foxR (PA2467, Q9I115) review notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE Q9I115 --alias foxR; accession matches the worklist.
Unreviewed entry. No deep-research provider was used; literature from the cached papers and
PubMed MCP. Read with the cognate sigma review (PA0472 / foxI) for consistency.

Literature

Seed paper PMID:16484199 (Llamas et al. 2006): cached file is abstract only; the full text was
read on the PMC article page (PMC1426570) on 2026-11-05. A foxR transposon mutant (UW library)
produces its receptor independent of the inducing siderophore, and the foxA promoter is
constitutively active (higher under iron restriction). The authors: "consistent with a role
for ... an anti-sigma factor"; FoxR and FiuR "are not required for maximal activities of FoxI
and FiuI". PMID:16484199.
PMID:35138377 (review, full text): PMID:35138377; the cytoplasmic
N-terminal fragments have pro-sigma activity.
PMID:39138320: the receptor (foxA) imports hydroxamate iron-siderophores.
PMID:25809487 (abstract): PMID:25809487; FoxR self-cleaves
between Gly191 and Thr192 by an N-O acyl rearrangement.
UniProt Q9I115: FecR_N, FecR, PIRSF018266, one Phobius TM helix (88-105).

Annotation decisions

GO:0016989 sigma factor antagonist activity (IMP): ACCEPT, core MF.
GO:0045892 (IEA, GO_REF:0000108): MODIFY to GO:2000143 negative regulation of DNA-templated
transcription initiation.
GO:0034756 regulation of iron ion transport (IMP): MODIFY to GO:0034757 negative regulation of
iron ion transport (mutant derepresses the receptor), non-core. Mirrors the MODIFY to
GO:0034758 positive regulation on the cognate sigma review.
NEW GO:0005886 plasma membrane (IC): TM helix plus published description.
Action counts: ACCEPT 1, MODIFY 2, NEW 1.
GOA has no IBA rows on foxR, although the PAINT leaf file assigns it the PTN001250434 IBA.

PseudoCAP IBA-seed assessment

Node-level assessment: see genes/PSEAE/fpvR/fpvR-notes.md (recorded once there); summary below.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN001250434	GO:0016989 sigma factor antagonist activity	4	53 (7 taxa)	GO:0016989, IMP, PMID:16484199	SOUND	Full text (PMC page): the foxR mutant expresses its receptor constitutively, independent of siderophore; derepression is the genetic signature of an anti-sigma factor, later confirmed (PMID:35138377).	fpvR (IMP, plus direct binding PMID:25433393), VreR (G3XCU5 merged into O69006), and PA0471/FiuR	Yes

No source defects: the PseudoCAP row is sound and the IBD is sound.