Rv0083 Resolved · high auto-curated
H37Rv Rv0083 · MTBC0 mtbc0_000093 ·
640 aa · 90563–92485 (+) ·
RefSeq NP_214597.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | oxidoreductase |
| Revised (this work) | Oxidoreductase. Pfam: Proton_antipo_M (PF00361.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIW3
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized protein Rv0083 |
UniProt still lists this protein as Uncharacterized protein Rv0083; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversionP Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | Proton-conducting membrane transporter |
| Orthologous group | COG0651 |
| KEGG orthology |
K12137
|
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 | 0.684 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 17 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 |
|---|---|---|---|---|
Proton_antipo_M | PF00361.26 | 1.2e-52 | 101–384 | NADH:quinone oxidoreductase/Mrp antiporter, TM |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hycE (formate hydrogenase HycE), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0087 hycE |
formate hydrogenase HycE | 999 | 1000 ctx | neighborhood:884 cooccurence:774 coexpression:899 experimental:995 textmining:453 |
Rv0082 |
oxidoreductase | 999 | 999 ctx | neighborhood:881 cooccurence:768 coexpression:884 experimental:784 |
Rv0084 hycD |
formate hydrogenlyase HycD | 998 | 998 ctx | neighborhood:881 cooccurence:774 coexpression:769 experimental:787 |
Rv0085 hycP |
hydrogenase HycP | 996 | 996 ctx | neighborhood:874 cooccurence:774 coexpression:860 |
Rv0086 hycQ |
hydrogenase HycQ | 987 | 987 ctx | neighborhood:874 coexpression:860 |
Rv0081 |
HTH-type transcriptional regulator | 979 | 974 ctx | neighborhood:881 coexpression:751 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 955 | 949 | coexpression:670 experimental:823 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 766 | 735 | experimental:697 |
Rv0088 |
polyketide cyclase/dehydrase | 653 | 653 ctx | neighborhood:644 |
Rv3146 nuoB |
NADH-quinone oxidoreductase subunit B | 631 | 599 | experimental:449 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 557 | 558 | experimental:449 |
Rv0080 hyp |
hypothetical protein | 551 | 551 ctx | neighborhood:548 |
Rv0079 hyp |
hypothetical protein | 550 | 550 ctx | neighborhood:548 |
Rv3147 nuoC |
NADH-quinone oxidoreductase subunit C | 502 | 443 | experimental:405 |
Rv0089 |
methyltransferase | 422 | 422 ctx | neighborhood:413 |
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: oxidoreductase
- Pfam (hmmscan --cut_ga): Proton_antipo_M PF00361.26 (E=1e-52)
- (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_214597.1)
- Domains: Pfam-A via hmmscan --cut_ga — Proton_antipo_M (PF00361.26)
- 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
COG0651 - Curated reference: UniProt P9WIW3 (SwissProt, reviewed; 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 —
17 functional partner(s); context anchor
hycE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000093|Rv0083| MTAAPTAGGVVTSGVGVAGVGVGLLGMFGPVRVVHVGWLLPLSGVHIELDRLGGFFMALTGAVAAPVGCYLIGYVRREHLGRVPMAVVPLFVAAMLLVPAAGSVTTFLLAWELMAIASLILVLSEHARPQVRSAGLWYAVMTQLGFIAILVGLVVLAAAGGSDRFAGLGAVCDGVRAAVFMLTLVGFGSKAGLVPLHAWLPRAHPEAPSPVSALMSAAMVNLGIYGIVRFDLQLLGPGPRWWGLALLAVGGTSALYGVLQASVAADLKRLLAYSTTENMGLITLALGAATLFADTGAYGPASIAAAAAMLHMIAHAAFKSLAFMAAGSVLAATGLRDLDLLGGLARRMPATTVFFGVAALGACGLPLGAGFVSEWLLVQSLIHAAPGHDPIVALTTPLAVGVVALATGLSVAAMTKAFGIGFLARPRSTQAEAAREAPASMRAGMAIAAGACLVLAVAPLLVAPMVRRAAATLPAAQAVKFTGLGAVVRLPAMSGSIAPGVIAAAVLAAALAVAVLARWRFRRRPAPARLPLWACGAADLTVRMQYTATSFAEPLQRVFGDVLRPDTDIEVTHTAESRYMAERITYRTAVADAIEQRLYTPVVGAVAAMAELLRRAHTGSVHRYLAYGALGVLIVLVVAR