PP_0076

Summary: Transport of a quaternary ammonium compound is supported at family level, but the choline-specific cargo is not.

Reason: The InterPro2GO mapping transfers choline transport from the choline-transporter substrate-binding family. The OpuAC-type binding-protein domain is shared by binding proteins for several quaternary ammonium compatible solutes, and PP_0076 sits beside the choline sulfatase gene in a locus induced by choline-O-sulfate in a second Pseudomonas, so its cargo could be choline-O-sulfate, choline or a related compound. The available sources do not resolve this for KT2440; the cited ATCC19151 locus study is a different-strain comparator, and its cached text is abstract-only. The supported claim is the class-level parent quaternary ammonium group transport (GO:0015697), whose definition covers any compound derived from ammonium by replacement of all four hydrogens with organic groups; choline and choline-O-sulfate both qualify.

Proposed replacements: quaternary ammonium group transport

Summary: A soluble periplasmic binding protein does not itself translocate substrate across a membrane.

Reason: The unqualified enables assertion attributes membrane translocation to a protein whose signal peptide and soluble substrate-binding architecture instead support ligand capture. No target-specific functional transport complex has been established that would justify a contributes_to qualifier. Retain transport-process participation and ligand binding, while rejecting independent transmembrane transporter activity for PP_0076; the absence of transmembrane helices alone would not exclude a qualified contribution in a demonstrated complex.

Summary: Exact choline binding is not established; binding of a quaternary ammonium ligand is the supported generalization.

Reason: The term is a family-based inference. Neither direct ligand-binding data nor target-specific genetics distinguishes choline from choline-O-sulfate or another quaternary ammonium solute for PP_0076. GO:0050997 quaternary ammonium group binding is defined as "Binding to a quaternary ammonium group, including glycine betaine, choline, carnitine and proline" and is the claim the OpuAC-type binding domain supports without committing to a ligand. This is a lateral generalization, not a parent: in GO, GO:0033265 choline binding is_a GO:0043169 cation binding (is_a ion binding, is_a binding), while GO:0050997 is_a GO:0036094 small molecule binding; neither term subsumes the other. Comparator: the KT2440 paralog CaiX (Q88R30, also NCBIfam TIGR03414 ABC_choline_bnd) is reviewed in this repository as the L-carnitine-binding component of the CbcWV importer, so membership of this NCBIfam family does not fix choline as the ligand.

Proposed replacements: quaternary ammonium group binding

Summary: The signal peptide and binding-protein architecture support a periplasmic location.

Reason: The predicted cleavable signal peptide and OpuAC-type substrate-binding architecture jointly support periplasmic localization. This is where the inferred ligand-capture activity occurs, so it is core functional localization even though the exact ligand and transport partner remain unresolved; it is not a target localization assay.

Summary: ABC-complex membership is an over-annotation from family architecture; no cognate KT2440 ABC permease or ATPase has been identified.

Reason: The target has ABC substrate-binding-family architecture and a syntenic Pseudomonas homolog is described in silico as an ABC substrate-binding protein, so complex membership is possible. However, the adjacent membrane protein PP_0075 is an SLC26A/SulP-STAS permease rather than an ABC permease, no ABC ATPase is encoded at the locus, and no assay has paired PP_0076 with any ABC transporter encoded elsewhere. Asserting part_of an ABC transporter complex goes beyond the evidence.

Summary: Retain generic transport-process participation for a periplasmic transporter binding protein.

Reason: The substrate-binding-protein architecture supports participation in a transport process, although the transported ligand and membrane partner remain unresolved.