Fetched with just fetch-gene PSEAE G3XD73 --alias motC; accession matches the
worklist. Unreviewed TrEMBL entry, named motC by the PAO1 annotation. No deep
research provider key was available; literature is the stator papers used for
motA and motB.
| PTN node | node term | n_seeds | leaf IBAs | seed annotation (term, evidence, PMID) | verdict | rationale | other seeds | IBD stands without this seed? |
|---|---|---|---|---|---|---|---|---|
| PTN001252377 | GO:0071978 bacterial-type flagellum-dependent swarming motility | 2 (G3XD73, Q9HUL1) | 29 (19 taxa) | GO:0071978, IMP, PMID:15629949 (PseudoCAP) | SOUND | Single-mutant swarming defect on 0.5% agar or firmer, with plasmid complementation, for a stator subunit that does part of the work of flagellar rotation. Doyle et al. report the same for PA1460 mutants. | motA (Q9HUL1): weak — the motAB single mutant swarms like wild type (PMID:15629949) or better (PMID:25349157) | No. Without the motC seed the IBD would rest only on the motA rows, whose phenotype is not a swarming requirement. The term is sound for this gene but too specific for the clade, so a GO_CENTRAL WRONG_TERM/REPOINT to GO:0071973 is filed here (PROBABLE), cross-referenced from motA. |
Clade composition checked with panther_tree.py node PTN001252377 --leaves:
29 leaves in 19 taxa, all in PTHR30433:SF2/SF3/SF4. The node-level objection is
to the term, not to the leaves. GO:0071978 is_a GO:0071973 (QuickGO) and its
definition adds a lifestyle context, requiring "the smooth movement of a group
of cells along a solid surface". The clade's one experimentally characterised
leaf, E. coli MotA (P09348), carries GO:0071973 by IMP, GO:0015252 proton
channel activity and GO:0120101 stator complex by IPI, and no experimental
swarming annotation; torque generation for flagellar rotation is the shared
role. The earlier version of this note argued from leaf names ("Aquifex,
Thermotoga, Helicobacter, Leptospira and Rhodopirellula have not been shown to
swarm"); that claim is withdrawn as absence of evidence. What was checked
instead is the annotation state: in QuickGO (2026-11-06) every GO:0071978 row
on the 24 non-PAO1 leaves is IBA or IEA. The same node also carries an E. coli
MotA-seeded (P09348) IBD of GO:0120101 stator complex, which is sound and suits
the whole clade.
Audit of the GO_CENTRAL defect on PTN001252377. The previous explanation
argued that "the leaves include Aquifex, Thermotoga, Helicobacter pylori,
Leptospira and Rhodopirellula stator proteins, which have not been shown to
swarm". Leaf membership is correct (panther_tree.py node PTN001252377
--leaves), but the claim itself is absence of evidence, and three of the five
names are submitter SubNames. The leaf list has been dropped from the
entry.
| Leaf | Name and its evidence | Experimental annotations found | Verdict |
|---|---|---|---|
| O67122 (Aquifex aeolicus motA) | Curated RecName "Motility protein A"; PE 1 |
None. GO:0120101 IBA, GO:0071978 IBA, GO:0006935 IEA only |
Claim dropped — no evidence either way |
| Q9WZE3 (Thermotoga maritima TM_0676) | SubName ECO:0000313 |
EMBL:AAD35759.1 — submitter name, unvetted | None (IBA/IEA only) |
| P65410 (Helicobacter pylori motA) | Curated RecName; PE 3 (inferred from homology) |
None (IBA/IEA only) | Claim dropped |
| Q8F0B9, Q8F896 (Leptospira interrogans) | SubName "Endoflagellar motor protein A" ECO:0000313 |
EMBL — submitter names | None (IBA/IEA only) |
| Q7ULV0 (Rhodopirellula baltica pomA) | SubName "Chemotaxis pomA protein" ECO:0000313 |
EMBL | None (IBA/IEA only) |
| P09348 (E. coli motA) | Curated RecName; PE 1 |
GO:0071973 IMP:EcoliWiki; GO:0120101 IPI:ComplexPortal; GO:0005886 IDA:EcoCyc; GO:0015252 proton channel activity TAS:EcoCyc. GO:0071978 only IBA |
New load-bearing leaf. The clade's one experimentally characterised member has the parent term by IMP and no experimental swarming annotation |
Replacement argument, as now written in the entry: GO:0071978 is_a
GO:0071973 (QuickGO), and its definition adds a lifestyle context — "the
smooth movement of a group of cells along a solid surface", and "Swarming
motility is observed in groups of bacteria". What a MotA-family protein
contributes is the ion-channel stator that generates torque, which is what
P09348's experimental annotations show. Whether an organism swarms depends on
surfactant, cell density and growth conditions, not on which stator it
encodes. One checked annotation-state fact replaces the behavioural absence
claim: in QuickGO (2026-11-06) every GO:0071978 row on the 24 non-PAO1
leaves is IBA or IEA, so no leaf besides the two P. aeruginosa seeds has
experimental support for the specific term.
Confidence unchanged at PROBABLE. The weak behavioural claim was withdrawn and
replaced with verified ones, but the call remains a term-scoping
recommendation that a PAINT curator could reasonably answer differently, so
CONFIRMED would overstate it.