dctQ

Summary: DctQ is a multi-pass inner (plasma) membrane permease subunit.

Reason: Seeded by E. coli YiaM and Vibrio cholerae TRAP small permeases. A membrane location is a family-wide property of TRAP small permeases, whatever their substrate, and DctQ has four predicted TM helices.

Summary: Inner-membrane location from the curated UniProt subcellular location.

Reason: Agrees with the IBA and ISS rows and with the predicted topology.

Summary: Curator transfer of inner-membrane location from a characterised DctQ ortholog.

Reason: The ISS source O07837 is a DctQ ortholog with an experimental inner membrane location, and DctQ is a polytopic permease.

Summary: IBA from PTN002169725, whose IBD for this term rests solely on DctQ's own PseudoCAP IMP. True for DctQ, where the specific substrates and direction (import) are known; but the node term does not suit the clade.

Reason: DctQ in its own WITH/FROM marks its experimental seed and is expected. For DctQ the claim is correct, and the precise terms are malate import across plasma membrane, succinate import across plasma membrane and fumarate transport, all descendants of C4-dicarboxylate transport and the same replacements as for the IMP row. The node is a different matter. PTN002169725 is a YiaM-type TRAP small-permease clade (PANTHER PTHR35011 is named for E. coli YiaM), with 24 leaves including E. coli and Salmonella YiaM, two Haemophilus, several Bradyrhizobium and Geobacter, Dictyoglomus and Yersinia members. E. coli YiaMNO transports 2,3-diketo-L-gulonate, not a C4-dicarboxylate. In TRAP transporters the substrate is set by the DctP-type binding protein, so a C4-dicarboxylate term placed on the whole clade is over-specific (see source_defects).

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 here the double mutant removes only the two transporters, the operon is induced by its substrates, and competition experiments separate DctPQM from DctA. DctQ, as a TRAP permease, forms part of the translocation pathway, so it does part of the work. The deletion is of the whole dctPQM operon, so the phenotype is not specific to DctQ, but DctQ is essential to TRAP function. The more precise terms are the substrate-specific import processes.

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

Summary: Correct but general for DctQ, whose TRAP system carries C4-dicarboxylates.

Reason: The YiaM-seeded node term is appropriate for the clade. For DctQ the specific activity is C4-dicarboxylate transmembrane transporter activity (GO:0015556, an is_a descendant). As in other TRAP systems the activity belongs to the DctPQM complex, so in core_functions it is recorded as contributes_to.

Proposed replacements: C4-dicarboxylate transmembrane transporter activity

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

Reason: Derived from the generic MF row. 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: DctQ is the small permease of the DctPQM TRAP transporter, made up of the binding protein DctP and the membrane proteins DctQ and DctM.

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