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upstream annotations for amino acid biosynthesis pathways #5618

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ValWood opened this issue Jan 23, 2025 · 1 comment
Open

upstream annotations for amino acid biosynthesis pathways #5618

ValWood opened this issue Jan 23, 2025 · 1 comment
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@ValWood
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ValWood commented Jan 23, 2025

These are all upstream of the first step in these pathways.
For example, the first step in de novo methionine biosynthesis is considered to be met6 (pombe) MET2 (S. cerevisiae)

If the GO annotations are kept they should be causally_upstream rather than involved_in (i.e part_of)

UniProtKB:O60163 | hom3 | 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:O60163 | hom3 | involved_in | GO:0009088    threonine biosynthetic process | ECO:0000250   ISS | GO_REF:0000024 | UniProtKB:P10869 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt |  
UniProtKB:O60163 | hom3 | involved_in | GO:0009088    threonine biosynthetic process | ECO:0000501   IEA | GO_REF:0000120 | UniProtKB-KW:KW-0791 more... | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt |  
UniProtKB:O60163 | hom3 | involved_in | GO:0009089    lysine biosynthetic process via diaminopimelate | ECO:0007322   IEA | GO_REF:0000041 | UniPathway:UPA00034 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt |  
UniProtKB:O60163 | hom3 | involved_in | GO:0071266    'de novo' L-methionine biosynthetic process | ECO:0000250   ISS | GO_REF:0000024 | UniProtKB:P10869 | 284812 Schizosaccharomyces pombe (strain 972 / ATCC 24843) | UniProt

I restricted to
homoserine biosynthesis

@ValWood ValWood changed the title upstream annotations foe amino acid biosynthesis upstream annotations for amino acid biosynthesis pathways Jan 23, 2025
@ValWood
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ValWood commented Jan 23, 2025

The same applies to hom2 and hom6

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