Rv2968c Family assigned · medium auto-curated
H37Rv Rv2968c · MTBC0 mtbc0_003152 ·
210 aa · 3344246–3344878 (-) ·
RefSeq NP_217484.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | vitamin K epoxide reductase family protein |
| Revised (this work) | Vitamin K epoxide reductase family protein. Pfam: VKOR (PF07884.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X5W1
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Vitamin K epoxide reductase |
| Orthologous group | COG4243 |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 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 |
|---|---|---|---|---|
VKOR | PF07884.20 | 8.3e-44 | 24–156 | Vitamin K epoxide reductase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lipN (lipase/esterase LipN), high confidence from genomic context alone (score 781 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2969c hyp |
hypothetical protein | 991 | 938 ctx | neighborhood:881 textmining:870 |
Rv2970c lipN |
lipase/esterase LipN | 780 | 781 ctx | neighborhood:775 |
Rv2967c pca |
pyruvate carboxylase | 742 | 742 ctx | neighborhood:738 |
Rv2966c rsmD |
methyltransferase | 693 | 694 ctx | neighborhood:689 |
Rv2970A hyp |
hypothetical protein | 641 | 642 ctx | neighborhood:640 |
Rv2971 |
oxidoreductase | 528 | 528 ctx | neighborhood:521 |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 447 | 223 | |
Rv0526 |
thioredoxin | 838 | 198 | textmining:807 |
Rv1677 dsbF |
lipoprotein DsbF | 428 | 184 | |
Rv3673c |
membrane-anchored thioredoxin-like protein | 609 | 178 | textmining:545 |
Rv0816c thiX |
thioredoxin ThiX | 598 | 160 | textmining:542 |
Rv0527 ccdA |
cytochrome C-type biogenesis protein CcdA | 698 | 82 | textmining:685 |
Rv0529 ccsA |
cytochrome C-type biogenesis protein CcsA | 549 | 47 | textmining:547 |
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: integral membrane protein
- MTBC0 PGAP product: vitamin K epoxide reductase family protein
- Pfam (hmmscan --cut_ga): VKOR PF07884.20 (E=8e-44)
- (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_217484.1)
- Domains: Pfam-A via hmmscan --cut_ga — VKOR (PF07884.20)
- 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
COG4243 - Curated reference: UniProt I6X5W1 (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 —
13 functional partner(s); context anchor
lipN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003152|Rv2968c| MVAARPAERSGDPAAVRVPVPSAWWVLIGGVIGLFASMTLTVEKVRILLDPIYVPSCNVNPIVSCGSVMTTPQASLLGFPNPLLGIAGFTVVVVTGVLAVAKVPLPRWYWIGLAVGILVGVAFVHWLIFQSLYRIGALCPYCMVVWAVIATLLVVVASIVFGPMRENRGSQERVGARLLYQWRWSLATLWFTTVFLLIMVRFWDYWSTLI