PA1054 (Q9I4S0, ShaAB) notes

2026-10-28 review (PseudoCAP IBA-seed worklist, rank 68)

No deep-research provider was available; literature collected by PubMed search
and cached abstracts or full texts. The PseudoCAP-cited paper (PMID:16030218,
Kosono et al. 2005) is abstract-only here (PMC1196046 is a scanned PDF). Sister
reviews of the same cluster: PA1055 (ShaC) and PA1057 (ShaE), with PA1056,
PA1058 and PA1059 reviewed in the same session.

Identity

UniProt Q9I4S0 (unreviewed, PE 4), 933 aa, about 22 predicted TM helices.
InterPro IPR050616 CPA3_Na-H_Antiporter_A, IPR001750 ND/Mrp_TM,
IPR001516 Proton_antipo_N, IPR025383/IPR046806 MrpA_C, IPR007182 MnhB;
Pfam PF00361, PF00662, PF13244 MbhD, PF20501 MbhE, PF04039 MnhB; PANTHER
PTHR43373:SF1 [file:PSEAE/PA1054/PA1054-uniprot.txt]. The UniProt name
"Probable NADH dehydrogenase" is the submitter's name, not a finding.
First gene of the six-gene sha cluster PA1054-PA1059. The MnhB Pfam match
in the C-terminal part matches the A-B fusion found in Gram-negative Mrp
operons PMID:29218041. So PA1054 = ShaAB.
Gene order and families give PA1055 = C, PA1056 = D, PA1057 = E,
PA1058 = F, PA1059 = G.

What PMID:16030218 shows for PA1054

Cluster lacking PA1054 fails to complement E. coli TO114 PMID:16030218.
PA1054 disruption in P. aeruginosa PMID:16030218 and attenuated virulence PMID:16030218.
So, unlike PA1055-PA1059, PA1054 has a real mutant phenotype. IMP is the
right code for both PseudoCAP rows on PA1054.

Mrp family biology for MrpA

No antiport with MrpA alone PMID:29218041;
complex needed PMID:20624916.
B. subtilis mrpA deletion is Na+-sensitive and complemented in trans
PMID:21236240; model
PMID:21236240. The structure
gives MrpA a proton path PMID:36241630. The MrpA C-terminal domain is needed at pH 8.4, where complex
formation is needed PMID:24021651.
Archaeal MBH lacks MrpA PMID:29754813.

PAINT node (PA1054-bioinformatics/RESULTS.md)

PTN000511949 = PTHR43373 root (LUCA), 16 leaves/15 taxa, 16 GO_Central IBAs
per term. GO:0015385 seeds: PA1054 and B. subtilis MrpA Q9K2S2 (IMP,
PMID:20509166). GO:0035725 seed: PA1054 only. No Thermococcus MBH leaf; one
hydrogenase-named leaf (Sulfolobus SSO1021 "HycC").

Annotation decisions

GO:0015385 (IBA, IMP): ACCEPT (core), qualifier should be contributes_to;
PSEUDOCAP WRONG_QUALIFIER REPOINT and GO_CENTRAL WRONG_QUALIFIER CHECK.
No evidence-code defect (PA1054 was mutated).
GO:0035725 (IBA, IMP): ACCEPT.
GO:0005886 plasma membrane: ACCEPT; GO:0016020 membrane: MODIFY to plasma
membrane.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN000511949	GO:0015385 sodium:proton antiporter activity	2	16	GO:0015385, IMP, PMID:16030218	SOUND	PA1054 is the one sha gene the abstract reports deleting: the cluster lacking PA1054 no longer restores antiport in E. coli TO114, and the P. aeruginosa disruptant loses Na+ tolerance and Na+ efflux. The node is the MrpA family root (no MBH members; one HycC-named Sulfolobus leaf). Caveat: activity is of the complex (no Mrp shows antiport with MrpA alone), so the qualifier should be `contributes_to`, for the seed and for the IBD. A second, independent seed (B. subtilis MrpA, IMP) supports the node.
PTN000511949	GO:0035725 sodium ion transmembrane transport	1 (sole)	16	GO:0035725, IMP, PMID:16030218	SOUND	Direct mutant evidence: PA1054 disruption decreases Na+ efflux. MrpA carries putative ion translocation pathways, and the process fits all MrpA-family members.

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

PMID:16030218 is still abstract-only (PubMed MCP returns no body text;
PMC1196046 is a scanned PDF not released as XML; PMC, Europe PMC and ASM
pages not retrievable). The two WRONG_QUALIFIER defects rest on positive
statements in other Mrp papers (no antiport with MrpA alone; complex
required) and stay PROBABLE. Wording that PA1054 is the only sha gene
mutated is now limited to what the abstract reports. No action changes.

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. So the IMP rows on PA1054 are supported; only the qualifier is in question.