PA5359 encodes a small, uncharacterised 151-residue protein of Pseudomonas aeruginosa PAO1 with an N-terminal signal peptide and two copies of the Lipoprotein_15 repeat (Pfam PF03640, InterPro IPR005297), placing it in a family of predicted bacterial lipoproteins that also has members in Streptomyces, Gloeobacter, Bradyrhizobium and plants. The protein has no recognisable catalytic domain, metal site or redox cofactor, and UniProt gives it no curated function, subcellular location or family statement; its "Lipoprotein" name comes from an automatic naming model. The locus lies between ubiA (PA5358) and phoB (PA5360), and is not part of the alkB1/alkB2/rubA1/rubA2/rubB system that carries out alkane oxidation in this organism. No publication accessible for this review describes an experiment on PA5359 itself, so its biological role remains unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0043448 alkane catabolic process | IBA GO_REF:0000033 | UNDECIDED | Summary: IBA from PTN002217427, the root of PTHR39335: seven leaves in five organisms, all small lipoprotein-repeat proteins, including two Streptomyces coelicolor lipoproteins, Gloeobacter glr0303, two Bradyrhizobium proteins and a tomato protein. The IBD is sole-seeded by this gene's PseudoCAP IMP row, whose supporting paper could not be read. GOA holds 764 rows with this node in with/from, 757 of them from TreeGrafter. Reason: The transfer cannot be endorsed and the underlying seed cannot be checked. Alkane catabolism requires an alkane hydroxylase with its rubredoxin and rubredoxin reductase partners; no member of this family has such a component, and the family spans actinobacteria, a cyanobacterium, an alphaproteobacterium and a flowering plant, so the process cannot be shared by descent. The right remedy is at the node, so a GO_CENTRAL defect is filed rather than a removal argued from an abstract we could not get behind. Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTN002217427 · PTN002217427 (PTHR39335 root) SOURCE BAD A family root over uncharacterised lipoprotein-repeat proteins including a plant protein; a bacterial alkane catabolic process cannot be an ancestral function of this clade. UniProtKB:Q9HTJ9 · PA5359 UNRESOLVED Sole seed. The supporting paper (PMID:14574114) is not in PMC and only its abstract is cached, so the experiment behind the IMP could not be examined. Supporting Evidence: file:PSEAE/PA5359/PA5359-bioinformatics/RESULTS.md GOA holds 764 GO:0043448 annotations with PTN002217427 in with/from: 7 from GO_Central (the reference leaves) and 757 from TreeGrafter. file:PSEAE/PA5359/PA5359-uniprot.txt DR Pfam; PF03640; Lipoprotein_15; 2. |
| GO:0043448 alkane catabolic process | IMP PMID:14574114 Functional characterization of genes involved in alkane oxid... | UNDECIDED | Summary: PseudoCAP IMP, the sole seed of the PTN002217427 IBD. The paper is Smits et al. 2003 on alkane oxidation in P. aeruginosa. It is not in PubMed Central and only the abstract is cached, so the experiment behind this row could not be read. The abstract describes AlkB1, AlkB2, RubA1, RubA2 and RubB, which are PA2574, PA1525, PA5351, PA5350 and PA5349; it does not mention PA5359, a 151-residue predicted lipoprotein lying between ubiA and phoB. A QuickGO query by reference shows this is the only annotation in GOA keyed to the paper, while the five genes it does describe carry GO:0043448 from UniProt keyword mapping instead. Reason: The full text was not accessible, and an experimental annotation is not overturned from an abstract. The circumstantial case for a locus-tag slip is strong enough to query but not to assert: PA5349 (rubB/alkT) differs by one digit, is in the paper, and would fit the evidence, whereas PA5359 has no component of an alkane oxidation system. Recorded as a SUSPECTED source defect for PseudoCAP to check against the full text. Supporting Evidence: PMID:14574114 Heterologous expression showed that the two alkane hydroxylase homologs of P. aeruginosa PAO1 (AlkB1 and AlkB2) oxidize C(12)-C(16)n-alkanes, while two rubredoxin (RubA1 and RubA2) and a rubredoxin reductase (RubB) homologs can replace their P. putida GPo1 counterparts in n-octane oxidation. file:PSEAE/PA5359/PA5359-uniprot.txt FT SIGNAL 1..45 |
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Download this section (compressed HTML)Q: Does the full text of PMID:14574114 contain any experiment on PA5359, or is the PseudoCAP row a locus-tag slip for PA5349 (rubB/alkT)?
Q: What does PA5359 actually do? It is a conserved, signal-peptide-bearing lipoprotein-repeat protein with no curated function, and the family (PTHR39335) is uncharacterised throughout.
Experiment: Delete PA5359 in PAO1 and test growth on C12-C16 n-alkanes and on hexadecane as sole carbon source, beside alkB1, alkB2 and rubB deletions, and localise a tagged copy by membrane fractionation and Triton X-114 partitioning. This would settle whether the organism's alkane phenotype involves this gene at all and would give the family its first functional anchor.
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