Rv0082 Family assigned · medium auto-curated
H37Rv Rv0082 · MTBC0 mtbc0_000092 ·
159 aa · 90087–90566 (+) ·
RefSeq NP_214596.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | NADH-quinone oxidoreductase subunit B family protein |
| Revised (this work) | NADH-quinone oxidoreductase subunit B family protein. Pfam: Oxidored_q6 (PF01058.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XUD2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | hycG |
| eggNOG description | oxidoreductase |
| Orthologous group | COG3260 |
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 | 0.193 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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 |
|---|---|---|---|---|
Oxidored_q6 | PF01058.30 | 1.2e-28 | 45–155 | NADH ubiquinone oxidoreductase, 20 Kd subunit |
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:926 experimental:999 textmining:835 |
Rv0084 hycD |
formate hydrogenlyase HycD | 999 | 1000 ctx | neighborhood:882 cooccurence:768 coexpression:844 experimental:899 |
Rv0083 |
oxidoreductase | 999 | 999 ctx | neighborhood:881 cooccurence:768 coexpression:884 experimental:784 |
Rv0086 hycQ |
hydrogenase HycQ | 998 | 999 ctx | neighborhood:874 cooccurence:770 coexpression:840 experimental:784 |
Rv0085 hycP |
hydrogenase HycP | 994 | 994 ctx | neighborhood:874 cooccurence:736 coexpression:824 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 986 | 983 ctx | cooccurence:534 coexpression:633 experimental:896 |
Rv0081 |
HTH-type transcriptional regulator | 985 | 975 ctx | neighborhood:881 coexpression:800 textmining:433 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 730 | 730 ctx | cooccurence:728 |
Rv0088 |
polyketide cyclase/dehydrase | 656 | 656 ctx | neighborhood:644 |
Rv0080 hyp |
hypothetical protein | 841 | 558 ctx | neighborhood:554 textmining:655 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 604 | 557 ctx | cooccurence:518 |
Rv0079 hyp |
hypothetical protein | 787 | 551 ctx | neighborhood:548 textmining:547 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 612 | 549 ctx | cooccurence:486 |
Rv3158 nuoN |
NADH-quinone oxidoreductase subunit N | 538 | 521 ctx | cooccurence:499 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 512 | 512 ctx | cooccurence:490 |
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: NADH-quinone oxidoreductase subunit B family protein
- Pfam (hmmscan --cut_ga): Oxidored_q6 PF01058.30 (E=1e-28)
- (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_214596.2)
- Domains: Pfam-A via hmmscan --cut_ga — Oxidored_q6 (PF01058.30)
- 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
COG3260 - Curated reference: UniProt I6XUD2 (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 —
22 functional partner(s); context anchor
hycE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000092|Rv0082| MGWVAKIFRVGRVVEPAAPLPAAIAEPPAGVRGSLQIRHVDAGSCNGCEVEISGAFGPVYDAERFGARLVASPRHADALLVTGVVTHNMAGPLRKTLEATPRPRVVIACGDCALNRGVFADAYGVVGAVGEVVPVDVEIAGCPPTPAAIMAALRSVTGK