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Accession number for GO_molecular function #1622

Closed guptapa closed 7 years ago

guptapa commented 7 years ago

Hi, I'm looking for the accession number for 4-aminobutyrate-pyruvate transaminase enzyme (EC: 2.6.1.96). I did not find it on GO live site. Following link is for more information about enzyme: http://www.brenda-enzymes.org/enzyme.php?ecno=2.6.1.96&Suchword=&reference=&UniProtAcc=&organism%5B%5D=Oryza+sativa&show_tm=0 Thanks.

krchristie commented 7 years ago

It looks like we do NOT have this EC number, though we do have a term with nearly that name, but a different EC#:

4-aminobutyrate:pyruvate transaminase activity (GO:0034387) Def: Catalysis of the reaction: 4-aminobutanoate + pyruvate = succinate semialdehyde + alanine. EC:2.6.1.19 GOC:mah

This looks like a mistake as the definition for this GO term looks like it matches the definition for EC:2.6.1.96, and not for EC:2.6.1.19, which is supposed to be "4-aminobutyrate—2-oxoglutarate transaminase". @hdrabkin Do you agree?

The only annotation to that term is a plant gene (http://amigo.geneontology.org/amigo/term/GO:0034387), so probably worth checking which EC number this gene actually has.

Here is info from the EC pages for these two EC numbers:

EC 2.6.1.19 (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/6/1/19.html) Accepted name: 4-aminobutyrate—2-oxoglutarate transaminase Reaction: 4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate Glossary: 4-aminobutanoate = γ-aminobutyrate = GABA

EC 2.6.1.96 (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/6/1/96.html) Accepted name: 4-aminobutyrate—pyruvate transaminase Reaction: (1) 4-aminobutanoate + pyruvate = succinate semialdehyde + L-alanine (2) 4-aminobutanoate + glyoxylate = succinate semialdehyde + glycine Systematic name: 4-aminobutanoate:pyruvate aminotransferase

This ticket should probably be transferred to the ontology tracker, but I don't know how to do that. Maybe @ukemi or @vanaukenk can move it.

hdrabkin commented 7 years ago

Yep, this is not right. These are two different critters. H

From: Karen R Christie notifications@github.com Reply-To: geneontology/go-annotation reply@reply.github.com Date: Friday, August 25, 2017 at 11:50 AM To: geneontology/go-annotation go-annotation@noreply.github.com Cc: me Harold.Drabkin@jax.org, Mention mention@noreply.github.com Subject: Re: [geneontology/go-annotation] Accession number for GO_molecular function (#1622)

It looks like we do NOT have this EC number, though we do have a term with nearly that name, but a different EC#:

4-aminobutyrate:pyruvate transaminase activity (GO:0034387) Def: Catalysis of the reaction: 4-aminobutanoate + pyruvate = succinate semialdehyde + alanine. EC:2.6.1.19 GOC:mah

This looks like a mistake as the definition for this GO term looks like it matches the definition for EC:2.6.1.96, and not for EC:2.6.1.19, which is supposed to be "4-aminobutyrate—2-oxoglutarate transaminase". @hdrabkinhttps://github.com/hdrabkin Do you agree?

The only annotation to that term is a plant gene (http://amigo.geneontology.org/amigo/term/GO:0034387), so probably worth checking which EC number this gene actually has.

Here is info from the EC pages for these two EC numbers:

EC 2.6.1.19 (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/6/1/19.html) Accepted name: 4-aminobutyrate—2-oxoglutarate transaminase Reaction: 4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate Glossary: 4-aminobutanoate = γ-aminobutyrate = GABA

EC 2.6.1.96 (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/6/1/96.html) Accepted name: 4-aminobutyrate—pyruvate transaminase Reaction: (1) 4-aminobutanoate + pyruvate = succinate semialdehyde + L-alanine (2) 4-aminobutanoate + glyoxylate = succinate semialdehyde + glycine Systematic name: 4-aminobutanoate:pyruvate aminotransferase

This ticket should probably be transferred to the ontology tracker, but I don't know how to do that. Maybe @ukemihttps://github.com/ukemi or @vanaukenkhttps://github.com/vanaukenk can move it.

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krchristie commented 7 years ago

This issue was moved to geneontology/go-ontology#14118

jaiswalp commented 7 years ago

So we need a new GO term for EC: 2.6.1.96 @deustp01 Please check when we get this term we need it in the Reactome central for curating a plant reaction

krchristie commented 7 years ago

PLEASE DO NOT COMMENT IN THIS TICKET

Please put all future comments to the ontology ticket that I moved this issue to: geneontology/go-ontology#14118