trmD Resolved · high auto-curated
H37Rv Rv2906c · MTBC0 mtbc0_003088 ·
230 aa · 3236494–3237186 (-) ·
RefSeq NP_217422.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA (guanine-N1)-methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (guanosine(37)-N1)-methyltransferase TrmD |
| Revised (this work) | TRNA (guanosine(37)-N1)-methyltransferase TrmD. Pfam: tRNA_m1G_MT (PF01746.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFY7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA |
| EC (curated) |
EC 2.1.1.228
|
| Curated function | Specifically methylates guanosine-37 in various tRNAs. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | trmD |
| eggNOG description | Belongs to the RNA methyltransferase TrmD family |
| Orthologous group | COG0336 |
| EC number |
EC 2.1.1.228
|
| KEGG orthology |
K00554
|
| Gene Ontology (46) |
GO:0001510, GO:0003674, GO:0003824, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006725, GO:0006807, GO:0008033, GO:0008150, GO:0008152 +34 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 | 0.346 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
tRNA_m1G_MT | PF01746.27 | 8.6e-93 | 1–227 | tRNA (Guanine-1)-methyltransferase TrmD |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rimM (16S rRNA processing protein RimM), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2907c rimM |
16S rRNA processing protein RimM | 989 | 985 ctx | neighborhood:882 coexpression:875 |
Rv2909c rpsP |
30S ribosomal protein S16 | 982 | 975 ctx | neighborhood:799 coexpression:858 |
Rv1307 atpH |
ATP synthase subunit b/delta | 981 | 970 | coexpression:968 textmining:413 |
Rv2904c rplS |
50S ribosomal protein L19 | 976 | 967 ctx | cooccurence:736 coexpression:853 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 920 | 909 ctx | cooccurence:531 coexpression:808 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 910 | 888 | coexpression:832 |
Rv2908c hyp |
hypothetical protein | 885 | 885 ctx | neighborhood:872 |
Rv3458c rpsD |
30S ribosomal protein S4 | 895 | 881 | coexpression:852 |
Rv0704 rplB |
50S ribosomal protein L2 | 880 | 879 | coexpression:861 |
Rv0732 secY |
preprotein translocase SecY | 880 | 874 | coexpression:857 |
Rv0716 rplE |
50S ribosomal protein L5 | 873 | 874 | coexpression:845 |
Rv2890c rpsB |
30S ribosomal protein S2 | 901 | 872 | coexpression:832 |
Rv0707 rpsC |
30S ribosomal protein S3 | 888 | 872 | coexpression:842 |
Rv0702 rplD |
50S ribosomal protein L4 | 862 | 862 | coexpression:861 |
Rv0703 rplW |
50S ribosomal protein L23 | 858 | 859 | coexpression:858 |
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-N1)-methyltransferase
- MTBC0 PGAP product: tRNA (guanosine(37)-N1)-methyltransferase TrmD
- Pfam (hmmscan --cut_ga): tRNA_m1G_MT PF01746.27 (E=9e-93)
- (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_217422.1)
- Domains: Pfam-A via hmmscan --cut_ga — tRNA_m1G_MT (PF01746.27)
- 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
COG0336 - Curated reference: UniProt P9WFY7 (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 —
165 functional partner(s); context anchor
rimM - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003088|Rv2906c|trmD MRIDIVTIFPACLDPLRQSLPGKAIESGLVDLNVHDLRRWTHDVHHSVDDAPYGGGPGMVMKAPVWGEALDEICSSETLLIVPTPAGVLFTQATAQRWTTESHLVFACGRYEGIDQRVVQDAARRMRVEEVSIGDYVLPGGESAAVVMVEAVLRLLAGVLGNPASHQDDSHSTGLDGLLEGPSYTRPASWRGLDVPEVLLSGDHARIAAWRREVSLQRTRERRPDLSHPD