nalC (PA3721, Q9HXS0) review notes

Literature

PA3721 was identified as nalC by transposon mutagenesis of nalC-type MexAB-OprM hyperexpressers; it represses the divergent PA3720-PA3719 operon PMID:15387820, and its effect on MexAB-OprM runs through PA3719 PMID:15387820. PA3719 is the ArmR anti-repressor of MexR.
Purified NalC binds an inverted repeat at the PA3720-armR promoter; PCP releases it PMID:22393435. Full text read: the nalC mutant K1454 shows increased PA3720-armR expression PMID:22393435.

Search: PubMed metadata for GOA-cited PMIDs; PMID:22393435 full text cached and read.

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?
PTN004738546	GO:0000976 transcription cis-regulatory region binding	7	411 (33 taxa)	GO:0000976, IDA, PMID:22393435	SOUND	EMSA with purified NalC, binding site mapped to an IR (full text). This is the only support for nalC as a seed (pseudocap_only_support).	AcrR P0ACS9 (IDA), VC_1746 Q9KR96, NfxB, MexZ, MexL, NalD	Yes
PTN004738546	GO:0006355 regulation of DNA-templated transcription	19	411 (33 taxa)	GO:0045892, IMP, PMID:22393435	SOUND	Increased PA3720-armR expression in the nalC mutant (full text).	18 other seeds incl. AcrR, RutR, KstR, EthR	Yes

Node-level verdict for PTN004738546 (all three IBDs stand on many experimentally characterised TetR regulators, no GO_CENTRAL defect) is recorded once in genes/PSEAE/nfxB/nfxB-notes.md.

Non-seed PseudoCAP rows: GO:0032410 (PMID:15387820) WRONG, DELETE_ROW defect PROBABLE (same pattern as nfxB/nalD/mexZ). GO:0034763 MARK_AS_OVER_ANNOTATED: NalC affects efflux only through the ArmR-MexR cascade; no defect filed.