Rv1523 Resolved · high auto-curated
H37Rv Rv1523 · MTBC0 mtbc0_001630 ·
347 aa · 1727462–1728505 (+) ·
RefSeq NP_216039.1
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), Methyltransf_29 (PF03141.23), 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 |
Q50584
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable methyltransferase |
| 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 |
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 | 1.531 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.16% of strains (228) · 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 |
|---|---|---|---|---|
Methyltransf_23 | PF13489.13 | 1.1e-12 | 145–269 | Methyltransferase domain |
Methyltransf_29 | PF03141.23 | 1.8e-05 | 155–263 | Putative S-adenosyl-L-methionine-dependent methyltransferase |
Ubie_methyltran | PF01209.25 | 2.1e-10 | 156–260 | ubiE/COQ5 methyltransferase family |
Methyltransf_31 | PF13847.13 | 1.6e-17 | 161–271 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 1.7e-22 | 164–256 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 2.7e-25 | 165–259 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 8.7e-14 | 165–258 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1524 (glycosyltransferase), high confidence from genomic context alone (score 898 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1524 |
glycosyltransferase | 898 | 898 ctx | neighborhood:721 coexpression:651 |
Rv1525 wbbL2 |
rhamnosyl transferase WbbL | 666 | 666 ctx | neighborhood:598 |
Rv1522c mmpL12 |
transmembrane transport protein MmpL12 | 833 | 575 ctx | neighborhood:567 textmining:624 |
Rv0558 menH |
demethylmenaquinone methyltransferase | 425 | 425 ctx | cooccurence:425 |
Rv2067c hyp |
hypothetical protein | 405 | 400 | |
Rv3322c |
methyltransferase | 887 | 166 | textmining:871 |
Rv1758 cut1 |
cutinase | 502 | 154 | textmining:436 |
Rv0131c fadE1 |
acyl-CoA dehydrogenase FadE1 | 520 | 59 | textmining:511 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 684 | 53 | textmining:680 |
Rv3392c cmaA1 |
cyclopropane mycolic acid synthase CmaA | 529 | 50 | textmining:525 |
Rv1832 gcvB |
glycine dehydrogenase | 467 | 49 | textmining:463 |
Rv1895 |
zinc-binding alcohol dehydrogenase | 871 | 46 | textmining:871 |
Rv3514 PE_PGRS57 |
PE-PGRS family protein PE_PGRS57 | 652 | 41 | textmining:652 |
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=1e-12), Methyltransf_29 PF03141.23 (E=2e-05), Ubie_methyltran PF01209.25 (E=2e-10), Methyltransf_31 PF13847.13 (E=2e-17), Methyltransf_25 PF13649.13 (E=2e-22), Methyltransf_11 PF08241.19 (E=3e-25), Methyltransf_12 PF08242.19 (E=9e-14)
- (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_216039.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), Methyltransf_29 (PF03141.23), 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 Q50584 (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 —
13 functional partner(s); context anchor
Rv1524 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001630|Rv1523| MTITALTVTLPLLWRRLTTAGVKYADQGHFVGSAGVPAADAGGRDAASEQIARWTQTCTVVLVCGHGPAKWAFRSWCTSRSCDTLPVALRYRLQSNPLVGKLTTKYFLPLGTRQVGDHVVFFNFGYEEDPPMALPLSESDEPNRYCIQLYHQTASQVDLTGKEVLEVSCGAGGGASYIARNLGPASYTGLDLNPASIDLCRAKHRLPGLQFVQGDAQNLPFPDESFDAVVNVEASHQYPDFRGFLAEVARVLRPGGHFLYTDSRRNPVVAEWEAALADAPLRTISQRDIGAQAKRGLDANTARSQEAIGRRAPVLLAGLTRCAVRVLDWDLRRGGGFSYRIYLFAKD