PA4912 (Q9HUQ1) notes

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

Fetched with just fetch-gene PSEAE Q9HUQ1 --alias PA4912; accession matches the
worklist. Unreviewed TrEMBL entry; no gene symbol, so the locus tag is the folder
name. No deep-research provider was used. NCBI E-utilities and Europe PMC search
were unavailable during this session; the only paper on the gene found in the
cache and UniProt is the Johnson et al. 2008 screen (PMID:18833300, full text).

Identity and literature

LivH-type HAAT permease, nine predicted TM helices (UniProt FT TRANSMEM),
PF02653 BPD_transp_2, PTHR11795:SF371.
Operon PA4909-PA4913, paralogous to braCDEFG (PA1070-PA1074)
PMID:18833300.
Phenotype PMID:18833300.
Table 2 gives D-Alanine N +/- and D-Valine N +/- for PA4912 (strain PAK); no
L-amino acid phenotype was recorded, although every bra mutant showed L-Ala
defects in the same screen.

Decisions

ACCEPT: plasma membrane (IBA, IEA), transmembrane transporter activity (IEA),
transmembrane transport (IEA).
TOO_GENERAL: membrane (IEA).
MARK_AS_OVER_ANNOTATED: L-phenylalanine transporter activity, phenylalanine
transport (IBA; E. coli binding-protein specificity), consistent with braD/braF.
UNDECIDED: L-valine, L-isoleucine, L-leucine transporter activity, L-leucine
import, L-valine transmembrane transport, L-isoleucine import, L-alanine
transport (IBA; the substrate of this paralogous system is unknown and set by
its own binding protein), D-alanine transmembrane transport (IBA, IMP).
Counts: ACCEPT 4, TOO_GENERAL 1, MARK_AS_OVER_ANNOTATED 2, UNDECIDED 9.

PseudoCAP IBA-seed assessment

Node-level assessment for both nodes was recorded in genes/PSEAE/braD/braD-notes.md
(braD, PA1073, is the co-seed); the verdicts below follow it.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000209860	GO:0055085 transmembrane transport	3	50 (15 taxa)	GO:0042941 D-alanine transmembrane transport, IMP, PMID:18833300 (PseudoCAP)	SOUND	For the generic node term, a permease mutant with a nutrient-utilisation defect is adequate, and the term suits a broad HAAT permease clade (includes urea permeases).	E. coli LivH (P0AEX7; IMP/IDA BCAA transport, EcoCyc), BraD (P21627; reconstituted LIV-I)	Yes
PTN000765102	GO:0042941 D-alanine transmembrane transport	2 (P21627, Q9HUQ1)	18 (16 taxa)	GO:0042941, IMP, PMID:18833300 (PseudoCAP)	INDIRECT-PHENOTYPE	Partial D-Ala/D-Val nitrogen-source growth defect from one Biolog screen; no uptake or binding assay for either system. Plausible, not established.	BraD (P21627), same screen and same kind of phenotype	No independent support; both seeds are the same kind of weak phenotype from one screen

No source_defects were recorded, consistent with braD: the D-alanine rows are
left UNDECIDED with a suggested question rather than filed as PseudoCAP or
GO_CENTRAL defects, because the claim is plausible and not refuted. If D-alanine
transport is later shown not to occur, the PTN000765102 D-alanine IBD would fall
with both seeds.