wapR (PA5000, Q9HUG5) notes

Literature (own research, 2026-11-05)

PMID:18178733; the alpha-1,3-L-Rha is where O antigen caps the core PMID:18178733; hence PMID:18178733.
PMID:22685285.
All cached papers abstract-only; full text not retrievable this session.
O antigen biosynthetic process (IMP) is a downstream effect of the missing acceptor: REMOVE, PSEUDOCAP WRONG_TERM PROBABLE.

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?
PTN000531320	GO:0016757 glycosyltransferase activity	7	44 (17 taxa)	GO:0016757, IDA, PMID:18178733	SOUND	Specific loss of alpha-1,3-L-Rha in the mutant; evidence is mutant structure, not an enzyme assay.	RfbV, WcaA, Rv2957, SunS, PA1014 (all IDA), MigA	Yes
PTN000531351	GO:0009244 lipopolysaccharide core region biosynthetic process	2	18 (10 taxa)	GO:0009244, IMP, PMID:18178733	SOUND	Mutant LPS structure lacks the sugar WapR adds.	MigA Q9I5M1 only	Yes, on MigA alone; but node term does not suit the clade
PTN000531351	GO:0009244 lipopolysaccharide core region biosynthetic process	2	18 (10 taxa)	GO:0009244, IDA, PMID:22685285	SOUND	wapR expression tracks the capped glycoform; term correct.	MigA	Yes

Node-level problem at PTN000531351, recorded here once (GO_CENTRAL WRONG_TERM, CONFIRMED, on the WapR GO:0009244 IBA row) and cross-referenced from genes/PSEAE/migA: both seeds are sound, but the 18 leaves include Salmonella RfbV (P26401; IDA GO:0009243 O antigen biosynthesis, GO:0047600 abequosyltransferase, PMID:7541787) and E. coli WcaA (P77414; IDA GO:0009242 colanic acid biosynthesis, PMID:30821147), plus Yersinia WbyL, five Geobacter paralogues and Haemophilus, Helicobacter and Coxiella GT2 proteins. An LPS-core term is wrong for at least RfbV and WcaA. Leaf list from .cache/paint/leaf.gaf.gz; seed experimental annotations from live QuickGO, 2026-11-05.

PseudoCAP defects: GO:0009243 O antigen biosynthetic process WRONG_TERM (PROBABLE); GO:0015920 lipopolysaccharide transport WRONG_TERM (PROBABLE).

Action counts

ACCEPT 4, TOO_GENERAL 3, REMOVE 2, MARK_AS_OVER_ANNOTATED 1.