fliI

Summary: FliI carries the Walker A/B nucleotide-binding fold of the F1/V1/A1 alpha/beta family (IPR000194, IPR020003) and binds ATP as its hydrolytic substrate; ATP binding drives FliI hexamerization in the Salmonella homolog.

Reason: Correct, but ATP binding is subsumed by the catalytic activity (ATP hydrolysis / protein-exporting ATPase activity), which is the informative molecular function.

Summary: FliI is a soluble protein lacking transmembrane segments; it acts from the cytoplasm, escorting substrates to the cytoplasmic face of the membrane export gate.

Reason: Correct location for the soluble ATPase component; the more specific location is the flagellar secretion apparatus (proposed as NEW GO:0120102).

Summary: Logical inference (GO_REF:0000108) from the TreeGrafter GO:0046933 row. FliI does not synthesise ATP: it is an ATP-hydrolysing export ATPase with no Fo proton-channel partner, and in the flagellar system the proton motive force is consumed by the membrane export gate to drive protein translocation, not to make ATP.

Reason: Inherits the error of the parent GO:0046933 annotation. Salmonella FliI ATPase activity is insensitive to F-type ATPase inhibitors, and the proton flux of the flagellar export machinery runs through the export gate (FlhA and partners), which acts as a proton-protein antiporter; nothing in this system couples proton flow to ATP formation by FliI. No H. pylori-specific evidence suggests otherwise.

Summary: FliI is an Mg2+-dependent ATPase (demonstrated for the Salmonella ortholog, with Walker-motif mutants abolishing activity and flagellar assembly). No kinetic measurement exists for H. pylori FliI, but the catalytic residues and the FliI/YscN family signature (IPR005714) are conserved.

Reason: Correct catalytic activity. Retained alongside the more informative protein-exporting ATPase activity (GO:0008564, proposed NEW), which is the core function.

Summary: The flagellar export apparatus is a type III secretion system; H. pylori fliI mutants fail to export/assemble flagellar axial proteins (aflagellate, reduced flagellin and hook), and FliI directly binds the FliH regulator and the FlgN export chaperone.

Reason: FliI does part of the work of type III export (substrate/chaperone docking and ATP-dependent release at the gate), so the process term is appropriate. The organismal evidence is from H. pylori strains N6 and CCUG 17874, not J99, but the gene is conserved within the species.

Summary: FliI is the cytoplasmic ATPase of the flagellar type III export apparatus; the GO term definition explicitly notes that type III secretion requires a cytoplasmic, membrane-associated ATPase.

Reason: Correct. The flagellum-specific child location GO:0120102 bacterial-type flagellum secretion apparatus (whose definition names FliI) is proposed as NEW for added specificity.

Summary: TreeGrafter transfer of the F1-beta catalytic-subunit function to FliI. The graft node PTN002689426 is, per QuickGO, used only for GO:0046933 IEA rows on epsilonproteobacterial FliI proteins (Helicobacter, Campylobacter, Arcobacter and relatives), i.e. the target sits in a FliI subfamily (PTHR15184:SF9, type III secretion ATPase) and has inherited a term that belongs to the F1-beta lineage of the PTHR15184 tree.

Reason: The term requires ATP synthesis from ADP and Pi driven by rotary proton transport through a membrane Fo sector. FliI is a soluble ATP-consuming export ATPase: its activity is insensitive to F-type ATPase inhibitors, it has no Fo partner, and in the flagellar export system protons are conducted by the membrane export gate (a proton-protein antiporter), with FliH-FliI-FliJ only boosting gate efficiency. The structural homology (F1-alpha/beta-like FliI hexamer around a gamma-like FliJ stalk) is real and a rotary mechanism for the FliI6-FliJ ring has been proposed, but even that model is one of ATP hydrolysis driving substrate handling, not proton transport or ATP synthesis. The node placement is therefore the error: ATP-synthase function arose in the F1-beta clade, and the FliI/SctN subfamily to which the target belongs diverged to protein-export function. REMOVE rather than MARK_AS_OVER_ANNOTATED because both halves of the term (ATP synthesis; proton transport) are contradicted for FliI itself. UniProt's companion EC 7.1.2.2 / "Flagellum-specific ATP synthase" name is the same family-signature error; EC 7.4.2.8 (protein-secreting ATPase) fits.

Summary: FliI couples ATP hydrolysis to the handling of flagellar export substrates at the type III export gate (docking, chaperone release, gate activation). The GO definition explicitly covers ATP-hydrolysing enzymes of the Type III pathway.

Reason: Most specific supported molecular function; missing from the GOA set, which instead carries the incorrect ATP-synthase term. Transferred from Salmonella FliI (functionally complementing His-FliI ATPase; Walker mutants block assembly) and supported by H. pylori fliI mutant phenotypes and FliI-FliH/FlgN interactions. Corresponds to EC 7.4.2.8.

Summary: Isogenic fliI mutants of H. pylori (strains N6 and CCUG 17874) are non-motile and almost completely aflagellate with reduced flagellin and hook.

Reason: Participation test: FliI performs part of the work of flagellum assembly by hydrolysing ATP to deliver axial subunits into the export gate; it is not merely required. Comparator check: flagellar export apparatus components (FliI orthologs in other reviews in this repository, FlhA, FliH) carry flagellum assembly. Evidence is from same-species strains other than J99, hence ISS rather than IMP.

Summary: The GO definition of the flagellar secretion apparatus lists FliI (with FliH and FliJ) as its soluble cytoplasmic components.

Reason: More precise complex than GO:0030257 for a flagellar (rather than injectisome) FliI. H. pylori FliI binds FliH and the FlgN chaperone directly.