cupA3 (PA2130, Q9I1Y5) review notes

Outer-membrane usher of the CupA chaperone-usher fimbrial system (fimbrial
export usher family; InterPro IPR000015). Unreviewed UniProt entry. Cluster
cupA1 (pilin), cupA2 (chaperone), cupA3 (usher), cupA4, cupA5.

Literature (no deep-research provider available; own reading)

Vallet et al. 2001 (full text read). Tn5 screen for attachment-defective
mutants of a non-piliated strain identified the cupA cluster. CupA3 is the
usher PMID:11381121. A cupA3 insertion mutant attaches at
10% of parent PMID:11381121. The usher's role is assembly
PMID:11381121.
Vallet et al. 2004 (abstract only; PMC387821 gave no full text). MvaT
represses cupA; restates that cupA is needed for biofilm formation
PMID:15090530.
Alvarez-Ortega and Harwood 2007 (abstract only): low-O2 transcriptome; cup
genes not mentioned in the abstract. IEP row left UNDECIDED.
Klebensberger et al. 2009 (abstract only): cupA operon needed for SDS-induced
aggregation PMID:19638175.

PseudoCAP IBA-seed assessment

Other seeds' experimental support queried live in QuickGO on 2026-11-05.

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN001252526	GO:0007155 cell adhesion	2	36 (5 taxa)	GO:0007155, IMP, PMID:11381121 (PseudoCAP)	INDIRECT-PHENOTYPE	Full text: real attachment defect of the cupA3 mutant, but CupA3 is the assembly pore; adhesion is done by the fimbria. Upstream role, not participation.	E. coli HtrE P33129 (EcoCyc IMP PMID:27696649, qualifier acts_upstream_of_or_within)	No. The only other seed is itself an upstream-qualified usher phenotype; the node term does not suit an usher clade
PTN001252526	GO:0007155 cell adhesion	2	36 (5 taxa)	GO:0007155, IMP, PMID:15090530 (PseudoCAP)	INDIRECT-PHENOTYPE (UNVERIFIABLE for cupA3)	Abstract only; MvaT paper restating the cupA biofilm requirement.	as above	as above

Defects:
- PSEUDOCAP WRONG_QUALIFIER on the PMID:11381121 row (PROBABLE; full text read,
call rests on the participation/upstream judgement) and on the PMID:15090530
row (SUSPECTED, CHECK; abstract only). Requested: acts_upstream_of_or_within,
or repoint to GO:0009297.
- GO_CENTRAL WRONG_TERM on PTN001252526 (PROBABLE, CHECK): withdraw the cell
adhesion IBD; the clade's role is GO:0015473 fimbrial usher porin activity and
GO:0009297 pilus assembly. The sibling IBDs at this node (GO:0015473 and
GO:0009279, seeded by E. coli FimD IDA) are sound.

Other PseudoCAP rows (not seeds)

term	verdict	defect
GO:0098743 cell aggregation (IMP, PMID:19638175)	INDIRECT-PHENOTYPE	none recorded (abstract does not name the gene mutated); MARK_AS_OVER_ANNOTATED
GO:0071453 cellular response to oxygen levels (IEP, PMID:17581126)	UNVERIFIABLE	none; UNDECIDED