Rv1403c Resolved · high auto-curated
H37Rv Rv1403c · MTBC0 mtbc0_001504 ·
274 aa · 1588942–1589766 (-) ·
RefSeq NP_215919.1
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: 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 |
P9WLY9
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized protein Rv1403c |
UniProt still lists this protein as Uncharacterized protein Rv1403c; 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 | Methyltransferase |
| 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 | 2.355 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.89% of strains (1291) · 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 |
|---|---|---|---|---|
Ubie_methyltran | PF01209.25 | 4.4e-11 | 44–151 | ubiE/COQ5 methyltransferase family |
Methyltransf_31 | PF13847.13 | 1.3e-09 | 49–148 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 1.3e-18 | 53–145 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 5.9e-18 | 54–147 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 1.7e-07 | 54–147 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1404 (transcriptional regulator), medium confidence from genomic context alone (score 580 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1405c |
methyltransferase | 741 | 736 | coexpression:729 |
Rv0575c |
oxidoreductase | 726 | 716 | coexpression:716 |
Rv1404 |
transcriptional regulator | 900 | 580 ctx | neighborhood:574 textmining:773 |
Rv0759c hyp |
hypothetical protein | 785 | 168 | textmining:753 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 886 | 163 | textmining:870 |
Rv1726 |
oxidoreductase | 816 | 98 | textmining:805 |
Rv0195 |
two component transcriptional regulator | 469 | 95 | textmining:438 |
Rv0059 darT hyp |
hypothetical protein | 568 | 65 | textmining:558 |
Rv3772 hisC2 |
histidinol-phosphate aminotransferase | 812 | 61 | textmining:808 |
Rv0194 |
multidrug ABC transporter ATPase/permease | 461 | 59 | textmining:451 |
Rv0193c hyp |
hypothetical protein | 871 | 55 | textmining:870 |
Rv1435c hyp |
hypothetical protein | 815 | 47 | textmining:815 |
Rv1185c fadD21 |
fatty-acid--CoA ligase FadD21 | 435 | 47 | textmining:432 |
Rv0917 betP |
glycine betaine transport integral membrane protein BetP | 809 | 46 | textmining:809 |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase | 634 | 46 | textmining:632 |
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): Ubie_methyltran PF01209.25 (E=4e-11), Methyltransf_31 PF13847.13 (E=1e-09), Methyltransf_25 PF13649.13 (E=1e-18), Methyltransf_11 PF08241.19 (E=6e-18), Methyltransf_12 PF08242.19 (E=2e-07)
- (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_215919.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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 P9WLY9 (SwissProt, reviewed; Inferred from homology)
- 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 —
20 functional partner(s); context anchor
Rv1404 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001504|Rv1403c| MTVYTPTSERQAPATTHRQMWALGDYAAIAEELLAPLGPILVSTSGIRRGDRVLDVAAGSGNVSIPAAMAGAHVTASDLTPELLRRAQARAAAAGLELGWREANAEALPFSAGEFDAVLSTIGVMFAPRHQRTADELARVCRRGGKISTLNWTPEGFYGKLLSTIRPYRPTLPAGAPHEVWWGSEDYVSGLFRDHVSDIRTRRGSLTVDRFGCPDECRDYFKNFYGPAINAYRSIADSPECVATLDAEITELCREYLCDGVMQWEYLIFTARKC