Rv0881 Resolved · high auto-curated
H37Rv Rv0881 · MTBC0 mtbc0_000936 ·
288 aa · 982576–983442 (+) ·
RefSeq NP_215396.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | tRNA/rRNA methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | RNA methyltransferase |
| Revised (this work) | RNA 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 |
P9WFY3
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized tRNA/rRNA methyltransferase Rv0881 |
| EC (curated) |
EC 2.1.1.-
|
UniProt still lists this protein as Uncharacterized tRNA/rRNA methyltransferase Rv0881; 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 | spoU2 |
| eggNOG description | rRNA methyltransferase |
| Orthologous group | COG0566 |
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 | 0.613 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
SpoU_methylase | PF00588.25 | 6.8e-32 | 132–275 | SpoU rRNA Methylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0882 (transmembrane protein), high confidence from genomic context alone (score 900 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0882 |
transmembrane protein | 900 | 900 ctx | neighborhood:882 |
Rv0880 |
HTH-type transcriptional regulator | 883 | 882 ctx | neighborhood:882 |
Rv2420c rsfS hyp |
hypothetical protein | 786 | 776 | experimental:763 |
Rv0879c |
transmembrane protein | 765 | 766 ctx | neighborhood:765 |
Rv3456c rplQ |
50S ribosomal protein L17 | 765 | 762 | experimental:739 |
Rv2442c rplU |
50S ribosomal protein L21 | 749 | 749 | experimental:739 |
Rv0723 rplO |
50S ribosomal protein L15 | 744 | 745 | experimental:732 |
Rv0640 rplK |
50S ribosomal protein L11 | 706 | 706 | experimental:696 |
Rv3443c rplM |
50S ribosomal protein L13 | 717 | 704 | experimental:687 |
Rv0715 rplX |
50S ribosomal protein L24 | 697 | 697 | experimental:676 |
Rv0701 rplC |
50S ribosomal protein L3 | 691 | 676 | experimental:664 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 678 | 649 ctx | neighborhood:456 |
Rv1023 eno |
enolase | 592 | 592 | database:546 |
Rv1630 rpsA |
30S ribosomal protein S1 | 563 | 563 | coexpression:420 |
Rv2298 |
oxidoreductase | 546 | 547 | 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: tRNA/rRNA methyltransferase
- MTBC0 PGAP product: RNA methyltransferase
- Pfam (hmmscan --cut_ga): SpoU_methylase PF00588.25 (E=7e-32)
- (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_215396.1)
- 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
COG0566 - Curated reference: UniProt P9WFY3 (SwissProt, reviewed; Inferred from homology)
- 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 —
70 functional partner(s); context anchor
Rv0882 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000936|Rv0881| MTEGRCAQHPDGLDVQDVCDPDDPRLDDFRDLNSIDRRPDLPTGKALVIAEGVLVVQRMLASRFTPLALFGTDRRLAELKDDLAGVGAPYYRASADVMARVIGFHLNRGVLAAARRVPEPSVAQVVAGARTVAVLEGVNDHENLGSIFRNAAGLSVDAVVFGTGCADPLYRRAVRVSMGHALLVPYARAADWPTELMTLKESGFRLLAMTPHGNACKLPEAIAAVSHERIALLVGAEGPGLTAAALRISDVRVRIPMSRGTDSLNVATAAALAFYERTRSGHHIGPGT