PA4910 (Q9HUQ3) notes

Review session 2026-11-05 (PseudoCAP IBA-seed protocol, tier 2)

Fetched with just fetch-gene PSEAE Q9HUQ3 --alias PA4910; accession matches the
worklist. Unreviewed TrEMBL entry with no gene symbol, so the locus tag is the
folder name. No deep-research provider key was available. The only paper on the
gene is the Johnson et al. 2008 transport-gene screen (PMID:18833300, full text
cached).

Identity and literature

LivG-type ABC ATPase: PF00005 ABC_tran plus PF12399 BCA_ABC_TP_C, both ABC
transporter PROSITE signatures, PTHR45772:SF11 (LivG). No TM segments.
Operon PA4909-PA4913, paralogous to braCDEFG (PA1070-PA1074)
PMID:18833300;
subunit assignment
PMID:18833300.
Phenotype
PMID:18833300.
No L-amino acid phenotype was recorded for PA4910, although every bra mutant
showed L-Ala defects in the same screen.
Substrate specificity in HAAT importers is set by the periplasmic binding
protein. PA4910's system has its own (PA4913), uncharacterised; this is why
the L-amino acid IBAs propagated from E. coli LivG and from BraF are left
UNDECIDED rather than accepted.

Consistency with the already-reviewed siblings

braG (P21630) is on a different node (PTN000657089, the LivF ATPase node),
so it does not share PA4910's node; its notes record that node separately.
PA4912 (Q9HUQ1) is the permease of the same operon, on the permease nodes
PTN000209860 and PTN000765102, not on PTN000656921. So PA4910 shares no node
with either already-reviewed gene; the shared element is the single seed
paper.
braF (P21629) is the gene that shares PTN000656921 with PA4910, and the
node-level assessment was recorded there. The present review follows it: the
D-alanine rows are UNDECIDED, the phenylalanine rows are
MARK_AS_OVER_ANNOTATED, and ATP binding/hydrolysis and plasma membrane are
accepted. braF and PA4912 recorded no source defects for the D-alanine rows,
and neither does this review.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000656921	GO:0042941 D-alanine transmembrane transport	2 (P21629 braF, Q9HUQ3 PA4910)	25 (15 taxa)	GO:0042941, IMP, PMID:18833300 (PseudoCAP)	INDIRECT-PHENOTYPE	A partial D-alanine nitrogen-source growth defect in one Biolog screen, with no uptake or binding assay and an uncharacterised binding protein for this system. Plausible for a D-amino acid importer, not established. The appearance of PA4910 in its own WITH/FROM is the expected seed self-reference.	braF (P21629), the LIV-I ATPase: the same screen, the same kind of partial phenotype	No independent support — both seeds are the same kind of weak phenotype from the same screen. Not filed as a GO_CENTRAL defect, following braF and PA4912: the claim is plausible and not refuted, and the node also carries well-grounded E. coli LivG-seeded MF IBDs.

Node composition (from braF's assessment): 25 leaves in 15 taxa, including
E. coli/Salmonella/Yersinia LivG, BraF, PA4910, seven Bradyrhizobium japonicum
HAAT ATPases, Geobacter, Deinococcus, Thermotoga, Chloroflexus, Streptomyces,
Fusobacterium and Streptococcus members — several paralogous systems per genome
whose substrates are unknown. That is the standing caveat on every
substrate-level term at this node.

Decisions summary

ACCEPT: ATP binding (IEA), ATP hydrolysis activity (IEA), plasma membrane
(IBA).
TOO_GENERAL: nucleotide binding (IEA; ATP binding is asserted).
MARK_AS_OVER_ANNOTATED: L-phenylalanine transporter activity (IBA),
phenylalanine transport (IEA).
UNDECIDED: L-valine and L-isoleucine transporter activity, L-alanine
transport, L-valine and L-isoleucine import, isoleucine and L-valine
transmembrane transport (ARBA), D-alanine transmembrane transport (IBA, IMP).
Counts: ACCEPT 3, TOO_GENERAL 1, MARK_AS_OVER_ANNOTATED 2, UNDECIDED 9.
Defects: none (PSEUDOCAP 0, GO_CENTRAL 0), consistent with braF, braD, braG
and PA4912.
One BIOLOGY knowledge gap recorded: the substrate range of the PA4909-PA4913
importer is undetermined.