Bacterial type IV secretion apparatus

A species-neutral module for the envelope-spanning machine that transfers macromolecules from a donor bacterium directly into a recipient cell or into the extracellular space. A coupling protein at the inner membrane receives the substrate and feeds it into a channel formed by a conserved three-protein envelope core complex; a VirB4-family ATPase, joined in many lineages by a second VirB11-family ATPase, energizes translocation and the assembly of an extracellular pilus built from processed pilin subunits. In conjugative systems an outer-membrane adhesin stabilizes the donor-recipient pair. The cargo is excluded from this module: the same apparatus transfers a relaxase covalently bound to plasmid DNA in conjugative systems and unrelated protein effectors in others. Relaxosome assembly and DNA nicking, plasmid replication, events inside the recipient cell, and transcriptional regulation of the transfer region are also outside this module.

## Boundary The module begins when the coupling protein engages a substrate at the cytoplasmic face of the inner membrane and ends when that substrate leaves the apparatus. Cargo is excluded for the same reason as in the sibling type II, type V, and type VI modules: the machine is defined by its architecture, and the cargo varies from a relaxase-DNA adduct to standalone protein effectors. ## The Tra naming hazard A naming hazard deserves recording, because it is easy to conflate proteins across plasmids. The Tra nomenclature is not stable between transfer systems: on the F plasmid TraC is the VirB4-family ATPase and TraB is a VirB10-family core-complex component, whereas on pKM101 TraB is itself the VirB4 homologue. Conserved-role assignments here therefore follow the VirB and VirD4 families, with F proteins named as counterparts, rather than following gene symbols across plasmids. Two consequences for grounding. The ATPase annoton is grounded on VirB4 and VirB11, which carry ATP hydrolysis annotations, and not on F TraC, whose GOA record currently holds only a plasma-membrane location. Conversely F TraB carries an experimentally supported ATP hydrolysis annotation whose cited source concerns the pKM101 VirB4 homologue of the same gene symbol; this module places TraB in the core complex on architectural grounds and asserts no ATPase activity for that part, leaving the annotation itself for gene-level review rather than adjudicating it here. 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 for the core-complex and chaperone roles Several components have no molecular function term that expresses what they do. The core-complex subunits carry the generic structural molecule activity, and the pilin maturation chaperone carries none at all, so the distinct architectural roles of the three core proteins are invisible to machine reasoning. **Asserted instead.** Keep structural molecule activity on the core subunits and assert no function for the maturation chaperone, recording the specific roles in prose instead of borrowing an inaccurate term. The coupling-protein molecular function is now a formal term request in `genes/ECOLI/traD/traD-ai-review.yaml` under `proposed_new_terms`. ## Curation gap: unstable gene symbols across transfer systems Conserved-role assignment across transfer systems is obstructed by unstable gene symbols, with the same symbol naming different families on different plasmids. Whether the resulting annotations have been affected has not been assessed systematically. **Asserted instead.** Assign every annoton by VirB or VirD4 family membership and name F proteins as counterparts, flagging on the affected annoton where an existing annotation may reflect a same-symbol protein from another plasmid.