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Source ontology files for the Gene Ontology
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Proposed obsoletions of some catalytic activity terms with no mappings #28382

Closed sjm41 closed 2 months ago

sjm41 commented 3 months ago

Some proposed obsoletions from reviewing catalytic activity leaf terms with no mappings but with an EC in the def xref (see https://docs.google.com/spreadsheets/d/1ytuqiOii6IYvMgy2rqRiy6JDCXIyucLcqcy5vFTO3bk/edit?gid=0#gid=0):

id: GO:0018071 name: NAD(P)-cysteine ADP-ribosyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: NAD(P)+ + L-cysteine = nicotinamide + N2-(ADP-D-ribosyl)-L-cysteine." [EC:2.4.2.-] is_a: GO:0016763 ! pentosyltransferase activity

id: GO:0018121 name: NAD(P)-asparagine ADP-ribosyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: NAD(P)+ + L-asparagine = nicotinamide + N2-(ADP-D-ribosyl)-L-asparagine." [EC:2.4.2.-] is_a: GO:0016763 ! pentosyltransferase activity

id: GO:0018127 name: NAD(P)-serine ADP-ribosyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: NAD(P)+ + L-serine = nicotinamide + N2-(ADP-D-ribosyl)-L-serine." [EC:2.4.2.-] is_a: GO:0016763 ! pentosyltransferase activity

None of these 3 terms have any annotations, and all of them are only defined by a partial EC (which corresponds to 'pentosyltransferases').

id: GO:0036136 name: kynurenine-oxaloacetate transaminase activity namespace: molecular_function def: "Catalysis of the reaction: L-kynurenine + 2-oxoglutarate = 4-(2-aminophenyl)-2,4-dioxobutanoate + L-aspartate." [EC:2.6.1.-, GOC:pde, PMID:15606768, PMID:4149765] synonym: "L-kynurenine-oxaloacetate transaminase activity" EXACT [GOC:bf] is_a: GO:0036137 ! kynurenine aminotransferase activity created_by: bf creation_date: 2012-03-06T02:14:11Z

This term has no annotations, and just has a partial EC in the def xref.

PMID:4149765 is a 1973 paper called 'Aromatic amino acid transaminase in rat intestine.' Can't tell which specific gene/protein that corresponds to.

PMID:15606768 is a 2004 paper. It says: 'In mammals, kynurenine aminotransferase I/glutamine transaminase K (EC2.6.1.64; KAT-I) is a multifunctional enzyme. In vitro, the enzyme catalyzes the transamination of several amino acids (e.g. glutamine, methionine, aromatic amino acids including kynurenine) and also possesses cysteine S-conjugate β-lyase activity (EC4.4.1.13)

I think that protein corresponds to KYAT1 (Q16773), which UniProt annotates to EC:2.6.1.7 (2-oxoglutarate + L-kynurenine = H2O + kynurenate + L-glutamate), as well as EC:2.6.1.64 (3-phenylpyruvate + L-glutamine = 2-oxoglutaramate + L-phenylalanine) and EC:4.4.1.13.

Searching in RHEA for the reaction given in GO:0036136, I can find this: RHEA:66088 L-kynurenine + oxaloacetate = 4-(2-aminophenyl)-2,4-dioxobutanoate + L-aspartate Three things to note:

So, overall, lots of reasons to obsolete GO:0036136.

id: GO:0004727 name: prenylated protein tyrosine phosphatase activity namespace: molecular_function def: "Catalysis of the reaction: prenylated-protein tyrosine phosphate + H2O = prenylated-protein tyrosine + phosphate." [EC:3.1.3.48] is_a: GO:0004725 ! protein tyrosine phosphatase activity

This term just has 3x TAS annotations, and the EC:3.1.3.48 def xref corresponds to the more general parent term 'protein tyrosine phosphatase activity'.

id: GO:0052789 name: mannan 1,3-beta-mannosidase activity namespace: molecular_function def: "Catalysis of the hydrolysis of (1->3)-beta-D-mannosidic linkages in mannans, releasing mannose." [EC:3.2.1.78, GOC:mengo_curators] synonym: "1,3-beta-D-mannan mannanohydrolase activity" RELATED [EC:3.2.1.78] synonym: "beta-1,3-mannan 3-mannanohydrolase activity" RELATED [EC:3.2.1.78] synonym: "exo-1,3-beta-mannanase activity" RELATED [EC:3.2.1.78] synonym: "exo-1,3-mannanase activity" RELATED [EC:3.2.1.78] synonym: "exo-beta-1,3-mannase activity" RELATED [EC:3.2.1.78] is_a: GO:0004567 ! beta-mannosidase activity created_by: ai creation_date: 2011-10-04T01:11:41Z

This term has no annotations, and the EC:3.2.1.78 number given in the def xref is actually for the hydrolysis of 1->4 linkages and is already correctly on a different GO term:

id: GO:0016985 name: mannan endo-1,4-beta-mannosidase activity namespace: molecular_function def: "Catalysis of the random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans." [EC:3.2.1.78] synonym: "1,4-beta-D-mannan mannanohydrolase activity" RELATED [EC:3.2.1.78] synonym: "beta-1,4-mannan 4-mannanohydrolase activity" RELATED [EC:3.2.1.78] synonym: "beta-D-mannanase activity" RELATED [EC:3.2.1.78] synonym: "beta-mannanase activity" BROAD [EC:3.2.1.78] synonym: "beta-mannanase B" RELATED [EC:3.2.1.78] synonym: "endo-1,4-beta-mannanase activity" RELATED [EC:3.2.1.78] synonym: "endo-1,4-mannanase activity" BROAD [EC:3.2.1.78] synonym: "endo-beta-1,4-mannase activity" RELATED [EC:3.2.1.78] synonym: "endo-beta-mannanase activity" BROAD [EC:3.2.1.78] xref: EC:3.2.1.78 xref: MetaCyc:3.2.1.78-RXN is_a: GO:0004567 ! beta-mannosidase activity

sjm41 commented 3 months ago

FYI, Sylvain at UP agrees with these obsoletions.

pgaudet commented 2 months ago