tsnR Resolved · high auto-curated
H37Rv Rv1644 · MTBC0 mtbc0_001753 ·
260 aa · 1865627–1866409 (+) ·
RefSeq NP_216160.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 23S rRNA methyltransferase TsnR |
|---|---|
| MTBC0 PGAP re-annotation | RNA methyltransferase |
| Revised (this work) | RNA methyltransferase. Pfam: MRM3-like_sub_bind (PF22435.2), SpoU_sub_bind (PF08032.18), SpoU_methylase (PF00588.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P94978
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible 23S rRNA methyltransferase TsnR |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | tsnR |
| eggNOG description | Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family |
| Orthologous group | COG0566 |
| KEGG orthology |
K03437
|
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 | 0.194 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 3 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 |
|---|---|---|---|---|
MRM3-like_sub_bind | PF22435.2 | 5.7e-11 | 8–90 | MRM3-like substrate binding domain |
SpoU_sub_bind | PF08032.18 | 2.5e-07 | 28–94 | RNA 2'-O ribose methyltransferase substrate binding |
SpoU_methylase | PF00588.25 | 2.4e-38 | 109–251 | SpoU rRNA Methylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplT (50S ribosomal protein L20), high confidence from genomic context alone (score 934 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1643 rplT |
50S ribosomal protein L20 | 936 | 934 ctx | neighborhood:833 experimental:400 |
Rv2420c rsfS hyp |
hypothetical protein | 819 | 811 | experimental:763 |
Rv1641 infC |
initiation factor IF-3 | 798 | 799 ctx | neighborhood:723 |
Rv1642 rpmI |
50S ribosomal protein L35 | 783 | 778 ctx | neighborhood:765 |
Rv3456c rplQ |
50S ribosomal protein L17 | 773 | 770 | experimental:739 |
Rv0723 rplO |
50S ribosomal protein L15 | 756 | 756 | experimental:732 |
Rv2442c rplU |
50S ribosomal protein L21 | 750 | 750 | experimental:739 |
Rv0715 rplX |
50S ribosomal protein L24 | 734 | 735 | experimental:676 |
Rv0640 rplK |
50S ribosomal protein L11 | 715 | 716 | experimental:696 |
Rv3443c rplM |
50S ribosomal protein L13 | 722 | 709 | experimental:687 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 727 | 703 ctx | neighborhood:456 |
Rv0701 rplC |
50S ribosomal protein L3 | 704 | 690 | experimental:664 |
Rv2902c rnhB |
ribonuclease HII | 678 | 662 | coexpression:594 |
Rv1540 |
RNA pseudouridine synthase | 647 | 629 | experimental:466 |
Rv1023 eno |
enolase | 592 | 592 | database:546 |
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: 23S rRNA methyltransferase TsnR
- MTBC0 PGAP product: RNA methyltransferase
- Pfam (hmmscan --cut_ga): MRM3-like_sub_bind PF22435.2 (E=6e-11), SpoU_sub_bind PF08032.18 (E=2e-07), SpoU_methylase PF00588.25 (E=2e-38)
- (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_216160.1)
- Domains: Pfam-A via hmmscan --cut_ga — MRM3-like_sub_bind (PF22435.2), SpoU_sub_bind (PF08032.18), SpoU_methylase (PF00588.25)
- 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
COG0566 - Curated reference: UniProt P94978 (TrEMBL, unreviewed; 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 —
82 functional partner(s); context anchor
rplT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001753|Rv1644|tsnR MLTERSARVATAVKLHRHVGRRRAGRFLAEGPNLVAAALARGLVREVFVTEVAARRHELLLAAHEASVHLVTERAAKALSDTVTPAGLVAVCDLPATRLEDVLAGSPQLIAVTVEIREPGNAGTVIRIADAMGAAAVILAGRSVDPYNGKCLRASTGSIFAIPVVVAPDVGAAIADLRAAGLQVLATAVDGEMALDDADRLLAEPTAWLFGPEAHGLSAEIAALADHRVHIPMSGGAESLNVAAAAAICLYESARALGRR