fpvR (PA2388, Q9I192) review notes

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

Fetched with just fetch-gene PSEAE Q9I192 --alias fpvR; accession matches the worklist.
Unreviewed entry. No deep-research provider was used; literature from the cached seed paper,
PubMed MCP and a web search ("FpvR cytoplasmic domain binds PvdS FpvI anti-sigma"). Read with
the cognate sigma reviews fpvI and pvdS for consistency.

Literature

Seed paper PMID:12492864 (Beare et al. 2003), abstract only (no PMC copy). PMID:12492864; FpvR also controls PvdS, which drives pyoverdine production.
PMID:25433393 (Edgar et al. 2014, full text cached): PMID:25433393; tandem affinity purification showed FpvR-PvdS binding in P. aeruginosa;
FpvI binding involves sigma region 4. PMID:25433393.
UniProt Q9I192: FecR_N (PF16220), FecR (PF04773), PIRSF018266, one Phobius TM helix (93-114).

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 (matches the GO:2000142 accepted on the cognate sigma reviews).
GO:1900705 negative regulation of siderophore biosynthetic process (IMP): KEEP_AS_NON_CORE
(via PvdS).
NEW GO:0005886 plasma membrane (IC): TM helix plus published description.
Action counts: ACCEPT 1, MODIFY 1, KEEP_AS_NON_CORE 1, NEW 1.
GOA has no IBA rows on fpvR, although the PAINT leaf file assigns it the PTN001250434 IBA.

PseudoCAP IBA-seed assessment

Node-level assessment recorded here once (fpvR has the most direct evidence: binding and
inhibition assays); PA0471 and foxR cross-reference it.

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:12492864	SOUND	The abstract states FpvR negatively regulates FpvI activity; direct binding and inhibition of FpvI and PvdS shown later (PMID:25433393).	VreR (G3XCU5, now merged into O69006), PA0471/FiuR and foxR (IMP, PMID:16484199, derepression in mutants)	Yes

Node PTN001250434

The four seeds are all P. aeruginosa FecR-family anti-sigma factors (PseudoCAP). G3XCU5 is
inactive in UniProt, merged into O69006 (vreR, PA0676). Leaf IBAs (.cache/paint/leaf.gaf.gz):
13 P. aeruginosa FecR-family proteins (including PA0150, PA1301, PA1364, PA2051, PA2094,
PA3409, PA3900, PA4895, femR, vreR, fiuR, foxR, fpvR), 26 Bacteroides thetaiotaomicron, 8
Rhodopirellula baltica, 3 Leptospira, 1 Xanthomonas, E. coli FecR (P23485) and one Ricinus
communis protein (B9TEC7, probably a bacterial contaminant sequence in the plant genome
assembly). The clade is the FecR anti-sigma family, whose members (FecR itself, the
Bacteroides PUL-associated anti-sigma factors) hold cognate ECF sigma factors inactive, so
the term suits the clade. FpvR's seed is supported by direct binding data; the FiuR and FoxR
seeds are sound derepression phenotypes. The IBD stands without any one seed. No GO_CENTRAL
defect. The dual pro-sigma role of the cytoplasmic fragments is not in conflict with the
term. No PSEUDOCAP defects.