Bacterial type III secretion injectisome

A species-neutral module for the injectisome, the envelope-spanning type III secretion machine that moves unfolded substrates from the bacterial cytoplasm through a continuous conduit and across a second, target-cell membrane in one step. A cytoplasmic sorting platform and ATPase select substrates and strip their chaperones; an inner-membrane export apparatus forms the narrow channel; rings in the inner membrane and an outer-membrane secretin complete the basal body; an inner rod and a helical needle extend the conduit beyond the cell surface; and a translocon inserted in the target membrane completes the passage. The substrates themselves are excluded from this module, as are chaperone-substrate pairing for individual cargo, transcriptional regulation of the locus, and the flagellar export system, which is homologous but builds a different structure.

## Boundary The module begins when the sorting platform selects a substrate in the cytoplasm and ends when that substrate passes through the translocon. Substrates are excluded for the same reason as in the sibling type II, type IV, type V, and type VI modules, and here the exclusion matters more than usual because injectisome substrate repertoires are large, lineage specific, and unrelated to each other in function. The flagellar export system is deliberately not admitted, although the export-apparatus and ATPase components are homologous and the repository has a separate module for flagellar assembly and export. The two systems build different structures from that shared core, and merging them would make the needle, secretin, and translocon parts inapplicable to half the module. ## Grounding Grounding is uneven by necessity. Every conserved role carries a reviewed Swiss-Prot exemplar, taken from Salmonella SPI-1 or Yersinia. The enteropathogenic Escherichia coli counterparts are given alongside them, but most of the Esc structural proteins exist only as unreviewed UniProt entries, which is noted on each annoton where it applies rather than hidden. Two Escherichia coli components are reviewed: the translocon protein EspB and the chaperone CesT. Ontology and curation gaps are recorded in these notes rather than as `knowledge_gaps`, which CLAUDE.md reserves for biological unknowns that only new experiments could close. None of the items below is a biological unknown: a term request or a curator would resolve each one. ## Ontology gap: no molecular function fits the chaperones or the gatekeeper Cytoplasmic chaperones and the gatekeeper have no molecular function term that fits. GOA gives the chaperone only protein binding, and unfolded protein binding, which would have been the natural choice, is obsolete, so the holdase-like role is inexpressible without overstating it. **Asserted instead.** Assert no molecular function for the chaperone or the gatekeeper and record their roles in prose, rather than borrowing the holdase term used for the periplasmic chaperones of the type V module. ## Curation gap: the Escherichia coli components are mostly unreviewed Most structural components of the Escherichia coli locus-of-enterocyte-effacement system exist only as unreviewed UniProt entries, and one of them carries a name suggesting proton transport that its role does not support. The conserved roles are therefore grounded on Salmonella and Yersinia exemplars with the Escherichia coli counterparts attached. **Asserted instead.** Mark every unreviewed exemplar as such on its annoton, and never let an unreviewed entry's name drive the asserted function.