PA2057 (PA2057, Q9I258) review notes

Literature

Uncharacterised TonB-dependent receptor (UniProt unreviewed, PE 3). Domain content from UniProt: TonB-dependent receptor plug and beta-barrel domains [file:PSEAE/PA2057/PA2057-uniprot.txt "PF00593; TonB_dep_Rec_b-barrel; 1."].
The PAO1 gene model is N-terminally truncated: it starts at an internal GTG, lacks a signal peptide, and the genome continues the frame upstream; the full-length protein (~985 aa) carries a signal peptide and an N-terminal extension. See PA2057-bioinformatics/RESULTS.md [file:PSEAE/PA2057/PA2057-bioinformatics/RESULTS.md "The PAO1 gene model starts too late."]. Recorded as a CONFIRMED WRONG_START_SITE gene_model_issue.
PseudoCAP cites Llamas et al. 2008 for an IDA outer-membrane annotation PMID:18086184. Abstract only (not in PMC; WebSearch found no open full text). The abstract does not name PA2057, so it was not possible to check whether it was among the proteins detected in outer membranes or was found only by microarray.

Search: PubMed metadata and cached abstract of PMID:18086184; WebSearch for the paper with the four locus tags (no full text, no other papers on PA2057 found); UniProt record. No other literature on this protein was found.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN002933024	GO:0019867 outer membrane	4	22 (3 taxa)	GO:0019867, IDA, PMID:18086184	UNVERIFIABLE	Abstract only and does not name PA2057; the location itself is correct on sequence grounds (TonB-dependent receptor plug and barrel), so no PSEUDOCAP defect.	PA2590, PA2070, PA2089 (all the same PseudoCAP IDA, same paper)	Yes as a term; its evidence base is the same paper for all four seeds (see below)

Node-level assessment for PTN002933024 is recorded once, in genes/PSEAE/PA2590/PA2590-notes.md: the IBD stands as a term (all leaves are TonB-dependent receptors), no GO_CENTRAL defect; all four seeds rest on the same paper.