Multifunctional transporter terms for obsoletion

[gocentral]

The following transporter terms represent more than one function. Recommend annotating one or more of the suggested alternatives. If there are no problems, I will do this in the first week of the new year.

GO:0015363 dicarboxylate (succinate/fumarate/malate) antiporter activity -->dicarboxylic acid transporter activity ; GO:0005310 succinate transporter activity ; GO:0015141 fumarate transporter activity ; GO:0015138 malate transporter activity ; GO:0015140 antiporter activity ; GO:0015297

GO:0015521 bicyclomycin/sulfathiazole:hydrogen antiporter activity -->bicyclomycin transporter activity ; GO:0015545 sulfathiazole transporter activity ; GO:0015546 azole:hydrogen antiporter activity ; GO:0045119

GO:0005311 sodium:dicarboxylate/tricarboxylate symporter activity -->dicarboxylic acid transporter activity ; GO:0005310 tricarboxylic acid transporter activity ; GO:0015142 organic acid:sodium symporter activity ; GO:0005343

GO:0015560 L-idonate/D-gluconate:hydrogen symporter activity -->solute:hydrogen symporter activity ; GO:0015295 L-idonate transporter activity ; GO:0015568 gluconate transporter activity ; GO:0015128

GO:0015376 betaine/GABA:sodium symporter activity -->betaine transporter activity ; GO:0015199 L-gamma-aminobutyric acid transporter activity ; GO: 0015185 gamma-aminobutyric acid:sodium symporter activity ; GO: 0005332 solute:sodium symporter activity ; GO:0015370

GO:0000258 isoleucine/valine:sodium symporter activity -->L-isoleucine transporter activity ; GO:0015188 L-valine transporter activity ; GO:0005304 NEW: amino acid:sodium symporter activity ; GO:0050new

GO:0015372 glutamate/aspartate:sodium symporter activity -->L-glutamate transporter activity ; GO:0005313 L-aspartate transporter activity ; GO:0015183 NEW: amino acid:sodium symporter activity ; GO:0050new

GO:0015500 threonine/serine:sodium symporter activity -->L-threonine transporter activity ; GO:0015195 L-serine transporter activity ; GO:0015194 NEW: amino acid:sodium symporter activity ; GO:0050new

GO:0015534 proline/glycine/betaine:hydrogen/sodium symporter activity -->betaine transporter activity ; GO:0015199 glycine transporter activity ; GO:0015187 L-proline transporter activity ; GO:0015193 solute:sodium symporter activity ; GO:0015370

GO:0005301 valine/tyrosine/tryptophan permease activity, 2.A.3.10.9 -->L-tryptophan transporter activity ; GO:0015196 L-tyrosine transporter activity ; GO:0005302 L-valine transporter activity ; GO:0005304 permease activity ; GO:0015646

GO:0015331 asparagine/glutamine permease activity, 2.A.3.10.7 -->L-asparagine transporter activity ; GO:0015182 L-glutamine transporter activity ; GO:0015186 permease activity ; GO:0015646

GO:0015332 leucine/valine/isoleucine permease activity, 2.A.3.10.6 -->L-leucine transporter activity ; GO:0015190 L-valine transporter activity ; GO:0005304 L-isoleucine transporter activity ; GO:0015188 permease activity ; GO:0015646

GO:0015356 monocarboxylate (lactate, pyruvate, mevalonate) uptake/efflux porter activity, 2.A.1.13.1 -->lactate transporter activity ; GO:0015129 mevalonate transporter activity ; GO:0015130 NEW: pyruvate transporter activity term ; GO:0050new uptake permease activity ; GO:0015563 efflux permease activity ; GO:0015562

GO:0015358 amino acid/choline transporter activity, 2.A.3.4.- -->choline transporter activity ; GO:0015220 amino acid transporter activity ; GO:0015171

GO:0015613 galactose/glucose (methylgalactoside) porter activity, 3.A.1.2.3 -->methylgalactoside transporter activity ; GO:0015592 glucose transporter activity ; GO:0005355 galactose transporter activity ; GO:0005354 porter activity ; GO:0015291

GO:0015316 nitrite/nitrate porter activity, 2.A.1.8.- -->nitrite transporter activity ; GO:0015113 nitrate transporter activity ; GO:0015112 porter activity ; GO:0015291

-->GO:0015393 uracil/uridine permease activity, 2.A.39.3.2 uridine transporter activity ; GO:0015213 uracil transporter activity ; GO:0015210 permease activity ; GO:0015646

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/1410":https://sourceforge.net/p/geneontology/ontology-requests/1410

[gocentral]

Logged In: YES user_id=451873

Might be worth sending this out to the list as I imagine it will affect a fair number of annotations...

Original comment by: jl242

[gocentral]

Logged In: YES user_id=482944

Hi, I am concerned about the obsoletion of these terms since many of them reflect the families of compounds that are transported by particular families of transporters. Sometimes during annotation we will know that a particular transporter belongs to a family of transporters that transports a few specific substrates, but we will not know which substrates our particular gene transports and which it does not. In these cases I have been able to annotate to the parent that represents the family of substrates. Now that I think about it in this context, perhaps that is wrong and implies that all of the substrates listed are known to be transported, but since the terms seem to be built around known familes of this type, its not clear.
Perhaps the names of these terms could be replaced with something that indicates the family nature of the substrates. If not, then during annotation, if we know that a certain family of substrates is transported but not which specific one, we will not be able to reflect that and will have to assign a more general term that gives less information than we know. For example "nitrite/nitrate substrate family porter activity" or something along those lines would be helpful to have. Michelle

Original comment by: mlgwinn

[gocentral]

Logged In: YES user_id=473796

For information, of the above terms, the following have annotations:

GO:0005311 sodium:dicarboxylate/tricarboxylate symporter activity - 4 GO:0015376 betaine/GABA:sodium symporter activity - 2 GO:0015372 glutamate/aspartate:sodium symporter activity - 1 GO:0015613 galactose/glucose (methylgalactoside) porter activity - 3 GO:0015393 uracil/uridine permease activity - 4

Michelle - I agree that it is useful to have transporter terms for families of compounds (eg. neutral amino acid transporter); however, with the above terms, I don't believe that they really represent useful groupings of compounds. They just represent gene products that can transport a couple of different substrates. Did you have any particular gene products in mind? You mentioned the nitrite/nitrate porter but that has 0 annotations. I would be happy to add any sensible grouping terms but I am not convinced by transporter terms which are just a list of diverse substrates with 'permease' or 'porter' stuck on the end.

addition to the suggested terms for GO:0015534: solute:cation symporter activity ; GO:0015294 solute:hydrogen symporter activity ; GO:0015295

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=546388

Haven't had time to go over each; but it might make sense when a protein product can do both (eg, glucose and galactose transport) to use concurrent annotation rather than a term for both?

Original comment by: hdrabkin

[gocentral]

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Are there any remaining reservations about these terms or can they be obsoleted?

Original comment by: girlwithglasses

[gocentral]

• priority: 5 --> 9

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=482944

I originally thought there would be more annotations affected, but there are very few - I have now had a chance to look at the TIGR annotations that will be affected and I agree that these terms should be deleted. Thanks for your time - sorry for holding up the ticket. Michelle

Original comment by: mlgwinn

[gocentral]

Logged In: YES user_id=473796

All gone!

Only one change - instead of adding 'amino acid:sodium symporter', I used the term 'sodium:amino acid transporter activity ; GO:0005283'.

New term added: pyruvate transporter activity ; GO:0050833

Original comment by: girlwithglasses

[gocentral]

• priority: 9 --> 5
• status: open --> closed-fixed

Original comment by: girlwithglasses