Rv2372c Resolved · high auto-curated
H37Rv Rv2372c · MTBC0 mtbc0_002524 ·
262 aa · 2676230–2677018 (-) ·
RefSeq NP_216888.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | rRNA small subunit methyltransferase E |
|---|---|
| MTBC0 PGAP re-annotation | 16S rRNA (uracil(1498)-N(3))-methyltransferase |
| Revised (this work) | 16S rRNA (uracil(1498)-N(3))-methyltransferase. Pfam: PUA_4 (PF20260.5), Methyltrans_RNA (PF04452.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGX1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribosomal RNA small subunit methyltransferase E |
| EC (curated) |
EC 2.1.1.193
|
| Curated function | Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rsmE |
| eggNOG description | Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit |
| Orthologous group | COG1385 |
| EC number |
EC 2.1.1.193
|
| KEGG orthology |
K09761
|
| Gene Ontology (47) |
GO:0000154, GO:0001510, GO:0003674, GO:0003824, GO:0006139, GO:0006364, GO:0006396, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0008168 +35 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 | 1.373 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (377) · 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 |
|---|---|---|---|---|
PUA_4 | PF20260.5 | 6.4e-12 | 20–66 | RNA methyltransferase PUA domain |
Methyltrans_RNA | PF04452.20 | 1.2e-46 | 78–240 | RNA methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dnaJ2 (chaperone protein DnaJ), high confidence from genomic context alone (score 966 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2373c dnaJ2 |
chaperone protein DnaJ | 967 | 966 ctx | neighborhood:872 coexpression:714 |
Rv2374c hrcA |
heat-inducible transcription repressor HrcA | 825 | 795 ctx | neighborhood:784 |
Rv2364c era |
GTPase Era | 621 | 621 ctx | neighborhood:544 |
Rv2365c hyp |
hypothetical protein | 548 | 549 ctx | neighborhood:544 |
Rv2366c |
transmembrane protein | 548 | 548 ctx | neighborhood:544 |
Rv2367c ybeY |
endoribonuclease | 545 | 546 ctx | neighborhood:543 |
Rv2375 hyp |
hypothetical protein | 539 | 539 ctx | neighborhood:535 |
Rv2368c phoH1 |
phosphate starvation-inducible protein PhoH | 517 | 517 ctx | neighborhood:514 |
Rv2733c miaB |
(dimethylallyl)adenosine tRNA methylthiotransferase | 515 | 461 | |
Rv0352 dnaJ1 |
chaperone protein DnaJ | 468 | 449 | |
Rv1402 priA |
primosomal protein N' | 438 | 438 | |
Rv1311 atpC |
ATP synthase subunit epsilon | 412 | 412 | |
Rv1703c |
methyltransferase | 410 | 411 | coexpression:411 |
Rv1220c |
methyltransferase | 410 | 411 | coexpression:411 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 410 | 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: rRNA small subunit methyltransferase E
- MTBC0 PGAP product: 16S rRNA (uracil(1498)-N(3))-methyltransferase
- Pfam (hmmscan --cut_ga): PUA_4 PF20260.5 (E=6e-12), Methyltrans_RNA PF04452.20 (E=1e-46)
- (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_216888.1)
- Domains: Pfam-A via hmmscan --cut_ga — PUA_4 (PF20260.5), Methyltrans_RNA (PF04452.20)
- 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
COG1385 - Curated reference: UniProt P9WGX1 (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 —
27 functional partner(s); context anchor
dnaJ2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002524|Rv2372c| MVAMLFYVDTLPDTGAVAVVDGDEGFHAATVRRIRPGEQLVLGDGVGRLARCVVEQAGRGGLRARVLRRWSVPPVRPPVTVVQALPKSERSELAIELATEAGADAFLAWQAARCVANWDGARVDKGLRRWRAVVRSAARQSRRARIPPVDGVLSTPMLVQRVREEVAAGAAVLVLHEEATERIVDIAAAQAGSLMLVVGPEGGIAPDELAALTDAGAVAVRLGPTVLRTSTAAAVALGAVGVLTSRWDASASDCEYCDVTRR