Rv0224c Resolved · high auto-curated
H37Rv Rv0224c · MTBC0 mtbc0_000238 ·
254 aa · 268244–269008 (-) ·
RefSeq NP_214738.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | class I SAM-dependent methyltransferase |
| Revised (this work) | Class I SAM-dependent methyltransferase. Pfam: Methyltransf_23 (PF13489.13), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJZ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized methyltransferase Rv0224c |
| EC (curated) |
EC 2.1.1.-
|
UniProt still lists this protein as Uncharacterized methyltransferase Rv0224c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Methyltransferase |
| Orthologous group | COG0500 |
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
Methyltransf_23 | PF13489.13 | 1.3e-09 | 56–158 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 1.2e-17 | 63–155 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 7.4e-11 | 63–152 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 4.0e-07 | 63–153 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aftD (alpha-(1->3)-arabinofuranosyltransferase), high confidence from genomic context alone (score 800 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0225 hyp |
hypothetical protein | 898 | 898 ctx | neighborhood:615 cooccurence:745 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 807 | 800 ctx | cooccurence:653 |
Rv0226c |
transmembrane protein | 749 | 749 ctx | cooccurence:743 |
Rv0227c |
membrane protein | 736 | 736 ctx | cooccurence:734 |
Rv2673 aftC |
alpha-(1->3)-arabinofuranosyltransferase | 629 | 630 ctx | cooccurence:628 |
Rv3802c |
membrane protein | 614 | 614 ctx | cooccurence:592 |
Rv3635 |
transmembrane protein | 613 | 614 ctx | cooccurence:607 |
Rv0228 |
acyltransferase | 571 | 571 ctx | cooccurence:567 |
Rv0223c |
aldehyde dehydrogenase | 547 | 543 ctx | neighborhood:543 |
Rv1489A hyp |
hypothetical protein | 473 | 474 ctx | cooccurence:472 |
Rv1684 hyp |
hypothetical protein | 465 | 465 | |
Rv1476 |
membrane protein | 450 | 451 ctx | cooccurence:448 |
Rv3794 embA |
arabinosyltransferase A | 434 | 434 ctx | cooccurence:429 |
Rv0885 hyp |
hypothetical protein | 431 | 432 ctx | cooccurence:430 |
Rv0555 menD |
bifunctional 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase | 451 | 152 |
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
- MTBC0 PGAP product: class I SAM-dependent methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_23 PF13489.13 (E=1e-09), Methyltransf_11 PF08241.19 (E=1e-17), Methyltransf_25 PF13649.13 (E=7e-11), Methyltransf_12 PF08242.19 (E=4e-07)
- (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_214738.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19)
- 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 P9WJZ9 (SwissProt, reviewed; 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 —
16 functional partner(s); context anchor
aftD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000238|Rv0224c| MAVTDVFARRATLRRSLRLLADFRYEQRDPARFYRTLAADTAAMIGDLWLATHSEPPVGRTLLDVGGGPGYFATAFSDAGVGYIGVEPDPDEMHAAGPAFTGRPGMFVRASGMALPFADDSVDICLSSNVAEHVPRPWQLGTEMLRVTKPGGLVVLSYTVWLGPFGGHEMGLSHYLGGARAAARYVRKHGHPAKNNYGSSLFAVSAAEGLRWAAGTGAALAVFPRYHPRWAWWLTSVPVLREFLVSNLVLVLTP