fpvI (PA2387, Q9I193) review notes

Reviewer: claude-code, 2026-11-05. PseudoCAP tier-2 IBA-seed batch (ECF sigma factors).

Literature

fpvI deletion abolishes pyoverdine-dependent fpvA expression, and cloned fpvI stimulates
it [PMID:12562796, full text]. A Fur box lies upstream of fpvI.
FpvR inhibits FpvI; ferri-pyoverdine signalling through FpvA increases FpvI activity
PMID:12492864. Abstract only.
Background: "Activated FpvI bound to the RNA polymerase initiates transcription of fpvA"
PMID:19730690.

Decisions

All sigma factor activity rows (IBA, IEA, IDA, 2 IMP): ACCEPT. The IDA from
PMID:12492864 is deferred to the curator, because the abstract does not name the assay.
GO:0006355: MODIFY to GO:2000142. GO:0003700: TOO_GENERAL. DNA binding: KEEP_AS_NON_CORE.
Curation gap, not proposed as NEW: FpvI's process role in ferri-pyoverdine import
(regulation of the fpvA receptor). No suitable regulation-of-siderophore-transport term
was checked here.

PseudoCAP IBA-seed assessment

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, IDA+IMP, PMID:12492864; IMP, PMID:12562796 (PseudoCAP)	SOUND	Loss- and gain-of-function control of fpvA transcription (full text of PMID:12562796 read) and FpvR-regulated FpvI activity.	15 others (FecI, Mtb SigD/SigE/SigL, Sco SigR, 10 PAO1 ECF sigmas incl. PvdS and AlgU with in vitro transcription)	Yes

Node PTN002455017 (shared by the whole ECF sigma batch)

PTN002455017 is the ECF sigma factor clade of PANTHER PTHR43133 (250 leaf IBAs, 29
taxa). It carries two IBDs (.cache/paint/IBD.gaf):

GO:0016987 sigma factor activity, 16 seeds: E. coli FecI (P23484), M. tuberculosis
SigE (P9WGG7), SigL (P9WGH5) and SigD (P9WGG9), S. coelicolor SigR (Q7AKG9), and 11
P. aeruginosa ECF sigmas: PA2093 (Q9I222), foxI (Q9I114), PA2050 (Q9I265), PA0149
(Q9I6Y3), PA0472 (Q9I646), PA4896 (Q9HUR7), vreI (Q9I5P9), sigX (Q9I2W5), fpvI
(Q9I193), algU (Q06198), pvdS (G3XCV1). Accessions were resolved against UniProt REST.
GO:0006355 regulation of DNA-templated transcription, 8 seeds: M. tuberculosis SigC
(P9WGH1), SigL (P9WGH5), SigH (P9WGH9) and SigM (O53590), V. cholerae RpoE (Q9KPA6),
E. coli RpoE (P0AGB6), algU (Q06198), pvdS (G3XCV1).

Both node terms suit a clade made up entirely of ECF sigma-70 family proteins. The
GO:0016987 IBD has direct biochemical seeds: PvdS (PMID:10873648, in vitro transcription)
and AlgU (PMID:7644517, in vitro transcription). It also has well-characterised
non-Pseudomonas seeds. It stands without any single seed. The GO:0016987 node is also
seeded by PA2093, foxI, PA2050, PA0149 and PA0472, which the parallel agent is reviewing,
and any node-level GO_CENTRAL defect for it is recorded there. I found none to record.
None of those five genes seeds the GO:0006355 IBD, so its node assessment belongs to
this batch (pvdS, algU). It is sound, and no GO_CENTRAL defect is needed.

Cross-reference: the same node is assessed in the reviews of PA4896, vreI, pvdS, sigX, fpvI and algU (this batch) and of PA2093, foxI, PA2050, PA0149 and PA0472 (parallel agent).