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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Obsoletion request: GO:0042960 antimonite secondary active transmembrane transporter activity #27767

Open pgaudet opened 2 months ago

pgaudet commented 2 months ago

GO:0042960 antimonite secondary active transmembrane transporter activity has a single annotation by EcoCyc to P0AB93. It seems this term has the same meaning as ATPase-coupled antimonite transmembrane transporter activity

Likewise for GO:0008490 arsenite secondary active transmembrane transporter activity ; should it be merged into ATPase-coupled arsenite transmembrane transporter activity; the same gene transports antimonite and arsenite.

@amandamackie Is this right? It certainly seems to be a primary active transporter.

Thanks, Pascale

amandamackie commented 2 months ago

Hi Pascale,

No this is not right. ArsB proteins in some bacteria (including P0AB93 in E. coli) are pmf-dependent efflux pumps. They are secondary transporters which belong to transport class 2.A.45 [https://tcdb.org/search/result.php?tc=2.A.45]

Amanda

pgaudet commented 2 months ago

Thanks @amandamackie

So is the UniProt description incorrect then ?

Thought to form the channel of an arsenite pump (By similarity).

pgaudet commented 2 months ago

Oh or maybe they mean that it's the 'pore'/channel part of the complex, but not that's is a 'channel' in terms of mechanism... ?

pgaudet commented 2 months ago

Can I move the term as a child of proton motive force dependent protein transmembrane transporter activity?

amandamackie commented 2 months ago

I think this is a case where the biology is not amenable to discrete categorisation. In some bacteria ArsB forms a complex with an ATPase (ArsA protein) and the complex functions to export arsenite. So these ArsAB protein complexes will be primary active transporters - Transport Classification DB has a nice explanantion (see [https://tcdb.org/search/result.php?tc=3.A.4]. BUT in other bacteria including E. coli K-12 there is no ArsA ATPase and the same ArsB protein functions as a pmf dependent arsenite exporter.

Re: GO:0009977: proton motive force dependent protein transmembrane transporter activity. My understanding is that this term refers to the pmf-dependent transport of proteins so it would not be an appropriate parent for pmf-dependent arsenite transport.