MTBC Gene Atlas

Rv0851c Family assigned · medium auto-curated

H37Rv Rv0851c · MTBC0 mtbc0_000906 · 275 aa · 950792–951619 (-) · RefSeq NP_215366.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)short-chain type dehydrogenase/reductase
MTBC0 PGAP re-annotationSDR family NAD(P)-dependent oxidoreductase
Revised (this work)SDR family NAD(P)-dependent oxidoreductase. Pfam: adh_short (PF00106.32), KR (PF08659.17), adh_short_C2 (PF13561.13).

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

Curated reference (UniProt)

UniProt O53863 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable short-chain type dehydrogenase/reductase

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category I Lipid transport and metabolism
Q Secondary metabolites biosynthesis, transport and catabolism
eggNOG descriptionBelongs to the short-chain dehydrogenases reductases (SDR) family
Orthologous groupCOG1028
Gene Ontology (62) GO:0003674, GO:0003824, GO:0004303, GO:0005488, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005777, GO:0006066, GO:0006629 +50 more

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) pseudogene candidate

pN/pS 2.486 · diversifying/relaxed
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 6 missense, 1 nonsense, 0 frameshift
Disruption 1 distinct premature-stop/frameshift site(s); most common in 2.15% of strains (3127) · clonal

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_shortPF00106.32 5.8e-479–197 short chain dehydrogenase
KRPF08659.17 1.6e-1710–172 KR domain
adh_short_C2PF13561.13 6.9e-3615–198 Enoyl-(Acyl carrier protein) reductase

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv0852 fadD16 hyp hypothetical protein 640 640 ctx neighborhood:550
Rv1932 tpx 2-Cys peroxiredoxin 408 408 coexpression:408

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: short-chain type dehydrogenase/reductase
  • MTBC0 PGAP product: SDR family NAD(P)-dependent oxidoreductase
  • Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=6e-47), KR PF08659.17 (E=2e-17), adh_short_C2 PF13561.13 (E=7e-36)
  • (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_215366.1)
  • Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), KR (PF08659.17), adh_short_C2 (PF13561.13)
  • 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 COG1028
  • Curated reference: UniProt O53863 (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 — 2 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000906|Rv0851c|
MDGFPGRGAVITGGASGIGLATGTEFARRGARVVLGDVDKPGLRQAVNHLRAEGFDVHGVMCDVRHREEVTHLADEAFRLLGHVDVVFSNAGIVVGGPIVEMTHDDWRWVIDVDLWGSIHTVEAFLPRLLEQGTGGHVVFTASFAGLVPNAGLGAYGVAKYGVVGLAETLAREVTADGIGVSVLCPMVVETNLVANSERIRGAACAQSSTTGSPGPLPLQDDNLGVDDIAQLTADAILANRLYVLPHAASRASIRRRFERIDRTFDEQAAEGWRH