Rv3057c Family assigned · medium auto-curated
H37Rv Rv3057c · MTBC0 mtbc0_003249 ·
287 aa · 3439095–3439958 (-) ·
RefSeq NP_217573.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | short chain alcohol dehydrogenase/reductase |
|---|---|
| MTBC0 PGAP re-annotation | SDR family oxidoreductase |
| Revised (this work) | SDR family oxidoreductase. Pfam: adh_short (PF00106.32), KR (PF08659.17), Epimerase (PF01370.28), 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 |
I6YB11
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable short chain alcohol dehydrogenase/reductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Belongs to the short-chain dehydrogenases reductases (SDR) family |
| Orthologous group | COG1028 |
| Gene Ontology (57) |
GO:0000166, GO:0003674, GO:0003824, GO:0004303, GO:0005488, GO:0005496, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006629 +45 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 | 0.577 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
adh_short | PF00106.32 | 1.5e-48 | 15–203 | short chain dehydrogenase |
KR | PF08659.17 | 1.4e-16 | 16–174 | KR domain |
Epimerase | PF01370.28 | 7.2e-05 | 16–133 | NAD dependent epimerase/dehydratase family |
adh_short_C2 | PF13561.13 | 4.6e-38 | 19–205 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3058c (TetR family transcriptional regulator), high confidence from genomic context alone (score 803 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3058c |
TetR family transcriptional regulator | 802 | 803 ctx | neighborhood:800 |
Rv0927c |
oxidoreductase | 793 | 788 ctx | cooccurence:759 |
Rv3059 cyp136 |
cytochrome P450 Cyp136 | 767 | 767 ctx | neighborhood:725 |
Rv1714 |
oxidoreductase | 431 | 416 | |
Rv3485c |
short-chain type dehydrogenase/reductase | 427 | 405 | |
Rv3530c |
oxidoreductase | 426 | 404 | |
Rv0769 |
oxidoreductase | 420 | 399 | |
Rv2766c |
short-chain type dehydrogenase/reductase | 412 | 390 | |
Rv3549c |
short-chain type dehydrogenase/reductase | 411 | 389 | |
Rv1483 fabG1 |
3-oxoacyl-ACP reductase FabG | 411 | 389 | |
Rv1928c |
short-chain type dehydrogenase/reductase | 408 | 386 | |
Rv3559c |
oxidoreductase | 407 | 384 | |
Rv1350 fabG2 |
3-oxoacyl-ACP reductase FabG | 406 | 384 | |
Rv3502c |
3-oxoacyl-ACP reductase | 406 | 384 | |
Rv2002 fabG3 |
3-alpha(or 20-beta)-hydroxysteroid dehydrogenase | 401 | 379 |
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 alcohol dehydrogenase/reductase
- MTBC0 PGAP product: SDR family oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=1e-48), KR PF08659.17 (E=1e-16), Epimerase PF01370.28 (E=7e-05), adh_short_C2 PF13561.13 (E=5e-38)
- (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_217573.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), KR (PF08659.17), Epimerase (PF01370.28), 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 I6YB11 (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 —
15 functional partner(s); context anchor
Rv3058c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003249|Rv3057c| MLQRGAGQYFAGKRCFVTGAASGIGRATALRLAAQGAELYLTDRDRDGLAQTVCDARALGAQVPEHRVLDVSDYQDVAAFAADIHARHPSMDVVLNIAGVSAWGTVDQLTHDQWSRMVAINLMGPIHVIETLVPPMVAAGRGGHLVNVSSAAGLVGLPWHAAYSASKYGLRGLSEVLRFDLARHGIGVSVVVPGAVKTPLVNTVEIAGVDRDDPRVNRWVERFSGHAVTPEKAADKILAGVTRNRYLVYTSADIRALYAFKRYAWWPYTLVMRRVNVFFTRALRPGP