PA1059 (Q9I4R5, ShaG) notes

2026-10-28 review (PseudoCAP IBA-seed worklist, rank 62)

No deep-research provider was available; literature collected by PubMed search
and cached abstracts or full texts. PMID:16030218 (Kosono et al. 2005) is
abstract-only here (PMC1196046 is a scanned PDF). Verdicts kept consistent
with the completed PA1055 (ShaC) and PA1057 (ShaE) reviews.

Identity

UniProt Q9I4R5 (unreviewed, PE 4), 115 aa, three predicted TM helices
(12-33, 45-64, 76-99). InterPro IPR005133 PhaG_MnhG_YufB; Pfam PF03334;
NCBIfam TIGR01300 CPA3_mnhG_phaG; PANTHER PTHR34703:SF1
[file:PSEAE/PA1059/PA1059-uniprot.txt]. The name "Na+/H+ antiporter
subunit G" is a ProtNLM prediction; the family matches are the evidence.
Sixth (last) gene of the sha cluster PA1054-PA1059; by gene order and
family, PA1059 = ShaG (MrpG).

What PMID:16030218 shows

Whole-cluster complementation of E. coli TO114, lost when PA1054 is
deleted; the abstract reports disruption of PA1054 only PMID:16030218. The abstract describes no PA1059 mutant, so IMP looks wrong for PA1059 (full text not read).

MrpG biology (family)

MrpG-P81A PMID:29218041.
MrpG = MBH subunit C PMID:29754813.
Three-TMH subunit PMID:36241630.

PAINT node (PA1059-bioinformatics/RESULTS.md)

PTN002162936 = PTHR34703 root (LUCA), 19 leaves/16 taxa. GOA: 19 GO_Central
GO:0015385 IBAs plus 263 TreeGrafter rows (live QuickGO). Sole seed PA1059.
B. subtilis MrpG (O05227) has no experimental GO:0015385 row. No GO:0035725
IBA from this node. Includes Thermococcus MBH subunit C proteins TK2082
(MbhC) and TK1224 (MbxC).

Annotation decisions

GO:0015385 (IBA, IMP): ACCEPT (core) as contributes_to; PSEUDOCAP
WRONG_EVIDENCE_CODE CHECK and WRONG_QUALIFIER REPOINT; GO_CENTRAL
WRONG_QUALIFIER CHECK (plus MBH reach).
GO:0035725 (IMP): ACCEPT; IMP code flagged. Seeds no IBD.
GO:0015297 antiporter activity: MODIFY to GO:0015385. GO:0055085
transmembrane transport: MODIFY to GO:0035725.
NEW GO:0005886 plasma membrane (IC): the gene has no CC row; TM helices and
complex membership agree.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002162936	GO:0015385 sodium:proton antiporter activity	1 (sole)	19 (GO_Central; plus 263 TreeGrafter)	GO:0015385, IMP, PMID:16030218	INDIRECT-PHENOTYPE	The abstract describes no PA1059 mutant. The evidence is a PA1054 disruption plus whole-cluster complementation of E. coli TO114. Right as `contributes_to` (MrpG Pro81 is needed for Mrp antiport), not as `enables` + IMP. The LUCA-root node also covers MBH/MBX hydrogenase subunit C proteins (TK2082, TK1224), for which a stand-alone antiporter MF is doubtful.

Audit 2026-10-29: confidence matched to what was read

PMID:16030218 is still abstract-only here: the PubMed MCP returns no body
text (the PMC copy, PMC1196046, is a scanned PDF the publisher does not
release as XML), and the PMC, Europe PMC and ASM pages were not retrievable.
The WRONG_EVIDENCE_CODE (IMP) defects on this gene rest on the abstract not
describing a mutant of this gene, so they are lowered from PROBABLE to
SUSPECTED. The WRONG_QUALIFIER defects (enables vs contributes_to) rest on
positive statements in other Mrp papers and stay PROBABLE. The reference
correctness for PMID:16030218 is changed from MISCITED to UNVERIFIED.
Annotation actions are unchanged.

Full-text check of PMID:16030218 (2026-11-05)

The full text of Kosono et al. 2005 was supplied by the user and read. It
supersedes the earlier notes above that describe this paper as abstract-only.
The only sha mutant the paper constructs is the PA1054 insertion; the
cluster-level evidence comes from expressing the whole PA1054-PA1059 cluster,
or the cluster with PA1054 disrupted, in an antiporter-deficient E. coli
strain. There is no PA1059 mutant, so the IMP evidence-code defects on PA1059 are CONFIRMED.