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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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acetyl-CoA C-acetyltransferase activity (GO:0003985) parentage #25289

Closed sjm41 closed 1 year ago

sjm41 commented 1 year ago

We currently have this arrangement:

C-acyltransferase activity
|__acetyl-CoA C-acyltransferase activity (GO:0003988, EC:2.3.1.16, RHEA:21564)
    |__acetyl-CoA C-acetyltransferase activity (GO:0003985, EC:2.3.1.9, RHEA:21036)

GO:0003988/EC:2.3.1.16 is: Catalysis of the reaction: acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA.

And GO:0003985/EC:2.3.1.9 is: Catalysis of the reaction: 2 acetyl-CoA = CoA + acetoacetyl-CoA

But I don't think the latter is a sub-class of the former? Supporting that, https://www.rhea-db.org/rhea/21564 doesn't list RHEA:21036 as a 'specific form of this reaction'.

So, I think the "is_a: GO:0003988 ! acetyl-CoA C-acyltransferase activity" should be removed from GO:0003985:

id: GO:0003985 name: acetyl-CoA C-acetyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: 2 acetyl-CoA = CoA + acetoacetyl-CoA." [EC:2.3.1.9] synonym: "2-methylacetoacetyl-CoA thiolase" BROAD [EC:2.3.1.9] synonym: "3-oxothiolase activity" RELATED [EC:2.3.1.9] synonym: "acetoacetyl-CoA thiolase activity" RELATED [EC:2.3.1.9] synonym: "acetyl coenzyme A thiolase activity" RELATED [EC:2.3.1.9] synonym: "acetyl-CoA acetyltransferase activity" RELATED [EC:2.3.1.9] synonym: "acetyl-CoA:acetyl-CoA C-acetyltransferase activity" RELATED [EC:2.3.1.9] synonym: "acetyl-CoA:N-acetyltransferase activity" RELATED [EC:2.3.1.9] synonym: "beta-acetoacetyl coenzyme A thiolase activity" RELATED [EC:2.3.1.9] synonym: "thiolase II" RELATED [EC:2.3.1.9] xref: EC:2.3.1.9 xref: MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN xref: RHEA:21036 xref: UM-BBD_enzymeID:e0144 is_a: GO:0003988 ! acetyl-CoA C-acyltransferase activity is_a: GO:0016453 ! C-acetyltransferase activity

pgaudet commented 1 year ago

@kaxelsen Isn't acetyl an acyl? why isn't RHEA:21036 a more specific reaction of RHEA:21564 ?

Thanks, Pascale

deustp01 commented 1 year ago

For what it's worth https://byjus.com/question-answer/is-acyl-and-acetyl-the-same/ says that an acetyl group is_a acyl group, specifically the one where the "R" moiety of the acyl is CH3.

kaxelsen commented 1 year ago

@kaxelsen Isn't acetyl an acyl? why isn't RHEA:21036 a more specific reaction of RHEA:21564 ?

Thanks, Pascale

@pgaudet, Yes acetyl is a very short acyl group, and I have now added the relationship.

sjm41 commented 1 year ago

Thanks @kaxelsen ! @pgaudet - there's nothing to do here, sorry for the trouble! (I think I was just foxed by the how the 2 reactions/definitions are written differently, but I see now that this is all correct.)