omt Resolved · high auto-curated
H37Rv Rv1153c · MTBC0 mtbc0_001239 ·
282 aa · 1288439–1289287 (-) ·
RefSeq NP_215669.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | O-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 |
O06551
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable O-methyltransferase Omt |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | omt |
| eggNOG description | O-Methyltransferase |
| Orthologous group | COG3315 |
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 | 1.064 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.28% of strains (1854) · 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 | 6.2e-11 | 20–178 | Leucine carboxyl methyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purD (phosphoribosylamine--glycine ligase), medium confidence from genomic context alone (score 611 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1154c hyp |
hypothetical protein | 883 | 883 ctx | neighborhood:882 |
Rv0772 purD |
phosphoribosylamine--glycine ligase | 612 | 611 ctx | fusion:611 |
Rv1155 |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 574 | 574 ctx | neighborhood:573 |
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: O-methyltransferase
- MTBC0 PGAP product: class I SAM-dependent methyltransferase
- Pfam (hmmscan --cut_ga): LCM PF04072.21 (E=6e-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_215669.1)
- 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 O06551 (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 —
3 functional partner(s); context anchor
purD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001239|Rv1153c|omt MSAHKPAKQRVALTGVSETALLTLNARAAEARRRDAIIDDPMAVALVESIDFDFAKFGPTGQGFALRARAFDMAAQHYLDQHPAATVVALAEGLQTSFWRLDVAIPGGQFRWLTVDLPPIVDLRTRLLPSSPRVSVCAQSALDYSWMDSVDPAGGVFITAEGLLMYLQPEQALGLIAQCAQTFPGGQMLFDLPPRWFAGWSRLGLRTSLRYKVPRMPFSMSVAQAADLVNKVPGVVAVRDLRVPPGRGLWVNMALSTVYRLPVFDPLRPCLTLLEFSRPARG