UniProtKB-KW:KW-0486 and KW:KW-0791 for Hom6

[ValWood]

• PTHR ID & PTN node:

From todays ontology editors discussion hom6 should not be annotated to methionine or threonine biosynthesis https://github.com/geneontology/go-ontology/issues/28911#issuecomment-2383682722

@Antonialock could you remove the UniProt ISS/ISO? UniProtKB:O94671 | hom6 | involved_in | GO:0009086    methionine biosynthetic process | ECO:0000250   ISS | GO_REF:0000024 | UniProtKB:P31116 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt |   UniProtKB:O94671 | hom6 | involved_in | GO:0009088    threonine biosynthetic process | ECO:0000250   ISS | GO_REF:0000024 | UniProtKB:P31116 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt |  

and these SPKW mappings UniProtKB:O94671 | hom6 | involved_in | GO:0009086    methionine biosynthetic process | ECO:0007322   IEA | GO_REF:0000043 | UniProtKB-KW:KW-0486 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt |   UniProtKB:O94671 | hom6 | involved_in | GO:0009088    threonine biosynthetic process | ECO:0007322   IEA | GO_REF:0000043 | UniProtKB-KW:KW-0791 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt |  

UniProtKB:O94671 | hom6 | involved_in | GO:0009088    threonine biosynthetic process | ECO:0007322   IEA | GO_REF:0000041 | UniPathway:UPA00050 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt |  

• Sequences with problematic annotation (ID + gene/protein name):

• Type of Issue: Erroneous source or erroneous propagation, or other issue

• Add the label 'high priority' if needed. Generally high priority issues affect a lot of proteins, and annotations are incorrect (as opposed to just imprecise).

[Antonialock]

I'm a bit unsure of this, we have this pathway annotation for hom6

CC PATHWAY: Amino-acid biosynthesis; L-threonine biosynthesis; L-threonine from L-aspartate; step 3/5

it would look odd to remove the KW when this pathway is annotated like this?

removing the kw2go mapping we would lose 150,621 annotations

@pgaudet ?

[pgaudet]

Hi @Antonialock

We have decided that the pathway ends at the homoserine intermediate, which is then used in multiple pathways: see https://github.com/geneontology/go-ontology/issues/28911#issuecomment-2353333179

This is consistent with how other pathways are annotated. I think the only pathway that should be in the CC PATHWAY line is 'L-homoserine from L-aspartate'.

Thanks, Pascale