diff --git a/src/ontology/go-edit.obo b/src/ontology/go-edit.obo index a5fb34ab6..cbffd6b02 100644 --- a/src/ontology/go-edit.obo +++ b/src/ontology/go-edit.obo @@ -46257,7 +46257,7 @@ is_a: GO:0042083 ! 5,10-methylenetetrahydrofolate-dependent methyltransferase ac id: GO:0004800 name: thyroxine 5'-deiodinase activity namespace: molecular_function -def: "Catalysis of the reaction: 3,5,3'-L-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + donor-H2." [EC:1.21.99.4] +def: "Catalysis of the reaction: 3,3',5-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + acceptor-H2." [RHEA:19745] synonym: "acceptor:3,5,3'-triiodo-L-thyronine oxidoreductase (iodinating)" RELATED [EC:1.21.99.4] synonym: "diiodothyronine 5'-deiodinase activity" RELATED [EC:1.21.99.4] synonym: "iodothyronine 5'-deiodinase activity" RELATED [EC:1.21.99.4] @@ -46271,7 +46271,8 @@ synonym: "type II iodothyronine deiodinase activity" NARROW [EC:1.21.99.4] xref: EC:1.21.99.4 xref: MetaCyc:THYROXINE-DEIODINASE-RXN xref: RHEA:19745 -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0004801 @@ -46907,8 +46908,11 @@ is_a: GO:0140096 ! catalytic activity, acting on a protein id: GO:0004836 name: tyramine-beta hydroxylase activity namespace: molecular_function -def: "Catalysis of the hydroxylation of tyramine to form octopamine." [PMID:10745161] -is_a: GO:0016491 ! oxidoreductase activity +def: "Catalysis of the reaction: tyramine + L-ascorbate + O2 = (R)-octopamine + L-dehydroascorbate + H2O." [PMID:10745161, RHEA:57132] +xref: MetaCyc:RXN-14645 +xref: RHEA:57132 {source="skos:exactMatch"} +is_a: GO:0016715 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0004837 @@ -83314,7 +83318,6 @@ xref: MetaCyc:RXN-982 xref: RHEA:22016 xref: UM-BBD_reactionID:r0635 is_a: GO:0030611 ! arsenate reductase activity -is_a: GO:0030614 ! oxidoreductase activity, acting on phosphorus or arsenic in donors, disulfide as acceptor [Term] id: GO:0008795 @@ -99620,8 +99623,9 @@ xref: MetaCyc:RXN-8678 {source="skos:narrowMatch"} xref: MetaCyc:RXN-8683 {source="skos:narrowMatch"} xref: RHEA:34419 {source="skos:narrowMatch"} xref: RHEA:34427 {source="skos:narrowMatch"} -is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor +is_a: GO:0120546 ! oxidoreductase activity, reducing C-O-C group as acceptor 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/29701" xsd:anyURI [Term] id: GO:0010284 @@ -99634,8 +99638,9 @@ xref: MetaCyc:RXN-8679 {source="skos:narrowMatch"} xref: MetaCyc:RXN-8684 {source="skos:narrowMatch"} xref: RHEA:34423 {source="skos:narrowMatch"} xref: RHEA:34431 {source="skos:narrowMatch"} -is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor +is_a: GO:0120546 ! oxidoreductase activity, reducing C-O-C group as acceptor 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/29701" xsd:anyURI [Term] id: GO:0010285 @@ -140864,12 +140869,15 @@ is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, [Term] id: GO:0019168 -name: 2-octaprenylphenol hydroxylase activity +name: 2-polyprenylphenol 6-hydroxylase activity namespace: molecular_function -def: "Catalysis of the reaction: 2-octaprenylphenol + NADPH + O2 + H+ = 2-octaprenyl-6-hydroxyphenol + NADP+ + H2O." [MetaCyc:2-OCTAPRENYLPHENOL-HYDROX-RXN] -xref: MetaCyc:2-OCTAPRENYLPHENOL-HYDROX-RXN -xref: RHEA:27790 -is_a: GO:0016491 ! oxidoreductase activity +def: "Catalysis of the reaction: a 2-(all-trans-polyprenyl)phenol + NADPH + O2 + H+ = a 3-(all-trans-polyprenyl)benzene-1,2-diol + NADP+ + H2O." [RHEA:55892] +synonym: "2-octaprenylphenol hydroxylase activity" NARROW [] +xref: EC:1.14.13.240 {source="skos:exactMatch"} +xref: MetaCyc:RXN-18459 +xref: RHEA:55892 {source="skos:exactMatch"} +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: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0019170 @@ -140922,7 +140930,8 @@ name: tetrahydrothiophene 1-oxide reductase activity namespace: molecular_function def: "Catalysis of the reaction: tetrahydrothiophene 1-oxide + reduced acceptor = tetrahydrothiophene + acceptor." [MetaCyc:THTOREDUCT-RXN] xref: MetaCyc:THTOREDUCT-RXN -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0016671 ! oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0019176 @@ -163163,15 +163172,18 @@ id: GO:0030611 name: arsenate reductase activity namespace: molecular_function def: "Catalysis of the interconversion of arsenate and arsenite." [GOC:mah] -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0030614 ! oxidoreductase activity, acting on phosphorus or arsenic in donors, disulfide as acceptor [Term] id: GO:0030612 name: arsenate reductase (thioredoxin) activity namespace: molecular_function -def: "Catalysis of the reaction: arsenate + thioredoxin = arsenite + thioredoxin disulfide. Thioredoxin disulfide is also known as oxidized thioredoxin." [MetaCyc:RXN-10737] +def: "Catalysis of the reaction: arsenate + [thioredoxin]-dithiol + H+ = arsenite + [thioredoxin]-disulfide + H2O." [RHEA:43848] +xref: EC:1.20.4.4 {source="skos:exactMatch"} xref: MetaCyc:RXN-10737 +xref: RHEA:43848 {source="skos:exactMatch"} is_a: GO:0030611 ! arsenate reductase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0030613 @@ -197221,7 +197233,8 @@ synonym: "sulphur reductase activity" EXACT [] xref: EC:1.12.98.4 xref: MetaCyc:RXN-8269 xref: RHEA:35591 -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0046995 ! oxidoreductase activity, acting on hydrogen as donor, with other known acceptors +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0033797 @@ -197240,7 +197253,7 @@ is_a: GO:0016491 ! oxidoreductase activity id: GO:0033798 name: thyroxine 5-deiodinase activity namespace: molecular_function -def: "Catalysis of the reaction: 3,3',5'-triiodo-L-thyronine + iodide + A + H+ = L-thyroxine + AH2." [EC:1.21.99.3] +def: "Catalysis of the reaction: 3,3',5'-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + acceptor-H2." [RHEA:18897] synonym: "acceptor:3,3',5'-triiodo-L-thyronine oxidoreductase (iodinating) activity" RELATED [EC:1.21.99.3] synonym: "diiodothyronine 5'-deiodinase activity" BROAD [EC:1.21.99.3] synonym: "inner ring-deiodinating pathway" EXACT [PMID:20403357] @@ -197250,7 +197263,8 @@ synonym: "type III iodothyronine deiodinase activity" NARROW [EC:1.21.99.3] xref: EC:1.21.99.3 xref: MetaCyc:1.97.1.11-RXN xref: RHEA:18897 -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0046992 ! oxidoreductase activity, acting on X-H and Y-H to form an X-Y bond +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0033799 @@ -225056,13 +225070,16 @@ creation_date: 2012-09-19T11:52:25Z [Term] id: GO:0036354 -name: 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase activity +name: bacteriochlorophyllide-a dehydrogenase activity namespace: molecular_function -def: "Catalysis of the reaction: 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a = bacteriochlorophyllide a + 2 H+." [GOC:crds, InterPro:IPR005903, MetaCyc:RXN-8787, PMID:8437569] +def: "Catalysis of the reaction: 3-deacetyl-3-(1-hydroxyethyl)bacteriochlorophyllide a + NAD+ = bacteriochlorophyllide a + NADH + H+." [PMID:8437569, RHEA:19733] +synonym: "2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase activity" EXACT [] +xref: EC:1.1.1.396 {source="skos:exactMatch"} xref: MetaCyc:RXN-8787 -xref: RHEA:19733 -is_a: GO:0016491 ! oxidoreductase activity +xref: RHEA:19733 {source="skos:exactMatch"} +is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor relationship: part_of GO:0030494 ! bacteriochlorophyll biosynthetic process +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI created_by: bf creation_date: 2012-09-19T14:46:31Z @@ -252157,8 +252174,9 @@ synonym: "MleS" RELATED [] xref: EC:4.1.1.101 {source="skos:exactMatch"} xref: MetaCyc:RXN-16819 {source="skos:exactMatch"} xref: RHEA:46276 {source="skos:exactMatch"} -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0016831 ! carboxy-lyase activity property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28324" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0043884 @@ -265600,14 +265618,18 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i [Term] id: GO:0045301 -name: tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity +name: tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase activity namespace: molecular_function -def: "Catalysis of the reaction: tRNA-(2-methylthio-N-6-isopentenyl adenosine) = tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine) + O2. 2-methylthio-N-6-isopentenyl adenosine is also known as ms2i6A; 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine is also known as ms2io6A and 2-methylthio-cis-ribozeatin." [GOC:mlg, PMID:8253666] +def: "Catalysis of the reaction: 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + acceptor-H2 + O2 = N(6)-[(2E)-4-hydroxy-3-methylbut-2-en-1-yl]-2-(methylsulfanyl)adenosine(37) in tRNA + acceptor + H2O." [PMID:8253666, RHEA:65812] synonym: "2-methylthio-cis-ribozeatin hydroxylase activity" EXACT [] +synonym: "tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine)-hydroxylase activity" EXACT [] synonym: "tRNA-(2-methylthio-N-6-(cis-hydroxy)isopentenyladenosine)-hydroxylase activity" EXACT [] synonym: "tRNA-(ms2io6A)-hydroxylase activity" EXACT [] -is_a: GO:0016491 ! oxidoreductase activity +xref: EC:1.14.99.69 {source="skos:exactMatch"} +xref: RHEA:65812 {source="skos:exactMatch"} +is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen is_a: GO:0140101 ! catalytic activity, acting on a tRNA +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0045302 @@ -278000,7 +278022,8 @@ synonym: "VDE" RELATED [EC:1.23.5.1] synonym: "violaxanthin:ascorbate oxidoreductase activity" RELATED [EC:1.23.5.1] xref: EC:1.23.5.1 xref: RHEA:32371 -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0120546 ! oxidoreductase activity, reducing C-O-C group as acceptor +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0046423 @@ -328740,12 +328763,14 @@ is_a: GO:0016636 ! oxidoreductase activity, acting on the CH-CH group of donors, [Term] id: GO:0051744 -name: 3,8-divinyl protochlorophyllide a 8-vinyl reductase activity +name: 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (NADPH) activity namespace: molecular_function -def: "Catalysis of the reaction: divinyl protochlorophyllide a + NADPH + H+ = monovinyl protochlorophyllide a + NADP+." [MetaCyc:RXN1F-72] +def: "Catalysis of the reaction: protochlorophyllide a + NADP+ = 3,8-divinyl protochlorophyllide a + NADPH + H+." [RHEA:48884] +synonym: "3,8-divinyl protochlorophyllide a 8-vinyl reductase activity" BROAD [] xref: MetaCyc:RXN1F-72 -xref: RHEA:48884 -is_a: GO:0016491 ! oxidoreductase activity +xref: RHEA:48884 {source="skos:exactMatch"} +is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0051745 @@ -337074,7 +337099,8 @@ synonym: "pyrimidine oxygenase activity" BROAD [MetaCyc:RXN0-6444] xref: EC:1.14.99.46 xref: MetaCyc:RXN0-6444 xref: RHEA:31587 -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI creation_date: 2010-08-26T10:11:11Z [Term] @@ -338137,7 +338163,8 @@ namespace: molecular_function def: "Catalysis of the reaction: epoxyqueuosine in tRNA + reductant = queuosine in tRNA + oxidised reductant." [PMID:21502530, RHEA:32159] xref: EC:1.17.99.6 xref: RHEA:32159 -is_a: GO:0016491 ! oxidoreductase activity +is_a: GO:0016725 ! oxidoreductase activity, acting on CH or CH2 groups +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI [Term] id: GO:0052694 @@ -339024,13 +339051,17 @@ creation_date: 2011-09-22T03:25:30Z [Term] id: GO:0052755 -name: reduced coenzyme F420:quinone oxidoreductase activity +name: coenzyme F420H2:quinone oxidoreductase activity namespace: molecular_function -def: "Catalysis of the reaction: reduced coenzyme F420 + 2,3-dimethyl-1,4-naphthoquinone = coenzyme F420 + reduced 2,3-dimethyl-1,4-naphthoquinone. Reduced 2,3-dimethyl-1,4-naphthoquinone is also known as 2,3-dimethyl-1,4-hydronaphthoquinone." [GOC:mengo_curators, PMID:10971593, PMID:8055920] +def: "Catalysis of the reaction: oxidized coenzyme F420-(gamma-L-Glu)(n) + a quinol + H+ = reduced coenzyme F420-(gamma-L-Glu)(n) + a quinone." [PMID:10971593, PMID:8055920, RHEA:39663] synonym: "F420H2-dependent quinone oxidoreductase activity" EXACT [] synonym: "F420H2:2,3-dimethyl-1,4-naphthoquinone oxidoreductase activity" EXACT [] synonym: "F420H2:quinone oxidoreductase activity" EXACT [] -is_a: GO:0016491 ! oxidoreductase activity +synonym: "reduced coenzyme F420:quinone oxidoreductase activity" EXACT [] +xref: EC:1.1.98.4 {source="skos:exactMatch"} +xref: RHEA:39663 {source="skos:exactMatch"} +is_a: GO:0016614 ! oxidoreductase activity, acting on CH-OH group of donors +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI created_by: ai creation_date: 2011-09-22T04:08:13Z @@ -339140,13 +339171,16 @@ creation_date: 2011-09-29T04:05:44Z [Term] id: GO:0052765 -name: reduced coenzyme F420 oxidase activity +name: coenzyme F420H2 oxidase activity namespace: molecular_function -def: "Catalysis of the reaction: 2 reduced coenzyme F420 + O2 = 2 coenzyme F420 + 2 H2O." [GOC:mengo_curators, PMID:15340796] -synonym: "coenzyme F420H2 oxidase activity" EXACT [] +def: "Catalysis of the reaction: 2 reduced coenzyme F420-(gamma-L-Glu)(n) + O2 = 2 oxidized coenzyme F420-(gamma-L-Glu)(n) + 2 H2O + 2 H+." [PMID:15340796, RHEA:39711] synonym: "F420H2 oxidase activity" EXACT [] synonym: "F420H2:oxygen oxidoreductase activity" EXACT [] -is_a: GO:0016491 ! oxidoreductase activity +synonym: "reduced coenzyme F420 oxidase activity" EXACT [] +xref: EC:1.5.3.22 {source="skos:exactMatch"} +xref: RHEA:39711 {source="skos:exactMatch"} +is_a: GO:0016647 ! oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI created_by: ai creation_date: 2011-09-29T04:33:54Z @@ -450607,6 +450641,17 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: sjm creation_date: 2025-02-11T09:55:25Z +[Term] +id: GO:0120546 +name: oxidoreductase activity, reducing C-O-C group as acceptor +namespace: molecular_function +def: "Catalysis of an oxidation-reduction (redox) reaction in which a reducing C-O-C group acts as acceptor." [EC:1.23.-.-] +xref: EC:1.23.-.- +is_a: GO:0016491 ! oxidoreductase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/29701" xsd:anyURI +created_by: sjm +creation_date: 2025-02-11T18:09:07Z + [Term] id: GO:0140001 name: morula formation