MTBC Gene Atlas

Rv0687 Family assigned · medium auto-curated

H37Rv Rv0687 · MTBC0 mtbc0_000726 · 275 aa · 791185–792012 (+) · RefSeq NP_215201.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)NAD-dependent oxidoreductase
MTBC0 PGAP re-annotationRv0687 family mycofactocin-dependent SDR oxidoreductase
Revised (this work)Rv0687 family mycofactocin-dependent SDR 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 P9WGS7 SwissProt · reviewed · Evidence at protein level
UniProt nameUncharacterized NAD-dependent oxidoreductase Rv0687
EC (curated) EC 1.-.-.-

UniProt still lists this protein as Uncharacterized NAD-dependent oxidoreductase Rv0687; the revised annotation above is ahead of the current UniProt record.

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

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 0.522 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 3 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_shortPF00106.32 2.3e-4612–212 short chain dehydrogenase
KRPF08659.17 5.0e-1614–185 KR domain
adh_short_C2PF13561.13 1.4e-4717–271 Enoyl-(Acyl carrier protein) reductase

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

Closest characterised functional partner: htdY (3-hydroxyacyl-thioester dehydratase HtdY), high confidence from genomic context alone (score 882 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv3389c htdY 3-hydroxyacyl-thioester dehydratase HtdY 882 882 ctx fusion:828
Rv0688 ferredoxin reductase 882 878 ctx neighborhood:867
Rv2524c fas fatty acid synthase 826 800 coexpression:506 experimental:475
Rv0686 membrane protein 753 753 ctx neighborhood:749
Rv3538 dehydrogenase 668 667 ctx fusion:514
Rv0685 tuf elongation factor Tu 655 635 ctx neighborhood:622
Rv1937 oxygenase 593 545
Rv2509 cmrA short-chain type dehydrogenase/reductase 560 523 ctx cooccurence:458
Rv2299c htpG chaperone protein HtpG 539 520 database:450
Rv0073 glutamine ABC transporter ATP-binding protein 533 512 database:431
Rv2564 glnQ glutamine ABC transporter ATP-binding protein 532 510 database:431
Rv3728 membrane protein 534 509 database:431
Rv0684 fusA1 elongation factor G 527 509 ctx neighborhood:429
Rv3239c transmembrane transport protein 532 506 database:431
Rv2565 NTE family protein 518 499 database:431

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: NAD-dependent oxidoreductase
  • MTBC0 PGAP product: Rv0687 family mycofactocin-dependent SDR oxidoreductase
  • Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=2e-46), KR PF08659.17 (E=5e-16), adh_short_C2 PF13561.13 (E=1e-47)
  • (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_215201.1)
  • 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 P9WGS7 (SwissProt, reviewed; 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 — 82 functional partner(s); context anchor htdY
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000726|Rv0687|
MSARGGSLHGRVAFVTGAARAQGRSHAVRLAREGADIVALDICAPVSGSVTYPPATSEDLGETVRAVEAEGRKVLAREVDIRDDAELRRLVADGVEQFGRLDIVVANAGVLGWGRLWELTDEQWETVIGVNLTGTWRTLRATVPAMIDAGNGGSIVVVSSSAGLKATPGNGHYAASKHALVALTNTLAIELGEFGIRVNSIHPYSVDTPMIEPEAMIQTFAKHPGYVHSFPPMPLQPKGFMTPDEISDVVVWLAGDGSGALSGNQIPVDKGALKY