dctP

Summary: IBA from PTN002121312, whose IBD rests solely on DctP's own PseudoCAP IMP. True for DctP, whose specific substrates and direction are known.

Reason: DctP in its own WITH/FROM marks its experimental seed and is expected. The node is a DctP-family TRAP binding-protein clade of 9 leaves in 5 taxa (P. aeruginosa DctP and its paralogs PA0884 and PA4616; three Bradyrhizobium binding proteins; Shewanella and Vibrio cholerae DctP; and a Nematostella genome entry that is probably a bacterial contaminant). No leaf other than DctP has experimental annotations, and none contradicts the C4-dicarboxylate term. Unlike the permease case (DctQ, a YiaM-type clade), here the seed is the binding protein, which sets substrate specificity, so the node term is a reasonable clade-level claim, with the caveat that within-genome paralogs may have diverged. For DctP itself the precise terms are the substrate-specific import processes, as for the IMP row.

Proposed replacements: malate import across plasma membrane succinate import across plasma membrane fumarate transport

Summary: Deleting dctPQM in a dctA background abolishes growth on malate and fumarate; competition experiments show DctPQM is the high-affinity succinate carrier. The claim is sound; the specific substrates and direction are known.

Reason: Growth on a sole carbon source is an indirect read-out of transport, but the double mutant removes only the two transporters, the operon is induced by its substrates, and competition experiments separate DctPQM from DctA. DctP, the TRAP binding protein, captures the substrate and delivers it to DctQM, so it does part of the work. The deletion covers the whole operon, so the phenotype is not specific to DctP, but TRAP transport requires the binding protein. The more precise terms are the substrate-specific import processes (the same replacements used for DctQ).

Proposed replacements: malate import across plasma membrane succinate import across plasma membrane fumarate transport

Summary: DctP is a soluble periplasmic binding protein of a Gram-negative bacterium.

Reason: DctP has a signal peptide and the TRAP DctP binding-protein fold; in a diderm bacterium the periplasm is bounded by the outer membrane, so this is the precise location term.

Summary: Correct but general; outer membrane-bounded periplasmic space is supported.

Reason: Outer membrane-bounded periplasmic space (an is_a descendant) is already annotated on this gene and is the precise term for a Gram-negative periplasmic binding protein.

Proposed replacements: outer membrane-bounded periplasmic space

Summary: Curator transfer of periplasmic location from Rhodobacter capsulatus DctP (P37735). Correct but general.

Reason: The transfer is sound; the more precise term, outer membrane-bounded periplasmic space, is already annotated on this gene.

Proposed replacements: outer membrane-bounded periplasmic space

Summary: Correct but uninformative; the specific import processes are known.

Reason: The supported specific processes are malate and succinate import across plasma membrane and fumarate transport.

Proposed replacements: malate import across plasma membrane succinate import across plasma membrane fumarate transport

Summary: DctP is the extracytoplasmic solute receptor of the DctPQM TRAP transporter.

Reason: The paper identifies dctPQM as a TRAP operon whose products function together, and UniProt's curated subunit statement records the DctPQM complex. As for DctQ, membership is inferred from the family architecture and operon phenotype rather than shown biochemically, hence IC.