Nitratidesulfovibrio vulgaris Hildenborough

GO review of four pathways in the model sulfate-reducing bacterium

AI Gene Review · projects/NITV2_PATHWAYS · 2026

Bottom line

  • We reviewed 23 genes in sulfate reduction, potassium transport, sigma factors and hydrogen metabolism; 20 are done (180 rows), 3 hydrogenase stubs are still PENDING.
  • The main fix is separating catalytic from accessory subunits: AprB, KdpC and the TrkA-type RCK proteins lose inherited catalytic or transporter terms.
  • A wrong reassignment of DVU0848–0849 to Flx–Hdr is reverted to QmoA/QmoB (PR #3226): they sit in the aprBA–qmoABC cluster; Flx–Hdr is DVU2399–2405.

Why this organism

  • Model sulfate reducer: sulfate is the terminal electron acceptor of anaerobic respiration.
  • Annotation is almost entirely electronic, so each pathway is a test of how well pipelines assign subunit roles.
  • Four pathways: sulfate reduction (AprAB, QmoABC, a SulP permease), K⁺ transport (Kdp, Trk), sigma factors, and periplasmic and cytoplasmic hydrogenases.

Who does the work in K⁺ uptake

KdpC is a chaperone, not an ATPase

kdpC (Q725T8): process row accepted; nucleotide binding, ATP binding and hydrolase activity removed; transporter MF replaced by ATPase activator activity (GO:0001671).

Other corrections

  • AprB (Q72DT3): adenylyl-sulfate reductase activity → electron transfer activity; AprA keeps the catalytic term and gains dissimilatory sulfate reduction.
  • AprA: succinate dehydrogenase activity (IEA) removed.
  • Sigma factors: DNA-binding TF activity → sigma factor activity (GO:0016987) on rpoD, rpoH, fliA; RNA polymerase activity removed from fliA.
  • rpoC is the RNA polymerase β′ core subunit, not a sigma factor.
  • DVU0279: a SulP-family transporter whose sulfate substrate is unproven.

Results

Status and next steps

  • ✅ Sulfate reduction (6), potassium transport (7), sigma factors (5) reviewed.
  • ◐ Hydrogenases: hydA and hynA1 reviewed; hysA, echA, cooH still PENDING.
  • ✅ DVU0848–0849 restored to QmoA/QmoB (PR #3226; QmoB drops two unsupported NEW rows).
  • ⬜ Update the status checklist on the project page.

Read more: projects/NITV2_PATHWAYS.md · genes/DESVH/<accession>/