spoU Resolved · high auto-curated
H37Rv Rv3366 · MTBC0 mtbc0_003581 ·
154 aa · 3804445–3804909 (+) ·
RefSeq NP_217883.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA/rRNA methylase SpoU |
|---|---|
| MTBC0 PGAP re-annotation | tRNA (cytidine(34)-2'-O)-methyltransferase |
| Revised (this work) | TRNA (cytidine(34)-2'-O)-methyltransferase. Pfam: 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 |
O50394
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative tRNA |
| EC (curated) |
EC 2.1.1.207
|
| Curated function | Could methylate the ribose at the nucleotide 34 wobble position in tRNA. |
UniProt still lists this protein as Putative tRNA; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | spoU |
| eggNOG description | Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family. TrmL subfamily |
| Orthologous group | COG0219 |
| EC number |
EC 2.1.1.207
|
| KEGG orthology |
K03216
|
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 0.11% of strains (156) · 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 |
|---|---|---|---|---|
SpoU_methylase | PF00588.25 | 2.2e-29 | 2–142 | SpoU rRNA Methylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3362c (ATP/GTP-binding protein), medium confidence from genomic context alone (score 495 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3361c mfpA hyp |
hypothetical protein | 547 | 548 ctx | neighborhood:541 |
Rv3365c hyp |
hypothetical protein | 529 | 529 ctx | neighborhood:526 |
Rv2462c tig |
trigger factor | 525 | 525 | |
Rv3363c hyp |
hypothetical protein | 523 | 523 ctx | neighborhood:518 |
Rv3362c |
ATP/GTP-binding protein | 494 | 495 ctx | neighborhood:491 |
Rv3364c hyp |
hypothetical protein | 493 | 492 ctx | neighborhood:486 |
Rv2882c frr |
ribosome recycling factor | 424 | 425 | coexpression:422 |
Rv3367 PE_PGRS51 |
PE-PGRS family protein PE_PGRS51 | 410 | 410 ctx | neighborhood:410 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 462 | 290 | |
Rv0208c trmB |
tRNA (guanine-N(7)-)-methyltransferase | 448 | 280 | |
Rv0557 mgtA |
GDP-mannose-dependent alpha-mannosyltransferase | 452 | 217 | |
Rv2966c rsmD |
methyltransferase | 830 | 153 | textmining:808 |
Rv3442c rpsI |
30S ribosomal protein S9 | 835 | 74 | textmining:830 |
Rv2765 |
hydrolase | 662 | 73 | textmining:651 |
Rv1781c malQ |
4-alpha-glucanotransferase | 628 | 51 | textmining:625 |
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/rRNA methylase SpoU
- MTBC0 PGAP product: tRNA (cytidine(34)-2'-O)-methyltransferase
- Pfam (hmmscan --cut_ga): SpoU_methylase PF00588.25 (E=2e-29)
- (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_217883.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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
COG0219 - Curated reference: UniProt O50394 (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 —
21 functional partner(s); context anchor
Rv3362c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003581|Rv3366|spoU MFRLLFVSPRIAPNTGNAIRTCAATGCELHLVEPLGFDLSEPKLRRAGLDYHDLASVTVHASLAHAWEALSPARVFAFTAQATTLFTNVGYRAGDVLMFGPEPTGLDEATLADTHITGQVRIPMLAGRRSLNLSNAAAVAVYEAWRQHGFAGAV