Rv0213c Resolved · high auto-curated
H37Rv Rv0213c · MTBC0 - ·
437 aa · 254637–255950 (-) ·
RefSeq NP_214727.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Methyltransferase. Pfam: B12-binding (PF02310.25), Radical_SAM (PF04055.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P96395
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible methyltransferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | Methyltransferase |
| Orthologous group | COG1032 |
| KEGG orthology |
K18564
|
| KEGG pathways |
map00332, map01130
|
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 | 0.412 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 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 |
|---|---|---|---|---|
B12-binding | PF02310.25 | 1.2e-11 | 37–110 | B12 binding domain |
Radical_SAM | PF04055.28 | 9.6e-17 | 170–342 | Radical SAM superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nadR (transcriptional regulator NadR), high confidence from genomic context alone (score 882 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0212c nadR |
transcriptional regulator NadR | 886 | 882 ctx | neighborhood:882 |
Rv3232c ppk2 |
polyphosphate kinase | 691 | 692 | coexpression:692 |
Rv0214 fadD4 |
fatty-acid--CoA ligase FadD4 | 595 | 596 ctx | neighborhood:571 |
Rv2388c hemN |
oxygen-independent coproporphyrinogen III oxidase | 518 | 446 | coexpression:420 |
Rv3729 |
transferase | 442 | 421 | |
Rv2954c hyp |
hypothetical protein | 410 | 380 | |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 408 | 292 | |
Rv3377c |
type B diterpene cyclase | 418 | 284 | |
Rv2530c vapC39 |
ribonuclease VapC39 | 611 | 237 | textmining:511 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 433 | 178 | |
Rv1833c dhmA2 |
haloalkane dehalogenase | 698 | 171 | textmining:652 |
Rv0245 |
oxidoreductase | 676 | 100 | textmining:655 |
Rv0326 hyp |
hypothetical protein | 655 | 87 | textmining:639 |
Rv3833 |
AraC family transcriptional regulator | 466 | 87 | textmining:440 |
Rv0325 hyp |
hypothetical protein | 545 | 76 | textmining:529 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): methyltransferase
- Pfam (hmmscan --cut_ga): B12-binding PF02310.25 (E=1e-11), Radical_SAM PF04055.28 (E=1e-16)
- (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_214727.1)
- Domains: Pfam-A via hmmscan --cut_ga — B12-binding (PF02310.25), Radical_SAM (PF04055.28)
- 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
COG1032 - Curated reference: UniProt P96395 (TrEMBL, unreviewed; Predicted)
- 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 —
30 functional partner(s); context anchor
nadR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0213c| MSIKAYAKTQGIAVTSVNGLVAGHGSVQETWLAMQSAAALSGTPRLVGFSCIDTFPEVLWLAQRARQAWDGVRIVIGNAMATLNYERILRQHDCFDYVVVGDGEVAFTKLALALANDAAVDDVPGLARRSEQGQILRTPSSLVDLDELPRPARDELPTVLADGFAASVFSTRGCPYRCTFCGTGAMSAMLGKDSYRAKSVDAVVDEIDYLVSDYDVNFLSITDDLFISKHPGSQQRAADFANAVLRRGISVNFMVDIRLDSVVDLDLFKHLHRAGLRRVFIGVETGSYEQLRAYRKQILTRGQDAADTINALQQLGIDVIPGTIMFHPTVQPDELRETVRLLRATKYTVGFKFMSRIVPYPGTPLYQAYSDAGYLTAKWPLGQWEFVDPEASRVYADVVAKVAPDVGISFDEAEAYFLSRLDEWENVIAGRIAEATS