Fetched with just fetch-gene PSEAE Q04804 --alias pfeS; accession matches the worklist.
No deep-research provider was used. PubMed esearch was unavailable (NCBI SOLR errors); a Europe
PMC query (PfeS AND aeruginosa) returned reviews and PfeE/enterobactin papers but no direct
biochemical study of PfeS. The seed paper PMID:8808923 is abstract-only here: the PMC record
(PMC178352) is a scanned PDF (checked with WebFetch) and the PubMed MCP returned no full text.
| PTN node | node term | n_seeds | leaf IBAs | seed annotation (term, evidence, PMID) | verdict | rationale | other seeds | IBD stands without this seed? |
|---|---|---|---|---|---|---|---|---|
| PTN002463889 | GO:0000160 phosphorelay signal transduction system | 3 | 200 (59 taxa) | GO:0000160, IDA, PMID:8808923 (PseudoCAP) | UNVERIFIABLE | Abstract only; it shows PfeS is required (probably genetic) and reports direct assays only for PfeR. The term is true of PfeS by architecture, but whether a PfeS IDA experiment exists could not be checked. | E. coli RcsC P0DMC5, M. tuberculosis PrrB P9WGK7 | Yes; the term suits a sensor-kinase clade |
Other IBD at the node, not seeded by pfeS: GO:0009927 histidine phosphotransfer kinase activity,
sole seed AT2G17820 (Arabidopsis AHK1); does not suit the bacterial classical-kinase members,
GO_CENTRAL defect recorded here. pfeS shares no PTN node with the already reviewed parS or
PA5484 (no PTN002463889 in their files).
The node's family was not resolvable from its IBD seeds, so it was looked up by hand.
This gene's UniProt record cross-references PTHR45436:SF15 / PTHR45436, but
PTN002463889 is not in PTHR45436. The IBD's seed, Arabidopsis AHK1 (AT2G17820,
UniProt Q9SXL4), cross-references PTHR43711, and the node is in that family, holding both
AHK1 and PfeS (Q04804, PTHR43711:SF1). This is the UniProt-vs-PANTHER family
disagreement CLAUDE.md warns about; PAINT propagates on PANTHER's own tree, so PTHR43711
is the relevant one and the node is correctly placed. No family id in the review was
changed.
PTN002463889: SPECIATION, LUCA, 200 leaves, ten subfamilies (SF1:80, SF31:43, SF26:42,
SF28:19, SF32:4, SF15:3, SF29:3, SF13:2, SF18:2, SF30:2).
| Child node | Event / taxon | Leaves | Subfamilies | Verdict |
|---|---|---|---|---|
| PTN001976854 | SPECIATION, Archaea-Eukaryota | 65 | SF1:60, SF15:3, SF18:2 | Holds the AHK1 seed (16 nodes deeper); the only clade the IBD could defensibly cover |
| PTN002463899 | DUPLICATION, bacteria | 135 | SF1:20, SF26:42, SF31:43, SF28:19, SF32:4, SF13:2, SF29:3, SF30:2 | Classical HisKA sensor kinases (PfeS, BaeS, RcsC, PrrB); no HPt domains |
Paths confirmed with the tree: Q9SXL4 (AHK1) runs through PTN001976854, while Q04804
(PfeS) runs PTN002463899 -> PTN008117710 (24) -> PTN008117711 (9) -> PTN008684377 (7) ->
PTN002536215 (3). P. aeruginosa contributes four leaves in all (Q04804 pfeS, Q9I528
PA0930, Q9HZ34 PA3206, Q9I0V9 PA2524), none with an HPt domain. PfeS's own architecture
is HK_sensor-HAMP-HisKA-HATPase_c (PF16750, PF00672, PF00512, PF02518) with no Hpt
(PF01627) and no receiver domain, so GO:0009927 histidine phosphotransfer kinase activity
is wrong for it. The earlier concern is confirmed and the diagnosis sharpened: one plant
hybrid-kinase seed at a LUCA node propagates across 135 bacterial leaves. Confidence
raised PROBABLE -> CONFIRMED; the requested change stays "withdraw", with PTN001976854 as
the minimum containment if the IBD is kept. The GO:0009927 row in this review remains
REMOVE/over-annotated as previously decided.