Rv0567 Resolved · high auto-curated
H37Rv Rv0567 · MTBC0 mtbc0_000597 ·
339 aa · 661872–662891 (+) ·
RefSeq NP_215081.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methyltransferase/methylase |
|---|---|
| MTBC0 PGAP re-annotation | methyltransferase |
| Revised (this work) | Methyltransferase. Pfam: Dimerisation (PF08100.19), Methyltransf_2 (PF00891.25), Methyltransf_23 (PF13489.13), MTS (PF05175.21), Methyltransf_12 (PF08242.19), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53764
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable methyltransferase/methylase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Dimerisation domain |
| Orthologous group | COG0500 |
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 | 1.474 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.39% of strains (565) · 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 |
|---|---|---|---|---|
Dimerisation | PF08100.19 | 1.7e-08 | 14–88 | O-methyltransferase dimerisation domain |
Methyltransf_2 | PF00891.25 | 2.0e-40 | 111–321 | O-methyltransferase domain |
Methyltransf_23 | PF13489.13 | 1.2e-06 | 157–321 | Methyltransferase domain |
MTS | PF05175.21 | 1.1e-06 | 161–275 | Methyltransferase small domain |
Methyltransf_12 | PF08242.19 | 1.1e-07 | 177–271 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 4.2e-07 | 177–270 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 6.9e-06 | 177–274 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cyp135B1 (cytochrome P450 Cyp135B1), medium confidence from genomic context alone (score 604 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0568 cyp135B1 |
cytochrome P450 Cyp135B1 | 604 | 604 ctx | neighborhood:513 |
Rv0566c hyp |
hypothetical protein | 429 | 429 ctx | neighborhood:423 |
Rv0569 hyp |
hypothetical protein | 415 | 415 | |
Rv1310 atpD |
ATP synthase subunit beta | 590 | 157 | textmining:534 |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 679 | 71 | textmining:670 |
Rv3375 amiD |
amidase | 864 | 47 | textmining:864 |
Rv1911c lppC |
lipoprotein LppC | 870 | 46 | textmining:870 |
Rv1038c esxJ |
ESAT-6 like protein EsxJ | 653 | 45 | textmining:652 |
Rv2809 hyp |
hypothetical protein | 870 | 44 | textmining:870 |
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: methyltransferase/methylase
- MTBC0 PGAP product: methyltransferase
- Pfam (hmmscan --cut_ga): Dimerisation PF08100.19 (E=2e-08), Methyltransf_2 PF00891.25 (E=2e-40), Methyltransf_23 PF13489.13 (E=1e-06), MTS PF05175.21 (E=1e-06), Methyltransf_12 PF08242.19 (E=1e-07), Methyltransf_25 PF13649.13 (E=4e-07), Methyltransf_11 PF08241.19 (E=7e-06)
- (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_215081.1)
- Domains: Pfam-A via hmmscan --cut_ga — Dimerisation (PF08100.19), Methyltransf_2 (PF00891.25), Methyltransf_23 (PF13489.13), MTS (PF05175.21), Methyltransf_12 (PF08242.19), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19)
- 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
COG0500 - Curated reference: UniProt O53764 (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 —
9 functional partner(s); context anchor
cyp135B1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000597|Rv0567| MELSPDRIMAIGGGYGPSKVLLTAVGLGLFTELGDEAMTAEAIADRLGLLKRPAIDFLDALVSLDLLARDGDGPGSHYRNTPETAHFLDEARPTYAGGLLKIWNERNYRFWADLTEALKTGKAQSEVKQTGRPFFEALYADPRRLEAFMAAMDAASRRNIELLAKRFPFERYRRLCDVGCADGLLSRIVAAAHPHLQCVSFDLPAVTEIARRKLTAEGLGERVQACAGDFLADPLPAADVITMGQILHDWNLDRKQQLVAKAYEALSKEGAFIVIETLIDDARRENTTGLMMSLNMLIEFGDAFDYSAADFRGWCGEAGFRSFEVIPLAGGSSAAVAYK