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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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where is "threonine deaminase" #26359

Closed ValWood closed 11 months ago

ValWood commented 12 months ago

We have some paper referring to threonine deaminase in fission yeast https://pubmed.ncbi.nlm.nih.gov/?term=%22threonine+deaminase%22+and+%22fission+yeast%22&sort=date

This is threonine deaminase

https://www.ebi.ac.uk/QuickGO/term/GO:0004794 Threonine deaminase is a related synonym of

GO:0004794 L-threonine ammonia-lyase activity L-threonine = 2-oxobutanoate + NH3

but are they the same thing ? If so can the synonym be exact. If not how do they differ?

Searching PubMed "Threonine deaminase" 319 "threonine ammonia-lyase" (10)

ValWood commented 12 months ago

OK I think they are the same:

Threonine deaminase (l-threonine dehydratase EC 4.2.1.16) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC251809/

with "threonine deaminase" appearing to be the most common name in the literature?

pgaudet commented 12 months ago

I think they are the same, an ammonium group is removed.

By default EC synonyms were added as 'related' rather than EXACT, we need to edit them as we see 'exact' ones. I dont think there is a way to automatically know which are exact.

pgaudet commented 12 months ago

WRT name: we have aligned to EC https://enzyme.expasy.org/EC/4.3.1.19 Maybe we shouldn't have, UniProt entries seem to use threonine deaminase: https://www.uniprot.org/uniprotkb/P20132/entry

pgaudet commented 12 months ago

Actions needed for this term:

ValWood commented 11 months ago

fix definition to match RHEA 4.3.1.19

do I change NH3 to NH4? And if so do I need to fix the subClass of, or is ammonium OK?

deustp01 commented 11 months ago

do I change NH3 to NH4?

NH4+ (CHEBI:28938) is the predominant form at pH 7.3 and is the one used in RHEA reactions BUT we don't add "zwitterion" to default names of amino acids who have that predomiant form at pH 7.3, so that is a separate issue (and maybe one to be ignored?)

ValWood commented 11 months ago

thanks @deustp01 !

pgaudet commented 11 months ago

I have been aligning chemicals with RHEA (also I usually change the def xref to the RHEA, since this is usually our 'source of truth).

ValWood commented 11 months ago

I looked at the Rhe reaction and aligned with that (I think), is it correct what I have done?

pgaudet commented 11 months ago

Yes, that was just to help in future definition changes. This one here is right.