PA1340

Summary: PA1340 is a polytopic inner (plasma) membrane ABC permease.

Reason: Seeded by experimentally localised E. coli HisMQ-subfamily permeases (including GltJ and GltK, plasma membrane by IDA). PA1340 has four predicted TM helices and the ABC transmembrane type-1 domain.

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

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

Summary: IBA from PTN000764525, whose IBD rests solely on PA1340's PseudoCAP row citing a P. putida paper. For PA1340 itself a weak glutamine phenotype exists in another paper, but glutamine is a secondary substrate and the node term does not suit this GltK clade.

Reason: PA1340 in its own WITH/FROM marks its seed, which is expected. On this leaf, glutamine is a plausible low-affinity substrate: the PA1340 transposon mutant used L-glutamine less well in the Biolog screen, and the orthologous P. putida binding protein binds Gln weakly. The more precise form is L-glutamine import across plasma membrane, kept as non-core. The node is another matter. PTN000764525 is a GltK-type permease clade (E. coli, Salmonella and Yersinia GltK, Bradyrhizobium bll7598 and blr3098, PA1340); E. coli GltIJKL is a glutamate/aspartate importer, and the sister GltJ node PTN004745596 carries L-glutamate import. Its only seed, the PseudoCAP IMP to PMID:18310026, is from a study of P. putida aatJ and aatP mutants whose abstract reports no test of PA1340 or of any GltK-type permease (see source_defects).

Proposed replacements: L-glutamine import across plasma membrane

Summary: PseudoCAP IMP citing Singh and Rohm 2008, a study of the orthologous P. putida KT2440 AatJMQP system. The abstract states the organism and the mutants (aatJ binding protein, aatP ATPase); no P. aeruginosa mutant is described, so this is unlikely to be an IMP for PA1340 (full text not read).

Reason: The claim that PA1340's system can carry L-glutamine is weakly supported for P. aeruginosa by the PA1340 Biolog phenotype in PMID:18833300 (already annotated as GO:1903803), and by the ortholog's weak Gln binding. The P. putida aatJ mutant's failure to grow on Gln could also reflect Gln deamidation to Glu by periplasmic glutaminase-asparaginase before uptake, which the same abstract places under the same regulator. The claim is therefore kept only in the precise, non-core form (L-glutamine import across plasma membrane), and the evidence code and reference of this row are flagged upstream.

Proposed replacements: L-glutamine import across plasma membrane

Summary: Correct for the HisMQ-subfamily clade; for PA1340 the main substrate (L-glutamate) and the ATP coupling are known.

Reason: The node term suits a clade of polar amino acid ABC permeases of varied specificity. PA1340 is the GltK/AatM permease of an L-glutamate ABC importer, so the specific activity is ATPase-coupled L-glutamate transmembrane transporter activity (GO:0102013). The activity belongs to the assembled complex; enables is kept for convention here and contributes_to is used in core_functions.

Proposed replacements: ATPase-coupled L-glutamate tranmembrane transporter activity

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

Reason: Plasma membrane, an is_a descendant, is already annotated on this gene by IBA and IEA.

Proposed replacements: plasma membrane

Summary: Correct but uninformative; the main substrate is known.

Reason: The specific activity supported for this gene is ATPase-coupled L-glutamate transmembrane transporter activity (GO:0102013).

Proposed replacements: ATPase-coupled L-glutamate tranmembrane transporter activity

Summary: He et al. 2014 report that the AatJMQP transporter is induced by D-Glu and essential for D-Glu utilisation in PAO1; the Johnson et al. screen independently found the PA1340 mutant unable to use D-glutamate as a nitrogen source.

Reason: Abstract only; which operon mutant was tested is not stated, so I defer to the curator who read the full text. The claim is independently supported for PA1340 by its loss of growth on D-Glu as N source in PMID:18833300. D-glutamate is a secondary substrate of an L-glutamate importer, and GO has no D-glutamate transport term, so D-amino acid transport is as precise as GO allows; kept as non-core.

Summary: PA1340 is a permease subunit of a binding protein-dependent ABC importer.

Reason: The orthologous P. putida AatJMQP system depends on its periplasmic solute-binding protein, 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: The PA1340 transposon mutant is defective in using L-glutamate as carbon and nitrogen source, and PA1340 expression is induced 9-fold by L-glutamate. Sound; refinable to import across the plasma membrane.

Reason: A growth defect is an indirect read-out of transport, but it is consistent across all three operon mutants, matches substrate induction, and the orthologous P. putida system imports Glu directly. As a permease, PA1340 forms part of the translocation pathway. The precise term is L-glutamate import across plasma membrane (GO:0098712, a descendant via L-glutamate transmembrane transport).

Proposed replacements: L-glutamate import across plasma membrane

Summary: Correct but uninformative for a glutamate ABC permease.

Reason: The specific process supported is L-glutamate import across plasma membrane (GO:0098712), a descendant of transmembrane transport.

Proposed replacements: L-glutamate import across plasma membrane

Summary: The PA1340 mutant showed a significant but partial decrease in using L-glutamine (C+/-) in the Biolog/plate screen.

Reason: A partial growth defect is an indirect read-out, and glutamine could in principle be deamidated to glutamate in the periplasm before uptake. The orthologous binding protein binds Gln, though weakly, so direct low-affinity glutamine uptake is plausible. Glutamine is a secondary substrate; kept as non-core.