PA5359 (Q9HTJ9) notes

2026-10-28 review (PseudoCAP IBA-seed worklist, rank 97)

No deep-research provider keys were available; literature gathered by PubMed
search and from the cached publications. The seeding paper (PMID:14574114,
Smits et al. 2003, Antonie Van Leeuwenhoek) is not in PubMed Central and only
its abstract is cached; pseudomonas.com is behind a bot challenge from this
environment. Several statements below are therefore limited, and the review
uses UNDECIDED accordingly.

Identity

UniProt Q9HTJ9 (unreviewed, PE 4 "Predicted"), 151 aa. The only name is
"Lipoprotein", generated by a machine-learning model
({ECO:0008006|Google:ProtNLM}), so it is not evidence of anything
[file:PSEAE/PA5359/PA5359-uniprot.txt].
Sequence features: a SignalP signal peptide at 1-45 and two copies of Pfam
PF03640 Lipoprotein_15, InterPro IPR005297 Lipoprotein_repeat and
IPR014558 UCP029720, PIRSF029720, PANTHER PTHR39335:SF1
[file:PSEAE/PA5359/PA5359-uniprot.txt]. Nothing in the record suggests a
catalytic activity, a redox cofactor or a membrane-bound monooxygenase fold.
The entry's only GO annotation is the PseudoCAP one under review:
"DR GO; GO:0043448; P:alkane catabolic process; IMP:PseudoCAP."
[file:PSEAE/PA5359/PA5359-uniprot.txt]. There is no UniProt FUNCTION,
SUBCELLULAR LOCATION or SIMILARITY line.

What PMID:14574114 is about

The abstract names the gene products that were characterised:
PMID:14574114 and the distribution of the hydroxylase genes
PMID:14574114.
Those five genes have PAO1 loci and UniProt entries of their own: alkB1 =
PA2574 (Q9I0R2), alkB2 = PA1525 (Q6H941), rubA1/alkG1 = PA5351 (Q9HTK7),
rubA2/alkG2 = PA5350 (Q9HTK8), rubB/alkT = PA5349 (Q9HTK9) (UniProt query).
PA5359 is not one of them; it lies about ten loci away, between ubiA (PA5358)
and phoB (PA5360).
A QuickGO query for annotations keyed to PMID:14574114 returns exactly one
row in the whole database: the PseudoCAP IMP on Q9HTJ9 (PA5359). None of the
five genes the abstract actually describes is annotated from this paper; their
GO:0043448 rows come from UniProt keyword mapping (GO_REF:0000041) instead.
A single annotation from an alkane-oxidation paper, landing on a gene the
abstract does not mention while the five it does mention get nothing, looks
like a locus-tag slip - PA5349 (rubB/alkT) differs from PA5359 by one digit.
This cannot be confirmed without the full text, so it is recorded as a
SUSPECTED source defect with requested_change: CHECK rather than asserted.

PAINT node (PA5359-bioinformatics/RESULTS.md)

PTN002217427 is the root of PTHR39335 (Eubacteria speciation node, 7 leaves in
5 organisms): two Streptomyces coelicolor lipoproteins (SCO0930, SCO7673),
Gloeobacter violaceus glr0303, two Bradyrhizobium diazoefficiens proteins
(bll4220, bll5559), a Solanum lycopersicum "lipoprotein with Yx(FWY)xxD
motif", and PA5359. The GO:0043448 IBD is sole-seeded by PA5359 and GOA now
holds 764 rows with this node in with/from (7 GO_Central and 757 TreeGrafter).

Whatever the status of the seed, the propagation is not defensible on its own
terms: alkane catabolism requires an alkane hydroxylase system, and this family
is a set of small, signal-peptide-bearing lipoprotein-repeat proteins with no
such component, spanning actinobacteria, a cyanobacterium, an
alphaproteobacterium and a flowering plant. A tomato protein annotated to
alkane catabolic process by descent from a P. aeruginosa mutant phenotype is a
clear taxon and role mismatch.

Annotation decisions

GO:0043448 (IMP and IBA): UNDECIDED for both. The full text of the seeding
paper is not available, and CLAUDE.md is explicit that an experimental
annotation whose evidence cannot be read is not to be removed on the strength
of an abstract. The doubts are recorded as source defects instead: a
SUSPECTED WRONG_GENE_PRODUCT query to PseudoCAP, and a PROBABLE
over-propagation report to GO_CENTRAL for the node.
No core function is asserted: nothing in the record or the accessible
literature establishes one for this protein.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002217427	GO:0043448 alkane catabolic process	1 (sole)	7 GO_Central (764 GOA rows incl. 757 TreeGrafter)	GO:0043448, IMP, PMID:14574114	UNVERIFIABLE seed, WRONG node	The seed cannot be checked: the paper is not in PMC and only the abstract is cached. What can be checked is suspicious. The abstract describes AlkB1, AlkB2, RubA1, RubA2 and RubB, which are PA2574, PA1525, PA5351, PA5350 and PA5349; PA5359 is a different locus one digit from PA5349, it is a 151-residue predicted lipoprotein with no alkane-oxidation component, and it is the only gene in GOA annotated from this paper. Independently of the seed, the node is the root of a family of small lipoprotein-repeat proteins from Streptomyces, Gloeobacter, Bradyrhizobium and tomato, which cannot share a bacterial alkane catabolic role; 764 GOA rows now carry the term from it, 757 of them by TreeGrafter.