Simplify labels for some transferases ?

[pgaudet]

Hello,

Some transferases have 'user friendly' labels, such as

GO:0042123 glucanosyltransferase activity GO:0000031 mannosylphosphate transferase activity GO:0042285 xylosyltransferase activity

We could simply those :

GO:0016746 transferase activity, transferring acyl groups => acyltransferase

GO:0016757 transferase activity, transferring glycosyl groups => glycosyltransferase ~Same as GO:0046527 glucosyltransferase activity ?~

GO:0016769 transferase activity, transferring nitrogenous groups => transaminase activity

GO:0016741 transferase activity, transferring one-carbon groups => ~methyltransferase activity~

GO:0016772 transferase activity, transferring phosphorus-containing groups => kinase activity (merge into GO:0016301 kinase activity)

GO:0016785 transferase activity, transferring selenium-containing groups => selenotransferase activity

GO:0016782 transferase activity, transferring sulfur-containing groups => sulfurtransferase activity

GO:0016744 transferase activity, transferring aldehyde or ketonic groups = > cannot change ? unless we split into individual substrates

GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups = > cannot change ? unless we split into individual substrates

Would this be OK @hdrabkin @deustp01 @cmungall ?

Thanks, Pascale

[hdrabkin]

I see no reason to do this as I have no problem with the current names; these are grouping terms that usually map to 3 digit (or less) ec ids, and the current names are more in line with what EC calls the groupings.

[ValWood]

I like the simpler more user friendly labels.

[ValWood]

although some of these are not possible GO:0016741 transferase activity, transferring one-carbon groups ->methyltransferase activity

methyltransferase is narrower, there are other transferases. So maybe not?

[hdrabkin]

IF we do this (again I think it is not needed), the old names must be synonyms. I often use these types of definitions to verifiy the 3 digit ec id (or add if needed).

[cmungall]

I agree with having the simpler names be primary, where unambiguous

of course we retain the syns. We can use systematic_synonym type

On Mon, Nov 30, 2020 at 6:37 AM Harold Drabkin notifications@github.com wrote:

IF we do this (again I think it is not needed), the old names must be synonyms. I often use these types of definitions to verifiy the 3 digit ec id (or add if needed).

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/geneontology/go-ontology/issues/20486#issuecomment-735823856, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOM4SKYJOVZTZ7S3PO3SSOUY3ANCNFSM4UCWQ66A .

[pgaudet]

• [x] GO:0016755 ! transferase activity, transferring amino-acyl groups -> change to aminoacyltransferase activity (same as https://enzyme.expasy.org/EC/2.3.-.-)

• [x] GO:0016747 ! transferase activity, transferring acyl groups other than amino-acyl groups -> change to ! acyltransferase activity, transferring groups other than amino-acyl groups (same as https://enzyme.expasy.org/EC/2.3.1.-)

• [x] GO:0016755 ! transferase activity, transferring amino-acyl groups -> change to aminoacyltransferase activity (same as https://enzyme.expasy.org/EC/2.3.2.-)

• [x] GO:0046912 ! transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer -> change to acyltransferase, acyl groups converted into alkyl on transfer (same as https://enzyme.expasy.org/EC/2.3.3.-)

• [x] GO:0004801 sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity -> change to transaldolase activity (same as https://enzyme.expasy.org/EC/2.2.1.2)

• [x] GO:0016758 ! transferase activity, transferring hexosyl groups -> change to hexosyltransferase activity (see https://enzyme.expasy.org/EC/2.4.1.-)

• [x] GO:0016757 ! transferase activity, transferring glycosyl groups -> change to GO:0016757 ! glycosyltransferase activity (see https://enzyme.expasy.org/EC/2.4.-.-)

• [x] GO:0016763 ! transferase activity, transferring pentosyl groups -> change to GO:0016763 ! pentosyltransferase activity (see https://enzyme.expasy.org/EC/2.4.1.-)

• [x] GO:0016744 ! transferase activity, transferring aldehyde or ketonic groups -> change to GO:0016744 ! transketolase or transaldolase activity

• [x] GO:0016785 ! transferase activity, transferring selenium-containing groups -> change to GO:0016785 ! selenotransferase activity

[pgaudet]

GO:0002948 archaeosine synthase activity EC:2.6.1.97 xref: RHEA:54084 changed parent from -is_a: GO:0015067 ! amidinotransferase activity +is_a: GO:0016769 ! transferase activity, transferring nitrogenous groups

[pgaudet]

GO:0030407 formimidoyltransferase activity

• has 2 EC: EC:2.1.2.4 and EC:2.1.2.5, which corresponds to its 2 children
• has 1 EXP, to an enzyme annotated in UniProt with EC:2.1.2.5 , which corresponds to the child, GO:0030409 glutamate formimidoyltransferase activity --> Merge down GO:0030407 into GO:0030409

[pgaudet]

Merge GO:0016770 oximinotransaminase activity linked to EC:2.6.3.-, into its single child GO:0050206 oximinotransferase activity linked to 2.6.3.1 (no annotations)

[pgaudet]

GO:0102192 neryl-diphosphate:isopentenyl-diphosphate cistransferase activity (xref: EC 2.5.1.92 (2Z,6Z)-farnesyl diphosphate synthase; no RHEA) - 0 annotations Def: Catalysis of the reaction: neryl diphosphate(3-) + isopentenyl diphosphate(3-) <=> diphosphoric acid + 2-cis,6-cis-farnesyl diphosphate(3-). is identical to GO:0102059 2-cis,6-cis-farnesyl pyrophosphate synthase activity (RHEA:27810) - also EC 2.5.1.92 Def: Catalysis of the reaction: prenyl diphosphate + 2 isopentenyl diphosphate <=> 2 diphosphoric acid + 2-cis,6-cis-farnesyl diphosphate. - 0 annotations

CHEBI:57623 prenyl diphosphate(3−) has synonyms:

dimethylallyl diphosphate | UniProt dimethylallyl pyrophosphate | ChEBI Dimethylallyl pyrophosphate trianion | ChEBI prenyl diphosphate trianion | ChEBI prenyl pyrophosphate trianion

= MERGE