The term GO:0046715 'active borate transmembrane transporter activity' is confusing and has been used to annotate NIPs and BOR/Solute Carriers and so should be obsoleted.
GO term ID and Label
GO:0046715 active borate transmembrane transporter activity
Reason for deprecation Put an x in the appropriate box:
[x] The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
[ ] The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
[ ] The reason for obsoletion is that this term represent an assay and not a GO process.
[ ] The reason for obsoletion is that this represents a phenotype.
[ ] The reason for obsoletion is that the data from the paper for which the term was requested can be accurately described using [appropriate GO term].
[ ] The reason for obsoletion is that this term represents a molecular function.
[ ] The reason for obsoletion is that this term represents a gene product.
[ ] The reason for obsoletion is that this term refers to a class of proteins.
[ ] The reason for obsoletion is that this term was added in error.
[x] The reason for obsoletion is that more specific terms were created.
[ ] The reason for obsoletion is that this term was an unnecessary grouping term.
[x] The reason for obsoletion is that the meaning of the term is ambiguous.
[] The reason for obsoletion is that is not known to be catalyzed by any gene product.
[ ] The reason for obsoletion is that it more specific than the specificity of any known gene product.
[] The reason for obsoletion is that there is no evidence that this function/process/component exists.
UniProtKB:Q8NBS3 ; SLC4A11 PMID:15525507 (https://www.rhea-db.org/rhea/66817)
UniProtKB:Q8VYR7 ; BOR1 PMID:12447444
should be reannotated to
GO:0080139 borate efflux transmembrane transporter activity
Any other information
For borate efflux the 'most likely form of borate is the charged borate [B(OH4)]−form' tetrahydroxoborate CHEBI:41132 (PMID:34112901)
maps to https://www.rhea-db.org/rhea/66817 for mouse and human SLC4A11.
For the NIPs channels it is
CHEBI:33118 boric acid
hattrill
commented
3 months ago
From 'Structural and functional insights into the mechanism of action of plant borate transporters' PMID:34112901
There are two types of 'borate' transporters:
channels: Nodulin 26-like intrinsic proteins (NIPs) (https://tcdb.org/search/result.php?tc=1.A.8.12#1.A.8.12) carriers which are responsible for the efflux of borate: BOR/Solute Carrier (SLC) 4 family of secondary active transporters (https://tcdb.org/search/result.php?tc=2.A.31)
The term GO:0046715 'active borate transmembrane transporter activity' is confusing and has been used to annotate NIPs and BOR/Solute Carriers and so should be obsoleted.
GO term ID and Label
GO:0046715 active borate transmembrane transporter activity
Reason for deprecation Put an x in the appropriate box:
There are 5 EXP annotations to these terms UniProtKB:Q8LAI1 ; NIP7-1 PMID:21710975 UniProtKB:Q9SAI4 ; NIP6-1 PMID:18952773 UniProtKB: Q9SV84 ; NIP5-1 PMID:16679457 There is a ticket for nodulin 26-like intrinsic proteins (NIPs) https://github.com/geneontology/go-annotation/issues/5156 for when borate channel activity becomes available (https://github.com/geneontology/go-ontology/issues/27487)
UniProtKB:Q8NBS3 ; SLC4A11 PMID:15525507 (https://www.rhea-db.org/rhea/66817) UniProtKB:Q8VYR7 ; BOR1 PMID:12447444 should be reannotated to GO:0080139 borate efflux transmembrane transporter activity
For borate efflux the 'most likely form of borate is the charged borate [B(OH4)]−form' tetrahydroxoborate CHEBI:41132 (PMID:34112901) maps to https://www.rhea-db.org/rhea/66817 for mouse and human SLC4A11.
For the NIPs channels it is CHEBI:33118 boric acid
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