foxI (Q9I114) review notes

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

Fetched with just fetch-gene PSEAE Q9I114 --alias foxI (the symbol-based fetch timed out on a UniProt
search; the accession fetch worked). Accession Q9I114 matches the worklist. Unreviewed entry. No
deep-research provider was used; literature searched in Europe PMC (queries: "foxI AND aeruginosa",
and FoxI/FiuI/PA0472/PA2468 variants) and PubMed MCP.

Identity

ECF (group IV) sigma-70 family factor: PF04542 Sigma70_r2, PF08281 Sigma70_r4_2, TIGR02937, PTHR43133:SF63. Locus PA2468; foxI-foxR (PA2468-PA2467) operon next to foxA (PA2466).
The UniProt "Belongs to the sigma-70 factor family. ECF subfamily" note is ARBA-only, so the
review cites the Pfam/NCBIfam DR lines instead.

Literature

Seed paper PMID:16484199: full text read on the PMC article page (PMC1426570); the XML route is blocked by the publisher, so the cached file is abstract-only.

PMID:16484199. Full text (PMC1426570, read 2026-11-05): plasmid pMUM8 expressing foxI induced FoxA (absent in a foxA mutant) and raised foxA-lacZ activity 25-fold without and 100-fold with ferrioxamine B under iron limitation; no foxI mutant was tested. PMID:25809487; PMID:35138377. FoxA imports ferric desferrioxamines PMID:39138320.

Annotation decisions

GO:0016987 sigma factor activity (IMP, IBA, IEA): ACCEPT, core MF.
GO:0003700 DNA-binding transcription factor activity (IEA): MODIFY to GO:0016987; sigma factors are
RNA polymerase specificity subunits, not stand-alone DNA-binding TFs.
GO:0006355 (IBA, IEA): TOO_GENERAL; GO:2000142 (accepted) is an is_a descendant.
GO:0006352 and GO:2000142 (IEA): ACCEPT.
Transport regulation IMP row: MODIFY to GO:0034758 positive regulation of iron ion transport (full text shows induction of the siderophore receptor, which imports iron), non-core.
Action counts: ACCEPT 6, KEEP_AS_NON_CORE 1, MODIFY 2, TOO_GENERAL 2.

PseudoCAP IBA-seed assessment

Node-level assessment: see genes/PSEAE/PA0472/PA0472-notes.md (recorded once there); summary repeated below.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN002455017	GO:0016987 sigma factor activity	16	250 (29 taxa)	GO:0016987, IMP, PMID:16484199	SOUND	Full text: FoxI expression specifically induces the foxA promoter and FoxA protein; overexpression is IMP-eligible. Direct target-promoter activation is the MF itself.	FecI, Mtb SigE/SigL (IDA), SigR, AlgU, PvdS, FpvI, SigX (IDA); Mtb SigD, VreI, PA4896 and four batch paralogues (IMP)	Yes; eight independent IDA seeds

No source_defects were recorded: the PseudoCAP row is sound and the IBD is sound.

The IBD at PTN002455017 (GO:0016987, 16 seeds, 250 leaf IBAs in 29 taxa) is also seeded by IDA rows for E. coli FecI (P23484, PMID:8596456), M. tuberculosis SigE (P9WGG7, PMID:9139909) and SigL (P9WGH5, PMID:16552079), S. coelicolor SigR (Q7AKG9, PMID:9755177), and P. aeruginosa AlgU (Q06198, PMID:7644517), PvdS (G3XCV1, PMID:10692351), FpvI (Q9I193, PMID:12492864) and SigX (Q9I2W5, PMID:10438740), plus IMP rows for Mtb SigD (P9WGG9) and VreI (Q9I5P9); queried live in QuickGO on 2026-11-05. The PseudoCAP seeds from this batch (PA2093, FoxI, PA2050, PA0149, PA0472) and PA4896 add nothing the IDA seeds do not already establish. The node is an ECF sigma clade of PTHR43133, so the term suits it. No GO_CENTRAL defect is needed for this node. The node-level assessment is recorded here once, on PA0472 (FiuI), the gene with the most direct evidence; the other genes in this batch, and the parallel PA4896/vreI/pvdS/sigX/fpvI/algU reviews, cross-reference it.