trmI Resolved · high auto-curated
H37Rv Rv2118c · MTBC0 mtbc0_002250 ·
280 aa · 2404733–2405575 (-) ·
RefSeq NP_216634.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA (adenine(58)-N(1))-methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (adenine(58)-N(1))-methyltransferase TrmI |
| Revised (this work) | TRNA (adenine(58)-N(1))-methyltransferase TrmI. Pfam: TrmI-like_N (PF14801.13), GCD14 (PF08704.17), PCMT (PF01135.26), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFZ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | tRNA |
| EC (curated) |
EC 2.1.1.220
|
| Curated function | Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | trmI |
| eggNOG description | Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA |
| Orthologous group | COG2519 |
| EC number |
EC 2.1.1.219, EC 2.1.1.220
|
| KEGG orthology |
K07442
|
| Gene Ontology (57) |
GO:0001510, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006139, GO:0006396, GO:0006399, GO:0006400 +45 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 | 0.366 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
TrmI-like_N | PF14801.13 | 1.2e-24 | 5–54 | TrmI-like N-terminal |
GCD14 | PF08704.17 | 1.7e-19 | 73–237 | tRNA methyltransferase complex GCD14 subunit |
PCMT | PF01135.26 | 9.6e-07 | 73–204 | Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) |
Methyltransf_25 | PF13649.13 | 1.2e-07 | 103–197 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 1.8e-04 | 104–200 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpoZ (DNA-directed RNA polymerase subunit omega), medium confidence from genomic context alone (score 629 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 886 | 859 | coexpression:643 database:540 |
Rv2119 hyp |
hypothetical protein | 785 | 786 ctx | neighborhood:785 |
Rv0722 rpmD |
50S ribosomal protein L30 | 719 | 720 | coexpression:684 |
Rv2689c hyp |
hypothetical protein | 705 | 662 | coexpression:662 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 628 | 629 ctx | cooccurence:559 |
Rv1440 secG |
protein-export membrane protein SecG | 585 | 586 ctx | cooccurence:585 |
Rv1830 |
HTH-type transcriptional regulator | 584 | 584 ctx | cooccurence:582 |
Rv3859c gltB |
glutamate synthase large subunit | 545 | 545 ctx | neighborhood:544 |
Rv1010 ksgA |
rRNA small subunit methyltransferase A | 539 | 512 | coexpression:414 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 510 | 511 ctx | cooccurence:508 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 507 | 508 ctx | cooccurence:505 |
Rv2613c |
AP-4-A phosphorylase | 486 | 486 ctx | cooccurence:482 |
Rv0651 rplJ |
50S ribosomal protein L10 | 484 | 485 | coexpression:426 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 541 | 475 | |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 473 | 473 | coexpression:410 |
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 (adenine(58)-N(1))-methyltransferase
- MTBC0 PGAP product: tRNA (adenine(58)-N(1))-methyltransferase TrmI
- Pfam (hmmscan --cut_ga): TrmI-like_N PF14801.13 (E=1e-24), GCD14 PF08704.17 (E=2e-19), PCMT PF01135.26 (E=1e-06), Methyltransf_25 PF13649.13 (E=1e-07), Methyltransf_11 PF08241.19 (E=2e-04)
- (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_216634.1)
- Domains: Pfam-A via hmmscan --cut_ga — TrmI-like_N (PF14801.13), GCD14 (PF08704.17), PCMT (PF01135.26), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19)
- 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
COG2519 - Curated reference: UniProt P9WFZ1 (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 —
42 functional partner(s); context anchor
rpoZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002250|Rv2118c|trmI MSATGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVAPAPLGRKREGRDG