ctpM (Q9I0I6, PA2652) review notes

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

Fetched with just fetch-gene PSEAE Q9I0I6 --alias ctpM (accession fetch); accession Q9I0I6 matches the worklist. Reviewed Swiss-Prot entry. No deep-research provider was used; literature found through the UniProt references and the PubMed MCP, and the cited papers were cached with ai-gene-review fetch-pmid. PMC full text could not be retrieved through the PubMed MCP for the PseudoCAP seed papers with PMC ids (empty body), so those were read as abstracts; the confidence rule is not engaged because no defect is recorded.

Identity

MCP with two TM helices (12-32, 206-226) around a periplasmic sCache_2 ligand binding domain (PF17200), cytoplasmic HAMP and MCPsignal domains (PTHR32089:SF119).

Literature

Seed paper PMID:17933940 (abstract only; PMC body not returned).
Follow-up, full text read PMID:29391435; PMID:29391435; PMID:29391435; PMID:29391435.

Annotation decisions

GO:0004888 IEA: ACCEPT, core MF. Positive chemotaxis IMP: ACCEPT, core.
Chemotaxis IBA, IEA and IMP: TOO_GENERAL (positive chemotaxis is_a chemotaxis, accepted here), following the tier-2 is_a convention.
Plasma membrane ACCEPT; membrane TOO_GENERAL; signal transduction MODIFY to GO:0007166.
No GO term for malate or C4-dicarboxylate binding; raised as a suggested question rather than a NEW row.
Action counts: ACCEPT 3, MODIFY 1, TOO_GENERAL 4.

PseudoCAP IBA-seed assessment

Node-level assessment: see genes/PSEAE/pctB/pctB-notes.md (recorded once there); summary repeated below.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN001280296	GO:0006935 chemotaxis	10	215 (22 taxa)	GO:0006935 and GO:0050918, IMP, PMID:17933940	SOUND	Abstract names PA2652 as the malate chemoreceptor from mutant screening; the 2018 paper confirms loss of malate taxis in the mutant and direct malate binding by the LBD.	PctA, PctB/PctC, CtpH, CtpL, CtpM, Aer (PseudoCAP IMP); B. subtilis McpC (IDA/IMP positive chemotaxis); B. subtilis and H. salinarum HemAT (IDA aerotaxis)	Yes; independent IDA seeds (McpC, two HemATs) and six other PseudoCAP seeds

No source_defects were recorded; no GO_CENTRAL defect for the shared node.