Prephenate pathway obsoletion

GO:0009095 → GO:0009094 L-phenylalanine and GO:0006571 L-tyrosine biosynthetic process

AI Gene Review · projects/PREPHENATE_PATHWAY_OBSOLETION · 2026

Bottom line

  • GO obsoleted GO:0009095, a pre-composed Phe + Tyr superpathway; the two component pathways already exist as separate terms.
  • 4 experimental annotations on 3 proteins must move; upstream proposes removal for 3 and GO:0009094 for Petunia PPA-AT.
  • Scoped, not yet started: none of the three proteins is reviewed in this repo.

One superpathway, two existing terms

Where the annotated enzymes act

Why most rows are removals

  • A move to a replacement is valid only if the paper shows a role in Phe or Tyr biosynthesis specifically.
  • PMID:20883697 (Arabidopsis PAT) and PMID:18727669 (Rv0948c) are biochemical or structural: no process claim.
  • Chorismate mutase acts upstream of both branches; mapping it to either needs in-vivo data.
  • No InterPro2GO, UniProt keyword or UniRule mappings point at GO:0009095, so there is no mapping fan-out.

Next steps

  1. Petunia PPA-AT (E9L7A5) first: check Fig 1 of PMID:21102469 supports Phe specifically; record MODIFY → GO:0009094.
  2. Arabidopsis PAT (Q9SIE1): both rows, likely REMOVE.
  3. M. tuberculosis Rv0948c (P9WIC1): likely REMOVE.

Each starts with just fetch-gene <organism> <gene>.
Upstream: go-annotation#6395 (open) · go-ontology#32005 (closed)
Read more: projects/PREPHENATE_PATHWAY_OBSOLETION.md