fleQ (PA1097, G3XCV0) review notes

Literature summary

FleQ heads the flagellar cascade as an NtrC/NifA-type activator PMID:12218010; the flhA site works in vivo PMID:12218010.
fleQ mutants are non-motile and lose mucin adhesion PMID:9287015; FleQ and RpoN drive fleSR PMID:9287015 and the class II genes PMID:14617143.
FleQ is a c-di-GMP receptor: it binds pel promoter DNA, and c-di-GMP inhibits the binding PMID:18485075; it binds c-di-GMP PMID:18485075.
At pelA it is both repressor and activator PMID:22581773, at two sites PMID:22581773.
c-di-GMP binds at the Walker A motif and inhibits ATPase [PMID:24167275 "a relatively low concentration of c-di-GMP competitively inhibited FleQ ATPase activity"; "a FleQ Walker A motif mutant failed to bind c-di-GMP"].
FleN is an antiactivator that does not block DNA binding PMID:11673434.

Literature search (2026-11-05): PubMed MCP and NCBI E-utilities returned server errors throughout; Europe PMC
was intermittently available. Review based on the cached PMIDs above (18485075, 22581773, 12218010, 11673434 full
text; 9287015, 14617143, 24167275 abstract only) and QuickGO queries of the node seeds.

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?
PTN000787214	GO:0000987 cis-regulatory region sequence-specific DNA binding	4	214 (28 taxa)	GO:0000987, IDA, PMID:18485075	SOUND	Full text: gel-shift binding of purified FleQ to pel promoter DNA, inhibited by c-di-GMP.	E. coli GlrR P0AFU4 (IDA PMID:19843219), FhlA P19323 (IDA PMID:8034727), NorR P37013 (IDA PMID:15375149)	Yes; three EcoCyc IDA seeds
PTN000787214	GO:0001216 DNA-binding transcription activator activity	6	214 (28 taxa)	GO:0001216, IMP, PMID:22581773	SOUND	Full text: footprinting at pelA box 1/box 2 and box-mutant lacZ fusions show c-di-GMP-dependent activation from box 1. The same row from CollecTF (IMP, IPI) is also a seed.	X. campestris FleQ Q8P9D2, P. aeruginosa CbrB Q9HV73, V. cholerae FlrA Q9KQ67 and VC_0665 Q9KU59, Geobacter GnfM Q74EF9 (CollecTF IMP/IPI)	Yes; five independent CollecTF-seeded orthologues/paralogues

Node-level assessment for PTN000787214 (recorded once here, on fleQ, the gene with the most direct evidence;
cross-referenced from genes/PSEAE/algB/algB-notes.md). The node is a clade of sigma-54 enhancer-binding proteins
(PTHR32071). All four IBD terms on it (GO:0000987, GO:0001216, GO:0032993, GO:0045893) rest on several independent
experimental seeds from E. coli (EcoCyc), Vibrio, Xanthomonas and Geobacter (CollecTF), checked live in QuickGO on
2026-11-05. The terms suit the clade. No GO_CENTRAL defect is needed; the IBDs stand without the FleQ and AlgB
seeds. One caveat for the clade: FleQ and AlgB can also act at sigma-70/sigma-22 promoters and FleQ also
represses, but that does not undermine the activator, DNA-binding and positive-regulation node terms.

Source defects (non-seed rows)

GO:2000155 positive regulation of cilium-dependent cell motility (IMP, PMID:12218010): eukaryote-only term
(only_in_taxon Eukaryota). PSEUDOCAP WRONG_TERM, CONFIRMED, repoint to GO:1902210.
GO:0006351 DNA-templated transcription (IDA, PMID:9287015): an activator annotated to transcription itself.
PSEUDOCAP WRONG_TERM, PROBABLE (abstract only), repoint to GO:0045893.

Action summary

32 rows. ACCEPT 16; KEEP_AS_NON_CORE 7 (GO:0032993 x5, GO:0010811, GO:1901202); TOO_GENERAL 7 (GO:0000976 x4,
GO:0006355 x2, GO:0043565); MODIFY 2 (GO:0006351, GO:2000155).