rocA1 (PA3948, Q9HX68) review notes

Literature

RocA1 was found in a transposon screen for loci controlling cupB/cupC fimbrial gene expression; it is the response regulator of the RocS1-RocR-RocA1 system PMID:15659157.
RocS1 interacts with the receiver domain of RocA1 and activates it through a phosphorelay PMID:15659157.
Domain architecture (UniProt Q9HX68): N-terminal receiver (PF00072), C-terminal LuxR-type HTH (GerE, PF00196); PANTHER PTHR43214 (NarL/FixJ family response regulators).
RocR, the EAL-domain antagonist, is reviewed in genes/PSEAE/rocR/.

Search: PubMed metadata for the GOA-cited PMID (abstract only; no PMC copy). NCBI E-utilities and Europe PMC search were unavailable (HTTP 500/503) during this session, so no further literature on direct RocA1-promoter binding was retrieved.

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?
PTN008449896	GO:0006355 regulation of DNA-templated transcription	9	167 (26 taxa)	GO:0045893, IMP, PMID:15659157	SOUND	The abstract states RocA1 is a DNA-binding response regulator that activates cup genes, identified as a locus controlling cupB/cupC transcription. Positive regulation of transcription is the right term for the gene and is subsumed by the node term.	E. coli NarL (P0AF28), NarP (P31802), UhpA (P0AGA6), RcsB (P0DMC7), BglJ (P39404); B. subtilis DegU (P13800); P. aeruginosa NarL (Q9HXD3); eraR (Q9I2C7)	Yes

Node-level verdict for PTN008449896 (recorded here once; eraR cross-references this table): the node is a NarL/FixJ (LuxR-type HTH) response-regulator clade. Its GO:0006355 IBD rests on nine seeds, seven of them classical, experimentally characterised transcription factors (NarL, NarP, UhpA, RcsB, BglJ, DegU, P. aeruginosa NarL); the GO:0003700 and GO:0000976 IBDs on the same node rest on NarL, RcsB, BglJ and PA NarL only, not on PseudoCAP. The generic node term suits a clade of DNA-binding response regulators. The IBD stands without either PseudoCAP seed (rocA1, eraR). No GO_CENTRAL defect.

Seed confidence: the abstract states the decisive facts (DNA-binding regulator that activates cup genes); full text not read.