pctA (PA4309, G3XD24) notes

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

Fetched with just fetch-gene PSEAE G3XD24 --alias pctA (accession fetch). Accession
G3XD24 matches the worklist. No deep-research keys available; literature from cached
publications (PMID:9353923, PMID:23650915, PMID:16233808 abstract-only) and the UniProt
record.

Identity

Major amino acid chemoreceptor MCP, PTHR32089 (UniProt lists subfamily SF39). Two TM
helices (11-31, 277-297) around a periplasmic dCache_1 (double PDC) ligand binding
region (36-259), then HAMP and MCPsignal domains. Crystal structures of the LBR with
bound amino acids (5LTX, 5T65, 5T7M, 9KOO). Paralog of PctB and PctC.

Literature

Major amino acid receptor. The pct deletion strain PCT2 shows no taxis to any of the
20 L-amino acids; cloned pctA restores taxis to 18
PMID:9353923;
PMID:9353923.
Direct binding of 17 L-amino acids to the recombinant LBR
PMID:23650915.
Repellent responses to TCE/chloroform/methylthiocyanate PMID:16233808. UniProt also
records histamine (indirect) and AI-2 chemotaxis.

Annotation decisions

Chemotaxis (IBA, IEA, IMP), response to amino acid (IEA, IMP): ACCEPT core.
Amino acid binding (IDA, IEA): ACCEPT. Transmembrane signaling receptor activity (IEA):
ACCEPT core MF. Plasma membrane (IEA): ACCEPT. Signal transduction (IEA): MODIFY to
GO:0007166. Membrane (IEA): TOO_GENERAL.
Action counts: ACCEPT 8, MODIFY 1, TOO_GENERAL 1.
No source defects; the PseudoCAP seed row is sound.

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?
PTN001280296	GO:0006935 chemotaxis	10	215 (22 taxa)	GO:0006935, IMP, PMID:9353923	SOUND	Deletion abolishes amino acid taxis; cloned pctA restores taxis to 18 amino acids; the LBR binds 17 amino acids directly. PctA performs the sensing step itself.	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 and six other PseudoCAP seeds

Node-level assessment of PTN001280296 is recorded once in pctB-notes.md; pctA is
consistent with it (SOUND, no GO_CENTRAL defect).