PA4912 is a predicted integral inner-membrane permease subunit of an uncharacterised hydrophobic amino acid (HAAT family, LivH-type) ABC importer of Pseudomonas aeruginosa, encoded in a five-gene operon (PA4909-PA4913) that is a paralogue of the braCDEFG (LIV-I) branched-chain amino acid transport operon. It has nine predicted transmembrane helices and the BPD_transp_2 permease domain. The substrate of this second system has not been determined biochemically; in a transposon-mutant growth screen the PA4912 mutant used D-alanine and D-valine less well as nitrogen sources.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005304 L-valine transmembrane transporter activity | IBA GO_REF:0000033 | UNDECIDED | Summary: Propagated from E. coli LivH at the LivH node PTN000765102. PA4912 belongs to a paralogous HAAT system whose substrate is unknown. Reason: In this family the substrate range is set by the partner periplasmic binding protein, not by the permease. The PA4909-PA4913 system has no transport or binding data, and its only phenotype is a weak D-alanine/D-valine growth defect; the screen recorded no L-valine phenotype for PA4912 (which could be masked by the Bra system). Branched-chain substrates are plausible from family membership but not shown. Propagation Review Root cause: UNRESOLVED Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000765102 · PTN000765102 UNRESOLVED LivH permease node spanning several paralogous HAAT systems per genome; substrate specificity is set by each system's binding protein, not by the permease. UniProtKB:P0AEX7 · E. coli LivH UNRESOLVED Experimental for E. coli LIV-I; transfer to the PA4909-PA4913 paralogous system is untested. Supporting Evidence: PMID:18833300 Disruption of PA4910 resulted in reduced utilization of D-Alanine (as a nitrogen source), while PA4912 mutants had disrupted D-Alanine and D-Valine utilization (Table 2). |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Integral inner-membrane permease with nine predicted transmembrane helices. Reason: The IBA from E. coli LivH agrees with the topology prediction; ABC permeases of this family sit in the inner membrane. Supporting Evidence: file:PSEAE/PA4912/PA4912-uniprot.txt Pfam; PF02653; BPD_transp_2; 1. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Same location as the IBA row. Reason: Consistent with nine predicted transmembrane helices and the permease family. Supporting Evidence: file:PSEAE/PA4912/PA4912-uniprot.txt InterPro; IPR001851; ABC_transp_permease. |
| GO:0015188 L-isoleucine transmembrane transporter activity | IBA GO_REF:0000033 | UNDECIDED | Summary: E. coli LivH-seeded substrate claim, transferred to an uncharacterised paralogous permease. Reason: Same reasoning as for L-valine: no substrate data for the PA4909-PA4913 system, whose substrate is set by its own binding protein. Propagation Review Root cause: UNRESOLVED Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000765102 · PTN000765102 UNRESOLVED LivH permease node spanning several paralogous HAAT systems per genome; substrate specificity is set by each system's binding protein, not by the permease. UniProtKB:P0AEX7 · E. coli LivH UNRESOLVED Experimental for E. coli LIV-I; transfer to the PA4909-PA4913 paralogous system is untested. Supporting Evidence: PMID:18833300 PA4910 encodes a putative ATP-binding protein, while PA4912 encodes a predicted membrane component of this ABC amino acid transporter. |
| GO:0015190 L-leucine transmembrane transporter activity | IBA GO_REF:0000033 | UNDECIDED | Summary: E. coli LivH-seeded substrate claim, transferred to an uncharacterised paralogous permease. Reason: No leucine transport or binding data exist for the PA4909-PA4913 system. Propagation Review Root cause: UNRESOLVED Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000765102 · PTN000765102 UNRESOLVED LivH permease node spanning several paralogous HAAT systems per genome; substrate specificity is set by each system's binding protein, not by the permease. UniProtKB:P0AEX7 · E. coli LivH UNRESOLVED Experimental for E. coli LIV-I; transfer to the PA4909-PA4913 paralogous system is untested. Supporting Evidence: PMID:18833300 PA4910 encodes a putative ATP-binding protein, while PA4912 encodes a predicted membrane component of this ABC amino acid transporter. |
| GO:0015192 L-phenylalanine transmembrane transporter activity | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Phenylalanine comes from E. coli LivH, whose phenylalanine transport depends on the E. coli LivK binding protein. Reason: Consistent with braD and braF. No P. aeruginosa HAAT system has been shown to carry phenylalanine, and the claim reflects the E. coli binding-protein repertoire rather than the permease lineage. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: UniProtKB:P0AEX7 · E. coli LivH SUPPORTS SOURCE BUT NOT TARGET Phenylalanine specificity is a property of the E. coli binding proteins. Supporting Evidence: PMID:18833300 PA4912 mutants had disrupted D-Alanine and D-Valine utilization |
| GO:0015808 L-alanine transport | IBA GO_REF:0000033 | UNDECIDED | Summary: Seeded by BraD (PA1073), whose LIV-I system carries alanine. PA4912 is in a different, uncharacterised system. Reason: The seed claim is sound for LIV-I (see genes/PSEAE/braD), but alanine is a secondary LIV-I substrate set by BraC, and nothing shows that the PA4909-PA4913 system carries L-alanine. The PA4912 mutant had no recorded L-alanine phenotype in the screen that found L-alanine defects for every bra mutant. Propagation Review Root cause: UNRESOLVED Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000765102 · PTN000765102 UNRESOLVED LivH permease node spanning several paralogous HAAT systems per genome; substrate specificity is set by each system's binding protein, not by the permease. UniProtKB:P21627 · braD (PA1073) UNRESOLVED PseudoCAP growth-screen IMP for the LIV-I permease; a different system from PA4912's. Supporting Evidence: PMID:18833300 PA4912 mutants had disrupted D-Alanine and D-Valine utilization |
| GO:0015823 phenylalanine transport | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Process counterpart of the phenylalanine transporter activity IBA. Reason: Same reasoning as GO:0015192; consistent with braD. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: UniProtKB:P0AEX7 · E. coli LivH SUPPORTS SOURCE BUT NOT TARGET Phenylalanine specificity is a property of the E. coli binding proteins. Supporting Evidence: PMID:18833300 PA4912 mutants had disrupted D-Alanine and D-Valine utilization |
| GO:0016020 membrane | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but general. Reason: GO:0005886 plasma membrane, accepted in this review, is_a membrane. Supporting Evidence: file:PSEAE/PA4912/PA4912-uniprot.txt InterPro; IPR001851; ABC_transp_permease. |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000002 | ACCEPT | Summary: Generic transporter activity from the ABC permease signature. Reason: As precise as the evidence allows. The HAAT permease clade includes non-amino acid substrates (for example urea permeases), and this system's substrate is unknown. Supporting Evidence: file:PSEAE/PA4912/PA4912-uniprot.txt Pfam; PF02653; BPD_transp_2; 1. |
| GO:0042941 D-alanine transmembrane transport | IBA GO_REF:0000033 | UNDECIDED | Summary: Propagated from two P. aeruginosa seeds, BraD and PA4912 itself, both resting on partial D-alanine growth defects in one Biolog screen. Reason: PA4912 in its own WITH/FROM is expected. No D-alanine uptake or binding has been shown for either system. The PA4912 phenotype (D-Ala and D-Val as nitrogen sources) fits a D-amino acid importer, but could also be indirect. Consistent with braD and braF. Propagation Review Root cause: UNRESOLVED Failure modes: SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTN000765102 · PTN000765102 UNRESOLVED LivH permease node spanning several paralogous HAAT systems per genome; substrate specificity is set by each system's binding protein, not by the permease. UniProtKB:P21627 · braD (PA1073) SOURCE WEAK OR INFERRED PseudoCAP growth-screen IMP for the LIV-I permease; a different system from PA4912's. UniProtKB:Q9HUQ1 · PA4912 (self; IBD seed, IMP PMID:18833300) SOURCE WEAK OR INFERRED Partial D-Ala/D-Val nitrogen-source growth defect; no uptake assay. Supporting Evidence: PMID:18833300 PA4912 mutants had disrupted D-Alanine and D-Valine utilization |
| GO:0042941 D-alanine transmembrane transport | IMP PMID:18833300 High-throughput phenotypic characterization of Pseudomonas a... | UNDECIDED | Summary: PseudoCAP IMP seed for PTN000209860 and PTN000765102. The PA4912 Tn5 mutant (strain PAK) grows less well (+/-) on D-alanine and D-valine as nitrogen sources. Reason: Seed verdict INDIRECT-PHENOTYPE for the D-alanine term. The phenotype is real but partial, with no uptake or binding assay. It is the only functional data on this system, so I neither accept nor reject it. Supporting Evidence: PMID:18833300 Disruption of PA4910 resulted in reduced utilization of D-Alanine (as a nitrogen source), while PA4912 mutants had disrupted D-Alanine and D-Valine utilization (Table 2). |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | ACCEPT | Summary: Generic transport process, also the term of the PTN000209860 IBD. Reason: As precise as the evidence allows, since the substrate is not established. PA4912 is an ABC permease, and its mutant has a nutrient-utilisation defect. Supporting Evidence: PMID:18833300 PA4910 encodes a putative ATP-binding protein, while PA4912 encodes a predicted membrane component of this ABC amino acid transporter. |
| GO:1903785 L-valine transmembrane transport | IBA GO_REF:0000033 | UNDECIDED | Summary: E. coli LivH-seeded substrate claim, transferred to an uncharacterised paralogous permease. Reason: No L-valine transport data for this system; the PA4912 screen phenotype is on D-valine, not L-valine. Propagation Review Root cause: UNRESOLVED Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000765102 · PTN000765102 UNRESOLVED LivH permease node spanning several paralogous HAAT systems per genome; substrate specificity is set by each system's binding protein, not by the permease. UniProtKB:P0AEX7 · E. coli LivH UNRESOLVED Experimental for E. coli LIV-I; transfer to the PA4909-PA4913 paralogous system is untested. Supporting Evidence: PMID:18833300 PA4912 mutants had disrupted D-Alanine and D-Valine utilization |
| GO:1903801 L-leucine import across plasma membrane | IBA GO_REF:0000033 | UNDECIDED | Summary: E. coli LivH-seeded substrate claim, transferred to an uncharacterised paralogous permease. Reason: No leucine transport data exist for the PA4909-PA4913 system. Propagation Review Root cause: UNRESOLVED Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000765102 · PTN000765102 UNRESOLVED LivH permease node spanning several paralogous HAAT systems per genome; substrate specificity is set by each system's binding protein, not by the permease. UniProtKB:P0AEX7 · E. coli LivH UNRESOLVED Experimental for E. coli LIV-I; transfer to the PA4909-PA4913 paralogous system is untested. Supporting Evidence: PMID:18833300 PA4910 encodes a putative ATP-binding protein, while PA4912 encodes a predicted membrane component of this ABC amino acid transporter. |
| GO:1903806 L-isoleucine import across plasma membrane | IBA GO_REF:0000033 | UNDECIDED | Summary: Seeded by BraD (sound for LIV-I); PA4912 is in a different, uncharacterised system. Reason: The screen tested L-isoleucine and recorded defects for braD/braF but not for PA4912. No transport data exist for the PA4909-PA4913 system. Propagation Review Root cause: UNRESOLVED Failure modes: WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000765102 · PTN000765102 UNRESOLVED LivH permease node spanning several paralogous HAAT systems per genome; substrate specificity is set by each system's binding protein, not by the permease. UniProtKB:P21627 · braD (PA1073) UNRESOLVED PseudoCAP growth-screen IMP for the LIV-I permease; a different system from PA4912's. Supporting Evidence: PMID:18833300 PA4912 mutants had disrupted D-Alanine and D-Valine utilization |
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Download this section (compressed HTML)Q: What does the PA4909-PA4913 HAAT system import? Its predicted periplasmic binding protein (probably PA4913) would set the substrate; the PA4912 and PA4910 mutants point to D-alanine and D-valine.
Experiment: Ligand screening (thermal shift or ITC) of the purified predicted periplasmic binding protein of the PA4909-PA4913 operon with D- and L-amino acids, and radiolabelled D-alanine uptake in wild-type, PA4912 and braC/PA4912 double mutants.
Type: transport assay
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