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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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EC xref for GO:0015419 ABC-type sulfate transporter activity #21236

Closed sjm41 closed 3 years ago

sjm41 commented 3 years ago

The EC xref on the following term should be EC:7.3.2.3

[Term] id: GO:0015419 name: ABC-type sulfate transporter activity namespace: molecular_function def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + sulfate(out) = ADP + phosphate + sulfate(in)." [RHEA:10192] synonym: "ATPase-coupled sulfate transmembrane transporter activity" RELATED [] synonym: "sulfate ABC transporter" EXACT [] synonym: "sulfate transmembrane-transporting ATPase activity" RELATED [] synonym: "sulfate-transporting ATPase activity" RELATED [EC:7.3.2.3] synonym: "sulfate/thiosulfate porter activity" BROAD [] synonym: "sulphate transporting ATPase activity" RELATED [] xref: EC:3.6.3.25 xref: MetaCyc:3.6.3.25-RXN xref: RHEA:10192 is_a: GO:0015116 ! sulfate transmembrane transporter activity is_a: GO:0043225 ! ATPase-coupled inorganic anion transmembrane transporter activity is_a: GO:0140359 ! ABC-type transporter activity

deustp01 commented 3 years ago

I think that EC recently (within the past 6 months) created a new category EC 7.- to house translocases, activities that mediate active transport, and re-classified a number of terms previously housed in various other EC categories. This looks like one of thenre-classified terms. It occurs to me, purely as a managerial time-efficiency issue, that finding and fixing such terms one at a time is terribly wasteful, and that some sort of scripted global fix is needed. @hdrabkin @cmungall

sjm41 commented 3 years ago

HI @deustp01 The vast majority have been fixed - I'm guessing this odd one got left behind somehow...

hdrabkin commented 3 years ago

I'll fix this one now since We know about it. Fortunately, the RHEA is also remapped and is for the sulfate ion.

hdrabkin commented 3 years ago

done. We'd need a list of all the ones that did get re-mapped, what they got remapped to, and access any RHEA changes needed.

sjm41 commented 3 years ago

I thought the bulk EC:7 xrefs transfer/match-up were handled in #15712 and #17127?

hdrabkin commented 3 years ago

I was pressed to undo #17127 (read details.) and #15712 was closed without comment (not by me). I was lead to believe that @pgaudet took on the transporters...

sjm41 commented 3 years ago

I'll note that all EC:3.6.3.- numbers were transferred to EC:7 (https://enzyme.expasy.org/EC/3.6.3.-), and the one noted above (EC:3.6.3.25) is the only one left in GO as a current xref. (So that's good!)

pgaudet commented 3 years ago

Is there anything that remains to be done here ?

We reverted #15712, ie the creation of a new term, translocase, because in GO that was equivalent to GO:0005215 transporter activity. But ECs can be added to any transporter as appropriate.

hdrabkin commented 3 years ago

Not that I know of.