Question on Revised D-glucosamine PTS permease activity,

[pgaudet]

Hi @raymond91125

For #27410 you updated GO:0103111 D-glucosamine PTS permease activity to narrowEC xref: [2.7.1.191] (https://enzyme.expasy.org/EC/2.7.1.191) (protein-N(pi)-phosphohistidine--D-mannose phosphotransferase)

How did you choose that one? Given that the previous EC matches many new ECs:
Transferred entry: 2.7.1.191
Transferred entry: 2.7.1.192
Transferred entry: 2.7.1.193
Transferred entry: 2.7.1.194
Transferred entry: 2.7.1.195,2.7.1.196
Transferred entry: 2.7.1.197
Transferred entry: 2.7.1.198
Transferred entry: 2.7.1.199
Transferred entry: 2.7.1.200
Transferred entry: 2.7.1.201,2.7.1.202
Transferred entry: 2.7.1.203
Transferred entry: 2.7.1.204
Transferred entry: 2.7.1.205
Transferred entry: 2.7.1.206
Transferred entry: 2.7.1.207
Transferred entry: 2.7.1.208

Also, the EC you picked corresponds to a RHEA that is different from the one we have a the GO term.

• EC:2.7.1.191 is mapped by RHEA to RHEA:49232 D-mannose(out) + Nπ-phospho-L-histidyl-[protein] = D-mannose 6-phosphate(in) + L-histidyl-[protein]
• GO:0103111 D-glucosamine PTS permease activity maps to RHEA:37359 (no EC mapped), in which glucosamine is a substrate, which seems more consistent with the GO term.

Can you confirm that this is the correct new EC mapping for this term?

[raymond91125]

Because of MetaCyc https://www.biocyc.org/reaction?orgid=META&id=TRANS-RXN-167A.
RHEA:37539 is an XREF but it doesn't specify the protein being a PTS enzyme. Thus I am not sure if RHEA should be used to replace the definition.

[pgaudet]

I'll put this on next Monday's agenda. I would like to understand how you selected MetaCyc as the source of truth here - and how that relates to the changes you've implemented.

Originally there were 3 xrefs:
xref: EC:2.7.1.69
xref: MetaCyc:TRANS-RXN-167A
xref: RHEA:37359

And you changed EC:2.7.1.69 to EC:2.7.1.191, and left the other two cross references.
Also, MetaCyc mentions mannose and the GO def mentions glucosamine.

MetaCyc has this comment: "Note that this reaction equation differs from the official Enzyme Commission reaction equation for this EC entry, which can be found here"

For reference, changes are here: d3b519b

Thanks, Pascale

[raymond91125]

EC 2.7.1.193, RHEA:49240