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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Parentage GO:0052593 tryptamine:oxygen oxidoreductase (deaminating) activity #26688

Closed lbreuza closed 10 months ago

lbreuza commented 11 months ago

Hi, why do you consider tryptamine has an aliphatic amine and not an aromatic amine. One should maybe change to GO:0008131 | primary amine oxidase activity. Best. Lionel

pgaudet commented 10 months ago

The confusion may have come from RHEA: https://www.rhea-db.org/rhea/59419 which has

More general form(s) of this reaction RHEA:16156 an aliphatic amine + H2O + O2 <=> an aldehyde + H2O2 + NH4+

A question for @kaxelsen ?

pgaudet commented 10 months ago

In GO we have xx reactions with the same EC: 'aliphatic amine oxidase activity' http://purl.obolibrary.org/obo/GO_0052595 'aminoacetone:oxygen oxidoreductase(deaminating) activity' http://purl.obolibrary.org/obo/GO_0052594 'phenethylamine:oxygen oxidoreductase (deaminating) activity' http://purl.obolibrary.org/obo/GO_0052596 'primary amine oxidase activity' http://purl.obolibrary.org/obo/GO_0008131 'tryptamine:oxygen oxidoreductase (deaminating) activity' http://purl.obolibrary.org/obo/GO_0052593

kaxelsen commented 10 months ago

The confusion may have come from RHEA: https://www.rhea-db.org/rhea/59419 which has

More general form(s) of this reaction RHEA:16156 an aliphatic amine + H2O + O2 <=> an aldehyde + H2O2 + NH4+

A question for @kaxelsen ?

RHEA:16153 used the wrong amine compound. The reaction has just been updated to use "a primary methyl amine" CHEBI:228804, which is equivalent to "a primary amine" and more general than "an aliphatic amine". The updated reaction will become public in 2024_03 scheduled for May 10.