Rv0149 Family assigned · medium auto-curated
H37Rv Rv0149 · MTBC0 mtbc0_000160 ·
322 aa · 176046–177014 (+) ·
RefSeq NP_214663.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | quinone oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | NADPH:quinone oxidoreductase family protein |
| Revised (this work) | NADPH:quinone oxidoreductase family protein. Pfam: ADH_N (PF08240.18), ADH_zinc_N (PF00107.33), ADH_zinc_N_2 (PF13602.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96826
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible quinone oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | alcohol dehydrogenase |
| Orthologous group | COG0604 |
| EC number |
EC 1.6.5.5
|
| KEGG orthology |
K00344
|
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 | 0.466 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 8 missense, 1 nonsense, 2 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 6.00% of strains (8708) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
ADH_N | PF08240.18 | 3.7e-13 | 28–108 | Alcohol dehydrogenase GroES-like domain |
ADH_zinc_N | PF00107.33 | 3.7e-28 | 150–272 | Zinc-binding dehydrogenase |
ADH_zinc_N_2 | PF13602.13 | 1.5e-12 | 183–320 | Zinc-binding dehydrogenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0148 (short-chain type dehydrogenase/reductase), high confidence from genomic context alone (score 903 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0148 |
short-chain type dehydrogenase/reductase | 903 | 903 ctx | neighborhood:882 |
Rv0147 |
aldehyde dehydrogenase | 835 | 830 ctx | neighborhood:789 |
Rv0130 htdZ |
3-hydroxyl-thioester dehydratase | 710 | 703 ctx | fusion:575 |
Rv0146 |
S-adenosylmethionine-dependent methyltransferase | 509 | 508 ctx | neighborhood:503 |
Rv0154c fadE2 |
acyl-CoA dehydrogenase FadE2 | 495 | 496 ctx | cooccurence:424 |
Rv3761c fadE36 |
acyl-CoA dehydrogenase FadE36 | 477 | 478 | |
Rv0145 |
S-adenosylmethionine-dependent methyltransferase | 476 | 477 ctx | neighborhood:470 |
Rv1240 mdh |
malate dehydrogenase | 405 | 96 |
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: quinone oxidoreductase
- MTBC0 PGAP product: NADPH:quinone oxidoreductase family protein
- Pfam (hmmscan --cut_ga): ADH_N PF08240.18 (E=4e-13), ADH_zinc_N PF00107.33 (E=4e-28), ADH_zinc_N_2 PF13602.13 (E=2e-12)
- (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_214663.1)
- Domains: Pfam-A via hmmscan --cut_ga — ADH_N (PF08240.18), ADH_zinc_N (PF00107.33), ADH_zinc_N_2 (PF13602.13)
- 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
COG0604 - Curated reference: UniProt P96826 (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 —
8 functional partner(s); context anchor
Rv0148 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000160|Rv0149| MKACVVKELSGPSGMVYTDIDEVSGDGGKVVIDVRAAGVCFPDLLLTKGEYQLKLTPPFVPGMETAGVVRSAPSDAGFHVGERVSAFGVLGGYAEQIAVPVANVVRSPVELDDAGAVSLLVNYNTMYFALARRAALRPGDTVLVLGAAGGVGTAAVQIAKAMQAGKVIAMVHREGAIDYVASLGADVVLPLTEGWAQQVRDHTYGQGVDIVVDPIGGPTFDDALGVLAIDGKLLLIGFAAGAVPTLKVNRLLVRNISVVGVGWGEYLNAVPGSAALFAWGLNQLVFLGLRPPPPQRYPLSEAQAALQSLDDGGVLGKVVLEP