Rv0146 Resolved · high auto-curated
H37Rv Rv0146 · MTBC0 mtbc0_000157 ·
310 aa · 172557–173489 (+) ·
RefSeq NP_214660.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | S-adenosylmethionine-dependent methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | class I SAM-dependent methyltransferase |
| Revised (this work) | Class I SAM-dependent methyltransferase. Pfam: LCM (PF04072.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFJ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative S-adenosyl-L-methionine-dependent methyltransferase Rv0146 |
| EC (curated) |
EC 2.1.1.-
|
| Curated function | Exhibits S-adenosyl-L-methionine-dependent methyltransferase activity. |
UniProt still lists this protein as Putative S-adenosyl-L-methionine-dependent methyltransferase Rv0146; 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 | Exhibits S-adenosyl-L-methionine-dependent methyltransferase activity |
| Orthologous group | COG3315 |
| Gene Ontology (44) |
GO:0002682, GO:0002684, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0009605, GO:0009607, GO:0016020 +32 more
|
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) pseudogene candidate
| pN/pS | 0.519 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 missense, 2 nonsense, 0 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 6.00% of strains (8716) · 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 |
|---|---|---|---|---|
LCM | PF04072.21 | 4.9e-67 | 18–204 | Leucine carboxyl methyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0145 (S-adenosylmethionine-dependent methyltransferase), high confidence from genomic context alone (score 837 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0145 |
S-adenosylmethionine-dependent methyltransferase | 836 | 837 ctx | neighborhood:816 |
Rv0147 |
aldehyde dehydrogenase | 785 | 785 ctx | neighborhood:775 |
Rv0144 |
transcriptional regulator | 743 | 743 ctx | neighborhood:739 |
Rv0148 |
short-chain type dehydrogenase/reductase | 708 | 708 ctx | neighborhood:699 |
Rv0149 |
quinone oxidoreductase | 509 | 508 ctx | neighborhood:503 |
Rv0143c |
transmembrane protein | 415 | 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: S-adenosylmethionine-dependent methyltransferase
- MTBC0 PGAP product: class I SAM-dependent methyltransferase
- Pfam (hmmscan --cut_ga): LCM PF04072.21 (E=5e-67)
- (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_214660.1)
- Domains: Pfam-A via hmmscan --cut_ga — LCM (PF04072.21)
- 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
COG3315 - Curated reference: UniProt P9WFJ3 (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 —
6 functional partner(s); context anchor
Rv0145 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000157|Rv0146| MRTHDDTWDIKTSVGATAVMVAAARAVETDRPDPLIRDPYARLLVTNAGAGAIWEAMLDPTLVAKAAAIDAETAAIVAYLRSYQAVRTNFFDTYFASAVAAGIRQVVILASGLDSRAYRLDWPAGTIVYEIDQPKVLSYKSTTLAENGVTPSAGRREVPADLRQDWPAALRDAGFDPTARTAWLAEGLLMYLPAEAQDRLFTQVGAVSVAGSRIAAETAPVHGEERRAEMRARFKKVADVLGIEQTIDVQELVYHDQDRASVADWLTDHGWRARSQRAPDEMRRVGRWVEGVPMADDPTAFAEFVTAERL