MTBC Gene Atlas

qor Resolved · high auto-curated

H37Rv Rv1454c · MTBC0 mtbc0_001556 · 328 aa · 1649426–1650412 (-) · RefSeq NP_215970.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)quinone reductase
MTBC0 PGAP re-annotationquinone oxidoreductase
Revised (this work)Quinone oxidoreductase. Pfam: ADH_N (PF08240.18), ADH_zinc_N (PF00107.33), ADH_zinc_N_2 (PF13602.13).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt O53146 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable quinone reductase Qor

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category C Energy production and conversion
Preferred nameqor
eggNOG descriptionNADPH quinone reductase
Orthologous groupCOG0604
EC number EC 1.6.5.5
KEGG orthology K00344

Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.

Conservation & selection (intra-MTBC, 145 209 strains)

pN/pS 0.737 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 4 missense, 0 nonsense, 0 frameshift

pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.

Domains (Pfam, hmmscan --cut_ga)

PfamAccessioni-EvalueResiduesDescription
ADH_NPF08240.18 1.2e-1527–112 Alcohol dehydrogenase GroES-like domain
ADH_zinc_NPF00107.33 3.6e-25153–283 Zinc-binding dehydrogenase
ADH_zinc_N_2PF13602.13 2.5e-16186–326 Zinc-binding dehydrogenase

Functional interaction network (STRING v12, guilt-by-association)

PartnerProductScoreNo text-miningChannels (≥400)
Rv1455 hyp hypothetical protein 878 792 ctx neighborhood:791 textmining:440
Rv3029c fixA electron transfer flavoprotein subunit beta 418 138
Rv1453 transcriptional activator protein 806 41 textmining:806

STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.

Evidence

  • Legacy H37Rv annotation: quinone reductase
  • MTBC0 PGAP product: quinone oxidoreductase
  • Pfam (hmmscan --cut_ga): ADH_N PF08240.18 (E=1e-15), ADH_zinc_N PF00107.33 (E=4e-25), ADH_zinc_N_2 PF13602.13 (E=3e-16)
  • (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)

Sources

  • Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
  • Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215970.1)
  • Domains: Pfam-A via hmmscan --cut_ga — ADH_N (PF08240.18), ADH_zinc_N (PF00107.33), ADH_zinc_N_2 (PF13602.13)
  • Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
  • Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021, doi:10.1093/molbev/msab293), eggNOG 5.0 DB (Huerta-Cepas et al. 2019) — OG COG0604
  • Curated reference: UniProt O53146 (TrEMBL, unreviewed; Evidence at protein level)
  • Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 3 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001556|Rv1454c|qor
MHAIEVTETGGPGVLRHVDQPQPQPGHGELLIKAEAIGVNFIDTYFRSGQYPRELPFVIGSEVCGTVEAVGPGVTAADTAISVGDRVVSASANGAYAEFCTAPASLTAKVPDDVTSEVAASALLKGLTAHYLLKSVYPVKRGDTVLVHAGAGGVGLILTQWATHLGVRVITTVSTAEKAKLSKDAGADVVLDYPEDAWQFAGRVRELTGGTGVQAVYDGVGATTFDASLASLAVRGTLALFGAASGPVPPVDPQRLNAAGSVYLTRPSLFHFTRTGEEFSWRAAELFDAIGSEAITVAVGGRYPLADALRAHQDLEARKTVGSVVLLP