cupA3

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0007155 cell adhesion	IBA GO_REF:0000033	MARK AS OVER ANNOTATED	Summary: IBA from PTN001252526, seeded only by this gene's PseudoCAP IMP rows and E. coli HtrE (P33129), whose EcoCyc row is IMP acts_upstream_of_or_within. Both seeds are attachment phenotypes of usher mutants. Reason: The usher assembles the fimbria; the adhesion itself is performed by the fimbrial subunits. The seeds support only an upstream role (as EcoCyc coded it), and the IBD turns that into involved_in for every usher in the clade. The usher's own process is pilus assembly (GO:0009297). Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN001252526 · PTN001252526 SOURCE WEAK OR INFERRED Usher clade; cell adhesion is the function of the fimbriae the ushers assemble, not of the ushers themselves. UniProtKB:P33129 · E. coli HtrE SOURCE WEAK OR INFERRED EcoCyc IMP qualified acts_upstream_of_or_within, not involved_in. UniProtKB:Q9I1Y5 · cupA3 (self; PseudoCAP IMP PMID:11381121, PMID:15090530) SOURCE WEAK OR INFERRED Mutant attachment phenotype; usher acts upstream of adhesion. Supporting Evidence: PMID:11381121 called usher, that forms a channel into the outer membrane through which the pilin subunits are sequentially assembled
GO:0007155 cell adhesion	IMP PMID:11381121 The chaperone/usher pathways of Pseudomonas aeruginosa: iden...	MARK AS OVER ANNOTATED	Summary: PseudoCAP seed row for PTN001252526. Full text: the cupA3 mutant attaches to plastic at 10% of the parental level. Seed verdict INDIRECT-PHENOTYPE: the data are real, but the usher acts upstream of adhesion by assembling the fimbria. Reason: CupA3 is required for CupA-dependent attachment, but as the assembly pore; it is not itself an adhesion molecule. acts_upstream_of_or_within is the fitting qualifier, as EcoCyc used for the homologous HtrE. Supporting Evidence: PMID:11381121 This strain, carrying a disrupted cupA3 gene, showed an adhesion-deficient phenotype, with only 10% of the bacteria adhering relative to the parental PAK-NP
GO:0007155 cell adhesion	IMP PMID:15090530 Biofilm formation in Pseudomonas aeruginosa: fimbrial cup ge...	MARK AS OVER ANNOTATED	Summary: PseudoCAP seed row for PTN001252526. Abstract only; it restates that the cupA cluster is needed for biofilm formation and concerns MvaT. Seed verdict INDIRECT-PHENOTYPE (and UNVERIFIABLE for cupA3 specifically). Reason: Same claim as the PMID:11381121 row; the usher acts upstream of adhesion. Supporting Evidence: PMID:15090530 The cupA gene cluster, but not the cupB or cupC cluster, is required for biofilm formation on abiotic surfaces.
GO:0009279 cell outer membrane	IBA GO_REF:0000033	ACCEPT	Summary: IBA from PTN001252526, seeded by E. coli FimD (IDA). Reason: Ushers are outer-membrane beta-barrel proteins.
GO:0009279 cell outer membrane	IEA GO_REF:0000044	ACCEPT	Summary: UniProt subcellular location mapping (cell outer membrane). Reason: Consistent with the IBA row.
GO:0009297 pilus assembly	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO from the fimbrial usher family signature. Reason: The usher's biological process is assembly of the CupA fimbria. Supporting Evidence: PMID:11381121 called usher, that forms a channel into the outer membrane through which the pilin subunits are sequentially assembled
GO:0015473 fimbrial usher porin activity	IBA GO_REF:0000033	ACCEPT	Summary: IBA from PTN001252526, seeded by E. coli FimD (IDA). Reason: Core activity of an usher; CupA3 is the CupA usher by similarity to FocD. Supporting Evidence: PMID:11381121 CupA3 appears to be the usher component of the system, based on its high similarity to FocD
GO:0015473 fimbrial usher porin activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO from the fimbrial usher family signature. Reason: Consistent with the IBA row; core activity.
GO:0016020 membrane	IEA GO_REF:0000002	TOO GENERAL	Summary: InterPro2GO membrane. Reason: Entailed by the accepted GO:0009279 cell outer membrane.
GO:0055085 transmembrane transport	IEA GO_REF:0000108	TOO GENERAL	Summary: Inter-ontology inference from GO:0015473. Reason: Entailed by the accepted GO:0015473 fimbrial usher porin activity.
GO:0071453 cellular response to oxygen levels	IEP PMID:17581126 Responses of Pseudomonas aeruginosa to low oxygen indicate t...	UNDECIDED	Summary: PseudoCAP IEP from a low-oxygen transcriptome study. The abstract does not mention cup genes and the full text was not available. Reason: Cannot verify the expression data for cupA3 without the full text.
GO:0098743 cell aggregation	IMP PMID:19638175 SiaA and SiaD are essential for inducing autoaggregation as ...	MARK AS OVER ANNOTATED	Summary: PseudoCAP row. The abstract says the cupA operon is essential for SDS-induced aggregation, without naming the gene mutated. Reason: As for cell adhesion, the usher acts upstream by assembling CupA fimbriae; the specific gene tested is not stated in the abstract. Supporting Evidence: PMID:19638175 Transposon and site-directed mutagenesis revealed that the cupA-operon and the co-transcribed genes siaA (PA0172) and siaD (PA0169) were essential for SDS-induced aggregation.