Rv2952 Resolved · high auto-curated
H37Rv Rv2952 · MTBC0 mtbc0_003134 ·
270 aa · 3325616–3326428 (+) ·
RefSeq NP_217468.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | phthiotriol/phenolphthiotriol dimycocerosates methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | phthiotriol/phenolphthiotriol dimycocerosates methyltransferase |
| Revised (this work) | Phthiotriol/phenolphthiotriol dimycocerosates 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 |
P9WIN3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phthiotriol/phenolphthiotriol dimycocerosates methyltransferase |
| EC (curated) |
EC 2.1.1.-
|
| Curated function | Catalyzes the methylation of the lipid moiety of the intermediate compounds phthiotriol and glycosylated phenolphthiotriol dimycoserosates to form phthiocerol dimycocerosates (DIM A) and glycosylated phenolphthiocerol dimycocerosates (PGL). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Catalyzes the methylation of the lipid moiety of the intermediate compounds phthiotriol and glycosylated phenolphthiotriol dimycoserosates to form phthiocerol dimycocerosates (DIM A) and glycosylated phenolphthiocerol dimycocerosates (PGL) |
| Orthologous group | COG0500 |
| Gene Ontology (25) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0008152, GO:0008168, GO:0008171, GO:0009273, GO:0009987, GO:0016020 +13 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)
| pN/pS | 1.132 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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 | 2.8e-07 | 71–183 | Methyltransferase domain |
Ubie_methyltran | PF01209.25 | 1.5e-09 | 77–178 | ubiE/COQ5 methyltransferase family |
Methyltransf_31 | PF13847.13 | 8.9e-16 | 81–184 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 1.8e-20 | 84–176 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 8.3e-24 | 85–178 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 2.9e-13 | 85–178 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2953 (trans-acting enoyl reductase), high confidence from genomic context alone (score 923 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2953 |
trans-acting enoyl reductase | 945 | 923 ctx | neighborhood:724 coexpression:733 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 881 | 799 ctx | neighborhood:597 database:500 textmining:435 |
Rv0329c hyp |
hypothetical protein | 553 | 553 ctx | cooccurence:553 |
Rv1405c |
methyltransferase | 530 | 530 ctx | cooccurence:530 |
Rv2067c hyp |
hypothetical protein | 453 | 450 | |
Rv1621c cydD |
cytochrome biosyntheisis ABC transporter ATP-binding protein/permease CydD | 569 | 319 | |
Rv1844c gnd1 |
6-phosphogluconate dehydrogenase | 529 | 73 | textmining:513 |
Rv3119 moaE1 |
molybdopterin synthase catalytic subunit 1 | 443 | 57 | textmining:434 |
Rv3221c TB7.3 |
acetyl-CoA carboxylase biotin carboxyl carrier protein subunit | 549 | 44 | textmining:548 |
Rv3324c moaC3 |
cyclic pyranopterin monophosphate synthase accessory protein | 436 | 41 | textmining:436 |
Rv0968 hyp |
hypothetical protein | 433 | 41 | textmining:433 |
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: phthiotriol/phenolphthiotriol dimycocerosates methyltransferase
- MTBC0 PGAP product: phthiotriol/phenolphthiotriol dimycocerosates methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_23 PF13489.13 (E=3e-07), Ubie_methyltran PF01209.25 (E=1e-09), Methyltransf_31 PF13847.13 (E=9e-16), Methyltransf_25 PF13649.13 (E=2e-20), Methyltransf_11 PF08241.19 (E=8e-24), Methyltransf_12 PF08242.19 (E=3e-13)
- (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_217468.1)
- 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 P9WIN3 (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 —
11 functional partner(s); context anchor
Rv2953 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003134|Rv2952| MAFSRTHSLLARAGSTSTYKRVWRYWYPLMTRGLGNDEIVFINWAYEEDPPMDLPLEASDEPNRAHINLYHRTATQVDLGGKQVLEVSCGHGGGASYLTRTLHPASYTGLDLNQAGIKLCKKRHRLPGLDFVRGDAENLPFDDESFDVVLNVEASHCYPHFRRFLAEVVRVLRPGGYFPYADLRPNNEIAAWEADLAATPLRQLSQRQINAEVLRGIGNNSQKSRDLVDRHLPAFLRFAGREFIGVQGTQLSRYLEGGELSYRMYCFTKD