Rv3174 Family assigned · medium auto-curated
H37Rv Rv3174 · MTBC0 mtbc0_003373 ·
235 aa · 3566986–3567693 (+) ·
RefSeq NP_217690.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | short-chain dehydrogenase/reductase |
|---|---|
| MTBC0 PGAP re-annotation | SDR family oxidoreductase |
| Revised (this work) | SDR family oxidoreductase. Pfam: adh_short (PF00106.32), 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 |
O53324
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable short-chain dehydrogenase/reductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | to the short-chain dehydrogenases reductases (SDR) family |
| Orthologous group | COG1028 |
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 | 0.806 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 9 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 | 4.3e-31 | 8–181 | short chain dehydrogenase |
adh_short_C2 | PF13561.13 | 7.6e-19 | 14–186 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3175 (amidase), high confidence from genomic context alone (score 953 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3175 |
amidase | 953 | 953 ctx | neighborhood:746 coexpression:822 |
Rv3173c |
TetR/Acr family transcriptional regulator | 672 | 672 ctx | neighborhood:598 |
Rv3172c hyp |
hypothetical protein | 431 | 431 ctx | neighborhood:427 |
Rv1050 |
oxidoreductase | 430 | 430 ctx | cooccurence:417 |
Rv2263 |
oxidoreductase | 427 | 427 | |
Rv1941 |
short-chain type dehydrogenase/reductase | 418 | 418 | |
Rv3502c |
3-oxoacyl-ACP reductase | 426 | 405 | |
Rv3177 |
peroxidase | 400 | 400 | |
Rv1714 |
oxidoreductase | 411 | 396 | |
Rv2750 |
dehydrogenase | 400 | 378 |
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 dehydrogenase/reductase
- MTBC0 PGAP product: SDR family oxidoreductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=4e-31), adh_short_C2 PF13561.13 (E=8e-19)
- (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_217690.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), 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 O53324 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
10 functional partner(s); context anchor
Rv3175 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003373|Rv3174| MTSLAERTVLVTGANRGMGREYVAQLLGRKVAKVYAATRNPLAIDVSDPRVIPLQLDVTDAVSVAEAADLATDVGILINNAGISRASSVLDKDTSALRGELETNLFGPLALASAFADRIAERSGAIVNVSSVLAWLPLGMSYGVSKAAMWSATESMRIELAPRGVQVVGVYVGLVDTDMGRFADAPKSDPADVVRQVLDGIEAGKEDVLADEMSRQVRASLNVPARERIARLMGN