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Accession number for GO_molecular function #14118

Closed krchristie closed 7 years ago

krchristie commented 7 years ago

From @guptapa on August 24, 2017 23:22

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.

Copied from original issue: geneontology/go-annotation#1622

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.

krchristie commented 7 years ago

From @hdrabkin on August 25, 2017 15:56

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

@ukemi - I'll just take this ticket since I already started looking into it.

@tberardini - Could you help me look into the single annotation to the term "4-aminobutyrate:pyruvate transaminase activity" (GO:0034387) (http://amigo.geneontology.org/amigo/term/GO:0034387).

The cited paper is in a plant journal I don't have access to: http://www.arabidopsis.org/servlets/TairObject?accession=Publication:501706563

From the abstract, it looks to me like this annotation is meant to be to the 4-aminobutyrate—pyruvate transaminase activity, which corresponds to the name of the term and NOT to the associated EC number for this term. Could you check the paper and see if you agree with that assessment? Thanks!

krchristie commented 7 years ago

@jaiswalp @deustp01 Note that it looks like the existing term 4-aminobutyrate:pyruvate transaminase activity (GO:0034387) is already defined with the definition of EC: 2.6.1.96 though it is associated with EC:2.6.1.19, and the sole existing annotation of an A. thaliana gene looks to me (from the abstract only) like it is probably meant to be to the pyruvate term (the .96 EC number), NOT to the .19 EC number that is actually associated with this GO term.

@ukemi - In a case like this, would it be OK to just change the EC number reference to the one that matches the term name and definition (assuming Tanya confirms my thought that the existing TAIR annotation is meant to be to the .96 EC#), or would we need would we need to obsolete this term and make a new term for the .96 EC#?

tberardini commented 7 years ago

Hi Karen,

@krchristie : I looked at the full text of the paper:

"The expression of GABA-T was corroborated by the presence of GABA:pyruvate-T activity in a crude extract from the GABAT :pTrcHis cell line (specific activity was 2.6 nmol·mg protein–1·min–1), whereas no activity was detected in the no-insert:pTrcHisB line. ...{snip} ..These data indicate that the GABA:pyruvate-T activity only could be attributed to the expression of the Arabidopsis GABA-T cDNA insert."

The experiments used GABA (4-aminobutyrate) and pyruvate as substrates and the amount of succinic semialdehyde produced was assessed.

It looks like the annotation to the term name + def is correct but the EC number is not.

krchristie commented 7 years ago

Thanks Tanya!

jaiswalp commented 7 years ago

Great. Changing the EC# would work.

krchristie commented 7 years ago

@ukemi - Any objection to just changing the EC number on the existing term "4-aminobutyrate:pyruvate transaminase activity" (GO:0034387), since the current usage of the term is consistent with the name/def and not with the EC number?

There doesn't seem to be any need to create a term for the EC number incorrectly referred to in the current GO term as there are no annotations for that activity, nor a request for it.

ukemi commented 7 years ago

No objection if the definitions match.

jaiswalp commented 7 years ago

@deustp01 can you comment on it, The above goes with the GO policy,. How much effort you may need in Reactome to make the change by replacing the assigned catalyst__activity to a new GO term.

guptapa commented 7 years ago

Assigning new EC # (2.6.1.96) with the existing term "4-aminobutyrate:pyruvate transaminase activity" (GO:0034387) would work for plants but not for animal folks. Go term for "4-aminobutyrate:alpha-ketoglutarate transaminase activity" (EC: 2.6.1.19) is required for animal enzyme as Human Reactome guys use this term.

krchristie commented 7 years ago

Definitely interested in opinion of @deustp01 . However, if we cannot correct this GO term (GO:0034387) that has a mismatch between its name/def (which matches EC:2.6.1.96) and its actual cross reference (to EC:2.6.1.19), then we would probably have to obsolete this term and make a new one, which could mean there is no difference in work for Reactome.

There is currently only 1 annotation in AmiGO to the existing GO term GO:0034387, and it should be to the EC:2.6.1.96.

Also, just searched for "EC:2.6.1.19" string and it is associated with three GO terms:

So, I propose fixing usage of EC:2.6.1.19 by:

The existing term "4-aminobutyrate:2-oxoglutarate transaminase activity" (GO:0034386) already has a correct reference to EC:2.6.1.19 and thus requires no edits in GO.

hdrabkin commented 7 years ago

at ec Search in ENZYME for: 4-aminobutyrate transaminase Release of 05-Jul-17 Please choose one of the following entries:

2.6.1.19 4-aminobutyrate--2-oxoglutarate transaminase. (AN: 4-aminobutyrate aminotransferase. Beta-alanine--oxoglutarate aminotransferase. GABA transaminase. Gamma-amino-N-butyrate transaminase.)

2.6.1.96 4-aminobutyrate--pyruvate transaminase. (AN: 4-aminobutyrate aminotransferase. GABA transaminase. Gamma-aminobutyrate aminotransaminase. Gamma-aminobutyric acid pyruvate transaminase.) Nothing above it 2.6.1: way too broad So I recommend removing the ec from the parent term,;

deustp01 commented 7 years ago

This term is not used to annotate any catalyst activities in human Reactome so the proposed changes will have no effect on us. In fact, if I'm reading the QuickGO entry for GO:0034387 correctly, it hasn't been used by anyone to annotate anything yet, so the proposed change looks safe.

tberardini commented 7 years ago

@deustp01 TAIR has one annotation to GO:0034387 and I reviewed it, see above for my comments.

http://amigo.geneontology.org/amigo/term/GO:0034387

I think removing the false EC from GO:0034387 and replacing with the correct one is the way to go. Fix of the more general term as suggested by Karen is also good.

My 2 cents.

jaiswalp commented 7 years ago

It works.

krchristie commented 7 years ago

I have removed all references to EC:2.6.1.19 from both "4-aminobutyrate transaminase activity" (GO:0003867) and "4-aminobutyrate:pyruvate transaminase activity" (GO:0034387), including synonym dbxrefs.

ukemi commented 7 years ago

But the GO term is connected to its definition, not the assigned EC number. The EC number association is a cross reference. So if the definition doesn't match the EC number, then the EC number should not be associated with the term.

krchristie commented 7 years ago

Yes, I have removed EC:2.6.1.19 from the two terms that it should not have been associated with:

I have left 2.6.1.19 on the term it belonged on: "4-aminobutyrate:2-oxoglutarate transaminase activity" (GO:0034386)