PA4503

Summary: DppB is a polytopic inner (plasma) membrane permease of an ABC importer.

Reason: The node is seeded by experimentally localised E. coli OppB-type permeases (DppB, SapB, NikB, DdpB and others). PA4503 has six predicted TM helices and the ABC_TM1 permease domain, so the location holds.

Summary: Inner-membrane location of an ABC permease subunit.

Reason: Agrees with the IBA row and with the predicted multi-pass topology.

Summary: Correct but general; the specific membrane is the plasma membrane.

Reason: DppB is an inner-membrane permease, and plasma membrane (an is_a descendant of membrane) is already annotated on this gene by IBA and IEA.

Proposed replacements: plasma membrane

Summary: Inferred from the MF row. Correct, but DppBCDF is an importer, so the import term is more precise.

Reason: The operon deletion loses the ability to use dipeptides as nitrogen source and becomes resistant to phaseolotoxin, both of which require uptake into the cytoplasm. Dipeptide import across plasma membrane (GO:0140206) is an is_a descendant of this term.

Proposed replacements: dipeptide import across plasma membrane

Summary: DppB is a permease subunit of a binding protein-dependent ABC importer.

Reason: The Dpp system depends on periplasmic substrate-binding proteins (a DppA1-A5 penta mutant phenocopies the dppBCDF deletion), so the precise complex is the substrate-binding subunit-containing ABC transporter complex (GO:0055052, an is_a descendant).

Proposed replacements: ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing

Summary: Correct but uninformative for a characterised dipeptide importer subunit.

Reason: The specific process supported for this gene is dipeptide import across plasma membrane (GO:0140206), a descendant of transmembrane transport.

Proposed replacements: dipeptide import across plasma membrane

Summary: IBA from PTN000765601, whose IBD rests solely on PA4503's own PseudoCAP row. True for PA4503, but the node term is over-specific for the clade.

Reason: PA4503 in its own WITH/FROM marks its experimental seed and is expected. For PA4503 the claim is correct: it is DppB of the DppBCDF dipeptide importer. Strictly, transport is an activity of the assembled DppA-BCDF complex, so contributes_to would be the more precise qualifier; comparators (E. coli DppB and DppC) use enables, and I keep the convention here and use contributes_to in core_functions. The problem lies at the node, not on this leaf: PTN000765601 also contains E. coli NikB (nickel import) and SapB (putrescine export) and nine Bradyrhizobium paralogs. In the OppBC family the binding protein sets the substrate, so a dipeptide term placed on the whole clade is over-specific (see notes and source_defects).

Summary: PseudoCAP row from Pletzer et al. 2014. The claim is correct, but the evidence is an operon-deletion phenotype, so the code should be IMP.

Reason: The paper deleted the whole dppBCDF operon in PA14 and found loss of dipeptide utilisation as nitrogen source (Biolog respiration and growth) and resistance to the tripeptide toxin phaseolotoxin. No uptake, binding or ATPase assay was done, and DppB was not mutated alone. This is a mutant phenotype, not a direct assay. It still supports the MF for DppB: the permeases form the translocation pathway of an ABC importer, and phaseolotoxin resistance shows a loss of uptake specifically. The claim is accepted and the evidence code is flagged upstream.