MTBC Gene Atlas

Rv0927c Family assigned · medium auto-curated

H37Rv Rv0927c · MTBC0 mtbc0_000985 · 263 aa · 1037057–1037848 (-) · RefSeq NP_215442.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)oxidoreductase
MTBC0 PGAP re-annotationSDR family oxidoreductase
Revised (this work)SDR family 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 P9WGQ5 SwissProt · reviewed · Evidence at protein level
UniProt nameUncharacterized oxidoreductase Rv0927c
EC (curated) EC 1.-.-.-

UniProt still lists this protein as Uncharacterized oxidoreductase Rv0927c; 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
Preferred namehdhA
eggNOG descriptionDehydrogenase
Orthologous groupCOG1028
EC number EC 1.1.1.159
KEGG orthology K00076
KEGG pathways map00121
Gene Ontology (39) GO:0002682, GO:0002684, GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0009605, GO:0009607, GO:0016020, GO:0035821, GO:0043207, GO:0044003 +27 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)

pN/pS 0.381 · purifying
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 2 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 1.7e-4511–199 short chain dehydrogenase
KRPF08659.17 3.4e-0814–167 KR domain
adh_short_C2PF13561.13 4.0e-5520–252 Enoyl-(Acyl carrier protein) reductase

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

Closest characterised functional partner: Rv3057c (short chain alcohol dehydrogenase/reductase), high confidence from genomic context alone (score 788 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv0926c hyp hypothetical protein 957 957 ctx neighborhood:684 cooccurence:451 coexpression:772
Rv2524c fas fatty acid synthase 826 800 coexpression:506 experimental:475
Rv3057c short chain alcohol dehydrogenase/reductase 793 788 ctx cooccurence:759
Rv1865c short-chain type dehydrogenase 790 785 ctx cooccurence:755
Rv0945 oxidoreductase 672 593 ctx cooccurence:536
Rv1937 oxygenase 592 544
Rv0925c hyp hypothetical protein 537 534 ctx neighborhood:511
Rv2299c htpG chaperone protein HtpG 542 523 database:450
Rv2243 fabD malonyl CoA-acyl carrier protein transacylase 538 521
Rv2564 glnQ glutamine ABC transporter ATP-binding protein 534 513 database:431
Rv2245 kasA 3-oxoacyl-ACP synthase 1 534 512
Rv0073 glutamine ABC transporter ATP-binding protein 532 511 database:431
Rv2246 kasB 3-oxoacyl-ACP synthase 2 532 510
Rv3728 membrane protein 546 507 database:431
Rv1882c short-chain type dehydrogenase/reductase 506 507 ctx cooccurence:496

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: oxidoreductase
  • MTBC0 PGAP product: SDR family oxidoreductase
  • Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=2e-45), KR PF08659.17 (E=3e-08), adh_short_C2 PF13561.13 (E=4e-55)
  • (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_215442.1)
  • 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 P9WGQ5 (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 — 88 functional partner(s); context anchor Rv3057c
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000985|Rv0927c|
MILDMFRLDDKVAVITGGGRGLGAAIALAFAQAGADVLIASRTSSELDAVAEQIRAAGRRAHTVAADLAHPEVTAQLAGQAVGAFGKLDIVVNNVGGTMPNTLLSTSTKDLADAFAFNVGTAHALTVAAVPLMLEHSGGGSVINISSTMGRLAARGFAAYGTAKAALAHYTRLAALDLCPRVRVNAIAPGSILTSALEVVAANDELRAPMEQATPLRRLGDPVDIAAAAVYLASPAGSFLTGKTLEVDGGLTFPNLDLPIPDL