Rv3342 Resolved · high auto-curated
H37Rv Rv3342 · MTBC0 mtbc0_003554 ·
243 aa · 3754610–3755341 (+) ·
RefSeq NP_217859.1
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), Ubie_methyltran (PF01209.25), Methyltransf_31 (PF13847.13), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19), 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 |
P9WK01
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized methyltransferase Rv3342 |
| EC (curated) |
EC 2.1.1.-
|
UniProt still lists this protein as Uncharacterized methyltransferase Rv3342; 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 |
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, 2 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 | 4.2e-07 | 25–144 | Methyltransferase domain |
Ubie_methyltran | PF01209.25 | 8.0e-07 | 39–132 | ubiE/COQ5 methyltransferase family |
Methyltransf_31 | PF13847.13 | 7.4e-09 | 40–131 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 1.8e-18 | 42–129 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 6.2e-23 | 43–131 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 2.7e-11 | 43–131 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: metA (homoserine O-acetyltransferase), high confidence from genomic context alone (score 984 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3341 metA |
homoserine O-acetyltransferase | 984 | 984 ctx | neighborhood:881 coexpression:868 |
Rv3340 metC |
O-acetylhomoserine sulfhydrylase | 925 | 922 ctx | neighborhood:872 coexpression:415 |
Rv3339c icd1 |
isocitrate dehydrogenase | 436 | 415 ctx | neighborhood:413 |
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=4e-07), Ubie_methyltran PF01209.25 (E=8e-07), Methyltransf_31 PF13847.13 (E=7e-09), Methyltransf_25 PF13649.13 (E=2e-18), Methyltransf_11 PF08241.19 (E=6e-23), Methyltransf_12 PF08242.19 (E=3e-11)
- (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_217859.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), Ubie_methyltran (PF01209.25), Methyltransf_31 (PF13847.13), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19), 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 P9WK01 (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 —
3 functional partner(s); context anchor
metA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003554|Rv3342| MTCSRRDMSLSFGSAVGAYERGRPSYPPEAIDWLLPAAARRVLDLGAGTGKLTTRLVERGLDVVAVDPIPEMLDVLRAALPQTVALLGTAEEIPLDDNSVDAVLVAQAWHWVDPARAIPEVARVLRPGGRLGLVWNTRDERLGWVRELGEIIGRDGDPVRDRVTLPEPFTTVQRHQVEWTNYLTPQALIDLVASRSYCITSPAQVRTKTLDRVRQLLATHPALANSNGLALPYVTVCVRATLA