Rv1498c Resolved · high auto-curated
H37Rv Rv1498c · MTBC0 - ·
205 aa · 1689303–1689920 (-) ·
RefSeq NP_216014.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Methyltransferase. Pfam: Methyltransf_31 (PF13847.13), Ubie_methyltran (PF01209.25), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19), Methyltransf_23 (PF13489.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WLW9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterised methyltransferase Rv1498c |
| EC (curated) |
EC 2.1.1.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Methyltransferase domain |
| Orthologous group | COG0500 |
| Gene Ontology (15) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0008150, GO:0008152, GO:0008168, GO:0008757, GO:0016740, GO:0016741 +3 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 | 0.246 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 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_31 | PF13847.13 | 4.6e-19 | 1–136 | Methyltransferase domain |
Ubie_methyltran | PF01209.25 | 7.0e-07 | 1–118 | ubiE/COQ5 methyltransferase family |
Methyltransf_11 | PF08241.19 | 4.3e-20 | 2–117 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 8.0e-19 | 2–113 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 4.4e-15 | 2–115 | Methyltransferase domain |
Methyltransf_23 | PF13489.13 | 3.3e-12 | 2–131 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqP (lipoprotein LpqP), medium confidence from genomic context alone (score 409 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1498A hyp |
hypothetical protein | 497 | 497 ctx | neighborhood:468 |
Rv2305 hyp |
hypothetical protein | 491 | 492 ctx | cooccurence:488 |
Rv1501 hyp |
hypothetical protein | 474 | 474 | |
Rv1500 pimF |
glycosyltransferase | 440 | 440 | |
Rv0671 lpqP |
lipoprotein LpqP | 409 | 409 ctx | cooccurence:401 |
Rv1963c mce3R |
transcriptional repressor Mce3R | 597 | 144 | textmining:549 |
Rv1938 ephB |
epoxide hydrolase EphB | 870 | 45 | textmining:870 |
Rv0234c gabD1 |
succinate-semialdehyde dehydrogenase | 862 | 44 | textmining:862 |
Rv2740 ephG |
epoxide hydrolase | 806 | 44 | textmining:806 |
Rv1936 |
monooxygenase | 692 | 43 | textmining:692 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_31 PF13847.13 (E=5e-19), Ubie_methyltran PF01209.25 (E=7e-07), Methyltransf_11 PF08241.19 (E=4e-20), Methyltransf_25 PF13649.13 (E=8e-19), Methyltransf_12 PF08242.19 (E=4e-15), Methyltransf_23 PF13489.13 (E=3e-12)
- (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_216014.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_31 (PF13847.13), Ubie_methyltran (PF01209.25), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19), Methyltransf_23 (PF13489.13)
- 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
COG0500 - Curated reference: UniProt P9WLW9 (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 —
10 functional partner(s); context anchor
lpqP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1498c| MLDVGCGSGRMALPLTGYLNSEGRYAGFDISQKAIAWCQEHITSAHPNFQFEVSDIYNSLYNPKGKYQSLDFRFPYPDASFDVVFLTSVFTHMFPPDVEHYLDEISRVLKPGGRCLCTYFLLNDESLAHIAEGKSAHNFQHEGPGYRTIHKKRPEEAIGLPETFVRDVYGKFGLAVHEPLHYGSWSGREPRLSFQDIVIATKTAS