Fur's experimental annotations seed five node-terms (local IBD.gaf, 2026-10-28): four at PTN002112386
(the Fur superfamily: 83 leaves, including Fur, Zur, PerR, Irr, Nur/Mur-like and archaeal paralogs) and one
at PTN002112483 (12 proteobacterial Fur leaves). Only the GO:1900705 PseudoCAP row is a PseudoCAP-only
seed; the other three PTN002112386 terms are multi-seeded from CollecTF and other MOD annotations.
| PTN node | node term | n_seeds | leaf IBAs | seed annotation (term, evidence, PMID) | verdict | rationale |
|---|---|---|---|---|---|---|
| PTN002112483 | GO:1900705 negative regulation of siderophore biosynthetic process | 1 (sole) | 12 (12 taxa) | GO:1900705, IMP, PMID:8885270 (PseudoCAP) | OVER-SPECIFIC | The seed is sound: Fur point mutants derepress siderophores and Fur-Fe(II) binds the pvdS/pchR promoters, so Fur itself does the regulating. But the node includes Fur of Neisseria meningitidis, Helicobacter pylori and Coxiella burnetii, not known to synthesise siderophores, so the term overreaches part of the clade (taxon/lineage mismatch). |
| PTN002112386 | GO:1900376 regulation of secondary metabolite biosynthetic process | 2 (Fur, Zur/np20) | 71 (33 taxa) | GO:1900705, IMP, PMID:8885270 (PseudoCAP) | OVER-SPECIFIC | Sound for Fur, but the node is the whole Fur superfamily; Zur, PerR, Irr and archaeal paralogs (about half the leaves) have no known secondary-metabolite role. A Fur-lineage-specific regulatory output placed at a superfamily node. |
| PTN002112386 | GO:0045892 negative regulation of DNA-templated transcription | 16 | 83 | GO:0045892, EXP/IEP, PMID:8633080 and others (CollecTF) | SOUND | Direct repression of Fur-box promoters; repression is conserved across the superfamily. |
| PTN002112386 | GO:0003700 DNA-binding transcription factor activity | 15 | 83 | GO:0001217, IPI, PMID:8633080 and others (CollecTF) | SOUND | Footprinting/EMSA on many promoters. |
| PTN002112386 | GO:0000976 transcription cis-regulatory region binding | 15 | 83 | GO:0000976, IPI, PMID:8633080 and others (CollecTF) | SOUND | Direct operator binding. |
GO_CENTRAL defects for PTN002112483 and PTN002112386 are recorded on the GO:1900705 rows (the gene
carries no GO:1900376 IBA row because it has the more specific term).
Topology fetched with projects/PSEUDOCAP/panther_tree.py node PTN002112483 --depth 3
--leaves (PTHR33202) plus a --contains query for the siderophore producers. The node
is a Proteobacteria SPECIATION node, 12 leaves, all PTHR33202:SF2, all Fur orthologues.
| Child node | Event / taxon | Leaves | Subfamilies | Verdict |
|---|---|---|---|---|
| PTN002848967 | LEAF, Helicobacter pylori | 1 (O25671) | SF2 | Fur, but no siderophore biosynthesis in the organism |
| PTN002848968 | LEAF, Neisseria meningitidis | 1 (P0A0S8) | SF2 | Same |
| PTN002112491 | LEAF, Geobacter sulfurreducens | 1 (Q74DD7) | SF2 | Same |
| PTN002112492 | SPECIATION, Gammaproteobacteria | 9 (Q83C33 Coxiella, P44561 Haemophilus, Q8EFN3, P0C6C8, Q8PAL3, Q03456, and PTN002112501 Enterobacteriaceae: Q7CQY3, P33086, P0A9A9) | SF2:9 | Mixed: producers plus Coxiella and Haemophilus |
--contains P0A9A9,P33086,P0C6C8,Q8EFN3,Q8PAL3,Q03456 returns PTN002112492 (9 leaves),
i.e. the smallest clade holding the siderophore producers still contains two
non-producers, and the other three non-producers are separate basal children rather than
one clade. The earlier concern is confirmed, with the diagnosis sharpened: this is not a
mis-rooted family (every leaf is a real Fur) but a term that encodes an organism trait
which does not track the phylogeny, so no "move the IBD" target exists. The remedy is to
retype the node-level IBD (negative regulation of DNA-templated transcription, or a
regulation-of-iron-import term) and leave GO:1900705 to leaf-level evidence in producers.
Confidence raised SUSPECTED -> CONFIRMED. The P. aeruginosa rows are unchanged: Fur
genuinely represses pvdS and pchR, so the IMP and the leaf IBA stay ACCEPT.