PA1058 (Q9I4R6, ShaF) notes

2026-10-28 review (PseudoCAP IBA-seed worklist, rank 63)

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 Q9I4R6 (unreviewed, PE 3), 89 aa, two predicted TM helices (34-53,
60-83). InterPro IPR007208 MrpF/PhaF-like; Pfam PF04066; NCBIfam
NF004812; PANTHER PTHR34702:SF1 [file:PSEAE/PA1058/PA1058-uniprot.txt].
The UniProt name "K+/H+ antiporter subunit F" is a ProtNLM prediction, not
evidence of K+ specificity.
Fifth gene of the sha cluster PA1054-PA1059; by gene order and family,
PA1058 = ShaF (MrpF).

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 PA1058 mutant, so IMP looks wrong for PA1058 (full text not read).

MrpF biology (family)

MrpF-D32A loses antiport and complex PMID:29218041.
MrpF = MBH subunit B PMID:29754813.
B. subtilis MrpF has a possible stand-alone role PMID:11004162.
This does not change the GO:0015385 assessment (Na+/H+ antiport of the
Sha complex), but is a question for ShaF.
Complex needed for antiport PMID:20624916.

PAINT node (PA1058-bioinformatics/RESULTS.md)

PTN002162906 = PTHR34702 root (LUCA), 19 leaves/16 taxa. GOA: 19 GO_Central
GO:0015385 IBAs plus 272 TreeGrafter rows with the same with/from (live
QuickGO). Sole seed PA1058. B. subtilis MrpF (O05228) has no experimental
GO:0015385 row. No GO:0035725 IBA from this node. Includes Thermococcus MBH
subunit B proteins TK2081 (MbhB) and TK1225 (MbxB).

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:0015075, GO:0015297: MODIFY to GO:0015385. GO:0034220: MODIFY to
GO:0035725. GO:0016020: MODIFY to GO:0005886. GO:0005886: ACCEPT.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002162906	GO:0015385 sodium:proton antiporter activity	1 (sole)	19 (GO_Central; plus 272 TreeGrafter)	GO:0015385, IMP, PMID:16030218	INDIRECT-PHENOTYPE	The abstract describes no PA1058 mutant. The evidence is a PA1054 disruption plus whole-cluster complementation of E. coli TO114, which shows the Sha complex is an antiporter. Right as `contributes_to` (MrpF Asp32 is needed for antiport and assembly), not as `enables` + IMP. The LUCA-root node also covers MBH/MBX hydrogenase subunit B proteins (TK2081, TK1225), 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 PA1058 mutant, so the IMP evidence-code defects on PA1058 are CONFIRMED.