No deep-research provider was available. PMC full text of PMID:17046787 was not returned by the PubMed
tool; the review uses the cached abstracts of PMID:17046787 and PMID:11065359 and the reviewed UniProt
entry (curated FUNCTION and binding sites cite PMID:17046787 as experimental).
| PTN node | node term | n_seeds | leaf IBAs | seed annotation (term, evidence, PMID) | verdict | rationale | other seeds | IBD stands without this seed? |
|---|---|---|---|---|---|---|---|---|
| PTN000471580 | GO:0000271 polysaccharide biosynthetic process | 3 | 38 (30 taxa) | GO:0009244, IDA, PMID:11065359 (PseudoCAP); also UniProt IDA GO:0000271 and GO:0009103, PMID:17046787 | SOUND | rmlC makes the L-Rha donor for the LPS outer core; mutants lack the O-antigen attachment site. Evidence is a mutant phenotype, so IMP not IDA (PROBABLE WRONG_EVIDENCE_CODE defect). | S. enterica RfbC P26394, M. tuberculosis RmlC P9WH11 | Yes. dTDP-L-Rha feeds O antigens and the mycobacterial linker; term suits the clade. |
| PTN000471580 | GO:0016854 racemase and epimerase activity | 3 | 13 (9 taxa) | GO:0008830, EXP, PMID:17046787 (PseudoCAP) and IDA (UniProt) | SOUND | Structure and mutant-assay paper; UniProt cites it as ECO:0000269 for function. Not a leaf row on rmlC (it carries the specific GO:0008830). | P26394, P9WH11 | Yes. |
| PTN000471594 | GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity | 3 | 25 (21 taxa) | GO:0008830, EXP, PMID:17046787 (PseudoCAP) | SOUND | As above; P. aeruginosa RmlC structures 2IXH-2IXK. | P26394, P9WH11 | Yes. |
| PTN000471594 | GO:0019305 dTDP-rhamnose biosynthetic process | 2 | 25 (21 taxa) | GO:0019305, IDA, PMID:17046787 (PseudoCAP) | SOUND | Characterises the third pathway enzyme; UniProt cites it for function in dTDP-rhamnose biosynthesis. | M. tuberculosis RmlC P9WH11 | Yes, on the single other seed, a characterised RmlC; the term is exact for the clade. |
One PSEUDOCAP defect (WRONG_EVIDENCE_CODE, PROBABLE) on GO:0009244. No GO_CENTRAL defect.
The seed verdict SOUND in the table above, and the "TOO_GENERAL, entailed by accepted GO:0009244"
decision under Other decisions, are both superseded. They stand above as written.
just validate-families flagged a PRUNING_CONFLICT after main was merged in: the PTHR21047 family
review assesses the PTN000471580 GO:0000271 IBD as WRONG_NODE, with the reasoning that the members
below the node make a soluble nucleotide-sugar donor and form no glycosidic bond, so the term
"supports this term at no node". That is right, and this review was wrong. RmlC supplies the
dTDP-L-rhamnose donor; the rhamnosyl transferases build the polymer. Under the project's rule on
involved_in (participation means doing some of the work; necessity evidence is not participation),
supplying a donor does not make the gene a participant in polysaccharide biosynthesis.
The GO:0009244 row had made the conflation explicit, calling precursor supply "a step of core
synthesis" on the strength of the mutant phenotype — which is necessity, not participation.
Now: GO:0000271 (IBA, IDA), GO:0009103 (IDA, IEA) and GO:0009244 (IDA) are all
MARK_AS_OVER_ANNOTATED; GO:0009244 is dropped from the core function, leaving GO:0019305
dTDP-rhamnose biosynthetic process, which is the process RmlC does perform a step of; and the IBA
row carries a propagation_review with root_cause: TERM_SCOPING_PROBLEM and SOURCE_BAD on
PTN000471580, so "No GO_CENTRAL defect" above no longer describes the review either.
This matches the three sibling reviews of the same clade, which already read the propagated row as
over-annotated: ECOLI rfbC (IBA and ISS), PSEPK rfbC and PSEPK rmlC. The comparison with the wbp
reviews in Other decisions above is the part that misled this pass: it reasoned by analogy with how
those reviews were written rather than from what the enzyme does.