PA4624

Summary: IBA from PTN002160772, whose MF IBD rests solely on CdrB's own PseudoCAP IMP row. The node is a TpsB subfamily and the term suits it.

Reason: PA4624 in its own WITH/FROM marks its experimental seed and is expected. TpsB proteins (FhaC, HxuB, HpmB, CdiB and others, all in this node) form the outer-membrane channel through which their partner exoprotein is translocated, so protein transmembrane transport is their own activity, not a complex property. CdrB has the POTRA plus ShlB barrel architecture, and CdrA is not secreted without it.

Summary: CdrA reaches the culture supernatant only when cdrB is co-expressed, which is the in vivo readout of the TpsB transport activity.

Reason: IMP can support an MF term when the perturbation abolishes the activity itself, as read out by an assay of that activity, rather than a downstream phenotype. Here the readout is the transport step: CdrA appears in supernatants from cells expressing cdrAB but not from cells expressing cdrA alone. This is not a cdrB deletion; it compares arabinose-inducible constructs in PAO1, where chromosomal cdrAB expression is low in planktonic culture. The genetic evidence is therefore moderate on its own. Combined with the TpsB architecture and the FhaC homology, which give the mechanism (CdrB is the channel), it supports the claim. The IMP code is acceptable (IGI would also be defensible).

Summary: Outer-membrane location of a TpsB beta-barrel transporter.

Reason: CdrB has a SignalP signal peptide, a POTRA domain and a ShlB-type beta-barrel domain, and is modelled on FhaC, an outer-membrane beta-barrel. No fractionation was done for CdrB, but family and domain evidence agree.

Summary: Biofilm phenotypes in the paper come from cdrA deletions and from overexpression of cdrAB together. CdrB acts upstream, by secreting the matrix adhesin CdrA.

Reason: The mutants tested were cdrA deletions; no cdrB mutant was made. The only phenotype involving cdrB is that overexpressing cdrAB increased biofilm biomass and aggregation, whereas cdrA or cdrB alone did not cause aggregation. This shows CdrB is required for CdrA's effect, through secretion. CdrB does none of the matrix work itself; CdrA cross-links or tethers Psl. The supported claims for CdrB are its transport activity and type V secretion. A biofilm role is at most acts_upstream_of_or_within, and is peripheral.

Summary: IBA from PTN002160772 seeded by the paralog PdtB (PA0692). CdrB is the TpsB of the CdrAB system and secretes CdrA.

Reason: The node is a TpsB subfamily; CdrB is inside it and its own data show CdrB-dependent secretion of CdrA. The process term fits a type Vb transporter, which performs the outer-membrane translocation step.

Summary: CdrB is the pore-forming component of the CdrAB two-partner secretion system.

Reason: The type V secretion system complex term covers the TpsB pore of two-partner secretion systems. The PdtB seed rests on an IMP export defect (an evidence-code issue recorded on PA0692), but the claim holds by family for CdrB.

Summary: Sequence similarity to Bordetella pertussis FhaC (P35077), the TpsB of the FHA two-partner secretion system.

Reason: ISS from FhaC is appropriate: the paper identified CdrB as an FhaC-like Omp85/TpsB transporter by Phyre and I-TASSER, and FhaC is the structurally characterised TpsB channel.