--- go-lastrelease.obo 2026-04-20 06:15:15.938939649 +0000
+++ go.obo 2026-04-20 06:24:05.643497390 +0000
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: releases/2026-03-25
+data-version: releases/2026-04-20
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_obsoletion_candidate "Terms planned for obsoletion"
@@ -44,7 +44,7 @@
property_value: has_ontology_root_term GO:0003674
property_value: has_ontology_root_term GO:0005575
property_value: has_ontology_root_term GO:0008150
-property_value: owl:versionInfo "2026-03-25" xsd:string
+property_value: owl:versionInfo "2026-04-20" xsd:string
property_value: terms:license http://creativecommons.org/licenses/by/4.0/
[Term]
@@ -86,7 +86,7 @@
is_obsolete: true
consider: GO:0042254
consider: GO:0044183
-consider: GO:0051082
+consider: GO:0140309
[Term]
id: GO:0000006
@@ -543,12 +543,15 @@
[Term]
id: GO:0000052
-name: citrulline metabolic process
+name: obsolete citrulline metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins." [ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins." [ISBN:0198506732]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "citrulline metabolism" EXACT []
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0019240
+consider: GO:0019241
[Term]
id: GO:0000053
@@ -1466,12 +1469,16 @@
xref: Reactome:R-HSA-75883 "DHRS7B reduces GO3P to HXDG3P"
xref: RHEA:17341
xref: RHEA:36175
+xref: RHEA:40939
+xref: RHEA:66452
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.101
property_value: skos:exactMatch MetaCyc:ACYLGLYCERONE-PHOSPHATE-REDUCTASE-RXN
property_value: skos:exactMatch RHEA:17341
property_value: skos:narrowMatch MetaCyc:RXN-15046
property_value: skos:narrowMatch RHEA:36175
+property_value: skos:narrowMatch RHEA:40939
+property_value: skos:narrowMatch RHEA:66452
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -1819,7 +1826,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "inactivation of MAPK (mating sensu Saccharomyces)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0000175
@@ -2816,10 +2823,16 @@
xref: Reactome:R-HSA-194718 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone)"
xref: Reactome:R-HSA-9945787 "NSDHL decarboxylates 4a-carboxy-5a-cholest-8-ene-3b-ol to 5a-cholest-8-en-3-one"
xref: Reactome:R-HSA-9945822 "NSDHL decarboxylates 4a-carboxy-4b-methyl-5a-cholest-8-en-3b-ol to 4a-methyl-5a-cholest-8-en-3b-ol"
+xref: RHEA:20673
+xref: RHEA:33447
xref: RHEA:34771
+xref: RHEA:60088
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.170
+property_value: skos:narrowMatch RHEA:20673
+property_value: skos:narrowMatch RHEA:33447
property_value: skos:narrowMatch RHEA:34771
+property_value: skos:narrowMatch RHEA:60088
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20597" xsd:anyURI
[Term]
@@ -5264,6 +5277,7 @@
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: 3-sulfino-L-alanine (cysteinesulfinate) (out) + H+(in) + L-glutamate(in) = 3-sulfino-L-alanine(in) + H+(out) + L-glutamate(out)." [PMID:11566871, RHEA:70967]
xref: RHEA:70967
is_a: GO:0000099 ! sulfur amino acid transmembrane transporter activity
+is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015078 ! proton transmembrane transporter activity
is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
@@ -5818,14 +5832,15 @@
[Term]
id: GO:0000750
-name: pheromone-dependent signal transduction involved in conjugation with cellular fusion
+name: obsolete pheromone-dependent signal transduction involved in conjugation with cellular fusion
namespace: biological_process
alt_id: GO:0007330
alt_id: GO:0030454
-def: "A signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae." [GOC:clt]
-synonym: "transduction of mating signal" BROAD []
-is_a: GO:0032005 ! signal transduction involved in positive regulation of conjugation with cellular fusion
-relationship: part_of GO:0000749 ! response to pheromone triggering conjugation with cellular fusion
+def: "OBSOLETE. A signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae." [GOC:clt]
+comment: This term was obsoleted because it is a pre-composed term that should be represented as a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31335" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0071507
[Term]
id: GO:0000751
@@ -6075,6 +6090,14 @@
xref: MetaCyc:RXN4FS-2
xref: RHEA:32735
xref: RHEA:32739
+xref: RHEA:46112
+xref: RHEA:70623
+xref: RHEA:70743
+xref: RHEA:70747
+xref: RHEA:70755
+xref: RHEA:70759
+xref: RHEA:70767
+xref: RHEA:70771
is_a: GO:0008170 ! N-methyltransferase activity
is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.71
@@ -6084,6 +6107,14 @@
property_value: skos:narrowMatch MetaCyc:RXN4FS-2
property_value: skos:narrowMatch RHEA:32735
property_value: skos:narrowMatch RHEA:32739
+property_value: skos:narrowMatch RHEA:46112
+property_value: skos:narrowMatch RHEA:70623
+property_value: skos:narrowMatch RHEA:70743
+property_value: skos:narrowMatch RHEA:70747
+property_value: skos:narrowMatch RHEA:70755
+property_value: skos:narrowMatch RHEA:70759
+property_value: skos:narrowMatch RHEA:70767
+property_value: skos:narrowMatch RHEA:70771
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -7172,36 +7203,46 @@
[Term]
id: GO:0000947
-name: amino acid catabolic process to alcohol via Ehrlich pathway
+name: obsolete amino acid catabolic process to alcohol via Ehrlich pathway
namespace: biological_process
-def: "The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432]
-is_a: GO:0000955 ! amino acid catabolic process via Ehrlich pathway
-is_a: GO:0046165 ! alcohol biosynthetic process
+def: "OBSOLETE. The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432]
+comment: This term was obsoleted because it represents multiple specific pathways. Consider specific amino acid catabolic processes.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0000948
-name: amino acid catabolic process to carboxylic acid via Ehrlich pathway
+name: obsolete amino acid catabolic process to carboxylic acid via Ehrlich pathway
namespace: biological_process
-def: "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432]
-is_a: GO:0000955 ! amino acid catabolic process via Ehrlich pathway
-is_a: GO:0046394 ! carboxylic acid biosynthetic process
+def: "OBSOLETE. The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432]
+comment: This term was obsoleted because it represents multiple specific pathways. Consider specific amino acid catabolic processes.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0000949
-name: aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
+name: obsolete aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
namespace: biological_process
-def: "The chemical reactions and pathways involving the catabolism of aromatic amino acids to produce aromatic alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanol, 4-hydroxyphenylethanol, or tryptophol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432]
-is_a: GO:0000947 ! amino acid catabolic process to alcohol via Ehrlich pathway
-is_a: GO:0009074 ! aromatic amino acid family catabolic process
+def: "OBSOLETE. The chemical reactions and pathways involving the catabolism of aromatic amino acids to produce aromatic alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanol, 4-hydroxyphenylethanol, or tryptophol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432]
+comment: This term was obsoleted because it represents multiple specific pathways. Consider specific amino acid catabolic processes.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
+is_obsolete: true
+consider: GO:0006559
+consider: GO:0006569
+consider: GO:0006572
[Term]
id: GO:0000950
-name: branched-chain amino acid catabolic process to alcohol via Ehrlich pathway
+name: obsolete branched-chain amino acid catabolic process to alcohol via Ehrlich pathway
namespace: biological_process
-def: "The chemical reactions and pathways involving the catabolism of branched chain amino acids to produce branched chain alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanol, 2-methylbutanol, or 2-methylpropanol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432]
+def: "OBSOLETE. The chemical reactions and pathways involving the catabolism of branched chain amino acids to produce branched chain alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanol, 2-methylbutanol, or 2-methylpropanol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432]
+comment: This term was obsoleted because it represents multiple specific pathways. Consider specific amino acid catabolic processes.
synonym: "branched chain family amino acid catabolic process to alcohol via Ehrlich pathway" EXACT [GOC:krc]
-is_a: GO:0000947 ! amino acid catabolic process to alcohol via Ehrlich pathway
-is_a: GO:0009083 ! branched-chain amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
+is_obsolete: true
+consider: GO:0006550
+consider: GO:0006552
+consider: GO:0006574
[Term]
id: GO:0000951
@@ -7215,20 +7256,28 @@
[Term]
id: GO:0000952
-name: aromatic amino acid family catabolic process to carboxylic acid via Ehrlich pathway
+name: obsolete aromatic amino acid family catabolic process to carboxylic acid via Ehrlich pathway
namespace: biological_process
-def: "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanoate, 4-hydroxyphenylethanoate, or 2-(Indol-3-yl)-ethanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432]
-is_a: GO:0000948 ! amino acid catabolic process to carboxylic acid via Ehrlich pathway
-is_a: GO:0009074 ! aromatic amino acid family catabolic process
+def: "OBSOLETE. The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanoate, 4-hydroxyphenylethanoate, or 2-(Indol-3-yl)-ethanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432]
+comment: This term was obsoleted because it represents multiple specific pathways. Consider specific amino acid catabolic processes.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
+is_obsolete: true
+consider: GO:0006559
+consider: GO:0006569
+consider: GO:0006572
[Term]
id: GO:0000953
-name: branched-chain amino acid catabolic process to carboxylic acid via Ehrlich pathway
+name: obsolete branched-chain amino acid catabolic process to carboxylic acid via Ehrlich pathway
namespace: biological_process
-def: "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanoate, 2-methylbutanoate, or 2-methylpropanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432]
+def: "OBSOLETE. The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanoate, 2-methylbutanoate, or 2-methylpropanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432]
+comment: This term was obsoleted because it represents multiple specific pathways. Consider specific amino acid catabolic processes.
synonym: "branched chain family amino acid catabolic process to carboxylic acid via Ehrlich pathway" EXACT [GOC:krc]
-is_a: GO:0000948 ! amino acid catabolic process to carboxylic acid via Ehrlich pathway
-is_a: GO:0009083 ! branched-chain amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
+is_obsolete: true
+consider: GO:0006550
+consider: GO:0006552
+consider: GO:0006574
[Term]
id: GO:0000954
@@ -7242,10 +7291,12 @@
[Term]
id: GO:0000955
-name: amino acid catabolic process via Ehrlich pathway
+name: obsolete amino acid catabolic process via Ehrlich pathway
namespace: biological_process
-def: "The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols or carboxylic acids containing one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives, sometimes referred to as fusel acids, may be produced instead of alcohols." [GOC:krc, PMID:18281432]
-is_a: GO:0009063 ! amino acid catabolic process
+def: "OBSOLETE. The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols or carboxylic acids containing one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives, sometimes referred to as fusel acids, may be produced instead of alcohols." [GOC:krc, PMID:18281432]
+comment: This term was obsoleted because it represents multiple specific pathways. Consider specific amino acid catabolic processes.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0000956
@@ -9883,7 +9934,6 @@
name: glycerophosphodiester transmembrane transport
namespace: biological_process
def: "The process in which a glycerophosphodiester is transported across a membrane. Glycerophosphodiesters are small molecules composed of glycerol-3-phosphate and an alcohol, for example, glycerophosphoinositol." [GOC:mcc, PMID:12912892]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
is_a: GO:0055085 ! transmembrane transport
@@ -13143,8 +13193,9 @@
synonym: "5-HT secretion" EXACT []
synonym: "5-hydroxytryptamine secretion" EXACT []
synonym: "serotonin release" RELATED [GOC:tb]
-is_a: GO:0006837 ! serotonin transport
+is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0023061 ! signal release
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0001821
@@ -16125,8 +16176,8 @@
def: "An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm." [PMID:12837608, PMID:15890982]
comment: Note that podosomes can be distinguished from other F-actin-rich structures or from other matrix contacts. For example, focal adhesions and focal contacts do not display a core structure of F-actin. Unlike focal adhesions, podosome assembly does not require de novo protein synthesis. However, most of the podosome ring components are found in focal adhesions and other cell-matrix contacts. Podosomes are typically found in cells that cross tissue boundaries, recruited to the leading edge of migrating cells, and are often sites of extracellular matrix degradation.
xref: Wikipedia:Podosome
-is_a: GO:0043232 ! intracellular membraneless organelle
-relationship: part_of GO:0015629 ! actin cytoskeleton
+is_a: GO:0098858 ! actin-based cell projection
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20443" xsd:anyURI
[Term]
id: GO:0002103
@@ -16456,7 +16507,7 @@
id: GO:0002143
name: tRNA wobble position uridine thiolation
namespace: biological_process
-def: "The process in which a uridine residue at position 34 in the anticodon of a tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps." [PMID:16871210]
+def: "The process in which a uridine residue at position 34 in the anticodon of a tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from L-cysteine to position C2 by several steps." [PMID:16871210]
comment: In E. coli, the first step of the reaction is reductive elimination of sulfur from L-cysteine by IscS cysteine desulfurase to form an enzyme-bound cysteine-persulfide intermediate. Then, five essential gene products, TusA, TusB, TusC, TusD and TusE, mediate a sulfur relay that delivers the terminal sulfur of persulfide from IscS to MnmA12. The last protein, MnmA catalyzes the transfer of the sulfur from IscS to an ATP activated U34 of the tRNA.
synonym: "tRNA wobble uridine thiolation" EXACT [GOC:mah]
synonym: "wobble position s2U biosynthesis" EXACT []
@@ -31376,7 +31427,7 @@
is_obsolete: true
consider: GO:0006457
consider: GO:0044183
-consider: GO:0051082
+consider: GO:0140309
[Term]
id: GO:0003755
@@ -31445,7 +31496,7 @@
is_obsolete: true
consider: GO:0006457
consider: GO:0044183
-consider: GO:0051082
+consider: GO:0140309
[Term]
id: GO:0003762
@@ -32283,17 +32334,25 @@
xref: Reactome:R-HSA-422454 "Polysialylation of NCAM1"
xref: Reactome:R-HSA-9845587 "ST8SIA5 transfers Neu5Ac to gangliosides"
xref: RHEA:19313
+xref: RHEA:41760
+xref: RHEA:41768
+xref: RHEA:41772
xref: RHEA:48288
xref: RHEA:48912
xref: RHEA:48924
+xref: RHEA:48928
xref: RHEA:48932
xref: RHEA:77387
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.8
property_value: skos:exactMatch RHEA:19313
+property_value: skos:narrowMatch RHEA:41760
+property_value: skos:narrowMatch RHEA:41768
+property_value: skos:narrowMatch RHEA:41772
property_value: skos:narrowMatch RHEA:48288
property_value: skos:narrowMatch RHEA:48912
property_value: skos:narrowMatch RHEA:48924
+property_value: skos:narrowMatch RHEA:48928
property_value: skos:narrowMatch RHEA:48932
property_value: skos:narrowMatch RHEA:77387
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -32459,6 +32518,7 @@
xref: RHEA:56268
xref: RHEA:82903
xref: RHEA:82947
+xref: RHEA:82983
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.1
property_value: skos:exactMatch RHEA:52104
@@ -32467,6 +32527,7 @@
property_value: skos:narrowMatch RHEA:56268
property_value: skos:narrowMatch RHEA:82903
property_value: skos:narrowMatch RHEA:82947
+property_value: skos:narrowMatch RHEA:82983
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -32602,10 +32663,15 @@
xref: RHEA:33187
xref: RHEA:33315
xref: RHEA:33319
+xref: RHEA:35903
+xref: RHEA:35907
xref: RHEA:35911
xref: RHEA:35915
+xref: RHEA:37131
xref: RHEA:37135
xref: RHEA:37139
+xref: RHEA:37143
+xref: RHEA:37147
xref: RHEA:37151
xref: RHEA:37155
xref: RHEA:37159
@@ -32619,10 +32685,14 @@
xref: RHEA:37427
xref: RHEA:37435
xref: RHEA:37439
+xref: RHEA:37443
xref: RHEA:37451
+xref: RHEA:37455
xref: RHEA:37595
xref: RHEA:37603
xref: RHEA:37607
+xref: RHEA:42588
+xref: RHEA:55304
is_a: GO:0016411 ! acylglycerol O-acyltransferase activity
is_a: GO:0042171 ! lysophosphatidic acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.51
@@ -32630,10 +32700,15 @@
property_value: skos:narrowMatch RHEA:33187
property_value: skos:narrowMatch RHEA:33315
property_value: skos:narrowMatch RHEA:33319
+property_value: skos:narrowMatch RHEA:35903
+property_value: skos:narrowMatch RHEA:35907
property_value: skos:narrowMatch RHEA:35911
property_value: skos:narrowMatch RHEA:35915
+property_value: skos:narrowMatch RHEA:37131
property_value: skos:narrowMatch RHEA:37135
property_value: skos:narrowMatch RHEA:37139
+property_value: skos:narrowMatch RHEA:37143
+property_value: skos:narrowMatch RHEA:37147
property_value: skos:narrowMatch RHEA:37151
property_value: skos:narrowMatch RHEA:37155
property_value: skos:narrowMatch RHEA:37159
@@ -32647,10 +32722,14 @@
property_value: skos:narrowMatch RHEA:37427
property_value: skos:narrowMatch RHEA:37435
property_value: skos:narrowMatch RHEA:37439
+property_value: skos:narrowMatch RHEA:37443
property_value: skos:narrowMatch RHEA:37451
+property_value: skos:narrowMatch RHEA:37455
property_value: skos:narrowMatch RHEA:37595
property_value: skos:narrowMatch RHEA:37603
property_value: skos:narrowMatch RHEA:37607
+property_value: skos:narrowMatch RHEA:42588
+property_value: skos:narrowMatch RHEA:55304
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -32781,6 +32860,16 @@
xref: Reactome:R-HSA-6800334 "MOGAT1,2,3 transfer acyl group from acyl-CoA to 2-acylglycerol to form DAG"
xref: RHEA:16741
xref: RHEA:32947
+xref: RHEA:37911
+xref: RHEA:38051
+xref: RHEA:38059
+xref: RHEA:38063
+xref: RHEA:38067
+xref: RHEA:38071
+xref: RHEA:38075
+xref: RHEA:38079
+xref: RHEA:38083
+xref: RHEA:38087
xref: RHEA:38467
xref: RHEA:39951
xref: RHEA:77271
@@ -32796,6 +32885,16 @@
property_value: skos:exactMatch EC:2.3.1.22
property_value: skos:exactMatch RHEA:16741
property_value: skos:narrowMatch RHEA:32947
+property_value: skos:narrowMatch RHEA:37911
+property_value: skos:narrowMatch RHEA:38051
+property_value: skos:narrowMatch RHEA:38059
+property_value: skos:narrowMatch RHEA:38063
+property_value: skos:narrowMatch RHEA:38067
+property_value: skos:narrowMatch RHEA:38071
+property_value: skos:narrowMatch RHEA:38075
+property_value: skos:narrowMatch RHEA:38079
+property_value: skos:narrowMatch RHEA:38083
+property_value: skos:narrowMatch RHEA:38087
property_value: skos:narrowMatch RHEA:38467
property_value: skos:narrowMatch RHEA:39951
property_value: skos:narrowMatch RHEA:77271
@@ -32935,11 +33034,13 @@
xref: Reactome:R-HSA-6785933 "UGT8 transfers Gal from UDP-Gal to CERA"
xref: RHEA:10856
xref: RHEA:13093
+xref: RHEA:43400
xref: RHEA:44896
is_a: GO:0035250 ! UDP-galactosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.47
property_value: skos:exactMatch RHEA:13093
property_value: skos:narrowMatch RHEA:10856
+property_value: skos:narrowMatch RHEA:43400
property_value: skos:narrowMatch RHEA:44896
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27679" xsd:anyURI
@@ -32986,11 +33087,13 @@
xref: MetaCyc:2-METHYLACYL-COA-DEHYDROGENASE-RXN
xref: RHEA:43780
xref: RHEA:44180
+xref: RHEA:48256
is_a: GO:0016937 ! short-chain fatty acyl-CoA dehydrogenase activity
property_value: skos:exactMatch EC:1.3.8.5
property_value: skos:narrowMatch MetaCyc:2-METHYLACYL-COA-DEHYDROGENASE-RXN
property_value: skos:narrowMatch RHEA:43780
property_value: skos:narrowMatch RHEA:44180
+property_value: skos:narrowMatch RHEA:48256
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23472" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23497" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26437" xsd:anyURI
@@ -33025,10 +33128,12 @@
xref: Reactome:R-HSA-196372 "17-Hydroxypregnenolone is dehydrogenated to form pregn-5-ene-3,20-dione-17-ol"
xref: RHEA:24076
xref: RHEA:43932
+xref: RHEA:56932
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.145
property_value: skos:narrowMatch RHEA:24076
property_value: skos:narrowMatch RHEA:43932
+property_value: skos:narrowMatch RHEA:56932
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28011" xsd:anyURI
[Term]
@@ -33100,18 +33205,36 @@
xref: Reactome:R-HSA-77331 "(S)-Hydroxyoctanoyl-CoA+NAD<=>3-Oxooctanoyl-CoA+NADH+H"
xref: Reactome:R-HSA-77342 "(S)-Hydroxydecanoyl-CoA+NAD<=>3-Oxodecanoyl-CoA+NADH+H"
xref: RHEA:22432
+xref: RHEA:30799
+xref: RHEA:31143
+xref: RHEA:31179
+xref: RHEA:31187
+xref: RHEA:31195
xref: RHEA:34851
xref: RHEA:40211
xref: RHEA:78919
xref: RHEA:78923
+xref: RHEA:83003
+xref: RHEA:84419
+xref: RHEA:84683
+xref: RHEA:84687
xref: UM-BBD_reactionID:r1063
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.35
property_value: skos:exactMatch RHEA:22432
+property_value: skos:narrowMatch RHEA:30799
+property_value: skos:narrowMatch RHEA:31143
+property_value: skos:narrowMatch RHEA:31179
+property_value: skos:narrowMatch RHEA:31187
+property_value: skos:narrowMatch RHEA:31195
property_value: skos:narrowMatch RHEA:34851
property_value: skos:narrowMatch RHEA:40211
property_value: skos:narrowMatch RHEA:78919
property_value: skos:narrowMatch RHEA:78923
+property_value: skos:narrowMatch RHEA:83003
+property_value: skos:narrowMatch RHEA:84419
+property_value: skos:narrowMatch RHEA:84683
+property_value: skos:narrowMatch RHEA:84687
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30577" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
@@ -33513,11 +33636,12 @@
[Term]
id: GO:0003875
-name: ADP-ribosylarginine hydrolase activity
+name: ADP-ribosylarginine-[protein] hydrolase activity
namespace: molecular_function
def: "Catalysis of the reactions: H2O + N(omega)-(ADP-D-ribosyl)-L-arginyl-[protein] = ADP-D-ribose + L-arginyl-[protein], and H2O + N(omega)-(ADP-D-ribosyl)-L-arginine = ADP-D-ribose + L-arginine." [EC:3.2.2.19]
synonym: "ADP-ribose-L-arginine cleavage enzyme activity" RELATED [EC:3.2.2.19]
synonym: "ADP-ribose-L-arginine cleaving enzyme activity" RELATED [EC:3.2.2.19]
+synonym: "ADP-ribosylarginine hydrolase activity" EXACT []
synonym: "ADPribosylarginine hydrolase activity" EXACT []
synonym: "N(omega)-(ADP-D-ribosyl)-L-arginine ADP-ribosylhydrolase activity" RELATED [EC:3.2.2.19]
synonym: "nomega-(ADP-D-ribosyl)-L-arginine ADP-ribosylhydrolase activity" RELATED [EC:3.2.2.19]
@@ -33525,8 +33649,10 @@
synonym: "protein ADP-ribosylarginine hydrolase activity" RELATED [EC:3.2.2.19]
synonym: "protein-nomega-(ADP-D-ribosyl)-L-arginine ADP-ribosylhydrolase activity" RELATED [EC:3.2.2.19]
xref: EC:3.2.2.19
+xref: MetaCyc:3.2.2.24-RXN {xref="skos:narrowMatch"}
xref: MetaCyc:ADP-RIBOSYLARGININE-HYDROLASE-RXN
xref: MetaCyc:RXN-8732
+xref: RHEA:14493
xref: RHEA:14885
xref: RHEA:20784
is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
@@ -33534,9 +33660,11 @@
property_value: skos:exactMatch EC:3.2.2.19
property_value: skos:narrowMatch MetaCyc:ADP-RIBOSYLARGININE-HYDROLASE-RXN
property_value: skos:narrowMatch MetaCyc:RXN-8732
+property_value: skos:narrowMatch RHEA:14493
property_value: skos:narrowMatch RHEA:14885
property_value: skos:narrowMatch RHEA:20784
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31850" xsd:anyURI
[Term]
id: GO:0003876
@@ -35786,24 +35914,102 @@
xref: Reactome:R-HSA-77340 "3-Oxodecanoyl-CoA+CoA-SH<=>Octanoyl-CoA"
xref: Reactome:R-HSA-8874745 "ACAA2 tetramer transfers acyl group from Ac-CoA to acyl-CoA forming 3OA-CoA and CoA-SH"
xref: RHEA:21564
+xref: RHEA:31087
+xref: RHEA:31091
+xref: RHEA:31111
+xref: RHEA:31183
+xref: RHEA:31203
xref: RHEA:34799
+xref: RHEA:35279
+xref: RHEA:39131
+xref: RHEA:39147
xref: RHEA:46312
+xref: RHEA:47400
+xref: RHEA:47444
+xref: RHEA:47460
xref: RHEA:67224
+xref: RHEA:78567
+xref: RHEA:78583
+xref: RHEA:78599
+xref: RHEA:78639
xref: RHEA:78895
xref: RHEA:78899
xref: RHEA:78903
xref: RHEA:78907
+xref: RHEA:82935
+xref: RHEA:82943
+xref: RHEA:83007
+xref: RHEA:83083
+xref: RHEA:83095
+xref: RHEA:83099
+xref: RHEA:83135
+xref: RHEA:83219
+xref: RHEA:83251
+xref: RHEA:83331
+xref: RHEA:83367
+xref: RHEA:83383
+xref: RHEA:83399
+xref: RHEA:84447
+xref: RHEA:84451
+xref: RHEA:84455
+xref: RHEA:84459
+xref: RHEA:84695
+xref: RHEA:84699
+xref: RHEA:84703
+xref: RHEA:84707
+xref: RHEA:84711
+xref: RHEA:84715
+xref: RHEA:84839
xref: UM-BBD_reactionID:r1051
-is_a: GO:0016408 ! C-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.16
property_value: skos:exactMatch RHEA:21564
+property_value: skos:narrowMatch RHEA:31087
+property_value: skos:narrowMatch RHEA:31091
+property_value: skos:narrowMatch RHEA:31111
+property_value: skos:narrowMatch RHEA:31183
+property_value: skos:narrowMatch RHEA:31203
property_value: skos:narrowMatch RHEA:34799
+property_value: skos:narrowMatch RHEA:35279
+property_value: skos:narrowMatch RHEA:39131
+property_value: skos:narrowMatch RHEA:39147
property_value: skos:narrowMatch RHEA:46312
+property_value: skos:narrowMatch RHEA:47400
+property_value: skos:narrowMatch RHEA:47444
+property_value: skos:narrowMatch RHEA:47460
property_value: skos:narrowMatch RHEA:67224
+property_value: skos:narrowMatch RHEA:78567
+property_value: skos:narrowMatch RHEA:78583
+property_value: skos:narrowMatch RHEA:78599
+property_value: skos:narrowMatch RHEA:78639
property_value: skos:narrowMatch RHEA:78895
property_value: skos:narrowMatch RHEA:78899
property_value: skos:narrowMatch RHEA:78903
property_value: skos:narrowMatch RHEA:78907
+property_value: skos:narrowMatch RHEA:82935
+property_value: skos:narrowMatch RHEA:82943
+property_value: skos:narrowMatch RHEA:83007
+property_value: skos:narrowMatch RHEA:83083
+property_value: skos:narrowMatch RHEA:83095
+property_value: skos:narrowMatch RHEA:83099
+property_value: skos:narrowMatch RHEA:83135
+property_value: skos:narrowMatch RHEA:83219
+property_value: skos:narrowMatch RHEA:83251
+property_value: skos:narrowMatch RHEA:83331
+property_value: skos:narrowMatch RHEA:83367
+property_value: skos:narrowMatch RHEA:83383
+property_value: skos:narrowMatch RHEA:83399
+property_value: skos:narrowMatch RHEA:84447
+property_value: skos:narrowMatch RHEA:84451
+property_value: skos:narrowMatch RHEA:84455
+property_value: skos:narrowMatch RHEA:84459
+property_value: skos:narrowMatch RHEA:84695
+property_value: skos:narrowMatch RHEA:84699
+property_value: skos:narrowMatch RHEA:84703
+property_value: skos:narrowMatch RHEA:84707
+property_value: skos:narrowMatch RHEA:84711
+property_value: skos:narrowMatch RHEA:84715
+property_value: skos:narrowMatch RHEA:84839
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -36397,12 +36603,136 @@
xref: Reactome:R-HSA-71707 "ethanol + NAD+ => acetaldehyde + NADH + H+"
xref: RHEA:10736
xref: RHEA:10740
+xref: RHEA:12216
+xref: RHEA:12785
+xref: RHEA:13221
+xref: RHEA:15757
+xref: RHEA:16317
+xref: RHEA:16821
+xref: RHEA:23552
+xref: RHEA:30027
+xref: RHEA:32343
+xref: RHEA:34347
+xref: RHEA:35463
+xref: RHEA:35615
+xref: RHEA:37167
+xref: RHEA:38215
+xref: RHEA:41984
+xref: RHEA:42012
+xref: RHEA:42016
+xref: RHEA:42020
+xref: RHEA:42052
+xref: RHEA:42056
+xref: RHEA:42060
+xref: RHEA:45120
+xref: RHEA:48728
+xref: RHEA:48748
+xref: RHEA:48756
+xref: RHEA:48760
+xref: RHEA:50704
+xref: RHEA:55936
+xref: RHEA:58848
+xref: RHEA:60632
+xref: RHEA:60668
+xref: RHEA:60672
+xref: RHEA:60676
+xref: RHEA:60712
+xref: RHEA:60972
+xref: RHEA:60976
+xref: RHEA:60980
+xref: RHEA:60984
+xref: RHEA:60988
+xref: RHEA:62064
+xref: RHEA:62392
+xref: RHEA:63260
+xref: RHEA:63740
+xref: RHEA:64060
+xref: RHEA:64068
+xref: RHEA:64516
+xref: RHEA:64560
+xref: RHEA:64692
+xref: RHEA:64700
+xref: RHEA:64704
+xref: RHEA:68108
+xref: RHEA:70231
+xref: RHEA:75115
+xref: RHEA:75419
+xref: RHEA:75423
+xref: RHEA:79419
+xref: RHEA:80735
+xref: RHEA:81603
+xref: RHEA:86103
+xref: RHEA:86111
+xref: RHEA:86115
+xref: RHEA:86119
is_a: GO:0018455 ! alcohol dehydrogenase [NAD(P)+] activity
property_value: skos:exactMatch EC:1.1.1.1
property_value: skos:narrowMatch MetaCyc:ALCOHOL-DEHYDROG-GENERIC-RXN
property_value: skos:narrowMatch MetaCyc:RXN-12448
property_value: skos:narrowMatch RHEA:10736
property_value: skos:narrowMatch RHEA:10740
+property_value: skos:narrowMatch RHEA:12216
+property_value: skos:narrowMatch RHEA:12785
+property_value: skos:narrowMatch RHEA:13221
+property_value: skos:narrowMatch RHEA:15757
+property_value: skos:narrowMatch RHEA:16317
+property_value: skos:narrowMatch RHEA:16821
+property_value: skos:narrowMatch RHEA:23552
+property_value: skos:narrowMatch RHEA:30027
+property_value: skos:narrowMatch RHEA:32343
+property_value: skos:narrowMatch RHEA:34347
+property_value: skos:narrowMatch RHEA:35463
+property_value: skos:narrowMatch RHEA:35615
+property_value: skos:narrowMatch RHEA:37167
+property_value: skos:narrowMatch RHEA:38215
+property_value: skos:narrowMatch RHEA:41984
+property_value: skos:narrowMatch RHEA:42012
+property_value: skos:narrowMatch RHEA:42016
+property_value: skos:narrowMatch RHEA:42020
+property_value: skos:narrowMatch RHEA:42052
+property_value: skos:narrowMatch RHEA:42056
+property_value: skos:narrowMatch RHEA:42060
+property_value: skos:narrowMatch RHEA:45120
+property_value: skos:narrowMatch RHEA:48728
+property_value: skos:narrowMatch RHEA:48748
+property_value: skos:narrowMatch RHEA:48756
+property_value: skos:narrowMatch RHEA:48760
+property_value: skos:narrowMatch RHEA:50704
+property_value: skos:narrowMatch RHEA:55936
+property_value: skos:narrowMatch RHEA:58848
+property_value: skos:narrowMatch RHEA:60632
+property_value: skos:narrowMatch RHEA:60668
+property_value: skos:narrowMatch RHEA:60672
+property_value: skos:narrowMatch RHEA:60676
+property_value: skos:narrowMatch RHEA:60712
+property_value: skos:narrowMatch RHEA:60972
+property_value: skos:narrowMatch RHEA:60976
+property_value: skos:narrowMatch RHEA:60980
+property_value: skos:narrowMatch RHEA:60984
+property_value: skos:narrowMatch RHEA:60988
+property_value: skos:narrowMatch RHEA:62064
+property_value: skos:narrowMatch RHEA:62392
+property_value: skos:narrowMatch RHEA:63260
+property_value: skos:narrowMatch RHEA:63740
+property_value: skos:narrowMatch RHEA:64060
+property_value: skos:narrowMatch RHEA:64068
+property_value: skos:narrowMatch RHEA:64516
+property_value: skos:narrowMatch RHEA:64560
+property_value: skos:narrowMatch RHEA:64692
+property_value: skos:narrowMatch RHEA:64700
+property_value: skos:narrowMatch RHEA:64704
+property_value: skos:narrowMatch RHEA:68108
+property_value: skos:narrowMatch RHEA:70231
+property_value: skos:narrowMatch RHEA:75115
+property_value: skos:narrowMatch RHEA:75419
+property_value: skos:narrowMatch RHEA:75423
+property_value: skos:narrowMatch RHEA:79419
+property_value: skos:narrowMatch RHEA:80735
+property_value: skos:narrowMatch RHEA:81603
+property_value: skos:narrowMatch RHEA:86103
+property_value: skos:narrowMatch RHEA:86111
+property_value: skos:narrowMatch RHEA:86115
+property_value: skos:narrowMatch RHEA:86119
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28532" xsd:anyURI
[Term]
@@ -36563,7 +36893,6 @@
xref: RHEA:42340
xref: RHEA:42384
xref: RHEA:45764
-xref: RHEA:47152
xref: RHEA:47932
xref: RHEA:59432
xref: RHEA:60688
@@ -36604,7 +36933,6 @@
property_value: skos:narrowMatch RHEA:42340
property_value: skos:narrowMatch RHEA:42384
property_value: skos:narrowMatch RHEA:45764
-property_value: skos:narrowMatch RHEA:47152
property_value: skos:narrowMatch RHEA:47932
property_value: skos:narrowMatch RHEA:59432
property_value: skos:narrowMatch RHEA:60688
@@ -36990,8 +37318,21 @@
xref: Reactome:R-HSA-9753944 "ACY1:Zn2+ dimer deacetylates NAC to L-Cys"
xref: RHEA:15565
xref: RHEA:36855
+xref: RHEA:49796
+xref: RHEA:51460
xref: RHEA:52628
xref: RHEA:54184
+xref: RHEA:54188
+xref: RHEA:64112
+xref: RHEA:64120
+xref: RHEA:64140
+xref: RHEA:64156
+xref: RHEA:64180
+xref: RHEA:64188
+xref: RHEA:64196
+xref: RHEA:64200
+xref: RHEA:64208
+xref: RHEA:64212
xref: RHEA:67368
xref: RHEA:67440
xref: RHEA:75515
@@ -37002,8 +37343,21 @@
property_value: skos:exactMatch EC:3.5.1.14
property_value: skos:exactMatch RHEA:15565
property_value: skos:narrowMatch RHEA:36855
+property_value: skos:narrowMatch RHEA:49796
+property_value: skos:narrowMatch RHEA:51460
property_value: skos:narrowMatch RHEA:52628
property_value: skos:narrowMatch RHEA:54184
+property_value: skos:narrowMatch RHEA:54188
+property_value: skos:narrowMatch RHEA:64112
+property_value: skos:narrowMatch RHEA:64120
+property_value: skos:narrowMatch RHEA:64140
+property_value: skos:narrowMatch RHEA:64156
+property_value: skos:narrowMatch RHEA:64180
+property_value: skos:narrowMatch RHEA:64188
+property_value: skos:narrowMatch RHEA:64196
+property_value: skos:narrowMatch RHEA:64200
+property_value: skos:narrowMatch RHEA:64208
+property_value: skos:narrowMatch RHEA:64212
property_value: skos:narrowMatch RHEA:67368
property_value: skos:narrowMatch RHEA:67440
property_value: skos:narrowMatch RHEA:75515
@@ -38075,6 +38429,7 @@
xref: RHEA:18941
xref: RHEA:19257
xref: RHEA:25960
+xref: RHEA:25964
xref: RHEA:31891
xref: RHEA:32339
xref: RHEA:32619
@@ -38086,6 +38441,8 @@
xref: RHEA:47540
xref: RHEA:53820
xref: RHEA:62068
+xref: RHEA:62072
+xref: RHEA:62080
xref: RHEA:62216
xref: RHEA:62268
xref: RHEA:63476
@@ -38120,6 +38477,7 @@
property_value: skos:narrowMatch RHEA:16817
property_value: skos:narrowMatch RHEA:18941
property_value: skos:narrowMatch RHEA:25960
+property_value: skos:narrowMatch RHEA:25964
property_value: skos:narrowMatch RHEA:31891
property_value: skos:narrowMatch RHEA:32339
property_value: skos:narrowMatch RHEA:32619
@@ -38131,6 +38489,8 @@
property_value: skos:narrowMatch RHEA:47540
property_value: skos:narrowMatch RHEA:53820
property_value: skos:narrowMatch RHEA:62068
+property_value: skos:narrowMatch RHEA:62072
+property_value: skos:narrowMatch RHEA:62080
property_value: skos:narrowMatch RHEA:62216
property_value: skos:narrowMatch RHEA:62268
property_value: skos:narrowMatch RHEA:63476
@@ -38880,12 +39240,13 @@
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 monoatomic ion transmembrane transporter activity
-relationship: has_part GO:0016675 ! oxidoreductase activity, acting on a heme group of donors
property_value: skos:exactMatch EC:7.1.1.9
property_value: skos:exactMatch RHEA:11436
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20924" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21275" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25935" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
[Term]
@@ -39482,11 +39843,15 @@
xref: Reactome:R-HSA-71130 "q-dihydrobiopterin + NADH + H+ => tetrahydrobiopterin + NAD+"
xref: RHEA:17865
xref: RHEA:17869
+xref: RHEA:32247
+xref: RHEA:32251
is_a: GO:0016646 ! oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.5.1.34
property_value: skos:exactMatch MetaCyc:1.5.1.34-RXN
property_value: skos:narrowMatch RHEA:17865
property_value: skos:narrowMatch RHEA:17869
+property_value: skos:narrowMatch RHEA:32247
+property_value: skos:narrowMatch RHEA:32251
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29460" xsd:anyURI
[Term]
@@ -39700,10 +40065,25 @@
xref: RHEA:23716
xref: RHEA:29847
xref: RHEA:45228
+xref: RHEA:45736
xref: RHEA:45748
+xref: RHEA:45752
xref: RHEA:45900
xref: RHEA:46044
+xref: RHEA:46068
+xref: RHEA:47464
+xref: RHEA:47476
+xref: RHEA:49852
+xref: RHEA:49932
xref: RHEA:77195
+xref: RHEA:83231
+xref: RHEA:84487
+xref: RHEA:84491
+xref: RHEA:84547
+xref: RHEA:84555
+xref: RHEA:84559
+xref: RHEA:84563
+xref: RHEA:84843
is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds
property_value: skos:exactMatch EC:5.3.3.8
property_value: skos:exactMatch RHEA:45900
@@ -39713,9 +40093,24 @@
property_value: skos:narrowMatch RHEA:23716
property_value: skos:narrowMatch RHEA:29847
property_value: skos:narrowMatch RHEA:45228
+property_value: skos:narrowMatch RHEA:45736
property_value: skos:narrowMatch RHEA:45748
+property_value: skos:narrowMatch RHEA:45752
property_value: skos:narrowMatch RHEA:46044
+property_value: skos:narrowMatch RHEA:46068
+property_value: skos:narrowMatch RHEA:47464
+property_value: skos:narrowMatch RHEA:47476
+property_value: skos:narrowMatch RHEA:49852
+property_value: skos:narrowMatch RHEA:49932
property_value: skos:narrowMatch RHEA:77195
+property_value: skos:narrowMatch RHEA:83231
+property_value: skos:narrowMatch RHEA:84487
+property_value: skos:narrowMatch RHEA:84491
+property_value: skos:narrowMatch RHEA:84547
+property_value: skos:narrowMatch RHEA:84555
+property_value: skos:narrowMatch RHEA:84559
+property_value: skos:narrowMatch RHEA:84563
+property_value: skos:narrowMatch RHEA:84843
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21637" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -39875,7 +40270,7 @@
xref: KEGG_REACTION:R02375
xref: MetaCyc:ECDYSONE-O-ACYLTRANSFERASE-RXN
xref: RHEA:15217
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.139
property_value: skos:exactMatch RHEA:15217
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -42285,6 +42680,17 @@
xref: RHEA:44044
xref: RHEA:44048
xref: RHEA:45352
+xref: RHEA:53972
+xref: RHEA:53976
+xref: RHEA:53980
+xref: RHEA:53984
+xref: RHEA:53992
+xref: RHEA:53996
+xref: RHEA:54000
+xref: RHEA:54004
+xref: RHEA:54008
+xref: RHEA:54012
+xref: RHEA:54016
xref: RHEA:56584
xref: RHEA:80591
xref: RHEA:80779
@@ -42303,6 +42709,17 @@
property_value: skos:narrowMatch RHEA:44044
property_value: skos:narrowMatch RHEA:44048
property_value: skos:narrowMatch RHEA:45352
+property_value: skos:narrowMatch RHEA:53972
+property_value: skos:narrowMatch RHEA:53976
+property_value: skos:narrowMatch RHEA:53980
+property_value: skos:narrowMatch RHEA:53984
+property_value: skos:narrowMatch RHEA:53992
+property_value: skos:narrowMatch RHEA:53996
+property_value: skos:narrowMatch RHEA:54000
+property_value: skos:narrowMatch RHEA:54004
+property_value: skos:narrowMatch RHEA:54008
+property_value: skos:narrowMatch RHEA:54012
+property_value: skos:narrowMatch RHEA:54016
property_value: skos:narrowMatch RHEA:56584
property_value: skos:narrowMatch RHEA:80591
property_value: skos:narrowMatch RHEA:80779
@@ -42787,7 +43204,7 @@
xref: EC:2.3.1.86
xref: MetaCyc:FATTY-ACYL-COA-SYNTHASE-RXN
xref: RHEA:22896
-is_a: GO:0016408 ! C-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.86
property_value: skos:exactMatch RHEA:22896
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -43850,7 +44267,7 @@
xref: RHEA:37199
xref: RHEA:37203
xref: RHEA:37463
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.15
property_value: skos:exactMatch RHEA:15325
property_value: skos:narrowMatch RHEA:35723
@@ -43877,13 +44294,17 @@
xref: MetaCyc:RXN-15745
xref: Reactome:R-HSA-188467 "Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)"
xref: RHEA:18977
+xref: RHEA:28751
xref: RHEA:28755
xref: RHEA:29219
+xref: RHEA:29223
is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:1.1.5.3
property_value: skos:exactMatch RHEA:18977
+property_value: skos:narrowMatch RHEA:28751
property_value: skos:narrowMatch RHEA:28755
property_value: skos:narrowMatch RHEA:29219
+property_value: skos:narrowMatch RHEA:29223
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25984" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -44112,7 +44533,6 @@
xref: Reactome:R-HSA-203611 "N-myristoylation of eNOS"
xref: Reactome:R-HSA-2534087 "NMT1/2 transfer MYS to GNAT1"
xref: RHEA:15521
-is_a: GO:0016410 ! N-acyltransferase activity
is_a: GO:0019107 ! myristoyltransferase activity
property_value: skos:exactMatch EC:2.3.1.97
property_value: skos:exactMatch RHEA:15521
@@ -46163,10 +46583,12 @@
xref: Reactome:R-HSA-9694721 "nsp16 acts as a cap 2'-O-methyltransferase to modify SARS-CoV-2 gRNA (plus strand)"
xref: Reactome:R-HSA-9834003 "L protein acts as a cap 2'-O-methyltransferase to modify RSV mRNAs"
xref: Reactome:R-HSA-9923097 "NS5 acts as a cap 2'-O-methyltransferase to methylate 5 m7GpppA of DENV genomic +ssRNA"
+xref: RHEA:19617
xref: RHEA:67020
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008173 ! RNA methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.57
+property_value: skos:narrowMatch RHEA:19617
property_value: skos:narrowMatch RHEA:67020
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27387" xsd:anyURI
@@ -46347,10 +46769,14 @@
xref: Reactome:R-HSA-70893 "methylmalonate semialdehyde + NAD+ + CoA + H2O => propionyl-CoA + HCO3- + NADH + H+"
xref: RHEA:20804
xref: RHEA:76615
+xref: RHEA:76623
+xref: RHEA:76627
is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.2.1.27
property_value: skos:narrowMatch RHEA:20804
property_value: skos:narrowMatch RHEA:76615
+property_value: skos:narrowMatch RHEA:76623
+property_value: skos:narrowMatch RHEA:76627
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25638" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30853" xsd:anyURI
@@ -48419,6 +48845,8 @@
xref: RHEA:50512
xref: RHEA:50516
xref: RHEA:57320
+xref: RHEA:57324
+xref: RHEA:57328
xref: RHEA:75243
xref: RHEA:75247
is_a: GO:0034212 ! protein N-acetyltransferase activity
@@ -48428,6 +48856,8 @@
property_value: skos:narrowMatch RHEA:50512
property_value: skos:narrowMatch RHEA:50516
property_value: skos:narrowMatch RHEA:57320
+property_value: skos:narrowMatch RHEA:57324
+property_value: skos:narrowMatch RHEA:57328
property_value: skos:narrowMatch RHEA:75243
property_value: skos:narrowMatch RHEA:75247
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24761" xsd:anyURI
@@ -48645,10 +49075,12 @@
xref: Reactome:R-HSA-264695 "cholesterol + phosphatidylcholine (lecithin) => cholesterol ester + 2-lysophosphatidylcholine (lysolecithin)"
xref: RHEA:21204
xref: RHEA:34087
-is_a: GO:0008374 ! O-acyltransferase activity
+xref: RHEA:53452
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.43
property_value: skos:exactMatch RHEA:21204
property_value: skos:narrowMatch RHEA:34087
+property_value: skos:narrowMatch RHEA:53452
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -49053,11 +49485,25 @@
xref: Reactome:R-HSA-1602446 "PA is hydrolyzed to 1-acyl LPA by PLA2[15]"
xref: Reactome:R-HSA-8848484 "PLA2s hydrolyze phospholipids at the Golgi membrane"
xref: RHEA:15801
+xref: RHEA:38779
+xref: RHEA:38847
+xref: RHEA:40643
+xref: RHEA:40651
+xref: RHEA:41223
+xref: RHEA:53500
+xref: RHEA:62036
is_a: GO:0004620 ! glycerophospholipase activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:exactMatch EC:3.1.1.4
property_value: skos:narrowMatch MetaCyc:RXN-15065
property_value: skos:narrowMatch RHEA:15801
+property_value: skos:narrowMatch RHEA:38779
+property_value: skos:narrowMatch RHEA:38847
+property_value: skos:narrowMatch RHEA:40643
+property_value: skos:narrowMatch RHEA:40651
+property_value: skos:narrowMatch RHEA:41223
+property_value: skos:narrowMatch RHEA:53500
+property_value: skos:narrowMatch RHEA:62036
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21259" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30258" xsd:anyURI
@@ -49159,10 +49605,14 @@
xref: Reactome:R-HSA-1483182 "PC is hydrolyzed to PA and choline by PLD1/2"
xref: Reactome:R-HSA-2029471 "Hydrolysis of PC to PA by PLD"
xref: RHEA:14445
+xref: RHEA:41412
+xref: RHEA:41416
is_a: GO:0004620 ! glycerophospholipase activity
is_a: GO:0008081 ! phosphoric diester hydrolase activity
property_value: skos:exactMatch EC:3.1.4.4
property_value: skos:narrowMatch RHEA:14445
+property_value: skos:narrowMatch RHEA:41412
+property_value: skos:narrowMatch RHEA:41416
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31049" xsd:anyURI
@@ -51983,12 +52433,16 @@
xref: Reactome:R-HSA-9865238 "PP2A dephosphorylates serine-715 of PDE4D5 in p-S715-PDE4D5:integrin alpha5:integrin beta1:fibronectin"
xref: Reactome:R-HSA-9912527 "H139Hfs13* PPM1K does not dephosphorylate BCKDH"
xref: Reactome:R-HSA-9970190 "PP1 dephosphorylates RNA Pol II"
+xref: RHEA:12849
xref: RHEA:20629
xref: RHEA:47004
+xref: RHEA:53988
is_a: GO:0004721 ! phosphoprotein phosphatase activity
property_value: skos:exactMatch EC:3.1.3.16
+property_value: skos:narrowMatch RHEA:12849
property_value: skos:narrowMatch RHEA:20629
property_value: skos:narrowMatch RHEA:47004
+property_value: skos:narrowMatch RHEA:53988
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22458" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25787" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -52955,6 +53409,7 @@
xref: RHEA:10100
xref: RHEA:33543
xref: RHEA:33547
+xref: RHEA:33875
xref: RHEA:36403
is_a: GO:0016298 ! lipase activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity
@@ -52963,6 +53418,7 @@
property_value: skos:exactMatch RHEA:10100
property_value: skos:narrowMatch RHEA:33543
property_value: skos:narrowMatch RHEA:33547
+property_value: skos:narrowMatch RHEA:33875
property_value: skos:narrowMatch RHEA:36403
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
@@ -52977,7 +53433,7 @@
xref: EC:2.3.1.26
xref: MetaCyc:RXN-20233
xref: RHEA:59816
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.26
property_value: skos:exactMatch MetaCyc:RXN-20233
property_value: skos:exactMatch RHEA:59816
@@ -53127,7 +53583,7 @@
id: GO:0004781
name: sulfate adenylyltransferase (ATP) activity
namespace: molecular_function
-def: "Catalysis of the reaction: ATP + H+ + sulfate = adenosine 5'-phosphosulfate + diphosphate." [EC:2.7.7.4]
+def: "Catalysis of the reaction: sulfate + ATP + H+ = adenosine 5'-phosphosulfate + diphosphate." [RHEA:18133]
synonym: "adenosine-5'-triphosphate sulfurylase activity" RELATED [EC:2.7.7.4]
synonym: "adenosinetriphosphate sulfurylase activity" RELATED [EC:2.7.7.4]
synonym: "adenylylsulfate pyrophosphorylase activity" RELATED [EC:2.7.7.4]
@@ -53691,14 +54147,28 @@
xref: Reactome:R-HSA-8848339 "PNPLA5 hydrolyzes TAG"
xref: RHEA:12044
xref: RHEA:35667
+xref: RHEA:38379
+xref: RHEA:38387
+xref: RHEA:38391
+xref: RHEA:38395
+xref: RHEA:38403
+xref: RHEA:38411
+xref: RHEA:38419
xref: RHEA:38495
xref: RHEA:38575
+xref: RHEA:39931
+xref: RHEA:40047
+xref: RHEA:40055
xref: RHEA:40475
+xref: RHEA:43732
+xref: RHEA:44864
xref: RHEA:47864
xref: RHEA:48024
xref: RHEA:48028
xref: RHEA:59020
xref: RHEA:59024
+xref: RHEA:63432
+xref: RHEA:63436
is_a: GO:0016298 ! lipase activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:broadMatch EC:3.1.1.79
@@ -53706,14 +54176,28 @@
property_value: skos:exactMatch MetaCyc:RXN-19278
property_value: skos:exactMatch RHEA:12044
property_value: skos:narrowMatch RHEA:35667
+property_value: skos:narrowMatch RHEA:38379
+property_value: skos:narrowMatch RHEA:38387
+property_value: skos:narrowMatch RHEA:38391
+property_value: skos:narrowMatch RHEA:38395
+property_value: skos:narrowMatch RHEA:38403
+property_value: skos:narrowMatch RHEA:38411
+property_value: skos:narrowMatch RHEA:38419
property_value: skos:narrowMatch RHEA:38495
property_value: skos:narrowMatch RHEA:38575
+property_value: skos:narrowMatch RHEA:39931
+property_value: skos:narrowMatch RHEA:40047
+property_value: skos:narrowMatch RHEA:40055
property_value: skos:narrowMatch RHEA:40475
+property_value: skos:narrowMatch RHEA:43732
+property_value: skos:narrowMatch RHEA:44864
property_value: skos:narrowMatch RHEA:47864
property_value: skos:narrowMatch RHEA:48024
property_value: skos:narrowMatch RHEA:48028
property_value: skos:narrowMatch RHEA:59020
property_value: skos:narrowMatch RHEA:59024
+property_value: skos:narrowMatch RHEA:63432
+property_value: skos:narrowMatch RHEA:63436
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28176" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
@@ -55980,10 +56464,10 @@
def: "Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts." [ISBN:0198506732]
comment: Note that this term represents an activity and not a gene product. Consider also annotating to the molecular function terms 'glutamate-gated ion channel activity ; GO:0005234' and 'cation channel activity ; GO:0005261'.
synonym: "ionotropic glutamate receptor activity" EXACT []
+is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0008066 ! glutamate receptor activity
is_a: GO:0015171 ! amino acid transmembrane transporter activity
is_a: GO:0022824 ! transmitter-gated monoatomic ion channel activity
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
relationship: part_of GO:0035235 ! ionotropic glutamate receptor signaling pathway
[Term]
@@ -59235,7 +59719,7 @@
name: creatine transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of creatine from one side of a membrane to the other. Creatine is a compound synthesized from the amino acids arginine, glycine, and methionine that occurs in muscle." [GOC:ai]
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
relationship: part_of GO:0015881 ! creatine transmembrane transport
@@ -59247,7 +59731,7 @@
synonym: "sodium/chloride-dependent creatine transporter" BROAD []
xref: Reactome:R-HSA-200396 "Creatine transport across the plasma membrane"
is_a: GO:0005308 ! creatine transmembrane transporter activity
-is_a: GO:0005343 ! organic acid:sodium symporter activity
+is_a: GO:0140161 ! monocarboxylate:sodium symporter activity
[Term]
id: GO:0005310
@@ -59290,6 +59774,7 @@
xref: Reactome:R-HSA-210444 "L-Glutamate loading of synaptic vesicle"
xref: Reactome:R-HSA-428052 "SLC17A6,7,8 exchange cytosolic L-Glu for synaptic vesicle H+"
xref: Reactome:R-HSA-5624256 "Defective SLC17A8 does not exchange cytosolic L-Glu for synaptic vesicle H+"
+is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015172 ! acidic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
relationship: part_of GO:0015813 ! L-glutamate transmembrane transport
@@ -59503,9 +59988,10 @@
xref: RHEA:70731
xref: TC:2.A.22.3.2
is_a: GO:0005283 ! amino acid:sodium symporter activity
+is_a: GO:0005343 ! organic acid:sodium symporter activity
is_a: GO:0015185 ! gamma-aminobutyric acid transmembrane transporter activity
+is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
is_a: GO:0015378 ! sodium:chloride symporter activity
-is_a: GO:0140161 ! monocarboxylate:sodium symporter activity
property_value: skos:narrowMatch RHEA:70687
property_value: skos:narrowMatch RHEA:70731
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23299" xsd:anyURI
@@ -65526,7 +66012,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism." [ISBN:0198506732]
synonym: "fructose 6-phosphate metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
@@ -65536,7 +66021,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving fructose 2,6-bisphosphate. The D enantiomer is an important regulator of the glycolytic and gluconeogenic pathways. It inhibits fructose 1,6-bisphosphatase and activates phosphofructokinase." [ISBN:0198506732]
synonym: "fructose 2,6-bisphosphate metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
@@ -65636,7 +66120,6 @@
synonym: "5-phosphoribosyl-1-pyrophosphate biosynthetic process" EXACT []
synonym: "PRPP biosynthetic process" EXACT []
xref: MetaCyc:PWY0-662
-xref: Reactome:R-HSA-73843 "5-Phosphoribose 1-diphosphate biosynthesis"
is_a: GO:0046390 ! ribose phosphate biosynthetic process
is_a: GO:0046391 ! 5-phosphoribose 1-diphosphate metabolic process
property_value: skos:narrowMatch MetaCyc:PWY0-662
@@ -65959,39 +66442,42 @@
[Term]
id: GO:0006041
-name: glucosamine metabolic process
+name: D-glucosamine metabolic process
namespace: biological_process
def: "The chemical reactions and pathways involving glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin." [GOC:jl, ISBN:0198506732]
synonym: "chitosamine metabolic process" EXACT []
synonym: "chitosamine metabolism" EXACT []
+synonym: "glucosamine metabolic process" EXACT []
synonym: "glucosamine metabolism" EXACT []
is_a: GO:0006040 ! amino sugar metabolic process
[Term]
id: GO:0006042
-name: glucosamine biosynthetic process
+name: D-glucosamine biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin." [GOC:jl, ISBN:0198506732]
synonym: "chitosamine biosynthesis" EXACT []
synonym: "chitosamine biosynthetic process" EXACT []
synonym: "glucosamine anabolism" EXACT []
synonym: "glucosamine biosynthesis" EXACT []
+synonym: "glucosamine biosynthetic process" EXACT []
synonym: "glucosamine formation" EXACT []
synonym: "glucosamine synthesis" EXACT []
-is_a: GO:0006041 ! glucosamine metabolic process
+is_a: GO:0006041 ! D-glucosamine metabolic process
is_a: GO:1901073 ! glucosamine-containing compound biosynthetic process
[Term]
id: GO:0006043
-name: glucosamine catabolic process
+name: D-glucosamine catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin." [GOC:jl, ISBN:0198506732]
synonym: "chitosamine catabolic process" EXACT []
synonym: "chitosamine catabolism" EXACT []
synonym: "glucosamine breakdown" EXACT []
+synonym: "glucosamine catabolic process" EXACT []
synonym: "glucosamine catabolism" EXACT []
synonym: "glucosamine degradation" EXACT []
-is_a: GO:0006041 ! glucosamine metabolic process
+is_a: GO:0006041 ! D-glucosamine metabolic process
is_a: GO:1901072 ! glucosamine-containing compound catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
@@ -66468,12 +66954,13 @@
[Term]
id: GO:0006082
-name: organic acid metabolic process
+name: obsolete organic acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732]
-subset: goslim_pir
-synonym: "organic acid metabolism" EXACT []
-is_a: GO:0044281 ! small molecule metabolic process
+def: "OBSOLETE. The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31816" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0008152
[Term]
id: GO:0006083
@@ -67521,6 +68008,7 @@
synonym: "dADP synthesis" EXACT []
is_a: GO:0009153 ! purine deoxyribonucleotide biosynthetic process
is_a: GO:0009183 ! purine deoxyribonucleoside diphosphate biosynthetic process
+is_a: GO:0009189 ! deoxyribonucleoside diphosphate biosynthetic process
is_a: GO:0046056 ! dADP metabolic process
[Term]
@@ -67541,6 +68029,7 @@
synonym: "dATP formation" EXACT []
synonym: "dATP synthesis" EXACT []
is_a: GO:0009153 ! purine deoxyribonucleotide biosynthetic process
+is_a: GO:0009202 ! deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009216 ! purine deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0046060 ! dATP metabolic process
@@ -67657,6 +68146,7 @@
synonym: "dGDP synthesis" EXACT []
is_a: GO:0009153 ! purine deoxyribonucleotide biosynthetic process
is_a: GO:0009183 ! purine deoxyribonucleoside diphosphate biosynthetic process
+is_a: GO:0009189 ! deoxyribonucleoside diphosphate biosynthetic process
is_a: GO:0046066 ! dGDP metabolic process
[Term]
@@ -67859,6 +68349,7 @@
synonym: "dGTP catabolism" EXACT []
synonym: "dGTP degradation" EXACT []
is_a: GO:0009155 ! purine deoxyribonucleotide catabolic process
+is_a: GO:0009204 ! deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009217 ! purine deoxyribonucleoside triphosphate catabolic process
is_a: GO:0046070 ! dGTP metabolic process
@@ -68128,6 +68619,7 @@
synonym: "dUDP biosynthesis" EXACT []
synonym: "dUDP formation" EXACT []
synonym: "dUDP synthesis" EXACT []
+is_a: GO:0009189 ! deoxyribonucleoside diphosphate biosynthetic process
is_a: GO:0009197 ! pyrimidine deoxyribonucleoside diphosphate biosynthetic process
is_a: GO:0009221 ! pyrimidine deoxyribonucleotide biosynthetic process
is_a: GO:0046077 ! dUDP metabolic process
@@ -68154,6 +68646,7 @@
synonym: "dUTP biosynthesis" EXACT []
synonym: "dUTP formation" EXACT []
synonym: "dUTP synthesis" EXACT []
+is_a: GO:0009202 ! deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009212 ! pyrimidine deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009221 ! pyrimidine deoxyribonucleotide biosynthetic process
is_a: GO:0046080 ! dUTP metabolic process
@@ -68232,6 +68725,7 @@
synonym: "dTTP biosynthesis" EXACT []
synonym: "dTTP formation" EXACT []
synonym: "dTTP synthesis" EXACT []
+is_a: GO:0009202 ! deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009212 ! pyrimidine deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009221 ! pyrimidine deoxyribonucleotide biosynthetic process
is_a: GO:0046075 ! dTTP metabolic process
@@ -68280,6 +68774,7 @@
synonym: "dCDP biosynthesis" EXACT []
synonym: "dCDP formation" EXACT []
synonym: "dCDP synthesis" EXACT []
+is_a: GO:0009189 ! deoxyribonucleoside diphosphate biosynthetic process
is_a: GO:0009197 ! pyrimidine deoxyribonucleoside diphosphate biosynthetic process
is_a: GO:0009221 ! pyrimidine deoxyribonucleotide biosynthetic process
is_a: GO:0046062 ! dCDP metabolic process
@@ -68306,6 +68801,7 @@
synonym: "dCTP biosynthesis" EXACT []
synonym: "dCTP formation" EXACT []
synonym: "dCTP synthesis" EXACT []
+is_a: GO:0009202 ! deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009212 ! pyrimidine deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009221 ! pyrimidine deoxyribonucleotide biosynthetic process
is_a: GO:0046065 ! dCTP metabolic process
@@ -68398,6 +68894,7 @@
synonym: "dCDP breakdown" EXACT []
synonym: "dCDP catabolism" EXACT []
synonym: "dCDP degradation" EXACT []
+is_a: GO:0009192 ! deoxyribonucleoside diphosphate catabolic process
is_a: GO:0009198 ! pyrimidine deoxyribonucleoside diphosphate catabolic process
is_a: GO:0009223 ! pyrimidine deoxyribonucleotide catabolic process
is_a: GO:0046062 ! dCDP metabolic process
@@ -68420,6 +68917,7 @@
synonym: "dCTP breakdown" EXACT []
synonym: "dCTP catabolism" EXACT []
synonym: "dCTP degradation" EXACT []
+is_a: GO:0009204 ! deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009213 ! pyrimidine deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009223 ! pyrimidine deoxyribonucleotide catabolic process
is_a: GO:0046065 ! dCTP metabolic process
@@ -68467,6 +68965,7 @@
synonym: "dUDP breakdown" EXACT []
synonym: "dUDP catabolism" EXACT []
synonym: "dUDP degradation" EXACT []
+is_a: GO:0009192 ! deoxyribonucleoside diphosphate catabolic process
is_a: GO:0009198 ! pyrimidine deoxyribonucleoside diphosphate catabolic process
is_a: GO:0009223 ! pyrimidine deoxyribonucleotide catabolic process
is_a: GO:0046077 ! dUDP metabolic process
@@ -70202,7 +70701,7 @@
id: GO:0006423
name: cysteinyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. A cysteinyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a cysteine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
+def: "The process of coupling L-cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. A cysteinyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a cysteine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification." [GOC:mcc, ISBN:0716730510]
is_a: GO:0006418 ! tRNA aminoacylation for protein translation
[Term]
@@ -70450,7 +70949,8 @@
synonym: "binding unfolded ER proteins" EXACT []
is_obsolete: true
consider: GO:0005783
-consider: GO:0051082
+consider: GO:0044183
+consider: GO:0140309
[Term]
id: GO:0006460
@@ -71162,7 +71662,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid." [GOC:curators]
synonym: "arginine metabolism" EXACT []
-xref: Wikipedia:Arginine
is_a: GO:1901605 ! alpha-amino acid metabolic process
[Term]
@@ -71350,7 +71849,6 @@
synonym: "glutamate metabolism" EXACT []
synonym: "glutamic acid metabolic process" EXACT []
synonym: "glutamic acid metabolism" EXACT []
-xref: Wikipedia:Glutamic_acid
is_a: GO:0043648 ! dicarboxylic acid metabolic process
is_a: GO:1901605 ! alpha-amino acid metabolic process
@@ -71579,12 +72077,15 @@
[Term]
id: GO:0006549
-name: isoleucine metabolic process
+name: obsolete isoleucine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways involving isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid." [GOC:ai]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "isoleucine metabolism" EXACT []
-is_a: GO:0009081 ! branched-chain amino acid metabolic process
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0006550
+consider: GO:1901705
[Term]
id: GO:0006550
@@ -71594,10 +72095,11 @@
synonym: "isoleucine breakdown" EXACT []
synonym: "isoleucine catabolism" EXACT []
synonym: "isoleucine degradation" EXACT []
+synonym: "L-isoleucine catabolic process via Ehrlich pathway" NARROW []
+synonym: "L-isoleucine degradation via Ehrlich pathway" NARROW []
xref: MetaCyc:ILEUDEG-PWY
xref: MetaCyc:PWY-5078
xref: MetaCyx:PWY-8184
-is_a: GO:0006549 ! isoleucine metabolic process
is_a: GO:0009083 ! branched-chain amino acid catabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
@@ -71605,6 +72107,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-5078
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30047" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
[Term]
id: GO:0006551
@@ -71625,6 +72128,8 @@
synonym: "L-leucine breakdown" EXACT []
synonym: "L-leucine catabolism" EXACT []
synonym: "L-leucine degradation" EXACT []
+synonym: "L-leucine degradation via Ehrlich pathway" NARROW []
+synonym: "L-methionine catabolic process via Ehrlich pathway" NARROW []
synonym: "leucine catabolic process" BROAD []
xref: MetaCyc:LEU-DEG2-PWY
xref: MetaCyc:PWY-5075
@@ -71642,6 +72147,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-8185
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30047" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
[Term]
id: GO:0006553
@@ -71678,7 +72184,6 @@
synonym: "methionine and threonine metabolic process" BROAD []
synonym: "methionine and threonine metabolism" BROAD []
synonym: "methionine metabolism" EXACT []
-xref: UM-BBD_pathwayID:met
is_a: GO:0000096 ! sulfur amino acid metabolic process
is_a: GO:0170033 ! L-amino acid metabolic process
is_a: GO:0170039 ! proteinogenic amino acid metabolic process
@@ -71734,8 +72239,10 @@
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of L-phenylalanine." [GOC:curators]
synonym: "L-phenylalanine breakdown" EXACT []
+synonym: "L-phenylalanine catabolic process via Ehrlich pathway" NARROW []
synonym: "L-phenylalanine catabolism" EXACT []
synonym: "L-phenylalanine degradation" EXACT []
+synonym: "L-phenylalanine degradation via Ehrlich pathway" NARROW []
synonym: "phenylalanine catabolic process" BROAD []
synonym: "phenylalanine catabolism" BROAD []
xref: MetaCyc:ANAPHENOXI-PWY
@@ -71754,6 +72261,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-8014
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
[Term]
id: GO:0006560
@@ -71852,7 +72360,8 @@
synonym: "methionine and threonine metabolism" BROAD []
synonym: "threonine metabolism" EXACT []
xref: UM-BBD_pathwayID:met
-is_a: GO:0019752 ! carboxylic acid metabolic process
+is_a: GO:0170033 ! L-amino acid metabolic process
+is_a: GO:0170039 ! proteinogenic amino acid metabolic process
[Term]
id: GO:0006567
@@ -71886,7 +72395,6 @@
def: "The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid." [ISBN:0198547684]
synonym: "tryptophan metabolic process" RELATED []
synonym: "tryptophan metabolism" RELATED []
-xref: Wikipedia:Tryptophan
is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:0042430 ! indole-containing compound metabolic process
is_a: GO:0170033 ! L-amino acid metabolic process
@@ -71897,6 +72405,8 @@
name: L-tryptophan catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of L-tryptophan." [GOC:curators]
+synonym: "L-tryptophan catabolic process via Ehrlich pathway" NARROW []
+synonym: "L-tryptophan degradation via Ehrlich pathway" NARROW []
synonym: "tryptophan breakdown" EXACT []
synonym: "tryptophan catabolic process" RELATED []
synonym: "tryptophan catabolic process, using tryptophanase" NARROW []
@@ -71937,18 +72447,19 @@
property_value: skos:narrowMatch MetaCyc:TRYPTOPHAN-DEGRADATION-1
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
[Term]
id: GO:0006570
-name: tyrosine metabolic process
+name: obsolete tyrosine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid." [GOC:curators]
+def: "OBSOLETE. The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid." [GOC:curators]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "tyrosine metabolism" EXACT []
-xref: UM-BBD_pathwayID:tyr
-xref: Wikipedia:Tyrosine
-is_a: GO:0009072 ! aromatic amino acid metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170039 ! proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0006571
+consider: GO:0006572
[Term]
id: GO:0006571
@@ -71964,7 +72475,6 @@
xref: MetaCyc:PWY-6120
xref: MetaCyc:PWY-6134
xref: MetaCyc:TYRSYN
-is_a: GO:0006570 ! tyrosine metabolic process
is_a: GO:0009073 ! aromatic amino acid family biosynthetic process
is_a: GO:1902223 ! erythrose 4-phosphate/phosphoenolpyruvate family amino acid biosynthetic process
property_value: skos:narrowMatch MetaCyc:PWY-3461
@@ -71988,7 +72498,7 @@
xref: MetaCyc:PWY3O-4108
xref: MetaCyc:TYRFUMCAT-PWY
xref: Reactome:R-HSA-8963684 "Tyrosine catabolism"
-is_a: GO:0006570 ! tyrosine metabolic process
+xref: UM-BBD_pathwayID:tyr
is_a: GO:0009074 ! aromatic amino acid family catabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
@@ -72002,12 +72512,15 @@
[Term]
id: GO:0006573
-name: valine metabolic process
+name: obsolete valine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid." [GOC:ai]
+def: "OBSOLETE. The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid." [GOC:ai]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "valine metabolism" EXACT []
-is_a: GO:0009081 ! branched-chain amino acid metabolic process
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0006574
+consider: GO:0009099
[Term]
id: GO:0006574
@@ -72018,10 +72531,10 @@
synonym: "valine breakdown" EXACT []
synonym: "valine catabolism" EXACT []
synonym: "valine degradation" EXACT []
+synonym: "valine degradation via Ehrlich pathway" NARROW []
xref: MetaCyc:PWY-5057
xref: MetaCyc:PWY-8183
xref: MetaCyc:VALDEG-PWY
-is_a: GO:0006573 ! valine metabolic process
is_a: GO:0009083 ! branched-chain amino acid catabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170040 ! proteinogenic amino acid catabolic process
@@ -72031,6 +72544,7 @@
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30047" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31221" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
[Term]
id: GO:0006575
@@ -72131,8 +72645,10 @@
synonym: "melanin anabolism from tyrosine" EXACT []
synonym: "melanin formation from tyrosine" EXACT []
synonym: "melanin synthesis from tyrosine" EXACT []
-is_a: GO:0006570 ! tyrosine metabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:0042438 ! melanin biosynthetic process
+is_a: GO:0170033 ! L-amino acid metabolic process
+is_a: GO:0170039 ! proteinogenic amino acid metabolic process
[Term]
id: GO:0006584
@@ -72151,8 +72667,10 @@
synonym: "dopamine anabolism from tyrosine" EXACT []
synonym: "dopamine formation from tyrosine" EXACT []
synonym: "dopamine synthesis from tyrosine" EXACT []
-is_a: GO:0006570 ! tyrosine metabolic process
+is_a: GO:0009072 ! aromatic amino acid metabolic process
is_a: GO:0042416 ! dopamine biosynthetic process
+is_a: GO:0170033 ! L-amino acid metabolic process
+is_a: GO:0170039 ! proteinogenic amino acid metabolic process
[Term]
id: GO:0006586
@@ -72168,17 +72686,18 @@
[Term]
id: GO:0006587
-name: serotonin biosynthetic process from L-tryptophan
+name: obsolete serotonin biosynthetic process from L-tryptophan
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation from L-tryptophan of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." [GOC:jl, ISBN:0198506732, PMID:30901029, PMID:35495641]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation from L-tryptophan of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." [GOC:jl, ISBN:0198506732, PMID:30901029, PMID:35495641]
+comment: The reason for obsoletion is that the term is too specific.
synonym: "serotonin anabolism from tryptophan" EXACT []
synonym: "serotonin formation from tryptophan" EXACT []
synonym: "serotonin synthesis from tryptophan" EXACT []
-is_a: GO:0006568 ! L-tryptophan metabolic process
-is_a: GO:0042427 ! serotonin biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31021" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31587" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31658" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0042427
[Term]
id: GO:0006588
@@ -72224,11 +72743,12 @@
[Term]
id: GO:0006592
-name: ornithine biosynthetic process
+name: L-ornithine biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis." [GOC:jl, ISBN:0192801023]
synonym: "ornithine anabolism" EXACT []
synonym: "ornithine biosynthesis" EXACT []
+synonym: "ornithine biosynthetic process" BROAD []
synonym: "ornithine formation" EXACT []
synonym: "ornithine synthesis" EXACT []
xref: MetaCyc:ARGININE-SYN4-PWY
@@ -72304,11 +72824,14 @@
name: polyamine catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of polyamines, any organic compound containing two or more amino groups." [ISBN:0198506732]
+synonym: "polyamine back-conversion" RELATED []
synonym: "polyamine breakdown" EXACT []
synonym: "polyamine catabolism" EXACT []
synonym: "polyamine degradation" EXACT []
+synonym: "polyamine interconversion" RELATED []
is_a: GO:0006595 ! polyamine metabolic process
is_a: GO:0042402 ! biogenic amine catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0006599
@@ -72363,7 +72886,6 @@
def: "The chemical reactions and pathways involving phosphocreatine, a phosphagen of creatine present in high concentration in striated muscle which is synthesized and broken down by creatine phosphokinase to buffer ATP concentration. It acts as an immediate energy reserve for muscle." [PMID:16371597]
synonym: "phosphocreatine metabolism" EXACT []
is_a: GO:0006575 ! modified amino acid metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
[Term]
@@ -72865,7 +73387,6 @@
xref: Reactome:R-HSA-1483152 "Hydrolysis of LPE"
xref: Reactome:R-HSA-1483257 "Phospholipid metabolism"
is_a: GO:0006629 ! lipid metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28908" xsd:anyURI
@@ -73802,6 +74323,7 @@
name: ommochrome biosynthetic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of ommochromes, any of a large group of natural polycyclic pigments commonly found in the Arthropoda, particularly in the ommatidia of the compound eye." [ISBN:0198506732]
+synonym: "kynurenine pathway" BROAD []
synonym: "ommochrome anabolism" EXACT []
synonym: "ommochrome biosynthesis" EXACT []
synonym: "ommochrome formation" EXACT []
@@ -73809,6 +74331,7 @@
is_a: GO:0006726 ! eye pigment biosynthetic process
is_a: GO:0008055 ! ocellus pigment biosynthetic process
is_a: GO:0046152 ! ommochrome metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31588" xsd:anyURI
[Term]
id: GO:0006728
@@ -74147,7 +74670,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving any phosphorylated nucleoside." [GOC:mah]
synonym: "nucleoside phosphate metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:0055086 ! nucleobase-containing small molecule metabolic process
@@ -74421,16 +74943,19 @@
[Term]
id: GO:0006782
-name: protoporphyrinogen IX biosynthetic process
+name: obsolete protoporphyrinogen IX biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX." [GOC:curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX." [GOC:curators]
+comment: This term was obsoleted because protoporphyrinogen IX is an intermediate in heme/chlorophyll/uroporphyrinogen biosynthesis.
synonym: "protoporphyrinogen IX anabolism" EXACT []
synonym: "protoporphyrinogen IX biosynthesis" EXACT []
synonym: "protoporphyrinogen IX formation" EXACT []
synonym: "protoporphyrinogen IX synthesis" EXACT []
-is_a: GO:0006779 ! porphyrin-containing compound biosynthetic process
-is_a: GO:0046501 ! protoporphyrinogen IX metabolic process
-relationship: part_of GO:0006783 ! heme biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31788" xsd:anyURI
+is_obsolete: true
+consider: GO:0006780
+consider: GO:0006783
+consider: GO:0033305
[Term]
id: GO:0006783
@@ -74599,7 +75124,7 @@
def: "The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid." [GOC:ai]
synonym: "phosphate metabolic process" RELATED []
synonym: "phosphate metabolism" EXACT []
-is_a: GO:0006793 ! phosphorus metabolic process
+is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0006797
@@ -74998,11 +75523,12 @@
[Term]
id: GO:0006837
-name: serotonin transport
+name: obsolete serotonin transport
namespace: biological_process
-def: "The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems." [GOC:ai]
-is_a: GO:0015844 ! monoamine transport
-is_a: GO:0015850 ! organic hydroxy compound transport
+def: "OBSOLETE. The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems." [GOC:ai]
+comment: The reason for obsoletion is that this is an unnecessary grouping term and annotations should be made to more mechanism/location specific terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0006838
@@ -75283,7 +75809,6 @@
alt_id: GO:0015815
def: "The directed movement of glutamine, 2-amino-4-carbamoylbutanoic 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: "glutamine transport" BROAD []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015804 ! neutral amino acid transport
is_a: GO:0015807 ! L-amino acid transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
@@ -76807,7 +77332,8 @@
namespace: biological_process
def: "Completion of folding of alpha- and beta-tubulin; takes place subsequent to chaperonin-mediated partial folding; mediated by a complex of folding cofactors." [PMID:10542094]
xref: Reactome:R-HSA-389977 "Post-chaperonin tubulin folding pathway"
-is_a: GO:0006457 ! protein folding
+is_a: GO:0007021 ! tubulin complex assembly
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31829" xsd:anyURI
[Term]
id: GO:0007026
@@ -79194,7 +79720,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "MAPKKK cascade (mating sensu Saccharomyces)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0007245
@@ -79204,7 +79730,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "activation of MAPKKK (mating sensu Saccharomyces)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0007246
@@ -79214,7 +79740,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "activation of MAPKK (mating sensu Saccharomyces)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0007247
@@ -79224,7 +79750,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "activation of MAPK (mating sensu Saccharomyces)" EXACT []
is_obsolete: true
-consider: GO:0000750
+consider: GO:0071507
[Term]
id: GO:0007248
@@ -79234,7 +79760,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "nuclear translocation of MAPK (mating sensu Saccharomyces)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0007249
@@ -79402,14 +79928,13 @@
[Term]
id: GO:0007263
-name: nitric oxide mediated signal transduction
+name: obsolete nitric oxide mediated signal transduction
namespace: biological_process
-def: "An intracellular signaling cassette that starts with production of nitric oxide, detection by receptors/sensors for nitric oxide (such as soluble guanylyl cyclase/sGC) and ends with the activation of downstream effectors that further transmit the signal within the cell. Nitric oxide transmits its downstream effects through either cyclic GMP (cGMP)-dependent or independent mechanisms." [GOC:jl, PMID:21549190]
-synonym: "nitric oxide signaling" EXACT [GOC:bf]
-synonym: "nitric oxide-mediated signal transduction" EXACT []
-synonym: "NO mediated signal transduction" EXACT []
-synonym: "NO-mediated signal transduction" EXACT []
-is_a: GO:0141124 ! intracellular signaling cassette
+def: "OBSOLETE. An intracellular signaling cassette that starts with production of nitric oxide, detection by receptors/sensors for nitric oxide (such as soluble guanylyl cyclase/sGC) and ends with the activation of downstream effectors that further transmit the signal within the cell. Nitric oxide transmits its downstream effects through either cyclic GMP (cGMP)-dependent or independent mechanisms." [GOC:jl, PMID:21549190]
+comment: The reason for obsoletion is that this term has been inconsistently used and NO signaling proceeds via cGMP, so the more specific replacement term is preferred.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26613" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0038060
[Term]
id: GO:0007264
@@ -83499,7 +84024,6 @@
xref: Reactome:R-HSA-9636560 "Eis acetylates DUSP16"
xref: Reactome:R-HSA-9913373 "AAC(6)-Ib acetylates ciprofloxacin"
is_a: GO:0016407 ! acetyltransferase activity
-is_a: GO:0016410 ! N-acyltransferase activity
[Term]
id: GO:0008081
@@ -83624,14 +84148,15 @@
[Term]
id: GO:0008093
-name: cytoskeletal anchor activity
+name: cytoskeletal adaptor activity
namespace: molecular_function
def: "The binding activity of a protein that brings together a cytoskeletal protein (either a microtubule or actin filament, spindle pole body, or protein directly bound to them) and one or more other molecules, permitting them to function in a coordinated way." [GOC:mtg_MIT_16mar07, PMID:30323238]
-synonym: "cytoskeletal adaptor activity" EXACT []
+synonym: "cytoskeletal anchor activity" NARROW []
is_a: GO:0030674 ! protein-macromolecule adaptor activity
relationship: has_part GO:0008092 ! cytoskeletal protein binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17668" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19119" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19185" xsd:anyURI
[Term]
id: GO:0008094
@@ -83749,10 +84274,46 @@
xref: Reactome:R-HSA-9027600 "Dehydrogenase dehydrogenates 17-HDPAn-3 to 17-oxo-DPAn-3"
xref: Reactome:R-HSA-9937340 "DHRSX reduces dolichal to dolichol"
xref: RHEA:15937
+xref: RHEA:20193
+xref: RHEA:38111
+xref: RHEA:54916
+xref: RHEA:54920
+xref: RHEA:58364
+xref: RHEA:58420
+xref: RHEA:58668
+xref: RHEA:59452
+xref: RHEA:59928
+xref: RHEA:63496
+xref: RHEA:64708
+xref: RHEA:64712
+xref: RHEA:66448
+xref: RHEA:76611
+xref: RHEA:80723
+xref: RHEA:84055
+xref: RHEA:84059
+xref: RHEA:84063
is_a: GO:0018455 ! alcohol dehydrogenase [NAD(P)+] activity
property_value: skos:exactMatch EC:1.1.1.2
property_value: skos:narrowMatch MetaCyc:ALCOHOL-DEHYDROGENASE-NADPORNOP+-RXN
property_value: skos:narrowMatch RHEA:15937
+property_value: skos:narrowMatch RHEA:20193
+property_value: skos:narrowMatch RHEA:38111
+property_value: skos:narrowMatch RHEA:54916
+property_value: skos:narrowMatch RHEA:54920
+property_value: skos:narrowMatch RHEA:58364
+property_value: skos:narrowMatch RHEA:58420
+property_value: skos:narrowMatch RHEA:58668
+property_value: skos:narrowMatch RHEA:59452
+property_value: skos:narrowMatch RHEA:59928
+property_value: skos:narrowMatch RHEA:63496
+property_value: skos:narrowMatch RHEA:64708
+property_value: skos:narrowMatch RHEA:64712
+property_value: skos:narrowMatch RHEA:66448
+property_value: skos:narrowMatch RHEA:76611
+property_value: skos:narrowMatch RHEA:80723
+property_value: skos:narrowMatch RHEA:84055
+property_value: skos:narrowMatch RHEA:84059
+property_value: skos:narrowMatch RHEA:84063
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28183" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28532" xsd:anyURI
@@ -83790,11 +84351,13 @@
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:32175
xref: RHEA:48792
xref: RHEA:50664
is_a: GO:0031127 ! alpha-(1,2)-fucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.69
property_value: skos:exactMatch RHEA:50664
+property_value: skos:narrowMatch RHEA:32175
property_value: skos:narrowMatch RHEA:48792
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -84021,15 +84584,19 @@
synonym: "neolactotetraosylceramide alpha-2,3-sialyltransferase activity" NARROW [EC:2.4.3.6]
xref: EC:2.4.3.6
xref: MetaCyc:2.4.99.6-RXN
+xref: RHEA:18913
xref: RHEA:52316
xref: RHEA:56264
xref: RHEA:65432
+xref: RHEA:80751
xref: RHEA:80755
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.6
property_value: skos:exactMatch RHEA:52316
+property_value: skos:narrowMatch RHEA:18913
property_value: skos:narrowMatch RHEA:56264
property_value: skos:narrowMatch RHEA:65432
+property_value: skos:narrowMatch RHEA:80751
property_value: skos:narrowMatch RHEA:80755
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28444" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -84110,12 +84677,13 @@
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 monoatomic ion transmembrane transporter activity
-relationship: has_part GO:0016679 ! oxidoreductase activity, acting on diphenols and related substances as donors
property_value: skos:exactMatch EC:7.1.1.8
property_value: skos:exactMatch RHEA:11484
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20616" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21275" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25935" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
@@ -84405,17 +84973,18 @@
xref: MetaCyc:NADH-DEHYDROG-A-RXN
xref: Reactome:R-HSA-163217 "Complex I oxidises NADH to NAD+, reduces CoQ to CoQH2"
xref: RHEA:29091
+is_a: GO:0003954 ! NADH dehydrogenase activity
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:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
is_a: GO:0022853 ! active monoatomic ion transmembrane transporter activity
-relationship: has_part GO:0003954 ! NADH dehydrogenase activity
-relationship: has_part GO:0016655 ! oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:7.1.1.2
property_value: skos:exactMatch RHEA:29091
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20616" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21275" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25784" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25935" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27641" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
@@ -84599,7 +85168,7 @@
id: GO:0008153
name: 4-aminobenzoate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of 4-aminobenzoate, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins." [ISBN:0198506732, MetaCyc:PWY-6543, PMID:11377864, PMID:11960743]
+def: "The chemical reactions and pathways resulting in the formation of 4-aminobenzoate, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins." [MetaCyc:PWY-6543, PMID:11377864, PMID:11960743]
synonym: "4-aminobenzoic acid biosynthesis" EXACT []
synonym: "4-aminobenzoic acid biosynthetic process" EXACT []
synonym: "p-aminobenzoic acid biosynthesis" EXACT []
@@ -84618,7 +85187,7 @@
xref: MetaCyc:PWY-8281
is_a: GO:0008652 ! amino acid biosynthetic process
is_a: GO:0009073 ! aromatic amino acid family biosynthetic process
-is_a: GO:0046482 ! para-aminobenzoic acid metabolic process
+is_a: GO:0042537 ! benzene-containing compound metabolic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
property_value: skos:narrowMatch MetaCyc:PWY-6543
property_value: skos:narrowMatch MetaCyc:PWY-8276
@@ -84894,6 +85463,8 @@
xref: Reactome:R-HSA-70994 "SDH complex dehydrogenates succinate"
xref: RHEA:13713
xref: RHEA:27834
+xref: RHEA:29215
+xref: RHEA:33863
xref: RHEA:40523
xref: RHEA:75711
is_a: GO:0000104 ! succinate dehydrogenase activity
@@ -84902,6 +85473,8 @@
property_value: skos:exactMatch RHEA:40523
property_value: skos:narrowMatch RHEA:13713
property_value: skos:narrowMatch RHEA:27834
+property_value: skos:narrowMatch RHEA:29215
+property_value: skos:narrowMatch RHEA:33863
property_value: skos:narrowMatch RHEA:75711
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26087" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27915" xsd:anyURI
@@ -87056,9 +87629,10 @@
[Term]
id: GO:0008374
-name: O-acyltransferase activity
+name: obsolete O-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of an acyl group to an oxygen atom on the acceptor molecule." [GOC:ai]
+def: "OBSOLETE. Catalysis of the transfer of an acyl group to an oxygen atom on the acceptor molecule." [GOC:ai]
+comment: This term was obsoleted because it represents an unnecessary grouping class that lacks an EC cross-reference and leads to misclassification of children.
xref: Reactome:R-HSA-1482775 "MLCL is acylated to CL by HADH (IM)"
xref: Reactome:R-HSA-1482781 "MLCL and PC are converted to CL and 1-acyl LPC by TAZ (IM) (Reversible)"
xref: Reactome:R-HSA-1482850 "MLCL and PE are converted to CL and 1-acyl LPE by TAZ (IM) (Reversible)"
@@ -87070,7 +87644,9 @@
xref: Reactome:R-HSA-422104 "Ghrelin O-acyltransferase octanoylates Proghrelin"
xref: Reactome:R-HSA-5358343 "HHAT palmitoylates Hh N-terminal fragment"
xref: Reactome:R-HSA-5483229 "HHAT G287V doesn't palmitoylate Hh-Np"
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31814" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0016747
[Term]
id: GO:0008375
@@ -87556,12 +88132,15 @@
[Term]
id: GO:0008411
-name: 4-hydroxybutyrate CoA-transferase activity
+name: obsolete 4-hydroxybutyrate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of a coenzyme A (CoA) group to 4-hydroxybutyrate." [GOC:jl, PMID:25452282]
+def: "OBSOLETE. Catalysis of the transfer of a coenzyme A (CoA) group to 4-hydroxybutyrate." [GOC:jl, PMID:25452282]
+comment: This term was obsoleted because it represents the same activity as 4-hydroxybutanoyl-CoA dehydratase activity ; GO:0043721. The term was incorrectly defined; the paper cited describes dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA ((2E)-butenoyl-CoA).
xref: MetaCyc:RXN-8889
-is_a: GO:0008410 ! CoA-transferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28340" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31862" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0043721
[Term]
id: GO:0008412
@@ -89012,7 +89591,6 @@
xref: Reactome:R-HSA-380620 "Reuptake of serotonin from the synapse"
xref: Reactome:R-HSA-5660706 "Defective SLC6A3 does not cotransport DA, Na+ from extracellular region to cytosol"
is_a: GO:0022804 ! active transmembrane transporter activity
-relationship: part_of GO:0015844 ! monoamine transport
[Term]
id: GO:0008506
@@ -89049,8 +89627,9 @@
xref: Reactome:R-HSA-194121 "SLC10A1 co-transport bile salts and Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-194187 "SLC10A2 transports bile salts and acids and Na+ from extracellular region to cytosol"
xref: Reactome:R-HSA-433089 "SOAT can transport taurolithocholate-3-sulphate"
+is_a: GO:0005343 ! organic acid:sodium symporter activity
is_a: GO:0015125 ! bile acid transmembrane transporter activity
-is_a: GO:0140161 ! monocarboxylate:sodium symporter activity
+is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
[Term]
id: GO:0008509
@@ -89169,7 +89748,7 @@
xref: Reactome:R-HSA-200652 "SLC19A1 transports 5-methyl-THF from extracellular region to cytosol"
xref: Reactome:R-HSA-200680 "SLC25A32 transports THF from cytosol to mitochondrial matrix"
xref: Reactome:R-HSA-200720 "SLC25A32 transports THF from mitochondrial matrix to cytosol"
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
is_a: GO:0090482 ! vitamin transmembrane transporter activity
relationship: part_of GO:0015884 ! folic acid transport
@@ -90258,11 +90837,11 @@
synonym: "protein hypusination" EXACT []
xref: MetaCyc:PWY-5905
xref: Reactome:R-HSA-204626 "Hypusine synthesis from eIF5A-lysine"
-is_a: GO:0018205 ! peptidyl-lysine modification
+is_a: GO:0009058 ! biosynthetic process
is_a: GO:0051604 ! protein maturation
-is_a: GO:1901607 ! alpha-amino acid biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31510" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31884" xsd:anyURI
[Term]
id: GO:0008613
@@ -90558,6 +91137,7 @@
synonym: "rRNA (uridine-2'-O-)-methyltransferase activity" EXACT []
xref: Reactome:R-HSA-6793127 "MRM2 (FTSJ2) methylates uridine-1369 of 16S rRNA yielding 2'-O-methyluridine"
xref: RHEA:42720
+xref: RHEA:42728
xref: RHEA:43092
xref: RHEA:47760
xref: RHEA:47764
@@ -90566,6 +91146,7 @@
is_a: GO:0062105 ! RNA 2'-O-methyltransferase activity
property_value: skos:exactMatch RHEA:54152
property_value: skos:narrowMatch RHEA:42720
+property_value: skos:narrowMatch RHEA:42728
property_value: skos:narrowMatch RHEA:43092
property_value: skos:narrowMatch RHEA:47760
property_value: skos:narrowMatch RHEA:47764
@@ -90860,12 +91441,16 @@
xref: MetaCyc:RXN-20995
xref: RHEA:12136
xref: RHEA:45232
+xref: RHEA:53296
+xref: RHEA:53708
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.3.1.34
property_value: skos:narrowMatch MetaCyc:RXN-20994
property_value: skos:narrowMatch MetaCyc:RXN-20995
property_value: skos:narrowMatch RHEA:12136
property_value: skos:narrowMatch RHEA:45232
+property_value: skos:narrowMatch RHEA:53296
+property_value: skos:narrowMatch RHEA:53708
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
[Term]
@@ -91330,7 +91915,7 @@
id: GO:0008695
name: 3-phenylpropionate dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-phenylpropionate + NADH + H+ + O2 = NAD+ + cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol." [UM-BBD_enzymeID:e0307]
+def: "Catalysis of the reaction: 3-phenylpropanoate + NADH + O2 + H+ = 3-(cis-5,6-dihydroxycyclohexa-1,3-dien-1-yl)propanoate + NAD+." [RHEA:20357]
synonym: "3-phenylpropanoate dioxygenase activity" RELATED [EC:1.14.12.19]
synonym: "3-phenylpropanoate,NADH:oxygen oxidoreductase (2,3-hydroxylating) activity" RELATED [EC:1.14.12.19]
synonym: "Hca dioxygenase activity" RELATED [EC:1.14.12.19]
@@ -91716,6 +92301,7 @@
xref: EC:1.4.5.1
xref: MetaCyc:RXN-11193
xref: RHEA:18125
+xref: RHEA:30091
xref: RHEA:37219
xref: RHEA:37255
xref: RHEA:43572
@@ -91725,6 +92311,7 @@
property_value: skos:exactMatch RHEA:18125
property_value: skos:narrowMatch EC:1.4.5.1
property_value: skos:narrowMatch MetaCyc:RXN-11193
+property_value: skos:narrowMatch RHEA:30091
property_value: skos:narrowMatch RHEA:37219
property_value: skos:narrowMatch RHEA:37255
property_value: skos:narrowMatch RHEA:43572
@@ -92247,6 +92834,7 @@
xref: RHEA:61980
xref: RHEA:63492
xref: RHEA:83239
+xref: RHEA:83247
is_a: GO:0003955 ! NAD(P)H dehydrogenase (quinone) activity
is_a: GO:0003959 ! NADPH dehydrogenase activity
property_value: skos:exactMatch EC:1.6.5.10
@@ -92257,6 +92845,7 @@
property_value: skos:narrowMatch RHEA:61980
property_value: skos:narrowMatch RHEA:63492
property_value: skos:narrowMatch RHEA:83239
+property_value: skos:narrowMatch RHEA:83247
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
[Term]
@@ -92635,7 +93224,7 @@
id: GO:0008775
name: acetate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acyl-CoA + acetate = a fatty acid anion + acetyl-CoA." [EC:2.8.3.8]
+def: "Catalysis of the reaction: an acyl-CoA + acetate = a carboxylate + acetyl-CoA." [RHEA:13381]
synonym: "acetate coenzyme A-transferase activity" RELATED [EC:2.8.3.8]
synonym: "acetyl-CoA:acetoacetate CoA transferase activity" RELATED [EC:2.8.3.8]
synonym: "acyl-CoA:acetate CoA-transferase activity" RELATED [EC:2.8.3.8]
@@ -92702,7 +93291,7 @@
xref: EC:2.3.1.40
xref: MetaCyc:ACYLGPEACYLTRANS-RXN
xref: RHEA:10304
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.40
property_value: skos:exactMatch RHEA:10304
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -92722,7 +93311,7 @@
xref: MetaCyc:RXN-22480
xref: RHEA:13925
xref: RHEA:67812
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.129
property_value: skos:exactMatch RHEA:67812
property_value: skos:narrowMatch RHEA:13925
@@ -93343,7 +93932,7 @@
id: GO:0008814
name: citrate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + citrate = acetate + (3S)-citryl-CoA." [EC:2.8.3.10]
+def: "Catalysis of the reaction: acetyl-CoA + citrate = acetate + (3S)-citryl-CoA." [RHEA:19405]
synonym: "acetyl-CoA:citrate CoA-transferase activity" RELATED [EC:2.8.3.10]
xref: EC:2.8.3.10
xref: MetaCyc:CITTRANS-RXN
@@ -95186,12 +95775,14 @@
xref: MetaCyc:ACYLACPSYNTH-RXN
xref: RHEA:10696
xref: RHEA:45588
+xref: RHEA:59164
xref: RHEA:63628
xref: RHEA:64888
is_a: GO:0015645 ! fatty acid ligase activity
property_value: skos:exactMatch EC:6.2.1.20
property_value: skos:exactMatch RHEA:45588
property_value: skos:narrowMatch RHEA:10696
+property_value: skos:narrowMatch RHEA:59164
property_value: skos:narrowMatch RHEA:63628
property_value: skos:narrowMatch RHEA:64888
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26445" xsd:anyURI
@@ -95226,6 +95817,7 @@
xref: MetaCyc:MALATE-DEHYDROGENASE-ACCEPTOR-RXN
xref: MetaCyc:RXNI-3
xref: RHEA:29083
+xref: RHEA:29087
xref: RHEA:30095
xref: RHEA:46012
is_a: GO:0016615 ! malate dehydrogenase activity
@@ -95235,6 +95827,7 @@
property_value: skos:exactMatch RHEA:46012
property_value: skos:narrowMatch MetaCyc:RXNI-3
property_value: skos:narrowMatch RHEA:29083
+property_value: skos:narrowMatch RHEA:29087
property_value: skos:narrowMatch RHEA:30095
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -95511,7 +96104,7 @@
[Term]
id: GO:0008941
-name: nitric oxide dioxygenase NAD(P)H activity
+name: nitric oxide dioxygenase [NAD(P)H] activity
namespace: molecular_function
def: "Catalysis of the reaction: 2 NO + 2 O2 + NAD(P)H + H+ = 2 nitrate + NAD(P)+." [EC:1.14.12.17]
comment: Note that this activity is similar to nitric oxide dioxygenase activity, heme protein ; GO:0141118, but GO:0141118 uses a heme protein as the electron donor.
@@ -95815,10 +96408,12 @@
xref: Reactome:R-HSA-1483197 "PTPMT1 dephosphorylates PGP to PG"
xref: RHEA:16725
xref: RHEA:33752
+xref: RHEA:42305
is_a: GO:0016791 ! phosphatase activity
property_value: skos:exactMatch EC:3.1.3.27
property_value: skos:exactMatch RHEA:16725
property_value: skos:narrowMatch RHEA:33752
+property_value: skos:narrowMatch RHEA:42305
[Term]
id: GO:0008963
@@ -95958,22 +96553,68 @@
xref: Reactome:R-HSA-8869425 "PLA1A hydrolyses PS to 2-acyl LPS"
xref: RHEA:18689
xref: RHEA:35263
+xref: RHEA:38783
+xref: RHEA:38787
+xref: RHEA:40487
+xref: RHEA:41167
+xref: RHEA:41171
+xref: RHEA:41207
xref: RHEA:42212
+xref: RHEA:43968
xref: RHEA:44408
xref: RHEA:44648
+xref: RHEA:53496
+xref: RHEA:56448
xref: RHEA:62032
+xref: RHEA:62044
+xref: RHEA:62464
+xref: RHEA:62480
+xref: RHEA:62484
+xref: RHEA:62488
+xref: RHEA:66708
xref: RHEA:67424
xref: RHEA:67428
+xref: RHEA:73971
+xref: RHEA:73975
+xref: RHEA:74103
+xref: RHEA:74247
+xref: RHEA:74251
+xref: RHEA:76971
+xref: RHEA:76979
+xref: RHEA:76983
is_a: GO:0140322 ! A1-type glycerophospholipase activity
property_value: skos:exactMatch EC:3.1.1.32
property_value: skos:exactMatch RHEA:67424
property_value: skos:narrowMatch RHEA:18689
property_value: skos:narrowMatch RHEA:35263
+property_value: skos:narrowMatch RHEA:38783
+property_value: skos:narrowMatch RHEA:38787
+property_value: skos:narrowMatch RHEA:40487
+property_value: skos:narrowMatch RHEA:41167
+property_value: skos:narrowMatch RHEA:41171
+property_value: skos:narrowMatch RHEA:41207
property_value: skos:narrowMatch RHEA:42212
+property_value: skos:narrowMatch RHEA:43968
property_value: skos:narrowMatch RHEA:44408
property_value: skos:narrowMatch RHEA:44648
+property_value: skos:narrowMatch RHEA:53496
+property_value: skos:narrowMatch RHEA:56448
property_value: skos:narrowMatch RHEA:62032
+property_value: skos:narrowMatch RHEA:62044
+property_value: skos:narrowMatch RHEA:62464
+property_value: skos:narrowMatch RHEA:62480
+property_value: skos:narrowMatch RHEA:62484
+property_value: skos:narrowMatch RHEA:62488
+property_value: skos:narrowMatch RHEA:66708
property_value: skos:narrowMatch RHEA:67428
+property_value: skos:narrowMatch RHEA:73971
+property_value: skos:narrowMatch RHEA:73975
+property_value: skos:narrowMatch RHEA:74103
+property_value: skos:narrowMatch RHEA:74247
+property_value: skos:narrowMatch RHEA:74251
+property_value: skos:narrowMatch RHEA:76971
+property_value: skos:narrowMatch RHEA:76979
+property_value: skos:narrowMatch RHEA:76983
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
[Term]
@@ -97770,6 +98411,8 @@
name: L-methionine catabolic process
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of L-methionine." [GOC:curators]
+synonym: "L-methionine catabolic process via Ehrlich pathway" NARROW []
+synonym: "L-methionine degradation via Ehrlich pathway" NARROW []
synonym: "methionine breakdown" EXACT []
synonym: "methionine catabolism" EXACT []
synonym: "methionine degradation" EXACT []
@@ -97786,6 +98429,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-701
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31405" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31839" xsd:anyURI
[Term]
id: GO:0009088
@@ -97955,7 +98599,6 @@
synonym: "valine formation" EXACT []
synonym: "valine synthesis" EXACT []
xref: MetaCyc:VALSYN-PWY
-is_a: GO:0006573 ! valine metabolic process
is_a: GO:0009079 ! pyruvate family amino acid biosynthetic process
is_a: GO:0009082 ! branched-chain amino acid biosynthetic process
relationship: has_part GO:0003984 ! acetolactate synthase activity
@@ -98863,7 +99506,6 @@
synonym: "purine deoxyribonucleoside diphosphate synthesis" EXACT []
is_a: GO:0009136 ! purine nucleoside diphosphate biosynthetic process
is_a: GO:0009182 ! purine deoxyribonucleoside diphosphate metabolic process
-is_a: GO:0009189 ! deoxyribonucleoside diphosphate biosynthetic process
[Term]
id: GO:0009184
@@ -98875,7 +99517,6 @@
synonym: "purine deoxyribonucleoside diphosphate degradation" EXACT []
is_a: GO:0009137 ! purine nucleoside diphosphate catabolic process
is_a: GO:0009182 ! purine deoxyribonucleoside diphosphate metabolic process
-is_a: GO:0009192 ! deoxyribonucleoside diphosphate catabolic process
[Term]
id: GO:0009185
@@ -98924,7 +99565,8 @@
synonym: "deoxyribonucleoside diphosphate biosynthesis" EXACT []
synonym: "deoxyribonucleoside diphosphate formation" EXACT []
synonym: "deoxyribonucleoside diphosphate synthesis" EXACT []
-is_a: GO:0009133 ! nucleoside diphosphate biosynthetic process
+is_a: GO:0006793 ! phosphorus metabolic process
+is_a: GO:0009058 ! biosynthetic process
[Term]
id: GO:0009190
@@ -98957,7 +99599,8 @@
synonym: "deoxyribonucleoside diphosphate breakdown" EXACT []
synonym: "deoxyribonucleoside diphosphate catabolism" EXACT []
synonym: "deoxyribonucleoside diphosphate degradation" EXACT []
-is_a: GO:0009134 ! nucleoside diphosphate catabolic process
+is_a: GO:0006793 ! phosphorus metabolic process
+is_a: GO:0009056 ! catabolic process
[Term]
id: GO:0009193
@@ -99011,7 +99654,6 @@
synonym: "pyrimidine deoxyribonucleoside diphosphate formation" EXACT []
synonym: "pyrimidine deoxyribonucleoside diphosphate synthesis" EXACT []
is_a: GO:0009139 ! pyrimidine nucleoside diphosphate biosynthetic process
-is_a: GO:0009189 ! deoxyribonucleoside diphosphate biosynthetic process
is_a: GO:0009196 ! pyrimidine deoxyribonucleoside diphosphate metabolic process
[Term]
@@ -99023,7 +99665,6 @@
synonym: "pyrimidine deoxyribonucleoside diphosphate catabolism" EXACT []
synonym: "pyrimidine deoxyribonucleoside diphosphate degradation" EXACT []
is_a: GO:0009140 ! pyrimidine nucleoside diphosphate catabolic process
-is_a: GO:0009192 ! deoxyribonucleoside diphosphate catabolic process
is_a: GO:0009196 ! pyrimidine deoxyribonucleoside diphosphate metabolic process
[Term]
@@ -99042,7 +99683,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "deoxyribonucleoside triphosphate metabolism" EXACT []
-is_a: GO:0009141 ! nucleoside triphosphate metabolic process
+is_a: GO:0009394 ! 2'-deoxyribonucleotide metabolic process
[Term]
id: GO:0009201
@@ -99064,8 +99705,8 @@
synonym: "deoxyribonucleoside triphosphate biosynthesis" EXACT []
synonym: "deoxyribonucleoside triphosphate formation" EXACT []
synonym: "deoxyribonucleoside triphosphate synthesis" EXACT []
-is_a: GO:0009142 ! nucleoside triphosphate biosynthetic process
is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
+is_a: GO:0009265 ! 2'-deoxyribonucleotide biosynthetic process
[Term]
id: GO:0009203
@@ -99085,8 +99726,9 @@
synonym: "deoxyribonucleoside triphosphate breakdown" EXACT []
synonym: "deoxyribonucleoside triphosphate catabolism" EXACT []
synonym: "deoxyribonucleoside triphosphate degradation" EXACT []
-is_a: GO:0009143 ! nucleoside triphosphate catabolic process
+is_a: GO:0009166 ! nucleotide catabolic process
is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
+is_a: GO:0046386 ! deoxyribose phosphate catabolic process
[Term]
id: GO:0009205
@@ -99203,7 +99845,6 @@
def: "The chemical reactions and pathways involving purine deoxyribonucleoside triphosphate, a compound consisting of a purine base linked to a deoxyribose sugar esterified with triphosphate on the sugar." [GOC:curators, ISBN:0198506732]
synonym: "purine deoxyribonucleoside triphosphate metabolism" EXACT []
is_a: GO:0009144 ! purine nucleoside triphosphate metabolic process
-is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
[Term]
id: GO:0009216
@@ -99215,7 +99856,6 @@
synonym: "purine deoxyribonucleoside triphosphate formation" EXACT []
synonym: "purine deoxyribonucleoside triphosphate synthesis" EXACT []
is_a: GO:0009145 ! purine nucleoside triphosphate biosynthetic process
-is_a: GO:0009202 ! deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009215 ! purine deoxyribonucleoside triphosphate metabolic process
[Term]
@@ -99227,7 +99867,6 @@
synonym: "purine deoxyribonucleoside triphosphate catabolism" EXACT []
synonym: "purine deoxyribonucleoside triphosphate degradation" EXACT []
is_a: GO:0009146 ! purine nucleoside triphosphate catabolic process
-is_a: GO:0009204 ! deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009215 ! purine deoxyribonucleoside triphosphate metabolic process
[Term]
@@ -101651,8 +102290,15 @@
synonym: "putrescine biosynthesis" EXACT []
synonym: "putrescine formation" EXACT []
synonym: "putrescine synthesis" EXACT []
+xref: MetaCyc:PWY-40
+xref: MetaCyc:PWY-43
+xref: MetaCyc:PWY-46
is_a: GO:0006596 ! polyamine biosynthetic process
is_a: GO:0009445 ! putrescine metabolic process
+property_value: skos:narrowMatch MetaCyc:PWY-40
+property_value: skos:narrowMatch MetaCyc:PWY-43
+property_value: skos:narrowMatch MetaCyc:PWY-46
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0009447
@@ -101662,15 +102308,26 @@
synonym: "putrescine breakdown" EXACT []
synonym: "putrescine catabolism" EXACT []
synonym: "putrescine degradation" EXACT []
+xref: MetaCyc:PUTDEG-PWY
+xref: MetaCyc:PWY-0
+xref: MetaCyc:PWY-2
+xref: MetaCyc:PWY-3
+xref: MetaCyc:PWY0-1221
is_a: GO:0006598 ! polyamine catabolic process
is_a: GO:0009445 ! putrescine metabolic process
+property_value: skos:narrowMatch MetaCyc:PUTDEG-PWY
+property_value: skos:narrowMatch MetaCyc:PWY-0
+property_value: skos:narrowMatch MetaCyc:PWY-2
+property_value: skos:narrowMatch MetaCyc:PWY-3
+property_value: skos:narrowMatch MetaCyc:PWY0-1221
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0009448
-name: GABA metabolic process
+name: obsolete GABA metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." [ISBN:0198506732]
-comment: See also the biological process term 'neurotransmitter metabolic process ; GO:0042133'.
+def: "OBSOLETE. The chemical reactions and pathways involving gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." [ISBN:0198506732]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "4-aminobutanoate metabolic process" EXACT []
synonym: "4-aminobutanoate metabolism" EXACT []
synonym: "4-aminobutyrate metabolic process" EXACT []
@@ -101678,9 +102335,11 @@
synonym: "GABA metabolism" EXACT []
synonym: "gamma-aminobutyric acid metabolic process" EXACT []
synonym: "gamma-aminobutyric acid metabolism" EXACT []
-is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31732" xsd:anyURI
+is_obsolete: true
+consider: GO:0009449
+consider: GO:0009450
[Term]
id: GO:0009449
@@ -101700,7 +102359,6 @@
synonym: "gamma-aminobutyric acid synthesis" EXACT []
xref: Reactome:R-HSA-888568 "GABA synthesis"
is_a: GO:0008652 ! amino acid biosynthetic process
-is_a: GO:0009448 ! GABA metabolic process
is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31732" xsd:anyURI
@@ -101726,7 +102384,6 @@
xref: MetaCyc:PWY-6537
xref: Reactome:R-HSA-916853 "Degradation of GABA"
is_a: GO:0009063 ! amino acid catabolic process
-is_a: GO:0009448 ! GABA metabolic process
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:PWY-5022
property_value: skos:narrowMatch MetaCyc:PWY-6473
@@ -109705,19 +110362,19 @@
id: GO:0010242
name: oxygen evolving activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2 H2O = O2 + 4 H+ + 4 e-. The evolution of oxygen from oxidizing water is carried out by the oxygen evolving complex in photosystem II of plants. P680+, the photochemically oxidized reaction-center chlorophyll of PSII, is a strong biological oxidant. The reduction potential of P680+ is more positive than that of water, and thus it can oxidize water to give O2 and H+ ions. The oxygen escapes as a gas while the H+ ions remain in solution inside the thylakoid vesicle." [GOC:kd, GOC:syr, PMID:17091926, PMID:7948862]
+def: "Catalysis of the reaction: 2 a plastoquinone + 4 hnu + 2 H2O = 2 a plastoquinol + O2. The evolution of oxygen from oxidizing water is carried out by the oxygen evolving complex in photosystem II of plants." [PMID:17091926, PMID:7948862, RHEA:36359]
synonym: "photosynthetic water oxidation" EXACT []
xref: EC:1.10.3.9
xref: MetaCyc:PSII-RXN
xref: RHEA:30247
xref: RHEA:36359
-is_a: GO:0016491 ! oxidoreductase activity
+is_a: GO:0016682 ! oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.10.3.9
property_value: skos:exactMatch MetaCyc:PSII-RXN
property_value: skos:exactMatch RHEA:36359
property_value: skos:narrowMatch RHEA:30247
-property_value: skos:relatedMatch MetaCyc:RXN0-5265
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31592" xsd:anyURI
[Term]
id: GO:0010243
@@ -110580,10 +111237,12 @@
xref: EC:2.6.1.88
xref: MetaCyc:R15-RXN
xref: RHEA:31763
+xref: RHEA:47084
xref: RHEA:47800
is_a: GO:0140385 ! amino acid transaminase activity
property_value: skos:exactMatch EC:2.6.1.88
property_value: skos:exactMatch RHEA:31763
+property_value: skos:narrowMatch RHEA:47084
property_value: skos:narrowMatch RHEA:47800
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -112356,20 +113015,23 @@
[Term]
id: GO:0010514
-name: induction of conjugation with cellular fusion
+name: obsolete induction of conjugation with cellular fusion
namespace: biological_process
-def: "The process in which a cell initiates conjugation with cellular fusion. Conjugation with cellular fusion is the process that results in the union of cellular and genetic information from compatible mating types." [GOC:dph, GOC:tb]
-is_a: GO:0031139 ! positive regulation of conjugation with cellular fusion
+def: "OBSOLETE. The process in which a cell initiates conjugation with cellular fusion. Conjugation with cellular fusion is the process that results in the union of cellular and genetic information from compatible mating types." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it is a pre-composed term that should be represented as a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31335" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0031139
[Term]
id: GO:0010515
-name: negative regulation of induction of conjugation with cellular fusion
+name: obsolete negative regulation of induction of conjugation with cellular fusion
namespace: biological_process
-def: "Any process that stops, prevents, or reduces the frequency or rate of initiation of conjugation with cellular fusion." [GOC:dph, GOC:tb]
-is_a: GO:0031138 ! negative regulation of conjugation with cellular fusion
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0010514 ! induction of conjugation with cellular fusion
-relationship: negatively_regulates GO:0010514 ! induction of conjugation with cellular fusion
+def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency or rate of initiation of conjugation with cellular fusion." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it is a pre-composed term that should be represented as a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31335" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0031138
[Term]
id: GO:0010516
@@ -114725,38 +115387,33 @@
[Term]
id: GO:0010749
-name: regulation of nitric oxide mediated signal transduction
+name: obsolete regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that modulates the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
-synonym: "regulation of nitric oxide-mediated signal transduction" EXACT []
-is_a: GO:1902531 ! regulation of intracellular signal transduction
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0007263 ! nitric oxide mediated signal transduction
-relationship: regulates GO:0007263 ! nitric oxide mediated signal transduction
+def: "OBSOLETE. Any process that modulates the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+comment: The reason for obsoletion is that this term has been inconsistently used and NO signaling proceeds via cGMP, so the more specific replacement term is preferred.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26613" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0141149
[Term]
id: GO:0010750
-name: positive regulation of nitric oxide mediated signal transduction
+name: obsolete positive regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that increases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
-synonym: "positive regulation of nitric oxide-mediated signal transduction" EXACT []
-is_a: GO:0010749 ! regulation of nitric oxide mediated signal transduction
-is_a: GO:1902533 ! positive regulation of intracellular signal transduction
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0007263 ! nitric oxide mediated signal transduction
-relationship: positively_regulates GO:0007263 ! nitric oxide mediated signal transduction
+def: "OBSOLETE. Any process that increases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+comment: The reason for obsoletion is that this term has been inconsistently used and NO signaling proceeds via cGMP, so the more specific replacement term is preferred.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26613" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0141150
[Term]
id: GO:0010751
-name: negative regulation of nitric oxide mediated signal transduction
+name: obsolete negative regulation of nitric oxide mediated signal transduction
namespace: biological_process
-def: "Any process that decreases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
-synonym: "negative regulation of nitric oxide-mediated signal transduction" EXACT []
-is_a: GO:0010749 ! regulation of nitric oxide mediated signal transduction
-is_a: GO:1902532 ! negative regulation of intracellular signal transduction
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0007263 ! nitric oxide mediated signal transduction
-relationship: negatively_regulates GO:0007263 ! nitric oxide mediated signal transduction
+def: "OBSOLETE. Any process that decreases the rate, frequency or extent of nitric oxide mediated signal transduction. Nitric oxide mediated signal transduction is The series of molecular signals mediated by the detection of nitric oxide (NO)." [GOC:BHF, GOC:dph, GOC:tb]
+comment: The reason for obsoletion is that this term has been inconsistently used and NO signaling proceeds via cGMP, so the more specific replacement term is preferred.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26613" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0141151
[Term]
id: GO:0010752
@@ -116497,9 +117154,9 @@
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of inositol phosphate biosynthesis. Inositol phosphate biosynthetic processes are the chemical reactions and pathways resulting in the formation of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached." [GOC:dph, GOC:tb]
synonym: "negative regulation of inositol phosphate biosynthesis" EXACT [GOC:dph, GOC:tb]
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0010919 ! regulation of inositol phosphate biosynthetic process
is_a: GO:0045912 ! negative regulation of carbohydrate metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:1902931 ! negative regulation of alcohol biosynthetic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0032958 ! inositol phosphate biosynthetic process
@@ -116765,13 +117422,55 @@
xref: Reactome:R-HSA-6809354 "NUDT7 hydrolyses CoA-SH to 3',5'-ADP and PPANT"
xref: Reactome:R-HSA-6810474 "NUDT19 hydrolyses acyl-CoA to 3',5'-ADP and acyl-PPANT"
xref: Reactome:R-HSA-9837354 "NUDT8 hydrolyzes CoA-SH to PPANT"
+xref: RHEA:49976
+xref: RHEA:49980
+xref: RHEA:50016
+xref: RHEA:50020
+xref: RHEA:50024
+xref: RHEA:50028
+xref: RHEA:50032
+xref: RHEA:50036
+xref: RHEA:50040
xref: RHEA:50044
xref: RHEA:64988
+xref: RHEA:64992
+xref: RHEA:65564
+xref: RHEA:65568
+xref: RHEA:67464
+xref: RHEA:67468
+xref: RHEA:67472
+xref: RHEA:67524
+xref: RHEA:67528
+xref: RHEA:67532
+xref: RHEA:67536
+xref: RHEA:67540
+xref: RHEA:67544
is_a: GO:0016462 ! pyrophosphatase activity
property_value: skos:narrowMatch EC:3.6.1.77
property_value: skos:narrowMatch MetaCyc:RXN-10811
+property_value: skos:narrowMatch RHEA:49976
+property_value: skos:narrowMatch RHEA:49980
+property_value: skos:narrowMatch RHEA:50016
+property_value: skos:narrowMatch RHEA:50020
+property_value: skos:narrowMatch RHEA:50024
+property_value: skos:narrowMatch RHEA:50028
+property_value: skos:narrowMatch RHEA:50032
+property_value: skos:narrowMatch RHEA:50036
+property_value: skos:narrowMatch RHEA:50040
property_value: skos:narrowMatch RHEA:50044
property_value: skos:narrowMatch RHEA:64988
+property_value: skos:narrowMatch RHEA:64992
+property_value: skos:narrowMatch RHEA:65564
+property_value: skos:narrowMatch RHEA:65568
+property_value: skos:narrowMatch RHEA:67464
+property_value: skos:narrowMatch RHEA:67468
+property_value: skos:narrowMatch RHEA:67472
+property_value: skos:narrowMatch RHEA:67524
+property_value: skos:narrowMatch RHEA:67528
+property_value: skos:narrowMatch RHEA:67532
+property_value: skos:narrowMatch RHEA:67536
+property_value: skos:narrowMatch RHEA:67540
+property_value: skos:narrowMatch RHEA:67544
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24569" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28938" xsd:anyURI
@@ -117061,14 +117760,13 @@
[Term]
id: GO:0010969
-name: regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion
+name: obsolete regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of pheromone-dependent signal transduction during conjugation with cellular fusion, a signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion." [GOC:dph, GOC:tb]
-is_a: GO:0009966 ! regulation of signal transduction
-is_a: GO:0031137 ! regulation of conjugation with cellular fusion
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0000750 ! pheromone-dependent signal transduction involved in conjugation with cellular fusion
-relationship: regulates GO:0000750 ! pheromone-dependent signal transduction involved in conjugation with cellular fusion
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of pheromone-dependent signal transduction during conjugation with cellular fusion, a signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it is a pre-composed term that should be represented as a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31335" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0180039
created_by: tb
creation_date: 2009-05-20T11:54:57Z
@@ -118043,7 +118741,6 @@
name: dopamine secretion
namespace: biological_process
def: "The regulated release of dopamine by a cell. Dopamine is a catecholamine and a precursor of adrenaline and noradrenaline. It acts as a neurotransmitter in the central nervous system but it is also produced peripherally and acts as a hormone." [GOC:ef]
-is_a: GO:0015872 ! dopamine transport
is_a: GO:0023061 ! signal release
is_a: GO:0050432 ! catecholamine secretion
@@ -120242,13 +120939,66 @@
xref: Reactome:R-HSA-9756183 "UGT1A3 lactonizes 4-OH-ATV to 4-OH-ATVL"
xref: Reactome:R-HSA-9758661 "UGT2B7,2B17,1A3 glucuronidates PRED metabolites"
xref: RHEA:21032
+xref: RHEA:30631
+xref: RHEA:31483
+xref: RHEA:52448
+xref: RHEA:52452
+xref: RHEA:52456
+xref: RHEA:52460
+xref: RHEA:52464
+xref: RHEA:52468
+xref: RHEA:52472
+xref: RHEA:52476
+xref: RHEA:52880
+xref: RHEA:52916
+xref: RHEA:52920
+xref: RHEA:52924
+xref: RHEA:52940
+xref: RHEA:52944
+xref: RHEA:52948
+xref: RHEA:52952
+xref: RHEA:52956
+xref: RHEA:52960
+xref: RHEA:52964
+xref: RHEA:52968
+xref: RHEA:53000
+xref: RHEA:53004
+xref: RHEA:53028
+xref: RHEA:53032
+xref: RHEA:53036
+xref: RHEA:53040
+xref: RHEA:53048
+xref: RHEA:53052
+xref: RHEA:53060
+xref: RHEA:53064
+xref: RHEA:53068
+xref: RHEA:53072
+xref: RHEA:53080
+xref: RHEA:53388
+xref: RHEA:55768
+xref: RHEA:55776
+xref: RHEA:55780
+xref: RHEA:55784
+xref: RHEA:55836
+xref: RHEA:55840
+xref: RHEA:55844
+xref: RHEA:56160
+xref: RHEA:56508
+xref: RHEA:63588
+xref: RHEA:63612
xref: RHEA:63616
xref: RHEA:63692
+xref: RHEA:63696
+xref: RHEA:63700
+xref: RHEA:63704
xref: RHEA:63716
xref: RHEA:63720
+xref: RHEA:63724
xref: RHEA:63728
+xref: RHEA:63732
xref: RHEA:63744
xref: RHEA:63748
+xref: RHEA:74563
xref: RHEA:75099
xref: RHEA:79067
xref: RHEA:79071
@@ -120257,13 +121007,66 @@
is_a: GO:0016758 ! hexosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.17
property_value: skos:exactMatch RHEA:21032
+property_value: skos:narrowMatch RHEA:30631
+property_value: skos:narrowMatch RHEA:31483
+property_value: skos:narrowMatch RHEA:52448
+property_value: skos:narrowMatch RHEA:52452
+property_value: skos:narrowMatch RHEA:52456
+property_value: skos:narrowMatch RHEA:52460
+property_value: skos:narrowMatch RHEA:52464
+property_value: skos:narrowMatch RHEA:52468
+property_value: skos:narrowMatch RHEA:52472
+property_value: skos:narrowMatch RHEA:52476
+property_value: skos:narrowMatch RHEA:52880
+property_value: skos:narrowMatch RHEA:52916
+property_value: skos:narrowMatch RHEA:52920
+property_value: skos:narrowMatch RHEA:52924
+property_value: skos:narrowMatch RHEA:52940
+property_value: skos:narrowMatch RHEA:52944
+property_value: skos:narrowMatch RHEA:52948
+property_value: skos:narrowMatch RHEA:52952
+property_value: skos:narrowMatch RHEA:52956
+property_value: skos:narrowMatch RHEA:52960
+property_value: skos:narrowMatch RHEA:52964
+property_value: skos:narrowMatch RHEA:52968
+property_value: skos:narrowMatch RHEA:53000
+property_value: skos:narrowMatch RHEA:53004
+property_value: skos:narrowMatch RHEA:53028
+property_value: skos:narrowMatch RHEA:53032
+property_value: skos:narrowMatch RHEA:53036
+property_value: skos:narrowMatch RHEA:53040
+property_value: skos:narrowMatch RHEA:53048
+property_value: skos:narrowMatch RHEA:53052
+property_value: skos:narrowMatch RHEA:53060
+property_value: skos:narrowMatch RHEA:53064
+property_value: skos:narrowMatch RHEA:53068
+property_value: skos:narrowMatch RHEA:53072
+property_value: skos:narrowMatch RHEA:53080
+property_value: skos:narrowMatch RHEA:53388
+property_value: skos:narrowMatch RHEA:55768
+property_value: skos:narrowMatch RHEA:55776
+property_value: skos:narrowMatch RHEA:55780
+property_value: skos:narrowMatch RHEA:55784
+property_value: skos:narrowMatch RHEA:55836
+property_value: skos:narrowMatch RHEA:55840
+property_value: skos:narrowMatch RHEA:55844
+property_value: skos:narrowMatch RHEA:56160
+property_value: skos:narrowMatch RHEA:56508
+property_value: skos:narrowMatch RHEA:63588
+property_value: skos:narrowMatch RHEA:63612
property_value: skos:narrowMatch RHEA:63616
property_value: skos:narrowMatch RHEA:63692
+property_value: skos:narrowMatch RHEA:63696
+property_value: skos:narrowMatch RHEA:63700
+property_value: skos:narrowMatch RHEA:63704
property_value: skos:narrowMatch RHEA:63716
property_value: skos:narrowMatch RHEA:63720
+property_value: skos:narrowMatch RHEA:63724
property_value: skos:narrowMatch RHEA:63728
+property_value: skos:narrowMatch RHEA:63732
property_value: skos:narrowMatch RHEA:63744
property_value: skos:narrowMatch RHEA:63748
+property_value: skos:narrowMatch RHEA:74563
property_value: skos:narrowMatch RHEA:75099
property_value: skos:narrowMatch RHEA:79067
property_value: skos:narrowMatch RHEA:79071
@@ -121336,7 +122139,7 @@
name: allantoate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of allantoate from one side of a membrane to the other. Allantoate is the end product of purine metabolism in mammals and some fish, formed form allantoin. It is widely distributed in plants as an important source of stored nitrogen." [GOC:ai, ISBN:0198547684]
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
relationship: part_of GO:0015719 ! allantoate transport
[Term]
@@ -121350,7 +122153,7 @@
xref: Reactome:R-HSA-5661184 "Defective SLCO1B1 does not transport BIL from extracellular region (blood) to cytosol (hepatocyte)"
xref: Reactome:R-HSA-5661198 "Defective SLCO1B3 does not transport BIL from extracellular region (blood) to cytosol (hepatocyte)"
xref: Reactome:R-HSA-9733964 "SLC51A:SLC51B transports bile salts from cytosol to extracellular region"
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0170055 ! lipid transmembrane transporter activity
relationship: part_of GO:0015721 ! bile acid and bile salt transport
@@ -121401,7 +122204,7 @@
namespace: molecular_function
def: "Enables the transfer of mevalonate from one side of a membrane to the other. Mevalonate is the anion of mevalonic acid; its (R)-enantiomer is a strategic intermediate derived from hydroxymethylglutaryl-CoA in the biosynthesis of polyprenyl compounds." [GOC:ai, ISBN:0198506732]
synonym: "monocarboxylate (lactate, pyruvate, mevalonate) uptake/efflux porter activity" RELATED []
-is_a: GO:0022857 ! transmembrane transporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
relationship: part_of GO:0015728 ! mevalonate transport
[Term]
@@ -121409,7 +122212,6 @@
name: oxaloacetate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of oxaloacetate, the anion of oxobutanedioic acid, from one side of a membrane to the other." [GOC:ai]
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
relationship: part_of GO:1902356 ! oxaloacetate(2-) transmembrane transport
@@ -121430,7 +122232,7 @@
name: uronic acid transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of uronic acid from one side of a membrane to the other. Uronic acids are any monocarboxylic acid formally derived by oxidizing to a carboxyl group the terminal hydroxymethylene group of either an aldose with four or more carbon atoms in the molecule, or of any glycoside derived from such an aldose." [GOC:ai]
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
relationship: part_of GO:0015735 ! uronic acid transmembrane transport
[Term]
@@ -121440,8 +122242,8 @@
alt_id: GO:0015163
def: "Enables the transfer of hexuronates from one side of a membrane to the other. A hexuronate is any monocarboxylic acid derived from a hexose by oxidation of C-6." [GOC:ai, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
synonym: "hexuronide transmembrane transporter activity" EXACT []
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015145 ! monosaccharide transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
relationship: part_of GO:0015736 ! hexuronate transmembrane transport
relationship: part_of GO:0015778 ! hexuronide transmembrane transport
@@ -121482,7 +122284,6 @@
namespace: molecular_function
def: "Enables the transfer of fumarate from one side of a membrane to the other. Fumarate is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate." [GOC:ai]
synonym: "dicarboxylate (succinate/fumarate/malate) antiporter activity" RELATED []
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
relationship: part_of GO:0015741 ! fumarate transport
@@ -121502,7 +122303,6 @@
namespace: molecular_function
def: "Enables the transfer of malate from one side of a membrane to the other. Malate is a chiral hydroxydicarboxylic acid, hydroxybutanedioic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle." [GOC:ai]
synonym: "dicarboxylate (succinate/fumarate/malate) antiporter activity" RELATED []
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
relationship: part_of GO:0071423 ! malate transmembrane transport
@@ -121512,7 +122312,6 @@
namespace: molecular_function
def: "Enables the transfer of succinate, the dianion of ethane dicarboxylic acid, from one side of a membrane to the other." [ISBN:0198506732]
synonym: "dicarboxylate (succinate/fumarate/malate) antiporter activity" RELATED []
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
relationship: part_of GO:0071422 ! succinate transmembrane transport
@@ -121926,7 +122725,6 @@
synonym: "glutamate/aspartate porter activity" NARROW []
synonym: "glutamate/aspartate:sodium symporter activity" NARROW []
synonym: "L-aspartate transporter activity" BROAD []
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015172 ! acidic amino acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
@@ -121954,8 +122752,8 @@
synonym: "4-aminobutyrate transporter activity" EXACT []
synonym: "betaine/GABA:sodium symporter activity" NARROW []
synonym: "GABA transporter activity" EXACT []
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015171 ! amino acid transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
relationship: part_of GO:0015812 ! gamma-aminobutyric acid transport
[Term]
@@ -122395,7 +123193,7 @@
namespace: molecular_function
def: "Enables the transfer of 5-formyltetrahydrofolate, the formylated derivative of tetrahydrofolate, from one side of a membrane to the other." [GOC:ai]
synonym: "5-formyltetrahydrofolate transporter activity" EXACT []
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
relationship: part_of GO:0015885 ! 5-formyltetrahydrofolate transport
@@ -122422,7 +123220,7 @@
def: "Enables the directed movement of pantothenate across a membrane. Pantothenate is the anion of pantothenic acid, the amide of beta-alanine and pantoic acid; it is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods." [GOC:ai, ISBN:0721662544]
synonym: "pantothenate transporter activity" BROAD [GOC:mah]
synonym: "vitamin B5 transmembrane transporter activity" EXACT []
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
is_a: GO:0090482 ! vitamin transmembrane transporter activity
relationship: part_of GO:0015887 ! pantothenate transmembrane transport
@@ -123167,6 +123965,7 @@
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: phosphate(out) + H+(out) = phosphate(in) + H+(in)." [TC:2.A.1.9.-]
synonym: "phosphate ion carrier activity" EXACT []
synonym: "phosphate:hydrogen symporter activity" EXACT []
+is_a: GO:0005315 ! phosphate transmembrane transporter activity
is_a: GO:0015295 ! solute:proton symporter activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14221" xsd:anyURI
@@ -123532,8 +124331,8 @@
namespace: molecular_function
def: "Catalysis of the movement of a monocarboxylate, any compound containing a single carboxyl group (COOH or COO-), by uniport, symport or antiport across a membrane by a carrier-mediated mechanism." [GOC:bf, GOC:jl]
synonym: "monocarboxylate porter activity" RELATED []
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015291 ! secondary active transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
[Term]
id: GO:0015356
@@ -124531,7 +125330,7 @@
xref: RHEA:50048
xref: TC:3.A.1.207.2
is_a: GO:0015125 ! bile acid transmembrane transporter activity
-is_a: GO:0033285 ! ATPase-coupled monocarboxylic acid transmembrane transporter activity
+is_a: GO:0033284 ! ATPase-coupled carboxylic acid transmembrane transporter activity
is_a: GO:0034040 ! ATPase-coupled lipid transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
property_value: skos:exactMatch RHEA:50048
@@ -124601,7 +125400,7 @@
synonym: "capsular-polysaccharide-transporting ATPase activity" EXACT []
xref: EC:7.6.2.12
xref: MetaCyc:3.6.3.38-RXN
-is_a: GO:0033284 ! ATPase-coupled carboxylic acid transmembrane transporter activity
+is_a: GO:0033285 ! ATPase-coupled monocarboxylic acid transmembrane transporter activity
is_a: GO:0140359 ! ABC-type transporter activity
relationship: part_of GO:0015776 ! capsular polysaccharide transport
property_value: skos:exactMatch EC:7.6.2.12
@@ -125032,7 +125831,7 @@
consider: GO:0009297
consider: GO:0030674
consider: GO:0044183
-consider: GO:0051082
+consider: GO:0140309
[Term]
id: GO:0015473
@@ -125276,9 +126075,8 @@
name: pantothenate:sodium symporter 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: pantothenate(out) + Na+(out) = pantothenate(in) + Na+(in)." [TC:2.A.21.1.1]
-is_a: GO:0005343 ! organic acid:sodium symporter activity
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
+is_a: GO:0140161 ! monocarboxylate:sodium symporter activity
relationship: part_of GO:0098719 ! sodium ion import across plasma membrane
[Term]
@@ -125318,8 +126116,7 @@
xref: MetaCyc:TRANS-RXN-122
xref: RHEA:29031
is_a: GO:0005283 ! amino acid:sodium symporter activity
-is_a: GO:0005343 ! organic acid:sodium symporter activity
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0017153 ! sodium:dicarboxylate symporter activity
property_value: skos:exactMatch RHEA:29031
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -125787,7 +126584,6 @@
name: tartrate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of tartrate from one side of a membrane to the other. Tartrate is the anion of 2,3-dihydroxybutanedioic acid, one of the aldaric acids. The L(+) enantiomer occurs widely in plants, especially in grape juice, and in fungi and bacteria." [GOC:ai]
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
is_a: GO:0042876 ! aldarate transmembrane transporter activity
@@ -125798,7 +126594,7 @@
name: C4-dicarboxylate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of C4-dicarboxylate from one side of a membrane to the other." [GOC:krc]
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
relationship: part_of GO:0015740 ! C4-dicarboxylate transport
[Term]
@@ -125890,7 +126686,6 @@
namespace: molecular_function
def: "Enables the transfer of L-idonate from one side of a membrane to the other. L-idonate is an aldonic acid derived from L-idose, an aldohexose which is epimeric with D-glucose." [GOC:ai]
synonym: "L-idonate/D-gluconate:hydrogen symporter activity" NARROW []
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
is_a: GO:0042879 ! aldonate transmembrane transporter activity
relationship: part_of GO:0015726 ! L-idonate transmembrane transport
@@ -126553,6 +127348,7 @@
xref: MetaCyc:TRANS-RXN-113
xref: RHEA:29943
is_a: GO:0005351 ! carbohydrate:proton symporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015145 ! monosaccharide transmembrane transporter activity
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
relationship: part_of GO:0046411 ! 2-keto-3-deoxygluconate transmembrane transport
@@ -126840,7 +127636,6 @@
namespace: biological_process
def: "A process in which ferric-enterobactin, the iron-bound form of the siderophore enterobactin, is transported into the cell by specific cell surface receptors." [GOC:pg, PMID:23192658]
synonym: "ferric-enterobactin transport" BROAD []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0033214 ! siderophore-iron import into cell
[Term]
@@ -126914,10 +127709,13 @@
[Term]
id: GO:0015695
-name: organic cation transport
+name: obsolete organic cation transport
namespace: biological_process
-def: "The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage." [GOC:ai]
-is_a: GO:0006810 ! transport
+def: "OBSOLETE. The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage." [GOC:ai]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0055085
[Term]
id: GO:0015697
@@ -126961,7 +127759,7 @@
xref: Reactome:R-HSA-1475029 "Reversible hydration of carbon dioxide"
xref: Reactome:R-HSA-1480926 "O2/CO2 exchange in erythrocytes"
xref: Reactome:R-HSA-425381 "Bicarbonate transporters"
-is_a: GO:0015711 ! organic anion transport
+is_a: GO:0006810 ! transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26780" xsd:anyURI
[Term]
@@ -127049,11 +127847,14 @@
[Term]
id: GO:0015711
-name: organic anion transport
+name: obsolete organic anion transport
namespace: biological_process
-def: "The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage." [GOC:ai, GOC:krc]
+def: "OBSOLETE. The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage." [GOC:ai, GOC:krc]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
xref: Reactome:R-HSA-9955298 "SLC-mediated transport of organic anions"
-is_a: GO:0006810 ! transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30715" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0055085
[Term]
id: GO:0015712
@@ -127191,7 +127992,8 @@
name: mevalonate transport
namespace: biological_process
def: "The directed movement of mevalonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
-is_a: GO:0006810 ! transport
+is_a: GO:0015718 ! monocarboxylic acid transport
+is_a: GO:0015850 ! organic hydroxy compound transport
[Term]
id: GO:0015729
@@ -127349,7 +128151,6 @@
def: "The directed movement of urate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc]
synonym: "urate transmembrane transport" EXACT [GOC:mah]
synonym: "uric acid transport" EXACT []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0071705 ! nitrogen compound transport
[Term]
@@ -127449,7 +128250,6 @@
name: glucose-6-phosphate transport
namespace: biological_process
def: "The directed movement of glucose-6-phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Glucose-6-phosphate is a monophosphorylated derivative of glucose with the phosphate group attached to C-6." [GOC:ai]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015712 ! hexose phosphate transport
[Term]
@@ -127614,7 +128414,6 @@
def: "The directed movement of CMP-N-acetylneuraminate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai]
synonym: "CMP-N-acetylneuraminate transport" RELATED []
synonym: "CMP-sialic acid transport" BROAD []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
[Term]
@@ -127630,7 +128429,6 @@
name: UDP-glucose transmembrane transport
namespace: biological_process
def: "The process in which UDP-glucose is transported across a membrane." [GOC:ai]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14450" xsd:anyURI
@@ -127651,7 +128449,6 @@
namespace: biological_process
def: "The directed movement of UDP-N-acetylgalactosamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. UDP-N-acetylgalactosamine is a substance composed of N-acetylgalactosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate." [GOC:ai]
synonym: "UDP-N-acetylgalactosamine transport" RELATED []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
[Term]
@@ -127660,7 +128457,6 @@
namespace: biological_process
def: "The directed movement of UDP-xylose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. UDP-xylose is a substance composed of xylose in glycosidic linkage with uridine diphosphate." [GOC:ai]
synonym: "UDP-xylose transport" RELATED []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
[Term]
@@ -127699,7 +128495,6 @@
namespace: biological_process
def: "The process in which glycerol-3-phosphate is transported across a membrane. Glycerol-3-phosphate is a phosphoric monoester of glycerol." [GOC:ai]
synonym: "glycerol-3-phosphate transport" RELATED []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
is_a: GO:0055085 ! transmembrane transport
is_a: GO:1901264 ! carbohydrate derivative transport
@@ -127802,7 +128597,6 @@
synonym: "S-adenosyl methionine transport" EXACT []
synonym: "S-adenosylmethionine transport" EXACT []
synonym: "SAM transport" EXACT []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0072348 ! sulfur compound transport
[Term]
@@ -127892,7 +128686,6 @@
name: glycine transport
namespace: biological_process
def: "The directed movement of glycine, aminoethanoic acid, 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:0015695 ! organic cation transport
is_a: GO:0015804 ! neutral amino acid transport
is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -127936,7 +128729,6 @@
namespace: biological_process
def: "The directed movement of L-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: "leucine transport" BROAD []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015803 ! branched-chain amino acid transport
is_a: GO:0015804 ! neutral amino acid transport
is_a: GO:0015807 ! L-amino acid transport
@@ -127949,7 +128741,6 @@
synonym: "L-methionine transport" NARROW []
is_a: GO:0000101 ! sulfur amino acid transport
is_a: GO:0006865 ! amino acid transport
-is_a: GO:0015695 ! organic cation transport
[Term]
id: GO:0015822
@@ -127958,7 +128749,6 @@
def: "The directed movement of ornithine, 2,5-diaminopentanoic 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-ornithine transport" NARROW []
is_a: GO:0006865 ! amino acid transport
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -127977,7 +128767,6 @@
namespace: biological_process
def: "The directed movement of proline, pyrrolidine-2-carboxylic 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-proline transport" NARROW []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015804 ! neutral amino acid transport
is_a: GO:0015807 ! L-amino acid transport
@@ -128010,7 +128799,6 @@
def: "The directed movement of tryptophan, 2-amino-3-(1H-indol-3-yl)propanoic 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-tryptophan transport" NARROW []
is_a: GO:0006865 ! amino acid transport
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015801 ! aromatic amino acid transport
[Term]
@@ -128019,7 +128807,6 @@
namespace: biological_process
def: "The directed movement of tyrosine, 2-amino-3-(4-hydroxyphenyl)propanoic 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-tyrosine transport" NARROW []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015801 ! aromatic amino acid transport
is_a: GO:0015807 ! L-amino acid transport
@@ -128111,7 +128898,6 @@
name: cadaverine transport
namespace: biological_process
def: "The directed movement of cadaverine, 1,5-pentanediamine, 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:0015695 ! organic cation transport
is_a: GO:0071705 ! nitrogen compound transport
[Term]
@@ -128142,17 +128928,18 @@
name: methylammonium transport
namespace: biological_process
def: "The directed movement of methylammonium 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:0015695 ! organic cation transport
is_a: GO:0015837 ! amine transport
is_a: GO:0019755 ! one-carbon compound transport
[Term]
id: GO:0015844
-name: monoamine transport
+name: obsolete monoamine transport
namespace: biological_process
alt_id: GO:0015873
-def: "The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
-is_a: GO:0071705 ! nitrogen compound transport
+def: "OBSOLETE. The directed movement of monoamines, organic compounds that contain one amino group that is connected to an aromatic ring by an ethylene group (-CH2-CH2-), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
+comment: The reason for obsoletion is that this is an unnecessary grouping term and annotations should be made to more mechanism/location specific terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0015846
@@ -128166,7 +128953,6 @@
name: putrescine transport
namespace: biological_process
def: "The directed movement of putrescine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Putrescine is 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine." [GOC:krc, ISBN:0198506732]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015846 ! polyamine transport
[Term]
@@ -128174,7 +128960,6 @@
name: spermidine transport
namespace: biological_process
def: "The directed movement of spermidine, N-(3-aminopropyl)-1,4-diaminobutane, a polyamine formed by the transfer of a propylamine group from decarboxylated S-adenosylmethionine to putrescine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc, ISBN:0198506732]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015846 ! polyamine transport
[Term]
@@ -128313,7 +129098,6 @@
name: ADP transport
namespace: biological_process
def: "The directed movement of ADP, adenosine diphosphate, 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:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
@@ -128322,7 +129106,6 @@
name: ATP transport
namespace: biological_process
def: "The directed movement of ATP, adenosine triphosphate, 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:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
@@ -128349,7 +129132,6 @@
name: acetylcholine transport
namespace: biological_process
def: "The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." [GOC:ai]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:1901374 ! acetate ester transport
@@ -128358,25 +129140,25 @@
name: choline transport
namespace: biological_process
def: "The directed movement of choline into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Choline (2-hydroxyethyltrimethylammonium) is an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine." [GOC:ai]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0015872
-name: dopamine transport
+name: obsolete dopamine transport
namespace: biological_process
-def: "The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." [GOC:ai]
-is_a: GO:0051937 ! catecholamine transport
+def: "OBSOLETE. The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." [GOC:ai]
+comment: The reason for obsoletion is that this is an unnecessary grouping term and annotations should be made to more mechanism/location specific terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0015874
-name: norepinephrine transport
+name: obsolete norepinephrine transport
namespace: biological_process
-def: "The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is 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, ISBN:0198506732]
-synonym: "levarterenol transport" EXACT []
-synonym: "noradrenaline transport" EXACT []
-is_a: GO:0015695 ! organic cation transport
-is_a: GO:0051937 ! catecholamine transport
+def: "OBSOLETE. The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is 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, ISBN:0198506732]
+comment: The reason for obsoletion is that this is an unnecessary grouping term and annotations should be made to more mechanism/location specific terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0015875
@@ -128420,7 +129202,6 @@
namespace: biological_process
def: "The directed movement of carnitine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carnitine is a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane." [GOC:ai]
synonym: "vitamin Bt transport" EXACT []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015838 ! amino-acid betaine transport
[Term]
@@ -128428,7 +129209,6 @@
name: coenzyme A transport
namespace: biological_process
def: "The directed movement of coenzyme A into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, is an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester." [GOC:ai]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
is_a: GO:0015931 ! nucleobase-containing compound transport
is_a: GO:0072348 ! sulfur compound transport
@@ -128466,7 +129246,6 @@
synonym: "flavin adenine dinucleotide transport" EXACT []
synonym: "flavin-adenine dinucleotide transport" EXACT []
is_a: GO:0006862 ! nucleotide transport
-is_a: GO:0015711 ! organic anion transport
[Term]
id: GO:0015884
@@ -128518,7 +129297,6 @@
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:0071705 ! nitrogen compound transport
is_a: GO:0072348 ! sulfur compound transport
@@ -128649,7 +129427,6 @@
def: "The directed movement of tetracycline from one side of a membrane to the other. Tetracycline is a broad spectrum antibiotic that blocks binding of aminoacyl tRNA to the ribosomes of both Gram-positive and Gram-negative organisms (and those of organelles)." [GOC:curators]
synonym: "tetracyclin transport" BROAD []
synonym: "tetracycline transport" BROAD []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0055085 ! transmembrane transport
@@ -128756,7 +129533,6 @@
synonym: "fatty acyl CoA transport" EXACT []
synonym: "fatty acyl coenzyme A transport" EXACT []
synonym: "fatty acyl-CoA transport" EXACT []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
is_a: GO:0015931 ! nucleobase-containing compound transport
is_a: GO:1901337 ! thioester transport
@@ -130103,26 +130879,23 @@
[Term]
id: GO:0016053
-name: organic acid biosynthetic process
+name: obsolete organic acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732]
-synonym: "organic acid anabolism" EXACT []
-synonym: "organic acid biosynthesis" EXACT []
-synonym: "organic acid formation" EXACT []
-synonym: "organic acid synthesis" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:0044283 ! small molecule biosynthetic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31816" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0008152
[Term]
id: GO:0016054
-name: organic acid catabolic process
+name: obsolete organic acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732]
-synonym: "organic acid breakdown" EXACT []
-synonym: "organic acid catabolism" EXACT []
-synonym: "organic acid degradation" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:0044282 ! small molecule catabolic process
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage." [ISBN:0198506732]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31816" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0008152
[Term]
id: GO:0016055
@@ -132359,7 +133132,9 @@
synonym: "selenocysteine catabolic process" EXACT []
synonym: "selenocysteine catabolism" EXACT []
synonym: "selenocysteine degradation" EXACT []
-is_a: GO:1901606 ! alpha-amino acid catabolic process
+is_a: GO:0042219 ! modified amino acid catabolic process
+is_a: GO:0170035 ! L-amino acid catabolic process
+is_a: GO:0170040 ! proteinogenic amino acid catabolic process
[Term]
id: GO:0016262
@@ -132601,12 +133376,18 @@
xref: Reactome:R-HSA-8932413 "METTL10 transfers 3xCH3 from 3xAdoMet to EEF1A1"
xref: Reactome:R-HSA-9844111 "EHMT1,EHMT2 trimethylates lysine-16 of ATF7IP"
xref: Reactome:R-HSA-9854315 "CSKMT methylates Citrate Synthase"
+xref: RHEA:51000
xref: RHEA:51736
xref: RHEA:54192
+xref: RHEA:55544
+xref: RHEA:67108
is_a: GO:0008276 ! protein methyltransferase activity
is_a: GO:0016278 ! lysine N-methyltransferase activity
+property_value: skos:narrowMatch RHEA:51000
property_value: skos:narrowMatch RHEA:51736
property_value: skos:narrowMatch RHEA:54192
+property_value: skos:narrowMatch RHEA:55544
+property_value: skos:narrowMatch RHEA:67108
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29483" xsd:anyURI
[Term]
@@ -132706,7 +133487,13 @@
xref: RHEA:19741
xref: RHEA:28542
xref: RHEA:31511
+xref: RHEA:38291
xref: RHEA:40219
+xref: RHEA:40575
+xref: RHEA:40583
+xref: RHEA:40587
+xref: RHEA:40591
+xref: RHEA:40595
xref: RHEA:45716
xref: RHEA:46224
xref: RHEA:49444
@@ -132725,7 +133512,13 @@
property_value: skos:narrowMatch RHEA:19741
property_value: skos:narrowMatch RHEA:28542
property_value: skos:narrowMatch RHEA:31511
+property_value: skos:narrowMatch RHEA:38291
property_value: skos:narrowMatch RHEA:40219
+property_value: skos:narrowMatch RHEA:40575
+property_value: skos:narrowMatch RHEA:40583
+property_value: skos:narrowMatch RHEA:40587
+property_value: skos:narrowMatch RHEA:40591
+property_value: skos:narrowMatch RHEA:40595
property_value: skos:narrowMatch RHEA:45716
property_value: skos:narrowMatch RHEA:46224
property_value: skos:narrowMatch RHEA:49444
@@ -133608,7 +134401,7 @@
namespace: molecular_function
def: "Catalysis of the transfer of an acyl group to an oxygen atom on the carnitine molecule." [GOC:ai]
xref: Reactome:R-HSA-200410 "CPT2 converts acylcarnitine to acyl-CoA"
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0016407
@@ -133627,10 +134420,13 @@
[Term]
id: GO:0016408
-name: C-acyltransferase activity
+name: obsolete C-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of an acyl group to a carbon atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+def: "OBSOLETE. Catalysis of the transfer of an acyl group to a carbon atom on the acceptor molecule." [GOC:ai]
+comment: This term was obsoleted because it represents an unnecessary grouping class that lacks an EC cross-reference and leads to misclassification of children.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31814" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0016747
[Term]
id: GO:0016409
@@ -133644,13 +134440,16 @@
[Term]
id: GO:0016410
-name: N-acyltransferase activity
+name: obsolete N-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule." [GOC:ai]
+def: "OBSOLETE. Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule." [GOC:ai]
+comment: This term was obsoleted because it represents an unnecessary grouping class that lacks an EC cross-reference and leads to misclassification of children.
xref: Reactome:R-HSA-177160 "phenylacetyl-CoA + glutamine => phenylacetyl glutamine + Coenzyme A"
xref: Reactome:R-HSA-6792572 "LIPT1 transfers lipoyl group from lipoyl-GCSH to DBT/DLST"
xref: Reactome:R-HSA-9858752 "LIPT1 transfers lipoyl group from lipoyl-GCSH to DLAT"
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31814" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0016747
[Term]
id: GO:0016411
@@ -133659,7 +134458,7 @@
def: "Catalysis of the transfer of an acyl group to an oxygen atom on the acylglycerol molecule." [GOC:ai]
xref: Reactome:R-HSA-1482647 "2-MAG and DAG are transacylated to TAG by PNPLA2/3"
xref: Reactome:R-HSA-1482654 "2-MAG is transacylated to DAG by PNPLA2/3"
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0016412
@@ -133676,7 +134475,7 @@
xref: RHEA:68292
xref: RHEA:68296
xref: RHEA:68300
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:68272
property_value: skos:narrowMatch RHEA:59964
property_value: skos:narrowMatch RHEA:59972
@@ -133693,7 +134492,6 @@
name: O-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of an acetyl group to an oxygen atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0008374 ! O-acyltransferase activity
is_a: GO:0016407 ! acetyltransferase activity
[Term]
@@ -133704,7 +134502,7 @@
synonym: "O-octanoyltransferase activity" BROAD []
xref: EC:2.3.1.273
xref: RHEA:56868
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.273
property_value: skos:exactMatch RHEA:56868
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
@@ -133727,15 +134525,17 @@
xref: Reactome:R-HSA-2404137 "LRAT esterifies RBP1:atROL and FACYLs to atREs"
xref: Reactome:R-HSA-2453855 "LRAT esterifies RBP1:atROL and FACYLs to atREs"
xref: Reactome:R-HSA-2466710 "Defective LRAT does not esterify RBP1:atROL and FACYLs to atREs"
-is_a: GO:0008374 ! O-acyltransferase activity
is_a: GO:0016409 ! palmitoyltransferase activity
[Term]
id: GO:0016417
-name: S-acyltransferase activity
+name: obsolete S-acyltransferase activity
namespace: molecular_function
-def: "Catalysis of the transfer of an acyl group to a sulfur atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
+def: "OBSOLETE. Catalysis of the transfer of an acyl group to a sulfur atom on the acceptor molecule." [GOC:ai]
+comment: This term was obsoleted because it represents an unnecessary grouping class that lacks an EC cross-reference and leads to misclassification of children.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31814" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0016747
[Term]
id: GO:0016418
@@ -133743,7 +134543,6 @@
namespace: molecular_function
def: "Catalysis of the transfer of an acetyl group to a sulfur atom on the acceptor molecule." [GOC:ai]
is_a: GO:0016407 ! acetyltransferase activity
-is_a: GO:0016417 ! S-acyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17828" xsd:anyURI
[Term]
@@ -133751,7 +134550,6 @@
name: S-malonyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a malonyl group to a sulfur atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0016417 ! S-acyltransferase activity
is_a: GO:0016420 ! malonyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
@@ -133830,6 +134628,7 @@
xref: Reactome:R-HSA-6785409 "NSUN2 methylates cytidine-48 and cytidine-49 of tRNA(Asp)(GUC)"
xref: Reactome:R-HSA-6785438 "NSUN2 methylates cytidine-40, cytidine-48, cytidine-49, cytidine-50 of tRNA(GLY)(GCC)"
xref: Reactome:R-HSA-8932765 "NSUN6 methylates cytidine-72 in tRNA(Cys) and tRNA(Thr)"
+xref: RHEA:21124
xref: RHEA:42940
xref: RHEA:42944
xref: RHEA:42948
@@ -133838,16 +134637,19 @@
xref: RHEA:51160
xref: RHEA:51164
xref: RHEA:51172
+xref: RHEA:51176
xref: RHEA:51180
xref: RHEA:53076
xref: RHEA:54136
xref: RHEA:54140
xref: RHEA:61468
xref: RHEA:61488
+xref: RHEA:61584
xref: RHEA:61988
is_a: GO:0016427 ! tRNA (cytidine) methyltransferase activity
property_value: skos:exactMatch RHEA:61468
property_value: skos:narrowMatch EC:2.1.1.202
+property_value: skos:narrowMatch RHEA:21124
property_value: skos:narrowMatch RHEA:42940
property_value: skos:narrowMatch RHEA:42944
property_value: skos:narrowMatch RHEA:42948
@@ -133856,11 +134658,13 @@
property_value: skos:narrowMatch RHEA:51160
property_value: skos:narrowMatch RHEA:51164
property_value: skos:narrowMatch RHEA:51172
+property_value: skos:narrowMatch RHEA:51176
property_value: skos:narrowMatch RHEA:51180
property_value: skos:narrowMatch RHEA:53076
property_value: skos:narrowMatch RHEA:54136
property_value: skos:narrowMatch RHEA:54140
property_value: skos:narrowMatch RHEA:61488
+property_value: skos:narrowMatch RHEA:61584
property_value: skos:narrowMatch RHEA:61988
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24771" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26109" xsd:anyURI
@@ -134036,14 +134840,12 @@
namespace: molecular_function
def: "Catalysis of the transfer of an acetyl group to a carbon atom on the acceptor molecule." [GOC:ai]
is_a: GO:0016407 ! acetyltransferase activity
-is_a: GO:0016408 ! C-acyltransferase activity
[Term]
id: GO:0016454
name: C-palmitoyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a palmitoyl group to a carbon atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0016408 ! C-acyltransferase activity
is_a: GO:0016409 ! palmitoyltransferase activity
[Term]
@@ -136788,12 +137590,22 @@
xref: Reactome:R-HSA-194678 "CYP51A1 demethylates LAN"
xref: Reactome:R-HSA-211966 "CYP2D6 4-hydroxylates debrisoquine"
xref: RHEA:17149
+xref: RHEA:51984
+xref: RHEA:68160
+xref: RHEA:75847
+xref: RHEA:75863
+xref: RHEA:76419
is_a: GO:0004497 ! monooxygenase activity
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
property_value: skos:exactMatch EC:1.14.14.-
property_value: skos:narrowMatch EC:1.14.14.1
property_value: skos:narrowMatch MetaCyc:UNSPECIFIC-MONOOXYGENASE-RXN
property_value: skos:narrowMatch RHEA:17149
+property_value: skos:narrowMatch RHEA:51984
+property_value: skos:narrowMatch RHEA:68160
+property_value: skos:narrowMatch RHEA:75847
+property_value: skos:narrowMatch RHEA:75863
+property_value: skos:narrowMatch RHEA:76419
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28295" xsd:anyURI
created_by: mah
@@ -137215,7 +138027,6 @@
name: N-succinyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a succinyl group to a nitrogen atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0016410 ! N-acyltransferase activity
is_a: GO:0016748 ! succinyltransferase activity
[Term]
@@ -137223,7 +138034,6 @@
name: O-succinyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a succinyl group to an oxygen atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0008374 ! O-acyltransferase activity
is_a: GO:0016748 ! succinyltransferase activity
[Term]
@@ -137231,7 +138041,6 @@
name: S-succinyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a succinyl group to a sulfur atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0016417 ! S-acyltransferase activity
is_a: GO:0016748 ! succinyltransferase activity
[Term]
@@ -137246,7 +138055,6 @@
name: O-sinapoyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a sinapoyl group to an oxygen atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0008374 ! O-acyltransferase activity
is_a: GO:0016752 ! sinapoyltransferase activity
[Term]
@@ -140611,12 +141419,14 @@
xref: Reactome:R-HSA-5693925 "FUT3 transfers L-fucose to Gal1,3GlcNAc"
xref: Reactome:R-HSA-9603986 "FUT3 transfers Fuc to Type 1 chains to form LeA"
xref: RHEA:23628
+xref: RHEA:48328
xref: RHEA:48824
xref: RHEA:62844
xref: RHEA:62848
is_a: GO:0008417 ! fucosyltransferase activity
property_value: skos:exactMatch EC:2.4.1.65
property_value: skos:exactMatch RHEA:23628
+property_value: skos:narrowMatch RHEA:48328
property_value: skos:narrowMatch RHEA:48824
property_value: skos:narrowMatch RHEA:62844
property_value: skos:narrowMatch RHEA:62848
@@ -141166,7 +141976,7 @@
id: GO:0017109
name: glutamate-cysteine ligase complex
namespace: cellular_component
-def: "An enzyme complex that catalyzes the ligation of glutamate to cysteine, forming glutamylcysteine." [PMID:9675072]
+def: "An enzyme complex that catalyzes the ligation of L-glutamate to L-cysteine, forming gamma-L-glutamyl-L-cysteine." [PMID:9675072]
synonym: "gamma-glutamylcysteine synthetase complex" EXACT []
is_a: GO:1902494 ! catalytic complex
relationship: part_of GO:0005737 ! cytoplasm
@@ -141589,12 +142399,20 @@
xref: MetaCyc:RXN0-1281
xref: Reactome:R-HSA-6782296 "DUS2:EPRS reduces uridine to dihydrouridine in tRNAs"
xref: RHEA:23624
+xref: RHEA:53336
+xref: RHEA:53340
+xref: RHEA:53360
+xref: RHEA:53364
xref: RHEA:54452
is_a: GO:0106413 ! RNA dihydrouridine synthase activity
is_a: GO:0140101 ! catalytic activity, acting on a tRNA
relationship: part_of GO:0002943 ! tRNA dihydrouridine synthesis
property_value: skos:narrowMatch MetaCyc:RXN0-1281
property_value: skos:narrowMatch RHEA:23624
+property_value: skos:narrowMatch RHEA:53336
+property_value: skos:narrowMatch RHEA:53340
+property_value: skos:narrowMatch RHEA:53360
+property_value: skos:narrowMatch RHEA:53364
property_value: skos:narrowMatch RHEA:54452
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25790" xsd:anyURI
@@ -142403,7 +143221,7 @@
name: peptidyl-lysine N6-palmitoyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a palmitoyl group to the N6 nitrogen atom on a lysine residue of a peptide or protein molecule." [GOC:mah, PMID:29074776]
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22878" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22968" xsd:anyURI
@@ -147639,12 +148457,11 @@
id: GO:0018554
name: 1,2-dihydroxynaphthalene dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 1,2-dihydroxynaphthalene + O2 = 2-hydroxychromene-2-carboxylate. C6 of the substrate molecular may have an NH2 group attached." [UM-BBD_enzymeID:r0336]
+def: "Catalysis of the reaction: naphthalene-1,2-diol + O2 = 2-hydroxychromene-2-carboxylate + H+." [RHEA:27310]
xref: EC:1.13.11.56
xref: RHEA:27310
xref: UM-BBD_enzymeID:r0336
-is_a: GO:0016701 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen
-is_a: GO:0051213 ! dioxygenase activity
+is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
property_value: skos:exactMatch EC:1.13.11.56
property_value: skos:exactMatch RHEA:27310
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -148267,7 +149084,7 @@
id: GO:0018610
name: dibenzofuran 4,4a-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: dibenzofuran + NADH + H+ + O2 = 2,2',3-trihydroxybiphenyl + NAD+." [MetaCyc:R606-RXN, RHEA:42460]
+def: "Catalysis of the reaction: dibenzofuran + NADH + H+ + O2 = 2,2',3-trihydroxybiphenyl + NAD+." [RHEA:42460]
xref: MetaCyc:R606-RXN
xref: RHEA:42460
xref: UM-BBD_enzymeID:r0026
@@ -148356,16 +149173,20 @@
synonym: "anthranilic hydroxylase activity" BROAD [EC:1.14.12.1]
xref: EC:1.14.12.1
xref: MetaCyc:1.14.12.1-RXN
+xref: RHEA:11072
+xref: RHEA:11076
xref: UM-BBD_reactionID:r0577
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
property_value: skos:exactMatch EC:1.14.12.1
+property_value: skos:narrowMatch RHEA:11072
+property_value: skos:narrowMatch RHEA:11076
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
id: GO:0018619
name: benzene 1,2-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzene + H+ + NADH + O2 = cis-cyclohexa-3,5-diene-1,2-diol + NAD+." [EC:1.14.12.3, RHEA:13813]
+def: "Catalysis of the reaction: benzene + NADH + O2 + H+ = cis-1,2-dihydrobenzene-1,2-diol + NAD+." [RHEA:13813]
synonym: "benzene dioxygenase activity" RELATED [EC:1.14.12.3]
synonym: "benzene hydroxylase activity" RELATED [EC:1.14.12.3]
synonym: "benzene,NADH:oxygen oxidoreductase (1,2-hydroxylating)" RELATED [EC:1.14.12.3]
@@ -148383,7 +149204,7 @@
id: GO:0018620
name: phthalate 4,5-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + NADH + O2 + phthalate = cis-4,5-dihydroxycyclohexa-2,6-diene-1,2-dicarboxylate + NAD+." [EC:1.14.12.7, RHEA:17489]
+def: "Catalysis of the reaction: phthalate + NADH + O2 + H+ = cis-4,5-dihydroxycyclohexa-2,6-diene-1,2-dicarboxylate + NAD+." [RHEA:17489]
synonym: "PDO activity" RELATED [EC:1.14.12.7]
synonym: "phthalate dioxygenase activity" BROAD [EC:1.14.12.7]
synonym: "phthalate,NADH:oxygen oxidoreductase (4,5-hydroxylating)" RELATED [EC:1.14.12.7]
@@ -148401,7 +149222,7 @@
id: GO:0018621
name: 4-sulfobenzoate 3,4-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-sulfobenzoate + H+ + NADH + O2 = 3,4-dihydroxybenzoate + NAD+ + sulfite." [EC:1.14.12.8, RHEA:13937]
+def: "Catalysis of the reaction: 4-sulfobenzoate + H+ + NADH + O2 = 3,4-dihydroxybenzoate + NAD+ + sulfite." [RHEA:13937]
synonym: "4-sulfobenzoate 3,4-dioxygenase system" RELATED [EC:1.14.12.8]
synonym: "4-sulfobenzoate dioxygenase activity" RELATED [EC:1.14.12.8]
synonym: "4-sulfobenzoate,NADH:oxygen oxidoreductase (3,4-hydroxylating, sulfite-forming)" RELATED [EC:1.14.12.8]
@@ -148420,7 +149241,7 @@
id: GO:0018622
name: 4-chlorophenylacetate 3,4-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-chlorophenylacetate + NADH + O2 = 3,4-dihydroxyphenylacetate + chloride + NAD+." [EC:1.14.12.9, RHEA:14689]
+def: "Catalysis of the reaction: 4-chlorophenylacetate + NADH + O2 = 3,4-dihydroxyphenylacetate + chloride + NAD+." [RHEA:14689]
synonym: "4-chlorophenylacetate,NADH:oxygen oxidoreductase (3,4-hydroxylating, dechlorinating)" RELATED [EC:1.14.12.9]
xref: EC:1.14.12.9
xref: KEGG_REACTION:R03306
@@ -148436,7 +149257,7 @@
id: GO:0018623
name: benzoate 1,2-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: benzoate + NADH + H+ + O2 = catechol + CO2 + NAD+." [EC:1.14.12.10]
+def: "Catalysis of the reaction: benzoate + NADH + O2 + H+ = (1R,6S)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate + NAD+." [RHEA:12633]
synonym: "benzoate dioxygenase activity" RELATED [EC:1.14.12.10]
synonym: "benzoate hydroxylase activity" RELATED [EC:1.14.12.10]
synonym: "benzoate,NADH:oxygen oxidoreductase (1,2-hydroxylating)" RELATED [EC:1.14.12.10]
@@ -148455,7 +149276,7 @@
id: GO:0018624
name: toluene dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + NADH + O2 + toluene = (1S,2R)-3-methylcyclohexa-3,5-diene-1,2-diol + NAD+." [EC:1.14.12.11, RHEA:16737]
+def: "Catalysis of the reaction: toluene + NADH + O2 + H+ = (1S,2R)-3-methylcyclohexa-3,5-diene-1,2-diol + NAD+." [RHEA:16737]
synonym: "toluene 1,2-dioxygenase activity" RELATED [EC:1.14.12.11]
synonym: "toluene 2,3-dioxygenase activity" RELATED [EC:1.14.12.11]
synonym: "toluene,NADH:oxygen oxidoreductase (1,2-hydroxylating)" RELATED [EC:1.14.12.11]
@@ -148509,7 +149330,7 @@
name: 2-aminobenzenesulfonate 2,3-dioxygenase activity
namespace: molecular_function
alt_id: GO:0018605
-def: "Catalysis of the reaction: 2-aminobenzenesulfonate + 2 H+ + NADH + O2 = 2,3-dihydroxybenzenesulfonate + NAD+ + NH4. 2,3-dihydroxybenzenesulfonate is also known as 3-sulfocatechol." [EC:1.14.12.14, RHEA:23468]
+def: "Catalysis of the reaction: 2-aminobenzenesulfonate + 2 H+ + NADH + O2 = 2,3-dihydroxybenzenesulfonate + NAD+ + NH4. 2,3-dihydroxybenzenesulfonate is also known as 3-sulfocatechol." [RHEA:23468]
synonym: "2-aminobenzenesulfonate dioxygenase activity" EXACT []
synonym: "2-aminobenzenesulfonate,NADH:oxygen oxidoreductase (2,3-hydroxylating, ammonia-forming)" RELATED [EC:1.14.12.14]
synonym: "2-aminobenzenesulphonate 2,3-dioxygenase activity" EXACT []
@@ -148529,7 +149350,7 @@
id: GO:0018628
name: terephthalate 1,2-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: H+ + NADH + O2 + terephthalate = (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD+." [EC:1.14.12.15, RHEA:10312]
+def: "Catalysis of the reaction: terephthalate + NADH + O2 + H+ = (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD+." [RHEA:10312]
synonym: "1,4-dicarboxybenzoate 1,2-dioxygenase activity" RELATED [EC:1.14.12.15]
synonym: "benzene-1,4-dicarboxylate 1,2-dioxygenase activity" RELATED [EC:1.14.12.15]
synonym: "benzene-1,4-dicarboxylate,NADH:oxygen oxidoreductase (1,2-hydroxylating)" RELATED [EC:1.14.12.15]
@@ -148547,7 +149368,7 @@
id: GO:0018629
name: 2-hydroxyquinoline 5,6-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: quinolin-2-ol + NADH + H+ + O2 = 2,5,6-trihydroxy-5,6-dihydroquinoline + NAD+." [EC:1.14.12.16]
+def: "Catalysis of the reaction: quinolin-2-ol + NADH + O2 + H+ = 5,6-dihydroquinoline-2,5,6-triol + NAD+." [RHEA:10976]
synonym: "2-oxo-1,2-dihydroquinoline 5,6-dioxygenase activity" EXACT []
synonym: "quinolin-2(1H)-one 5,6-dioxygenase activity" RELATED [EC:1.14.12.16]
synonym: "quinolin-2-ol 5,6-dioxygenase activity" RELATED [EC:1.14.12.16]
@@ -149399,7 +150220,7 @@
id: GO:0018687
name: biphenyl 2,3-dioxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: biphenyl + NADH + H+ + O2 = (2R,3S)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+. This reaction requires Fe2+." [EC:1.14.12.18]
+def: "Catalysis of the reaction: biphenyl + NADH + H+ + O2 = (2R,3S)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+. This reaction requires Fe2+." [RHEA:18165]
synonym: "biphenyl dioxygenase activity" RELATED [EC:1.14.12.18]
synonym: "biphenyl,NADH:oxygen oxidoreductase (2,3-hydroxylating)" RELATED [EC:1.14.12.18]
xref: EC:1.14.12.18
@@ -149818,7 +150639,7 @@
id: GO:0018729
name: propionate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + propanoate = acetate + propanoyl-CoA." [EC:2.8.3.1]
+def: "Catalysis of the reaction: acetyl-CoA + propanoate = acetate + propanoyl-CoA." [RHEA:23520]
synonym: "acetyl-CoA:propanoate CoA-transferase activity" RELATED [EC:2.8.3.1]
synonym: "propionate coenzyme A-transferase activity" RELATED [EC:2.8.3.1]
synonym: "propionate-CoA:lactoyl-CoA transferase activity" RELATED [EC:2.8.3.1]
@@ -149837,7 +150658,7 @@
id: GO:0018730
name: glutaconate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + (E)-glutaconate = acetate + glutaconyl-1-CoA." [EC:2.8.3.12]
+def: "Catalysis of the reaction: trans-glutaconate + acetyl-CoA = (2E)-glutaconyl-CoA + acetate." [RHEA:23208]
synonym: "acetyl-CoA:(E)-glutaconate CoA-transferase activity" RELATED [EC:2.8.3.12]
xref: EC:2.8.3.12
xref: MetaCyc:GLUTACONATE-COA-TRANSFERASE-RXN
@@ -150844,27 +151665,61 @@
xref: Reactome:R-HSA-6809263 "EHHADH hydrates trans-2,3-dehydrohexacosanoyl-CoA"
xref: Reactome:R-HSA-8957389 "RPP14 (HTD2) dehydrates 3HA-CoA to t2E-CoA"
xref: RHEA:16105
+xref: RHEA:30547
+xref: RHEA:31075
+xref: RHEA:31191
+xref: RHEA:31199
xref: RHEA:33767
xref: RHEA:35347
xref: RHEA:35355
xref: RHEA:35359
+xref: RHEA:39123
+xref: RHEA:39139
+xref: RHEA:40187
+xref: RHEA:40207
+xref: RHEA:45992
xref: RHEA:46348
xref: RHEA:46352
xref: RHEA:52664
xref: RHEA:71647
+xref: RHEA:72579
+xref: RHEA:76647
+xref: RHEA:78911
+xref: RHEA:78915
+xref: RHEA:82959
+xref: RHEA:84407
+xref: RHEA:84659
+xref: RHEA:84663
is_a: GO:0004300 ! enoyl-CoA hydratase activity
property_value: skos:exactMatch RHEA:33767
property_value: skos:narrowMatch EC:4.2.1.150
property_value: skos:narrowMatch EC:4.2.1.74
property_value: skos:narrowMatch MetaCyc:ENOYL-COA-HYDRAT-RXN
property_value: skos:narrowMatch RHEA:16105
+property_value: skos:narrowMatch RHEA:30547
+property_value: skos:narrowMatch RHEA:31075
+property_value: skos:narrowMatch RHEA:31191
+property_value: skos:narrowMatch RHEA:31199
property_value: skos:narrowMatch RHEA:35347
property_value: skos:narrowMatch RHEA:35355
property_value: skos:narrowMatch RHEA:35359
+property_value: skos:narrowMatch RHEA:39123
+property_value: skos:narrowMatch RHEA:39139
+property_value: skos:narrowMatch RHEA:40187
+property_value: skos:narrowMatch RHEA:40207
+property_value: skos:narrowMatch RHEA:45992
property_value: skos:narrowMatch RHEA:46348
property_value: skos:narrowMatch RHEA:46352
property_value: skos:narrowMatch RHEA:52664
property_value: skos:narrowMatch RHEA:71647
+property_value: skos:narrowMatch RHEA:72579
+property_value: skos:narrowMatch RHEA:76647
+property_value: skos:narrowMatch RHEA:78911
+property_value: skos:narrowMatch RHEA:78915
+property_value: skos:narrowMatch RHEA:82959
+property_value: skos:narrowMatch RHEA:84407
+property_value: skos:narrowMatch RHEA:84659
+property_value: skos:narrowMatch RHEA:84663
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24738" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28557" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29788" xsd:anyURI
@@ -152203,6 +153058,7 @@
xref: UM-BBD_pathwayID:msa
is_a: GO:0006805 ! xenobiotic metabolic process
is_a: GO:0019694 ! alkanesulfonate metabolic process
+is_a: GO:0044281 ! small molecule metabolic process
[Term]
id: GO:0018927
@@ -152588,8 +153444,8 @@
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
@@ -152834,7 +153690,6 @@
synonym: "naphthalenesulphonate metabolic process" EXACT []
synonym: "naphthalenesulphonate metabolism" EXACT []
xref: UM-BBD_pathwayID:nphs
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
[Term]
@@ -154034,7 +154889,7 @@
comment: This term has been obsoleted because it represents an unnecessary grouping class and is not consistent with the ontology structure.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22971" xsd:anyURI
is_obsolete: true
-consider: GO:0016410
+consider: GO:0016747
[Term]
id: GO:0019107
@@ -155631,15 +156486,15 @@
[Term]
id: GO:0019240
-name: citrulline biosynthetic process
+name: L-citrulline biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of L-citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins." [ISBN:0198506732]
synonym: "citrulline anabolism" EXACT []
synonym: "citrulline biosynthesis" EXACT []
+synonym: "citrulline biosynthetic process" BROAD []
synonym: "citrulline formation" EXACT []
synonym: "citrulline synthesis" EXACT []
xref: MetaCyc:CITRULBIO-PWY
-is_a: GO:0000052 ! citrulline metabolic process
is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
is_a: GO:1901607 ! alpha-amino acid biosynthetic process
@@ -155652,7 +156507,6 @@
synonym: "citrulline catabolism" EXACT []
synonym: "citrulline degradation" EXACT []
xref: MetaCyc:CITRULLINE-DEG-PWY
-is_a: GO:0000052 ! citrulline metabolic process
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
is_a: GO:1901606 ! alpha-amino acid catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30202" xsd:anyURI
@@ -155840,7 +156694,6 @@
synonym: "glucose 1-phosphate metabolism" EXACT []
synonym: "glucose 1-phosphate utilization" RELATED [GOC:mah]
xref: MetaCyc:GLUCOSE1PMETAB-PWY
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
@@ -156345,7 +157198,6 @@
synonym: "coenzyme M synthesis" EXACT []
xref: MetaCyc:P261-PWY
xref: MetaCyc:PWY-6643
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0044272 ! sulfur compound biosynthetic process
property_value: skos:narrowMatch MetaCyc:P261-PWY
property_value: skos:narrowMatch MetaCyc:PWY-6643
@@ -156864,7 +157716,6 @@
synonym: "parathion degradation" EXACT []
xref: MetaCyc:PARATHION-DEGRADATION-PWY
xref: UM-BBD_pathwayID:pthn
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
is_a: GO:0046434 ! organophosphate catabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
@@ -157028,8 +157879,8 @@
synonym: "teichoic acid formation" EXACT []
synonym: "teichoic acid synthesis" EXACT []
xref: MetaCyc:TEICHOICACID-PWY
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0044038 ! cell wall macromolecule biosynthetic process
+is_a: GO:0044283 ! small molecule biosynthetic process
is_a: GO:0046374 ! teichoic acid metabolic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
relationship: part_of GO:0009273 ! peptidoglycan-based cell wall biogenesis
@@ -157051,26 +157902,31 @@
[Term]
id: GO:0019352
-name: protoporphyrinogen IX biosynthetic process from glycine
+name: obsolete protoporphyrinogen IX biosynthetic process from glycine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from other compounds, including glycine." [GOC:curators]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from other compounds, including glycine." [GOC:curators]
+comment: This term was obsoleted because protoporphyrinogen IX is an intermediate in heme/chlorophyll/uroporphyrinogen biosynthesis.
synonym: "protoporphyrinogen IX anabolism from glycine" EXACT []
synonym: "protoporphyrinogen IX formation from glycine" EXACT []
synonym: "protoporphyrinogen IX synthesis from glycine" EXACT []
-is_a: GO:0006544 ! glycine metabolic process
-is_a: GO:0006782 ! protoporphyrinogen IX biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31788" xsd:anyURI
+is_obsolete: true
+consider: GO:0006780
+consider: GO:0006783
+consider: GO:0015995
[Term]
id: GO:0019353
-name: protoporphyrinogen IX biosynthetic process from glutamate
+name: obsolete protoporphyrinogen IX biosynthetic process from glutamate
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from other compounds, including glutamate." [PMID:32976912]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from other compounds, including glutamate." [PMID:32976912]
+comment: This term was obsoleted because protoporphyrinogen IX is an intermediate in heme/chlorophyll/uroporphyrinogen biosynthesis.
synonym: "protoporphyrinogen IX anabolism from glutamate" EXACT []
synonym: "protoporphyrinogen IX formation from glutamate" EXACT []
synonym: "protoporphyrinogen IX synthesis from glutamate" EXACT []
-is_a: GO:0006782 ! protoporphyrinogen IX biosynthetic process
-is_a: GO:0033526 ! tetrapyrrole biosynthetic process from glutamate
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17053" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31788" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0019354
@@ -157357,13 +158213,16 @@
synonym: "atrazine breakdown" EXACT []
synonym: "atrazine catabolism" EXACT []
synonym: "atrazine degradation" EXACT []
+xref: MetaCyc:P141-PWY
xref: MetaCyc:PWY-5724
xref: UM-BBD_pathwayID:atr
is_a: GO:0006598 ! polyamine catabolic process
is_a: GO:0042204 ! s-triazine compound catabolic process
is_a: GO:0090345 ! organohalogen metabolic process
+property_value: skos:narrowMatch MetaCyc:P141-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0019382
@@ -157502,14 +158361,17 @@
[Term]
id: GO:0019393
-name: glucarate biosynthetic process
+name: obsolete glucarate biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of glucarate, the anion of glucaric acid." [ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of glucarate, the anion of glucaric acid." [ISBN:0198506732]
+comment: This term was obsoleted because it represents the same process as D-glucarate biosynthetic process ; GO:0042837.
synonym: "glucarate anabolism" EXACT []
synonym: "glucarate biosynthesis" EXACT []
synonym: "glucarate formation" EXACT []
synonym: "glucarate synthesis" EXACT []
-is_a: GO:0019578 ! aldaric acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0042837
[Term]
id: GO:0019394
@@ -158575,12 +159437,15 @@
[Term]
id: GO:0019482
-name: beta-alanine metabolic process
+name: obsolete beta-alanine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins." [GOC:jl, ISBN:0198506732]
+def: "OBSOLETE. The chemical reactions and pathways involving beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins." [GOC:jl, ISBN:0198506732]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "beta-alanine metabolism" EXACT []
-xref: Wikipedia:Beta-alanine
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0019483
+consider: GO:0019484
[Term]
id: GO:0019483
@@ -158597,7 +159462,6 @@
xref: MetaCyc:PWY-5155
xref: MetaCyc:PWY-5760
is_a: GO:0008652 ! amino acid biosynthetic process
-is_a: GO:0019482 ! beta-alanine metabolic process
is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
property_value: skos:narrowMatch MetaCyc:PWY-3941
property_value: skos:narrowMatch MetaCyc:PWY-3981
@@ -158618,7 +159482,6 @@
xref: MetaCyc:PWY-1781
xref: MetaCyc:PWY-8120
is_a: GO:0009063 ! amino acid catabolic process
-is_a: GO:0019482 ! beta-alanine metabolic process
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
property_value: skos:narrowMatch MetaCyc:BETA-ALA-DEGRADATION-I-PWY
property_value: skos:narrowMatch MetaCyc:PWY-1781
@@ -159739,7 +160602,7 @@
synonym: "aldaric acid biosynthesis" EXACT []
synonym: "aldaric acid formation" EXACT []
synonym: "aldaric acid synthesis" EXACT []
-is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
[Term]
id: GO:0019579
@@ -159749,7 +160612,7 @@
synonym: "aldaric acid breakdown" EXACT []
synonym: "aldaric acid catabolism" EXACT []
synonym: "aldaric acid degradation" EXACT []
-is_a: GO:0043649 ! dicarboxylic acid catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
[Term]
id: GO:0019580
@@ -160219,35 +161082,41 @@
[Term]
id: GO:0019623
-name: atrazine catabolic process to urea
+name: obsolete atrazine catabolic process to urea
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of atrazine, a triazine ring-containing herbicide, into urea." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of atrazine, a triazine ring-containing herbicide, into urea." [GOC:jl]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "atrazine breakdown to urea" EXACT []
synonym: "atrazine degradation to urea" EXACT []
-is_a: GO:0019381 ! atrazine catabolic process
-is_a: GO:0019627 ! urea metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019381
[Term]
id: GO:0019624
-name: atrazine catabolic process to isopropylamine
+name: obsolete atrazine catabolic process to isopropylamine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of atrazine, a triazine ring-containing herbicide, into isopropylamine." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of atrazine, a triazine ring-containing herbicide, into isopropylamine." [GOC:jl]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "atrazine breakdown to isopropylamine" EXACT []
synonym: "atrazine degradation to isopropylamine" EXACT []
-is_a: GO:0019381 ! atrazine catabolic process
-property_value: skos:broadMatch MetaCyc:P141-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019381
[Term]
id: GO:0019625
-name: atrazine catabolic process to cyanuric acid
+name: obsolete atrazine catabolic process to cyanuric acid
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of atrazine, a triazine ring-containing herbicide, into cyanuric acid." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of atrazine, a triazine ring-containing herbicide, into cyanuric acid." [GOC:jl]
+comment: The reason for obsoletion is that this term represents a GO-CAM model.
synonym: "atrazine breakdown to cyanuric acid" EXACT []
synonym: "atrazine degradation to cyanuric acid" EXACT []
-is_a: GO:0019381 ! atrazine catabolic process
-property_value: skos:broadMatch MetaCyc:P141-PWY
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28388" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0019381
[Term]
id: GO:0019626
@@ -160756,7 +161625,6 @@
is_a: GO:0006089 ! lactate metabolic process
is_a: GO:0006103 ! 2-oxoglutarate metabolic process
is_a: GO:0006105 ! succinate metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0015942 ! formate metabolic process
is_a: GO:0046434 ! organophosphate catabolic process
is_a: GO:0072329 ! monocarboxylic acid catabolic process
@@ -161013,7 +161881,6 @@
synonym: "glyceraldehyde 3-phosphate metabolism" EXACT []
synonym: "glyceraldehyde-3-phosphate metabolism" EXACT []
is_a: GO:0006081 ! aldehyde metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
@@ -161114,7 +161981,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar." [GOC:ai]
synonym: "ribose phosphate metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
@@ -161127,7 +161993,6 @@
synonym: "alkanesulphonate metabolic process" EXACT []
synonym: "alkanesulphonate metabolism" EXACT []
xref: MetaCyc:ALKANEMONOX-PWY
-is_a: GO:0006082 ! organic acid metabolic process
is_a: GO:0006790 ! sulfur compound metabolic process
[Term]
@@ -161290,7 +162155,7 @@
xref: Reactome:R-HSA-158832 "The acetyl group from acetyl-CoA is transferred to NAT2"
xref: Reactome:R-HSA-174959 "The acetyl group from acetyl-CoA is transferred to NAT1"
xref: RHEA:63372
-is_a: GO:0016417 ! S-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch RHEA:63372
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18882" xsd:anyURI
@@ -172542,15 +173407,17 @@
id: GO:0030150
name: protein import into mitochondrial matrix
namespace: biological_process
-def: "The import of proteins across the outer and inner mitochondrial membranes into the matrix. Unfolded proteins enter the mitochondrial matrix with a chaperone protein; the information required to target the precursor protein from the cytosol to the mitochondrial matrix is contained within its N-terminal matrix-targeting sequence. Translocation of precursors to the matrix occurs at the rare sites where the outer and inner membranes are close together." [ISBN:0716731363]
+def: "The import of proteins with mitochondrial targeting sequence from the cytosol across the mitochondrial outer and inner membranes into the matrix via TOM-TIM23-PAM." [ISBN:0716731363, PMID:36931257]
synonym: "mitochondrial matrix protein import" EXACT []
synonym: "mitochondrial translocation" BROAD []
synonym: "protein transport into mitochondrial matrix" EXACT []
-is_a: GO:0010496 ! intercellular transport
+synonym: "TOM-TIM23-PAM presequence matrix import pathway" EXACT []
+is_a: GO:0044743 ! protein transmembrane import into intracellular organelle
is_a: GO:0070585 ! protein localization to mitochondrion
-is_a: GO:0071806 ! protein transmembrane transport
-is_a: GO:0072594 ! establishment of protein localization to organelle
-property_value: term_tracker_item "/github.com/geneontology/go-ontology/issues/29962" xsd:anyURI
+is_a: GO:0170036 ! import into the mitochondrion
+is_a: GO:7770058 ! mitochondrial protein import pathway
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29962" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
[Term]
id: GO:0030151
@@ -173008,8 +173875,9 @@
synonym: "chaperone regulator activity" EXACT []
is_obsolete: true
consider: GO:0006457
-consider: GO:0051082
+consider: GO:0044183
consider: GO:0051787
+consider: GO:0140309
[Term]
id: GO:0030189
@@ -173020,8 +173888,9 @@
synonym: "chaperone activator activity" EXACT []
is_obsolete: true
consider: GO:0006457
-consider: GO:0051082
+consider: GO:0044183
consider: GO:0051787
+consider: GO:0140309
[Term]
id: GO:0030190
@@ -173032,8 +173901,9 @@
synonym: "chaperone inhibitor activity" EXACT []
is_obsolete: true
consider: GO:0006457
-consider: GO:0051082
+consider: GO:0044183
consider: GO:0051787
+consider: GO:0140309
[Term]
id: GO:0030191
@@ -173044,8 +173914,9 @@
synonym: "Hsp70/Hsc70 protein inhibitor activity" EXACT []
is_obsolete: true
consider: GO:0006457
-consider: GO:0051082
+consider: GO:0044183
consider: GO:0051787
+consider: GO:0140309
[Term]
id: GO:0030192
@@ -173056,8 +173927,9 @@
synonym: "Hsp70/Hsc70 protein regulator activity" EXACT []
is_obsolete: true
consider: GO:0006457
-consider: GO:0051082
+consider: GO:0044183
consider: GO:0051787
+consider: GO:0140309
[Term]
id: GO:0030193
@@ -173988,7 +174860,7 @@
xref: MetaCyc:2.3.1.101-RXN
xref: RHEA:18061
xref: UM-BBD_reactionID:r0346
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.101
property_value: skos:exactMatch RHEA:18061
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -175098,7 +175970,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving fructose 1,6-bisphosphate, also known as FBP. The D enantiomer is a metabolic intermediate in glycolysis and gluconeogenesis." [ISBN:0198506732]
synonym: "fructose 1,6-bisphosphate metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
@@ -175785,7 +176656,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "MAPKKK cascade (mating sensu Fungi)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0030456
@@ -175795,7 +176666,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "activation of MAPK (mating sensu Fungi)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0030457
@@ -175805,7 +176676,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "activation of MAPKK (mating sensu Fungi)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0030458
@@ -175815,7 +176686,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "activation of MAPKKK (mating sensu Fungi)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0030459
@@ -175825,7 +176696,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "inactivation of MAPK (mating sensu Fungi)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0030460
@@ -175835,7 +176706,7 @@
comment: This term was made obsolete because it is a gene product specific term.
synonym: "nuclear translocation of MAPK (mating sensu Fungi)" EXACT []
is_obsolete: true
-replaced_by: GO:0000750
+replaced_by: GO:0071507
[Term]
id: GO:0030463
@@ -177892,12 +178763,11 @@
name: protein-macromolecule adaptor activity
namespace: molecular_function
def: "An adaptor activity 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]
+comment: Note that protein complex scaffolds should use GO:0140378 protein complex scaffold activity.
subset: goslim_chembl
subset: goslim_yeast
synonym: "protein binding, bridging" EXACT []
-synonym: "protein complex scaffold activity" BROAD []
synonym: "protein recruiting activity" RELATED []
-synonym: "protein-containing complex scaffold activity" BROAD []
synonym: "protein-protein adaptor" NARROW []
xref: Reactome:R-HSA-3780997 "PPP1R3C binds to glycogen:GYG2:GYS2"
xref: Reactome:R-HSA-3781001 "EPM2A dimer binds PPP1R3C:phosphoglycogen-GYG1 complex"
@@ -177910,6 +178780,7 @@
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/18655" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19409" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22925" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31444" xsd:anyURI
[Term]
id: GO:0030677
@@ -181692,7 +182563,6 @@
synonym: "thiamine pyrophosphate transport" NARROW []
synonym: "TPP transport" EXACT []
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:0071934 ! thiamine transmembrane transport
@@ -183404,7 +184274,7 @@
name: induction of conjugation upon nutrient starvation
namespace: biological_process
def: "The process in which a cell initiates conjugation with cellular fusion upon starvation for one or more nutrients." [GOC:mah]
-is_a: GO:0010514 ! induction of conjugation with cellular fusion
+is_a: GO:0031139 ! positive regulation of conjugation with cellular fusion
[Term]
id: GO:0031141
@@ -184348,11 +185218,14 @@
[Term]
id: GO:0031249
-name: denatured protein binding
+name: obsolete denatured protein binding
namespace: molecular_function
-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
+def: "OBSOLETE. Binding to a denatured protein." [GOC:mlg]
+comment: The reason for obsoletion is that this binding term should be replaced by an activity term such as protein folding chaperone (GO:0044183) or unfolded protein holdase activity (GO:0140309).
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30962" xsd:anyURI
+is_obsolete: true
+consider: GO:0044183
+consider: GO:0140309
[Term]
id: GO:0031250
@@ -185974,11 +186847,13 @@
[Term]
id: GO:0031388
-name: organic acid phosphorylation
+name: obsolete organic acid phosphorylation
namespace: biological_process
-def: "The process of introducing one or more phosphate groups into an organic acid." [GOC:mah]
-is_a: GO:0006082 ! organic acid metabolic process
-is_a: GO:0016310 ! phosphorylation
+def: "OBSOLETE. The process of introducing one or more phosphate groups into an organic acid." [GOC:mah]
+comment: The reason for obsoletion is that this term was an unnecessary grouping term.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31816" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0008152
[Term]
id: GO:0031389
@@ -186799,7 +187674,6 @@
namespace: biological_process
def: "The directed movement of glycine betaine, N-trimethylglycine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
synonym: "N-trimethylglycine transport" EXACT []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015838 ! amino-acid betaine transport
[Term]
@@ -191110,7 +191984,6 @@
name: pyridoxal transport
namespace: biological_process
def: "The directed movement of pyridoxal into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Pyridoxal, 3-hydroxy-5-(hydroxymethyl)-2-methyl-4-pyridinecarboxaldehyde, is one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate." [GOC:mah]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0031919 ! vitamin B6 transport
@@ -191119,7 +191992,6 @@
name: pyridoxal phosphate transport
namespace: biological_process
def: "The directed movement of pyridoxal phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore; pyridoxal phosphate is pyridoxal phosphorylated at the hydroxymethyl group of C-5, and is the active form of vitamin B6." [GOC:mah]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0031919 ! vitamin B6 transport
@@ -191129,7 +192001,6 @@
name: pyridoxamine transport
namespace: biological_process
def: "The directed movement of pyridoxamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Pyridoxamine, 4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol, is one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate." [GOC:mah]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0031919 ! vitamin B6 transport
@@ -192064,13 +192935,13 @@
[Term]
id: GO:0032005
-name: signal transduction involved in positive regulation of conjugation with cellular fusion
+name: obsolete signal transduction involved in positive regulation of conjugation with cellular fusion
namespace: biological_process
-def: "The series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion." [GOC:mah]
-is_a: GO:0007165 ! signal transduction
-is_a: GO:0031139 ! positive regulation of conjugation with cellular fusion
-intersection_of: GO:0007165 ! signal transduction
-intersection_of: positively_regulates GO:0000747 ! conjugation with cellular fusion
+def: "OBSOLETE. The series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion." [GOC:mah]
+comment: This term was obsoleted because it is a pre-composed term that should be represented as a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31335" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0071507
[Term]
id: GO:0032006
@@ -194366,7 +195237,7 @@
synonym: "GPI-inositol acyltransferase" RELATED []
xref: RHEA:60496
xref: RHEA:83759
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:60496
property_value: skos:narrowMatch RHEA:83759
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30693" xsd:anyURI
@@ -194387,7 +195258,6 @@
name: riboflavin transport
namespace: biological_process
def: "The directed movement of riboflavin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Riboflavin (vitamin B2) is a water-soluble B-complex vitamin, converted in the cell to FMN and FAD, cofactors required for the function of flavoproteins." [GOC:rn, PMID:16204239]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0051180 ! vitamin transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -195040,7 +195910,7 @@
namespace: biological_process
def: "The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone." [GOC:mah, ISBN:0721662544]
synonym: "gonadotrophin secretion" EXACT []
-is_a: GO:0060986 ! endocrine hormone secretion
+is_a: GO:0046879 ! hormone secretion
[Term]
id: GO:0032275
@@ -195542,7 +196412,6 @@
name: alanine transport
namespace: biological_process
def: "The directed movement of alanine, 2-aminopropanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015804 ! neutral amino acid transport
is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -195554,7 +196423,6 @@
alt_id: GO:0090478
def: "The directed movement of L-serine, 2-amino-3-hydroxypropanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
synonym: "serine import" NARROW []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015804 ! neutral amino acid transport
is_a: GO:0046942 ! carboxylic acid transport
is_a: GO:0071705 ! nitrogen compound transport
@@ -195617,7 +196485,7 @@
name: inhibin secretion
namespace: biological_process
def: "The regulated release of an inhibin, either of two glycoproteins (designated A and B), secreted by the gonads and present in seminal plasma and follicular fluid, that inhibit pituitary production of follicle-stimulating hormone." [GOC:mah]
-is_a: GO:0060986 ! endocrine hormone secretion
+is_a: GO:0046879 ! hormone secretion
[Term]
id: GO:0032335
@@ -196649,7 +197517,6 @@
is_a: GO:0043005 ! neuron projection
is_a: GO:0098858 ! actin-based cell projection
relationship: part_of GO:0032421 ! stereocilium bundle
-relationship: part_of GO:0043226 ! organelle
[Term]
id: GO:0032421
@@ -198225,7 +199092,7 @@
name: O-linoleoyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a linoleoyl ((9Z,12Z)-octadeca-9,12-dienoyl) group to an oxygen atom on the acceptor molecule." [GOC:cb]
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0032577
@@ -203023,34 +203890,47 @@
[Term]
id: GO:0032917
-name: polyamine acetylation
+name: obsolete polyamine acetylation
namespace: biological_process
-def: "The modification of polyamines by addition of acetyl groups." [GOC:mlg]
-is_a: GO:0006595 ! polyamine metabolic process
+def: "OBSOLETE. The modification of polyamines by addition of acetyl groups." [GOC:mlg]
+comment: The reason for obsoletion is that this term represents a molecular function.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31741" xsd:anyURI
+is_obsolete: true
+consider: GO:0004145
+consider: GO:0006598
[Term]
id: GO:0032918
-name: spermidine acetylation
+name: obsolete spermidine acetylation
namespace: biological_process
-def: "The modification of spermidine by addition of acetyl groups." [GOC:mlg]
-is_a: GO:0008216 ! spermidine metabolic process
-is_a: GO:0032917 ! polyamine acetylation
+def: "OBSOLETE. The modification of spermidine by addition of acetyl groups." [GOC:mlg]
+comment: The reason for obsoletion is that this term represents a molecular function.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31741" xsd:anyURI
+is_obsolete: true
+consider: GO:0004145
+consider: GO:0046203
[Term]
id: GO:0032919
-name: spermine acetylation
+name: obsolete spermine acetylation
namespace: biological_process
-def: "The modification of spermine by addition of acetyl groups." [GOC:mlg]
-is_a: GO:0008215 ! spermine metabolic process
-is_a: GO:0032917 ! polyamine acetylation
+def: "OBSOLETE. The modification of spermine by addition of acetyl groups." [GOC:mlg]
+comment: The reason for obsoletion is that this term represents a molecular function.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31741" xsd:anyURI
+is_obsolete: true
+consider: GO:0004145
+consider: GO:0046208
[Term]
id: GO:0032920
-name: putrescine acetylation
+name: obsolete putrescine acetylation
namespace: biological_process
-def: "The modification of putrescine by addition of acetyl groups." [GOC:mlg]
-is_a: GO:0009445 ! putrescine metabolic process
-is_a: GO:0032917 ! polyamine acetylation
+def: "OBSOLETE. The modification of putrescine by addition of acetyl groups." [GOC:mlg]
+comment: The reason for obsoletion is that this term represents a molecular function.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31741" xsd:anyURI
+is_obsolete: true
+consider: GO:0004145
+consider: GO:0009447
[Term]
id: GO:0032921
@@ -203808,7 +204688,8 @@
synonym: "insertion of proteins into the mitochondrial membrane from the inner side" EXACT []
synonym: "protein insertion into mitochondrial inner membrane from matrix side" EXACT []
synonym: "protein insertion into mitochondrial membrane from inner side" EXACT []
-is_a: GO:0045039 ! protein insertion into mitochondrial inner membrane
+is_a: GO:0007007 ! inner mitochondrial membrane organization
+is_a: GO:0051204 ! protein insertion into mitochondrial membrane
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25265" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30453" xsd:anyURI
@@ -206254,9 +207135,10 @@
namespace: biological_process
def: "A process in which iron is solubilized by reduction from Fe3+ to Fe2+ via a cell surface reductase and subsequent transport of the iron across the membrane by iron uptake proteins." [GOC:cjm, GOC:mah, PMID:16963626]
synonym: "iron assimilation by reduction and transport" EXACT []
-is_a: GO:0033212 ! iron import into cell
+is_a: GO:0098711 ! iron ion import across plasma membrane
relationship: has_part GO:0000293 ! ferric-chelate reductase activity
relationship: has_part GO:0034755 ! iron ion transmembrane transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31750" xsd:anyURI
[Term]
id: GO:0033217
@@ -206366,46 +207248,54 @@
[Term]
id: GO:0033228
-name: cysteine export across plasma membrane
+name: L-cysteine export across plasma membrane
namespace: biological_process
-def: "The directed movement of cysteine from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:mlg]
+def: "The directed movement of L-cysteine from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:mlg]
synonym: "cysteine export" BROAD []
+synonym: "cysteine export across plasma membrane" BROAD []
+synonym: "L-cysteine export" BROAD []
is_a: GO:0032973 ! amino acid export across plasma membrane
-is_a: GO:1903712 ! cysteine transmembrane transport
+is_a: GO:1903712 ! L-cysteine transmembrane transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27479" xsd:anyURI
[Term]
id: GO:0033229
-name: cysteine transmembrane transporter activity
+name: L-cysteine transmembrane transporter activity
namespace: molecular_function
-def: "Enables the transfer of cysteine from one side of a membrane to the other." [GOC:mah]
+def: "Enables the transfer of L-cysteine from one side of a membrane to the other." [GOC:mah]
+synonym: "cysteine transmembrane transporter activity" BROAD []
is_a: GO:0000099 ! sulfur amino acid transmembrane transporter activity
is_a: GO:0015175 ! neutral L-amino acid transmembrane transporter activity
-relationship: part_of GO:1903712 ! cysteine transmembrane transport
+is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
+relationship: part_of GO:1903712 ! L-cysteine transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17289" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24076" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27479" xsd:anyURI
[Term]
id: GO:0033230
-name: ABC-type cysteine transporter activity
+name: ABC-type L-cysteine transporter activity
namespace: molecular_function
alt_id: GO:0032519
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + L-cysteine(in) = ADP + H+ + L-cysteine(out) + phosphate." [PMID:25837721, PMID:32144203, RHEA:29783]
-synonym: "ATP-dependent cysteine transporter activity" EXACT []
+synonym: "ABC-type cysteine transporter activity" BROAD []
+synonym: "ATP-dependent cysteine transporter activity" BROAD []
synonym: "ATPase-coupled cysteine transmembrane transporter activity" RELATED []
synonym: "ATPase-coupled cysteine transporter activity" RELATED []
synonym: "cysteine exporter" RELATED []
synonym: "cysteine-exporting ATPase activity" RELATED []
-synonym: "cysteine-transporting ATPase activity" EXACT []
+synonym: "cysteine-transporting ATPase activity" BROAD []
xref: MetaCyc:RXN0-3
xref: RHEA:29783
is_a: GO:0015424 ! ABC-type amino acid transporter activity
-is_a: GO:0033229 ! cysteine transmembrane transporter activity
+is_a: GO:0033229 ! L-cysteine transmembrane transporter activity
is_a: GO:0033284 ! ATPase-coupled carboxylic acid transmembrane transporter activity
property_value: skos:exactMatch MetaCyc:RXN0-3
property_value: skos:exactMatch RHEA:29783
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17289" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24076" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27479" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
[Term]
@@ -206909,7 +207799,6 @@
namespace: biological_process
def: "The directed movement of myo-inositol hexakisphosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
synonym: "phytate transport" EXACT []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0033271 ! myo-inositol phosphate transport
[Term]
@@ -207723,10 +208612,15 @@
synonym: "SAM cycle" EXACT []
xref: MetaCyc:PWY-5041
xref: MetyaCyc:PWY-6151
+is_a: GO:0006555 ! L-methionine metabolic process
+is_a: GO:0006575 ! modified amino acid metabolic process
+is_a: GO:0046128 ! purine ribonucleoside metabolic process
is_a: GO:0046500 ! S-adenosylmethionine metabolic process
+is_a: GO:0050667 ! homocysteine metabolic process
property_value: skos:narrowMatch MetaCyc:PWY-5041
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31318" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31634" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31840" xsd:anyURI
[Term]
id: GO:0033354
@@ -208128,59 +209022,65 @@
[Term]
id: GO:0033387
-name: putrescine biosynthetic process from arginine, via ornithine
+name: obsolete putrescine biosynthetic process from arginine, via ornithine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine, via decarboxylation of ornithine." [GOC:mah, MetaCyc:PWY-46]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine, via decarboxylation of ornithine." [GOC:mah, MetaCyc:PWY-46]
+comment: The reason for obsoletion is that this term represents a GO-CAM.
synonym: "putrescine anabolism from ornithine" EXACT []
synonym: "putrescine biosynthesis from ornithine" EXACT []
synonym: "putrescine biosynthetic process from ornithine" EXACT []
synonym: "putrescine formation from ornithine" EXACT []
synonym: "putrescine synthesis from ornithine" EXACT []
-xref: MetaCyc:PWY-46
-is_a: GO:0033388 ! putrescine biosynthetic process from arginine
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009446
[Term]
id: GO:0033388
-name: putrescine biosynthetic process from arginine
+name: obsolete putrescine biosynthetic process from arginine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine." [GOC:mah]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine." [GOC:mah]
+comment: The reason for obsoletion is that this term represents a GO-CAM.
synonym: "putrescine anabolism from arginine" EXACT []
synonym: "putrescine biosynthesis from arginine" EXACT []
synonym: "putrescine formation from arginine" EXACT []
synonym: "putrescine synthesis from arginine" EXACT []
-is_a: GO:0006525 ! arginine metabolic process
-is_a: GO:0009446 ! putrescine biosynthetic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170039 ! proteinogenic amino acid metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009446
[Term]
id: GO:0033389
-name: putrescine biosynthetic process from arginine, via agmatine
+name: obsolete putrescine biosynthetic process from arginine, via agmatine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine via agmatine." [GOC:mah, MetaCyc:PWY-40]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine via agmatine." [GOC:mah, MetaCyc:PWY-40]
+comment: The reason for obsoletion is that this term represents a GO-CAM.
synonym: "putrescine anabolism from arginine, using agmatinase" EXACT []
synonym: "putrescine biosynthesis from arginine, using agmatinase" EXACT []
synonym: "putrescine biosynthetic process from arginine, using agmatinase" EXACT []
synonym: "putrescine formation from arginine, using agmatinase" EXACT []
synonym: "putrescine synthesis from arginine, using agmatinase" EXACT []
-xref: MetaCyc:PWY-40
-is_a: GO:0033388 ! putrescine biosynthetic process from arginine
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009446
[Term]
id: GO:0033390
-name: putrescine biosynthetic process from arginine via N-carbamoylputrescine
+name: obsolete putrescine biosynthetic process from arginine via N-carbamoylputrescine
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine, via the intermediate N-carbamoylputrescine; in this pathway, arginine is converted to agmatine, and agmatine is converted to putrescine in two single enzymatic steps." [GOC:mah, MetaCyc:PWY-43]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine, via the intermediate N-carbamoylputrescine; in this pathway, arginine is converted to agmatine, and agmatine is converted to putrescine in two single enzymatic steps." [GOC:mah, MetaCyc:PWY-43]
+comment: The reason for obsoletion is that this term represents a GO-CAM.
synonym: "putrescine anabolism from arginine via N-carbamoylputrescine" EXACT []
synonym: "putrescine biosynthesis from arginine via N-carbamoylputrescine" EXACT []
synonym: "putrescine formation from arginine via N-carbamoylputrescine" EXACT []
synonym: "putrescine synthesis from arginine via N-carbamoylputrescine" EXACT []
-xref: MetaCyc:PWY-43
-is_a: GO:0033388 ! putrescine biosynthetic process from arginine
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28523" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0009446
[Term]
id: GO:0033391
@@ -209340,7 +210240,6 @@
synonym: "Leloir Pathway" EXACT [PMID:14741191]
xref: MetaCyc:PWY-6317
xref: Reactome:R-HSA-70370 "Galactose catabolism"
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019388 ! galactose catabolic process
is_a: GO:0046434 ! organophosphate catabolic process
is_a: GO:1901136 ! carbohydrate derivative catabolic process
@@ -210524,7 +211423,7 @@
id: GO:0033608
name: formyl-CoA transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: formyl-CoA + oxalate = formate + oxalyl-CoA." [EC:2.8.3.16, RHEA:16545]
+def: "Catalysis of the reaction: formyl-CoA + oxalate = formate + oxalyl-CoA." [RHEA:16545]
synonym: "formyl-CoA oxalate CoA-transferase activity" RELATED [EC:2.8.3.16]
synonym: "formyl-CoA:oxalate CoA-transferase activity" RELATED [EC:2.8.3.16]
synonym: "formyl-coenzyme A transferase activity" RELATED [EC:2.8.3.16]
@@ -211874,6 +212773,8 @@
xref: RHEA:72535
xref: RHEA:72539
xref: RHEA:76671
+xref: RHEA:76967
+xref: RHEA:80815
xref: RHEA:80823
xref: RHEA:81423
is_a: GO:0004030 ! aldehyde dehydrogenase [NAD(P)+] activity
@@ -211895,6 +212796,8 @@
property_value: skos:narrowMatch RHEA:72535
property_value: skos:narrowMatch RHEA:72539
property_value: skos:narrowMatch RHEA:76671
+property_value: skos:narrowMatch RHEA:76967
+property_value: skos:narrowMatch RHEA:80815
property_value: skos:narrowMatch RHEA:80823
property_value: skos:narrowMatch RHEA:81423
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29544" xsd:anyURI
@@ -213115,12 +214018,14 @@
xref: KEGG_REACTION:R07229
xref: MetaCyc:RXN0-2101
xref: RHEA:14029
+xref: RHEA:34939
xref: RHEA:51636
xref: RHEA:80603
xref: UM-BBD_reactionID:r0828
is_a: GO:0016491 ! oxidoreductase activity
property_value: skos:exactMatch EC:1.97.1.9
property_value: skos:exactMatch RHEA:14029
+property_value: skos:narrowMatch RHEA:34939
property_value: skos:narrowMatch RHEA:51636
property_value: skos:narrowMatch RHEA:80603
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -213389,7 +214294,7 @@
xref: KEGG_REACTION:R03064
xref: MetaCyc:2.3.1.175-RXN
xref: RHEA:23860
-is_a: GO:0016408 ! C-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.175
property_value: skos:exactMatch RHEA:23860
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -213408,7 +214313,7 @@
synonym: "sterol carrier protein-X" RELATED [EC:2.3.1.176]
xref: MetaCyc:2.3.1.176-RXN
xref: RHEA:16865
-is_a: GO:0016408 ! C-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:broadMatch EC:2.3.1.176
property_value: skos:exactMatch RHEA:16865
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
@@ -214403,7 +215308,7 @@
name: succinyl-CoA:(R)-benzylsuccinate CoA-transferase activity
namespace: molecular_function
alt_id: GO:0018728
-def: "Catalysis of the reaction: (R)-2-benzylsuccinate + succinyl-CoA = (R)-2-benzylsuccinyl-CoA + succinate." [EC:2.8.3.15, RHEA:16469]
+def: "Catalysis of the reaction: (R)-2-benzylsuccinate + succinyl-CoA = (R)-2-benzylsuccinyl-CoA + succinate." [RHEA:16469]
synonym: "benzylsuccinate CoA-transferase activity" RELATED [EC:2.8.3.15]
synonym: "succinyl-CoA:(R)-2-benzylsuccinate CoA-transferase activity" RELATED [EC:2.8.3.15]
synonym: "succinyl-CoA:benzylsuccinate CoA-transferase activity" EXACT []
@@ -219104,7 +220009,6 @@
def: "The directed movement of ethanolamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ethanolamine (2-aminoethanol, monoethanolamine) is an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids, such as phosphatidylethanolamine." [GOC:rn, PMID:3514579]
synonym: "2-aminoethanol transport" EXACT []
synonym: "monoethanolamine transport" EXACT []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015837 ! amine transport
is_a: GO:0015850 ! organic hydroxy compound transport
@@ -219630,8 +220534,10 @@
synonym: "kynurenic acid biosynthesis" EXACT []
synonym: "kynurenic acid formation" RELATED []
synonym: "kynurenic acid synthesis" EXACT []
+synonym: "kynurenine pathway" BROAD []
is_a: GO:0034275 ! kynurenic acid metabolic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31588" xsd:anyURI
[Term]
id: GO:0034277
@@ -220061,7 +220967,7 @@
synonym: "acyl-coenzymeA:ethanol O-acyltransferase activity" NARROW []
synonym: "AEATase activity" NARROW []
synonym: "alcohol acyltransferase activity" EXACT []
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0034319
@@ -220456,6 +221362,7 @@
synonym: "'de novo' NAD biosynthetic process from L-tryptophan" EXACT []
synonym: "'de novo' NAD biosynthetic process from tryptophan" BROAD []
synonym: "de novo NAD biosynthetic process from tryptophan" RELATED []
+synonym: "kynurenine pathway" BROAD []
xref: MetaCyc:NADSYN-PWY
xref: MetaCyc:PWY-5653
is_a: GO:0006568 ! L-tryptophan metabolic process
@@ -220464,6 +221371,7 @@
property_value: skos:narrowMatch MetaCyc:PWY-5653
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29050" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29666" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31588" xsd:anyURI
[Term]
id: GO:0034355
@@ -222830,7 +223738,6 @@
def: "Enables the transfer of L-hydroxyproline from one side of a membrane to the other." [GOC:mah, PMID:14502423]
synonym: "4-hydroxyproline transmembrane transporter activity" BROAD []
xref: Reactome:R-HSA-6784213 "Unknown hydroxyproline carrier transports cytosolic HPRO into the mitochondrial matrix"
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015179 ! L-amino acid transmembrane transporter activity
is_a: GO:0072349 ! modified amino acid transmembrane transporter activity
relationship: part_of GO:0034589 ! hydroxyproline transport
@@ -223232,7 +224139,6 @@
name: glutathione transport
namespace: biological_process
def: "The directed movement of glutathione, the tripeptide glutamylcysteinylglycine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0042939 ! tripeptide transport
is_a: GO:0072337 ! modified amino acid transport
is_a: GO:0072348 ! sulfur compound transport
@@ -229604,7 +230510,7 @@
name: regulation of dephosphorylation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of removal of phosphate groups from a molecule." [GOC:bf]
-is_a: GO:0051174 ! regulation of phosphorus metabolic process
+is_a: GO:0019222 ! regulation of metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0016311 ! dephosphorylation
relationship: regulates GO:0016311 ! dephosphorylation
@@ -231122,7 +232028,6 @@
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 []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015717 ! triose phosphate transport
is_a: GO:0055085 ! transmembrane transport
created_by: bf
@@ -233981,6 +234886,7 @@
def: "The process in which a tricarboxylic acid is transported across a membrane." [GOC:vw]
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "tricarboxylic acid membrane transport" EXACT []
+is_a: GO:0006842 ! tricarboxylic acid transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
created_by: bf
creation_date: 2011-02-08T02:37:31Z
@@ -235892,13 +236798,16 @@
[Term]
id: GO:0035842
-name: old cell tip after activation of bipolar cell growth
+name: obsolete old cell tip after activation of bipolar cell growth
namespace: cellular_component
-def: "A cell tip which has existed for at least one complete cell cycle, and at which polarized growth occurs, which is part of a cell that has activated bipolar cell growth (i.e. in which new end take-off, NETO, has taken place). For example, in fission yeast the cell end that existed prior to cell division grows immediately after division, and contains a distinctive complement of proteins including actin cytoskeletal structures." [GOC:expert_jd, GOC:mah]
+def: "OBSOLETE. A cell tip which has existed for at least one complete cell cycle, and at which polarized growth occurs, which is part of a cell that has activated bipolar cell growth (i.e. in which new end take-off, NETO, has taken place). For example, in fission yeast the cell end that existed prior to cell division grows immediately after division, and contains a distinctive complement of proteins including actin cytoskeletal structures." [GOC:expert_jd, GOC:mah]
+comment: This term was obsoleted because the parent process, activation of bipolar cell growth, GO:0051519, was obsoleted.
synonym: "post-NETO old cell end" EXACT [GOC:mah]
synonym: "post-NETO old cell tip" EXACT [GOC:mah]
synonym: "post-new end take-off old cell tip" EXACT [GOC:mah]
-is_a: GO:0035840 ! old growing cell tip
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31746" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0035840
created_by: bf
creation_date: 2011-05-06T01:37:23Z
@@ -236148,6 +237057,7 @@
synonym: "dITP catabolism" EXACT [GOC:bf]
synonym: "dITP degradation" EXACT [GOC:bf]
is_a: GO:0009155 ! purine deoxyribonucleotide catabolic process
+is_a: GO:0009204 ! deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009217 ! purine deoxyribonucleoside triphosphate catabolic process
created_by: bf
creation_date: 2011-05-25T02:55:21Z
@@ -236580,7 +237490,7 @@
synonym: "parathormone secretion" EXACT [PR:000013429]
synonym: "parathyrin secretion" EXACT [PR:000013429]
synonym: "PTH secretion" EXACT [PMID:12171519, PR:000013429]
-is_a: GO:0060986 ! endocrine hormone secretion
+is_a: GO:0046879 ! hormone secretion
created_by: bf
creation_date: 2011-06-22T09:28:54Z
@@ -236944,7 +237854,7 @@
name: steroid hormone secretion
namespace: biological_process
def: "The regulated release of any steroid that acts as a hormone into the circulatory system." [GOC:sl]
-is_a: GO:0060986 ! endocrine hormone secretion
+is_a: GO:0046879 ! hormone secretion
is_a: GO:0140353 ! lipid export from cell
created_by: bf
creation_date: 2011-07-20T01:01:00Z
@@ -242661,12 +243571,14 @@
xref: KEGG_REACTION:R09494
xref: MetaCyc:FORMATEDEHYDROG-RXN
xref: RHEA:29063
+xref: RHEA:29067
xref: RHEA:29071
xref: RHEA:48592
is_a: GO:0033695 ! oxidoreductase activity, acting on CH or CH2 groups, quinone or similar compound as acceptor
property_value: skos:exactMatch EC:1.17.5.3
property_value: skos:exactMatch RHEA:48592
property_value: skos:narrowMatch RHEA:29063
+property_value: skos:narrowMatch RHEA:29067
property_value: skos:narrowMatch RHEA:29071
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21412" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -244053,10 +244965,14 @@
[Term]
id: GO:0036506
-name: maintenance of unfolded protein
+name: obsolete maintenance of unfolded protein
namespace: biological_process
-def: "Maintaining a protein in an unfolded, soluble state." [GOC:bf, GOC:BHF, GOC:nc, GOC:PARL, PMID:21636303]
-is_a: GO:0031647 ! regulation of protein stability
+def: "OBSOLETE. Maintaining a protein in an unfolded, soluble state." [GOC:bf, GOC:BHF, GOC:nc, GOC:PARL, PMID:21636303]
+comment: The reason for obsoletion is that this term describes a molecular function (holdase activity) rather than a biological process.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31758" xsd:anyURI
+is_obsolete: true
+consider: GO:0140309
+consider: GO:0140597
created_by: bf
creation_date: 2015-06-11T10:17:36Z
@@ -245141,7 +246057,7 @@
synonym: "nitric oxide-cGMP-mediated signaling pathway" EXACT []
synonym: "nitric oxide-cGMP-mediated signalling pathway" EXACT [GOC:mah]
synonym: "NO-cGMP signaling pathway" EXACT [PMID:22019632]
-is_a: GO:0007263 ! nitric oxide mediated signal transduction
+is_a: GO:0141124 ! intracellular signaling cassette
created_by: bf
creation_date: 2012-01-10T05:32:39Z
@@ -248776,9 +249692,9 @@
name: RNA translocase activity
namespace: molecular_function
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 ! ATP-dependent activity, acting on RNA
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21612" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31772" xsd:anyURI
created_by: bf
creation_date: 2012-08-06T13:24:51Z
@@ -250781,9 +251697,15 @@
xref: Reactome:R-HSA-5216234 "PRMT5:pT5-WDR77 methylates arginine-4 of histone H2A (H2AR3)"
xref: Reactome:R-HSA-9822583 "METTL23 dimethylates histone H3.3 arginine-17 (arginine-18 in the preprotein)"
xref: RHEA:10024
+xref: RHEA:60312
+xref: RHEA:67112
+xref: RHEA:67808
is_a: GO:0008276 ! protein methyltransferase activity
is_a: GO:0140993 ! histone modifying activity
property_value: skos:narrowMatch RHEA:10024
+property_value: skos:narrowMatch RHEA:60312
+property_value: skos:narrowMatch RHEA:67112
+property_value: skos:narrowMatch RHEA:67808
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22588" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24397" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29483" xsd:anyURI
@@ -253372,7 +254294,7 @@
def: "Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule." [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_obsoletion_candidate
-is_a: GO:0051174 ! regulation of phosphorus metabolic process
+is_a: GO:0019222 ! regulation of metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0016310 ! phosphorylation
relationship: regulates GO:0016310 ! phosphorylation
@@ -253730,7 +254652,6 @@
synonym: "thiamine pyrophosphate metabolism" EXACT []
synonym: "TPP metabolic process" EXACT []
synonym: "TPP metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:0042723 ! thiamine-containing compound metabolic process
@@ -254177,7 +255098,6 @@
synonym: "phosphagen biosynthesis" EXACT []
synonym: "phosphagen formation" EXACT []
synonym: "phosphagen synthesis" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0042398 ! modified amino acid biosynthetic process
is_a: GO:0090407 ! organophosphate biosynthetic process
@@ -254189,7 +255109,6 @@
synonym: "phosphagen breakdown" EXACT []
synonym: "phosphagen catabolism" EXACT []
synonym: "phosphagen degradation" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0042219 ! modified amino acid catabolic process
is_a: GO:0046434 ! organophosphate catabolic process
@@ -256260,7 +257179,7 @@
synonym: "PHB metabolic process" EXACT []
synonym: "PHB metabolism" EXACT []
synonym: "poly-hydroxybutyrate metabolism" EXACT []
-is_a: GO:1901440 ! poly(hydroxyalkanoate) metabolic process
+is_a: GO:0008152 ! metabolic process
[Term]
id: GO:0042619
@@ -256273,8 +257192,8 @@
synonym: "poly-hydroxybutyrate biosynthesis" EXACT []
synonym: "poly-hydroxybutyrate formation" EXACT []
synonym: "poly-hydroxybutyrate synthesis" EXACT []
+is_a: GO:0009058 ! biosynthetic process
is_a: GO:0042618 ! poly-hydroxybutyrate metabolic process
-is_a: GO:1901441 ! poly(hydroxyalkanoate) biosynthetic process
[Term]
id: GO:0042620
@@ -258409,7 +259328,9 @@
def: "The chemical reactions and pathways involving any of the vitamin B6 compounds: pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate." [GOC:jl, PMID:30037155, PMID:30671974]
synonym: "vitamin B6 metabolism" EXACT []
xref: Reactome:R-HSA-964975 "Vitamin B6 activation to pyridoxal phosphate"
+is_a: GO:0006766 ! vitamin metabolic process
is_a: GO:0072524 ! pyridine-containing compound metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31855" xsd:anyURI
[Term]
id: GO:0042817
@@ -258476,7 +259397,6 @@
synonym: "active vitamin B6 metabolism" EXACT []
synonym: "pyridoxal phosphate metabolism" EXACT []
is_a: GO:0006081 ! aldehyde metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:0042816 ! vitamin B6 metabolic process
@@ -258577,7 +259497,7 @@
synonym: "saccharate metabolic process" EXACT []
synonym: "saccharate metabolism" EXACT []
is_a: GO:0005975 ! carbohydrate metabolic process
-is_a: GO:0043648 ! dicarboxylic acid metabolic process
+is_a: GO:0019752 ! carboxylic acid metabolic process
[Term]
id: GO:0042837
@@ -258591,7 +259511,7 @@
synonym: "saccharate biosynthesis" EXACT []
synonym: "saccharate biosynthetic process" EXACT []
is_a: GO:0016051 ! carbohydrate biosynthetic process
-is_a: GO:0019393 ! glucarate biosynthetic process
+is_a: GO:0019578 ! aldaric acid biosynthetic process
is_a: GO:0042836 ! D-glucarate metabolic process
[Term]
@@ -259034,7 +259954,6 @@
namespace: biological_process
def: "The process in which aldarate is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:curators]
synonym: "aldarate transport" RELATED []
-is_a: GO:0006835 ! dicarboxylic acid transport
is_a: GO:1905039 ! carboxylic acid transmembrane transport
[Term]
@@ -259085,7 +260004,6 @@
name: D-glucarate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of D-glucarate, the D-enantiomer of glucarate, from one side of a membrane to the other." [GOC:jl, GOC:jsg, GOC:mah, GOC:mtg_transport, ISBN:0198506732, ISBN:0815340729]
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
is_a: GO:0042876 ! aldarate transmembrane transporter activity
relationship: part_of GO:0042870 ! D-glucarate transmembrane transport
@@ -259095,7 +260013,7 @@
name: aldonate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of aldonate from one side of a membrane to the other." [GOC:jl, GOC:mtg_transport, ISBN:0815340729]
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
relationship: part_of GO:0042873 ! aldonate transmembrane transport
[Term]
@@ -259129,13 +260047,13 @@
[Term]
id: GO:0042883
-name: cysteine transport
+name: L-cysteine transport
namespace: biological_process
-def: "The directed movement of cysteine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732]
-synonym: "L-cysteine transport" NARROW []
+def: "The directed movement of L-cysteine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732]
+synonym: "cysteine transport" BROAD []
is_a: GO:0000101 ! sulfur amino acid transport
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015804 ! neutral amino acid transport
+is_a: GO:0015807 ! L-amino acid transport
[Term]
id: GO:0042884
@@ -259447,7 +260365,6 @@
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." [PMID:31802112]
synonym: "alkanesulfonate transport" BROAD []
synonym: "alkanesulphonate transport" BROAD []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015849 ! organic acid transport
is_a: GO:0055085 ! transmembrane transport
is_a: GO:0072348 ! sulfur compound transport
@@ -259508,8 +260425,8 @@
namespace: molecular_function
def: "Enables the directed movement of benzoate, the anion of benzoic acid (benzenecarboxylic acid) from one side of a membrane to the other." [GOC:jl, ISBN:0721662544]
synonym: "benzoate transporter activity" RELATED []
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0042910 ! xenobiotic transmembrane transporter activity
-is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
relationship: part_of GO:0042919 ! benzoate transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27521" xsd:anyURI
@@ -259549,7 +260466,6 @@
namespace: biological_process
def: "The directed movement of the siderochrome enterobactin, a cyclic trimer of 2, 3 dihydroxybenzoylserine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl]
synonym: "enterochelin transport" EXACT []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0015891 ! siderophore transport
@@ -259581,9 +260497,9 @@
namespace: molecular_function
def: "Enables the directed movement of the siderophore chrysobactin (alpha-N-(2,3-dihydroxybenzoyl)-D-lysyl-L-serine) from one side of a membrane to the other." [GOC:jl, PMID:8837459]
synonym: "chrysobactin transporter activity" RELATED []
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015343 ! siderophore-iron transmembrane transporter activity
is_a: GO:0015665 ! alcohol transmembrane transporter activity
+is_a: GO:0046943 ! carboxylic acid transmembrane transporter activity
is_a: GO:0071916 ! dipeptide transmembrane transporter activity
relationship: part_of GO:0042932 ! chrysobactin transport
@@ -262376,7 +263292,6 @@
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:0071705 ! nitrogen compound transport
is_a: GO:1901656 ! glycoside transport
@@ -262738,7 +263653,7 @@
name: sodium-dependent organic anion transport
namespace: biological_process
def: "The directed, sodium-dependent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators]
-is_a: GO:0015711 ! organic anion transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0043252
@@ -262746,7 +263661,7 @@
namespace: biological_process
def: "The directed, sodium-independent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:curators]
xref: Reactome:R-HSA-879518 "Organic anion transport by SLCO transporters"
-is_a: GO:0015711 ! organic anion transport
+is_a: GO:0055085 ! transmembrane transport
[Term]
id: GO:0043253
@@ -264862,13 +265777,14 @@
synonym: "oxo acid metabolic process" EXACT []
synonym: "oxo acid metabolism" EXACT []
synonym: "oxoacid metabolism" EXACT []
-is_a: GO:0006082 ! organic acid metabolic process
+is_a: GO:0044281 ! small molecule metabolic process
[Term]
id: GO:0043438
-name: acetoacetic acid metabolic process
+name: obsolete acetoacetic acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving acetoacetic acid, 3-oxobutanoic acid; the empirical formula is C4H6O3 or CH3COCH2COOH." [Wikipedia:Acetoacetic_acid]
+def: "OBSOLETE. The chemical reactions and pathways involving acetoacetic acid, 3-oxobutanoic acid; the empirical formula is C4H6O3 or CH3COCH2COOH." [Wikipedia:Acetoacetic_acid]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "3-oxobutanoate metabolic process" EXACT []
synonym: "3-oxobutanoate metabolism" EXACT []
synonym: "3-oxobutanoic acid metabolic process" EXACT []
@@ -264882,33 +265798,35 @@
synonym: "beta-ketobutyric acid metabolism" EXACT []
synonym: "diacetic acid metabolic process" EXACT []
synonym: "diacetic acid metabolism" EXACT []
-is_a: GO:0046459 ! short-chain fatty acid metabolic process
-is_a: GO:1902224 ! ketone body metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31806" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0043441
-name: acetoacetic acid biosynthetic process
+name: obsolete acetoacetic acid biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of acetoacetic acid, a beta-keto acid of the keto acid group, empirical formula is C4H6O3 or CH3COCH2COOH." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of acetoacetic acid, a beta-keto acid of the keto acid group, empirical formula is C4H6O3 or CH3COCH2COOH." [GOC:jl]
+comment: This term was obsoleted because it represents a specific substrate of ketone body biosynthetic process ; GO:0046951.
synonym: "acetoacetic acid anabolism" EXACT []
synonym: "acetoacetic acid biosynthesis" EXACT []
synonym: "acetoacetic acid formation" EXACT []
synonym: "acetoacetic acid synthesis" EXACT []
-is_a: GO:0043438 ! acetoacetic acid metabolic process
-is_a: GO:0046951 ! ketone body biosynthetic process
-is_a: GO:0051790 ! short-chain fatty acid biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31806" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0046951
[Term]
id: GO:0043442
-name: acetoacetic acid catabolic process
+name: obsolete acetoacetic acid catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of acetoacetic acid, a beta-keto acid of the keto acid group, empirical formula is C4H6O3 or CH3COCH2COOH." [GOC:jl]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of acetoacetic acid, a beta-keto acid of the keto acid group, empirical formula is C4H6O3 or CH3COCH2COOH." [GOC:jl]
+comment: This term was obsoleted because it represents a specific substrate of \nketone body catabolic process ; GO:0046952.
synonym: "acetoacetic acid breakdown" EXACT []
synonym: "acetoacetic acid catabolism" EXACT []
synonym: "acetoacetic acid degradation" EXACT []
-is_a: GO:0019626 ! short-chain fatty acid catabolic process
-is_a: GO:0043438 ! acetoacetic acid metabolic process
-is_a: GO:0046952 ! ketone body catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31806" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0046952
[Term]
id: GO:0043443
@@ -266071,7 +266989,6 @@
synonym: "Moco metabolic process" EXACT []
synonym: "Moco metabolism" EXACT []
synonym: "molybdopterin cofactor metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:0051189 ! prosthetic group metabolic process
@@ -267149,7 +268066,6 @@
synonym: "myo-inositol phosphate metabolic process" NARROW []
synonym: "myo-inositol phosphate metabolism" NARROW []
xref: Reactome:R-HSA-1483249 "Inositol phosphate metabolism"
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:0019751 ! polyol metabolic process
@@ -267743,12 +268659,17 @@
[Term]
id: GO:0043712
-name: 2-hydroxyisocaproate CoA-transferase activity
+name: (R)-2-hydroxy-4-methylpentanoate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-2-hydroxyisocaproate + isocaproyl-CoA = (R)-2-hydroxyisocaproyl-CoA + isocaproate." [PMID:16957230]
+def: "Catalysis of the reaction: 4-methylpentanoyl-CoA + (2R)-hydroxy-4-methylpentanoate = (R)-2-hydroxy-4-methylpentanoyl-CoA + 4-methylpentanoate." [PMID:16957230, RHEA:49440]
synonym: "(R)-2-hydroxyisocaproate CoA transferase activity" EXACT []
-synonym: "(R)-2-hydroxyisocaproate CoA-transferase activity" EXACT []
+synonym: "2-hydroxyisocaproate CoA-transferase activity" EXACT []
+synonym: "https://github.com/geneontology/go-ontology/issues/31862" EXACT []
+xref: EC:2.8.3.24
+xref: RHEA:49440
is_a: GO:0008410 ! CoA-transferase activity
+property_value: skos:exactMatch EC:2.8.3.24
+property_value: skos:exactMatch RHEA:49440
[Term]
id: GO:0043713
@@ -267863,7 +268784,7 @@
id: GO:0043721
name: 4-hydroxybutanoyl-CoA dehydratase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 4-hydroxybutanoyl-CoA = vinylacetyl-CoA + H2O." [EC:4.2.1.120]
+def: "Catalysis of the reaction: 4-hydroxybutanoyl-CoA = (2E)-butenoyl-CoA + H2O." [RHEA:26530]
synonym: "4-hydroxybutanoyl-CoA hydro-lyase" EXACT []
synonym: "4-hydroxybutyryl-CoA dehydratase activity" EXACT []
synonym: "gamma-hydroxybutanoyl-CoA dehydratase activity" EXACT []
@@ -268482,14 +269403,30 @@
xref: MetaCyc:RXN-11046
xref: MetaCyc:RXN-9191
xref: RHEA:26466
+xref: RHEA:30063
+xref: RHEA:33255
xref: RHEA:42640
+xref: RHEA:44776
+xref: RHEA:44780
+xref: RHEA:44784
+xref: RHEA:44788
+xref: RHEA:44792
+xref: RHEA:44796
is_a: GO:0008168 ! methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.163
property_value: skos:exactMatch MetaCyc:RXN-11046
property_value: skos:narrowMatch MetaCyc:ADOMET-DMK-METHYLTRANSFER-RXN
property_value: skos:narrowMatch MetaCyc:RXN-9191
property_value: skos:narrowMatch RHEA:26466
+property_value: skos:narrowMatch RHEA:30063
+property_value: skos:narrowMatch RHEA:33255
property_value: skos:narrowMatch RHEA:42640
+property_value: skos:narrowMatch RHEA:44776
+property_value: skos:narrowMatch RHEA:44780
+property_value: skos:narrowMatch RHEA:44784
+property_value: skos:narrowMatch RHEA:44788
+property_value: skos:narrowMatch RHEA:44792
+property_value: skos:narrowMatch RHEA:44796
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -268663,7 +269600,7 @@
id: GO:0043785
name: cinnamoyl-CoA:phenyllactate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (R)-3-phenyllactate + [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonatooxy)oxolan-2-yl]methyl {[(3R)-3-hydroxy-2,2-dimethyl-3-({2-[(2-{[(2E)-3-phenylprop-2-enoyl]sulfanyl}ethyl)carbamoyl]ethyl}carbamoyl)propyl phosphonato]oxy}phosphonate = (R)-3-phenyllactoyl-CoA + trans-cinnamate." [EC:2.8.3.17, RHEA:15601]
+def: "Catalysis of the reaction: (E)-cinnamoyl-CoA + (R)-3-phenyllactate = (R)-3-phenyllactoyl-CoA + (E)-cinnamate." [RHEA:15601]
synonym: "(E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase activity" EXACT []
synonym: "FldA" RELATED []
xref: EC:2.8.3.17
@@ -268973,7 +269910,7 @@
name: lyso-ornithine lipid acyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: lyso-ornithine lipid + acyl-[acyl-carrier protein] = ornithine lipid + [acyl-carrier protein]." [PMID:15341653]
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
[Term]
id: GO:0043810
@@ -268984,7 +269921,7 @@
synonym: "ornithine-acyl[acyl carrier protein] N-acyltransferase activity" EXACT []
xref: EC:2.3.2.30
xref: RHEA:20633
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
relationship: part_of GO:0140371 ! ornithine lipid biosynthetic process
property_value: skos:exactMatch EC:2.3.2.30
property_value: skos:exactMatch RHEA:20633
@@ -269151,7 +270088,7 @@
id: GO:0043821
name: propionyl-CoA:succinate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: succinate + propionyl-CoA = succinyl-CoA + propionate." [PMID:10769117]
+def: "Catalysis of the reaction: succinate + propionyl-CoA = succinyl-CoA + propionate." [PMID:10769117, RHEA:28010]
synonym: "propionyl-CoA succinate CoA-transferase activity" EXACT []
synonym: "propionyl-CoA:succinate CoA transferase activity" EXACT []
xref: MetaCyc:RXN0-268
@@ -271016,7 +271953,7 @@
id: GO:0043961
name: succinyl-CoA:(R)-citramalate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: succinyl-CoA + (R)-citramalate = succinate + (R)-citramalyl-CoA." [GOC:jl, PMID:17259315]
+def: "Catalysis of the reaction: succinyl-CoA + (R)-citramalate = succinate + (R)-citramalyl-CoA." [PMID:17259315, RHEA:38279]
synonym: "L-carnitine dehydratase/bile acid-inducible protein F" RELATED []
synonym: "succinyl-CoA:(R)-citramalate CoA transferase activity" EXACT []
synonym: "succinyl-CoA:R-citramalate CoA transferase" EXACT []
@@ -272625,10 +273562,14 @@
id: GO:0044104
name: 2,5-dioxovalerate dehydrogenase (NAD+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,5-dioxopentanoate + NAD+ + H2O = 2-oxoglutarate + NADH + H+." [PMID:16835232, PMID:17202142]
+def: "Catalysis of the reaction: 2,5-dioxopentanoate + NAD+ + H2O = 2-oxoglutarate + NADH + 2 H+." [PMID:16835232, PMID:17202142, RHEA:47152]
synonym: "2,5-dioxopentanoate dehydrogenase (NAD+) activity" EXACT []
synonym: "2,5-dioxopentanoate:NAD+ 5-oxidoreductase activity" EXACT []
-is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
+xref: MetaCyc:RXN-8775
+xref: RHEA:47152
+is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
+property_value: skos:exactMatch RHEA:47152
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31862" xsd:anyURI
created_by: jl
creation_date: 2009-07-09T04:15:14Z
@@ -273385,7 +274326,6 @@
xref: Reactome:R-HSA-9865893 "MT-CYB is translated"
xref: Reactome:R-HSA-9866253 "apo-UQCRFS1 binds LYRM7"
is_a: GO:0003674 ! molecular_function
-relationship: has_part GO:0051082 ! unfolded protein binding
relationship: part_of GO:0006457 ! protein folding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30552" xsd:anyURI
created_by: jl
@@ -278889,9 +279829,19 @@
id: GO:0044688
name: 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate phosphodiesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate + H2O = 7,8-dihydroneopterin 3'-phosphate + H+." [GOC:mengo_curators, PMID:19746965]
+def: "Catalysis of the reaction: 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate + H2O = 7,8-dihydroneopterin 3'-phosphate or 7,8-dihydroneopterin 2'-phosphate + H+." [EC:3.1.4.56]
+xref: EC:3.1.4.56
+xref: MetaCyc:RXN-12356
+xref: MetaCyc:RXN-12357 {xref="skos:narrowMatch"}
+xref: RHEA:35799
+xref: RHEA:35803
is_a: GO:0008081 ! phosphoric diester hydrolase activity
relationship: part_of GO:2001116 ! methanopterin-containing compound biosynthetic process
+property_value: skos:exactMatch EC:3.1.4.56
+property_value: skos:narrowMatch MetaCyc:RXN-12356
+property_value: skos:narrowMatch RHEA:35799
+property_value: skos:narrowMatch RHEA:35803
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31862" xsd:anyURI
created_by: jl
creation_date: 2012-08-15T14:28:30Z
@@ -281170,9 +282120,10 @@
synonym: "protein import into mitochondrial inner membrane" EXACT []
synonym: "protein transport into mitochondrial inner membrane" EXACT []
is_a: GO:0007007 ! inner mitochondrial membrane organization
-is_a: GO:0051204 ! protein insertion into mitochondrial membrane
+is_a: GO:7770058 ! mitochondrial protein import pathway
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15800" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29962" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
[Term]
id: GO:0045040
@@ -281193,18 +282144,16 @@
namespace: biological_process
alt_id: GO:0045043
alt_id: GO:0045044
-def: "The import of proteins into the space between the inner and outer mitochondrial membranes." [ISBN:0716731363]
+def: "The import of proteins from the cytosol across the outer mitochondrial membrane into the intermembrane space." [ISBN:0716731363]
synonym: "mitochondrial intermembrane space protein import" EXACT []
synonym: "protein import into mitochondrial IMS" EXACT []
synonym: "protein import into mitochondrial intermembrane space, direct" NARROW [GOC:mcc]
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:0010496 ! intercellular transport
-is_a: GO:0070585 ! protein localization to mitochondrion
-is_a: GO:0071806 ! protein transmembrane transport
-is_a: GO:0072594 ! establishment of protein localization to organelle
+is_a: GO:7770058 ! mitochondrial protein import pathway
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29962" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
[Term]
id: GO:0045042
@@ -283622,6 +284571,7 @@
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]
id: GO:0045276
@@ -283653,6 +284603,7 @@
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
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27727" xsd:anyURI
[Term]
@@ -283964,8 +284915,10 @@
synonym: "nor-spermidine biosynthesis" EXACT []
synonym: "nor-spermidine formation" EXACT []
synonym: "nor-spermidine synthesis" EXACT []
+xref: MetaCyc:PWY-6562
is_a: GO:0006596 ! polyamine biosynthetic process
is_a: GO:0046204 ! nor-spermidine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0045313
@@ -284621,7 +285574,7 @@
namespace: biological_process
def: "The regulated release of juvenile hormones, 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:curators, ISBN:0198547684]
is_a: GO:0046865 ! terpenoid transport
-is_a: GO:0060986 ! endocrine hormone secretion
+is_a: GO:0046879 ! hormone secretion
is_a: GO:0140353 ! lipid export from cell
[Term]
@@ -291251,7 +292204,7 @@
synonym: "downregulation of phosphate metabolic process" EXACT []
synonym: "inhibition of phosphate metabolic process" NARROW []
synonym: "negative regulation of phosphate metabolism" EXACT []
-is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
+is_a: GO:0009892 ! negative regulation of metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0006796 ! phosphate-containing compound metabolic process
relationship: negatively_regulates GO:0006796 ! phosphate-containing compound metabolic process
@@ -291267,7 +292220,7 @@
synonym: "up regulation of phosphate metabolic process" EXACT []
synonym: "up-regulation of phosphate metabolic process" EXACT []
synonym: "upregulation of phosphate metabolic process" EXACT []
-is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
+is_a: GO:0009893 ! positive regulation of metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0006796 ! phosphate-containing compound metabolic process
relationship: positively_regulates GO:0006796 ! phosphate-containing compound metabolic process
@@ -291963,8 +292916,8 @@
synonym: "inhibition of nucleotide metabolic process" NARROW []
synonym: "negative regulation of nucleotide metabolism" EXACT []
is_a: GO:0006140 ! regulation of nucleotide metabolic process
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0009117 ! nucleotide metabolic process
@@ -291982,7 +292935,7 @@
synonym: "up-regulation of nucleotide metabolic process" EXACT []
synonym: "upregulation of nucleotide metabolic process" EXACT []
is_a: GO:0006140 ! regulation of nucleotide metabolic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0009117 ! nucleotide metabolic process
@@ -292985,6 +293938,7 @@
synonym: "dADP degradation" EXACT []
is_a: GO:0009155 ! purine deoxyribonucleotide catabolic process
is_a: GO:0009184 ! purine deoxyribonucleoside diphosphate catabolic process
+is_a: GO:0009192 ! deoxyribonucleoside diphosphate catabolic process
is_a: GO:0046056 ! dADP metabolic process
[Term]
@@ -293024,6 +293978,7 @@
def: "The chemical reactions and pathways involving dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate)." [GOC:curators]
synonym: "dATP metabolism" EXACT []
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
+is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009215 ! purine deoxyribonucleoside triphosphate metabolic process
[Term]
@@ -293035,6 +293990,7 @@
synonym: "dATP catabolism" EXACT []
synonym: "dATP degradation" EXACT []
is_a: GO:0009155 ! purine deoxyribonucleotide catabolic process
+is_a: GO:0009204 ! deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009217 ! purine deoxyribonucleoside triphosphate catabolic process
is_a: GO:0046060 ! dATP metabolic process
@@ -293075,6 +294031,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving dCTP, deoxycytidine triphosphate." [GOC:curators]
synonym: "dCTP metabolism" EXACT []
+is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009211 ! pyrimidine deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -293097,6 +294054,7 @@
synonym: "dGDP degradation" EXACT []
is_a: GO:0009155 ! purine deoxyribonucleotide catabolic process
is_a: GO:0009184 ! purine deoxyribonucleoside diphosphate catabolic process
+is_a: GO:0009192 ! deoxyribonucleoside diphosphate catabolic process
is_a: GO:0046066 ! dGDP metabolic process
[Term]
@@ -293127,6 +294085,7 @@
def: "The chemical reactions and pathways involving dGTP, guanosine triphosphate." [GOC:curators]
synonym: "dGTP metabolism" EXACT []
is_a: GO:0009151 ! purine deoxyribonucleotide metabolic process
+is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009215 ! purine deoxyribonucleoside triphosphate metabolic process
[Term]
@@ -293139,6 +294098,7 @@
synonym: "dGTP formation" EXACT []
synonym: "dGTP synthesis" EXACT []
is_a: GO:0009153 ! purine deoxyribonucleotide biosynthetic process
+is_a: GO:0009202 ! deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0009216 ! purine deoxyribonucleoside triphosphate biosynthetic process
is_a: GO:0046070 ! dGTP metabolic process
@@ -293178,6 +294138,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving dTTP, deoxyribosylthymine triphosphate." [GOC:curators]
synonym: "dTTP metabolism" EXACT []
+is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009211 ! pyrimidine deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -293189,6 +294150,7 @@
synonym: "dTTP breakdown" EXACT []
synonym: "dTTP catabolism" EXACT []
synonym: "dTTP degradation" EXACT []
+is_a: GO:0009204 ! deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009213 ! pyrimidine deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009223 ! pyrimidine deoxyribonucleotide catabolic process
is_a: GO:0046075 ! dTTP metabolic process
@@ -293229,6 +294191,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate." [GOC:curators]
synonym: "dUTP metabolism" EXACT []
+is_a: GO:0009200 ! deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009211 ! pyrimidine deoxyribonucleoside triphosphate metabolic process
is_a: GO:0009219 ! pyrimidine deoxyribonucleotide metabolic process
@@ -293240,6 +294203,7 @@
synonym: "dUTP breakdown" EXACT []
synonym: "dUTP catabolism" EXACT []
synonym: "dUTP degradation" EXACT []
+is_a: GO:0009204 ! deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009213 ! pyrimidine deoxyribonucleoside triphosphate catabolic process
is_a: GO:0009223 ! pyrimidine deoxyribonucleotide catabolic process
is_a: GO:0046080 ! dUTP metabolic process
@@ -294650,6 +295614,10 @@
synonym: "spermidine degradation" EXACT []
is_a: GO:0006598 ! polyamine catabolic process
is_a: GO:0008216 ! spermidine metabolic process
+property_value: skos:broadMatch MetaCyc:PWY-6117
+property_value: skos:broadMatch MetaCyc:PWY-6440
+property_value: skos:broadMatch MetaCyc:PWY-6441
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0046204
@@ -294699,6 +295667,10 @@
synonym: "spermine degradation" EXACT []
is_a: GO:0006598 ! polyamine catabolic process
is_a: GO:0008215 ! spermine metabolic process
+property_value: skos:broadMatch MetaCyc:PWY-6117
+property_value: skos:broadMatch MetaCyc:PWY-6440
+property_value: skos:broadMatch MetaCyc:PWY-6441
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
[Term]
id: GO:0046209
@@ -294966,7 +295938,6 @@
synonym: "2-aminobenzenesulphonate catabolic process" EXACT []
synonym: "2-aminobenzenesulphonate catabolism" EXACT []
is_a: GO:0009310 ! amine catabolic process
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0042178 ! xenobiotic catabolic process
is_a: GO:0042537 ! benzene-containing compound metabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
@@ -295083,7 +296054,7 @@
synonym: "phthalate degradation" EXACT []
is_a: GO:0018963 ! phthalate metabolic process
is_a: GO:0042178 ! xenobiotic catabolic process
-is_a: GO:0046395 ! carboxylic acid catabolic process
+is_a: GO:0043649 ! dicarboxylic acid catabolic process
[Term]
id: GO:0046240
@@ -295468,8 +296439,8 @@
synonym: "toluene-4-sulfonate degradation" EXACT []
synonym: "toluene-4-sulphonate catabolic process" EXACT []
synonym: "toluene-4-sulphonate catabolism" EXACT []
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
+is_a: GO:0044282 ! small molecule catabolic process
is_a: GO:0072491 ! toluene-containing compound catabolic process
[Term]
@@ -295916,7 +296887,6 @@
synonym: "alkanesulfonate synthesis" EXACT []
synonym: "alkanesulphonate biosynthesis" EXACT []
synonym: "alkanesulphonate biosynthetic process" EXACT []
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0019694 ! alkanesulfonate metabolic process
is_a: GO:0044272 ! sulfur compound biosynthetic process
@@ -295930,7 +296900,6 @@
synonym: "alkanesulfonate degradation" EXACT []
synonym: "alkanesulphonate catabolic process" EXACT []
synonym: "alkanesulphonate catabolism" EXACT []
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019694 ! alkanesulfonate metabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
@@ -296597,6 +297566,7 @@
is_a: GO:0016051 ! carbohydrate biosynthetic process
is_a: GO:0019578 ! aldaric acid biosynthetic process
is_a: GO:0019580 ! galactarate metabolic process
+is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
[Term]
@@ -296912,7 +297882,6 @@
synonym: "deoxyribose phosphate biosynthesis" EXACT []
synonym: "deoxyribose phosphate formation" EXACT []
synonym: "deoxyribose phosphate synthesis" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0090407 ! organophosphate biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
@@ -296924,7 +297893,6 @@
synonym: "deoxyribose phosphate breakdown" EXACT []
synonym: "deoxyribose phosphate catabolism" EXACT []
synonym: "deoxyribose phosphate degradation" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0046434 ! organophosphate catabolic process
is_a: GO:1901136 ! carbohydrate derivative catabolic process
@@ -296988,6 +297956,7 @@
is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019579 ! aldaric acid catabolic process
is_a: GO:0019580 ! galactarate metabolic process
+is_a: GO:0043649 ! dicarboxylic acid catabolic process
property_value: skos:narrowMatch MetaCyc:GALACTARDEG-PWY
property_value: skos:narrowMatch MetaCyc:PWY-6497
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
@@ -297002,8 +297971,8 @@
synonym: "carboxylic acid biosynthesis" EXACT []
synonym: "carboxylic acid formation" EXACT []
synonym: "carboxylic acid synthesis" EXACT []
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0019752 ! carboxylic acid metabolic process
+is_a: GO:0044283 ! small molecule biosynthetic process
[Term]
id: GO:0046395
@@ -297013,8 +297982,8 @@
synonym: "carboxylic acid breakdown" EXACT []
synonym: "carboxylic acid catabolism" EXACT []
synonym: "carboxylic acid degradation" EXACT []
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0019752 ! carboxylic acid metabolic process
+is_a: GO:0044282 ! small molecule catabolic process
[Term]
id: GO:0046396
@@ -298044,9 +299013,10 @@
[Term]
id: GO:0046482
-name: para-aminobenzoic acid metabolic process
+name: obsolete para-aminobenzoic acid metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving para-aminobenzoic acid, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins." [PMID:11960743]
+def: "OBSOLETE. The chemical reactions and pathways involving para-aminobenzoic acid, an intermediate in the synthesis of folic acid, a compound which some organisms, e.g. prokaryotes, eukaryotic microbes, and plants, can synthesize de novo. Others, notably mammals, cannot. In yeast, it is present as a factor in the B complex of vitamins." [PMID:11960743]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "4-aminobenzoic acid metabolic process" EXACT []
synonym: "4-aminobenzoic acid metabolism" EXACT []
synonym: "p-aminobenzoic acid metabolic process" EXACT []
@@ -298056,9 +299026,8 @@
synonym: "para-aminobenzoic acid metabolism" EXACT []
synonym: "vitamin Bx metabolic process" EXACT []
synonym: "vitamin Bx metabolism" EXACT []
-is_a: GO:0009072 ! aromatic amino acid metabolic process
-is_a: GO:0032787 ! monocarboxylic acid metabolic process
-is_a: GO:0042537 ! benzene-containing compound metabolic process
+is_obsolete: true
+consider: GO:0008153
[Term]
id: GO:0046483
@@ -298239,12 +299208,13 @@
[Term]
id: GO:0046501
-name: protoporphyrinogen IX metabolic process
+name: obsolete protoporphyrinogen IX metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving protoporphyrinogen IX, the specific substrate for the enzyme ferrochelatase, which catalyzes the insertion of iron to form protoheme. It is probably also the substrate for chlorophyll formation." [ISBN:0198506732]
-comment: See also the molecular function term 'ferrochelatase activity ; GO:0004325'.
+def: "OBSOLETE. The chemical reactions and pathways involving protoporphyrinogen IX, the specific substrate for the enzyme ferrochelatase, which catalyzes the insertion of iron to form protoheme. It is probably also the substrate for chlorophyll formation." [ISBN:0198506732]
+comment: This term was obsoleted because protoporphyrinogen IX is an intermediate in heme/chlorophyll/uroporphyrinogen biosynthesis.
synonym: "protoporphyrinogen IX metabolism" EXACT []
-is_a: GO:0006778 ! porphyrin-containing compound metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31788" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0046502
@@ -300891,18 +301861,15 @@
[Term]
id: GO:0046715
-name: active borate transmembrane transporter activity
+name: obsolete active borate transmembrane transporter activity
namespace: molecular_function
alt_id: GO:0080138
-def: "Enables the transport of borate across a membrane against the concentration gradient." [PMID:12447444]
-synonym: "borate transmembrane transporter activity" BROAD []
-synonym: "borate uptake transmembrane transporter activity" RELATED []
-synonym: "boron transmembrane transporter activity" RELATED []
-synonym: "boron uptake transmembrane transporter activity" RELATED []
-synonym: "efflux-type borate transporter" NARROW []
-synonym: "efflux-type boron transporter" RELATED []
-is_a: GO:0022804 ! active transmembrane transporter activity
-relationship: part_of GO:0035445 ! borate transmembrane transport
+def: "OBSOLETE. Enables the transport of borate across a membrane against the concentration gradient." [PMID:12447444]
+comment: The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27488" xsd:anyURI
+is_obsolete: true
+consider: GO:0080139
+consider: GO:0180044
created_by: dhl
creation_date: 2009-05-19T04:09:56Z
@@ -303290,7 +304257,6 @@
name: carboxylic acid transport
namespace: biological_process
def: "The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:ai]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015849 ! organic acid transport
[Term]
@@ -303381,27 +304347,30 @@
synonym: "cellular ketone body metabolism" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29021" xsd:anyURI
is_obsolete: true
-replaced_by: GO:1902224
+consider: GO:0046951
+consider: GO:0046952
[Term]
id: GO:0046951
name: ketone body biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA." [MetaCyc:PWY66-367]
+synonym: "ketogenesis" EXACT []
synonym: "ketone body anabolism" EXACT []
synonym: "ketone body biosynthesis" EXACT []
synonym: "ketone body formation" EXACT []
synonym: "ketone body synthesis" EXACT []
+xref: MetaCyc:PWY66-367
xref: Reactome:R-HSA-77111 "Synthesis of Ketone Bodies"
is_a: GO:0044283 ! small molecule biosynthetic process
is_a: GO:1901570 ! fatty acid derivative biosynthetic process
-is_a: GO:1902224 ! ketone body metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31806" xsd:anyURI
[Term]
id: GO:0046952
name: ketone body catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Ketone bodies can be used as an energy source as an alternative to glucose. Utilization of ketone bodies in peripheral tissues involves conversion of acetoacetate to acetoacetyl-CoA, which is then converted to two molecules of acetyl-CoA." [ISBN:0198506732]
+def: "The chemical reactions and pathways resulting in the breakdown of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Ketone bodies can be used as an energy source as an alternative to glucose. Utilization of ketone bodies in peripheral tissues involves conversion of acetoacetate to acetoacetyl-CoA, which is then converted to two molecules of acetyl-CoA." [MetaCyc:PWY66-367]
synonym: "ketolysis" EXACT [MetaCyc:PWY66-368]
synonym: "ketone body breakdown" EXACT []
synonym: "ketone body catabolism" EXACT []
@@ -303411,7 +304380,7 @@
xref: Reactome:R-HSA-77108 "Utilization of Ketone Bodies"
is_a: GO:0044282 ! small molecule catabolic process
is_a: GO:1901569 ! fatty acid derivative catabolic process
-is_a: GO:1902224 ! ketone body metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31806" xsd:anyURI
[Term]
id: GO:0046956
@@ -303534,7 +304503,6 @@
synonym: "3'-phosphoadenosine 5'-phosphosulphate transport" EXACT []
synonym: "adenosine 3'-phosphate 5'-phosphosulfate transport" EXACT []
synonym: "PAPS transport" EXACT []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
is_a: GO:0072348 ! sulfur compound transport
@@ -305328,7 +306296,7 @@
id: GO:0047077
name: Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity
namespace: molecular_function
-def: "Catalysis of the reaction: O2 + ATP + Photinus luciferin = light + diphosphate + AMP + CO2 + oxidized Photinus luciferin." [EC:1.13.12.7, MetaCyc:1.13.12.7-RXN]
+def: "Catalysis of the reaction: O2 + ATP + Photinus luciferin = light + diphosphate + AMP + CO2 + oxidized Photinus luciferin." [EC:1.13.12.7]
synonym: "firefly luciferase activity" RELATED [EC:1.13.12.7]
synonym: "firefly luciferin luciferase activity" RELATED [EC:1.13.12.7]
synonym: "luciferase (firefly luciferin)" RELATED [EC:1.13.12.7]
@@ -305407,9 +306375,9 @@
[Term]
id: GO:0047081
-name: 3-hydroxy-2-methylpyridinecarboxylate dioxygenase activity
+name: 3-hydroxy-2-methylpyridinecarboxylate dioxygenase [NAD(P)H] activity
namespace: molecular_function
-def: "Catalysis of the reaction: O2 + NADPH + H+ + 3-hydroxy-2-methylpyridine-5-carboxylate = NADP+ + 2-(acetamidomethylene)succinate." [EC:1.14.13.242, MetaCyc:1.14.12.4-RXN]
+def: "Catalysis of the reaction: O2 + NAD(P)H + H+ + 3-hydroxy-2-methylpyridine-5-carboxylate = NAD(P)+ + 2-(acetamidomethylene)succinate." [EC:1.14.13.242]
synonym: "2-methyl-3-hydroxypyridine 5-carboxylic acid dioxygenase activity" RELATED [EC:1.14.13.242]
synonym: "3-hydroxy-2-methylpyridine-5-carboxylate,NADPH:oxygen oxidoreductase (decyclizing)" RELATED [EC:1.14.13.242]
synonym: "3-hydroxy-3-methylpyridinecarboxylate dioxygenase activity" RELATED [EC:1.14.13.242]
@@ -305417,10 +306385,12 @@
synonym: "methylhydroxypyridinecarboxylate oxidase activity" RELATED [EC:1.14.13.242]
xref: EC:1.14.13.242
xref: MetaCyc:1.14.12.4-RXN
+xref: RHEA:10860
xref: RHEA:10864
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
property_value: skos:exactMatch EC:1.14.13.242
-property_value: skos:exactMatch RHEA:10864
+property_value: skos:narrowMatch RHEA:10860
+property_value: skos:narrowMatch RHEA:10864
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -305583,7 +306553,6 @@
xref: KEGG_REACTION:R00448
xref: MetaCyc:1.14.13.59-RXN
xref: RHEA:23228
-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)
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
property_value: skos:exactMatch EC:1.14.13.59
property_value: skos:exactMatch RHEA:23228
@@ -306495,7 +307464,6 @@
xref: Reactome:R-HSA-1482646 "2-acyl LPE is acylated to PE by LPEAT"
xref: Reactome:R-HSA-1482691 "2-acyl LPS is acylated to PS by LPSAT"
xref: RHEA:14233
-is_a: GO:0008374 ! O-acyltransferase activity
is_a: GO:0042171 ! lysophosphatidic acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.52
property_value: skos:exactMatch RHEA:14233
@@ -306774,7 +307742,7 @@
xref: RHEA:37627
xref: RHEA:37711
xref: RHEA:37819
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.25
property_value: skos:exactMatch RHEA:10344
property_value: skos:narrowMatch RHEA:37627
@@ -306910,7 +307878,7 @@
xref: RHEA:37755
xref: RHEA:37759
xref: RHEA:37763
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.121
property_value: skos:exactMatch RHEA:16245
property_value: skos:narrowMatch RHEA:37631
@@ -306930,7 +307898,7 @@
xref: EC:2.3.1.125
xref: MetaCyc:2.3.1.125-RXN
xref: RHEA:21996
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.125
property_value: skos:exactMatch RHEA:21996
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -307025,7 +307993,7 @@
xref: RHEA:55320
xref: RHEA:56244
xref: RHEA:56248
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.135
property_value: skos:exactMatch RHEA:17469
property_value: skos:narrowMatch RHEA:55320
@@ -307049,7 +308017,6 @@
xref: KEGG_REACTION:R01944
xref: MetaCyc:2.3.1.138-RXN
xref: RHEA:12436
-is_a: GO:0016410 ! N-acyltransferase activity
is_a: GO:0050734 ! hydroxycinnamoyltransferase activity
property_value: skos:exactMatch EC:2.3.1.138
property_value: skos:exactMatch RHEA:12436
@@ -307066,7 +308033,7 @@
xref: EC:2.3.1.141
xref: MetaCyc:2.3.1.141-RXN
xref: RHEA:17057
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.141
property_value: skos:exactMatch RHEA:17057
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -307211,30 +308178,62 @@
xref: Reactome:R-HSA-1482794 "CL and 1-acyl LPC are converted to MLCL and PC by TAZ (IM) (Reversible)"
xref: RHEA:12937
xref: RHEA:33359
+xref: RHEA:35983
xref: RHEA:35987
+xref: RHEA:35991
+xref: RHEA:35995
+xref: RHEA:35999
+xref: RHEA:37383
+xref: RHEA:37387
+xref: RHEA:37391
+xref: RHEA:37395
xref: RHEA:37475
+xref: RHEA:37479
+xref: RHEA:37483
+xref: RHEA:37487
+xref: RHEA:37511
xref: RHEA:37515
+xref: RHEA:37519
+xref: RHEA:37527
xref: RHEA:37559
xref: RHEA:37563
+xref: RHEA:37655
xref: RHEA:37703
xref: RHEA:37707
xref: RHEA:37803
+xref: RHEA:37843
xref: RHEA:37855
xref: RHEA:37859
xref: RHEA:37863
xref: RHEA:37867
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.23
property_value: skos:exactMatch RHEA:12937
property_value: skos:narrowMatch RHEA:33359
+property_value: skos:narrowMatch RHEA:35983
property_value: skos:narrowMatch RHEA:35987
+property_value: skos:narrowMatch RHEA:35991
+property_value: skos:narrowMatch RHEA:35995
+property_value: skos:narrowMatch RHEA:35999
+property_value: skos:narrowMatch RHEA:37383
+property_value: skos:narrowMatch RHEA:37387
+property_value: skos:narrowMatch RHEA:37391
+property_value: skos:narrowMatch RHEA:37395
property_value: skos:narrowMatch RHEA:37475
+property_value: skos:narrowMatch RHEA:37479
+property_value: skos:narrowMatch RHEA:37483
+property_value: skos:narrowMatch RHEA:37487
+property_value: skos:narrowMatch RHEA:37511
property_value: skos:narrowMatch RHEA:37515
+property_value: skos:narrowMatch RHEA:37519
+property_value: skos:narrowMatch RHEA:37527
property_value: skos:narrowMatch RHEA:37559
property_value: skos:narrowMatch RHEA:37563
+property_value: skos:narrowMatch RHEA:37655
property_value: skos:narrowMatch RHEA:37703
property_value: skos:narrowMatch RHEA:37707
property_value: skos:narrowMatch RHEA:37803
+property_value: skos:narrowMatch RHEA:37843
property_value: skos:narrowMatch RHEA:37855
property_value: skos:narrowMatch RHEA:37859
property_value: skos:narrowMatch RHEA:37863
@@ -307357,7 +308356,7 @@
xref: RHEA:74807
xref: RHEA:74811
xref: RHEA:74823
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.62
property_value: skos:exactMatch RHEA:10332
property_value: skos:narrowMatch RHEA:74799
@@ -307377,14 +308376,18 @@
xref: MetaCyc:2.3.1.63-RXN
xref: RHEA:23992
xref: RHEA:37715
+xref: RHEA:37747
xref: RHEA:37783
+xref: RHEA:37787
xref: RHEA:37811
xref: RHEA:37839
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.63
property_value: skos:exactMatch RHEA:23992
property_value: skos:narrowMatch RHEA:37715
+property_value: skos:narrowMatch RHEA:37747
property_value: skos:narrowMatch RHEA:37783
+property_value: skos:narrowMatch RHEA:37787
property_value: skos:narrowMatch RHEA:37811
property_value: skos:narrowMatch RHEA:37839
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -307444,7 +308447,7 @@
xref: KEGG_REACTION:R04333
xref: MetaCyc:2.3.1.72-RXN
xref: RHEA:21180
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.72
property_value: skos:exactMatch RHEA:21180
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -307459,7 +308462,7 @@
xref: EC:2.3.1.73
xref: MetaCyc:2.3.1.73-RXN
xref: RHEA:13301
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.73
property_value: skos:exactMatch RHEA:13301
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -307494,7 +308497,7 @@
xref: RHEA:81803
xref: RHEA:81807
xref: RHEA:81811
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.75
property_value: skos:exactMatch MetaCyc:2.3.1.75-RXN
property_value: skos:exactMatch RHEA:38443
@@ -307528,7 +308531,7 @@
xref: RHEA:16897
xref: RHEA:78195
xref: RHEA:78199
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.77
property_value: skos:exactMatch RHEA:16897
property_value: skos:narrowMatch RHEA:78195
@@ -307566,7 +308569,7 @@
xref: KEGG_REACTION:R04227
xref: MetaCyc:2.3.1.83-RXN
xref: RHEA:19285
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.83
property_value: skos:exactMatch RHEA:19285
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -309171,20 +310174,24 @@
xref: KEGG_REACTION:R04635
xref: MetaCyc:2.4.99.7-RXN
xref: Reactome:R-HSA-981809 "ST6GALNAC3/4 transfers sialic acid to the sialyl T antigen to form the disialyl T antigen"
+xref: RHEA:41968
xref: RHEA:48316
xref: RHEA:53896
xref: RHEA:56088
xref: RHEA:65280
xref: RHEA:65284
xref: RHEA:65288
+xref: RHEA:77679
is_a: GO:0008373 ! sialyltransferase activity
property_value: skos:exactMatch EC:2.4.3.7
property_value: skos:exactMatch RHEA:53896
+property_value: skos:narrowMatch RHEA:41968
property_value: skos:narrowMatch RHEA:48316
property_value: skos:narrowMatch RHEA:56088
property_value: skos:narrowMatch RHEA:65280
property_value: skos:narrowMatch RHEA:65284
property_value: skos:narrowMatch RHEA:65288
+property_value: skos:narrowMatch RHEA:77679
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -310695,7 +311702,7 @@
id: GO:0047369
name: succinate-hydroxymethylglutarate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (S)-3-hydroxy-3-methylglutarate + succinyl-CoA = 3-hydroxy-3-methyl-glutaryl-CoA + succinate." [EC:2.8.3.13, MetaCyc:2.8.3.13-RXN]
+def: "Catalysis of the reaction: 3-hydroxy-3-methylglutarate + succinyl-CoA = (3S)-3-hydroxy-3-methylglutaryl-CoA + succinate." [RHEA:12284]
synonym: "dicarboxyl-CoA:dicarboxylic acid coenzyme A transferase activity" RELATED [EC:2.8.3.13]
synonym: "hydroxymethylglutarate coenzyme A-transferase activity" RELATED [EC:2.8.3.13]
synonym: "succinate:(S)-3-hydroxy-3-methylglutarate CoA-transferase activity" RELATED [EC:2.8.3.13]
@@ -310726,7 +311733,7 @@
id: GO:0047371
name: butyrate-acetoacetate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetoacetate + butanoyl-CoA = acetoacetyl-CoA + butanoate." [EC:2.8.3.9, RHEA:12961]
+def: "Catalysis of the reaction: acetoacetate + butanoyl-CoA = acetoacetyl-CoA + butanoate." [RHEA:12961]
synonym: "butanoyl-CoA:acetoacetate CoA-transferase activity" RELATED [EC:2.8.3.9]
synonym: "butyryl coenzyme A-acetoacetate coenzyme A-transferase activity" RELATED [EC:2.8.3.9]
synonym: "butyryl-CoA-acetoacetate CoA-transferase activity" RELATED [EC:2.8.3.9]
@@ -310767,16 +311774,54 @@
xref: Reactome:R-HSA-426043 "2-AG hydrolysis to arachidonate by MAGL"
xref: Reactome:R-HSA-5694462 "ABHD6,12 hydrolyse 3AG"
xref: RHEA:15245
+xref: RHEA:32875
xref: RHEA:34019
+xref: RHEA:38363
+xref: RHEA:38487
+xref: RHEA:38491
+xref: RHEA:39959
+xref: RHEA:44312
+xref: RHEA:44316
+xref: RHEA:44320
xref: RHEA:44688
+xref: RHEA:44728
+xref: RHEA:47072
+xref: RHEA:58040
+xref: RHEA:58076
+xref: RHEA:58080
+xref: RHEA:58084
+xref: RHEA:58088
+xref: RHEA:58092
+xref: RHEA:58096
+xref: RHEA:58100
+xref: RHEA:78151
is_a: GO:0016298 ! lipase activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity
property_value: skos:broadMatch EC:3.1.1.79
property_value: skos:exactMatch EC:3.1.1.23
property_value: skos:exactMatch MetaCyc:RXN-19280
property_value: skos:exactMatch RHEA:15245
+property_value: skos:narrowMatch RHEA:32875
property_value: skos:narrowMatch RHEA:34019
+property_value: skos:narrowMatch RHEA:38363
+property_value: skos:narrowMatch RHEA:38487
+property_value: skos:narrowMatch RHEA:38491
+property_value: skos:narrowMatch RHEA:39959
+property_value: skos:narrowMatch RHEA:44312
+property_value: skos:narrowMatch RHEA:44316
+property_value: skos:narrowMatch RHEA:44320
property_value: skos:narrowMatch RHEA:44688
+property_value: skos:narrowMatch RHEA:44728
+property_value: skos:narrowMatch RHEA:47072
+property_value: skos:narrowMatch RHEA:58040
+property_value: skos:narrowMatch RHEA:58076
+property_value: skos:narrowMatch RHEA:58080
+property_value: skos:narrowMatch RHEA:58084
+property_value: skos:narrowMatch RHEA:58088
+property_value: skos:narrowMatch RHEA:58092
+property_value: skos:narrowMatch RHEA:58096
+property_value: skos:narrowMatch RHEA:58100
+property_value: skos:narrowMatch RHEA:78151
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
[Term]
@@ -311367,9 +312412,10 @@
[Term]
id: GO:0047407
-name: ADP-ribosyl-[dinitrogen reductase] hydrolase activity
+name: obsolete ADP-ribosyl-[dinitrogen reductase] hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ADP-ribosyl-[dinitrogen reductase] = adenosine diphosphate ribose + [dinitrogen reductase]." [EC:3.2.2.24, MetaCyc:3.2.2.24-RXN]
+def: "OBSOLETE. Catalysis of the reaction: ADP-ribosyl-[dinitrogen reductase] = adenosine diphosphate ribose + [dinitrogen reductase]." [MetaCyc:3.2.2.24-RXN]
+comment: This term was obsoleted because it is beyond the specificity of GO.
synonym: "ADP-D-ribosyl-dinitrogen reductase ADP-ribosylhydrolase activity" RELATED [EC:3.2.2.24]
synonym: "ADP-ribosyl glycohydrolase activity" RELATED [EC:3.2.2.24]
synonym: "ADP-ribosyl-dinitrogen reductase hydrolase activity" RELATED [EC:3.2.2.24]
@@ -311377,13 +312423,10 @@
synonym: "azoferredoxin-activating enzymes" RELATED [EC:3.2.2.24]
synonym: "dinitrogenase reductase activating glycohydrolase activity" RELATED [EC:3.2.2.24]
synonym: "dinitrogenase reductase-activating glycohydrolase activity" RELATED [EC:3.2.2.24]
-xref: EC:3.2.2.24
-xref: MetaCyc:3.2.2.24-RXN
-xref: RHEA:14493
-is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
-property_value: skos:exactMatch EC:3.2.2.24
-property_value: skos:exactMatch RHEA:14493
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31850" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0003875
[Term]
id: GO:0047408
@@ -311683,7 +312726,7 @@
id: GO:0047426
name: ricinine nitrilase activity
namespace: molecular_function
-def: "Catalysis of the reaction: ricinine + 2 H2O = 4-methoxy-1-methyl-2-oxo-1,2-dihydropyridine-3-carboxylate + NH4+." [RHEA:22704]
+def: "Catalysis of the reaction: ricinine + 2 H2O = 4-methoxy-1-methyl-2-oxo-1,2-dihydropyridine-3-carboxylate + NH4+." [RHEA:22704]
synonym: "ricinine aminohydrolase activity" RELATED [EC:3.5.5.2]
xref: EC:3.5.5.2
xref: MetaCyc:3.5.5.2-RXN
@@ -311737,11 +312780,21 @@
xref: MetaCyc:NUCLEOTIDE-PYROPHOSPHATASE-RXN
xref: Reactome:R-HSA-9755030 "ITPA dimer dephosphorylates RBV-TP to RBV-MP"
xref: RHEA:23996
+xref: RHEA:27762
xref: RHEA:44644
+xref: RHEA:58732
+xref: RHEA:58736
+xref: RHEA:58740
+xref: RHEA:58744
is_a: GO:0016462 ! pyrophosphatase activity
property_value: skos:exactMatch EC:3.6.1.9
property_value: skos:narrowMatch RHEA:23996
+property_value: skos:narrowMatch RHEA:27762
property_value: skos:narrowMatch RHEA:44644
+property_value: skos:narrowMatch RHEA:58732
+property_value: skos:narrowMatch RHEA:58736
+property_value: skos:narrowMatch RHEA:58740
+property_value: skos:narrowMatch RHEA:58744
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23401" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27991" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -313502,7 +314555,7 @@
id: GO:0047533
name: 2,5-dioxovalerate dehydrogenase (NADP+) activity
namespace: molecular_function
-def: "Catalysis of the reaction: 2,5-dioxopentanoate + NADP+ + H2O = 2-oxoglutarate + NADPH + H+." [EC:1.2.1.26, MetaCyc:25-DIOXOVALERATE-DEHYDROGENASE-RXN]
+def: "Catalysis of the reaction: 2,5-dioxopentanoate + NADP+ + H2O = 2-oxoglutarate + NADPH + H+." [RHEA:11296]
synonym: "2,5-dioxopentanoate:NADP+ 5-oxidoreductase activity" RELATED [EC:1.2.1.26]
synonym: "2-oxoglutarate semialdehyde dehydrogenase activity" RELATED [EC:1.2.1.26]
synonym: "alpha-ketoglutaric semialdehyde dehydrogenase activity" RELATED [EC:1.2.1.26]
@@ -314164,7 +315217,7 @@
id: GO:0047569
name: 3-oxoadipate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: succinyl-CoA + 3-oxoadipate = succinate + 3-oxoadipyl-CoA." [EC:2.8.3.6, MetaCyc:3-OXOADIPATE-COA-TRANSFERASE-RXN]
+def: "Catalysis of the reaction: 3-oxoadipate + succinyl-CoA = 3-oxoadipyl-CoA + succinate." [RHEA:12048]
synonym: "3-oxoadipate coenzyme A-transferase activity" RELATED [EC:2.8.3.6]
synonym: "3-oxoadipate succinyl-CoA transferase activity" RELATED [EC:2.8.3.6]
synonym: "beta-ketoadipate:succinyl-CoA transferase activity" RELATED [EC:2.8.3.6]
@@ -314547,7 +315600,7 @@
id: GO:0047591
name: 5-hydroxypentanoate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-hydroxypentanoate + acetyl-CoA = 5-hydroxy-pentanoyl-CoA + acetate." [EC:2.8.3.14, RHEA:23496]
+def: "Catalysis of the reaction: 5-hydroxypentanoate + acetyl-CoA = 5-hydroxy-pentanoyl-CoA + acetate." [RHEA:23496]
synonym: "5-hydroxyvalerate CoA-transferase activity" RELATED [EC:2.8.3.14]
synonym: "5-hydroxyvalerate coenzyme A transferase activity" RELATED [EC:2.8.3.14]
synonym: "acetyl-CoA:5-hydroxypentanoate CoA-transferase activity" RELATED [EC:2.8.3.14]
@@ -315055,12 +316108,22 @@
xref: RHEA:19293
xref: RHEA:33747
xref: RHEA:39847
+xref: RHEA:41079
+xref: RHEA:43308
+xref: RHEA:43316
+xref: RHEA:43328
+xref: RHEA:63328
is_a: GO:0016301 ! kinase activity
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
property_value: skos:exactMatch EC:2.7.1.94
property_value: skos:exactMatch RHEA:19293
property_value: skos:narrowMatch RHEA:33747
property_value: skos:narrowMatch RHEA:39847
+property_value: skos:narrowMatch RHEA:41079
+property_value: skos:narrowMatch RHEA:43308
+property_value: skos:narrowMatch RHEA:43316
+property_value: skos:narrowMatch RHEA:43328
+property_value: skos:narrowMatch RHEA:63328
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -315520,6 +316583,8 @@
xref: MetaCyc:ALKAN-1-OL-DEHYDROGENASE-ACCEPTOR-RXN
xref: RHEA:14685
xref: RHEA:17085
+xref: RHEA:27538
+xref: RHEA:27542
xref: RHEA:33567
xref: RHEA:33571
xref: RHEA:48076
@@ -315532,6 +316597,8 @@
property_value: skos:exactMatch EC:1.1.99.20
property_value: skos:exactMatch RHEA:14685
property_value: skos:narrowMatch RHEA:17085
+property_value: skos:narrowMatch RHEA:27538
+property_value: skos:narrowMatch RHEA:27542
property_value: skos:narrowMatch RHEA:33567
property_value: skos:narrowMatch RHEA:33571
property_value: skos:narrowMatch RHEA:48076
@@ -316762,7 +317829,7 @@
id: GO:0047712
name: Cypridina-luciferin 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: Cypridina luciferin + O2 = oxidized Cypridina luciferin + CO2 + light." [EC:1.13.12.6, MetaCyc:CYPRIDINA-LUCIFERIN-2-MONOOXYGENASE-RXN]
+def: "Catalysis of the reaction: Cypridina luciferin + O2 = oxidized Cypridina luciferin + CO2 + light." [EC:1.13.12.6]
synonym: "Cypridina luciferase activity" RELATED [EC:1.13.12.6]
synonym: "Cypridina-luciferin:oxygen 2-oxidoreductase (decarboxylating)" RELATED [EC:1.13.12.6]
synonym: "Cypridina-type luciferase activity" RELATED [EC:1.13.12.6]
@@ -317827,7 +318894,7 @@
id: GO:0047775
name: citramalate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + citramalate = acetate + (3S)-citramalyl-CoA." [EC:2.8.3.11, MetaCyc:CITRAMALATE-COA-TRANSFERASE-RXN]
+def: "Catalysis of the reaction: citramalate + acetyl-CoA = (3S)-citramalyl-CoA + acetate." [RHEA:17621]
synonym: "acetyl-CoA:citramalate CoA-transferase activity" RELATED [EC:2.8.3.11]
xref: EC:2.8.3.11
xref: MetaCyc:CITRAMALATE-COA-TRANSFERASE-RXN
@@ -318411,6 +319478,7 @@
xref: RHEA:64748
xref: RHEA:64752
xref: RHEA:64756
+xref: RHEA:64760
is_a: GO:0016846 ! carbon-sulfur lyase activity
property_value: skos:exactMatch EC:4.4.1.13
property_value: skos:exactMatch MetaCyc:RXN-6763
@@ -318423,6 +319491,7 @@
property_value: skos:narrowMatch RHEA:64748
property_value: skos:narrowMatch RHEA:64752
property_value: skos:narrowMatch RHEA:64756
+property_value: skos:narrowMatch RHEA:64760
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27673" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
@@ -319614,7 +320683,7 @@
xref: EC:2.3.1.123
xref: MetaCyc:DOLICHOL-O-ACYLTRANSFERASE-RXN
xref: RHEA:16685
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.123
property_value: skos:exactMatch RHEA:16685
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -319695,6 +320764,7 @@
xref: RHEA:65548
xref: RHEA:65552
xref: RHEA:65556
+xref: RHEA:77675
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds
property_value: skos:exactMatch EC:3.2.1.123
property_value: skos:exactMatch RHEA:22288
@@ -319703,6 +320773,7 @@
property_value: skos:narrowMatch RHEA:65548
property_value: skos:narrowMatch RHEA:65552
property_value: skos:narrowMatch RHEA:65556
+property_value: skos:narrowMatch RHEA:77675
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
[Term]
@@ -320259,7 +321330,7 @@
synonym: "mono-beta-D-galactosyldiacylglycerol:mono-beta-D-galactosyldiacylglycerol acyltransferase activity" RELATED [EC:2.3.1.134]
xref: EC:2.3.1.134
xref: MetaCyc:GALACTOLIPID-O-ACYLTRANSFERASE-RXN
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.134
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -321178,13 +322249,39 @@
xref: MetaCyc:GLYCINE-N-ACYLTRANSFERASE-RXN
xref: Reactome:R-HSA-2534040 "Unknown NAT N-acylates Gly in GNAT1"
xref: RHEA:19869
+xref: RHEA:49772
+xref: RHEA:49780
xref: RHEA:49788
+xref: RHEA:49792
+xref: RHEA:51272
+xref: RHEA:51364
+xref: RHEA:51368
+xref: RHEA:51372
+xref: RHEA:58536
+xref: RHEA:64240
xref: RHEA:64244
+xref: RHEA:64248
+xref: RHEA:64252
+xref: RHEA:64256
+xref: RHEA:64260
is_a: GO:0140379 ! amino acid acyltransferase activity
property_value: skos:exactMatch EC:2.3.1.13
property_value: skos:exactMatch RHEA:19869
+property_value: skos:narrowMatch RHEA:49772
+property_value: skos:narrowMatch RHEA:49780
property_value: skos:narrowMatch RHEA:49788
+property_value: skos:narrowMatch RHEA:49792
+property_value: skos:narrowMatch RHEA:51272
+property_value: skos:narrowMatch RHEA:51364
+property_value: skos:narrowMatch RHEA:51368
+property_value: skos:narrowMatch RHEA:51372
+property_value: skos:narrowMatch RHEA:58536
+property_value: skos:narrowMatch RHEA:64240
property_value: skos:narrowMatch RHEA:64244
+property_value: skos:narrowMatch RHEA:64248
+property_value: skos:narrowMatch RHEA:64252
+property_value: skos:narrowMatch RHEA:64256
+property_value: skos:narrowMatch RHEA:64260
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
@@ -323861,12 +324958,12 @@
[Term]
id: GO:0048241
-name: epinephrine transport
+name: obsolete epinephrine transport
namespace: biological_process
-def: "The directed movement of epinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jid]
-synonym: "adrenaline transport" EXACT []
-is_a: GO:0015695 ! organic cation transport
-is_a: GO:0051937 ! catecholamine transport
+def: "OBSOLETE. The directed movement of epinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jid]
+comment: The reason for obsoletion is that this is an unnecessary grouping term and annotations should be made to more mechanism/location specific terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0048242
@@ -323874,7 +324971,6 @@
namespace: biological_process
def: "The regulated release of epinephrine by a cell. Epinephrine is a catecholamine hormone secreted by the adrenal medulla and a neurotransmitter, released by certain neurons and active in the central nervous system." [GOC:ef, GOC:jid]
synonym: "adrenaline secretion" EXACT []
-is_a: GO:0048241 ! epinephrine transport
is_a: GO:0050432 ! catecholamine secretion
[Term]
@@ -323883,7 +324979,6 @@
namespace: biological_process
def: "The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system." [GOC:ef, GOC:jid]
synonym: "noradrenaline secretion" EXACT []
-is_a: GO:0015874 ! norepinephrine transport
is_a: GO:0023061 ! signal release
is_a: GO:0050432 ! catecholamine secretion
@@ -330844,9 +331939,19 @@
xref: EC:1.4.1.5
xref: MetaCyc:L-AMINO-ACID-DEHYDROGENASE-RXN
xref: RHEA:10396
+xref: RHEA:32959
+xref: RHEA:37035
+xref: RHEA:37259
+xref: RHEA:47632
+xref: RHEA:65196
is_a: GO:0016639 ! oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor
property_value: skos:narrowMatch EC:1.4.1.5
property_value: skos:narrowMatch RHEA:10396
+property_value: skos:narrowMatch RHEA:32959
+property_value: skos:narrowMatch RHEA:37035
+property_value: skos:narrowMatch RHEA:37259
+property_value: skos:narrowMatch RHEA:47632
+property_value: skos:narrowMatch RHEA:65196
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30646" xsd:anyURI
@@ -331694,11 +332799,12 @@
[Term]
id: GO:0050067
-name: lysine 2-monooxygenase activity
+name: L-lysine 2-monooxygenase activity
namespace: molecular_function
def: "Catalysis of the reaction: L-lysine + O2 = 5-aminopentanamide + CO2 + H2O." [EC:1.13.12.2, RHEA:14601]
synonym: "L-lysine-2-monooxygenase activity" RELATED [EC:1.13.12.2]
synonym: "L-lysine:oxygen 2-oxidoreductase (decarboxylating)" RELATED [EC:1.13.12.2]
+synonym: "lysine 2-monooxygenase activity" EXACT []
synonym: "lysine monooxygenase activity" RELATED [EC:1.13.12.2]
synonym: "lysine oxygenase activity" RELATED [EC:1.13.12.2]
xref: EC:1.13.12.2
@@ -331869,7 +332975,7 @@
id: GO:0050078
name: malonate CoA-transferase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acetyl-CoA + malonate = acetate + malonyl-CoA." [EC:2.8.3.3, RHEA:18817]
+def: "Catalysis of the reaction: acetyl-CoA + malonate = acetate + malonyl-CoA." [RHEA:18817]
synonym: "acetyl-CoA:malonate CoA-transferase activity" RELATED [EC:2.8.3.3]
synonym: "malonate coenzyme A-transferase activity" RELATED [EC:2.8.3.3]
xref: EC:2.8.3.3
@@ -332884,6 +333990,7 @@
xref: RHEA:74075
xref: RHEA:74079
xref: RHEA:83235
+xref: RHEA:83243
is_a: GO:0003954 ! NADH dehydrogenase activity
is_a: GO:0003955 ! NAD(P)H dehydrogenase (quinone) activity
property_value: skos:exactMatch EC:1.6.5.9
@@ -332894,6 +334001,7 @@
property_value: skos:narrowMatch RHEA:74075
property_value: skos:narrowMatch RHEA:74079
property_value: skos:narrowMatch RHEA:83235
+property_value: skos:narrowMatch RHEA:83243
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25784" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27410" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30272" xsd:anyURI
@@ -334139,6 +335247,7 @@
xref: EC:1.14.19.77
xref: MetaCyc:RXN-17732
xref: RHEA:22956
+xref: RHEA:61956
xref: RHEA:61960
xref: RHEA:61964
xref: RHEA:61968
@@ -334146,6 +335255,7 @@
is_a: 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
property_value: skos:exactMatch EC:1.14.19.77
property_value: skos:exactMatch RHEA:22956
+property_value: skos:narrowMatch RHEA:61956
property_value: skos:narrowMatch RHEA:61960
property_value: skos:narrowMatch RHEA:61964
property_value: skos:narrowMatch RHEA:61968
@@ -334838,7 +335948,7 @@
id: GO:0050248
name: Renilla-luciferin 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: Renilla luciferin + O2 = oxidized Renilla luciferin + CO2 + light." [EC:1.13.12.5, MetaCyc:RENILLA-LUCIFERIN-2-MONOOXYGENASE-RXN]
+def: "Catalysis of the reaction: Renilla luciferin + O2 = oxidized Renilla luciferin + CO2 + light." [EC:1.13.12.5]
synonym: "aequorin activity" NARROW [EC:1.13.12.5]
synonym: "luciferase (Renilla luciferin)" RELATED [EC:1.13.12.5]
synonym: "luciferase activity" BROAD [EC:1.13.12.5]
@@ -334901,7 +336011,7 @@
xref: RHEA:11488
xref: RHEA:38175
xref: RHEA:55284
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
relationship: part_of GO:0042572 ! retinol metabolic process
property_value: skos:exactMatch EC:2.3.1.76
property_value: skos:exactMatch RHEA:11488
@@ -335593,15 +336703,17 @@
xref: RHEA:23768
xref: RHEA:36687
xref: RHEA:36691
+xref: RHEA:37111
xref: RHEA:37115
xref: RHEA:37123
xref: RHEA:45284
xref: RHEA:64044
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.24
property_value: skos:exactMatch RHEA:23768
property_value: skos:narrowMatch RHEA:36687
property_value: skos:narrowMatch RHEA:36691
+property_value: skos:narrowMatch RHEA:37111
property_value: skos:narrowMatch RHEA:37115
property_value: skos:narrowMatch RHEA:37123
property_value: skos:narrowMatch RHEA:45284
@@ -335907,7 +337019,7 @@
id: GO:0050308
name: sugar-phosphatase activity
namespace: molecular_function
-def: "Catalysis of the reaction: sugar phosphate + H2O = sugar + phosphate." [EC:3.1.3.23, MetaCyc:SUGAR-PHOSPHATASE-RXN]
+def: "Catalysis of the reaction: sugar phosphate + H2O = sugar + phosphate." [EC:3.1.3.23]
synonym: "sugar-phosphate phosphatase activity" EXACT []
synonym: "sugar-phosphate phosphohydrolase activity" EXACT systematic_synonym [EC:3.1.3.23]
xref: EC:3.1.3.23
@@ -337418,7 +338530,7 @@
id: GO:0050397
name: Watasenia-luciferin 2-monooxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: Watasenia luciferin + O2 = oxidized Watasenia luciferin + CO2 + light." [EC:1.13.12.8, MetaCyc:WATASEMIA-LUCIFERIN-2-MONOOXYGENASE-RXN]
+def: "Catalysis of the reaction: Watasenia luciferin + O2 = oxidized Watasenia luciferin + CO2 + light." [EC:1.13.12.8]
synonym: "luciferase activity" BROAD [EC:1.13.12.8]
synonym: "Watasenia-luciferin:oxygen 2-oxidoreductase (decarboxylating)" RELATED [EC:1.13.12.8]
synonym: "Watasenia-type luciferase activity" RELATED [EC:1.13.12.8]
@@ -338001,8 +339113,9 @@
name: catecholamine secretion
namespace: biological_process
def: "The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." [GOC:ai, GOC:ef]
+is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0032940 ! secretion by cell
-is_a: GO:0051937 ! catecholamine transport
+is_a: GO:0071705 ! nitrogen compound transport
[Term]
id: GO:0050433
@@ -341305,7 +342418,6 @@
xref: EC:2.3.1.155
xref: MetaCyc:2.3.1.155-RXN
xref: RHEA:18161
-is_a: GO:0016408 ! C-acyltransferase activity
is_a: GO:0019107 ! myristoyltransferase activity
property_value: skos:exactMatch EC:2.3.1.155
property_value: skos:exactMatch RHEA:18161
@@ -341425,7 +342537,7 @@
xref: EC:2.3.1.164
xref: MetaCyc:2.3.1.164-RXN
xref: RHEA:20720
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.164
property_value: skos:exactMatch RHEA:20720
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -342342,7 +343454,6 @@
name: N-malonyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a malonyl group to a nitrogen atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0016410 ! N-acyltransferase activity
is_a: GO:0016420 ! malonyltransferase activity
[Term]
@@ -342350,7 +343461,6 @@
name: O-malonyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a malonyl group to an oxygen atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0008374 ! O-acyltransferase activity
is_a: GO:0016420 ! malonyltransferase activity
[Term]
@@ -342358,7 +343468,6 @@
name: O-hydroxycinnamoyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a hydroxycinnamoyl group to an oxygen atom on the acceptor molecule." [GOC:ai]
-is_a: GO:0008374 ! O-acyltransferase activity
is_a: GO:0050734 ! hydroxycinnamoyltransferase activity
[Term]
@@ -343546,8 +344655,8 @@
synonym: "teichuronic acid biosynthesis" EXACT []
synonym: "teichuronic acid formation" EXACT []
synonym: "teichuronic acid synthesis" EXACT []
-is_a: GO:0016053 ! organic acid biosynthetic process
is_a: GO:0044038 ! cell wall macromolecule biosynthetic process
+is_a: GO:0044283 ! small molecule biosynthetic process
relationship: part_of GO:0009273 ! peptidoglycan-based cell wall biogenesis
[Term]
@@ -346394,17 +347503,17 @@
[Term]
id: GO:0051082
-name: unfolded protein binding
+name: obsolete unfolded protein binding
namespace: molecular_function
-def: "Binding to an unfolded protein." [GOC:ai]
-subset: goslim_chembl
-subset: goslim_drosophila
-subset: goslim_yeast
-synonym: "chaperone activity" BROAD []
+def: "OBSOLETE. Binding to an unfolded protein." [GOC:ai]
+comment: The reason for obsoletion is that this binding term should be replaced by an activity term such as protein folding chaperone (GO:0044183) or unfolded protein holdase activity (GO:0140309).
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
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21436" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30962" xsd:anyURI
+is_obsolete: true
+consider: GO:0044183
+consider: GO:0140309
[Term]
id: GO:0051083
@@ -347431,7 +348540,6 @@
def: "The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6." [GOC:ai]
synonym: "glucose 6-phosphate metabolism" EXACT []
synonym: "glucose 6-phosphate utilization" RELATED [GOC:mah]
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
@@ -347556,7 +348664,6 @@
synonym: "xylulose 5-phosphate metabolism" EXACT []
synonym: "xylulose-5-phosphate metabolic process" EXACT []
synonym: "xylulose-5-phosphate metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28597" xsd:anyURI
@@ -351145,7 +352252,6 @@
synonym: "adrenotropin secretion" EXACT []
synonym: "corticotropic hormone secretion" EXACT []
is_a: GO:0030072 ! peptide hormone secretion
-is_a: GO:0060986 ! endocrine hormone secretion
[Term]
id: GO:0051459
@@ -351922,10 +353028,13 @@
[Term]
id: GO:0051519
-name: activation of bipolar cell growth
+name: obsolete activation of bipolar cell growth
namespace: biological_process
-def: "Any process that initiates the inactive process of bipolar cell growth, polarized growth from both ends of a cell." [GOC:ai]
-is_a: GO:0051518 ! positive regulation of bipolar cell growth
+def: "OBSOLETE. Any process that initiates the inactive process of bipolar cell growth, polarized growth from both ends of a cell." [GOC:ai]
+comment: This term was obsoleted because it represented the same process as its parent, positive regulation of bipolar cell growth ; GO:0051518.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31746" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0051518
[Term]
id: GO:0051520
@@ -352850,7 +353959,8 @@
synonym: "5-hydroxytryptamine uptake" EXACT []
synonym: "5HT uptake" EXACT []
synonym: "serotonin import" EXACT [GOC:dph, GOC:tb]
-is_a: GO:0006837 ! serotonin transport
+is_a: GO:0015850 ! organic hydroxy compound transport
+is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:0098810 ! neurotransmitter reuptake
[Term]
@@ -352989,7 +354099,6 @@
synonym: "noradrenaline uptake" EXACT []
synonym: "norepinephrine import" EXACT [GOC:dph, GOC:tb]
synonym: "norepinephrine reuptake" EXACT []
-is_a: GO:0015874 ! norepinephrine transport
is_a: GO:0090493 ! catecholamine uptake
[Term]
@@ -356624,11 +357733,12 @@
[Term]
id: GO:0051937
-name: catecholamine transport
+name: obsolete catecholamine transport
namespace: biological_process
-def: "The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." [GOC:ai, ISBN:0198506732]
-is_a: GO:0015844 ! monoamine transport
-is_a: GO:0015850 ! organic hydroxy compound transport
+def: "OBSOLETE. The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." [GOC:ai, ISBN:0198506732]
+comment: The reason for obsoletion is that this is an unnecessary grouping term and annotations should be made to more mechanism/location specific terms.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0051938
@@ -363609,7 +364719,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving alditol phosphates, any phosphorylated polyhydric alcohol derived from the acyclic form of a monosaccharide by reduction of its aldehyde or keto group to an alcoholic group." [PMID:30240188]
synonym: "alditol phosphate metabolism" EXACT []
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
created_by: ai
@@ -363927,6 +365036,7 @@
xref: MetaCyc:RXN-11045
xref: RHEA:20976
xref: RHEA:26490
+xref: RHEA:50772
is_a: GO:0016663 ! oxidoreductase activity, acting on other nitrogenous compounds as donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.7.3.1
property_value: skos:narrowMatch KEGG_REACTION:R00799
@@ -363935,6 +365045,7 @@
property_value: skos:narrowMatch MetaCyc:RXN-11045
property_value: skos:narrowMatch RHEA:20976
property_value: skos:narrowMatch RHEA:26490
+property_value: skos:narrowMatch RHEA:50772
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
creation_date: 2010-10-11T10:50:59Z
@@ -364410,15 +365521,18 @@
[Term]
id: GO:0052698
-name: ergothioneine metabolic process
+name: obsolete ergothioneine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving ergothioneine, a naturally occurring metabolite of histidine with antioxidant properties." [Wikipedia:Ergothioneine]
+def: "OBSOLETE. The chemical reactions and pathways involving ergothioneine, a naturally occurring metabolite of histidine with antioxidant properties." [Wikipedia:Ergothioneine]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "(2S)-3-(2-mercapto-1H-imidazol-5-yl)-2-(trimethylazaniumyl)propanoate metabolic process" EXACT [CHEBI:4828]
synonym: "2-mercaptoergothioneine trimethylbetaine metabolic process" EXACT [CHEBI:4828]
synonym: "2-mercaptoergothioneine trimethylbetaine metabolism" EXACT [CHEBI:4828]
synonym: "ergothioneine metabolism" EXACT []
-is_a: GO:0000096 ! sulfur amino acid metabolic process
-is_a: GO:0006577 ! amino-acid betaine metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0052699
+consider: GO:0052700
created_by: ai
creation_date: 2011-08-01T03:52:11Z
@@ -364439,7 +365553,6 @@
synonym: "ergothioneine synthesis" EXACT []
is_a: GO:0000097 ! sulfur amino acid biosynthetic process
is_a: GO:0006578 ! amino-acid betaine biosynthetic process
-is_a: GO:0052698 ! ergothioneine metabolic process
is_a: GO:0052703 ! modified histidine biosynthetic process
created_by: ai
creation_date: 2011-08-01T03:56:19Z
@@ -364459,7 +365572,6 @@
synonym: "ergothioneine degradation" EXACT []
is_a: GO:0000098 ! sulfur amino acid catabolic process
is_a: GO:0006579 ! amino-acid betaine catabolic process
-is_a: GO:0052698 ! ergothioneine metabolic process
is_a: GO:0052702 ! modified histidine catabolic process
created_by: ai
creation_date: 2011-08-01T03:56:22Z
@@ -365825,9 +366937,14 @@
id: GO:0052797
name: 4-O-methyl-glucuronoyl methylesterase activity
namespace: molecular_function
-def: "Catalysis of the reaction: [X]-4-O-methyl-D-glucuronic acid + H2O = [X]-OH + methyl-D-glucuronic acid. This reaction is the hydrolysis of the ester linkage between 4-O-methyl-D-glucuronic acid (MeGlcA) and an alcohol (-OH) group attached to a molecule, denoted here as [X]." [GOC:mengo_curators, PMID:16876163]
+def: "Catalysis of the reaction: a 4-O-methyl-alpha-D-glucuronosyl ester derivative + H2O = 4-O-methyl-alpha-D-glucuronate derivative + an alcohol + H+." [PMID:16876163, RHEA:67452]
synonym: "glucuronoyl esterase activity" BROAD [PMID:16876163]
+xref: EC:3.1.1.117
+xref: RHEA:67452
is_a: GO:0052689 ! carboxylic ester hydrolase activity
+property_value: skos:exactMatch EC:3.1.1.117
+property_value: skos:exactMatch RHEA:67452
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31862" xsd:anyURI
[Term]
id: GO:0052798
@@ -367203,9 +368320,41 @@
xref: MetaCyc:RXN-11731
xref: RHEA:56588
xref: RHEA:56592
+xref: RHEA:77395
+xref: RHEA:77399
+xref: RHEA:77403
+xref: RHEA:77407
+xref: RHEA:77411
+xref: RHEA:77415
+xref: RHEA:77419
+xref: RHEA:77423
+xref: RHEA:77471
+xref: RHEA:77479
+xref: RHEA:77483
+xref: RHEA:77487
+xref: RHEA:77491
+xref: RHEA:77523
+xref: RHEA:77527
+xref: RHEA:77531
is_a: GO:0047606 ! (S)-hydroxynitrile lyase activity
property_value: skos:narrowMatch RHEA:56588
property_value: skos:narrowMatch RHEA:56592
+property_value: skos:narrowMatch RHEA:77395
+property_value: skos:narrowMatch RHEA:77399
+property_value: skos:narrowMatch RHEA:77403
+property_value: skos:narrowMatch RHEA:77407
+property_value: skos:narrowMatch RHEA:77411
+property_value: skos:narrowMatch RHEA:77415
+property_value: skos:narrowMatch RHEA:77419
+property_value: skos:narrowMatch RHEA:77423
+property_value: skos:narrowMatch RHEA:77471
+property_value: skos:narrowMatch RHEA:77479
+property_value: skos:narrowMatch RHEA:77483
+property_value: skos:narrowMatch RHEA:77487
+property_value: skos:narrowMatch RHEA:77491
+property_value: skos:narrowMatch RHEA:77523
+property_value: skos:narrowMatch RHEA:77527
+property_value: skos:narrowMatch RHEA:77531
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/16166" xsd:anyURI
[Term]
@@ -370861,7 +372010,6 @@
namespace: cellular_component
def: "The portion of the plasma membrane surrounding a stereocilium." [GOC:dph, GOC:rph]
is_a: GO:0032589 ! neuron projection membrane
-relationship: part_of GO:0005622 ! intracellular anatomical structure
relationship: part_of GO:0032420 ! stereocilium
[Term]
@@ -372211,6 +373359,7 @@
synonym: "regulation of phosphoinositide dephosphorylation" EXACT []
is_a: GO:0019216 ! regulation of lipid metabolic process
is_a: GO:0035303 ! regulation of dephosphorylation
+is_a: GO:0051174 ! regulation of phosphorus metabolic process
is_a: GO:0060255 ! regulation of macromolecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0046856 ! phosphatidylinositol dephosphorylation
@@ -374749,7 +375898,7 @@
name: positive regulation of fructose 1,6-bisphosphate metabolic process
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of fructose 1,6-bisphosphate metabolism. Fructose 1,6-bisphosphate metabolism is the chemical reactions and pathways involving fructose 1,6-bisphosphate, also known as FBP. The D enantiomer is a metabolic intermediate in glycolysis and gluconeogenesis." [GOC:BHF, GOC:dph, GOC:tb]
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0030388 ! fructose 1,6-bisphosphate metabolic process
relationship: positively_regulates GO:0030388 ! fructose 1,6-bisphosphate metabolic process
@@ -376832,9 +377981,9 @@
name: positive regulation of inositol phosphate biosynthetic process
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of inositol phosphate biosynthesis. Inositol phosphate biosynthetic processes are the chemical reactions and pathways resulting in the formation of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached." [GOC:dph, GOC:tb]
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0010919 ! regulation of inositol phosphate biosynthetic process
is_a: GO:0045913 ! positive regulation of carbohydrate metabolic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
is_a: GO:1902932 ! positive regulation of alcohol biosynthetic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0032958 ! inositol phosphate biosynthetic process
@@ -379779,11 +380928,13 @@
[Term]
id: GO:0060986
-name: endocrine hormone secretion
+name: obsolete endocrine hormone secretion
namespace: biological_process
-def: "The regulated release of a hormone into the circulatory system." [GOC:dph]
-is_a: GO:0046879 ! hormone secretion
-relationship: part_of GO:0050886 ! endocrine process
+def: "OBSOLETE. The regulated release of a hormone into the circulatory system." [GOC:dph]
+comment: The reason for obsoletion is that this term represents fake precision. The distinction between endocrine and other modes of hormone dispersal (paracrine, autocrine) is not always clear-cut, and this term was unevenly used relative to its parent.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17084" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0046879
created_by: dph
creation_date: 2010-01-11T09:03:48Z
@@ -385846,7 +386997,6 @@
def: "The controlled release of histamine by a cell, in which the histamine acts as a neurotransmitter." [GOC:dph]
is_a: GO:0001821 ! histamine secretion
is_a: GO:0007269 ! neurotransmitter secretion
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015801 ! aromatic amino acid transport
is_a: GO:0015807 ! L-amino acid transport
created_by: dph
@@ -385946,8 +387096,8 @@
name: tyramine secretion
namespace: biological_process
def: "The regulated release of a tyramine by a cell." [GOC:dph]
+is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0061531 ! primary amine secretion
-is_a: GO:7770032 ! tyramine transport
created_by: dph
creation_date: 2013-06-25T09:14:07Z
@@ -386327,7 +387477,7 @@
synonym: "autoinducer-1 synthase" RELATED [GOC:dph]
xref: EC:2.3.1.184
xref: RHEA:10096
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.184
property_value: skos:exactMatch RHEA:10096
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -386688,7 +387838,6 @@
synonym: "glycerol metabolism to glycerone phosphate" EXACT [GOC:dph]
synonym: "glycerol to DHAP metabolic process" EXACT [GOC:dph]
synonym: "glycerol to dihydroxyacetone phosphate metabolic process" EXACT [GOC:dph]
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019563 ! glycerol catabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:0034308 ! primary alcohol metabolic process
@@ -388141,7 +389290,6 @@
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of 6-sulfoquinovose(1-) resulting in the formation of glycerone phosphate (DHAP) and 3-sulfolactaldehyde (SLA)." [GOC:dph, PMID:24463506]
is_a: GO:0006081 ! aldehyde metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:0019694 ! alkanesulfonate metabolic process
is_a: GO:0034308 ! primary alcohol metabolic process
@@ -390242,7 +391390,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: propionyl-CoA + lysine in peptide = CoA + N-propionyl-lysine-peptide." [PMID:17267393]
xref: RHEA:54020
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:54020
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: dph
@@ -391873,7 +393021,6 @@
def: "Any process that modulates the rate, frequency or extent of taurine biosynthesis." [GOC:BHF, PMID:18648510, PMID:24911144]
is_a: GO:0009889 ! regulation of biosynthetic process
is_a: GO:0042762 ! regulation of sulfur metabolic process
-is_a: GO:0062012 ! regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0042412 ! taurine biosynthetic process
relationship: regulates GO:0042412 ! taurine biosynthetic process
@@ -391886,7 +393033,6 @@
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of taurine biosynthesis." [GOC:BHF, PMID:18648510, PMID:24911144]
is_a: GO:0009891 ! positive regulation of biosynthetic process
-is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:0062089 ! regulation of taurine biosynthetic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0042412 ! taurine biosynthetic process
@@ -392017,11 +393163,13 @@
xref: Reactome:R-HSA-9631355 "ASPH:Fe2+ hydroxylates an aspartate residue of F9"
xref: RHEA:11508
xref: RHEA:54276
+xref: RHEA:54280
is_a: GO:0016706 ! 2-oxoglutarate-dependent dioxygenase activity
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch EC:1.14.11.16
property_value: skos:exactMatch RHEA:11508
property_value: skos:narrowMatch RHEA:54276
+property_value: skos:narrowMatch RHEA:54280
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17842" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: dph
@@ -392051,18 +393199,36 @@
name: RNA 2'-O-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + RNA = S-adenosyl-L-homocysteine + RNA containing 2'-O-methylribonucleotide." [PMID:30626973, RHEA:58956]
+xref: RHEA:24140
xref: RHEA:42724
+xref: RHEA:42788
+xref: RHEA:42924
+xref: RHEA:43200
+xref: RHEA:43204
+xref: RHEA:47756
+xref: RHEA:47772
+xref: RHEA:47776
xref: RHEA:48628
xref: RHEA:56884
xref: RHEA:58956
xref: RHEA:65380
+xref: RHEA:73759
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008173 ! RNA methyltransferase activity
property_value: skos:exactMatch RHEA:58956
+property_value: skos:narrowMatch RHEA:24140
property_value: skos:narrowMatch RHEA:42724
+property_value: skos:narrowMatch RHEA:42788
+property_value: skos:narrowMatch RHEA:42924
+property_value: skos:narrowMatch RHEA:43200
+property_value: skos:narrowMatch RHEA:43204
+property_value: skos:narrowMatch RHEA:47756
+property_value: skos:narrowMatch RHEA:47772
+property_value: skos:narrowMatch RHEA:47776
property_value: skos:narrowMatch RHEA:48628
property_value: skos:narrowMatch RHEA:56884
property_value: skos:narrowMatch RHEA:65380
+property_value: skos:narrowMatch RHEA:73759
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: dph
creation_date: 2019-01-23T14:23:00Z
@@ -392305,7 +393471,7 @@
id: GO:0062131
name: 3-butenylglucosinolate 2-hydroxylase activity
namespace: molecular_function
-def: "Catalysis of the reaction: gluconapin + a reduced electron acceptor + O2 = xi-progoitrin + an oxidized electron acceptor + H2O." [PMID:18945935]
+def: "Catalysis of the reaction: gluconapin + a reduced electron acceptor + O2 = progoitrin + an oxidized electron acceptor + H2O." [PMID:18945935, RHEA:60628]
synonym: "But-3-enyl Glucosinolate-2-hydroxylase activity" EXACT []
xref: MetaCyc:RXNQT-4343
xref: RHEA:60628
@@ -393728,12 +394894,14 @@
[Term]
id: GO:0070007
-name: obsolete glutamic-type endopeptidase activity
+name: glutamic-type endopeptidase activity
namespace: molecular_function
-def: "OBSOLETE. Catalysis of the hydrolysis of internal peptide bonds in a polypeptide chain by a mechanism involving a glutamate/glutamine catalytic dyad." [GOC:mah, https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE, https://www.ebi.ac.uk/merops/about/glossary.shtml#ENDOPEPTIDASE]
-comment: This term was obsoleted because it represents a specific substrate.
+def: "Catalysis of the hydrolysis of internal peptide bonds in a polypeptide chain by a mechanism involving a glutamate/glutamine catalytic dyad." [GOC:mah, https://www.ebi.ac.uk/merops/about/glossary.shtml#CATTYPE, https://www.ebi.ac.uk/merops/about/glossary.shtml#ENDOPEPTIDASE]
+comment: Unobsoleted, since similar terms exist.
+is_a: GO:0004175 ! endopeptidase activity
+is_a: GO:0070002 ! glutamic-type peptidase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31581" xsd:anyURI
-is_obsolete: true
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31893" xsd:anyURI
[Term]
id: GO:0070008
@@ -395081,7 +396249,7 @@
id: GO:0070147
name: mitochondrial cysteinyl-tRNA aminoacylation
namespace: biological_process
-def: "The process of coupling cysteine to cysteinyl-tRNA in a mitochondrion, catalyzed by cysteinyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
+def: "The process of coupling L-cysteine to cysteinyl-tRNA in a mitochondrion, catalyzed by cysteinyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA." [GOC:mah, GOC:mcc]
is_a: GO:0006423 ! cysteinyl-tRNA aminoacylation
is_a: GO:0070127 ! tRNA aminoacylation for mitochondrial protein translation
intersection_of: GO:0006423 ! cysteinyl-tRNA aminoacylation
@@ -395231,7 +396399,7 @@
namespace: biological_process
def: "The regulated release of adiponectin, a protein hormone, by adipose tissue." [GOC:BHF, GOC:rl]
is_a: GO:0009306 ! protein secretion
-is_a: GO:0060986 ! endocrine hormone secretion
+is_a: GO:0046879 ! hormone secretion
[Term]
id: GO:0070163
@@ -395508,14 +396676,16 @@
[Term]
id: GO:0070189
-name: kynurenine metabolic process
+name: obsolete kynurenine metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving kynurenine, the amino acid 3-(2-aminobenzoyl)-alanine." [CHEBI:28683, GOC:mah, GOC:rph]
+def: "OBSOLETE. The chemical reactions and pathways involving kynurenine, the amino acid 3-(2-aminobenzoyl)-alanine." [CHEBI:28683, GOC:mah, GOC:rph]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "kynurenine metabolism" EXACT []
-is_a: GO:0042180 ! ketone metabolic process
-is_a: GO:0042537 ! benzene-containing compound metabolic process
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
-is_a: GO:1901605 ! alpha-amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31172" xsd:anyURI
+is_obsolete: true
+consider: GO:0006569
+consider: GO:0006727
+consider: GO:0034354
[Term]
id: GO:0070190
@@ -396688,10 +397858,13 @@
xref: MetaCyc:RXN-12116
xref: Reactome:R-HSA-2466831 "A2PE hydrolyses to A2E"
xref: RHEA:33159
+xref: RHEA:45528
xref: RHEA:45532
xref: RHEA:45536
+xref: RHEA:45540
xref: RHEA:45552
xref: RHEA:45556
+xref: RHEA:45596
xref: RHEA:45608
xref: RHEA:45612
xref: RHEA:45616
@@ -396701,10 +397874,13 @@
is_a: GO:0004630 ! D-type glycerophospholipase activity
property_value: skos:exactMatch EC:3.1.4.54
property_value: skos:exactMatch RHEA:33159
+property_value: skos:narrowMatch RHEA:45528
property_value: skos:narrowMatch RHEA:45532
property_value: skos:narrowMatch RHEA:45536
+property_value: skos:narrowMatch RHEA:45540
property_value: skos:narrowMatch RHEA:45552
property_value: skos:narrowMatch RHEA:45556
+property_value: skos:narrowMatch RHEA:45596
property_value: skos:narrowMatch RHEA:45608
property_value: skos:narrowMatch RHEA:45612
property_value: skos:narrowMatch RHEA:45616
@@ -397980,7 +399156,6 @@
def: "The chemical reactions and pathways involving carbamoyl phosphate, an intermediate in the urea cycle and other nitrogen compound metabolic pathways." [CHEBI:17672, GOC:mah, GOC:rph]
synonym: "carbamoyl phosphate metabolism" EXACT [GOC:mah]
xref: UM-BBD_pathwayID:bzn
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
[Term]
@@ -400361,7 +401536,7 @@
synonym: "negative regulation of thiamine diphosphate formation" EXACT [GOC:mah]
synonym: "negative regulation of thiamine diphosphate synthesis" EXACT [GOC:mah]
is_a: GO:0009890 ! negative regulation of biosynthetic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0046137 ! negative regulation of vitamin metabolic process
is_a: GO:0070616 ! regulation of thiamine diphosphate biosynthetic process
intersection_of: GO:0065007 ! biological regulation
@@ -401481,7 +402656,7 @@
name: sodium-dependent organic cation transport
namespace: biological_process
def: "The directed, sodium-dependent, movement of organic cations 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]
-is_a: GO:0015695 ! organic cation transport
+is_a: GO:0055085 ! transmembrane transport
created_by: mah
creation_date: 2009-06-09T03:26:27Z
@@ -401639,7 +402814,6 @@
namespace: biological_process
def: "The directed movement of cyclic AMP (cAMP), into, out of or within a cell." [GOC:mah, ISBN:0198506732]
synonym: "cyclic AMP transport" EXACT [GOC:mah]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
is_a: GO:0070729 ! cyclic nucleotide transport
@@ -401653,7 +402827,6 @@
def: "The directed movement of cyclic GMP (cGMP), into, out of or within a cell." [GOC:mah, ISBN:0198506732]
synonym: "cyclic GMP transport" EXACT [GOC:mah]
is_a: GO:0001408 ! guanine nucleotide transport
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0070729 ! cyclic nucleotide transport
created_by: mah
@@ -402628,7 +403801,6 @@
namespace: biological_process
def: "The process in which glycerol-2-phosphate is transported across a membrane. Glycerol-2-phosphate is a phosphoric monoester of glycerol." [GOC:mah]
synonym: "glycerol-2-phosphate transport" RELATED []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015748 ! organophosphate ester transport
is_a: GO:0055085 ! transmembrane transport
is_a: GO:1901264 ! carbohydrate derivative transport
@@ -402932,7 +404104,6 @@
namespace: biological_process
def: "The directed movement of dehydroascorbate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dehydroascorbate, 5-(1,2-dihydroxyethyl)furan-2,3,4(5H)-trione, is an oxidized form of vitamin C." [GOC:sl]
synonym: "dehydroascorbate transport" EXACT [GOC:sl]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0051180 ! vitamin transport
created_by: mah
creation_date: 2009-07-30T05:24:31Z
@@ -403279,6 +404450,8 @@
intersection_of: GO:0098590 ! plasma membrane region
intersection_of: part_of GO:0043332 ! mating projection tip
relationship: part_of GO:0043332 ! mating projection tip
+relationship: part_of GO:0070250 ! mating projection membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31775" xsd:anyURI
created_by: mah
creation_date: 2009-08-19T04:05:58Z
@@ -403749,7 +404922,6 @@
synonym: "aspartate-alanine antiporter activity" EXACT [GOC:mah]
synonym: "aspartate/alanine antiporter activity" EXACT [GOC:mah]
xref: RHEA:33139
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015297 ! antiporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
is_a: GO:0022858 ! alanine transmembrane transporter activity
@@ -403793,6 +404965,7 @@
synonym: "glutamate-gamma-aminobutyric acid antiporter activity" EXACT [GOC:mah]
synonym: "glutamate/gamma-aminobutyric acid antiporter activity" EXACT [GOC:mah]
synonym: "glutamate: GABA antiporter activity" EXACT [GOC:dh]
+is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015185 ! gamma-aminobutyric acid transmembrane transporter activity
is_a: GO:0015297 ! antiporter activity
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
@@ -410713,7 +411886,6 @@
intersection_of: GO:0000165 ! MAPK cascade
intersection_of: part_of GO:0000747 ! conjugation with cellular fusion
relationship: part_of GO:0000747 ! conjugation with cellular fusion
-relationship: part_of GO:0000750 ! pheromone-dependent signal transduction involved in conjugation with cellular fusion
created_by: mah
creation_date: 2010-01-05T01:43:47Z
@@ -414312,7 +415484,7 @@
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:0140694 ! membraneless organelle assembly
+is_a: GO:0120031 ! plasma membrane bounded cell projection assembly
created_by: mah
creation_date: 2010-09-03T11:00:45Z
@@ -414323,7 +415495,7 @@
def: "Any process that modulates the frequency, rate or extent of podosome assembly." [GOC:mah, GOC:sl]
comment: Note that the assembly is regulated by several small GTPases of the Rab and Rho families.
is_a: GO:0043254 ! regulation of protein-containing complex assembly
-is_a: GO:1902115 ! regulation of organelle assembly
+is_a: GO:0120032 ! regulation of plasma membrane bounded cell projection assembly
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0071800 ! podosome assembly
relationship: regulates GO:0071800 ! podosome assembly
@@ -414341,7 +415513,7 @@
synonym: "inhibition of podosome assembly" NARROW [GOC:mah]
is_a: GO:0031333 ! negative regulation of protein-containing complex assembly
is_a: GO:0071801 ! regulation of podosome assembly
-is_a: GO:1902116 ! negative regulation of organelle assembly
+is_a: GO:0120033 ! negative regulation of plasma membrane bounded cell projection assembly
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0071800 ! podosome assembly
relationship: negatively_regulates GO:0071800 ! podosome assembly
@@ -414360,7 +415532,7 @@
synonym: "upregulation of podosome assembly" EXACT [GOC:mah]
is_a: GO:0031334 ! positive regulation of protein-containing complex assembly
is_a: GO:0071801 ! regulation of podosome assembly
-is_a: GO:1902117 ! positive regulation of organelle assembly
+is_a: GO:0120034 ! positive regulation of plasma membrane bounded cell projection assembly
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0071800 ! podosome assembly
relationship: positively_regulates GO:0071800 ! podosome assembly
@@ -416412,7 +417584,6 @@
namespace: biological_process
def: "The directed movement of a phytochelatin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phytochelatins are a group of peptides that bind metals (Cd, Zn, Cu, Pb, Hg) in thiolate coordination complexes." [GOC:mah, ISBN:0198506732]
synonym: "cadystin transport" RELATED [GOC:vw, Wikipedia:Phytochelatin#History]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0071705 ! nitrogen compound transport
created_by: mah
creation_date: 2010-10-25T01:57:55Z
@@ -420147,7 +421318,6 @@
comment: Note that this term is not intended for use in annotating lateral movement within membranes.
synonym: "UDP-galactose membrane transport" EXACT []
synonym: "UDP-galactose transport" RELATED []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
created_by: mah
creation_date: 2010-11-03T02:03:36Z
@@ -428106,7 +429276,15 @@
xref: EC:4.2.1.119
xref: MetaCyc:RXN-7699
xref: RHEA:26526
+xref: RHEA:39155
+xref: RHEA:39159
+xref: RHEA:39175
+xref: RHEA:39187
+xref: RHEA:39247
+xref: RHEA:39259
xref: RHEA:39303
+xref: RHEA:39315
+xref: RHEA:39327
xref: RHEA:39343
xref: RHEA:39351
xref: RHEA:39363
@@ -428116,6 +429294,8 @@
xref: RHEA:39411
xref: RHEA:39423
xref: RHEA:39439
+xref: RHEA:39451
+xref: RHEA:39463
xref: RHEA:39475
xref: RHEA:39487
xref: RHEA:39499
@@ -428132,10 +429312,12 @@
xref: RHEA:39639
xref: RHEA:39687
xref: RHEA:39699
+xref: RHEA:44024
xref: RHEA:46720
xref: RHEA:67216
xref: RHEA:67228
xref: RHEA:72575
+xref: RHEA:78643
xref: RHEA:78863
xref: RHEA:78867
xref: RHEA:78931
@@ -428143,7 +429325,15 @@
property_value: skos:exactMatch EC:4.2.1.119
property_value: skos:exactMatch MetaCyc:RXN-7699
property_value: skos:exactMatch RHEA:26526
+property_value: skos:narrowMatch RHEA:39155
+property_value: skos:narrowMatch RHEA:39159
+property_value: skos:narrowMatch RHEA:39175
+property_value: skos:narrowMatch RHEA:39187
+property_value: skos:narrowMatch RHEA:39247
+property_value: skos:narrowMatch RHEA:39259
property_value: skos:narrowMatch RHEA:39303
+property_value: skos:narrowMatch RHEA:39315
+property_value: skos:narrowMatch RHEA:39327
property_value: skos:narrowMatch RHEA:39343
property_value: skos:narrowMatch RHEA:39351
property_value: skos:narrowMatch RHEA:39363
@@ -428153,6 +429343,8 @@
property_value: skos:narrowMatch RHEA:39411
property_value: skos:narrowMatch RHEA:39423
property_value: skos:narrowMatch RHEA:39439
+property_value: skos:narrowMatch RHEA:39451
+property_value: skos:narrowMatch RHEA:39463
property_value: skos:narrowMatch RHEA:39475
property_value: skos:narrowMatch RHEA:39487
property_value: skos:narrowMatch RHEA:39499
@@ -428169,10 +429361,12 @@
property_value: skos:narrowMatch RHEA:39639
property_value: skos:narrowMatch RHEA:39687
property_value: skos:narrowMatch RHEA:39699
+property_value: skos:narrowMatch RHEA:44024
property_value: skos:narrowMatch RHEA:46720
property_value: skos:narrowMatch RHEA:67216
property_value: skos:narrowMatch RHEA:67228
property_value: skos:narrowMatch RHEA:72575
+property_value: skos:narrowMatch RHEA:78643
property_value: skos:narrowMatch RHEA:78863
property_value: skos:narrowMatch RHEA:78867
property_value: skos:narrowMatch RHEA:78931
@@ -428671,7 +429865,7 @@
name: spermidine:sinapoyl CoA N-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a sinapoyl group to a nitrogen atom on the spermidine molecule." [PMID:19077165]
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
created_by: dhl
creation_date: 2009-04-13T04:16:28Z
@@ -428680,7 +429874,7 @@
name: spermidine:coumaroyl CoA N-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a coumaroyl group to a nitrogen atom on the spermidine molecule." [PMID:19077165]
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
created_by: dhl
creation_date: 2009-04-13T04:16:59Z
@@ -428689,7 +429883,7 @@
name: spermidine:caffeoyl CoA N-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a caffeoyl group to a nitrogen atom on the spermidine molecule." [PMID:19077165]
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
created_by: dhl
creation_date: 2009-04-13T04:17:23Z
@@ -428698,7 +429892,7 @@
name: spermidine:feruloyl CoA N-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a feruloyl group to a nitrogen atom on the spermidine molecule." [PMID:19077165]
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
created_by: dhl
creation_date: 2009-04-13T04:17:50Z
@@ -428819,7 +430013,7 @@
name: sinapoyl spermidine:sinapoyl CoA N-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the transfer of a sinapoyl group to a nitrogen atom on a sinapoyl spermidine molecule resulting in the formation of a disinapoyl spermidine derivative." [PMID:19168716]
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
created_by: dhl
creation_date: 2009-04-22T03:27:55Z
@@ -428891,7 +430085,7 @@
name: phosphatidylethanolamine-sterol O-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: a phosphatidylethanolamine + a sterol = a sterol ester + a lysophosphatidylethanolamine." [PMID:16020547]
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
created_by: dhl
creation_date: 2009-04-23T03:39:33Z
@@ -428900,7 +430094,7 @@
name: phosphatidate-sterol O-acyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: a phosphatidate + a sterol = a sterol ester + a lysophosphatidate." [PMID:16020547]
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
created_by: dhl
creation_date: 2009-04-23T03:41:42Z
@@ -429183,8 +430377,6 @@
namespace: biological_process
def: "The directed movement of AMP, adenosine monophosphate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [PMID:18923018]
synonym: "adenosine monophosphate transport" EXACT []
-is_a: GO:0015695 ! organic cation transport
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
created_by: dhl
@@ -429478,7 +430670,7 @@
id: GO:0080145
name: intracellular cysteine homeostasis
namespace: biological_process
-def: "A homeostatic process involved in the maintenance of a steady state level of cysteine within a cell." [PMID:19955263]
+def: "A homeostatic process involved in the maintenance of a steady state level of L-cysteine within a cell." [PMID:19955263]
synonym: "cellular cysteine homeostasis" EXACT []
synonym: "cysteine homeostasis" EXACT []
is_a: GO:0080144 ! intracellular amino acid homeostasis
@@ -431835,7 +433027,6 @@
name: L-histidine transmembrane transport
namespace: biological_process
def: "The directed movement of L-histidine across a membrane." [PMID:21307582]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015801 ! aromatic amino acid transport
is_a: GO:0045117 ! azole transmembrane transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
@@ -432249,19 +433440,19 @@
comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31306" xsd:anyURI
is_obsolete: true
+replaced_by: GO:0062038
created_by: tb
creation_date: 2009-08-03T10:25:27Z
[Term]
id: GO:0090029
-name: negative regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion
+name: obsolete negative regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion
namespace: biological_process
-def: "Any process that decreases the frequency, rate or extent of pheromone-dependent signal transduction during conjugation with cellular fusion, a signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion." [GOC:dph, GOC:tb]
-is_a: GO:0009968 ! negative regulation of signal transduction
-is_a: GO:0010969 ! regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0000750 ! pheromone-dependent signal transduction involved in conjugation with cellular fusion
-relationship: negatively_regulates GO:0000750 ! pheromone-dependent signal transduction involved in conjugation with cellular fusion
+def: "OBSOLETE. Any process that decreases the frequency, rate or extent of pheromone-dependent signal transduction during conjugation with cellular fusion, a signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion." [GOC:dph, GOC:tb]
+comment: This term was obsoleted because it is a pre-composed term that should be represented as a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31335" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0180040
created_by: tb
creation_date: 2009-08-03T10:27:04Z
@@ -437284,7 +438475,7 @@
def: "Catalysis of the reaction: an acyl-CoA + sn-glycerol 3-phosphate = CoA + a 2-acyl-sn-glycerol 3-phosphate." [RHEA:33559]
xref: EC:2.3.1.198
xref: RHEA:33559
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.198
property_value: skos:exactMatch RHEA:33559
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -437680,7 +438871,8 @@
name: catecholamine uptake
namespace: biological_process
def: "The directed movement of catecholamine into a cell." [GOC:dph, GOC:tb]
-is_a: GO:0051937 ! catecholamine transport
+is_a: GO:0015850 ! organic hydroxy compound transport
+is_a: GO:0071705 ! nitrogen compound transport
created_by: tb
creation_date: 2012-10-17T11:06:17Z
@@ -437689,7 +438881,6 @@
name: dopamine uptake
namespace: biological_process
def: "The directed movement of dopamine into a cell." [GOC:dph, GOC:tb]
-is_a: GO:0015872 ! dopamine transport
is_a: GO:0090493 ! catecholamine uptake
created_by: tb
creation_date: 2012-10-17T11:12:09Z
@@ -440792,16 +441983,15 @@
[Term]
id: GO:0097053
-name: L-kynurenine catabolic process
+name: obsolete L-kynurenine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine)." [GOC:yaf]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-kynurenine, the L-enantiomer of the amino acid kynurenine (3-(2-aminobenzoyl)-alanine)." [GOC:yaf]
+comment: This term was obsoleted because there is no evidence that this compound is specifically degraded.
synonym: "L-kynurenine breakdown" EXACT []
synonym: "L-kynurenine catabolism" EXACT []
synonym: "L-kynurenine degradation" EXACT []
-is_a: GO:0042182 ! ketone catabolic process
-is_a: GO:0070189 ! kynurenine metabolic process
-is_a: GO:0170035 ! L-amino acid catabolic process
-is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31588" xsd:anyURI
+is_obsolete: true
created_by: pr
creation_date: 2011-05-24T03:30:58Z
@@ -443160,12 +444350,15 @@
id: GO:0097265
name: 5(S)-hydroxyeicosatetraenoic acid dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 5-HETE + NADP+ = 5-oxo-ETE + NADPH + H+." [GOC:mw, PMID:1326548]
+def: "Catalysis of the reaction: 5-hydroxy-(6E,8Z,11Z,14Z)-eicosatetraenoate (5-HETE) + reduced [NADPH-hemoprotein reductase] + O2 = 5,20-dihydroxy-(6E,8Z,11Z,14Z)-eicosatetraenoate (5-oxo-ETE) + oxidized [NADPH-hemoprotein reductase] + H2O + H+." [PMID:1326548, PMID:9675028, RHEA:48656]
synonym: "5(S)-HETE dehydrogenase activity" EXACT []
synonym: "5-HETE dehydrogenase activity" EXACT []
synonym: "5-hydroxy-eicosatetraenoic acid dehydrogenase activity" EXACT []
xref: Reactome:R-HSA-2161776 "5S-HETE is oxidised to 5-oxoETE by 5-HEDH"
+xref: RHEA:48656
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+property_value: skos:exactMatch RHEA:48656
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31862" xsd:anyURI
created_by: pr
creation_date: 2012-03-09T12:46:02Z
@@ -447105,9 +448298,11 @@
synonym: "amine:oxygen oxidoreductase (deaminating) activity" EXACT []
xref: EC:1.4.3.4
xref: RHEA:26414
+xref: RHEA:51168
is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
property_value: skos:exactMatch EC:1.4.3.4
property_value: skos:narrowMatch RHEA:26414
+property_value: skos:narrowMatch RHEA:51168
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22282" xsd:anyURI
created_by: pr
creation_date: 2014-07-30T10:23:57Z
@@ -447306,9 +448501,8 @@
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:0015695 ! organic cation transport
is_a: GO:0089718 ! amino acid import across plasma membrane
-is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
+is_a: GO:1903826 ! L-arginine transmembrane transport
created_by: tb
creation_date: 2012-09-24T14:28:58Z
@@ -452547,7 +453741,8 @@
namespace: cellular_component
def: "A cell projection supported by an assembly of actin filaments, and which lacks microtubules." [PMID:15661519]
is_a: GO:0120025 ! plasma membrane bounded cell projection
-relationship: has_part GO:0005884 ! actin filament
+relationship: part_of GO:0015629 ! actin cytoskeleton
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20443" xsd:anyURI
[Term]
id: GO:0098859
@@ -452757,14 +453952,12 @@
[Term]
id: GO:0098881
-name: exocytic insertion of neurotransmitter receptor to plasma membrane
+name: obsolete exocytic insertion of neurotransmitter receptor to plasma membrane
namespace: biological_process
-def: "The exocytic fusion of neurotransmitter receptor-containing vesicles with plasma membrane, resulting in the integration of neurotransmitter receptors into the plasma membrane. This process includes tethering and docking steps that prepare vesicles for fusion." [GOC:aruk, GOC:bc, PMID:19503082]
-subset: goslim_synapse
-synonym: "neurotransmitter receptor insertion" EXACT []
-is_a: GO:0006904 ! vesicle docking involved in exocytosis
-is_a: GO:0090522 ! vesicle tethering involved in exocytosis
-relationship: part_of GO:0098877 ! neurotransmitter receptor transport to plasma membrane
+def: "OBSOLETE. The exocytic fusion of neurotransmitter receptor-containing vesicles with plasma membrane, resulting in the integration of neurotransmitter receptors into the plasma membrane. This process includes tethering and docking steps that prepare vesicles for fusion." [GOC:aruk, GOC:bc, PMID:19503082]
+comment: The reason for obsoletion is that the meaning of the term is ambiguous. It was placed under both tethering and docking involved in exocytosis, but it is unclear which part of exocytosis it refers to, and it has not been used.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31869" xsd:anyURI
+is_obsolete: true
[Term]
id: GO:0098882
@@ -458816,7 +460009,7 @@
id: GO:0102045
name: 3-chlorobenzoate-3,4-oxygenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: 3-chlorobenzoate + O2 + a reduced electron acceptor = 3-chlorobenzoate-cis-3,4-diol + an oxidized electron acceptor." [GOC:pz, PMID:8285670]
+def: "Catalysis of the reaction: 3-chlorobenzoate + O2 + a reduced electron acceptor = 3-chlorobenzoate-cis-3,4-diol + an oxidized electron acceptor." [PMID:38488372, PMID:8285670]
xref: MetaCyc:RXN-10422
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
@@ -459883,11 +461076,15 @@
[Term]
id: GO:0102157
-name: (R)-sulfopropanediol 2-dehydrogenase activity
+name: sulfopropanediol 3-dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2R)-3-sulfopropanediol(1-) + NAD = 2-oxo-3-hydroxy-propane-1-sulfonate + NADH + H+." [GOC:pz, PMID:20150239]
-xref: MetaCyc:RXN-11729
+def: "Catalysis of the reaction: (2R)-3-sulfopropanediol + 2 NAD+ + H2O = (2R)-3-sulfolactate + 2 NADH + 3 H+." [PMID:20150239, RHEA:28074]
+xref: EC:1.1.1.308
+xref: MetaCyc:RXN-11727
+xref: RHEA:28074 {status="skos:exactMatch"}
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+property_value: skos:exactMatch EC:1.1.1.308
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31862" xsd:anyURI
[Term]
id: GO:0102158
@@ -460125,12 +461322,14 @@
xref: RHEA:34775
xref: RHEA:59016
xref: RHEA:60084
+xref: RHEA:60092
is_a: GO:0000252 ! 3-beta-hydroxysteroid dehydrogenase [NAD(P)+]/C4-decarboxylase activity
property_value: skos:exactMatch EC:1.1.1.418
property_value: skos:exactMatch RHEA:34775
property_value: skos:narrowMatch RHEA:20669
property_value: skos:narrowMatch RHEA:59016
property_value: skos:narrowMatch RHEA:60084
+property_value: skos:narrowMatch RHEA:60092
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29311" xsd:anyURI
[Term]
@@ -460675,9 +461874,12 @@
id: GO:0102232
name: acrolein reductase activity
namespace: molecular_function
-def: "Catalysis of the reaction: acrolein + NADPH + H+ = propanal + NADP." [GOC:pz, PMID:21169366]
+def: "Catalysis of the reaction: propanal + NADP+ = acrolein + NADPH + H+." [PMID:21169366, RHEA:64716]
xref: MetaCyc:RXN-12281
+xref: RHEA:64716
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
+property_value: skos:exactMatch RHEA:64716
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31862" xsd:anyURI
[Term]
id: GO:0102233
@@ -461488,7 +462690,7 @@
id: GO:0102313
name: 1,8-cineole synthase activity
namespace: molecular_function
-def: "Catalysis of the reaction: geranyl diphosphate(3-) + H2O = 1,8-cineole + diphosphoric acid." [GOC:pz, RHEA:32543]
+def: "Catalysis of the reaction: geranyl diphosphate(3-) + H2O = 1,8-cineole + diphosphoric acid." [RHEA:32543]
xref: EC:4.2.3.108
xref: MetaCyc:RXN-12980
xref: RHEA:32543
@@ -462306,9 +463508,14 @@
id: GO:0102394
name: 4-hydroxy-L-isoleucine dehydrogenase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (2S,3R,4S)-4-hydroxy-L-isoleucine + NAD = (2S,3R)-2-amino-3-methyl-4-ketopentanoate + NADH + H+." [GOC:pz, PMID:21069315]
+def: "Catalysis of the reaction: L-isoleucine + 2-oxoglutarate + O2 = (4S)-4-hydroxy-L-isoleucine + succinate + CO2." [PMID:21069315, RHEA:41448]
+xref: EC:1.14.11.45
xref: MetaCyc:RXN-13637
+xref: RHEA:41448
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
+property_value: skos:exactMatch EC:1.14.11.45
+property_value: skos:exactMatch RHEA:41448
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31862" xsd:anyURI
[Term]
id: GO:0102395
@@ -465093,11 +466300,15 @@
synonym: "fatty aldehyde dehydrogenase activity" EXACT []
xref: MetaCyc:RXN-4142
xref: RHEA:44008
+xref: RHEA:44016
xref: RHEA:49832
+xref: RHEA:69092
xref: RHEA:69771
is_a: GO:0004029 ! aldehyde dehydrogenase (NAD+) activity
property_value: skos:exactMatch RHEA:49832
property_value: skos:narrowMatch RHEA:44008
+property_value: skos:narrowMatch RHEA:44016
+property_value: skos:narrowMatch RHEA:69092
property_value: skos:narrowMatch RHEA:69771
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28142" xsd:anyURI
@@ -466140,6 +467351,9 @@
xref: EC:1.14.18.5
xref: MetaCyc:RXN-14250
xref: Reactome:R-HSA-428260 "DEGS2 oxygenates dihydroceramide"
+xref: RHEA:33599
+xref: RHEA:33679
+xref: RHEA:43116
xref: RHEA:46364
xref: RHEA:55476
xref: RHEA:55808
@@ -466147,6 +467361,9 @@
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
property_value: skos:exactMatch EC:1.14.18.5
property_value: skos:exactMatch RHEA:55808
+property_value: skos:narrowMatch RHEA:33599
+property_value: skos:narrowMatch RHEA:33679
+property_value: skos:narrowMatch RHEA:43116
property_value: skos:narrowMatch RHEA:46364
property_value: skos:narrowMatch RHEA:55476
property_value: skos:narrowMatch RHEA:81475
@@ -468479,6 +469696,9 @@
xref: MetaCyc:RXN-9667
xref: RHEA:46408
xref: RHEA:46412
+xref: RHEA:66512
+xref: RHEA:66516
+xref: RHEA:66520
is_a: 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
property_value: skos:exactMatch EC:1.14.19.35
property_value: skos:exactMatch MetaCyc:RXN-9667
@@ -468495,6 +469715,9 @@
property_value: skos:narrowMatch MetaCyc:RXN-8366
property_value: skos:narrowMatch RHEA:46408
property_value: skos:narrowMatch RHEA:46412
+property_value: skos:narrowMatch RHEA:66512
+property_value: skos:narrowMatch RHEA:66516
+property_value: skos:narrowMatch RHEA:66520
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
[Term]
@@ -469666,7 +470889,7 @@
synonym: "membrane-cytoskeletal protein anchor activity" BROAD []
synonym: "membrane-cytoskeletal protein tether activity" BROAD []
synonym: "microtubule cortical anchor activity" NARROW []
-is_a: GO:0008093 ! cytoskeletal anchor activity
+is_a: GO:0008093 ! cytoskeletal adaptor activity
is_a: GO:0043495 ! protein-membrane adaptor activity
relationship: has_part GO:0008289 ! lipid binding
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/17668" xsd:anyURI
@@ -470120,22 +471343,27 @@
[Term]
id: GO:0106047
-name: polyamine deacetylation
+name: obsolete polyamine deacetylation
namespace: biological_process
-def: "The modification of acetylpolyamine by the removal of acetyl groups." [PMID:28516954]
-is_a: GO:0006595 ! polyamine metabolic process
-is_a: GO:0098732 ! macromolecule deacylation
+def: "OBSOLETE. The modification of acetylpolyamine by the removal of acetyl groups." [PMID:28516954]
+comment: The reason for obsoletion is that this term represents a molecular function.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31741" xsd:anyURI
+is_obsolete: true
+consider: GO:0006598
+consider: GO:0019213
created_by: hjd
creation_date: 2017-08-01T18:36:46Z
[Term]
id: GO:0106048
-name: spermidine deacetylation
+name: obsolete spermidine deacetylation
namespace: biological_process
-def: "The modification of acetylspermadine by the removal of acetyl groups." [PMID:28516954]
-synonym: "N8-acetylspermidine deacetylation" EXACT []
-is_a: GO:0008216 ! spermidine metabolic process
-is_a: GO:0106047 ! polyamine deacetylation
+def: "OBSOLETE. The modification of acetylspermadine by the removal of acetyl groups." [PMID:28516954]
+comment: The reason for obsoletion is that this term represents a molecular function.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31741" xsd:anyURI
+is_obsolete: true
+consider: GO:0046203
+consider: GO:0047611
created_by: hjd
creation_date: 2017-08-01T18:39:17Z
@@ -470412,7 +471640,7 @@
name: peptide N-succinyltransferase activity
namespace: molecular_function
def: "Catalysis of the acetylation of an amino acid residue of a peptide or protein, according to the reaction: succinyl-CoA + peptide = CoA + N-succinylpeptide." [PMID:29211711]
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
created_by: hjd
creation_date: 2017-12-15T18:23:58Z
@@ -471911,7 +473139,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: 2-hydroxyisobutyryl-CoA + lysine in peptide = CoA + N-2-hydroxyisobutyryl-lysine-peptide." [GOC:sp, PMID:29775581]
xref: RHEA:24180
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:24180
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -471934,7 +473162,7 @@
def: "Catalysis of the reaction: glutaryl-CoA + L-lysyl-[protein] = CoA + H+ + N6-glutaryl-L-lysyl-[protein]." [GOC:sp, PMID:31542297]
xref: Reactome:R-HSA-9858590 "DLST transfers glutaryl to CoA"
xref: RHEA:18009
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:18009
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -472017,9 +473245,11 @@
def: "Catalysis of the reaction: ceramide-1-phosphate + H2O = ceramide+ phosphate." [GOC:lb, PMID:10359651]
xref: RHEA:33743
xref: RHEA:50888
+xref: RHEA:62040
is_a: GO:0042577 ! lipid phosphatase activity
property_value: skos:exactMatch RHEA:50888
property_value: skos:narrowMatch RHEA:33743
+property_value: skos:narrowMatch RHEA:62040
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
creation_date: 2019-11-21T20:40:39Z
@@ -472361,6 +473591,7 @@
xref: RHEA:36015
xref: RHEA:36019
xref: RHEA:36023
+xref: RHEA:37419
xref: RHEA:37495
xref: RHEA:37499
xref: RHEA:37503
@@ -472372,12 +473603,15 @@
xref: RHEA:37767
xref: RHEA:37771
xref: RHEA:37775
-is_a: GO:0008374 ! O-acyltransferase activity
+xref: RHEA:64204
+xref: RHEA:64228
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.n7
property_value: skos:exactMatch RHEA:32995
property_value: skos:narrowMatch RHEA:36015
property_value: skos:narrowMatch RHEA:36019
property_value: skos:narrowMatch RHEA:36023
+property_value: skos:narrowMatch RHEA:37419
property_value: skos:narrowMatch RHEA:37495
property_value: skos:narrowMatch RHEA:37499
property_value: skos:narrowMatch RHEA:37503
@@ -472389,6 +473623,8 @@
property_value: skos:narrowMatch RHEA:37767
property_value: skos:narrowMatch RHEA:37771
property_value: skos:narrowMatch RHEA:37775
+property_value: skos:narrowMatch RHEA:64204
+property_value: skos:narrowMatch RHEA:64228
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27226" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -472401,22 +473637,30 @@
def: "Catalysis of the reaction:a 1-acyl-sn-glycero-3-phospho-L-serine + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phospho-L-serine + CoA." [PMID:18287005, RHEA:33191]
xref: EC:2.3.1.n6
xref: RHEA:33191
+xref: RHEA:37375
+xref: RHEA:37379
xref: RHEA:37399
xref: RHEA:37403
+xref: RHEA:37407
xref: RHEA:37415
xref: RHEA:37531
+xref: RHEA:37535
xref: RHEA:37539
xref: RHEA:37567
xref: RHEA:37571
xref: RHEA:37735
xref: RHEA:37739
-is_a: GO:0008374 ! O-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.n6
property_value: skos:exactMatch RHEA:33191
+property_value: skos:narrowMatch RHEA:37375
+property_value: skos:narrowMatch RHEA:37379
property_value: skos:narrowMatch RHEA:37399
property_value: skos:narrowMatch RHEA:37403
+property_value: skos:narrowMatch RHEA:37407
property_value: skos:narrowMatch RHEA:37415
property_value: skos:narrowMatch RHEA:37531
+property_value: skos:narrowMatch RHEA:37535
property_value: skos:narrowMatch RHEA:37539
property_value: skos:narrowMatch RHEA:37567
property_value: skos:narrowMatch RHEA:37571
@@ -472609,8 +473853,8 @@
synonym: "negative regulation of UDP-N-acetylglucosamine formation" RELATED []
synonym: "negative regulation of UDP-N-acetylglucosamine synthesis" RELATED []
is_a: GO:0009890 ! negative regulation of biosynthetic process
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:0106278 ! regulation of UDP-N-acetylglucosamine biosynthetic process
intersection_of: GO:0065007 ! biological regulation
@@ -472630,7 +473874,7 @@
synonym: "positive regulation of UDP-N-acetylglucosamine biosynthesis" RELATED []
synonym: "positive regulation of UDP-N-acetylglucosamine synthesis" RELATED []
is_a: GO:0009891 ! positive regulation of biosynthetic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:0106278 ! regulation of UDP-N-acetylglucosamine biosynthetic process
intersection_of: GO:0065007 ! biological regulation
@@ -473299,14 +474543,36 @@
xref: EC:2.3.1.296
xref: MetaCyc:RXN-20362
xref: RHEA:61528
+xref: RHEA:65648
+xref: RHEA:65652
+xref: RHEA:65668
+xref: RHEA:65672
+xref: RHEA:65676
+xref: RHEA:65680
+xref: RHEA:65684
+xref: RHEA:65688
xref: RHEA:65692
+xref: RHEA:65696
+xref: RHEA:78007
+xref: RHEA:78011
xref: RHEA:78115
xref: RHEA:78119
is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch EC:2.3.1.296
property_value: skos:exactMatch MetaCyc:RXN-20362
property_value: skos:exactMatch RHEA:61528
+property_value: skos:narrowMatch RHEA:65648
+property_value: skos:narrowMatch RHEA:65652
+property_value: skos:narrowMatch RHEA:65668
+property_value: skos:narrowMatch RHEA:65672
+property_value: skos:narrowMatch RHEA:65676
+property_value: skos:narrowMatch RHEA:65680
+property_value: skos:narrowMatch RHEA:65684
+property_value: skos:narrowMatch RHEA:65688
property_value: skos:narrowMatch RHEA:65692
+property_value: skos:narrowMatch RHEA:65696
+property_value: skos:narrowMatch RHEA:78007
+property_value: skos:narrowMatch RHEA:78011
property_value: skos:narrowMatch RHEA:78115
property_value: skos:narrowMatch RHEA:78119
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30910" xsd:anyURI
@@ -473493,11 +474759,13 @@
xref: RHEA:25375
xref: RHEA:25379
xref: RHEA:67444
+xref: RHEA:67448
is_a: GO:0016832 ! aldehyde-lyase activity
property_value: skos:exactMatch EC:4.1.2.63
property_value: skos:narrowMatch RHEA:25375
property_value: skos:narrowMatch RHEA:25379
property_value: skos:narrowMatch RHEA:67444
+property_value: skos:narrowMatch RHEA:67448
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20787" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23412" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25060" xsd:anyURI
@@ -473842,21 +475110,43 @@
xref: EC:1.1.1.n12
xref: MetaCyc:RXN66-485
xref: RHEA:32711
+xref: RHEA:40191
+xref: RHEA:40243
+xref: RHEA:45832
xref: RHEA:67220
xref: RHEA:67232
+xref: RHEA:78563
+xref: RHEA:78579
+xref: RHEA:78595
+xref: RHEA:78607
+xref: RHEA:78635
+xref: RHEA:78667
+xref: RHEA:78671
xref: RHEA:78871
xref: RHEA:78875
xref: RHEA:78879
xref: RHEA:78935
+xref: RHEA:79191
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:exactMatch EC:1.1.1.n12
property_value: skos:exactMatch RHEA:32711
+property_value: skos:narrowMatch RHEA:40191
+property_value: skos:narrowMatch RHEA:40243
+property_value: skos:narrowMatch RHEA:45832
property_value: skos:narrowMatch RHEA:67220
property_value: skos:narrowMatch RHEA:67232
+property_value: skos:narrowMatch RHEA:78563
+property_value: skos:narrowMatch RHEA:78579
+property_value: skos:narrowMatch RHEA:78595
+property_value: skos:narrowMatch RHEA:78607
+property_value: skos:narrowMatch RHEA:78635
+property_value: skos:narrowMatch RHEA:78667
+property_value: skos:narrowMatch RHEA:78671
property_value: skos:narrowMatch RHEA:78871
property_value: skos:narrowMatch RHEA:78875
property_value: skos:narrowMatch RHEA:78879
property_value: skos:narrowMatch RHEA:78935
+property_value: skos:narrowMatch RHEA:79191
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27180" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30577" xsd:anyURI
created_by: hjd
@@ -473879,6 +475169,7 @@
def: "Catalysis of the reaction: N1-methylpseudouridine in small subunit rRNA + S-adenosyl-L-methionine = H+ + N1-methyl-N3-[(3S)-3-amino-3-carboxypropyl]pseudouridine in small subunit rRNA + S-methyl-5'-thioadenosine." [PMID:27084949, RHEA:63296]
synonym: "18S rRNA aminocarboxypropyltransferase activity" NARROW []
xref: EC:2.5.1.157
+xref: RHEA:31479
xref: RHEA:63292
xref: RHEA:63296
xref: RHEA:63300
@@ -473886,6 +475177,7 @@
is_a: GO:0140102 ! catalytic activity, acting on a rRNA
property_value: skos:exactMatch EC:2.5.1.157
property_value: skos:exactMatch RHEA:63296
+property_value: skos:narrowMatch RHEA:31479
property_value: skos:narrowMatch RHEA:63292
property_value: skos:narrowMatch RHEA:63300
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29843" xsd:anyURI
@@ -474343,15 +475635,19 @@
namespace: molecular_function
def: "(S)-dihydroorotate + a quinone = orotate + a quinol." [RHEA:30187]
xref: EC:1.3.5.2
+xref: RHEA:28687
xref: RHEA:28691
xref: RHEA:29195
+xref: RHEA:29199
xref: RHEA:30187
is_a: GO:0004152 ! dihydroorotate dehydrogenase activity
is_a: GO:0016635 ! oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor
property_value: skos:exactMatch EC:1.3.5.2
property_value: skos:exactMatch RHEA:30187
+property_value: skos:narrowMatch RHEA:28687
property_value: skos:narrowMatch RHEA:28691
property_value: skos:narrowMatch RHEA:29195
+property_value: skos:narrowMatch RHEA:29199
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23786" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: hjd
@@ -474434,6 +475730,15 @@
xref: RHEA:21164
xref: RHEA:31779
xref: RHEA:38555
+xref: RHEA:47348
+xref: RHEA:47352
+xref: RHEA:47356
+xref: RHEA:47360
+xref: RHEA:47364
+xref: RHEA:47388
+xref: RHEA:47392
+xref: RHEA:50136
+xref: RHEA:50144
xref: RHEA:50148
xref: RHEA:59388
xref: RHEA:63052
@@ -474442,6 +475747,15 @@
property_value: skos:exactMatch RHEA:21164
property_value: skos:narrowMatch RHEA:31779
property_value: skos:narrowMatch RHEA:38555
+property_value: skos:narrowMatch RHEA:47348
+property_value: skos:narrowMatch RHEA:47352
+property_value: skos:narrowMatch RHEA:47356
+property_value: skos:narrowMatch RHEA:47360
+property_value: skos:narrowMatch RHEA:47364
+property_value: skos:narrowMatch RHEA:47388
+property_value: skos:narrowMatch RHEA:47392
+property_value: skos:narrowMatch RHEA:50136
+property_value: skos:narrowMatch RHEA:50144
property_value: skos:narrowMatch RHEA:50148
property_value: skos:narrowMatch RHEA:59388
property_value: skos:narrowMatch RHEA:63052
@@ -474475,9 +475789,11 @@
def: "Catalytic reaction: ATP + L-glutamate + L-glutamyl-[protein] = ADP + H+ + L-gamma-glutamyl-L-glutamyl-[protein] + phosphate." [PMID:32747782, RHEA:60144]
xref: RHEA:60144
xref: RHEA:69192
+xref: RHEA:69196
is_a: GO:0070739 ! protein-glutamic acid ligase activity
property_value: skos:exactMatch RHEA:60144
property_value: skos:narrowMatch RHEA:69192
+property_value: skos:narrowMatch RHEA:69196
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21309" xsd:anyURI
created_by: hjd
creation_date: 2022-10-21T21:11:47Z
@@ -474489,9 +475805,11 @@
def: "Catalytic reaction :(L-glutamyl)n-L-gamma-glutamyl-L-glutamyl-[protein] + ATP + L-glutamate = (L-glutamyl)n+1-L-gamma-glutamyl-L-glutamyl-[protein] + ADP + H+ + phosphate." [PMID:32747782, RHEA:60148]
xref: RHEA:60148
xref: RHEA:69208
+xref: RHEA:69212
is_a: GO:0070739 ! protein-glutamic acid ligase activity
property_value: skos:exactMatch RHEA:60148
property_value: skos:narrowMatch RHEA:69208
+property_value: skos:narrowMatch RHEA:69212
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21309" xsd:anyURI
created_by: hjd
creation_date: 2022-10-21T21:15:15Z
@@ -480186,7 +481504,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: L-glutaminyl-[protein] + serotonin = 5-serotonyl-L-glutamyl-[protein] + NH4+." [GOC:sp, PMID:14697203]
xref: RHEA:66552
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:66552
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20685" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -480212,7 +481530,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: dopamine + L-glutaminyl-[protein] = 5-dopaminyl-L-glutamyl-[protein] + NH4+." [GOC:sp, PMID:22858378, PMID:32273471]
xref: RHEA:66556
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:66556
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20685" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -480238,7 +481556,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: (R)-noradrenaline + L-glutaminyl-[protein] = 5-(R)-noradrenalinyl-L-glutamyl-[protein] + NH4+." [GOC:sp, PMID:22858378]
xref: RHEA:66560
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:66560
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20685" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -480251,7 +481569,7 @@
namespace: molecular_function
def: "Catalysis of the reaction: histamine + L-glutaminyl-[protein] = 5-histaminyl-L-glutamyl-[protein]." [GOC:sp, PMID:23022564, PMID:23797785]
xref: RHEA:66564
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:66564
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20685" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
@@ -480267,7 +481585,7 @@
synonym: "peptide lactyltransferase activity" BROAD []
synonym: "peptide lactyltransferase activity (CoA-dependent)" BROAD []
xref: RHEA:61996
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:61996
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20685" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28015" xsd:anyURI
@@ -480863,11 +482181,13 @@
def: "Catalysis of the reaction: an (omega-1)-ethyl fatty acid + O2 + reduced [NADPH--hemoprotein reductase] = an (omega-1)-hydroxy fatty acid + H+ + H2O + oxidized [NADPH--hemoprotein reductase]." [RHEA:44548]
xref: RHEA:39751
xref: RHEA:39759
+xref: RHEA:41724
xref: RHEA:44548
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
property_value: skos:exactMatch RHEA:44548
property_value: skos:narrowMatch RHEA:39751
property_value: skos:narrowMatch RHEA:39759
+property_value: skos:narrowMatch RHEA:41724
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24661" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: sjm
@@ -481042,11 +482362,13 @@
xref: MetaCyc:BUTYRATE--COA-LIGASE-RXN
xref: RHEA:38883
xref: RHEA:44004
+xref: RHEA:44196
is_a: GO:0015645 ! fatty acid ligase activity
is_a: GO:0016405 ! CoA-ligase activity
property_value: skos:exactMatch MetaCyc:BUTYRATE--COA-LIGASE-RXN
property_value: skos:exactMatch RHEA:38883
property_value: skos:narrowMatch RHEA:44004
+property_value: skos:narrowMatch RHEA:44196
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28199" xsd:anyURI
created_by: sjm
creation_date: 2024-06-25T12:17:07Z
@@ -481057,17 +482379,39 @@
namespace: molecular_function
def: "Catalysis of the reaction: a diacylglycerol + H2O = a fatty acid + a monoacylglycerol + H+." [RHEA:32731]
xref: MetaCyc:RXN-19279
+xref: RHEA:18761
xref: RHEA:32731
+xref: RHEA:38383
+xref: RHEA:38455
+xref: RHEA:38483
+xref: RHEA:39935
+xref: RHEA:39939
+xref: RHEA:42604
xref: RHEA:44444
+xref: RHEA:44712
+xref: RHEA:44876
xref: RHEA:47868
+xref: RHEA:48596
xref: RHEA:78019
+xref: RHEA:78147
is_a: GO:0016298 ! lipase activity
property_value: skos:broadMatch EC:3.1.1.79
property_value: skos:exactMatch MetaCyc:RXN-19279
property_value: skos:exactMatch RHEA:32731
+property_value: skos:narrowMatch RHEA:18761
+property_value: skos:narrowMatch RHEA:38383
+property_value: skos:narrowMatch RHEA:38455
+property_value: skos:narrowMatch RHEA:38483
+property_value: skos:narrowMatch RHEA:39935
+property_value: skos:narrowMatch RHEA:39939
+property_value: skos:narrowMatch RHEA:42604
property_value: skos:narrowMatch RHEA:44444
+property_value: skos:narrowMatch RHEA:44712
+property_value: skos:narrowMatch RHEA:44876
property_value: skos:narrowMatch RHEA:47868
+property_value: skos:narrowMatch RHEA:48596
property_value: skos:narrowMatch RHEA:78019
+property_value: skos:narrowMatch RHEA:78147
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI
created_by: sjm
creation_date: 2024-06-28T12:36:24Z
@@ -481329,10 +482673,18 @@
xref: EC:4.2.1.170
xref: RHEA:50632
xref: RHEA:50636
+xref: RHEA:50648
+xref: RHEA:50652
+xref: RHEA:50656
+xref: RHEA:50660
is_a: GO:0016836 ! hydro-lyase activity
property_value: skos:exactMatch EC:4.2.1.170
property_value: skos:narrowMatch RHEA:50632
property_value: skos:narrowMatch RHEA:50636
+property_value: skos:narrowMatch RHEA:50648
+property_value: skos:narrowMatch RHEA:50652
+property_value: skos:narrowMatch RHEA:50656
+property_value: skos:narrowMatch RHEA:50660
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28776" xsd:anyURI
created_by: sjm
creation_date: 2024-09-05T08:00:08Z
@@ -481657,11 +483009,13 @@
synonym: "mRNA (nucleoside-2'-O-)-methyltransferase activity" RELATED [EC:2.1.1.296]
xref: EC:2.1.1.296
xref: MetaCyc:RXN-14928
+xref: RHEA:53044
xref: RHEA:67024
is_a: GO:0008171 ! O-methyltransferase activity
is_a: GO:0008173 ! RNA methyltransferase activity
property_value: skos:exactMatch EC:2.1.1.296
property_value: skos:narrowMatch MetaCyc:RXN-14928
+property_value: skos:narrowMatch RHEA:53044
property_value: skos:narrowMatch RHEA:67024
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27387" xsd:anyURI
created_by: sjm
@@ -481947,7 +483301,7 @@
name: dihydrolipoyllysine-residue glutaryltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: N6-[(R)-dihydrolipoyl]-L-lysyl-[protein] + glutaryl-CoA = CoA + N6-[(R)-S8-glutaryldihydrolipoyl]-L-lysyl-[protein]." [PMID:29191460]
-is_a: GO:0016417 ! S-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31280" xsd:anyURI
created_by: sjm
creation_date: 2026-01-07T15:48:37Z
@@ -482029,7 +483383,6 @@
is_a: GO:0042219 ! modified amino acid catabolic process
is_a: GO:0170035 ! L-amino acid catabolic process
is_a: GO:0170044 ! non-proteinogenic amino acid catabolic process
-is_a: GO:1903184 ! L-dopa metabolic process
property_value: skos:narrowMatch MetaCyc:PWY-6334
property_value: skos:narrowMatch MetaCyc:PWY-8110
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31703" xsd:anyURI
@@ -482145,7 +483498,6 @@
name: D-aspartate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of D-aspartate from one side of a membrane to the other." [GO_REF:0000070, PMID:7914198]
-is_a: GO:0005310 ! dicarboxylic acid transmembrane transporter activity
is_a: GO:0015556 ! C4-dicarboxylate transmembrane transporter activity
is_a: GO:0042943 ! D-amino acid transmembrane transporter activity
relationship: part_of GO:0070777 ! D-aspartate transmembrane transport
@@ -482640,13 +483992,14 @@
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]
+def: "The process of transcribing and translating the mitochondrial genome (mtDNA) to produce at least a subset of oxidative phosphorylation (OXPHOS) proteins, 2 rRNAs, and mitochondrial tRNAs, which are critical for ATP production. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [PMID:27058308, PMID:31861673, PMID:38117001]
subset: goslim_generic
subset: goslim_pombe
is_a: GO:0010467 ! gene expression
intersection_of: GO:0010467 ! gene expression
intersection_of: occurs_in GO:0005739 ! mitochondrion
relationship: occurs_in GO:0005739 ! mitochondrion
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31659" xsd:anyURI
created_by: pg
creation_date: 2017-06-26T10:57:45Z
@@ -482772,7 +484125,7 @@
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
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:53908
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: pg
@@ -482785,7 +484138,7 @@
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
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
property_value: skos:exactMatch RHEA:53912
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: pg
@@ -483021,8 +484374,14 @@
name: L-amino-acid N-acetyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: acetyl-CoA + a L-amino acid = CoA + an N-acetyl-L-amino-acid. In some cases other acetyl containing molecules can be used as donor." [GOC:pg, RHEA:83863]
+xref: RHEA:47656
+xref: RHEA:47660
+xref: RHEA:52680
xref: RHEA:83863
is_a: GO:0140379 ! amino acid acyltransferase activity
+property_value: skos:narrowMatch RHEA:47656
+property_value: skos:narrowMatch RHEA:47660
+property_value: skos:narrowMatch RHEA:52680
property_value: skos:narrowMatch RHEA:83863
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29604" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31474" xsd:anyURI
@@ -483938,7 +485297,7 @@
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: monocarboxylate(out) + Na+(out) = monocarboxylate(in) + Na+(in)." [GOC:ln, PMID:15322102]
is_a: GO:0005343 ! organic acid:sodium symporter activity
-is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
created_by: pg
creation_date: 2018-02-05T10:33:55Z
@@ -484041,6 +485400,13 @@
xref: EC:1.1.1.50
xref: RHEA:34779
xref: RHEA:34783
+xref: RHEA:42116
+xref: RHEA:69016
+xref: RHEA:69028
+xref: RHEA:84155
+xref: RHEA:84199
+xref: RHEA:85551
+xref: RHEA:85559
is_a: GO:0033764 ! steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: skos:broadMatch MetaCyc:1.1.1.209-RXN
property_value: skos:exactMatch EC:1.1.1.357
@@ -484048,6 +485414,13 @@
property_value: skos:narrowMatch EC:1.1.1.50
property_value: skos:narrowMatch RHEA:34779
property_value: skos:narrowMatch RHEA:34783
+property_value: skos:narrowMatch RHEA:42116
+property_value: skos:narrowMatch RHEA:69016
+property_value: skos:narrowMatch RHEA:69028
+property_value: skos:narrowMatch RHEA:84155
+property_value: skos:narrowMatch RHEA:84199
+property_value: skos:narrowMatch RHEA:85551
+property_value: skos:narrowMatch RHEA:85559
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29921" xsd:anyURI
created_by: pg
creation_date: 2025-04-09T15:19:24Z
@@ -484171,7 +485544,7 @@
id: GO:0140177
name: membrane-membrane adaptor activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together two membranes, either via membrane lipid binding or by interacting with a membrane protein, to establish or maintain the localization of the protein, protein complex or organelle." [GOC:curators]
+def: "The binding activity of a molecule that brings together two membranes, either via membrane lipid binding or by interacting with a membrane protein, to establish or maintain the localization of the protein, protein complex, vesicle or organelle." [GOC:curators]
is_a: GO:0060090 ! molecular adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24964" xsd:anyURI
created_by: pg
@@ -484284,7 +485657,7 @@
xref: RHEA:59800
xref: RHEA:83531
xref: RHEA:85279
-is_a: GO:0016410 ! N-acyltransferase activity
+is_a: GO:0016747 ! acyltransferase activity, transferring groups other than amino-acyl groups
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch RHEA:53916
property_value: skos:narrowMatch RHEA:59764
@@ -485639,24 +487012,31 @@
[Term]
id: GO:0140292
-name: ADP-ribosylserine hydrolase activity
+name: ADP-ribosylserine-[protein] hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (ADP-D-ribosyl)-L-seryl-[protein] + H2O = L-seryl-[protein] + ADP-ribose." [PMID:28650317, PMID:29234005, RHEA:58256]
+def: "Catalysis of the reaction: O-(ADP-D-ribosyl)-L-seryl-[protein] + H2O = ADP-D-ribose + L-seryl-[protein]." [PMID:28650317, PMID:29234005, RHEA:58256]
+synonym: "ADP-ribosylserine hydrolase activity" EXACT []
xref: RHEA:58256
is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
is_a: GO:0140096 ! catalytic activity, acting on a protein
property_value: skos:exactMatch RHEA:58256
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28476" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31850" xsd:anyURI
created_by: pg
creation_date: 2018-11-22T14:35:39Z
[Term]
id: GO:0140293
-name: ADP-ribosylglutamate hydrolase activity
+name: ADP-ribosylglutamate-[protein] hydrolase activity
namespace: molecular_function
-def: "Catalysis of the reaction: (ADP-D-ribosyl)-L-glutamyl-[protein] + H2O = L-glutamyl-[protein] + ADP-ribose." [PMID:23481255]
+def: "Catalysis of the reaction: 5-O-(ADP-D-ribosyl)-L-glutamyl-[protein] + H2O = L-glutamyl-[protein] + ADP-D-ribose + H+." [PMID:23481255, RHEA:58248]
+synonym: "ADP-ribosylglutamate hydrolase activity" EXACT []
+xref: RHEA:58248
is_a: GO:0016799 ! hydrolase activity, hydrolyzing N-glycosyl compounds
is_a: GO:0140096 ! catalytic activity, acting on a protein
+property_value: skos:exactMatch RHEA:58248
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31849" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31850" xsd:anyURI
created_by: pg
creation_date: 2018-11-22T14:36:37Z
@@ -486056,11 +487436,15 @@
name: lysophospholipase C activity
namespace: molecular_function
def: "Hydrolysis of a lysoglycerophospholipid at the first phosphodiester bond between the phosphate and glycerol." [PMID:32917725]
+xref: RHEA:86371
xref: RHEA:86375
xref: RHEA:86379
+xref: RHEA:86383
is_a: GO:0004629 ! C-type glycerophospholipase activity
+property_value: skos:narrowMatch RHEA:86371
property_value: skos:narrowMatch RHEA:86375
property_value: skos:narrowMatch RHEA:86379
+property_value: skos:narrowMatch RHEA:86383
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30949" xsd:anyURI
created_by: pg
creation_date: 2025-11-10T12:35:51Z
@@ -486538,7 +487922,6 @@
name: cyclic-GMP-AMP transmembrane import across plasma membrane
namespace: biological_process
def: "The directed movement of cyclic-GMP-AMP from outside of a cell, across the plasma membrane and into the cytosol." [PMID:31126740]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
is_a: GO:0070729 ! cyclic nucleotide transport
@@ -486737,7 +488120,6 @@
def: "The chemical reactions and pathways resulting in the formation of psilocybin, a psychotropic tryptamine-derived natural product." [MetaCyc:PWY-7936, PMID:28763571]
xref: MetaCyc:PWY-7936
is_a: GO:0006568 ! L-tryptophan metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0035835 ! indole alkaloid biosynthetic process
is_a: GO:0042435 ! indole-containing compound biosynthetic process
is_a: GO:0043386 ! mycotoxin biosynthetic process
@@ -486880,7 +488262,7 @@
namespace: biological_process
def: "Any process that increases the rate, frequency, or extent of acetyl-CoA biosynthetic process." [PMID:41730913]
is_a: GO:0009891 ! positive regulation of biosynthetic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0050812 ! regulation of acyl-CoA biosynthetic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
@@ -486896,8 +488278,8 @@
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of acetyl-CoA biosynthetic process." [PMID:39019872]
is_a: GO:0009890 ! negative regulation of biosynthetic process
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:0050812 ! regulation of acyl-CoA biosynthetic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
intersection_of: GO:0065007 ! biological regulation
@@ -487051,6 +488433,26 @@
creation_date: 2026-03-06T09:07:34Z
[Term]
+id: GO:0140401
+name: 4-phosphoerythronate phosphatase activity
+namespace: molecular_function
+def: "Catalysis of the reaction: 4-phospho-D-erythronate + H2O = D-erythronate + phosphate." [PMID:27294321]
+is_a: GO:0016791 ! phosphatase activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31118" xsd:anyURI
+created_by: pg
+creation_date: 2026-04-02T12:52:47Z
+
+[Term]
+id: GO:0140402
+name: symbiont-mediated disassembly of host stress granules
+namespace: biological_process
+def: "The process in which an organism effects a change that impairs the structure or function of the stress granule of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. Stress granules are dynamic cytoplasmic condensates formed through liquid-liquid phase separation. They act as a critical hub for both cellular stress adaptation and defense against viruses." [PMID:32353859, PMID:39345463]
+is_a: GO:0052008 ! symbiont-mediated disruption of host cellular anatomical structure
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31751" xsd:anyURI
+created_by: pg
+creation_date: 2026-04-07T12:22:21Z
+
+[Term]
id: GO:0140403
name: effector-mediated suppression of host innate immune response
namespace: biological_process
@@ -487163,6 +488565,18 @@
creation_date: 2020-01-07T16:58:49Z
[Term]
+id: GO:0140411
+name: symbiont-mediated suppression of host stress granule assembly
+namespace: biological_process
+def: "A process in which a symbiont inhibits or disrupts the normal assembly of stress granule of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. Stress granules are dynamic cytoplasmic condensates formed through liquid-liquid phase separation. They act as a critical hub for both cellular stress adaptation and defense against viruses." [PMID:32353859, PMID:39345463]
+synonym: "symbiont-mediated inhibition of host stress granule assembly" EXACT []
+synonym: "symbiont-mediated inhibition of host stress granule formation" EXACT []
+is_a: GO:0044068 ! symbiont-mediated perturbation of host cellular process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31751" xsd:anyURI
+created_by: pg
+creation_date: 2026-04-07T12:38:51Z
+
+[Term]
id: GO:0140412
name: zinc:bicarbonate symporter activity
namespace: molecular_function
@@ -487481,13 +488895,14 @@
id: GO:0140443
name: mitochondrion-plasma membrane adaptor activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together a mitochondrion and a plasma membrane either via membrane lipid binding or by interacting with a mitochondrial outer membrane protein, to establish or maintain the localization of the mitochondrion." [PMID:31582398]
+def: "The binding activity of a molecule that brings together a mitochondrial outer membrane and a plasma membrane either via membrane lipid binding or by interacting with a mitochondrial outer membrane protein, to establish or maintain the localization of the mitochondrion." [PMID:31582398]
synonym: "mitochondrion plasma membrane adaptor activity" EXACT []
synonym: "mitochondrion plasma membrane tether activity" EXACT []
synonym: "plasma membrane-mitochondrion adaptor activity" EXACT []
synonym: "plasma membrane-mitochondrion tether activity" EXACT []
-is_a: GO:0043495 ! protein-membrane adaptor activity
+is_a: GO:0140177 ! membrane-membrane adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19090" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: pg
creation_date: 2020-03-24T13:11:20Z
@@ -487823,7 +489238,7 @@
id: GO:0140474
name: mitochondrion-endoplasmic reticulum membrane tether activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together a mitochondrion and an ER membrane either via membrane lipid binding or by interacting with a mitochondrial outer membrane protein, to establish or maintain the localization of the mitochondrion." [PMID:19556461, PMID:27875684]
+def: "The binding activity of a molecule that brings together a mitochondrial outer membrane and an ER membrane either via membrane lipid binding or by interacting with a mitochondrial outer membrane protein, to establish or maintain the localization of the mitochondrion." [PMID:19556461, PMID:27875684]
synonym: "endoplasmic reticulum-mitochondrion membrane adaptor activity" EXACT []
synonym: "endoplasmic reticulum-mitochondrion membrane tether activity" EXACT []
synonym: "ER-mitochondrion membrane adaptor activity" EXACT []
@@ -487833,6 +489248,7 @@
synonym: "mitochondrion-ER membrane tether activity" EXACT []
is_a: GO:0170009 ! endoplasmic reticulum-organelle membrane tether activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19634" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: pg
creation_date: 2020-06-22T07:01:14Z
@@ -487841,7 +489257,7 @@
name: spindle pole body anchor activity
namespace: molecular_function
def: "The binding activity of a protein that brings together the spindle pole body and one or more other molecules, permitting them to function in a coordinated way." [PMID:19942852]
-is_a: GO:0008093 ! cytoskeletal anchor activity
+is_a: GO:0008093 ! cytoskeletal adaptor activity
created_by: pg
creation_date: 2020-06-23T15:54:56Z
@@ -487908,7 +489324,6 @@
name: 5-aminolevulinic acid import across plasma membrane
namespace: biological_process
def: "The directed movement of 5-aminolevulinic acid from outside of a cell, across the plasma membrane and into the cytosol." [PMID:31989647]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015718 ! monocarboxylic acid transport
is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:0089718 ! amino acid import across plasma membrane
@@ -488163,13 +489578,14 @@
id: GO:0140506
name: endoplasmic reticulum-autophagosome adaptor activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together an ER membrane and an autophagosome during reticulophagy." [PMID:32735772]
+def: "The binding activity of a molecule that brings together an ER membrane and an autophagosome membrane during reticulophagy." [PMID:32735772]
synonym: "autophagosome-endoplasmic reticulum anchor" EXACT []
synonym: "autophagosome-ER anchor" EXACT []
synonym: "ER- autophagosome anchor" EXACT []
is_a: GO:0160183 ! autophagosome-membrane adaptor activity
is_a: GO:0170009 ! endoplasmic reticulum-organelle membrane tether activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19873" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: pg
creation_date: 2020-08-27T11:04:43Z
@@ -488847,10 +490263,11 @@
id: GO:0140580
name: mitochondrion autophagosome adaptor activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together a mitochondrial membrane and an autophagosome during mitophagy." [PMID:33138913]
+def: "The binding activity of a molecule that brings together a mitochondrial membrane and an autophagosome membrane during mitophagy." [PMID:33138913]
synonym: "mitophagy receptor" EXACT []
is_a: GO:0160183 ! autophagosome-membrane adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20668" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: pg
creation_date: 2021-01-18T11:03:49Z
@@ -490858,10 +492275,11 @@
[Term]
id: GO:0140740
-name: ADP-riboxanase activity
+name: ADP-riboxanase-[protein] activity
namespace: molecular_function
def: "Catalysis of the reaction: L-arginyl-[protein] + NAD+ = ADP-riboxanated L-argininyl-[protein] + H+ + NH4+ + nicotinamide." [PMID:34671164, RHEA:69500]
comment: Note that this activity has two steps: a transfer of an ADP-ribose group, followed by the elimination of an ammonia group.
+synonym: "ADP-riboxanase activity" EXACT []
xref: Reactome:R-HSA-9956624 "OspC3 ADP-riboxanates CASP4"
xref: RHEA:69500
xref: RHEA:75883
@@ -490873,6 +492291,7 @@
property_value: skos:narrowMatch RHEA:75883
property_value: skos:narrowMatch RHEA:75887
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22480" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31850" xsd:anyURI
created_by: pg
creation_date: 2021-11-30T08:29:49Z
@@ -491863,6 +493282,7 @@
def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: orotate(out) + anion (in) = orotate (in) + anion (out)." [PMID:21350910, PMID:35144162]
synonym: "orotate:anion antiporter activity" BROAD []
synonym: "orotate:organic anion antiporter activity" NARROW []
+is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0008509 ! monoatomic anion transmembrane transporter activity
is_a: GO:0015297 ! antiporter activity
is_a: GO:0015355 ! secondary active monocarboxylate transmembrane transporter activity
@@ -491954,12 +493374,16 @@
xref: EC:3.6.1.74
xref: MetaCyc:POLYNUCLEOTIDE-5-PHOSPHATASE-RXN
xref: RHEA:11008
+xref: RHEA:60828
+xref: RHEA:60832
xref: RHEA:67004
is_a: GO:0016462 ! pyrophosphatase activity
is_a: GO:0140098 ! catalytic activity, acting on RNA
property_value: skos:exactMatch EC:3.6.1.74
property_value: skos:exactMatch RHEA:67004
property_value: skos:narrowMatch RHEA:11008
+property_value: skos:narrowMatch RHEA:60828
+property_value: skos:narrowMatch RHEA:60832
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23319" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25810" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26929" xsd:anyURI
@@ -491994,7 +493418,6 @@
namespace: biological_process
def: "The directed movement of UDP-beta-L-arabinofuranose from the cytosol to the Golgi apparatus of a cell." [PMID:28373556]
synonym: "cytosol to Golgi apparatus UDP-beta-L-arabinofuranose transport" EXACT []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
is_a: GO:0140820 ! cytosol to Golgi apparatus transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21524" xsd:anyURI
@@ -493462,7 +494885,6 @@
name: L-phenylalanine import across plasma membrane
namespace: biological_process
def: "The directed movement of L-phenylalanine from outside of a cell, across the plasma membrane and into the cytosol." [PMID:11069779]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015801 ! aromatic amino acid transport
is_a: GO:0015823 ! phenylalanine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
@@ -493550,10 +494972,14 @@
synonym: "m(7)GpppX diphosphatase activity" EXACT [EC:3.6.1.59]
synonym: "m(7)GpppX pyrophosphatase activity" EXACT [EC:3.6.1.59]
xref: EC:3.6.1.59
+xref: RHEA:37099
+xref: RHEA:37103
xref: RHEA:65384
xref: RHEA:65388
is_a: GO:0016462 ! pyrophosphatase activity
property_value: skos:exactMatch EC:3.6.1.59
+property_value: skos:narrowMatch RHEA:37099
+property_value: skos:narrowMatch RHEA:37103
property_value: skos:narrowMatch RHEA:65384
property_value: skos:narrowMatch RHEA:65388
created_by: pg
@@ -493567,11 +494993,15 @@
synonym: "m(7)GpppN-mRNA hydrolase activity" EXACT []
xref: EC:3.6.1.62
xref: RHEA:37371
+xref: RHEA:60868
+xref: RHEA:60872
xref: RHEA:67484
is_a: GO:0016462 ! pyrophosphatase activity
property_value: skos:exactMatch EC:3.6.1.62
property_value: skos:exactMatch RHEA:67484
property_value: skos:narrowMatch RHEA:37371
+property_value: skos:narrowMatch RHEA:60868
+property_value: skos:narrowMatch RHEA:60872
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23290" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30193" xsd:anyURI
created_by: pg
@@ -496305,7 +497735,7 @@
name: regulation of nitric oxide-cGMP mediated signal transduction
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of nitric oxide-cGMP mediated signal transduction." [PMID:35931019]
-is_a: GO:0010749 ! regulation of nitric oxide mediated signal transduction
+is_a: GO:1902531 ! regulation of intracellular signal transduction
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
relationship: regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
@@ -496318,8 +497748,8 @@
name: positive regulation of nitric oxide-cGMP mediated signal transduction
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of nitric oxide-cGMP mediated signal transduction." [PMID:14615391]
-is_a: GO:0010750 ! positive regulation of nitric oxide mediated signal transduction
is_a: GO:0141149 ! regulation of nitric oxide-cGMP mediated signal transduction
+is_a: GO:1902533 ! positive regulation of intracellular signal transduction
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
relationship: positively_regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
@@ -496332,8 +497762,8 @@
name: negative regulation of nitric oxide-cGMP mediated signal transduction
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of nitric oxide-cGMP mediated signal transduction." [PMID:35931019]
-is_a: GO:0010751 ! negative regulation of nitric oxide mediated signal transduction
is_a: GO:0141149 ! regulation of nitric oxide-cGMP mediated signal transduction
+is_a: GO:1902532 ! negative regulation of intracellular signal transduction
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
relationship: negatively_regulates GO:0038060 ! nitric oxide-cGMP-mediated signaling
@@ -500877,13 +502307,17 @@
synonym: "quinol-nitrate oxidoreductase activity" RELATED [EC:1.7.5.1]
xref: EC:1.7.5.1
xref: RHEA:29119
+xref: RHEA:29123
xref: RHEA:29127
+xref: RHEA:29131
xref: RHEA:56144
is_a: GO:0008940 ! nitrate reductase activity
property_value: skos:exactMatch EC:1.7.5.1
property_value: skos:exactMatch RHEA:56144
property_value: skos:narrowMatch RHEA:29119
+property_value: skos:narrowMatch RHEA:29123
property_value: skos:narrowMatch RHEA:29127
+property_value: skos:narrowMatch RHEA:29131
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27675" xsd:anyURI
created_by: rynl
creation_date: 2024-04-24T22:45:01Z
@@ -500892,11 +502326,12 @@
id: GO:0160183
name: autophagosome-membrane adaptor activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together a target membrane and an autophagosome during autophagy." [PMID:30544615, PMID:36635405]
-is_a: GO:0043495 ! protein-membrane adaptor activity
+def: "The binding activity of a molecule that brings together a target membrane and an autophagosome membrane during autophagy." [PMID:30544615, PMID:36635405]
+is_a: GO:0140177 ! membrane-membrane adaptor activity
is_a: GO:0160247 ! autophagy cargo adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27704" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28285" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: rynl
creation_date: 2024-04-25T00:20:20Z
@@ -500970,9 +502405,10 @@
id: GO:0160190
name: peroxisome-mitochondrion membrane tether activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together the peroxisome and the mitochondrial outer membrane, establishing the localization of the peroxisome close to the mitochondrion." [PMID:29720625, PMID:38669296]
-is_a: GO:0043495 ! protein-membrane adaptor activity
+def: "The binding activity of a molecule that brings together the peroxisome membrane and the mitochondrial outer membrane, establishing the localization of the peroxisome close to the mitochondrion." [PMID:29720625, PMID:38669296]
+is_a: GO:0140177 ! membrane-membrane adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28255" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: rynl
creation_date: 2024-06-24T22:53:31Z
@@ -500986,18 +502422,30 @@
xref: MetaCyc:RXN-22825
xref: MetaCyc:RXN-22826
xref: MetaCyc:RXN-22827
+xref: RHEA:69831
+xref: RHEA:69835
+xref: RHEA:69839
+xref: RHEA:69871
+xref: RHEA:70003
xref: RHEA:70059
xref: RHEA:70063
xref: RHEA:70067
+xref: RHEA:70071
is_a: GO:0008395 ! steroid hydroxylase 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
property_value: skos:exactMatch EC:1.14.14.178
property_value: skos:narrowMatch MetaCyc:RXN-22825
property_value: skos:narrowMatch MetaCyc:RXN-22826
property_value: skos:narrowMatch MetaCyc:RXN-22827
+property_value: skos:narrowMatch RHEA:69831
+property_value: skos:narrowMatch RHEA:69835
+property_value: skos:narrowMatch RHEA:69839
+property_value: skos:narrowMatch RHEA:69871
+property_value: skos:narrowMatch RHEA:70003
property_value: skos:narrowMatch RHEA:70059
property_value: skos:narrowMatch RHEA:70063
property_value: skos:narrowMatch RHEA:70067
+property_value: skos:narrowMatch RHEA:70071
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28221" xsd:anyURI
created_by: rynl
creation_date: 2024-06-27T00:40:39Z
@@ -501136,14 +502584,16 @@
[Term]
id: GO:0160203
-name: mitochondrial disulfide relay system
+name: protein import into the intermembrane space via the disulfide relay system
namespace: biological_process
-def: "A protein folding process that facilitates the import of a subset of soluble proteins into mitochondrial intermembrane space via disulfide bond formation." [PMID:32936885, PMID:37159021]
+def: "The import of small cysteine-containing proteins from the cytosol across the outer mitochondrial membrane via the TOM complex driven by oxidative folding." [PMID:32936885, PMID:37159021]
+synonym: "CHCHD4/Mia40-dependent import" NARROW []
synonym: "MIA pathway" EXACT []
+synonym: "mitochondrial disulfide relay system" EXACT []
synonym: "mitochondrial intermembrane space assembly pathway" EXACT []
-is_a: GO:0006457 ! protein folding
-relationship: part_of GO:0045041 ! protein import into mitochondrial intermembrane space
+is_a: GO:0045041 ! protein import into mitochondrial intermembrane space
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28663" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
created_by: rynl
creation_date: 2024-08-05T23:59:12Z
@@ -501154,8 +502604,9 @@
def: "The binding activity of a molecule that brings together two mitochondrion membranes via membrane lipid binding or by interacting with a mitochondrial outer membrane protein, to establish or maintain the localization of the mitochondrion." [PMID:38843396]
synonym: "mitochondrion membrane tether activity" RELATED []
synonym: "mitochondrion outer membrane tether activity" RELATED []
-is_a: GO:0043495 ! protein-membrane adaptor activity
+is_a: GO:0140177 ! membrane-membrane adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28694" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: rynl
creation_date: 2024-08-15T17:06:16Z
@@ -501280,8 +502731,9 @@
name: endoplasmic reticulum-plasma membrane adaptor activity
namespace: molecular_function
def: "The binding activity of a molecule that brings together a plasma membrane with an endoplasmic reticulum membrane, via membrane lipid binding, to establish membrane contact sites and mediate exchange and communication." [PMID:23041194, PMID:39239853]
-is_a: GO:0043495 ! protein-membrane adaptor activity
+is_a: GO:0140177 ! membrane-membrane adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28899" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: rynl
creation_date: 2024-09-12T20:22:40Z
@@ -501478,9 +502930,10 @@
id: GO:0160229
name: peroxisome-endoplasmic reticulum membrane tether activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together a peroxisome and an ER membrane, either via membrane lipid binding or by interacting with a membrane protein." [PMID:39271061]
+def: "The binding activity of a molecule that brings together a peroxisome membrane and an ER membrane, either via membrane lipid binding or by interacting with a membrane protein." [PMID:39271061]
is_a: GO:0170009 ! endoplasmic reticulum-organelle membrane tether activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29432" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: rynl
creation_date: 2024-12-17T01:17:43Z
@@ -502345,9 +503798,11 @@
name: 6-carboxymethyl-5-methyl-4-hydroxypyridin-2-ol 3-C-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: 6-carboxymethyl-5-methyl-4-hydroxypyridin-2-ol + S-adenosyl-L-methionine = 6-carboxymethyl-3,5-dimethyl-4-hydroxypyridin-2-ol + S-adenosyl-L-homocysteine + H+." [PMID:27391308, RHEA:85483]
+xref: EC:2.1.1.400
xref: KEGG_REACTION:R13499
xref: RHEA:85483
is_a: GO:0008168 ! methyltransferase activity
+property_value: skos:exactMatch EC:2.1.1.400
property_value: skos:exactMatch RHEA:85483
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/30721" xsd:anyURI
created_by: rynl
@@ -502445,8 +503900,8 @@
name: dopamine loading into synaptic vesicle
namespace: biological_process
def: "The active transport of dopamine neurotransmitters into a synaptic vesicle." [PMID:29666153]
-is_a: GO:0015872 ! dopamine transport
-is_a: GO:0098700 ! neurotransmitter loading into synaptic vesicle
+is_a: GO:0015842 ! aminergic neurotransmitter loading into synaptic vesicle
+is_a: GO:0015850 ! organic hydroxy compound transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
created_by: rynl
creation_date: 2025-12-02T22:02:35Z
@@ -502456,8 +503911,8 @@
name: tyramine loading into synaptic vesicle
namespace: biological_process
def: "The active transport of tyramine neurotransmitters into a synaptic vesicle." [PMID:15849736, PMID:9870940]
-is_a: GO:0098700 ! neurotransmitter loading into synaptic vesicle
-is_a: GO:7770032 ! tyramine transport
+is_a: GO:0015842 ! aminergic neurotransmitter loading into synaptic vesicle
+is_a: GO:0015850 ! organic hydroxy compound transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
created_by: rynl
creation_date: 2025-12-02T23:16:14Z
@@ -502467,7 +503922,7 @@
name: octopamine loading into synaptic vesicle
namespace: biological_process
def: "The active transport of octopamine neurotransmitters into a synaptic vesicle." [PMID:15849736, PMID:9870940]
-is_a: GO:0098700 ! neurotransmitter loading into synaptic vesicle
+is_a: GO:0015842 ! aminergic neurotransmitter loading into synaptic vesicle
is_a: GO:7770033 ! octopamine transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
created_by: rynl
@@ -502584,6 +504039,17 @@
replaced_by: GO:0004447
[Term]
+id: GO:0160321
+name: vesicle docking activity
+namespace: molecular_function
+def: "The binding activity of a protein that directly mediates the stable attachment of a transport vesicle to a target membrane, bringing the two membranes into close apposition." [PMID:28237810]
+comment: Vesicle docking activity succeeds vesicle tethering activity and precedes fusogenic activity in the vesicle membrane fusion pathway.
+is_a: GO:0140177 ! membrane-membrane adaptor activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31880" xsd:anyURI
+created_by: rynl
+creation_date: 2026-04-17T21:35:33Z
+
+[Term]
id: GO:0170001
name: ergothioneine transmembrane transporter activity
namespace: molecular_function
@@ -502674,8 +504140,9 @@
name: endoplasmic reticulum-organelle membrane tether activity
namespace: molecular_function
def: "The binding activity of a molecule that brings together two membranes, either via membrane lipid binding or by interacting with a membrane protein, to establish or maintain membrane contact sites and mediate organelle exchange and communication." [PMID:29858488]
-is_a: GO:0043495 ! protein-membrane adaptor activity
+is_a: GO:0140177 ! membrane-membrane adaptor activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25429" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: ew
creation_date: 2023-06-29T16:28:28Z
@@ -502751,9 +504218,10 @@
id: GO:0170016
name: endoplasmic reticulum-endosome tether activity
namespace: molecular_function
-def: "The binding activity of a molecule that brings together an endosome and an ER membrane either via membrane lipid binding or by interacting with an endosome protein, to establish and facilitate organelle exchange." [PMID:33124732]
+def: "The binding activity of a molecule that brings together an endosome membrane and an ER membrane either via membrane lipid binding or by interacting with an endosome protein, to establish and facilitate organelle exchange." [PMID:33124732]
is_a: GO:0170009 ! endoplasmic reticulum-organelle membrane tether activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25429" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31866" xsd:anyURI
created_by: ew
creation_date: 2023-06-29T16:31:41Z
@@ -502976,7 +504444,6 @@
name: isopentenyl pyrophosphate import into mitochondrion
namespace: biological_process
def: "The process in which isopentenyl pyrophosphate is transported across a membrane into the mitochondrion." [GOC:ew, PMID:37813972]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015914 ! phospholipid transport
is_a: GO:0032365 ! intracellular lipid transport
is_a: GO:0170036 ! import into the mitochondrion
@@ -509241,16 +510708,13 @@
[Term]
id: GO:1900237
-name: positive regulation of induction of conjugation with cellular fusion
+name: obsolete positive regulation of induction of conjugation with cellular fusion
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of induction of conjugation with cellular fusion." [GOC:TermGenie]
-synonym: "up regulation of induction of conjugation with cellular fusion" EXACT [GOC:TermGenie]
-synonym: "up-regulation of induction of conjugation with cellular fusion" EXACT [GOC:TermGenie]
-synonym: "upregulation of induction of conjugation with cellular fusion" EXACT [GOC:TermGenie]
-is_a: GO:0031139 ! positive regulation of conjugation with cellular fusion
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0010514 ! induction of conjugation with cellular fusion
-relationship: positively_regulates GO:0010514 ! induction of conjugation with cellular fusion
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of induction of conjugation with cellular fusion." [GOC:TermGenie]
+comment: This term was obsoleted because it is a pre-composed term that should be represented as a GO-CAM model.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31335" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0031139
created_by: al
creation_date: 2012-03-26T10:14:16Z
@@ -514483,9 +515947,9 @@
synonym: "inhibition of butyryl-CoA biosynthesis from acetyl-CoA" EXACT [GOC:TermGenie]
synonym: "inhibition of butyryl-CoA biosynthetic process from acetyl-CoA" NARROW [GOC:TermGenie]
synonym: "negative regulation of butyryl-CoA biosynthesis from acetyl-CoA" EXACT [GOC:TermGenie]
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0045717 ! negative regulation of fatty acid biosynthetic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:1900494 ! regulation of butyryl-CoA biosynthetic process from acetyl-CoA
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0044579 ! butyryl-CoA biosynthetic process from acetyl-CoA
@@ -514507,8 +515971,8 @@
synonym: "up-regulation of butyryl-CoA biosynthetic process from acetyl-CoA" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA biosynthesis from acetyl-CoA" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA biosynthetic process from acetyl-CoA" EXACT [GOC:TermGenie]
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0045723 ! positive regulation of fatty acid biosynthetic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
is_a: GO:1900494 ! regulation of butyryl-CoA biosynthetic process from acetyl-CoA
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0044579 ! butyryl-CoA biosynthetic process from acetyl-CoA
@@ -514549,9 +516013,9 @@
synonym: "inhibition of butyryl-CoA catabolic process to butanol" NARROW [GOC:TermGenie]
synonym: "inhibition of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGenie]
synonym: "negative regulation of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGenie]
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0045922 ! negative regulation of fatty acid metabolic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:0050995 ! negative regulation of lipid catabolic process
is_a: GO:0051055 ! negative regulation of lipid biosynthetic process
is_a: GO:1900497 ! regulation of butyryl-CoA catabolic process to butanol
@@ -514576,8 +516040,8 @@
synonym: "up-regulation of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA catabolic process to butanol" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA catabolism to butanol" EXACT [GOC:TermGenie]
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0045923 ! positive regulation of fatty acid metabolic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
is_a: GO:0046889 ! positive regulation of lipid biosynthetic process
is_a: GO:0050996 ! positive regulation of lipid catabolic process
is_a: GO:1900497 ! regulation of butyryl-CoA catabolic process to butanol
@@ -514619,9 +516083,9 @@
synonym: "inhibition of butyryl-CoA catabolic process to butyrate" NARROW [GOC:TermGenie]
synonym: "inhibition of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGenie]
synonym: "negative regulation of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGenie]
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0045717 ! negative regulation of fatty acid biosynthetic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:0050995 ! negative regulation of lipid catabolic process
is_a: GO:1900500 ! regulation of butyryl-CoA catabolic process to butyrate
intersection_of: GO:0065007 ! biological regulation
@@ -514644,8 +516108,8 @@
synonym: "up-regulation of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA catabolic process to butyrate" EXACT [GOC:TermGenie]
synonym: "upregulation of butyryl-CoA catabolism to butyrate" EXACT [GOC:TermGenie]
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0045723 ! positive regulation of fatty acid biosynthetic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
is_a: GO:0050996 ! positive regulation of lipid catabolic process
is_a: GO:1900500 ! regulation of butyryl-CoA catabolic process to butyrate
intersection_of: GO:0065007 ! biological regulation
@@ -520018,7 +521482,6 @@
synonym: "deoxycarnitine transport" RELATED [GOC:TermGenie]
synonym: "gamma-Butyrobetain transport" EXACT [GOC:TermGenie]
synonym: "gamma-butyrobetaine transport" EXACT [GOC:TermGenie]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015838 ! amino-acid betaine transport
created_by: jl
creation_date: 2012-05-29T02:32:37Z
@@ -520049,7 +521512,6 @@
synonym: "Adriamycin transport" RELATED [GOC:TermGenie]
synonym: "doxorubicine transport" RELATED [GOC:TermGenie]
synonym: "doxorubicinum transport" RELATED [GOC:TermGenie]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0071705 ! nitrogen compound transport
is_a: GO:1901656 ! glycoside transport
@@ -521829,7 +523291,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving sarcinapterin." [GOC:mengo_curators, GOC:TermGenie]
synonym: "sarcinapterin metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:0042558 ! pteridine-containing compound metabolic process
is_a: GO:0072350 ! tricarboxylic acid metabolic process
@@ -524107,7 +525568,7 @@
synonym: "negative regulation of sarcinapterin formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of sarcinapterin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0009890 ! negative regulation of biosynthetic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1900971 ! regulation of sarcinapterin biosynthetic process
intersection_of: GO:0065007 ! biological regulation
@@ -524146,7 +525607,7 @@
synonym: "upregulation of sarcinapterin formation" EXACT [GOC:TermGenie]
synonym: "upregulation of sarcinapterin synthesis" EXACT [GOC:TermGenie]
is_a: GO:0009891 ! positive regulation of biosynthetic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1900971 ! regulation of sarcinapterin biosynthetic process
intersection_of: GO:0065007 ! biological regulation
@@ -525610,13 +527071,15 @@
[Term]
id: GO:1901056
-name: trimethylenediamine catabolic process
+name: obsolete trimethylenediamine catabolic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the breakdown of trimethylenediamine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00010]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the breakdown of trimethylenediamine." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00010]
+comment: The reason for obsoletion is that this term was made in error.
synonym: "trimethylenediamine breakdown" EXACT [GOC:TermGenie]
synonym: "trimethylenediamine catabolism" EXACT [GOC:TermGenie]
synonym: "trimethylenediamine degradation" EXACT [GOC:TermGenie]
-is_a: GO:0006598 ! polyamine catabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31766" xsd:anyURI
+is_obsolete: true
created_by: yaf
creation_date: 2012-06-28T04:53:06Z
@@ -526593,7 +528056,7 @@
synonym: "actinorhodin breakdown" EXACT [GOC:TermGenie]
synonym: "actinorhodin catabolism" EXACT [GOC:TermGenie]
synonym: "actinorhodin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0043649 ! dicarboxylic acid catabolic process
+is_a: GO:0046395 ! carboxylic acid catabolic process
created_by: yaf
creation_date: 2012-07-11T03:06:00Z
@@ -526606,7 +528069,7 @@
synonym: "actinorhodin biosynthesis" EXACT [GOC:TermGenie]
synonym: "actinorhodin formation" EXACT [GOC:TermGenie]
synonym: "actinorhodin synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
+is_a: GO:0046394 ! carboxylic acid biosynthetic process
created_by: yaf
creation_date: 2012-07-11T03:06:08Z
@@ -526807,8 +528270,7 @@
namespace: biological_process
def: "The chemical reactions and pathways involving gentamycin." [GOC:TermGenie, GOC:yaf, UniPathway:UPA00967]
synonym: "gentamycin metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0016137 ! glycoside metabolic process
-is_a: GO:0019751 ! polyol metabolic process
+is_a: GO:0008152 ! metabolic process
created_by: yaf
creation_date: 2012-07-11T03:26:25Z
@@ -526820,8 +528282,7 @@
synonym: "gentamycin breakdown" EXACT [GOC:TermGenie]
synonym: "gentamycin catabolism" EXACT [GOC:TermGenie]
synonym: "gentamycin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0030649 ! aminoglycoside antibiotic catabolic process
-is_a: GO:0046174 ! polyol catabolic process
+is_a: GO:0009056 ! catabolic process
is_a: GO:1901128 ! gentamycin metabolic process
created_by: yaf
creation_date: 2012-07-11T03:26:51Z
@@ -526835,8 +528296,7 @@
synonym: "gentamycin biosynthesis" EXACT [GOC:TermGenie]
synonym: "gentamycin formation" EXACT [GOC:TermGenie]
synonym: "gentamycin synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0030648 ! aminoglycoside antibiotic biosynthetic process
-is_a: GO:0046173 ! polyol biosynthetic process
+is_a: GO:0009058 ! biosynthetic process
is_a: GO:1901128 ! gentamycin metabolic process
created_by: yaf
creation_date: 2012-07-11T03:26:59Z
@@ -529504,6 +530964,7 @@
synonym: "tartrate degradation" EXACT [GOC:TermGenie]
is_a: GO:0016052 ! carbohydrate catabolic process
is_a: GO:0019579 ! aldaric acid catabolic process
+is_a: GO:0043649 ! dicarboxylic acid catabolic process
is_a: GO:1901275 ! tartrate metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
created_by: yaf
@@ -529520,6 +530981,7 @@
synonym: "tartrate synthesis" EXACT [GOC:TermGenie]
is_a: GO:0016051 ! carbohydrate biosynthetic process
is_a: GO:0019578 ! aldaric acid biosynthetic process
+is_a: GO:0043650 ! dicarboxylic acid biosynthetic process
is_a: GO:1901275 ! tartrate metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
created_by: yaf
@@ -529615,7 +531077,6 @@
synonym: "5,6,7,8-tetrahydromethanopterin breakdown" EXACT [GOC:TermGenie]
synonym: "5,6,7,8-tetrahydromethanopterin catabolism" EXACT [GOC:TermGenie]
synonym: "5,6,7,8-tetrahydromethanopterin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0042560 ! pteridine-containing compound catabolic process
is_a: GO:0043649 ! dicarboxylic acid catabolic process
is_a: GO:0046434 ! organophosphate catabolic process
@@ -531070,7 +532531,6 @@
synonym: "cyclic 2,3-bisphospho-D-glyceric acid formation" EXACT [GOC:TermGenie]
synonym: "cyclic 2,3-bisphospho-D-glyceric acid synthesis" EXACT [GOC:TermGenie]
synonym: "cyclic 2,3-diphosphoglycerate biosynthesis" EXACT [CHEBI:28699]
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0072330 ! monocarboxylic acid biosynthetic process
is_a: GO:0090407 ! organophosphate biosynthetic process
is_a: GO:1901137 ! carbohydrate derivative biosynthetic process
@@ -532173,9 +533633,9 @@
synonym: "negative regulation of tetrapyrrole biosynthesis from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "negative regulation of tetrapyrrole formation from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "negative regulation of tetrapyrrole synthesis from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0045763 ! negative regulation of amino acid metabolic process
is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:0062014 ! negative regulation of small molecule metabolic process
is_a: GO:1901413 ! regulation of tetrapyrrole biosynthetic process from glycine and succinyl-CoA
is_a: GO:1901464 ! negative regulation of tetrapyrrole biosynthetic process
@@ -532214,8 +533674,8 @@
synonym: "upregulation of tetrapyrrole biosynthetic process from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "upregulation of tetrapyrrole formation from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
synonym: "upregulation of tetrapyrrole synthesis from glycine and succinyl-CoA" EXACT [GOC:TermGenie]
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0045764 ! positive regulation of amino acid metabolic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
is_a: GO:0062013 ! positive regulation of small molecule metabolic process
is_a: GO:1901413 ! regulation of tetrapyrrole biosynthetic process from glycine and succinyl-CoA
is_a: GO:1901465 ! positive regulation of tetrapyrrole biosynthetic process
@@ -537077,7 +538537,6 @@
xref: MetaCyc:PWY-5103
xref: MetaCyc:PWY-5104
xref: MetaCyc:PWY-5108
-is_a: GO:0006549 ! isoleucine metabolic process
is_a: GO:0009067 ! aspartate family amino acid biosynthetic process
is_a: GO:0009082 ! branched-chain amino acid biosynthetic process
property_value: skos:narrowMatch MetaCyc:ILEUSYN-PWY
@@ -539461,7 +540920,6 @@
synonym: "5,6,7,8-tetrahydrosarcinapterin breakdown" EXACT [GOC:TermGenie]
synonym: "5,6,7,8-tetrahydrosarcinapterin catabolism" EXACT [GOC:TermGenie]
synonym: "5,6,7,8-tetrahydrosarcinapterin degradation" EXACT [GOC:TermGenie]
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0042560 ! pteridine-containing compound catabolic process
is_a: GO:0046434 ! organophosphate catabolic process
is_a: GO:0072352 ! tricarboxylic acid catabolic process
@@ -541567,7 +543025,6 @@
name: glycerate transmembrane transporter activity
namespace: molecular_function
def: "Enables the transfer of glycerate from one side of a membrane to the other." [GOC:TermGenie, PMID:23382251]
-is_a: GO:0008028 ! monocarboxylic acid transmembrane transporter activity
is_a: GO:0015144 ! carbohydrate transmembrane transporter activity
is_a: GO:0042879 ! aldonate transmembrane transporter activity
relationship: part_of GO:1901975 ! glycerate transmembrane transport
@@ -542412,7 +543869,6 @@
name: L-lysine transport
namespace: biological_process
def: "The directed movement of a L-lysine 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]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015807 ! L-amino acid transport
created_by: kmv
creation_date: 2013-03-27T16:09:06Z
@@ -542422,7 +543878,6 @@
name: L-histidine transport
namespace: biological_process
def: "The directed movement of a L-histidine 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]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015801 ! aromatic amino acid transport
is_a: GO:0015802 ! basic amino acid transport
is_a: GO:0015807 ! L-amino acid transport
@@ -546091,15 +547546,15 @@
[Term]
id: GO:1902224
-name: ketone body metabolic process
+name: obsolete ketone body metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving ketone body." [GOC:pr, GOC:TermGenie]
+def: "OBSOLETE. The chemical reactions and pathways involving ketone body." [GOC:pr, GOC:TermGenie]
+comment: This term was obsoleted because it is an unnecessary grouping term.
synonym: "ketone body metabolism" EXACT [GOC:TermGenie]
xref: Reactome:R-HSA-74182 "Ketone body metabolism"
-is_a: GO:0006091 ! generation of precursor metabolites and energy
-is_a: GO:0044281 ! small molecule metabolic process
-is_a: GO:1901568 ! fatty acid derivative metabolic process
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22938" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31806" xsd:anyURI
+is_obsolete: true
created_by: pr
creation_date: 2013-06-13T10:37:54Z
@@ -549014,7 +550469,6 @@
name: ceramide 1-phosphate transport
namespace: biological_process
def: "The directed movement of a ceramide 1-phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:TermGenie, PMID:23863933]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015914 ! phospholipid transport
is_a: GO:0035627 ! ceramide transport
created_by: uh
@@ -551452,7 +552906,6 @@
namespace: biological_process
def: "The process in which 5'-adenylyl sulfate is transported across a membrane." [GOC:TermGenie, PMID:24296033]
synonym: "adenosine 5'-phosphosulfate transmembrane transport" EXACT [PMID:24296033]
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0015868 ! purine ribonucleotide transport
is_a: GO:0051503 ! adenine nucleotide transport
is_a: GO:0072348 ! sulfur compound transport
@@ -555090,7 +556543,6 @@
synonym: "6-sulfoquinovose(1-) breakdown" EXACT [GOC:TermGenie]
synonym: "6-sulfoquinovose(1-) catabolism" EXACT [GOC:TermGenie]
synonym: "6-sulfoquinovose(1-) degradation" EXACT [GOC:TermGenie]
-is_a: GO:0016054 ! organic acid catabolic process
is_a: GO:0044273 ! sulfur compound catabolic process
is_a: GO:1901136 ! carbohydrate derivative catabolic process
created_by: dph
@@ -557718,7 +559170,7 @@
synonym: "poly(hydroxyvalerate) biosynthesis" EXACT [GOC:TermGenie]
synonym: "poly(hydroxyvalerate) formation" EXACT [GOC:TermGenie]
synonym: "poly(hydroxyvalerate) synthesis" EXACT [GOC:TermGenie]
-is_a: GO:1901441 ! poly(hydroxyalkanoate) biosynthetic process
+is_a: GO:0009058 ! biosynthetic process
created_by: tt
creation_date: 2014-04-21T19:12:38Z
@@ -557757,7 +559209,7 @@
synonym: "poly(hydroxyalkanoate) formation from glucose" EXACT [GOC:TermGenie]
synonym: "poly(hydroxyalkanoate) synthesis from glucose" EXACT [GOC:TermGenie]
is_a: GO:0006006 ! glucose metabolic process
-is_a: GO:1901441 ! poly(hydroxyalkanoate) biosynthetic process
+is_a: GO:0009058 ! biosynthetic process
created_by: tt
creation_date: 2014-04-21T22:49:07Z
@@ -557771,7 +559223,7 @@
synonym: "poly(hydroxyalkanoate) formation from fatty acid" EXACT [GOC:TermGenie]
synonym: "poly(hydroxyalkanoate) synthesis from fatty acid" EXACT [GOC:TermGenie]
is_a: GO:0006631 ! fatty acid metabolic process
-is_a: GO:1901441 ! poly(hydroxyalkanoate) biosynthetic process
+is_a: GO:0009058 ! biosynthetic process
created_by: tt
creation_date: 2014-04-21T22:53:59Z
@@ -563310,31 +564762,29 @@
[Term]
id: GO:1903184
-name: L-dopa metabolic process
+name: obsolete L-dopa metabolic process
namespace: biological_process
-def: "The chemical reactions and pathways involving L-dopa." [GO_REF:0000068, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:8822146]
+def: "OBSOLETE. The chemical reactions and pathways involving L-dopa." [GO_REF:0000068, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:8822146]
+comment: This term was obsoleted because there is no evidence that this process exists; L-dopa metabolism has been used in the literature to mean L-dopa degradation.
synonym: "L-dopa metabolism" EXACT [GOC:TermGenie]
-is_a: GO:0006575 ! modified amino acid metabolic process
-is_a: GO:0009072 ! aromatic amino acid metabolic process
-is_a: GO:0170033 ! L-amino acid metabolic process
-is_a: GO:0170041 ! non-proteinogenic amino acid metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31703" xsd:anyURI
+is_obsolete: true
+replaced_by: GO:0120575
created_by: bf
creation_date: 2014-07-14T15:06:00Z
[Term]
id: GO:1903185
-name: L-dopa biosynthetic process
+name: obsolete L-dopa biosynthetic process
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of L-dopa." [GO_REF:0000068, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:8822146]
+def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of L-dopa." [GO_REF:0000068, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:8822146]
+comment: This term was obsoleted because there is no evidence that this process exists.
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:0009073 ! aromatic amino acid family biosynthetic process
-is_a: GO:0042398 ! modified amino acid biosynthetic process
-is_a: GO:0170034 ! L-amino acid biosynthetic process
-is_a: GO:0170043 ! non-proteinogenic amino acid biosynthetic process
-is_a: GO:1903184 ! L-dopa metabolic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31703" xsd:anyURI
+is_obsolete: true
created_by: bf
creation_date: 2014-07-14T15:06:06Z
@@ -563462,26 +564912,25 @@
[Term]
id: GO:1903195
-name: regulation of L-dopa biosynthetic process
+name: obsolete regulation of L-dopa biosynthetic process
namespace: biological_process
-def: "Any process that modulates the frequency, rate or extent of L-dopa biosynthetic process." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
+def: "OBSOLETE. Any process that modulates the frequency, rate or extent of L-dopa biosynthetic process." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "regulation of L-dopa anabolism" EXACT [GOC:TermGenie]
synonym: "regulation of L-dopa biosynthesis" EXACT [GOC:TermGenie]
synonym: "regulation of L-dopa formation" EXACT [GOC:TermGenie]
synonym: "regulation of L-dopa synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0062012 ! regulation of small molecule metabolic process
-is_a: GO:2000282 ! regulation of amino acid biosynthetic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:1903185 ! L-dopa biosynthetic process
-relationship: regulates GO:1903185 ! L-dopa biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31703" xsd:anyURI
+is_obsolete: true
created_by: bf
creation_date: 2014-07-21T09:12:37Z
[Term]
id: GO:1903196
-name: negative regulation of L-dopa biosynthetic process
+name: obsolete negative regulation of L-dopa biosynthetic process
namespace: biological_process
-def: "Any process that stops, prevents or reduces the frequency, rate or extent of L-dopa biosynthetic process." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
+def: "OBSOLETE. Any process that stops, prevents or reduces the frequency, rate or extent of L-dopa biosynthetic process." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "down regulation of L-dopa anabolism" EXACT [GOC:TermGenie]
synonym: "down regulation of L-dopa biosynthesis" EXACT [GOC:TermGenie]
synonym: "down regulation of L-dopa biosynthetic process" EXACT [GOC:TermGenie]
@@ -563506,20 +564955,17 @@
synonym: "negative regulation of L-dopa biosynthesis" EXACT [GOC:TermGenie]
synonym: "negative regulation of L-dopa formation" EXACT [GOC:TermGenie]
synonym: "negative regulation of L-dopa synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0062014 ! negative regulation of small molecule metabolic process
-is_a: GO:1903195 ! regulation of L-dopa biosynthetic process
-is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:1903185 ! L-dopa biosynthetic process
-relationship: negatively_regulates GO:1903185 ! L-dopa biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31703" xsd:anyURI
+is_obsolete: true
created_by: bf
creation_date: 2014-07-21T09:12:44Z
[Term]
id: GO:1903197
-name: positive regulation of L-dopa biosynthetic process
+name: obsolete positive regulation of L-dopa biosynthetic process
namespace: biological_process
-def: "Any process that activates or increases the frequency, rate or extent of L-dopa biosynthetic process." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:16731528]
+def: "OBSOLETE. Any process that activates or increases the frequency, rate or extent of L-dopa biosynthetic process." [GO_REF:0000058, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:16731528]
+comment: This term was obsoleted because there is no evidence that this process exists.
synonym: "activation of L-dopa anabolism" NARROW [GOC:TermGenie]
synonym: "activation of L-dopa biosynthesis" NARROW [GOC:TermGenie]
synonym: "activation of L-dopa biosynthetic process" NARROW [GOC:TermGenie]
@@ -563544,12 +564990,8 @@
synonym: "upregulation of L-dopa biosynthetic process" EXACT [GOC:TermGenie]
synonym: "upregulation of L-dopa formation" EXACT [GOC:TermGenie]
synonym: "upregulation of L-dopa synthesis" EXACT [GOC:TermGenie]
-is_a: GO:0062013 ! positive regulation of small molecule metabolic process
-is_a: GO:1903195 ! regulation of L-dopa biosynthetic process
-is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
-intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:1903185 ! L-dopa biosynthetic process
-relationship: positively_regulates GO:1903185 ! L-dopa biosynthetic process
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31703" xsd:anyURI
+is_obsolete: true
created_by: bf
creation_date: 2014-07-21T09:12:49Z
@@ -564608,8 +566050,8 @@
is_a: GO:0062012 ! regulation of small molecule metabolic process
is_a: GO:2000282 ! regulation of amino acid biosynthetic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: regulates GO:0019240 ! citrulline biosynthetic process
-relationship: regulates GO:0019240 ! citrulline biosynthetic process
+intersection_of: regulates GO:0019240 ! L-citrulline biosynthetic process
+relationship: regulates GO:0019240 ! L-citrulline biosynthetic process
created_by: rl
creation_date: 2014-08-04T15:24:34Z
@@ -564646,8 +566088,8 @@
is_a: GO:1903248 ! regulation of citrulline biosynthetic process
is_a: GO:2000283 ! negative regulation of amino acid biosynthetic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: negatively_regulates GO:0019240 ! citrulline biosynthetic process
-relationship: negatively_regulates GO:0019240 ! citrulline biosynthetic process
+intersection_of: negatively_regulates GO:0019240 ! L-citrulline biosynthetic process
+relationship: negatively_regulates GO:0019240 ! L-citrulline biosynthetic process
created_by: rl
creation_date: 2014-08-04T15:24:46Z
@@ -564684,8 +566126,8 @@
is_a: GO:1903248 ! regulation of citrulline biosynthetic process
is_a: GO:2000284 ! positive regulation of amino acid biosynthetic process
intersection_of: GO:0065007 ! biological regulation
-intersection_of: positively_regulates GO:0019240 ! citrulline biosynthetic process
-relationship: positively_regulates GO:0019240 ! citrulline biosynthetic process
+intersection_of: positively_regulates GO:0019240 ! L-citrulline biosynthetic process
+relationship: positively_regulates GO:0019240 ! L-citrulline biosynthetic process
created_by: rl
creation_date: 2014-08-04T15:24:52Z
@@ -573769,12 +575211,13 @@
[Term]
id: GO:1903712
-name: cysteine transmembrane transport
+name: L-cysteine transmembrane transport
namespace: biological_process
-def: "The directed movement of cysteine across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:17435223]
-is_a: GO:0003333 ! amino acid transmembrane transport
-is_a: GO:0042883 ! cysteine transport
-is_a: GO:1905039 ! carboxylic acid transmembrane transport
+def: "The directed movement of L-cysteine across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:17435223]
+synonym: "cysteine transmembrane transport" BROAD []
+is_a: GO:0042883 ! L-cysteine transport
+is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27479" xsd:anyURI
created_by: vw
creation_date: 2014-12-06T08:15:06Z
@@ -573977,8 +575420,8 @@
synonym: "inhibition of phospholipid metabolic process" NARROW [GOC:TermGenie]
synonym: "inhibition of phospholipid metabolism" NARROW [GOC:TermGenie]
synonym: "negative regulation of phospholipid metabolism" EXACT [GOC:TermGenie]
+is_a: GO:0010563 ! negative regulation of phosphorus metabolic process
is_a: GO:0045833 ! negative regulation of lipid metabolic process
-is_a: GO:0045936 ! negative regulation of phosphate metabolic process
is_a: GO:1903725 ! regulation of phospholipid metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0006644 ! phospholipid metabolic process
@@ -574000,8 +575443,8 @@
synonym: "up-regulation of phospholipid metabolism" EXACT [GOC:TermGenie]
synonym: "upregulation of phospholipid metabolic process" EXACT [GOC:TermGenie]
synonym: "upregulation of phospholipid metabolism" EXACT [GOC:TermGenie]
+is_a: GO:0010562 ! positive regulation of phosphorus metabolic process
is_a: GO:0045834 ! positive regulation of lipid metabolic process
-is_a: GO:0045937 ! positive regulation of phosphate metabolic process
is_a: GO:1903725 ! regulation of phospholipid metabolic process
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0006644 ! phospholipid metabolic process
@@ -575021,7 +576464,6 @@
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:0015695 ! organic cation transport
is_a: GO:0015829 ! valine transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
created_by: al
@@ -575473,7 +576915,6 @@
synonym: "isoleucine import" BROAD []
synonym: "L-isoleucine import" BROAD []
synonym: "L-isoleucine import into cell" EXACT []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0089718 ! amino acid import across plasma membrane
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
is_a: GO:1903714 ! isoleucine transmembrane transport
@@ -575489,7 +576930,6 @@
synonym: "L-threonine import" BROAD []
synonym: "L-threonine import into cell" EXACT []
synonym: "L-threonine uptake" EXACT [GOC:bf]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015826 ! threonine transport
is_a: GO:0089718 ! amino acid import across plasma membrane
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
@@ -575535,7 +576975,6 @@
synonym: "asparagine import" BROAD []
synonym: "L-asparagine import into cell" EXACT []
is_a: GO:0006867 ! asparagine transport
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0089718 ! amino acid import across plasma membrane
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
is_a: GO:1903713 ! asparagine transmembrane transport
@@ -575796,10 +577235,10 @@
synonym: "L-arginine import" NARROW []
synonym: "L-arginine transport" BROAD []
synonym: "L-arginine uptake" NARROW []
-is_a: GO:0015695 ! organic cation transport
is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
is_a: GO:1990822 ! basic amino acid transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22228" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31823" xsd:anyURI
created_by: vw
creation_date: 2015-01-20T10:38:15Z
@@ -581520,7 +582959,7 @@
synonym: "protein localisation in microvillus" EXACT [GOC:TermGenie]
synonym: "protein localisation to microvillus" EXACT [GOC:TermGenie]
synonym: "protein localization in microvillus" EXACT [GOC:TermGenie]
-is_a: GO:0008104 ! intracellular protein localization
+is_a: GO:1903119 ! protein localization to actin cytoskeleton
created_by: kmv
creation_date: 2015-04-01T18:14:41Z
@@ -590185,15 +591624,17 @@
[Term]
id: GO:1904541
-name: fungal-type cell wall disassembly involved in conjugation with cellular fusion
+name: mating projection tip cell wall disassembly
namespace: biological_process
-def: "Any fungal-type cell wall disassembly that is involved in conjugation with cellular fusion." [GO_REF:0000060, GOC:TermGenie, PMID:25825517]
+def: "Any fungal-type cell wall disassembly that is involved in conjugation with cellular fusion, where the cell wall is locally disassembled to enable conjugation with cellular fusion." [GO_REF:0000060, GOC:TermGenie, PMID:25825517]
synonym: "fungal-type cell wall disassembly involved in cell fusion" RELATED [GOC:TermGenie]
+synonym: "fungal-type cell wall disassembly involved in conjugation with cellular fusion" EXACT []
synonym: "fungal-type cell wall disassembly involved in mating" RELATED [GOC:TermGenie]
is_a: GO:0071853 ! fungal-type cell wall disassembly
intersection_of: GO:0071853 ! fungal-type cell wall disassembly
intersection_of: part_of GO:0000747 ! conjugation with cellular fusion
relationship: part_of GO:0000747 ! conjugation with cellular fusion
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31753" xsd:anyURI
created_by: al
creation_date: 2015-08-10T17:12:51Z
@@ -591188,10 +592629,10 @@
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 assembly" BROAD []
synonym: "actin fusion focus formation" EXACT [GOC:TermGenie]
-is_a: GO:0010927 ! cellular component assembly involved in morphogenesis
is_a: GO:0030036 ! actin cytoskeleton organization
-relationship: part_of GO:0031382 ! mating projection formation
+relationship: part_of GO:0000755 ! cytogamy
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21688" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31774" xsd:anyURI
created_by: al
creation_date: 2015-08-26T10:34:48Z
@@ -591204,6 +592645,8 @@
synonym: "protein localisation to actin fusion focus" EXACT [GOC:TermGenie]
synonym: "protein localization in actin fusion focus" EXACT [GOC:TermGenie]
is_a: GO:0015031 ! protein transport
+relationship: part_of GO:0000755 ! cytogamy
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31774" xsd:anyURI
created_by: al
creation_date: 2015-08-26T10:36:22Z
@@ -598910,6 +600353,7 @@
synonym: "regulation of warburg's respiratory enzyme activity" RELATED [GOC:TermGenie]
is_a: GO:0010155 ! regulation of proton transport
is_a: GO:0022898 ! regulation of transmembrane transporter activity
+is_a: GO:0051341 ! regulation of oxidoreductase activity
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0004129 ! cytochrome-c oxidase activity
relationship: regulates GO:0004129 ! cytochrome-c oxidase activity
@@ -599002,6 +600446,7 @@
synonym: "upregulation of NADH cytochrome c oxidase" EXACT [GOC:TermGenie]
synonym: "upregulation of warburg's respiratory enzyme activity" RELATED [GOC:TermGenie]
is_a: GO:0032414 ! positive regulation of ion transmembrane transporter activity
+is_a: GO:0051353 ! positive regulation of oxidoreductase activity
is_a: GO:1904959 ! regulation of cytochrome-c oxidase activity
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0004129 ! cytochrome-c oxidase activity
@@ -602559,7 +604004,6 @@
name: carcinine import across plasma membrane
namespace: biological_process
def: "The directed movement of carcinine from outside of a cell, across the plasma membrane and into the cytosol." [GO_REF:0000075, GOC:dph, GOC:TermGenie, PMID:26653853, PMID:26713872]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0045117 ! azole transmembrane transport
is_a: GO:0072337 ! modified amino acid transport
is_a: GO:0098739 ! import across plasma membrane
@@ -606131,7 +607575,6 @@
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
created_by: tb
creation_date: 2016-07-22T01:40:59Z
@@ -624842,7 +626285,6 @@
alt_id: GO:0015788
def: "The process in which UDP-N-acetylglucosamine is transported across a membrane." [PMID:10788474]
synonym: "UDP-N-acetylglucosamine transport" RELATED []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0090481 ! pyrimidine nucleotide-sugar transmembrane transport
created_by: vw
creation_date: 2014-11-27T11:56:35Z
@@ -624854,7 +626296,6 @@
alt_id: GO:0015784
def: "The process in which GDP-mannose is transported across a membrane." [PMID:9395539]
synonym: "GDP-mannose transport" RELATED []
-is_a: GO:0015711 ! organic anion transport
is_a: GO:0090480 ! purine nucleotide-sugar transmembrane transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27059" xsd:anyURI
created_by: vw
@@ -626604,10 +628045,12 @@
[Term]
id: GO:1990727
-name: tubulin folding cofactor complex
+name: obsolete tubulin folding cofactor complex
namespace: cellular_component
-def: "A multimeric protein complex involved in tubulin alpha-beta-subunit folding assembly consisting of beta-tubulin-TFC-D, alpha-tubulin-TFC-E and TFC-C, through which tubulin subunit association and dimer release occur." [GOC:vw, PMID:12445400]
-is_a: GO:0032991 ! protein-containing complex
+def: "OBSOLETE. A multimeric protein complex involved in tubulin alpha-beta-subunit folding assembly consisting of beta-tubulin-TFC-D, alpha-tubulin-TFC-E and TFC-C, through which tubulin subunit association and dimer release occur." [GOC:vw, PMID:12445400]
+comment: This term was obsoleted because it was created by mistake; this is a pathway, not a complex.
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31828" xsd:anyURI
+is_obsolete: true
created_by: pr
creation_date: 2015-04-08T10:29:43Z
@@ -627333,7 +628776,7 @@
id: GO:1990799
name: mitochondrial tRNA wobble position uridine thiolation
namespace: biological_process
-def: "The process in which a uridine residue at position 34 in the anticodon of a mitochondrial tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from cysteine to position C2 by several steps." [PMID:15509579]
+def: "The process in which a uridine residue at position 34 in the anticodon of a mitochondrial tRNA is post-transcriptionally thiolated at the C2 position. This process involves transfer of a sulfur from L-cysteine to position C2 by several steps." [PMID:15509579]
is_a: GO:0002143 ! tRNA wobble position uridine thiolation
is_a: GO:0070899 ! mitochondrial tRNA wobble uridine modification
is_a: GO:0070903 ! mitochondrial tRNA thio-modification
@@ -627571,9 +629014,8 @@
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:0015695 ! organic cation transport
is_a: GO:0032974 ! amino acid transmembrane export from vacuole
-is_a: GO:1902475 ! L-alpha-amino acid transmembrane transport
+is_a: GO:1903826 ! L-arginine transmembrane transport
created_by: vw
creation_date: 2015-08-06T15:06:33Z
@@ -627581,13 +629023,14 @@
id: GO:1990819
name: mating projection actin fusion focus
namespace: cellular_component
-def: "A focus at the mating projection tip where the cell wall is degraded during conjugation with cellular fusion. Actin filaments form an aster-like structure from this location." [PMID:25825517]
+def: "A focus at the mating projection tip where the cell wall is degraded during cytogamy. Actin filaments form an aster-like structure from this location." [PMID:25825517]
synonym: "actin fusion focus" BROAD []
is_a: GO:0110165 ! cellular anatomical structure
relationship: has_part GO:0005884 ! actin filament
relationship: part_of GO:0015629 ! actin cytoskeleton
relationship: part_of GO:0043332 ! mating projection tip
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21449" xsd:anyURI
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31774" xsd:anyURI
created_by: al
creation_date: 2015-08-10T16:52:15Z
@@ -644347,7 +645790,6 @@
def: "The chemical reactions and pathways resulting in the breakdown of a D-tagatose 6-phosphate." [GOC:mengo_curators]
synonym: "D-tagatose 6-phosphate catabolism" EXACT [GOC:obol]
xref: UniPathway:UPA00704
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0046434 ! organophosphate catabolic process
is_a: GO:1901136 ! carbohydrate derivative catabolic process
created_by: jl
@@ -644359,7 +645801,6 @@
namespace: biological_process
def: "The chemical reactions and pathways involving a D-glycero-D-manno-heptose 7-phosphate." [GOC:mengo_curators]
synonym: "D-glycero-D-manno-heptose 7-phosphate metabolism" EXACT [GOC:obol]
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
is_a: GO:1901135 ! carbohydrate derivative metabolic process
created_by: jl
@@ -644944,7 +646385,6 @@
namespace: biological_process
def: "The chemical reactions and pathways resulting in the formation of a methanopterin." [GOC:mengo_curators]
synonym: "methanopterin biosynthesis" EXACT [GOC:obol]
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0042559 ! pteridine-containing compound biosynthetic process
is_a: GO:0090407 ! organophosphate biosynthetic process
created_by: jl
@@ -645257,7 +646697,6 @@
name: N-methylnicotinate transport
namespace: biological_process
def: "The directed movement of a N-methylnicotinateacetate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:obol]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015697 ! quaternary ammonium group transport
created_by: tb
creation_date: 2011-10-18T05:16:08Z
@@ -647297,7 +648736,6 @@
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 metabolism" EXACT [GOC:obol]
is_a: GO:0006040 ! amino sugar metabolic process
-is_a: GO:0006796 ! phosphate-containing compound metabolic process
is_a: GO:0019637 ! organophosphate metabolic process
created_by: tb
creation_date: 2012-01-13T11:28:58Z
@@ -648086,20 +649524,18 @@
[Term]
id: GO:7770032
-name: tyramine transport
+name: obsolete tyramine transport
namespace: biological_process
-def: "The directed movement of tyramine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Tyramine is a monoamine neurotransmitter occurring predominantly in invertebrates." [PMID:15849736, PMID:32305263, PMID:9870940]
-is_a: GO:0015844 ! monoamine transport
-is_a: GO:0015850 ! organic hydroxy compound transport
+def: "OBSOLETE. The directed movement of tyramine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Tyramine is a monoamine neurotransmitter occurring predominantly in invertebrates." [PMID:15849736, PMID:32305263, PMID:9870940]
+comment: The reason for obsoletion is that this is an unnecessary grouping term and annotations should be made to more mechanism/location specific terms.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
-created_by: dragon-ai-agent
+is_obsolete: true
[Term]
id: GO:7770033
name: octopamine transport
namespace: biological_process
def: "The directed movement of octopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Octopamine is a monoamine neurotransmitter occurring predominantly in invertebrates." [PMID:15849736, PMID:32305263, PMID:9870940]
-is_a: GO:0015695 ! organic cation transport
is_a: GO:0015850 ! organic hydroxy compound transport
is_a: GO:0071705 ! nitrogen compound transport
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31143" xsd:anyURI
@@ -648387,6 +649823,117 @@
created_by: dragon-ai-agent
creation_date: 2026-03-24T17:37:00Z
+[Term]
+id: GO:7770057
+name: copper ion import into Golgi lumen
+namespace: biological_process
+def: "The directed import of copper cation from the cytosol across the Golgi membrane into the Golgi lumen." [PMID:7708696, PMID:9325307]
+synonym: "copper ion import across Golgi membrane" EXACT []
+synonym: "copper ion import into Golgi apparatus" EXACT []
+synonym: "copper ion import into the Golgi" EXACT []
+synonym: "cytosol to Golgi apparatus copper transport" EXACT []
+is_a: GO:0035434 ! copper ion transmembrane transport
+is_a: GO:0140820 ! cytosol to Golgi apparatus transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31723" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-04-01T09:01:56Z
+
+[Term]
+id: GO:7770058
+name: mitochondrial protein import pathway
+namespace: biological_process
+def: "The import of proteins from the cytosol to their final destination in the mitochondria." [PMID:36931257]
+synonym: "mitochondrial protein import" EXACT []
+is_a: GO:0006839 ! mitochondrial transport
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-04-01T10:06:36Z
+
+[Term]
+id: GO:7770059
+name: alpha helical protein insertion into mitochondrial outer membrane
+namespace: biological_process
+def: "The import of alpha helical and tail-anchored proteins from the cytosol and their insertion into the mitochondrial outer membrane." [PMID:40782022]
+comment: In yeast, the insertase is the mitochondrial import (MIM) complex, composed of Mim1 and Mim2. In higher eukaryotes, the functional counterpart MTCH performs a similar role despite lacking sequence and structural homology, reflecting convergent evolution.
+synonym: "MIM pathway" NARROW []
+synonym: "MTCH pathway" NARROW []
+is_a: GO:0006886 ! intracellular protein transport
+is_a: GO:0010496 ! intercellular transport
+is_a: GO:0045040 ! protein insertion into mitochondrial outer membrane
+is_a: GO:0070585 ! protein localization to mitochondrion
+is_a: GO:0072657 ! protein localization to membrane
+is_a: GO:7770058 ! mitochondrial protein import pathway
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-04-01T12:53:29Z
+
+[Term]
+id: GO:7770060
+name: TOM-TIM23-SORT-mediated protein insertion into the mitochondrial inner membrane
+namespace: biological_process
+def: "The import of proteins from the cytosol across the outer mitochondrial membrane and laterally inserted into the inner membrane. Typically acting on single-pass transmembrane proteins with an N-terminal targeting sequence and an internal hydrophobic stop-transfer sequence which targets them for lateral insertion." [PMID:36931257]
+comment: Some proteins utilize this pathway but can be further processed and released from the inner membrane into the IMS.
+synonym: "stop-transfer pathway" RELATED []
+synonym: "TOM-TIM23-SORT pathway" EXACT []
+is_a: GO:0045039 ! protein insertion into mitochondrial inner membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-04-01T13:32:53Z
+
+[Term]
+id: GO:7770061
+name: TOM-TIM22-mediated mitochondrial inner membrane protein insertion
+namespace: biological_process
+def: "The import of multipass-membrane proteins from the cytosol and their insertion into the mitochondrial inner membrane, supported by tiny-tim chaperones." [PMID:36931257]
+synonym: "carrier import pathway" NARROW []
+synonym: "carrier pathway" NARROW []
+is_a: GO:0045039 ! protein insertion into mitochondrial inner membrane
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-04-01T16:37:07Z
+
+[Term]
+id: GO:7770062
+name: vesicle membrane tethering activity
+namespace: molecular_function
+def: "A membrane-membrane adaptor activity that provides the first point of contact and physically bridges the vesicle membrane and its target membrane prior to vesicle docking and fusion." [PMID:19575650, PMID:19887069]
+synonym: "vesicle membrane tether activity" EXACT []
+synonym: "vesicle tethering activity" EXACT []
+is_a: GO:0140177 ! membrane-membrane adaptor activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31863" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-04-13T23:43:55Z
+
+[Term]
+id: GO:7770063
+name: beta barrel protein insertion into mitochondrial outer membrane
+namespace: biological_process
+def: "The import of beta barrel proteins from the cytosol and their insertion into the mitochondrial outer membrane." [PMID:36931257]
+synonym: "TOM-SAM pathway" EXACT []
+is_a: GO:0006886 ! intracellular protein transport
+is_a: GO:0010496 ! intercellular transport
+is_a: GO:0045040 ! protein insertion into mitochondrial outer membrane
+is_a: GO:0070585 ! protein localization to mitochondrion
+is_a: GO:0072657 ! protein localization to membrane
+is_a: GO:7770058 ! mitochondrial protein import pathway
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/31711" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-04-15T13:26:12Z
+
+[Term]
+id: GO:7770064
+name: actin-filament cross-linking activity
+namespace: molecular_function
+def: "An adaptor activity that brings together two actin filaments, enabling the bundling or networking of actin filaments (F-actin)." [GOC:vw, PMID:37025173]
+synonym: "actin filament cross-linking activity" EXACT []
+synonym: "actin filament crosslinking activity" EXACT []
+synonym: "F-actin cross-linking activity" EXACT []
+is_a: GO:0008093 ! cytoskeletal adaptor activity
+relationship: has_part GO:0051015 ! actin filament binding
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19185" xsd:anyURI
+created_by: dragon-ai-agent
+creation_date: 2026-04-16T11:21:46Z
+
[Typedef]
id: ends_during
name: ends during