "sterol 14alpha-demethylase activity" RELATED [EC:1.14.13.70]
-synonym: "sterol,NADPH:oxygen oxidoreductase (14-methyl cleaving)" RELATED [EC:1.14.13.70]
-xref: EC:1.14.13.70
+synonym: "lanosterol 14-alpha-demethylase activity" NARROW [EC:1.14.14.154]
+synonym: "lanosterol 14-demethylase activity" NARROW [EC:1.14.14.154]
+synonym: "lanosterol 14alpha-demethylase activity" RELATED [EC:1.14.14.154]
+synonym: "obtusufoliol 14-demethylase activity" NARROW [EC:1.14.14.154]
+synonym: "sterol 14-alpha-demethylase activity" RELATED []
+synonym: "sterol 14alpha-demethylase activity" RELATED []
+xref: EC:1.14.14.154
xref: MetaCyc:1.14.13.70-RXN
xref: Reactome:R-HSA-194678 "CYP51A1 demethylates LNSOL"
-xref: RHEA:14917
+xref: RHEA:54028
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
is_a: GO:0032451 ! demethylase activity
@@ -78031,27 +77887,27 @@ id: GO:0008428
name: ribonuclease inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents or reduces the activity of ribonuclease." [GOC:ai]
-is_a: GO:0004857 ! enzyme inhibitor activity
+is_a: GO:0140721 ! nuclease inhibitor activity
[Term]
id: GO:0008429
name: phosphatidylethanolamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine." [ISBN:0198506732]
+def: "Binding to a phosphatidylethanolamine, a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine." [ISBN:0198506732]
is_a: GO:0005543 ! phospholipid binding
[Term]
id: GO:0008430
name: selenium binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with selenium (Se)." [GOC:ai]
+def: "Binding to a selenium (Se) ion." [GOC:ai]
is_a: GO:0005488 ! binding
[Term]
id: GO:0008431
name: vitamin E binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with vitamin E, tocopherol, which includes a series of eight structurally similar compounds. Alpha-tocopherol is the most active form in humans and is a powerful biological antioxidant." [ISBN:0721662544]
+def: "Binding to a vitamin E, tocopherol, which includes a series of eight structurally similar compounds. Alpha-tocopherol is the most active form in humans and is a powerful biological antioxidant." [ISBN:0721662544]
synonym: "alpha-tocopherol binding" NARROW []
synonym: "tocopherol binding" EXACT []
is_a: GO:0019842 ! vitamin binding
@@ -78062,7 +77918,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0008432
name: JUN kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with JUN kinase, an enzyme that catalyzes the phosphorylation and activation of members of the JUN family." [GOC:jl]
+def: "Binding to JUN kinase, an enzyme that catalyzes the phosphorylation and activation of members of the JUN family." [GOC:jl]
synonym: "JNK binding" EXACT [GOC:BHF, GOC:ebc]
is_a: GO:0019901 ! protein kinase binding
@@ -78315,7 +78171,7 @@ replaced_by: GO:0004222
id: GO:0008451
name: obsolete X-Pro aminopeptidase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the release of any N-terminal amino acid, including proline, that is linked with proline, even from a dipeptide or tripeptide." [EC:3.4.11.9]
+def: "OBSOLETE. Catalysis of the release of an N-terminal amino acid, including proline, that is linked with proline, even from a dipeptide or tripeptide." [EC:3.4.11.9]
comment: This term was made obsolete because it represents a gene product.
synonym: "aminoacylproline aminopeptidase activity" RELATED [EC:3.4.11.9]
synonym: "aminopeptidase P" EXACT []
@@ -78836,6 +78692,7 @@ id: GO:0008482
name: sulfite oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: H(2)O + O(2) + sulfite = H(2)O(2) + H(+) + sulfate." [EC:1.8.3.1, RHEA:24600]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "sulfite:oxygen oxidoreductase activity" RELATED [EC:1.8.3.1]
synonym: "sulphite oxidase activity" EXACT []
xref: EC:1.8.3.1
@@ -78860,7 +78717,7 @@ is_a: GO:0016769 ! transferase activity, transferring nitrogenous groups
id: GO:0008484
name: sulfuric ester hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: RSO-R' + H2O = RSOOH + R'H. This reaction is the hydrolysis of any sulfuric ester bond, any ester formed from sulfuric acid, O=SO(OH)2." [GOC:ai]
+def: "Catalysis of the reaction: RSO-R' + H2O = RSOOH + R'H. This reaction is the hydrolysis of a sulfuric ester bond, an ester formed from sulfuric acid, O=SO(OH)2." [GOC:ai]
synonym: "sulfatase activity" EXACT []
synonym: "sulphuric ester hydrolase activity" EXACT []
xref: EC:3.1.6.-
@@ -78966,7 +78823,7 @@ is_a: GO:0090079 ! translation regulator activity, nucleic acid binding
id: GO:0008495
name: protoheme IX farnesyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protoheme IX + (2E,6E)-farnesyl diphosphate + H2O = heme o + diphosphate." [RHEA:28070]
+def: "Catalysis of the reaction: protoheme IX + (2E,6E)-farnesyl diphosphate + H2O = heme O + diphosphate." [RHEA:28070]
synonym: "haem O synthase activity" EXACT []
synonym: "heme A:farnesyltransferase activity" EXACT [PMID:9177788]
synonym: "heme O synthase activity" EXACT []
@@ -79215,8 +79072,8 @@ id: GO:0008519
name: ammonium transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0051739
-def: "Enables the transfer of ammonium from one side of a membrane to the other. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals." [GOC:go_curators, ISBN:0198506732]
-synonym: "ammonia transmembrane transporter activity" EXACT []
+def: "Enables the transfer of ammonium from one side of a membrane to the other. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals." [PMID:17710640]
+synonym: "ammonia transmembrane transporter activity" RELATED []
xref: Reactome:R-HSA-444393 "RhCG mediates ammonium influx into kidney collecting duct cells"
xref: Reactome:R-HSA-444416 "RHAG transports NH4+ from cytosol to extracellular region (red blood cells)"
xref: Reactome:R-HSA-444419 "RhBG mediates ammonium effflux out of kidney collecting duct cells"
@@ -79224,6 +79081,7 @@ xref: Reactome:R-HSA-446277 "RhCG mediates ammonium efflux out of kidney collect
xref: Reactome:R-HSA-446278 "RhBG mediates ammonium influx into kidney collecting duct cells"
xref: Reactome:R-HSA-5623051 "Defective RHAG does not transport NH4+ from cytosol to extracellular region (rbc)"
xref: RHEA:28747
+xref: TCBD:1.A.11
is_a: GO:0022890 ! inorganic cation transmembrane transporter activity
[Term]
@@ -79282,7 +79140,6 @@ def: "Removes phosphatidylinositol from a membrane or a monolayer lipid particle
synonym: "intermembrane phosphatidylinositol transfer activity" NARROW []
synonym: "intermembrane phosphotidylinositol transfer activity" NARROW []
synonym: "phosphatidylinositol carrier activity" EXACT []
-synonym: "phosphatidylinositol transfer activity" EXACT []
synonym: "phosphatidylinositol transporter activity" BROAD []
xref: Reactome:R-HSA-8869241 "PITPNM1,2,3 exchange PI for PA"
xref: Reactome:R-HSA-8874470 "TNFAIP8 proteins transfer PI(4,5)P2, PI(3,4,5)P3 from cytosolic vesicles to plasma membrane"
@@ -79629,17 +79486,16 @@ is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
id: GO:0008554
name: P-type sodium transporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) -> ADP + phosphate + Na+(out); by a phosphorylative mechanism." [RHEA:14633]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) -> ADP + phosphate + Na+(out); by a phosphorylative mechanism." [PMID:9224683]
comment: Note that RHEA:14633 represents both the ABC and the P-type sodium transporters.
-synonym: "hydrogen-/sodium-translocating ATPase activity" RELATED []
-synonym: "Na(+)-exporting ATPase activity" RELATED [EC:7.2.2.3]
+synonym: "Na(+)-exporting ATPase activity" BROAD [EC:7.2.2.3]
synonym: "Na(+)-transporting ATPase activity" BROAD [EC:7.2.2.3]
-synonym: "Na+-exporting ATPase activity" RELATED [EC:7.2.2.3]
-synonym: "Na+-transporting ATPase activity" RELATED [EC:7.2.2.3]
+synonym: "Na+-exporting ATPase activity" BROAD [EC:7.2.2.3]
+synonym: "Na+-transporting ATPase activity" BROAD [EC:7.2.2.3]
synonym: "sodium exporting ATPase activity, phosphorylative mechanism" EXACT []
synonym: "sodium transmembrane transporter activity, phosphorylative mechanism" EXACT []
-synonym: "sodium transport ATPase activity" RELATED [EC:7.2.2.3]
-synonym: "sodium-exporting ATPase activity" RELATED [EC:7.2.2.3]
+synonym: "sodium transport ATPase activity" BROAD [EC:7.2.2.3]
+synonym: "sodium-exporting ATPase activity" BROAD [EC:7.2.2.3]
synonym: "sodium-exporting ATPase activity, phosphorylative mechanism" EXACT []
synonym: "sodium-translocating P-type ATPase activity" EXACT [EC:7.2.2.3]
xref: EC:7.2.2.3
@@ -79727,12 +79583,11 @@ id: GO:0008564
name: protein-exporting ATPase activity
namespace: molecular_function
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + protein+(in) -> ADP + phosphate + protein+(out); drives the concomitant secretion of proteins." [PMID:30346996]
-synonym: "ATP phosphohydrolase (protein-secreting)" RELATED [EC:7.4.2.8]
+comment: Represents ATP- hydrolyzing enzymes of the general secretory pathway (Sec or Type II), of the virulence-related secretory pathway (Type III) and of the conjugal DNA-protein transfer pathway (Type IV). Type II enzymes occur in bacteria, archaea and eukaryotes, whereas type III and type IV enzymes occur in bacteria where they form components of a multi-subunit complex.
synonym: "ATPase-coupled protein transporter activity" EXACT []
-synonym: "protein-secreting ATPase activity" EXACT []
xref: EC:7.4.2.8
xref: MetaCyc:3.6.3.50-RXN
-is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
+is_a: GO:0015450 ! protein-transporting ATPase activity
[Term]
id: GO:0008565
@@ -79755,7 +79610,7 @@ comment: See also the cellular component term 'mitochondrial inner membrane pres
synonym: "ATPase-coupled mitochondrial protein transporter activity" EXACT []
xref: EC:7.4.2.3
xref: MetaCyc:3.6.3.51-RXN
-is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
+is_a: GO:0015450 ! protein-transporting ATPase activity
[Term]
id: GO:0008567
@@ -79779,22 +79634,23 @@ synonym: "katanin activity" NARROW [EC:5.6.1.1]
xref: EC:5.6.1.1
xref: MetaCyc:3.6.4.3-RXN
xref: Reactome:R-HSA-9668419 "SPAST (spastin) mediates the severing of microtubules at chromosome attachment sites"
-is_a: GO:0016887 ! ATPase
is_a: GO:0140096 ! catalytic activity, acting on a protein
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0008569
-name: ATP-dependent microtubule motor activity, minus-end-directed
+name: minus-end-directed microtubule motor activity
namespace: molecular_function
-def: "Catalysis of movement along a microtubule toward the minus end, coupled to the hydrolysis of ATP." [GOC:mah, GOC:vw]
+def: "A motor activity that generates movement along a microtubule toward the minus end, driven by ATP hydrolysis." [GOC:mah, GOC:vw, PMID:15659646, PMID:32842864]
+synonym: "ATP-dependent microtubule motor activity, minus-end-directed" EXACT []
synonym: "ATP-dependent minus-end-directed microtubule motor activity" EXACT []
synonym: "dynein ATPase" NARROW []
-synonym: "kinesin ATP phosphohydrolase (minus-end-directed)" EXACT []
+synonym: "kinesin ATP phosphohydrolase (minus-end-directed)" NARROW []
+synonym: "microtubule motor activity, minus-end-directed" EXACT []
synonym: "minus-end-directed ATP-dependent microtubule motor activity" EXACT []
-synonym: "minus-end-directed kinesin ATPase activity" EXACT []
-synonym: "minus-end-directed microtubule motor activity" BROAD []
+synonym: "minus-end-directed kinesin ATPase activity" NARROW []
xref: MetaCyc:3.6.4.5-RXN
-is_a: GO:1990939 ! ATP-dependent microtubule motor activity
+is_a: GO:0003777 ! microtubule motor activity
[Term]
id: GO:0008570
@@ -79842,18 +79698,19 @@ consider: GO:0007031
[Term]
id: GO:0008574
-name: ATP-dependent microtubule motor activity, plus-end-directed
+name: plus-end-directed microtubule motor activity
namespace: molecular_function
-def: "Catalysis of movement along a microtubule toward the plus end, coupled to the hydrolysis of ATP." [EC:5.6.1.3, GOC:vw]
+def: "A motor activity that generates movement along a microtubule toward the plus end, driven by ATP hydrolysis." [GOC:vw, PMID:32842864]
+synonym: "ATP-dependent microtubule motor activity, plus-end-directed" EXACT []
synonym: "ATP-dependent plus-end-directed microtubule motor activity" EXACT []
synonym: "kinesin activity" RELATED [EC:5.6.1.3]
-synonym: "kinesin ATP phosphohydrolase (plus-end-directed)" EXACT []
+synonym: "kinesin ATP phosphohydrolase (plus-end-directed)" NARROW []
+synonym: "microtubule motor activity, plus-end-directed" EXACT []
synonym: "plus-end-directed ATP-dependent microtubule motor activity" EXACT []
-synonym: "plus-end-directed kinesin ATPase activity" EXACT []
-synonym: "plus-end-directed microtubule motor activity" BROAD []
+synonym: "plus-end-directed kinesin ATPase activity" NARROW []
xref: EC:5.6.1.3
xref: MetaCyc:3.6.4.4-RXN
-is_a: GO:1990939 ! ATP-dependent microtubule motor activity
+is_a: GO:0003777 ! microtubule motor activity
[Term]
id: GO:0008575
@@ -80037,7 +79894,7 @@ relationship: part_of GO:0007351 ! tripartite regional subdivision
id: GO:0008597
name: calcium-dependent protein serine/threonine phosphatase regulator activity
namespace: molecular_function
-def: "Binds to and modulates of the activity of the enzyme calcium-dependent protein serine/threonine phosphatase." [EC:3.1.3.16, GOC:ai]
+def: "Binds to and modulates of the activity of the enzyme calcium-dependent protein serine/threonine phosphatase." [GOC:ai]
synonym: "calcium-dependent protein serine/threonine phosphatase, intrinsic regulator activity" NARROW []
xref: Reactome:R-HSA-139906 "Activation of BAD by calcineurin"
is_a: GO:0019888 ! protein phosphatase regulator activity
@@ -80070,9 +79927,8 @@ replaced_by: GO:0019887
id: GO:0008607
name: phosphorylase kinase regulator activity
namespace: molecular_function
-def: "Modulation of the activity of the enzyme phosphorylase kinase." [EC:2.7.11.19]
+def: "Modulation of the activity of the enzyme phosphorylase kinase." [GOC:curators]
synonym: "phosphorylase kinase, intrinsic regulator activity" NARROW []
-xref: EC:2.7.1.-
is_a: GO:0019887 ! protein kinase regulator activity
[Term]
@@ -80170,7 +80026,7 @@ is_a: GO:0051604 ! protein maturation
id: GO:0008613
name: diuretic hormone activity
namespace: molecular_function
-def: "The action characteristic of a diuretic hormone, any peptide hormone that, upon receptor binding, regulates water balance and fluid secretion." [GOC:mah, InterPro:IPR003621, PMID:8618894]
+def: "The action characteristic of a diuretic hormone, a peptide hormone that, upon receptor binding, regulates water balance and fluid secretion." [GOC:mah, InterPro:IPR003621, PMID:8618894]
is_a: GO:0005179 ! hormone activity
[Term]
@@ -80202,7 +80058,7 @@ is_a: GO:1901617 ! organic hydroxy compound biosynthetic process
id: GO:0008616
name: queuosine biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of queuosines, a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents." [GOC:go_curators, ISBN:0198506732]
synonym: "queuosine anabolism" EXACT []
synonym: "queuosine biosynthesis" EXACT []
synonym: "queuosine formation" EXACT []
@@ -80356,7 +80212,7 @@ is_a: GO:0006919 ! activation of cysteine-type endopeptidase activity involved i
id: GO:0008636
name: obsolete activation of caspase activity by protein phosphorylation
namespace: biological_process
-def: "OBSOLETE. Upregulation of the activity of a caspase, any of a group of cysteine proteases involved in apoptosis, by the addition of a phosphate group." [GOC:dph, GOC:jl, GOC:tb, PMID:14744432, Wikipedia:Caspase]
+def: "OBSOLETE. Upregulation of the activity of a caspase, a group of cysteine proteases involved in apoptosis, by the addition of a phosphate group." [GOC:dph, GOC:jl, GOC:tb, PMID:14744432, Wikipedia:Caspase]
comment: This term was made obsolete because it is ill-defined: phosphorylation regulates the activity of caspases, but it doesn't activate them (caspases are only activated upon cleavage).
synonym: "activation of caspase activity by protein amino acid phosphorylation" EXACT [GOC:bf]
synonym: "activation of caspase activity by protein phosphorylation" EXACT []
@@ -80401,7 +80257,7 @@ name: carbohydrate transport
namespace: biological_process
alt_id: GO:0006861
alt_id: GO:0008644
-def: "The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y." [GOC:ai]
+def: "The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y." [GOC:ai]
subset: goslim_pir
subset: goslim_yeast
synonym: "sugar transport" NARROW []
@@ -80414,7 +80270,7 @@ namespace: biological_process
alt_id: GO:0008646
alt_id: GO:0008647
alt_id: GO:0035428
-def: "The process in which hexose is transported across a membrane. Hexoses are any aldoses with a chain of six carbon atoms in the molecule." [GOC:vw]
+def: "The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule." [GOC:vw]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "hexose membrane transport" RELATED []
synonym: "hexose transport" RELATED []
@@ -80483,7 +80339,7 @@ is_a: GO:1901566 ! organonitrogen compound biosynthetic process
id: GO:0008653
name: lipopolysaccharide metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide." [ISBN:0198506732]
+def: "The chemical reactions and pathways involving lipopolysaccharides, a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide." [ISBN:0198506732]
synonym: "lipopolysaccharide metabolism" EXACT []
synonym: "LPS metabolic process" EXACT []
is_a: GO:0044255 ! cellular lipid metabolic process
@@ -80494,7 +80350,7 @@ is_a: GO:1903509 ! liposaccharide metabolic process
id: GO:0008654
name: phospholipid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester." [ISBN:0198506732]
synonym: "phospholipid anabolism" EXACT []
synonym: "phospholipid biosynthesis" EXACT []
synonym: "phospholipid formation" EXACT []
@@ -80511,7 +80367,7 @@ is_a: GO:0090407 ! organophosphate biosynthetic process
id: GO:0008655
name: pyrimidine-containing compound salvage
namespace: biological_process
-def: "Any process that generates a pyrimidine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis." [GOC:jl]
+def: "Any process that generates a pyrimidine-containing compound, a nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis." [GOC:jl]
subset: goslim_pir
synonym: "pyrimidine salvage" RELATED []
is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process
@@ -80535,6 +80391,7 @@ name: DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor a
namespace: molecular_function
def: "Binds to and stops, prevents or reduces the activity of ATP-hydrolyzing DNA topoisomerase. ATP-hydrolyzing DNA topoisomerase catalyzes the DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2." [GOC:mah]
synonym: "DNA gyrase inhibitor activity" EXACT [GOC:dph, GOC:tb]
+is_a: GO:0004857 ! enzyme inhibitor activity
is_a: GO:0042030 ! ATPase inhibitor activity
is_a: GO:0072586 ! DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) regulator activity
@@ -80542,9 +80399,8 @@ is_a: GO:0072586 ! DNA topoisomerase type II (double strand cut, ATP-hydrolyzing
id: GO:0008658
name: penicillin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system." [GOC:ai]
+def: "Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system." [GOC:ai]
subset: goslim_metagenomics
-is_a: GO:0008144 ! drug binding
is_a: GO:0033218 ! amide binding
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0043177 ! organic acid binding
@@ -82509,7 +82365,6 @@ id: GO:0008796
name: bis(5'-nucleosyl)-tetraphosphatase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of P(1),P(4)-bis(5'-nucleosyl)tetraphosphate into two nucleotides." [GOC:ai]
-xref: EC:3.6.1.-
is_a: GO:0004551 ! nucleotide diphosphatase activity
[Term]
@@ -83274,7 +83129,6 @@ id: GO:0008847
name: Enterobacter ribonuclease activity
namespace: molecular_function
def: "Catalysis of the endonucleolytic cleavage to 3'-phosphomononucleotides and 3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates." [EC:4.6.1.21]
-synonym: "enterobacter ribonuclease activity" RELATED [EC:4.6.1.21]
synonym: "Enterobacter RNase activity" EXACT []
xref: EC:4.6.1.21
xref: MetaCyc:3.1.27.6-RXN
@@ -83446,19 +83300,13 @@ name: formate dehydrogenase (NAD+) activity
namespace: molecular_function
alt_id: GO:0018476
def: "Catalysis of the reaction: formate + NAD(+) = CO(2) + NADH." [EC:1.17.1.9, RHEA:15985]
-synonym: "FDH I" RELATED [EC:1.17.1.9]
-synonym: "FDH II" RELATED [EC:1.17.1.9]
-synonym: "formate benzyl-viologen oxidoreductase" RELATED [EC:1.17.1.9]
synonym: "formate dehydrogenase (NAD)" RELATED [EC:1.17.1.9]
synonym: "formate hydrogenlyase" RELATED [EC:1.17.1.9]
-synonym: "formate-NAD oxidoreductase" RELATED [EC:1.17.1.9]
-synonym: "formate:NAD+ oxidoreductase" RELATED [EC:1.17.1.9]
+synonym: "formate-NAD oxidoreductase" RELATED []
synonym: "formic acid dehydrogenase" RELATED [EC:1.17.1.9]
synonym: "formic hydrogen-lyase" RELATED [EC:1.17.1.9]
-synonym: "N-FDH" RELATED [EC:1.17.1.9]
-synonym: "NAD-dependent formate dehydrogenase" RELATED [EC:1.17.1.9]
+synonym: "NAD-dependent formate dehydrogenase" RELATED []
synonym: "NAD-formate dehydrogenase" RELATED [EC:1.17.1.9]
-synonym: "NAD-linked formate dehydrogenase" RELATED [EC:1.17.1.9]
xref: EC:1.17.1.9
xref: KEGG_REACTION:R00519
xref: MetaCyc:1.2.1.2-RXN
@@ -83631,7 +83479,7 @@ id: GO:0008876
name: quinoprotein glucose dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol." [EC:1.1.5.2]
-comment: Note that this was EC:1.1.99.17.
+comment: Formerly EC:1.1.99.17.
synonym: "D-glucose:(pyrroloquinoline-quinone) 1-oxidoreductase activity" RELATED [EC:1.1.5.2]
synonym: "D-glucose:ubiquinone oxidoreductase activity" RELATED [EC:1.1.5.2]
synonym: "glucose dehydrogenase (PQQ-dependent) activity" RELATED [EC:1.1.5.2]
@@ -83871,16 +83719,6 @@ xref: MetaCyc:AKBLIG-RXN
xref: RHEA:20736
is_a: GO:0016453 ! C-acetyltransferase activity
-[Term]
-id: GO:0008891
-name: glycolate oxidase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: glycolate + O2 = glyoxylate + hydrogen peroxide." [EC:1.1.3.15]
-xref: MetaCyc:RXN-969
-xref: Reactome:R-HSA-389842 "HAO1 tetramer oxidizes glycolate to glyoxylate"
-xref: RHEA:25311
-is_a: GO:0003973 ! (S)-2-hydroxy-acid oxidase activity
-
[Term]
id: GO:0008892
name: guanine deaminase activity
@@ -83952,7 +83790,6 @@ synonym: "alphaaminoadipic semialdehyde dehydrogenase-phosphopantetheinyl transf
synonym: "CoA-[4'-phosphopantetheine]:apo-acyl-carrier-protein 4'-pantetheinephosphotransferase activity" RELATED [EC:2.7.8.7]
synonym: "CoA:apo-acyl-carrier-protein pantetheinephosphotransferase activity" RELATED [EC:2.7.8.7]
synonym: "coenzyme A:fatty acid synthetase apoenzyme 4'-phosphopantetheine transferase activity" RELATED [EC:2.7.8.7]
-synonym: "holo-[acyl-carrier-protein] synthase activity" NARROW []
synonym: "holo-[peptidyl-carrier protein] synthase activity" NARROW []
synonym: "holo-ACP synthase activity" RELATED [EC:2.7.8.7]
synonym: "holo-ACP synthetase activity" RELATED [EC:2.7.8.7]
@@ -84137,7 +83974,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0008907
name: integrase activity
namespace: molecular_function
-def: "Catalysis of the integration of one segment of DNA into another." [GOC:mah]
+def: "Catalysis of the integration of one DNA segment into another." [GOC:mah]
subset: goslim_pir
xref: Reactome:R-HSA-164523 "Transesterification to connect viral DNA 3' ends to host DNA 5' ends"
is_a: GO:0140097 ! catalytic activity, acting on DNA
@@ -84359,14 +84196,14 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0008924
name: malate dehydrogenase (quinone) activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-malate + a quinone = oxaloacetate + a quinol." [MetaCyc:MALATE-DEHYDROGENASE-ACCEPTOR-RXN]
+def: "Catalysis of the reaction: (S)-malate + a quinone = oxaloacetate + a quinol." [PMID:234747, RHEA:46012]
synonym: "(S)-malate:(quinone) oxidoreductase activity" RELATED [EC:1.1.5.4]
synonym: "(S)-malate:quinone oxidoreductase activity" RELATED [EC:1.1.5.4]
synonym: "FAD-dependent malate dehydrogenase activity" RELATED [EC:1.1.5.4]
synonym: "MQO activity" BROAD [EC:1.1.5.4]
xref: EC:1.1.5.4
xref: MetaCyc:MALATE-DEHYDROGENASE-ACCEPTOR-RXN
-xref: RHEA:22556
+xref: RHEA:46012
is_a: GO:0016615 ! malate dehydrogenase activity
is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor
@@ -84513,18 +84350,16 @@ is_a: GO:0052834 ! inositol monophosphate phosphatase activity
id: GO:0008935
name: 1,4-dihydroxy-2-naphthoyl-CoA synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-napthoyl-CoA + H2O." [EC:4.1.3.36]
-synonym: "1,4-dihydroxy-2-naphthoate synthase activity" RELATED [EC:4.1.3.36]
+def: "Catalysis of the reaction: 2-succinylbenzoyl-CoA + H+ = 1,4-dihydroxy-2-naphthoyl-CoA + H2O." [RHEA:26562]
synonym: "DHNA synthetase activity" RELATED [EC:4.1.3.36]
-synonym: "dihydroxynaphthoate synthase activity" RELATED [EC:4.1.3.36]
+synonym: "dihydroxynaphthoate synthase activity" RELATED []
synonym: "dihydroxynaphthoic acid synthetase activity" RELATED [EC:4.1.3.36]
+synonym: "naphthoate synthase activity" RELATED [EC:4.1.3.36]
synonym: "O-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing) activity" RELATED [EC:4.1.3.36]
-synonym: "O-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing; CoA-forming)" RELATED [EC:4.1.3.36]
-synonym: "O-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase activity" RELATED [KEGG_REACTION:R04150]
xref: EC:4.1.3.36
xref: KEGG_REACTION:R04150
xref: MetaCyc:NAPHTHOATE-SYN-RXN
-xref: RHEA:15525
+xref: RHEA:26562
is_a: GO:0016833 ! oxo-acid-lyase activity
[Term]
@@ -84547,9 +84382,8 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0008937
name: ferredoxin-NAD(P) reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: reduced ferredoxin + NAD(P)+ = oxidized ferredoxin + NAD(P)H + H+." [EC:1.18.1.-]
+def: "Catalysis of the reaction: reduced ferredoxin + NAD(P)+ = oxidized ferredoxin + NAD(P)H + H+." [GOC:curators]
synonym: "ferredoxin reductase activity" BROAD []
-xref: EC:1.18.1.-
is_a: GO:0016731 ! oxidoreductase activity, acting on iron-sulfur proteins as donors, NAD or NADP as acceptor
[Term]
@@ -84856,7 +84690,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0008962
name: phosphatidylglycerophosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: phosphatidylglycerophosphate + H2O = phosphatidylglycerol + phosphate." [EC:3.1.3.27]
+def: "Catalysis of the reaction: phosphatidylglycerophosphate + H2O = phosphatidylglycerol + phosphate." [PMID:4292860]
synonym: "PGP phosphatase activity" RELATED [EC:3.1.3.27]
synonym: "phosphatidylglycerol phosphatase activity" RELATED [EC:3.1.3.27]
synonym: "phosphatidylglycerol phosphate phosphatase activity" RELATED [EC:3.1.3.27]
@@ -85385,13 +85219,14 @@ is_a: GO:0016728 ! oxidoreductase activity, acting on CH or CH2 groups, disulfid
[Term]
id: GO:0008999
-name: ribosomal-protein-alanine N-acetyltransferase activity
+name: ribosomal protein S5-alanine N-acetyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + ribosomal-protein L-alanine = CoA + ribosomal-protein N-acetyl-L-alanine." [EC:2.3.1.267]
-synonym: "acetyl-CoA:ribosomal-protein-L-alanine N-acetyltransferase activity" RELATED [EC:2.3.1.128]
-synonym: "ribosomal protein S18 acetyltransferase activity" RELATED [EC:2.3.1.128]
-xref: EC:2.3.1.267
+def: "Catalysis of the reaction: acetyl-CoA + N-terminal L-alanyl-[ribosomal protein] = CoA + H+ + N-terminal N-alpha-acetyl-L-alanyl-[ribosomal protein]." [RHEA:43752]
+synonym: "acetyl-CoA:ribosomal-protein-L-alanine N-acetyltransferase activity" RELATED []
+synonym: "ribosomal protein S18 acetyltransferase activity" RELATED []
+synonym: "ribosomal-protein-alanine N-acetyltransferase activity" BROAD []
xref: MetaCyc:2.3.1.128-RXN
+xref: RHEA:16433
is_a: GO:0004596 ! peptide alpha-N-acetyltransferase activity
[Term]
@@ -85880,16 +85715,11 @@ is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor
id: GO:0009032
name: thymidine phosphorylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: thymidine + phosphate = thymine + 2-deoxy-D-ribose 1-phosphate." [EC:2.4.2.4]
-synonym: "animal growth regulators, blood platelet-derived endothelial cell growth factors" RELATED [EC:2.4.2.4]
-synonym: "blood platelet-derived endothelial cell growth factor" RELATED [EC:2.4.2.4]
-synonym: "deoxythymidine phosphorylase activity" RELATED [EC:2.4.2.4]
-synonym: "gliostatins" RELATED [EC:2.4.2.4]
-synonym: "pyrimidine deoxynucleoside phosphorylase activity" RELATED [EC:2.4.2.4]
+def: "Catalysis of the reaction: thymidine + phosphate = thymine + 2-deoxy-D-ribose 1-phosphate." [RHEA:16037]
synonym: "pyrimidine phosphorylase activity" BROAD [EC:2.4.2.4]
-synonym: "thymidine-orthophosphate deoxyribosyltransferase activity" RELATED [EC:2.4.2.4]
-synonym: "thymidine:phosphate deoxy-alpha-D-ribosyltransferase activity" RELATED [EC:2.4.2.4]
-synonym: "thymidine:phosphate deoxy-D-ribosyltransferase activity" RELATED [EC:2.4.2.4]
+synonym: "thymidine-orthophosphate deoxyribosyltransferase activity" RELATED []
+synonym: "thymidine:phosphate deoxy-alpha-D-ribosyltransferase activity" RELATED []
+synonym: "thymidine:phosphate deoxy-D-ribosyltransferase activity" RELATED []
xref: EC:2.4.2.4
xref: MetaCyc:THYM-PHOSPH-RXN
xref: RHEA:16037
@@ -85899,7 +85729,7 @@ is_a: GO:0016763 ! pentosyltransferase activity
id: GO:0009033
name: trimethylamine-N-oxide reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADH + H+ + trimethylamine-N-oxide = NAD+ + trimethylamine + H2O." [GOC:curators, RHEA:22024]
+def: "Catalysis of the reaction: NADH + H+ + trimethylamine-N-oxide = NAD+ + trimethylamine + H2O." [RHEA:22024]
synonym: "NADH:trimethylamine-N-oxide oxidoreductase" EXACT []
synonym: "trimethylamine N-oxide reductase" EXACT []
synonym: "trimethylamine oxidase activity" EXACT []
@@ -85912,7 +85742,7 @@ is_a: GO:0016657 ! oxidoreductase activity, acting on NAD(P)H, nitrogenous group
id: GO:0009034
name: tryptophanase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + H(2)O = indole + NH(4)(+) + pyruvate." [EC:4.1.99.1, RHEA:19553]
+def: "Catalysis of the reaction: L-tryptophan + H(2)O = indole + NH(4)(+) + pyruvate." [RHEA:19553]
comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "L-tryptophan indole-lyase (deaminating) activity" RELATED [EC:4.1.99.1]
synonym: "L-tryptophan indole-lyase (deaminating; pyruvate forming) activity" RELATED [EC:4.1.99.1]
@@ -85933,13 +85763,12 @@ is_a: GO:0016830 ! carbon-carbon lyase activity
id: GO:0009035
name: type I site-specific deoxyribonuclease activity
namespace: molecular_function
-def: "Catalysis of the endonucleolytic cleavage of DNA to give random double-stranded fragments with terminal 5' or 3' protrusions; ATP is simultaneously hydrolyzed. Cleavage is dependent on the presence in the DNA of a specific recognition site. Cleavage may occur hundreds or thousands of base pairs away from the recognition site due to translocation of DNA." [PMID:15300241, PMID:15788748]
+def: "Catalysis of the endonucleolytic cleavage of DNA to give random double-stranded fragments with terminal 5' or 3' protrusions, driven by ATP hydrolysis. Cleavage is dependent on the presence in the DNA of a specific recognition site. Cleavage may occur hundreds or thousands of base pairs away from the recognition site due to translocation of DNA." [PMID:15300241, PMID:15788748]
synonym: "adenosine triphosphate-dependent deoxyribonuclease activity" RELATED [EC:3.1.21.3]
synonym: "ATP-dependent DNase activity" RELATED [EC:3.1.21.3]
synonym: "deoxyribonuclease (adenosine triphosphate-hydrolyzing)" RELATED [EC:3.1.21.3]
synonym: "deoxyribonuclease (ATP- and S-adenosyl-L-methionine-dependent)" RELATED [EC:3.1.21.3]
synonym: "type I restriction enzyme activity" EXACT []
-synonym: "type I site-specific deoxyribonuclease activity" RELATED [EC:3.1.21.3]
xref: EC:3.1.21.3
xref: MetaCyc:3.1.21.3-RXN
is_a: GO:0015616 ! DNA translocase activity
@@ -86110,7 +85939,7 @@ replaced_by: GO:0004190
id: GO:0009050
name: glycopeptide catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of glycopeptides, any compound in which carbohydrate is covalently attached to an oligopeptide composed of residues of L and/or D-amino acids. The term usually denotes a product of proteolytic degradation of a glycoprotein but includes glycated peptide." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of glycopeptides, a compound in which carbohydrate is covalently attached to an oligopeptide composed of residues of L and/or D-amino acids. The term usually denotes a product of proteolytic degradation of a glycoprotein but includes glycated peptide." [GOC:go_curators, ISBN:0198506732]
synonym: "glycopeptide breakdown" EXACT []
synonym: "glycopeptide catabolism" EXACT []
synonym: "glycopeptide degradation" EXACT []
@@ -86153,6 +85982,7 @@ namespace: molecular_function
alt_id: GO:0009053
alt_id: GO:0009054
def: "Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [ISBN:0198506732]
+comment: Note that this term should only be be used for electron transfer that generates a transmembrane electrochemical gradient, e.g. components of the respiratory or photosynthetic electron transport chain.
subset: goslim_metagenomics
subset: goslim_pir
synonym: "electron acceptor activity" NARROW []
@@ -86172,7 +86002,6 @@ alt_id: GO:0044712
def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684]
subset: goslim_agr
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_plant
synonym: "breakdown" EXACT []
synonym: "catabolism" EXACT []
@@ -86206,7 +86035,6 @@ alt_id: GO:0044274
alt_id: GO:0044711
def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_plant
synonym: "anabolism" EXACT []
@@ -86365,10 +86193,9 @@ name: aromatic amino acid family metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan)." [GOC:go_curators]
synonym: "aromatic amino acid family metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0006520 ! cellular amino acid metabolic process
is_a: GO:0006725 ! cellular aromatic compound metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
-is_a: GO:1901564 ! organonitrogen compound metabolic process
[Term]
id: GO:0009073
@@ -86477,8 +86304,7 @@ name: branched-chain amino acid metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine." [GOC:ai]
synonym: "branched chain family amino acid metabolism" EXACT [GOC:ai]
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:1901564 ! organonitrogen compound metabolic process
+is_a: GO:0006520 ! cellular amino acid metabolic process
[Term]
id: GO:0009082
@@ -86503,9 +86329,8 @@ synonym: "branched chain family amino acid breakdown" EXACT []
synonym: "branched chain family amino acid catabolic process" EXACT [GOC:ai]
synonym: "branched chain family amino acid catabolism" EXACT []
synonym: "branched chain family amino acid degradation" EXACT []
+is_a: GO:0009063 ! cellular amino acid catabolic process
is_a: GO:0009081 ! branched-chain amino acid metabolic process
-is_a: GO:0016054 ! organic acid catabolic process
-is_a: GO:1901565 ! organonitrogen compound catabolic process
[Term]
id: GO:0009084
@@ -86530,7 +86355,6 @@ synonym: "lysine formation" EXACT []
synonym: "lysine synthesis" EXACT []
xref: MetaCyc:PWY-5097
is_a: GO:0006553 ! lysine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
[Term]
@@ -86544,7 +86368,6 @@ synonym: "methionine formation" EXACT []
synonym: "methionine synthesis" EXACT []
is_a: GO:0000097 ! sulfur amino acid biosynthetic process
is_a: GO:0006555 ! methionine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
[Term]
@@ -86573,7 +86396,6 @@ synonym: "threonine synthesis" EXACT []
xref: MetaCyc:HOMOSER-THRESYN-PWY
xref: MetaCyc:THRESYN-PWY
is_a: GO:0006566 ! threonine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
[Term]
@@ -86601,7 +86423,6 @@ synonym: "homoserine biosynthesis" EXACT []
synonym: "homoserine formation" EXACT []
synonym: "homoserine synthesis" EXACT []
xref: MetaCyc:HOMOSERSYN-PWY
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009070 ! serine family amino acid biosynthetic process
is_a: GO:0009092 ! homoserine metabolic process
@@ -86656,7 +86477,6 @@ synonym: "phenylalanine biosynthetic process" BROAD []
synonym: "phenylalanine biosynthetic process, prephenate pathway" RELATED []
synonym: "phenylalanine biosynthetic process, shikimate pathway" RELATED []
is_a: GO:0006558 ! L-phenylalanine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009095 ! aromatic amino acid family biosynthetic process, prephenate pathway
is_a: GO:1902223 ! erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process
@@ -86697,7 +86517,8 @@ synonym: "leucine formation" EXACT []
synonym: "leucine synthesis" EXACT []
xref: MetaCyc:LEUSYN-PWY
is_a: GO:0006551 ! leucine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0009082 ! branched-chain amino acid biosynthetic process
+is_a: GO:1901607 ! alpha-amino acid biosynthetic process
[Term]
id: GO:0009099
@@ -86710,13 +86531,14 @@ synonym: "valine formation" EXACT []
synonym: "valine synthesis" EXACT []
xref: MetaCyc:VALSYN-PWY
is_a: GO:0006573 ! valine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
+is_a: GO:0009082 ! branched-chain amino acid biosynthetic process
+is_a: GO:1901607 ! alpha-amino acid biosynthetic process
[Term]
id: GO:0009100
name: glycoprotein metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732]
subset: goslim_drosophila
synonym: "glycoprotein metabolism" EXACT []
is_a: GO:0019538 ! protein metabolic process
@@ -86727,7 +86549,7 @@ is_a: GO:1901135 ! carbohydrate derivative metabolic process
id: GO:0009101
name: glycoprotein biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:go_curators, ISBN:0198506732]
synonym: "glycoprotein anabolism" EXACT []
synonym: "glycoprotein biosynthesis" EXACT []
synonym: "glycoprotein formation" EXACT []
@@ -88130,6 +87952,7 @@ synonym: "vitamin B1 biosynthesis" EXACT []
synonym: "vitamin B1 biosynthetic process" EXACT []
xref: MetaCyc:THISYN-PWY
is_a: GO:0006772 ! thiamine metabolic process
+is_a: GO:0034309 ! primary alcohol biosynthetic process
is_a: GO:0042724 ! thiamine-containing compound biosynthetic process
[Term]
@@ -88148,10 +87971,8 @@ synonym: "thiamine pyrophosphate biosynthesis" EXACT []
synonym: "thiamine pyrophosphate biosynthetic process" EXACT []
synonym: "TPP biosynthesis" EXACT []
synonym: "TPP biosynthetic process" EXACT []
-is_a: GO:0019438 ! aromatic compound biosynthetic process
is_a: GO:0042357 ! thiamine diphosphate metabolic process
-is_a: GO:0044272 ! sulfur compound biosynthetic process
-is_a: GO:0072528 ! pyrimidine-containing compound biosynthetic process
+is_a: GO:0042724 ! thiamine-containing compound biosynthetic process
is_a: GO:0090407 ! organophosphate biosynthetic process
[Term]
@@ -88166,6 +87987,7 @@ synonym: "thiamine degradation" EXACT []
synonym: "vitamin B1 catabolic process" EXACT []
synonym: "vitamin B1 catabolism" EXACT []
is_a: GO:0006772 ! thiamine metabolic process
+is_a: GO:0034310 ! primary alcohol catabolic process
is_a: GO:0042725 ! thiamine-containing compound catabolic process
[Term]
@@ -88809,7 +88631,6 @@ def: "The directed movement of DNA into a cell that contributes to the process o
synonym: "cellular DNA import during transformation" RELATED []
synonym: "cellular DNA uptake" BROAD []
synonym: "DNA import into cell" BROAD []
-synonym: "DNA import into cell involved in transformation" RELATED [GOC:dph, GOC:tb]
synonym: "DNA transport into cell during transformation" RELATED []
is_a: GO:0051027 ! DNA transport
is_a: GO:0098657 ! import into cell
@@ -88917,14 +88738,15 @@ id: GO:0009300
name: antisense RNA transcription
namespace: biological_process
def: "The synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:jl]
-is_a: GO:0006351 ! transcription, DNA-templated
is_a: GO:0042868 ! antisense RNA metabolic process
+is_a: GO:0098781 ! ncRNA transcription
[Term]
id: GO:0009301
name: snRNA transcription
namespace: biological_process
def: "The synthesis of small nuclear RNA (snRNA) from a DNA template." [GOC:jl, ISBN:0321000382]
+is_a: GO:0016073 ! snRNA metabolic process
is_a: GO:0098781 ! ncRNA transcription
[Term]
@@ -88945,6 +88767,7 @@ def: "The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribo
synonym: "rRNA biosynthesis" BROAD []
synonym: "rRNA biosynthetic process" BROAD []
synonym: "rRNA synthesis" BROAD []
+is_a: GO:0016072 ! rRNA metabolic process
is_a: GO:0098781 ! ncRNA transcription
[Term]
@@ -88955,6 +88778,7 @@ def: "The synthesis of transfer RNA (tRNA) from a DNA template." [GOC:jl]
synonym: "tRNA biosynthesis" BROAD []
synonym: "tRNA biosynthetic process" BROAD []
synonym: "tRNA synthesis" BROAD []
+is_a: GO:0006399 ! tRNA metabolic process
is_a: GO:0098781 ! ncRNA transcription
[Term]
@@ -88972,7 +88796,6 @@ namespace: biological_process
alt_id: GO:0045166
alt_id: GO:0045731
def: "The controlled release of proteins from a cell." [GOC:ai]
-subset: goslim_drosophila
synonym: "glycoprotein secretion" NARROW []
synonym: "protein secretion during cell fate commitment" NARROW []
synonym: "protein secretion resulting in cell fate commitment" NARROW []
@@ -89077,7 +88900,7 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:go_curators]
comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process.
synonym: "drug resistance" EXACT []
is_obsolete: true
-replaced_by: GO:0042493
+replaced_by: GO:0009410
[Term]
id: GO:0009316
@@ -89117,9 +88940,8 @@ def: "A protein complex that possesses cytochrome o ubiquinol oxidase activity;
comment: See also the molecular function term 'cytochrome o ubiquinol oxidase activity ; GO:0008827'.
xref: MetaCyc:CYT-O-UBIOX-CPLX
is_a: GO:0070069 ! cytochrome complex
-is_a: GO:0098796 ! membrane protein complex
+is_a: GO:1902495 ! transmembrane transporter complex
is_a: GO:1990204 ! oxidoreductase complex
-relationship: part_of GO:0016021 ! integral component of membrane
[Term]
id: GO:0009320
@@ -89148,11 +88970,11 @@ is_a: GO:1990204 ! oxidoreductase complex
[Term]
id: GO:0009323
-name: ribosomal-protein-alanine N-acetyltransferase complex
+name: obsolete ribosomal-protein-alanine N-acetyltransferase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the transfer of an acetyl group to ribosomal-protein alanine, forming ribosomal-protein acetylalanine." [EC:2.3.1.128]
-xref: EC:2.3.1.128
-is_a: GO:0031248 ! protein acetyltransferase complex
+def: "OBSOLETE. An enzyme complex that catalyzes the transfer of an acetyl group to ribosomal-protein alanine, forming ribosomal-protein acetylalanine." [EC:2.3.1.128]
+comment: This term was obsoleted because there is no evidence that this complex exists. Enzymes with that activity, such as E. coli rimJ (UniProt:P0A948), act as monomoers.
+is_obsolete: true
[Term]
id: GO:0009324
@@ -89174,7 +88996,7 @@ is_a: GO:1990204 ! oxidoreductase complex
id: GO:0009326
name: formate dehydrogenase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2)." [EC:1.17.1.9]
+def: "An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2)." [PMID:1504073, PMID:8566699]
xref: EC:1.17.1.9
is_a: GO:1990204 ! oxidoreductase complex
@@ -89297,7 +89119,7 @@ is_a: GO:0009330 ! DNA topoisomerase type II (double strand cut, ATP-hydrolyzing
id: GO:0009341
name: beta-galactosidase complex
namespace: cellular_component
-def: "A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species." [BRENDA:3.2.1.2, EC:3.2.1.23, PMID:15950161]
+def: "A protein complex that possesses beta-galactosidase activity, i.e. catalyzes the hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. In E. coli, the complex is a homotetramer; dimeric and hexameric beta-galactosidase complexes have been observed in other species." [PMID:15950161]
subset: goslim_metagenomics
is_a: GO:1902494 ! catalytic complex
@@ -89404,7 +89226,7 @@ consider: GO:0045254
id: GO:0009353
name: mitochondrial oxoglutarate dehydrogenase complex
namespace: cellular_component
-def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) ; EC:1.2.4.2 (E1), dihydrolipoamide S-succinyltransferase ; EC:2.3.1.61 (E2) and dihydrolipoamide dehydrogenase ; EC:1.8.1.4 (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2) within the mitochondrial matrix. An example of this complex is found in Mus musculus." [GOC:mtg_sensu, MetaCyc:CPLX66-42, PMID:10848975]
+def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2) within the mitochondrial matrix. An example of this complex is found in Mus musculus." [GOC:mtg_sensu, MetaCyc:CPLX66-42, PMID:10848975]
comment: See also the molecular functions term 'oxoglutarate dehydrogenase (succinyl-transferring) activity ; GO:0004591', 'dihydrolipoyllysine-residue succinyltransferase activity ; GO:0004149' and 'dihydrolipoyl dehydrogenase activity ; GO:0004148'.
is_a: GO:0005947 ! mitochondrial alpha-ketoglutarate dehydrogenase complex
is_a: GO:0045252 ! oxoglutarate dehydrogenase complex
@@ -89474,7 +89296,7 @@ is_a: GO:0042575 ! DNA polymerase complex
id: GO:0009361
name: succinate-CoA ligase complex (ADP-forming)
namespace: cellular_component
-def: "A heterodimeric enzyme complex, composed of an alpha and beta chain, most usually found in (but not limited to) bacteria. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP." [EC:6.2.1.5, GOC:jl]
+def: "A heterodimeric enzyme complex, composed of an alpha and beta chain, most usually found in (but not limited to) bacteria. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP." [GOC:jl, PMID:9874242]
synonym: "succinyl-CoA synthetase, ADP-forming" EXACT [CORUM:394]
is_a: GO:0042709 ! succinate-CoA ligase complex
@@ -89553,7 +89375,7 @@ relationship: part_of GO:0071444 ! cellular response to pheromone
id: GO:0009374
name: biotin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with biotin (cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid), the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [GOC:jl, ISBN:0198506732]
+def: "Binding to biotin (cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid), the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions." [GOC:jl, ISBN:0198506732]
synonym: "vitamin B7 binding" EXACT []
synonym: "vitamin H binding" EXACT []
is_a: GO:0019842 ! vitamin binding
@@ -89580,7 +89402,6 @@ namespace: cellular_component
def: "A protein complex that possesses ATP-dependent protease activity; consists of an ATPase large subunit with homology to other ClpX family ATPases and a peptidase small subunit related to the proteasomal beta-subunits of eukaryotes. In the E. coli complex, a double ring-shaped homohexamer of HslV is capped on each side by a ring-shaped HslU homohexamer." [GOC:bhm, PMID:12670962, UniProt:P0A6H5]
synonym: "ClpYQ protease complex" EXACT []
is_a: GO:0031597 ! cytosolic proteasome complex
-is_a: GO:1904949 ! ATPase complex
[Term]
id: GO:0009377
@@ -89597,7 +89418,7 @@ id: GO:0009378
name: four-way junction helicase activity
namespace: molecular_function
alt_id: GO:1990163
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, where this reaction drives the unwinding of the DNA helix of DNA containing four-way junctions, including Holliday junctions." [GOC:al, PMID:22723423, PMID:9442895]
+def: "Unwinding a DNA helix of DNA containing four-way junctions, including Holliday junctions, driven by ATP hydrolysis." [GOC:al, PMID:22723423, PMID:9442895]
synonym: "ATP-dependent four-way junction DNA helicase activity" EXACT []
synonym: "ATP-dependent four-way junction helicase activity" EXACT []
synonym: "ATP-dependent Holliday junction helicase activity" NARROW []
@@ -89930,8 +89751,14 @@ is_a: GO:0009266 ! response to temperature stimulus
id: GO:0009410
name: response to xenobiotic stimulus
namespace: biological_process
+alt_id: GO:0017035
alt_id: GO:0017104
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms." [GOC:jl]
+alt_id: GO:0042493
+def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a xenobiotic, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:jl, GOC:krc]
+subset: goslim_candida
+synonym: "drug resistance" RELATED []
+synonym: "drug susceptibility/resistance" RELATED []
+synonym: "response to drug" RELATED []
is_a: GO:0042221 ! response to chemical
[Term]
@@ -90719,6 +90546,7 @@ xref: MetaCyc:RXN0-5268
xref: RHEA:30251
xref: TC:3.D.4.5.1
is_a: GO:0009055 ! electron transfer activity
+is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity
is_a: GO:0016675 ! oxidoreductase activity, acting on a heme group of donors
[Term]
@@ -90828,6 +90656,7 @@ xref: EC:7.1.1.6
xref: KEGG_REACTION:R03817
xref: MetaCyc:PLASTOQUINOL--PLASTOCYANIN-REDUCTASE-RXN
xref: RHEA:22148
+is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity
is_a: GO:0052880 ! oxidoreductase activity, acting on diphenols and related substances as donors, with copper protein as acceptor
[Term]
@@ -90938,7 +90767,7 @@ id: GO:0009508
name: plastid chromosome
namespace: cellular_component
def: "A circular DNA molecule containing plastid encoded genes." [ISBN:0943088399]
-is_a: GO:0000229 ! cytoplasmic chromosome
+is_a: GO:0005694 ! chromosome
relationship: part_of GO:0042646 ! plastid nucleoid
[Term]
@@ -91207,17 +91036,6 @@ synonym: "photosystem II reaction centre" EXACT []
is_a: GO:0098796 ! membrane protein complex
relationship: part_of GO:0009523 ! photosystem II
-[Term]
-id: GO:0009540
-name: zeaxanthin epoxidase [overall] activity
-namespace: molecular_function
-def: "Catalysis of the reactions: zeaxanthin + NAD(P)H + H+ + O2 = antheraxanthin + NAD(P)+ + H2O; and antheraxanthin + NAD(P)H + H+ + O2 = violaxanthin + NAD(P)+ + H2O." [EC:1.14.13.90]
-comment: This is a process composed of two reactions represented by the terms 'GO:0052662 : zeaxanthin epoxidase activity' and 'GO:0052663 : antheraxanthin epoxidase activity'.
-synonym: "zea-epoxidase activity" RELATED [EC:1.14.13.90]
-synonym: "zeaxanthin,NAD(P)H:oxygen oxidoreductase activity" RELATED [EC:1.14.13.90]
-xref: EC:1.14.13.90
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
-
[Term]
id: GO:0009541
name: etioplast prolamellar body
@@ -93361,11 +93179,11 @@ relationship: part_of GO:0019684 ! photosynthesis, light reaction
[Term]
id: GO:0009766
-name: primary charge separation
+name: obsolete primary charge separation
namespace: biological_process
-def: "In the photosynthetic reaction centers, primary charge separation is initiated by the excitation of a molecule followed by the transfer of an electron to an electron acceptor molecule following energy transfer from light harvesting complexes." [ISBN:0792361431]
-is_a: GO:0022904 ! respiratory electron transport chain
-relationship: part_of GO:0019684 ! photosynthesis, light reaction
+def: "OBSOLETE. In the photosynthetic reaction centers, primary charge separation is initiated by the excitation of a molecule followed by the transfer of an electron to an electron acceptor molecule following energy transfer from light harvesting complexes." [ISBN:0792361431]
+comment: This term was obsoleted because it represents a mechanism, and is outside the scope of GO.
+is_obsolete: true
[Term]
id: GO:0009767
@@ -93398,17 +93216,19 @@ is_a: GO:0009765 ! photosynthesis, light harvesting
[Term]
id: GO:0009770
-name: primary charge separation in photosystem I
+name: obsolete primary charge separation in photosystem I
namespace: biological_process
-def: "Energized reaction-center P700 chlorophylls on photosystem I donate an electron to a loosely bound Quinone acceptor molecule X, on the stromal surface of the thylakoid membrane. The result is charge separation; a negative charge on the stromal side of the thylakoid membrane and a positive charge on the luminal side." [GOC:jid, ISBN:0716731363, ISBN:0816017360]
-is_a: GO:0009766 ! primary charge separation
+def: "OBSOLETE. Energized reaction-center P700 chlorophylls on photosystem I donate an electron to a loosely bound Quinone acceptor molecule X, on the stromal surface of the thylakoid membrane. The result is charge separation; a negative charge on the stromal side of the thylakoid membrane and a positive charge on the luminal side." [GOC:jid, ISBN:0716731363, ISBN:0816017360]
+comment: This term was obsoleted because it represents a mechanism, and is outside the scope of GO.
+is_obsolete: true
[Term]
id: GO:0009771
-name: primary charge separation in photosystem II
+name: obsolete primary charge separation in photosystem II
namespace: biological_process
-def: "Energized reaction-center P680 chlorophylls on photosystem II donate an electron to a loosely bound acceptor molecule, the quinone Q, on the stromal surface of the thylakoid membrane. The result is charge separation; a negative charge on the stromal side of the thylakoid membrane and a positive charge on the luminal side." [GOC:jid, ISBN:0716731363, ISBN:0816017360]
-is_a: GO:0009766 ! primary charge separation
+def: "OBSOLETE. Energized reaction-center P680 chlorophylls on photosystem II donate an electron to a loosely bound acceptor molecule, the quinone Q, on the stromal surface of the thylakoid membrane. The result is charge separation; a negative charge on the stromal side of the thylakoid membrane and a positive charge on the luminal side." [GOC:jid, ISBN:0716731363, ISBN:0816017360]
+comment: This term was obsoleted because it represents a mechanism, and is outside the scope of GO.
+is_obsolete: true
[Term]
id: GO:0009772
@@ -93558,7 +93378,6 @@ alt_id: GO:0009795
def: "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu]
subset: gocheck_do_not_manually_annotate
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_plant
synonym: "embryogenesis" EXACT []
synonym: "embryogenesis and morphogenesis" BROAD []
@@ -94116,7 +93935,7 @@ namespace: biological_process
alt_id: GO:0075005
def: "The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall)." [GOC:lr]
synonym: "spore germination on or near host" NARROW []
-is_a: GO:0032502 ! developmental process
+is_a: GO:0030154 ! cell differentiation
[Term]
id: GO:0009848
@@ -94184,6 +94003,7 @@ id: GO:0009853
name: photorespiration
namespace: biological_process
def: "A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria." [ISBN:0198506732]
+synonym: "photorespiratory pathway" EXACT [GOC:cjm]
xref: MetaCyc:PWY-181
xref: Wikipedia:Photorespiration
is_a: GO:0043094 ! cellular metabolic compound salvage
@@ -94813,7 +94633,6 @@ namespace: biological_process
def: "The process in which the cellular identity of auditory hair cells is acquired and determined." [GOC:lr]
synonym: "auditory hair cell fate commitment" EXACT []
is_a: GO:0060120 ! inner ear receptor cell fate commitment
-is_a: GO:0072148 ! epithelial cell fate commitment
relationship: part_of GO:0042491 ! inner ear auditory receptor cell differentiation
[Term]
@@ -95065,7 +94884,7 @@ relationship: positively_regulates GO:0009740 ! gibberellic acid mediated signal
id: GO:0009940
name: amino-terminal vacuolar sorting propeptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an amino terminal propeptide, which functions as a sorting signal to sort away the soluble vacuolar protein from Golgi to lytic vacuole via clathrin-coated vesicles." [GOC:sm, PMID:10871276]
+def: "Binding to an amino terminal propeptide, which functions as a sorting signal to sort away the soluble vacuolar protein from Golgi to lytic vacuole via clathrin-coated vesicles." [GOC:sm, PMID:10871276]
is_a: GO:0010209 ! vacuolar sorting signal binding
[Term]
@@ -95429,6 +95248,7 @@ id: GO:0009975
name: cyclase activity
namespace: molecular_function
def: "Catalysis of a ring closure reaction." [ISBN:0198547684]
+subset: goslim_generic
subset: goslim_pir
is_a: GO:0003824 ! catalytic activity
@@ -95456,11 +95276,17 @@ is_a: GO:0015291 ! secondary active transmembrane transporter activity
id: GO:0009978
name: allene oxide synthase activity
namespace: molecular_function
+alt_id: GO:0047987
def: "Catalysis of the reaction: 13(S)-hydroperoxylinolenate = 12,13(S)-epoxylinolenate + H2O." [EC:4.2.1.92, MetaCyc:RXN1F-19, PMID:9778849]
synonym: "(9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate 12,13-hydro-lyase [(9Z)-(13S)-12,13-epoxyoctadeca-9,11-dienoate-forming]" RELATED [EC:4.2.1.92]
+synonym: "(9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate 12,13-hydro-lyase activity" RELATED [EC:4.2.1.92]
synonym: "HPI" RELATED [EC:4.2.1.92]
+synonym: "hydroperoxide dehydratase activity" RELATED []
+synonym: "hydroperoxide isomerase activity" RELATED [EC:4.2.1.92]
synonym: "linoleate hydroperoxide isomerase" RELATED [EC:4.2.1.92]
synonym: "linoleic acid hydroperoxide isomerase" RELATED [EC:4.2.1.92]
+xref: EC:4.2.1.92
+xref: MetaCyc:HYDROPEROXIDE-DEHYDRATASE-RXN
xref: MetaCyc:RXN1F-19
xref: RHEA:25074
is_a: GO:0016836 ! hydro-lyase activity
@@ -95551,6 +95377,7 @@ alt_id: GO:0008151
alt_id: GO:0044763
alt_id: GO:0050875
def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
+subset: gocheck_do_not_annotate
subset: goslim_plant
synonym: "cell growth and/or maintenance" NARROW []
synonym: "cell physiology" EXACT []
@@ -95738,7 +95565,7 @@ namespace: cellular_component
def: "The lipid bilayer surrounding an endosome." [GOC:mah]
synonym: "endosomal membrane" EXACT [NIF_Subcellular:sao978443756]
xref: NIF_Subcellular:sao978443756
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
is_a: GO:0098588 ! bounding membrane of organelle
relationship: part_of GO:0005768 ! endosome
@@ -95756,7 +95583,7 @@ relationship: part_of GO:0010008 ! endosome membrane
id: GO:0010011
name: auxin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with auxin, plant hormones that regulate aspects of plant growth." [GOC:sm]
+def: "Binding to auxin, a plant hormone that regulates aspects of plant growth." [GOC:sm]
synonym: "auxin receptor" NARROW []
is_a: GO:0042562 ! hormone binding
@@ -95771,8 +95598,7 @@ is_a: GO:0008395 ! steroid hydroxylase activity
id: GO:0010013
name: N-1-naphthylphthalamic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with N-1-naphthylphthalamic acid, an auxin transport inhibitor." [GOC:sm]
-is_a: GO:0008144 ! drug binding
+def: "Binding to N-1-naphthylphthalamic acid, an auxin transport inhibitor." [GOC:sm]
is_a: GO:0033218 ! amide binding
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0043177 ! organic acid binding
@@ -96680,7 +96506,6 @@ def: "Any process that modulates the frequency, rate or extent of systemic acqui
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0050776 ! regulation of immune response
relationship: regulates GO:0009627 ! systemic acquired resistance
[Term]
@@ -96696,7 +96521,6 @@ is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0010112 ! regulation of systemic acquired resistance
is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
-is_a: GO:0050777 ! negative regulation of immune response
relationship: negatively_regulates GO:0009627 ! systemic acquired resistance
[Term]
@@ -97369,7 +97193,7 @@ is_a: GO:0010178 ! IAA-amino acid conjugate hydrolase activity
id: GO:0010180
name: thioglucosidase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme thioglucosidase." [GOC:tb]
+def: "Binding to a thioglucosidase enzyme." [GOC:tb]
synonym: "myrosinase binding" EXACT []
is_a: GO:0019899 ! enzyme binding
@@ -97377,7 +97201,7 @@ is_a: GO:0019899 ! enzyme binding
id: GO:0010181
name: FMN binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:tb]
+def: "Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:tb]
synonym: "flavin mononucleotide binding" EXACT []
is_a: GO:0032553 ! ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -97622,7 +97446,7 @@ id: GO:0010207
name: photosystem II assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a photosystem II complex on the thylakoid membrane. The photosystem II complex consists of at least 20 polypeptides and around 80 cofactors in most organisms." [GOC:aa, GOC:pz]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0019684 ! photosynthesis, light reaction
[Term]
@@ -97639,7 +97463,7 @@ relationship: part_of GO:0009555 ! pollen development
id: GO:0010209
name: vacuolar sorting signal binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a vacuolar sorting signal, a specific peptide sequence that acts as a signal to localize the protein within the vacuole." [GOC:mah]
+def: "Binding to a vacuolar sorting signal, a specific peptide sequence that acts as a signal to localize the protein within the vacuole." [GOC:mah]
is_a: GO:0005048 ! signal sequence binding
[Term]
@@ -98071,7 +97895,7 @@ id: GO:0010257
name: NADH dehydrogenase complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form an NADH dehydrogenase complex." [GOC:sm]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0010258
@@ -98150,6 +97974,7 @@ synonym: "response to thiamine" EXACT []
is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0033273 ! response to vitamin
+is_a: GO:0097305 ! response to alcohol
[Term]
id: GO:0010267
@@ -98219,7 +98044,7 @@ name: NAD(P)H dehydrogenase complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form NAD(P)H dehydrogenase complex, which is involved in electron transport from an unidentified electron donor, possibly NAD(P)H or ferredoxin(Fd) to the plastoquinone pool." [GOC:sm]
synonym: "NAD(P)H dehydrogenase complex (plastoquinone) assembly" NARROW []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0010276
@@ -98434,7 +98259,7 @@ is_a: GO:0051723 ! protein methylesterase activity
id: GO:0010297
name: heteropolysaccharide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with heteropolysaccharides. A heteropolysaccharide is a glycan composed of more than one type of monosaccharide residue." [PMID:16640603]
+def: "Binding to a heteropolysaccharide, a glycan composed of more than one type of monosaccharide residue." [PMID:16640603]
synonym: "heteroglycan binding" EXACT []
is_a: GO:0030247 ! polysaccharide binding
@@ -98583,14 +98408,14 @@ relationship: part_of GO:1990359 ! stress response to zinc ion
id: GO:0010313
name: phytochrome binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phytochrome." [PMID:15486102]
+def: "Binding to a phytochrome." [PMID:15486102]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0010314
name: phosphatidylinositol-5-phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol-5-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 5' position." [GOC:bf, GOC:tair_curators]
+def: "Binding to phosphatidylinositol-5-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 5' position." [GOC:bf, GOC:tair_curators]
is_a: GO:1901981 ! phosphatidylinositol phosphate binding
[Term]
@@ -98750,7 +98575,7 @@ is_a: GO:1990234 ! transferase complex
id: GO:0010331
name: gibberellin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with gibberellins, plant hormones that regulate aspects of plant growth." [GOC:tair_curators]
+def: "Binding to a gibberellin, a plant hormone that regulates aspects of plant growth." [GOC:tair_curators]
synonym: "gibberellic acid receptor" RELATED []
synonym: "gibberellin receptor" RELATED []
is_a: GO:0019840 ! isoprenoid binding
@@ -98905,11 +98730,12 @@ is_a: GO:0046873 ! metal ion transmembrane transporter activity
id: GO:0010349
name: L-galactose dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-galactose + NAD+ = L-galactono-1,4-lactone + NADH + H+." [PMID:12047629]
+def: "Catalysis of the reaction: L-galactose + NAD+ = L-galactono-1,4-lactone + NADH + H+." [PMID:12047629, RHEA:31559]
synonym: "L-galactose 1-dehydrogenase activity" RELATED []
+xref: EC:1.1.1.316
xref: MetaCyc:RXN-1884
xref: RHEA:31559
-is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0010350
@@ -98924,7 +98750,7 @@ name: lithium ion transport
namespace: biological_process
def: "The directed movement of lithium ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [PMID:17270011]
synonym: "lithium transport" EXACT []
-is_a: GO:0006812 ! cation transport
+is_a: GO:0030001 ! metal ion transport
[Term]
id: GO:0010352
@@ -99224,7 +99050,7 @@ is_a: GO:0044036 ! cell wall macromolecule metabolic process
id: GO:0010385
name: double-stranded methylated DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded methylated DNA. Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks." [GOC:imk, PMID:17242155]
+def: "Binding to double-stranded methylated DNA. Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks." [GOC:imk, PMID:17242155]
is_a: GO:0003690 ! double-stranded DNA binding
[Term]
@@ -99233,7 +99059,7 @@ name: COP9 signalosome assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a COP9 signalosome." [PMID:17307927]
synonym: "signalosome assembly" BROAD [GOC:krc]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0010389
@@ -99563,7 +99389,7 @@ is_a: GO:0032776 ! DNA methylation on cytosine
id: GO:0010427
name: abscisic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with abscisic acid, plant hormones that regulate aspects of plant growth." [PMID:17347412]
+def: "Binding to abscisic acid, a plant hormone that regulates aspects of plant growth." [PMID:17347412]
synonym: "ABA binding" RELATED []
synonym: "abscisate binding" RELATED []
is_a: GO:0019840 ! isoprenoid binding
@@ -99576,14 +99402,14 @@ is_a: GO:0043178 ! alcohol binding
id: GO:0010428
name: methyl-CpNpG binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a methylated cytosine/unspecified/guanine trinucleotide." [PMID:17239600]
+def: "Binding to a methylated cytosine/unspecified/guanine trinucleotide." [PMID:17239600]
is_a: GO:0000166 ! nucleotide binding
[Term]
id: GO:0010429
name: methyl-CpNpN binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a methylated cytosine/unspecified/unspecified trinucleotide." [PMID:17239600]
+def: "Binding to a methylated cytosine/unspecified/unspecified trinucleotide." [PMID:17239600]
is_a: GO:0000166 ! nucleotide binding
[Term]
@@ -99909,7 +99735,7 @@ is_a: GO:0052547 ! regulation of peptidase activity
id: GO:0010467
name: gene expression
namespace: biological_process
-def: "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb]
+def: "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes." [GOC:txnOH-2018, PMID:25934543, PMID:31580950]
subset: goslim_flybase_ribbon
xref: Wikipedia:Gene_expression
is_a: GO:0043170 ! macromolecule metabolic process
@@ -99918,8 +99744,9 @@ is_a: GO:0043170 ! macromolecule metabolic process
id: GO:0010468
name: regulation of gene expression
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb]
+def: "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." [GOC:txnOH-2018]
comment: This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation.
+synonym: "gene regulation" RELATED [GOC:cjm]
synonym: "regulation of gene product expression" RELATED []
synonym: "regulation of protein expression" NARROW []
xref: Wikipedia:Regulation_of_gene_expression
@@ -100655,7 +100482,7 @@ relationship: negatively_regulates GO:0009059 ! macromolecule biosynthetic proce
id: GO:0010559
name: regulation of glycoprotein biosynthetic process
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
+def: "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
is_a: GO:1903018 ! regulation of glycoprotein metabolic process
is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0009101 ! glycoprotein biosynthetic process
@@ -100664,7 +100491,7 @@ relationship: regulates GO:0009101 ! glycoprotein biosynthetic process
id: GO:0010560
name: positive regulation of glycoprotein biosynthetic process
namespace: biological_process
-def: "Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
+def: "Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process
is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
@@ -100675,7 +100502,7 @@ relationship: positively_regulates GO:0009101 ! glycoprotein biosynthetic proces
id: GO:0010561
name: negative regulation of glycoprotein biosynthetic process
namespace: biological_process
-def: "Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of glycoproteins, any protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
+def: "Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." [GOC:dph, GOC:tb]
is_a: GO:0010559 ! regulation of glycoprotein biosynthetic process
is_a: GO:1903019 ! negative regulation of glycoprotein metabolic process
is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
@@ -101235,7 +101062,7 @@ relationship: negatively_regulates GO:0014010 ! Schwann cell proliferation
id: GO:0010628
name: positive regulation of gene expression
namespace: biological_process
-def: "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb]
+def: "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." [GOC:txnOH-2018]
is_a: GO:0010468 ! regulation of gene expression
is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
relationship: positively_regulates GO:0010467 ! gene expression
@@ -101244,8 +101071,9 @@ relationship: positively_regulates GO:0010467 ! gene expression
id: GO:0010629
name: negative regulation of gene expression
namespace: biological_process
-def: "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb]
+def: "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." [GOC:txnOH-2018]
comment: This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation.
+synonym: "gene silencing" RELATED []
is_a: GO:0010468 ! regulation of gene expression
is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
relationship: negatively_regulates GO:0010467 ! gene expression
@@ -102234,8 +102062,7 @@ is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
id: GO:0010736
name: serum response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the serum response element (SRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to a serum response element (SRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:dph, GOC:rl, GOC:tb]
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
[Term]
@@ -103146,7 +102973,7 @@ relationship: part_of GO:0060042 ! retina morphogenesis in camera-type eye
id: GO:0010843
name: obsolete promoter binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factor complexes of the basal transcription machinery." [GOC:dph, GOC:tb, SO:0000167]
+def: "OBSOLETE. Binding to a regulatory region composed of the transcription start site and binding sites for transcription factor complexes of the basal transcription machinery." [GOC:dph, GOC:tb, SO:0000167]
comment: This term was made obsolete because the word "promoter" is used ambiguously in the literature. It sometimes is used to refer specifically to the "core promoter" region recognized by the basal transcription machinery, and other times is used to refer to a larger regulatory region composed of the core promoter and also the regulatory region adjacent (proximal) to the core promoter. The core promoter proximal region is typically recognized by "regulatory transcription factors", such as Gal4 in S. cerevisiae.
synonym: "DNA binding, transcription promoter" EXACT [GOC:dph, GOC:tb]
synonym: "promoter binding" EXACT []
@@ -103158,7 +102985,7 @@ consider: GO:0001046
id: GO:0010844
name: recombination hotspot binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a region in a genome which promotes recombination." [GOC:dph, GOC:tb]
+def: "Binding to a genomic region which promotes recombination." [GOC:dph, GOC:tb]
synonym: "DNA binding, recombination hotspot" EXACT [GOC:dph, GOC:tb]
is_a: GO:0003677 ! DNA binding
@@ -103207,7 +103034,7 @@ synonym: "regulation of hydrogen ion transporting ATPase activity, rotational me
synonym: "regulation of V-type ATPase activity" BROAD [GOC:dph, GOC:tb]
is_a: GO:0010155 ! regulation of proton transport
is_a: GO:0032412 ! regulation of ion transmembrane transporter activity
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
[Term]
id: GO:0010850
@@ -103260,6 +103087,7 @@ name: adenylate cyclase activator activity
namespace: molecular_function
def: "Increases the activity of the enzyme that catalyzes the reaction: ATP = 3',5'-cyclic AMP + diphosphate." [GOC:dph, GOC:tb]
is_a: GO:0008047 ! enzyme activator activity
+is_a: GO:0010851 ! cyclase regulator activity
[Term]
id: GO:0010857
@@ -104234,15 +104062,6 @@ is_a: GO:0032885 ! regulation of polysaccharide biosynthetic process
is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process
relationship: regulates GO:0009250 ! glucan biosynthetic process
-[Term]
-id: GO:0010963
-name: regulation of L-arginine import
-namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of L-arginine import. L-arginine import is the directed movement of L-arginine, the L-enantiomer of 2-amino-5-guanidinopentanoic acid, into a cell or organelle." [GOC:dph, GOC:tb]
-is_a: GO:0044070 ! regulation of anion transport
-is_a: GO:0051955 ! regulation of amino acid transport
-relationship: regulates GO:1902023 ! L-arginine transport
-
[Term]
id: GO:0010964
name: regulation of heterochromatin assembly by small RNA
@@ -104556,7 +104375,7 @@ is_a: GO:0009612 ! response to mechanical stimulus
id: GO:0010997
name: anaphase-promoting complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an anaphase-promoting complex. A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis." [GOC:BHF, GOC:dph, GOC:tb]
+def: "Binding to an anaphase-promoting complex. A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis." [GOC:BHF, GOC:dph, GOC:tb]
synonym: "APC binding" EXACT [GOC:dph, GOC:tb]
is_a: GO:0044877 ! protein-containing complex binding
@@ -104595,6 +104414,7 @@ namespace: biological_process
alt_id: GO:0016244
def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis]
comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children.
+subset: goslim_generic
synonym: "caspase-independent apoptosis" RELATED []
synonym: "caspase-independent cell death" NARROW []
synonym: "non-apoptotic programmed cell death" NARROW []
@@ -107205,7 +107025,6 @@ namespace: biological_process
alt_id: GO:0015831
def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
subset: goslim_yeast
synonym: "enzyme transport" NARROW []
@@ -107677,7 +107496,7 @@ replaced_by: GO:0046935
id: GO:0015074
name: DNA integration
namespace: biological_process
-def: "The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome." [GOC:mah]
+def: "The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome." [GOC:mah]
subset: goslim_pir
is_a: GO:0006259 ! DNA metabolic process
@@ -107993,8 +107812,9 @@ is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
id: GO:0015112
name: nitrate transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of nitrate ions (NO3-) from one side of a membrane to the other." [GOC:ai]
+def: "Enables the transfer of nitrate ions (NO3-) from one side of a membrane to the other." [GOC:ai, RHEA:34923]
synonym: "nitrite/nitrate porter activity" RELATED []
+xref: RHEA:34923
is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
[Term]
@@ -108602,20 +108422,6 @@ synonym: "L-alanine transporter activity" BROAD []
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0022858 ! alanine transmembrane transporter activity
-[Term]
-id: GO:0015181
-name: arginine transmembrane transporter activity
-namespace: molecular_function
-alt_id: GO:0005288
-def: "Enables the stereospecific transfer of arginine, 2-amino-5-guanidinopentanoic acid, across a biological membrane." [GOC:go_curators, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
-synonym: "arginine permease activity" EXACT []
-synonym: "histidine/arginine/lysine/ornithine porter activity" NARROW []
-synonym: "L-arginine transporter activity" NARROW []
-xref: RHEA:32143
-is_a: GO:0008324 ! cation transmembrane transporter activity
-is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015174 ! basic amino acid transmembrane transporter activity
-
[Term]
id: GO:0015182
name: L-asparagine transmembrane transporter activity
@@ -109130,6 +108936,7 @@ synonym: "thiamine uptake transmembrane transporter activity" RELATED []
synonym: "vitamin B1 transporter activity" EXACT []
xref: Reactome:R-HSA-199626 "SLC19A2/3 transport extracellular THMN to cytosol"
xref: RHEA:34919
+is_a: GO:0015101 ! organic cation transmembrane transporter activity
is_a: GO:0090482 ! vitamin transmembrane transporter activity
is_a: GO:1901474 ! azole transmembrane transporter activity
is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
@@ -109365,7 +109172,7 @@ namespace: molecular_function
alt_id: GO:0015249
alt_id: GO:0015268
alt_id: GO:0022838
-def: "Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729, TC:1.-.-.-.-]
+def: "Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729]
synonym: "alpha-type channel activity" RELATED []
synonym: "channel-forming toxin activity" RELATED []
synonym: "channel/pore class transporter activity" EXACT []
@@ -109375,7 +109182,6 @@ synonym: "pore class transporter activity" RELATED []
synonym: "substrate-specific channel activity" RELATED []
xref: Reactome:R-HSA-3779381 "H2O2 diffuses from the mitochondrial matrix to the cytosol"
xref: Reactome:R-HSA-8953430 "PXMP2 trimer transports glycolate from cytosol to peroxisomal matrix"
-xref: RHEA:29447
xref: TC:1
is_a: GO:0022803 ! passive transmembrane transporter activity
@@ -110606,14 +110412,15 @@ is_a: GO:0140359 ! ABC-type transporter activity
id: GO:0015411
name: ABC-type taurine transporter transporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + taurine(out) = ADP + phosphate + taurine(in)." [RHEA:14614]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + taurine(out) = ADP + phosphate + taurine(in)." [RHEA:14613]
synonym: "ATP-dependent taurine transporter activity" RELATED []
synonym: "ATPase-coupled taurine transporter activity" RELATED []
synonym: "taurine ABC transporter" EXACT [EC:7.6.2.7]
synonym: "taurine-transporting ATPase activity" RELATED [EC:7.6.2.7]
xref: EC:7.6.2.7
xref: MetaCyc:3.6.3.36-RXN
-xref: RHEA:14614
+xref: MetaCyc:ABC-64-RXN
+xref: RHEA:14613
is_a: GO:0005368 ! taurine transmembrane transporter activity
is_a: GO:0008559 ! ABC-type xenobiotic transporter activity
is_a: GO:0022853 ! active ion transmembrane transporter activity
@@ -110948,7 +110755,7 @@ name: ABC-type glycerol-3-phosphate transporter activity
namespace: molecular_function
alt_id: GO:0015610
alt_id: GO:0070812
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + glycerol-3-phosphate(out) = ADP + phosphate + glycerol-3-phosphate(in)." [RHEA:21669]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + glycerol-3-phosphate(out) = ADP + phosphate + glycerol-3-phosphate(in)." [RHEA:21668]
synonym: "ABC-type glycerol 3-phosphate transporter" EXACT [EC:7.6.2.10]
synonym: "ATP-dependent glycerol-2-phosphate transmembrane transporter activity" NARROW []
synonym: "ATPase-coupled glycerol-2-phosphate transmembrane transporter activity" NARROW []
@@ -110960,7 +110767,7 @@ synonym: "glycerol-3-phosphate-transporting ATPase" RELATED [EC:7.6.2.10]
synonym: "glycerol-phosphate porter activity" NARROW []
xref: EC:7.6.2.10
xref: MetaCyc:3.6.3.20-RXN
-xref: RHEA:21669
+xref: RHEA:21668
is_a: GO:0015169 ! glycerol-3-phosphate transmembrane transporter activity
is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
@@ -111254,15 +111061,14 @@ is_obsolete: true
[Term]
id: GO:0015450
-name: P-P-bond-hydrolysis-driven protein transmembrane transporter activity
+name: protein-transporting ATPase activity
namespace: molecular_function
def: "Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated." [GOC:mtg_transport, ISBN:0815340729]
+synonym: "P-P-bond-hydrolysis-driven protein transmembrane transporter activity" RELATED []
synonym: "protein translocase activity" EXACT []
-xref: EC:7.4.2.3
-xref: EC:7.4.2.4
xref: Reactome:R-HSA-1222523 "SodB gets secreted"
is_a: GO:0008320 ! protein transmembrane transporter activity
-is_a: GO:0015399 ! primary active transmembrane transporter activity
+is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
[Term]
id: GO:0015451
@@ -111312,7 +111118,6 @@ name: potassium channel regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of a potassium channel." [GOC:dos, GOC:mah]
synonym: "potassium channel gating activity" EXACT []
-is_a: GO:0016247 ! channel regulator activity
is_a: GO:0099106 ! ion channel regulator activity
[Term]
@@ -111339,7 +111144,7 @@ synonym: "protein ABC transporter" EXACT []
synonym: "protein-transmembrane transporting ATPase activity" RELATED []
synonym: "protein-transporting ATPase activity" BROAD []
xref: EC:7.4.2.5
-is_a: GO:0008320 ! protein transmembrane transporter activity
+is_a: GO:0015450 ! protein-transporting ATPase activity
is_a: GO:0140359 ! ABC-type transporter activity
[Term]
@@ -111557,7 +111362,7 @@ consider: GO:0019836
id: GO:0015485
name: cholesterol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones." [GOC:jl, ISBN:0198506732]
+def: "Binding to cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones." [GOC:jl, ISBN:0198506732]
is_a: GO:0032934 ! sterol binding
is_a: GO:0043178 ! alcohol binding
@@ -112207,6 +112012,7 @@ name: efflux transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of a specific substance or related group of substances from the inside of the cell to the outside of the cell across a membrane." [GOC:ai, GOC:mtg_transport, ISBN:0815340729]
synonym: "efflux permease activity" EXACT []
+synonym: "efflux transporter activity" EXACT [GOC:cjm]
synonym: "monocarboxylate (lactate, pyruvate, mevalonate) uptake/efflux porter activity" RELATED []
is_a: GO:0022857 ! transmembrane transporter activity
@@ -112288,6 +112094,7 @@ namespace: molecular_function
alt_id: GO:0015584
def: "Enables the transfer of trehalose from one side of a membrane to the other. Trehalose is the disaccharide alpha-D-glucopyranosyl-alpha-D-glucopyranoside that acts of a reserve carbohydrate in certain fungi, algae and lichens." [GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "trehalose permease activity" EXACT []
+xref: RHEA:17629
is_a: GO:0015154 ! disaccharide transmembrane transporter activity
[Term]
@@ -112401,9 +112208,9 @@ synonym: "histidine/arginine/lysine/ornithine porter activity" EXACT []
is_obsolete: true
consider: GO:0000064
consider: GO:0005290
-consider: GO:0015181
consider: GO:0015189
consider: GO:0015426
+consider: GO:0061459
[Term]
id: GO:0015599
@@ -112550,12 +112357,12 @@ consider: GO:0015592
id: GO:0015614
name: ABC-type D-xylose transporter activity
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + D-xylose(out) -> ADP + phosphate + D-xylose(in)." [RHEA:29902]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + D-xylose(out) -> ADP + phosphate + D-xylose(in)." [RHEA:29899]
synonym: "ATPase-coupled D-xylose transmembrane transporter activity" RELATED []
synonym: "D-xylose porter activity" BROAD []
synonym: "D-xylose-importing ATPase activity" RELATED []
xref: EC:7.5.2.10
-xref: RHEA:29902
+xref: RHEA:29899
is_a: GO:0015148 ! D-xylose transmembrane transporter activity
is_a: GO:0015407 ! ABC-type monosaccharide transporter activity
@@ -112572,9 +112379,9 @@ is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
id: GO:0015616
name: DNA translocase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule." [GOC:mah, PMID:16428451, PMID:17631491]
+def: "Generation of movement along a single- or double-stranded DNA molecule, driven by ATP hydrolysis." [GOC:mah, PMID:16428451, PMID:17631491]
comment: Note that some gene products that possess DNA translocase activity, such as members of the FtsK/SpoIIIE family, can be fixed in place by interactions with other components of the cell; the relative movement between the protein and DNA bound to it results in movement of the DNA within the cell, often across a membrane.
-is_a: GO:0008094 ! ATPase, acting on DNA
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
[Term]
id: GO:0015617
@@ -112699,7 +112506,7 @@ is_a: GO:0005856 ! cytoskeleton
id: GO:0015631
name: tubulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules." [GOC:clt]
+def: "Binding to monomeric or multimeric forms of tubulin, including microtubules." [GOC:clt]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
@@ -112779,7 +112586,7 @@ consider: GO:0019835
id: GO:0015643
name: toxic substance binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems." [GOC:bf, GOC:curators, GOC:jl, GOC:pr]
+def: "Binding to a toxic substance, a poisonous substance that causes damage to biological systems." [GOC:bf, GOC:curators, GOC:jl, GOC:pr]
synonym: "antitoxin activity" RELATED []
synonym: "lipoprotein antitoxin" RELATED []
is_a: GO:0005488 ! binding
@@ -112803,7 +112610,7 @@ synonym: "fatty acid CoA ligase activity" RELATED []
synonym: "fatty acyl-coenzyme A synthetase activity" RELATED []
synonym: "fatty-acid ligase activity" EXACT []
is_a: GO:0016878 ! acid-thiol ligase activity
-is_a: GO:0016887 ! ATPase
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0015647
@@ -113123,7 +112930,7 @@ synonym: "aluminium ion transport" EXACT []
synonym: "aluminium transport" EXACT []
synonym: "aluminum ion transport" RELATED []
synonym: "aluminum transport" EXACT []
-is_a: GO:0006812 ! cation transport
+is_a: GO:0030001 ! metal ion transport
[Term]
id: GO:0015691
@@ -113132,14 +112939,13 @@ namespace: biological_process
def: "The directed movement of cadmium (Cd) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "cadmium transport" EXACT []
is_a: GO:0000041 ! transition metal ion transport
-is_a: GO:0030001 ! metal ion transport
[Term]
id: GO:0015692
name: lead ion transport
namespace: biological_process
def: "The directed movement of lead (Pb) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
-is_a: GO:0006812 ! cation transport
+is_a: GO:0030001 ! metal ion transport
[Term]
id: GO:0015693
@@ -113168,15 +112974,6 @@ def: "The directed movement of organic cations into, out of or within a cell, or
is_a: GO:0006812 ! cation transport
is_a: GO:0071702 ! organic substance transport
-[Term]
-id: GO:0015696
-name: ammonium transport
-namespace: biological_process
-def: "The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals." [ISBN:0198506732]
-synonym: "ammonia transport" RELATED []
-is_a: GO:0006812 ! cation transport
-is_a: GO:0071705 ! nitrogen compound transport
-
[Term]
id: GO:0015697
name: quaternary ammonium group transport
@@ -114065,16 +113862,6 @@ def: "The directed movement of L-alanine, the L-enantiomer of 2-aminopropanoic a
is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0032328 ! alanine transport
-[Term]
-id: GO:0015809
-name: arginine transport
-namespace: biological_process
-def: "The directed movement of arginine, 2-amino-5-guanidinopentanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators, ISBN:0198506732]
-synonym: "L-arginine transport" NARROW []
-is_a: GO:0006812 ! cation transport
-is_a: GO:0015802 ! basic amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
-
[Term]
id: GO:0015810
name: aspartate transmembrane transport
@@ -114181,8 +113968,8 @@ name: leucine transport
namespace: biological_process
def: "The directed movement of leucine, 2-amino-4-methylpentanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-leucine transport" NARROW []
+is_a: GO:0015803 ! branched-chain amino acid transport
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015821
@@ -114265,8 +114052,8 @@ name: valine transport
namespace: biological_process
def: "The directed movement of valine, 2-amino-3-methylbutanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "L-valine transport" NARROW []
+is_a: GO:0015803 ! branched-chain amino acid transport
is_a: GO:0015804 ! neutral amino acid transport
-is_a: GO:0046942 ! carboxylic acid transport
[Term]
id: GO:0015830
@@ -114759,8 +114546,8 @@ namespace: biological_process
def: "The directed movement of thiamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Thiamine is vitamin B1, a water soluble vitamin present in fresh vegetables and meats, especially liver." [GOC:ai]
synonym: "thiamin transport" EXACT []
synonym: "vitamin B1 transport" EXACT []
+is_a: GO:0015695 ! organic cation transport
is_a: GO:0051180 ! vitamin transport
-is_a: GO:0071702 ! organic substance transport
is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:0072348 ! sulfur compound transport
@@ -114796,15 +114583,6 @@ synonym: "siderochrome transport" NARROW []
synonym: "siderophore-iron transport" EXACT []
is_a: GO:1901678 ! iron coordination entity transport
-[Term]
-id: GO:0015893
-name: drug transport
-namespace: biological_process
-def: "The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
-subset: goslim_pir
-is_a: GO:0006810 ! transport
-relationship: part_of GO:0042493 ! response to drug
-
[Term]
id: GO:0015894
name: acriflavine transport
@@ -114827,7 +114605,6 @@ namespace: biological_process
def: "The directed movement of nalidixic acid into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Nalidixic acid is a synthetic antibiotic that interferes with DNA gyrase and inhibits prokaryotic replication." [GOC:curators, PMID:12702699, PubChem_Compound:4221]
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015849 ! organic acid transport
-is_a: GO:0042908 ! xenobiotic transport
is_a: GO:0071705 ! nitrogen compound transport
[Term]
@@ -114843,7 +114620,6 @@ id: GO:0015898
name: amiloride transport
namespace: biological_process
def: "The directed movement amiloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Amiloride is a potent and specific inhibitor of sodium ion entry into cells. It is used as a potassium-sparing diuretic." [GOC:ai]
-is_a: GO:0015893 ! drug transport
is_a: GO:0071702 ! organic substance transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -114861,7 +114637,6 @@ name: benomyl transport
namespace: biological_process
def: "The directed movement of benomyl into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Benomyl, methyl 1-(butylcarbamoyl)-2-benzimidazolecarbamate, is a systemic agricultural fungicide used for control of certain fungal diseases of stone fruit." [GOC:curators]
is_a: GO:0042886 ! amide transport
-is_a: GO:0042908 ! xenobiotic transport
is_a: GO:0071702 ! organic substance transport
[Term]
@@ -114878,7 +114653,6 @@ name: carbonyl cyanide m-chlorophenylhydrazone transport
namespace: biological_process
def: "The directed movement of carbonyl cyanide m-chlorophenylhydrazone into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbonyl cyanide m-chlorophenylhydrazone is a proton ionophore, commonly used as an uncoupling agent and inhibitor of photosynthesis because of its effects on mitochondrial and chloroplast membranes." [GOC:curators]
synonym: "CCCP transport" EXACT []
-is_a: GO:0015893 ! drug transport
is_a: GO:0071702 ! organic substance transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -115074,9 +114848,8 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0015927
name: trehalase activity
namespace: molecular_function
-def: "Catalysis of the hydrolysis of trehalose or a trehalose derivative." [GOC:ai]
+def: "Catalysis of the hydrolysis of trehalose or a trehalose derivative." [GOC:ai, PMID:31925485]
xref: MetaCyc:TREHALA-RXN
-xref: RHEA:32675
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
[Term]
@@ -115921,9 +115694,8 @@ consider: GO:0046876
id: GO:0016018
name: cyclosporin A binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cyclosporin A, a cyclic undecapeptide that contains several N-methylated and unusual amino acids." [GOC:mb]
+def: "Binding to cyclosporin A, a cyclic undecapeptide that contains several N-methylated and unusual amino acids." [GOC:mb]
synonym: "cyclophilin" RELATED []
-is_a: GO:0008144 ! drug binding
is_a: GO:0042277 ! peptide binding
[Term]
@@ -116137,6 +115909,7 @@ id: GO:0016041
name: glutamate synthase (ferredoxin) activity
namespace: molecular_function
def: "Catalysis of the reaction: 2 L-glutamate + 2 oxidized ferredoxin = L-glutamine + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+. This is a two-step reaction: (a) L-glutamate + NH3 = L-glutamine + H2O, (b) L-glutamate + 2 oxidized ferredoxin + H2O = NH3 + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+." [EC:1.4.7.1]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "ferredoxin-dependent glutamate synthase activity" RELATED [EC:1.4.7.1]
synonym: "ferredoxin-glutamate synthase activity" RELATED [EC:1.4.7.1]
synonym: "glutamate synthase (ferredoxin-dependent)" RELATED [EC:1.4.7.1]
@@ -116463,6 +116236,7 @@ name: mRNA metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes." [ISBN:0198506732]
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pombe
synonym: "mRNA metabolism" EXACT []
is_a: GO:0016070 ! RNA metabolic process
@@ -116482,6 +116256,7 @@ name: snRNA metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving snRNA, small nuclear RNA, any of various low-molecular-mass RNA molecules found in the eukaryotic nucleus as components of the small nuclear ribonucleoprotein." [ISBN:0198506732]
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pombe
synonym: "snRNA metabolism" EXACT []
is_a: GO:0034660 ! ncRNA metabolic process
@@ -116584,7 +116359,7 @@ namespace: biological_process
def: "A process that converts synaptic vesicles to a state of competence for calcium triggered fusion with the active zone membrane by bringing the two membranes into very close proximity. Priming typically (but not always) occurs after docking (Jahn and Fasshauer, 2012). Primed vesicles are also capable of spontaneously fusing with the active zone membrane." [GOC:mah, PMID:15217342, PMID:23060190]
comment: Although this process can occur outside of synaptic transmission, by convention we treat it as a part of synaptic transmission. (dos, pvn, fk synapse project 2015)
subset: goslim_synapse
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
is_a: GO:0140029 ! exocytic process
relationship: part_of GO:0016079 ! synaptic vesicle exocytosis
@@ -117306,7 +117081,8 @@ is_a: GO:0003747 ! translation release factor activity
id: GO:0016151
name: nickel cation binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with nickel (Ni) cations." [GOC:ai]
+def: "Binding to a nickel (Ni) cation." [GOC:ai]
+synonym: "Ni binding" EXACT []
synonym: "nickel binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
@@ -117484,7 +117260,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0016163
name: nitrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + nitrogen + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate." [EC:1.18.6.1]
+def: "Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + N2 + 16 ATP + 16 H2O = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate." [PMID:15382920, RHEA:21448]
synonym: "iron-iron nitrogenase activity" NARROW []
synonym: "molybdenum-iron nitrogenase activity" NARROW []
synonym: "reduced ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing) activity" RELATED [EC:1.18.6.1]
@@ -117544,21 +117320,21 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0016168
name: chlorophyll binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chlorophyll; any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment." [GOC:jl]
+def: "Binding to a chlorophyll; a compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment." [GOC:jl]
is_a: GO:0046906 ! tetrapyrrole binding
[Term]
id: GO:0016169
name: bacteriochlorophyll c binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with bacteriochlorophyll c, a chlorophyll of photosynthetic bacteria, for example green sulfur bacteria." [ISBN:0192800981]
+def: "Binding to bacteriochlorophyll c, a chlorophyll of photosynthetic bacteria, for example green sulfur bacteria." [ISBN:0192800981]
is_a: GO:0042314 ! bacteriochlorophyll binding
[Term]
id: GO:0016170
name: interleukin-15 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-15 receptor." [GOC:ai]
+def: "Binding to an interleukin-15 receptor." [GOC:ai]
synonym: "IL-15" NARROW []
synonym: "interleukin-15 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -117763,7 +117539,6 @@ synonym: "vesicle trafficking" RELATED []
synonym: "vesicle transport" EXACT []
synonym: "vesicular transport" EXACT [GOC:mah]
is_a: GO:0006810 ! transport
-is_a: GO:0009987 ! cellular process
[Term]
id: GO:0016197
@@ -117899,7 +117674,7 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0016208
name: AMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with AMP, adenosine monophosphate." [GOC:go_curators]
+def: "Binding to AMP, adenosine monophosphate." [GOC:go_curators]
is_a: GO:0032559 ! adenyl ribonucleotide binding
is_a: GO:0043168 ! anion binding
is_a: GO:0043169 ! cation binding
@@ -117909,6 +117684,7 @@ id: GO:0016209
name: antioxidant activity
namespace: molecular_function
def: "Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage." [ISBN:0198506732]
+subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:0003674 ! molecular_function
@@ -117957,7 +117733,7 @@ is_a: GO:0036137 ! kynurenine aminotransferase activity
id: GO:0016213
name: linoleoyl-CoA desaturase activity
namespace: molecular_function
-def: "Catalysis of the reaction: linoleoyl-CoA + reduced acceptor + O2 = gamma-linolenoyl-CoA + acceptor + 2 H2O." [RHEA:22196]
+def: "Catalysis of the reaction: linoleoyl-CoA + reduced acceptor + O2 = gamma-linolenoyl-CoA + acceptor + 2 H2O." [PMID:12713571, PMID:7212717, RHEA:47140]
comment: Note that this function was formerly EC:1.14.99.25.
synonym: "delta(6)-acyl CoA desaturase activity" BROAD []
synonym: "delta(6)-desaturase activity" BROAD []
@@ -117981,7 +117757,7 @@ xref: Reactome:R-HSA-2046084 "Desaturation of alpha-linoleoyl-CoA to Stearidonoy
xref: Reactome:R-HSA-2046096 "Desaturation of Linoleoyl-CoA to gamma-linolenoyl-CoA"
xref: Reactome:R-HSA-2046097 "Desaturation of tetracosatetraenoyl-CoA to tetracosapentaenoyl-CoA"
xref: Reactome:R-HSA-2046099 "Desaturation of tetracosapentaenoyl-CoA to tetracosahexaenoyl-CoA"
-xref: RHEA:22196
+xref: RHEA:47140
is_a: GO:0016215 ! acyl-CoA desaturase activity
[Term]
@@ -118236,6 +118012,7 @@ name: channel inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of a channel." [GOC:mah]
is_a: GO:0016247 ! channel regulator activity
+is_a: GO:0140678 ! molecular function inhibitor activity
[Term]
id: GO:0016250
@@ -118637,6 +118414,7 @@ name: palmitoyl-CoA hydrolase activity
namespace: molecular_function
alt_id: GO:0016293
def: "Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate." [EC:3.1.2.2]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
subset: goslim_chembl
synonym: "fatty acyl thioesterase I" RELATED [EC:3.1.2.2]
synonym: "long-chain fatty-acyl-CoA hydrolase activity" BROAD []
@@ -118747,7 +118525,6 @@ def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a sub
comment: Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_plant
subset: goslim_yeast
@@ -119227,7 +119004,7 @@ def: "OBSOLETE. (Was not defined before being made obsolete)." [GOC:ai]
comment: This term was made obsolete because 'susceptibility/resistance' implies a phenotype rather than a biological process.
synonym: "drug susceptibility/resistance" EXACT []
is_obsolete: true
-replaced_by: GO:0042493
+replaced_by: GO:0009410
[Term]
id: GO:0016352
@@ -119710,7 +119487,7 @@ synonym: "PTGS" EXACT []
synonym: "quelling" EXACT []
xref: Wikipedia:Post_transcriptional_gene_silencing
is_a: GO:0010608 ! posttranscriptional regulation of gene expression
-is_a: GO:0016458 ! gene silencing
+is_a: GO:0010629 ! negative regulation of gene expression
[Term]
id: GO:0016442
@@ -119805,16 +119582,14 @@ relationship: part_of GO:0009047 ! dosage compensation by hyperactivation of X c
[Term]
id: GO:0016458
-name: gene silencing
+name: obsolete gene silencing
namespace: biological_process
-def: "Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression." [GOC:dos, GOC:dph, GOC:jid, GOC:tb]
-comment: This is a rather broad grouping term. While it was originally defined for long-term, heritable, epigenetic effects, short term effects on expression mediated by RNA are also frequently referred to as gene silencing, and are grouped under this class.
-subset: goslim_drosophila
-subset: goslim_pir
-synonym: "long-term maintenance of gene inactivation" NARROW []
+def: "OBSOLETE. Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression." [GOC:dos, GOC:dph, GOC:jid, GOC:tb]
+comment: This term was obsoleted because its definition was too broad, and not distinct from 'GO:0045814 negative regulation of gene expression, epigenetic'.
xref: Wikipedia:Gene_silencing
-is_a: GO:0009987 ! cellular process
-is_a: GO:0010629 ! negative regulation of gene expression
+is_obsolete: true
+consider: GO:0010629
+consider: GO:0031507
[Term]
id: GO:0016459
@@ -119880,7 +119655,7 @@ synonym: "AAA chloroplast protein-transporting ATPase" EXACT []
synonym: "ATPase-coupled chloroplast protein transporter activity" EXACT []
xref: EC:7.4.2.4
xref: MetaCyc:3.6.3.52-RXN
-is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
+is_a: GO:0015450 ! protein-transporting ATPase activity
[Term]
id: GO:0016465
@@ -120379,12 +120154,13 @@ is_a: GO:0004896 ! cytokine receptor activity
[Term]
id: GO:0016518
-name: interleukin-14 receptor activity
+name: obsolete interleukin-14 receptor activity
namespace: molecular_function
-def: "Combining with interleukin-14 and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:jl, GOC:signaling]
+def: "OBSOLETE. Combining with interleukin-14 and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:jl, GOC:signaling]
+comment: This term was obsoleted because the gene was shown not to exist, see PMID:8755619.
synonym: "IL-14 receptor activity" EXACT [GOC:mah]
synonym: "IL-14R" EXACT []
-is_a: GO:0004896 ! cytokine receptor activity
+is_obsolete: true
[Term]
id: GO:0016519
@@ -120514,7 +120290,6 @@ synonym: "cyclin-dependent protein kinase regulator activity" BROAD []
synonym: "cyclin-dependent protein kinase, intrinsic regulator activity" NARROW []
synonym: "G1/S-specific cyclin" NARROW []
synonym: "G2/M-specific cyclin" NARROW []
-xref: EC:2.7.1.-
xref: Reactome:R-HSA-3215385 "CDK4 in CCND1:CDK4:PRMT5:WDR77 phosphorylates WDR77"
is_a: GO:0019887 ! protein kinase regulator activity
@@ -120787,12 +120562,12 @@ is_a: GO:0032446 ! protein modification by small protein conjugation
[Term]
id: GO:0016569
-name: covalent chromatin modification
+name: obsolete covalent chromatin modification
namespace: biological_process
-def: "The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups." [GOC:mah, GOC:vw]
+def: "OBSOLETE. The alteration of DNA or protein in chromatin by the covalent addition or removal of chemical groups." [GOC:mah, GOC:vw]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "chromatin modification" EXACT []
-is_a: GO:0006325 ! chromatin organization
-is_a: GO:0043412 ! macromolecule modification
+is_obsolete: true
[Term]
id: GO:0016570
@@ -120802,7 +120577,6 @@ def: "The covalent alteration of one or more amino acid residues within a histon
subset: goslim_yeast
xref: Wikipedia:Histone#Histone_modifications_in_chromatin_regulation
is_a: GO:0006464 ! cellular protein modification process
-is_a: GO:0016569 ! covalent chromatin modification
[Term]
id: GO:0016571
@@ -121014,7 +120788,7 @@ relationship: part_of GO:0016591 ! RNA polymerase II, holoenzyme
id: GO:0016594
name: glycine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with glycine, aminoethanoic acid." [GOC:ai]
+def: "Binding to glycine, aminoethanoic acid." [GOC:ai]
synonym: "aminoacetic acid binding" EXACT []
synonym: "aminoethanoic acid binding" EXACT []
synonym: "Gly binding" EXACT []
@@ -121026,7 +120800,7 @@ is_a: GO:0043169 ! cation binding
id: GO:0016595
name: glutamate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with glutamate, the anion of 2-aminopentanedioic acid." [GOC:ai]
+def: "Binding to glutamate, the anion of 2-aminopentanedioic acid." [GOC:ai]
synonym: "glutamic acid binding" EXACT []
is_a: GO:0016597 ! amino acid binding
is_a: GO:0031406 ! carboxylic acid binding
@@ -121035,9 +120809,8 @@ is_a: GO:0031406 ! carboxylic acid binding
id: GO:0016596
name: thienylcyclohexylpiperidine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with thienylcyclohexylpiperidine." [GOC:jl]
+def: "Binding to thienylcyclohexylpiperidine." [GOC:jl]
synonym: "TCP binding" BROAD []
-is_a: GO:0008144 ! drug binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
is_a: GO:1901681 ! sulfur compound binding
@@ -121046,7 +120819,7 @@ is_a: GO:1901681 ! sulfur compound binding
id: GO:0016597
name: amino acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents." [GOC:ai]
+def: "Binding to an amino acid, organic acids containing one or more amino substituents." [GOC:ai]
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:0043177 ! organic acid binding
@@ -122449,6 +122222,8 @@ def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group,
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
+subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
@@ -122505,8 +122280,6 @@ alt_id: GO:0008415
def: "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
-synonym: "acyltransferase activity" EXACT []
synonym: "transferase activity, transferring acyl groups" EXACT []
xref: EC:2.3.-.-
xref: Reactome:R-HSA-159431 "Cytosolic chenodeoxycholoyl-CoA or choloyl-CoA are conjugated with glycine or taurine"
@@ -122591,7 +122364,6 @@ id: GO:0016755
name: aminoacyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of an amino-acyl group from one compound (donor) to another (acceptor)." [GOC:jl]
-synonym: "aminoacyltransferase activity" EXACT []
synonym: "transferase activity, transferring amino-acyl groups" EXACT []
xref: EC:2.3.2.-
is_a: GO:0016746 ! acyltransferase activity
@@ -122619,7 +122391,6 @@ alt_id: GO:0016932
def: "Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_yeast
synonym: "transferase activity, transferring glycosyl groups" EXACT []
synonym: "transferase activity, transferring other glycosyl groups" NARROW []
@@ -122735,7 +122506,6 @@ alt_id: GO:0016766
def: "Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
synonym: "transferase activity, transferring alkyl or aryl groups, other than methyl groups" EXACT []
xref: EC:2.5.1.-
xref: Reactome:R-HSA-4419978 "DHDDS:NUS1 elongates E,E-FPP with (n)IPPP to form pPPP"
@@ -122851,7 +122621,6 @@ subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_yeast
xref: EC:2.7.7.-
@@ -122881,7 +122650,6 @@ id: GO:0016782
name: transferase activity, transferring sulphur-containing groups
namespace: molecular_function
def: "Catalysis of the transfer of a sulfur-containing group from one compound (donor) to another (acceptor)." [GOC:jl, ISBN:0198506732]
-synonym: "transferase activity, transferring sulphur-containing groups" EXACT []
xref: EC:2.8.-.-
is_a: GO:0016740 ! transferase activity
@@ -122934,6 +122702,8 @@ def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphor
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
+subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_mouse
subset: goslim_pir
@@ -122983,7 +122753,6 @@ subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_yeast
synonym: "4-nitrophenylphosphatase activity" NARROW []
@@ -123055,7 +122824,6 @@ namespace: molecular_function
def: "Catalysis of the hydrolysis of any glycosyl bond." [GOC:jl]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_yeast
synonym: "glycosidase activity" EXACT []
synonym: "glycosylase" NARROW []
@@ -123165,7 +122933,6 @@ namespace: molecular_function
def: "Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds." [GOC:jl]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
synonym: "hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in other compounds" NARROW []
xref: EC:3.5.-.-
xref: Reactome:R-HSA-6803753 "NAAA hydrolyses NAEs to FAs and ethanolamine"
@@ -123289,7 +123056,7 @@ id: GO:0016825
name: hydrolase activity, acting on acid phosphorus-nitrogen bonds
namespace: molecular_function
def: "Catalysis of the hydrolysis of any acid phosphorus-nitrogen bond." [GOC:jl]
-xref: EC:3.9.-.-
+xref: EC:3.9.1.-
is_a: GO:0016787 ! hydrolase activity
[Term]
@@ -123913,17 +123680,18 @@ is_a: GO:0016874 ! ligase activity
[Term]
id: GO:0016887
-name: ATPase
+name: ATP hydrolysis activity
namespace: molecular_function
alt_id: GO:0004002
alt_id: GO:0042623
-def: "A molecular function characterized by the use of ATP hydrolysis as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient." [GOC:curators]
-subset: gocheck_do_not_annotate
-subset: goslim_chembl
-subset: goslim_drosophila
-subset: goslim_generic
-subset: goslim_yeast
-synonym: "ATPase activity, coupled" RELATED []
+def: "Catalysis of the reaction: ATP + H2O = ADP + H+ Pi. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient." [RHEA:13065]
+comment: Note that this term is meant to specifically represent the ATPase activity of proteins using ATPase as a source of energy to drive a reaction. If possible, gene products should also be annotated to a child of 'ATP-dependent activity ; GO:0140657', to capture their overall function.
+synonym: "adenosine 5'-triphosphatase activity" EXACT []
+synonym: "adenosine triphosphatase activity" EXACT []
+synonym: "adenosinetriphosphatase activity" EXACT []
+synonym: "ATP hydrolase activity" EXACT []
+synonym: "ATP monophosphatase activity" RELATED []
+synonym: "ATP phosphohydrolase activity" EXACT []
xref: Reactome:R-HSA-159101 "NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)"
xref: Reactome:R-HSA-3371422 "ATP hydrolysis by HSP70"
xref: Reactome:R-HSA-416985 "Trafficking of GluR2-containing AMPA receptors to synapse"
@@ -123944,7 +123712,9 @@ xref: Reactome:R-HSA-917693 "ESCRT Disassembly"
xref: Reactome:R-HSA-9609860 "Tail-anchored protein:SGTA:BAG6:GET4:UBL4A:ASNA1:ATP dissociates and ASNA1 hydrolyzes ATP yielding Tail-anchored protein:ASNA1:ADP"
xref: Reactome:R-HSA-9668415 "VPS4 mediates disassembly of ESCRTIII subunits to promote sealing of holes in the nuclear envelope"
xref: Reactome:R-HSA-9706399 "RHOBTB3 hydrolyzes ATP"
-is_a: GO:0003674 ! molecular_function
+xref: RHEA:13065
+is_a: GO:0017111 ! nucleoside-triphosphatase activity
+relationship: part_of GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0016888
@@ -124255,7 +124025,7 @@ is_a: GO:0004888 ! transmembrane signaling receptor activity
id: GO:0016918
name: retinal binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with retinal, one of the forms of vitamin A. Retinal plays an important role in the visual process in most vertebrates, combining with opsins to form visual pigments in the retina." [ISBN:0198506732]
+def: "Binding to retinal, one of the forms of vitamin A. Retinal plays an important role in the visual process in most vertebrates, combining with opsins to form visual pigments in the retina." [ISBN:0198506732]
synonym: "blue-sensitive opsin" RELATED []
synonym: "green-sensitive opsin" RELATED []
synonym: "long-wave-sensitive opsin" RELATED []
@@ -124323,7 +124093,7 @@ name: nuclear receptor binding
namespace: molecular_function
alt_id: GO:0035257
alt_id: GO:0035258
-def: "Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein." [GOC:mah, PMID:7776974]
+def: "Binding to a nuclear receptor protein. Nuclear receptor proteins are DNA-binding transcription factors which are regulated by binding to a ligand." [PMID:7776974]
synonym: "ligand-dependent nuclear receptor binding" EXACT []
synonym: "ligand-dependent nuclear receptor interactor activity" RELATED []
synonym: "nuclear hormone receptor binding" EXACT []
@@ -124347,9 +124117,13 @@ name: protein sumoylation
namespace: biological_process
alt_id: GO:0006485
alt_id: GO:0016927
+alt_id: GO:0019947
+alt_id: GO:0019951
def: "The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxy-terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein." [GOC:jl, PMID:11265250]
synonym: "protein sumolation" EXACT []
synonym: "small ubiquitin-related protein 1 conjugation" EXACT []
+synonym: "Smt3-protein conjugation" RELATED []
+synonym: "Smt3p-protein conjugation" RELATED []
synonym: "SUMO-protein conjugation" EXACT []
synonym: "sumoylation" EXACT []
xref: Wikipedia:SUMO_protein
@@ -124415,7 +124189,7 @@ relationship: part_of GO:0005887 ! integral component of plasma membrane
id: GO:0016936
name: galactoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any glycoside in which the sugar group is galactose." [GOC:jl, ISBN:0198506732]
+def: "Binding to a glycoside in which the sugar group is galactose." [GOC:jl, ISBN:0198506732]
subset: goslim_chembl
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -124662,23 +124436,20 @@ is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0016984
name: ribulose-bisphosphate carboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-ribulose 1,5-bisphosphate + CO2 + H2O = 2 3-phospho-D-glycerate." [EC:4.1.1.39]
-synonym: "3-phospho-D-glycerate carboxy-lyase (dimerizing)" RELATED [EC:4.1.1.39]
-synonym: "3-phospho-D-glycerate carboxy-lyase (dimerizing; D-ribulose-1,5-bisphosphate-forming)" RELATED [EC:4.1.1.39]
+def: "Catalysis of the reaction: 2 (2R)-3-phosphoglycerate + 2 H+ = CO2 + D-ribulose 1,5-bisphosphate + H2O." [RHEA:23124]
synonym: "carboxydismutase activity" RELATED [EC:4.1.1.39]
-synonym: "D-ribulose 1,5-diphosphate carboxylase activity" RELATED [EC:4.1.1.39]
-synonym: "D-ribulose-1,5-bisphosphate carboxylase activity" RELATED [EC:4.1.1.39]
-synonym: "diphosphoribulose carboxylase activity" RELATED [EC:4.1.1.39]
-synonym: "ribulose 1,5-bisphosphate carboxylase activity" RELATED [EC:4.1.1.39]
+synonym: "D-ribulose 1,5-diphosphate carboxylase activity" EXACT [EC:4.1.1.39]
+synonym: "D-ribulose-1,5-bisphosphate carboxylase activity" EXACT [EC:4.1.1.39]
+synonym: "diphosphoribulose carboxylase activity" EXACT [EC:4.1.1.39]
+synonym: "ribulose 1,5-bisphosphate carboxylase activity" EXACT [EC:4.1.1.39]
synonym: "ribulose 1,5-bisphosphate carboxylase/oxygenase activity" EXACT []
-synonym: "ribulose 1,5-diphosphate carboxylase activity" RELATED [EC:4.1.1.39]
-synonym: "ribulose 1,5-diphosphate carboxylase/oxygenase activity" RELATED [EC:4.1.1.39]
-synonym: "ribulose bisphosphate carboxylase/oxygenase activity" RELATED [EC:4.1.1.39]
-synonym: "ribulose diphosphate carboxylase activity" RELATED [EC:4.1.1.39]
-synonym: "ribulose diphosphate carboxylase/oxygenase activity" RELATED [EC:4.1.1.39]
-synonym: "RuBisCO activity" RELATED [EC:4.1.1.39]
-synonym: "rubisco activity" EXACT []
-synonym: "RuBP carboxylase activity" RELATED [EC:4.1.1.39]
+synonym: "ribulose 1,5-diphosphate carboxylase activity" EXACT [EC:4.1.1.39]
+synonym: "ribulose 1,5-diphosphate carboxylase/oxygenase activity" EXACT [EC:4.1.1.39]
+synonym: "ribulose bisphosphate carboxylase/oxygenase activity" EXACT [EC:4.1.1.39]
+synonym: "ribulose diphosphate carboxylase activity" EXACT [EC:4.1.1.39]
+synonym: "ribulose diphosphate carboxylase/oxygenase activity" EXACT [EC:4.1.1.39]
+synonym: "RuBisCO activity" EXACT [EC:4.1.1.39]
+synonym: "RuBP carboxylase activity" EXACT [EC:4.1.1.39]
xref: EC:4.1.1.39
xref: MetaCyc:RIBULOSE-BISPHOSPHATE-CARBOXYLASE-RXN
xref: RHEA:23124
@@ -124725,7 +124496,6 @@ synonym: "core DNA-dependent RNA polymerase binding promoter specificity activit
synonym: "DNA-dependent RNA polymerase promoter selection factor" EXACT []
synonym: "plastid sigma factor activity" NARROW []
synonym: "promoter selection factor activity" NARROW []
-synonym: "sigma factor activity" EXACT []
synonym: "sigma transcription factor" EXACT []
is_a: GO:0003700 ! DNA-binding transcription factor activity
@@ -124870,7 +124640,7 @@ name: antibiotic metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms." [GOC:cab2]
synonym: "antibiotic metabolism" EXACT []
-is_a: GO:0017144 ! drug metabolic process
+is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0017000
@@ -124920,7 +124690,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions." [GOC:jl, GOC:mah]
subset: goslim_metagenomics
synonym: "cytochrome biogenesis" BROAD []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0017005
@@ -125037,9 +124807,8 @@ is_a: GO:0004722 ! protein serine/threonine phosphatase activity
id: GO:0017020
name: myosin phosphatase regulator activity
namespace: molecular_function
-def: "Binds to and modulates of the activity of myosin phosphatase." [EC:3.1.3.16, GOC:ai]
+def: "Binds to and modulates of the activity of myosin phosphatase." [GOC:ai, PMID:10491107]
synonym: "myosin phosphatase, intrinsic regulator activity" NARROW []
-is_a: GO:0019208 ! phosphatase regulator activity
is_a: GO:0019888 ! protein phosphatase regulator activity
[Term]
@@ -125057,7 +124826,7 @@ consider: GO:0017022
id: GO:0017022
name: myosin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments." [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
+def: "Binding to a myosin; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments." [GOC:mah]
synonym: "myosin phosphatase myosin binding" NARROW []
is_a: GO:0008092 ! cytoskeletal protein binding
@@ -125065,21 +124834,21 @@ is_a: GO:0008092 ! cytoskeletal protein binding
id: GO:0017023
name: myosin phosphatase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the removal of the phosphate group from phosphomyosin." [EC:3.1.3.16]
+def: "An enzyme complex that catalyzes the removal of the phosphate group from phosphomyosin. Composed of a PP1 catalytic subunit (PP1c/PPP1CB) and a myosin phosphatase targeting subunit (MYPT1/PPP1R12A)." [PMID:30076859]
is_a: GO:0008287 ! protein serine/threonine phosphatase complex
[Term]
id: GO:0017024
name: myosin I binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a class I myosin; myosin I heavy chains are single-headed, possess tails of various lengths, and do not self-associate into bipolar filaments." [GOC:bf, GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
+def: "Binding to a class I myosin; myosin I heavy chains are single-headed, possess tails of various lengths, and do not self-associate into bipolar filaments." [GOC:bf, GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
is_a: GO:0017022 ! myosin binding
[Term]
id: GO:0017025
name: TBP-class protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs)." [GOC:jl, GOC:txnOH, http://www.mblab.gla.ac.uk/, PMID:16858867]
+def: "Binding to a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs)." [GOC:jl, GOC:txnOH, http://www.mblab.gla.ac.uk/, PMID:16858867]
synonym: "TATA-binding protein binding" NARROW []
synonym: "TBP binding" NARROW []
synonym: "TBP-related factor (TRF) protein binding" NARROW []
@@ -125184,7 +124953,6 @@ namespace: molecular_function
def: "Catalysis of the reaction: N-acylsphingosine + H2O = a fatty acid + sphingosine." [EC:3.5.1.23]
synonym: "acylsphingosine deacylase activity" RELATED [EC:3.5.1.23]
synonym: "glycosphingolipid ceramide deacylase" BROAD [EC:3.5.1.23]
-synonym: "N-acylsphingosine amidohydrolase activity" RELATED [EC:3.5.1.23]
xref: EC:3.5.1.23
xref: MetaCyc:CERAMIDASE-RXN
xref: Reactome:R-HSA-1606583 "Neutral ceramidase hydrolyses ceramide into sphingosine and free fatty acid (plasma membrane)"
@@ -125263,7 +125031,7 @@ is_a: GO:0005179 ! hormone activity
id: GO:0017046
name: peptide hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any peptide with hormonal activity in animals." [GOC:jl, ISBN:0198506732]
+def: "Binding to a peptide with hormonal activity in animals." [GOC:jl, ISBN:0198506732]
synonym: "polypeptide hormone binding" EXACT []
is_a: GO:0042277 ! peptide binding
is_a: GO:0042562 ! hormone binding
@@ -125376,7 +125144,7 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0017058
name: FH1 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a FH1 domain of a protein, a proline-rich domain, usually located in front of a FH2 domain." [GOC:go_curators]
+def: "Binding to a FH1 domain of a protein, a proline-rich domain, usually located in front of a FH2 domain." [GOC:go_curators]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -125403,6 +125171,7 @@ synonym: "beta-acetylglucosaminylsaccharide fucosyltransferase activity" BROAD [
synonym: "blood group Lewis alpha-4-fucosyltransferase activity" BROAD [EC:2.4.1.65]
synonym: "blood-group substance Le(a)-dependent fucosyltransferase activity" BROAD [EC:2.4.1.65]
synonym: "blood-group substance Lea-dependent fucosyltransferase" BROAD [EC:2.4.1.65]
+synonym: "fuca(1,3)-glycosidic linkage formation" RELATED []
synonym: "FucT-II activity" BROAD [EC:2.4.1.65]
synonym: "galactoside 3(4)-L-fucosyltransferase activity" BROAD []
synonym: "GDP-beta-L-fucose:3-beta-D-galactosyl-N-acetyl-D-glucosaminyl-R 4I-alpha-L-fucosyltransferase activity" RELATED [EC:2.4.1.65]
@@ -125509,7 +125278,7 @@ id: GO:0017069
name: snRNA binding
namespace: molecular_function
alt_id: GO:0000945
-def: "Interacting selectively and non-covalently with a small nuclear RNA (snRNA)." [GOC:mah]
+def: "Binding to a small nuclear RNA (snRNA)." [GOC:mah]
synonym: "base pairing with snRNA" NARROW []
synonym: "small nuclear RNA binding" EXACT []
is_a: GO:0003723 ! RNA binding
@@ -125518,8 +125287,7 @@ is_a: GO:0003723 ! RNA binding
id: GO:0017070
name: U6 snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U6 small nuclear RNA (U6 snRNA)." [GOC:mah]
-comment: Note that this term may be useful for annotating small nuclear RNAs (snRNAs).
+def: "Binding to a U6 small nuclear RNA (U6 snRNA)." [GOC:mah]
is_a: GO:0017069 ! snRNA binding
[Term]
@@ -125562,14 +125330,14 @@ replaced_by: GO:0004222
id: GO:0017075
name: syntaxin-1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the SNAP receptor syntaxin-1." [GOC:ai]
+def: "Binding to a syntaxin-1 SNAP receptor." [GOC:ai]
is_a: GO:0019905 ! syntaxin binding
[Term]
id: GO:0017076
name: purine nucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with purine nucleotides, any compound consisting of a purine nucleoside esterified with (ortho)phosphate." [GOC:ai]
+def: "Binding to a purine nucleotide, a compound consisting of a purine nucleoside esterified with (ortho)phosphate." [GOC:ai]
is_a: GO:0000166 ! nucleotide binding
[Term]
@@ -125601,7 +125369,6 @@ id: GO:0017080
name: sodium channel regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of a sodium channel." [GOC:mah]
-is_a: GO:0016247 ! channel regulator activity
is_a: GO:0099106 ! ion channel regulator activity
[Term]
@@ -125610,14 +125377,13 @@ name: chloride channel regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of a chloride channel." [GOC:mah]
xref: Reactome:R-HSA-383190 "HCO3- transport through ion channel"
-is_a: GO:0016247 ! channel regulator activity
is_a: GO:0099106 ! ion channel regulator activity
[Term]
id: GO:0017082
name: obsolete mineralocorticoid receptor activity
namespace: molecular_function
-def: "OBSOLETE. Combining with a mineralocorticoid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:20932876]
+def: "OBSOLETE. Combining with a mineralocorticoid and transmitting the signal to the transcriptional machinery by binding to a specific DNA sequence in order to modulate transcription by RNA polymerase II." [GOC:signaling, PMID:20932876]
synonym: "aldosterone receptor" NARROW []
is_obsolete: true
@@ -125634,7 +125400,6 @@ synonym: "GDP-L-fucose:1,4-beta-D-galactosyl-N-acetyl-D-glucosaminyl-R 3-L-fucos
synonym: "guanosine diphosphofucose-glucoside alpha-1->3-fucosyltransferase activity" RELATED [EC:2.4.1.152]
synonym: "guanosine diphosphofucose-glucoside alpha1->3-fucosyltransferase activity" RELATED [EC:2.4.1.152]
synonym: "Lewis-negative alpha-3-fucosyltransferase activity" NARROW [EC:2.4.1.152]
-synonym: "lewis-negative alpha-3-fucosyltransferase activity" RELATED [EC:2.4.1.152]
synonym: "plasma alpha-3-fucosyltransferase activity" NARROW [EC:2.4.1.152]
xref: EC:2.4.1.152
xref: MetaCyc:GALACTOSIDE-3-FUCOSYLTRANSFERASE-RXN
@@ -125780,7 +125545,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0017098
name: sulfonylurea receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the sulfonylurea receptor, a regulatory subunit of the ATP-sensitive potassium ion channel." [GOC:ceb, PMID:11938023]
+def: "Binding to a sulfonylurea receptor, a regulatory subunit of the ATP-sensitive potassium ion channel." [GOC:ceb, PMID:11938023]
synonym: "sulfonylurea receptor ligand" NARROW []
synonym: "sulphonylurea receptor binding" EXACT []
is_a: GO:0005102 ! signaling receptor binding
@@ -126051,7 +125816,7 @@ is_a: GO:1990234 ! transferase complex
id: GO:0017124
name: SH3 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins." [GOC:go_curators, Pfam:PF00018]
+def: "Binding to a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins." [GOC:go_curators, Pfam:PF00018]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -126087,7 +125852,7 @@ is_a: GO:0140303 ! intramembrane lipid transporter activity
id: GO:0017129
name: triglyceride binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any triester of glycerol." [GOC:jl, ISBN:0198506732]
+def: "Binding to a triester of glycerol." [GOC:jl, ISBN:0198506732]
synonym: "triacylglycerol binding" EXACT [GOC:mah]
is_a: GO:0008289 ! lipid binding
@@ -126095,7 +125860,7 @@ is_a: GO:0008289 ! lipid binding
id: GO:0017130
name: poly(C) RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a sequence of cytosine residues in an RNA molecule." [GOC:mah]
+def: "Binding to a sequence of cytosine residues in an RNA molecule." [GOC:mah]
synonym: "poly(C) binding" BROAD [GOC:mah]
synonym: "poly(rC) binding" EXACT [GOC:mah]
is_a: GO:0008187 ! poly-pyrimidine tract binding
@@ -126104,7 +125869,7 @@ is_a: GO:0008187 ! poly-pyrimidine tract binding
id: GO:0017131
name: uridine-rich cytoplasmic polyadenylylation element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with U-rich sequence in the 3'-end of nuclear-transcribed mRNAs; required for cytoplasmic polyadenylylation." [GOC:krc, PMID:7954828]
+def: "Binding to a U-rich sequence in the 3'-end of nuclear-transcribed mRNAs; required for cytoplasmic polyadenylylation." [GOC:krc, PMID:7954828]
synonym: "U-rich CPE binding" EXACT [PMID:7954828]
synonym: "uridine-rich cytoplasmic polyadenylation element binding" EXACT []
is_a: GO:0008187 ! poly-pyrimidine tract binding
@@ -126128,7 +125893,7 @@ alt_id: GO:0048604
alt_id: GO:0048605
alt_id: GO:0048606
alt_id: GO:0048607
-def: "Interacting selectively and non-covalently with a fibroblast growth factor." [PMID:9806903]
+def: "Binding to a fibroblast growth factor." [PMID:9806903]
synonym: "FGF 1 binding" NARROW []
synonym: "FGF 2 binding" NARROW []
synonym: "FGF 3 binding" NARROW []
@@ -126158,7 +125923,7 @@ consider: GO:0019899
id: GO:0017136
name: NAD-dependent histone deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone." [EC:3.5.1.17, RHEA:24548]
+def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone." [PMID:28450737]
synonym: "SIR2" RELATED []
is_a: GO:0004407 ! histone deacetylase activity
is_a: GO:0034979 ! NAD-dependent protein deacetylase activity
@@ -126204,17 +125969,6 @@ is_a: GO:0006805 ! xenobiotic metabolic process
is_a: GO:0009404 ! toxin metabolic process
relationship: part_of GO:0017085 ! response to insecticide
-[Term]
-id: GO:0017144
-name: drug metabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice." [GOC:cab2]
-subset: goslim_chembl
-subset: goslim_pir
-synonym: "drug metabolism" EXACT []
-xref: Wikipedia:Drug_metabolism
-is_a: GO:0044237 ! cellular metabolic process
-
[Term]
id: GO:0017145
name: stem cell division
@@ -126237,7 +125991,7 @@ is_a: GO:0034703 ! cation channel complex
id: GO:0017147
name: Wnt-protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling." [GOC:jl]
+def: "Binding to a Wnt-protein, a secreted growth factor involved in signaling." [GOC:jl]
subset: goslim_chembl
is_a: GO:0005515 ! protein binding
@@ -126286,14 +126040,14 @@ def: "Catalysis of the reaction: tRNA-uracil + acceptor = tRNA-dihydrouridine +
xref: MetaCyc:RXN0-1281
xref: Reactome:R-HSA-6782296 "DUS2:EPRS reduces uridine to dihydrouridine in tRNAs"
xref: RHEA:23624
-is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
+is_a: GO:0106413 ! dihydrouridine synthase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
id: GO:0017151
name: DEAD/H-box RNA helicase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme DEAD/H-box RNA helicase." [GOC:jl]
+def: "Binding to a DEAD/H-box RNA helicase." [GOC:jl]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -126378,7 +126132,7 @@ is_a: GO:0046030 ! inositol trisphosphate phosphatase activity
id: GO:0017162
name: aryl hydrocarbon receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an aryl hydrocarbon receptor." [GOC:ai]
+def: "Binding to an aryl hydrocarbon receptor." [GOC:ai]
is_a: GO:0005102 ! signaling receptor binding
is_a: GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor binding
@@ -126423,7 +126177,7 @@ replaced_by: GO:0016805
id: GO:0017166
name: vinculin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with vinculin, a protein found in muscle, fibroblasts, and epithelial cells that binds actin and appears to mediate attachment of actin filaments to integral proteins of the plasma membrane." [ISBN:0721662544]
+def: "Binding to vinculin, a protein found in muscle, fibroblasts, and epithelial cells that binds actin and appears to mediate attachment of actin filaments to integral proteins of the plasma membrane." [ISBN:0721662544]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
@@ -126463,7 +126217,7 @@ is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate
id: GO:0017170
name: obsolete KU70 binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with Ku70, a protein involved in non-homologous DNA end joining." [GOC:mah, PMID:14739985]
+def: "OBSOLETE. Binding to Ku70, a protein involved in non-homologous DNA end joining." [GOC:mah, PMID:14739985]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "KU70 binding" EXACT []
is_obsolete: true
@@ -128311,7 +128065,6 @@ synonym: "peptidyl-1-thioglycine anabolism from peptidyl-glycine" EXACT []
synonym: "peptidyl-1-thioglycine formation from peptidyl-glycine" EXACT []
synonym: "peptidyl-1-thioglycine synthesis from peptidyl-glycine" EXACT []
xref: RESID:AA0265
-is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:0018201 ! peptidyl-glycine modification
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
is_a: GO:0044249 ! cellular biosynthetic process
@@ -130408,7 +130161,7 @@ id: GO:0018419
name: protein catenane formation
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a protein structure comprising two or more rings that are interlocked but not covalently joined; resembling the links of a chain." [ISBN:0198506732]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0018420
@@ -130464,7 +130217,6 @@ synonym: "O3-(N-acetylglucosamine-1-phosphoryl)-L-serine biosynthesis" EXACT []
synonym: "O3-(N-acetylglucosamine-1-phosphoryl)-L-serine formation" EXACT []
synonym: "O3-(N-acetylglucosamine-1-phosphoryl)-L-serine synthesis" EXACT []
xref: RESID:AA0296
-is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0042077 ! protein phosphate-linked glycosylation via serine
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
@@ -130824,23 +130576,6 @@ xref: RHEA:16425
xref: UM-BBD_reactionID:r0240
is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
-[Term]
-id: GO:0018468
-name: alcohol dehydrogenase (acceptor) activity
-namespace: molecular_function
-def: "Catalysis of the reaction: a primary alcohol + acceptor = an aldehyde + reduced acceptor." [EC:1.1.99.8]
-synonym: "alcohol:(acceptor) oxidoreductase activity" RELATED [EC:1.1.99.8]
-synonym: "alcohol:acceptor oxidoreductase activity" RELATED [EC:1.1.99.8]
-synonym: "MDH" RELATED [EC:1.1.99.8]
-synonym: "PQQ-dependent alcohol dehydrogenase activity" EXACT []
-synonym: "primary alcohol dehydrogenase" BROAD [EC:1.1.99.8]
-synonym: "quinohemoprotein alcohol dehydrogenase activity" RELATED [EC:1.1.99.8]
-synonym: "quinoprotein alcohol dehydrogenase activity" RELATED [EC:1.1.99.8]
-synonym: "quinoprotein ethanol dehydrogenase activity" RELATED [EC:1.1.99.8]
-xref: EC:1.1.99.8
-xref: UM-BBD_enzymeID:e0004
-is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
-
[Term]
id: GO:0018469
name: myrtenal dehydrogenase activity
@@ -132036,13 +131771,13 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0018580
name: nitronate monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ethylnitronate + O(2) = acetaldehyde + nitrite." [EC:1.13.12.16, RHEA:28770]
+def: "Catalysis of the reaction: ethylnitronate + O(2) = acetaldehyde + nitrite." [EC:1.13.12.16, RHEA:28767]
comment: Where non-covalently bound FMN is used as the cofactor, see instead 'nitronate monooxygenase (FMN-linked) activity ; GO:0036434'.
synonym: "2-nitropropane dioxygenase activity" RELATED [EC:1.13.11.32]
synonym: "nitronate:oxygen 2-oxidoreductase (nitrite-forming) activity" EXACT systematic_synonym [EC:1.13.12.16]
xref: EC:1.13.12.16
xref: MetaCyc:2-NITROPROPANE-DIOXYGENASE-RXN
-xref: RHEA:28770
+xref: RHEA:28767
is_a: GO:0016703 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases)
[Term]
@@ -132812,7 +132547,7 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0018652
name: toluene-sulfonate methyl-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: toluene-4-sulfonate + NADH + O2 = NAD+ + OH- + 4-sulfobenzyl alcohol." [RHEA:510240]
+def: "Catalysis of the reaction: toluene-4-sulfonate + NADH + O2 = NAD+ + OH- + 4-sulfobenzyl alcohol." [RHEA:51024]
synonym: "toluene-sulphonate methyl-monooxygenase activity" EXACT []
xref: MetaCyc:TSMOS-RXN
xref: RHEA:51024
@@ -132907,12 +132642,12 @@ id: GO:0018660
name: 4-hydroxyphenylacetate,NADH:oxygen oxidoreductase (3-hydroxylating) activity
namespace: molecular_function
def: "Catalysis of the reaction: 4-hydroxyphenylacetate + NADH + H+ + O2 = 3,4-dihydroxyphenylacetate + NAD+ + H2O." [RHEA:16681]
-synonym: "4 HPA 3-hydroxylase activity" BROAD [EC:1.14.13.3]
+synonym: "4 HPA 3-hydroxylase activity" BROAD [EC:1.14.14.9]
synonym: "4-hydroxyphenylacetate 3-hydroxylase activity" BROAD []
-synonym: "4-hydroxyphenylacetate 3-monooxygenase activity" BROAD [EC:1.14.13.3]
-synonym: "p-hydroxyphenylacetate 3-hydroxylase activity" BROAD [EC:1.14.13.3]
-synonym: "p-hydroxyphenylacetate hydroxylase activity" BROAD [EC:1.14.13.3]
-xref: EC:1.14.13.3
+synonym: "4-hydroxyphenylacetate 3-monooxygenase activity" BROAD []
+synonym: "p-hydroxyphenylacetate 3-hydroxylase activity" BROAD [EC:1.14.14.9]
+synonym: "p-hydroxyphenylacetate hydroxylase activity" BROAD [EC:1.14.14.9]
+xref: EC:1.14.14.9
xref: KEGG_REACTION:R02698
xref: RHEA:16681
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
@@ -133254,18 +132989,19 @@ is_a: GO:0016713 ! oxidoreductase activity, acting on paired donors, with incorp
[Term]
id: GO:0018684
-name: camphor 1,2-monooxygenase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: (1R)-bornane-2,5-dione + reduced rubredoxin + O2 = 5-oxo-1,2-campholide + oxidized rubredoxin + H2O." [EC:1.14.15.2]
-synonym: "(+)-camphor,reduced-rubredoxin:oxygen oxidoreductase (1,2-lactonizing)" RELATED [EC:1.14.15.2]
-synonym: "2,5-diketocamphane lactonizing enzyme activity" RELATED [EC:1.14.15.2]
-synonym: "camphor ketolactonase I activity" RELATED [EC:1.14.15.2]
-synonym: "ketolactonase I" RELATED [EC:1.14.15.2]
-synonym: "oxygenase, camphor 1,2-mono" RELATED [EC:1.14.15.2]
-xref: EC:1.14.15.2
+name: 2,5-diketocamphane 1,2-monooxygenase
+namespace: molecular_function
+def: "Catalysis of the reaction: 1R,4R)-bornane-2,5-dione + FMNH2 + O2 = (1R,4R)-5-oxo-1,2-campholide + FMN + H+ + H2O." [PMID:3944058, PMID:8515237, RHEA:34415]
+comment: Formerly EC:1.14.15.2.
+synonym: "(+)-camphor,reduced-rubredoxin:oxygen oxidoreductase (1,2-lactonizing)" RELATED []
+synonym: "2,5-diketocamphane lactonizing enzyme activity" RELATED [EC:1.14.14.108]
+synonym: "camphor 1,2-monooxygenase activity" EXACT []
+synonym: "camphor ketolactonase I activity" RELATED [EC:1.14.14.108]
+xref: EC:1.14.14.108
xref: MetaCyc:CAMPHOR-12-MONOOXYGENASE-RXN
+xref: RHEA:34415
xref: UM-BBD_enzymeID:e0302
-is_a: GO:0016713 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0018685
@@ -134262,13 +133998,13 @@ is_a: GO:0019120 ! hydrolase activity, acting on acid halide bonds, in C-halide
id: GO:0018786
name: haloalkane dehalogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1-haloalkane + H2O = a primary alcohol + halide." [EC:3.8.1.5]
+def: "Catalysis of the reaction: 1-haloalkane + H2O = a primary alcohol + halide." [RHEA:19081]
synonym: "1-chlorohexane halidohydrolase activity" RELATED [EC:3.8.1.5]
synonym: "1-haloalkane dehalogenase activity" RELATED [EC:3.8.1.5]
synonym: "1-haloalkane halidohydrolase activity" RELATED [EC:3.8.1.5]
xref: EC:3.8.1.5
xref: MetaCyc:HALOALKANE-DEHALOGENASE-RXN
-xref: RHEA:25185
+xref: RHEA:19081
xref: UM-BBD_enzymeID:e0003
is_a: GO:0019120 ! hydrolase activity, acting on acid halide bonds, in C-halide compounds
@@ -134420,7 +134156,7 @@ is_a: GO:0016831 ! carboxy-lyase activity
id: GO:0018801
name: glutaconyl-CoA decarboxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: trans-glutaconyl-CoA + H(+) = but-2-enoyl-CoA + CO(2)." [EC:7.2.4.5, RHEA:23972]
+def: "Catalysis of the reaction: trans-glutaconyl-CoA + H(+) = but-2-enoyl-CoA + CO(2)." [PMID:11248185, RHEA:23972]
synonym: "4-carboxybut-2-enoyl-CoA carboxy-lyase (but-2-enoyl-CoA-forming)" EXACT []
synonym: "4-carboxybut-2-enoyl-CoA carboxy-lyase activity" RELATED [EC:7.2.4.5]
synonym: "glutaconyl coenzyme A decarboxylase activity" RELATED [EC:7.2.4.5]
@@ -134430,6 +134166,7 @@ xref: KEGG_REACTION:R03028
xref: MetaCyc:GLUTACONYL-COA-DECARBOXYLASE-RXN
xref: RHEA:23972
xref: UM-BBD_reactionID:r0199
+is_a: GO:0015451 ! decarboxylation-driven active transmembrane transporter activity
is_a: GO:0016831 ! carboxy-lyase activity
[Term]
@@ -134840,15 +134577,6 @@ xref: EC:5.2.1.-
xref: UM-BBD_reactionID:r0163
is_a: GO:0016859 ! cis-trans isomerase activity
-[Term]
-id: GO:0018842
-name: 3-carboxymuconate cycloisomerase type II activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 3-sulfomuconate = 4-sulfolactone." [UM-BBD_reactionID:r0582]
-xref: EC:5.5.1.2
-xref: UM-BBD_reactionID:r0582
-is_a: GO:0016872 ! intramolecular lyase activity
-
[Term]
id: GO:0018844
name: 2-hydroxytetrahydrofuran isomerase activity
@@ -134907,17 +134635,15 @@ is_a: GO:0016872 ! intramolecular lyase activity
id: GO:0018849
name: muconate cycloisomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,5-dihydro-5-oxofuran-2-acetate = cis,cis-hexadienedioate." [EC:5.5.1.1]
-synonym: "2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)" RELATED [EC:5.5.1.1]
-synonym: "4-carboxymethyl-4-hydroxyisocrotonolactone lyase (decyclizing)" RELATED [EC:5.5.1.1]
+def: "Catalysis of the reaction: 2,5-dihydro-5-oxofuran-2-acetate = cis,cis-hexadienedioate." [RHEA:30031]
synonym: "cis,cis-muconate cycloisomerase activity" RELATED [EC:5.5.1.1]
-synonym: "cis,cis-muconate lactonizing enzyme I activity" RELATED [EC:5.5.1.1]
synonym: "cis,cis-muconate-lactonizing enzyme" RELATED [EC:5.5.1.1]
synonym: "muconate cycloisomerase I activity" RELATED [EC:5.5.1.1]
synonym: "muconate lactonizing enzyme activity" RELATED [EC:5.5.1.1]
+synonym: "muconate lactonizing enzyme I activity" RELATED [EC:5.5.1.1]
xref: EC:5.5.1.1
xref: MetaCyc:MUCONATE-CYCLOISOMERASE-RXN
-xref: RHEA:10640
+xref: RHEA:30031
xref: UM-BBD_enzymeID:e0133
is_a: GO:0016872 ! intramolecular lyase activity
@@ -136146,8 +135872,8 @@ synonym: "phthalate metabolism" EXACT []
synonym: "phthalic acid metabolic process" EXACT []
synonym: "phthalic acid metabolism" EXACT []
xref: UM-BBD_pathwayID:pth
+is_a: GO:0019752 ! carboxylic acid metabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
-is_a: GO:0043648 ! dicarboxylic acid metabolic process
[Term]
id: GO:0018964
@@ -136510,7 +136236,7 @@ consider: GO:0004521
id: GO:0019001
name: guanyl nucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with guanyl nucleotides, any compound consisting of guanosine esterified with (ortho)phosphate." [ISBN:0198506732]
+def: "Binding to a guanyl nucleotide, consisting of guanosine esterified with (ortho)phosphate." [ISBN:0198506732]
xref: Reactome:R-HSA-156909 "eEF1A complexes with GTP"
is_a: GO:0017076 ! purine nucleotide binding
@@ -136518,7 +136244,7 @@ is_a: GO:0017076 ! purine nucleotide binding
id: GO:0019002
name: GMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with GMP, guanosine monophosphate." [GOC:ai]
+def: "Binding to GMP, guanosine monophosphate." [GOC:ai]
is_a: GO:0032561 ! guanyl ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -136526,7 +136252,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0019003
name: GDP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate." [GOC:ai]
+def: "Binding to GDP, guanosine 5'-diphosphate." [GOC:ai]
is_a: GO:0032561 ! guanyl ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -136755,11 +136481,12 @@ is_a: GO:0044094 ! host cell nuclear part
id: GO:0019035
name: viral integration complex
namespace: cellular_component
-def: "A nucleoprotein complex containing viral genetic material and associated viral and host proteins, which is capable of inserting a viral genome into a host genome." [ISBN:0781718325, PMID:16712776, Wikipedia:Pre-integration_complex]
-synonym: "PIC" EXACT [PMID:16712776]
-synonym: "pre-integration complex" EXACT [PMID:16712776]
+def: "A nucleoprotein complex containing viral genetic material and the viral integrase, required for genome integration into the host's genome. May contain other proteins." [PMID:21037296, PMID:2721960, PMID:29900498]
+synonym: "PIC" BROAD []
+synonym: "pre-integration complex" EXACT []
+xref: Wikipedia:Pre-integration_complex
is_a: GO:0032991 ! protein-containing complex
-relationship: part_of GO:0042025 ! host cell nucleus
+relationship: part_of GO:0043657 ! host cell
[Term]
id: GO:0019036
@@ -136948,7 +136675,6 @@ namespace: biological_process
def: "Any process in which a virus modulates the frequency, rate or extent of its host's transcription." [ISBN:0781718325]
synonym: "modification by virus of host transcription" EXACT []
synonym: "viral perturbation of host cell transcription" EXACT []
-is_a: GO:0010468 ! regulation of gene expression
is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0039656 ! modulation by virus of host gene expression
is_a: GO:0052026 ! modulation by symbiont of host transcription
@@ -137012,7 +136738,6 @@ synonym: "nuclear viral capsid transport" NARROW []
synonym: "viral capsid transport in host cell cytoplasm" NARROW []
synonym: "viral capsid transport in host cell nucleus" NARROW []
is_a: GO:0030581 ! symbiont intracellular protein transport in host
-is_a: GO:0044766 ! multi-organism transport
relationship: part_of GO:0046719 ! regulation by virus of viral protein levels in host cell
[Term]
@@ -137050,6 +136775,7 @@ synonym: "viral penetration via membrane fusion" BROAD []
synonym: "viral-cell fusion molecule activity" RELATED []
xref: VZ:987 "Fusion of virus membrane with host cell membrane"
is_a: GO:0039663 ! membrane fusion involved in viral entry into host cell
+is_a: GO:0061025 ! membrane fusion
[Term]
id: GO:0019065
@@ -137377,8 +137103,9 @@ name: reproductive behavior
namespace: biological_process
alt_id: GO:0033057
alt_id: GO:0044704
+alt_id: GO:0044705
def: "The specific behavior of an organism that is associated with reproduction." [GOC:jl, GOC:pr]
-subset: goslim_drosophila
+synonym: "multi-organism reproductive behavior" NARROW []
synonym: "multicellular organism reproductive behavior" NARROW []
synonym: "reproductive behavior in a multicellular organism" EXACT []
synonym: "reproductive behaviour" EXACT []
@@ -137426,7 +137153,7 @@ is_a: GO:0030238 ! male sex determination
id: GO:0019103
name: pyrimidine nucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pyrimidine nucleotide, any compound consisting of a pyrimidine nucleoside esterified with (ortho)phosphate." [GOC:ai]
+def: "Binding to a pyrimidine nucleotide, a pyrimidine nucleoside esterified with (ortho)phosphate." [GOC:ai]
is_a: GO:0000166 ! nucleotide binding
[Term]
@@ -137437,7 +137164,6 @@ alt_id: GO:0008578
def: "Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site." [GOC:elh, PMID:11554296]
synonym: "DNA glycosylase activity" EXACT []
synonym: "endonuclease VIII activity" RELATED []
-xref: EC:3.2.2.-
xref: Reactome:R-HSA-110218 "Cleavage of uracil by TDG glycosylase"
xref: Reactome:R-HSA-110219 "Cleavage of thymine by TDG glycosylase"
xref: Reactome:R-HSA-110231 "Cleavage of uracil by MBD4 glycosylase"
@@ -137758,6 +137484,7 @@ name: cytokinin dehydrogenase activity
namespace: molecular_function
alt_id: GO:0046420
def: "Catalysis of the reaction: N6-dimethylallyladenine + acceptor + H2O = adenine + 3-methylbut-2-enal + reduced electron acceptor." [EC:1.5.99.12]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "6-N-dimethylallyladenine:acceptor oxidoreductase activity" RELATED [EC:1.5.99.12]
synonym: "cytokinin oxidase activity" RELATED []
synonym: "N6-dimethylallyladenine:(acceptor) oxidoreductase activity" RELATED [EC:1.5.99.12]
@@ -137961,7 +137688,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0019153
name: protein-disulfide reductase (glutathione) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 glutathione + protein-disulfide = oxidized glutathione + protein-dithiol." [EC:1.8.4.2]
+def: "Catalysis of the reaction: 2 glutathione + protein-disulfide = oxidized glutathione + protein-dithiol." [RHEA:21064]
synonym: "glutaredoxin reductase" RELATED []
synonym: "glutathione--insulin transhydrogenase activity" RELATED [EC:1.8.4.2]
synonym: "glutathione-insulin transhydrogenase activity" EXACT []
@@ -137980,6 +137707,7 @@ synonym: "thiol:protein-disulfide oxidoreductase activity" RELATED [EC:1.8.4.2]
xref: EC:1.8.4.2
xref: MetaCyc:PRODISULFREDUCT-RXN
xref: RHEA:21064
+is_a: GO:0015035 ! protein-disulfide reductase activity
is_a: GO:0016671 ! oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor
[Term]
@@ -138471,7 +138199,7 @@ id: GO:0019207
name: kinase regulator activity
namespace: molecular_function
def: "Modulates the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:ai]
-is_a: GO:0003674 ! molecular_function
+is_a: GO:0030234 ! enzyme regulator activity
[Term]
id: GO:0019208
@@ -138502,6 +138230,7 @@ name: phosphatase activator activity
namespace: molecular_function
def: "Binds to and increases the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule." [GOC:ai]
is_a: GO:0008047 ! enzyme activator activity
+is_a: GO:0019208 ! phosphatase regulator activity
[Term]
id: GO:0019212
@@ -138534,7 +138263,7 @@ consider: GO:0050828
id: GO:0019215
name: intermediate filament binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an intermediate filament, a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space." [ISBN:0198506732]
+def: "Binding to an intermediate filament, a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space." [ISBN:0198506732]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -138708,7 +138437,7 @@ is_a: GO:0010033 ! response to organic substance
id: GO:0019237
name: centromeric DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis." [GOC:jl, SO:0000577]
+def: "Binding to a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis." [GOC:jl, SO:0000577]
synonym: "centromere binding" EXACT []
is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
@@ -139967,7 +139696,6 @@ synonym: "cysteine formation" EXACT []
synonym: "cysteine synthesis" EXACT []
is_a: GO:0000097 ! sulfur amino acid biosynthetic process
is_a: GO:0006534 ! cysteine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009070 ! serine family amino acid biosynthetic process
[Term]
@@ -141094,7 +140822,7 @@ is_obsolete: true
id: GO:0019447
name: D-cysteine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of D-cysteine, (S)-2-amino-3-mercaptopropanoic acid, which occurs naturally in firefly luciferin." [GOC:go_curators, ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of D-cysteine, (S)-2-amino-3-mercaptopropanoic acid, which occurs naturally in firefly luciferin." [PMID:11527960]
synonym: "D-cysteine breakdown" EXACT []
synonym: "D-cysteine catabolism" EXACT []
synonym: "D-cysteine degradation" EXACT []
@@ -141166,7 +140894,7 @@ is_a: GO:0019448 ! L-cysteine catabolic process
id: GO:0019454
name: L-cysteine catabolic process via cystine, using glutathione-cystine transhydrogenase
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme glutathione-cystine transhydrogenase (EC:1.8.4.4)." [GOC:jl]
+def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme glutathione-cystine transhydrogenase." [GOC:jl]
synonym: "L-cysteine breakdown via cystine, using glutathione-cystine transhydrogenase" EXACT []
synonym: "L-cysteine degradation via cystine, using glutathione-cystine transhydrogenase" EXACT []
is_a: GO:0019453 ! L-cysteine catabolic process via cystine
@@ -141175,7 +140903,7 @@ is_a: GO:0019453 ! L-cysteine catabolic process via cystine
id: GO:0019455
name: L-cysteine catabolic process via cystine, using cystine reductase
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cystine reductase (EC:1.8.1.6)." [GOC:jl]
+def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cystine reductase." [GOC:jl]
synonym: "L-cysteine breakdown via cystine, using cystine reductase" EXACT []
synonym: "L-cysteine degradation via cystine, using cystine reductase" EXACT []
is_a: GO:0019453 ! L-cysteine catabolic process via cystine
@@ -141184,7 +140912,7 @@ is_a: GO:0019453 ! L-cysteine catabolic process via cystine
id: GO:0019456
name: L-cysteine catabolic process via cystine, using cysteine transaminase
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cysteine transaminase (EC:2.6.1.3)." [GOC:jl]
+def: "The chemical reactions and pathways resulting in the breakdown, via the compound cystine, of L-cysteine, catalyzed by the enzyme cysteine transaminase." [GOC:jl]
synonym: "L-cysteine breakdown via cystine, using cysteine transaminase" EXACT []
synonym: "L-cysteine degradation via cystine, using cysteine transaminase" EXACT []
is_a: GO:0019453 ! L-cysteine catabolic process via cystine
@@ -141352,7 +141080,6 @@ synonym: "4-hydroxyproline anabolism" EXACT []
synonym: "4-hydroxyproline biosynthesis" EXACT []
synonym: "4-hydroxyproline formation" EXACT []
synonym: "4-hydroxyproline synthesis" EXACT []
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0019471 ! 4-hydroxyproline metabolic process
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -141800,7 +141527,7 @@ is_a: GO:0005990 ! lactose catabolic process
id: GO:0019513
name: lactose catabolic process, using glucoside 3-dehydrogenase
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of lactose, catalyzed by the enzyme glucoside 3-dehydrogenase (EC:1.1.99.13)." [GOC:jl]
+def: "The chemical reactions and pathways resulting in the breakdown of lactose, catalyzed by the enzyme glucoside 3-dehydrogenase." [GOC:jl]
synonym: "lactose breakdown, using glucoside 3-dehydrogenase" EXACT []
synonym: "lactose degradation, using glucoside 3-dehydrogenase" EXACT []
xref: MetaCyc:LACTOSEUTIL-PWY
@@ -143880,7 +143607,6 @@ synonym: "peptidyl-glycine cholesteryl ester formation from peptidyl-glycine" EX
synonym: "peptidyl-glycine cholesteryl ester synthesis from peptidyl-glycine" EXACT []
xref: RESID:AA0309
is_a: GO:0006501 ! C-terminal protein lipidation
-is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:0008203 ! cholesterol metabolic process
is_a: GO:0018201 ! peptidyl-glycine modification
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
@@ -144217,7 +143943,6 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." [GOC:go_curators]
subset: goslim_aspergillus
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_pombe
@@ -144521,6 +144246,7 @@ namespace: molecular_function
alt_id: GO:0019944
def: "Catalysis of the initiation of the NEDD8 (RUB1) conjugation cascade." [PMID:12646924]
synonym: "RUB1 activating enzyme activity" EXACT []
+xref: EC:6.2.1.64
is_a: GO:0008641 ! ubiquitin-like modifier activating enzyme activity
[Term]
@@ -144978,14 +144704,14 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0019808
name: polyamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with polyamines, organic compounds containing two or more amino groups." [GOC:ai]
+def: "Binding to a polyamine, an organic compound containing two or more amino groups." [GOC:ai]
is_a: GO:0005488 ! binding
[Term]
id: GO:0019809
name: spermidine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with spermidine, N-(3-aminopropyl)-1,4-diaminobutane." [GOC:ai]
+def: "Binding to spermidine, N-(3-aminopropyl)-1,4-diaminobutane." [GOC:ai]
is_a: GO:0019808 ! polyamine binding
is_a: GO:0043169 ! cation binding
@@ -144993,7 +144719,7 @@ is_a: GO:0043169 ! cation binding
id: GO:0019810
name: putrescine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with putrescine, 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine." [GOC:ai]
+def: "Binding to putrescine, 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine." [GOC:ai]
is_a: GO:0019808 ! polyamine binding
is_a: GO:0043169 ! cation binding
@@ -145001,8 +144727,7 @@ is_a: GO:0043169 ! cation binding
id: GO:0019811
name: cocaine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cocaine (2-beta-carbomethoxy-3-beta-benzoxytropane), an alkaloid obtained from dried leaves of the South American shrub Erythroxylon coca or by chemical synthesis." [GOC:jl, ISBN:0198506732]
-is_a: GO:0008144 ! drug binding
+def: "Binding to cocaine (2-beta-carbomethoxy-3-beta-benzoxytropane), an alkaloid obtained from dried leaves of the South American shrub Erythroxylon coca or by chemical synthesis." [GOC:jl, ISBN:0198506732]
is_a: GO:0043169 ! cation binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -145013,7 +144738,6 @@ name: type I site-specific deoxyribonuclease complex
namespace: cellular_component
def: "A multisubunit complex composed of two copies of a restriction (R) subunit, two copies of a methylation (M) subunit, and one copy of a specificity (S) subunit. This complex recognizes specific short DNA sequences (through the S subunit), and binds to them. If the recognition site is hemimethylated, the complex acts as a methyltransferase which modifies the recognition site, using S-adenosylmethionine as the methyl donor. Only the M and S subunits are required for this reaction. If the complex binds to an unmethylated recognition site, then the complex translocates the DNA bidirectionally in an ATP-dependent manner. When the translocation is stalled by impact with another complex or unusual DNA structure, the enzyme functions as an endonuclease and cleavage of the DNA will occur, hundreds or thousands of base pairs away from the recognition site. These DNA restriction systems are used by bacteria to defend against phage and other foreign DNA that may enter a cell." [PMID:12654995, PMID:15788748]
synonym: "type I restriction enzyme complex" EXACT []
-is_a: GO:1904949 ! ATPase complex
is_a: GO:1905347 ! endodeoxyribonuclease complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -145129,7 +144853,7 @@ is_a: GO:0005777 ! peroxisome
id: GO:0019825
name: oxygen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with oxygen (O2)." [GOC:jl]
+def: "Binding to oxygen (O2)." [GOC:jl]
subset: goslim_pir
subset: goslim_plant
synonym: "cytochrome P450" NARROW []
@@ -145140,7 +144864,7 @@ is_a: GO:0036094 ! small molecule binding
id: GO:0019826
name: oxygen sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of oxygen (O2)." [GOC:mah]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of oxygen (O2)." [GOC:mah]
is_a: GO:0019825 ! oxygen binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -145249,10 +144973,9 @@ synonym: "haemolysis in host" EXACT []
synonym: "hemolysin activity" RELATED []
synonym: "hemolysis by symbiont of host RBCs" EXACT [CL:0000232]
synonym: "hemolysis by symbiont of host red blood cells" EXACT [CL:0000232]
-synonym: "pathogenesis" NARROW []
+synonym: "pathogenesis" RELATED []
synonym: "regulation of cytolysis of host cells by symbiont" EXACT [GOC:dph, GOC:tb]
is_a: GO:0001897 ! cytolysis by symbiont of host cells
-is_a: GO:0052331 ! hemolysis in other organism involved in symbiotic interaction
[Term]
id: GO:0019837
@@ -145268,7 +144991,7 @@ replaced_by: GO:0009635
id: GO:0019838
name: growth factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate." [GOC:curators]
+def: "Binding to a growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate." [GOC:curators]
subset: goslim_chembl
synonym: "neurotrophin TRK receptor activity" RELATED []
is_a: GO:0005515 ! protein binding
@@ -145277,7 +145000,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0019840
name: isoprenoid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [GOC:jl]
+def: "Binding to an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues." [GOC:jl]
subset: goslim_pir
is_a: GO:0008289 ! lipid binding
@@ -145285,7 +145008,7 @@ is_a: GO:0008289 ! lipid binding
id: GO:0019841
name: retinol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation." [GOC:curators]
+def: "Binding to retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation." [GOC:curators]
synonym: "vitamin A1 alcohol binding" EXACT []
synonym: "vitamin A1 binding" EXACT []
is_a: GO:0005501 ! retinoid binding
@@ -145296,7 +145019,7 @@ is_a: GO:0043178 ! alcohol binding
id: GO:0019842
name: vitamin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:ai]
+def: "Binding to a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body." [GOC:ai]
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:0036094 ! small molecule binding
@@ -145306,9 +145029,8 @@ id: GO:0019843
name: rRNA binding
namespace: molecular_function
alt_id: GO:0000944
-def: "Interacting selectively and non-covalently with ribosomal RNA." [GOC:jl]
+def: "Binding to a ribosomal RNA." [GOC:jl]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_yeast
synonym: "base pairing with rRNA" NARROW []
is_a: GO:0003723 ! RNA binding
@@ -145389,6 +145111,7 @@ synonym: "vitamin C metabolism" EXACT []
is_a: GO:0005996 ! monosaccharide metabolic process
is_a: GO:0006767 ! water-soluble vitamin metabolic process
is_a: GO:0019752 ! carboxylic acid metabolic process
+is_a: GO:1901334 ! lactone metabolic process
[Term]
id: GO:0019853
@@ -145408,6 +145131,7 @@ is_a: GO:0019852 ! L-ascorbic acid metabolic process
is_a: GO:0042364 ! water-soluble vitamin biosynthetic process
is_a: GO:0046364 ! monosaccharide biosynthetic process
is_a: GO:0046394 ! carboxylic acid biosynthetic process
+is_a: GO:1901336 ! lactone biosynthetic process
[Term]
id: GO:0019854
@@ -145426,6 +145150,7 @@ is_a: GO:0019852 ! L-ascorbic acid metabolic process
is_a: GO:0042365 ! water-soluble vitamin catabolic process
is_a: GO:0046365 ! monosaccharide catabolic process
is_a: GO:0046395 ! carboxylic acid catabolic process
+is_a: GO:1901335 ! lactone catabolic process
[Term]
id: GO:0019855
@@ -145499,21 +145224,21 @@ consider: GO:0009288
id: GO:0019862
name: IgA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an immunoglobulin of an IgA isotype." [GOC:add, ISBN:0781735149]
+def: "Binding to an immunoglobulin of an IgA isotype." [GOC:add, ISBN:0781735149]
is_a: GO:0019865 ! immunoglobulin binding
[Term]
id: GO:0019863
name: IgE binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an immunoglobulin of the IgE isotype." [GOC:add, ISBN:0781735149]
+def: "Binding to an immunoglobulin of the IgE isotype." [GOC:add, ISBN:0781735149]
is_a: GO:0019865 ! immunoglobulin binding
[Term]
id: GO:0019864
name: IgG binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype." [GOC:add, ISBN:0781735149]
+def: "Binding to an immunoglobulin of an IgG isotype." [GOC:add, ISBN:0781735149]
subset: goslim_chembl
is_a: GO:0019865 ! immunoglobulin binding
@@ -145521,7 +145246,7 @@ is_a: GO:0019865 ! immunoglobulin binding
id: GO:0019865
name: immunoglobulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an immunoglobulin." [GOC:ma]
+def: "Binding to an immunoglobulin." [GOC:ma]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -145546,7 +145271,6 @@ id: GO:0019869
name: chloride channel inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of a chloride channel." [GOC:mah]
-is_a: GO:0008200 ! ion channel inhibitor activity
is_a: GO:0017081 ! chloride channel regulator activity
[Term]
@@ -145769,7 +145493,7 @@ synonym: "protein phosphatase type 2B, intrinsic regulator activity" NARROW []
synonym: "protein phosphatase type 4 regulator activity" NARROW []
synonym: "protein phosphatase type 4, intrinsic regulator activity" NARROW []
xref: Reactome:R-HSA-180038 "DARPP-32 phosphorylated on T34 binds to PP1, inhibiting its function"
-is_a: GO:0003674 ! molecular_function
+is_a: GO:0019208 ! phosphatase regulator activity
[Term]
id: GO:0019889
@@ -145844,10 +145568,8 @@ relationship: part_of GO:0016020 ! membrane
id: GO:0019899
name: enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any enzyme." [GOC:jl]
+def: "Binding to an enzyme, a protein with catalytic activity." [GOC:jl]
subset: goslim_chembl
-subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_yeast
is_a: GO:0005515 ! protein binding
@@ -145855,35 +145577,35 @@ is_a: GO:0005515 ! protein binding
id: GO:0019900
name: kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group." [GOC:jl]
+def: "Binding to a kinase, any enzyme that catalyzes the transfer of a phosphate group." [GOC:jl]
is_a: GO:0019899 ! enzyme binding
[Term]
id: GO:0019901
name: protein kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate." [GOC:jl]
+def: "Binding to a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate." [GOC:jl]
is_a: GO:0019900 ! kinase binding
[Term]
id: GO:0019902
name: phosphatase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any phosphatase." [GOC:jl]
+def: "Binding to a phosphatase." [GOC:jl]
is_a: GO:0019899 ! enzyme binding
[Term]
id: GO:0019903
name: protein phosphatase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein phosphatase." [GOC:jl]
+def: "Binding to a protein phosphatase." [GOC:jl]
is_a: GO:0019902 ! phosphatase binding
[Term]
id: GO:0019904
name: protein domain specific binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a specific domain of a protein." [GOC:go_curators]
+def: "Binding to a specific domain of a protein." [GOC:go_curators]
subset: goslim_chembl
synonym: "protein domain-specific binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -145896,7 +145618,7 @@ alt_id: GO:0030347
alt_id: GO:0030349
alt_id: GO:0050430
alt_id: GO:0051535
-def: "Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse." [ISBN:0198506732]
+def: "Binding to a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse." [ISBN:0198506732]
synonym: "syntaxin-13 binding" NARROW []
synonym: "syntaxin-2 binding" NARROW []
synonym: "syntaxin-5 binding" NARROW []
@@ -145929,7 +145651,6 @@ name: [pyruvate dehydrogenase (lipoamide)] phosphatase regulator activity
namespace: molecular_function
def: "Binds to and modulates of the activity of [pyruvate dehydrogenase (lipoamide)] phosphatase." [EC:3.1.3.43, GOC:ai]
synonym: "[pyruvate dehydrogenase (lipoamide)] phosphatase, intrinsic regulator activity" NARROW []
-is_a: GO:0019208 ! phosphatase regulator activity
is_a: GO:0019888 ! protein phosphatase regulator activity
[Term]
@@ -145967,7 +145688,6 @@ name: cyclin-dependent protein kinase activating kinase regulator activity
namespace: molecular_function
def: "Modulation of the activity of the enzyme cyclin-dependent protein kinase activating kinase." [GOC:ai]
synonym: "cyclin-dependent protein kinase activating kinase, intrinsic regulator activity" NARROW []
-xref: EC:2.7.1.-
is_a: GO:0019887 ! protein kinase regulator activity
[Term]
@@ -146271,24 +145991,15 @@ is_a: GO:0008641 ! ubiquitin-like modifier activating enzyme activity
[Term]
id: GO:0019950
-name: SMT3-dependent protein catabolic process
+name: obsolete SMT3-dependent protein catabolic process
namespace: biological_process
alt_id: GO:0019946
-def: "The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by covalent attachment of the ubiquitin-like protein SMT3 to the target protein." [GOC:jl, PMID:9435231]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by covalent attachment of the ubiquitin-like protein SMT3 to the target protein." [GOC:jl, PMID:9435231]
+comment: See issue #21890. SMT3 protein mod is sumoylation and does not always lead to degradation.
synonym: "SMT3-dependent protein breakdown" EXACT []
synonym: "SMT3-dependent protein catabolism" EXACT []
synonym: "SMT3-dependent protein degradation" EXACT []
-is_a: GO:0019941 ! modification-dependent protein catabolic process
-
-[Term]
-id: GO:0019951
-name: Smt3-protein conjugation
-namespace: biological_process
-alt_id: GO:0019947
-def: "The covalent addition to a protein of Smt3, a ubiquitin-like protein." [GOC:jl]
-synonym: "Smt3p-protein conjugation" EXACT []
-is_a: GO:0032446 ! protein modification by small protein conjugation
-relationship: part_of GO:0019950 ! SMT3-dependent protein catabolic process
+is_obsolete: true
[Term]
id: GO:0019953
@@ -146314,7 +146025,7 @@ id: GO:0019955
name: cytokine binding
namespace: molecular_function
alt_id: GO:0019965
-def: "Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." [GOC:ai, GOC:bf, ISBN:0198599471]
+def: "Binding to a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." [GOC:ai, GOC:bf, ISBN:0198599471]
synonym: "IL binding" NARROW []
synonym: "interleukin binding" NARROW []
is_a: GO:0005515 ! protein binding
@@ -146323,28 +146034,28 @@ is_a: GO:0005515 ! protein binding
id: GO:0019956
name: chemokine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chemokine. Chemokines are a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria." [GOC:ai, GOC:BHF, GOC:rl, PMID:12183377, Wikipedia:Chemokine]
+def: "Binding to a chemokine. Chemokines are a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria." [GOC:ai, GOC:BHF, GOC:rl, PMID:12183377, Wikipedia:Chemokine]
is_a: GO:0019955 ! cytokine binding
[Term]
id: GO:0019957
name: C-C chemokine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a C-C chemokine; C-C chemokines do not have an amino acid between the first two cysteines of the characteristic four-cysteine motif." [GOC:ai]
+def: "Binding to a C-C chemokine; C-C chemokines do not have an amino acid between the first two cysteines of the characteristic four-cysteine motif." [GOC:ai]
is_a: GO:0019956 ! chemokine binding
[Term]
id: GO:0019958
name: C-X-C chemokine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a C-X-C chemokine; C-X-C chemokines have a single amino acid between the first two cysteines of the characteristic four cysteine motif." [GOC:ai]
+def: "Binding to a C-X-C chemokine; C-X-C chemokines have a single amino acid between the first two cysteines of the characteristic four cysteine motif." [GOC:ai]
is_a: GO:0019956 ! chemokine binding
[Term]
id: GO:0019959
name: interleukin-8 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-8." [GOC:jl]
+def: "Binding to interleukin-8." [GOC:jl]
synonym: "IL-8 binding" EXACT []
is_a: GO:0019958 ! C-X-C chemokine binding
@@ -146352,14 +146063,14 @@ is_a: GO:0019958 ! C-X-C chemokine binding
id: GO:0019960
name: C-X3-C chemokine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a C-X3-C chemokine; C-X3-C chemokines have three amino acids between the first two cysteines of the characteristic four-cysteine motif." [GOC:ai]
+def: "Binding to a C-X3-C chemokine; C-X3-C chemokines have three amino acids between the first two cysteines of the characteristic four-cysteine motif." [GOC:ai]
is_a: GO:0019956 ! chemokine binding
[Term]
id: GO:0019961
name: interferon binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an interferon, a protein produced by the immune systems of many animals in response to a challenge by a foreign agent." [PMID:9607096, Wikipedia:Interferon]
+def: "Binding to an interferon, a protein produced by the immune systems of many animals in response to a challenge by a foreign agent." [PMID:9607096, Wikipedia:Interferon]
synonym: "IFN binding" EXACT [GOC:mah]
is_a: GO:0019955 ! cytokine binding
@@ -146367,7 +146078,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019962
name: type I interferon binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type I interferon. Type I interferons include the interferon-alpha, beta, delta, epsilon, zeta, kappa, tau, and omega gene families." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16681834]
+def: "Binding to a type I interferon. Type I interferons include the interferon-alpha, beta, delta, epsilon, zeta, kappa, tau, and omega gene families." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16681834]
synonym: "interferon-alpha binding" NARROW []
synonym: "interferon-alpha/beta binding" NARROW []
synonym: "interferon-beta binding" NARROW []
@@ -146384,7 +146095,7 @@ is_a: GO:0019961 ! interferon binding
id: GO:0019964
name: interferon-gamma binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interferon-gamma. Interferon gamma is the only member of the type II interferon found so far." [GOC:add, GOC:ai, ISBN:0126896631, PMID:15546383]
+def: "Binding to interferon-gamma. Interferon gamma is the only member of the type II interferon found so far." [GOC:add, GOC:ai, ISBN:0126896631, PMID:15546383]
synonym: "IFN-gamma binding" EXACT [GOC:mah]
synonym: "IFNG binding" EXACT [GOC:mah]
synonym: "type II interferon binding" BROAD [PMID:15546383, PR:000024990]
@@ -146394,7 +146105,7 @@ is_a: GO:0019961 ! interferon binding
id: GO:0019966
name: interleukin-1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-1." [GOC:jl, ISBN:0198506732]
+def: "Binding to interleukin-1." [GOC:jl, ISBN:0198506732]
synonym: "IL-1 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146403,7 +146114,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019969
name: interleukin-10 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-10." [GOC:jl]
+def: "Binding to interleukin-10." [GOC:jl]
synonym: "IL-10 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146412,7 +146123,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019970
name: interleukin-11 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-11." [GOC:jl]
+def: "Binding to interleukin-11." [GOC:jl]
synonym: "IL-11 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146421,7 +146132,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019972
name: interleukin-12 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-12." [GOC:jl]
+def: "Binding to interleukin-12." [GOC:jl]
synonym: "IL-12 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -146429,23 +146140,24 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019973
name: interleukin-13 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-13." [GOC:jl]
+def: "Binding to interleukin-13." [GOC:jl]
synonym: "IL-13 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
[Term]
id: GO:0019974
-name: interleukin-14 binding
+name: obsolete interleukin-14 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-14." [GOC:jl]
+def: "OBSOLETE. Binding to interleukin-14." [GOC:jl]
+comment: This term was obsoleted because the gene was shown not to exist, see PMID:8755619.
synonym: "IL-14 binding" EXACT []
-is_a: GO:0019955 ! cytokine binding
+is_obsolete: true
[Term]
id: GO:0019975
name: interleukin-17 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the interleukin-17 family of cytokines." [GOC:add, GOC:jl]
+def: "Binding to a member of the interleukin-17 family of cytokines." [GOC:add, GOC:jl]
synonym: "IL-17 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -146453,7 +146165,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019976
name: interleukin-2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-2." [GOC:jl]
+def: "Binding to interleukin-2." [GOC:jl]
synonym: "IL-2 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146462,7 +146174,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019977
name: interleukin-21 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-21." [GOC:jl]
+def: "Binding to interleukin-21." [GOC:jl]
synonym: "IL-21 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -146470,7 +146182,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019978
name: interleukin-3 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-3." [GOC:jl]
+def: "Binding to interleukin-3." [GOC:jl]
synonym: "IL-3 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146479,7 +146191,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019979
name: interleukin-4 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-4." [GOC:jl]
+def: "Binding to interleukin-4." [GOC:jl]
synonym: "IL-4 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146488,7 +146200,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019980
name: interleukin-5 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-5." [GOC:jl]
+def: "Binding to interleukin-5." [GOC:jl]
synonym: "IL-5 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146497,7 +146209,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019981
name: interleukin-6 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-6." [GOC:jl]
+def: "Binding to interleukin-6." [GOC:jl]
synonym: "IL-6 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146506,7 +146218,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019982
name: interleukin-7 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-7." [GOC:jl]
+def: "Binding to interleukin-7." [GOC:jl]
synonym: "IL-7 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146515,7 +146227,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0019983
name: interleukin-9 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-9." [GOC:jl]
+def: "Binding to interleukin-9." [GOC:jl]
synonym: "IL-9 binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0019955 ! cytokine binding
@@ -146581,7 +146293,7 @@ relationship: part_of GO:0043297 ! apical junction assembly
id: GO:0019992
name: diacylglycerol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with diacylglycerol, a diester of glycerol and two fatty acids." [GOC:ma]
+def: "Binding to a diacylglycerol, a diester of glycerol and two fatty acids." [GOC:ma]
is_a: GO:0008289 ! lipid binding
[Term]
@@ -146865,7 +146577,7 @@ is_a: GO:0033655 ! host cell cytoplasm part
id: GO:0020037
name: heme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring." [GOC:ai]
+def: "Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring." [GOC:ai]
synonym: "haem binding" EXACT []
is_a: GO:0046906 ! tetrapyrrole binding
@@ -148660,7 +148372,6 @@ name: developmental maturation
namespace: biological_process
def: "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid]
subset: goslim_chembl
-subset: goslim_generic
is_a: GO:0032502 ! developmental process
[Term]
@@ -149519,9 +149230,11 @@ is_a: GO:0021795 ! cerebral cortex cell migration
[Term]
id: GO:0021801
-name: cerebral cortex radial glia guided migration
+name: cerebral cortex radial glia-guided migration
namespace: biological_process
def: "The radial migration of neuronal or glial precursor cells along radial glial cells during the development of the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695]
+synonym: "cerebral cortex radial glia guided migration" EXACT []
+synonym: "cerebral cortex radial glia-dependent cell migration" EXACT []
synonym: "glial-guided locomotion" RELATED [PMID:12626695]
is_a: GO:0021799 ! cerebral cortex radially oriented cell migration
is_a: GO:0022030 ! telencephalon glial cell migration
@@ -149624,7 +149337,7 @@ namespace: biological_process
def: "The changes in adhesion between neuronal cells and glial cells as a component of the process of cerebral cortex glial-mediated radial cell migration." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695]
synonym: "neuronal-glial interaction involved in cerebral cortex glial-mediated radial migration" EXACT [GOC:dph]
is_a: GO:0098609 ! cell-cell adhesion
-relationship: part_of GO:0021801 ! cerebral cortex radial glia guided migration
+relationship: part_of GO:0021801 ! cerebral cortex radial glia-guided migration
[Term]
id: GO:0021813
@@ -149643,7 +149356,7 @@ def: "The movement of a cell along the process of a radial glial cell involved i
synonym: "cell locomotion involved in cerebral cortex glial-mediated radial migration" EXACT [GOC:dph]
synonym: "cell locomotion involved in cerebral cortex radial glia guided migration" RELATED [GOC:dph]
is_a: GO:0048870 ! cell motility
-relationship: part_of GO:0021801 ! cerebral cortex radial glia guided migration
+relationship: part_of GO:0021801 ! cerebral cortex radial glia-guided migration
[Term]
id: GO:0021815
@@ -149688,7 +149401,7 @@ namespace: biological_process
def: "The detachment of cells from radial glial fibers at the appropriate time when they cease to migrate and form distinct layer in the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695]
synonym: "cerebral cortex lamination" RELATED [PMID:12626695]
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
-relationship: part_of GO:0021801 ! cerebral cortex radial glia guided migration
+relationship: part_of GO:0021801 ! cerebral cortex radial glia-guided migration
[Term]
id: GO:0021820
@@ -149974,12 +149687,13 @@ is_a: GO:0021848 ! neuroblast division in subpallium
[Term]
id: GO:0021852
-name: pyramidal neuron migration
+name: pyramidal neuron migration to cerebral cortex
namespace: biological_process
-def: "The migration of pyramidal a neuron precursor from the ventricular zone to the correct layer of the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695]
+def: "The migration of a pyramidal neuron precursor from the ventricular zone to the correct layer of the cerebral cortex." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695, PMID:22192824]
synonym: "projection neuron migration" RELATED [PMID:12626695]
-is_a: GO:0001764 ! neuron migration
-is_a: GO:0021801 ! cerebral cortex radial glia guided migration
+synonym: "pyramidal neuron migration" BROAD []
+is_a: GO:0021801 ! cerebral cortex radial glia-guided migration
+is_a: GO:0140650 ! radial glia-guided pyramidal neuron migration
relationship: part_of GO:0021860 ! pyramidal neuron development
[Term]
@@ -150028,7 +149742,7 @@ name: pyramidal neuron differentiation
namespace: biological_process
def: "The process in which a neuroblast or one of its progeny commits to a pyramidal neuron fate, migrates from the ventricular zone to the appropriate layer in the cortex and develops into a mature neuron." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid]
synonym: "projection neuron differentiation" BROAD [PMID:16226447]
-is_a: GO:0021953 ! central nervous system neuron differentiation
+is_a: GO:0030182 ! neuron differentiation
[Term]
id: GO:0021860
@@ -150215,7 +149929,6 @@ namespace: biological_process
def: "The series of molecular signals initiated by binding of Wnt protein to a receptor on the surface of the target cell that contributes to the commitment of a neuroblast to aneuronal fate. The neuron will reside in the forebrain." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:16226447]
synonym: "Wnt receptor signaling pathway involved in forebrain neuron fate commitment" EXACT []
synonym: "Wnt receptor signalling pathway involved in forebrain neuron fate commitment" EXACT []
-synonym: "Wnt-activated signaling pathway involved in forebrain neuron fate commitment" RELATED [GOC:signaling]
is_a: GO:0016055 ! Wnt signaling pathway
relationship: part_of GO:0021898 ! commitment of multipotent stem cells to neuronal lineage in forebrain
@@ -150284,7 +149997,7 @@ id: GO:0021889
name: olfactory bulb interneuron differentiation
namespace: biological_process
def: "The process in which a neuroblast acquires specialized features of an interneuron residing in the olfactory bulb." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695]
-is_a: GO:0021879 ! forebrain neuron differentiation
+is_a: GO:0030182 ! neuron differentiation
relationship: part_of GO:0021772 ! olfactory bulb development
[Term]
@@ -150300,7 +150013,7 @@ id: GO:0021891
name: olfactory bulb interneuron development
namespace: biological_process
def: "The process whose specific outcome is the progression of an interneuron residing in the olfactory bulb, from its initial commitment, to the fully functional differentiated cell." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:12626695]
-is_a: GO:0021884 ! forebrain neuron development
+is_a: GO:0048666 ! neuron development
relationship: part_of GO:0021889 ! olfactory bulb interneuron differentiation
[Term]
@@ -151345,7 +151058,6 @@ name: central nervous system vasculogenesis
namespace: biological_process
def: "The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid]
is_a: GO:0001570 ! vasculogenesis
-relationship: part_of GO:0014045 ! establishment of endothelial blood-brain barrier
[Term]
id: GO:0022010
@@ -151646,7 +151358,6 @@ name: membrane docking
namespace: biological_process
def: "The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere." [GOC:isa_complete, PMID:27875684]
subset: goslim_pir
-synonym: "membrane docking" EXACT []
is_a: GO:0009987 ! cellular process
[Term]
@@ -151727,6 +151438,7 @@ name: reproductive process
namespace: biological_process
alt_id: GO:0044702
def: "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:dph, GOC:isa_complete]
+subset: goslim_generic
synonym: "single organism reproductive process" RELATED []
is_a: GO:0008150 ! biological_process
relationship: part_of GO:0000003 ! reproduction
@@ -151752,6 +151464,7 @@ id: GO:0022600
name: digestive system process
namespace: biological_process
def: "A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." [GOC:isa_complete, GOC:jid, GOC:mtg_cardio]
+subset: goslim_generic
is_a: GO:0003008 ! system process
relationship: part_of GO:0007586 ! digestion
@@ -151818,7 +151531,6 @@ namespace: biological_process
alt_id: GO:0071844
def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
synonym: "cell structure assembly" EXACT []
synonym: "cellular component assembly at cellular level" EXACT []
@@ -151912,11 +151624,10 @@ name: ribonucleoprotein complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl]
subset: goslim_chembl
-subset: goslim_generic
synonym: "protein-RNA complex assembly" EXACT []
synonym: "RNA-protein complex assembly" EXACT []
synonym: "RNP complex assembly" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
is_a: GO:0071826 ! ribonucleoprotein complex subunit organization
relationship: part_of GO:0022613 ! ribonucleoprotein complex biogenesis
@@ -152325,7 +152036,6 @@ alt_id: GO:0022892
def: "Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other." [GOC:jid, GOC:mtg_transport, ISBN:0815340729]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_yeast
synonym: "substrate-specific transmembrane transporter activity" RELATED []
synonym: "substrate-specific transporter activity" RELATED []
@@ -152611,7 +152321,7 @@ is_a: GO:0034762 ! regulation of transmembrane transport
id: GO:0022900
name: electron transport chain
namespace: biological_process
-def: "A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient." [GOC:mtg_electron_transport]
+def: "A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors." [GOC:mtg_electron_transport]
subset: goslim_pir
xref: Wikipedia:Electron_transport_chain
is_a: GO:0006091 ! generation of precursor metabolites and energy
@@ -152816,35 +152526,35 @@ relationship: part_of GO:0050852 ! T cell receptor signaling pathway
id: GO:0023023
name: MHC protein complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the major histocompatibility complex." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a major histocompatibility complex." [GOC:mtg_signal, GOC:vw]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0023024
name: MHC class I protein complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the class I major histocompatibility complex." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a class I major histocompatibility complex." [GOC:mtg_signal, GOC:vw]
is_a: GO:0023023 ! MHC protein complex binding
[Term]
id: GO:0023025
name: MHC class Ib protein complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the class Ib major histocompatibility complex." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a class Ib major histocompatibility complex." [GOC:mtg_signal, GOC:vw]
is_a: GO:0023023 ! MHC protein complex binding
[Term]
id: GO:0023026
name: MHC class II protein complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the class II major histocompatibility complex." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a class II major histocompatibility complex." [GOC:mtg_signal, GOC:vw]
is_a: GO:0023023 ! MHC protein complex binding
[Term]
id: GO:0023027
name: MHC class I protein binding, via antigen binding groove
namespace: molecular_function
-def: "Interacting selectively and non-covalently with major histocompatibility complex class I molecules via the antigen binding groove." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a major histocompatibility complex class I molecules via the antigen binding groove." [GOC:mtg_signal, GOC:vw]
is_a: GO:0042288 ! MHC class I protein binding
relationship: part_of GO:0023024 ! MHC class I protein complex binding
@@ -152852,21 +152562,21 @@ relationship: part_of GO:0023024 ! MHC class I protein complex binding
id: GO:0023028
name: MHC class I protein binding, via lateral surface
namespace: molecular_function
-def: "Interacting selectively and non-covalently with major histocompatibility complex class I molecules via the lateral surface." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a major histocompatibility complex class I molecules via the lateral surface." [GOC:mtg_signal, GOC:vw]
is_a: GO:0042288 ! MHC class I protein binding
[Term]
id: GO:0023029
name: MHC class Ib protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with major histocompatibility complex class Ib molecules." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a major histocompatibility complex class Ib molecules." [GOC:mtg_signal, GOC:vw]
is_a: GO:0042287 ! MHC protein binding
[Term]
id: GO:0023030
name: MHC class Ib protein binding, via antigen binding groove
namespace: molecular_function
-def: "Interacting selectively and non-covalently with major histocompatibility complex class Ib molecules via the antigen binding groove." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a major histocompatibility complex class Ib molecules via the antigen binding groove." [GOC:mtg_signal, GOC:vw]
is_a: GO:0023029 ! MHC class Ib protein binding
relationship: part_of GO:0023025 ! MHC class Ib protein complex binding
@@ -152874,7 +152584,7 @@ relationship: part_of GO:0023025 ! MHC class Ib protein complex binding
id: GO:0023031
name: MHC class Ib protein binding, via lateral surface
namespace: molecular_function
-def: "Interacting selectively and non-covalently with major histocompatibility complex class Ib molecules via the lateral surface." [GOC:mtg_signal, GOC:vw]
+def: "Binding to a major histocompatibility complex class Ib molecules via the lateral surface." [GOC:mtg_signal, GOC:vw]
is_a: GO:0023029 ! MHC class Ib protein binding
[Term]
@@ -153053,6 +152763,7 @@ def: "The entirety of a process in which information is transmitted within a bio
comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
subset: goslim_agr
subset: goslim_flybase_ribbon
+subset: goslim_generic
subset: goslim_mouse
subset: goslim_pombe
subset: goslim_yeast
@@ -153536,7 +153247,6 @@ id: GO:0030036
name: actin cytoskeleton organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins." [GOC:dph, GOC:jl, GOC:mah]
-subset: goslim_drosophila
subset: goslim_pombe
synonym: "actin cytoskeleton organisation" EXACT []
synonym: "actin cytoskeleton organization and biogenesis" RELATED [GOC:mah]
@@ -153718,16 +153428,13 @@ is_a: GO:0005911 ! cell-cell junction
id: GO:0030058
name: amine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: R-CH2-NH2 + H2O + acceptor = R-CHO + NH3 + reduced acceptor." [EC:1.4.9.1]
-synonym: "amine: (acceptor) oxidoreductase (deaminating)" RELATED [EC:1.4.9.1]
-synonym: "MADH activity" RELATED [EC:1.4.9.1]
-synonym: "methylamine dehydrogenase activity" RELATED [EC:1.4.9.1]
-synonym: "primary-amine dehydrogenase activity" BROAD [EC:1.4.9.1]
-synonym: "primary-amine:(acceptor) oxidoreductase (deaminating)" RELATED [EC:1.4.9.1]
-synonym: "primary-amine:acceptor oxidoreductase (deaminating)" RELATED [EC:1.4.9.1]
-xref: EC:1.4.9.1
-xref: MetaCyc:AMINE-DEHYDROGENASE-RXN
-xref: RHEA:30207
+def: "Catalysis of the reaction: an aliphatic amine + an acceptor (A) + H2O = an aldehyde + a reduced acceptor (AH2) + NH4+." [PMID:6246962, RHEA:51128]
+synonym: "amine: (acceptor) oxidoreductase (deaminating)" RELATED []
+synonym: "MADH activity" RELATED []
+synonym: "methylamine dehydrogenase activity" RELATED []
+synonym: "primary-amine dehydrogenase activity" BROAD []
+synonym: "primary-amine:acceptor oxidoreductase (deaminating)" RELATED []
+xref: RHEA:51128
xref: UM-BBD_enzymeID:e0058
is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
@@ -153735,12 +153442,9 @@ is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors
id: GO:0030059
name: aralkylamine dehydrogenase (azurin) activity
namespace: molecular_function
-def: "Catalysis of the reaction: H(2)O + arCH(2)NH(2) + 2 azurin = 2 reduced azurin + ArCHO + NH(3). The symbol arCH(2)NH(2) represents an aralkylamine and ArCHO is an aryl aldehyde." [EC:1.4.9.2]
-synonym: "aralkylamine:(azurin) oxidoreductase (deaminating) activity" RELATED [EC:1.4.9.2]
-synonym: "aromatic amine dehydrogenase (azurin) activity" RELATED [EC:1.4.9.2]
-synonym: "arylamine dehydrogenase activity" BROAD [EC:1.4.9.2]
-synonym: "dehydrogenase, arylamine (azurin) activity" RELATED [EC:1.4.9.2]
-synonym: "tyramine dehydrogenase (azurin) activity" NARROW [EC:1.4.9.2]
+def: "Catalysis of the reaction: an aralkylamine + H2O + 2 oxidized [azurin] = an aromatic aldehyde + 2 H+ + NH4+ + 2 reduced [azurin]." [PMID:10506161, RHEA:47796]
+synonym: "aralkylamine:(azurin) oxidoreductase (deaminating) activity" EXACT [EC:1.4.9.2]
+synonym: "aromatic amine dehydrogenase (azurin) activity" EXACT [EC:1.4.9.2]
xref: EC:1.4.9.2
xref: MetaCyc:ARALKYLAMINE-DEHYDROGENASE-RXN
xref: RHEA:47796
@@ -154543,8 +154247,9 @@ is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
id: GO:0030145
name: manganese ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with manganese (Mn) ions." [GOC:ai]
+def: "Binding to a manganese ion (Mn)." [GOC:ai]
synonym: "manganese binding" EXACT []
+synonym: "Mn binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
[Term]
@@ -154606,6 +154311,7 @@ def: "The import of proteins across the outer and inner mitochondrial membranes
synonym: "mitochondrial matrix protein import" EXACT []
synonym: "mitochondrial translocation" BROAD []
synonym: "protein transport into mitochondrial matrix" EXACT []
+is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0044743 ! protein transmembrane import into intracellular organelle
is_a: GO:0065002 ! intracellular protein transmembrane transport
is_a: GO:0072655 ! establishment of protein localization to mitochondrion
@@ -154616,7 +154322,8 @@ relationship: part_of GO:0006626 ! protein targeting to mitochondrion
id: GO:0030151
name: molybdenum ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with molybdenum (Mo) ions." [GOC:ai]
+def: "Binding to a molybdenum ion (Mo)." [GOC:ai]
+synonym: "Mo ion binding" EXACT []
synonym: "molybdenum binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
@@ -154667,7 +154374,7 @@ relationship: regulates GO:0007155 ! cell adhesion
id: GO:0030156
name: benzodiazepine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the peripheral benzodiazepine receptor (PBR)." [GOC:ceb, GOC:mah, PMID:9915832]
+def: "Binding to a peripheral benzodiazepine receptor (PBR)." [GOC:ceb, GOC:mah, PMID:9915832]
synonym: "benzodiazepine receptor ligand" NARROW []
synonym: "diazepam binding inhibitor activity" RELATED []
is_a: GO:0005102 ! signaling receptor binding
@@ -154752,6 +154459,7 @@ comment: This term refers to the breakdown of mature proteins. For cleavage even
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pombe
synonym: "multicellular organismal protein catabolic process" NARROW []
synonym: "pheromone catabolic process" RELATED []
@@ -154776,7 +154484,7 @@ is_a: GO:0044257 ! cellular protein catabolic process
id: GO:0030165
name: PDZ domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins." [GOC:go_curators, Pfam:PF00595]
+def: "Binding to a PDZ domain of a protein, a domain found in diverse signaling proteins." [GOC:go_curators, Pfam:PF00595]
synonym: "DHR-domain binding" EXACT []
synonym: "GLGF-domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -154817,7 +154525,7 @@ relationship: part_of GO:0007596 ! blood coagulation
id: GO:0030169
name: low-density lipoprotein particle binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a low-density lipoprotein particle, a lipoprotein particle that is rich in cholesterol esters and low in triglycerides, is typically composed of APOB100 and APOE, and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm." [GOC:mah]
+def: "Binding to a low-density lipoprotein particle, a lipoprotein particle that is rich in cholesterol esters and low in triglycerides, is typically composed of APOB100 and APOE, and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm." [GOC:mah]
subset: goslim_chembl
synonym: "LDL binding" EXACT []
is_a: GO:0071813 ! lipoprotein particle binding
@@ -154826,7 +154534,7 @@ is_a: GO:0071813 ! lipoprotein particle binding
id: GO:0030170
name: pyridoxal phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6." [GOC:mah, ISBN:0198506732]
+def: "Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6." [GOC:mah, ISBN:0198506732]
subset: goslim_metagenomics
is_a: GO:0043168 ! anion binding
is_a: GO:0070279 ! vitamin B6 binding
@@ -154845,7 +154553,7 @@ is_a: GO:0022843 ! voltage-gated cation channel activity
id: GO:0030172
name: troponin C binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with troponin C, the calcium-binding subunit of the troponin complex." [GOC:mah, ISBN:0815316194]
+def: "Binding to troponin C, the calcium-binding subunit of the troponin complex." [GOC:mah, ISBN:0815316194]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
@@ -155156,6 +154864,7 @@ name: extracellular matrix organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix." [GOC:mah]
subset: goslim_chembl
+subset: goslim_drosophila
subset: goslim_generic
synonym: "extracellular matrix organisation" EXACT []
synonym: "extracellular matrix organization and biogenesis" RELATED [GOC:mah]
@@ -155211,7 +154920,7 @@ is_a: GO:1903510 ! mucopolysaccharide metabolic process
id: GO:0030203
name: glycosaminoglycan metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties." [ISBN:0192800981]
+def: "The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars." [ISBN:0192800981]
synonym: "glycosaminoglycan metabolism" EXACT []
is_a: GO:0006022 ! aminoglycan metabolic process
@@ -155367,7 +155076,7 @@ is_a: GO:0030212 ! hyaluronan metabolic process
id: GO:0030215
name: semaphorin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with semaphorin receptors." [GOC:ceb, PMID:12001990]
+def: "Binding to a semaphorin receptor." [GOC:ceb, PMID:12001990]
synonym: "plexin binding" NARROW []
synonym: "plexin ligand" NARROW []
synonym: "semaphorin receptor ligand" NARROW []
@@ -155535,13 +155244,12 @@ name: enzyme regulator activity
namespace: molecular_function
alt_id: GO:0010576
def: "Binds to and modulates the activity of an enzyme." [GOC:dph, GOC:mah, GOC:tb]
-comment: GO:0030234 is reserved for cases when the regulator directly interacts with the enzyme. When regulation of enzyme activity is achieved without enzyme binding, or when the mechanism of regulation is unknown, instead annotate to 'regulation of catalytic activity ; GO:0050790'.
+comment: This term should only be used in cases when the regulator directly interacts with the enzyme.
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_mouse
subset: goslim_pir
subset: goslim_plant
@@ -155583,8 +155291,8 @@ namespace: biological_process
def: "Formation of myofibrils, the repeating units of striated muscle." [GOC:mah]
is_a: GO:0010927 ! cellular component assembly involved in morphogenesis
is_a: GO:0031032 ! actomyosin structure organization
-is_a: GO:0070925 ! organelle assembly
is_a: GO:0097435 ! supramolecular fiber organization
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
relationship: part_of GO:0055002 ! striated muscle cell development
[Term]
@@ -155652,7 +155360,7 @@ id: GO:0030246
name: carbohydrate binding
namespace: molecular_function
alt_id: GO:0005529
-def: "Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates." [GOC:mah]
+def: "Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates." [GOC:mah]
subset: goslim_agr
subset: goslim_chembl
subset: goslim_drosophila
@@ -155669,7 +155377,7 @@ id: GO:0030247
name: polysaccharide binding
namespace: molecular_function
alt_id: GO:0002506
-def: "Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [GOC:mah]
+def: "Binding to a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [GOC:mah]
synonym: "polysaccharide assembly with MHC class II protein complex" NARROW []
is_a: GO:0030246 ! carbohydrate binding
@@ -155677,7 +155385,7 @@ is_a: GO:0030246 ! carbohydrate binding
id: GO:0030248
name: cellulose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cellulose." [GOC:mah]
+def: "Binding to cellulose." [GOC:mah]
is_a: GO:0030247 ! polysaccharide binding
[Term]
@@ -155971,21 +155679,21 @@ is_a: GO:0016500 ! protein-hormone receptor activity
id: GO:0030274
name: LIM domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a LIM domain (for Lin-11 Isl-1 Mec-3) of a protein, a domain with seven conserved cysteine residues and a histidine, that binds two zinc ions and acts as an interface for protein-protein interactions." [GOC:go_curators, Pfam:PF00412]
+def: "Binding to a LIM domain (for Lin-11 Isl-1 Mec-3) of a protein, a domain with seven conserved cysteine residues and a histidine, that binds two zinc ions and acts as an interface for protein-protein interactions." [GOC:go_curators, Pfam:PF00412]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0030275
name: LRR domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a LRR domain (leucine rich repeats) of a protein." [GOC:go_curators, Pfam:PF00560]
+def: "Binding to a LRR domain (leucine rich repeats) of a protein." [GOC:go_curators, Pfam:PF00560]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0030276
name: clathrin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles." [GOC:jl, GOC:mah, ISBN:0198506732]
+def: "Binding to a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles." [GOC:jl, GOC:mah, ISBN:0198506732]
is_a: GO:0005515 ! protein binding
[Term]
@@ -156138,7 +155846,6 @@ name: protein tyrosine kinase inhibitor activity
namespace: molecular_function
def: "Stops, prevents or reduces the activity of a protein tyrosine kinase." [GOC:mah]
is_a: GO:0004860 ! protein kinase inhibitor activity
-is_a: GO:0030234 ! enzyme regulator activity
[Term]
id: GO:0030293
@@ -156490,7 +156197,7 @@ name: prenylcysteine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving prenylcysteine, 3-methyl-2-buten-1-yl-cysteine, a derivative of the amino acid cysteine formed by the covalent addition of a prenyl residue." [GOC:ai, PMID:16627894]
synonym: "prenylcysteine metabolism" EXACT []
-is_a: GO:1901564 ! organonitrogen compound metabolic process
+is_a: GO:0006575 ! cellular modified amino acid metabolic process
[Term]
id: GO:0030330
@@ -156509,14 +156216,14 @@ is_a: GO:0072331 ! signal transduction by p53 class mediator
id: GO:0030331
name: estrogen receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an estrogen receptor." [GOC:ai]
+def: "Binding to an estrogen receptor." [GOC:ai]
is_a: GO:0016922 ! nuclear receptor binding
[Term]
id: GO:0030332
name: cyclin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cyclins, proteins whose levels in a cell varies markedly during the cell cycle, rising steadily until mitosis, then falling abruptly to zero. As cyclins reach a threshold level, they are thought to drive cells into G2 phase and thus to mitosis." [GOC:ai]
+def: "Binding to cyclins, proteins whose levels in a cell varies markedly during the cell cycle, rising steadily until mitosis, then falling abruptly to zero. As cyclins reach a threshold level, they are thought to drive cells into G2 phase and thus to mitosis." [GOC:ai]
is_a: GO:0005515 ! protein binding
[Term]
@@ -156660,7 +156367,7 @@ is_a: GO:0030021 ! extracellular matrix structural constituent conferring compre
id: GO:0030346
name: protein phosphatase 2B binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme protein phosphatase 2B." [GOC:jl]
+def: "Binding to a protein phosphatase 2B." [GOC:jl]
synonym: "calcineurin binding" EXACT []
synonym: "protein phosphatase 3 binding" RELATED [GOC:dph, GOC:rl]
is_a: GO:0019903 ! protein phosphatase binding
@@ -156669,14 +156376,14 @@ is_a: GO:0019903 ! protein phosphatase binding
id: GO:0030348
name: syntaxin-3 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the SNAP receptor syntaxin-3." [GOC:ai]
+def: "Binding to a syntaxin-3 SNAP receptor." [GOC:ai]
is_a: GO:0019905 ! syntaxin binding
[Term]
id: GO:0030350
name: iron-responsive element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the iron-responsive element, a regulatory sequence found in the 5'- and 3'-untranslated regions of mRNAs encoding many iron-binding proteins." [PMID:3198610, PMID:8710843]
+def: "Binding to an iron-responsive element, a regulatory sequence found in the 5'- and 3'-untranslated regions of mRNAs encoding many iron-binding proteins." [PMID:3198610, PMID:8710843]
synonym: "IRE binding" EXACT []
is_a: GO:0003729 ! mRNA binding
@@ -156785,7 +156492,7 @@ is_a: GO:0016783 ! sulfurtransferase activity
id: GO:0030367
name: interleukin-17 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-17 receptor." [GOC:ai]
+def: "Binding to an interleukin-17 receptor." [GOC:ai]
synonym: "IL-17" NARROW []
synonym: "interleukin-17 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -156812,7 +156519,7 @@ is_a: GO:0004888 ! transmembrane signaling receptor activity
id: GO:0030370
name: intercellular adhesion molecule-3 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with receptors for intercellular adhesion molecule-3 (ICAM-3), such as DC-SIGN and LFA-1." [GOC:ceb, PMID:11473836]
+def: "Binding to a receptor for intercellular adhesion molecule-3 (ICAM-3), such as DC-SIGN and LFA-1." [GOC:ceb, PMID:11473836]
synonym: "ICAM-3 receptor binding" EXACT []
synonym: "ICAM-3 receptor ligand" NARROW []
synonym: "intercellular adhesion molecule-3 receptor ligand" NARROW []
@@ -156829,7 +156536,7 @@ is_a: GO:0045182 ! translation regulator activity
id: GO:0030372
name: high molecular weight B cell growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the high molecular weight B cell growth factor receptor." [GOC:ai]
+def: "Binding to a high molecular weight B cell growth factor receptor." [GOC:ai]
synonym: "high molecular weight B cell growth factor receptor ligand" NARROW []
synonym: "high molecular weight B lymphocyte growth factor receptor binding" EXACT []
synonym: "high molecular weight B-cell growth factor receptor binding" EXACT []
@@ -156910,7 +156617,7 @@ is_a: GO:0004888 ! transmembrane signaling receptor activity
id: GO:0030380
name: interleukin-17E receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-17E receptor." [GOC:ai]
+def: "Binding to an interleukin-17E receptor." [GOC:ai]
synonym: "IL-17E" NARROW []
synonym: "interleukin-17E receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -157018,7 +156725,7 @@ is_a: GO:0030389 ! fructosamine metabolic process
id: GO:0030395
name: lactose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lactose, a disaccharide of glucose and galactose, the carbohydrate of milk." [GOC:jl, ISBN:0192800981]
+def: "Binding to lactose, a disaccharide of glucose and galactose, the carbohydrate of milk." [GOC:jl, ISBN:0192800981]
is_a: GO:0048030 ! disaccharide binding
[Term]
@@ -157306,6 +157013,7 @@ namespace: biological_process
def: "The expulsion of feces from the rectum." [GOC:mah]
xref: Wikipedia:Defecation
is_a: GO:0007588 ! excretion
+is_a: GO:0022600 ! digestive system process
[Term]
id: GO:0030422
@@ -157716,7 +157424,7 @@ synonym: "chromatin silencing at silent mating-type cassette" EXACT []
synonym: "establishment of chromatin silencing at silent mating-type cassette" RELATED []
synonym: "heterochromatic silencing at silent mating-type cassette" EXACT []
synonym: "silent mating-type cassette chromatin silencing" EXACT [GOC:mah]
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0140719 ! constitutive heterochromatin assembly
[Term]
id: GO:0030470
@@ -157882,7 +157590,7 @@ is_a: GO:0006259 ! DNA metabolic process
id: GO:0030492
name: hemoglobin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin." [GOC:jl]
+def: "Binding to hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin." [GOC:jl]
synonym: "globin binding" BROAD []
synonym: "haemoglobin binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -157993,14 +157701,14 @@ is_a: GO:0015698 ! inorganic anion transport
id: GO:0030506
name: ankyrin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ankyrin, a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane proteins." [GOC:mah, ISBN:0198506732]
+def: "Binding to ankyrin, a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane proteins." [GOC:mah, ISBN:0198506732]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
id: GO:0030507
name: spectrin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers." [GOC:mah, ISBN:0198506732]
+def: "Binding to spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers." [GOC:mah, ISBN:0198506732]
is_a: GO:0008092 ! cytoskeletal protein binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -158136,7 +157844,7 @@ relationship: negatively_regulates GO:0030509 ! BMP signaling pathway
id: GO:0030515
name: snoRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with small nucleolar RNA." [GOC:mah]
+def: "Binding to a small nucleolar RNA." [GOC:mah]
is_a: GO:0003723 ! RNA binding
[Term]
@@ -158177,7 +157885,7 @@ is_a: GO:0043401 ! steroid hormone mediated signaling pathway
id: GO:0030519
name: snoRNP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of a small nucleolar ribonucleoprotein particle." [GOC:mah]
+def: "Binding to a small nucleolar ribonucleoprotein particle." [GOC:mah]
is_a: GO:0043021 ! ribonucleoprotein complex binding
[Term]
@@ -158291,7 +157999,6 @@ comment: Note that this term can be used in place of the obsolete term 'transfer
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_yeast
synonym: "transfer RNA" RELATED []
synonym: "tRNA" RELATED []
@@ -158388,7 +158095,7 @@ is_a: GO:0030541 ! plasmid partitioning
id: GO:0030544
name: Hsp70 protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size." [ISBN:0198506732]
+def: "Binding to a Hsp70 protein, heat shock proteins around 70kDa in size." [ISBN:0198506732]
is_a: GO:0031072 ! heat shock protein binding
[Term]
@@ -158406,7 +158113,7 @@ namespace: molecular_function
def: "The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased." [GOC:ceb]
synonym: "receptor activator activity" BROAD []
synonym: "signalling receptor activator activity" EXACT []
-is_a: GO:0003674 ! molecular_function
+is_a: GO:0030545 ! signaling receptor regulator activity
[Term]
id: GO:0030547
@@ -158421,7 +158128,6 @@ id: GO:0030548
name: acetylcholine receptor regulator activity
namespace: molecular_function
def: "Interacting (directly or indirectly) with acetylcholine receptors such that the proportion of receptors in the active form is changed." [GOC:mah]
-is_a: GO:0030545 ! signaling receptor regulator activity
is_a: GO:0099602 ! neurotransmitter receptor regulator activity
[Term]
@@ -158444,14 +158150,14 @@ is_a: GO:0030548 ! acetylcholine receptor regulator activity
id: GO:0030551
name: cyclic nucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:ai]
+def: "Binding to a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue." [GOC:ai]
is_a: GO:0000166 ! nucleotide binding
[Term]
id: GO:0030552
name: cAMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate)." [GOC:ai]
+def: "Binding to cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate)." [GOC:ai]
synonym: "3',5' cAMP binding" EXACT []
synonym: "3',5'-cAMP binding" EXACT []
synonym: "adenosine 3',5'-cyclophosphate binding" EXACT []
@@ -158464,7 +158170,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0030553
name: cGMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate)." [GOC:ai]
+def: "Binding to cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate)." [GOC:ai]
synonym: "3',5' cGMP binding" EXACT []
synonym: "3',5'-cGMP binding" EXACT []
synonym: "cyclic GMP binding" EXACT []
@@ -158476,7 +158182,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0030554
name: adenyl nucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with adenyl nucleotides, any compound consisting of adenosine esterified with (ortho)phosphate." [ISBN:0198506732]
+def: "Binding to an adenyl nucleotide, an adenosine esterified with (ortho)phosphate." [ISBN:0198506732]
subset: goslim_chembl
is_a: GO:0017076 ! purine nucleotide binding
@@ -158486,7 +158192,6 @@ name: RNA modification guide activity
namespace: molecular_function
def: "Specifies the site of a posttranscriptional modification in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
comment: Note that this term describes the activity of a nucleic acid, usually RNA, gene product that interacts with other RNA molecules via base pairing; it should not be used to annotate proteins.
-subset: goslim_generic
subset: goslim_yeast
is_a: GO:0003723 ! RNA binding
@@ -158807,7 +158512,7 @@ is_a: GO:0004611 ! phosphoenolpyruvate carboxykinase activity
id: GO:0030586
name: [methionine synthase] reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: [methionine synthase]-cob(II)alamin + NADPH + H+ + S-adenosyl methionine => [methionine synthase]-methylcob(I)alamin + S-adenosylhomocysteine + NADP+." [RHEA:23910]
+def: "Catalysis of the reaction: [methionine synthase]-cob(II)alamin + NADPH + H+ + S-adenosyl methionine = [methionine synthase]-methylcob(I)alamin + S-adenosylhomocysteine + NADP+." [RHEA:23908]
comment: Formerly EC:2.1.1.135.
synonym: "5-methyltetrahydrofolate-homocysteine methyltransferase reductase" RELATED []
synonym: "[methionine synthase]-cobalamin methyltransferase (cob(II)alamin reducing) activity" EXACT []
@@ -158818,7 +158523,7 @@ synonym: "methionine synthase-methylcob(I)alamin,S-adenosylhomocysteine:NADP+ ox
xref: EC:1.16.1.8
xref: MetaCyc:2.1.1.135-RXN
xref: Reactome:R-HSA-3149518 "MTRR reduces cob(II)alamin to meCbl"
-xref: RHEA:23910
+xref: RHEA:23908
is_a: GO:0016723 ! oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor
[Term]
@@ -158830,7 +158535,7 @@ synonym: "fruiting body development" BROAD []
synonym: "fruiting body formation" BROAD []
synonym: "sorocarp biosynthesis" EXACT []
synonym: "sorocarp formation" EXACT []
-is_a: GO:0090702 ! non-reproductive fruiting body development
+is_a: GO:0099120 ! socially cooperative development
[Term]
id: GO:0030588
@@ -159113,7 +158818,7 @@ consider: GO:0003712
id: GO:0030619
name: U1 snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U1 small nuclear RNA (U1 snRNA)." [GOC:mah]
+def: "Binding to a U1 small nuclear RNA (U1 snRNA)." [GOC:mah]
comment: Note that this term may be useful for annotating other small nuclear RNAs (snRNAs).
is_a: GO:0017069 ! snRNA binding
@@ -159121,56 +158826,56 @@ is_a: GO:0017069 ! snRNA binding
id: GO:0030620
name: U2 snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U2 small nuclear RNA (U2 snRNA)." [GOC:jl]
+def: "Binding to a U2 small nuclear RNA (U2 snRNA)." [GOC:jl]
is_a: GO:0017069 ! snRNA binding
[Term]
id: GO:0030621
name: U4 snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U4 small nuclear RNA (U4 snRNA)." [GOC:jl]
+def: "Binding to a U4 small nuclear RNA (U4 snRNA)." [GOC:jl]
is_a: GO:0017069 ! snRNA binding
[Term]
id: GO:0030622
name: U4atac snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U4atac small nuclear RNA (U4atac snRNA)." [GOC:jl]
+def: "Binding to a U4atac small nuclear RNA (U4atac snRNA)." [GOC:jl]
is_a: GO:0017069 ! snRNA binding
[Term]
id: GO:0030623
name: U5 snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U5 small nuclear RNA (U5 snRNA)." [GOC:jl]
+def: "Binding to a U5 small nuclear RNA (U5 snRNA)." [GOC:jl]
is_a: GO:0017069 ! snRNA binding
[Term]
id: GO:0030624
name: U6atac snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U6atac small nuclear RNA (U6atac snRNA)." [GOC:jl]
+def: "Binding to a U6atac small nuclear RNA (U6atac snRNA)." [GOC:jl]
is_a: GO:0017069 ! snRNA binding
[Term]
id: GO:0030625
name: U11 snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U11 small nuclear RNA (U11 snRNA)." [GOC:jl]
+def: "Binding to a U11 small nuclear RNA (U11 snRNA)." [GOC:jl]
is_a: GO:0017069 ! snRNA binding
[Term]
id: GO:0030626
name: U12 snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U12 small nuclear RNA (U12 snRNA)." [GOC:jl]
+def: "Binding to a U12 small nuclear RNA (U12 snRNA)." [GOC:jl]
is_a: GO:0017069 ! snRNA binding
[Term]
id: GO:0030627
name: pre-mRNA 5'-splice site binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the pre-mRNA 5' splice site sequence." [GOC:jl]
+def: "Binding to a pre-mRNA 5' splice site sequence." [GOC:jl]
synonym: "pre-mRNA 5' splice site binding" EXACT []
is_a: GO:0036002 ! pre-mRNA binding
@@ -159178,7 +158883,7 @@ is_a: GO:0036002 ! pre-mRNA binding
id: GO:0030628
name: pre-mRNA 3'-splice site binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the pre-mRNA 3' splice site sequence." [GOC:jl]
+def: "Binding to a pre-mRNA 3' splice site sequence." [GOC:jl]
synonym: "pre-mRNA 3' splice site binding" EXACT []
is_a: GO:0036002 ! pre-mRNA binding
@@ -159186,7 +158891,7 @@ is_a: GO:0036002 ! pre-mRNA binding
id: GO:0030629
name: U6 snRNA 3'-end binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the 3' end of the U6 small nuclear RNA (U6 snRNA)." [GOC:mah]
+def: "Binding to a U6 small nuclear RNA (U6 snRNA) at the 3' end." [GOC:mah]
comment: Note that this term may be useful for annotating small nuclear RNAs (snRNAs).
synonym: "U6 snRNA 3' end binding" EXACT []
is_a: GO:0017070 ! U6 snRNA binding
@@ -159498,7 +159203,6 @@ name: cytoplasmic vesicle membrane
namespace: cellular_component
def: "The lipid bilayer surrounding a cytoplasmic vesicle." [GOC:mah]
is_a: GO:0012506 ! vesicle membrane
-is_a: GO:0043229 ! intracellular organelle
relationship: part_of GO:0031410 ! cytoplasmic vesicle
[Term]
@@ -159507,7 +159211,7 @@ name: Golgi-associated vesicle membrane
namespace: cellular_component
def: "The lipid bilayer surrounding a vesicle associated with the Golgi apparatus." [GOC:mah]
synonym: "Golgi vesicle membrane" RELATED []
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
is_a: GO:0098588 ! bounding membrane of organelle
relationship: part_of GO:0005798 ! Golgi-associated vesicle
@@ -159629,7 +159333,6 @@ name: protein-macromolecule adaptor activity
namespace: molecular_function
def: "The binding activity of a protein that brings together two or more macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid." [GOC:bf, GOC:mah, GOC:vw]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_yeast
synonym: "protein binding, bridging" EXACT []
synonym: "protein-protein adaptor" NARROW []
@@ -159958,7 +159661,6 @@ namespace: biological_process
def: "The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell." [GOC:mah]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
is_a: GO:0046907 ! intracellular transport
[Term]
@@ -160386,7 +160088,7 @@ is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
id: GO:0030742
name: GTP-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) when at least one of the interacting partners is in the GTP-bound state." [GOC:go_curators, GOC:krc]
+def: "Binding to a protein or protein complex when at least one of the interacting partners is in the GTP-bound state." [GOC:go_curators, GOC:krc]
comment: This term may be used to annotate both partners in a GTP-dependent binding interaction, both the GTP-bound protein and the protein(s) which interact with it.
is_a: GO:0005515 ! protein binding
@@ -161320,7 +161022,6 @@ synonym: "regulation of nucleotide breakdown" EXACT []
synonym: "regulation of nucleotide catabolism" EXACT []
synonym: "regulation of nucleotide degradation" EXACT []
is_a: GO:0006140 ! regulation of nucleotide metabolic process
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0031329 ! regulation of cellular catabolic process
relationship: regulates GO:0009166 ! nucleotide catabolic process
@@ -161337,7 +161038,6 @@ synonym: "negative regulation of nucleotide breakdown" EXACT []
synonym: "negative regulation of nucleotide catabolism" EXACT []
synonym: "negative regulation of nucleotide degradation" EXACT []
is_a: GO:0030811 ! regulation of nucleotide catabolic process
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
is_a: GO:0031330 ! negative regulation of cellular catabolic process
is_a: GO:0045980 ! negative regulation of nucleotide metabolic process
relationship: negatively_regulates GO:0009166 ! nucleotide catabolic process
@@ -161356,7 +161056,6 @@ synonym: "up regulation of nucleotide catabolic process" EXACT []
synonym: "up-regulation of nucleotide catabolic process" EXACT []
synonym: "upregulation of nucleotide catabolic process" EXACT []
is_a: GO:0030811 ! regulation of nucleotide catabolic process
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
is_a: GO:0031331 ! positive regulation of cellular catabolic process
is_a: GO:0045981 ! positive regulation of nucleotide metabolic process
relationship: positively_regulates GO:0009166 ! nucleotide catabolic process
@@ -162232,7 +161931,7 @@ is_a: GO:0140535 ! intracellular protein-containing complex
id: GO:0030881
name: beta-2-microglobulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with beta-2-microglobulin." [GOC:mah]
+def: "Binding to beta-2-microglobulin." [GOC:mah]
subset: goslim_chembl
is_a: GO:0005515 ! protein binding
@@ -162240,7 +161939,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0030882
name: lipid antigen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lipid antigen." [PMID:14500461]
+def: "Binding to a lipid antigen." [PMID:14500461]
is_a: GO:0003823 ! antigen binding
is_a: GO:0008289 ! lipid binding
@@ -162248,14 +161947,14 @@ is_a: GO:0008289 ! lipid binding
id: GO:0030883
name: endogenous lipid antigen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an endogenous cellular lipid antigen." [PMID:14500461]
+def: "Binding to an endogenous cellular lipid antigen." [PMID:14500461]
is_a: GO:0030882 ! lipid antigen binding
[Term]
id: GO:0030884
name: exogenous lipid antigen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an exogenous lipid antigen (examples include microbial lipids and glycolipids)." [PMID:14500461]
+def: "Binding to an exogenous lipid antigen (examples include microbial lipids and glycolipids)." [PMID:14500461]
is_a: GO:0030882 ! lipid antigen binding
[Term]
@@ -162410,7 +162109,7 @@ id: GO:0030899
name: calcium-dependent ATPase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate. This reaction requires the presence of calcium ion (Ca2+)." [GOC:mah]
-is_a: GO:0016887 ! ATPase
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0030900
@@ -162517,7 +162216,7 @@ relationship: part_of GO:0071699 ! olfactory placode morphogenesis
id: GO:0030911
name: TPR domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a tetratricopeptide repeat (TPR) domain of a protein, the consensus sequence of which is defined by a pattern of small and large hydrophobic amino acids and a structure composed of helices." [GOC:mah]
+def: "Binding to a tetratricopeptide repeat (TPR) domain of a protein, the consensus sequence of which is defined by a pattern of small and large hydrophobic amino acids and a structure composed of helices." [GOC:mah]
synonym: "tetratricopeptide repeat domain binding" EXACT [GOC:sl]
is_a: GO:0019904 ! protein domain specific binding
@@ -162541,16 +162240,6 @@ is_a: GO:0007043 ! cell-cell junction assembly
is_a: GO:0010927 ! cellular component assembly involved in morphogenesis
relationship: part_of GO:0032288 ! myelin assembly
-[Term]
-id: GO:0030914
-name: STAGA complex
-namespace: cellular_component
-def: "A large multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. The composition is similar to that of the SAGA complex; for example, the human complex contains the transcription-transformation cofactor TRRAP, hGCN5L acetylase, novel human ADA-like and SPT-like cofactors, and a subset of TAFs." [PMID:11564863]
-comment: See also the cellular component term 'SAGA complex ; GO:0000124'.
-synonym: "SPT3-TAF9-GCN5 acetylase complex" EXACT [GOC:rl, PMID:18838386]
-synonym: "STAGA coactivator complex" EXACT []
-is_a: GO:0070461 ! SAGA-type complex
-
[Term]
id: GO:0030915
name: Smc5-Smc6 complex
@@ -162760,14 +162449,14 @@ consider: GO:0048572
id: GO:0030941
name: chloroplast targeting sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chloroplast targeting sequence, a specific peptide sequence that acts as a signal to localize the protein within the chloroplast." [GOC:mah]
+def: "Binding to a chloroplast targeting sequence, a specific peptide sequence that acts as a signal to localize the protein within the chloroplast." [GOC:mah]
is_a: GO:0005048 ! signal sequence binding
[Term]
id: GO:0030942
name: endoplasmic reticulum signal peptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an endoplasmic reticulum signal peptide, a specific peptide sequence that acts as a signal to localize the protein within the endoplasmic reticulum." [GOC:mah]
+def: "Binding to an endoplasmic reticulum signal peptide, a specific peptide sequence that acts as a signal to localize the protein within the endoplasmic reticulum." [GOC:mah]
synonym: "ER signal peptide binding" EXACT []
is_a: GO:0005048 ! signal sequence binding
@@ -162775,7 +162464,7 @@ is_a: GO:0005048 ! signal sequence binding
id: GO:0030943
name: mitochondrion targeting sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mitochondrion targeting sequence, a specific peptide sequence that acts as a signal to localize the protein within the mitochondrion." [GOC:mah]
+def: "Binding to a mitochondrion targeting sequence, a specific peptide sequence that acts as a signal to localize the protein within the mitochondrion." [GOC:mah]
synonym: "mitochondrial targeting sequence binding" EXACT []
is_a: GO:0005048 ! signal sequence binding
@@ -162783,7 +162472,7 @@ is_a: GO:0005048 ! signal sequence binding
id: GO:0030944
name: DDEL sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a KDEL sequence, the C terminus tetrapeptide sequence Asp-Asp-Glu-Leu found in proteins that are to be retained in the endoplasmic reticulum." [GOC:mah]
+def: "Binding to a KDEL sequence, the C terminus tetrapeptide sequence Asp-Asp-Glu-Leu found in proteins that are to be retained in the endoplasmic reticulum." [GOC:mah]
is_a: GO:0046923 ! ER retention sequence binding
[Term]
@@ -162893,7 +162582,8 @@ is_a: GO:0051418 ! microtubule nucleation by microtubule organizing center
id: GO:0030955
name: potassium ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with potassium (K+) ions." [GOC:mah]
+def: "Binding to a potassium ion (K+)." [GOC:mah]
+synonym: "K ion binding" EXACT []
is_a: GO:0031420 ! alkali metal ion binding
[Term]
@@ -162911,7 +162601,7 @@ is_a: GO:0140535 ! intracellular protein-containing complex
id: GO:0030957
name: Tat protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with Tat, a viral transactivating regulatory protein from the human immunodeficiency virus, or the equivalent protein from another virus." [GOC:mah, PMID:9094689]
+def: "Binding to Tat, a viral transactivating regulatory protein from the human immunodeficiency virus, or the equivalent protein from another virus." [GOC:mah, PMID:9094689]
is_a: GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor binding
[Term]
@@ -163051,7 +162741,7 @@ relationship: part_of GO:0036503 ! ERAD pathway
id: GO:0030971
name: receptor tyrosine kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity." [GOC:mah]
+def: "Binding to a receptor that possesses protein tyrosine kinase activity." [GOC:mah]
synonym: "transmembrane receptor protein tyrosine kinase ligand binding" RELATED []
is_a: GO:0005102 ! signaling receptor binding
is_a: GO:1990782 ! protein tyrosine kinase binding
@@ -163072,7 +162762,8 @@ consider: GO:0097200
id: GO:0030973
name: molybdate ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with molybdate (MoO4 2-) ions." [GOC:mlg]
+def: "Binding to a molybdate ion (MoO4 2-)." [GOC:mlg]
+synonym: "MoO4 ion binding" EXACT []
is_a: GO:0043168 ! anion binding
[Term]
@@ -163085,23 +162776,22 @@ synonym: "thiamin pyrophosphate transport" EXACT []
synonym: "thiamine diphosphate transport" EXACT []
synonym: "thiamine pyrophosphate transport" NARROW []
synonym: "TPP transport" EXACT []
-is_a: GO:0015695 ! organic cation transport
+is_a: GO:0015697 ! quaternary ammonium group transport
is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
-is_a: GO:0045117 ! azole transmembrane transport
-is_a: GO:0072348 ! sulfur compound transport
-is_a: GO:0072531 ! pyrimidine-containing compound transmembrane transport
-is_a: GO:0098655 ! cation transmembrane transport
+is_a: GO:0071934 ! thiamine transmembrane transport
is_a: GO:0098656 ! anion transmembrane transport
[Term]
id: GO:0030975
name: thiamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver." [GOC:mlg]
+def: "Binding to thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver." [GOC:mlg]
synonym: "thiamin binding" EXACT []
synonym: "vitamin B1 binding" EXACT []
is_a: GO:0019842 ! vitamin binding
+is_a: GO:0043169 ! cation binding
+is_a: GO:0043178 ! alcohol binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
is_a: GO:1901681 ! sulfur compound binding
@@ -163110,7 +162800,7 @@ is_a: GO:1901681 ! sulfur compound binding
id: GO:0030976
name: thiamine pyrophosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases." [GOC:mlg]
+def: "Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases." [GOC:mlg]
synonym: "aneurine pyrophosphate binding" EXACT []
synonym: "cocarboxylase binding" EXACT []
synonym: "diphosphothiamin binding" EXACT []
@@ -163119,6 +162809,7 @@ synonym: "TPP binding" EXACT []
is_a: GO:0019842 ! vitamin binding
is_a: GO:0043168 ! anion binding
is_a: GO:0043169 ! cation binding
+is_a: GO:0050997 ! quaternary ammonium group binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
is_a: GO:1901681 ! sulfur compound binding
@@ -163127,7 +162818,7 @@ is_a: GO:1901681 ! sulfur compound binding
id: GO:0030977
name: taurine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with taurine." [GOC:mlg]
+def: "Binding to taurine." [GOC:mlg]
is_a: GO:0043177 ! organic acid binding
is_a: GO:0043210 ! alkanesulfonate binding
is_a: GO:1901681 ! sulfur compound binding
@@ -163185,7 +162876,7 @@ id: GO:0030983
name: mismatched DNA binding
namespace: molecular_function
alt_id: GO:0032134
-def: "Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches." [GOC:mah]
+def: "Binding to a double-stranded DNA region containing one or more mismatches." [GOC:mah]
synonym: "mispair binding" EXACT []
synonym: "mispaired DNA binding" EXACT []
is_a: GO:0003690 ! double-stranded DNA binding
@@ -163194,14 +162885,14 @@ is_a: GO:0003690 ! double-stranded DNA binding
id: GO:0030984
name: kininogen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a kininogen, any of a group of plasma proteins that are kinin precursors." [GOC:mah, PMID:9520414]
+def: "Binding to a kininogen, a kinin precursor." [GOC:mah, PMID:9520414]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0030985
name: high molecular weight kininogen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a kininogen of high molecular mass." [GOC:mah, PMID:9520414]
+def: "Binding to a kininogen of high molecular mass." [GOC:mah, PMID:9520414]
synonym: "HK binding" EXACT []
synonym: "HMW kininogen binding" EXACT []
is_a: GO:0030984 ! kininogen binding
@@ -163210,7 +162901,7 @@ is_a: GO:0030984 ! kininogen binding
id: GO:0030986
name: low molecular weight kininogen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a kininogen of low molecular mass." [GOC:mah, PMID:9520414]
+def: "Binding to a kininogen of low molecular mass." [GOC:mah, PMID:9520414]
synonym: "LK binding" EXACT []
synonym: "LMW kininogen binding" EXACT []
is_a: GO:0030984 ! kininogen binding
@@ -163219,7 +162910,7 @@ is_a: GO:0030984 ! kininogen binding
id: GO:0030987
name: high molecular weight kininogen receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a high molecular weight kininogen receptor." [GOC:mah]
+def: "Binding to a high molecular weight kininogen receptor." [GOC:mah]
is_a: GO:0005102 ! signaling receptor binding
[Term]
@@ -163394,7 +163085,7 @@ namespace: molecular_function
alt_id: GO:0031006
alt_id: GO:0031007
alt_id: GO:0031008
-def: "Interacting selectively and non-covalently with a filamin, any member of a family of high molecular mass cytoskeletal proteins that crosslink actin filaments to form networks and stress fibers. Filamins contain an amino-terminal alpha-actinin-like actin binding domain, which is followed by a rod-domain composed of 4 to 24 100-residue repetitive segments including a carboxy-terminal dimerization domain." [GOC:mah, PMID:11336782]
+def: "Binding to a filamin, any member of a family of high molecular mass cytoskeletal proteins that crosslink actin filaments to form networks and stress fibers. Filamins contain an amino-terminal alpha-actinin-like actin binding domain, which is followed by a rod-domain composed of 4 to 24 100-residue repetitive segments including a carboxy-terminal dimerization domain." [GOC:mah, PMID:11336782]
synonym: "ABP-278/276 binding" NARROW []
synonym: "ABP-280 binding" NARROW []
synonym: "ABPL binding" NARROW []
@@ -163431,9 +163122,8 @@ is_a: GO:0070603 ! SWI/SNF superfamily-type complex
id: GO:0031011
name: Ino80 complex
namespace: cellular_component
-def: "A multisubunit protein complex that contains the Ino80p ATPase; exhibits chromatin remodeling activity and 3' to 5' DNA helicase activity." [GOC:jh, GOC:rb, PMID:19355820]
+def: "A multisubunit protein complex that contains the Ino80p ATPase; exhibits chromatin remodeling activity." [GOC:jh, GOC:rb, PMID:19355820]
synonym: "INO80 chromatin remodeling complex" EXACT []
-is_a: GO:0033202 ! DNA helicase complex
is_a: GO:0097346 ! INO80-type complex
relationship: part_of GO:0000228 ! nuclear chromosome
@@ -163457,14 +163147,14 @@ is_a: GO:0030312 ! external encapsulating structure
id: GO:0031013
name: troponin I binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with troponin I, the inhibitory subunit of the troponin complex." [GOC:mah, ISBN:0815316194]
+def: "Binding to troponin I, the inhibitory subunit of the troponin complex." [GOC:mah, ISBN:0815316194]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
id: GO:0031014
name: troponin T binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with troponin T, the tropomyosin-binding subunit of the troponin complex." [GOC:mah, ISBN:0815316194]
+def: "Binding to troponin T, the tropomyosin-binding subunit of the troponin complex." [GOC:mah, ISBN:0815316194]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
@@ -163681,7 +163371,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a filament composed of myosin molecules." [GOC:mah]
synonym: "myosin polymerization" RELATED []
is_a: GO:0031033 ! myosin filament organization
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0031035
@@ -163690,7 +163380,7 @@ namespace: biological_process
def: "The disassembly of a filament composed of myosin molecules." [GOC:mah]
synonym: "myosin depolymerization" RELATED []
is_a: GO:0031033 ! myosin filament organization
-is_a: GO:0043624 ! cellular protein complex disassembly
+is_a: GO:0032984 ! protein-containing complex disassembly
[Term]
id: GO:0031036
@@ -163778,8 +163468,10 @@ id: GO:0031047
name: gene silencing by RNA
namespace: biological_process
def: "Any process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:mah, GOC:tb, PMID:15020054]
+subset: goslim_drosophila
+subset: goslim_generic
synonym: "RNA-mediated gene silencing" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0016458 ! gene silencing
+is_a: GO:0010629 ! negative regulation of gene expression
[Term]
id: GO:0031048
@@ -163868,7 +163560,6 @@ name: regulation of histone modification
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the covalent alteration of a histone." [GOC:mah]
is_a: GO:0031399 ! regulation of protein modification process
-is_a: GO:1902275 ! regulation of chromatin organization
relationship: regulates GO:0016570 ! histone modification
[Term]
@@ -163882,7 +163573,6 @@ synonym: "downregulation of histone modification" EXACT []
synonym: "inhibition of histone modification" NARROW []
is_a: GO:0031056 ! regulation of histone modification
is_a: GO:0031400 ! negative regulation of protein modification process
-is_a: GO:1905268 ! negative regulation of chromatin organization
relationship: negatively_regulates GO:0016570 ! histone modification
[Term]
@@ -163897,7 +163587,6 @@ synonym: "up-regulation of histone modification" EXACT []
synonym: "upregulation of histone modification" EXACT []
is_a: GO:0031056 ! regulation of histone modification
is_a: GO:0031401 ! positive regulation of protein modification process
-is_a: GO:1905269 ! positive regulation of chromatin organization
relationship: positively_regulates GO:0016570 ! histone modification
[Term]
@@ -164051,7 +163740,7 @@ is_a: GO:0016783 ! sulfurtransferase activity
id: GO:0031072
name: heat shock protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock." [GOC:mah, GOC:vw]
+def: "Binding to a heat shock protein, a protein synthesized or activated in response to heat shock." [GOC:mah, GOC:vw]
is_a: GO:0005515 ! protein binding
[Term]
@@ -164094,7 +163783,7 @@ relationship: part_of GO:0009791 ! post-embryonic development
id: GO:0031078
name: histone deacetylase activity (H3-K14 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein." [EC:3.5.1.17, RHEA:24548]
+def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein." [PMID:28450737]
is_a: GO:0004407 ! histone deacetylase activity
[Term]
@@ -164654,7 +164343,6 @@ synonym: "down regulation of conjugation" EXACT []
synonym: "down-regulation of conjugation" EXACT []
synonym: "downregulation of conjugation" EXACT []
synonym: "inhibition of conjugation" NARROW []
-is_a: GO:0043901 ! negative regulation of multi-organism process
is_a: GO:0046999 ! regulation of conjugation
is_a: GO:0048523 ! negative regulation of cellular process
relationship: negatively_regulates GO:0000746 ! conjugation
@@ -164669,7 +164357,6 @@ synonym: "stimulation of conjugation" NARROW []
synonym: "up regulation of conjugation" EXACT []
synonym: "up-regulation of conjugation" EXACT []
synonym: "upregulation of conjugation" EXACT []
-is_a: GO:0043902 ! positive regulation of multi-organism process
is_a: GO:0046999 ! regulation of conjugation
is_a: GO:0048522 ! positive regulation of cellular process
relationship: positively_regulates GO:0000746 ! conjugation
@@ -164755,7 +164442,7 @@ namespace: biological_process
def: "Any process in which the proteasome is transported to, or maintained in, a specific location." [GOC:mah]
synonym: "establishment and maintenance of proteasome localization" EXACT []
synonym: "proteasome localisation" EXACT [GOC:mah]
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
[Term]
id: GO:0031145
@@ -164981,7 +164668,7 @@ namespace: cellular_component
def: "The lipid bilayer surrounding the contractile vacuole." [GOC:pg]
synonym: "contractile vacuole membrane" EXACT [GOC:mah, GOC:pf]
is_a: GO:0005774 ! vacuolar membrane
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
relationship: part_of GO:0000331 ! contractile vacuole
[Term]
@@ -165123,7 +164810,7 @@ is_a: GO:0097599 ! xylanase activity
id: GO:0031177
name: phosphopantetheine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate)." [GOC:mah, GOC:vw]
+def: "Binding to phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate)." [GOC:mah, GOC:vw]
is_a: GO:0019842 ! vitamin binding
is_a: GO:0033218 ! amide binding
is_a: GO:0072341 ! modified amino acid binding
@@ -165151,7 +164838,7 @@ def: "The process in which the signal sequence of a translated protein binds to
synonym: "posttranslational protein membrane targeting, docking" EXACT []
synonym: "protein docking during posttranslational protein targeting to membrane" EXACT []
synonym: "Sec-translated protein complex assembly" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0006620 ! posttranslational protein targeting to endoplasmic reticulum membrane
[Term]
@@ -165189,7 +164876,7 @@ relationship: part_of GO:0031205 ! endoplasmic reticulum Sec complex
id: GO:0031208
name: POZ domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a POZ (poxvirus and zinc finger) domain of a protein, a protein-protein interaction domain found in many transcription factors." [PMID:7958847]
+def: "Binding to a POZ (poxvirus and zinc finger) domain of a protein, a protein-protein interaction domain found in many transcription factors." [PMID:7958847]
synonym: "broad-complex, tramtrack, and bric-a-brac domain binding" EXACT []
synonym: "BTB domain" EXACT [PMID:22621901]
is_a: GO:0019904 ! protein domain specific binding
@@ -165209,7 +164896,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0031210
name: phosphatidylcholine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylcholine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of choline." [GOC:mah, ISBN:0198506732]
+def: "Binding to a phosphatidylcholine, a glycophospholipid in which a phosphatidyl group is esterified to the hydroxyl group of choline." [GOC:mah, ISBN:0198506732]
is_a: GO:0005543 ! phospholipid binding
is_a: GO:0043169 ! cation binding
is_a: GO:0050997 ! quaternary ammonium group binding
@@ -165445,7 +165132,6 @@ synonym: "extrinsic to cytoplasmic side of plasma membrane" NARROW []
synonym: "extrinsic to internal leaflet of plasma membrane" EXACT [GOC:ab]
synonym: "extrinsic to internal side of plasma membrane" EXACT []
is_a: GO:0019897 ! extrinsic component of plasma membrane
-relationship: part_of GO:0005622 ! intracellular anatomical structure
relationship: part_of GO:0009898 ! cytoplasmic side of plasma membrane
[Term]
@@ -165580,7 +165266,7 @@ is_a: GO:1902493 ! acetyltransferase complex
id: GO:0031249
name: denatured protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with denatured proteins." [GOC:mlg]
+def: "Binding to a denatured protein." [GOC:mlg]
comment: Note that this term should not be confused with 'unfolded protein binding ; GO:0051082', which usually refers to proteins that have not yet folded into their active states. Denatured proteins once were in their correct functional conformations, but have become incorrectly folded, and often form aggregates.
is_a: GO:0005515 ! protein binding
@@ -165763,7 +165449,7 @@ alt_id: GO:0017160
alt_id: GO:0030306
alt_id: GO:0034989
alt_id: GO:0048365
-def: "Interacting selectively and non-covalently with a small monomeric GTPase." [GOC:mah, PMID:27218782]
+def: "Binding to a small monomeric GTPase." [GOC:mah, PMID:27218782]
synonym: "ADP-ribosylation factor binding" NARROW []
synonym: "ARF binding" NARROW []
synonym: "GTP-Ral binding" NARROW []
@@ -165805,7 +165491,8 @@ is_a: GO:0120031 ! plasma membrane bounded cell projection assembly
id: GO:0031270
name: pseudopodium retraction
namespace: biological_process
-def: "The myosin-based contraction and retraction of the pseudopodium." [GOC:pg]
+def: "The myosin-based contraction and retraction of a pseudopodium." [GOC:pg]
+is_a: GO:0022411 ! cellular component disassembly
is_a: GO:0031268 ! pseudopodium organization
[Term]
@@ -165856,41 +165543,40 @@ relationship: positively_regulates GO:0031269 ! pseudopodium assembly
[Term]
id: GO:0031275
-name: regulation of lateral pseudopodium assembly
+name: obsolete regulation of lateral pseudopodium assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the assembly of pseudopodia from the lateral side of the cell." [GOC:dph, GOC:pg, GOC:tb]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the assembly of pseudopodia from the lateral side of the cell." [GOC:dph, GOC:pg, GOC:tb]
+comment: The regulation of lateral pseudopodium assembly terms were not used consistently. The negative regulation term has been replaced by GO:0120320 lateral pseudopodium retraction.
synonym: "regulation of lateral pseudopodium formation" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0031272 ! regulation of pseudopodium assembly
-relationship: regulates GO:0031271 ! lateral pseudopodium assembly
+is_obsolete: true
[Term]
id: GO:0031276
-name: negative regulation of lateral pseudopodium assembly
+name: obsolete negative regulation of lateral pseudopodium assembly
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of pseudopodia from the lateral side of the cell." [GOC:dph, GOC:pg, GOC:tb]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of pseudopodia from the lateral side of the cell." [GOC:dph, GOC:pg, GOC:tb]
+comment: The regulation of lateral pseudopodium assembly terms were not used consistently. The negative regulation term has been replaced by GO:0120320 lateral pseudopodium retraction.
synonym: "down regulation of lateral pseudopodium formation" RELATED []
synonym: "down-regulation of lateral pseudopodium formation" RELATED []
synonym: "downregulation of lateral pseudopodium formation" RELATED []
synonym: "inhibition of lateral pseudopodium formation" NARROW []
synonym: "negative regulation of lateral pseudopodium formation" RELATED [GOC:dph]
-is_a: GO:0031273 ! negative regulation of pseudopodium assembly
-is_a: GO:0031275 ! regulation of lateral pseudopodium assembly
-relationship: negatively_regulates GO:0031271 ! lateral pseudopodium assembly
+is_obsolete: true
+replaced_by: GO:0120320
[Term]
id: GO:0031277
-name: positive regulation of lateral pseudopodium assembly
+name: obsolete positive regulation of lateral pseudopodium assembly
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the assembly of pseudopodia from the lateral side of the cell." [GOC:dph, GOC:pg, GOC:tb]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the assembly of pseudopodia from the lateral side of the cell." [GOC:dph, GOC:pg, GOC:tb]
+comment: The regulation of lateral pseudopodium assembly terms were not used consistently. The negative regulation term has been replaced by GO:0120320 lateral pseudopodium retraction.
synonym: "activation of lateral pseudopodium formation" NARROW []
synonym: "positive regulation of lateral pseudopodium formation" RELATED []
synonym: "stimulation of lateral pseudopodium formation" NARROW []
synonym: "up regulation of lateral pseudopodium formation" RELATED []
synonym: "up-regulation of lateral pseudopodium formation" RELATED []
synonym: "upregulation of lateral pseudopodium formation" RELATED []
-is_a: GO:0031274 ! positive regulation of pseudopodium assembly
-is_a: GO:0031275 ! regulation of lateral pseudopodium assembly
-relationship: positively_regulates GO:0031271 ! lateral pseudopodium assembly
+is_obsolete: true
[Term]
id: GO:0031278
@@ -166361,6 +166047,7 @@ id: GO:0031323
name: regulation of cellular metabolic process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah]
+subset: gocheck_do_not_annotate
synonym: "regulation of cellular metabolism" EXACT []
is_a: GO:0019222 ! regulation of metabolic process
is_a: GO:0050794 ! regulation of cellular process
@@ -166371,6 +166058,7 @@ id: GO:0031324
name: negative regulation of cellular metabolic process
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah]
+subset: gocheck_do_not_annotate
synonym: "down regulation of cellular metabolic process" EXACT []
synonym: "down-regulation of cellular metabolic process" EXACT []
synonym: "downregulation of cellular metabolic process" EXACT []
@@ -166386,6 +166074,7 @@ id: GO:0031325
name: positive regulation of cellular metabolic process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah]
+subset: gocheck_do_not_annotate
synonym: "activation of cellular metabolic process" NARROW []
synonym: "positive regulation of cellular metabolism" EXACT []
synonym: "stimulation of cellular metabolic process" NARROW []
@@ -166901,14 +166590,14 @@ consider: GO:0008233
id: GO:0031369
name: translation initiation factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation." [GOC:mah]
+def: "Binding to a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation." [GOC:mah]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0031370
name: eukaryotic initiation factor 4G binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with eukaryotic initiation factor 4G, a polypeptide factor involved in the initiation of ribosome-mediated translation." [GOC:mah]
+def: "Binding to eukaryotic initiation factor 4G, a polypeptide factor involved in the initiation of ribosome-mediated translation." [GOC:mah]
synonym: "eIF4G binding" EXACT []
is_a: GO:0031369 ! translation initiation factor binding
@@ -167038,6 +166727,8 @@ name: protein tag
namespace: molecular_function
def: "A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation." [GOC:dos, GOC:go_curators, PMID:19028679, PMID:20054389, PMID:6305978]
comment: Use this term to annotate conjugated tags, not for conjugating enzymes. At the time of writing, all known gene products with this activity are ubiquitin-like, either based on overall sequence similarity or the presence of common motifs and structures.
+subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pir
synonym: "covalent modifier" RELATED [GOC:vw]
synonym: "protein tagging activity" RELATED []
@@ -167092,7 +166783,6 @@ synonym: "Elg1-RFC" EXACT []
synonym: "Elg1-RLC" EXACT []
synonym: "RFC (Elg1)" EXACT []
is_a: GO:1902494 ! catalytic complex
-is_a: GO:1904949 ! ATPase complex
relationship: part_of GO:0005694 ! chromosome
[Term]
@@ -167225,29 +166915,32 @@ relationship: positively_regulates GO:0006464 ! cellular protein modification pr
id: GO:0031402
name: sodium ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with sodium ions (Na+)." [GOC:mah]
+def: "Binding to a sodium ion (Na+)." [GOC:mah]
+synonym: "Na+ ion binding" EXACT []
is_a: GO:0031420 ! alkali metal ion binding
[Term]
id: GO:0031403
name: lithium ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lithium ions (Li+)." [GOC:mah]
+def: "Binding to a lithium ion (Li+)." [GOC:mah]
+synonym: "Li+ ion binding" EXACT []
is_a: GO:0031420 ! alkali metal ion binding
[Term]
id: GO:0031404
name: chloride ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chloride ions (Cl-)." [GOC:mah]
+def: "Binding to a chloride ion (Cl-)." [GOC:mah]
synonym: "chloride binding" EXACT []
+synonym: "Cl- ion binding" EXACT []
is_a: GO:0043168 ! anion binding
[Term]
id: GO:0031405
name: lipoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lipoic acid, 1,2-dithiolane-3-pentanoic acid." [GOC:mah, ISBN:0198506732]
+def: "Binding to lipoic acid, 1,2-dithiolane-3-pentanoic acid." [GOC:mah, ISBN:0198506732]
is_a: GO:0005504 ! fatty acid binding
is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -167258,7 +166951,7 @@ is_a: GO:1901681 ! sulfur compound binding
id: GO:0031406
name: carboxylic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:mah, ISBN:0198506732]
+def: "Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:mah, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0043168 ! anion binding
@@ -167286,7 +166979,7 @@ is_a: GO:0046394 ! carboxylic acid biosynthetic process
id: GO:0031409
name: pigment binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pigment, any general or particular coloring matter in living organisms, e.g. melanin." [GOC:mah]
+def: "Binding to a pigment, a general or particular coloring matter in living organisms, e.g. melanin." [GOC:mah]
subset: goslim_pir
is_a: GO:0005488 ! binding
@@ -167376,19 +167069,21 @@ is_a: GO:0031414 ! N-terminal protein acetyltransferase complex
id: GO:0031418
name: L-ascorbic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species." [GOC:mah]
+def: "Binding to L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species." [GOC:mah]
synonym: "L-ascorbate binding" EXACT []
synonym: "vitamin C binding" EXACT []
is_a: GO:0019842 ! vitamin binding
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043177 ! organic acid binding
is_a: GO:0048029 ! monosaccharide binding
+is_a: GO:0097159 ! organic cyclic compound binding
+is_a: GO:1901363 ! heterocyclic compound binding
[Term]
id: GO:0031419
name: cobalamin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom." [GOC:mah]
+def: "Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom." [GOC:mah]
synonym: "vitamin B12 binding" EXACT []
is_a: GO:0019842 ! vitamin binding
is_a: GO:0046906 ! tetrapyrrole binding
@@ -167397,7 +167092,7 @@ is_a: GO:0046906 ! tetrapyrrole binding
id: GO:0031420
name: alkali metal ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any alkali metal ion; alkali metals are those elements in group Ia of the periodic table, with the exception of hydrogen." [GOC:mah]
+def: "Binding to an alkali metal ion; alkali metals are those elements in group Ia of the periodic table, with the exception of hydrogen." [GOC:mah]
is_a: GO:0046872 ! metal ion binding
[Term]
@@ -167422,7 +167117,7 @@ relationship: part_of GO:0005694 ! chromosome
id: GO:0031423
name: hexon binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a hexon, the major protein component of the icosahedral capsid of an adenovirus." [GOC:mah, PMID:12915569]
+def: "Binding to a hexon, the major protein component of the icosahedral capsid of an adenovirus." [GOC:mah, PMID:12915569]
is_a: GO:0005515 ! protein binding
[Term]
@@ -167507,21 +167202,21 @@ is_a: GO:0140535 ! intracellular protein-containing complex
id: GO:0031432
name: titin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with titin, any of a family of giant proteins found in striated and smooth muscle. In striated muscle, single titin molecules span half the sarcomere, with their N- and C-termini in the Z-disc and M-line, respectively." [GOC:mah, PMID:10481174]
+def: "Binding to titin, any of a family of giant proteins found in striated and smooth muscle. In striated muscle, single titin molecules span half the sarcomere, with their N- and C-termini in the Z-disc and M-line, respectively." [GOC:mah, PMID:10481174]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
id: GO:0031433
name: telethonin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with telethonin, a protein found in the Z disc of striated muscle and which is a substrate of the titin kinase." [GOC:mah, PMID:10481174]
+def: "Binding to telethonin, a protein found in the Z disc of striated muscle and which is a substrate of the titin kinase." [GOC:mah, PMID:10481174]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
id: GO:0031434
name: mitogen-activated protein kinase kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase, any protein that can phosphorylate a MAP kinase." [GOC:mah]
+def: "Binding to a mitogen-activated protein kinase kinase, a protein that can phosphorylate a MAP kinase." [GOC:mah]
synonym: "MAPKK binding" EXACT []
is_a: GO:0019901 ! protein kinase binding
@@ -167529,7 +167224,7 @@ is_a: GO:0019901 ! protein kinase binding
id: GO:0031435
name: mitogen-activated protein kinase kinase kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase kinase, any protein that can phosphorylate a MAP kinase kinase." [GOC:bf]
+def: "Binding to a mitogen-activated protein kinase kinase kinase, a protein that can phosphorylate a MAP kinase kinase." [GOC:bf]
synonym: "MAPKKK binding" EXACT []
is_a: GO:0019901 ! protein kinase binding
@@ -167636,8 +167331,8 @@ name: regulation of heterochromatin assembly
namespace: biological_process
def: "Any process that modulates the frequency, rate, extent or location of heterochromatin formation." [GOC:mah]
synonym: "regulation of heterochromatin formation" EXACT []
+is_a: GO:0010468 ! regulation of gene expression
is_a: GO:0010847 ! regulation of chromatin assembly
-is_a: GO:0033044 ! regulation of chromosome organization
is_a: GO:0120261 ! regulation of heterochromatin organization
relationship: regulates GO:0031507 ! heterochromatin assembly
@@ -167727,10 +167422,10 @@ synonym: "down-regulation of heterochromatin formation" EXACT []
synonym: "downregulation of heterochromatin formation" EXACT []
synonym: "inhibition of heterochromatin formation" NARROW []
synonym: "negative regulation of heterochromatin formation" EXACT []
+is_a: GO:0010628 ! positive regulation of gene expression
is_a: GO:0031445 ! regulation of heterochromatin assembly
is_a: GO:0045798 ! negative regulation of chromatin assembly or disassembly
is_a: GO:0120262 ! negative regulation of heterochromatin organization
-is_a: GO:2001251 ! negative regulation of chromosome organization
relationship: negatively_regulates GO:0031507 ! heterochromatin assembly
[Term]
@@ -167750,15 +167445,6 @@ is_a: GO:0045799 ! positive regulation of chromatin assembly or disassembly
is_a: GO:0120263 ! positive regulation of heterochromatin organization
relationship: positively_regulates GO:0031507 ! heterochromatin assembly
-[Term]
-id: GO:0031454
-name: regulation of extent of heterochromatin assembly
-namespace: biological_process
-def: "Any process that modulates the extent or location of heterochromatin formation." [GOC:mah]
-synonym: "regulation of extent of heterochromatin formation" EXACT []
-synonym: "regulation of heterochromatin spreading" RELATED []
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-
[Term]
id: GO:0031455
name: glycine betaine metabolic process
@@ -167926,12 +167612,14 @@ is_a: GO:0071763 ! nuclear membrane organization
[Term]
id: GO:0031469
-name: polyhedral organelle
+name: bacterial microcompartment
namespace: cellular_component
-def: "An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy." [GOC:js, PMID:10498708, PMID:11844753, PMID:12923081]
+def: "An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy." [GOC:js, PMID:10498708, PMID:11844753, PMID:12923081, PMID:34058518, PMID:34340100]
subset: goslim_pir
synonym: "BAC" BROAD []
-synonym: "bacterial microcompartment" EXACT []
+synonym: "BMC" BROAD []
+synonym: "MCP" BROAD []
+synonym: "polyhedral organelle" RELATED []
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
[Term]
@@ -167940,7 +167628,7 @@ name: carboxysome
namespace: cellular_component
def: "An organelle consisting of a proteinaceous coat and enzymes for the fixation of CO(2). It augments the concentration of CO(2) in the vicinity of RuBisCO to increase the efficiency of CO(2) fixation under atmospheric conditions." [GOC:js, PMID:28934381, PMID:8157606, PMID:8491708]
xref: Wikipedia:Carboxysome
-is_a: GO:0031469 ! polyhedral organelle
+is_a: GO:0031469 ! bacterial microcompartment
[Term]
id: GO:0031471
@@ -167948,20 +167636,20 @@ name: ethanolamine degradation polyhedral organelle
namespace: cellular_component
def: "An organelle found in bacteria consisting of a proteinaceous coat containing enzymes for the degradation of ethanolamine whose purpose is the protection of the rest of the cell from the toxic acetaldehyde product of the enzyme ethanolamine ammonia lyase." [GOC:js, PMID:11844753]
synonym: "ethanolamine metabolosome" RELATED []
-is_a: GO:0031469 ! polyhedral organelle
+is_a: GO:0031469 ! bacterial microcompartment
[Term]
id: GO:0031472
name: propanediol degradation polyhedral organelle
namespace: cellular_component
def: "An organelle found in bacteria consisting of a proteinaceous coat containing enzymes for the degradation of 1,2-propanediol whose purpose is the protection of the rest of the cell from the toxic propionaldehyde product of the enzyme diol dehydratase." [GOC:js, PMID:10498708, PMID:11844753, PMID:12923081]
-is_a: GO:0031469 ! polyhedral organelle
+is_a: GO:0031469 ! bacterial microcompartment
[Term]
id: GO:0031473
name: myosin III binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a class III myosin; myosin III is monomeric and has an N terminal kinase domain." [GOC:mah]
+def: "Binding to a class III myosin; myosin III is monomeric and has an N terminal kinase domain." [GOC:mah]
is_a: GO:0017022 ! myosin binding
[Term]
@@ -168073,14 +167761,14 @@ is_a: GO:0016461 ! unconventional myosin complex
id: GO:0031489
name: myosin V binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a class V myosin; myosin V is a dimeric molecule involved in intracellular transport." [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
+def: "Binding to a class V myosin; myosin V is a dimeric molecule involved in intracellular transport." [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
is_a: GO:0017022 ! myosin binding
[Term]
id: GO:0031490
name: chromatin DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA that is assembled into chromatin." [GOC:mah]
+def: "Binding to DNA that is assembled into chromatin." [GOC:mah]
is_a: GO:0003677 ! DNA binding
is_a: GO:0003682 ! chromatin binding
@@ -168088,7 +167776,7 @@ is_a: GO:0003682 ! chromatin binding
id: GO:0031491
name: nucleosome binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC:mah]
+def: "Binding to a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC:mah]
is_a: GO:0003682 ! chromatin binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -168096,17 +167784,19 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0031492
name: nucleosomal DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the DNA portion of a nucleosome." [GOC:mah]
+def: "Binding to the DNA portion of a nucleosome." [GOC:mah]
is_a: GO:0031490 ! chromatin DNA binding
is_a: GO:0031491 ! nucleosome binding
[Term]
id: GO:0031493
-name: nucleosomal histone binding
+name: obsolete nucleosomal histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone that is assembled into a nucleosome." [GOC:mah]
-is_a: GO:0031491 ! nucleosome binding
-is_a: GO:0042393 ! histone binding
+def: "OBSOLETE. Binding to a histone that is assembled into a nucleosome." [GOC:mah]
+comment: This term was obsoleted because it represents both an activity and a cellular component.
+is_obsolete: true
+consider: GO:0000786
+consider: GO:0042393
[Term]
id: GO:0031494
@@ -168151,6 +167841,7 @@ id: GO:0031497
name: chromatin assembly
namespace: biological_process
def: "The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus." [http://www.infobiogen.fr/services/chromcancer/IntroItems/ChromatinEducEng.html, PMID:20404130]
+synonym: "chromatin maintenance" BROAD []
synonym: "establishment of chromatin architecture" EXACT [GOC:mah]
is_a: GO:0006333 ! chromatin assembly or disassembly
is_a: GO:0022607 ! cellular component assembly
@@ -168161,6 +167852,7 @@ id: GO:0031498
name: chromatin disassembly
namespace: biological_process
def: "The controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, other proteins, and sometimes RNA." [http://www.infobiogen.fr/services/chromcancer/IntroItems/ChromatinEducEng.html, PMID:20404130]
+synonym: "chromatin maintenance" BROAD []
is_a: GO:0006333 ! chromatin assembly or disassembly
is_a: GO:0022411 ! cellular component disassembly
@@ -168211,7 +167903,12 @@ relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
id: GO:0031503
name: protein-containing complex localization
namespace: biological_process
+alt_id: GO:0034629
def: "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location." [GOC:mah]
+synonym: "cellular protein complex localisation" RELATED [GOC:mah]
+synonym: "cellular protein complex localization" RELATED []
+synonym: "cellular protein-containing complex localization" RELATED []
+synonym: "establishment and maintenance of cellular protein complex localization" RELATED []
synonym: "establishment and maintenance of protein complex localization" EXACT []
synonym: "protein complex localisation" EXACT [GOC:mah]
synonym: "protein complex localization" RELATED []
@@ -168255,15 +167952,20 @@ is_a: GO:0044038 ! cell wall macromolecule biosynthetic process
id: GO:0031507
name: heterochromatin assembly
namespace: biological_process
+alt_id: GO:0006342
alt_id: GO:0006343
+alt_id: GO:0016440
alt_id: GO:0070869
alt_id: GO:1904497
-def: "The assembly of chromatin into heterochromatin, a compact and highly condensed form that is often, but not always, transcriptionally silent." [GOC:mah]
+def: "An epigenetic gene silencing mechanism that involves the assembly of chromatin into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation." [GOC:mah, PMID:25192661, PMID:33827924]
+synonym: "chromatin silencing" EXACT []
+synonym: "chromatin-mediated silencing" EXACT []
synonym: "establishment of chromatin silencing" RELATED []
synonym: "establishment of heterochromatic silencing" RELATED []
synonym: "establishment of heterochromatin architecture" EXACT [GOC:mah]
synonym: "establishment of heterochromatin architecture involved in chromatin silencing at centromere outer repeat region" NARROW [GOC:TermGenie]
synonym: "establishment of heterochromatin architecture involved in chromatin silencing at pericentric region" NARROW [GOC:TermGenie]
+synonym: "heterochromatic silencing" RELATED []
synonym: "heterochromatin assembly involved in chromatin silencing" RELATED []
synonym: "heterochromatin assembly involved in chromatin silencing at centromere outer repeat region" NARROW []
synonym: "heterochromatin assembly involved in chromatin silencing at pericentric region" NARROW [GOC:TermGenie]
@@ -168271,11 +167973,12 @@ synonym: "heterochromatin formation" EXACT []
synonym: "heterochromatin formation involved in chromatin silencing" RELATED []
synonym: "heterochromatin formation involved in chromatin silencing at centromere outer repeat region" NARROW [GOC:TermGenie]
synonym: "heterochromatin formation involved in chromatin silencing at pericentric region" NARROW [GOC:TermGenie]
-is_a: GO:0006338 ! chromatin remodeling
+synonym: "heterochromatin maintenance" BROAD []
+synonym: "TGS" BROAD []
+synonym: "transcriptional gene silencing" EXACT []
is_a: GO:0031497 ! chromatin assembly
-is_a: GO:0051276 ! chromosome organization
+is_a: GO:0045814 ! negative regulation of gene expression, epigenetic
is_a: GO:0070828 ! heterochromatin organization
-is_a: GO:0097549 ! chromatin organization involved in negative regulation of transcription
[Term]
id: GO:0031508
@@ -168293,29 +167996,34 @@ synonym: "chromatin silencing at centromere" EXACT []
synonym: "chromatin silencing at centromere outer repeat region" NARROW []
synonym: "chromatin silencing at pericentric region" RELATED [GOC:mah]
synonym: "heterochromatic silencing at centromere" EXACT []
-is_a: GO:0010629 ! negative regulation of gene expression
is_a: GO:0031055 ! chromatin remodeling at centromere
-is_a: GO:0031507 ! heterochromatin assembly
is_a: GO:0140462 ! pericentric heterochromatin organization
+is_a: GO:0140719 ! constitutive heterochromatin assembly
relationship: part_of GO:0034508 ! centromere complex assembly
[Term]
id: GO:0031509
name: subtelomeric heterochromatin assembly
namespace: biological_process
+alt_id: GO:0006348
alt_id: GO:0035390
alt_id: GO:0099114
-def: "The assembly of chromatin into heterochromatin at the subtelomeric region." [GOC:mah, PMID:26205977]
+def: "The assembly of chromatin into heterochromatin at the subtelomeric region, resulting in a chromatin conformation refractory to transcription." [GOC:mah, PMID:10219245, PMID:26205977]
synonym: "chromatin silencing at subtelomere" RELATED []
+synonym: "chromatin silencing at telomere" EXACT []
synonym: "establishment of chromatin silencing at telomere" RELATED []
synonym: "heterochromatic silencing at subtelomere" RELATED []
+synonym: "heterochromatic silencing at telomere" EXACT []
+synonym: "regulation of chromatin silencing at telomere" RELATED []
+synonym: "regulation of subtelomeric heterochromatin assembly" RELATED []
synonym: "subtelomere chromatin silencing" RELATED [GOC:mah]
synonym: "subtelomeric silencing" EXACT [GOC:mah]
+synonym: "telomere chromatin silencing" EXACT [GOC:mah]
+synonym: "Telomere Position Effect" EXACT [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:21847107]
synonym: "telomeric heterochromatin assembly" RELATED []
synonym: "telomeric heterochromatin formation" RELATED []
-is_a: GO:0031507 ! heterochromatin assembly
-is_a: GO:0032202 ! telomere assembly
-is_a: GO:0140461 ! subtelomeric heterochromatin organization
+synonym: "telomeric silencing" EXACT [GOC:bf]
+is_a: GO:0140719 ! constitutive heterochromatin assembly
relationship: part_of GO:0032200 ! telomere organization
[Term]
@@ -168489,7 +168197,7 @@ is_a: GO:0120036 ! plasma membrane bounded cell projection organization
id: GO:0031530
name: gonadotropin-releasing hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a receptor for gonadotropin-releasing hormone (GnRH), a peptide hormone that is synthesized and released by the hypothalamus and is responsible for the release of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) from the anterior pituitary." [GOC:pr, PMID:15196882]
+def: "Binding to a receptor for gonadotropin-releasing hormone (GnRH), a peptide hormone that is synthesized and released by the hypothalamus and is responsible for the release of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) from the anterior pituitary." [GOC:pr, PMID:15196882]
synonym: "GnRH receptor binding" EXACT []
synonym: "gonadotrophin-releasing hormone receptor binding" EXACT [GOC:dph]
is_a: GO:0051428 ! peptide hormone receptor binding
@@ -168499,7 +168207,7 @@ id: GO:0031531
name: thyrotropin-releasing hormone receptor binding
namespace: molecular_function
alt_id: GO:0031888
-def: "Interacting selectively and non-covalently with a receptor for thyrotropin-releasing hormone, a tripeptide hormone that is produced by the hypothalamus and stimulates the release of thyroid-stimulating hormone (TSH) and prolactin by the anterior pituitary." [PMID:8592728]
+def: "Binding to a receptor for thyrotropin-releasing hormone, a tripeptide hormone that is produced by the hypothalamus and stimulates the release of thyroid-stimulating hormone (TSH) and prolactin by the anterior pituitary." [PMID:8592728]
synonym: "thyrotropin releasing hormone receptor binding" EXACT []
synonym: "thyrotropin-releasing hormone receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -168679,7 +168387,7 @@ is_a: GO:0031543 ! peptidyl-proline dioxygenase activity
id: GO:0031546
name: brain-derived neurotrophic factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the brain-derived neurotrophic factor receptor." [GOC:mah]
+def: "Binding to a brain-derived neurotrophic factor receptor." [GOC:mah]
synonym: "BDNF receptor binding" EXACT []
synonym: "brain-derived neurotrophic factor ligand" NARROW []
is_a: GO:0005165 ! neurotrophin receptor binding
@@ -169184,7 +168892,7 @@ relationship: part_of GO:0005813 ! centrosome
id: GO:0031593
name: polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein." [GOC:pg]
+def: "Binding to a protein upon poly-ubiquitination of the target protein." [GOC:pg]
is_a: GO:0140030 ! modification-dependent protein binding
[Term]
@@ -169456,14 +169164,14 @@ is_a: GO:0043112 ! receptor metabolic process
id: GO:0031624
name: ubiquitin conjugating enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins." [GOC:vp]
+def: "Binding to a ubiquitin conjugating enzyme, any of the E2 proteins." [GOC:vp]
is_a: GO:0044390 ! ubiquitin-like protein conjugating enzyme binding
[Term]
id: GO:0031625
name: ubiquitin protein ligase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins." [GOC:vp]
+def: "Binding to a ubiquitin protein ligase enzyme, any of the E3 proteins." [GOC:vp]
synonym: "ubiquitin ligase binding" EXACT []
is_a: GO:0044389 ! ubiquitin-like protein ligase binding
@@ -169471,7 +169179,7 @@ is_a: GO:0044389 ! ubiquitin-like protein ligase binding
id: GO:0031626
name: beta-endorphin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with beta-endorphin, a peptide generated by the cleavage of pro-opiomelanocortin." [GOC:nln, PMID:6267560]
+def: "Binding to beta-endorphin, a peptide generated by the cleavage of pro-opiomelanocortin." [GOC:nln, PMID:6267560]
is_a: GO:0042165 ! neurotransmitter binding
is_a: GO:0042277 ! peptide binding
@@ -169490,7 +169198,7 @@ is_a: GO:0000723 ! telomere maintenance
id: GO:0031628
name: opioid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an opioid receptor." [GOC:nln]
+def: "Binding to an opioid receptor." [GOC:nln]
is_a: GO:0001664 ! G protein-coupled receptor binding
[Term]
@@ -169570,7 +169278,7 @@ is_a: GO:0042716 ! plasma membrane-derived chromatophore
id: GO:0031634
name: replication fork barrier binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with replication fork barriers, sites that inhibit the progress of replication forks." [GOC:mah]
+def: "Binding to replication fork barriers, sites that inhibit the progress of replication forks." [GOC:mah]
is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
[Term]
@@ -169612,13 +169320,12 @@ is_a: GO:0031638 ! zymogen activation
[Term]
id: GO:0031640
-name: killing of cells of other organism
+name: killing of cells of another organism
namespace: biological_process
alt_id: GO:0001908
def: "Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add]
subset: goslim_pir
-synonym: "killing of cells of another organism" EXACT [GOC:bf]
-synonym: "killing of cells of another, non-host, organism" NARROW []
+synonym: "killing of cells of other organism" EXACT []
is_a: GO:0001906 ! cell killing
is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms
@@ -169851,20 +169558,22 @@ is_obsolete: true
[Term]
id: GO:0031660
-name: regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle
+name: obsolete regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity contributing to the G2/M transition of the cell cycle." [GOC:dph, GOC:mah, GOC:pr, GOC:tb]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity contributing to the G2/M transition of the cell cycle." [GOC:dph, GOC:mah, GOC:pr, GOC:tb]
+comment: This term was obsoleted because it is a MF represented as a BP.
synonym: "G2/M-specific regulation of cyclin-dependent protein kinase activity" EXACT [GOC:dph, GOC:tb]
synonym: "regulation of cyclin-dependent protein kinase activity during G2/M" RELATED [GOC:dph, GOC:tb]
synonym: "regulation of cyclin-dependent protein kinase activity involved in G2/M" BROAD []
-is_a: GO:0000079 ! regulation of cyclin-dependent protein serine/threonine kinase activity
-is_a: GO:0010389 ! regulation of G2/M transition of mitotic cell cycle
+is_obsolete: true
+consider: GO:0010389
[Term]
id: GO:0031661
-name: negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle
+name: obsolete negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity contributing to the G2/M transition of the cell cycle." [GOC:dph, GOC:mah, GOC:pr, GOC:tb]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity contributing to the G2/M transition of the cell cycle." [GOC:dph, GOC:mah, GOC:pr, GOC:tb]
+comment: This term was obsoleted because it is a MF represented as a BP.
synonym: "G2/M-specific down regulation of cyclin-dependent protein kinase activity" EXACT []
synonym: "G2/M-specific down-regulation of cyclin-dependent protein kinase activity" EXACT []
synonym: "G2/M-specific downregulation of cyclin-dependent protein kinase activity" EXACT []
@@ -169872,8 +169581,8 @@ synonym: "G2/M-specific inhibition of cyclin-dependent protein kinase activity"
synonym: "G2/M-specific negative regulation of cyclin-dependent protein kinase activity" EXACT [GOC:dph, GOC:tb]
synonym: "negative regulation of cyclin-dependent protein kinase activity during G2/M" RELATED [GOC:dph, GOC:tb]
synonym: "negative regulation of cyclin-dependent protein kinase activity involved in G2/M" BROAD []
-is_a: GO:0031660 ! regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle
-is_a: GO:0045736 ! negative regulation of cyclin-dependent protein serine/threonine kinase activity
+is_obsolete: true
+consider: GO:0010389
[Term]
id: GO:0031663
@@ -169895,7 +169604,6 @@ synonym: "regulation of LPS-mediated signaling pathway" EXACT []
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0009966 ! regulation of signal transduction
is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0043900 ! regulation of multi-organism process
relationship: regulates GO:0031663 ! lipopolysaccharide-mediated signaling pathway
[Term]
@@ -169913,7 +169621,6 @@ is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0009968 ! negative regulation of signal transduction
is_a: GO:0031664 ! regulation of lipopolysaccharide-mediated signaling pathway
is_a: GO:0032102 ! negative regulation of response to external stimulus
-is_a: GO:0043901 ! negative regulation of multi-organism process
relationship: negatively_regulates GO:0031663 ! lipopolysaccharide-mediated signaling pathway
[Term]
@@ -169932,7 +169639,6 @@ is_a: GO:0002833 ! positive regulation of response to biotic stimulus
is_a: GO:0009967 ! positive regulation of signal transduction
is_a: GO:0031664 ! regulation of lipopolysaccharide-mediated signaling pathway
is_a: GO:0032103 ! positive regulation of response to external stimulus
-is_a: GO:0043902 ! positive regulation of multi-organism process
relationship: positively_regulates GO:0031663 ! lipopolysaccharide-mediated signaling pathway
[Term]
@@ -170049,7 +169755,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0031681
name: G-protein beta-subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a G-protein beta subunit." [GOC:mah]
+def: "Binding to a G-protein beta subunit." [GOC:mah]
synonym: "G-beta protein subunit binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -170057,7 +169763,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0031682
name: G-protein gamma-subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a G-protein gamma subunit." [GOC:mah]
+def: "Binding to a G-protein gamma subunit." [GOC:mah]
synonym: "G-gamma protein subunit binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -170065,7 +169771,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0031683
name: G-protein beta/gamma-subunit complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a complex of G-protein beta/gamma subunits." [GOC:nln, GOC:vw]
+def: "Binding to a complex of G-protein beta/gamma subunits." [GOC:nln, GOC:vw]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -170080,7 +169786,7 @@ is_obsolete: true
id: GO:0031685
name: adenosine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an adenosine receptor." [GOC:mah, GOC:nln]
+def: "Binding to an adenosine receptor." [GOC:mah, GOC:nln]
synonym: "adenosine receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170088,7 +169794,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031686
name: A1 adenosine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an A1 adenosine receptor." [GOC:mah, GOC:nln]
+def: "Binding to an A1 adenosine receptor." [GOC:mah, GOC:nln]
synonym: "A1 adenosine receptor ligand" NARROW []
is_a: GO:0031685 ! adenosine receptor binding
@@ -170096,7 +169802,7 @@ is_a: GO:0031685 ! adenosine receptor binding
id: GO:0031687
name: A2A adenosine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an A2A adenosine receptor." [GOC:mah, GOC:nln]
+def: "Binding to an A2A adenosine receptor." [GOC:mah, GOC:nln]
synonym: "A2A adenosine receptor ligand" NARROW []
is_a: GO:0031685 ! adenosine receptor binding
@@ -170104,7 +169810,7 @@ is_a: GO:0031685 ! adenosine receptor binding
id: GO:0031688
name: A2B adenosine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an A2B adenosine receptor." [GOC:mah, GOC:nln]
+def: "Binding to an A2B adenosine receptor." [GOC:mah, GOC:nln]
synonym: "A2B adenosine receptor ligand" NARROW []
is_a: GO:0031685 ! adenosine receptor binding
@@ -170112,7 +169818,7 @@ is_a: GO:0031685 ! adenosine receptor binding
id: GO:0031689
name: A3 adenosine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an A3 adenosine receptor." [GOC:mah, GOC:nln]
+def: "Binding to an A3 adenosine receptor." [GOC:mah, GOC:nln]
synonym: "A3 adenosine receptor ligand" NARROW []
is_a: GO:0031685 ! adenosine receptor binding
@@ -170120,7 +169826,7 @@ is_a: GO:0031685 ! adenosine receptor binding
id: GO:0031690
name: adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to an adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "adrenergic receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170128,7 +169834,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031691
name: alpha-1A adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alpha-1A adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to an alpha-1A adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "alpha-1A adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170136,7 +169842,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031692
name: alpha-1B adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alpha-1B adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to an alpha-1B adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "alpha-1B adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170144,7 +169850,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031693
name: alpha-1D adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alpha-1D adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to an alpha-1D adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "alpha-1D adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170152,7 +169858,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031694
name: alpha-2A adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alpha-2A adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to an alpha-2A adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "alpha-2A adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170160,7 +169866,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031695
name: alpha-2B adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alpha-2B adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to an alpha-2B adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "alpha-2B adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170168,7 +169874,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031696
name: alpha-2C adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alpha-2C adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to an alpha-2C adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "alpha-2C adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170176,7 +169882,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031697
name: beta-1 adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a beta-1 adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to a beta-1 adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "beta-1 adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170184,7 +169890,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031698
name: beta-2 adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a beta-2 adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to a beta-2 adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "beta-2 adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170192,7 +169898,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031699
name: beta-3 adrenergic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a beta-3 adrenergic receptor." [GOC:mah, GOC:nln]
+def: "Binding to a beta-3 adrenergic receptor." [GOC:mah, GOC:nln]
synonym: "beta-3 adrenergic receptor ligand" NARROW []
is_a: GO:0031690 ! adrenergic receptor binding
@@ -170200,7 +169906,7 @@ is_a: GO:0031690 ! adrenergic receptor binding
id: GO:0031700
name: adrenomedullin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an adrenomedullin receptor." [GOC:mah, GOC:nln]
+def: "Binding to an adrenomedullin receptor." [GOC:mah, GOC:nln]
synonym: "adrenomedullin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170208,7 +169914,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031701
name: angiotensin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an angiotensin receptor." [GOC:mah, GOC:nln]
+def: "Binding to an angiotensin receptor." [GOC:mah, GOC:nln]
synonym: "angiotensin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170216,7 +169922,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031702
name: type 1 angiotensin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 angiotensin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 angiotensin receptor." [GOC:mah, GOC:nln]
synonym: "AT1 receptor binding" EXACT []
synonym: "type 1 angiotensin receptor ligand" NARROW []
is_a: GO:0031701 ! angiotensin receptor binding
@@ -170225,7 +169931,7 @@ is_a: GO:0031701 ! angiotensin receptor binding
id: GO:0031703
name: type 2 angiotensin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 angiotensin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 angiotensin receptor." [GOC:mah, GOC:nln]
synonym: "AT2 receptor binding" EXACT []
synonym: "type 2 angiotensin receptor ligand" NARROW []
is_a: GO:0031701 ! angiotensin receptor binding
@@ -170235,7 +169941,7 @@ id: GO:0031704
name: apelin receptor binding
namespace: molecular_function
alt_id: GO:0042569
-def: "Interacting selectively and non-covalently with an apelin receptor." [GOC:mah, GOC:nln, GOC:vp, PMID:12787050]
+def: "Binding to an apelin receptor." [GOC:mah, GOC:nln, GOC:vp, PMID:12787050]
synonym: "apelin receptor ligand" NARROW []
synonym: "APJ receptor binding" EXACT []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -170244,7 +169950,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031705
name: bombesin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a bombesin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a bombesin receptor." [GOC:mah, GOC:nln]
synonym: "bombesin receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -170252,7 +169958,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031706
name: subtype 3 bombesin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a subtype 3 bombesin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a subtype 3 bombesin receptor." [GOC:mah, GOC:nln]
synonym: "subtype 3 bombesin receptor ligand" NARROW []
is_a: GO:0031705 ! bombesin receptor binding
@@ -170260,7 +169966,7 @@ is_a: GO:0031705 ! bombesin receptor binding
id: GO:0031707
name: endothelin A receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an endothelin A receptor." [GOC:mah, GOC:nln]
+def: "Binding to an endothelin A receptor." [GOC:mah, GOC:nln]
synonym: "endothelin A receptor ligand" NARROW []
synonym: "endothelin-1 receptor binding" EXACT []
is_a: GO:0031705 ! bombesin receptor binding
@@ -170269,7 +169975,7 @@ is_a: GO:0031705 ! bombesin receptor binding
id: GO:0031708
name: endothelin B receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an endothelin B receptor." [GOC:mah, GOC:nln]
+def: "Binding to an endothelin B receptor." [GOC:mah, GOC:nln]
synonym: "endothelin B receptor ligand" NARROW []
is_a: GO:0031705 ! bombesin receptor binding
@@ -170277,7 +169983,7 @@ is_a: GO:0031705 ! bombesin receptor binding
id: GO:0031709
name: gastrin-releasing peptide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a gastrin-releasing peptide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a gastrin-releasing peptide receptor." [GOC:mah, GOC:nln]
synonym: "gastrin-releasing peptide receptor ligand" NARROW []
synonym: "GRP receptor binding" EXACT []
is_a: GO:0031705 ! bombesin receptor binding
@@ -170286,7 +169992,7 @@ is_a: GO:0031705 ! bombesin receptor binding
id: GO:0031710
name: neuromedin B receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neuromedin B receptor." [GOC:mah, GOC:nln]
+def: "Binding to a neuromedin B receptor." [GOC:mah, GOC:nln]
synonym: "neuromedin B receptor ligand" NARROW []
is_a: GO:0031705 ! bombesin receptor binding
@@ -170294,7 +170000,7 @@ is_a: GO:0031705 ! bombesin receptor binding
id: GO:0031711
name: bradykinin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a bradykinin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a bradykinin receptor." [GOC:mah, GOC:nln]
synonym: "bradykinin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170302,7 +170008,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031712
name: B1 bradykinin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a B1 bradykinin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a B1 bradykinin receptor." [GOC:mah, GOC:nln]
synonym: "B1 bradykinin receptor ligand" NARROW []
is_a: GO:0031711 ! bradykinin receptor binding
@@ -170310,7 +170016,7 @@ is_a: GO:0031711 ! bradykinin receptor binding
id: GO:0031713
name: B2 bradykinin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a B2 bradykinin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a B2 bradykinin receptor." [GOC:mah, GOC:nln]
synonym: "B2 bradykinin receptor ligand" NARROW []
is_a: GO:0031711 ! bradykinin receptor binding
@@ -170318,7 +170024,7 @@ is_a: GO:0031711 ! bradykinin receptor binding
id: GO:0031714
name: C5a anaphylatoxin chemotactic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a C5a anaphylatoxin chemotactic receptor." [GOC:mah, GOC:nln]
+def: "Binding to a C5a anaphylatoxin chemotactic receptor." [GOC:mah, GOC:nln]
synonym: "C5a anaphylatoxin chemotactic receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170326,7 +170032,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031715
name: C5L2 anaphylatoxin chemotactic receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a C5L2 anaphylatoxin chemotactic receptor." [GOC:mah, GOC:nln]
+def: "Binding to a C5L2 anaphylatoxin chemotactic receptor." [GOC:mah, GOC:nln]
synonym: "C5L2 anaphylatoxin chemotactic receptor ligand" NARROW []
is_a: GO:0031714 ! C5a anaphylatoxin chemotactic receptor binding
@@ -170334,7 +170040,7 @@ is_a: GO:0031714 ! C5a anaphylatoxin chemotactic receptor binding
id: GO:0031716
name: calcitonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a calcitonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a calcitonin receptor." [GOC:mah, GOC:nln]
synonym: "calcitonin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170342,7 +170048,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031717
name: cannabinoid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cannabinoid receptor." [GOC:mah, GOC:nln]
+def: "Binding to a cannabinoid receptor." [GOC:mah, GOC:nln]
synonym: "cannabinoid receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170350,7 +170056,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031718
name: type 1 cannabinoid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 cannabinoid receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 cannabinoid receptor." [GOC:mah, GOC:nln]
synonym: "type 1 cannabinoid receptor ligand" NARROW []
is_a: GO:0031717 ! cannabinoid receptor binding
@@ -170358,7 +170064,7 @@ is_a: GO:0031717 ! cannabinoid receptor binding
id: GO:0031719
name: type 2 cannabinoid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 cannabinoid receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 cannabinoid receptor." [GOC:mah, GOC:nln]
synonym: "type 2 cannabinoid receptor ligand" NARROW []
is_a: GO:0031717 ! cannabinoid receptor binding
@@ -170366,28 +170072,28 @@ is_a: GO:0031717 ! cannabinoid receptor binding
id: GO:0031720
name: haptoglobin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a haptoglobin, any alpha2 globulin of blood plasma that can combine with free oxyhemoglobin to form a stable complex." [GOC:mah, ISBN:0198506732]
+def: "Binding to a haptoglobin, any alpha2 globulin of blood plasma that can combine with free oxyhemoglobin to form a stable complex." [GOC:mah, ISBN:0198506732]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0031721
name: hemoglobin alpha binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a hemoglobin alpha chain." [GOC:mah]
+def: "Binding to a hemoglobin alpha chain." [GOC:mah]
is_a: GO:0030492 ! hemoglobin binding
[Term]
id: GO:0031722
name: hemoglobin beta binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a hemoglobin beta chain." [GOC:mah]
+def: "Binding to a hemoglobin beta chain." [GOC:mah]
is_a: GO:0030492 ! hemoglobin binding
[Term]
id: GO:0031723
name: CXCR4 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CXCR4 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CXCR4 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CXCR4 chemokine receptor ligand" NARROW []
synonym: "stromal cell-derived factor 1 receptor binding" EXACT []
is_a: GO:0045236 ! CXCR chemokine receptor binding
@@ -170396,7 +170102,7 @@ is_a: GO:0045236 ! CXCR chemokine receptor binding
id: GO:0031724
name: CXCR5 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CXCR5 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CXCR5 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CXCR5 chemokine receptor ligand" NARROW []
synonym: "type 1 Burkitt's lymphoma receptor binding" EXACT []
is_a: GO:0045236 ! CXCR chemokine receptor binding
@@ -170405,7 +170111,7 @@ is_a: GO:0045236 ! CXCR chemokine receptor binding
id: GO:0031725
name: CXCR6 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CXCR6 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CXCR6 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "bonzo receptor binding" EXACT []
synonym: "CXCR6 chemokine receptor ligand" NARROW []
synonym: "STRL33 receptor binding" EXACT []
@@ -170415,7 +170121,7 @@ is_a: GO:0045236 ! CXCR chemokine receptor binding
id: GO:0031726
name: CCR1 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR1 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR1 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR1 chemokine receptor ligand" NARROW []
synonym: "macrophage inflammatory protein-1 alpha receptor binding" EXACT []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170424,7 +170130,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031727
name: CCR2 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR2 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR2 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR2 chemokine receptor ligand" NARROW []
synonym: "monocyte chemoattractant protein 1 receptor binding" EXACT []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170433,7 +170139,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031728
name: CCR3 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR3 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR3 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR3 chemokine receptor ligand" NARROW []
synonym: "eosinophil eotaxin receptor binding" EXACT []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170442,7 +170148,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031729
name: CCR4 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR4 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR4 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR4 chemokine receptor ligand" NARROW []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170450,7 +170156,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031730
name: CCR5 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR5 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR5 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR5 chemokine receptor ligand" NARROW []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170458,7 +170164,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031731
name: CCR6 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR6 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR6 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR6 chemokine receptor ligand" NARROW []
synonym: "LARC receptor binding" EXACT []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170467,7 +170173,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031732
name: CCR7 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR7 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR7 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR7 chemokine receptor ligand" NARROW []
synonym: "MIP-3 beta receptor binding" EXACT []
synonym: "type 1 EBV-induced G-protein coupled receptor binding" EXACT []
@@ -170477,7 +170183,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031733
name: CCR8 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR8 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR8 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR8 chemokine receptor ligand" NARROW []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170485,7 +170191,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031734
name: CCR9 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR9 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR9 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR9 chemokine receptor ligand" NARROW []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170493,7 +170199,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031735
name: CCR10 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR10 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR10 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR10 chemokine receptor ligand" NARROW []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170501,7 +170207,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031736
name: CCR11 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR11 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CCR11 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CCR11 chemokine receptor ligand" NARROW []
is_a: GO:0048020 ! CCR chemokine receptor binding
@@ -170509,7 +170215,7 @@ is_a: GO:0048020 ! CCR chemokine receptor binding
id: GO:0031737
name: CX3C chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CX3C chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a CX3C chemokine receptor." [GOC:mah, GOC:nln]
synonym: "CX3C chemokine receptor ligand" NARROW []
synonym: "fractalkine receptor binding" EXACT []
is_a: GO:0042379 ! chemokine receptor binding
@@ -170518,7 +170224,7 @@ is_a: GO:0042379 ! chemokine receptor binding
id: GO:0031738
name: XCR1 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a XCR1 chemokine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a XCR1 chemokine receptor." [GOC:mah, GOC:nln]
synonym: "lymphotactin receptor binding" EXACT []
synonym: "XCR1 chemokine receptor ligand" NARROW []
is_a: GO:0042379 ! chemokine receptor binding
@@ -170527,7 +170233,7 @@ is_a: GO:0042379 ! chemokine receptor binding
id: GO:0031739
name: cholecystokinin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cholecystokinin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a cholecystokinin receptor." [GOC:mah, GOC:nln]
synonym: "cholecystokinin receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -170535,7 +170241,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031740
name: type A cholecystokinin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type A cholecystokinin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type A cholecystokinin receptor." [GOC:mah, GOC:nln]
synonym: "type A cholecystokinin receptor ligand" NARROW []
is_a: GO:0031739 ! cholecystokinin receptor binding
@@ -170543,7 +170249,7 @@ is_a: GO:0031739 ! cholecystokinin receptor binding
id: GO:0031741
name: type B gastrin/cholecystokinin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type B gastrin/cholecystokinin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type B gastrin/cholecystokinin receptor." [GOC:mah, GOC:nln]
synonym: "type B gastrin/cholecystokinin receptor ligand" NARROW []
is_a: GO:0031739 ! cholecystokinin receptor binding
@@ -170551,7 +170257,7 @@ is_a: GO:0031739 ! cholecystokinin receptor binding
id: GO:0031745
name: cysteinyl leukotriene receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cysteinyl leukotriene receptor." [GOC:mah, GOC:nln]
+def: "Binding to a cysteinyl leukotriene receptor." [GOC:mah, GOC:nln]
synonym: "cysteinyl leukotriene receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170559,7 +170265,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031746
name: type 1 cysteinyl leukotriene receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 cysteinyl leukotriene receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 cysteinyl leukotriene receptor." [GOC:mah, GOC:nln]
synonym: "type 1 cysteinyl leukotriene receptor ligand" NARROW []
is_a: GO:0031745 ! cysteinyl leukotriene receptor binding
@@ -170567,7 +170273,7 @@ is_a: GO:0031745 ! cysteinyl leukotriene receptor binding
id: GO:0031747
name: type 2 cysteinyl leukotriene receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 cysteinyl leukotriene receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 cysteinyl leukotriene receptor." [GOC:mah, GOC:nln]
synonym: "type 2 cysteinyl leukotriene receptor ligand" NARROW []
is_a: GO:0031745 ! cysteinyl leukotriene receptor binding
@@ -170575,7 +170281,7 @@ is_a: GO:0031745 ! cysteinyl leukotriene receptor binding
id: GO:0031748
name: D1 dopamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a D1 dopamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a D1 dopamine receptor." [GOC:mah, GOC:nln]
synonym: "D1 dopamine receptor ligand" NARROW []
synonym: "D1A dopamine receptor binding" EXACT []
is_a: GO:0050780 ! dopamine receptor binding
@@ -170584,7 +170290,7 @@ is_a: GO:0050780 ! dopamine receptor binding
id: GO:0031749
name: D2 dopamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a D2 dopamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a D2 dopamine receptor." [GOC:mah, GOC:nln]
synonym: "D2 dopamine receptor ligand" NARROW []
is_a: GO:0050780 ! dopamine receptor binding
@@ -170592,7 +170298,7 @@ is_a: GO:0050780 ! dopamine receptor binding
id: GO:0031750
name: D3 dopamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a D3 dopamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a D3 dopamine receptor." [GOC:mah, GOC:nln]
synonym: "D3 dopamine receptor ligand" NARROW []
is_a: GO:0050780 ! dopamine receptor binding
@@ -170600,7 +170306,7 @@ is_a: GO:0050780 ! dopamine receptor binding
id: GO:0031751
name: D4 dopamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a D4 dopamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a D4 dopamine receptor." [GOC:mah, GOC:nln]
synonym: "D4 dopamine receptor ligand" NARROW []
is_a: GO:0050780 ! dopamine receptor binding
@@ -170608,7 +170314,7 @@ is_a: GO:0050780 ! dopamine receptor binding
id: GO:0031752
name: D5 dopamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a D5 dopamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a D5 dopamine receptor." [GOC:mah, GOC:nln]
synonym: "D1B dopamine receptor binding" EXACT []
synonym: "D5 dopamine receptor ligand" NARROW []
is_a: GO:0050780 ! dopamine receptor binding
@@ -170617,7 +170323,7 @@ is_a: GO:0050780 ! dopamine receptor binding
id: GO:0031753
name: endothelial differentiation G protein-coupled receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an endothelial differentiation G protein-coupled receptor." [GOC:mah, GOC:nln]
+def: "Binding to an endothelial differentiation G protein-coupled receptor." [GOC:mah, GOC:nln]
synonym: "endothelial differentiation G-protein coupled receptor binding" EXACT []
synonym: "endothelial differentiation G-protein coupled receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170626,7 +170332,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031754
name: Edg-1 sphingosine 1-phosphate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an Edg-1 sphingosine 1-phosphate receptor." [GOC:mah, GOC:nln]
+def: "Binding to an Edg-1 sphingosine 1-phosphate receptor." [GOC:mah, GOC:nln]
synonym: "Edg-1 sphingosine 1-phosphate receptor ligand" NARROW []
is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor binding
@@ -170634,7 +170340,7 @@ is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor bindin
id: GO:0031755
name: Edg-2 lysophosphatidic acid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an Edg-2 lysophosphatidic acid receptor." [GOC:mah, GOC:nln]
+def: "Binding to an Edg-2 lysophosphatidic acid receptor." [GOC:mah, GOC:nln]
synonym: "Edg-2 lysophosphatidic acid receptor ligand" NARROW []
synonym: "LPA1 receptor binding" EXACT []
is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor binding
@@ -170643,7 +170349,7 @@ is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor bindin
id: GO:0031756
name: Edg-3 sphingosine 1-phosphate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an Edg-3 sphingosine 1-phosphate receptor." [GOC:mah, GOC:nln]
+def: "Binding to an Edg-3 sphingosine 1-phosphate receptor." [GOC:mah, GOC:nln]
synonym: "Edg-3 sphingosine 1-phosphate receptor ligand" NARROW []
is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor binding
@@ -170651,7 +170357,7 @@ is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor bindin
id: GO:0031757
name: Edg-4 lysophosphatidic acid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an Edg-4 lysophosphatidic acid receptor." [GOC:mah, GOC:nln]
+def: "Binding to an Edg-4 lysophosphatidic acid receptor." [GOC:mah, GOC:nln]
synonym: "Edg-4 lysophosphatidic acid receptor ligand" NARROW []
synonym: "LPA2 receptor binding" EXACT []
is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor binding
@@ -170660,7 +170366,7 @@ is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor bindin
id: GO:0031758
name: Edg-5 sphingosine 1-phosphate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an Edg-5 sphingosine 1-phosphate receptor." [GOC:mah, GOC:nln]
+def: "Binding to an Edg-5 sphingosine 1-phosphate receptor." [GOC:mah, GOC:nln]
synonym: "Edg-5 sphingosine 1-phosphate receptor ligand" NARROW []
is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor binding
@@ -170668,7 +170374,7 @@ is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor bindin
id: GO:0031759
name: Edg-6 sphingosine 1-phosphate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an Edg-6 sphingosine 1-phosphate receptor." [GOC:mah, GOC:nln]
+def: "Binding to an Edg-6 sphingosine 1-phosphate receptor." [GOC:mah, GOC:nln]
synonym: "Edg-6 sphingosine 1-phosphate receptor ligand" NARROW []
is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor binding
@@ -170676,7 +170382,7 @@ is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor bindin
id: GO:0031760
name: Edg-7 lysophosphatidic acid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an Edg-7 lysophosphatidic acid receptor." [GOC:mah, GOC:nln]
+def: "Binding to an Edg-7 lysophosphatidic acid receptor." [GOC:mah, GOC:nln]
synonym: "Edg-7 lysophosphatidic acid receptor ligand" NARROW []
synonym: "LPA3 receptor binding" EXACT []
is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor binding
@@ -170685,7 +170391,7 @@ is_a: GO:0031753 ! endothelial differentiation G protein-coupled receptor bindin
id: GO:0031761
name: fMet-Leu-Phe receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a fMet-Leu-Phe receptor." [GOC:mah, GOC:nln]
+def: "Binding to a fMet-Leu-Phe receptor." [GOC:mah, GOC:nln]
synonym: "fMet-Leu-Phe receptor ligand" NARROW []
synonym: "N-formyl peptide receptor binding" EXACT []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170694,7 +170400,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031762
name: follicle-stimulating hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a follicle-stimulating hormone receptor." [GOC:mah, GOC:nln]
+def: "Binding to a follicle-stimulating hormone receptor." [GOC:mah, GOC:nln]
synonym: "follicle stimulating hormone receptor binding" EXACT []
synonym: "follicle stimulating hormone receptor ligand" NARROW []
synonym: "FSH receptor binding" EXACT []
@@ -170704,7 +170410,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031763
name: galanin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a galanin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a galanin receptor." [GOC:mah, GOC:nln]
synonym: "galanin receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -170712,7 +170418,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031764
name: type 1 galanin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 galanin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 galanin receptor." [GOC:mah, GOC:nln]
synonym: "type 1 galanin receptor ligand" NARROW []
is_a: GO:0031763 ! galanin receptor binding
@@ -170720,7 +170426,7 @@ is_a: GO:0031763 ! galanin receptor binding
id: GO:0031765
name: type 2 galanin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 galanin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 galanin receptor." [GOC:mah, GOC:nln]
synonym: "type 2 galanin receptor ligand" NARROW []
is_a: GO:0031763 ! galanin receptor binding
@@ -170728,7 +170434,7 @@ is_a: GO:0031763 ! galanin receptor binding
id: GO:0031766
name: type 3 galanin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 3 galanin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 3 galanin receptor." [GOC:mah, GOC:nln]
synonym: "type 3 galanin receptor ligand" NARROW []
is_a: GO:0031763 ! galanin receptor binding
@@ -170736,7 +170442,7 @@ is_a: GO:0031763 ! galanin receptor binding
id: GO:0031767
name: gastric inhibitory polypeptide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a gastric inhibitory polypeptide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a gastric inhibitory polypeptide receptor." [GOC:mah, GOC:nln]
synonym: "gastric inhibitory polypeptide receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170744,7 +170450,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031768
name: ghrelin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ghrelin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a ghrelin receptor." [GOC:mah, GOC:nln]
synonym: "ghrelin receptor ligand" NARROW []
synonym: "type 1 growth hormone secretagogue GH-releasing peptide receptor binding" EXACT []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170753,7 +170459,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031769
name: glucagon receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a glucagon receptor." [GOC:mah, GOC:nln]
+def: "Binding to a glucagon receptor." [GOC:mah, GOC:nln]
synonym: "glucagon receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170761,7 +170467,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031770
name: growth hormone-releasing hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a growth hormone-releasing hormone receptor." [GOC:mah, GOC:nln]
+def: "Binding to a growth hormone-releasing hormone receptor." [GOC:mah, GOC:nln]
synonym: "growth hormone-releasing hormone receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -170769,7 +170475,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031771
name: type 1 hypocretin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 hypocretin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 hypocretin receptor." [GOC:mah, GOC:nln]
synonym: "type 1 hypocretin receptor ligand" NARROW []
synonym: "type 1 orexin receptor binding" EXACT []
is_a: GO:0042324 ! hypocretin receptor binding
@@ -170778,7 +170484,7 @@ is_a: GO:0042324 ! hypocretin receptor binding
id: GO:0031772
name: type 2 hypocretin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 hypocretin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 hypocretin receptor." [GOC:mah, GOC:nln]
synonym: "type 2 hypocretin receptor ligand" NARROW []
synonym: "type 2 orexin receptor binding" EXACT []
is_a: GO:0042324 ! hypocretin receptor binding
@@ -170787,7 +170493,7 @@ is_a: GO:0042324 ! hypocretin receptor binding
id: GO:0031773
name: kisspeptin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a kisspeptin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a kisspeptin receptor." [GOC:mah, GOC:nln]
synonym: "G-protein coupled receptor 54 binding" EXACT []
synonym: "hOT7T175 receptor binding" EXACT []
synonym: "hypogonadotropin-1 receptor binding" EXACT []
@@ -170800,7 +170506,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031774
name: leukotriene receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a leukotriene receptor." [GOC:mah, GOC:nln]
+def: "Binding to a leukotriene receptor." [GOC:mah, GOC:nln]
synonym: "leukotriene receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170808,7 +170514,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031775
name: lutropin-choriogonadotropic hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lutropin-choriogonadotropic hormone receptor." [GOC:mah, GOC:nln]
+def: "Binding to a lutropin-choriogonadotropic hormone receptor." [GOC:mah, GOC:nln]
synonym: "lutropin-choriogonadotropic hormone receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170816,7 +170522,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031776
name: melanin-concentrating hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a melanin-concentrating hormone receptor." [GOC:mah, GOC:nln]
+def: "Binding to a melanin-concentrating hormone receptor." [GOC:mah, GOC:nln]
synonym: "melanin-concentrating hormone receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -170824,7 +170530,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031777
name: type 1 melanin-concentrating hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 melanin-concentrating hormone receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 melanin-concentrating hormone receptor." [GOC:mah, GOC:nln]
synonym: "type 1 melanin-concentrating hormone receptor ligand" NARROW []
is_a: GO:0031776 ! melanin-concentrating hormone receptor binding
@@ -170832,7 +170538,7 @@ is_a: GO:0031776 ! melanin-concentrating hormone receptor binding
id: GO:0031778
name: type 2 melanin-concentrating hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 melanin-concentrating hormone receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 melanin-concentrating hormone receptor." [GOC:mah, GOC:nln]
synonym: "type 2 melanin-concentrating hormone receptor ligand" NARROW []
is_a: GO:0031776 ! melanin-concentrating hormone receptor binding
@@ -170840,7 +170546,7 @@ is_a: GO:0031776 ! melanin-concentrating hormone receptor binding
id: GO:0031779
name: melanocortin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a melanocortin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a melanocortin receptor." [GOC:mah, GOC:nln]
synonym: "melanocortin receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -170849,7 +170555,7 @@ id: GO:0031780
name: corticotropin hormone receptor binding
namespace: molecular_function
alt_id: GO:0071856
-def: "Interacting selectively and non-covalently with a corticotropin hormone receptor." [GOC:dph, GOC:mah, GOC:nln]
+def: "Binding to a corticotropin hormone receptor." [GOC:dph, GOC:mah, GOC:nln]
synonym: "ACTH receptor binding" EXACT []
synonym: "adrenocorticotropic hormone receptor ligand" NARROW []
synonym: "adrenocorticotropin hormone receptor binding" EXACT [GOC:dph, GOC:tb]
@@ -170861,7 +170567,7 @@ is_a: GO:0031779 ! melanocortin receptor binding
id: GO:0031781
name: type 3 melanocortin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 3 melanocortin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 3 melanocortin receptor." [GOC:mah, GOC:nln]
synonym: "type 3 melanocortin receptor ligand" NARROW []
is_a: GO:0031779 ! melanocortin receptor binding
@@ -170869,7 +170575,7 @@ is_a: GO:0031779 ! melanocortin receptor binding
id: GO:0031782
name: type 4 melanocortin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 4 melanocortin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 4 melanocortin receptor." [GOC:mah, GOC:nln]
synonym: "type 4 melanocortin receptor ligand" NARROW []
is_a: GO:0031779 ! melanocortin receptor binding
@@ -170877,7 +170583,7 @@ is_a: GO:0031779 ! melanocortin receptor binding
id: GO:0031783
name: type 5 melanocortin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 5 melanocortin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 5 melanocortin receptor." [GOC:mah, GOC:nln]
synonym: "type 5 melanocortin receptor ligand" NARROW []
is_a: GO:0031779 ! melanocortin receptor binding
@@ -170885,7 +170591,7 @@ is_a: GO:0031779 ! melanocortin receptor binding
id: GO:0031784
name: melatonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a melatonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a melatonin receptor." [GOC:mah, GOC:nln]
synonym: "melatonin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170893,7 +170599,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031785
name: type 1A melatonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1A melatonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1A melatonin receptor." [GOC:mah, GOC:nln]
synonym: "type 1A melatonin receptor ligand" NARROW []
is_a: GO:0031784 ! melatonin receptor binding
@@ -170901,7 +170607,7 @@ is_a: GO:0031784 ! melatonin receptor binding
id: GO:0031786
name: type 1B melatonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1B melatonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1B melatonin receptor." [GOC:mah, GOC:nln]
synonym: "type 1B melatonin receptor ligand" NARROW []
is_a: GO:0031784 ! melatonin receptor binding
@@ -170909,7 +170615,7 @@ is_a: GO:0031784 ! melatonin receptor binding
id: GO:0031787
name: H9 melatonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a H9 melatonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a H9 melatonin receptor." [GOC:mah, GOC:nln]
synonym: "H9 melatonin receptor ligand" NARROW []
is_a: GO:0031784 ! melatonin receptor binding
@@ -170917,7 +170623,7 @@ is_a: GO:0031784 ! melatonin receptor binding
id: GO:0031788
name: motilin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a motilin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a motilin receptor." [GOC:mah, GOC:nln]
synonym: "motilin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -170930,7 +170636,7 @@ alt_id: GO:0031791
alt_id: GO:0031792
alt_id: GO:0031793
alt_id: GO:0031794
-def: "Interacting selectively and non-covalently with a G protein-coupled acetylcholine receptor." [GOC:bf, GOC:mah, GOC:nln]
+def: "Binding to a G protein-coupled acetylcholine receptor." [GOC:bf, GOC:mah, GOC:nln]
synonym: "G-protein coupled acetylcholine receptor binding" EXACT []
synonym: "M1 muscarinic acetylcholine receptor binding" NARROW []
synonym: "M1 muscarinic acetylcholine receptor ligand" NARROW []
@@ -170950,7 +170656,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031795
name: G protein-coupled GABA receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a G protein-coupled (metabotropic) GABA receptor." [GOC:mah, GOC:nln]
+def: "Binding to a G protein-coupled (metabotropic) GABA receptor." [GOC:mah, GOC:nln]
synonym: "G-protein coupled GABA receptor binding" EXACT []
synonym: "GABAB receptor binding" EXACT []
synonym: "metabotropic GABA receptor binding" EXACT [GOC:bf]
@@ -170962,7 +170668,7 @@ is_a: GO:0050811 ! GABA receptor binding
id: GO:0031796
name: type 1 metabotropic GABA receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 metabotropic GABA receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 metabotropic GABA receptor." [GOC:mah, GOC:nln]
synonym: "type 1 metabotropic GABA receptor ligand" NARROW []
is_a: GO:0031795 ! G protein-coupled GABA receptor binding
@@ -170970,7 +170676,7 @@ is_a: GO:0031795 ! G protein-coupled GABA receptor binding
id: GO:0031797
name: type 2 metabotropic GABA receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 metabotropic GABA receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 metabotropic GABA receptor." [GOC:mah, GOC:nln]
synonym: "type 2 metabotropic GABA receptor ligand" NARROW []
is_a: GO:0031795 ! G protein-coupled GABA receptor binding
@@ -170978,7 +170684,7 @@ is_a: GO:0031795 ! G protein-coupled GABA receptor binding
id: GO:0031798
name: type 1 metabotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
synonym: "type 1 metabotropic glutamate receptor ligand" NARROW []
is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
@@ -170986,7 +170692,7 @@ is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
id: GO:0031799
name: type 2 metabotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
synonym: "type 2 metabotropic glutamate receptor ligand" NARROW []
is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
@@ -170994,7 +170700,7 @@ is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
id: GO:0031800
name: type 3 metabotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 3 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 3 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
synonym: "type 3 metabotropic glutamate receptor ligand" NARROW []
is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
@@ -171002,7 +170708,7 @@ is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
id: GO:0031801
name: type 4 metabotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 4 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 4 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
synonym: "type 4 metabotropic glutamate receptor ligand" NARROW []
is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
@@ -171010,7 +170716,7 @@ is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
id: GO:0031802
name: type 5 metabotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 5 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 5 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
synonym: "type 5 metabotropic glutamate receptor ligand" NARROW []
is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
@@ -171018,7 +170724,7 @@ is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
id: GO:0031803
name: type 6 metabotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 6 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 6 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
synonym: "type 6 metabotropic glutamate receptor ligand" NARROW []
is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
@@ -171026,7 +170732,7 @@ is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
id: GO:0031804
name: type 7 metabotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 7 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 7 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
synonym: "type 7 metabotropic glutamate receptor ligand" NARROW []
is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
@@ -171034,7 +170740,7 @@ is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
id: GO:0031805
name: type 8 metabotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 8 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 8 metabotropic glutamate receptor." [GOC:mah, GOC:nln]
synonym: "type 8 metabotropic glutamate receptor ligand" NARROW []
is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
@@ -171042,7 +170748,7 @@ is_a: GO:0035256 ! G protein-coupled glutamate receptor binding
id: GO:0031806
name: G protein-coupled histamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a G protein-coupled (metabotropic) histamine receptor." [GOC:mah, GOC:nln, PMID:12679144]
+def: "Binding to a G protein-coupled (metabotropic) histamine receptor." [GOC:mah, GOC:nln, PMID:12679144]
synonym: "G-protein coupled histamine receptor binding" EXACT []
synonym: "metabotropic histamine receptor binding" EXACT [GOC:bf]
synonym: "metabotropic histamine receptor ligand" NARROW []
@@ -171052,7 +170758,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031807
name: H1 histamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a H1 histamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a H1 histamine receptor." [GOC:mah, GOC:nln]
synonym: "H1 histamine receptor ligand" NARROW []
is_a: GO:0031806 ! G protein-coupled histamine receptor binding
@@ -171060,7 +170766,7 @@ is_a: GO:0031806 ! G protein-coupled histamine receptor binding
id: GO:0031808
name: H2 histamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a H2 histamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a H2 histamine receptor." [GOC:mah, GOC:nln]
synonym: "H2 histamine receptor ligand" NARROW []
is_a: GO:0031806 ! G protein-coupled histamine receptor binding
@@ -171068,7 +170774,7 @@ is_a: GO:0031806 ! G protein-coupled histamine receptor binding
id: GO:0031809
name: H3 histamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a H3 histamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a H3 histamine receptor." [GOC:mah, GOC:nln]
synonym: "H3 histamine receptor ligand" NARROW []
is_a: GO:0031806 ! G protein-coupled histamine receptor binding
@@ -171076,7 +170782,7 @@ is_a: GO:0031806 ! G protein-coupled histamine receptor binding
id: GO:0031810
name: H4 histamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a H4 histamine receptor." [GOC:mah, GOC:nln]
+def: "Binding to a H4 histamine receptor." [GOC:mah, GOC:nln]
synonym: "H4 histamine receptor ligand" NARROW []
is_a: GO:0031806 ! G protein-coupled histamine receptor binding
@@ -171084,7 +170790,7 @@ is_a: GO:0031806 ! G protein-coupled histamine receptor binding
id: GO:0031811
name: G protein-coupled nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a G protein-coupled (metabotropic) nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a G protein-coupled (metabotropic) nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "G-protein coupled nucleotide receptor binding" EXACT []
synonym: "metabotropic nucleotide receptor binding" EXACT [GOC:bf]
synonym: "metabotropic nucleotide receptor ligand" NARROW []
@@ -171095,7 +170801,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031812
name: P2Y1 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y1 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y1 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y1 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171103,7 +170809,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031813
name: P2Y2 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y2 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y2 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y2 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171111,7 +170817,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031814
name: P2Y4 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y4 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y4 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y4 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171119,7 +170825,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031815
name: P2Y5 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y5 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y5 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y5 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171127,7 +170833,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031816
name: P2Y6 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y6 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y6 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y6 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171135,7 +170841,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031817
name: P2Y8 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y8 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y8 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y8 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171143,7 +170849,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031818
name: P2Y9 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y9 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y9 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y9 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171151,7 +170857,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031819
name: P2Y10 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y10 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y10 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y10 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171159,7 +170865,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031820
name: P2Y11 nucleotide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a P2Y11 nucleotide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a P2Y11 nucleotide receptor." [GOC:mah, GOC:nln]
synonym: "P2Y11 nucleotide receptor ligand" NARROW []
is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
@@ -171167,7 +170873,7 @@ is_a: GO:0031811 ! G protein-coupled nucleotide receptor binding
id: GO:0031821
name: G protein-coupled serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a metabotropic serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a metabotropic serotonin receptor." [GOC:mah, GOC:nln]
synonym: "G-protein coupled serotonin receptor binding" EXACT []
synonym: "metabotropic 5-hydroxytryptamine receptor binding" EXACT []
synonym: "metabotropic serotonin receptor binding" EXACT [GOC:bf]
@@ -171178,7 +170884,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031822
name: type 1B serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1B serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1B serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 1B receptor binding" EXACT []
synonym: "type 1B serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171187,7 +170893,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031823
name: type 1D serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1D serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1D serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 1D receptor binding" EXACT []
synonym: "type 1D serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171196,7 +170902,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031824
name: type 1E serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1E serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1E serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 1E receptor binding" EXACT []
synonym: "type 1E serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171205,7 +170911,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031825
name: type 1F serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1F serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1F serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 1F receptor binding" EXACT []
synonym: "type 1F serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171214,7 +170920,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031826
name: type 2A serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2A serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2A serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 2A receptor binding" EXACT []
synonym: "type 2A serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171223,7 +170929,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031827
name: type 2B serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2B serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2B serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 2B receptor binding" EXACT []
synonym: "type 2B serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171232,7 +170938,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031828
name: type 2C serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2C serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2C serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 2C receptor binding" EXACT []
synonym: "type 2C serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171241,7 +170947,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031829
name: type 4 serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 4 serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 4 serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 4 receptor binding" EXACT []
synonym: "type 4 serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171250,7 +170956,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031830
name: type 5A serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 5A serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 5A serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 5A receptor binding" EXACT []
synonym: "type 5A serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171259,7 +170965,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031831
name: type 5B serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 5B serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 5B serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 5B receptor binding" EXACT []
synonym: "type 5B serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171268,7 +170974,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031832
name: type 6 serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 6 serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 6 serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 6 receptor binding" EXACT []
synonym: "type 6 serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171277,7 +170983,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031833
name: type 7 serotonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 7 serotonin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 7 serotonin receptor." [GOC:mah, GOC:nln]
synonym: "5-hydroxytryptamine 7 receptor binding" EXACT []
synonym: "type 7 serotonin receptor ligand" NARROW []
is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
@@ -171286,7 +170992,7 @@ is_a: GO:0031821 ! G protein-coupled serotonin receptor binding
id: GO:0031834
name: neurokinin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neurokinin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a neurokinin receptor." [GOC:mah, GOC:nln]
synonym: "neurokinin receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -171294,7 +171000,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031835
name: substance P receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a substance P receptor." [GOC:mah, GOC:nln]
+def: "Binding to a substance P receptor." [GOC:mah, GOC:nln]
synonym: "neurokinin-1 receptor binding" EXACT []
synonym: "substance P receptor ligand" NARROW []
is_a: GO:0031834 ! neurokinin receptor binding
@@ -171303,7 +171009,7 @@ is_a: GO:0031834 ! neurokinin receptor binding
id: GO:0031836
name: neuromedin K receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neuromedin K receptor." [GOC:mah, GOC:nln]
+def: "Binding to a neuromedin K receptor." [GOC:mah, GOC:nln]
synonym: "neurokinin-B receptor binding" EXACT []
synonym: "neuromedin K receptor ligand" NARROW []
is_a: GO:0031834 ! neurokinin receptor binding
@@ -171312,7 +171018,7 @@ is_a: GO:0031834 ! neurokinin receptor binding
id: GO:0031837
name: substance K receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a substance K receptor." [GOC:mah, GOC:nln]
+def: "Binding to a substance K receptor." [GOC:mah, GOC:nln]
synonym: "neurokinin-A receptor binding" EXACT []
synonym: "substance K receptor ligand" NARROW []
is_a: GO:0031834 ! neurokinin receptor binding
@@ -171328,7 +171034,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0031839
name: type 1 neuromedin U receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 neuromedin U receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 neuromedin U receptor." [GOC:mah, GOC:nln]
synonym: "type 1 neuromedin U receptor ligand" NARROW []
is_a: GO:0042922 ! neuromedin U receptor binding
@@ -171336,7 +171042,7 @@ is_a: GO:0042922 ! neuromedin U receptor binding
id: GO:0031840
name: type 2 neuromedin U receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 neuromedin U receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 neuromedin U receptor." [GOC:mah, GOC:nln]
synonym: "type 2 neuromedin U receptor ligand" NARROW []
is_a: GO:0042922 ! neuromedin U receptor binding
@@ -171344,7 +171050,7 @@ is_a: GO:0042922 ! neuromedin U receptor binding
id: GO:0031841
name: neuropeptide Y receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neuropeptide Y receptor." [GOC:mah, GOC:nln]
+def: "Binding to a neuropeptide Y receptor." [GOC:mah, GOC:nln]
synonym: "neuropeptide Y receptor ligand" NARROW []
synonym: "NPY receptor binding" EXACT []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -171353,7 +171059,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031842
name: type 1 neuropeptide Y receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 neuropeptide Y receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 neuropeptide Y receptor." [GOC:mah, GOC:nln]
synonym: "type 1 neuropeptide Y receptor ligand" NARROW []
is_a: GO:0031841 ! neuropeptide Y receptor binding
@@ -171361,7 +171067,7 @@ is_a: GO:0031841 ! neuropeptide Y receptor binding
id: GO:0031843
name: type 2 neuropeptide Y receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 neuropeptide Y receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 neuropeptide Y receptor." [GOC:mah, GOC:nln]
synonym: "type 2 neuropeptide Y receptor ligand" NARROW []
is_a: GO:0031841 ! neuropeptide Y receptor binding
@@ -171369,7 +171075,7 @@ is_a: GO:0031841 ! neuropeptide Y receptor binding
id: GO:0031844
name: type 4 neuropeptide Y receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 4 neuropeptide Y receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 4 neuropeptide Y receptor." [GOC:mah, GOC:nln]
synonym: "pancreatic polypeptide receptor binding" EXACT []
synonym: "type 4 neuropeptide Y receptor ligand" NARROW []
is_a: GO:0031841 ! neuropeptide Y receptor binding
@@ -171378,7 +171084,7 @@ is_a: GO:0031841 ! neuropeptide Y receptor binding
id: GO:0031845
name: type 5 neuropeptide Y receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 5 neuropeptide Y receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 5 neuropeptide Y receptor." [GOC:mah, GOC:nln]
synonym: "type 5 neuropeptide Y receptor ligand" NARROW []
is_a: GO:0031841 ! neuropeptide Y receptor binding
@@ -171386,7 +171092,7 @@ is_a: GO:0031841 ! neuropeptide Y receptor binding
id: GO:0031846
name: neurotensin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neurotensin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a neurotensin receptor." [GOC:mah, GOC:nln]
synonym: "neurotensin receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -171394,7 +171100,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031847
name: type 1 neurotensin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 neurotensin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 neurotensin receptor." [GOC:mah, GOC:nln]
synonym: "type 1 neurotensin receptor ligand" NARROW []
is_a: GO:0031846 ! neurotensin receptor binding
@@ -171411,7 +171117,7 @@ relationship: part_of GO:0016233 ! telomere capping
id: GO:0031849
name: olfactory receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an olfactory receptor." [GOC:mah, GOC:nln]
+def: "Binding to an olfactory receptor." [GOC:mah, GOC:nln]
synonym: "olfactory receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171419,7 +171125,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031850
name: delta-type opioid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a delta-type opioid receptor." [GOC:mah, GOC:nln]
+def: "Binding to a delta-type opioid receptor." [GOC:mah, GOC:nln]
synonym: "delta-type opioid receptor ligand" NARROW []
synonym: "enkephalin receptor binding" RELATED [GOC:sl]
is_a: GO:0031628 ! opioid receptor binding
@@ -171428,7 +171134,7 @@ is_a: GO:0031628 ! opioid receptor binding
id: GO:0031851
name: kappa-type opioid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a kappa-type opioid receptor." [GOC:mah, GOC:nln]
+def: "Binding to a kappa-type opioid receptor." [GOC:mah, GOC:nln]
synonym: "dynorphin receptor binding" RELATED []
synonym: "kappa-type opioid receptor ligand" NARROW [GOC:sl]
is_a: GO:0031628 ! opioid receptor binding
@@ -171437,7 +171143,7 @@ is_a: GO:0031628 ! opioid receptor binding
id: GO:0031852
name: mu-type opioid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mu-type opioid receptor." [GOC:mah, GOC:nln, GOC:sl]
+def: "Binding to a mu-type opioid receptor." [GOC:mah, GOC:nln, GOC:sl]
synonym: "morphine receptor binding" RELATED [GOC:sl]
synonym: "mu-type opioid receptor ligand" NARROW []
is_a: GO:0031628 ! opioid receptor binding
@@ -171446,7 +171152,7 @@ is_a: GO:0031628 ! opioid receptor binding
id: GO:0031853
name: nociceptin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nociceptin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a nociceptin receptor." [GOC:mah, GOC:nln]
synonym: "nociceptin receptor ligand" NARROW []
is_a: GO:0031628 ! opioid receptor binding
@@ -171454,7 +171160,7 @@ is_a: GO:0031628 ! opioid receptor binding
id: GO:0031854
name: orexigenic neuropeptide QRFP receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an orexigenic neuropeptide QRFP receptor." [GOC:mah, GOC:nln]
+def: "Binding to an orexigenic neuropeptide QRFP receptor." [GOC:mah, GOC:nln]
synonym: "orexigenic neuropeptide QRFP receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -171462,7 +171168,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031855
name: oxytocin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an oxytocin receptor." [GOC:mah, GOC:nln]
+def: "Binding to an oxytocin receptor." [GOC:mah, GOC:nln]
synonym: "oxytocin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171470,7 +171176,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031856
name: parathyroid hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a parathyroid hormone receptor." [GOC:mah, GOC:nln]
+def: "Binding to a parathyroid hormone receptor." [GOC:mah, GOC:nln]
synonym: "parathyroid hormone receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171478,7 +171184,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031857
name: type 1 parathyroid hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 parathyroid hormone receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 parathyroid hormone receptor." [GOC:mah, GOC:nln]
synonym: "type 1 parathyroid hormone receptor ligand" NARROW []
is_a: GO:0031856 ! parathyroid hormone receptor binding
@@ -171486,7 +171192,7 @@ is_a: GO:0031856 ! parathyroid hormone receptor binding
id: GO:0031858
name: pituitary adenylate cyclase-activating polypeptide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pituitary adenylate cyclase-activating polypeptide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a pituitary adenylate cyclase-activating polypeptide receptor." [GOC:mah, GOC:nln]
synonym: "PACAP receptor binding" EXACT []
synonym: "pituitary adenylate cyclase activating peptide receptor binding" EXACT [GOC:dph, GOC:tb]
synonym: "pituitary adenylate cyclase-activating peptide receptor ligand" NARROW []
@@ -171496,7 +171202,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031859
name: platelet activating factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a platelet activating factor receptor." [GOC:mah, GOC:nln]
+def: "Binding to a platelet activating factor receptor." [GOC:mah, GOC:nln]
synonym: "platelet activating factor receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171514,7 +171220,7 @@ relationship: part_of GO:0016233 ! telomere capping
id: GO:0031861
name: prolactin-releasing peptide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a prolactin-releasing peptide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a prolactin-releasing peptide receptor." [GOC:mah, GOC:nln]
synonym: "prolactin-releasing peptide receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -171522,7 +171228,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031862
name: prostanoid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a prostanoid receptor." [GOC:mah, GOC:nln]
+def: "Binding to a prostanoid receptor." [GOC:mah, GOC:nln]
synonym: "prostanoid receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171530,7 +171236,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031863
name: prostaglandin D2 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a prostaglandin D2 receptor." [GOC:mah, GOC:nln]
+def: "Binding to a prostaglandin D2 receptor." [GOC:mah, GOC:nln]
synonym: "prostaglandin D2 receptor ligand" NARROW []
synonym: "prostanoid DP receptor binding" EXACT []
is_a: GO:0031862 ! prostanoid receptor binding
@@ -171539,7 +171245,7 @@ is_a: GO:0031862 ! prostanoid receptor binding
id: GO:0031864
name: EP1 subtype prostaglandin E2 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an EP1 subtype prostaglandin E2 receptor." [GOC:mah, GOC:nln]
+def: "Binding to an EP1 subtype prostaglandin E2 receptor." [GOC:mah, GOC:nln]
synonym: "EP1 subtype prostaglandin E2 receptor ligand" NARROW []
synonym: "prostanoid EP1 receptor binding" EXACT []
is_a: GO:0031862 ! prostanoid receptor binding
@@ -171548,7 +171254,7 @@ is_a: GO:0031862 ! prostanoid receptor binding
id: GO:0031865
name: EP2 subtype prostaglandin E2 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an EP2 subtype prostaglandin E2 receptor." [GOC:mah, GOC:nln]
+def: "Binding to an EP2 subtype prostaglandin E2 receptor." [GOC:mah, GOC:nln]
synonym: "EP2 subtype prostaglandin E2 receptor ligand" NARROW []
synonym: "prostanoid EP2 receptor binding" EXACT []
is_a: GO:0031862 ! prostanoid receptor binding
@@ -171557,7 +171263,7 @@ is_a: GO:0031862 ! prostanoid receptor binding
id: GO:0031866
name: EP3 subtype prostaglandin E2 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an EP3 subtype prostaglandin E2 receptor." [GOC:mah, GOC:nln]
+def: "Binding to an EP3 subtype prostaglandin E2 receptor." [GOC:mah, GOC:nln]
synonym: "EP3 subtype prostaglandin E2 receptor ligand" NARROW []
synonym: "prostanoid EP3 receptor binding" EXACT []
is_a: GO:0031862 ! prostanoid receptor binding
@@ -171566,7 +171272,7 @@ is_a: GO:0031862 ! prostanoid receptor binding
id: GO:0031867
name: EP4 subtype prostaglandin E2 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an EP4 subtype prostaglandin E2 receptor." [GOC:mah, GOC:nln]
+def: "Binding to an EP4 subtype prostaglandin E2 receptor." [GOC:mah, GOC:nln]
synonym: "EP4 subtype prostaglandin E2 receptor ligand" NARROW []
synonym: "prostanoid EP4 receptor binding" EXACT []
is_a: GO:0031862 ! prostanoid receptor binding
@@ -171575,7 +171281,7 @@ is_a: GO:0031862 ! prostanoid receptor binding
id: GO:0031868
name: prostaglandin F2-alpha receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a prostaglandin F2-alpha receptor." [GOC:mah, GOC:nln]
+def: "Binding to a prostaglandin F2-alpha receptor." [GOC:mah, GOC:nln]
synonym: "prostaglandin F2-alpha receptor ligand" NARROW []
synonym: "prostanoid FP receptor binding" EXACT []
is_a: GO:0031862 ! prostanoid receptor binding
@@ -171584,7 +171290,7 @@ is_a: GO:0031862 ! prostanoid receptor binding
id: GO:0031869
name: prostacyclin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a prostacyclin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a prostacyclin receptor." [GOC:mah, GOC:nln]
synonym: "prostacyclin receptor ligand" NARROW []
synonym: "prostanoid IP receptor binding" EXACT []
is_a: GO:0031862 ! prostanoid receptor binding
@@ -171593,7 +171299,7 @@ is_a: GO:0031862 ! prostanoid receptor binding
id: GO:0031870
name: thromboxane A2 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a thromboxane A2 receptor." [GOC:mah, GOC:nln]
+def: "Binding to a thromboxane A2 receptor." [GOC:mah, GOC:nln]
synonym: "prostanoid TP receptor binding" EXACT []
synonym: "thromboxane A2 receptor ligand" NARROW []
is_a: GO:0031862 ! prostanoid receptor binding
@@ -171602,7 +171308,7 @@ is_a: GO:0031862 ! prostanoid receptor binding
id: GO:0031871
name: proteinase activated receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a proteinase activated receptor." [GOC:mah, GOC:nln]
+def: "Binding to a proteinase activated receptor." [GOC:mah, GOC:nln]
synonym: "proteinase activated receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171610,7 +171316,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031872
name: type 1 proteinase activated receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 proteinase activated receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 proteinase activated receptor." [GOC:mah, GOC:nln]
synonym: "thrombin receptor binding" EXACT []
synonym: "type 1 proteinase activated receptor ligand" NARROW []
is_a: GO:0031871 ! proteinase activated receptor binding
@@ -171619,7 +171325,7 @@ is_a: GO:0031871 ! proteinase activated receptor binding
id: GO:0031873
name: type 2 proteinase activated receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 proteinase activated receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 proteinase activated receptor." [GOC:mah, GOC:nln]
synonym: "type 2 proteinase activated receptor ligand" NARROW []
is_a: GO:0031871 ! proteinase activated receptor binding
@@ -171627,7 +171333,7 @@ is_a: GO:0031871 ! proteinase activated receptor binding
id: GO:0031874
name: type 3 proteinase activated receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 3 proteinase activated receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 3 proteinase activated receptor." [GOC:mah, GOC:nln]
synonym: "type 3 proteinase activated receptor ligand" NARROW []
is_a: GO:0031871 ! proteinase activated receptor binding
@@ -171635,7 +171341,7 @@ is_a: GO:0031871 ! proteinase activated receptor binding
id: GO:0031875
name: type 4 proteinase activated receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 4 proteinase activated receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 4 proteinase activated receptor." [GOC:mah, GOC:nln]
synonym: "type 4 proteinase activated receptor ligand" NARROW []
is_a: GO:0031871 ! proteinase activated receptor binding
@@ -171643,7 +171349,7 @@ is_a: GO:0031871 ! proteinase activated receptor binding
id: GO:0031876
name: secretin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a secretin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a secretin receptor." [GOC:mah, GOC:nln]
synonym: "secretin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171651,7 +171357,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031877
name: somatostatin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a somatostatin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a somatostatin receptor." [GOC:mah, GOC:nln]
synonym: "somatostatin receptor ligand" NARROW []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -171659,7 +171365,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031878
name: type 1 somatostatin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 somatostatin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 somatostatin receptor." [GOC:mah, GOC:nln]
synonym: "type 1 somatostatin receptor ligand" NARROW []
is_a: GO:0031877 ! somatostatin receptor binding
@@ -171667,7 +171373,7 @@ is_a: GO:0031877 ! somatostatin receptor binding
id: GO:0031879
name: type 2 somatostatin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 somatostatin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 somatostatin receptor." [GOC:mah, GOC:nln]
synonym: "type 2 somatostatin receptor ligand" NARROW []
is_a: GO:0031877 ! somatostatin receptor binding
@@ -171675,7 +171381,7 @@ is_a: GO:0031877 ! somatostatin receptor binding
id: GO:0031880
name: type 3 somatostatin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 3 somatostatin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 3 somatostatin receptor." [GOC:mah, GOC:nln]
synonym: "type 3 somatostatin receptor ligand" NARROW []
is_a: GO:0031877 ! somatostatin receptor binding
@@ -171683,7 +171389,7 @@ is_a: GO:0031877 ! somatostatin receptor binding
id: GO:0031881
name: type 4 somatostatin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 4 somatostatin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 4 somatostatin receptor." [GOC:mah, GOC:nln]
synonym: "type 4 somatostatin receptor ligand" NARROW []
is_a: GO:0031877 ! somatostatin receptor binding
@@ -171691,7 +171397,7 @@ is_a: GO:0031877 ! somatostatin receptor binding
id: GO:0031882
name: type 5 somatostatin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 5 somatostatin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 5 somatostatin receptor." [GOC:mah, GOC:nln]
synonym: "type 5 somatostatin receptor ligand" NARROW []
is_a: GO:0031877 ! somatostatin receptor binding
@@ -171699,7 +171405,7 @@ is_a: GO:0031877 ! somatostatin receptor binding
id: GO:0031883
name: taste receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a taste receptor." [GOC:mah, GOC:nln]
+def: "Binding to a taste receptor." [GOC:mah, GOC:nln]
synonym: "taste receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171707,7 +171413,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031884
name: type 1 member 1 taste receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 member 1 taste receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 member 1 taste receptor." [GOC:mah, GOC:nln]
synonym: "type 1 member 1 taste receptor ligand" NARROW []
is_a: GO:0031883 ! taste receptor binding
@@ -171715,7 +171421,7 @@ is_a: GO:0031883 ! taste receptor binding
id: GO:0031885
name: type 1 member 2 taste receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 member 2 taste receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 member 2 taste receptor." [GOC:mah, GOC:nln]
synonym: "type 1 member 2 taste receptor ligand" NARROW []
is_a: GO:0031883 ! taste receptor binding
@@ -171723,7 +171429,7 @@ is_a: GO:0031883 ! taste receptor binding
id: GO:0031886
name: type 1 member 3 taste receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 member 3 taste receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 member 3 taste receptor." [GOC:mah, GOC:nln]
synonym: "sweet taste receptor binding" EXACT []
synonym: "type 1 member 3 taste receptor ligand" NARROW []
is_a: GO:0031883 ! taste receptor binding
@@ -171742,7 +171448,7 @@ is_a: GO:0072384 ! organelle transport along microtubule
id: GO:0031889
name: urotensin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a urotensin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a urotensin receptor." [GOC:mah, GOC:nln]
synonym: "urotensin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171750,7 +171456,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031890
name: vasoactive intestinal polypeptide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a vasoactive intestinal polypeptide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a vasoactive intestinal polypeptide receptor." [GOC:mah, GOC:nln]
synonym: "vasoactive intestinal polypeptide receptor ligand" NARROW []
synonym: "VIP receptor binding" EXACT []
is_a: GO:0071855 ! neuropeptide receptor binding
@@ -171759,7 +171465,7 @@ is_a: GO:0071855 ! neuropeptide receptor binding
id: GO:0031891
name: type 1 vasoactive intestinal polypeptide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 vasoactive intestinal polypeptide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 1 vasoactive intestinal polypeptide receptor." [GOC:mah, GOC:nln]
synonym: "type 1 vasoactive intestinal polypeptide receptor ligand" NARROW []
synonym: "type 2 PACAP receptor binding" EXACT []
is_a: GO:0031890 ! vasoactive intestinal polypeptide receptor binding
@@ -171768,7 +171474,7 @@ is_a: GO:0031890 ! vasoactive intestinal polypeptide receptor binding
id: GO:0031892
name: type 2 vasoactive intestinal polypeptide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 2 vasoactive intestinal polypeptide receptor." [GOC:mah, GOC:nln]
+def: "Binding to a type 2 vasoactive intestinal polypeptide receptor." [GOC:mah, GOC:nln]
synonym: "type 2 vasoactive intestinal polypeptide receptor ligand" NARROW []
synonym: "type 3 PACAP receptor binding" EXACT []
is_a: GO:0031890 ! vasoactive intestinal polypeptide receptor binding
@@ -171777,7 +171483,7 @@ is_a: GO:0031890 ! vasoactive intestinal polypeptide receptor binding
id: GO:0031893
name: vasopressin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a vasopressin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a vasopressin receptor." [GOC:mah, GOC:nln]
synonym: "vasopressin receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -171785,7 +171491,7 @@ is_a: GO:0001664 ! G protein-coupled receptor binding
id: GO:0031894
name: V1A vasopressin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a V1A vasopressin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a V1A vasopressin receptor." [GOC:mah, GOC:nln]
synonym: "V1A vasopressin receptor ligand" NARROW []
is_a: GO:0031893 ! vasopressin receptor binding
@@ -171793,7 +171499,7 @@ is_a: GO:0031893 ! vasopressin receptor binding
id: GO:0031895
name: V1B vasopressin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a V1B vasopressin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a V1B vasopressin receptor." [GOC:mah, GOC:nln]
synonym: "V1B vasopressin receptor ligand" NARROW []
is_a: GO:0031893 ! vasopressin receptor binding
@@ -171801,7 +171507,7 @@ is_a: GO:0031893 ! vasopressin receptor binding
id: GO:0031896
name: V2 vasopressin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a V2 vasopressin receptor." [GOC:mah, GOC:nln]
+def: "Binding to a V2 vasopressin receptor." [GOC:mah, GOC:nln]
synonym: "V2 vasopressin receptor ligand" NARROW []
is_a: GO:0031893 ! vasopressin receptor binding
@@ -172150,86 +171856,78 @@ is_a: GO:0000792 ! heterochromatin
[Term]
id: GO:0031935
-name: regulation of chromatin silencing
+name: obsolete regulation of chromatin silencing
namespace: biological_process
-def: "Any process that affects the rate, extent or location of chromatin silencing." [GOC:mah]
+def: "OBSOLETE. Any process that affects the rate, extent or location of chromatin silencing." [GOC:mah]
+comment: This term was obsoleted because it was too vague: regulation of chromatin (gene) silencing takes place via upstream signaling pathways.
synonym: "regulation of heterochromatic silencing" RELATED []
-is_a: GO:0006355 ! regulation of transcription, DNA-templated
-is_a: GO:0060968 ! regulation of gene silencing
-is_a: GO:1902275 ! regulation of chromatin organization
-relationship: regulates GO:0006342 ! chromatin silencing
+is_obsolete: true
[Term]
id: GO:0031936
-name: negative regulation of chromatin silencing
+name: obsolete negative regulation of chromatin silencing
namespace: biological_process
alt_id: GO:0006345
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing." [GOC:mah]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing." [GOC:mah]
+comment: This term was obsoleted because it was too vague: regulation of chromatin (gene) silencing takes place via upstream signaling pathways.
synonym: "down regulation of chromatin silencing" EXACT []
synonym: "down-regulation of chromatin silencing" EXACT []
synonym: "downregulation of chromatin silencing" EXACT []
synonym: "inhibition of chromatin silencing" NARROW []
synonym: "loss of chromatin silencing" EXACT []
synonym: "negative regulation of heterochromatic silencing" EXACT []
-is_a: GO:0031935 ! regulation of chromatin silencing
-is_a: GO:0045815 ! positive regulation of gene expression, epigenetic
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
-is_a: GO:0060969 ! negative regulation of gene silencing
-is_a: GO:1905268 ! negative regulation of chromatin organization
-relationship: negatively_regulates GO:0006342 ! chromatin silencing
+is_obsolete: true
[Term]
id: GO:0031937
-name: positive regulation of chromatin silencing
+name: obsolete positive regulation of chromatin silencing
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of chromatin silencing." [GOC:mah]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of chromatin silencing." [GOC:mah]
+comment: This term was obsoleted because it was too vague: regulation of chromatin (gene) silencing takes place via upstream signaling pathways.
synonym: "activation of chromatin silencing" NARROW []
synonym: "positive regulation of heterochromatic silencing" EXACT []
synonym: "stimulation of chromatin silencing" NARROW []
synonym: "up regulation of chromatin silencing" EXACT []
synonym: "up-regulation of chromatin silencing" EXACT []
synonym: "upregulation of chromatin silencing" EXACT []
-is_a: GO:0031935 ! regulation of chromatin silencing
-is_a: GO:1905269 ! positive regulation of chromatin organization
-relationship: positively_regulates GO:0006342 ! chromatin silencing
+is_obsolete: true
[Term]
id: GO:0031938
-name: regulation of chromatin silencing at telomere
+name: obsolete regulation of chromatin silencing at telomere
namespace: biological_process
-def: "Any process that affects the rate, extent or location of chromatin silencing at telomeres." [GOC:mah]
+def: "OBSOLETE. Any process that affects the rate, extent or location of chromatin silencing at telomeres." [GOC:mah]
+comment: This term was obsoleted because there is no evidence that chromatin silencing /heterochromatin assembly are directly regulated.
synonym: "regulation of heterochromatic silencing at telomere" EXACT []
-is_a: GO:0031935 ! regulation of chromatin silencing
-relationship: regulates GO:0006348 ! chromatin silencing at telomere
+is_obsolete: true
+consider: GO:0031509
[Term]
id: GO:0031939
-name: negative regulation of chromatin silencing at telomere
+name: obsolete negative regulation of chromatin silencing at telomere
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing at telomeres." [GOC:mah]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing at telomeres." [GOC:mah]
+comment: This term was obsoleted because there is no evidence that chromatin silencing /heterochromatin assembly are directly regulated.
synonym: "down regulation of chromatin silencing at telomere" EXACT []
synonym: "down-regulation of chromatin silencing at telomere" EXACT []
synonym: "downregulation of chromatin silencing at telomere" EXACT []
synonym: "inhibition of chromatin silencing at telomere" NARROW []
synonym: "negative regulation of heterochromatic silencing at telomere" EXACT []
-is_a: GO:0031936 ! negative regulation of chromatin silencing
-is_a: GO:0031938 ! regulation of chromatin silencing at telomere
-relationship: negatively_regulates GO:0006348 ! chromatin silencing at telomere
+is_obsolete: true
[Term]
id: GO:0031940
-name: positive regulation of chromatin silencing at telomere
+name: obsolete positive regulation of chromatin silencing at telomere
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of chromatin silencing at telomeres." [GOC:mah]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of chromatin silencing at telomeres." [GOC:mah]
+comment: This term was obsoleted because there is no evidence that chromatin silencing /heterochromatin assembly are directly regulated.
synonym: "activation of chromatin silencing at telomere" NARROW []
synonym: "positive regulation of heterochromatic silencing at telomere" EXACT []
synonym: "stimulation of chromatin silencing at telomere" NARROW []
synonym: "up regulation of chromatin silencing at telomere" EXACT []
synonym: "up-regulation of chromatin silencing at telomere" EXACT []
synonym: "upregulation of chromatin silencing at telomere" EXACT []
-is_a: GO:0031937 ! positive regulation of chromatin silencing
-is_a: GO:0031938 ! regulation of chromatin silencing at telomere
-relationship: positively_regulates GO:0006348 ! chromatin silencing at telomere
+is_obsolete: true
[Term]
id: GO:0031941
@@ -172476,14 +172174,14 @@ is_a: GO:0048545 ! response to steroid hormone
id: GO:0031961
name: cortisol receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cortisol receptor." [GOC:mah, PMID:12511169]
+def: "Binding to a cortisol receptor." [GOC:mah, PMID:12511169]
is_a: GO:0035259 ! glucocorticoid receptor binding
[Term]
id: GO:0031962
name: mineralocorticoid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mineralocorticoid receptor." [GOC:mah, PMID:12511169]
+def: "Binding to a mineralocorticoid receptor." [GOC:mah, PMID:12511169]
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -172716,6 +172414,7 @@ id: GO:0031991
name: regulation of actomyosin contractile ring contraction
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of contraction of the actomyosin ring involved in cytokinesis that takes place as part of a cell cycle." [GOC:dph, GOC:mah, GOC:tb]
+synonym: "regulation of actomyosin contractile ring constriction" EXACT [GOC:vw]
synonym: "regulation of contractile ring contraction involved in cell cycle cytokinesis" EXACT [GOC:mah, GOC:vw]
synonym: "regulation of contractile ring contraction involved in cytokinesis during cell cycle" RELATED [GOC:dph, GOC:tb]
is_a: GO:0032506 ! cytokinetic process
@@ -172743,7 +172442,7 @@ is_a: GO:0031992 ! energy transducer activity
id: GO:0031994
name: insulin-like growth factor I binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with insulin-like growth factor I." [GOC:mah]
+def: "Binding to insulin-like growth factor I." [GOC:mah]
subset: goslim_chembl
synonym: "IGF-I binding" EXACT []
is_a: GO:0005520 ! insulin-like growth factor binding
@@ -172752,7 +172451,7 @@ is_a: GO:0005520 ! insulin-like growth factor binding
id: GO:0031995
name: insulin-like growth factor II binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with insulin-like growth factor II." [GOC:mah]
+def: "Binding to insulin-like growth factor II." [GOC:mah]
subset: goslim_chembl
synonym: "IGF-II binding" EXACT []
is_a: GO:0005520 ! insulin-like growth factor binding
@@ -172761,7 +172460,7 @@ is_a: GO:0005520 ! insulin-like growth factor binding
id: GO:0031996
name: thioesterase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any thioesterase enzyme." [GOC:dl]
+def: "Binding to a thioesterase." [GOC:dl]
synonym: "thiolesterase binding" EXACT []
is_a: GO:0019899 ! enzyme binding
@@ -172769,7 +172468,7 @@ is_a: GO:0019899 ! enzyme binding
id: GO:0031997
name: N-terminal myristoylation domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the N-terminus of a protein that has the potential to be, or has been, modified by N-terminal myristoylation. Binding affinity is typically altered by myristoylation; for example, N-terminal myristoylation of HIV Nef increases its affinity for calmodulin." [GOC:dl, GOC:jsg, PMID:15632291]
+def: "Binding to the N-terminus of a protein that has the potential to be, or has been, modified by N-terminal myristoylation. Binding affinity is typically altered by myristoylation; for example, N-terminal myristoylation of HIV Nef increases its affinity for calmodulin." [GOC:dl, GOC:jsg, PMID:15632291]
is_a: GO:0047485 ! protein N-terminus binding
[Term]
@@ -172840,7 +172539,7 @@ relationship: part_of GO:0005887 ! integral component of plasma membrane
id: GO:0032003
name: interleukin-28 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-28 receptor." [GOC:rph]
+def: "Binding to an interleukin-28 receptor." [GOC:rph]
synonym: "IL-28" NARROW []
synonym: "interleukin-28 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -172915,7 +172614,7 @@ is_a: GO:0045335 ! phagocytic vesicle
id: GO:0032010
name: phagolysosome
namespace: cellular_component
-def: "A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes." [GOC:mah, PMID:12388753]
+def: "A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes." [GOC:mah, PMID:12388753, PMID:14733906]
synonym: "late phagocytic vesicle" RELATED []
synonym: "late phagosome" RELATED []
xref: Wikipedia:Phagolysosome
@@ -173023,7 +172722,7 @@ id: GO:0032020
name: ISG15-protein conjugation
namespace: biological_process
def: "The covalent addition to a protein of ISG15, a ubiquitin-like protein." [GOC:mah]
-is_a: GO:0006464 ! cellular protein modification process
+is_a: GO:0032446 ! protein modification by small protein conjugation
[Term]
id: GO:0032021
@@ -173074,28 +172773,28 @@ is_a: GO:0010038 ! response to metal ion
id: GO:0032027
name: myosin light chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a light chain of a myosin complex." [GOC:mah]
+def: "Binding to a light chain of a myosin complex." [GOC:mah]
is_a: GO:0017022 ! myosin binding
[Term]
id: GO:0032028
name: myosin head/neck binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the head/neck region of a myosin heavy chain." [GOC:mah]
+def: "Binding to the head/neck region of a myosin heavy chain." [GOC:mah]
is_a: GO:0032036 ! myosin heavy chain binding
[Term]
id: GO:0032029
name: myosin tail binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the tail region of a myosin heavy chain." [GOC:mah]
+def: "Binding to the tail region of a myosin heavy chain." [GOC:mah]
is_a: GO:0032036 ! myosin heavy chain binding
[Term]
id: GO:0032030
name: myosin I light chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a light chain of a myosin I complex." [GOC:mah]
+def: "Binding to a light chain of a myosin I complex." [GOC:mah]
is_a: GO:0017024 ! myosin I binding
is_a: GO:0032027 ! myosin light chain binding
@@ -173103,7 +172802,7 @@ is_a: GO:0032027 ! myosin light chain binding
id: GO:0032031
name: myosin I head/neck binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the head/neck region of a myosin I heavy chain." [GOC:mah]
+def: "Binding to the head/neck region of a myosin I heavy chain." [GOC:mah]
is_a: GO:0032028 ! myosin head/neck binding
is_a: GO:0032037 ! myosin I heavy chain binding
@@ -173111,7 +172810,7 @@ is_a: GO:0032037 ! myosin I heavy chain binding
id: GO:0032032
name: myosin I tail binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the tail region of a myosin I heavy chain." [GOC:mah]
+def: "Binding to the tail region of a myosin I heavy chain." [GOC:mah]
is_a: GO:0032029 ! myosin tail binding
is_a: GO:0032037 ! myosin I heavy chain binding
@@ -173119,7 +172818,7 @@ is_a: GO:0032037 ! myosin I heavy chain binding
id: GO:0032033
name: myosin II light chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a light chain of a myosin II complex." [GOC:mah]
+def: "Binding to a light chain of a myosin II complex." [GOC:mah]
is_a: GO:0032027 ! myosin light chain binding
is_a: GO:0045159 ! myosin II binding
@@ -173127,7 +172826,7 @@ is_a: GO:0045159 ! myosin II binding
id: GO:0032034
name: myosin II head/neck binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the head/neck region of a myosin II heavy chain." [GOC:mah]
+def: "Binding to the head/neck region of a myosin II heavy chain." [GOC:mah]
is_a: GO:0032028 ! myosin head/neck binding
is_a: GO:0032038 ! myosin II heavy chain binding
@@ -173135,7 +172834,7 @@ is_a: GO:0032038 ! myosin II heavy chain binding
id: GO:0032035
name: myosin II tail binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the tail region of a myosin II heavy chain." [GOC:mah]
+def: "Binding to the tail region of a myosin II heavy chain." [GOC:mah]
is_a: GO:0032029 ! myosin tail binding
is_a: GO:0032038 ! myosin II heavy chain binding
@@ -173143,14 +172842,14 @@ is_a: GO:0032038 ! myosin II heavy chain binding
id: GO:0032036
name: myosin heavy chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a heavy chain of a myosin complex." [GOC:mah]
+def: "Binding to a heavy chain of a myosin complex." [GOC:mah]
is_a: GO:0017022 ! myosin binding
[Term]
id: GO:0032037
name: myosin I heavy chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a heavy chain of a myosin I complex." [GOC:mah]
+def: "Binding to a heavy chain of a myosin I complex." [GOC:mah]
is_a: GO:0017024 ! myosin I binding
is_a: GO:0032036 ! myosin heavy chain binding
@@ -173158,7 +172857,7 @@ is_a: GO:0032036 ! myosin heavy chain binding
id: GO:0032038
name: myosin II heavy chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a heavy chain of a myosin II complex." [GOC:mah]
+def: "Binding to a heavy chain of a myosin II complex." [GOC:mah]
is_a: GO:0032036 ! myosin heavy chain binding
is_a: GO:0045159 ! myosin II binding
@@ -173182,8 +172881,7 @@ is_a: GO:0030684 ! preribosome
id: GO:0032041
name: NAD-dependent histone deacetylase activity (H3-K14 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein." [EC:3.5.1.17, RHEA:24548]
-xref: EC:3.5.1.98
+def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein." [PMID:28450737]
is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
is_a: GO:0031078 ! histone deacetylase activity (H3-K14 specific)
@@ -173230,7 +172928,6 @@ name: guanyl-nucleotide exchange factor complex
namespace: cellular_component
def: "A protein complex that stimulates the exchange of guanyl nucleotides associated with a GTPase." [GOC:mah]
is_a: GO:0140535 ! intracellular protein-containing complex
-is_a: GO:1902773 ! GTPase activator complex
[Term]
id: GO:0032046
@@ -173278,21 +172975,21 @@ is_a: GO:0032048 ! cardiolipin metabolic process
id: GO:0032050
name: clathrin heavy chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a clathrin heavy chain." [GOC:mah]
+def: "Binding to a clathrin heavy chain." [GOC:mah]
is_a: GO:0030276 ! clathrin binding
[Term]
id: GO:0032051
name: clathrin light chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a clathrin light chain." [GOC:mah]
+def: "Binding to a clathrin light chain." [GOC:mah]
is_a: GO:0030276 ! clathrin binding
[Term]
id: GO:0032052
name: bile acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile." [GOC:rph]
+def: "Binding to a bile acid, a steroid carboxylic acids occurring in bile." [GOC:rph]
is_a: GO:0033293 ! monocarboxylic acid binding
[Term]
@@ -173340,9 +173037,8 @@ synonym: "down regulation of translation initiation in response to stress" EXACT
synonym: "down-regulation of translation initiation in response to stress" EXACT []
synonym: "downregulation of translation initiation in response to stress" EXACT []
synonym: "inhibition of translation initiation in response to stress" NARROW []
-is_a: GO:0032055 ! negative regulation of translation in response to stress
-is_a: GO:0043558 ! regulation of translational initiation in response to stress
is_a: GO:0045947 ! negative regulation of translational initiation
+relationship: part_of GO:0006950 ! response to stress
[Term]
id: GO:0032058
@@ -173354,9 +173050,8 @@ synonym: "stimulation of translation initiation in response to stress" NARROW []
synonym: "up regulation of translation initiation in response to stress" EXACT []
synonym: "up-regulation of translation initiation in response to stress" EXACT []
synonym: "upregulation of translation initiation in response to stress" EXACT []
-is_a: GO:0032056 ! positive regulation of translation in response to stress
-is_a: GO:0043558 ! regulation of translational initiation in response to stress
is_a: GO:0045948 ! positive regulation of translational initiation
+relationship: part_of GO:0006950 ! response to stress
[Term]
id: GO:0032059
@@ -173438,7 +173133,6 @@ name: maintenance of protein location in cell cortex
namespace: biological_process
def: "A process in which a protein or protein complex is maintained in a specific location in the cell cortex." [GOC:vw]
synonym: "cortical protein anchoring" RELATED []
-synonym: "maintenance of protein location in cell cortex" EXACT [GOC:dph, GOC:tb]
is_a: GO:0032507 ! maintenance of protein location in cell
[Term]
@@ -173608,7 +173302,7 @@ synonym: "type I restriction endodeoxyribonuclease inhibitor" RELATED []
synonym: "type I restriction enzyme inhibitor" RELATED []
is_a: GO:0032073 ! negative regulation of restriction endodeoxyribonuclease activity
is_a: GO:0032084 ! regulation of type I site-specific deoxyribonuclease activity
-is_a: GO:0032780 ! negative regulation of ATPase activity
+is_a: GO:0032780 ! negative regulation of ATP-dependent activity
[Term]
id: GO:0032081
@@ -173664,7 +173358,7 @@ synonym: "regulation of type I restriction endodeoxyribonuclease activity" EXACT
synonym: "type I restriction endodeoxyribonuclease regulator" RELATED []
synonym: "type I restriction enzyme regulator" RELATED []
is_a: GO:0032072 ! regulation of restriction endodeoxyribonuclease activity
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
[Term]
id: GO:0032085
@@ -173709,14 +173403,14 @@ is_a: GO:0043433 ! negative regulation of DNA-binding transcription factor activ
id: GO:0032089
name: NACHT domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a NACHT (NAIP, CIITA, HET-E and TP1) domain. The NACHT domain consists of seven distinct conserved motifs, including an ATP/GTPase specific P-loop, a Mg(2+)-binding site and five more specific motifs." [GOC:rl]
+def: "Binding to a NACHT (NAIP, CIITA, HET-E and TP1) domain. The NACHT domain consists of seven distinct conserved motifs, including an ATP/GTPase specific P-loop, a Mg(2+)-binding site and five more specific motifs." [GOC:rl]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0032090
name: Pyrin domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Pyrin (PAAD/DAPIN) domain, a protein-protein interaction domain that has the same fold as the Death domain." [GOC:rl]
+def: "Binding to a Pyrin (PAAD/DAPIN) domain, a protein-protein interaction domain that has the same fold as the Death domain." [GOC:rl]
synonym: "DAPIN domain binding" EXACT []
synonym: "PAAD domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -173750,7 +173444,7 @@ is_a: GO:0051099 ! positive regulation of binding
id: GO:0032093
name: SAM domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a SAM (Sterile Alpha Motif) domain, which is a 70-amino acid protein sequence that participates in protein-protein, protein-lipid, and protein-RNA interactions and is conserved from lower to higher eukaryotes." [GOC:mcc, PMID:16337230]
+def: "Binding to a SAM (Sterile Alpha Motif) domain, which is a 70-amino acid protein sequence that participates in protein-protein, protein-lipid, and protein-RNA interactions and is conserved from lower to higher eukaryotes." [GOC:mcc, PMID:16337230]
synonym: "Sterile Alpha Motif domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -174134,7 +173828,7 @@ relationship: part_of GO:0031045 ! dense core granule
id: GO:0032129
name: histone deacetylase activity (H3-K9 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein." [EC:3.5.1.17, RHEA:24548]
+def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein." [PMID:28450737]
is_a: GO:0004407 ! histone deacetylase activity
[Term]
@@ -174150,14 +173844,14 @@ is_a: GO:1902410 ! mitotic cytokinetic process
id: GO:0032131
name: alkylated DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with alkylated residues in DNA." [GOC:mah]
+def: "Binding to an alkylated residue in DNA." [GOC:mah]
is_a: GO:0003684 ! damaged DNA binding
[Term]
id: GO:0032132
name: O6-alkylguanine-DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with O6-alkylguanine adducts in DNA." [GOC:mah, PMID:16679453]
+def: "Binding to an O6-alkylguanine adduct in DNA." [GOC:mah, PMID:16679453]
is_a: GO:0032131 ! alkylated DNA binding
[Term]
@@ -174174,7 +173868,7 @@ is_a: GO:0005875 ! microtubule associated complex
id: GO:0032135
name: DNA insertion or deletion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing insertions or deletions." [GOC:vk]
+def: "Binding to a double-stranded DNA region containing an insertion or a deletion." [GOC:vk]
synonym: "DNA insertion binding" NARROW []
synonym: "insertion binding" EXACT []
is_a: GO:0030983 ! mismatched DNA binding
@@ -174183,7 +173877,7 @@ is_a: GO:0030983 ! mismatched DNA binding
id: GO:0032136
name: adenine/cytosine mispair binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing an A/C mispair." [GOC:vk]
+def: "Binding to a double-stranded DNA region containing an A/C mispair." [GOC:vk]
synonym: "A/C mispair binding" EXACT [GOC:bf]
synonym: "C/A mispair binding" EXACT [GOC:bf]
synonym: "cytosine/adenine mispair binding" RELATED [GOC:bf]
@@ -174193,7 +173887,7 @@ is_a: GO:0030983 ! mismatched DNA binding
id: GO:0032137
name: guanine/thymine mispair binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a G/T mispair." [GOC:vk]
+def: "Binding to a double-stranded DNA region containing a G/T mispair." [GOC:vk]
synonym: "G/T mispair binding" EXACT [GOC:bf]
synonym: "T/G mispair binding" EXACT [GOC:bf]
synonym: "thymine/guanine mispair binding" EXACT [GOC:bf]
@@ -174203,7 +173897,7 @@ is_a: GO:0030983 ! mismatched DNA binding
id: GO:0032138
name: single base insertion or deletion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a single base insertion or deletion." [GOC:vk]
+def: "Binding to a double-stranded DNA region containing a single base insertion or deletion." [GOC:vk]
synonym: "single base insertion binding" NARROW []
is_a: GO:0032135 ! DNA insertion or deletion binding
@@ -174211,7 +173905,7 @@ is_a: GO:0032135 ! DNA insertion or deletion binding
id: GO:0032139
name: dinucleotide insertion or deletion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide insertion or deletion." [GOC:vk]
+def: "Binding to a double-stranded DNA region containing a dinucleotide insertion or deletion." [GOC:vk]
synonym: "dinucleotide insertion binding" NARROW []
is_a: GO:0032135 ! DNA insertion or deletion binding
@@ -174219,28 +173913,28 @@ is_a: GO:0032135 ! DNA insertion or deletion binding
id: GO:0032140
name: single adenine insertion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a single adenine insertion or a deletion that results in an unpaired adenine." [GOC:mah, GOC:vk]
+def: "Binding to a double-stranded DNA region containing a single adenine insertion or a deletion that results in an unpaired adenine." [GOC:mah, GOC:vk]
is_a: GO:0032138 ! single base insertion or deletion binding
[Term]
id: GO:0032141
name: single cytosine insertion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a single cytosine insertion or a deletion that results in an unpaired cytosine." [GOC:mah, GOC:vk]
+def: "Binding to a double-stranded DNA region containing a single cytosine insertion or a deletion that results in an unpaired cytosine." [GOC:mah, GOC:vk]
is_a: GO:0032138 ! single base insertion or deletion binding
[Term]
id: GO:0032142
name: single guanine insertion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a single guanine insertion or a deletion that results in an unpaired guanine." [GOC:mah, GOC:vk]
+def: "Binding to a double-stranded DNA region containing a single guanine insertion or a deletion that results in an unpaired guanine." [GOC:mah, GOC:vk]
is_a: GO:0032138 ! single base insertion or deletion binding
[Term]
id: GO:0032143
name: single thymine insertion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a single thymine insertion or a deletion that results in an unpaired thymine." [GOC:mah, GOC:vk]
+def: "Binding to a double-stranded DNA region containing a single thymine insertion or a deletion that results in an unpaired thymine." [GOC:mah, GOC:vk]
is_a: GO:0032138 ! single base insertion or deletion binding
[Term]
@@ -174258,7 +173952,7 @@ is_a: GO:1990234 ! transferase complex
id: GO:0032145
name: succinate-semialdehyde dehydrogenase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with succinate-semialdehyde dehydrogenase." [GOC:mah]
+def: "Binding to succinate-semialdehyde dehydrogenase." [GOC:mah]
synonym: "succinic semialdehyde dehydrogenase binding" EXACT []
is_a: GO:0019899 ! enzyme binding
@@ -174551,16 +174245,15 @@ is_a: GO:0006744 ! ubiquinone biosynthetic process
id: GO:0032181
name: dinucleotide repeat insertion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide repeat insertion or a deletion resulting in unpaired dinucleotide repeats." [GOC:mah, GOC:vk]
+def: "Binding to a double-stranded DNA region containing a dinucleotide repeat insertion or a deletion resulting in unpaired dinucleotide repeats." [GOC:mah, GOC:vk]
is_a: GO:0032139 ! dinucleotide insertion or deletion binding
[Term]
id: GO:0032182
name: ubiquitin-like protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein." [GOC:mah]
+def: "Binding to a small conjugating protein such as ubiquitin or a ubiquitin-like protein." [GOC:mah]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_yeast
synonym: "small conjugating protein binding" EXACT [GOC:dph]
is_a: GO:0005515 ! protein binding
@@ -174569,7 +174262,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0032183
name: SUMO binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the small ubiquitin-like protein SUMO." [GOC:mah]
+def: "Binding to the small ubiquitin-like protein SUMO." [GOC:mah]
synonym: "Smt3 binding" RELATED []
synonym: "Smt3 monomer binding" NARROW []
is_a: GO:0032182 ! ubiquitin-like protein binding
@@ -174578,7 +174271,7 @@ is_a: GO:0032182 ! ubiquitin-like protein binding
id: GO:0032184
name: SUMO polymer binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a polymer of the small ubiquitin-like protein SUMO." [GOC:mah]
+def: "Binding to a polymer of the small ubiquitin-like protein SUMO." [GOC:mah]
synonym: "Smt3 polymer binding" EXACT []
is_a: GO:0032183 ! SUMO binding
@@ -174643,7 +174336,7 @@ name: acrosin binding
namespace: molecular_function
alt_id: GO:0032191
alt_id: GO:0032192
-def: "Interacting selectively and non-covalently with acrosin, a protein that is found in the acrosomes of sperm and possesses protease and carbohydrate binding activities." [GOC:mah, PMID:12398221]
+def: "Binding to acrosin, a protein that is found in the acrosomes of sperm and possesses protease and carbohydrate binding activities." [GOC:mah, PMID:12398221]
synonym: "acrosin heavy chain binding" NARROW []
synonym: "acrosin light chain binding" NARROW []
is_a: GO:0019899 ! enzyme binding
@@ -174666,8 +174359,9 @@ is_a: GO:0006744 ! ubiquinone biosynthetic process
id: GO:0032195
name: post-lysosomal vacuole
namespace: cellular_component
-def: "A membrane-bounded intracellular vesicle formed late in the endocytic pathway when the pH in the vacuole becomes neutral prior to exocytosis." [GOC:pf, PMID:9276759, PMID:9394012]
+def: "A membrane-bounded intracellular vesicle formed late in the endocytic pathway when the pH in the vacuole becomes neutral prior to exocytosis." [GOC:pf, PMID:23494323, PMID:9276759, PMID:9394012]
synonym: "post-lysosome" EXACT [GOC:dph]
+synonym: "postlysosome" EXACT []
is_a: GO:0005773 ! vacuole
is_a: GO:0030139 ! endocytic vesicle
@@ -174679,7 +174373,6 @@ def: "Any process involved in mediating the movement of discrete segments of DNA
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
subset: goslim_yeast
xref: Wikipedia:Transposon
@@ -174728,6 +174421,7 @@ id: GO:0032200
name: telomere organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins." [GOC:dph, GOC:jl, GOC:mah]
+subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
synonym: "chromosome organization, telomeric" EXACT []
@@ -174745,7 +174439,6 @@ synonym: "equal telomere replication" RELATED []
synonym: "telomeric fork progression" NARROW []
synonym: "telomeric replication fork progression" NARROW []
is_a: GO:0000723 ! telomere maintenance
-is_a: GO:0019725 ! cellular homeostasis
is_a: GO:0022402 ! cell cycle process
relationship: part_of GO:0033260 ! nuclear DNA replication
@@ -174772,7 +174465,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA." [GOC:mah]
is_a: GO:0033044 ! regulation of chromosome organization
is_a: GO:0051052 ! regulation of DNA metabolic process
-is_a: GO:0065008 ! regulation of biological quality
relationship: regulates GO:0000723 ! telomere maintenance
[Term]
@@ -175449,7 +175141,7 @@ name: GMP salvage
namespace: biological_process
def: "Any process which produces guanosine monophosphate from derivatives of it, without de novo synthesis." [GOC:mah]
is_a: GO:0006177 ! GMP biosynthetic process
-is_a: GO:0032261 ! purine nucleotide salvage
+is_a: GO:0106380 ! purine ribonucleotide salvage
[Term]
id: GO:0032264
@@ -175457,21 +175149,21 @@ name: IMP salvage
namespace: biological_process
def: "Any process which produces inosine monophosphate from derivatives of it, without de novo synthesis." [GOC:mah]
is_a: GO:0006188 ! IMP biosynthetic process
-is_a: GO:0032261 ! purine nucleotide salvage
+is_a: GO:0106380 ! purine ribonucleotide salvage
[Term]
id: GO:0032265
name: XMP salvage
namespace: biological_process
def: "Any process which produces xanthosine monophosphate from derivatives of it, without de novo synthesis." [GOC:mah]
-is_a: GO:0032261 ! purine nucleotide salvage
is_a: GO:0097293 ! XMP biosynthetic process
+is_a: GO:0106380 ! purine ribonucleotide salvage
[Term]
id: GO:0032266
name: phosphatidylinositol-3-phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position." [GOC:bf, PMID:10209156, PMID:11395417, PMID:11557775]
+def: "Binding to phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position." [GOC:bf, PMID:10209156, PMID:11395417, PMID:11557775]
synonym: "phosphatidylinositol 3-phosphate binding" EXACT []
synonym: "PtdIns-3-P binding" EXACT []
is_a: GO:1901981 ! phosphatidylinositol phosphate binding
@@ -176386,7 +176078,7 @@ is_a: GO:1901700 ! response to oxygen-containing compound
id: GO:0032356
name: oxidized DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with oxidized residues in DNA." [GOC:vk]
+def: "Binding to a DNA region containing an oxidized residue." [GOC:vk]
synonym: "oxidised DNA binding" EXACT []
is_a: GO:0003684 ! damaged DNA binding
@@ -176394,7 +176086,7 @@ is_a: GO:0003684 ! damaged DNA binding
id: GO:0032357
name: oxidized purine DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with oxidized purine residues in DNA." [GOC:vk]
+def: "Binding to a DNA region containing an oxidized purine residue." [GOC:vk]
synonym: "oxidised purine DNA binding" EXACT []
synonym: "oxidized purine base DNA binding" EXACT []
synonym: "oxidized purine nucleobase DNA binding" EXACT []
@@ -176404,7 +176096,7 @@ is_a: GO:0032356 ! oxidized DNA binding
id: GO:0032358
name: oxidized pyrimidine DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with oxidized pyrimidine residues in DNA." [GOC:vk]
+def: "Binding to a DNA region containing an oxidized pyrimidine residue." [GOC:vk]
synonym: "oxidised pyrimidine DNA binding" EXACT []
synonym: "oxidized pyrimidine base DNA binding" EXACT []
synonym: "oxidized pyrimidine nucleobase DNA binding" EXACT []
@@ -176843,7 +176535,7 @@ is_a: GO:0042611 ! MHC protein complex
id: GO:0032399
name: HECT domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a HECT, 'Homologous to the E6-AP Carboxy-Terminus', domain of a protein." [GOC:mah, Pfam:PF00632]
+def: "Binding to a HECT, 'Homologous to the E6-AP Carboxy-Terminus', domain of a protein." [GOC:mah, Pfam:PF00632]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -176876,35 +176568,35 @@ is_a: GO:0051904 ! pigment granule transport
id: GO:0032404
name: mismatch repair complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mismatch repair complex." [GOC:vk]
+def: "Binding to a mismatch repair complex." [GOC:vk]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0032405
name: MutLalpha complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the mismatch repair complex MutLalpha." [GOC:vk]
+def: "Binding to a MutLalpha mismatch repair complex." [GOC:vk]
is_a: GO:0032404 ! mismatch repair complex binding
[Term]
id: GO:0032406
name: MutLbeta complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the mismatch repair complex MutLbeta." [GOC:vk]
+def: "Binding to a MutLbeta mismatch repair complex." [GOC:vk]
is_a: GO:0032404 ! mismatch repair complex binding
[Term]
id: GO:0032407
name: MutSalpha complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the mismatch repair complex MutSalpha." [GOC:vk]
+def: "Binding to a MutSalpha mismatch repair complex." [GOC:vk]
is_a: GO:0032404 ! mismatch repair complex binding
[Term]
id: GO:0032408
name: MutSbeta complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the mismatch repair complex MutSbeta." [GOC:vk]
+def: "Binding to a MutSbeta mismatch repair complex." [GOC:vk]
is_a: GO:0032404 ! mismatch repair complex binding
[Term]
@@ -177021,7 +176713,7 @@ name: lysosome localization
namespace: biological_process
def: "Any process in which a lysosome is transported to, and/or maintained in, a specific location." [GOC:mah]
synonym: "lysosome localisation" EXACT [GOC:mah]
-is_a: GO:0051640 ! organelle localization
+is_a: GO:1990849 ! vacuolar localization
[Term]
id: GO:0032419
@@ -177056,7 +176748,7 @@ is_a: GO:0098862 ! cluster of actin-based cell projections
id: GO:0032422
name: purine-rich negative regulatory element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 30-bp purine-rich negative regulatory element; the best characterized such element is found in the first intronic region of the rat cardiac alpha-myosin heavy chain gene, and contains two palindromic high-affinity Ets-binding sites (CTTCCCTGGAAG). The presence of this element restricts expression of the gene containing it to cardiac myocytes." [GOC:mah, PMID:9819411]
+def: "Binding to a 30-bp purine-rich negative regulatory element; the best characterized such element is found in the first intronic region of the rat cardiac alpha-myosin heavy chain gene, and contains two palindromic high-affinity Ets-binding sites (CTTCCCTGGAAG). The presence of this element restricts expression of the gene containing it to cardiac myocytes." [GOC:mah, PMID:9819411]
synonym: "PNR element binding" BROAD []
is_a: GO:0000976 ! transcription cis-regulatory region binding
@@ -177107,7 +176799,7 @@ relationship: part_of GO:0032420 ! stereocilium
id: GO:0032427
name: GBD domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the GTPase protein binding domain (GDB) domain of a protein. The GBD is a short motif, including a minimum region of 16 amino acids, identified in proteins that bind to small GTPases such as Cdc42 and Rac." [GOC:mah, GOC:pg, PMID:9119069]
+def: "Binding to a GTPase protein binding domain (GDB) domain. The GBD is a short motif, including a minimum region of 16 amino acids, identified in proteins that bind to small GTPases such as Cdc42 and Rac." [GOC:mah, GOC:pg, PMID:9119069]
synonym: "Cdc42/Rac interactive binding motif binding" EXACT [PMID:9119069]
synonym: "CRIB motif binding" EXACT [PMID:9119069]
synonym: "P21-Rho-binding domain binding" EXACT [GOC:rl]
@@ -177298,7 +176990,7 @@ is_a: GO:0032446 ! protein modification by small protein conjugation
id: GO:0032448
name: DNA hairpin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA containing a hairpin. A hairpin structure forms when a DNA strand folds back on itself and intrachain base pairing occurs between inverted repeat sequences." [GOC:mah, ISBN:0198506732]
+def: "Binding to a DNA region containing a hairpin. A hairpin structure forms when a DNA strand folds back on itself and intrachain base pairing occurs between inverted repeat sequences." [GOC:mah, ISBN:0198506732]
is_a: GO:0000217 ! DNA secondary structure binding
[Term]
@@ -177357,18 +177049,20 @@ is_a: GO:0140457 ! protein demethylase activity
[Term]
id: GO:0032453
-name: histone demethylase activity (H3-K4 specific)
+name: histone H3-methyl-lysine-4 demethylase activity
namespace: molecular_function
-def: "Catalysis of the removal of a methyl group from lysine at position 4 of the histone H3 protein." [GOC:mah]
+def: "Catalysis of the removal of a methyl group from a modified lysine residue at position 4 of the histone H3 protein." [GOC:mah]
+synonym: "histone demethylase activity (H3-K4 specific)" EXACT []
+synonym: "histone H3K4 demethylase activity" EXACT []
is_a: GO:0032452 ! histone demethylase activity
[Term]
id: GO:0032454
-name: histone demethylase activity (H3-K9 specific)
+name: histone H3-methyl-lysine-9 demethylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein." [PMID:16362057]
-xref: EC:1.14.11.65
-xref: EC:1.14.11.66
+def: "Catalysis of the removal of a methyl group from a modified lysine residue at position 9 of the histone H3 protein." [PMID:16362057]
+synonym: "H3K49 demethylase activity" EXACT []
+synonym: "histone demethylase activity (H3-K9 specific)" EXACT []
xref: Reactome:R-HSA-9011949 "KDM4B demethylates H3K9me3 on estrogen-responsive target enhancers"
xref: Reactome:R-HSA-9011985 "KDM1A demethylates H3 on MYC and BCL genes in response to estrogen"
xref: Reactome:R-HSA-997263 "JMJD1C demethylates H3K9 mono- and di-methylation"
@@ -177846,6 +177540,7 @@ namespace: biological_process
alt_id: GO:0044707
alt_id: GO:0050874
def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb]
+subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "organismal physiological process" EXACT []
synonym: "single-multicellular organism process" RELATED []
@@ -177870,6 +177565,7 @@ id: GO:0032504
name: multicellular organism reproduction
namespace: biological_process
def: "The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." [GOC:isa_complete, GOC:jid]
+subset: goslim_drosophila
is_a: GO:0000003 ! reproduction
is_a: GO:0032501 ! multicellular organismal process
@@ -178227,7 +177923,6 @@ id: GO:0032543
name: mitochondrial translation
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code." [GOC:go_curators]
-subset: goslim_drosophila
subset: goslim_yeast
synonym: "mitochondrial protein anabolism" EXACT []
synonym: "mitochondrial protein biosynthesis" EXACT []
@@ -178261,14 +177956,14 @@ is_a: GO:0140513 ! nuclear protein-containing complex
id: GO:0032546
name: deoxyribonucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a deoxyribonucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked to deoxyribose." [GOC:mah]
+def: "Binding to a deoxyribonucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked to deoxyribose." [GOC:mah]
is_a: GO:0001882 ! nucleoside binding
[Term]
id: GO:0032547
name: purine deoxyribonucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a purine deoxyribonucleoside, a compound consisting of a purine base linked to deoxyribose." [GOC:mah]
+def: "Binding to a purine deoxyribonucleoside, a compound consisting of a purine base linked to deoxyribose." [GOC:mah]
is_a: GO:0001883 ! purine nucleoside binding
is_a: GO:0032546 ! deoxyribonucleoside binding
@@ -178276,7 +177971,7 @@ is_a: GO:0032546 ! deoxyribonucleoside binding
id: GO:0032548
name: pyrimidine deoxyribonucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pyrimidine deoxyribonucleoside, a compound consisting of a pyrimidine base linked to deoxyribose." [GOC:mah]
+def: "Binding to a pyrimidine deoxyribonucleoside, a compound consisting of a pyrimidine base linked to deoxyribose." [GOC:mah]
is_a: GO:0001884 ! pyrimidine nucleoside binding
is_a: GO:0032546 ! deoxyribonucleoside binding
@@ -178284,14 +177979,14 @@ is_a: GO:0032546 ! deoxyribonucleoside binding
id: GO:0032549
name: ribonucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ribonucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked to ribose." [GOC:mah]
+def: "Binding to a ribonucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked to ribose." [GOC:mah]
is_a: GO:0001882 ! nucleoside binding
[Term]
id: GO:0032550
name: purine ribonucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a purine ribonucleoside, a compound consisting of a purine base linked to ribose." [GOC:mah]
+def: "Binding to a purine ribonucleoside, a compound consisting of a purine base linked to ribose." [GOC:mah]
is_a: GO:0001883 ! purine nucleoside binding
is_a: GO:0032549 ! ribonucleoside binding
@@ -178299,7 +177994,7 @@ is_a: GO:0032549 ! ribonucleoside binding
id: GO:0032551
name: pyrimidine ribonucleoside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pyrimidine ribonucleoside, a compound consisting of a pyrimidine base linked to ribose." [GOC:mah]
+def: "Binding to a pyrimidine ribonucleoside, a compound consisting of a pyrimidine base linked to ribose." [GOC:mah]
is_a: GO:0001884 ! pyrimidine nucleoside binding
is_a: GO:0032549 ! ribonucleoside binding
@@ -178307,7 +178002,7 @@ is_a: GO:0032549 ! ribonucleoside binding
id: GO:0032552
name: deoxyribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a deoxyribonucleotide, any compound consisting of a deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
+def: "Binding to a deoxyribonucleotide, any compound consisting of a deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
is_a: GO:0000166 ! nucleotide binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -178315,7 +178010,7 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:0032553
name: ribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ribonucleotide, any compound consisting of a ribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
+def: "Binding to a ribonucleotide, any compound consisting of a ribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
is_a: GO:0000166 ! nucleotide binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -178323,7 +178018,7 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:0032554
name: purine deoxyribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a purine deoxyribonucleotide, any compound consisting of a purine deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
+def: "Binding to a purine deoxyribonucleotide, any compound consisting of a purine deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
is_a: GO:0017076 ! purine nucleotide binding
is_a: GO:0032552 ! deoxyribonucleotide binding
@@ -178331,7 +178026,7 @@ is_a: GO:0032552 ! deoxyribonucleotide binding
id: GO:0032555
name: purine ribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a purine ribonucleotide, any compound consisting of a purine ribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
+def: "Binding to a purine ribonucleotide, any compound consisting of a purine ribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
is_a: GO:0017076 ! purine nucleotide binding
is_a: GO:0032553 ! ribonucleotide binding
@@ -178339,7 +178034,7 @@ is_a: GO:0032553 ! ribonucleotide binding
id: GO:0032556
name: pyrimidine deoxyribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pyrimidine deoxyribonucleotide, any compound consisting of a pyrimidine deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
+def: "Binding to a pyrimidine deoxyribonucleotide, any compound consisting of a pyrimidine deoxyribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
is_a: GO:0019103 ! pyrimidine nucleotide binding
is_a: GO:0032552 ! deoxyribonucleotide binding
@@ -178347,7 +178042,7 @@ is_a: GO:0032552 ! deoxyribonucleotide binding
id: GO:0032557
name: pyrimidine ribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pyrimidine ribonucleotide, any compound consisting of a pyrimidine ribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
+def: "Binding to a pyrimidine ribonucleotide, any compound consisting of a pyrimidine ribonucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
is_a: GO:0019103 ! pyrimidine nucleotide binding
is_a: GO:0032553 ! ribonucleotide binding
@@ -178355,7 +178050,7 @@ is_a: GO:0032553 ! ribonucleotide binding
id: GO:0032558
name: adenyl deoxyribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an adenyl deoxyribonucleotide, any compound consisting of adenosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
+def: "Binding to an adenyl deoxyribonucleotide, any compound consisting of adenosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
is_a: GO:0030554 ! adenyl nucleotide binding
is_a: GO:0032554 ! purine deoxyribonucleotide binding
@@ -178363,7 +178058,7 @@ is_a: GO:0032554 ! purine deoxyribonucleotide binding
id: GO:0032559
name: adenyl ribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an adenyl ribonucleotide, any compound consisting of adenosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
+def: "Binding to an adenyl ribonucleotide, any compound consisting of adenosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
is_a: GO:0030554 ! adenyl nucleotide binding
is_a: GO:0032555 ! purine ribonucleotide binding
@@ -178371,7 +178066,7 @@ is_a: GO:0032555 ! purine ribonucleotide binding
id: GO:0032560
name: guanyl deoxyribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a guanyl deoxyribonucleotide, any compound consisting of guanosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
+def: "Binding to a guanyl deoxyribonucleotide, any compound consisting of guanosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety." [GOC:mah]
is_a: GO:0019001 ! guanyl nucleotide binding
is_a: GO:0032554 ! purine deoxyribonucleotide binding
@@ -178379,7 +178074,7 @@ is_a: GO:0032554 ! purine deoxyribonucleotide binding
id: GO:0032561
name: guanyl ribonucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a guanyl ribonucleotide, any compound consisting of guanosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
+def: "Binding to a guanyl ribonucleotide, any compound consisting of guanosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose moiety." [GOC:mah]
is_a: GO:0019001 ! guanyl nucleotide binding
is_a: GO:0032555 ! purine ribonucleotide binding
@@ -178387,7 +178082,7 @@ is_a: GO:0032555 ! purine ribonucleotide binding
id: GO:0032562
name: dAMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dAMP, deoxyadenosine monophosphate." [GOC:mah]
+def: "Binding to dAMP, deoxyadenosine monophosphate." [GOC:mah]
is_a: GO:0032558 ! adenyl deoxyribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -178395,7 +178090,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0032563
name: dADP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dADP, deoxyadenosine diphosphate." [GOC:mah]
+def: "Binding to dADP, deoxyadenosine diphosphate." [GOC:mah]
is_a: GO:0032558 ! adenyl deoxyribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -178403,7 +178098,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0032564
name: dATP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dATP, deoxyadenosine triphosphate." [GOC:mah]
+def: "Binding to dATP, deoxyadenosine triphosphate." [GOC:mah]
is_a: GO:0032558 ! adenyl deoxyribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -178411,7 +178106,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0032565
name: dGMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dGMP, deoxyguanosine monophosphate." [GOC:mah]
+def: "Binding to dGMP, deoxyguanosine monophosphate." [GOC:mah]
is_a: GO:0032560 ! guanyl deoxyribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -178419,7 +178114,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0032566
name: dGDP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dGDP, deoxyguanosine diphosphate." [GOC:mah]
+def: "Binding to dGDP, deoxyguanosine diphosphate." [GOC:mah]
is_a: GO:0032560 ! guanyl deoxyribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -178427,7 +178122,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0032567
name: dGTP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dGTP, deoxyguanosine triphosphate." [GOC:mah]
+def: "Binding to dGTP, deoxyguanosine triphosphate." [GOC:mah]
is_a: GO:0032560 ! guanyl deoxyribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -178446,6 +178141,7 @@ name: response to vitamin K
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin K stimulus." [GOC:sl]
is_a: GO:0033273 ! response to vitamin
+is_a: GO:1901654 ! response to ketone
[Term]
id: GO:0032572
@@ -178454,7 +178150,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a menaquinone (vitamin K2) stimulus." [GOC:sl]
synonym: "response to menatetrenone" EXACT []
synonym: "response to vitamin K2" EXACT []
-is_a: GO:1901654 ! response to ketone
+is_a: GO:0032571 ! response to vitamin K
[Term]
id: GO:0032573
@@ -178462,14 +178158,14 @@ name: response to phylloquinone
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a phylloquinone (vitamin K1) stimulus." [GOC:sl]
synonym: "response to vitamin K1" EXACT []
-is_a: GO:1901654 ! response to ketone
+is_a: GO:0032571 ! response to vitamin K
[Term]
id: GO:0032574
name: 5'-3' RNA helicase activity
namespace: molecular_function
alt_id: GO:0032575
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix in the direction 5' to 3'." [GOC:jp]
+def: "Unwinding of an RNA helix in the 5' to 3' direction, driven by ATP hydrolysis." [GOC:jp]
synonym: "5' to 3' RNA helicase activity" EXACT []
synonym: "ATP-dependent 5' to 3' RNA helicase activity" EXACT []
synonym: "ATP-dependent 5'-3' RNA helicase activity" EXACT []
@@ -178515,7 +178211,7 @@ name: Golgi cisterna membrane
namespace: cellular_component
def: "The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex." [GOC:ecd, GOC:mah]
synonym: "Golgi stack membrane" EXACT []
-is_a: GO:0000139 ! Golgi membrane
+is_a: GO:0031090 ! organelle membrane
relationship: part_of GO:0031985 ! Golgi cisterna
[Term]
@@ -178573,7 +178269,7 @@ namespace: cellular_component
def: "The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network." [GOC:mah]
synonym: "Golgi trans face membrane" RELATED []
synonym: "trans Golgi network membrane" EXACT []
-is_a: GO:0000139 ! Golgi membrane
+is_a: GO:0031090 ! organelle membrane
relationship: part_of GO:0005802 ! trans-Golgi network
[Term]
@@ -178928,16 +178624,17 @@ is_a: GO:0001816 ! cytokine production
[Term]
id: GO:0032617
-name: interleukin-14 production
+name: obsolete interleukin-14 production
namespace: biological_process
alt_id: GO:0042232
alt_id: GO:0072612
-def: "The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah]
+def: "OBSOLETE. The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:mah]
+comment: This term was obsoleted because the gene was shown not to exist, see PMID:8755619.
subset: gocheck_do_not_annotate
synonym: "IL-14 production" EXACT []
synonym: "interleukin-14 biosynthetic process" NARROW []
synonym: "interleukin-14 secretion" NARROW []
-is_a: GO:0001816 ! cytokine production
+is_obsolete: true
[Term]
id: GO:0032618
@@ -179496,14 +179193,14 @@ relationship: regulates GO:0032616 ! interleukin-13 production
[Term]
id: GO:0032657
-name: regulation of interleukin-14 production
+name: obsolete regulation of interleukin-14 production
namespace: biological_process
alt_id: GO:0045369
-def: "Any process that modulates the frequency, rate, or extent of interleukin-14 production." [GOC:mah]
+def: "OBSOLETE. Any process that modulates the frequency, rate, or extent of interleukin-14 production." [GOC:mah]
+comment: This term was obsoleted because the gene was shown not to exist, see PMID:8755619.
synonym: "regulation of IL-14 production" EXACT []
synonym: "regulation of interleukin-14 biosynthetic process" NARROW []
-is_a: GO:0001817 ! regulation of cytokine production
-relationship: regulates GO:0032617 ! interleukin-14 production
+is_obsolete: true
[Term]
id: GO:0032658
@@ -180077,19 +179774,18 @@ relationship: negatively_regulates GO:0032616 ! interleukin-13 production
[Term]
id: GO:0032697
-name: negative regulation of interleukin-14 production
+name: obsolete negative regulation of interleukin-14 production
namespace: biological_process
alt_id: GO:0045370
-def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-14 production." [GOC:mah]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-14 production." [GOC:mah]
+comment: This term was obsoleted because the gene was shown not to exist, see PMID:8755619.
synonym: "down regulation of interleukin-14 production" EXACT []
synonym: "down-regulation of interleukin-14 production" EXACT []
synonym: "downregulation of interleukin-14 production" EXACT []
synonym: "inhibition of interleukin-14 production" NARROW []
synonym: "negative regulation of IL-14 production" EXACT []
synonym: "negative regulation of interleukin-14 biosynthetic process" NARROW []
-is_a: GO:0001818 ! negative regulation of cytokine production
-is_a: GO:0032657 ! regulation of interleukin-14 production
-relationship: negatively_regulates GO:0032617 ! interleukin-14 production
+is_obsolete: true
[Term]
id: GO:0032698
@@ -180786,10 +180482,11 @@ relationship: positively_regulates GO:0032616 ! interleukin-13 production
[Term]
id: GO:0032737
-name: positive regulation of interleukin-14 production
+name: obsolete positive regulation of interleukin-14 production
namespace: biological_process
alt_id: GO:0045371
-def: "Any process that activates or increases the frequency, rate, or extent of interleukin-14 production." [GOC:mah]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate, or extent of interleukin-14 production." [GOC:mah]
+comment: This term was obsoleted because the gene was shown not to exist, see PMID:8755619.
synonym: "activation of interleukin-14 production" NARROW []
synonym: "positive regulation of IL-14 production" EXACT []
synonym: "positive regulation of interleukin-14 biosynthetic process" NARROW []
@@ -180797,9 +180494,7 @@ synonym: "stimulation of interleukin-14 production" NARROW []
synonym: "up regulation of interleukin-14 production" EXACT []
synonym: "up-regulation of interleukin-14 production" EXACT []
synonym: "upregulation of interleukin-14 production" EXACT []
-is_a: GO:0001819 ! positive regulation of cytokine production
-is_a: GO:0032657 ! regulation of interleukin-14 production
-relationship: positively_regulates GO:0032617 ! interleukin-14 production
+is_obsolete: true
[Term]
id: GO:0032738
@@ -181298,7 +180993,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0032767
name: copper-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of copper." [GOC:ecd, PMID:16884690]
+def: "Binding to a protein or protein complex, in the presence of copper." [GOC:ecd, PMID:16884690]
is_a: GO:0005515 ! protein binding
[Term]
@@ -181335,38 +181030,41 @@ is_a: GO:0051353 ! positive regulation of oxidoreductase activity
[Term]
id: GO:0032771
-name: regulation of monophenol monooxygenase activity
+name: regulation of tyrosinase activity
namespace: biological_process
-def: "Any process that modulates the activity of the enzyme monophenol monooxygenase. Monophenol monooxygenase catalyzes the reaction: L-tyrosine + L-DOPA + O2 = L-DOPA + DOPAquinone + H2O." [GOC:dph, GOC:mah, GOC:tb, PMID:2494997]
+def: "Any process that modulates the activity of a tyrosinase enzyme." [GOC:dph, GOC:mah, GOC:tb, PMID:2494997]
+synonym: "regulation of monophenol monooxygenase activity" RELATED []
synonym: "regulation of monophenol oxygenase activity" EXACT [GOC:dph, GOC:tb]
is_a: GO:0032768 ! regulation of monooxygenase activity
[Term]
id: GO:0032772
-name: negative regulation of monophenol monooxygenase activity
+name: negative regulation of tyrosinase activity
namespace: biological_process
-def: "Any process that stops or reduces the activity of the enzyme monophenol monooxygenase. Monophenol monooxygenase catalyzes the reaction: L-tyrosine + L-DOPA + O2 = L-DOPA + DOPAquinone + H2O." [GOC:dph, GOC:mah, GOC:tb]
+def: "Any process that stops or reduces the activity of a tyrosinase enzyme." [GOC:dph, GOC:mah, GOC:tb]
synonym: "down regulation of monophenol oxygenase activity" EXACT []
synonym: "down-regulation of monophenol oxygenase activity" EXACT []
synonym: "downregulation of monophenol oxygenase activity" EXACT []
synonym: "inhibition of monophenol oxygenase activity" NARROW []
+synonym: "negative regulation of monophenol monooxygenase activity" RELATED []
synonym: "negative regulation of monophenol oxygenase activity" EXACT [GOC:dph, GOC:tb, PMID:2494997]
is_a: GO:0032769 ! negative regulation of monooxygenase activity
-is_a: GO:0032771 ! regulation of monophenol monooxygenase activity
+is_a: GO:0032771 ! regulation of tyrosinase activity
[Term]
id: GO:0032773
-name: positive regulation of monophenol monooxygenase activity
+name: positive regulation of tyrosinase activity
namespace: biological_process
-def: "Any process that activates or increases the activity of the enzyme monophenol oxygenase. Monophenol monooxygenase catalyzes the reaction: L-tyrosine + L-DOPA + O2 = L-DOPA + DOPAquinone + H2O." [GOC:dph, GOC:mah, GOC:tb, PMID:2494997]
+def: "Any process that activates or increases the activity of a tyrosinase enzyme monophenol oxygenase." [GOC:dph, GOC:mah, GOC:tb, PMID:2494997]
synonym: "activation of monophenol oxygenase activity" NARROW []
+synonym: "positive regulation of monophenol monooxygenase activity" RELATED []
synonym: "positive regulation of monophenol oxygenase activity" EXACT [GOC:dph, GOC:tb, PMID:2494997]
synonym: "stimulation of monophenol oxygenase activity" NARROW []
synonym: "up regulation of monophenol oxygenase activity" EXACT []
synonym: "up-regulation of monophenol oxygenase activity" EXACT []
synonym: "upregulation of monophenol oxygenase activity" EXACT []
is_a: GO:0032770 ! positive regulation of monooxygenase activity
-is_a: GO:0032771 ! regulation of monophenol monooxygenase activity
+is_a: GO:0032771 ! regulation of tyrosinase activity
[Term]
id: GO:0032774
@@ -181423,29 +181121,31 @@ is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
[Term]
id: GO:0032780
-name: negative regulation of ATPase activity
+name: negative regulation of ATP-dependent activity
namespace: biological_process
-def: "Any process that stops or reduces the rate of ATP hydrolysis by an ATPase." [GOC:mah]
+def: "Any process that stops or reduces the rate of an ATP-dependent activity." [GOC:mah]
synonym: "down regulation of ATPase activity" EXACT []
synonym: "down-regulation of ATPase activity" EXACT []
synonym: "downregulation of ATPase activity" EXACT []
synonym: "inhibition of ATPase activity" NARROW []
synonym: "negative regulation of adenosinetriphosphatase activity" EXACT []
-is_a: GO:0043462 ! regulation of ATPase activity
+synonym: "negative regulation of ATPase activity" EXACT []
+is_a: GO:0043462 ! regulation of ATP-dependent activity
is_a: GO:0044092 ! negative regulation of molecular function
[Term]
id: GO:0032781
-name: positive regulation of ATPase activity
+name: positive regulation of ATP-dependent activity
namespace: biological_process
-def: "Any process that activates or increases the rate of ATP hydrolysis by an ATPase." [GOC:mah]
+def: "Any process that activates or increases the rate of an ATP-dependent activity." [GOC:mah]
synonym: "activation of ATPase activity" NARROW []
synonym: "positive regulation of adenosinetriphosphatase activity" EXACT []
+synonym: "positive regulation of ATPase activity" EXACT []
synonym: "stimulation of ATPase activity" NARROW []
synonym: "up regulation of ATPase activity" EXACT []
synonym: "up-regulation of ATPase activity" EXACT []
synonym: "upregulation of ATPase activity" EXACT []
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
is_a: GO:0044093 ! positive regulation of molecular function
[Term]
@@ -181556,7 +181256,7 @@ is_a: GO:1903008 ! organelle disassembly
id: GO:0032791
name: lead ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lead (Pb) ions." [GOC:mah]
+def: "Binding to lead (Pb) ions." [GOC:mah]
is_a: GO:0046872 ! metal ion binding
[Term]
@@ -181582,7 +181282,7 @@ is_a: GO:0051091 ! positive regulation of DNA-binding transcription factor activ
id: GO:0032794
name: GTPase activating protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a GTPase activating protein." [GOC:nln]
+def: "Binding to a GTPase activating protein." [GOC:nln]
synonym: "GAP binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -181590,7 +181290,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0032795
name: heterotrimeric G-protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a heterotrimeric G-protein." [GOC:nln]
+def: "Binding to a heterotrimeric G-protein." [GOC:nln]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -181641,7 +181341,7 @@ id: GO:0032800
name: obsolete receptor biosynthetic process
namespace: biological_process
def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." [GOC:mah]
-comment: The reason for obsoletion is that those represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
+comment: The reason for obsoletion is that this represent specific gene products, and genes annotated to those terms should be annotated to 'regulation of gene expression' or 'regulation of transcription' or some signaling term.
synonym: "receptor anabolism" EXACT []
synonym: "receptor biosynthesis" EXACT []
synonym: "receptor formation" EXACT []
@@ -181768,8 +181468,7 @@ relationship: part_of GO:0043025 ! neuronal cell body
id: GO:0032810
name: sterol response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the sterol response element (SRE), a nonpalindromic sequence found in the promoters of genes involved in lipid metabolism." [GOC:vk, PMID:11994399]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to a sterol response element (SRE), a nonpalindromic sequence found in the promoters of genes involved in lipid metabolism." [GOC:vk, PMID:11994399]
synonym: "SRE binding" EXACT []
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
@@ -181806,7 +181505,7 @@ relationship: positively_regulates GO:0048242 ! epinephrine secretion
id: GO:0032813
name: tumor necrosis factor receptor superfamily binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the tumor necrosis factor receptor superfamily." [GOC:add]
+def: "Binding to a member of the tumor necrosis factor receptor superfamily." [GOC:add]
synonym: "TNF receptor superfamily binding" EXACT []
is_a: GO:0005126 ! cytokine receptor binding
@@ -182192,7 +181891,7 @@ relationship: part_of GO:0030425 ! dendrite
id: GO:0032840
name: intramolecular proline-rich ligand binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a proline-rich region within the same polypeptide." [GOC:pf]
+def: "Binding to a proline-rich region within the same polypeptide." [GOC:pf]
synonym: "intramolecular proline-rich region binding" EXACT []
is_a: GO:0043621 ! protein self-association
is_a: GO:0070064 ! proline-rich region binding
@@ -182201,7 +181900,7 @@ is_a: GO:0070064 ! proline-rich region binding
id: GO:0032841
name: calcitonin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with calcitonin, a peptide hormone responsible for reducing serum calcium levels by inhibiting osteoclastic bone reabsorption and promoting renal calcium excretion. It is synthesized and released by the C cells of the thyroid." [GOC:ecd]
+def: "Binding to calcitonin, a peptide hormone responsible for reducing serum calcium levels by inhibiting osteoclastic bone reabsorption and promoting renal calcium excretion. It is synthesized and released by the C cells of the thyroid." [GOC:ecd]
is_a: GO:0097644 ! calcitonin family binding
[Term]
@@ -182460,8 +182159,11 @@ relationship: regulates GO:0051179 ! localization
id: GO:0032880
name: regulation of protein localization
namespace: biological_process
+alt_id: GO:1903827
def: "Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location." [GOC:dph, GOC:mah, GOC:tb]
subset: goslim_chembl
+synonym: "regulation of cellular protein localisation" EXACT [GOC:TermGenie]
+synonym: "regulation of cellular protein localization" EXACT []
synonym: "regulation of protein localisation" EXACT [GOC:mah]
is_a: GO:0032879 ! regulation of localization
relationship: regulates GO:0008104 ! protein localization
@@ -182544,6 +182246,7 @@ name: regulation of mitotic spindle elongation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle." [GOC:mah]
is_a: GO:0032887 ! regulation of spindle elongation
+relationship: part_of GO:0033047 ! regulation of mitotic sister chromatid segregation
relationship: regulates GO:0000022 ! mitotic spindle elongation
[Term]
@@ -183052,7 +182755,7 @@ id: GO:0032934
name: sterol binding
namespace: molecular_function
alt_id: GO:0005498
-def: "Interacting selectively and non-covalently with a sterol, any steroid containing a hydroxy group in the 3 position, closely related to cholestan-3-ol." [GOC:mah]
+def: "Binding to a sterol, a steroid containing a hydroxy group in the 3 position, closely related to cholestan-3-ol." [GOC:mah]
synonym: "sterol carrier activity" RELATED [GOC:mah]
is_a: GO:0005496 ! steroid binding
@@ -183060,7 +182763,7 @@ is_a: GO:0005496 ! steroid binding
id: GO:0032935
name: sterol sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of a sterol." [GOC:mah]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of a sterol." [GOC:mah]
synonym: "sterol-sensing domain" NARROW []
is_a: GO:0032934 ! sterol binding
is_a: GO:0106254 ! lipid sensor activity
@@ -183087,8 +182790,9 @@ id: GO:0032938
name: negative regulation of translation in response to oxidative stress
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translation as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:mah]
-is_a: GO:0032055 ! negative regulation of translation in response to stress
+is_a: GO:0032057 ! negative regulation of translational initiation in response to stress
is_a: GO:0043556 ! regulation of translation in response to oxidative stress
+is_a: GO:0043558 ! regulation of translational initiation in response to stress
[Term]
id: GO:0032939
@@ -183101,7 +182805,7 @@ synonym: "up regulation of translation in response to oxidative stress" EXACT []
synonym: "up-regulation of translation in response to oxidative stress" EXACT []
synonym: "upregulation of translation in response to oxidative stress" EXACT []
is_a: GO:0032056 ! positive regulation of translation in response to stress
-is_a: GO:0043556 ! regulation of translation in response to oxidative stress
+relationship: part_of GO:0034599 ! cellular response to oxidative stress
[Term]
id: GO:0032940
@@ -183131,7 +182835,6 @@ def: "Catalysis of the reaction: 1D-myo-inositol tetrakisphosphate + ATP = 1D-my
synonym: "1D-myo-inositol-tetrakisphosphate 2-kinase activity" EXACT []
synonym: "inositol 1,3,4,6-tetrakisphosphate 2-kinase activity" EXACT []
synonym: "inositol-tetrakisphosphate 2-kinase activity" EXACT []
-xref: EC:2.7.1.-
is_a: GO:0051765 ! inositol tetrakisphosphate kinase activity
[Term]
@@ -183532,7 +183235,7 @@ def: "Binds transmembrane domain-containing proteins and mediates their integrat
xref: Reactome:R-HSA-1268025 "SAM50 complex inserts proteins into mitochondrial outer membrane"
xref: Reactome:R-HSA-1299482 "TIMM23 SORT inserts proteins into inner membrane"
xref: Reactome:R-HSA-1307803 "TIMM22 inserts proteins into inner membrane"
-is_a: GO:0140597 ! protein carrier activity
+is_a: GO:0140597 ! protein carrier chaperone
[Term]
id: GO:0032978
@@ -183596,12 +183299,14 @@ name: protein-containing complex disassembly
namespace: biological_process
alt_id: GO:0034623
alt_id: GO:0043241
+alt_id: GO:0043624
def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah]
synonym: "cellular macromolecule complex disassembly" RELATED []
+synonym: "cellular protein complex disassembly" RELATED []
synonym: "macromolecule complex disassembly" RELATED []
synonym: "protein complex disassembly" EXACT []
is_a: GO:0022411 ! cellular component disassembly
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0032985
@@ -184856,7 +184561,7 @@ id: GO:0033108
name: mitochondrial respiratory chain complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a mitochondrial respiratory chain complex." [GOC:mah]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0007005 ! mitochondrion organization
[Term]
@@ -185061,7 +184766,7 @@ relationship: positively_regulates GO:0016572 ! histone phosphorylation
id: GO:0033130
name: acetylcholine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an acetylcholine receptor." [GOC:mah]
+def: "Binding to an acetylcholine receptor." [GOC:mah]
is_a: GO:0005102 ! signaling receptor binding
[Term]
@@ -185103,7 +184808,7 @@ is_a: GO:1903301 ! positive regulation of hexokinase activity
id: GO:0033134
name: ubiquitin activating enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ubiquitin activating enzyme, any of the E1 proteins." [GOC:mah]
+def: "Binding to a ubiquitin activating enzyme, any of the E1 proteins." [GOC:mah]
is_a: GO:0044388 ! small protein activating enzyme binding
[Term]
@@ -185176,7 +184881,7 @@ relationship: positively_regulates GO:0042501 ! serine phosphorylation of STAT p
id: GO:0033142
name: progesterone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a progesterone receptor." [GOC:mah]
+def: "Binding to a progesterone receptor." [GOC:mah]
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -185247,7 +184952,7 @@ relationship: positively_regulates GO:0030520 ! intracellular estrogen receptor
id: GO:0033149
name: FFAT motif binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the FFAT motif, a short motif containing diphenylalanine in an acidic tract that targets proteins to the cytosolic surface of the ER and to the nuclear membrane by binding directly to members of the VAP (VAMP-associated protein) protein family." [PMID:12727870, PMID:15455074, PMID:16004875]
+def: "Binding to a FFAT motif, a short motif containing diphenylalanine in an acidic tract that targets proteins to the cytosolic surface of the ER and to the nuclear membrane by binding directly to members of the VAP (VAMP-associated protein) protein family." [PMID:12727870, PMID:15455074, PMID:16004875]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -185327,8 +185032,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells." [GOC:mah]
is_a: GO:0032386 ! regulation of intracellular transport
is_a: GO:0051223 ! regulation of protein transport
-is_a: GO:1903827 ! regulation of cellular protein localization
relationship: regulates GO:0006886 ! intracellular protein transport
+relationship: regulates GO:0034613 ! cellular protein localization
[Term]
id: GO:0033158
@@ -185361,7 +185066,7 @@ is_obsolete: true
id: GO:0033161
name: mitogen-activated protein kinase kinase kinase kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase kinase kinase, any protein that can phosphorylate a MAP kinase kinase kinase." [GOC:mah]
+def: "Binding to a mitogen-activated protein kinase kinase kinase kinase, a protein that can phosphorylate a MAP kinase kinase kinase." [GOC:mah]
synonym: "MAPKKKK binding" EXACT []
is_a: GO:0019901 ! protein kinase binding
@@ -185370,7 +185075,6 @@ id: GO:0033162
name: melanosome membrane
namespace: cellular_component
def: "The lipid bilayer surrounding a melanosome." [GOC:mah]
-is_a: GO:0030659 ! cytoplasmic vesicle membrane
is_a: GO:0090741 ! pigment granule membrane
relationship: part_of GO:0042470 ! melanosome
relationship: part_of GO:0045009 ! chitosome
@@ -185423,12 +185127,14 @@ is_a: GO:0140513 ! nuclear protein-containing complex
[Term]
id: GO:0033168
-name: conversion of ds siRNA to ss siRNA involved in RNA interference
+name: obsolete conversion of ds siRNA to ss siRNA involved in RNA interference
namespace: biological_process
-def: "The process in which double-stranded siRNA molecules are converted to single-stranded siRNAs; required for the formation of a mature RITS complex during RNA interference." [GOC:mah, PMID:17310250]
+def: "OBSOLETE. The process in which double-stranded siRNA molecules are converted to single-stranded siRNAs; required for the formation of a mature RITS complex during RNA interference." [GOC:mah, PMID:17310250]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "RNA interference, conversion of ds siRNA to ss siRNA" EXACT [GOC:mah]
-is_a: GO:0036404 ! conversion of ds siRNA to ss siRNA
-relationship: part_of GO:0030422 ! production of siRNA involved in RNA interference
+is_obsolete: true
+consider: GO:0004521
+consider: GO:0016246
[Term]
id: GO:0033169
@@ -185746,7 +185452,6 @@ def: "A protein complex that possesses DNA helicase activity." [GOC:mah]
subset: goslim_metagenomics
subset: goslim_pir
is_a: GO:1902494 ! catalytic complex
-is_a: GO:1904949 ! ATPase complex
relationship: part_of GO:0005622 ! intracellular anatomical structure
[Term]
@@ -185761,7 +185466,7 @@ is_a: GO:0140513 ! nuclear protein-containing complex
id: GO:0033204
name: ribonuclease P RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the RNA subunit of ribonuclease P." [GOC:pg, PMID:11455963]
+def: "Binding to RNA subunit of ribonuclease P." [GOC:pg, PMID:11455963]
synonym: "RNase P RNA binding" EXACT []
is_a: GO:0003723 ! RNA binding
@@ -185873,7 +185578,7 @@ is_a: GO:0043618 ! regulation of transcription from RNA polymerase II promoter i
id: GO:0033218
name: amide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [GOC:mah]
+def: "Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [GOC:mah]
subset: goslim_pir
is_a: GO:0005488 ! binding
@@ -185881,7 +185586,7 @@ is_a: GO:0005488 ! binding
id: GO:0033219
name: urea binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with urea, a water-soluble carboxamide with the structure H2N-CO-NH2." [GOC:mah, ISBN:0198506732]
+def: "Binding to urea, a water-soluble carboxamide with the structure H2N-CO-NH2." [GOC:mah, ISBN:0198506732]
is_a: GO:0033218 ! amide binding
is_a: GO:0036094 ! small molecule binding
@@ -185911,7 +185616,7 @@ is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
id: GO:0033222
name: xylose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the D- or L-enantiomer of xylose." [GOC:mah]
+def: "Binding to the D- or L-enantiomer of xylose." [GOC:mah]
is_a: GO:0048029 ! monosaccharide binding
[Term]
@@ -185946,7 +185651,7 @@ is_a: GO:0042626 ! ATPase-coupled transmembrane transporter activity
id: GO:0033226
name: 2-aminoethylphosphonate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 2-aminoethylphosphonate." [GOC:mlg]
+def: "Binding to 2-aminoethylphosphonate." [GOC:mlg]
synonym: "2-phosphonoethylamine binding" EXACT []
synonym: "ciliatine binding" EXACT []
is_a: GO:0005488 ! binding
@@ -186371,7 +186076,7 @@ replaced_by: GO:0004222
id: GO:0033265
name: choline binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with choline, the amine 2-hydroxy-N,N,N-trimethylethanaminium." [GOC:mlg]
+def: "Binding to choline, the amine 2-hydroxy-N,N,N-trimethylethanaminium." [GOC:mlg]
is_a: GO:0043169 ! cation binding
[Term]
@@ -186463,6 +186168,7 @@ synonym: "response to riboflavin" EXACT []
is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0033273 ! response to vitamin
+is_a: GO:1901700 ! response to oxygen-containing compound
[Term]
id: GO:0033275
@@ -186637,14 +186343,14 @@ relationship: part_of GO:0055001 ! muscle cell development
id: GO:0033293
name: monocarboxylic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a monocarboxylic acid, any organic acid containing one carboxyl (COOH) group or anion (COO-)." [GOC:mah]
+def: "Binding to a monocarboxylic acid, any organic acid containing one carboxyl (COOH) group or anion (COO-)." [GOC:mah]
is_a: GO:0031406 ! carboxylic acid binding
[Term]
id: GO:0033294
name: ectoine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ectoine, 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid." [GOC:mah]
+def: "Binding to ectoine, 1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid." [GOC:mah]
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -186654,7 +186360,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0033295
name: hydroxyectoine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with hydroxyectoine." [GOC:mlg]
+def: "Binding to hydroxyectoine." [GOC:mlg]
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0043177 ! organic acid binding
is_a: GO:0043178 ! alcohol binding
@@ -186666,7 +186372,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0033296
name: rhamnose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the D- or L-enantiomer of rhamnose." [GOC:mah]
+def: "Binding to the D- or L-enantiomer of rhamnose." [GOC:mah]
is_a: GO:0048029 ! monosaccharide binding
[Term]
@@ -186985,7 +186691,7 @@ relationship: part_of GO:0008584 ! male gonad development
id: GO:0033328
name: peroxisome membrane targeting sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a peroxisomal membrane targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome membrane." [GOC:rb, PMID:15133130, PMID:17020786]
+def: "Binding to a peroxisomal membrane targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome membrane." [GOC:rb, PMID:15133130, PMID:17020786]
synonym: "mPTS binding" EXACT []
synonym: "peroxisomal membrane protein (PMP) targeting signal (mPTS) binding" EXACT [PMID:14709540]
synonym: "PMP targeting signal (mPTS) binding" EXACT [PMID:14709540]
@@ -187662,7 +187368,7 @@ is_a: GO:0036464 ! cytoplasmic ribonucleoprotein granule
id: GO:0033392
name: obsolete actin homodimerization activity
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an identical actin monomer to form a homodimer." [GOC:mah]
+def: "OBSOLETE. Binding to an identical actin monomer to form a homodimer." [GOC:mah]
comment: This term was made obsolete because it was added in error; formation of an actin dimer is simply a transient step in the polymerization of actin. Also, this term may not represent a real molecular function in GO, but rather that a gene product (actin itself) is part of an actin homodimer transient protein complex.
synonym: "actin dimerization activity" BROAD []
synonym: "actin homodimerization activity" EXACT []
@@ -188824,10 +188530,10 @@ is_a: GO:0055082 ! cellular chemical homeostasis
id: GO:0033503
name: HULC complex
namespace: cellular_component
-def: "A ubiquitin-conjugating enzyme complex that contains two RING finger proteins, which have ubiquitin ligase activity, in addition to a protein with ubiquitin-conjugating enzyme activity; catalyzes the ubiquitination of histone H2B at lysine 119 (or the equivalent residue). In Schizosaccharomyces the subunits are Rhp1, Brl2/Rfp1 and Brl1/Rfp2." [GOC:mah, PMID:17363370, PMID:17374714]
+def: "A ubiquitin ligase complex that contains two RING finger proteins, which have ubiquitin ligase activity, in addition to a protein with ubiquitin-conjugating enzyme activity; catalyzes the ubiquitination of histone H2B at lysine 119 (or the equivalent residue). In Schizosaccharomyces the subunits are Rhp6, Shf1, Brl2/Rfp1 and Brl1/Rfp2." [GOC:mah, PMID:17363370, PMID:17374714]
is_a: GO:0000151 ! ubiquitin ligase complex
is_a: GO:0031371 ! ubiquitin conjugating enzyme complex
-relationship: part_of GO:0000792 ! heterochromatin
+relationship: part_of GO:0000785 ! chromatin
[Term]
id: GO:0033504
@@ -189476,7 +189182,7 @@ namespace: biological_process
def: "Any process in which a gamma-tubulin complex is transported to, or maintained in, a specific location." [GOC:mah]
synonym: "establishment and maintenance of gamma-tubulin complex localization" EXACT []
synonym: "gamma-tubulin complex localisation" EXACT [GOC:mah]
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
[Term]
id: GO:0033567
@@ -189668,10 +189374,9 @@ id: GO:0033588
name: elongator holoenzyme complex
namespace: cellular_component
alt_id: GO:0033589
-def: "A heterohexameric protein complex that is involved in modification of wobble nucleosides in tRNA. The complex can associate physically with hyperphosphorylated RNA polymerase II; it contains two discrete heterotrimeric subcomplexes." [GOC:bhm, GOC:jh, GOC:mah, GOC:vw, PMID:11435442, PMID:11689709, PMID:15769872, PMID:17018299, PMID:18755837, PMID:23165209]
-comment: Despite its name, this complex is no longer thought to be directly involved in transcriptional elongation (PMID:23165209).
+def: "A heterohexameric protein complex composed two discrete heterotrimeric subcomplexes that is involved in modification of wobble nucleosides in tRNA." [GOC:bhm, GOC:jh, GOC:mah, GOC:vw, PMID:11435442, PMID:11689709, PMID:15769872, PMID:17018299, PMID:18755837, PMID:23165209]
+comment: Despite its name, this complex is not directly involved in transcriptional elongation (PMID:23165209).
synonym: "Elongator core complex" RELATED []
-synonym: "Elongator holoenzyme complex" EXACT []
is_a: GO:0140535 ! intracellular protein-containing complex
[Term]
@@ -189683,6 +189388,7 @@ synonym: "response to vitamin B12" EXACT []
is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0033273 ! response to vitamin
+is_a: GO:1901700 ! response to oxygen-containing compound
[Term]
id: GO:0033591
@@ -189692,6 +189398,7 @@ def: "Any process that results in a change in state or activity of a cell or an
synonym: "response to ascorbic acid" BROAD []
synonym: "response to L-ascorbate" EXACT []
synonym: "response to vitamin C" EXACT []
+is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0033273 ! response to vitamin
is_a: GO:0034284 ! response to monosaccharide
@@ -189699,10 +189406,9 @@ is_a: GO:0034284 ! response to monosaccharide
id: GO:0033592
name: RNA strand annealing activity
namespace: molecular_function
-def: "Facilitates the base-pairing of complementary single-stranded RNA." [GOC:mah]
-is_a: GO:0003725 ! double-stranded RNA binding
+def: "An activity that facilitates the formation of a complementary double-stranded RNA molecule." [GOC:mah, PMID:7543843]
is_a: GO:0003727 ! single-stranded RNA binding
-is_a: GO:0097617 ! annealing activity
+is_a: GO:0140666 ! annealing activity
[Term]
id: GO:0033593
@@ -189921,7 +189627,7 @@ is_a: GO:0043649 ! dicarboxylic acid catabolic process
id: GO:0033612
name: receptor serine/threonine kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a receptor that possesses protein serine/threonine kinase activity." [GOC:mah]
+def: "Binding to a receptor that possesses protein serine/threonine kinase activity." [GOC:mah]
synonym: "transmembrane receptor protein serine/threonine kinase ligand binding" RELATED []
is_a: GO:0005102 ! signaling receptor binding
@@ -190333,7 +190039,6 @@ synonym: "down-regulation by symbiont of host gene-for-gene resistance" EXACT []
synonym: "downregulation by symbiont of pathogen-race/host plant cultivar-specific resistance in symbiont" EXACT []
synonym: "inhibition by symbiont of host resistance gene-dependent defense response" NARROW []
synonym: "negative regulation by symbiont of host resistance gene-dependent defense response" EXACT []
-synonym: "suppression by symbiont of host resistance gene-dependent defense response" EXACT []
is_a: GO:0044414 ! suppression of host defenses by symbiont
is_a: GO:0052158 ! modulation by symbiont of host resistance gene-dependent defense response
@@ -190514,9 +190219,11 @@ id: GO:0033677
name: DNA/RNA helicase activity
namespace: molecular_function
alt_id: GO:0033680
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of a DNA/RNA duplex, i.e. a double helix in which a strand of DNA pairs with a complementary strand of RNA." [GOC:mah]
+def: "Unwinding of a DNA/RNA duplex, i.e. a double helix in which a strand of DNA pairs with a complementary strand of RNA, driven by ATP hydrolysis." [GOC:mah]
synonym: "ATP-dependent DNA/RNA helicase activity" EXACT []
is_a: GO:0004386 ! helicase activity
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
+is_a: GO:0008186 ! ATP-dependent activity, acting on RNA
is_a: GO:0140098 ! catalytic activity, acting on RNA
[Term]
@@ -190524,7 +190231,7 @@ id: GO:0033678
name: 5'-3' DNA/RNA helicase activity
namespace: molecular_function
alt_id: GO:0033682
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of a DNA/RNA duplex in the direction 5' to 3'." [GOC:mah]
+def: "Unwinding of a DNA/RNA duplex in the 5' to 3' direction, driven by ATP hydrolysis." [GOC:mah]
synonym: "5' to 3' DNA/RNA helicase activity" EXACT []
synonym: "ATP-dependent 5' to 3' DNA/RNA helicase activity" EXACT []
synonym: "ATP-dependent 5'-3' DNA/RNA helicase activity" EXACT []
@@ -190536,7 +190243,7 @@ id: GO:0033679
name: 3'-5' DNA/RNA helicase activity
namespace: molecular_function
alt_id: GO:0033681
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of a DNA/RNA duplex in the direction 3' to 5'." [GOC:mah]
+def: "Unwinding of a DNA/RNA duplex in the 3' to 5' direction, driven by ATP hydrolysis." [GOC:mah]
synonym: "3' to 5' DNA/RNA helicase activity" EXACT []
synonym: "ATP-dependent 3' to 5' DNA/RNA helicase activity" EXACT []
synonym: "ATP-dependent 3'-5' DNA/RNA helicase activity" EXACT []
@@ -190633,7 +190340,7 @@ relationship: positively_regulates GO:0033687 ! osteoblast proliferation
id: GO:0033691
name: sialic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with sialic acid, any of a variety of N- or O- substituted derivatives of neuraminic acid, a nine carbon monosaccharide. Sialic acids often occur in polysaccharides, glycoproteins, and glycolipids in animals and bacteria." [GOC:add, ISBN:9780721601465]
+def: "Binding to a sialic acid, a N- or O- substituted derivative of neuraminic acid, a nine carbon monosaccharide. Sialic acids often occur in polysaccharides, glycoproteins, and glycolipids in animals and bacteria." [GOC:add, ISBN:9780721601465]
synonym: "N-acetylneuraminic acid binding" NARROW []
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -190680,24 +190387,30 @@ is_a: GO:0016725 ! oxidoreductase activity, acting on CH or CH2 groups
[Term]
id: GO:0033696
-name: negative regulation of extent of heterochromatin assembly
+name: heterochromatin boundary formation
namespace: biological_process
-def: "Any process that reduces the extent of heterochromatin formation; reduces the size of a chromosomal region converted to heterochromatin." [GOC:mah]
+alt_id: GO:0031454
+def: "A process that forms a boundary that limits the spreading of heterochromatin along a chromosome." [GOC:mah]
synonym: "maintenance of heterochromatin boundaries" RELATED []
-synonym: "negative regulation of extent of heterochromatin formation" EXACT []
+synonym: "negative regulation of extent of heterochromatin assembly" RELATED []
+synonym: "negative regulation of extent of heterochromatin formation" RELATED []
synonym: "negative regulation of heterochromatin spreading" RELATED []
-is_a: GO:0031452 ! negative regulation of heterochromatin assembly
-is_a: GO:0031454 ! regulation of extent of heterochromatin assembly
+synonym: "regulation of extent of heterochromatin assembly" RELATED []
+synonym: "regulation of extent of heterochromatin formation" EXACT []
+synonym: "regulation of heterochromatin spreading" RELATED []
+is_a: GO:0070828 ! heterochromatin organization
+relationship: part_of GO:0031507 ! heterochromatin assembly
[Term]
id: GO:0033697
-name: positive regulation of extent of heterochromatin assembly
+name: obsolete positive regulation of extent of heterochromatin assembly
namespace: biological_process
-def: "Any process that increases the extent of heterochromatin formation; increases the size of a chromosomal region converted to heterochromatin." [GOC:mah]
+def: "OBSOLETE. Any process that increases the extent of heterochromatin formation; increases the size of a chromosomal region converted to heterochromatin." [GOC:mah]
+comment: This term has been obsoleted because there is no evidence it exists.
synonym: "positive regulation of extent of heterochromatin formation" EXACT []
synonym: "positive regulation of heterochromatin spreading" RELATED []
-is_a: GO:0031453 ! positive regulation of heterochromatin assembly
-is_a: GO:0031454 ! regulation of extent of heterochromatin assembly
+is_obsolete: true
+consider: GO:0031507
[Term]
id: GO:0033698
@@ -191295,9 +191008,12 @@ is_a: GO:0016671 ! oxidoreductase activity, acting on a sulfur group of donors,
[Term]
id: GO:0033746
-name: histone demethylase activity (H3-R2 specific)
+name: histone H3-methyl-arginine-2 demethylase activity
namespace: molecular_function
-def: "Catalysis of the removal of a methyl group from arginine at position 2 of the histone H3 protein." [GOC:mah]
+def: "Catalysis of the removal of the methyl group from a modified arginine residue at position 2 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:17947579, PMID:22483719, PMID:29233856]
+synonym: "histone demethylase activity (H3-R2 specific)" EXACT []
+synonym: "histone H3R2me demethylase activity" EXACT []
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032452 ! histone demethylase activity
[Term]
@@ -191333,9 +191049,12 @@ is_a: GO:0016695 ! oxidoreductase activity, acting on hydrogen as donor
[Term]
id: GO:0033749
-name: histone demethylase activity (H4-R3 specific)
+name: histone H3-methyl-arginine-3 demethylase activity
namespace: molecular_function
-def: "Catalysis of the removal of a methyl group from arginine at position 3 of the histone H4 protein." [GOC:mah]
+def: "Catalysis of the removal of the methyl group from a modified arginine residue at position 3 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:17947579]
+synonym: "histone demethylase activity (H4-R3 specific)" EXACT []
+synonym: "histone H3R3me demethylase activity" EXACT []
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032452 ! histone demethylase activity
[Term]
@@ -191351,14 +191070,14 @@ is_a: GO:0051640 ! organelle localization
[Term]
id: GO:0033751
-name: linoleate 8R-lipoxygenase
+name: obsolete linoleate 8R-lipoxygenase
namespace: molecular_function
-def: "Catalysis of the reaction: linoleate + O2 = (9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate." [RHEA:22392]
-synonym: "5,8-linoleate diol synthase (bifunctional enzyme)" RELATED [EC:1.13.11.60]
-synonym: "7,8-linoleate diol synthase (bifunctional enzyme)" RELATED [EC:1.13.11.60]
+def: "OBSOLETE. Catalysis of the reaction: linoleate + O2 = (9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate." [GOC:curators]
+comment: The reason for obsoletion is because there is no support for the reaction. EC and RHEA mappings have been obsoleted at their source.
+synonym: "5,8-linoleate diol synthase (bifunctional enzyme)" RELATED []
+synonym: "7,8-linoleate diol synthase (bifunctional enzyme)" RELATED []
synonym: "linoleate diol synthase activity" RELATED []
-xref: RHEA:22392
-is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
+is_obsolete: true
[Term]
id: GO:0033752
@@ -191608,14 +191327,15 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033773
name: isoflavone 2'-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: an isoflavone + NADPH + H+ + O2 = a 2'-hydroxyisoflavone + NADP+ + H2O." [EC:1.14.13.89]
-synonym: "CYP Ge-3" RELATED [EC:1.14.13.89]
-synonym: "CYP81E1" RELATED [EC:1.14.13.89]
-synonym: "isoflavone 2'-monooxygenase activity" BROAD [EC:1.14.13.89]
-synonym: "isoflavone,NADPH:oxygen oxidoreductase (2'-hydroxylating) activity" RELATED [EC:1.14.13.89]
-xref: EC:1.14.13.89
+def: "Catalysis of the reaction: an isoflavone + O2 + reduced [NADPH-hemoprotein reductase] = a 2'-hydroxyisoflavone + H+ + H2O + oxidized [NADPH-hemoprotein reductase]." [RHEA:18849]
+comment: Formerly EC:1.14.13.89.
+synonym: "CYP Ge-3" RELATED [EC:1.14.14.90]
+synonym: "CYP81E1" RELATED [EC:1.14.14.90]
+synonym: "isoflavone 2'-monooxygenase activity" BROAD [EC:1.14.14.90]
+xref: EC:1.14.14.90
xref: MetaCyc:ISOFLAVONE-2-HYDROXYLASE-RXN
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+xref: RHEA:18849
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0033774
@@ -191671,13 +191391,13 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033778
name: 7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7alpha-hydroxycholest-4-en-3-one + H(+) + NADPH + O(2) = 7alpha,12alpha-dihydroxycholest-4-en-3-one + H(2)O + NADP(+)." [EC:1.14.13.95, RHEA:46752]
+def: "Catalysis of the reaction: 7alpha-hydroxycholest-4-en-3-one + H(+) + NADPH + O(2) = 7alpha,12alpha-dihydroxycholest-4-en-3-one + H(2)O + NADP(+)." [PMID:10051404, PMID:1400444, RHEA:46752]
synonym: "7alpha-hydroxy-4-cholesten-3-one 12alpha-monooxygenase activity" RELATED [EC:1.14.13.95]
synonym: "7alpha-hydroxycholest-4-en-3-one,NADPH:oxygen oxidoreductase (12alpha-hydroxylating) activity" RELATED [EC:1.14.13.95]
synonym: "CYP12" RELATED [EC:1.14.13.95]
synonym: "HCO 12alpha-hydroxylase activity" RELATED [EC:1.14.13.95]
synonym: "sterol 12alpha-hydroxylase activity" BROAD [EC:1.14.13.95]
-xref: EC:1.14.13.95
+xref: EC:1.14.14.139
xref: KEGG_REACTION:R04826
xref: MetaCyc:1.14.13.95-RXN
xref: Reactome:R-HSA-192157 "CYP8B1 12-hydroxylates 4CHOL7aOLONE"
@@ -191738,16 +191458,15 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0033782
name: 24-hydroxycholesterol 7alpha-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (24R)-cholest-5-ene-3beta,24-diol + H(+) + NADPH + O(2) = (24R)-7alpha,24-dihydroxycholesterol + H(2)O + NADP(+)." [EC:1.14.13.99, RHEA:16093]
-synonym: "(24R)-cholest-5-ene-3beta,24-diol,NADPH:oxygen oxidoreductase (7alpha-hydroxylating) activity" RELATED [EC:1.14.13.99]
-synonym: "24-hydroxycholesterol 7alpha-monooxygenase activity" RELATED [EC:1.14.13.99]
-synonym: "CYP39A1" RELATED [EC:1.14.13.99]
-synonym: "CYP39A1 oxysterol 7alpha-hydroxylase activity" RELATED [EC:1.14.13.99]
-xref: EC:1.14.13.99
+def: "Catalysis of the reaction: (24S)-hydroxycholesterol + O2 + reduced [NADPH-hemoprotein reductase] = (24S)-7alpha-dihydroxycholesterol + H+ + H2O + oxidized [NADPH-hemoprotein reductase]." [PMID:10748047, PMID:11013305, RHEA:46124]
+comment: Formerly EC:1.14.13.99.
+synonym: "24-cholest-5-ene-3beta,24-diol,NADPH:oxygen oxidoreductase (7alpha-hydroxylating) activity" RELATED []
+synonym: "24-hydroxycholesterol 7alpha-monooxygenase activity" RELATED [EC:1.14.14.26]
+xref: EC:1.14.14.26
xref: KEGG_REACTION:R07208
xref: MetaCyc:1.14.13.99-RXN
-xref: RHEA:16093
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+xref: RHEA:46124
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0033783
@@ -191835,7 +191554,7 @@ is_a: GO:0016726 ! oxidoreductase activity, acting on CH or CH2 groups, NAD or N
id: GO:0033789
name: phenylacetyl-CoA dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 1,4-benzoquinone + H(2)O + phenylacetyl-CoA = 2 hydroquinone + phenylglyoxylyl-CoA." [EC:1.17.5.1, RHEA:15705]
+def: "Catalysis of the reaction: 2 1,4-benzoquinone + H(2)O + phenylacetyl-CoA = 2 hydroquinone + phenylglyoxylyl-CoA." [RHEA:15705]
synonym: "phenylacetyl-CoA:acceptor oxidoreductase activity" RELATED [EC:1.17.5.1]
synonym: "phenylacetyl-CoA:quinone oxidoreductase activity" RELATED [EC:1.17.5.1]
xref: EC:1.17.5.1
@@ -191927,12 +191646,12 @@ is_a: GO:0016491 ! oxidoreductase activity
id: GO:0033797
name: selenate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 e(-) + 2 H(+) + selenate = H(2)O + selenite." [EC:1.97.1.9, RHEA:14031]
+def: "Catalysis of the reaction: 2 e(-) + 2 H(+) + selenate = H(2)O + selenite." [EC:1.97.1.9, RHEA:14029]
synonym: "selenite:reduced acceptor oxidoreductase activity" RELATED [EC:1.97.1.9]
xref: EC:1.97.1.9
xref: KEGG_REACTION:R07229
xref: MetaCyc:RXN0-2101
-xref: RHEA:14031
+xref: RHEA:14029
xref: UM-BBD_reactionID:r0828
is_a: GO:0016491 ! oxidoreductase activity
@@ -192211,22 +191930,6 @@ xref: MetaCyc:R102-RXN
xref: RHEA:16901
is_a: GO:0016407 ! acetyltransferase activity
-[Term]
-id: GO:0033817
-name: beta-ketoacyl-acyl-carrier-protein synthase II activity
-namespace: molecular_function
-def: "Catalysis of the reaction: (Z)-hexadec-11-enoyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = (Z)-3-oxooctadec-13-enoyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein]." [EC:2.3.1.179]
-synonym: "(Z)-hexadec-11-enoyl-acyl-carrier-protein:malonyl-acyl-carrier-protein C-acyltransferase (decarboxylating) activity" RELATED [EC:2.3.1.179]
-synonym: "3-oxoacyl-acyl carrier protein synthase I activity" RELATED [EC:2.3.1.179]
-synonym: "beta-ketoacyl-ACP synthase II activity" RELATED [EC:2.3.1.179]
-synonym: "FabF" RELATED [EC:2.3.1.179]
-synonym: "KAS II" RELATED [EC:2.3.1.179]
-synonym: "KASII" RELATED [EC:2.3.1.179]
-xref: EC:2.3.1.179
-xref: MetaCyc:2.3.1.179-RXN
-xref: RHEA:14565
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
-
[Term]
id: GO:0033818
name: beta-ketoacyl-acyl-carrier-protein synthase III activity
@@ -193295,23 +192998,24 @@ synonym: "non-base specific ribonuclease activity" EXACT []
synonym: "nonbase-specific RNase activity" EXACT []
synonym: "nonspecific RNase activity" EXACT []
synonym: "ribonnuclease (non-base specific) activity" EXACT []
-synonym: "ribonuclease (non-base specific) activity" RELATED [EC:3.1.27.1]
+synonym: "ribonuclease (non-base specific) activity" RELATED []
synonym: "ribonuclease II activity" BROAD [EC:4.6.1.19]
synonym: "ribonuclease M activity" EXACT []
synonym: "ribonuclease N2 activity" EXACT []
-synonym: "ribonuclease PP3 activity" RELATED [EC:3.1.27.1]
+synonym: "ribonuclease PP3 activity" RELATED []
synonym: "ribonuclease U4 activity" EXACT []
synonym: "ribonucleate 3'-oligonucleotide hydrolase activity" EXACT []
synonym: "ribonucleate nucleotido-2'-transferase (cyclizing) activity" BROAD []
synonym: "RNAase CL activity" EXACT []
synonym: "RNase (non-base specific) activity" EXACT []
synonym: "RNase II activity" BROAD [EC:4.6.1.19]
-synonym: "RNase M activity" RELATED [EC:3.1.27.1]
+synonym: "RNase M activity" RELATED []
synonym: "RNase Ms activity" EXACT []
synonym: "RNase T2 activity" RELATED [EC:4.6.1.19]
xref: EC:4.6.1.19
xref: MetaCyc:3.1.27.1-RXN
-is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters
+is_a: GO:0004521 ! endoribonuclease activity
+is_a: GO:0016849 ! phosphorus-oxygen lyase activity
[Term]
id: GO:0033898
@@ -193334,7 +193038,6 @@ synonym: "purine specific endoribonuclease activity" EXACT []
synonym: "purine-specific ribonuclease activity" EXACT []
synonym: "purine-specific RNase activity" EXACT []
synonym: "ribonuclease (purine) activity" EXACT []
-synonym: "ribonuclease U2 activity" RELATED [EC:4.6.1.20]
synonym: "RNase U2 activity" RELATED [EC:4.6.1.20]
synonym: "trichoderma koningi RNase III activity" EXACT []
xref: EC:4.6.1.20
@@ -193596,7 +193299,6 @@ namespace: molecular_function
def: "Catalysis of the hydrolysis of terminal (1->3)-alpha-D-glucosidic links in 1,3-alpha-D-glucans." [EC:3.2.1.84]
synonym: "1,3-alpha-D-glucan 3-glucohydrolase activity" RELATED [EC:3.2.1.84]
synonym: "exo-1,3-alpha-glucanase activity" RELATED [EC:3.2.1.84]
-synonym: "glucosidase II activity" RELATED [EC:3.2.1.84, GOC:vw]
xref: EC:3.2.1.84
xref: MetaCyc:3.2.1.84-RXN
xref: Reactome:R-HSA-532667 "Removal of the second glucose by glucosidase II"
@@ -194167,7 +193869,7 @@ def: "The aggregation, arrangement and bonding together of proteins and RNA mole
synonym: "cytoplasmic mRNA processing body assembly" EXACT []
synonym: "P body assembly" EXACT []
synonym: "P body biogenesis" RELATED []
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:0033963
@@ -194884,7 +194586,7 @@ is_a: GO:1901700 ! response to oxygen-containing compound
id: GO:0034015
name: L-ribulose-5-phosphate 3-epimerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-ribulose 5-phosphate = L-xylulose 5-phosphate." [EC:5.1.3.22]
+def: "Catalysis of the reaction: L-ribulose 5-phosphate = L-xylulose 5-phosphate." [EC:5.1.3.22, RHEA:18497]
synonym: "L-xylulose 5-phosphate 3-epimerase activity" RELATED [EC:5.1.3.22]
synonym: "SgaU" RELATED [EC:5.1.3.22]
synonym: "UlaE" RELATED [EC:5.1.3.22]
@@ -195194,11 +194896,11 @@ is_a: GO:0034035 ! purine ribonucleoside bisphosphate metabolic process
id: GO:0034038
name: deoxyhypusine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: [eIF5A-precursor]-lysine + spermidine = [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine. Four sub-reactions have been identified,in which the intermediates remain tightly associated with the enzyme: spermidine + NAD+ = dehydrospermidine + NADH; dehydrospermidine + [enzyme]-lysine = N-(4-aminobutylidene)-[enzyme]-lysine + propane-1,3-diamine; N-(4-aminobutylidene)-[enzyme]-lysine + [eIF5A-precursor]-lysine = N-(4-aminobutylidene)-[eIF5A-precursor]-lysine + [enzyme]-lysine; N-(4-aminobutylidene)-[eIF5A-precursor]-lysine + NADH + H+ = [eIF5A-precursor]-deoxyhypusine + NAD+." [EC:2.5.1.46, GOC:pde, MetaCyc:2.5.1.46-RXN]
+def: "Catalysis of the reaction: [eIF5A-precursor]-lysine + spermidine = [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine. Four sub-reactions have been identified,in which the intermediates remain tightly associated with the enzyme: spermidine + NAD+ = dehydrospermidine + NADH; dehydrospermidine + [enzyme]-lysine = N-(4-aminobutylidene)-[enzyme]-lysine + propane-1,3-diamine; N-(4-aminobutylidene)-[enzyme]-lysine + [eIF5A-precursor]-lysine = N-(4-aminobutylidene)-[eIF5A-precursor]-lysine + [enzyme]-lysine; N-(4-aminobutylidene)-[eIF5A-precursor]-lysine + NADH + H+ = [eIF5A-precursor]-deoxyhypusine + NAD+." [GOC:pde, RHEA:33299]
comment: Note that this term is equivalent to the obsolete molecular function term 'deoxyhypusine synthase activity ; GO:0004171' and corresponds closely to the biological process term 'deoxyhypusine biosynthetic process from spermidine, using deoxyhypusine synthase ; GO:0050983'.
+synonym: "(4-aminobutyl)lysine synthase" BROAD [EC:2.5.1.46]
synonym: "eIF-5A-deoxyhypusine synthase activity" RELATED [EC:2.5.1.46]
-synonym: "eIF5A-precursor-lysine:spermidine 4-aminobutyltransferase (propane-1,3-diamine-forming) activity" RELATED [EC:2.5.1.46]
-synonym: "spermidine:eIF5A-lysine 4-aminobutyltransferase (propane-1,3-diamine-forming) activity" RELATED [EC:2.5.1.46]
+synonym: "spermidine dehydrogenase" BROAD [EC:2.5.1.46]
xref: EC:2.5.1.46
xref: MetaCyc:2.5.1.46-RXN
xref: Reactome:R-HSA-204617 "DHPS tetramer synthesizes EIF5A and spermidine from Dhp-K50-EIF5A"
@@ -195279,7 +194981,7 @@ relationship: part_of GO:0000407 ! phagophore assembly site
id: GO:0034046
name: poly(G) binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a sequence of guanine residues in an RNA molecule." [GOC:mah]
+def: "Binding to a sequence of guanine residues in an RNA molecule." [GOC:mah]
synonym: "poly(G) binding, within an RNA molecule" EXACT []
synonym: "poly(rG) binding" EXACT [GOC:mah]
is_a: GO:0070717 ! poly-purine tract binding
@@ -195362,7 +195064,6 @@ synonym: "negative regulation by symbiont of host defense-related PCD" EXACT [GO
synonym: "negative regulation by symbiont of host defense-related programmed cell death" EXACT []
synonym: "negative regulation by symbiont of plant HR" NARROW [GOC:pamgo_curators]
synonym: "negative regulation by symbiont of plant hypersensitive response" NARROW [GOC:pamgo_curators]
-synonym: "suppression by symbiont of host defense-related programmed cell death" NARROW [GOC:pamgo_curators]
synonym: "suppression of HR" NARROW [GOC:pamgo_curators]
is_a: GO:0034053 ! modulation by symbiont of host defense-related programmed cell death
is_a: GO:0043069 ! negative regulation of programmed cell death
@@ -195392,8 +195093,7 @@ is_a: GO:0140418 ! effector-mediated modulation of host process by symbiont
id: GO:0034056
name: estrogen response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the estrogen response element (ERE), a conserved sequence found in the promoters of genes whose expression is regulated in response to estrogen." [GOC:ecd, PMID:15036253, PMID:17975005]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to an estrogen response element (ERE), a conserved sequence found in the promoters of genes whose expression is regulated in response to estrogen." [GOC:ecd, PMID:15036253, PMID:17975005]
synonym: "ERE binding" EXACT []
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
@@ -195472,7 +195172,7 @@ name: stress granule assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule." [GOC:mah, PMID:17392519]
synonym: "SG assembly" EXACT [PMID:19825938]
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:0034064
@@ -195541,7 +195241,7 @@ name: aminoglycoside phosphotransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + aminoglycoside = ADP + phosphoaminoglycoside." [GOC:cb, GOC:mah]
synonym: "aminoglycoside kinase activity" EXACT []
-xref: EC:2.7.1.-
+xref: EC 2.7.1.190
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
@@ -195628,11 +195328,12 @@ is_a: GO:1902653 ! secondary alcohol biosynthetic process
[Term]
id: GO:0034080
-name: CENP-A containing nucleosome assembly
+name: CENP-A containing chromatin assembly
namespace: biological_process
alt_id: GO:0034509
-def: "The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GOC:mah, GOC:vw, PMID:18158900, PMID:19217403]
+def: "The formation of chromatin containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres." [GOC:mah, GOC:vw, PMID:18158900, PMID:19217403]
synonym: "CenH3-containing nucleosome assembly at centromere" RELATED []
+synonym: "CENP-A containing nucleosome assembly" RELATED []
synonym: "CENP-A containing nucleosome assembly at centromere" EXACT [GOC:vw]
synonym: "CENP-A deposition" RELATED [GOC:vw]
synonym: "CENP-A loading" RELATED [GOC:vw]
@@ -195640,7 +195341,8 @@ synonym: "centromere specific nucleosome exchange" RELATED [GOC:mah]
synonym: "centromere-specific histone exchange" EXACT [GOC:mah, GOC:vw]
synonym: "centromeric DNA replication-independent nucleosome assembly" EXACT [GOC:mah]
synonym: "DNA replication-independent nucleosome assembly at centromere" EXACT [GOC:mah]
-is_a: GO:0006336 ! DNA replication-independent nucleosome assembly
+is_a: GO:0006334 ! nucleosome assembly
+is_a: GO:0006336 ! DNA replication-independent chromatin assembly
is_a: GO:0031055 ! chromatin remodeling at centromere
is_a: GO:0043486 ! histone exchange
relationship: part_of GO:0034508 ! centromere complex assembly
@@ -196673,21 +196375,21 @@ relationship: positively_regulates GO:0034088 ! maintenance of mitotic sister ch
id: GO:0034185
name: apolipoprotein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex." [GOC:BHF, GOC:rl]
+def: "Binding to an apolipoprotein, the protein component of a lipoprotein complex." [GOC:BHF, GOC:rl]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0034186
name: apolipoprotein A-I binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with apolipoprotein A-I." [GOC:BHF, GOC:rl]
+def: "Binding to apolipoprotein A-I." [GOC:BHF, GOC:rl]
is_a: GO:0034185 ! apolipoprotein binding
[Term]
id: GO:0034187
name: obsolete apolipoprotein E binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with apolipoprotein E." [GOC:BHF, GOC:rl]
+def: "OBSOLETE. Binding to apolipoprotein E." [GOC:BHF, GOC:rl]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "apolipoprotein E binding" EXACT []
is_obsolete: true
@@ -196705,7 +196407,7 @@ is_a: GO:0030226 ! apolipoprotein receptor activity
id: GO:0034189
name: very-low-density lipoprotein particle binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a very-low-density lipoprotein particle, a triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm." [GOC:BHF, GOC:mah]
+def: "Binding to a very-low-density lipoprotein particle, a triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm." [GOC:BHF, GOC:mah]
synonym: "very-low-density lipoprotein binding" EXACT [GOC:bf, GOC:dph]
synonym: "VLDL binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -196715,14 +196417,14 @@ is_a: GO:0071813 ! lipoprotein particle binding
id: GO:0034190
name: apolipoprotein receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an apolipoprotein receptor." [GOC:BHF, GOC:rl]
+def: "Binding to an apolipoprotein receptor." [GOC:BHF, GOC:rl]
is_a: GO:0005102 ! signaling receptor binding
[Term]
id: GO:0034191
name: apolipoprotein A-I receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an apolipoprotein A-I receptor." [GOC:BHF, GOC:rl]
+def: "Binding to an apolipoprotein A-I receptor." [GOC:BHF, GOC:rl]
comment: Note that this term is to be used only to annotate gene products that bind to lipid-free APOA1. For receptors that bind lipid-associated apolipoproteins (plasma lipoprotein particles), consider annotating to 'lipoprotein receptor activity ; GO:0030228' or its child terms.
is_a: GO:0034190 ! apolipoprotein receptor binding
@@ -197075,7 +196777,6 @@ id: GO:0034227
name: tRNA thio-modification
namespace: biological_process
def: "The addition a sulfur atom to a nucleotide in a tRNA molecule." [GOC:mcc, PMID:12549933, PMID:14722066]
-synonym: "tRNA sulfurtransferase activity" RELATED [GOC:mah]
synonym: "tRNA thiolation" EXACT [PMID:24774365]
is_a: GO:0006400 ! tRNA modification
@@ -197168,7 +196869,7 @@ relationship: regulates GO:0034232 ! ascospore wall chitin catabolic process
id: GO:0034235
name: GPI anchor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any glycosylphosphatidylinositol anchor. GPI anchors serve to attach membrane proteins to the lipid bilayer of cell membranes." [GOC:vw]
+def: "Binding to a glycosylphosphatidylinositol anchor. GPI anchors serve to attach membrane proteins to the lipid bilayer of cell membranes." [GOC:vw]
comment: Note that this term should be used to annotate gene products that interact non-covalently with GPI anchors, and not proteins that have GPI anchors covalently attached.
synonym: "glycosylphosphatidylinositol binding" EXACT []
is_a: GO:0035091 ! phosphatidylinositol binding
@@ -197178,7 +196879,7 @@ is_a: GO:0051861 ! glycolipid binding
id: GO:0034236
name: protein kinase A catalytic subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A." [GOC:mah]
+def: "Binding to one or both of the catalytic subunits of protein kinase A." [GOC:mah]
synonym: "PKA catalytic subunit binding" EXACT []
is_a: GO:0019901 ! protein kinase binding
is_a: GO:0051018 ! protein kinase A binding
@@ -197187,7 +196888,7 @@ is_a: GO:0051018 ! protein kinase A binding
id: GO:0034237
name: protein kinase A regulatory subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with one or both of the regulatory subunits of protein kinase A." [GOC:mah]
+def: "Binding to one or both of the regulatory subunits of protein kinase A." [GOC:mah]
synonym: "PKA regulatory subunit binding" EXACT []
synonym: "protein kinase A anchoring activity" RELATED []
is_a: GO:0051018 ! protein kinase A binding
@@ -197286,7 +196987,6 @@ synonym: "mitochondrial RNA polymerase promoter specificity activity" RELATED []
synonym: "mitochondrial RNA polymerase transcription factor activity, sequence-specific DNA binding" EXACT []
synonym: "mitochondrial sequence-specific DNA binding transcription factor activity" EXACT []
synonym: "mitochondrial sequence-specific DNA-binding transcription factor activity" NARROW []
-synonym: "mitochondrial transcription factor activity" RELATED []
synonym: "mitochondrial transcription initiation factor activity" EXACT []
synonym: "sequence-specific DNA binding mitochondrial RNA polymerase transcription factor activity" EXACT []
synonym: "transcription factor activity, mitochondrial proximal promoter sequence-specific binding" EXACT []
@@ -197527,7 +197227,6 @@ synonym: "discadenine anabolism" EXACT []
synonym: "discadenine biosynthesis" EXACT []
synonym: "discadenine formation" EXACT []
synonym: "discadenine synthesis" EXACT []
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009691 ! cytokinin biosynthetic process
is_a: GO:0034267 ! discadenine metabolic process
is_a: GO:0072522 ! purine-containing compound biosynthetic process
@@ -198175,7 +197874,7 @@ is_a: GO:0003918 ! DNA topoisomerase type II (double strand cut, ATP-hydrolyzing
id: GO:0034336
name: misfolded RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA molecule that has assumed an incorrect conformation." [GOC:mah, PMID:10393192]
+def: "Binding to an RNA molecule that has assumed an incorrect conformation." [GOC:mah, PMID:10393192]
synonym: "RNA chaperone" RELATED []
is_a: GO:0003723 ! RNA binding
@@ -198301,7 +198000,7 @@ relationship: positively_regulates GO:0034343 ! type III interferon production
id: GO:0034347
name: type III interferon binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type III interferon. Interferon lambda is the only member of the type III interferon found so far." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16734557]
+def: "Binding to a type III interferon. Interferon lambda is the only member of the type III interferon found so far." [GOC:add, ISBN:0126896631, PMID:15546383, PMID:16734557]
comment: Note that IL-28A, IL-28B, and IL-29 are types of interferon-lambda.
synonym: "interferon-lambda binding" NARROW []
is_a: GO:0019961 ! interferon binding
@@ -198503,7 +198202,7 @@ name: protein-containing complex remodeling
namespace: biological_process
def: "The acquisition, loss, or modification of macromolecules within a complex, resulting in the alteration of an existing complex." [GOC:BHF, GOC:mah, GOC:mtg_mpo, GOC:rl]
synonym: "macromolecular complex remodeling" RELATED []
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0034368
@@ -198839,11 +198538,12 @@ is_a: GO:0009536 ! plastid
[Term]
id: GO:0034401
-name: chromatin organization involved in regulation of transcription
+name: obsolete chromatin organization involved in regulation of transcription
namespace: biological_process
alt_id: GO:1903756
alt_id: GO:1903757
-def: "Any cellular process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin that modulates the rate, frequency or extent of DNA-dependent transcription." [GOC:curators, PMID:21102443]
+def: "OBSOLETE. Any cellular process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin that modulates the rate, frequency or extent of DNA-dependent transcription." [GOC:curators, PMID:21102443]
+comment: This term was obsoleted because these it was redundant with other terms: heterochromatin assembly and regulation of gene expression, epigenetic.
synonym: "activation of global transcription from RNA polymerase II promoter by histone modification" NARROW [GOC:TermGenie]
synonym: "activation of transcription from RNA polymerase II promoter by histone modification" NARROW [GOC:TermGenie]
synonym: "establishment or maintenance of chromatin architecture during transcription" EXACT [GOC:mah]
@@ -198867,8 +198567,7 @@ synonym: "up-regulation of global transcription from RNA polymerase II promoter
synonym: "up-regulation of transcription from RNA polymerase II promoter by histone modification" NARROW [GOC:TermGenie]
synonym: "upregulation of global transcription from RNA polymerase II promoter by histone modification" NARROW [GOC:TermGenie]
synonym: "upregulation of transcription from RNA polymerase II promoter by histone modification" NARROW [GOC:TermGenie]
-is_a: GO:0006325 ! chromatin organization
-relationship: part_of GO:0006355 ! regulation of transcription, DNA-templated
+is_obsolete: true
[Term]
id: GO:0034402
@@ -199080,10 +198779,12 @@ is_a: GO:1901576 ! organic substance biosynthetic process
[Term]
id: GO:0034419
-name: L-2-hydroxyglutarate oxidase activity
+name: obsolete L-2-hydroxyglutarate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-2-hydroxyglutarate + O2 = 2-oxoglutarate + hydrogen peroxide." [PMID:18390652]
-is_a: GO:0003973 ! (S)-2-hydroxy-acid oxidase activity
+def: "OBSOLETE. Catalysis of the reaction: L-2-hydroxyglutarate + O2 = 2-oxoglutarate + hydrogen peroxide." [PMID:18390652]
+comment: This term was obsoleted because this activity is not believed to exist.
+is_obsolete: true
+consider: GO:0140696
[Term]
id: GO:0034420
@@ -199234,7 +198935,7 @@ is_a: GO:0034434 ! sterol esterification
id: GO:0034436
name: glycoprotein transport
namespace: biological_process
-def: "The directed movement of a glycoprotein, any protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:BHF, GOC:mah, GOC:rl]
+def: "The directed movement of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:BHF, GOC:mah, GOC:rl]
is_a: GO:0015031 ! protein transport
is_a: GO:1901264 ! carbohydrate derivative transport
@@ -199358,7 +199059,7 @@ relationship: part_of GO:0005813 ! centrosome
id: GO:0034452
name: dynactin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of a dynactin complex; dynactin is a large protein complex that activates dynein-based motor activity." [GOC:BHF, GOC:mah]
+def: "Binding to a dynactin complex; a large protein complex that activates dynein-based motor activity." [GOC:BHF, GOC:mah]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
@@ -199411,7 +199112,7 @@ id: GO:0034458
name: 3'-5' RNA helicase activity
namespace: molecular_function
alt_id: GO:0034459
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix in the direction 3' to 5'." [GOC:jp]
+def: "Unwinding of an RNA helix in the 3' to 5' direction, driven by ATP hydrolysis." [GOC:jp]
synonym: "3' to 5' RNA helicase activity" EXACT []
synonym: "ATP-dependent 3' to 5' RNA helicase activity" EXACT []
synonym: "ATP-dependent 3'-5' RNA helicase activity" EXACT []
@@ -199654,7 +199355,6 @@ namespace: biological_process
def: "The process in which a solute is transported from one side of the vacuolar membrane to the other." [GOC:mah]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "vacuolar membrane transport" EXACT []
-is_a: GO:0007034 ! vacuolar transport
is_a: GO:0055085 ! transmembrane transport
[Term]
@@ -199864,14 +199564,14 @@ relationship: part_of GO:0098813 ! nuclear chromosome segregation
id: GO:0034511
name: U3 snoRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with U3 small nucleolar RNA." [GOC:mah]
+def: "Binding to a U3 small nucleolar RNA." [GOC:mah]
is_a: GO:0030515 ! snoRNA binding
[Term]
id: GO:0034512
name: box C/D RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with box C/D small nucleolar RNA." [GOC:mah]
+def: "Binding to a box C/D small nucleolar RNA." [GOC:mah]
synonym: "box C/D snoRNA binding" NARROW []
synonym: "box C/D sRNA binding" NARROW []
is_a: GO:0030515 ! snoRNA binding
@@ -199880,7 +199580,7 @@ is_a: GO:0030515 ! snoRNA binding
id: GO:0034513
name: box H/ACA snoRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with box H/ACA small nucleolar RNA." [GOC:mah]
+def: "Binding to a box H/ACA small nucleolar RNA." [GOC:mah]
is_a: GO:0030515 ! snoRNA binding
[Term]
@@ -199908,6 +199608,7 @@ def: "Any process that results in a change in state or activity of a cell or an
is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:0014070 ! response to organic cyclic compound
is_a: GO:0033273 ! response to vitamin
+is_a: GO:1901700 ! response to oxygen-containing compound
[Term]
id: GO:0034517
@@ -200214,7 +199915,7 @@ id: GO:0034552
name: respiratory chain complex II assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex II." [GOC:dgf]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0034553
@@ -200468,14 +200169,14 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0034583
name: 21U-RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 21U-RNA, a 21-nucleotide RNA characterized by a uridine 5'-monophosphate and a modified 3' end resistant to periodate degradation. 21U-RNAs are derived from distinct, autonomously expressed loci within the genome." [GOC:kmv]
+def: "Binding to a 21U-RNA, a 21-nucleotide RNA characterized by a uridine 5'-monophosphate and a modified 3' end resistant to periodate degradation. 21U-RNAs are derived from distinct, autonomously expressed loci within the genome." [GOC:kmv]
is_a: GO:0003723 ! RNA binding
[Term]
id: GO:0034584
name: piRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a piRNA, a Piwi-associated RNA, a 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv]
+def: "Binding to a piRNA, a Piwi-associated RNA, a 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [GOC:kmv]
synonym: "Piwi-associated RNA binding" EXACT []
is_a: GO:0061980 ! regulatory RNA binding
@@ -200745,7 +200446,6 @@ name: cellular protein localization
namespace: biological_process
alt_id: GO:0016249
def: "Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah]
-subset: goslim_drosophila
synonym: "cellular protein localisation" EXACT [GOC:mah]
synonym: "channel localizer activity" NARROW [GOC:mah]
is_a: GO:0008104 ! protein localization
@@ -200786,7 +200486,7 @@ is_a: GO:0034405 ! response to fluid shear stress
id: GO:0034617
name: tetrahydrobiopterin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a tetrahydrobiopterin, 5,6,7,8-tetrahydrobiopterin or a derivative thereof; tetrahydrobiopterins are enzyme cofactors that carry electrons in redox reactions." [GOC:BHF, GOC:mah, GOC:rl]
+def: "Binding to a tetrahydrobiopterin, 5,6,7,8-tetrahydrobiopterin or a derivative thereof; tetrahydrobiopterins are enzyme cofactors that carry electrons in redox reactions." [GOC:BHF, GOC:mah, GOC:rl]
synonym: "BH4 binding" EXACT []
synonym: "H4biopterin binding" EXACT []
synonym: "sapropterin binding" EXACT []
@@ -200797,7 +200497,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0034618
name: arginine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:BHF, GOC:rl]
+def: "Binding to 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:BHF, GOC:rl]
synonym: "aminopentanoic acid binding" RELATED []
synonym: "Arg binding" EXACT []
is_a: GO:0016597 ! amino acid binding
@@ -200814,16 +200514,6 @@ synonym: "heat shock protein activity" RELATED []
is_a: GO:0006986 ! response to unfolded protein
is_a: GO:0035967 ! cellular response to topologically incorrect protein
-[Term]
-id: GO:0034622
-name: cellular protein-containing complex assembly
-namespace: biological_process
-alt_id: GO:0043623
-def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell." [GOC:jl]
-synonym: "cellular macromolecule complex assembly" RELATED []
-synonym: "cellular protein complex assembly" EXACT []
-is_a: GO:0065003 ! protein-containing complex assembly
-
[Term]
id: GO:0034624
name: obsolete DNA recombinase assembly involved in gene conversion at mating-type locus
@@ -200863,17 +200553,6 @@ synonym: "de novo NAD biosynthetic process from aspartate" RELATED []
is_a: GO:0019355 ! nicotinamide nucleotide biosynthetic process from aspartate
is_a: GO:0034627 ! 'de novo' NAD biosynthetic process
-[Term]
-id: GO:0034629
-name: cellular protein-containing complex localization
-namespace: biological_process
-def: "A protein complex localization process that takes place at the cellular level; as a result, a protein complex is transported to, or maintained in, a specific location within a cell." [GOC:mah]
-synonym: "cellular protein complex localisation" EXACT [GOC:mah]
-synonym: "cellular protein complex localization" RELATED []
-synonym: "establishment and maintenance of cellular protein complex localization" EXACT []
-is_a: GO:0031503 ! protein-containing complex localization
-is_a: GO:0034613 ! cellular protein localization
-
[Term]
id: GO:0034630
name: RITS complex localization
@@ -200881,7 +200560,7 @@ namespace: biological_process
def: "Any process in which a RITS complex is transported to, or maintained in, a specific location." [GOC:mah]
synonym: "establishment and maintenance of RITS complex localization" EXACT []
synonym: "RITS complex localisation" EXACT [GOC:mah]
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
[Term]
id: GO:0034631
@@ -200987,7 +200666,6 @@ name: cellular nitrogen compound metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah]
subset: goslim_chembl
-subset: goslim_generic
synonym: "cellular nitrogen compound metabolism" EXACT []
is_a: GO:0006807 ! nitrogen compound metabolic process
is_a: GO:0044237 ! cellular metabolic process
@@ -201054,29 +200732,41 @@ relationship: part_of GO:0043229 ! intracellular organelle
[Term]
id: GO:0034647
-name: histone demethylase activity (H3-trimethyl-K4 specific)
+name: histone H3-tri/di/monomethyl-lysine-4 demethylase activity
namespace: molecular_function
-def: "Catalysis of the removal of a methyl group from trimethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:17550896]
+def: "Catalysis of the removal of a methyl group from a tri, a di or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:17550896, PMID:22473470]
+synonym: "H3K4me3 demethylase activity" RELATED []
synonym: "histone demethylase activity (H3-K4-me3 specific)" EXACT []
+synonym: "histone demethylase activity (H3-trimethyl-K4 specific)" EXACT []
+synonym: "histone H3-K4me2 demethylase activity" BROAD []
+synonym: "histone H3-K4me3 demethylase activity" RELATED []
+synonym: "histone H3K4me2 demethylase activity" BROAD []
xref: EC:1.14.11.67
-is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific)
+xref: RHEA:60208
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
+is_a: GO:0032453 ! histone H3-methyl-lysine-4 demethylase activity
[Term]
id: GO:0034648
-name: histone demethylase activity (H3-dimethyl-K4 specific)
+name: obsolete histone demethylase activity (H3-dimethyl-K4 specific)
namespace: molecular_function
-def: "Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:17550896]
+def: "OBSOLETE. Catalysis of the removal of a methyl group from dimethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:17550896]
+comment: This term was obsoleted to align with RHEA and EC: this is a sub-reaction both in RHEA:60208 and EC:1.14.11.67.
synonym: "histone demethylase activity (H3-K4-me2 specific)" EXACT []
-is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific)
+is_obsolete: true
+consider: GO:0034647
+consider: GO:0140682
[Term]
id: GO:0034649
-name: histone demethylase activity (H3-monomethyl-K4 specific)
+name: obsolete histone demethylase activity (H3-monomethyl-K4 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 4) + O2 + FAD + H2O = histone H3 L-lysine (position 4) + H2O2 + formaldehyde + FADH2. This reaction is the removal of a methyl group from monomethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:16223729]
+def: "OBSOLETE. Catalysis of the removal of a methyl group from monomethylated lysine at position 4 of the histone H3 protein." [GOC:mah, PMID:16223729]
+comment: This term was obsoleted to align with RHEA and EC: this is a sub-reaction both in RHEA:60208 and EC:1.14.11.67.
synonym: "histone demethylase activity (H3-K4-me1 specific)" EXACT []
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
-is_a: GO:0032453 ! histone demethylase activity (H3-K4 specific)
+is_obsolete: true
+consider: GO:0034647
+consider: GO:0140682
[Term]
id: GO:0034650
@@ -201152,7 +200842,6 @@ name: nucleobase-containing compound catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah]
subset: goslim_chembl
-subset: goslim_generic
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" EXACT []
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process" RELATED [GOC:dph, GOC:tb]
synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" EXACT []
@@ -201639,7 +201328,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0034710
name: inhibin complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an inhibin complex, a dimer of one inhibin-alpha subunit and one inhibin-beta subunit." [GOC:BHF, GOC:mah]
+def: "Binding to an inhibin complex, a dimer of one inhibin-alpha subunit and one inhibin-beta subunit." [GOC:BHF, GOC:mah]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -201649,7 +201338,7 @@ namespace: molecular_function
alt_id: GO:0034712
alt_id: GO:0048186
alt_id: GO:0048187
-def: "Interacting selectively and non-covalently with an inhibin monomer, any of the polypeptides that combine to form activin and inhibin dimers." [GOC:BHF, GOC:mah]
+def: "Binding to an inhibin monomer, any of the polypeptides that combine to form activin and inhibin dimers." [GOC:BHF, GOC:mah]
synonym: "inhibin alpha binding" NARROW []
synonym: "inhibin beta-A binding" NARROW []
synonym: "inhibin beta-B binding" NARROW []
@@ -201663,7 +201352,7 @@ namespace: molecular_function
alt_id: GO:0005103
alt_id: GO:0005116
alt_id: GO:0005120
-def: "Interacting selectively and non-covalently with a type I transforming growth factor beta receptor." [GOC:BHF, GOC:mah]
+def: "Binding to a type I transforming growth factor beta receptor." [GOC:BHF, GOC:mah]
synonym: "babo binding" NARROW []
synonym: "babo ligand" NARROW []
synonym: "baboon binding" NARROW []
@@ -201687,7 +201376,7 @@ is_a: GO:0005160 ! transforming growth factor beta receptor binding
id: GO:0034714
name: type III transforming growth factor beta receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type III transforming growth factor beta receptor." [GOC:BHF, GOC:mah]
+def: "Binding to a type III transforming growth factor beta receptor." [GOC:BHF, GOC:mah]
synonym: "betaglycan binding" RELATED []
synonym: "TGF-beta type III binding" EXACT []
synonym: "transforming growth factor beta ligand binding to type III receptor" RELATED []
@@ -201767,37 +201456,39 @@ is_a: GO:0008242 ! omega peptidase activity
[Term]
id: GO:0034723
-name: DNA replication-dependent nucleosome organization
+name: DNA replication-dependent chromatin organization
namespace: biological_process
def: "The formation or destruction of chromatin structures on newly replicated DNA, coupled to strand elongation." [GOC:mah, PMID:17510629]
synonym: "DNA replication-dependent nucleosome organisation" EXACT []
-is_a: GO:0006333 ! chromatin assembly or disassembly
-is_a: GO:0034728 ! nucleosome organization
+synonym: "DNA replication-dependent nucleosome organization" EXACT []
+is_a: GO:0006325 ! chromatin organization
[Term]
id: GO:0034724
-name: DNA replication-independent nucleosome organization
+name: DNA replication-independent chromatin organization
namespace: biological_process
def: "The formation or destruction of chromatin structures, occurring outside the context of DNA replication." [GOC:mah, PMID:17510629]
synonym: "DNA replication-independent nucleosome organisation" EXACT []
-is_a: GO:0006333 ! chromatin assembly or disassembly
-is_a: GO:0034728 ! nucleosome organization
+is_a: GO:0006325 ! chromatin organization
[Term]
id: GO:0034725
-name: DNA replication-dependent nucleosome disassembly
+name: obsolete DNA replication-dependent nucleosome disassembly
namespace: biological_process
-def: "The controlled breakdown of nucleosomes on newly replicated DNA, coupled to strand elongation." [GOC:mah, PMID:17510629]
-is_a: GO:0006337 ! nucleosome disassembly
-is_a: GO:0034723 ! DNA replication-dependent nucleosome organization
+def: "OBSOLETE. The controlled breakdown of nucleosomes on newly replicated DNA, coupled to strand elongation." [GOC:mah, PMID:17510629]
+comment: This term was obsoleted because it did not describe a different process from that described by its parent.
+synonym: "DNA replication-dependent chromatin disassembly" EXACT []
+is_obsolete: true
+consider: GO:0006337
[Term]
id: GO:0034726
-name: DNA replication-independent nucleosome disassembly
+name: obsolete DNA replication-independent nucleosome disassembly
namespace: biological_process
-def: "The controlled breakdown of nucleosomes outside the context of DNA replication." [GOC:mah, PMID:17510629]
-is_a: GO:0006337 ! nucleosome disassembly
-is_a: GO:0034724 ! DNA replication-independent nucleosome organization
+def: "OBSOLETE. The controlled disassembly of chromatin outside the context of DNA replication." [GOC:mah, PMID:17510629]
+comment: This term was obsoleted because it did not describe a different process from that described by its parent.
+synonym: "DNA replication-independent chromatin disassembly" RELATED []
+is_obsolete: true
[Term]
id: GO:0034727
@@ -201814,7 +201505,7 @@ name: nucleosome organization
namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of one or more nucleosomes." [GOC:mah]
synonym: "nucleosome organisation" EXACT []
-is_a: GO:0006325 ! chromatin organization
+is_a: GO:0006338 ! chromatin remodeling
is_a: GO:0071824 ! protein-DNA complex subunit organization
[Term]
@@ -201912,7 +201603,7 @@ is_a: GO:0004772 ! sterol O-acyltransferase activity
id: GO:0034739
name: histone deacetylase activity (H4-K16 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein." [EC:3.5.1.17, GOC:vw, RHEA:24548]
+def: "Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein." [GOC:vw, PMID:28450737]
is_a: GO:0004407 ! histone deacetylase activity
[Term]
@@ -202078,7 +201769,7 @@ synonym: "regulation of Fe transport" EXACT []
synonym: "regulation of iron import" NARROW [GOC:TermGenie]
synonym: "regulation of iron ion import" NARROW []
synonym: "regulation of iron transport" EXACT []
-is_a: GO:0043269 ! regulation of ion transport
+is_a: GO:0010959 ! regulation of metal ion transport
relationship: regulates GO:0006826 ! iron ion transport
[Term]
@@ -203169,8 +202860,9 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0034875
name: caffeine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: caffeine + O2 + 2 H+ + 2 e- = 1,3,7-trimethyluric acid + H2O." [UM-BBD_reactionID:r1321]
-xref: EC:1.17.5.-
+def: "Catalysis of the reaction: caffeine + O2 + 2 H+ + 2 e- = 1,3,7-trimethyluric acid + H2O." [RHEA:47148]
+xref: EC:1.17.5.2
+xref: RHEA:47148
xref: UM-BBD_reactionID:r1321
is_a: GO:0033695 ! oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor
@@ -204041,7 +203733,7 @@ is_a: GO:0140513 ! nuclear protein-containing complex
id: GO:0034979
name: NAD-dependent protein deacetylase activity
namespace: molecular_function
-def: "Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD." [GOC:BHF, GOC:mah]
+def: "Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD." [GOC:BHF, GOC:mah, PMID:28450737]
xref: Reactome:R-HSA-3371467 "SIRT1 deacetylates HSF1"
xref: Reactome:R-HSA-5211239 "SIRT1 deacetylates TAF1B in SL1 complex"
xref: Reactome:R-HSA-5685953 "SIRT6 deacetylates RBBP8"
@@ -204104,7 +203796,7 @@ is_a: GO:0016530 ! metallochaperone activity
id: GO:0034987
name: immunoglobulin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule." [GOC:BHF, GOC:vk]
+def: "Binding to one or more specific sites on an immunoglobulin receptor molecule." [GOC:BHF, GOC:vk]
synonym: "Fc receptor binding" RELATED []
is_a: GO:0005102 ! signaling receptor binding
@@ -204112,7 +203804,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0034988
name: Fc-gamma receptor I complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with one or more specific sites on the Fc-gamma receptor I complex. The complex functions primarily as an activating receptor for IgG." [GOC:BHF, GOC:vk]
+def: "Binding to one or more specific sites on the Fc-gamma receptor I complex. The complex functions primarily as an activating receptor for IgG." [GOC:BHF, GOC:vk]
is_a: GO:0034987 ! immunoglobulin receptor binding
is_a: GO:0044877 ! protein-containing complex binding
@@ -204543,7 +204235,7 @@ is_a: GO:0030234 ! enzyme regulator activity
id: GO:0035035
name: histone acetyltransferase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme histone acetyltransferase." [GOC:bf]
+def: "Binding to an histone acetyltransferase." [GOC:bf]
synonym: "histone acetylase binding" EXACT []
is_a: GO:0019899 ! enzyme binding
@@ -204570,7 +204262,6 @@ id: GO:0035038
name: female pronucleus assembly
namespace: biological_process
def: "Assembly of the haploid nucleus of the unfertilized egg." [GOC:bf, ISBN:0582227089]
-synonym: "female pronucleus assembly" RELATED [GOC:dph]
is_a: GO:0006997 ! nucleus organization
is_a: GO:0022414 ! reproductive process
is_a: GO:0070925 ! organelle assembly
@@ -204598,9 +204289,10 @@ relationship: part_of GO:0035039 ! male pronucleus assembly
[Term]
id: GO:0035041
-name: sperm chromatin decondensation
+name: sperm DNA decondensation
namespace: biological_process
def: "Unwinding of the condensed nuclear chromatin of an inactive sperm nucleus." [GOC:bf, PMID:11735001]
+synonym: "sperm chromatin decondensation" EXACT []
is_a: GO:0006325 ! chromatin organization
is_a: GO:0022414 ! reproductive process
relationship: part_of GO:0035039 ! male pronucleus assembly
@@ -204614,7 +204306,7 @@ synonym: "sperm-specific histone exchange" EXACT []
synonym: "sperm-specific histone replacement" EXACT []
is_a: GO:0022414 ! reproductive process
is_a: GO:0043486 ! histone exchange
-relationship: part_of GO:0035041 ! sperm chromatin decondensation
+relationship: part_of GO:0035041 ! sperm DNA decondensation
[Term]
id: GO:0035043
@@ -204776,7 +204468,7 @@ is_a: GO:0030575 ! nuclear body organization
id: GO:0035064
name: methylated histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:bf, PMID:14585615]
+def: "Binding to a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:bf, PMID:14585615]
is_a: GO:0042393 ! histone binding
is_a: GO:0140034 ! methylation-dependent protein binding
@@ -204995,15 +204687,16 @@ is_a: GO:0035088 ! establishment or maintenance of apical/basal cell polarity
id: GO:0035091
name: phosphatidylinositol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives." [GOC:bf, ISBN:0198506732, PMID:11395417]
+def: "Binding to an inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives." [GOC:bf, ISBN:0198506732, PMID:11395417]
synonym: "phosphoinositide binding" EXACT []
is_a: GO:0005543 ! phospholipid binding
[Term]
id: GO:0035092
-name: sperm chromatin condensation
+name: sperm DNA condensation
namespace: biological_process
def: "The progressive compaction of the spermatid chromatin so that it reaches a level of condensation that is not compatible with nuclear activities such as transcription or DNA replication." [GOC:bf, PMID:11735001]
+synonym: "sperm chromatin condensation" EXACT []
is_a: GO:0006323 ! DNA packaging
is_a: GO:0006325 ! chromatin organization
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
@@ -205014,11 +204707,9 @@ id: GO:0035093
name: spermatogenesis, exchange of chromosomal proteins
namespace: biological_process
def: "The replacement of somatic histones within sperm chromatin with sperm-specific histones or protamines with unique DNA-binding properties, resulting in condensation of the sperm chromatin." [GOC:bf, PMID:11735001]
-synonym: "somatic histone exchange" EXACT []
-synonym: "somatic histone replacement" RELATED []
is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
is_a: GO:0043486 ! histone exchange
-relationship: part_of GO:0035092 ! sperm chromatin condensation
+relationship: part_of GO:0035092 ! sperm DNA condensation
[Term]
id: GO:0035094
@@ -205080,7 +204771,7 @@ relationship: part_of GO:0035162 ! embryonic hemopoiesis
id: GO:0035100
name: ecdysone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 20-hydroxyecdysone (ecdysone). Ecdysone is an ecdysteroid produced by the prothoracic glands of immature insects and the ovaries of adult females, which stimulates growth and molting." [GOC:bf, ISBN:0198506732, ISBN:0582227089]
+def: "Binding to 20-hydroxyecdysone (ecdysone). Ecdysone is an ecdysteroid produced by the prothoracic glands of immature insects and the ovaries of adult females, which stimulates growth and molting." [GOC:bf, ISBN:0198506732, ISBN:0582227089]
is_a: GO:0032934 ! sterol binding
is_a: GO:0042562 ! hormone binding
is_a: GO:0043178 ! alcohol binding
@@ -205089,7 +204780,7 @@ is_a: GO:0043178 ! alcohol binding
id: GO:0035101
name: FACT complex
namespace: cellular_component
-def: "An abundant nuclear complex, which was originally identified in mammalian systems as a factor required for transcription elongation on chromatin templates. The FACT complex has been shown to destablilize the interaction between the H2A/H2B dimer and the H3/H4 tetramer of the nucleosome, thus reorganizing the structure of the nucleosome. In this way, the FACT complex may play a role in DNA replication and other processes that traverse the chromatin, as well as in transcription elongation. FACT is composed of two proteins that are evolutionarily conserved in all eukaryotes and homologous to mammalian Spt16 and SSRP1. In metazoans, the SSRP1 homolog contains an HMG domain; however in fungi and protists, it does not. For example, in S. cerevisiae the Pob3 protein is homologous to SSRP1, but lacks the HMG chromatin binding domain. Instead, the yFACT complex of Spt16p and Pob3p, binds to nucleosomes where multiple copies of the HMG-domain containing protein Nhp6p have already bound, but Nhp6p does not form a stable complex with the Spt16p/Pob3p heterodimer." [GOC:bf, GOC:expert_ks, GOC:expert_ras, GOC:expert_tf, GOC:krc, PMID:12934006, PMID:12934007, PMID:16678108]
+def: "A histone chaperone complex that facilitates nucleosome disassembly and reassembly upon DNA or RNA polymerase passage." [PMID:12934006, PMID:12934007, PMID:16678108, PMID:34731638]
synonym: "Facilitates chromatin transcription complex" EXACT []
is_a: GO:0008023 ! transcription elongation factor complex
relationship: part_of GO:0000785 ! chromatin
@@ -205948,6 +205639,7 @@ synonym: "microRNA metabolism" RELATED []
synonym: "microRNA processing" BROAD []
synonym: "microRNA-mediated gene silencing, production of microRNAs" EXACT []
synonym: "miRNA biogenesis" RELATED [GOC:tb]
+synonym: "miRNA biosynthetic process" EXACT []
synonym: "miRNA processing" EXACT []
synonym: "miRNA-mediated gene silencing, production of miRNAs" EXACT [GOC:dph, GOC:tb]
synonym: "production of microRNAs involved in gene silencing by microRNA" EXACT [GOC:pr]
@@ -205958,7 +205650,7 @@ relationship: part_of GO:0035195 ! gene silencing by miRNA
id: GO:0035197
name: siRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme." [PMID:15066275, PMID:15066283]
+def: "Binding to a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme." [PMID:15066275, PMID:15066283]
synonym: "small interfering RNA binding" EXACT []
is_a: GO:0061980 ! regulatory RNA binding
@@ -205966,7 +205658,7 @@ is_a: GO:0061980 ! regulatory RNA binding
id: GO:0035198
name: miRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes." [PMID:15066283]
+def: "Binding to a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes." [PMID:15066283]
synonym: "microRNA binding" EXACT []
is_a: GO:0061980 ! regulatory RNA binding
@@ -206217,7 +205909,7 @@ relationship: part_of GO:0035215 ! genital disc development
id: GO:0035226
name: glutamate-cysteine ligase catalytic subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the catalytic subunit of glutamate-cysteine ligase." [PMID:12954617]
+def: "Binding to the catalytic subunit of glutamate-cysteine ligase." [PMID:12954617]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -206309,6 +206001,7 @@ namespace: biological_process
def: "A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:0198506732]
synonym: "ionotropic glutamate receptor signalling pathway" EXACT []
is_a: GO:0007215 ! glutamate receptor signaling pathway
+is_a: GO:1990806 ! ligand-gated ion channel signaling pathway
[Term]
id: GO:0035236
@@ -206349,7 +206042,7 @@ relationship: part_of GO:0035295 ! tube development
id: GO:0035240
name: dopamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dopamine, a catecholamine neurotransmitter formed by aromatic-L-amino-acid decarboxylase from 3,4-dihydroxy-L-phenylalanine." [ISBN:0198506732]
+def: "Binding to dopamine, a catecholamine neurotransmitter formed by aromatic-L-amino-acid decarboxylase from 3,4-dihydroxy-L-phenylalanine." [ISBN:0198506732]
is_a: GO:0043169 ! cation binding
is_a: GO:1901338 ! catecholamine binding
@@ -206490,7 +206183,7 @@ relationship: part_of GO:0005929 ! cilium
id: GO:0035254
name: glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a glutamate receptor." [GOC:bf]
+def: "Binding to a glutamate receptor." [GOC:bf]
subset: goslim_chembl
is_a: GO:0005102 ! signaling receptor binding
@@ -206498,14 +206191,14 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0035255
name: ionotropic glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels." [GOC:bf, ISBN:0198506732]
+def: "Binding to an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels." [GOC:bf, ISBN:0198506732]
is_a: GO:0035254 ! glutamate receptor binding
[Term]
id: GO:0035256
name: G protein-coupled glutamate receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a G protein-coupled glutamate receptor (a metabotropic glutamate receptor)." [GOC:bf, ISBN:0198506732, PMID:9069287]
+def: "Binding to a G protein-coupled glutamate receptor (a metabotropic glutamate receptor)." [GOC:bf, ISBN:0198506732, PMID:9069287]
synonym: "G-protein coupled glutamate receptor binding" EXACT []
synonym: "metabotropic glutamate receptor binding" EXACT [GOC:bf]
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -206515,7 +206208,7 @@ is_a: GO:0035254 ! glutamate receptor binding
id: GO:0035259
name: glucocorticoid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a glucocorticoid receptor." [GOC:bf]
+def: "Binding to a glucocorticoid receptor." [GOC:bf]
is_a: GO:0016922 ! nuclear receptor binding
[Term]
@@ -206630,7 +206323,7 @@ is_a: GO:0048731 ! system development
id: GO:0035273
name: phthalate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a phthalate, any ester or salt of phthalic acid." [http://umbbd.ahc.umn.edu/pth/pth_map.html]
+def: "Binding to a phthalate, any ester or salt of phthalic acid." [http://umbbd.ahc.umn.edu/pth/pth_map.html]
subset: goslim_pir
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -206639,7 +206332,7 @@ is_a: GO:0097159 ! organic cyclic compound binding
id: GO:0035274
name: diphenyl phthalate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with diphenyl phthalate, C(20)H(14)O(4)." [http://www.sigmaaldrich.com]
+def: "Binding to diphenyl phthalate, C(20)H(14)O(4)." [http://www.sigmaaldrich.com]
synonym: "DPP binding" EXACT []
is_a: GO:0097159 ! organic cyclic compound binding
@@ -206647,7 +206340,7 @@ is_a: GO:0097159 ! organic cyclic compound binding
id: GO:0035275
name: dibutyl phthalate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dibutyl phthalate, C(16)H(22)O(4)." [http://www.sigmaaldrich.com]
+def: "Binding to dibutyl phthalate, C(16)H(22)O(4)." [http://www.sigmaaldrich.com]
synonym: "DBP binding" EXACT []
synonym: "phthalic acid dibutyl ester binding" EXACT []
is_a: GO:0097159 ! organic cyclic compound binding
@@ -206656,7 +206349,7 @@ is_a: GO:0097159 ! organic cyclic compound binding
id: GO:0035276
name: ethanol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ethanol, CH(3)-CH(2)-OH." [ISBN:0198506732]
+def: "Binding to ethanol, CH(3)-CH(2)-OH." [ISBN:0198506732]
is_a: GO:0043168 ! anion binding
is_a: GO:0043178 ! alcohol binding
@@ -206671,7 +206364,7 @@ relationship: part_of GO:0007424 ! open tracheal system development
[Term]
id: GO:0035278
-name: miRNA mediated inhibition of translation
+name: miRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
def: "The process in which microRNAs (miRNAs) block the translation of target mRNAs into proteins. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA will typically mediate repression of translation if the miRNA imperfectly base-pairs with the 3' untranslated regions of target mRNAs." [PMID:14744438, PMID:15196554]
synonym: "down regulation of translation involved in gene silencing by miRNA" EXACT [GOC:mah]
@@ -206679,21 +206372,24 @@ synonym: "down-regulation of translation involved in gene silencing by miRNA" EX
synonym: "downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:mah]
synonym: "gene silencing by miRNA, negative regulation of translation" EXACT [GOC:mah]
synonym: "inhibition of translation involved in gene silencing by miRNA" NARROW [GOC:mah]
+synonym: "miRNA mediated inhibition of translation" EXACT []
synonym: "miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:dph, GOC:tb]
synonym: "negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:pr]
-is_a: GO:0040033 ! negative regulation of translation, ncRNA-mediated
-relationship: part_of GO:0035195 ! gene silencing by miRNA
+is_a: GO:0035195 ! gene silencing by miRNA
+is_a: GO:0040033 ! RNA-mediated gene silencing by inhibition of translation
[Term]
id: GO:0035279
-name: mRNA cleavage involved in gene silencing by miRNA
+name: miRNA-mediated gene silencing by mRNA destabilization
namespace: biological_process
def: "The process in which microRNAs (miRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA base pairing with near-perfect complementarity to the target mRNA will typically direct targeted endonucleolytic cleavage of the mRNA. Many plant miRNAs downregulate gene expression through this mechanism." [GOC:dph, GOC:mtg_lung, PMID:14744438, PMID:15196554]
synonym: "gene silencing by miRNA, mRNA cleavage" EXACT [GOC:mah]
synonym: "miRNA-mediated gene silencing, mRNA cleavage" EXACT [GOC:dph, GOC:tb]
synonym: "mRNA cleavage involved in gene silencing by microRNA" EXACT [GOC:pr]
-is_a: GO:0098795 ! mRNA cleavage involved in gene silencing
-relationship: part_of GO:0035195 ! gene silencing by miRNA
+synonym: "mRNA cleavage involved in gene silencing by miRNA" EXACT []
+synonym: "mRNA destabilization-mediated gene silencing by miRNA" EXACT []
+is_a: GO:0035195 ! gene silencing by miRNA
+is_a: GO:0098795 ! mRNA destabilization-mediated gene silencing
[Term]
id: GO:0035280
@@ -207149,25 +206845,10 @@ is_a: GO:0045172 ! germline ring canal
id: GO:0035325
name: Toll-like receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Toll-like protein, a pattern recognition receptor that binds pattern motifs from a variety of microbial sources to initiate an innate immune response." [PMID:19076341]
+def: "Binding to a Toll-like protein, a pattern recognition receptor that binds pattern motifs from a variety of microbial sources to initiate an innate immune response." [PMID:19076341]
synonym: "TLR binding" EXACT []
is_a: GO:0005102 ! signaling receptor binding
-[Term]
-id: GO:0035327
-name: transcriptionally active chromatin
-namespace: cellular_component
-def: "The ordered and organized complex of DNA and protein that forms regions of the chromosome that are being actively transcribed." [GOC:sart, PMID:17965872]
-is_a: GO:0000785 ! chromatin
-
-[Term]
-id: GO:0035328
-name: transcriptionally silent chromatin
-namespace: cellular_component
-def: "The ordered and organized complex of DNA and protein that forms regions of the chromosome that are not being actively transcribed." [GOC:sart, PMID:17965872]
-synonym: "transcriptionally inactive chromatin" EXACT []
-is_a: GO:0000785 ! chromatin
-
[Term]
id: GO:0035329
name: hippo signaling
@@ -207563,7 +207244,7 @@ relationship: positively_regulates GO:0035364 ! thymine transport
id: GO:0035368
name: selenocysteine insertion sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the selenocysteine insertion sequence (SECIS), a regulatory sequence within mRNA which directs incorporation of a selenocysteine at a stop codon (UGA) during translation." [GOC:imk, PMID:10760958]
+def: "Binding to a selenocysteine insertion sequence (SECIS), a regulatory sequence within mRNA which directs incorporation of a selenocysteine at a stop codon (UGA) during translation." [GOC:imk, PMID:10760958]
synonym: "SECIS binding" EXACT []
is_a: GO:0003729 ! mRNA binding
@@ -207604,7 +207285,7 @@ is_a: GO:0072698 ! protein localization to microtubule cytoskeleton
id: GO:0035373
name: chondroitin sulfate proteoglycan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chondroitin sulfate proteoglycan, any proteoglycan containing chondroitin sulfate as the glycosaminoglycan carbohydrate unit." [GOC:kmv, ISBN:0198506732]
+def: "Binding to a chondroitin sulfate proteoglycan, any proteoglycan containing chondroitin sulfate as the glycosaminoglycan carbohydrate unit." [GOC:kmv, ISBN:0198506732]
is_a: GO:0005539 ! glycosaminoglycan binding
is_a: GO:0043394 ! proteoglycan binding
is_a: GO:1901681 ! sulfur compound binding
@@ -207613,7 +207294,7 @@ is_a: GO:1901681 ! sulfur compound binding
id: GO:0035374
name: chondroitin sulfate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chondroitin sulfate, a glycosaminoglycan made up of two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc)." [GOC:kmv, ISBN:0198506732]
+def: "Binding to chondroitin sulfate, a glycosaminoglycan made up of two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc)." [GOC:kmv, ISBN:0198506732]
is_a: GO:0005539 ! glycosaminoglycan binding
is_a: GO:1901681 ! sulfur compound binding
@@ -207621,7 +207302,7 @@ is_a: GO:1901681 ! sulfur compound binding
id: GO:0035375
name: zymogen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a zymogen, an enzymatically inactive precursor of an enzyme that is often convertible to an active enzyme by proteolysis." [ISBN:0198506732]
+def: "Binding to a zymogen, an enzymatically inactive precursor of an enzyme that is often convertible to an active enzyme by proteolysis." [ISBN:0198506732]
synonym: "proenzyme binding" NARROW [ISBN:0198506732]
is_a: GO:0019899 ! enzyme binding
@@ -208128,7 +207809,6 @@ namespace: biological_process
def: "The process in which triose phosphate (glyceraldehyde 3-phosphate) is transported across a membrane. Glyceraldehyde 3-phosphate is any organic three carbon compound phosphate ester." [GOC:bf, ISBN:0198506732]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "triose phosphate membrane transport" EXACT []
-synonym: "triose phosphate transmembrane transport" EXACT []
is_a: GO:0015711 ! organic anion transport
is_a: GO:0015717 ! triose phosphate transport
is_a: GO:0098656 ! anion transmembrane transport
@@ -208153,7 +207833,7 @@ relationship: part_of GO:0070972 ! protein localization to endoplasmic reticulum
id: GO:0035438
name: cyclic-di-GMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cyclic-di-GMP, cyclic dimeric guanosine monophosphate." [GOC:bf]
+def: "Binding to cyclic-di-GMP, cyclic dimeric guanosine monophosphate." [GOC:bf]
synonym: "3',5'-cyclic di-GMP binding" EXACT []
synonym: "c-di-GMP binding" EXACT []
synonym: "cyclic dinucleotide di-GMP binding" EXACT []
@@ -208496,7 +208176,7 @@ is_a: GO:0016500 ! protein-hormone receptor activity
id: GO:0035473
name: lipase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any lipase." [GOC:BHF]
+def: "Binding to a lipase." [GOC:BHF]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -208537,7 +208217,7 @@ relationship: regulates GO:0035475 ! angioblast cell migration involved in selec
id: GO:0035478
name: chylomicron binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chylomicron, a large lipoprotein particle (diameter 75-1200 nm) composed of a central core of triglycerides and cholesterol surrounded by a protein-phospholipid coating. The proteins include one molecule of apolipoprotein B-48 and may include a variety of apolipoproteins, including APOAs, APOCs and APOE." [GOC:BHF, http://www.britannica.com/EBchecked/topic/117461/chylomicron]
+def: "Binding to a chylomicron, a large lipoprotein particle (diameter 75-1200 nm) composed of a central core of triglycerides and cholesterol surrounded by a protein-phospholipid coating. The proteins include one molecule of apolipoprotein B-48 and may include a variety of apolipoproteins, including APOAs, APOCs and APOE." [GOC:BHF, PMID:17403372]
is_a: GO:0071813 ! lipoprotein particle binding
[Term]
@@ -208584,7 +208264,7 @@ is_a: GO:0035482 ! gastric motility
id: GO:0035484
name: adenine/adenine mispair binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing an A/A mispair." [GOC:bf, GOC:jh]
+def: "Binding to a double-stranded DNA region containing an A/A mispair." [GOC:bf, GOC:jh]
synonym: "A/A mispair binding" EXACT [GOC:jh]
is_a: GO:0030983 ! mismatched DNA binding
@@ -208592,7 +208272,7 @@ is_a: GO:0030983 ! mismatched DNA binding
id: GO:0035485
name: adenine/guanine mispair binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing an A/G mispair." [GOC:bf, GOC:jh]
+def: "Binding to a double-stranded DNA region containing an A/G mispair." [GOC:bf, GOC:jh]
synonym: "A/G mispair binding" EXACT [GOC:jh]
synonym: "G/A mispair binding" RELATED [GOC:bf]
synonym: "guanine-adenine mispair binding" EXACT [GOC:bf]
@@ -208602,7 +208282,7 @@ is_a: GO:0030983 ! mismatched DNA binding
id: GO:0035486
name: cytosine/cytosine mispair binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a C/C mispair." [GOC:bf, GOC:jh]
+def: "Binding to a double-stranded DNA region containing a C/C mispair." [GOC:bf, GOC:jh]
synonym: "C/C mispair binding" EXACT [GOC:jh]
is_a: GO:0030983 ! mismatched DNA binding
@@ -208610,7 +208290,7 @@ is_a: GO:0030983 ! mismatched DNA binding
id: GO:0035487
name: thymine/thymine mispair binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a T/T mispair." [GOC:bf, GOC:jh]
+def: "Binding to a double-stranded DNA region containing a T/T mispair." [GOC:bf, GOC:jh]
synonym: "T/T mispair binding" EXACT []
is_a: GO:0030983 ! mismatched DNA binding
@@ -208618,7 +208298,7 @@ is_a: GO:0030983 ! mismatched DNA binding
id: GO:0035488
name: cytosine/thymine mispair binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a C/T mispair." [GOC:bf, GOC:jh]
+def: "Binding to a double-stranded DNA region containing a C/T mispair." [GOC:bf, GOC:jh]
synonym: "C/T mispair binding" EXACT [GOC:jh]
synonym: "T/C mispair binding" EXACT [GOC:bf]
synonym: "thymine/cytosine mispair binding" EXACT [GOC:bf]
@@ -208628,7 +208308,7 @@ is_a: GO:0030983 ! mismatched DNA binding
id: GO:0035489
name: guanine/guanine mispair binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA containing a G/G mispair." [GOC:bf, GOC:jh]
+def: "Binding to a double-stranded DNA region containing a G/G mispair." [GOC:bf, GOC:jh]
synonym: "G/G mispair binding" EXACT [GOC:jh]
is_a: GO:0030983 ! mismatched DNA binding
@@ -208665,7 +208345,7 @@ id: GO:0035493
name: SNARE complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a SNARE complex, a protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers." [GOC:rb, PMID:10872468]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0006906 ! vesicle fusion
[Term]
@@ -208673,7 +208353,7 @@ id: GO:0035494
name: SNARE complex disassembly
namespace: biological_process
def: "The disaggregation of the SNARE protein complex into its constituent components. The SNARE complex is a protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers." [GOC:rb, PMID:11697877]
-is_a: GO:0043624 ! cellular protein complex disassembly
+is_a: GO:0032984 ! protein-containing complex disassembly
relationship: part_of GO:0016192 ! vesicle-mediated transport
[Term]
@@ -208697,8 +208377,7 @@ is_a: GO:0035250 ! UDP-galactosyltransferase activity
id: GO:0035497
name: cAMP response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the cyclic AMP response element (CRE), a short palindrome-containing sequence found in the promoters of genes whose expression is regulated in response to cyclic AMP." [PMID:2875459, PMID:2900470]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to a cyclic AMP response element (CRE), a short palindrome-containing sequence found in the promoters of genes whose expression is regulated in response to cyclic AMP." [PMID:2875459, PMID:2900470]
synonym: "cAMP-responsive element binding" EXACT [PMID:2875459]
synonym: "CRE binding" EXACT [PMID:2900470]
synonym: "cyclic AMP response element binding" EXACT [PMID:2900470]
@@ -208732,7 +208411,7 @@ is_a: GO:0046394 ! carboxylic acid biosynthetic process
id: GO:0035500
name: MH2 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the MH2 (MAD homology 2) domain of a protein. The MH2 domain is found at the carboxy-terminus of MAD related proteins such as Smads. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers." [GOC:curators]
+def: "Binding to a MH2 (MAD homology 2) protein domain. The MH2 domain is found at the carboxy-terminus of MAD related proteins such as Smads. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers." [GOC:curators]
synonym: "MAD homology 2 domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -208740,7 +208419,7 @@ is_a: GO:0019904 ! protein domain specific binding
id: GO:0035501
name: MH1 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the MH1 (MAD homology 1) domain of a protein. The MH1 domain is found at the amino terminus of MAD related proteins such as Smads and can mediate DNA binding in some proteins. Smads also use the MH1 domain to interact with some transcription factors." [Pfam:PF03165]
+def: "Binding to a MH1 (MAD homology 1) protein domain. The MH1 domain is found at the amino terminus of MAD related proteins such as Smads and can mediate DNA binding in some proteins. Smads also use the MH1 domain to interact with some transcription factors." [Pfam:PF03165]
synonym: "MAD homology 1 domain binding" EXACT [Pfam:PF03165]
is_a: GO:0019904 ! protein domain specific binding
@@ -208853,7 +208532,7 @@ namespace: molecular_function
def: "Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms." [PMID:12594517, PMID:16482161, PMID:18775698]
synonym: "2-oxoglutarate-dependent RNA demethylase" EXACT [PMID:17991826]
xref: Reactome:R-HSA-8857692 "RNA demethylases demethylate N6-methyladenosine RNA"
-is_a: GO:0016491 ! oxidoreductase activity
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032451 ! demethylase activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
@@ -208861,9 +208540,20 @@ is_a: GO:0140098 ! catalytic activity, acting on RNA
id: GO:0035516
name: oxidative DNA demethylase activity
namespace: molecular_function
-def: "Catalysis of the removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms." [PMID:12594517, PMID:16482161, PMID:18775698]
+alt_id: GO:0103051
+alt_id: GO:0103052
+alt_id: GO:0103053
+def: "Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O(2) = a nucleobase within DNA + formaldehyde + succinate + CO(2)." [PMID:12594517, PMID:16482161, PMID:18775698, RHEA:30299]
+synonym: "1-ethyladenine demethylase activity" NARROW []
synonym: "2-oxoglutarate-dependent DNA demethylase" EXACT [PMID:17991826]
-is_a: GO:0016491 ! oxidoreductase activity
+synonym: "N1-methyladenine demethylase activity" NARROW []
+synonym: "N3-methylcytosine demethylase activity" NARROW []
+xref: EC:1.14.11.33
+xref: MetaCyc:RXN0-984
+xref: MetaCyc:RXN0-985
+xref: MetaCyc:RXN0-986
+xref: RHEA:30299
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0035514 ! DNA demethylase activity
[Term]
@@ -209048,8 +208738,7 @@ relationship: positively_regulates GO:0035530 ! chemokine (C-C motif) ligand 6 p
id: GO:0035538
name: carbohydrate response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the carbohydrate response element (ChoRE) found in the promoters of genes whose expression is regulated in response to carbohydrates, such as the triglyceride synthesis genes." [GOC:BHF, PMID:20001964]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to a carbohydrate response element (ChoRE) found in the promoters of genes whose expression is regulated in response to carbohydrates, such as the triglyceride synthesis genes." [GOC:BHF, PMID:20001964]
synonym: "ChoRE binding" EXACT [PMID:20001964]
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
@@ -209367,10 +209056,13 @@ is_a: GO:0070076 ! histone lysine demethylation
[Term]
id: GO:0035575
-name: histone demethylase activity (H4-K20 specific)
+name: histone H4-methyl-lysine-20 demethylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein." [PMID:20622853]
+def: "Catalysis of the removal of the methyl group from a modified lysine residue at position 20 of the histone H4 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:20622853, PMID:26214369, PMID:32209475]
+synonym: "histone demethylase activity (H4-K20 specific)" EXACT []
+synonym: "histone H4K20me demethylase activity" EXACT []
xref: Reactome:R-HSA-2172678 "PHF8 demethylates histone H4K20me1"
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032452 ! histone demethylase activity
[Term]
@@ -209550,7 +209242,7 @@ is_a: GO:0035592 ! establishment of protein localization to extracellular region
id: GO:0035594
name: ganglioside binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ganglioside, a ceramide oligosaccharide carrying in addition to other sugar residues, one or more sialic acid residues." [GOC:yaf]
+def: "Binding to a ganglioside, a ceramide oligosaccharide carrying in addition to other sugar residues, one or more sialic acid residues." [GOC:yaf]
is_a: GO:0043208 ! glycosphingolipid binding
is_a: GO:0097001 ! ceramide binding
@@ -209726,7 +209418,7 @@ is_a: GO:0035608 ! protein deglutamylation
id: GO:0035612
name: AP-2 adaptor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the AP-2 adaptor complex. The AP-2 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of alpha, beta2, mu2 and sigma2 subunits and links clathrin to the membrane surface of a vesicle. In at least humans, the AP-2 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different alpha genes (alphaA and alphaC)." [GOC:BHF, PMID:12221107, PMID:15728179, PMID:21097499]
+def: "Binding to an AP-2 adaptor complex. The AP-2 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of alpha, beta2, mu2 and sigma2 subunits and links clathrin to the membrane surface of a vesicle. In at least humans, the AP-2 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different alpha genes (alphaA and alphaC)." [GOC:BHF, PMID:12221107, PMID:15728179, PMID:21097499]
synonym: "AP-2 clathrin adaptor complex binding" RELATED [GOC:bf]
is_a: GO:0044877 ! protein-containing complex binding
@@ -209734,7 +209426,7 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0035613
name: RNA stem-loop binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a stem-loop in an RNA molecule. An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop." [GOC:sart, PMID:16568238, PMID:20455544]
+def: "Binding to a stem-loop in an RNA molecule. An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop." [GOC:sart, PMID:16568238, PMID:20455544]
synonym: "RNA hairpin binding" EXACT [PMID:16568238]
synonym: "RNA hairpin loop binding" EXACT [PMID:16568238]
is_a: GO:0003723 ! RNA binding
@@ -209743,7 +209435,7 @@ is_a: GO:0003723 ! RNA binding
id: GO:0035614
name: snRNA stem-loop binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a stem-loop in a small nuclear RNA (snRNA). An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop." [GOC:sart, PMID:16568238, PMID:20455544]
+def: "Binding to a stem-loop in a small nuclear RNA (snRNA). An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop." [GOC:sart, PMID:16568238, PMID:20455544]
synonym: "small nuclear RNA stem-loop binding" EXACT []
synonym: "snRNA hairpin binding" EXACT [PMID:16568238]
synonym: "snRNA hairpin loop binding" EXACT [PMID:16568238]
@@ -209956,7 +209648,7 @@ is_a: GO:0032501 ! multicellular organismal process
id: GO:0035639
name: purine ribonucleoside triphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:BHF, GOC:ebc, ISBN:0198506732]
+def: "Binding to a purine ribonucleoside triphosphate, a compound consisting of a purine base linked to a ribose sugar esterified with triphosphate on the sugar." [GOC:BHF, GOC:ebc, ISBN:0198506732]
synonym: "purine NTP binding" BROAD [GOC:ebc]
is_a: GO:0043168 ! anion binding
is_a: GO:1901265 ! nucleoside phosphate binding
@@ -209996,7 +209688,6 @@ name: L-DOPA receptor activity
namespace: molecular_function
def: "Combining with L-DOPA to initiate a change in cell activity. L-DOPA is the modified amino acid (2S)-2-amino-3-(3,4-dihydroxyphenyl) propanoic acid, and is the precursor to dopamine, norepinephrine (noradrenaline) and epinephrine." [PMID:18828673, Wikipedia:L-DOPA]
synonym: "L-beta-(3,4-Dihydroxyphenyl)alanine receptor activity" EXACT []
-synonym: "L-dopa receptor activity" EXACT []
is_a: GO:0008188 ! neuropeptide receptor activity
[Term]
@@ -210051,14 +209742,14 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0035650
name: AP-1 adaptor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the AP-1 adaptor complex. The AP-1 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of beta1, gamma, mu1 and sigma1 subunits and links clathrin to the membrane surface of a vesicle. In at least humans, the AP-1 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (gamma1 and gamma2, mu1A and mu1B, and sigma1A, sigma1B and sigma1C)." [PMID:21097499]
+def: "Binding to an AP-1 adaptor complex. The AP-1 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of beta1, gamma, mu1 and sigma1 subunits and links clathrin to the membrane surface of a vesicle. In at least humans, the AP-1 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (gamma1 and gamma2, mu1A and mu1B, and sigma1A, sigma1B and sigma1C)." [PMID:21097499]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0035651
name: AP-3 adaptor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the AP-3 adaptor complex. The AP-3 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of beta3, delta, mu3 and sigma3 subunits and is found associated with endosomal membranes. In at least humans, the AP-3 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (beta3A and beta3B, mu3A and mu3B, and sigma3A and sigma3B)." [PMID:21097499]
+def: "Binding to an AP-3 adaptor complex. The AP-3 adaptor complex is a heterotetrameric AP-type membrane coat adaptor complex that consists of beta3, delta, mu3 and sigma3 subunits and is found associated with endosomal membranes. In at least humans, the AP-3 complex can be heterogeneric due to the existence of multiple subunit isoforms encoded by different genes (beta3A and beta3B, mu3A and mu3B, and sigma3A and sigma3B)." [PMID:21097499]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -210156,7 +209847,7 @@ is_a: GO:0034134 ! toll-like receptor 2 signaling pathway
id: GO:0035662
name: Toll-like receptor 4 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Toll-like 4 protein, a pattern recognition receptor that binds bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:18304834]
+def: "Binding to a Toll-like 4 protein, a pattern recognition receptor that binds bacterial lipopolysaccharide (LPS) to initiate an innate immune response." [GOC:BHF, PMID:18304834]
synonym: "TLR4 binding" EXACT [GOC:bf]
is_a: GO:0035325 ! Toll-like receptor binding
@@ -210164,7 +209855,7 @@ is_a: GO:0035325 ! Toll-like receptor binding
id: GO:0035663
name: Toll-like receptor 2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Toll-like 2 protein, a pattern recognition receptor that binds microbial pattern motifs to initiate an innate immune response." [GOC:BHF]
+def: "Binding to a Toll-like 2 protein, a pattern recognition receptor that binds microbial pattern motifs to initiate an innate immune response." [GOC:BHF]
synonym: "TLR2 binding" EXACT [GOC:bf]
is_a: GO:0035325 ! Toll-like receptor binding
@@ -210407,15 +210098,6 @@ synonym: "chemokine (C-C motif) ligand 5 signalling pathway" EXACT [GOC:mah]
synonym: "RANTES-mediated signaling pathway" EXACT [PMID:19122644]
is_a: GO:0070098 ! chemokine-mediated signaling pathway
-[Term]
-id: GO:0035690
-name: cellular response to drug
-namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease." [GOC:sl]
-subset: goslim_chembl
-is_a: GO:0042493 ! response to drug
-is_a: GO:0070887 ! cellular response to chemical stimulus
-
[Term]
id: GO:0035691
name: macrophage migration inhibitory factor signaling pathway
@@ -210618,7 +210300,7 @@ is_a: GO:1901701 ! cellular response to oxygen-containing compound
id: GO:0035715
name: chemokine (C-C motif) ligand 2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chemokine (C-C motif) ligand 2." [GOC:BHF]
+def: "Binding to chemokine (C-C motif) ligand 2." [GOC:BHF]
synonym: "CCL2 binding" EXACT [GOC:ebc]
is_a: GO:0019957 ! C-C chemokine binding
@@ -210626,7 +210308,7 @@ is_a: GO:0019957 ! C-C chemokine binding
id: GO:0035716
name: chemokine (C-C motif) ligand 12 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chemokine (C-C motif) ligand 12." [GOC:BHF]
+def: "Binding to chemokine (C-C motif) ligand 12." [GOC:BHF]
synonym: "CCL12 binding" EXACT [GOC:ebc]
is_a: GO:0019957 ! C-C chemokine binding
@@ -210634,7 +210316,7 @@ is_a: GO:0019957 ! C-C chemokine binding
id: GO:0035717
name: chemokine (C-C motif) ligand 7 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chemokine (C-C motif) ligand 7." [GOC:BHF]
+def: "Binding to chemokine (C-C motif) ligand 7." [GOC:BHF]
synonym: "CCL7 binding" EXACT [GOC:ebc]
is_a: GO:0019957 ! C-C chemokine binding
@@ -210642,7 +210324,7 @@ is_a: GO:0019957 ! C-C chemokine binding
id: GO:0035718
name: macrophage migration inhibitory factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the cytokine, macrophage migration inhibitory factor." [GOC:BHF, PMID:19601712]
+def: "Binding to the cytokine, macrophage migration inhibitory factor." [GOC:BHF, PMID:19601712]
synonym: "MIF binding" EXACT [PMID:19601712]
is_a: GO:0019955 ! cytokine binding
@@ -210726,7 +210408,7 @@ is_a: GO:0008283 ! cell population proliferation
id: GO:0035727
name: lysophosphatidic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lysophosphatidic acid (LPA), a phospholipid derivative that acts as a potent mitogen due to its activation of high-affinity G protein-coupled receptors." [GOC:curators]
+def: "Binding to lysophosphatidic acid (LPA), a phospholipid derivative that acts as a potent mitogen due to its activation of high-affinity G protein-coupled receptors." [GOC:curators]
synonym: "LPA binding" EXACT []
is_a: GO:0005543 ! phospholipid binding
is_a: GO:0043168 ! anion binding
@@ -210754,7 +210436,7 @@ is_a: GO:0071363 ! cellular response to growth factor stimulus
id: GO:0035730
name: S-nitrosoglutathione binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with S-nitrosoglutathione, a nitrosothiol considered to be a natural nitric oxide (NO) donor involved in S-nitrosylation, and in the storage and transport of nitric oxide in biological systems." [GOC:BHF]
+def: "Binding to S-nitrosoglutathione, a nitrosothiol considered to be a natural nitric oxide (NO) donor involved in S-nitrosylation, and in the storage and transport of nitric oxide in biological systems." [GOC:BHF]
synonym: "GSNO binding" EXACT []
is_a: GO:1901681 ! sulfur compound binding
@@ -210762,7 +210444,7 @@ is_a: GO:1901681 ! sulfur compound binding
id: GO:0035731
name: dinitrosyl-iron complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a dinitrosyl-iron complex. Nitric oxide (NO) is stored as dinitrosyl-iron complexes, which form spontaneously from Glutathione (GSH), S-nitrosoglutathione, and trace amounts of ferrous ions, or by reaction of iron-sulfur centers with NO." [GOC:BHF, PMID:10534443]
+def: "Binding to a dinitrosyl-iron complex. Nitric oxide (NO) is stored as dinitrosyl-iron complexes, which form spontaneously from Glutathione (GSH), S-nitrosoglutathione, and trace amounts of ferrous ions, or by reaction of iron-sulfur centers with NO." [GOC:BHF, PMID:10534443]
synonym: "dinitrosyl-diglutathionyl-iron complex binding" EXACT [PMID:12871931]
synonym: "DNDGIC binding" EXACT [PMID:12871931]
synonym: "DNIC binding" EXACT [PMID:10534443]
@@ -210813,10 +210495,11 @@ is_a: GO:0044419 ! biological process involved in interspecies interaction betwe
[Term]
id: GO:0035738
-name: envenomation resulting in modulation of process in other organism
+name: envenomation resulting in modulation of process in another organism
namespace: biological_process
def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the manifestation of some change or damage to the bitten organism." [GOC:pamgo_curators]
synonym: "envenomation resulting in modification of morphology or physiology of other organism" EXACT []
+synonym: "envenomation resulting in modulation of process in other organism" EXACT []
is_a: GO:0035737 ! injection of substance in to other organism
[Term]
@@ -210974,7 +210657,7 @@ is_a: GO:0044001 ! migration in host
id: GO:0035757
name: chemokine (C-C motif) ligand 19 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chemokine (C-C motif) ligand 19." [GOC:BHF]
+def: "Binding to chemokine (C-C motif) ligand 19." [GOC:BHF]
synonym: "CCL19 binding" EXACT [GOC:bf]
is_a: GO:0019957 ! C-C chemokine binding
@@ -210982,7 +210665,7 @@ is_a: GO:0019957 ! C-C chemokine binding
id: GO:0035758
name: chemokine (C-C motif) ligand 21 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chemokine (C-C motif) ligand 21." [GOC:BHF]
+def: "Binding to chemokine (C-C motif) ligand 21." [GOC:BHF]
synonym: "CCL21 binding" EXACT [GOC:bf]
is_a: GO:0019957 ! C-C chemokine binding
@@ -211415,27 +211098,29 @@ is_a: GO:0031012 ! extracellular matrix
[Term]
id: GO:0035806
-name: modulation of blood coagulation in other organism
+name: modulation of blood coagulation in another organism
namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of blood coagulation in another organism. Blood coagulation is the sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot." [GOC:bf, GOC:fj]
synonym: "modulation by organism of blood clotting in other organism" EXACT [GOC:bf]
synonym: "modulation by organism of blood coagulation in other organism" EXACT [GOC:bf]
+synonym: "modulation of blood coagulation in other organism" EXACT [GOC:bf]
synonym: "regulation by organism of blood clotting in other organism" EXACT [GOC:bf]
synonym: "regulation of blood clotting in other organism" EXACT [GOC:bf]
synonym: "regulation of blood coagulation in other organism" EXACT [GOC:bf]
is_a: GO:0030193 ! regulation of blood coagulation
-is_a: GO:0035821 ! modulation of process of other organism
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0035807
-name: positive regulation of blood coagulation in other organism
+name: positive regulation of blood coagulation in another organism
namespace: biological_process
def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of blood coagulation in another organism. Blood coagulation is the sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot." [GOC:bf, GOC:fj, PMID:12362232]
synonym: "positive regulation by organism of blood clotting in other organism" EXACT [GOC:bf]
synonym: "positive regulation by organism of blood coagulation in other organism" EXACT [GOC:bf]
synonym: "positive regulation of blood clotting in other organism" EXACT [GOC:bf]
+synonym: "positive regulation of blood coagulation in other organism" EXACT []
is_a: GO:0030194 ! positive regulation of blood coagulation
-is_a: GO:0035806 ! modulation of blood coagulation in other organism
+is_a: GO:0035806 ! modulation of blood coagulation in another organism
[Term]
id: GO:0035808
@@ -211479,9 +211164,8 @@ is_a: GO:0035809 ! regulation of urine volume
id: GO:0035812
name: renal sodium excretion
namespace: biological_process
-def: "The elimination by an organism of sodium in the urine." [GOC:mtg_25march11, GOC:yaf]
-is_a: GO:0003014 ! renal system process
-is_a: GO:0007588 ! excretion
+def: "The elimination of sodium ions from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine." [GOC:mtg_25march11, GOC:yaf, PMID:25287933]
+is_a: GO:0097254 ! renal tubular secretion
relationship: part_of GO:0055078 ! sodium ion homeostasis
[Term]
@@ -211561,10 +211245,11 @@ is_a: GO:0035814 ! negative regulation of renal sodium excretion
[Term]
id: GO:0035821
-name: modulation of process of other organism
+name: modulation of process of another organism
namespace: biological_process
def: "The process in which an organism effects a change in the structure or processes of another organism." [GOC:bf]
synonym: "modification of morphology or physiology of other organism" EXACT []
+synonym: "modulation of process of other organism" EXACT []
synonym: "regulation of morphology of other organism" NARROW [GOC:bf]
synonym: "regulation of morphology or physiology of other organism" RELATED [GOC:bf]
synonym: "regulation of physiological process of other organism" NARROW [GOC:bf]
@@ -211852,7 +211537,7 @@ is_a: GO:0061005 ! cell differentiation involved in kidney development
id: GO:0035851
name: Krueppel-associated box domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Krueppel-associated box (KRAB) domain of a protein. The approximately 75 amino acid KRAB domain is enriched in charged amino acids, and is found in the N-terminal regions of many zinc finger-containing transcription factors." [InterPro:IPR001909]
+def: "Binding to a Krueppel-associated box (KRAB) domain of a protein. The approximately 75 amino acid KRAB domain is enriched in charged amino acids, and is found in the N-terminal regions of many zinc finger-containing transcription factors." [InterPro:IPR001909]
synonym: "KRAB domain binding" EXACT [InterPro:IPR001909]
synonym: "Krueppel-associated box binding" EXACT [InterPro:IPR001909]
is_a: GO:0019904 ! protein domain specific binding
@@ -211880,7 +211565,7 @@ synonym: "chromosome passenger complex localization to central spindle" EXACT [P
synonym: "chromosome passenger complex localization to spindle equator" EXACT [GOC:bf]
synonym: "CPC complex localization to spindle midzone" EXACT [GOC:bf]
synonym: "CPC localization to spindle midzone" EXACT [GOC:bf]
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
is_a: GO:0044380 ! protein localization to cytoskeleton
[Term]
@@ -211924,7 +211609,8 @@ relationship: part_of GO:0035854 ! eosinophil fate commitment
id: GO:0035859
name: Seh1-associated complex
namespace: cellular_component
-def: "A protein complex that associates dynamically with the vacuolar membrane, and is proposed to have a role in membrane-associated trafficking or regulatory processes. In S. cerevisiae the complex contains Seh1p, Sec13p, Npr2p, Npr3p, Iml1p, Mtc5p, Rtc1p, and Sea4p." [GOC:jh, PMID:21454883, PMID:23974112]
+def: "A GTPase-activating protein (GAP) complex that regulates TORC1 signaling by interacting with the Rag GTPase. In S. cerevisiae the complex contains Seh1p, Sec13p, Npr2p, Npr3p, Iml1p, Mtc5p, Rtc1p, and Sea4p." [GOC:jh, PMID:21454883, PMID:23974112]
+comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
synonym: "GATOR complex" EXACT [GOC:rb, PMID:23723238]
synonym: "SEA complex" EXACT [GOC:jh, PMID:21454883]
is_a: GO:0032991 ! protein-containing complex
@@ -212022,7 +211708,6 @@ name: alphav-beta3 integrin-HMGB1 complex
namespace: cellular_component
def: "A protein complex that consists of an alphav-beta3 integrin complex bound to high mobility group box 1 protein." [GOC:BHF, GOC:ebc, PMID:20826760]
synonym: "alphav-beta3 integrin-high mobility group box 1 complex" EXACT [GOC:bf]
-synonym: "alphaV-beta3 integrin-HMGB1 complex" EXACT [GOC:ebc]
is_a: GO:0098797 ! plasma membrane protein complex
[Term]
@@ -212119,7 +211804,7 @@ relationship: part_of GO:0051760 ! meiotic sister chromatid cohesion, arms
id: GO:0035877
name: death effector domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DED domain (death effector domain) of a protein, a homotypic protein interaction module composed of a bundle of six alpha-helices that is related in structure to the death domain (DD)." [GOC:ecd, InterPro:IPR001875]
+def: "Binding to a DED domain (death effector domain) of a protein, a homotypic protein interaction module composed of a bundle of six alpha-helices that is related in structure to the death domain (DD)." [GOC:ecd, InterPro:IPR001875]
comment: For binding to the death domain, consider instead the term 'death domain binding ; GO:0070513'.
synonym: "DED binding" EXACT [InterPro:IPR001875]
is_a: GO:0019904 ! protein domain specific binding
@@ -212199,7 +211884,6 @@ id: GO:0035886
name: vascular associated smooth muscle cell differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a vascular smooth muscle cell." [GOC:sl, PMID:16151017, PMID:18267954]
-synonym: "vascular associated smooth muscle cell differentiation" EXACT [CL:0000359]
synonym: "vascular smooth muscle cell differentiation" EXACT []
synonym: "VSMC differentiation" EXACT [PMID:16151017]
is_a: GO:0051145 ! smooth muscle cell differentiation
@@ -212249,65 +211933,70 @@ is_a: GO:0035890 ! exit from host
[Term]
id: GO:0035892
-name: modulation of platelet aggregation in other organism
+name: modulation of platelet aggregation in another organism
namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of platelet aggregation in another organism. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules." [GOC:bf, GOC:fj, PMID:15922770]
synonym: "modulation by organism of platelet aggregation in other organism" EXACT [GOC:bf]
+synonym: "modulation of platelet aggregation in other organism" EXACT []
synonym: "regulation of platelet aggregation in other organism" RELATED [GOC:bf]
-is_a: GO:0035806 ! modulation of blood coagulation in other organism
-is_a: GO:0044364 ! disruption of cells of other organism
+is_a: GO:0035806 ! modulation of blood coagulation in another organism
+is_a: GO:0044364 ! disruption of cells of another organism
is_a: GO:0090330 ! regulation of platelet aggregation
[Term]
id: GO:0035893
-name: negative regulation of platelet aggregation in other organism
+name: negative regulation of platelet aggregation in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of platelet aggregation in a second organism." [GOC:bf, GOC:fj, PMID:15922770]
synonym: "down-regulation of platelet aggregation in other organism" EXACT [GOC:bf]
synonym: "downregulation of platelet aggregation in other organism" EXACT [GOC:bf]
synonym: "inhibition of platelet aggregation in other organism" EXACT [GOC:bf]
+synonym: "negative regulation of platelet aggregation in other organism" EXACT []
synonym: "suppression of platelet aggregation in other organism" EXACT [GOC:bf]
-is_a: GO:0035892 ! modulation of platelet aggregation in other organism
-is_a: GO:0035899 ! negative regulation of blood coagulation in other organism
+is_a: GO:0035892 ! modulation of platelet aggregation in another organism
+is_a: GO:0035899 ! negative regulation of blood coagulation in another organism
is_a: GO:0090331 ! negative regulation of platelet aggregation
[Term]
id: GO:0035894
-name: positive regulation of platelet aggregation in other organism
+name: positive regulation of platelet aggregation in another organism
namespace: biological_process
def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of platelet aggregation in another organism." [GOC:bf, GOC:fj, PMID:11453648, PMID:18804547]
+synonym: "positive regulation of platelet aggregation in other organism" EXACT []
synonym: "up-regulation of platelet aggregation in other organism" RELATED [GOC:bf]
synonym: "upregulation of platelet aggregation in other organism" EXACT [GOC:bf]
-is_a: GO:0035807 ! positive regulation of blood coagulation in other organism
-is_a: GO:0035892 ! modulation of platelet aggregation in other organism
+is_a: GO:0035807 ! positive regulation of blood coagulation in another organism
+is_a: GO:0035892 ! modulation of platelet aggregation in another organism
is_a: GO:1901731 ! positive regulation of platelet aggregation
[Term]
id: GO:0035895
-name: modulation of mast cell degranulation in other organism
+name: modulation of mast cell degranulation in another organism
namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of blood mast cell degranulation in another organism. Mast cell degranulation is the regulated exocytosis of secretory granules containing preformed mediators such as histamine, serotonin, and neutral proteases by a mast cell." [GOC:bf, GOC:fj, PMID:21549739]
+synonym: "modulation of mast cell degranulation in other organism" EXACT []
synonym: "regulation of mast cell degranulation in other organism" EXACT [GOC:bf]
-is_a: GO:0035821 ! modulation of process of other organism
+is_a: GO:0035821 ! modulation of process of another organism
is_a: GO:0043304 ! regulation of mast cell degranulation
[Term]
id: GO:0035896
-name: positive regulation of mast cell degranulation in other organism
+name: positive regulation of mast cell degranulation in another organism
namespace: biological_process
def: "Any process in which an organism increases the frequency, rate or extent of blood mast cell degranulation in another organism." [GOC:bf, GOC:fj]
+synonym: "positive regulation of mast cell degranulation in other organism" EXACT []
synonym: "up-regulation of mast cell degranulation in other organism" RELATED [GOC:bf]
synonym: "upregulation of mast cell degranulation in other organism" EXACT [GOC:bf]
-is_a: GO:0035895 ! modulation of mast cell degranulation in other organism
+is_a: GO:0035895 ! modulation of mast cell degranulation in another organism
is_a: GO:0043306 ! positive regulation of mast cell degranulation
[Term]
id: GO:0035897
-name: proteolysis in other organism
+name: obsolete proteolysis in other organism
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the hydrolysis of proteins in another organism by cleavage of their peptide bonds." [GOC:bf, GOC:fj, PMID:15922779]
-is_a: GO:0006508 ! proteolysis
-is_a: GO:0044033 ! multi-organism metabolic process
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the hydrolysis of proteins in another organism by cleavage of their peptide bonds." [GOC:bf, GOC:fj, PMID:15922779]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0035898
@@ -212321,16 +212010,17 @@ is_a: GO:0060986 ! endocrine hormone secretion
[Term]
id: GO:0035899
-name: negative regulation of blood coagulation in other organism
+name: negative regulation of blood coagulation in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents or reduces the frequency, rate or extent of blood coagulation in another organism. Blood coagulation is the sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot." [GOC:fj]
synonym: "down-regulation of blood coagulation in other organism" EXACT [GOC:bf]
synonym: "downregulation of blood coagulation in other organism" EXACT [GOC:bf]
synonym: "inhibition of blood coagulation in other organism" NARROW [GOC:bf]
synonym: "negative regulation of blood clotting in other organism" EXACT [GOC:bf]
+synonym: "negative regulation of blood coagulation in other organism" EXACT []
synonym: "suppression of blood coagulation in other organism" EXACT [GOC:bf]
is_a: GO:0030195 ! negative regulation of blood coagulation
-is_a: GO:0035806 ! modulation of blood coagulation in other organism
+is_a: GO:0035806 ! modulation of blood coagulation in another organism
[Term]
id: GO:0035900
@@ -212457,37 +212147,38 @@ relationship: part_of GO:0007519 ! skeletal muscle tissue development
[Term]
id: GO:0035915
-name: pore formation in membrane of other organism
+name: pore formation in membrane of another organism
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components by an organism to form a pore complex in a membrane of another organism." [GOC:bf, GOC:fj, PMID:21549739]
-synonym: "pore biosynthesis in other organism" EXACT [GOC:bf]
synonym: "pore complex assembly in other organism" EXACT []
synonym: "pore complex biogenesis in other organism" EXACT [GOC:bf]
+synonym: "pore formation in membrane of other organism" EXACT []
synonym: "pore formation in other organism" EXACT [GOC:bf]
synonym: "pore-forming toxin activity" RELATED [GOC:bf]
-is_a: GO:0051673 ! membrane disruption in other organism
+is_a: GO:0051673 ! membrane disruption in another organism
[Term]
id: GO:0035916
-name: modulation of calcium channel activity in other organism
+name: modulation of calcium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism effects a change in the frequency, rate or extent of the activity of a calcium channel in another organism." [GOC:bf, GOC:fj, PMID:20920515]
-is_a: GO:0044561 ! modulation of ion channel activity in other organism
+synonym: "modulation of calcium channel activity in other organism" EXACT []
+is_a: GO:0044561 ! modulation of ion channel activity in another organism
[Term]
id: GO:0035917
-name: negative regulation of calcium channel activity in other organism
+name: negative regulation of calcium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the activity of a calcium channel in another organism." [GOC:bf, GOC:fj, PMID:20920515]
synonym: "down-regulation of calcium channel activity in other organism" EXACT [GOC:bf]
synonym: "downregulation of calcium channel activity in other organism" EXACT [GOC:bf]
synonym: "inhibition of calcium channel activity in other organism" NARROW [GOC:bf]
-is_a: GO:0035916 ! modulation of calcium channel activity in other organism
-is_a: GO:0052204 ! negative regulation of molecular function in other organism involved in symbiotic interaction
+synonym: "negative regulation of calcium channel activity in other organism" EXACT [GOC:bf]
+is_a: GO:0035916 ! modulation of calcium channel activity in another organism
[Term]
id: GO:0035918
-name: negative regulation of voltage-gated calcium channel activity in other organism
+name: negative regulation of voltage-gated calcium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the activity of a voltage-gated calcium channel in another organism. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded." [GOC:bf, GOC:fj, ISBN:0815340729, PMID:20920515]
synonym: "down-regulation of voltage-gated calcium channel activity in other organism" EXACT [GOC:bf]
@@ -212495,12 +212186,13 @@ synonym: "downregulation of voltage-gated calcium channel activity in other orga
synonym: "inhibition of voltage-gated calcium channel activity in other organism" NARROW [GOC:bf]
synonym: "negative regulation of voltage gated calcium channel activity in other organism" EXACT [GOC:bf]
synonym: "negative regulation of voltage-dependent calcium channel activity in other organism" EXACT [GOC:bf]
+synonym: "negative regulation of voltage-gated calcium channel activity in other organism" EXACT []
synonym: "negative regulation of voltage-sensitive calcium channel activity in other organism" EXACT [GOC:bf]
-is_a: GO:0035917 ! negative regulation of calcium channel activity in other organism
+is_a: GO:0035917 ! negative regulation of calcium channel activity in another organism
[Term]
id: GO:0035919
-name: negative regulation of low voltage-gated calcium channel activity in other organism
+name: negative regulation of low voltage-gated calcium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the activity of a low voltage-gated calcium channel in another organism. A low voltage-gated channel is a channel whose open state is dependent on low voltage across the membrane in which it is embedded." [GOC:bf, GOC:fj, ISBN:0815340729, PMID:20920515]
synonym: "down-regulation of low voltage-gated calcium channel activity in other organism" EXACT [GOC:bf]
@@ -212508,11 +212200,12 @@ synonym: "downregulation of low voltage-gated calcium channel activity in other
synonym: "inhibition of low voltage-gated calcium channel activity in other organism" NARROW [GOC:bf]
synonym: "negative regulation of low voltage gated calcium channel activity in other organism" EXACT [GOC:bf]
synonym: "negative regulation of low voltage-dependent calcium channel activity in other organism" EXACT [GOC:bf]
-is_a: GO:0035918 ! negative regulation of voltage-gated calcium channel activity in other organism
+synonym: "negative regulation of low voltage-gated calcium channel activity in other organism" EXACT []
+is_a: GO:0035918 ! negative regulation of voltage-gated calcium channel activity in another organism
[Term]
id: GO:0035920
-name: negative regulation of high voltage-gated calcium channel activity in other organism
+name: negative regulation of high voltage-gated calcium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the activity of a high voltage-gated calcium channel in another organism. A high voltage-gated channel is a channel whose open state is dependent on high voltage across the membrane in which it is embedded." [GOC:bf, GOC:fj, ISBN:0815340729, PMID:20920515]
synonym: "down-regulation of high voltage-gated calcium channel activity in other organism" EXACT [GOC:bf]
@@ -212520,7 +212213,8 @@ synonym: "downregulation of high voltage-gated calcium channel activity in other
synonym: "inhibition of high voltage-gated calcium channel activity in other organism" NARROW [GOC:bf]
synonym: "negative regulation of high voltage gated calcium channel activity in other organism" EXACT [GOC:bf]
synonym: "negative regulation of high voltage-dependent calcium channel activity in other organism" EXACT [GOC:bf]
-is_a: GO:0035918 ! negative regulation of voltage-gated calcium channel activity in other organism
+synonym: "negative regulation of high voltage-gated calcium channel activity in other organism" EXACT [GOC:bf]
+is_a: GO:0035918 ! negative regulation of voltage-gated calcium channel activity in another organism
[Term]
id: GO:0035921
@@ -212544,7 +212238,7 @@ relationship: part_of GO:0060411 ! cardiac septum morphogenesis
id: GO:0035923
name: flurbiprofen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with flurbiprofen." [GOC:BHF, GOC:rl]
+def: "Binding to flurbiprofen." [GOC:BHF, GOC:rl]
synonym: "2-(2-fluoro-[1,1'-biphenyl-4-yl])propanoic acid binding" EXACT []
is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -212565,7 +212259,7 @@ id: GO:0035925
name: mRNA 3'-UTR AU-rich region binding
namespace: molecular_function
alt_id: GO:0017091
-def: "Interacting selectively and non-covalently with a region containing frequent adenine and uridine bases within the 3' untranslated region of a mRNA molecule or in pre-mRNA intron. The ARE-binding element consensus is UUAUUUAUU. ARE-binding proteins control the stability and/or translation of mRNAs." [GOC:vw, PMID:31511872, PMID:7892223, PMID:8578590]
+def: "Binding to a region containing frequent adenine and uridine bases within the 3' untranslated region of a mRNA molecule or in pre-mRNA intron. The ARE-binding element consensus is UUAUUUAUU. ARE-binding proteins control the stability and/or translation of mRNAs." [GOC:vw, PMID:31511872, PMID:7892223, PMID:8578590]
synonym: "adenylate/uridylate-rich element binding" EXACT []
synonym: "ARE binding" RELATED []
synonym: "AU-rich element binding" RELATED []
@@ -212676,7 +212370,7 @@ is_a: GO:0140353 ! lipid export from cell
id: GO:0035939
name: microsatellite binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a microsatellite, a repeat_region in DNA containing repeat units (2 to 4 base pairs) that is repeated multiple times in tandem." [GOC:yaf, PMID:21290414, SO:0000289]
+def: "Binding to a microsatellite, a repeat_region in DNA containing repeat units (2 to 4 base pairs) that is repeated multiple times in tandem." [GOC:yaf, PMID:21290414, SO:0000289]
synonym: "microsatellite DNA binding" EXACT [GOC:bf]
synonym: "variable number tandem repeat binding" EXACT [PMID:21290414]
synonym: "VNTR binding" EXACT [SO:0000289]
@@ -212684,16 +212378,16 @@ is_a: GO:0003696 ! satellite DNA binding
[Term]
id: GO:0035940
-name: negative regulation of peptidase activity in other organism
+name: obsolete negative regulation of peptidase activity in other organism
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of peptidase activity, the catalysis of the hydrolysis of peptide bonds in a protein, in a second organism." [GOC:klp, PMID:10595640]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of peptidase activity, the catalysis of the hydrolysis of peptide bonds in a protein, in a second organism." [GOC:klp, PMID:10595640]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of peptidase activity in other organism" EXACT [GOC:bf]
synonym: "down-regulation of protease activity in other organism" NARROW [GOC:bf]
synonym: "downregulation of peptidase activity in other organism" EXACT [GOC:bf]
synonym: "inhibition of protease activity in other organism" NARROW [GOC:bf]
synonym: "negative regulation of protease activity in other organism" NARROW [GOC:bf]
-is_a: GO:0010466 ! negative regulation of peptidase activity
-is_a: GO:0044362 ! negative regulation of molecular function in other organism
+is_obsolete: true
[Term]
id: GO:0035941
@@ -213233,13 +212927,15 @@ is_a: GO:0000792 ! heterochromatin
[Term]
id: GO:0035986
-name: senescence-associated heterochromatin focus assembly
+name: obsolete senescence-associated heterochromatin focus assembly
namespace: biological_process
-def: "The assembly of chromatin into senescence-associated heterochromatin foci (SAHF), transcriptionally-silent heterochromatin structures present in senescent cells, containing the condensed chromatin of one chromosome, and enriched for histone modifications. Formation of these chromatin structures is thought to repress expression of proliferation-promoting genes." [GOC:yaf, PMID:15621527, PMID:21248468]
+def: "OBSOLETE. The assembly of chromatin into senescence-associated heterochromatin foci (SAHF), transcriptionally-silent heterochromatin structures present in senescent cells, containing the condensed chromatin of one chromosome, and enriched for histone modifications. Formation of these chromatin structures is thought to repress expression of proliferation-promoting genes." [GOC:yaf, PMID:15621527, PMID:21248468]
+comment: This term was obsoleted because there is no evidence that this is a distinct process; this should be captured as an extension
synonym: "SAHF formation" EXACT [GOC:yaf]
synonym: "senescence-associated heterochromatin foci formation" EXACT [GOC:yaf]
synonym: "senescence-associated heterochromatin focus formation" EXACT []
-is_a: GO:0031507 ! heterochromatin assembly
+is_obsolete: true
+consider: GO:0031507
[Term]
id: GO:0035987
@@ -213281,7 +212977,7 @@ relationship: part_of GO:0035992 ! tendon formation
id: GO:0035991
name: nitric oxide sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of nitric oxide (NO)." [GOC:kmv, PMID:21491957]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of nitric oxide (NO)." [GOC:kmv, PMID:21491957]
synonym: "NO sensor activity" EXACT []
is_a: GO:0070026 ! nitric oxide binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -213385,7 +213081,7 @@ is_a: GO:0042823 ! pyridoxal phosphate biosynthetic process
id: GO:0036002
name: pre-mRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a mRNA molecule." [GOC:bf, GOC:kmv, PMID:21901112, SO:0000120]
+def: "Binding to a pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a mRNA molecule." [GOC:bf, GOC:kmv, PMID:21901112, SO:0000120]
synonym: "protein-coding primary transcript binding" RELATED [SO:0000120]
is_a: GO:0003723 ! RNA binding
@@ -213401,7 +213097,7 @@ is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
id: GO:0036004
name: GAF domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the GAF domain of a protein." [GOC:yaf, InterPro:IPR003018]
+def: "Binding to a GAF protein domain." [GOC:yaf, InterPro:IPR003018]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -213410,7 +213106,6 @@ name: response to macrophage colony-stimulating factor
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a macrophage colony-stimulating factor stimulus." [GOC:yaf, PMID:14687666]
synonym: "response to M-CSF" EXACT [GOC:bf, PMID:14687666]
-synonym: "response to macrophage colony-stimulating factor" EXACT [GOC:bf]
synonym: "response to macrophage colony-stimulating factor stimulus" EXACT [GOC:dos]
is_a: GO:0034097 ! response to cytokine
@@ -213689,7 +213384,7 @@ is_a: GO:0060232 ! delamination
id: GO:0036033
name: mediator complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mediator complex. The mediator complex is a protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins." [GOC:yaf, PMID:18391015]
+def: "Binding to a mediator complex. The mediator complex is a protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins." [GOC:yaf, PMID:18391015]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -213697,7 +213392,7 @@ id: GO:0036034
name: mediator complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a mediator complex. The mediator complex is a protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins." [GOC:yaf, PMID:17641689]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0036035
@@ -213784,7 +213479,7 @@ is_a: GO:1901502 ! ether catabolic process
id: GO:0036041
name: long-chain fatty acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a long-chain fatty acid. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [GOC:pm, PMID:12641450]
+def: "Binding to a long-chain fatty acid. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [GOC:pm, PMID:12641450]
synonym: "long chain fatty acid binding" EXACT [PMID:12641450]
is_a: GO:0005504 ! fatty acid binding
@@ -213792,7 +213487,7 @@ is_a: GO:0005504 ! fatty acid binding
id: GO:0036042
name: long-chain fatty acyl-CoA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a long-chain fatty acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more." [GOC:krc, GOC:pm]
+def: "Binding to a long-chain fatty acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more." [GOC:krc, GOC:pm]
synonym: "long-chain fatty acyl-coenyme A binding" EXACT []
is_a: GO:0000062 ! fatty-acyl-CoA binding
@@ -214260,7 +213955,7 @@ relationship: part_of GO:0007276 ! gamete generation
id: GO:0036094
name: small molecule binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:pm]
+def: "Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule." [GOC:curators, GOC:pde, GOC:pm]
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
subset: goslim_agr
subset: goslim_flybase_ribbon
@@ -214381,7 +214076,7 @@ is_a: GO:1901271 ! lipooligosaccharide biosynthetic process
id: GO:0036105
name: peroxisome membrane class-1 targeting sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a class I peroxisomal membrane targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome membrane in a PEX19-dependent manner." [GOC:pm, PMID:14709540, PMID:17020786]
+def: "Binding to a class I peroxisomal membrane targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome membrane in a PEX19-dependent manner." [GOC:pm, PMID:14709540, PMID:17020786]
comment: Currently identified mPTSs vary greatly in length, and cannot be distinguished by primary structure analysis, suggesting that the peroxisomal sorting information is not contained within a specific amino acid sequence. There do however appear to be two classes of mPTSs: class 1 mPTSs that are bound by PEX19 and imported in a PEX19-dependent manner, and class 2 mPTSs that are not bound by PEX19 and mediate protein import independently of PEX19. The two classes cannot be defined based on their amino acid sequence.
synonym: "class 1 mPTS binding" EXACT [PMID:14709540]
synonym: "PEX19-dependent mPTS binding" RELATED [PMID:14709540]
@@ -214391,7 +214086,7 @@ is_a: GO:0033328 ! peroxisome membrane targeting sequence binding
id: GO:0036106
name: peroxisome membrane class-2 targeting sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a class II peroxisomal membrane targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome membrane in a PEX19-independent manner." [GOC:pm, PMID:14709540, PMID:17020786]
+def: "Binding to a class II peroxisomal membrane targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome membrane in a PEX19-independent manner." [GOC:pm, PMID:14709540, PMID:17020786]
comment: Currently identified mPTSs vary greatly in length, and cannot be distinguished by primary structure analysis, suggesting that the peroxisomal sorting information is not contained within a specific amino acid sequence. There do however appear to be two classes of mPTSs: class 1 mPTSs that are bound by PEX19 and imported in a PEX19-dependent manner, and class 2 mPTSs that are not bound by PEX19 and mediate protein import independently of PEX19. The two classes cannot be defined based on their amino acid sequence.
synonym: "class 2 mPTS binding" EXACT [PMID:14709540]
synonym: "PEX19-independent mPTS binding" RELATED [PMID:14709540]
@@ -214561,7 +214256,7 @@ is_a: GO:0003678 ! DNA helicase activity
id: GO:0036122
name: BMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a member of the bone morphogenetic protein (BMP) family." [GOC:BHF, PMID:9660951]
+def: "Binding to a member of the bone morphogenetic protein (BMP) family." [GOC:BHF, PMID:9660951]
synonym: "bone morphogenetic protein binding" EXACT [GOC:bf]
is_a: GO:0019955 ! cytokine binding
@@ -214605,7 +214300,7 @@ is_a: GO:0097729 ! 9+2 motile cilium
id: GO:0036127
name: 3-sulfino-L-alanine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 3-sulfino-L-alanine (cysteine sulfinate)." [GOC:al, PMID:8346915]
+def: "Binding to 3-sulfino-L-alanine (cysteine sulfinate)." [GOC:al, PMID:8346915]
synonym: "cysteine sulfinate binding" EXACT [GOC:al]
is_a: GO:0016597 ! amino acid binding
is_a: GO:0031406 ! carboxylic acid binding
@@ -214755,7 +214450,7 @@ is_a: GO:0070546 ! L-phenylalanine aminotransferase activity
id: GO:0036143
name: kringle domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a kringle domain. Kringle domains are protein domains that fold into large loops stabilized by 3 disulfide linkages, and are important in protein-protein interactions with blood coagulation factors." [GOC:yaf, Wikipedia:Kringle_domain]
+def: "Binding to a kringle domain. Kringle domains are protein domains that fold into large loops stabilized by 3 disulfide linkages, and are important in protein-protein interactions with blood coagulation factors." [GOC:yaf, Wikipedia:Kringle_domain]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -214893,10 +214588,13 @@ is_a: GO:0030072 ! peptide hormone secretion
[Term]
id: GO:0036162
-name: oxytocin secretion
+name: oxytocin production
namespace: biological_process
-def: "The regulated release of oxytocin, a cyclic nonapeptide hormone with amino acid sequence CYIQNCPLG that also acts as a neurotransmitter in the brain, from a cell. Oxytocin is the principal uterine-contracting and milk-ejecting hormone of the posterior pituitary, and together with the neuropeptide vasopressin, is believed to influence social cognition and behavior." [GOC:cjm, Wikipedia:Oxytocin]
-is_a: GO:0030072 ! peptide hormone secretion
+def: "The appearance of oxytocin, a cyclic nonapeptide hormone with amino acid sequence CYIQNCPLG, due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Oxytocin is the principal uterine-contracting and milk-ejecting hormone of the posterior pituitary, and together with the neuropeptide vasopressin, is believed to influence social cognition and behavior. It also acts as a neurotransmitter in the brain." [GOC:cjm, Wikipedia:Oxytocin]
+comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular oxytocin levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting oxytocin molecules, or increased conversion from precursor molecules.
+synonym: "oxytocin biosynthesis" NARROW []
+synonym: "oxytocin secretion" NARROW []
+is_a: GO:0010467 ! gene expression
[Term]
id: GO:0036163
@@ -214990,7 +214688,7 @@ is_a: GO:0009228 ! thiamine biosynthetic process
id: GO:0036173
name: thiosulfate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the inorganic anion thiosulfate, a sulfur oxide that has formula O3S2." [GOC:db, PMID:2188959]
+def: "Binding to a thiosulfate, a sulfur oxide that has formula O3S2." [GOC:db, PMID:2188959]
is_a: GO:0043168 ! anion binding
is_a: GO:1901681 ! sulfur compound binding
@@ -215352,26 +215050,31 @@ consider: GO:0000122
id: GO:0036209
name: 9beta-pimara-7,15-diene oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 9beta-pimara-7,15-diene + 3 O2 + 3 NADPH + 3 H+ = 9beta-pimara-7,15-dien-19-oate + 3 NADP+ + 4 H2O. This is a three-step reaction: (a) 9beta-pimara-7,15-diene + O2 + NADPH + H+ = 9beta-pimara-7,15-dien-19-ol + NADP+ + H2O, (b) 9beta-pimara-7,15-dien-19-ol + O2 + NADPH + H+ = 9neta-pimara-7,15-dien-19-al + NADP+ + 2 H2O, (c) 9beta-pimara-7,15-dien-19-al + O2 + NADPH + H+ = 9beta-pimara-7,15-dien-19-oate + NADP+ + H2O." [EC:1.14.14.111]
+alt_id: GO:0102609
+def: "Catalysis of the reaction: 9beta-pimara-7,15-diene + 3 O2 + 3 reduced [NADPH-hemoprotein reductase] = 9beta-pimara-7,15-dien-19-oate + 4 H+ + 4 H2O + 3 oxidized [NADPH-hemoprotein reductase]." [RHEA:31951]
+comment: Formerly EC:1.14.13.144.
+synonym: "9-beta-stemod-13(17)-ene oxidase activity" RELATED []
xref: EC:1.14.14.111
xref: KEGG_REACTION:R09865
+xref: MetaCyc:RXN-15437
xref: RHEA:31951
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0036210
-name: protein modification process in other organism
+name: protein modification process in another organism
namespace: biological_process
def: "The covalent alteration performed by one organism of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) in another organism. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl]
synonym: "protein modification in other organism" EXACT [GOC:bf]
-is_a: GO:0036211 ! protein modification process
-is_a: GO:0044033 ! multi-organism metabolic process
+synonym: "protein modification process in other organism" EXACT []
+is_a: GO:0052027 ! modulation by symbiont of host signal transduction pathway
[Term]
id: GO:0036211
name: protein modification process
namespace: biological_process
def: "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." [GOC:bf, GOC:jl]
+subset: goslim_generic
synonym: "protein modification" EXACT [GOC:bf]
is_a: GO:0019538 ! protein metabolic process
is_a: GO:0043412 ! macromolecule modification
@@ -215392,6 +215095,7 @@ name: contractile ring contraction
namespace: biological_process
def: "The process of an actomyosin ring getting smaller in diameter." [GOC:mah, GOC:vw]
comment: This term can be used to annotate contraction of either bacterial or fungal contractile rings.
+synonym: "contractile ring constriction" EXACT [GOC:vw]
is_a: GO:0032506 ! cytokinetic process
relationship: part_of GO:0061640 ! cytoskeleton-dependent cytokinesis
@@ -215668,8 +215372,8 @@ name: cellular response to menadione
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a menadione stimulus. Menadione (also called vitamin K3) is a naphthoquinone having a methyl substituent at the 2-position." [GOC:al, Wikipedia:Menadione]
synonym: "cellular response to vitamin K3" EXACT [GOC:al]
+is_a: GO:0071307 ! cellular response to vitamin K
is_a: GO:0071310 ! cellular response to organic substance
-is_a: GO:1901655 ! cellular response to ketone
[Term]
id: GO:0036246
@@ -215828,20 +215532,6 @@ comment: Note that this term is in the subset of terms that should not be used f
subset: gocheck_do_not_annotate
is_a: GO:0002440 ! production of molecular mediator of immune response
-[Term]
-id: GO:0036263
-name: L-DOPA monooxygenase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: L-DOPA + O2 = ? + H2O. This reaction catalyzes the oxygenation of the dopamine precursor L-DOPA, to the corresponding o-quinone." [GOC:sart, PMID:22120533]
-is_a: GO:0004097 ! catechol oxidase activity
-
-[Term]
-id: GO:0036264
-name: dopamine monooxygenase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: dopamine + O2 = ? + H2O. This reaction catalyzes the oxygenation of dopamine to the corresponding o-quinone." [GOC:sart, PMID:22120533]
-is_a: GO:0004097 ! catechol oxidase activity
-
[Term]
id: GO:0036265
name: RNA (guanine-N7)-methylation
@@ -215890,7 +215580,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a diuretic stimulus. A diuretic is an agent that promotes the excretion of urine through its effects on kidney function." [GOC:hp]
comment: Note that this term is in the subset of terms that should not be used for direct manual annotation of gene products. It was created to be used for cross-referencing by other ontologies. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_manually_annotate
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0036271
@@ -215958,7 +215648,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antidepressant stimulus, a mood-stimulating drug." [GOC:hp]
comment: Note that this term is in the subset of terms that should not be used for direct manual annotation of gene products. It was created to be used for cross-referencing by other ontologies. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_manually_annotate
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0036277
@@ -215967,7 +215657,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an anticonvulsant stimulus, a drug used to prevent seizures or reduce their severity." [GOC:hp]
comment: Note that this term is in the subset of terms that should not be used for direct manual annotation of gene products. It was created to be used for cross-referencing by other ontologies. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_manually_annotate
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0036278
@@ -216018,7 +215708,7 @@ name: SAGA complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a SAGA complex, a SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof." [GOC:mah, PMID:10637607, PMID:22456315]
synonym: "SAGA complex formation" EXACT [GOC:bf]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0036286
@@ -216138,7 +215828,7 @@ is_a: GO:0006281 ! DNA repair
id: GO:0036298
name: recombinational interstrand cross-link repair
namespace: biological_process
-def: "Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA by a mechanism that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC:vw, PMID:20658649]
+def: "Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA by a mechanism that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region." [GOC:vw, PMID:20658649]
synonym: "recombination-dependent interstrand cross-link repair" EXACT [GOC:vw]
is_a: GO:0000725 ! recombinational repair
is_a: GO:0036297 ! interstrand cross-link repair
@@ -216237,14 +215927,16 @@ is_a: GO:0033365 ! protein localization to organelle
[Term]
id: GO:0036310
-name: annealing helicase activity
+name: ATP-dependent DNA/DNA annealing activity
namespace: molecular_function
-def: "Catalysis of the ATP-dependent rewinding of single-stranded DNA (ssDNA) to reform base pairs between strands. Often acts on ssDNA bubbles bound by replication protein A (RPA)." [GOC:bf, GOC:sp, PMID:21078962, PMID:22704558, PMID:22705370, PMID:22759634]
-synonym: "annealing activity" BROAD [GOC:bf]
+def: "An ATP-dependent activity that facilitates the formation of a complementary double-stranded DNA molecule." [PMID:21078962, PMID:22704558, PMID:22705370, PMID:22759634, PMID:22888405]
+synonym: "annealing helicase activity" RELATED [PMID:22888405]
synonym: "ATP-dependent DNA annealing activity" RELATED [GOC:sp]
+synonym: "DNA rewinding activity" RELATED [PMID:22888405]
synonym: "nucleoside-triphosphatase activity involved in DNA annealing" EXACT [GOC:bf]
-is_a: GO:0016887 ! ATPase
-is_a: GO:0097617 ! annealing activity
+xref: Reactome:R-HSA-5686642 "RAD52 promotes single strand annealing at resected DNA DSBs"
+is_a: GO:0140657 ! ATP-dependent activity
+is_a: GO:1990814 ! DNA/DNA annealing activity
[Term]
id: GO:0036311
@@ -216261,7 +215953,7 @@ is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0036312
name: phosphatidylinositol 3-kinase regulatory subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a regulatory subunit of phosphatidylinositol 3-kinase. The regulatory subunit associates with the catalytic subunit to regulate both its activity and subcellular location." [GOC:bf, PMID:20505341]
+def: "Binding to a regulatory subunit of phosphatidylinositol 3-kinase. The regulatory subunit associates with the catalytic subunit to regulate both its activity and subcellular location." [GOC:bf, PMID:20505341]
synonym: "p85 binding" RELATED [PMID:10627473, PMID:20505341]
synonym: "PI3K regulatory subunit binding" EXACT [GOC:bf]
is_a: GO:0043548 ! phosphatidylinositol 3-kinase binding
@@ -216270,7 +215962,7 @@ is_a: GO:0043548 ! phosphatidylinositol 3-kinase binding
id: GO:0036313
name: phosphatidylinositol 3-kinase catalytic subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the catalytic subunit of a phosphatidylinositol 3-kinase. The catalytic subunit catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring." [GOC:bf, PMID:17475214]
+def: "Binding to the catalytic subunit of a phosphatidylinositol 3-kinase. The catalytic subunit catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring." [GOC:bf, PMID:17475214]
synonym: "p110 binding" RELATED [PMID:17475214]
synonym: "PI3K catalytic subunit binding" EXACT [GOC:bf]
is_a: GO:0019900 ! kinase binding
@@ -216602,7 +216294,6 @@ def: "Catalysis of the reaction: 2,3-diphosphoglycerate (DPG) + ATP = cyclic 2,3
comment: This reaction is the intramolecular cyclization of 2,3-diphosphoglycerate to cyclic 2,3-diphosphoglycerate and is the second step in the biosynthesis of cyclic 2,3-diphosphoglycerate (cDPG).
synonym: "cDPGS activity" EXACT [PMID:9811660]
synonym: "CPGS activity" EXACT [GOC:bf]
-xref: EC:4.6.1.-
is_a: GO:0009975 ! cyclase activity
[Term]
@@ -216629,12 +216320,11 @@ is_a: GO:0070400 ! teichoic acid D-alanylation
id: GO:0036359
name: renal potassium excretion
namespace: biological_process
-def: "The elimination by an organism of potassium in the urine." [GOC:gap, PMID:15034090, PMID:16014448]
+def: "The elimination of potassium ions from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine." [GOC:gap, PMID:15034090, PMID:25287933]
synonym: "renal K(+) excretion" EXACT [PMID:16014448]
synonym: "renal K+ elimination" EXACT [PMID:15034090]
synonym: "renal potassium ion excretion" EXACT [GOC:bf]
-is_a: GO:0003014 ! renal system process
-is_a: GO:0007588 ! excretion
+is_a: GO:0097254 ! renal tubular secretion
[Term]
id: GO:0036360
@@ -217040,14 +216730,16 @@ is_a: GO:0045293 ! mRNA editing complex
id: GO:0036397
name: formate dehydrogenase (quinone) activity
namespace: molecular_function
-def: "Catalysis of the reaction: formate + a quinone = CO2 + a quinol." [EC:1.1.5.6, GOC:bhm]
-synonym: "Fdh-N activity" RELATED [EC:1.1.5.6]
-synonym: "formate dehydrogenase-N activity" RELATED [EC:1.1.5.6]
-synonym: "formate:quinone oxidoreductase activity" RELATED [EC:1.1.5.6]
-xref: EC:1.1.5.6
+def: "Catalysis of the reaction: formate + a quinone = CO2 + a quinol." [GOC:bhm, RHEA:48592]
+comment: Formerly EC:1.1.5.6.
+synonym: "Fdh-N activity" RELATED []
+synonym: "formate dehydrogenase-N activity" RELATED [EC:1.17.5.3]
+synonym: "formate:quinone oxidoreductase activity" RELATED []
+xref: EC:1.17.5.3
xref: KEGG_REACTION:R09494
xref: MetaCyc:FORMATEDEHYDROG-RXN
-is_a: GO:0052738 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, with a quinone or similar compound as acceptor
+xref: RHEA:48592
+is_a: GO:0033695 ! oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor
[Term]
id: GO:0036398
@@ -217095,7 +216787,7 @@ synonym: "proteasome channel gating activity" NARROW [GOC:rb]
synonym: "proteasome channel opening activity" NARROW [GOC:rb]
synonym: "proteasome-activating ATPase activity" EXACT []
xref: EC:5.6.1.5
-is_a: GO:0016887 ! ATPase
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0036403
@@ -217111,12 +216803,13 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
[Term]
id: GO:0036404
-name: conversion of ds siRNA to ss siRNA
+name: obsolete conversion of ds siRNA to ss siRNA
namespace: biological_process
-def: "The process in which double-stranded small interfering RNA (ds siRNA) molecules are converted to single-stranded small interfering RNA (ss siRNA)." [GOC:vw]
+def: "OBSOLETE. The process in which double-stranded small interfering RNA (ds siRNA) molecules are converted to single-stranded small interfering RNA (ss siRNA)." [GOC:vw]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA" RELATED [GOC:bf]
-is_a: GO:0006396 ! RNA processing
-relationship: part_of GO:0031050 ! dsRNA processing
+is_obsolete: true
+consider: GO:0004521
[Term]
id: GO:0036405
@@ -217144,7 +216837,6 @@ namespace: cellular_component
def: "A mycolic acid-rich cell outer membrane containing a lipid bilayer and long-chain mycolic acids (hydroxylated branched-chain fatty acids) that are covalently linked to the cell wall peptidoglycan via an arabinogalactan network. Found in mycobacteria and related genera (e.g. corynebacteria)." [GOC:bf, GOC:das, GOC:md, PMID:18316738, PMID:18567661]
synonym: "MOM" EXACT [GOC:md]
synonym: "mycobacterial outer membrane" EXACT [GOC:md]
-synonym: "mycolate outer membrane" NARROW [GOC:md]
synonym: "mycomembrane" EXACT [GOC:das, GOC:md]
is_a: GO:0009279 ! cell outer membrane
@@ -217311,20 +217003,27 @@ is_a: GO:0004659 ! prenyltransferase activity
id: GO:0036424
name: L-phosphoserine phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-phospho-L-serine + H2O <=> L-serine + phosphate, on a free amino acid." [PMID:25037224, PMID:9188776, RHEA:21208]
+alt_id: GO:0004647
+def: "Catalysis of the reaction: O-phospho-L-serine + H2O = L-serine + phosphate, on a free amino acid." [PMID:25037224, PMID:9188776, RHEA:21208]
+comment: Do not confuse with protein phosphatases. For protein phosphatases, consider GO:0004722 ; protein serine/threonine phosphatase activity or GO:0008138 ; protein tyrosine/serine/threonine phosphatase activity.
+synonym: "O-phosphoserine phosphohydrolase activity" RELATED [EC:3.1.3.3]
+synonym: "phosphoserine phosphatase activity" RELATED []
+xref: EC:3.1.3.3
xref: KEGG_REACTION:R00582
+xref: MetaCyc:PSERPHOSPHA-RXN
xref: MetaCyc:RXN0-5114
+xref: Reactome:R-HSA-977324 "PSPH:Mg2+ dimer dephosphorylates O-P-Ser"
xref: RHEA:21208
-is_a: GO:0004647 ! phosphoserine phosphatase activity
+is_a: GO:0016791 ! phosphatase activity
[Term]
id: GO:0036425
-name: D-phosphoserine phosphatase activity
+name: obsolete D-phosphoserine phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: O-phospho-D-serine + H2O <=> L-serine + phosphate, on a free amino acid." [RHEA:24873]
-xref: KEGG_REACTION:R02853
-xref: RHEA:24873
-is_a: GO:0004647 ! phosphoserine phosphatase activity
+def: "OBSOLETE. Catalysis of the reaction: O-phospho-D-serine + H2O = L-serine + phosphate, on a free amino acid." [GOC:curators]
+comment: This term was obsoleted because there is no evidence that this function exisis. This reaction corresponds to RHEA:24873 and KEGG_REACTION:R02853.
+is_obsolete: true
+consider: GO:0036424
[Term]
id: GO:0036426
@@ -217417,7 +217116,7 @@ is_a: GO:0016703 ! oxidoreductase activity, acting on single donors with incorpo
id: GO:0036435
name: K48-linked polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 48 in the target protein." [GOC:al, PMID:20739285]
+def: "Binding to a protein upon poly-ubiquitination formed by linkages between lysine residues at position 48 in the target protein." [GOC:al, PMID:20739285]
xref: Reactome:R-HSA-5683077 "RNF8 and RNF168 ubiquitinate KDM4A,B"
is_a: GO:0031593 ! polyubiquitin modification-dependent protein binding
@@ -217482,7 +217181,6 @@ synonym: "mitochondrial calcium uptake" EXACT []
is_a: GO:0006851 ! mitochondrial calcium ion transmembrane transport
is_a: GO:0060401 ! cytosolic calcium ion transport
is_a: GO:0070509 ! calcium ion import
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0036445
@@ -217593,7 +217291,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0036458
name: hepatocyte growth factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a hepatocyte growth factor." [GOC:curators]
+def: "Binding to a hepatocyte growth factor." [GOC:curators]
synonym: "HGF binding" EXACT [PR:000008534]
is_a: GO:0019838 ! growth factor binding
@@ -217609,7 +217307,7 @@ is_a: GO:0033554 ! cellular response to stress
id: GO:0036461
name: BLOC-2 complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a BLOC-2 complex, a protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules." [GOC:bf, GOC:PARL, PMID:22511774]
+def: "Binding to a BLOC-2 complex, a protein complex required for the biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules." [GOC:bf, GOC:PARL, PMID:22511774]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -217687,7 +217385,6 @@ id: GO:0036469
name: L-tryptophan decarboxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-tryptophan + H+ = CO2 + tryptamine." [GOC:bf, GOC:PARL, RHEA:30339]
-synonym: "L-tryptophan decarboxylase activity" RELATED [EC:4.1.1.105]
xref: EC:4.1.1.105
xref: RHEA:30339
is_a: GO:0004058 ! aromatic-L-amino-acid decarboxylase activity
@@ -217902,8 +217599,8 @@ name: regulation of translation in response to endoplasmic reticulum stress
namespace: biological_process
def: "Modulation of the frequency, rate or extent of translation as a result of endoplasmic reticulum stress." [GOC:bf, GOC:PARL, PMID:14676213, PMID:16835242]
synonym: "regulation of translation in response to ER stress" EXACT [GOC:bf]
-is_a: GO:0034976 ! response to endoplasmic reticulum stress
is_a: GO:0043555 ! regulation of translation in response to stress
+relationship: part_of GO:0034976 ! response to endoplasmic reticulum stress
[Term]
id: GO:0036491
@@ -218256,14 +217953,14 @@ is_a: GO:1905170 ! negative regulation of protein localization to phagocytic ves
[Term]
id: GO:0036523
-name: induction by symbiont of host cytokine production
+name: obsolete induction by symbiont of host cytokine production
namespace: biological_process
-def: "Any process in which a symbiont activates, maintains or increases the frequency, rate or extent of cytokine production by the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:bf, GOC:PARL, PMID:25063865]
+def: "OBSOLETE. Any process in which a symbiont activates, maintains or increases the frequency, rate or extent of cytokine production by the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:bf, GOC:PARL, PMID:25063865]
+comment: This term was obsoleted because it does not represent a real process.
synonym: "'induction by symbiont of host cytokine secretion'" NARROW []
synonym: "induction by symbiont of host cytokine secretion" RELATED [PMID:25063865]
synonym: "positive regulation by symbiont of host cytokine secretion" NARROW []
-is_a: GO:0001819 ! positive regulation of cytokine production
-is_a: GO:0052390 ! induction by symbiont of host innate immune response
+is_obsolete: true
[Term]
id: GO:0036524
@@ -218584,6 +218281,8 @@ name: cargo receptor activity
namespace: molecular_function
def: "Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span a membrane (either the plasma membrane or a vesicle membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit soluble proteins to nascent vesicles." [PMID:15239958, PMID:27903609]
comment: Notes: (1) this term and its child terms are intended for receptors that bind to and internalize molecules by receptor-mediated endocytosis. For receptors that are coupled to a signal transduction pathway, consider instead the term 'signaling receptor activity ; GO:0038023' and its children. (2) Cargo receptors transport substances by vesicular transport, not by transmembrane transport. For transmembrane transporters, consider instead the term 'transmembrane transporter activity ; GO:0022857.
+subset: goslim_drosophila
+subset: goslim_generic
synonym: "endocytic receptor activity" NARROW [GOC:signaling, ISBN:0123645387, PMID:12671190]
synonym: "receptor activity" BROAD []
synonym: "receptor activity involved in receptor-mediated endocytosis" NARROW [GOC:bf]
@@ -218816,7 +218515,7 @@ is_a: GO:0004985 ! G protein-coupled opioid receptor activity
id: GO:0038053
name: obsolete transcription factor activity, estrogen-activated RNA polymerase II transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Combining with estrogen and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. For example, estrogen-bound receptors can bind to transcription factor complexes to regulate transcription of genes whose promoters do not contain estrogen response elements." [GOC:signaling, PMID:17615392]
+def: "OBSOLETE. Combining with estrogen and transmitting the signal to the transcriptional machinery by binding to an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. For example, estrogen-bound receptors can bind to transcription factor complexes to regulate transcription of genes whose promoters do not contain estrogen response elements." [GOC:signaling, PMID:17615392]
comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "estrogen nuclear receptor activity" BROAD [GOC:bf]
synonym: "estrogen-activated RNA polymerase II transcription factor binding transcription factor activity" EXACT []
@@ -218855,7 +218554,7 @@ is_a: GO:2001285 ! negative regulation of BMP secretion
id: GO:0038057
name: TNFSF11 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with tumor necrosis factor ligand superfamily member 11 (TNFSF11), a member of the tumor necrosis factor (TNF) cytokine family." [GOC:cjm]
+def: "Binding to tumor necrosis factor ligand superfamily member 11 (TNFSF11), a member of the tumor necrosis factor (TNF) cytokine family." [GOC:cjm]
synonym: "CD254 binding" EXACT [GOC:sl, PR:000002107]
synonym: "ODF binding" EXACT [GOC:sl, PR:000002107]
synonym: "OPGL binding" EXACT [GOC:sl, PR:000002107]
@@ -219075,11 +218774,12 @@ is_obsolete: true
[Term]
id: GO:0038078
-name: MAP kinase phosphatase activity involved in regulation of innate immune response
+name: obsolete MAP kinase phosphatase activity involved in regulation of innate immune response
namespace: molecular_function
-def: "Catalysis of the reaction: a phosphorylated MAP kinase + H2O = a MAP kinase + phosphate, where the MAP kinase (MAPK) is part of a MAPK signaling cascade that contributes to an innate immune response." [GOC:signaling]
+def: "OBSOLETE. Catalysis of the reaction: a phosphorylated MAP kinase + H2O = a MAP kinase + phosphate, where the MAP kinase (MAPK) is part of a MAPK signaling cascade that contributes to an innate immune response." [GOC:signaling]
+comment: This term was obsoleted because it represents a biological process within the molecular function branch.
synonym: "MAPK phosphatase activity involved in regulation of innate immune response" EXACT [GOC:bf]
-is_a: GO:0033549 ! MAP kinase phosphatase activity
+is_obsolete: true
[Term]
id: GO:0038079
@@ -219151,7 +218851,7 @@ relationship: part_of GO:0035924 ! cellular response to vascular endothelial gro
id: GO:0038085
name: vascular endothelial growth factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a vascular endothelial growth factor." [PMID:17470632]
+def: "Binding to a vascular endothelial growth factor." [PMID:17470632]
synonym: "VEGF binding" EXACT [GOC:bf]
is_a: GO:0019838 ! growth factor binding
@@ -219303,14 +219003,14 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a complex containing a type II activin receptor, a type I activin receptor, and a coreceptor of the EGF-CFC family (e.g. Cripto or Cryptic, in mammals)." [GOC:bf, GOC:signaling, PMID:15062104]
synonym: "ActRIIB.ALK4.EGF-CFC complex formation" EXACT [GOC:bf]
synonym: "nodal receptor complex formation" EXACT [GOC:bf]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0038092 ! nodal signaling pathway
[Term]
id: GO:0038100
name: nodal binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nodal protein, a member of the transforming growth factor-beta superfamily." [GOC:bf, PMID:20629020]
+def: "Binding to a nodal protein, a member of the transforming growth factor-beta superfamily." [GOC:bf, PMID:20629020]
is_a: GO:0005515 ! protein binding
[Term]
@@ -219364,7 +219064,7 @@ is_a: GO:0035581 ! sequestering of extracellular ligand from receptor
id: GO:0038106
name: choriogonadotropin hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with choriogonadotropin hormone, a heterodimer, with an alpha subunit identical to that of luteinizing hormone (LH), follicle-stimulating hormone (FSH) and thyroid-stimulating hormone (TSH), and a unique beta subunit." [GOC:BHF, GOC:rl, Wikipedia:Human_chorionic_gonadotropin]
+def: "Binding to choriogonadotropin hormone, a heterodimer, with an alpha subunit identical to that of luteinizing hormone (LH), follicle-stimulating hormone (FSH) and thyroid-stimulating hormone (TSH), and a unique beta subunit." [GOC:BHF, GOC:rl, Wikipedia:Human_chorionic_gonadotropin]
synonym: "chorionic gonadotrophin binding" EXACT [Wikipedia:Human_chorionic_gonadotropin]
synonym: "chorionic gonadotropin binding" EXACT [Wikipedia:Human_chorionic_gonadotropin]
is_a: GO:0042562 ! hormone binding
@@ -219605,7 +219305,7 @@ is_a: GO:0004888 ! transmembrane signaling receptor activity
id: GO:0038132
name: neuregulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neuregulin, a member of the EGF family of growth factors." [GOC:bf, GOC:signaling]
+def: "Binding to a neuregulin, a member of the EGF family of growth factors." [GOC:bf, GOC:signaling]
is_a: GO:0019838 ! growth factor binding
[Term]
@@ -220001,7 +219701,6 @@ namespace: biological_process
def: "A series of molecular signals initiated by the binding of interleukin-17A to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription." [GOC:jc, GOC:signaling]
synonym: "IL-17A-mediated signaling pathway" EXACT [GOC:bf]
synonym: "IL17A signaling pathway" EXACT [PR:000001138, Wikipedia:IL17A]
-synonym: "IL17a signaling pathway" EXACT [GOC:jc]
synonym: "interleukin-17A signaling pathway" RELATED [GOC:jc]
synonym: "interleukin-17A-mediated signalling pathway" EXACT [GOC:bf]
is_a: GO:0019221 ! cytokine-mediated signaling pathway
@@ -220173,7 +219872,7 @@ is_a: GO:0038189 ! neuropilin signaling pathway
id: GO:0038191
name: neuropilin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a member of the neuropilin family." [GOC:bf, PMID:23871893]
+def: "Binding to a member of the neuropilin family." [GOC:bf, PMID:23871893]
synonym: "neuropilin-binding" EXACT [PMID:12852851]
synonym: "Nrp binding" EXACT [PMID:23871893]
synonym: "Nrp ligand" NARROW [PMID:23871893]
@@ -220523,11 +220222,10 @@ synonym: "inhibition of host adaptive immune response by virus" EXACT [UniProtKB
synonym: "negative regulation by virus of host adaptive immune response" EXACT [GOC:bf]
synonym: "negative regulation by virus of host adaptive immunity" EXACT [GOC:bf]
synonym: "suppression by virus of host acquired immune response" EXACT [ISBN:068340007X]
-is_a: GO:0002820 ! negative regulation of adaptive immune response
is_a: GO:0030683 ! mitigation of host immune response by virus
-is_a: GO:0050794 ! regulation of cellular process
is_a: GO:0052562 ! suppression by symbiont of host immune response
is_a: GO:0075528 ! modulation by virus of host immune response
+relationship: negatively_regulates GO:0002250 ! adaptive immune response
[Term]
id: GO:0039505
@@ -220537,7 +220235,9 @@ def: "Any viral process that inhibits a host antigen-presenting cell expressing
synonym: "inhibition of host MHC class II molecule presentation by virus" RELATED [UniProtKB-KW:KW-1116]
xref: VZ:820 "Inhibition of host MHC class II molecule presentation by virus"
is_a: GO:0002587 ! negative regulation of antigen processing and presentation of peptide antigen via MHC class II
+is_a: GO:0002820 ! negative regulation of adaptive immune response
is_a: GO:0039588 ! suppression by virus of host antigen processing and presentation
+is_a: GO:0050794 ! regulation of cellular process
[Term]
id: GO:0039506
@@ -220559,8 +220259,8 @@ synonym: "inhibition by virus of host protein function" NARROW [GOC:bf]
synonym: "inhibition of host protein function" NARROW [GOC:bf]
synonym: "negative regulation by virus of host molecular function" EXACT [GOC:bf]
synonym: "negative regulation by virus of host protein function" EXACT [GOC:bf]
-is_a: GO:0039506 ! modulation by virus of host molecular function
-is_a: GO:0052056 ! negative regulation by symbiont of host molecular function
+is_a: GO:0039516 ! modulation by virus of host catalytic activity
+is_a: GO:0052053 ! negative regulation by symbiont of host catalytic activity
[Term]
id: GO:0039508
@@ -220590,14 +220290,15 @@ is_a: GO:0039508 ! suppression by virus of host receptor activity
[Term]
id: GO:0039510
-name: suppression by virus of host ATP-dependent RNA helicase activity
+name: obsolete suppression by virus of host ATP-dependent RNA helicase activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ATP-dependent RNA helicase activity." [GOC:bf, GOC:sp]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ATP-dependent RNA helicase activity." [GOC:bf, GOC:sp]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down-regulation by virus of host ATP-dependent RNA helicase activity" EXACT [GOC:bf]
synonym: "downregulation by virus of host ATP-dependent RNA helicase activity" EXACT [GOC:bf]
synonym: "inhibition by virus of host ATP-dependent RNA helicase activity" NARROW [GOC:bf]
synonym: "negative regulation by virus of host ATP-dependent RNA helicase activity" EXACT [GOC:bf]
-is_a: GO:0039513 ! suppression by virus of host catalytic activity
+is_obsolete: true
[Term]
id: GO:0039511
@@ -220633,8 +220334,6 @@ synonym: "downregulation by virus of host catalytic activity" EXACT [GOC:bf]
synonym: "inhibition by virus of host catalytic activity" NARROW [GOC:bf]
synonym: "negative regulation by virus of host catalytic activity" EXACT [GOC:bf]
is_a: GO:0039507 ! suppression by virus of host molecular function
-is_a: GO:0039516 ! modulation by virus of host catalytic activity
-is_a: GO:0052053 ! negative regulation by symbiont of host catalytic activity
[Term]
id: GO:0039514
@@ -220645,7 +220344,6 @@ synonym: "down-regulation by virus of host JAK-STAT cascade" EXACT [GOC:bf]
synonym: "downregulation by virus of host JAK-STAT cascade" EXACT [GOC:bf]
synonym: "inhibition by virus of host JAK-STAT cascade" NARROW [GOC:bf]
synonym: "negative regulation by virus of host JAK-STAT cascade" EXACT [GOC:bf]
-is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0052029 ! suppression by symbiont of host signal transduction pathway
[Term]
@@ -220668,7 +220366,6 @@ synonym: "modulation by virus of protein serine/threonine phosphatase activity i
synonym: "regulation by virus of host protein serine/threonine phosphatase activity" EXACT [GOC:bf]
is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0039516 ! modulation by virus of host catalytic activity
-is_a: GO:0043666 ! regulation of phosphoprotein phosphatase activity
[Term]
id: GO:0039518
@@ -220733,14 +220430,13 @@ is_a: GO:0052038 ! modulation by symbiont of host intracellular transport
[Term]
id: GO:0039523
-name: suppression by virus of host RNA polymerase II activity
+name: suppression by virus of host mRNA transcription via inhibition of RNA polymerase II activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host RNA polymerase II activity." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1104, VZ:905]
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host mRNA transcription by directly inhibiting RNA polymerase II activity." [GOC:bf, GOC:sp, PMID:25233083]
synonym: "inhibition of host RNA polymerase II activity by virus" EXACT [GOC:bf]
-synonym: "inhibition of host RNA polymerase II by virus" EXACT [UniProtKB-KW:KW-1104]
+synonym: "inhibition of host RNA polymerase II by virus" EXACT []
synonym: "negative regulation by virus of host RNA polymerase II activity" BROAD [GOC:bf]
-xref: VZ:905 "Inhibition of host RNA polymerase II by virus"
-is_a: GO:0039507 ! suppression by virus of host molecular function
+synonym: "suppression by virus of host RNA polymerase II activity" EXACT []
is_a: GO:0039653 ! suppression by virus of host transcription
[Term]
@@ -220789,7 +220485,6 @@ def: "Any process in which a virus stops, prevents, or reduces the frequency, ra
synonym: "inhibition of host TRAF-mediated signal transduction by virus" EXACT [GOC:bf]
synonym: "negative regulation by virus of host TRAF-mediated signal transduction" BROAD [GOC:bf]
synonym: "suppression by virus of host tumor necrosis factor receptor-associated factor signaling" EXACT [GOC:bf]
-is_a: GO:0019054 ! modulation by virus of host cellular process
is_a: GO:0052029 ! suppression by symbiont of host signal transduction pathway
[Term]
@@ -220922,44 +220617,28 @@ synonym: "suppression by virus of host viral-induced cytoplasmic pattern recogni
is_a: GO:0039503 ! suppression by virus of host innate immune response
is_a: GO:0075111 ! suppression by symbiont of host receptor-mediated signal transduction
-[Term]
-id: GO:0039538
-name: suppression by virus of host RIG-I signaling pathway
-namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA. This is a mechanism by which the virus evades the host innate immune response." [GOC:bf, GOC:jl]
-synonym: "inhibition by virus of host RIG-I signaling" EXACT [GOC:bf]
-synonym: "suppression by virus of host DDX58 signaling pathway" EXACT [GOC:bf]
-synonym: "suppression by virus of host RIG-I signalling pathway" EXACT [GOC:mah]
-is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
-
-[Term]
-id: GO:0039539
-name: suppression by virus of host MDA-5 signaling pathway
-namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1) binding to viral RNA. This is a mechanism by which the virus evades the host innate immune response." [GOC:bf, GOC:jl]
-synonym: "inhibition by virus of host MDA-5 signaling" EXACT [GOC:bf]
-synonym: "suppression by virus of host IFIH1 signaling pathway" EXACT [GOC:bf]
-synonym: "suppression by virus of host MDA-5 signalling pathway" EXACT [GOC:mah]
-is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
-
[Term]
id: GO:0039540
-name: suppression by virus of host RIG-I activity
+name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of host RIG-I activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of RIG-1 (also known as DDX58). The cytoplasmic pattern recognition RIG-I recognizes viral RNA synthesized during active viral replication and signals to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [GOC:bf, GOC:sp, UniProtKB-KW:KW-1088, VZ:856]
+alt_id: GO:0039538
+def: "Any process in which a virus stops, prevents, or reduces a host viral-induced cytoplasmic pattern recognition receptor signaling pathway by inhibiting the activity of RIG-1 (also known as DDX58). The cytoplasmic pattern recognition RIG-I recognizes viral RNA synthesized during active viral replication and signals to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [PMID:19454348, PMID:26138103]
comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response initiated by host RIG-I, either by binding and inhibiting host RIG-I directly, or by interfering with other processes so that RIG-I is unable to carry out its normal function (e.g. by processing viral RNA so it cannot be recognized by RIG-I, or by promoting the degradation of RIG-I).
-synonym: "inhibition by virus of host DDX58 activity" EXACT [GOC:sp]
-synonym: "inhibition by virus of host RIG-I" RELATED [GOC:bf]
-synonym: "inhibition of host DDX58/RIG-I by virus" EXACT [UniProtKB-KW:KW-1088]
-xref: VZ:856 "Inhibition of host RIG-I by virus"
-is_a: GO:0039509 ! suppression by virus of host pattern recognition receptor activity
-is_a: GO:0039538 ! suppression by virus of host RIG-I signaling pathway
+synonym: "inhibition by virus of host DDX58 activity" RELATED [GOC:sp]
+synonym: "inhibition by virus of host RIG-I" RELATED []
+synonym: "inhibition by virus of host RIG-I signaling" RELATED []
+synonym: "inhibition of host DDX58/RIG-I by virus" EXACT []
+synonym: "suppression by virus of host DDX58 signaling pathway" RELATED []
+synonym: "suppression by virus of host RIG-I activity" RELATED []
+synonym: "suppression by virus of host RIG-I signaling pathway" RELATED []
+synonym: "suppression by virus of host RIG-I signalling pathway" EXACT []
+is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
[Term]
id: GO:0039541
name: obsolete suppression by virus of host RIG-I via RIG-I binding
namespace: biological_process
-def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the activity of RIG-I (also known as DDX58) by interacting selectively and non-covalently with RIG-I itself." [PMID:19193793, PMID:20007272, VZ:856]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the activity of RIG-I (also known as DDX58) by binding to RIG-I itself." [PMID:19193793, PMID:20007272, VZ:856]
comment: The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
synonym: "inhibition by virus of host DDX58:MAVS binding" EXACT [GOC:bf]
is_obsolete: true
@@ -220996,14 +220675,13 @@ is_obsolete: true
[Term]
id: GO:0039545
-name: suppression by virus of host MAVS activity
+name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of MAVS (mitochondrial antiviral signaling protein), a signal transducer that lies downstream of the viral RNA receptors MDA-5 and RIG-I to coordinate host innate immune responses." [UniProtKB-KW:KW-1097, VZ:704]
+def: "Any process in which a virus stops, prevents, or reduces a viral-induced cytoplasmic pattern recognition receptor signaling pathway in a host organism by reducing the activity of host MAVS (mitochondrial antiviral signaling protein). MAVS is a signal transducer that lies downstream of the viral RNA receptors MDA-5 and RIG-I to coordinate host innate immune responses." [PMID:17438296, PMID:22674996]
comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response.
-synonym: "inhibition of host MAVS by virus" EXACT [UniProtKB-KW:KW-1097, VZ:704]
-synonym: "suppression by virus of host mitochondrial antiviral-signaling protein" EXACT [PR:000010210]
-xref: VZ:704 "Inhibition of host MAVS by virus"
-is_a: GO:0039507 ! suppression by virus of host molecular function
+synonym: "inhibition of host MAVS by virus" RELATED []
+synonym: "suppression by virus of host MAVS activity" RELATED []
+synonym: "suppression by virus of host mitochondrial antiviral-signaling protein" RELATED []
is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
[Term]
@@ -221027,17 +220705,15 @@ relationship: part_of GO:0039527 ! suppression by virus of host TRAF-mediated si
[Term]
id: GO:0039548
-name: suppression by virus of host IRF3 activity
+name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF3 (interferon regulatory factor-3), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes." [PMID:21632562, UniProtKB-KW:KW-1092, VZ:757]
+def: "Any process in which a virus stops, prevents, or reduces a viral-induced cytoplasmic pattern recognition receptor signaling pathway in a host organism by reducing the activity of host IRF3 (interferon regulatory factor-3). IRF3 is a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF3, which allows IRF3 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes." [PMID:21632562]
comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response.
-synonym: "inhibition of host IRF3 by virus" EXACT [UniProtKB-KW:KW-1092]
-synonym: "Inhibition of IRF3-dependent antiviral response" BROAD [PMID:19125153]
-synonym: "suppression by virus of host interferon regulatory factor 3" EXACT [PR:000002045]
-xref: VZ:757 "Inhibition of host IRF3 by virus"
-is_a: GO:0039503 ! suppression by virus of host innate immune response
-is_a: GO:0039507 ! suppression by virus of host molecular function
-is_a: GO:0039653 ! suppression by virus of host transcription
+synonym: "inhibition of host IRF3 by virus" RELATED []
+synonym: "inhibition of IRF3-dependent antiviral response" RELATED [PMID:19125153]
+synonym: "suppression by virus of host interferon regulatory factor 3" RELATED []
+synonym: "suppression by virus of host IRF3 activity" RELATED []
+is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
[Term]
id: GO:0039549
@@ -221071,7 +220747,7 @@ is_obsolete: true
id: GO:0039552
name: RIG-I binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with RIG-I, a cytosolic pattern recognition receptor that initiates an antiviral signaling pathway upon binding to viral RNA." [GOC:bf, PMID:21233210]
+def: "Binding to RIG-I, a cytosolic pattern recognition receptor that initiates an antiviral signaling pathway upon binding to viral RNA." [GOC:bf, PMID:21233210]
synonym: "DDX58 binding" EXACT [GOC:sp]
synonym: "DDX58/RIG-I binding" EXACT [GOC:sp]
is_a: GO:0005102 ! signaling receptor binding
@@ -221091,20 +220767,24 @@ is_a: GO:0039518 ! suppression by virus of host cytokine activity
[Term]
id: GO:0039554
-name: suppression by virus of host MDA-5 activity
-namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of MDA-5 (also known as IFIH1). The cytoplasmic pattern recognition receptor MDA-5 detects dsRNA synthesized during active viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [UniProtKB-KW:KW-1089, VZ:603]
-synonym: "inhibition of host IFIH1/MDA5 by virus" RELATED [UniProtKB-KW:KW-1089]
-synonym: "Inhibition of host MDA5 by virus" EXACT [VZ:603]
-xref: VZ:603 "Inhibition of host MDA5 by virus"
-is_a: GO:0039509 ! suppression by virus of host pattern recognition receptor activity
-is_a: GO:0039539 ! suppression by virus of host MDA-5 signaling pathway
+name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of host MDA-5 activity
+namespace: biological_process
+alt_id: GO:0039539
+def: "Any process in which a virus stops, prevents, or reduces a host viral-induced cytoplasmic pattern recognition receptor signaling pathway by inhibiting the activity of MDA-5 (also known as IFIH1). The cytoplasmic pattern recognition receptor MDA-5 detects dsRNA synthesized during active viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [PMID:19019954, PMID:33727702]
+synonym: "inhibition by virus of host MDA-5 signaling" RELATED []
+synonym: "inhibition of host IFIH1/MDA5 by virus" RELATED []
+synonym: "Inhibition of host MDA5 by virus" RELATED []
+synonym: "suppression by virus of host IFIH1 signaling pathway" RELATED []
+synonym: "suppression by virus of host MDA-5 activity" RELATED []
+synonym: "suppression by virus of host MDA-5 signaling pathway" RELATED []
+synonym: "suppression by virus of host MDA-5 signalling pathway" RELATED []
+is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
[Term]
id: GO:0039555
name: obsolete suppression by virus of host MDA-5 activity via MDA-5 binding
namespace: biological_process
-def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the activity of MDA-5 (also known as IFIH1) by interacting selectively and non-covalently with MDA-5 itself. For example, direct binding of viral proteins to the host MDA-5 protein can inhibit interaction of MDA-5 with MAVS, its downstream signaling effector." [PMID:19019954, VZ:603]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the activity of MDA-5 (also known as IFIH1) by binding to MDA-5 itself. For example, direct binding of viral proteins to the host MDA-5 protein can inhibit interaction of MDA-5 with MAVS, its downstream signaling effector." [PMID:19019954, VZ:603]
comment: The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
synonym: "suppression by virus of host MDA5 activity by MDA-5 binding" EXACT [GOC:bf]
is_obsolete: true
@@ -221113,23 +220793,21 @@ is_obsolete: true
id: GO:0039556
name: MDA-5 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with MDA-5, a cytosolic pattern recognition receptor that initiates an antiviral signaling pathway upon binding to viral dsRNA." [PMID:19019954]
+def: "Binding to MDA-5, a cytosolic pattern recognition receptor that initiates an antiviral signaling pathway upon binding to viral dsRNA." [PMID:19019954]
synonym: "MDA5 binding" EXACT [GOC:bf]
is_a: GO:0005102 ! signaling receptor binding
[Term]
id: GO:0039557
-name: suppression by virus of host IRF7 activity
+name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF7 (interferon regulatory factor-7), a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF7, which allows IRF7 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes." [UniProtKB-KW:KW-1093, VZ:653]
+def: "Any process in which a virus stops, prevents, or reduces a host viral-induced cytoplasmic pattern recognition receptor signaling pathway by reducing the activity of IRF7 (interferon regulatory factor-7). IRF7 a transcription factor in the RIG-I/MDA-5 signaling pathway. Viral infection triggers phosphorylation of cytoplasmic IRF7, which allows IRF7 to form a homodimer, migrate to the nucleus, and activate transcription of IFN-alpha and IFN-beta genes." [PMID:11943871, PMID:16014964, PMID:19557165]
comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response.
-synonym: "inhibition of host interferon regulatory factor-7 by virus" EXACT [VZ:653]
-synonym: "inhibition of host IRF7 by virus" EXACT [UniProtKB-KW:KW-1093]
-synonym: "suppression by virus of host interferon regulatory factor 7 activity" EXACT [PR:000002049]
-xref: VZ:653 "Inhibition of host IRF7 by virus"
-is_a: GO:0039503 ! suppression by virus of host innate immune response
-is_a: GO:0039507 ! suppression by virus of host molecular function
-is_a: GO:0039653 ! suppression by virus of host transcription
+synonym: "inhibition of host interferon regulatory factor-7 by virus" RELATED []
+synonym: "inhibition of host IRF7 by virus" RELATED []
+synonym: "suppression by virus of host interferon regulatory factor 7 activity" RELATED []
+synonym: "suppression by virus of host IRF7 activity" RELATED []
+is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
[Term]
id: GO:0039558
@@ -221152,17 +220830,16 @@ is_obsolete: true
[Term]
id: GO:0039560
-name: suppression by virus of host IRF9 activity
+name: suppression by virus of host JAK-STAT cascade via inhibition of host IRF9 activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of host IRF9 (interferon regulatory factor-9), a transcription factor involved in the innate immune response. Viral infection triggers binding of IRF9 to phosphorylated STAT1 and STAT2, forming the ISGF3 complex. The ISGF3 complex migrates to the nucleus and activates transcription of IFN-responsive genes." [UniProtKB-KW:KW-1094, VZ:683]
+def: "Any process in which a virus stops, prevents, or reduces a JAK1-STAT signaling cascade in a host organism by reducing the activity of host IRF9 (interferon regulatory factor-9), a transcription factor involved in the innate immune response. Viral infection triggers binding of IRF9 to phosphorylated STAT1 and STAT2, forming the ISGF3 complex. The ISGF3 complex migrates to the nucleus and activates transcription of IFN-responsive genes." [PMID:10388655, PMID:19109390]
comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response.
synonym: "inhibition of host interferon regulatory factor-9 by virus" EXACT [GOC:bf]
-synonym: "inhibition of host IRF9 by virus" EXACT [UniProtKB-KW:KW-1094]
-synonym: "suppression by virus of host interferon regulatory factor 9 activity" EXACT [PR:000002051]
-xref: VZ:683 "Inhibition of host IRF9 by virus"
+synonym: "inhibition of host IRF9 by virus" EXACT []
+synonym: "suppression by virus of host interferon regulatory factor 9 activity" RELATED []
+synonym: "suppression by virus of host IRF9 activity" RELATED []
is_a: GO:0039503 ! suppression by virus of host innate immune response
-is_a: GO:0039507 ! suppression by virus of host molecular function
-is_a: GO:0039653 ! suppression by virus of host transcription
+is_a: GO:0039514 ! suppression by virus of host JAK-STAT cascade
[Term]
id: GO:0039561
@@ -221176,36 +220853,35 @@ is_obsolete: true
[Term]
id: GO:0039562
-name: suppression by virus of host STAT activity
+name: suppression by virus of host JAK-STAT cascade via inhibition of STAT activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT (signal transducer and activator of transcription) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes." [GOC:bf]
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of a JAK-STAT signal cascade in a host organism by reducing the activity of host STAT (signal transducer and activator of transcription). STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes." [GOC:bf]
comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response.
synonym: "inhibition by virus of host STAT activity" NARROW [GOC:bf]
synonym: "suppression by virus of host signal transducer and activator of transcription activity" EXACT [GOC:bf]
-is_a: GO:0039507 ! suppression by virus of host molecular function
+synonym: "suppression by virus of host STAT activity" EXACT []
is_a: GO:0039514 ! suppression by virus of host JAK-STAT cascade
-is_a: GO:0050794 ! regulation of cellular process
[Term]
id: GO:0039563
-name: suppression by virus of host STAT1 activity
+name: suppression by virus of host JAK-STAT cascade via inhibition of STAT1 activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT1 (signal transducer and activator of transcription-1) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes." [UniProtKB-KW:KW-1105, VZ:282]
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of a JAK-STAT signal cascade in a host organism by reducing the activity of host STAT1 (signal transducer and activator of transcription 1)." [PMID:32699158]
comment: This term is for annotation of viral proteins that counteract the host anti-viral innate immune response.
synonym: "inhibition by virus of host STAT1 activity" NARROW [GOC:bf]
-synonym: "Inhibition of host STAT1 by virus" NARROW [VZ:282]
-xref: VZ:282 "Inhibition of host STAT1 by virus"
-is_a: GO:0039562 ! suppression by virus of host STAT activity
+synonym: "inhibition of host STAT1 by virus" NARROW []
+synonym: "suppression by virus of host STAT1 activity" RELATED []
+is_a: GO:0039562 ! suppression by virus of host JAK-STAT cascade via inhibition of STAT activity
[Term]
id: GO:0039564
-name: suppression by virus of host STAT2 activity
+name: suppression by virus of host JAK-STAT cascade via inhibition of STAT2 activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host STAT2 (signal transducer and activator of transcription-2) activity. STATs are SH2 domain-containing proteins which lie downstream of many signaling receptors. Upon phosphorylation by JAKs, STAT proteins hetero- or homo-dimerize and translocate to the nucleus to activate transcription of target genes." [UniProtKB-KW:KW-1106, VZ:257]
-synonym: "inhibition by virus of host STAT2 activity" NARROW [GOC:bf]
-synonym: "Inhibition of host STAT2 by virus" EXACT [VZ:257]
-xref: VZ:257 "Inhibition of host STAT2 by virus"
-is_a: GO:0039562 ! suppression by virus of host STAT activity
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of a JAK-STAT signal cascade in a host organism by reducing the activity of host STAT2 (signal transducer and activator of transcription 2)." [PMID:32699158]
+synonym: "inhibition by virus of host STAT2 activity" RELATED [GOC:bf]
+synonym: "inhibition of host STAT2 by virus" RELATED []
+synonym: "suppression by virus of host STAT2 activity" RELATED []
+is_a: GO:0039562 ! suppression by virus of host JAK-STAT cascade via inhibition of STAT activity
[Term]
id: GO:0039565
@@ -221303,13 +220979,13 @@ is_a: GO:0075528 ! modulation by virus of host immune response
[Term]
id: GO:0039574
-name: suppression by virus of host TYK2 activity
+name: suppression by virus of host JAK-STAT cascade via inhibition of host TYK2 activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host TYK2 (tyrosine kinase 2) activity. TYK2 is an intracellular signal-transducing tyrosine kinase that associates with the cytoplasmic tails of cytokine receptors and transmits the cytokine signal by phosphorylating receptor subunits." [UniProtKB-KW:KW-1112, VZ:720]
-synonym: "suppression by virus of host non-receptor tyrosine-protein kinase TYK2 activity" EXACT [PR:000016874]
-xref: VZ:720 "Inhibition of host TYK2 by virus"
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of a JAK1-STAT signaling cascade in a host organism by reducing the activity of host TYK2 (tyrosine kinase 2). TYK2 is an intracellular signal-transducing tyrosine kinase that associates with the cytoplasmic tails of cytokine receptors and transmits the cytokine signal by phosphorylating receptor subunits." [PMID:16987978, PMID:19085955]
+synonym: "suppression by virus of host non-receptor tyrosine-protein kinase TYK2 activity" EXACT []
+synonym: "suppression by virus of host TYK2 activity" RELATED []
is_a: GO:0039503 ! suppression by virus of host innate immune response
-is_a: GO:0039512 ! suppression by virus of host protein tyrosine kinase activity
+is_a: GO:0039514 ! suppression by virus of host JAK-STAT cascade
[Term]
id: GO:0039575
@@ -221323,18 +220999,18 @@ is_obsolete: true
[Term]
id: GO:0039576
-name: suppression by virus of host JAK1 activity
+name: suppression by virus of host JAK-STAT cascade via inhibition of JAK1 activity
namespace: biological_process
alt_id: GO:0039515
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host JAK1 (Janus Kinase 1) activity. In the host, binding of a ligand to a receptor triggers activation of JAK proteins, which phosphorylate tyrosine residues on the receptor creating sites for STAT proteins to bind, which are in turn phosphorylated and activated by JAK proteins. By blocking JAK1 activity, many viruses block the host signal transduction pathway." [UniProtKB-KW:KW-1096, VZ:784]
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of a JAK-STAT signal cascade in a host organism by reducing the activity of host JAK1 (Janus Kinase 1)." [PMID:16188985]
synonym: "inhibition of host JAK activity by virus" NARROW [GOC:bf]
synonym: "negative regulation by virus of host JAK" EXACT [GOC:bf]
synonym: "negative regulation by virus of tyrosine phosphorylation of host STAT protein" NARROW [GOC:bf]
+synonym: "suppression by virus of host JAK1 activity" EXACT []
synonym: "suppression by virus of host janus kinase 1 activity" EXACT [PR:000009196]
synonym: "suppression by virus of tyrosine phosphorylation of host STAT protein" NARROW []
synonym: "viral inhibition of tyrosine phosphorylation of host STAT protein" NARROW [GOC:bf]
xref: VZ:784 "Inhibition of host JAK1 by virus"
-is_a: GO:0039512 ! suppression by virus of host protein tyrosine kinase activity
is_a: GO:0039514 ! suppression by virus of host JAK-STAT cascade
[Term]
@@ -221355,28 +221031,27 @@ is_obsolete: true
[Term]
id: GO:0039579
-name: suppression by virus of host ISG15 activity
+name: suppression by virus of host ISG15-protein conjugation
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ubiquitin-like protein ISG15 activity. ISG15 is a ubiquitin-like protein that is conjugated to lysine residues on various target proteins. Viruses escape from the antiviral activity of ISG15 by using different mechanisms; the influenza B virus NS1 protein for instance blocks the covalent linkage of ISG15 to its target proteins by directly interacting with ISG15. The papain-like protease from the coronavirus cleaves ISG15 derivatives." [PMID:11157743, PMID:18604270, UniProtKB-KW:KW-1095, VZ:723]
-xref: VZ:723 "Inhibition of host ISG15 by virus"
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host ubiquitin-like protein ISG15 conjugation to a susbtrate. ISG15 is a ubiquitin-like protein that is conjugated to lysine residues on various target proteins. Viruses escape from the antiviral activity of ISG15 by using different mechanisms; the influenza B virus NS1 protein for instance blocks the covalent linkage of ISG15 to its target proteins by directly interacting with ISG15. The papain-like protease from the coronavirus cleaves ISG15 derivatives." [PMID:11157743, PMID:18604270]
+synonym: "suppression by virus of host ISG15 activity" RELATED []
is_a: GO:0039503 ! suppression by virus of host innate immune response
-is_a: GO:0039507 ! suppression by virus of host molecular function
[Term]
id: GO:0039580
-name: suppression by virus of host PKR activity
+name: suppression by virus of host PKR signaling
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (protein kinase regulated by RNA) activity. Activation of PKR involves dsRNA binding followed by autophosphorylation. Phosphorylated PKR can then phosphorylate downstream targets such as the translation initiation factor eIF2 to inhibit protein synthesis. Viruses encode a number of mechanisms to inhibit the host antiviral response via PKR, including direct interaction with PKR, promoting degradation of PKR or altering the subcellular location of PKR." [PMID:15207627, UniProtKB-KW:KW-1102, VZ:554]
-synonym: "suppression by virus of host EIF2AK2 activity" EXACT [PR:000006959, UniProtKB-KW:KW-1102]
-xref: VZ:554 "Inhibition of host PKR by virus"
+def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (Protein Kinase regulated by RNA) signaling. Host PKR signaling includes targets such as the translation initiation factor eIF2alpha, inhibiting protein synthesis as an antiviral response." [PMID:15207627]
+synonym: "suppression by virus of host EIF2AK2 activity" NARROW []
+synonym: "suppression by virus of host PKR activity" NARROW []
+is_a: GO:0019057 ! modulation by virus of host translation
is_a: GO:0039503 ! suppression by virus of host innate immune response
-is_a: GO:0039584 ! suppression by virus of host protein kinase activity
[Term]
id: GO:0039581
name: obsolete suppression by virus of host PKR activity via double-stranded RNA binding
namespace: biological_process
-def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (protein kinase regulated by RNA) activity by interacting selectively and non-covalently with double-stranded RNA (dsRNA). Binding of viral proteins to RNA may sequester or alter the RNA so it can not be recognized by host PKR, or may compete with PKR for dsRNA binding." [PMID:7514679]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (protein kinase regulated by RNA) activity by binding to double-stranded RNA (dsRNA). Binding of viral proteins to RNA may sequester or alter the RNA so it can not be recognized by host PKR, or may compete with PKR for dsRNA binding." [PMID:7514679]
comment: The reason for obsoleting this term is that it is too specific. The exact molecular roles of the individual proteins should be captured separately.
synonym: "suppression by virus of host PKR activity by binding to dsRNA" EXACT [GOC:bf]
is_obsolete: true
@@ -221409,6 +221084,7 @@ namespace: biological_process
def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host protein kinase activity." [GOC:bf]
is_a: GO:0039513 ! suppression by virus of host catalytic activity
is_a: GO:0039613 ! suppression by virus of host protein phosphorylation
+is_a: GO:0043086 ! negative regulation of catalytic activity
[Term]
id: GO:0039585
@@ -221437,11 +221113,9 @@ is_a: GO:0039517 ! modulation by virus of host protein serine/threonine phosphat
id: GO:0039587
name: suppression by virus of host tetherin activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of host tetherin activity. Tetherin (also known as BST2) is an alpha interferon-inducible cellular factor that impairs the release of many enveloped viruses. By blocking tetherin activity, many viruses circumvent its antiviral effects." [PMID:22493439, UniProtKB-KW:KW-1084, VZ:665]
-synonym: "inhibition of host BST2/Tetherin by virus" EXACT [UniProtKB-KW:KW-1084]
-synonym: "suppression by virus of host BST-2 activity" EXACT [PMID:22493439]
-xref: VZ:665 "Inhibition of host tetherin by virus"
-is_a: GO:0039506 ! modulation by virus of host molecular function
+def: "Any process in which a virus stops, prevents, or reduces the activity of host tetherin activity. Tetherin (also known as BST2) is an alpha interferon-inducible cellular factor that impairs the release of many enveloped viruses. By blocking tetherin activity, many viruses circumvent its antiviral effects." [PMID:22493439]
+synonym: "inhibition of host BST2/Tetherin by virus" EXACT []
+is_a: GO:0019049 ! mitigation of host defenses by virus
[Term]
id: GO:0039588
@@ -221450,11 +221124,7 @@ namespace: biological_process
def: "Any viral process that inhibits a host antigen-presenting cell expressing a peptide antigen on its cell surface in association with an MHC protein complex." [UniProtKB-KW:KW-1117, VZ:815]
synonym: "inhibition of host proteasome antigen processing by virus" EXACT [UniProtKB-KW:KW-1117]
xref: VZ:815 "Inhibition of host proteasome antigen processing by virus"
-is_a: GO:0002578 ! negative regulation of antigen processing and presentation
-is_a: GO:0030683 ! mitigation of host immune response by virus
-is_a: GO:0050776 ! regulation of immune response
-is_a: GO:0050794 ! regulation of cellular process
-is_a: GO:0075528 ! modulation by virus of host immune response
+is_a: GO:0039504 ! suppression by virus of host adaptive immune response
[Term]
id: GO:0039589
@@ -221467,19 +221137,6 @@ xref: VZ:817 "Inhibition of host TAP by virus"
is_obsolete: true
consider: GO:0039588
-[Term]
-id: GO:0039591
-name: suppression by virus of host tapasin activity
-namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host tapasin (TAP binding protein/TAPBP) activity. Tapasin is a type I transmembrane protein essential for the optimal expression of stable MHC class I molecules on the host cell surface. By inhibiting host tapasin activity, viruses can prevent presentation of their antigens at the cell surface, and thereby evade the host anti-viral immune response." [UniProtKB-KW:KW-1108, VZ:818]
-comment: Consider also annotating to 'tapasin binding ; GO:0046980'.
-synonym: "inhibition of host tapasin by virus" EXACT [UniProtKB-KW:KW-1108]
-synonym: "inhibition of host TAPBP by virus" EXACT [UniProtKB-KW:KW-1108]
-synonym: "suppression by virus of host TAP binding protein" EXACT [HGNC:11566]
-xref: VZ:818 "Inhibition of host tapasin by virus"
-is_a: GO:0039507 ! suppression by virus of host molecular function
-is_a: GO:0046776 ! suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I
-
[Term]
id: GO:0039592
name: suppression by virus of G2/M transition of host mitotic cell cycle
@@ -221531,13 +221188,12 @@ is_a: GO:0035304 ! regulation of protein dephosphorylation
[Term]
id: GO:0039597
-name: induction by virus of host endoribonuclease activity
+name: obsolete induction by virus of host endoribonuclease activity
namespace: biological_process
-def: "Any viral process that activates or increases the frequency, rate or extent of host endoribonuclease activity." [PMID:22174690]
-comment: GO:0039597 should be used to annotate viral proteins which utilize a host RNase to induce endonucleolytic cleavage of mRNAs (e.g. the NSP1 protein of SARS coronavirus). For viral proteins that have endoribonuclease activity themselves, consider instead annotating to: 'endoribonuclease activity involved in viral induction of host mRNA catabolic process ; GO:0039594'.
+def: "OBSOLETE. Any viral process that activates or increases the frequency, rate or extent of host endoribonuclease activity." [PMID:22174690]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "viral induction of host RNAse activity" EXACT [GOC:bf]
-is_a: GO:0039600 ! induction by virus of host endonucleolytic cleavage-dependent mRNA catabolic process
-is_a: GO:0039712 ! induction by virus of host catalytic activity
+is_obsolete: true
[Term]
id: GO:0039598
@@ -221558,7 +221214,6 @@ def: "Any process in which a host pre-mRNA or mRNA molecule is cleaved at specif
synonym: "host mRNA cleavage by viral endoribonuclease" EXACT [GOC:bf]
synonym: "viral endoribonuclease activity involved in degradation of host mRNA" RELATED [GOC:bf]
is_a: GO:0019048 ! modulation by virus of host process
-is_a: GO:0044033 ! multi-organism metabolic process
[Term]
id: GO:0039600
@@ -221647,6 +221302,7 @@ synonym: "Inhibition of host translation factors by virus" BROAD [UniProtKB-KW:K
synonym: "suppression by virus of host EIF-4E activity" EXACT [GOC:bf]
is_a: GO:0039507 ! suppression by virus of host molecular function
is_a: GO:0039606 ! suppression by virus of host translation initiation
+is_a: GO:0043086 ! negative regulation of catalytic activity
[Term]
id: GO:0039612
@@ -221801,9 +221457,9 @@ is_a: GO:0019030 ! icosahedral viral capsid
id: GO:0039630
name: RNA translocase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded RNA molecule." [GOC:bm, PMID:22713318]
+def: "Generating a movement along a single- or double-stranded RNA molecule, driven by ATP hydrolysis." [GOC:bm, PMID:22713318]
comment: Note that some gene products that possess DNA translocase activity, such as members of the FtsK/SpoIIIE family, can be fixed in place by interactions with other components of the cell; the relative movement between the protein and DNA bound to it results in movement of the DNA within the cell, often across a membrane.
-is_a: GO:0008186 ! ATPase, acting on RNA
+is_a: GO:0008186 ! ATP-dependent activity, acting on RNA
[Term]
id: GO:0039631
@@ -221919,13 +221575,13 @@ is_a: GO:0033646 ! host intracellular part
[Term]
id: GO:0039644
-name: suppression by virus of host NF-kappaB transcription factor activity
+name: suppression by virus of host NF-kappaB cascade
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of host NF-kappaB activity." [UniProtKB-KW:KW-1100, VZ:695]
-synonym: "inhibition of host NF-kappa-B by virus" EXACT [UniProtKB-KW:KW-1100, VZ:695]
-xref: VZ:695 "Inhibition of host NF-kappa-B by virus"
-is_a: GO:0039507 ! suppression by virus of host molecular function
-is_a: GO:0039653 ! suppression by virus of host transcription
+def: "Any process in which a virus stops, prevents, or reduces a host NF-kappaB cascade." [PMID:10920188, PMID:25275128]
+synonym: "inhibition of host NF-kappa-B by virus" EXACT []
+synonym: "suppression by virus of host NF-kappaB transcription factor activity" RELATED []
+is_a: GO:0019049 ! mitigation of host defenses by virus
+is_a: GO:0019054 ! modulation by virus of host cellular process
[Term]
id: GO:0039645
@@ -221947,13 +221603,14 @@ is_a: GO:0060153 ! modulation by virus of host cell cycle
[Term]
id: GO:0039647
-name: suppression by virus of host poly(A)-binding protein activity
+name: obsolete suppression by virus of host poly(A)-binding protein activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host poly(A)-binding protein (PABP) activity. PABP binds to the poly(A) tail of mRNA to facilitate translation." [UniProtKB-KW:KW-1101]
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host poly(A)-binding protein (PABP) activity. PABP binds to the poly(A) tail of mRNA to facilitate translation." [UniProtKB-KW:KW-1101]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "inhibition of host poly(A)-binding protein by virus" EXACT [UniProtKB-KW:KW-1101]
synonym: "suppression by virus of host PABP activity" EXACT [Wikipedia:Poly(A)-binding_protein]
-is_a: GO:0039507 ! suppression by virus of host molecular function
-is_a: GO:0039604 ! suppression by virus of host translation
+is_obsolete: true
+consider: GO:0039604
[Term]
id: GO:0039648
@@ -221971,7 +221628,6 @@ namespace: biological_process
def: "The process in which a virus effects a change in host ubiquitin-protein ligase activity. Ubiquitin-protein ligase activity catalyzes the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine." [UniProtKB-KW:KW-1123]
synonym: "modulation of host E3 ubiquitin ligases by virus" NARROW [UniProtKB-KW:KW-1123]
is_a: GO:0039516 ! modulation by virus of host catalytic activity
-is_a: GO:1904666 ! regulation of ubiquitin protein ligase activity
[Term]
id: GO:0039650
@@ -221981,6 +221637,7 @@ def: "Any process in which a virus stops, prevents, or reduces the frequency, ra
synonym: "inhibition of host caspases by virus" NARROW [UniProtKB-KW:KW-1085, VZ:912]
is_a: GO:0019050 ! suppression by virus of host apoptotic process
is_a: GO:0039513 ! suppression by virus of host catalytic activity
+is_a: GO:0043086 ! negative regulation of catalytic activity
[Term]
id: GO:0039651
@@ -221990,18 +221647,17 @@ def: "Any process in which a virus increases the frequency, rate or extent of ho
synonym: "activation of host caspases by virus" NARROW [UniProtKB-KW:KW-1073]
synonym: "induction by virus of host caspase activity" NARROW [GOC:bf, GOC:jl]
is_a: GO:0019051 ! induction by virus of host apoptotic process
-is_a: GO:0039712 ! induction by virus of host catalytic activity
[Term]
id: GO:0039652
-name: activation by virus of host NF-kappaB transcription factor activity
+name: induction by virus of host NF-kappaB cascade
namespace: biological_process
-def: "Any process in which a virus starts, promotes, or enhances the activity of the host transcription factor NF-kappaB." [UniProtKB-KW:KW-1074]
+def: "Any process in which a virus starts, promotes, or enhances a host NF-kappaB cascade." [PMID:11907233, PMID:7845680]
+synonym: "activation by virus of host NF-kappaB transcription factor activity" RELATED []
synonym: "activation of host NF-kappa-B by virus" EXACT [UniProtKB-KW:KW-1074]
xref: VZ:841 "Activation of host NF-kappa-B by virus"
-is_a: GO:0019056 ! modulation by virus of host transcription
-is_a: GO:0039506 ! modulation by virus of host molecular function
-is_a: GO:0065009 ! regulation of molecular function
+is_a: GO:0019054 ! modulation by virus of host cellular process
+is_a: GO:0085033 ! induction by symbiont of host I-kappaB kinase/NF-kappaB cascade
[Term]
id: GO:0039653
@@ -222013,6 +221669,7 @@ synonym: "suppression by virus of host DNA-dependent transcription" EXACT [GOC:b
xref: VZ:1577 "Host transcription shutoff by virus"
is_a: GO:0019056 ! modulation by virus of host transcription
is_a: GO:0039657 ! suppression by virus of host gene expression
+is_a: GO:0050794 ! regulation of cellular process
[Term]
id: GO:0039654
@@ -222113,8 +221770,7 @@ def: "Merging of the virion membrane and a host membrane (host plasma membrane o
synonym: "fusion of virus membrane with host membrane" RELATED [UniProtKB-KW:KW-1168]
synonym: "fusion of virus membrane with host membrane during viral entry" RELATED [UniProtKB-KW:KW-1168]
synonym: "viral entry into host cell via membrane fusion" RELATED [GOC:bf, GOC:jl]
-is_a: GO:0044800 ! multi-organism membrane fusion
-relationship: part_of GO:0046718 ! viral entry into host cell
+is_a: GO:0016032 ! viral process
[Term]
id: GO:0039664
@@ -222441,7 +222097,7 @@ namespace: biological_process
def: "Fusion of a viral primary envelope with the host outer nuclear membrane during nuclear egress. The transitory primary envelope is acquired by the virus as it buds at the inner nuclear membrane and gains access to the perinuclear space. This membrane is lost by fusing with the host outer nuclear membrane during nuclear exit." [PMID:23057731, UniProtKB-KW:KW-1181]
synonym: "fusion of viral membrane with host outer nuclear membrane involved in nuclear egress" EXACT [GOC:bf]
synonym: "viral primary envelope fusion with host outer nuclear membrane" EXACT [UniProtKB-KW:KW-1181]
-is_a: GO:0044800 ! multi-organism membrane fusion
+is_a: GO:0016032 ! viral process
relationship: part_of GO:0046802 ! exit of virus from host cell nucleus by nuclear egress
[Term]
@@ -222495,7 +222151,7 @@ relationship: part_of GO:0019081 ! viral translation
id: GO:0039706
name: co-receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a coreceptor. A coreceptor acts in cooperation with a primary receptor to transmit a signal within the cell." [GOC:bf, GOC:jl]
+def: "Binding to a coreceptor. A coreceptor acts in cooperation with a primary receptor to transmit a signal within the cell." [GOC:bf, GOC:jl]
is_a: GO:0005515 ! protein binding
[Term]
@@ -222540,12 +222196,12 @@ is_a: GO:0039709 ! cytoplasmic capsid assembly
[Term]
id: GO:0039712
-name: induction by virus of host catalytic activity
+name: obsolete induction by virus of host catalytic activity
namespace: biological_process
-def: "Any viral process that activates or increases the frequency, rate or extent of host catalytic activity." [GOC:bf, GOC:jl]
+def: "OBSOLETE. Any viral process that activates or increases the frequency, rate or extent of host catalytic activity." [GOC:bf, GOC:jl]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "induction by virus of host enzyme activity" EXACT [GOC:bf, GOC:jl]
-is_a: GO:0039516 ! modulation by virus of host catalytic activity
-is_a: GO:0043948 ! induction by symbiont of host catalytic activity
+is_obsolete: true
[Term]
id: GO:0039713
@@ -222631,23 +222287,21 @@ is_a: GO:0039503 ! suppression by virus of host innate immune response
[Term]
id: GO:0039723
-name: suppression by virus of host TBK1 activity
+name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of the host serine/threonine kinase TBK1." [UniProtKB-KW:KW-1223]
-comment: When TBK1 acts as part of a TBK1-IKBKE-DDX3 complex, consider also annotating to: suppression by virus of host TBK1-IKBKE-DDX3 complex activity ; GO:0039659.
-synonym: "inhibition of host TBK1 by virus" EXACT [UniProtKB-KW:KW-1223]
-is_a: GO:0039503 ! suppression by virus of host innate immune response
-is_a: GO:0039584 ! suppression by virus of host protein kinase activity
+def: "Any process in which a virus stops, prevents, or reduces a viral-induced cytoplasmic pattern recognition receptor signaling pathway in a host organism by reducing the activity of a host serine/threonine kinase TBK1." [PMID:22171259, PMID:34084167]
+synonym: "inhibition of host TBK1 by virus" RELATED []
+synonym: "suppression by virus of host TBK1 activity" RELATED []
+is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
[Term]
id: GO:0039724
-name: suppression by virus of host IKBKE activity
+name: suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the activity of the host I-kappa-B kinase epsilon (IKBKE/IKK-epsilon/IKK-E)." [UniProtKB-KW:KW-1224]
-comment: When IKBKE acts as part of a TBK1-IKBKE-DDX3 complex, consider also annotating to: suppression by virus of host TBK1-IKBKE-DDX3 complex activity ; GO:0039659.
-synonym: "inhibition of host IKBKE by virus" EXACT [UniProtKB-KW:KW-1224]
-is_a: GO:0039503 ! suppression by virus of host innate immune response
-is_a: GO:0039507 ! suppression by virus of host molecular function
+def: "Any process in which a virus stops, prevents, or reduces a host viral-induced cytoplasmic pattern recognition receptor signaling pathway by reducing the activity of host I-kappa-B kinase epsilon (IKBKE/IKK-epsilon/IKK-E)." [PMID:19153231, PMID:22532683, PMID:24173023]
+synonym: "inhibition of host IKBKE by virus" RELATED []
+synonym: "suppression by virus of host IKBKE activity" RELATED []
+is_a: GO:0039537 ! suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway
[Term]
id: GO:0040001
@@ -222729,7 +222383,6 @@ def: "The increase in size or mass of an entire organism, a part of an organism
comment: See also the biological process term 'cell growth ; GO:0016049'.
subset: gocheck_do_not_annotate
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "growth pattern" RELATED []
@@ -222772,7 +222425,6 @@ name: locomotion
namespace: biological_process
def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
is_a: GO:0008150 ! biological_process
@@ -222949,17 +222601,19 @@ relationship: regulates GO:0040025 ! vulval development
id: GO:0040029
name: regulation of gene expression, epigenetic
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582]
+def: "A process that modulates the frequency, rate or extent of gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA. Once established, this regulation may be maintained over many cell divisions. It can also be heritable in the absence of the instigating signal." [PMID:10521337, PMID:11498582, PMID:22243696, PMID:34414474]
subset: goslim_plant
is_a: GO:0010468 ! regulation of gene expression
+relationship: part_of GO:0006325 ! chromatin organization
[Term]
id: GO:0040030
-name: regulation of molecular function, epigenetic
+name: obsolete regulation of molecular function, epigenetic
namespace: biological_process
-def: "Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:dph, GOC:ems, GOC:tb, PMID:10611975, PMID:11050225, PMID:11447696, PMID:11685242, PMID:11782551]
+def: "OBSOLETE. Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:dph, GOC:ems, GOC:tb, PMID:10611975, PMID:11050225, PMID:11447696, PMID:11685242, PMID:11782551]
+comment: This term was obsoleted because it is not an active process.
synonym: "regulation of protein activity, epigenetic" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0065009 ! regulation of molecular function
+is_obsolete: true
[Term]
id: GO:0040031
@@ -222980,15 +222634,16 @@ is_a: GO:0010171 ! body morphogenesis
[Term]
id: GO:0040033
-name: negative regulation of translation, ncRNA-mediated
+name: RNA-mediated gene silencing by inhibition of translation
namespace: biological_process
def: "Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein." [GOC:dph, GOC:ems, GOC:tb]
synonym: "down regulation of mRNA translation, ncRNA-mediated" EXACT []
synonym: "down-regulation of mRNA translation, ncRNA-mediated" EXACT []
synonym: "downregulation of mRNA translation, ncRNA-mediated" EXACT []
synonym: "inhibition of mRNA translation, ncRNA-mediated" NARROW []
+synonym: "negative regulation of translation, ncRNA-mediated" EXACT []
is_a: GO:0017148 ! negative regulation of translation
-is_a: GO:0045974 ! regulation of translation, ncRNA-mediated
+is_a: GO:0035194 ! post-transcriptional gene silencing by RNA
[Term]
id: GO:0040034
@@ -223110,7 +222765,7 @@ is_a: GO:0040021 ! hermaphrodite germ-line sex determination
id: GO:0042007
name: interleukin-18 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-18." [GOC:jl]
+def: "Binding to interleukin-18." [GOC:jl]
synonym: "IL-18 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -223127,7 +222782,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0042009
name: interleukin-15 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-15." [GOC:jl]
+def: "Binding to interleukin-15." [GOC:jl]
synonym: "IL-15 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -223144,7 +222799,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0042011
name: interleukin-16 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-16." [GOC:jl]
+def: "Binding to interleukin-16." [GOC:jl]
synonym: "IL-16 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -223161,7 +222816,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0042013
name: interleukin-19 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-19." [GOC:jl]
+def: "Binding to interleukin-19." [GOC:jl]
synonym: "IL-19 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -223178,7 +222833,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0042015
name: interleukin-20 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-20." [GOC:jl]
+def: "Binding to interleukin-20." [GOC:jl]
synonym: "IL-20 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -223195,7 +222850,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0042017
name: interleukin-22 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-22." [GOC:jl]
+def: "Binding to interleukin-22." [GOC:jl]
synonym: "IL-22 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -223212,7 +222867,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0042019
name: interleukin-23 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-23." [GOC:jl]
+def: "Binding to interleukin-23." [GOC:jl]
synonym: "IL-23 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -223229,7 +222884,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0042021
name: granulocyte macrophage colony-stimulating factor complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the granulocyte macrophage colony-stimulating factor complex." [GOC:ai]
+def: "Binding to a granulocyte macrophage colony-stimulating factor complex." [GOC:ai]
synonym: "GM-CSF complex binding" EXACT []
synonym: "GMC-SF complex binding" EXACT []
synonym: "granulocyte macrophage colony stimulating factor complex binding" EXACT []
@@ -223300,8 +222955,7 @@ name: ATPase inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents or reduces an ATP hydrolysis activity." [GOC:jl]
synonym: "adenosinetriphosphatase inhibitor" EXACT []
-is_a: GO:0004857 ! enzyme inhibitor activity
-is_a: GO:0060590 ! ATPase regulator activity
+is_a: GO:0140678 ! molecular function inhibitor activity
[Term]
id: GO:0042031
@@ -223373,7 +223027,7 @@ id: GO:0042043
name: neurexin family protein binding
namespace: molecular_function
alt_id: GO:0019963
-def: "Interacting selectively and non-covalently with neurexins, synaptic cell surface proteins related to latrotoxin receptor, laminin and agrin. Neurexins act as cell recognition molecules at nerve terminals." [GOC:curators, GOC:pr, PMID:18923512]
+def: "Binding to a neurexin, a synaptic cell surface protein related to latrotoxin receptor, laminin and agrin. Neurexins act as cell recognition molecules at nerve terminals." [GOC:curators, GOC:pr, PMID:18923512]
synonym: "neuroligin" RELATED []
is_a: GO:0005102 ! signaling receptor binding
@@ -223533,6 +223187,7 @@ id: GO:0042060
name: wound healing
namespace: biological_process
def: "The series of events that restore integrity to a damaged tissue, following an injury." [GOC:bf, PMID:15269788]
+subset: goslim_generic
xref: Wikipedia:Wound_healing
is_a: GO:0009611 ! response to wounding
@@ -224167,7 +223822,7 @@ is_a: GO:0044237 ! cellular metabolic process
id: GO:0042134
name: rRNA primary transcript binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an unprocessed ribosomal RNA transcript." [GOC:jl]
+def: "Binding to an unprocessed ribosomal RNA transcript." [GOC:jl]
synonym: "pre-rRNA binding" EXACT [PMID:3327689]
is_a: GO:0019843 ! rRNA binding
@@ -224326,7 +223981,7 @@ is_a: GO:0006310 ! DNA recombination
id: GO:0042153
name: obsolete RPTP-like protein binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with proteins with similar structure/function to receptor protein tyrosine phosphatases." [GOC:jl]
+def: "OBSOLETE. Binding to proteins with similar structure/function to receptor protein tyrosine phosphatases." [GOC:jl]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "receptor protein tyrosine phosphatase-like protein binding" EXACT []
synonym: "RPTP-like protein binding" EXACT []
@@ -224355,6 +224010,7 @@ id: GO:0042158
name: lipoprotein biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids." [ISBN:0198506732]
+subset: goslim_pombe
synonym: "lipoprotein anabolism" EXACT []
synonym: "lipoprotein biosynthesis" EXACT []
synonym: "lipoprotein formation" EXACT []
@@ -224392,7 +224048,7 @@ is_a: GO:0042160 ! lipoprotein modification
id: GO:0042162
name: telomeric DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end." [GOC:jl, SO:0000624]
+def: "Binding to a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end." [GOC:jl, SO:0000624]
synonym: "telomere binding" EXACT []
synonym: "telomeric repeat binding" EXACT []
is_a: GO:0043565 ! sequence-specific DNA binding
@@ -224401,7 +224057,7 @@ is_a: GO:0043565 ! sequence-specific DNA binding
id: GO:0042163
name: interleukin-12 beta subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the beta subunit of interleukin-12." [GOC:mah]
+def: "Binding to the beta subunit of interleukin-12." [GOC:mah]
synonym: "CLMFp40 binding" EXACT []
synonym: "IL-12B binding" EXACT []
synonym: "IL-12p40 binding" EXACT []
@@ -224412,7 +224068,7 @@ is_a: GO:0019972 ! interleukin-12 binding
id: GO:0042164
name: interleukin-12 alpha subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the alpha subunit of interleukin-12." [GOC:mah]
+def: "Binding to the alpha subunit of interleukin-12." [GOC:mah]
synonym: "CLMFp35 binding" EXACT []
synonym: "IL-12A binding" EXACT []
synonym: "IL-12p35 binding" EXACT []
@@ -224423,7 +224079,7 @@ is_a: GO:0019972 ! interleukin-12 binding
id: GO:0042165
name: neurotransmitter binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neurotransmitter, any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [ISBN:0198506732]
+def: "Binding to a neurotransmitter, any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." [ISBN:0198506732]
subset: goslim_pir
is_a: GO:0005488 ! binding
@@ -224431,7 +224087,7 @@ is_a: GO:0005488 ! binding
id: GO:0042166
name: acetylcholine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." [GOC:ai]
+def: "Binding to acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." [GOC:ai]
is_a: GO:0042165 ! neurotransmitter binding
is_a: GO:0043169 ! cation binding
@@ -224464,7 +224120,7 @@ is_a: GO:0042440 ! pigment metabolic process
id: GO:0042169
name: SH2 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class." [GOC:go_curators, Pfam:PF00017]
+def: "Binding to a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class." [GOC:go_curators, Pfam:PF00017]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -224554,7 +224210,17 @@ relationship: negatively_regulates GO:0030163 ! protein catabolic process
id: GO:0042178
name: xenobiotic catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide." [GOC:jl]
+alt_id: GO:0042737
+alt_id: GO:0042738
+def: "The chemical reactions and pathways resulting in the breakdown of a xenobiotic compound, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:jl, GOC:krc]
+synonym: "drug breakdown" RELATED []
+synonym: "drug catabolic process" RELATED []
+synonym: "drug catabolism" RELATED []
+synonym: "drug degradation" RELATED []
+synonym: "exogenous drug breakdown" RELATED []
+synonym: "exogenous drug catabolic process" RELATED []
+synonym: "exogenous drug catabolism" RELATED []
+synonym: "exogenous drug degradation" RELATED []
synonym: "xenobiotic breakdown" EXACT []
synonym: "xenobiotic catabolism" EXACT []
synonym: "xenobiotic degradation" EXACT []
@@ -225062,7 +224728,6 @@ synonym: "1-aminocyclopropane-1-carboxylate anabolism" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate biosynthesis" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate formation" EXACT []
synonym: "1-aminocyclopropane-1-carboxylate synthesis" EXACT []
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0018871 ! 1-aminocyclopropane-1-carboxylate metabolic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -225081,6 +224746,7 @@ synonym: "cellular modified amino acid catabolism" EXACT [GOC:mah]
synonym: "cellular modified amino acid degradation" EXACT [GOC:mah]
synonym: "modified amino acid catabolic process" EXACT [GOC:mah]
synonym: "modified amino acid catabolism" EXACT [GOC:mah]
+is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:1901565 ! organonitrogen compound catabolic process
[Term]
@@ -225228,7 +224894,7 @@ alt_id: GO:0042257
def: "The aggregation, arrangement and bonding together of the mature ribosome and of its subunits." [GOC:ma]
subset: goslim_yeast
synonym: "ribosomal subunit assembly" NARROW [GOC:mah, GOC:vw]
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
relationship: part_of GO:0042254 ! ribosome biogenesis
[Term]
@@ -225420,7 +225086,7 @@ is_a: GO:0019985 ! translesion synthesis
id: GO:0042277
name: peptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds." [GOC:jl]
+def: "Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds." [GOC:jl]
subset: goslim_chembl
subset: goslim_pir
is_a: GO:0033218 ! amide binding
@@ -225475,25 +225141,6 @@ xref: MetaCyc:RXN-5470
xref: RHEA:30635
is_a: GO:0046527 ! glucosyltransferase activity
-[Term]
-id: GO:0042282
-name: hydroxymethylglutaryl-CoA reductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: (R)-mevalonate + CoA + 2 NAD(+) = (S)-3-hydroxy-3-methylglutaryl-CoA + 2 H(+) + 2 NADH." [EC:1.1.1.88, RHEA:14833]
-synonym: "(R)-mevalonate:NAD+ oxidoreductase (CoA-acylating)" RELATED [EC:1.1.1.88]
-synonym: "3-hydroxy-3-methylglutaryl coenzyme A reductase activity" RELATED [EC:1.1.1.88]
-synonym: "3-hydroxy-3-methylglutaryl-coenzyme A reductase activity" BROAD [EC:1.1.1.88]
-synonym: "beta-hydroxy-beta-methylglutaryl CoA-reductase activity" BROAD [EC:1.1.1.88]
-synonym: "beta-hydroxy-beta-methylglutaryl coenzyme A reductase activity" BROAD [EC:1.1.1.88]
-synonym: "HMG-CoA reductase activity" BROAD [EC:1.1.1.88]
-synonym: "hydroxymethylglutaryl coenzyme A reductase activity" BROAD [EC:1.1.1.88]
-synonym: "hydroxymethylglutaryl-CoA reductase (NADH) activity" RELATED [EC:1.1.1.88]
-xref: EC:1.1.1.88
-xref: KEGG_REACTION:R02081
-xref: MetaCyc:HYDROXYMETHYLGLUTARYL-COA-REDUCTASE-RXN
-xref: RHEA:14833
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
-
[Term]
id: GO:0042283
name: dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase activity
@@ -225540,7 +225187,7 @@ is_a: GO:0016869 ! intramolecular transferase activity, transferring amino group
id: GO:0042287
name: MHC protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with major histocompatibility complex molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation." [GOC:jl]
+def: "Binding to a major histocompatibility complex molecule; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation." [GOC:jl]
comment: Note that this term does not include binding to the antigen peptide bound to the MHC protein, for this also annotate to 'peptide antigen binding ; GO:0042605' or one of its children.
synonym: "major histocompatibility complex binding" EXACT []
synonym: "major histocompatibility complex ligand" NARROW []
@@ -225550,7 +225197,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0042288
name: MHC class I protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation." [GOC:jl]
+def: "Binding to a major histocompatibility complex class I molecule; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation." [GOC:jl]
comment: Note that this term does not include binding to the antigen peptide bound to the MHC protein. Consider also annotating to the molecular function term 'peptide antigen binding ; GO:0042605' or one of its children.
synonym: "alpha-beta T cell receptor activity" RELATED []
synonym: "gamma-delta T cell receptor activity" RELATED []
@@ -225563,7 +225210,7 @@ is_a: GO:0042287 ! MHC protein binding
id: GO:0042289
name: MHC class II protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with major histocompatibility complex class II molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation." [GOC:jl]
+def: "Binding to a major histocompatibility complex class II molecule; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation." [GOC:jl]
comment: Note that this term does not include binding to the antigen peptide bound to the MHC protein. Consider also annotating to the molecular function term 'peptide antigen binding ; GO:0042605' or one of its children.
synonym: "major histocompatibility complex class II binding" EXACT []
synonym: "major histocompatibility complex class II ligand" NARROW []
@@ -225655,7 +225302,7 @@ is_a: GO:0031559 ! oxidosqualene cyclase activity
id: GO:0042301
name: phosphate ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphate." [GOC:jl]
+def: "Binding to a phosphate ion." [GOC:jl]
is_a: GO:0043168 ! anion binding
[Term]
@@ -225794,7 +225441,7 @@ is_a: GO:0008277 ! regulation of G protein-coupled receptor signaling pathway
id: GO:0042314
name: bacteriochlorophyll binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants." [ISBN:0192800981]
+def: "Binding to bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants." [ISBN:0192800981]
is_a: GO:0016168 ! chlorophyll binding
[Term]
@@ -225927,7 +225574,7 @@ relationship: negatively_regulates GO:0042748 ! circadian sleep/wake cycle, non-
id: GO:0042324
name: hypocretin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the hypocretin receptor." [GOC:ceb, PMID:11988773]
+def: "Binding to a hypocretin receptor." [GOC:ceb, PMID:11988773]
synonym: "hypocretin receptor ligand" NARROW []
synonym: "orexin receptor binding" EXACT []
synonym: "orexin receptor ligand" NARROW []
@@ -226267,11 +225914,9 @@ synonym: "thiamine pyrophosphate metabolic process" EXACT []
synonym: "thiamine pyrophosphate metabolism" EXACT []
synonym: "TPP metabolic process" EXACT []
synonym: "TPP metabolism" EXACT []
-is_a: GO:0006725 ! cellular aromatic compound metabolic process
-is_a: GO:0006790 ! sulfur compound metabolic process
is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
-is_a: GO:0072527 ! pyrimidine-containing compound metabolic process
+is_a: GO:0042723 ! thiamine-containing compound metabolic process
[Term]
id: GO:0042358
@@ -226289,11 +225934,9 @@ synonym: "thiamine pyrophosphate catabolic process" EXACT []
synonym: "thiamine pyrophosphate catabolism" EXACT []
synonym: "TPP catabolic process" EXACT []
synonym: "TPP catabolism" EXACT []
-is_a: GO:0019439 ! aromatic compound catabolic process
is_a: GO:0042357 ! thiamine diphosphate metabolic process
-is_a: GO:0044273 ! sulfur compound catabolic process
+is_a: GO:0042725 ! thiamine-containing compound catabolic process
is_a: GO:0046434 ! organophosphate catabolic process
-is_a: GO:0072529 ! pyrimidine-containing compound catabolic process
[Term]
id: GO:0042359
@@ -226485,6 +226128,7 @@ synonym: "vitamin K formation" EXACT []
synonym: "vitamin K synthesis" EXACT []
is_a: GO:0042362 ! fat-soluble vitamin biosynthetic process
is_a: GO:0042373 ! vitamin K metabolic process
+is_a: GO:1901663 ! quinone biosynthetic process
[Term]
id: GO:0042372
@@ -226504,8 +226148,8 @@ synonym: "phytylmenaquinone biosynthetic process" EXACT []
synonym: "vitamin K1 biosynthesis" EXACT []
synonym: "vitamin K1 biosynthetic process" EXACT []
xref: MetaCyc:PWY-5027
+is_a: GO:0042371 ! vitamin K biosynthetic process
is_a: GO:0042374 ! phylloquinone metabolic process
-is_a: GO:1901663 ! quinone biosynthetic process
[Term]
id: GO:0042373
@@ -226516,6 +226160,7 @@ synonym: "naphthoquinone metabolic process" BROAD []
synonym: "naphthoquinone metabolism" BROAD []
synonym: "vitamin K metabolism" EXACT []
is_a: GO:0006775 ! fat-soluble vitamin metabolic process
+is_a: GO:1901661 ! quinone metabolic process
[Term]
id: GO:0042374
@@ -226531,7 +226176,7 @@ synonym: "phytylmenaquinone metabolic process" EXACT []
synonym: "phytylmenaquinone metabolism" EXACT []
synonym: "vitamin K1 metabolic process" EXACT []
synonym: "vitamin K1 metabolism" EXACT []
-is_a: GO:1901661 ! quinone metabolic process
+is_a: GO:0042373 ! vitamin K metabolic process
[Term]
id: GO:0042376
@@ -226550,7 +226195,7 @@ synonym: "phytylmenaquinone catabolism" EXACT []
synonym: "vitamin K1 catabolic process" EXACT []
synonym: "vitamin K1 catabolism" EXACT []
is_a: GO:0042374 ! phylloquinone metabolic process
-is_a: GO:1901662 ! quinone catabolic process
+is_a: GO:0042377 ! vitamin K catabolic process
[Term]
id: GO:0042377
@@ -226564,12 +226209,13 @@ synonym: "vitamin K catabolism" EXACT []
synonym: "vitamin K degradation" EXACT []
is_a: GO:0042363 ! fat-soluble vitamin catabolic process
is_a: GO:0042373 ! vitamin K metabolic process
+is_a: GO:1901662 ! quinone catabolic process
[Term]
id: GO:0042379
name: chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any chemokine receptor." [GOC:ai]
+def: "Binding to a chemokine receptor." [GOC:ai]
synonym: "chemokine receptor ligand" NARROW []
is_a: GO:0001664 ! G protein-coupled receptor binding
is_a: GO:0005126 ! cytokine receptor binding
@@ -226682,7 +226328,7 @@ is_a: GO:0042577 ! lipid phosphatase activity
id: GO:0042393
name: histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity." [GOC:jl]
+def: "Binding to a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity." [GOC:jl]
subset: goslim_chembl
subset: goslim_drosophila
subset: goslim_generic
@@ -226749,6 +226395,7 @@ synonym: "cellular modified amino acid anabolism" EXACT [GOC:mah]
synonym: "cellular modified amino acid biosynthesis" EXACT [GOC:mah]
synonym: "cellular modified amino acid formation" EXACT [GOC:mah]
synonym: "cellular modified amino acid synthesis" EXACT [GOC:mah]
+is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
@@ -227249,6 +226896,7 @@ id: GO:0042440
name: pigment metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving pigment, any general or particular coloring matter in living organisms, e.g. melanin." [GOC:jl, ISBN:0198506732]
+subset: goslim_drosophila
subset: goslim_pir
synonym: "pigment metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
@@ -227741,17 +227389,6 @@ synonym: "gamma-delta T-lymphocyte differentiation" EXACT []
is_a: GO:0030217 ! T cell differentiation
is_a: GO:0046629 ! gamma-delta T cell activation
-[Term]
-id: GO:0042493
-name: response to drug
-namespace: biological_process
-alt_id: GO:0017035
-def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease." [GOC:jl]
-subset: goslim_candida
-synonym: "drug resistance" RELATED []
-synonym: "drug susceptibility/resistance" RELATED []
-is_a: GO:0042221 ! response to chemical
-
[Term]
id: GO:0042494
name: detection of bacterial lipoprotein
@@ -227794,7 +227431,7 @@ is_a: GO:0071724 ! response to diacyl bacterial lipopeptide
id: GO:0042497
name: triacyl lipopeptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lipopeptide containing a nonprotein moiety consisting of three acyl groups." [GOC:add, PMID:12077222, PMID:12524386, PMID:2757794]
+def: "Binding to a lipopeptide containing a nonprotein moiety consisting of three acyl groups." [GOC:add, PMID:12077222, PMID:12524386, PMID:2757794]
comment: Note that bacterial lipopeptides are derived from bacterial lipoproteins, but the two terms are sometimes used interchangeably in the literature.
synonym: "bacterial triacyl lipopeptide binding" NARROW [GOC:add]
synonym: "bacterial triacyl lipoprotein binding" RELATED [GOC:add]
@@ -227805,7 +227442,7 @@ is_a: GO:0071723 ! lipopeptide binding
id: GO:0042498
name: diacyl lipopeptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lipopeptide containing a nonprotein moiety consisting of two acyl groups." [GOC:add, PMID:12077222, PMID:12524386, PMID:2757794]
+def: "Binding to a lipopeptide containing a nonprotein moiety consisting of two acyl groups." [GOC:add, PMID:12077222, PMID:12524386, PMID:2757794]
comment: Note that bacterial lipopeptides are derived from bacterial lipoproteins, but the two terms are sometimes used interchangeably in the literature.
synonym: "bacterial diacyl lipopeptide binding" NARROW [GOC:add]
synonym: "bacterial diacyl lipoprotein binding" RELATED [GOC:add]
@@ -228244,7 +227881,7 @@ is_a: GO:0031559 ! oxidosqualene cyclase activity
id: GO:0042562
name: hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of cells possessing functional receptors for the hormone. Hormones may be produced by the same, or different, cell as express the receptor." [GOC:jl]
+def: "Binding to an hormone, a naturally occurring substance secreted by specialized cells that affect the metabolism or behavior of cells possessing functional receptors for the hormone. Hormones may be produced by the same, or different, cell as express the receptor." [GOC:jl]
subset: goslim_chembl
subset: goslim_pir
is_a: GO:0005488 ! binding
@@ -228322,6 +227959,7 @@ xref: Wikipedia:Retinol
is_a: GO:0001523 ! retinoid metabolic process
is_a: GO:0034308 ! primary alcohol metabolic process
is_a: GO:0034754 ! cellular hormone metabolic process
+is_a: GO:0120254 ! olefinic compound metabolic process
[Term]
id: GO:0042573
@@ -228502,7 +228140,6 @@ alt_id: GO:0032846
def: "Any biological process involved in the maintenance of an internal steady state." [GOC:jl, ISBN:0395825172]
subset: goslim_agr
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_mouse
synonym: "activation of homeostatic process" NARROW []
synonym: "homeostasis" EXACT []
@@ -228637,7 +228274,7 @@ name: peptide antigen binding
namespace: molecular_function
alt_id: GO:0042606
alt_id: GO:0042607
-def: "Interacting selectively and non-covalently with an antigen peptide." [GOC:add, GOC:jl, GOC:rv]
+def: "Binding to an antigen peptide." [GOC:add, GOC:jl, GOC:rv]
comment: Note that this term can be used to describe the binding of a peptide to an MHC molecule.
subset: goslim_chembl
synonym: "endogenous peptide antigen binding" NARROW []
@@ -228649,7 +228286,7 @@ is_a: GO:0042277 ! peptide binding
id: GO:0042608
name: T cell receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a T cell receptor, the antigen-recognizing receptor on the surface of T cells." [GOC:jl]
+def: "Binding to a T cell receptor, the antigen-recognizing receptor on the surface of T cells." [GOC:jl]
synonym: "T lymphocyte receptor binding" EXACT []
synonym: "T-cell receptor binding" EXACT []
synonym: "T-lymphocyte receptor binding" EXACT []
@@ -228661,14 +228298,14 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:0042609
name: CD4 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CD4, a receptor found on the surface of T cells, monocytes and macrophages." [GOC:jl, MSH:D015704]
+def: "Binding to a CD4, a receptor found on the surface of T cells, monocytes and macrophages." [GOC:jl, MSH:D015704]
is_a: GO:0005102 ! signaling receptor binding
[Term]
id: GO:0042610
name: CD8 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CD8, a receptor found on the surface of thymocytes and cytotoxic and suppressor T-lymphocytes." [GOC:jl, MSH:D016827]
+def: "Binding to a CD8, a receptor found on the surface of thymocytes and cytotoxic and suppressor T-lymphocytes." [GOC:jl, MSH:D016827]
is_a: GO:0005102 ! signaling receptor binding
[Term]
@@ -228698,7 +228335,7 @@ is_a: GO:0042611 ! MHC protein complex
id: GO:0042614
name: CD70 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CD70, a receptor found on the surface of most activated B cells and some activated T cells." [GOC:jl, ISBN:0120781859]
+def: "Binding to a CD70, a receptor found on the surface of most activated B cells and some activated T cells." [GOC:jl, ISBN:0120781859]
synonym: "CD27 receptor activity" RELATED []
synonym: "CD27L binding" EXACT []
is_a: GO:0005102 ! signaling receptor binding
@@ -228707,7 +228344,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0042615
name: CD154 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with CD154, a receptor found on the surface of some activated lymphocytes." [GOC:jl, ISBN:0120781859]
+def: "Binding to CD154, a receptor found on the surface of some activated lymphocytes." [GOC:jl, ISBN:0120781859]
synonym: "CD40 receptor activity" RELATED []
synonym: "CD40L binding" EXACT []
is_a: GO:0005102 ! signaling receptor binding
@@ -228716,7 +228353,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0042616
name: paclitaxel metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving paclitaxel, an alkaloid compound used as an anticancer treatment." [GOC:jl]
+def: "The chemical reactions and pathways involving paclitaxel, a tetracyclic diterpenoid isolated originally from the bark of the Pacific yew tree, Taxus brevifolia." [GOC:jl, GOC:krc]
synonym: "paclitaxel metabolism" EXACT []
synonym: "taxol metabolic process" NARROW []
synonym: "taxol metabolism" NARROW []
@@ -228727,7 +228364,7 @@ is_a: GO:0034641 ! cellular nitrogen compound metabolic process
id: GO:0042617
name: paclitaxel biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of paclitaxel, an alkaloid compound used as an anticancer treatment." [GOC:jl]
+def: "The chemical reactions and pathways resulting in the formation of paclitaxel, a tetracyclic diterpenoid isolated originally from the bark of the Pacific yew tree, Taxus brevifolia." [GOC:jl, GOC:krc]
synonym: "paclitaxel anabolism" EXACT []
synonym: "paclitaxel biosynthesis" EXACT []
synonym: "paclitaxel formation" EXACT []
@@ -228833,7 +228470,7 @@ xref: Reactome:R-HSA-2161538 "abacavir [cytosol] + ATP + H2O => abacavir[extrace
xref: Reactome:R-HSA-9033499 "PEX1:PEX6:PEX26:ZFAND6 dissociates Ub:PEX5L and PEX7 from PEX14:PEX13:PEX2:PEX10:PEX12 and translocates PEX5L and PEX7 from the peroxisomal membrane to the cytosol"
xref: Reactome:R-HSA-9033505 "PEX1:PEX6:PEX26:ZFAND6:Ub:PEX5S,L:PEX14:PEX13:PEX2:PEX10:PEX12 dissociates yielding cytosolic Ub:PEX5S,L and membrane PEX14:PEX13:PEX2:PEX10:PEX12"
is_a: GO:0015399 ! primary active transmembrane transporter activity
-is_a: GO:0016887 ! ATPase
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0042627
@@ -229103,13 +228740,15 @@ is_a: GO:0004930 ! G protein-coupled receptor activity
[Term]
id: GO:0042655
-name: activation of JNKKK activity
+name: obsolete activation of JNKKK activity
namespace: biological_process
-def: "The initiation of the activity of the inactive enzyme JUN kinase kinase kinase (JNKKK) activity." [GOC:bf]
+def: "OBSOLETE. The initiation of the activity of the inactive enzyme JUN kinase kinase kinase (JNKKK) activity." [GOC:bf]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of JUN kinase kinase kinase activity" EXACT []
synonym: "positive regulation of JUNKKK activity" BROAD []
-is_a: GO:0000185 ! activation of MAPKKK activity
-relationship: part_of GO:0007254 ! JNK cascade
+is_obsolete: true
+consider: GO:0007254
+consider: GO:0043539
[Term]
id: GO:0042656
@@ -229123,7 +228762,7 @@ is_a: GO:0008349 ! MAP kinase kinase kinase kinase activity
id: GO:0042657
name: MHC class II protein binding, via lateral surface
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the lateral surface of major histocompatibility complex class II molecules." [GOC:jl]
+def: "Binding to the lateral surface of major histocompatibility complex class II molecules." [GOC:jl]
synonym: "major histocompatibility complex class II protein binding, via lateral surface" EXACT []
is_a: GO:0042289 ! MHC class II protein binding
@@ -229131,7 +228770,7 @@ is_a: GO:0042289 ! MHC class II protein binding
id: GO:0042658
name: MHC class II protein binding, via antigen binding groove
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the antigen binding groove of major histocompatibility complex class II molecules." [GOC:jl]
+def: "Binding to the antigen binding groove of major histocompatibility complex class II molecules." [GOC:jl]
synonym: "major histocompatibility complex class II protein binding, via antigen binding groove" EXACT []
is_a: GO:0042289 ! MHC class II protein binding
relationship: part_of GO:0023026 ! MHC class II protein complex binding
@@ -229259,7 +228898,6 @@ name: regulation of inner ear auditory receptor cell fate specification
namespace: biological_process
def: "Any process that mediates the specification of a cell into an auditory hair cell." [GOC:go_curators]
synonym: "regulation of auditory hair cell fate specification" EXACT []
-synonym: "regulation of inner ear auditory receptor cell fate specification" RELATED []
is_a: GO:0042659 ! regulation of cell fate specification
is_a: GO:0045607 ! regulation of inner ear auditory receptor cell differentiation
relationship: regulates GO:0042667 ! auditory receptor cell fate specification
@@ -229580,7 +229218,7 @@ replaced_by: GO:0004175
id: GO:0042709
name: succinate-CoA ligase complex
namespace: cellular_component
-def: "A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP or GTP." [EC:6.2.1.4, EC:6.2.1.5, GOC:jl]
+def: "A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP or GTP." [GOC:jl, PMID:10671455]
is_a: GO:0045239 ! tricarboxylic acid cycle enzyme complex
is_a: GO:1902494 ! catalytic complex
@@ -229624,7 +229262,7 @@ id: GO:0042714
name: dosage compensation complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins on DNA or RNA to form the complex that mediates dosage compensation on one or more X chromosomes." [GOC:jl, PMID:11102361, PMID:12672493]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0007549 ! dosage compensation
[Term]
@@ -229842,7 +229480,7 @@ is_a: GO:0030195 ! negative regulation of blood coagulation
id: GO:0042731
name: PH domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a PH domain (pleckstrin homology) of a protein, a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton." [GOC:jl, Pfam:PF00169]
+def: "Binding to a PH domain (pleckstrin homology) of a protein, a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton." [GOC:jl, Pfam:PF00169]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -229896,37 +229534,16 @@ xref: RHEA:12260
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
-[Term]
-id: GO:0042737
-name: drug catabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a drug, a substance used in the diagnosis, treatment or prevention of a disease." [GOC:go_curators]
-synonym: "drug breakdown" EXACT []
-synonym: "drug catabolism" EXACT []
-synonym: "drug degradation" EXACT []
-is_a: GO:0017144 ! drug metabolic process
-is_a: GO:0044248 ! cellular catabolic process
-
-[Term]
-id: GO:0042738
-name: exogenous drug catabolic process
-namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a drug that has originated externally to the cell or organism." [GOC:jl]
-synonym: "exogenous drug breakdown" EXACT []
-synonym: "exogenous drug catabolism" EXACT []
-synonym: "exogenous drug degradation" EXACT []
-is_a: GO:0042737 ! drug catabolic process
-relationship: part_of GO:0042493 ! response to drug
-
[Term]
id: GO:0042739
-name: endogenous drug catabolic process
+name: obsolete endogenous drug catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of a drug that has originated internally within the cell or organism." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of a drug that has originated internally within the cell or organism." [GOC:jl]
+comment: The reason for obsoletion is that there is no evidence that this process exists as a drug is by definition exogenous.
synonym: "endogenous drug breakdown" EXACT []
synonym: "endogenous drug catabolism" EXACT []
synonym: "endogenous drug degradation" EXACT []
-is_a: GO:0042737 ! drug catabolic process
+is_obsolete: true
[Term]
id: GO:0042740
@@ -229937,7 +229554,7 @@ synonym: "exogenous antibiotic breakdown" EXACT []
synonym: "exogenous antibiotic catabolism" EXACT []
synonym: "exogenous antibiotic degradation" EXACT []
is_a: GO:0017001 ! antibiotic catabolic process
-is_a: GO:0042738 ! exogenous drug catabolic process
+is_a: GO:0042178 ! xenobiotic catabolic process
relationship: part_of GO:0046677 ! response to antibiotic
[Term]
@@ -229949,7 +229566,6 @@ synonym: "endogenous antibiotic breakdown" EXACT []
synonym: "endogenous antibiotic catabolism" EXACT []
synonym: "endogenous antibiotic degradation" EXACT []
is_a: GO:0017001 ! antibiotic catabolic process
-is_a: GO:0042739 ! endogenous drug catabolic process
[Term]
id: GO:0042742
@@ -230041,7 +229657,6 @@ namespace: biological_process
def: "Any process in which an organism enters and maintains a period of dormancy in which to pass the winter. It is characterized by narcosis and by sharp reduction in body temperature and metabolic activity and by a depression of vital signs." [GOC:jl, PMID:1945046]
xref: Wikipedia:Hibernation
is_a: GO:0022611 ! dormancy process
-is_a: GO:0030431 ! sleep
[Term]
id: GO:0042751
@@ -230051,7 +229666,6 @@ def: "Any process in which an organism enters and maintains a period of dormancy
synonym: "aestivation" EXACT [GOC:pr]
xref: Wikipedia:Estivation
is_a: GO:0022611 ! dormancy process
-is_a: GO:0030431 ! sleep
[Term]
id: GO:0042752
@@ -230204,7 +229818,6 @@ name: nucleosome mobilization
namespace: biological_process
def: "The movement of nucleosomes along a DNA fragment." [PMID:12006495]
synonym: "nucleosome sliding" EXACT [GOC:dph]
-is_a: GO:0006338 ! chromatin remodeling
is_a: GO:0034728 ! nucleosome organization
[Term]
@@ -230225,13 +229838,16 @@ is_a: GO:0008395 ! steroid hydroxylase activity
[Term]
id: GO:0042769
-name: DNA damage response, detection of DNA damage
+name: obsolete DNA damage response, detection of DNA damage
namespace: biological_process
-def: "The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal." [GOC:go_curators]
+def: "OBSOLETE. The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal." [GOC:go_curators]
+comment: This term has been obsoleted because it represents a molecular function.
synonym: "detection of DNA damage during DNA damage response" EXACT []
synonym: "DNA damage response, perception of DNA damage" RELATED []
-is_a: GO:0006974 ! cellular response to DNA damage stimulus
-is_a: GO:0051606 ! detection of stimulus
+is_obsolete: true
+consider: GO:0006281
+consider: GO:0140612
+consider: GO:0140664
[Term]
id: GO:0042770
@@ -230289,8 +229905,8 @@ name: mitochondrial ATP synthesis coupled proton transport
namespace: biological_process
def: "The transport of protons across a mitochondrial membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis." [GOC:mtg_sensu, ISBN:0716731363]
synonym: "mitochondrial proton transport" BROAD []
+is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0015986 ! ATP synthesis coupled proton transport
-is_a: GO:0046907 ! intracellular transport
is_a: GO:1990542 ! mitochondrial transmembrane transport
relationship: part_of GO:0006119 ! oxidative phosphorylation
@@ -230332,7 +229948,7 @@ is_a: GO:0043628 ! ncRNA 3'-end processing
id: GO:0042781
name: 3'-tRNA processing endoribonuclease activity
namespace: molecular_function
-def: "Catalysis of the endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule." [EC:3.1.26.11]
+def: "Catalysis of the endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule." [PMID:12032089, PMID:21208191]
synonym: "3 tRNase activity" RELATED [EC:3.1.26.11]
synonym: "3' tRNA processing endoribonuclease activity" EXACT []
synonym: "3' tRNase activity" EXACT []
@@ -230341,8 +229957,10 @@ synonym: "RNase Z activity" BROAD []
synonym: "tRNA 3 endonuclease activity" RELATED [EC:3.1.26.11]
synonym: "tRNA 3' endonuclease activity" EXACT []
synonym: "tRNAse Z" RELATED [EC:3.1.26.11]
+xref: EC:3.1.26.11
xref: MetaCyc:3.1.26.11-RXN
is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
+is_a: GO:0140101 ! catalytic activity, acting on a tRNA
[Term]
id: GO:0042783
@@ -230557,7 +230175,7 @@ is_obsolete: true
id: GO:0042802
name: identical protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an identical protein or proteins." [GOC:jl]
+def: "Binding to an identical protein or proteins." [GOC:jl]
subset: goslim_chembl
synonym: "isoform-specific homophilic binding" EXACT [PMID:17889655]
synonym: "protein homopolymerization" RELATED []
@@ -230567,7 +230185,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0042803
name: protein homodimerization activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an identical protein to form a homodimer." [GOC:jl]
+def: "Binding to an identical protein to form a homodimer." [GOC:jl]
subset: goslim_chembl
synonym: "dimerization activity" BROAD []
is_a: GO:0042802 ! identical protein binding
@@ -230589,7 +230207,7 @@ id: GO:0042805
name: actinin binding
namespace: molecular_function
alt_id: GO:0051406
-def: "Interacting selectively and non-covalently with actinin, any member of a family of proteins that crosslink F-actin." [GOC:jl, ISBN:0198506732]
+def: "Binding to actinin, any member of a family of proteins that crosslink F-actin." [GOC:jl, ISBN:0198506732]
synonym: "beta-actinin binding" NARROW []
synonym: "capZ binding" EXACT []
is_a: GO:0008092 ! cytoskeletal protein binding
@@ -230598,7 +230216,7 @@ is_a: GO:0008092 ! cytoskeletal protein binding
id: GO:0042806
name: fucose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with fucose, the pentose 6-deoxygalactose." [ISBN:0582227089]
+def: "Binding to fucose, the pentose 6-deoxygalactose." [ISBN:0582227089]
is_a: GO:0048029 ! monosaccharide binding
[Term]
@@ -230612,7 +230230,7 @@ is_a: GO:0000325 ! plant-type vacuole
id: GO:0042808
name: obsolete neuronal Cdc2-like kinase binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with neuronal Cdc2-like kinase, an enzyme involved in the regulation of neuronal differentiation and neuro-cytoskeleton dynamics." [GOC:jl, PMID:10721722]
+def: "OBSOLETE. Binding to neuronal Cdc2-like kinase, an enzyme involved in the regulation of neuronal differentiation and neuro-cytoskeleton dynamics." [GOC:jl, PMID:10721722]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "neuronal Cdc2-like kinase binding" EXACT []
is_obsolete: true
@@ -230622,7 +230240,7 @@ replaced_by: GO:0019901
id: GO:0042809
name: vitamin D receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes." [GOC:jl, PMID:12637589]
+def: "Binding to a vitamin D receptor, a nuclear receptor that mediates the action of vitamin D by binding DNA and controlling the transcription of hormone-sensitive genes." [GOC:jl, PMID:12637589]
synonym: "calciferol receptor binding" NARROW []
synonym: "VDR binding" EXACT []
is_a: GO:0016922 ! nuclear receptor binding
@@ -230830,7 +230448,7 @@ relationship: part_of GO:0042824 ! MHC class I peptide loading complex
id: GO:0042826
name: histone deacetylase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme histone deacetylase." [GOC:jl]
+def: "Binding to histone deacetylase." [GOC:jl]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -230871,7 +230489,7 @@ is_a: GO:0005539 ! glycosaminoglycan binding
id: GO:0042835
name: BRE binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the RNA element BRE (Bruno response element)." [PMID:10893231]
+def: "Binding to a BRE RNA element (Bruno response element)." [PMID:10893231]
is_a: GO:0003723 ! RNA binding
[Term]
@@ -231613,8 +231231,10 @@ is_a: GO:0005345 ! purine nucleobase transmembrane transporter activity
id: GO:0042908
name: xenobiotic transport
namespace: biological_process
-def: "The directed movement of a xenobiotic, a compound foreign to living organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:go_curators]
+alt_id: GO:0015893
+def: "The directed movement of a xenobiotic into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A xenobiotic is a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators, GOC:krc]
subset: goslim_pir
+synonym: "drug transport" RELATED []
is_a: GO:0006810 ! transport
[Term]
@@ -231622,7 +231242,6 @@ id: GO:0042909
name: acridine transport
namespace: biological_process
def: "The directed movement of acridine (10-azaanthracene), a heterocyclic ring compound found in crude coal-tar anthracene, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, Wikipedia:Acridine]
-is_a: GO:0042908 ! xenobiotic transport
is_a: GO:0071702 ! organic substance transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -231635,7 +231254,7 @@ alt_id: GO:0015239
alt_id: GO:0015559
alt_id: GO:0015564
alt_id: GO:0090484
-def: "Enables the directed movement of a xenobiotic from one side of a membrane to the other. A xenobiotic is a compound foreign the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators]
+def: "Enables the directed movement of a xenobiotic from one side of a membrane to the other. A xenobiotic is a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators, GOC:krc]
subset: goslim_metagenomics
synonym: "drug transmembrane transporter activity" RELATED []
synonym: "drug transporter activity" RELATED []
@@ -231688,7 +231307,6 @@ namespace: biological_process
def: "The directed movement of an alkanesulfonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Alkanesulfonates are organic esters or salts of sulfonic acid containing an aliphatic hydrocarbon radical." [GOC:jl]
synonym: "alkanesulphonate transport" EXACT []
is_a: GO:0015711 ! organic anion transport
-is_a: GO:0042908 ! xenobiotic transport
[Term]
id: GO:0042919
@@ -231697,7 +231315,6 @@ namespace: biological_process
def: "The directed movement of benzoate, the anion of benzoic acid (benzenecarboxylic acid) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0721662544]
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015849 ! organic acid transport
-is_a: GO:0042908 ! xenobiotic transport
[Term]
id: GO:0042920
@@ -231710,7 +231327,6 @@ synonym: "m-hydroxyphenylpropionic acid transport" EXACT []
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0015849 ! organic acid transport
is_a: GO:0015850 ! organic hydroxy compound transport
-is_a: GO:0042908 ! xenobiotic transport
[Term]
id: GO:0042921
@@ -231724,7 +231340,7 @@ is_a: GO:0031958 ! corticosteroid receptor signaling pathway
id: GO:0042922
name: neuromedin U receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with one or more specific sites on a neuromedin U receptor." [GOC:jl, PMID:10899166]
+def: "Binding to one or more specific sites on a neuromedin U receptor." [GOC:jl, PMID:10899166]
is_a: GO:0071855 ! neuropeptide receptor binding
[Term]
@@ -232191,7 +231807,7 @@ is_a: GO:0008422 ! beta-glucosidase activity
id: GO:0042974
name: retinoic acid receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily." [GOC:jl, PMID:12476796]
+def: "Binding to a retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily." [GOC:jl, PMID:12476796]
synonym: "RAR binding" EXACT []
is_a: GO:0016922 ! nuclear receptor binding
@@ -232199,7 +231815,7 @@ is_a: GO:0016922 ! nuclear receptor binding
id: GO:0042975
name: peroxisome proliferator activated receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any of the peroxisome proliferator activated receptors, alpha, beta or gamma." [GOC:jl, PMID:12769781]
+def: "Binding to a peroxisome proliferator activated receptor, alpha, beta or gamma." [GOC:jl, PMID:12769781]
synonym: "PPAR binding" EXACT []
is_a: GO:0005102 ! signaling receptor binding
@@ -232244,7 +231860,7 @@ is_a: GO:0030234 ! enzyme regulator activity
id: GO:0042980
name: obsolete cystic fibrosis transmembrane conductance regulator binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein." [GOC:jl]
+def: "OBSOLETE. Binding to a Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein." [GOC:jl]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "CFTR binding" EXACT []
synonym: "cystic fibrosis transmembrane conductance regulator binding" EXACT []
@@ -232356,7 +231972,7 @@ is_a: GO:0042982 ! amyloid precursor protein metabolic process
id: GO:0042988
name: X11-like protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with X11-like protein, a neuron-specific adaptor protein." [GOC:jl, PMID:12780348]
+def: "Binding to X11-like protein, a neuron-specific adaptor protein." [GOC:jl, PMID:12780348]
synonym: "X11L binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -232610,7 +232226,7 @@ is_a: GO:0043570 ! maintenance of DNA repeat elements
id: GO:0043008
name: ATP-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) using energy from the hydrolysis of ATP." [GOC:jl]
+def: "Binding to a protein or protein complex using energy from ATP hydrolysis." [GOC:jl]
subset: goslim_chembl
is_a: GO:0005515 ! protein binding
@@ -232672,7 +232288,7 @@ relationship: negatively_regulates GO:0007342 ! fusion of sperm to egg plasma me
id: GO:0043014
name: alpha-tubulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the microtubule constituent protein alpha-tubulin." [GOC:jl]
+def: "Binding to the microtubule constituent protein alpha-tubulin." [GOC:jl]
synonym: "alpha tubulin binding" EXACT []
is_a: GO:0015631 ! tubulin binding
@@ -232680,7 +232296,7 @@ is_a: GO:0015631 ! tubulin binding
id: GO:0043015
name: gamma-tubulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the microtubule constituent protein gamma-tubulin." [GOC:jl]
+def: "Binding to the microtubule constituent protein gamma-tubulin." [GOC:jl]
synonym: "gamma tubulin binding" EXACT []
is_a: GO:0015631 ! tubulin binding
@@ -232699,7 +232315,7 @@ relationship: part_of GO:0005887 ! integral component of plasma membrane
id: GO:0043021
name: ribonucleoprotein complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any complex of RNA and protein." [GOC:bf, GOC:go_curators, GOC:vk]
+def: "Binding to a complex of RNA and protein." [GOC:bf, GOC:go_curators, GOC:vk]
subset: goslim_pir
synonym: "protein-RNA complex binding" EXACT [GOC:bf, GOC:vk]
synonym: "ribonucleoprotein binding" EXACT [GOC:bf, GOC:vk]
@@ -232711,7 +232327,7 @@ id: GO:0043022
name: ribosome binding
namespace: molecular_function
alt_id: GO:0030376
-def: "Interacting selectively and non-covalently with any part of a ribosome." [GOC:go_curators]
+def: "Binding to a ribosome." [GOC:go_curators]
synonym: "ribosome receptor activity" NARROW []
is_a: GO:0043021 ! ribonucleoprotein complex binding
@@ -232719,14 +232335,14 @@ is_a: GO:0043021 ! ribonucleoprotein complex binding
id: GO:0043023
name: ribosomal large subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of the larger ribosomal subunit." [GOC:go_curators]
+def: "Binding to a large ribosomal subunit." [GOC:go_curators]
is_a: GO:0043021 ! ribonucleoprotein complex binding
[Term]
id: GO:0043024
name: ribosomal small subunit binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of the small ribosomal subunit." [GOC:go_curators]
+def: "Binding to a small ribosomal subunit." [GOC:go_curators]
is_a: GO:0043021 ! ribonucleoprotein complex binding
[Term]
@@ -232904,14 +232520,6 @@ is_a: GO:0006518 ! peptide metabolic process
is_a: GO:0043604 ! amide biosynthetic process
is_a: GO:1901566 ! organonitrogen compound biosynthetic process
-[Term]
-id: GO:0043044
-name: ATP-dependent chromatin remodeling
-namespace: biological_process
-def: "Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors." [GOC:jl, PMID:12042764]
-synonym: "ATP-dependent chromatin remodelling" EXACT []
-is_a: GO:0006338 ! chromatin remodeling
-
[Term]
id: GO:0043045
name: DNA methylation involved in embryo development
@@ -232935,7 +232543,7 @@ relationship: part_of GO:0007276 ! gamete generation
id: GO:0043047
name: single-stranded telomeric DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with single-stranded telomere-associated DNA." [GOC:jl, ISBN:0321000382]
+def: "Binding to single-stranded telomere-associated DNA." [GOC:jl, ISBN:0321000382]
synonym: "telomeric ssDNA binding" EXACT [GOC:mah]
is_a: GO:0042162 ! telomeric DNA binding
is_a: GO:0098847 ! sequence-specific single stranded DNA binding
@@ -233470,7 +233078,7 @@ is_a: GO:0043711 ! pilus organization
id: GO:0043110
name: rDNA spacer replication fork barrier binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with replication fork barriers found in rDNA spacers, sites that inhibit replication forks in the direction opposite to rDNA transcription." [GOC:jl, GOC:mah, PMID:14645529]
+def: "Binding to replication fork barriers found in rDNA spacers, sites that inhibit replication forks in the direction opposite to rDNA transcription." [GOC:jl, GOC:mah, PMID:14645529]
synonym: "RFB binding" EXACT []
is_a: GO:0000182 ! rDNA binding
is_a: GO:0031634 ! replication fork barrier binding
@@ -233557,7 +233165,7 @@ is_a: GO:0043114 ! regulation of vascular permeability
id: GO:0043120
name: tumor necrosis factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages." [GOC:jl, http://lookwayup.com/]
+def: "Binding to tumor necrosis factor, a proinflammatory cytokine produced by monocytes and macrophages." [GOC:jl, http://lookwayup.com/]
is_a: GO:0019955 ! cytokine binding
[Term]
@@ -233566,7 +233174,7 @@ name: neurotrophin binding
namespace: molecular_function
alt_id: GO:0048404
alt_id: GO:0048405
-def: "Interacting selectively and non-covalently with a neurotrophin, any of a family of growth factors that prevent apoptosis in neurons and promote nerve growth." [GOC:jl]
+def: "Binding to a neurotrophin, any of a family of growth factors that prevent apoptosis in neurons and promote nerve growth." [GOC:jl]
comment: Note that mammalian NT-5 was initially named differently from amphibian NT-4 because of sequence differences, but the two genes were later shown to be functionally equivalent [SF:919858].
synonym: "neurotrophic factor binding" EXACT [GOC:aruk, GOC:bc]
synonym: "neurotrophin 3 binding" NARROW []
@@ -233629,7 +233237,7 @@ relationship: negatively_regulates GO:0007249 ! I-kappaB kinase/NF-kappaB signal
id: GO:0043125
name: ErbB-3 class receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the protein-tyrosine kinase receptor ErbB-3/HER3." [GOC:jl]
+def: "Binding to the protein-tyrosine kinase receptor ErbB-3/HER3." [GOC:jl]
synonym: "HER3 receptor binding" EXACT []
synonym: "Neu/ErbB-2 receptor activity" RELATED []
is_a: GO:0005102 ! signaling receptor binding
@@ -233680,7 +233288,7 @@ is_a: GO:0048875 ! chemical homeostasis within a tissue
id: GO:0043130
name: ubiquitin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation." [GOC:ecd]
+def: "Binding to ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation." [GOC:ecd]
xref: Reactome:R-HSA-1169404 "Transfer of ISG15 from E1 to E2 (UBCH8)"
xref: Reactome:R-HSA-205008 "Polyubiquitinated NRIF binds to p62 (Sequestosome)"
xref: Reactome:R-HSA-983152 "Transfer of ubiquitin from E1 to E2"
@@ -233750,15 +233358,15 @@ name: DNA replication, removal of RNA primer
namespace: biological_process
def: "Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease." [GOC:jl, PMID:12424238]
synonym: "Okazaki initiator RNA removal" EXACT []
-is_a: GO:0006259 ! DNA metabolic process
is_a: GO:0006401 ! RNA catabolic process
+relationship: part_of GO:0006260 ! DNA replication
[Term]
id: GO:0043138
name: 3'-5' DNA helicase activity
namespace: molecular_function
alt_id: GO:0043140
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; drives the unwinding of the DNA helix in the direction 3' to 5'." [GOC:jl]
+def: "Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis." [GOC:jl]
synonym: "3' to 5' DNA helicase activity" EXACT []
synonym: "ATP-dependent 3' to 5' DNA helicase activity" EXACT []
synonym: "ATP-dependent 3'-5' DNA helicase activity" EXACT []
@@ -233778,7 +233386,7 @@ name: 5'-3' DNA helicase activity
namespace: molecular_function
alt_id: GO:0008722
alt_id: GO:0043141
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate; drives the unwinding of the DNA helix in the direction 5' to 3'." [GOC:jl]
+def: "Unwinding a DNA helix in the 5' to 3' direction, driven by ATP hydrolysis." [GOC:jl]
synonym: "5' to 3' DNA helicase activity" EXACT []
synonym: "ATP-dependent 5' to 3' DNA helicase activity" EXACT []
synonym: "ATP-dependent 5'-3' DNA helicase activity" EXACT []
@@ -233898,11 +233506,11 @@ relationship: negatively_regulates GO:0019684 ! photosynthesis, light reaction
[Term]
id: GO:0043156
-name: chromatin remodeling in response to cation stress
+name: obsolete chromatin remodeling in response to cation stress
namespace: biological_process
-def: "Structural changes to eukaryotic chromatin occurring as a result of cation stress, an increase or decrease in the concentration of positively charged ions in the environment." [GOC:jl, GOC:vw, PMID:14762213]
-is_a: GO:0006338 ! chromatin remodeling
-is_a: GO:0071473 ! cellular response to cation stress
+def: "OBSOLETE. Structural changes to eukaryotic chromatin occurring as a result of cation stress, an increase or decrease in the concentration of positively charged ions in the environment." [GOC:jl, GOC:vw, PMID:14762213]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
[Term]
id: GO:0043157
@@ -234001,9 +233609,8 @@ relationship: part_of GO:0043163 ! cell envelope organization
id: GO:0043167
name: ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ions, charged atoms or groups of atoms." [GOC:jl]
+def: "Binding to an ion, a charged atoms or groups of atoms." [GOC:jl]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_yeast
@@ -234014,14 +233621,14 @@ is_a: GO:0005488 ! binding
id: GO:0043168
name: anion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with anions, charged atoms or groups of atoms with a net negative charge." [GOC:jl]
+def: "Binding to an anion, a charged atom or group of atoms with a net negative charge." [GOC:jl]
is_a: GO:0043167 ! ion binding
[Term]
id: GO:0043169
name: cation binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge." [GOC:jl]
+def: "Binding to a cation, a charged atom or group of atoms with a net positive charge." [GOC:jl]
is_a: GO:0043167 ! ion binding
[Term]
@@ -234083,14 +233690,14 @@ is_a: GO:0043094 ! cellular metabolic compound salvage
id: GO:0043175
name: RNA polymerase core enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA polymerase core enzyme, containing a specific subunit composition defined as the core enzyme." [GOC:jl, GOC:txnOH]
+def: "Binding to an RNA polymerase core enzyme, containing a specific subunit composition defined as the core enzyme." [GOC:jl, GOC:txnOH]
is_a: GO:0070063 ! RNA polymerase binding
[Term]
id: GO:0043176
name: amine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any organic compound that is weakly basic in character and contains an amino or a substituted amino group." [GOC:jl]
+def: "Binding to an amine, a weakly basic organic compound that contains an amino or a substituted amino group." [GOC:jl]
subset: goslim_pir
is_a: GO:0005488 ! binding
@@ -234098,14 +233705,14 @@ is_a: GO:0005488 ! binding
id: GO:0043177
name: organic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an organic acid, any acidic compound containing carbon in covalent linkage." [GOC:jl, ISBN:0198506732]
+def: "Binding to an organic acid, any acidic compound containing carbon in covalent linkage." [GOC:jl, ISBN:0198506732]
is_a: GO:0036094 ! small molecule binding
[Term]
id: GO:0043178
name: alcohol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alcohol, any of a class of alkyl compounds containing a hydroxyl group." [GOC:jl, ISBN:0198506732]
+def: "Binding to an alcohol, any of a class of alkyl compounds containing a hydroxyl group." [GOC:jl, ISBN:0198506732]
subset: goslim_pir
is_a: GO:0036094 ! small molecule binding
@@ -234157,7 +233764,7 @@ relationship: part_of GO:0006883 ! cellular sodium ion homeostasis
id: GO:0043183
name: vascular endothelial growth factor receptor 1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with vascular endothelial growth factor receptor 1." [GOC:st]
+def: "Binding to a vascular endothelial growth factor receptor 1." [GOC:st]
synonym: "Flt-1 binding" EXACT []
synonym: "VEGF receptor 1 binding" EXACT []
synonym: "VEGFR 1 binding" EXACT []
@@ -234167,7 +233774,7 @@ is_a: GO:0005172 ! vascular endothelial growth factor receptor binding
id: GO:0043184
name: vascular endothelial growth factor receptor 2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with vascular endothelial growth factor receptor 2." [GOC:st]
+def: "Binding to a vascular endothelial growth factor receptor 2." [GOC:st]
synonym: "Flk-1 binding" EXACT []
synonym: "KDR binding" BROAD []
synonym: "kinase domain region binding" EXACT []
@@ -234179,7 +233786,7 @@ is_a: GO:0005172 ! vascular endothelial growth factor receptor binding
id: GO:0043185
name: vascular endothelial growth factor receptor 3 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with vascular endothelial growth factor receptor 3." [GOC:st]
+def: "Binding to a vascular endothelial growth factor receptor 3." [GOC:st]
synonym: "fms-like-tyrosine kinase (Flt)-4 binding" EXACT []
synonym: "VEGF receptor 3 binding" EXACT []
synonym: "VEGFR 3 binding" EXACT []
@@ -234292,7 +233899,7 @@ relationship: part_of GO:0030425 ! dendrite
id: GO:0043199
name: sulfate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with sulfate, SO4(2-), a negatively charged small molecule." [GOC:mlg]
+def: "Binding to sulfate, SO4(2-), a negatively charged small molecule." [GOC:mlg]
is_a: GO:0043168 ! anion binding
is_a: GO:1901681 ! sulfur compound binding
@@ -234354,7 +233961,7 @@ is_a: GO:0009607 ! response to biotic stimulus
id: GO:0043208
name: glycosphingolipid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide." [GOC:jl]
+def: "Binding to glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide." [GOC:jl]
is_a: GO:0046625 ! sphingolipid binding
is_a: GO:0051861 ! glycolipid binding
@@ -234375,7 +233982,7 @@ is_a: GO:0110165 ! cellular anatomical entity
id: GO:0043210
name: alkanesulfonate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with alkanesulfonates, the anion of alkanesulfonic acids, sulfonic acid derivatives containing an aliphatic hydrocarbon group." [GOC:mlg]
+def: "Binding to alkanesulfonates, the anion of alkanesulfonic acids, sulfonic acid derivatives containing an aliphatic hydrocarbon group." [GOC:mlg]
is_a: GO:0043168 ! anion binding
[Term]
@@ -234423,7 +234030,6 @@ name: daunorubicin transport
namespace: biological_process
def: "The directed movement of daunorubicin, an anthracycline antibiotic produced by Streptomyces coeruleorubidus or S. peucetius and used as an antineoplastic into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, GOC:mlg]
is_a: GO:0015695 ! organic cation transport
-is_a: GO:0015893 ! drug transport
is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:1901656 ! glycoside transport
@@ -234487,7 +234093,7 @@ relationship: part_of GO:0043218 ! compact myelin
id: GO:0043221
name: SMC family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein from the structural maintenance of chromosomes (SMC) family, a group of chromosomal ATPases with a role in mitotic chromosome organization." [GOC:jl, GOC:vw, InterPro:IPR024704, PMID:9640531]
+def: "Binding to a protein from the structural maintenance of chromosomes (SMC) family, a group of chromosomal ATPases with a role in mitotic chromosome organization." [GOC:jl, GOC:vw, InterPro:IPR024704, PMID:9640531]
synonym: "structural maintenance of chromosomes family protein binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -234555,6 +234161,7 @@ id: GO:0043228
name: non-membrane-bounded organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators]
+synonym: "biological condensate" NARROW []
synonym: "non-membrane-enclosed organelle" EXACT []
xref: NIF_Subcellular:sao1456184038
is_a: GO:0043226 ! organelle
@@ -234620,7 +234227,7 @@ name: laminin binding
namespace: molecular_function
alt_id: GO:0043238
alt_id: GO:0043239
-def: "Interacting selectively and non-covalently with laminins, glycoproteins that are major constituents of the basement membrane of cells." [GOC:ecd]
+def: "Binding to a laminin, a major glycoprotein constituent of the basement membrane of cells." [GOC:ecd]
synonym: "laminin-2 binding" NARROW []
synonym: "laminin-4 binding" NARROW []
is_a: GO:0005515 ! protein binding
@@ -234630,7 +234237,7 @@ is_a: GO:0050840 ! extracellular matrix binding
id: GO:0043237
name: laminin-1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with laminin-1, a glycoprotein trimer with the subunit composition alpha1, beta1, gamma1." [GOC:go_curators]
+def: "Binding to laminin-1, a glycoprotein trimer with the subunit composition alpha1, beta1, gamma1." [GOC:go_curators]
synonym: "laminin-111 binding" EXACT [GOC:dph, PMID:15979864]
is_a: GO:0043236 ! laminin binding
@@ -234715,7 +234322,7 @@ def: "The aggregation, arrangement and bonding together of a mature, active prot
synonym: "26S proteasome assembly" NARROW []
synonym: "proteasome complex assembly" EXACT []
synonym: "proteasome maturation" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0043249
@@ -234879,7 +234486,7 @@ synonym: "regulation of K+ transport" EXACT []
synonym: "regulation of potassium conductance" NARROW []
synonym: "regulation of potassium ion conductance" NARROW []
synonym: "regulation of potassium transport" EXACT []
-is_a: GO:0043269 ! regulation of ion transport
+is_a: GO:0010959 ! regulation of metal ion transport
relationship: regulates GO:0006813 ! potassium ion transport
[Term]
@@ -234983,7 +234590,7 @@ is_a: GO:0017111 ! nucleoside-triphosphatase activity
id: GO:0043274
name: phospholipase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid." [GOC:jl]
+def: "Binding to a phospholipase." [GOC:jl]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -235102,7 +234709,7 @@ relationship: regulates GO:0042621 ! poly(3-hydroxyalkanoate) biosynthetic proce
id: GO:0043287
name: poly(3-hydroxyalkanoate) binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with poly(3-hydroxyalkanoate)s, polyesters of 3-hydroxyacids produced as intracellular granules by a large variety of bacteria." [GOC:jl]
+def: "Binding to a poly(3-hydroxyalkanoate), a polyester of 3-hydroxyacids produced as intracellular granules by a large variety of bacteria." [GOC:jl]
synonym: "PHA binding" EXACT []
is_a: GO:0005488 ! binding
@@ -235181,7 +234788,7 @@ relationship: part_of GO:0005759 ! mitochondrial matrix
id: GO:0043295
name: glutathione binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with glutathione; a tripeptide composed of the three amino acids cysteine, glutamic acid and glycine." [GOC:bf, ISBN:0198506732]
+def: "Binding to glutathione; a tripeptide composed of the three amino acids cysteine, glutamic acid and glycine." [GOC:bf, ISBN:0198506732]
is_a: GO:0043168 ! anion binding
is_a: GO:0072341 ! modified amino acid binding
is_a: GO:1900750 ! oligopeptide binding
@@ -235595,7 +235202,7 @@ relationship: part_of GO:0048066 ! developmental pigmentation
id: GO:0043325
name: phosphatidylinositol-3,4-bisphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions." [GOC:bf, GOC:go_curators]
+def: "Binding to phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions." [GOC:bf, GOC:go_curators]
is_a: GO:0043168 ! anion binding
[Term]
@@ -236175,7 +235782,7 @@ is_a: GO:0051098 ! regulation of binding
id: GO:0043394
name: proteoglycan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans." [ISBN:0198506732]
+def: "Binding to a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans." [ISBN:0198506732]
is_a: GO:0005515 ! protein binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -236183,7 +235790,7 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:0043395
name: heparan sulfate proteoglycan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a heparan sulfate proteoglycan, any proteoglycan containing heparan sulfate as the glycosaminoglycan carbohydrate unit." [ISBN:0198506732]
+def: "Binding to a heparan sulfate proteoglycan, any proteoglycan containing heparan sulfate as the glycosaminoglycan carbohydrate unit." [ISBN:0198506732]
synonym: "heparin proteoglycan binding" RELATED []
is_a: GO:0043394 ! proteoglycan binding
is_a: GO:1901681 ! sulfur compound binding
@@ -236213,7 +235820,7 @@ relationship: regulates GO:0043396 ! corticotropin-releasing hormone secretion
id: GO:0043398
name: HLH domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with Helix Loop Helix, a domain of 40-50 residues that occurs in specific DNA-binding proteins that act as transcription factors. The domain is formed of two amphipathic helices joined by a variable length linker region that can form a loop and it mediates protein dimerization." [GOC:go_curators, Prosite:PDOC0038]
+def: "Binding to a Helix Loop Helix domain, a domain of 40-50 residues that occurs in specific DNA-binding proteins that act as transcription factors. The domain is formed of two amphipathic helices joined by a variable length linker region that can form a loop and it mediates protein dimerization." [GOC:go_curators, Prosite:PDOC0038]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -236379,7 +235986,7 @@ relationship: positively_regulates GO:0000165 ! MAPK cascade
id: GO:0043411
name: obsolete myopalladin binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with myopalladin, a myofibrillar protein with titin-like Ig domains." [GOC:go_curators]
+def: "OBSOLETE. Binding to myopalladin, a myofibrillar protein with titin-like Ig domains." [GOC:go_curators]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "myopalladin binding" EXACT []
is_obsolete: true
@@ -236520,7 +236127,7 @@ is_a: GO:0072329 ! monocarboxylic acid catabolic process
id: GO:0043422
name: protein kinase B binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with protein kinase B, an intracellular kinase that is important in regulating glucose metabolism." [GOC:jl, http://www.heartandmetabolism.org/]
+def: "Binding to protein kinase B, an intracellular kinase that is important in regulating glucose metabolism." [GOC:jl, http://www.heartandmetabolism.org/]
synonym: "Akt binding" EXACT []
synonym: "PKB binding" EXACT []
is_a: GO:0019901 ! protein kinase binding
@@ -236529,7 +236136,7 @@ is_a: GO:0019901 ! protein kinase binding
id: GO:0043423
name: 3-phosphoinositide-dependent protein kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 3-phosphoinositide-dependent protein kinase." [GOC:jl]
+def: "Binding to a 3-phosphoinositide-dependent protein kinase." [GOC:jl]
synonym: "phosphatidylinositol-3-phosphate-dependent protein kinase binding" EXACT []
is_a: GO:0019901 ! protein kinase binding
@@ -236537,7 +236144,7 @@ is_a: GO:0019901 ! protein kinase binding
id: GO:0043424
name: protein histidine kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with protein histidine kinase." [GOC:jl]
+def: "Binding to a protein histidine kinase." [GOC:jl]
synonym: "histidine kinase binding" EXACT []
synonym: "histidine-protein kinase binding" EXACT []
synonym: "protein-histidine kinase binding" EXACT []
@@ -236547,7 +236154,7 @@ is_a: GO:0019901 ! protein kinase binding
id: GO:0043425
name: bHLH transcription factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways." [PMID:9144210]
+def: "Binding to a basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways." [PMID:9144210]
is_a: GO:0140297 ! DNA-binding transcription factor binding
[Term]
@@ -236558,7 +236165,7 @@ alt_id: GO:0051576
alt_id: GO:0051577
alt_id: GO:0051578
alt_id: GO:0051579
-def: "Interacting selectively and non-covalently with Myogenic Regulatory Factor (MRF), a member of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors." [PMID:10966875]
+def: "Binding to Myogenic Regulatory Factor (MRF), a member of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors." [PMID:10966875]
synonym: "Mrf4 binding" NARROW []
synonym: "Myf5 binding" NARROW []
synonym: "MyoD binding" NARROW []
@@ -236950,10 +236557,11 @@ is_a: GO:0070071 ! proton-transporting two-sector ATPase complex assembly
[Term]
id: GO:0043462
-name: regulation of ATPase activity
+name: regulation of ATP-dependent activity
namespace: biological_process
-def: "Any process that modulates the rate of ATP hydrolysis by an ATPase." [GOC:jl]
+def: "Any process that modulates the rate of an ATP-dependent activity." [GOC:jl]
synonym: "regulation of adenosinetriphosphatase activity" EXACT []
+synonym: "regulation of ATPase activity" EXACT []
is_a: GO:0065009 ! regulation of molecular function
[Term]
@@ -237048,7 +236656,7 @@ relationship: regulates GO:0044275 ! cellular carbohydrate catabolic process
id: GO:0043472
name: IgD binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an immunoglobulin of a D isotype." [PMID:12886015]
+def: "Binding to an immunoglobulin of a D isotype." [PMID:12886015]
is_a: GO:0019865 ! immunoglobulin binding
[Term]
@@ -237057,7 +236665,6 @@ name: pigmentation
namespace: biological_process
def: "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." [GOC:jl]
subset: goslim_chembl
-subset: goslim_generic
subset: goslim_pir
is_a: GO:0008150 ! biological_process
@@ -237178,7 +236785,6 @@ comment: Note that this term also includes the exchange of sperm-specific histon
synonym: "histone chaperone" RELATED [GOC:vw]
synonym: "histone replacement" EXACT []
is_a: GO:0034728 ! nucleosome organization
-is_a: GO:0043044 ! ATP-dependent chromatin remodeling
[Term]
id: GO:0043487
@@ -237290,7 +236896,7 @@ is_a: GO:0043393 ! regulation of protein binding
id: GO:0043498
name: obsolete cell surface binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with any component on the surface of a cell." [GOC:jl]
+def: "OBSOLETE. Binding to a component on the surface of a cell." [GOC:jl]
comment: This term was made obsolete because it is ambiguous and causing confusion, and is an unnecessary grouping term.
synonym: "cell surface binding" EXACT []
is_obsolete: true
@@ -237304,7 +236910,7 @@ consider: GO:0046812
id: GO:0043499
name: obsolete eukaryotic cell surface binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with any component on the surface of a eukaryotic cell." [GOC:jl]
+def: "OBSOLETE. Binding to a component on the surface of a eukaryotic cell." [GOC:jl]
comment: This term was made obsolete because it is ambiguous and causing confusion, and is an unnecessary grouping term.
synonym: "eukaryotic cell surface binding" EXACT []
is_obsolete: true
@@ -237473,7 +237079,7 @@ relationship: part_of GO:0005615 ! extracellular space
id: GO:0043515
name: kinetochore binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a kinetochore, a proteinaceous structure on a condensed chromosome, beside the centromere, to which the spindle fibers are attached." [GOC:jl]
+def: "Binding to a kinetochore, a proteinaceous structure on a condensed chromosome, beside the centromere, to which the spindle fibers are attached." [GOC:jl]
is_a: GO:0005488 ! binding
[Term]
@@ -237550,7 +237156,7 @@ relationship: regulates GO:0031037 ! myosin II filament disassembly
id: GO:0043522
name: leucine zipper domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a leucine zipper domain, a protein secondary structure exhibiting a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns." [GOC:jl, InterPro:IPR002158]
+def: "Binding to a leucine zipper domain, a protein secondary structure exhibiting a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns." [GOC:jl, InterPro:IPR002158]
synonym: "leucine zipper binding" EXACT []
is_a: GO:0030275 ! LRR domain binding
@@ -237640,16 +237246,17 @@ is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
id: GO:0043530
name: adenosine 5'-monophosphoramidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: adenosine 5'-monophosphoramidate = AMP + NH2. Other substrates include AMP-morpholidate, AMP-N-alanine methyl ester and AMP-alpha-acetyl lysine methyl ester." [PMID:11805111]
+def: "Catalysis of the reaction: adenosine 5'-monophosphoramidate + H2O = AMP + NH4+. Other substrates include AMP-morpholidate, AMP-N-alanine methyl ester and AMP-alpha-acetyl lysine methyl ester." [PMID:11805111, RHEA:67916]
synonym: "adenosine 5' monophosphoramidase activity" EXACT []
synonym: "adenosine 5'-monophosphoramidate hydrolase activity" EXACT []
+xref: RHEA:67916
is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
[Term]
id: GO:0043531
name: ADP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate." [GOC:jl]
+def: "Binding to ADP, adenosine 5'-diphosphate." [GOC:jl]
synonym: "adenosine 5'-diphosphate binding" EXACT []
synonym: "adenosine diphosphate binding" EXACT []
is_a: GO:0032559 ! adenyl ribonucleotide binding
@@ -237659,14 +237266,14 @@ is_a: GO:0043168 ! anion binding
id: GO:0043532
name: angiostatin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with angiostatin, a proteolytic product of plasminogen or plasmin containing at least one intact kringle domain, and which is an inhibitor of angiogenesis." [PMID:16043488]
+def: "Binding to angiostatin, a proteolytic product of plasminogen or plasmin containing at least one intact kringle domain, and which is an inhibitor of angiogenesis." [PMID:16043488]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0043533
name: inositol 1,3,4,5 tetrakisphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with inositol 1,3,4,5 tetrakisphosphate." [GOC:go_curators]
+def: "Binding to inositol 1,3,4,5 tetrakisphosphate." [GOC:go_curators]
synonym: "InsP4 binding" EXACT []
synonym: "IP4 binding" EXACT []
is_a: GO:0043168 ! anion binding
@@ -237774,7 +237381,7 @@ is_a: GO:0006464 ! cellular protein modification process
id: GO:0043544
name: lipoamide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group." [GOC:go_curators]
+def: "Binding to lipoamide, the functional form of lipoic acid in which the carboxyl group is attached to protein by an amide linkage to a lysine amino group." [GOC:go_curators]
is_a: GO:0033218 ! amide binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -237799,7 +237406,7 @@ is_a: GO:1901564 ! organonitrogen compound metabolic process
id: GO:0043546
name: molybdopterin cofactor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands." [ISSN:09498257]
+def: "Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands." [ISSN:09498257]
synonym: "Moco binding" EXACT []
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -237875,7 +237482,7 @@ is_a: GO:0051345 ! positive regulation of hydrolase activity
id: GO:0043548
name: phosphatidylinositol 3-kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a phosphatidylinositol 3-kinase, any enzyme that catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring." [PMID:10209156, PMID:9255069]
+def: "Binding to a phosphatidylinositol 3-kinase, any enzyme that catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring." [PMID:10209156, PMID:9255069]
synonym: "phosphoinositide 3-kinase binding" EXACT []
synonym: "PI3K binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -237946,14 +237553,14 @@ namespace: biological_process
def: "Modulation of the frequency, rate or extent of translation as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:jl]
synonym: "translational stress response" EXACT []
is_a: GO:0006417 ! regulation of translation
-is_a: GO:0033554 ! cellular response to stress
+relationship: part_of GO:0033554 ! cellular response to stress
[Term]
id: GO:0043556
name: regulation of translation in response to oxidative stress
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of translation as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals." [GOC:jl]
-is_a: GO:0043555 ! regulation of translation in response to stress
+is_a: GO:0032055 ! negative regulation of translation in response to stress
relationship: part_of GO:0034599 ! cellular response to oxidative stress
[Term]
@@ -237961,8 +237568,8 @@ id: GO:0043557
name: regulation of translation in response to osmotic stress
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the frequency, rate or extent of translation as a result of a stimulus indicating an increase or decrease in the concentration of solutes outside the organism or cell." [GOC:jl]
-is_a: GO:0006970 ! response to osmotic stress
is_a: GO:0043555 ! regulation of translation in response to stress
+relationship: part_of GO:0071470 ! cellular response to osmotic stress
[Term]
id: GO:0043558
@@ -237977,7 +237584,7 @@ is_a: GO:0043555 ! regulation of translation in response to stress
id: GO:0043559
name: insulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with insulin, a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." [ISBN:0198506732]
+def: "Binding to insulin, a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." [ISBN:0198506732]
is_a: GO:0005515 ! protein binding
is_a: GO:0017046 ! peptide hormone binding
@@ -237985,7 +237592,7 @@ is_a: GO:0017046 ! peptide hormone binding
id: GO:0043560
name: insulin receptor substrate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any of the insulin receptor substrate (IRS) proteins, adaptor proteins that bind to the transphosphorylated insulin and insulin-like growth factor receptors, are themselves phosphorylated and in turn recruit SH2 domain-containing signaling molecules to form a productive signaling complex." [PMID:12829233]
+def: "Binding to an insulin receptor substrate (IRS) protein, an adaptor protein that bind to the transphosphorylated insulin and insulin-like growth factor receptors, are themselves phosphorylated and in turn recruit SH2 domain-containing signaling molecules to form a productive signaling complex." [PMID:12829233]
synonym: "insulin receptor substrate [protein] binding" EXACT []
synonym: "IRS [protein] binding" EXACT []
synonym: "IRS binding" EXACT []
@@ -238025,7 +237632,7 @@ is_a: GO:0140513 ! nuclear protein-containing complex
id: GO:0043565
name: sequence-specific DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [GOC:jl]
+def: "Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [GOC:jl]
synonym: "sequence specific DNA binding" EXACT []
is_a: GO:0003677 ! DNA binding
@@ -238314,7 +237921,7 @@ name: cytoplasmic replication fork
namespace: cellular_component
def: "The Y-shaped region of a cytoplasmic replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes." [GOC:jl, GOC:mtg_sensu]
is_a: GO:0005657 ! replication fork
-relationship: part_of GO:0000229 ! cytoplasmic chromosome
+relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0043598
@@ -238533,7 +238140,7 @@ is_a: GO:0033554 ! cellular response to stress
id: GO:0043621
name: protein self-association
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a domain within the same polypeptide." [GOC:jl]
+def: "Binding to a domain within the same polypeptide." [GOC:jl]
subset: goslim_chembl
synonym: "intramolecular protein binding" EXACT []
synonym: "protein self association" EXACT []
@@ -238551,13 +238158,6 @@ synonym: "cortical microtubule organization and biogenesis" RELATED [GOC:mah]
is_a: GO:0030865 ! cortical cytoskeleton organization
is_a: GO:0031122 ! cytoplasmic microtubule organization
-[Term]
-id: GO:0043624
-name: cellular protein complex disassembly
-namespace: biological_process
-def: "The disaggregation of a protein complex into its constituent components, occurring at the level of an individual cell. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups." [GOC:jl]
-is_a: GO:0032984 ! protein-containing complex disassembly
-
[Term]
id: GO:0043625
name: delta DNA polymerase complex
@@ -238636,7 +238236,6 @@ id: GO:0043633
name: polyadenylation-dependent RNA catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of an RNA molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3'-end of the target RNA." [GOC:dgf, GOC:jl, GOC:krc]
-synonym: "polyadenylation-dependent RNA catabolic process" RELATED [GOC:vw]
is_a: GO:0006401 ! RNA catabolic process
is_a: GO:0043632 ! modification-dependent macromolecule catabolic process
@@ -238891,7 +238490,6 @@ name: host extracellular space
namespace: cellular_component
def: "The space within a host but external to the plasma membrane of host cells, e.g. within host bloodstream." [GOC:cc]
synonym: "extracellular space of host" EXACT []
-synonym: "host extracellular space" EXACT []
is_a: GO:0018995 ! host cellular component
[Term]
@@ -239597,7 +239195,6 @@ def: "Catalysis of the reaction: DNA containing 3-methylbase + H2O = DNA with ab
synonym: "DNA-3-methyladenine glycosylase III" RELATED []
synonym: "Mag III" NARROW []
synonym: "MagIII" NARROW []
-xref: EC:3.2.2.-
is_a: GO:0003905 ! alkylbase DNA N-glycosylase activity
[Term]
@@ -240303,9 +239900,9 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0043804
name: imidazolone hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-formimidoylglycine => H2O + imidazol-4-one." [PMID:27286964, RHEA:24937]
+def: "Catalysis of the reaction: N-formimidoylglycine => H2O + imidazol-4-one." [PMID:27286964, RHEA:24935]
comment: Note that this reaction can occur spontaneously (see RHEA:24937).
-xref: RHEA:24937
+xref: RHEA:24935
is_a: GO:0016812 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
[Term]
@@ -240941,7 +240538,8 @@ def: "Catalysis of the reaction: arginine(out) + ornithine(in) = arginine(in) +
synonym: "ArcD" RELATED []
synonym: "arginine-ornithine antiporter activity" EXACT []
synonym: "arginine/ornithine antiporter activity" EXACT []
-is_a: GO:0015181 ! arginine transmembrane transporter activity
+is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0015171 ! amino acid transmembrane transporter activity
is_a: GO:0015301 ! anion:anion antiporter activity
is_a: GO:0015491 ! cation:cation antiporter activity
@@ -240983,8 +240581,9 @@ synonym: "AdiC" RELATED []
synonym: "arginine-agmatine antiporter activity" EXACT []
synonym: "arginine-agmatine exchange transporter activity" EXACT []
synonym: "arginine/agmatine antiporter activity" EXACT []
+is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015101 ! organic cation transmembrane transporter activity
-is_a: GO:0015181 ! arginine transmembrane transporter activity
+is_a: GO:0015171 ! amino acid transmembrane transporter activity
is_a: GO:0015491 ! cation:cation antiporter activity
[Term]
@@ -241176,11 +240775,12 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0043879
name: glycolate transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of glycolate from one side of a membrane to the other. Glycolate is the smallest alpha-hydroxy acid (AHA)." [GOC:jl]
+def: "Enables the transfer of glycolate from one side of a membrane to the other. Glycolate is the smallest alpha-hydroxy acid (AHA)." [GOC:jl, RHEA:29447]
synonym: "glcA" RELATED []
synonym: "glycolate permease" RELATED []
synonym: "glycolic acid transmembrane transporter activity" EXACT []
synonym: "hydroxyacetic acid transmembrane transporter activity" EXACT []
+xref: RHEA:29447
is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0008514 ! organic anion transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
@@ -241466,29 +241066,27 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
id: GO:0043900
-name: regulation of multi-organism process
+name: obsolete regulation of multi-organism process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl]
-is_a: GO:0050789 ! regulation of biological process
-relationship: regulates GO:0051704 ! multi-organism process
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl]
+comment: This term was obsoleted because it is an unnecessary grouping term.
+is_obsolete: true
[Term]
id: GO:0043901
-name: negative regulation of multi-organism process
+name: obsolete negative regulation of multi-organism process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl]
-is_a: GO:0043900 ! regulation of multi-organism process
-is_a: GO:0048519 ! negative regulation of biological process
-relationship: negatively_regulates GO:0051704 ! multi-organism process
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl]
+comment: This term was obsoleted because it is an unnecessary grouping term.
+is_obsolete: true
[Term]
id: GO:0043902
-name: positive regulation of multi-organism process
+name: obsolete positive regulation of multi-organism process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl]
-is_a: GO:0043900 ! regulation of multi-organism process
-is_a: GO:0048518 ! positive regulation of biological process
-relationship: positively_regulates GO:0051704 ! multi-organism process
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl]
+comment: This term was obsoleted because it is an unnecessary grouping term.
+is_obsolete: true
[Term]
id: GO:0043903
@@ -241671,8 +241269,9 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0043920
name: aminopropylagmatine ureohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N1-aminopropylagmatine + H2O = spermidine + urea." [GOC:jl, PMID:15983049]
-xref: RHEA:35828
+def: "Catalysis of the reaction: N1-aminopropylagmatine + H2O = spermidine + urea." [GOC:jl, PMID:15983049, RHEA:35827]
+xref: EC:3.5.3.24
+xref: RHEA:35827
is_a: GO:0016813 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
[Term]
@@ -241707,7 +241306,7 @@ relationship: positively_regulates GO:0019083 ! viral transcription
id: GO:0043924
name: suramin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with suramin, a naphthalenesulfonic acid compound which is used in the treatment of diseases caused by trypanosomes and worms." [GOC:jl, Wikipedia:Suramin]
+def: "Binding to suramin, a naphthalenesulfonic acid compound which is used in the treatment of diseases caused by trypanosomes and worms." [GOC:jl, Wikipedia:Suramin]
synonym: "Germanin binding" EXACT []
is_a: GO:0033218 ! amide binding
is_a: GO:0043177 ! organic acid binding
@@ -241769,7 +241368,7 @@ relationship: part_of GO:0046849 ! bone remodeling
[Term]
id: GO:0043933
-name: protein-containing complex subunit organization
+name: protein-containing complex organization
namespace: biological_process
alt_id: GO:0034600
alt_id: GO:0034621
@@ -241783,6 +241382,7 @@ synonym: "macromolecular complex subunit organisation" RELATED []
synonym: "macromolecular complex subunit organization" RELATED []
synonym: "protein complex subunit organisation" EXACT [GOC:mah]
synonym: "protein complex subunit organization" EXACT []
+synonym: "protein-containing complex subunit organization" RELATED []
is_a: GO:0016043 ! cellular component organization
[Term]
@@ -241903,36 +241503,39 @@ relationship: positively_regulates GO:0043936 ! asexual sporulation resulting in
[Term]
id: GO:0043946
-name: positive regulation of catalytic activity in other organism involved in symbiotic interaction
+name: obsolete positive regulation of catalytic activity in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, GOC:tb]
+def: "OBSOLETE. Any process in which an organism activates, maintains or increases the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of enzyme activity in other organism" NARROW []
synonym: "activation of enzyme activity in other organism during symbiotic interaction" NARROW []
synonym: "positive regulation of catalytic activity in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "up regulation of enzyme activity in other organism during symbiotic interaction" RELATED []
synonym: "up-regulation of enzyme activity in other organism during symbiotic interaction" RELATED []
synonym: "upregulation of enzyme activity in other organism during symbiotic interaction" RELATED []
-is_a: GO:0052203 ! modulation of catalytic activity in other organism involved in symbiotic interaction
+is_obsolete: true
+consider: GO:0140677
[Term]
id: GO:0043947
-name: positive regulation by host of symbiont catalytic activity
+name: obsolete positive regulation by host of symbiont catalytic activity
namespace: biological_process
-def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of symbiont enzyme activity. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+def: "OBSOLETE. Any process in which an organism activates, maintains or increases the frequency, rate or extent of symbiont enzyme activity. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation by host of symbiont enzyme activity" NARROW []
synonym: "activation of symbiont enzyme activity" NARROW []
synonym: "positive regulation by host of symbiont enzyme activity" EXACT []
synonym: "up regulation by host of symbiont enzyme activity" EXACT []
synonym: "up-regulation by host of symbiont enzyme activity" EXACT []
synonym: "upregulation by host of symbiont enzyme activity" EXACT []
-is_a: GO:0043946 ! positive regulation of catalytic activity in other organism involved in symbiotic interaction
-is_a: GO:0052422 ! modulation by host of symbiont catalytic activity
+is_obsolete: true
[Term]
id: GO:0043948
-name: induction by symbiont of host catalytic activity
+name: obsolete induction by symbiont of host catalytic activity
namespace: biological_process
-def: "Any process in which the symbiont activates, maintains or increases the frequency, rate or extent of host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. Any process in which the symbiont activates, maintains or increases the frequency, rate or extent of host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation by symbiont of host enzyme activity" NARROW []
synonym: "activation of host enzyme activity" NARROW []
synonym: "positive regulation by symbiont of host catalytic activity" EXACT []
@@ -241940,9 +241543,7 @@ synonym: "positive regulation by symbiont of host enzyme activity" EXACT []
synonym: "up regulation by symbiont of host enzyme activity" EXACT []
synonym: "up-regulation by symbiont of host enzyme activity" EXACT []
synonym: "upregulation by symbiont of host enzyme activity" EXACT []
-is_a: GO:0043085 ! positive regulation of catalytic activity
-is_a: GO:0043946 ! positive regulation of catalytic activity in other organism involved in symbiotic interaction
-is_a: GO:0052148 ! modulation by symbiont of host catalytic activity
+is_obsolete: true
[Term]
id: GO:0043949
@@ -242042,7 +241643,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0043957
name: acryloyl-CoA reductase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: acryloyl-CoA + NADPH + H+ = propionyl-CoA + NADP+." [GOC:jl, PMID:11821399]
+def: "Catalysis of the reaction: acryloyl-CoA + NADPH + H+ = propionyl-CoA + NADP+." [GOC:jl, PMID:11821399, RHEA:26454]
comment: Note that this function is one of the activities of the trifunctional enzyme propionyl-coenzyme A synthase. See PMID:11821399.
synonym: "acetyl-coenzyme A synthetase" BROAD []
synonym: "acetyl-coenzyme A synthetase/GroES-like domain" BROAD []
@@ -242054,7 +241655,7 @@ synonym: "enoyl-CoA hydratase/isomerase" BROAD []
xref: EC:1.3.1.84
xref: KEGG_REACTION:R00919
xref: MetaCyc:RXN-9087
-xref: RHEA:26456
+xref: RHEA:26454
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
[Term]
@@ -242436,7 +242037,6 @@ name: acquisition of nutrients from host
namespace: biological_process
def: "The process that begins with the production and formation of structures and molecules in an organism that are required for the acquisition and utilization of nutrients from its host organism, and the ends with the acquirement of the nutrients. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:cc, GOC:jl]
is_a: GO:0051701 ! biological process involved in interaction with host
-is_a: GO:0051816 ! acquisition of nutrients from other organism during symbiotic interaction
[Term]
id: GO:0044003
@@ -242449,10 +242049,9 @@ synonym: "disruption by symbiont of host cell" RELATED []
synonym: "modification by symbiont of host biological process" RELATED []
synonym: "modification by symbiont of host morphology or physiology" RELATED []
synonym: "modulation by symbiont of host system process" NARROW []
-synonym: "pathogenesis" NARROW []
+synonym: "pathogenesis" RELATED []
synonym: "regulation by symbiont of host system process" NARROW []
is_a: GO:0051701 ! biological process involved in interaction with host
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
[Term]
id: GO:0044007
@@ -242651,11 +242250,11 @@ relationship: regulates GO:0006306 ! DNA methylation
[Term]
id: GO:0044031
-name: modification by symbiont of host protein by phosphorylation
+name: obsolete modification by symbiont of host protein by phosphorylation
namespace: biological_process
-def: "The process in which an organism adds a phosphate group to a protein of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is intended for use in annotation of symbiont gene products. For host gene products that phosphorylate host proteins, consider annotation to 'protein amino acid phosphorylation ; GO:0006468'. Consider also annotation to the molecular function term 'protein kinase activity ; GO:0004672'.
-is_a: GO:0075345 ! modification by symbiont of host protein
+def: "OBSOLETE. The process in which an organism adds a phosphate group to a protein of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0044032
@@ -242669,14 +242268,14 @@ is_a: GO:0052019 ! modulation by symbiont of host hormone or growth regulator le
[Term]
id: GO:0044033
-name: multi-organism metabolic process
+name: obsolete multi-organism metabolic process
namespace: biological_process
-def: "A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves more than one organism." [GOC:jl]
+def: "OBSOLETE. A metabolic process - chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances - which involves more than one organism." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi-organism metabolism" EXACT []
synonym: "multi-organismal metabolic process" EXACT []
synonym: "multi-organismal metabolism" EXACT []
-is_a: GO:0008152 ! metabolic process
-is_a: GO:0051704 ! multi-organism process
+is_obsolete: true
[Term]
id: GO:0044034
@@ -242691,14 +242290,14 @@ is_obsolete: true
[Term]
id: GO:0044035
-name: multi-organism catabolic process
+name: obsolete multi-organism catabolic process
namespace: biological_process
-def: "A catabolic process - chemical reactions and pathways resulting in the breakdown of substances - which involves more than one organism." [GOC:jl]
+def: "OBSOLETE. A catabolic process - chemical reactions and pathways resulting in the breakdown of substances - which involves more than one organism." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi-organism catabolism" EXACT []
synonym: "multi-organismal catabolic process" EXACT []
synonym: "multi-organismal catabolism" EXACT []
-is_a: GO:0009056 ! catabolic process
-is_a: GO:0044033 ! multi-organism metabolic process
+is_obsolete: true
[Term]
id: GO:0044036
@@ -242713,13 +242312,12 @@ relationship: part_of GO:0071554 ! cell wall organization or biogenesis
[Term]
id: GO:0044037
-name: multi-organism cell wall macromolecule metabolic process
+name: obsolete multi-organism cell wall macromolecule metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving macromolecules forming, or destined to form, part of a cell wall, involving more than one organism. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis." [GOC:mah, GOC:tair_curators]
+def: "OBSOLETE. The chemical reactions and pathways involving macromolecules forming, or destined to form, part of a cell wall, involving more than one organism. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis." [GOC:mah, GOC:tair_curators]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi-organism cell wall macromolecule metabolism" EXACT [GOC:mah]
-is_a: GO:0044033 ! multi-organism metabolic process
-is_a: GO:0044036 ! cell wall macromolecule metabolic process
-is_a: GO:0044764 ! multi-organism cellular process
+is_obsolete: true
[Term]
id: GO:0044038
@@ -242737,26 +242335,25 @@ relationship: part_of GO:0042546 ! cell wall biogenesis
[Term]
id: GO:0044040
-name: multi-organism carbohydrate metabolic process
+name: obsolete multi-organism carbohydrate metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, that involve more than one organism." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, that involve more than one organism." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "main pathways of carbohydrate metabolic process" NARROW []
synonym: "main pathways of carbohydrate metabolism" NARROW []
synonym: "multi-organism carbohydrate metabolism" EXACT []
-is_a: GO:0005975 ! carbohydrate metabolic process
-is_a: GO:0044033 ! multi-organism metabolic process
+is_obsolete: true
[Term]
id: GO:0044041
-name: multi-organism carbohydrate catabolic process
+name: obsolete multi-organism carbohydrate catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, involving more than one organism." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y, involving more than one organism." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi-organism carbohydrate breakdown" EXACT []
synonym: "multi-organism carbohydrate catabolism" EXACT []
synonym: "multi-organism carbohydrate degradation" EXACT []
-is_a: GO:0016052 ! carbohydrate catabolic process
-is_a: GO:0044035 ! multi-organism catabolic process
-is_a: GO:0044040 ! multi-organism carbohydrate metabolic process
+is_obsolete: true
[Term]
id: GO:0044042
@@ -242768,12 +242365,12 @@ is_a: GO:0005976 ! polysaccharide metabolic process
[Term]
id: GO:0044043
-name: multi-organism glucan metabolic process
+name: obsolete multi-organism glucan metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, involving more than one organism." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues, involving more than one organism." [ISBN:0198547684]
+comment: This term was obsoleted because there is no evidence it exists.
synonym: "multi-organism glucan metabolism" EXACT []
-is_a: GO:0044040 ! multi-organism carbohydrate metabolic process
-is_a: GO:0044042 ! glucan metabolic process
+is_obsolete: true
[Term]
id: GO:0044044
@@ -242906,12 +242503,12 @@ relationship: regulates GO:0050886 ! endocrine process
[Term]
id: GO:0044061
-name: modulation by symbiont of host excretion
+name: obsolete modulation by symbiont of host excretion
namespace: biological_process
-def: "The alteration by a symbiont organism of the functioning of excretion, the elimination by the host organism of the waste products that arise as a result of metabolic activity." [MITRE:tk]
+def: "OBSOLETE. The alteration by a symbiont organism of the functioning of excretion, the elimination by the host organism of the waste products that arise as a result of metabolic activity." [MITRE:tk]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "regulation by symbiont of host excretion" EXACT []
-is_a: GO:0044003 ! modulation by symbiont of host process
-is_a: GO:0044062 ! regulation of excretion
+is_obsolete: true
[Term]
id: GO:0044062
@@ -243315,7 +242912,6 @@ id: GO:0044105
name: L-xylulose reductase (NAD+) activity
namespace: molecular_function
def: "Catalysis of the reaction: xylitol + NAD+ = L-xylulose + NADH + H+." [PMID:14736891]
-xref: EC:1.1.1.10
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
@@ -243861,15 +243457,16 @@ relationship: part_of GO:0044177 ! host cell Golgi apparatus
[Term]
id: GO:0044179
-name: hemolysis in other organism
+name: hemolysis in another organism
namespace: biological_process
def: "The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another." [GOC:jl]
subset: goslim_chembl
+synonym: "hemolysis in other organism" EXACT []
synonym: "hemolysis of cells in other organism" EXACT [GOC:bf]
synonym: "hemolysis of erythrocytes in other organism" EXACT []
synonym: "hemolysis of RBCs in other organism" EXACT []
synonym: "hemolysis of red blood cells in other organism" EXACT []
-is_a: GO:0051715 ! cytolysis in other organism
+is_a: GO:0051715 ! cytolysis in another organism
[Term]
id: GO:0044180
@@ -243899,6 +243496,8 @@ name: protein folding chaperone
namespace: molecular_function
def: "Binding to a protein or a protein-containing complex to assist the protein folding process." [GOC:mtg_cambridge_2009]
subset: goslim_chembl
+subset: goslim_drosophila
+subset: goslim_generic
synonym: "chaperone activity" BROAD []
synonym: "protein binding involved in protein folding" EXACT []
xref: Reactome:R-HSA-9018785 "RHOBTB2 binds GTP"
@@ -244014,7 +243613,7 @@ is_a: GO:0044094 ! host cell nuclear part
id: GO:0044197
name: Rel homology domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Rel Homology Domain (RHD) of a protein. The RHD is found in a family of eukaryotic transcription factors, which includes NF-kappaB, Dorsal, Relish and NFAT." [InterPro:IPR011539, Wikipedia:Rel_homology_domain]
+def: "Binding to a Rel Homology Domain (RHD) of a protein. The RHD is found in a family of eukaryotic transcription factors, which includes NF-kappaB, Dorsal, Relish and NFAT." [InterPro:IPR011539, Wikipedia:Rel_homology_domain]
synonym: "RHD binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -244022,7 +243621,7 @@ is_a: GO:0019904 ! protein domain specific binding
id: GO:0044198
name: zf-TRAF domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a TRAF-type zinc finger domain of a protein." [InterPro:IPR001293]
+def: "Binding to a TRAF-type zinc finger domain of a protein." [InterPro:IPR001293]
synonym: "TRAF-type zinc finger domain binding" EXACT []
synonym: "zinc finger TRAF-type domain binding" EXACT []
synonym: "zinc-finger-TRAF domain binding" EXACT []
@@ -244117,7 +243716,7 @@ def: "The chemical reactions and pathways resulting in the formation of adenosin
synonym: "adenosine monophosphate salvage" EXACT []
synonym: "AMP biosynthetic process via salvage pathway" EXACT []
is_a: GO:0006167 ! AMP biosynthetic process
-is_a: GO:0032261 ! purine nucleotide salvage
+is_a: GO:0106380 ! purine ribonucleotide salvage
[Term]
id: GO:0044210
@@ -244314,7 +243913,6 @@ synonym: "endoplasmic reticulum-mitochondrion membrane contact site" EXACT []
synonym: "ER-mitochondrion membrane contact site" EXACT []
synonym: "MAM" RELATED []
synonym: "mitochondria-associated ER membrane" EXACT []
-synonym: "Mitochondria-associated Membrane" RELATED []
synonym: "mitochondria-associated membrane" EXACT []
synonym: "mitochondria-endoplasmic reticulum (ER) contact" EXACT [PMID:29870872]
is_a: GO:0044232 ! organelle membrane contact site
@@ -244324,6 +243922,7 @@ id: GO:0044237
name: cellular metabolic process
namespace: biological_process
def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators]
+subset: gocheck_do_not_annotate
synonym: "cellular metabolism" EXACT []
synonym: "intermediary metabolism" RELATED [GOC:mah]
is_a: GO:0008152 ! metabolic process
@@ -244618,10 +244217,11 @@ is_a: GO:0071555 ! cell wall organization
[Term]
id: GO:0044278
-name: cell wall disruption in other organism
+name: cell wall disruption in another organism
namespace: biological_process
def: "A process carried out by an organism that results in the breakdown of the cell wall of a second organism." [GOC:jl]
-is_a: GO:0035821 ! modulation of process of other organism
+synonym: "cell wall disruption in other organism" EXACT []
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0044280
@@ -244640,7 +244240,6 @@ def: "The chemical reactions and pathways involving small molecules, any low mol
comment: Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
subset: goslim_chembl
subset: goslim_flybase_ribbon
-subset: goslim_generic
subset: goslim_metagenomics
synonym: "small molecule metabolism" EXACT []
is_a: GO:0008152 ! metabolic process
@@ -245012,8 +244611,7 @@ relationship: part_of GO:0005783 ! endoplasmic reticulum
id: GO:0044323
name: retinoic acid-responsive element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a retinoic acid-responsive element, a variable direct repeat of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [GOC:jl, GOC:vw, GOC:yaf, PMID:11327309, PMID:19917671]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to a retinoic acid-responsive element, a variable direct repeat of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [GOC:jl, GOC:vw, GOC:yaf, PMID:11327309, PMID:19917671]
synonym: "RARE binding" EXACT []
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
@@ -245027,10 +244625,11 @@ relationship: part_of GO:0009948 ! anterior/posterior axis specification
[Term]
id: GO:0044325
-name: ion channel binding
+name: transmembrane transporter binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient." [GOC:BHF, GOC:jl]
+def: "Binding to a transmembrane transporter, a protein or protein complex that enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other." [GOC:BHF, GOC:jl, PMID:33199372]
subset: goslim_chembl
+synonym: "ion channel binding" NARROW []
is_a: GO:0005515 ! protein binding
[Term]
@@ -245341,68 +244940,76 @@ is_a: GO:1902374 ! regulation of rRNA catabolic process
[Term]
id: GO:0044358
-name: envenomation resulting in hemorrhagic damage to other organism
+name: envenomation resulting in hemorrhagic damage in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with vascular damage and hemorrhage in the bitten organism." [PMID:10441379, PMID:20614020]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in hemorrhagic damage to other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044359
-name: modulation of molecular function in other organism
+name: modulation of molecular function in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the function of proteins in a second organism." [GOC:jl]
-is_a: GO:0035821 ! modulation of process of other organism
+synonym: "modulation of molecular function in other organism" EXACT []
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0044360
-name: modulation of voltage-gated potassium channel activity in other organism
+name: modulation of voltage-gated potassium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism effects a change in the frequency, rate or extent of the activity of a voltage-gated potassium channel in another organism." [GOC:jl]
-is_a: GO:0044363 ! modulation of potassium channel activity in other organism
+synonym: "modulation of voltage-gated potassium channel activity in other organism" EXACT []
+is_a: GO:0044363 ! modulation of potassium channel activity in another organism
[Term]
id: GO:0044361
-name: negative regulation of voltage-gated potassium channel activity in other organism
+name: negative regulation of voltage-gated potassium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the activity of a voltage-gated potassium channel in another organism." [GOC:jl]
-is_a: GO:0044360 ! modulation of voltage-gated potassium channel activity in other organism
-is_a: GO:0044362 ! negative regulation of molecular function in other organism
+synonym: "negative regulation of voltage-gated potassium channel activity in other organism" EXACT []
+is_a: GO:0044360 ! modulation of voltage-gated potassium channel activity in another organism
+is_a: GO:0044362 ! negative regulation of molecular function in another organism
[Term]
id: GO:0044362
-name: negative regulation of molecular function in other organism
+name: negative regulation of molecular function in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the function of proteins in a second organism." [GOC:jl]
+synonym: "negative regulation of molecular function in other organism" EXACT []
is_a: GO:0044092 ! negative regulation of molecular function
-is_a: GO:0044359 ! modulation of molecular function in other organism
+is_a: GO:0044359 ! modulation of molecular function in another organism
[Term]
id: GO:0044363
-name: modulation of potassium channel activity in other organism
+name: modulation of potassium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism effects a change in the frequency, rate or extent of the activity of a potassium channel in another organism." [GOC:jl]
-is_a: GO:0044561 ! modulation of ion channel activity in other organism
+synonym: "modulation of potassium channel activity in other organism" EXACT []
+is_a: GO:0044561 ! modulation of ion channel activity in another organism
[Term]
id: GO:0044364
-name: disruption of cells of other organism
+name: disruption of cells of another organism
namespace: biological_process
def: "A process in which an organism has a negative effect on the functioning of the second organism's cells." [GOC:jl]
-is_a: GO:0035821 ! modulation of process of other organism
+synonym: "disruption of cells of other organism" EXACT []
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0044365
-name: envenomation resulting in modulation of platelet aggregation in other organism
+name: envenomation resulting in modulation of platelet aggregation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change to the frequency, rate or extent of platelet aggregation in the bitten organism." [GOC:fj, GOC:jl]
+synonym: "envenomation resulting in modulation of platelet aggregation in other organism" EXACT []
synonym: "envenomation resulting in regulation of platelet aggregation in other organism" EXACT []
-is_a: GO:0044468 ! envenomation resulting in modulation of blood coagulation in other organism
+is_a: GO:0044468 ! envenomation resulting in modulation of blood coagulation in another organism
[Term]
id: GO:0044373
name: cytokinin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cytokinin, any of a class of adenine-derived compounds that can function in plants as growth regulators." [GOC:jl]
+def: "Binding to a cytokinin, any of a class of adenine-derived compounds that can function in plants as growth regulators." [GOC:jl]
is_a: GO:0042562 ! hormone binding
[Term]
@@ -245439,7 +245046,7 @@ consider: GO:0006606
id: GO:0044377
name: RNA polymerase II cis-regulatory region sequence-specific DNA binding, bending
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase II, and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:jl, GOC:pg]
+def: "Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by RNA polymerase II, and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence." [GOC:jl, GOC:pg]
synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding, bending" RELATED []
synonym: "RNA polymerase II promoter proximal region sequence-specific DNA binding, bending" RELATED []
synonym: "RNA polymerase II proximal promoter region sequence-specific DNA binding, bending" RELATED []
@@ -245488,7 +245095,7 @@ namespace: biological_process
def: "The process by which a CLRC complex is transported to, or maintained in, heterochromatin. CLRC complex is an active cullin-dependent E3 ubiquitin ligase complex essential for heterochromatin assembly by RNAi and histone H3K9 methylation." [GOC:jl]
synonym: "CLRC ubiquitin ligase complex localisation to heterochromatin" EXACT [GOC:mah]
synonym: "CLRC ubiquitin ligase complex localization to heterochromatin" EXACT []
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
is_a: GO:0097355 ! protein localization to heterochromatin
[Term]
@@ -245534,14 +245141,14 @@ is_a: GO:0006469 ! negative regulation of protein kinase activity
id: GO:0044388
name: small protein activating enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a small protein activating enzyme, such as ubiquitin-activating enzyme." [GOC:jl]
+def: "Binding to a small protein activating enzyme, such as ubiquitin-activating enzyme." [GOC:jl]
is_a: GO:0019899 ! enzyme binding
[Term]
id: GO:0044389
name: ubiquitin-like protein ligase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ubiquitin-like protein ligase, such as ubiquitin-ligase." [GOC:jl]
+def: "Binding to a ubiquitin-like protein ligase, such as ubiquitin-ligase." [GOC:jl]
synonym: "E3 protein ligase binding" EXACT []
synonym: "small conjugating protein ligase binding" EXACT [GOC:dph]
is_a: GO:0019899 ! enzyme binding
@@ -245550,7 +245157,7 @@ is_a: GO:0019899 ! enzyme binding
id: GO:0044390
name: ubiquitin-like protein conjugating enzyme binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ubiquitin-like protein conjugating enzyme such as ubiquitin conjugating enzyme." [GOC:jl]
+def: "Binding to a ubiquitin-like protein conjugating enzyme such as ubiquitin conjugating enzyme." [GOC:jl]
synonym: "E2 protein ligase binding" EXACT []
synonym: "small protein conjugating enzyme binding" EXACT [GOC:dph]
is_a: GO:0019899 ! enzyme binding
@@ -245616,11 +245223,12 @@ replaced_by: GO:0006897
[Term]
id: GO:0044398
-name: envenomation resulting in induction of edema in other organism
+name: envenomation resulting in induction of edema in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the swelling of soft tissues of the bitten organism as a result of excess water accumulation." [GOC:jl, PMID:20562011]
+synonym: "envenomation resulting in induction of edema in other organism" EXACT []
synonym: "envenomation resulting in induction of oedema in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044399
@@ -245658,7 +245266,6 @@ alt_id: GO:0072519
alt_id: GO:0085031
def: "A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts." [GOC:cc, PMID:31257129]
subset: goslim_chembl
-subset: goslim_generic
synonym: "commensalism" NARROW []
synonym: "host-pathogen interaction" NARROW []
synonym: "parasitism" NARROW []
@@ -245753,13 +245360,14 @@ is_a: GO:0052126 ! movement in host environment
[Term]
id: GO:0044410
-name: entry into host through natural portals
+name: obsolete entry into host through natural portals
namespace: biological_process
alt_id: GO:0051829
-def: "Penetration by a symbiont into a host organism via naturally occurring openings in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:cc]
+def: "OBSOLETE. Penetration by a symbiont into a host organism via naturally occurring openings in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:cc]
+comment: This is an unnecessary grouping term.
synonym: "entry into other organism through natural portals during symbiotic interaction" RELATED [GOC:tb]
synonym: "entry into other organism through natural portals involved in symbiotic interaction" RELATED []
-is_a: GO:0044409 ! entry into host
+is_obsolete: true
[Term]
id: GO:0044412
@@ -245900,8 +245508,6 @@ name: virion component
namespace: cellular_component
alt_id: GO:0019012
def: "Any constituent part of a virion, a complete fully infectious extracellular virus particle." [GOC:jl]
-comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
-subset: gocheck_do_not_annotate
subset: goslim_chembl
subset: goslim_metagenomics
subset: goslim_pir
@@ -246364,11 +245970,12 @@ consider: CL:0000000
[Term]
id: GO:0044465
-name: modulation of sensory perception of pain in other organism
+name: modulation of sensory perception of pain in another organism
namespace: biological_process
def: "A process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal, in a different organism." [GOC:ed, PMID:18579526]
+synonym: "modulation of sensory perception of pain in other organism" EXACT []
synonym: "regulation of sensory perception of pain in another organism" EXACT []
-is_a: GO:0035821 ! modulation of process of other organism
+is_a: GO:0035821 ! modulation of process of another organism
is_a: GO:0051930 ! regulation of sensory perception of pain
[Term]
@@ -246393,303 +246000,341 @@ is_a: GO:0001816 ! cytokine production
[Term]
id: GO:0044468
-name: envenomation resulting in modulation of blood coagulation in other organism
+name: envenomation resulting in modulation of blood coagulation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the modulation of the frequency, rate or extent of blood coagulation in the bitten organism." [GOC:jl]
+synonym: "envenomation resulting in modulation of blood coagulation in other organism" EXACT []
synonym: "envenomation resulting in regulation of blood coagulation in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044469
-name: envenomation resulting in positive regulation of blood coagulation in other organism
+name: envenomation resulting in positive regulation of blood coagulation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant activation, maintenance or an increase in the frequency, rate or extent of blood coagulation in the bitten organism." [GOC:jl]
-is_a: GO:0044468 ! envenomation resulting in modulation of blood coagulation in other organism
-is_a: GO:0044483 ! envenomation resulting in impairment of hemostasis in other organism
+synonym: "envenomation resulting in positive regulation of blood coagulation in other organism" EXACT []
+is_a: GO:0044468 ! envenomation resulting in modulation of blood coagulation in another organism
+is_a: GO:0044483 ! envenomation resulting in impairment of hemostasis in another organism
[Term]
id: GO:0044470
-name: envenomation resulting in negative regulation of blood coagulation in other organism
+name: envenomation resulting in negative regulation of blood coagulation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction in the frequency, rate or extent of blood coagulation in the bitten organism." [GOC:jl]
-is_a: GO:0044468 ! envenomation resulting in modulation of blood coagulation in other organism
-is_a: GO:0044483 ! envenomation resulting in impairment of hemostasis in other organism
+synonym: "envenomation resulting in negative regulation of blood coagulation in other organism" EXACT []
+is_a: GO:0044468 ! envenomation resulting in modulation of blood coagulation in another organism
+is_a: GO:0044483 ! envenomation resulting in impairment of hemostasis in another organism
[Term]
id: GO:0044471
-name: envenomation resulting in pore formation in membrane of other organism
+name: envenomation resulting in pore formation in membrane of another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the aggregation, arrangement and bonding together of a set of components to form a pore complex in a membrane of the bitten organism." [GOC:fj, GOC:jl, PMID:21549739]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in pore formation in membrane of other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044472
-name: envenomation resulting in modulation of calcium channel activity in other organism
+name: envenomation resulting in modulation of calcium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of a calcium channel in the bitten organism." [GOC:fj, GOC:jl, PMID:20920515]
-is_a: GO:0044560 ! envenomation resulting in modulation of ion channel activity in other organism
+synonym: "envenomation resulting in modulation of calcium channel activity in other organism" EXACT []
+is_a: GO:0044560 ! envenomation resulting in modulation of ion channel activity in another organism
[Term]
id: GO:0044473
-name: envenomation resulting in negative regulation of calcium channel activity in other organism
+name: envenomation resulting in negative regulation of calcium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a calcium channel in the bitten organism." [GOC:fj, GOC:jl, PMID:20920515]
-is_a: GO:0044472 ! envenomation resulting in modulation of calcium channel activity in other organism
+synonym: "envenomation resulting in negative regulation of calcium channel activity in other organism" EXACT []
+is_a: GO:0044472 ! envenomation resulting in modulation of calcium channel activity in another organism
[Term]
id: GO:0044474
-name: envenomation resulting in negative regulation of voltage-gated calcium channel activity in other organism
+name: envenomation resulting in negative regulation of voltage-gated calcium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a voltage-gated calcium channel in the bitten organism." [GOC:fj, GOC:jl, PMID:20920515]
-is_a: GO:0044473 ! envenomation resulting in negative regulation of calcium channel activity in other organism
+synonym: "envenomation resulting in negative regulation of voltage-gated calcium channel activity in other organism" EXACT []
+is_a: GO:0044473 ! envenomation resulting in negative regulation of calcium channel activity in another organism
[Term]
id: GO:0044475
-name: envenomation resulting in negative regulation of high voltage-gated calcium channel activity in other organism
+name: envenomation resulting in negative regulation of high voltage-gated calcium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a high voltage-gated calcium channel in the bitten organism." [GOC:fj, GOC:jl, PMID:20920515]
-is_a: GO:0044474 ! envenomation resulting in negative regulation of voltage-gated calcium channel activity in other organism
+synonym: "envenomation resulting in negative regulation of high voltage-gated calcium channel activity in other organism" EXACT []
+is_a: GO:0044474 ! envenomation resulting in negative regulation of voltage-gated calcium channel activity in another organism
[Term]
id: GO:0044476
-name: envenomation resulting in negative regulation of low voltage-gated calcium channel activity in other organism
+name: envenomation resulting in negative regulation of low voltage-gated calcium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a low voltage-gated calcium channel in the bitten organism." [GOC:fj, GOC:jl, PMID:20920515]
-is_a: GO:0044474 ! envenomation resulting in negative regulation of voltage-gated calcium channel activity in other organism
+synonym: "envenomation resulting in negative regulation of low voltage-gated calcium channel activity in other organism" EXACT []
+is_a: GO:0044474 ! envenomation resulting in negative regulation of voltage-gated calcium channel activity in another organism
[Term]
id: GO:0044477
-name: envenomation resulting in negative regulation of platelet aggregation in other organism
+name: envenomation resulting in negative regulation of platelet aggregation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction in the frequency, rate or extent of platelet aggregation in the bitten organism." [GOC:fj, GOC:jl]
-is_a: GO:0044365 ! envenomation resulting in modulation of platelet aggregation in other organism
+synonym: "envenomation resulting in negative regulation of platelet aggregation in other organism" EXACT []
+is_a: GO:0044365 ! envenomation resulting in modulation of platelet aggregation in another organism
[Term]
id: GO:0044478
-name: envenomation resulting in positive regulation of platelet aggregation in other organism
+name: envenomation resulting in positive regulation of platelet aggregation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant activation, maintenance or an increase in the frequency, rate or extent of platelet aggregation in the bitten organism." [GOC:fj, GOC:jl]
-is_a: GO:0044365 ! envenomation resulting in modulation of platelet aggregation in other organism
-is_a: GO:0044469 ! envenomation resulting in positive regulation of blood coagulation in other organism
+synonym: "envenomation resulting in positive regulation of platelet aggregation in other organism" EXACT []
+is_a: GO:0044365 ! envenomation resulting in modulation of platelet aggregation in another organism
+is_a: GO:0044469 ! envenomation resulting in positive regulation of blood coagulation in another organism
[Term]
id: GO:0044479
-name: envenomation resulting in modulation of mast cell degranulation in other organism
+name: envenomation resulting in modulation of mast cell degranulation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of blood mast cell degranulation in the bitten organism." [GOC:fj, GOC:jl, PMID:21549739]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in modulation of mast cell degranulation in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044480
-name: envenomation resulting in positive regulation of mast cell degranulation in other organism
+name: envenomation resulting in positive regulation of mast cell degranulation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of blood mast cell degranulation in the bitten organism." [GOC:fj, GOC:jl, PMID:21549739]
-is_a: GO:0044479 ! envenomation resulting in modulation of mast cell degranulation in other organism
+synonym: "envenomation resulting in positive regulation of mast cell degranulation in other organism" EXACT []
+is_a: GO:0044479 ! envenomation resulting in modulation of mast cell degranulation in another organism
[Term]
id: GO:0044481
-name: envenomation resulting in proteolysis in other organism
+name: envenomation resulting in proteolysis in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant hydrolysis of proteins in of the bitten organism." [GOC:fj, GOC:jl, PMID:15922779]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in proteolysis in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044482
-name: envenomation resulting in blood vessel extracellular matrix damage, causing hemorrhagic damage in other organism
+name: envenomation resulting in blood vessel extracellular matrix damage, causing hemorrhagic damage in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism which causes damage to the extracellular matrix of the blood vessels of the bitten organism, ultimately resulting in hemorrhage in the bitten organism." [GOC:fj, GOC:jl, PMID:10441379, PMID:19485419]
synonym: "envenomation resulting in blood vessel ECM, causing hemorrhagic damage in other organism" EXACT []
-is_a: GO:0044358 ! envenomation resulting in hemorrhagic damage to other organism
+synonym: "envenomation resulting in blood vessel extracellular matrix damage, causing hemorrhagic damage in other organism" EXACT []
+is_a: GO:0044358 ! envenomation resulting in hemorrhagic damage in another organism
[Term]
id: GO:0044483
-name: envenomation resulting in impairment of hemostasis in other organism
+name: envenomation resulting in impairment of hemostasis in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the inhibition of the process of hemostasis - the stopping of bleeding or the arrest of the circulation to an organ or part - in the bitten organism." [GOC:fj, GOC:jl]
+synonym: "envenomation resulting in impairment of hemostasis in other organism" EXACT []
synonym: "envenomation resulting in negative regulation of hemostasis in other organism" EXACT []
synonym: "envenomation, impairing hemostasis in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044484
-name: envenomation resulting in fibrinolysis in other organism
+name: envenomation resulting in fibrinolysis in another organism
namespace: biological_process
def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with fibrinolysis, a process that solubilizes fibrin, chiefly by the proteolytic action of plasmin, in the bloodstream of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:17433397, PMID:17544404]
-is_a: GO:0044483 ! envenomation resulting in impairment of hemostasis in other organism
+synonym: "envenomation resulting in fibrinolysis in other organism" EXACT []
+is_a: GO:0044483 ! envenomation resulting in impairment of hemostasis in another organism
[Term]
id: GO:0044485
-name: envenomation resulting in fibrinogenolysis in other organism
+name: envenomation resulting in fibrinogenolysis in another organism
namespace: biological_process
def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with fibrinogenolysis, a process that degrades fibrinogen at a variety of Arg-Lys bonds, thus impairing fibrinogen clotting in the bloodstream of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:17433397, PMID:17544404]
-is_a: GO:0044536 ! envenomation resulting in depletion of circulating fibrinogen in other organism
+synonym: "envenomation resulting in fibrinogenolysis in other organism" EXACT []
+is_a: GO:0044536 ! envenomation resulting in depletion of circulating fibrinogen in another organism
[Term]
id: GO:0044486
-name: modulation of transmission of nerve impulse in other organism
+name: modulation of transmission of nerve impulse in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the transmission of a nerve impulse in another organism." [GOC:jl]
synonym: "modulation of conduction of nerve impulse in other organism" EXACT [GOC:dph]
+synonym: "modulation of transmission of nerve impulse in other organism" EXACT []
synonym: "regulation of transmission of nerve impulse in other organism" EXACT []
-is_a: GO:0035821 ! modulation of process of other organism
+is_a: GO:0035821 ! modulation of process of another organism
is_a: GO:0051969 ! regulation of transmission of nerve impulse
[Term]
id: GO:0044487
-name: envenomation resulting in modulation of transmission of nerve impulse in other organism
+name: envenomation resulting in modulation of transmission of nerve impulse in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of the transmission of nerve impulses in the bitten organism." [GOC:fj, GOC:jl]
synonym: "envenomation resulting in modulation of conduction of nerve impulse in other organism" EXACT [GOC:dph]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in modulation of transmission of nerve impulse in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044488
-name: modulation of voltage-gated sodium channel activity in other organism
+name: modulation of voltage-gated sodium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism effects a change in the frequency, rate or extent of the activity of a voltage-gated sodium channel in another organism." [GOC:fj, GOC:jl, PMID:21781281]
-is_a: GO:0044561 ! modulation of ion channel activity in other organism
+synonym: "modulation of voltage-gated sodium channel activity in other organism" EXACT []
+is_a: GO:0044561 ! modulation of ion channel activity in another organism
[Term]
id: GO:0044489
-name: negative regulation of voltage-gated sodium channel activity in other organism
+name: negative regulation of voltage-gated sodium channel activity in another organism
namespace: biological_process
def: "Any process in which an organism stops, prevents or reduces the frequency, rate or extent of the activity of a voltage-gated sodium channel in another organism." [GOC:fj, GOC:jl, PMID:21781281]
-is_a: GO:0044362 ! negative regulation of molecular function in other organism
-is_a: GO:0044488 ! modulation of voltage-gated sodium channel activity in other organism
+synonym: "negative regulation of voltage-gated sodium channel activity in other organism" EXACT []
+is_a: GO:0044362 ! negative regulation of molecular function in another organism
+is_a: GO:0044488 ! modulation of voltage-gated sodium channel activity in another organism
[Term]
id: GO:0044490
-name: positive regulation of voltage-gated sodium channel activity in other organism
+name: positive regulation of voltage-gated sodium channel activity in another organism
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the activity of a voltage-gated sodium channel in another organism." [GOC:fj, GOC:jl, PMID:21781281]
-is_a: GO:0044488 ! modulation of voltage-gated sodium channel activity in other organism
-is_a: GO:0044491 ! positive regulation of molecular function in other organism
+synonym: "positive regulation of voltage-gated sodium channel activity in other organism" EXACT []
+is_a: GO:0044488 ! modulation of voltage-gated sodium channel activity in another organism
+is_a: GO:0044491 ! positive regulation of molecular function in another organism
[Term]
id: GO:0044491
-name: positive regulation of molecular function in other organism
+name: positive regulation of molecular function in another organism
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of the function of proteins in a second organism." [GOC:jl]
+synonym: "positive regulation of molecular function in other organism" EXACT []
is_a: GO:0044092 ! negative regulation of molecular function
is_a: GO:0044093 ! positive regulation of molecular function
-is_a: GO:0044359 ! modulation of molecular function in other organism
+is_a: GO:0044359 ! modulation of molecular function in another organism
[Term]
id: GO:0044492
-name: envenomation resulting in modulation of voltage-gated sodium channel activity in other organism
+name: envenomation resulting in modulation of voltage-gated sodium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of a voltage-gated sodium channel in the bitten organism." [GOC:fj, GOC:jl, PMID:21781281]
-is_a: GO:0044560 ! envenomation resulting in modulation of ion channel activity in other organism
+synonym: "envenomation resulting in modulation of voltage-gated sodium channel activity in other organism" EXACT []
+is_a: GO:0044560 ! envenomation resulting in modulation of ion channel activity in another organism
[Term]
id: GO:0044493
-name: envenomation resulting in negative regulation of voltage-gated sodium channel activity in other organism
+name: envenomation resulting in negative regulation of voltage-gated sodium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant stopping, prevention or reduction of the activity of a voltage-gated sodium channel in the bitten organism." [GOC:fj, GOC:jl, PMID:21781281]
-is_a: GO:0044492 ! envenomation resulting in modulation of voltage-gated sodium channel activity in other organism
+synonym: "envenomation resulting in negative regulation of voltage-gated sodium channel activity in other organism" EXACT []
+is_a: GO:0044492 ! envenomation resulting in modulation of voltage-gated sodium channel activity in another organism
[Term]
id: GO:0044494
-name: envenomation resulting in positive regulation of voltage-gated sodium channel activity in other organism
+name: envenomation resulting in positive regulation of voltage-gated sodium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant activation or increase in the activity of the activity of a voltage-gated sodium channel in the bitten organism." [GOC:fj, GOC:jl, PMID:21781281]
-is_a: GO:0044492 ! envenomation resulting in modulation of voltage-gated sodium channel activity in other organism
+synonym: "envenomation resulting in positive regulation of voltage-gated sodium channel activity in other organism" EXACT []
+is_a: GO:0044492 ! envenomation resulting in modulation of voltage-gated sodium channel activity in another organism
[Term]
id: GO:0044495
-name: modulation of blood pressure in other organism
+name: modulation of blood pressure in another organism
namespace: biological_process
def: "A process by which one organism modulates the force with which blood travels through the circulatory system of another organism." [GOC:fj, GOC:jl, PMID:19837656]
+synonym: "modulation of blood pressure in other organism" EXACT []
synonym: "regulation of blood pressure in other organism" EXACT []
is_a: GO:0008217 ! regulation of blood pressure
[Term]
id: GO:0044496
-name: negative regulation of blood pressure in other organism
+name: negative regulation of blood pressure in another organism
namespace: biological_process
def: "A process by which one organism decreases the force with which blood travels through the circulatory system of another organism." [GOC:fj, GOC:jl, PMID:19837656]
-is_a: GO:0044495 ! modulation of blood pressure in other organism
+synonym: "negative regulation of blood pressure in other organism" EXACT []
+is_a: GO:0044495 ! modulation of blood pressure in another organism
is_a: GO:0045776 ! negative regulation of blood pressure
[Term]
id: GO:0044497
-name: positive regulation of blood pressure in other organism
+name: positive regulation of blood pressure in another organism
namespace: biological_process
def: "A process by which one organism increases the force with which blood travels through the circulatory system of another organism." [GOC:fj, GOC:jl, PMID:19837656]
-is_a: GO:0044495 ! modulation of blood pressure in other organism
+synonym: "positive regulation of blood pressure in other organism" EXACT []
+is_a: GO:0044495 ! modulation of blood pressure in another organism
is_a: GO:0045777 ! positive regulation of blood pressure
[Term]
id: GO:0044498
-name: envenomation resulting in modulation of blood pressure in other organism
+name: envenomation resulting in modulation of blood pressure in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of the force with which blood travels through the circulatory system of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:19837656]
+synonym: "envenomation resulting in modulation of blood pressure in other organism" EXACT []
synonym: "envenomation resulting in regulation of blood pressure in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044499
-name: envenomation resulting in positive regulation of blood pressure in other organism
+name: envenomation resulting in positive regulation of blood pressure in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant increase of the force with which blood travels through the circulatory system of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:19837656]
-is_a: GO:0044498 ! envenomation resulting in modulation of blood pressure in other organism
+synonym: "envenomation resulting in positive regulation of blood pressure in other organism" EXACT []
+is_a: GO:0044498 ! envenomation resulting in modulation of blood pressure in another organism
[Term]
id: GO:0044500
-name: envenomation resulting in negative regulation of blood pressure in other organism
+name: envenomation resulting in negative regulation of blood pressure in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant decrease of the force with which blood travels through the circulatory system of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:19837656]
+synonym: "envenomation resulting in negative regulation of blood pressure in other organism" EXACT []
synonym: "hypotensive activity in other organism" EXACT []
-is_a: GO:0044498 ! envenomation resulting in modulation of blood pressure in other organism
+is_a: GO:0044498 ! envenomation resulting in modulation of blood pressure in another organism
[Term]
id: GO:0044501
-name: modulation of signal transduction in other organism
+name: modulation of signal transduction in another organism
namespace: biological_process
def: "The process in which an organism effects a change in a signal transduction process - a cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell - in a second organism." [GOC:fj, GOC:jl]
-is_a: GO:0035821 ! modulation of process of other organism
+synonym: "modulation of signal transduction in other organism" EXACT []
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0044503
-name: modulation of G protein-coupled receptor activity in other organism
+name: modulation of G protein-coupled receptor activity in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the activity of a G protein-coupled receptor in a second organism." [GOC:fj, GOC:jl, PMID:8405712]
+synonym: "modulation of G protein-coupled receptor activity in other organism" EXACT []
synonym: "modulation of G-protein coupled receptor activity in other organism" EXACT []
-is_a: GO:0044504 ! modulation of receptor activity in other organism
+is_a: GO:0044504 ! modulation of receptor activity in another organism
[Term]
id: GO:0044504
-name: modulation of receptor activity in other organism
+name: modulation of receptor activity in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the activity of a receptor in a second organism." [GOC:fj, GOC:jl, PMID:8405712]
-is_a: GO:0044359 ! modulation of molecular function in other organism
+synonym: "modulation of receptor activity in other organism" EXACT []
+is_a: GO:0044359 ! modulation of molecular function in another organism
[Term]
id: GO:0044505
-name: positive regulation of G protein-coupled receptor activity in other organism
+name: positive regulation of G protein-coupled receptor activity in another organism
namespace: biological_process
def: "A process that activates or increases the frequency, rate or extent of the activity of a G protein-coupled receptor in a second organism." [GOC:fj, GOC:jl, PMID:8405712]
+synonym: "positive regulation of G protein-coupled receptor activity in other organism" EXACT []
synonym: "positive regulation of G-protein coupled receptor activity in other organism" EXACT []
-synonym: "regulation of G-protein coupled receptor activity in other organism" EXACT []
-is_a: GO:0044503 ! modulation of G protein-coupled receptor activity in other organism
-is_a: GO:0044507 ! positive regulation of receptor activity in other organism
+is_a: GO:0044503 ! modulation of G protein-coupled receptor activity in another organism
+is_a: GO:0044507 ! positive regulation of receptor activity in another organism
is_a: GO:2000273 ! positive regulation of signaling receptor activity
[Term]
id: GO:0044506
-name: modulation of glucagon-like peptide receptor 1 activity in other organism
+name: modulation of glucagon-like peptide receptor 1 activity in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the activity of a glucagon-like peptide receptor 1 in a second organism." [GOC:fj, GOC:jl, PMID:8405712]
+synonym: "modulation of glucagon-like peptide receptor 1 activity in other organism" EXACT []
synonym: "regulation of glucagon-like peptide receptor activity in other organism" EXACT []
-is_a: GO:0044504 ! modulation of receptor activity in other organism
+is_a: GO:0044504 ! modulation of receptor activity in another organism
[Term]
id: GO:0044507
-name: positive regulation of receptor activity in other organism
+name: positive regulation of receptor activity in another organism
namespace: biological_process
def: "A process that activates or increases the frequency, rate or extent of the activity of a receptor in a second organism." [GOC:fj, GOC:jl, PMID:8405712]
-is_a: GO:0044491 ! positive regulation of molecular function in other organism
-is_a: GO:0044504 ! modulation of receptor activity in other organism
+synonym: "positive regulation of receptor activity in other organism" EXACT []
+is_a: GO:0044491 ! positive regulation of molecular function in another organism
+is_a: GO:0044504 ! modulation of receptor activity in another organism
[Term]
id: GO:0044508
@@ -246700,121 +246345,136 @@ is_a: GO:0008528 ! G protein-coupled peptide receptor activity
[Term]
id: GO:0044509
-name: envenomation resulting in modulation of signal transduction in other organism
+name: envenomation resulting in modulation of signal transduction in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of signal transduction in the bitten organism." [GOC:fj, GOC:jl, PMID:8405712]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in modulation of signal transduction in other organismm" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044510
-name: envenomation resulting in positive regulation of signal transduction in other organism
+name: envenomation resulting in positive regulation of signal transduction in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of signal transduction in the bitten organism." [GOC:fj, GOC:jl, PMID:8405712]
-is_a: GO:0044509 ! envenomation resulting in modulation of signal transduction in other organism
+synonym: "envenomation resulting in positive regulation of signal transduction in other organism" EXACT []
+is_a: GO:0044509 ! envenomation resulting in modulation of signal transduction in another organism
[Term]
id: GO:0044511
-name: envenomation resulting in modulation of receptor activity in other organism
+name: envenomation resulting in modulation of receptor activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of receptor activity in of the bitten organism." [GOC:fj, GOC:jl, PMID:8405712]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in modulation of receptor activity in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044512
-name: envenomation resulting in modulation of glucagon-like peptide receptor 1 activity in other organism
+name: envenomation resulting in modulation of glucagon-like peptide receptor 1 activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of glucagon-like peptide receptor 1 activity in of the bitten organism." [GOC:fj, GOC:jl, PMID:8405712]
-is_a: GO:0044511 ! envenomation resulting in modulation of receptor activity in other organism
+synonym: "envenomation resulting in modulation of glucagon-like peptide receptor 1 activity in other organism" EXACT []
+is_a: GO:0044511 ! envenomation resulting in modulation of receptor activity in another organism
[Term]
id: GO:0044513
-name: envenomation resulting in modulation of G protein-coupled receptor activity in other organism
+name: envenomation resulting in modulation of G protein-coupled receptor activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of G protein-coupled receptor activity in of the bitten organism." [GOC:fj, GOC:jl, PMID:8405712]
+synonym: "envenomation resulting in modulation of G protein-coupled receptor activity in other organism" EXACT []
synonym: "envenomation resulting in modulation of G-protein coupled receptor activity in other organism" EXACT []
-is_a: GO:0044511 ! envenomation resulting in modulation of receptor activity in other organism
+is_a: GO:0044511 ! envenomation resulting in modulation of receptor activity in another organism
[Term]
id: GO:0044514
-name: envenomation resulting in positive regulation of G protein-coupled receptor activity in other organism
+name: envenomation resulting in positive regulation of G protein-coupled receptor activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of G protein-coupled receptor activity in of the bitten organism." [GOC:fj, GOC:jl, PMID:8405712]
+synonym: "envenomation resulting in positive regulation of G protein-coupled receptor activity in other organism" EXACT []
synonym: "envenomation resulting in positive regulation of G-protein coupled receptor activity in other organism" EXACT []
-is_a: GO:0044513 ! envenomation resulting in modulation of G protein-coupled receptor activity in other organism
+is_a: GO:0044513 ! envenomation resulting in modulation of G protein-coupled receptor activity in another organism
[Term]
id: GO:0044515
-name: envenomation resulting in positive regulation of glucagon-like peptide receptor 1 activity in other organism
+name: envenomation resulting in positive regulation of glucagon-like peptide receptor 1 activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of glucagon-like peptide receptor 1 activity in of the bitten organism." [GOC:fj, GOC:jl, PMID:8405712]
-is_a: GO:0044512 ! envenomation resulting in modulation of glucagon-like peptide receptor 1 activity in other organism
+synonym: "envenomation resulting in positive regulation of glucagon-like peptide receptor 1 activity in other organism" EXACT []
+is_a: GO:0044512 ! envenomation resulting in modulation of glucagon-like peptide receptor 1 activity in another organism
[Term]
id: GO:0044516
-name: positive regulation of glucagon-like peptide receptor 1 activity in other organism
+name: positive regulation of glucagon-like peptide receptor 1 activity in another organism
namespace: biological_process
def: "A process that activates or increases the frequency, rate or extent of the activity of a glucagon-like peptide receptor 1 in a second organism." [GOC:fj, GOC:jl, PMID:8405712]
-is_a: GO:0044506 ! modulation of glucagon-like peptide receptor 1 activity in other organism
-is_a: GO:0044507 ! positive regulation of receptor activity in other organism
+synonym: "positive regulation of glucagon-like peptide receptor 1 activity in other organism" EXACT []
+is_a: GO:0044506 ! modulation of glucagon-like peptide receptor 1 activity in another organism
+is_a: GO:0044507 ! positive regulation of receptor activity in another organism
[Term]
id: GO:0044517
-name: modulation of vasoactive intestinal polypeptide receptor activity in other organism
+name: modulation of vasoactive intestinal polypeptide receptor activity in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the activity of a vasoactive intestinal polypeptide receptor in a second organism." [GOC:fj, GOC:jl]
+synonym: "modulation of vasoactive intestinal polypeptide receptor activity in other organism" EXACT []
synonym: "modulation of VIP receptor activity in other organism" EXACT []
synonym: "regulation of vasoactive intestinal polypeptide receptor activity in other organism" EXACT []
-is_a: GO:0044504 ! modulation of receptor activity in other organism
+is_a: GO:0044504 ! modulation of receptor activity in another organism
[Term]
id: GO:0044518
-name: positive regulation of vasoactive intestinal polypeptide receptor activity in other organism
+name: positive regulation of vasoactive intestinal polypeptide receptor activity in another organism
namespace: biological_process
def: "A process that activates or increases the frequency, rate or extent of the activity of a vasoactive intestinal polypeptide receptor in a second organism." [GOC:fj, GOC:jl]
+synonym: "positive regulation of vasoactive intestinal polypeptide receptor activity in other organism" EXACT []
synonym: "positive regulation of VIP receptor activity in other organism" EXACT []
-is_a: GO:0044507 ! positive regulation of receptor activity in other organism
-is_a: GO:0044517 ! modulation of vasoactive intestinal polypeptide receptor activity in other organism
+is_a: GO:0044507 ! positive regulation of receptor activity in another organism
+is_a: GO:0044517 ! modulation of vasoactive intestinal polypeptide receptor activity in another organism
[Term]
id: GO:0044519
-name: envenomation resulting in modulation of vasoactive intestinal polypeptide receptor activity in other organism
+name: envenomation resulting in modulation of vasoactive intestinal polypeptide receptor activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of the activity of a vasoactive intestinal polypeptide receptor in the bitten organism." [GOC:fj, GOC:jl]
+synonym: "envenomation resulting in modulation of vasoactive intestinal polypeptide receptor activity in other organism" EXACT []
synonym: "envenomation resulting in modulation of VIP receptor activity in other organism" EXACT []
synonym: "envenomation resulting in regulation of vasoactive intestinal polypeptide receptor activity in other organism" EXACT []
synonym: "envenomation resulting in regulation of VIP receptor activity in other organism" EXACT []
-is_a: GO:0044511 ! envenomation resulting in modulation of receptor activity in other organism
+is_a: GO:0044511 ! envenomation resulting in modulation of receptor activity in another organism
[Term]
id: GO:0044520
-name: envenomation resulting in positive regulation of vasoactive intestinal polypeptide receptor activity in other organism
+name: envenomation resulting in positive regulation of vasoactive intestinal polypeptide receptor activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of the activity of a vasoactive intestinal polypeptide receptor in the bitten organism." [GOC:fj, GOC:jl]
+synonym: "envenomation resulting in positive regulation of vasoactive intestinal polypeptide receptor activity in other organism" EXACT []
synonym: "envenomation resulting in positive regulation of VIP receptor activity in other organism" EXACT []
-is_a: GO:0044519 ! envenomation resulting in modulation of vasoactive intestinal polypeptide receptor activity in other organism
+is_a: GO:0044519 ! envenomation resulting in modulation of vasoactive intestinal polypeptide receptor activity in another organism
[Term]
id: GO:0044521
-name: envenomation resulting in muscle damage in other organism
+name: envenomation resulting in muscle damage in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with resultant muscle damage in the bitten organism." [GOC:fj, GOC:jl, PMID:10620318, PMID:21150580]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in muscle damage in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044522
-name: envenomation resulting in myocyte killing in other organism
+name: envenomation resulting in myocyte killing in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, killing heart myocytes and ultimately resulting in muscle damage in the bitten organism." [GOC:fj, GOC:jl, PMID:10620318, PMID:21150580]
synonym: "envenomation resulting in myocyte killing causing muscle damage in other organism" EXACT []
-is_a: GO:0044521 ! envenomation resulting in muscle damage in other organism
+synonym: "envenomation resulting in myocyte killing in other organism" EXACT []
+is_a: GO:0044521 ! envenomation resulting in muscle damage in another organism
[Term]
id: GO:0044523
-name: envenomation resulting in damage of muscle extracellular matrix in other organism
+name: envenomation resulting in damage of muscle extracellular matrix in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, damaging the extracellular matrix of muscle cells and ultimately resulting in muscle necrosis in the bitten organism." [GOC:fj, GOC:jl, PMID:10620318, PMID:21150580]
synonym: "envenomation resulting in damage of muscle extracellular matrix causing muscle necrosis in other organism" EXACT []
-is_a: GO:0044521 ! envenomation resulting in muscle damage in other organism
+synonym: "envenomation resulting in damage of muscle extracellular matrix in other organism" EXACT []
+is_a: GO:0044521 ! envenomation resulting in muscle damage in another organism
[Term]
id: GO:0044524
@@ -246868,27 +246528,30 @@ is_a: GO:0005681 ! spliceosomal complex
[Term]
id: GO:0044532
-name: modulation of apoptotic process in other organism
+name: modulation of apoptotic process in another organism
namespace: biological_process
def: "A process in which an organism modulates the frequency, rate or extent of apoptosis in a second organism." [GOC:jl]
+synonym: "modulation of apoptotic process in other organism" EXACT []
synonym: "regulation of apoptotic process in other organism" EXACT []
is_a: GO:0042981 ! regulation of apoptotic process
-is_a: GO:0051709 ! regulation of killing of cells of other organism
+is_a: GO:0051709 ! regulation of killing of cells of another organism
[Term]
id: GO:0044533
-name: positive regulation of apoptotic process in other organism
+name: positive regulation of apoptotic process in another organism
namespace: biological_process
def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism." [GOC:jl, PMID:17983639]
+synonym: "positive regulation of apoptotic process in other organism" EXACT []
is_a: GO:0043065 ! positive regulation of apoptotic process
-is_a: GO:0044532 ! modulation of apoptotic process in other organism
+is_a: GO:0044532 ! modulation of apoptotic process in another organism
[Term]
id: GO:0044534
-name: envenomation resulting in modulation of apoptotic process in other organism
+name: envenomation resulting in modulation of apoptotic process in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of apoptosis in the bitten organism." [GOC:fj, GOC:jl, PMID:17983639]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in modulation of apoptotic process in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044535
@@ -246903,11 +246566,12 @@ is_a: GO:0003997 ! acyl-CoA oxidase activity
[Term]
id: GO:0044536
-name: envenomation resulting in depletion of circulating fibrinogen in other organism
+name: envenomation resulting in depletion of circulating fibrinogen in another organism
namespace: biological_process
def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with a reduction in the quantity of fibrinogen found in the bloodstream of the bitten/stung organism." [GOC:fj, GOC:jl]
+synonym: "envenomation resulting in depletion of circulating fibrinogen in other organism" EXACT []
synonym: "envenomation resulting in negative regulation of circulating fibrinogen in other organism" EXACT []
-is_a: GO:0044483 ! envenomation resulting in impairment of hemostasis in other organism
+is_a: GO:0044483 ! envenomation resulting in impairment of hemostasis in another organism
is_a: GO:0061754 ! negative regulation of circulating fibrinogen levels
[Term]
@@ -246946,33 +246610,36 @@ is_a: GO:0016846 ! carbon-sulfur lyase activity
[Term]
id: GO:0044541
-name: zymogen activation in other organism
+name: zymogen activation in another organism
namespace: biological_process
def: "The chemical reactions and pathways performed by an organism resulting in the proteolytic processing of an inactive enzyme to an active form in another organism." [GOC:fj, GOC:jl]
+synonym: "zymogen activation in other organism" EXACT []
is_a: GO:0031638 ! zymogen activation
-is_a: GO:0044033 ! multi-organism metabolic process
[Term]
id: GO:0044542
-name: plasminogen activation in other organism
+name: plasminogen activation in another organism
namespace: biological_process
def: "The chemical reactions and pathways performed by an organism resulting in the processing of inactive plasminogen to active plasmin in another organism." [GOC:fj, GOC:jl]
+synonym: "plasminogen activation in other organism" EXACT []
is_a: GO:0031639 ! plasminogen activation
-is_a: GO:0044541 ! zymogen activation in other organism
+is_a: GO:0044541 ! zymogen activation in another organism
[Term]
id: GO:0044543
-name: envenomation resulting in zymogen activation in other organism
+name: envenomation resulting in zymogen activation in another organism
namespace: biological_process
def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the proteolytic processing of an inactive enzyme to an active form." [GOC:fj, GOC:jl]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in zymogen activation in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044544
-name: envenomation resulting in plasminogen activation in other organism
+name: envenomation resulting in plasminogen activation in another organism
namespace: biological_process
def: "The process which begins with venom being forced into an organism by the bite or sting of another organism, and ends with the activation of plasminogen into plasmin in the bitten organism. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide." [GOC:fj, GOC:jl]
-is_a: GO:0044484 ! envenomation resulting in fibrinolysis in other organism
+synonym: "envenomation resulting in plasminogen activation in other organism" EXACT []
+is_a: GO:0044484 ! envenomation resulting in fibrinolysis in another organism
[Term]
id: GO:0044545
@@ -246996,7 +246663,7 @@ id: GO:0044547
name: DNA topoisomerase binding
namespace: molecular_function
alt_id: GO:0017033
-def: "Interacting selectively and non-covalently with a DNA topoisomerase." [GOC:jl]
+def: "Binding to a DNA topoisomerase." [GOC:jl]
synonym: "DNA topoisomerase I binding" NARROW []
is_a: GO:0019899 ! enzyme binding
@@ -247006,7 +246673,7 @@ name: S100 protein binding
namespace: molecular_function
alt_id: GO:0048154
alt_id: GO:0048155
-def: "Interacting selectively and non-covalently with a S100 protein. S100 is a small calcium and zinc binding protein produced in astrocytes that is implicated in Alzheimer's disease, Down Syndrome and ALS." [GOC:jid]
+def: "Binding to a S100 protein. S100 is a small calcium and zinc binding protein produced in astrocytes that is implicated in Alzheimer's disease, Down Syndrome and ALS." [GOC:jid]
synonym: "S100 alpha binding" NARROW []
synonym: "S100 beta binding" NARROW []
synonym: "S100 binding" EXACT []
@@ -247017,7 +246684,7 @@ id: GO:0044549
name: GTP cyclohydrolase binding
namespace: molecular_function
alt_id: GO:0043106
-def: "Interacting selectively and non-covalently with a GTP cyclohydrolase." [GOC:jl]
+def: "Binding to a GTP cyclohydrolase." [GOC:jl]
synonym: "GTP cyclohydrolase I binding" NARROW []
is_a: GO:0019899 ! enzyme binding
@@ -247032,54 +246699,60 @@ is_a: GO:0019748 ! secondary metabolic process
[Term]
id: GO:0044551
-name: envenomation resulting in vasodilation in other organism
+name: envenomation resulting in vasodilation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with resultant vasodilation of blood vessels, usually causing a reduction in blood pressure, in the bitten/stung organism." [GOC:ecd, GOC:jl, PMID:21050868]
synonym: "envenomation resulting in modulation of vasodilation in other organism" RELATED []
synonym: "envenomation resulting in regulation of vasodilation in other organism" RELATED []
-is_a: GO:0044500 ! envenomation resulting in negative regulation of blood pressure in other organism
+synonym: "envenomation resulting in vasodilation in other organism" EXACT []
+is_a: GO:0044500 ! envenomation resulting in negative regulation of blood pressure in another organism
[Term]
id: GO:0044552
-name: vasodilation in other organism
+name: vasodilation in another organism
namespace: biological_process
def: "A process by which an organism causes vasodilation of blood vessels, usually causing a reduction in blood pressure, in another organism." [GOC:ecd, GOC:jl, PMID:21050868]
synonym: "modulation of vasodilation in other organism" RELATED []
synonym: "regulation of vasodilation in other organism" RELATED []
+synonym: "vasodilation in other organism" EXACT []
is_a: GO:0042311 ! vasodilation
-is_a: GO:0044553 ! modulation of biological quality in other organism
+is_a: GO:0044553 ! modulation of biological quality in another organism
[Term]
id: GO:0044553
-name: modulation of biological quality in other organism
+name: modulation of biological quality in another organism
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of a biological quality in another organism. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." [GOC:jl]
+synonym: "modulation of biological quality in other organism" EXACT []
synonym: "regulation of biological quality in other organism" EXACT []
-is_a: GO:0035821 ! modulation of process of other organism
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0044554
-name: modulation of heart rate in other organism
+name: modulation of heart rate in another organism
namespace: biological_process
def: "Any process that modulates the frequency or rate of heart contraction of another organism." [GOC:jl, PMID:20923766]
+synonym: "modulation of heart rate in other organism" EXACT []
synonym: "regulation of heart rate in other organism" EXACT []
is_a: GO:0002027 ! regulation of heart rate
-is_a: GO:0044553 ! modulation of biological quality in other organism
+is_a: GO:0044553 ! modulation of biological quality in another organism
[Term]
id: GO:0044555
-name: negative regulation of heart rate in other organism
+name: negative regulation of heart rate in another organism
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency of heart contraction of another organism." [GOC:ecd, GOC:jl, PMID:20923766]
+synonym: "negative regulation of heart rate in other organism" EXACT []
is_a: GO:0010459 ! negative regulation of heart rate
-is_a: GO:0044554 ! modulation of heart rate in other organism
+is_a: GO:0044554 ! modulation of heart rate in another organism
[Term]
id: GO:0044556
-name: envenomation resulting in negative regulation of heart rate of other organism
+name: envenomation resulting in negative regulation of heart rate in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the negative regulation of the heart rate of the bitten/stung organism." [GOC:ecd, GOC:jl, PMID:20923766]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in negative regulation of heart rate of other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044557
@@ -247099,48 +246772,54 @@ is_a: GO:0044557 ! relaxation of smooth muscle
[Term]
id: GO:0044559
-name: envenomation resulting in modulation of voltage-gated potassium channel activity in other organism
+name: envenomation resulting in modulation of voltage-gated potassium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of a voltage-gated potassium channel in the bitten/stung organism." [GOC:fj, GOC:jl]
-is_a: GO:0044560 ! envenomation resulting in modulation of ion channel activity in other organism
+synonym: "envenomation resulting in modulation of voltage-gated potassium channel activity in other organism" EXACT []
+is_a: GO:0044560 ! envenomation resulting in modulation of ion channel activity in another organism
[Term]
id: GO:0044560
-name: envenomation resulting in modulation of ion channel activity in other organism
+name: envenomation resulting in modulation of ion channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of an ion channel in the bitten organism." [GOC:fj, GOC:jl]
+synonym: "envenomation resulting in modulation of ion channel activity in other organism" EXACT []
synonym: "envenomation resulting in regulation of ion channel activity in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044561
-name: modulation of ion channel activity in other organism
+name: modulation of ion channel activity in another organism
namespace: biological_process
def: "Any process in which an organism effects a change in the frequency, rate or extent of the activity of an ion channel in another organism." [GOC:jl]
+synonym: "modulation of ion channel activity in other organism" EXACT []
synonym: "regulation of ion channel activity in other organism" EXACT []
-is_a: GO:0044359 ! modulation of molecular function in other organism
+is_a: GO:0044359 ! modulation of molecular function in another organism
[Term]
id: GO:0044562
-name: envenomation resulting in negative regulation of voltage-gated potassium channel activity in other organism
+name: envenomation resulting in negative regulation of voltage-gated potassium channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant negative regulation of the activity of a voltage-gated potassium channel in the bitten/stung organism." [GOC:fj, GOC:jl]
-is_a: GO:0044559 ! envenomation resulting in modulation of voltage-gated potassium channel activity in other organism
+synonym: "envenomation resulting in negative regulation of voltage-gated potassium channel activity in other organism" EXACT []
+is_a: GO:0044559 ! envenomation resulting in modulation of voltage-gated potassium channel activity in another organism
[Term]
id: GO:0044563
-name: envenomation resulting in slowing of activation kinetics of voltage-gated potassium channel in other organism
+name: envenomation resulting in slowing of activation kinetics of voltage-gated potassium channel in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant slowing of the activation kinetics of the activity of a voltage-gated potassium channel in the bitten/stung organism." [GOC:fj, GOC:jl]
+synonym: "envenomation resulting in slowing of activation kinetics of voltage-gated potassium channel in other organism" EXACT []
synonym: "voltage-dependence of activation shift (to the left)" EXACT []
-is_a: GO:0044562 ! envenomation resulting in negative regulation of voltage-gated potassium channel activity in other organism
+is_a: GO:0044562 ! envenomation resulting in negative regulation of voltage-gated potassium channel activity in another organism
[Term]
id: GO:0044564
-name: envenomation resulting in occlusion of the pore of voltage-gated potassium channel in other organism
+name: envenomation resulting in occlusion of the pore of voltage-gated potassium channel in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant blocking of a voltage-gated potassium channel, inhibiting the pore's activity, in the bitten/stung organism." [GOC:fj, GOC:jl]
-is_a: GO:0044562 ! envenomation resulting in negative regulation of voltage-gated potassium channel activity in other organism
+synonym: "envenomation resulting in occlusion of the pore of voltage-gated potassium channel in other organism" EXACT []
+is_a: GO:0044562 ! envenomation resulting in negative regulation of voltage-gated potassium channel activity in another organism
[Term]
id: GO:0044565
@@ -247171,7 +246850,6 @@ name: secondary cell wall cellulose synthase complex
namespace: cellular_component
def: "A large, multimeric protein complex which catalyzes the biosynthesis of cellulose for the plant secondary cell wall. In Arabidopsis, contains the essential component proteins CESA8, CESA7, and CESA4." [GOC:mengo_curators, GOC:tt, PMID:21307367]
synonym: "secondary cell wall CESA complex" EXACT []
-synonym: "secondary cell wall CesA complex" EXACT []
synonym: "secondary cell-wall cellulose synthase complex" EXACT []
is_a: GO:0010330 ! cellulose synthase complex
@@ -247234,7 +246912,7 @@ id: GO:0044575
name: cellulosome assembly
namespace: biological_process
def: "The assembly of a cellulosome, a macromolecular multi-enzyme complex in bacteria that facilitates the breakdown of cellulase, hemicellulase and pectin in the plant cell wall." [GOC:mengo_curators, GOC:tt, PMID:20373916]
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:0044576
@@ -247303,14 +246981,14 @@ is_a: GO:0071271 ! 1-butanol biosynthetic process
id: GO:0044583
name: cellotriose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cellotriose." [GOC:mengo_curators, GOC:tt]
+def: "Binding to cellotriose." [GOC:mengo_curators, GOC:tt]
is_a: GO:0048031 ! trisaccharide binding
[Term]
id: GO:0044584
name: cellodextrin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cellodextrin, a glucose polymer of 2 or more glucose monomers." [GOC:mengo_curators, GOC:tt, PMID:18952792]
+def: "Binding to a cellodextrin, a glucose polymer of 2 or more glucose monomers." [GOC:mengo_curators, GOC:tt, PMID:18952792]
is_a: GO:0030247 ! polysaccharide binding
is_a: GO:0070492 ! oligosaccharide binding
@@ -247318,42 +246996,42 @@ is_a: GO:0070492 ! oligosaccharide binding
id: GO:0044585
name: cellobiose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cellobiose, a disaccharide that represents the basic repeating unit of cellulose." [GOC:mengo_curators, GOC:tt]
+def: "Binding to cellobiose, a disaccharide that represents the basic repeating unit of cellulose." [GOC:mengo_curators, GOC:tt]
is_a: GO:0048030 ! disaccharide binding
[Term]
id: GO:0044586
name: cellotetraose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cellotetraose, an oligosaccharide consisting of four glucose residues resulting from hydrolysis of cellulose." [GOC:mengo_curators, GOC:tt]
+def: "Binding to a cellotetraose, an oligosaccharide consisting of four glucose residues resulting from hydrolysis of cellulose." [GOC:mengo_curators, GOC:tt]
is_a: GO:0070492 ! oligosaccharide binding
[Term]
id: GO:0044587
name: cellopentaose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cellopentaose, an oligosaccharide consisting of four glucose residues resulting from hydrolysis of cellulose." [GOC:mengo_curators, GOC:tt]
+def: "Binding to a cellopentaose, an oligosaccharide consisting of four glucose residues resulting from hydrolysis of cellulose." [GOC:mengo_curators, GOC:tt]
is_a: GO:0070492 ! oligosaccharide binding
[Term]
id: GO:0044588
name: laminaribiose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with laminaribiose, a disaccharide." [GOC:mengo_curators, GOC:tt]
+def: "Binding to laminaribiose, a disaccharide." [GOC:mengo_curators, GOC:tt]
is_a: GO:0070492 ! oligosaccharide binding
[Term]
id: GO:0044589
name: pectin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pectin." [GOC:mengo_curators, GOC:tt]
+def: "Binding to pectin." [GOC:mengo_curators, GOC:tt]
is_a: GO:0048028 ! galacturonan binding
[Term]
id: GO:0044590
name: iron-sulfur-molybdenum cofactor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with iron molybdenum cofactor, the cofactor located at the active site of the molybdenum nitrogenase." [GOC:mengo_curators, GOC:tt, PMID:18429691]
+def: "Binding to iron molybdenum cofactor, the cofactor located at the active site of the molybdenum nitrogenase." [GOC:mengo_curators, GOC:tt, PMID:18429691]
synonym: "FeMo co binding" EXACT []
synonym: "FeMoco binding" EXACT []
is_a: GO:0005488 ! binding
@@ -247598,249 +247276,279 @@ relationship: part_of GO:0005643 ! nuclear pore
[Term]
id: GO:0044616
-name: modulation of relaxation of muscle in other organism
+name: modulation of relaxation of muscle in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the relaxation of muscle in a second organism." [GOC:jl]
+synonym: "modulation of relaxation of muscle in other organism" EXACT []
synonym: "regulation of relaxation of muscle in other organism" EXACT []
-is_a: GO:0035821 ! modulation of process of other organism
+is_a: GO:0035821 ! modulation of process of another organism
is_a: GO:1901077 ! regulation of relaxation of muscle
[Term]
id: GO:0044617
-name: modulation of relaxation of smooth muscle in other organism
+name: modulation of relaxation of smooth muscle in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the relaxation of smooth muscle in a second organism." [GOC:jl]
+synonym: "modulation of relaxation of smooth muscle in other organism" EXACT []
synonym: "regulation of relaxation of smooth muscle in other organism" EXACT []
-is_a: GO:0044616 ! modulation of relaxation of muscle in other organism
+is_a: GO:0044616 ! modulation of relaxation of muscle in another organism
is_a: GO:1901080 ! regulation of relaxation of smooth muscle
[Term]
id: GO:0044618
-name: modulation of relaxation of uterine smooth muscle in other organism
+name: modulation of relaxation of uterine smooth muscle in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the relaxation of smooth muscle in the uterus of a second organism." [GOC:jl]
+synonym: "modulation of relaxation of uterine smooth muscle in other organism" EXACT []
synonym: "regulation of relaxation of uterine smooth muscle in other organism" EXACT []
-is_a: GO:0044617 ! modulation of relaxation of smooth muscle in other organism
+is_a: GO:0044617 ! modulation of relaxation of smooth muscle in another organism
is_a: GO:1900719 ! regulation of uterine smooth muscle relaxation
[Term]
id: GO:0044619
-name: positive regulation of relaxation of uterine smooth muscle in other organism
+name: positive regulation of relaxation of uterine smooth muscle in another organism
namespace: biological_process
def: "The process in which an organism increases the extent of relaxation of smooth muscle in the uterus of a second organism." [GOC:jl]
-is_a: GO:0044618 ! modulation of relaxation of uterine smooth muscle in other organism
+synonym: "positive regulation of relaxation of uterine smooth muscle in other organism" EXACT []
+is_a: GO:0044618 ! modulation of relaxation of uterine smooth muscle in another organism
is_a: GO:1900721 ! positive regulation of uterine smooth muscle relaxation
[Term]
id: GO:0044620
name: ACP phosphopantetheine attachment site binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP)." [GOC:jl, GOC:vw]
+def: "Binding to the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP)." [GOC:jl, GOC:vw]
is_a: GO:0051192 ! prosthetic group binding
[Term]
id: GO:0044621
-name: modulation of cell migration in other organism
+name: modulation of cell migration in another organism
namespace: biological_process
def: "The process in which an organism effects a change in the process of cell migration in a second organism." [GOC:jl]
+synonym: "modulation of cell migration in other organism" EXACT []
synonym: "regulation of cell migration in other organism" EXACT []
is_a: GO:0030334 ! regulation of cell migration
-is_a: GO:0035821 ! modulation of process of other organism
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0044622
-name: negative regulation of cell migration in other organism
+name: negative regulation of cell migration in another organism
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration in a second organism." [GOC:jl]
+synonym: "negative regulation of cell migration in other organism" EXACT []
is_a: GO:0030336 ! negative regulation of cell migration
-is_a: GO:0044621 ! modulation of cell migration in other organism
+is_a: GO:0044621 ! modulation of cell migration in another organism
[Term]
id: GO:0044623
-name: positive regulation of cell migration in other organism
+name: positive regulation of cell migration in another organism
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of cell migration in a second organism." [GOC:jl]
+synonym: "positive regulation of cell migration in other organism" EXACT []
is_a: GO:0030335 ! positive regulation of cell migration
-is_a: GO:0044621 ! modulation of cell migration in other organism
+is_a: GO:0044621 ! modulation of cell migration in another organism
[Term]
id: GO:0044624
-name: envenomation resulting in modulation of cell migration in other organism
+name: envenomation resulting in modulation of cell migration in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the modulation of cell migration in the bitten organism." [GOC:jl, PMID:19932752]
+synonym: "envenomation resulting in modulation of cell migration in other organism" EXACT []
synonym: "envenomation resulting in regulation of cell migration in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044625
-name: envenomation resulting in negative regulation of cell migration in other organism
+name: envenomation resulting in negative regulation of cell migration in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the negative regulation of cell migration in the bitten organism." [GOC:jl, PMID:19932752]
-is_a: GO:0044624 ! envenomation resulting in modulation of cell migration in other organism
+synonym: "envenomation resulting in negative regulation of cell migration in other organism" EXACT []
+is_a: GO:0044624 ! envenomation resulting in modulation of cell migration in another organism
[Term]
id: GO:0044626
-name: envenomation resulting in positive regulation of cell migration in other organism
+name: envenomation resulting in positive regulation of cell migration in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the positive regulation of cell migration in the bitten organism." [GOC:jl, PMID:19932752]
-is_a: GO:0044624 ! envenomation resulting in modulation of cell migration in other organism
+synonym: "envenomation resulting in positive regulation of cell migration in other organism" EXACT []
+is_a: GO:0044624 ! envenomation resulting in modulation of cell migration in another organism
[Term]
id: GO:0044627
-name: modulation of complement activation, classical pathway in other organism
+name: modulation of complement activation, classical pathway in another organism
namespace: biological_process
def: "A process that modulates the frequency, rate or extent of the classical pathway of complement activation, in a different organism." [GOC:jl, PMID:20837040]
+synonym: "modulation of complement activation, classical pathway in other organism" EXACT []
synonym: "regulation of complement activation, classical pathway in other organism" EXACT []
is_a: GO:0030450 ! regulation of complement activation, classical pathway
-is_a: GO:0044645 ! modulation of complement activation in other organism
+is_a: GO:0044645 ! modulation of complement activation in another organism
[Term]
id: GO:0044628
-name: positive regulation of complement activation, classical pathway in other organism
+name: positive regulation of complement activation, classical pathway in another organism
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of complement activation by the classical pathway, in a different organism." [GOC:jl, PMID:20837040]
-is_a: GO:0044627 ! modulation of complement activation, classical pathway in other organism
+synonym: "positive regulation of complement activation, classical pathway in other organism" EXACT []
+is_a: GO:0044627 ! modulation of complement activation, classical pathway in another organism
is_a: GO:0045960 ! positive regulation of complement activation, classical pathway
[Term]
id: GO:0044629
-name: negative regulation of complement activation, classical pathway in other organism
+name: negative regulation of complement activation, classical pathway in another organism
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the classical pathway, in a different organism." [GOC:jl, PMID:20837040]
-is_a: GO:0044627 ! modulation of complement activation, classical pathway in other organism
+synonym: "negative regulation of complement activation, classical pathway in other organism" EXACT []
+is_a: GO:0044627 ! modulation of complement activation, classical pathway in another organism
is_a: GO:0045959 ! negative regulation of complement activation, classical pathway
[Term]
id: GO:0044630
-name: modulation of complement activation, lectin pathway in other organism
+name: modulation of complement activation, lectin pathway in another organism
namespace: biological_process
def: "A process that modulates the frequency, rate or extent of the lectin pathway of complement activation, in a different organism." [GOC:jl, PMID:20837040]
+synonym: "modulation of complement activation, lectin pathway in other organism" EXACT []
synonym: "regulation of complement activation, lectin pathway in other organism" EXACT []
is_a: GO:0001868 ! regulation of complement activation, lectin pathway
-is_a: GO:0044645 ! modulation of complement activation in other organism
+is_a: GO:0044645 ! modulation of complement activation in another organism
[Term]
id: GO:0044631
-name: positive regulation of complement activation, lectin pathway in other organism
+name: positive regulation of complement activation, lectin pathway in another organism
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of complement activation by the lectin pathway, in a different organism." [GOC:jl, PMID:20837040]
+synonym: "positive regulation of complement activation, lectin pathway in other organism" EXACT []
is_a: GO:0001870 ! positive regulation of complement activation, lectin pathway
-is_a: GO:0044630 ! modulation of complement activation, lectin pathway in other organism
+is_a: GO:0044630 ! modulation of complement activation, lectin pathway in another organism
[Term]
id: GO:0044632
-name: negative regulation of complement activation, lectin pathway in other organism
+name: negative regulation of complement activation, lectin pathway in another organism
namespace: biological_process
def: "Any process that stops, prevents, or reduces the rate of complement activation by the lectin pathway, in a different organism." [GOC:jl, PMID:20837040]
+synonym: "negative regulation of complement activation, lectin pathway in other organism" EXACT []
is_a: GO:0001869 ! negative regulation of complement activation, lectin pathway
-is_a: GO:0044630 ! modulation of complement activation, lectin pathway in other organism
+is_a: GO:0044630 ! modulation of complement activation, lectin pathway in another organism
[Term]
id: GO:0044633
-name: modulation of complement activation, alternative pathway in other organism
+name: modulation of complement activation, alternative pathway in another organism
namespace: biological_process
def: "A process that modulates the frequency, rate or extent of complement activation, via the alternative pathway, in a different organism." [GOC:jl, PMID:20837040]
+synonym: "modulation of complement activation, alternative pathway in other organism" EXACT []
synonym: "regulation of complement activation, alternative pathway in other organism" RELATED []
is_a: GO:0030451 ! regulation of complement activation, alternative pathway
-is_a: GO:0044645 ! modulation of complement activation in other organism
+is_a: GO:0044645 ! modulation of complement activation in another organism
[Term]
id: GO:0044634
-name: negative regulation of complement activation, alternative pathway in other organism
+name: negative regulation of complement activation, alternative pathway in another organism
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the alternative pathway, in a different organism." [GOC:jl, PMID:20837040]
-is_a: GO:0044633 ! modulation of complement activation, alternative pathway in other organism
+synonym: "negative regulation of complement activation, alternative pathway in other organism" EXACT []
+is_a: GO:0044633 ! modulation of complement activation, alternative pathway in another organism
is_a: GO:0045957 ! negative regulation of complement activation, alternative pathway
[Term]
id: GO:0044635
-name: positive regulation of complement activation, alternative pathway in other organism
+name: positive regulation of complement activation, alternative pathway in another organism
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of complement activation by the alternative pathway, in a different organism." [GOC:jl, PMID:20837040]
-is_a: GO:0044633 ! modulation of complement activation, alternative pathway in other organism
+synonym: "positive regulation of complement activation, alternative pathway in other organism" EXACT []
+is_a: GO:0044633 ! modulation of complement activation, alternative pathway in another organism
is_a: GO:0045958 ! positive regulation of complement activation, alternative pathway
[Term]
id: GO:0044636
-name: envenomation resulting in modulation of complement activation, classical pathway in other organism
+name: envenomation resulting in modulation of complement activation, classical pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the regulation of complement activation via the classical pathway of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
-is_a: GO:0044646 ! envenomation resulting in modulation of complement activation in other organism
+synonym: "envenomation resulting in modulation of complement activation, classical pathway in other organism" EXACT []
+is_a: GO:0044646 ! envenomation resulting in modulation of complement activation in another organism
[Term]
id: GO:0044637
-name: envenomation resulting in negative regulation of complement activation, classical pathway in other organism
+name: envenomation resulting in negative regulation of complement activation, classical pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the negative regulation of complement activation via the classical pathway of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
-is_a: GO:0044636 ! envenomation resulting in modulation of complement activation, classical pathway in other organism
+synonym: "envenomation resulting in negative regulation of complement activation, classical pathway in other organism" EXACT []
+is_a: GO:0044636 ! envenomation resulting in modulation of complement activation, classical pathway in another organism
[Term]
id: GO:0044638
-name: envenomation resulting in positive regulation of complement activation, classical pathway in other organism
+name: envenomation resulting in positive regulation of complement activation, classical pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the positive regulation of complement activation via the classical pathway of the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
-is_a: GO:0044636 ! envenomation resulting in modulation of complement activation, classical pathway in other organism
+synonym: "envenomation resulting in positive regulation of complement activation, classical pathway in other organism" EXACT []
+is_a: GO:0044636 ! envenomation resulting in modulation of complement activation, classical pathway in another organism
[Term]
id: GO:0044639
-name: envenomation resulting in modulation of complement activation, lectin pathway in other organism
+name: envenomation resulting in modulation of complement activation, lectin pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of complement activation via the lectin pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
+synonym: "envenomation resulting in modulation of complement activation, lectin pathway in other organism" EXACT []
synonym: "envenomation resulting in regulation of complement activation, lectin pathway in other organism" EXACT []
-is_a: GO:0044646 ! envenomation resulting in modulation of complement activation in other organism
+is_a: GO:0044646 ! envenomation resulting in modulation of complement activation in another organism
[Term]
id: GO:0044640
-name: envenomation resulting in negative regulation of complement activation, lectin pathway in other organism
+name: envenomation resulting in negative regulation of complement activation, lectin pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant negative regulation of complement activation via the lectin pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
-is_a: GO:0044639 ! envenomation resulting in modulation of complement activation, lectin pathway in other organism
+synonym: "envenomation resulting in negative regulation of complement activation, lectin pathway in other organism" EXACT []
+is_a: GO:0044639 ! envenomation resulting in modulation of complement activation, lectin pathway in another organism
[Term]
id: GO:0044641
-name: envenomation resulting in positive regulation of complement activation, lectin pathway in other organism
+name: envenomation resulting in positive regulation of complement activation, lectin pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of complement activation via the lectin pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
-is_a: GO:0044639 ! envenomation resulting in modulation of complement activation, lectin pathway in other organism
+synonym: "envenomation resulting in positive regulation of complement activation, lectin pathway in other organism" EXACT []
+is_a: GO:0044639 ! envenomation resulting in modulation of complement activation, lectin pathway in another organism
[Term]
id: GO:0044642
-name: envenomation resulting in modulation of complement activation, alternative pathway in other organism
+name: envenomation resulting in modulation of complement activation, alternative pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of complement activation via the alternative pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
+synonym: "envenomation resulting in modulation of complement activation, alternative pathway in other organism" EXACT []
synonym: "envenomation resulting in regulation of complement activation, alternative pathway in other organism" EXACT []
-is_a: GO:0044646 ! envenomation resulting in modulation of complement activation in other organism
+is_a: GO:0044646 ! envenomation resulting in modulation of complement activation in another organism
[Term]
id: GO:0044643
-name: envenomation resulting in positive regulation of complement activation, alternative pathway in other organism
+name: envenomation resulting in positive regulation of complement activation, alternative pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant positive regulation of complement activation via the alternative pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
-is_a: GO:0044642 ! envenomation resulting in modulation of complement activation, alternative pathway in other organism
+synonym: "envenomation resulting in positive regulation of complement activation, alternative pathway in other organism" EXACT []
+is_a: GO:0044642 ! envenomation resulting in modulation of complement activation, alternative pathway in another organism
[Term]
id: GO:0044644
-name: envenomation resulting in negative regulation of complement activation, alternative pathway in other organism
+name: envenomation resulting in negative regulation of complement activation, alternative pathway in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant negative regulation of complement activation via the alternative pathway in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
-is_a: GO:0044642 ! envenomation resulting in modulation of complement activation, alternative pathway in other organism
+synonym: "envenomation resulting in negative regulation of complement activation, alternative pathway in other organism" EXACT []
+is_a: GO:0044642 ! envenomation resulting in modulation of complement activation, alternative pathway in another organism
[Term]
id: GO:0044645
-name: modulation of complement activation in other organism
+name: modulation of complement activation in another organism
namespace: biological_process
def: "A process that modulates the frequency, rate or extent of complement activation in a different organism." [GOC:fj, GOC:jl, PMID:20837040]
+synonym: "modulation of complement activation in other organism" EXACT []
synonym: "regulation of complement activation in other organism" EXACT []
-is_a: GO:0035821 ! modulation of process of other organism
+is_a: GO:0035821 ! modulation of process of another organism
is_a: GO:0045088 ! regulation of innate immune response
[Term]
id: GO:0044646
-name: envenomation resulting in modulation of complement activation in other organism
+name: envenomation resulting in modulation of complement activation in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the resultant modulation of complement activation in the bitten/stung organism." [GOC:fj, GOC:jl, PMID:20837040]
+synonym: "envenomation resulting in modulation of complement activation in other organism" EXACT []
synonym: "envenomation resulting in regulation of complement activation in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044647
@@ -247861,10 +247569,11 @@ is_a: GO:0051568 ! histone H3-K4 methylation
[Term]
id: GO:0044649
-name: envenomation resulting in cytolysis in other organism
+name: envenomation resulting in cytolysis in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with cytolysis in the bitten organism." [GOC:fj, GOC:jl, PMID:22484288]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in cytolysis in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044650
@@ -247919,22 +247628,24 @@ name: regulation of post-lysosomal vacuole size
namespace: biological_process
def: "Any process that modulates the volume of a post-lysosomal vacuole, a membrane-bounded intracellular vesicle formed late in the endocytic pathway when the pH in the vacuole becomes neutral prior to exocytosis." [GOC:rjd, PMID:22008230]
synonym: "regulation of post-lysosome size" EXACT [GOC:dph]
+synonym: "regulation of postlysosomal vacuole size" EXACT []
+synonym: "regulation of postlysosome vacuole size" EXACT []
is_a: GO:0032535 ! regulation of cellular component size
[Term]
id: GO:0044657
-name: pore formation in membrane of other organism during symbiotic interaction
+name: obsolete pore formation in membrane of other organism during symbiotic interaction
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components by an organism to form a pore complex in a membrane of another organism, occurring as part of a symbiotic interaction." [GOC:jl]
-is_a: GO:0035915 ! pore formation in membrane of other organism
-is_a: GO:0052025 ! modification by symbiont of host cell membrane
+def: "OBSOLETE. The aggregation, arrangement and bonding together of a set of components by an organism to form a pore complex in a membrane of another organism, occurring as part of a symbiotic interaction." [GOC:jl]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0044658
name: pore formation in membrane of host by symbiont
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components by an organism to form a pore complex in a membrane of a host organism." [GOC:jl]
-is_a: GO:0044657 ! pore formation in membrane of other organism during symbiotic interaction
+is_a: GO:0052111 ! modification by symbiont of host structure
[Term]
id: GO:0044659
@@ -247968,9 +247679,8 @@ name: disruption by virus of host cell membrane
namespace: biological_process
def: "A process by which a virus has a negative effect on the functioning of a host cellular membrane." [GOC:jl]
synonym: "disruption by organism of host cell membrane" EXACT []
-synonym: "disruption by virus of host cell membrane" NARROW [GOC:bf, GOC:jl]
is_a: GO:0019048 ! modulation by virus of host process
-is_a: GO:0051673 ! membrane disruption in other organism
+is_a: GO:0051673 ! membrane disruption in another organism
is_a: GO:0052025 ! modification by symbiont of host cell membrane
[Term]
@@ -248202,7 +247912,6 @@ def: "Catalysis of the reaction: 5-amino-6-(D-ribitylamino)uracil + 4-hydroxyphe
synonym: "FO synthase" EXACT []
xref: EC:2.5.1.147
xref: MetaCyc:RXN-8079
-xref: RHEA:27373
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
[Term]
@@ -248294,15 +248003,8 @@ id: GO:0044703
name: multi-organism reproductive process
namespace: biological_process
def: "A biological process that directly contributes to the process of producing new individuals, involving another organism." [GOC:jl]
+subset: goslim_drosophila
is_a: GO:0022414 ! reproductive process
-is_a: GO:0051704 ! multi-organism process
-
-[Term]
-id: GO:0044705
-name: multi-organism reproductive behavior
-namespace: biological_process
-def: "The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species." [GOC:jl, GOC:pr]
-is_a: GO:0019098 ! reproductive behavior
[Term]
id: GO:0044706
@@ -248310,7 +248012,6 @@ name: multi-multicellular organism process
namespace: biological_process
def: "A multicellular organism process which involves another multicellular organism of the same or different species." [GOC:jl]
is_a: GO:0032501 ! multicellular organismal process
-is_a: GO:0051704 ! multi-organism process
[Term]
id: GO:0044715
@@ -248370,17 +248071,16 @@ id: GO:0044721
name: protein import into peroxisome matrix, substrate release
namespace: biological_process
def: "The process by which the cargo protein is released into the peroxisomal matrix, following translocation across the membrane." [PMID:21976670]
-is_a: GO:0043624 ! cellular protein complex disassembly
+is_a: GO:0032984 ! protein-containing complex disassembly
relationship: part_of GO:0016558 ! protein import into peroxisome matrix
[Term]
id: GO:0044722
name: renal phosphate excretion
namespace: biological_process
-def: "The elimination by an organism of phosphate ions in the urine." [GOC:jl, PMID:21451460]
+def: "The elimination of phosphate ions from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine." [GOC:jl, PMID:25287933]
synonym: "renal phosphate ion excretion" EXACT []
-is_a: GO:0003014 ! renal system process
-is_a: GO:0007588 ! excretion
+is_a: GO:0097254 ! renal tubular secretion
[Term]
id: GO:0044725
@@ -248417,7 +248117,7 @@ is_a: GO:0006304 ! DNA modification
id: GO:0044729
name: hemi-methylated DNA-binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks." [GOC:imk, GOC:sp, PMID:18772889]
+def: "Binding to double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks." [GOC:imk, GOC:sp, PMID:18772889]
synonym: "double-stranded hemi-methylated DNA binding" EXACT []
is_a: GO:0003690 ! double-stranded DNA binding
@@ -248425,7 +248125,7 @@ is_a: GO:0003690 ! double-stranded DNA binding
id: GO:0044730
name: bone sialoprotein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a bone sialoprotein, an extracellular matrix glycoprotein found on the surface of bones and dentin." [PMID:10642520]
+def: "Binding to a bone sialoprotein, an extracellular matrix glycoprotein found on the surface of bones and dentin." [PMID:10642520]
synonym: "bone sialoprotein II binding" EXACT []
xref: InterPro:IPR008412
is_a: GO:0005515 ! protein binding
@@ -248450,27 +248150,30 @@ is_a: GO:0005816 ! spindle pole body
[Term]
id: GO:0044733
-name: envenomation resulting in modulation of acid-sensing ion channel activity in other organism
+name: envenomation resulting in modulation of acid-sensing ion channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant change in the activity of an acid-sensing ion channel (ASIC) in the bitten organism." [GOC:fj, GOC:jl, PMID:23034652]
+synonym: "envenomation resulting in modulation of acid-sensing ion channel activity in other organism" EXACT []
synonym: "envenomation resulting in modulation of ASIC channel activity in other organism" EXACT []
-is_a: GO:0044560 ! envenomation resulting in modulation of ion channel activity in other organism
+is_a: GO:0044560 ! envenomation resulting in modulation of ion channel activity in another organism
[Term]
id: GO:0044734
-name: envenomation resulting in positive regulation of acid-sensing ion channel activity in other organism
+name: envenomation resulting in positive regulation of acid-sensing ion channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant positive regulation in the activity of an acid-sensing ion channel (ASIC) in the bitten organism." [GOC:fj, GOC:jl, PMID:23034652]
+synonym: "envenomation resulting in positive regulation of acid-sensing ion channel activity in other organism" EXACT []
synonym: "envenomation resulting in positive regulation of ASIC channel activity in other organism" EXACT []
-is_a: GO:0044733 ! envenomation resulting in modulation of acid-sensing ion channel activity in other organism
+is_a: GO:0044733 ! envenomation resulting in modulation of acid-sensing ion channel activity in another organism
[Term]
id: GO:0044735
-name: envenomation resulting in negative regulation of acid-sensing ion channel activity in other organism
+name: envenomation resulting in negative regulation of acid-sensing ion channel activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with a resultant negative regulation in the activity of an acid-sensing ion channel (ASIC) in the bitten organism." [GOC:fj, GOC:jl, PMID:23034652]
+synonym: "envenomation resulting in negative regulation of acid-sensing ion channel activity in other organism" EXACT []
synonym: "envenomation resulting in negative regulation of ASIC channel activity in other organism" EXACT []
-is_a: GO:0044733 ! envenomation resulting in modulation of acid-sensing ion channel activity in other organism
+is_a: GO:0044733 ! envenomation resulting in modulation of acid-sensing ion channel activity in another organism
[Term]
id: GO:0044736
@@ -248484,53 +248187,59 @@ is_a: GO:0015280 ! ligand-gated sodium channel activity
[Term]
id: GO:0044737
-name: modulation of acid-sensing ion channel in other organism
+name: modulation of acid-sensing ion channel in another organism
namespace: biological_process
def: "Any process in which an organism effects a change in the frequency, rate or extent of the activity of an acid-sensing ion channel (ASIC) in another organism." [GOC:jl]
+synonym: "modulation of acid-sensing ion channel in other organism" EXACT []
synonym: "regulation of acid-sensing ion channel in other organism" EXACT []
synonym: "regulation of ASIC channel in other organism" EXACT []
-is_a: GO:0044561 ! modulation of ion channel activity in other organism
+is_a: GO:0044561 ! modulation of ion channel activity in another organism
[Term]
id: GO:0044738
-name: negative regulation of acid-sensing ion channel in other organism
+name: negative regulation of acid-sensing ion channel in another organism
namespace: biological_process
def: "Any process in which an organism negatively regulates the activity of a voltage-gated sodium channel in another organism." [GOC:jl]
+synonym: "negative regulation of acid-sensing ion channel in other organism" EXACT []
synonym: "negative regulation of ASIC channel in other organism" EXACT []
-is_a: GO:0044737 ! modulation of acid-sensing ion channel in other organism
+is_a: GO:0044737 ! modulation of acid-sensing ion channel in another organism
[Term]
id: GO:0044739
-name: positive regulation of acid-sensing ion channel in other organism
+name: positive regulation of acid-sensing ion channel in another organism
namespace: biological_process
def: "Any process in which an organism positively regulates the activity of a voltage-gated sodium channel in another organism." [GOC:jl]
+synonym: "positive regulation of acid-sensing ion channel in other organism" EXACT []
synonym: "positive regulation of ASIC channel in other organism" EXACT []
-is_a: GO:0044737 ! modulation of acid-sensing ion channel in other organism
+is_a: GO:0044737 ! modulation of acid-sensing ion channel in another organism
[Term]
id: GO:0044740
-name: negative regulation of sensory perception of pain in other organism
+name: negative regulation of sensory perception of pain in another organism
namespace: biological_process
def: "A process that negatively regulates the sensory perception of pain in a different organism." [GOC:fj, GOC:jl]
synonym: "inhibition of sensory perception of pain in another organism" EXACT []
+synonym: "negative regulation of sensory perception of pain in other organism" EXACT []
is_a: GO:0031645 ! negative regulation of nervous system process
-is_a: GO:0044465 ! modulation of sensory perception of pain in other organism
+is_a: GO:0044465 ! modulation of sensory perception of pain in another organism
[Term]
id: GO:0044741
-name: envenomation resulting in negative regulation of sensory perception of pain in other organism
+name: envenomation resulting in negative regulation of sensory perception of pain in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the inhibition of the sensory perception of pain in the bitten organism." [GOC:fj, GOC:jl, PMID:23034652]
synonym: "envenomation resulting in inhibition of sensory perception of pain in other organism" EXACT []
-is_a: GO:0044742 ! envenomation resulting in modulation of sensory perception of pain in other organism
+synonym: "envenomation resulting in negative regulation of sensory perception of pain in other organism" EXACT []
+is_a: GO:0044742 ! envenomation resulting in modulation of sensory perception of pain in another organism
[Term]
id: GO:0044742
-name: envenomation resulting in modulation of sensory perception of pain in other organism
+name: envenomation resulting in modulation of sensory perception of pain in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the modulation of the sensory perception of pain in the bitten organism." [GOC:fj, GOC:jl, PMID:23034652]
+synonym: "envenomation resulting in modulation of sensory perception of pain in other organism" EXACT []
synonym: "envenomation resulting in regulation of sensory perception of pain in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0044743
@@ -248653,15 +248362,14 @@ name: multi-organism cellular process
namespace: biological_process
def: "Any process that is carried out at the cellular level which involves another organism of the same or different species." [GOC:jl]
is_a: GO:0009987 ! cellular process
-is_a: GO:0051704 ! multi-organism process
[Term]
id: GO:0044766
-name: multi-organism transport
+name: obsolete multi-organism transport
namespace: biological_process
-def: "The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving more than one organism." [GOC:jl]
-is_a: GO:0006810 ! transport
-is_a: GO:1902579 ! multi-organism localization
+def: "OBSOLETE. The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving more than one organism." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:0044768
@@ -248816,7 +248524,7 @@ def: "The assembly of a bacterial-type flagellum, a motor complex composed of an
synonym: "bacterial flagellum assembly" EXACT []
is_a: GO:0030031 ! cell projection assembly
is_a: GO:0044781 ! bacterial-type flagellum organization
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:0044781
@@ -248833,6 +248541,7 @@ namespace: biological_process
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:cilia, GOC:jl]
comment: Note that we deem cilium and microtubule-based flagellum to be equivalent.
subset: goslim_drosophila
+subset: goslim_generic
synonym: "microtubule-based flagellum organization" EXACT []
is_a: GO:0006996 ! organelle organization
is_a: GO:0120036 ! plasma membrane bounded cell projection organization
@@ -248879,29 +248588,55 @@ is_a: GO:0051851 ! modulation by host of symbiont process
[Term]
id: GO:0044789
-name: modulation by host of viral release from host cell
+name: obsolete modulation by host of viral release from host cell
namespace: biological_process
-def: "A process in which a host organism modulates the frequency, rate or extent of the release of a virus with which it is infected, from its cells." [GOC:jl, PMID:18305167]
-is_a: GO:0044788 ! modulation by host of viral process
-is_a: GO:1902186 ! regulation of viral release from host cell
+def: "OBSOLETE. A process in which a host organism modulates the frequency, rate or extent of the release of a virus with which it is infected, from its cells." [GOC:jl, PMID:18305167]
+comment: This term was obsoleted because there is no evidence that it is a regulated process.
+is_obsolete: true
+replaced_by: GO:0019076
[Term]
id: GO:0044790
-name: negative regulation by host of viral release from host cell
+name: suppression of viral release by host
namespace: biological_process
+alt_id: GO:1902187
def: "A process in which a host organism stops, prevents or reduces the frequency, rate or extent of the release of a virus with which it is infected, from its cells." [GOC:jl, PMID:18305167]
-is_a: GO:0044789 ! modulation by host of viral release from host cell
-is_a: GO:0044793 ! negative regulation by host of viral process
-is_a: GO:1902187 ! negative regulation of viral release from host cell
+synonym: "down regulation of release of virus from host" EXACT [GOC:TermGenie]
+synonym: "down regulation of viral exit" EXACT [GOC:TermGenie]
+synonym: "down regulation of viral release" EXACT [GOC:TermGenie]
+synonym: "down regulation of viral release from host cell" EXACT [GOC:TermGenie]
+synonym: "down regulation of viral shedding" EXACT [GOC:TermGenie]
+synonym: "down-regulation of release of virus from host" EXACT [GOC:TermGenie]
+synonym: "down-regulation of viral exit" EXACT [GOC:TermGenie]
+synonym: "down-regulation of viral release" EXACT [GOC:TermGenie]
+synonym: "down-regulation of viral release from host cell" EXACT [GOC:TermGenie]
+synonym: "down-regulation of viral shedding" EXACT [GOC:TermGenie]
+synonym: "downregulation of release of virus from host" EXACT [GOC:TermGenie]
+synonym: "downregulation of viral exit" EXACT [GOC:TermGenie]
+synonym: "downregulation of viral release" EXACT [GOC:TermGenie]
+synonym: "downregulation of viral release from host cell" EXACT [GOC:TermGenie]
+synonym: "downregulation of viral shedding" EXACT [GOC:TermGenie]
+synonym: "inhibition of release of virus from host" EXACT [GOC:TermGenie]
+synonym: "inhibition of viral exit" EXACT [GOC:TermGenie]
+synonym: "inhibition of viral release" EXACT [GOC:TermGenie]
+synonym: "inhibition of viral release from host cell" NARROW [GOC:TermGenie]
+synonym: "inhibition of viral shedding" EXACT [GOC:TermGenie]
+synonym: "negative regulation by host of viral release from host cell" EXACT []
+synonym: "negative regulation of release of virus from host" EXACT [GOC:TermGenie]
+synonym: "negative regulation of viral exit" EXACT [GOC:TermGenie]
+synonym: "negative regulation of viral release" EXACT [GOC:TermGenie]
+synonym: "negative regulation of viral release from host cell" EXACT []
+synonym: "negative regulation of viral shedding" EXACT [GOC:TermGenie]
+is_a: GO:0051607 ! defense response to virus
[Term]
id: GO:0044791
-name: positive regulation by host of viral release from host cell
+name: obsolete positive regulation by host of viral release from host cell
namespace: biological_process
-def: "A process in which a host organism activates or increases the frequency, rate or extent of the release of a virus with which it is infected, from its cells." [GOC:jl]
-is_a: GO:0044789 ! modulation by host of viral release from host cell
-is_a: GO:0044794 ! positive regulation by host of viral process
-is_a: GO:1902188 ! positive regulation of viral release from host cell
+def: "OBSOLETE. A process in which a host organism activates or increases the frequency, rate or extent of the release of a virus with which it is infected, from its cells." [GOC:jl]
+comment: This term was obsoleted because there is no evidence that it is a regulated process.
+is_obsolete: true
+replaced_by: GO:0019076
[Term]
id: GO:0044793
@@ -248948,18 +248683,17 @@ relationship: part_of GO:0070470 ! plasma membrane respirasome
[Term]
id: GO:0044800
-name: multi-organism membrane fusion
+name: obsolete multi-organism membrane fusion
namespace: biological_process
-def: "The membrane organization process that joins two lipid bilayers to form a single membrane, involving more than one organism." [GOC:jl]
-is_a: GO:0044803 ! multi-organism membrane organization
-is_a: GO:0061025 ! membrane fusion
+def: "OBSOLETE. The membrane organization process that joins two lipid bilayers to form a single membrane, involving more than one organism." [GOC:jl]
+comment: This term was obsoleted because it is not a biologically meaningful grouping class.
+is_obsolete: true
[Term]
id: GO:0044803
name: multi-organism membrane organization
namespace: biological_process
def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane, involving more than one organism." [GOC:jl]
-is_a: GO:0044764 ! multi-organism cellular process
is_a: GO:0061024 ! membrane organization
[Term]
@@ -249001,7 +248735,6 @@ name: oncostatin M production
namespace: biological_process
def: "The appearance of oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:rv]
subset: gocheck_do_not_annotate
-synonym: "Oncostatin M production" EXACT []
synonym: "OSM production" EXACT []
is_a: GO:0001816 ! cytokine production
@@ -249115,12 +248848,13 @@ relationship: part_of GO:0044823 ! retroviral integrase activity
[Term]
id: GO:0044825
-name: retroviral strand transfer activity
+name: obsolete retroviral strand transfer activity
namespace: molecular_function
-def: "Catalysis of the covalent insertion of processed 3'-viral DNA ends into host chromosomal DNA by a trans-esterification reaction." [PMID:22580823]
+def: "OBSOLETE. Catalysis of the covalent insertion of processed 3'-viral DNA ends into host chromosomal DNA by a trans-esterification reaction." [PMID:22580823]
+comment: This term was obsoleted because it represents part of an activity.
synonym: "strand transfer reaction" EXACT []
-is_a: GO:0140097 ! catalytic activity, acting on DNA
-relationship: part_of GO:0044823 ! retroviral integrase activity
+is_obsolete: true
+consider: GO:0044823
[Term]
id: GO:0044826
@@ -249194,8 +248928,8 @@ name: modulation by virus of host protein transport
namespace: biological_process
def: "Any viral process that modulates the frequency, rate or extent of protein transport in its host organism." [GOC:jl, PMID:22334672]
is_a: GO:0019054 ! modulation by virus of host cellular process
-is_a: GO:0051223 ! regulation of protein transport
is_a: GO:0052038 ! modulation by symbiont of host intracellular transport
+relationship: regulates GO:0015031 ! protein transport
[Term]
id: GO:0044834
@@ -249262,7 +248996,7 @@ id: GO:0044841
name: gut granule membrane
namespace: cellular_component
def: "The membrane of a gut granule, a lysosome-related organelle contained within the intestinal cells of the nematode C. elegans." [GOC:kmv, PMID:22916203, PMID:24204312]
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
relationship: part_of GO:0044840 ! gut granule
[Term]
@@ -249503,7 +249237,6 @@ namespace: biological_process
def: "The process in which a host organism decreases viral exo-alpha-sialidase activity, the catalysis of the hydrolysis of peptide bonds in a protein." [GOC:jl]
is_a: GO:0044866 ! modulation by host of viral exo-alpha-sialidase activity
is_a: GO:0052403 ! negative regulation by host of symbiont catalytic activity
-is_a: GO:1903016 ! negative regulation of exo-alpha-sialidase activity
[Term]
id: GO:0044870
@@ -249560,9 +249293,9 @@ is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0044876
name: hercynylselenocysteine synthase
namespace: molecular_function
-def: "Catalysis of the reaction: 2 L-selenocysteine + 2 hercynine + O2 <=> 2 H2O + 2 hercynylselenocysteine." [GOC:jl, PMID:24828577]
+def: "Catalysis of the reaction: 2 L-selenocysteine + 2 hercynine + O2 <=> 2 H2O + 2 hercynylselenocysteine." [GOC:jl, PMID:24828577, RHEA:42680]
xref: MetaCyc:RXN-15803
-xref: RHEA:42683
+xref: RHEA:42680
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
[Term]
@@ -249570,7 +249303,7 @@ id: GO:0044877
name: protein-containing complex binding
namespace: molecular_function
alt_id: GO:0032403
-def: "Interacting selectively and non-covalently with a macromolecular complex." [GOC:jl]
+def: "Binding to a macromolecular complex." [GOC:jl]
subset: goslim_chembl
synonym: "macromolecular complex binding" RELATED []
synonym: "protein complex binding" EXACT []
@@ -249685,7 +249418,6 @@ namespace: biological_process
def: "The initial step in the formation of an actin filament, in which actin monomers combine to form a new filament. Nucleation is slow relative to the subsequent addition of more monomers to extend the filament." [ISBN:0815316194]
synonym: "actin filament nucleation" EXACT []
is_a: GO:0007015 ! actin filament organization
-is_a: GO:0030838 ! positive regulation of actin filament polymerization
[Term]
id: GO:0045012
@@ -249729,7 +249461,7 @@ is_a: GO:0061986 ! negative regulation of transcription by glucose
id: GO:0045015
name: HDEL sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a HDEL sequence, the C terminus tetrapeptide sequence His-Asp-Glu-Leu found in proteins that are to be retained in the endoplasmic reticulum." [PMID:1327759]
+def: "Binding to a HDEL sequence, the C terminus tetrapeptide sequence His-Asp-Glu-Leu found in proteins that are to be retained in the endoplasmic reticulum." [PMID:1327759]
synonym: "HDEL receptor activity" NARROW []
is_a: GO:0046923 ! ER retention sequence binding
@@ -249853,7 +249585,7 @@ is_a: GO:0061025 ! membrane fusion
id: GO:0045027
name: DNA end binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the ends of DNA that are exposed by the creation of double-strand breaks (DSBs)." [GOC:jl]
+def: "Binding to DNA ends exposed by the creation of double-strand breaks (DSBs)." [GOC:jl]
is_a: GO:0003677 ! DNA binding
[Term]
@@ -250000,6 +249732,7 @@ synonym: "protein import into mitochondrial intermembrane space, direct" NARROW
synonym: "protein import into mitochondrial intermembrane space, nonconservative" NARROW [GOC:mcc]
synonym: "protein transport into mitochondrial IMS" EXACT []
synonym: "protein transport into mitochondrial intermembrane space" EXACT []
+is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0044743 ! protein transmembrane import into intracellular organelle
is_a: GO:0065002 ! intracellular protein transmembrane transport
is_a: GO:0072655 ! establishment of protein localization to mitochondrion
@@ -250155,6 +249888,7 @@ namespace: biological_process
def: "The directed movement of endocytosed material through the cell and its exocytosis from the plasma membrane at the opposite side." [ISBN:0716731363]
xref: Wikipedia:Transcytosis
is_a: GO:0016192 ! vesicle-mediated transport
+is_a: GO:0032501 ! multicellular organismal process
[Term]
id: GO:0045057
@@ -250273,7 +250007,6 @@ id: GO:0045067
name: positive extrathymic T cell selection
namespace: biological_process
def: "The process of sparing extrathymically maturing T cells which react with self-MHC protein complexes with low affinity levels from apoptotic death." [ISBN:0781735149, PMID:7880383]
-synonym: "positive extrathymic T cell selection" RELATED [GOC:add]
synonym: "positive extrathymic T lymphocyte selection" EXACT []
synonym: "positive extrathymic T-cell selection" EXACT []
synonym: "positive extrathymic T-lymphocyte selection" EXACT []
@@ -250335,6 +250068,7 @@ def: "Innate immune responses are defense responses mediated by germline encoded
synonym: "innate immunity" EXACT [GOC:pg]
synonym: "nonspecific immune response" EXACT []
xref: Wikipedia:Innate_immune_system
+is_a: GO:0006955 ! immune response
is_a: GO:0098542 ! defense response to other organism
[Term]
@@ -250386,7 +250120,7 @@ relationship: part_of GO:0005887 ! integral component of plasma membrane
id: GO:0045093
name: obsolete interleukin-18 alpha subunit binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with the alpha subunit of interleukin-18. IL-18a is a component of IL-18 that is essential for IL-18 binding on the surface of T-helper 1 cells." [PMID:10653850]
+def: "OBSOLETE. Binding to alpha subunit of interleukin-18. IL-18a is a component of IL-18 that is essential for IL-18 binding on the surface of T-helper 1 cells." [PMID:10653850]
comment: This term was obsoleted because interleukin-18 is a single polypeptide and has no subunits
synonym: "IL-18Ra binding" EXACT []
is_obsolete: true
@@ -250395,7 +250129,7 @@ is_obsolete: true
id: GO:0045094
name: obsolete interleukin-18 beta subunit binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with the beta subunit of interleukin-18. IL-18b is a ligand non-binding chain and is required for signaling of IL-18 that binds with IL-18a." [PMID:10653850]
+def: "OBSOLETE. Binding to beta subunit of interleukin-18. IL-18b is a ligand non-binding chain and is required for signaling of IL-18 that binds with IL-18a." [PMID:10653850]
comment: This term was obsoleted because interleukin-18 is a single polypeptide and has no subunits.
synonym: "IL-18Rb binding" EXACT []
is_obsolete: true
@@ -250506,7 +250240,7 @@ id: GO:0045105
name: intermediate filament polymerization or depolymerization
namespace: biological_process
def: "Assembly or disassembly of intermediate filaments by the addition or removal of component parts from a filament." [GOC:ai]
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
relationship: part_of GO:0045104 ! intermediate filament cytoskeleton organization
[Term]
@@ -250733,7 +250467,7 @@ relationship: negatively_regulates GO:0007131 ! reciprocal meiotic recombination
id: GO:0045129
name: NAD-independent histone deacetylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction does not require the presence of NAD, and represents the removal of an acetyl group from a histone." [EC:3.5.1.17, RHEA:24548]
+def: "Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction does not require the presence of NAD, and represents the removal of an acetyl group from a histone." [PMID:28450737]
synonym: "AcuC" RELATED []
is_a: GO:0004407 ! histone deacetylase activity
@@ -250757,7 +250491,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0045131
name: pre-mRNA branch point binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pre-mRNA branch point sequence, located upstream of the 3' splice site." [PMID:11691992, PMID:9722632]
+def: "Binding to a pre-mRNA branch point sequence, located upstream of the 3' splice site." [PMID:11691992, PMID:9722632]
is_a: GO:0036002 ! pre-mRNA binding
[Term]
@@ -250876,7 +250610,7 @@ is_a: GO:0090220 ! chromosome localization to nuclear envelope involved in homol
id: GO:0045142
name: triplex DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DNA triple helix. The formation of triple helical DNA has been evoked in several cellular processes including transcription, replication, and recombination." [PMID:10681538]
+def: "Binding to a DNA triple helix. The formation of triple helical DNA has been evoked in several cellular processes including transcription, replication, and recombination." [PMID:10681538]
is_a: GO:0003677 ! DNA binding
[Term]
@@ -250986,7 +250720,7 @@ is_a: GO:1902653 ! secondary alcohol biosynthetic process
id: GO:0045152
name: antisigma factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an antisigma factor, a factor which inhibits the ability of the sigma factor to function as a transcriptional initiator." [GOC:mlg]
+def: "Binding to an antisigma factor, a factor which inhibits the ability of the sigma factor to function as a transcriptional initiator." [GOC:mlg]
synonym: "antisigma factor antagonist activity" NARROW []
is_a: GO:0005515 ! protein binding
@@ -251032,7 +250766,7 @@ is_a: GO:0009055 ! electron transfer activity
id: GO:0045159
name: myosin II binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a class II myosin, any member of the class of 'conventional' double-headed myosins that includes muscle myosin." [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
+def: "Binding to a class II myosin, any member of the class of 'conventional' double-headed myosins that includes muscle myosin." [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html]
is_a: GO:0017022 ! myosin binding
[Term]
@@ -251251,6 +250985,7 @@ def: "Any molecular function involved in the initiation, activation, perpetuatio
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
synonym: "translation factor activity" EXACT []
@@ -251851,7 +251586,7 @@ is_a: GO:0043543 ! protein acylation
id: GO:0045236
name: CXCR chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chemokine receptor in the CXCR family." [GOC:ceb, PMID:11910892]
+def: "Binding to a chemokine receptor in the CXCR family." [GOC:ceb, PMID:11910892]
synonym: "alpha chemokine receptor binding" EXACT []
synonym: "alpha chemokine receptor ligand" NARROW []
synonym: "C-X-C chemokine receptor ligand" NARROW []
@@ -251862,7 +251597,7 @@ is_a: GO:0042379 ! chemokine receptor binding
id: GO:0045237
name: CXCR1 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the CXCR1 chemokine receptor." [GOC:ceb, PMID:11910892]
+def: "Binding to a CXCR1 chemokine receptor." [GOC:ceb, PMID:11910892]
synonym: "CXCR1 chemokine receptor ligand" NARROW []
is_a: GO:0005153 ! interleukin-8 receptor binding
@@ -251870,7 +251605,7 @@ is_a: GO:0005153 ! interleukin-8 receptor binding
id: GO:0045238
name: CXCR2 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the CXCR2 chemokine receptor." [GOC:ceb, PMID:11910892]
+def: "Binding to a CXCR2 chemokine receptor." [GOC:ceb, PMID:11910892]
synonym: "CXCR2 chemokine receptor ligand" NARROW []
is_a: GO:0005153 ! interleukin-8 receptor binding
@@ -251926,7 +251661,7 @@ name: succinate-CoA ligase complex (GDP-forming)
namespace: cellular_component
alt_id: GO:0008325
alt_id: GO:0045245
-def: "A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming GTP." [EC:6.2.1.4, GOC:jl]
+def: "A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming GTP." [GOC:jl, PMID:27487822]
synonym: "succinyl-CoA synthetase, GDP-forming" EXACT [CORUM:392]
is_a: GO:0030062 ! mitochondrial tricarboxylic acid cycle enzyme complex
is_a: GO:0042709 ! succinate-CoA ligase complex
@@ -251953,8 +251688,7 @@ relationship: part_of GO:0005829 ! cytosol
id: GO:0045248
name: cytosolic oxoglutarate dehydrogenase complex
namespace: cellular_component
-def: "A cytosolic complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) ; EC:1.2.4.2 (E1), dihydrolipoamide S-succinyltransferase ; EC:2.3.1.61 (E2) and dihydrolipoamide dehydrogenase ; EC:1.8.1.4 (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [GOC:mtg_sensu, PMID:10848975]
-comment: See also the molecular functions term 'oxoglutarate dehydrogenase (succinyl-transferring) activity ; GO:0004591', 'dihydrolipoyllysine-residue succinyltransferase activity ; GO:0004149' and 'dihydrolipoyl dehydrogenase activity ; GO:0004148'.
+def: "A cytosolic complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [GOC:mtg_sensu, PMID:10848975]
is_a: GO:0045252 ! oxoglutarate dehydrogenase complex
relationship: part_of GO:0005829 ! cytosol
@@ -251991,8 +251725,7 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0045252
name: oxoglutarate dehydrogenase complex
namespace: cellular_component
-def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) ; EC:1.2.4.2 (E1), dihydrolipoamide S-succinyltransferase ; EC:2.3.1.61 (E2) and dihydrolipoamide dehydrogenase ; EC:1.8.1.4 (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [MetaCyc:CPLX66-42, PMID:10848975]
-comment: See also the molecular functions term 'oxoglutarate dehydrogenase (succinyl-transferring) activity ; GO:0004591', 'dihydrolipoyllysine-residue succinyltransferase activity ; GO:0004149' and 'dihydrolipoyl dehydrogenase activity ; GO:0004148'.
+def: "A complex of multiple copies of three enzymatic components: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3); catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and carbon dioxide (CO2)." [MetaCyc:CPLX66-42, PMID:10848975]
subset: goslim_pir
synonym: "dihydrolipoamide S-succinyltransferase complex" EXACT []
is_a: GO:0045240 ! dihydrolipoyl dehydrogenase complex
@@ -252182,6 +251915,7 @@ synonym: "NADH dehydrogenase complex (ubiquinone)" EXACT []
synonym: "NADH-Q oxidoreductase complex" EXACT []
is_a: GO:0030964 ! NADH dehydrogenase complex
is_a: GO:0098803 ! respiratory chain complex
+is_a: GO:1902495 ! transmembrane transporter complex
[Term]
id: GO:0045272
@@ -252234,6 +251968,7 @@ synonym: "ubiquinol-cytochrome-c reductase complex" EXACT []
xref: Wikipedia:Coenzyme_Q_-_cytochrome_c_reductase
is_a: GO:0070069 ! cytochrome complex
is_a: GO:0098803 ! respiratory chain complex
+is_a: GO:1902495 ! transmembrane transporter complex
is_a: GO:1990204 ! oxidoreductase complex
[Term]
@@ -252367,14 +252102,14 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0045294
name: alpha-catenin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the alpha subunit of the catenin complex." [GOC:bf]
+def: "Binding to catenin complex alpha subunit." [GOC:bf]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0045295
name: gamma-catenin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the gamma subunit of the catenin complex." [GOC:bf]
+def: "Binding to catenin complex gamma subunit." [GOC:bf]
synonym: "plakoglobin binding" EXACT [GOC:BHF]
is_a: GO:0005515 ! protein binding
@@ -252382,7 +252117,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0045296
name: cadherin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion." [GOC:bf]
+def: "Binding to cadherin, a type I membrane protein involved in cell adhesion." [GOC:bf]
is_a: GO:0050839 ! cell adhesion molecule binding
[Term]
@@ -252516,7 +252251,7 @@ replaced_by: GO:0045809
id: GO:0045309
name: protein phosphorylated amino acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a phosphorylated amino acid residue within a protein." [GOC:go_curators]
+def: "Binding to a phosphorylated amino acid residue within a protein." [GOC:go_curators]
synonym: "phosphoprotein amino acid binding" RELATED []
is_a: GO:0051219 ! phosphoprotein binding
@@ -252642,7 +252377,7 @@ is_a: GO:0002376 ! immune system process
id: GO:0045322
name: unmethylated CpG binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters." [GOC:ai, PMID:10688657]
+def: "Binding to uan nmethylated CpG motif. Unmethylated CpG dinucleotides are often associated with gene promoters." [GOC:ai, PMID:10688657]
is_a: GO:0043565 ! sequence-specific DNA binding
[Term]
@@ -252661,7 +252396,6 @@ namespace: biological_process
def: "The directed movement of substances from late endosomes to the vacuole. In yeast, after transport to the prevacuolar compartment, endocytic content is delivered to the late endosome and on to the vacuole. This pathway is analogous to endosome to lysosome transport." [PMID:11872141]
is_a: GO:0007034 ! vacuolar transport
is_a: GO:0016192 ! vesicle-mediated transport
-is_a: GO:0046907 ! intracellular transport
[Term]
id: GO:0045325
@@ -252825,7 +252559,8 @@ is_a: GO:0045338 ! farnesyl diphosphate metabolic process
id: GO:0045340
name: mercury ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with mercury (Hg) ions." [GOC:go_curators]
+def: "Binding to a mercury ion (Hg)." [GOC:go_curators]
+synonym: "Hg ion binding" EXACT []
synonym: "mercury binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
@@ -253723,21 +253458,21 @@ relationship: regulates GO:0045500 ! sevenless signaling pathway
id: GO:0045503
name: dynein light chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a light chain of the dynein complex." [GOC:bf]
+def: "Binding to a light chain of the dynein complex." [GOC:bf]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0045504
name: dynein heavy chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a heavy chain of the dynein complex." [GOC:bf]
+def: "Binding to a heavy chain of the dynein complex." [GOC:bf]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0045505
name: dynein intermediate chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an intermediate chain of the dynein complex." [GOC:bf]
+def: "Binding to an intermediate chain of the dynein complex." [GOC:bf]
is_a: GO:0005515 ! protein binding
[Term]
@@ -253780,7 +253515,7 @@ is_a: GO:0030368 ! interleukin-17 receptor activity
id: GO:0045510
name: interleukin-24 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-24." [GOC:go_curators]
+def: "Binding to interleukin-24." [GOC:go_curators]
synonym: "IL-24 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -253788,7 +253523,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0045511
name: interleukin-25 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-25." [GOC:go_curators]
+def: "Binding to interleukin-25." [GOC:go_curators]
synonym: "IL-25 binding" EXACT []
is_a: GO:0019975 ! interleukin-17 binding
@@ -253796,7 +253531,7 @@ is_a: GO:0019975 ! interleukin-17 binding
id: GO:0045512
name: interleukin-26 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-26." [GOC:go_curators]
+def: "Binding to interleukin-26." [GOC:go_curators]
synonym: "IL-26 binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -253804,7 +253539,7 @@ is_a: GO:0019955 ! cytokine binding
id: GO:0045513
name: interleukin-27 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-27." [GOC:go_curators]
+def: "Binding to interleukin-27." [GOC:go_curators]
synonym: "IL-27 binding" EXACT []
is_a: GO:0019975 ! interleukin-17 binding
@@ -253812,7 +253547,7 @@ is_a: GO:0019975 ! interleukin-17 binding
id: GO:0045514
name: interleukin-16 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-16 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-16 receptor." [GOC:go_curators]
synonym: "IL-16" NARROW []
synonym: "interleukin-16 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253821,7 +253556,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045515
name: interleukin-18 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-18 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-18 receptor." [GOC:go_curators]
synonym: "IL-18" NARROW []
synonym: "interleukin-18 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253830,7 +253565,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045516
name: interleukin-19 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-19 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-19 receptor." [GOC:go_curators]
synonym: "IL-19" NARROW []
synonym: "interleukin-19 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253839,7 +253574,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045517
name: interleukin-20 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-20 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-20 receptor." [GOC:go_curators]
synonym: "IL-20" NARROW []
synonym: "interleukin-20 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253848,7 +253583,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045518
name: interleukin-22 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-22 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-22 receptor." [GOC:go_curators]
synonym: "IL-22" NARROW []
synonym: "interleukin-22 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253857,7 +253592,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045519
name: interleukin-23 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-23 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-23 receptor." [GOC:go_curators]
synonym: "IL-23" NARROW []
synonym: "interleukin-23 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253866,7 +253601,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045520
name: interleukin-24 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-24 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-24 receptor." [GOC:go_curators]
synonym: "IL-24" NARROW []
synonym: "interleukin-24 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253875,7 +253610,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045521
name: interleukin-25 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-25 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-25 receptor." [GOC:go_curators]
synonym: "IL-25" NARROW []
synonym: "interleukin-25 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253884,7 +253619,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045522
name: interleukin-26 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-26 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-26 receptor." [GOC:go_curators]
synonym: "IL-26" NARROW []
synonym: "interleukin-26 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253893,7 +253628,7 @@ is_a: GO:0005126 ! cytokine receptor binding
id: GO:0045523
name: interleukin-27 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-27 receptor." [GOC:go_curators]
+def: "Binding to an interleukin-27 receptor." [GOC:go_curators]
synonym: "IL-27" NARROW []
synonym: "interleukin-27 receptor ligand" NARROW []
is_a: GO:0005126 ! cytokine receptor binding
@@ -253977,7 +253712,7 @@ is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
id: GO:0045545
name: syndecan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with syndecan, an integral membrane proteoglycan (250-300 kDa) associated largely with epithelial cells." [GOC:go_curators, PMID:9355727]
+def: "Binding to syndecan, an integral membrane proteoglycan (250-300 kDa) associated largely with epithelial cells." [GOC:go_curators, PMID:9355727]
is_a: GO:0043394 ! proteoglycan binding
[Term]
@@ -254230,7 +253965,7 @@ is_obsolete: true
id: GO:0045569
name: TRAIL binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with TRAIL (TNF-related apoptosis inducing ligand), a member of the tumor necrosis factor ligand family that rapidly induces apoptosis in a variety of transformed cell lines." [GOC:go_curators, PMID:9082980]
+def: "Binding to TRAIL (TNF-related apoptosis inducing ligand), a member of the tumor necrosis factor ligand family that rapidly induces apoptosis in a variety of transformed cell lines." [GOC:go_curators, PMID:9082980]
subset: goslim_chembl
synonym: "Apo-2L binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -256427,6 +256162,7 @@ name: nutrient reservoir activity
namespace: molecular_function
def: "Functions in the storage of nutritious substrates." [GOC:ai]
comment: Note that this term can be used in place of the obsolete terms 'storage protein ; GO:0005187' and 'storage protein of fat body (sensu Insecta) ; GO:0008041'.
+subset: goslim_generic
subset: goslim_pir
synonym: "storage protein" RELATED []
synonym: "storage protein of fat body" RELATED []
@@ -257466,21 +257202,31 @@ relationship: positively_regulates GO:0007223 ! Wnt signaling pathway, calcium m
id: GO:0045814
name: negative regulation of gene expression, epigenetic
namespace: biological_process
-def: "Any epigenetic process that stops, prevents or reduces the rate of gene expression." [GOC:go_curators]
+def: "An epigenetic process that stops, prevents or reduces the rate of gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA." [PMID:22243696]
synonym: "down regulation of gene expression, epigenetic" EXACT []
synonym: "down-regulation of gene expression, epigenetic" EXACT []
synonym: "downregulation of gene expression, epigenetic" EXACT []
+synonym: "gene silencing" RELATED []
synonym: "inhibition of gene expression, epigenetic" NARROW []
is_a: GO:0010629 ! negative regulation of gene expression
is_a: GO:0040029 ! regulation of gene expression, epigenetic
[Term]
id: GO:0045815
-name: positive regulation of gene expression, epigenetic
-namespace: biological_process
-def: "Any epigenetic process that activates or increases the rate of gene expression." [GOC:go_curators]
-synonym: "activation of gene expression, epigenetic" NARROW []
-synonym: "stimulation of gene expression, epigenetic" NARROW []
+name: epigenetic maintenance of chromatin in transcription-competent conformation
+namespace: biological_process
+alt_id: GO:0048096
+def: "An epigenetic process that capacitates gene expression by remodelling of chromatin by either modifying the chromatin fiber, the nucleosomal histones, or the DNA." [PMID:34414474]
+comment: This regulation is exemplified by members of the trithorax group, which maintain the active state of homeotic gene transcription. Do not confuse with GO:0140673 ; co-transcriptional chromatin reassembly, which describes the reforming of chromatin after RNA polymerase II passage.
+synonym: "activation of gene expression, epigenetic" RELATED []
+synonym: "chromatin-mediated maintenance of transcription" EXACT []
+synonym: "euchromatin assembly" RELATED []
+synonym: "euchromatin organisation" RELATED []
+synonym: "euchromatin organization" RELATED []
+synonym: "long-term maintenance of gene activation" RELATED []
+synonym: "maintenance of chromatin in transcription-competent conformation" EXACT []
+synonym: "positive regulation of gene expression, epigenetic" EXACT []
+synonym: "stimulation of gene expression, epigenetic" RELATED []
synonym: "up regulation of gene expression, epigenetic" EXACT []
synonym: "up-regulation of gene expression, epigenetic" EXACT []
synonym: "upregulation of gene expression, epigenetic" EXACT []
@@ -258047,30 +257793,30 @@ relationship: positively_regulates GO:0045451 ! pole plasm oskar mRNA localizati
[Term]
id: GO:0045857
-name: negative regulation of molecular function, epigenetic
+name: obsolete negative regulation of molecular function, epigenetic
namespace: biological_process
-def: "Any heritable epigenetic process that stops, prevents, or reduces the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "OBSOLETE. Any heritable epigenetic process that stops, prevents, or reduces the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:dph, GOC:go_curators, GOC:tb]
+comment: This term was obsoleted because it is not an active process.
synonym: "down regulation of protein activity, epigenetic" EXACT []
synonym: "down-regulation of protein activity, epigenetic" EXACT []
synonym: "downregulation of protein activity, epigenetic" EXACT []
synonym: "inhibition of protein activity, epigenetic" NARROW []
synonym: "negative regulation of protein activity, epigenetic" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0040030 ! regulation of molecular function, epigenetic
-is_a: GO:0044092 ! negative regulation of molecular function
+is_obsolete: true
[Term]
id: GO:0045858
-name: positive regulation of molecular function, epigenetic
+name: obsolete positive regulation of molecular function, epigenetic
namespace: biological_process
-def: "Any heritable epigenetic process that increases the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:dph, GOC:go_curators, GOC:tb]
+def: "OBSOLETE. Any heritable epigenetic process that increases the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [GOC:dph, GOC:go_curators, GOC:tb]
+comment: This term was obsoleted because it is not an active process.
synonym: "activation of protein activity, epigenetic" NARROW []
synonym: "positive regulation of protein activity, epigenetic" EXACT [GOC:dph, GOC:tb]
synonym: "stimulation of protein activity, epigenetic" NARROW []
synonym: "up regulation of protein activity, epigenetic" EXACT []
synonym: "up-regulation of protein activity, epigenetic" EXACT []
synonym: "upregulation of protein activity, epigenetic" EXACT []
-is_a: GO:0040030 ! regulation of molecular function, epigenetic
-is_a: GO:0044093 ! positive regulation of molecular function
+is_obsolete: true
[Term]
id: GO:0045859
@@ -258500,7 +258246,6 @@ synonym: "negative regulation of transcription, DNA-dependent" EXACT [GOC:txnOH]
synonym: "transcription repressor activity" RELATED []
is_a: GO:0006355 ! regulation of transcription, DNA-templated
is_a: GO:1903507 ! negative regulation of nucleic acid-templated transcription
-is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process
relationship: negatively_regulates GO:0006351 ! transcription, DNA-templated
[Term]
@@ -262838,7 +262583,7 @@ synonym: "phthalate degradation" EXACT []
is_a: GO:0018963 ! phthalate metabolic process
is_a: GO:0019439 ! aromatic compound catabolic process
is_a: GO:0042178 ! xenobiotic catabolic process
-is_a: GO:0043649 ! dicarboxylic acid catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
[Term]
@@ -263790,7 +263535,6 @@ synonym: "phosphoarginine biosynthesis" EXACT []
synonym: "phosphoarginine formation" EXACT []
synonym: "phosphoarginine synthesis" EXACT []
is_a: GO:0006604 ! phosphoarginine metabolic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0042396 ! phosphagen biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -264034,7 +263778,7 @@ is_a: GO:0045168 ! cell-cell signaling involved in cell fate commitment
id: GO:0046332
name: SMAD binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a SMAD signaling protein." [GOC:ai]
+def: "Binding to a SMAD signaling protein." [GOC:ai]
is_a: GO:0005515 ! protein binding
[Term]
@@ -264834,11 +264578,12 @@ is_a: GO:0098518 ! polynucleotide phosphatase activity
[Term]
id: GO:0046404
-name: ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity
+name: polydeoxyribonucleotide 5'-hydroxyl-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA." [EC:2.7.1.78]
+def: "Catalysis of the reaction: ATP + 5'-dephospho-DNA = ADP + 5'-phospho-DNA." [RHEA:15669]
synonym: "ATP-dependent DNA 5'-hydroxyl-kinase activity" EXACT []
synonym: "ATP-dependent DNA kinase activity" EXACT []
+synonym: "ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity" RELATED []
synonym: "ATP-dependent polynucleotide 5'-hydroxyl-kinase activity" BROAD []
synonym: "ATP:5'-dephosphopolydeoxyribonucleotide 5'-phosphotransferase activity" EXACT []
xref: EC:2.7.1.78
@@ -264846,7 +264591,7 @@ xref: KEGG_REACTION:R03840
xref: MetaCyc:POLYNUCLEOTIDE-5-HYDROXYL-KINASE-RXN
xref: RHEA:15669
is_a: GO:0051733 ! polydeoxyribonucleotide kinase activity
-is_a: GO:0051734 ! ATP-dependent polynucleotide kinase activity
+is_a: GO:0051734 ! polynucleotide kinase activity
[Term]
id: GO:0046405
@@ -265199,7 +264944,6 @@ synonym: "D-amino acid anabolism" EXACT []
synonym: "D-amino acid biosynthesis" EXACT []
synonym: "D-amino acid formation" EXACT []
synonym: "D-amino acid synthesis" EXACT []
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0046416 ! D-amino acid metabolic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -265689,7 +265433,6 @@ synonym: "PABA metabolism" EXACT []
synonym: "para-aminobenzoic acid metabolism" EXACT []
synonym: "vitamin Bx metabolic process" EXACT []
synonym: "vitamin Bx metabolism" EXACT []
-is_a: GO:0006520 ! cellular amino acid metabolic process
is_a: GO:0009072 ! aromatic amino acid family metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
@@ -266443,7 +266186,6 @@ synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine formation f
synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine synthesis from asparagine" EXACT []
xref: RESID:AA0328
is_a: GO:0006528 ! asparagine metabolic process
-is_a: GO:0006575 ! cellular modified amino acid metabolic process
is_a: GO:0009165 ! nucleotide biosynthetic process
is_a: GO:0018196 ! peptidyl-asparagine modification
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
@@ -267218,19 +266960,21 @@ consider: GO:0007576
[Term]
id: GO:0046618
-name: drug export
+name: xenobiotic export
namespace: biological_process
-def: "The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, out of a cell or organelle." [GOC:go_curators]
-is_a: GO:0015893 ! drug transport
+def: "The directed movement of a xenobiotic, a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:go_curators, GOC:krc]
+synonym: "drug export" RELATED []
+is_a: GO:0042908 ! xenobiotic transport
[Term]
id: GO:0046619
-name: optic placode formation involved in camera-type eye formation
+name: lens placode formation involved in camera-type eye formation
namespace: biological_process
def: "Establishment and formation of the optic placode, paired ectodermal placodes that become invaginated to form the embryonic lens vesicles." [GOC:dph, GOC:mtg_sensu, GOC:sdb_2009, GOC:tb]
synonym: "optic placode formation in camera-type eye" EXACT []
synonym: "optic placode formation involved in camera-style eye" EXACT []
-is_a: GO:0001743 ! optic placode formation
+synonym: "optic placode formation involved in camera-type eye formation" RELATED []
+is_a: GO:0001743 ! lens placode formation
relationship: part_of GO:0060900 ! embryonic camera-type eye formation
[Term]
@@ -267285,7 +267029,7 @@ is_a: GO:0005319 ! lipid transporter activity
id: GO:0046625
name: sphingolipid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with sphingolipids, a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid)." [ISBN:0198506732]
+def: "Binding to a sphingolipid, a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid)." [ISBN:0198506732]
is_a: GO:0008289 ! lipid binding
[Term]
@@ -268075,7 +267819,7 @@ is_a: GO:0046692 ! sperm competition
id: GO:0046695
name: SLIK (SAGA-like) complex
namespace: cellular_component
-def: "A SAGA-type histone acetyltransferase complex that contains Rtg2 and a smaller form of Spt7 than the fungal SAGA complex, and lacks Spt8. The complex is involved in the yeast retrograde response pathway, which is important for gene expression changes during mitochondrial dysfunction." [PMID:12101232, PMID:12186975, PMID:17337012]
+def: "A SAGA-type histone acetyltransferase complex that contains a smaller form of Spt7 (lacking the SPT8 binding region) than the fungal SAGA complex, and consequently lacks Spt8. The complex is involved in the yeast retrograde response pathway, which is important for gene expression changes during mitochondrial dysfunction." [PMID:33864814]
comment: See also the cellular component term 'SAGA complex ; GO:0000124'.
synonym: "SAGA (alt) complex" EXACT []
synonym: "SALSA complex" EXACT []
@@ -268138,7 +267882,7 @@ is_a: GO:0046921 ! alpha-(1->6)-fucosyltransferase activity
id: GO:0046703
name: natural killer cell lectin-like receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lectin-like natural killer cell receptor." [GOC:ai]
+def: "Binding to a lectin-like natural killer cell receptor." [GOC:ai]
synonym: "KLRC4 receptor binding" NARROW []
synonym: "NK cell lectin-like receptor binding" EXACT []
synonym: "NKG2D receptor binding" NARROW []
@@ -268258,7 +268002,7 @@ is_a: GO:0015698 ! inorganic anion transport
id: GO:0046714
name: borate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with borate, the anion (BO3)3-." [GOC:curators]
+def: "Binding to borate, the anion (BO3)3-." [GOC:curators]
synonym: "boron binding" RELATED []
is_a: GO:0043168 ! anion binding
@@ -268494,7 +268238,6 @@ synonym: "spread of virus within host, cell to cell" EXACT []
synonym: "viral spread within host, cell to cell" EXACT []
xref: VZ:1018
is_a: GO:0046739 ! transport of virus in multicellular host
-is_a: GO:1902586 ! multi-organism intercellular transport
[Term]
id: GO:0046741
@@ -268760,15 +268503,15 @@ is_a: GO:0050794 ! regulation of cellular process
id: GO:0046776
name: suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I
namespace: biological_process
-def: "Any viral process that inhibits a host antigen-presenting cell expressing a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules." [GOC:add, GOC:bf, PMID:10859382, UniProtKB-KW:KW-1115, VZ:819]
-synonym: "inhibition of host MHC class I molecule presentation by virus" EXACT [UniProtKB-KW:KW-1115]
-synonym: "major histocompatibility complex" RELATED []
+alt_id: GO:0039591
+def: "Any viral process that inhibits a host antigen-presenting cell expressing a peptide antigen on its cell surface in association with an MHC class I transmembrane protein complex. One mechanism of suppression is by direct inhibition of host tapasin, a type I transmembrane protein essential for the optimal expression of stable MHC class I molecules on the host cell surface. By inhibiting host tapasin activity, viruses can prevent presentation of their antigens at the cell surface, and thereby evade the host anti-viral immune response." [GOC:add, GOC:bf, PMID:10859382]
+synonym: "inhibition of host MHC class I molecule presentation by virus" EXACT []
synonym: "negative regulation by virus of MHC class I cell surface presentation" EXACT []
synonym: "suppression by virus of host MHC class I cell surface presentation" EXACT [GOC:add]
+synonym: "suppression by virus of host tapasin activity" NARROW []
synonym: "suppression by virus of MHC class I cell surface presentation in host" EXACT []
-xref: VZ:819 "Inhibition of host MHC class I molecule presentation by virus"
-is_a: GO:0002590 ! negative regulation of antigen processing and presentation of peptide antigen via MHC class I
is_a: GO:0039588 ! suppression by virus of host antigen processing and presentation
+relationship: negatively_regulates GO:0002474 ! antigen processing and presentation of peptide antigen via MHC class I
[Term]
id: GO:0046777
@@ -268873,7 +268616,7 @@ relationship: part_of GO:0016032 ! viral process
id: GO:0046789
name: host cell surface receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a receptor on the host cell surface." [GOC:ai, PMID:11511370]
+def: "Binding to a receptor on the host cell surface." [GOC:ai, PMID:11511370]
subset: goslim_chembl
synonym: "cell surface antigen activity, host-interacting" RELATED []
synonym: "cell surface receptor ligand" RELATED []
@@ -268883,7 +268626,7 @@ is_a: GO:0046812 ! host cell surface binding
id: GO:0046790
name: virion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a virion, either by binding to components of the capsid or the viral envelope." [GOC:ai]
+def: "Binding to a virion, either by binding to components of the capsid or the viral envelope." [GOC:ai]
is_a: GO:0005488 ! binding
[Term]
@@ -268912,6 +268655,7 @@ namespace: biological_process
def: "Any process in which a virus activates the frequency, rate or extent of phosphorylation of host RNA polymerase II." [PMID:7637000]
synonym: "induction by virus of modification of host RNA polymerase II" BROAD [GOC:bf, GOC:jl]
synonym: "virus-induced modification of host RNA polymerase II" EXACT []
+is_a: GO:0010468 ! regulation of gene expression
is_a: GO:0019056 ! modulation by virus of host transcription
is_a: GO:0039614 ! induction by virus of host protein phosphorylation
@@ -268924,7 +268668,6 @@ subset: goslim_pir
synonym: "viral transport" EXACT [GOC:bf, GOC:jl]
synonym: "virion transport" NARROW [GOC:bf, GOC:jl]
is_a: GO:0016032 ! viral process
-is_a: GO:0044766 ! multi-organism transport
[Term]
id: GO:0046797
@@ -269044,7 +268787,7 @@ is_a: GO:0039715 ! nuclear viral factory
id: GO:0046810
name: host cell extracellular matrix binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the extracellular matrix of a host cell." [PMID:7996163]
+def: "Binding to the extracellular matrix of a host cell." [PMID:7996163]
is_a: GO:0050840 ! extracellular matrix binding
[Term]
@@ -269059,7 +268802,7 @@ is_a: GO:0035033 ! histone deacetylase regulator activity
id: GO:0046812
name: host cell surface binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the surface of a host cell." [GOC:ai]
+def: "Binding to the surface of a host cell." [GOC:ai]
subset: goslim_pir
is_a: GO:0005488 ! binding
@@ -269431,7 +269174,7 @@ is_a: GO:0120031 ! plasma membrane bounded cell projection assembly
id: GO:0046848
name: hydroxyapatite binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with hydroxyapatite, the calcium phosphate mineral of formula Ca10(PO4)6(OH)2 found both in rocks of nonorganic origin and as a component of bone and dentin." [PMID:2438276]
+def: "Binding to hydroxyapatite, the calcium phosphate mineral of formula Ca10(PO4)6(OH)2 found both in rocks of nonorganic origin and as a component of bone and dentin." [PMID:2438276]
synonym: "hydroxylapatite binding" EXACT [GOC:vk]
is_a: GO:0005488 ! binding
@@ -269500,7 +269243,6 @@ namespace: biological_process
alt_id: GO:0046837
def: "The chemical reactions and pathways resulting in the formation of phosphatidylinositol phosphate." [ISBN:0198506732]
synonym: "phosphatidylinositol phosphate biosynthesis" EXACT []
-synonym: "phosphatidylinositol phosphate biosynthetic process" NARROW []
synonym: "phosphatidylinositol phosphate phosphorylation" NARROW []
synonym: "phosphatidylinositol phosphorylation" RELATED []
synonym: "phosphoinositide phosphorylation" NARROW []
@@ -269646,8 +269388,9 @@ is_a: GO:0018283 ! iron incorporation into metallo-sulfur cluster
id: GO:0046870
name: cadmium ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cadmium (Cd) ions." [GOC:ai]
+def: "Binding to a cadmium ion (Cd)." [GOC:ai]
synonym: "cadmium binding" EXACT []
+synonym: "Cd ion binding" EXACT []
synonym: "copper/cadmium binding" BROAD []
is_a: GO:0046914 ! transition metal ion binding
@@ -269655,7 +269398,7 @@ is_a: GO:0046914 ! transition metal ion binding
id: GO:0046871
name: N-acetylgalactosamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with N-acetylgalactosamine, 2-acetamido-2-deoxygalactopyranose, the n-acetyl derivative of galactosamine." [GOC:ai, PMID:18384150]
+def: "Binding to N-acetylgalactosamine, 2-acetamido-2-deoxygalactopyranose, the n-acetyl derivative of galactosamine." [GOC:ai, PMID:18384150]
synonym: "N-acetylgalactosamine lectin" RELATED []
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -269663,7 +269406,7 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:0046872
name: metal ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any metal ion." [GOC:ai]
+def: "Binding to a metal ion." [GOC:ai]
subset: goslim_agr
subset: goslim_drosophila
subset: goslim_flybase_ribbon
@@ -269698,7 +269441,7 @@ is_a: GO:0072524 ! pyridine-containing compound metabolic process
id: GO:0046875
name: ephrin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an ephrin receptor." [GOC:ai]
+def: "Binding to an ephrin receptor." [GOC:ai]
synonym: "Eph receptor binding" EXACT []
synonym: "ephrin" NARROW []
synonym: "GPI-linked ephrin" NARROW []
@@ -269709,7 +269452,7 @@ is_a: GO:0005102 ! signaling receptor binding
id: GO:0046876
name: 3,4-didehydroretinal binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 3,4-didehydroretinal, a form of retinal that plays a role in the visual process in freshwater fish and some amphibians analogous to that of all-trans retinal in other vertebrates. 3,4-didehydro-11-cis-retinal combines with an opsin to form cyanopsin (cone) or porphyropsin (rod)." [GOC:ai, ISBN:0198506732]
+def: "Binding to 3,4-didehydroretinal, a form of retinal that plays a role in the visual process in freshwater fish and some amphibians analogous to that of all-trans retinal in other vertebrates. 3,4-didehydro-11-cis-retinal combines with an opsin to form cyanopsin (cone) or porphyropsin (rod)." [GOC:ai, ISBN:0198506732]
synonym: "blue-sensitive opsin" NARROW []
synonym: "green-sensitive opsin" NARROW []
synonym: "long-wave-sensitive opsin" NARROW []
@@ -270053,7 +269796,7 @@ is_a: GO:0006810 ! transport
id: GO:0046904
name: calcium oxalate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with calcium oxalate, CaC2O4, a salt of oxalic acid. In animals, it may be excreted in urine or retained in the form of urinary calculi." [ISBN:0721662544]
+def: "Binding to calcium oxalate, CaC2O4, a salt of oxalic acid. In animals, it may be excreted in urine or retained in the form of urinary calculi." [ISBN:0721662544]
is_a: GO:0005488 ! binding
[Term]
@@ -270070,7 +269813,7 @@ is_a: GO:0016462 ! pyrophosphatase activity
id: GO:0046906
name: tetrapyrrole binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position." [GOC:curators, ISBN:0198506732]
+def: "Binding to a tetrapyrrole, a compound containing four pyrrole nuclei variously substituted and linked to each other through carbons at the alpha position." [GOC:curators, ISBN:0198506732]
subset: goslim_metagenomics
subset: goslim_pir
synonym: "porphyrin binding" NARROW []
@@ -270140,7 +269883,7 @@ is_a: GO:0016746 ! acyltransferase activity
id: GO:0046914
name: transition metal ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [ISBN:0198506732]
+def: "Binding to a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [ISBN:0198506732]
is_a: GO:0046872 ! metal ion binding
[Term]
@@ -270232,7 +269975,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0046923
name: ER retention sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an endoplasmic reticulum (ER) retention sequence, a specific peptide sequence that ensures a protein is retained within the ER." [GOC:ai]
+def: "Binding to an endoplasmic reticulum (ER) retention sequence, a specific peptide sequence that ensures a protein is retained within the ER." [GOC:ai]
synonym: "endoplasmic reticulum retention sequence binding" EXACT []
is_a: GO:0005048 ! signal sequence binding
@@ -270333,6 +270076,7 @@ synonym: "sodium-translocating F-type ATPase activity" EXACT []
synonym: "sodium-transporting two-sector ATPase activity" EXACT []
xref: EC:7.2.2.1
xref: MetaCyc:3.6.3.15-RXN
+xref: RHEA:58156
xref: RHEA:58158
xref: TC:3.A.2.1.2
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
@@ -270342,7 +270086,7 @@ is_a: GO:0016874 ! ligase activity
id: GO:0046933
name: proton-transporting ATP synthase activity, rotational mechanism
namespace: molecular_function
-def: "Enables the synthesis of ATP from ADP and phosphate by the transfer of protons from one side of a membrane to the other by a rotational mechanism driven by a gradient according to the reaction: ADP + H2O + phosphate + H+(in) = ATP + H+(out)." [RHEA:57722]
+def: "Enables the synthesis of ATP from ADP and phosphate by the transfer of protons from one side of a membrane to the other by a rotational mechanism driven by a gradient according to the reaction: ADP + H2O + phosphate + H+(in) -> ATP + H+(out)." [RHEA:57720]
synonym: "H+-transporting ATP synthase activity" RELATED [EC:7.1.2.2]
synonym: "hydrogen ion translocating F-type ATPase activity" EXACT []
synonym: "hydrogen ion transporting ATP synthase activity, rotational mechanism" EXACT []
@@ -270350,7 +270094,7 @@ synonym: "hydrogen ion transporting two-sector ATPase activity" EXACT []
xref: EC:7.1.2.2
xref: MetaCyc:ATPSYN-RXN
xref: Reactome:R-HSA-164832 "ATPase synthesizes ATP"
-xref: RHEA:57722
+xref: RHEA:57720
xref: TC:3.A.2.1.1
is_a: GO:0015252 ! proton channel activity
is_a: GO:0016874 ! ligase activity
@@ -270535,7 +270279,6 @@ synonym: "hydroxylysine anabolism" EXACT []
synonym: "hydroxylysine biosynthesis" EXACT []
synonym: "hydroxylysine formation" EXACT []
synonym: "hydroxylysine synthesis" EXACT []
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
is_a: GO:0046946 ! hydroxylysine metabolic process
@@ -270689,7 +270432,8 @@ is_a: GO:0044769 ! ATPase activity, coupled to transmembrane movement of ions, r
id: GO:0046962
name: sodium-transporting ATPase activity, rotational mechanism
namespace: molecular_function
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) => ADP + phosphate + Na+(out), by a rotational mechanism." [RHEA:58157]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) -> ADP + phosphate + Na+(out), by a rotational mechanism." [PMID:30791207, RHEA:58157]
+comment: Found in some halophilic or alkalophilic bacteria that functions in maintaining sodium homeostasis; similar to EC:7.1.2.2 but pumps Na(+) rather than H(+). (Source: EC:7.2.2.1)
synonym: "ATP phosphohydrolase (Na+-transporting) activity" RELATED []
synonym: "ATP synthase, sodium ion specific activity" RELATED [EC:7.2.2.1]
synonym: "Na(+)-translocating ATPase activity" BROAD []
@@ -270705,6 +270449,7 @@ synonym: "vacuolar-type Na+-ATPase" NARROW []
synonym: "vacuolar-type Na+-translocating ATPase" NARROW []
xref: EC:7.2.2.1
xref: MetaCyc:3.6.3.15-RXN
+xref: RHEA:58156
xref: RHEA:58157
is_a: GO:0015081 ! sodium ion transmembrane transporter activity
is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
@@ -270741,7 +270486,7 @@ is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
id: GO:0046965
name: retinoid X receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a retinoid X receptor." [GOC:ai]
+def: "Binding to a retinoid X receptor." [GOC:ai]
synonym: "RXR binding" EXACT []
is_a: GO:0042974 ! retinoic acid receptor binding
@@ -270749,7 +270494,7 @@ is_a: GO:0042974 ! retinoic acid receptor binding
id: GO:0046966
name: thyroid hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a thyroid hormone receptor." [GOC:ai]
+def: "Binding to a thyroid hormone receptor." [GOC:ai]
synonym: "ligand-dependent thyroid hormone receptor interactor activity" NARROW []
is_a: GO:0016922 ! nuclear receptor binding
@@ -270758,7 +270503,6 @@ id: GO:0046967
name: cytosol to endoplasmic reticulum transport
namespace: biological_process
def: "The directed movement of substances from the cytosol to the endoplasmic reticulum of a cell." [GOC:ai]
-synonym: "cytosol to endoplasmic reticulum transport" EXACT []
synonym: "cytosol to ER transport" EXACT []
is_a: GO:0046907 ! intracellular transport
is_a: GO:0055085 ! transmembrane transport
@@ -270775,7 +270519,7 @@ relationship: part_of GO:0048002 ! antigen processing and presentation of peptid
id: GO:0046969
name: NAD-dependent histone deacetylase activity (H3-K9 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein." [EC:3.5.1.17, RHEA:24548]
+def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 9) + H2O = histone H3 L-lysine (position 9) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 9 of the histone H3 protein." [PMID:28450737]
xref: Reactome:R-HSA-9604829 "SIRT6 deacetylates histones at NOTCH1 and NOTCH4 gene promoters"
is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
is_a: GO:0032129 ! histone deacetylase activity (H3-K9 specific)
@@ -270784,9 +270528,9 @@ is_a: GO:0032129 ! histone deacetylase activity (H3-K9 specific)
id: GO:0046970
name: NAD-dependent histone deacetylase activity (H4-K16 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein." [EC:3.5.1.17, GOC:vw, RHEA:24548]
-is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
+def: "Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein." [GOC:vw, PMID:28450737]
is_a: GO:0034739 ! histone deacetylase activity (H4-K16 specific)
+is_a: GO:0046969 ! NAD-dependent histone deacetylase activity (H3-K9 specific)
[Term]
id: GO:0046972
@@ -270840,28 +270584,28 @@ is_a: GO:0018024 ! histone-lysine N-methyltransferase activity
id: GO:0046977
name: TAP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with TAP protein, transporter associated with antigen processing protein. TAP protein is a heterodimeric peptide transporter consisting of the subunits TAP1 and TAP2." [PMID:11133832]
+def: "Binding to TAP protein, transporter associated with antigen processing protein. TAP protein is a heterodimeric peptide transporter consisting of the subunits TAP1 and TAP2." [PMID:11133832]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0046978
name: TAP1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the TAP1 subunit of TAP (transporter associated with antigen processing) protein." [PMID:11133832]
+def: "Binding to the TAP1 subunit of TAP (transporter associated with antigen processing) protein." [PMID:11133832]
is_a: GO:0046977 ! TAP binding
[Term]
id: GO:0046979
name: TAP2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the TAP2 subunit of TAP (transporter associated with antigen processing) protein." [PMID:11133832]
+def: "Binding to the TAP2 subunit of TAP (transporter associated with antigen processing) protein." [PMID:11133832]
is_a: GO:0046977 ! TAP binding
[Term]
id: GO:0046980
name: tapasin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with tapasin, a member of the MHC class I loading complex which bridges the TAP peptide transporter to class I molecules." [PMID:12594855]
+def: "Binding to tapasin, a member of the MHC class I loading complex which bridges the TAP peptide transporter to class I molecules." [PMID:12594855]
synonym: "TAP binding protein binding" EXACT [HGNC:11566]
synonym: "TAPBP binding" RELATED [HGNC:11566]
is_a: GO:0005515 ! protein binding
@@ -270878,7 +270622,7 @@ is_a: GO:0008375 ! acetylglucosaminyltransferase activity
id: GO:0046982
name: protein heterodimerization activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer." [GOC:ai]
+def: "Binding to a nonidentical protein to form a heterodimer." [GOC:ai]
subset: goslim_chembl
is_a: GO:0046983 ! protein dimerization activity
@@ -271050,7 +270794,6 @@ id: GO:0046999
name: regulation of conjugation
namespace: biological_process
def: "Any process that modulates the rate or frequency of conjugation, the union or introduction of genetic information from compatible mating types that results in a genetically different individual." [GOC:ai]
-is_a: GO:0043900 ! regulation of multi-organism process
is_a: GO:0050794 ! regulation of cellular process
relationship: regulates GO:0000746 ! conjugation
@@ -271502,14 +271245,15 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
[Term]
id: GO:0047029
-name: (R)-4-hydroxyphenyllactate dehydrogenase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: NAD(P)+ + (R)-3-(4-hydroxyphenyl)lactate = NAD(P)H + H+ + 3-(4-hydroxyphenyl)pyruvate." [EC:1.1.1.222, MetaCyc:1.1.1.222-RXN]
-synonym: "(R)-3-(4-hydroxyphenyl)lactate:NAD(P)+ 2-oxidoreductase activity" RELATED [EC:1.1.1.222]
-synonym: "(R)-aromatic lactate dehydrogenase activity" RELATED [EC:1.1.1.222]
-synonym: "D-hydrogenase, D-aryllactate" RELATED [EC:1.1.1.222]
-xref: EC:1.1.1.222
-xref: MetaCyc:1.1.1.222-RXN
+name: (R)-4-hydroxyphenyllactate dehydrogenase (NADPH) activity
+namespace: molecular_function
+def: "Catalysis of the reaction: NADP+ + (R)-3-(4-hydroxyphenyl)lactate = NADPH + H+ + 3-(4-hydroxyphenyl)pyruvate." [RHEA:52692]
+synonym: "aromatic 2-oxoacid reductase activity" BROAD []
+synonym: "hydroxyphenylpyruvate reductase activity" BROAD []
+synonym: "phenylpyruvate reductase activity" RELATED []
+xref: https://github.com/geneontology/go-ontology/issues/21412
+xref: MetaCyc:RXN-7632
+xref: RHEA:52692
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
@@ -271832,7 +271576,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047051
name: D-lactate dehydrogenase (cytochrome c-553) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 ferricytochrome C-553 + D-lactate = 2 ferrocytochrome C-553 + pyruvate." [EC:1.1.2.5, MetaCyc:1.1.2.5-RXN]
+def: "Catalysis of the reaction: (R)-lactate + 2 [Fe(III)cytochrome c553] = 2 [Fe(II)cytochrome c553] + 2 H+ + pyruvate." [RHEA:16465]
synonym: "(R)-lactate:ferricytochrome-c-553 2-oxidoreductase activity" RELATED [EC:1.1.2.5]
xref: EC:1.1.2.5
xref: MetaCyc:1.1.2.5-RXN
@@ -271905,25 +271649,25 @@ is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidat
id: GO:0047057
name: vitamin-K-epoxide reductase (warfarin-sensitive) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-methyl-3-phytyl-1,4-naphthoquinone + oxidized dithiothreitol + H2O = 2,3-epoxy-2,3-dihydro-2-methyl-3-phytyl-1,4-naphthoquinone + 1,4-dithiothreitol." [EC:1.1.4.1, MetaCyc:1.1.4.1-RXN]
-synonym: "2-methyl-3-phytyl-1,4-naphthoquinone:oxidized-dithiothreitol oxidoreductase activity" RELATED [EC:1.1.4.1]
-synonym: "phylloquinone epoxide reductase activity" RELATED [EC:1.1.4.1]
-synonym: "vitamin K1 epoxide reductase activity" NARROW [EC:1.1.4.1]
-xref: EC:1.1.4.1
+def: "Catalysis of the reaction: phylloquinol + a protein with a disulfide bond = phylloquinone + a protein with reduced L-cysteine residues." [RHEA:57744]
+comment: Formerly EC:1.1.4.1.
+synonym: "phylloquinone epoxide reductase activity" RELATED [EC:1.17.4.4]
+synonym: "vitamin K1 epoxide reductase activity" NARROW [EC:1.17.4.4]
+xref: EC:1.17.4.4
xref: MetaCyc:1.1.4.1-RXN
xref: Reactome:R-HSA-159790 "VKORC1 reduces vitamin K epoxide to MK4 (vitamin K hydroquinone)"
xref: Reactome:R-HSA-6806647 "VKORC1L1 reduces vitamin K epoxide to MK4 (vitamin K hydroquinone)"
-xref: RHEA:13817
+xref: RHEA:57744
is_a: GO:0016900 ! oxidoreductase activity, acting on the CH-OH group of donors, disulfide as acceptor
[Term]
id: GO:0047058
name: vitamin-K-epoxide reductase (warfarin-insensitive) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-hydroxy-2-methyl-3-phytyl-2,3-dihydronaphthoquinone + oxidized dithiothreitol + H2O = 2,3-epoxy-2,3-dihydro-2-methyl-3-phytyl-1,4-naphthoquinone + 1,4-dithiothreitol." [EC:1.1.4.2, MetaCyc:1.1.4.2-RXN]
-synonym: "3-hydroxy-2-methyl-3-phytyl-2,3-dihydronaphthoquinone:oxidized-dithiothreitol oxidoreductase activity" RELATED [EC:1.1.4.2]
-synonym: "vitamin K 2,3-epoxide reductase activity" RELATED [EC:1.1.4.2]
-xref: EC:1.1.4.2
+def: "Catalysis of the reaction: 3-hydroxy-2-methyl-3-phytyl-2,3-dihydronaphthoquinone + oxidized dithiothreitol + H2O = 2,3-epoxy-2,3-dihydro-2-methyl-3-phytyl-1,4-naphthoquinone + 1,4-dithiothreitol." [RHEA:21560]
+comment: Formerly EC:1.1.4.2.
+synonym: "vitamin K 2,3-epoxide reductase activity" RELATED [EC:1.17.4.5]
+xref: EC:1.17.4.5
xref: MetaCyc:1.1.4.2-RXN
xref: RHEA:21560
is_a: GO:0016900 ! oxidoreductase activity, acting on the CH-OH group of donors, disulfide as acceptor
@@ -271933,10 +271677,11 @@ id: GO:0047059
name: polyvinyl alcohol dehydrogenase (cytochrome) activity
namespace: molecular_function
def: "Catalysis of the reaction: polyvinyl alcohol + ferricytochrome c = oxidized polyvinyl alcohol + ferrocytochrome c + H+." [EC:1.1.2.6]
-synonym: "polyvinyl alcohol:ferricytochrome-c oxidoreductase activity" EXACT systematic_synonym [EC:1.1.2.6]
-synonym: "polyvinyl-alcohol:(acceptor) oxidoreductase activity" BROAD [EC:1.1.99.23]
-synonym: "polyvinyl-alcohol:acceptor oxidoreductase activity" BROAD [EC:1.1.99.23]
-synonym: "PVA dehydrogenase activity" BROAD [EC:1.1.99.23]
+comment: Formerly EC:1.1.99.23.
+synonym: "polyvinyl alcohol:ferricytochrome-c oxidoreductase activity" EXACT []
+synonym: "polyvinyl-alcohol:(acceptor) oxidoreductase activity" BROAD []
+synonym: "polyvinyl-alcohol:acceptor oxidoreductase activity" BROAD []
+synonym: "PVA dehydrogenase activity" BROAD [EC:1.1.2.6]
xref: EC:1.1.2.6
xref: KEGG_REACTION:R03136
xref: MetaCyc:RXN-11316
@@ -271987,13 +271732,11 @@ is_a: GO:0016680 ! oxidoreductase activity, acting on diphenols and related subs
id: GO:0047063
name: obsolete L-ascorbate-cytochrome-b5 reductase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the reaction: ferricytochrome B5 + ascorbate = ferrocytochrome B5 + monodehydroascorbate." [EC:1.10.2.1, RHEA:18677]
-comment: This term was obsoleted because the EC and RHEA it represented was obsoleted.
+def: "OBSOLETE. Catalysis of the reaction: ferricytochrome B5 + ascorbate = ferrocytochrome B5 + monodehydroascorbate." [GOC:curators]
+comment: This term was obsoleted because the EC (EC:1.10.2.1) and RHEA (RHEA:18677) it represented was obsoleted.
synonym: "ascorbate-cytochrome b5 reductase activity" RELATED [EC:1.10.2.1]
synonym: "L-ascorbate:ferricytochrome-b5 oxidoreductase activity" RELATED [EC:1.10.2.1]
-xref: EC:1.10.2.1
xref: MetaCyc:1.10.2.1-RXN
-xref: RHEA:18677
is_obsolete: true
[Term]
@@ -272570,17 +272313,18 @@ is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group
id: GO:0047103
name: 3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-oxidoreductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + NAD+ + 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestan-26-al = NADH + 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanate." [MetaCyc:1.2.1.40-RXN]
+def: "Catalysis of the reaction: H2O + NAD+ + 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestan-26-al = NADH + 3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanate." [PMID:8496170, RHEA:34627]
synonym: "3-alpha,7-alpha,12-alpha-trihydroxycholestan-26-al 26-dehydrogenase activity" EXACT []
synonym: "3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-al dehydrogenase activity" EXACT []
synonym: "3alpha,7alpha,12alpha-trihydroxy-5beta-cholestan-26-al:NAD+ 26-oxidoreductase activity" EXACT []
synonym: "3alpha,7alpha,12alpha-trihydroxycholestan-26-al 26-dehydrogenase activity" EXACT []
synonym: "3alpha,7alpha,12alpha-trihydroxycholestan-26-al 26-oxidoreductase activity" EXACT []
-synonym: "cholestanetriol-26-al 26-dehydrogenase activity" RELATED [EC:1.2.1.40]
+synonym: "cholestanetriol-26-al 26-dehydrogenase activity" RELATED []
synonym: "THAL-NAD oxidoreductase activity" EXACT []
synonym: "trihydroxydeoxycoprostanal dehydrogenase activity" EXACT []
+xref: EC:1.14.15.15
xref: MetaCyc:1.2.1.40-RXN
-xref: RHEA:24584
+xref: RHEA:34627
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
[Term]
@@ -272795,12 +272539,12 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0047119
name: 2-methyl-branched-chain-enoyl-CoA reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-methylbutanoyl-CoA + NAD(+) = 2-methylbut-2-enoyl-CoA + H(+) + NADH." [EC:1.3.1.52, RHEA:24532]
+def: "Catalysis of the reaction: 2-methylbutanoyl-CoA + NAD(+) = 2-methylbut-2-enoyl-CoA + H(+) + NADH." [PMID:10989435, PMID:6401712, RHEA:43780]
synonym: "2-methyl-branched-chain-acyl-CoA:NAD+ 2-oxidoreductase activity" RELATED [EC:1.3.1.52]
-xref: EC:1.3.1.52
+xref: EC:1.3.8.5
xref: KEGG_REACTION:R03169
xref: MetaCyc:1.3.1.52-RXN
-xref: RHEA:24532
+xref: RHEA:43780
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
[Term]
@@ -273082,7 +272826,6 @@ synonym: "vitamin B(12a) reductase activity" RELATED [EC:1.16.1.3]
synonym: "vitamin B12a reductase activity" RELATED [EC:1.16.1.3]
xref: EC:1.16.1.3
xref: MetaCyc:AQUACOBALAMIN-REDUCTASE-RXN
-xref: RHEA:24472
is_obsolete: true
[Term]
@@ -273281,7 +273024,7 @@ id: GO:0047152
name: methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase activity
namespace: molecular_function
alt_id: GO:1990087
-def: "Catalysis of the reaction: 5-hydroxybenzimidazolylcobamide + methanol = H2O + Co-methyl-Co-5-hydroxybenzimidazolylcob(I)amide." [EC:2.1.1.90, MetaCyc:2.1.1.90-RXN]
+def: "Catalysis of the reaction: 5-hydroxybenzimidazolylcobamide + methanol = H2O + Co-methyl-Co-5-hydroxybenzimidazolylcob(I)amide." [PMID:6438059, RHEA:45204]
comment: This function is the first step in the pathway of methanogenesis from methanol.
synonym: "methanol cobalamin methyltransferase activity" RELATED [EC:2.1.1.90]
synonym: "methanol-corrinoid protein Co-methyltransferase" EXACT []
@@ -273294,7 +273037,7 @@ synonym: "MT1" RELATED []
synonym: "MtaB" RELATED []
xref: EC:2.1.1.90
xref: MetaCyc:2.1.1.90-RXN
-xref: RHEA:21344
+xref: RHEA:45204
is_a: GO:0008168 ! methyltransferase activity
[Term]
@@ -273819,7 +273562,7 @@ is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amin
id: GO:0047190
name: 2-acylglycerophosphocholine O-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-acyl-sn-glycero-3-phosphocholine + acyl-CoA = 1,2-diacyl-sn-glycero-3-phosphocholine + CoA." [EC:2.3.1.62, RHEA:10332]
+def: "Catalysis of the reaction: 2-acyl-sn-glycero-3-phosphocholine + acyl-CoA = 1,2-diacyl-sn-glycero-3-phosphocholine + CoA." [RHEA:10332]
synonym: "2-acylglycerol-3-phosphorylcholine acyltransferase activity" RELATED [EC:2.3.1.62]
synonym: "2-acylglycerophosphocholine acyltransferase activity" RELATED [EC:2.3.1.62]
synonym: "acyl-CoA:2-acyl-sn-glycero-3-phosphocholine O-acyltransferase activity" RELATED [EC:2.3.1.62]
@@ -273855,7 +273598,6 @@ synonym: "blood platelet-activating factor acetyltransferase activity" BROAD [EC
synonym: "lyso-GPC:acetyl CoA acetyltransferase activity" BROAD [EC:2.3.1.67]
synonym: "lyso-platelet activating factor:acetyl-CoA acetyltransferase activity" BROAD [EC:2.3.1.67]
synonym: "lyso-platelet-activating factor:acetyl-CoA acetyltransferase activity" BROAD [EC:2.3.1.67]
-synonym: "lysoPAF:acetyl CoA acetyltransferase activity" RELATED [EC:2.3.1.67]
synonym: "lysopaf:acetyl CoA acetyltransferase activity" BROAD [EC:2.3.1.67]
synonym: "platelet-activating factor acylhydrolase activity" BROAD [EC:2.3.1.67]
synonym: "platelet-activating factor-synthesizing enzyme activity" BROAD [EC:2.3.1.67]
@@ -274328,7 +274070,6 @@ synonym: "UDP-N-acetyl-D-glucosamine:O-glycosyl-glycoprotein (N-acetyl-D-glucosa
synonym: "uridine diphosphoacetylglucosamine-mucin beta(1->3)-acetylglucosaminyltransferase activity" RELATED [EC:2.4.1.147]
xref: EC:2.4.1.147
xref: MetaCyc:2.4.1.147-RXN
-xref: RHEA:14252
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
@@ -274345,7 +274086,6 @@ synonym: "UDP-N-acetyl-D-glucosamine:O-oligosaccharide-glycoprotein (N-acetyl-D-
synonym: "uridine diphosphoacetylglucosamine-mucin beta(1->6)-acetylglucosaminyltransferase B" RELATED [EC:2.4.1.148]
xref: EC:2.4.1.148
xref: MetaCyc:2.4.1.148-RXN
-xref: RHEA:16552
is_a: GO:0008375 ! acetylglucosaminyltransferase activity
is_a: GO:0140103 ! catalytic activity, acting on a glycoprotein
@@ -275118,7 +274858,6 @@ name: globoside alpha-N-acetylgalactosaminyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: N-acetyl-D-galactosaminyl-(1,3)-D-galactosyl-(1,4)-D-galactosyl-(1,4)-D-glucosylceramide + UDP-N-acetylgalactosamine = N-acetyl-D-galactosaminyl-N-acetyl-D-galactosaminyl-(1,3)-D-galactosyl-(1,4)-D-galactosyl-(1,4)-D-glucosylceramide + UDP." [EC:2.4.1.88, MetaCyc:2.4.1.88-RXN]
synonym: "Forssman synthase activity" RELATED [EC:2.4.1.88]
-synonym: "forssman synthase activity" RELATED [EC:2.4.1.88]
synonym: "globoside acetylgalactosaminyltransferase activity" RELATED [EC:2.4.1.88]
synonym: "UDP-N-acetyl-D-galactosamine:N-acetyl-D-galactosaminyl-1,3-D-galactosyl-1,4-D-galactosyl-1,4-D-glucosylceramide alpha-N-acetyl-D-galactosaminyltransferase activity" RELATED [EC:2.4.1.88]
synonym: "uridine diphosphoacetylgalactosamine-globoside alpha-acetylgalactosaminyltransferase activity" RELATED [EC:2.4.1.88]
@@ -275488,7 +275227,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0047302
name: UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + UDP-2-acetamido-4-amino-2,4,6-trideoxy-D-glucose = L-glutamate + UDP-2-acetamido-4-dehydro-2,6-dideoxy-beta-D-glucose." [EC:2.6.1.34, RHEA:18713]
+def: "Catalysis of the reaction: 2-oxoglutarate + UDP-2-acetamido-4-amino-2,4,6-trideoxy-D-glucose = L-glutamate + UDP-2-acetamido-4-dehydro-2,6-dideoxy-beta-D-glucose." [PMID:16286454, RHEA:31663]
synonym: "UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose:2-oxoglutarate aminotransferase activity" RELATED [EC:2.6.1.34]
synonym: "UDP-4-amino-2-acetamido-2,4,6-trideoxyglucose aminotransferase activity" EXACT []
synonym: "UDP-4-amino-2-acetamido-2,4,6-trideoxyglucose transaminase activity" EXACT []
@@ -275496,7 +275235,7 @@ synonym: "uridine diphospho-4-amino-2-acetamido-2,4,6-trideoxyglucose aminotrans
xref: EC:2.6.1.34
xref: KEGG_REACTION:R04529
xref: MetaCyc:2.6.1.34-RXN
-xref: RHEA:18713
+xref: RHEA:31663
is_a: GO:0008483 ! transaminase activity
[Term]
@@ -276394,7 +276133,7 @@ synonym: "CDP-choline-1-alkenyl-2-acyl-glycerol phosphocholinetransferase activi
synonym: "CDP-choline:1-alkenyl-2-acylglycerol cholinephosphotransferase activity" RELATED [EC:2.7.8.22]
xref: EC:2.7.8.22
xref: MetaCyc:2.7.8.22-RXN
-xref: RHEA:21072
+xref: RHEA:36227
is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate groups
[Term]
@@ -276543,13 +276282,13 @@ is_a: GO:0008410 ! CoA-transferase activity
id: GO:0047370
name: succinate-citramalate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: S-citramalate + succinyl-CoA = citramalyl-CoA + succinate." [MetaCyc:2.8.3.7-RXN]
+def: "Catalysis of the reaction: S-citramalate + succinyl-CoA = citramalyl-CoA + succinate." [PMID:16547052, RHEA:38287]
synonym: "citramalate coenzyme A-transferase activity" EXACT []
synonym: "itaconate CoA-transferase activity" EXACT []
synonym: "succinyl coenzyme A-citramalyl coenzyme A transferase activity" EXACT []
synonym: "succinyl-CoA:citramalate CoA-transferase activity" EXACT []
xref: MetaCyc:2.8.3.7-RXN
-xref: RHEA:23528
+xref: RHEA:38287
is_a: GO:0008410 ! CoA-transferase activity
[Term]
@@ -277749,7 +277488,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0047453
name: ATP-dependent NAD(P)H-hydrate dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ATP = ADP + 3 H(+) + NADH + phosphate." [EC:4.2.1.93, RHEA:19017]
+def: "Catalysis of the reaction: (6S)-6beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide + ATP = ADP + 3 H(+) + NADH + phosphate." [PMID:3061454, RHEA:19017]
synonym: "(6S)-beta-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ATP-hydrolysing)" RELATED [EC:4.2.1.93]
synonym: "(6S)-beta-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase(ATP-hydrolysing; NADH-forming)" RELATED [EC:4.2.1.93]
synonym: "ATP-dependent H(4)NAD(P)OH dehydratase activity" EXACT []
@@ -278026,16 +277765,18 @@ is_a: GO:0016866 ! intramolecular transferase activity
id: GO:0047472
name: 3-carboxy-cis,cis-muconate cycloisomerase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate = 3-carboxy-cis,cis-muconate + H(+)." [EC:5.5.1.2, RHEA:23656]
-synonym: "2-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)" RELATED [EC:5.5.1.2]
+alt_id: GO:0018842
+def: "Catalysis of the reaction: 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate = 3-carboxy-cis,cis-muconate + H(+)." [PMID:15301541, PMID:17054713, RHEA:23656]
+synonym: "3-carboxymuconate cycloisomerase type II activity" RELATED []
synonym: "3-carboxymuconate lactonizing enzyme activity" RELATED [EC:5.5.1.2]
-synonym: "3-carboxymuconolactone hydrolase activity" RELATED [EC:5.5.1.2]
+synonym: "3-carboxymuconolactone hydrolase activity" RELATED []
synonym: "beta-carboxymuconate lactonizing enzyme activity" RELATED [EC:5.5.1.2]
synonym: "CMLE activity" RELATED [EC:5.5.1.2]
xref: EC:5.5.1.2
xref: KEGG_REACTION:R03307
xref: MetaCyc:5.5.1.2-RXN
xref: RHEA:23656
+xref: UM-BBD_reactionID:r0582
is_a: GO:0016872 ! intramolecular lyase activity
[Term]
@@ -278204,7 +277945,7 @@ relationship: regulates GO:0006970 ! response to osmotic stress
id: GO:0047485
name: protein N-terminus binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732]
+def: "Binding to a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue." [ISBN:0198506732]
synonym: "amino-terminal binding" RELATED [GOC:jsg]
synonym: "amino-terminus binding" RELATED [GOC:jsg]
synonym: "N-terminal binding" EXACT []
@@ -279701,14 +279442,14 @@ is_a: GO:0008410 ! CoA-transferase activity
id: GO:0047592
name: 5-pyridoxate dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-pyridoxate + NADPH + O(2) = (2Z)-2-(acetamidomethylene)-3-(hydroxymethyl)succinate + NADP(+)." [EC:1.14.12.5, RHEA:11152]
-synonym: "5-pyridoxate oxidase activity" RELATED [EC:1.14.12.5]
-synonym: "5-pyridoxate,NADPH:oxygen oxidoreductase (decyclizing)" RELATED [EC:1.14.12.5]
-xref: EC:1.14.12.5
+def: "Catalysis of the reaction: 5-pyridoxate + NADPH + O(2) = 2-(acetamidomethylene)-3-(hydroxymethyl)succinate) + NADP(+)." [RHEA:11152]
+comment: Formerly EC:1.14.12.5.
+synonym: "5-pyridoxate oxidase activity" RELATED [EC:1.14.13.241]
+xref: EC:1.14.13.241
xref: KEGG_REACTION:R04570
xref: MetaCyc:5-PYRIDOXATE-DIOXYGENASE-RXN
xref: RHEA:11152
-is_a: GO:0016708 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor
+is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0047593
@@ -280845,14 +280586,14 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0047671
name: anthranilate adenylyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: anthranilate + ATP = N-adenylylanthranilate + diphosphate + H(+)." [EC:2.7.7.55, RHEA:22412]
+def: "Catalysis of the reaction: anthranilate + ATP = N-adenylylanthranilate + diphosphate + H(+)." [PMID:2995633, RHEA:35091]
synonym: "anthranilic acid adenylyltransferase activity" RELATED [EC:2.7.7.55]
synonym: "ATP:anthranilate adenylyltransferase activity" EXACT []
synonym: "ATP:anthranilate N-adenylyltransferase activity" RELATED [EC:2.7.7.55]
-xref: EC:2.7.7.55
+xref: EC:6.3.2.40
xref: KEGG_REACTION:R00979
xref: MetaCyc:ANTHRANILATE-ADENYLYLTRANSFERASE-RXN
-xref: RHEA:22412
+xref: RHEA:35091
is_a: GO:0070566 ! adenylyltransferase activity
[Term]
@@ -281576,9 +281317,9 @@ is_a: GO:0010279 ! indole-3-acetic acid amido synthetase activity
[Term]
id: GO:0047722
-name: indolelactate dehydrogenase activity
+name: indolelactate dehydrogenase (NADH) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-(indol-3-yl)lactate + NAD(+) = 3-(indol-3-yl)pyruvate + H(+) + NADH." [EC:1.1.1.110, RHEA:20133]
+def: "Catalysis of the reaction: 3-(indol-3-yl)lactate + NAD(+) = 3-(indol-3-yl)pyruvate + H(+) + NADH." [RHEA:20133]
synonym: "(indol-3-yl)lactate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.110]
synonym: "indole-3-lactate dehydrogenase activity" EXACT []
synonym: "indolelactate:NAD+ oxidoreductase activity" RELATED [EC:1.1.1.110]
@@ -282711,13 +282452,12 @@ is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorpo
[Term]
id: GO:0047801
-name: L-cysteine:2-oxoglutarate aminotransferase activity
+name: L-cysteine transaminase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-cysteine + 2-oxoglutarate = mercaptopyruvate + L-glutamate." [EC:2.6.1.3, MetaCyc:CYSTEINE-AMINOTRANSFERASE-RXN]
-synonym: "CGT" RELATED [EC:2.6.1.3]
+def: "Catalysis of the reaction: L-cysteine + 2-oxoglutarate = mercaptopyruvate + L-glutamate." [RHEA:17441]
synonym: "cysteine aminotransferase activity" BROAD []
-synonym: "cysteine transaminase activity" BROAD [EC:2.6.1.3]
-synonym: "L-cysteine aminotransferase activity" BROAD [EC:2.6.1.3]
+synonym: "cysteine transaminase activity" EXACT [EC:2.6.1.3]
+synonym: "L-cysteine:2-oxoglutarate aminotransferase activity" EXACT []
xref: EC:2.6.1.3
xref: MetaCyc:CYSTEINE-AMINOTRANSFERASE-RXN
xref: Reactome:R-HSA-9012597 "GOT2 dimer transfers amino group from L-Cys to 2OG to form 3MPYR and Glu"
@@ -283931,7 +283671,7 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0047887
name: farnesyl diphosphate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate + ATP = 2-trans,6-trans-farnesyl triphosphate + ADP." [EC:2.7.4.18, RHEA:21544]
+def: "Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate + ATP = 2-trans,6-trans-farnesyl triphosphate + ADP." [RHEA:21544]
synonym: "ATP:farnesyl-diphosphate phosphotransferase activity" RELATED [EC:2.7.4.18]
synonym: "farnesyl pyrophosphate kinase activity" RELATED [EC:2.7.4.18]
synonym: "farnesyl-diphosphate kinase activity" EXACT []
@@ -284641,13 +284381,14 @@ is_a: GO:0047936 ! glucose 1-dehydrogenase [NAD(P)] activity
id: GO:0047936
name: glucose 1-dehydrogenase [NAD(P)] activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-D-glucose + NAD(P)+ = D-glucono-1,5-lactone + NAD(P)H." [EC:1.1.1.47, MetaCyc:GLUCOSE-1-DEHYDROGENASE-RXN]
+def: "Catalysis of the reaction: beta-D-glucose + NAD(P)+ = D-glucono-1,5-lactone + NAD(P)H." [EC:1.1.1.47]
synonym: "beta-D-glucose:NAD(P)+ 1-oxidoreductase activity" RELATED [EC:1.1.1.47]
synonym: "D-glucose dehydrogenase (NAD(P))" RELATED [EC:1.1.1.47]
synonym: "hexose phosphate dehydrogenase activity" RELATED [EC:1.1.1.47]
xref: EC:1.1.1.47
xref: MetaCyc:GLUCOSE-1-DEHYDROGENASE-RXN
is_a: GO:0004344 ! glucose dehydrogenase activity
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
id: GO:0047937
@@ -285334,22 +285075,6 @@ xref: MetaCyc:HYDROGEN-SULFIDE-S-ACETYLTRANSFERASE-RXN
xref: RHEA:16625
is_a: GO:0016418 ! S-acetyltransferase activity
-[Term]
-id: GO:0047987
-name: hydroperoxide dehydratase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: (9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate = (9Z)-(13S)-12,13-epoxyoctadeca-9,11-dienoate + H2O." [EC:4.2.1.92, MetaCyc:HYDROPEROXIDE-DEHYDRATASE-RXN]
-synonym: "(9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate 12,13-hydro-lyase [(9Z)-(13S)-12,13-epoxyoctadeca-9,11-dienoate-forming]" RELATED [EC:4.2.1.92]
-synonym: "(9Z,11E,14Z)-(13S)-hydroperoxyoctadeca-9,11,14-trienoate 12,13-hydro-lyase activity" RELATED [EC:4.2.1.92]
-synonym: "HPI" RELATED [EC:4.2.1.92]
-synonym: "hydroperoxide isomerase activity" RELATED [EC:4.2.1.92]
-synonym: "linoleate hydroperoxide isomerase" RELATED [EC:4.2.1.92]
-synonym: "linoleic acid hydroperoxide isomerase" RELATED [EC:4.2.1.92]
-xref: EC:4.2.1.92
-xref: MetaCyc:HYDROPEROXIDE-DEHYDRATASE-RXN
-xref: RHEA:25075
-is_a: GO:0016836 ! hydro-lyase activity
-
[Term]
id: GO:0047988
name: hydroxyacid-oxoacid transhydrogenase activity
@@ -285715,7 +285440,7 @@ is_a: GO:0030547 ! signaling receptor inhibitor activity
id: GO:0048020
name: CCR chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR chemokine receptor." [GOC:ai]
+def: "Binding to a CCR chemokine receptor." [GOC:ai]
synonym: "beta chemokine receptor binding" EXACT []
synonym: "beta chemokine receptor ligand" NARROW []
synonym: "CCR chemokine receptor ligand" NARROW []
@@ -285834,7 +285559,7 @@ relationship: positively_regulates GO:0000398 ! mRNA splicing, via spliceosome
id: GO:0048027
name: mRNA 5'-UTR binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the 5' untranslated region of an mRNA molecule." [GOC:jid]
+def: "Binding to an mRNA molecule at its 5' untranslated region." [GOC:jid]
synonym: "mRNA 5' UTR binding" EXACT []
is_a: GO:0003729 ! mRNA binding
@@ -285842,7 +285567,7 @@ is_a: GO:0003729 ! mRNA binding
id: GO:0048028
name: galacturonan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any simple or complex galacturonan. Galacturonan is any glycan composed solely of galacturonic acid residues, a specific type of glycuronan, and a constituent of some pectins." [GOC:jid]
+def: "Binding to a simple or complex galacturonan. Galacturonan is any glycan composed solely of galacturonic acid residues, a specific type of glycuronan, and a constituent of some pectins." [GOC:jid]
synonym: "polygalacturonide binding" RELATED []
is_a: GO:0030247 ! polysaccharide binding
@@ -285850,7 +285575,7 @@ is_a: GO:0030247 ! polysaccharide binding
id: GO:0048029
name: monosaccharide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides." [GOC:jid]
+def: "Binding to a monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides." [GOC:jid]
is_a: GO:0030246 ! carbohydrate binding
is_a: GO:0036094 ! small molecule binding
@@ -285858,32 +285583,32 @@ is_a: GO:0036094 ! small molecule binding
id: GO:0048030
name: disaccharide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any disaccharide. Disaccharides are sugars composed of two monosaccharide units." [GOC:jid]
+def: "Binding to a disaccharide. Disaccharides are sugars composed of two monosaccharide units." [GOC:jid]
is_a: GO:0070492 ! oligosaccharide binding
[Term]
id: GO:0048031
name: trisaccharide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any trisaccharide. Trisaccharides are sugars composed of three monosaccharide units." [GOC:jid]
+def: "Binding to a trisaccharide. Trisaccharides are sugars composed of three monosaccharide units." [GOC:jid]
is_a: GO:0070492 ! oligosaccharide binding
[Term]
id: GO:0048032
name: galacturonate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any galacturonate. Galacturonate is the anion of galacturonic acid, the uronic acid formally derived from galactose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group." [GOC:jid]
+def: "Binding to a galacturonate. Galacturonate is the anion of galacturonic acid, the uronic acid formally derived from galactose by oxidation of the hydroxymethylene group at C-6 to a carboxyl group." [GOC:jid]
synonym: "galacturonic acid binding" EXACT []
is_a: GO:0033293 ! monocarboxylic acid binding
[Term]
id: GO:0048033
-name: heme o metabolic process
+name: heme O metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving heme O, a derivative of heme containing a 17-carbon hydroxyethylfarnesyl side chain at position 8 of the tetrapyrrole macrocycle." [GOC:jid]
-synonym: "haem o metabolic process" EXACT []
-synonym: "haem o metabolism" EXACT []
-synonym: "heme o metabolism" EXACT []
+synonym: "haem O metabolic process" EXACT []
+synonym: "haem O metabolism" EXACT []
+synonym: "heme O metabolism" EXACT []
is_a: GO:0042168 ! heme metabolic process
[Term]
@@ -285898,20 +285623,20 @@ synonym: "heme O biosynthesis" EXACT []
synonym: "heme O formation" EXACT []
synonym: "heme O synthesis" EXACT []
is_a: GO:0006783 ! heme biosynthetic process
-is_a: GO:0048033 ! heme o metabolic process
+is_a: GO:0048033 ! heme O metabolic process
[Term]
id: GO:0048035
-name: heme o catabolic process
+name: heme O catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of heme O, a derivative of heme containing a 17-carbon hydroxyethylfarnesyl side chain at position 8 of the tetrapyrrole macrocycle." [GOC:jid]
-synonym: "haem o catabolic process" EXACT []
-synonym: "haem o catabolism" EXACT []
-synonym: "heme o breakdown" EXACT []
-synonym: "heme o catabolism" EXACT []
-synonym: "heme o degradation" EXACT []
+synonym: "haem O catabolic process" EXACT []
+synonym: "haem O catabolism" EXACT []
+synonym: "heme O breakdown" EXACT []
+synonym: "heme O catabolism" EXACT []
+synonym: "heme O degradation" EXACT []
is_a: GO:0042167 ! heme catabolic process
-is_a: GO:0048033 ! heme o metabolic process
+is_a: GO:0048033 ! heme O metabolic process
[Term]
id: GO:0048036
@@ -285926,7 +285651,7 @@ relationship: part_of GO:0007420 ! brain development
id: GO:0048037
name: obsolete cofactor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate." [ISBN:0198506732]
+def: "OBSOLETE. Binding to a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate." [ISBN:0198506732]
comment: 1. Making inferences in GO about compounds based on the cofactor role curated by ChEBI creates relationships that are not always true which violates ontological principles for GO; therefore we will cease making these inferences. 2. It is not meaningful to group binding interactions that are not all chemically related by the fact that they may be used as a cofactor.
is_obsolete: true
@@ -285934,14 +285659,14 @@ is_obsolete: true
id: GO:0048038
name: quinone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds." [ISBN:0198506732]
+def: "Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds." [ISBN:0198506732]
is_a: GO:0005488 ! binding
[Term]
id: GO:0048039
name: ubiquinone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ubiquinone, a quinone derivative with a tail of isoprene units." [GOC:jid, ISBN:0582227089]
+def: "Binding to ubiquinone, a quinone derivative with a tail of isoprene units." [GOC:jid, ISBN:0582227089]
synonym: "coenzyme Q binding" EXACT []
synonym: "coenzyme Q6 binding" NARROW []
is_a: GO:0048038 ! quinone binding
@@ -286445,23 +286170,14 @@ def: "Establishment of a pattern of pigment in females." [GOC:jid]
is_a: GO:0048071 ! sex-specific pigmentation
relationship: part_of GO:0046660 ! female sex differentiation
-[Term]
-id: GO:0048096
-name: chromatin-mediated maintenance of transcription
-namespace: biological_process
-def: "Maintenance of transcription by remodelling of chromatin into an 'open configuration'. Once established, this regulation is mitotically stable and is maintained over many cell divisions. It is also heritable." [GOC:jid]
-comment: Note that this process is the opposite of chromatin silencing. This regulation is exemplified by members of the trithorax group, which maintain the active state of homeotic gene transcription.
-is_a: GO:0034401 ! chromatin organization involved in regulation of transcription
-is_a: GO:0045815 ! positive regulation of gene expression, epigenetic
-is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
-
[Term]
id: GO:0048097
-name: long-term maintenance of gene activation
+name: obsolete long-term maintenance of gene activation
namespace: biological_process
-def: "Any mechanism, at the level of transcription or post-transcription, maintaining gene activation in the long-term." [GOC:jid]
-comment: Note that this process is the opposite of gene silencing.
-is_a: GO:0045815 ! positive regulation of gene expression, epigenetic
+def: "OBSOLETE. Any mechanism, at the level of transcription or post-transcription, maintaining gene activation in the long-term." [GOC:jid]
+comment: This term has been obsoleted because its definition was not clear, and had no references and no annotations.
+is_obsolete: true
+consider: GO:0045815
[Term]
id: GO:0048098
@@ -286781,7 +286497,7 @@ is_obsolete: true
id: GO:0048156
name: tau protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS." [GOC:jid]
+def: "Binding to tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS." [GOC:jid]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
@@ -286976,7 +286692,7 @@ is_a: GO:0048180 ! activin complex
id: GO:0048184
name: obsolete follistatin binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with the peptide hormone follistatin." [GOC:jid, GOC:mah]
+def: "OBSOLETE. Binding to the peptide hormone follistatin." [GOC:jid, GOC:mah]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "follistatin binding" EXACT []
is_obsolete: true
@@ -286986,7 +286702,7 @@ replaced_by: GO:0017046
id: GO:0048185
name: activin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with activin, a dimer of inhibin-beta subunits." [GOC:jid, GOC:mah]
+def: "Binding to activin, a dimer of inhibin-beta subunits." [GOC:jid, GOC:mah]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -287003,7 +286719,7 @@ is_a: GO:0035097 ! histone methyltransferase complex
id: GO:0048189
name: Lid2 complex
namespace: cellular_component
-def: "A protein complex that is thought to be involved in regulation of chromatin remodeling. In Schizosaccharomyces the complex contains Lid1p, Ash2p, Ecm5p, Snt2p, and Sdc1p." [PMID:12488447]
+def: "A protein complex involved in regulation of chromatin remodeling. In Schizosaccharomyces the complex contains Lid2, Ash2, Jmj3, Snt2, and Sdc1." [PMID:12488447]
is_a: GO:0140513 ! nuclear protein-containing complex
[Term]
@@ -287062,7 +286778,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a membrane priming complex. An incoming coat component recognizes both GTPase and a membrane protein to form the priming complex." [GOC:jid, ISBN:0716731363, PMID:10219233]
synonym: "formation of dictyosome membrane priming complex" NARROW []
synonym: "formation of Golgi membrane priming complex" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0048200 ! Golgi transport vesicle coating
[Term]
@@ -287083,7 +286799,7 @@ def: "The aggregation, arrangement and bonding together of priming complexes to
synonym: "dictyosome membrane binding by cytosolic coat proteins" NARROW []
synonym: "dictyosome membrane bud coat oligomerisation" NARROW []
synonym: "Golgi membrane bud coat oligomerisation" NARROW []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0048200 ! Golgi transport vesicle coating
[Term]
@@ -287169,7 +286885,6 @@ namespace: biological_process
def: "The process in which vesicles are directed to specific destination membranes during transport from the cis-Golgi to the rough ER." [GOC:jid, GOC:mah, ISBN:0716731363, PMID:10219233]
synonym: "cis-Golgi to rough endoplasmic reticulum targeting" EXACT []
synonym: "cis-Golgi to rough ER targeting" EXACT []
-synonym: "vesicle targeting, cis-Golgi to rough endoplasmic reticulum" EXACT []
synonym: "vesicle targeting, cis-Golgi to rough ER" EXACT []
is_a: GO:0006890 ! retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
is_a: GO:0048199 ! vesicle targeting, to, from or within Golgi
@@ -287250,7 +286965,7 @@ def: "The binding of specific proteins to the t-SNARE/v-SNARE/SNAP25 complex, by
synonym: "dictyosome vesicle prefusion complex stabilisation" NARROW []
synonym: "Golgi vesicle prefusion complex assembly" EXACT []
synonym: "Golgi-derived vesicle prefusion complex stabilization" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0048193 ! Golgi vesicle transport
[Term]
@@ -287527,7 +287242,7 @@ is_a: GO:0072676 ! lymphocyte migration
id: GO:0048248
name: CXCR3 chemokine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a the CXCR3 chemokine receptor." [GOC:jid, PMID:10556837]
+def: "Binding to a CXCR3 chemokine receptor." [GOC:jid, PMID:10556837]
is_a: GO:0045236 ! CXCR chemokine receptor binding
[Term]
@@ -287706,7 +287421,7 @@ name: clathrin coat assembly
namespace: biological_process
def: "The process that results in the assembly of clathrin triskelia into the ordered structure known as a clathrin cage." [GOC:jid, PMID:11460887, PMID:11977118, PMID:9531549]
synonym: "clathrin cage assembly" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0048269
@@ -287730,7 +287445,7 @@ is_a: GO:0030234 ! enzyme regulator activity
id: GO:0048273
name: mitogen-activated protein kinase p38 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with mitogen-activated protein kinase p38, an enzyme that catalyzes the transfer of phosphate from ATP to hydroxyl side chains on proteins in response to mitogen activation." [GOC:curators, PMID:17827184]
+def: "Binding to mitogen-activated protein kinase p38, an enzyme that catalyzes the transfer of phosphate from ATP to hydroxyl side chains on proteins in response to mitogen activation." [GOC:curators, PMID:17827184]
synonym: "MAPK p38 binding" EXACT []
is_a: GO:0051019 ! mitogen-activated protein kinase binding
@@ -288060,7 +287775,7 @@ relationship: positively_regulates GO:0048291 ! isotype switching to IgG isotype
id: GO:0048306
name: calcium-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium." [GOC:jid, PMID:10485905]
+def: "Binding to a protein or protein complex in the presence of calcium." [GOC:jid, PMID:10485905]
is_a: GO:0005515 ! protein binding
[Term]
@@ -289038,7 +288753,7 @@ relationship: part_of GO:0048390 ! intermediate mesoderm morphogenesis
id: GO:0048403
name: brain-derived neurotrophic factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with brain-derived neurotrophic factor." [GOC:dgh]
+def: "Binding to brain-derived neurotrophic factor." [GOC:dgh]
synonym: "BDNF binding" EXACT []
synonym: "neurotrophin TRKB receptor activity" RELATED []
is_a: GO:0043121 ! neurotrophin binding
@@ -289047,7 +288762,7 @@ is_a: GO:0043121 ! neurotrophin binding
id: GO:0048406
name: nerve growth factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with nerve growth factor (NGF)." [GOC:dgh]
+def: "Binding to nerve growth factor (NGF)." [GOC:dgh]
synonym: "beta-nerve growth factor binding" EXACT [PR:000011194]
synonym: "neurotrophin TRKA receptor activity" RELATED []
synonym: "NGF binding" EXACT [PR:000011194]
@@ -289057,7 +288772,7 @@ is_a: GO:0043121 ! neurotrophin binding
id: GO:0048407
name: platelet-derived growth factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with platelet-derived growth factor." [GOC:dgh]
+def: "Binding to platelet-derived growth factor." [GOC:dgh]
synonym: "PDGF binding" EXACT []
is_a: GO:0019838 ! growth factor binding
@@ -289065,7 +288780,7 @@ is_a: GO:0019838 ! growth factor binding
id: GO:0048408
name: epidermal growth factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with epidermal growth factor." [GOC:dgh]
+def: "Binding to epidermal growth factor." [GOC:dgh]
synonym: "EGF binding" EXACT []
is_a: GO:0019838 ! growth factor binding
is_a: GO:0042562 ! hormone binding
@@ -289539,7 +289254,7 @@ relationship: part_of GO:0048483 ! autonomic nervous system development
id: GO:0048487
name: beta-tubulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin." [GOC:krc]
+def: "Binding to the microtubule constituent protein beta-tubulin." [GOC:krc]
synonym: "beta tubulin binding" EXACT []
is_a: GO:0015631 ! tubulin binding
@@ -289623,7 +289338,7 @@ relationship: part_of GO:0042716 ! plasma membrane-derived chromatophore
id: GO:0048495
name: Roundabout binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the Roundabout (ROBO) receptor, a transmembrane receptor." [GOC:ecd, PMID:10102268, PMID:10197527]
+def: "Binding to Roundabout (ROBO) receptor, a transmembrane receptor." [GOC:ecd, PMID:10102268, PMID:10197527]
synonym: "Roundabout receptor binding" RELATED []
is_a: GO:0005102 ! signaling receptor binding
@@ -289660,7 +289375,6 @@ def: "A process that is carried out at the cellular level which results in the a
synonym: "SLMV biogenesis" NARROW []
synonym: "synaptic vesicle membrane organisation" EXACT []
synonym: "synaptic vesicle membrane organization and biogenesis" RELATED [GOC:mah]
-is_a: GO:0006996 ! organelle organization
is_a: GO:0061024 ! membrane organization
relationship: part_of GO:0010256 ! endomembrane system organization
@@ -289702,6 +289416,7 @@ xref: EC:7.6.2.15
xref: RHEA:29811
xref: TC:3.A.1.19.1
is_a: GO:0015234 ! thiamine transmembrane transporter activity
+is_a: GO:0022853 ! active ion transmembrane transporter activity
is_a: GO:0140394 ! ABC-type azole transporter activity
[Term]
@@ -289904,6 +289619,7 @@ name: positive regulation of cellular process
namespace: biological_process
alt_id: GO:0051242
def: "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid]
+subset: gocheck_do_not_annotate
synonym: "activation of cellular process" NARROW []
synonym: "positive regulation of cellular physiological process" EXACT []
synonym: "stimulation of cellular process" NARROW []
@@ -289920,6 +289636,7 @@ name: negative regulation of cellular process
namespace: biological_process
alt_id: GO:0051243
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jid]
+subset: gocheck_do_not_annotate
synonym: "down regulation of cellular process" EXACT []
synonym: "down-regulation of cellular process" EXACT []
synonym: "downregulation of cellular process" EXACT []
@@ -290283,7 +290000,7 @@ name: photosystem I assembly
namespace: biological_process
alt_id: GO:0010251
def: "The aggregation, arrangement and bonding together of a set of components to form a photosystem I complex on the thylakoid membrane." [GOC:go_curators]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0019684 ! photosynthesis, light reaction
[Term]
@@ -290302,7 +290019,6 @@ id: GO:0048566
name: embryonic digestive tract development
namespace: biological_process
def: "The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus." [GOC:go_curators]
-synonym: "embryonic digestive tract development" BROAD [GOC:dph]
is_a: GO:0048565 ! digestive tract development
is_a: GO:0048568 ! embryonic organ development
@@ -290661,7 +290377,7 @@ relationship: part_of GO:0048599 ! oocyte development
id: GO:0048608
name: reproductive structure development
namespace: biological_process
-def: "The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures." [GOC:dph, GOC:isa_complete, GOC:jid]
+def: "The reproductive developmental process whose specific outcome is the progression of somatic structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures." [GOC:dph, GOC:isa_complete, GOC:jid]
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0048856 ! anatomical structure development
relationship: part_of GO:0061458 ! reproductive system development
@@ -290813,7 +290529,6 @@ synonym: "vegetative vivipary" BROAD []
synonym: "vivipary" BROAD []
is_a: GO:0003006 ! developmental process involved in reproduction
is_a: GO:0019954 ! asexual reproduction
-is_a: GO:0044703 ! multi-organism reproductive process
is_a: GO:0044706 ! multi-multicellular organism process
is_a: GO:0048507 ! meristem development
is_a: GO:0048609 ! multicellular organismal reproductive process
@@ -291043,7 +290758,6 @@ namespace: biological_process
def: "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:jid, GOC:tb]
comment: Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.
subset: goslim_chembl
-subset: goslim_generic
synonym: "formation of an anatomical structure involved in morphogenesis" EXACT [GOC:dph, GOC:tb]
is_a: GO:0032502 ! developmental process
relationship: part_of GO:0009653 ! anatomical structure morphogenesis
@@ -293938,18 +293652,19 @@ is_a: GO:0016836 ! hydro-lyase activity
[Term]
id: GO:0050012
-name: juglone 3-monooxygenase activity
+name: juglone 3-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-hydroxy-1,4-naphthoquinone + AH(2) + O(2) = 3,5-dihydroxy-1,4-naphthoquinone + A + H(2)O + H(+)." [EC:1.14.99.27, RHEA:18745]
-synonym: "5-hydroxy-1,4-naphthoquinone,hydrogen-donor:oxygen oxidoreductase (3-hydroxylating)" RELATED [EC:1.14.99.27]
+def: "Catalysis of the reaction: 2 juglone + O2 = 2 3,5-dihydroxy-1,4-naphthoquinone + 2 H+." [PMID:4041238, RHEA:18745]
+comment: Formerly EC:1.14.99.27.
+synonym: "5-hydroxy-1,4-naphthoquinone,hydrogen-donor:oxygen oxidoreductase (3-hydroxylating)" RELATED []
+synonym: "juglone 3-monooxygenase activity" EXACT []
synonym: "juglone hydroxylase activity" EXACT []
-synonym: "naphthoquinone hydroxylase activity" RELATED [EC:1.14.99.27]
-synonym: "naphthoquinone-hydroxylase activity" RELATED [EC:1.14.99.27]
-xref: EC:1.14.99.27
+synonym: "naphthoquinone hydroxylase activity" RELATED [EC:1.17.3.4]
+xref: EC:1.17.3.4
xref: KEGG_REACTION:R04327
xref: MetaCyc:JUGLONE-3-MONOOXYGENASE-RXN
xref: RHEA:18745
-is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0016727 ! oxidoreductase activity, acting on CH or CH2 groups, oxygen as acceptor
[Term]
id: GO:0050013
@@ -294182,6 +293897,7 @@ id: GO:0050029
name: L-lysine oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-lysine + H(2)O + O(2) = 6-amino-2-oxohexanoate + H(2)O(2) + NH(4)(+)." [EC:1.4.3.14, RHEA:14437]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "L-lysine alpha-oxidase activity" RELATED [EC:1.4.3.14]
synonym: "L-lysine:oxygen 2-oxidoreductase (deaminating)" RELATED [EC:1.4.3.14]
synonym: "L-lysyl-alpha-oxidase activity" RELATED [EC:1.4.3.14]
@@ -294487,7 +294203,7 @@ is_a: GO:0008080 ! N-acetyltransferase activity
id: GO:0050051
name: leukotriene-B4 20-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6Z,8E,10E,14Z)-(5S,12R)-5,12-dihydroxyicosa-6,8,10,14-tetraenoate + NADPH + H+ + O2 = (6Z,8E,10E,14Z)-(5S,12R)-5,12,20-trihydroxyicosa-6,8,10,14-tetraenoate + NADP+ + H2O." [MetaCyc:LEUKOTRIENE-B4-20-MONOOXYGENASE-RXN, RHEA:22176]
+def: "Catalysis of the reaction: leukotriene B4 + O2 + reduced [NADPH-hemoprotein reductase] = 20-hydroxy-leukotriene B4 + H+ + H2O + oxidized [NADPH-hemoprotein reductase]." [PMID:11461919, PMID:15364545, PMID:8486631, PMID:9675028, RHEA:22176]
synonym: "leukotriene-B4 20-hydroxylase activity" RELATED [EC:1.14.14.94]
synonym: "leukotriene-B4 omega-hydroxylase activity" RELATED [EC:1.14.14.94]
synonym: "LTB(4) 20-hydroxylase activity" RELATED [EC:1.14.14.94]
@@ -294498,7 +294214,7 @@ xref: EC:1.14.14.94
xref: MetaCyc:LEUKOTRIENE-B4-20-MONOOXYGENASE-RXN
xref: Reactome:R-HSA-211873 "CYP4F2, 4F3 20-hydroxylate LTB4"
xref: RHEA:22176
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0050052
@@ -294561,12 +294277,12 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0050056
name: linalool 8-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: AH(2) + linalool + O(2) = (2E)-2,6-dimethylocta-2,7-diene-1,6-diol + A + H(2)O." [EC:1.14.99.28, RHEA:20760]
+def: "Catalysis of the reaction: AH(2) + linalool + O(2) = (2E)-2,6-dimethylocta-2,7-diene-1,6-diol + A + H(2)O." [EC:1.14.14.84, RHEA:32635]
synonym: "3,7-dimethylocta-1,6-dien-3-ol,hydrogen-donor:oxygen oxidoreductase (8-hydroxylating)" RELATED [EC:1.14.99.28]
-xref: EC:1.14.99.28
+xref: EC:1.14.14.84
xref: KEGG_REACTION:R04366
xref: MetaCyc:LINALOOL-8-MONOOXYGENASE-RXN
-xref: RHEA:20760
+xref: RHEA:32635
is_a: GO:0004497 ! monooxygenase activity
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
@@ -294695,6 +294411,7 @@ id: GO:0050065
name: lysine-pyruvate 6-transaminase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-lysine + pyruvate = L-alanine + L-allysine." [EC:2.6.1.71, RHEA:19393]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "L-lysine:pyruvate aminotransferase activity" RELATED [EC:2.6.1.71]
synonym: "Lys-AT" RELATED [EC:2.6.1.71]
synonym: "lysine--pyruvate 6-aminotransferase activity" EXACT []
@@ -294987,8 +294704,8 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050087
name: mannitol dehydrogenase (cytochrome) activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-mannitol + ferricytochrome c = D-fructose + ferrocytochrome c." [EC:1.1.2.2, MetaCyc:MANNITOL-DEHYDROGENASE-CYTOCHROME-RXN]
-synonym: "D-mannitol:ferricytochrome-c 2-oxidoreductase activity" RELATED [EC:1.1.2.2]
+def: "Catalysis of the reaction: 2 [Fe(III)cytochrome c] + D-mannitol = 2 [Fe(II)cytochrome c] + D-fructose + 2 H+." [RHEA:17597]
+synonym: "D-mannitol:ferricytochrome-c 2-oxidoreductase activity" RELATED []
synonym: "polyol dehydrogenase activity" BROAD [EC:1.1.2.2]
xref: EC:1.1.2.2
xref: MetaCyc:MANNITOL-DEHYDROGENASE-CYTOCHROME-RXN
@@ -295825,7 +295542,6 @@ alt_id: GO:0019201
def: "Catalysis of the reaction: ATP + nucleoside monophosphate = ADP + nucleoside diphosphate." [GOC:ai, ISBN:0198506732]
synonym: "ATP:nucleoside-phosphate phosphotransferase activity" RELATED [EC:2.7.4.4]
synonym: "NMP-kinase activity" RELATED [EC:2.7.4.4]
-synonym: "nucleoside monophosphate kinase activity" EXACT [GOC:dph, GOC:tb]
synonym: "nucleoside-phosphate kinase activity" EXACT []
synonym: "nucleotide kinase activity" RELATED []
xref: EC:2.7.4.4
@@ -296063,14 +295779,14 @@ is_a: GO:0008410 ! CoA-transferase activity
id: GO:0050162
name: oxalate oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H(+) + O(2) + oxalate = 2 CO(2) + H(2)O(2)." [EC:1.2.3.4, RHEA:21881]
+def: "Catalysis of the reaction: 2 H(+) + O(2) + oxalate = 2 CO(2) + H(2)O(2)." [RHEA:21880]
synonym: "aero-oxalo dehydrogenase activity" RELATED [EC:1.2.3.4]
synonym: "oxalate:oxygen oxidoreductase activity" RELATED [EC:1.2.3.4]
synonym: "oxalic acid oxidase activity" RELATED [EC:1.2.3.4]
xref: EC:1.2.3.4
xref: KEGG_REACTION:R00273
xref: MetaCyc:OXALATE-OXIDASE-RXN
-xref: RHEA:21881
+xref: RHEA:21880
is_a: GO:0016623 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor
[Term]
@@ -298102,6 +297818,7 @@ id: GO:0050303
name: lysine 6-dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + NAD+ + L-lysine = NH3 + NADH + allysine." [EC:1.4.1.18, MetaCyc:LYSINE-6-DEHYDROGENASE-RXN, RHEA:12408]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "L-lysine 6-dehydrogenase activity" RELATED [EC:1.4.1.18]
synonym: "L-lysine epsilon-dehydrogenase activity" RELATED [EC:1.4.1.18]
synonym: "L-lysine:NAD+ 6-oxidoreductase (deaminating)" RELATED [EC:1.4.1.18]
@@ -299172,6 +298889,7 @@ id: GO:0050378
name: UDP-glucuronate 4-epimerase activity
namespace: molecular_function
def: "Catalysis of the reaction: UDP-alpha-D-glucuronate = UDP-alpha-D-galacturonate." [EC:5.1.3.6, RHEA:11404]
+comment: Note that this term has a MetaCyc pathway reference as the pathway only has a single step.
synonym: "UDP glucuronic epimerase activity" RELATED [EC:5.1.3.6]
synonym: "UDP-D-galacturonic acid 4-epimerase activity" RELATED [EC:5.1.3.6]
synonym: "UDP-galacturonate 4-epimerase activity" RELATED [EC:5.1.3.6]
@@ -299207,7 +298925,7 @@ is_a: GO:0016857 ! racemase and epimerase activity, acting on carbohydrates and
id: GO:0050380
name: undecaprenyl-diphosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: all-trans-undecaprenyl diphosphate + H(2)O = all-trans-undecaprenyl phosphate + H(+) + phosphate." [EC:3.6.1.27, RHEA:17069]
+def: "Catalysis of the reaction: di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-trans,octa-cis-undecaprenyl phosphate + H+ + phosphate." [PMID:18411271, RHEA:28094]
synonym: "C(55)-isoprenyl diphosphatase activity" RELATED [EC:3.6.1.27]
synonym: "C(55)-isoprenyl pyrophosphatase activity" RELATED [EC:3.6.1.27]
synonym: "C55-isoprenyl diphosphatase activity" RELATED [EC:3.6.1.27]
@@ -299217,7 +298935,7 @@ synonym: "undecaprenyl-diphosphate phosphohydrolase activity" RELATED [EC:3.6.1.
xref: EC:3.6.1.27
xref: KEGG_REACTION:R05627
xref: MetaCyc:UNDECAPRENYL-DIPHOSPHATASE-RXN
-xref: RHEA:17069
+xref: RHEA:28094
is_a: GO:0016462 ! pyrophosphatase activity
[Term]
@@ -299925,7 +299643,7 @@ is_a: GO:0004629 ! phospholipase C activity
id: GO:0050431
name: transforming growth factor beta binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with TGF-beta, transforming growth factor beta, a multifunctional peptide that controls proliferation, differentiation and other functions in many cell types." [ISBN:0198506732]
+def: "Binding to TGF-beta, transforming growth factor beta, a multifunctional peptide that controls proliferation, differentiation and other functions in many cell types." [ISBN:0198506732]
synonym: "TGF-beta binding" EXACT []
synonym: "TGFbeta binding" EXACT []
synonym: "transforming growth factor beta ligand binding to type I receptor" RELATED []
@@ -299978,7 +299696,7 @@ is_a: GO:0006518 ! peptide metabolic process
id: GO:0050436
name: microfibril binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a microfibril, any small fibril occurring in biological material." [GOC:ai]
+def: "Binding to a microfibril, any small fibril occurring in biological material." [GOC:ai]
comment: See also the cellular component term 'microfibril ; GO:0001527'.
is_a: GO:0005488 ! binding
@@ -300166,7 +299884,7 @@ is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than
id: GO:0050448
name: beta-cyclopiazonate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: beta-cyclopiazonate + A = alpha-cyclopiazonate + AH(2)." [EC:1.21.99.1, RHEA:14526]
+def: "Catalysis of the reaction: beta-cyclopiazonate + A = alpha-cyclopiazonate + AH(2)." [RHEA:14525]
synonym: "b-cyclopiazonate dehydrogenase activity" EXACT []
synonym: "beta-cyclopiazonate oxidocyclase activity" RELATED [EC:1.21.99.1]
synonym: "beta-cyclopiazonate:(acceptor) oxidoreductase (cyclizing)" RELATED [EC:1.21.99.1]
@@ -300175,7 +299893,7 @@ synonym: "beta-cyclopiazonic oxidocyclase activity" RELATED [EC:1.21.99.1]
xref: EC:1.21.99.1
xref: KEGG_REACTION:R04080
xref: MetaCyc:BETA-CYCLOPIAZONATE-DEHYDROGENASE-RXN
-xref: RHEA:14526
+xref: RHEA:14525
is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond
[Term]
@@ -301460,7 +301178,7 @@ is_a: GO:0016634 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0050542
name: icosanoid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with icosanoids, any C20 polyunsaturated fatty acids or their derivatives, including the leukotrienes and the prostanoids." [ISBN:0198506732]
+def: "Binding to icosanoids, any C20 polyunsaturated fatty acids or their derivatives, including the leukotrienes and the prostanoids." [ISBN:0198506732]
synonym: "eicosanoid binding" EXACT []
is_a: GO:0031406 ! carboxylic acid binding
@@ -301468,7 +301186,7 @@ is_a: GO:0031406 ! carboxylic acid binding
id: GO:0050543
name: icosatetraenoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with icosatetraenoic acid, any straight-chain fatty acid with twenty carbon atoms and four double bonds per molecule." [ISBN:0198506732]
+def: "Binding to icosatetraenoic acid, any straight-chain fatty acid with twenty carbon atoms and four double bonds per molecule." [ISBN:0198506732]
synonym: "eicosatetraenoic acid binding" EXACT []
is_a: GO:0036041 ! long-chain fatty acid binding
@@ -301476,7 +301194,7 @@ is_a: GO:0036041 ! long-chain fatty acid binding
id: GO:0050544
name: arachidonic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer." [GOC:ai]
+def: "Binding to arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer." [GOC:ai]
synonym: "arachidonate binding" EXACT []
is_a: GO:0043177 ! organic acid binding
is_a: GO:0050542 ! icosanoid binding
@@ -301731,7 +301449,7 @@ id: GO:0050563
name: trans-feruloyl-CoA synthase activity
namespace: molecular_function
alt_id: GO:0106287
-def: "Catalysis of the reaction: ATP + CoA + trans-ferulate = (E)-feruloyl-CoA + ADP + phosphate." [PMID:22649270, RHEA:19389]
+def: "Catalysis of the reaction: ATP + CoA + trans-ferulate = (E)-feruloyl-CoA + ADP + phosphate." [PMID:22649270]
synonym: "ferulate-CoA ligase activity" RELATED []
synonym: "trans-ferulate:CoASH ligase (ATP-hydrolysing)" RELATED [EC:6.2.1.34]
synonym: "trans-feruloyl-CoA synthetase activity" RELATED [EC:6.2.1.34]
@@ -301881,13 +301599,13 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0050573
name: dTDP-4-dehydro-6-deoxyglucose reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-D-fucose + NADP(+) = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(+) + NADPH." [EC:1.1.1.266, RHEA:36586]
+def: "Catalysis of the reaction: dTDP-D-fucose + NADP(+) = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H(+) + NADPH." [EC:1.1.1.266, RHEA:36583]
synonym: "dTDP-4-keto-6-deoxyglucose reductase activity" RELATED [EC:1.1.1.266]
synonym: "dTDP-D-fucose:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.266]
xref: EC:1.1.1.266
xref: KEGG_REACTION:R05687
xref: MetaCyc:1.1.1.266-RXN
-xref: RHEA:36586
+xref: RHEA:36583
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
[Term]
@@ -302888,7 +302606,7 @@ is_a: GO:0035251 ! UDP-glucosyltransferase activity
id: GO:0050646
name: 5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
+def: "Binding to 5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
synonym: "5-oxo-6E,8Z,11Z,14Z-eicosatetraenoic acid binding" EXACT []
is_a: GO:0036041 ! long-chain fatty acid binding
is_a: GO:0043177 ! organic acid binding
@@ -302898,7 +302616,7 @@ is_a: GO:0050542 ! icosanoid binding
id: GO:0050647
name: 5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
+def: "Binding to 5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
synonym: "5-hydroxy-6E,8Z,11Z,14Z-eicosatetraenoic acid binding" EXACT []
is_a: GO:0036041 ! long-chain fatty acid binding
is_a: GO:0043177 ! organic acid binding
@@ -302909,7 +302627,7 @@ is_a: GO:1901567 ! fatty acid derivative binding
id: GO:0050648
name: 5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
+def: "Binding to 5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid, a straight-chain fatty acid with twenty carbon atoms and four double bonds." [GOC:ai]
synonym: "5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-eicosatetraenoic acid binding" EXACT []
is_a: GO:0036041 ! long-chain fatty acid binding
is_a: GO:0043177 ! organic acid binding
@@ -303013,7 +302731,7 @@ is_a: GO:0006029 ! proteoglycan metabolic process
id: GO:0050656
name: 3'-phosphoadenosine 5'-phosphosulfate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 3'-phosphoadenosine 5'-phosphosulfate (PAPS), a naturally occurring mixed anhydride. It is an intermediate in the formation of a variety of sulfo compounds in biological systems." [GOC:ai]
+def: "Binding to 3'-phosphoadenosine 5'-phosphosulfate (PAPS), a naturally occurring mixed anhydride. It is an intermediate in the formation of a variety of sulfo compounds in biological systems." [GOC:ai]
synonym: "3'-phosphoadenosine 5'-phosphosulphate binding" EXACT []
synonym: "3'-phosphoadenylyl-sulfate binding" EXACT []
synonym: "adenosine 3'-phosphate 5'-phosphosulfate binding" EXACT []
@@ -303059,7 +302777,7 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0050660
name: flavin adenine dinucleotide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2." [GOC:ai, GOC:imk, ISBN:0198506732]
+def: "Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2." [GOC:ai, GOC:imk, ISBN:0198506732]
synonym: "FAD or FADH2 binding" EXACT []
synonym: "flavine-adenine dinucleotide binding" EXACT []
is_a: GO:0000166 ! nucleotide binding
@@ -303069,7 +302787,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0050661
name: NADP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH." [GOC:ai]
+def: "Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH." [GOC:ai]
synonym: "NADP or NADPH binding" RELATED [GOC:mah]
synonym: "NADP+ or NADPH binding" RELATED []
synonym: "nicotinamide adenine dinucleotide phosphate binding" EXACT []
@@ -303079,7 +302797,7 @@ is_a: GO:0000166 ! nucleotide binding
id: GO:0050662
name: obsolete coenzyme binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed." [ISBN:0198506732]
+def: "OBSOLETE. Binding to a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed." [ISBN:0198506732]
comment: 1. Making inferences in GO about compounds based on the coenzyme role curated by ChEBI creates relationships that are not always true which violates ontological principles for GO; therefore we will cease making these inferences. 2. It is not meaningful to group binding interactions that are not all chemically related by the fact that they may be used as a coenzyme.
is_obsolete: true
@@ -303291,7 +303009,7 @@ relationship: negatively_regulates GO:0050673 ! epithelial cell proliferation
id: GO:0050681
name: androgen receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an androgen receptor." [GOC:ai]
+def: "Binding to an androgen receptor." [GOC:ai]
synonym: "AR binding" EXACT []
is_a: GO:0016922 ! nuclear receptor binding
@@ -303299,14 +303017,14 @@ is_a: GO:0016922 ! nuclear receptor binding
id: GO:0050682
name: AF-2 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the AF-2 domain of a protein, a highly conserved ligand-dependent transactivation domain which is essential for receptor-mediated transcriptional activation." [PMID:9682036]
+def: "Binding to an AF-2 protein domain, a highly conserved ligand-dependent transactivation domain which is essential for receptor-mediated transcriptional activation." [PMID:9682036]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0050683
name: AF-1 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the AF-1 domain of a protein, a ligand-independent transactivation domain which is required for the full transcriptional activity of the receptor." [PMID:9682036]
+def: "Binding to an AF-1 protein domain, a ligand-independent transactivation domain which is required for the full transcriptional activity of the receptor." [PMID:9682036]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -303358,7 +303076,6 @@ is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
is_a: GO:0050688 ! regulation of defense response to virus
-is_a: GO:0050777 ! negative regulation of immune response
relationship: negatively_regulates GO:0051607 ! defense response to virus
[Term]
@@ -303370,7 +303087,6 @@ synonym: "regulation of antiviral response" EXACT []
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0050776 ! regulation of immune response
relationship: regulates GO:0051607 ! defense response to virus
[Term]
@@ -303411,7 +303127,7 @@ is_a: GO:0050688 ! regulation of defense response to virus
id: GO:0050692
name: DNA binding domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the DBD, DNA binding domain, of a protein." [PMID:9682036]
+def: "Binding to a protein's DNA binding domain (DBD)." [PMID:9682036]
synonym: "DBD binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -303419,7 +303135,7 @@ is_a: GO:0019904 ! protein domain specific binding
id: GO:0050693
name: LBD domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the LBD, the ligand binding domain found in nuclear receptors. In general, the LBDs consist of three layers comprised of twelve alpha-helices and several beta-strands that are organized around a lipophilic ligand-binding pocket." [PMID:9682036]
+def: "Binding to a protein's ligand binding domain (LBD) domain, found in nuclear receptors. In general, the LBDs consist of three layers comprised of twelve alpha-helices and several beta-strands that are organized around a lipophilic ligand-binding pocket." [PMID:9682036]
synonym: "ligand binding domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -303483,14 +303199,14 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0050699
name: WW domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a WW domain of a protein, a small module composed of 40 amino acids and plays a role in mediating protein-protein interactions via proline-rich regions." [PMID:14531730]
+def: "Binding to a WW domain of a protein, a small module composed of 40 amino acids and plays a role in mediating protein-protein interactions via proline-rich regions." [PMID:14531730]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0050700
name: CARD domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CARD (N-terminal caspase recruitment) domain, a protein-protein interaction domain that belongs to the death domain-fold superfamily. These protein molecule families are similar in structure with each consisting of six or seven anti-parallel alpha-helices that form highly specific homophilic interactions between signaling partners. CARD exists in the N-terminal prodomains of several caspases and in apoptosis-regulatory proteins and mediates the assembly of CARD-containing proteins that participate in activation or suppression of CARD carrying members of the caspase family." [PMID:12054670]
+def: "Binding to a CARD (N-terminal caspase recruitment) domain, a protein-protein interaction domain that belongs to the death domain-fold superfamily. These protein molecule families are similar in structure with each consisting of six or seven anti-parallel alpha-helices that form highly specific homophilic interactions between signaling partners. CARD exists in the N-terminal prodomains of several caspases and in apoptosis-regulatory proteins and mediates the assembly of CARD-containing proteins that participate in activation or suppression of CARD carrying members of the caspase family." [PMID:12054670]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -303610,7 +303326,7 @@ relationship: negatively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylatio
id: GO:0050733
name: RS domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RS domain of a protein; RS domains are usually highly phosphorylated and characterized by the presence of arginine (R)/serine (S) dipeptides. The RS domain promotes protein-protein interactions and directs subcellular localization and, in certain situations, nucleocytoplasmic shuttling of individual SR proteins. They also play a role in splicing." [PMID:11684676, PMID:12215544]
+def: "Binding to an RS domain of a protein; RS domains are usually highly phosphorylated and characterized by the presence of arginine (R)/serine (S) dipeptides. The RS domain promotes protein-protein interactions and directs subcellular localization and, in certain situations, nucleocytoplasmic shuttling of individual SR proteins. They also play a role in splicing." [PMID:11684676, PMID:12215544]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -303766,42 +303482,41 @@ replaced_by: GO:0070326
id: GO:0050750
name: low-density lipoprotein particle receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a low-density lipoprotein receptor." [GOC:ai]
+def: "Binding to a low-density lipoprotein receptor." [GOC:ai]
synonym: "LDL receptor binding" EXACT []
synonym: "low-density lipoprotein receptor binding" EXACT [GOC:dph]
is_a: GO:0070325 ! lipoprotein particle receptor binding
[Term]
id: GO:0050757
-name: thymidylate synthase biosynthetic process
+name: obsolete thymidylate synthase biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of the enzyme thymidylate synthase, which catalyzes the reaction: 5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP." [EC:2.1.1.45]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of the enzyme thymidylate synthase, which catalyzes the reaction: 5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP." [GOC:curators]
+comment: This term was obsoleted because it represent a specific gene product. Consider annotating to 'regulation of gene expression', 'regulation of transcription' or some signaling term.
synonym: "thymidylate synthase anabolism" EXACT []
synonym: "thymidylate synthase biosynthesis" EXACT []
synonym: "thymidylate synthase formation" EXACT []
synonym: "thymidylate synthase synthesis" EXACT []
-is_a: GO:0009059 ! macromolecule biosynthetic process
-is_a: GO:0019538 ! protein metabolic process
-is_a: GO:1901566 ! organonitrogen compound biosynthetic process
+is_obsolete: true
[Term]
id: GO:0050758
-name: regulation of thymidylate synthase biosynthetic process
+name: obsolete regulation of thymidylate synthase biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the enzyme thymidylate synthase." [GOC:ai]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the enzyme thymidylate synthase." [GOC:ai]
+comment: This term was obsoleted because it represent a specific gene product. Consider annotating to 'regulation of gene expression', 'regulation of transcription' or some signaling term.
synonym: "regulation of thymidylate synthase anabolism" EXACT []
synonym: "regulation of thymidylate synthase biosynthesis" EXACT []
synonym: "regulation of thymidylate synthase formation" EXACT []
synonym: "regulation of thymidylate synthase synthesis" EXACT []
-is_a: GO:0010556 ! regulation of macromolecule biosynthetic process
-is_a: GO:0051246 ! regulation of protein metabolic process
-relationship: regulates GO:0050757 ! thymidylate synthase biosynthetic process
+is_obsolete: true
[Term]
id: GO:0050759
-name: positive regulation of thymidylate synthase biosynthetic process
+name: obsolete positive regulation of thymidylate synthase biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the enzyme thymidylate synthase." [GOC:ai]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the enzyme thymidylate synthase." [GOC:ai]
+comment: This term was obsoleted because it represent a specific gene product. Consider annotating to 'positive regulation of gene expression', 'positive regulation of transcription' or some signaling term.
synonym: "activation of thymidylate synthase biosynthetic process" NARROW []
synonym: "positive regulation of thymidylate synthase anabolism" EXACT []
synonym: "positive regulation of thymidylate synthase biosynthesis" EXACT []
@@ -303811,16 +303526,14 @@ synonym: "stimulation of thymidylate synthase biosynthetic process" NARROW []
synonym: "up regulation of thymidylate synthase biosynthetic process" EXACT []
synonym: "up-regulation of thymidylate synthase biosynthetic process" EXACT []
synonym: "upregulation of thymidylate synthase biosynthetic process" EXACT []
-is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process
-is_a: GO:0050758 ! regulation of thymidylate synthase biosynthetic process
-is_a: GO:0051247 ! positive regulation of protein metabolic process
-relationship: positively_regulates GO:0050757 ! thymidylate synthase biosynthetic process
+is_obsolete: true
[Term]
id: GO:0050760
-name: negative regulation of thymidylate synthase biosynthetic process
+name: obsolete negative regulation of thymidylate synthase biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the enzyme thymidylate synthase." [GOC:ai]
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the enzyme thymidylate synthase." [GOC:ai]
+comment: This term was obsoleted because it represent a specific gene product. Consider annotating to 'negative regulation of gene expression', 'negative regulation of transcription' or some signaling term.
synonym: "down regulation of thymidylate synthase biosynthetic process" EXACT []
synonym: "down-regulation of thymidylate synthase biosynthetic process" EXACT []
synonym: "downregulation of thymidylate synthase biosynthetic process" EXACT []
@@ -303829,10 +303542,7 @@ synonym: "negative regulation of thymidylate synthase anabolism" EXACT []
synonym: "negative regulation of thymidylate synthase biosynthesis" EXACT []
synonym: "negative regulation of thymidylate synthase formation" EXACT []
synonym: "negative regulation of thymidylate synthase synthesis" EXACT []
-is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process
-is_a: GO:0050758 ! regulation of thymidylate synthase biosynthetic process
-is_a: GO:0051248 ! negative regulation of protein metabolic process
-relationship: negatively_regulates GO:0050757 ! thymidylate synthase biosynthetic process
+is_obsolete: true
[Term]
id: GO:0050761
@@ -303883,7 +303593,6 @@ synonym: "down regulation of phagocytosis" EXACT []
synonym: "down-regulation of phagocytosis" EXACT []
synonym: "downregulation of phagocytosis" EXACT []
synonym: "inhibition of phagocytosis" NARROW []
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0050764 ! regulation of phagocytosis
is_a: GO:0051051 ! negative regulation of transport
relationship: negatively_regulates GO:0006909 ! phagocytosis
@@ -303898,7 +303607,6 @@ synonym: "stimulation of phagocytosis" NARROW []
synonym: "up regulation of phagocytosis" EXACT []
synonym: "up-regulation of phagocytosis" EXACT []
synonym: "upregulation of phagocytosis" EXACT []
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0050764 ! regulation of phagocytosis
is_a: GO:0051050 ! positive regulation of transport
relationship: positively_regulates GO:0006909 ! phagocytosis
@@ -304070,7 +303778,7 @@ relationship: positively_regulates GO:0006401 ! RNA catabolic process
id: GO:0050780
name: dopamine receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a dopamine receptor." [GOC:ai]
+def: "Binding to a dopamine receptor." [GOC:ai]
is_a: GO:0001664 ! G protein-coupled receptor binding
[Term]
@@ -304098,7 +303806,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving cocaine, an alkaloid obtained from the dried leaves of the shrub Erythroxylon coca. It is a cerebral stimulant and narcotic." [ISBN:0198506732]
synonym: "cocaine metabolism" EXACT []
is_a: GO:0006725 ! cellular aromatic compound metabolic process
-is_a: GO:0017144 ! drug metabolic process
is_a: GO:0046448 ! tropane alkaloid metabolic process
[Term]
@@ -304111,7 +303818,6 @@ synonym: "cocaine catabolism" EXACT []
synonym: "cocaine degradation" EXACT []
is_a: GO:0009822 ! alkaloid catabolic process
is_a: GO:0019439 ! aromatic compound catabolic process
-is_a: GO:0042737 ! drug catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:0050783 ! cocaine metabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
@@ -304129,7 +303835,7 @@ is_a: GO:0038023 ! signaling receptor activity
id: GO:0050786
name: RAGE receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the RAGE receptor, the receptor for advanced glycation end-products." [GOC:ai]
+def: "Binding to a RAGE receptor, the receptor for advanced glycation end-products." [GOC:ai]
synonym: "advanced glycation end-product receptor binding" EXACT []
is_a: GO:0005102 ! signaling receptor binding
@@ -304191,7 +303897,6 @@ id: GO:0050792
name: regulation of viral process
namespace: biological_process
def: "Any process that modulates the rate or extent of the viral life cycle, the set of processes by which a virus reproduces and spreads among hosts." [GOC:go_curators, GOC:tb]
-synonym: "regulation of viral process" BROAD []
synonym: "regulation of viral reproduction" NARROW [GOC:bf, GOC:jl]
is_a: GO:0050789 ! regulation of biological process
relationship: regulates GO:0016032 ! viral process
@@ -304210,6 +303915,7 @@ name: regulation of cellular process
namespace: biological_process
alt_id: GO:0051244
def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators]
+subset: gocheck_do_not_annotate
synonym: "regulation of cellular physiological process" EXACT []
is_a: GO:0050789 ! regulation of biological process
relationship: regulates GO:0009987 ! cellular process
@@ -304381,10 +304087,9 @@ is_a: GO:0034330 ! cell junction organization
id: GO:0050809
name: diazepam binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with diazepam, one of the most widely used benzodiazepine drugs. It is used as an anti-anxiety-hypnotic agent and has the proprietary name Valium." [ISBN:0198506732]
+def: "Binding to diazepam, one of the most widely used benzodiazepine drugs. It is used as an anti-anxiety-hypnotic agent and has the proprietary name Valium." [ISBN:0198506732]
synonym: "diazepam binding inhibitor activity" RELATED []
synonym: "Valium binding" EXACT []
-is_a: GO:0008144 ! drug binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -304406,7 +304111,7 @@ relationship: regulates GO:0006694 ! steroid biosynthetic process
id: GO:0050811
name: GABA receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the gamma-aminobutyric acid (GABA, 4-aminobutyrate) receptor." [GOC:ai]
+def: "Binding to a gamma-aminobutyric acid (GABA, 4-aminobutyrate) receptor." [GOC:ai]
synonym: "4-aminobutanoate receptor binding" EXACT []
synonym: "4-aminobutyrate receptor binding" EXACT []
synonym: "diazepam binding inhibitor activity" RELATED []
@@ -304460,7 +304165,7 @@ is_a: GO:1901566 ! organonitrogen compound biosynthetic process
id: GO:0050815
name: phosphoserine residue binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a phosphorylated serine residue within a protein." [GOC:ai]
+def: "Binding to a phosphorylated serine residue within a protein." [GOC:ai]
synonym: "phosphoserine binding" RELATED []
is_a: GO:0045309 ! protein phosphorylated amino acid binding
@@ -304468,7 +304173,7 @@ is_a: GO:0045309 ! protein phosphorylated amino acid binding
id: GO:0050816
name: phosphothreonine residue binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a phosphorylated threonine residue within a protein." [GOC:ai]
+def: "Binding to a phosphorylated threonine residue within a protein." [GOC:ai]
synonym: "phosphothreonine binding" RELATED []
is_a: GO:0045309 ! protein phosphorylated amino acid binding
@@ -304555,7 +304260,7 @@ relationship: part_of GO:0048002 ! antigen processing and presentation of peptid
id: GO:0050824
name: obsolete water binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with water (H2O)." [GOC:ai]
+def: "OBSOLETE. Binding to water (H2O)." [GOC:ai]
comment: This term was obsoleted because water binding is non-specific.
is_obsolete: true
@@ -304563,7 +304268,7 @@ is_obsolete: true
id: GO:0050825
name: ice binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ice, water reduced to the solid state by cold temperature. It is a white or transparent colorless substance, crystalline, brittle, and viscoidal." [GOC:curators]
+def: "Binding to ice, water reduced to the solid state by cold temperature. It is a white or transparent colorless substance, crystalline, brittle, and viscoidal." [GOC:curators]
synonym: "antifreeze activity" RELATED []
synonym: "ice crystal binding" EXACT []
synonym: "ice nucleation activity" RELATED []
@@ -304701,7 +304406,7 @@ is_a: GO:0018022 ! peptidyl-lysine methylation
id: GO:0050839
name: cell adhesion molecule binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cell adhesion molecule." [GOC:ai]
+def: "Binding to a cell adhesion molecule." [GOC:ai]
synonym: "adhesive extracellular matrix constituent" RELATED []
synonym: "CAM binding" EXACT []
synonym: "cell adhesion molecule activity" RELATED []
@@ -304712,7 +304417,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0050840
name: extracellular matrix binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a component of the extracellular matrix." [GOC:ai]
+def: "Binding to a component of the extracellular matrix." [GOC:ai]
subset: goslim_chembl
subset: goslim_pir
synonym: "adhesive extracellular matrix constituent" RELATED []
@@ -305235,6 +304940,7 @@ id: GO:0050886
name: endocrine process
namespace: biological_process
def: "The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system." [ISBN:0721662544]
+subset: goslim_generic
subset: goslim_pir
synonym: "endocrine physiological process" EXACT []
synonym: "endocrine physiology" EXACT []
@@ -305322,7 +305028,8 @@ is_a: GO:0008150 ! biological_process
id: GO:0050897
name: cobalt ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cobalt (Co) ion." [GOC:ai]
+def: "Binding to a cobalt ion (Co)." [GOC:ai]
+synonym: "Co ion binding" EXACT []
synonym: "cobalt binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
@@ -305999,6 +305706,7 @@ id: GO:0050959
name: echolocation
namespace: biological_process
def: "Echolocation is the method used by some animals (e.g. bats, dolphins and some whales) to determine the location of something by measuring the time it takes for an echo to return from it. These animals emit sound waves and listen for the echo, calculating the distance to the object from the time lapse between sound emission and the echo returning." [PMID:16005275, Wikipedia:Animal_echolocation]
+synonym: "biological sonar" EXACT [https://en.wikipedia.org/wiki/Animal_echolocation]
synonym: "perception of environment using reflected sound waves" EXACT []
xref: Wikipedia:Echolocation
is_a: GO:0050877 ! nervous system process
@@ -306327,9 +306035,7 @@ id: GO:0050983
name: obsolete deoxyhypusine biosynthetic process from spermidine
namespace: biological_process
def: "OBSOLETE. The chemical reactions resulting in the formation of deoxyhypusine from spermidine by the enzyme [eIF-5A]-deoxyhypusine synthase. The reaction occurs in four steps: 1. spermidine + NAD+ = dehydrospermidine + NADH + H+; 2. dehydrospermidine + [enzyme]-lysine = 1,3-diaminopropane + [enzyme]-lysine-N6=CH(CH2)3NH2; 3. [enzyme]-lysine-N6=CH(CH2)3NH2 = [eIF-5A]-lysine-N6=CH(CH2)3NH2; 4. [eIF-5A]-lysine-N6=CH(CH2)3NH2 + NADH + H+ = [eIF-5A]-deoxyhypusine + NAD+." [MetaCyc:1.1.1.249-RXN]
-comment: The reason for obsoletion is that although GO:0050983 is described as a multistep process, the entire reaction is carried out by a single enzyme, therefore we would define it as the molecular function GO:0034038 deoxyhypusine synthase activity.
-synonym: "(4-aminobutyl)lysine synthase activity" RELATED [EC:2.5.1.46]
-synonym: "[eIF-5A]-deoxyhypusine synthase activity" RELATED [EC:2.5.1.46]
+comment: The reason for obsoletion is that although GO:0050983 is described as a multistep process, the entire reaction is carried out by a single enzyme, therefore was replacey by the molecular function GO:0034038 deoxyhypusine synthase activity.
synonym: "deoxyhypusine anabolism from spermidine, using deoxyhypusine synthase" EXACT []
synonym: "deoxyhypusine biosynthesis from spermidine, using deoxyhypusine synthase" EXACT []
synonym: "deoxyhypusine biosynthetic process from spermidine, using deoxyhypusine synthase" EXACT []
@@ -306337,8 +306043,6 @@ synonym: "deoxyhypusine formation from spermidine, using deoxyhypusine synthase"
synonym: "spermidine breakdown to deoxyhypusine, using deoxyhypusine synthase" EXACT []
synonym: "spermidine catabolic process to deoxyhypusine, using deoxyhypusine synthase" EXACT []
synonym: "spermidine degradation to deoxyhypusine, using deoxyhypusine synthase" EXACT []
-xref: EC:2.5.1.46
-xref: MetaCyc:2.5.1.46-RXN
is_obsolete: true
consider: GO:0034038
@@ -306491,7 +306195,7 @@ relationship: positively_regulates GO:0016042 ! lipid catabolic process
id: GO:0050997
name: quaternary ammonium group binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a quaternary ammonium group, including glycine betaine, choline, carnitine and proline. A quaternary ammonium group is any compound that can be regarded as derived from ammonium hydroxide or an ammonium salt by replacement of all four hydrogen atoms of the NH4+ ion by organic groups." [GOC:ai]
+def: "Binding to a quaternary ammonium group, including glycine betaine, choline, carnitine and proline. A quaternary ammonium group is any compound that can be regarded as derived from ammonium hydroxide or an ammonium salt by replacement of all four hydrogen atoms of the NH4+ ion by organic groups." [GOC:ai]
synonym: "quaternary amine binding" EXACT []
is_a: GO:0005488 ! binding
@@ -306499,7 +306203,7 @@ is_a: GO:0005488 ! binding
id: GO:0050998
name: nitric-oxide synthase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme nitric-oxide synthase." [GOC:ai]
+def: "Binding to nitric-oxide synthase." [GOC:ai]
synonym: "NOS binding" EXACT []
is_a: GO:0019899 ! enzyme binding
@@ -306609,7 +306313,7 @@ is_a: GO:0034072 ! squalene cyclase activity
id: GO:0051008
name: Hsp27 protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with Hsp27 proteins, a lightweight heat shock protein." [GOC:ai]
+def: "Binding to Hsp27 proteins, a lightweight heat shock protein." [GOC:ai]
is_a: GO:0031072 ! heat shock protein binding
[Term]
@@ -306625,14 +306329,14 @@ is_a: GO:0016835 ! carbon-oxygen lyase activity
id: GO:0051010
name: microtubule plus-end binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the plus end of a microtubule." [GOC:ai, PMID:14557818, PMID:14614826]
+def: "Binding to the plus end of a microtubule." [GOC:ai, PMID:14557818, PMID:14614826]
is_a: GO:0008017 ! microtubule binding
[Term]
id: GO:0051011
name: microtubule minus-end binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the minus end of a microtubule." [GOC:ai, PMID:14557818, PMID:14614826]
+def: "Binding to the minus end of a microtubule." [GOC:ai, PMID:14557818, PMID:14614826]
is_a: GO:0008017 ! microtubule binding
[Term]
@@ -306665,7 +306369,7 @@ is_a: GO:0030029 ! actin filament-based process
id: GO:0051015
name: actin filament binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits." [ISBN:0198506732]
+def: "Binding to an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits." [ISBN:0198506732]
synonym: "actin cross-linking activity" RELATED []
synonym: "F-actin binding" EXACT []
is_a: GO:0003779 ! actin binding
@@ -306698,7 +306402,7 @@ is_a: GO:0061572 ! actin filament bundle organization
id: GO:0051018
name: protein kinase A binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any subunit of protein kinase A." [GOC:ai]
+def: "Binding to a protein kinase A." [GOC:ai]
comment: Note that this term is a direct child of 'protein binding ; GO:0005515' because it encompasses binding to either the catalytic or regulatory subunit of protein kinase A, and the latter does not have kinase activity.
synonym: "PKA binding" EXACT []
synonym: "protein kinase A anchoring activity" RELATED []
@@ -306708,7 +306412,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0051019
name: mitogen-activated protein kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mitogen-activated protein kinase." [GOC:ai]
+def: "Binding to a mitogen-activated protein kinase." [GOC:ai]
synonym: "MAP kinase binding" EXACT []
synonym: "MAP-kinase anchoring activity" RELATED []
synonym: "MAPK binding" EXACT []
@@ -306718,14 +306422,14 @@ is_a: GO:0019901 ! protein kinase binding
id: GO:0051020
name: GTPase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a GTPase, any enzyme that catalyzes the hydrolysis of GTP." [GOC:ai]
+def: "Binding to a GTPase, any enzyme that catalyzes the hydrolysis of GTP." [GOC:ai]
is_a: GO:0019899 ! enzyme binding
[Term]
id: GO:0051021
name: GDP-dissociation inhibitor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a GDP-dissociation inhibitor protein." [GOC:ai]
+def: "Binding to a GDP-dissociation inhibitor protein." [GOC:ai]
synonym: "GDI binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -306733,7 +306437,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0051022
name: Rho GDP-dissociation inhibitor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Rho GDP-dissociation inhibitor protein." [GOC:ai]
+def: "Binding to a Rho GDP-dissociation inhibitor protein." [GOC:ai]
synonym: "Rho GDI binding" EXACT []
is_a: GO:0051021 ! GDP-dissociation inhibitor binding
@@ -307112,7 +306816,7 @@ relationship: negatively_regulates GO:0007264 ! small GTPase mediated signal tra
id: GO:0051059
name: NF-kappaB binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters." [GOC:ai]
+def: "Binding to NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters." [GOC:ai]
is_a: GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor binding
[Term]
@@ -307358,18 +307062,11 @@ is_a: GO:0071763 ! nuclear membrane organization
id: GO:0051082
name: unfolded protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an unfolded protein." [GOC:ai]
+def: "Binding to an unfolded protein." [GOC:ai]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_yeast
-synonym: "binding unfolded ER proteins" NARROW []
-synonym: "chaperone activity" RELATED []
-synonym: "fimbrium-specific chaperone activity" NARROW []
-synonym: "glycoprotein-specific chaperone activity" NARROW []
-synonym: "histone-specific chaperone activity" NARROW []
-synonym: "ribosomal chaperone activity" NARROW []
-synonym: "tubulin-specific chaperone activity" NARROW []
+synonym: "chaperone activity" BROAD []
xref: Reactome:R-HSA-9683772 "Trimmed spike protein binds to calnexin"
xref: Reactome:R-HSA-9694337 "Trimmed spike protein binds to calnexin"
is_a: GO:0005515 ! protein binding
@@ -307420,7 +307117,7 @@ is_a: GO:0061077 ! chaperone-mediated protein folding
id: GO:0051087
name: chaperone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport." [PMID:10585443]
+def: "Binding to a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport." [PMID:10585443]
synonym: "chaperone protein binding" EXACT []
synonym: "co-chaperone activity" RELATED []
synonym: "co-chaperonin activity" RELATED []
@@ -307516,7 +307213,7 @@ id: GO:0051095
name: regulation of helicase activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of helicase activity." [GOC:ai]
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
is_a: GO:0050790 ! regulation of catalytic activity
[Term]
@@ -307529,7 +307226,7 @@ synonym: "stimulation of helicase activity" NARROW []
synonym: "up regulation of helicase activity" EXACT []
synonym: "up-regulation of helicase activity" EXACT []
synonym: "upregulation of helicase activity" EXACT []
-is_a: GO:0032781 ! positive regulation of ATPase activity
+is_a: GO:0032781 ! positive regulation of ATP-dependent activity
is_a: GO:0043085 ! positive regulation of catalytic activity
is_a: GO:0051095 ! regulation of helicase activity
@@ -307542,7 +307239,7 @@ synonym: "down regulation of helicase activity" EXACT []
synonym: "down-regulation of helicase activity" EXACT []
synonym: "downregulation of helicase activity" EXACT []
synonym: "inhibition of helicase activity" NARROW []
-is_a: GO:0032780 ! negative regulation of ATPase activity
+is_a: GO:0032780 ! negative regulation of ATP-dependent activity
is_a: GO:0043086 ! negative regulation of catalytic activity
is_a: GO:0051095 ! regulation of helicase activity
@@ -307743,7 +307440,7 @@ is_a: GO:0051003 ! ligase activity, forming nitrogen-metal bonds, forming coordi
id: GO:0051117
name: ATPase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP." [GOC:ai]
+def: "Binding to an ATPase, any enzyme that catalyzes the hydrolysis of ATP." [GOC:ai]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -307830,7 +307527,7 @@ id: GO:0051125
name: regulation of actin nucleation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of actin nucleation, the initial step in the formation of an actin filament in which actin monomers combine to form a new filament." [GOC:ai]
-is_a: GO:0030833 ! regulation of actin filament polymerization
+is_a: GO:0110053 ! regulation of actin filament organization
relationship: regulates GO:0045010 ! actin nucleation
[Term]
@@ -307857,8 +307554,9 @@ synonym: "stimulation of actin nucleation" NARROW []
synonym: "up regulation of actin nucleation" EXACT []
synonym: "up-regulation of actin nucleation" EXACT []
synonym: "upregulation of actin nucleation" EXACT []
-is_a: GO:0030838 ! positive regulation of actin filament polymerization
is_a: GO:0051125 ! regulation of actin nucleation
+is_a: GO:0051495 ! positive regulation of cytoskeleton organization
+is_a: GO:1902905 ! positive regulation of supramolecular fiber organization
relationship: positively_regulates GO:0045010 ! actin nucleation
[Term]
@@ -307913,7 +307611,7 @@ def: "The aggregation, arrangement and bonding together of a set of components t
synonym: "cellular chaperone-mediated protein complex assembly" EXACT []
synonym: "chaperone activity" RELATED []
synonym: "protein complex assembly, multichaperone pathway" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0051132
@@ -308669,7 +308367,7 @@ relationship: part_of GO:0009059 ! macromolecule biosynthetic process
id: GO:0051192
name: prosthetic group binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a prosthetic group, the non-amino acid portion of certain protein molecules. Prosthetic groups may be inorganic or organic and are usually required for the biological activity of the protein." [GOC:ai, GOC:vw]
+def: "Binding to a prosthetic group, the non-amino acid portion of certain protein molecules. Prosthetic groups may be inorganic or organic and are usually required for the biological activity of the protein." [GOC:ai, GOC:vw]
is_a: GO:0005488 ! binding
[Term]
@@ -308910,7 +308608,8 @@ is_a: GO:0016049 ! cell growth
id: GO:0051212
name: vanadium ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with vanadium (V) ions." [GOC:ai]
+def: "Binding to a vanadium ion (V)." [GOC:ai]
+synonym: "V ion binding" EXACT []
is_a: GO:0046914 ! transition metal ion binding
[Term]
@@ -308983,7 +308682,7 @@ is_a: GO:0050844 ! peptidyl-selenocysteine modification
id: GO:0051219
name: phosphoprotein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a phosphorylated protein." [GOC:ai]
+def: "Binding to a phosphorylated protein." [GOC:ai]
subset: goslim_chembl
synonym: "phosphorylated protein binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -309061,7 +308760,7 @@ synonym: "bipolar spindle formation" EXACT []
synonym: "spindle biosynthesis" EXACT []
synonym: "spindle formation" EXACT []
is_a: GO:0007051 ! spindle organization
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:0051228
@@ -309412,7 +309111,7 @@ subset: goslim_pir
synonym: "protein polymer biosynthesis" EXACT []
synonym: "protein polymer biosynthetic process" EXACT []
synonym: "protein polymer formation" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0051259
@@ -309450,7 +309149,7 @@ synonym: "protein polymer breakdown" EXACT []
synonym: "protein polymer catabolic process" EXACT []
synonym: "protein polymer catabolism" EXACT []
synonym: "protein polymer degradation" EXACT []
-is_a: GO:0043624 ! cellular protein complex disassembly
+is_a: GO:0032984 ! protein-containing complex disassembly
[Term]
id: GO:0051262
@@ -309616,7 +309315,6 @@ alt_id: GO:0051277
def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [GOC:ai, GOC:dph, GOC:jl, GOC:mah]
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_pir
synonym: "chromosome organisation" EXACT []
synonym: "chromosome organization and biogenesis" RELATED [GOC:mah]
@@ -309790,7 +309488,7 @@ id: GO:0051287
name: NAD binding
namespace: molecular_function
alt_id: GO:0051288
-def: "Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH." [GOC:ai]
+def: "Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH." [GOC:ai]
subset: goslim_chembl
synonym: "NAD or NADH binding" RELATED [GOC:mah]
synonym: "NAD+ or NADH binding" RELATED []
@@ -309846,7 +309544,6 @@ synonym: "nuclear pore complex biosynthesis" EXACT []
synonym: "nuclear pore complex formation" EXACT []
synonym: "nuclear pore formation" EXACT []
is_a: GO:0006999 ! nuclear pore organization
-is_a: GO:0034622 ! cellular protein-containing complex assembly
is_a: GO:0046931 ! pore complex assembly
[Term]
@@ -309934,7 +309631,6 @@ def: "The process resulting in division and partitioning of components of a cell
comment: Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
subset: goslim_chembl
subset: goslim_drosophila
-subset: goslim_generic
subset: goslim_pir
xref: Wikipedia:Cell_division
is_a: GO:0009987 ! cellular process
@@ -310248,6 +309944,7 @@ namespace: biological_process
def: "The cell cycle phase, following G1, during which DNA synthesis takes place as part of a meiotic cell cycle." [GOC:mtg_cell_cycle]
comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
subset: gocheck_do_not_annotate
+synonym: "premeiotic S-phase" EXACT []
synonym: "S phase of meiotic cell cycle" EXACT []
synonym: "S-phase of meiotic cell cycle" EXACT []
is_a: GO:0051320 ! S phase
@@ -310284,7 +309981,7 @@ relationship: part_of GO:0007135 ! meiosis II
id: GO:0051336
name: regulation of hydrolase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [EC:3.-.-.-, GOC:ai]
+def: "Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [GOC:ai]
synonym: "hydrolase regulator" EXACT []
is_a: GO:0050790 ! regulation of catalytic activity
@@ -310301,7 +309998,7 @@ is_a: GO:0000280 ! nuclear division
id: GO:0051338
name: regulation of transferase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [EC:2.-.-.-, GOC:ai]
+def: "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [GOC:ai]
comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
subset: gocheck_do_not_manually_annotate
synonym: "transferase regulator" EXACT []
@@ -310311,7 +310008,7 @@ is_a: GO:0050790 ! regulation of catalytic activity
id: GO:0051339
name: regulation of lyase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [EC:4.-.-.-, GOC:ai]
+def: "Any process that modulates the frequency, rate or extent of lyase activity, the catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring." [GOC:ai]
synonym: "lyase regulator" EXACT []
is_a: GO:0050790 ! regulation of catalytic activity
@@ -310319,7 +310016,7 @@ is_a: GO:0050790 ! regulation of catalytic activity
id: GO:0051340
name: regulation of ligase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6." [EC:6.-.-.-, GOC:ai]
+def: "Any process that modulates the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6." [GOC:ai]
synonym: "ligase regulator" EXACT []
is_a: GO:0050790 ! regulation of catalytic activity
@@ -310327,7 +310024,7 @@ is_a: GO:0050790 ! regulation of catalytic activity
id: GO:0051341
name: regulation of oxidoreductase activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [EC:1.-.-.-, GOC:ai]
+def: "Any process that modulates the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GOC:ai]
synonym: "oxidoreductase regulator" EXACT []
is_a: GO:0050790 ! regulation of catalytic activity
@@ -310704,7 +310401,7 @@ is_a: GO:0051366 ! protein decanoylation
id: GO:0051370
name: obsolete ZASP binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with Z-band alternatively spliced PDZ motif protein (ZASP). ZASP is a Z-band protein specifically expressed in heart and skeletal muscle. This protein contains N-terminal PDZ domain and C-terminal LIM domain." [PMID:10427098, PMID:11699871]
+def: "OBSOLETE. Binding to Z-band alternatively spliced PDZ motif protein (ZASP). ZASP is a Z-band protein specifically expressed in heart and skeletal muscle. This protein contains N-terminal PDZ domain and C-terminal LIM domain." [PMID:10427098, PMID:11699871]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "Z-band alternatively spliced PDZ-motif protein binding" EXACT []
synonym: "ZASP binding" EXACT []
@@ -310715,7 +310412,7 @@ replaced_by: GO:0008092
id: GO:0051371
name: muscle alpha-actinin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with muscle isoforms of actinin. Muscle alpha-actinin isoforms are found in skeletal and cardiac muscle and are localized to the Z-disc." [PMID:10984498, PMID:11699871, PMID:15014165]
+def: "Binding to muscle isoforms of actinin. Muscle alpha-actinin isoforms are found in skeletal and cardiac muscle and are localized to the Z-disc." [PMID:10984498, PMID:11699871, PMID:15014165]
synonym: "alpha-actinin 2 binding" NARROW []
synonym: "alpha-actinin 3 binding" NARROW []
is_a: GO:0051393 ! alpha-actinin binding
@@ -310727,7 +310424,7 @@ namespace: molecular_function
alt_id: GO:0051374
alt_id: GO:0051375
alt_id: GO:0051376
-def: "Interacting selectively and non-covalently with a member of the FATZ family of proteins, filamin-, actinin-, and telethonin-binding proteins of the Z-disc of striated muscle. FATZ proteins are located in the Z-disc of the sarcomere and are involved in a complex network of interactions with other Z-band components." [PMID:10984498, PMID:11699871]
+def: "Binding to a member of the FATZ family of proteins, filamin-, actinin-, and telethonin-binding proteins of the Z-disc of striated muscle. FATZ proteins are located in the Z-disc of the sarcomere and are involved in a complex network of interactions with other Z-band components." [PMID:10984498, PMID:11699871]
synonym: "calsarcin 1 binding" EXACT []
synonym: "calsarcin 2 binding" EXACT []
synonym: "calsarcin 3 binding" EXACT []
@@ -310754,7 +310451,7 @@ is_a: GO:0016780 ! phosphotransferase activity, for other substituted phosphate
id: GO:0051378
name: serotonin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." [GOC:ai]
+def: "Binding to serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." [GOC:ai]
synonym: "5-hydroxytryptamine binding" EXACT []
is_a: GO:0043169 ! cation binding
is_a: GO:0043176 ! amine binding
@@ -310765,7 +310462,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0051379
name: epinephrine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine." [GOC:ai]
+def: "Binding to epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine." [GOC:ai]
synonym: "adrenaline binding" EXACT []
is_a: GO:1901338 ! catecholamine binding
@@ -310773,7 +310470,7 @@ is_a: GO:1901338 ! catecholamine binding
id: GO:0051380
name: norepinephrine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with norepinephrine, (3,4-dihydroxyphenyl-2-aminoethanol), a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine." [GOC:ai]
+def: "Binding to norepinephrine, (3,4-dihydroxyphenyl-2-aminoethanol), a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine." [GOC:ai]
synonym: "noradrenaline binding" EXACT []
is_a: GO:1901338 ! catecholamine binding
@@ -310781,7 +310478,7 @@ is_a: GO:1901338 ! catecholamine binding
id: GO:0051381
name: histamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:ai]
+def: "Binding to histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:ai]
is_a: GO:0043169 ! cation binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -310796,9 +310493,9 @@ synonym: "centromere and kinetochore complex maturation" NARROW []
synonym: "centromere/kinetochore complex maturation" NARROW []
synonym: "chromosome-kinetochore attachment" NARROW [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "kinetochore formation" RELATED []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
is_a: GO:0051383 ! kinetochore organization
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0065003 ! protein-containing complex assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
relationship: part_of GO:0034508 ! centromere complex assembly
[Term]
@@ -310877,27 +310574,29 @@ relationship: positively_regulates GO:0048011 ! neurotrophin TRK receptor signal
[Term]
id: GO:0051389
-name: inactivation of MAPKK activity
+name: obsolete inactivation of MAPKK activity
namespace: biological_process
-def: "Any process that terminates the activity of the active enzyme MAP kinase kinase (MAPKK)." [GOC:ai]
+def: "OBSOLETE. Any process that terminates the activity of the active enzyme MAP kinase kinase (MAPKK)." [GOC:ai]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "inactivation of MAP kinase kinase activity" EXACT []
synonym: "termination of MAP kinase kinase activity" EXACT []
synonym: "termination of MAPKK activity" EXACT []
-is_a: GO:0006469 ! negative regulation of protein kinase activity
-is_a: GO:0043405 ! regulation of MAP kinase activity
-is_a: GO:0043409 ! negative regulation of MAPK cascade
+is_obsolete: true
+consider: GO:0030291
+consider: GO:0043409
[Term]
id: GO:0051390
-name: inactivation of MAPKKK activity
+name: obsolete inactivation of MAPKKK activity
namespace: biological_process
-def: "Any process that terminates the activity of the active enzyme MAP kinase kinase kinase (MAPKKK)." [GOC:ai]
+def: "OBSOLETE. Any process that terminates the activity of the active enzyme MAP kinase kinase kinase (MAPKKK)." [GOC:ai]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "inactivation of MAP kinase kinase kinase activity" EXACT []
synonym: "termination of MAP kinase kinase kinase activity" EXACT []
synonym: "termination of MAPKKK activity" EXACT []
-is_a: GO:0043405 ! regulation of MAP kinase activity
-is_a: GO:0043409 ! negative regulation of MAPK cascade
-is_a: GO:0071901 ! negative regulation of protein serine/threonine kinase activity
+is_obsolete: true
+consider: GO:0030291
+consider: GO:0043409
[Term]
id: GO:0051391
@@ -310920,7 +310619,7 @@ id: GO:0051393
name: alpha-actinin binding
namespace: molecular_function
alt_id: GO:0051372
-def: "Interacting selectively and non-covalently with alpha-actinin, one of a family of proteins that cross-link F-actin as antiparallel homodimers. Alpha-actinin has a molecular mass of 93-103 KDa; at the N-terminus there are two calponin homology domains, at the C-terminus there are two EF-hands. These two domains are connected by the rod domain. This domain is formed by triple-helical spectrin repeats." [PMID:10984498, PMID:11699871, PMID:15014165]
+def: "Binding to alpha-actinin, one of a family of proteins that cross-link F-actin as antiparallel homodimers. Alpha-actinin has a molecular mass of 93-103 KDa; at the N-terminus there are two calponin homology domains, at the C-terminus there are two EF-hands. These two domains are connected by the rod domain. This domain is formed by triple-helical spectrin repeats." [PMID:10984498, PMID:11699871, PMID:15014165]
synonym: "alpha-actinin 1 binding" NARROW []
synonym: "alpha-actinin 4 binding" NARROW []
synonym: "nonmuscle alpha-actinin binding" NARROW []
@@ -311002,7 +310701,7 @@ replaced_by: GO:0004177
id: GO:0051400
name: BH domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the Bcl-2 homology (BH) domain of a protein. Bcl-2-related proteins share homology in one to four conserved regions designated the Bcl-2 homology (BH) domains BH1, BH2, BH3 and BH4. These domains contribute at multiple levels to the function of these proteins in cell death and survival. Anti-apoptotic members of the Bcl-2 family have four BH domains (BH1-BH4). Pro-apoptotic members have fewer BH domains." [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409]
+def: "Binding to a Bcl-2 homology (BH) protein domain. Bcl-2-related proteins share homology in one to four conserved regions designated the Bcl-2 homology (BH) domains BH1, BH2, BH3 and BH4. These domains contribute at multiple levels to the function of these proteins in cell death and survival. Anti-apoptotic members of the Bcl-2 family have four BH domains (BH1-BH4). Pro-apoptotic members have fewer BH domains." [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409]
subset: goslim_chembl
synonym: "Bcl-2 homology domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -311011,7 +310710,7 @@ is_a: GO:0019904 ! protein domain specific binding
id: GO:0051401
name: CH domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the calponin homology domain of a protein, a domain of 100 residues that occurs in signaling and cytoskeletal proteins." [PMID:11911887, Prosite:PDOC50021]
+def: "Binding to a calponin homology protein domain, a domain of 100 residues that occurs in signaling and cytoskeletal proteins." [PMID:11911887, Prosite:PDOC50021]
synonym: "calponin homology domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -311198,7 +310897,7 @@ is_a: GO:0051418 ! microtubule nucleation by microtubule organizing center
id: GO:0051416
name: obsolete myotilin binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with myotilin, a structural component of the Z-discs in human skeletal and cardiac muscle. Its C-terminus contains two immunoglobulin-like domains and the unique N-terminal half has a serine-rich region, with numerous potential phosphorylation sites, and a stretch of hydrophobic amino acids. Myotilin forms homodimers and binds to alpha-actinin, F-actin, and filamin C." [PMID:11699871, PMID:15752755]
+def: "OBSOLETE. Binding to myotilin, a structural component of the Z-discs in human skeletal and cardiac muscle. Its C-terminus contains two immunoglobulin-like domains and the unique N-terminal half has a serine-rich region, with numerous potential phosphorylation sites, and a stretch of hydrophobic amino acids. Myotilin forms homodimers and binds to alpha-actinin, F-actin, and filamin C." [PMID:11699871, PMID:15752755]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "myotilin binding" EXACT []
is_obsolete: true
@@ -311229,7 +310928,7 @@ is_a: GO:0007020 ! microtubule nucleation
id: GO:0051419
name: obsolete nebulin binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with nebulin, a large protein (approximately 800kD) that is anchored at the Z-disc by its C-terminal region and spans the length of the thin filament, ending at the edge of the H-zone." [PMID:11699871]
+def: "OBSOLETE. Binding to nebulin, a large protein (approximately 800kD) that is anchored at the Z-disc by its C-terminal region and spans the length of the thin filament, ending at the edge of the H-zone." [PMID:11699871]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "nebulin binding" EXACT []
is_obsolete: true
@@ -311239,7 +310938,7 @@ replaced_by: GO:0008092
id: GO:0051420
name: obsolete nebulette binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with nebulette, a 107 kDa protein associated with the I-Z-I complex of cardiac myofibrils. It shows a high degree of homology with skeletal muscle nebulin." [PMID:11699871]
+def: "OBSOLETE. Binding to nebulette, a 107 kDa protein associated with the I-Z-I complex of cardiac myofibrils. It shows a high degree of homology with skeletal muscle nebulin." [PMID:11699871]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "nebulette binding" EXACT []
is_obsolete: true
@@ -311288,7 +310987,7 @@ id: GO:0051424
name: corticotropin-releasing hormone binding
namespace: molecular_function
alt_id: GO:0017047
-def: "Interacting selectively and non-covalently with corticotropin-releasing hormone, a polypeptide hormone involved in the stress response. It is released by the hypothalamus and stimulates the release of corticotropin by the anterior pituitary gland." [PMID:7556876]
+def: "Binding to corticotropin-releasing hormone, a polypeptide hormone involved in the stress response. It is released by the hypothalamus and stimulates the release of corticotropin by the anterior pituitary gland." [PMID:7556876]
synonym: "corticoliberin binding" EXACT []
synonym: "corticotropin-releasing factor binding" EXACT []
synonym: "CRF binding" EXACT [GOC:bf]
@@ -311299,7 +310998,7 @@ is_a: GO:0017046 ! peptide hormone binding
id: GO:0051425
name: PTB domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a phosphotyrosine-binding (PTB) domain of a protein." [Pfam:PF02174.5, PMID:15924411]
+def: "Binding to a phosphotyrosine-binding (PTB) Binding to a phosphotyrosine-bindin domain." [Pfam:PF02174.5, PMID:15924411]
synonym: "phosphotyrosine-interacting domain binding" EXACT []
synonym: "PID binding" BROAD []
is_a: GO:0019904 ! protein domain specific binding
@@ -311308,14 +311007,14 @@ is_a: GO:0019904 ! protein domain specific binding
id: GO:0051427
name: hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a receptor for hormones." [GOC:ai]
+def: "Binding to a receptor for a hormone." [GOC:ai]
is_a: GO:0005102 ! signaling receptor binding
[Term]
id: GO:0051428
name: peptide hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a receptor for peptide hormones." [GOC:ai]
+def: "Binding to a receptor for a peptide hormone." [GOC:ai]
subset: goslim_chembl
synonym: "polypeptide hormone receptor binding" EXACT []
is_a: GO:0051427 ! hormone receptor binding
@@ -311325,7 +311024,7 @@ id: GO:0051429
name: corticotropin-releasing hormone receptor binding
namespace: molecular_function
alt_id: GO:0031742
-def: "Interacting selectively and non-covalently with a receptor for corticotropin-releasing hormone (CRH), a polypeptide hormone involved in the stress response. It is released by the hypothalamus and stimulates the release of corticotropin by the anterior pituitary gland." [GOC:ai]
+def: "Binding to a receptor for corticotropin-releasing hormone (CRH), a polypeptide hormone involved in the stress response. It is released by the hypothalamus and stimulates the release of corticotropin by the anterior pituitary gland." [GOC:ai]
synonym: "corticotropin releasing factor receptor binding" EXACT []
synonym: "corticotropin releasing factor receptor ligand" NARROW []
synonym: "corticotropin-releasing factor receptor binding" EXACT [GOC:bf]
@@ -311340,7 +311039,7 @@ id: GO:0051430
name: corticotropin-releasing hormone receptor 1 binding
namespace: molecular_function
alt_id: GO:0031743
-def: "Interacting selectively and non-covalently with the corticotropin-releasing hormone receptor 1 (CRHR1). CRHR1 is the major subtype in the pituitary corticotroph, and mediates the stimulatory actions of corticotropin-releasing hormone on corticotropin hormone secretion. CRHR1 are also located in cortical areas of the brain, cerebellum and limbic system." [PMID:15134857]
+def: "Binding to a corticotropin-releasing hormone receptor 1 (CRHR1). CRHR1 is the major subtype in the pituitary corticotroph, and mediates the stimulatory actions of corticotropin-releasing hormone on corticotropin hormone secretion. CRHR1 are also located in cortical areas of the brain, cerebellum and limbic system." [PMID:15134857]
synonym: "CRHR1 binding" EXACT []
synonym: "type 1 corticotropin releasing factor receptor binding" EXACT []
synonym: "type 1 corticotropin releasing factor receptor ligand" NARROW []
@@ -311352,7 +311051,7 @@ id: GO:0051431
name: corticotropin-releasing hormone receptor 2 binding
namespace: molecular_function
alt_id: GO:0031744
-def: "Interacting selectively and non-covalently with the corticotropin-releasing hormone receptor type 2 (CRHR2). The CRHR2 has several splice variants that are located in sub-cortical areas of the brain and in the periphery." [PMID:15134857]
+def: "Binding to a corticotropin-releasing hormone receptor type 2 (CRHR2). The CRHR2 has several splice variants that are located in sub-cortical areas of the brain and in the periphery." [PMID:15134857]
synonym: "CRHR2 binding" EXACT []
synonym: "type 2 corticotropin releasing factor receptor binding" EXACT []
synonym: "type 2 corticotropin releasing factor receptor ligand" NARROW []
@@ -311363,21 +311062,21 @@ is_a: GO:0051429 ! corticotropin-releasing hormone receptor binding
id: GO:0051432
name: BH1 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the BH1 domain of a protein of the Bcl-2 family. Proteins that act as inhibitors of apoptosis harbour at least three BH domains: BH1, BH2 and BH3; the BH1 and BH2 domains are found in all death antagonists of the Bcl-2 family but only in one class of death agonists." [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01080]
+def: "Binding to a BH1 protein domain, present in Bcl-2 family members. Proteins that act as inhibitors of apoptosis harbour at least three BH domains: BH1, BH2 and BH3; the BH1 and BH2 domains are found in all death antagonists of the Bcl-2 family but only in one class of death agonists." [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01080]
is_a: GO:0051400 ! BH domain binding
[Term]
id: GO:0051433
name: BH2 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the BH2 domain of a protein of the Bcl-2 family. Proteins that act as inhibitors of apoptosis harbour at least three BH domains: BH1, BH2 and BH3; the BH1 and BH2 domains are found in all death antagonists of the Bcl-2 family but only in one class of death agonists." [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01258]
+def: "Binding to a BH2 protein domain, present in Bcl-2 family members. Proteins that act as inhibitors of apoptosis harbour at least three BH domains: BH1, BH2 and BH3; the BH1 and BH2 domains are found in all death antagonists of the Bcl-2 family but only in one class of death agonists." [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01258]
is_a: GO:0051400 ! BH domain binding
[Term]
id: GO:0051434
name: BH3 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the BH3 domain of a protein of the Bcl-2 family. The BH3 domain is a potent death domain and has an important role in protein-protein interactions and in cell death." [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01259]
+def: "Binding to a BH3 protein domain, present in Bcl-2 family members. The BH3 domain is a potent death domain and has an important role in protein-protein interactions and in cell death." [PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01259]
subset: goslim_chembl
is_a: GO:0051400 ! BH domain binding
is_a: GO:0070513 ! death domain binding
@@ -311386,7 +311085,7 @@ is_a: GO:0070513 ! death domain binding
id: GO:0051435
name: BH4 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the BH4 domain of a protein of the Bcl-2 family. All anti-apoptotic proteins contain BH1 and BH2 domains; some also contain an additional N-terminal BH4 domain, which is almost never seen in pro-apoptotic proteins. Loss of the BH4 domain can diminish or abrogate anti-apoptotic function or even impart outright death-promoting properties to the protein." [InterPro:IPR003093, PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01260, Prosite:PS50063]
+def: "Binding to a BH4 protein domain, present in Bcl-2 family members. All anti-apoptotic proteins contain BH1 and BH2 domains; some also contain an additional N-terminal BH4 domain, which is almost never seen in pro-apoptotic proteins. Loss of the BH4 domain can diminish or abrogate anti-apoptotic function or even impart outright death-promoting properties to the protein." [InterPro:IPR003093, PMID:11048732, PMID:12133724, PMID:9020082, PMID:9704409, Prosite:PS01260, Prosite:PS50063]
is_a: GO:0051400 ! BH domain binding
[Term]
@@ -311624,7 +311323,7 @@ relationship: negatively_regulates GO:0051321 ! meiotic cell cycle
id: GO:0051448
name: gonadotropin-releasing hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with gonadotropin-releasing hormone (GnRH), a peptide hormone responsible for the release of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) from the anterior pituitary. GnRH is synthesized and released by the hypothalamus." [GOC:pr, PMID:1984190]
+def: "Binding to gonadotropin-releasing hormone (GnRH), a peptide hormone responsible for the release of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) from the anterior pituitary. GnRH is synthesized and released by the hypothalamus." [GOC:pr, PMID:1984190]
synonym: "GnRH binding" EXACT []
synonym: "gonadotrophin releasing hormone binding" EXACT []
is_a: GO:0017046 ! peptide hormone binding
@@ -311633,7 +311332,7 @@ is_a: GO:0017046 ! peptide hormone binding
id: GO:0051449
name: thyrotropin-releasing hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with thyrotropin-releasing hormone, a tripeptide hormone that stimulates the release of thyroid-stimulating hormone (TSH) and prolactin by the anterior pituitary and it is produced by the hypothalamus and travels across the median eminence to the pituitary via the pituitary portal system." [GOC:ai]
+def: "Binding to thyrotropin-releasing hormone, a tripeptide hormone that stimulates the release of thyroid-stimulating hormone (TSH) and prolactin by the anterior pituitary and it is produced by the hypothalamus and travels across the median eminence to the pituitary via the pituitary portal system." [GOC:ai]
synonym: "thyrotropin releasing hormone binding" EXACT []
is_a: GO:0017046 ! peptide hormone binding
@@ -312003,7 +311702,6 @@ synonym: "cytosolic calcium ion concentration regulation" EXACT []
synonym: "regulation of calcium ion concentration in cytoplasm" BROAD []
synonym: "regulation of calcium ion concentration in cytosol" EXACT []
synonym: "regulation of cytoplasmic calcium ion concentration" BROAD []
-synonym: "regulation of cytosolic calcium ion concentration" EXACT []
is_a: GO:0006874 ! cellular calcium ion homeostasis
[Term]
@@ -312486,7 +312184,7 @@ alt_id: GO:0051527
alt_id: GO:0051528
alt_id: GO:0051529
alt_id: GO:0051530
-def: "Interacting selectively and non-covalently with NFAT (nuclear factor of activated T cells) proteins, a family of transcription factors. NFAT proteins have crucial roles in the development and function of the immune system." [PMID:15928679]
+def: "Binding to NFAT (nuclear factor of activated T cells) proteins, a family of transcription factors. NFAT proteins have crucial roles in the development and function of the immune system." [PMID:15928679]
synonym: "NFAT binding" EXACT []
synonym: "NFAT1 protein binding" NARROW []
synonym: "NFAT2 protein binding" NARROW []
@@ -312508,7 +312206,7 @@ is_a: GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor b
id: GO:0051536
name: iron-sulfur cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms." [GOC:ai]
+def: "Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms." [GOC:ai]
subset: goslim_metagenomics
synonym: "Fe/S binding" EXACT []
synonym: "iron sulfur cluster binding" EXACT []
@@ -312520,7 +312218,7 @@ is_a: GO:0051540 ! metal cluster binding
id: GO:0051537
name: 2 iron, 2 sulfur cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands." [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
+def: "Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands." [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
synonym: "2 Fe 2 S cluster binding" EXACT []
synonym: "2 iron, 2 sulphur cluster binding" EXACT []
synonym: "2Fe-2S cluster binding" EXACT []
@@ -312534,7 +312232,7 @@ is_a: GO:0051536 ! iron-sulfur cluster binding
id: GO:0051538
name: 3 iron, 4 sulfur cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing." [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
+def: "Binding to a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing." [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
synonym: "3 Fe 4 S cluster binding" EXACT []
synonym: "3 iron, 4 sulphur cluster binding" EXACT []
synonym: "3Fe-4S cluster binding" EXACT []
@@ -312548,7 +312246,7 @@ is_a: GO:0051536 ! iron-sulfur cluster binding
id: GO:0051539
name: 4 iron, 4 sulfur cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands." [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
+def: "Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands." [GOC:ai, PMID:15952888, Wikipedia:Iron-sulfur_cluster]
synonym: "4 Fe 4 S cluster binding" EXACT []
synonym: "4 iron, 4 sulphur cluster binding" EXACT []
synonym: "4Fe-4S cluster binding" EXACT []
@@ -312562,7 +312260,7 @@ is_a: GO:0051536 ! iron-sulfur cluster binding
id: GO:0051540
name: metal cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a cluster of atoms including both metal ions and nonmetal atoms, usually sulfur and oxygen. Examples include iron-sulfur clusters and nickel-iron-sulfur clusters." [GOC:jsg]
+def: "Binding to a cluster of atoms including both metal ions and nonmetal atoms, usually sulfur and oxygen. Examples include iron-sulfur clusters and nickel-iron-sulfur clusters." [GOC:jsg]
subset: goslim_pir
is_a: GO:0005488 ! binding
@@ -313211,7 +312909,7 @@ namespace: biological_process
def: "Any process in which an exocyst is transported to, or maintained in, a specific location. An exocyst is a protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse." [GOC:ai]
synonym: "establishment and maintenance of exocyst localization" EXACT []
synonym: "exocyst localisation" EXACT [GOC:mah]
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
[Term]
id: GO:0051602
@@ -313613,7 +313311,7 @@ id: GO:0051635
name: obsolete bacterial cell surface binding
namespace: molecular_function
alt_id: GO:0008367
-def: "OBSOLETE. Interacting selectively and non-covalently with any component on the surface of a bacterial cell." [GOC:ai]
+def: "OBSOLETE. Binding to a component on the surface of a bacterial cell." [GOC:ai]
comment: This term was made obsolete because it is ambiguous and causing confusion, and is an unnecessary grouping term.
synonym: "bacterial binding" EXACT []
synonym: "bacterial cell surface binding" EXACT []
@@ -313630,7 +313328,7 @@ id: GO:0051636
name: obsolete Gram-negative bacterial cell surface binding
namespace: molecular_function
alt_id: GO:0008368
-def: "OBSOLETE. Interacting selectively and non-covalently with any component on the surface of a Gram-negative bacterial cell." [GOC:ai]
+def: "OBSOLETE. Binding to a component on the surface of a Gram-negative bacterial cell." [GOC:ai]
comment: This term was made obsolete because it is an unnecessary grouping term and was causing confusion.
synonym: "binding to Gram-negative bacterium" EXACT []
synonym: "Gram-negative bacterial binding" EXACT []
@@ -313646,7 +313344,7 @@ id: GO:0051637
name: obsolete Gram-positive bacterial cell surface binding
namespace: molecular_function
alt_id: GO:0051076
-def: "OBSOLETE. Interacting selectively and non-covalently with any component on the surface of a Gram-positive bacterium." [GOC:ai]
+def: "OBSOLETE. Binding to a component on the surface of a Gram-positive bacterium." [GOC:ai]
comment: This term was made obsolete because it is an unnecessary grouping term and was causing confusion.
synonym: "binding to Gram-positive bacterium" EXACT []
synonym: "Gram-positive bacterial binding" EXACT []
@@ -313955,8 +313653,8 @@ synonym: "nuclear pore distribution" RELATED []
synonym: "nuclear pore localisation" EXACT [GOC:mah]
synonym: "positioning of nuclear pores" RELATED []
is_a: GO:0006997 ! nucleus organization
-is_a: GO:0034629 ! cellular protein-containing complex localization
-is_a: GO:0072657 ! protein localization to membrane
+is_a: GO:0031503 ! protein-containing complex localization
+is_a: GO:0051668 ! localization within membrane
[Term]
id: GO:0051665
@@ -314031,9 +313729,10 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
[Term]
id: GO:0051671
-name: induction of autolysin activity in other organism
+name: obsolete induction of autolysin activity in other organism
namespace: biological_process
-def: "Any process in which an organism initiates the activity of the inactive enzyme autolysin in another organism. The autolysin enzyme belongs to, and is active in, the other organism." [GOC:ai]
+def: "OBSOLETE. Any process in which an organism initiates the activity of the inactive enzyme autolysin in another organism. The autolysin enzyme belongs to, and is active in, the other organism." [GOC:ai]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of autolysin activity in another organism" EXACT []
synonym: "activation of autolysis in other organism" NARROW []
synonym: "activation of autolytic activity in other organism" NARROW []
@@ -314041,31 +313740,29 @@ synonym: "induction of autolysin activity in another organism" EXACT [GOC:bf]
synonym: "induction of autolysis in other organism" NARROW []
synonym: "induction of autolytic activity in other organism" NARROW []
synonym: "positive regulation of autolysin activity in another organism" BROAD []
-is_a: GO:0043946 ! positive regulation of catalytic activity in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0051672
-name: catabolism by organism of cell wall peptidoglycan in other organism
+name: obsolete catabolism by organism of cell wall peptidoglycan in other organism
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of the cell wall peptidoglycans of another organism." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of the cell wall peptidoglycans of another organism." [GOC:ai]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolic process of cell wall peptidoglycans of other organism" EXACT []
synonym: "catabolism of cell wall peptidoglycans of other organism" EXACT []
synonym: "cell wall catabolic process in other organism" NARROW []
synonym: "cell wall catabolism in other organism" NARROW []
synonym: "cell wall peptidoglycan catabolic process in another organism" EXACT []
-is_a: GO:0009253 ! peptidoglycan catabolic process
-is_a: GO:0044041 ! multi-organism carbohydrate catabolic process
-relationship: part_of GO:0009617 ! response to bacterium
-relationship: part_of GO:0044278 ! cell wall disruption in other organism
+is_obsolete: true
[Term]
id: GO:0051673
-name: membrane disruption in other organism
+name: membrane disruption in another organism
namespace: biological_process
def: "The disruption of the membranes of another organism, leading to damage to its cells and possibly death of that organism." [GOC:ai]
synonym: "cytolysis, by membrane disruption, in other organism" NARROW []
-synonym: "membrane disruption in another organism" EXACT [GOC:bf]
-is_a: GO:0035821 ! modulation of process of other organism
+synonym: "membrane disruption in other organism" EXACT []
+is_a: GO:0035821 ! modulation of process of another organism
[Term]
id: GO:0051674
@@ -314353,16 +314050,17 @@ is_a: GO:0008150 ! biological_process
[Term]
id: GO:0051704
-name: multi-organism process
+name: obsolete multi-organism process
namespace: biological_process
alt_id: GO:0051706
-def: "A biological process which involves another organism of the same or different species." [GOC:jl]
+def: "OBSOLETE. A biological process which involves another organism of the same or different species." [GOC:jl]
+comment: This term was obsoleted because it was not a biologically meaningful grouping class.
subset: gocheck_do_not_annotate
subset: goslim_pir
synonym: "interaction between organisms" EXACT []
synonym: "physiological interaction between organisms" EXACT []
synonym: "physiological interaction with other organism" EXACT []
-is_a: GO:0008150 ! biological_process
+is_obsolete: true
[Term]
id: GO:0051705
@@ -314391,7 +314089,7 @@ is_a: GO:0044419 ! biological process involved in interspecies interaction betwe
[Term]
id: GO:0051709
-name: regulation of killing of cells of other organism
+name: regulation of killing of cells of another organism
namespace: biological_process
alt_id: GO:0044531
alt_id: GO:0052248
@@ -314401,26 +314099,26 @@ def: "Any process that modulates the frequency, rate or extent of the killing by
synonym: "modulation by organism of apoptotic process in other organism involved in symbiotic interaction" NARROW []
synonym: "modulation of programmed cell death in other organism" NARROW []
synonym: "modulation of programmed cell death in other organism involved in symbiotic interaction" NARROW []
-synonym: "regulation of killing of cells of another organism" EXACT [GOC:bf]
+synonym: "regulation of killing of cells of other organism" EXACT [GOC:bf]
is_a: GO:0031341 ! regulation of cell killing
-is_a: GO:0035821 ! modulation of process of other organism
-relationship: regulates GO:0031640 ! killing of cells of other organism
+is_a: GO:0035821 ! modulation of process of another organism
+relationship: regulates GO:0031640 ! killing of cells of another organism
[Term]
id: GO:0051710
-name: regulation of cytolysis in other organism
+name: regulation of cytolysis in another organism
namespace: biological_process
alt_id: GO:0001902
def: "Any process that modulates the frequency, rate or extent of the cytolysis by an organism of cells in another organism." [GOC:ai]
+synonym: "regulation of cytolysis in other organism" EXACT []
synonym: "regulation of cytolysis of cells of another organism" EXACT [GOC:bf]
-synonym: "regulation of cytolysis of cells of another, non-host, organism" NARROW []
is_a: GO:0042268 ! regulation of cytolysis
-is_a: GO:0051709 ! regulation of killing of cells of other organism
-relationship: regulates GO:0051715 ! cytolysis in other organism
+is_a: GO:0051709 ! regulation of killing of cells of another organism
+relationship: regulates GO:0051715 ! cytolysis in another organism
[Term]
id: GO:0051711
-name: negative regulation of killing of cells of other organism
+name: negative regulation of killing of cells of another organism
namespace: biological_process
alt_id: GO:0052490
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the killing by an organism of cells in another organism." [GOC:ai]
@@ -314428,15 +314126,14 @@ synonym: "down regulation of killing of cells of another organism" EXACT []
synonym: "down-regulation of killing of cells of another organism" EXACT []
synonym: "downregulation of killing of cells of another organism" EXACT []
synonym: "inhibition of killing of cells of another organism" NARROW []
-synonym: "negative regulation by organism of programmed cell death in other organism involved in symbiotic interaction" NARROW []
-synonym: "negative regulation of killing of cells of another organism" EXACT [GOC:bf]
+synonym: "negative regulation of killing of cells of other organism" EXACT []
is_a: GO:0031342 ! negative regulation of cell killing
-is_a: GO:0051709 ! regulation of killing of cells of other organism
-relationship: negatively_regulates GO:0031640 ! killing of cells of other organism
+is_a: GO:0051709 ! regulation of killing of cells of another organism
+relationship: negatively_regulates GO:0031640 ! killing of cells of another organism
[Term]
id: GO:0051712
-name: positive regulation of killing of cells of other organism
+name: positive regulation of killing of cells of another organism
namespace: biological_process
alt_id: GO:0052330
alt_id: GO:0052388
@@ -314447,23 +314144,19 @@ def: "Any process that activates or increases the frequency, rate or extent of t
synonym: "activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction" RELATED []
synonym: "activation of killing of cells of another organism" NARROW []
synonym: "enhancement of other organism programmed cell death by organism" RELATED []
-synonym: "induction by organism of apoptosis in other organism during symbiotic interaction" RELATED [GOC:tb]
-synonym: "induction by organism of apoptosis in other organism involved in symbiotic interaction" EXACT []
-synonym: "positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction" NARROW []
-synonym: "positive regulation by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction" NARROW []
-synonym: "positive regulation by organism of programmed cell death in other organism involved in symbiotic interaction" NARROW []
+synonym: "positive regulation of killing of cells of other organism" EXACT []
synonym: "stimulation of killing of cells of another organism" NARROW []
synonym: "up regulation of killing of cells of another organism" EXACT []
synonym: "up-regulation of killing of cells of another organism" EXACT []
synonym: "upregulation of killing of cells of another organism" EXACT []
is_a: GO:0031343 ! positive regulation of cell killing
is_a: GO:0043068 ! positive regulation of programmed cell death
-is_a: GO:0051709 ! regulation of killing of cells of other organism
-relationship: positively_regulates GO:0031640 ! killing of cells of other organism
+is_a: GO:0051709 ! regulation of killing of cells of another organism
+relationship: positively_regulates GO:0031640 ! killing of cells of another organism
[Term]
id: GO:0051713
-name: negative regulation of cytolysis in other organism
+name: negative regulation of cytolysis in another organism
namespace: biological_process
alt_id: GO:0001903
def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the cytolysis of cells in another organism." [GOC:ai]
@@ -314471,42 +314164,41 @@ synonym: "down regulation of cytolysis of cells of another organism" EXACT []
synonym: "down-regulation of cytolysis of cells of another organism" EXACT []
synonym: "downregulation of cytolysis of cells of another organism" EXACT []
synonym: "inhibition of cytolysis of cells of another organism" NARROW []
+synonym: "negative regulation of cytolysis in other organism" EXACT []
synonym: "negative regulation of cytolysis of cells of another organism" EXACT [GOC:bf]
-synonym: "negative regulation of cytolysis of cells of another, non-host, organism" NARROW []
is_a: GO:0045918 ! negative regulation of cytolysis
-is_a: GO:0051710 ! regulation of cytolysis in other organism
-is_a: GO:0051711 ! negative regulation of killing of cells of other organism
-relationship: negatively_regulates GO:0051715 ! cytolysis in other organism
+is_a: GO:0051710 ! regulation of cytolysis in another organism
+is_a: GO:0051711 ! negative regulation of killing of cells of another organism
+relationship: negatively_regulates GO:0051715 ! cytolysis in another organism
[Term]
id: GO:0051714
-name: positive regulation of cytolysis in other organism
+name: positive regulation of cytolysis in another organism
namespace: biological_process
alt_id: GO:0001904
def: "Any process that activates or increases the frequency, rate or extent of the cytolysis by an organism of cells in another organism." [GOC:ai]
synonym: "activation of cytolysis of cells of another organism" NARROW []
+synonym: "positive regulation of cytolysis in other organism" EXACT []
synonym: "positive regulation of cytolysis of cells of another organism" EXACT [GOC:bf]
-synonym: "positive regulation of cytolysis of cells of another, non-host, organism" NARROW []
synonym: "stimulation of cytolysis of cells of another organism" NARROW []
synonym: "up regulation of cytolysis of cells of another organism" EXACT []
synonym: "up-regulation of cytolysis of cells of another organism" EXACT []
synonym: "upregulation of cytolysis of cells of another organism" EXACT []
is_a: GO:0045919 ! positive regulation of cytolysis
-is_a: GO:0051710 ! regulation of cytolysis in other organism
-is_a: GO:0051712 ! positive regulation of killing of cells of other organism
-relationship: positively_regulates GO:0051715 ! cytolysis in other organism
+is_a: GO:0051710 ! regulation of cytolysis in another organism
+is_a: GO:0051712 ! positive regulation of killing of cells of another organism
+relationship: positively_regulates GO:0051715 ! cytolysis in another organism
[Term]
id: GO:0051715
-name: cytolysis in other organism
+name: cytolysis in another organism
namespace: biological_process
alt_id: GO:0001901
def: "The killing by an organism of a cell in another organism by means of the rupture of cell membranes and the loss of cytoplasm." [GOC:ai]
+synonym: "cytolysis in other organism" EXACT []
synonym: "cytolysis of cells of another organism" EXACT [GOC:bf]
-synonym: "cytolysis of cells of another, non-host, organism" NARROW []
-synonym: "cytolysis of cells of competing organism" NARROW []
is_a: GO:0019835 ! cytolysis
-is_a: GO:0031640 ! killing of cells of other organism
+is_a: GO:0031640 ! killing of cells of another organism
[Term]
id: GO:0051716
@@ -314563,7 +314255,7 @@ is_a: GO:0003886 ! DNA (cytosine-5-)-methyltransferase activity
id: GO:0051721
name: protein phosphatase 2A binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme protein phosphatase 2A." [GOC:ai]
+def: "Binding to protein phosphatase 2A." [GOC:ai]
synonym: "protein phosphatase 2 binding" RELATED [GOC:rl]
is_a: GO:0019903 ! protein phosphatase binding
@@ -314750,10 +314442,11 @@ is_a: GO:0051731 ! polynucleotide 5'-hydroxyl-kinase activity
[Term]
id: GO:0051734
-name: ATP-dependent polynucleotide kinase activity
+name: polynucleotide kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + 5'-dephosphopolynucleotide = ADP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA." [EC:2.7.1.78]
+def: "Catalysis of the reaction: ATP + 5'-dephosphopolynucleotide = ADP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA." [RHEA:54580]
synonym: "ATP-dependent polynucleotide 5'-hydroxyl-kinase activity" EXACT []
+synonym: "ATP-dependent polynucleotide kinase activity" RELATED []
synonym: "ATP:5'-dephosphopolynucleotide 5'-phosphatase activity" RELATED [EC:2.7.1.78]
synonym: "ATP:5'-dephosphopolynucleotide 5'-phosphotransferase activity" EXACT []
xref: EC:2.7.1.78
@@ -314771,16 +314464,17 @@ is_a: GO:0051731 ! polynucleotide 5'-hydroxyl-kinase activity
[Term]
id: GO:0051736
-name: ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity
+name: polyribonucleotide 5'-hydroxyl-kinase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + 5'-dephospho-RNA = ADP + 5'-phospho-RNA." [EC:2.7.1.78]
synonym: "ATP-dependent polynucleotide 5'-hydroxyl-kinase activity" BROAD []
+synonym: "ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity" RELATED []
synonym: "ATP-dependent polyribonucleotide kinase activity" EXACT []
synonym: "ATP-dependent RNA 5'-hydroxyl-kinase activity" EXACT []
synonym: "ATP-dependent RNA kinase activity" EXACT []
synonym: "ATP:5'-dephosphopolyribonucleotide 5'-phosphotransferase activity" EXACT []
is_a: GO:0051732 ! polyribonucleotide kinase activity
-is_a: GO:0051734 ! ATP-dependent polynucleotide kinase activity
+is_a: GO:0051734 ! polynucleotide kinase activity
[Term]
id: GO:0051737
@@ -314799,7 +314493,7 @@ is_a: GO:0051735 ! GTP-dependent polynucleotide kinase activity
id: GO:0051738
name: xanthophyll binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with xanthophylls, any of several neutral yellow to orange carotenoid pigments containing oxygen." [ISBN:0122146743]
+def: "Binding to xanthophylls, any of several neutral yellow to orange carotenoid pigments containing oxygen." [ISBN:0122146743]
is_a: GO:0019840 ! isoprenoid binding
is_a: GO:0031409 ! pigment binding
@@ -314807,7 +314501,7 @@ is_a: GO:0031409 ! pigment binding
id: GO:0051740
name: ethylene binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ethylene (C2-H4, ethene), a simple hydrocarbon gas that can function in plants as a growth regulator." [GOC:ai]
+def: "Binding to ethylene (C2-H4, ethene), a simple hydrocarbon gas that can function in plants as a growth regulator." [GOC:ai]
synonym: "ethene binding" EXACT []
is_a: GO:0072328 ! alkene binding
@@ -314865,9 +314559,9 @@ is_a: GO:0016726 ! oxidoreductase activity, acting on CH or CH2 groups, NAD or N
id: GO:0051746
name: thalianol synthase activity
namespace: molecular_function
-def: "Catalysis of the cyclization of 3(S)-oxidosqualene to (3S,13S,14R)-malabarica-8,17,21-trien-3-ol (thalianol)." [PMID:15125655]
+def: "Catalysis of the cyclization of 3(S)-oxidosqualene to (3S,13S,14R)-malabarica-8,17,21-trien-3-ol (thalianol)." [PMID:15125655, RHEA:26160]
xref: EC:5.4.99.31
-xref: RHEA:26163
+xref: RHEA:26160
is_a: GO:0031559 ! oxidosqualene cyclase activity
[Term]
@@ -315313,7 +315007,7 @@ is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
id: GO:0051787
name: misfolded protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a misfolded protein." [GOC:ai]
+def: "Binding to a misfolded protein." [GOC:ai]
xref: Reactome:R-HSA-5324632 "Dissociation of cytosolic HSF1:HSP90:HDAC6:PTGES3 upon sensing protein aggregates"
is_a: GO:0005515 ! protein binding
@@ -315478,45 +315172,44 @@ is_a: GO:0106017 ! phosphatidylinositol-3,4-bisphosphate phosphatase activity
[Term]
id: GO:0051801
-name: cytolysis in other organism involved in symbiotic interaction
+name: obsolete cytolysis in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The killing by an organism of a cell in a second organism by means of the rupture of cell membranes and the loss of cytoplasm, where the two organisms are in a symbiotic interaction." [GOC:add]
+def: "OBSOLETE. The killing by an organism of a cell in a second organism by means of the rupture of cell membranes and the loss of cytoplasm, where the two organisms are in a symbiotic interaction." [GOC:add]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "cytolysis of cells in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "cytolysis of cells in other organism involved in symbiotic interaction" EXACT [GOC:bf]
-is_a: GO:0051715 ! cytolysis in other organism
-is_a: GO:0051883 ! killing of cells in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0051802
-name: regulation of cytolysis in other organism involved in symbiotic interaction
+name: obsolete regulation of cytolysis in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism modulates the frequency, rate or extent of the cytolysis by that organism of cells in a second organism, where the two organisms are in a symbiotic interaction." [GOC:add]
+def: "OBSOLETE. Any process in which an organism modulates the frequency, rate or extent of the cytolysis by that organism of cells in a second organism, where the two organisms are in a symbiotic interaction." [GOC:add]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "regulation of cytolysis of cells in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "regulation of cytolysis of cells in other organism involved in symbiotic interaction" EXACT [GOC:bf]
-is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
-is_a: GO:0051710 ! regulation of cytolysis in other organism
-relationship: regulates GO:0051801 ! cytolysis in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0051803
-name: negative regulation of cytolysis in other organism involved in symbiotic interaction
+name: obsolete negative regulation of cytolysis in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of cytolysis by that organism of cells in a second organism, where the two organisms are in a symbiotic interaction." [GOC:add]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of cytolysis by that organism of cells in a second organism, where the two organisms are in a symbiotic interaction." [GOC:add]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "down regulation of cytolysis of cells in other organism during symbiotic interaction" RELATED []
synonym: "down-regulation of cytolysis of cells in other organism during symbiotic interaction" RELATED []
synonym: "downregulation of cytolysis of cells in other organism during symbiotic interaction" RELATED []
synonym: "inhibition of cytolysis of cells in other organism during symbiotic interaction" NARROW []
synonym: "negative regulation of cytolysis of cells in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "negative regulation of cytolysis of cells in other organism involved in symbiotic interaction" EXACT [GOC:bf]
-is_a: GO:0051713 ! negative regulation of cytolysis in other organism
-is_a: GO:0051802 ! regulation of cytolysis in other organism involved in symbiotic interaction
-relationship: negatively_regulates GO:0051801 ! cytolysis in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0051804
-name: positive regulation of cytolysis in other organism involved in symbiotic interaction
+name: obsolete positive regulation of cytolysis in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism activates or increases the frequency, rate or extent of cytolysis by that organism of cells in a second organism, where the two organisms are in a symbiotic interaction." [GOC:add]
+def: "OBSOLETE. Any process in which an organism activates or increases the frequency, rate or extent of cytolysis by that organism of cells in a second organism, where the two organisms are in a symbiotic interaction." [GOC:add]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "activation of cytolysis of cells in other organism during symbiotic interaction" NARROW []
synonym: "positive regulation of cytolysis of cells in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "positive regulation of cytolysis of cells in other organism involved in symbiotic interaction" EXACT [GOC:bf]
@@ -315524,9 +315217,7 @@ synonym: "stimulation of cytolysis of cells in other organism during symbiotic i
synonym: "up regulation of cytolysis of cells in other organism during symbiotic interaction" EXACT []
synonym: "up-regulation of cytolysis of cells in other organism during symbiotic interaction" EXACT []
synonym: "upregulation of cytolysis of cells in other organism during symbiotic interaction" EXACT []
-is_a: GO:0051714 ! positive regulation of cytolysis in other organism
-is_a: GO:0051802 ! regulation of cytolysis in other organism involved in symbiotic interaction
-relationship: positively_regulates GO:0051801 ! cytolysis in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0051814
@@ -315550,16 +315241,18 @@ is_obsolete: true
[Term]
id: GO:0051816
-name: acquisition of nutrients from other organism during symbiotic interaction
+name: obsolete acquisition of nutrients from other organism during symbiotic interaction
namespace: biological_process
-def: "The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from a second organism, where the two organisms are in a symbiotic interaction." [GOC:cc]
-is_a: GO:0044403 ! biological process involved in symbiotic interaction
+def: "OBSOLETE. The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from a second organism, where the two organisms are in a symbiotic interaction." [GOC:cc]
+comment: This term was obsoleted because it represented an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0051817
-name: modulation of process of other organism involved in symbiotic interaction
+name: obsolete modulation of process of other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction." [GOC:cc]
+def: "OBSOLETE. The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction." [GOC:cc]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modification of morphology or physiology of other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "modification of morphology or physiology of other organism involved in symbiotic interaction" RELATED []
synonym: "modulation of biological process of other organism involved in symbiotic interaction" RELATED []
@@ -315568,16 +315261,16 @@ synonym: "regulation of morphology of other organism during symbiotic interactio
synonym: "regulation of morphology or physiology of other organism during symbiotic interaction" RELATED []
synonym: "regulation of physiological process in other organism during symbiotic interaction" NARROW []
synonym: "regulation of physiology of other organism during symbiotic interaction" NARROW []
-is_a: GO:0035821 ! modulation of process of other organism
+is_obsolete: true
[Term]
id: GO:0051818
-name: disruption of cells of other organism involved in symbiotic interaction
+name: obsolete disruption of cells of other organism involved in symbiotic interaction
namespace: biological_process
-def: "A process in which an organism has a negative effect on the functioning of the second organism's cells, where the two organisms are in a symbiotic interaction." [GOC:cc]
+def: "OBSOLETE. A process in which an organism has a negative effect on the functioning of the second organism's cells, where the two organisms are in a symbiotic interaction." [GOC:cc]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "disruption of cells of other organism during symbiotic interaction" RELATED [GOC:tb]
-is_a: GO:0044364 ! disruption of cells of other organism
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0051819
@@ -315673,7 +315366,6 @@ id: GO:0051838
name: cytolysis by host of symbiont cells
namespace: biological_process
def: "The killing by an organism of a cell in its symbiont organism by means of the rupture of cell membranes and the loss of cytoplasm. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:add]
-is_a: GO:0051801 ! cytolysis in other organism involved in symbiotic interaction
is_a: GO:0051873 ! killing by host of symbiont cells
[Term]
@@ -315684,8 +315376,8 @@ def: "Any process in which an organism modulates the frequency, rate or extent o
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0050776 ! regulation of immune response
-is_a: GO:0051802 ! regulation of cytolysis in other organism involved in symbiotic interaction
+is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
+is_a: GO:0051709 ! regulation of killing of cells of another organism
relationship: regulates GO:0051838 ! cytolysis by host of symbiont cells
[Term]
@@ -315697,7 +315389,6 @@ synonym: "down regulation by host of cytolysis of symbiont cells" EXACT []
synonym: "down-regulation by host of cytolysis of symbiont cells" EXACT []
synonym: "downregulation by host of cytolysis of symbiont cells" EXACT []
synonym: "inhibition by host of cytolysis of symbiont cells" NARROW []
-is_a: GO:0051803 ! negative regulation of cytolysis in other organism involved in symbiotic interaction
is_a: GO:0051839 ! regulation by host of cytolysis of symbiont cells
[Term]
@@ -315710,7 +315401,6 @@ synonym: "stimulation by host of cytolysis of symbiont cells" NARROW []
synonym: "up regulation by host of cytolysis of symbiont cells" EXACT []
synonym: "up-regulation by host of cytolysis of symbiont cells" EXACT []
synonym: "upregulation by host of cytolysis of symbiont cells" EXACT []
-is_a: GO:0051804 ! positive regulation of cytolysis in other organism involved in symbiotic interaction
is_a: GO:0051839 ! regulation by host of cytolysis of symbiont cells
[Term]
@@ -315802,7 +315492,6 @@ name: acquisition of nutrients from symbiont
namespace: biological_process
def: "The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:cc]
is_a: GO:0051702 ! biological process involved in interaction with symbiont
-is_a: GO:0051816 ! acquisition of nutrients from other organism during symbiotic interaction
[Term]
id: GO:0051851
@@ -315811,7 +315500,6 @@ namespace: biological_process
def: "The process in which an organism effects a change in the structure or processes of a symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:cc]
synonym: "modification by host of symbiont morphology or physiology" RELATED []
is_a: GO:0051702 ! biological process involved in interaction with symbiont
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
[Term]
id: GO:0051853
@@ -315869,7 +315557,7 @@ is_obsolete: true
id: GO:0051861
name: glycolipid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a glycolipid, any compound containing one or more monosaccharide residues bound by a glycosidic linkage to a hydrophobic group such as an acylglycerol, a sphingoid, a ceramide (N-acylsphingoid) or a prenyl phosphate." [PMID:19635802]
+def: "Binding to a glycolipid, any compound containing one or more monosaccharide residues bound by a glycosidic linkage to a hydrophobic group such as an acylglycerol, a sphingoid, a ceramide (N-acylsphingoid) or a prenyl phosphate." [PMID:19635802]
is_a: GO:0008289 ! lipid binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -315892,23 +315580,16 @@ is_obsolete: true
[Term]
id: GO:0051864
-name: histone demethylase activity (H3-K36 specific)
+name: histone H3-methyl-lysine-36 demethylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein." [PMID:16362057]
+def: "Catalysis of the removal of a methyl group from a modified lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:16362057]
synonym: "[histone-H3]-lysine-36 demethylase activity" EXACT []
-synonym: "H3-K36-specific demethylase activity" RELATED [EC:1.14.11.27]
-synonym: "histone H3-lysine-36 demethylase activity" RELATED [EC:1.14.11.27]
-synonym: "histone-lysine (H3-K36) demethylase activity" RELATED [EC:1.14.11.27]
+synonym: "histone demethylase activity (H3-K36 specific)" EXACT []
+synonym: "histone H3-lysine-36 demethylase activity" RELATED []
+synonym: "histone H3K36 demethylase activity" RELATED []
+synonym: "histone-lysine (H3-K36) demethylase activity" RELATED []
synonym: "histone-lysine demethylase activity (H3-K36 specific)" EXACT []
synonym: "histone-lysine(H3-K36) demethylase activity" EXACT []
-synonym: "JHDM1A activity" NARROW [EC:1.14.11.27]
-synonym: "JmjC domain-containing histone demethylase 1A activity" NARROW [EC:1.14.11.27]
-synonym: "protein-6-N,6-N-dimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase activity" RELATED [EC:1.14.11.27]
-synonym: "protein-N6,N6-dimethyl-L-lysine,2-oxoglutarate:oxygen oxidoreductase activity" RELATED [EC:1.14.11.27]
-xref: EC:1.14.11.27
-xref: MetaCyc:RXN-8660
-xref: MetaCyc:RXN-8661
-xref: RHEA:42032
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032452 ! histone demethylase activity
@@ -315955,8 +315636,7 @@ relationship: part_of GO:0051866 ! general adaptation syndrome
id: GO:0051870
name: methotrexate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with methotrexate, an antineoplastic antimetabolite with immunosuppressant properties. It is an inhibitor of tetrahydrofolate reductase and prevents the formation of tetrahydrofolate, necessary for synthesis of thymidylate, an essential component of DNA." [GOC:nln]
-is_a: GO:0008144 ! drug binding
+def: "Binding to methotrexate, an antineoplastic antimetabolite with immunosuppressant properties. It is an inhibitor of tetrahydrofolate reductase and prevents the formation of tetrahydrofolate, necessary for synthesis of thymidylate, an essential component of DNA." [GOC:nln]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0033218 ! amide binding
is_a: GO:0043177 ! organic acid binding
@@ -315967,7 +315647,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0051871
name: dihydrofolic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dihydrofolic acid, a folic acid in which the bicyclic pteridine structure is in the dihydro, partially reduced form; they are intermediates in folate metabolism and are reduced to their tetrahydro, reduced forms." [ISBN:0721662544]
+def: "Binding to dihydrofolic acid, a folic acid in which the bicyclic pteridine structure is in the dihydro, partially reduced form; they are intermediates in folate metabolism and are reduced to their tetrahydro, reduced forms." [ISBN:0721662544]
synonym: "DHF binding" RELATED []
synonym: "dihydrofolate binding" RELATED []
is_a: GO:0031406 ! carboxylic acid binding
@@ -315996,7 +315676,6 @@ alt_id: GO:0051852
def: "Any process mediated by an organism that results in the death of cells in the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:add]
synonym: "disruption by host of symbiont cells" BROAD []
is_a: GO:0051702 ! biological process involved in interaction with symbiont
-is_a: GO:0051883 ! killing of cells in other organism involved in symbiotic interaction
is_a: GO:0098542 ! defense response to other organism
[Term]
@@ -316046,7 +315725,7 @@ relationship: part_of GO:0007130 ! synaptonemal complex assembly
id: GO:0051879
name: Hsp90 protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size." [GOC:ai]
+def: "Binding to Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size." [GOC:ai]
synonym: "Hsp90 binding" EXACT []
synonym: "Hsp90 class protein binding" EXACT []
is_a: GO:0031072 ! heat shock protein binding
@@ -316055,7 +315734,7 @@ is_a: GO:0031072 ! heat shock protein binding
id: GO:0051880
name: G-quadruplex DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome." [PMID:16142245, PMID:9512530]
+def: "Binding to G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome." [PMID:16142245, PMID:9512530]
synonym: "G quadruplex DNA binding" EXACT [GOC:mah]
synonym: "G quartet binding" BROAD [GOC:mah]
synonym: "G quartet DNA binding" EXACT [GOC:mah]
@@ -316087,12 +315766,12 @@ is_a: GO:0051899 ! membrane depolarization
[Term]
id: GO:0051883
-name: killing of cells in other organism involved in symbiotic interaction
+name: obsolete killing of cells in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process mediated by an organism that results in the death of cells in a second organism, where the two organisms are in a symbiotic interaction." [GOC:add]
+def: "OBSOLETE. Any process mediated by an organism that results in the death of cells in a second organism, where the two organisms are in a symbiotic interaction." [GOC:add]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "killing of cells in other organism during symbiotic interaction" RELATED [GOC:tb]
-is_a: GO:0031640 ! killing of cells of other organism
-is_a: GO:0044403 ! biological process involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0051884
@@ -316502,7 +316181,7 @@ is_a: GO:0051914 ! positive regulation of synaptic plasticity by chemical substa
id: GO:0051916
name: granulocyte colony-stimulating factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with granulocyte colony-stimulating factor, G-CSF." [GOC:ai]
+def: "Binding to granulocyte colony-stimulating factor, G-CSF." [GOC:ai]
synonym: "G-CSF binding" EXACT []
synonym: "granulocyte colony stimulating factor binding" EXACT []
is_a: GO:0019955 ! cytokine binding
@@ -317082,14 +316761,13 @@ namespace: biological_process
def: "The directed movement of methotrexate, 4-amino-10-methylformic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Methotrexate is a folic acid analogue and a potent competitive inhibitor of dihydrofolate reductase." [GOC:ai]
is_a: GO:0006835 ! dicarboxylic acid transport
is_a: GO:0015849 ! organic acid transport
-is_a: GO:0015893 ! drug transport
is_a: GO:0042886 ! amide transport
[Term]
id: GO:0051959
name: dynein light intermediate chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a light intermediate chain of the dynein complex." [GOC:bf]
+def: "Binding to a light intermediate chain of the dynein complex." [GOC:bf]
is_a: GO:0005515 ! protein binding
[Term]
@@ -317568,11 +317246,11 @@ is_a: GO:0044406 ! adhesion of symbiont to host
[Term]
id: GO:0052002
-name: metabolism by symbiont of substance in host
+name: obsolete metabolism by symbiont of substance in host
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0044003 ! modulation by symbiont of host process
-is_a: GO:0052214 ! metabolism of substance in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052003
@@ -317606,7 +317284,6 @@ is_a: GO:0044414 ! suppression of host defenses by symbiont
is_a: GO:0052029 ! suppression by symbiont of host signal transduction pathway
is_a: GO:0052081 ! modulation by symbiont of defense-related host salicylic acid-mediated signal transduction pathway
is_a: GO:0052089 ! modulation by symbiont of host salicylic acid-mediated defense response
-is_a: GO:2001039 ! negative regulation of cellular response to drug
relationship: negatively_regulates GO:0009862 ! systemic acquired resistance, salicylic acid mediated signaling pathway
[Term]
@@ -317631,12 +317308,12 @@ is_a: GO:0052084 ! modulation by symbiont of host ethylene-mediated defense resp
[Term]
id: GO:0052006
-name: catabolism by symbiont of substance in host
+name: obsolete catabolism by symbiont of substance in host
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism in its host resulting in the breakdown of substances. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism in its host resulting in the breakdown of substances. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of substance in host" EXACT []
-is_a: GO:0052002 ! metabolism by symbiont of substance in host
-is_a: GO:0052227 ! catabolism of substance in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052007
@@ -317658,7 +317335,6 @@ synonym: "degradation of host cellular component by organism" EXACT []
synonym: "disassembly by organism of host cellular component" EXACT []
synonym: "disassembly by symbiont of host cellular component" RELATED []
is_a: GO:0052043 ! modification by symbiont of host cellular component
-is_a: GO:0052368 ! disruption by organism of cellular component in other organism involved in symbiotic interaction
[Term]
id: GO:0052009
@@ -317670,86 +317346,75 @@ is_a: GO:0098933 ! disruption by symbiont of host cell envelope
[Term]
id: GO:0052010
-name: catabolism by symbiont of host cell wall cellulose
+name: obsolete catabolism by symbiont of host cell wall cellulose
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of cellulose in the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of cellulose in the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of host cell wall cellulose" EXACT []
-is_a: GO:0052015 ! catabolism by symbiont of host carbohydrate
-is_a: GO:0052172 ! metabolism by symbiont of host cell wall cellulose
-is_a: GO:0052340 ! catabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
-relationship: part_of GO:0052009 ! disruption by symbiont of host cell wall
+is_obsolete: true
[Term]
id: GO:0052011
-name: catabolism by symbiont of host cell wall pectin
+name: obsolete catabolism by symbiont of host cell wall pectin
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of pectin in the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of pectin in the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of host cell wall pectin" EXACT []
-is_a: GO:0052015 ! catabolism by symbiont of host carbohydrate
-is_a: GO:0052179 ! metabolism by symbiont of host cell wall pectin
-is_a: GO:0052341 ! catabolism by organism of cell wall pectin in other organism involved in symbiotic interaction
-relationship: part_of GO:0052009 ! disruption by symbiont of host cell wall
+is_obsolete: true
[Term]
id: GO:0052012
-name: catabolism by symbiont of host cell wall chitin
+name: obsolete catabolism by symbiont of host cell wall chitin
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of chitin in the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of chitin in the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of host cell wall chitin" EXACT []
-is_a: GO:0052015 ! catabolism by symbiont of host carbohydrate
-is_a: GO:0052178 ! metabolism by symbiont of host cell wall chitin
-is_a: GO:0052342 ! catabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
-relationship: part_of GO:0052009 ! disruption by symbiont of host cell wall
+is_obsolete: true
[Term]
id: GO:0052013
-name: catabolism by symbiont of host macromolecule
+name: obsolete catabolism by symbiont of host macromolecule
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of macromolecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of macromolecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of host macromolecule" EXACT []
-is_a: GO:0052006 ! catabolism by symbiont of substance in host
-is_a: GO:0052174 ! metabolism by symbiont of host macromolecule
-is_a: GO:0052361 ! catabolism by organism of macromolecule in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052014
-name: catabolism by symbiont of host protein
+name: obsolete catabolism by symbiont of host protein
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of protein macromolecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of protein macromolecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of host protein" EXACT []
-is_a: GO:0052013 ! catabolism by symbiont of host macromolecule
-is_a: GO:0052228 ! metabolism by symbiont of host protein
-is_a: GO:0052363 ! catabolism by organism of protein in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052015
-name: catabolism by symbiont of host carbohydrate
+name: obsolete catabolism by symbiont of host carbohydrate
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of carbohydrate molecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of carbohydrate molecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of host carbohydrate" EXACT []
-is_a: GO:0052013 ! catabolism by symbiont of host macromolecule
-is_a: GO:0052175 ! metabolism by symbiont of host carbohydrate
-is_a: GO:0052354 ! catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052016
-name: catabolism by symbiont of host glucan
+name: obsolete catabolism by symbiont of host glucan
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of glucan molecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of glucan molecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of host glucan" EXACT []
-is_a: GO:0052015 ! catabolism by symbiont of host carbohydrate
-is_a: GO:0052176 ! metabolism by symbiont of host glucan
-is_a: GO:0052359 ! catabolism by organism of glucan in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052017
-name: catabolism by symbiont of host xylan
+name: obsolete catabolism by symbiont of host xylan
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of xylan within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of xylan within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of host xylan" EXACT []
-is_a: GO:0052015 ! catabolism by symbiont of host carbohydrate
-is_a: GO:0052177 ! metabolism by symbiont of host xylan
-is_a: GO:0052366 ! catabolism by organism of xylan in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052018
@@ -317758,7 +317423,6 @@ namespace: biological_process
def: "The alteration by an organism of the levels of RNA in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "modulation by symbiont of host RNA levels" EXACT []
is_a: GO:0044003 ! modulation by symbiont of host process
-is_a: GO:0052249 ! modulation of RNA levels in other organism involved in symbiotic interaction
[Term]
id: GO:0052019
@@ -317776,7 +317440,6 @@ namespace: biological_process
def: "The process in which an organism effects a change in the structure or function of the host cell wall. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
synonym: "metabolism of host cell wall by organism" EXACT []
is_a: GO:0052043 ! modification by symbiont of host cellular component
-is_a: GO:0052333 ! modification by organism of cell wall of other organism involved in symbiotic interaction
[Term]
id: GO:0052021
@@ -317825,9 +317488,7 @@ id: GO:0052025
name: modification by symbiont of host cell membrane
namespace: biological_process
def: "The process in which an organism effects a change in the structure or function of a host cellular membrane. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-synonym: "modification by symbiont of host cell membrane" NARROW [GOC:bf, GOC:jl]
is_a: GO:0052043 ! modification by symbiont of host cellular component
-is_a: GO:0052332 ! modification by organism of membrane in other organism involved in symbiotic interaction
[Term]
id: GO:0052026
@@ -317835,7 +317496,6 @@ name: modulation by symbiont of host transcription
namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of its host's transcription. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0044068 ! modulation by symbiont of host cellular process
-is_a: GO:0052312 ! modulation of transcription in other organism involved in symbiotic interaction
[Term]
id: GO:0052027
@@ -317848,7 +317508,7 @@ synonym: "modulation of host signal transduction by symbiont" EXACT []
synonym: "modulation of signal transduction in other organism involved in symbiotic interaction" BROAD []
synonym: "regulation by symbiont of host signal transduction pathway" EXACT []
is_a: GO:0044068 ! modulation by symbiont of host cellular process
-is_a: GO:0044501 ! modulation of signal transduction in other organism
+is_a: GO:0044501 ! modulation of signal transduction in another organism
[Term]
id: GO:0052028
@@ -317890,7 +317550,7 @@ alt_id: GO:0052255
def: "Any process in which an organism modulates the frequency, rate or extent of the defense response of its host, the response mounted by the host in response to the presence of the organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "mitigation by symbiont of host defense response" EXACT []
synonym: "modulation by organism of defense response of other organism involved in symbiotic interaction" BROAD []
-synonym: "pathogenesis" NARROW []
+synonym: "pathogenesis" RELATED []
is_a: GO:0044003 ! modulation by symbiont of host process
is_a: GO:0052200 ! response to host defenses
@@ -317945,7 +317605,6 @@ synonym: "suppression of MAMP-induced host innate immunity" RELATED []
synonym: "suppression of PAMP induced host innate immunity" RELATED []
synonym: "suppression of PAMP-induced host innate immunity" RELATED []
synonym: "suppression of pathogen-associated molecular pattern-induced host innate immunity" RELATED []
-is_a: GO:0052170 ! suppression by symbiont of host innate immune response
is_a: GO:0140403 ! effector-mediated suppression of host innate immune response
[Term]
@@ -317985,17 +317644,17 @@ namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of the directed movement of substances within the cell or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "modulation of host intracellular trafficking" EXACT []
is_a: GO:0044068 ! modulation by symbiont of host cellular process
-is_a: GO:0052230 ! modulation of intracellular transport in other organism involved in symbiotic interaction
+relationship: regulates GO:0046907 ! intracellular transport
[Term]
id: GO:0052039
-name: modification by symbiont of host cytoskeleton
+name: disruption by symbiont of host cytoskeleton
namespace: biological_process
alt_id: GO:0044054
-def: "The process in which an organism effects a change in the structure or function of the host cytoskeleton. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "The process in which an organism effects a change that impairs the structure or function of the host cytoskeleton. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+synonym: "modification by symbiont of host cytoskeleton" RELATED []
synonym: "rounding by symbiont of host cells" NARROW []
is_a: GO:0052043 ! modification by symbiont of host cellular component
-is_a: GO:0052334 ! modification by organism of cytoskeleton of other organism involved in symbiotic interaction
[Term]
id: GO:0052040
@@ -318045,11 +317704,11 @@ synonym: "induction by organism of programmed cell death in other organism durin
synonym: "induction by organism of programmed cell death in other organism involved in symbiotic interaction" EXACT []
synonym: "induction by symbiont of host programmed cell death" EXACT []
synonym: "induction of non-apoptotic programmed cell death by other organism" RELATED []
-synonym: "pathogenesis" NARROW []
+synonym: "pathogenesis" RELATED []
synonym: "positive regulation by symbiont of host non-apoptotic programmed cell death" NARROW []
synonym: "stimulation by symbiont of host programmed cell death" NARROW []
synonym: "upregulation by symbiont of host programmed cell death" EXACT []
-is_a: GO:0051712 ! positive regulation of killing of cells of other organism
+is_a: GO:0051712 ! positive regulation of killing of cells of another organism
is_a: GO:0052040 ! modulation by symbiont of host programmed cell death
relationship: part_of GO:0001907 ! killing by symbiont of host cells
@@ -318059,7 +317718,6 @@ name: modification by symbiont of host cellular component
namespace: biological_process
def: "The process in which an organism effects a change in the structure or function of a host cellular component. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0052111 ! modification by symbiont of host structure
-is_a: GO:0052188 ! modification of cellular component in other organism involved in symbiotic interaction
[Term]
id: GO:0052046
@@ -318127,6 +317785,7 @@ is_obsolete: true
id: GO:0052053
name: negative regulation by symbiont of host catalytic activity
namespace: biological_process
+alt_id: GO:0052056
def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of host enzyme activity. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "down regulation by symbiont of host enzyme activity" EXACT []
synonym: "down-regulation by symbiont of host enzyme activity" EXACT []
@@ -318134,25 +317793,22 @@ synonym: "downregulation by symbiont of host enzyme activity" EXACT []
synonym: "inhibition by symbiont of host enzyme activity" NARROW []
synonym: "inhibition of host enzyme activity" EXACT []
synonym: "negative regulation by symbiont of host enzyme activity" EXACT []
-is_a: GO:0052056 ! negative regulation by symbiont of host molecular function
+synonym: "negative regulation by symbiont of host molecular function" BROAD []
is_a: GO:0052148 ! modulation by symbiont of host catalytic activity
-is_a: GO:0052199 ! negative regulation of catalytic activity in other organism involved in symbiotic interaction
[Term]
id: GO:0052054
-name: negative regulation by symbiont of host peptidase activity
+name: obsolete negative regulation by symbiont of host peptidase activity
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of host protease activity, the catalysis of the hydrolysis of peptide bonds in a protein. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of host protease activity, the catalysis of the hydrolysis of peptide bonds in a protein. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation by symbiont of host protease activity" NARROW []
synonym: "down-regulation by symbiont of host protease activity" NARROW []
synonym: "downregulation by symbiont of host protease activity" NARROW []
synonym: "inhibition by symbiont of host protease activity" NARROW []
synonym: "inhibition of host protease activity" NARROW []
synonym: "negative regulation by symbiont of host protease activity" NARROW [GOC:dph, GOC:tb]
-is_a: GO:0044068 ! modulation by symbiont of host cellular process
-is_a: GO:0052053 ! negative regulation by symbiont of host catalytic activity
-is_a: GO:0052149 ! modulation by symbiont of host peptidase activity
-is_a: GO:0052180 ! negative regulation of peptidase activity in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052055
@@ -318162,21 +317818,6 @@ def: "The process in which an organism effects a change in the function of a hos
synonym: "modification by symbiont of host molecular function" EXACT []
synonym: "modification by symbiont of host protein function" EXACT [GOC:dph, GOC:tb]
is_a: GO:0044003 ! modulation by symbiont of host process
-is_a: GO:0052205 ! modulation of molecular function in other organism involved in symbiotic interaction
-
-[Term]
-id: GO:0052056
-name: negative regulation by symbiont of host molecular function
-namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of host proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
-synonym: "down regulation by symbiont of host protein function" EXACT []
-synonym: "down-regulation by symbiont of host protein function" EXACT []
-synonym: "downregulation by symbiont of host protein function" EXACT []
-synonym: "inhibition by symbiont of host protein function" NARROW []
-synonym: "inhibition of host protein function" EXACT []
-synonym: "negative regulation by symbiont of host protein function" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0052055 ! modulation by symbiont of host molecular function
-is_a: GO:0052204 ! negative regulation of molecular function in other organism involved in symbiotic interaction
[Term]
id: GO:0052057
@@ -318289,7 +317930,6 @@ synonym: "negative regulation by organism of entry into host cell via host phago
synonym: "negative regulation by symbiont of entry into host cell via phagocytosis" RELATED []
synonym: "phagocytosis avoidence" EXACT []
is_a: GO:0030682 ! mitigation of host defenses by symbiont
-is_a: GO:0052372 ! modulation by symbiont of entry into host
[Term]
id: GO:0052072
@@ -318561,26 +318201,26 @@ relationship: regulates GO:0009862 ! systemic acquired resistance, salicylic aci
[Term]
id: GO:0052091
-name: modulation by symbiont of nutrient release from host
+name: modulation of nutrient release by host
namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of the release of nutrients from its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+synonym: "modulation by symbiont of nutrient release from host" EXACT []
is_a: GO:0044003 ! modulation by symbiont of host process
-is_a: GO:0052313 ! modulation of nutrient release from other organism involved in symbiotic interaction
relationship: part_of GO:0044002 ! acquisition of nutrients from host
[Term]
id: GO:0052092
-name: positive regulation by symbiont of nutrient release from host
+name: positive regulation of nutrient release by host
namespace: biological_process
def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of the release of nutrients from its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "activation by symbiont of nutrient release from host" NARROW []
+synonym: "positive regulation by symbiont of nutrient release from host" EXACT []
synonym: "promotion of nutrient release from host" EXACT []
synonym: "stimulation by symbiont of nutrient release from host" NARROW []
synonym: "up regulation by symbiont of nutrient release from host" EXACT []
synonym: "up-regulation by symbiont of nutrient release from host" EXACT []
synonym: "upregulation by symbiont of nutrient release from host" EXACT []
-is_a: GO:0052091 ! modulation by symbiont of nutrient release from host
-is_a: GO:0052520 ! positive regulation by organism of nutrient release from other organism involved in symbiotic interaction
+is_a: GO:0052091 ! modulation of nutrient release by host
[Term]
id: GO:0052093
@@ -318605,13 +318245,12 @@ is_a: GO:0052093 ! formation of specialized structure for nutrient acquisition
[Term]
id: GO:0052095
-name: formation of specialized structure for nutrient acquisition from other organism involved in symbiotic interaction
+name: obsolete formation of specialized structure for nutrient acquisition from other organism involved in symbiotic interaction
namespace: biological_process
-def: "The assembly by an organism of a cellular component or anatomical structure for the purpose of obtaining nutrients from a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The assembly by an organism of a cellular component or anatomical structure for the purpose of obtaining nutrients from a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "formation of specialized structure for nutrient acquisition from other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044111 ! formation of structure involved in a symbiotic process
-is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
-relationship: part_of GO:0051816 ! acquisition of nutrients from other organism during symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052096
@@ -318620,7 +318259,6 @@ namespace: biological_process
def: "The assembly of a syncytium, a multi-nucleate and physiologically active aggregation of fused root cells induced by a symbiotic nematode in a plant host. The syncytium exclusively provides the nematode with nourishment during its sedentary life, for the purpose of obtaining nutrients from its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
synonym: "formation by organism of syncytium involving giant cell for nutrient acquisition from host" EXACT []
synonym: "formation by symbiont of syncytium involving giant cell for nutrient acquisition from host" RELATED []
-synonym: "https://github.com/geneontology/go-ontology/issues/20305" RELATED []
is_a: GO:0052093 ! formation of specialized structure for nutrient acquisition
[Term]
@@ -318636,7 +318274,7 @@ id: GO:0052098
name: formation by host of specialized structure for nutrient acquisition from symbiont
namespace: biological_process
def: "The assembly by an organism of a cellular component or anatomical structure for the purpose of obtaining nutrients from a symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052095 ! formation of specialized structure for nutrient acquisition from other organism involved in symbiotic interaction
+is_a: GO:0051702 ! biological process involved in interaction with symbiont
relationship: part_of GO:0051850 ! acquisition of nutrients from symbiont
[Term]
@@ -318781,7 +318419,6 @@ name: occlusion by symbiont of host vascular system
namespace: biological_process
def: "The process in which an organism reduces the flow of fluid within its host's vascular system, the vessels and tissue that carry or circulate fluids, such as blood, lymph or sap, through the body of an animal or plant. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, http://www.thefreedictionary.com]
is_a: GO:0052111 ! modification by symbiont of host structure
-is_a: GO:0052495 ! occlusion by organism of vascular system in other organism involved in symbiotic interaction
[Term]
id: GO:0052111
@@ -318789,7 +318426,6 @@ name: modification by symbiont of host structure
namespace: biological_process
def: "The process in which an organism effects a change in an anatomical part or cellular component of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0044003 ! modulation by symbiont of host process
-is_a: GO:0052185 ! modification of structure of other organism involved in symbiotic interaction
[Term]
id: GO:0052112
@@ -318797,7 +318433,6 @@ name: occlusion by symbiont of host xylem
namespace: biological_process
def: "The process in which an organism reduces the flow of fluid within the host xylem, the tissue in plants that carries water and nutrients up from the roots to the shoot and leaves. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0052110 ! occlusion by symbiont of host vascular system
-is_a: GO:0052497 ! occlusion by organism of xylem in other organism involved in symbiotic interaction
[Term]
id: GO:0052113
@@ -319111,17 +318746,15 @@ synonym: "regulation by symbiont of host catalytic activity" EXACT []
synonym: "regulation of catalytic activity of host by symbiont" EXACT []
synonym: "regulation of host catalytic activity by symbiont" EXACT []
is_a: GO:0052055 ! modulation by symbiont of host molecular function
-is_a: GO:0052203 ! modulation of catalytic activity in other organism involved in symbiotic interaction
[Term]
id: GO:0052149
-name: modulation by symbiont of host peptidase activity
+name: obsolete modulation by symbiont of host peptidase activity
namespace: biological_process
-def: "The process in which an organism effects a change in host peptidase activity, the catalysis of the hydrolysis of peptide bonds in a protein. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism effects a change in host peptidase activity, the catalysis of the hydrolysis of peptide bonds in a protein. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "modulation by symbiont of host protease activity" NARROW [GOC:bf]
-is_a: GO:0052148 ! modulation by symbiont of host catalytic activity
-is_a: GO:0052198 ! modulation of peptidase activity in other organism involved in symbiotic interaction
-is_a: GO:0052547 ! regulation of peptidase activity
+is_obsolete: true
[Term]
id: GO:0052150
@@ -319132,7 +318765,7 @@ comment: Note that term is to be used to annotate gene products in the symbiont.
synonym: "modulation by organism of host apoptotic programmed cell death" EXACT []
synonym: "modulation by symbiont of host apoptosis" NARROW []
is_a: GO:0042981 ! regulation of apoptotic process
-is_a: GO:0051709 ! regulation of killing of cells of other organism
+is_a: GO:0051709 ! regulation of killing of cells of another organism
is_a: GO:0052040 ! modulation by symbiont of host programmed cell death
[Term]
@@ -319408,11 +319041,11 @@ consider: GO:0044111
[Term]
id: GO:0052172
-name: metabolism by symbiont of host cell wall cellulose
+name: obsolete metabolism by symbiont of host cell wall cellulose
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving cellulose in the cell wall of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052175 ! metabolism by symbiont of host carbohydrate
-is_a: GO:0052409 ! metabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving cellulose in the cell wall of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052173
@@ -319425,65 +319058,66 @@ is_a: GO:0051707 ! response to other organism
[Term]
id: GO:0052174
-name: metabolism by symbiont of host macromolecule
+name: obsolete metabolism by symbiont of host macromolecule
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving macromolecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052002 ! metabolism by symbiont of substance in host
-is_a: GO:0052229 ! metabolism of macromolecule in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving macromolecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052175
-name: metabolism by symbiont of host carbohydrate
+name: obsolete metabolism by symbiont of host carbohydrate
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving carbohydrates within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052174 ! metabolism by symbiont of host macromolecule
-is_a: GO:0052407 ! metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving carbohydrates within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052176
-name: metabolism by symbiont of host glucan
+name: obsolete metabolism by symbiont of host glucan
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving glucans within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052175 ! metabolism by symbiont of host carbohydrate
-is_a: GO:0052415 ! metabolism by organism of glucan in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving glucans within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052177
-name: metabolism by symbiont of host xylan
+name: obsolete metabolism by symbiont of host xylan
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving xylan within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052175 ! metabolism by symbiont of host carbohydrate
-is_a: GO:0052421 ! metabolism by organism of xylan in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving xylan within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
+is_obsolete: true
[Term]
id: GO:0052178
-name: metabolism by symbiont of host cell wall chitin
+name: obsolete metabolism by symbiont of host cell wall chitin
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving chitin in the cell wall of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052175 ! metabolism by symbiont of host carbohydrate
-is_a: GO:0052411 ! metabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving chitin in the cell wall of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052179
-name: metabolism by symbiont of host cell wall pectin
+name: obsolete metabolism by symbiont of host cell wall pectin
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving pectin in the cell wall of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052175 ! metabolism by symbiont of host carbohydrate
-is_a: GO:0052413 ! metabolism by organism of cell wall pectin in other organism involved in symbiotic interaction
+alt_id: GO:0052413
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving pectin in the cell wall of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+synonym: "metabolism by organism of cell wall pectin in other organism involved in symbiotic interaction" NARROW []
+is_obsolete: true
[Term]
id: GO:0052180
-name: negative regulation of peptidase activity in other organism involved in symbiotic interaction
+name: obsolete negative regulation of peptidase activity in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of protease activity, the catalysis of the hydrolysis of peptide bonds in a protein, in a second organism, where the two organisms are in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of protease activity, the catalysis of the hydrolysis of peptide bonds in a protein, in a second organism, where the two organisms are in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of protease activity in other organism during symbiotic interaction" EXACT []
synonym: "down-regulation of protease activity in other organism during symbiotic interaction" EXACT []
synonym: "downregulation of protease activity in other organism during symbiotic interaction" EXACT []
synonym: "inhibition of protease activity in other organism during symbiotic interaction" NARROW []
synonym: "negative regulation of protease activity in other organism during symbiotic interaction" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0035940 ! negative regulation of peptidase activity in other organism
-is_a: GO:0052198 ! modulation of peptidase activity in other organism involved in symbiotic interaction
-is_a: GO:0052199 ! negative regulation of catalytic activity in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052181
@@ -319507,7 +319141,6 @@ name: modification by host of symbiont structure
namespace: biological_process
def: "The process in which an organism effects a change in an anatomical part or cellular component of the host organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0051851 ! modulation by host of symbiont process
-is_a: GO:0052185 ! modification of structure of other organism involved in symbiotic interaction
[Term]
id: GO:0052184
@@ -319520,11 +319153,12 @@ is_obsolete: true
[Term]
id: GO:0052185
-name: modification of structure of other organism involved in symbiotic interaction
+name: obsolete modification of structure of other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in an anatomical part or cellular component of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism effects a change in an anatomical part or cellular component of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modification of structure of other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052187
@@ -319532,15 +319166,15 @@ name: modification by host of symbiont cellular component
namespace: biological_process
def: "The process in which an organism effects a change in the structure or function of a symbiont cellular component. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0052183 ! modification by host of symbiont structure
-is_a: GO:0052188 ! modification of cellular component in other organism involved in symbiotic interaction
[Term]
id: GO:0052188
-name: modification of cellular component in other organism involved in symbiotic interaction
+name: obsolete modification of cellular component in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of a cellular component in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism effects a change in the structure or function of a cellular component in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modification of cellular component in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0052185 ! modification of structure of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052189
@@ -319637,27 +319271,27 @@ is_obsolete: true
[Term]
id: GO:0052198
-name: modulation of peptidase activity in other organism involved in symbiotic interaction
+name: obsolete modulation of peptidase activity in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in peptidase activity, the catalysis of the hydrolysis of peptide bonds in a protein, in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism effects a change in peptidase activity, the catalysis of the hydrolysis of peptide bonds in a protein, in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "modulation of protease activity in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "modulation of protease activity in other organism involved in symbiotic interaction" NARROW [GOC:bf]
-is_a: GO:0052203 ! modulation of catalytic activity in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052199
-name: negative regulation of catalytic activity in other organism involved in symbiotic interaction
+name: obsolete negative regulation of catalytic activity in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, GOC:tb]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, GOC:tb]
+comment: This term was obsoleted because it was an unnecessary grouping term.
synonym: "down regulation of enzyme activity in other organism during symbiotic interaction" RELATED []
synonym: "down-regulation of enzyme activity in other organism during symbiotic interaction" RELATED []
synonym: "downregulation of enzyme activity in other organism during symbiotic interaction" RELATED []
synonym: "inhibition of enzyme activity in other organism" EXACT []
synonym: "inhibition of enzyme activity in other organism during symbiotic interaction" NARROW []
synonym: "negative regulation of enzyme activity in other organism during symbiotic interaction" EXACT [GOC:tb]
-is_a: GO:0043086 ! negative regulation of catalytic activity
-is_a: GO:0052203 ! modulation of catalytic activity in other organism involved in symbiotic interaction
-is_a: GO:0052204 ! negative regulation of molecular function in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052200
@@ -319701,37 +319335,37 @@ is_obsolete: true
[Term]
id: GO:0052203
-name: modulation of catalytic activity in other organism involved in symbiotic interaction
+name: obsolete modulation of catalytic activity in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in enzyme activity in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, GOC:tb]
+def: "OBSOLETE. The process in which an organism effects a change in enzyme activity in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, GOC:tb]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modulation of enzyme activity within other organism during symbiotic interaction" EXACT [GOC:tb]
-is_a: GO:0050790 ! regulation of catalytic activity
-is_a: GO:0052205 ! modulation of molecular function in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052204
-name: negative regulation of molecular function in other organism involved in symbiotic interaction
+name: obsolete negative regulation of molecular function in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of proteins in a second organism, where the two organisms are in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of proteins in a second organism, where the two organisms are in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "down regulation of protein function in other organism during symbiotic interaction" EXACT []
synonym: "down-regulation of protein function in other organism during symbiotic interaction" EXACT []
synonym: "downregulation of protein function in other organism during symbiotic interaction" EXACT []
synonym: "inhibition of protein function in other organism" EXACT []
synonym: "inhibition of protein function in other organism during symbiotic interaction" NARROW []
synonym: "negative regulation of protein function in other organism during symbiotic interaction" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0044362 ! negative regulation of molecular function in other organism
-is_a: GO:0052205 ! modulation of molecular function in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052205
-name: modulation of molecular function in other organism involved in symbiotic interaction
+name: obsolete modulation of molecular function in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in the function of proteins in a second organism, where the two organisms are in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+def: "OBSOLETE. The process in which an organism effects a change in the function of proteins in a second organism, where the two organisms are in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modification of molecular function in other organism during symbiotic interaction" EXACT []
synonym: "modification of protein function in other organism during symbiotic interaction" EXACT [GOC:dph, GOC:tb]
synonym: "modulation of molecular function in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044359 ! modulation of molecular function in other organism
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052206
@@ -319810,12 +319444,12 @@ is_obsolete: true
[Term]
id: GO:0052214
-name: metabolism of substance in other organism involved in symbiotic interaction
+name: obsolete metabolism of substance in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "metabolism of substance in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044033 ! multi-organism metabolic process
-is_a: GO:0044419 ! biological process involved in interspecies interaction between organisms
+is_obsolete: true
[Term]
id: GO:0052215
@@ -319937,39 +319571,39 @@ is_obsolete: true
[Term]
id: GO:0052227
-name: catabolism of substance in other organism involved in symbiotic interaction
+name: obsolete catabolism of substance in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism in a second organism resulting in the breakdown of substances, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism in a second organism resulting in the breakdown of substances, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism of substance in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044035 ! multi-organism catabolic process
-is_a: GO:0052214 ! metabolism of substance in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052228
-name: metabolism by symbiont of host protein
+name: obsolete metabolism by symbiont of host protein
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving protein macromolecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052174 ! metabolism by symbiont of host macromolecule
-is_a: GO:0052418 ! metabolism by organism of protein in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving protein macromolecules within the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052229
-name: metabolism of macromolecule in other organism involved in symbiotic interaction
+name: obsolete metabolism of macromolecule in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving macromolecules within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving macromolecules within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "metabolism of macromolecule in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0043170 ! macromolecule metabolic process
-is_a: GO:0052214 ! metabolism of substance in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052230
-name: modulation of intracellular transport in other organism involved in symbiotic interaction
+name: obsolete modulation of intracellular transport in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism modulates the frequency, rate or extent of the directed movement of substances within the cell or cells of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. Any process in which an organism modulates the frequency, rate or extent of the directed movement of substances within the cell or cells of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modulation of intracellular trafficking in other organism" EXACT []
synonym: "modulation of intracellular transport in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0032386 ! regulation of intracellular transport
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052231
@@ -320134,11 +319768,12 @@ is_obsolete: true
[Term]
id: GO:0052249
-name: modulation of RNA levels in other organism involved in symbiotic interaction
+name: obsolete modulation of RNA levels in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The alteration by an organism of the levels of RNA in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The alteration by an organism of the levels of RNA in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modulation of RNA levels in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052257
@@ -320174,21 +319809,21 @@ consider: GO:0052034
[Term]
id: GO:0052312
-name: modulation of transcription in other organism involved in symbiotic interaction
+name: obsolete modulation of transcription in other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism modulates the frequency, rate or extent of transcription in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. Any process in which an organism modulates the frequency, rate or extent of transcription in a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modulation of transcription in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
-is_a: GO:2001141 ! regulation of RNA biosynthetic process
+is_obsolete: true
[Term]
id: GO:0052313
-name: modulation of nutrient release from other organism involved in symbiotic interaction
+name: obsolete modulation of nutrient release from other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism modulates the frequency, rate or extent of the release of nutrients from a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. Any process in which an organism modulates the frequency, rate or extent of the release of nutrients from a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modulation of nutrient release from other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0051817 ! modulation of process of other organism involved in symbiotic interaction
-relationship: part_of GO:0051816 ! acquisition of nutrients from other organism during symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052314
@@ -320362,9 +319997,10 @@ is_obsolete: true
[Term]
id: GO:0052331
-name: hemolysis in other organism involved in symbiotic interaction
+name: obsolete hemolysis in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another, where two organisms are in a symbiotic interaction." [GOC:add, UniProtKB-KW:KW-0354]
+def: "OBSOLETE. The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another, where two organisms are in a symbiotic interaction." [GOC:add, UniProtKB-KW:KW-0354]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "haemolysis in other organism involved in symbiotic interaction" EXACT []
synonym: "hemolysin activity" RELATED []
synonym: "hemolysis by organism of erythrocytes in other organism during symbiotic interaction" RELATED []
@@ -320372,35 +320008,36 @@ synonym: "hemolysis by organism of RBCs in other organism during symbiotic inter
synonym: "hemolysis by organism of red blood cells in other organism during symbiotic interaction" RELATED [CL:0000232]
synonym: "hemolysis of cells in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "hemolysis of cells in other organism involved in symbiotic interaction" EXACT [GOC:bf]
-is_a: GO:0044179 ! hemolysis in other organism
-is_a: GO:0051801 ! cytolysis in other organism involved in symbiotic interaction
-relationship: part_of GO:0044403 ! biological process involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052332
-name: modification by organism of membrane in other organism involved in symbiotic interaction
+name: obsolete modification by organism of membrane in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of a cellular membrane of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism effects a change in the structure or function of a cellular membrane of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modification by organism of cell membrane in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "modification by organism of cell membrane in other organism involved in symbiotic interaction" NARROW [GOC:bf, GOC:jl]
-is_a: GO:0052188 ! modification of cellular component in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052333
-name: modification by organism of cell wall of other organism involved in symbiotic interaction
+name: obsolete modification by organism of cell wall of other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism effects a change in the structure or function of the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "metabolism by organism of cell wall of other organism" RELATED []
synonym: "modification by organism of cell wall of other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0052188 ! modification of cellular component in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052334
-name: modification by organism of cytoskeleton of other organism involved in symbiotic interaction
+name: obsolete modification by organism of cytoskeleton of other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism effects a change in the structure or function of the cytoskeleton of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism effects a change in the structure or function of the cytoskeleton of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "modification by organism of cytoskeleton of other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0052188 ! modification of cellular component in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052335
@@ -320408,7 +320045,6 @@ name: modification by host of symbiont cytoskeleton
namespace: biological_process
def: "The process in which an organism effects a change in the structure or function of the symbiont cytoskeleton. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0052187 ! modification by host of symbiont cellular component
-is_a: GO:0052334 ! modification by organism of cytoskeleton of other organism involved in symbiotic interaction
[Term]
id: GO:0052336
@@ -320417,7 +320053,6 @@ namespace: biological_process
def: "The process in which an organism effects a change in the structure or function of the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
synonym: "metabolism of symbiont cell wall by organism" EXACT []
is_a: GO:0052187 ! modification by host of symbiont cellular component
-is_a: GO:0052333 ! modification by organism of cell wall of other organism involved in symbiotic interaction
[Term]
id: GO:0052337
@@ -320426,7 +320061,6 @@ namespace: biological_process
def: "The process in which an organism effects a change in the structure or function of a symbiont cellular membrane. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "modification by host of symbiont cell membrane" NARROW [GOC:bf, GOC:jl]
is_a: GO:0052187 ! modification by host of symbiont cellular component
-is_a: GO:0052332 ! modification by organism of membrane in other organism involved in symbiotic interaction
[Term]
id: GO:0052338
@@ -320437,51 +320071,42 @@ synonym: "catabolism of symbiont cell wall by organism" EXACT []
synonym: "degradation of symbiont cell wall by organism" EXACT []
synonym: "disassembly by host of symbiont cell wall" EXACT []
is_a: GO:0052336 ! modification by host of symbiont cell wall
-is_a: GO:0052339 ! disruption by organism of cell wall of other organism involved in symbiotic interaction
-is_a: GO:0052367 ! disruption by host of symbiont cellular component
[Term]
id: GO:0052339
-name: disruption by organism of cell wall of other organism involved in symbiotic interaction
+name: obsolete disruption by organism of cell wall of other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "disassembly by organism of cell wall of other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0052333 ! modification by organism of cell wall of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052340
-name: catabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
+name: obsolete catabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of cellulose in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of cellulose in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "catabolism by organism of cell wall cellulose in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0030245 ! cellulose catabolic process
-is_a: GO:0044347 ! cell wall polysaccharide catabolic process
-is_a: GO:0052354 ! catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052409 ! metabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
-relationship: part_of GO:0044278 ! cell wall disruption in other organism
-relationship: part_of GO:0052339 ! disruption by organism of cell wall of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052341
-name: catabolism by organism of cell wall pectin in other organism involved in symbiotic interaction
+name: obsolete catabolism by organism of cell wall pectin in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of pectin in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of pectin in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "catabolism by organism of cell wall pectin in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0052354 ! catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052413 ! metabolism by organism of cell wall pectin in other organism involved in symbiotic interaction
-relationship: part_of GO:0044278 ! cell wall disruption in other organism
-relationship: part_of GO:0052339 ! disruption by organism of cell wall of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052342
-name: catabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
+name: obsolete catabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of chitin in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of chitin in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "catabolism by organism of cell wall chitin in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0006039 ! cell wall chitin catabolic process
-is_a: GO:0052354 ! catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052411 ! metabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
-relationship: part_of GO:0052339 ! disruption by organism of cell wall of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052343
@@ -320568,136 +320193,120 @@ is_obsolete: true
[Term]
id: GO:0052353
-name: catabolism by host of symbiont carbohydrate
+name: obsolete catabolism by host of symbiont carbohydrate
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of carbohydrate molecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052354 ! catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052360 ! catabolism by host of symbiont macromolecule
-is_a: GO:0052406 ! metabolism by host of symbiont carbohydrate
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of carbohydrate molecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052354
-name: catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
+name: obsolete catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of carbohydrate molecules within a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of carbohydrate molecules within a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "catabolism by organism of carbohydrate in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044041 ! multi-organism carbohydrate catabolic process
-is_a: GO:0052361 ! catabolism by organism of macromolecule in other organism involved in symbiotic interaction
-is_a: GO:0052407 ! metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052355
-name: catabolism by host of symbiont cell wall cellulose
+name: obsolete catabolism by host of symbiont cell wall cellulose
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of cellulose in the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052340 ! catabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
-is_a: GO:0052353 ! catabolism by host of symbiont carbohydrate
-is_a: GO:0052408 ! metabolism by host of symbiont cell wall cellulose
-relationship: part_of GO:0052338 ! disruption by host of symbiont cell wall
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of cellulose in the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052356
-name: catabolism by host of symbiont cell wall chitin
+name: obsolete catabolism by host of symbiont cell wall chitin
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of chitin in the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052342 ! catabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
-is_a: GO:0052353 ! catabolism by host of symbiont carbohydrate
-is_a: GO:0052410 ! metabolism by host of symbiont cell wall chitin
-relationship: part_of GO:0052338 ! disruption by host of symbiont cell wall
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of chitin in the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [PMID:11085997]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052357
-name: catabolism by host of symbiont cell wall pectin
+name: obsolete catabolism by host of symbiont cell wall pectin
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of pectin in the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052341 ! catabolism by organism of cell wall pectin in other organism involved in symbiotic interaction
-is_a: GO:0052353 ! catabolism by host of symbiont carbohydrate
-is_a: GO:0052412 ! metabolism by host of symbiont cell wall pectin
-relationship: part_of GO:0052338 ! disruption by host of symbiont cell wall
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of pectin in the symbiont cell wall. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because there is no evidence it exists.
+is_obsolete: true
[Term]
id: GO:0052358
-name: catabolism by host of symbiont glucan
+name: obsolete catabolism by host of symbiont glucan
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of glucan molecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052353 ! catabolism by host of symbiont carbohydrate
-is_a: GO:0052359 ! catabolism by organism of glucan in other organism involved in symbiotic interaction
-is_a: GO:0052414 ! metabolism by host of symbiont glucan
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of glucan molecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because there is no evidence it exists.
+is_obsolete: true
[Term]
id: GO:0052359
-name: catabolism by organism of glucan in other organism involved in symbiotic interaction
+name: obsolete catabolism by organism of glucan in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of glucan molecules within a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of glucan molecules within a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "catabolism by organism of glucan in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0000272 ! polysaccharide catabolic process
-is_a: GO:0052354 ! catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052415 ! metabolism by organism of glucan in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052360
-name: catabolism by host of symbiont macromolecule
+name: obsolete catabolism by host of symbiont macromolecule
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of macromolecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052361 ! catabolism by organism of macromolecule in other organism involved in symbiotic interaction
-is_a: GO:0052364 ! catabolism by host of substance in symbiont
-is_a: GO:0052416 ! metabolism by host of symbiont macromolecule
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of macromolecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052361
-name: catabolism by organism of macromolecule in other organism involved in symbiotic interaction
+name: obsolete catabolism by organism of macromolecule in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of macromolecules within a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of macromolecules within a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "catabolism by organism of macromolecule in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0009057 ! macromolecule catabolic process
-is_a: GO:0052227 ! catabolism of substance in other organism involved in symbiotic interaction
-is_a: GO:0052229 ! metabolism of macromolecule in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052362
-name: catabolism by host of symbiont protein
+name: obsolete catabolism by host of symbiont protein
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of protein macromolecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052360 ! catabolism by host of symbiont macromolecule
-is_a: GO:0052363 ! catabolism by organism of protein in other organism involved in symbiotic interaction
-is_a: GO:0052417 ! metabolism by host of symbiont protein
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of protein macromolecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052363
-name: catabolism by organism of protein in other organism involved in symbiotic interaction
+name: obsolete catabolism by organism of protein in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of protein macromolecules within the second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of protein macromolecules within the second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "catabolism by organism of protein in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0030163 ! protein catabolic process
-is_a: GO:0052361 ! catabolism by organism of macromolecule in other organism involved in symbiotic interaction
-is_a: GO:0052418 ! metabolism by organism of protein in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052364
-name: catabolism by host of substance in symbiont
+name: obsolete catabolism by host of substance in symbiont
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism in its symbiont resulting in the breakdown of substances. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052227 ! catabolism of substance in other organism involved in symbiotic interaction
-is_a: GO:0052419 ! metabolism by host of substance in symbiont
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism in its symbiont resulting in the breakdown of substances. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052365
-name: catabolism by host of symbiont xylan
+name: obsolete catabolism by host of symbiont xylan
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of xylan within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052353 ! catabolism by host of symbiont carbohydrate
-is_a: GO:0052366 ! catabolism by organism of xylan in other organism involved in symbiotic interaction
-is_a: GO:0052420 ! metabolism by host of symbiont xylan
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of xylan within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because there is no evidence it exists.
+is_obsolete: true
[Term]
id: GO:0052366
-name: catabolism by organism of xylan in other organism involved in symbiotic interaction
+name: obsolete catabolism by organism of xylan in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of xylan within a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of xylan within a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "catabolism by organism of xylan in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0045493 ! xylan catabolic process
-is_a: GO:0052354 ! catabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052421 ! metabolism by organism of xylan in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052367
@@ -320709,19 +320318,19 @@ synonym: "catabolism of symbiont structural constituent by organism" EXACT []
synonym: "degradation of symbiont cellular component by organism" EXACT []
synonym: "disassembly by host of symbiont cellular component" RELATED []
is_a: GO:0052187 ! modification by host of symbiont cellular component
-is_a: GO:0052368 ! disruption by organism of cellular component in other organism involved in symbiotic interaction
[Term]
id: GO:0052368
-name: disruption by organism of cellular component in other organism involved in symbiotic interaction
+name: obsolete disruption by organism of cellular component in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism resulting in the breakdown of cellular components of a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism resulting in the breakdown of cellular components of a second organism, where the two organisms are in a symbiotic interaction." [ISBN:0198547684]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "catabolism of cellular component in other organism" EXACT []
synonym: "catabolism of structural constituent in other organism" EXACT []
synonym: "degradation of cellular component in other organism" EXACT []
synonym: "disassembly by organism of cellular component in other organism during symbiotic interaction" RELATED [GOC:dph]
synonym: "disassembly by organism of cellular component in other organism involved in symbiotic interaction" RELATED []
-is_a: GO:0052185 ! modification of structure of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052372
@@ -320730,7 +320339,6 @@ namespace: biological_process
alt_id: GO:0052371
def: "Any process in which an organism modulates the frequency, rate or extent to which it enters into the host organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "modulation by organism of entry into other organism during symbiotic interaction" RELATED []
-synonym: "modulation by symbiont of entry into host" RELATED []
synonym: "regulation by organism of entry into other organism during symbiotic interaction" RELATED [GOC:tb]
synonym: "regulation by organism of entry into other organism involved in symbiotic interaction" RELATED []
is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
@@ -320738,7 +320346,7 @@ relationship: regulates GO:0044409 ! entry into host
[Term]
id: GO:0052373
-name: suppression of symbiont entry into host by host
+name: suppression of symbiont entry into host
namespace: biological_process
def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent to which it enters into a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "down regulation by organism of entry into other organism during symbiotic interaction" RELATED []
@@ -320747,8 +320355,8 @@ synonym: "downregulation by organism of entry into other organism during symbiot
synonym: "inhibition by organism of entry into other organism during symbiotic interaction" NARROW []
synonym: "negative regulation by organism of entry into other organism during symbiotic interaction" RELATED [GOC:tb]
synonym: "negative regulation by organism of entry into other organism involved in symbiotic interaction" BROAD []
-is_a: GO:0043901 ! negative regulation of multi-organism process
-is_a: GO:0098542 ! defense response to other organism
+synonym: "suppression of symbiont entry into host by host" EXACT []
+is_a: GO:0140546 ! defense response to symbiont
[Term]
id: GO:0052374
@@ -321037,194 +320645,171 @@ is_obsolete: true
id: GO:0052403
name: negative regulation by host of symbiont catalytic activity
namespace: biological_process
+alt_id: GO:0052405
def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of symbiont enzyme activity. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "down regulation by host of symbiont enzyme activity" EXACT []
+synonym: "down regulation by host of symbiont protein function" BROAD []
synonym: "down-regulation by host of symbiont enzyme activity" EXACT []
+synonym: "down-regulation by host of symbiont protein function" BROAD []
synonym: "downregulation by host of symbiont enzyme activity" EXACT []
+synonym: "downregulation by host of symbiont protein function" BROAD []
synonym: "inhibition by host of symbiont enzyme activity" NARROW []
+synonym: "inhibition by host of symbiont protein function" NARROW []
synonym: "inhibition of symbiont enzyme activity" EXACT []
+synonym: "inhibition of symbiont protein function" BROAD []
synonym: "negative regulation by host of symbiont enzyme activity" EXACT []
-is_a: GO:0052199 ! negative regulation of catalytic activity in other organism involved in symbiotic interaction
-is_a: GO:0052405 ! negative regulation by host of symbiont molecular function
+synonym: "negative regulation by host of symbiont molecular function" BROAD []
is_a: GO:0052422 ! modulation by host of symbiont catalytic activity
[Term]
id: GO:0052404
-name: negative regulation by host of symbiont peptidase activity
+name: obsolete negative regulation by host of symbiont peptidase activity
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of symbiont protease activity, the catalysis of the hydrolysis of peptide bonds in a protein. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of symbiont protease activity, the catalysis of the hydrolysis of peptide bonds in a protein. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation by host of symbiont protease activity" NARROW []
synonym: "down-regulation by host of symbiont protease activity" NARROW []
synonym: "downregulation by host of symbiont protease activity" NARROW []
synonym: "inhibition by host of symbiont protease activity" NARROW []
synonym: "inhibition of symbiont protease activity" NARROW []
synonym: "negative regulation by host of symbiont protease activity" NARROW [GOC:dph, GOC:tb]
-is_a: GO:0052180 ! negative regulation of peptidase activity in other organism involved in symbiotic interaction
-is_a: GO:0052403 ! negative regulation by host of symbiont catalytic activity
-is_a: GO:0052427 ! modulation by host of symbiont peptidase activity
-
-[Term]
-id: GO:0052405
-name: negative regulation by host of symbiont molecular function
-namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the functional activity of symbiont proteins. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
-synonym: "down regulation by host of symbiont protein function" EXACT []
-synonym: "down-regulation by host of symbiont protein function" EXACT []
-synonym: "downregulation by host of symbiont protein function" EXACT []
-synonym: "inhibition by host of symbiont protein function" NARROW []
-synonym: "inhibition of symbiont protein function" EXACT []
-synonym: "negative regulation by host of symbiont protein function" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0052204 ! negative regulation of molecular function in other organism involved in symbiotic interaction
-is_a: GO:0052428 ! modulation by host of symbiont molecular function
+is_obsolete: true
[Term]
id: GO:0052406
-name: metabolism by host of symbiont carbohydrate
+name: obsolete metabolism by host of symbiont carbohydrate
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving carbohydrates within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052407 ! metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052416 ! metabolism by host of symbiont macromolecule
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving carbohydrates within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052407
-name: metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
+name: obsolete metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving carbohydrates within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving carbohydrates within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "metabolism by organism of carbohydrate in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044040 ! multi-organism carbohydrate metabolic process
-is_a: GO:0052229 ! metabolism of macromolecule in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052408
-name: metabolism by host of symbiont cell wall cellulose
+name: obsolete metabolism by host of symbiont cell wall cellulose
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving cellulose in the cell wall of the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052406 ! metabolism by host of symbiont carbohydrate
-is_a: GO:0052409 ! metabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving cellulose in the cell wall of the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052409
-name: metabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
+name: obsolete metabolism by organism of cell wall cellulose in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving cellulose in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving cellulose in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "metabolism by organism of cell wall cellulose in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044037 ! multi-organism cell wall macromolecule metabolic process
-is_a: GO:0044043 ! multi-organism glucan metabolic process
-is_a: GO:0052407 ! metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052541 ! plant-type cell wall cellulose metabolic process
+is_obsolete: true
[Term]
id: GO:0052410
-name: metabolism by host of symbiont cell wall chitin
+name: obsolete metabolism by host of symbiont cell wall chitin
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving chitin in the cell wall of the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052406 ! metabolism by host of symbiont carbohydrate
-is_a: GO:0052411 ! metabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving chitin in the cell wall of the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052411
-name: metabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
+name: obsolete metabolism by organism of cell wall chitin in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving chitin in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving chitin in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "metabolism by organism of cell wall chitin in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0006037 ! cell wall chitin metabolic process
-is_a: GO:0044037 ! multi-organism cell wall macromolecule metabolic process
-is_a: GO:0052407 ! metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052412
-name: metabolism by host of symbiont cell wall pectin
+name: obsolete metabolism by host of symbiont cell wall pectin
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving pectin in the cell wall of the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052406 ! metabolism by host of symbiont carbohydrate
-is_a: GO:0052413 ! metabolism by organism of cell wall pectin in other organism involved in symbiotic interaction
-
-[Term]
-id: GO:0052413
-name: metabolism by organism of cell wall pectin in other organism involved in symbiotic interaction
-namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving pectin in the cell wall of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-synonym: "metabolism by organism of cell wall pectin in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044037 ! multi-organism cell wall macromolecule metabolic process
-is_a: GO:0052407 ! metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
-is_a: GO:0052546 ! cell wall pectin metabolic process
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving pectin in the cell wall of the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because there is no evidence it exists.
+is_obsolete: true
[Term]
id: GO:0052414
-name: metabolism by host of symbiont glucan
+name: obsolete metabolism by host of symbiont glucan
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving glucans within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052406 ! metabolism by host of symbiont carbohydrate
-is_a: GO:0052415 ! metabolism by organism of glucan in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving glucans within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052415
-name: metabolism by organism of glucan in other organism involved in symbiotic interaction
+name: obsolete metabolism by organism of glucan in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving glucans within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving glucans within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "metabolism by organism of glucan in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044043 ! multi-organism glucan metabolic process
-is_a: GO:0052407 ! metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052416
-name: metabolism by host of symbiont macromolecule
+name: obsolete metabolism by host of symbiont macromolecule
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving macromolecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052229 ! metabolism of macromolecule in other organism involved in symbiotic interaction
-is_a: GO:0052419 ! metabolism by host of substance in symbiont
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving macromolecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052417
-name: metabolism by host of symbiont protein
+name: obsolete metabolism by host of symbiont protein
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving protein macromolecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052416 ! metabolism by host of symbiont macromolecule
-is_a: GO:0052418 ! metabolism by organism of protein in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving protein macromolecules within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052418
-name: metabolism by organism of protein in other organism involved in symbiotic interaction
+name: obsolete metabolism by organism of protein in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving protein macromolecules within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving protein macromolecules within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "metabolism by organism of protein in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0019538 ! protein metabolic process
-is_a: GO:0052229 ! metabolism of macromolecule in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052419
-name: metabolism by host of substance in symbiont
+name: obsolete metabolism by host of substance in symbiont
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism in its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0051851 ! modulation by host of symbiont process
-is_a: GO:0052214 ! metabolism of substance in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism in its symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0052420
-name: metabolism by host of symbiont xylan
+name: obsolete metabolism by host of symbiont xylan
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving xylan within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
-is_a: GO:0052406 ! metabolism by host of symbiont carbohydrate
-is_a: GO:0052421 ! metabolism by organism of xylan in other organism involved in symbiotic interaction
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving xylan within the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because there is no evidence it exists.
+is_obsolete: true
[Term]
id: GO:0052421
-name: metabolism by organism of xylan in other organism involved in symbiotic interaction
+name: obsolete metabolism by organism of xylan in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The chemical reactions and pathways performed by an organism involving xylan within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The chemical reactions and pathways performed by an organism involving xylan within a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was deprecated because it represents an unnecessary grouping class.
synonym: "metabolism by organism of xylan in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0044037 ! multi-organism cell wall macromolecule metabolic process
-is_a: GO:0045491 ! xylan metabolic process
-is_a: GO:0052407 ! metabolism by organism of carbohydrate in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052422
name: modulation by host of symbiont catalytic activity
namespace: biological_process
+alt_id: GO:0052428
def: "The process in which a host organism effects a change in the enzyme activity of its symbiont organism." [GOC:mtg_pamgo_17jul06, GOC:tb]
synonym: "modulation by host of symbiont enzyme activity" EXACT [GOC:tb]
-is_a: GO:0052203 ! modulation of catalytic activity in other organism involved in symbiotic interaction
-is_a: GO:0052428 ! modulation by host of symbiont molecular function
+synonym: "modulation by host of symbiont molecular function" BROAD []
+is_a: GO:0051851 ! modulation by host of symbiont process
[Term]
id: GO:0052424
@@ -321255,23 +320840,12 @@ is_obsolete: true
[Term]
id: GO:0052427
-name: modulation by host of symbiont peptidase activity
+name: obsolete modulation by host of symbiont peptidase activity
namespace: biological_process
-def: "The process in which an organism effects a change in symbiont peptidase activity, the catalysis of the hydrolysis of peptide bonds in a protein. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism effects a change in symbiont peptidase activity, the catalysis of the hydrolysis of peptide bonds in a protein. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "modulation by host of symbiont protease activity" NARROW [GOC:bf]
-is_a: GO:0052198 ! modulation of peptidase activity in other organism involved in symbiotic interaction
-is_a: GO:0052422 ! modulation by host of symbiont catalytic activity
-is_a: GO:0052547 ! regulation of peptidase activity
-
-[Term]
-id: GO:0052428
-name: modulation by host of symbiont molecular function
-namespace: biological_process
-def: "The process in which an organism effects a change in the function of proteins in the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:mtg_pamgo_17jul06, GOC:tb]
-synonym: "modification by host of symbiont molecular function" EXACT []
-synonym: "modification by host of symbiont protein function" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0051851 ! modulation by host of symbiont process
-is_a: GO:0052205 ! modulation of molecular function in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052429
@@ -321289,7 +320863,6 @@ name: modulation by host of symbiont RNA levels
namespace: biological_process
def: "The alteration by an organism of the levels of RNA in a symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0051851 ! modulation by host of symbiont process
-is_a: GO:0052249 ! modulation of RNA levels in other organism involved in symbiotic interaction
[Term]
id: GO:0052431
@@ -321503,11 +321076,11 @@ is_obsolete: true
[Term]
id: GO:0052460
-name: modulation by host of nutrient release from symbiont
+name: modulation of nutrient release by symbiont
namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of the release of nutrients from a symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+synonym: "modulation by host of nutrient release from symbiont" EXACT []
is_a: GO:0051851 ! modulation by host of symbiont process
-is_a: GO:0052313 ! modulation of nutrient release from other organism involved in symbiotic interaction
relationship: part_of GO:0051850 ! acquisition of nutrients from symbiont
[Term]
@@ -321620,7 +321193,6 @@ name: modulation by host of symbiont transcription
namespace: biological_process
def: "Any process in which an organism modulates the frequency, rate or extent of its symbiont's transcription." [GOC:mtg_pamgo_17jul06]
is_a: GO:0051851 ! modulation by host of symbiont process
-is_a: GO:0052312 ! modulation of transcription in other organism involved in symbiotic interaction
[Term]
id: GO:0052473
@@ -321788,7 +321360,7 @@ synonym: "down-regulation by host of symbiont programmed cell death" EXACT []
synonym: "downregulation by host of symbiont programmed cell death" EXACT []
synonym: "inhibition by host of symbiont programmed cell death" NARROW []
synonym: "inhibition of symbiont programmed cell death" EXACT []
-is_a: GO:0051711 ! negative regulation of killing of cells of other organism
+is_a: GO:0051711 ! negative regulation of killing of cells of another organism
[Term]
id: GO:0052491
@@ -321821,15 +321393,15 @@ name: occlusion by host of symbiont vascular system
namespace: biological_process
def: "The process in which an organism reduces the flow of fluid within its symbiont's vascular system, the vessels and tissue that carry or circulate fluids, such as blood, lymph or sap, through the body of an animal or plant. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, http://www.thefreedictionary.com]
is_a: GO:0052183 ! modification by host of symbiont structure
-is_a: GO:0052495 ! occlusion by organism of vascular system in other organism involved in symbiotic interaction
[Term]
id: GO:0052495
-name: occlusion by organism of vascular system in other organism involved in symbiotic interaction
+name: obsolete occlusion by organism of vascular system in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism reduces the flow of fluid within its second organism's vascular system, the vessels and tissue that carry or circulate fluids, such as blood, lymph or sap, through the body of an animal or plant, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, http://www.thefreedictionary.com]
+def: "OBSOLETE. The process in which an organism reduces the flow of fluid within its second organism's vascular system, the vessels and tissue that carry or circulate fluids, such as blood, lymph or sap, through the body of an animal or plant, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06, http://www.thefreedictionary.com]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "occlusion by organism of vascular system in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0052185 ! modification of structure of other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052496
@@ -321837,15 +321409,15 @@ name: occlusion by host of symbiont xylem
namespace: biological_process
def: "The process in which an organism reduces the flow of fluid within the symbiont xylem, the tissue in plants that carries water and nutrients up from the roots to the shoot and leaves. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
is_a: GO:0052494 ! occlusion by host of symbiont vascular system
-is_a: GO:0052497 ! occlusion by organism of xylem in other organism involved in symbiotic interaction
[Term]
id: GO:0052497
-name: occlusion by organism of xylem in other organism involved in symbiotic interaction
+name: obsolete occlusion by organism of xylem in other organism involved in symbiotic interaction
namespace: biological_process
-def: "The process in which an organism reduces the flow of fluid within the xylem, the tissue in plants that carries water and nutrients up from the roots to the shoot and leaves, of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. The process in which an organism reduces the flow of fluid within the xylem, the tissue in plants that carries water and nutrients up from the roots to the shoot and leaves, of a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "occlusion by organism of xylem in other organism during symbiotic interaction" RELATED [GOC:dph]
-is_a: GO:0052495 ! occlusion by organism of vascular system in other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052498
@@ -322040,23 +321612,24 @@ is_obsolete: true
[Term]
id: GO:0052519
-name: positive regulation by host of nutrient release from symbiont
+name: positive regulation of nutrient release by symbiont
namespace: biological_process
def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of the release of nutrients from a symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
synonym: "activation by host of nutrient release from symbiont" NARROW []
+synonym: "positive regulation by host of nutrient release from symbiont" EXACT []
synonym: "promotion of nutrient release from symbiont" EXACT []
synonym: "stimulation by host of nutrient release from symbiont" NARROW []
synonym: "up regulation by host of nutrient release from symbiont" EXACT []
synonym: "up-regulation by host of nutrient release from symbiont" EXACT []
synonym: "upregulation by host of nutrient release from symbiont" EXACT []
-is_a: GO:0052460 ! modulation by host of nutrient release from symbiont
-is_a: GO:0052520 ! positive regulation by organism of nutrient release from other organism involved in symbiotic interaction
+is_a: GO:0052460 ! modulation of nutrient release by symbiont
[Term]
id: GO:0052520
-name: positive regulation by organism of nutrient release from other organism involved in symbiotic interaction
+name: obsolete positive regulation by organism of nutrient release from other organism involved in symbiotic interaction
namespace: biological_process
-def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of the release of nutrients from a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+def: "OBSOLETE. Any process in which an organism activates, maintains or increases the frequency, rate or extent of the release of nutrients from a second organism, where the two organisms are in a symbiotic interaction." [GOC:mtg_pamgo_17jul06]
+comment: This term was obsoleted because it represents an unnecessary grouping class.
synonym: "activation by organism of nutrient release from other organism during symbiotic interaction" NARROW []
synonym: "positive regulation by organism of nutrient release from other organism during symbiotic interaction" RELATED [GOC:tb]
synonym: "promotion of nutrient release from other organism" EXACT []
@@ -322064,7 +321637,7 @@ synonym: "stimulation by organism of nutrient release from other organism during
synonym: "up regulation by organism of nutrient release from other organism during symbiotic interaction" RELATED []
synonym: "up-regulation by organism of nutrient release from other organism during symbiotic interaction" RELATED []
synonym: "upregulation by organism of nutrient release from other organism during symbiotic interaction" RELATED []
-is_a: GO:0052313 ! modulation of nutrient release from other organism involved in symbiotic interaction
+is_obsolete: true
[Term]
id: GO:0052521
@@ -322485,12 +322058,12 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
id: GO:0052581
name: (-)-isopiperitenone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (6R)-isoperitenone + H(+) + NADPH = (2R,5R)-isopulegone + NADP(+)." [EC:1.3.1.82, RHEA:25651]
+def: "Catalysis of the reaction: (6R)-isoperitenone + H(+) + NADPH = (2R,5R)-isopulegone + NADP(+)." [EC:1.3.1.82, RHEA:25649]
synonym: "(+)-cis-isopulegone:NADP+ oxidoreductase activity" RELATED [EC:1.3.1.82]
xref: EC:1.3.1.82
xref: KEGG_REACTION:R06417
xref: MetaCyc:RXN-5161
-xref: RHEA:25651
+xref: RHEA:25649
is_a: GO:0035671 ! enone reductase activity
[Term]
@@ -322824,7 +322397,6 @@ id: GO:0052611
name: beta-carotene 3-hydroxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: beta-carotene + a reduced electron acceptor + oxygen = beta-cryptoxanthin + an oxidized electron acceptor + H2O." [RHEA:30323]
-synonym: "beta-carotene 3-hydroxylase activity" BROAD [MetaCyc:MONOMER-12386]
synonym: "beta-carotene hydroxylase activity" BROAD []
synonym: "carotene beta-ring hydroxylase activity" BROAD []
xref: MetaCyc:RXN-8025
@@ -323466,28 +323038,22 @@ is_a: GO:0008912 ! lactaldehyde reductase activity
id: GO:0052662
name: zeaxanthin epoxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: zeaxanthin + NAD(P)H + H+ + O2 = antheraxanthin + NAD(P)+ + H2O." [EC:1.14.13.90, RHEA:24084]
-synonym: "zea-epoxidase activity" RELATED [EC:1.14.13.90]
-synonym: "zeaxanthin,NAD(P)H:oxygen oxidoreductase activity" RELATED [EC:1.14.13.90]
-xref: EC:1.14.13.90
+alt_id: GO:0009540
+alt_id: GO:0052663
+def: "Catalysis of the reaction: all-trans-zeaxanthin + 4 H+ + 2 O2 + 4 reduced [2Fe-2S]-[ferredoxin] = all-trans-violaxanthin + 2 H2O + 4 oxidized [2Fe-2S]-[ferredoxin]." [RHEA:32443]
+comment: Multi-step reaction: RHEA:14937 and RHEA:24084. Formerly EC:1.14.13.90.
+synonym: "antheraxanthin epoxidase activity" NARROW []
+synonym: "zea-epoxidase activity" RELATED [EC:1.14.15.21]
+synonym: "zeaxanthin epoxidase [overall] activity" RELATED []
+xref: EC:1.14.15.21
xref: KEGG_REACTION:R06946 "zeaxanthin,NADH:oxygen oxidoreductase activity"
-xref: KEGG_REACTION:R07199 "zeaxanthin,NADPH:oxygen oxidoreductase activity"
-xref: MetaCyc:RXN-7978
-xref: RHEA:24084
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
-
-[Term]
-id: GO:0052663
-name: antheraxanthin epoxidase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: antheraxanthin + NAD(P)H + H+ + O2 = all-trans-violaxanthin + NAD(P)+ + H2O." [MetaCyc:RXN-7979, RHEA:14937]
-synonym: "antheraxanthin,NAD(P)H:oxygen oxidoreductase activity" RELATED [EC:1.14.13.90]
-xref: EC:1.14.13.90
xref: KEGG_REACTION:R06947 "antheraxanthin,NADH:oxygen oxidoreductase activity"
+xref: KEGG_REACTION:R07199 "zeaxanthin,NADPH:oxygen oxidoreductase activity"
xref: KEGG_REACTION:R07200 "antheraxanthin,NADPH:oxygen oxidoreductase activity"
+xref: MetaCyc:RXN-7978
xref: MetaCyc:RXN-7979
-xref: RHEA:14937
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
+xref: RHEA:24084
+is_a: GO:0016713 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0052664
@@ -323541,35 +323107,31 @@ is_a: GO:0016427 ! tRNA (cytosine) methyltransferase activity
id: GO:0052667
name: phosphomethylethanolamine N-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+)." [KEGG_REACTION:R06868, MetaCyc:RXN-5642, RHEA:25322]
+def: "Catalysis of the reaction: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+)." [RHEA:25321]
synonym: "N-methylethanolamine phosphate N-methyltransferase activity" EXACT []
synonym: "S-adenosyl-L-methionine:methylethanolamine phosphate N-methyltransferase activity" EXACT systematic_synonym [KEGG_REACTION:R06868]
+xref: EC:2.1.1.103
xref: KEGG_REACTION:R06868
xref: MetaCyc:RXN-5642
-xref: RHEA:25322
+xref: RHEA:25321
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:0052668
-name: farnesol kinase activity
+name: CTP:farnesol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: farnesol + nucleoside triphosphate = farnesyl monophosphate + nucleoside diphosphate." [GOC:kd, MetaCyc:RXN-11625]
+alt_id: GO:0052669
+def: "Catalysis of the reaction: 2-trans,-6-trans-farnesol + CTP = 2-trans,-6-trans-farnesyl monophosphate + CDP + H+." [PMID:21395888, RHEA:51680]
+synonym: "CTP:2-trans,-6-trans-farnesol kinase activity" EXACT []
+synonym: "CTP:2-trans,-6-trans-farnesol phosphotransferase activity" EXACT []
+synonym: "farnesol kinase activity" RELATED []
synonym: "farnesol phosphotransferase activity" EXACT []
synonym: "trans,trans-farnesol kinase activity" NARROW []
xref: EC:2.7.1.216
-is_a: GO:0052673 ! prenol kinase activity
-
-[Term]
-id: GO:0052669
-name: CTP:2-trans,-6-trans-farnesol kinase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 2-trans,-6-trans-farnesol + CTP = 2-trans,-6-trans-farnesyl monophosphate + CDP + H+." [MetaCyc:RXN-11625]
-synonym: "CTP:2-trans,-6-trans-farnesol phosphotransferase activity" EXACT []
-xref: EC:2.7.1.216
xref: MetaCyc:RXN-11625
xref: RHEA:51680
-is_a: GO:0052668 ! farnesol kinase activity
+is_a: GO:0052673 ! prenol kinase activity
[Term]
id: GO:0052670
@@ -323806,7 +323368,6 @@ synonym: "carboxyl ester hydrolase activity" RELATED [EC:3.1.1.1]
synonym: "carboxylate esterase activity" RELATED [EC:3.1.1.1]
synonym: "carboxylesterase activity" EXACT []
synonym: "carboxylic acid esterase activity" EXACT []
-synonym: "carboxylic ester hydrolase activity" RELATED []
synonym: "carboxylic esterase activity" RELATED [EC:3.1.1.1]
synonym: "cocaine esterase activity" NARROW [EC:3.1.1.1]
synonym: "esterase A" NARROW [EC:3.1.1.1]
@@ -325402,15 +324963,14 @@ is_a: GO:0052745 ! inositol phosphate phosphatase activity
id: GO:0052835
name: inositol-3,4,6-trisphosphate 1-kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1D-myo-inositol 3,4,6-trisphosphate + ATP = 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ADP + 2 H(+)." [EC:2.7.1.134]
+def: "Catalysis of the reaction: 1D-myo-inositol 3,4,6-trisphosphate + ATP = 1D-myo-inositol 1,3,4,6-tetrakisphosphate + ADP + 2 H(+)." [GOC:curators]
synonym: "1D-myo-inositol-trisphosphate 1-kinase activity" BROAD []
-synonym: "ATP:1D-myo-inositol-3,4,6-trisphosphate 1-phosphotransferase activity" RELATED [EC:2.7.1.127]
+synonym: "ATP:1D-myo-inositol-3,4,6-trisphosphate 1-phosphotransferase activity" RELATED []
synonym: "inositol 3,4,6-trisphosphate 1-kinase activity" EXACT []
synonym: "inositol-trisphosphate 1-kinase activity" BROAD []
-synonym: "ins(3,4,6)P(3) 1-kinase activity" RELATED [EC:2.7.1.127]
-synonym: "Ins(3,4,6)P3 1-kinase activity" RELATED [EC:2.7.1.127]
-synonym: "IP3 1-kinase activity" BROAD [EC:2.7.1.127]
-xref: EC:2.7.1.-
+synonym: "ins(3,4,6)P(3) 1-kinase activity" RELATED []
+synonym: "Ins(3,4,6)P3 1-kinase activity" RELATED []
+synonym: "IP3 1-kinase activity" BROAD []
xref: Reactome:R-HSA-1855169 "I(3,4,6)P3 is phosphorylated to I(1,3,4,6)P4 by ITPK1 in the cytosol"
is_a: GO:0051766 ! inositol trisphosphate kinase activity
@@ -325456,7 +325016,7 @@ is_a: GO:1901564 ! organonitrogen compound metabolic process
id: GO:0052839
name: inositol diphosphate tetrakisphosphate kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: Catalysis of the reaction: ATP + inositol diphosphate tetrakisphosphate = ADP + inositol bisdiphosphate trisphosphate." [PMID:10827188, PMID:11502751, PMID:18355727]
+def: "Catalysis of the reaction: ATP + inositol diphosphate tetrakisphosphate = ADP + inositol bisdiphosphate trisphosphate." [PMID:10827188, PMID:11502751, PMID:18355727]
xref: Reactome:R-HSA-1855193 "1-PP-IP4 is phosphorylated to 1,5-(PP)2-IP3 by IP6K1/3 in the cytosol"
xref: Reactome:R-HSA-1855230 "5-PP-IP4 is phosphorylated to 1,5-(PP)2-IP3 by IP6K1/2 in the nucleus"
is_a: GO:0016301 ! kinase activity
@@ -325574,52 +325134,6 @@ xref: RHEA:28795
is_a: GO:0000293 ! ferric-chelate reductase activity
is_a: GO:0016723 ! oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor
-[Term]
-id: GO:0052852
-name: very-long-chain-(S)-2-hydroxy-acid oxidase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: very-long-chain (S)-2-hydroxy-acid + O2 = very-long-chain 2-oxo acid + hydrogen peroxide. Very long chain refers to a chain length of greater than 18 carbons." [EC:1.1.3.15]
-synonym: "oxidase, very-long-chain L-2-hydroxy acid" RELATED [EC:1.1.3.15]
-synonym: "very-long-chain L-2-hydroxy acid oxidase" RELATED [EC:1.1.3.15]
-synonym: "very-long-chain L-alpha-hydroxy acid oxidase" RELATED [EC:1.1.3.15]
-synonym: "very-long-chain-(S)-2-hydroxy-acid:oxygen 2-oxidoreductase" RELATED [EC:1.1.3.15]
-synonym: "very-long-chain-hydroxy-acid oxidase A activity" NARROW [EC:1.1.3.15]
-synonym: "very-long-chain-hydroxy-acid oxidase B activity" NARROW [EC:1.1.3.15]
-synonym: "very-long-chain-hydroxyacid oxidase A" RELATED [EC:1.1.3.15]
-xref: EC:1.1.3.15
-is_a: GO:0003973 ! (S)-2-hydroxy-acid oxidase activity
-
-[Term]
-id: GO:0052853
-name: long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: long-chain-(S)-2-hydroxy-acid + O2 = long-chain-2-oxo acid + hydrogen peroxide. Long chain refers to a chain length of 14 to 18 carbons." [EC:1.1.3.15]
-synonym: "long-chain-(S)-2-hydroxy-acid:oxygen 2-oxidoreductase" RELATED [EC:1.1.3.15]
-synonym: "long-chain-hydroxy-acid oxidase A activity" NARROW [EC:1.1.3.15]
-synonym: "long-chain-hydroxy-acid oxidase B activity" NARROW [EC:1.1.3.15]
-synonym: "long-chain-hydroxyacid oxidase A" RELATED [EC:1.1.3.15]
-synonym: "long-chain-L-2-hydroxy acid oxidase" RELATED [EC:1.1.3.15]
-synonym: "long-chain-L-alpha-hydroxy acid oxidase" RELATED [EC:1.1.3.15]
-synonym: "oxidase, long-chain-L-2-hydroxy acid" RELATED [EC:1.1.3.15]
-xref: EC:1.1.3.15
-xref: Reactome:R-HSA-6787811 "HAO2 tetramer oxidises 2OH-PALM"
-is_a: GO:0003973 ! (S)-2-hydroxy-acid oxidase activity
-
-[Term]
-id: GO:0052854
-name: medium-chain-(S)-2-hydroxy-acid oxidase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: medium-chain-(S)-2-hydroxy-acid + O2 = medium-chain-2-oxo acid + hydrogen peroxide. Medium chain refers to a chain length of between 8 and 12 carbons." [EC:1.1.3.15]
-synonym: "medium-chain-(S)-2-hydroxy-acid:oxygen 2-oxidoreductase" RELATED [EC:1.1.3.15]
-synonym: "medium-chain-hydroxy-acid oxidase A activity" NARROW [EC:1.1.3.15]
-synonym: "medium-chain-hydroxy-acid oxidase B activity" NARROW [EC:1.1.3.15]
-synonym: "medium-chain-hydroxyacid oxidase A" RELATED [EC:1.1.3.15]
-synonym: "medium-chain-L-2-hydroxy acid oxidase" RELATED [EC:1.1.3.15]
-synonym: "medium-chain-L-alpha-hydroxy acid oxidase" RELATED [EC:1.1.3.15]
-synonym: "oxidase, medium-chain-L-2-hydroxy acid" RELATED [EC:1.1.3.15]
-xref: EC:1.1.3.15
-is_a: GO:0003973 ! (S)-2-hydroxy-acid oxidase activity
-
[Term]
id: GO:0052855
name: ADP-dependent NAD(P)H-hydrate dehydratase activity
@@ -325906,16 +325420,15 @@ is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors,
id: GO:0052876
name: methylamine dehydrogenase (amicyanin) activity
namespace: molecular_function
-def: "Catalysis of the reaction: methylamine + H2O + amicyanin = formaldehyde + ammonia + reduced amicyanin." [KEGG_REACTION:R00606]
-synonym: "amine dehydrogenase activity" BROAD [EC:1.4.9.1]
-synonym: "amine:(acceptor) oxidoreductase (deaminating) activity" BROAD [EC:1.4.9.1]
+def: "Catalysis of the reaction: 2O + methylamine + 2 oxidized [amicyanin] = formaldehyde + 2 H+ + NH4+ + 2 reduced [amicyanin]." [RHEA:30207]
+synonym: "amine dehydrogenase" BROAD [EC:1.4.9.1]
synonym: "MADH activity" BROAD [EC:1.4.9.1]
-synonym: "methylamine dehydrogenase activity" BROAD [EC:1.4.9.1]
-synonym: "methylamine:amicyanin oxidoreductase (deaminating) activity" EXACT systematic_synonym [EC:1.4.9.1]
-synonym: "primary-amine dehydrogenase activity" BROAD [EC:1.4.9.1]
-synonym: "primary-amine:(acceptor) oxidoreductase (deaminating) activity" BROAD [EC:1.4.9.1]
+synonym: "methylamine dehydrogenase activity" EXACT [EC:1.4.9.1]
+synonym: "methylamine:amicyanin oxidoreductase (deaminating) activity" EXACT systematic_synonym []
+synonym: "primary-amine dehydrogenase" BROAD [EC:1.4.9.1]
xref: EC:1.4.9.1
xref: KEGG_REACTION:R00606
+xref: RHEA:30207
xref: UM-BBD_reactionID:r0075
is_a: GO:0052877 ! oxidoreductase activity, acting on the CH-NH2 group of donors, with a copper protein as acceptor
@@ -326602,48 +326115,24 @@ xref: RHEA:60012
is_a: GO:0004810 ! tRNA adenylyltransferase activity
[Term]
-id: GO:0052930
-name: methanol ferricytochrome-c oxidoreductase activity
+id: GO:0052933
+name: alcohol dehydrogenase (cytochrome c(L)) activity
namespace: molecular_function
-def: "Catalysis of the reaction: methanol + 2 ferricytochrome c = formaldehyde + 2 ferrocytochrome c + 2 H+." [KEGG_REACTION:R01146]
-synonym: "methanol dehydrogenase (cytochrome c) activity" BROAD [EC:1.1.2.7]
-synonym: "methanol dehydrogenase activity" BROAD [EC:1.1.2.7]
+alt_id: GO:0052930
+alt_id: GO:0052931
+alt_id: GO:0052932
+def: "Catalysis of the reaction: 2 [Fe(III)cytochrome cL] + a primary alcohol = 2 [Fe(II)cytochrome cL] + an aldehyde + 2 H+." [RHEA:51004]
+synonym: "2-chloroethanol cytochrome-c oxidoreductase activity" NARROW []
+synonym: "alcohol:cytochrome c(L) oxidoreductase activity" EXACT []
+synonym: "ethanol cytochrome-c oxidoreductase activity" NARROW []
+synonym: "methanol dehydrogenase activity" NARROW [EC:1.1.2.7]
+synonym: "methanol ferricytochrome-c oxidoreductase activity" NARROW []
xref: EC:1.1.2.7
xref: KEGG_REACTION:R01146
-xref: MetaCyc:RXN-2861
-xref: RHEA:51008
-is_a: GO:0016898 ! oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor
-
-[Term]
-id: GO:0052931
-name: ethanol cytochrome-c oxidoreductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: ethanol + 2 cytochrome c(L) = acetaldehyde + 2 reduced cytochrome c(L) + 2 H+." [KEGG_REACTION:R09127]
-synonym: "ethanol dehydrogenase (cytochrome c) activity" BROAD [EC:1.1.2.7]
-synonym: "ethanol dehydrogenase activity" BROAD [EC:1.1.2.7]
-xref: EC:1.1.2.7
xref: KEGG_REACTION:R09127
-is_a: GO:0052933 ! alcohol dehydrogenase (cytochrome c(L)) activity
-
-[Term]
-id: GO:0052932
-name: 2-chloroethanol cytochrome-c oxidoreductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 2-chloroethanol + 2 cytochrome c(L) = chloroacetaldehyde + 2 reduced cytochrome c(L)." [KEGG_REACTION:R09128]
-synonym: "2-chloroethanol dehydrogenase (cytochrome c) activity" BROAD [EC:1.1.2.7]
-synonym: "2-chloroethanol dehydrogenase activity" BROAD [EC:1.1.2.7]
-xref: EC:1.1.2.7
xref: KEGG_REACTION:R09128
-is_a: GO:0052933 ! alcohol dehydrogenase (cytochrome c(L)) activity
-
-[Term]
-id: GO:0052933
-name: alcohol dehydrogenase (cytochrome c(L)) activity
-namespace: molecular_function
-def: "Catalysis of the reaction: primary alcohol + 2 cytochrome c(L) = 2 reduced cytochrome c(L) + an aldehyde + 2 H+." [EC:1.1.2.7]
-synonym: "alcohol:cytochrome c(L) oxidoreductase activity" EXACT systematic_synonym [EC:1.1.2.7]
-xref: EC:1.1.2.7
xref: MetaCyc:RXN-11332
+xref: MetaCyc:RXN-2861
xref: RHEA:51004
is_a: GO:0016898 ! oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor
@@ -326651,32 +326140,25 @@ is_a: GO:0016898 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0052934
name: alcohol dehydrogenase (cytochrome c) activity
namespace: molecular_function
-def: "Catalysis of the reaction: primary alcohol + 2 cytochrome c = 2 reduced cytochrome c + an aldehyde + 2 H+." [EC:1.1.2.8]
-synonym: "alcohol:cytochrome c oxidoreductase activity" EXACT systematic_synonym [EC:1.1.2.8]
-synonym: "quinoprotein alcohol dehydrogenase activity" RELATED [EC:1.1.2.8]
-xref: EC:1.1.2.8
-xref: MetaCyc:RXN-11333
-is_a: GO:0016898 ! oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor
-
-[Term]
-id: GO:0052935
-name: ethanol:cytochrome c oxidoreductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: ethanol + 2 cytochrome c = 2 reduced cytochrome c + acetaldehyde." [KEGG_REACTION:R05198]
-synonym: "ethanol dehydrogenase (cytochrome c) activity" RELATED [EC:1.1.2.8]
+alt_id: GO:0018468
+alt_id: GO:0052935
+alt_id: GO:0052936
+def: "Catalysis of the reaction: 2 [Fe(III)cytochrome c] + a primary alcohol = 2 [Fe(II)cytochrome c] + an aldehyde + 2 H+." [RHEA:51020]
+synonym: "2-chloroethanol:cytochrome c oxidoreductase activity" NARROW []
+synonym: "alcohol dehydrogenase (acceptor) activity" BROAD []
+synonym: "alcohol:(acceptor) oxidoreductase activity" RELATED []
+synonym: "alcohol:acceptor oxidoreductase activity" RELATED []
+synonym: "alcohol:cytochrome c oxidoreductase activity" EXACT []
+synonym: "ethanol:cytochrome c oxidoreductase activity" NARROW []
+synonym: "PQQ-dependent alcohol dehydrogenase activity" EXACT []
+synonym: "quinoprotein alcohol dehydrogenase activity" RELATED []
xref: EC:1.1.2.8
xref: KEGG_REACTION:R05198
-xref: RHEA:51020
-is_a: GO:0052934 ! alcohol dehydrogenase (cytochrome c) activity
-
-[Term]
-id: GO:0052936
-name: 2-chloroethanol:cytochrome c oxidoreductase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 2-chloroethanol + 2 cytochrome c = chloroacetaldehyde + 2 reduced cytochrome c." [KEGG_REACTION:R05285]
xref: KEGG_REACTION:R05285
-xref: RHEA:55947
-is_a: GO:0052934 ! alcohol dehydrogenase (cytochrome c) activity
+xref: MetaCyc:RXN-11333
+xref: RHEA:51020
+xref: UM-BBD_enzymeID:e0004
+is_a: GO:0016898 ! oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor
[Term]
id: GO:0055001
@@ -327265,6 +326747,7 @@ id: GO:0055065
name: metal ion homeostasis
namespace: biological_process
def: "Any process involved in the maintenance of an internal steady state of metal ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah]
+subset: goslim_generic
subset: goslim_pombe
is_a: GO:0055080 ! cation homeostasis
is_a: GO:0098771 ! inorganic ion homeostasis
@@ -327425,6 +326908,7 @@ alt_id: GO:0090662
def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid]
comment: Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes.
subset: goslim_chembl
+subset: goslim_drosophila
subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
@@ -327439,6 +326923,7 @@ name: nucleobase-containing small molecule metabolic process
namespace: biological_process
def: "The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide." [GOC:vw]
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pombe
subset: goslim_yeast
synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED []
@@ -327547,7 +327032,7 @@ relationship: part_of GO:0071403 ! cellular response to high density lipoprotein
id: GO:0055100
name: adiponectin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with adiponectin, a protein hormone produced by adipose tissue that modulates a number of metabolic processes, including glucose regulation and fatty acid catabolism." [GOC:BHF, GOC:rl, PMID:15210937]
+def: "Binding to adiponectin, a protein hormone produced by adipose tissue that modulates a number of metabolic processes, including glucose regulation and fatty acid catabolism." [GOC:BHF, GOC:rl, PMID:15210937]
is_a: GO:0005515 ! protein binding
is_a: GO:0042562 ! hormone binding
@@ -327580,6 +327065,7 @@ name: ligase inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents or reduces the activity of a ligase." [GOC:BHF, GOC:rl]
is_a: GO:0004857 ! enzyme inhibitor activity
+is_a: GO:0055103 ! ligase regulator activity
[Term]
id: GO:0055105
@@ -327795,14 +327281,14 @@ is_a: GO:0046436 ! D-alanine metabolic process
id: GO:0055131
name: C3HC4-type RING finger domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a C3HC4-type zinc finger domain of a protein. The C3HC4-type zinc finger is a variant of RING finger, is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C, where X is any amino acid. Many proteins containing a C3HC4-type RING finger play a key role in the ubiquitination pathway." [GOC:amm, InterPro:IPR001841, InterPro:IPR018957]
+def: "Binding to a C3HC4-type zinc finger domain of a protein. The C3HC4-type zinc finger is a variant of RING finger, is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C, where X is any amino acid. Many proteins containing a C3HC4-type RING finger play a key role in the ubiquitination pathway." [GOC:amm, InterPro:IPR001841, InterPro:IPR018957]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0060001
name: minus-end directed microfilament motor activity
namespace: molecular_function
-def: "Catalysis of movement along a microfilament towards the minus end, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP). The minus end of an actin filament is the end that does not preferentially add actin monomers." [GOC:dph, PMID:10519557]
+def: "A motor activity that generates movement along a microfilament towards the minus end, driven by ATP hydrolysis. The minus end of an actin filament is the end that does not preferentially add actin monomers." [GOC:dph, PMID:10519557]
synonym: "minus-end directed actin filament motor activity" RELATED [GOC:dph]
synonym: "minus-end directed actin-filament motor activity" EXACT [GOC:dph]
synonym: "pointed-end directed actin-filament motor activity" EXACT [GOC:dph]
@@ -327812,7 +327298,7 @@ is_a: GO:0000146 ! microfilament motor activity
id: GO:0060002
name: plus-end directed microfilament motor activity
namespace: molecular_function
-def: "Catalysis of movement along a microfilament towards the plus end, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP). The plus end of an actin filament is the end that preferentially adds actin monomers." [GOC:dph, PMID:10519557]
+def: "A motor activity that generates movement along a microfilament towards the plus end, driven by ATP hydrolysis. The minus end of an actin filament is the end that does not preferentially add actin monomers." [GOC:dph, PMID:10519557]
synonym: "barbed-end directed actin-filament motor activity" EXACT [GOC:dph]
synonym: "plus-end directed actin filament motor activity" RELATED [GOC:dph]
synonym: "plus-end directed actin-filament motor activity" EXACT [GOC:dph]
@@ -328612,6 +328098,7 @@ name: molecular transducer activity
namespace: molecular_function
def: "A compound molecular function in which an effector function is controlled by one or more regulatory components." [GOC:dos, GOC:pdt]
subset: gocheck_do_not_manually_annotate
+subset: goslim_generic
subset: goslim_pir
is_a: GO:0003674 ! molecular_function
@@ -328622,6 +328109,7 @@ namespace: molecular_function
alt_id: GO:0032947
def: "The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." [GOC:mtg_MIT_16mar07, GOC:vw]
subset: goslim_drosophila
+subset: goslim_generic
subset: goslim_pir
synonym: "binding, bridging" EXACT []
synonym: "protein complex scaffold activity" RELATED []
@@ -328878,7 +328366,6 @@ name: auditory receptor cell development
namespace: biological_process
def: "The process whose specific outcome is the progression of an auditory receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:dph]
synonym: "auditory hair cell development" EXACT []
-is_a: GO:0002064 ! epithelial cell development
is_a: GO:0060119 ! inner ear receptor cell development
relationship: part_of GO:0042491 ! inner ear auditory receptor cell differentiation
@@ -329183,7 +328670,7 @@ id: GO:0060147
name: regulation of posttranscriptional gene silencing
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph]
-is_a: GO:0060968 ! regulation of gene silencing
+is_a: GO:0010468 ! regulation of gene expression
relationship: regulates GO:0016441 ! posttranscriptional gene silencing
[Term]
@@ -329191,7 +328678,7 @@ id: GO:0060148
name: positive regulation of posttranscriptional gene silencing
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph]
-is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:0048518 ! positive regulation of biological process
is_a: GO:0060147 ! regulation of posttranscriptional gene silencing
relationship: positively_regulates GO:0016441 ! posttranscriptional gene silencing
@@ -329200,8 +328687,9 @@ id: GO:0060149
name: negative regulation of posttranscriptional gene silencing
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph]
+is_a: GO:0010628 ! positive regulation of gene expression
+is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0060147 ! regulation of posttranscriptional gene silencing
-is_a: GO:0060969 ! negative regulation of gene silencing
relationship: negatively_regulates GO:0016441 ! posttranscriptional gene silencing
[Term]
@@ -329473,7 +328961,7 @@ name: regulation of exocyst localization
namespace: biological_process
def: "Any process that modulates the localization of exocysts. An exocyst is a protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse." [GOC:dph, GOC:tb]
synonym: "regulation of exocyst localisation" EXACT [GOC:mah]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032879 ! regulation of localization
relationship: regulates GO:0051601 ! exocyst localization
[Term]
@@ -330286,7 +329774,6 @@ alt_id: GO:0042384
def: "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GOC:BHF, GOC:cilia, GOC:dph, GOC:kmv, GOC:pr, GOC:vw, ISBN:0198506732, PMID:13978319, PMID:27350441, Reactome:R-HSA-5617833.2]
comment: Note that we deem cilium and microtubule-based flagellum to be equivalent.
synonym: "ciliogenesis" EXACT []
-synonym: "cilium assembly" EXACT []
synonym: "cilium biogenesis" RELATED [GOC:mah]
synonym: "cilium formation" EXACT []
synonym: "cilium morphogenesis" RELATED []
@@ -331322,7 +330809,6 @@ id: GO:0060378
name: regulation of brood size
namespace: biological_process
def: "Any process that modulates brood size. Brood size is the number of progeny that survive embryogenesis and are cared for at one time." [GOC:dph, GOC:tb]
-is_a: GO:0044703 ! multi-organism reproductive process
is_a: GO:0044706 ! multi-multicellular organism process
is_a: GO:0048609 ! multicellular organismal reproductive process
is_a: GO:0065008 ! regulation of biological quality
@@ -331561,7 +331047,6 @@ id: GO:0060405
name: regulation of penile erection
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of penile erection. Penile erection is the hardening, enlarging and rising of the penis which often occurs in the sexually aroused male and enables sexual intercourse. Achieved by increased inflow of blood into the vessels of erectile tissue, and decreased outflow." [GOC:add, GOC:dph, GOC:tb]
-is_a: GO:0043900 ! regulation of multi-organism process
is_a: GO:0051239 ! regulation of multicellular organismal process
is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0043084 ! penile erection
@@ -331571,7 +331056,6 @@ id: GO:0060406
name: positive regulation of penile erection
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of penile erection. Penile erection is the hardening, enlarging and rising of the penis which often occurs in the sexually aroused male and enables sexual intercourse. Achieved by increased inflow of blood into the vessels of erectile tissue, and decreased outflow." [GOC:dph, GOC:tb]
-is_a: GO:0043902 ! positive regulation of multi-organism process
is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:0060405 ! regulation of penile erection
is_a: GO:2000243 ! positive regulation of reproductive process
@@ -331582,7 +331066,6 @@ id: GO:0060407
name: negative regulation of penile erection
namespace: biological_process
def: "Any process that stops, prevents, or reduces the rate, frequency or extent of penile erection. Penile erection is the hardening, enlarging and rising of the penis which often occurs in the sexually aroused male and enables sexual intercourse. Achieved by increased inflow of blood into the vessels of erectile tissue, and decreased outflow." [GOC:dph, GOC:tb]
-is_a: GO:0043901 ! negative regulation of multi-organism process
is_a: GO:0051241 ! negative regulation of multicellular organismal process
is_a: GO:0060405 ! regulation of penile erection
is_a: GO:2000242 ! negative regulation of reproductive process
@@ -332111,7 +331594,6 @@ id: GO:0060467
name: negative regulation of fertilization
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." [GOC:dph]
-is_a: GO:0043901 ! negative regulation of multi-organism process
is_a: GO:0080154 ! regulation of fertilization
is_a: GO:2000242 ! negative regulation of reproductive process
relationship: negatively_regulates GO:0009566 ! fertilization
@@ -333221,7 +332703,7 @@ name: ATPase regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of an ATP hydrolysis activity." [GOC:dph, GOC:tb]
synonym: "ATP hydrolysis regulator activity" EXACT []
-is_a: GO:0060589 ! nucleoside-triphosphatase regulator activity
+is_a: GO:0098772 ! molecular function regulator
[Term]
id: GO:0060591
@@ -334216,7 +333698,7 @@ name: deoxyribonuclease inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents or reduces the activity of deoxyribonuclease." [GOC:dph, GOC:tb]
synonym: "DNase inhibitor activity" RELATED [GOC:dph, GOC:tb]
-is_a: GO:0004857 ! enzyme inhibitor activity
+is_a: GO:0140721 ! nuclease inhibitor activity
[Term]
id: GO:0060704
@@ -335090,7 +334572,6 @@ name: positive regulation of Wnt signaling pathway by BMP signaling pathway
namespace: biological_process
def: "A series of molecular signals generated as a consequence of any member of the BMP (bone morphogenetic protein) family binding to a cell surface receptor that results in an increase in the rate, frequency or extent of a Wnt signaling pathway." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "positive regulation of WNT receptor signaling pathway by BMP signaling pathway" EXACT [GOC:bf]
-synonym: "positive regulation of Wnt receptor signaling pathway by BMP signaling pathway" EXACT []
synonym: "positive regulation of WNT receptor signalling pathway by BMP signalling pathway" EXACT [GOC:mah]
synonym: "positive regulation of Wnt-activated signaling pathway by BMP signaling pathway" EXACT [GOC:signaling]
is_a: GO:0030177 ! positive regulation of Wnt signaling pathway
@@ -335207,18 +334688,20 @@ is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome
[Term]
id: GO:0060818
-name: inactivation of paternal X chromosome by genetic imprinting
+name: inactivation of paternal X chromosome by genomic imprinting
namespace: biological_process
-def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on the paternal X-chromosome in the XX sex by genetic imprinting." [GOC:dph, GOC:sdb_2009, GOC:tb]
+def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on the paternal X-chromosome in the XX sex by genomic imprinting." [GOC:dph, GOC:sdb_2009, GOC:tb]
+synonym: "inactivation of paternal X chromosome by genetic imprinting" RELATED []
is_a: GO:0060817 ! inactivation of paternal X chromosome
-is_a: GO:0060819 ! inactivation of X chromosome by genetic imprinting
+is_a: GO:0060819 ! inactivation of X chromosome by genomic imprinting
[Term]
id: GO:0060819
-name: inactivation of X chromosome by genetic imprinting
+name: inactivation of X chromosome by genomic imprinting
namespace: biological_process
-def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by genetic imprinting." [GOC:dph, GOC:sdb_2009, GOC:tb]
-is_a: GO:0006349 ! regulation of gene expression by genetic imprinting
+def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by genomic imprinting." [GOC:dph, GOC:sdb_2009, GOC:tb]
+synonym: "inactivation of X chromosome by genetic imprinting" RELATED []
+is_a: GO:0006349 ! regulation of gene expression by genomic imprinting
is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome
[Term]
@@ -335228,14 +334711,17 @@ namespace: biological_process
def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by the mechanism of heterochromatin formation." [GOC:dph, GOC:sdb_2009, GOC:tb]
synonym: "inactivation of X chromosome by heterochromatin formation" EXACT []
is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0140719 ! constitutive heterochromatin assembly
[Term]
id: GO:0060821
-name: inactivation of X chromosome by DNA methylation
+name: obsolete inactivation of X chromosome by DNA methylation
namespace: biological_process
-def: "Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by a mechanism of DNA methylation." [GOC:dph, GOC:sdb_2009, GOC:tb]
-is_a: GO:0009048 ! dosage compensation by inactivation of X chromosome
+def: "OBSOLETE. Compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex by a mechanism of DNA methylation." [GOC:dph, GOC:sdb_2009, GOC:tb]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0009048
+consider: GO:0035514
[Term]
id: GO:0060822
@@ -335907,7 +335393,7 @@ name: eye field cell fate commitment involved in camera-type eye formation
namespace: biological_process
def: "The commitment of neurectodermal cells to cells of the eye field and their capacity to differentiate into eye field cells. Eye field cells are neurectodermal cells that will form the optic placode." [GOC:dph, GOC:sdb_2009, GOC:tb]
is_a: GO:0060581 ! cell fate commitment involved in pattern specification
-relationship: part_of GO:0046619 ! optic placode formation involved in camera-type eye formation
+relationship: part_of GO:0046619 ! lens placode formation involved in camera-type eye formation
relationship: part_of GO:0060897 ! neural plate regionalization
[Term]
@@ -336507,7 +335993,7 @@ id: GO:0060966
name: regulation of gene silencing by RNA
namespace: biological_process
def: "Any process that regulates the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:tb]
-is_a: GO:0060968 ! regulation of gene silencing
+is_a: GO:0010468 ! regulation of gene expression
relationship: regulates GO:0031047 ! gene silencing by RNA
[Term]
@@ -336515,28 +336001,30 @@ id: GO:0060967
name: negative regulation of gene silencing by RNA
namespace: biological_process
def: "Any process that decreases the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:tb]
+is_a: GO:0010628 ! positive regulation of gene expression
+is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0060966 ! regulation of gene silencing by RNA
-is_a: GO:0060969 ! negative regulation of gene silencing
relationship: negatively_regulates GO:0031047 ! gene silencing by RNA
[Term]
id: GO:0060968
-name: regulation of gene silencing
+name: obsolete regulation of gene silencing
namespace: biological_process
-def: "Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:tb]
-is_a: GO:0010468 ! regulation of gene expression
-is_a: GO:0050794 ! regulation of cellular process
-relationship: regulates GO:0016458 ! gene silencing
+def: "OBSOLETE. Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it was too broadly defined and could not be distinguished from 'GO:0040029 regulation of gene expression, epigenetic'.
+is_obsolete: true
+consider: GO:0040029
[Term]
id: GO:0060969
-name: negative regulation of gene silencing
+name: obsolete negative regulation of gene silencing
namespace: biological_process
-def: "Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:tb]
-is_a: GO:0010628 ! positive regulation of gene expression
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0060968 ! regulation of gene silencing
-relationship: negatively_regulates GO:0016458 ! gene silencing
+def: "OBSOLETE. Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because its definition was too broad.
+is_obsolete: true
+consider: GO:0010629
+consider: GO:0031047
+consider: GO:0031507
[Term]
id: GO:0060970
@@ -336705,7 +336193,6 @@ name: lipid tube assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a macromolecular complex that contains a tube of lipid surrounded by a protein coat involved in membrane shaping of vesicle membranes as they fuse or undergo fission." [GOC:ascb_2009, GOC:dph, GOC:tb]
synonym: "lipid tubulation" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
is_a: GO:0065005 ! protein-lipid complex assembly
[Term]
@@ -336878,6 +336365,7 @@ id: GO:0061007
name: hepaticobiliary system process
namespace: biological_process
def: "An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins." [GOC:dph]
+subset: goslim_generic
synonym: "hepatobiliary system process" EXACT [GOC:dph]
is_a: GO:0003008 ! system process
@@ -337270,7 +336758,7 @@ synonym: "Imd signalling pathway" EXACT [GOC:dph]
synonym: "immune deficiency pathway" RELATED [GOC:dph]
synonym: "immune deficiency signaling pathway" RELATED [GOC:dph]
synonym: "PGRP signaling pathway" RELATED [GOC:dph]
-is_a: GO:0007165 ! signal transduction
+is_a: GO:0002764 ! immune response-regulating signaling pathway
relationship: part_of GO:0042742 ! defense response to bacterium
[Term]
@@ -337280,6 +336768,7 @@ namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of the peptidoglycan recognition protein signaling pathway." [GOC:dph]
synonym: "regulation of peptidoglycan recognition protein signalling pathway" EXACT [GOC:mah]
is_a: GO:0009966 ! regulation of signal transduction
+is_a: GO:0050776 ! regulation of immune response
relationship: regulates GO:0061057 ! peptidoglycan recognition protein signaling pathway
[Term]
@@ -337289,7 +336778,6 @@ namespace: biological_process
def: "Any process that increases the rate, frequency, or extent of the peptidoglycan recognition protein signaling pathway." [GOC:dph]
synonym: "positive regulation of peptidoglycan recognition protein signalling pathway" EXACT [GOC:mah]
is_a: GO:0009967 ! positive regulation of signal transduction
-is_a: GO:0043902 ! positive regulation of multi-organism process
is_a: GO:0061058 ! regulation of peptidoglycan recognition protein signaling pathway
is_a: GO:1900426 ! positive regulation of defense response to bacterium
relationship: positively_regulates GO:0061057 ! peptidoglycan recognition protein signaling pathway
@@ -337301,7 +336789,6 @@ namespace: biological_process
def: "Any process that decreases the rate, frequency, or extent of the peptidoglycan recognition protein signaling pathway." [GOC:dph]
synonym: "negative regulation of peptidoglycan recognition protein signalling pathway" EXACT [GOC:mah]
is_a: GO:0009968 ! negative regulation of signal transduction
-is_a: GO:0043901 ! negative regulation of multi-organism process
is_a: GO:0061058 ! regulation of peptidoglycan recognition protein signaling pathway
is_a: GO:1900425 ! negative regulation of defense response to bacterium
relationship: negatively_regulates GO:0061057 ! peptidoglycan recognition protein signaling pathway
@@ -340701,16 +340188,25 @@ is_a: GO:0048731 ! system development
id: GO:0061459
name: L-arginine transmembrane transporter activity
namespace: molecular_function
+alt_id: GO:0005288
+alt_id: GO:0015181
alt_id: GO:0015598
alt_id: GO:0102022
-def: "Enables the stereospecific transfer of L-arginine, 2-amino-5-guanidinopentanoic acid, across a biological membrane." [GOC:dph]
+def: "Enables the transfer of L-arginine from one side of a membrane to the other." [GOC:dph, RHEA:32143]
+synonym: "arginine permease activity" BROAD []
synonym: "arginine porter activity" NARROW []
+synonym: "arginine transmembrane transporter activity" EXACT []
synonym: "arginine-importing ATPase activity" NARROW []
synonym: "ATP-dependent L-arginine transmembrane transporter activity" NARROW []
synonym: "ATPase-coupled L-arginine transmembrane transporter activity" NARROW []
+synonym: "histidine/arginine/lysine/ornithine porter activity" NARROW []
+synonym: "L-arginine transporter activity" EXACT []
synonym: "L-arginine-importing ATPase activity" NARROW []
+xref: RHEA:32143
+is_a: GO:0008324 ! cation transmembrane transporter activity
+is_a: GO:0008514 ! organic anion transmembrane transporter activity
+is_a: GO:0015174 ! basic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
-is_a: GO:0015181 ! arginine transmembrane transporter activity
[Term]
id: GO:0061462
@@ -340819,7 +340315,7 @@ id: GO:0061476
name: response to anticoagulant
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an anticoagulant stimulus." [GOC:dph]
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0061477
@@ -340833,7 +340329,7 @@ id: GO:0061478
name: response to platelet aggregation inhibitor
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platelet aggregation inhibitor stimulus." [GOC:dph]
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0061479
@@ -340952,12 +340448,17 @@ relationship: part_of GO:0044732 ! mitotic spindle pole body
[Term]
id: GO:0061501
-name: cyclic-GMP-AMP synthase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: ATP + GTP = 2 diphosphate + cyclic GMP-AMP." [GOC:dph, PMID:23258413]
+name: 2',3'-cyclic GMP-AMP synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + GTP = 2 diphosphate + cyclic G-P(2'-5')A-P(3'-5') (cyclic 2',3' GAMP)." [GOC:dph, PMID:23258413, RHEA:42064]
+synonym: "2',3' cyclic GMP-AMP synthase activity" EXACT []
+synonym: "2',3' cyclic-GMP-AMP synthase activity" EXACT []
+synonym: "cyclic 2',3' GAMP synthase activity" EXACT []
+synonym: "cyclic-GMP-AMP synthase activity" BROAD []
+xref: EC:2.7.7.86
xref: Reactome:R-HSA-3244614 "cGAS produces cyclic GMP-AMP"
-xref: RHEA:35647
-is_a: GO:0016779 ! nucleotidyltransferase activity
+xref: RHEA:42064
+is_a: GO:0140699 ! cyclic GMP-AMP synthase activity
[Term]
id: GO:0061502
@@ -340992,9 +340493,17 @@ is_obsolete: true
[Term]
id: GO:0061507
-name: cyclic-GMP-AMP binding
-namespace: molecular_function
-def: "Interacting selectively and non-covalently with cyclic-GMP-AMP (cGAMP) cyclic nucleotide." [GOC:dph, PMID:23258412]
+name: 2',3'-cyclic GMP-AMP binding
+namespace: molecular_function
+alt_id: GO:0098546
+def: "Binding to 2',3' cyclic GMP-AMP (cGAMP) nucleotide, a cyclic purine dinucleotide that consists of AMP and GMP units cyclized via 2',5' and 3',5' linkages." [GOC:dph, PMID:23258412, PMID:23910378]
+synonym: "2',3' cGAMP binding" EXACT []
+synonym: "2',3' cyclic GAMP binding" EXACT []
+synonym: "2',3'-cGAMP binding" EXACT []
+synonym: "2',3'-cyclic GAMP binding" EXACT []
+synonym: "2',5-3',5'-cyclic GMP-AMP binding" EXACT []
+synonym: "c[G(2',5')pA(3',5')p] binding" EXACT [PMID:23910378]
+synonym: "cyclic-GMP-AMP binding" BROAD []
is_a: GO:0030551 ! cyclic nucleotide binding
is_a: GO:0032559 ! adenyl ribonucleotide binding
is_a: GO:0032561 ! guanyl ribonucleotide binding
@@ -341680,8 +341189,7 @@ synonym: "transfer RNA gene-mediated chromatin silencing" EXACT [GOC:dph]
synonym: "transfer RNA gene-mediated gene silencing" EXACT [GOC:dph]
synonym: "tRNA gene-mediated chromatin silencing" EXACT [GOC:dph]
synonym: "tRNA gene-mediated gene silencing" EXACT [GOC:dph]
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:0006342 ! chromatin silencing
+is_a: GO:0140458 ! pre-transcriptional gene silencing by RNA
[Term]
id: GO:0061588
@@ -341887,11 +341395,15 @@ is_a: GO:0019563 ! glycerol catabolic process
[Term]
id: GO:0061614
-name: pri-miRNA transcription by RNA polymerase II
+name: miRNA transcription
namespace: biological_process
-def: "The cellular synthesis of primary microRNA (pri-miRNA) transcripts from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. pri-miRNA transcripts are subsequently processed to produce the ~22nt miRNAs that function in gene regulation." [GOC:dph, GOC:kmv, PMID:18778799]
+def: "The cellular synthesis of microRNA (miRNA) transcripts. MicroRNA genes are synthesized as primary (pri) miRNA transcripts and subsequently processed to produce the ~22nt miRNAs that function in gene regulation." [GOC:dph, GOC:kmv, PMID:18778799]
+synonym: "microRNA gene transcription" EXACT []
+synonym: "miRNA gene transcription" EXACT []
+synonym: "pri-miRNA transcription by RNA polymerase II" EXACT []
synonym: "pri-miRNA transcription from RNA polymerase II promoter" EXACT []
-is_a: GO:0006366 ! transcription by RNA polymerase II
+synonym: "primary miRNA gene transcription" EXACT []
+is_a: GO:0006351 ! transcription, DNA-templated
[Term]
id: GO:0061615
@@ -342018,7 +341530,7 @@ is_a: GO:0008172 ! S-methyltransferase activity
id: GO:0061628
name: H3K27me3 modified histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone H3 in which the lysine residue at position 27 has been modified by trimethylation." [GOC:dph, PMID:23948251]
+def: "Binding to a histone H3 in which the lysine residue at position 27 has been modified by trimethylation." [GOC:dph, PMID:23948251]
synonym: "H3-K27me3 modified histone binding" EXACT [GOC:dph]
is_a: GO:0035064 ! methylated histone binding
@@ -342029,7 +341541,7 @@ namespace: molecular_function
alt_id: GO:0001085
alt_id: GO:0001102
alt_id: GO:0001103
-def: "Interacting selectively and non-covalently with a sequence-specific DNA binding RNA polymerase II transcription factor, any of the factors that interact selectively and non-covalently with a specific DNA sequence in order to modulate transcription." [GOC:dph, GOC:vw]
+def: "Binding to a sequence-specific DNA binding RNA polymerase II transcription factor, any of the factors that interact selectively and non-covalently with a specific DNA sequence in order to modulate transcription." [GOC:dph, GOC:vw]
synonym: "RNA polymerase II activating transcription factor binding" RELATED []
synonym: "RNA polymerase II repressing transcription factor binding" RELATED []
synonym: "RNA polymerase II sequence-specific DNA binding transcription factor binding" EXACT []
@@ -342282,7 +341794,7 @@ is_a: GO:0042476 ! odontogenesis
id: GO:0061649
name: ubiquitin modification-dependent histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone protein in which a residue has been modified by ubiquitination. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:dph, PMID:24526689]
+def: "Binding to a histone protein in which a residue has been modified by ubiquitination. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:dph, PMID:24526689]
synonym: "ubiquitinated histone binding" RELATED []
is_a: GO:0042393 ! histone binding
is_a: GO:0140036 ! ubiquitin-dependent protein binding
@@ -342510,7 +342022,7 @@ relationship: part_of GO:0006303 ! double-strand break repair via nonhomologous
id: GO:0061675
name: RBL family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the rhamnose-binding lectin (RBL) family, a family of animal lectins that show specific binding activities to L-rhamnose or D-galactose." [PMID:22312473]
+def: "Binding to a member of the rhamnose-binding lectin (RBL) family, a family of animal lectins that show specific binding activities to L-rhamnose or D-galactose." [PMID:22312473]
synonym: "rhamnose-binding lectin family protein binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -342518,7 +342030,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0061676
name: importin-alpha family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the importin-alpha family." [PMID:15350979, PMID:17170104, PMID:23734157]
+def: "Binding to a member of the importin-alpha family." [PMID:15350979, PMID:17170104, PMID:23734157]
is_a: GO:0005515 ! protein binding
[Term]
@@ -342731,7 +342243,8 @@ is_a: GO:0061698 ! protein deglutarylation
id: GO:0061700
name: GATOR2 complex
namespace: cellular_component
-def: "A multiprotein subcomplex of the GATOR complex that regulates mTOR signaling by interacting with the Rag GTPases. In humans, this complex consists of WDR24, WDR59, MIOS, SEH1L, and SEC13. In S. cerevisiae, this complex is referred to as SEACAT and contains the Sea2p, Sea3p, Sea4p, Seh1p, Sec13p proteins." [GOC:krc, GOC:rb, PMID:23723238, PMID:25934700]
+def: "A multiprotein subcomplex of the GATOR complex that regulates TORC1 signaling by interacting with the Rag GTPase. In human, this complex consists of WDR24, WDR59, MIOS, SEH1L, and SEC13. In S. cerevisiae, this complex is referred to as SEACAT and contains the Sea2p, Sea3p, Sea4p, Seh1p, Sec13p proteins." [GOC:krc, GOC:rb, PMID:23723238, PMID:25934700]
+comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
synonym: "SEACAT complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0035859 ! Seh1-associated complex
@@ -342998,7 +342511,7 @@ is_a: GO:0019637 ! organophosphate metabolic process
id: GO:0061730
name: C-rich strand telomeric DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with C-rich, single-stranded, telomere-associated DNA." [GOC:dph, GOC:kmv, PMID:18329362]
+def: "Binding to C-rich, single-stranded, telomere-associated DNA." [GOC:dph, GOC:kmv, PMID:18329362]
is_a: GO:0043047 ! single-stranded telomeric DNA binding
[Term]
@@ -343144,7 +342657,7 @@ is_obsolete: true
id: GO:0061749
name: forked DNA-dependent helicase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA helix containing forked DNA." [GOC:dph, PMID:26277776]
+def: "Unwinding a DNA helix containing forked DNA, driven by ATP hydrolysis." [GOC:dph, PMID:26277776]
is_a: GO:0003678 ! DNA helicase activity
[Term]
@@ -343169,7 +342682,7 @@ is_a: GO:0004767 ! sphingomyelin phosphodiesterase activity
id: GO:0061752
name: telomeric repeat-containing RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with long non-coding RNA molecules transcribed from subtelomeric regions in most eukaryotes. Telomeric repeat-containing RNA (TERRA) molecules consist of subtelomeric-derived sequences and G-rich telomeric repeats." [GOC:BHF, GOC:BHF_telomere, GOC:dph, GOC:jbu, PMID:20655916]
+def: "Binding to long non-coding RNA molecules transcribed from subtelomeric regions in most eukaryotes. Telomeric repeat-containing RNA (TERRA) molecules consist of subtelomeric-derived sequences and G-rich telomeric repeats." [GOC:BHF, GOC:BHF_telomere, GOC:dph, GOC:jbu, PMID:20655916]
synonym: "TERRA binding" EXACT [PMID:20655916]
is_a: GO:0003723 ! RNA binding
@@ -343224,7 +342737,7 @@ is_a: GO:0047545 ! 2-hydroxyglutarate dehydrogenase activity
id: GO:0061759
name: alpha-ketoglutarate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-oxoglutarate + reduced acceptor -> (S)-2-hydroxyglutarate + acceptor." [EC:1.1.99.2, GOC:dph, PMID:26774271]
+def: "Catalysis of the reaction: 2-oxoglutarate + reduced acceptor = (S)-2-hydroxyglutarate + acceptor." [EC:1.1.99.2, GOC:dph, PMID:26774271, RHEA:21254]
synonym: "2-hydroxyglutarate dehydrogenase activity, reverse reaction" EXACT [GOC:dph]
synonym: "2-ketoglutarate reductase activity" RELATED [GOC:dph]
synonym: "2-oxoglutarate reductase activity" RELATED [GOC:dph]
@@ -343244,7 +342757,7 @@ is_a: GO:0050832 ! defense response to fungus
id: GO:0061761
name: alpha-latrotoxin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alpha-latrotoxin receptor." [GOC:dph, PMID:21724987]
+def: "Binding to an alpha-latrotoxin receptor." [GOC:dph, PMID:21724987]
synonym: "lasso receptor binding" EXACT [GOC:dph, PMID:21724987]
synonym: "latrophilin binding" EXACT [GOC:dph, PMID:21724987]
is_a: GO:0001664 ! G protein-coupled receptor binding
@@ -343281,11 +342794,11 @@ is_a: GO:1902774 ! late endosome to lysosome transport
[Term]
id: GO:0061765
-name: modulation by virus of host NIK/NF-kappaB signaling
+name: modulation by virus of host NIK/NF-kappaB cascade
namespace: biological_process
def: "Any process in which a virus effect a change in the frequency, rate or extent of NIK/NF-kappaB signaling in the host." [GOC:bc, GOC:BHF, GOC:BHF_miRNA, PMID:26764146]
-is_a: GO:0019054 ! modulation by virus of host cellular process
-is_a: GO:1901222 ! regulation of NIK/NF-kappaB signaling
+synonym: "modulation by virus of host NIK/NF-kappaB signaling" EXACT []
+is_a: GO:0085032 ! modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade
[Term]
id: GO:0061766
@@ -343324,7 +342837,7 @@ is_a: GO:0016301 ! kinase activity
id: GO:0061770
name: translation elongation factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a translation elongation factor, any polypeptide factor involved in the peptide elongation in ribosome-mediated translation." [GOC:dph]
+def: "Binding to a translation elongation factor, any polypeptide factor involved in the peptide elongation in ribosome-mediated translation." [GOC:dph]
is_a: GO:0005515 ! protein binding
[Term]
@@ -343364,10 +342877,13 @@ is_a: GO:0045875 ! negative regulation of sister chromatid cohesion
[Term]
id: GO:0061775
-name: cohesin ATPase activity
+name: cohesin loading activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, coupled to the topological linking or unlinking of a cohesin ring complex around homologous chromosomes." [GOC:dph, GOC:vw, PMID:26687354]
-is_a: GO:0008094 ! ATPase, acting on DNA
+def: "Facilitating a conformational change to load a cohesin complex around sister chromatids, driven by ATP hydrolysis." [GOC:vw, PMID:26687354]
+synonym: "ATP-dependent cohesin loading activity" EXACT []
+synonym: "cohesin ATPase activity" EXACT []
+synonym: "cohesin loading ATPase" EXACT []
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
[Term]
id: GO:0061776
@@ -343469,7 +342985,7 @@ is_a: GO:0061785 ! peptidoglycan endopeptidase activity
id: GO:0061788
name: EGF repeat binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with Epidermal Growth Factor (EGF) repeats." [GOC:25700513, GOC:dph, PMID:25155514]
+def: "Binding to Epidermal Growth Factor (EGF) repeats." [GOC:25700513, GOC:dph, PMID:25155514]
synonym: "Epidermal growth factor domain binding" BROAD [GOC:dph]
synonym: "Epidermal Growth Factor repeat binding" RELATED [GOC:dph]
is_a: GO:0019904 ! protein domain specific binding
@@ -343482,7 +342998,7 @@ def: "A process that converts unprimed dense core granules (DCVs) to a pool of p
synonym: "dense core vesicle priming" EXACT [PMID:26575293]
synonym: "large dense-core vesicle priming" EXACT [PMID:10899113]
synonym: "LDCV priming" EXACT [PMID:26575293]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
is_a: GO:0140029 ! exocytic process
relationship: part_of GO:1990504 ! dense core granule exocytosis
@@ -343499,7 +343015,7 @@ id: GO:0061791
name: GTPase motor activity
namespace: molecular_function
def: "A motor activity driven by GTP hydrolysis." [GOC:dph, GOC:vw, PMID:11242086]
-is_a: GO:0003774 ! motor activity
+is_a: GO:0003774 ! cytoskeletal motor activity
is_a: GO:0003924 ! GTPase activity
[Term]
@@ -343683,7 +343199,7 @@ is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
id: GO:0061813
name: obsolete ARID domain binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a ARID domain. The AT-rich interaction domain (ARID) is an ~100-amino acid DNA-binding module found in a large number of eukaryotic transcription factors." [GOC:dph, InterPro:IPR001606, PMID:18270511]
+def: "OBSOLETE. Binding to a ARID domain. The AT-rich interaction domain (ARID) is an ~100-amino acid DNA-binding module found in a large number of eukaryotic transcription factors." [GOC:dph, InterPro:IPR001606, PMID:18270511]
is_obsolete: true
[Term]
@@ -343738,7 +343254,7 @@ is_a: GO:0090657 ! telomeric loop disassembly
id: GO:0061821
name: telomeric D-loop binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a telomeric D-loop. A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus." [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:19734539]
+def: "Binding to a telomeric D-loop. A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus." [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:19734539]
synonym: "telomeric Displacement-loop binding" EXACT []
is_a: GO:0062037 ! D-loop DNA binding
@@ -343967,7 +343483,7 @@ is_a: GO:0071375 ! cellular response to peptide hormone stimulus
id: GO:0061849
name: telomeric G-quadruplex DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with telomeric G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures in telomeres." [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:16142245, PMID:9512530]
+def: "Binding to telomeric G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures in telomeres." [GOC:BHF, GOC:BHF_telomere, GOC:nc, PMID:16142245, PMID:9512530]
is_a: GO:0042162 ! telomeric DNA binding
is_a: GO:0051880 ! G-quadruplex DNA binding
@@ -344046,8 +343562,8 @@ is_a: GO:0034976 ! response to endoplasmic reticulum stress
id: GO:0061860
name: DNA clamp unloader activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their removal from the DNA duplex." [GOC:vw, PMID:23499004]
-is_a: GO:0008094 ! ATPase, acting on DNA
+def: "Facilitating the opening of the ring structure of the PCNA complex, or any of the related sliding clamp complexes, and their removal from the DNA duplex, driven by ATP hydrolysis." [GOC:vw, PMID:23499004]
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
[Term]
id: GO:0061862
@@ -344201,7 +343717,7 @@ name: clathrin-dependent endocytosis involved in vitellogenesis
namespace: biological_process
def: "A clathrin-mediated endocytosis process whereby yolk proteins are internalized and trafficked through the endocytic pathway for yolk deposition." [PMID:26265702]
synonym: "clathrin-dependent endocytosis involved in yolk formation" EXACT []
-is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism
+is_a: GO:0022414 ! reproductive process
is_a: GO:0072583 ! clathrin-dependent endocytosis
relationship: part_of GO:0007296 ! vitellogenesis
@@ -344274,7 +343790,7 @@ relationship: positively_regulates GO:0048143 ! astrocyte activation
id: GO:0061891
name: calcium ion sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of calcium ions (Ca2+)." [PMID:16005298, PMID:17020874, PMID:28151650]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of calcium ions (Ca2+)." [PMID:16005298, PMID:17020874, PMID:28151650]
is_a: GO:0005509 ! calcium ion binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -344344,7 +343860,7 @@ id: GO:0061906
name: autophagosome localization
namespace: biological_process
def: "Any process in which an autophagosome is transported to, and/or maintained in, a specific location within the cell." [PMID:26763909]
-is_a: GO:0051640 ! organelle localization
+is_a: GO:1990849 ! vacuolar localization
[Term]
id: GO:0061907
@@ -344763,14 +344279,14 @@ id: GO:0061960
name: regulation of heme oxygenase activity
namespace: biological_process
def: "Any process that modulates the frequency, or rate of heme oxygenase activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:24844779]
-is_a: GO:0051341 ! regulation of oxidoreductase activity
+is_a: GO:0032768 ! regulation of monooxygenase activity
[Term]
id: GO:0061961
name: positive regulation of heme oxygenase activity
namespace: biological_process
def: "Any process that activates or increases the frequency or rate of heme oxygenase activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:24844779]
-is_a: GO:0051353 ! positive regulation of oxidoreductase activity
+is_a: GO:0032770 ! positive regulation of monooxygenase activity
is_a: GO:0061960 ! regulation of heme oxygenase activity
[Term]
@@ -344778,7 +344294,7 @@ id: GO:0061962
name: negative regulation of heme oxygenase activity
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency or rate of heme oxygenase activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:24844779]
-is_a: GO:0051354 ! negative regulation of oxidoreductase activity
+is_a: GO:0032769 ! negative regulation of monooxygenase activity
is_a: GO:0061960 ! regulation of heme oxygenase activity
[Term]
@@ -344911,7 +344427,7 @@ is_a: GO:0061977 ! hip joint articular cartilage development
id: GO:0061980
name: regulatory RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a small regulatory RNA, a short RNA (usually 50-200 nt long) that is either independently transcribed or processed from a longer RNA by an RNAse enzyme." [PMID:14622403, PMID:23475961]
+def: "Binding to a small regulatory RNA, a short RNA (usually 50-200 nt long) that is either independently transcribed or processed from a longer RNA by an RNAse enzyme." [PMID:14622403, PMID:23475961]
is_a: GO:0003723 ! RNA binding
[Term]
@@ -344997,10 +344513,13 @@ is_a: GO:0016415 ! octanoyltransferase activity
[Term]
id: GO:0061992
-name: ATP-dependent chaperone mediated protein folding
+name: obsolete ATP-dependent chaperone mediated protein folding
namespace: biological_process
-def: "The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone, and dependent on ATP hydrolysis." [PMID:18311152]
-is_a: GO:0061077 ! chaperone-mediated protein folding
+def: "OBSOLETE. The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone, and dependent on ATP hydrolysis." [PMID:18311152]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0006457
+consider: GO:0140662
[Term]
id: GO:0061993
@@ -345012,19 +344531,14 @@ synonym: "CAX1-CAX3 complex" NARROW [GOC:bhm]
synonym: "CAX3 homodimer" NARROW [GOC:bhm]
is_a: GO:1902495 ! transmembrane transporter complex
-[Term]
-id: GO:0061994
-name: ATP-dependent protein-nucleic acid complex displacement activity
-namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate coupled to the displacement of proteins or protein complexes from nucleic acid, sometimes in a 'wire stripping' fashion." [PMID:18593879]
-is_a: GO:0008094 ! ATPase, acting on DNA
-
[Term]
id: GO:0061995
name: ATP-dependent protein-DNA complex displacement activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate coupled to the displacement of proteins or protein complexes from DNA, sometimes in a 'wire stripping' fashion." [PMID:18593879]
-is_a: GO:0061994 ! ATP-dependent protein-nucleic acid complex displacement activity
+alt_id: GO:0061994
+def: "An activity that displaces proteins or protein complexes from DNA, sometimes in a 'wire stripping' fashion, driven by ATP hydrolysis." [PMID:18593879]
+synonym: "ATP-dependent protein-nucleic acid complex displacement activity" NARROW []
+is_a: GO:0140083 ! ATP-dependent protein-DNA unloading activity
[Term]
id: GO:0061999
@@ -345255,7 +344769,7 @@ is_a: GO:0050955 ! thermoception
id: GO:0062037
name: D-loop DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DNA D-loop. A D-loop is a three-stranded DNA structure formed by the invasion of a single DNA strand that base pairs with one strand of duplex DNA, while the rest of the double-stranded DNA does not unwind." [PMID:20924116]
+def: "Binding to a DNA D-loop. A D-loop is a three-stranded DNA structure formed by the invasion of a single DNA strand that base pairs with one strand of duplex DNA, while the rest of the double-stranded DNA does not unwind." [PMID:20924116]
synonym: "DNA displacement loop binding" EXACT []
is_a: GO:0000217 ! DNA secondary structure binding
@@ -345364,7 +344878,6 @@ id: GO:0062051
name: lipopolysaccharide transport system
namespace: cellular_component
def: "A protein-containing complex that functions to transport lipopolysaccharide from its site of synthesis at the cytoplasmic membrane across the periplasm to the outer membrane in an ATP-dependent manner." [PMID:29449493]
-is_a: GO:1904949 ! ATPase complex
is_a: GO:1990351 ! transporter complex
[Term]
@@ -345410,91 +344923,91 @@ is_a: GO:0015301 ! anion:anion antiporter activity
id: GO:0062058
name: transcription factor TFIIH holo complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a transcription factor TFIIH holo complex." [PMID:11259578]
+def: "Binding to a transcription factor TFIIH holo complex." [PMID:11259578]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062059
name: FACT complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a FACT complex." [PMID:10682845]
+def: "Binding to a FACT complex." [PMID:10682845]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062060
name: NuA4 histone acetyltransferase complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a NuA4 histone acetyltransferase complex." [PMID:15528408]
+def: "Binding to a NuA4 histone acetyltransferase complex." [PMID:15528408]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062061
name: TAP complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a TAP complex." [PMID:17947644]
+def: "Binding to a TAP complex." [PMID:17947644]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062062
name: oligosaccharyltransferase complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an oligosaccharyltransferase complex." [PMID:12887896]
+def: "Binding to an oligosaccharyltransferase complex." [PMID:12887896]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062063
name: BBSome binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a BBSome complex." [PMID:20603001]
+def: "Binding to a BBSome complex." [PMID:20603001]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062064
name: box C/D snoRNP complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a box C/D snoRNP complex." [PMID:10679015]
+def: "Binding to a box C/D snoRNP complex." [PMID:10679015]
is_a: GO:0030519 ! snoRNP binding
[Term]
id: GO:0062065
name: box H/ACA snoRNP complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a box H/ACA snoRNP complex." [PMID:10679015]
+def: "Binding to a box H/ACA snoRNP complex." [PMID:10679015]
is_a: GO:0030519 ! snoRNP binding
[Term]
id: GO:0062066
name: PSII associated light-harvesting complex II binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a PSII associated light-harvesting complex II." [PMID:17400553]
+def: "Binding to a PSII associated light-harvesting complex II." [PMID:17400553]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062067
name: chloroplast photosystem I binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chloroplast photosystem I." [PMID:17400553]
+def: "Binding to a chloroplast photosystem I." [PMID:17400553]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062068
name: chloroplast photosystem II binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chloroplast photosystem II." [PMID:17400553]
+def: "Binding to a chloroplast photosystem II." [PMID:17400553]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062069
name: GARP complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a GARP complex." [PMID:20163565]
+def: "Binding to a GARP complex." [PMID:20163565]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0062070
name: SAGA complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a SAGA complex." [PMID:27185460]
+def: "Binding to a SAGA complex." [PMID:27185460]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -345508,7 +345021,7 @@ is_a: GO:0090575 ! RNA polymerase II transcription regulator complex
id: GO:0062072
name: H3K9me3 modified histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone H3 in which the lysine residue at position 9 has been modified by trimethylation." [PMID:30110338]
+def: "Binding to a histone H3 in which the lysine residue at position 9 has been modified by trimethylation." [PMID:30110338]
is_a: GO:0035064 ! methylated histone binding
[Term]
@@ -345561,7 +345074,7 @@ is_a: GO:1990204 ! oxidoreductase complex
id: GO:0062078
name: TSC1-TSC2 complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a TSC1-TSC2 complex." [PMID:28561066]
+def: "Binding to a TSC1-TSC2 complex." [PMID:28561066]
synonym: "tuberin sclerosis complex binding" EXACT []
synonym: "tuberin-hamartin complex binding" EXACT []
is_a: GO:0044877 ! protein-containing complex binding
@@ -345796,7 +345309,7 @@ is_a: GO:0032774 ! RNA biosynthetic process
id: GO:0062104
name: pumilio-response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a region of RNA containing a Pumilio-response element element. The consensus sequence for the element is UGUAAAUA." [PMID:30601114]
+def: "Binding to a region of RNA containing a Pumilio-response element element. The consensus sequence for the element is UGUAAAUA." [PMID:30601114]
synonym: "PRE binding" EXACT [PMID:30601114]
is_a: GO:0003723 ! RNA binding
@@ -345892,7 +345405,7 @@ id: GO:0062120
name: LinE complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components during meiotic prophase to form a LinE complex, the protein complex that associates with chromatin to form linear elements in fission yeast. In S. pombe, the LinE complex contains four main structural components (Rec10, Rec25, Rec27, and Mug20) and other associated proteins." [PMID:30640914]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0030999 ! linear element assembly
@@ -345935,7 +345448,7 @@ is_a: GO:0038023 ! signaling receptor activity
id: GO:0062125
name: regulation of mitochondrial gene expression
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of mitochondrial gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA)." [PMID:28285835]
+def: "Any process that modulates the frequency, rate or extent of mitochondrial gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." [PMID:28285835]
is_a: GO:0010468 ! regulation of gene expression
relationship: regulates GO:0140053 ! mitochondrial gene expression
@@ -346158,7 +345671,7 @@ is_a: GO:0008174 ! mRNA methyltransferase activity
id: GO:0062153
name: C5-methylcytidine-containing RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA molecule modified by C5-methylcytidine." [PMID:28418038]
+def: "Binding to an RNA molecule modified by C5-methylcytidine." [PMID:28418038]
synonym: "C5-methylcytosine-containing RNA binding" EXACT []
is_a: GO:0003723 ! RNA binding
@@ -346644,6 +346157,7 @@ name: regulation of pattern recognition receptor signaling pathway
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of a pattern recognition receptor signaling pathway." [PMID:30610168]
is_a: GO:0009966 ! regulation of signal transduction
+is_a: GO:0050776 ! regulation of immune response
relationship: regulates GO:0002221 ! pattern recognition receptor signaling pathway
[Term]
@@ -346842,27 +346356,27 @@ relationship: part_of GO:0000228 ! nuclear chromosome
id: GO:0062239
name: heterochromatin-nuclear membrane anchor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with heterochromatin and the nuclear inner membrane, in order to establish and maintain the heterochromatin location and organization." [PMID:31635174]
+def: "Binding to heterochromatin and the nuclear inner membrane, in order to establish and maintain the heterochromatin location and organization." [PMID:31635174]
synonym: "heterochromatin-nuclear membrane tether activity" EXACT []
synonym: "nuclear membrane-heterochromatin anchor activity" EXACT []
synonym: "nuclear membrane-heterochromatin tether activity" EXACT []
-is_a: GO:0043495 ! protein-membrane adaptor activity
+is_a: GO:0140707 ! chromatin-nuclear membrane anchor activity
[Term]
id: GO:0062240
name: euchromatin-nuclear membrane anchor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with euchromatin and the nuclear inner membrane, in order to establish and maintain the euchromatin location and organization." [PMID:31635174]
+def: "Binding to euchromatin and the nuclear inner membrane, in order to establish and maintain the euchromatin location and organization." [PMID:31635174]
synonym: "euchromatin-nuclear membrane tether activity" EXACT []
synonym: "nuclear membrane-euchromatin anchor activity" EXACT []
synonym: "nuclear membrane-euchromatin tether activity" EXACT []
-is_a: GO:0043495 ! protein-membrane adaptor activity
+is_a: GO:0140707 ! chromatin-nuclear membrane anchor activity
[Term]
id: GO:0062241
name: double strand break-nuclear membrane anchor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA double strand breaks and the nuclear inner membrane, in order to facilitate DNA repair." [PMID:31635174]
+def: "Binding to DNA double strand breaks and the nuclear inner membrane, in order to facilitate DNA repair." [PMID:31635174]
synonym: "DNA repair factory" RELATED []
is_a: GO:0043495 ! protein-membrane adaptor activity
@@ -346950,19 +346464,25 @@ id: GO:0065003
name: protein-containing complex assembly
namespace: biological_process
alt_id: GO:0006461
+alt_id: GO:0034622
+alt_id: GO:0043623
def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl]
subset: goslim_chembl
+subset: goslim_drosophila
subset: goslim_generic
subset: goslim_metagenomics
subset: goslim_pir
subset: goslim_pombe
+synonym: "cellular macromolecule complex assembly" RELATED []
+synonym: "cellular protein complex assembly" EXACT []
+synonym: "cellular protein-containing complex assembly" RELATED []
synonym: "chaperone activity" RELATED []
synonym: "macromolecular complex assembly" RELATED []
synonym: "macromolecule complex assembly" RELATED []
synonym: "protein complex assembly" RELATED []
synonym: "protein complex formation" RELATED []
is_a: GO:0022607 ! cellular component assembly
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0065004
@@ -346970,7 +346490,7 @@ name: protein-DNA complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex." [GOC:jl]
synonym: "DNA-protein complex assembly" EXACT [GOC:mah]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
is_a: GO:0071824 ! protein-DNA complex subunit organization
[Term]
@@ -347123,7 +346643,7 @@ relationship: part_of GO:0005887 ! integral component of plasma membrane
id: GO:0070016
name: armadillo repeat domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the armadillo repeat domain of a protein, an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity protein armadillo. Arm-repeat proteins are involved in various processes, including intracellular signalling and cytoskeletal regulation." [GOC:BHF, GOC:mah, GOC:vk, InterPro:IPR000225]
+def: "Binding to an armadillo repeat domain, an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity protein armadillo. Arm-repeat proteins are involved in various processes, including intracellular signalling and cytoskeletal regulation." [GOC:BHF, GOC:mah, GOC:vk, InterPro:IPR000225]
synonym: "Arm repeat domain binding" EXACT []
synonym: "armadillo domain binding" EXACT []
synonym: "armadillo repeat binding" EXACT []
@@ -347223,7 +346743,7 @@ is_a: GO:0098797 ! plasma membrane protein complex
id: GO:0070025
name: carbon monoxide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with carbon monoxide (CO)." [GOC:ecd]
+def: "Binding to carbon monoxide (CO)." [GOC:ecd]
synonym: "CO binding" EXACT []
is_a: GO:0005488 ! binding
@@ -347231,7 +346751,7 @@ is_a: GO:0005488 ! binding
id: GO:0070026
name: nitric oxide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with nitric oxide (NO)." [GOC:ecd]
+def: "Binding to nitric oxide (NO)." [GOC:ecd]
synonym: "nitrogen monoxide binding" EXACT []
synonym: "nitrosyl binding" EXACT [CHEBI:16480]
synonym: "NO binding" EXACT []
@@ -347241,7 +346761,7 @@ is_a: GO:0005488 ! binding
id: GO:0070027
name: carbon monoxide sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of carbon monoxide (CO)." [GOC:ecd]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of carbon monoxide (CO)." [GOC:ecd]
is_a: GO:0070025 ! carbon monoxide binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -347301,7 +346821,7 @@ is_a: GO:0031201 ! SNARE complex
id: GO:0070034
name: telomerase RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the telomerase RNA template." [GOC:krc, PMID:16884717]
+def: "Binding to the telomerase RNA template." [GOC:krc, PMID:16884717]
synonym: "TERC binding" RELATED [GOC:dph]
is_a: GO:0003723 ! RNA binding
@@ -347450,14 +346970,14 @@ is_a: GO:0060249 ! anatomical structure homeostasis
id: GO:0070051
name: fibrinogen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with fibrinogen, a highly soluble hexameric glycoprotein complex that is found in blood plasma and is converted to fibrin by thrombin in the coagulation cascade." [GOC:BHF, GOC:mah, GOC:vk]
+def: "Binding to fibrinogen, a highly soluble hexameric glycoprotein complex that is found in blood plasma and is converted to fibrin by thrombin in the coagulation cascade." [GOC:BHF, GOC:mah, GOC:vk]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0070052
name: collagen V binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type V collagen trimer." [GOC:BHF, GOC:mah]
+def: "Binding to a type V collagen trimer." [GOC:BHF, GOC:mah]
is_a: GO:0005518 ! collagen binding
[Term]
@@ -347546,7 +347066,7 @@ is_a: GO:0045010 ! actin nucleation
id: GO:0070061
name: fructose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the D- or L-enantiomer of fructose, the ketohexose arabino-hex-2-ulose." [CHEBI:28757, GOC:BHF, GOC:mah]
+def: "Binding to the D- or L-enantiomer of fructose, the ketohexose arabino-hex-2-ulose." [CHEBI:28757, GOC:BHF, GOC:mah]
is_a: GO:0048029 ! monosaccharide binding
[Term]
@@ -347563,14 +347083,14 @@ relationship: part_of GO:0005615 ! extracellular space
id: GO:0070063
name: RNA polymerase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA polymerase molecule or complex." [GOC:BHF, GOC:mah, GOC:txnOH]
+def: "Binding to an RNA polymerase molecule or complex." [GOC:BHF, GOC:mah, GOC:txnOH]
is_a: GO:0019899 ! enzyme binding
[Term]
id: GO:0070064
name: proline-rich region binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein." [GOC:mah]
+def: "Binding to a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein." [GOC:mah]
is_a: GO:0005515 ! protein binding
[Term]
@@ -347628,7 +347148,7 @@ id: GO:0070071
name: proton-transporting two-sector ATPase complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a proton-transporting two-sector ATPase complex, a large protein complex that catalyzes the synthesis or hydrolysis of ATP by a rotational mechanism, coupled to the transport of protons across a membrane." [GOC:mah]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0070072
@@ -347697,7 +347217,7 @@ is_a: GO:0070077 ! histone arginine demethylation
id: GO:0070080
name: titin Z domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the titin Z domain, which recognizes and binds to the C-terminal calmodulin-like domain of alpha-actinin-2 (Act-EF34), adopts a helical structure, and binds in a groove formed by the two planes between the helix pairs of Act-EF34." [GOC:mah, InterPro:IPR015129]
+def: "Binding to a titin Z protein domain, which recognizes and binds to the C-terminal calmodulin-like domain of alpha-actinin-2 (Act-EF34), adopts a helical structure, and binds in a groove formed by the two planes between the helix pairs of Act-EF34." [GOC:mah, InterPro:IPR015129]
synonym: "Z repeat domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -347763,7 +347283,7 @@ is_a: GO:0098657 ! import into cell
id: GO:0070087
name: chromo shadow domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain." [GOC:BHF, GOC:vk, InterPro:IPR008251, PMID:7667093]
+def: "Binding to a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain." [GOC:BHF, GOC:vk, InterPro:IPR008251, PMID:7667093]
synonym: "chromoshadow domain binding" EXACT [GOC:vk]
is_a: GO:0019904 ! protein domain specific binding
@@ -347839,7 +347359,7 @@ relationship: positively_regulates GO:0070091 ! glucagon secretion
id: GO:0070095
name: fructose-6-phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with fructose 6-phosphate." [GOC:mah]
+def: "Binding to fructose 6-phosphate." [GOC:mah]
synonym: "D-fructose 6-phosphate binding" NARROW []
synonym: "fructose 6-phosphate binding" EXACT []
is_a: GO:0043168 ! anion binding
@@ -347852,14 +347372,14 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a mitochondrial outer membrane translocase complex." [GOC:BHF, GOC:vk]
synonym: "mitochondrion outer membrane translocase complex assembly" EXACT []
synonym: "TOM complex assembly" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0007008 ! outer mitochondrial membrane organization
[Term]
id: GO:0070097
name: delta-catenin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the delta subunit of the catenin complex." [GOC:rph]
+def: "Binding to the delta subunit of the catenin complex." [GOC:rph]
is_a: GO:0005515 ! protein binding
[Term]
@@ -348009,7 +347529,7 @@ name: organellar chromatophore membrane
namespace: cellular_component
def: "Either of the lipid bilayers that surround an organellar chromatophore." [GOC:mah]
synonym: "Paulinella-type chromatophore membrane" EXACT [GOC:mah]
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
relationship: part_of GO:0070111 ! organellar chromatophore
[Term]
@@ -348070,7 +347590,7 @@ relationship: part_of GO:0070116 ! organellar chromatophore thylakoid
id: GO:0070119
name: ciliary neurotrophic factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the cytokine ciliary neurotrophic factor." [GOC:BHF, GOC:mah]
+def: "Binding to the cytokine ciliary neurotrophic factor." [GOC:BHF, GOC:mah]
synonym: "CNTF binding" EXACT [GOC:mah]
is_a: GO:0019955 ! cytokine binding
@@ -348203,7 +347723,6 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the process preceding formation of the peptide bond between the first two amino acids of a protein in a mitochondrion." [GOC:mah]
synonym: "negative regulation of mitochondrial translation initiation" EXACT [GOC:mah]
is_a: GO:0045947 ! negative regulation of translational initiation
-is_a: GO:0070130 ! negative regulation of mitochondrial translation
is_a: GO:0070132 ! regulation of mitochondrial translational initiation
relationship: negatively_regulates GO:0070124 ! mitochondrial translational initiation
@@ -348630,7 +348149,7 @@ is_a: GO:0070178 ! D-serine metabolic process
id: GO:0070180
name: large ribosomal subunit rRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA." [GOC:elh]
+def: "Binding to large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA." [GOC:elh]
synonym: "25S rRNA binding" EXACT [GOC:elh]
synonym: "LSU rRNA binding" EXACT []
is_a: GO:0019843 ! rRNA binding
@@ -348639,7 +348158,7 @@ is_a: GO:0019843 ! rRNA binding
id: GO:0070181
name: small ribosomal subunit rRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA." [GOC:elh]
+def: "Binding to small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA." [GOC:elh]
synonym: "18S rRNA binding" EXACT [GOC:elh]
synonym: "SSU rRNA binding" EXACT []
is_a: GO:0019843 ! rRNA binding
@@ -348648,7 +348167,7 @@ is_a: GO:0019843 ! rRNA binding
id: GO:0070182
name: DNA polymerase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DNA polymerase." [GOC:BHF, GOC:mah]
+def: "Binding to a DNA polymerase." [GOC:BHF, GOC:mah]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -348772,7 +348291,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the eukaryotic translation initiation factor 3 complex." [GOC:mah]
synonym: "eIF-3 assembly" EXACT [GOC:mah]
synonym: "eIF3 assembly" EXACT [GOC:mah]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0070197
@@ -348781,7 +348300,6 @@ namespace: biological_process
def: "The meiotic cell cycle process in which physical connections are formed between telomeric heterochromatin and the nuclear envelope, facilitating bouquet formation." [GOC:jp, GOC:pr, GOC:vw, PMID:18818742]
synonym: "attachment of telomeres to nuclear envelope" BROAD []
synonym: "attachment of telomeric chromatin to nuclear envelope" BROAD []
-synonym: "attachment of telomeric heterochromatin to nuclear envelope" EXACT []
is_a: GO:0097240 ! chromosome attachment to the nuclear envelope
is_a: GO:1903046 ! meiotic cell cycle process
relationship: part_of GO:0044821 ! meiotic telomere tethering at nuclear periphery
@@ -348829,8 +348347,8 @@ name: regulation of establishment of protein localization to chromosome
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome." [GOC:BHF, GOC:mah]
synonym: "regulation of establishment of protein localisation to chromosome" EXACT [GOC:mah]
+is_a: GO:0060341 ! regulation of cellular localization
is_a: GO:0070201 ! regulation of establishment of protein localization
-is_a: GO:1903827 ! regulation of cellular protein localization
relationship: regulates GO:0070199 ! establishment of protein localization to chromosome
[Term]
@@ -348968,7 +348486,7 @@ relationship: part_of GO:0031252 ! cell leading edge
id: GO:0070215
name: obsolete MDM2 binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with any isoform of the MDM2 protein, a negative regulator of p53." [GOC:mah, GOC:nln]
+def: "OBSOLETE. Binding to an isoform of the MDM2 protein, a negative regulator of p53." [GOC:mah, GOC:nln]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "MDM2 binding" EXACT []
is_obsolete: true
@@ -348978,7 +348496,7 @@ replaced_by: GO:0097371
id: GO:0070216
name: obsolete MDM4 binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with any isoform of the MDM4 protein, a negative regulator of p53." [GOC:mah, GOC:nln]
+def: "OBSOLETE. Binding to an isoform of the MDM4 protein, a negative regulator of p53." [GOC:mah, GOC:nln]
comment: This term was made obsolete because it represents binding to an individual protein.
synonym: "MDM4 binding" EXACT []
synonym: "MDMX binding" EXACT [GOC:nln]
@@ -348991,7 +348509,7 @@ name: transcription factor TFIIIB complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a transcription factor TFIIIB complex." [GOC:mah]
synonym: "TFIIIB assembly" EXACT [GOC:mah]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0070218
@@ -349651,7 +349169,7 @@ is_obsolete: true
id: GO:0070273
name: phosphatidylinositol-4-phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position." [GOC:bf, GOC:mah]
+def: "Binding to phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position." [GOC:bf, GOC:mah]
is_a: GO:1901981 ! phosphatidylinositol phosphate binding
[Term]
@@ -349699,7 +349217,7 @@ relationship: part_of GO:0030198 ! extracellular matrix organization
id: GO:0070279
name: vitamin B6 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate." [GOC:mah]
+def: "Binding to a vitamin B6 compound: pyridoxal, pyridoxamine, pyridoxine, or the active form, pyridoxal phosphate." [GOC:mah]
is_a: GO:0019842 ! vitamin binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -349708,7 +349226,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0070280
name: pyridoxal binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pyridoxal, 3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde, a form of vitamin B6." [CHEBI:17310, GOC:mah]
+def: "Binding to pyridoxal, 3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde, a form of vitamin B6." [CHEBI:17310, GOC:mah]
is_a: GO:0043169 ! cation binding
is_a: GO:0070279 ! vitamin B6 binding
@@ -349716,7 +349234,7 @@ is_a: GO:0070279 ! vitamin B6 binding
id: GO:0070281
name: pyridoxamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pyridoxamine, 4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol, a form of vitamin B6." [CHEBI:16410, GOC:mah]
+def: "Binding to pyridoxamine, 4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol, a form of vitamin B6." [CHEBI:16410, GOC:mah]
is_a: GO:0043169 ! cation binding
is_a: GO:0070279 ! vitamin B6 binding
@@ -349724,7 +349242,7 @@ is_a: GO:0070279 ! vitamin B6 binding
id: GO:0070282
name: pyridoxine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pyridoxine, 4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol, a form of vitamin B6." [CHEBI:16709, GOC:mah]
+def: "Binding to pyridoxine, 4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol, a form of vitamin B6." [CHEBI:16709, GOC:mah]
is_a: GO:0070279 ! vitamin B6 binding
[Term]
@@ -349750,7 +349268,7 @@ name: axonemal dynein complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form an axonemal dynein complex, a dynein complex found in eukaryotic cilia and flagella, in which the motor domain heads interact with adjacent microtubules to generate a sliding force which is converted to a bending motion." [GOC:cilia, GOC:mah, PMID:19052621]
synonym: "dynein arm assembly" EXACT [GOC:vk, PMID:19944405]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0035082 ! axoneme assembly
[Term]
@@ -349895,7 +349413,7 @@ relationship: positively_regulates GO:0000160 ! phosphorelay signal transduction
id: GO:0070300
name: phosphatidic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidic acid, any of a class of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids." [CHEBI:16337, GOC:jp, ISBN:0198506732]
+def: "Binding to phosphatidic acid, any of a class of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids." [CHEBI:16337, GOC:jp, ISBN:0198506732]
synonym: "phosphatidate binding" EXACT [GOC:jp]
is_a: GO:0005543 ! phospholipid binding
is_a: GO:0043168 ! anion binding
@@ -350143,7 +349661,7 @@ consider: GO:1903833
id: GO:0070324
name: thyroid hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland." [GOC:rph]
+def: "Binding to thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland." [GOC:rph]
subset: goslim_chembl
synonym: "thyroxine binding" NARROW [GOC:mah]
synonym: "triiodothyronine binding" NARROW [GOC:mah]
@@ -350153,14 +349671,14 @@ is_a: GO:0042562 ! hormone binding
id: GO:0070325
name: lipoprotein particle receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lipoprotein particle receptor." [GOC:BHF, GOC:rl]
+def: "Binding to a lipoprotein particle receptor." [GOC:BHF, GOC:rl]
is_a: GO:0005102 ! signaling receptor binding
[Term]
id: GO:0070326
name: very-low-density lipoprotein particle receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a very-low-density lipoprotein receptor." [GOC:BHF, GOC:mah]
+def: "Binding to a very-low-density lipoprotein receptor." [GOC:BHF, GOC:mah]
synonym: "apolipoprotein E receptor binding" RELATED [GOC:rl]
synonym: "very-low-density lipoprotein receptor binding" EXACT [GOC:bf, GOC:dph]
synonym: "VLDL receptor binding" EXACT [GOC:mah]
@@ -350240,7 +349758,7 @@ is_a: GO:0098797 ! plasma membrane protein complex
id: GO:0070335
name: aspartate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with aspartate, the alpha-amino-acid anion of 2-aminobutanedioic acid that has formula C4H5NO4." [CHEBI:29995, GOC:mah]
+def: "Binding to aspartate, the alpha-amino-acid anion of 2-aminobutanedioic acid that has formula C4H5NO4." [CHEBI:29995, GOC:mah]
synonym: "aspartic acid binding" EXACT [GOC:mah]
is_a: GO:0016597 ! amino acid binding
is_a: GO:0031406 ! carboxylic acid binding
@@ -350249,21 +349767,21 @@ is_a: GO:0031406 ! carboxylic acid binding
id: GO:0070336
name: flap-structured DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a flap structure in DNA. A DNA flap structure is one in which a single-stranded length of DNA or RNA protrudes from a double-stranded DNA molecule." [GOC:mah, PMID:15189154]
+def: "Binding to a flap structure in DNA. A DNA flap structure is one in which a single-stranded length of DNA or RNA protrudes from a double-stranded DNA molecule." [GOC:mah, PMID:15189154]
is_a: GO:0003677 ! DNA binding
[Term]
id: GO:0070337
name: 3'-flap-structured DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 3'-flap structure in DNA. A DNA flap structure is one in which a single-stranded 3'-end of DNA or RNA protrudes from a double-stranded DNA molecule." [GOC:mah, PMID:15189154]
+def: "Binding to a 3'-flap structure in DNA. A DNA flap structure is one in which a single-stranded 3'-end of DNA or RNA protrudes from a double-stranded DNA molecule." [GOC:mah, PMID:15189154]
is_a: GO:0070336 ! flap-structured DNA binding
[Term]
id: GO:0070338
name: 5'-flap-structured DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 5'-flap structure in DNA. A DNA flap structure is one in which a single-stranded 5'-end of DNA or RNA protrudes from a double-stranded DNA molecule. 5'-flap structures can be formed during DNA repair or lagging strand synthesis; in the latter case RNA flaps form from lagging strand RNA primers." [GOC:mah, PMID:15189154]
+def: "Binding to a 5'-flap structure in DNA. A DNA flap structure is one in which a single-stranded 5'-end of DNA or RNA protrudes from a double-stranded DNA molecule. 5'-flap structures can be formed during DNA repair or lagging strand synthesis; in the latter case RNA flaps form from lagging strand RNA primers." [GOC:mah, PMID:15189154]
is_a: GO:0070336 ! flap-structured DNA binding
[Term]
@@ -350711,7 +350229,7 @@ relationship: positively_regulates GO:0070375 ! ERK5 cascade
id: GO:0070379
name: high mobility group box 1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with high mobility group box 1 (HMBGB1)." [GOC:add, PMID:18431461]
+def: "Binding to high mobility group box 1 (HMBGB1)." [GOC:add, PMID:18431461]
synonym: "HMGB1 binding" EXACT [GOC:add]
is_a: GO:0019955 ! cytokine binding
@@ -350907,7 +350425,7 @@ is_a: GO:0019350 ! teichoic acid biosynthetic process
id: GO:0070401
name: NADP+ binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions." [GOC:mah]
+def: "Binding to the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions." [GOC:mah]
synonym: "NADP (oxidized) binding" EXACT [GOC:mah]
synonym: "NADP binding" RELATED [GOC:mah]
synonym: "oxidized NADP binding" EXACT [GOC:mah]
@@ -350919,7 +350437,7 @@ is_a: GO:0050661 ! NADP binding
id: GO:0070402
name: NADPH binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions." [GOC:mah]
+def: "Binding to the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions." [GOC:mah]
synonym: "NADP (reduced) binding" EXACT [GOC:mah]
synonym: "reduced NADP binding" EXACT [GOC:mah]
synonym: "reduced nicotinamide adenine dinucleotide phosphate binding" EXACT [GOC:mah]
@@ -350930,7 +350448,7 @@ is_a: GO:0050661 ! NADP binding
id: GO:0070403
name: NAD+ binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions." [GOC:mah]
+def: "Binding to the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions." [GOC:mah]
synonym: "NAD (oxidized) binding" EXACT [GOC:mah]
synonym: "NAD binding" RELATED [GOC:mah]
synonym: "oxidized NAD binding" EXACT [GOC:mah]
@@ -350942,7 +350460,7 @@ is_a: GO:0051287 ! NAD binding
id: GO:0070404
name: NADH binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions." [GOC:mah]
+def: "Binding to the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions." [GOC:mah]
synonym: "NAD (reduced) binding" EXACT [GOC:mah]
synonym: "reduced NAD binding" EXACT [GOC:mah]
synonym: "reduced nicotinamide adenine dinucleotide binding" EXACT [GOC:mah]
@@ -350953,7 +350471,7 @@ is_a: GO:0051287 ! NAD binding
id: GO:0070405
name: ammonium ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ammonium ions (NH4+)." [CHEBI:28938, GOC:ecd]
+def: "Binding to ammonium ions (NH4+)." [CHEBI:28938, GOC:ecd]
synonym: "ammonium binding" RELATED []
is_a: GO:0043169 ! cation binding
@@ -350961,7 +350479,7 @@ is_a: GO:0043169 ! cation binding
id: GO:0070406
name: glutamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with glutamine, 2,5-diamino-5-oxopentanoic acid." [CHEBI:28300, GOC:ecd]
+def: "Binding to glutamine, 2,5-diamino-5-oxopentanoic acid." [CHEBI:28300, GOC:ecd]
is_a: GO:0031406 ! carboxylic acid binding
[Term]
@@ -351005,7 +350523,7 @@ is_a: GO:0090407 ! organophosphate biosynthetic process
id: GO:0070410
name: co-SMAD binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a common mediator SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992]
+def: "Binding to a common mediator SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992]
synonym: "common mediator SMAD binding" EXACT [GOC:rl]
synonym: "common partner SMAD binding" EXACT [GOC:rl]
synonym: "common-mediator SMAD binding" EXACT [GOC:rl]
@@ -351016,14 +350534,14 @@ is_a: GO:0046332 ! SMAD binding
id: GO:0070411
name: I-SMAD binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an inhibitory SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992]
+def: "Binding to an inhibitory SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992]
is_a: GO:0046332 ! SMAD binding
[Term]
id: GO:0070412
name: R-SMAD binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992]
+def: "Binding to a receptor-regulated SMAD signaling protein." [GOC:BHF, GOC:vk, PMID:19114992]
synonym: "pathway restricted SMAD binding" EXACT [GOC:rl]
synonym: "pathway-restricted SMAD binding" EXACT [GOC:rl]
synonym: "receptor regulated SMAD binding" EXACT [GOC:rl]
@@ -351523,7 +351041,7 @@ is_a: GO:0030072 ! peptide hormone secretion
id: GO:0070461
name: SAGA-type complex
namespace: cellular_component
-def: "A histone acetyltransferase complex that acetylates nucleosomal H3 and H2B and is required for the expression of a subset of Pol II-transcribed genes. The budding yeast complex includes the acetyltransferase Gcn5p, several proteins of the Spt and Ada families, and several TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins." [GOC:mah, PMID:10637607, PMID:17337012]
+def: "A histone acetyltransferase complex that acetylates nucleosomal histones H2B, H3, or H4 and is required for the expression of a subset of Pol II-transcribed genes. This complex includes the acetyltransferases GCN5/KAT2A or PCAF/KAT2B, several proteins of the ADA, SGF and SPT families, and several TBP-associate proteins (TAFs)." [GOC:mah, PMID:10637607, PMID:17337012]
synonym: "SAGA family complex" EXACT [PMID:17337012]
is_a: GO:0000123 ! histone acetyltransferase complex
@@ -351540,7 +351058,7 @@ name: tubulin-dependent ATPase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate. This reaction requires the presence of a tubulin dimer to accelerate release of ADP and phosphate." [GOC:mah, PMID:16906148]
synonym: "tubulin-activated ATPase activity" EXACT []
-is_a: GO:0016887 ! ATPase
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0070464
@@ -351826,7 +351344,7 @@ is_a: GO:0032446 ! protein modification by small protein conjugation
id: GO:0070492
name: oligosaccharide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any oligosaccharide, a molecule with between two and (about) 20 monosaccharide residues connected by glycosidic linkages." [GOC:mah]
+def: "Binding to an oligosaccharide, a molecule with between two and (about) 20 monosaccharide residues connected by glycosidic linkages." [GOC:mah]
is_a: GO:0030246 ! carbohydrate binding
[Term]
@@ -352043,7 +351561,7 @@ relationship: positively_regulates GO:0034770 ! histone H4-K20 methylation
id: GO:0070513
name: death domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a death domain of a protein. The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD bind each other forming oligomers. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB." [GOC:BHF, GOC:rl, InterPro:IPR000488, Pfam:PF00531]
+def: "Binding to a death domain of a protein. The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD bind each other forming oligomers. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB." [GOC:BHF, GOC:rl, InterPro:IPR000488, Pfam:PF00531]
comment: For binding to the death effector domain, consider instead the term 'death effector domain binding ; GO:0035877'.
is_a: GO:0019904 ! protein domain specific binding
@@ -352124,20 +351642,21 @@ is_a: GO:0000109 ! nucleotide-excision repair complex
id: GO:0070523
name: 11-beta-hydroxysteroid dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NAD+ = an 11-oxosteroid + NADH + H+." [PMID:15761036]
+def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NAD+ = an 11-oxosteroid + NADH + H+." [PMID:15761036, RHEA:53116]
+xref: RHEA:53116
+xref: Wikipedia:11beta-hydroxysteroid_dehydrogenase
is_a: GO:0003845 ! 11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity
[Term]
id: GO:0070524
name: 11-beta-hydroxysteroid dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NADP+ = an 11-oxosteroid + NADPH + H+." [EC:1.1.1.146]
-synonym: "11beta-hydroxysteroid:NADP+ 11-oxidoreductase" RELATED [EC:1.1.1.146]
-synonym: "beta-hydroxysteroid dehydrogenase" BROAD [EC:1.1.1.146]
+def: "Catalysis of the reaction: an 11-beta-hydroxysteroid + NADP+ = an 11-oxosteroid + NADPH + H+." [RHEA:11388]
+synonym: "beta-hydroxysteroid dehydrogenase" BROAD []
synonym: "corticosteroid 11-beta-dehydrogenase activity" RELATED [EC:1.1.1.146]
xref: EC:1.1.1.146
-xref: MetaCyc:11-BETA-HYDROXYSTEROID-DEHYDROGENASE-RXN
xref: RHEA:11388
+xref: Wikipedia:11beta-hydroxysteroid_dehydrogenase
is_a: GO:0003845 ! 11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity
[Term]
@@ -352183,7 +351702,7 @@ is_a: GO:0008483 ! transaminase activity
id: GO:0070530
name: K63-linked polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 63 in the target protein." [GOC:mah, PMID:15556404, PMID:17525341]
+def: "Binding to a protein upon poly-ubiquitination formed by linkages between lysine residues at position 63 in the target protein." [GOC:mah, PMID:15556404, PMID:17525341]
is_a: GO:0031593 ! polyubiquitin modification-dependent protein binding
[Term]
@@ -352242,7 +351761,7 @@ is_a: GO:0070536 ! protein K63-linked deubiquitination
id: GO:0070538
name: oleic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with oleic acid, the 18-carbon monounsaturated fatty acid (9Z)-octadec-9-enoic acid." [GOC:lp, GOC:mah]
+def: "Binding to oleic acid, the 18-carbon monounsaturated fatty acid (9Z)-octadec-9-enoic acid." [GOC:lp, GOC:mah]
is_a: GO:0005504 ! fatty acid binding
is_a: GO:0043177 ! organic acid binding
@@ -352250,7 +351769,7 @@ is_a: GO:0043177 ! organic acid binding
id: GO:0070539
name: linoleic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with linoleic acid, the 18-carbon unsaturated fatty acid (9Z,12Z)-octadeca-9,12-dienoic acid." [GOC:lp, GOC:mah]
+def: "Binding to linoleic acid, the 18-carbon unsaturated fatty acid (9Z,12Z)-octadeca-9,12-dienoic acid." [GOC:lp, GOC:mah]
is_a: GO:0036041 ! long-chain fatty acid binding
is_a: GO:0043177 ! organic acid binding
@@ -352258,7 +351777,7 @@ is_a: GO:0043177 ! organic acid binding
id: GO:0070540
name: stearic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with stearic acid, the 18-carbon saturated fatty acid octadecanoic acid." [GOC:lp, GOC:mah]
+def: "Binding to stearic acid, the 18-carbon saturated fatty acid octadecanoic acid." [GOC:lp, GOC:mah]
is_a: GO:0036041 ! long-chain fatty acid binding
is_a: GO:0043177 ! organic acid binding
@@ -352326,16 +351845,16 @@ is_a: GO:0008483 ! transaminase activity
[Term]
id: GO:0070549
-name: negative regulation of translation involved in RNA interference
+name: siRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
def: "A process of negative regulation of translation that is mediated by the association of small interfering RNAs (siRNAs) with a cognate target mRNA." [GOC:mah, PMID:18771919]
synonym: "down regulation of translation involved in RNA interference" EXACT [GOC:mah]
synonym: "down-regulation of translation involved in RNA interference" EXACT [GOC:mah]
synonym: "downregulation of translation involved in RNA interference" EXACT [GOC:mah]
synonym: "inhibition of translation involved in RNA interference" NARROW [GOC:mah]
+synonym: "negative regulation of translation involved in RNA interference" EXACT []
synonym: "RNA interference, negative regulation of translation" EXACT [GOC:mah]
-is_a: GO:0040033 ! negative regulation of translation, ncRNA-mediated
-relationship: part_of GO:0016246 ! RNA interference
+is_a: GO:0040033 ! RNA-mediated gene silencing by inhibition of translation
[Term]
id: GO:0070550
@@ -352345,6 +351864,7 @@ def: "The process in which the chromatin structure of the rDNA repeats is compac
synonym: "rDNA packaging" EXACT []
is_a: GO:0006323 ! DNA packaging
relationship: part_of GO:0030261 ! chromosome condensation
+relationship: part_of GO:1990700 ! nucleolar chromatin organization
[Term]
id: GO:0070551
@@ -352604,7 +352124,7 @@ is_a: GO:0004497 ! monooxygenase activity
id: GO:0070577
name: lysine-acetylated histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation." [GOC:BHF, GOC:mah, GOC:rl, PMID:17582821]
+def: "Binding to a histone in which a lysine residue has been modified by acetylation." [GOC:BHF, GOC:mah, GOC:rl, PMID:17582821]
synonym: "acetylated histone residue binding" BROAD [GOC:rl]
is_a: GO:0042393 ! histone binding
is_a: GO:0140033 ! acetylation-dependent protein binding
@@ -352763,8 +352283,7 @@ is_a: GO:0008038 ! neuron recognition
id: GO:0070594
name: juvenile hormone response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the juvenile hormone response element (JHRE), a conserved sequence found in the promoters of genes whose expression is regulated in response to juvenile hormone." [GOC:sart, PMID:17956872]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to a juvenile hormone response element (JHRE), a conserved sequence found in the promoters of genes whose expression is regulated in response to juvenile hormone." [GOC:sart, PMID:17956872]
synonym: "JHRE binding" EXACT [GOC:mah]
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
@@ -353010,7 +352529,7 @@ id: GO:0070613
name: regulation of protein processing
namespace: biological_process
alt_id: GO:0010953
-def: "Any process that modulates the frequency, rate or extent of protein processing, any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein." [GOC:mah]
+def: "Any process that modulates the frequency, rate or extent of protein processing, a protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein." [GOC:mah]
synonym: "regulation of protein maturation by peptide bond cleavage" EXACT []
is_a: GO:0030162 ! regulation of proteolysis
is_a: GO:1903317 ! regulation of protein maturation
@@ -353023,14 +352542,6 @@ namespace: biological_process
def: "The directed movement of tungstate (WO4 2-) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Tungstate is a bivalent oxoanion of tungsten." [GOC:dh]
is_a: GO:0015698 ! inorganic anion transport
-[Term]
-id: GO:0070615
-name: nucleosome-dependent ATPase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate. This reaction requires the presence of one or more nucleosomes." [GOC:mah, PMID:19165147]
-synonym: "nucleosome-activated ATPase activity" EXACT [GOC:mah]
-is_a: GO:0016887 ! ATPase
-
[Term]
id: GO:0070616
name: regulation of thiamine diphosphate biosynthetic process
@@ -353125,6 +352636,7 @@ is_a: GO:0030656 ! regulation of vitamin metabolic process
is_a: GO:0031326 ! regulation of cellular biosynthetic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
is_a: GO:0051171 ! regulation of nitrogen compound metabolic process
+is_a: GO:1902930 ! regulation of alcohol biosynthetic process
relationship: regulates GO:0009228 ! thiamine biosynthetic process
[Term]
@@ -353146,6 +352658,7 @@ is_a: GO:0046137 ! negative regulation of vitamin metabolic process
is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process
is_a: GO:0051175 ! negative regulation of sulfur metabolic process
is_a: GO:0070623 ! regulation of thiamine biosynthetic process
+is_a: GO:1902931 ! negative regulation of alcohol biosynthetic process
relationship: negatively_regulates GO:0009228 ! thiamine biosynthetic process
[Term]
@@ -353157,11 +352670,13 @@ is_a: GO:0017156 ! calcium-ion regulated exocytosis
[Term]
id: GO:0070626
-name: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity
+name: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity
namespace: molecular_function
def: "Catalysis of the reaction: (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide." [GOC:mah, GOC:pde]
+synonym: "(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity" RELATED []
synonym: "adenylosuccinase activity" BROAD [EC:4.3.2.2, GOC:mah]
synonym: "adenylosuccinate lyase activity" BROAD [GOC:mah]
+synonym: "SAICAR-lyase (fumarate forming) activity" RELATED []
synonym: "succino AMP-lyase activity" BROAD [EC:4.3.2.2, GOC:mah]
xref: EC:4.3.2.2
xref: KEGG_REACTION:R04559
@@ -353173,7 +352688,7 @@ is_a: GO:0016842 ! amidine-lyase activity
id: GO:0070628
name: proteasome binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a proteasome, a large multisubunit protein complex that catalyzes protein degradation." [GOC:mah]
+def: "Binding to a proteasome, a large multisubunit protein complex that catalyzes protein degradation." [GOC:mah]
subset: goslim_chembl
is_a: GO:0044877 ! protein-containing complex binding
@@ -353235,8 +352750,9 @@ id: GO:0070634
name: transepithelial ammonium transport
namespace: biological_process
def: "The directed movement of ammonium ions from one side of an epithelium to the other." [GOC:mah, GOC:yaf]
-is_a: GO:0015696 ! ammonium transport
+is_a: GO:0006812 ! cation transport
is_a: GO:0070633 ! transepithelial transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0070635
@@ -353333,8 +352849,7 @@ is_a: GO:0004497 ! monooxygenase activity
id: GO:0070644
name: vitamin D response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:vk, PMID:17426122]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to a vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum." [GOC:BHF, GOC:vk, PMID:17426122]
synonym: "VDRE binding" EXACT [GOC:vk, PMID:17426122]
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
@@ -353408,7 +352923,7 @@ is_a: GO:0005875 ! microtubule associated complex
id: GO:0070653
name: high-density lipoprotein particle receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a high-density lipoprotein receptor." [GOC:BHF, GOC:mah]
+def: "Binding to a high-density lipoprotein receptor." [GOC:BHF, GOC:mah]
synonym: "HDL receptor binding" EXACT [GOC:mah]
synonym: "high-density lipoprotein receptor binding" EXACT [GOC:dph]
is_a: GO:0070325 ! lipoprotein particle receptor binding
@@ -353639,7 +353154,7 @@ is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
id: GO:0070678
name: preprotein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a preprotein, the unprocessed form of a protein destined to undergo co- or post-translational processing." [GOC:imk, GOC:mah, PMID:12914940]
+def: "Binding to a preprotein, the unprocessed form of a protein destined to undergo co- or post-translational processing." [GOC:imk, GOC:mah, PMID:12914940]
synonym: "unprocessed protein binding" EXACT [GOC:imk]
is_a: GO:0005515 ! protein binding
@@ -353647,7 +353162,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0070679
name: inositol 1,4,5 trisphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with inositol 1,4,5 trisphosphate." [GOC:BHF, GOC:mah]
+def: "Binding to inositol 1,4,5 trisphosphate." [GOC:BHF, GOC:mah]
synonym: "InsP3 binding" EXACT [GOC:mah]
synonym: "IP3 binding" EXACT [GOC:mah]
is_a: GO:0043168 ! anion binding
@@ -353785,7 +353300,6 @@ name: deoxyribonucleoside 5'-monophosphate N-glycosidase activity
namespace: molecular_function
def: "Catalysis of the reaction: a deoxyribonucleoside 5'-monophosphate + H2O = deoxyribose 5-monophosphate + a purine or pyrimidine base." [GOC:ab, PMID:17234634]
synonym: "deoxynucleoside 5'-monophosphate N-glycosidase activity" EXACT []
-xref: EC:3.2.2.-
xref: Reactome:R-HSA-8953339 "DNPH1 hydrolyses dGMP"
is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
@@ -353802,35 +353316,35 @@ relationship: part_of GO:0005737 ! cytoplasm
id: GO:0070696
name: transmembrane receptor protein serine/threonine kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a receptor that spans a cell membrane and possesses protein serine/threonine kinase activity." [GOC:BHF, GOC:mah]
+def: "Binding to a receptor that spans a cell membrane and possesses protein serine/threonine kinase activity." [GOC:BHF, GOC:mah]
is_a: GO:0033612 ! receptor serine/threonine kinase binding
[Term]
id: GO:0070697
name: activin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an activin receptor." [GOC:BHF, GOC:vk]
+def: "Binding to an activin receptor." [GOC:BHF, GOC:vk]
is_a: GO:0070696 ! transmembrane receptor protein serine/threonine kinase binding
[Term]
id: GO:0070698
name: type I activin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type I activin receptor." [GOC:BHF, GOC:vk]
+def: "Binding to a type I activin receptor." [GOC:BHF, GOC:vk]
is_a: GO:0070697 ! activin receptor binding
[Term]
id: GO:0070699
name: type II activin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type II activin receptor." [GOC:BHF, GOC:vk]
+def: "Binding to a type II activin receptor." [GOC:BHF, GOC:vk]
is_a: GO:0070697 ! activin receptor binding
[Term]
id: GO:0070700
name: BMP receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a BMP receptor." [GOC:BHF, GOC:vk]
+def: "Binding to a BMP receptor." [GOC:BHF, GOC:vk]
synonym: "bone morphogenetic protein receptor binding" EXACT [GOC:mah]
is_a: GO:0070696 ! transmembrane receptor protein serine/threonine kinase binding
@@ -353966,7 +353480,7 @@ relationship: part_of GO:0045005 ! DNA-dependent DNA replication maintenance of
id: GO:0070717
name: poly-purine tract binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any stretch of purines (adenine or guanine) in an RNA molecule." [GOC:mah]
+def: "Binding to a stretch of purines (adenine or guanine) in an RNA molecule." [GOC:mah]
is_a: GO:0003727 ! single-stranded RNA binding
[Term]
@@ -354055,9 +353569,9 @@ is_a: GO:0051641 ! cellular localization
id: GO:0070728
name: leucine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 2-amino-4-methylpentanoic acid." [GOC:BHF, GOC:mah]
+def: "Binding to 2-amino-4-methylpentanoic acid." [GOC:BHF, GOC:mah]
synonym: "Leu binding" EXACT [GOC:mah]
-is_a: GO:0031406 ! carboxylic acid binding
+is_a: GO:0016597 ! amino acid binding
[Term]
id: GO:0070729
@@ -354183,7 +353697,7 @@ is_a: GO:0034097 ! response to cytokine
id: GO:0070742
name: C2H2 zinc finger domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion." [GOC:BHF, GOC:mah, Pfam:PF00096]
+def: "Binding to a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion." [GOC:BHF, GOC:mah, Pfam:PF00096]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -354230,7 +353744,7 @@ relationship: part_of GO:0005615 ! extracellular space
id: GO:0070746
name: interleukin-35 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with interleukin-35." [GOC:add]
+def: "Binding to interleukin-35." [GOC:add]
synonym: "IL-35 binding" EXACT [GOC:add]
is_a: GO:0019955 ! cytokine binding
@@ -354247,7 +353761,7 @@ is_a: GO:0004896 ! cytokine receptor activity
id: GO:0070748
name: interleukin-35 receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the interleukin-35 receptor." [GOC:add]
+def: "Binding to an interleukin-35 receptor." [GOC:add]
synonym: "IL-35" NARROW [GOC:add]
synonym: "interleukin-35 receptor ligand" NARROW [GOC:add]
is_a: GO:0005126 ! cytokine receptor binding
@@ -354885,7 +354399,7 @@ namespace: biological_process
def: "Any process in which the P-TEFb-cap methyltransferase complex is transported to, or maintained in, a specific location." [GOC:mah]
synonym: "establishment and maintenance of P-TEFb-cap methyltransferase complex localization" EXACT [GOC:MAH]
synonym: "P-TEFb-cap methyltransferase complex localisation" EXACT [GOC:mah]
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
[Term]
id: GO:0070818
@@ -354966,11 +354480,11 @@ relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0070827
-name: chromatin maintenance
+name: obsolete chromatin maintenance
namespace: biological_process
-def: "The chromatin organization process that preserves chromatin in a stable functional or structural state." [GOC:mah]
-is_a: GO:0006325 ! chromatin organization
-is_a: GO:0043954 ! cellular component maintenance
+def: "OBSOLETE. The chromatin organization process that preserves chromatin in a stable functional or structural state." [GOC:mah]
+comment: This term was obsoleted because it is redundant with chromatin organization and assembly terms.
+is_obsolete: true
[Term]
id: GO:0070828
@@ -354982,17 +354496,16 @@ is_a: GO:0006325 ! chromatin organization
[Term]
id: GO:0070829
-name: heterochromatin maintenance
+name: obsolete heterochromatin maintenance
namespace: biological_process
alt_id: GO:0006344
alt_id: GO:0070870
-def: "The chromatin organization process that preserves heterochromatin in a stable functional or structural state." [GOC:mah]
+def: "OBSOLETE. The chromatin organization process that preserves heterochromatin in a stable functional or structural state." [GOC:mah]
+comment: This term was obsoleted because it is redundant with heterochromatin organization and assembly terms.
synonym: "heterochromatin maintenance involved in chromatin silencing" RELATED []
synonym: "maintenance of chromatin silencing" RELATED []
synonym: "maintenance of heterochromatic silencing" RELATED []
-is_a: GO:0051276 ! chromosome organization
-is_a: GO:0070827 ! chromatin maintenance
-is_a: GO:0070868 ! heterochromatin organization involved in chromatin silencing
+is_obsolete: true
[Term]
id: GO:0070830
@@ -355076,7 +354589,7 @@ id: GO:0070840
name: dynein complex binding
namespace: molecular_function
alt_id: GO:0045502
-def: "Interacting selectively and non-covalently with a dynein complex, a protein complex that contains two or three dynein heavy chains and several light chains, and has microtubule motor activity." [GOC:bf, GOC:BHF, GOC:mah]
+def: "Binding to a dynein complex, a protein complex that contains two or three dynein heavy chains and several light chains, and has microtubule motor activity." [GOC:bf, GOC:BHF, GOC:mah]
synonym: "dynein binding" RELATED []
is_a: GO:0044877 ! protein-containing complex binding
@@ -355164,7 +354677,7 @@ is_a: GO:0140535 ! intracellular protein-containing complex
id: GO:0070851
name: growth factor receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a growth factor receptor." [GOC:mah, GOC:vw]
+def: "Binding to a growth factor receptor." [GOC:mah, GOC:vw]
is_a: GO:0005102 ! signaling receptor binding
[Term]
@@ -355180,14 +354693,14 @@ is_a: GO:0043005 ! neuron projection
id: GO:0070853
name: myosin VI binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a class VI myosin. The myosin VI heavy chain has a single IQ motif in the neck and a tail region with a coiled coil domain followed by a unique globular domain, a unique insertion that enables myosin VI to move towards the pointed or minus end of actin filaments." [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html, PMID:15473855]
+def: "Binding to a class VI myosin. The myosin VI heavy chain has a single IQ motif in the neck and a tail region with a coiled coil domain followed by a unique globular domain, a unique insertion that enables myosin VI to move towards the pointed or minus end of actin filaments." [GOC:mah, http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html, PMID:15473855]
is_a: GO:0017022 ! myosin binding
[Term]
id: GO:0070854
name: myosin VI heavy chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a heavy chain of a myosin VI complex." [GOC:sart]
+def: "Binding to a heavy chain of a myosin VI complex." [GOC:sart]
is_a: GO:0032036 ! myosin heavy chain binding
is_a: GO:0070853 ! myosin VI binding
@@ -355195,7 +354708,7 @@ is_a: GO:0070853 ! myosin VI binding
id: GO:0070855
name: myosin VI head/neck binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the head/neck region of a myosin VI heavy chain." [GOC:sart]
+def: "Binding to the head/neck region of a myosin VI heavy chain." [GOC:sart]
is_a: GO:0032028 ! myosin head/neck binding
is_a: GO:0070854 ! myosin VI heavy chain binding
@@ -355203,7 +354716,7 @@ is_a: GO:0070854 ! myosin VI heavy chain binding
id: GO:0070856
name: myosin VI light chain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a light chain of a myosin VI complex." [GOC:sart]
+def: "Binding to a light chain of a myosin VI complex." [GOC:sart]
is_a: GO:0032027 ! myosin light chain binding
is_a: GO:0070853 ! myosin VI binding
@@ -355334,7 +354847,7 @@ relationship: part_of GO:0070864 ! sperm individualization complex
id: GO:0070866
name: sterol-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) in the presence of sterols." [GOC:ecd]
+def: "Binding to a protein or protein complex in the presence of sterols." [GOC:ecd]
is_a: GO:0005515 ! protein binding
[Term]
@@ -355349,13 +354862,12 @@ relationship: part_of GO:0043332 ! mating projection tip
[Term]
id: GO:0070868
-name: heterochromatin organization involved in chromatin silencing
+name: obsolete heterochromatin organization involved in chromatin silencing
namespace: biological_process
-def: "Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin and contributes to chromatin silencing." [GOC:mah]
+def: "OBSOLETE. Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin and contributes to chromatin silencing." [GOC:mah]
+comment: This term was obsoleted because it was not clearly defined, and used incorrectly.
synonym: "heterochromatin organisation involved in chromatin silencing" EXACT [GOC:mah]
-is_a: GO:0070828 ! heterochromatin organization
-is_a: GO:0097549 ! chromatin organization involved in negative regulation of transcription
-relationship: part_of GO:0006342 ! chromatin silencing
+is_obsolete: true
[Term]
id: GO:0070871
@@ -355419,7 +354931,7 @@ is_a: GO:1903095 ! ribonuclease III complex
id: GO:0070878
name: primary miRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding." [GOC:sl, PMID:15531877, PMID:15574589]
+def: "Binding to a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding." [GOC:sl, PMID:15531877, PMID:15574589]
synonym: "pri-miRNA binding" EXACT []
synonym: "primary microRNA binding" EXACT [PMID:15531877, PMID:15574589]
is_a: GO:0003723 ! RNA binding
@@ -355460,7 +354972,7 @@ relationship: regulates GO:0015824 ! proline transport
id: GO:0070883
name: pre-miRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA." [PMID:18951094]
+def: "Binding to a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA." [PMID:18951094]
synonym: "pre-microRNA binding" EXACT [GOC:pr]
synonym: "precursor microRNA binding" EXACT [PMID:18951094]
is_a: GO:0003723 ! RNA binding
@@ -355530,8 +355042,7 @@ is_a: GO:0051716 ! cellular response to stimulus
id: GO:0070888
name: E-box binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues." [GOC:BHF, GOC:vk, PMID:11812799]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues." [GOC:BHF, GOC:vk, PMID:11812799]
synonym: "E-box promoter binding" EXACT [GOC:vk]
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
@@ -355549,7 +355060,7 @@ is_a: GO:0033363 ! secretory granule organization
id: GO:0070891
name: lipoteichoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lipoteichoic acid." [GOC:add, PMID:14665680]
+def: "Binding to lipoteichoic acid." [GOC:add, PMID:14665680]
is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
@@ -355610,7 +355121,11 @@ relationship: positively_regulates GO:0070893 ! transposon integration
id: GO:0070897
name: transcription preinitiation complex assembly
namespace: biological_process
+alt_id: GO:0001126
def: "The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), required for transcription." [GOC:jp, GOC:txnOH]
+synonym: "bacterial-type RNA polymerase preinitiation complex assembly" NARROW []
+synonym: "bacterial-type RNA polymerase transcription PIC formation" NARROW []
+synonym: "bacterial-type RNA polymerase transcriptional preinitiation complex formation" NARROW []
synonym: "DNA-dependent transcriptional preinitiation complex assembly" EXACT [GOC:txnOH]
synonym: "DNA-templated transcriptional preinitiation complex assembly" EXACT []
synonym: "transcription PIC biosynthesis" BROAD [GOC:mah]
@@ -355697,7 +355212,7 @@ is_a: GO:0070633 ! transepithelial transport
id: GO:0070905
name: serine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 2-amino-3-hydroxypropanoic acid." [GOC:rph]
+def: "Binding to 2-amino-3-hydroxypropanoic acid." [GOC:rph]
synonym: "Ser binding" EXACT [GOC:mah]
is_a: GO:0016597 ! amino acid binding
is_a: GO:0031406 ! carboxylic acid binding
@@ -355837,12 +355352,13 @@ relationship: part_of GO:0031047 ! gene silencing by RNA
[Term]
id: GO:0070919
-name: production of siRNA involved in chromatin silencing by small RNA
+name: production of siRNA involved in gene silencing by small RNA
namespace: biological_process
-def: "Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of chromatin silencing by small RNA." [GOC:mah, PMID:19239886]
+def: "Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of gene silencing by small RNA." [GOC:mah, PMID:19239886]
synonym: "chromatin silencing by small RNA, production of guide RNAs" EXACT []
synonym: "chromatin silencing by small RNA, production of siRNA" EXACT [GOC:mah]
synonym: "production of guide RNAs involved in chromatin silencing by small RNA" EXACT [GOC:mah]
+synonym: "production of siRNA involved in chromatin silencing by small RNA" EXACT []
is_a: GO:0070918 ! production of small RNA involved in gene silencing by RNA
relationship: part_of GO:0031048 ! heterochromatin assembly by small RNA
@@ -355859,10 +355375,11 @@ relationship: regulates GO:0070918 ! production of small RNA involved in gene si
[Term]
id: GO:0070921
-name: regulation of production of siRNA involved in chromatin silencing by small RNA
+name: regulation of production of siRNA involved in gene silencing by small RNA
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of chromatin silencing by small RNA." [GOC:mah]
+def: "Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of gene silencing by small RNA." [GOC:mah]
synonym: "regulation of chromatin silencing by small RNA, production of siRNA" EXACT [GOC:mah]
+synonym: "regulation of production of siRNA involved in chromatin silencing by small RNA" EXACT []
is_a: GO:0070920 ! regulation of production of small RNA involved in gene silencing by RNA
[Term]
@@ -355877,10 +355394,11 @@ relationship: part_of GO:0031047 ! gene silencing by RNA
[Term]
id: GO:0070923
-name: siRNA loading onto RISC involved in chromatin silencing by small RNA
+name: siRNA loading onto RISC involved in gene silencing by small RNA
namespace: biological_process
-def: "The process in which a single-stranded small RNA associates with the RNA-initiated silencing complex (RISC); occurs as part of a process of chromatin silencing by small RNA." [GOC:mah, PMID:19239886]
+def: "The process in which a single-stranded small RNA associates with the RNA-initiated silencing complex (RISC); occurs as part of a process of chromatin gene by small RNA." [GOC:mah, PMID:19239886]
synonym: "chromatin silencing by small RNA, siRNA loading onto RISC" EXACT [GOC:mah]
+synonym: "siRNA loading onto RISC involved in chromatin silencing by small RNA" EXACT []
is_a: GO:0070922 ! small RNA loading onto RISC
relationship: part_of GO:0031048 ! heterochromatin assembly by small RNA
@@ -356113,8 +355631,6 @@ is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
-is_a: GO:0050776 ! regulation of immune response
-is_a: GO:0051709 ! regulation of killing of cells of other organism
is_a: GO:0070948 ! regulation of neutrophil mediated cytotoxicity
relationship: regulates GO:0070943 ! neutrophil-mediated killing of symbiont cell
@@ -356178,8 +355694,6 @@ synonym: "inhibition of neutrophil mediated killing of symbiont cell" NARROW [GO
is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
-is_a: GO:0050777 ! negative regulation of immune response
-is_a: GO:0051711 ! negative regulation of killing of cells of other organism
is_a: GO:0070949 ! regulation of neutrophil mediated killing of symbiont cell
is_a: GO:0070954 ! negative regulation of neutrophil mediated cytotoxicity
relationship: negatively_regulates GO:0070943 ! neutrophil-mediated killing of symbiont cell
@@ -356265,8 +355779,6 @@ synonym: "upregulation of neutrophil mediated killing of symbiont cell" EXACT [G
is_a: GO:0002833 ! positive regulation of response to biotic stimulus
is_a: GO:0031349 ! positive regulation of defense response
is_a: GO:0032103 ! positive regulation of response to external stimulus
-is_a: GO:0050778 ! positive regulation of immune response
-is_a: GO:0051712 ! positive regulation of killing of cells of other organism
is_a: GO:0070949 ! regulation of neutrophil mediated killing of symbiont cell
is_a: GO:0070960 ! positive regulation of neutrophil mediated cytotoxicity
relationship: positively_regulates GO:0070943 ! neutrophil-mediated killing of symbiont cell
@@ -356344,7 +355856,7 @@ is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process
id: GO:0070967
name: coenzyme F420 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with F420, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:dh]
+def: "Binding to F420, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:dh]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -356354,7 +355866,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0070968
name: pyrroloquinoline quinone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pyrroloquinoline quinone, PQQ, the coenzyme or the prosthetic group of certain alcohol dehydrogenases and glucose dehydrogenases." [GOC:dh]
+def: "Binding to pyrroloquinoline quinone, PQQ, the coenzyme or the prosthetic group of certain alcohol dehydrogenases and glucose dehydrogenases." [GOC:dh]
synonym: "PQQ binding" EXACT [GOC:dh]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043177 ! organic acid binding
@@ -356396,14 +355908,14 @@ is_a: GO:0070972 ! protein localization to endoplasmic reticulum
id: GO:0070974
name: POU domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a POU domain of a protein. The POU domain is a bipartite DNA binding domain composed of two subunits separated by a non-conserved region of 15-55 amino acids; it is found in several eukaryotic transcription factors." [GOC:mah, GOC:yaf, InterPro:IPR000327]
+def: "Binding to a POU domain of a protein. The POU domain is a bipartite DNA binding domain composed of two subunits separated by a non-conserved region of 15-55 amino acids; it is found in several eukaryotic transcription factors." [GOC:mah, GOC:yaf, InterPro:IPR000327]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0070975
name: FHA domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a FHA domain of a protein. The FHA domain is a phosphopeptide recognition domain found in many regulatory proteins, and consists of approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich." [GOC:mah, InterPro:IPR000253]
+def: "Binding to a FHA domain of a protein. The FHA domain is a phosphopeptide recognition domain found in many regulatory proteins, and consists of approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich." [GOC:mah, InterPro:IPR000253]
synonym: "Forkhead-associated domain binding" EXACT [InterPro:IPR000253]
is_a: GO:0019904 ! protein domain specific binding
@@ -356411,7 +355923,7 @@ is_a: GO:0019904 ! protein domain specific binding
id: GO:0070976
name: TIR domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Toll-Interleukin receptor (TIR) domain of a protein. The TIR domain is an intracellular 200 residue domain that is found in the Toll protein, the interleukin-1 receptor (IL-1R), and MyD88; it contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components." [GOC:mah, InterPro:IPR000157]
+def: "Binding to a Toll-Interleukin receptor (TIR) domain of a protein. The TIR domain is an intracellular 200 residue domain that is found in the Toll protein, the interleukin-1 receptor (IL-1R), and MyD88; it contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components." [GOC:mah, InterPro:IPR000157]
subset: goslim_chembl
synonym: "Toll-Interleukin receptor domain binding" EXACT [InterPro:IPR000157]
is_a: GO:0019904 ! protein domain specific binding
@@ -356429,7 +355941,7 @@ id: GO:0070978
name: voltage-gated calcium channel complex assembly
namespace: biological_process
def: "Cellular protein complex assembly that results in the formation of a voltage-gated calcium channel complex." [GOC:mh]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0070979
@@ -356486,7 +355998,7 @@ relationship: part_of GO:0048813 ! dendrite morphogenesis
id: GO:0070984
name: SET domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a SET domain of a protein. SET domains are named after three Drosophila proteins that contain this domain: Su(var), E(z) and trithorax. SET domains are associated with histone lysine methylation." [GOC:sart, Pfam:PF00856, PMID:12575990]
+def: "Binding to a SET domain of a protein. SET domains are named after three Drosophila proteins that contain this domain: Su(var), E(z) and trithorax. SET domains are associated with histone lysine methylation." [GOC:sart, Pfam:PF00856, PMID:12575990]
synonym: "SET binding" EXACT [GOC:sart]
is_a: GO:0019904 ! protein domain specific binding
@@ -356538,7 +356050,7 @@ is_a: GO:0070988 ! demethylation
id: GO:0070990
name: snRNP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of a small nuclear ribonucleoprotein particle." [GOC:BHF, GOC:mah, GOC:rl]
+def: "Binding to a small nuclear ribonucleoprotein particle." [GOC:BHF, GOC:mah, GOC:rl]
is_a: GO:0043021 ! ribonucleoprotein complex binding
[Term]
@@ -356591,7 +356103,7 @@ is_a: GO:0006739 ! NADP metabolic process
id: GO:0070996
name: type 1 melanocortin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type 1 melanocortin receptor." [GOC:BHF, GOC:mah]
+def: "Binding to a type 1 melanocortin receptor." [GOC:BHF, GOC:mah]
synonym: "type 1 melanocortin receptor ligand" NARROW [GOC:mah]
is_a: GO:0031779 ! melanocortin receptor binding
@@ -356889,7 +356401,7 @@ is_a: GO:0097525 ! spliceosomal snRNP complex
id: GO:0071025
name: RNA surveillance
namespace: biological_process
-def: "The set of processes involved in identifying and degrading defective or aberrant RNAs." [GOC:dgf, GOC:krc, PMID:18644474]
+def: "A process that identifies and degrades defective or aberrant RNAs." [GOC:dgf, GOC:krc, PMID:18644474]
synonym: "aberrant RNA catabolic process" EXACT [GOC:dgf, GOC:krc]
synonym: "RNA quality control" EXACT [GOC:dgf, GOC:krc]
is_a: GO:0006401 ! RNA catabolic process
@@ -356907,7 +356419,7 @@ is_a: GO:0071025 ! RNA surveillance
id: GO:0071027
name: nuclear RNA surveillance
namespace: biological_process
-def: "The set of processes involved in identifying and degrading defective or aberrant RNAs within the nucleus." [GOC:dgf, GOC:krc, PMID:18644474]
+def: "A process that identifies and degrades defective or aberrant RNAs within the nucleus." [GOC:dgf, GOC:krc, PMID:18644474]
synonym: "nuclear aberrant RNA catabolic process" EXACT [GOC:dgf, GOC:krc]
synonym: "nuclear RNA quality control" EXACT [GOC:dgf, GOC:krc]
is_a: GO:0071025 ! RNA surveillance
@@ -356916,9 +356428,15 @@ is_a: GO:0071025 ! RNA surveillance
id: GO:0071028
name: nuclear mRNA surveillance
namespace: biological_process
-def: "The set of processes involved in identifying and degrading defective or aberrant mRNAs within the nucleus." [GOC:dgf, GOC:krc, PMID:18644474]
+alt_id: GO:0071033
+alt_id: GO:0071048
+alt_id: GO:0071049
+def: "A process that identifies and degrades defective or aberrant mRNAs within the nucleus." [GOC:dgf, GOC:krc, PMID:11586364, PMID:12417728, PMID:14718167, PMID:18644474]
synonym: "nuclear aberrant mRNA catabolic process" EXACT [GOC:dgf, GOC:krc]
synonym: "nuclear mRNA quality control" EXACT [GOC:dgf, GOC:krc]
+synonym: "nuclear retention of pre-mRNA at the site of transcription" NARROW []
+synonym: "nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription" NARROW []
+synonym: "nuclear retention of unspliced pre-mRNA at the site of transcription" NARROW []
is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process
is_a: GO:0071027 ! nuclear RNA surveillance
@@ -356959,14 +356477,6 @@ synonym: "nuclear mRNA catabolic process of mRNAs in aberrant mRNPs" EXACT [GOC:
synonym: "nuclear mRNA quality control of mRNAs in aberrant mRNPs" EXACT [GOC:dgf, GOC:krc]
is_a: GO:0071028 ! nuclear mRNA surveillance
-[Term]
-id: GO:0071033
-name: nuclear retention of pre-mRNA at the site of transcription
-namespace: biological_process
-def: "The process involved in retention of aberrant or improperly formed mRNAs, e.g. those that are incorrectly or incompletely spliced or that have incorrectly formed 3'-ends, within the nucleus at the site of transcription." [GOC:dgf, GOC:krc, PMID:11586364, PMID:12417728, PMID:14718167, PMID:18644474]
-is_a: GO:0008298 ! intracellular mRNA localization
-relationship: part_of GO:0071028 ! nuclear mRNA surveillance
-
[Term]
id: GO:0071034
name: CUT catabolic process
@@ -357087,22 +356597,6 @@ is_a: GO:0006402 ! mRNA catabolic process
is_a: GO:0043633 ! polyadenylation-dependent RNA catabolic process
is_a: GO:0061157 ! mRNA destabilization
-[Term]
-id: GO:0071048
-name: nuclear retention of unspliced pre-mRNA at the site of transcription
-namespace: biological_process
-def: "The process involved in retention of incorrectly or incompletely spliced pre-mRNA within the nucleus at the site of transcription." [GOC:dgf, GOC:krc, PMID:14718167]
-is_a: GO:0071033 ! nuclear retention of pre-mRNA at the site of transcription
-relationship: part_of GO:0071030 ! nuclear mRNA surveillance of spliceosomal pre-mRNA splicing
-
-[Term]
-id: GO:0071049
-name: nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription
-namespace: biological_process
-def: "The process involved in retention of mRNAs that have incorrectly formed 3'-ends within the nucleus at the site of transcription." [GOC:dgf, GOC:krc, PMID:11586364, PMID:12417728]
-is_a: GO:0071033 ! nuclear retention of pre-mRNA at the site of transcription
-relationship: part_of GO:0071031 ! nuclear mRNA surveillance of mRNA 3'-end processing
-
[Term]
id: GO:0071050
name: sno(s)RNA polyadenylation
@@ -357340,7 +356834,7 @@ relationship: positively_regulates GO:0008654 ! phospholipid biosynthetic proces
id: GO:0071074
name: eukaryotic initiation factor eIF2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with eukaryotic initiation factor eIF2, a protein complex involved in the initiation of ribosome-mediated translation." [GOC:hjd]
+def: "Binding to eukaryotic initiation factor eIF2, a protein complex involved in the initiation of ribosome-mediated translation." [GOC:hjd]
is_a: GO:0031369 ! translation initiation factor binding
[Term]
@@ -358081,6 +357575,7 @@ id: GO:0071171
name: site-specific DNA replication termination at RTS1 barrier
namespace: biological_process
def: "A DNA replication termination process that takes place at the RTS1 termination site in the mating type locus, in a specific direction required for subsequent imprinting and mating-type switching." [GOC:vw, PMID:12009298, PMID:18723894]
+is_a: GO:0022414 ! reproductive process
is_a: GO:0071170 ! site-specific DNA replication termination
relationship: part_of GO:0071516 ! establishment of imprinting at mating-type locus
@@ -358388,21 +357883,21 @@ is_a: GO:0071205 ! protein localization to juxtaparanode region of axon
id: GO:0071207
name: histone pre-mRNA stem-loop binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a conserved stem-loop structure found in histone pre-mRNAs." [PMID:19470752]
+def: "Binding to a conserved stem-loop structure found in histone pre-mRNAs." [PMID:19470752]
is_a: GO:0036002 ! pre-mRNA binding
[Term]
id: GO:0071208
name: histone pre-mRNA DCP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the downstream cleavage product (DCP) generated by histone pre-mRNA 3'-end processing." [PMID:19470752]
+def: "Binding to the downstream cleavage product (DCP) generated by histone pre-mRNA 3'-end processing." [PMID:19470752]
is_a: GO:0003723 ! RNA binding
[Term]
id: GO:0071209
name: U7 snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the U7 small nuclear RNA (U7 snRNA)." [GOC:mah, PMID:12975319]
+def: "Binding to a U7 small nuclear RNA (U7 snRNA)." [GOC:mah, PMID:12975319]
comment: Note that this term may be useful for annotating other small nuclear RNAs (snRNAs).
is_a: GO:0017069 ! snRNA binding
@@ -358820,7 +358315,7 @@ is_a: GO:1901701 ! cellular response to oxygen-containing compound
id: GO:0071253
name: connexin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a connexin, any of a group of related proteins that assemble to form gap junctions." [GOC:mah, PMID:19864490]
+def: "Binding to a connexin, any of a group of related proteins that assemble to form gap junctions." [GOC:mah, PMID:19864490]
is_a: GO:0005515 ! protein binding
[Term]
@@ -358909,8 +358404,8 @@ name: regulation of translational initiation in response to starvation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of translation initiation, as a result of deprivation of nourishment." [GOC:mah]
synonym: "regulation of translational initiation in response to nutrient starvation" EXACT [GOC:vw]
-is_a: GO:0009267 ! cellular response to starvation
is_a: GO:0043558 ! regulation of translational initiation in response to stress
+relationship: part_of GO:0009267 ! cellular response to starvation
[Term]
id: GO:0071263
@@ -358922,6 +358417,7 @@ synonym: "down-regulation of translation initiation in response to starvation" E
synonym: "downregulation of translation initiation in response to starvation" EXACT [GOC:mah]
synonym: "inhibition of translation initiation in response to starvation" NARROW [GOC:mah]
synonym: "negative regulation of translational initiation in response to nutrient starvation" EXACT [GOC:vw]
+is_a: GO:0032055 ! negative regulation of translation in response to stress
is_a: GO:0032057 ! negative regulation of translational initiation in response to stress
is_a: GO:0071262 ! regulation of translational initiation in response to starvation
@@ -358936,6 +358432,7 @@ synonym: "stimulation of translation initiation in response to starvation" NARRO
synonym: "up regulation of translation initiation in response to starvation" EXACT [GOC:mah]
synonym: "up-regulation of translation initiation in response to starvation" EXACT [GOC:mah]
synonym: "upregulation of translation initiation in response to starvation" EXACT [GOC:mah]
+is_a: GO:0032056 ! positive regulation of translation in response to stress
is_a: GO:0032058 ! positive regulation of translational initiation in response to stress
is_a: GO:0071262 ! regulation of translational initiation in response to starvation
@@ -358979,7 +358476,6 @@ synonym: "homocysteine biosynthesis" EXACT [GOC:mah]
synonym: "homocysteine formation" EXACT [GOC:mah]
synonym: "homocysteine synthesis" EXACT [GOC:mah]
is_a: GO:0000097 ! sulfur amino acid biosynthetic process
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0050667 ! homocysteine metabolic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -359268,6 +358764,7 @@ is_a: GO:0033590 ! response to cobalamin
is_a: GO:0071295 ! cellular response to vitamin
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
[Term]
id: GO:0071298
@@ -359280,6 +358777,7 @@ synonym: "cellular response to vitamin C" EXACT [GOC:mah]
is_a: GO:0033591 ! response to L-ascorbic acid
is_a: GO:0071295 ! cellular response to vitamin
is_a: GO:0071326 ! cellular response to monosaccharide stimulus
+is_a: GO:0071407 ! cellular response to organic cyclic compound
[Term]
id: GO:0071299
@@ -359312,6 +358810,7 @@ is_a: GO:0010266 ! response to vitamin B1
is_a: GO:0071295 ! cellular response to vitamin
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
+is_a: GO:0097306 ! cellular response to alcohol
[Term]
id: GO:0071302
@@ -359323,6 +358822,7 @@ is_a: GO:0033274 ! response to vitamin B2
is_a: GO:0071295 ! cellular response to vitamin
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
[Term]
id: GO:0071303
@@ -359343,6 +358843,7 @@ is_a: GO:0034516 ! response to vitamin B6
is_a: GO:0071295 ! cellular response to vitamin
is_a: GO:0071407 ! cellular response to organic cyclic compound
is_a: GO:0071417 ! cellular response to organonitrogen compound
+is_a: GO:1901701 ! cellular response to oxygen-containing compound
[Term]
id: GO:0071305
@@ -359378,6 +358879,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin K stimulus." [GOC:mah]
is_a: GO:0032571 ! response to vitamin K
is_a: GO:0071295 ! cellular response to vitamin
+is_a: GO:1901655 ! cellular response to ketone
[Term]
id: GO:0071308
@@ -359387,8 +358889,8 @@ def: "Any process that results in a change in state or activity of a cell (in te
synonym: "cellular response to menatetrenone" EXACT [GOC:mah]
synonym: "cellular response to vitamin K2" EXACT [GOC:mah]
is_a: GO:0032572 ! response to menaquinone
+is_a: GO:0071307 ! cellular response to vitamin K
is_a: GO:0071310 ! cellular response to organic substance
-is_a: GO:1901655 ! cellular response to ketone
[Term]
id: GO:0071309
@@ -359397,7 +358899,7 @@ namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a phylloquinone (vitamin K1) stimulus." [GOC:mah]
synonym: "cellular response to vitamin K1" EXACT [GOC:mah]
is_a: GO:0032573 ! response to phylloquinone
-is_a: GO:1901655 ! cellular response to ketone
+is_a: GO:0071307 ! cellular response to vitamin K
[Term]
id: GO:0071310
@@ -360353,7 +359855,7 @@ def: "Any process that results in a change in state or activity of a cell (in te
comment: Note that this term is in the subset of terms that should not be used for direct manual annotation of gene products. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_manually_annotate
is_a: GO:0014076 ! response to fluoxetine
-is_a: GO:0035690 ! cellular response to drug
+is_a: GO:0070887 ! cellular response to chemical stimulus
[Term]
id: GO:0071412
@@ -360492,72 +359994,78 @@ relationship: part_of GO:0030097 ! hemopoiesis
[Term]
id: GO:0071426
-name: ribonucleoprotein complex export from nucleus
+name: obsolete ribonucleoprotein complex export from nucleus
namespace: biological_process
-def: "The directed movement of a ribonucleoprotein complex from the nucleus to the cytoplasm." [GOC:mah]
+def: "OBSOLETE. The directed movement of a ribonucleoprotein complex from the nucleus to the cytoplasm." [GOC:mah]
+comment: This term has been obsoleted because it represents the transport of a carrier bound to its substrate.
synonym: "ribonucleoprotein complex export from cell nucleus" EXACT [GOC:mah]
synonym: "ribonucleoprotein complex nucleus export" EXACT [GOC:mah]
synonym: "ribonucleoprotein complex transport from nucleus to cytoplasm" EXACT [GOC:mah]
synonym: "RNP export from nucleus" EXACT [GOC:mah]
-is_a: GO:0031503 ! protein-containing complex localization
-is_a: GO:0051168 ! nuclear export
-relationship: part_of GO:0071166 ! ribonucleoprotein complex localization
+is_obsolete: true
[Term]
id: GO:0071427
-name: mRNA-containing ribonucleoprotein complex export from nucleus
+name: obsolete mRNA-containing ribonucleoprotein complex export from nucleus
namespace: biological_process
-def: "The directed movement of a ribonucleoprotein complex that contains messenger RNA from the nucleus to the cytoplasm." [GOC:mah]
+def: "OBSOLETE. The directed movement of a ribonucleoprotein complex that contains messenger RNA from the nucleus to the cytoplasm." [GOC:mah]
+comment: This term has been obsoleted because it represents the transport of a carrier bound to its substrate.
synonym: "mRNA-containing ribonucleoprotein complex export from cell nucleus" EXACT [GOC:mah]
synonym: "mRNA-containing ribonucleoprotein complex nucleus export" EXACT [GOC:mah]
synonym: "mRNA-containing ribonucleoprotein complex transport from nucleus to cytoplasm" EXACT [GOC:mah]
synonym: "mRNA-containing RNP export from nucleus" EXACT [GOC:mah]
-is_a: GO:0071426 ! ribonucleoprotein complex export from nucleus
+is_obsolete: true
+consider: GO:0006406
[Term]
id: GO:0071428
-name: rRNA-containing ribonucleoprotein complex export from nucleus
+name: obsolete rRNA-containing ribonucleoprotein complex export from nucleus
namespace: biological_process
-def: "The directed movement of a ribonucleoprotein complex that contains ribosomal RNA from the nucleus to the cytoplasm." [GOC:mah]
+def: "OBSOLETE. The directed movement of a ribonucleoprotein complex that contains ribosomal RNA from the nucleus to the cytoplasm." [GOC:mah]
+comment: This term has been obsoleted because it represents the transport of a carrier bound to its substrate.
synonym: "rRNA-containing ribonucleoprotein complex export from cell nucleus" EXACT [GOC:mah]
synonym: "rRNA-containing ribonucleoprotein complex nucleus export" EXACT [GOC:mah]
synonym: "rRNA-containing ribonucleoprotein complex transport from nucleus to cytoplasm" EXACT [GOC:mah]
synonym: "rRNA-containing RNP export from nucleus" EXACT [GOC:mah]
-is_a: GO:0071426 ! ribonucleoprotein complex export from nucleus
+is_obsolete: true
[Term]
id: GO:0071429
-name: snRNA-containing ribonucleoprotein complex export from nucleus
+name: obsolete snRNA-containing ribonucleoprotein complex export from nucleus
namespace: biological_process
-def: "The directed movement of a ribonucleoprotein complex that contains small nuclear RNA from the nucleus to the cytoplasm." [GOC:mah]
+def: "OBSOLETE. The directed movement of a ribonucleoprotein complex that contains small nuclear RNA from the nucleus to the cytoplasm." [GOC:mah]
+comment: This term has been obsoleted because it represents the transport of a carrier bound to its substrate.
synonym: "snRNA-containing ribonucleoprotein complex export from cell nucleus" EXACT [GOC:mah]
synonym: "snRNA-containing ribonucleoprotein complex nucleus export" EXACT [GOC:mah]
synonym: "snRNA-containing ribonucleoprotein complex transport from nucleus to cytoplasm" EXACT [GOC:mah]
synonym: "snRNA-containing RNP export from nucleus" EXACT [GOC:mah]
-is_a: GO:0071426 ! ribonucleoprotein complex export from nucleus
+is_obsolete: true
[Term]
id: GO:0071430
-name: pre-miRNA-containing ribonucleoprotein complex export from nucleus
+name: obsolete pre-miRNA-containing ribonucleoprotein complex export from nucleus
namespace: biological_process
-def: "The directed movement of a ribonucleoprotein complex that contains pre-microRNA from the nucleus to the cytoplasm." [GOC:mah, GOC:sl]
+def: "OBSOLETE. The directed movement of a ribonucleoprotein complex that contains pre-microRNA from the nucleus to the cytoplasm." [GOC:mah, GOC:sl]
+comment: This term has been obsoleted because it represents the transport of a carrier bound to its substrate.
synonym: "pre-microRNA-containing ribonucleoprotein complex export from cell nucleus" EXACT [GOC:mah]
synonym: "pre-microRNA-containing ribonucleoprotein complex export from nucleus" EXACT []
synonym: "pre-microRNA-containing ribonucleoprotein complex nucleus export" EXACT [GOC:mah]
synonym: "pre-microRNA-containing ribonucleoprotein complex transport from nucleus to cytoplasm" EXACT [GOC:mah]
synonym: "pre-microRNA-containing RNP export from nucleus" EXACT [GOC:mah]
-is_a: GO:0071426 ! ribonucleoprotein complex export from nucleus
+is_obsolete: true
[Term]
id: GO:0071431
-name: tRNA-containing ribonucleoprotein complex export from nucleus
+name: obsolete tRNA-containing ribonucleoprotein complex export from nucleus
namespace: biological_process
-def: "The directed movement of a ribonucleoprotein complex that contains transfer RNA from the nucleus to the cytoplasm." [GOC:mah]
+def: "OBSOLETE. The directed movement of a ribonucleoprotein complex that contains transfer RNA from the nucleus to the cytoplasm." [GOC:mah]
+comment: This term has been obsoleted because it represents the transport of a carrier bound to its substrate.
synonym: "tRNA-containing ribonucleoprotein complex export from cell nucleus" EXACT [GOC:mah]
synonym: "tRNA-containing ribonucleoprotein complex nucleus export" EXACT [GOC:mah]
synonym: "tRNA-containing ribonucleoprotein complex transport from nucleus to cytoplasm" EXACT [GOC:mah]
synonym: "tRNA-containing RNP export from nucleus" EXACT [GOC:mah]
-is_a: GO:0071426 ! ribonucleoprotein complex export from nucleus
+is_obsolete: true
+consider: GO:0051168
[Term]
id: GO:0071432
@@ -360658,7 +360166,7 @@ relationship: positively_regulates GO:0044154 ! histone H3-K14 acetylation
id: GO:0071443
name: tDNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with DNA sequences encoding transfer RNA." [GOC:mah]
+def: "Binding to DNA sequences encoding transfer RNA." [GOC:mah]
is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
[Term]
@@ -360876,7 +360384,10 @@ is_a: GO:0042631 ! cellular response to water deprivation
id: GO:0071466
name: cellular response to xenobiotic stimulus
namespace: biological_process
-def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms." [GOC:mah]
+alt_id: GO:0035690
+def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a xenobiotic, a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GOC:krc, GOC:mah]
+subset: goslim_chembl
+synonym: "cellular response to drug" RELATED []
is_a: GO:0009410 ! response to xenobiotic stimulus
is_a: GO:0070887 ! cellular response to chemical stimulus
@@ -361344,22 +360855,24 @@ relationship: part_of GO:0005737 ! cytoplasm
[Term]
id: GO:0071514
-name: genetic imprinting
+name: genomic imprinting
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules by a mechanism that is mediated by DNA, is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [GOC:mah, GOC:vw]
+def: "The establishment of epigenetic modifications (imprints) during gametogenesis, leading to an asymmetry in the heterochromatin between the maternal and paternal alleles, and differential expression of the corresponding alleles. This asymmetry results from the different epigenetic pathways acting in maternal and paternal gametes." [PMID:31896690]
synonym: "DNA imprinting" EXACT [GOC:mah]
-is_a: GO:0006139 ! nucleobase-containing compound metabolic process
-is_a: GO:0060255 ! regulation of macromolecule metabolic process
+synonym: "genetic imprinting" EXACT []
+is_a: GO:0031507 ! heterochromatin assembly
[Term]
id: GO:0071515
-name: genetic imprinting at mating-type locus
+name: mating-type locus imprinting
namespace: biological_process
-def: "A genetic imprinting process in which a stable single-strand DNA lesion triggers programmed gene conversion at the mating-type locus, thereby restricting mating-type interconversion to one of the two sister chromatids during DNA replication." [GOC:mah, PMID:14765111, PMID:18723894]
+def: "A genomic imprinting process in which a stable single-strand DNA lesion triggers programmed gene conversion at the mating-type locus, thereby restricting mating-type interconversion to one of the two sister chromatids during DNA replication." [GOC:mah, PMID:14765111, PMID:18723894]
+synonym: "genetic imprinting at mating-type locus" EXACT []
+synonym: "genomic imprinting at mating-type locus" EXACT []
synonym: "mating type determination, imprinting" EXACT [GOC:vw]
-is_a: GO:0006259 ! DNA metabolic process
-is_a: GO:0031494 ! regulation of mating type switching
-is_a: GO:0071514 ! genetic imprinting
+is_a: GO:0022414 ! reproductive process
+is_a: GO:0031507 ! heterochromatin assembly
+relationship: part_of GO:0007533 ! mating type switching
[Term]
id: GO:0071516
@@ -361368,7 +360881,8 @@ namespace: biological_process
def: "The initial formation of a stable single-strand DNA lesion that triggers programmed gene conversion at the mating-type locus, thereby restricting mating-type interconversion to one of the two sister chromatids during DNA replication." [GOC:mah, PMID:18723894]
synonym: "mating type determination, establishment of imprinting" EXACT [GOC:vw]
is_a: GO:0006259 ! DNA metabolic process
-relationship: part_of GO:0071515 ! genetic imprinting at mating-type locus
+is_a: GO:0022414 ! reproductive process
+relationship: part_of GO:0071515 ! mating-type locus imprinting
[Term]
id: GO:0071517
@@ -361377,7 +360891,8 @@ namespace: biological_process
def: "Any process involved in preserving the structure of a stable single-strand DNA lesion that triggers programmed gene conversion at the mating-type locus, thereby restricting mating-type interconversion to one of the two sister chromatids during DNA replication." [GOC:mah, PMID:14765111, PMID:18723894]
synonym: "mating type determination, maintenance of imprinting" EXACT [GOC:mah]
is_a: GO:0006259 ! DNA metabolic process
-relationship: part_of GO:0071515 ! genetic imprinting at mating-type locus
+is_a: GO:0022414 ! reproductive process
+relationship: part_of GO:0071515 ! mating-type locus imprinting
[Term]
id: GO:0071518
@@ -361522,7 +361037,7 @@ is_obsolete: true
id: GO:0071532
name: ankyrin repeat binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an ankyrin repeat of a protein. Ankyrin repeats are tandemly repeated modules of about 33 amino acids; each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90-degree angle, and repeats stack to form an L-shaped structure." [GOC:mah, InterPro:IPR002110]
+def: "Binding to an ankyrin repeat of a protein. Ankyrin repeats are tandemly repeated modules of about 33 amino acids; each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90-degree angle, and repeats stack to form an L-shaped structure." [GOC:mah, InterPro:IPR002110]
synonym: "ANK repeat binding" EXACT [GOC:amm]
is_a: GO:0019904 ! protein domain specific binding
@@ -361550,7 +361065,7 @@ is_obsolete: true
id: GO:0071535
name: RING-like zinc finger domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a RING-like zinc finger domain domain of a protein. The RING-like domain is a zinc finger domain that is related to the C3HC4 RING finger domain." [GOC:mah, InterPro:IPR014857]
+def: "Binding to a RING-like zinc finger domain domain of a protein. The RING-like domain is a zinc finger domain that is related to the C3HC4 RING finger domain." [GOC:mah, InterPro:IPR014857]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -361695,7 +361210,7 @@ relationship: part_of GO:0097191 ! extrinsic apoptotic signaling pathway
id: GO:0071551
name: RIP homotypic interaction motif binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a RIP homotypic interaction motif (RHIM) of a protein. The RHIM is a 16-amino-acid motif found in some members, including RIP3, of a family of related kinases." [GOC:mah, PMID:11734559]
+def: "Binding to a RIP homotypic interaction motif (RHIM) of a protein. The RHIM is a 16-amino-acid motif found in some members, including RIP3, of a family of related kinases." [GOC:mah, PMID:11734559]
synonym: "RHIM binding" EXACT [GOC:mah]
is_a: GO:0019904 ! protein domain specific binding
@@ -361777,13 +361292,18 @@ is_a: GO:0070076 ! histone lysine demethylation
[Term]
id: GO:0071558
-name: histone demethylase activity (H3-K27 specific)
+name: histone H3-tri/di-methyl-lysine-27 demethylase activity
namespace: molecular_function
-def: "Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein." [GOC:sp, PMID:20622853]
+def: "Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 27 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [GOC:sp, PMID:20622853]
+synonym: "histone demethylase activity (H3-K27 specific)" BROAD []
+synonym: "histone H3K27me2 demethylase activity" RELATED []
+synonym: "histone H3K27me3 demethylase activity" RELATED []
xref: EC:1.14.11.68
xref: Reactome:R-HSA-3222593 "KDM6B demethylates H3K27me3 on p16INK4A promoter"
xref: Reactome:R-HSA-5617431 "Retinoic acid activates HOXA1 chromatin"
xref: Reactome:R-HSA-5617887 "HOXC4 chromatin is activated"
+xref: RHEA:60224
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0032452 ! histone demethylase activity
[Term]
@@ -361940,7 +361460,7 @@ is_a: GO:0031233 ! intrinsic component of external side of plasma membrane
id: GO:0071576
name: tetrahydrodictyopterin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with tetrahydrodictyopterin, the pterin 2-amino-6-[(1R,2R)-1,2-dihydroxypropyl]-5,6,7,8-tetrahydropteridin-4(3H)-one." [GOC:mah, GOC:vw]
+def: "Binding to tetrahydrodictyopterin, the pterin 2-amino-6-[(1R,2R)-1,2-dihydroxypropyl]-5,6,7,8-tetrahydropteridin-4(3H)-one." [GOC:mah, GOC:vw]
synonym: "D-threo-tetrahydrobiopterin" EXACT [GOC:mah]
synonym: "DH4 binding" EXACT [GOC:mah]
is_a: GO:0034617 ! tetrahydrobiopterin binding
@@ -362904,7 +362424,7 @@ is_a: GO:0032992 ! protein-carbohydrate complex
id: GO:0071667
name: DNA/RNA hybrid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a RNA/DNA hybrid." [GOC:ecd]
+def: "Binding to a RNA/DNA hybrid." [GOC:ecd]
synonym: "RNA/DNA hybrid binding" EXACT [GOC:ecd]
is_a: GO:0003676 ! nucleic acid binding
@@ -363411,7 +362931,7 @@ relationship: part_of GO:0046685 ! response to arsenic-containing substance
id: GO:0071723
name: lipopeptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lipopeptide, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds and containing a nonprotein group consisting of a lipid or lipids." [GOC:add, PMID:12077222, PMID:12524386, PMID:2757794]
+def: "Binding to a lipopeptide, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds and containing a nonprotein group consisting of a lipid or lipids." [GOC:add, PMID:12077222, PMID:12524386, PMID:2757794]
comment: Note that bacterial lipopeptides are derived from bacterial lipoproteins, but the two terms are sometimes used interchangeably in the literature.
synonym: "bacterial lipopeptide binding" NARROW [GOC:add]
synonym: "bacterial lipoprotein binding" RELATED [GOC:add]
@@ -364039,7 +363559,7 @@ is_a: GO:0071786 ! endoplasmic reticulum tubular network organization
id: GO:0071791
name: chemokine (C-C motif) ligand 5 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chemokine (C-C motif) ligand 5." [GOC:add, GOC:amm]
+def: "Binding to chemokine (C-C motif) ligand 5." [GOC:add, GOC:amm]
synonym: "CCL5 binding" EXACT [GOC:add, GOC:amm]
synonym: "RANTES binding" EXACT [GOC:bf]
synonym: "Regulated upon Activation, Normal T-cell Expressed, and Secreted binding" EXACT [GOC:add]
@@ -364073,21 +363593,21 @@ is_a: GO:0071792 ! bacillithiol metabolic process
id: GO:0071794
name: CAP-Gly domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CAP-Gly domain of a protein. The CAP_Gly domain is a conserved, glycine-rich domain of about 42 residues found in some cytoskeleton-associated proteins, and features a novel protein fold containing three beta-sheets." [GOC:mah, InterPro:IPR000938]
+def: "Binding to a CAP-Gly domain of a protein. The CAP_Gly domain is a conserved, glycine-rich domain of about 42 residues found in some cytoskeleton-associated proteins, and features a novel protein fold containing three beta-sheets." [GOC:mah, InterPro:IPR000938]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0071795
name: K11-linked polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 11 in the target protein." [GOC:sp, PMID:18775313]
+def: "Binding to a protein upon poly-ubiquitination formed by linkages between lysine residues at position 11 in the target protein." [GOC:sp, PMID:18775313]
is_a: GO:0031593 ! polyubiquitin modification-dependent protein binding
[Term]
id: GO:0071796
name: K6-linked polyubiquitin modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 6 in the target protein." [GOC:sp, PMID:17525341, PMID:20351172]
+def: "Binding to a protein upon poly-ubiquitination formed by linkages between lysine residues at position 6 in the target protein." [GOC:sp, PMID:17525341, PMID:20351172]
is_a: GO:0031593 ! polyubiquitin modification-dependent protein binding
[Term]
@@ -364123,7 +363643,7 @@ name: podosome assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a podosome, an actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell." [GOC:mah, GOC:sl]
is_a: GO:0065003 ! protein-containing complex assembly
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:0071801
@@ -364185,7 +363705,6 @@ name: protein transmembrane transport
namespace: biological_process
def: "The process in which a protein is transported across a membrane." [GOC:mah, GOC:vw]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
-subset: goslim_drosophila
synonym: "protein membrane transport" EXACT []
is_a: GO:0015031 ! protein transport
is_a: GO:0055085 ! transmembrane transport
@@ -364244,7 +363763,7 @@ is_a: GO:0032308 ! positive regulation of prostaglandin secretion
id: GO:0071813
name: lipoprotein particle binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a lipoprotein particle. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." [GOC:BHF, GOC:mah]
+def: "Binding to a lipoprotein particle. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." [GOC:BHF, GOC:mah]
synonym: "lipoprotein binding" RELATED [GOC:mah]
synonym: "plasma lipoprotein binding" RELATED [GOC:mah]
synonym: "plasma lipoprotein particle binding" EXACT [GOC:mah]
@@ -364254,14 +363773,14 @@ is_a: GO:0071814 ! protein-lipid complex binding
id: GO:0071814
name: protein-lipid complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein-lipid complex, any macromolecular complex that contains both protein and lipid molecules." [GOC:BHF, GOC:mah]
+def: "Binding to a protein-lipid complex, any macromolecular complex that contains both protein and lipid molecules." [GOC:BHF, GOC:mah]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0071815
name: intermediate-density lipoprotein particle binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a intermediate-density lipoprotein particle, a triglyceride-rich lipoprotein particle that typically contains APOB100, APOE and APOCs and has a density of 1.006-1.019 g/ml and a diameter of between 25-30 nm." [GOC:BHF, GOC:mah]
+def: "Binding to a intermediate-density lipoprotein particle, a triglyceride-rich lipoprotein particle that typically contains APOB100, APOE and APOCs and has a density of 1.006-1.019 g/ml and a diameter of between 25-30 nm." [GOC:BHF, GOC:mah]
synonym: "IDL binding" EXACT [GOC:BHF]
synonym: "intermediate-density lipoprotein binding" EXACT [GOC:dph]
is_a: GO:0071813 ! lipoprotein particle binding
@@ -364309,8 +363828,7 @@ is_a: GO:0140513 ! nuclear protein-containing complex
id: GO:0071820
name: N-box binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an N-box, a DNA motif with the consensus sequence CACNAG that is found in the promoters of genes expressed preferentially at synapses." [GOC:yaf, PMID:11498047]
-comment: Note that as agreed during the transcription overhaul, terms specifying binding to specific transcription regulatory motifs are no longer being created. The level of specificity GO has decided to go to is the "core promoter", "core promoter proximal region" and "enhancer". To capture more detail, please consider using column 16.
+def: "Binding to an N-box, a DNA motif with the consensus sequence CACNAG that is found in the promoters of genes expressed preferentially at synapses." [GOC:yaf, PMID:11498047]
synonym: "N box binding" EXACT [GOC:mah]
synonym: "N-box promoter binding" EXACT [GOC:mah]
is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
@@ -364328,7 +363846,7 @@ name: protein-carbohydrate complex subunit organization
namespace: biological_process
def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-carbohydrate complex." [GOC:mah]
synonym: "protein-carbohydrate complex subunit organisation" EXACT [GOC:mah]
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0071824
@@ -364337,7 +363855,7 @@ namespace: biological_process
def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex." [GOC:mah]
synonym: "DNA-protein complex subunit organization" EXACT [GOC:mah]
synonym: "protein-DNA complex subunit organisation" EXACT [GOC:mah]
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0071825
@@ -364345,7 +363863,7 @@ name: protein-lipid complex subunit organization
namespace: biological_process
def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-lipid complex." [GOC:mah]
synonym: "protein-lipid complex subunit organisation" EXACT [GOC:mah]
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0071826
@@ -364355,7 +363873,7 @@ def: "Any process in which macromolecules aggregate, disaggregate, or are modifi
synonym: "protein-RNA complex subunit organization" EXACT [GOC:mah]
synonym: "ribonucleoprotein complex subunit organisation" EXACT [GOC:mah]
synonym: "RNA-protein complex subunit organization" EXACT [GOC:mah]
-is_a: GO:0043933 ! protein-containing complex subunit organization
+is_a: GO:0043933 ! protein-containing complex organization
[Term]
id: GO:0071827
@@ -364445,7 +363963,7 @@ is_a: GO:0046903 ! secretion
id: GO:0071837
name: HMG box domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin." [GOC:yaf, InterPro:IPR009071, PMID:18445004]
+def: "Binding to an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin." [GOC:yaf, InterPro:IPR009071, PMID:18445004]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -364462,7 +363980,6 @@ name: apoptotic process in bone marrow cell
namespace: biological_process
def: "The apoptotic process in cells in the bone marrow." [GOC:mah, GOC:mtg_apoptosis, PMID:17063141]
synonym: "apoptosis in bone marrow" NARROW []
-synonym: "apoptotic process in bone marrow cell" EXACT []
synonym: "bone marrow cell apoptosis" EXACT [GOC:yaf]
synonym: "bone marrow cell programmed cell death by apoptosis" EXACT [GOC:mah]
synonym: "killing of bone marrow cells" EXACT [GOC:mah]
@@ -364558,42 +364075,42 @@ relationship: part_of GO:0071853 ! fungal-type cell wall disassembly
id: GO:0071855
name: neuropeptide receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neuropeptide receptor." [GOC:kmv, GOC:mah]
+def: "Binding to a neuropeptide receptor." [GOC:kmv, GOC:mah]
is_a: GO:0001664 ! G protein-coupled receptor binding
[Term]
id: GO:0071857
name: beta-endorphin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a beta-endorphin receptor." [GOC:kmv, GOC:mah]
+def: "Binding to a beta-endorphin receptor." [GOC:kmv, GOC:mah]
is_a: GO:0071855 ! neuropeptide receptor binding
[Term]
id: GO:0071858
name: corazonin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a corazonin receptor." [GOC:kmv, GOC:mah]
+def: "Binding to a corazonin receptor." [GOC:kmv, GOC:mah]
is_a: GO:0071855 ! neuropeptide receptor binding
[Term]
id: GO:0071859
name: neuropeptide F receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a neuropeptide F receptor." [GOC:kmv, GOC:mah]
+def: "Binding to a neuropeptide F receptor." [GOC:kmv, GOC:mah]
is_a: GO:0071855 ! neuropeptide receptor binding
[Term]
id: GO:0071860
name: proctolin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a proctolin receptor." [GOC:kmv, GOC:mah]
+def: "Binding to a proctolin receptor." [GOC:kmv, GOC:mah]
is_a: GO:0071855 ! neuropeptide receptor binding
[Term]
id: GO:0071861
name: tachykinin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a tachykinin receptor." [GOC:kmv, GOC:mah]
+def: "Binding to a tachykinin receptor." [GOC:kmv, GOC:mah]
is_a: GO:0071855 ! neuropeptide receptor binding
[Term]
@@ -364754,7 +364271,7 @@ id: GO:0071877
name: regulation of adenylate cyclase-inhibiting adrenergic receptor signaling pathway
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of an adenylate cyclase-inhibiting adrenergic receptor signaling pathway activity. An adrenergic receptor signaling pathway is the series of molecular signals generated as a consequence of an adrenergic receptor binding to one of its physiological ligands." [GOC:BHF, GOC:mah]
-synonym: "false" BROAD []
+synonym: "regulation of adrenergic receptor signaling pathway" EXACT []
synonym: "regulation of adrenergic receptor signalling pathway" EXACT [GOC:mah]
is_a: GO:0008277 ! regulation of G protein-coupled receptor signaling pathway
relationship: regulates GO:0071881 ! adenylate cyclase-inhibiting adrenergic receptor signaling pathway
@@ -364764,7 +364281,7 @@ id: GO:0071878
name: negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of an adenylate cyclase-activating adrenergic receptor protein signaling pathway activity. An adrenergic receptor signaling pathway is the series of molecular signals generated as a consequence of an adrenergic receptor binding to one of its physiological ligands." [GOC:BHF, GOC:mah]
-synonym: "false" BROAD []
+synonym: "negative regulation of adrenergic receptor signaling pathway" EXACT []
synonym: "negative regulation of adrenergic receptor signalling pathway" EXACT [GOC:mah]
is_a: GO:0106072 ! negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway
relationship: negatively_regulates GO:0071880 ! adenylate cyclase-activating adrenergic receptor signaling pathway
@@ -364816,13 +364333,13 @@ is_a: GO:0071875 ! adrenergic receptor signaling pathway
[Term]
id: GO:0071883
-name: activation of MAPK activity by adrenergic receptor signaling pathway
+name: MAPK-activating adrenergic receptor signaling pathway
namespace: biological_process
-def: "The series of molecular signals generated as a consequence of an adrenergic receptor binding to its physiological ligand, followed by the activation of a MAP kinase." [GOC:BHF, GOC:mah]
+def: "The series of molecular signals generated as a consequence of an adrenergic receptor binding to its physiological ligand and leading to the activation of a MAP kinase cascade." [GOC:BHF, GOC:mah]
synonym: "activation of MAP kinase activity by adrenergic receptor signaling pathway" EXACT [GOC:mah]
synonym: "activation of MAP kinase activity by adrenergic receptor signalling pathway" EXACT [GOC:mah]
+synonym: "activation of MAPK activity by adrenergic receptor signaling pathway" EXACT []
synonym: "activation of MAPK activity by adrenergic receptor signalling pathway" EXACT [GOC:mah]
-is_a: GO:0000187 ! activation of MAPK activity
is_a: GO:0071875 ! adrenergic receptor signaling pathway
[Term]
@@ -364837,7 +364354,7 @@ is_a: GO:0008276 ! protein methyltransferase activity
id: GO:0071886
name: 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the amine 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine, a serotonin receptor agonist that can act as a psychedelic drug." [GOC:yaf, PMID:19057895]
+def: "Binding to the amine 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine, a serotonin receptor agonist that can act as a psychedelic drug." [GOC:yaf, PMID:19057895]
synonym: "(+/-)2-(4-iodo-2,5-dimethoxy-phenyl)-1-methyl-ethylamine binding" EXACT [CHEBI:100436]
synonym: "1-(4-iodo-2,5-dimethoxyphenyl)-2-aminopropane binding" EXACT [PMID:19057895]
synonym: "4-iodo-2,5-dimethoxyphenylisopropylamine binding" EXACT [PubChem_Compound:1229]
@@ -364870,14 +364387,15 @@ is_a: GO:0071887 ! leukocyte apoptotic process
id: GO:0071889
name: 14-3-3 protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 14-3-3 protein. A 14-3-3 protein is any of a large family of approximately 30kDa acidic proteins which exist primarily as homo- and heterodimers within all eukaryotic cells, and have been implicated in the modulation of distinct biological processes by binding to specific phosphorylated sites on diverse target proteins, thereby forcing conformational changes or influencing interactions between their targets and other molecules. Each 14-3-3 protein sequence can be roughly divided into three sections: a divergent amino terminus, the conserved core region and a divergent carboxy-terminus. The conserved middle core region of the 14-3-3s encodes an amphipathic groove that forms the main functional domain, a cradle for interacting with client proteins." [GOC:cna, GOC:mah, PMID:15167810, PMID:19575580]
+def: "Binding to a 14-3-3 protein. A 14-3-3 protein is any of a large family of approximately 30kDa acidic proteins which exist primarily as homo- and heterodimers within all eukaryotic cells, and have been implicated in the modulation of distinct biological processes by binding to specific phosphorylated sites on diverse target proteins, thereby forcing conformational changes or influencing interactions between their targets and other molecules. Each 14-3-3 protein sequence can be roughly divided into three sections: a divergent amino terminus, the conserved core region and a divergent carboxy-terminus. The conserved middle core region of the 14-3-3s encodes an amphipathic groove that forms the main functional domain, a cradle for interacting with client proteins." [GOC:cna, GOC:mah, PMID:15167810, PMID:19575580]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0071890
name: bicarbonate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with bicarbonate (CHO3-) ions." [GOC:curators]
+def: "Binding to bicarbonate ions (CHO3-)." [GOC:curators]
+synonym: "CHO3- ion binding binding" EXACT []
synonym: "hydrogencarbonate binding" EXACT [CHEBI:17544]
is_a: GO:0043168 ! anion binding
@@ -365024,7 +364542,7 @@ is_a: GO:0018279 ! protein N-linked glycosylation via asparagine
id: GO:0071906
name: CRD domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CRD (context dependent regulatory) domain, a domain of about 130 residues that is the most divergent region among the LEF/TCF proteins." [GOC:yaf, PMID:19460168]
+def: "Binding to a CRD (context dependent regulatory) domain, a domain of about 130 residues that is the most divergent region among the LEF/TCF proteins." [GOC:yaf, PMID:19460168]
synonym: "context dependent regulatory domain binding" EXACT [GOC:mah]
is_a: GO:0019904 ! protein domain specific binding
@@ -365264,7 +364782,7 @@ is_a: GO:0031297 ! replication fork processing
id: GO:0071933
name: Arp2/3 complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an Arp2/3 complex, a protein complex that contains two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5)." [GOC:mah]
+def: "Binding to an Arp2/3 complex, a protein complex that contains two actin-related proteins, Arp2 and Arp3, and five novel proteins (ARPC1-5)." [GOC:mah]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -365280,6 +364798,7 @@ is_a: GO:0015888 ! thiamine transport
is_a: GO:0035461 ! vitamin transmembrane transport
is_a: GO:0045117 ! azole transmembrane transport
is_a: GO:0072531 ! pyrimidine-containing compound transmembrane transport
+is_a: GO:0098655 ! cation transmembrane transport
[Term]
id: GO:0071935
@@ -365409,7 +364928,7 @@ is_a: GO:0001783 ! B cell apoptotic process
id: GO:0071949
name: FAD binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:mah]
+def: "Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:mah]
synonym: "oxidized flavin adenine dinucleotide binding" EXACT [GOC:mah]
synonym: "oxidized flavine-adenine dinucleotide binding" EXACT [GOC:mah]
is_a: GO:0050660 ! flavin adenine dinucleotide binding
@@ -365418,7 +364937,7 @@ is_a: GO:0050660 ! flavin adenine dinucleotide binding
id: GO:0071950
name: FADH2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the reduced form, FADH2, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:mah]
+def: "Binding to the reduced form, FADH2, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes." [GOC:mah]
synonym: "reduced flavin adenine dinucleotide binding" EXACT [GOC:mah]
synonym: "reduced flavine-adenine dinucleotide binding" EXACT [GOC:mah]
is_a: GO:0050660 ! flavin adenine dinucleotide binding
@@ -365727,12 +365246,14 @@ name: Ragulator complex
namespace: cellular_component
alt_id: GO:0034448
alt_id: GO:0034449
-def: "A eukaryotic vacuolar membrane-associated protein; in humans, it is comprised of LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4, and LAMTOR5. In budding yeast, S. cerevisiae, this complex includes Gtr1p, Gtr2p, Meh1p, and Slm4p. The complex is anchored to lipid rafts in vacuole/lysosome membrane via LAMTOR1 and acts as a guanine nucleotide exchange factor (GEF) for the Rag GTPases." [GOC:krc, GOC:lb, GOC:vw, PMID:15989961, PMID:16732272, PMID:19177150, PMID:19748353, PMID:20381137, PMID:22980980, PMID:29199950]
+def: "A vacuolar membrane-anchored guanine nucleotide exchange factor (GEF) complex for the Rag GTPases (Gtr1-Gtr2 GTPase complex GO:1990131) in TORC1 signalling pathway. In human, Ragulator is comprised of the membrane anchor subunit LAMTOR1 (Meh1p in S. cerevisiae, Lam1 in S. pombe), a GEF subunit LAMTOR2 ( Slm4 in S. cerevisiae , Lam2 in S. pombe ) , LAMTOR3 (no S. cerevisiae ortholog identified, Lam3 in S. pombe) , LAMTOR4 (no S. cerevisiae ortholog identified, Lam4 in S. pombe), and LAMTOR5 (no S. cerevisiae or S. pombe ortholog identified)." [GOC:vw, PMID:15989961, PMID:16732272, PMID:19177150, PMID:19748353, PMID:20381137, PMID:22980980, PMID:29199950]
synonym: "EGO complex" RELATED []
synonym: "EGO-GSE complex" RELATED []
synonym: "GSE complex" RELATED []
synonym: "GTPase-containing complex for Gap1p sorting in the endosome" RELATED []
synonym: "MAPKSP1/ROBLD3/C11orf59 complex" EXACT [GOC:mah]
+synonym: "Rag GEF" EXACT []
+is_a: GO:0032045 ! guanyl-nucleotide exchange factor complex
is_a: GO:0098796 ! membrane protein complex
relationship: part_of GO:0005774 ! vacuolar membrane
relationship: part_of GO:0031902 ! late endosome membrane
@@ -365742,7 +365263,7 @@ relationship: part_of GO:0045121 ! membrane raft
id: GO:0071987
name: WD40-repeat domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a WD40 repeat domain of a protein. The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Several of these repeats are combined to form a type of protein domain called the WD domain." [GOC:yaf, InterPro:IPR017986]
+def: "Binding to a WD40 repeat domain of a protein. The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Several of these repeats are combined to form a type of protein domain called the WD domain." [GOC:yaf, InterPro:IPR017986]
synonym: "beta-transducin repeat domain binding" EXACT [GOC:yaf]
synonym: "WD domain binding" EXACT [GOC:yaf]
is_a: GO:0019904 ! protein domain specific binding
@@ -367460,7 +366981,6 @@ id: GO:0072189
name: ureter development
namespace: biological_process
def: "The process whose specific outcome is the progression of the ureter over time, from its formation to the mature structure. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut." [GOC:mtg_kidney_jan10]
-is_a: GO:0035295 ! tube development
is_a: GO:0048513 ! animal organ development
relationship: part_of GO:0072001 ! renal system development
@@ -368692,7 +368212,7 @@ relationship: part_of GO:0072325 ! vulval cell fate commitment
id: GO:0072328
name: alkene binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an alkene, any acyclic branched or unbranched hydrocarbon having one carbon-carbon double bond and the general formula CnH2n." [GOC:mah]
+def: "Binding to an alkene, any acyclic branched or unbranched hydrocarbon having one carbon-carbon double bond and the general formula CnH2n." [GOC:mah]
is_a: GO:0005488 ! binding
[Term]
@@ -368829,7 +368349,7 @@ is_a: GO:0072338 ! cellular lactam metabolic process
id: GO:0072341
name: modified amino acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a modified amino acid." [GOC:mah]
+def: "Binding to a modified amino acid." [GOC:mah]
synonym: "amino acid derivative binding" EXACT []
is_a: GO:0005488 ! binding
@@ -368853,7 +368373,6 @@ name: rescue of stalled ribosome
namespace: biological_process
def: "A process of translational elongation that takes place when a ribosome has stalled during translation, and results in freeing the ribosome from the stalled translation complex." [GOC:jh2, GOC:mah, PMID:18557701, PMID:19170872, PMID:20117091, PMID:20185543]
is_a: GO:0006414 ! translational elongation
-is_a: GO:0006417 ! regulation of translation
[Term]
id: GO:0072345
@@ -368876,7 +368395,7 @@ name: response to anesthetic
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an anesthetic stimulus. An anesthetic is a substance that causes loss of feeling, awareness, or sensation." [GOC:sart]
synonym: "response to anaesthetic" EXACT [GOC:mah]
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0072348
@@ -368963,8 +368482,8 @@ synonym: "chromosomal passenger complex localization to kinetochore" EXACT [GOC:
synonym: "chromosome passenger complex localisation to kinetochore" RELATED [GOC:mah]
synonym: "CPC complex localization to kinetochore" EXACT [GOC:vw]
synonym: "CPC localization to kinetochore" EXACT [GOC:mah]
+is_a: GO:0031503 ! protein-containing complex localization
is_a: GO:0034501 ! protein localization to kinetochore
-is_a: GO:0034629 ! cellular protein-containing complex localization
[Term]
id: GO:0072357
@@ -368979,6 +368498,7 @@ name: circulatory system development
namespace: biological_process
alt_id: GO:0072358
def: "The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis." [GOC:mah, UBERON:0001009]
+subset: goslim_drosophila
synonym: "cardiovascular system development" NARROW []
is_a: GO:0048731 ! system development
@@ -369887,10 +369407,13 @@ is_a: GO:1902562 ! H4 histone acetyltransferase complex
id: GO:0072488
name: ammonium transmembrane transport
namespace: biological_process
+alt_id: GO:0015696
def: "The process in which ammonium is transported across a membrane. Ammonium is the cation NH4+." [GOC:mah]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
+synonym: "ammonia transport" BROAD []
synonym: "ammonium membrane transport" EXACT []
-is_a: GO:0015696 ! ammonium transport
+synonym: "ammonium transport" BROAD []
+is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:0098662 ! inorganic cation transmembrane transport
[Term]
@@ -370387,7 +369910,6 @@ def: "Binds to and increases the activity of a protein phosphatase, an enzyme wh
synonym: "protein phosphatase 2 activator activity" NARROW [GOC:dph, GOC:rl]
synonym: "protein phosphatase type 1 activator activity" NARROW []
synonym: "protein phosphatase type 2A activator activity" NARROW []
-is_a: GO:0019208 ! phosphatase regulator activity
is_a: GO:0019211 ! phosphatase activator activity
is_a: GO:0019888 ! protein phosphatase regulator activity
@@ -370395,8 +369917,7 @@ is_a: GO:0019888 ! protein phosphatase regulator activity
id: GO:0072544
name: L-DOPA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with L-DOPA, the modified amino acid (2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid." [GOC:mah, GOC:vw]
-synonym: "L-dopa binding" EXACT [CHEBI:15765]
+def: "Binding to L-DOPA, the modified amino acid (2S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid." [GOC:mah, GOC:vw]
is_a: GO:0016597 ! amino acid binding
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0072341 ! modified amino acid binding
@@ -370406,7 +369927,7 @@ is_a: GO:0097159 ! organic cyclic compound binding
id: GO:0072545
name: tyrosine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 2-amino-3-(4-hydroxyphenyl)propanoic acid." [GOC:mah]
+def: "Binding to 2-amino-3-(4-hydroxyphenyl)propanoic acid." [GOC:mah]
synonym: "Tyr binding" EXACT [GOC:mah]
is_a: GO:0016597 ! amino acid binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -370595,7 +370116,7 @@ is_a: GO:0032602 ! chemokine production
id: GO:0072570
name: ADP-D-ribose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ADP-D-ribose, an ADP-aldose having ribose as the aldose fragment." [GOC:mah, GOC:sart, PMID:20088964]
+def: "Binding to ADP-D-ribose, an ADP-aldose having ribose as the aldose fragment." [GOC:mah, GOC:sart, PMID:20088964]
synonym: "ADP-ribose binding" BROAD [GOC:mah]
is_a: GO:0043168 ! anion binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -370606,7 +370127,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0072571
name: mono-ADP-D-ribose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with monomeric ADP-D-ribose, an ADP-aldose having ribose as the aldose fragment." [GOC:mah, GOC:sart, PMID:20088964]
+def: "Binding to monomeric ADP-D-ribose, an ADP-aldose having ribose as the aldose fragment." [GOC:mah, GOC:sart, PMID:20088964]
synonym: "mADPr binding" EXACT [PMID:20088964]
synonym: "mono-ADP-ribose binding" BROAD [GOC:mah]
is_a: GO:0072570 ! ADP-D-ribose binding
@@ -370615,7 +370136,7 @@ is_a: GO:0072570 ! ADP-D-ribose binding
id: GO:0072572
name: poly-ADP-D-ribose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with polymeric ADP-D-ribose, a polymer that is composed of poly-ADP-D-ribose units linked through 1,2-glycosidic bonds at the ribose ring." [GOC:mah, GOC:sart, PMID:20088964]
+def: "Binding to polymeric ADP-D-ribose, a polymer that is composed of poly-ADP-D-ribose units linked through 1,2-glycosidic bonds at the ribose ring." [GOC:mah, GOC:sart, PMID:20088964]
synonym: "pADPr binding" EXACT [PMID:20088964]
synonym: "poly-ADP-ribose binding" BROAD [GOC:mah]
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -370705,7 +370226,6 @@ id: GO:0072582
name: 17-beta-hydroxysteroid dehydrogenase (NADP+) activity
namespace: molecular_function
def: "Catalysis of the reaction: a 17-beta-hydroxysteroid + NADP+ = a 17-oxosteroid + NADPH + H+." [GOC:kad, PMID:17074428]
-xref: RHEA:24616
is_a: GO:0004303 ! estradiol 17-beta-dehydrogenase activity
[Term]
@@ -370714,7 +370234,6 @@ name: clathrin-dependent endocytosis
namespace: biological_process
def: "An endocytosis process that begins when material is taken up into clathrin-coated pits, which then pinch off to form clathrin-coated endocytic vesicles." [GOC:BHF, GOC:mah, PMID:18498251, PMID:8970738, PMID:9234965]
synonym: "clathrin coated pit-dependent endocytosis" EXACT [GOC:BHF]
-synonym: "clathrin-dependent endocytosis" EXACT [GOC:mah]
synonym: "clathrin-mediated endocytosis" EXACT []
synonym: "CME" EXACT [PMID:20074057]
is_a: GO:0006898 ! receptor-mediated endocytosis
@@ -370744,6 +370263,7 @@ id: GO:0072586
name: DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) regulator activity
namespace: molecular_function
def: "Binds to and modulates the activity of ATP-hydrolyzing DNA topoisomerase. DNA topoisomerase (ATP-hydrolyzing) regulator activity catalyzes a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2." [GOC:mah]
+is_a: GO:0030234 ! enzyme regulator activity
is_a: GO:0060590 ! ATPase regulator activity
[Term]
@@ -370752,6 +370272,7 @@ name: DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activator a
namespace: molecular_function
def: "Binds to and increases the activity of ATP-hydrolyzing DNA topoisomerase. DNA topoisomerase (ATP-hydrolyzing) regulator activity catalyzes a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined; product release is coupled to ATP binding and hydrolysis; changes the linking number in multiples of 2." [GOC:mah]
is_a: GO:0001671 ! ATPase activator activity
+is_a: GO:0008047 ! enzyme activator activity
is_a: GO:0072586 ! DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) regulator activity
[Term]
@@ -371070,6 +370591,7 @@ namespace: biological_process
alt_id: GO:0072661
alt_id: GO:0090002
def: "A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane." [GOC:mah]
+subset: goslim_generic
subset: goslim_pombe
synonym: "protein localisation in plasma membrane" RELATED [GOC:mah]
synonym: "protein localization in plasma membrane" RELATED []
@@ -371312,7 +370834,7 @@ synonym: "Rad50 complex assembly" EXACT [GOC:mah]
synonym: "RAD50-MRE11-NBN complex assembly" EXACT [CORUM:2767, GOC:mah]
synonym: "Rad50-Rad32-Nbs1 complex assembly" EXACT [GOC:mah]
synonym: "RMX complex assembly" EXACT [GOC:mah]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0072686
@@ -371335,14 +370857,14 @@ namespace: biological_process
def: "Any process in which a SHREC complex is transported to, or maintained in, a specific location." [GOC:mah]
synonym: "establishment and maintenance of SHREC complex localization" EXACT [GOC:mah]
synonym: "SHREC complex localisation" EXACT [GOC:mah]
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
[Term]
id: GO:0072689
name: MCM complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form an MCM complex, a hexameric protein complex required for the initiation and regulation of DNA replication." [GOC:mah, PMID:21813639]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0072690
@@ -371803,7 +371325,7 @@ namespace: biological_process
def: "Any process in which a SAGA complex is transported to, or maintained in, a specific location in the transcription regulatory region of a gene." [GOC:mah]
synonym: "SAGA complex localization to promoter" EXACT [GOC:mah]
synonym: "SAGA complex recruitment" EXACT [GOC:mah]
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
[Term]
id: GO:0072743
@@ -372018,7 +371540,7 @@ def: "A cellular localization process in which a centromere/kinetochore is trans
synonym: "establishment and maintenance of kinetochore localization" EXACT [GOC:mah]
synonym: "kinetochore localisation" EXACT [GOC:mah]
synonym: "kinetochore localization" EXACT []
-is_a: GO:0034629 ! cellular protein-containing complex localization
+is_a: GO:0031503 ! protein-containing complex localization
is_a: GO:0051640 ! organelle localization
[Term]
@@ -372073,6 +371595,7 @@ def: "The attachment of an appressorium of the symbiont to its host via adhesion
comment: Note that this term should not be used to annotate gene products of the host. It should only be used to annotate those gene products from the symbiont involved in this process.
synonym: "adhesion of symbiont appressorium to host during symbiotic interaction" EXACT []
is_a: GO:0075001 ! adhesion of symbiont infection structure to host
+relationship: part_of GO:0075016 ! appressorium formation
[Term]
id: GO:0075004
@@ -372333,25 +371856,24 @@ relationship: negatively_regulates GO:0075029 ! formation of appressorium germ t
[Term]
id: GO:0075033
-name: appressorium septum formation
+name: obsolete appressorium septum formation
namespace: biological_process
-def: "The process in which a symbiont partition is formed to separate the appressorium from the germination tube, occurring during appressorium formation." [GOC:pamgo_curators]
+def: "OBSOLETE. The process in which a symbiont partition is formed to separate the appressorium from the germination tube, occurring during appressorium formation." [GOC:pamgo_curators]
+comment: The reason for obsoletion is that there is no evidence that this process exists.
synonym: "septum formation during appressorium formation on or near host" RELATED [GOC:tb]
synonym: "septum formation involved in appressorium formation" EXACT []
synonym: "septum formation involved in appressorium formation on or near host" EXACT []
-is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
-relationship: part_of GO:0075016 ! appressorium formation
+is_obsolete: true
[Term]
id: GO:0075034
-name: nuclear division involved in appressorium formation
+name: obsolete nuclear division involved in appressorium formation
namespace: biological_process
-def: "The process in which nuclear division occurs within a symbiont spore that contributes to appressorium formation. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:pamgo_curators]
-comment: Note that this term should not be used to annotate gene products of the host. It should only be used to annotate those gene products from the symbiont involved in this process.
+def: "OBSOLETE. The process in which nuclear division occurs within a symbiont spore that contributes to appressorium formation. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:dph, GOC:pamgo_curators]
+comment: The reason for obsoletion is that there is no evidence that this process exists.
synonym: "nuclear division during appressorium formation on or near host" RELATED [GOC:dph]
synonym: "nuclear division involved in appressorium formation on or near host" RELATED []
-is_a: GO:0000280 ! nuclear division
-relationship: part_of GO:0075016 ! appressorium formation
+is_obsolete: true
[Term]
id: GO:0075035
@@ -372442,10 +371964,11 @@ relationship: negatively_regulates GO:0075039 ! establishment of turgor in appre
id: GO:0075043
name: melanization of appressorium wall
namespace: biological_process
-def: "The process in which melanin is produced in the appressorium of the symbiont. Melanization of the appressorium increases turgor pressure in the appressorium." [GOC:pamgo_curators, Wikipedia:Appressorium]
+def: "The process in which melanin is produced in the appressorium of the symbiont. Melanization of the appressorium increases turgor pressure in the appressorium." [GOC:pamgo_curators, PMID:28165657, Wikipedia:Appressorium]
synonym: "maintenance of turgor in appressorium by melanization" RELATED []
synonym: "melanization of appressorium to maintain turgor pressure" EXACT []
-is_a: GO:0075035 ! appressorium maturation
+is_a: GO:0043476 ! pigment accumulation
+relationship: part_of GO:0075035 ! appressorium maturation
[Term]
id: GO:0075044
@@ -372706,31 +372229,27 @@ is_obsolete: true
[Term]
id: GO:0075075
-name: modulation by host of symbiont adenylate cyclase activity
+name: obsolete modulation by host of symbiont adenylate cyclase activity
namespace: biological_process
-def: "Any process in which the host organism modulates the frequency, rate or extent of the symbiont adenylate cyclase activity, which catalyze the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the host. To annotate symbiont gene products, consider the biological process term "modulation by symbiont of host adenylate cyclase activity ; GO:0075106".
-is_a: GO:0045761 ! regulation of adenylate cyclase activity
-is_a: GO:0052422 ! modulation by host of symbiont catalytic activity
+def: "OBSOLETE. Any process in which the host organism modulates the frequency, rate or extent of the symbiont adenylate cyclase activity, which catalyze the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0075076
-name: positive regulation by host of symbiont adenylate cyclase activity
+name: obsolete positive regulation by host of symbiont adenylate cyclase activity
namespace: biological_process
-def: "Any process in which the host organism activates, maintains or increases the frequency, rate or extent of the symbiont adenylate cyclase activity, which catalyze the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-is_a: GO:0043947 ! positive regulation by host of symbiont catalytic activity
-is_a: GO:0045762 ! positive regulation of adenylate cyclase activity
-is_a: GO:0075075 ! modulation by host of symbiont adenylate cyclase activity
+def: "OBSOLETE. Any process in which the host organism activates, maintains or increases the frequency, rate or extent of the symbiont adenylate cyclase activity, which catalyze the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0075077
-name: negative regulation by host of symbiont adenylate cyclase activity
+name: obsolete negative regulation by host of symbiont adenylate cyclase activity
namespace: biological_process
-def: "Any process in which the host organism stops, prevents, or reduces the frequency, rate or extent of the symbiont adenylate cyclase activity, which catalyze the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the host. To annotate symbiont gene products, consider the biological process term "negative regulation by symbiont of host adenylate cyclase activity ; GO:0075108".
-is_a: GO:0007194 ! negative regulation of adenylate cyclase activity
-is_a: GO:0052403 ! negative regulation by host of symbiont catalytic activity
-is_a: GO:0075075 ! modulation by host of symbiont adenylate cyclase activity
+def: "OBSOLETE. Any process in which the host organism stops, prevents, or reduces the frequency, rate or extent of the symbiont adenylate cyclase activity, which catalyze the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0075078
@@ -372973,10 +372492,10 @@ is_obsolete: true
[Term]
id: GO:0075106
-name: modulation by symbiont of host adenylate cyclase activity
+name: obsolete modulation by symbiont of host adenylate cyclase activity
namespace: biological_process
-def: "Any process in which the symbiont modulates the frequency, rate or extent of the host adenylate cyclase activity, which involves catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the symbiont. To annotate host gene products, consider the biological process term "modulation by host of symbiont adenylate cyclase activity ; GO:0075075".
+def: "OBSOLETE. Any process in which the symbiont modulates the frequency, rate or extent of the host adenylate cyclase activity, which involves catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "Modulation by symbiont of host 3',5'-cyclic AMP synthetase activity" EXACT []
synonym: "Modulation by symbiont of host adenyl cyclase activity" EXACT []
synonym: "Modulation by symbiont of host adenylyl cyclase activity" EXACT []
@@ -372985,30 +372504,27 @@ synonym: "Modulation by symbiont of host ATP diphosphate-lyase (cyclizing ; 3',5
synonym: "Modulation by symbiont of host ATP diphosphate-lyase (cyclizing) activity" EXACT []
synonym: "Modulation by symbiont of host ATP pyrophosphate-lyase activity" EXACT []
synonym: "Modulation by symbiont of host cAMP generating peptide activity" RELATED []
-is_a: GO:0045761 ! regulation of adenylate cyclase activity
-is_a: GO:0052148 ! modulation by symbiont of host catalytic activity
+is_obsolete: true
[Term]
id: GO:0075107
-name: positive regulation by symbiont of host adenylate cyclase activity
+name: obsolete positive regulation by symbiont of host adenylate cyclase activity
namespace: biological_process
-def: "Any process in which the symbiont activates, maintains or increases the frequency, rate or extent of the host adenylate cyclase activity, which involves catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the symbiont. To annotate host gene products, consider the biological process term "positive regulation by host of symbiont adenylate cyclase activity ; GO:0075076".
+def: "OBSOLETE. Any process in which the symbiont activates, maintains or increases the frequency, rate or extent of the host adenylate cyclase activity, which involves catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "positive regulation by symbiont of host 3',5'-cyclic AMP synthetase activity" EXACT []
synonym: "positive regulation by symbiont of host adenyl cyclase activity" EXACT []
synonym: "positive regulation by symbiont of host adenylyl cyclase activity" EXACT []
synonym: "positive regulation by symbiont of host adenylylcyclase activity" EXACT []
synonym: "positive regulation by symbiont of host ATP diphosphate-lyase (cyclizing ; 3',5'-cyclic-AMP-forming) activity" EXACT []
-is_a: GO:0043948 ! induction by symbiont of host catalytic activity
-is_a: GO:0045762 ! positive regulation of adenylate cyclase activity
-is_a: GO:0075106 ! modulation by symbiont of host adenylate cyclase activity
+is_obsolete: true
[Term]
id: GO:0075108
-name: negative regulation by symbiont of host adenylate cyclase activity
+name: obsolete negative regulation by symbiont of host adenylate cyclase activity
namespace: biological_process
-def: "Any process in which the symbiont stops, prevents, or reduces the frequency, rate or extent of the host adenylate cyclase activity, which catalyze the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the symbiont. To annotate host gene products, consider the biological process term "negative regulation by host of symbiont adenylate cyclase activity ; GO:0075077".
+def: "OBSOLETE. Any process in which the symbiont stops, prevents, or reduces the frequency, rate or extent of the host adenylate cyclase activity, which catalyze the reaction: ATP = 3',5'-cyclic AMP + diphosphate. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "Negative regulation by symbiont of host 3',5'-cyclic AMP synthetase activity" EXACT []
synonym: "Negative regulation by symbiont of host adenyl cyclase activity" EXACT []
synonym: "Negative regulation by symbiont of host adenylyl cyclase activity" EXACT []
@@ -373017,9 +372533,7 @@ synonym: "Negative regulation by symbiont of host ATP diphosphate-lyase (cyclizi
synonym: "Negative regulation by symbiont of host ATP diphosphate-lyase (cyclizing) activity" EXACT []
synonym: "Negative regulation by symbiont of host ATP pyrophosphate-lyase activity" EXACT []
synonym: "Negative regulation by symbiont of host cAMP generating peptide activity" RELATED []
-is_a: GO:0007194 ! negative regulation of adenylate cyclase activity
-is_a: GO:0052053 ! negative regulation by symbiont of host catalytic activity
-is_a: GO:0075106 ! modulation by symbiont of host adenylate cyclase activity
+is_obsolete: true
[Term]
id: GO:0075109
@@ -373591,31 +373105,30 @@ is_obsolete: true
[Term]
id: GO:0075180
-name: regulation of transcription in response to host
+name: obsolete regulation of transcription in response to host
namespace: biological_process
-def: "Any process in which the symbiont organism modulates the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the symbiont.
-synonym: "regulation of symbiont transcription in response to host" EXACT []
-is_a: GO:0075136 ! response to host
-is_a: GO:2001141 ! regulation of RNA biosynthetic process
+def: "OBSOLETE. Any process in which the symbiont organism modulates the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0006355
[Term]
id: GO:0075181
-name: positive regulation of symbiont transcription in response to host
+name: obsolete positive regulation of symbiont transcription in response to host
namespace: biological_process
-def: "Any process in which an organism activates, maintains or increases the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the symbiont.
-is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process
-is_a: GO:0075180 ! regulation of transcription in response to host
+def: "OBSOLETE. Any process in which an organism activates, maintains or increases the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0006355
[Term]
id: GO:0075182
-name: negative regulation of symbiont transcription in response to host
+name: obsolete negative regulation of symbiont transcription in response to host
namespace: biological_process
-def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is used to annotate gene products of the symbiont.
-is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0075180 ! regulation of transcription in response to host
+def: "OBSOLETE. Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a GO-CAM model.
+is_obsolete: true
+consider: GO:0045892
[Term]
id: GO:0075183
@@ -374037,7 +373550,7 @@ relationship: negatively_regulates GO:0075222 ! sporangium germination
id: GO:0075226
name: encysted zoospore germination
namespace: biological_process
-def: "The physiological, developmental and morphological changes that occur in an encysted zoospore, that germinates by developing a germ tube that may penetrate the host directly or indirectly through an appresorium. An encysted zoospore is a zoospore which has shed its flagellum and whose membrane has fused to form a walled cyst. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+def: "The physiological, developmental and morphological changes that occur in an encysted zoospore, that germinates by developing a germ tube that may penetrate the host directly or indirectly through an appressorium. An encysted zoospore is a zoospore which has shed its flagellum and whose membrane has fused to form a walled cyst. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
comment: Note that this term should not be used to annotate gene products of the host. It should only be used to annotate those gene products from the symbiont involved in this process.
synonym: "encysted zoospore germination on or near host" EXACT []
is_a: GO:0009847 ! spore germination
@@ -375062,21 +374575,21 @@ is_obsolete: true
[Term]
id: GO:0075345
-name: modification by symbiont of host protein
+name: obsolete modification by symbiont of host protein
namespace: biological_process
-def: "The covalent alteration by an organism of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is intended for use in annotation of symbiont gene products. For host gene products that modify host proteins, consider annotation to 'protein modification process' GO:0006464.
-is_a: GO:0052228 ! metabolism by symbiont of host protein
+def: "OBSOLETE. The covalent alteration by an organism of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0075346
-name: modification by symbiont of host protein by ubiquitination
+name: obsolete modification by symbiont of host protein by ubiquitination
namespace: biological_process
-def: "The process in which an organism adds one or more ubiquitin groups to a protein of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
-comment: Note that this term is intended for use in annotation of symbiont gene products. For host gene products that ubiquitinate host proteins, consider annotation to 'protein ubiquitination ; GO:0016567'.
+def: "OBSOLETE. The process in which an organism adds one or more ubiquitin groups to a protein of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "modification by symbiont of host protein by ubiquitinylation" EXACT []
synonym: "modification by symbiont of host protein by ubiquitylation" EXACT []
-is_a: GO:0075345 ! modification by symbiont of host protein
+is_obsolete: true
[Term]
id: GO:0075502
@@ -375149,7 +374662,6 @@ synonym: "viral penetration via endocytosis followed by endosome disruption" EXA
synonym: "virus endocytosis by host" EXACT [UniProtKB-KW:KW-1164]
xref: VZ:977 "Virus endocytosis by host"
is_a: GO:0006897 ! endocytosis
-is_a: GO:0044764 ! multi-organism cellular process
is_a: GO:0046794 ! transport of virus
relationship: part_of GO:0046718 ! viral entry into host cell
@@ -375161,7 +374673,6 @@ def: "Any macropinocytosis that is involved in the uptake of a virus into a host
synonym: "viral entry into host cell via macropinocytosis" RELATED [GOC:bf, GOC:jl]
xref: VZ:800 "Macropinocytosis of virus by host"
is_a: GO:0075509 ! endocytosis involved in viral entry into host cell
-is_a: GO:1902539 ! multi-organism macropinocytosis
[Term]
id: GO:0075511
@@ -375623,7 +375134,7 @@ is_a: GO:0042430 ! indole-containing compound metabolic process
id: GO:0080025
name: phosphatidylinositol-3,5-bisphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions." [GOC:bf, PMID:18397324]
+def: "Binding to phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions." [GOC:bf, PMID:18397324]
synonym: "PtdIns(3,5)P2 binding" EXACT []
is_a: GO:0043168 ! anion binding
is_a: GO:1902936 ! phosphatidylinositol bisphosphate binding
@@ -375675,7 +375186,6 @@ def: "Catalysis of the reaction: methyl indole-3-acetate + H2O = indole-3-acetat
synonym: "indole-3-Acetic acid methyl ester esterase activity" EXACT []
synonym: "MeIAA esterase activity" EXACT []
synonym: "Methyl IAA esterase activity" EXACT []
-synonym: "methyl indole-3-acetate esterase activity" RELATED []
xref: EC:3.1.1.1
xref: MetaCyc:RXN-10711
is_a: GO:0052689 ! carboxylic ester hydrolase activity
@@ -376091,7 +375601,7 @@ is_a: GO:0008422 ! beta-glucosidase activity
id: GO:0080084
name: 5S rDNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the 5S rDNA sequence encoding ribosomal 5S rRNA, which is individually transcribed by RNA polymerase III, rather than by RNA polymerase I, in species where it exists." [PMID:12711688]
+def: "Binding to a 5S rDNA sequence, encoding ribosomal 5S rRNA, which is individually transcribed by RNA polymerase III, rather than by RNA polymerase I, in species where it exists." [PMID:12711688]
is_a: GO:0000182 ! rDNA binding
[Term]
@@ -376188,11 +375698,11 @@ is_a: GO:0008374 ! O-acyltransferase activity
id: GO:0080097
name: L-tryptophan:pyruvate aminotransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-tryptophan + pyruvate = 3-(indol-3-yl)pyruvate + L-alanine." [MetaCyc:RXN-10139]
+def: "Catalysis of the reaction: L-tryptophan + pyruvate = 3-(indol-3-yl)pyruvate + L-alanine." [RHEA:27586]
comment: This reaction falls within the larger set of reactions associated with EC:2.6.1.28 (See BRENDA: http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.6.1.28; note: 3-indole-2-oxopropanoate = indolepyruvate = 3-(indol-3-yl)pyruvate).
-xref: EC:2.6.1.28
+xref: EC:2.6.1.99
xref: MetaCyc:RXN-10139
-xref: RHEA:27587
+xref: RHEA:27586
is_a: GO:0070529 ! L-tryptophan aminotransferase activity
[Term]
@@ -376345,7 +375855,7 @@ is_a: GO:0051347 ! positive regulation of transferase activity
id: GO:0080115
name: myosin XI tail binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the tail region of a myosin XI heavy chain." [PMID:18703495]
+def: "Binding to the tail region of a myosin XI heavy chain." [PMID:18703495]
is_a: GO:0032029 ! myosin tail binding
[Term]
@@ -376669,7 +376179,6 @@ def: "Any process that activates or increases the frequency, rate or extent of s
synonym: "positive regulation of salicylic acid mediated signalling pathway" EXACT [GOC:mah]
is_a: GO:0009967 ! positive regulation of signal transduction
is_a: GO:2000031 ! regulation of salicylic acid mediated signaling pathway
-is_a: GO:2001040 ! positive regulation of cellular response to drug
relationship: positively_regulates GO:0009863 ! salicylic acid mediated signaling pathway
[Term]
@@ -376700,7 +376209,6 @@ id: GO:0080154
name: regulation of fertilization
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." [GOC:DHL, PMID:20478994]
-is_a: GO:0043900 ! regulation of multi-organism process
is_a: GO:2000241 ! regulation of reproductive process
relationship: regulates GO:0009566 ! fertilization
@@ -377007,9 +376515,11 @@ relationship: part_of GO:0048437 ! floral organ development
id: GO:0080188
name: gene silencing by RNA-directed DNA methylation
namespace: biological_process
-def: "An epigenetic RNA-based gene silencing process first elucidated in plants whereby 24-nt small interfering RNAs (siRNAs) guide DNA methyltransferases to the siRNA-generating genomic loci and other loci that are homologous to the siRNAs for de novo DNA methylation. In general this process consists of three phases: biogenesis of siRNAs, scaffold RNA production, and the formation of the guiding complex that recruits de novo DNA methyltransferases to the target loci." [PMID:21420348]
+def: "A small RNA-based epigenetic gene silencing process in which small interfering RNAs (siRNAs) guide DNA methylation to the siRNA-generating genomic loci and other loci that are homologous to the siRNAs for de novo DNA methylation. This results in a heterochromatin assembly, a chromatin conformation that is refractory to transcription. In general this process consists of three phases: biogenesis of siRNAs, scaffold RNA production, and the formation of the guiding complex that recruits de novo DNA methyltransferases to the target loci. Transposable elements are silenced by this mechanism." [PMID:21420348]
+comment: This process has been shown in plants and in yeasts, but so far has not been detected in vertebrates, organisms that lack RNA-dependent RNA polymerase.
synonym: "RdDM" EXACT []
synonym: "RNA-directed DNA methylation" RELATED []
+is_a: GO:0006346 ! DNA methylation-dependent heterochromatin assembly
is_a: GO:0140458 ! pre-transcriptional gene silencing by RNA
[Term]
@@ -377209,13 +376719,14 @@ is_a: GO:0044409 ! entry into host
[Term]
id: GO:0085018
-name: maintenance of symbiont-containing vacuole by host
+name: obsolete maintenance of symbiont-containing vacuole by host
namespace: biological_process
-def: "The process in which a host organism maintains the structure and function of a symbiont-containing vacuole. The symbiont-containing vacuole is a membrane-bounded vacuole within a host cell in which a symbiont organism resides, and can serve to reduce pathogenicity of invading symbionts by restricting them to the vacuolar compartment." [GOC:jl, GOC:yaf, PMID:18665841]
+def: "OBSOLETE. The process in which a host organism maintains the structure and function of a symbiont-containing vacuole. The symbiont-containing vacuole is a membrane-bounded vacuole within a host cell in which a symbiont organism resides, and can serve to reduce pathogenicity of invading symbionts by restricting them to the vacuolar compartment." [GOC:jl, GOC:yaf, PMID:18665841]
+comment: This term has been obsoleted because there is no evidence that this process exists.
synonym: "maintenance of parasitophorous vacuole" EXACT []
synonym: "maintenance of pathogen-containing vacuole" EXACT []
synonym: "maintenance of vacuolar integrity during bacterial infection" NARROW []
-is_a: GO:0051851 ! modulation by host of symbiont process
+is_obsolete: true
[Term]
id: GO:0085019
@@ -377317,7 +376828,6 @@ name: induction by symbiont of host I-kappaB kinase/NF-kappaB cascade
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of host NF-kappaB-mediated signal transduction pathways during the host defense response. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:pamgo_curators]
synonym: "activation by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT []
-synonym: "induction by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT []
synonym: "positive regulation by symbiont of host I-kappaB kinase/NF-kappaB cascade" EXACT []
synonym: "positive regulation by symbiont of host NF-kappaB-mediated signal transduction pathway" EXACT []
synonym: "positive regulation by symbiont of nuclear factor kappa-light-chain-enhancer of activated B cells mediated signal transduction pathway" EXACT []
@@ -377676,7 +377186,6 @@ id: GO:0086030
name: adenylate cyclase-activating adrenergic receptor signaling pathway involved in cardiac muscle relaxation
namespace: biological_process
def: "An adrenergic receptor signaling pathway that contributes to a reduction in cardiac muscle contraction. Beta-adrenergic receptor-induced cardiac relaxation is achieved by a GPCR-activated adenylate cyclase generating cAMP; cAMP then activates the cAMP-dependent protein kinase A (PKA), which phosphorylates the sarcoplasmic reticulum (SR) membrane protein PLB. In its non-phosphorylated state, PLB acts as an inhibitor of the ATPase Ca(2+) pump of the cardiac SR (SERCA2a); inhibition of the pump is relieved upon phosphorylation. The pump removes Ca(2+) from the cytoplasm, thereby preventing cytosolic Ca(2+)-dependent activation of contractile proteins, leading to enhanced muscle relaxation." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, PMID:10571541]
-synonym: "adenylate cyclase-activating adrenergic receptor signaling pathway involved in cardiac muscle relaxation" EXACT [GOC:mtg_cardiac_conduct_nov11]
synonym: "adrenergic receptor signaling pathway involved in cardiac muscle relaxation" EXACT []
synonym: "adrenergic receptor signaling pathway involved in cardiac muscle relaxation via activation of AC" RELATED [GOC:mtg_cardiac_conduct_nov11]
synonym: "adrenergic receptor-induced cardiac relaxation" RELATED [PMID:10571541]
@@ -378089,14 +377598,14 @@ is_a: GO:0086075 ! gap junction channel activity involved in cardiac conduction
id: GO:0086080
name: protein binding involved in heterotypic cell-cell adhesion
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex contributing to the adhesion of two different types of cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "Binding to a protein or protein complex contributing to the adhesion of two different types of cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
is_a: GO:0098632 ! cell-cell adhesion mediator activity
[Term]
id: GO:0086081
name: cell adhesive protein binding involved in atrial cardiac muscle cell-AV node cell communication
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex that results in the connection of an atrial cardiomyocyte with an AV node cell and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "Binding to a protein or protein complex that results in the connection of an atrial cardiomyocyte with an AV node cell and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
synonym: "cell adhesive protein binding involved in atrial cardiomyocyte-atrioventricular node cell communication" EXACT []
synonym: "cell adhesive protein binding involved in atrial cardiomyocyte-AV node cell communication" EXACT []
is_a: GO:0086080 ! protein binding involved in heterotypic cell-cell adhesion
@@ -378105,7 +377614,7 @@ is_a: GO:0086080 ! protein binding involved in heterotypic cell-cell adhesion
id: GO:0086082
name: cell adhesive protein binding involved in AV node cell-bundle of His cell communication
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex that results in the connection of an AV node cell with a bundle of His cell and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "Binding to a protein or protein complex that results in the connection of an AV node cell with a bundle of His cell and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
synonym: "cell adhesive protein binding involved in atrioventricular node cell-bundle of His cell communication" EXACT []
is_a: GO:0086080 ! protein binding involved in heterotypic cell-cell adhesion
@@ -378113,21 +377622,21 @@ is_a: GO:0086080 ! protein binding involved in heterotypic cell-cell adhesion
id: GO:0086083
name: cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex that results in the connection of a bundle of His cell with a Purkinje myocyte and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "Binding to a protein or protein complex that results in the connection of a bundle of His cell with a Purkinje myocyte and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
is_a: GO:0086080 ! protein binding involved in heterotypic cell-cell adhesion
[Term]
id: GO:0086084
name: cell adhesive protein binding involved in Purkinje myocyte-ventricular cardiac muscle cell communication
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex that results in the connection of a Purkinje myocyte with an ventricular cardiac muscle cell and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "Binding to a protein or protein complex that results in the connection of a Purkinje myocyte with an ventricular cardiac muscle cell and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
is_a: GO:0086080 ! protein binding involved in heterotypic cell-cell adhesion
[Term]
id: GO:0086085
name: cell adhesive protein binding involved in SA cardiac muscle cell-atrial cardiac muscle cell communication
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex that results in the connection of an SA cardiomyocyte with an atrial cardiomyocyte and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
+def: "Binding to a protein or protein complex that results in the connection of an SA cardiomyocyte with an atrial cardiomyocyte and contributes to the communication between the two cells." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11]
synonym: "cell adhesive protein binding involved in SA cardiomyocyte-atrial cardiomyocyte communication" EXACT []
is_a: GO:0086080 ! protein binding involved in heterotypic cell-cell adhesion
@@ -378413,7 +377922,7 @@ is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
id: GO:0089710
name: endocytic targeting sequence binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a endocytic signal sequence, a specific peptide sequence, of 4-6 amino acids with an essential tyrosine (Y), found on cytoplasmic tails of some cell surface membrane proteins, which directs internalization by clathrin-coated pits." [PMID:8918456]
+def: "Binding to a endocytic signal sequence, a specific peptide sequence, of 4-6 amino acids with an essential tyrosine (Y), found on cytoplasmic tails of some cell surface membrane proteins, which directs internalization by clathrin-coated pits." [PMID:8918456]
is_a: GO:0005515 ! protein binding
[Term]
@@ -378476,7 +377985,7 @@ is_a: GO:0098739 ! import across plasma membrane
id: GO:0089719
name: RHG protein domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RHG (reaper/hid/grimm) domain/motif (AKA iap binding motif)." [GOC:dos, GOC:ha]
+def: "Binding to an RHG (reaper/hid/grimm) domain/motif (AKA iap binding motif)." [GOC:dos, GOC:ha]
synonym: "iap binding domain binding" EXACT []
synonym: "inhibitor of apoptosis binding domain binding" EXACT []
synonym: "reaper hid grim domain binding" EXACT []
@@ -378487,7 +377996,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0089720
name: caspase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a caspase family protein." [GOC:dos, GOC:ha]
+def: "Binding to a caspase family protein." [GOC:dos, GOC:ha]
is_a: GO:0002020 ! protease binding
[Term]
@@ -378520,7 +378029,6 @@ id: GO:0090006
name: regulation of linear element assembly
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of linear element assembly. Linear element assembly is the cell cycle process in which a proteinaceous scaffold, related to the synaptonemal complex, is assembled in association with S. pombe chromosomes during meiotic prophase." [GOC:tb]
-synonym: "regulation of linear element assembly" RELATED [GOC:dph]
is_a: GO:0044087 ! regulation of cellular component biogenesis
is_a: GO:0051128 ! regulation of cellular component organization
is_a: GO:0060629 ! regulation of homologous chromosome segregation
@@ -378919,7 +378427,6 @@ name: regulation of pericentric heterochromatin assembly
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of chromatin silencing at the centromere. Chromatin silencing at the centromere is the repression of transcription of centromeric DNA by altering the structure of chromatin." [GOC:dph, GOC:tb]
synonym: "regulation of chromatin silencing at centromere" EXACT []
-is_a: GO:0010468 ! regulation of gene expression
is_a: GO:0031445 ! regulation of heterochromatin assembly
relationship: regulates GO:0031508 ! pericentric heterochromatin assembly
@@ -380018,6 +379525,7 @@ is_a: GO:0046136 ! positive regulation of vitamin metabolic process
is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process
is_a: GO:0051176 ! positive regulation of sulfur metabolic process
is_a: GO:0070623 ! regulation of thiamine biosynthetic process
+is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
relationship: positively_regulates GO:0009228 ! thiamine biosynthetic process
[Term]
@@ -381138,10 +380646,10 @@ is_a: GO:0090304 ! nucleic acid metabolic process
[Term]
id: GO:0090306
-name: spindle assembly involved in meiosis
+name: meiotic spindle assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of meiosis." [GOC:tb, GOC:vw]
-synonym: "meiotic spindle assembly" EXACT [GOC:vw]
+synonym: "spindle assembly involved in meiosis" EXACT []
is_a: GO:0000212 ! meiotic spindle organization
is_a: GO:0051225 ! spindle assembly
relationship: part_of GO:0140013 ! meiotic nuclear division
@@ -381163,7 +380671,6 @@ namespace: biological_process
def: "Any process that modulates the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF]
synonym: "regulation of methylation-dependent chromatin silencing" BROAD []
is_a: GO:0031445 ! regulation of heterochromatin assembly
-is_a: GO:0060255 ! regulation of macromolecule metabolic process
relationship: regulates GO:0006346 ! DNA methylation-dependent heterochromatin assembly
[Term]
@@ -381172,7 +380679,6 @@ name: positive regulation of DNA methylation-dependent heterochromatin assembly
namespace: biological_process
def: "Any process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF]
synonym: "positive regulation of methylation-dependent chromatin silencing" BROAD []
-is_a: GO:0010604 ! positive regulation of macromolecule metabolic process
is_a: GO:0031453 ! positive regulation of heterochromatin assembly
is_a: GO:0090308 ! regulation of DNA methylation-dependent heterochromatin assembly
relationship: positively_regulates GO:0006346 ! DNA methylation-dependent heterochromatin assembly
@@ -381183,7 +380689,6 @@ name: negative regulation of DNA methylation-dependent heterochromatin assembly
namespace: biological_process
def: "Any process that decreases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:BHF]
synonym: "negative regulation of methylation-dependent chromatin silencing" BROAD []
-is_a: GO:0010605 ! negative regulation of macromolecule metabolic process
is_a: GO:0031452 ! negative regulation of heterochromatin assembly
is_a: GO:0090308 ! regulation of DNA methylation-dependent heterochromatin assembly
relationship: negatively_regulates GO:0006346 ! DNA methylation-dependent heterochromatin assembly
@@ -381254,8 +380759,8 @@ def: "Any process that decreases the frequency, rate or extent of the directed m
is_a: GO:0032387 ! negative regulation of intracellular transport
is_a: GO:0033157 ! regulation of intracellular protein transport
is_a: GO:0051224 ! negative regulation of protein transport
-is_a: GO:1903828 ! negative regulation of cellular protein localization
relationship: negatively_regulates GO:0006886 ! intracellular protein transport
+relationship: negatively_regulates GO:0034613 ! cellular protein localization
[Term]
id: GO:0090318
@@ -381414,6 +380919,7 @@ synonym: "regulation of cell wall 1,3-beta-D-glucan biosynthetic process" BROAD
synonym: "regulation of cell wall 1,3-beta-glucan biosynthetic process" BROAD []
is_a: GO:0010981 ! regulation of cell wall macromolecule metabolic process
is_a: GO:0032953 ! regulation of (1->3)-beta-D-glucan biosynthetic process
+is_a: GO:1903338 ! regulation of cell wall organization or biogenesis
relationship: regulates GO:0034411 ! cell wall (1->3)-beta-D-glucan biosynthetic process
[Term]
@@ -382094,7 +381600,7 @@ is_a: GO:0043649 ! dicarboxylic acid catabolic process
id: GO:0090411
name: brassinosteroid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a brassinosteroid." [GOC:tb]
+def: "Binding to a brassinosteroid." [GOC:tb]
is_a: GO:0005496 ! steroid binding
[Term]
@@ -382201,11 +381707,9 @@ synonym: "thiamine diphosphate transporter activity" EXACT [GOC:tb]
synonym: "thiamine pyrophosphate transporter activity" NARROW []
xref: Reactome:R-HSA-8875838 "SLC25A19 transports ThDP from cytosol to mitochondrial matrix"
is_a: GO:0008514 ! organic anion transmembrane transporter activity
-is_a: GO:0015101 ! organic cation transmembrane transporter activity
+is_a: GO:0015234 ! thiamine transmembrane transporter activity
is_a: GO:0015605 ! organophosphate ester transmembrane transporter activity
-is_a: GO:0090482 ! vitamin transmembrane transporter activity
-is_a: GO:1901474 ! azole transmembrane transporter activity
-is_a: GO:1901682 ! sulfur compound transmembrane transporter activity
+is_a: GO:0015651 ! quaternary ammonium group transmembrane transporter activity
[Term]
id: GO:0090423
@@ -382664,7 +382168,7 @@ is_a: GO:0019748 ! secondary metabolic process
id: GO:0090488
name: polo box domain specific binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a polo box domain of a protein. The polo box domain is involved in binding substrates of polo kinases." [GOC:al, GOC:tb, Pfam:PF00659, PMID:12352953]
+def: "Binding to a polo box domain of a protein. The polo box domain is involved in binding substrates of polo kinases." [GOC:al, GOC:tb, Pfam:PF00659, PMID:12352953]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -382910,7 +382414,7 @@ def: "The directed movement of L-arginine into the vacuole across the vacuolar m
synonym: "arginine transmembrane import into vacuole" BROAD []
synonym: "vacuolar arginine import" EXACT [GOC:tb]
is_a: GO:0034490 ! basic amino acid transmembrane import into vacuole
-is_a: GO:1903400 ! L-arginine transmembrane transport
+is_a: GO:1903826 ! L-arginine transmembrane transport
[Term]
id: GO:0090519
@@ -383074,14 +382578,14 @@ is_a: GO:0030244 ! cellulose biosynthetic process
id: GO:0090541
name: MIT domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the MIT domain of a protein. The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking." [GOC:pm, InterPro:IPR007330]
+def: "Binding to a MIT protein domain. The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking." [GOC:pm, InterPro:IPR007330]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0090542
name: ELYC domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the ELYC domain of a protein. The ELYC domain is an approximately 150 amino acid sequence which contains a highly conserved tetrapeptide sequence, ELYC." [GOC:pm, PMID:18032582, PMID:19525971]
+def: "Binding to a ELYC protein domain. The ELYC domain is an approximately 150 amino acid sequence which contains a highly conserved tetrapeptide sequence, ELYC." [GOC:pm, PMID:18032582, PMID:19525971]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -383162,12 +382666,12 @@ relationship: part_of GO:0090552 ! unicellular trichome apex
id: GO:0090554
name: phosphatidylcholine floppase activity
namespace: molecular_function
-def: "Catalysis of the movement of phosphatidylcholine from the cytosolic to the exoplasmic leaftlet of a membrane, using energy from the hydrolysis of ATP." [GOC:ab, PMID:16452632, RHEA:38584]
+def: "Catalysis of the movement of phosphatidylcholine from the cytosolic to the exoplasmic leaftlet of a membrane, using energy from the hydrolysis of ATP." [GOC:ab, PMID:16452632, RHEA:38583]
synonym: "ATP-dependent phosphatidylcholine transporter activity" BROAD []
synonym: "ATPase-coupled phosphatidylcholine transporter activity" BROAD []
synonym: "phosphatidylcholine floppase activity (cytosolic to exoplasmic leaftlet)" EXACT []
synonym: "phosphatidylcholine-translocating ATPase activity" BROAD []
-xref: RHEA:38584
+xref: RHEA:38583
is_a: GO:0008525 ! phosphatidylcholine transporter activity
is_a: GO:0140328 ! floppase activity
@@ -383181,19 +382685,19 @@ synonym: "ATP-dependent phosphatidylethanolamine transporter activity" RELATED [
synonym: "ATPase-coupled phosphatidylethanolamine transporter activity" BROAD []
synonym: "phosphatidylethanolamine flippase activity (exoplasmic to cytosolic leaftlet)" EXACT []
synonym: "phosphatidylethanolamine-translocating ATPase activity" RELATED []
-xref: RHEA:36440
+xref: RHEA:66132
is_a: GO:0140333 ! glycerophospholipid flippase activity
[Term]
id: GO:0090556
name: phosphatidylserine floppase activity
namespace: molecular_function
-def: "Catalysis of the movement of phosphatidylserine from the cytosolic to the exoplasmic leaftlet of a membrane, using energy from the hydrolysis of ATP." [GOC:ab, PMID:16452632, PMID:20224745, RHEA:38568]
+def: "Catalysis of the movement of phosphatidylserine from the cytosolic to the exoplasmic leaftlet of a membrane, using energy from the hydrolysis of ATP." [GOC:ab, PMID:16452632, PMID:20224745, RHEA:38567]
synonym: "ATPase-coupled phosphatidylserine transporter activity" BROAD []
synonym: "ATPase-dependent phosphatidylserine transporter activity" BROAD []
synonym: "phosphatidylserine floppase activity (cytosolic to exoplasmic leaftlet)" EXACT []
synonym: "phosphatidylserine-translocating ATPase activity" BROAD []
-xref: RHEA:38568
+xref: RHEA:38567
is_a: GO:0005548 ! phospholipid transporter activity
is_a: GO:0140328 ! floppase activity
@@ -383222,7 +382726,8 @@ is_a: GO:0065008 ! regulation of biological quality
id: GO:0090560
name: 2-(3-amino-3-carboxypropyl)histidine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2] = S-methyl-5-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]." [BRENDA:2.5.1.108, GOC:pde, PMID:15485916]
+def: "Catalysis of the reaction S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2] = S-methyl-5-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]." [GOC:pde, PMID:15485916]
+xref: EC:2.5.1.108
xref: MetaCyc:RXN-11371
xref: Reactome:R-HSA-5358494 "DPH2 transfers a 3-amino-3-carboxypropyl group from AdoMet to residue 715 of nascent EEF2"
xref: RHEA:36783
@@ -383691,11 +383196,12 @@ is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
[Term]
id: GO:0090625
-name: mRNA cleavage involved in gene silencing by siRNA
+name: mRNA destabilization-mediated gene silencing by siRNA
namespace: biological_process
def: "The process in which small interfering RNAs (siRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a siRNA will typically direct cleavage by base pairing with perfect or near-perfect complementarity to the target mRNA." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:15260970]
-is_a: GO:0098795 ! mRNA cleavage involved in gene silencing
-relationship: part_of GO:0016246 ! RNA interference
+synonym: "mRNA cleavage involved in gene silencing by siRNA" EXACT []
+is_a: GO:0035194 ! post-transcriptional gene silencing by RNA
+is_a: GO:0098795 ! mRNA destabilization-mediated gene silencing
[Term]
id: GO:0090626
@@ -383952,7 +383458,7 @@ relationship: part_of GO:0090652 ! basolateral cytoplasm
id: GO:0090655
name: double-stranded/single-stranded junction telomeric DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the junction formed at the point where double-stranded telomeric DNA becomes a single-stranded G-rich telomeric DNA 3' overhang." [GOC:BHF, GOC:BHF_telomere, GOC:bhm, GOC:nc, PMID:21852327]
+def: "Binding to a junction formed at the point where double-stranded telomeric DNA becomes a single-stranded G-rich telomeric DNA 3' overhang." [GOC:BHF, GOC:BHF_telomere, GOC:bhm, GOC:nc, PMID:21852327]
is_a: GO:0000406 ! double-strand/single-strand DNA junction binding
is_a: GO:0042162 ! telomeric DNA binding
@@ -384310,13 +383816,6 @@ def: "The regionalization process in which the identity of a plant organ primord
is_a: GO:0003002 ! regionalization
relationship: part_of GO:1905393 ! plant organ formation
-[Term]
-id: GO:0090702
-name: non-reproductive fruiting body development
-namespace: biological_process
-def: "The process whose specific outcome is the progression of a non-reproductive fruiting body over time, from its formation to the mature structure. A non-reproductive fruiting body is a colonial multicellular structure consisting of co-operating unicellular organisms, some of which are spores. An example of such a process is found in Dictyostelium discoideum and Myxococcus xanthus colonies." [GOC:pf]
-is_a: GO:0099120 ! socially cooperative development
-
[Term]
id: GO:0090703
name: obsolete triplex DNA unwinding
@@ -384523,6 +384022,7 @@ name: toxin activity
namespace: molecular_function
alt_id: GO:0050827
def: "Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom." [GOC:pt]
+subset: goslim_generic
synonym: "toxin receptor binding" EXACT []
xref: Wikipedia:Toxin
is_a: GO:0003674 ! molecular_function
@@ -384588,7 +384088,7 @@ is_a: GO:0065003 ! protein-containing complex assembly
id: GO:0090736
name: MATH domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a meprin and TRAF homology (MATH) domain." [InterPro:IPR002083, PMID:22621901]
+def: "Binding to a meprin and TRAF homology (MATH) domain." [InterPro:IPR002083, PMID:22621901]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -384611,7 +384111,7 @@ id: GO:0090741
name: pigment granule membrane
namespace: cellular_component
def: "Any membrane that is part of a pigment granule." [PMID:11294610]
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
is_a: GO:0098588 ! bounding membrane of organelle
relationship: part_of GO:0048770 ! pigment granule
@@ -384645,7 +384145,7 @@ relationship: part_of GO:1905145 ! cellular response to acetylcholine
id: GO:0097001
name: ceramide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any ceramide, a class of lipids that is composed of sphingosine linked to a fatty acid. Ceramides are a major component of cell membranes." [GOC:sart]
+def: "Binding to a ceramide, a class of lipids composed of sphingosine linked to a fatty acid. Ceramides are a major component of cell membranes." [GOC:sart]
is_a: GO:0033218 ! amide binding
is_a: GO:0046625 ! sphingolipid binding
@@ -384671,7 +384171,7 @@ is_a: GO:0016500 ! protein-hormone receptor activity
id: GO:0097004
name: adipokinetic hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an adipokinetic hormone. Adipokinetic hormones (AKHs) are peptide hormones that are involved in the mobilization of sugar and lipids from the insect fat body during energy-requiring activities such as flight and locomotion. They also contribute to hemolymph sugar homeostasis." [GOC:sart, PMID:11904407]
+def: "Binding to an adipokinetic hormone. Adipokinetic hormones (AKHs) are peptide hormones that are involved in the mobilization of sugar and lipids from the insect fat body during energy-requiring activities such as flight and locomotion. They also contribute to hemolymph sugar homeostasis." [GOC:sart, PMID:11904407]
synonym: "AKH binding" EXACT []
is_a: GO:0017046 ! peptide hormone binding
@@ -384679,7 +384179,7 @@ is_a: GO:0017046 ! peptide hormone binding
id: GO:0097005
name: adipokinetic hormone receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an adipokinetic hormone receptor. Adipokinetic hormones (AKHs) are peptide hormones that are involved in the mobilization of sugar and lipids from the insect fat body during energy-requiring activities such as flight and locomotion. They also contribute to hemolymph sugar homeostasis." [GOC:sart, PMID:11904407]
+def: "Binding to an adipokinetic hormone receptor. Adipokinetic hormones (AKHs) are peptide hormones that are involved in the mobilization of sugar and lipids from the insect fat body during energy-requiring activities such as flight and locomotion. They also contribute to hemolymph sugar homeostasis." [GOC:sart, PMID:11904407]
synonym: "AKH receptor binding" EXACT []
is_a: GO:0051428 ! peptide hormone receptor binding
@@ -384732,7 +384232,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the eukaryotic translation initiation factor 4F complex." [GOC:BHF, GOC:ebc, PMID:18337562]
synonym: "eIF-4F assembly" EXACT [GOC:pr]
synonym: "eIF4F assembly" EXACT [GOC:pr]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0097011
@@ -384790,7 +384290,7 @@ is_obsolete: true
id: GO:0097016
name: L27 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a L27 domain of a protein. L27 is composed of conserved negatively charged amino acids and a conserved aromatic amino acid. L27 domains can assemble proteins involved in signaling and establishment and maintenance of cell polarity into complexes by interacting in a heterodimeric manner." [GOC:BHF, PMID:15241471, PMID:17237226, Prosite:PDOC51022]
+def: "Binding to a L27 domain of a protein. L27 is composed of conserved negatively charged amino acids and a conserved aromatic amino acid. L27 domains can assemble proteins involved in signaling and establishment and maintenance of cell polarity into complexes by interacting in a heterodimeric manner." [GOC:BHF, PMID:15241471, PMID:17237226, Prosite:PDOC51022]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -384895,7 +384395,7 @@ is_a: GO:0097028 ! dendritic cell differentiation
id: GO:0097030
name: CENP-A containing nucleosome binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a centromere-specific nucleosome, a form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3)." [GOC:jp, PMID:21412236]
+def: "Binding to a centromere-specific nucleosome, a form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3)." [GOC:jp, PMID:21412236]
synonym: "centromere-specific nucleosome binding" RELATED [GOC:vw]
synonym: "centromeric nucleosome binding" RELATED []
is_a: GO:0031491 ! nucleosome binding
@@ -385198,7 +384698,7 @@ is_a: GO:0097061 ! dendritic spine organization
id: GO:0097063
name: cadmium ion sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of cadmium (Cd++)." [GOC:rs, PMID:19456862]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of cadmium (Cd++)." [GOC:rs, PMID:19456862]
is_a: GO:0046870 ! cadmium ion binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -385317,7 +384817,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0097077
name: copper ion sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+)." [GOC:rs, PMID:19928961]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+)." [GOC:rs, PMID:19928961]
is_a: GO:0005507 ! copper ion binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -385502,9 +385002,9 @@ is_a: GO:0097096 ! facial suture morphogenesis
id: GO:0097098
name: DNA/RNA hybrid annealing activity
namespace: molecular_function
-def: "Facilitates the base-pairing of single-stranded RNA to double-stranded DNA resulting in the formation of R-loops." [GOC:imk, PMID:21699496]
+def: "An activity that facilitates the base-pairing of single-stranded RNA to double-stranded DNA resulting in the formation of R-loops." [GOC:imk, PMID:21699496]
is_a: GO:0071667 ! DNA/RNA hybrid binding
-is_a: GO:0097617 ! annealing activity
+is_a: GO:0140666 ! annealing activity
[Term]
id: GO:0097099
@@ -385518,7 +385018,7 @@ is_a: GO:0005198 ! structural molecule activity
id: GO:0097100
name: supercoiled DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with supercoiled DNA. For example, during replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA." [GOC:pr, GOC:rph, PMID:20723754, PMID:21345933, Wikipedia:DNA_supercoil]
+def: "Binding to supercoiled DNA. For example, during replication and transcription, template DNA is negatively supercoiled in the receding downstream DNA and positively supercoiled in the approaching downstream DNA." [GOC:pr, GOC:rph, PMID:20723754, PMID:21345933, Wikipedia:DNA_supercoil]
is_a: GO:0003690 ! double-stranded DNA binding
[Term]
@@ -385598,21 +385098,21 @@ relationship: part_of GO:1904861 ! excitatory synapse assembly
id: GO:0097108
name: hedgehog family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a member of the hedgehog protein family, signaling proteins involved in development." [GOC:BHF, GOC:pr, PMID:10050855]
+def: "Binding to a member of the hedgehog protein family, signaling proteins involved in development." [GOC:BHF, GOC:pr, PMID:10050855]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0097109
name: neuroligin family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a member of the neuroligin protein family, neuronal cell surface proteins that mediate synapse formation." [GOC:BHF, GOC:pr, GOC:sjp, PMID:21424692]
+def: "Binding to a member of the neuroligin protein family, neuronal cell surface proteins that mediate synapse formation." [GOC:BHF, GOC:pr, GOC:sjp, PMID:21424692]
is_a: GO:0005102 ! signaling receptor binding
[Term]
id: GO:0097110
name: scaffold protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes." [GOC:BHF, GOC:sjp, PMID:10433269, Wikipedia:Scaffold_protein]
+def: "Binding to a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes." [GOC:BHF, GOC:sjp, PMID:10433269, Wikipedia:Scaffold_protein]
is_a: GO:0005515 ! protein binding
[Term]
@@ -385980,7 +385480,7 @@ is_a: GO:0007413 ! axonal fasciculation
id: GO:0097157
name: pre-mRNA intronic binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an intronic sequence of a pre-messenger RNA (pre-mRNA)." [GOC:ans, PMID:16260624]
+def: "Binding to an intronic sequence of a pre-messenger RNA (pre-mRNA)." [GOC:ans, PMID:16260624]
synonym: "pre-messenger RNA intronic binding" EXACT []
is_a: GO:0036002 ! pre-mRNA binding
@@ -385988,7 +385488,7 @@ is_a: GO:0036002 ! pre-mRNA binding
id: GO:0097158
name: pre-mRNA intronic pyrimidine-rich binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a pyrimidine-rich (CU-rich) intronic sequence of a pre-messenger RNA (pre-mRNA)." [GOC:ans, PMID:16260624, PMID:16777844]
+def: "Binding to a pyrimidine-rich (CU-rich) intronic sequence of a pre-messenger RNA (pre-mRNA)." [GOC:ans, PMID:16260624, PMID:16777844]
synonym: "pre-messenger RNA intronic pyrimidine-rich binding" EXACT []
is_a: GO:0097157 ! pre-mRNA intronic binding
@@ -385996,14 +385496,14 @@ is_a: GO:0097157 ! pre-mRNA intronic binding
id: GO:0097159
name: organic cyclic compound binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [GOC:sjw, PMID:7583672]
+def: "Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [GOC:sjw, PMID:7583672]
is_a: GO:0005488 ! binding
[Term]
id: GO:0097160
name: polychlorinated biphenyl binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a polychlorinated biphenyl (PCB), a biphenyl compound containing between 2 and 10 chlorine atoms attached to the two benzene rings." [GOC:sjw, PMID:7583672]
+def: "Binding to a polychlorinated biphenyl (PCB), a biphenyl compound containing between 2 and 10 chlorine atoms attached to the two benzene rings." [GOC:sjw, PMID:7583672]
synonym: "PCB binding" EXACT []
synonym: "polychlorobiphenyl binding" EXACT []
is_a: GO:0097159 ! organic cyclic compound binding
@@ -386012,14 +385512,14 @@ is_a: GO:0097159 ! organic cyclic compound binding
id: GO:0097161
name: DH domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DH (Dbl homology) domain of a protein. The DH domain contains three structurally conserved regions separated by more variable regions. It is composed of 11 alpha helices that are folded into a flattened, elongated alpha-helix bundle in which two of the three conserved regions, conserved region 1 (CR1) and conserved region 3 (CR3), are exposed near the centre of one surface. CR1 and CR3, together with a part of alpha-6 and the DH/PH (pleckstrin homology) junction site, constitute the Rho GTPase interacting pocket." [GOC:yaf, InterPro:IPR000219, PMID:12775584]
+def: "Binding to a DH (Dbl homology) domain of a protein. The DH domain contains three structurally conserved regions separated by more variable regions. It is composed of 11 alpha helices that are folded into a flattened, elongated alpha-helix bundle in which two of the three conserved regions, conserved region 1 (CR1) and conserved region 3 (CR3), are exposed near the centre of one surface. CR1 and CR3, together with a part of alpha-6 and the DH/PH (pleckstrin homology) junction site, constitute the Rho GTPase interacting pocket." [GOC:yaf, InterPro:IPR000219, PMID:12775584]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:0097162
name: MADS box domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a MADS box domain, a protein domain that encodes the DNA-binding MADS domain. The MADS domain binds to DNA sequences of high similarity to the motif CC[A/T]6GG termed the CArG-box. MADS-domain proteins are generally transcription factors. The length of the MADS-box is in the range of 168 to 180 base pairs." [GOC:yaf, InterPro:IPR002100, PMID:18296735, Wikipedia:MADS-box]
+def: "Binding to a MADS box domain, a protein domain that encodes the DNA-binding MADS domain. The MADS domain binds to DNA sequences of high similarity to the motif CC[A/T]6GG termed the CArG-box. MADS-domain proteins are generally transcription factors. The length of the MADS-box is in the range of 168 to 180 base pairs." [GOC:yaf, InterPro:IPR002100, PMID:18296735, Wikipedia:MADS-box]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -386174,7 +385674,7 @@ is_a: GO:1901360 ! organic cyclic compound metabolic process
id: GO:0097177
name: mitochondrial ribosome binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of a mitochondrial ribosome, a ribosome found in the mitochondrion of a eukaryotic cell." [GOC:ans, PMID:20739282]
+def: "Binding to a mitochondrial ribosome." [GOC:ans, PMID:20739282]
is_a: GO:0043022 ! ribosome binding
[Term]
@@ -386545,7 +386045,7 @@ is_a: GO:1905709 ! negative regulation of membrane permeability
id: GO:0097216
name: guanosine tetraphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with guanosine tetraphosphate (5'-ppGpp-3'), a guanosine bisphosphate having diphosphate groups at both the 3' and 5'-positions." [GOC:imk, PMID:15109491, PMID:16968770, PMID:18359660]
+def: "Binding to guanosine tetraphosphate (5'-ppGpp-3'), a guanosine bisphosphate having diphosphate groups at both the 3' and 5'-positions." [GOC:imk, PMID:15109491, PMID:16968770, PMID:18359660]
synonym: "5'-ppGpp-3' binding" EXACT []
is_a: GO:0032561 ! guanyl ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -386780,14 +386280,14 @@ is_a: GO:0032501 ! multicellular organismal process
id: GO:0097243
name: flavonoid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a flavonoid, a compound containing two or more aromatic rings, each bearing at least one aromatic hydroxyl and connected with a carbon bridge." [GOC:sl, PMID:20599706]
+def: "Binding to a flavonoid, a compound containing two or more aromatic rings, each bearing at least one aromatic hydroxyl and connected with a carbon bridge." [GOC:sl, PMID:20599706]
is_a: GO:0005488 ! binding
[Term]
id: GO:0097244
name: flavonol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a flavonol, a flavonoid that contains a 3-hydroxy-2-phenylchromen-4-one backbone." [GOC:sl]
+def: "Binding to a flavonol, a flavonoid that contains a 3-hydroxy-2-phenylchromen-4-one backbone." [GOC:sl]
is_a: GO:0043168 ! anion binding
is_a: GO:0097243 ! flavonoid binding
@@ -386795,7 +386295,7 @@ is_a: GO:0097243 ! flavonoid binding
id: GO:0097245
name: flavanol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a flavanol." [GOC:sl]
+def: "Binding to a flavanol." [GOC:sl]
synonym: "flavan-3-ol binding" NARROW []
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:0097243 ! flavonoid binding
@@ -386805,14 +386305,14 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0097246
name: catechin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a catechin, a polyphenolic antioxidant plant metabolite with a flavonoid or flavan-3-ol structure." [GOC:sl]
+def: "Binding to a catechin, a polyphenolic antioxidant plant metabolite with a flavonoid or flavan-3-ol structure." [GOC:sl]
is_a: GO:0097245 ! flavanol binding
[Term]
id: GO:0097247
name: epigallocatechin 3-gallate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with epigallocatechin 3-gallate, a compound that is a gallic acid ester of a catechin." [GOC:sl, PMID:21307292]
+def: "Binding to epigallocatechin 3-gallate, a compound that is a gallic acid ester of a catechin." [GOC:sl, PMID:21307292]
synonym: "catechin gallate binding" BROAD []
synonym: "EGCG binding" EXACT []
is_a: GO:0097159 ! organic cyclic compound binding
@@ -386834,7 +386334,7 @@ def: "The aggregation, arrangement and bonding together of a set of respiratory
synonym: "mitochondrial respiratory chain supercomplex assembly" EXACT []
synonym: "mitochondrial respiratory supercomplex assembly" EXACT []
is_a: GO:0007005 ! mitochondrion organization
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0097251
@@ -386879,9 +386379,9 @@ is_a: GO:0015665 ! alcohol transmembrane transporter activity
id: GO:0097254
name: renal tubular secretion
namespace: biological_process
-def: "Secretion of substances from peritubular capillaries into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs." [GOC:rph, PMID:10049739, Wikipedia:Renal_secretion#Secretion]
+def: "The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs." [GOC:rph, PMID:25287933, Wikipedia:Renal_secretion#Secretion]
is_a: GO:0003014 ! renal system process
-is_a: GO:0046903 ! secretion
+is_a: GO:0007588 ! excretion
[Term]
id: GO:0097255
@@ -386894,8 +386394,9 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:0097256
name: phenyllactate dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the oxidation of phenyllactate to produce phenylpyruvate." [GOC:pde, PMID:15421980]
+def: "Catalysis of the reaction: (R)-3-phenyllactate + NAD+ = 3-phenylpyruvate + H+ + NADH." [GOC:pde, PMID:10849007, RHEA:38351]
comment: This enzymatic activity is usually negligible, but may become prominent when phenylalanine levels are abnormally high as in the human disease phenylketonuria (PKU).
+xref: RHEA:38351
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
[Term]
@@ -386912,19 +386413,22 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0097258
name: 20-hydroxy-leukotriene B4 omega oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 20-hydroxy-leukotriene B4 + O2 + NADPH + H(+) = 20-aldehyde-leukotriene B4 + 2H2O + NADP(+)." [GOC:mw, PMID:2836406]
+def: "Catalysis of the reaction: 20-hydroxy-leukotriene B4 + O2 + reduced [NADPH-hemoprotein reductase] = 20-oxo-leukotriene B4 + H+ + 2 H2O + oxidized [NADPH-hemoprotein reductase]." [GOC:mw, PMID:2836406, PMID:9675028, RHEA:48668]
synonym: "20-hydroxy-leukotriene B4 omega-oxidase activity" EXACT []
synonym: "20-hydroxy-leukotriene B4 omega-oxidation" RELATED []
xref: Reactome:R-HSA-2161745 "20oh-LTB4 is oxidised to 20cho-LTB4 by CYP4F2/4F3"
+xref: RHEA:48668
+is_a: GO:0004497 ! monooxygenase activity
is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
[Term]
id: GO:0097259
name: 20-aldehyde-leukotriene B4 20-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 20-aldehyde-leukotriene B4 + O2 + NADPH + H(+) = 20-carboxy-leukotriene B4 + H2O + NADP(+)." [GOC:mw, PMID:2549038, PMID:2836406]
+def: "Catalysis of the reaction: 20-oxo-leukotriene B4 + O2 + reduced [NADPH-hemoprotein reductase] = 20-carboxy-leukotriene B4 + 2 H+ + H2O + oxidized [NADPH-hemoprotein reductase]." [GOC:mw, PMID:2549038, PMID:2836406, PMID:9675028, RHEA:48672]
xref: Reactome:R-HSA-2161792 "20cho-LTB4 is oxidised to 20cooh-LTB4 by CYP4F2/4F3"
xref: Reactome:R-HSA-2161979 "20cho-LTB4 is oxidised to 20cooh-LTB4 by ALDH"
+xref: RHEA:48672
is_a: GO:0004497 ! monooxygenase activity
[Term]
@@ -387474,7 +386978,7 @@ is_a: GO:0070784 ! regulation of growth of unicellular organism as a thread of a
id: GO:0097322
name: 7SK snRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 7SK small nuclear RNA (7SK snRNA)." [GOC:nhn, PMID:21853533]
+def: "Binding to a 7SK small nuclear RNA (7SK snRNA)." [GOC:nhn, PMID:21853533]
synonym: "7SK small nuclear RNA binding" EXACT []
is_a: GO:0017069 ! snRNA binding
@@ -387511,7 +387015,7 @@ id: GO:0097327
name: response to antineoplastic agent
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antineoplastic agent stimulus. An antineoplastic agent is a substance that inhibits or prevents the proliferation of neoplasms." [GOC:pr]
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0097328
@@ -387550,7 +387054,7 @@ id: GO:0097332
name: response to antipsychotic drug
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antipsychotic drug stimulus. Antipsychotic drugs are agents that control agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect." [GOC:pr]
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0097333
@@ -387665,7 +387169,6 @@ name: mitochondrial outer membrane permeabilization
namespace: biological_process
def: "The process by which the mitochondrial outer membrane becomes permeable to the passing of proteins and other molecules from the intermembrane space to the cytosol as part of the apoptotic signaling pathway." [GOC:BHF, GOC:mtg_apoptosis, GOC:pg, PMID:21041309]
comment: BAX and BAK are involved in this process, as reviewed in PMID:21760595 (the human proteins have UniProt symbols Q07812 and Q16611 respectively).
-synonym: "mitochondrial outer membrane permeabilization" BROAD []
synonym: "mitochondrial outer membrane permeabilization during apoptotic cell death" BROAD []
synonym: "mitochondrion outer membrane permeabilization" EXACT []
synonym: "MOMP" EXACT []
@@ -387704,10 +387207,12 @@ relationship: part_of GO:0001780 ! neutrophil homeostasis
[Term]
id: GO:0097351
-name: toxin-antitoxin pair type II binding
+name: toxin sequestering activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a toxic protein, disabling its function. There may be more than one antitoxin to a toxic protein. Instances of this activity are known only in prokaryotes, where the toxic protein may be a ribonuclease, a DNA gyrase, or other." [GOC:rs, PMID:19143615, PMID:19325885, PMID:21819231, PMID:22545240, Wikipedia:Toxin-antitoxin_system#Type_II]
-is_a: GO:0005515 ! protein binding
+def: "Binding to a toxic protein, disabling its function. There may be more than one antitoxin to a toxic protein. Instances of this activity are known only in prokaryotes, where the toxic protein may be a ribonuclease, a DNA gyrase, or other." [GOC:rs, PMID:19143615, PMID:19325885, PMID:21819231, PMID:22545240, PMID:24806488, Wikipedia:Toxin-antitoxin_system#Type_II]
+synonym: "toxin-antitoxin pair type I binding" NARROW []
+synonym: "toxin-antitoxin pair type II binding" NARROW []
+is_a: GO:0140313 ! molecular sequestering activity
[Term]
id: GO:0097352
@@ -387827,13 +387332,13 @@ comment: Note that this term is in the subset of terms that should not be used f
subset: gocheck_do_not_manually_annotate
synonym: "response to bronchodilator agent" EXACT []
synonym: "response to broncholytic agent" RELATED []
-is_a: GO:0042493 ! response to drug
+is_a: GO:0042221 ! response to chemical
[Term]
id: GO:0097367
name: carbohydrate derivative binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a carbohydrate derivative." [GOC:pr]
+def: "Binding to a carbohydrate derivative." [GOC:pr]
subset: goslim_agr
subset: goslim_mouse
is_a: GO:0005488 ! binding
@@ -387860,14 +387365,14 @@ is_a: GO:1901135 ! carbohydrate derivative metabolic process
id: GO:0097371
name: MDM2/MDM4 family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any isoform of the MDM2/MDM4 protein family, comprising negative regulators of p53." [InterPro:IPR016495]
+def: "Binding to a member of the MDM2/MDM4 protein family, comprising negative regulators of p53." [InterPro:IPR016495]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0097372
name: NAD-dependent histone deacetylase activity (H3-K18 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 18) + H2O = histone H3 L-lysine (position 18) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 18 of the histone H3 protein." [EC:3.5.1.17, GOC:sp, PMID:22722849, RHEA:24548]
+def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 18) + H2O = histone H3 L-lysine (position 18) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 18 of the histone H3 protein." [GOC:sp, PMID:22722849, PMID:28450737]
is_a: GO:0017136 ! NAD-dependent histone deacetylase activity
is_a: GO:0034739 ! histone deacetylase activity (H4-K16 specific)
@@ -388050,7 +387555,8 @@ name: telomeric repeat-containing RNA transcription
namespace: biological_process
def: "The synthesis of telomeric repeat-containing RNA from a DNA template. A telomere is a complex of DNA and proteins that seals the end of a chromosome." [GOC:al, PMID:22139915]
synonym: "TERRA transcription" EXACT [PMID:22139915]
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0034660 ! ncRNA metabolic process
+is_a: GO:0098781 ! ncRNA transcription
[Term]
id: GO:0097394
@@ -388179,8 +387685,7 @@ id: GO:0097410
name: hippocampal interneuron differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a hippocampal interneuron." [CL:1001569, GOC:jc, PMID:19655320]
-is_a: GO:0021879 ! forebrain neuron differentiation
-is_a: GO:0021895 ! cerebral cortex neuron differentiation
+is_a: GO:0030182 ! neuron differentiation
relationship: part_of GO:0021766 ! hippocampus development
[Term]
@@ -388361,7 +387866,6 @@ id: GO:0097430
name: copper ion import across prospore membrane
namespace: biological_process
def: "The directed movement of copper ions from outside of a cell, across an ascospore-type prospore membrane and into the cytosol." [GOC:al, GOC:vw, PMID:21828039]
-synonym: "copper ion import across prospore membrane" EXACT []
synonym: "copper ion import into ascospore-type prospore" RELATED []
synonym: "copper ion transport into forespores" RELATED []
is_a: GO:0015677 ! copper ion import
@@ -388381,8 +387885,6 @@ name: hippocampal pyramidal neuron differentiation
namespace: biological_process
def: "The process in which a relatively unspecialized cell acquires specialized features of a hippocampal pyramidal neuron, a pyramidal cell of the hippocampus." [CL:1001571, GOC:jc, PMID:19342486]
is_a: GO:0021859 ! pyramidal neuron differentiation
-is_a: GO:0021879 ! forebrain neuron differentiation
-is_a: GO:0021895 ! cerebral cortex neuron differentiation
[Term]
id: GO:0097433
@@ -388832,7 +388334,6 @@ id: GO:0097487
name: multivesicular body, internal vesicle
namespace: cellular_component
def: "A membrane-bounded vesicle wholly contained within a multivesicular body." [GOC:pde, PMID:21183070]
-is_a: GO:0030659 ! cytoplasmic vesicle membrane
is_a: GO:0031410 ! cytoplasmic vesicle
relationship: part_of GO:0005771 ! multivesicular body
@@ -388841,7 +388342,7 @@ id: GO:0097488
name: multivesicular body, internal vesicle membrane
namespace: cellular_component
def: "The lipid bilayer surrounding a multivesicular body internal vesicle." [GOC:pde, PMID:21183070]
-is_a: GO:0012506 ! vesicle membrane
+is_a: GO:0030659 ! cytoplasmic vesicle membrane
is_a: GO:0098588 ! bounding membrane of organelle
relationship: part_of GO:0097487 ! multivesicular body, internal vesicle
@@ -389380,19 +388881,18 @@ is_a: GO:0009838 ! abscission
[Term]
id: GO:0097549
-name: chromatin organization involved in negative regulation of transcription
+name: obsolete chromatin organization involved in negative regulation of transcription
namespace: biological_process
alt_id: GO:1903758
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription by chromatin organization." [GOC:di, PMID:23123093]
-subset: gocheck_do_not_manually_annotate
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription by chromatin organization." [GOC:di, PMID:23123093]
+comment: This term was obsoleted because these it was redundant with other terms: heterochromatin assembly and negative regulation of gene expression, epigenetic.
synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter by histone modification" NARROW [GOC:TermGenie]
synonym: "negative regulation of global transcription from Pol II promoter by histone modification" NARROW [GOC:TermGenie]
synonym: "negative regulation of transcription by chromatin organization" EXACT []
synonym: "negative regulation of transcription from Pol II promoter by histone modification" NARROW [GOC:TermGenie]
synonym: "negative regulation of transcription from RNA polymerase II promoter by histone modification" NARROW []
synonym: "negative regulation of transcription from RNA polymerase II promoter, global by histone modification" NARROW [GOC:TermGenie]
-is_a: GO:0034401 ! chromatin organization involved in regulation of transcription
-relationship: part_of GO:0045892 ! negative regulation of transcription, DNA-templated
+is_obsolete: true
[Term]
id: GO:0097550
@@ -389402,7 +388902,6 @@ def: "A protein-DNA complex composed of proteins binding promoter DNA to form th
synonym: "DNA-templated transcriptional preinitiation complex" EXACT []
synonym: "PIC" NARROW []
synonym: "preinitiation complex" NARROW []
-synonym: "transcription preinitiation complex" EXACT []
synonym: "transcriptional pre-initiation complex" EXACT []
synonym: "transcriptional preinitiation complex" EXACT []
is_a: GO:0032993 ! protein-DNA complex
@@ -389861,7 +389360,7 @@ comment: Due to the asymmetric nature of the Giardia trophozoite, this term is d
synonym: "adhesive disc" RELATED []
synonym: "ventral adhesive disc" EXACT []
synonym: "ventral disk" RELATED []
-is_a: GO:0043226 ! organelle
+is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
[Term]
id: GO:0097598
@@ -389869,7 +389368,7 @@ name: sperm cytoplasmic droplet
namespace: cellular_component
def: "A small amount of cytoplasm surrounded by a cell membrane that is generally retained in spermatozoa after spermiogenesis, when the majority of the cytoplasm is phagocytosed by Sertoli cells to produce what are called residual bodies. Initially, the droplet is located at the neck just behind the head of an elongated spermatid. During epididymal transit, the cytoplasmic droplet migrates caudally to the annulus at the end of the midpiece; the exact position and time varies by species. The cytoplasmic droplet consists of lipids, lipoproteins, RNAs, a variety of hydrolytic enzymes, receptors, ion channels, and Golgi-derived vesicles. The droplet may be involved in regulatory volume loss (RVD) at ejaculation, and in most species, though not in humans, the cytoplasmic droplet is lost at ejaculation. Note that the cytoplasmic droplet is distinct from 'excessive residual cytoplasm' that sometimes remains in epididymal spermatozoa, particularly when spermiogenesis has been disrupted." [GOC:krc, GOC:vesicles, PMID:12672117, PMID:21076437, PMID:23159014]
synonym: "sperm residual cytoplasm" EXACT []
-is_a: GO:0097708 ! intracellular vesicle
+is_a: GO:0031410 ! cytoplasmic vesicle
[Term]
id: GO:0097599
@@ -389900,7 +389399,7 @@ is_a: GO:0001895 ! retina homeostasis
id: GO:0097602
name: cullin family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the cullin family, hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3)." [GOC:ha, InterPro:IPR016158, PMID:18698375]
+def: "Binding to a member of the cullin family, hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3)." [GOC:ha, InterPro:IPR016158, PMID:18698375]
synonym: "cullin binding" NARROW []
is_a: GO:0005515 ! protein binding
@@ -390044,16 +389543,6 @@ def: "Any process in which an organism activates, maintains or increases the fre
synonym: "positive regulation by host of bacterial type IV pilus-dependent motility" EXACT []
is_a: GO:0097615 ! modulation by host of symbiont type IV pilus-dependent motility
-[Term]
-id: GO:0097617
-name: annealing activity
-namespace: molecular_function
-def: "A nucleic acid binding activity that brings together complementary sequences of nucleic acids so that they pair by hydrogen bonds to form a double-stranded polynucleotide." [GOC:mba, Wikipedia:Nucleic_acid_thermodynamics#Annealing]
-comment: The term 'annealing' is often used to describe the binding of a DNA probe, or the binding of a primer to a DNA strand during a polymerase chain reaction. The term is also often used to describe the reformation (renaturation) of complementary strands that were separated by heat (thermally denatured). For example, proteins such as RAD52 can help DNA anneal. If at all possible, please annotate to the more specific terms GO:0036310 'annealing helicase activity', GO:0097098 'DNA/RNA hybrid annealing activity' or GO:0033592 'RNA strand annealing activity'.
-synonym: "renaturation" RELATED []
-xref: Reactome:R-HSA-5686642 "RAD52 promotes single strand annealing at resected DNA DSBs"
-is_a: GO:0003676 ! nucleic acid binding
-
[Term]
id: GO:0097618
name: dinoflagellate sulcal notch
@@ -390087,9 +389576,10 @@ is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors
id: GO:0097621
name: monoamine oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: RCH2NHR' + H2O + O2 = RCHO + R'NH2 + H2O2." [EC:1.4.3.4, GOC:pr, RHEA:26414]
+def: "Catalysis of the reaction: RCH2NHR' + H2O + O2 = RCHO + R'NH2 + H2O2." [GOC:pr, RHEA:26414]
comment: Acts on primary amines, and also on some secondary and tertiary amines. It differs from EC:1.4.3.21, primary-amine oxidase as it can oxidize secondary and tertiary amines but not methylamine.
synonym: "amine:oxygen oxidoreductase (deaminating) activity" EXACT []
+xref: EC:1.4.3.4
xref: RHEA:26414
is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
@@ -390255,8 +389745,11 @@ alt_id: GO:1902765
def: "The directed movement of L-arginine from outside of a cell, across the plasma membrane and into the cytosol." [GOC:krc, PMID:8195186]
synonym: "arginine import" BROAD []
synonym: "L-arginine import into cell" EXACT []
+is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:1903400 ! L-arginine transmembrane transport
+is_a: GO:0098655 ! cation transmembrane transport
+is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
id: GO:0097639
@@ -390307,14 +389800,14 @@ is_a: GO:0097642 ! calcitonin family receptor activity
id: GO:0097644
name: calcitonin family binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs))." [GOC:bhm, InterPro:IPR021116, PMID:10871296, PMID:12037140, PMID:18687416]
+def: "Binding to a member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs))." [GOC:bhm, InterPro:IPR021116, PMID:10871296, PMID:12037140, PMID:18687416]
is_a: GO:0017046 ! peptide hormone binding
[Term]
id: GO:0097645
name: amylin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with amylin." [GOC:bhm, PMID:10871296, PMID:12037140, PMID:18687416]
+def: "Binding to amylin." [GOC:bhm, PMID:10871296, PMID:12037140, PMID:18687416]
is_a: GO:0097644 ! calcitonin family binding
[Term]
@@ -390397,8 +389890,7 @@ is_a: GO:0031201 ! SNARE complex
id: GO:0097655
name: serpin family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the serpin protein family (serine protease inhibitors or classified inhibitor family I4). Serpins are a broadly distributed family of protease inhibitors that use a conformational change to inhibit target enzymes. They are central in controlling many important proteolytic cascades. The majority of serpins inhibit serine proteases, but serpins that inhibit caspases and papain-like cysteine proteases have also been identified. Rarely, serpins perform a non-inhibitory function; for example, several human serpins function as hormone transporters and certain serpins function as molecular chaperones or tumor suppressors." [GOC:mr, InterPro:IPR000215, PMID:16737556]
-synonym: "SERPIN family protein binding" EXACT []
+def: "Binding to a member of the serpin protein family (serine protease inhibitors or classified inhibitor family I4). Serpins are a broadly distributed family of protease inhibitors that use a conformational change to inhibit target enzymes. They are central in controlling many important proteolytic cascades. The majority of serpins inhibit serine proteases, but serpins that inhibit caspases and papain-like cysteine proteases have also been identified. Rarely, serpins perform a non-inhibitory function; for example, several human serpins function as hormone transporters and certain serpins function as molecular chaperones or tumor suppressors." [GOC:mr, InterPro:IPR000215, PMID:16737556]
is_a: GO:0005515 ! protein binding
[Term]
@@ -390439,6 +389931,7 @@ comment: Note that this term is in the subset of terms that should not be used f
subset: gocheck_do_not_manually_annotate
subset: goslim_mouse
is_a: GO:0032774 ! RNA biosynthetic process
+relationship: part_of GO:0010467 ! gene expression
[Term]
id: GO:0097660
@@ -390566,7 +390059,7 @@ is_a: GO:0018027 ! peptidyl-lysine dimethylation
id: GO:0097677
name: STAT family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the signal transducers and activators of transcription (STAT) protein family. STATs are, as the name indicates, both signal transducers and transcription factors. STATs are activated by cytokines and some growth factors and thus control important biological processes including cell growth, cell differentiation, apoptosis and immune responses." [GOC:mr, InterPro:IPR001217, PMID:21447371, PMID:24470978]
+def: "Binding to a member of the signal transducers and activators of transcription (STAT) protein family. STATs are, as the name indicates, both signal transducers and transcription factors. STATs are activated by cytokines and some growth factors and thus control important biological processes including cell growth, cell differentiation, apoptosis and immune responses." [GOC:mr, InterPro:IPR001217, PMID:21447371, PMID:24470978]
synonym: "signal transducers and activators of transcription family protein binding" EXACT []
is_a: GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor binding
@@ -390574,7 +390067,7 @@ is_a: GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor b
id: GO:0097678
name: SOCS family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the suppressor of cytokine signaling (SOCS) family of proteins. SOCS represent an important mechanism to extinguish cytokine and growth factor receptor signaling. Individual SOCS proteins are typically induced by specific cytokines and growth factors, thereby generating a negative feedback loop. SOCS proteins have important functions in development and homeostasis, and in disease, particularly tumor suppression and anti-inflammatory functions." [GOC:mr, InterPro:IPR028413, PMID:23885323, PMID:24705897]
+def: "Binding to a member of the suppressor of cytokine signaling (SOCS) family of proteins. SOCS represent an important mechanism to extinguish cytokine and growth factor receptor signaling. Individual SOCS proteins are typically induced by specific cytokines and growth factors, thereby generating a negative feedback loop. SOCS proteins have important functions in development and homeostasis, and in disease, particularly tumor suppression and anti-inflammatory functions." [GOC:mr, InterPro:IPR028413, PMID:23885323, PMID:24705897]
synonym: "suppressor of cytokine signaling family protein binding" EXACT []
is_a: GO:0005515 ! protein binding
@@ -390665,7 +390158,7 @@ namespace: molecular_function
def: "Binds to and stops, prevents, or reduces the activity of an iron ion transmembrane transporter." [GOC:BHF, GOC:kom, PMID:15514116]
comment: An example of this is human hepcidin (UniProt symbol P81172), which regulates iron transport out of cells (see PMID:15514116).
synonym: "iron channel inhibitor activity" EXACT []
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0140678 ! molecular function inhibitor activity
[Term]
id: GO:0097691
@@ -390899,7 +390392,7 @@ is_a: GO:0150195 ! transport across blood-cerebrospinal fluid barrier
id: GO:0097718
name: disordered domain specific binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a disordered domain of a protein." [GOC:gg, PMID:11746698]
+def: "Binding to a disordered domain of a protein." [GOC:gg, PMID:11746698]
synonym: "disordered protein domain specific binding" RELATED []
is_a: GO:0019904 ! protein domain specific binding
@@ -390963,7 +390456,7 @@ is_a: GO:0034729 ! histone H3-K79 methylation
id: GO:0097726
name: LEM domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a LEM domain. The LEM domain (for lamina-associated polypeptide, emerin, MAN1 domain) is present in a group of nuclear proteins that bind chromatin through interaction of the LEM motif with the conserved DNA crosslinking protein, barrier-to-autointegration factor (BAF)." [GOC:rz, InterPro:IPR003887, PMID:22399800]
+def: "Binding to a LEM domain. The LEM domain (for lamina-associated polypeptide, emerin, MAN1 domain) is present in a group of nuclear proteins that bind chromatin through interaction of the LEM motif with the conserved DNA crosslinking protein, barrier-to-autointegration factor (BAF)." [GOC:rz, InterPro:IPR003887, PMID:22399800]
synonym: "lamina-associated polypeptide, emerin, MAN1 domain binding" EXACT []
synonym: "LAP2, emerin, MAN1 domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -391139,11 +390632,12 @@ is_a: GO:0097742 ! de novo centriole assembly
[Term]
id: GO:0097744
-name: urate salt excretion
+name: renal urate salt excretion
namespace: biological_process
-def: "The elimination by an organism of urate salt or uric acid." [GOC:jl, Wikipedia:Uric_acid#Biology]
+def: "The elimination of urate salt or uric acid from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine." [GOC:jl, PMID:25287933, PMID:3906799, Wikipedia:Renal_physiology#Secretion]
synonym: "urate excretion" BROAD []
-is_a: GO:0007588 ! excretion
+synonym: "urate salt excretion" BROAD []
+is_a: GO:0097254 ! renal tubular secretion
[Term]
id: GO:0097745
@@ -391316,7 +390810,6 @@ def: "The part of the viral terminase complex that contains the translocase and
comment: This term should only be used when the large subunit consists of more than one polypeptide.
synonym: "virus terminase, large subunit" EXACT []
is_a: GO:1902494 ! catalytic complex
-is_a: GO:1904949 ! ATPase complex
relationship: part_of GO:0043493 ! viral terminase complex
[Term]
@@ -391583,7 +391076,7 @@ is_obsolete: true
id: GO:0098505
name: G-rich strand telomeric DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with G-rich, single-stranded, telomere-associated DNA." [PMID:11349150]
+def: "Binding to G-rich, single-stranded, telomere-associated DNA." [PMID:11349150]
is_a: GO:0043047 ! single-stranded telomeric DNA binding
[Term]
@@ -391814,7 +391307,6 @@ namespace: cellular_component
def: "A transmembrane protein complex that functions in ATPase dependent active transport across a membrane." [GOC:dos]
comment: The location of this complex is implicit in its activity, so its location is asserted as a regular relationship rather than as a part of an intersection.
is_a: GO:1902495 ! transmembrane transporter complex
-is_a: GO:1904949 ! ATPase complex
[Term]
id: GO:0098534
@@ -391822,7 +391314,7 @@ name: centriole assembly
namespace: biological_process
def: "A cellular process that results in the assembly of one or more centrioles." [GOC:dos, PMID:24075808]
is_a: GO:0031023 ! microtubule organizing center organization
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:0098535
@@ -391898,12 +391390,12 @@ name: defense response to other organism
namespace: biological_process
alt_id: GO:0009814
def: "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." [GOC:dos]
+subset: goslim_generic
synonym: "defence response incompatible interaction" NARROW []
synonym: "defence response to pathogen, incompatible interaction" NARROW []
synonym: "defense response, incompatible interaction" NARROW []
synonym: "resistance response to pathogen" NARROW []
is_a: GO:0006952 ! defense response
-is_a: GO:0006955 ! immune response
is_a: GO:0051707 ! response to other organism
[Term]
@@ -391933,17 +391425,6 @@ def: "Any process in which a protein complex is maintained in a specific locatio
is_a: GO:0051651 ! maintenance of location in cell
is_a: GO:0098544 ! maintenance of protein complex location
-[Term]
-id: GO:0098546
-name: 2',5-3',5'-cyclic GMP-AMP binding
-namespace: molecular_function
-def: "Interacting selectively and non-covalently with c[G(2',5')pA(2',5')p], a cyclic purine dinucleotide that consists of AMP and GMP units cyclized via 2',5' and 3',5' linkages." [GOC:dos, PMID:23910378]
-synonym: "c[G(2',5')pA(3',5')p] binding" EXACT [PMID:23910378]
-is_a: GO:0030551 ! cyclic nucleotide binding
-is_a: GO:0032559 ! adenyl ribonucleotide binding
-is_a: GO:0032561 ! guanyl ribonucleotide binding
-is_a: GO:0043168 ! anion binding
-
[Term]
id: GO:0098547
name: lumenal side of Golgi membrane
@@ -392578,9 +392059,12 @@ is_a: GO:0016651 ! oxidoreductase activity, acting on NAD(P)H
id: GO:0098627
name: protein arginine phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein arginine phosphate + H2O = protein arginine + phosphate." [PMID:23770242]
+def: "Catalysis of the reaction: protein arginine phosphate + H2O = protein arginine + phosphate." [PMID:23770242, RHEA:43380]
comment: Made part of peptidyl-N-phospho-arginine phosphatase activity on the assumption that arginine phosphorylation in proteins occurs via an N link.
+xref: EC:3.9.1.2
+xref: RHEA:43380
is_a: GO:0004721 ! phosphoprotein phosphatase activity
+is_a: GO:0016825 ! hydrolase activity, acting on acid phosphorus-nitrogen bonds
[Term]
id: GO:0098628
@@ -392609,6 +392093,7 @@ id: GO:0098631
name: cell adhesion mediator activity
namespace: molecular_function
def: "The binding by a cell-adhesion protein on a cell surface to an adhesion molecule on another cell surface, to mediate adhesion of the cell to the external substrate or to another cell." [GOC:vw, Wikipedia:Cell_adhesion]
+subset: goslim_generic
synonym: "cell adhesion molecule" EXACT []
synonym: "protein binding involved in cell adhesion" EXACT []
is_a: GO:0050839 ! cell adhesion molecule binding
@@ -392626,7 +392111,7 @@ is_a: GO:0098631 ! cell adhesion mediator activity
id: GO:0098633
name: collagen fibril binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a collagen fibril." [GOC:dos, PMID:21421911]
+def: "Binding to a collagen fibril." [GOC:dos, PMID:21421911]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -392764,7 +392249,7 @@ is_obsolete: true
id: GO:0098650
name: peptidyl-proline 4-dioxygenase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a peptidyl-proline 4-dioxygenase." [GOC:dos, GOC:kvm]
+def: "Binding to a peptidyl-proline 4-dioxygenase." [GOC:dos, GOC:kvm]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -392947,10 +392432,12 @@ is_a: GO:0046813 ! receptor-mediated virion attachment to host cell
[Term]
id: GO:0098672
-name: evasion by virus of CRISPR-cas system
+name: inhibition of host CRISPR-cas system by virus
namespace: biological_process
-def: "Any process, either active or passive, by which a virus evades the CRISPR-cas system of its host. Some viruses can directly suppress the CRISPR system." [PMID:23242138, PMID:23446421, PMID:26416740, VZ:3962]
+def: "A process by which a virus inhibits the CRISPR-cas system of its host." [PMID:23242138, PMID:23446421, PMID:26416740]
+synonym: "anti-CRISPR" BROAD []
synonym: "CRISPR-cas system evasion by virus" EXACT [VZ:3962]
+synonym: "evasion by virus of CRISPR-cas system" RELATED []
xref: VZ:3962
is_a: GO:0019049 ! mitigation of host defenses by virus
@@ -393347,7 +392834,7 @@ alt_id: GO:1990122
def: "The directed movement of leucine from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos]
synonym: "L-leucine import into cell" NARROW [GOC:mah]
synonym: "leucine import into cell" EXACT []
-is_a: GO:0015803 ! branched-chain amino acid transport
+is_a: GO:0015820 ! leucine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
[Term]
@@ -393628,14 +393115,14 @@ id: GO:0098749
name: cerebellar neuron development
namespace: biological_process
def: "The process whose specific outcome is the progression of a cerebellar neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." [GOC:dos]
-is_a: GO:0021954 ! central nervous system neuron development
+is_a: GO:0048666 ! neuron development
relationship: part_of GO:0021549 ! cerebellum development
[Term]
id: GO:0098750
name: FYXD domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a FXYD domain." [GOC:dos, GOC:mr, PMID:10950925, PMID:16403837, PMID:18000745]
+def: "Binding to a FXYD domain." [GOC:dos, GOC:mr, PMID:10950925, PMID:16403837, PMID:18000745]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -393670,6 +393157,7 @@ id: GO:0098754
name: detoxification
namespace: biological_process
def: "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." [GOC:dos]
+subset: goslim_generic
subset: goslim_pombe
is_a: GO:0008150 ! biological_process
relationship: part_of GO:0009636 ! response to toxic substance
@@ -393799,14 +393287,14 @@ is_a: GO:0098764 ! meiosis I cell cycle phase
id: GO:0098769
name: TIMP family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the Tissue inhibitors of metalloproteinases (TIMPs) family. TIMPs are endogenous protein regulators of the matrix metalloproteinase (MMPs) family." [PMID:22078297]
+def: "Binding to a member of the Tissue inhibitors of metalloproteinases (TIMPs) family. TIMPs are endogenous protein regulators of the matrix metalloproteinase (MMPs) family." [PMID:22078297]
is_a: GO:0005515 ! protein binding
[Term]
id: GO:0098770
name: FBXO family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the FBXO protein family. Members of this family have an F-box protein motif of approximately 50 amino acids that functions as a site of protein-protein interaction." [PMID:11178263]
+def: "Binding to a member of the FBXO protein family. Members of this family have an F-box protein motif of approximately 50 amino acids that functions as a site of protein-protein interaction." [PMID:11178263]
is_a: GO:0005515 ! protein binding
[Term]
@@ -393823,6 +393311,7 @@ namespace: molecular_function
def: "A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition." [GOC:dos, GOC:pt]
subset: gocheck_do_not_annotate
subset: goslim_flybase_ribbon
+subset: goslim_generic
is_a: GO:0003674 ! molecular_function
[Term]
@@ -394006,11 +393495,11 @@ relationship: part_of GO:0045202 ! synapse
[Term]
id: GO:0098795
-name: mRNA cleavage involved in gene silencing
+name: mRNA destabilization-mediated gene silencing
namespace: biological_process
-def: "Cleavage of an mRNA occurring as part of the mechanism of gene silencing." [GOC:BHF, GOC:BHF_miRNA, GOC:dos]
-is_a: GO:0006379 ! mRNA cleavage
-relationship: part_of GO:0016458 ! gene silencing
+def: "A gene silencing mechanism that involves the destabilization of an mRNA." [GOC:BHF, GOC:BHF_miRNA, GOC:dos]
+synonym: "mRNA cleavage involved in gene silencing" EXACT []
+is_a: GO:0016441 ! posttranscriptional gene silencing
[Term]
id: GO:0098796
@@ -394095,12 +393584,11 @@ relationship: part_of GO:0097730 ! non-motile cilium
[Term]
id: GO:0098806
-name: deadenylation involved in gene silencing by miRNA
+name: mRNA deadenylation-mediated gene silencing by miRNA
namespace: biological_process
def: "Shortening of the poly(A) tail of a nuclear-transcribed mRNA following miRNA binding to mRNA, resulting in destabilization of the mRNA and a reduction in the efficiency of its translation." [GOC:BHF, GOC:dos, PMID:21118121, PMID:23209154]
-is_a: GO:0000289 ! nuclear-transcribed mRNA poly(A) tail shortening
-is_a: GO:0061157 ! mRNA destabilization
-relationship: part_of GO:0035195 ! gene silencing by miRNA
+synonym: "deadenylation involved in gene silencing by miRNA" EXACT []
+is_a: GO:0035279 ! miRNA-mediated gene silencing by mRNA destabilization
[Term]
id: GO:0098807
@@ -394114,7 +393602,7 @@ relationship: part_of GO:0009535 ! chloroplast thylakoid membrane
id: GO:0098808
name: mRNA cap binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 7-methylguanosine (m7G) group or derivative located at the 5' end of an mRNA molecule." [GOC:dos]
+def: "Binding to a 7-methylguanosine (m7G) group or derivative located at the 5' end of an mRNA molecule." [GOC:dos]
is_a: GO:0000339 ! RNA cap binding
is_a: GO:0003729 ! mRNA binding
@@ -394138,7 +393626,7 @@ is_a: GO:0051649 ! establishment of localization in cell
id: GO:0098811
name: obsolete transcriptional repressor activity, RNA polymerase II activating transcription factor binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II activating transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription." [GOC:BHF, GOC:dos, GOC:rl, GOC:txnOH]
+def: "OBSOLETE. Binding to an RNA polymerase II activating transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription." [GOC:BHF, GOC:dos, GOC:rl, GOC:txnOH]
comment: The reason for obsoletion is that this concept is partly covered by other concepts in the ontology and usage has been inconsistent.
synonym: "RNA polymerase II activating transcription factor binding transcription factor activity involved in negative regulation of transcription" EXACT []
synonym: "RNA polymerase II activating transcription factor binding transcription repressor activity" EXACT []
@@ -394465,7 +393953,7 @@ is_a: GO:0120025 ! plasma membrane bounded cell projection
id: GO:0098847
name: sequence-specific single stranded DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with single-stranded DNA of a specific nucleotide composition." [PMID:9531483]
+def: "Binding to single-stranded DNA of a specific nucleotide composition." [PMID:9531483]
is_a: GO:0003697 ! single-stranded DNA binding
is_a: GO:0043565 ! sequence-specific DNA binding
@@ -394501,7 +393989,7 @@ relationship: part_of GO:0030672 ! synaptic vesicle membrane
id: GO:0098851
name: double-stranded miRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded miRNA. double-stranded miRNA is formed by processing of pre-miRNA stem-loop structures." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:19966796]
+def: "Binding to double-stranded miRNA. double-stranded miRNA is formed by processing of pre-miRNA stem-loop structures." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:19966796]
synonym: "miRNA duplex binding" EXACT []
is_a: GO:0003725 ! double-stranded RNA binding
@@ -394518,7 +394006,6 @@ id: GO:0098853
name: endoplasmic reticulum-vacuole membrane contact site
namespace: cellular_component
def: "A zone of apposition between endoplasmic-reticulum and lytic vacuole membranes, structured by bridging complexes." [GOC:dos, PMID:26283797]
-synonym: "endoplasmic reticulum-vacuole membrane contact site" EXACT []
synonym: "ER-vacuole membrane contact site" EXACT []
is_a: GO:0044232 ! organelle membrane contact site
@@ -395258,9 +394745,7 @@ id: GO:0098933
name: disruption by symbiont of host cell envelope
namespace: biological_process
def: "The process by which a symbiont breaks down the cell wall of its host. The host is defined as the larger of the organisms involved in a symbiotic interaction." [ISBN:0198547684]
-is_a: GO:0052008 ! disruption by symbiont of host cellular component
is_a: GO:0052020 ! modification by symbiont of host cell wall
-is_a: GO:0052339 ! disruption by organism of cell wall of other organism involved in symbiotic interaction
[Term]
id: GO:0098934
@@ -395349,8 +394834,8 @@ namespace: biological_process
def: "The directed movement of neurotransmitter receptor from the postsynaptic endosome in tranpsort vesicles to the lysosome for degradation." [GOC:dos]
subset: goslim_synapse
synonym: "postsynaptic neurotransmitter receptor endosomal trafficking" BROAD []
-is_a: GO:0007041 ! lysosomal transport
-is_a: GO:0016192 ! vesicle-mediated transport
+is_a: GO:0006886 ! intracellular protein transport
+is_a: GO:0008333 ! endosome to lysosome transport
is_a: GO:0061462 ! protein localization to lysosome
is_a: GO:0072666 ! establishment of protein localization to vacuole
is_a: GO:0099637 ! neurotransmitter receptor transport
@@ -396017,7 +395502,7 @@ is_a: GO:0039637 ! catabolism by virus of host DNA
id: GO:0099016
name: DNA end degradation evasion by virus
namespace: biological_process
-def: "Any process, either active or passive, by which a virus evades and ends degradation of its DNA when free viral-DNA ends are exposed as part of its life-cycle. For example, some bacteriophages encode proteins that bind to free viral DNA ends, protecting them from degradation by host exonucleases." [GOC:dos, VZ:3963]
+def: "A process by which a virus evades and ends degradation of its DNA when free viral-DNA ends are exposed as part of its life-cycle. For example, some bacteriophages encode proteins that bind to free viral DNA ends, protecting them from degradation by host exonucleases." [GOC:dos]
xref: VZ:3963
is_a: GO:0019049 ! mitigation of host defenses by virus
@@ -396514,6 +395999,7 @@ id: GO:0099074
name: mitochondrion to lysosome transport
namespace: biological_process
def: "Transport from the mitochondrion to the lysosome, mediated by mitochondrion-derived vesicles." [GOC:bc, GOC:pad, GOC:PARL-UCL, PMID:20619655]
+is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0007041 ! lysosomal transport
is_a: GO:0099075 ! mitochondrion-derived vesicle mediated transport
@@ -396522,7 +396008,6 @@ id: GO:0099075
name: mitochondrion-derived vesicle mediated transport
namespace: biological_process
def: "Transport from the mitochondrion, mediated by mitochondrion derived vesicles." [GOC:bc, GOC:pad, GOC:PARL-UCL, PMID:2061965, PMID:20619655]
-is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0016192 ! vesicle-mediated transport
[Term]
@@ -396543,7 +396028,7 @@ is_a: GO:0003677 ! DNA binding
id: GO:0099078
name: BORC complex
namespace: cellular_component
-def: "A protein complex that is invovled in positioning of the lysosome within the cytoplasm and which is composed of BLOC1S1, BLOC1S2, BORCS5, BORCS6, BORCS7, BORCS8, KXD1 and SNAPIN. The BORC complex recruits ARL8 at the cytosolic face of lysosomes and couples them to microtubule plus-end-directed kinesin motors." [GOC:dos, GOC:li, PMID:25898167]
+def: "A protein complex that is involved in positioning of the lysosome within the cytoplasm and which is composed of BLOC1S1, BLOC1S2, BORCS5, BORCS6, BORCS7, BORCS8, KXD1 and SNAPIN. The BORC complex recruits ARL8 at the cytosolic face of lysosomes and couples them to microtubule plus-end-directed kinesin motors." [GOC:dos, GOC:li, PMID:25898167]
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0005829 ! cytosol
@@ -396656,7 +396141,7 @@ name: postsynaptic specialization, intracellular component
namespace: cellular_component
def: "A network of proteins adjacent to the postsynaptic membrane. Its major components include the proteins that spatially and functionally organize neurotransmitter receptors in the adjacent membrane, such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components." [GOC:dos]
subset: goslim_synapse
-is_a: GO:0043228 ! non-membrane-bounded organelle
+is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
relationship: part_of GO:0099572 ! postsynaptic specialization
[Term]
@@ -396679,7 +396164,6 @@ synonym: "mitochondrial calcium release" EXACT []
is_a: GO:0006851 ! mitochondrial calcium ion transmembrane transport
is_a: GO:0051209 ! release of sequestered calcium ion into cytosol
is_a: GO:1901660 ! calcium ion export
-is_a: GO:1990542 ! mitochondrial transmembrane transport
[Term]
id: GO:0099094
@@ -396749,7 +396233,8 @@ name: channel activator activity
namespace: molecular_function
def: "Direct interaction with a channel (binding or modification), resulting in its opening. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel." [GOC:dos]
synonym: "channel gating activity" EXACT []
-is_a: GO:0003674 ! molecular_function
+is_a: GO:0016247 ! channel regulator activity
+is_a: GO:0140677 ! molecular function activator activity
[Term]
id: GO:0099104
@@ -396772,7 +396257,7 @@ id: GO:0099106
name: ion channel regulator activity
namespace: molecular_function
def: "Modulates the activity of a channel via direct interaction with it. A channel catalyzes energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel." [GOC:dos]
-is_a: GO:0003674 ! molecular_function
+is_a: GO:0016247 ! channel regulator activity
[Term]
id: GO:0099107
@@ -396848,7 +396333,6 @@ synonym: "subtelomere" EXACT []
synonym: "subtelomeric heterochromatin" RELATED []
xref: SO:0001997
is_a: GO:0000781 ! chromosome, telomeric region
-is_a: GO:0000792 ! heterochromatin
[Term]
id: GO:0099116
@@ -396886,8 +396370,10 @@ is_a: GO:0061542 ! 3-demethylubiquinol-n 3-O-methyltransferase activity
id: GO:0099120
name: socially cooperative development
namespace: biological_process
-def: "Development a structure consisting of multiple co-operating unicellular organisms of the same species. Examples include sorocarp development in Dictystelia and co-operative colonial structures formed by Myxococcus xanthus for the purpose of predation and fruiting body formation." [PMID:12448714]
+alt_id: GO:0090702
+def: "The process whose specific outcome is the progression of a non-reproductive fruiting body over time, from its formation to the mature structure. A non-reproductive fruiting body is a colonial multicellular structure consisting of co-operating unicellular organisms, some of which are spores. An example of such a process is found in Dictyostelium discoideum and Myxococcus xanthus colonies." [GOC:pf, PMID:12448714]
synonym: "colonial development" EXACT []
+synonym: "non-reproductive fruiting body development" RELATED []
synonym: "socially co-operative development" EXACT []
is_a: GO:0048856 ! anatomical structure development
is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms
@@ -396903,7 +396389,7 @@ is_a: GO:0048608 ! reproductive structure development
id: GO:0099122
name: RNA polymerase II C-terminal domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. The CTD is comprised of repeats of a heptapeptide with the consensus sequence YSPTSPS. The number of repeats varies with the species and a minimum number of repeats is required for RNAP II function." [PMID:20889714]
+def: "Binding to the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. The CTD is comprised of repeats of a heptapeptide with the consensus sequence YSPTSPS. The number of repeats varies with the species and a minimum number of repeats is required for RNAP II function." [PMID:20889714]
synonym: "RNAP II C-terminal binding" EXACT []
is_a: GO:0000993 ! RNA polymerase II complex binding
@@ -396951,10 +396437,11 @@ relationship: part_of GO:0062023 ! collagen-containing extracellular matrix
[Term]
id: GO:0099127
-name: envenomation resulting in positive regulation of argininosuccinate synthase activity in other organism
+name: envenomation resulting in positive regulation of argininosuccinate synthase activity in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with the activation of the cytosolic argininosuccinate synthase in the bitten organism." [PMID:19491403]
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+synonym: "envenomation resulting in positive regulation of argininosuccinate synthase activity in other organism" EXACT []
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0099128
@@ -396974,7 +396461,7 @@ is_a: GO:0006928 ! movement of cell or subcellular component
id: GO:0099130
name: estrogen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any estrogen." [GOC:dos]
+def: "Binding to an estrogen." [GOC:dos]
is_a: GO:0042562 ! hormone binding
[Term]
@@ -397000,7 +396487,6 @@ name: chimeric non-reproductive fruiting body development
namespace: biological_process
def: "Development of a non-reproductive fruiting body formed by aggregation of cells with different genotypes." [PMID:18272966]
subset: gocheck_do_not_manually_annotate
-is_a: GO:0090702 ! non-reproductive fruiting body development
is_a: GO:0099135 ! chimeric colonial development
[Term]
@@ -397233,7 +396719,9 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of presynaptic dense core granule exocytosis." [GOC:dos, PMID:17881523]
subset: goslim_synapse
synonym: "regulation of presynaptic dense core vesicle exocytosis" EXACT syngo_official_label []
+is_a: GO:0099171 ! presynaptic modulation of chemical synaptic transmission
is_a: GO:1903233 ! regulation of calcium ion-dependent exocytosis of neurotransmitter
+is_a: GO:1905413 ! regulation of dense core granule exocytosis
relationship: regulates GO:0099525 ! presynaptic dense core vesicle exocytosis
[Term]
@@ -397764,7 +397252,6 @@ id: GO:0099519
name: dense core granule cytoskeletal transport
namespace: biological_process
def: "The directed movement of dense core granules along cytoskeletal fibers, such as microtubules or actin filaments." [GOC:kmv, PMID:23358451]
-synonym: "dense core granule cytoskeletal transport" EXACT []
synonym: "dense core vesicle cytoskeletal trafficking" EXACT []
is_a: GO:0099518 ! vesicle cytoskeletal trafficking
is_a: GO:1901950 ! dense core granule transport
@@ -397790,9 +397277,11 @@ is_a: GO:0042625 ! ATPase-coupled ion transmembrane transporter activity
[Term]
id: GO:0099522
-name: region of cytosol
+name: cytosolic region
namespace: cellular_component
def: "Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol." [GOC:dos]
+subset: gocheck_do_not_annotate
+synonym: "region of cytosol" EXACT []
is_a: GO:0005829 ! cytosol
[Term]
@@ -397801,7 +397290,7 @@ name: presynaptic cytosol
namespace: cellular_component
def: "The region of the cytosol consisting of all cytosol that is part of the presynapse." [GOC:dos]
subset: goslim_synapse
-is_a: GO:0099522 ! region of cytosol
+is_a: GO:0099522 ! cytosolic region
relationship: part_of GO:0098793 ! presynapse
[Term]
@@ -397810,7 +397299,7 @@ name: postsynaptic cytosol
namespace: cellular_component
def: "The region of the cytosol consisting of all cytosol that is part of the postsynapse." [GOC:dos]
subset: goslim_synapse
-is_a: GO:0099522 ! region of cytosol
+is_a: GO:0099522 ! cytosolic region
relationship: part_of GO:0098794 ! postsynapse
[Term]
@@ -397921,6 +397410,7 @@ id: GO:0099536
name: synaptic signaling
namespace: biological_process
def: "Cell-cell signaling to, from or within a synapse." [GOC:dos]
+subset: goslim_drosophila
subset: goslim_synapse
is_a: GO:0007267 ! cell-cell signaling
@@ -398220,6 +397710,7 @@ id: GO:0099568
name: cytoplasmic region
namespace: cellular_component
def: "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm." [GOC:dos]
+subset: gocheck_do_not_annotate
is_a: GO:0005737 ! cytoplasm
[Term]
@@ -398441,7 +397932,7 @@ id: GO:0099602
name: neurotransmitter receptor regulator activity
namespace: molecular_function
def: "A molecular function that directly (via physical interaction or direct modification) activates, inhibits or otherwise modulates the activity of a neurotransmitter receptor. Modulation of activity includes changes in desensitization rate, ligand affinity, ion selectivity and pore-opening/closing." [GOC:dos, PMID:12740117, PMID:18387948]
-is_a: GO:0003674 ! molecular_function
+is_a: GO:0030545 ! signaling receptor regulator activity
[Term]
id: GO:0099604
@@ -398489,7 +397980,7 @@ relationship: regulates GO:0098874 ! spike train
id: GO:0099609
name: microtubule lateral binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the side of a microtubule." [GOC:dos]
+def: "Binding to the side of a microtubule." [GOC:dos]
is_a: GO:0008017 ! microtubule binding
[Term]
@@ -398686,7 +398177,6 @@ name: postsynaptic endocytic zone cytoplasmic component
namespace: cellular_component
def: "The cytoplasmic component of the postsynaptic endocytic zone." [GOC:dos]
subset: goslim_synapse
-synonym: "postsynaptic endocytic zone cytoplasmic component" EXACT []
is_a: GO:0099738 ! cell cortex region
relationship: part_of GO:0098843 ! postsynaptic endocytic zone
@@ -398858,6 +398348,7 @@ id: GO:0099738
name: cell cortex region
namespace: cellular_component
def: "The complete extent of cell cortex that underlies some some region of the plasma membrane." [GOC:dos]
+subset: gocheck_do_not_annotate
synonym: "perimembrane region" EXACT []
is_a: GO:0005938 ! cell cortex
is_a: GO:0099568 ! cytoplasmic region
@@ -399447,7 +398938,6 @@ namespace: molecular_function
alt_id: GO:1904265
def: "Catalysis of the hydrolysis of ubiquitin from proteins." [GOC:mec]
comment: There are two main classes of deubiquitinating enzymes: cysteine proteases (i.e., thiol dependent) and metalloproteases.
-synonym: "deubiquitinase activity" EXACT []
synonym: "ubiquitinyl hydrolase activity" EXACT []
xref: Reactome:R-HSA-9674127 "USP30 deubiquitinates ATM dimer:Ub-p-PEX5"
is_a: GO:0019783 ! ubiquitin-like protein-specific protease activity
@@ -399457,9 +398947,13 @@ id: GO:0101006
name: protein histidine phosphatase activity
namespace: molecular_function
alt_id: GO:0008969
-def: "Catalysis of the reaction: protein histidine phosphate + H2O = protein histidine + phosphate." [GOC:mec]
+def: "Catalysis of the reaction: protein histidine phosphate + H2O = protein histidine + phosphate." [GOC:mec, RHEA:47964]
+comment: This eukaryotic enzyme dephosphorylates phosphorylated histidine residues within proteins and peptides. The enzyme acts on phosphate groups attached to both the pros- (RHEA:47964) and tele- (RHEA:47960) nitrogen atoms, but the pros- position is somewhat preferred (by a factor of two at the most) (EC:3.9.1.3).
synonym: "phosphohistidine phosphatase activity" BROAD []
+xref: EC:3.9.1.3
+xref: RHEA:47964
is_a: GO:0004721 ! phosphoprotein phosphatase activity
+is_a: GO:0016825 ! hydrolase activity, acting on acid phosphorus-nitrogen bonds
[Term]
id: GO:0101007
@@ -399526,7 +399020,7 @@ is_a: GO:0004721 ! phosphoprotein phosphatase activity
id: GO:0101016
name: FMN-binding domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the FMN-binding domain of a protein." [PMID:15752726]
+def: "Binding to the FMN-binding domain of a protein." [PMID:15752726]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -399737,7 +399231,7 @@ id: GO:0102025
name: ABC-type thiosulfate transporter activity
namespace: molecular_function
alt_id: GO:0032146
-def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + thiosulfate(out) = ADP + phosphate + thiosulfate(in)." [GOC:mlg, GOC:pz, RHEA:29871]
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + thiosulfate(out) = ADP + phosphate + thiosulfate(in)." [GOC:mlg, GOC:pz]
synonym: "ATPase-coupled thiosulfate transmembrane transporter activity" RELATED []
synonym: "thiosulfate transmembrane-transporting ATPase activity" RELATED []
synonym: "thiosulphate ABC transporter activity" EXACT []
@@ -399974,7 +399468,8 @@ is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
id: GO:0102054
name: maleylpyruvate hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-maleylpyruvate(2-) + H2O <=> H+ + maleate(2-) + pyruvate." [EC:3.7.1.-, GOC:pz]
+def: "Catalysis of the reaction: 3-maleylpyruvate(2-) + H2O <=> H+ + maleate(2-) + pyruvate." [GOC:pz, PMID:7400101, RHEA:47956]
+xref: EC:3.7.1.23
xref: MetaCyc:RXN-10447
xref: RHEA:47956
is_a: GO:0016823 ! hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances
@@ -400003,16 +399498,20 @@ is_a: GO:0008146 ! sulfotransferase activity
id: GO:0102057
name: jasmonoyl-valine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-valine + ATP(4-) + a jasmonic acid <=> AMP(2-) + diphosphoric acid + a jasmonoyl-valine." [EC:6.3.-.-, GOC:pz]
+def: "Catalysis of the reaction: L-valine + ATP(4-) + a jasmonic acid <=> AMP(2-) + diphosphoric acid + a jasmonoyl-valine." [GOC:pz, PMID:17291501]
+xref: EC:6.3.2.52
xref: MetaCyc:RXN-10457
+xref: RHEA:55772
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
[Term]
id: GO:0102058
name: jasmonoyl-leucine synthetase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-leucine + ATP(4-) + a jasmonic acid <=> AMP(2-) + diphosphoric acid + a jasmonoyl-leucine." [EC:6.3.-.-, GOC:pz]
+def: "Catalysis of the reaction: L-leucine + ATP(4-) + a jasmonic acid <=> AMP(2-) + diphosphoric acid + a jasmonoyl-leucine." [GOC:pz, PMID:17291501]
+xref: EC:6.3.2.52
xref: MetaCyc:RXN-10459
+xref: RHEA:55772
is_a: GO:0016879 ! ligase activity, forming carbon-nitrogen bonds
[Term]
@@ -400130,7 +399629,8 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0102070
name: 18-hydroxyoleate peroxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 18-hydroxyoleate + a lipid hydroperoxide <=> 9,10-epoxy-18-hydroxystearate + a lipid alcohol." [EC:1.11.-.-, GOC:pz]
+def: "Catalysis of the reaction: 18-hydroxyoleate + a lipid hydroperoxide <=> 9,10-epoxy-18-hydroxystearate + a lipid alcohol." [GOC:pz, PMID:12226220, PMID:14535881, PMID:468835]
+xref: EC:1.11.2.3
xref: MetaCyc:RXN-1064
is_a: GO:0016684 ! oxidoreductase activity, acting on peroxide as acceptor
@@ -400144,11 +399644,12 @@ is_a: GO:0016803 ! ether hydrolase activity
[Term]
id: GO:0102072
-name: 3-oxo-cis-Delta9-hexadecenoyl-[acp] reductase activity
+name: obsolete 3-oxo-cis-Delta9-hexadecenoyl-[acp] reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP + a 3R-hydroxy cis Delta9-hexadecenoyl-[acp] <=> NADPH + H+ + a 3-oxo-cis-Delta9-hexadecenoyl-[acp]." [EC:1.1.1.100, GOC:pz]
-xref: MetaCyc:RXN-10659
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+def: "OBSOLETE. Catalysis of the reaction: NADP + a 3R-hydroxy cis Delta9-hexadecenoyl-[acp] <=> NADPH + H+ + a 3-oxo-cis-Delta9-hexadecenoyl-[acp]." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate, and is beyond the specificity of GO.
+is_obsolete: true
+consider: GO:0004316
[Term]
id: GO:0102073
@@ -400562,7 +400063,8 @@ is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptid
id: GO:0102128
name: chalcone synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-dihydrocoumaroyl-CoA + 3 malonyl-CoA + 3 H+ = phloretin + 4 coenzyme A + 3 carbon dioxide." [EC:2.3.1.-, GOC:pz]
+def: "Catalysis of the reaction: 4-dihydrocoumaroyl-CoA + 3 malonyl-CoA + 3 H+ = phloretin + 4 coenzyme A + 3 carbon dioxide." [GOC:pz, PMID:20356611]
+xref: EC:2.3.1.74
xref: MetaCyc:RXN-11468
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
@@ -400578,21 +400080,21 @@ is_a: GO:0008168 ! methyltransferase activity
[Term]
id: GO:0102131
-name: 3-oxo-glutaryl-[acp] methyl ester reductase activity
+name: obsolete 3-oxo-glutaryl-[acp] methyl ester reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP + a 3R-hydroxyglutaryl-[acp] methyl ester <=> NADPH + H+ + a 3-oxo-glutaryl-[acp] methyl ester." [EC:1.1.1.100, GOC:pz]
-xref: EC:1.1.1.100
-xref: MetaCyc:RXN-11476
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+def: "OBSOLETE. Catalysis of the reaction: NADP + a 3R-hydroxyglutaryl-[acp] methyl ester <=> NADPH + H+ + a 3-oxo-glutaryl-[acp] methyl ester." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate, and is beyond the specificity of GO.
+is_obsolete: true
+consider: GO:0004316
[Term]
id: GO:0102132
-name: 3-oxo-pimeloyl-[acp] methyl ester reductase activity
+name: obsolete 3-oxo-pimeloyl-[acp] methyl ester reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: NADP + a 3R-hydroxypimeloyl-[acp] methyl ester <=> NADPH + H+ + a 3-oxo-pimeloyl-[acp] methyl ester." [EC:1.1.1.100, GOC:pz]
-xref: EC:1.1.1.100
-xref: MetaCyc:RXN-11480
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+def: "OBSOLETE. Catalysis of the reaction: NADP + a 3R-hydroxypimeloyl-[acp] methyl ester <=> NADPH + H+ + a 3-oxo-pimeloyl-[acp] methyl ester." [GOC:pz]
+comment: This term was obsoleted because it represents a specific substrate, and is beyond the specificity of GO.
+is_obsolete: true
+consider: GO:0004316
[Term]
id: GO:0102133
@@ -400914,7 +400416,8 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102169
name: pyocyanin hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-methylphenazine-1-carboxylate + NADH + O2 + 2 H+ <=> pyocyanin + NAD + carbon dioxide + H2O." [EC:1.14.13.-, GOC:pz]
+def: "Catalysis of the reaction: 5-methylphenazine-1-carboxylate + NADH + O2 + 2 H+ = pyocyanin + NAD + carbon dioxide + H2O." [GOC:pz, PMID:11591691]
+xref: EC:1.14.13.218
xref: MetaCyc:RXN-11898
xref: RHEA:48976
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
@@ -400978,7 +400481,8 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0102176
name: cycloeucalenone reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cycloeucalenone + NADPH + H+ <=> cycloeucalenol + NADP." [EC:1.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: cycloeucalenone + NADPH + H+ <=> cycloeucalenol + NADP." [GOC:pz, PMID:4387005]
+xref: EC:1.1.1.270
xref: MetaCyc:RXN-11929
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -400986,7 +400490,8 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0102177
name: 24-methylenelophenol methyl oxidase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 24-methylenelophenol + O2 + NADH + H+ <=> 4alpha-hydroxymethyl-ergosta-7,24(241)-dien-3beta-ol + NAD + H2O." [EC:1.14.13.-, GOC:pz]
+def: "Catalysis of the reaction: 24-methylenelophenol + O2 + NADH + H+ <=> 4alpha-hydroxymethyl-ergosta-7,24(241)-dien-3beta-ol + NAD + H2O." [GOC:pz, PMID:11707264, RHEA:58872]
+xref: EC:1.14.18.11
xref: MetaCyc:RXN-11930
xref: RHEA:58872
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
@@ -401147,7 +400652,8 @@ is_a: GO:0016881 ! acid-amino acid ligase activity
id: GO:0102196
name: cortisol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: cortisol + NADP <=> cortisone + NADPH + H+." [EC:1.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: cortisol + NADP <=> cortisone + NADPH + H+." [GOC:pz, PMID:16216911]
+xref: EC:1.1.1.146
xref: MetaCyc:RXN-12085
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -401411,7 +400917,7 @@ is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
id: GO:0102232
name: acrolein reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acrolein + NADPH + H+ <=> propanal + NADP." [EC:1.3.1.-, GOC:pz]
+def: "Catalysis of the reaction: acrolein + NADPH + H+ <=> propanal + NADP." [GOC:pz, PMID:21169366]
xref: MetaCyc:RXN-12281
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
@@ -401449,11 +400955,13 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors,
[Term]
id: GO:0102237
-name: ATP-dependent farnesol kinase activity
+name: ATP:farnesol kinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2-trans,6-trans)-farnesol + ATP(4-) <=> H+ + 2-trans,-6-trans-farnesyl monophosphate + ADP(3-)." [EC:2.7.1.-, GOC:pz]
+def: "Catalysis of the reaction: 2-trans,-6-trans-farnesol + ATP = 2-trans,-6-trans-farnesyl monophosphate + ADP + H+." [GOC:pz, RHEA:61656]
+synonym: "ATP-dependent farnesol kinase activity" RELATED []
xref: MetaCyc:RXN-12304
-is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
+xref: RHEA:61656
+is_a: GO:0052673 ! prenol kinase activity
[Term]
id: GO:0102238
@@ -401633,16 +401141,6 @@ def: "Catalysis of the reaction: H2O + a 1,2-diacyl-sn-glycerol = a monoglycerid
xref: MetaCyc:RXN-12434
is_a: GO:0052689 ! carboxylic ester hydrolase activity
-[Term]
-id: GO:0102260
-name: germacrene A alcohol dehydrogenase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: germacra-1(10),4,11(13)-trien-12-ol + 2 NADP + H2O <=> germacra-1(10),4,11(13)-trien-12-oate + 2 NADPH + 3 H+." [EC:1.1.1.314, GOC:pz]
-xref: EC:1.1.1.314
-xref: MetaCyc:RXN-12449
-xref: RHEA:30667
-is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
-
[Term]
id: GO:0102261
name: 8-hydroxy-5-deazaflavin:NADPH oxidoreductase activity
@@ -402057,7 +401555,8 @@ is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors,
id: GO:0102312
name: 4-coumaroyl 2'-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-coumaryl-CoA + 2-oxoglutarate + O2 <=> 2,4-dihydroxycinnamoyl-CoA + succinate + carbon dioxide." [EC:1.14.11.-, GOC:pz]
+def: "Catalysis of the reaction: 4-coumaryl-CoA + 2-oxoglutarate + O2 <=> 2,4-dihydroxycinnamoyl-CoA + succinate + carbon dioxide." [GOC:pz, PMID:22168819, PMID:22169019]
+xref: EC:1.14.11.62
xref: MetaCyc:RXN-12963
xref: RHEA:57868
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
@@ -402072,14 +401571,6 @@ xref: MetaCyc:RXN-12980
xref: RHEA:32543
is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
-[Term]
-id: GO:0102316
-name: L-dopa oxidase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: L-dopa + 0.5 O2 = L-dopaquinone + H2O." [EC:1.10.3.-, GOC:pz]
-xref: MetaCyc:RXN-13061
-is_a: GO:0016682 ! oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
-
[Term]
id: GO:0102317
name: 4-methylaminobutyrate oxidase (demethylating) activity
@@ -402134,18 +401625,16 @@ is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorp
id: GO:0102322
name: 2-propylphenol monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-propylphenol + O2 + NADH + H+ = 3-propylcatechol + H2O + NAD." [GOC:pz, RHEA:63524]
+def: "Catalysis of the reaction: 2-propylphenol + O2 + NADH + H+ = 3-propylcatechol + H2O + NAD." [GOC:pz]
xref: MetaCyc:RXN-13151
-xref: RHEA:63524
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0102323
name: 2-isopropylphenol monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-isopropylphenol + O2 + NADH + H+ = 3-isopropylcatechol + H2O + NAD." [GOC:pz, RHEA:63520]
+def: "Catalysis of the reaction: 2-isopropylphenol + O2 + NADH + H+ = 3-isopropylcatechol + H2O + NAD." [GOC:pz]
xref: MetaCyc:RXN-13152
-xref: RHEA:63520
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
@@ -402253,27 +401742,27 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0102336
name: 3-oxo-arachidoyl-CoA synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: stearoyl-CoA(4-) + malonyl-CoA(5-) + H+ <=> 3-oxoicosanoyl-CoA. + carbon dioxide + coenzyme A." [EC:2.3.1.199, GOC:pz]
-xref: EC:2.3.1.199
+def: "Catalysis of the reaction: stearoyl-CoA(4-) + malonyl-CoA(5-) + H+ <=> 3-oxoicosanoyl-CoA. + carbon dioxide + coenzyme A." [GOC:pz, RHEA:35319]
xref: MetaCyc:RXN-13294
+xref: RHEA:35319
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0102337
name: 3-oxo-cerotoyl-CoA synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: tetracosanoyl-CoA(4-) + malonyl-CoA(5-) + H+ <=> 3-oxohexacosanoyl-CoA + carbon dioxide + coenzyme A." [EC:2.3.1.199, GOC:pz]
-xref: EC:2.3.1.199
+def: "Catalysis of the reaction: tetracosanoyl-CoA(4-) + malonyl-CoA(5-) + H+ <=> 3-oxohexacosanoyl-CoA + carbon dioxide + coenzyme A." [GOC:pz, RHEA:36515]
xref: MetaCyc:RXN-13296
+xref: RHEA:36515
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0102338
name: 3-oxo-lignoceronyl-CoA synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: behenoyl-CoA(4-) + malonyl-CoA(5-) + H+ <=> 3-oxotetracosanoyl-CoA. + carbon dioxide + coenzyme A." [EC:2.3.1.199, GOC:pz]
-xref: EC:2.3.1.199
+def: "Catalysis of the reaction: behenoyl-CoA(4-) + malonyl-CoA(5-) + H+ <=> 3-oxotetracosanoyl-CoA. + carbon dioxide + coenzyme A." [GOC:pz, RHEA:36507]
xref: MetaCyc:RXN-13297
+xref: RHEA:36507
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
@@ -403608,7 +403097,7 @@ is_a: GO:0016758 ! hexosyltransferase activity
id: GO:0102501
name: D-fructuronate reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: D-mannonate + NADP = NADPH + H+ + D-fructuronate." [EC:1.1.1.-, GOC:pz]
+def: "Catalysis of the reaction: D-mannonate + NADP = NADPH + H+ + D-fructuronate." [GOC:pz, PMID:22925190]
xref: MetaCyc:RXN-14368
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
@@ -403760,7 +403249,7 @@ is_a: GO:0016791 ! phosphatase activity
id: GO:0102521
name: tRNA-4-demethylwyosine synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: pyruvate + S-adenosyl-L-methionine + N1-methylguanine37 in tRNAPhe = L-methionine + 5'-deoxyadenosine + carbon dioxide + H2O + 4-demethylwyosine37 in tRNAPhe." [GOC:pz, RHEA:36347]
+def: "Catalysis of the reaction: pyruvate + S-adenosyl-L-methionine + N1-methylguanine37 in tRNAPhe = L-methionine + 5'-deoxyadenosine + carbon dioxide + H2O + 4-demethylwyosine37 in tRNAPhe." [GOC:pz, PMID:34184886, RHEA:36347]
xref: EC:4.1.3.44
xref: MetaCyc:RXN-14516
xref: RHEA:36347
@@ -403859,8 +403348,9 @@ is_a: GO:0052689 ! carboxylic ester hydrolase activity
id: GO:0102531
name: ecdysteroid-phosphate phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + an ecdysteroid 22-phosphate <=> hydrogenphosphate + an ecdysteroid." [EC:3.1.3.-, GOC:pz]
+def: "Catalysis of the reaction: H2O + an ecdysteroid 22-phosphate = hydrogenphosphate + an ecdysteroid." [GOC:pz, PMID:12721294]
xref: MetaCyc:RXN-14734
+xref: RHEA:63576
is_a: GO:0016791 ! phosphatase activity
[Term]
@@ -404106,10 +403596,10 @@ is_a: GO:0008081 ! phosphoric diester hydrolase activity
id: GO:0102561
name: D-ribose 2,5-bisphosphate 2-phosphohydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + D-ribofuranose 2,5-bisphosphate <=> hydrogenphosphate + D-ribofuranose 5-phosphate." [EC:3.1.4.57, GOC:pz]
+def: "Catalysis of the reaction: H2O + D-ribofuranose 2,5-bisphosphate <=> hydrogenphosphate + D-ribofuranose 5-phosphate." [GOC:pz, RHEA:41616]
xref: EC:3.1.4.57
xref: MetaCyc:RXN-14996
-xref: RHEA:41617
+xref: RHEA:41616
is_a: GO:0008081 ! phosphoric diester hydrolase activity
[Term]
@@ -404147,24 +403637,6 @@ xref: EC:1.1.1.101
xref: MetaCyc:RXN-15046
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
-[Term]
-id: GO:0102567
-name: phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine)
-namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphocholine + hexadecanoate + H+." [EC:3.1.1.4, GOC:pz]
-xref: EC:3.1.1.4
-xref: MetaCyc:RXN-15065
-is_a: GO:0052689 ! carboxylic ester hydrolase activity
-
-[Term]
-id: GO:0102568
-name: phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)
-namespace: molecular_function
-def: "Catalysis of the reaction: 1-18:1-2-18:1-phosphatidylethanolamine + H2O = 1-oleoyl-sn-glycero-3-phosphoethanolamine + oleate + H+." [EC:3.1.1.4, GOC:pz]
-xref: EC:3.1.1.4
-xref: MetaCyc:RXN-15067
-is_a: GO:0052689 ! carboxylic ester hydrolase activity
-
[Term]
id: GO:0102569
name: FR-33289 synthase activity
@@ -404489,15 +403961,6 @@ def: "Catalysis of the reaction: tetracenomycin B3 + S-adenosyl-L-methionine <=
xref: MetaCyc:RXN-15435
is_a: GO:0008168 ! methyltransferase activity
-[Term]
-id: GO:0102609
-name: 9-beta-stemod-13(17)-ene oxidase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: stemod-13(17)-ene + 3 NADPH + 3 O2 + 3 H+ <=> 9beta-stemod-13(17)-en-19-oate + 3 NADP + 4 H2O." [EC:1.14.13.144, GOC:pz]
-xref: EC:1.14.13.144
-xref: MetaCyc:RXN-15437
-is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
-
[Term]
id: GO:0102610
name: (+)-secoisolariciresinol glucosyltransferase activity
@@ -404781,7 +404244,7 @@ is_a: GO:0016836 ! hydro-lyase activity
id: GO:0102645
name: 17(E)-cheilanthenediol synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 17(E)-cheilanthenediol <=> all-trans-geranylfarnesol + H2O." [EC:4.2.1.-, GOC:pz]
+def: "Catalysis of the reaction: 17(E)-cheilanthenediol <=> all-trans-geranylfarnesol + H2O." [GOC:pz, PMID:24200803]
xref: MetaCyc:RXN-15758
is_a: GO:0016836 ! hydro-lyase activity
@@ -405243,7 +404706,7 @@ is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
id: GO:0102702
name: 2-carene synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: geranyl diphosphate <=> (+)-2-carene + diphosphoric acid." [EC:4.2.3.-, GOC:pz]
+def: "Catalysis of the reaction: geranyl diphosphate <=> (+)-2-carene + diphosphoric acid." [GOC:pz, PMID:10700382]
xref: MetaCyc:RXN-5122
is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
@@ -407082,8 +406545,10 @@ is_a: GO:0008168 ! methyltransferase activity
id: GO:0102915
name: piperitol synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + (+)-pinoresinol + NADPH + O2 <=> (+)-piperitol + NADP + 2 H2O." [EC:1.14.13.-, GOC:pz]
+def: "Catalysis of the reaction: H+ + (+)-pinoresinol + NADPH + O2 <=> (+)-piperitol + NADP + 2 H2O." [GOC:pz, PMID:16785429, RHEA:56776]
+xref: EC:1.14.19.74
xref: MetaCyc:RXN-8695
+xref: RHEA:56776
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
@@ -407417,7 +406882,7 @@ is_a: GO:0016755 ! aminoacyltransferase activity
id: GO:0102954
name: dalcochinase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dalcochinin-8'-O-beta-glucoside + H2O <=> dalcochinin + D-glucopyranose." [EC:3.2.1.-, GOC:pz]
+def: "Catalysis of the reaction: dalcochinin-8'-O-beta-glucoside + H2O <=> dalcochinin + D-glucopyranose." [GOC:pz, PMID:16814564]
xref: MetaCyc:RXN-9162
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
@@ -407955,7 +407420,8 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
id: GO:0103023
name: ITPase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ITP + H2O <=> H+ + IDP + hydrogenphosphate." [EC:3.6.1.-, GOC:pz]
+def: "Catalysis of the reaction: ITP + H2O <=> H+ + IDP + hydrogenphosphate." [GOC:pz, PMID:16216582, RHEA:28330]
+xref: EC:3.6.1.73
xref: MetaCyc:RXN0-5073
xref: RHEA:28330
is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
@@ -408151,32 +407617,6 @@ def: "Catalysis of the reaction: isobutanol + NADP <=> isobutyraldehyde + NADPH
xref: MetaCyc:RXN0-7119
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
-[Term]
-id: GO:0103051
-name: N1-methyladenine demethylase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 1-methyladenine + O2 + 2-oxoglutarate <=> adenine + carbon dioxide + formaldehyde + succinate." [EC:1.14.11.33, GOC:pz]
-xref: MetaCyc:RXN0-984
-is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-
-[Term]
-id: GO:0103052
-name: N3-methylcytosine demethylase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: N3-methylcytosine + O2 + 2-oxoglutarate <=> H+ + cytosine + carbon dioxide + formaldehyde + succinate." [EC:1.14.11.33, GOC:pz]
-xref: MetaCyc:RXN0-985
-is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-
-[Term]
-id: GO:0103053
-name: 1-ethyladenine demethylase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: 1-ethyladenine + O2 + 2-oxoglutarate(2-) <=> adenine + carbon dioxide + acetaldehyde + succinate." [GOC:pz, RHEA:30299]
-xref: EC:1.14.11.33
-xref: MetaCyc:RXN0-986
-xref: RHEA:30299
-is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-
[Term]
id: GO:0103054
name: gibberellin A12, 2-oxoglutarate:oxygen oxidoreductase activity (gibberellin A15-forming)
@@ -408265,9 +407705,11 @@ is_a: GO:0016878 ! acid-thiol ligase activity
id: GO:0103064
name: inositol phosphorylceramide mannosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: GDP-alpha-D-mannose + an inositol-phospho-alpha hydroxyphytoceramide = H+ + GDP + a mannosyl-inositol-phospho-alpha hydroxyphytoceramide." [EC:2.4.1.-, GOC:pz]
+def: "Catalysis of the reaction: a 1D-myo-inositol-1-phospho-N-[(R)-2-hydroxy-very-long-chain fatty acyl]-(R)-4-hydroxysphingoid base + GDP-alpha-D-mannose = an alpha-D-mannosyl-(1,6)-1D-myo-inositol-1-phospho-N-[(R)-2-hydroxy-very-long-chain fatty acyl]-(R)-4-hydroxysphingoid base + GDP + H+." [GOC:pz, RHEA:64596]
+xref: EC:2.4.1.370
+xref: https://github.com/geneontology/go-ontology/issues/21803
xref: MetaCyc:RXN3O-663
-xref: RHEA:61496
+xref: RHEA:64596
is_a: GO:0016758 ! hexosyltransferase activity
[Term]
@@ -409118,10 +408560,11 @@ is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
[Term]
id: GO:0106054
-name: tRNA U34 thiol-transferase activity
+name: tRNA U34 sulfurtransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: uridine34 in tRNA + a [TusE sulfur carrier protein]-S-sulfanylcysteine + ATP + a reduced electron acceptor = a 2-thiouridine34 in tRNA + a [TusE sulfur carrier protein]-L-cysteine + AMP + an oxidized electron acceptor + diphosphate + H+." [PMID:12549933, PMID:16387657]
synonym: "tRNA U34 2-thiouridylase" EXACT []
+synonym: "tRNA U34 thiol-transferase activity" EXACT []
synonym: "tRNA-specific 2-thiouridylase" RELATED []
is_a: GO:0016783 ! sulfurtransferase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
@@ -409313,7 +408756,7 @@ is_a: GO:0106075 ! peptide N-succinyltransferase activity
id: GO:0106080
name: GATOR1 complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the GATOR1 complex." [PMID:28199306]
+def: "Binding to a GATOR1 complex." [PMID:28199306]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -409542,14 +408985,24 @@ relationship: positively_regulates GO:1901737 ! (R)-mevalonic acid biosynthetic
id: GO:0106110
name: vomitoxin biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of type B trichothecene vomitoxin, a poisonous substance produced by some species of fungi and predominantly occurs in grains such as wheat, barley and oats." [http://www.inchem.org/documents/jecfa/jecmono/v47je05.htm, https://doi.org/10.1007/BF03356188, PMID:19333439, PMID:25680507, PMID:25758923, PMID:8637056]
+def: "The chemical reactions and pathways resulting in the formation of type B trichothecene vomitoxin, also known as deoxynivalenol, a poisonous substance produced by some species of fungi and predominantly occurs in grains such as wheat, barley and oats." [http://www.inchem.org/documents/jecfa/jecmono/v47je05.htm, https://doi.org/10.1007/BF03356188, PMID:19333439, PMID:25680507, PMID:25758923, PMID:8637056]
synonym: "deoxynivalenol biosynthetic process" EXACT []
synonym: "DON biosynthetic process" EXACT []
synonym: "vomitoxin anabolism" EXACT []
synonym: "vomitoxin biosynthesis" EXACT []
synonym: "vomitoxin formation" EXACT []
synonym: "vomitoxin synthesis" EXACT []
+is_a: GO:0016106 ! sesquiterpenoid biosynthetic process
+is_a: GO:0018130 ! heterocycle biosynthetic process
+is_a: GO:0034309 ! primary alcohol biosynthetic process
+is_a: GO:0042181 ! ketone biosynthetic process
is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0046173 ! polyol biosynthetic process
+is_a: GO:0097176 ! epoxide metabolic process
+is_a: GO:0120255 ! olefinic compound biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_a: GO:1901503 ! ether biosynthetic process
+is_a: GO:1902653 ! secondary alcohol biosynthetic process
[Term]
id: GO:0106111
@@ -409750,14 +409203,14 @@ is_a: GO:0051702 ! biological process involved in interaction with symbiont
id: GO:0106137
name: IkappaB kinase complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the IkappaB kinase complex." [GOC:pga, PMID:12492477]
+def: "Binding to a IkappaB kinase complex." [GOC:pga, PMID:12492477]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0106138
name: Sec61 translocon complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Sec61 translocon complex." [GOC:pga, PMID:9792704]
+def: "Binding to a Sec61 translocon complex." [GOC:pga, PMID:9792704]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -409772,7 +409225,7 @@ is_a: GO:0044217 ! other organism part
id: GO:0106140
name: P-TEFb complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the P-TEFb complex." [GOC:pga, PMID:18391197]
+def: "Binding to a P-TEFb complex." [GOC:pga, PMID:18391197]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -409874,7 +409327,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0106153
name: phosphorylated histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone in which a residue has been modified by phosphorylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:mah, PMID:20679485]
+def: "Binding to a histone in which a residue has been modified by phosphorylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes." [GOC:mah, PMID:20679485]
is_a: GO:0042393 ! histone binding
is_a: GO:0140031 ! phosphorylation-dependent protein binding
@@ -409889,8 +409342,9 @@ is_a: GO:0120165 ! perithecium development
id: GO:0106155
name: peptidyl-lysine 3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein L-lysine + 2-oxoglutarate + O2 = protein 3-hydroxy-L-lysine + succinate + CO2." [GOC:al, PMID:29915238]
-xref: RHEA:57153
+def: "Catalysis of the reaction: protein L-lysine + 2-oxoglutarate + O2 = protein 3-hydroxy-L-lysine + succinate + CO2." [GOC:al, PMID:29915238, RHEA:57152]
+xref: EC:1.14.11.63
+xref: RHEA:57152
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -409907,7 +409361,10 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:0106157
name: peptidyl-arginine 3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: protein L-arginie + 2-oxoglutarate + O2 = protein 3-hydroxy-L-arginine + succinate + CO2." [GOC:pde, PMID:29563586]
+alt_id: GO:0140554
+def: "Catalyzes the reaction: 2-oxoglutarate + [protein]-L-arginine + O2 = [protein]-(3R)-3-hydroxy-L-arginine + CO2 + succinate." [PMID:29563586]
+synonym: "L-arginine 3-hydroxylase activity" EXACT []
+xref: RHEA:56744
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -409916,7 +409373,6 @@ id: GO:0106158
name: glycero-3-phosphocholine acyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction:acyl-CoA + glycerophosphocholine = CoA + 1-acyl-sn-glycero-3-phosphocholine." [PMID:18430972, PMID:27758859, RHEA:58476]
-synonym: "glycero-3-phosphocholine acyltransferase activity" EXACT []
synonym: "glycerophosphocholine O-acyltransferase activity" EXACT []
synonym: "GPACT activity" EXACT []
xref: RHEA:58476
@@ -410283,8 +409739,12 @@ synonym: "culmorin anabolism" EXACT []
synonym: "culmorin biosynthesis" EXACT []
synonym: "culmorin formation" EXACT []
synonym: "culmorin synthesis" EXACT []
+is_a: GO:0016106 ! sesquiterpenoid biosynthetic process
+is_a: GO:0034312 ! diol biosynthetic process
is_a: GO:0043386 ! mycotoxin biosynthetic process
is_a: GO:0051762 ! sesquiterpene biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_a: GO:1902653 ! secondary alcohol biosynthetic process
[Term]
id: GO:0106211
@@ -410364,7 +409824,7 @@ is_a: GO:0051278 ! fungal-type cell wall polysaccharide biosynthetic process
id: GO:0106219
name: zinc ion sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of zinc." [GOC:vw, PMID:31239353]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of zinc." [GOC:vw, PMID:31239353]
is_a: GO:0008270 ! zinc ion binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -410380,20 +409840,24 @@ is_a: GO:1901566 ! organonitrogen compound biosynthetic process
[Term]
id: GO:0106222
-name: long noncoding RNA binding
+name: lncRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a long noncoding RNA (lncRNA)." [PMID:25578728]
-synonym: "lncRNA binding" EXACT []
+def: "Binding to a long noncoding RNA (lncRNA)." [PMID:25578728]
+synonym: "long noncoding RNA binding" EXACT []
is_a: GO:0003723 ! RNA binding
[Term]
id: GO:0106223
name: germacrene A hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction:(+)-(R)-germacrene A + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = germacra-1(10),4,11(13)-trien-12-oate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase]." [PMID:11299372, PMID:20351109]
+alt_id: GO:0102260
+def: "Catalysis of the reaction:(+)-(R)-germacrene A + 3 O2 + 3 reduced [NADPH--hemoprotein reductase] = germacra-1(10),4,11(13)-trien-12-oate + 4 H(+) + 4 H2O + 3 oxidized [NADPH--hemoprotein reductase]." [PMID:11299372, PMID:20351109, RHEA:30303]
+comment: Formerly EC:1.1.1.314.
+synonym: "germacrene A alcohol dehydrogenase activity" RELATED []
xref: EC:1.14.14.95
+xref: MetaCyc:RXN-12449
xref: RHEA:30303
-is_a: GO:0004497 ! monooxygenase activity
+is_a: GO:0016712 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0106225
@@ -410589,6 +410053,7 @@ id: GO:0106249
name: Nicalin-NOMO complex
namespace: cellular_component
def: "A protein complex regulating Nodal signaling. Subunits are highly conserved in vertebrates and include Nicalin, NOMO and TMEM147." [GOC:al, GOC:bhm, PMID:20538592]
+synonym: "Nicalin-TMEM147-NOMO complex" EXACT [PMID:32820719]
is_a: GO:0032991 ! protein-containing complex
[Term]
@@ -410620,7 +410085,7 @@ relationship: positively_regulates GO:0110025 ! DNA strand resection involved in
id: GO:0106254
name: lipid sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of a lipid." [GOC:vw, PMID:30075144]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of a lipid." [GOC:vw, PMID:30075144]
is_a: GO:0140299 ! small molecule sensor activity
[Term]
@@ -410703,8 +410168,9 @@ is_a: GO:0008374 ! O-acyltransferase activity
id: GO:0106264
name: protein serine kinase activity (using GTP as donor)
namespace: molecular_function
-def: "Catalysis of the reactions: GTP + L-seryl-[protein] = GDP + H(+) + O-phospho-L-seryl-[protein]." [GOC:sp, PMID:32322062, Rhea:64020]
-is_a: GO:0004672 ! protein kinase activity
+def: "Catalysis of the reactions: GTP + L-seryl-[protein] = GDP + H(+) + O-phospho-L-seryl-[protein]." [GOC:sp, PMID:32322062, RHEA:64020]
+xref: RHEA:64020
+is_a: GO:0106310 ! protein serine kinase activity
[Term]
id: GO:0106265
@@ -411033,24 +410499,6 @@ synonym: "mannogen catabolism" RELATED []
synonym: "mannogen degradation" RELATED []
is_a: GO:0106303 ! mannogen metabolic process
-[Term]
-id: GO:0106306
-name: protein serine phosphatase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate." [RHEA:20629]
-xref: EC:3.1.3.16
-xref: RHEA:20629
-is_a: GO:0004722 ! protein serine/threonine phosphatase activity
-
-[Term]
-id: GO:0106307
-name: protein threonine phosphatase activity
-namespace: molecular_function
-def: "Catalysis of the reaction: protein threonine phosphate + H2O = protein threonine + phosphate." [RHEA:47004]
-xref: EC:3.1.3.16
-xref: RHEA:47004
-is_a: GO:0004722 ! protein serine/threonine phosphatase activity
-
[Term]
id: GO:0106309
name: progesterone 21-hydroxylase activity
@@ -411064,18 +410512,9 @@ id: GO:0106310
name: protein serine kinase activity
namespace: molecular_function
def: "Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate." [RHEA:17989]
-xref: EC:2.7.11.1
+comment: Note that this term is to annotate proteins the specifically phosphorylate a serine residue on a protein. An example is human PIKFYVE (UniProt:Q9Y2I7). For dual specificity protein kinases, use 'protein serine/threonine kinase activity' ; GO:0004712.
xref: RHEA:17989
-is_a: GO:0004674 ! protein serine/threonine kinase activity
-
-[Term]
-id: GO:0106311
-name: protein threonine kinase activity
-namespace: molecular_function
-def: "Catalysis of the reactions: ATP + protein threonine = ADP + threonine phosphate." [RHEA:46608]
-xref: EC:2.7.11.1
-xref: RHEA:46608
-is_a: GO:0004674 ! protein serine/threonine kinase activity
+is_a: GO:0004672 ! protein kinase activity
[Term]
id: GO:0106312
@@ -411328,7 +410767,6 @@ id: GO:0106344
name: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP
namespace: molecular_function
def: "Catalysis of the reaction: 2 Fe(3+) + 4 H2O + L-histidyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] + N(6)-(pyridoxal phosphate)-L-lysyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] = (2S)-2-amino-5-hydroxy-4-oxopentanoyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase] + 3-oxopropanoate + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 2 Fe(2+) + 2 H(+) + L-lysyl-[4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase]." [PMID:22568620, RHEA:65756]
-synonym: "4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP" EXACT []
xref: RHEA:65756
is_a: GO:0016740 ! transferase activity
@@ -411367,6 +410805,7 @@ name: snRNA methylation
namespace: biological_process
def: "The posttranscriptional addition of methyl groups to specific residues in an snRNA molecule." [PMID:21823225]
is_a: GO:0001510 ! RNA methylation
+is_a: GO:0040031 ! snRNA modification
[Term]
id: GO:0106350
@@ -411452,14 +410891,16 @@ is_a: GO:0106359 ! 2-hydroxyacyl-CoA lyase activity
id: GO:0106361
name: protein-arginine rhamnosyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dTDP-beta-L-rhamnose + L-arginyl-[protein] = dTDP + H(+) + N(omega)-(L-rhamnosyl)-L-arginyl-[protein]." [GOC:sp, PMID:25686373, PMID:26060278]
+def: "Catalysis of the reaction: dTDP-beta-L-rhamnose + L-arginyl-[protein] = dTDP + H(+) + N(omega)-(L-rhamnosyl)-L-arginyl-[protein]." [GOC:sp, PMID:25686373, PMID:26060278, RHEA:66692]
+xref: RHEA:66692
is_a: GO:0046527 ! glucosyltransferase activity
[Term]
id: GO:0106362
name: protein-arginine N-acetylglucosaminyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-arginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = H(+) + N(omega)-(N-acetyl-beta-D-glucosaminyl)-L-arginyl-[protein] + UDP." [GOC:sp, PMID:23955153, PMID:30619781]
+def: "Catalysis of the reaction: L-arginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = H(+) + N(omega)-(N-acetyl-beta-D-glucosaminyl)-L-arginyl-[protein] + UDP." [GOC:sp, PMID:23955153, PMID:30619781, RHEA:66632]
+xref: RHEA:66632
is_a: GO:0016262 ! protein N-acetylglucosaminyltransferase activity
[Term]
@@ -411469,6 +410910,8 @@ namespace: molecular_function
def: "Catalysis of the reaction: L-cysteinyl-[protein] + S-adenosyl-L-methionine = H(+) + S-adenosyl-L-homocysteine + S-methyl-L-cysteinyl-[protein]." [GOC:sp, PMID:21481189, PMID:22158122, PMID:24235145, PMID:25412445, RHEA:66544]
xref: RHEA:66544
is_a: GO:0008172 ! S-methyltransferase activity
+is_a: GO:0008276 ! protein methyltransferase activity
+is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:0106364
@@ -411499,7 +410942,7 @@ is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
[Term]
id: GO:0106367
-name: dGTP dependent (deoxy)nucleoside -phosphate kinase activity
+name: (deoxy)nucleoside phosphate kinase activity, dGTP as phosphate donor
namespace: molecular_function
def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + dGTP = a 2'-deoxyribonucleoside 5'-diphosphate + dGDP." [PMID:20497505, RHEA:62128]
xref: RHEA:62128
@@ -411508,7 +410951,7 @@ is_a: GO:0019205 ! nucleobase-containing compound kinase activity
[Term]
id: GO:0106368
-name: dTTP dependent (deoxy)nucleoside - phosphate kinase activity
+name: (deoxy)nucleoside phosphate kinase activity, dTTP as phosphate donor
namespace: molecular_function
def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + dTTP = a 2'-deoxyribonucleoside 5'-diphosphate + dTDP." [PMID:20497505, RHEA:62132]
xref: RHEA:62132
@@ -411517,7 +410960,7 @@ is_a: GO:0019205 ! nucleobase-containing compound kinase activity
[Term]
id: GO:0106369
-name: GTP dependent (deoxy)nucleoside -phosphate kinase activity
+name: (deoxy)nucleoside phosphate kinase activity, GTP as phosphate donor
namespace: molecular_function
def: "Catalysis of the reaction: a 2'-deoxyribonucleoside 5'-phosphate + GTP = a 2'-deoxyribonucleoside 5'-diphosphate + GDP." [PMID:20497505, RHEA:62124]
xref: RHEA:62124
@@ -411528,28 +410971,34 @@ is_a: GO:0019205 ! nucleobase-containing compound kinase activity
id: GO:0106370
name: protein-L-histidine N-pros-methyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: L-histidyl-[protein] + S-adenosyl-L-methionine = N(pros)-methyl-L-histidyl-[protein] + S-adenosyl-L-homocysteine." [PMID:33563959]
+def: "Catalysis of the reaction: L-histidyl-[protein] + S-adenosyl-L-methionine = N(pros)-methyl-L-histidyl-[protein] + S-adenosyl-L-homocysteine." [PMID:33563959, RHEA:67076]
+xref: RHEA:67076
+is_a: GO:0008170 ! N-methyltransferase activity
+is_a: GO:0008276 ! protein methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
[Term]
id: GO:0106371
name: fluorescent chlorophyll catabolite monooxygenase (deformylase) activity
namespace: molecular_function
-def: "Catalysis of the reaction: O2 + primary fluorescent chlorophyll catabolite + reduced [NADPH--hemoprotein reductase] = formate + 2 H+ + oxidized [NADPH--hemoprotein reductase] + primary fluorescent dioxobilin-type chlorophyll catabolite." [PMID:23723324]
+def: "Catalysis of the reaction: O2 + primary fluorescent chlorophyll catabolite + reduced [NADPH--hemoprotein reductase] = formate + 2 H+ + oxidized [NADPH--hemoprotein reductase] + primary fluorescent dioxobilin-type chlorophyll catabolite." [PMID:23723324, RHEA:67172]
+xref: RHEA:67172
is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
[Term]
id: GO:0106372
name: primary fluorescent dioxobilin-type chlorophyll catabolite methylesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H2O + primary fluorescent dioxobilin-type chlorophyll catabolite = H+ + methanol + O13(4)-desmethyl pFCC." [PMID:23723324]
+def: "Catalysis of the reaction: H2O + primary fluorescent dioxobilin-type chlorophyll catabolite = H+ + methanol + O13(4)-desmethyl pFCC." [PMID:23723324, RHEA:67176]
+xref: RHEA:67176
is_a: GO:0052689 ! carboxylic ester hydrolase activity
[Term]
id: GO:0106373
name: 3-deoxyglucosone dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-deoxyglucosone + H2O + NAD(+) = 2-dehydro-3-deoxy-D-gluconate + 2 H(+) + NADH." [PMID:17175089]
+def: "Catalysis of the reaction: 3-deoxyglucosone + H2O + NAD(+) = 2-dehydro-3-deoxy-D-gluconate + 2 H(+) + NADH." [PMID:17175089, RHEA:67244]
+xref: RHEA:67244
is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
[Term]
@@ -411572,7 +411021,8 @@ is_a: GO:0016832 ! aldehyde-lyase activity
id: GO:0106377
name: 2-hydroxy-ATP hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2-hydroxy-ATP + H2O = 2-hydroxy-AMP + diphosphate." [PMID:11139615]
+def: "Catalysis of the reaction: 2-hydroxy-ATP + H2O = 2-hydroxy-AMP + diphosphate." [PMID:11139615, RHEA:67392]
+xref: RHEA:67392
is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
[Term]
@@ -411583,6 +411033,254 @@ def: "Catalysis of the reaction: 2-hydroxy-dATP + H2O = 2-hydroxy-dAMP + diphosp
xref: RHEA:31583
is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+[Term]
+id: GO:0106379
+name: 8-oxo-(d)RTP hydrolase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 8-oxo-(d)RTP + H20 = 8-oxo-(d)RMP + diphosphate + H+." [PMID:11139615]
+is_a: GO:0016818 ! hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
+
+[Term]
+id: GO:0106380
+name: purine ribonucleotide salvage
+namespace: biological_process
+def: "Any process which produces a purine ribonucleotide from derivatives of it, without de novo synthesis." [PMID:8864750]
+is_a: GO:0009152 ! purine ribonucleotide biosynthetic process
+is_a: GO:0032261 ! purine nucleotide salvage
+
+[Term]
+id: GO:0106381
+name: purine deoxyribonucleotide salvage
+namespace: biological_process
+def: "Any process which produces a purine deoxyribonucleotide from derivatives of it, without de novo synthesis." [PMID:6605343]
+is_a: GO:0009153 ! purine deoxyribonucleotide biosynthetic process
+is_a: GO:0032261 ! purine nucleotide salvage
+
+[Term]
+id: GO:0106383
+name: dAMP salvage
+namespace: biological_process
+def: "Any process which produces a dAMP from derivatives of it, without de novo synthesis." [PMID:21829339, PMID:6605343]
+is_a: GO:0006170 ! dAMP biosynthetic process
+is_a: GO:0106381 ! purine deoxyribonucleotide salvage
+
+[Term]
+id: GO:0106384
+name: dGMP salvage
+namespace: biological_process
+def: "Any process which produces a dGMP from derivatives of it, without de novo synthesis." [PMID:21829339, PMID:6605343]
+is_a: GO:0006181 ! dGMP biosynthetic process
+is_a: GO:0106381 ! purine deoxyribonucleotide salvage
+
+[Term]
+id: GO:0106385
+name: dIMP salvage
+namespace: biological_process
+def: "Any process which produces a dIMP from derivatives of it, without de novo synthesis." [PMID:8692979]
+is_a: GO:0009171 ! purine deoxyribonucleoside monophosphate biosynthetic process
+is_a: GO:0106381 ! purine deoxyribonucleotide salvage
+
+[Term]
+id: GO:0106386
+name: (3R)-hydroxyacyl-CoA dehydrogenase (NAD) activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 3R-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH." [PMID:19571038, PMID:25203508]
+xref: EC:1.1.1.n12
+xref: RHEA:32711
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+
+[Term]
+id: GO:0106387
+name: 'de novo' GMP biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of guanosine 5'-monophosphate (GMP) through an inosine 5'-monophosphate (IMP) intermediate." [PMID:25605736]
+synonym: "'de novo' guanosine 5'-monophosphate biosynthetic process" EXACT []
+is_a: GO:0006177 ! GMP biosynthetic process
+
+[Term]
+id: GO:0106388
+name: 18S rRNA aminocarboxypropyltransferase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: N1-methylpseudouridine in 18S rRNA + S-adenosyl-L-methionine = H+ + N1-methyl-N3-[(3S)-3-amino-3-carboxypropyl]pseudouridine in 18S rRNA + S-methyl-5'-thioadenosine." [PMID:27084949]
+xref: RHEA:63296
+is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups
+is_a: GO:0140102 ! catalytic activity, acting on a rRNA
+
+[Term]
+id: GO:0106389
+name: ecdysteroid 22-kinase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: an ecdysteroid + ATP = an ecdysteroid 22-phosphate + ADP + H+." [PMID:16899460]
+xref: MetaCyc:RXN-14755
+is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
+
+[Term]
+id: GO:0106391
+name: bI4 intron splicing complex
+namespace: cellular_component
+def: "A protein complex required for the splicing of intron 4 of the cytochrome b (COB) gene. In S. cerevisiae, the complex contains the maturase bI4 (which derives from one of the products of the splicing), Leucyl-tRNA synthetase NAM2 and the intron 4 of the cytochrome b pre-mRNA. The two proteins stimulate the ribozyme activity of the pre-mRNA which autoctalyse a group I intron splicing." [GOC:lnp, PMID:19622748]
+xref: Intact:EBI-16420264
+is_a: GO:1902555 ! endoribonuclease complex
+
+[Term]
+id: GO:0106392
+name: bI3 intron splicing complex
+namespace: cellular_component
+def: "Aprotein complex required for the splicing of intron 3 of the cytochrome b (COB) gene. In S. cerevisiae, the complex contains the maturase bI3 (which derives from one of the products of the splicing), the MRS1 cofactor and the intron 4 of the cytochrome b pre-mRNA. The two proteins stimulate the ribozyme activity of the pre-mRNA which autoctalyse a group I intron splicing." [GOC:lnp, PMID:11773622]
+xref: Intact:EBI-16426213
+is_a: GO:1902555 ! endoribonuclease complex
+
+[Term]
+id: GO:0106393
+name: regulation of palmitic acid catabolic process
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of a palmitic acid catabolic process." [PMID:14677856]
+is_a: GO:0019217 ! regulation of fatty acid metabolic process
+is_a: GO:0031329 ! regulation of cellular catabolic process
+is_a: GO:0050994 ! regulation of lipid catabolic process
+relationship: regulates GO:1900534 ! palmitic acid catabolic process
+
+[Term]
+id: GO:0106394
+name: negative regulation of palmitic acid catabolic process
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of a palmitic acid catabolic process." [PMID:14677856]
+is_a: GO:0031330 ! negative regulation of cellular catabolic process
+is_a: GO:0045922 ! negative regulation of fatty acid metabolic process
+is_a: GO:0050995 ! negative regulation of lipid catabolic process
+is_a: GO:0106393 ! regulation of palmitic acid catabolic process
+relationship: negatively_regulates GO:1900534 ! palmitic acid catabolic process
+
+[Term]
+id: GO:0106395
+name: positive regulation of palmitic acid catabolic process
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of a palmitic acid catabolic process." [PMID:14677856]
+is_a: GO:0031331 ! positive regulation of cellular catabolic process
+is_a: GO:0045923 ! positive regulation of fatty acid metabolic process
+is_a: GO:0050996 ! positive regulation of lipid catabolic process
+is_a: GO:0106393 ! regulation of palmitic acid catabolic process
+relationship: positively_regulates GO:1900534 ! palmitic acid catabolic process
+
+[Term]
+id: GO:0106396
+name: regulation of R7 cell fate commitment
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of R7 cell fate commitment." [GOC:ha, PMID:22878552]
+is_a: GO:0010453 ! regulation of cell fate commitment
+relationship: regulates GO:0007465 ! R7 cell fate commitment
+
+[Term]
+id: GO:0106397
+name: positive regulation of R7 cell fate commitment
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of R7 cell fate commitment." [GOC:ha, PMID:22878552]
+is_a: GO:0010455 ! positive regulation of cell fate commitment
+is_a: GO:0106396 ! regulation of R7 cell fate commitment
+relationship: positively_regulates GO:0007465 ! R7 cell fate commitment
+
+[Term]
+id: GO:0106398
+name: negative regulation of R7 cell fate commitment
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of R7 cell fate commitment." [GOC:ha, PMID:22878552]
+is_a: GO:0010454 ! negative regulation of cell fate commitment
+is_a: GO:0106396 ! regulation of R7 cell fate commitment
+relationship: negatively_regulates GO:0007465 ! R7 cell fate commitment
+
+[Term]
+id: GO:0106399
+name: acyl-coenzyme A diphosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: an acyl-CoA + H2O = adenosine 3',5'-bisphosphate + an acyl-4'-phosphopantetheine + 2 H(+)." [PMID:32915949, RHEA:50044]
+xref: RHEA:50044
+is_a: GO:0016462 ! pyrophosphatase activity
+
+[Term]
+id: GO:0106400
+name: double-strand break repair via transcription-associated homologous recombination
+namespace: biological_process
+def: "A mechanism of homologous recombination and DNA repair in which transcript RNA is used as a template for DSB repair." [PMID:25186730]
+is_a: GO:0000724 ! double-strand break repair via homologous recombination
+
+[Term]
+id: GO:0106402
+name: Lewis x epitope biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of a Lewis x epitope, a trisaccharide (beta-D-galactosyl-(1,4)-[alpha-L-fucosyl-(1,3)]-N-acetyl-beta-D-glucosamine) expressed on several glycolipids, glycoproteins, and proteoglycans of the nervous system. The related Lewis x epitope is formed by alpha(1,3) fucosylation of the N-acetylglucosaminyl residue of a type 2 histo-blood group antigen precursor disaccharide." [PMID:16973732, PMID:23000574]
+synonym: "sialyl-Lewis X biosynthetic process" RELATED []
+synonym: "sLeX biosynthetic process" RELATED []
+is_a: GO:0005975 ! carbohydrate metabolic process
+
+[Term]
+id: GO:0106405
+name: isoprenoid diphosphate phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the dephosphorylation of isoprenoid diphosphates." [PMID:33246356]
+is_a: GO:0016462 ! pyrophosphatase activity
+
+[Term]
+id: GO:0106407
+name: Glc2Man9GlcNAc2 oligosaccharide glucosidase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: Glc(2)Man(9)GlcNAc(2)-[protein] + H(2)O = GlcMan(9)GlcNAc(2)-[protein] + beta-D-glucopyranose." [PMID:30389790]
+comment: Trims Glc alpha 1,3 Glc bond in Glc2Man9GlcNAc2 oligosaccharide in inmature glycoproteins.
+synonym: "Glucosidase II" BROAD []
+is_a: GO:0004573 ! Glc3Man9GlcNAc2 oligosaccharide glucosidase activity
+
+[Term]
+id: GO:0106408
+name: diadenylate cyclase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 2 ATP = 3',3'-c-di-AMP + 2 diphosphate." [PMID:30884174, RHEA:35655]
+synonym: "cyclic-di-AMP synthase" EXACT [EC:2.7.7.85]
+xref: EC:2.7.7.85
+xref: MetaCyc:RXN-14338
+xref: RHEA:35655
+is_a: GO:0016779 ! nucleotidyltransferase activity
+
+[Term]
+id: GO:0106409
+name: cyclic-di-AMP phosphodiesterase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 3',3'-c-di-AMP + H2O = 5'-O-phosphonoadenylyl-(3'-5')-adenosine + H+." [PMID:21909268, RHEA:54420]
+xref: EC:3.1.4.59
+xref: MetaCyc:RXN-19814
+xref: RHEA:54420
+is_a: GO:0016779 ! nucleotidyltransferase activity
+
+[Term]
+id: GO:0106410
+name: box C/D RNA 5'-end processing
+namespace: biological_process
+def: "Any process involved in forming the mature 5' end of a box C/D RNA molecule." [PMID:34352089]
+is_a: GO:0034471 ! ncRNA 5'-end processing
+is_a: GO:0034963 ! box C/D RNA processing
+
+[Term]
+id: GO:0106411
+name: XMP 5'-nucleosidase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 5'XMP + H20 = phosphate + xanthosine." [PMID:34824243, RHEA:28530]
+xref: EC:3.1.3.5
+xref: MetaCyc:XMPXAN-RXN
+xref: RHEA:28530
+is_a: GO:0008253 ! 5'-nucleotidase activity
+
+[Term]
+id: GO:0106413
+name: dihydrouridine synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: RNA-uracil + acceptor = RNA-dihydrouridine + reduced acceptor." [PMID:12581659, PMID:25073379]
+is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors
+
+[Term]
+id: GO:0106414
+name: mRNA dihydrouridine synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: mRNA-uracil + acceptor = mRNA-dihydrouridine + reduced acceptor." [PMID:34798057]
+is_a: GO:0106413 ! dihydrouridine synthase activity
+
[Term]
id: GO:0110001
name: toxin-antitoxin complex
@@ -411878,7 +411576,7 @@ is_a: GO:0044374 ! sequence-specific DNA binding, bending
id: GO:0110036
name: C2 domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the C2 domain of a protein, a protein structural domain involved in targeting proteins to cell membranes." [GOC:sl, PMID:24882364]
+def: "Binding to the C2 domain of a protein, a protein structural domain involved in targeting proteins to cell membranes." [GOC:sl, PMID:24882364]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -412139,7 +411837,7 @@ id: GO:0110070
name: cellularization cleavage furrow
namespace: cellular_component
def: "A plasma membrane invagination at the site of separation of a multi-nucleate cell or syncytium into individual cells." [GOC:ha, PMID:27226317]
-is_a: GO:0032154 ! cleavage furrow
+is_a: GO:0098590 ! plasma membrane region
[Term]
id: GO:0110071
@@ -412256,7 +411954,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly." [GOC:vw, PMID:29343550]
is_a: GO:0090068 ! positive regulation of cell cycle process
is_a: GO:0110082 ! regulation of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:1903476 ! protein localization to cell division site involved in mitotic actomyosin contractile ring assembly
[Term]
@@ -412266,7 +411964,7 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly." [GOC:vw, PMID:29343550]
is_a: GO:0110082 ! regulation of protein localization to cell division site involved in mitotic actomyosin contractile ring assembly
is_a: GO:1903500 ! negative regulation of mitotic actomyosin contractile ring assembly
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:1903476 ! protein localization to cell division site involved in mitotic actomyosin contractile ring assembly
[Term]
@@ -412285,10 +411983,11 @@ is_a: GO:0005826 ! actomyosin contractile ring
[Term]
id: GO:0110087
-name: suppression by virus of host protease activator activity
+name: obsolete suppression by virus of host protease activator activity
namespace: biological_process
-def: "Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host protease activator activity." [PMID:23303392]
-is_a: GO:0039507 ! suppression by virus of host molecular function
+def: "OBSOLETE. Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host protease activator activity." [PMID:23303392]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
[Term]
id: GO:0110088
@@ -412417,8 +412116,7 @@ name: ribulose bisphosphate carboxylase complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a ribulose bisphosphate carboxylase complex." [GOC:krc, GOC:tb, PMID:29396988, PMID:29589905]
synonym: "RuBisCO assembly" EXACT [GOC:krc]
-synonym: "rubisco assembly" EXACT [GOC:krc, GOC:tb]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0110103
@@ -412442,7 +412140,7 @@ id: GO:0110105
name: mRNA cleavage and polyadenylation specificity factor complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the mRNA cleavage and polyadenylation specificity factor complex." [GOC:mah, PMID:27401558]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
relationship: part_of GO:0031123 ! RNA 3'-end processing
[Term]
@@ -412658,26 +412356,20 @@ relationship: part_of GO:0030479 ! actin cortical patch
[Term]
id: GO:0110132
-name: regulation of CRISPR-cas system
+name: obsolete regulation of CRISPR-cas system
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of a CRISPR-cas system." [PMID:30190307, PMID:30190308]
-is_a: GO:0002831 ! regulation of response to biotic stimulus
-is_a: GO:0031347 ! regulation of defense response
-is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0050776 ! regulation of immune response
-relationship: regulates GO:0099048 ! CRISPR-cas system
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of a CRISPR-cas system." [PMID:30190307, PMID:30190308]
+comment: This term was obsoleted because it does not accurately capture the process described in the literature.
+is_obsolete: true
[Term]
id: GO:0110133
-name: negative regulation of CRISPR-cas system
+name: obsolete negative regulation of CRISPR-cas system
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a CRISPR-cas system." [PMID:30190307, PMID:30190308]
-is_a: GO:0002832 ! negative regulation of response to biotic stimulus
-is_a: GO:0031348 ! negative regulation of defense response
-is_a: GO:0032102 ! negative regulation of response to external stimulus
-is_a: GO:0050777 ! negative regulation of immune response
-is_a: GO:0110132 ! regulation of CRISPR-cas system
-relationship: negatively_regulates GO:0099048 ! CRISPR-cas system
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of a CRISPR-cas system." [PMID:30190307, PMID:30190308]
+comment: This term was obsoleted because it does not accurately capture the process described in the literature.
+is_obsolete: true
+consider: GO:0098672
[Term]
id: GO:0110134
@@ -412760,7 +412452,7 @@ id: GO:0110143
name: magnetosome
namespace: cellular_component
def: "A membrane-bound organelle that envelops particles of magnetic iron minerals in magnetotactic bacteria. Magnetosomes form linear chains that align along the cellular motility axis at midcell and function in bacterial navigation along the Earth's magnetic field. They are formed by invagination of the cell inner membrane; in some species they remain connected to the inner membrane, in others they pinch off to form independent intracellular vesicles." [GOC:aa, PMID:27620945]
-is_a: GO:0043226 ! organelle
+is_a: GO:0043231 ! intracellular membrane-bounded organelle
[Term]
id: GO:0110144
@@ -412775,7 +412467,7 @@ id: GO:0110145
name: magnetosome lumen
namespace: cellular_component
def: "The volume enclosed by the membrane of a magnetosome." [GOC:aa, PMID:27620945]
-is_a: GO:0043233 ! organelle lumen
+is_a: GO:0070013 ! intracellular organelle lumen
relationship: part_of GO:0110143 ! magnetosome
[Term]
@@ -412783,7 +412475,7 @@ id: GO:0110146
name: magnetosome membrane
namespace: cellular_component
def: "The lipid bilayer surrounding a magnetosome." [GOC:aa, PMID:27620945]
-is_a: GO:0016020 ! membrane
+is_a: GO:0031090 ! organelle membrane
relationship: part_of GO:0110143 ! magnetosome
[Term]
@@ -412908,6 +412600,7 @@ name: regulation of mitotic spindle formation (spindle phase one)
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the cell cycle process in which the distance is lengthened between poles of the mitotic spindle during mitotic prophase (spindle phase one)." [GOC:vw, PMID:27697865]
is_a: GO:1901673 ! regulation of mitotic spindle assembly
+relationship: part_of GO:0032888 ! regulation of mitotic spindle elongation
relationship: regulates GO:0061804 ! mitotic spindle formation (spindle phase one)
[Term]
@@ -413147,23 +412840,19 @@ is_a: GO:0120015 ! sterol transfer activity
[Term]
id: GO:0120022
-name: glucagon binding
+name: glucagon family peptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with glucagon, a polypeptide hormone involved in glucose response. It is produced by pancreatic alpha cells and raises the concentration of glucose in the blood." [GOC:cvs]
+alt_id: GO:0120024
+def: "Binding to a member of the glucagon family peptide hormone (e.g. glucagon, glucagon-like peptides, oxyntomodulin, glicentin, ADCYAP1, GHRH, secretin, VIP, GIP)." [PMID:17715056]
+synonym: "glucagon binding" NARROW []
+synonym: "glucagon-like peptide binding" NARROW []
is_a: GO:0017046 ! peptide hormone binding
[Term]
id: GO:0120023
name: somatostatin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with somatostatin, a polypeptide hormone involved in regulating pancreatic alpha and pancreatic beta cells and controlling growth hormone secretion as well as many other functions. Somatostatin is produced by several cell types including pancreatic delta cells. There are several different mature forms of somatostatin." [GOC:cvs, PMID:20472043]
-is_a: GO:0017046 ! peptide hormone binding
-
-[Term]
-id: GO:0120024
-name: glucagon-like peptide binding
-namespace: molecular_function
-def: "Interacting selectively and non-covalently with glucagon-like peptide, a antihyperglycemic hormone. Glucagon-like peptide is derived from the glucagon gene produced by pancreatic alpha cells." [GOC:cvs]
+def: "Binding to somatostatin, a polypeptide hormone involved in regulating pancreatic alpha and pancreatic beta cells and controlling growth hormone secretion as well as many other functions. Somatostatin is produced by several cell types including pancreatic delta cells. There are several different mature forms of somatostatin." [GOC:cvs, PMID:20472043]
is_a: GO:0017046 ! peptide hormone binding
[Term]
@@ -413206,7 +412895,6 @@ namespace: biological_process
def: "The directed movement of hydrogen ions (protons) from inside a cell, across the plasma membrane and into the extracellular region." [GOC:mah, PMID:9762918]
synonym: "hydrogen ion export across plasma membrane" EXACT []
synonym: "hydrogen ion export from cell" BROAD []
-synonym: "proton export across plasma membrane" EXACT []
synonym: "proton export from cell" BROAD []
is_a: GO:0140115 ! export across plasma membrane
is_a: GO:1902600 ! proton transmembrane transport
@@ -413580,7 +413268,6 @@ id: GO:0120077
name: angiogenic sprout fusion
namespace: biological_process
def: "The connection of an angiogenic sprout to another vessel or sprout during the formation of vascular networks by sprouting angiogenesis." [GOC:cvs, PMID:28264837]
-synonym: "angiogenic sprout fusion" EXACT []
synonym: "blood vessel anastomosis" EXACT []
is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
relationship: part_of GO:0002040 ! sprouting angiogenesis
@@ -413597,25 +413284,27 @@ relationship: part_of GO:0120077 ! angiogenic sprout fusion
[Term]
id: GO:0120079
-name: regulation of microfilament motor activity
+name: obsolete regulation of microfilament motor activity
namespace: biological_process
alt_id: GO:1904621
-def: "Any process that modulates the frequency, rate or extent of microfilament motor activity." [GOC:mah, PMID:20705471, PMID:8621557]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of microfilament motor activity." [GOC:mah, PMID:20705471, PMID:8621557]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of actin filament motor activity" EXACT []
synonym: "regulation of actin-activated ATPase activity" RELATED [GOC:TermGenie]
synonym: "regulation of actin-dependent ATPase activity" RELATED []
synonym: "regulation of actin-filament motor activity" EXACT []
synonym: "regulation of muscle motor activity" NARROW []
synonym: "regulation of myosin ATPase activity" RELATED []
-is_a: GO:0043462 ! regulation of ATPase activity
-is_a: GO:0051336 ! regulation of hydrolase activity
+is_obsolete: true
+consider: GO:0140659
[Term]
id: GO:0120080
-name: negative regulation of microfilament motor activity
+name: obsolete negative regulation of microfilament motor activity
namespace: biological_process
alt_id: GO:1904622
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of microfilament motor activity." [GOC:mah, PMID:20705471, PMID:8621557]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of microfilament motor activity." [GOC:mah, PMID:20705471, PMID:8621557]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of actin-activated ATPase activity" RELATED [GOC:TermGenie]
synonym: "down regulation of actin-dependent ATPase activity" EXACT [GOC:TermGenie]
synonym: "inhibition of actin-activated ATPase activity" NARROW [GOC:TermGenie]
@@ -413626,16 +413315,16 @@ synonym: "negative regulation of actin-dependent ATPase activity" RELATED []
synonym: "negative regulation of actin-filament motor activity" EXACT []
synonym: "negative regulation of muscle motor activity" NARROW []
synonym: "negative regulation of myosin ATPase activity" RELATED []
-is_a: GO:0032780 ! negative regulation of ATPase activity
-is_a: GO:0051346 ! negative regulation of hydrolase activity
-is_a: GO:0120079 ! regulation of microfilament motor activity
+is_obsolete: true
+consider: GO:0140661
[Term]
id: GO:0120081
-name: positive regulation of microfilament motor activity
+name: obsolete positive regulation of microfilament motor activity
namespace: biological_process
alt_id: GO:1904623
-def: "Any process that activates or increases the frequency, rate or extent of microfilament motor activity." [GOC:mah, PMID:20705471, PMID:8621557]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of microfilament motor activity." [GOC:mah, PMID:20705471, PMID:8621557]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of actin-activated ATPase activity" NARROW [GOC:TermGenie]
synonym: "activation of actin-dependent ATPase activity" NARROW [GOC:TermGenie]
synonym: "positive regulation of actin filament motor activity" EXACT []
@@ -413645,9 +413334,8 @@ synonym: "positive regulation of actin-filament motor activity" EXACT []
synonym: "positive regulation of muscle motor activity" NARROW []
synonym: "positive regulation of myosin ATPase activity" BROAD []
synonym: "upregulation of actin-dependent ATPase activity" NARROW [GOC:TermGenie]
-is_a: GO:0032781 ! positive regulation of ATPase activity
-is_a: GO:0051345 ! positive regulation of hydrolase activity
-is_a: GO:0120079 ! regulation of microfilament motor activity
+is_obsolete: true
+consider: GO:0140660
[Term]
id: GO:0120082
@@ -414136,7 +413824,7 @@ is_a: GO:0150105 ! protein localization to cell-cell junction
id: GO:0120146
name: sulfatide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with sulfatide, also known as 3-O-sulfogalactosylceramide, SM4, or sulfated galactocerebroside. Sulfatide is a class of sulfoglycolipid, which are glycolipids that contain a sulfate group." [GOC:krc, PMID:21525289, PMID:22619219, PMID:22977233, PMID:23574804, PMID:29497057, PMID:3549017, Wikipedia:Sulfatide]
+def: "Binding to sulfatide, also known as 3-O-sulfogalactosylceramide, SM4, or sulfated galactocerebroside. Sulfatide is a class of sulfoglycolipid, which are glycolipids that contain a sulfate group." [GOC:krc, PMID:21525289, PMID:22619219, PMID:22977233, PMID:23574804, PMID:29497057, PMID:3549017, Wikipedia:Sulfatide]
synonym: "3-O-sulfogalactosylceramide binding" EXACT []
synonym: "SM4 binding" EXACT []
synonym: "sulfated galactocerebroside binding" EXACT []
@@ -414202,14 +413890,14 @@ relationship: positively_regulates GO:1990274 ! mitotic actomyosin contractile r
id: GO:0120152
name: calcium-dependent outer dynein arm binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an outer dynein arm in the presence of calcium." [GOC:krc, PMID:18620543]
+def: "Binding to an outer dynein arm in the presence of calcium." [GOC:krc, PMID:18620543]
is_a: GO:0048306 ! calcium-dependent protein binding
[Term]
id: GO:0120153
name: calcium-dependent carbohydrate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any carbohydrate in the presence of calcium." [PMID:25912189]
+def: "Binding to a carbohydrate in the presence of calcium." [PMID:25912189]
is_a: GO:0030246 ! carbohydrate binding
[Term]
@@ -414288,7 +413976,7 @@ is_a: GO:0140098 ! catalytic activity, acting on RNA
id: GO:0120160
name: intraciliary transport particle A binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an intraciliary transport particle A (IFT A) complex." [PMID:20889716]
+def: "Binding to an intraciliary transport particle A (IFT A) complex." [PMID:20889716]
synonym: "IFT A complex binding" RELATED []
synonym: "intraciliary transport complex A binding" EXACT []
synonym: "intraflagellar transport complex A binding" EXACT []
@@ -414382,7 +414070,7 @@ relationship: part_of GO:0062035 ! sensory perception of cold stimulus
id: GO:0120170
name: intraciliary transport particle B binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an intraciliary transport particle B (IFT B) complex." [PMID:20889716]
+def: "Binding to an intraciliary transport particle B (IFT B) complex." [PMID:20889716]
synonym: "IFT B complex binding" RELATED []
synonym: "intraciliary transport complex B binding" EXACT []
synonym: "intraflagellar transport complex B binding" EXACT []
@@ -414518,7 +414206,7 @@ def: "The aggregation, arrangement and bonding together of a set of components t
synonym: "DSC1 transcription factor complex assembly" EXACT []
synonym: "MBF complex assembly" EXACT []
synonym: "Mlu1-box binding factor assembly" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0120186
@@ -414526,7 +414214,8 @@ name: negative regulation of protein localization to chromatin
namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin." [PMID:20889714, PMID:29899453]
synonym: "negative regulation of protein localisation to chromatin" EXACT [GOC:krc]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905634 ! regulation of protein localization to chromatin
relationship: negatively_regulates GO:0071168 ! protein localization to chromatin
@@ -414536,7 +414225,8 @@ name: positive regulation of protein localization to chromatin
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein localization to chromatin." [PMID:20889714, PMID:29899453]
synonym: "positive regulation of protein localisation to chromatin" EXACT [GOC:krc]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905634 ! regulation of protein localization to chromatin
relationship: positively_regulates GO:0071168 ! protein localization to chromatin
@@ -414943,7 +414633,7 @@ relationship: part_of GO:0060541 ! respiratory system development
id: GO:0120225
name: coenzyme A binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester." [GOC:krc, ISBN:0198547684]
+def: "Binding to coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester." [GOC:krc, ISBN:0198547684]
synonym: "CoA binding" EXACT []
is_a: GO:0032559 ! adenyl ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -414952,7 +414642,7 @@ is_a: GO:0043168 ! anion binding
id: GO:0120226
name: succinyl-CoA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with succinyl-CoA, an omega-carboxyacyl-CoA having succinoyl as the S-acyl component." [GOC:krc]
+def: "Binding to succinyl-CoA, an omega-carboxyacyl-CoA having succinoyl as the S-acyl component." [GOC:krc]
synonym: "succinyl-coenzyme A binding" EXACT []
is_a: GO:0043168 ! anion binding
is_a: GO:0120227 ! acyl-CoA binding
@@ -414961,7 +414651,7 @@ is_a: GO:0120227 ! acyl-CoA binding
id: GO:0120227
name: acyl-CoA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an acyl-CoA, a thioester that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any carboxylic acid." [GOC:krc]
+def: "Binding to an acyl-CoA, a thioester that results from the formal condensation of the thiol group of coenzyme A with the carboxy group of any carboxylic acid." [GOC:krc]
synonym: "acyl binding" BROAD []
synonym: "acyl-coenzyme A binding" EXACT []
is_a: GO:0032559 ! adenyl ribonucleotide binding
@@ -415024,7 +414714,7 @@ is_a: GO:0042727 ! flavin-containing compound biosynthetic process
id: GO:0120233
name: prenyl-FMNH2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with prenyl-FMNH2, a flavin mononucleotide obtained by prenylation of the N-10 position of FMNH2 followed by cyclisation. An essential cofactor for the decarboxylase enzymes UbiD and Fdc1." [GOC:krc, PMID:25647642, PMID:26083743, PMID:26083754]
+def: "Binding to prenyl-FMNH2, a flavin mononucleotide obtained by prenylation of the N-10 position of FMNH2 followed by cyclisation. An essential cofactor for the decarboxylase enzymes UbiD and Fdc1." [GOC:krc, PMID:25647642, PMID:26083743, PMID:26083754]
synonym: "prenylated FMNH2 binding" EXACT []
is_a: GO:0032553 ! ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -415206,6 +414896,7 @@ name: fatty acid omega-hydroxylase activity
namespace: molecular_function
def: "Catalysis of the reaction: an omega-methyl fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an omega-hydroxy fatty acid + H(+) + H2O + oxidized [NADPH--hemoprotein reductase]." [GOC:krc, RHEA:39023]
xref: RHEA:39023
+is_a: GO:0004497 ! monooxygenase activity
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
[Term]
@@ -415325,7 +415016,6 @@ synonym: "down regulation of heterochromatin organization" EXACT []
synonym: "down-regulation of heterochromatin organization" EXACT []
synonym: "downregulation of heterochromatin organization" EXACT []
synonym: "inhibition of heterochromatin organization" NARROW []
-synonym: "negative regulation of heterochromatin organization" EXACT []
is_a: GO:0120261 ! regulation of heterochromatin organization
is_a: GO:1905268 ! negative regulation of chromatin organization
relationship: negatively_regulates GO:0070828 ! heterochromatin organization
@@ -415336,7 +415026,6 @@ name: positive regulation of heterochromatin organization
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of heterochromatin organization." [GOC:krc]
synonym: "activation of heterochromatin organization" NARROW []
-synonym: "positive regulation of heterochromatin organization" EXACT []
synonym: "stimulation of heterochromatin organization" NARROW []
synonym: "up regulation of heterochromatin organization" EXACT []
synonym: "up-regulation of heterochromatin organization" EXACT []
@@ -415546,14 +415235,14 @@ relationship: part_of GO:0044754 ! autolysosome
id: GO:0120283
name: protein serine/threonine kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein serine/threonine kinase." [GOC:krc, GOC:sl, PMID:28608965]
+def: "Binding to a protein serine/threonine kinase." [GOC:krc, GOC:sl, PMID:28608965]
is_a: GO:0019901 ! protein kinase binding
[Term]
id: GO:0120284
name: tryptophan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 2-amino-3-(1H-indol-3-yl)propanoic acid." [GOC:krc]
+def: "Binding to 2-amino-3-(1H-indol-3-yl)propanoic acid." [GOC:krc]
synonym: "Trp binding" EXACT [GOC:krc]
is_a: GO:0016597 ! amino acid binding
is_a: GO:0031406 ! carboxylic acid binding
@@ -415565,7 +415254,7 @@ is_a: GO:1901363 ! heterocyclic compound binding
id: GO:0120285
name: tyrosine sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of tyrosine." [GOC:krc, PMID:31498992]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of tyrosine." [GOC:krc, PMID:31498992]
is_a: GO:0072545 ! tyrosine binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -415573,7 +415262,7 @@ is_a: GO:0140299 ! small molecule sensor activity
id: GO:0120286
name: tryptophan sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of tryptophan." [GOC:krc, PMID:31498992]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of tryptophan." [GOC:krc, PMID:31498992]
is_a: GO:0120284 ! tryptophan binding
is_a: GO:0140299 ! small molecule sensor activity
@@ -415697,8 +415386,8 @@ is_a: GO:0016410 ! N-acyltransferase activity
id: GO:0120300
name: peptide lactyltransferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (L-lysyl-[protein] + lactoyl-CoA = CoA + H(+) + N(6)-lactoyl-L-lysyl-[protein]." [GOC:sp, PMID:31645732]
-xref: RHEA:61997
+def: "Catalysis of the reaction: (L-lysyl-[protein] + lactoyl-CoA = CoA + H(+) + N(6)-lactoyl-L-lysyl-[protein]." [GOC:sp, PMID:31645732, RHEA:61996]
+xref: RHEA:61996
is_a: GO:0016410 ! N-acyltransferase activity
[Term]
@@ -415867,6 +415556,97 @@ def: "The assembly and organization of the sperm mitochondrial sheath, the tight
is_a: GO:0003006 ! developmental process involved in reproduction
relationship: part_of GO:0120316 ! sperm flagellum assembly
+[Term]
+id: GO:0120318
+name: olfactory sociosexual communication
+namespace: biological_process
+def: "The use of external chemical cues called pheromones to send social and sexual information between members of the same species, leading to specific behavioral responses. Pheromones may be detected by two olfactory sensory circuits, the main olfactory pathway and the vomeronasal system." [GOC:krc, PMID:17935991]
+comment: Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior.
+is_a: GO:0007610 ! behavior
+is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms
+
+[Term]
+id: GO:0120319
+name: long-chain fatty acid omega-1 hydroxylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: an (omega-1)-ethyl long-chain fatty acid + O2 + reduced [NADPH-hemoprotein reductase] = an (omega-1)-hydroxy-long-chain fatty acid + H+ + H2O + oxidized [NADPH-hemoprotein reductase." [GOC:nhn, PMID:18577768, PMID:22772592, PMID:24242247, RHEA:60936]
+synonym: "cytochrome P450 fatty acid omega-1 hydroxylase activity" RELATED []
+xref: RHEA:60936
+is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+
+[Term]
+id: GO:0120320
+name: lateral pseudopodium retraction
+namespace: biological_process
+def: "The myosin-based contraction and retraction of a lateral pseudopodium." [GOC:krc, GOC:pf, PMID:12953059, PMID:15483055, PMID:17623773]
+synonym: "lateral pseudopodium suppression" RELATED []
+is_a: GO:0031270 ! pseudopodium retraction
+
+[Term]
+id: GO:0120321
+name: nuclear envelope adjacent to nuclear pore complex
+namespace: cellular_component
+def: "The region of the nuclear envelope situated in close proximity to a nuclear pore complex." [GOC:mah, PMID:21802294, PMID:24184107]
+synonym: "associated with the nuclear pore" RELATED [GOC:mah]
+synonym: "nuclear envelope adjacent to NPC" EXACT [GOC:mah]
+synonym: "nuclear envelope periphery of the nuclear pore complex" EXACT [GOC:mah]
+is_a: GO:0110165 ! cellular anatomical entity
+relationship: part_of GO:0005635 ! nuclear envelope
+
+[Term]
+id: GO:0120322
+name: lipid modification by small protein conjugation
+namespace: biological_process
+def: "A lipid modification process in which one or more groups of a small protein, such as ubiquitin or a ubiquitin-like protein, are covalently attached to a target lipid." [GOC:sp, PMID:34012115]
+is_a: GO:0030258 ! lipid modification
+
+[Term]
+id: GO:0120323
+name: lipid ubiquitination
+namespace: biological_process
+def: "The process in which one or more ubiquitin groups are added to a lipid." [GOC:sp, PMID:34012115]
+is_a: GO:0120322 ! lipid modification by small protein conjugation
+
+[Term]
+id: GO:0120324
+name: procyclogenesis
+namespace: biological_process
+def: "The morphological, biochemical and genetic changes that induce the differentiation of bloodstream form trypomastigotes into procyclic trypomastigotes in some of the Trypanosomatidae species such as Trypanosoma brucei. This process occurs inside the midgut of the tsetse fly vectors in T. brucei." [GOC:ach, https://www.cdc.gov/parasites/sleepingsickness/biology.html, PMID:10593184, PMID:1698624, PMID:17997129, PMID:3194362, PMID:3194363]
+is_a: GO:0044114 ! development of symbiont in host
+
+[Term]
+id: GO:0120325
+name: NuRD complex binding
+namespace: molecular_function
+def: "Binding to a NuRD complex." [GOC:krc, GOC:lb, PMID:25150861]
+is_a: GO:0044877 ! protein-containing complex binding
+
+[Term]
+id: GO:0120326
+name: appressorium-mediated entry into host
+namespace: biological_process
+def: "Penetration by a symbiont into a host organism via an appressorium. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:ach, GOC:krc, PMID:14731267, PMID:22589729]
+synonym: "appressorium-mediated host invasion" EXACT [GOC:ach]
+synonym: "appressorium-mediated host penetration" EXACT [GOC:ach]
+synonym: "appressorium-mediated invasion into host" EXACT [GOC:ach]
+synonym: "appressorium-mediated penetration into host" EXACT [] {EXACT="GOC:ach"}
+is_a: GO:0044409 ! entry into host
+
+[Term]
+id: GO:0120327
+name: telopode
+namespace: cellular_component
+def: "A telopode is a plasma membrane bounded cell projection that is present on a telocyte and is tens to hundreds of microns long. Telopodes form a labyrinthine system communicating through gap junctions." [GOC:krc, MESH:D000067617, PMID:20367664]
+is_a: GO:0120025 ! plasma membrane bounded cell projection
+
+[Term]
+id: GO:0120328
+name: ATP-dependent DNA (cytosine-5-)-methyltransferase activity
+namespace: molecular_function
+def: "Catalytic activity that acts to transfer a methyl group to a DNA molecule, driven by ATP hydrolysis." [GOC:krc, PMID:31955845, PMID:32437639]
+is_a: GO:0003886 ! DNA (cytosine-5-)-methyltransferase activity
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
+
[Term]
id: GO:0140007
name: KICSTOR complex
@@ -415896,6 +415676,7 @@ id: GO:0140013
name: meiotic nuclear division
namespace: biological_process
def: "One of the two nuclear divisions that occur as part of the meiotic cell cycle." [PMID:9334324]
+subset: goslim_generic
synonym: "meiosis" EXACT []
is_a: GO:0000280 ! nuclear division
is_a: GO:1903046 ! meiotic cell cycle process
@@ -415980,10 +415761,12 @@ is_a: GO:0016192 ! vesicle-mediated transport
[Term]
id: GO:0140027
-name: establishment of contractile vacuole localization
+name: contractile vacuole localization
namespace: biological_process
def: "The directed movement of the contractile vacuole to a specific location." [PMID:19687255]
-is_a: GO:0051656 ! establishment of organelle localization
+synonym: "establishment of contractile vacuole localization" NARROW []
+is_a: GO:0051648 ! vesicle localization
+is_a: GO:1990849 ! vacuolar localization
[Term]
id: GO:0140028
@@ -416006,7 +415789,7 @@ relationship: part_of GO:0006887 ! exocytosis
id: GO:0140030
name: modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon post-translation modification of the target protein." [PMID:26060076]
+def: "Binding to a protein upon post-translation modification of the target protein." [PMID:26060076]
comment: This term should only be used when the binding is shown to require a post-translational modification: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of the modification. It may be that the PTM causes a conformational change that allows binding of the protein to another region; this type of modification-dependent protein binding is valid for annotation to this term.
synonym: "modified protein binding" RELATED []
is_a: GO:0005515 ! protein binding
@@ -416015,7 +415798,7 @@ is_a: GO:0005515 ! protein binding
id: GO:0140031
name: phosphorylation-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon phosphorylation of the target protein." [PMID:26060076]
+def: "Binding to a protein upon phosphorylation of the target protein." [PMID:26060076]
comment: This term should only be used when the binding is shown to require phosphorylation of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of phosphorylation. It may be that the phosphorylation causes a conformational change that allows binding of the protein to another region; this type of phosphorylation-dependent protein binding is valid for annotation to this term.
is_a: GO:0140030 ! modification-dependent protein binding
@@ -416023,7 +415806,7 @@ is_a: GO:0140030 ! modification-dependent protein binding
id: GO:0140032
name: glycosylation-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon glycosylation of the target protein." [PMID:26060076]
+def: "Binding to a protein upon glycosylation of the target protein." [PMID:26060076]
comment: This term should only be used when the binding is shown to require glycosylation of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of glycosylation. It may be that the glycosylation causes a conformational change that allows binding of the protein to another region; this type of glycosylation-dependent protein binding is valid for annotation to this term.
is_a: GO:0140030 ! modification-dependent protein binding
@@ -416031,7 +415814,7 @@ is_a: GO:0140030 ! modification-dependent protein binding
id: GO:0140033
name: acetylation-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon acetylation of the target protein." [PMID:26060076]
+def: "Binding to a protein upon acetylation of the target protein." [PMID:26060076]
comment: This term should only be used when the binding is shown to require acetylation of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of acetylation. It may be that the acetylation causes a conformational change that allows binding of the protein to another region; this type of acetylation-dependent protein binding is valid for annotation to this term.
is_a: GO:0140030 ! modification-dependent protein binding
@@ -416039,7 +415822,7 @@ is_a: GO:0140030 ! modification-dependent protein binding
id: GO:0140034
name: methylation-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon methylation of the target protein." [PMID:26060076]
+def: "Binding to a protein upon methylation of the target protein." [PMID:26060076]
comment: This term should only be used when the binding is shown to require methylation of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of methylation. It may be that the methylation causes a conformational change that allows binding of the protein to another region; this type of methylation-dependent protein binding is valid for annotation to this term.
is_a: GO:0140030 ! modification-dependent protein binding
@@ -416047,7 +415830,7 @@ is_a: GO:0140030 ! modification-dependent protein binding
id: GO:0140035
name: ubiquitination-like modification-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon modification by a ubiquitin-like protein of the target protein." [PMID:26060076]
+def: "Binding to a protein upon modification by a ubiquitin-like protein of the target protein." [PMID:26060076]
comment: This term should only be used when the binding is shown to require a ubiquitin-like modification in the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of ubiquitin-like modification. It may be that the modification causes a conformational change that allows binding of the protein to another region; this type of modification-dependent protein binding is valid for annotation to this term.
is_a: GO:0140030 ! modification-dependent protein binding
@@ -416055,7 +415838,7 @@ is_a: GO:0140030 ! modification-dependent protein binding
id: GO:0140036
name: ubiquitin-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon ubiquitination of the target protein." [PMID:26060076]
+def: "Binding to a protein upon ubiquitination of the target protein." [PMID:26060076]
comment: This term should only be used when the binding is shown to require ubiquitination of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of ubiquitination. It may be that the ubiquitination causes a conformational change that allows binding of the protein to another region; this type of ubiquitination-dependent protein binding is valid for annotation to this term.
is_a: GO:0140035 ! ubiquitination-like modification-dependent protein binding
@@ -416063,7 +415846,7 @@ is_a: GO:0140035 ! ubiquitination-like modification-dependent protein binding
id: GO:0140037
name: sumo-dependent protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein upon sumoylation of the target protein." [PMID:26060076]
+def: "Binding to a protein upon sumoylation of the target protein." [PMID:26060076]
comment: This term should only be used when the binding is shown to require sumoylation of the target protein: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of sumoylation. It may be that the sumoylation causes a conformational change that allows binding of the protein to another region; this type of sumoylation-dependent protein binding is valid for annotation to this term.
is_a: GO:0140035 ! ubiquitination-like modification-dependent protein binding
@@ -416101,7 +415884,7 @@ synonym: "adiposome formation" EXACT []
synonym: "lipid body formation" EXACT []
synonym: "lipid particle formation" EXACT []
is_a: GO:0034389 ! lipid droplet organization
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
relationship: part_of GO:0019915 ! lipid storage
[Term]
@@ -416175,6 +415958,7 @@ id: GO:0140053
name: mitochondrial gene expression
namespace: biological_process
def: "The process in which a mitochondrial gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [PMID:27058308]
+subset: goslim_generic
subset: goslim_pombe
is_a: GO:0010467 ! gene expression
@@ -416244,6 +416028,7 @@ name: peptide crotonyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: crotonyl-CoA + lysine in peptide = CoA + N-crotonyl-lysine-peptide." [PMID:25818647]
synonym: "protein crotonyltransferase activity" RELATED []
+xref: RHEA:53908
is_a: GO:0016410 ! N-acyltransferase activity
[Term]
@@ -416252,6 +416037,7 @@ name: peptide butyryltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: butyryl-CoA + lysine in peptide = CoA + N-butyryl-lysine-peptide." [PMID:27105113]
synonym: "protein butyryltransferase activity" RELATED []
+xref: RHEA:53912
is_a: GO:0016410 ! N-acyltransferase activity
[Term]
@@ -416321,7 +416107,8 @@ relationship: positively_regulates GO:0042953 ! lipoprotein transport
id: GO:0140078
name: class I DNA-(apurinic or apyrimidinic site) endonuclease activity
namespace: molecular_function
-def: "Catalysis of the cleavage of an AP site 3' of the baseless site by a beta-lyase mechanism, leaving an unsaturated aldehyde, termed a 3'-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5'-phosphate." [PMID:1698278, Wikipedia:AP_endonuclease]
+def: "Catalysis of the cleavage of an AP site 3' of the baseless site by a beta-lyase mechanism, leaving an unsaturated aldehyde, termed a 3'-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5'-phosphate." [PMID:1698278, RHEA:66592]
+comment: Note that this term is does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. Class II AP endonuclease is a nuclease, but not Class I, III and IV.
synonym: "AP endonuclease class I activity" RELATED []
synonym: "AP site-DNA 5'-phosphomonoester-lyase activity" EXACT []
synonym: "class I DNA-(apurinic or apyrimidinic site) lyase activity" EXACT []
@@ -416329,6 +416116,8 @@ synonym: "DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase activity
synonym: "DNA-(apurinic or apyrimidinic site) lyase activity" EXACT []
xref: EC:4.2.99.18
xref: MetaCyc:4.2.99.18-RXN
+xref: RHEA:66592
+xref: Wikipedia:AP_endonuclease
is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) endonuclease activity
is_a: GO:0016835 ! carbon-oxygen lyase activity
@@ -416336,17 +416125,18 @@ is_a: GO:0016835 ! carbon-oxygen lyase activity
id: GO:0140080
name: class III/IV DNA-(apurinic or apyrimidinic site) endonuclease activity
namespace: molecular_function
-def: "Catalysis of the cleavage of an AP site 3' and 5' of the baseless site, generating a 3'-phosphate and a 5'-OH." [PMID:2519777, Wikipedia:AP_endonuclease]
+def: "Catalysis of the cleavage of an AP site 3' and 5' of the baseless site, generating a 3'-phosphate and a 5'-OH." [PMID:2519777]
+comment: Note that this term is does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. Class II AP endonuclease is a nuclease, but not Class I, III and IV.
synonym: "endonuclease III" RELATED []
synonym: "endonuclease IV" RELATED []
+xref: Wikipedia:AP_endonuclease
is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) endonuclease activity
-is_a: GO:0016889 ! endodeoxyribonuclease activity, producing 3'-phosphomonoesters
[Term]
id: GO:0140081
name: glycosylated region protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a glycosylated region of a protein." [GOC:pg]
+def: "Binding to a glycosylated region of a protein." [GOC:pg]
is_a: GO:0005515 ! protein binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -416359,10 +416149,11 @@ is_a: GO:0061665 ! SUMO ligase activity
[Term]
id: GO:0140083
-name: protein-DNA unloading ATPase activity
+name: ATP-dependent protein-DNA unloading activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate , this reaction drives the unwinding of the DNA helix and drives the removal of a protein or protein complex from a DNA molecule, by introducing non-canonical DNA structures or generating torque to directly inhibit a protein-DNA binding interaction." [PMID:28552615]
-is_a: GO:0008094 ! ATPase, acting on DNA
+def: "Facilitating the removal of a protein or protein complex from a DNA molecule driven by ATP hydrolysis. This can be achieved for example by introducing non-canonical DNA structures or generating torque to directly inhibit a protein-DNA binding interaction." [PMID:28552615]
+synonym: "protein-DNA unloading ATPase activity" EXACT []
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
[Term]
id: GO:0140084
@@ -416414,6 +416205,7 @@ id: GO:0140096
name: catalytic activity, acting on a protein
namespace: molecular_function
def: "Catalytic activity that acts to modify a protein." [GOC:molecular_function_refactoring, GOC:pdt]
+subset: goslim_generic
is_a: GO:0003824 ! catalytic activity
[Term]
@@ -416421,14 +416213,16 @@ id: GO:0140097
name: catalytic activity, acting on DNA
namespace: molecular_function
def: "Catalytic activity that acts to modify DNA." [GOC:molecular_function_refactoring, GOC:pdt]
-is_a: GO:0003824 ! catalytic activity
+subset: goslim_generic
+is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid
[Term]
id: GO:0140098
name: catalytic activity, acting on RNA
namespace: molecular_function
-def: "Catalytic activity that acts to modify RNA." [GOC:molecular_function_refactoring, GOC:pdt]
-is_a: GO:0003824 ! catalytic activity
+def: "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis." [GOC:molecular_function_refactoring, GOC:pdt]
+subset: goslim_generic
+is_a: GO:0140640 ! catalytic activity, acting on a nucleic acid
[Term]
id: GO:0140101
@@ -416458,6 +416252,7 @@ namespace: molecular_function
def: "Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location." [GOC:molecular_function_refactoring, GOC:pdt]
comment: Note that a carrier moves with its substrate/cargo, while a transporter does not move with the cargo, but facilitates the change in localization.
subset: gocheck_do_not_annotate
+subset: goslim_generic
is_a: GO:0003674 ! molecular_function
[Term]
@@ -416646,7 +416441,7 @@ subset: gocheck_do_not_annotate
synonym: "miRNA transporter activity" NARROW []
synonym: "nucleocytoplasmic importin/exportin activity" EXACT []
synonym: "pre-miRNA transporter activity" NARROW []
-is_a: GO:0140597 ! protein carrier activity
+is_a: GO:0140104 ! molecular carrier activity
[Term]
id: GO:0140145
@@ -416704,7 +416499,7 @@ is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter ac
id: GO:0140164
name: Golgi transport complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the Golgi transport complex, a multisubunit tethering complex of the CATCHR family." [GOC:ha, PMID:28100664]
+def: "Binding to a Golgi transport complex, a multisubunit tethering complex of the CATCHR family." [GOC:ha, PMID:28100664]
synonym: "COG complex binding" EXACT []
is_a: GO:0044877 ! protein-containing complex binding
@@ -416966,6 +416761,8 @@ name: general transcription initiation factor activity
namespace: molecular_function
def: "A molecular function required for core promoter activity that mediates the assembly of the RNA polymerase holoenzyme at promoter DNA to form the pre-initiation complex (PIC). General transcription factors (GTFs) bind to and open promoter DNA, initiate RNA synthesis and stimulate the escape of the polymerase from the promoter. Not all subunits of the general transcription factor are necessarily present at all promoters to initiate transcription. GTFs act at each promoter, although the exact subunit composition at individual promoters may vary." [GOC:txnOH-2018]
comment: Usage guidance: The distinction between general transcription factors and DNA-binding transcription factors is that the latter modulate the selection of which genes are expressed under specific conditions, while general transcription factors are the constitutive machinery required for transcription initiation.
+subset: goslim_drosophila
+subset: goslim_generic
synonym: "basal transcription factor activity" EXACT []
synonym: "general transcription factor activity" EXACT []
synonym: "GTF activity" EXACT []
@@ -417228,14 +417025,14 @@ relationship: negatively_regulates GO:0016036 ! cellular response to phosphate s
id: GO:0140259
name: PRC1 complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a PRC1 complex." [PMID:15280237]
+def: "Binding to a PRC1 complex." [PMID:15280237]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:0140260
name: mitochondrial proton-transporting ATP synthase complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mitochondrial proton-transporting ATP synthase complex." [PMID:12110673]
+def: "Binding to a mitochondrial proton-transporting ATP synthase complex." [PMID:12110673]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -417254,7 +417051,7 @@ is_a: GO:0000152 ! nuclear ubiquitin ligase complex
id: GO:0140262
name: mRNA cap binding complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a mRNA cap binding complex." [PMID:16938833]
+def: "Binding to a mRNA cap binding complex." [PMID:16938833]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -417304,7 +417101,7 @@ is_a: GO:0098704 ! carbohydrate import across plasma membrane
id: GO:0140272
name: exogenous protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein or protein complex from a different species, for example a pathogen molecule binding to a host protein (a complex of two or more proteins that may include other nonprotein molecules)." [PMID:28861068]
+def: "Binding to a protein or protein complex from a different species, for example a pathogen molecule binding to a host protein." [PMID:28861068]
comment: Note that as GO captures normal processes, it may be that exogenous proteins interactions are normal for one of the participating species but not the other. Therefore reciprocal annotations should not be made without confirming that it is physiological relevant.
is_a: GO:0005488 ! binding
@@ -417417,7 +417214,6 @@ synonym: "activation of septin assembly and septum biosynthesis involved in mito
synonym: "activation of septin assembly and septum formation involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "positive regulation of division septum formation involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "positive regulation of formation of division septum involved in mitotic cell cycle" EXACT [GOC:TermGenie]
-synonym: "positive regulation of mitotic division septum assembly" EXACT []
synonym: "positive regulation of septin assembly and septum biosynthesis involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "positive regulation of septin assembly and septum formation involved in mitotic cell cycle" RELATED [GOC:TermGenie]
synonym: "up regulation of division septum formation involved in mitotic cell cycle" EXACT [GOC:TermGenie]
@@ -417444,7 +417240,6 @@ id: GO:0140282
name: carbon-nitrogen ligase activity on lipid II
namespace: molecular_function
def: "Catalysis of the reaction: L-glutamine + lipid II + ATP + H2O = L-glutamate + beta-D-GlcNAc(1->4)-Mur2Ac(oyl-L-Ala-D-isoGln-L-Lys-D-Ala-D-Ala)-diphospho-di-trans,octa-cis-undecaprenol + ADP + phosphate." [PMID:22291598, PMID:30093673, PMID:30154570, RHEA:57928]
-synonym: "carbon-nitrogen ligase activity on lipid II" EXACT []
synonym: "L-glutamate--lipid II transaminase activity" EXACT []
synonym: "undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl pentapeptide amidotransferase (glutamine-hydrolyzing) activity" EXACT []
xref: EC:6.3.5.13
@@ -417528,7 +417323,7 @@ is_a: GO:0048018 ! receptor ligand activity
id: GO:0140296
name: general transcription initiation factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a general transcription initiation factor, a protein that contributes to transcription start site selection and transcription initiation." [GOC:txnOH-2018]
+def: "Binding to a general transcription initiation factor, a protein that contributes to transcription start site selection and transcription initiation." [GOC:txnOH-2018]
is_a: GO:0008134 ! transcription factor binding
[Term]
@@ -417538,7 +417333,7 @@ namespace: molecular_function
alt_id: GO:0001107
alt_id: GO:0033613
alt_id: GO:0070491
-def: "Interacting selectively and non-covalently with a DNA-binding transcription factor, a protein that interacts with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription." [GOC:txnOH-2018]
+def: "Binding to a DNA-binding transcription factor, a protein that interacts with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription." [GOC:txnOH-2018]
synonym: "activating transcription factor binding" RELATED []
synonym: "repressing transcription factor binding" RELATED []
synonym: "transcription activator binding" RELATED []
@@ -417558,6 +417353,8 @@ id: GO:0140299
name: small molecule sensor activity
namespace: molecular_function
def: "Binding to a small molecule and eliciting a change in the protein's activity in response to the intracellular level of that small molecule." [PMID:26328879]
+subset: goslim_drosophila
+subset: goslim_generic
synonym: "small molecular sensor activity" EXACT []
is_a: GO:0003674 ! molecular_function
@@ -417624,6 +417421,8 @@ id: GO:0140313
name: molecular sequestering activity
namespace: molecular_function
def: "The selective interaction of a protein with a specific molecule to prevent it from interacting with other partners or inhibiting its localization to other areas of the cell." [PMID:13130076]
+subset: goslim_drosophila
+subset: goslim_generic
is_a: GO:0003674 ! molecular_function
[Term]
@@ -417719,7 +417518,7 @@ name: ATPase-coupled intramembrane lipid transporter activity
namespace: molecular_function
alt_id: GO:0004012
alt_id: GO:0008557
-def: "Catalysis of the movement of lipids from one membrane leaflet to the other, using energy from the hydrolysis of ATP. This includes flippases and floppases." [PMID:16828084]
+def: "Catalysis of the movement of lipids from one membrane leaflet to the other, driven by ATP hydrolysis. This includes flippases and floppases." [PMID:16828084]
synonym: "aminophospholipid-transporting ATPase" RELATED []
synonym: "ATPase-coupled phospholipid transporter activity" RELATED []
synonym: "ATPase-dependent phospholipid transporter activity" RELATED []
@@ -417731,8 +417530,8 @@ xref: EC:7.6.2.1
xref: MetaCyc:3.6.3.1-RXN
xref: Reactome:R-HSA-939763 "P-type ATPases type IV transport external-facing APLs to internal side of the plasma membrane"
xref: Reactome:R-HSA-947591 "P-type ATPases type IV transport internal-facing APLs to external side of the plasma membrane"
-is_a: GO:0016887 ! ATPase
is_a: GO:0140303 ! intramembrane lipid transporter activity
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0140327
@@ -417765,7 +417564,7 @@ id: GO:0140330
name: xenobiotic detoxification by transmembrane export across the cell outer membrane
namespace: biological_process
def: "A process that reduces or removes the toxicity of a xenobiotic by exporting it outside the cell through the outer membrane." [PMID:11948170]
-is_a: GO:0042908 ! xenobiotic transport
+is_a: GO:0046618 ! xenobiotic export
is_a: GO:0140317 ! export across cell outer membrane
relationship: part_of GO:0098754 ! detoxification
@@ -418237,6 +418036,7 @@ synonym: "effector-mediated suppression of host immune innate response by symbio
synonym: "effector-mediated suppression of host innate immune response by symbiont" EXACT []
synonym: "effector-mediated suppression of host innate immunity" EXACT []
synonym: "effector-triggered suppression of host immune innate response by symbiont" EXACT []
+is_a: GO:0052170 ! suppression by symbiont of host innate immune response
is_a: GO:0140404 ! effector-mediated modulation of host innate immune response by symbiont
is_a: GO:0140590 ! effector-mediated suppression of host defenses
@@ -418344,7 +418144,7 @@ namespace: molecular_function
def: "A molecular function regulator that inhibits the activity of a transcription regulator via direct binding and/or post-translational modification." [PMID:10652346]
comment: Usage guidance: transcription regulator inhibitors bind to a transcription regulator to prevent it from reaching the chromatin. This activity does not occur at the promoter. For activities that do occur at the promoter, consider GO:0001217 ; DNA-binding transcription repressor activity or GO:0003714 ; transcription corepressor activity. An example of a transcription regulator is TCF23 Q7RTU1 is an example of a protein that regulates transcription factors by heterodimerising or binding to DbTFs and prevent DNA binding and their specific genomic binding site where the dbTF would have activated or repressed transcription. Also an example is NFKBIA P25963 which has a different way of regulating transcription factor activity by sequestering the dbTF (complex) in the cytoplasm. Another example is the HSP90 and HSP23 proteins that sequester steroid receptors away from the DNA.
synonym: "DNA-binding transcription factor inhibitor activity" NARROW []
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0140678 ! molecular function inhibitor activity
[Term]
id: GO:0140417
@@ -418444,7 +418244,7 @@ relationship: positively_regulates GO:0072356 ! chromosome passenger complex loc
id: GO:0140431
name: DNA-(abasic site) binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a DNA site that has neither a purine nor a pyrimidine base. Apurinic sites can form spontaneously or when DNA glycosylase removes a damaged base." [PMID:23245849]
+def: "Binding to a DNA site that has neither a purine nor a pyrimidine base. Apurinic sites can form spontaneously or when DNA glycosylase removes a damaged base." [PMID:23245849]
synonym: "DNA AP site binding" EXACT []
synonym: "DNA-(apurinic site) binding" NARROW []
synonym: "DNA-(apurinic site/apyrimidinic site) binding" EXACT []
@@ -418660,7 +418460,7 @@ is_a: GO:1903046 ! meiotic cell cycle process
id: GO:0140457
name: protein demethylase activity
namespace: molecular_function
-def: "Catalysis of the removal of a methyl group from a protein." [PMID:24498420]
+def: "Catalysis of the removal of a methyl group from a protein." [PMID:24498420, PMID:28360925]
is_a: GO:0032451 ! demethylase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
@@ -418670,6 +418470,7 @@ name: pre-transcriptional gene silencing by RNA
namespace: biological_process
def: "Any gene inactivation (silencing) process mediated by small RNA molecules that occur before the trancription begins." [PMID:21420348]
is_a: GO:0031047 ! gene silencing by RNA
+is_a: GO:0031507 ! heterochromatin assembly
[Term]
id: GO:0140459
@@ -418687,11 +418488,11 @@ is_a: GO:0009617 ! response to bacterium
[Term]
id: GO:0140461
-name: subtelomeric heterochromatin organization
+name: obsolete subtelomeric heterochromatin organization
namespace: biological_process
-def: "The organization of chromatin into heterochromatin at the subtelomeric region of a chromosome." [PMID:26744419]
-is_a: GO:0032200 ! telomere organization
-is_a: GO:0070828 ! heterochromatin organization
+def: "OBSOLETE. The organization of chromatin into heterochromatin at the subtelomeric region of a chromosome." [PMID:26744419]
+comment: This term has been obsoleted because it represents a different process, GO:0097240 attachment of telomeric heterochromatin to nuclear envelope.
+is_obsolete: true
[Term]
id: GO:0140462
@@ -418833,7 +418634,7 @@ is_a: GO:0140359 ! ABC-type transporter activity
id: GO:0140482
name: iron sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of iron." [PMID:11956219, PMID:25806539]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of iron." [PMID:11956219, PMID:25806539]
is_a: GO:0140299 ! small molecule sensor activity
[Term]
@@ -418934,7 +418735,7 @@ id: GO:0140494
name: migrasome
namespace: cellular_component
def: "A vesicular organelle that forms on retraction fibers behind migrating cells and mediates the release of cytoplasmic contents during cell migration." [PMID:25342562, PMID:31371827]
-is_a: GO:0043226 ! organelle
+is_a: GO:0043231 ! intracellular membrane-bounded organelle
[Term]
id: GO:0140495
@@ -418947,7 +418748,7 @@ is_a: GO:0016477 ! cell migration
id: GO:0140496
name: gamma-tubulin complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a gamma-tubulin complex." [PMID:30174135]
+def: "Binding to a gamma-tubulin complex." [PMID:30174135]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -419109,7 +418910,6 @@ def: "The mitotic cell cycle process in which the controlled breakdown of the nu
synonym: "nuclear pore complex disassembly during mitosis" EXACT []
is_a: GO:0006999 ! nuclear pore organization
is_a: GO:0007077 ! mitotic nuclear membrane disassembly
-is_a: GO:0022607 ! cellular component assembly
is_a: GO:0032984 ! protein-containing complex disassembly
[Term]
@@ -419244,7 +419044,7 @@ name: transcription regulator activator activity
namespace: molecular_function
def: "A molecular function regulator that increases the activity of a transcription regulator via direct binding and/or post-translational modification." [PMID:9597751]
comment: Usage guidance: transcription regulator activators bind to a transcription regulator to allow it to reach the chromatin or to contact other transcriptional regulators. This activity does not occur at the promoter. For activities that do occur at the promoter, consider GO:0001216 ; DNA-binding transcription activator activity or GO:0003713; transcription coactivator activity; those activities respectively bind DNA themselves or positively regulate a transcription regulator when it is located at the chromatin.
-is_a: GO:0098772 ! molecular function regulator
+is_a: GO:0140677 ! molecular function activator activity
[Term]
id: GO:0140538
@@ -419279,7 +419079,8 @@ namespace: biological_process
def: "The cellular synthesis of Piwi-interacting RNA piRNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism." [PMID:28847004]
synonym: "Piwi-associated RNA transcription" EXACT []
synonym: "PIWI-interacting RNA transcription" EXACT []
-is_a: GO:0006351 ! transcription, DNA-templated
+is_a: GO:0034660 ! ncRNA metabolic process
+is_a: GO:0098781 ! ncRNA transcription
[Term]
id: GO:0140542
@@ -419311,7 +419112,7 @@ id: GO:0140545
name: protein disaggregase activity
namespace: molecular_function
def: "An ATP-dependent molecular chaperone activity that mediates the solubilization of ordered protein aggregates." [PMID:26312418]
-is_a: GO:0016887 ! ATPase
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0140546
@@ -419331,12 +419132,13 @@ relationship: part_of GO:0048316 ! seed development
[Term]
id: GO:0140548
-name: envenomation resulting in blood agglutination in other organism
+name: envenomation resulting in blood agglutination in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with specific proteins binding to cell-surface carbohydrates and causing calcium-dependent agglutination of blood cells in the bitten organism." [PMID:10484740]
+synonym: "envenomation resulting in blood agglutination in other organism" EXACT []
synonym: "envenomation resulting in erythrocytes agglutination in other organism" EXACT []
synonym: "envenomation resulting in red blood cells agglutination in other organism" EXACT []
-is_a: GO:0035738 ! envenomation resulting in modulation of process in other organism
+is_a: GO:0035738 ! envenomation resulting in modulation of process in another organism
[Term]
id: GO:0140549
@@ -419350,7 +419152,7 @@ is_a: GO:0016020 ! membrane
id: GO:0140550
name: phosphatidylinositol-4,5-bisphosphate sensor activity
namespace: molecular_function
-def: "Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of phosphatidylinositol-4,5-bisphosphate." [PMID:33172987]
+def: "Binding to and responding, e.g. by conformational change, to changes in the cellular level of phosphatidylinositol-4,5-bisphosphate." [PMID:33172987]
is_a: GO:0140299 ! small molecule sensor activity
[Term]
@@ -419371,14 +419173,6 @@ synonym: "TEAD-4-YAP complex" NARROW []
xref: CORUM:2870
is_a: GO:0090575 ! RNA polymerase II transcription regulator complex
-[Term]
-id: GO:0140554
-name: L-arginine 3-hydroxylase activity
-namespace: molecular_function
-def: "Catalyzes the reaction: 2-oxoglutarate + [protein]-L-arginine + O2 = [protein]-(3R)-3-hydroxy-L-arginine + CO2 + succinate." [PMID:29563586, RHEA:56744]
-xref: RHEA:56744
-is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
-
[Term]
id: GO:0140560
name: xylosyl alpha-1,3-xylosyltransferase activity
@@ -419417,19 +419211,21 @@ is_a: GO:0035252 ! UDP-xylosyltransferase activity
[Term]
id: GO:0140566
-name: epigenetic reader
+name: histone reader
namespace: molecular_function
-def: "A transcription regulator that recognizes epigenetic marks such as methylated cytosines in CpG islands and modified histones, and modulates the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:32260176]
-is_a: GO:0140110 ! transcription regulator activity
+def: "A chromatin adaptor that recognizes specific forms of histones, either modified by a post-translational modification, or the unmodified form. Histone readers have roles in many processes, including in centromere function or in modulating the accessibility of cis-regulatory regions to the transcription machinery." [PMID:11498575, PMID:25688442, PMID:31082667, PMID:32260176, PMID:34726351]
+synonym: "epigenetic reader" BROAD []
+is_a: GO:0140463 ! chromatin-protein adaptor
[Term]
id: GO:0140567
name: transmembrane protein dislocase activity
namespace: molecular_function
-def: "The activity of removing a protein from a membrane, by binding to a transmembrane helical fragment of a tail-anchored protein and releasing it from the the hydrophobic region of one or both lipid bilayers." [PMID:24821790, PMID:28712723, PMID:32973005]
+def: "The activity of removing a protein from a membrane, by binding to a transmembrane helical fragment of a tail-anchored protein and releasing it from the the hydrophobic region of one or both lipid bilayers. The reaction is driven by ATP hydrolysis." [PMID:24821790, PMID:28712723, PMID:32973005]
synonym: "transmembrane helix dislocase" RELATED []
xref: RHEA:66168
is_a: GO:0140318 ! protein transporter activity
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:0140568
@@ -419464,6 +419260,7 @@ synonym: "L-ascorbate:ferricytochrome-b5 oxidoreductase activity" EXACT []
xref: EC:7.2.1.3
xref: MetaCyc:1.10.2.1-RXN
xref: RHEA:30403
+is_a: GO:0015453 ! oxidoreduction-driven active transmembrane transporter activity
is_a: GO:0016722 ! oxidoreductase activity, acting on metal ions
[Term]
@@ -419538,7 +419335,7 @@ is_a: GO:0007189 ! adenylate cyclase-activating G protein-coupled receptor signa
id: GO:0140584
name: chromatin extrusion motor activity
namespace: molecular_function
-def: "A DNA translocase activity that folds chromosomal DNA and catalytically extends the newly formed loop." [PMID:23074191, PMID:26499245, PMID:27210764]
+def: "A DNA translocase activity that folds chromosomal DNA and catalytically extends the newly formed loop, driven by ATP hydrolysis." [PMID:23074191, PMID:26499245, PMID:27210764]
synonym: "chromatin extrusion activity" EXACT []
is_a: GO:0015616 ! DNA translocase activity
@@ -419574,8 +419371,11 @@ id: GO:0140588
name: chromatin looping
namespace: biological_process
def: "A chromatin organization process that starts with the loading of an extrusion motor (by an SMC family complex) onto the chromatin, followed by chromatin extrusion that stops at loop anchoring sites on the chromosome." [PMID:32213323]
+comment: To describe the molecular function associated with chromatin looping, consider 'chromatin extrusion motor activity'; GO:0140584.
synonym: "chromatin folding" RELATED []
synonym: "chromatin loop assembly" EXACT []
+synonym: "DNA loop extrusion" EXACT []
+synonym: "DNA looping" BROAD []
is_a: GO:0006325 ! chromatin organization
[Term]
@@ -419634,10 +419434,10 @@ is_a: GO:0005742 ! mitochondrial outer membrane translocase complex
[Term]
id: GO:0140597
-name: protein carrier activity
+name: protein carrier chaperone
namespace: molecular_function
-def: "Binding to and carrying a protein between two different cellular locations by moving along with the target protein." [PMID:7628437]
-synonym: "protein carrier chaperone" EXACT []
+def: "Binding to and carrying a protein between two different cellular components by moving along with the target protein." [PMID:7628437]
+synonym: "protein carrier activity" EXACT []
synonym: "protein chaperone" BROAD []
is_a: GO:0140104 ! molecular carrier activity
@@ -419646,7 +419446,7 @@ id: GO:0140598
name: lipoprotein carrier activity
namespace: molecular_function
def: "Binding to and carrying a lipoprotein between two different cellular locations by moving along with the target lipoprotein." [PMID:7628437]
-is_a: GO:0140597 ! protein carrier activity
+is_a: GO:0140597 ! protein carrier chaperone
[Term]
id: GO:0140599
@@ -419666,18 +419466,12 @@ is_a: GO:0042405 ! nuclear inclusion body
[Term]
id: GO:0140603
-name: ATP hydrolysis activity
+name: obsolete ATP hydrolysis activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H2O = ADP + H+ Pi. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient." [RHEA:13065]
-synonym: "adenosine 5'-triphosphatase activity" RELATED []
-synonym: "adenosine triphosphatase activity" RELATED []
-synonym: "adenosinetriphosphatase activity" EXACT []
-synonym: "ATP hydrolase activity" RELATED []
-synonym: "ATP monophosphatase activity" RELATED []
-synonym: "ATP phosphohydrolase activity" EXACT []
-xref: MetaCyc:ADENOSINETRIPHOSPHATASE-RXN
-xref: RHEA:13065
-is_a: GO:0017111 ! nucleoside-triphosphatase activity
+def: "OBSOLETE. Catalysis of the reaction: ATP + H2O = ADP + H+ Pi. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient." [GOC:curators]
+comment: This term was deprecated because it was created in the wrong branch on the ontology.
+is_obsolete: true
+replaced_by: GO:0016887
[Term]
id: GO:0140604
@@ -419693,8 +419487,7 @@ id: GO:0140605
name: proton motive force-driven motor activity
namespace: molecular_function
def: "A motor activity driven by an electrochemical proton gradient (proton-motive force). PMF-driven motors are used by bacterial flagella." [PMID:18216858]
-synonym: "proton motive force-driven motor activity" EXACT []
-is_a: GO:0003774 ! motor activity
+is_a: GO:0003774 ! cytoskeletal motor activity
[Term]
id: GO:0140608
@@ -419762,7 +419555,6 @@ namespace: molecular_function
def: "Catalyzes the reaction: 2 iodide + L-tyrosine + 2 NADP+ = 3,5-diiodo-L-tyrosine + H+ + 2 NADPH." [PMID:15289438, PMID:18434651, PMID:25395621, PMID:27643701, RHEA:32479]
synonym: "iodide peroxidase-tyrosine iodinase activity" RELATED []
synonym: "iodotyrosine deiodase activity" RELATED []
-synonym: "iodotyrosine deiodinase activity" RELATED []
synonym: "monoiodotyrosine deiodinase activity" RELATED []
synonym: "tyrosine iodinase activity" RELATED []
xref: EC:1.21.1.1
@@ -419796,8 +419588,7 @@ id: GO:0140619
name: DNA strand exchange activator activity
namespace: molecular_function
def: "Binds to and increases a DNA strand exchange activity." [PMID:33493431]
-is_a: GO:0030234 ! enzyme regulator activity
-is_a: GO:0120230 ! recombinase activator activity
+is_a: GO:0008047 ! enzyme activator activity
[Term]
id: GO:0140620
@@ -419805,7 +419596,6 @@ name: DNA strand exchange inhibitor activity
namespace: molecular_function
def: "Binds to and stops, prevents or reduces a DNA strand exchange activity." [PMID:33493431]
is_a: GO:0004857 ! enzyme inhibitor activity
-is_a: GO:0030234 ! enzyme regulator activity
[Term]
id: GO:0140621
@@ -419911,7 +419701,7 @@ id: GO:0140632
name: inflammasome complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form an inflammasome complex." [PMID:33420028, PMID:33420033, PMID:33542150]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:0140633
@@ -419951,6 +419741,973 @@ def: "A small heterodimeric protein complex that is required during early matura
synonym: "small ribosomal subunit maturation complex" RELATED []
is_a: GO:1905348 ! endonuclease complex
+[Term]
+id: GO:0140639
+name: positive regulation of pyroptosis
+namespace: biological_process
+def: "Any process that increases the frequency, rate or extent of pyroptosis." [PMID:24626226]
+is_a: GO:0043068 ! positive regulation of programmed cell death
+relationship: positively_regulates GO:0070269 ! pyroptosis
+
+[Term]
+id: GO:0140640
+name: catalytic activity, acting on a nucleic acid
+namespace: molecular_function
+def: "Catalytic activity that acts to modify a nucleic acid." [GOC:pg]
+is_a: GO:0003824 ! catalytic activity
+
+[Term]
+id: GO:0140641
+name: mitotic spindle formation (spindle phase two)
+namespace: biological_process
+def: "The spindle organization process in which the spindle is maintained at a constant length during mitotic metaphase." [PMID:32723864]
+synonym: "metaphase spindle stability" EXACT []
+synonym: "metaphase spindle stabilization" EXACT []
+is_a: GO:0090307 ! mitotic spindle assembly
+
+[Term]
+id: GO:0140642
+name: meiotic spindle formation (spindle phase two)
+namespace: biological_process
+def: "The spindle organization process in which the spindle is maintained at a constant length during meiotic metaphase." [PMID:32723864]
+is_a: GO:0090306 ! meiotic spindle assembly
+
+[Term]
+id: GO:0140643
+name: hydroxymethylglutaryl-CoA reductase (NADH) activity
+namespace: molecular_function
+def: "Catalysis of the reaction: (R)-mevalonate + CoA + 2 NAD(+) <=> 3-hydroxy-3-methylglutaryl-CoA + 2 NADH." [PMID:29224355, RHEA:14833]
+comment: Note that this activity is not present in eukaryotes, see PMID:29224355.
+synonym: "3-hydroxy-3-methylglutaryl coenzyme A reductase activity" BROAD [EC:1.1.1.88]
+synonym: "beta-hydroxy-beta-methylglutaryl CoA-reductase activity" BROAD [EC:1.1.1.88]
+synonym: "beta-hydroxy-beta-methylglutaryl coenzyme A reductase activity" BROAD [EC:1.1.1.88]
+synonym: "HMG-CoA reductase activity" BROAD [EC:1.1.1.88]
+synonym: "hydroxymethylglutaryl coenzyme A reductase activity" BROAD [EC:1.1.1.88]
+xref: EC:1.1.1.88
+xref: KEGG_REACTION:R02081
+xref: MetaCyc:HYDROXYMETHYLGLUTARYL-COA-REDUCTASE-RXN
+xref: RHEA:14833
+is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+
+[Term]
+id: GO:0140644
+name: neutrophil extracellular trap
+namespace: cellular_component
+def: "Extracellular microbicidal structure composed of nuclear chromatin, histones and granular antimicrobial proteins. Histones and several neutrophil granule proteins associated with the DNA framework damage entrapped microorganisms." [PMID:31172493]
+synonym: "NET" BROAD []
+is_a: GO:0043264 ! extracellular non-membrane-bounded organelle
+
+[Term]
+id: GO:0140645
+name: neutrophic extracellular trap formation
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a neutrophil extracellular trap, a network of extracellular fibers primarily composed of DNA from neutrophils, which bind and neutralizes pathogens." [PMID:28267716]
+synonym: "NET formation" BROAD []
+xref: http://purl.obolibrary.org/obo/TXPO_0002149
+is_a: GO:0022607 ! cellular component assembly
+
+[Term]
+id: GO:0140646
+name: negative regulation of pre-B cell receptor expression
+namespace: biological_process
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of the process leading up to expression of the pre-B cell receptor on the surface of pre-B cells." [PMID:22949502]
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:0051093 ! negative regulation of developmental process
+relationship: negatively_regulates GO:0002330 ! pre-B cell receptor expression
+
+[Term]
+id: GO:0140647
+name: P450-containing electron transport chain
+namespace: biological_process
+def: "A electron transport chain in which one or more electron carriers operate to transfer electrons from donors to a cytochrome P450 protein or domain. Electron carriers operating in this chain include FAD-containing flavoproteins or domains, FMN domains, ferredoxins and cytochrome b5. The reduced cytochrome P450 functions as the terminal oxidase and participates in a wide range of biochemical pathways." [PMID:16042601]
+synonym: "P450-containing system" RELATED []
+xref: Wikipedia:P450-containing_systems
+is_a: GO:0022900 ! electron transport chain
+
+[Term]
+id: GO:0140648
+name: positive regulation of cell cycle switching, mitotic to meiotic cell cycle
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of mitotic to meiotic cell cycle switching, the process in which a cell switches cell cycle mode from mitotic to meiotic division." [PMID:22375066]
+is_a: GO:0051446 ! positive regulation of meiotic cell cycle
+is_a: GO:0090068 ! positive regulation of cell cycle process
+is_a: GO:0110044 ! regulation of cell cycle switching, mitotic to meiotic cell cycle
+relationship: positively_regulates GO:0051728 ! cell cycle switching, mitotic to meiotic cell cycle
+
+[Term]
+id: GO:0140649
+name: cell-to-cell migration by invasive hypha
+namespace: biological_process
+def: "The directional movement of a hyphal filament from one host cell to another. This process involves the clearance of plant-derived plasmodesmal occlusion materials, cytoskeleton based constriction of invasive hypha to traverse plasmodesmata. Septins and F-actin are reorganized into an hourglass shape at the point of maximum hyphal constriction." [PMID:29567712]
+comment: Do not confuse with ' GO:0036267 invasive filamentous growth ', which doesn't include invasion of cells within the host.
+synonym: "host tissue colonization" BROAD []
+synonym: "invasive growth" BROAD []
+synonym: "invasive hyphae formation" EXACT []
+synonym: "plant tissue colonization" BROAD []
+is_a: GO:0106259 ! cell-to-cell migration in host
+
+[Term]
+id: GO:0140650
+name: radial glia-guided pyramidal neuron migration
+namespace: biological_process
+def: "The radial migration of a pyramidal neuron along radial glial cells." [PMID:3760547]
+synonym: "radial glia-dependent neuronal migration" EXACT []
+is_a: GO:0001764 ! neuron migration
+
+[Term]
+id: GO:0140651
+name: futile creatine cycle
+namespace: biological_process
+def: "The phosphorylation and dephosphorylation of creatine in a futile cycle, which dissipates the high energy charge of phosphocreatine as heat without performing any mechanical or chemical work. The futile creatine cycle takes place in thermogenic fat cells and is part of adaptive thermogenesis." [PMID:33597756, PMID:33981039]
+is_a: GO:0008152 ! metabolic process
+relationship: part_of GO:1990845 ! adaptive thermogenesis
+
+[Term]
+id: GO:0140652
+name: pyripyropene A biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of pyripyropene A." [GOC:ach, PMID:21224862, PMID:26019565]
+synonym: "pyripyropene A anabolism" EXACT []
+synonym: "pyripyropene A biosynthesis" EXACT []
+synonym: "pyripyropene A formation" EXACT []
+synonym: "pyripyropene A synthesis" EXACT []
+is_a: GO:0016106 ! sesquiterpenoid biosynthetic process
+is_a: GO:0018130 ! heterocycle biosynthetic process
+is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+
+[Term]
+id: GO:0140653
+name: fumitremorgin C biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of fumitremorgin C." [GOC:ach, PMID:19226505]
+synonym: "fumitremorgin C anabolism" EXACT []
+synonym: "fumitremorgin C biosynthesis" EXACT []
+synonym: "fumitremorgin C formation" EXACT []
+synonym: "fumitremorgin C synthesis" EXACT []
+is_a: GO:0019438 ! aromatic compound biosynthetic process
+is_a: GO:0035835 ! indole alkaloid biosynthetic process
+is_a: GO:1901378 ! organic heteropentacyclic compound biosynthetic process
+is_a: GO:1901503 ! ether biosynthetic process
+
+[Term]
+id: GO:0140654
+name: tryprostatin A biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of tryprostatin A." [GOC:ach, PMID:19226505]
+synonym: "tryprostatin A anabolism" EXACT []
+synonym: "tryprostatin A biosynthesis" EXACT []
+synonym: "tryprostatin A formation" EXACT []
+synonym: "tryprostatin A synthesis" EXACT []
+is_a: GO:0035835 ! indole alkaloid biosynthetic process
+is_a: GO:0042435 ! indole-containing compound biosynthetic process
+is_a: GO:0043043 ! peptide biosynthetic process
+is_a: GO:1901503 ! ether biosynthetic process
+
+[Term]
+id: GO:0140655
+name: mitochondrial proliferation
+namespace: biological_process
+def: "The multiplication of mitochondria, resulting in the expansion of the number of mitochondria within a cell." [PMID:28301064]
+is_a: GO:0007005 ! mitochondrion organization
+
+[Term]
+id: GO:0140656
+name: endodeoxyribonuclease activator activity
+namespace: molecular_function
+def: "Binds to and increases the activity of an endodeoxyribonuclease." [PMID:33836577]
+is_a: GO:0008047 ! enzyme activator activity
+
+[Term]
+id: GO:0140657
+name: ATP-dependent activity
+namespace: molecular_function
+def: "A molecular function characterized by the coupling of ATP hydrolysis to other steps of a reaction mechanism to make the reaction energetically favorable, for example to catalyze a reaction or drive transport against a concentration gradient." [PMID:24878343, PMID:25750732, PMID:32933017, PMID:33818025, PMID:33873056, PMID:33988324]
+comment: Note that this term represents a grouping class that includes all proteins that use ATP hydrolysis to drive a reaction; it is not meant to capture the ATP hydrolysis reaction itself. To annotate ATP hydrolysis, please use 'ATP hydrolysis activity ; GO:0016887'.
+subset: gocheck_do_not_annotate
+subset: goslim_chembl
+subset: goslim_drosophila
+subset: goslim_generic
+subset: goslim_yeast
+synonym: "ATP hydrolysis-dependent activity" EXACT []
+synonym: "ATPase activity" EXACT []
+synonym: "ATPase activity, coupled" EXACT []
+synonym: "ATPase-dependent activity" EXACT []
+is_a: GO:0003674 ! molecular_function
+
+[Term]
+id: GO:0140658
+name: ATP-dependent chromatin remodeler activity
+namespace: molecular_function
+alt_id: GO:0070615
+def: "An activity, driven by ATP hydrolysis, that modulates the contacts between histones and DNA, resulting in a change in chromosome architecture within the nucleosomal array, leading to chromatin remodeling." [PMID:14729263, PMID:19165147, PMID:21862382, PMID:30867599, PMID:34313222]
+synonym: "ATP hydrolysis-dependent chromatin remodeler activity" EXACT []
+synonym: "ATPase-dependent chromatin remodeler activity" EXACT []
+synonym: "nucleosome-activated ATPase activity" RELATED [GOC:mah]
+synonym: "nucleosome-dependent ATPase activity" RELATED []
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
+
+[Term]
+id: GO:0140659
+name: cytoskeletal motor regulator activity
+namespace: molecular_function
+def: "Binds to and modulates the activity of a motor protein." [PMID:23142046, PMID:33221250]
+synonym: "motor activity regulator activity" BROAD []
+is_a: GO:0098772 ! molecular function regulator
+
+[Term]
+id: GO:0140660
+name: cytoskeletal motor activator activity
+namespace: molecular_function
+def: "Binds to and increases the activity of a motor protein." [PMID:33221250]
+synonym: "motor activity activator activity" BROAD []
+is_a: GO:0140659 ! cytoskeletal motor regulator activity
+is_a: GO:0140677 ! molecular function activator activity
+
+[Term]
+id: GO:0140661
+name: cytoskeletal motor inhibitor activity
+namespace: molecular_function
+def: "Binds to and stops, prevents, or reduces the activity of a motor protein." [PMID:23142046]
+synonym: "motor activity inhibitor activity" BROAD []
+is_a: GO:0140659 ! cytoskeletal motor regulator activity
+is_a: GO:0140678 ! molecular function inhibitor activity
+
+[Term]
+id: GO:0140662
+name: ATP-dependent protein folding chaperone
+namespace: molecular_function
+def: "Binding to a protein or a protein-containing complex to assist the protein folding process, driven by ATP hydrolysis." [PMID:27365453]
+is_a: GO:0044183 ! protein folding chaperone
+is_a: GO:0140657 ! ATP-dependent activity
+
+[Term]
+id: GO:0140663
+name: ATP-dependent FeS chaperone activity
+namespace: molecular_function
+def: "Binding to and delivering metal ions to a target protein, driven by ATP hydrolysis." [PMID:16843540]
+is_a: GO:0016530 ! metallochaperone activity
+is_a: GO:0140657 ! ATP-dependent activity
+
+[Term]
+id: GO:0140664
+name: ATP-dependent DNA damage sensor activity
+namespace: molecular_function
+def: "A molecule that recognises toxic DNA structures, and initiates a signalling response, driven by ATP hydrolysis." [PMID:33302090, PMID:33510387]
+is_a: GO:0008094 ! ATP-dependent activity, acting on DNA
+is_a: GO:0140612 ! DNA damage sensor activity
+
+[Term]
+id: GO:0140665
+name: ATP-dependent H3-H4 histone complex loader activity
+namespace: molecular_function
+def: "Loading of a histone H3-H4 complex onto DNA, driven by ATP hydrolysis." [PMID:31848341, PMID:33658433]
+synonym: "H3-H4 dimer loading activity" EXACT []
+synonym: "H3-H4 histone chaperone" BROAD []
+synonym: "H3-H4 histone complex loader activity" BROAD []
+synonym: "histone chaperone" RELATED []
+synonym: "histone H3-H4 dimer loading activity" EXACT []
+is_a: GO:0140674 ! ATP-dependent histone loader activity
+
+[Term]
+id: GO:0140666
+name: annealing activity
+namespace: molecular_function
+alt_id: GO:0097617
+def: "An activity that facilitates the formation of a complementary double-stranded polynucleotide molecule." [PMID:22888405]
+synonym: "renaturation" RELATED []
+is_a: GO:0003676 ! nucleic acid binding
+
+[Term]
+id: GO:0140667
+name: regulation of oxytocin production
+namespace: biological_process
+def: "Any process that modulates the frequency, rate, or extent of production of oxytocin." [PMID:25096581]
+is_a: GO:0010468 ! regulation of gene expression
+relationship: regulates GO:0036162 ! oxytocin production
+
+[Term]
+id: GO:0140668
+name: positive regulation of oxytocin production
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of production of oxytocin." [PMID:25096581]
+is_a: GO:0010628 ! positive regulation of gene expression
+is_a: GO:0140667 ! regulation of oxytocin production
+relationship: positively_regulates GO:0036162 ! oxytocin production
+
+[Term]
+id: GO:0140669
+name: negative regulation of oxytocin production
+namespace: biological_process
+def: "Any process that stops, prevents, or reduces the rate of production of oxytocin." [PMID:25096581]
+is_a: GO:0010629 ! negative regulation of gene expression
+is_a: GO:0140667 ! regulation of oxytocin production
+relationship: negatively_regulates GO:0036162 ! oxytocin production
+
+[Term]
+id: GO:0140670
+name: ATP-dependent cohesin unloading activity
+namespace: molecular_function
+def: "Facilitating a conformational change to unload a cohesin complex from sister chromatids, driven by ATP hydrolysis." [PMID:26687354]
+is_a: GO:0140083 ! ATP-dependent protein-DNA unloading activity
+
+[Term]
+id: GO:0140671
+name: ADA complex
+namespace: cellular_component
+def: "A chromatin remodelling complex that regulates transcription via acetylation primarily of nucleosomal histones H3 and H2B. In budding yeast shares the histone acetylation (HAT) module of ADA2-GCN5-NGG1-SGF29 with the related SAGA complex." [GOC:bhm, PMID:21734642, PMID:28966424]
+synonym: "ADA HAT complex" EXACT []
+synonym: "ADA histone acetyltransferase complex" EXACT []
+synonym: "Ada2/Gcn5/Ada3 transcription activator complex" RELATED []
+synonym: "scADA" NARROW []
+is_a: GO:0070461 ! SAGA-type complex
+
+[Term]
+id: GO:0140672
+name: ATAC complex
+namespace: cellular_component
+def: "A chromatin remodelling complex that regulates transcription via acetylation primarily of nucleosomal histones H3 and possibly H4. Shares the histone acetylation (HAT) module of GCN5/PCAF-ADA2-ADA3-SGF29 (or orthologs) with the related SAGA complex (GO:0000124). Contains HAT subunits GCN5 or PCAF in a mutually exclusive manner. In addition to the HAT module contains DR1/NC2B, KAT14, MBIP, WDR5, YEATS2 and ZZZ3 or orthologs. Also regulates the activity of non-histone targets and orchestrates mitotic progression by regulating Cyclin A degradation through acetylation." [GOC:bhm, PMID:19936620, PMID:20562830, PMID:28966424]
+synonym: "Ada two A containing complex" EXACT []
+synonym: "Ada Two-A containing complex" EXACT []
+synonym: "Ada-Two-A-containing complex" EXACT []
+synonym: "ADA2A-containing complex" EXACT []
+synonym: "G-ATAC complex" EXACT []
+synonym: "KAT2A-containing ATAC complex" EXACT []
+synonym: "KAT2B-containing ATAC complex" EXACT []
+is_a: GO:0070461 ! SAGA-type complex
+
+[Term]
+id: GO:0140673
+name: co-transcriptional chromatin reassembly
+namespace: biological_process
+def: "The reestablishment of chromatin structure that was disrupted upon passage of RNA polymerase II during transcription elongation. This process prevents cryptic intragenic transcription initiation." [PMID:22922743]
+comment: Note: Do not confuse with 'GO:0045815 epigenetic maintenance of chromatin in transcription-competent conformation', which describes the maintenance of chromatin in an open conformation (indeendent of transcription).
+synonym: "chromatin maintenance during transcription elongation" RELATED []
+synonym: "euchromatin maintenance during transcription elongation" EXACT []
+synonym: "maintainance of chromatin integrity during transcription elongation by RNAPII" EXACT []
+synonym: "maintenance of transcriptionally active chromatin during transcription elongation" EXACT []
+is_a: GO:0031497 ! chromatin assembly
+relationship: part_of GO:0006368 ! transcription elongation from RNA polymerase II promoter
+
+[Term]
+id: GO:0140674
+name: ATP-dependent histone loader activity
+namespace: molecular_function
+def: "Depositing a histone or a histone complex onto DNA." [PMID:26459557]
+synonym: "histone loader activity" BROAD []
+synonym: "histone loading activity" EXACT []
+is_a: GO:0140658 ! ATP-dependent chromatin remodeler activity
+
+[Term]
+id: GO:0140675
+name: ATP-dependent histone unloader activity
+namespace: molecular_function
+def: "Removing a histone or a histone complex from DNA." [PMID:26459557]
+synonym: "histone unloader activity" BROAD []
+synonym: "histone unloading activity" EXACT []
+is_a: GO:0140658 ! ATP-dependent chromatin remodeler activity
+
+[Term]
+id: GO:0140676
+name: oscillatory cAMP signaling
+namespace: biological_process
+def: "Fluctuation in the extracellular cAMP levels due to the alternate activation of adenylate cyclase, which produces cAMP, and phosphodiesterase, which degrades it. Occurs in Dictyostelium during early sorocarp development. Oscillation in signaling result is directional chemotaxis of cells towards the center of the aggregate." [PMID:18657484]
+synonym: "cAMP relay" EXACT []
+is_a: GO:0007267 ! cell-cell signaling
+
+[Term]
+id: GO:0140677
+name: molecular function activator activity
+namespace: molecular_function
+def: "A molecular function regulator that activates or increases the activity of its target via non-covalent binding that does not result in covalent modification to the target." [GOC:curators]
+is_a: GO:0098772 ! molecular function regulator
+
+[Term]
+id: GO:0140678
+name: molecular function inhibitor activity
+namespace: molecular_function
+def: "A molecular function regulator that inhibits or decreases the activity of its target via non-covalent binding that does not result in covalent modification to the target." [GOC:curators]
+is_a: GO:0098772 ! molecular function regulator
+
+[Term]
+id: GO:0140679
+name: ABC-type sodium transporter activity
+namespace: molecular_function
+def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na(in) -> ADP + phosphate + Na(out)." [PMID:9106203]
+xref: EC:7.2.2.4
+xref: RHEA:14633
+xref: TC:3.A.1.115.1
+is_a: GO:0015081 ! sodium ion transmembrane transporter activity
+is_a: GO:0019829 ! ATPase-coupled cation transmembrane transporter activity
+is_a: GO:0140359 ! ABC-type transporter activity
+
+[Term]
+id: GO:0140680
+name: histone H3-di/monomethyl-lysine-36 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:20531378]
+synonym: "histone H3K36me demethylase activity" RELATED []
+synonym: "histone H3K36me2 demethylase activity" BROAD []
+xref: EC:1.14.11.27
+xref: MetaCyc:RXN-8661
+xref: RHEA:42032
+is_a: GO:0051864 ! histone H3-methyl-lysine-36 demethylase activity
+
+[Term]
+id: GO:0140681
+name: histone H3-tri/dimethyl-lysine-36 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:21914792]
+synonym: "histone H3K36me2 demethylase activity" BROAD []
+synonym: "histone H3K36me3 demethylase activity" RELATED []
+xref: EC:1.14.11.69
+xref: MetaCyc:RXN-8660
+xref: RHEA:60236
+is_a: GO:0051864 ! histone H3-methyl-lysine-36 demethylase activity
+
+[Term]
+id: GO:0140682
+name: histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction." [PMID:22473470]
+synonym: "histone H3K4me demethylase activity" RELATED []
+synonym: "histone H3K4me2 demethylase activity" BROAD []
+xref: EC:1.14.99.66
+xref: RHEA:60244
+is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0032453 ! histone H3-methyl-lysine-4 demethylase activity
+
+[Term]
+id: GO:0140683
+name: histone H3-di/monomethyl-lysine-9 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a di or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:16603238]
+synonym: "histone H3K9me demethylase activity" BROAD []
+synonym: "histone H3K9me2 demethylase activity" BROAD []
+xref: EC:1.14.11.65
+xref: RHEA:60188
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
+is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+
+[Term]
+id: GO:0140684
+name: histone H3-tri/dimethyl-lysine-9 demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate." [PMID:20208542, PMID:20531378]
+synonym: "histone H3K9me2 demethylase activity" BROAD []
+synonym: "histone H3K9me3 demethylase activity" RELATED []
+xref: EC:1.14.11.66
+xref: RHEA:60200
+is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
+is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+
+[Term]
+id: GO:0140685
+name: histone H3-di/monomethyl-lysine-9 FAD-dependent demethylase activity
+namespace: molecular_function
+def: "Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction." [PMID:22473470]
+synonym: "histone H3K9me demethylase activity" BROAD []
+synonym: "histone H3K9me2 demethylase activity" BROAD []
+is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
+is_a: GO:0032454 ! histone H3-methyl-lysine-9 demethylase activity
+
+[Term]
+id: GO:0140690
+name: dihydropyrimidine dehydrogenase (NAD+) complex
+namespace: cellular_component
+def: "A heteromultimeric complex capable of dihydropyrimidine dehydrogenase (NAD+); in E. coli, composed of PreA and PreT." [PMID:21169495, PMID:34097066]
+xref: MetaCyc:CPLX0-7788
+is_a: GO:1990204 ! oxidoreductase complex
+
+[Term]
+id: GO:0140691
+name: RNA folding chaperone
+namespace: molecular_function
+def: "Binding to an RNA or an RNA-containing complex to assist the folding process." [PMID:31165735]
+subset: goslim_generic
+is_a: GO:0003674 ! molecular_function
+
+[Term]
+id: GO:0140692
+name: very long-chain fatty acid omega-hydroxylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: an omega-methyl-very-long-chain fatty acid + O2 + reduced [NADPH-hemoprotein reductase] = an omega-hydroxy-very-long-chain fatty acid + H+ + H2O + oxidized [NADPH-hemoprotein reductase]." [PMID:16547005]
+is_a: GO:0120250 ! fatty acid omega-hydroxylase activity
+
+[Term]
+id: GO:0140693
+name: molecular condensate scaffold activity
+namespace: molecular_function
+def: "Binding and bringing together two or more macromolecules in contact, permitting those molecules to organize as a molecular condensate." [PMID:28225081]
+is_a: GO:0030674 ! protein-macromolecule adaptor activity
+
+[Term]
+id: GO:0140694
+name: non-membrane-bounded organelle assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle." [PMID:28225081]
+synonym: "non-membrane-bounded organelle formation" EXACT []
+synonym: "non-membrane-enclosed organelle assembly" EXACT []
+synonym: "non-membrane-enclosed organelle formation" EXACT []
+is_a: GO:0070925 ! organelle assembly
+
+[Term]
+id: GO:0140696
+name: (S)-2-hydroxyglutarate dehydrogenase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: (S)-2-hydroxyglutarate + a quinone = 2-oxoglutarate + a quinol." [PMID:30498244, RHEA:58664]
+synonym: "L-2-hydroxyglutarate dehydrogenase activity" EXACT []
+xref: EC:1.1.5.13
+xref: RHEA:58664
+is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor
+
+[Term]
+id: GO:0140698
+name: attachment of telomeric heterochromatin to nuclear envelope
+namespace: biological_process
+def: "The process in which physical connections are formed between sub-telomeric heterochromatin and the nuclear envelope facilitating bouquet formation." [PMID:31635174]
+synonym: "attachment of telomeres to nuclear envelope" BROAD []
+synonym: "attachment of telomeric chromatin to nuclear envelope" BROAD []
+synonym: "heterochromatin organization" BROAD []
+is_a: GO:0097240 ! chromosome attachment to the nuclear envelope
+
+[Term]
+id: GO:0140699
+name: cyclic GMP-AMP synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + GTP = 2 diphosphate + cyclic GMP-AMP." [PMID:23258413]
+comment: Note that this term should not be used for direct annotation. It should be possible to annotate to a more specific child term that descibes the position of the phosphate group on the cGAMP molecule.
+subset: gocheck_do_not_annotate
+synonym: "cyclic-GMP-AMP synthase activity" EXACT []
+is_a: GO:0016779 ! nucleotidyltransferase activity
+
+[Term]
+id: GO:0140700
+name: 3',2'-cyclic GMP-AMP synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + GTP = 2 diphosphate + cyclic G-P(3'-5')A-P(2'-5') (cyclic 3',2' GAMP)." [PMID:34261127]
+synonym: "3',2' cyclic-GMP-AMP synthase activity" EXACT []
+synonym: "3',2'-cyclic GAMP synthase activity" EXACT []
+is_a: GO:0140699 ! cyclic GMP-AMP synthase activity
+
+[Term]
+id: GO:0140701
+name: 3',3'-cyclic GMP-AMP synthase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: ATP + GTP = 2 diphosphate + cyclic G-P(3'-5')A-P(3'-5') (cyclic 3',3' GAMP)." [PMID:30787435, RHEA:35647]
+synonym: "3',3' cyclic-GAMP synthase activity" EXACT []
+synonym: "3',3' cyclic-GMP-AMP synthase activity" EXACT []
+synonym: "3',3'-cyclic GAMP synthase activity" EXACT []
+xref: RHEA:35647
+is_a: GO:0140699 ! cyclic GMP-AMP synthase activity
+
+[Term]
+id: GO:0140702
+name: cyclic GMP-AMP binding
+namespace: molecular_function
+def: "Binding to cyclic GMP-AMP (cGAMP) nucleotide." [PMID:23258412]
+subset: gocheck_do_not_annotate
+is_a: GO:0030551 ! cyclic nucleotide binding
+is_a: GO:0032559 ! adenyl ribonucleotide binding
+is_a: GO:0032561 ! guanyl ribonucleotide binding
+is_a: GO:0043168 ! anion binding
+
+[Term]
+id: GO:0140703
+name: 3',3'-cyclic GMP-AMP binding
+namespace: molecular_function
+def: "Binding to 3',3' cyclic GMP-AMP (cGAMP) nucleotide, a cyclic purine dinucleotide that consists of AMP and GMP units cyclized via 3',5' and 3',5' linkages." [PMID:30787435]
+synonym: "3',3' cyclic-GMP-AMP binding" EXACT []
+synonym: "3',3'-cGAMP binding" EXACT []
+synonym: "3',3'-cGMP-AMP binding" EXACT []
+synonym: "3',3'-cyclic GAMP binding" EXACT []
+is_a: GO:0030551 ! cyclic nucleotide binding
+
+[Term]
+id: GO:0140704
+name: 3',2'-cyclic GMP-AMP binding
+namespace: molecular_function
+def: "Binding to 3',2' cyclic GMP-AMP (cGAMP) nucleotide, a cyclic purine dinucleotide that consists of AMP and GMP units cyclized via 3',5' and 2',5' linkages." [PMID:34261127]
+synonym: "3',2' cyclic-GMP-AMP binding" EXACT []
+synonym: "3',2'-cGAMP binding" EXACT []
+synonym: "3',2'-cyclic GAMP binding" EXACT []
+is_a: GO:0030551 ! cyclic nucleotide binding
+
+[Term]
+id: GO:0140706
+name: protein-containing complex localization to centriolar satellite
+namespace: biological_process
+def: "A protein-containing complex localization by which the complex is transported to, or maintained in, the centriolar satellite." [PMID:27979967]
+is_a: GO:0031503 ! protein-containing complex localization
+
+[Term]
+id: GO:0140707
+name: chromatin-nuclear membrane anchor activity
+namespace: molecular_function
+def: "Binding to chromatin and the nuclear inner membrane, in order to establish and maintain the heterochromatin location and organization, or to enable equal segregation of the nuclear membrane during mitosis." [PMID:24184107]
+is_a: GO:0043495 ! protein-membrane adaptor activity
+
+[Term]
+id: GO:0140708
+name: CAT tailing
+namespace: biological_process
+def: "The C-terminal elongation of 60S-anchored stalled nascent polypeptide chains with untemplated alanine and threonine tails (CAT tails). CAT tails participate in the recognition of stalled nascent chains by the ribosome quality control sytem." [PMID:25554787, PMID:32934225]
+is_a: GO:0002182 ! cytoplasmic translational elongation
+relationship: part_of GO:1990116 ! ribosome-associated ubiquitin-dependent protein catabolic process
+
+[Term]
+id: GO:0140709
+name: Frizzled Nuclear Import pathway
+namespace: biological_process
+def: "The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by internalization and cleavage of the frizzled receptor to yeild a C-terminal fragment that is imported into the nucleus. The frizzled C-terminal fragment is incorporated into large ribonucleoprotein particles and stimulates their egress via nuclear budding." [PMID:22510459, PMID:22579286]
+synonym: "FNI" BROAD []
+synonym: "Frizzled Nuclear Import Wnt Pathway" EXACT []
+is_a: GO:0035567 ! non-canonical Wnt signaling pathway
+
+[Term]
+id: GO:0140710
+name: regulation of Frizzled Nuclear Import pathway
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of a Frizzled Nuclear Import pathway." [PMID:22510459, PMID:22579286]
+synonym: "regulation of FNI" BROAD []
+synonym: "regulation of Frizzled Nuclear Import Wnt Pathway" EXACT []
+is_a: GO:2000050 ! regulation of non-canonical Wnt signaling pathway
+relationship: regulates GO:0140709 ! Frizzled Nuclear Import pathway
+
+[Term]
+id: GO:0140711
+name: positive regulation of Frizzled Nuclear Import pathway
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of a Frizzled Nuclear Import pathway." [PMID:22510459, PMID:22579286]
+synonym: "positive regulation of FNI" BROAD []
+synonym: "positive regulation of Frizzled Nuclear Import Wnt Pathway" EXACT []
+is_a: GO:0140710 ! regulation of Frizzled Nuclear Import pathway
+is_a: GO:2000052 ! positive regulation of non-canonical Wnt signaling pathway
+relationship: positively_regulates GO:0140709 ! Frizzled Nuclear Import pathway
+
+[Term]
+id: GO:0140712
+name: negative regulation of Frizzled Nuclear Import pathway
+namespace: biological_process
+def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a Frizzled Nuclear Import pathway." [PMID:22510459, PMID:22579286]
+synonym: "negative regulation of FNI" BROAD []
+synonym: "negative regulation of Frizzled Nuclear Import Wnt Pathway" EXACT []
+is_a: GO:0140710 ! regulation of Frizzled Nuclear Import pathway
+is_a: GO:2000051 ! negative regulation of non-canonical Wnt signaling pathway
+relationship: negatively_regulates GO:0140709 ! Frizzled Nuclear Import pathway
+
+[Term]
+id: GO:0140713
+name: histone chaperone activity
+namespace: molecular_function
+def: "Binding to and carrying a histone or a histone complex until it is deposited on DNA, or degraded." [PMID:26459557]
+synonym: "histone carrier activity" EXACT []
+is_a: GO:0140597 ! protein carrier chaperone
+
+[Term]
+id: GO:0140714
+name: large ribosomal subunit pre-assembly complex
+namespace: cellular_component
+def: "A protein complex that assists early maturation of nascent 60S ribosomal subunits. The complex interacts with the large ribosomal subunit rRNA via one of the components (Urb2 in S. cerevisiae) and requires a RNA helicase (Dbp6 in S. cerevisiae)." [GOC:lnp, PMID:17145778, PMID:9528757]
+is_a: GO:0101031 ! chaperone complex
+
+[Term]
+id: GO:0140715
+name: serine-tRNA ligase complex
+namespace: cellular_component
+def: "A heterodimeric enzyme complex that catalyzes the ligation of serine to tRNA(Ser), forming L-seryl-tRNA(Ser)." [PMID:30943413]
+is_a: GO:1902494 ! catalytic complex
+
+[Term]
+id: GO:0140717
+name: entry into host through the stromata
+namespace: biological_process
+def: "Entry of a symbiont into host plant tissue via the stromata, microscopic pores in the epidermis of the aerial parts of terrestrial plants. These pores are essential for photosynthesis, as they allow CO(2) to diffuse into the plant. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:16959560, PMID:17419713, PMID:29307013]
+is_a: GO:0044409 ! entry into host
+
+[Term]
+id: GO:0140718
+name: facultative heterochromatin assembly
+namespace: biological_process
+def: "The assembly of facultative heterochromatin, heterochromatin that can be converted to euchromatin and allow transcription under specific contexts. These can be temporal (e.g., developmental states or specific cell-cycle stages), spatial (e.g., nuclear localization changes from the center to the periphery or vice versa due to exogenous factors/signals), or parental/heritable (e.g., monoallelic gene expression)." [PMID:17936700]
+synonym: "fHC assembly" EXACT []
+is_a: GO:0031507 ! heterochromatin assembly
+
+[Term]
+id: GO:0140719
+name: constitutive heterochromatin assembly
+namespace: biological_process
+def: "The assembly of constitutive heterochromatin, heterochromatin that is always in a conformation refactory to transcription." [PMID:17936700]
+is_a: GO:0031507 ! heterochromatin assembly
+
+[Term]
+id: GO:0140720
+name: subtelomeric heterochromatin
+namespace: cellular_component
+def: "Heterochromatin that is located adjacent to the telomere, and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3)." [PMID:34576871]
+is_a: GO:0000792 ! heterochromatin
+relationship: part_of GO:0099115 ! chromosome, subtelomeric region
+
+[Term]
+id: GO:0140721
+name: nuclease inhibitor activity
+namespace: molecular_function
+def: "Binds to and modulates the activity of a nuclease." [PMID:28785032, PMID:29554913, PMID:30046034]
+is_a: GO:0004857 ! enzyme inhibitor activity
+
+[Term]
+id: GO:0140722
+name: mycophenolic acid biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of mycophenolic acid (MPA). MPA is the first isolated antibiotic natural product in the world obtained from a culture of Penicillium brevicompactum in 1893." [PMID:21398490, PMID:26751579, PMID:31209052]
+synonym: "MPA anabolism" BROAD []
+synonym: "MPA biosynthesis" BROAD []
+synonym: "MPA formation" BROAD []
+synonym: "MPA synthesis" BROAD []
+synonym: "mycophenolic acid anabolism" EXACT []
+synonym: "mycophenolic acid biosynthesis" EXACT []
+synonym: "mycophenolic acid formation" EXACT []
+synonym: "mycophenolic acid synthesis" EXACT []
+is_a: GO:0017000 ! antibiotic biosynthetic process
+is_a: GO:0030639 ! polyketide biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:0046189 ! phenol-containing compound biosynthetic process
+is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
+is_a: GO:1901336 ! lactone biosynthetic process
+
+[Term]
+id: GO:0140723
+name: patulin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of patulin, an acetate-derived tetraketide mycotoxin produced by several fungal species that shows antimicrobial properties against several bacteria." [PMID:25120234, PMID:30680886]
+synonym: "patulin anabolism" EXACT []
+synonym: "patulin biosynthesis" EXACT []
+synonym: "patulin formation" EXACT []
+synonym: "patulin synthesis" EXACT []
+is_a: GO:0030639 ! polyketide biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+
+[Term]
+id: GO:0140724
+name: positive regulation of patulin biosynthetic process
+namespace: biological_process
+def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of patulin." [PMID:25625822]
+synonym: "positive regulation of patulin anabolism" EXACT []
+synonym: "positive regulation of patulin formation" EXACT []
+synonym: "positive regulation of patulin synthesis" EXACT []
+is_a: GO:1900734 ! positive regulation of polyketide biosynthetic process
+relationship: positively_regulates GO:0140723 ! patulin biosynthetic process
+
+[Term]
+id: GO:0140725
+name: detoxification of free heme
+namespace: biological_process
+def: "Any process that reduces or removes the toxicity of free heme. These include transport of heme away from sensitive areas and to compartments or complexes whose purpose is sequestration of heme." [PMID:26741528, PMID:32983129]
+synonym: "free heme detoxification" EXACT []
+is_a: GO:0098754 ! detoxification
+
+[Term]
+id: GO:0140727
+name: siRNA-dependent pericentric heterochromatin assembly
+namespace: biological_process
+def: "The assembly of pericentric heterochromatin by a process mediated by a small interfering RNA." [PMID:15289661]
+synonym: "siRNA dependent pericentric heterochromatin assembly" EXACT []
+is_a: GO:0031508 ! pericentric heterochromatin assembly
+
+[Term]
+id: GO:0140728
+name: GC-box binding
+namespace: molecular_function
+def: "Binding to a GC-box, a DNA motif with the consensus sequence GGGCGG that is located upstream of the start point of eukaryotic transcription units. The GC-box may occur in multiple copies or in either orientation relative to the transcription start site." [PMID:14701757]
+synonym: "GC box binding" EXACT []
+synonym: "GC rich promoter region binding" BROAD []
+synonym: "GC-rich region binding" BROAD []
+synonym: "GC_rich_promoter_region binding" BROAD []
+is_a: GO:0000978 ! RNA polymerase II cis-regulatory region sequence-specific DNA binding
+
+[Term]
+id: GO:0140729
+name: self-resistance to endogenously produced metabolite
+namespace: biological_process
+def: "A process that reduces or removes the toxicity of an endogenously produced substance. Mechanisms of resistance to endogenously produced compounds include modification the compound, export, sequestration, or mutations in the target enzyme." [PMID:21923907, PMID:29763292]
+synonym: "prevention of self-toxicity" EXACT []
+synonym: "self-resistance to bioactive secondary metabolite" EXACT []
+synonym: "self-resistance to endogenously produced compound" EXACT []
+synonym: "self-resistance to endogenously produced toxin" EXACT []
+is_a: GO:0098754 ! detoxification
+
+[Term]
+id: GO:0140730
+name: amphiregulin production
+namespace: biological_process
+def: "The appearance of amphiregulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Amphiregulin (AREG) is a ligand of the epidermal growth factor receptor (EGFR), a widely expressed transmembrane tyrosine kinase. AREG is synthesized as a membrane-anchored precursor protein that can engage in juxtacrine signaling on adjacent cells. Alternatively, after proteolytic processing by cell membrane proteases, mainly TACE/ADAM17, AREG is secreted and behaves as an autocrine or paracrine factor." [PMID:24463227]
+comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
+subset: gocheck_do_not_annotate
+synonym: "AREG production" BROAD []
+is_a: GO:0001816 ! cytokine production
+
+[Term]
+id: GO:0140731
+name: regulation of amphiregulin production
+namespace: biological_process
+def: "Any process that modulates the frequency, rate, or extent of production of amphiregulin." [PMID:24463227]
+synonym: "regulation of AREG production" BROAD []
+is_a: GO:0001817 ! regulation of cytokine production
+relationship: regulates GO:0140730 ! amphiregulin production
+
+[Term]
+id: GO:0140732
+name: positive regulation of amphiregulin production
+namespace: biological_process
+def: "Any process that activates or increases the frequency, rate or extent of production of amphiregulin." [PMID:24463227]
+synonym: "positive regulation of AREG production" BROAD []
+is_a: GO:0001819 ! positive regulation of cytokine production
+is_a: GO:0140731 ! regulation of amphiregulin production
+relationship: positively_regulates GO:0140730 ! amphiregulin production
+
+[Term]
+id: GO:0140733
+name: tRNA ligase activator activity
+namespace: molecular_function
+def: "Binds to and increases the activity of a tRNA ligase, an enzyme that catalyzes the formation of aminoacyl-tRNA." [PMID:30943413]
+is_a: GO:0008047 ! enzyme activator activity
+is_a: GO:0055103 ! ligase regulator activity
+
+[Term]
+id: GO:0140734
+name: ammonium excretion
+namespace: biological_process
+def: "The elimination of ammonium ions from an excretory cell." [PMID:25740900]
+synonym: "ammonia excretion" RELATED []
+is_a: GO:0007588 ! excretion
+
+[Term]
+id: GO:0140735
+name: lovastatin biosynthetic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the formation of lovastatin (also known as mevinolin, mevacor or monacolin K), a hypolipidemic inhibitor of (3S)-hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR)." [PMID:10334994, PMID:10381407]
+synonym: "lovastatin anabolism" EXACT []
+synonym: "lovastatin biosynthesis" EXACT []
+synonym: "lovastatin formation" EXACT []
+synonym: "lovastatin synthesis" EXACT []
+synonym: "mevacor anabolism" EXACT []
+synonym: "mevacor biosynthesis" EXACT []
+synonym: "mevacor biosynthetic process" EXACT []
+synonym: "mevacor formation" EXACT []
+synonym: "mevacor synthesis" EXACT []
+synonym: "mevinolin anabolism" EXACT []
+synonym: "mevinolin biosynthesis" EXACT []
+synonym: "mevinolin biosynthetic process" EXACT []
+synonym: "mevinolin formation," EXACT []
+synonym: "mevinolin synthesis" EXACT []
+synonym: "monacolin K anabolism" EXACT []
+synonym: "monacolin K biosynthesis" EXACT []
+synonym: "monacolin K biosynthetic process" EXACT []
+synonym: "monacolin K formation" EXACT []
+synonym: "monacolin K synthesis" EXACT []
+xref: KEGG_PATHWAY:M00893
+xref: MetaCyc:PWY-7535
+is_a: GO:0008610 ! lipid biosynthetic process
+is_a: GO:0030639 ! polyketide biosynthetic process
+is_a: GO:0043386 ! mycotoxin biosynthetic process
+is_a: GO:1901336 ! lactone biosynthetic process
+
+[Term]
+id: GO:0140736
+name: positive regulation of lovastatin biosynthetic process
+namespace: biological_process
+def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of lovastin." [PMID:10334994, PMID:19781329]
+synonym: "positive regulation of mevacor biosynthetic process" EXACT []
+synonym: "positive regulation of mevinolin biosynthetic process" EXACT []
+synonym: "positive regulation of monacolin K biosynthetic process" EXACT []
+is_a: GO:0046889 ! positive regulation of lipid biosynthetic process
+is_a: GO:1900734 ! positive regulation of polyketide biosynthetic process
+relationship: positively_regulates GO:0140735 ! lovastatin biosynthetic process
+
+[Term]
+id: GO:0140737
+name: encapsulin nanocompartment
+namespace: cellular_component
+def: "Intracellular non-membrane bound organelle, consisting of proteinaceous polyhedral shells that encapsulate enzymes, protecting the contents from their surrounding milieu and/or the milieu from reactants in their interior. The self-assembling, 25-42 nm nanocompartment shell, unlike larger bacterial microcompartments, is made of only one protein, and has only a few proteins inside. Shells about vary from about 25-42 nm in diameter. The shell protein has an HK97-like fold and probably evolved from a viral protein. Artificial encapsulin nanocompartments can be expressed and filled with cargo proteins for biotechnological uses. They are found in many bacterial and a few archaeal phyla." [PMID:32918485]
+synonym: "protein nanocompartment" BROAD []
+is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
+
+[Term]
+id: GO:0140738
+name: NLRP6 inflammasome complex
+namespace: cellular_component
+def: "An inflammasome complex that consists of NLRP6, PYCARD/ASC and caspase-1 or caspase-4/caspase-11." [PMID:30674671, PMID:34678144]
+is_a: GO:0061702 ! inflammasome complex
+
+[Term]
+id: GO:0140739
+name: NLRP6 inflammasome complex assembly
+namespace: biological_process
+def: "The aggregation, arrangement and bonding together of a set of components to form a NLRP6 inflammasome complex." [PMID:30674671, PMID:34678144]
+is_a: GO:0140632 ! inflammasome complex assembly
+
+[Term]
+id: GO:0140740
+name: ADP-riboxanase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: L-arginyl-[protein] + NAD(+) = ADP-riboxanated L-argininyl-[protein] + H(+) + NH4(+) + nicotinamide." [PMID:34671164]
+comment: Note that this activity has two steps: a transfer of an ADP-robose group, followed by the elimitation of an ammonia group.
+xref: EC:4.3.99.-
+is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups
+is_a: GO:0016841 ! ammonia-lyase activity
+is_a: GO:0140096 ! catalytic activity, acting on a protein
+
+[Term]
+id: GO:0140741
+name: tRNA U4 sulfurtransferase
+namespace: molecular_function
+def: "Catalyzes the reaction: ATP + [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + uracil in tRNA + 2 reduced ferredoxin [iron-sulfur] cluster <=> AMP + diphosphate + 4-thiouracil in tRNA + [ThiI sulfur-carrier protein]-L-cysteine + 2 oxidized ferredoxin [iron-sulfur] cluster." [PMID:27791189, PMID:5541999, RHEA:24176]
+synonym: "tRNA uracil 4 sulfurtransferase" EXACT []
+synonym: "tRNA uracil 4-sulfurtransferase" EXACT []
+xref: EC:2.8.1.4
+xref: MetaCyc:TRNA-S-TRANSFERASE-RXN
+xref: RHEA:24176
+is_a: GO:0016783 ! sulfurtransferase activity
+is_a: GO:0140101 ! catalytic activity, acting on a tRNA
+
+[Term]
+id: GO:0140742
+name: lncRNA transcription
+namespace: biological_process
+def: "The transcription of lncRNAs, non-coding RNAs over 200 nucleotides in length, from a DNA template." [PMID:33767452, PMID:33913806]
+is_a: GO:0034660 ! ncRNA metabolic process
+is_a: GO:0098781 ! ncRNA transcription
+
+[Term]
+id: GO:0140743
+name: regulation of lncRNA transcription
+namespace: biological_process
+def: "Any process that modulates the frequency, rate or extent of the synthesis of a lncRNA." [PMID:33767452, PMID:33913806]
+is_a: GO:0006355 ! regulation of transcription, DNA-templated
+relationship: regulates GO:0140742 ! lncRNA transcription
+
+[Term]
+id: GO:0140744
+name: negative regulation of lncRNA transcription
+namespace: biological_process
+def: "Any process that decreases the frequency, rate or extent of the synthesis of a lncRNA." [PMID:33767452, PMID:33913806]
+is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:0140743 ! regulation of lncRNA transcription
+relationship: negatively_regulates GO:0140742 ! lncRNA transcription
+
+[Term]
+id: GO:0140745
+name: siRNA transcription
+namespace: biological_process
+def: "The transcription of a small interfering RNA from an RNA template." [PMID:23001036]
+is_a: GO:0001172 ! transcription, RNA-templated
+
+[Term]
+id: GO:0140746
+name: siRNA catabolic process
+namespace: biological_process
+def: "The chemical reactions and pathways resulting in the breakdown of small interfering RNA transcripts (siRNAs)." [PMID:25928405]
+is_a: GO:0034661 ! ncRNA catabolic process
+
[Term]
id: GO:0150001
name: primary dendrite
@@ -420167,7 +420924,8 @@ id: GO:0150031
name: regulation of protein localization to lysosome
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to lysosome." [GOC:aruk, GOC:bc, PMID:24305806]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0061462 ! protein localization to lysosome
[Term]
@@ -420175,8 +420933,9 @@ id: GO:0150032
name: positive regulation of protein localization to lysosome
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein localization to lysosome." [GOC:aruk, GOC:bc]
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0150031 ! regulation of protein localization to lysosome
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0061462 ! protein localization to lysosome
[Term]
@@ -420184,8 +420943,9 @@ id: GO:0150033
name: negative regulation of protein localization to lysosome
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to lysosome." [GOC:aruk, GOC:bc, PMID:24305806]
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0150031 ! regulation of protein localization to lysosome
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0061462 ! protein localization to lysosome
[Term]
@@ -420254,7 +421014,7 @@ name: regulation of postsynaptic dense core vesicle exocytosis
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of postsynaptic dense core vesicle exocytosis." [GOC:aruk, GOC:bc, PMID:19448629]
subset: goslim_synapse
-is_a: GO:0017158 ! regulation of calcium ion-dependent exocytosis
+is_a: GO:1905413 ! regulation of dense core granule exocytosis
relationship: regulates GO:0150038 ! postsynaptic dense core vesicle exocytosis
[Term]
@@ -420733,8 +421493,8 @@ id: GO:0150107
name: positive regulation of protein localization to cell-cell junction
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein localization to cell-cell junction." [GOC:aruk, GOC:bc, PMID:26706435]
-is_a: GO:0048518 ! positive regulation of biological process
is_a: GO:0150106 ! regulation of protein localization to cell-cell junction
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0150105 ! protein localization to cell-cell junction
[Term]
@@ -420794,8 +421554,8 @@ name: negative regulation of protein localization to cell-cell junction
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell-cell junction." [GOC:aruk, GOC:bc]
synonym: "negative regulation of protein localisation to cell-cell junction" EXACT []
-is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0150106 ! regulation of protein localization to cell-cell junction
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0150105 ! protein localization to cell-cell junction
[Term]
@@ -421243,6 +422003,109 @@ namespace: biological_process
def: "Cell-cell signaling that starts with the activation of extrasynaptic GABA receptors in neurons through binding of ambient gamma-aminobutyric acid present in the extracellular fluid." [PMID:23038269, PMID:9364051]
is_a: GO:0007214 ! gamma-aminobutyric acid signaling pathway
+[Term]
+id: GO:0160002
+name: ADP-D-ribose modification-dependent protein binding
+namespace: molecular_function
+def: "Binding to a protein upon ADP-ribosylation of the target protein." [PMID:26673700]
+comment: This term should only be used when the binding is shown to require a ADP-D-ribose post-translational modification: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of the ADP-D-ribose modification. It may be that the PTM causes a conformational change that allows binding of the protein to another region; this type of modification-dependent protein binding is valid for annotation to this term.
+is_a: GO:0140030 ! modification-dependent protein binding
+
+[Term]
+id: GO:0160003
+name: mono-ADP-D-ribose modification-dependent protein binding
+namespace: molecular_function
+def: "Binding to a protein upon mono-ADP-ribosylation of the target protein." [PMID:34023495]
+comment: This term should only be used when the binding is shown to require a mono-ADP-D-ribose post-translational modification: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of the ADP-D-ribose modification. It may be that the PTM causes a conformational change that allows binding of the protein to another region; this type of modification-dependent protein binding is valid for annotation to this term.
+is_a: GO:0160002 ! ADP-D-ribose modification-dependent protein binding
+
+[Term]
+id: GO:0160004
+name: poly-ADP-D-ribose modification-dependent protein binding
+namespace: molecular_function
+def: "Binding to a protein upon poly-ADP-ribosylation of the target protein." [PMID:26673700]
+comment: This term should only be used when the binding is shown to require a poly-ADP-D-ribose post-translational modification: the interaction needs to be tested with and without the PTM. The binding does not need to be at the site of the ADP-D-ribose modification. It may be that the PTM causes a conformational change that allows binding of the protein to another region; this type of modification-dependent protein binding is valid for annotation to this term.
+is_a: GO:0160002 ! ADP-D-ribose modification-dependent protein binding
+
+[Term]
+id: GO:0160005
+name: PAT complex
+namespace: cellular_component
+def: "A transmembrane protein complex located in the endoplasmic reticulum (ER) involved in the correct folding of multipass membrane proteins in the ER membrane after their release from the Sec61 translocon. In human, the substrate-binding Asterix (PAT10, WDR83OS) forms an obligate heterodimer with CCDC47." [PMID:32814900, PMID:33082068, PMID:33960686]
+comment: PAT complex functions by shielding exposed hydrophilicity of transmembrane domains (TMDs) to prevent premature degradation and promote proper folding and bundling of TMDs.
+is_a: GO:0098796 ! membrane protein complex
+is_a: GO:0140534 ! endoplasmic reticulum protein-containing complex
+relationship: part_of GO:0030176 ! integral component of endoplasmic reticulum membrane
+
+[Term]
+id: GO:0160006
+name: Fc receptor-mediated immune complex endocytosis
+namespace: biological_process
+def: "An endocytosis process mediated by the Fc receptor for the purpose of delivery of antigen-bound immunoglobulin to an intracellular compartment where the antigen can be processed and loaded onto MHC molecules. This process selectively targets antigens for presentation by MHC class II or cross-presentation by MHC class I." [PMID:28389502, PMID:9143687, PMID:9463401]
+synonym: "antigen-antibody immune complex uptake via Fc receptor" EXACT []
+synonym: "Fc receptor-mediated immune complex internalization" RELATED []
+synonym: "Ig-complexed antigen endocytosis via Fc receptor" EXACT []
+is_a: GO:0006898 ! receptor-mediated endocytosis
+is_a: GO:0031503 ! protein-containing complex localization
+
+[Term]
+id: GO:0160007
+name: glutathione import into mitochondrion
+namespace: biological_process
+def: "The process in which glutathione is transported from the cytosol into the mitochondrial matrix." [PMID:34707288]
+is_a: GO:0034775 ! glutathione transmembrane transport
+is_a: GO:1990542 ! mitochondrial transmembrane transport
+
+[Term]
+id: GO:0160008
+name: protein decrotonylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[protein] = (2E)-2-butenoate + L-lysyl-[protein]." [PMID:28497810, PMID:30279482, PMID:34608293]
+is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
+
+[Term]
+id: GO:0160009
+name: histone decrotonylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone] = (2E)-2-butenoate + L-lysyl-[histone]." [PMID:28497810]
+is_a: GO:0160008 ! protein decrotonylase activity
+
+[Term]
+id: GO:0160010
+name: protein de-2-hydroxyisobutyrylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + N6-(2-hydroxyisobutanoyl)-L-lysyl-[protein] = 2-hydroxy-2-methylpropanoate + L-lysyl-[protein]." [PMID:29192674]
+is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
+
+[Term]
+id: GO:0160011
+name: NAD-dependent protein decrotonylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[protein] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [PMID:28497810]
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+
+[Term]
+id: GO:0160012
+name: NAD-dependent histone decrotonylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + N6-(2E)-butenoyl-L-lysyl-[histone] + NAD+ = 2''-O-(2E)-but-2-enoyl-ADP-D-ribose + L-lysyl-[histone] + nicotinamide." [PMID:28497810]
+is_a: GO:0160011 ! NAD-dependent protein decrotonylase activity
+
+[Term]
+id: GO:0160013
+name: NAD-dependent protein de-2-hydroxyisobutyrylase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: H2O + N6-(2-hydroxyisobutanoyl)-L-lysyl-[protein] + NAD+ = 2''-O-(2-hydroxyisobutanoyl)-ADP-D-ribose + L-lysyl-[protein] + nicotinamide." [PMID:31328167]
+xref: RHEA:24364
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+
+[Term]
+id: GO:0160014
+name: exopher
+namespace: cellular_component
+def: "An extracellular vesicle that is approximately four microns in diameter, released by budding out of cells into the extracellular space, and hypothesized to be a mechanism for disposal of unwanted cellular material including protein aggregates and damaged organelles." [PMID:28178240, PMID:33016946, PMID:33027673, PMID:33659873, PMID:34288362, PMID:34475208]
+is_a: GO:1903561 ! extracellular vesicle
+
[Term]
id: GO:0198738
name: cell-cell signaling by wnt
@@ -423814,7 +424677,6 @@ synonym: "regulation of response to pathogenic fungus (incompatible interaction)
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0050776 ! regulation of immune response
relationship: regulates GO:0050832 ! defense response to fungus
[Term]
@@ -424316,7 +425178,8 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
synonym: "regulation of protein localisation to nucleus" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in cell nucleus" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in nucleus" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0034504 ! protein localization to nucleus
[Term]
@@ -424343,8 +425206,9 @@ synonym: "inhibition of protein localization to nucleus" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to nucleus" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in cell nucleus" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in nucleus" EXACT [GOC:TermGenie]
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1900180 ! regulation of protein localization to nucleus
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0034504 ! protein localization to nucleus
[Term]
@@ -424371,8 +425235,9 @@ synonym: "upregulation of protein localisation to nucleus" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in cell nucleus" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in nucleus" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to nucleus" EXACT [GOC:TermGenie]
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1900180 ! regulation of protein localization to nucleus
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0034504 ! protein localization to nucleus
[Term]
@@ -424496,7 +425361,6 @@ synonym: "inhibition of clathrin coated pit-dependent endocytosis" EXACT [GOC:Te
synonym: "inhibition of clathrin-dependent endocytosis" EXACT [GOC:TermGenie]
synonym: "inhibition of clathrin-mediated endocytosis" NARROW [GOC:TermGenie]
synonym: "negative regulation of clathrin coated pit-dependent endocytosis" EXACT [GOC:TermGenie]
-synonym: "negative regulation of clathrin-dependent endocytosis" EXACT [GOC:TermGenie]
synonym: "negative regulation of clathrin-mediated endocytosis" EXACT []
is_a: GO:0048261 ! negative regulation of receptor-mediated endocytosis
is_a: GO:2000369 ! regulation of clathrin-dependent endocytosis
@@ -427768,7 +428632,6 @@ synonym: "susceptibility to insect" RELATED []
is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
-is_a: GO:0050777 ! negative regulation of immune response
is_a: GO:2000068 ! regulation of defense response to insect
relationship: negatively_regulates GO:0002213 ! defense response to insect
@@ -427789,7 +428652,6 @@ synonym: "upregulation of physiological defense response to insect" EXACT [GOC:T
is_a: GO:0002833 ! positive regulation of response to biotic stimulus
is_a: GO:0031349 ! positive regulation of defense response
is_a: GO:0032103 ! positive regulation of response to external stimulus
-is_a: GO:0050778 ! positive regulation of immune response
is_a: GO:2000068 ! regulation of defense response to insect
relationship: positively_regulates GO:0002213 ! defense response to insect
@@ -428776,7 +429638,6 @@ synonym: "regulation of resistance response to pathogenic bacterium" NARROW [GOC
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0050776 ! regulation of immune response
relationship: regulates GO:0042742 ! defense response to bacterium
[Term]
@@ -428820,7 +429681,6 @@ synonym: "negative regulation of defense response to bacterium, incompatible int
is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
-is_a: GO:0050777 ! negative regulation of immune response
is_a: GO:1900424 ! regulation of defense response to bacterium
relationship: negatively_regulates GO:0042742 ! defense response to bacterium
@@ -428860,7 +429720,6 @@ synonym: "upregulation of defense response to bacterium" EXACT [GOC:TermGenie]
is_a: GO:0002833 ! positive regulation of response to biotic stimulus
is_a: GO:0031349 ! positive regulation of defense response
is_a: GO:0032103 ! positive regulation of response to external stimulus
-is_a: GO:0050778 ! positive regulation of immune response
is_a: GO:1900424 ! regulation of defense response to bacterium
relationship: positively_regulates GO:0042742 ! defense response to bacterium
@@ -429778,9 +430637,10 @@ relationship: positively_regulates GO:0044571 ! [2Fe-2S] cluster assembly
[Term]
id: GO:1900490
-name: positive regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity
+name: obsolete positive regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of hydroxymethylglutaryl-CoA reductase (NADPH) activity." [GOC:TermGenie]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of hydroxymethylglutaryl-CoA reductase (NADPH) activity." [GOC:TermGenie]
+comment: This term has been obsoleted because it represents a molecular function.
synonym: "activation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase activity" BROAD [GOC:TermGenie]
synonym: "activation of HMG-CoA reductase activity" BROAD [GOC:TermGenie]
synonym: "activation of hydroxymethylglutaryl-CoA reductase (NADPH) activity" NARROW [GOC:TermGenie]
@@ -429795,8 +430655,9 @@ synonym: "up-regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity"
synonym: "upregulation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase activity" BROAD [GOC:TermGenie]
synonym: "upregulation of HMG-CoA reductase activity" BROAD [GOC:TermGenie]
synonym: "upregulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity" EXACT [GOC:TermGenie]
-is_a: GO:0051353 ! positive regulation of oxidoreductase activity
-is_a: GO:2001215 ! regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity
+is_obsolete: true
+consider: GO:0008047
+consider: GO:0106109
[Term]
id: GO:1900491
@@ -434747,7 +435608,6 @@ def: "The directed movement of a (R)-carnitine into, out of or within a cell, or
synonym: "(-)-Carnitine transport" RELATED [GOC:TermGenie]
synonym: "(-)-L-Carnitine transport" RELATED [GOC:TermGenie]
synonym: "(3R)-3-hydroxy-4-(trimethylammonio)butanoate transport" EXACT [GOC:TermGenie]
-synonym: "(R)-Carnitine transport" EXACT [GOC:TermGenie]
synonym: "C7H15NO3 transport" RELATED [GOC:TermGenie]
synonym: "Carnicor transport" RELATED [GOC:TermGenie]
synonym: "Carnitene transport" RELATED [GOC:TermGenie]
@@ -434762,7 +435622,7 @@ is_a: GO:0015879 ! carnitine transport
id: GO:1900750
name: oligopeptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an oligopeptide." [GOC:TermGenie, PMID:21854595]
+def: "Binding to an oligopeptide." [GOC:TermGenie, PMID:21854595]
synonym: "Oligopeptid binding" RELATED [GOC:TermGenie]
synonym: "oligopeptides binding" EXACT [GOC:TermGenie]
synonym: "oligopeptido binding" RELATED [GOC:TermGenie]
@@ -435787,33 +436647,32 @@ id: GO:1900816
name: ochratoxin A metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving ochratoxin A." [GOC:di, GOC:TermGenie]
-synonym: "Ochratoxin A metabolic process" EXACT [GOC:TermGenie]
synonym: "Ochratoxin A metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006575 ! cellular modified amino acid metabolic process
+is_a: GO:0006629 ! lipid metabolic process
is_a: GO:0019748 ! secondary metabolic process
is_a: GO:0032787 ! monocarboxylic acid metabolic process
is_a: GO:0043603 ! cellular amide metabolic process
is_a: GO:0046483 ! heterocycle metabolic process
is_a: GO:1901360 ! organic cyclic compound metabolic process
+is_a: GO:1901568 ! fatty acid derivative metabolic process
[Term]
id: GO:1900817
name: ochratoxin A catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of ochratoxin A." [GOC:di, GOC:TermGenie]
-synonym: "Ochratoxin A breakdown" EXACT [GOC:TermGenie]
synonym: "ochratoxin A breakdown" EXACT [GOC:TermGenie]
-synonym: "Ochratoxin A catabolic process" EXACT [GOC:TermGenie]
-synonym: "Ochratoxin A catabolism" EXACT [GOC:TermGenie]
synonym: "ochratoxin A catabolism" EXACT [GOC:TermGenie]
-synonym: "Ochratoxin A degradation" EXACT [GOC:TermGenie]
synonym: "ochratoxin A degradation" EXACT [GOC:TermGenie]
+is_a: GO:0016042 ! lipid catabolic process
is_a: GO:0042219 ! cellular modified amino acid catabolic process
is_a: GO:0046700 ! heterocycle catabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
is_a: GO:0090487 ! secondary metabolite catabolic process
is_a: GO:1900816 ! ochratoxin A metabolic process
is_a: GO:1901361 ! organic cyclic compound catabolic process
+is_a: GO:1901569 ! fatty acid derivative catabolic process
[Term]
id: GO:1900818
@@ -435822,9 +436681,9 @@ namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of ochratoxin A." [GOC:di, GOC:TermGenie]
synonym: "Ochratoxin A anabolism" EXACT [GOC:TermGenie]
synonym: "Ochratoxin A biosynthesis" EXACT [GOC:TermGenie]
-synonym: "Ochratoxin A biosynthetic process" EXACT [GOC:TermGenie]
synonym: "Ochratoxin A formation" EXACT [GOC:TermGenie]
synonym: "Ochratoxin A synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0018130 ! heterocycle biosynthetic process
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
is_a: GO:0043604 ! amide biosynthetic process
@@ -435832,6 +436691,7 @@ is_a: GO:0044550 ! secondary metabolite biosynthetic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
is_a: GO:1900816 ! ochratoxin A metabolic process
is_a: GO:1901362 ! organic cyclic compound biosynthetic process
+is_a: GO:1901570 ! fatty acid derivative biosynthetic process
[Term]
id: GO:1900819
@@ -436031,7 +436891,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving D-leucine." [GOC:TermGenie, PMID:10918062]
synonym: "D-leucine metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006551 ! leucine metabolic process
-is_a: GO:0009081 ! branched-chain amino acid metabolic process
is_a: GO:0046416 ! D-amino acid metabolic process
[Term]
@@ -436043,7 +436902,6 @@ synonym: "D-leucine breakdown" EXACT [GOC:TermGenie]
synonym: "D-leucine catabolism" EXACT [GOC:TermGenie]
synonym: "D-leucine degradation" EXACT [GOC:TermGenie]
is_a: GO:0006552 ! leucine catabolic process
-is_a: GO:0009083 ! branched-chain amino acid catabolic process
is_a: GO:0019478 ! D-amino acid catabolic process
is_a: GO:1900831 ! D-leucine metabolic process
@@ -436056,7 +436914,6 @@ synonym: "D-leucine anabolism" EXACT [GOC:TermGenie]
synonym: "D-leucine biosynthesis" EXACT [GOC:TermGenie]
synonym: "D-leucine formation" EXACT [GOC:TermGenie]
synonym: "D-leucine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0009082 ! branched-chain amino acid biosynthetic process
is_a: GO:0009098 ! leucine biosynthetic process
is_a: GO:0046437 ! D-amino acid biosynthetic process
is_a: GO:1900831 ! D-leucine metabolic process
@@ -439000,7 +439857,7 @@ is_a: GO:1901806 ! beta-glucoside biosynthetic process
id: GO:1900995
name: ubiquinone-6 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ubiquinone-6. Ubiquinone-6 is a ubiquinone compound having a (2E,6E,10E,14E,18E)-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl substituent at position 2." [GOC:al, GOC:TermGenie]
+def: "Binding to ubiquinone-6. Ubiquinone-6 is a ubiquinone compound having a (2E,6E,10E,14E,18E)-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl substituent at position 2." [GOC:al, GOC:TermGenie]
is_a: GO:0048039 ! ubiquinone binding
[Term]
@@ -439837,7 +440694,6 @@ synonym: "sarcosine anabolism" EXACT [GOC:TermGenie]
synonym: "sarcosine biosynthesis" EXACT [GOC:TermGenie]
synonym: "sarcosine formation" EXACT [GOC:TermGenie]
synonym: "sarcosine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
is_a: GO:1901052 ! sarcosine metabolic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -440459,7 +441315,6 @@ synonym: "regulation of amphisome-lysosome fusion" NARROW [GOC:TermGenie]
synonym: "regulation of autolysosome formation" NARROW [GOC:TermGenie]
synonym: "regulation of autophagic vacuole fusion" EXACT [GOC:autophagy]
synonym: "regulation of autophagosome fusion" EXACT []
-synonym: "regulation of autophagosome maturation" EXACT [GOC:TermGenie]
synonym: "regulation of fusion of autophagosome with lysosome" NARROW [GOC:TermGenie]
is_a: GO:0016241 ! regulation of macroautophagy
is_a: GO:0033043 ! regulation of organelle organization
@@ -440500,7 +441355,6 @@ synonym: "negative regulation of amphisome-lysosome fusion" NARROW [GOC:TermGeni
synonym: "negative regulation of autolysosome formation" NARROW [GOC:TermGenie]
synonym: "negative regulation of autophagic vacuole fusion" EXACT [GOC:autophagy]
synonym: "negative regulation of autophagosome fusion" EXACT []
-synonym: "negative regulation of autophagosome maturation" EXACT [GOC:TermGenie]
synonym: "negative regulation of fusion of autophagosome with lysosome" NARROW [GOC:TermGenie]
is_a: GO:0016242 ! negative regulation of macroautophagy
is_a: GO:0043242 ! negative regulation of protein-containing complex disassembly
@@ -440523,7 +441377,6 @@ synonym: "positive regulation of amphisome-lysosome fusion" NARROW [GOC:TermGeni
synonym: "positive regulation of autolysosome formation" NARROW [GOC:TermGenie]
synonym: "positive regulation of autophagic vacuole fusion" EXACT [GOC:autophagy]
synonym: "positive regulation of autophagosome fusion" EXACT []
-synonym: "positive regulation of autophagosome maturation" EXACT [GOC:TermGenie]
synonym: "positive regulation of fusion of autophagosome with lysosome" NARROW [GOC:TermGenie]
synonym: "up regulation of amphisome-lysosome fusion" NARROW [GOC:TermGenie]
synonym: "up regulation of autolysosome formation" NARROW [GOC:TermGenie]
@@ -440960,6 +441813,7 @@ name: carbohydrate derivative metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving carbohydrate derivative." [GOC:TermGenie]
subset: goslim_agr
+subset: goslim_generic
subset: goslim_mouse
synonym: "carbohydrate derivative metabolism" EXACT [GOC:TermGenie]
is_a: GO:0071704 ! organic substance metabolic process
@@ -441080,7 +441934,7 @@ relationship: part_of GO:0030198 ! extracellular matrix organization
id: GO:1901149
name: salicylic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with salicylic acid." [GOC:TermGenie, PMID:22699612]
+def: "Binding to salicylic acid." [GOC:TermGenie, PMID:22699612]
synonym: "salicylic acid receptor" NARROW [PMID:22699612]
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0043177 ! organic acid binding
@@ -442093,7 +442947,9 @@ name: regulation of holin activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of holin activity." [GOC:bm, GOC:TermGenie]
is_a: GO:0022898 ! regulation of transmembrane transporter activity
-is_a: GO:1902186 ! regulation of viral release from host cell
+is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
+is_a: GO:0050792 ! regulation of viral process
+relationship: regulates GO:0019076 ! viral release from host cell
[Term]
id: GO:1901218
@@ -442108,9 +442964,10 @@ synonym: "inhibition of holin activity" NARROW [GOC:TermGenie]
synonym: "phage antiholin" NARROW [GOC:bm]
is_a: GO:0032410 ! negative regulation of transporter activity
is_a: GO:0034763 ! negative regulation of transmembrane transport
-is_a: GO:0051711 ! negative regulation of killing of cells of other organism
+is_a: GO:0048525 ! negative regulation of viral process
+is_a: GO:0051711 ! negative regulation of killing of cells of another organism
is_a: GO:1901217 ! regulation of holin activity
-is_a: GO:1902187 ! negative regulation of viral release from host cell
+relationship: negatively_regulates GO:0019076 ! viral release from host cell
[Term]
id: GO:1901219
@@ -442871,8 +443728,6 @@ def: "Any process that modulates the frequency, rate or extent of egress of viru
synonym: "regulation of egress of virus within host cell" RELATED []
synonym: "regulation of movement of virus within host cell" EXACT [GOC:TermGenie]
synonym: "regulation of viral egress" EXACT [GOC:TermGenie]
-is_a: GO:0043900 ! regulation of multi-organism process
-is_a: GO:0051049 ! regulation of transport
is_a: GO:1903900 ! regulation of viral life cycle
relationship: regulates GO:0075733 ! intracellular transport of virus
@@ -442896,8 +443751,6 @@ synonym: "inhibition of viral egress" EXACT [GOC:TermGenie]
synonym: "negative regulation of egress of virus within host cell" RELATED []
synonym: "negative regulation of movement of virus within host cell" EXACT [GOC:TermGenie]
synonym: "negative regulation of viral egress" EXACT [GOC:TermGenie]
-is_a: GO:0043901 ! negative regulation of multi-organism process
-is_a: GO:0051051 ! negative regulation of transport
is_a: GO:1901252 ! regulation of intracellular transport of viral material
is_a: GO:1903901 ! negative regulation of viral life cycle
relationship: negatively_regulates GO:0075733 ! intracellular transport of virus
@@ -442922,8 +443775,6 @@ synonym: "up-regulation of viral egress" EXACT [GOC:TermGenie]
synonym: "upregulation of egress of virus within host cell" EXACT [GOC:TermGenie]
synonym: "upregulation of movement of virus within host cell" EXACT [GOC:TermGenie]
synonym: "upregulation of viral egress" EXACT [GOC:TermGenie]
-is_a: GO:0043902 ! positive regulation of multi-organism process
-is_a: GO:0051050 ! positive regulation of transport
is_a: GO:1901252 ! regulation of intracellular transport of viral material
is_a: GO:1903902 ! positive regulation of viral life cycle
relationship: positively_regulates GO:0075733 ! intracellular transport of virus
@@ -443046,7 +443897,7 @@ is_a: GO:0071702 ! organic substance transport
id: GO:1901265
name: nucleoside phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with nucleoside phosphate." [GOC:TermGenie]
+def: "Binding to nucleoside phosphate." [GOC:TermGenie]
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -443378,7 +444229,6 @@ synonym: "nucleoside phosphate breakdown" EXACT [GOC:TermGenie]
synonym: "nucleoside phosphate catabolism" EXACT [GOC:TermGenie]
synonym: "nucleoside phosphate degradation" EXACT [GOC:TermGenie]
is_a: GO:0006753 ! nucleoside phosphate metabolic process
-is_a: GO:0034404 ! nucleobase-containing small molecule biosynthetic process
is_a: GO:0034655 ! nucleobase-containing compound catabolic process
is_a: GO:0046434 ! organophosphate catabolic process
@@ -444042,7 +444892,7 @@ is_a: GO:0072348 ! sulfur compound transport
id: GO:1901338
name: catecholamine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with catecholamine." [GOC:TermGenie]
+def: "Binding to catecholamine." [GOC:TermGenie]
is_a: GO:0097159 ! organic cyclic compound binding
[Term]
@@ -444395,7 +445245,7 @@ is_a: GO:1901356 ! beta-D-galactofuranose metabolic process
id: GO:1901359
name: tungstate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with tungstate." [GOC:TermGenie]
+def: "Binding to tungstate." [GOC:TermGenie]
is_a: GO:0043168 ! anion binding
[Term]
@@ -444433,7 +445283,7 @@ is_a: GO:1901576 ! organic substance biosynthetic process
id: GO:1901363
name: heterocyclic compound binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with heterocyclic compound." [GOC:TermGenie]
+def: "Binding to heterocyclic compound." [GOC:TermGenie]
is_a: GO:0005488 ! binding
[Term]
@@ -447070,7 +447920,7 @@ is_a: GO:0010035 ! response to inorganic substance
id: GO:1901531
name: hypochlorite binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with hypochlorite." [GOC:pr, GOC:TermGenie, PMID:22223481]
+def: "Binding to hypochlorite." [GOC:pr, GOC:TermGenie, PMID:22223481]
is_a: GO:0043168 ! anion binding
[Term]
@@ -447527,7 +448377,7 @@ is_a: GO:1901576 ! organic substance biosynthetic process
id: GO:1901567
name: fatty acid derivative binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with fatty acid derivative." [GOC:pr, GOC:TermGenie]
+def: "Binding to fatty acid derivative." [GOC:pr, GOC:TermGenie]
is_a: GO:0005488 ! binding
[Term]
@@ -447960,7 +448810,7 @@ is_a: GO:1901600 ! strigolactone metabolic process
id: GO:1901602
name: dethiobiotin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dethiobiotin." [GOC:TermGenie]
+def: "Binding to dethiobiotin." [GOC:TermGenie]
is_a: GO:0033218 ! amide binding
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0043177 ! organic acid binding
@@ -448005,8 +448855,7 @@ synonym: "alpha-amino acid anabolism" EXACT [GOC:TermGenie]
synonym: "alpha-amino acid biosynthesis" EXACT [GOC:TermGenie]
synonym: "alpha-amino acid formation" EXACT [GOC:TermGenie]
synonym: "alpha-amino acid synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0016053 ! organic acid biosynthetic process
-is_a: GO:1901566 ! organonitrogen compound biosynthetic process
+is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
@@ -448060,7 +448909,7 @@ relationship: positively_regulates GO:0047496 ! vesicle transport along microtub
id: GO:1901611
name: phosphatidylglycerol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylglycerol." [GOC:kmv, GOC:TermGenie]
+def: "Binding to phosphatidylglycerol." [GOC:kmv, GOC:TermGenie]
is_a: GO:0005543 ! phospholipid binding
is_a: GO:0043168 ! anion binding
@@ -448068,7 +448917,7 @@ is_a: GO:0043168 ! anion binding
id: GO:1901612
name: cardiolipin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cardiolipin." [GOC:kmv, GOC:TermGenie]
+def: "Binding to cardiolipin." [GOC:kmv, GOC:TermGenie]
is_a: GO:1901611 ! phosphatidylglycerol binding
[Term]
@@ -448394,7 +449243,7 @@ def: "Any process that modulates the frequency, rate or extent of synaptic vesic
synonym: "regulation of SLMV biogenesis" NARROW [GOC:TermGenie]
synonym: "regulation of synaptic vesicle membrane organisation" EXACT [GOC:TermGenie]
synonym: "regulation of synaptic vesicle membrane organization and biogenesis" RELATED [GOC:TermGenie]
-is_a: GO:0033043 ! regulation of organelle organization
+is_a: GO:0051128 ! regulation of cellular component organization
relationship: regulates GO:0048499 ! synaptic vesicle membrane organization
[Term]
@@ -448421,7 +449270,7 @@ synonym: "inhibition of synaptic vesicle membrane organization and biogenesis" N
synonym: "negative regulation of SLMV biogenesis" NARROW [GOC:TermGenie]
synonym: "negative regulation of synaptic vesicle membrane organisation" EXACT [GOC:TermGenie]
synonym: "negative regulation of synaptic vesicle membrane organization and biogenesis" RELATED [GOC:TermGenie]
-is_a: GO:0010639 ! negative regulation of organelle organization
+is_a: GO:0051129 ! negative regulation of cellular component organization
is_a: GO:1901632 ! regulation of synaptic vesicle membrane organization
relationship: negatively_regulates GO:0048499 ! synaptic vesicle membrane organization
@@ -448449,7 +449298,7 @@ synonym: "upregulation of SLMV biogenesis" NARROW [GOC:TermGenie]
synonym: "upregulation of synaptic vesicle membrane organisation" EXACT [GOC:TermGenie]
synonym: "upregulation of synaptic vesicle membrane organization" EXACT [GOC:TermGenie]
synonym: "upregulation of synaptic vesicle membrane organization and biogenesis" RELATED [GOC:TermGenie]
-is_a: GO:0010638 ! positive regulation of organelle organization
+is_a: GO:0051130 ! positive regulation of cellular component organization
is_a: GO:1901632 ! regulation of synaptic vesicle membrane organization
relationship: positively_regulates GO:0048499 ! synaptic vesicle membrane organization
@@ -448513,7 +449362,7 @@ is_obsolete: true
id: GO:1901640
name: XTP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with XTP." [GOC:TermGenie]
+def: "Binding to XTP." [GOC:TermGenie]
is_a: GO:0032555 ! purine ribonucleotide binding
is_a: GO:0035639 ! purine ribonucleoside triphosphate binding
@@ -448521,7 +449370,7 @@ is_a: GO:0035639 ! purine ribonucleoside triphosphate binding
id: GO:1901641
name: ITP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ITP." [GOC:TermGenie]
+def: "Binding to ITP." [GOC:TermGenie]
is_a: GO:0032555 ! purine ribonucleotide binding
is_a: GO:0035639 ! purine ribonucleoside triphosphate binding
@@ -449270,7 +450119,6 @@ is_a: GO:0002833 ! positive regulation of response to biotic stimulus
is_a: GO:0010112 ! regulation of systemic acquired resistance
is_a: GO:0031349 ! positive regulation of defense response
is_a: GO:0032103 ! positive regulation of response to external stimulus
-is_a: GO:0050778 ! positive regulation of immune response
relationship: positively_regulates GO:0009627 ! systemic acquired resistance
[Term]
@@ -449368,7 +450216,7 @@ is_a: GO:0015291 ! secondary active transmembrane transporter activity
id: GO:1901681
name: sulfur compound binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a sulfur compound." [GOC:pr, GOC:TermGenie]
+def: "Binding to a sulfur compound." [GOC:pr, GOC:TermGenie]
synonym: "sulfur molecular entity binding" EXACT []
is_a: GO:0005488 ! binding
@@ -449433,7 +450281,7 @@ is_a: GO:1901685 ! glutathione derivative metabolic process
id: GO:1901691
name: proton binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with proton." [GOC:TermGenie]
+def: "Binding to proton." [GOC:TermGenie]
synonym: "hydrogen ion binding" EXACT [GOC:bm]
is_a: GO:0043169 ! cation binding
@@ -449582,7 +450430,6 @@ synonym: "L-isoleucine anabolism" EXACT [GOC:TermGenie]
synonym: "L-isoleucine biosynthesis" EXACT [GOC:TermGenie]
synonym: "L-isoleucine formation" EXACT [GOC:TermGenie]
synonym: "L-isoleucine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
is_a: GO:0009097 ! isoleucine biosynthetic process
@@ -449598,7 +450445,7 @@ relationship: part_of GO:0060348 ! bone development
id: GO:1901707
name: leptomycin B binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with leptomycin B." [GOC:TermGenie]
+def: "Binding to leptomycin B." [GOC:TermGenie]
is_a: GO:0008289 ! lipid binding
is_a: GO:0043177 ! organic acid binding
is_a: GO:0097159 ! organic cyclic compound binding
@@ -452344,7 +453191,7 @@ synonym: "regulation of calcium-transporting ATPase activity" EXACT []
synonym: "regulation of plasma membrane Ca-ATPase" NARROW [GOC:TermGenie]
synonym: "regulation of sarco(endo)plasmic reticulum Ca2+-ATPase" NARROW [GOC:TermGenie]
synonym: "regulation of sarcoplasmic reticulum ATPase" NARROW [GOC:TermGenie]
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
is_a: GO:1901019 ! regulation of calcium ion transmembrane transporter activity
[Term]
@@ -452417,7 +453264,7 @@ synonym: "negative regulation of calcium-transporting ATPase activity" EXACT []
synonym: "negative regulation of plasma membrane Ca-ATPase" NARROW [GOC:TermGenie]
synonym: "negative regulation of sarco(endo)plasmic reticulum Ca2+-ATPase" NARROW [GOC:TermGenie]
synonym: "negative regulation of sarcoplasmic reticulum ATPase" NARROW [GOC:TermGenie]
-is_a: GO:0032780 ! negative regulation of ATPase activity
+is_a: GO:0032780 ! negative regulation of ATP-dependent activity
is_a: GO:1901020 ! negative regulation of calcium ion transmembrane transporter activity
is_a: GO:1901894 ! regulation of ATPase-coupled calcium transmembrane transporter activity
@@ -452491,7 +453338,7 @@ synonym: "upregulation of calcium-transporting ATPase activity" EXACT [GOC:TermG
synonym: "upregulation of plasma membrane Ca-ATPase" NARROW [GOC:TermGenie]
synonym: "upregulation of sarco(endo)plasmic reticulum Ca2+-ATPase" NARROW [GOC:TermGenie]
synonym: "upregulation of sarcoplasmic reticulum ATPase" NARROW [GOC:TermGenie]
-is_a: GO:0032781 ! positive regulation of ATPase activity
+is_a: GO:0032781 ! positive regulation of ATP-dependent activity
is_a: GO:1901021 ! positive regulation of calcium ion transmembrane transporter activity
is_a: GO:1901894 ! regulation of ATPase-coupled calcium transmembrane transporter activity
@@ -452535,7 +453382,8 @@ name: regulation of protein localization to cell division site
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to cell division site." [GOC:dph, GOC:TermGenie, PMID:22573892]
synonym: "regulation of protein localisation to cell division site" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0072741 ! protein localization to cell division site
[Term]
@@ -453438,7 +454286,7 @@ is_a: GO:1902546 ! positive regulation of DNA N-glycosylase activity
id: GO:1901973
name: proline binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with proline." [GOC:pm, GOC:TermGenie, PMID:7730362]
+def: "Binding to proline." [GOC:pm, GOC:TermGenie, PMID:7730362]
is_a: GO:0016597 ! amino acid binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -453540,14 +454388,14 @@ is_a: GO:1903818 ! positive regulation of voltage-gated potassium channel activi
id: GO:1901981
name: phosphatidylinositol phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol phosphate." [GOC:TermGenie, PMID:23445487]
+def: "Binding to phosphatidylinositol phosphate." [GOC:TermGenie, PMID:23445487]
is_a: GO:0035091 ! phosphatidylinositol binding
[Term]
id: GO:1901982
name: maltose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with maltose." [GOC:TermGenie, PMID:21566157]
+def: "Binding to maltose." [GOC:TermGenie, PMID:21566157]
is_a: GO:0048030 ! disaccharide binding
[Term]
@@ -454130,17 +454978,6 @@ is_a: GO:0006812 ! cation transport
is_a: GO:0006865 ! amino acid transport
is_a: GO:0015807 ! L-amino acid transport
-[Term]
-id: GO:1902023
-name: L-arginine transport
-namespace: biological_process
-alt_id: GO:0043091
-def: "The directed movement of a L-arginine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:kmv, GOC:TermGenie, PMID:22822152]
-synonym: "L-arginine import" NARROW []
-synonym: "L-arginine uptake" NARROW []
-is_a: GO:0015807 ! L-amino acid transport
-is_a: GO:0015809 ! arginine transport
-
[Term]
id: GO:1902024
name: L-histidine transport
@@ -454659,7 +455496,7 @@ is_a: GO:1902645 ! tertiary alcohol biosynthetic process
id: GO:1902051
name: (25S)-Delta(4)-dafachronate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with (25S)-Delta(4)-dafachronate." [GOC:TermGenie, PMID:16529801]
+def: "Binding to (25S)-Delta(4)-dafachronate." [GOC:TermGenie, PMID:16529801]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043177 ! organic acid binding
is_a: GO:1990239 ! steroid hormone binding
@@ -454668,7 +455505,7 @@ is_a: GO:1990239 ! steroid hormone binding
id: GO:1902052
name: (25S)-Delta(7)-dafachronate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with (25S)-Delta(7)-dafachronate." [GOC:TermGenie, PMID:16529801]
+def: "Binding to (25S)-Delta(7)-dafachronate." [GOC:TermGenie, PMID:16529801]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043177 ! organic acid binding
is_a: GO:1990239 ! steroid hormone binding
@@ -454816,7 +455653,6 @@ synonym: "negative regulation of ascus development" NARROW [GOC:TermGenie]
synonym: "negative regulation of fruiting body development involved in sexual reproduction" BROAD [GOC:TermGenie]
synonym: "negative regulation of fruiting body formation involved in sexual reproduction" BROAD [GOC:TermGenie]
synonym: "negative regulation of perfect stage fruiting body development" NARROW [GOC:TermGenie]
-is_a: GO:0043901 ! negative regulation of multi-organism process
is_a: GO:0075262 ! negative regulation of spore-bearing organ development
is_a: GO:1902058 ! regulation of sporocarp development involved in sexual reproduction
relationship: negatively_regulates GO:0000909 ! sporocarp development involved in sexual reproduction
@@ -455088,7 +455924,6 @@ synonym: "D-valine breakdown" EXACT [GOC:TermGenie]
synonym: "D-valine catabolism" EXACT [GOC:TermGenie]
synonym: "D-valine degradation" EXACT [GOC:TermGenie]
is_a: GO:0006574 ! valine catabolic process
-is_a: GO:0009083 ! branched-chain amino acid catabolic process
is_a: GO:0019478 ! D-amino acid catabolic process
is_a: GO:1902114 ! D-valine metabolic process
@@ -455405,7 +456240,7 @@ relationship: part_of GO:0050829 ! defense response to Gram-negative bacterium
id: GO:1902098
name: calcitriol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with calcitriol. Calcitriol (1,25-dihydroxycholecalciferol) is the hormonally active form of vitamin D3." [GOC:TermGenie, PMID:21872797, Wikipedia:Calcitriol_receptor]
+def: "Binding to calcitriol. Calcitriol (1,25-dihydroxycholecalciferol) is the hormonally active form of vitamin D3." [GOC:TermGenie, PMID:21872797, Wikipedia:Calcitriol_receptor]
synonym: "1,25-dihydroxycholecalciferol binding" EXACT [Wikipedia:Calcitriol]
synonym: "1,25-dihydroxyvitamin D3 binding" EXACT [Wikipedia:Calcitriol]
synonym: "1alpha,25(OH)2 vitamin D3 binding" EXACT [PMID:21872797]
@@ -455701,7 +456536,6 @@ namespace: biological_process
def: "The chemical reactions and pathways involving D-valine." [GOC:TermGenie, PMID:23085840]
synonym: "D-valine metabolism" EXACT [GOC:TermGenie]
is_a: GO:0006573 ! valine metabolic process
-is_a: GO:0009081 ! branched-chain amino acid metabolic process
is_a: GO:0046416 ! D-amino acid metabolic process
[Term]
@@ -455744,7 +456578,7 @@ relationship: positively_regulates GO:0070925 ! organelle assembly
id: GO:1902118
name: calcidiol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with calcidiol." [GOC:bf, GOC:TermGenie, PMID:11799400]
+def: "Binding to calcidiol." [GOC:bf, GOC:TermGenie, PMID:11799400]
synonym: "25(OH)D3 binding" EXACT [CHEBI:17933]
synonym: "25-hydroxycholecalciferol binding" EXACT [CHEBI:17933]
synonym: "25-hydroxyvitamin D3 binding" EXACT [CHEBI:17933]
@@ -455784,7 +456618,7 @@ relationship: negatively_regulates GO:0051232 ! meiotic spindle elongation
id: GO:1902121
name: lithocholic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lithocholic acid." [GOC:bf, GOC:TermGenie, PMID:20371703]
+def: "Binding to lithocholic acid." [GOC:bf, GOC:TermGenie, PMID:20371703]
synonym: "LCA binding" EXACT [PMID:20371703]
is_a: GO:0005496 ! steroid binding
is_a: GO:0032052 ! bile acid binding
@@ -455794,7 +456628,7 @@ is_a: GO:0043177 ! organic acid binding
id: GO:1902122
name: chenodeoxycholic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chenodeoxycholic acid." [GOC:bf, GOC:TermGenie, PMID:10334992]
+def: "Binding to chenodeoxycholic acid." [GOC:bf, GOC:TermGenie, PMID:10334992]
synonym: "CDCA binding" EXACT [CHEBI:16755]
is_a: GO:0005496 ! steroid binding
is_a: GO:0032052 ! bile acid binding
@@ -456706,55 +457540,23 @@ relationship: positively_regulates GO:1902182 ! shoot apical meristem developmen
[Term]
id: GO:1902186
-name: regulation of viral release from host cell
+name: obsolete regulation of viral release from host cell
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of viral release from host cell." [GOC:TermGenie, PMID:18305167]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of viral release from host cell." [GOC:TermGenie, PMID:18305167]
+comment: This term was obsoleted because there is no evidence that it is a regulated process.
synonym: "regulation of release of virus from host" EXACT [GOC:TermGenie]
synonym: "regulation of viral exit" EXACT [GOC:TermGenie]
synonym: "regulation of viral release" EXACT [GOC:TermGenie]
synonym: "regulation of viral shedding" EXACT [GOC:TermGenie]
-is_a: GO:0043903 ! regulation of biological process involved in symbiotic interaction
-is_a: GO:1903900 ! regulation of viral life cycle
-relationship: regulates GO:0019076 ! viral release from host cell
-
-[Term]
-id: GO:1902187
-name: negative regulation of viral release from host cell
-namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of viral release from host cell." [GOC:TermGenie, PMID:18305167]
-synonym: "down regulation of release of virus from host" EXACT [GOC:TermGenie]
-synonym: "down regulation of viral exit" EXACT [GOC:TermGenie]
-synonym: "down regulation of viral release" EXACT [GOC:TermGenie]
-synonym: "down regulation of viral release from host cell" EXACT [GOC:TermGenie]
-synonym: "down regulation of viral shedding" EXACT [GOC:TermGenie]
-synonym: "down-regulation of release of virus from host" EXACT [GOC:TermGenie]
-synonym: "down-regulation of viral exit" EXACT [GOC:TermGenie]
-synonym: "down-regulation of viral release" EXACT [GOC:TermGenie]
-synonym: "down-regulation of viral release from host cell" EXACT [GOC:TermGenie]
-synonym: "down-regulation of viral shedding" EXACT [GOC:TermGenie]
-synonym: "downregulation of release of virus from host" EXACT [GOC:TermGenie]
-synonym: "downregulation of viral exit" EXACT [GOC:TermGenie]
-synonym: "downregulation of viral release" EXACT [GOC:TermGenie]
-synonym: "downregulation of viral release from host cell" EXACT [GOC:TermGenie]
-synonym: "downregulation of viral shedding" EXACT [GOC:TermGenie]
-synonym: "inhibition of release of virus from host" EXACT [GOC:TermGenie]
-synonym: "inhibition of viral exit" EXACT [GOC:TermGenie]
-synonym: "inhibition of viral release" EXACT [GOC:TermGenie]
-synonym: "inhibition of viral release from host cell" NARROW [GOC:TermGenie]
-synonym: "inhibition of viral shedding" EXACT [GOC:TermGenie]
-synonym: "negative regulation of release of virus from host" EXACT [GOC:TermGenie]
-synonym: "negative regulation of viral exit" EXACT [GOC:TermGenie]
-synonym: "negative regulation of viral release" EXACT [GOC:TermGenie]
-synonym: "negative regulation of viral shedding" EXACT [GOC:TermGenie]
-is_a: GO:0048525 ! negative regulation of viral process
-is_a: GO:1902186 ! regulation of viral release from host cell
-relationship: negatively_regulates GO:0019076 ! viral release from host cell
+is_obsolete: true
+replaced_by: GO:0019076
[Term]
id: GO:1902188
-name: positive regulation of viral release from host cell
+name: obsolete positive regulation of viral release from host cell
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of viral release from host cell." [GOC:TermGenie, PMID:18305167]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of viral release from host cell." [GOC:TermGenie, PMID:18305167]
+comment: This term was obsoleted because there is no evidence that it is a regulated process.
synonym: "activation of release of virus from host" EXACT [GOC:TermGenie]
synonym: "activation of viral exit" EXACT [GOC:TermGenie]
synonym: "activation of viral release" EXACT [GOC:TermGenie]
@@ -456779,9 +457581,8 @@ synonym: "upregulation of viral exit" EXACT [GOC:TermGenie]
synonym: "upregulation of viral release" EXACT [GOC:TermGenie]
synonym: "upregulation of viral release from host cell" EXACT [GOC:TermGenie]
synonym: "upregulation of viral shedding" EXACT [GOC:TermGenie]
-is_a: GO:1902186 ! regulation of viral release from host cell
-is_a: GO:1903902 ! positive regulation of viral life cycle
-relationship: positively_regulates GO:0019076 ! viral release from host cell
+is_obsolete: true
+replaced_by: GO:0019076
[Term]
id: GO:1902189
@@ -457698,7 +458499,7 @@ is_a: GO:0033385 ! geranylgeranyl diphosphate metabolic process
id: GO:1902248
name: 5-O-phosphono-alpha-D-ribofuranosyl diphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 5-O-phosphono-alpha-D-ribofuranosyl diphosphate." [GOC:mah, GOC:TermGenie, PMID:4314233]
+def: "Binding to 5-O-phosphono-alpha-D-ribofuranosyl diphosphate." [GOC:mah, GOC:TermGenie, PMID:4314233]
synonym: "5-phosphoribose 1-diphosphate binding" EXACT []
synonym: "phosphoribosylpyrophosphate binding" EXACT [GOC:al]
is_a: GO:0043168 ! anion binding
@@ -457708,7 +458509,7 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:1902249
name: IMP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with IMP, inosine monophosphate." [GOC:mah, GOC:TermGenie, PMID:4314233]
+def: "Binding to IMP, inosine monophosphate." [GOC:mah, GOC:TermGenie, PMID:4314233]
is_a: GO:0032555 ! purine ribonucleotide binding
is_a: GO:0043168 ! anion binding
@@ -458033,7 +458834,7 @@ is_a: GO:1902603 ! carnitine transmembrane transport
id: GO:1902271
name: D3 vitamins binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with D3 vitamins." [GOC:bf, GOC:TermGenie, PMID:9127467]
+def: "Binding to D3 vitamins." [GOC:bf, GOC:TermGenie, PMID:9127467]
is_a: GO:0005499 ! vitamin D binding
[Term]
@@ -458268,7 +459069,6 @@ def: "Any process that modulates the frequency, rate or extent of defense respon
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0050776 ! regulation of immune response
relationship: regulates GO:0002229 ! defense response to oomycetes
[Term]
@@ -458283,7 +459083,6 @@ synonym: "inhibition of defense response to oomycetes" NARROW [GOC:TermGenie]
is_a: GO:0002832 ! negative regulation of response to biotic stimulus
is_a: GO:0031348 ! negative regulation of defense response
is_a: GO:0032102 ! negative regulation of response to external stimulus
-is_a: GO:0050777 ! negative regulation of immune response
is_a: GO:1902288 ! regulation of defense response to oomycetes
relationship: negatively_regulates GO:0002229 ! defense response to oomycetes
@@ -458299,7 +459098,6 @@ synonym: "upregulation of defense response to oomycetes" EXACT [GOC:TermGenie]
is_a: GO:0002833 ! positive regulation of response to biotic stimulus
is_a: GO:0031349 ! positive regulation of defense response
is_a: GO:0032103 ! positive regulation of response to external stimulus
-is_a: GO:0050778 ! positive regulation of immune response
is_a: GO:1902288 ! regulation of defense response to oomycetes
relationship: positively_regulates GO:0002229 ! defense response to oomycetes
@@ -458502,6 +459300,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of copper ion transmembrane transport." [GOC:di, GOC:TermGenie, PMID:21489137]
synonym: "regulation of copper cation transmembrane transport" EXACT [GOC:TermGenie]
synonym: "regulation of copper ion membrane transport" EXACT [GOC:TermGenie]
+is_a: GO:0010959 ! regulation of metal ion transport
is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:0035434 ! copper ion transmembrane transport
@@ -458555,7 +459354,7 @@ relationship: positively_regulates GO:0035434 ! copper ion transmembrane transpo
id: GO:1902314
name: hydroquinone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with hydroquinone." [GOC:bhm, GOC:TermGenie, pmid:15667223]
+def: "Binding to hydroquinone." [GOC:bhm, GOC:TermGenie, pmid:15667223]
synonym: "quinol binding" EXACT []
is_a: GO:0097159 ! organic cyclic compound binding
@@ -459195,9 +459994,10 @@ relationship: part_of GO:0001756 ! somitogenesis
[Term]
id: GO:1902360
-name: conversion of ds siRNA to ss siRNA involved in chromatin silencing by small RNA
+name: obsolete conversion of ds siRNA to ss siRNA involved in gene silencing by small RNA
namespace: biological_process
-def: "Any conversion of ds siRNA to ss siRNA that is involved in chromatin silencing by small RNA." [GOC:TermGenie, GOC:vw, PMID:19239886]
+def: "OBSOLETE. Any conversion of ds siRNA to ss siRNA that is involved in gene silencing by small RNA." [GOC:TermGenie, GOC:vw, PMID:19239886]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA involved in chromatin silencing by small RNA" RELATED [GOC:TermGenie]
synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA involved in RNA interference-like chromatin silencing" RELATED [GOC:TermGenie]
synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA involved in RNA-mediated chromatin silencing" RELATED [GOC:TermGenie]
@@ -459205,14 +460005,16 @@ synonym: "conversion of double-stranded small interfering RNA to single-stranded
synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA involved in RNAi-directed chromatin silencing" RELATED [GOC:TermGenie]
synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA involved in RNAi-like chromatin silencing" RELATED [GOC:TermGenie]
synonym: "conversion of double-stranded small interfering RNA to single-stranded small interfering RNA involved in small RNA-mediated heterochromatic silencing" RELATED [GOC:TermGenie]
+synonym: "conversion of ds siRNA to ss siRNA involved in chromatin silencing by small RNA" EXACT []
synonym: "conversion of ds siRNA to ss siRNA involved in RNA interference-like chromatin silencing" EXACT [GOC:TermGenie]
synonym: "conversion of ds siRNA to ss siRNA involved in RNA-mediated chromatin silencing" EXACT [GOC:TermGenie]
synonym: "conversion of ds siRNA to ss siRNA involved in RNA-mediated transcriptional silencing" EXACT [GOC:TermGenie]
synonym: "conversion of ds siRNA to ss siRNA involved in RNAi-directed chromatin silencing" EXACT [GOC:TermGenie]
synonym: "conversion of ds siRNA to ss siRNA involved in RNAi-like chromatin silencing" EXACT [GOC:TermGenie]
synonym: "conversion of ds siRNA to ss siRNA involved in small RNA-mediated heterochromatic silencing" EXACT [GOC:TermGenie]
-is_a: GO:0036404 ! conversion of ds siRNA to ss siRNA
-relationship: part_of GO:0031048 ! heterochromatin assembly by small RNA
+is_obsolete: true
+consider: GO:0004521
+consider: GO:0031047
[Term]
id: GO:1902362
@@ -459230,7 +460032,8 @@ name: regulation of protein localization to spindle pole body
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to spindle pole body." [GOC:TermGenie, PMID:21131906]
synonym: "regulation of protein localisation to spindle pole body" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0071988 ! protein localization to spindle pole body
[Term]
@@ -459247,8 +460050,9 @@ synonym: "downregulation of protein localization to spindle pole body" EXACT [GO
synonym: "inhibition of protein localisation to spindle pole body" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to spindle pole body" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to spindle pole body" EXACT [GOC:TermGenie]
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1902363 ! regulation of protein localization to spindle pole body
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0071988 ! protein localization to spindle pole body
[Term]
@@ -459265,8 +460069,9 @@ synonym: "up-regulation of protein localisation to spindle pole body" EXACT [GOC
synonym: "up-regulation of protein localization to spindle pole body" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localisation to spindle pole body" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to spindle pole body" EXACT [GOC:TermGenie]
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1902363 ! regulation of protein localization to spindle pole body
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0071988 ! protein localization to spindle pole body
[Term]
@@ -459677,7 +460482,7 @@ is_a: GO:1902384 ! glycyrrhetinate metabolic process
id: GO:1902387
name: ceramide 1-phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ceramide 1-phosphate." [GOC:TermGenie, PMID:23863933]
+def: "Binding to ceramide 1-phosphate." [GOC:TermGenie, PMID:23863933]
is_a: GO:0005543 ! phospholipid binding
is_a: GO:0043168 ! anion binding
is_a: GO:0097001 ! ceramide binding
@@ -459826,6 +460631,7 @@ namespace: biological_process
def: "Any actomyosin contractile ring contraction that is involved in mitotic cell cycle." [GOC:mtg_cell_cycle, GOC:TermGenie]
synonym: "contractile ring contraction involved in cell cycle cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "cytokinesis, actomyosin ring contraction involved in mitotic cell cycle" EXACT [GOC:TermGenie]
+synonym: "mitotic actomyosin contractile ring constriction" EXACT [GOC:vw]
is_a: GO:0000916 ! actomyosin contractile ring contraction
is_a: GO:1902410 ! mitotic cytokinetic process
@@ -460322,7 +461128,7 @@ relationship: negatively_regulates GO:1901026 ! ripoptosome assembly involved in
id: GO:1902444
name: riboflavin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with riboflavin." [GOC:TermGenie, PMID:12083520]
+def: "Binding to riboflavin." [GOC:TermGenie, PMID:12083520]
is_a: GO:0043168 ! anion binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -460572,8 +461378,8 @@ synonym: "up-regulation of protein localisation to synapse" EXACT [GOC:TermGenie
synonym: "up-regulation of protein localization to synapse" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localisation to synapse" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to synapse" EXACT [GOC:TermGenie]
-is_a: GO:0048518 ! positive regulation of biological process
is_a: GO:1902473 ! regulation of protein localization to synapse
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0035418 ! protein localization to synapse
[Term]
@@ -460650,7 +461456,7 @@ is_a: GO:1904019 ! epithelial cell apoptotic process
id: GO:1902485
name: L-cysteine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with L-cysteine." [GOC:bhm, GOC:TermGenie, PMID:12941942]
+def: "Binding to L-cysteine." [GOC:bhm, GOC:TermGenie, PMID:12941942]
is_a: GO:0016597 ! amino acid binding
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0043169 ! cation binding
@@ -460700,7 +461506,6 @@ name: regulation of sperm capacitation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of sperm capacitation." [GOC:hjd, GOC:TermGenie, PMID:22539676]
synonym: "regulation of sperm activation" RELATED [GOC:TermGenie]
-is_a: GO:0043900 ! regulation of multi-organism process
is_a: GO:0051239 ! regulation of multicellular organismal process
is_a: GO:1903429 ! regulation of cell maturation
is_a: GO:2000241 ! regulation of reproductive process
@@ -460720,7 +461525,6 @@ synonym: "downregulation of sperm capacitation" EXACT [GOC:TermGenie]
synonym: "inhibition of sperm activation" RELATED [GOC:TermGenie]
synonym: "inhibition of sperm capacitation" NARROW [GOC:TermGenie]
synonym: "negative regulation of sperm activation" RELATED [GOC:TermGenie]
-is_a: GO:0043901 ! negative regulation of multi-organism process
is_a: GO:0051241 ! negative regulation of multicellular organismal process
is_a: GO:1902490 ! regulation of sperm capacitation
is_a: GO:1903430 ! negative regulation of cell maturation
@@ -460741,7 +461545,6 @@ synonym: "up-regulation of sperm activation" RELATED [GOC:TermGenie]
synonym: "up-regulation of sperm capacitation" EXACT [GOC:TermGenie]
synonym: "upregulation of sperm activation" RELATED [GOC:TermGenie]
synonym: "upregulation of sperm capacitation" EXACT [GOC:TermGenie]
-is_a: GO:0043902 ! positive regulation of multi-organism process
is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:1902490 ! regulation of sperm capacitation
is_a: GO:1903431 ! positive regulation of cell maturation
@@ -461016,7 +461819,7 @@ is_a: GO:1990204 ! oxidoreductase complex
id: GO:1902516
name: sn-glycerol 3-phosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with sn-glycerol 3-phosphate." [GOC:bhm, GOC:TermGenie, PMID:23013274]
+def: "Binding to sn-glycerol 3-phosphate." [GOC:bhm, GOC:TermGenie, PMID:23013274]
comment: An example of this is UgpB in E. coli [P0AG80] - see PMID:23013274.
is_a: GO:0043168 ! anion binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -461334,11 +462137,11 @@ relationship: positively_regulates GO:0035556 ! intracellular signal transductio
[Term]
id: GO:1902535
-name: multi-organism membrane invagination
+name: obsolete multi-organism membrane invagination
namespace: biological_process
-def: "A membrane invagination which involves another organism." [GOC:bf, GOC:jl, GOC:TermGenie]
-is_a: GO:0010324 ! membrane invagination
-is_a: GO:0044803 ! multi-organism membrane organization
+def: "OBSOLETE. A membrane invagination which involves another organism." [GOC:bf, GOC:jl, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:1902537
@@ -461350,21 +462153,19 @@ is_obsolete: true
[Term]
id: GO:1902539
-name: multi-organism macropinocytosis
+name: obsolete multi-organism macropinocytosis
namespace: biological_process
-def: "A macropinocytosis which involves another organism." [GOC:bf, GOC:jl, GOC:TermGenie]
-is_a: GO:0044351 ! macropinocytosis
-is_a: GO:0044764 ! multi-organism cellular process
-is_a: GO:0044766 ! multi-organism transport
+def: "OBSOLETE. A macropinocytosis which involves another organism." [GOC:bf, GOC:jl, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:1902541
-name: multi-organism micropinocytosis
+name: obsolete multi-organism micropinocytosis
namespace: biological_process
-def: "A micropinocytosis which involves another organism." [GOC:bf, GOC:jl, GOC:TermGenie]
-is_a: GO:0044350 ! micropinocytosis
-is_a: GO:0044764 ! multi-organism cellular process
-is_a: GO:0044766 ! multi-organism transport
+def: "OBSOLETE. A micropinocytosis which involves another organism." [GOC:bf, GOC:jl, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
+is_obsolete: true
[Term]
id: GO:1902542
@@ -461997,22 +462798,21 @@ is_a: GO:0071574 ! protein localization to medial cortex
[Term]
id: GO:1902579
-name: multi-organism localization
+name: obsolete multi-organism localization
namespace: biological_process
-def: "A localization which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+def: "OBSOLETE. A localization which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi organism localization" EXACT [GOC:TermGenie]
-is_a: GO:0051179 ! localization
-is_a: GO:0051704 ! multi-organism process
+is_obsolete: true
[Term]
id: GO:1902581
-name: multi-organism cellular localization
+name: obsolete multi-organism cellular localization
namespace: biological_process
-def: "A cellular localization which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+def: "OBSOLETE. A cellular localization which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi organism cellular localization" EXACT [GOC:TermGenie]
-is_a: GO:0044764 ! multi-organism cellular process
-is_a: GO:0051641 ! cellular localization
-is_a: GO:1902579 ! multi-organism localization
+is_obsolete: true
[Term]
id: GO:1902583
@@ -462058,11 +462858,12 @@ relationship: positively_regulates GO:0009414 ! response to water deprivation
[Term]
id: GO:1902586
-name: multi-organism intercellular transport
+name: obsolete multi-organism intercellular transport
namespace: biological_process
-def: "An intercellular transport which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+def: "OBSOLETE. An intercellular transport which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi organism intercellular transport" EXACT [GOC:TermGenie]
-is_a: GO:0044766 ! multi-organism transport
+is_obsolete: true
[Term]
id: GO:1902588
@@ -462075,12 +462876,12 @@ is_obsolete: true
[Term]
id: GO:1902590
-name: multi-organism organelle organization
+name: obsolete multi-organism organelle organization
namespace: biological_process
-def: "An organelle organization which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+def: "OBSOLETE. An organelle organization which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi organism organelle organization" EXACT [GOC:TermGenie]
-is_a: GO:0006996 ! organelle organization
-is_a: GO:0044764 ! multi-organism cellular process
+is_obsolete: true
[Term]
id: GO:1902592
@@ -462093,13 +462894,12 @@ is_obsolete: true
[Term]
id: GO:1902594
-name: multi-organism nuclear import
+name: obsolete multi-organism nuclear import
namespace: biological_process
-def: "A nuclear import which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+def: "OBSOLETE. A nuclear import which involves another organism." [GO_REF:0000089, GOC:jl, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "multi organism nuclear import" EXACT [GOC:TermGenie]
-is_a: GO:0044766 ! multi-organism transport
-is_a: GO:0051170 ! import into nucleus
-is_a: GO:1902581 ! multi-organism cellular localization
+is_obsolete: true
[Term]
id: GO:1902595
@@ -462170,7 +462970,6 @@ synonym: "hydrogen ion transport" RELATED []
synonym: "hydrogen transmembrane transport" EXACT []
synonym: "hydrogen transport" BROAD []
synonym: "passive proton transport, down the electrochemical gradient" NARROW []
-synonym: "proton transmembrane transport" EXACT []
synonym: "proton transport" BROAD []
is_a: GO:0098662 ! inorganic cation transmembrane transport
@@ -462833,37 +463632,38 @@ relationship: positively_regulates GO:1902635 ! 1-phosphatidyl-1D-myo-inositol 4
[Term]
id: GO:1902649
-name: regulation of histone H2A-H2B dimer displacement
+name: obsolete regulation of histone H2A-H2B dimer displacement
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of histone H2A-H2B dimer displacement." [GO_REF:0000058, GOC:di, GOC:TermGenie, PMID:22199252]
-is_a: GO:1902275 ! regulation of chromatin organization
-relationship: regulates GO:0001208 ! histone H2A-H2B dimer displacement
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of histone H2A-H2B dimer displacement." [GO_REF:0000058, GOC:di, GOC:TermGenie, PMID:22199252]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0140713
[Term]
id: GO:1902650
-name: negative regulation of histone H2A-H2B dimer displacement
+name: obsolete negative regulation of histone H2A-H2B dimer displacement
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of histone H2A-H2B dimer displacement." [GO_REF:0000058, GOC:di, GOC:TermGenie, PMID:22199252]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of histone H2A-H2B dimer displacement." [GO_REF:0000058, GOC:di, GOC:TermGenie, PMID:22199252]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of histone H2A-H2B dimer displacement" EXACT [GOC:TermGenie]
synonym: "down-regulation of histone H2A-H2B dimer displacement" EXACT [GOC:TermGenie]
synonym: "downregulation of histone H2A-H2B dimer displacement" EXACT [GOC:TermGenie]
synonym: "inhibition of histone H2A-H2B dimer displacement" NARROW [GOC:TermGenie]
-is_a: GO:1902649 ! regulation of histone H2A-H2B dimer displacement
-is_a: GO:1905268 ! negative regulation of chromatin organization
-relationship: negatively_regulates GO:0001208 ! histone H2A-H2B dimer displacement
+is_obsolete: true
+consider: GO:0140713
[Term]
id: GO:1902651
-name: positive regulation of histone H2A-H2B dimer displacement
+name: obsolete positive regulation of histone H2A-H2B dimer displacement
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of histone H2A-H2B dimer displacement." [GO_REF:0000058, GOC:di, GOC:TermGenie, PMID:22199252]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of histone H2A-H2B dimer displacement." [GO_REF:0000058, GOC:di, GOC:TermGenie, PMID:22199252]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of histone H2A-H2B dimer displacement" NARROW [GOC:TermGenie]
synonym: "up regulation of histone H2A-H2B dimer displacement" EXACT [GOC:TermGenie]
synonym: "up-regulation of histone H2A-H2B dimer displacement" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H2A-H2B dimer displacement" EXACT [GOC:TermGenie]
-is_a: GO:1902649 ! regulation of histone H2A-H2B dimer displacement
-is_a: GO:1905269 ! positive regulation of chromatin organization
-relationship: positively_regulates GO:0001208 ! histone H2A-H2B dimer displacement
+is_obsolete: true
+consider: GO:0140713
[Term]
id: GO:1902652
@@ -463167,7 +463967,7 @@ relationship: positively_regulates GO:0007411 ! axon guidance
id: GO:1902670
name: carbon dioxide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with carbon dioxide." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:15491402]
+def: "Binding to carbon dioxide." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:15491402]
synonym: "CO2 binding" EXACT []
is_a: GO:0005488 ! binding
@@ -463419,7 +464219,6 @@ name: protein localization to pericentric heterochromatin
namespace: biological_process
def: "A process in which a protein is transported to, or maintained in the pericentric heterochromatin." [GO_REF:0000087, GOC:TermGenie, PMID:20211136]
synonym: "protein localisation in centromeric heterochromatin" EXACT [GOC:TermGenie]
-synonym: "protein localization to pericentric heterochromatin" RELATED []
is_a: GO:0071459 ! protein localization to chromosome, centromeric region
is_a: GO:0097355 ! protein localization to heterochromatin
@@ -463734,8 +464533,7 @@ def: "The chemical reactions and pathways resulting in the breakdown of valine t
synonym: "valine breakdown to isobutanol" EXACT [GOC:TermGenie]
synonym: "valine catabolism to isobutanol" EXACT [GOC:TermGenie]
synonym: "valine degradation to isobutanol" EXACT [GOC:TermGenie]
-is_a: GO:0009083 ! branched-chain amino acid catabolic process
-is_a: GO:1901606 ! alpha-amino acid catabolic process
+is_a: GO:0006574 ! valine catabolic process
is_a: GO:1901960 ! isobutanol metabolic process
[Term]
@@ -464859,21 +465657,24 @@ is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:1902794
-name: heterochromatin island assembly
+name: siRNA-independent facultative heterochromatin assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a heterochromatin island." [GO_REF:0000079, GOC:TermGenie, PMID:24210919]
+def: "The assembly of facultative heterochromatin to form a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process independent of small interfering RNAs." [GO_REF:0000079, GOC:TermGenie, PMID:22144463, PMID:24210919]
+synonym: "heterochromatin island assembly" EXACT []
synonym: "heterochromatin island formation" EXACT [GOC:TermGenie]
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0140718 ! facultative heterochromatin assembly
[Term]
id: GO:1902795
-name: heterochromatin domain assembly
+name: siRNA-dependent facultative heterochromatin assembly
namespace: biological_process
-def: "The aggregation, arrangement and bonding together of a set of components to form a heterochromatin domain." [GO_REF:0000079, GOC:TermGenie, PMID:24210919]
+def: "The assembly of facultative heterochromatin to form a heterochromatin domain, enriched in histone H3 methylated on lysine 9 (H3K9me), by a process mediated by a small interfering RNA." [GO_REF:0000079, GOC:TermGenie, PMID:23151475, PMID:24210919]
+synonym: "heterochromatin domain assembly" EXACT []
synonym: "heterochromatin domain formation" EXACT [GOC:TermGenie]
synonym: "HOOD assembly" EXACT [GOC:TermGenie]
synonym: "HOOD formation" EXACT [GOC:TermGenie]
-is_a: GO:0031507 ! heterochromatin assembly
+is_a: GO:0031048 ! heterochromatin assembly by small RNA
+is_a: GO:0140718 ! facultative heterochromatin assembly
[Term]
id: GO:1902796
@@ -465018,23 +465819,25 @@ is_a: GO:1905779 ! positive regulation of exonuclease activity
[Term]
id: GO:1902801
-name: regulation of heterochromatin island assembly
+name: regulation of siRNA-independent facultative heterochromatin assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of heterochromatin island assembly." [GO_REF:0000058, GOC:TermGenie, PMID:24210919]
+def: "Any process that modulates the frequency, rate or extent of siRNA-independent facultative heterochromatin assembly." [GO_REF:0000058, GOC:TermGenie, PMID:24210919]
+synonym: "regulation of heterochromatin island assembly" EXACT []
synonym: "regulation of heterochromatin island formation" EXACT [GOC:TermGenie]
is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:1902794 ! heterochromatin island assembly
+relationship: regulates GO:1902794 ! siRNA-independent facultative heterochromatin assembly
[Term]
id: GO:1902802
-name: regulation of heterochromatin domain assembly
+name: regulation of siRNA-dependent facultative heterochromatin assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of heterochromatin domain assembly." [GO_REF:0000058, GOC:TermGenie, PMID:24210919]
+def: "Any process that modulates the frequency, rate or extent of siRNA-dependent facultative heterochromatin assembly." [GO_REF:0000058, GOC:TermGenie, PMID:24210919]
+synonym: "regulation of heterochromatin domain assembly" EXACT []
synonym: "regulation of heterochromatin domain formation" EXACT [GOC:TermGenie]
synonym: "regulation of HOOD assembly" EXACT [GOC:TermGenie]
synonym: "regulation of HOOD formation" EXACT [GOC:TermGenie]
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:1902795 ! heterochromatin domain assembly
+is_a: GO:0010964 ! regulation of heterochromatin assembly by small RNA
+relationship: regulates GO:1902795 ! siRNA-dependent facultative heterochromatin assembly
[Term]
id: GO:1902803
@@ -465237,7 +466040,8 @@ name: regulation of protein localization to microtubule
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to microtubule." [GO_REF:0000058, GOC:TermGenie, GOC:vw, PMID:23087209]
synonym: "regulation of protein localisation to microtubule" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0035372 ! protein localization to microtubule
[Term]
@@ -465254,8 +466058,9 @@ synonym: "downregulation of protein localization to microtubule" EXACT [GOC:Term
synonym: "inhibition of protein localisation to microtubule" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to microtubule" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to microtubule" EXACT [GOC:TermGenie]
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1902816 ! regulation of protein localization to microtubule
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0035372 ! protein localization to microtubule
[Term]
@@ -465869,6 +466674,7 @@ name: propionyl-CoA metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving propionyl-CoA." [GO_REF:0000068, GOC:mengo_curators, GOC:TermGenie, PMID:15514053]
synonym: "propionyl-CoA metabolism" EXACT [GOC:TermGenie]
+is_a: GO:0006629 ! lipid metabolic process
is_a: GO:0006637 ! acyl-CoA metabolic process
[Term]
@@ -465880,6 +466686,7 @@ synonym: "propionyl-CoA breakdown" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA catabolism" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA degradation" EXACT [GOC:TermGenie]
is_a: GO:0009154 ! purine ribonucleotide catabolic process
+is_a: GO:0016042 ! lipid catabolic process
is_a: GO:0034031 ! ribonucleoside bisphosphate catabolic process
is_a: GO:0034034 ! purine nucleoside bisphosphate catabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
@@ -465894,6 +466701,7 @@ synonym: "propionyl-CoA anabolism" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA biosynthesis" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA formation" EXACT [GOC:TermGenie]
synonym: "propionyl-CoA synthesis" EXACT [GOC:TermGenie]
+is_a: GO:0008610 ! lipid biosynthetic process
is_a: GO:0071616 ! acyl-CoA biosynthetic process
is_a: GO:1902858 ! propionyl-CoA metabolic process
@@ -466420,40 +467228,52 @@ relationship: positively_regulates GO:0048767 ! root hair elongation
[Term]
id: GO:1902893
-name: regulation of pri-miRNA transcription by RNA polymerase II
+name: regulation of miRNA transcription
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of pri-miRNA transcription mediated by RNA polymerase II." [GO_REF:0000058, GOC:dph, GOC:kmv, GOC:TermGenie, PMID:24699545]
+def: "Any process that modulates the frequency, rate or extent of microRNA (miRNA) gene transcription." [GO_REF:0000058, GOC:dph, GOC:kmv, GOC:TermGenie, PMID:24699545]
+synonym: "regulation of microRNA gene transcription" EXACT []
+synonym: "regulation of miRNA gene transcription" EXACT []
+synonym: "regulation of pri-miRNA transcription by RNA polymerase II" EXACT []
synonym: "regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT []
-is_a: GO:0006357 ! regulation of transcription by RNA polymerase II
-relationship: regulates GO:0061614 ! pri-miRNA transcription by RNA polymerase II
+synonym: "regulation of primary miRNA gene transcription" EXACT []
+is_a: GO:0006355 ! regulation of transcription, DNA-templated
+relationship: regulates GO:0061614 ! miRNA transcription
[Term]
id: GO:1902894
-name: negative regulation of pri-miRNA transcription by RNA polymerase II
+name: negative regulation of miRNA transcription
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of pri-miRNA transcription mediated by RNA polymerase II." [GO_REF:0000058, GOC:dph, GOC:kmv, GOC:TermGenie, PMID:24699545]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of microRNA (miRNA) gene transcription." [GO_REF:0000058, GOC:dph, GOC:kmv, GOC:TermGenie, PMID:24699545]
synonym: "down regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "down-regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "downregulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "inhibition of pri-miRNA transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie]
+synonym: "negative regulation of microRNA gene transcription" EXACT []
+synonym: "negative regulation of miRNA gene transcription" EXACT []
+synonym: "negative regulation of pri-miRNA transcription by RNA polymerase II" EXACT []
synonym: "negative regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT []
-is_a: GO:0000122 ! negative regulation of transcription by RNA polymerase II
-is_a: GO:1902893 ! regulation of pri-miRNA transcription by RNA polymerase II
-relationship: negatively_regulates GO:0061614 ! pri-miRNA transcription by RNA polymerase II
+synonym: "negative regulation of primary miRNA gene transcription" EXACT []
+is_a: GO:0045892 ! negative regulation of transcription, DNA-templated
+is_a: GO:1902893 ! regulation of miRNA transcription
+relationship: negatively_regulates GO:0061614 ! miRNA transcription
[Term]
id: GO:1902895
-name: positive regulation of pri-miRNA transcription by RNA polymerase II
+name: positive regulation of miRNA transcription
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of pri-miRNA transcription mediated by RNA polymerase II." [GO_REF:0000058, GOC:dph, GOC:kmv, GOC:TermGenie, PMID:24699545]
+def: "Any process that activates or increases the frequency, rate or extent of microRNA (miRNA) gene transcription." [GO_REF:0000058, GOC:dph, GOC:kmv, GOC:TermGenie, PMID:24699545]
synonym: "activation of pri-miRNA transcription from RNA polymerase II promoter" NARROW [GOC:TermGenie]
+synonym: "positive regulation of microRNA gene transcription" EXACT []
+synonym: "positive regulation of pri-miRNA gene transcription" EXACT []
+synonym: "positive regulation of pri-miRNA transcription by RNA polymerase II" EXACT []
synonym: "positive regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT []
+synonym: "positive regulation of primary miRNA gene transcription" EXACT []
synonym: "up regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "up-regulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
synonym: "upregulation of pri-miRNA transcription from RNA polymerase II promoter" EXACT [GOC:TermGenie]
-is_a: GO:0045944 ! positive regulation of transcription by RNA polymerase II
-is_a: GO:1902893 ! regulation of pri-miRNA transcription by RNA polymerase II
-relationship: positively_regulates GO:0061614 ! pri-miRNA transcription by RNA polymerase II
+is_a: GO:0045893 ! positive regulation of transcription, DNA-templated
+is_a: GO:1902893 ! regulation of miRNA transcription
+relationship: positively_regulates GO:0061614 ! miRNA transcription
[Term]
id: GO:1902896
@@ -466462,7 +467282,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a terminal web." [GO_REF:0000079, GOC:kmv, GOC:TermGenie, pmid:21949650]
synonym: "terminal web formation" EXACT [GOC:TermGenie]
is_a: GO:0030866 ! cortical actin cytoskeleton organization
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:1902897
@@ -466650,7 +467470,7 @@ synonym: "proteasome storage granule formation" EXACT [GOC:TermGenie]
synonym: "PSG assembly" RELATED [GOC:TermGenie]
synonym: "PSG formation" RELATED [GOC:TermGenie]
synonym: "sequestration of proteasome core complex in proteasome storage granule" NARROW []
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:1902907
@@ -466810,6 +467630,7 @@ is_a: GO:0031383 ! regulation of mating projection assembly
is_a: GO:0051094 ! positive regulation of developmental process
is_a: GO:0120034 ! positive regulation of plasma membrane bounded cell projection assembly
is_a: GO:2000243 ! positive regulation of reproductive process
+relationship: part_of GO:0031139 ! positive regulation of conjugation with cellular fusion
relationship: positively_regulates GO:0031382 ! mating projection formation
[Term]
@@ -467063,7 +467884,7 @@ is_a: GO:0072697 ! protein localization to cell cortex
id: GO:1902936
name: phosphatidylinositol bisphosphate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphatidylinositol bisphosphate." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:18690034]
+def: "Binding to phosphatidylinositol bisphosphate." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:18690034]
comment: An example of this is KCNJ2 in human (P63252) in PMID:18690034 (inferred from direct assay)
is_a: GO:1901981 ! phosphatidylinositol phosphate binding
@@ -468387,7 +469208,6 @@ synonym: "DNA replication initiation involved in meiotic DNA replication" EXACT
synonym: "initiation of meiotic DNA synthesis" RELATED [GOC:mah]
synonym: "initiation of premeiotic DNA replication" RELATED []
synonym: "initiation of premeiotic DNA synthesis" RELATED [GOC:mah]
-synonym: "meiotic DNA replication initiation" RELATED [GOC:mah]
synonym: "premeiotic DNA replication initiation" RELATED [GOC:mah]
is_a: GO:1902315 ! nuclear cell cycle DNA replication initiation
is_a: GO:1903046 ! meiotic cell cycle process
@@ -469297,6 +470117,7 @@ synonym: "up regulation of opsonization" EXACT [GOC:TermGenie]
synonym: "up-regulation of opsonization" EXACT [GOC:TermGenie]
synonym: "upregulation of opsonization" EXACT [GOC:TermGenie]
is_a: GO:0002699 ! positive regulation of immune effector process
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0050766 ! positive regulation of phagocytosis
is_a: GO:1903027 ! regulation of opsonization
relationship: positively_regulates GO:0008228 ! opsonization
@@ -469879,7 +470700,8 @@ name: regulation of protein localization to cell tip
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to cell tip." [GO_REF:0000058, GOC:TermGenie, PMID:24554432]
synonym: "regulation of protein localisation to cell tip" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1990151 ! protein localization to cell tip
[Term]
@@ -469896,8 +470718,9 @@ synonym: "downregulation of protein localization to cell tip" EXACT [GOC:TermGen
synonym: "inhibition of protein localisation to cell tip" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to cell tip" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to cell tip" EXACT [GOC:TermGenie]
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903066 ! regulation of protein localization to cell tip
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:1990151 ! protein localization to cell tip
[Term]
@@ -469914,8 +470737,9 @@ synonym: "up-regulation of protein localisation to cell tip" EXACT [GOC:TermGeni
synonym: "up-regulation of protein localization to cell tip" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localisation to cell tip" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to cell tip" EXACT [GOC:TermGenie]
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903066 ! regulation of protein localization to cell tip
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:1990151 ! protein localization to cell tip
[Term]
@@ -470473,7 +471297,7 @@ synonym: "regulation of DNA replication-independent nucleosome assembly at centr
is_a: GO:0010847 ! regulation of chromatin assembly
is_a: GO:0090230 ! regulation of centromere complex assembly
is_a: GO:1900049 ! regulation of histone exchange
-relationship: regulates GO:0034080 ! CENP-A containing nucleosome assembly
+relationship: regulates GO:0034080 ! CENP-A containing chromatin assembly
[Term]
id: GO:1903098
@@ -470528,7 +471352,7 @@ is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
is_a: GO:0045798 ! negative regulation of chromatin assembly or disassembly
is_a: GO:1900050 ! negative regulation of histone exchange
is_a: GO:1903097 ! regulation of CENP-A containing nucleosome assembly
-relationship: negatively_regulates GO:0034080 ! CENP-A containing nucleosome assembly
+relationship: negatively_regulates GO:0034080 ! CENP-A containing chromatin assembly
[Term]
id: GO:1903099
@@ -470583,7 +471407,7 @@ is_a: GO:0031334 ! positive regulation of protein-containing complex assembly
is_a: GO:0045799 ! positive regulation of chromatin assembly or disassembly
is_a: GO:1900051 ! positive regulation of histone exchange
is_a: GO:1903097 ! regulation of CENP-A containing nucleosome assembly
-relationship: positively_regulates GO:0034080 ! CENP-A containing nucleosome assembly
+relationship: positively_regulates GO:0034080 ! CENP-A containing chromatin assembly
[Term]
id: GO:1903100
@@ -470710,7 +471534,6 @@ id: GO:1903108
name: regulation of mitochondrial transcription
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcription occuring in the mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:21357609]
-synonym: "regulation of mitochondrial transcription" EXACT [GOC:TermGenie]
synonym: "regulation of transcription from mitochondrial promoter" EXACT []
is_a: GO:0006355 ! regulation of transcription, DNA-templated
is_a: GO:0062125 ! regulation of mitochondrial gene expression
@@ -470723,7 +471546,6 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of transcription occuring in the mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:21357609]
synonym: "activation of mitochondrial transcription" NARROW [GOC:TermGenie]
synonym: "activation of transcription from mitochondrial promoter" NARROW [GOC:TermGenie]
-synonym: "positive regulation of mitochondrial transcription" EXACT [GOC:TermGenie]
synonym: "positive regulation of transcription from mitochondrial promoter" EXACT []
synonym: "up regulation of mitochondrial transcription" EXACT [GOC:TermGenie]
synonym: "up regulation of transcription from mitochondrial promoter" EXACT [GOC:TermGenie]
@@ -471025,7 +471847,7 @@ is_obsolete: true
id: GO:1903135
name: cupric ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cupric ion, copper(2+)." [GO_REF:0000067, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24567322]
+def: "Binding to a cupric ion, copper(2+)." [GO_REF:0000067, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24567322]
synonym: "copper(2+)binding" EXACT [CHEBI:29036]
synonym: "Cu(2+) binding" EXACT [CHEBI:29036]
synonym: "Cu(II) binding" EXACT [PMID:24567322]
@@ -471035,7 +471857,7 @@ is_a: GO:0005507 ! copper ion binding
id: GO:1903136
name: cuprous ion binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cuprous ion, copper(1+)." [GO_REF:0000067, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24567322]
+def: "Binding to a cuprous ion, copper(1+)." [GO_REF:0000067, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24567322]
synonym: "copper(1+) binding" EXACT [CHEBI:49552]
synonym: "Cu(+) binding" EXACT [CHEBI:49552]
synonym: "Cu(I) binding" EXACT [PMID:24567322]
@@ -471823,7 +472645,6 @@ synonym: "L-dopa anabolism" EXACT [GOC:TermGenie]
synonym: "L-dopa biosynthesis" EXACT [GOC:TermGenie]
synonym: "L-dopa formation" EXACT [GOC:TermGenie]
synonym: "L-dopa synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0009073 ! aromatic amino acid family biosynthetic process
is_a: GO:0042398 ! cellular modified amino acid biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -472926,8 +473747,7 @@ synonym: "regulation of citrulline anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of citrulline biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of citrulline formation" EXACT [GOC:TermGenie]
synonym: "regulation of citrulline synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0006521 ! regulation of cellular amino acid metabolic process
-is_a: GO:0031326 ! regulation of cellular biosynthetic process
+is_a: GO:2000282 ! regulation of cellular amino acid biosynthetic process
relationship: regulates GO:0019240 ! citrulline biosynthetic process
[Term]
@@ -472959,9 +473779,8 @@ synonym: "negative regulation of citrulline anabolism" EXACT [GOC:TermGenie]
synonym: "negative regulation of citrulline biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of citrulline formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of citrulline synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031327 ! negative regulation of cellular biosynthetic process
-is_a: GO:0045763 ! negative regulation of cellular amino acid metabolic process
is_a: GO:1903248 ! regulation of citrulline biosynthetic process
+is_a: GO:2000283 ! negative regulation of cellular amino acid biosynthetic process
relationship: negatively_regulates GO:0019240 ! citrulline biosynthetic process
[Term]
@@ -472993,9 +473812,8 @@ synonym: "upregulation of citrulline biosynthesis" EXACT [GOC:TermGenie]
synonym: "upregulation of citrulline biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of citrulline formation" EXACT [GOC:TermGenie]
synonym: "upregulation of citrulline synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0031328 ! positive regulation of cellular biosynthetic process
-is_a: GO:0045764 ! positive regulation of cellular amino acid metabolic process
is_a: GO:1903248 ! regulation of citrulline biosynthetic process
+is_a: GO:2000284 ! positive regulation of cellular amino acid biosynthetic process
relationship: positively_regulates GO:0019240 ! citrulline biosynthetic process
[Term]
@@ -473271,7 +474089,6 @@ def: "Any process that modulates the frequency, rate or extent of sodium ion exp
synonym: "regulation of sodium export" RELATED [GOC:TermGenie]
synonym: "regulation of sodium ion export" RELATED []
synonym: "regulation of sodium ion export from cell" EXACT []
-is_a: GO:0010959 ! regulation of metal ion transport
is_a: GO:1902305 ! regulation of sodium ion transmembrane transport
relationship: regulates GO:0036376 ! sodium ion export across plasma membrane
@@ -474468,8 +475285,7 @@ id: GO:1903335
name: regulation of vacuolar transport
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of vacuolar transport." [GO_REF:0000058, GOC:TermGenie, GOC:vw]
-is_a: GO:0050794 ! regulation of cellular process
-is_a: GO:0051049 ! regulation of transport
+is_a: GO:0032386 ! regulation of intracellular transport
relationship: regulates GO:0007034 ! vacuolar transport
[Term]
@@ -474481,8 +475297,7 @@ synonym: "down regulation of vacuolar transport" EXACT [GOC:TermGenie]
synonym: "down-regulation of vacuolar transport" EXACT [GOC:TermGenie]
synonym: "downregulation of vacuolar transport" EXACT [GOC:TermGenie]
synonym: "inhibition of vacuolar transport" NARROW [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:0051051 ! negative regulation of transport
+is_a: GO:0032387 ! negative regulation of intracellular transport
is_a: GO:1903335 ! regulation of vacuolar transport
relationship: negatively_regulates GO:0007034 ! vacuolar transport
@@ -474495,8 +475310,7 @@ synonym: "activation of vacuolar transport" NARROW [GOC:TermGenie]
synonym: "up regulation of vacuolar transport" EXACT [GOC:TermGenie]
synonym: "up-regulation of vacuolar transport" EXACT [GOC:TermGenie]
synonym: "upregulation of vacuolar transport" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
-is_a: GO:0051050 ! positive regulation of transport
+is_a: GO:0032388 ! positive regulation of intracellular transport
is_a: GO:1903335 ! regulation of vacuolar transport
relationship: positively_regulates GO:0007034 ! vacuolar transport
@@ -475076,7 +475890,7 @@ synonym: "spatium leptomeningeum development" RELATED [GOC:TermGenie]
synonym: "spatium subarachnoideum development" RELATED [GOC:TermGenie]
synonym: "subarachnoid cavity development" RELATED [GOC:TermGenie]
is_a: GO:0048856 ! anatomical structure development
-relationship: part_of GO:0007420 ! brain development
+relationship: part_of GO:0007417 ! central nervous system development
[Term]
id: GO:1903375
@@ -475507,15 +476321,6 @@ synonym: "upregulation of m7G(5')pppN pyrophosphatase activity" EXACT [GOC:TermG
is_a: GO:0051345 ! positive regulation of hydrolase activity
is_a: GO:1903398 ! regulation of m7G(5')pppN diphosphatase activity
-[Term]
-id: GO:1903400
-name: L-arginine transmembrane transport
-namespace: biological_process
-def: "The directed movement of L-arginine across a membrane." [GO_REF:0000069, GOC:krc, GOC:TermGenie, PMID:8195186]
-is_a: GO:1902023 ! L-arginine transport
-is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
-is_a: GO:1903826 ! arginine transmembrane transport
-
[Term]
id: GO:1903401
name: L-lysine transmembrane transport
@@ -475603,7 +476408,7 @@ synonym: "regulation of sodium/potassium-exchanging ATPase activity" EXACT [GOC:
synonym: "regulation of sodium/potassium-transporting ATPase activity" EXACT [GOC:TermGenie]
synonym: "regulation of sodium:potassium exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "regulation of sodium:potassium-exchanging ATPase activity" EXACT []
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
is_a: GO:1901016 ! regulation of potassium ion transmembrane transporter activity
is_a: GO:2000649 ! regulation of sodium ion transmembrane transporter activity
@@ -475687,7 +476492,7 @@ synonym: "negative regulation of sodium/potassium-exchanging ATPase activity" EX
synonym: "negative regulation of sodium/potassium-transporting ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of sodium:potassium exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of sodium:potassium-exchanging ATPase activity" EXACT []
-is_a: GO:0032780 ! negative regulation of ATPase activity
+is_a: GO:0032780 ! negative regulation of ATP-dependent activity
is_a: GO:1901017 ! negative regulation of potassium ion transmembrane transporter activity
is_a: GO:1903406 ! regulation of P-type sodium:potassium-exchanging transporter activity
is_a: GO:2000650 ! negative regulation of sodium ion transmembrane transporter activity
@@ -475772,7 +476577,7 @@ synonym: "upregulation of sodium/potassium-exchanging ATPase activity" EXACT [GO
synonym: "upregulation of sodium/potassium-transporting ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of sodium:potassium exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of sodium:potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
-is_a: GO:0032781 ! positive regulation of ATPase activity
+is_a: GO:0032781 ! positive regulation of ATP-dependent activity
is_a: GO:1901018 ! positive regulation of potassium ion transmembrane transporter activity
is_a: GO:1903406 ! regulation of P-type sodium:potassium-exchanging transporter activity
is_a: GO:2000651 ! positive regulation of sodium ion transmembrane transporter activity
@@ -475817,7 +476622,6 @@ name: flavonoid transport from endoplasmic reticulum to plant-type vacuole
namespace: biological_process
def: "The directed movement of flavonoid from endoplasmic reticulum to plant-type vacuole." [GO_REF:0000078, GOC:tb, GOC:TermGenie, PMID:25116949]
synonym: "flavonoid accumulation in vacuole" RELATED []
-is_a: GO:0007034 ! vacuolar transport
is_a: GO:0071702 ! organic substance transport
[Term]
@@ -476723,6 +477527,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of mitotic actomyosin contractile ring contraction." [GO_REF:0000058, GOC:mtg_cell_cycle, GOC:TermGenie, PMID:1234]
synonym: "regulation of contractile ring contraction involved in cell cycle cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "regulation of cytokinesis, actomyosin ring contraction involved in mitotic cell cycle" EXACT [GOC:TermGenie]
+synonym: "regulation of mitotic actomyosin contractile ring constriction" EXACT [GOC:vw]
is_a: GO:0031991 ! regulation of actomyosin contractile ring contraction
is_a: GO:1903436 ! regulation of mitotic cytokinetic process
relationship: regulates GO:1902404 ! mitotic actomyosin contractile ring contraction
@@ -476746,6 +477551,7 @@ synonym: "inhibition of cytokinesis, actomyosin ring contraction involved in mit
synonym: "inhibition of mitotic actomyosin contractile ring contraction" NARROW [GOC:TermGenie]
synonym: "negative regulation of contractile ring contraction involved in cell cycle cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "negative regulation of cytokinesis, actomyosin ring contraction involved in mitotic cell cycle" EXACT [GOC:TermGenie]
+synonym: "negative regulation of mitotic actomyosin contractile ring constriction" EXACT [GOC:vw]
is_a: GO:1903437 ! negative regulation of mitotic cytokinetic process
is_a: GO:1903471 ! regulation of mitotic actomyosin contractile ring contraction
relationship: negatively_regulates GO:1902404 ! mitotic actomyosin contractile ring contraction
@@ -476760,6 +477566,7 @@ synonym: "activation of cytokinesis, actomyosin ring contraction involved in mit
synonym: "activation of mitotic actomyosin contractile ring contraction" NARROW [GOC:TermGenie]
synonym: "positive regulation of contractile ring contraction involved in cell cycle cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "positive regulation of cytokinesis, actomyosin ring contraction involved in mitotic cell cycle" EXACT [GOC:TermGenie]
+synonym: "positive regulation of mitotic actomyosin contractile ring constriction" EXACT [GOC:vw]
synonym: "up regulation of contractile ring contraction involved in cell cycle cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "up regulation of cytokinesis, actomyosin ring contraction involved in mitotic cell cycle" EXACT [GOC:TermGenie]
synonym: "up regulation of mitotic actomyosin contractile ring contraction" EXACT [GOC:TermGenie]
@@ -477719,6 +478526,7 @@ synonym: "regulation of exosomal secretory pathway" EXACT [GOC:TermGenie]
synonym: "regulation of extracellular vesicular exosome secretion" EXACT [GOC:TermGenie]
synonym: "regulation of secretion of exosome" EXACT [GOC:TermGenie]
is_a: GO:0017157 ! regulation of exocytosis
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1990182 ! exosomal secretion
[Term]
@@ -478059,7 +478867,6 @@ synonym: "3-cyano-L-alanine anabolism" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine biosynthesis" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine formation" EXACT [GOC:TermGenie]
synonym: "3-cyano-L-alanine synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0008652 ! cellular amino acid biosynthetic process
is_a: GO:0080028 ! nitrile biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
is_a: GO:1903558 ! 3-cyano-L-alanine metabolic process
@@ -478078,7 +478885,6 @@ id: GO:1903562
name: microtubule bundle formation involved in mitotic spindle midzone assembly
namespace: biological_process
def: "Any microtubule bundle formation that is involved in spindle midzone assembly involved in mitosis." [GO_REF:0000060, GOC:TermGenie, PMID:15647375]
-synonym: "microtubule bundle formation involved in mitotic spindle midzone assembly" EXACT [GOC:TermGenie]
synonym: "microtubule bundle formation involved in mitotic spindle midzone formation" EXACT [GOC:TermGenie]
synonym: "microtubule bundle formation involved in spindle midzone assembly involved in mitosis" EXACT [GOC:dos]
synonym: "microtubule bundling involved in mitotic spindle midzone assembly" RELATED [GOC:TermGenie]
@@ -478109,7 +478915,8 @@ id: GO:1903564
name: regulation of protein localization to cilium
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to cilium." [GO_REF:0000058, GOC:cilia, GOC:krc, GOC:TermGenie, PMID:22072986]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0061512 ! protein localization to cilium
[Term]
@@ -478121,8 +478928,9 @@ synonym: "down regulation of protein localization to cilium" EXACT [GOC:TermGeni
synonym: "down-regulation of protein localization to cilium" EXACT [GOC:TermGenie]
synonym: "downregulation of protein localization to cilium" EXACT [GOC:TermGenie]
synonym: "inhibition of protein localization to cilium" NARROW [GOC:TermGenie]
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903564 ! regulation of protein localization to cilium
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0061512 ! protein localization to cilium
[Term]
@@ -478134,8 +478942,9 @@ synonym: "activation of protein localization to cilium" NARROW [GOC:TermGenie]
synonym: "up regulation of protein localization to cilium" EXACT [GOC:TermGenie]
synonym: "up-regulation of protein localization to cilium" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to cilium" EXACT [GOC:TermGenie]
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903564 ! regulation of protein localization to cilium
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0061512 ! protein localization to cilium
[Term]
@@ -478922,7 +479731,7 @@ id: GO:1903610
name: regulation of calcium-dependent ATPase activity
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of calcium-dependent ATPase activity." [GO_REF:0000059, GOC:TermGenie, PMID:10861851]
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
[Term]
id: GO:1903611
@@ -478933,7 +479742,7 @@ synonym: "down regulation of calcium-dependent ATPase activity" EXACT [GOC:TermG
synonym: "down-regulation of calcium-dependent ATPase activity" EXACT [GOC:TermGenie]
synonym: "downregulation of calcium-dependent ATPase activity" EXACT [GOC:TermGenie]
synonym: "inhibition of calcium-dependent ATPase activity" NARROW [GOC:TermGenie]
-is_a: GO:0032780 ! negative regulation of ATPase activity
+is_a: GO:0032780 ! negative regulation of ATP-dependent activity
is_a: GO:1903610 ! regulation of calcium-dependent ATPase activity
[Term]
@@ -478945,7 +479754,7 @@ synonym: "activation of calcium-dependent ATPase activity" NARROW [GOC:TermGenie
synonym: "up regulation of calcium-dependent ATPase activity" EXACT [GOC:TermGenie]
synonym: "up-regulation of calcium-dependent ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of calcium-dependent ATPase activity" EXACT [GOC:TermGenie]
-is_a: GO:0032781 ! positive regulation of ATPase activity
+is_a: GO:0032781 ! positive regulation of ATP-dependent activity
is_a: GO:1903610 ! regulation of calcium-dependent ATPase activity
[Term]
@@ -479839,8 +480648,7 @@ synonym: "regulation by virus of host cytoplasmic streaming" EXACT []
synonym: "regulation by virus of host cytoplasmic transport" EXACT []
synonym: "viral modulation of host cytoplasmic trafficking" EXACT []
is_a: GO:0019054 ! modulation by virus of host cellular process
-is_a: GO:0052038 ! modulation by symbiont of host intracellular transport
-is_a: GO:1903649 ! regulation of cytoplasmic transport
+relationship: regulates GO:0016482 ! cytosolic transport
[Term]
id: GO:1903653
@@ -481132,8 +481940,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of establishment of protein localization to mitochondrion." [GO_REF:0000058, GOC:TermGenie, PMID:16857185]
synonym: "regulation of establishment of protein localisation to mitochondrion" EXACT [GOC:TermGenie]
synonym: "regulation of establishment of protein localization in mitochondrion" EXACT [GOC:TermGenie]
+is_a: GO:0060341 ! regulation of cellular localization
is_a: GO:0070201 ! regulation of establishment of protein localization
-is_a: GO:1903827 ! regulation of cellular protein localization
relationship: regulates GO:0072655 ! establishment of protein localization to mitochondrion
[Term]
@@ -481155,8 +481963,8 @@ synonym: "inhibition of establishment of protein localization in mitochondrion"
synonym: "inhibition of establishment of protein localization to mitochondrion" NARROW [GOC:TermGenie]
synonym: "negative regulation of establishment of protein localisation to mitochondrion" EXACT [GOC:TermGenie]
synonym: "negative regulation of establishment of protein localization in mitochondrion" EXACT [GOC:TermGenie]
+is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:1903747 ! regulation of establishment of protein localization to mitochondrion
-is_a: GO:1903828 ! negative regulation of cellular protein localization
is_a: GO:1904950 ! negative regulation of establishment of protein localization
relationship: negatively_regulates GO:0072655 ! establishment of protein localization to mitochondrion
@@ -481179,8 +481987,8 @@ synonym: "up-regulation of establishment of protein localization to mitochondrio
synonym: "upregulation of establishment of protein localisation to mitochondrion" EXACT [GOC:TermGenie]
synonym: "upregulation of establishment of protein localization in mitochondrion" EXACT [GOC:TermGenie]
synonym: "upregulation of establishment of protein localization to mitochondrion" EXACT [GOC:TermGenie]
+is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:1903747 ! regulation of establishment of protein localization to mitochondrion
-is_a: GO:1903829 ! positive regulation of cellular protein localization
is_a: GO:1904951 ! positive regulation of establishment of protein localization
relationship: positively_regulates GO:0072655 ! establishment of protein localization to mitochondrion
@@ -481418,7 +482226,6 @@ def: "Any process that modulates the frequency, rate or extent of potassium ion
synonym: "regulation of potassium export" BROAD [GOC:TermGenie]
synonym: "regulation of potassium export across plasma membrane" BROAD [GOC:TermGenie]
synonym: "regulation of potassium ion export" BROAD []
-is_a: GO:0010959 ! regulation of metal ion transport
is_a: GO:1901379 ! regulation of potassium ion transmembrane transport
relationship: regulates GO:0097623 ! potassium ion export across plasma membrane
@@ -481720,7 +482527,7 @@ relationship: regulates GO:0000736 ! double-strand break repair via single-stran
id: GO:1903777
name: melibiose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with melibiose." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:11471732]
+def: "Binding to melibiose." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:11471732]
is_a: GO:0048030 ! disaccharide binding
[Term]
@@ -481810,7 +482617,6 @@ id: GO:1903785
name: L-valine transmembrane transport
namespace: biological_process
def: "The directed movement of L-valine across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:20944394]
-is_a: GO:0015803 ! branched-chain amino acid transport
is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0015829 ! valine transport
is_a: GO:0098655 ! cation transmembrane transport
@@ -481959,7 +482765,7 @@ relationship: positively_regulates GO:0006820 ! anion transport
id: GO:1903794
name: cortisol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cortisol." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:18483153]
+def: "Binding to cortisol." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:18483153]
is_a: GO:0043178 ! alcohol binding
is_a: GO:1990239 ! steroid hormone binding
@@ -482191,7 +482997,6 @@ synonym: "L-leucine uptake" NARROW []
synonym: "leucine import" BROAD []
synonym: "leucine uptake" EXACT []
is_a: GO:0015807 ! L-amino acid transport
-is_a: GO:0015820 ! leucine transport
is_a: GO:0098655 ! cation transmembrane transport
is_a: GO:0098656 ! anion transmembrane transport
is_a: GO:0098713 ! leucine import across plasma membrane
@@ -482515,70 +483320,59 @@ is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:1903826
-name: arginine transmembrane transport
+name: L-arginine transmembrane transport
namespace: biological_process
-def: "The directed movement of arginine across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:18357653]
-is_a: GO:0015809 ! arginine transport
+alt_id: GO:0015809
+alt_id: GO:0043091
+alt_id: GO:1902023
+alt_id: GO:1903400
+def: "The directed movement of L-arginine across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:18357653, PMID:22822152, PMID:8195186]
+synonym: "arginine transmembrane transport" RELATED []
+synonym: "arginine transport" BROAD []
+synonym: "L-arginine import" NARROW []
+synonym: "L-arginine transport" BROAD []
+synonym: "L-arginine uptake" NARROW []
+is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0098655 ! cation transmembrane transport
is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
is_a: GO:1990822 ! basic amino acid transmembrane transport
-[Term]
-id: GO:1903827
-name: regulation of cellular protein localization
-namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GO_REF:0000058, GOC:TermGenie, GOC:vw]
-synonym: "regulation of cellular protein localisation" EXACT [GOC:TermGenie]
-synonym: "regulation of channel localizer activity" NARROW [GOC:TermGenie]
-is_a: GO:0032880 ! regulation of protein localization
-is_a: GO:0060341 ! regulation of cellular localization
-relationship: regulates GO:0034613 ! cellular protein localization
-
[Term]
id: GO:1903828
-name: negative regulation of cellular protein localization
+name: negative regulation of protein localization
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GO_REF:0000058, GOC:TermGenie, GOC:vw]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization." [GO_REF:0000058, GOC:TermGenie, GOC:vw]
synonym: "down regulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "down regulation of cellular protein localization" EXACT [GOC:TermGenie]
-synonym: "down regulation of channel localizer activity" NARROW [GOC:TermGenie]
synonym: "down-regulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "down-regulation of cellular protein localization" EXACT [GOC:TermGenie]
-synonym: "down-regulation of channel localizer activity" NARROW [GOC:TermGenie]
synonym: "downregulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "downregulation of cellular protein localization" EXACT [GOC:TermGenie]
-synonym: "downregulation of channel localizer activity" NARROW [GOC:TermGenie]
synonym: "inhibition of cellular protein localisation" NARROW [GOC:TermGenie]
synonym: "inhibition of cellular protein localization" NARROW [GOC:TermGenie]
-synonym: "inhibition of channel localizer activity" NARROW [GOC:TermGenie]
synonym: "negative regulation of cellular protein localisation" EXACT [GOC:TermGenie]
-synonym: "negative regulation of channel localizer activity" NARROW [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
-is_a: GO:1903827 ! regulation of cellular protein localization
-relationship: negatively_regulates GO:0034613 ! cellular protein localization
+synonym: "negative regulation of cellular protein localization" EXACT []
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0048519 ! negative regulation of biological process
+relationship: negatively_regulates GO:0008104 ! protein localization
[Term]
id: GO:1903829
-name: positive regulation of cellular protein localization
+name: positive regulation of protein localization
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GO_REF:0000058, GOC:TermGenie, GOC:vw]
-synonym: "activation of cellular protein localisation" NARROW [GOC:TermGenie]
-synonym: "activation of cellular protein localization" NARROW [GOC:TermGenie]
-synonym: "activation of channel localizer activity" NARROW [GOC:TermGenie]
+def: "Any process that activates or increases the frequency, rate or extent of a protein localization." [GO_REF:0000058, GOC:TermGenie, GOC:vw]
synonym: "positive regulation of cellular protein localisation" EXACT [GOC:TermGenie]
-synonym: "positive regulation of channel localizer activity" NARROW [GOC:TermGenie]
+synonym: "positive regulation of cellular protein localization" EXACT []
synonym: "up regulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "up regulation of cellular protein localization" EXACT [GOC:TermGenie]
-synonym: "up regulation of channel localizer activity" NARROW [GOC:TermGenie]
synonym: "up-regulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "up-regulation of cellular protein localization" EXACT [GOC:TermGenie]
-synonym: "up-regulation of channel localizer activity" NARROW [GOC:TermGenie]
synonym: "upregulation of cellular protein localisation" EXACT [GOC:TermGenie]
synonym: "upregulation of cellular protein localization" EXACT [GOC:TermGenie]
-synonym: "upregulation of channel localizer activity" NARROW [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
-is_a: GO:1903827 ! regulation of cellular protein localization
-relationship: positively_regulates GO:0034613 ! cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0048518 ! positive regulation of biological process
+relationship: positively_regulates GO:0008104 ! protein localization
[Term]
id: GO:1903830
@@ -483010,7 +483804,7 @@ synonym: "P granule formation" EXACT [GOC:TermGenie]
synonym: "polar granule assembly" EXACT [GOC:TermGenie]
synonym: "polar granule formation" EXACT [GOC:TermGenie]
is_a: GO:0030719 ! P granule organization
-is_a: GO:0070925 ! organelle assembly
+is_a: GO:0140694 ! non-membrane-bounded organelle assembly
[Term]
id: GO:1903864
@@ -483363,7 +484157,7 @@ relationship: negatively_regulates GO:1903871 ! DNA recombinase mediator complex
id: GO:1903875
name: corticosterone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with corticosterone." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
+def: "Binding to corticosterone." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
is_a: GO:0043178 ! alcohol binding
is_a: GO:1990239 ! steroid hormone binding
@@ -483371,7 +484165,7 @@ is_a: GO:1990239 ! steroid hormone binding
id: GO:1903876
name: 11-deoxycortisol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 11-deoxycortisol." [GO_REF:0000067, GOC:TermGenie, PMID:10802282]
+def: "Binding to 11-deoxycortisol." [GO_REF:0000067, GOC:TermGenie, PMID:10802282]
is_a: GO:0043178 ! alcohol binding
is_a: GO:1990239 ! steroid hormone binding
@@ -483379,7 +484173,7 @@ is_a: GO:1990239 ! steroid hormone binding
id: GO:1903877
name: 21-deoxycortisol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 21-deoxycortisol." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
+def: "Binding to 21-deoxycortisol." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
is_a: GO:0005496 ! steroid binding
is_a: GO:0043178 ! alcohol binding
@@ -483387,7 +484181,7 @@ is_a: GO:0043178 ! alcohol binding
id: GO:1903878
name: 11-deoxycorticosterone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 11-deoxycorticosterone." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
+def: "Binding to 11-deoxycorticosterone." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
is_a: GO:0043178 ! alcohol binding
is_a: GO:1990239 ! steroid hormone binding
@@ -483395,14 +484189,14 @@ is_a: GO:1990239 ! steroid hormone binding
id: GO:1903879
name: 11beta-hydroxyprogesterone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 11beta-hydroxyprogesterone." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
+def: "Binding to 11beta-hydroxyprogesterone." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
is_a: GO:0005496 ! steroid binding
[Term]
id: GO:1903880
name: 17alpha-hydroxyprogesterone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 17alpha-hydroxyprogesterone." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
+def: "Binding to 17alpha-hydroxyprogesterone." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10802282]
is_a: GO:0005496 ! steroid binding
is_a: GO:0043178 ! alcohol binding
@@ -484164,7 +484958,6 @@ synonym: "negative regulation of ER stress-induced eIF2 alpha phosphorylation" E
synonym: "negative regulation of regulation of translation initiation by eiF2alpha phosphorylation in response to endoplasmic reticulum stress" EXACT [GOC:TermGenie]
is_a: GO:0001933 ! negative regulation of protein phosphorylation
is_a: GO:0006446 ! regulation of translational initiation
-is_a: GO:1903573 ! negative regulation of response to endoplasmic reticulum stress
relationship: negatively_regulates GO:0036492 ! eiF2alpha phosphorylation in response to endoplasmic reticulum stress
[Term]
@@ -484179,7 +484972,6 @@ synonym: "regulation of viral envelope fusion with host membrane" EXACT [GOC:Ter
synonym: "regulation of viral envelope fusion with host plasma membrane" EXACT [GOC:TermGenie]
synonym: "regulation of viral penetration via membrane fusion" EXACT [GOC:TermGenie]
synonym: "regulation of viral-cell fusion molecule activity" RELATED [GOC:TermGenie]
-is_a: GO:0043900 ! regulation of multi-organism process
is_a: GO:0046596 ! regulation of viral entry into host cell
is_a: GO:0051128 ! regulation of cellular component organization
relationship: regulates GO:0019064 ! fusion of virus membrane with host plasma membrane
@@ -484223,7 +485015,6 @@ synonym: "negative regulation of viral envelope fusion with host membrane" EXACT
synonym: "negative regulation of viral envelope fusion with host plasma membrane" EXACT [GOC:TermGenie]
synonym: "negative regulation of viral penetration via membrane fusion" EXACT [GOC:TermGenie]
synonym: "negative regulation of viral-cell fusion molecule activity" RELATED [GOC:TermGenie]
-is_a: GO:0043901 ! negative regulation of multi-organism process
is_a: GO:0046597 ! negative regulation of viral entry into host cell
is_a: GO:0051129 ! negative regulation of cellular component organization
is_a: GO:1903913 ! regulation of fusion of virus membrane with host plasma membrane
@@ -484268,7 +485059,6 @@ synonym: "upregulation of viral envelope fusion with host membrane" EXACT [GOC:T
synonym: "upregulation of viral envelope fusion with host plasma membrane" EXACT [GOC:TermGenie]
synonym: "upregulation of viral penetration via membrane fusion" EXACT [GOC:TermGenie]
synonym: "upregulation of viral-cell fusion molecule activity" RELATED [GOC:TermGenie]
-is_a: GO:0043902 ! positive regulation of multi-organism process
is_a: GO:0046598 ! positive regulation of viral entry into host cell
is_a: GO:0051130 ! positive regulation of cellular component organization
is_a: GO:1903913 ! regulation of fusion of virus membrane with host plasma membrane
@@ -484287,7 +485077,6 @@ is_a: GO:0006446 ! regulation of translational initiation
is_a: GO:0032535 ! regulation of cellular component size
is_a: GO:0035304 ! regulation of protein dephosphorylation
is_a: GO:0051128 ! regulation of cellular component organization
-is_a: GO:1905897 ! regulation of response to endoplasmic reticulum stress
relationship: regulates GO:0036497 ! eIF2alpha dephosphorylation in response to endoplasmic reticulum stress
[Term]
@@ -484314,7 +485103,6 @@ synonym: "upregulation of regulation of translation initiation by eIF2alpha deph
is_a: GO:0035307 ! positive regulation of protein dephosphorylation
is_a: GO:0051130 ! positive regulation of cellular component organization
is_a: GO:1903916 ! regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation
-is_a: GO:1905898 ! positive regulation of response to endoplasmic reticulum stress
relationship: positively_regulates GO:0036497 ! eIF2alpha dephosphorylation in response to endoplasmic reticulum stress
[Term]
@@ -484521,7 +485309,7 @@ relationship: positively_regulates GO:1900756 ! protein processing in phagocytic
id: GO:1903924
name: estradiol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with estradiol." [GO_REF:0000067, GOC:TermGenie, PMID:9048584]
+def: "Binding to estradiol." [GO_REF:0000067, GOC:TermGenie, PMID:9048584]
is_a: GO:0005496 ! steroid binding
[Term]
@@ -485077,7 +485865,6 @@ name: regulation of response to macrophage colony-stimulating factor
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of response to macrophage colony-stimulating factor." [GO_REF:0000058, GOC:BHF, GOC:nc, GOC:TermGenie, PMID:19100238]
synonym: "regulation of response to M-CSF" EXACT [GOC:TermGenie]
-synonym: "regulation of response to macrophage colony-stimulating factor" EXACT [GOC:TermGenie]
synonym: "regulation of response to macrophage colony-stimulating factor stimulus" EXACT [GOC:TermGenie]
is_a: GO:0060759 ! regulation of response to cytokine stimulus
relationship: regulates GO:0036005 ! response to macrophage colony-stimulating factor
@@ -485100,7 +485887,6 @@ synonym: "inhibition of response to M-CSF" NARROW [GOC:TermGenie]
synonym: "inhibition of response to macrophage colony-stimulating factor" NARROW [GOC:TermGenie]
synonym: "inhibition of response to macrophage colony-stimulating factor stimulus" NARROW [GOC:TermGenie]
synonym: "negative regulation of response to M-CSF" EXACT [GOC:TermGenie]
-synonym: "negative regulation of response to macrophage colony-stimulating factor" EXACT [GOC:TermGenie]
synonym: "negative regulation of response to macrophage colony-stimulating factor stimulus" EXACT [GOC:TermGenie]
is_a: GO:0060761 ! negative regulation of response to cytokine stimulus
is_a: GO:1903969 ! regulation of response to macrophage colony-stimulating factor
@@ -485115,7 +485901,6 @@ synonym: "activation of response to M-CSF" NARROW [GOC:TermGenie]
synonym: "activation of response to macrophage colony-stimulating factor" NARROW [GOC:TermGenie]
synonym: "activation of response to macrophage colony-stimulating factor stimulus" NARROW [GOC:TermGenie]
synonym: "positive regulation of response to M-CSF" EXACT [GOC:TermGenie]
-synonym: "positive regulation of response to macrophage colony-stimulating factor" EXACT [GOC:TermGenie]
synonym: "positive regulation of response to macrophage colony-stimulating factor stimulus" EXACT [GOC:TermGenie]
synonym: "up regulation of response to M-CSF" EXACT [GOC:TermGenie]
synonym: "up regulation of response to macrophage colony-stimulating factor" EXACT [GOC:TermGenie]
@@ -485275,7 +486060,7 @@ relationship: positively_regulates GO:0001774 ! microglial cell activation
id: GO:1903981
name: enterobactin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with enterobactin." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:21951132]
+def: "Binding to enterobactin." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:21951132]
synonym: "enterochelin binding" EXACT []
synonym: "siderophore binding" BROAD []
is_a: GO:0005527 ! macrolide binding
@@ -485785,7 +486570,7 @@ is_a: GO:1904010 ! response to Aroclor 1254
id: GO:1904012
name: obsolete platinum binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with platinum." [GO_REF:0000067, GOC:TermGenie, PMID:10089464]
+def: "OBSOLETE. Binding to platinum." [GO_REF:0000067, GOC:TermGenie, PMID:10089464]
comment: The reason for obsoletion is that binding to platinum does not have physiological relevance.
is_obsolete: true
@@ -485793,7 +486578,7 @@ is_obsolete: true
id: GO:1904013
name: obsolete xenon atom binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with xenon atom." [GO_REF:0000067, GOC:TermGenie, PMID:10089464]
+def: "OBSOLETE. Binding to xenon atom." [GO_REF:0000067, GOC:TermGenie, PMID:10089464]
comment: The reason for obsoletion is that binding to xenon does not have physiological relevance.
is_obsolete: true
@@ -486210,7 +486995,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region." [GO_REF:0000058, GOC:BHF, GOC:kom, GOC:TermGenie, PMID:15514116]
synonym: "regulation of ferrous iron export" NARROW []
synonym: "regulation of iron(2+) export" NARROW []
-is_a: GO:0010959 ! regulation of metal ion transport
is_a: GO:0034759 ! regulation of iron ion transmembrane transport
relationship: regulates GO:1903988 ! iron ion export across plasma membrane
@@ -486392,7 +487176,7 @@ id: GO:1904047
name: S-adenosyl-L-methionine binding
namespace: molecular_function
alt_id: GO:0070283
-def: "Interacting selectively and non-covalently with S-adenosyl-L-methionine." [GO_REF:0000067, GOC:BHF, GOC:hal, GOC:TermGenie, PMID:22985361]
+def: "Binding to S-adenosyl-L-methionine." [GO_REF:0000067, GOC:BHF, GOC:hal, GOC:TermGenie, PMID:22985361]
synonym: "radical SAM enzyme activity" NARROW []
xref: Reactome:R-HSA-947535 "Cyclisation of GTP to precursor Z"
is_a: GO:0043169 ! cation binding
@@ -486484,7 +487268,6 @@ synonym: "up-regulation of protein targeting to vacuole involved in autophagy" E
synonym: "upregulation of protein targeting to vacuole involved in autophagy" EXACT [GOC:TermGenie]
is_a: GO:0090316 ! positive regulation of intracellular protein transport
is_a: GO:1903337 ! positive regulation of vacuolar transport
-is_a: GO:1903829 ! positive regulation of cellular protein localization
is_a: GO:1904051 ! regulation of protein targeting to vacuole involved in autophagy
relationship: positively_regulates GO:0071211 ! protein targeting to vacuole involved in autophagy
@@ -486707,7 +487490,7 @@ relationship: part_of GO:0040024 ! dauer larval development
id: GO:1904067
name: ascr#2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ascr#2." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:22665789]
+def: "Binding to ascr#2." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:22665789]
is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
@@ -487490,19 +488273,22 @@ relationship: positively_regulates GO:0070508 ! cholesterol import
[Term]
id: GO:1904110
-name: regulation of plus-end directed microfilament motor activity
+name: obsolete regulation of plus-end directed microfilament motor activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of plus-end directed microfilament motor activity." [GO_REF:0000059, GOC:kmv, GOC:TermGenie, PMID:25717181]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of plus-end directed microfilament motor activity." [GO_REF:0000059, GOC:kmv, GOC:TermGenie, PMID:25717181]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of barbed-end directed actin-filament motor activity" EXACT [GOC:TermGenie]
synonym: "regulation of plus-end directed actin filament motor activity" RELATED [GOC:TermGenie]
synonym: "regulation of plus-end directed actin-filament motor activity" EXACT [GOC:TermGenie]
-is_a: GO:0120079 ! regulation of microfilament motor activity
+is_obsolete: true
+consider: GO:0140659
[Term]
id: GO:1904111
-name: negative regulation of plus-end directed microfilament motor activity
+name: obsolete negative regulation of plus-end directed microfilament motor activity
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of plus-end directed microfilament motor activity." [GO_REF:0000059, GOC:kmv, GOC:TermGenie, PMID:25717181]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of plus-end directed microfilament motor activity." [GO_REF:0000059, GOC:kmv, GOC:TermGenie, PMID:25717181]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "down regulation of barbed-end directed actin-filament motor activity" EXACT [GOC:TermGenie]
synonym: "down regulation of plus-end directed actin filament motor activity" RELATED [GOC:TermGenie]
synonym: "down regulation of plus-end directed actin-filament motor activity" EXACT [GOC:TermGenie]
@@ -487522,14 +488308,15 @@ synonym: "inhibition of plus-end directed microfilament motor activity" NARROW [
synonym: "negative regulation of barbed-end directed actin-filament motor activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of plus-end directed actin filament motor activity" RELATED [GOC:TermGenie]
synonym: "negative regulation of plus-end directed actin-filament motor activity" EXACT [GOC:TermGenie]
-is_a: GO:0120080 ! negative regulation of microfilament motor activity
-is_a: GO:1904110 ! regulation of plus-end directed microfilament motor activity
+is_obsolete: true
+consider: GO:0140661
[Term]
id: GO:1904112
-name: positive regulation of plus-end directed microfilament motor activity
+name: obsolete positive regulation of plus-end directed microfilament motor activity
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of plus-end directed microfilament motor activity." [GO_REF:0000059, GOC:kmv, GOC:TermGenie, PMID:25717181]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of plus-end directed microfilament motor activity." [GO_REF:0000059, GOC:kmv, GOC:TermGenie, PMID:25717181]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "activation of barbed-end directed actin-filament motor activity" NARROW [GOC:TermGenie]
synonym: "activation of plus-end directed actin filament motor activity" RELATED [GOC:TermGenie]
synonym: "activation of plus-end directed actin-filament motor activity" NARROW [GOC:TermGenie]
@@ -487549,8 +488336,8 @@ synonym: "upregulation of barbed-end directed actin-filament motor activity" EXA
synonym: "upregulation of plus-end directed actin filament motor activity" RELATED [GOC:TermGenie]
synonym: "upregulation of plus-end directed actin-filament motor activity" EXACT [GOC:TermGenie]
synonym: "upregulation of plus-end directed microfilament motor activity" EXACT [GOC:TermGenie]
-is_a: GO:0120081 ! positive regulation of microfilament motor activity
-is_a: GO:1904110 ! regulation of plus-end directed microfilament motor activity
+is_obsolete: true
+consider: GO:0140659
[Term]
id: GO:1904113
@@ -488845,7 +489632,6 @@ synonym: "upregulation of protein import into chloroplast stroma" EXACT [GOC:Ter
synonym: "upregulation of protein transport into chloroplast stroma" EXACT [GOC:TermGenie]
is_a: GO:0034764 ! positive regulation of transmembrane transport
is_a: GO:0090316 ! positive regulation of intracellular protein transport
-is_a: GO:1903829 ! positive regulation of cellular protein localization
is_a: GO:1904215 ! regulation of protein import into chloroplast stroma
is_a: GO:1904591 ! positive regulation of protein import
relationship: positively_regulates GO:0045037 ! protein import into chloroplast stroma
@@ -491032,7 +491818,7 @@ relationship: positively_regulates GO:0018352 ! protein-pyridoxal-5-phosphate li
id: GO:1904288
name: BAT3 complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a BAT3 complex." [GOC:bf, GOC:PARL, GOC:TermGenie, PMID:23246001]
+def: "Binding to a BAT3 complex." [GOC:bf, GOC:PARL, GOC:TermGenie, PMID:23246001]
synonym: "Bag6 complex binding" EXACT [GOC:TermGenie]
synonym: "BAG6-UBL4A-TRC35 complex binding" EXACT [GOC:TermGenie]
synonym: "BAT3-TRC35-UBL4A complex binding" RELATED [GOC:TermGenie]
@@ -491185,6 +491971,7 @@ id: GO:1904298
name: regulation of transcytosis
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of transcytosis." [GO_REF:0000058, GOC:TermGenie, PMID:9664076]
+is_a: GO:0051239 ! regulation of multicellular organismal process
is_a: GO:0060627 ! regulation of vesicle-mediated transport
relationship: regulates GO:0045056 ! transcytosis
@@ -491197,8 +491984,8 @@ synonym: "down regulation of transcytosis" EXACT [GOC:TermGenie]
synonym: "down-regulation of transcytosis" EXACT [GOC:TermGenie]
synonym: "downregulation of transcytosis" EXACT [GOC:TermGenie]
synonym: "inhibition of transcytosis" NARROW [GOC:TermGenie]
-is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0051051 ! negative regulation of transport
+is_a: GO:0051241 ! negative regulation of multicellular organismal process
is_a: GO:1904298 ! regulation of transcytosis
relationship: negatively_regulates GO:0045056 ! transcytosis
@@ -491211,8 +491998,8 @@ synonym: "activation of transcytosis" NARROW [GOC:TermGenie]
synonym: "up regulation of transcytosis" EXACT [GOC:TermGenie]
synonym: "up-regulation of transcytosis" EXACT [GOC:TermGenie]
synonym: "upregulation of transcytosis" EXACT [GOC:TermGenie]
-is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:0051050 ! positive regulation of transport
+is_a: GO:0051240 ! positive regulation of multicellular organismal process
is_a: GO:1904298 ! regulation of transcytosis
relationship: positively_regulates GO:0045056 ! transcytosis
@@ -492013,7 +492800,7 @@ namespace: biological_process
alt_id: GO:0075006
def: "Any process that modulates the frequency, rate or extent of spore germination." [GO_REF:0000058, GOC:TermGenie, PMID:14718564, PMID:8798577]
synonym: "modulation of spore germination on or near host" NARROW []
-is_a: GO:0050793 ! regulation of developmental process
+is_a: GO:0045595 ! regulation of cell differentiation
relationship: regulates GO:0009847 ! spore germination
[Term]
@@ -492027,7 +492814,7 @@ synonym: "down-regulation of spore germination" EXACT [GOC:TermGenie]
synonym: "downregulation of spore germination" EXACT [GOC:TermGenie]
synonym: "inhibition of spore germination" NARROW [GOC:TermGenie]
synonym: "negative regulation of spore germination on or near host" NARROW []
-is_a: GO:0051093 ! negative regulation of developmental process
+is_a: GO:0045596 ! negative regulation of cell differentiation
is_a: GO:1904359 ! regulation of spore germination
relationship: negatively_regulates GO:0009847 ! spore germination
@@ -492042,7 +492829,7 @@ synonym: "positive regulation of spore germination on or near host" NARROW []
synonym: "up regulation of spore germination" EXACT [GOC:TermGenie]
synonym: "up-regulation of spore germination" EXACT [GOC:TermGenie]
synonym: "upregulation of spore germination" EXACT [GOC:TermGenie]
-is_a: GO:0051094 ! positive regulation of developmental process
+is_a: GO:0045597 ! positive regulation of cell differentiation
is_a: GO:1904359 ! regulation of spore germination
relationship: positively_regulates GO:0009847 ! spore germination
@@ -492201,7 +492988,8 @@ id: GO:1904375
name: regulation of protein localization to cell periphery
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to cell periphery." [GO_REF:0000058, GOC:TermGenie, PMID:18216290]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1990778 ! protein localization to cell periphery
[Term]
@@ -492213,7 +493001,8 @@ synonym: "down regulation of protein localization to cell periphery" EXACT [GOC:
synonym: "down-regulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
synonym: "downregulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
synonym: "inhibition of protein localization to cell periphery" NARROW [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1904375 ! regulation of protein localization to cell periphery
relationship: negatively_regulates GO:1990778 ! protein localization to cell periphery
@@ -492226,7 +493015,8 @@ synonym: "activation of protein localization to cell periphery" NARROW [GOC:Term
synonym: "up regulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
synonym: "up-regulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to cell periphery" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1904375 ! regulation of protein localization to cell periphery
relationship: positively_regulates GO:1990778 ! protein localization to cell periphery
@@ -492536,7 +493326,7 @@ relationship: positively_regulates GO:0007528 ! neuromuscular junction developme
id: GO:1904399
name: heparan sulfate binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with heparan sulfate." [GO_REF:0000067, GOC:TermGenie, PMID:8567685]
+def: "Binding to heparan sulfate." [GO_REF:0000067, GOC:TermGenie, PMID:8567685]
is_a: GO:0005539 ! glycosaminoglycan binding
is_a: GO:1901681 ! sulfur compound binding
@@ -492630,7 +493420,7 @@ relationship: positively_regulates GO:0046209 ! nitric oxide metabolic process
id: GO:1904408
name: melatonin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with melatonin." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10379923]
+def: "Binding to melatonin." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10379923]
is_a: GO:0033218 ! amide binding
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -493286,7 +494076,7 @@ synonym: "regulation of hydrogen:potassium exchanging ATPase activity" EXACT [GO
synonym: "regulation of hydrogen:potassium-exchanging ATPase activity" EXACT []
synonym: "regulation of proton pump activity" BROAD [GOC:TermGenie]
is_a: GO:0010155 ! regulation of proton transport
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
is_a: GO:1901016 ! regulation of potassium ion transmembrane transporter activity
[Term]
@@ -493359,7 +494149,7 @@ synonym: "negative regulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of hydrogen/potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of hydrogen:potassium exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "negative regulation of hydrogen:potassium-exchanging ATPase activity" EXACT []
-is_a: GO:0032780 ! negative regulation of ATPase activity
+is_a: GO:0032780 ! negative regulation of ATP-dependent activity
is_a: GO:1901017 ! negative regulation of potassium ion transmembrane transporter activity
is_a: GO:1904451 ! regulation of potassium:proton exchanging ATPase activity
@@ -493433,7 +494223,7 @@ synonym: "upregulation of H,K-ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of hydrogen/potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of hydrogen:potassium exchanging ATPase activity" EXACT [GOC:TermGenie]
synonym: "upregulation of hydrogen:potassium-exchanging ATPase activity" EXACT [GOC:TermGenie]
-is_a: GO:0032781 ! positive regulation of ATPase activity
+is_a: GO:0032781 ! positive regulation of ATP-dependent activity
is_a: GO:1901018 ! positive regulation of potassium ion transmembrane transporter activity
is_a: GO:1904451 ! regulation of potassium:proton exchanging ATPase activity
@@ -493800,7 +494590,7 @@ id: GO:1904481
name: response to tetrahydrofolate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tetrahydrofolate stimulus." [GO_REF:0000071, GOC:BHF, GOC:hal, GOC:TermGenie, PMID:24698160]
-is_a: GO:0010033 ! response to organic substance
+is_a: GO:0010243 ! response to organonitrogen compound
is_a: GO:1901700 ! response to oxygen-containing compound
[Term]
@@ -493808,6 +494598,7 @@ id: GO:1904482
name: cellular response to tetrahydrofolate
namespace: biological_process
def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tetrahydrofolate stimulus." [GO_REF:0000071, GOC:BHF, GOC:hal, GOC:TermGenie, PMID:24698160]
+is_a: GO:0071417 ! cellular response to organonitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
is_a: GO:1904481 ! response to tetrahydrofolate
@@ -493815,7 +494606,7 @@ is_a: GO:1904481 ! response to tetrahydrofolate
id: GO:1904483
name: synthetic cannabinoid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with synthetic cannabinoid." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10700562]
+def: "Binding to synthetic cannabinoid." [GO_REF:0000067, GOC:mr, GOC:TermGenie, PMID:10700562]
is_a: GO:0005488 ! binding
[Term]
@@ -493991,7 +494782,7 @@ is_a: GO:0061512 ! protein localization to cilium
id: GO:1904492
name: Ac-Asp-Glu binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with Ac-Asp-Glu." [GO_REF:0000067, GOC:BHF, GOC:hal, GOC:TermGenie, PMID:24863754]
+def: "Binding to Ac-Asp-Glu." [GO_REF:0000067, GOC:BHF, GOC:hal, GOC:TermGenie, PMID:24863754]
is_a: GO:0043168 ! anion binding
is_a: GO:1900750 ! oligopeptide binding
@@ -493999,7 +494790,7 @@ is_a: GO:1900750 ! oligopeptide binding
id: GO:1904493
name: tetrahydrofolyl-poly(glutamate) polymer binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with tetrahydrofolyl-poly(glutamate) polymer." [GO_REF:0000067, GOC:BHF, GOC:hal, GOC:TermGenie, PMID:24863754]
+def: "Binding to tetrahydrofolyl-poly(glutamate) polymer." [GO_REF:0000067, GOC:BHF, GOC:hal, GOC:TermGenie, PMID:24863754]
is_a: GO:0005488 ! binding
[Term]
@@ -494049,7 +494840,6 @@ synonym: "protein localisation to actomyosin contractile ring involved in mitoti
synonym: "protein localization to actomyosin contractile ring during mitotic cytokinesis" RELATED []
synonym: "protein localization to actomyosin contractile ring involved in cytokinesis after mitosis" EXACT [GOC:TermGenie]
synonym: "protein localization to actomyosin contractile ring involved in mitotic cytokinesis" EXACT []
-synonym: "protein localization to mitotic actomyosin contractile ring" EXACT []
is_a: GO:1903047 ! mitotic cell cycle process
is_a: GO:1990179 ! protein localization to actomyosin contractile ring
relationship: part_of GO:0000281 ! mitotic cytokinesis
@@ -494368,7 +495158,7 @@ is_a: GO:0006915 ! apoptotic process
id: GO:1904517
name: MgATP(2-) binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with MgATP(2-)." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:20086079]
+def: "Binding to MgATP(2-)." [GO_REF:0000067, GOC:bhm, GOC:TermGenie, PMID:20086079]
is_a: GO:0005488 ! binding
[Term]
@@ -495432,7 +496222,7 @@ relationship: positively_regulates GO:0042026 ! protein refolding
id: GO:1904593
name: prostaglandin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with prostaglandin." [GO_REF:0000067, GOC:TermGenie, PMID:21445266]
+def: "Binding to prostaglandin." [GO_REF:0000067, GOC:TermGenie, PMID:21445266]
is_a: GO:1901567 ! fatty acid derivative binding
[Term]
@@ -495546,7 +496336,7 @@ relationship: positively_regulates GO:0002248 ! connective tissue replacement in
id: GO:1904599
name: advanced glycation end-product binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with advanced glycation end-product." [GO_REF:0000067, GOC:krc, GOC:TermGenie, PMID:1650387]
+def: "Binding to advanced glycation end-product." [GO_REF:0000067, GOC:krc, GOC:TermGenie, PMID:1650387]
is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
@@ -495555,10 +496345,10 @@ name: actin fusion focus assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form an actin fusion focus." [GO_REF:0000079, GOC:TermGenie, PMID:25825517]
synonym: "actin fusion focus formation" EXACT [GOC:TermGenie]
-is_a: GO:0022414 ! reproductive process
-is_a: GO:0022607 ! cellular component assembly
+is_a: GO:0003006 ! developmental process involved in reproduction
+is_a: GO:0010927 ! cellular component assembly involved in morphogenesis
is_a: GO:0030036 ! actin cytoskeleton organization
-relationship: part_of GO:0000747 ! conjugation with cellular fusion
+relationship: part_of GO:0031382 ! mating projection formation
[Term]
id: GO:1904601
@@ -496570,7 +497360,7 @@ relationship: positively_regulates GO:0048103 ! somatic stem cell division
id: GO:1904678
name: alpha-aminoacyl-tRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with alpha-aminoacyl-tRNA." [GO_REF:0000067, GOC:TermGenie, ISBN:155581073X]
+def: "Binding to an alpha-aminoacyl-tRNA." [GO_REF:0000067, GOC:TermGenie, ISBN:155581073X]
synonym: "aminoacyl-tRNA binding" RELATED []
is_a: GO:0003723 ! RNA binding
@@ -496745,7 +497535,6 @@ synonym: "downregulation of cytoplasmic translational initiation" EXACT [GOC:Ter
synonym: "inhibition of cytoplasmic translational initiation" NARROW [GOC:TermGenie]
is_a: GO:0045947 ! negative regulation of translational initiation
is_a: GO:1904688 ! regulation of cytoplasmic translational initiation
-is_a: GO:2000766 ! negative regulation of cytoplasmic translation
relationship: negatively_regulates GO:0002183 ! cytoplasmic translational initiation
[Term]
@@ -496759,7 +497548,6 @@ synonym: "up-regulation of cytoplasmic translational initiation" EXACT [GOC:Term
synonym: "upregulation of cytoplasmic translational initiation" EXACT [GOC:TermGenie]
is_a: GO:0045948 ! positive regulation of translational initiation
is_a: GO:1904688 ! regulation of cytoplasmic translational initiation
-is_a: GO:2000767 ! positive regulation of cytoplasmic translation
relationship: positively_regulates GO:0002183 ! cytoplasmic translational initiation
[Term]
@@ -497197,7 +497985,7 @@ relationship: positively_regulates GO:1904701 ! Wnt-Frizzled-LRP5/6 complex asse
id: GO:1904713
name: beta-catenin destruction complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a beta-catenin destruction complex." [GOC:bf, GOC:PARL, GOC:TermGenie, PMID:22899650]
+def: "Binding to a beta-catenin destruction complex." [GOC:bf, GOC:PARL, GOC:TermGenie, PMID:22899650]
synonym: "23S APC complex binding" NARROW [GOC:TermGenie]
synonym: "APC-Axin-1-beta-catenin complex binding" EXACT [GOC:TermGenie]
synonym: "Axin-APC-beta-catenin-GSK3B complex binding" EXACT [GOC:TermGenie]
@@ -498679,7 +499467,7 @@ is_a: GO:0038202 ! TORC1 signaling
id: GO:1904767
name: octanoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with octanoic acid." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
+def: "Binding to octanoic acid." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
synonym: "caprylic acid binding" EXACT [CHEBI:28837]
is_a: GO:0005504 ! fatty acid binding
is_a: GO:0043177 ! organic acid binding
@@ -498688,14 +499476,14 @@ is_a: GO:0043177 ! organic acid binding
id: GO:1904768
name: all-trans-retinol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with all-trans-retinol." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
+def: "Binding to all-trans-retinol." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
is_a: GO:0019841 ! retinol binding
[Term]
id: GO:1904769
name: isopentadecanoic acid binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with isopentadecanoic acid." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
+def: "Binding to isopentadecanoic acid." [GO_REF:0000067, GOC:kmv, GOC:TermGenie, PMID:19828452]
synonym: "13-methylmyristic acid binding" EXACT [CHEBI:39250]
is_a: GO:0036041 ! long-chain fatty acid binding
is_a: GO:0043177 ! organic acid binding
@@ -498959,7 +499747,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to centrosome." [GO_REF:0000058, GOC:TermGenie, PMID:17115027]
comment: An example is cdk-2 in C. elegans (UniProt ID O61847) in PMID:17115027 (inferred from mutant phenotype).
synonym: "regulation of protein localisation to centrosome" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0071539 ! protein localization to centrosome
[Term]
@@ -498977,7 +499766,8 @@ synonym: "downregulation of protein localization to centrosome" EXACT [GOC:TermG
synonym: "inhibition of protein localisation to centrosome" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to centrosome" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to centrosome" EXACT [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1904779 ! regulation of protein localization to centrosome
relationship: negatively_regulates GO:0071539 ! protein localization to centrosome
@@ -498996,7 +499786,8 @@ synonym: "up-regulation of protein localisation to centrosome" EXACT [GOC:TermGe
synonym: "up-regulation of protein localization to centrosome" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localisation to centrosome" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to centrosome" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1904779 ! regulation of protein localization to centrosome
relationship: positively_regulates GO:0071539 ! protein localization to centrosome
@@ -499101,7 +499892,7 @@ synonym: "negative regulation of asymmetric protein localisation involved in cel
synonym: "negative regulation of asymmetric protein localization involved in cell fate commitment" EXACT [GOC:TermGenie]
synonym: "negative regulation of asymmetric protein localization resulting in cell fate commitment" EXACT [GOC:TermGenie]
synonym: "negative regulation of cell fate commitment, asymmetric protein localization" EXACT [GOC:TermGenie]
-is_a: GO:0048519 ! negative regulation of biological process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1904785 ! regulation of asymmetric protein localization involved in cell fate determination
relationship: negatively_regulates GO:0045167 ! asymmetric protein localization involved in cell fate determination
@@ -499135,7 +499926,7 @@ synonym: "upregulation of asymmetric protein localization involved in cell fate
synonym: "upregulation of asymmetric protein localization involved in cell fate determination" EXACT [GOC:TermGenie]
synonym: "upregulation of asymmetric protein localization resulting in cell fate commitment" EXACT [GOC:TermGenie]
synonym: "upregulation of cell fate commitment, asymmetric protein localization" EXACT [GOC:TermGenie]
-is_a: GO:0048518 ! positive regulation of biological process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1904785 ! regulation of asymmetric protein localization involved in cell fate determination
relationship: positively_regulates GO:0045167 ! asymmetric protein localization involved in cell fate determination
@@ -499500,7 +500291,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to chromosome, telomeric region." [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:19487455]
synonym: "regulation of protein localisation to chromosome, telomeric region" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization to telomere" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0070198 ! protein localization to chromosome, telomeric region
[Term]
@@ -499522,7 +500314,8 @@ synonym: "inhibition of protein localization to chromosome, telomeric region" NA
synonym: "inhibition of protein localization to telomere" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to chromosome, telomeric region" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization to telomere" EXACT [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1904814 ! regulation of protein localization to chromosome, telomeric region
relationship: negatively_regulates GO:0070198 ! protein localization to chromosome, telomeric region
@@ -499545,7 +500338,8 @@ synonym: "up-regulation of protein localization to telomere" EXACT [GOC:TermGeni
synonym: "upregulation of protein localisation to chromosome, telomeric region" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to chromosome, telomeric region" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to telomere" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1904814 ! regulation of protein localization to chromosome, telomeric region
relationship: positively_regulates GO:0070198 ! protein localization to chromosome, telomeric region
@@ -499920,8 +500714,8 @@ relationship: positively_regulates GO:0048133 ! male germ-line stem cell asymmet
id: GO:1904841
name: TORC2 complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a TORC2 complex." [GOC:TermGenie, PMID:20660630]
-comment: Interacting selectively and non-covalently with a TORC2 complex, a protein complex that mediates the phosphorylation of protein kinase B
+def: "Binding to a TORC2 complex." [GOC:TermGenie, PMID:20660630]
+comment: Binding to a TORC2 complex, a protein complex that mediates the phosphorylation of protein kinase B
synonym: "mTORC2 binding" NARROW [GOC:TermGenie]
synonym: "rapamycin and nutrient-insensitive TOR complex binding" EXACT [GOC:TermGenie]
synonym: "TOR complex 2 binding" EXACT [GOC:TermGenie]
@@ -499939,7 +500733,6 @@ synonym: "response to nitroglycerol" EXACT []
synonym: "response to trinitroglycerin" EXACT []
synonym: "response to trinitroglycerol" EXACT []
is_a: GO:0010033 ! response to organic substance
-is_a: GO:0042493 ! response to drug
is_a: GO:1901698 ! response to nitrogen compound
is_a: GO:1901700 ! response to oxygen-containing compound
@@ -499952,7 +500745,6 @@ synonym: "cellular response to nitroglycerine" EXACT []
synonym: "cellular response to nitroglycerol" EXACT []
synonym: "cellular response to trinitroglycerin" EXACT []
synonym: "cellular response to trinitroglycerol" EXACT []
-is_a: GO:0035690 ! cellular response to drug
is_a: GO:1901699 ! cellular response to nitrogen compound
is_a: GO:1901701 ! cellular response to oxygen-containing compound
is_a: GO:1904842 ! response to nitroglycerin
@@ -500094,7 +500886,7 @@ is_a: GO:0099614 ! protein localization to spore cell wall
id: GO:1904854
name: proteasome core complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a proteasome core complex." [GOC:TermGenie, PMID:16096059]
+def: "Binding to a proteasome core complex." [GOC:TermGenie, PMID:16096059]
synonym: "20S core complex binding" NARROW [GOC:TermGenie]
synonym: "20S proteasome binding" NARROW [GOC:TermGenie]
synonym: "macropain binding" EXACT [GOC:TermGenie]
@@ -500105,7 +500897,7 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:1904855
name: proteasome regulatory particle binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a proteasome regulatory particle." [GOC:TermGenie, PMID:16096059]
+def: "Binding to a proteasome regulatory particle." [GOC:TermGenie, PMID:16096059]
synonym: "19S regulatory particle binding" NARROW [GOC:TermGenie]
synonym: "modulator complex binding" RELATED [GOC:TermGenie]
synonym: "PA700 proteasome activator binding" NARROW [GOC:TermGenie]
@@ -501163,8 +501955,11 @@ namespace: biological_process
def: "The directed movement of L-arginine across a membrane from lysosomal lumen to cytosol." [GO_REF:0000078, GOC:kmv, GOC:TermGenie, PMID:22822152]
synonym: "transmembrane L-arginine transport from lysosomal lumen to cytosol" EXACT []
is_a: GO:0007041 ! lysosomal transport
+is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0034486 ! vacuolar transmembrane transport
-is_a: GO:1903400 ! L-arginine transmembrane transport
+is_a: GO:0098655 ! cation transmembrane transport
+is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
id: GO:1904918
@@ -501441,7 +502236,7 @@ relationship: part_of GO:0044753 ! amphisome
id: GO:1904931
name: MCM complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an MCM complex." [GOC:TermGenie, PMID:12604790]
+def: "Binding to an MCM complex." [GOC:TermGenie, PMID:12604790]
synonym: "mini-chromosome maintenance complex binding" EXACT [GOC:TermGenie]
is_a: GO:0044877 ! protein-containing complex binding
@@ -501545,7 +502340,6 @@ synonym: "PCP pathway involved in axon guidance" EXACT [GOC:TermGenie]
synonym: "PCP pathway involved in axon pathfinding" EXACT [GOC:TermGenie]
synonym: "planar cell polarity pathway involved in axon chemotaxis" RELATED [GOC:TermGenie]
synonym: "planar cell polarity pathway involved in axon growth cone guidance" NARROW [GOC:TermGenie]
-synonym: "planar cell polarity pathway involved in axon guidance" EXACT [GOC:TermGenie]
synonym: "planar cell polarity pathway involved in axon pathfinding" EXACT [GOC:TermGenie]
synonym: "Wnt receptor signaling pathway, planar cell polarity pathway involved in axon chemotaxis" RELATED [GOC:TermGenie]
synonym: "Wnt receptor signaling pathway, planar cell polarity pathway involved in axon growth cone guidance" NARROW [GOC:TermGenie]
@@ -501796,7 +502590,6 @@ synonym: "DA neurogenesis from midbrain floor plate" EXACT [PMID:19122665]
synonym: "mDA neuron differentiation" EXACT [PMID:24287202]
synonym: "midbrain DA neurogenesis" EXACT [PMID:19122665]
synonym: "midbrain dopaminergic neuron production" EXACT [PMID:19122665]
-is_a: GO:0021953 ! central nervous system neuron differentiation
is_a: GO:0071542 ! dopaminergic neuron differentiation
relationship: part_of GO:0030901 ! midbrain development
@@ -501807,7 +502600,7 @@ namespace: cellular_component
def: "A protein complex which is capable of ATPase activity." [GO_REF:0000088, GOC:bhm, GOC:TermGenie, PMID:9606181]
comment: An example of this is VPS4 in Saccharomyces cerevisiae (UniProt ID P52917) in PMID:9606181 (inferred from direct assay).
synonym: "VPS4 complex" NARROW []
-is_a: GO:0032991 ! protein-containing complex
+is_a: GO:1902494 ! catalytic complex
[Term]
id: GO:1904950
@@ -501833,8 +502626,8 @@ synonym: "inhibition of protein recruitment" NARROW [GOC:TermGenie]
synonym: "negative regulation of establishment of protein localisation" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein positioning" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein recruitment" EXACT [GOC:TermGenie]
-is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0070201 ! regulation of establishment of protein localization
+is_a: GO:1903828 ! negative regulation of protein localization
relationship: negatively_regulates GO:0045184 ! establishment of protein localization
[Term]
@@ -501861,8 +502654,8 @@ synonym: "upregulation of establishment of protein localisation" EXACT [GOC:Term
synonym: "upregulation of establishment of protein localization" EXACT [GOC:TermGenie]
synonym: "upregulation of protein positioning" EXACT [GOC:TermGenie]
synonym: "upregulation of protein recruitment" EXACT [GOC:TermGenie]
-is_a: GO:0048518 ! positive regulation of biological process
is_a: GO:0070201 ! regulation of establishment of protein localization
+is_a: GO:1903829 ! positive regulation of protein localization
relationship: positively_regulates GO:0045184 ! establishment of protein localization
[Term]
@@ -501992,7 +502785,6 @@ synonym: "PCP pathway involved in midbrain dopaminergic neuron production" EXACT
synonym: "planar cell polarity pathway involved in DA neurogenesis from midbrain floor plate" EXACT [GOC:TermGenie]
synonym: "planar cell polarity pathway involved in mDA neuron differentiation" EXACT [GOC:TermGenie]
synonym: "planar cell polarity pathway involved in midbrain DA neurogenesis" EXACT [GOC:TermGenie]
-synonym: "planar cell polarity pathway involved in midbrain dopaminergic neuron differentiation" EXACT [GOC:TermGenie]
synonym: "planar cell polarity pathway involved in midbrain dopaminergic neuron production" EXACT [GOC:TermGenie]
synonym: "Wnt receptor signaling pathway, planar cell polarity pathway involved in DA neurogenesis from midbrain floor plate" EXACT [GOC:TermGenie]
synonym: "Wnt receptor signaling pathway, planar cell polarity pathway involved in mDA neuron differentiation" EXACT [GOC:TermGenie]
@@ -504232,7 +505024,6 @@ synonym: "inhibition of occluding cell junction disassembly" NARROW [GOC:TermGen
synonym: "inhibition of occluding junction disassembly" NARROW [GOC:TermGenie]
synonym: "inhibition of tight junction disassembly" NARROW [GOC:TermGenie]
synonym: "negative regulation of occluding cell junction disassembly" EXACT [GOC:TermGenie]
-synonym: "negative regulation of tight junction disassembly" EXACT [GOC:TermGenie]
is_a: GO:0051129 ! negative regulation of cellular component organization
is_a: GO:1905073 ! regulation of tight junction disassembly
relationship: negatively_regulates GO:1905071 ! tight junction disassembly
@@ -504598,7 +505389,6 @@ synonym: "upregulation of GNRP" NARROW [GOC:TermGenie]
synonym: "upregulation of guanyl-nucleotide exchange factor activity" EXACT [GOC:TermGenie]
synonym: "upregulation of guanyl-nucleotide release factor activity" EXACT [GOC:TermGenie]
synonym: "upregulation of guanyl-nucleotide releasing factor" EXACT [GOC:TermGenie]
-is_a: GO:0043547 ! positive regulation of GTPase activity
is_a: GO:1904426 ! positive regulation of GTP binding
is_a: GO:1905097 ! regulation of guanyl-nucleotide exchange factor activity
@@ -504694,7 +505484,7 @@ is_obsolete: true
id: GO:1905108
name: guanosine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with guanosine." [GO_REF:0000067, GOC:TermGenie, PMID:26007660]
+def: "Binding to guanosine." [GO_REF:0000067, GOC:TermGenie, PMID:26007660]
is_a: GO:0032550 ! purine ribonucleoside binding
[Term]
@@ -505877,7 +506667,8 @@ synonym: "regulation of protein localisation to phagocytic vesicle" EXACT [GOC:T
synonym: "regulation of protein localisation to phagosome" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in phagocytic vesicle" EXACT [GOC:TermGenie]
synonym: "regulation of protein recruitment to phagosome" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1905161 ! protein localization to phagocytic vesicle
[Term]
@@ -505914,7 +506705,8 @@ synonym: "negative regulation of protein localisation to phagocytic vesicle" EXA
synonym: "negative regulation of protein localisation to phagosome" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in phagocytic vesicle" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein recruitment to phagosome" EXACT [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905169 ! regulation of protein localization to phagocytic vesicle
relationship: negatively_regulates GO:1905161 ! protein localization to phagocytic vesicle
@@ -505952,7 +506744,8 @@ synonym: "upregulation of protein localisation to phagosome" EXACT [GOC:TermGeni
synonym: "upregulation of protein localization in phagocytic vesicle" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to phagocytic vesicle" EXACT [GOC:TermGenie]
synonym: "upregulation of protein recruitment to phagosome" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905169 ! regulation of protein localization to phagocytic vesicle
relationship: positively_regulates GO:1905161 ! protein localization to phagocytic vesicle
@@ -505960,7 +506753,7 @@ relationship: positively_regulates GO:1905161 ! protein localization to phagocyt
id: GO:1905172
name: RISC complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a RISC complex." [GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24882364]
+def: "Binding to a RISC complex." [GOC:bf, GOC:PARL, GOC:TermGenie, PMID:24882364]
synonym: "RNA-induced silencing complex binding" EXACT [GOC:TermGenie]
is_a: GO:0043021 ! ribonucleoprotein complex binding
@@ -506998,7 +507791,6 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to nitrosative stress." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:14752510]
synonym: "regulation of intrinsic apoptotic signaling pathway in response to nitrosative stress" EXACT [GOC:bf]
synonym: "regulation of nitrosative stress-induced apoptosis" RELATED [GOC:TermGenie]
-synonym: "regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway" EXACT [GOC:TermGenie]
is_a: GO:0080135 ! regulation of cellular response to stress
is_a: GO:2001242 ! regulation of intrinsic apoptotic signaling pathway
relationship: regulates GO:1990442 ! intrinsic apoptotic signaling pathway in response to nitrosative stress
@@ -507022,7 +507814,6 @@ synonym: "inhibition of nitrosative stress-induced apoptosis" RELATED [GOC:TermG
synonym: "inhibition of nitrosative stress-induced intrinsic apoptotic signaling pathway" NARROW [GOC:TermGenie]
synonym: "negative regulation of intrinsic apoptotic signaling pathway in response to nitrosative stress" EXACT [GOC:bf]
synonym: "negative regulation of nitrosative stress-induced apoptosis" RELATED [GOC:TermGenie]
-synonym: "negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway" EXACT [GOC:TermGenie]
is_a: GO:1905258 ! regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway
is_a: GO:2001243 ! negative regulation of intrinsic apoptotic signaling pathway
relationship: negatively_regulates GO:1990442 ! intrinsic apoptotic signaling pathway in response to nitrosative stress
@@ -507037,7 +507828,6 @@ synonym: "activation of nitrosative stress-induced apoptosis" RELATED [GOC:TermG
synonym: "activation of nitrosative stress-induced intrinsic apoptotic signaling pathway" NARROW [GOC:TermGenie]
synonym: "positive regulation of intrinsic apoptotic signaling pathway in response to nitrosative stress" EXACT [GOC:bf]
synonym: "positive regulation of nitrosative stress-induced apoptosis" RELATED [GOC:TermGenie]
-synonym: "positive regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway" EXACT [GOC:TermGenie]
synonym: "up regulation of intrinsic apoptotic signaling pathway in response to nitrosative stress" EXACT [GOC:TermGenie]
synonym: "up regulation of nitrosative stress-induced apoptosis" RELATED [GOC:TermGenie]
synonym: "up regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway" EXACT [GOC:TermGenie]
@@ -507056,7 +507846,9 @@ id: GO:1905261
name: regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination." [GO_REF:0000058, GOC:TermGenie, PMID:26653857]
+is_a: GO:0022414 ! reproductive process
is_a: GO:1903341 ! regulation of meiotic DNA double-strand break formation
+relationship: part_of GO:0007131 ! reciprocal meiotic recombination
relationship: regulates GO:0010780 ! meiotic DNA double-strand break formation involved in reciprocal meiotic recombination
[Term]
@@ -508099,6 +508891,7 @@ synonym: "phytosphingosine transport" NARROW []
synonym: "sphingoid base(1+) transport" EXACT []
synonym: "sphingoid transport" RELATED []
synonym: "sphingosine transport" NARROW []
+is_a: GO:0006869 ! lipid transport
is_a: GO:0015695 ! organic cation transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -508162,7 +508955,7 @@ relationship: regulates GO:0035482 ! gastric motility
id: GO:1905334
name: Swi5-Sfr1 complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Swi5-Sfr1 complex." [GOC:TermGenie, PMID:16921379]
+def: "Binding to a Swi5-Sfr1 complex." [GOC:TermGenie, PMID:16921379]
synonym: "Sae3-Mei5 complex binding" EXACT [GOC:TermGenie]
is_a: GO:0044877 ! protein-containing complex binding
@@ -508236,7 +509029,8 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
comment: Q9H211 in Human in PMID:22581055
synonym: "regulation of condensin localization to kinetochore" NARROW [GOC:TermGenie]
synonym: "regulation of protein localisation to kinetochore" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0034501 ! protein localization to kinetochore
[Term]
@@ -508259,7 +509053,8 @@ synonym: "inhibition of protein localisation to kinetochore" NARROW [GOC:TermGen
synonym: "inhibition of protein localization to kinetochore" NARROW [GOC:TermGenie]
synonym: "negative regulation of condensin localization to kinetochore" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation to kinetochore" EXACT [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905340 ! regulation of protein localization to kinetochore
relationship: negatively_regulates GO:0034501 ! protein localization to kinetochore
@@ -508283,7 +509078,8 @@ synonym: "up-regulation of protein localization to kinetochore" EXACT [GOC:TermG
synonym: "upregulation of condensin localization to kinetochore" NARROW [GOC:TermGenie]
synonym: "upregulation of protein localisation to kinetochore" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to kinetochore" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905340 ! regulation of protein localization to kinetochore
relationship: positively_regulates GO:0034501 ! protein localization to kinetochore
@@ -508891,7 +509687,7 @@ synonym: "negative regulation of protein localisation in presynapse" EXACT [GOC:
synonym: "negative regulation of protein localisation to presynapse" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in presynapse" EXACT [GOC:TermGenie]
synonym: "negative regulation of recruitment of presynaptic proteins" EXACT [GOC:TermGenie]
-is_a: GO:0048519 ! negative regulation of biological process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905384 ! regulation of protein localization to presynapse
relationship: negatively_regulates GO:1905383 ! protein localization to presynapse
@@ -508993,7 +509789,7 @@ is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis
id: GO:1905394
name: retromer complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a retromer complex." [GOC:bc, GOC:PARL, GOC:TermGenie, PMID:27385586]
+def: "Binding to a retromer complex." [GOC:bc, GOC:PARL, GOC:TermGenie, PMID:27385586]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
@@ -509343,7 +510139,7 @@ name: regulation of dense core granule exocytosis
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of dense core granule exocytosis." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:18468511]
synonym: "regulation of dense core vesicle exocytosis" EXACT [GOC:TermGenie]
-is_a: GO:0008150 ! biological_process
+is_a: GO:0017158 ! regulation of calcium ion-dependent exocytosis
relationship: regulates GO:1990504 ! dense core granule exocytosis
[Term]
@@ -509361,6 +510157,7 @@ synonym: "inhibition of dense core granule exocytosis" NARROW [GOC:TermGenie]
synonym: "inhibition of dense core vesicle exocytosis" NARROW [GOC:TermGenie]
synonym: "negative regulation of dense core vesicle exocytosis" EXACT [GOC:TermGenie]
is_a: GO:0045955 ! negative regulation of calcium ion-dependent exocytosis
+is_a: GO:1905413 ! regulation of dense core granule exocytosis
relationship: negatively_regulates GO:1990504 ! dense core granule exocytosis
[Term]
@@ -509378,6 +510175,7 @@ synonym: "up-regulation of dense core vesicle exocytosis" EXACT [GOC:TermGenie]
synonym: "upregulation of dense core granule exocytosis" EXACT [GOC:TermGenie]
synonym: "upregulation of dense core vesicle exocytosis" EXACT [GOC:TermGenie]
is_a: GO:0045956 ! positive regulation of calcium ion-dependent exocytosis
+is_a: GO:1905413 ! regulation of dense core granule exocytosis
relationship: positively_regulates GO:1990504 ! dense core granule exocytosis
[Term]
@@ -509456,7 +510254,6 @@ name: vascular associated smooth muscle cell differentiation involved in phenoty
namespace: biological_process
def: "Any vascular smooth muscle cell differentiation that is involved in phenotypic switching." [GO_REF:0000060, GOC:BHF, GOC:BHF_miRNA, GOC:rph, GOC:TermGenie, PMID:25089138]
synonym: "vascular associated smooth muscle cell differentiation involved in phenotypic dimorphism" RELATED [GOC:TermGenie]
-synonym: "vascular associated smooth muscle cell differentiation involved in phenotypic switching" EXACT [GOC:TermGenie]
synonym: "vascular smooth muscle cell differentiation involved in phenotypic dimorphism" RELATED [GOC:TermGenie]
synonym: "vascular smooth muscle cell differentiation involved in phenotypic switching" EXACT []
synonym: "VSMC differentiation involved in phenotypic dimorphism" RELATED [GOC:TermGenie]
@@ -510902,7 +511699,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to membrane." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:26911690]
synonym: "regulation of protein localisation in membrane" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in membrane" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0072657 ! protein localization to membrane
[Term]
@@ -510924,7 +511722,8 @@ synonym: "inhibition of protein localization in membrane" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to membrane" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation in membrane" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in membrane" EXACT [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905475 ! regulation of protein localization to membrane
relationship: negatively_regulates GO:0072657 ! protein localization to membrane
@@ -510947,7 +511746,8 @@ synonym: "up-regulation of protein localization to membrane" EXACT [GOC:TermGeni
synonym: "upregulation of protein localisation in membrane" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in membrane" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to membrane" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905475 ! regulation of protein localization to membrane
relationship: positively_regulates GO:0072657 ! protein localization to membrane
@@ -511341,7 +512141,7 @@ is_obsolete: true
id: GO:1905502
name: acetyl-CoA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with acetyl-CoA, an acyl-CoA having acetyl as its S-acetyl component." [GO_REF:0000067, GOC:bc, GOC:krc, GOC:PARL, GOC:TermGenie, PMID:24927529]
+def: "Binding to acetyl-CoA, an acyl-CoA having acetyl as its S-acetyl component." [GO_REF:0000067, GOC:bc, GOC:krc, GOC:PARL, GOC:TermGenie, PMID:24927529]
synonym: "acetyl-coenzyme A binding" EXACT []
is_a: GO:0043168 ! anion binding
is_a: GO:0120227 ! acyl-CoA binding
@@ -511589,7 +512389,6 @@ synonym: "up-regulation of fertilization" EXACT [GOC:TermGenie]
synonym: "up-regulation of syngamy" EXACT [GOC:TermGenie]
synonym: "upregulation of fertilization" EXACT [GOC:TermGenie]
synonym: "upregulation of syngamy" EXACT [GOC:TermGenie]
-is_a: GO:0043902 ! positive regulation of multi-organism process
is_a: GO:0080154 ! regulation of fertilization
is_a: GO:2000243 ! positive regulation of reproductive process
relationship: positively_regulates GO:0009566 ! fertilization
@@ -511984,7 +512783,7 @@ relationship: positively_regulates GO:0097010 ! eukaryotic translation initiatio
id: GO:1905538
name: polysome binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a polysome." [GOC:bc, GOC:PARL, GOC:TermGenie, PMID:18426977]
+def: "Binding to a polysome." [GOC:bc, GOC:PARL, GOC:TermGenie, PMID:18426977]
synonym: "polyribosome binding" EXACT [GOC:TermGenie]
is_a: GO:0043021 ! ribonucleoprotein complex binding
@@ -512014,11 +512813,12 @@ is_a: GO:0043235 ! receptor complex
id: GO:1905541
name: regulation of L-arginine import across plasma membrane
namespace: biological_process
+alt_id: GO:0010963
alt_id: GO:1902826
def: "Any process that modulates the frequency, rate or extent of L-arginine import across plasma membrane." [GO_REF:0000058, GOC:TermGenie, PMID:14718525]
+synonym: "regulation of L-arginine import" BROAD []
synonym: "regulation of L-arginine import into cell" EXACT []
is_a: GO:0010958 ! regulation of amino acid import across plasma membrane
-is_a: GO:0010963 ! regulation of L-arginine import
is_a: GO:1903959 ! regulation of anion transmembrane transport
is_a: GO:1904062 ! regulation of cation transmembrane transport
relationship: regulates GO:0097638 ! L-arginine import across plasma membrane
@@ -512289,19 +513089,20 @@ is_a: GO:0080184 ! response to phenylpropanoid
[Term]
id: GO:1905547
-name: regulation of subtelomeric heterochromatin assembly
+name: obsolete regulation of subtelomeric heterochromatin assembly
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of subtelomeric heterochromatin assembly." [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:25819580]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of subtelomeric heterochromatin assembly." [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:25819580]
+comment: This term was obsoleted because there is no evidence that chromatin silencing /heterochromatin assembly are directly regulated.
synonym: "regulation of telomeric heterochromatin assembly" RELATED []
synonym: "regulation of telomeric heterochromatin formation" RELATED [GOC:TermGenie]
-is_a: GO:0031445 ! regulation of heterochromatin assembly
-relationship: regulates GO:0031509 ! subtelomeric heterochromatin assembly
+is_obsolete: true
[Term]
id: GO:1905548
-name: negative regulation of subtelomeric heterochromatin assembly
+name: obsolete negative regulation of subtelomeric heterochromatin assembly
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of subtelomeric heterochromatin assembly." [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:25819580]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of subtelomeric heterochromatin assembly." [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:25819580]
+comment: This term was obsoleted because there is no evidence that chromatin silencing /heterochromatin assembly are directly regulated.
synonym: "down regulation of telomeric heterochromatin assembly" RELATED [GOC:TermGenie]
synonym: "down regulation of telomeric heterochromatin formation" RELATED [GOC:TermGenie]
synonym: "down-regulation of telomeric heterochromatin assembly" RELATED [GOC:TermGenie]
@@ -512312,15 +513113,14 @@ synonym: "inhibition of telomeric heterochromatin assembly" NARROW [GOC:TermGeni
synonym: "inhibition of telomeric heterochromatin formation" NARROW [GOC:TermGenie]
synonym: "negative regulation of telomeric heterochromatin assembly" RELATED []
synonym: "negative regulation of telomeric heterochromatin formation" RELATED [GOC:TermGenie]
-is_a: GO:0031452 ! negative regulation of heterochromatin assembly
-is_a: GO:1905547 ! regulation of subtelomeric heterochromatin assembly
-relationship: negatively_regulates GO:0031509 ! subtelomeric heterochromatin assembly
+is_obsolete: true
[Term]
id: GO:1905549
-name: positive regulation of subtelomeric heterochromatin assembly
+name: obsolete positive regulation of subtelomeric heterochromatin assembly
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of subtelomeric heterochromatin assembly." [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:25819580]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of subtelomeric heterochromatin assembly." [GO_REF:0000058, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:25819580]
+comment: This term was obsoleted because there is no evidence that chromatin silencing /heterochromatin assembly are directly regulated.
synonym: "activation of telomeric heterochromatin assembly" NARROW [GOC:TermGenie]
synonym: "activation of telomeric heterochromatin formation" NARROW [GOC:TermGenie]
synonym: "positive regulation of telomeric heterochromatin assembly" RELATED []
@@ -512331,9 +513131,7 @@ synonym: "up-regulation of telomeric heterochromatin assembly" RELATED [GOC:Term
synonym: "up-regulation of telomeric heterochromatin formation" RELATED [GOC:TermGenie]
synonym: "upregulation of telomeric heterochromatin assembly" RELATED [GOC:TermGenie]
synonym: "upregulation of telomeric heterochromatin formation" RELATED [GOC:TermGenie]
-is_a: GO:0031453 ! positive regulation of heterochromatin assembly
-is_a: GO:1905547 ! regulation of subtelomeric heterochromatin assembly
-relationship: positively_regulates GO:0031509 ! subtelomeric heterochromatin assembly
+is_obsolete: true
[Term]
id: GO:1905550
@@ -512343,7 +513141,8 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
synonym: "regulation of protein localisation in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in ER" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0070972 ! protein localization to endoplasmic reticulum
[Term]
@@ -512370,7 +513169,8 @@ synonym: "inhibition of protein localization to endoplasmic reticulum" NARROW [G
synonym: "negative regulation of protein localisation in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in ER" EXACT [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905550 ! regulation of protein localization to endoplasmic reticulum
relationship: negatively_regulates GO:0070972 ! protein localization to endoplasmic reticulum
@@ -512398,7 +513198,8 @@ synonym: "upregulation of protein localisation in endoplasmic reticulum" EXACT [
synonym: "upregulation of protein localization in endoplasmic reticulum" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in ER" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to endoplasmic reticulum" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905550 ! regulation of protein localization to endoplasmic reticulum
relationship: positively_regulates GO:0070972 ! protein localization to endoplasmic reticulum
@@ -512819,7 +513620,7 @@ is_a: GO:0051668 ! localization within membrane
id: GO:1905573
name: ganglioside GM1 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ganglioside GM1." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
+def: "Binding to ganglioside GM1." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0035594 ! ganglioside binding
@@ -512827,7 +513628,7 @@ is_a: GO:0035594 ! ganglioside binding
id: GO:1905574
name: ganglioside GM2 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ganglioside GM2." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
+def: "Binding to ganglioside GM2." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0035594 ! ganglioside binding
@@ -512835,7 +513636,7 @@ is_a: GO:0035594 ! ganglioside binding
id: GO:1905575
name: ganglioside GM3 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ganglioside GM3." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
+def: "Binding to ganglioside GM3." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
is_a: GO:0033293 ! monocarboxylic acid binding
is_a: GO:0035594 ! ganglioside binding
@@ -512843,7 +513644,7 @@ is_a: GO:0035594 ! ganglioside binding
id: GO:1905576
name: ganglioside GT1b binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ganglioside GT1b." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
+def: "Binding to ganglioside GT1b." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0035594 ! ganglioside binding
@@ -512851,7 +513652,7 @@ is_a: GO:0035594 ! ganglioside binding
id: GO:1905577
name: ganglioside GP1c binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with ganglioside GP1c." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
+def: "Binding to ganglioside GP1c." [GO_REF:0000067, GOC:TermGenie, PMID:1454804]
is_a: GO:0031406 ! carboxylic acid binding
is_a: GO:0035594 ! ganglioside binding
@@ -512964,7 +513765,6 @@ synonym: "cochlear outer hair cell apoptosis" NARROW [GOC:TermGenie]
synonym: "cochlear outer hair cell apoptotic process" EXACT [GOC:TermGenie]
synonym: "outer hair cell apoptosis" NARROW [GOC:TermGenie]
is_a: GO:0051402 ! neuron apoptotic process
-is_a: GO:1904019 ! epithelial cell apoptotic process
[Term]
id: GO:1905585
@@ -512975,7 +513775,6 @@ synonym: "regulation of cochlear outer hair cell apoptosis" NARROW [GOC:TermGeni
synonym: "regulation of cochlear outer hair cell apoptotic process" EXACT [GOC:TermGenie]
synonym: "regulation of outer hair cell apoptosis" NARROW [GOC:TermGenie]
is_a: GO:0043523 ! regulation of neuron apoptotic process
-is_a: GO:1904035 ! regulation of epithelial cell apoptotic process
relationship: regulates GO:1905584 ! outer hair cell apoptotic process
[Term]
@@ -513003,7 +513802,6 @@ synonym: "negative regulation of cochlear outer hair cell apoptosis" NARROW [GOC
synonym: "negative regulation of cochlear outer hair cell apoptotic process" EXACT [GOC:TermGenie]
synonym: "negative regulation of outer hair cell apoptosis" NARROW [GOC:TermGenie]
is_a: GO:0043524 ! negative regulation of neuron apoptotic process
-is_a: GO:1904036 ! negative regulation of epithelial cell apoptotic process
is_a: GO:1905585 ! regulation of outer hair cell apoptotic process
relationship: negatively_regulates GO:1905584 ! outer hair cell apoptotic process
@@ -513032,7 +513830,6 @@ synonym: "upregulation of cochlear outer hair cell apoptotic process" EXACT [GOC
synonym: "upregulation of outer hair cell apoptosis" NARROW [GOC:TermGenie]
synonym: "upregulation of outer hair cell apoptotic process" EXACT [GOC:TermGenie]
is_a: GO:0043525 ! positive regulation of neuron apoptotic process
-is_a: GO:1904037 ! positive regulation of epithelial cell apoptotic process
is_a: GO:1905585 ! regulation of outer hair cell apoptotic process
relationship: positively_regulates GO:1905584 ! outer hair cell apoptotic process
@@ -513118,7 +513915,7 @@ relationship: positively_regulates GO:0101027 ! optical nerve axon regeneration
id: GO:1905594
name: resveratrol binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with resveratrol." [GO_REF:0000067, GOC:TermGenie, PMID:18254726]
+def: "Binding to resveratrol." [GO_REF:0000067, GOC:TermGenie, PMID:18254726]
comment: (5-(aziridin-1-yl)-2,4-dinitrobenzamide
is_a: GO:0097159 ! organic cyclic compound binding
@@ -513483,25 +514280,26 @@ relationship: positively_regulates GO:0080186 ! developmental vegetative growth
[Term]
id: GO:1905616
-name: regulation of miRNA mediated inhibition of translation
+name: regulation of miRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of miRNA mediated inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+def: "Any process that modulates the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
synonym: "regulation of down regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "regulation of down-regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "regulation of downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "regulation of gene silencing by miRNA, negative regulation of translation" EXACT [GOC:TermGenie]
synonym: "regulation of inhibition of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
+synonym: "regulation of miRNA mediated inhibition of translation" EXACT []
synonym: "regulation of miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:TermGenie]
synonym: "regulation of negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
is_a: GO:0006417 ! regulation of translation
is_a: GO:0060964 ! regulation of gene silencing by miRNA
-relationship: regulates GO:0035278 ! miRNA mediated inhibition of translation
+relationship: regulates GO:0035278 ! miRNA-mediated gene silencing by inhibition of translation
[Term]
id: GO:1905617
-name: negative regulation of miRNA mediated inhibition of translation
+name: negative regulation of miRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of miRNA mediated inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
synonym: "down regulation of down regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "down regulation of down-regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "down regulation of downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
@@ -513539,18 +514337,19 @@ synonym: "negative regulation of down-regulation of translation involved in gene
synonym: "negative regulation of downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "negative regulation of gene silencing by miRNA, negative regulation of translation" EXACT [GOC:TermGenie]
synonym: "negative regulation of inhibition of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
+synonym: "negative regulation of miRNA mediated inhibition of translation" EXACT []
synonym: "negative regulation of miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:TermGenie]
synonym: "negative regulation of negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
is_a: GO:0045727 ! positive regulation of translation
is_a: GO:0060965 ! negative regulation of gene silencing by miRNA
-is_a: GO:1905616 ! regulation of miRNA mediated inhibition of translation
-relationship: negatively_regulates GO:0035278 ! miRNA mediated inhibition of translation
+is_a: GO:1905616 ! regulation of miRNA-mediated gene silencing by inhibition of translation
+relationship: negatively_regulates GO:0035278 ! miRNA-mediated gene silencing by inhibition of translation
[Term]
id: GO:1905618
-name: positive regulation of miRNA mediated inhibition of translation
+name: positive regulation of miRNA-mediated gene silencing by inhibition of translation
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of miRNA mediated inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
+def: "Any process that activates or increases the frequency, rate or extent of miRNA-mediated gene silencing by inhibition of translation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:23409027]
synonym: "activation of down regulation of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
synonym: "activation of down-regulation of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
synonym: "activation of downregulation of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
@@ -513564,6 +514363,7 @@ synonym: "positive regulation of down-regulation of translation involved in gene
synonym: "positive regulation of downregulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
synonym: "positive regulation of gene silencing by miRNA, negative regulation of translation" EXACT [GOC:TermGenie]
synonym: "positive regulation of inhibition of translation involved in gene silencing by miRNA" NARROW [GOC:TermGenie]
+synonym: "positive regulation of miRNA mediated inhibition of translation" EXACT []
synonym: "positive regulation of miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:TermGenie]
synonym: "positive regulation of negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
synonym: "up regulation of down regulation of translation involved in gene silencing by miRNA" EXACT [GOC:TermGenie]
@@ -513590,9 +514390,9 @@ synonym: "upregulation of inhibition of translation involved in gene silencing b
synonym: "upregulation of miRNA mediated inhibition of translation" EXACT [GOC:TermGenie]
synonym: "upregulation of miRNA-mediated gene silencing, negative regulation of translation" RELATED [GOC:TermGenie]
synonym: "upregulation of negative regulation of translation involved in gene silencing by microRNA" EXACT [GOC:TermGenie]
-is_a: GO:1905616 ! regulation of miRNA mediated inhibition of translation
+is_a: GO:1905616 ! regulation of miRNA-mediated gene silencing by inhibition of translation
is_a: GO:2000637 ! positive regulation of gene silencing by miRNA
-relationship: positively_regulates GO:0035278 ! miRNA mediated inhibition of translation
+relationship: positively_regulates GO:0035278 ! miRNA-mediated gene silencing by inhibition of translation
[Term]
id: GO:1905619
@@ -513842,7 +514642,8 @@ name: regulation of protein localization to chromatin
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to chromatin." [GO_REF:0000058, GOC:TermGenie, PMID:20889714]
synonym: "regulation of protein localisation to chromatin" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0071168 ! protein localization to chromatin
[Term]
@@ -514233,7 +515034,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to endosome." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:22732145]
synonym: "regulation of protein localisation in endosome" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in endosome" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0036010 ! protein localization to endosome
[Term]
@@ -514255,7 +515057,8 @@ synonym: "inhibition of protein localization in endosome" NARROW [GOC:TermGenie]
synonym: "inhibition of protein localization to endosome" NARROW [GOC:TermGenie]
synonym: "negative regulation of protein localisation in endosome" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in endosome" EXACT [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905666 ! regulation of protein localization to endosome
relationship: negatively_regulates GO:0036010 ! protein localization to endosome
@@ -514278,7 +515081,8 @@ synonym: "up-regulation of protein localization to endosome" EXACT [GOC:TermGeni
synonym: "upregulation of protein localisation in endosome" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in endosome" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to endosome" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905666 ! regulation of protein localization to endosome
relationship: positively_regulates GO:0036010 ! protein localization to endosome
@@ -514826,7 +515630,7 @@ is_a: GO:1905696 ! regulation of polysome binding
id: GO:1905699
name: regulation of xenobiotic detoxification by transmembrane export across the plasma membrane
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of drug transmembrane export." [GO_REF:0000058, GOC:TermGenie, PMID:15198509]
+def: "Any process that modulates the frequency, rate or extent of xenobiotic transmembrane export. A xenobiotic is a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:15198509]
synonym: "regulation of drug transmembrane export" NARROW []
synonym: "regulation of xenobiotic transmembrane export" NARROW []
is_a: GO:0034762 ! regulation of transmembrane transport
@@ -514837,7 +515641,7 @@ relationship: regulates GO:1990961 ! xenobiotic detoxification by transmembrane
id: GO:1905700
name: negative regulation of xenobiotic detoxification by transmembrane export across the plasma membrane
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of drug transmembrane export." [GO_REF:0000058, GOC:TermGenie, PMID:15198509]
+def: "Any process that stops, prevents or reduces the frequency, rate or extent of xenobiotic transmembrane export. A xenobiotic is a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:15198509]
synonym: "down regulation of drug transmembrane export" NARROW [GOC:TermGenie]
synonym: "down-regulation of drug transmembrane export" NARROW [GOC:TermGenie]
synonym: "downregulation of drug transmembrane export" NARROW [GOC:TermGenie]
@@ -514853,7 +515657,7 @@ relationship: negatively_regulates GO:1990961 ! xenobiotic detoxification by tra
id: GO:1905701
name: positive regulation of xenobiotic detoxification by transmembrane export across the plasma membrane
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of drug transmembrane export." [GO_REF:0000058, GOC:TermGenie, PMID:15198509]
+def: "Any process that activates or increases the frequency, rate or extent of xenobiotic transmembrane export. A xenobiotic is a compound foreign to the organim exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical." [GO_REF:0000058, GOC:krc, GOC:TermGenie, PMID:15198509]
synonym: "activation of drug transmembrane export" NARROW [GOC:TermGenie]
synonym: "positive regulation of drug transmembrane export" NARROW []
synonym: "positive regulation of xenobiotic transmembrane export" NARROW []
@@ -515480,7 +516284,7 @@ relationship: part_of GO:1905759 ! post-anaphase array microtubule
id: GO:1905761
name: SCF ubiquitin ligase complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a SCF ubiquitin ligase complex." [GOC:dph, GOC:ha, GOC:TermGenie, PMID:19723762]
+def: "Binding to a SCF ubiquitin ligase complex." [GOC:dph, GOC:ha, GOC:TermGenie, PMID:19723762]
synonym: "CDL1 complex binding" EXACT [GOC:TermGenie]
synonym: "CRL1 complex binding" EXACT [GOC:TermGenie]
synonym: "Cul1-RING ubiquitin ligase complex binding" EXACT [GOC:TermGenie]
@@ -515494,14 +516298,14 @@ is_a: GO:0044877 ! protein-containing complex binding
id: GO:1905762
name: CCR4-NOT complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a CCR4-NOT complex." [GOC:TermGenie, PMID:26942678]
+def: "Binding to a CCR4-NOT complex." [GOC:TermGenie, PMID:26942678]
is_a: GO:0044877 ! protein-containing complex binding
[Term]
id: GO:1905763
name: MTREC complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a MTREC complex." [GOC:TermGenie, PMID:26942678]
+def: "Binding to a MTREC complex." [GOC:TermGenie, PMID:26942678]
synonym: "Mtl1-Red1 core complex binding" EXACT [GOC:TermGenie]
synonym: "NURS complex binding" EXACT []
synonym: "PAXT complex binding" EXACT []
@@ -515634,7 +516438,7 @@ relationship: positively_regulates GO:0048333 ! mesodermal cell differentiation
id: GO:1905773
name: 8-hydroxy-2'-deoxyguanosine DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 8-hydroxy-2'-deoxyguanosine an oxidized purine residue found in damaged DNA." [GO_REF:0000067, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:19734539]
+def: "Binding to 8-hydroxy-2'-deoxyguanosine an oxidized purine residue found in damaged DNA." [GO_REF:0000067, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:19734539]
is_a: GO:0032357 ! oxidized purine DNA binding
[Term]
@@ -515776,13 +516580,15 @@ relationship: positively_regulates GO:0070782 ! phosphatidylserine exposure on a
[Term]
id: GO:1905783
-name: CENP-A containing nucleosome disassembly
+name: obsolete CENP-A containing nucleosome disassembly
namespace: biological_process
-def: "The disaggregation of a CENP-A containing nucleosome into its constituent components." [GO_REF:0000079, GOC:TermGenie, PMID:27666591]
+def: "OBSOLETE. The disaggregation of a CENP-A containing nucleosome into its constituent components." [GO_REF:0000079, GOC:TermGenie, PMID:27666591]
+comment: This term was obsoleted because it did not describe a different process from that described by its parent.
synonym: "centromere specific nucleosome disassembly" RELATED [GOC:TermGenie]
synonym: "centromere-specific nucleosome disassembly" RELATED [GOC:TermGenie]
synonym: "centromeric nucleosome disassembly" RELATED [GOC:TermGenie]
-is_a: GO:0006337 ! nucleosome disassembly
+is_obsolete: true
+consider: GO:0006337
[Term]
id: GO:1905784
@@ -517334,7 +518140,8 @@ def: "Any process that modulates the frequency, rate or extent of protein locali
synonym: "regulation of protein localisation in cell leading edge" EXACT [GOC:TermGenie]
synonym: "regulation of protein localisation to cell leading edge" EXACT [GOC:TermGenie]
synonym: "regulation of protein localization in cell leading edge" EXACT [GOC:TermGenie]
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:1902463 ! protein localization to cell leading edge
[Term]
@@ -517361,7 +518168,8 @@ synonym: "inhibition of protein localization to cell leading edge" NARROW [GOC:T
synonym: "negative regulation of protein localisation in cell leading edge" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localisation to cell leading edge" EXACT [GOC:TermGenie]
synonym: "negative regulation of protein localization in cell leading edge" EXACT [GOC:TermGenie]
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:1905871 ! regulation of protein localization to cell leading edge
relationship: negatively_regulates GO:1902463 ! protein localization to cell leading edge
@@ -517389,7 +518197,8 @@ synonym: "upregulation of protein localisation in cell leading edge" EXACT [GOC:
synonym: "upregulation of protein localisation to cell leading edge" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization in cell leading edge" EXACT [GOC:TermGenie]
synonym: "upregulation of protein localization to cell leading edge" EXACT [GOC:TermGenie]
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:1905871 ! regulation of protein localization to cell leading edge
relationship: positively_regulates GO:1902463 ! protein localization to cell leading edge
@@ -517595,15 +518404,15 @@ relationship: positively_regulates GO:0034197 ! triglyceride transport
[Term]
id: GO:1905886
-name: chromatin remodeling involved in meiosis I
+name: obsolete chromatin remodeling involved in meiosis I
namespace: biological_process
-def: "Any chromatin remodeling that is involved in meiosis I." [GO_REF:0000060, GOC:TermGenie, PMID:19139281, PMID:25934010, PMID:9106659]
+def: "OBSOLETE. Any chromatin remodeling that is involved in meiosis I." [GO_REF:0000060, GOC:TermGenie, PMID:19139281, PMID:25934010, PMID:9106659]
+comment: This term was obsoleted because it represents a GO-CAM model.
synonym: "chromatin modeling involved in meiosis I" EXACT [GOC:TermGenie]
synonym: "chromatin modelling involved in meiosis I" EXACT [GOC:TermGenie]
synonym: "chromatin remodelling involved in meiosis I" EXACT [GOC:TermGenie]
synonym: "meiosis-specific chromatin remodeling" EXACT [PMID:19139281]
-is_a: GO:0006338 ! chromatin remodeling
-is_a: GO:0061982 ! meiosis I cell cycle process
+is_obsolete: true
[Term]
id: GO:1905887
@@ -518287,7 +519096,6 @@ synonym: "inhibition of vascular smooth muscle cell differentiation involved in
synonym: "inhibition of VSMC differentiation involved in phenotypic dimorphism" RELATED [GOC:TermGenie]
synonym: "inhibition of VSMC differentiation involved in phenotypic switching" NARROW [GOC:TermGenie]
synonym: "negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic dimorphism" RELATED [GOC:TermGenie]
-synonym: "negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching" EXACT [GOC:TermGenie]
synonym: "negative regulation of vascular smooth muscle cell differentiation involved in phenotypic dimorphism" RELATED [GOC:TermGenie]
synonym: "negative regulation of vascular smooth muscle cell differentiation involved in phenotypic switching" EXACT []
synonym: "negative regulation of VSMC differentiation involved in phenotypic dimorphism" RELATED [GOC:TermGenie]
@@ -518757,7 +519565,6 @@ def: "Catalysis of the reaction: IDP + H2O = IMP + phosphate." [PMID:20385596, P
synonym: "IDP phosphatase activity" EXACT []
synonym: "IDPase activity" EXACT []
synonym: "inosine diphosphatase activity" EXACT []
-synonym: "inosine-diphosphatase activity" EXACT []
xref: EC:3.6.1.64
xref: Reactome:R-HSA-2509816 "NUDT16 hydrolyses IDP to IMP"
xref: RHEA:35207
@@ -519709,7 +520516,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the eukaryotic RNA polymerase I complex." [GOC:rb, PMID:23459708]
synonym: "DNA-directed RNA polymerase I complex assembly" EXACT []
synonym: "RNA Polymerase I complex assembly" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:1990114
@@ -519718,7 +520525,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the eukaryotic RNA polymerase II core complex." [GOC:rb, PMID:23459708]
synonym: "DNA-directed RNA polymerase II, core complex assembly" EXACT []
synonym: "RNA Polymerase II assembly" BROAD []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:1990115
@@ -519727,7 +520534,7 @@ namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form the eukaryotic RNA polymerase III complex." [GOC:rb, PMID:23459708]
synonym: "DNA-directed RNA polymerase III complex assembly" EXACT []
synonym: "RNA Polymerase III complex assembly" EXACT []
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:1990116
@@ -519755,9 +520562,11 @@ relationship: part_of GO:0001783 ! B cell apoptotic process
[Term]
id: GO:1990119
-name: ATP-dependent RNA helicase inhibitor activity
+name: RNA helicase inhibitor activity
namespace: molecular_function
-def: "Binds to and stops, prevents or reduces the activity of an ATP-dependent RNA helicase." [GOC:rb, PMID:23721653]
+def: "Binds to and stops, prevents or reduces the activity of an RNA helicase." [GOC:rb, PMID:23721653]
+synonym: "ATP-dependent RNA helicase inhibitor activity" EXACT []
+is_a: GO:0004857 ! enzyme inhibitor activity
is_a: GO:0042030 ! ATPase inhibitor activity
[Term]
@@ -519831,7 +520640,8 @@ is_obsolete: true
id: GO:1990130
name: GATOR1 complex
namespace: cellular_component
-def: "A protein complex involved in regulation of non-nitrogen-starvation (NNS) autophagic process. In humans, the GATOR1 complex consists of DEPDC5, NPRL2, and NPRL3). In S. cerevisiae, this complex is referred to as SEACIT AND contains the Iml1p, Npr2p, and Npr3p proteins." [GOC:krc, GOC:rb, PMID:21900499, PMID:23723238, PMID:23974112, PMID:25934700, PMID:28199306]
+def: "A GTPase-activating protein (GAP) complex that regulates TORC1 signaling by interacting with the Rag GTPase. In human, the GATOR1 complex consists of DEPDC5, NPRL2, and NPRL3. In S. cerevisiae, this complex is referred to as SEACIT and contains the Iml1p, Npr2p, and Npr3p proteins." [GOC:krc, GOC:rb, PMID:21900499, PMID:23723238, PMID:23974112, PMID:25934700, PMID:28199306, PMID:29199950]
+comment: The Rag GTPase complex corresponds to Gtr1-Gtr2 GTPase complex ; GO:1990131.
synonym: "IML1 complex" EXACT []
synonym: "SEACIT complex" EXACT []
is_a: GO:0032991 ! protein-containing complex
@@ -519930,10 +520740,11 @@ is_a: GO:1990228 ! sulfurtransferase complex
[Term]
id: GO:1990142
-name: envenomation resulting in hemolysis in other organism
+name: envenomation resulting in hemolysis in another organism
namespace: biological_process
def: "A process that begins with venom being forced into an organism by the bite or sting of another organism, and ends with hemolysis in the bitten organism." [PMID:21590705]
-is_a: GO:0044649 ! envenomation resulting in cytolysis in other organism
+synonym: "envenomation resulting in hemolysis in other organism" EXACT []
+is_a: GO:0044649 ! envenomation resulting in cytolysis in another organism
[Term]
id: GO:1990143
@@ -519971,7 +520782,7 @@ is_a: GO:0034613 ! cellular protein localization
id: GO:1990147
name: talin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a talin, a family of related cytoskeletal proteins that play a role in assembly of actin filaments and migration of various cell types." [GOC:hjd, PMID:23372168]
+def: "Binding to a talin, a family of related cytoskeletal proteins that play a role in assembly of actin filaments and migration of various cell types." [GOC:hjd, PMID:23372168]
is_a: GO:0008092 ! cytoskeletal protein binding
[Term]
@@ -520042,7 +520853,7 @@ name: Dsc E3 ubiquitin ligase complex assembly
namespace: biological_process
def: "The aggregation, arrangement and bonding together of a set of components to form a Dsc E3 ubiquitin ligase complex, an E3 ubiquitin ligase complex localized to the ER and Golgi membrane." [GOC:mah, PMID:23760507]
synonym: "Dsc complex assembly" EXACT [PMID:23760507]
-is_a: GO:0034622 ! cellular protein-containing complex assembly
+is_a: GO:0065003 ! protein-containing complex assembly
[Term]
id: GO:1990156
@@ -520099,7 +520910,7 @@ is_a: GO:0033202 ! DNA helicase complex
id: GO:1990162
name: histone deacetylase activity (H3-K4 specific)
namespace: molecular_function
-def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 4) + H2O = histone H3 L-lysine (position 4) + acetate. This reaction represents the removal of an acetyl group from lysine at position 4 of the histone H3 protein." [GOC:al, PMID:23771057]
+def: "Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 4) + H2O = histone H3 L-lysine (position 4) + acetate. This reaction represents the removal of an acetyl group from lysine at position 4 of the histone H3 protein." [GOC:al, PMID:23771057, PMID:28450737]
is_a: GO:0004407 ! histone deacetylase activity
[Term]
@@ -520113,7 +520924,7 @@ is_a: GO:0016572 ! histone phosphorylation
id: GO:1990165
name: single-strand break-containing DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with damaged DNA containing single-strand breaks (SSBs)." [GOC:al, PMID:21984210]
+def: "Binding to damaged DNA containing single-strand breaks (SSBs)." [GOC:al, PMID:21984210]
synonym: "single-strand break-containing damaged DNA binding" EXACT []
synonym: "SSB-containing DNA binding" EXACT []
is_a: GO:0003684 ! damaged DNA binding
@@ -520203,7 +521014,7 @@ is_a: GO:0016891 ! endoribonuclease activity, producing 5'-phosphomonoesters
id: GO:1990175
name: EH domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an EH domain of a protein. The EH stand for Eps15 homology. This was originally identified as a motif present in three copies at the NH2-termini of Eps15 and of the related molecule Eps15R." [GOC:hjd, PMID:11911876, PMID:21115825]
+def: "Binding to an EH domain of a protein. The EH stand for Eps15 homology. This was originally identified as a motif present in three copies at the NH2-termini of Eps15 and of the related molecule Eps15R." [GOC:hjd, PMID:11911876, PMID:21115825]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -520285,6 +521096,7 @@ synonym: "extracellular vesicular exosome secretion" EXACT [GOC:hjd]
synonym: "multi-vesicular body fusion with plasma membrane" EXACT []
synonym: "secretion of exosome" EXACT [PMID:18617898]
is_a: GO:0006887 ! exocytosis
+is_a: GO:0051650 ! establishment of vesicle localization
relationship: part_of GO:0097734 ! extracellular exosome biogenesis
[Term]
@@ -520331,7 +521143,7 @@ is_obsolete: true
id: GO:1990188
name: euchromatin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with euchromatin, a dispersed and relatively uncompacted form of chromatin." [GOC:vw, PMID:22431512]
+def: "Binding to euchromatin, a dispersed and relatively uncompacted form of chromatin." [GOC:vw, PMID:22431512]
is_a: GO:0003682 ! chromatin binding
[Term]
@@ -520406,12 +521218,13 @@ is_a: GO:1990195 ! macrolide transmembrane transporter complex
[Term]
id: GO:1990197
-name: ATP-dependent methionine-importing complex
+name: methionine-importing ABC transporter complex
namespace: cellular_component
def: "An ATP-binding cassette (ABC) transporter complex that is capable of methionine-importing activity. An example is the bacterial MetNIQ methionine transporter, that consists of the dimeric ATPase subunit MetN located at the cytoplasmic side of the plasma membrane and the dimeric transmembrane subunit MetI. MetQ is regarded as the periplasmic methionine-binding chaperon subunit, and is capable of transporting methionine from the periplasm into the cytoplasm in an ATP-dependent manner." [GOC:bhm, PMID:22095702]
synonym: "ATP-binding cassette (ABC) methionine importer complex" EXACT []
synonym: "ATP-dependent methionine importer complex" EXACT []
synonym: "ATP-dependent methionine importing complex" EXACT []
+synonym: "ATP-dependent methionine-importing complex" EXACT []
synonym: "methionine transport complex" BROAD []
synonym: "methionine transporter" RELATED []
synonym: "methionine transporter complex" BROAD []
@@ -520584,8 +521397,8 @@ id: GO:1990215
name: negative regulation by symbiont of host intracellular transport
namespace: biological_process
def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of intracellular transport in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [PMID:22319451]
-is_a: GO:0032387 ! negative regulation of intracellular transport
is_a: GO:0052038 ! modulation by symbiont of host intracellular transport
+relationship: negatively_regulates GO:0046907 ! intracellular transport
[Term]
id: GO:1990216
@@ -520632,7 +521445,6 @@ name: L-cysteine desulfurase complex
namespace: cellular_component
def: "A protein complex capable of cysteine desulfurase activity decomposing L-cysteine to L-alanine and sulfur. It belongs to a ubiquitous family of pyridoxal 5-phosphate (PLP)-dependent enzymes. In E. coli it consists of a SufS dimer." [GOC:bhm, PMID:11827487]
synonym: "IscS" NARROW [GOC:bhm, GOC:dph]
-synonym: "NIFS" NARROW [GOC:bhm, GOC:dph]
synonym: "NifS" NARROW [GOC:bhm, GOC:dph]
synonym: "SufS complex" NARROW []
is_a: GO:0032991 ! protein-containing complex
@@ -520675,7 +521487,7 @@ relationship: part_of GO:0020008 ! rhoptry
id: GO:1990226
name: histone methyltransferase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone methyltransferase enzyme." [GOC:ame, GOC:BHF, PMID:19486527]
+def: "Binding to a histone methyltransferase enzyme." [GOC:ame, GOC:BHF, PMID:19486527]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -520788,7 +521600,7 @@ is_a: GO:0004520 ! endodeoxyribonuclease activity
id: GO:1990239
name: steroid hormone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a steroid hormone." [GOC:ln]
+def: "Binding to a steroid hormone." [GOC:ln]
is_a: GO:0005496 ! steroid binding
is_a: GO:0042562 ! hormone binding
@@ -520849,7 +521661,7 @@ is_a: GO:0098800 ! inner mitochondrial membrane protein complex
id: GO:1990247
name: N6-methyladenosine-containing RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA molecule modified by N6-methyladenosine (m6A), a modification present at internal sites of mRNAs and some non-coding RNAs." [PMID:22575960, PMID:24284625]
+def: "Binding to an RNA molecule modified by N6-methyladenosine (m6A), a modification present at internal sites of mRNAs and some non-coding RNAs." [PMID:22575960, PMID:24284625]
is_a: GO:0003723 ! RNA binding
[Term]
@@ -520903,7 +521715,7 @@ is_a: GO:0034198 ! cellular response to amino acid starvation
id: GO:1990254
name: keratin filament binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a keratin filament, an intermediate filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells." [GOC:krc, PMID:6170061]
+def: "Binding to a keratin filament, an intermediate filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells." [GOC:krc, PMID:6170061]
is_a: GO:0019215 ! intermediate filament binding
[Term]
@@ -520927,7 +521739,7 @@ name: piccolo-bassoon transport vesicle
namespace: cellular_component
def: "A cytoplasmic dense-core vesicle that transports a range of proteins including piccolo, bassoon, N-cadherin and syntaxin. The transported proteins may be associated with the external side of the vesicle, rather than being contained within the vesicle, therefore forming an aggregate of vesicle and proteins. Piccolo-bassoon transport vesicles (or PTVs) range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. They are packaged via the trans-Golgi network before being transported through the axon." [GOC:dr, PMID:21569270]
synonym: "PTV" RELATED []
-is_a: GO:0031410 ! cytoplasmic vesicle
+is_a: GO:0030133 ! transport vesicle
[Term]
id: GO:1990258
@@ -521029,7 +521841,7 @@ is_a: GO:1990267 ! response to transition metal nanoparticle
id: GO:1990269
name: RNA polymerase II C-terminal domain phosphoserine binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with phosphorylated serine residues in the C-terminal domain of RNA polymerase II." [GOC:di, PMID:22796944]
+def: "Binding to phosphorylated serine residues in the C-terminal domain of RNA polymerase II." [GOC:di, PMID:22796944]
synonym: "RNA Pol II C-terminal domain phosphoserine binding" EXACT [GOC:di]
synonym: "RNAP II C-terminal domain phosphoserine binding" EXACT []
is_a: GO:0050815 ! phosphoserine residue binding
@@ -521100,7 +521912,7 @@ is_a: GO:1902621 ! actomyosin contractile ring disassembly
id: GO:1990275
name: preribosome binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of a preribosome." [GOC:di, PMID:22735702]
+def: "Binding to a preribosome." [GOC:di, PMID:22735702]
is_a: GO:0043021 ! ribonucleoprotein complex binding
[Term]
@@ -521108,6 +521920,7 @@ id: GO:1990276
name: RNA 5'-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the 5'-gamma-phosphate in an RNA molecule." [GOC:al, GOC:vw, PMID:22740346]
+is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008173 ! RNA methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
@@ -521193,15 +522006,15 @@ id: GO:1990299
name: Bub1-Bub3 complex localization to kinetochore
namespace: biological_process
def: "A cellular protein complex localization that acts on a Bub1-Bub3 complex; as a result, the complex is transported to, or maintained in, a specific location at the kinetochore." [PMID:22521786]
+is_a: GO:0031503 ! protein-containing complex localization
is_a: GO:0034501 ! protein localization to kinetochore
-is_a: GO:0034629 ! cellular protein-containing complex localization
[Term]
id: GO:1990300
name: cellulosome binding
namespace: molecular_function
alt_id: GO:1990301
-def: "Interacting selectively and non-covalently with the cellulosome, an extracellular multi-enzyme complex containing several enzymes aligned on a non-catalytic scaffolding that functions to hydrolyze plant cell wall polysaccharides." [GOC:mengo_curators, PMID:11893054, PMID:15197390]
+def: "Binding to a cellulosome, an extracellular multi-enzyme complex containing several enzymes aligned on a non-catalytic scaffolding that functions to hydrolyze plant cell wall polysaccharides." [GOC:mengo_curators, PMID:11893054, PMID:15197390]
synonym: "scaffoldin complex binding" NARROW []
is_a: GO:0005488 ! binding
@@ -521259,42 +522072,42 @@ is_a: GO:1990234 ! transferase complex
id: GO:1990308
name: type-I dockerin domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type-I dockerin domain of a protein. Type-I dockerin domain is the binding partner of type-1 cohesin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
+def: "Binding to a type-I dockerin domain of a protein. Type-I dockerin domain is the binding partner of type-1 cohesin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:1990309
name: type-II dockerin domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type-II dockerin domain of a protein. Type-II dockerin domain is the binding partner of type-II cohesin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
+def: "Binding to a type-II dockerin domain of a protein. Type-II dockerin domain is the binding partner of type-II cohesin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:1990310
name: type-III dockerin domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type-III dockerin domain of a protein. Type-III dockerin domain is the binding partner of type-III cohesin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
+def: "Binding to a type-III dockerin domain of a protein. Type-III dockerin domain is the binding partner of type-III cohesin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:1990311
name: type-I cohesin domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type-I cohesin domain of a protein. Type-I cohesin domain is the binding partner of type-I dockerin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
+def: "Binding to a type-I cohesin domain of a protein. Type-I cohesin domain is the binding partner of type-I dockerin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:1990312
name: type-II cohesin domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type-II cohesin domain of a protein. Type-II cohesin domain is the binding partner of type-II dockerin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
+def: "Binding to a type-II cohesin domain of a protein. Type-II cohesin domain is the binding partner of type-II dockerin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
is_a: GO:0019904 ! protein domain specific binding
[Term]
id: GO:1990313
name: type-III cohesin domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a type-III cohesin domain of a protein. Type-III cohesin domain is the binding partner of type-III dockerin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
+def: "Binding to a type-III cohesin domain of a protein. Type-III cohesin domain is the binding partner of type-III dockerin domain." [GOC:mengo_curators, PMID:23195689, PMID:24080387]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -521677,8 +522490,8 @@ is_a: GO:1902912 ! pyruvate kinase complex
id: GO:1990362
name: butanol dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+." [GOC:mengo_curators, PMID:1999395]
-xref: RHEA:33200
+def: "Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+." [GOC:mengo_curators, PMID:1999395, RHEA:33199]
+xref: RHEA:33199
is_a: GO:0004022 ! alcohol dehydrogenase (NAD+) activity
[Term]
@@ -521821,7 +522634,7 @@ is_a: GO:0101005 ! deubiquitinase activity
id: GO:1990381
name: ubiquitin-specific protease binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ubiquitin-specific protease." [GOC:bf, GOC:PARL, PMID:24063750]
+def: "Binding to a ubiquitin-specific protease." [GOC:bf, GOC:PARL, PMID:24063750]
synonym: "deubiquitinase binding" EXACT [GOC:bf]
synonym: "deubiquitinating enzyme binding" EXACT [PMID:24063750]
is_a: GO:0002020 ! protease binding
@@ -521986,7 +522799,7 @@ is_a: GO:0060429 ! epithelium development
id: GO:1990400
name: mitochondrial ribosomal large subunit rRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the mitochondrial large ribosomal subunit RNA (LSU rRNA), a constituent of the mitochondrial large ribosomal subunit." [PMID:24206665]
+def: "Binding to a mitochondrial large ribosomal subunit RNA (LSU rRNA)." [PMID:24206665]
comment: In S. cerevisiae, this is the mitochondrial 21S rRNA
synonym: "21S rRNA binding" NARROW []
synonym: "mitochondrial LSU rRNA binding" EXACT []
@@ -522026,7 +522839,7 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein
id: GO:1990405
name: protein antigen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein antigen." [PMID:9360996]
+def: "Binding to a protein antigen." [PMID:9360996]
is_a: GO:0003823 ! antigen binding
is_a: GO:0005515 ! protein binding
@@ -522045,7 +522858,7 @@ is_a: GO:1903439 ! calcitonin family receptor complex
id: GO:1990407
name: calcitonin gene-related peptide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with calcitonin gene-related peptide (CGRP)." [GOC:bhm, PMID:10882736]
+def: "Binding to calcitonin gene-related peptide (CGRP)." [GOC:bhm, PMID:10882736]
comment: An example of this is CALCRL in human (Q16602) in PMID:10882736 (inferred from direct assay/mutant phenotype/etc.).
synonym: "calcitonin-gene-related peptide binding" EXACT []
synonym: "calcitonin-gene-related polypeptide binding" EXACT []
@@ -522067,7 +522880,7 @@ is_a: GO:0097646 ! calcitonin family receptor signaling pathway
id: GO:1990409
name: adrenomedullin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with adrenomedullin (AM)." [GOC:bhm, PMID:10882736]
+def: "Binding to adrenomedullin (AM)." [GOC:bhm, PMID:10882736]
comment: An example of a protein that could be annotated to this term is CALCRL in human (Q16602) in PMID:10882736.
synonym: "AM binding" EXACT []
is_a: GO:0097644 ! calcitonin family binding
@@ -522105,7 +522918,7 @@ namespace: cellular_component
def: "A small pigmented organelle used in single-celled organisms to detect light." [Wikipedia:Eyespot_apparatus]
synonym: "eyespot" RELATED []
synonym: "stigma" RELATED []
-is_a: GO:0043229 ! intracellular organelle
+is_a: GO:0043231 ! intracellular membrane-bounded organelle
[Term]
id: GO:1990414
@@ -522115,13 +522928,6 @@ def: "The repair of a replication-born double-strand DNA break in which the DNA
synonym: "replication-born DSB repair by SCE" EXACT []
is_a: GO:0000724 ! double-strand break repair via homologous recombination
-[Term]
-id: GO:1990415
-name: Pex17p-Pex14p docking complex
-namespace: cellular_component
-def: "A protein complex involved in the peroxisomal import machinery. In S. cerevisiae, this complex contains the proteins Pex17p, Pex14p, Pex19, and Pex13p." [GOC:rb, PMID:12667447]
-is_a: GO:0032991 ! protein-containing complex
-
[Term]
id: GO:1990416
name: cellular response to brain-derived neurotrophic factor stimulus
@@ -522229,18 +523035,19 @@ is_a: GO:0050658 ! RNA transport
id: GO:1990429
name: peroxisomal importomer complex
namespace: cellular_component
-def: "A protein complex responsible for transporting proteins into the peroxisomal matrix. An example of this complex is Pex14 found in S. cerevisae which has 9 core components and 12 transient interaction partners." [PMID:20154681, PMID:22375831]
+alt_id: GO:1990415
+def: "A protein complex responsible for transporting proteins into the peroxisomal matrix. An example of this complex is Pex14 found in S. cerevisae which has 9 core components and 12 transient interaction partners." [PMID:12667447, PMID:20154681, PMID:22375831]
synonym: "peroxisomal import pore" EXACT []
synonym: "peroxisomal protein import machinery" EXACT []
synonym: "Pex14 complex" NARROW []
+synonym: "Pex17p-Pex14p docking complex" RELATED []
is_a: GO:1990351 ! transporter complex
-is_a: GO:1990415 ! Pex17p-Pex14p docking complex
[Term]
id: GO:1990430
name: extracellular matrix protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a protein that is part of an extracellular matrix." [PMID:22355679]
+def: "Binding to a protein that is part of an extracellular matrix." [PMID:22355679]
is_a: GO:0005515 ! protein binding
[Term]
@@ -522299,7 +523106,6 @@ id: GO:1990437
name: snRNA 2'-O-methylation
namespace: biological_process
def: "The posttranscriptional addition of a methyl group to the 2' oxygen atom of a nucleotide residue in an snRNA molecule." [PMID:11842100, PMID:9844635]
-is_a: GO:0040031 ! snRNA modification
is_a: GO:0106349 ! snRNA methylation
[Term]
@@ -522370,7 +523176,7 @@ is_a: GO:0046777 ! protein autophosphorylation
id: GO:1990444
name: F-box domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an F-box domain of a protein." [GOC:bf, GOC:PARL, InterPro:IPR001810, PMID:12628165]
+def: "Binding to an F-box domain of a protein." [GOC:bf, GOC:PARL, InterPro:IPR001810, PMID:12628165]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -522386,21 +523192,21 @@ is_obsolete: true
id: GO:1990446
name: U1 snRNP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of a U1 small nuclear ribonucleoprotein particle." [PMID:14713954]
+def: "Binding to a U1 small nuclear ribonucleoprotein particle." [PMID:14713954]
is_a: GO:0070990 ! snRNP binding
[Term]
id: GO:1990447
name: U2 snRNP binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any part of a U2 small nuclear ribonucleoprotein particle." [PMID:14713954]
+def: "Binding to a U2 small nuclear ribonucleoprotein particle." [PMID:14713954]
is_a: GO:0070990 ! snRNP binding
[Term]
id: GO:1990448
name: exon-exon junction complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an exon-exon junction complex, a protein complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay." [GOC:sart, PMID:24967911]
+def: "Binding to an exon-exon junction complex, a protein complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay." [GOC:sart, PMID:24967911]
synonym: "EJC binding" EXACT []
is_a: GO:0044877 ! protein-containing complex binding
@@ -522423,7 +523229,7 @@ is_obsolete: true
id: GO:1990450
name: linear polyubiquitin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a linear polymer of ubiquitin. Linear ubiquitin polymers are formed by linking the amino-terminal methionine (M1) of one ubiquitin molecule to the carboxy-terminal glycine (G76) of the next." [GOC:bf, GOC:PARL, PMID:23453807]
+def: "Binding to a linear polymer of ubiquitin. Linear ubiquitin polymers are formed by linking the amino-terminal methionine (M1) of one ubiquitin molecule to the carboxy-terminal glycine (G76) of the next." [GOC:bf, GOC:PARL, PMID:23453807]
synonym: "M1-linked ubiquitin chain binding" EXACT [PMID:23453807]
is_a: GO:0043130 ! ubiquitin binding
@@ -522504,7 +523310,7 @@ is_a: GO:0045335 ! phagocytic vesicle
id: GO:1990458
name: lipooligosaccharide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with lipooligosaccharide. Lipooligosaccharides (LOSs) are the major glycolipids expressed on mucosal Gram-negative bacteria." [GOC:hjd, PMID:8894399]
+def: "Binding to lipooligosaccharide. Lipooligosaccharides (LOSs) are the major glycolipids expressed on mucosal Gram-negative bacteria." [GOC:hjd, PMID:8894399]
comment: ChEBI distinguishes an oligosaccharide from a polysaccharide as the latter being anything of length 10 or greater.
synonym: "endotoxin binding" RELATED []
synonym: "LOS binding" RELATED []
@@ -522514,14 +523320,14 @@ is_a: GO:0097367 ! carbohydrate derivative binding
id: GO:1990459
name: transferrin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the transferrin receptor." [GOC:pm, PMID:9819414]
+def: "Binding to a transferrin receptor." [GOC:pm, PMID:9819414]
is_a: GO:0005102 ! signaling receptor binding
[Term]
id: GO:1990460
name: leptin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the leptin receptor." [GOC:pm, PMID:22405007]
+def: "Binding to a leptin receptor." [GOC:pm, PMID:22405007]
is_a: GO:0005102 ! signaling receptor binding
[Term]
@@ -522610,7 +523416,7 @@ relationship: part_of GO:0043073 ! germ cell nucleus
id: GO:1990470
name: piRNA cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs)." [GOC:bhm, PMID:24906153]
+def: "Binding to piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs)." [GOC:bhm, PMID:24906153]
comment: An example of this is rhi in Drosophila melanogaster (Q7JXA8) in PMID:24906153 (inferred from direct assay).
is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
@@ -522618,14 +523424,14 @@ is_a: GO:1990837 ! sequence-specific double-stranded DNA binding
id: GO:1990471
name: piRNA uni-strand cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with uni-strand piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs) that map predominantly to only one strand and exhibit hallmarks of canonical Pol II transcription. Uni-strand piRNA clusters are found in many taxa." [GOC:bhm, PMID:24906153]
+def: "Binding to uni-strand piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs) that map predominantly to only one strand and exhibit hallmarks of canonical Pol II transcription. Uni-strand piRNA clusters are found in many taxa." [GOC:bhm, PMID:24906153]
is_a: GO:1990470 ! piRNA cluster binding
[Term]
id: GO:1990472
name: piRNA dual-strand cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with dual-strand piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs) where piRNAs originate from both DNA strands via noncanonical transcription." [GOC:bhm, PMID:24906153]
+def: "Binding to dual-strand piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs) where piRNAs originate from both DNA strands via noncanonical transcription." [GOC:bhm, PMID:24906153]
comment: An example of this is rhi in Drosophila melanogaster (Q7JXA8) in PMID:24906153 (inferred from direct assay).
is_a: GO:1990470 ! piRNA cluster binding
@@ -522633,7 +523439,7 @@ is_a: GO:1990470 ! piRNA cluster binding
id: GO:1990473
name: ciliary targeting signal binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a ciliary targeting sequence, a specific peptide sequence that acts as a signal to localize a membrane protein to the ciliary membrane." [GOC:krc, PMID:18256283, PMID:19575670, PMID:20603001, PMID:20697559]
+def: "Binding to a ciliary targeting sequence, a specific peptide sequence that acts as a signal to localize a membrane protein to the ciliary membrane." [GOC:krc, PMID:18256283, PMID:19575670, PMID:20603001, PMID:20697559]
synonym: "CTS binding" EXACT []
is_a: GO:0005048 ! signal sequence binding
@@ -522924,7 +523730,6 @@ alt_id: GO:1990510
def: "Any maintenance of fidelity that is involved in mitotic cell cycle DNA replication." [PMID:19185548]
synonym: "maintenance of fidelity involved in mitotic cell cycle DNA replication" EXACT []
synonym: "maintenance of fidelity involved in mitotic DNA replication" EXACT []
-synonym: "mitotic DNA replication maintenance of fidelity" EXACT []
is_a: GO:1902298 ! cell cycle DNA replication maintenance of fidelity
is_a: GO:1903047 ! mitotic cell cycle process
relationship: part_of GO:1902969 ! mitotic DNA replication
@@ -522938,10 +523743,13 @@ is_a: GO:1902969 ! mitotic DNA replication
[Term]
id: GO:1990507
-name: ATP-independent chaperone mediated protein folding
+name: obsolete ATP-independent chaperone mediated protein folding
namespace: biological_process
-def: "The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone, and independent of ATP hydrolysis." [GOC:rb, PMID:25242142]
-is_a: GO:0061077 ! chaperone-mediated protein folding
+def: "OBSOLETE. The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone, and independent of ATP hydrolysis." [GOC:rb, PMID:25242142]
+comment: This term was obsoleted because it represents a molecular function.
+is_obsolete: true
+consider: GO:0006457
+consider: GO:0044183
[Term]
id: GO:1990508
@@ -523082,7 +523890,7 @@ relationship: part_of GO:0031304 ! intrinsic component of mitochondrial inner me
id: GO:1990525
name: BIR domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a Baculovirus Inhibitor of apoptosis protein Repeat (BIR) domain." [GOC:ha, InterPro:IPR001370]
+def: "Binding to a Baculovirus Inhibitor of apoptosis protein Repeat (BIR) domain." [GOC:ha, InterPro:IPR001370]
comment: An example of this is the Drosophila reaper gene in PMID:21886178.
synonym: "Baculovirus Inhibitor of apoptosis protein Repeat domain binding" EXACT []
is_a: GO:0019904 ! protein domain specific binding
@@ -523141,7 +523949,6 @@ synonym: "Lem3-Dnf1 complex" NARROW []
synonym: "Lem3p-Dnf1p complex" NARROW []
synonym: "P4-ATPase complex" EXACT []
synonym: "phospholipid flippase complex" EXACT []
-is_a: GO:1904949 ! ATPase complex
is_a: GO:1990351 ! transporter complex
[Term]
@@ -523225,7 +524032,6 @@ id: GO:1990542
name: mitochondrial transmembrane transport
namespace: biological_process
def: "The process in which a solute is transported from one side of a membrane to the other into, out of or within a mitochondrion." [PMID:20533899]
-is_a: GO:0006839 ! mitochondrial transport
is_a: GO:0055085 ! transmembrane transport
[Term]
@@ -523369,7 +524175,7 @@ is_a: GO:1990542 ! mitochondrial transmembrane transport
id: GO:1990560
name: obsolete DNA methyltransferase binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a DNA methyltransferase." [PMID:22880885]
+def: "OBSOLETE. Binding to a DNA methyltransferase." [PMID:22880885]
comment: This term was obsoleted at the TermGenie Gatekeeper stage.
synonym: "DNA methyltransferase binding" EXACT []
is_obsolete: true
@@ -523476,8 +524282,6 @@ synonym: "centromere clustering during meiosis" EXACT []
synonym: "homologous chromosome movement towards spindle pole in meiosis I prometaphase" EXACT []
is_a: GO:0016344 ! meiotic chromosome movement towards spindle pole
is_a: GO:0070192 ! chromosome organization involved in meiotic cell cycle
-is_a: GO:0072594 ! establishment of protein localization to organelle
-is_a: GO:0072698 ! protein localization to microtubule cytoskeleton
is_a: GO:0098653 ! centromere clustering
[Term]
@@ -523669,7 +524473,7 @@ is_a: GO:1990564 ! protein polyufmylation
id: GO:1990593
name: nascent polypeptide-associated complex binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the nascent polypeptide-associated complex, which is a heterodimeric protein complex that can reversibly bind to ribosomes and is located in direct proximity to newly synthesized polypeptide chains as they emerge from the ribosome." [PMID:25487825]
+def: "Binding to nascent polypeptide-associated complex, a heterodimeric protein complex that can reversibly bind to ribosomes and is located in direct proximity to newly synthesized polypeptide chains as they emerge from the ribosome." [PMID:25487825]
synonym: "NAC binding" EXACT []
synonym: "NACA binding" EXACT []
is_a: GO:0044877 ! protein-containing complex binding
@@ -523760,7 +524564,7 @@ relationship: part_of GO:0005789 ! endoplasmic reticulum membrane
id: GO:1990605
name: GU repeat RNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an RNA molecule containing GU repeats." [PMID:20081200]
+def: "Binding to an RNA molecule containing GU repeats." [PMID:20081200]
is_a: GO:0003723 ! RNA binding
[Term]
@@ -523817,6 +524621,7 @@ name: regulation of cytoplasmic translational initiation in response to stress
namespace: biological_process
def: "Modulation of the frequency, rate or extent of cytoplasmic translational initiation as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [PMID:16278445]
is_a: GO:0043558 ! regulation of translational initiation in response to stress
+is_a: GO:1904688 ! regulation of cytoplasmic translational initiation
is_a: GO:1990497 ! regulation of cytoplasmic translation in response to stress
[Term]
@@ -523938,9 +524743,10 @@ id: GO:1990625
name: negative regulation of cytoplasmic translational initiation in response to stress
namespace: biological_process
def: "Any process that stops, prevents or reduces the rate of cytoplasmic translation initiation as a result of a stimulus indicating the organism is under stress." [GOC:vw, PMID:12242291]
+is_a: GO:0032055 ! negative regulation of translation in response to stress
is_a: GO:0032057 ! negative regulation of translational initiation in response to stress
+is_a: GO:1904689 ! negative regulation of cytoplasmic translational initiation
is_a: GO:1990611 ! regulation of cytoplasmic translational initiation in response to stress
-is_a: GO:2000766 ! negative regulation of cytoplasmic translation
[Term]
id: GO:1990626
@@ -523996,7 +524802,7 @@ is_a: GO:0032991 ! protein-containing complex
id: GO:1990631
name: ErbB-4 class receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the protein-tyrosine kinase receptor ErbB-4/HER4." [GOC:sl, PMID:18523588]
+def: "Binding to the protein-tyrosine kinase receptor ErbB-4/HER4." [GOC:sl, PMID:18523588]
synonym: "HER4 receptor binding" EXACT []
is_a: GO:0005102 ! signaling receptor binding
@@ -524021,7 +524827,7 @@ relationship: part_of GO:0048471 ! perinuclear region of cytoplasm
id: GO:1990634
name: protein phosphatase 5 binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the enzyme protein phosphatase 5." [PMID:8943293]
+def: "Binding to protein phosphatase 5." [PMID:8943293]
synonym: "protein phosphatase T binding" EXACT []
is_a: GO:0019903 ! protein phosphatase binding
@@ -524189,7 +524995,7 @@ is_a: GO:0008283 ! cell population proliferation
id: GO:1990655
name: 4 iron, 3 sulfur cluster binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a 4 iron, 3 sulfur (4Fe-3S) cluster, an uncommon iron-sulfur cluster with unique properties found in oxygen-tolerant Ni-Fe hydrogenases of various bacteria." [GOC:am, PMID:23267108]
+def: "Binding to a 4 iron, 3 sulfur (4Fe-3S) cluster, an uncommon iron-sulfur cluster with unique properties found in oxygen-tolerant Ni-Fe hydrogenases of various bacteria." [GOC:am, PMID:23267108]
synonym: "4Fe-3S cluster binding" RELATED []
is_a: GO:0051536 ! iron-sulfur cluster binding
@@ -524545,7 +525351,7 @@ name: intrinsic component of Golgi cis cisterna membrane
namespace: cellular_component
def: "The component of the Golgi cis cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
synonym: "intrinsic component of cis-Golgi cisterna membrane" EXACT []
-is_a: GO:0031228 ! intrinsic component of Golgi membrane
+is_a: GO:0031300 ! intrinsic component of organelle membrane
relationship: part_of GO:1990674 ! Golgi cis cisterna membrane
[Term]
@@ -524554,7 +525360,7 @@ name: intrinsic component of Golgi medial cisterna membrane
namespace: cellular_component
def: "The component of the Golgi medial cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
synonym: "intrinsic component of medial-Golgi cisterna membrane" EXACT []
-is_a: GO:0031228 ! intrinsic component of Golgi membrane
+is_a: GO:0031300 ! intrinsic component of organelle membrane
relationship: part_of GO:1990675 ! Golgi medial cisterna membrane
[Term]
@@ -524563,7 +525369,7 @@ name: intrinsic component of Golgi trans cisterna membrane
namespace: cellular_component
def: "The component of the Golgi trans cisterna membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
synonym: "intrinsic component of trans-Golgi cisterna membrane" EXACT []
-is_a: GO:0031228 ! intrinsic component of Golgi membrane
+is_a: GO:0031300 ! intrinsic component of organelle membrane
relationship: part_of GO:1990676 ! Golgi trans cisterna membrane
[Term]
@@ -524605,6 +525411,7 @@ synonym: "establishment or maintenance of nucleolar chromatin architecture" EXAC
synonym: "nucleolar chromatin organisation" EXACT []
is_a: GO:0016043 ! cellular component organization
relationship: part_of GO:0006325 ! chromatin organization
+relationship: part_of GO:0007000 ! nucleolus organization
[Term]
id: GO:1990701
@@ -524623,7 +525430,7 @@ name: integral component of Golgi cis cisterna membrane
namespace: cellular_component
def: "The component of the Golgi cis membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
synonym: "integral component of cis-Golgi cisterna membrane" EXACT []
-is_a: GO:0030173 ! integral component of Golgi membrane
+is_a: GO:0031301 ! integral component of organelle membrane
is_a: GO:1990693 ! intrinsic component of Golgi cis cisterna membrane
[Term]
@@ -524632,7 +525439,7 @@ name: integral component of Golgi medial cisterna membrane
namespace: cellular_component
def: "The component of the Golgi medial membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
synonym: "integral component of medial-Golgi cisterna membrane" EXACT []
-is_a: GO:0030173 ! integral component of Golgi membrane
+is_a: GO:0031301 ! integral component of organelle membrane
is_a: GO:1990694 ! intrinsic component of Golgi medial cisterna membrane
[Term]
@@ -524641,7 +525448,7 @@ name: integral component of Golgi trans cisterna membrane
namespace: cellular_component
def: "The component of the Golgi trans membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane." [GOC:bhm, PMID:16038056, PMID:24119662]
synonym: "integral component of trans-Golgi cisterna membrane" EXACT []
-is_a: GO:0030173 ! integral component of Golgi membrane
+is_a: GO:0031301 ! integral component of organelle membrane
is_a: GO:1990695 ! intrinsic component of Golgi trans cisterna membrane
[Term]
@@ -524685,7 +525492,6 @@ comment: An example of this is MutS in E. coli (UniProt symbol P23909) in PMID:2
synonym: "MutS mismatch repair complex" EXACT []
is_a: GO:0032300 ! mismatch repair complex
is_a: GO:1902494 ! catalytic complex
-is_a: GO:1904949 ! ATPase complex
[Term]
id: GO:1990711
@@ -524693,7 +525499,6 @@ name: beta-catenin-ICAT complex
namespace: cellular_component
def: "Transcription factor complex that inhibits binding of Tcf to beta-catenin while preserving interaction of catenin with cadherin thus inhibiting transcription mediated by beta-catenin-Tcf complex." [GOC:bhm, PMID:12408824]
comment: An example of this is Catenin beta-1 in human (UniProt symbol P35222) in PMID:12408824 (inferred from physical interaction).
-synonym: "Beta-catenin-ICAT complex" EXACT []
synonym: "CTNNB1-CTNNBIP1 complex" EXACT []
is_a: GO:0090571 ! RNA polymerase II transcription repressor complex
@@ -524726,7 +525531,7 @@ is_a: GO:0008378 ! galactosyltransferase activity
id: GO:1990715
name: mRNA CDS binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the coding sequence (CDS) of an mRNA molecule." [GOC:kmv, PMID:25805859, SO:0000316]
+def: "Binding to an mRNA molecule coding sequence (CDS)." [GOC:kmv, PMID:25805859, SO:0000316]
synonym: "mRNA coding region binding" EXACT []
synonym: "mRNA coding sequence binding" EXACT []
is_a: GO:0003729 ! mRNA binding
@@ -524797,6 +525602,7 @@ id: GO:1990723
name: cytoplasmic periphery of the nuclear pore complex
namespace: cellular_component
def: "Cytoplasm situated in close proximity to a nuclear pore complex." [PMID:9398662]
+synonym: "associated with the nuclear pore" RELATED [GOC:mah]
is_a: GO:0048471 ! perinuclear region of cytoplasm
[Term]
@@ -524913,7 +525719,6 @@ synonym: "establishment and maintenance of gamma-tubulin complex localization to
synonym: "gamma-tubulin complex localisation to mitotic spindle pole body" EXACT []
synonym: "gamma-tubulin complex localization to mitotic SPB" EXACT []
is_a: GO:0033566 ! gamma-tubulin complex localization
-is_a: GO:1902440 ! protein localization to mitotic spindle pole body
[Term]
id: GO:1990736
@@ -525136,7 +525941,7 @@ relationship: part_of GO:0002181 ! cytoplasmic translation
id: GO:1990763
name: arrestin family protein binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any member of the arrestin family, proteins involved in agonist-mediated desensitization of G protein-coupled receptors." [PMID:23911909]
+def: "Binding to a member of the arrestin family, proteins involved in agonist-mediated desensitization of G protein-coupled receptors." [PMID:23911909]
is_a: GO:0005515 ! protein binding
[Term]
@@ -525281,7 +526086,7 @@ is_a: GO:0051602 ! response to electrical stimulus
id: GO:1990782
name: protein tyrosine kinase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with protein tyrosine kinase." [PMID:25499537]
+def: "Binding to protein tyrosine kinase." [PMID:25499537]
synonym: "tyrosine kinase binding" EXACT []
is_a: GO:0019901 ! protein kinase binding
@@ -525516,7 +526321,7 @@ is_obsolete: true
id: GO:1990808
name: F-bar domain binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an F-BAR domain of a protein, a domain of about 60 residues that occurs in a wide range of cytoskeletal proteins." [PMID:20603077]
+def: "Binding to an F-BAR domain of a protein, a domain of about 60 residues that occurs in a wide range of cytoskeletal proteins." [PMID:20603077]
is_a: GO:0019904 ! protein domain specific binding
[Term]
@@ -525566,9 +526371,10 @@ relationship: part_of GO:0051455 ! monopolar spindle attachment to meiosis I kin
id: GO:1990814
name: DNA/DNA annealing activity
namespace: molecular_function
-def: "A nucleic acid binding activity that brings together complementary sequences of ssDNA so that they pair by hydrogen bonds to form a double-stranded DNA." [PMID:25520186]
+def: "An activity that faciliates the formation of a complementary double-stranded DNA molecule." [PMID:22888405, PMID:25520186]
synonym: "DNA reannealing activity" EXACT []
-is_a: GO:0097617 ! annealing activity
+is_a: GO:0003697 ! single-stranded DNA binding
+is_a: GO:0140666 ! annealing activity
[Term]
id: GO:1990815
@@ -525599,8 +526405,11 @@ id: GO:1990818
name: L-arginine transmembrane export from vacuole
namespace: biological_process
def: "The directed movement of L-arginine out of the vacuole, across the vacuolar membrane." [PMID:26083598]
+is_a: GO:0015807 ! L-amino acid transport
is_a: GO:0032974 ! amino acid transmembrane export from vacuole
-is_a: GO:1903400 ! L-arginine transmembrane transport
+is_a: GO:0098655 ! cation transmembrane transport
+is_a: GO:0098656 ! anion transmembrane transport
+is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
[Term]
id: GO:1990819
@@ -525650,7 +526459,7 @@ is_obsolete: true
id: GO:1990825
name: sequence-specific mRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with messenger RNA (mRNA) of a specific nucleotide composition or a specific sequence motif." [PMID:11886857]
+def: "Binding to messenger RNA (mRNA) of a specific nucleotide composition or a specific sequence motif." [PMID:11886857]
is_a: GO:0003729 ! mRNA binding
[Term]
@@ -525658,6 +526467,7 @@ id: GO:1990826
name: nucleoplasmic periphery of the nuclear pore complex
namespace: cellular_component
def: "Nucleoplasm situated in close proximity and peripheral to a nuclear pore complex." [PMID:10633080]
+synonym: "associated with the nuclear pore" RELATED [GOC:mah]
is_a: GO:0110165 ! cellular anatomical entity
relationship: part_of GO:0005654 ! nucleoplasm
@@ -525665,7 +526475,7 @@ relationship: part_of GO:0005654 ! nucleoplasm
id: GO:1990827
name: deaminase binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with an enzyme that catalyzes the removal of an amino group from a substrate, producing ammonia (NH3)." [PMID:9792439]
+def: "Binding to an enzyme that catalyzes the removal of an amino group from a substrate, producing ammonia (NH3)." [PMID:9792439]
is_a: GO:0019899 ! enzyme binding
[Term]
@@ -525679,7 +526489,7 @@ is_a: GO:0043697 ! cell dedifferentiation
id: GO:1990829
name: C-rich single-stranded DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with C-rich, single-stranded DNA." [PMID:8127654]
+def: "Binding to C-rich, single-stranded DNA." [PMID:8127654]
synonym: "C-rich ssDNA binding" EXACT []
is_a: GO:0003697 ! single-stranded DNA binding
@@ -525713,7 +526523,7 @@ id: GO:1990833
name: clathrin-uncoating ATPase activity
namespace: molecular_function
def: "Catalysis of the reaction: ATP + H2O = ADP + phosphate. Catalysis of the removal of clathrin from vesicle membranes, coupled to the hydrolysis of ATP." [PMID:6146630, PMID:8363588]
-is_a: GO:0016887 ! ATPase
+is_a: GO:0140657 ! ATP-dependent activity
[Term]
id: GO:1990834
@@ -525743,7 +526553,7 @@ relationship: part_of GO:0043202 ! lysosomal lumen
id: GO:1990837
name: sequence-specific double-stranded DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with double-stranded DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA, e.g. promotor binding or rDNA binding." [GOC:dos, GOC:sl]
+def: "Binding to double-stranded DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA, e.g. promotor binding or rDNA binding." [GOC:dos, GOC:sl]
synonym: "sequence-specific dsDNA binding" EXACT []
is_a: GO:0003690 ! double-stranded DNA binding
is_a: GO:0043565 ! sequence-specific DNA binding
@@ -525774,7 +526584,7 @@ is_a: GO:0009607 ! response to biotic stimulus
id: GO:1990841
name: promoter-specific chromatin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a section of chromatin that is associated with gene promoter sequences of DNA." [PMID:19948729]
+def: "Binding to a section of chromatin that is associated with gene promoter sequences of DNA." [PMID:19948729]
is_a: GO:0003682 ! chromatin binding
[Term]
@@ -525840,14 +526650,14 @@ is_obsolete: true
[Term]
id: GO:1990849
-name: maintenance of vacuolar location
+name: vacuolar localization
namespace: biological_process
-def: "Any process in which the vacuole is maintained in a specific location within a cell and prevented from moving elsewhere." [PMID:26283797]
+def: "Any process in which the vacuole is transported to, and/or maintained in, a specific location within the cell." [PMID:26283797]
synonym: "maintenance of vacuolar localization" EXACT []
+synonym: "maintenance of vacuolar location" NARROW []
synonym: "maintenance of vacuole localization" EXACT []
synonym: "maintenance of vacuole location" EXACT []
is_a: GO:0051640 ! organelle localization
-is_a: GO:0051657 ! maintenance of organelle location
[Term]
id: GO:1990850
@@ -525902,7 +526712,7 @@ synonym: "vacuole-ER attachment" EXACT []
is_a: GO:0016043 ! cellular component organization
is_a: GO:0051685 ! maintenance of ER location
is_a: GO:0140056 ! organelle localization by membrane tethering
-is_a: GO:1990849 ! maintenance of vacuolar location
+is_a: GO:1990849 ! vacuolar localization
[Term]
id: GO:1990855
@@ -525916,7 +526726,7 @@ is_obsolete: true
id: GO:1990856
name: methionyl-initiator methionine tRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with methionine-initator methionine tRNA." [GOC:hjd, ISBN:9781555810733]
+def: "Binding to methionine-initator methionine tRNA." [GOC:hjd, ISBN:9781555810733]
comment: An example of this is eukaryotic initiation factor 2 complex, which binds the methionyl-initiator methionine tRNA during ternary complex formation. The non-acylated tRNA is not bound.
is_a: GO:0000049 ! tRNA binding
@@ -526186,7 +526996,7 @@ is_a: GO:0009451 ! RNA modification
id: GO:1990885
name: obsolete protein serine/threonine kinase binding
namespace: molecular_function
-def: "OBSOLETE. Interacting selectively and non-covalently with a protein serine/threonine kinase." [PMID:16982699]
+def: "OBSOLETE. Binding to a protein serine/threonine kinase." [PMID:16982699]
comment: This term was obsoleted at the TermGenie Gatekeeper stage.
is_obsolete: true
@@ -526208,14 +527018,14 @@ is_a: GO:0008171 ! O-methyltransferase activity
id: GO:1990889
name: H4K20me3 modified histone binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a histone H4 in which the lysine residue at position 20 has been modified by trimethylation." [PMID:22150589]
+def: "Binding to a histone H4 in which the lysine residue at position 20 has been modified by trimethylation." [PMID:22150589]
is_a: GO:0035064 ! methylated histone binding
[Term]
id: GO:1990890
name: netrin receptor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a netrin receptor." [GOC:kmv, PMID:8861902, PMID:9126742]
+def: "Binding to a netrin receptor." [GOC:kmv, PMID:8861902, PMID:9126742]
is_a: GO:0005102 ! signaling receptor binding
[Term]
@@ -526332,7 +527142,6 @@ subset: goslim_pir
synonym: "extracellular ribonucleoprotein complex" NARROW []
synonym: "intracellular ribonucleoprotein complex" NARROW []
synonym: "protein-RNA complex" EXACT []
-synonym: "ribonucleoprotein complex" EXACT []
synonym: "RNA-protein complex" EXACT []
synonym: "RNP" EXACT []
xref: Wikipedia:Ribonucleoprotein
@@ -526474,7 +527283,6 @@ name: proteasome localization to nuclear periphery
namespace: biological_process
def: "Any process in which the proteasome is transported to, or maintained at the nuclear periphery." [PMID:11084332]
is_a: GO:0031144 ! proteasome localization
-is_a: GO:1990139 ! protein localization to nuclear periphery
[Term]
id: GO:1990921
@@ -526543,23 +527351,32 @@ is_a: GO:0016798 ! hydrolase activity, acting on glycosyl bonds
[Term]
id: GO:1990930
-name: RNA N1-methyladenosine dioxygenase activity
+name: mRNA N1-methyladenosine dioxygenase activity
namespace: molecular_function
def: "Catalysis of the oxidative demethylation of N1-methyladenosine RNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N1-methyladenosine as formaldehyde." [PMID:26863196, PMID:26863410]
+synonym: "RNA N(1)-methyladenosine dioxygenase activity" RELATED []
+synonym: "RNA N1-methyladenosine dioxygenase activity" RELATED []
+xref: EC:1.14.11.54
+xref: RHEA:49516
is_a: GO:0035515 ! oxidative RNA demethylase activity
[Term]
id: GO:1990931
-name: RNA N6-methyladenosine dioxygenase activity
+name: mRNA N6-methyladenosine dioxygenase activity
namespace: molecular_function
def: "Catalysis of the oxidative demethylation of N6-methyladenosine RNA, with concomitant decarboxylation of 2-oxoglutarate and releases oxidized methyl group on N6-methyladenosine as formaldehyde." [PMID:22002720, PMID:26458103]
+synonym: "mRNA N(6)-methyladenine demethylase" EXACT []
+synonym: "mRNA N(6)-methyladenosine dioxygenase activity" EXACT []
+synonym: "RNA N6-methyladenosine dioxygenase activity" RELATED []
+xref: EC:1.14.11.53
+xref: RHEA:49520
is_a: GO:0035515 ! oxidative RNA demethylase activity
[Term]
id: GO:1990932
name: 5.8S rRNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with 5.8S ribosomal RNA, a eukaryotic ribosomal RNA which forms a complex with 28S RNA." [PMID:11716358, PMID:15527424]
+def: "Binding to 5.8S ribosomal RNA, a eukaryotic ribosomal RNA which forms a complex with 28S RNA." [PMID:11716358, PMID:15527424]
is_a: GO:0019843 ! rRNA binding
[Term]
@@ -526576,7 +527393,6 @@ namespace: cellular_component
def: "A nuclear compartment containing significant amounts of non-nucleolar, spliceosomal components. It is commonly found in germinal vesicle (GV) stage oocytes, and is similar to both nucleoli and sphere organelles." [PMID:26226217, PMID:9021878]
synonym: "compact nucleolus" EXACT []
synonym: "NLB" EXACT []
-synonym: "nucleolus-like body" EXACT []
is_a: GO:0043232 ! intracellular non-membrane-bounded organelle
relationship: part_of GO:0031981 ! nuclear lumen
@@ -526584,7 +527400,7 @@ relationship: part_of GO:0031981 ! nuclear lumen
id: GO:1990935
name: splicing factor binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with any protein involved in the process of removing sections of the primary RNA transcript to form the mature form of the RNA." [PMID:11118435]
+def: "Binding to a protein involved in the process of removing sections of the primary RNA transcript to form the mature form of the RNA." [PMID:11118435]
is_a: GO:0005515 ! protein binding
[Term]
@@ -526613,15 +527429,6 @@ synonym: "peptidyl-aspartate autophosphorylation" EXACT [GOC:bf]
is_a: GO:0018217 ! peptidyl-aspartic acid phosphorylation
is_a: GO:0046777 ! protein autophosphorylation
-[Term]
-id: GO:1990939
-name: ATP-dependent microtubule motor activity
-namespace: molecular_function
-def: "Catalysis of movement along a microtubule, coupled to the hydrolysis of ATP." [PMID:19686686]
-xref: Reactome:R-HSA-9610627 "KIF17 transports GluN1:GluN2B (GRIN1:GRIN2B) NMDA receptors to the plasma membrane"
-is_a: GO:0003777 ! microtubule motor activity
-is_a: GO:0016887 ! ATPase
-
[Term]
id: GO:1990940
name: obsolete microtubule sliding involved in mitotic spindle elongation
@@ -526659,7 +527466,7 @@ relationship: part_of GO:0007080 ! mitotic metaphase plate congression
id: GO:1990943
name: mating type region replication fork barrier binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with the replication fork barrier found in the mating type region of fission yeast." [PMID:18723894]
+def: "Binding to the replication fork barrier found in the mating type region of fission yeast." [PMID:18723894]
synonym: "RTS1 barrier binding" EXACT []
synonym: "RTS1 element binding" EXACT []
is_a: GO:0031634 ! replication fork barrier binding
@@ -526742,7 +527549,7 @@ relationship: part_of GO:0007286 ! spermatid development
id: GO:1990955
name: G-rich single-stranded DNA binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with G-rich, single-stranded DNA." [GOC:hjd, PMID:8493094]
+def: "Binding to G-rich, single-stranded DNA." [GOC:hjd, PMID:8493094]
is_a: GO:0003697 ! single-stranded DNA binding
[Term]
@@ -526798,7 +527605,7 @@ name: xenobiotic detoxification by transmembrane export across the plasma membra
namespace: biological_process
def: "A process that reduces or removes the toxicity of a xenobiotic by exporting it outside the cell." [PMID:28355133]
synonym: "drug transmembrane export" NARROW []
-is_a: GO:0042908 ! xenobiotic transport
+is_a: GO:0046618 ! xenobiotic export
is_a: GO:0140115 ! export across plasma membrane
relationship: part_of GO:0098754 ! detoxification
@@ -526872,13 +527679,13 @@ namespace: biological_process
def: "A process in which a host organism modulates the frequency, rate or extent of the activity of a viral RNA-binding transcription factor." [GOC:bf, GOC:PARL, PMID:25116364]
synonym: "modulation by host of viral Tat activity" NARROW [PMID:25116364]
is_a: GO:0043921 ! modulation by host of viral transcription
-is_a: GO:0052428 ! modulation by host of symbiont molecular function
+is_a: GO:0052422 ! modulation by host of symbiont catalytic activity
[Term]
id: GO:1990970
name: trans-activation response element binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with a trans-activation response (TAR) element, a hairpin RNA structure located at the 5' end of all HIV-1 transcripts, and which is required for trans-activation of a viral promoter." [GOC:bf, GOC:PARL, PMID:25116364, Wikipedia:Trans-activation_response_element_(TAR)]
+def: "Binding to a trans-activation response (TAR) element, a hairpin RNA structure located at the 5' end of all HIV-1 transcripts, and which is required for trans-activation of a viral promoter." [GOC:bf, GOC:PARL, PMID:25116364, Wikipedia:Trans-activation_response_element_(TAR)]
synonym: "TAR binding" EXACT [PMID:25116364]
is_a: GO:0070883 ! pre-miRNA binding
@@ -527018,7 +527825,6 @@ namespace: biological_process
def: "The disaggregation of a DNA recombinase complex into its constituent strand exchange proteins (recombinases)." [GOC:pg, PMID:19540122]
synonym: "Rad51 nucleoprotein filament disassembly" RELATED []
is_a: GO:0032986 ! protein-DNA complex disassembly
-is_a: GO:0043624 ! cellular protein complex disassembly
[Term]
id: GO:2000001
@@ -527093,7 +527899,8 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of protein localization to the cell surface." [GOC:obol]
synonym: "regulation of protein localisation at cell surface" EXACT [GOC:mah]
synonym: "regulation of protein localization at cell surface" EXACT []
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0032880 ! regulation of protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0034394 ! protein localization to cell surface
[Term]
@@ -527103,7 +527910,8 @@ namespace: biological_process
def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to the cell surface." [GOC:obol]
synonym: "negative regulation of protein localisation at cell surface" EXACT [GOC:mah]
synonym: "negative regulation of protein localization at cell surface" EXACT []
-is_a: GO:1903828 ! negative regulation of cellular protein localization
+is_a: GO:0048523 ! negative regulation of cellular process
+is_a: GO:1903828 ! negative regulation of protein localization
is_a: GO:2000008 ! regulation of protein localization to cell surface
relationship: negatively_regulates GO:0034394 ! protein localization to cell surface
@@ -527114,7 +527922,8 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of protein localization to the cell surface." [GOC:obol]
synonym: "positive regulation of protein localisation at cell surface" EXACT [GOC:mah]
synonym: "positive regulation of protein localization at cell surface" EXACT []
-is_a: GO:1903829 ! positive regulation of cellular protein localization
+is_a: GO:0048522 ! positive regulation of cellular process
+is_a: GO:1903829 ! positive regulation of protein localization
is_a: GO:2000008 ! regulation of protein localization to cell surface
relationship: positively_regulates GO:0034394 ! protein localization to cell surface
@@ -527737,7 +528546,6 @@ synonym: "regulation of physiological defense response to insect" EXACT [GOC:obo
is_a: GO:0002831 ! regulation of response to biotic stimulus
is_a: GO:0031347 ! regulation of defense response
is_a: GO:0032101 ! regulation of response to external stimulus
-is_a: GO:0050776 ! regulation of immune response
relationship: regulates GO:0002213 ! defense response to insect
[Term]
@@ -530099,6 +530907,7 @@ id: GO:2000292
name: regulation of defecation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of defecation." [GOC:obol]
+is_a: GO:0044058 ! regulation of digestive system process
is_a: GO:0044062 ! regulation of excretion
relationship: regulates GO:0030421 ! defecation
@@ -530108,7 +530917,7 @@ name: negative regulation of defecation
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of defecation." [GOC:obol]
is_a: GO:0051048 ! negative regulation of secretion
-is_a: GO:0051241 ! negative regulation of multicellular organismal process
+is_a: GO:0060457 ! negative regulation of digestive system process
is_a: GO:2000292 ! regulation of defecation
relationship: negatively_regulates GO:0030421 ! defecation
@@ -530118,7 +530927,7 @@ name: positive regulation of defecation
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of defecation." [GOC:obol]
is_a: GO:0051047 ! positive regulation of secretion
-is_a: GO:0051240 ! positive regulation of multicellular organismal process
+is_a: GO:0060456 ! positive regulation of digestive system process
is_a: GO:2000292 ! regulation of defecation
relationship: positively_regulates GO:0030421 ! defecation
@@ -530951,7 +531760,6 @@ name: regulation of clathrin-dependent endocytosis
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of clathrin-mediated endocytosis." [GOC:mah]
synonym: "regulation of clathrin coated pit-dependent endocytosis" EXACT [GOC:obol]
-synonym: "regulation of clathrin-dependent endocytosis" EXACT [GOC:obol]
synonym: "regulation of clathrin-mediated endocytosis" EXACT []
is_a: GO:0048259 ! regulation of receptor-mediated endocytosis
relationship: regulates GO:0072583 ! clathrin-dependent endocytosis
@@ -530962,7 +531770,6 @@ name: positive regulation of clathrin-dependent endocytosis
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of clathrin-mediated endocytosis." [GOC:BHF, GOC:mah]
synonym: "positive regulation of clathrin coated pit-dependent endocytosis" EXACT [GOC:obol]
-synonym: "positive regulation of clathrin-dependent endocytosis" EXACT [GOC:obol]
synonym: "positive regulation of clathrin-mediated endocytosis" EXACT []
is_a: GO:0048260 ! positive regulation of receptor-mediated endocytosis
is_a: GO:2000369 ! regulation of clathrin-dependent endocytosis
@@ -530983,7 +531790,7 @@ synonym: "regulation of topoisomerase" RELATED [GOC:obol]
synonym: "regulation of topoisomerase II" EXACT [GOC:obol]
synonym: "regulation of type II DNA topoisomerase activity" EXACT [GOC:obol]
is_a: GO:0010911 ! regulation of isomerase activity
-is_a: GO:0043462 ! regulation of ATPase activity
+is_a: GO:0043462 ! regulation of ATP-dependent activity
[Term]
id: GO:2000372
@@ -530999,7 +531806,7 @@ synonym: "negative regulation of DNA topoisomerase type II activity" EXACT [GOC:
synonym: "negative regulation of topoisomerase" RELATED [GOC:obol]
synonym: "negative regulation of topoisomerase II" EXACT [GOC:obol]
synonym: "negative regulation of type II DNA topoisomerase activity" EXACT [GOC:obol]
-is_a: GO:0032780 ! negative regulation of ATPase activity
+is_a: GO:0032780 ! negative regulation of ATP-dependent activity
is_a: GO:0043086 ! negative regulation of catalytic activity
is_a: GO:2000371 ! regulation of DNA topoisomerase (ATP-hydrolyzing) activity
@@ -531018,7 +531825,7 @@ synonym: "positive regulation of topoisomerase" RELATED [GOC:obol]
synonym: "positive regulation of topoisomerase II" EXACT [GOC:obol]
synonym: "positive regulation of type II DNA topoisomerase activity" EXACT [GOC:obol]
is_a: GO:0010912 ! positive regulation of isomerase activity
-is_a: GO:0032781 ! positive regulation of ATPase activity
+is_a: GO:0032781 ! positive regulation of ATP-dependent activity
is_a: GO:2000371 ! regulation of DNA topoisomerase (ATP-hydrolyzing) activity
[Term]
@@ -531236,7 +532043,7 @@ def: "Any process that modulates the frequency, rate or extent of ubiquitin-depe
synonym: "regulation of ubiquitin-mediated endocytosis" EXACT [GOC:obol]
is_a: GO:0030100 ! regulation of endocytosis
is_a: GO:0051223 ! regulation of protein transport
-is_a: GO:1903827 ! regulation of cellular protein localization
+is_a: GO:0060341 ! regulation of cellular localization
relationship: regulates GO:0070086 ! ubiquitin-dependent endocytosis
[Term]
@@ -531247,7 +532054,6 @@ def: "Any process that stops, prevents or reduces the frequency, rate or extent
synonym: "negative regulation of ubiquitin-mediated endocytosis" EXACT [GOC:obol]
is_a: GO:0045806 ! negative regulation of endocytosis
is_a: GO:0051224 ! negative regulation of protein transport
-is_a: GO:1903828 ! negative regulation of cellular protein localization
is_a: GO:2000395 ! regulation of ubiquitin-dependent endocytosis
relationship: negatively_regulates GO:0070086 ! ubiquitin-dependent endocytosis
@@ -531259,7 +532065,6 @@ def: "Any process that activates or increases the frequency, rate or extent of u
synonym: "positive regulation of ubiquitin-mediated endocytosis" EXACT [GOC:obol]
is_a: GO:0045807 ! positive regulation of endocytosis
is_a: GO:0051222 ! positive regulation of protein transport
-is_a: GO:1903829 ! positive regulation of cellular protein localization
is_a: GO:2000395 ! regulation of ubiquitin-dependent endocytosis
relationship: positively_regulates GO:0070086 ! ubiquitin-dependent endocytosis
@@ -533041,117 +533846,129 @@ relationship: positively_regulates GO:0071897 ! DNA biosynthetic process
[Term]
id: GO:2000574
-name: regulation of microtubule motor activity
+name: obsolete regulation of microtubule motor activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of microtubule motor activity." [GOC:kmv]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of microtubule motor activity." [GOC:kmv]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of axonemal motor activity" RELATED [GOC:obol]
synonym: "regulation of dynein" RELATED [GOC:obol]
synonym: "regulation of dynein ATPase activity" RELATED [GOC:obol]
synonym: "regulation of kinesin" RELATED [GOC:obol]
synonym: "regulation of kinesin motor activity" RELATED [GOC:obol]
synonym: "regulation of kinetochore motor activity" RELATED [GOC:obol]
-is_a: GO:0051336 ! regulation of hydrolase activity
+is_obsolete: true
+consider: GO:0140659
[Term]
id: GO:2000575
-name: negative regulation of microtubule motor activity
+name: obsolete negative regulation of microtubule motor activity
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of microtubule motor activity." [GOC:kmv]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of microtubule motor activity." [GOC:kmv]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "negative regulation of axonemal motor activity" RELATED [GOC:obol]
synonym: "negative regulation of dynein" RELATED [GOC:obol]
synonym: "negative regulation of dynein ATPase activity" RELATED [GOC:obol]
synonym: "negative regulation of kinesin" RELATED [GOC:obol]
synonym: "negative regulation of kinesin motor activity" RELATED [GOC:obol]
synonym: "negative regulation of kinetochore motor activity" RELATED [GOC:obol]
-is_a: GO:0051346 ! negative regulation of hydrolase activity
-is_a: GO:2000574 ! regulation of microtubule motor activity
+is_obsolete: true
+consider: GO:0140661
[Term]
id: GO:2000576
-name: positive regulation of microtubule motor activity
+name: obsolete positive regulation of microtubule motor activity
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of microtubule motor activity." [GOC:kmv]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of microtubule motor activity." [GOC:kmv]
+comment: This term was obsoleted because it represents a molecular function.
synonym: "positive regulation of axonemal motor activity" RELATED [GOC:obol]
synonym: "positive regulation of dynein" RELATED [GOC:obol]
synonym: "positive regulation of dynein ATPase activity" RELATED [GOC:obol]
synonym: "positive regulation of kinesin" RELATED [GOC:obol]
synonym: "positive regulation of kinesin motor activity" RELATED [GOC:obol]
synonym: "positive regulation of kinetochore motor activity" RELATED [GOC:obol]
-is_a: GO:0051345 ! positive regulation of hydrolase activity
-is_a: GO:2000574 ! regulation of microtubule motor activity
+is_obsolete: true
+consider: GO:0140660
[Term]
id: GO:2000577
-name: regulation of ATP-dependent microtubule motor activity, minus-end-directed
+name: obsolete regulation of microtubule motor activity, minus-end-directed
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of ATP-dependent microtubule motor activity, minus-end-directed." [GOC:kmv, GOC:vw]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of ATP-dependent microtubule motor activity, minus-end-directed." [GOC:kmv, GOC:vw]
+comment: This term was obsoleted because it represents a molecular function.
+synonym: "regulation of ATP-dependent microtubule motor activity, minus-end-directed" EXACT []
synonym: "regulation of kinesin ATP phosphohydrolase (minus-end-directed)" EXACT [GOC:obol]
synonym: "regulation of minus-end-directed kinesin ATPase activity" RELATED [GOC:obol]
synonym: "regulation of minus-end-directed microtubule motor activity" BROAD []
-is_a: GO:0043462 ! regulation of ATPase activity
-is_a: GO:2000574 ! regulation of microtubule motor activity
+is_obsolete: true
+consider: GO:0140659
[Term]
id: GO:2000578
-name: negative regulation of ATP-dependent microtubule motor activity, minus-end-directed
+name: obsolete negative regulation of microtubule motor activity, minus-end-directed
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of ATP-dependent microtubule motor activity, minus-end-directed." [GOC:kmv, GOC:vw]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of ATP-dependent microtubule motor activity, minus-end-directed." [GOC:kmv, GOC:vw]
+comment: This term was obsoleted because it represents a molecular function.
+synonym: "negative regulation of ATP-dependent microtubule motor activity, minus-end-directed" EXACT []
synonym: "negative regulation of kinesin ATP phosphohydrolase (minus-end-directed)" EXACT [GOC:obol]
synonym: "negative regulation of minus-end-directed kinesin ATPase activity" EXACT [GOC:obol]
synonym: "negative regulation of minus-end-directed microtubule motor activity" BROAD []
-is_a: GO:0032780 ! negative regulation of ATPase activity
-is_a: GO:2000575 ! negative regulation of microtubule motor activity
-is_a: GO:2000577 ! regulation of ATP-dependent microtubule motor activity, minus-end-directed
+is_obsolete: true
+consider: GO:0140661
[Term]
id: GO:2000579
-name: positive regulation of ATP-dependent microtubule motor activity, minus-end-directed
+name: obsolete positive regulation of microtubule motor activity, minus-end-directed
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of ATP-dependent microtubule motor activity, minus-end-directed." [GOC:kmv, GOC:vw]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of ATP-dependent microtubule motor activity, minus-end-directed." [GOC:kmv, GOC:vw]
+comment: This term was obsoleted because it represents a molecular function.
+synonym: "positive regulation of ATP-dependent microtubule motor activity, minus-end-directed" EXACT []
synonym: "positive regulation of kinesin ATP phosphohydrolase (minus-end-directed)" EXACT [GOC:obol]
synonym: "positive regulation of minus-end-directed kinesin ATPase activity" EXACT [GOC:obol]
synonym: "positive regulation of minus-end-directed microtubule motor activity" BROAD []
-is_a: GO:0032781 ! positive regulation of ATPase activity
-is_a: GO:2000576 ! positive regulation of microtubule motor activity
-is_a: GO:2000577 ! regulation of ATP-dependent microtubule motor activity, minus-end-directed
+is_obsolete: true
+consider: GO:0140660
[Term]
id: GO:2000580
-name: regulation of ATP-dependent microtubule motor activity, plus-end-directed
+name: obsolete regulation of microtubule motor activity, plus-end-directed
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of ATP-dependent microtubule motor activity, plus-end-directed." [GOC:kmv, GOC:vw]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of ATP-dependent microtubule motor activity, plus-end-directed." [GOC:kmv, GOC:vw]
+comment: This term was obsoleted because it represents a molecular function.
+synonym: "regulation of ATP-dependent microtubule motor activity, plus-end-directed" EXACT []
synonym: "regulation of kinesin activity" RELATED [GOC:obol]
synonym: "regulation of kinesin ATP phosphohydrolase (plus-end-directed)" EXACT [GOC:obol]
synonym: "regulation of plus-end-directed kinesin ATPase activity" EXACT [GOC:obol]
synonym: "regulation of plus-end-directed microtubule motor activity" BROAD []
-is_a: GO:0043462 ! regulation of ATPase activity
-is_a: GO:2000574 ! regulation of microtubule motor activity
+is_obsolete: true
+consider: GO:0140659
[Term]
id: GO:2000581
-name: negative regulation of ATP-dependent microtubule motor activity, plus-end-directed
+name: obsolete negative regulation of microtubule motor activity, plus-end-directed
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of ATP-dependent microtubule motor activity, plus-end-directed." [GOC:kmv, GOC:vw]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of ATP-dependent microtubule motor activity, plus-end-directed." [GOC:kmv, GOC:vw]
+comment: This term was obsoleted because it represents a molecular function.
+synonym: "negative regulation of ATP-dependent microtubule motor activity, plus-end-directed" EXACT []
synonym: "negative regulation of kinesin activity" RELATED [GOC:obol]
synonym: "negative regulation of kinesin ATP phosphohydrolase (plus-end-directed)" EXACT [GOC:obol]
synonym: "negative regulation of plus-end-directed kinesin ATPase activity" EXACT [GOC:obol]
synonym: "negative regulation of plus-end-directed microtubule motor activity" BROAD []
-is_a: GO:0032780 ! negative regulation of ATPase activity
-is_a: GO:2000575 ! negative regulation of microtubule motor activity
-is_a: GO:2000580 ! regulation of ATP-dependent microtubule motor activity, plus-end-directed
+is_obsolete: true
+consider: GO:0140661
[Term]
id: GO:2000582
-name: positive regulation of ATP-dependent microtubule motor activity, plus-end-directed
+name: obsolete positive regulation of microtubule motor activity, plus-end-directed
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of ATP-dependent microtubule motor activity, plus-end-directed." [GOC:kmv, GOC:vw]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of ATP-dependent microtubule motor activity, plus-end-directed." [GOC:kmv, GOC:vw]
+comment: This term was obsoleted because it represents a molecular function.
+synonym: "positive regulation of ATP-dependent microtubule motor activity, plus-end-directed" EXACT []
synonym: "positive regulation of kinesin activity" RELATED [GOC:obol]
synonym: "positive regulation of kinesin ATP phosphohydrolase (plus-end-directed)" EXACT [GOC:obol]
synonym: "positive regulation of plus-end-directed kinesin ATPase activity" EXACT [GOC:obol]
synonym: "positive regulation of plus-end-directed microtubule motor activity" BROAD []
-is_a: GO:0032781 ! positive regulation of ATPase activity
-is_a: GO:2000576 ! positive regulation of microtubule motor activity
-is_a: GO:2000580 ! regulation of ATP-dependent microtubule motor activity, plus-end-directed
+is_obsolete: true
+consider: GO:0140660
[Term]
id: GO:2000583
@@ -533637,7 +534454,7 @@ name: regulation of pre-miRNA processing
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of pre-microRNA processing." [GOC:dph, GOC:sl]
synonym: "regulation of pre-microRNA processing" EXACT []
-is_a: GO:1903798 ! regulation of production of miRNAs involved in gene silencing by miRNA
+is_a: GO:0051252 ! regulation of RNA metabolic process
relationship: regulates GO:0031054 ! pre-miRNA processing
[Term]
@@ -533646,7 +534463,7 @@ name: negative regulation of pre-miRNA processing
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of pre-microRNA processing." [GOC:dph, GOC:sl]
synonym: "negative regulation of pre-microRNA processing" EXACT [GOC:obol]
-is_a: GO:1903799 ! negative regulation of production of miRNAs involved in gene silencing by miRNA
+is_a: GO:0051253 ! negative regulation of RNA metabolic process
is_a: GO:2000631 ! regulation of pre-miRNA processing
relationship: negatively_regulates GO:0031054 ! pre-miRNA processing
@@ -533667,7 +534484,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl]
synonym: "regulation of pri-miRNA processing" EXACT [GOC:obol]
synonym: "regulation of primary microRNA processing" EXACT [GOC:obol]
-is_a: GO:1903798 ! regulation of production of miRNAs involved in gene silencing by miRNA
+is_a: GO:0051252 ! regulation of RNA metabolic process
relationship: regulates GO:0031053 ! primary miRNA processing
[Term]
@@ -533677,7 +534494,7 @@ namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl]
synonym: "negative regulation of pri-miRNA processing" EXACT [GOC:obol]
synonym: "negative regulation of primary microRNA processing" EXACT [GOC:obol]
-is_a: GO:1903799 ! negative regulation of production of miRNAs involved in gene silencing by miRNA
+is_a: GO:0051253 ! negative regulation of RNA metabolic process
is_a: GO:2000634 ! regulation of primary miRNA processing
relationship: negatively_regulates GO:0031053 ! primary miRNA processing
@@ -533688,7 +534505,7 @@ namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of primary microRNA processing." [GOC:dph, GOC:sl]
synonym: "positive regulation of pri-miRNA processing" EXACT [GOC:obol]
synonym: "positive regulation of primary microRNA processing" EXACT [GOC:obol]
-is_a: GO:1903800 ! positive regulation of production of miRNAs involved in gene silencing by miRNA
+is_a: GO:0051254 ! positive regulation of RNA metabolic process
is_a: GO:2000634 ! regulation of primary miRNA processing
relationship: positively_regulates GO:0031053 ! primary miRNA processing
@@ -533870,9 +534687,8 @@ name: regulation of genetic imprinting
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of genetic imprinting." [GOC:BHF]
synonym: "regulation of DNA imprinting" EXACT [GOC:obol]
-is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process
-is_a: GO:0060255 ! regulation of macromolecule metabolic process
-relationship: regulates GO:0071514 ! genetic imprinting
+is_a: GO:0031445 ! regulation of heterochromatin assembly
+relationship: regulates GO:0071514 ! genomic imprinting
[Term]
id: GO:2000654
@@ -535178,14 +535994,13 @@ relationship: positively_regulates GO:0090398 ! cellular senescence
[Term]
id: GO:2000775
-name: histone H3-S10 phosphorylation involved in chromosome condensation
+name: obsolete histone H3-S10 phosphorylation involved in chromosome condensation
namespace: biological_process
-def: "Any histone H3-S10 phosphorylation that is involved in chromosome condensation." [GOC:obol]
+def: "OBSOLETE. Any histone H3-S10 phosphorylation that is involved in chromosome condensation." [GOC:obol]
+comment: This term was obsoleted because it is a molecular function represented as a biological process.
synonym: "histone H3 phosphorylation at S10 of chromosome condensation" EXACT [GOC:obol]
synonym: "histone H3-S10 phosphorylation of chromosome condensation" EXACT [GOC:obol]
-synonym: "histone H3S10 phosphorylation of chromosome condensation" EXACT [GOC:obol]
-is_a: GO:0043987 ! histone H3-S10 phosphorylation
-relationship: part_of GO:0030261 ! chromosome condensation
+is_obsolete: true
[Term]
id: GO:2000776
@@ -537842,7 +538657,7 @@ def: "Any process that modulates the frequency, rate or extent of response to dr
synonym: "regulation of drug resistance" RELATED [GOC:obol]
synonym: "regulation of drug susceptibility/resistance" RELATED [GOC:obol]
is_a: GO:0048583 ! regulation of response to stimulus
-relationship: regulates GO:0042493 ! response to drug
+relationship: regulates GO:0009410 ! response to xenobiotic stimulus
[Term]
id: GO:2001024
@@ -537853,7 +538668,7 @@ synonym: "negative regulation of drug resistance" RELATED [GOC:obol]
synonym: "negative regulation of drug susceptibility/resistance" RELATED [GOC:obol]
is_a: GO:0048585 ! negative regulation of response to stimulus
is_a: GO:2001023 ! regulation of response to drug
-relationship: negatively_regulates GO:0042493 ! response to drug
+relationship: negatively_regulates GO:0009410 ! response to xenobiotic stimulus
[Term]
id: GO:2001025
@@ -537864,7 +538679,7 @@ synonym: "positive regulation of drug resistance" RELATED [GOC:obol]
synonym: "positive regulation of drug susceptibility/resistance" RELATED [GOC:obol]
is_a: GO:0048584 ! positive regulation of response to stimulus
is_a: GO:2001023 ! regulation of response to drug
-relationship: positively_regulates GO:0042493 ! response to drug
+relationship: positively_regulates GO:0009410 ! response to xenobiotic stimulus
[Term]
id: GO:2001026
@@ -537998,7 +538813,7 @@ namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of cellular response to drug." [GOC:obol]
is_a: GO:0050794 ! regulation of cellular process
is_a: GO:2001023 ! regulation of response to drug
-relationship: regulates GO:0035690 ! cellular response to drug
+relationship: regulates GO:0071466 ! cellular response to xenobiotic stimulus
[Term]
id: GO:2001039
@@ -538008,7 +538823,7 @@ def: "Any process that stops, prevents or reduces the frequency, rate or extent
is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:2001024 ! negative regulation of response to drug
is_a: GO:2001038 ! regulation of cellular response to drug
-relationship: negatively_regulates GO:0035690 ! cellular response to drug
+relationship: negatively_regulates GO:0071466 ! cellular response to xenobiotic stimulus
[Term]
id: GO:2001040
@@ -538018,7 +538833,7 @@ def: "Any process that activates or increases the frequency, rate or extent of c
is_a: GO:0048522 ! positive regulation of cellular process
is_a: GO:2001025 ! positive regulation of response to drug
is_a: GO:2001038 ! regulation of cellular response to drug
-relationship: positively_regulates GO:0035690 ! cellular response to drug
+relationship: positively_regulates GO:0071466 ! cellular response to xenobiotic stimulus
[Term]
id: GO:2001042
@@ -538197,28 +539012,28 @@ is_a: GO:2001060 ! D-glycero-D-manno-heptose 7-phosphate metabolic process
id: GO:2001062
name: xylan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with xylan." [GOC:mengo_curators]
+def: "Binding to xylan." [GOC:mengo_curators]
is_a: GO:0030247 ! polysaccharide binding
[Term]
id: GO:2001063
name: glucomannan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with glucomannan." [GOC:mengo_curators]
+def: "Binding to glucomannan." [GOC:mengo_curators]
is_a: GO:0010297 ! heteropolysaccharide binding
[Term]
id: GO:2001064
name: cellooligosaccharide binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cellooligosaccharide." [GOC:mengo_curators]
+def: "Binding to cellooligosaccharide." [GOC:mengo_curators]
is_a: GO:0070492 ! oligosaccharide binding
[Term]
id: GO:2001065
name: mannan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with mannan." [GOC:mengo_curators]
+def: "Binding to mannan." [GOC:mengo_curators]
synonym: "mannoglycan binding" RELATED [GOC:obol]
is_a: GO:0030247 ! polysaccharide binding
@@ -538226,28 +539041,28 @@ is_a: GO:0030247 ! polysaccharide binding
id: GO:2001066
name: amylopectin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with amylopectin." [GOC:mengo_curators]
+def: "Binding to amylopectin." [GOC:mengo_curators]
is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
id: GO:2001067
name: pullulan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with pullulan." [GOC:mengo_curators]
+def: "Binding to pullulan." [GOC:mengo_curators]
is_a: GO:0030247 ! polysaccharide binding
[Term]
id: GO:2001068
name: arabinoxylan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with arabinoxylan." [GOC:mengo_curators]
+def: "Binding to arabinoxylan." [GOC:mengo_curators]
is_a: GO:2001062 ! xylan binding
[Term]
id: GO:2001069
name: glycogen binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with glycogen." [GOC:mengo_curators]
+def: "Binding to glycogen." [GOC:mengo_curators]
synonym: "animal starch binding" RELATED [GOC:obol]
synonym: "liver starch binding" RELATED [GOC:obol]
is_a: GO:0030247 ! polysaccharide binding
@@ -538256,7 +539071,7 @@ is_a: GO:0030247 ! polysaccharide binding
id: GO:2001070
name: starch binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with starch." [GOC:mengo_curators]
+def: "Binding to starch." [GOC:mengo_curators]
synonym: "amidon binding" RELATED [GOC:obol]
synonym: "amylum binding" RELATED [GOC:obol]
is_a: GO:0030247 ! polysaccharide binding
@@ -538265,21 +539080,21 @@ is_a: GO:0030247 ! polysaccharide binding
id: GO:2001071
name: maltoheptaose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with maltoheptaose." [GOC:mengo_curators]
+def: "Binding to maltoheptaose." [GOC:mengo_curators]
is_a: GO:0070492 ! oligosaccharide binding
[Term]
id: GO:2001072
name: galactomannan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with galactomannan." [GOC:mengo_curators]
+def: "Binding to galactomannan." [GOC:mengo_curators]
is_a: GO:0010297 ! heteropolysaccharide binding
[Term]
id: GO:2001073
name: cyclodextrin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with cyclodextrin." [GOC:mengo_curators]
+def: "Binding to cyclodextrin." [GOC:mengo_curators]
is_a: GO:0030247 ! polysaccharide binding
is_a: GO:0070492 ! oligosaccharide binding
@@ -538313,7 +539128,7 @@ relationship: positively_regulates GO:0035502 ! metanephric part of ureteric bud
id: GO:2001077
name: (1->3),(1->4)-beta-glucan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with (1->3),(1->4)-beta-glucan." [GOC:mengo_curators]
+def: "Binding to (1->3),(1->4)-beta-glucan." [GOC:mengo_curators]
synonym: "(1,3),(1,4)-beta-glucan binding" EXACT []
synonym: "1->3,1->4-beta-glucan binding" EXACT []
synonym: "beta-(1,3),(1,4)-glucan binding" EXACT []
@@ -538326,7 +539141,7 @@ is_a: GO:0030247 ! polysaccharide binding
id: GO:2001078
name: (1->6)-beta-D-glucan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with (1->6)-beta-D-glucan." [GOC:mengo_curators]
+def: "Binding to (1->6)-beta-D-glucan." [GOC:mengo_curators]
synonym: "(1,6)-beta-D-glucan binding" EXACT []
synonym: "1,6-beta-D-glucan binding" EXACT []
synonym: "1->6-beta-D-glucan binding" EXACT []
@@ -538340,21 +539155,21 @@ is_a: GO:0030247 ! polysaccharide binding
id: GO:2001079
name: beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc." [GOC:mengo_curators]
+def: "Binding to beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc." [GOC:mengo_curators]
is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
id: GO:2001080
name: chitosan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with chitosan." [GOC:mengo_curators]
+def: "Binding to chitosan." [GOC:mengo_curators]
is_a: GO:0097367 ! carbohydrate derivative binding
[Term]
id: GO:2001081
name: (1->4)-beta-D-galactan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with (1->4)-beta-D-galactan." [GOC:mengo_curators]
+def: "Binding to (1->4)-beta-D-galactan." [GOC:mengo_curators]
synonym: "(1,4)-beta-D-galactan binding" EXACT []
is_a: GO:0030247 ! polysaccharide binding
@@ -538362,28 +539177,28 @@ is_a: GO:0030247 ! polysaccharide binding
id: GO:2001082
name: inulin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with inulin." [GOC:mengo_curators]
+def: "Binding to inulin." [GOC:mengo_curators]
is_a: GO:0030247 ! polysaccharide binding
[Term]
id: GO:2001083
name: alpha-D-glucan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with alpha-D-glucan." [GOC:mengo_curators]
+def: "Binding to alpha-D-glucan." [GOC:mengo_curators]
is_a: GO:0030247 ! polysaccharide binding
[Term]
id: GO:2001084
name: L-arabinofuranose binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with L-arabinofuranose." [GOC:mengo_curators]
+def: "Binding to L-arabinofuranose." [GOC:mengo_curators]
is_a: GO:0048029 ! monosaccharide binding
[Term]
id: GO:2001085
name: arabinogalactan binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with arabinogalactan." [GOC:mengo_curators]
+def: "Binding to arabinogalactan." [GOC:mengo_curators]
is_a: GO:0030247 ! polysaccharide binding
[Term]
@@ -538902,7 +539717,7 @@ is_a: GO:2001144 ! regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phos
id: GO:2001147
name: camalexin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with camalexin." [GOC:obol]
+def: "Binding to camalexin." [GOC:obol]
synonym: "3-(1,3-thiazol-2-yl)-1H-indole binding" EXACT [GOC:obol]
is_a: GO:0097159 ! organic cyclic compound binding
is_a: GO:1901363 ! heterocyclic compound binding
@@ -539558,22 +540373,27 @@ relationship: positively_regulates GO:0001570 ! vasculogenesis
[Term]
id: GO:2001215
-name: regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity
+name: obsolete regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of hydroxymethylglutaryl-CoA reductase (NADPH) activity." [GOC:al]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of hydroxymethylglutaryl-CoA reductase (NADPH) activity." [GOC:al]
+comment: This term has been obsoleted because it represents a molecular function.
synonym: "regulation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase activity" RELATED [GOC:obol]
synonym: "regulation of HMG-CoA reductase activity" RELATED [GOC:obol]
-is_a: GO:0051341 ! regulation of oxidoreductase activity
+is_obsolete: true
+consider: GO:0030234
+consider: GO:0106107
[Term]
id: GO:2001216
-name: negative regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity
+name: obsolete negative regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of hydroxymethylglutaryl-CoA reductase (NADPH) activity." [GOC:al]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of hydroxymethylglutaryl-CoA reductase (NADPH) activity." [GOC:al]
+comment: This term has been obsoleted because it represents a molecular function.
synonym: "negative regulation of 3-hydroxy-3-methylglutaryl-coenzyme A reductase activity" RELATED [GOC:obol]
synonym: "negative regulation of HMG-CoA reductase activity" RELATED [GOC:obol]
-is_a: GO:0051354 ! negative regulation of oxidoreductase activity
-is_a: GO:2001215 ! regulation of hydroxymethylglutaryl-CoA reductase (NADPH) activity
+is_obsolete: true
+consider: GO:0004857
+consider: GO:0106108
[Term]
id: GO:2001217
@@ -539677,7 +540497,7 @@ relationship: negatively_regulates GO:0006821 ! chloride transport
id: GO:2001227
name: quercitrin binding
namespace: molecular_function
-def: "Interacting selectively and non-covalently with quercitrin." [GOC:obol]
+def: "Binding to quercitrin." [GOC:obol]
is_a: GO:0043168 ! anion binding
is_a: GO:0097243 ! flavonoid binding
is_a: GO:0097367 ! carbohydrate derivative binding
@@ -540395,8 +541215,6 @@ synonym: "2,3-Bis(beta-hydoroxymyristoyl)-beta-D-glucosaminyl 1-phosphate metabo
synonym: "2,3-Bis(beta-hydoroxymyristoyl)-beta-D-glucosaminyl 1-phosphate metabolism" RELATED [GOC:obol]
synonym: "2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose metabolic process" EXACT [GOC:obol]
synonym: "2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose metabolism" EXACT [GOC:obol]
-synonym: "Lipid X metabolic process" EXACT [GOC:obol]
-synonym: "Lipid X metabolism" EXACT [GOC:obol]
synonym: "lipid X metabolism" EXACT [GOC:obol]
is_a: GO:0006040 ! amino sugar metabolic process
is_a: GO:0006796 ! phosphate-containing compound metabolic process
@@ -540824,4 +541642,3 @@ namespace: external
xref: IAO:0000233
is_metadata_tag: true
is_class_level: true
-
diff --git a/dist/pantools.jar b/dist/pantools.jar
index 41e5e4bcf498d55b7ab637fd6d872283ad38d947..14f17f78f847a5a09374f8d031930651165e096d 100644
Binary files a/dist/pantools.jar and b/dist/pantools.jar differ
diff --git a/nbproject/private/private.xml b/nbproject/private/private.xml
index cb57780334cd51f51a56b664b1cd8eeb4782f8a2..700418731b56aa13278cdb2013ee3dc9f6ac3338 100755
--- a/nbproject/private/private.xml
+++ b/nbproject/private/private.xml
@@ -13,7 +13,8 @@
<open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
<group>
<file>file:/local/jonkh004/git_branch/pantools/src/pangenome/Classification.java</file>
- <file>file:/local/jonkh004/git_branch/pantools/src/pangenome/FunctionalAnnotations.java</file>
+ <file>file:/local/jonkh004/git_branch/pantools/src/pangenome/Phylogeny.java</file>
+ <file>file:/local/jonkh004/git_branch/pantools/src/pangenome/AnnotationLayer.java</file>
<file>file:/local/jonkh004/git_branch/pantools/src/pantools/Pantools.java</file>
</group>
</open-files>
diff --git a/src/pangenome/AnnotationLayer.java b/src/pangenome/AnnotationLayer.java
index 10d465dc3200e01a9053dd51ddf2a77f53962421..063d98b017a2e49c9a985651c73ad7579808e4af 100755
--- a/src/pangenome/AnnotationLayer.java
+++ b/src/pangenome/AnnotationLayer.java
@@ -35,7 +35,6 @@ import org.neo4j.graphdb.NotFoundException;
import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.ResourceIterator;
import org.neo4j.graphdb.Transaction;
-import static pangenome.Classification.annotation_overview;
import static pangenome.Classification.try_incr_hashmap;
import static pangenome.GenomeLayer.locate;
@@ -81,6 +80,7 @@ import static pantools.Pantools.stop_if_panproteome;
import static pantools.Pantools.pangenome_label;
import static pangenome.create_skip_arrays.create_skip_arrays;
import static pantools.Pantools.skip_array;
+import static pantools.Pantools.write_string_to_file_in_DB;
/**
* Implements all the functionalities related to the annotation layer of the pangenome
@@ -181,9 +181,17 @@ public class AnnotationLayer {
genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexDb.get_pre_len());
num_proteins = 0;
- try{
+ try (Transaction tx = graphDb.beginTx()) {
+ Node pangenome_node = graphDb.findNodes(pangenome_label).next();
+ stop_if_panproteome(pangenome_node, "add_annotations"); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
+ tx.success();
+ }
+
+ try {
BufferedReader paths = new BufferedReader(new FileReader(PATH_TO_THE_ANNOTATIONS_FILE));
- log_file = new BufferedWriter(new FileWriter(OUTPUT_PATH + "/log/annotation.log"));
+ log_file = new BufferedWriter(new FileWriter(OUTPUT_PATH + "/log/annotation.log", true)); // true allows to append the original instead of overwriting
+ String date = new SimpleDateFormat("dd-MM-yyyy HH:mm:ss").format(new Date());
+ log_file.write("## LOG of run on " + date + "\n");
if (! new File(OUTPUT_PATH + "/proteins").exists()) {
Files.createDirectory(Paths.get(OUTPUT_PATH + "/proteins"));
}
@@ -204,9 +212,9 @@ public class AnnotationLayer {
continue;
}
genome = Integer.parseInt(fields[0]);
- log_file.write("#Genome " + genome + "\n");
+ log_file.write("#Genome " + genome +".");
if (! new File(annotation_file).exists()) {
- log_file.write("Genome " + genome + "'s annotation file not found.");
+ log_file.write(" annotation file not found: " + annotation_file + "\n");
System.out.println("Genome " + genome + "'s annotation file not found.");
continue;
}
@@ -223,7 +231,9 @@ public class AnnotationLayer {
annotation_node.setProperty("genome", genome);
annotation_node.setProperty("number", degree);
annotation_node.setProperty("identifier", genome + "_" + degree);
- log_file.write("Used annotation file " + annotation_file + "\n");
+ log_file.write(" Annotation identifier: " + genome + "_" + degree + "\n"
+ + "Used annotation file " + annotation_file + "\n");
+
if (annotation_file.endsWith(".gff") || annotation_file.endsWith(".gff3")) {
//parse_gff(genome, genome + "_" + degree, log_file, annotation_file, OUTPUT_PATH + "/proteins", annotation_node);
annotation_node.setProperty("type", "GFF");
@@ -250,9 +260,9 @@ public class AnnotationLayer {
} else if (annotation_file.endsWith(".gbk") || annotation_file.endsWith(".gbff")) {
parse_gbk(genome, genome + "_" + degree, log_file, annotation_file, OUTPUT_PATH + "/proteins", annotation_node);
}
-
} // for genomes
paths.close();
+ log_file.write("\n");
log_file.close();
} catch (IOException ioe) {
System.out.println("Failed to open " + PATH_TO_THE_ANNOTATIONS_FILE);
@@ -263,17 +273,59 @@ public class AnnotationLayer {
Node pangenome_node = graphDb.findNodes(pangenome_label).next();
pangenome_node.removeProperty("num_proteins");
pangenome_node.setProperty("num_proteins", num_proteins);
- annotation_overview();
+ create_annotation_overview();
tx.success();
}
disconnect_pangenome();
System.out.println("\nAnnotated proteins available in:\n "
+ WORKING_DIRECTORY + "proteins/\n\n"
+ "Log output written to:\n "
- + WORKING_DIRECTORY + "log/annotation.log\n "
- + WORKING_DIRECTORY + "databases/genome.db/annotations.txt\n");
+ + WORKING_DIRECTORY + "annotation_overview.txt\n "
+ + WORKING_DIRECTORY + "log/annotation.log\n ");
}
-
+
+ /**
+ * Creates annotation_overview.txt, an overview of the .gff and .gbk files incorporated in the pangenome
+ */
+ public static void create_annotation_overview() {
+ int total_genomes = (int) graphDb.findNodes(pangenome_label).next().getProperty("num_genomes");
+ StringBuilder output_builder = new StringBuilder();
+ int annotation_count = 0;
+ for (int i = 1; i <= total_genomes; i++) {
+ StringBuilder genome_builder = new StringBuilder();
+ ResourceIterator<Node> annotation_nodes = graphDb.findNodes(annotation_label, "genome", i);
+ HashSet<String> id_set = new HashSet<>();
+ while (annotation_nodes.hasNext()) {
+ Node genome_node = annotation_nodes.next();
+ long genome_node_id = genome_node.getId();
+ String genome_path = (String) genome_node.getProperty("path");
+ String identifier = (String) genome_node.getProperty("identifier");
+ id_set.add(identifier);
+ String date = (String) genome_node.getProperty("date");
+ String type = (String) genome_node.getProperty("type");
+ genome_builder.append("\nAnnotation id: ").append(identifier)
+ .append("\nAnnotation file: ").append(genome_path)
+ .append("\nFiletype: ").append(type)
+ .append("\nStored in node: ").append(genome_node_id)
+ .append("\nCreation date ").append(date).append("\n");
+ annotation_count ++;
+ }
+ String ids = id_set.toString().replace("[","").replace("]","").replace(", ",",");
+ String total = "No annotations";
+ if (id_set.size() == 1) {
+ total = "1 annotation: ";
+ } else if (id_set.size() > 1) {
+ total = id_set.size() + " annotations: ";
+ }
+ output_builder.append("\n#Genome ").append(i).append("\n")
+ .append(total).append(ids).append("\n")
+ .append(genome_builder.toString());
+ }
+
+ String anno_str = "Total annotations included in the pangenome: " + annotation_count + "\n";
+ write_string_to_file_in_DB(anno_str + output_builder.toString(), "annotation_overview.txt");
+ }
+
/**
* Parses a GFF3 file and annotates the genomes at the same time.
*
@@ -818,7 +870,7 @@ public class AnnotationLayer {
continue;
}
if (first) {
- log_file.write("\nThe following mRNAs have the same identifier. This is caused by incorrect naming in your GFF file."
+ log_file.write("\nThe following mRNAs have the same identifier. This is caused by incorrect naming in your GFF file. "
+ "The 'protein_ID' property is incremented by an underscore and a number for the following mrna's/proteins: \n");
first = false;
}
diff --git a/src/pangenome/Classification.java b/src/pangenome/Classification.java
index add0c9253e94fc972a794be445b6b767f739c1d5..0709d60bdf894b1c3831591c9970a75bd3725014 100644
--- a/src/pangenome/Classification.java
+++ b/src/pangenome/Classification.java
@@ -1426,7 +1426,7 @@ public class Classification {
}
String prot_size_freq = determine_frequency_list_int(psize_list);
- if (SELECTED_LABEL != null) { // user has given --label that matches the mrna node
+ if (SELECTED_LABEL != null) { // user has given --label with a function identifier
check_function_output_matches(function_node_set, group_id, groups_with_function_or_name);
}
@@ -2375,7 +2375,7 @@ public class Classification {
/**
* The function id from GO, TIGRFAM, PFAM or InterPRO must exactly match one of the user input IDs
- * For phobius there are 3 user input options: 'secreted', 'transmembrane' and 'receptor'. These match the three different labels.
+ * For phobius/signalp there are 2 user input options: 'signal_peptide' and 'transmembrane'
*
* @param function_node_set
* @param hm_id_str
@@ -2476,7 +2476,7 @@ public class Classification {
if (mrna_node.hasProperty("phobius_signal_peptide")) {
String phobius_signalpep = (String) mrna_node.getProperty("phobius_signal_peptide");
- if (phobius_signalpep.equals("yes")){
+ if (phobius_signalpep.equals("yes")) {
function_set.add("Phobius_signal_peptide");
output_builder.append("Phobius signalpeptide, ");
function_node_set.add(mrna_node);
@@ -2639,12 +2639,12 @@ public class Classification {
boolean ignore_first = true;
for (String value : line_array) {
- if (ignore_first) {
+ if (ignore_first) { // is 'Genome'
ignore_first = false;
column ++;
continue;
}
- String trim_value = value.toLowerCase().trim();
+ String trim_value = value.trim();
if (existing_phenotypes.contains(trim_value)) {
already_present.add(trim_value);
} else {
@@ -2662,7 +2662,7 @@ public class Classification {
}
}
- if (line_array.length < 2){
+ if (line_array.length < 2) {
System.out.println("\rThe input file must have at least two columns. The first column must always be the genome numbers\n");
System.exit(1);
}
@@ -3687,7 +3687,7 @@ public class Classification {
header_builder.append(seq_name);
shared_pos_builder.append(seq_name).append(",");
distance_builder.append(seq_name).append(",");
- if (i != protein_id_list.size()-1){
+ if (i != protein_id_list.size()-1) {
header_builder.append(",");
}
for (int j=0; j < protein_id_list.size(); j++) {
@@ -3708,7 +3708,7 @@ public class Classification {
double distance = 1 - divide(shared_sites, total_sites);
shared_pos_builder.append(shared_sites);
distance_builder.append(fmt.format(distance));
- if (j != protein_id_list.size()-1){
+ if (j != protein_id_list.size()-1) {
distance_builder.append(",");
shared_pos_builder.append(",");
}
@@ -4531,7 +4531,8 @@ public class Classification {
}
/**
- * Stop PanTools when less than 3 genomes are included in the analysis
+ * Stop PanTools when less than ? genomes are included in the analysis
+ * @param genome_threshold minimum required genomes
*/
public static void stop_with_less_than_X_genomes(int genome_threshold) {
if (adj_total_genomes < genome_threshold) {
@@ -4554,7 +4555,7 @@ public class Classification {
int[][] all_core, all_accessory, all_unique;
create_directory_in_DB("pangenome_size/gene/gains_losses");
check_if_graphDb_is_available(); // starts up the graph database if needed
- retrieve_number_of_loops_for_size(1000);
+ retrieve_number_of_loops_for_size(10000);
try (Transaction tx = graphDb.beginTx()) { // start database transaction
Node pangenome_node = graphDb.findNodes(pangenome_label).next();
@@ -4600,6 +4601,14 @@ public class Classification {
create_pangenome_size_rscript("gene","");
create_pangenome_size_rscript("gene","_unique");
create_pangenome_size_gains_losses_rscript();
+ System.out.println("\n\nOutput written to:\n "
+ + WORKING_DIRECTORY + "pangenome_size/gene/pangenome_size.txt\n "
+ + WORKING_DIRECTORY + "pangenome_size/gene/pangenome_growth.R\n "
+ + WORKING_DIRECTORY + "pangenome_size/gene/gains_losses.txt\n "
+ + WORKING_DIRECTORY + "pangenome_size/gene/gains_losses_last_genome.txt\n "
+ + WORKING_DIRECTORY + "pangenome_size/gene/gains_losses_median_or_average.R\n "
+ + WORKING_DIRECTORY + "pangenome_size/gene/gains_losses_median_and_average.R\n "
+ + WORKING_DIRECTORY + "pangenome_size/gene/heaps_law.R\n");
}
/**
@@ -4715,6 +4724,10 @@ public class Classification {
write_string_to_file_in_DB(header + output_builder.toString(), "pangenome_size/gene/gains_losses_last_genome.txt");
}
+ /**
+ *
+ * @param default_nr_loops
+ */
public void retrieve_number_of_loops_for_size(int default_nr_loops) {
if (NODE_VALUE == null) {
total_loops = default_nr_loops;
@@ -5409,6 +5422,11 @@ public class Classification {
}
/**
+ * Creates the input files for the gains and losses rscripts
+ * - average_all.csv
+ * - median_all.csv
+ * - average_core_accessory.csv
+ * - median_core_accessory.csv
*
* @param all_core
* @param all_accessory
@@ -5550,6 +5568,10 @@ public class Classification {
}
/**
+ * Creates
+ * - pangenome_size.txt
+ * - core_accessory_unique_size.csv
+ * - core_accessory_size.csv
*
* @param all_core
* @param all_accessory
@@ -5621,14 +5643,7 @@ public class Classification {
write_SB_to_file_in_DB(output_builder, "pangenome_size/gene/pangenome_size.txt");
write_SB_to_file_in_DB(input_builder, "pangenome_size/gene/core_accessory_unique_size.csv");
write_SB_to_file_in_DB(input_builder2, "pangenome_size/gene/core_accessory_size.csv");
- System.out.println("\n\nOutput written to:\n "
- + WORKING_DIRECTORY + "pangenome_size/gene/pangenome_size.txt\n "
- + WORKING_DIRECTORY + "pangenome_size/gene/pangenome_growth.R\n "
- + WORKING_DIRECTORY + "pangenome_size/gene/gains_losses.txt\n "
- + WORKING_DIRECTORY + "pangenome_size/gene/gains_losses_last_genome.txt\n "
- + WORKING_DIRECTORY + "pangenome_size/gene/gains_losses_median_or_average.R\n "
- + WORKING_DIRECTORY + "pangenome_size/gene/gains_losses_median_and_average.R\n "
- + WORKING_DIRECTORY + "pangenome_size/gene/heaps_law.R\n");
+
}
/**
@@ -6224,7 +6239,7 @@ public class Classification {
genome_i_distinct_shared_builder.append(seq_id).append(",");
genome_j_distinct_shared_builder.append(seq_id).append(",");
sequence_counter ++;
- if (sequence_counter % 100 == 0 ){
+ if (sequence_counter % 100 == 0 ) {
System.out.print("\rWriting shared k-mers between sequences " + (i+1));
}
for (int j = 0; j < all_sequences.size(); j ++) {
@@ -6349,10 +6364,10 @@ public class Classification {
/**
* Loop over all nucleotide nodes of the pangenome
- * @param kmer_occur_map
+ * @param kmer_occur_map is null except when --mode OCCURANCE is included
* @param kmer_freq_map
* @param pheno_kmer_map
- * @param freq_per_genome
+ * @param freq_per_genome is null except when --mode OCCURANCE is included
* @param kmer_class_count
*
* @return
@@ -6498,12 +6513,12 @@ public class Classification {
/**
*/
- public long determine_appropriate_nr_for_printing(){
+ public long determine_appropriate_nr_for_printing() {
long nr_for_printing = 1000;
- if (all_sequences.size() >= 1000){
+ if (all_sequences.size() >= 1000) {
nr_for_printing = 100;
}
- if (all_sequences.size() >= 10000){
+ if (all_sequences.size() >= 10000) {
nr_for_printing = 10;
}
return nr_for_printing;
@@ -6539,13 +6554,11 @@ public class Classification {
}
}
- //System.out.println(nuc_node + " " + positions + " missing " + missing_positions);
for (int i = 0; i < positions.size(); i++) {
for (int j = i; j < positions.size(); j++) {
- //System.out.println(positions.size() + ". " + i + " " + j + " -> " + positions.get(i) + " " + positions.get(j));
int i_pos = positions.get(i);
int j_pos = positions.get(j);
- if (j_pos < i_pos){
+ if (j_pos < i_pos) {
i_pos = positions.get(j);
j_pos = positions.get(i);
}
@@ -6573,8 +6586,7 @@ public class Classification {
int i_pos = positions.get(i);
int j_pos = missing_positions.get(j);
int i_freq = freq_array[i_pos];
- //System.out.println("ifreg " + i_freq);
- if (j_pos < i_pos){
+ if (j_pos < i_pos) {
i_pos = missing_positions.get(j);
j_pos = positions.get(i);
}
@@ -6644,7 +6656,7 @@ public class Classification {
}
}
- public static HashMap<String, Integer> create_seq_nr_map(){
+ public static HashMap<String, Integer> create_seq_nr_map() {
HashMap<String, Integer> seq_nr_map = new HashMap<>();
int counter = 0;
for (String seq_id : all_sequences) {
@@ -6654,14 +6666,14 @@ public class Classification {
return seq_nr_map;
}
- /**
+ /**
*
*/
public class find_shared_kmers2 implements Runnable {
- ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map;
+ ConcurrentHashMap<Long, ArrayList<Node>> kmer_occur_map; // is null except when --mode OCCURANCE is included
ConcurrentHashMap<Integer, long[]> kmer_freq_map;
ConcurrentHashMap<String, ArrayList<Node>> pheno_kmer_map;
- ConcurrentHashMap<Integer, HashMap<Long,Long>> freq_per_genome;
+ ConcurrentHashMap<Integer, HashMap<Long,Long>> freq_per_genome; // is null except when --mode OCCURANCE is included
long[] kmer_class_count;
int[][] distinct_shared_array = new int[total_genomes][total_genomes];
int[][] distinct_total_array = new int[total_genomes][total_genomes];
@@ -6842,15 +6854,15 @@ public class Classification {
/**
*/
- public int get_number_of_kmers_for_printing(){
+ public int get_number_of_kmers_for_printing() {
int nr_kmers = 10000;
- if (total_genomes > 100 ){
+ if (total_genomes > 100 ) {
nr_kmers = 5000;
}
- if (total_genomes > 1000 ){
+ if (total_genomes > 1000 ) {
nr_kmers = 1000;
}
- if (total_genomes >= 10000 ){
+ if (total_genomes >= 10000 ) {
nr_kmers = 100;
}
return nr_kmers;
@@ -6938,7 +6950,7 @@ public class Classification {
all_shared_array[i-1][j-1] += lowest;
all_total_array[i-1][j-1] += highest;
} else {
- if (lowest > 0){
+ if (lowest > 0) {
distinct_shared_array[i-1][j-1] += actual_kmers;
}
distinct_total_array[i-1][j-1] += actual_kmers;
@@ -7028,7 +7040,7 @@ public class Classification {
}
int[] freq_of_seq = (int[]) nuc_node.getProperty("freq_per_seq_genome_" + i);
ArrayList<Integer> selected_sequences = sequences_per_genome.get(i);
- if (selected_sequences == null){
+ if (selected_sequences == null) {
continue;
}
for (int j : selected_sequences) { // j is a sequence number
@@ -7056,7 +7068,7 @@ public class Classification {
int[][] freq_per_seq = new int[total_genomes][0];
for (int i = 1; i <= total_genomes; i++) {
ArrayList<Integer> sequences = sequences_per_genome.get(i);
- //if (number_of_sequences == null){
+ //if (number_of_sequences == null) {
// continue;
//}
freq_per_seq[i-1] = new int[sequences.size()];
@@ -7144,7 +7156,7 @@ public class Classification {
continue;
}
genome_counter ++;
- if (genome_counter % 100 == 0 ){
+ if (genome_counter % 100 == 0 ) {
System.out.print("\rWriting shared k-mers between genomes " + i);
}
String phenotype = get_phenotype_for_genome(i, true);
@@ -7653,7 +7665,7 @@ public class Classification {
if (degen_node_count.containsKey(seq_id)) {
values = degen_node_count.get(seq_id);
values[0] += 1;
- if (compressed_kmers){
+ if (compressed_kmers) {
values[1] += 1;
values[2] += kmer_count_per_seq.get(seq_id);
} else {
@@ -7724,7 +7736,7 @@ public class Classification {
}
for (int i = 1; i < freq_array.length; i++) { // first value is always a 0
- if (freq_array[i] == 0 || skip_array[i-1]){
+ if (freq_array[i] == 0 || skip_array[i-1]) {
continue;
}
long[] degen_counts = degen_node_count.get("genome_" + i);
@@ -7762,7 +7774,7 @@ public class Classification {
Node genome_node = genome_nodes.next();
int genome_nr = (int) genome_node.getProperty("number");
counter ++;
- if (counter % 10 == 0){
+ if (counter % 10 == 0) {
System.out.print("\rRetrieving sequences: genome " + counter);
}
int num_sequences = (int) genome_node.getProperty("num_sequences");
@@ -8853,7 +8865,7 @@ public class Classification {
}
no_other_pheno = true;// disrupted by presence of other phenotype
}
- if (pass_threshold){
+ if (pass_threshold) {
try_incr_AL_chashmap(pheno_kmer_map, phenotype + "#shared", nuc_node); // kmer is phenotype shared
}
if (no_other_pheno && pass_threshold) {
@@ -9005,7 +9017,7 @@ public class Classification {
}
/**
- * Create Rscript for pangenome_size_genes
+ * Creates gains_losses_median_or_average.R & gains_losses_median_and_average.R rscripts for pangenome_structure
*/
public void create_pangenome_size_gains_losses_rscript() {
String R_LIB = check_r_libraries_environment();
@@ -9097,7 +9109,8 @@ public class Classification {
}
/**
- * Used by pangenome_size_gene/kmer functions
+ * Creates the pangenome_growth.R rscript. Used by pangenome_structure_gene/kmer functions
+ *
* @param gene_or_kmer
* @param unique string can be empty or 'unique'
*/
@@ -9848,13 +9861,13 @@ public class Classification {
/**
* Read a txt file given by --regions-file/-rf
*
- * The reverse complement of a region is retrieved when 'rv' is placed behind it.
- * if #reverse is found. all other regions will be reverse complement
+ * The reverse complement of a region is retrieved when a minus is placed behind it.
+ * If #reverse is found, all other regions will be reverse complement
*
* @return
*/
public static String[] read_regions_file() {
- String regions_str = "";
+ StringBuilder regions_builder = new StringBuilder();
if (PATH_TO_THE_REGIONS_FILE == null) {
System.out.println("\nNo regions provided via --regions-file or -rf\n");
System.exit(1);
@@ -9872,60 +9885,18 @@ public class Classification {
continue;
}
if (reverse) {
- line += "rv";
+ line += "-";
}
- regions_str += line + ",";
+ regions_builder.append(line + ",");
}
} catch (IOException ioe) {
- System.out.println("\nUnable to read: " + PATH_TO_THE_REGIONS_FILE + "\n");
+ System.out.println("\nUnable to read the --regions-file: " + PATH_TO_THE_REGIONS_FILE + "\n");
System.exit(1);
}
- String[] regions_array = regions_str.split(",");
+ String[] regions_array = regions_builder.toString().split(",");
return regions_array;
}
- /**
- * Is run after add_annotations().
- * A transaction must already be opened
- */
- public static void annotation_overview() {
- total_genomes = (int) graphDb.findNodes(pangenome_label).next().getProperty("num_genomes");
- StringBuilder output_builder = new StringBuilder();
- int annotation_count = 0;
- for (int i = 1; i <= total_genomes; i++) {
- StringBuilder genome_builder = new StringBuilder();
- ResourceIterator<Node> annotation_nodes = graphDb.findNodes(annotation_label, "genome", i);
- HashSet<String> id_set = new HashSet<>();
- while (annotation_nodes.hasNext()) {
- Node genome_node = annotation_nodes.next();
- long genome_node_id = genome_node.getId();
- String genome_path = (String) genome_node.getProperty("path");
- String identifier = (String) genome_node.getProperty("identifier");
- id_set.add(identifier);
- String date = (String) genome_node.getProperty("date");
- String type = (String) genome_node.getProperty("type");
- genome_builder.append("\nAnnotation id: ").append(identifier)
- .append("\nAnnotation file: ").append(genome_path)
- .append("\nFiletype: ").append(type)
- .append("\nStored in node: ").append(genome_node_id)
- .append("\nCreation date ").append(date).append("\n\n");
- annotation_count ++;
- }
- String ids = id_set.toString().replace("[","").replace("]","").replace(", ",",");
- String total = "";
- if (id_set.size() == 1) {
- total = "1 annotation: ";
- } else if (id_set.size() > 1) {
- total = id_set.size() + " annotations: ";
- }
- output_builder.append("#Genome ").append(i).append("\n")
- .append(total).append(ids).append("\n")
- .append(genome_builder.toString());
- }
- String anno_str = "Total annotations: " + annotation_count + "\n";
- write_string_to_file_in_DB(anno_str + output_builder.toString(), "databases/genome.db/annotations.txt");
- }
-
/*
Requires
-dp
@@ -9988,16 +9959,16 @@ public class Classification {
check_if_program_exists_stderr("FastTree -h", 100, "Fasttree", true); // check if program is set to $PATH
report_number_of_threads(true, true); // prints how many threads were selected by user
check_if_graphDb_is_available(); // starts up the graph database if needed
- create_directory_in_DB("alignments/regions/");
+ create_directory_in_DB("alignments/regions/var_inf_positions");
if (target_genome != null || skip_genomes != null) {
- System.out.println("'msa_of_regions' is unable to use --reference/-ref or --skip\n");
+ System.out.println("\r'msa_of_regions' is unable to use --reference/-ref or --skip. You should exclude these genomes from your --regions-file\n");
}
try (Transaction tx = graphDb.beginTx()) { // start database transaction
Node pangenome_node = graphDb.findNodes(pangenome_label).next();
stop_if_panproteome(pangenome_node, "msa_of_regions"); // stops the progam when run on a panproteome, retrieves K_size & total_genomes
create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
if (PHENOTYPE == null) {
- System.out.println("No --phenotype was provided, unable to find phenotype specific SNPs\n");
+ System.out.println("\rNo --phenotype was provided, unable to find phenotype specific SNPs");
} else {
retrieve_phenotypes(); // Creates and fills geno_pheno_map and phenotype_map when a phenotype was provided by the user
}
@@ -10012,41 +9983,6 @@ public class Classification {
genomeSc = new SequenceScanner(genomeDb, 1, 1, K_SIZE, indexSc.get_pre_len());
regions_to_search = read_regions_file();
prepare_region_msa_input();
- run_msa_region(); // step 1/3 & step 2/3
-
- HashMap<String, Integer> shared_snps_map = new HashMap<>();
- StringBuilder pheno_specific_output = new StringBuilder("# Each row contains: position in the alignment, reference allele,other alleles, "
- + "phenotype, number of sequences with the phenotype and letter/total sequences with phenotype\n");
- HashMap<String, Integer> pheno_specific_group_sites = new HashMap<>();
- String output_path = WORKING_DIRECTORY + "alignments/regions/";
-
- System.out.println("Step 3/3. Reading the alignment");
- int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output, pheno_specific_group_sites,
- output_path + "nuc.afa", "MSA", "nucleotide", output_path + "nuc_input_genomes.txt"); // variable, informative, conserved sites
- create_identity_matrices(shared_snps_map, var_inf_sites[0], var_inf_sites[2], "nucleotide",
- output_path + "nuc_identity.csv", output_path + "nuc_input_genomes.txt");
- prepare_phenotype_results_msa_regions(pheno_specific_group_sites, output_path, pheno_specific_output);
- System.out.print("\nNucleotide variable/informative sites: " + var_inf_sites[0] + "/" + var_inf_sites[1]
- + "\nOutput written to:\n "
- + output_path + "nuc_input.fasta\n "
- + output_path + "nuc.fasta\n "
- + output_path + "nuc.afa\n "
- + output_path + "nuc.newick\n "
- + output_path + "nuc_alignment.info\n "
- + output_path + "nuc_identity.csv\n ");
-
- if (PHENOTYPE != null) {
- System.out.println("\n " + output_path + "nuc_phenotype_specific_changes.txt\n "
- + output_path + "nuc_phenotype_specific_changes.info\n");
- } else {
- System.out.println("");
- }
- }
-
- /**
- * Run alignment and infer phylogeny on extracted regions
- */
- public void run_msa_region() {
System.out.println("\nStep 1/3. Performing the alignment");
String[] msa_command = {"mafft", "--auto", "--anysymbol", "--thread", THREADS + "", "--clustalout",
WORKING_DIRECTORY + "/alignments/regions/nuc_input.fasta"};
@@ -10064,28 +10000,36 @@ public class Classification {
System.out.println("Step 2/3. Inferring phylogeny");
String[] run_fasttree = {"FastTree","-out", WORKING_DIRECTORY + "alignments/regions/nuc.newick",
WORKING_DIRECTORY + "alignments/regions/nuc.fasta"};
- ExecCommand.ExecCommand(run_fasttree);
- }
-
- /**
- *
- * @param pheno_specific_group_sites
- * @param output_path
- * @param pheno_specific_output
- */
- public static void prepare_phenotype_results_msa_regions(HashMap<String, Integer> pheno_specific_group_sites,
- String output_path, StringBuilder pheno_specific_output) {
+ ExecCommand.ExecCommand(run_fasttree);
- StringBuilder pheno_spec_builder = new StringBuilder("Total phenotype specific SNPs\n");
- for (String pheno_key : pheno_specific_group_sites.keySet()) {
- if (pheno_key.endsWith("_groups")) {
- continue;
- }
- int value = pheno_specific_group_sites.get(pheno_key);
- pheno_spec_builder.append(" ").append(pheno_key).append(": ").append(value).append("\n");
+ System.out.println("Step 3/3. Reading the alignment");
+ HashMap<String, Integer> shared_snps_map = new HashMap<>();
+ StringBuilder pheno_specific_output = new StringBuilder("# Each row contains: position in the alignment, reference allele,other alleles, "
+ + "phenotype, number of sequences with the phenotype and letter/total sequences with phenotype\n");
+ HashMap<String, Integer> pheno_specific_group_sites = new HashMap<>();
+ String output_path = WORKING_DIRECTORY + "alignments/regions/";
+ String genome_order_file = output_path + "nuc_input_genomes.txt";
+ int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output, pheno_specific_group_sites,
+ output_path + "nuc.afa", "MSA", "nucleotide", genome_order_file); // variable, informative, conserved sites
+ create_shared_site_matrices(shared_snps_map, output_path +"var_inf_positions/", var_inf_sites[0], "", "nucleotide", genome_order_file);
+ create_shared_site_matrices(shared_snps_map, output_path +"var_inf_positions/", var_inf_sites[1], "#inf", "nucleotide", genome_order_file);
+ create_identity_matrices(shared_snps_map, var_inf_sites[0], var_inf_sites[2], "nucleotide",
+ output_path + "nuc_identity.csv", output_path + "nuc_input_genomes.txt");
+
+ System.out.print("\nNucleotide variable/informative sites: " + var_inf_sites[0] + "/" + var_inf_sites[1] + "\n"
+ + "\n"
+ + "Output written to:\n "
+ + output_path + "nuc_input.fasta\n "
+ + output_path + "nuc.fasta\n "
+ + output_path + "nuc.afa\n "
+ + output_path + "nuc.newick\n "
+ + output_path + "nuc_identity.csv\n "
+ + output_path + "nuc_alignment.info\n ");
+
+ if (PHENOTYPE != null) {
+ System.out.print(output_path + "nuc_phenotype_specific_changes.info\n ");
}
- write_string_to_file_in_DB(pheno_spec_builder.toString() +"\n" + pheno_specific_output.toString(),
- "alignments/regions/nuc_phenotype_specific_changes.txt");
+ System.out.println(output_path + "var_inf_positions/\n ");
}
/**
@@ -11641,7 +11585,7 @@ public class Classification {
}
public static void initialize_BLOSUM() {
- if (BLOSUM != 45 && BLOSUM != 62 && BLOSUM != 80){
+ if (BLOSUM != 45 && BLOSUM != 62 && BLOSUM != 80) {
System.out.println("BLOSUM value must be 45, 62 or 80. Using BLOSUM62");
BLOSUM = 62;
}
@@ -11836,6 +11780,11 @@ public class Classification {
}
/**
+ * Create
+ * - nuc_phenotype_specific_changes.info
+ * - prot_phenotype_specific_changes.info
+ * - nuc_trimmed_phenotype_specific_changes.info
+ * - prot_trimmed_phenotype_specific_changes.info
*
* @param position_map
* @param pheno_specific_output
@@ -11843,20 +11792,25 @@ public class Classification {
* @param pheno_specific_group_sites
* @param alignment_info
* @param genome_order_file
- * @return
+ * @param trim can be "trimmed" or ""
+ * @param output_path
*/
- public static String find_pheno_specific_sites(HashMap<String, ArrayList<Integer>> position_map, StringBuilder pheno_specific_output,
- String nuc_or_prot, HashMap<String, Integer> pheno_specific_group_sites, StringBuilder alignment_info, String genome_order_file) {
+ public static void find_pheno_specific_sites(HashMap<String, ArrayList<Integer>> position_map, StringBuilder pheno_specific_output,
+ String nuc_or_prot, HashMap<String, Integer> pheno_specific_group_sites, StringBuilder alignment_info, String genome_order_file, String trim,
+ String output_path) {
+
if (pheno_specific_output == null || PHENOTYPE == null) {
- return "";
+ return;
}
StringBuilder pheno_log_builder = new StringBuilder("\n#All variable positions of the alignment");
String pheno_log_header = "#Use this file to see why a position is phenotype specific or not. The overview shows the number of phenotype "
+ "members with a specific letter on variable positions in the alignment followed by the required threshold to be phenotype specific\n";
String SNP_or_substi = "SNPs", nuc_or_prot_cap = "Nucleotide";
+ String nuc_or_prot_short = "nuc";
if (nuc_or_prot.equals("protein")) {
SNP_or_substi = "Substitutions";
nuc_or_prot_cap = "Amino acid";
+ nuc_or_prot_short = "prot";
}
prepare_phenotype_threshold_msa_no_genome_nrs(position_map, genome_order_file);
ArrayList<Integer> genome_order_list = read_genome_order_file(genome_order_file, false);
@@ -11864,6 +11818,7 @@ public class Classification {
StringBuilder pheno_specific_sites = new StringBuilder("Phenotype specific " + SNP_or_substi + " per position in the alignment."
+ " Each row contains: position in the alignment, reference allele/other alleles, phenotype,"
+ " number of sequences with the phenotype and letter/total sequences with phenotype\n");
+
TreeSet<Integer> positions_set = new TreeSet<>();
HashMap<Integer, ArrayList<String>> found_pos_map = new HashMap<>(); // key is position, value is list with
for (String key : position_map.keySet()) {
@@ -11872,7 +11827,7 @@ public class Classification {
positions_set.add(pos_nr);
try_incr_AL_hashmap(found_pos_map, pos_nr, key);
}
- ArrayList<String> added_phenotypes = new ArrayList<>(); // prevents the counter for groups with e incremented more than once
+
for (int position : positions_set) { // go over all variable sites
boolean first_pos = true;
ArrayList<String> position_keys = found_pos_map.get(position);
@@ -11894,12 +11849,24 @@ public class Classification {
pheno_log_builder.append("\n").append(nuc_or_prot_cap).append(" ").append(actual_position).append(character).append(": ")
.append(present_genomes.toString().replace("[","").replace(" ","").replace("]","")).append("\n");
determine_pheno_specific_sites_msa(phenotype_occurance, pheno_log_builder, position, character, other_characters, pheno_specific_sites,
- pheno_specific_output, added_phenotypes, pheno_specific_group_sites, pheno_specific_counter);
+ pheno_specific_output, pheno_specific_counter);
}
}
- //pheno_specific_output.append("\n");
+
+ StringBuilder pheno_site_count_builder = new StringBuilder();
+ if (!pheno_specific_counter.isEmpty()) {
+ pheno_site_count_builder.append("Number of phenotype specific SNPs per phenotype:\n");
+ for (String key : pheno_specific_counter.keySet()) { // increase the number of shared SNPs found in this alignment to the total number for all alignments
+ pheno_site_count_builder.append(key).append(": ").append(pheno_specific_counter.get(key)).append("\n");
+ try_incr_hashmap(pheno_specific_group_sites, key, pheno_specific_counter.get(key));
+ try_incr_hashmap(pheno_specific_group_sites, key + "_groups", 1);
+ }
+ pheno_site_count_builder.append("\n");
+ }
+
add_pheno_specific_to_alignment_info(nuc_or_prot, pheno_specific_sites.toString(), alignment_info, pheno_specific_counter);
- return pheno_log_header + pheno_specific_sites.toString() + pheno_log_builder.toString();
+ write_string_to_file_full_path(pheno_log_header + pheno_site_count_builder.toString() + pheno_specific_sites.toString() + pheno_log_builder.toString(),
+ output_path + "/" + nuc_or_prot_short + trim + "_phenotype_specific_changes.info");
}
/**
@@ -11935,12 +11902,10 @@ public class Classification {
* @param pheno_specific_sites
* @param pheno_specific_output
* @param added_phenotypes
- * @param pheno_specific_group_sites
* @param pheno_specific_counter
*/
- public static void determine_pheno_specific_sites_msa(HashMap<String, Integer> phenotype_occurance, StringBuilder pheno_log_builder,
- int position, String character, String other_characters, StringBuilder pheno_specific_sites, StringBuilder pheno_specific_output,
- ArrayList<String> added_phenotypes, HashMap<String, Integer> pheno_specific_group_sites, HashMap<String, Integer> pheno_specific_counter) {
+ public static void determine_pheno_specific_sites_msa(HashMap<String, Integer> phenotype_occurance, StringBuilder pheno_log_builder, int position, String character,
+ String other_characters, StringBuilder pheno_specific_sites, StringBuilder pheno_specific_output, HashMap<String, Integer> pheno_specific_counter) {
for (String current_phenotype : phenotype_occurance.keySet()) {
int threshold = phenotype_threshold_map.get(current_phenotype);
@@ -11972,11 +11937,6 @@ public class Classification {
pheno_specific_sites.append(info);
try_incr_hashmap(pheno_specific_counter, current_phenotype, 1);
pheno_log_builder.append(" Phenotype specific!");
- try_incr_hashmap(pheno_specific_group_sites, current_phenotype, 1);
- if (!added_phenotypes.contains(current_phenotype)) {
- added_phenotypes.add(current_phenotype);
- try_incr_hashmap(pheno_specific_group_sites, current_phenotype + "_groups", 1);
- }
}
pheno_log_builder.append("\n");
}
@@ -12538,7 +12498,6 @@ public class Classification {
* @param genome_order_file
* @return
*/
-
public static int[] count_var_inf_sites_in_msa(HashMap<String, Integer> shared_snps_map, StringBuilder pheno_specific_output,
HashMap<String, Integer> pheno_specific_group_sites, String input_file, String hmgroup, String nuc_or_prot, String genome_order_file) {
@@ -12572,9 +12531,9 @@ public class Classification {
StringBuilder alignment_info = prepare_alignment_info(hmgroup, sequence_skip_counter[0], sequence_skip_counter[1], alignment_length, genome_set, input_file,
conserved_sites.get(), informative_sites_overview, variable_positions, uninformative_positions, pheno_specific_output);
- String pheno_specific_log = find_pheno_specific_sites(position_map, pheno_specific_output, nuc_or_prot, pheno_specific_group_sites, alignment_info, genome_order_file);
+ find_pheno_specific_sites(position_map, pheno_specific_output, nuc_or_prot, pheno_specific_group_sites, alignment_info, genome_order_file, trim, output_path);
write_SB_to_file_full_path(alignment_info, output_path + "/" + nuc_or_prot_short + trim + "_alignment.info");
- write_string_to_file_full_path(pheno_specific_log, output_path + "/" + nuc_or_prot_short + trim + "_phenotype_specific_changes.info");
+
return new int[] {variable_positions.size(), variable_positions.size()-uninformative_positions.size(), conserved_sites.get()}; // variable, informative, conserved
}
@@ -12624,7 +12583,13 @@ public class Classification {
}
/**
- * Available keys: sequence combi (1), sequence combi + '#inf' (2), sequence combi + '#nogap' (3), sequence combi + "#similar" (4)
+ * Creates a csv formatted table with the counts of A, T, C, G, or gap for every variable position in the alignment
+ * Possible output files:
+ * - nuc_variable_positions.csv
+ * - prot_variable_positions.csv
+ * - prot_trimmed_variable_positions.csv
+ * - nuc_trimmed_variable_positions.csv
+ *
* @param variable_positions
* @param uninformative_positions
* @param position_map
@@ -12636,7 +12601,8 @@ public class Classification {
*/
public static void create_matrix_with_var_inf_positions(ArrayList<String> variable_positions, ArrayList<String> uninformative_positions,
LinkedHashMap<String, ArrayList<Integer>> position_map, int total_sequences, String nuc_or_prot, String output_path, String trim) {
- if (output_path.contains("/mlsa/")){
+
+ if (output_path.contains("mlsa/input")) { // do not create this file when running the mlsa_concatenate function
return;
}
StringBuilder matrix_builder = new StringBuilder();
@@ -12646,14 +12612,14 @@ public class Classification {
counts_per_position = new int[22]; // A R N D C Q E G H I L K M F P S T W Y V - other
matrix_builder.append("Position,Informative,A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y,V,gap,other\n");
} else {
- counts_per_position = new int[6]; // a t c g gap other
+ counts_per_position = new int[6]; // a t c g - other
matrix_builder.append("Position,Informative,A,T,C,G,gap,other\n");
}
String prev_position = "";
for (String position_character_key : position_map.keySet()) {
ArrayList<Integer> sequence_numbers = position_map.get(position_character_key);
- boolean informative = true;
+
String position = position_character_key.replaceFirst(".$",""); // remove last character
String character = position_character_key.replace(position, "");
@@ -12674,50 +12640,47 @@ public class Classification {
if (!variable_positions.contains(position)) {
continue;
}
- if (uninformative_positions.contains(position)) {
- informative = false;
- }
-
+
if (nuc_or_prot.equals("protein")) { // A R N D C Q E G H I L K M F P S T W Y V gap other
- if (character.equals("A")){
+ if (character.equals("A")) {
counts_per_position[0] += sequence_numbers.size();
- } else if (character.equals("R")){
+ } else if (character.equals("R")) {
counts_per_position[1] += sequence_numbers.size();
- } else if (character.equals("N")){
+ } else if (character.equals("N")) {
counts_per_position[2] += sequence_numbers.size();
- } else if (character.equals("D")){
+ } else if (character.equals("D")) {
counts_per_position[3] += sequence_numbers.size();
- } else if (character.equals("C")){
+ } else if (character.equals("C")) {
counts_per_position[4] += sequence_numbers.size();
- } else if (character.equals("Q")){
+ } else if (character.equals("Q")) {
counts_per_position[5] += sequence_numbers.size();
- } else if (character.equals("E")){
+ } else if (character.equals("E")) {
counts_per_position[6] += sequence_numbers.size();
- } else if (character.equals("G")){
+ } else if (character.equals("G")) {
counts_per_position[7] += sequence_numbers.size();
- } else if (character.equals("H")){
+ } else if (character.equals("H")) {
counts_per_position[8] += sequence_numbers.size();
- } else if (character.equals("I")){
+ } else if (character.equals("I")) {
counts_per_position[9] += sequence_numbers.size();
- } else if (character.equals("L")){
+ } else if (character.equals("L")) {
counts_per_position[10] += sequence_numbers.size();
- } else if (character.equals("K")){
+ } else if (character.equals("K")) {
counts_per_position[11] += sequence_numbers.size();
- } else if (character.equals("M")){
+ } else if (character.equals("M")) {
counts_per_position[12] += sequence_numbers.size();
- } else if (character.equals("F")){
+ } else if (character.equals("F")) {
counts_per_position[13] += sequence_numbers.size();
- } else if (character.equals("P")){
+ } else if (character.equals("P")) {
counts_per_position[15] += sequence_numbers.size();
- } else if (character.equals("S")){
+ } else if (character.equals("S")) {
counts_per_position[15] += sequence_numbers.size();
- } else if (character.equals("T")){
+ } else if (character.equals("T")) {
counts_per_position[16] += sequence_numbers.size();
- }else if (character.equals("W")){
+ }else if (character.equals("W")) {
counts_per_position[17] += sequence_numbers.size();
- }else if (character.equals("Y")){
+ }else if (character.equals("Y")) {
counts_per_position[18] += sequence_numbers.size();
- }else if (character.equals("V")){
+ }else if (character.equals("V")) {
counts_per_position[19] += sequence_numbers.size();
} else if (character.equals("-")) {
counts_per_position[20] += sequence_numbers.size();
@@ -12726,11 +12689,11 @@ public class Classification {
}
} else {
- if (character.equals("A")){
+ if (character.equals("A")) {
counts_per_position[0] += sequence_numbers.size();
- } else if (character.equals("T")){
+ } else if (character.equals("T")) {
counts_per_position[1] += sequence_numbers.size();
- } else if (character.equals("C")){
+ } else if (character.equals("C")) {
counts_per_position[2] += sequence_numbers.size();
} else if (character.equals("G")) {
counts_per_position[3] += sequence_numbers.size();
@@ -12742,17 +12705,22 @@ public class Classification {
}
prev_position = position;
}
- int pos_int = Integer.parseInt(prev_position);
- if (uninformative_positions.contains(prev_position)) {
- matrix_builder.append((pos_int+1)).append(",,").append(Arrays.toString(counts_per_position).replace("[","") .replace("]","").replace(" ","")).append("\n");
- } else {
- matrix_builder.append((pos_int+1)).append(",I,").append(Arrays.toString(counts_per_position).replace("[","") .replace("]","").replace(" ","")).append("\n");
- }
-
+
String nuc_or_prot_short = "prot";
if (nuc_or_prot.equals("nucleotide")) {
nuc_or_prot_short = "nuc";
}
+
+ if (!prev_position.equals("")) { // there are variable positions in the alignment
+ int pos_int = Integer.parseInt(prev_position);
+ if (uninformative_positions.contains(prev_position)) {
+ matrix_builder.append((pos_int+1)).append(",,").append(Arrays.toString(counts_per_position).replace("[","") .replace("]","").replace(" ","")).append("\n");
+ } else {
+ matrix_builder.append((pos_int+1)).append(",I,").append(Arrays.toString(counts_per_position).replace("[","") .replace("]","").replace(" ","")).append("\n");
+ }
+ } else { // no variable positions
+ matrix_builder = new StringBuilder("Alignment does not contain variable positions");
+ }
write_SB_to_file_full_path(matrix_builder, output_path + "var_inf_positions/" + nuc_or_prot_short + trim + "_variable_positions.csv");
}
@@ -15298,28 +15266,44 @@ public class Classification {
}
/**
- * Step 1 of X , msa_of_regions. Retrieval of the regions from the pangenome
+ * First step of msa_of_regions. Retrieval of regions from the pangenome
*/
public static void prepare_region_msa_input() {
- StringBuilder output_builder = new StringBuilder();
+ StringBuilder fasta_builder = new StringBuilder();
StringBuilder genome_nrs_builder = new StringBuilder();
+
int counter = 1;
if (regions_to_search.length > 100) {
System.out.println("\nRetrieving regions");
}
- for (String region_str: regions_to_search) {
+ for (String region_str : regions_to_search) {
if (regions_to_search.length > 100) {
printProgressBar(regions_to_search.length, counter, "regions", false);
}
+
+ String[] region_array = region_str.split(" ");
+ int genome_nr;
+ int sequence_nr;
+ int start_pos;
+ int end_pos;
+ try {
+ genome_nr = Integer.parseInt(region_array[0]);
+ sequence_nr = Integer.parseInt(region_array[1]);
+ start_pos = Integer.parseInt(region_array[2]);
+ end_pos = Integer.parseInt(region_array[3]);
+ } catch (NumberFormatException nfe) {
+ System.out.println("Unable to correctly retrieve four numbers in: " + region_str);
+ continue;
+ }
+
boolean reverse = false;
- if (region_str.contains("rv")) {
+ String rev_complement = "";
+ if (region_str.endsWith("-")) {
reverse = true;
- region_str = region_str.replace("rv","").replace("_","").replaceFirst(".$","");;
+ region_str = region_str.replace(" -","");
+ rev_complement = "_rvComplement";
}
- String[] region_array = region_str.split(" ");
- int genome_nr = Integer.parseInt(region_array[0]);
- int start_pos = Integer.parseInt(region_array[2]);
- int end_pos = Integer.parseInt(region_array[3]);
+
if (genome_nr > total_genomes) {
System.out.println("A genome with number " + genome_nr + " does not exists! Only " + total_genomes + " genomes in pangenome\n");
System.exit(1);
@@ -15329,22 +15313,24 @@ public class Classification {
System.exit(1);
}
- region_str = region_str.replace(" ","_");
+ region_str = region_str.replace(" ","_"); // 1 1 1 1000 becomes 1_1_1_1000
String region;
if (!reverse) {
- region = get_region(genome_nr, Integer.parseInt(region_array[1]), start_pos-1, end_pos-1, true);
+ region = get_region(genome_nr, sequence_nr, start_pos-1, end_pos-1, true);
} else {
- region = get_region(genome_nr, Integer.parseInt(region_array[1]), start_pos-1, end_pos-1, false);
+ region = get_region(genome_nr, sequence_nr, start_pos-1, end_pos-1, false);
}
- output_builder.append(">").append(region_str).append("\n").append(region).append("\n");
- genome_nrs_builder.append(region_array[0]).append(",").append(region_str).append("\n");
+ fasta_builder.append(">").append(region_str).append(rev_complement).append("\n")
+ .append(region).append("\n");
+
+ genome_nrs_builder.append(genome_nr).append(",").append(region_str).append(rev_complement).append("\n");
if (region.length() < 10) {
System.out.println("The length of " + region_str + " is below 10 characters.");
System.exit(1);
}
counter ++;
}
- write_SB_to_file_in_DB(output_builder, "/alignments/regions/nuc_input.fasta");
+ write_SB_to_file_in_DB(fasta_builder, "/alignments/regions/nuc_input.fasta");
write_SB_to_file_in_DB(genome_nrs_builder, "/alignments/regions/nuc_input_genomes.txt");
}
diff --git a/src/pangenome/FunctionalAnnotations.java b/src/pangenome/FunctionalAnnotations.java
index 234cafdd3b72918cd13c1ac915d6485548392ce8..dc560c2e4051f264b811cd5de816eeb4834cee77 100644
--- a/src/pangenome/FunctionalAnnotations.java
+++ b/src/pangenome/FunctionalAnnotations.java
@@ -7,15 +7,12 @@ package pangenome;
import cern.jet.stat.Gamma;
import java.io.BufferedReader;
-import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
-import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.text.DecimalFormat;
import java.util.ArrayList;
-import static pantools.Pantools.write_log;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
@@ -31,9 +28,7 @@ import org.neo4j.graphdb.NotFoundException;
import org.neo4j.graphdb.Relationship;
import org.neo4j.graphdb.RelationshipType;
import org.neo4j.graphdb.ResourceIterator;
-import static pantools.Pantools.target_genome;
import org.neo4j.graphdb.Transaction;
-import static pantools.Pantools.OVERWRITE;
import static pangenome.Classification.try_incr_SB_hashmap;
import static pangenome.Classification.try_incr_hashset_hashmap;
import static pangenome.Classification.incr_array_hashmap;
@@ -43,7 +38,6 @@ import static pangenome.Classification.get_percentage_str;
import static pantools.Pantools.geno_pheno_map;
import static pantools.Pantools.phenotype_map;
import pantools.Pantools;
-import static pantools.Pantools.APPEND;
import static pantools.Pantools.K_SIZE;
import static pantools.Pantools.Mode;
import static pantools.Pantools.NODE_ID;
@@ -51,7 +45,6 @@ import static pantools.Pantools.PATH_TO_THE_ANNOTATIONS_FILE;
import static pantools.Pantools.PHENOTYPE;
import pantools.Pantools.RelTypes;
import static pantools.Pantools.SELECTED_NAME;
-import static pantools.Pantools.THREADS;
import static pantools.Pantools.WD_full_path;
import static pantools.Pantools.WORKING_DIRECTORY;
import static pantools.Pantools.adj_total_genomes;
@@ -62,7 +55,6 @@ import static pantools.Pantools.gene_label;
import static pantools.Pantools.go_label;
import static pantools.Pantools.graphDb;
import static pantools.Pantools.homology_group_label;
-import static pantools.Pantools.annotation_label;
import static pantools.Pantools.interpro_label;
import static pantools.Pantools.mRNA_label;
import static pantools.Pantools.pangenome_label;
@@ -76,7 +68,6 @@ import static pantools.Pantools.phenotype_threshold_map;
import static pantools.Pantools.count_nodes;
import static pantools.Pantools.check_if_panproteome;
import static pantools.Pantools.create_directory_in_DB;
-import static pantools.Pantools.delete_directory;
import static pantools.Pantools.write_SB_to_file_in_DB;
import static pantools.Pantools.write_string_to_file_in_DB;
import static pantools.Pantools.SELECTED_LABEL;
@@ -96,22 +87,16 @@ import static pantools.Pantools.PROTEOME;
import static pantools.Pantools.stop_if_panproteome;
import static pantools.Pantools.core_threshold;
import static pantools.Pantools.unique_threshold;
-import static pangenome.Classification.create_mrna_node_map_for_genome;
-import static pangenome.Classification.determine_genome_freq_absence_presence_freq;
import static pangenome.Classification.find_last_correct_rank;
import static pangenome.Classification.get_annotation_identifiers;
-import static pangenome.Classification.get_num_proteins_from_individual_genomes_map;
-import static pangenome.Classification.get_protein_sequence;
-import static pangenome.Classification.incr_hashmap;
import static pangenome.Classification.percentage;
+import static pangenome.Classification.create_mrna_node_map_for_genome;
import static pangenome.Classification.try_incr_treeset_hashmap;
import static pantools.Pantools.INPUT_FILE;
import static pantools.Pantools.NODE_VALUE;
import static pantools.Pantools.SELECTED_HMGROUPS;
-import static pantools.Pantools.report_number_of_threads;
import static pantools.Pantools.classification;
import static pantools.Pantools.NODE_ID_long;
-import static pantools.Pantools.check_if_program_exists_stdout;
import static pantools.Pantools.genome_label;
import static pantools.Pantools.skip_array;
import static pantools.Pantools.append_string_to_file_full_path;
@@ -765,8 +750,8 @@ public class FunctionalAnnotations {
+ "protein name, protein node id, homology group node id\n");
}
results.append(output_builder.toString())
- .append("#Not connected functions\n")
- .append("#function id, function name, node id\n")
+ .append("\n#Not connected functions\n")
+ .append("function id, function name, node id\n")
.append(missing.toString()).append("\n");
add_missing_groups_to_stringbuilder(hmgroups_per_class, results, label_str);
System.out.print("\r "); // spaces are intentional
@@ -906,7 +891,7 @@ public class FunctionalAnnotations {
HashMap<String, Integer> class_counter = count_hmgroups_per_class(hmgroups_per_class);
add_annotated_to_stringbuilder(class_counter, hmgroups_per_class, output_builder, "phobius");
output_builder.append("# File consists of 4 parts.\n"
- + "# Part 1. Total number of mRNA's/proteins found per genome\n"
+ + "# Part 1. Total number of mRNA's/proteins with signal peptides & transmembrane domains found per genome\n"
+ "# Part 2. SignalP signal peptides\n"
+ "# Part 3. Phobius signal peptides\n"
+ "# Part 4. Phobius transmembrane domains\n\n");
@@ -922,7 +907,7 @@ public class FunctionalAnnotations {
.append("Phobius transmembrane domains: ").append(counts[0]).append("\n\n");
}
- StringBuilder signalp_signalpep_builder = new StringBuilder("#Part 2. SignalP signal peptides\n# Signal peptide type, mRNA/gene name, mRNA id, mRNA node id, homology group node id\n\n");
+ StringBuilder signalp_signalpep_builder = new StringBuilder("#Part 2. SignalP signal peptides\n# Signal peptide type (only v5.0 has types), mRNA/gene name, mRNA id, mRNA node id, homology group node id\n\n");
StringBuilder phobius_signalpep_builder = new StringBuilder("#Part 3. Phobius signal peptides\n# mRNA/gene name, mRNA id, mRNA node id, homology group node id\n\n");
StringBuilder transmembrane_builder = new StringBuilder("#Part 4. Phobius transmembrane domains\n# mRNA/gene name, mRNA id, mRNA node id, homology group node id\n\n");
if (PROTEOME) {
@@ -950,7 +935,7 @@ public class FunctionalAnnotations {
add_missing_groups_to_stringbuilder(hmgroups_per_class, output_builder, "phobius");
if (output_builder.length() > 0) {
- write_SB_to_file_in_DB(output_builder, "function/phobius_signalp_overview.txt");
+ write_SB_to_file_in_DB(output_builder, "function/phobius_signalp_overview.csv");
}
System.out.println("\r ");
}
@@ -1745,8 +1730,8 @@ public class FunctionalAnnotations {
* @param cog_cat_counter_map
* @return
*/
- public static String create_COG_rscript_input(HashMap<String, Integer> cog_counter_map, HashMap<String, int[]> cog_cat_counter_map) {
- StringBuilder abundance_builder = new StringBuilder();
+ public static HashMap<String, String> create_COG_rscript_input(HashMap<String, Integer> cog_counter_map, HashMap<String, int[]> cog_cat_counter_map) {
+
DecimalFormat formatter = new DecimalFormat("0.00");
String[] class_array = {"core", "accessory", "unique"};
StringBuilder output_builder = new StringBuilder("Category;Class;Value\n");
@@ -1789,19 +1774,7 @@ public class FunctionalAnnotations {
}
write_SB_to_file_in_DB(output_builder, "function/cog_per_class_hmgroups.csv");
write_SB_to_file_in_DB(output_builder2, "function/cog_per_class_percentage.csv");
- for (String category : cog_category_array) {
- String[] category_array = category.split(":");
- int[] occurance = cog_cat_counter_map.get(category_array[0]);
- String presence_freq = determine_genome_freq_absence_presence_freq(occurance);
- abundance_builder.append(category).append("\n");
- for (String class1 : class_array) {
- String log2_pc = cog_log2_map.get(category + "#" + class1);
- abundance_builder.append(class1).append(" ").append(log2_pc).append("\n");
- }
- abundance_builder.append("Occurance per genome: ").append(presence_freq).append("\n");
- abundance_builder.append("\n");
- }
- return abundance_builder.toString();
+ return cog_log2_map;
}
/**
@@ -1812,143 +1785,8 @@ public class FunctionalAnnotations {
public static int log2(int x) {
return (int) (Math.log(x) / Math.log(2));
}
-
- /*
-
- Does not work on a panproteome
- Requires
- -dp
-
- Optional
- -skip/-ref
- --label
- --append
- --overwrite
- -af
- */
- public void blast_cog() {
- System.out.println("\nAdding COG results to database\n");
- create_directory_in_DB("function");
- create_directory_in_DB("function/COG");
- check_if_cog_input_files_are_present();
- check_if_graphDb_is_available(); // starts up the graph database if needed
- try (Transaction tx = graphDb.beginTx()) {
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- stop_if_panproteome(pangenome_node, "blast_cog"); // stops the progam when run on a panproteome, retrieves K_size & total_genomes
- create_skip_arrays(false, true); // create skip array if -skip/-ref is provided by user
- report_number_of_threads(true, true); // prints how many threads were selected by user
- annotation_identifiers = get_annotation_identifiers(false, false); // do not print, USE the -af input file
- if (!APPEND) {
- System.out.println("No --overwrite provided. First deleting current COG information before adding new");
- }
- tx.success();
- } catch (NotFoundException nfe) {
- System.out.println("Unable to start the database\n");
- System.exit(1);
- }
- String[] blast_output_locations = new String[0];
- if (INPUT_FILE == null) { // user input --input-file/-if
- create_cog_BLAST_DB();
- blast_against_COG();
- } else {
- blast_output_locations = read_provided_blast_output();
- }
- HashMap<String, String> cog_map = read_COG_database();
- include_blast_cog_results(cog_map, blast_output_locations);
- graphDb.shutdown();
- System.out.println("\n\nLog written to:\n "
- + WORKING_DIRECTORY + "function/COG/blast_results/cog.log\n");
- }
-
- /**
- * Verify if the 2 ( or 3) required COG files were downloaded
- */
- public void check_if_cog_input_files_are_present() {
- boolean stop = false;
- if (!check_if_file_exists(pantools_path + "addons/cog-20.def.tab")) {
- System.out.println(pantools_path + "addons/cog-20.def.tab does not exist!\nFollow the following two steps to continue\n"
- + " cd " + pantools_path + "addons\n"
- + " wget ftp://ftp.ncbi.nih.gov/pub/COG/COG2020/data/cog-20.def.tab\n");
- stop = true;
- }
-
- if (!check_if_file_exists(pantools_path + "addons/cog-20.cog.csv")) {
- System.out.println(pantools_path + "addons/cog-20.cog.csv does not exist!\nFollow the following two steps to continue\n"
- + " cd " + pantools_path + "addons\n"
- + " wget ftp://ftp.ncbi.nih.gov/pub/COG/COG2020/data/cog-20.cog.csv\n");
- stop = true;
- }
- if (INPUT_FILE == null) { // user input --input-file/-if
- // if no -if is given, sequences will be blasted against a database constructed from cog-20.fa
- if (!check_if_file_exists(pantools_path + "addons/cog-20.fa")) {
- System.out.println(pantools_path + "addons/cog-20.fa does not exist!\nFollow the following three steps to continue\n"
- + " cd " + pantools_path + "addons\n"
- + " wget ftp://ftp.ncbi.nih.gov/pub/COG/COG2020/data/cog-20.fa.gz\n"
- + " gzip -d cog-20.fa.gz\n");
- stop = true;
- }
- check_if_program_exists_stdout("blastp -h", 100, "blastp"); // check if program is set to $PATH
- check_if_program_exists_stdout("makeblastdb -h", 100, "makeblastdb"); // check if program is set to $PATH
- }
- if (stop) { // stop when 1 of the 3 files is not present
- System.out.println("The files must be downloaded before you can continue.");
- System.exit(1);
- }
- }
-
- /**
- * When the user already has BLAST output against the COG database
- *
- * Assumes only 1 file per genome
- * @return array
- */
- public static String[] read_provided_blast_output() {
- if (INPUT_FILE == null) {
- return new String[0];
- }
- String[] file_locations = new String[total_genomes];
- target_genome = "";
- try (BufferedReader in = new BufferedReader(new FileReader(INPUT_FILE))) { // read the GFF file
- for (int c = 0; in.ready();) {
- String line = in.readLine().trim();
- String[] line_array = line.split(" ");
- if (line_array.length != 2) {
- System.out.println("The format of the given -af is not correct. Needs to have two columns\n");
- System.exit(1);
- }
- target_genome += line_array[0] + ",";
- int genome_nr = Integer. parseInt(line_array[0]);
- file_locations[genome_nr-1] = line_array[1];
- }
- } catch (IOException ioe) {
- System.out.println("\nFailed to read: " + INPUT_FILE + "\n");
- System.exit(1);
- }
- target_genome = target_genome.replaceFirst(".$",""); // remove last character
- return file_locations;
- }
+
- /**
- * Only works on a pangenome
- * @param genome_nr
- */
- public static void remove_previous_COG_properties(int genome_nr) {
- try (Transaction tx = graphDb.beginTx()) {
- if (!APPEND) { // If no --append is given, remove all properties related to COG
- String annotation_id = annotation_identifiers.get(genome_nr-1);
- ResourceIterator<Node> mrna_nodes = graphDb.findNodes(COG_label, "annotation_id", annotation_id);
- while (mrna_nodes.hasNext()) {
- Node mrna_node = mrna_nodes.next();
- mrna_node.removeProperty("COG_id");
- mrna_node.removeProperty("COG_category");
- mrna_node.removeProperty("COG_name");
- mrna_node.removeProperty("COG_description");
- mrna_node.removeLabel(COG_label);
- }
- }
- tx.success();
- }
- }
/**
*
@@ -1970,339 +1808,7 @@ public class FunctionalAnnotations {
return strictness;
}
- /**
- * Does not work on a panproteome
- * @param cog_map
- * @param blast_output_locations
- */
- public static void include_blast_cog_results(HashMap<String, String> cog_map, String[] blast_output_locations) {
- StringBuilder log_builder = new StringBuilder();
- String strictness = check_blast_strictness(); // strong, normal, soft
- HashMap<String, Integer> proteins_per_genome = new HashMap<>();
- try (Transaction tx = graphDb.beginTx()) {
- proteins_per_genome = get_num_proteins_from_individual_genomes_map();
- tx.success();
- }
- for (int i=1; i <= total_genomes; i++) {
- if (skip_array[i-1]) {
- continue;
- }
- int[] count_array = new int[4];
- remove_previous_COG_properties(i);
- try (Transaction tx = graphDb.beginTx()) {
- String input_file = WORKING_DIRECTORY + "function/COG/blast_results/" + i;
- if (blast_output_locations.length > 0) { // when BLAST output was provided via --input-file/-if
- input_file = blast_output_locations[i-1];
- }
- if (!check_if_file_exists(input_file)) {
- System.out.println(input_file + " does not exist");
- tx.success();
- continue;
- }
- HashMap<String, Node> mrna_node_map = create_mrna_node_map_for_genome(i, "Including COGs into database", "mrna");
- try (BufferedReader in = new BufferedReader(new FileReader(input_file))) { // read BLAST output format 6
- String prev_seq_name = "", best_hit = "";
- double best_score = 0;
- for (int c = 0; in.ready();) {
- String line = in.readLine().trim();
- String[] line_array = line.split("\t");
- String seq_name = line_array[0];
- if (!seq_name.equals(prev_seq_name) && !prev_seq_name.equals("")) {
- int new_hit = add_cog_to_database(best_hit, mrna_node_map, cog_map, strictness);
- count_array[new_hit] ++;
- best_score = 0;
- best_hit = "";
- }
-
- double identity = Double.parseDouble(line_array[2]);
- double ali_length = Double.parseDouble(line_array[3]);
- double score = identity*ali_length;
- //System.out.println(identity + " " + ali_length + " " + score);
- if (score > best_score) {
- best_score = score;
- best_hit = line_array[0] + "#" + line_array[1] + "#" + identity + "#" + ali_length;
- }
- prev_seq_name = seq_name;
- }
- int new_hit = add_cog_to_database(best_hit, mrna_node_map, cog_map, strictness);
- count_array[new_hit] ++;
- } catch (IOException ioe) {
- System.out.println("\nUnable to read: " + input_file + "\n");
- System.exit(1);
- }
- tx.success();
- }
-
- int proteins = proteins_per_genome.get(i +"");
- int missing = proteins-count_array[0]-count_array[1]-count_array[2]-count_array[3];
- if (APPEND) {
- log_builder.append("Genome ").append(i).append(", ").append(count_array[1]).append(" new, ").append(count_array[3])
- .append(" already known were overwritten, ").append(count_array[0]).append(" below threshold, ").append(missing).append(" without hit\n");
- } else {
- log_builder.append("Genome ").append(i).append(", ").append(count_array[1]).append(" new, ").append(count_array[2])
- .append(" already known, ").append(count_array[0]).append(" below threshold, ").append(missing).append(" without hit\n");
- }
- }
- write_SB_to_file_in_DB(log_builder, "function/COG/blast_results/cog.log");
- }
-
/**
- *
- * @param best_hit
- * @param mrna_node_map
- * @param cog_map
- * @param strictness
- * @return
- */
- public static int add_cog_to_database(String best_hit, HashMap<String, Node> mrna_node_map, HashMap<String, String> cog_map, String strictness) {
- int new_hit = 2; // 0 missing, 1 new, 2 known, counted outside this function
- int threshold = 65;
- double threshold2 = 0.65;
- if (strictness.equals("normal")) {
- threshold = 50;
- threshold2 = 0.5;
- } else if (strictness.equals("soft")) {
- threshold = 35;
- threshold2 = 0.35;
- }
- String[] best_hit_array = best_hit.split("#");
- String[] mrna_name_array = best_hit_array[0].split("_genome_");
- try {
- Node mrna_node = mrna_node_map.get(mrna_name_array[0]);
- int length = (int) mrna_node.getProperty("length");
- double identity = Double.parseDouble(best_hit_array[2]);
- double ali_length = Double.parseDouble(best_hit_array[3]); // alignment length
- boolean pass = true;
- if (identity < threshold) {
- pass = false;
- new_hit = 0;
- }
- if (ali_length > length * threshold2) {
- pass = false;
- new_hit = 0;
- }
- if (pass) {
- //System.out.println(best_hit_array[1]);
- //String[] hit_array = best_hit_array[1].split("\\|");
- //System.out.println(mrna_node + " " + pass + " " + hit_array[1]);
- String cog = cog_map.get(best_hit_array[1]);
- //System.out.println(mrna_node + " " + pass + " " + hit_array[1] + " " + cog);
- if (!mrna_node.hasLabel(COG_label) || OVERWRITE) {
- if (mrna_node.hasLabel(COG_label) && OVERWRITE) {
- mrna_node.removeProperty("COG_id"); // old, can be removed later
- mrna_node.removeProperty("COG_category");
- mrna_node.removeProperty("COG_name"); // old, can be removed later
- mrna_node.removeProperty("COG_description");
- new_hit = 3;
- } else {
- new_hit = 1;
- }
- String[] cog_array = cog.split("#");
- mrna_node.addLabel(COG_label);
- mrna_node.setProperty("COG_category", cog_array[1]);
- mrna_node.setProperty("COG_description", cog_array[2]);
- }
- }
- } catch (NullPointerException nee) {
- System.out.println(mrna_name_array[0] + " cannot be found");
- System.exit(1);
- }
- return new_hit;
- }
-
- /**
- * Read two COG input files inside the pantools/addons/ directory
- *
- *
- * cog-20.def.tab file has 7 columns
- * 1. COG ID
- * 2. COG functional category (could include multiple letters in the order of importance)
- * 3. COG name
- * 4. Gene associated with the COG (optional)
- * 5. Functional pathway associated with the COG (optional)
- * 6. PubMed ID, associated with the COG (multiple entries are semicolon-separated; optional)
- * 7. PDB ID of the structure associated with the COG (multiple entries are semicolon-separated; optional)
-
- * cog-20.cog.csv has 13 columns
- * 1. Gene ID (GenBank or ad hoc)
- * 2. NCBI Assembly ID
- * 3. Protein ID (GenBank if conforms to [A-Za-z0-9_]+\.[0-9]+ regex; ad hoc otherwise)
- * 4. Protein length
- * 5. COG footprint coordinates on the protein.
- * "201-400" means "from position 201 to position 400"; "1-100=201-300" indicates a segmented footprint, 1-100 AND 201-300
- * 6. Length of the COG footprint on the proteins
- * 7. COG ID
- * 8. reserved
- * 9. COG membership class (0: footprint covers most of the protein and most of the COG profile;
- * 1: footprint covers most of the COG profile and part of the protein;
- * 2: footprint covers most of the protein and part of the COG profile; 3: partial match on both protein and COG profile)
- *
- * 10. PSI-BLAST bit score for the match between the protein and COG profile
- * 11. PSI-BLAST e-value for the match between the protein and COG profile
- * 12. COG profile length
- * 13. Protein footprint coordinates on the COG profile
- * @return
- */
- public static HashMap<String, String> read_COG_database() {
- HashMap<String, String> temp_cog_map = new HashMap<>();
- HashMap<String, String> cog_map = new HashMap<>();
- try (BufferedReader in = new BufferedReader(new FileReader(pantools_path + "addons/cog-20.def.tab"))) { // read the GFF file
- for (int c = 0; in.ready();) {
- String line = in.readLine().trim();
- String[] line_array = line.split("\t");
- temp_cog_map.put(line_array[0], line_array[1] + "#" + line_array[2]); // key is COG ID, values are COG functional category + "#+ COG name
- }
- } catch (IOException ioe) {
- System.out.println("\nFailed to read: " + pantools_path + "addons/cog-20.def.tab\n");
- System.exit(1);
- }
-
- try (BufferedReader in = new BufferedReader(new FileReader(pantools_path + "addons/cog-20.cog.csv"))) { // read the GFF file
- for (int c = 0; in.ready();) {
- String[] line_array = in.readLine().trim().split(",");
- String cog_info = temp_cog_map.get(line_array[6]);
- cog_map.put(line_array[2].replace(".","_"), line_array[6] + "#" + cog_info);
- }
- } catch (IOException ioe) {
- System.out.println("\nFailed to read: " + pantools_path + "addons/cog-20.cog.csv\n");
- System.exit(1);
- }
- return cog_map;
- }
-
- /**
- *
- */
- public static void blast_against_COG() {
- if (INPUT_FILE != null) { // user already gave an -if, not need to blast
- return;
- }
- write_log = true;
- for (int i=1; i<= total_genomes; i++) {
- if (skip_array[i-1]) {
- continue;
- }
- if (check_if_file_exists(WORKING_DIRECTORY + "function/COG/blast_results/" + i)) {
- continue;
- }
- System.out.print("\rBLASTING sequences of genome " + i);
- String[] blast_command = new String[]{"blastp", "-db", pantools_path + "addons/COG_protein_DB/COG_protein_DB", "-num_threads", THREADS + "",
- "-query", WORKING_DIRECTORY + "proteins/proteins_" + i + ".fasta", "-outfmt", "6", "-max_target_seqs", "10", "-out",
- WORKING_DIRECTORY + "function/COG/blast_results/" + i};
- ExecCommand.ExecCommand(blast_command); //
- }
- System.out.println("");
- }
-
- /**
- * Make a COG BLAST database when no output files (-if) are included
- */
- public void create_cog_BLAST_DB() {
- boolean exists = check_if_file_exists(pantools_path + "addons/COG_protein_DB/COG_protein_DB.pal");
- if (exists || INPUT_FILE != null) {
- return;
- }
- System.out.println("Building the COG protein database");
- create_directory_in_DB("function/COG/blast_results");
- String[] protein_command = {"makeblastdb", "-in", pantools_path + "addons/cog-20.fa", "-dbtype", "prot", "-out",
- pantools_path + "addons/COG_protein_DB/COG_protein_DB"};
- ExecCommand.ExecCommand(protein_command);
- try (Transaction tx = graphDb.beginTx()) {
- prepare_proteins_add_genome_in_header();
- tx.success();
- }
- }
-
- /**
- *
- */
- public static void prepare_proteins_add_genome_in_header() {
- HashMap<String, StringBuilder> protein_map = new HashMap<>();
- create_directory_in_DB("proteins");
- create_directory_in_DB("proteins/for_blast/");
- StringBuilder not_protein_builder = new StringBuilder("The following mRNA's do not have a protein sequence.\n"
- + "Was your GFF correctly formatted? Does the gene/mRNA have have a CDS property?\n"
- + "If everything is correct, please submit a bug to our GIT page\n"
- + "#mRNA node id, mRNa id, mRNA name, address\n");
- int warning_counter = 0;
- for (int i=1; i <= total_genomes; i++) {
- String i_str = Integer.toString(i);
- StringBuilder seq = new StringBuilder();
- protein_map.put(i_str, seq);
- }
-
- if (!PROTEOME) { // pangenome can have multiple annotations
- for (String anno_id : annotation_identifiers) {
- ResourceIterator<Node> mrna_nodes = graphDb.findNodes(mRNA_label, "annotation_id", anno_id);
- String[] anno_id_array = anno_id.split("_");
- warning_counter = prepare_proteins_add_genome_in_header_inner(mrna_nodes, Integer.parseInt(anno_id_array[0]), not_protein_builder, protein_map, warning_counter);
- }
- } else {
- for (int i=1; i <= total_genomes; i++) {
- ResourceIterator<Node> mrna_nodes = graphDb.findNodes(mRNA_label, "genome", i);
- warning_counter = prepare_proteins_add_genome_in_header_inner(mrna_nodes, i, not_protein_builder, protein_map, warning_counter);
- }
- }
-
- for (String genome_nr_str : protein_map.keySet()) {
- StringBuilder values = protein_map.get(genome_nr_str);
- if (!check_if_file_exists(WORKING_DIRECTORY + "proteins/for_blast/proteins_" + genome_nr_str + ".fasta")) {
- write_SB_to_file_in_DB(values, "proteins/for_blast/proteins_" + genome_nr_str + ".fasta");
- }
- }
- if (warning_counter > 1) {
- System.out.println("\n" + warning_counter + " mRNAs did not have a protein sequence. Please check " + WORKING_DIRECTORY + "BLAST/no_protein_seq.txt");
- write_SB_to_file_in_DB(not_protein_builder, "BLAST/no_protein_seq.txt");
- }
- }
-
- /**
- *
- * @param mrna_nodes
- * @param genome_nr
- * @param not_protein_builder
- * @param protein_map
- * @param warning_counter
- * @return
- */
- public static int prepare_proteins_add_genome_in_header_inner(ResourceIterator<Node> mrna_nodes, int genome_nr, StringBuilder not_protein_builder,
- HashMap<String, StringBuilder> protein_map, int warning_counter) {
-
- int mrna_counter = 0;
- not_protein_builder.append("#Genome ").append(genome_nr).append("\n");
- while (mrna_nodes.hasNext()) {
- mrna_counter++;
- Node mrna_node = mrna_nodes.next();
- if (mrna_counter % 1000 == 0) {
- System.out.print("\rGathering mRNA nodes: Genome " + genome_nr + ". " + mrna_counter);
- }
- if (skip_array[genome_nr-1]) {
- continue;
- }
- String mrna_name = "", mrna_protein = "";
- if (mrna_node.hasProperty("protein_ID")) {
- mrna_protein = get_protein_sequence(mrna_node);
- mrna_name = (String) mrna_node.getProperty("protein_ID");
- } else { // this can only happen in pangenomes
- String mrna_name2 = (String) mrna_node.getProperty("name");
- String mrna_id2 = (String) mrna_node.getProperty("id");
- int[] mrna_address = (int[]) mrna_node.getProperty("address");
- not_protein_builder.append(mrna_node.getId()).append(",").append(mrna_id2).append(",").append(mrna_name2).append(",")
- .append(mrna_address[0]).append(" ").append(mrna_address[1]).append(" ").append(mrna_address[2]).append(" ").append(mrna_address[3]).append("\n");
- warning_counter ++;
- continue;
- }
- String genome_str = Integer.toString(genome_nr);
- StringBuilder all_proteins = protein_map.get(genome_str);
- all_proteins.append(">").append(mrna_name).append("_genome_").append(genome_nr).append("\n")
- .append(mrna_protein).append("\n");
- protein_map.put(genome_str, all_proteins);
- }
- return warning_counter;
- }
-
-
- /**
*
* @param genes_per_genome
* @param go_hits_per_genome
@@ -2974,7 +2480,7 @@ public class FunctionalAnnotations {
try (Transaction tx = graphDb.beginTx()) {
Node pangenome_node = graphDb.findNodes(pangenome_label).next();
check_if_panproteome(pangenome_node); // sets PROTEOME boolean that controls functions, retrieves K_size & total_genomes
- stop_if_no_active_grouping_present(); // stops if there are no active homology groups
+ stop_if_no_active_grouping_present(); // stop if there is active homology grouping
create_skip_arrays(false, true);
annotation_identifiers = get_annotation_identifiers(false, false); // do not print, USE the input via -af
tx.success();
@@ -3017,7 +2523,7 @@ public class FunctionalAnnotations {
public static void count_COGs_for_function_overview() {
HashMap<String, HashSet<Node>> hmgroups_per_class = new HashMap<>();
HashMap<String, Integer> cog_counter_map = new HashMap<>();
- StringBuilder output_builder = new StringBuilder();
+ StringBuilder missing_builder = new StringBuilder("\n#Part 4. Homology groups without COG category\n");
int[] counter_array = new int[total_genomes+1]; // total COG nodes per genome
int total_cog_nodes = (int) count_nodes(COG_label); // count nodes with a specific label
int node_counter = 0;
@@ -3033,7 +2539,7 @@ public class FunctionalAnnotations {
while (cog_nodes.hasNext()) {
node_counter ++;
if (node_counter % 100 == 0 || node_counter == total_cog_nodes) {
- System.out.print("\rExtracting 'COG' nodes: " + node_counter + "/" + total_cog_nodes + " ");
+ System.out.print("\rExtracting 'COG' nodes: " + node_counter + "/" + total_cog_nodes + " "); // spaces are intentional
}
Node cog_node = cog_nodes.next();
long node_id = cog_node.getId();
@@ -3099,10 +2605,18 @@ public class FunctionalAnnotations {
StringBuilder header_builder = new StringBuilder();
HashMap<String, Integer> class_counter = count_hmgroups_per_class(hmgroups_per_class);
add_annotated_to_stringbuilder(class_counter, hmgroups_per_class, header_builder, "COG") ;
- add_missing_groups_to_stringbuilder(hmgroups_per_class, output_builder, "COG");
+ add_missing_groups_to_stringbuilder(hmgroups_per_class, missing_builder, "COG");
+
+ StringBuilder all_mrnas_with_cog = new StringBuilder();
+ if (!PROTEOME) {
+ all_mrnas_with_cog.append("\n#Part 3. mRNAs per COG category. ")
+ .append("Information on each line: genome number, mRNA/gene name, mRNA id, mRNA node id, homology group id\n");
+ } else {
+ all_mrnas_with_cog.append("\n#Part 3. Proteins per COG category. ")
+ .append("Information on each line: genome number, protein id, protein node id, homology group node id\n");
+ }
- StringBuilder all_mrnas_with_cog = new StringBuilder();
- for (String cog_category : cog_category_array) { // maak nu de all mrnas
+ for (String cog_category : cog_category_array) {
String[] cog_cat_array = cog_category.split(": ");
all_mrnas_with_cog.append("#").append(cog_category).append("\n");
StringBuilder mrna_per_category = all_mrnas_per_cog.get(cog_cat_array[0]);
@@ -3113,26 +2627,53 @@ public class FunctionalAnnotations {
}
}
- String cog_categories_abundance = create_COG_rscript_input(cog_counter_map, cog_cat_counter_map);
- String cog_results_header = "\n#Part 1. Abundance of COGs within a category (core,accessory unique). Two numbers after each category. "
- + "The first is the percentage abundances of COG functional categories within a category. "
- + "The second is the log2(relative abundance)\n\n" + cog_categories_abundance;
-
- if (!PROTEOME) {
- cog_results_header += "\n#Part 2. mRNAs per COG category. "
- + "Information on each line: genome number, mRNA/gene name, mRNA id, mRNA node id, homology group id\n" + all_mrnas_with_cog.toString();
- } else {
- cog_results_header += "\n#Part 2. Proteins per COG category. "
- + "Information on each line: genome number, protein id, protein node id, homology group node id\n" + all_mrnas_with_cog.toString();
- }
- cog_results_header += "\n#Part 3. Homology groups without COG category\n";
-
- write_string_to_file_in_DB(header_builder.toString() + output_builder2.toString() + cog_results_header + output_builder.toString(),
- "function/cog_overview.txt");
+ HashMap<String, String> cog_log2_map = create_COG_rscript_input(cog_counter_map, cog_cat_counter_map);
+ String freq_abundance_output = create_COG_abundance_frequency_tables(cog_log2_map, cog_cat_counter_map);
+
+
+ write_string_to_file_in_DB(header_builder.toString() + output_builder2.toString() +
+ freq_abundance_output + all_mrnas_with_cog.toString() + missing_builder.toString(),
+ "function/cog_overview.csv");
create_COG_rscript();
System.out.print("\r ");
}
+ /**
+ *
+ * @param cog_log2_map
+ * @param cog_cat_counter_map
+ * @return
+ */
+ public static String create_COG_abundance_frequency_tables(HashMap<String, String> cog_log2_map, HashMap<String, int[]> cog_cat_counter_map) {
+ String[] class_array = {"core", "accessory", "unique"};
+ StringBuilder frequency_builder = new StringBuilder("#Part 2. COG category frequency per genome\nCOG category;");
+ for (int i = 1; i <= total_genomes; i++) {
+ frequency_builder.append(i);
+ if (i != total_genomes) {
+ frequency_builder.append(";");
+ }
+ }
+ frequency_builder.append("\n");
+
+ StringBuilder abundance_builder = new StringBuilder();
+ abundance_builder.append("\n#Part 1. Abundance of COGs within a category (core,accessory unique). Two numbers after each category. "
+ + "The first is the percentage abundances of COG functional categories within a category. "
+ + "The second is the log2(relative abundance)\n\n");
+
+ for (String category : cog_category_array) {
+ String[] category_array = category.split(":");
+ int[] occurance = cog_cat_counter_map.get(category_array[0]);
+ frequency_builder.append(category).append(";").append(Arrays.toString(occurance).replace("[","").replace("]","").replace(" ","").replace(",",";")).append("\n");
+ abundance_builder.append(category).append("\n");
+ for (String class1 : class_array) {
+ String log2_pc = cog_log2_map.get(category + "#" + class1);
+ abundance_builder.append(class1).append(" ").append(log2_pc).append("\n");
+ }
+ abundance_builder.append("\n");
+ }
+ return abundance_builder.toString() + frequency_builder.toString();
+ }
+
/**
* Print output files nmaes if they were created
*/
@@ -3170,7 +2711,7 @@ public class FunctionalAnnotations {
System.out.print(dir + "phobius_signalp_overview.csv\n ");
}
if (cog_present) {
- System.out.print(dir + "cog_overview.txt\n "
+ System.out.print(dir + "cog_overview.csv\n "
+ dir + "cog_per_class.R\n\n");
} else {
System.out.println("");
@@ -4179,7 +3720,7 @@ public class FunctionalAnnotations {
mRNA-cox2 0.107 25 0.132 12 0.270 4 0.162 0.148 N 0.450 SignalP-noTM
mRNA-cox2_1 0.850 17 0.776 17 0.785 2 0.717 0.753 Y 0.500 SignalP-TM
- output of 5.1, OTHER means there is no signal peptide
+ output of 5.0, OTHER means there is no signal peptide
# SignalP-5.0 Organism: Eukarya Timestamp: 20211122233246
# ID Prediction SP(Sec/SPI) OTHER CS Position
diff --git a/src/pangenome/GenomeLayer.java b/src/pangenome/GenomeLayer.java
index 870dea06fd10add27f121b0ab89f2c75e4f599b9..8f18f751f1c083023f11a4d61ae4f2470ec1259e 100755
--- a/src/pangenome/GenomeLayer.java
+++ b/src/pangenome/GenomeLayer.java
@@ -2290,6 +2290,7 @@ public class GenomeLayer {
/**
* Retrieves some genomic regions from the genome database.
+ *
*/
public void retrieve_regions() {
String[] fields;
@@ -2331,10 +2332,16 @@ public class GenomeLayer {
continue;
}
fields = line.trim().split("\\s");
- genome = Integer.parseInt(fields[0]);
- sequence = Integer.parseInt(fields[1]);
- begin = Integer.parseInt(fields[2]);
- end = Integer.parseInt(fields[3]);
+ try {
+ genome = Integer.parseInt(fields[0]);
+ sequence = Integer.parseInt(fields[1]);
+ begin = Integer.parseInt(fields[2]);
+ end = Integer.parseInt(fields[3]);
+ } catch(NumberFormatException e) {
+ System.out.println("Unable to correctly retrieve four numbers in: " + line);
+ out.close();
+ continue;
+ }
if (genome >= 1 && genome <= genomeDb.num_genomes && sequence <= genomeDb.num_sequences[genome] &&
begin >= 1 && end <= genomeDb.sequence_length[genome][sequence]) {
@@ -2344,7 +2351,7 @@ public class GenomeLayer {
end -= 1;
seq.setLength(0);
genomeSc.get_sub_sequence(seq, genome, sequence, begin, end - begin + 1, true);
- if (line.endsWith("-") || line.endsWith("rv")) {
+ if (line.endsWith("-") || line.endsWith("rv")) { // manual only mentions '-'
String rv_sequence = get_rv_complement(seq.toString());
write_fasta(out, rv_sequence, 70);
} else {
@@ -2401,7 +2408,7 @@ public class GenomeLayer {
continue;
try{
genome = Integer.parseInt(genome_number);
- }catch(NumberFormatException e) {
+ } catch(NumberFormatException e) {
System.out.println(genome_number + "is not a valid genome number.");
continue;
}
@@ -2414,8 +2421,6 @@ public class GenomeLayer {
out = new BufferedWriter(new FileWriter(OUTPUT_PATH + "/Genome_" + genome_number + ".fasta"));
for (sequence = 1; sequence <= genomeDb.num_sequences[genome]; ++sequence) {
System.out.println("Sequence " + sequence + " length = " + genomeDb.sequence_length[genome][sequence]);
- //begin = 1;
- //end = (int)genomeDb.sequence_length[genome][sequence];
out.write(">" + genomeDb.sequence_titles[genome][sequence] + "\n");
begin = 0;
end = (int)genomeDb.sequence_length[genome][sequence] - 1;
diff --git a/src/pangenome/Phylogeny.java b/src/pangenome/Phylogeny.java
index 3e72392556b2343cbb3b74531b018c6b2a6b8e3a..2bfbc349d98c3b13939f5f649899c5172b9f48fb 100644
--- a/src/pangenome/Phylogeny.java
+++ b/src/pangenome/Phylogeny.java
@@ -63,70 +63,10 @@ import static pantools.Pantools.WD_full_path;
import static pantools.Pantools.geno_pheno_map;
import static pantools.Pantools.check_if_graphDb_is_available;
import static pantools.Pantools.connect_pangenome;
-import static pantools.Pantools.copy_file;
import static pantools.Pantools.create_directory_in_DB;
import static pantools.Pantools.delete_directory;;
-import static pantools.Pantools.indexDb;
-import static pantools.Pantools.print_runtime;
-import static pantools.Pantools.append_string_to_file_full_path;
-import static pantools.Pantools.pantools_path;
-import static pantools.Pantools.write_SB_to_file_in_DB;
-import static pantools.Pantools.write_string_to_file_in_DB;
-import static pantools.Pantools.write_SB_to_file_full_path;
-import static pantools.Pantools.append_SB_to_file_full_path;
-import static pantools.Pantools.check_if_file_exists;
-import static pantools.Pantools.delete_file_in_DB;
-import static pantools.Pantools.delete_file_full_path;
-import static pantools.Pantools.check_if_program_exists_stdout;
-import static pantools.Pantools.check_if_program_exists_stderr;
-import static pangenome.create_skip_arrays.create_skip_arrays;
-import static pantools.Pantools.retrieve_phenotypes;
-import static pantools.Pantools.count_nodes;
-import static pantools.Pantools.stop_if_panproteome;
-import static pantools.Pantools.classification;
-import static pantools.Pantools.genome_label;
-import static pantools.Pantools.phenotype_label;
-import java.io.BufferedWriter;
-import java.io.FileWriter;
-import java.util.Date;
-import java.text.SimpleDateFormat;
-import static pantools.Pantools.genomeDb;
-import static pantools.Pantools.genomeSc;
-import static pantools.Pantools.indexSc;
-import java.text.DecimalFormat;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.LinkedBlockingQueue;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.atomic.AtomicInteger;
-import java.util.concurrent.atomic.AtomicLong;
-import static pangenome.Classification.check_if_msa_is_complete;
-import static pangenome.Classification.divide;
-import static pangenome.Classification.stop_with_less_than_X_genomes;
-import static pangenome.Classification.trim_prealigned_proteins;
-import static pangenome.Classification.try_incr_hashset_hashmap;
-import static pangenome.Classification.try_incr_hashmap;
-import static pangenome.Classification.check_if_informative_position;
-import static pangenome.Classification.get_full_protein_identifiers;
-import static pangenome.Classification.read_genome_order_file;
-import static pangenome.Classification.read_mafft_alignment;
-import static pantools.Pantools.INPUT_FILE;
-import static pantools.Pantools.SELECTED_HMGROUPS;
-import static pantools.Pantools.annotation_identifiers;
-import static pantools.Pantools.check_current_grouping_version;
-import static pantools.Pantools.check_if_panproteome;
-import static pantools.Pantools.check_r_libraries_environment;
-import static pantools.Pantools.grouping_version;
-import static pantools.Pantools.write_fasta;
-import static pantools.Pantools.write_string_to_file_full_path;
-import static pantools.Pantools.PROTEOME;
-import static pantools.Pantools.FAST;
import static pantools.Pantools.K_SIZE;
-import static pantools.Pantools.print_runtime;
-import sequence.SequenceScanner;
import static pantools.Pantools.indexDb;
-import static pantools.Pantools.print_runtime;
import static pantools.Pantools.append_string_to_file_full_path;
import static pantools.Pantools.pantools_path;
import static pantools.Pantools.write_SB_to_file_in_DB;
@@ -219,7 +159,7 @@ public class Phylogeny {
}
if (Mode.equals("0")) {
- System.out.println("--mode extensive was NOT included. Can only find exact (& case insensitive) matches!");
+ System.out.println("--mode extensive was NOT included. Can only find exact (and case insensitive) matches!");
} else if (Mode.equals("EXTENSIVE")) {
System.out.println("Extensive search mode was selected. Can find exactly matching or shorter gene names!");
} else {
@@ -438,232 +378,7 @@ public class Phylogeny {
+ WORKING_DIRECTORY + "mlsa/input/concatenated.fasta\n\n"
+ "Log file:\n " + WORKING_DIRECTORY + "mlsa/mlsa.info\n");
}
-
- /**
- *
- */
- public void mlsa_check_seq_verify_input() {
- if (SELECTED_NAME == null) { // no input
- System.out.println("No genes were provided via --name\n");
- System.exit(1);
- }
- boolean exists = check_if_file_exists(WORKING_DIRECTORY + "mlsa/input/protein/" + SELECTED_NAME + ".fasta");
- boolean exists2 = check_if_file_exists(SELECTED_NAME);
- if (!exists && !exists2) {
- System.out.println("No directory or fasta file can be found on:\n "
- + SELECTED_NAME + " \n "
- + WORKING_DIRECTORY + "mlsa/input/protein/" + SELECTED_NAME + ".fasta\n");
- System.exit(1);
- }
- }
-
- /**
- *
- */
- public void mlsa_check_sequences() {
- System.out.println("\nMLSA. Check sequences\n");
- mlsa_check_seq_verify_input();
- create_directory_in_DB("mlsa/check_sequences/var_inf_positions");
- create_directory_in_DB("mlsa/check_sequences/similarity_identity");
- check_if_graphDb_is_available(); // starts up the graph database if needed
- try (Transaction tx = graphDb.beginTx()) { // start database transaction
- Node pangenome_node = graphDb.findNodes(pangenome_label).next();
- stop_if_panproteome(pangenome_node, "MLSA_check_sequences"); // stops the progam when run on a panproteome, retrieves K_size & total_genomes
- create_skip_arrays(false, true); // create skip array if --skip/-ref is provided by user
- retrieve_phenotypes(); // create geno_pheno_map and new_phenotype_map when a phenotype was provided by the user
- tx.success(); // transaction successful, commit changes
- } catch (NotFoundException nfe) {
- System.out.println("Unable to start the database");
- }
- String threads_str = report_number_of_threads(true, true); // prints how many threads were selected by user
- String output_path = WD_full_path + "mlsa/check_sequences/";
- String genome_order = WORKING_DIRECTORY + "mlsa/check_sequences/genome_order.info";
- String nuc_or_prot_short = "nuc";
- String[] type_array;
-
- if (SELECTED_NAME.contains("protein")) { // if a path is given, check if its protein or nucleotide sequences
- type_array = new String[]{"protein"};
- } else if (SELECTED_NAME.contains("nucleotide")) {
- type_array = new String[]{"nucleotide"};
- } else {
- type_array = new String[]{"protein", "nucleotide"};
- }
-
- for (String nuc_or_prot : type_array) {
- String output_path2 = output_path + "var_inf_positions/";
- String output_path3 = output_path + "similarity_identity/";
- if (nuc_or_prot.equals("protein")) {
- nuc_or_prot_short = "prot";
- }
-
- int sequences_present = change_headers_fasta_for_check(nuc_or_prot); // creates ..._input.fasta
- boolean pass = false;
- while (!pass) {
- String[] command = new String[] {"mafft", "--auto", "--anysymbol", "--clustalout", "--thread", threads_str,
- WORKING_DIRECTORY + "mlsa/check_sequences/" + nuc_or_prot_short + "_input.fasta"};
- System.out.print("\r2/3. Aligning " + sequences_present + " " + nuc_or_prot + " sequences ");
- String mafft_output = ExecCommand.ExecCommand(command);
- if (!mafft_output.equals("")) {
- pass = true;
- write_string_to_file_full_path(mafft_output, output_path + nuc_or_prot_short + "_alignment.afa");
- }
- }
-
- convert_afa_to_aligned_fasta(output_path + nuc_or_prot_short + "_input.fasta", output_path + nuc_or_prot_short + "_alignment.afa");
- String[] tree = new String[]{"FastTree","-out", output_path + SELECTED_NAME + "_" + nuc_or_prot_short + ".newick",
- output_path + nuc_or_prot_short + "_alignment.fasta"};
- ExecCommand.ExecCommand(tree);
-
- System.out.print("\r3/3. Reading " + nuc_or_prot + " alignment ");
- HashMap<String, Integer> shared_snps_map = new HashMap<>();
- int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, null, null, output_path + nuc_or_prot_short + "_alignment.afa",
- "Multiple sequence alignment", "nucleotide", genome_order); // variable, informative, shared between all
- System.out.print("\rVariable/informative positions in " + nuc_or_prot + " sequences: " + var_inf_sites[0] + "/" + var_inf_sites[1] + "\n");
- classification.create_shared_site_matrices(shared_snps_map, output_path2, var_inf_sites[0], "", nuc_or_prot_short, genome_order);
- classification.create_shared_site_matrices(shared_snps_map, output_path2, var_inf_sites[1], "#inf", nuc_or_prot_short, genome_order);
- classification.create_identity_matrices(shared_snps_map, var_inf_sites[0], var_inf_sites[2], nuc_or_prot,
- output_path3 + nuc_or_prot_short + "_identity.csv", genome_order);
-
- Mode = "DESC";
- if (nuc_or_prot.equals("protein")) {
- create_similarity_matrices(shared_snps_map, output_path3 + "prot_similarity.csv", var_inf_sites[0], var_inf_sites[2], genome_order);
- INPUT_FILE = output_path3 + "prot_similarity.csv";
- rename_headers_matrix_for_mlsa(INPUT_FILE);
- classification.order_matrix(false);
- copy_file(PATH_TO_THE_ANNOTATIONS_FILE + "_ORDERED", output_path3 + "prot_similarity_ordered.txt");
- copy_file(PATH_TO_THE_ANNOTATIONS_FILE + "_PHENOTYPE", output_path3 + "prot_similarity_phenotype.txt");
- delete_file_full_path(INPUT_FILE + "_ORDERED");
- delete_file_full_path(INPUT_FILE + "_PHENOTYPE");
- }
- System.out.println("rest is disabled");
- boolean test = true;
- if (test) {
- System.exit(1);
- }
-
- PATH_TO_THE_ANNOTATIONS_FILE = output_path3 + nuc_or_prot_short + "_identity.csv";
- rename_headers_matrix_for_mlsa(PATH_TO_THE_ANNOTATIONS_FILE);
- classification.order_matrix(false);
- copy_file(PATH_TO_THE_ANNOTATIONS_FILE + "_ORDERED", output_path3 + nuc_or_prot_short + "_identity_ordered.txt");
- copy_file(PATH_TO_THE_ANNOTATIONS_FILE + "_PHENOTYPE", output_path3 + nuc_or_prot_short + "_identity_phenotype.txt");
- delete_file_full_path(PATH_TO_THE_ANNOTATIONS_FILE + "_ORDERED");
- delete_file_full_path(PATH_TO_THE_ANNOTATIONS_FILE + "_PHENOTYPE");
-
- Mode = "ASC";
- PATH_TO_THE_ANNOTATIONS_FILE = output_path2 + "informative_" + nuc_or_prot_short + "_distance.csv";
- rename_headers_matrix_for_mlsa(PATH_TO_THE_ANNOTATIONS_FILE);
- classification.order_matrix(false);
- copy_file(PATH_TO_THE_ANNOTATIONS_FILE + "_ORDERED", PATH_TO_THE_ANNOTATIONS_FILE + "/informative_" + nuc_or_prot_short + "_distances_ordered.txt");
- copy_file(PATH_TO_THE_ANNOTATIONS_FILE + "_PHENOTYPE", PATH_TO_THE_ANNOTATIONS_FILE + "/informative_" + nuc_or_prot_short + "_distances_phenotype.txt");
- delete_file_in_DB(PATH_TO_THE_ANNOTATIONS_FILE + "_ORDERED");
- delete_file_in_DB(PATH_TO_THE_ANNOTATIONS_FILE + "_PHENOTYPE");
-
- PATH_TO_THE_ANNOTATIONS_FILE = output_path2 + "variable_" + nuc_or_prot_short + "_distance.csv";
- rename_headers_matrix_for_mlsa(PATH_TO_THE_ANNOTATIONS_FILE);
- classification.order_matrix(false);
- copy_file(PATH_TO_THE_ANNOTATIONS_FILE + "_ORDERED", PATH_TO_THE_ANNOTATIONS_FILE + "/variable_" + nuc_or_prot_short + "_distances_ordered.txt");
- copy_file(PATH_TO_THE_ANNOTATIONS_FILE + "_PHENOTYPE", PATH_TO_THE_ANNOTATIONS_FILE + "/variable/" + nuc_or_prot_short + "_distances_phenotype.txt");
- delete_file_in_DB(PATH_TO_THE_ANNOTATIONS_FILE +"_ORDERED");
- delete_file_in_DB(PATH_TO_THE_ANNOTATIONS_FILE +"_PHENOTYPE");
- }
- delete_file_in_DB("mlsa/check_sequences/genome_order.info");
- System.out.println("\nOutput written to:\n "
- + WORKING_DIRECTORY + "mlsa/check_sequences/\n "
- + WORKING_DIRECTORY + "mlsa/check_sequences/var_inf_positions\n "
- + WORKING_DIRECTORY + "mlsa/check_sequences/similarity_identity\n");
- graphDb.shutdown();
- }
-
- /**
- *
- * @param input_file
- */
- public void rename_headers_matrix_for_mlsa(String input_file) {
- StringBuilder output_builder = new StringBuilder ();
- try (BufferedReader in = new BufferedReader(new FileReader(input_file))) {
- boolean first = true;
- for (int c = 0; in.ready();) {
- String line = in.readLine().trim();
- String[] line_array = line.split(",");
- if (first) {
- output_builder.append(line_array[0]).append(",");
- for (int i = 1; i < line_array.length; i++) {
- String[] line_array2 = line_array[i].split(" ");
- int genome_nr = Integer.valueOf(line_array2[2]);
- String phenotype = get_phenotype_for_genome(genome_nr, true);
- output_builder.append(line_array2[1]).append(phenotype).append(",");
- }
- first = false;
- } else {
- String[] line_array2 = line_array[0].split(" ");
- int genome_nr = Integer.valueOf(line_array2[2]);
- String phenotype = get_phenotype_for_genome(genome_nr, true);
- output_builder.append(line_array2[1]).append(phenotype).append(",");
- for (int i = 1; i < line_array.length; i++) {
- output_builder.append(line_array[i]).append(",");
- }
- }
- output_builder.append("\n");
- }
- } catch (IOException ioe) {
- System.out.println("Failed to read:" + input_file);
- System.exit(1);
- }
- write_SB_to_file_full_path(output_builder, input_file);
- }
-
- /**
- *
- * @param nuc_or_prot
- * @return
- */
- public int change_headers_fasta_for_check(String nuc_or_prot) {
- String nuc_or_prot_short = "nuc";
- if (nuc_or_prot.equals("protein")) {
- nuc_or_prot_short = "prot";
- }
- ArrayList <String> files_to_change = new ArrayList<>();
- if (SELECTED_NAME.contains("/") && SELECTED_NAME.contains("mlsa")) { // path was given to multiple homology groups
- File folder = new File(SELECTED_NAME);
- String[] files = folder.list();
- for (String file : files) {
- files_to_change.add(folder + "/" + file);
- }
- } else { // only the gene name is given, add 1 file
- files_to_change.add(WORKING_DIRECTORY + "mlsa/input/" + nuc_or_prot + "/" + SELECTED_NAME + ".fasta");
- }
- System.out.print("\r1/3. Changing fasta header of " + files_to_change.size() + " files");
- int counter = 0;
- StringBuilder new_fasta = new StringBuilder();
- StringBuilder genome_order = new StringBuilder();
- for (String file : files_to_change) {
- try {
- BufferedReader in = new BufferedReader(new FileReader(file));
- while (in.ready()) {
- String line = in.readLine().trim();
- if (line.startsWith(">")) {
- counter ++;
- String[] line_array = line.split(" ");
- String[] line_array2 = line_array[1].split("_");
- String prot_id = line_array[0].replace(">","");
- String phenotype = get_phenotype_with_underscore(Integer.parseInt(line_array2[2]));
- new_fasta.append(">").append(prot_id).append(" genome ").append(line_array2[2]).append(phenotype).append("\n");
- genome_order.append(line_array2[2]).append(",").append(prot_id).append(" genome ")
- .append(line_array2[2]).append(phenotype).append("\n");
- } else {
- new_fasta.append(line).append("\n");
- }
- }
- } catch (IOException ioe) {
- System.out.println("\nUnable to read: " + file + "\n");
- System.exit(1);
- }
- }
- write_SB_to_file_in_DB(new_fasta, "mlsa/check_sequences/" + nuc_or_prot_short + "_input.fasta");
- write_SB_to_file_in_DB(genome_order, "mlsa/check_sequences/genome_order.info");
- return counter;
- }
-
+
/*
--mode 1, skip over IQ-tree (this option is hidden in the manual)
*/
@@ -680,11 +395,11 @@ public class Phylogeny {
retrieve_phenotypes(); // create geno_pheno_map and new_phenotype_map when a phenotype was provided by the user
tx.success(); // transaction successful, commit changes
} catch (NotFoundException nfe) {
- System.out.println("Unable to start the database");
+ System.out.println("\rUnable to start the database");
return;
}
if (Mode.equals("1") || Mode.contains("SKIP")) {
- System.out.println("--mode skip selected. Skipping over IQtree");
+ System.out.println("\r--mode skip selected. Skipping over IQtree");
}
read_concatenated_fasta_for_genome_order();
@@ -693,50 +408,68 @@ public class Phylogeny {
check_if_program_exists_stdout("iqtree -h", 100, "IQtree");
String path = WORKING_DIRECTORY + "mlsa/";
if (!check_if_file_exists(WORKING_DIRECTORY+ "mlsa/input/concatenated.fasta")) {
- System.out.println("Please run 'MLSA_concatenate' first!"
+ System.out.println("\rPlease run 'MLSA_concatenate' first!"
+ "\nNo sequences found in " + WORKING_DIRECTORY + "mlsa/input/concatenated.fasta\n");
System.exit(1);
}
- System.out.print("Step 1/3. Aligning sequences using MAFFT.");
+ System.out.print("\rStep 1/3. Aligning sequences using MAFFT");
run_alignment_for_mlsa();
- System.out.println("\nStep 2/3. Running IQtree");
- if (!Mode.equals("1") && !Mode.contains("SKIP")) { // these two modes were only created for development, not shown in manual
- LOG = true; // to print the iq-tree log output to the screen
- String[] iq_command = {"iqtree", "-nt", threads_str, "-s", path + "output/mlsa.fasta","-redo","-bb", "1000"};
- ExecCommand.ExecCommand(iq_command);
- }
- System.out.println("\nStep 3/3. Extracting SNPs from alignment");
+
+ System.out.println("\nStep 2/3. Identifying SNPs in the alignment.");
HashMap<String, Integer> shared_snps_map = new HashMap<>();
- int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, null,
- null, path + "output/mlsa.afa", "MLSA", "nucleotide", path + "input/genome_order.info"); // variable, informative, shared between all
+ StringBuilder pheno_specific_output = new StringBuilder("# Each row contains: position in the alignment,"
+ + " reference letter/other letters found, phenotype, "
+ + "number of sequences with the phenotype and letter/total sequences with phenotype\n");
+ HashMap<String, Integer> pheno_specific_group_sites = new HashMap<>();
+ if (PHENOTYPE == null) {
+ pheno_specific_output = null;
+ pheno_specific_group_sites = null;
+ }
+ int[] var_inf_sites = count_var_inf_sites_in_msa(shared_snps_map, pheno_specific_output,
+ pheno_specific_group_sites, path + "output/mlsa.afa", "MLSA", "nucleotide", path + "input/genome_order.info"); // variable, informative, shared between all
System.out.println("\nTotal variable/informative sites: " + var_inf_sites[0] + "/" + var_inf_sites[1]);
classification.create_shared_site_matrices(shared_snps_map, path + "output/var_inf_positions/", var_inf_sites[0], "", "nuc", path + "input/genome_order.info");
classification.create_shared_site_matrices(shared_snps_map, path + "output/var_inf_positions/", var_inf_sites[1], "#inf", "nuc", path + "input/genome_order.info");
delete_file_full_path(WORKING_DIRECTORY + "mlsa/input/genome_order.info");
+
+ System.out.println("\nStep 3/3. Running IQtree");
+ if (!Mode.equals("1") && !Mode.contains("SKIP") && var_inf_sites[1] > 0) { // these two modes were only created for development, not shown in manual
+ LOG = true; // to print the iq-tree log output to the screen
+ String[] iq_command = {"iqtree", "-nt", threads_str, "-s", path + "output/mlsa.fasta","-redo","-bb", "1000"};
+ ExecCommand.ExecCommand(iq_command);
+ }
+
System.out.print("\nOutput written to:\n "
+ path + "output/\n "
+ path + "output/mlsa.afa\n "
+ path + "output/mlsa.fasta\n "
- + path + "output/nuc_alignment_info\n ");
- if (!Mode.equals("1") && !Mode.contains("SKIP")) {
+ + path + "output/nuc_alignment.info\n ");
+
+ if (PHENOTYPE != null) {
+ System.out.print(path + "output/nuc_phenotype_specific_changes.info\n ");
+ }
+ if (!Mode.equals("1") && !Mode.contains("SKIP")) { // these two modes were only created for development, not shown in manual
System.out.print(path + "output/mlsa.fasta.treefile\n "
+ + path + "output/mlsa.fasta.contree\n "
+ path + "output/mlsa.fasta.iqtree\n");
}
+
System.out.print("\n " + path + "output/var_inf_positions/variable_nuc_distance.csv\n "
- + path + "output/var_inf_positions/variable_nuc_sites.csv\n ");
+ + path + "output/var_inf_positions/variable_nuc_site_counts.csv\n ");
if (var_inf_sites[1] > 0) {
System.out.print(path + "output/var_inf_positions/informative_nuc_distance.csv\n "
- + path + "output/var_inf_positions/informative_nuc_sites.csv\n\n");
+ + path + "output/var_inf_positions/informative_nuc_site_counts.csv\n\n");
} else {
- System.out.println("");
+ System.out.println("The alignment does not contains parsimony informative sites.\n"
+ + "Unable to infer a phylogeny!\n");
}
}
/**
- *
+ * Creates a genome_order.info file, used by the functions that count SNPs in the alignment
*/
public void read_concatenated_fasta_for_genome_order() {
StringBuilder genome_order = new StringBuilder();
@@ -747,7 +480,7 @@ public class Phylogeny {
if (line.startsWith(">")) {
String[] line_array = line.split("_");
String genome_nr = line_array[0].replace(">","");
- genome_order.append(genome_nr).append(",genome_").append(genome_nr).append("\n");
+ genome_order.append(genome_nr).append(",").append(genome_nr).append("\n");
target_genomes.append(genome_nr).append(",");
}
}
@@ -755,6 +488,7 @@ public class Phylogeny {
System.out.println("\nUnable to read: " + WORKING_DIRECTORY + "mlsa/input/concatenated.fasta\n");
System.exit(1);
}
+
String target_genomes_str = target_genomes.toString().replaceFirst(".$","");
target_genome = target_genomes_str;
create_skip_arrays(false, false); // create skip array if --skip/-ref is provided by user
@@ -786,7 +520,7 @@ public class Phylogeny {
public static void run_alignment_for_mlsa_concatenate(String gene_name, String path) {
boolean pass = false;
while (!pass) {
- String[] command = new String[] {"mafft","--auto", "--anysymbol", "--thread", THREADS + "", "--clustalout", path + gene_name + ".fasta"};
+ String[] command = new String[] {"mafft","--auto", "--anysymbol", "--thread", THREADS + "", "--clustalout", path + gene_name + ".fasta"};
String mafft_output = ExecCommand.ExecCommand(command);
if (!mafft_output.equals("")) {
pass = true;
@@ -975,8 +709,9 @@ public class Phylogeny {
counter ++;
}
- String info = counter + " genomes\nGenes: " + SELECTED_NAME +
- "\nAll sizes: " + all_sizes + "\n\n";
+ String info = counter + " genomes\n"
+ + "Genes: " + SELECTED_NAME + "\n"
+ + "All sizes: " + all_sizes + "\n\n";
if (all_sizes.size() == 1) {
System.out.println("All concatenated sequences have the same length: " + all_sizes.iterator().next());
} else {
@@ -2175,7 +1910,7 @@ public class Phylogeny {
}
check_if_node_exists_in_tree();
create_reroot_script();
- System.out.println("\nRscript written to:\n " +WORKING_DIRECTORY + "reroot.R\n");
+ System.out.println("\nRscript written to:\n " + WORKING_DIRECTORY + "reroot.R\n");
}
/**
diff --git a/src/pangenome/ProteomeLayer.java b/src/pangenome/ProteomeLayer.java
index d685c04d2969161f4b5644d7666abf56766fad76..46de4cc4d52a726a20a90a841dd154f5e70184bd 100755
--- a/src/pangenome/ProteomeLayer.java
+++ b/src/pangenome/ProteomeLayer.java
@@ -1212,7 +1212,7 @@ public class ProteomeLayer {
print_info = true; // compare_busco_to_grouping() now prints some info to user
compare_busco_to_grouping(skip_groupings);
String dir = WORKING_DIRECTORY + "optimal_grouping/";
- if (grouping_version == -1){
+ if (grouping_version == -1) {
System.out.println("\rNo grouping is currently active. Use 'change_active_grouping'");
} else {
System.out.println("\rGrouping " + grouping_version + " is currently active.");
@@ -2695,7 +2695,7 @@ public class ProteomeLayer {
if (annotation_identifiers.contains(identifier)) { // the number of proteins for genomes that are skipped are not present
int prot_count = (int) annotation_node.getProperty("num_proteins");
updated_num_proteins += prot_count;
- if (prot_count == 0){ // even though the genome is annotated, there are no protein coding genes
+ if (prot_count == 0) { // even though the genome is annotated, there are no protein coding genes
int genome_nr = Integer.parseInt(id_array[0]);
skip_array[genome_nr -1] = true;
skip_list.add(genome_nr);
@@ -2802,14 +2802,14 @@ public class ProteomeLayer {
}
if (longest_transcript_length > 0) {
- if (!longest_transcript_node.hasProperty("longest_transcript")){
+ if (!longest_transcript_node.hasProperty("longest_transcript")) {
longest_transcript_node.setProperty("longest_transcript", "yes");
}
Iterable<Relationship> relations = longest_transcript_node.getRelationships(RelTypes.is_parent_of);
for (Relationship rel : relations) {
Node cds_intron_exon_node = rel.getEndNode(); // CDS, intron or exon
if (cds_intron_exon_node.hasLabel(exon_label) || cds_intron_exon_node.hasLabel(CDS_label) || cds_intron_exon_node.hasLabel(intron_label)) {
- if (!cds_intron_exon_node.hasProperty("longest_transcript")){
+ if (!cds_intron_exon_node.hasProperty("longest_transcript")) {
cds_intron_exon_node.setProperty("longest_transcript", "yes");
}
}
@@ -2819,7 +2819,7 @@ public class ProteomeLayer {
for (Relationship rel : relations) {
Node cds_node = rel.getStartNode(); // CDS
if (cds_node.hasLabel(CDS_label)) {
- if (!cds_node.hasProperty("longest_transcript")){
+ if (!cds_node.hasProperty("longest_transcript")) {
cds_node.setProperty("longest_transcript", "yes");
}
}
@@ -2850,7 +2850,7 @@ public class ProteomeLayer {
When a genome does not have an annotation (or is skipped) the id will end with '_0'.
*/
public void update_skip_array_based_on_anno_ids() {
- if (annotation_identifiers == null){
+ if (annotation_identifiers == null) {
annotation_identifiers = get_annotation_identifiers(true, true);
}
for (String anno_id : annotation_identifiers) {
@@ -2876,7 +2876,6 @@ public class ProteomeLayer {
check_if_graphDb_is_available(); // starts up the graph database if needed
report_number_of_threads(true, true); // prints how many threads were selected by user
delete_files_from_previous_group_run();
- //connect_panproteome();
create_directory_in_DB("group");
proteins = new LinkedBlockingQueue<>();
@@ -3012,7 +3011,6 @@ public class ProteomeLayer {
tx.success();
}
copy_file(WORKING_DIRECTORY + "pantools_homology_groups.txt", WORKING_DIRECTORY + "/group/" + MIN_NORMALIZED_SIMILARITY);
- //disconnect_panproteome();
System.out.println("\nComponents = " + num_components);
System.out.println("Groups = " + num_groups + "\n");
System.out.println("Database size = " + getFolderSize(new File(WORKING_DIRECTORY + GRAPH_DATABASE_PATH)) + " MB");
diff --git a/src/pantools/Pantools.java b/src/pantools/Pantools.java
index 2123e68e46b610c9b628c7b33f69678e606221d9..441b34394cf2458317764bdbb7550833587f4e9f 100644
--- a/src/pantools/Pantools.java
+++ b/src/pantools/Pantools.java
@@ -266,6 +266,7 @@ public class Pantools {
public static Classification classification;
public static Phylogeny phylogeny;
public static FunctionalAnnotations functionalAnnotations;
+ private static final String PANTOOLS_VERSION = "3.2";
/**
* The main function of PanTools.
@@ -309,17 +310,15 @@ public class Pantools {
for (i = 0; i < label_strings.length; ++i) {
labels.put(label_strings[i], Label.label(label_strings[i]));
}
- System.out.println("\n------------------------------- PanTools ------------------------------");
+ System.out.println("\n------------------------------- PanTools " + PANTOOLS_VERSION + " ------------------------------");
pantools_path = Pantools.class.getProtectionDomain().getCodeSource().getLocation().getPath().replace("dist/pantools.jar", ""); // retrieve location of jar
StringBuilder command = new StringBuilder();
int loop_counter = 0; // to prevent an endless loop
Path currentRelativePath = Paths.get("");
current_path = currentRelativePath.toAbsolutePath().toString() + "/";
SELECTED_FUNCTION = args[0];
- if (SELECTED_FUNCTION.startsWith("-")) {
- System.out.println("\nNo subcommand was included\n");
- System.exit(1);
- }
+
+ verify_correct_subcommand();
try {
for (i = 1; i < args.length;) {
loop_counter ++;
@@ -496,7 +495,7 @@ public class Pantools {
case "--gap-open": case "-go":
x = Integer.parseInt(args[i + 1]);
i += 2;
- if ((x >= -50 && x <= -1) || args[0].equals("locate_genes")){
+ if ((x >= -50 && x <= -1) || args[0].equals("locate_genes")) {
GAP_OPEN = x;
} else {
System.out.println("Choose GAP_OPEN in the range [-50..-1] or do not specify it to use the default value. " + x);
@@ -733,7 +732,7 @@ public class Pantools {
System.out.println("RAW_ABUNDANCE_FILE = " + RAW_ABUNDANCE_FILE);
break;
case "--phenotype": case "-ph":
- if (!args[i + 1].equals(".") && !args[i + 1].equals("-") ){
+ if (!args[i + 1].equals(".") && !args[i + 1].equals("-") ) {
PHENOTYPE = args[i + 1];
System.out.println("SELECTED PHENOTYPE = '" + PHENOTYPE + "'");
}
@@ -809,7 +808,7 @@ public class Pantools {
System.out.println("Input file = " + INPUT_FILE);
i += 2;
break;
- case "--skip":
+ case "--skip": case "-sk":
skip_genomes = args[i + 1];
i += 2;
break;
@@ -892,7 +891,7 @@ public class Pantools {
case "pangenome_size_genes": case "pangenome_size_gene": case "pangenome_structure_genes":
classification.pangenome_size_genes();
break;
- case "pangenome_size_kmer": case "pangenome_size_kmers":
+ case "pangenome_size_kmer": case "pangenome_size_kmers": case "pangenome_structure_kmers":
classification.pangenome_size_kmer();
break;
case "kmer_classification":
@@ -935,7 +934,7 @@ public class Pantools {
case "find_genes_in_region":
classification.find_genes_in_region();
break;
- case "find_genes_by_annotation":
+ case "find_genes_by_function":
classification.find_genes_by_annotation();
break;
@@ -965,13 +964,10 @@ public class Pantools {
case "mlsa_concatenate": case "MLSA_concatenate":
phylogeny.mlsa_concatenate();
break;
- case "mlsa_check_sequences": case "MLSA_check_sequences":
- phylogeny.mlsa_check_sequences();
- break;
case "MLSA": case "mlsa": case "run_MLSA": case "run_mlsa":
phylogeny.run_MLSA();
break;
- case "consensus_tree": // added by Dirk-Jan
+ case "consensus_tree":
phylogeny.consensus_tree();
break;
@@ -991,7 +987,7 @@ public class Pantools {
case "add_functional_annotations": case "add_functions":
functionalAnnotations.add_functional_annotations();
break;
- case "functional_annotation_overview": case "FA_overview": case "fa_overview": case "function_overview":
+ case "functional_annotation_overview": case "function_overview":
functionalAnnotations.functional_annotation_overview();
break;
case "functional_classification": case "function_classification":
@@ -1000,9 +996,6 @@ public class Pantools {
case "go_enrichment": case "GO_enrichment":
functionalAnnotations.go_enrichment();
break;
- case "cog": case "COG": case "blast_cog":
- functionalAnnotations.blast_cog();
- break;
// construction
case "bpg": case "build_pangenome":
@@ -1044,11 +1037,11 @@ public class Pantools {
break;
case "h": case "help": case "-h": case "--help":
print_help_message("global");
- System.exit(1);
+ System.exit(0);
break;
case "v": case "version":
- System.out.println("PanTools version 3\nNeo4j community edition 3.5.3\nJDK 1.8");
- System.exit(1);
+ print_pantools_version();
+ System.exit(0);
default:
System.out.println(args[0] + " is not a valid PanTools command, type 'pantools.jar h [or help]' to see the manual.");
System.exit(1);
@@ -1069,6 +1062,41 @@ public class Pantools {
System.out.println("-----------------------------------------------------------------------");
}
+ public static void print_pantools_version() {
+ System.out.println("PanTools version " + PANTOOLS_VERSION + "\n"
+ + "Neo4j community edition 3.5.3\n"
+ + "JDK 1.8, You are using Java " + System.getProperty("java.version") +"\n");
+ }
+
+ /**
+ * Prevents starting PanTools when a subcommand is missing.
+ */
+ public static void verify_correct_subcommand() {
+ String[] help_commands = new String[]{"--help","-h"};
+ String[] version_commands = new String[]{"--version","-v"};
+ boolean stop = false; // when true, input starts with '-' meaning no subcommand was given
+ if (SELECTED_FUNCTION.startsWith("-") ) {
+ stop = true;
+ for (String help_command : help_commands) {
+ if (SELECTED_FUNCTION.equals(help_command)) {
+ print_help_message("global");
+ System.exit(0);
+ }
+ }
+ for (String version_command : version_commands) {
+ if (SELECTED_FUNCTION.equals(version_command)) {
+ print_pantools_version();
+ System.exit(0);
+ }
+ }
+ }
+
+ if (stop) {
+ System.out.println("\nNo subcommand was included\n");
+ System.exit(1);
+ }
+ }
+
/**
* Connects to genome, index and graph databases of the pangenome.
*/
@@ -1370,18 +1398,21 @@ public class Pantools {
/**
* Prints the manual of the software.
- * Put the manual in a textfile and let the function read and print the file
- * Thanks DJ!
+ * Put the manual in a textfile and let the function read and print the file?
*/
private static void print_help_message(String help) {
- System.out.println("\nPanTools version 3\n" +
+ System.out.println("\nPanTools version " + PANTOOLS_VERSION + "\n" +
"PanTools is pangenomic toolkit for comparative analysis of large number of genomes developed in the " +
"Bioinformatics group of Wageningen University, the Netherlands.\n" +
"Please cite the relevant publication(s) from the list of publications if you use PanTools in your research.\n");
+
switch (help) {
case "global":
System.out.println("Usage:\n" +
- "java <JVM options> -jar <path to pantools.jar> <command> <arguments>\n" +
+ " java <JVM options> -jar <path to pantools.jar> <subcommand> <arguments>\n" +
+ "\n" +
+ "Obtain the manual of a specific function:\n" +
+ " java -jar <path to pantools.jar> <subcommand> --help\n" +
"\n" +
" Construction of a pangenome\n" +
" build_pangenome : Build a pangenome out of a set of genomes.\n" +
@@ -1397,7 +1428,7 @@ public class Pantools {
" busco_protein : Identify BUSCO genes in the pangenome.\n" +
"\n" +
" Removing data from a pangenome or panproteome\n" +
- " remove_annotations : Remove all the genomic features belonging to structural annotations\n" +
+ " remove_annotations : Remove all the genomic features belonging to structural annotations.\n" +
" remove_nodes : To remove a selection of nodes from a pangenome.\n" +
" remove_phenotype : Remove phenotypes nodes or specific phenotype properties from nodes.\n" +
" remove_grouping : Remove an homology grouping from the pangenome.\n" +
@@ -1405,8 +1436,8 @@ public class Pantools {
" Detecting homology groups based on similarity of proteins\n" +
" group : Create homology groups in the protein space of the pangenome.\n" +
" optimal_grouping : Identify the optimal grouping in the protein space of the pangenome.\n" +
- " move_grouping : Inactivate the current homology grouping\n" +
- " change_grouping : Activate one of inactive homology groupings\n" +
+ " move_grouping : Inactivate the current homology grouping.\n" +
+ " change_grouping : Activate one of inactive homology groupings.\n" +
"\n" +
" Retrieving features/regions/genomes\n" +
" retrieve_features : Retrieve the sequence of annotated features from the pangenome.\n" +
@@ -1417,48 +1448,48 @@ public class Pantools {
" map : Map single or paired-end short reads to all or a sebset of the constituent genomes.\n" +
"\n" +
" Pangenome characterization\n" +
- " metrics : Report metrics for all available features of the pangenome \n" +
+ " metrics : Report metrics for all available features of the pangenome.\n" +
"\n" +
" Characterization of gene content\n" +
- " gene_classification : Classify the gene repertoire as core, accessory or unique\n" +
- " pangenome_size_genes : Determine the openess of the pangenome based on homology groups\n" +
- " core_unique_threshold : Test the effect of changing the --core-threshold and --unique-threshold\n" +
- " grouping_overview : Create an overview table for every homology grouping in the pangenome\n" +
- " grouping_info : Create an overview table for every homology grouping in the pangenome\n" +
- " locate_genes : Identify co-localized genes in a set of homology groups\n" +
+ " gene_classification : Classify the gene repertoire as core, accessory or unique.\n" +
+ " pangenome_size_genes : Determine the openness of the pangenome based on homology groups.\n" +
+ " core_unique_thresholds : Test the effect of changing the --core-threshold and --unique-threshold.\n" +
+ " grouping_overview : Create an overview table for every homology grouping in the pangenome.\n" +
+ " locate_genes : Identify co-localized genes in a set of homology groups.\n" +
+ " group_info : Report all available information of one or multiple homology groups.\n" +
"\n" +
" Characterization of k-mer content\n" +
- " kmer_classification : Classify the k-mer content as core, accessory or unique\n" +
- " pangenome_size_kmers : Determine the openess of the pangenome based on k-mer sequences\n" +
+ " kmer_classification : Classify the k-mer content as core, accessory or unique.\n" +
+ " pangenome_size_kmers : Determine the openess of the pangenome based on k-mer sequences.\n" +
"\n" +
" Characterization of functional annotations\n" +
- " functional_classification: Classify functional annotations as core, accessory or unique\n" +
- " function_overview : Create an overview table for each type of functional annotation in the pangenome\n" +
- " go_enrichment : Identify over or underrepresented GO terms in a set of genes\n" +
+ " functional_classification: Classify functional annotations as core, accessory or unique.\n" +
+ " function_overview : Create an overview table for each functional annotation type in the pangenome.\n" +
+ " go_enrichment : Identify over or underrepresented GO terms in a set of genes.\n" +
"\n" +
" Alignment functions\n" +
- " msa_of_group : Align the protein and nucleotide sequences of homology groups\n" +
- " msa_of_multiple_groups : Combine multiple homology groups into a single alignment\n" +
- " msa_of_regions : Align a selection of genomic regions\n" +
+ " msa_of_group : Align the protein and nucleotide sequences of homology groups.\n" +
+ " msa_of_multiple_groups : Use sequences from multiple homology groups for a single alignment.\n" +
+ " msa_of_regions : Align a selection of genomic regions.\n" +
"\n" +
" Find genes\n" +
- " find_genes_by_name : Find genes matching a gene name\n" +
- " find_genes_by_annotation : Find genes connected to a functional annotation \n" +
- " find_genes_in_region : Find genes in a given genomic region\n" +
+ " find_genes_by_name : Find genes matching a gene name.\n" +
+ " find_genes_by_function : Find genes connected to a functional annotation.\n" +
+ " find_genes_in_region : Find genes in a given genomic region.\n" +
"\n" +
" Phylogeny\n" +
" Phylogenetic methods\n" +
- " core_snp_tree : Create a SNP tree from single-copy genes\n" +
- " consensus_tree : Create a consensus tree from gene trees\n" +
- " ani : Create an ANI distance tree\n" +
- " mlsa_find_genes : Step 1/3 of MLSA. Search and filter suitable genes for the MLSA\n" +
- " mlsa_concatenate : Step 2/3 of MLSA. Concatenate the gene selection into a single continuous sequence \n" +
- " mlsa : Step 3/3 of MLSA. Run IQ-tree on the concatenated sequences\n" +
+ " core_snp_tree : Create a SNP tree from single-copy genes.\n" +
+ " consensus_tree : Create a consensus tree from gene trees.\n" +
+ " ani : Create an ANI distance tree.\n" +
+ " mlsa_find_genes : Step 1/3 of MLSA. Search and filter suitable genes for the MLSA.\n" +
+ " mlsa_concatenate : Step 2/3 of MLSA. Concatenate the gene selection into a single continuous sequence.\n" +
+ " mlsa : Step 3/3 of MLSA. Run IQ-tree on the concatenated sequences.\n" +
"\n" +
" Phylogenetic tree editing\n" +
- " rename_phylogeny : Update the terminal nodes (leaves) of a phylogenic tree\n" +
- " reroot_phylogeny : (Re) root a phylogenetic tree\n" +
- " create_tree_template : Create templates for coloring phylogenetic trees in iTOL\n" +
+ " rename_phylogeny : Update the terminal nodes (leaves) of a phylogenic tree.\n" +
+ " reroot_phylogeny : (Re) root a phylogenetic tree.\n" +
+ " create_tree_template : Create templates for coloring phylogenetic trees in iTOL.\n" +
"\n" +
" General:\n" +
" version or v : To show the versions of PanTools, JVM and Neo4j.\n" +
@@ -1483,31 +1514,40 @@ public class Pantools {
"Licence:\n" +
"PanTools has been licensed under GNU GENERAL PUBLIC LICENSE version 3.\n");
break;
-
case "bpg": case "build_pangenome":
System.out.println("build_pangenome or bpg : To build a pangenome out of a set of genomes.\n" +
"\n" +
- "Required software: KMC 2.3 or 3.0\n" +
+ "Required software: KMC 2.3 or 3.0.\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
" --genomes-file or -gf : A text file containing paths to FASTA files of genomes; each in a seperated line.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --kmer-size or -ks : The size of k-mers. If it is not given or is out of valid range (6 <= K_SIZE <= 255), " +
- "then an optimal value would be calculated automatically.\n");
+ " --kmer-size or -ks : The size of k-mers. If it is not given or is out of valid range (6 <= K_SIZE <= 255), " +
+ "then an optimal value would be calculated automatically.\n" +
+ "\n" +
+ "Example --genomes-file input file:\n" +
+ "/always/genome1.fasta\n" +
+ "/use_the/genome2.fasta\n" +
+ "/full_path/genome3.fasta\n");
break;
case "bpp": case "build_panproteome":
System.out.println("build_panproteome or bpp : To build a panproteome out of a set of proteins.\n" +
"\n" +
- "Required software: KMC 2.3 or 3.0\n" +
+ "Required software: KMC 2.3 or 3.0.\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --proteomes-file or -pf : A text file containing paths to FASTA files of proteomes; each in a seperated line.\n");
+ " --proteomes-file or -pf: A text file containing paths to FASTA files of proteomes; each in a seperated line.\n" +
+ "\n" +
+ "Example --proteomes-file input file:\n" +
+ "/always/genome1.fasta\n" +
+ "/use_the/genome2.fasta\n" +
+ "/full_path/genome3.fasta\n");
break;
case "ag": case "add_genomes":
System.out.println("add_genomes or ag : To add new genomes to an available pangenome.\n" +
@@ -1515,150 +1555,168 @@ public class Pantools {
"Required software: KMC 2.3 or 3.0\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
- " --genomes-file or -gf : A text file containing paths to FASTA files of the new genomes to be added to the pangeome; each in a seperated line.\n");
+ " --genomes-file or -gf : A text file containing paths to FASTA files of the new genomes to be added to the pangeome, " +
+ "each on a seperate line.\n" +
+ "\n" +
+ "Example --genomes-file input file:\n" +
+ "/always/genome4.fasta\n" +
+ "/use_the/genome5.fasta\n" +
+ "/full_path/genome6.fasta\n");
break;
case "aa": case "add_annotations":
System.out.println("add_annotations or aa : To add annotations to existing genomes.\n" +
+ "\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --annotations-file or -af : A text file each line of which contains genome number and path to the corresponding GFF file seperated by one space. "
- + "Genomes are numbered in the same order they have been added to the pangenome. "
- + "The protein sequence of the annotated genes will be also stored in the folder \"/proteins\" in the output path.\n" +
+ " --annotations-file or -af : "
+ + "A text file with on each line a genome number and the full path to the corresponding annotation file, separated by a space.\n" +
"\n" +
- " --connect-annotations or -ca : Connects the annotated genomic features to the nodes of gDBG.\n");
+ " --connect-annotations or -ca: Connect the annotated genomic features to the nodes of gDBG.\n" +
+ "\n" +
+ "Example --annotations-file input file:\n" +
+ "1 /always/genome1.gff\n" +
+ "2 /use_the/genome2.gff\n" +
+ "3 /full_path/genome3.gbk\n");
break;
case "g": case "group":
- System.out.println("group or g : To create homology groups in the protein space of the pangenome (panproteome). "
- + "The resulting homology groups will be stored in the output path.\n" +
+ System.out.println("group or g : Create homology groups in the protein space of the pangenome (panproteome).\n" +
"\n" +
"Required software: MCL\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --threads or -tn (default value: 1) : The number of parallel working threads.\n" +
+ " --threads or -tn : The number of parallel working threads (default is 3 threads).\n" +
"\n" +
- " --skip : Exclude a selection of genomes.\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference: or -ref : Only include a selection of genomes.\n" +
+ " --reference: or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line. " +
- "The most recent annotation is taken for genomes without an identifier.\n" +
+ " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " The most recent annotation is selected for genomes without an identifier.\n" +
"\n" +
"Optional arguments that influence the clustering sensivity:\n" +
"\n" +
- " --relaxation or -rn : The relaxation in homology calls. Should be in range [1-8], from strict to relaxed (default 1). " +
+ " --relaxation or -rn : The relaxation in homology calls. Should be in range [1-8], from strict to relaxed (default 1). " +
"Automatically sets the four remaining arguments, stated here below.\n" +
"\n" +
- " --intersection-rate or -ir (default valuue: 0.09, valid range: [0.001..0.1]) : The fraction of k-mers needs to be shared by two intersecting proteins.\n" +
+ " --intersection-rate or -ir : The fraction of k-mers needs to be shared by two intersecting proteins "
+ + "(default value: 0.09, valid range: [0.001..0.1]).\n" +
"\n" +
- " --min-normalized-similarity or -mns (default value: 95, valid range: [1..99]) : The minimum normalized similarity score of two proteins.\n" +
+ " --min-normalized-similarity or -mns: The minimum normalized similarity score of two proteins (default value: 95, valid range: [1..99]).\n" +
"\n" +
- " --mcl-inflation or -mi (default value: 9.6, valid range: (1..19)) : The MCL inflation.\n" +
+ " --mcl-inflation or -mi : The MCL inflation (default value: 9.6, valid range: (1..19)).\n" +
"\n" +
- " --contrast or -ct (default value: 8, valid range: (0..10)) : The contrast factor.\n");
+ " --contrast or -ct : The contrast factor (default value: 8, valid range: (0..10)).\n");
break;
case "rf": case "retrieve_features":
- System.out.println("retrieve_features or rf : To retrieve the sequence of annotated features from the pangenome. "
- + "For each genome a FASTA file containing the retrieved features will be stored in the output path. "
- + "For example, genes.1.fasta contains all the genes annotated in genome 1.\n" +
+ System.out.println("retrieve_features or rf : To retrieve the sequence of annotated features from the pangenome.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --genome-numbers or -gn : A text file containing genome_numbers for which the features will be retrieved.\n" +
+ " --genome-numbers or -gn: A text file containing genome_numbers for which the features will be retrieved.\n" +
"\n" +
- " --feature-type or -ft : The feature name; for example gene, mRNA, exon, tRNA, etc. (default value: gene)\n" +
+ " --feature-type or -ft : The feature name; for example gene, mRNA, exon, tRNA, etc. (default value: gene).\n" +
"\n" +
"Optional argument:\n" +
"\n" +
- " --output-path or -op (default value: Database path determined by -dp) : Path to the output files.\n");
+ " --output-path or -op : Path to the output files (default value: Database path determined by -dp).\n");
break;
case "rr": case "retrieve_regions":
- System.out.println("retrieve_regions or rr : To retrieve the sequence of some genomic regios from the pangenome. "
- + "The resulting FASTA files will be stored in the output path.\n" +
+ System.out.println("retrieve_regions or rr : To retrieve the sequence of some genomic regios from the pangenome.\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
" --regions-file or -rf : A text file containing records with genome_number, sequence_number, " +
"begin and end positions seperated by one space for each region.\n" +
+ " Place a minus symbol behind a region to extract the reverse complement sequence.\n" +
"\n" +
"Optional argument:\n" +
"\n" +
- " --output-path or -op (default value: Database path determined by -dp) : Path to the output files.\n");
+ " --output-path or -op : Path to the output files (default value: Database path determined by -dp).\n" +
+ "\n" +
+ "Example --regions-file input file:\n" +
+ "1 1 1 10000\n" +
+ "195 1 477722 478426\n" +
+ "71 10 17346 18056 -\n" +
+ "138 47 159593 160300 -\n");
break;
case "rg": case "retrieve_genomes":
- System.out.println("retrieve_genomes or rg : To retrieve the full sequence of some genomes. The resulting FASTA files will be stored in the output path.\n" +
+ System.out.println("retrieve_genomes or rg : To retrieve the full sequence of some genomes.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --genome-numbers or -gn : A text file containing genome numbers to be retrieved in each line.\n" +
+ " --genome-numbers or -gn: A text file containing genome numbers to be retrieved in each line.\n" +
"\n" +
"Optional argument:\n" +
"\n" +
- " --output-path or -op (default value: Database path determined by -dp) : Path to the output files.\n");
+ " --output-path or -op : Path to the output files (default value: Database path determined by -dp).\n");
break;
case "m": case "map":
- System.out.println("map or m : To map single or paired-end short reads to all or a sebset of the constituent genomes. "
- + "The resulting SAM/BAM files will be stored in the output path.\n" +
- "argument:\n" +
+ System.out.println("map or m : To map single or paired-end short reads to all or a sebset of the constituent genomes.\n" +
+ "\n" +
+ "Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " -1 : The first short-read archive in FASTQ format, which can be gz/bz2 compressed. This file can be precessed interleaved by -il option.\n" +
+ " -1 : The first short-read archive in FASTQ format, which can be gz/bz2 compressed. "
+ + "This file can be precessed interleaved by -il option.\n" +
+ "\n" +
+ " --genome-numbers or -gn: A text file containing genome_numbers to map reads against in each line.\n" +
"\n" +
- " -2 : Optionally, the second short-read archive in FASTQ format, which can be gz/bz2 compressed.\n" +
+ "Optional arguments:\n" +
"\n" +
- " --genome-numbers or -gn : A text file containing genome_numbers to map reads against in each line.\n" +
+ " -2 : Optionally, the second short-read archive in FASTQ format, which can be gz/bz2 compressed.\n" +
"\n" +
- " --output-path or -op (default value: Database path determined by -dp) : Path to the output files.\n" +
+ " --output-path or -op : Path to the output files (default value: Database path determined by -dp).\n" +
"\n" +
- " --threads or -tn (default value: 1) : The number of parallel working threads.\n" +
+ " --threads or -tn : The number of parallel working threads (default value: 1).\n" +
"\n" +
- " --min-mapping-identity or -mmi (default value: 0.5, valid range: [0..1)) : The minimum acceptable identity of the alignment.\n" +
+ " --min-mapping-identity or -mmi: The minimum acceptable identity of the alignment (default value: 0.5, valid range: [0..1)).\n" +
"\n" +
- " --num-kmer-samples or *-nks (default value: 15, valid range: [1..r-k+1]) : The number of kmers sampled from read.\n" +
+ " --num-kmer-samples or -nks : The number of kmers sampled from read (default value: 15, valid range: [1..r-k+1]).\n" +
"\n" +
- " --min-hit-length or -mhl (default value: 13, valid range: [10..100]) : The minimum acceptable length of alignment after soft-clipping.\n" +
+ " --min-hit-length or -mhl : The minimum acceptable length of alignment after soft-clipping (default value: 13, valid range: [10..100]).\n" +
"\n" +
- " --max-alignment-length or -mal (default value: 1000, valid range: [50..5000]) : The maximum acceptable length of alignment.\n" +
+ " --max-alignment-length or -mal: The maximum acceptable length of alignment (default value: 1000, valid range: [50..5000]).\n" +
"\n" +
- " --max-fragment-length or -mfl (default value: 2000, valid range: [50..5000]) : The maximum acceptable length of fragment.\n" +
+ " --max-fragment-length or -mfl : The maximum acceptable length of fragment (default value: 2000, valid range: [50..5000]).\n" +
"\n" +
- " --max-num-locations or -mnl (default value: 15, valid range: [1..100]) : The maximum number of location of candidate hits to examine.\n" +
+ " --max-num-locations or -mnl : The maximum number of location of candidate hits to examine (default value: 15, valid range: [1..100]).\n" +
"\n" +
- " --alignment-band or -ab (default value: 5, valid range: [1..100]) : The length of bound of banded alignment.\n" +
+ " --alignment-band or -ab : The length of bound of banded alignment (default value: 5, valid range: [1..100]).\n" +
"\n" +
- " --clipping-stringency or -ci : The stringency of soft-clipping (default value: 1).\n" +
+ " --clipping-stringency or -ci : The stringency of soft-clipping (default value: 1).\n" +
" 0 : no soft clipping\n" +
" 1 : low\n" +
" 2 : medium\n" +
" 3 : high\n" +
"\n" +
- " --out-format or -of : Writes the alignment files to BAM or SAM format. (default is SAM)\n" +
+ " --out-format or -of : Writes the alignment files to BAM or SAM format (default is SAM). \n" +
"\n" +
- "--alignment-mode or -am (default value: 2) : The alignment mode.\n" +
+ "--alignment-mode or -am: The alignment mode (default value: 2).\n" +
" -1 : Competitive, none-bests\n" +
" -2 : Competitive, random-best\n" +
" -3 : Competitive, all-bests\n" +
- " 1 : Normal, none-bests\n" +
- " 2 : Normal, random-best\n" +
- " 3 : Normal, all-bests\n" +
- " 0 : Normal, all-hits\n" +
+ " 1 : Normal, none-bests\n" +
+ " 2 : Normal, random-best\n" +
+ " 3 : Normal, all-bests\n" +
+ " 0 : Normal, all-hits\n" +
"\n" +
- " --interleaved or -i : Process the fastq file as an interleaved paired-end archive.\n" +
+ " --interleaved or -i : Process the fastq file as an interleaved paired-end archive.\n" +
"\n" +
- "--raw-abundance-file or -raf : The mapping_summary.txt file from a previous mapping run (random-best competitive mode) "
+ "--raw-abundance-file or -raf : The mapping_summary.txt file from a previous mapping run (random-best competitive mode) "
+ "for a better estimation of coverage in a metagenomic setting.");
break;
case "gene_classification":
@@ -1672,15 +1730,15 @@ public class Pantools {
"\n" +
" --phenotype or -ph : A phenotype name, used to find genes specific to the phenotype.\n" +
"\n" +
- " --skip : Exclude a selection of genomes. This automatically lowers the threshold for core genes.\n" +
+ " --skip or -sk : Exclude a selection of genomes. This automatically lowers the threshold for core genes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core genes.\n" +
+ " --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core and phenotype genes.\n" +
"\n" +
" --core-threshold or -ct : Threshold (%) for core/softcore genes. Default is the total number of genomes, not a percentage.\n" +
"\n" +
" --unique-threshold or -ut : Threshold (%) for unique/cloud genes. Default is a single genome, not a percentage.\n" +
"\n" +
- " --phenotype-threshold or -pt: Threshold (%) for phenotype specific/shared genes. Default is 100%" +
+ " --phenotype-threshold or -pt: Threshold (%) for phenotype specific/shared genes. Default is 100% of genomes with phenotype.\n" +
"\n" +
" --mode MLSA : Find suitable single-copy groups for a MLSA.\n") ;
break;
@@ -1693,62 +1751,77 @@ public class Pantools {
"\n" +
"Optional arguments:\n" +
"\n" +
- " --skip : Exclude a selection of genomes.\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
" --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --annotations-file or -af: A text file with the identifiers of annotations that should be used. " +
- "The most recent annotation is taken for genomes without an identifier.\n");
+ " --annotations-file or -af: A text file with the identifiers of annotations that should be used.\n" +
+ " The most recent annotation is selected for genomes without an identifier.\n");
break;
case "add_phenotypes": case "add_phenotype":
System.out.println("add_phenotypes : Include phenotype data to the pangenome.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
- " --phenotype or -ph : A CSV file containing the phenotype information. Example file shown in online manual.\n" +
+ " --phenotype or -ph : A CSV file containing the phenotype information. File requirements and an example file are shown below.\n" +
"\n" +
"Optional argument:\n" +
"\n" +
- " --append : Do not remove existing phenotype nodes but only add new properties to it. "
- + "If a property already exists, values from the new file will overwrite the old.\n");
+ " --append : Do not remove existing phenotype nodes but only add new properties to it. "
+ + "If a property already exists, values from the new file will overwrite the old.\n" +
+ "\n" +
+ "Phenotype CSV file:\n" +
+ " - The first row should start with 'Genome,' followed by the phenotype names and/or identifiers.\n"+
+ " - The first column must start with genome numbers corresponding to the one in your pangennome.\n"+
+ " - Phenotypes/metadata are placed on the same line as their genome number.\n" +
+ " - A field can remain empty when the phenotype for a genome is missing or unknown.\n" +
+ "\n" +
+ "Example CSV file:\n" +
+ "Genome,Gram,Region,Pathogenicity,Boolean,float,species\n" +
+ "1,+,NL,3,True,0.1,Species\n" +
+ "2,+,BE,,False,0.1,Species3\n" +
+ "3,+,LUX,7,true,0.1,Species3\n" +
+ "4,+,NL,9,FALSE,0.1,Species3\n" +
+ "5,,,,TRUE,,\n");
break;
case "change_active_grouping": case "change_grouping":
System.out.println("change_active_grouping : Change the active version of the homology grouping.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
- " --version : The version of homology grouping to become active.\n");
+ " --version : The version of homology grouping to become active.\n");
break;
case "grouping_overview":
System.out.println("grouping_overview : Report the content of all (active & inactive) different homology groupings in the pangenome.\n" +
"\n" +
"Required argument:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
"Optional argument:\n" +
"\n" +
- " --fast : Only show which grouping is active and which groupings can be activated.\n");
+ " --fast : Only show which grouping is active and which groupings can be activated.\n");
break;
case "remove_nodes":
System.out.println("remove nodes : Remove a selection of nodes including their relationships from the pangenome.\n" +
+ "\n" +
"Required argument:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
"Requires either one of the following arguments:\n" +
"\n" +
- " --node : One or mulitple node identifiers, separated by a comma.\n" +
+ " --node : One or mulitple node identifiers, separated by a comma.\n" +
"\n" +
- " --label : A node label, all nodes matching the label are removed.\n" +
+ " --label : A node label, all nodes matching the label are removed.\n" +
"\n" +
"Optional argument:\n" +
"\n" +
- " --skip : Do not remove nodes of the selected genomes. This can only be used in combination with --label.\n");
+ " --skip or -sk : Do not remove nodes of the selected genomes. This can only be used in combination with --label.\n");
break;
case "remove_grouping":
System.out.println("remove_grouping : Remove an homology grouping from the pangenome.\n" +
@@ -1768,71 +1841,76 @@ public class Pantools {
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp Path to the database.\n" +
+ " --database-path or -dp : Path to the database.\n" +
"\n" +
" --homology-groups or -hm : A text file with homology group node identifiers, seperated by a comma.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --label : name of function identifiers from GO, PFAM, InterPro or TIGRAM. " +
- "The second option is to include 'secreted', 'receptor', or transmembrane for Phobius annotations.\n" +
+ " --label : Report homology groups matching a function.\n" +
+ " Option 1, name of function identifier from GO, PFAM, InterPro or TIGRAM (example GO:1990620).\n" +
+ " Option 2, 'signal_peptide' or 'transmembrane' for Phobius and SignalP annotations.\n" +
"\n" +
- " --name : One or multiple gene names, seperated by a comma.\n" +
+ " --name : One or multiple gene names, seperated by a comma.\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n");
+ " --reference or -ref : Only include a selection of genomes.\n");
break;
- case "pangenome_size_genes": case "pangenome_size_gene":
- System.out.println("pangenome_size_genes : Estimate the size of the pangenome using homology groups.\n" +
+ case "pangenome_size_genes": case "pangenome_size_gene": case "pangenome_structure_genes":
+ System.out.println("pangenome_structure_genes : Determine the openness of the pangenome based on homology groups.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
"Optional arguments: \n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --value : Number of loops (default is 10.000).\n");
+ " --value : Number of loops (default is 10.000).\n");
break;
- case "pangenome_size_kmer": case "pangenome_size_kmers":
- System.out.println("pangenome_size_kmers : Estimate the size and openness of the pangenome based on k-mer sequences.\n" +
+ case "pangenome_size_kmer": case "pangenome_size_kmers": case "pangenome_structure_kmers":
+ System.out.println("pangenome_structure_kmers : Determine the size and openness of the pangenome based on k-mer sequences.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
"Optional arguments: \n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --value : Number of loops (default is 100).\n");
+ " --value : Number of loops (default is 100).\n");
break;
case "kmer_classification":
- System.out.println("kmer_classification : Calculate the number of core, accessory and unique k-mer sequences\n" +
+ System.out.println("kmer_classification : Calculate the number of core, accessory and unique k-mer sequences.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
"Optional arguments: \n" +
"\n" +
- " --phenotype or -ph : A phenotype name, used to identify phenotype specific k-mers.\n" +
+ " --phenotype or -ph : A phenotype name, used to identify phenotype specific k-mers.\n" +
+ "\n" +
+ " --skip or -sk : Exclude a selection of genomes. "
+ + "This automatically lowers the threshold for core and phenotype k-mers.\n" +
"\n" +
- " --skip : Exclude a selection of genomes. This automatically lowers the threshold for core genes.\n" +
+ " --reference or -ref : Only include a selection of genomes. "
+ + "This automatically lowers the threshold for core and phenotype k-mers.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core k-mers.\n" +
+ " --core-threshold or -ct : Threshold (%) for core/softcore k-mers (default is the total number of genomes, not a percentage).\n" +
"\n" +
- " --core-threshold or -ct : Threshold (%) for core/softcore k-mers (default is the total number of genomes, not a percentage).\n" +
+ " --unique-threshold or -ut : Threshold (%) for unique/cloud k-mers (default is a single genome, not a percentage).\n" +
"\n" +
- " --unique-threshold or -ut : Threshold (%) for unique/cloud k-mers (default is a single genome, not a percentage).\n" +
+ " --phenotype-threshold or -pt: Threshold (%) for phenotype specific/shared k-mers. Default is 100% of genomes with phenotype.\n" +
"\n" +
- " --mode compressed : Count unitigs (collapsed non-branching k-mers) instead of k-mers.\n");
+ " --mode compressed : Count k-mer nodes (collapsed non-branching k-mers) instead of all k-mers.\n");
break;
case "locate_genes":
System.out.println("locate_genes : Identify and compare gene clusters of from a set of homology groups.\n" +
@@ -1841,278 +1919,317 @@ public class Pantools {
"\n" +
" --database-path or -dp : Path to the database.\n" +
"\n" +
- " --homology-groups -hm : A text file with homology group node identifiers, seperated by a comma.\n" +
+ " --homology-groups -hm : A text file with homology group node identifiers, seperated by a comma.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --phenotype or -ph : A phenotype name, used to identify gene clusters shared by all phenotype members.\n" +
+ " --phenotype or -ph : A phenotype name, used to identify gene clusters shared by all phenotype members.\n" +
"\n" +
- " --value : Number of allowed nucleotides between two neighbouring genes (default is 1 MB).\n" +
+ " --value : Number of allowed nucleotides between two neighbouring genes (default is 1 MB).\n" +
"\n" +
- " --gap-open or -go : When constucting the clusters, allow a number of genes for each cluster that are not originally part of the input groups (default is 0).\n" +
+ " --gap-open or -go : When constucting the clusters, "
+ + "allow a number of genes for each cluster that are not originally part of the input groups (default is 0).\n" +
"\n" +
- " --core-threshold : Lower the threshold (%) for a group to be considered core/softcore " +
+ " --core-threshold : Lower the threshold (%) for a group to be considered core/softcore " +
"(default is the total number of genomes found in the groups, not a percentage).\n" +
"\n" +
- " --skip : Exclude a selection of genomes. This automatically lowers the threshold for core genes.\n" +
+ " --skip or -sk : Exclude a selection of genomes. This automatically lowers the threshold for core genes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core genes.\n" +
+ " --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core genes.\n" +
"\n" +
- " --mode ignore-copies : Duplicated and co-localized genes no longer break up clusters.\n");
+ " --mode ignore-copies : Duplicated and co-localized genes no longer break up clusters.\n");
break;
case "msa_of_group": case "msa_of_groups":
System.out.println("msa_of_group : Multiple sequence alignments of one or multiple homology groups.\n" +
"\n" +
- "Required software: MAFFT, FastTree\n" +
+ "Required software: MAFFT, FastTree.\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp : Path to the database.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --homology-groups or -hm : Text file with homology group node identifiers (default is all groups).\n" +
+ " --homology-groups or -hm : Text file with homology group node identifiers (default is all groups).\n" +
"\n" +
- " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
+ " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
"\n" +
- " --core-threshold or -ct : Threshold for phenotype specific SNPs (default is 100%).\n" +
+ " --phenotype-threshold or -pt: Threshold for phenotype specific SNPs. "
+ + "Default is 100% of the sequences with the phenotype present in an homology group.\n" +
"\n" +
- " --skip : Exclude a selection of genomes. " +
+ " --skip or -sk : Exclude a selection of genomes. " +
"The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes. " +
+ " --reference or -ref : Only include a selection of genomes. " +
"The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n" +
"\n" +
- " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n" +
+ " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n" +
"\n" +
- " --mode nucleotide or --mode protein : Choose to only align nucleotide or protein sequences (default is both).\n" +
+ " --mode nucleotide or protein: Choose to only align nucleotide or protein sequences (default is both).\n" +
"\n" +
- " --mode no-trimming : Align the sequences only once.\n");
+ " --mode no-trimming : Align the sequences only once.\n");
break;
case "msa_of_multiple_groups":
- System.out.println("msa_of_multiple_groups : To perform an alignment on sequences from multiple homology groups\n" +
+ System.out.println("msa_of_multiple_groups : Use sequences from multiple homology groups for a single alignment\n" +
"\n" +
"Required software: MAFFT, FastTree\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp : Path to the database.\n" +
"\n" +
- " --homology-groups or -hm : Text file with homology group node identifiers.\n" +
+ " --homology-groups or -hm : Text file with homology group node identifiers.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- "--phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions." +
+ " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- "--core-threshold or -ct : Threshold for phenotype specific SNPs (Default is 100%).\n" +
+ " --phenotype-threshold or -pt: Threshold for phenotype specific SNPs. Default is 100% of the sequences with the phenotype.\n" +
"\n" +
- "--mode nucleotide or --mode protein : Choose to only align nucleotide or protein sequences (default is both).\n" +
+ " --mode nucleotide or protein: Choose to only align nucleotide or protein sequences (default is both).\n" +
"\n" +
- "--threads or -tn The number of parallel working threads for MAFFT (default is 1).\n");
+ " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n");
break;
case "move_grouping":
System.out.println("move_grouping : Inactivate the currently active homology grouping\n" +
"\n" +
"Required argument:\n" +
"\n" +
- "--database-path or -dp Path to the pangenome database.\n");
+ "--database-path or -dp : Path to the pangenome database.\n");
break;
case "core_unique_thresholds":
System.out.println("core_unique_thresholds : Test the effect of different core and unique thresholds on the homology group classification.\n" +
"\n" +
"Required argument:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp: Path to the pangenome database.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes. This automatically lowers the threshold for core genes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n");
+ " --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core genes.\n");
break;
case "msa_of_regions":
- System.out.println("msa_of_regions : ...\n" +
+ System.out.println("msa_of_regions : Align a selection of genomic regions\n" +
"\n" +
"Required software: MAFFT, FastTree\n" +
"Required arguments:\n" +
"\n" +
- "--regions-file or -rf : A text file containing genome locations with on each line:" +
+ "--regions-file or -rf : A text file containing genome locations with on each line:" +
" a genome number, sequence number, begin and end positions separated by one space.\n" +
+ " Place a minus symbol behind a region to extract the reverse complement sequence." +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
+ " --phenotype or -ph : A phenotype name, used to identify phenotype specific SNPs/substitutions.\n" +
+ "\n" +
+ " --phenotype-threshold or -pt : Threshold for phenotype specific SNPs. Default is 100% of the sequences with the phenoptype.\n" +
"\n" +
- " --core-threshold or -ct : Threshold for phenotype specific SNPs (Default is 100%).\n" +
+ " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n" +
"\n" +
- " --threads or -tn : The number of parallel working threads for MAFFT (Highly recommended! default is 1).\n");
+ "Example --regions-file input file:\n" +
+ "1 1 1 10000\n" +
+ "195 1 477722 478426\n" +
+ "71 10 17346 18056 -\n" +
+ "138 47 159593 160300 -\n");
break;
case "order_matrix":
- System.out.println("order matrix : ...\n" +
+ System.out.println("order matrix : Order the values of a matrix file created by PanTools\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp: Path to the database.\n" +
"\n" +
- " --input-file or -af : A CSV formatted matrix file.\n" +
+ " --input-file or -af : A CSV formatted matrix file.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --mode asc or desc : Order the matrix in ascending or descending order (ascending is default).\n" );
+ " --mode asc desc : Order the matrix in ascending or descending order (ascending is default).\n");
break;
case "rename_matrix":
- System.out.println("rename matrix : ...\n" +
+ System.out.println("rename matrix : Add phenotype values to the header of a matrix file created by PanTools\n" +
+ "\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp: Path to the database.\n" +
"\n" +
- " --input-file or -if : A matrix file with numerical values.\n" +
+ " --input-file or -if : A matrix file with numerical values.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --phenotype or -ph : A phenotype name, used to include phenotype information into the headers.\n" +
+ " --phenotype or -ph : A phenotype name, used to include phenotype information into the headers.\n" +
"\n" +
- " --skip : Exclude a selection of genomes from the new matrix file.\n" +
+ " --skip or -sk : Exclude a selection of genomes from the new matrix file.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes from the new matrix file.\n" +
+ " --reference or -ref : Only include a selection of genomes in the new matrix file.\n" +
"\n" +
- " --mode no-numbers : Exclude genome numbers from the headers.\n");
+ " --mode no-numbers : Exclude genome numbers from the headers.\n");
break;
case "busco_protein":
- System.out.println("busco_protein : Run BUSCO v3 or v4 against a selection of proteomes.\n" +
+ System.out.println("busco_protein : Identify BUSCO genes in the pangenome.\n" +
"\n" +
"Required software: BUSCO v3, v4 or v5\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --input-file or -if : A BUSCO benchmark dataset.\n" +
+ " --input-file or -if : A BUSCO benchmark dataset.\n" +
+ " BUSCO v3 requires the full path to a dataset.\n" +
+ " BUSCO v4 & v5 only require the dataset name, option to include the full path to a dataset is also available.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --name : A list of questionable BUSCOs. The completeness score is recalculated by excluding these.\n" +
+ " --name : A list of questionable BUSCOs. The completeness score is recalculated by excluding these.\n" +
"\n" +
- " --version : The BUSCO version. Select either 'busco3', 'busco4' or 'busco5' (default).\n" +
+ " --version : The BUSCO version. Select either 'busco3', 'busco4' or 'busco5' (default).\n" +
"\n" +
- " --mode longest-transcript : Only search against the longest protein-coding transcript of genes.\n" +
+ " --longest-transcript or -lt: Only search against the longest protein-coding transcript of genes.\n" +
"\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line. " +
- "The most recent annotation is taken for genomes without an identifier.\n");
+ " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " The most recent annotation is selected for genomes without an identifier.\n");
break;
- case "find_genes_in_region":
- System.out.println("The manual for this functionality will soon be included here. For now, please use the online manual");
+ case "find_genes_in_region": case "find_genes_in_regions":
+ System.out.println("find_genes_in_region : Find genes in a given genomic region.\n" +
+ "\n" +
+ "Required arguments:\n" +
+ "\n" +
+ " --database-path or -dp: Path to the database.\n" +
+ "\n" +
+ " --regions-file or -rf : A text file containing genome locations with on each line:" +
+ " a genome number, sequence number, begin and end positions separated by one space.\n" +
+ "\n" +
+ "Optional arguments:\n" +
+ "\n" +
+ "--mode partial : Also retrieve genes that only partially overlap the input regions.\n" +
+ "\n" +
+ "Example --regions-file input file:\n" +
+ "1 1 1 10000\n" +
+ "195 1 477722 478426\n" +
+ "71 10 17346 18056\n" +
+ "138 47 159593 160300\n");
break;
- case "find_genes_by_annotation":
- System.out.println("The manual for this functionality will soon be included here. For now, please use the online manual");
+ case "find_genes_by_function":
+ System.out.println("find_genes_by_function : Find genes connected to a functional annotation.\n" +
+ "\n" +
+ "Required arguments:\n" +
+ "\n" +
+ " --database-path or -dp: Path to the database.\n" +
+ "\n" +
+ "Requires either one of the following arguments:\n" +
+ "\n" +
+ " --node : One or multiple identifiers of function nodes (GO, InterPro, PFAM, TIGRFAM), seperated by a comma.\n" +
+ "\n" +
+ " --name : One or multiple function identifiers (GO, InterPro, PFAM, TIGRFAM), seperated by a comma.\n");
break;
case "core_snp_tree":
- System.out.println("core_snp_tree : ...\n" +
- "Required software: MAFFT, IQ-tree (Only required for Maximum-Likelihood)\n" +
+ System.out.println("core_snp_tree : Create a SNP tree from single-copy genes\n" +
"\n" +
+ "Required software: MAFFT, IQ-tree (Only required for Maximum-Likelihood).\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp : Path to the database.\n" +
"\n" +
- "Optional arguments: \n" +
+ "Optional arguments:\n" +
"\n" +
- " --mode ML or NJ : Neighbour joining or Maximum likelihood (default).\n" +
+ " --mode ML or NJ : Neighbour joining or Maximum likelihood (default).\n" +
"\n" +
- " --mode protein : ...\n" +
+ " --mode nucleotide or protein: Infer the tree on informative positions in nucleotide or protein alignments.\n" +
"\n" +
- " --threads or -tn : Number of threads (default is 1).\n" +
+ " --threads or -tn : Number of threads (default is 1).\n" +
"\n" +
- " --phenotype or -ph : Include phenotype information in the output files.\n" +
+ " --phenotype or -ph : Include phenotype information in the output files.\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n");
+ " --reference or -ref : Only include a selection of genomes.\n");
break;
case "rename_phylogeny":
- System.out.println("rename_phylogeny : Change the values of terminal nodes (leaves) of a phylogenic tree\n" +
+ System.out.println("rename_phylogeny : Change the values of terminal nodes (leaves) of a phylogenic tree.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the database.\n" +
"\n" +
- " --input-file or -if : A phylogenetic tree in newick format.\n" +
+ " --input-file or -if : A phylogenetic tree in newick format.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --phenotype or -ph : The phenotype used to rename the terminal nodes (leaves) of selected tree.\n" +
+ " --phenotype or -ph : The phenotype used to rename the terminal nodes (leaves) of selected tree.\n" +
"\n" +
- " --mode no-numbers : Exclude genome numbers from the terminal nodes (leaves).\n");
+ " --mode no-numbers : Exclude genome numbers from the terminal nodes (leaves).\n");
break;
case "root_phylogeny":
- System.out.println("root_phylogeny : Root a phylogenic tree by selecting one of the terminal nodes (leaves)\n" +
+ System.out.println("root_phylogeny : Root a phylogenic tree by selecting one of the terminal nodes (leaves).\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --input-file or -if : A phylogenetic tree in newick format.\n" +
+ " --input-file or -if: A phylogenetic tree in newick format.\n" +
"\n" +
- " --value : The name of the terminal node that will root the tree.\n");
+ " --value : The name of the terminal node that will root the tree.\n");
break;
case "create_tree_templates": case "create_tree_template":
- System.out.println("create_tree_templates : ...\n" +
+ System.out.println("create_tree_templates : Create templates for coloring phylogenetic trees in iTOL.\n" +
+ "\n" +
"Required argument:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp: Path to the database.\n" +
"\n" +
"Optional argument:\n" +
"\n" +
- "--phenotype or -ph : Use the names from this phenotype\n" +
+ " --phenotype or -ph : The terminal nodes in the tree must match the the names from this phenotype.\n" +
"\n" +
- "--value : the number of genomes a phenotype should have before a color is assigned. Default is 2.\n");
+ " --value : The number of genomes a phenotype should have before a color is assigned. Default is 2.\n");
break;
- case "ani": case "calculate_ani": case "calculate_ANI": case "ANI":
- System.out.println("ANI : Calculate Average Nucleotide Identity (ANI) scores between genomes" +
+ case "ani": case "ANI": case "calculate_ani": case "calculate_ANI":
+ System.out.println("ANI : Calculate Average Nucleotide Identity (ANI) scores between genomes.\n" +
"\n" +
- "Required software: MASH or fastANI\n" +
+ "Required software: MASH or fastANI.\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the database.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --mode mash or fastani : Software to calculate ANI score (default is MASH)\n" +
+ " --mode mash or fastani : Software to calculate ANI score (default is MASH).\n" +
"\n" +
- " --phenotype or -ph : Add phenotype information/values to the phylogeny.\n" +
+ " --phenotype or -ph : Add phenotype information/values to the phylogeny.\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --threads or -tn Number of threads used by FastANI (default is 1). MASH is single threaded (and currently not parallelized).\n");
+ " --threads or -tn : Number of threads used by FastANI (default is 1). MASH is single threaded (and currently not parallelized).\n");
break;
case "mlsa_find_genes": case "MLSA_find_genes": case "find_genes_by_name":
if (help.equals("mlsa_find_genes") || (help.equals("mlsa_find_genes"))) {
- System.out.println("MLSA_find_genes : Step 1/3 of MLSA. Find and retrieve genes of interest using the gene name.");
+ System.out.println("MLSA_find_genes : Step 1/3 of MLSA. Find and retrieve genes of interest using the gene name.\n");
} else {
- System.out.println("find_genes_by_name : Find and retrieve genes of interest using the gene name.");
+ System.out.println("find_genes_by_name : Find and retrieve genes of interest using the gene name.\n");
}
- System.out.println("\n" +
- "Required arguments:\n" +
+ System.out.println("Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp: Path to the database.\n" +
"\n" +
- " --name : One or multiple gene names, seperated by a comma.\n" +
+ " --name : One or multiple gene names, seperated by a comma.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --mode extensive : Perform a more extensive gene search. For more information, see online manual.\n" +
+ " --mode extensive : Perform a more extensive gene search. For more information, see online manual.\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n");
+ " --reference or -ref : Only include a selection of genomes.\n");
break;
case "mlsa_concatenate": case "MLSA_concatenate":
System.out.println("MLSA_concatenate : Step 2/3 of MLSA. Concatenate sequences obtained by 'MLSA_find_genes' into a single sequence per genome." +
@@ -2120,249 +2237,223 @@ public class Pantools {
"Required software: MAFFT\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp: Path to the database.\n" +
"\n" +
- " --name : One or multiple names of genes to be included in the concatenated sequence, seperated by a comma.\n" +
+ " --name : One or multiple names of genes to be included in the concatenated sequence, seperated by a comma.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --threads or -tn : Number of threads for MAFFT (default is 1).\n" +
+ " --threads or -tn : Number of threads for MAFFT (default is 1).\n" +
"\n" +
- " --skip : Exclude a selection of genomes\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --phenotype or -ph : Add phenotype information/values to the phylogeny\n");
- break;
- case "mlsa_check_sequences": case "MLSA_check_sequences":
- System.out.println("mlsa_check_sequences : ...\n" +
- "Required software: MAFFT, FastTree\n" +
- "\n" +
- "Required argument\n" +
- "\n" +
- " --database-path or -dp : Path to the database.\n" +
- "\n" +
- " --name : Gene name or the path to the protein sequences of the gene (when found in multiple homology groups).\n" +
- "\n" +
- "Optional arguments:\n" +
- "\n" +
- " --threads or -tn : Number of threads used by MAFFT (default is 1).\n");
+ " --phenotype or -ph : Add phenotype information/values to the phylogeny (next step).\n");
break;
case "MLSA": case "mlsa": case "run_MLSA": case "run_mlsa":
System.out.println("MLSA : Step 3/3 of MLSA. Align the concatenated sequences and run IQ-tree to infer the phylogeny\n" +
"\n" +
- "Required software: MAFFT, IQ-tree\n" +
+ "Required software: MAFFT, IQ-tree.\n" +
"Required arguments:\n" +
"\n" +
" --database-path or -dp : Path to the database.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --threads or tn : Number of threads (default is 1).\n");
+ " --threads or tn : Number of threads (default is 1).\n");
break;
case "consensus_tree":
- System.out.println("Build a consensus tree for all genomes in the pangenome (or proteomes in panproteome) using ASTRAL-PRO\n"
+ System.out.println("Build a consensus tree for all genomes in the pangenome (or proteomes in panproteome) using ASTRAL-Pro\n"
+ "(https://github.com/chaoszhang/ASTER at commit 2c1c469 is used for this, but NOT needed as required software "
+ "since it is already installed)\n"
+ "\n"
- + "Required software: MAFFT FastTree (ASTRAL-Pro)\n"
+ + "Required software: MAFFT FastTree (ASTRAL-Pro).\n"
+ "\n"
+ "Required arguments:\n"
+ "\n"
- + " --database-path or -dp : Path to the database.\n"
+ + " --database-path or -dp : Path to the database.\n"
+ "\n"
+ " --homology-groups or -hm : Text file with homology group node identifiers (default is all groups).\n"
+ "\n"
- + "Optional arguments:\n"
+ + "Optional arguments:\n"
+ "\n"
- + " --skip : Exclude a selection of genomes. "
- + "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n"
- + "\n"
- + " --reference or -ref : Only include a selection of genomes. "
- + "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n"
- + "\n"
- + " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n");
-
+ // skip currently does not work for the consensus tree
+ //+ " --skip or -sk : Exclude a selection of genomes. "
+ //+ "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n"
+ //+ "\n"
+ //+ " --reference or -ref : Only include a selection of genomes. "
+ //+ "The alignment is still made with all sequences in the homology group and this only effects the SNPs/substitutions counting.\n"
+ //+ "\n"
+ + " --threads or -tn : The number of parallel working threads for MAFFT (default is 1).\n");
// + "\n"
// + " --mode nucleotide or --mode protein : Choose to only align nucleotide or protein sequences (default is both).\n");
break;
case "show_go":
- System.out.println("show_go : ... \n " +
+ System.out.println("show_go : For a given GO term, show the child terms, all parent terms higher in the hierarchy, and connected mRNA nodes\n" +
"\n" +
"Required argument:\n" +
"\n" +
- " --database-path or -dp : Path to the database\n" +
+ " --database-path or -dp: Path to the database.\n" +
"\n" +
"Requires either one of the following arguments:\n" +
"\n" +
- " --node : One or multiple identifiers of GO nodes, seperated by a comma.\n" +
+ " --node : One or multiple identifiers of GO nodes, seperated by a comma.\n" +
"\n" +
- " --name : One or multiple GO term identifiers, seperated by a comma.\n");
+ " --name : One or multiple GO term identifiers, seperated by a comma.\n");
break;
case "compare_go":
- System.out.println("compare_go : ...\n" +
+ System.out.println("compare_go : For two given GO terms, move up in the GO hierarchy to see if they are related.\n" +
"\n" +
"Required argument:\n" +
"\n" +
- " --database-path or -dp : Path to the database\n" +
+ " --database-path or -dp: Path to the database\n" +
"\n" +
"Requires either one of the following arguments:\n" +
"\n" +
- " --node : Two node identifiers of 'GO' nodes, seperated by a comma..\n" +
+ " --node : Two node identifiers of 'GO' nodes, seperated by a comma.\n" +
"\n" +
- " --name : Two GO identifiers, seperated by a comma.\n");
+ " --name : Two GO identifiers, seperated by a comma.\n");
break;
case "add_antismash_results": case "add_gene_clusters":
- System.out.println("add_antismash_results : Include antiSMASH output to the pangenome\n" +
+ System.out.println("add_antismash_results : Include antiSMASH output to the pangenome.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --input-file or -if : A text file with on each line a genome number and the full path to the corresponding antiSMASH output file, separated by a space.\n" +
+ " --input-file or -if : A text file with on each line a genome number and the full path to the corresponding antiSMASH output file,"
+ + " separated by a space.\n" +
"\n" +
"Optional argument:\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line. " +
- "The most recent annotation is taken for genomes without an identifier.\n");
+ " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " The most recent annotation is selected for genomes without an identifier.\n");
break;
- case "add_functional_annotations":
- System.out.println("add_functional_annotations : Include functional annotations from BLAST2GO, InterProScan or eggNOG-mapper output\n" +
+ case "add_functional_annotations": case "add_functions":
+ System.out.println("add_functional_annotations : "
+ + "Include functional annotations from InterProScan, eggNOG-mapper, Phobius, SignalP, or a custom format.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --input-file or -if : A text file with on each line a genome number and the full path to the corresponding annotation file, separated by a space.\n" +
+ " --input-file or -if : A text file with on each line a genome number and the full path to the corresponding annotation file, "
+ + "separated by a space.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --mode shared-functions : Find shared functions between similar sequences and put these on the 'is_similar' relationships.\n" +
+ " --mode shared-functions : Find shared functions between similar sequences and put these on the 'is_similar' relationships.\n" +
"\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line. " +
- "The most recent annotation is taken for genomes without an identifier.\n");
+ " --annotations-file or -af: A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " The most recent annotation is selected for genomes without an identifier.\n");
break;
- case "add_phobius":
- System.out.println("add_phobius : Include Phobius predictions to the pangenome\n" +
+ case "functional_annotation_overview": case "function_overview":
+ System.out.println("function overview : Create an overview table for each functional annotation type in the pangenome.\n" +
"\n" +
- "Required software: Phobius 1.01\n" +
- "Required argument: \n" +
+ "Required argument:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
"Optional arguments:\n" +
+ "\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --skip : Exclude a selection of genomes.\n" +
- "\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
- "\n" +
- " --input-file or -if : A text file with on each line a genome number and the full path to the corresponding Phobius output file, separated by a space.\n" +
- "\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line. " +
- "The most recent annotation is taken for genomes without an identifier.\n");
- break;
- case "functional_annotation_overview": case "FA_overview": case "fa_overview":
- System.out.println("The manual for this functionality will soon be included here. For now, please use the online manual");
+ " --reference or -ref : Only include a selection of genomes.\n" +
+ "\n" +
+ " --annotations-file or -af: A text file with the identifiers of annotations to be included, each on a seperate line.\n" +
+ " The most recent annotation is selected for genomes without an identifier.\n");
break;
case "functional_classification": case "function_classification":
- System.out.println("functional_classification : Calculate the number of core, accessory and unique functional annotations\n" +
+ System.out.println("functional_classification : Calculate the number of core, accessory and unique functional annotations.\n" +
"\n" +
"Required argument:\n" +
"\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --phenotype or -ph : A phenotype name, used to find functions specific to a phenotype.\n" +
+ " --phenotype or -ph : A phenotype name, used to find functions specific to a phenotype.\n" +
"\n" +
- " --skip : Exclude a selection of genomes. This automatically lowers the threshold for core genes.\n" +
+ " --skip or -sk : Exclude a selection of genomes. This automatically lowers the threshold for core genes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core genes.\n" +
+ " --reference or -ref : Only include a selection of genomes. This automatically lowers the threshold for core genes.\n" +
"\n" +
- " --core-threshold or -ct : Threshold (%) For core/softcore functions (default is 100%).\n" +
+ " --core-threshold or -ct : Threshold (%) For core/softcore functions (default is 100%).\n" +
"\n" +
- " --unique-threshold -ut : Threshold (%) For unique/cloud functions (default is a single genome, not a percentage).\n" +
+ " --unique-threshold -ut : Threshold (%) For unique/cloud functions (default is a single genome, not a percentage).\n" +
"\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations that should be used. " +
- "The most recent annotation is taken for genomes without an identifier.\n");
+ " --phenotype-threshold or -pt: Threshold (%) for phenotype specific/shared functions. Default is 100% of genomes with phenotype.\n" +
+ "\n" +
+ " --annotations-file or -af : A text file with the identifiers of annotations that should be used.\n" +
+ " The most recent annotation is selected for genomes without an identifier.\n");
break;
case "go_enrichment": case "GO_enrichment":
System.out.println("go_enrichment : Identify over or under-repressented GO terms for a given set of mRNA's or homology groups.\n" +
"\n" +
- "Required software: dot\n" +
+ "Required software: dot (part of graphviz).\n" +
"Required arguments:\n" +
"\n" +
- " --database-path or -dp : Path to the database.\n" +
+ " --database-path or -dp : Path to the database.\n" +
"\n" +
"Requires either one of the following arguments:\n" +
"\n" +
- " --homology-groups or -hm : A text file with homology group node identifiers, seperated by a comma\n" +
+ " --homology-groups or -hm: A text file with homology group node identifiers, seperated by a comma.\n" +
"\n" +
- " --node : mRNA node identifiers, seperated by a comma on the command line\n" +
+ " --node : mRNA node identifiers, seperated by a comma on the command line.\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --skip : Exclude a selection of genomes.\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
"\n" +
- " --value : the desired false discovery rate (default is 5%).\n");
- break;
- case "cog": case "COG": case "blast_cog":
- System.out.println("blast_cog : ..." +
- "\n" +
- "Required software: BLAST\n" +
- "Required argument:\n" +
- "\n" +
- " --database-path or -dp : Path to the pangenome database.\n" +
- "\n" +
- "Optional arguments:\n" +
- "\n" +
- " --input-file or -if : A text file with on each line a genome number and the full path to the corresponding BLAST output (format 6) file, " +
- "separated by a space. Will not run BLAST when included.\n" +
- "\n" +
- " --skip : Exclude a selection of genomes.\n" +
- "\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
- "\n" +
- " --label strict normal soft : The strictness of accepting a hit; Use strict (> 65% similarity & > 65% alignment length of query sequence, default), " +
- "normal (> 50%) or soft (> 35%).\n" +
- "\n" +
- " --append : COG information already present in the pangenome is not initially removed before the new data is added (default is false).\n" +
- "\n" +
- " --overwrite : Older COG categories on mRNAs are overwritten when the new data has a different category (default is false).\n"+
- "\n" +
- " --annotations-file or -af : A text file with the identifiers of annotations to be included, each on a seperate line. " +
- "The most recent annotation is taken for genomes without an identifier.\n");
+ " --value : the desired false discovery rate (default is 5%).\n");
break;
case "optimal_grouping":
- System.out.println("optimal_grouping : ...\n" +
+ System.out.println("optimal_grouping : Identify the optimal grouping in the protein space of the pangenome.\n" +
"\n" +
"Required arguments:\n" +
"\n" +
- " --database-path/-dp Path to the pangenome database.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --input-file or -af : The output directory created by 'busco_protein'. This directory is found inside the pangenome database ( in the busco directory).\n" +
+ " --input-file or -af : The output directory created by 'busco_protein'. "
+ + "This directory is found inside the pangenome database (in the busco directory).\n" +
"\n" +
"Optional arguments:\n" +
"\n" +
- " --skip : Exclude a selection of genomes.\n" +
+ " --skip or -sk : Exclude a selection of genomes.\n" +
+ "\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
+ "\n" +
+ " --threads or tn : Number of threads (default is 1).\n" +
"\n" +
- " --reference or -ref : Only include a selection of genomes.\n" +
+ " --value : Only consider a selection of relaxation settings (1-8 allowed).\n" +
"\n" +
- " --threads or tn : Number of threads (default is 1).\n" +
+ " --fast : Assume the optimal grouping is found when the F1-score drops compared to the previous clustering round.\n" +
"\n" +
- " --value : Only consider a selection of relaxation settings (1-8 allowed).\n" +
+ " --longest-transcripts or -lt: Only cluster protein sequences of the largest transcript per gene.\n" +
+ "\n" +
+ " --annotations-file or -af : A text file with identifiers of the annotations that should be used.\n" +
+ " The most recent annotation is selected for genomes without an identifier.\n");
+ break;
+ case "remove_annotations":
+ System.out.println("remove_annotations : Remove all the genomic features belonging to structural annotations\n" +
+ "\n" +
+ "Required arguments:\n" +
"\n" +
- " --mode fast or fastest : Assume the optimal grouping is found when the F-score drops one (fastest) or two (fast) consecutive clustering rounds.\n" +
+ " --database-path or -dp : Path to the pangenome database.\n" +
"\n" +
- " --mode longest-transcript : Only cluster protein sequences of the largest transcript per gene.\n" +
+ "Requires one of three following arguments:\n" +
"\n" +
- " --annotations-file or -af : A text file with identifiers of the annotations that should be used. " +
- "The most recent annotation is taken for genomes without an identifier.\n");
+ " --skip or -sk : Exclude a selection of genomes.\n" +
+ "\n" +
+ " --reference or -ref : Only include a selection of genomes.\n" +
+ "\n" +
+ " --annotations-file or -af: A text file with the identifiers of annotations to be removed, each on a seperate line.\n");
+ break;
default:
- System.out.println("There is no help available yet for this subcommand. ");
+ System.out.println("The provided subcommand '" + help + "' was not recognized, no manual available!\n");
break;
-
}
System.out.println("-----------------------------------------------------------------------" +
"\nManual and tutorial available at http://bioinformatics.nl/pangenomics/manual/" +
@@ -2447,7 +2538,7 @@ public class Pantools {
}
/**
- * The 'last_grouping_successful' is created at the end of group()
+ * The 'last_grouping_successful' property is created at the end of the 'group' function
*/
public static void stop_if_no_active_grouping_present() {
Node pangenome_node = graphDb.findNodes(pangenome_label).next();
@@ -2456,7 +2547,7 @@ public class Pantools {
last_grouping_successful = (boolean) pangenome_node.getProperty("last_grouping_successful");
}
if (!last_grouping_successful) {
- System.out.println("\nNo (correct) grouping is present. Run 'group'\n");
+ System.out.println("\nNo (correct) grouping is present. Please run 'group'\n");
System.exit(1);
}
}
@@ -2605,9 +2696,9 @@ public class Pantools {
String line;
while ((line = in.readLine()) != null) {
line = line.trim();
- if (line.equals(""))
- continue;
- else {
+ if (line.equals("")) {
+ // do nothing
+ } else {
in.close();
return line.charAt(0) == '>';
}
@@ -2815,7 +2906,7 @@ public class Pantools {
*/
public static void append_SB_to_file_in_DB(StringBuilder output_builder, String output_file) {
String output_str = output_builder.toString();
- try (FileWriter fw = new FileWriter(WORKING_DIRECTORY + output_file, true)) { //the true will append the new data
+ try (FileWriter fw = new FileWriter(WORKING_DIRECTORY + output_file, true)) { // true allows to append the original instead of overwriting
fw.write(output_str);
fw.close();
} catch(IOException ioe) {
@@ -3024,7 +3115,7 @@ public class Pantools {
System.exit(1);
} else if (!new File(PATH_TO_THE_PANGENOME_DATABASE + GRAPH_DATABASE_PATH).exists()) {
System.out.println("Unable to open the database provided via --database-path/-dp\n");
- System.exit(0);
+ System.exit(1);
}
}
@@ -3108,7 +3199,7 @@ public class Pantools {
float allowed_float = (float) (value.length-skip_counter) * Math.round(phenotype_threshold) / 100;
allowed = Math.round(allowed_float);
}
- if (allowed == 0){
+ if (allowed == 0) {
allowed ++;
}
phenotype_threshold_map.put(phenotype, allowed);
@@ -3327,7 +3418,7 @@ public class Pantools {
* @param pangenome_node
*/
public static void check_if_panproteome(Node pangenome_node) {
- if (pangenome_node.hasProperty("k_mer_size")) { // The "k_mer_size" property is only present in pangenomes
+ if (pangenome_node.hasProperty("k_mer_size")) { // The "k_mer_size" property is only present in pangenomes
K_SIZE = (int) pangenome_node.getProperty("k_mer_size");
} else {
PROTEOME = true;