Rv0089 Resolved · high auto-curated
H37Rv Rv0089 · MTBC0 - ·
197 aa · 97758–98351 (+) ·
RefSeq NP_214603.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Methyltransferase. Pfam: Methyltransf_9 (PF08003.18), RrnaAD (PF00398.27), Methyltransf_2 (PF00891.25), MTS (PF05175.21), Ubie_methyltran (PF01209.25), PrmA (PF06325.20), Methyltransf_23 (PF13489.13), NodS (PF05401.17), Methyltransf_25 (PF13649.13), Methyltransf_31 (PF13847.13), 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.
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 |
P9WK03
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized methyltransferase Rv0089 |
| EC (curated) |
EC 2.1.1.-
|
UniProt still lists this protein as Uncharacterized methyltransferase Rv0089; 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 domain |
| Orthologous group | COG0500 |
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.368 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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_9 | PF08003.18 | 2.8e-05 | 2–125 | Protein of unknown function (DUF1698) |
RrnaAD | PF00398.27 | 6.8e-09 | 10–95 | Ribosomal RNA adenine dimethylase |
Methyltransf_2 | PF00891.25 | 6.7e-06 | 11–132 | O-methyltransferase domain |
MTS | PF05175.21 | 1.4e-09 | 14–105 | Methyltransferase small domain |
Ubie_methyltran | PF01209.25 | 7.7e-09 | 14–127 | ubiE/COQ5 methyltransferase family |
PrmA | PF06325.20 | 3.9e-05 | 21–103 | Ribosomal protein L11 methyltransferase (PrmA) |
Methyltransf_23 | PF13489.13 | 2.7e-12 | 24–168 | Methyltransferase domain |
NodS | PF05401.17 | 3.6e-08 | 25–118 | Nodulation protein S (NodS) |
Methyltransf_25 | PF13649.13 | 7.1e-20 | 26–116 | Methyltransferase domain |
Methyltransf_31 | PF13847.13 | 8.6e-11 | 26–124 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 2.5e-20 | 27–119 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 8.9e-16 | 27–118 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0090 (membrane protein), medium confidence from genomic context alone (score 623 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0090 |
membrane protein | 622 | 623 ctx | neighborhood:581 |
Rv0088 |
polyketide cyclase/dehydrase | 564 | 564 ctx | neighborhood:499 |
Rv0084 hycD |
formate hydrogenlyase HycD | 435 | 435 ctx | neighborhood:419 |
Rv0086 hycQ |
hydrogenase HycQ | 435 | 435 ctx | neighborhood:427 |
Rv0085 hycP |
hydrogenase HycP | 435 | 435 ctx | neighborhood:427 |
Rv0087 hycE |
formate hydrogenase HycE | 434 | 434 ctx | neighborhood:420 |
Rv0082 |
oxidoreductase | 431 | 431 ctx | neighborhood:419 |
Rv0083 |
oxidoreductase | 422 | 422 ctx | neighborhood:413 |
Rv0081 |
HTH-type transcriptional regulator | 423 | 419 ctx | neighborhood:414 |
Rv1570 bioD |
ATP-dependent dethiobiotin synthetase BioD | 848 | 204 | textmining:818 |
Rv1568 bioA |
adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA | 828 | 134 | textmining:811 |
Rv2715 |
hydrolase | 870 | 45 | textmining:870 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 618 | 43 | textmining:618 |
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_9 PF08003.18 (E=3e-05), RrnaAD PF00398.27 (E=7e-09), Methyltransf_2 PF00891.25 (E=7e-06), MTS PF05175.21 (E=1e-09), Ubie_methyltran PF01209.25 (E=8e-09), PrmA PF06325.20 (E=4e-05), Methyltransf_23 PF13489.13 (E=3e-12), NodS PF05401.17 (E=4e-08), Methyltransf_25 PF13649.13 (E=7e-20), Methyltransf_31 PF13847.13 (E=9e-11), Methyltransf_11 PF08241.19 (E=2e-20), Methyltransf_12 PF08242.19 (E=9e-16)
- (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_214603.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_9 (PF08003.18), RrnaAD (PF00398.27), Methyltransf_2 (PF00891.25), MTS (PF05175.21), Ubie_methyltran (PF01209.25), PrmA (PF06325.20), Methyltransf_23 (PF13489.13), NodS (PF05401.17), Methyltransf_25 (PF13649.13), Methyltransf_31 (PF13847.13), 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 P9WK03 (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 —
13 functional partner(s); context anchor
Rv0090 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0089| MDQPWNANIHYDALLDAMVPLGTQCVLDVGCGDGLLAARLARRIPYVTAVDIDAPVLRRAQTRFANAPIRWLHADIMTAELPNAGFDAVVSNAALHHIEDTRTALSRLGGLVTPGGTLAVVTFVTPSLRNGLWHLTSWVACGMANRVKGKWEHSAPIKWPPPQTLHELRSHVRALLPGACIRRLLYGRVLVTWRAPV