Rv2959c Resolved · high auto-curated
H37Rv Rv2959c · MTBC0 mtbc0_003142 ·
245 aa · 3333276–3334013 (-) ·
RefSeq NP_217475.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | rhamnosyl O-methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | rhamnosyl O-methyltransferase |
| Revised (this work) | Rhamnosyl O-methyltransferase. Pfam: RMNT_CmcI (PF04989.19), Methyltransf_24 (PF13578.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIM5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Rhamnosyl O-methyltransferase |
| EC (curated) |
EC 2.1.1.-
|
| Curated function | Catalyzes the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| eggNOG description | Catalyzes the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD) |
| Orthologous group | COG3510 |
| Gene Ontology (52) |
GO:0005575, GO:0005623, GO:0005886, GO:0006022, GO:0006023, GO:0006024, GO:0006029, GO:0006082, GO:0006790, GO:0006807, GO:0008150, GO:0008152 +40 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 | 0.862 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 3.32% of strains (4817) · 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 |
|---|---|---|---|---|
RMNT_CmcI | PF04989.19 | 1.8e-78 | 50–244 | Rhamnosyl O-methyltransferase/CmcI |
Methyltransf_24 | PF13578.13 | 1.0e-06 | 84–191 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2958c (PGL/p-HBAD biosynthesis glycosyltransferase), high confidence from genomic context alone (score 814 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2958c |
PGL/p-HBAD biosynthesis glycosyltransferase | 979 | 814 ctx | neighborhood:529 database:500 textmining:891 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 633 | 633 ctx | cooccurence:633 |
Rv2075c hyp |
hypothetical protein | 626 | 626 ctx | cooccurence:626 |
Rv2231A vapC16 |
ribonuclease VapC16 | 602 | 602 ctx | cooccurence:602 |
Rv0355c PPE8 |
PPE family protein PPE8 | 600 | 600 ctx | cooccurence:598 |
Rv3350c PPE56 |
PPE family protein PPE56 | 592 | 592 ctx | cooccurence:590 |
Rv2082 hyp |
hypothetical protein | 586 | 586 ctx | cooccurence:584 |
Rv0104 hyp |
hypothetical protein | 586 | 586 ctx | cooccurence:586 |
Rv3347c PPE55 |
PPE family protein PPE55 | 580 | 580 ctx | cooccurence:578 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 571 | 571 ctx | cooccurence:571 |
Rv3343c PPE54 |
PPE family protein PPE54 | 565 | 566 ctx | cooccurence:560 |
Rv0304c PPE5 |
PPE family protein PPE5 | 564 | 565 ctx | cooccurence:562 |
Rv2949c |
chorismate pyruvate-lyase | 905 | 545 ctx | cooccurence:517 textmining:800 |
Rv2209 |
integral membrane protein | 543 | 543 ctx | cooccurence:543 |
Rv1004c |
membrane protein | 543 | 543 ctx | cooccurence:543 |
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: rhamnosyl O-methyltransferase
- MTBC0 PGAP product: rhamnosyl O-methyltransferase
- Pfam (hmmscan --cut_ga): RMNT_CmcI PF04989.19 (E=2e-78), Methyltransf_24 PF13578.13 (E=1e-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_217475.1)
- Domains: Pfam-A via hmmscan --cut_ga — RMNT_CmcI (PF04989.19), Methyltransf_24 (PF13578.13)
- 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
COG3510 - Curated reference: UniProt P9WIM5 (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 —
47 functional partner(s); context anchor
Rv2958c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003142|Rv2959c| MGLVWRSRTSLVGQLIGLVRLVASFAAQLFYRPSDAVAEEYHKWYYGNLVWTKTTYMGINCWKSVSDMWNYQEILSELQPSLVIEFGTRYGGSAVYFANIMRQIGQPFKVLTVDNSHKALDPRARREPDVLFVESSSTDPAIAEQIQRLKNEYPGKIFAILDSDHSMNHVLAEMKLLRPLLSAGDYLVVEDSNINGHPVLPGFGPGPYEAIEAYEDEFPNDYKHDAERENKFGWTSAPNGFLIRN