trmB Resolved · high auto-curated
H37Rv Rv0208c · MTBC0 mtbc0_000222 ·
263 aa · 248467–249258 (-) ·
RefSeq NP_214722.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA (guanine-N(7)-)-methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (guanosine(46)-N7)-methyltransferase TrmB |
| Revised (this work) | TRNA (guanosine(46)-N7)-methyltransferase TrmB. Pfam: Methyltransf_4 (PF02390.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFY9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA |
| EC (curated) |
EC 2.1.1.33
|
| Curated function | Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | trmB |
| eggNOG description | Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA |
| Orthologous group | COG0220 |
| EC number |
EC 2.1.1.33
|
| KEGG orthology |
K03439
|
| Gene Ontology (56) |
GO:0001510, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006725 +44 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.30% of strains (430) · 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_4 | PF02390.24 | 1.6e-55 | 76–247 | Putative methyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL3 (transmembrane transport protein MmpL3), high confidence from genomic context alone (score 837 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0207c hyp |
hypothetical protein | 989 | 973 ctx | neighborhood:882 coexpression:783 textmining:604 |
Rv2118c trmI |
tRNA (adenine(58)-N(1))-methyltransferase | 886 | 859 | coexpression:643 database:540 |
Rv0206c mmpL3 |
transmembrane transport protein MmpL3 | 862 | 837 ctx | neighborhood:798 |
Rv0210 hyp |
hypothetical protein | 801 | 801 ctx | neighborhood:775 |
Rv0209 hyp |
hypothetical protein | 776 | 776 ctx | neighborhood:775 |
Rv2793c truB |
tRNA pseudouridine synthase B | 817 | 758 | coexpression:648 |
Rv0722 rpmD |
50S ribosomal protein L30 | 650 | 651 | coexpression:650 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 747 | 645 | coexpression:425 |
Rv0823c dusB |
tRNA-dihydrouridine synthase | 657 | 579 | |
Rv3455c truA |
tRNA pseudouridine synthase A | 657 | 550 | coexpression:400 |
Rv3834c serS |
serine--tRNA ligase | 547 | 519 | experimental:490 |
Rv1340 rphA |
ribonuclease PH | 527 | 498 | |
Rv1112 ychF |
GTP-binding protein | 504 | 494 | coexpression:402 |
Rv2963 |
integral membrane protein | 484 | 485 | coexpression:483 |
Rv3396c guaA |
GMP synthase | 478 | 478 | coexpression:409 |
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: tRNA (guanine-N(7)-)-methyltransferase
- MTBC0 PGAP product: tRNA (guanosine(46)-N7)-methyltransferase TrmB
- Pfam (hmmscan --cut_ga): Methyltransf_4 PF02390.24 (E=2e-55)
- (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_214722.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_4 (PF02390.24)
- 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
COG0220 - Curated reference: UniProt P9WFY9 (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 —
57 functional partner(s); context anchor
mmpL3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000222|Rv0208c|trmB MVHHGQMHAQPGVGLRPDTPVASGQLPSTSIRSRRSGISKAQRETWERLWPELGLLALPQSPRGTPVDTRAWFGRDAPVVLEIGSGSGTSTLAMAKAEPHVDVIAVDVYRRGLAQLLCAIDKVGSDGINIRLILGNAVDVLQHLIAPDSLCGVRVFFPDPWPKARHHKRRLLQPATMALIADRLVPSGVLHAATDHPGYAEHIAAAGDAEPRLVRVDPDTELLPISVVRPATKYERKAQLGGGAVIELLWKKHGCSERDLKIR