nalD (PA3574, Q9HY46) review notes

Literature

nalD (PA3574) mutations cause MexAB-OprM overexpression in a transposon mutant and clinical isolates, reversed by the cloned gene PMID:15855496.
NalD binds an operator overlapping a second mexAB-oprM promoter, whose activity rises in a nalD mutant PMID:17028276.
Pyocyanin binds NalD and MexR and releases them from the mexA promoter PMID:40794867.

Search: PubMed metadata for GOA-cited PMIDs; PMID:15855496 and PMID:40794867 full text cached.

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:0006355 regulation of DNA-templated transcription	19	411 (33 taxa)	GO:0045892, IMP, PMID:17028276	SOUND	Abstract states NalD binding and increased promoter expression in the nalD mutant.	18 other seeds incl. AcrR, RutR, KstR, EthR	Yes
PTN004738546	GO:0000976 (not in worklist for this gene)	7	411	UniProt IDA, PMID:40794867	SOUND	EMSA on the mexA promoter (not PseudoCAP).	AcrR, VC_1746, NfxB, nalC, MexL, MexZ	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:17028276) DELETE_ROW defect PROBABLE. GO:0034763 and GO:0051051 MODIFY to GO:1905700 (direct repressor of a xenobiotic efflux pump; same choice as mexZ).