Rv0380c Resolved · high auto-curated
H37Rv Rv0380c · MTBC0 - ·
183 aa · 456268–456819 (-) ·
RefSeq NP_214894.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | RNA methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O53715
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible RNA methyltransferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | trmH |
| eggNOG description | tRNA rRNA methyltransferase, SpoU |
| Orthologous group | COG0566 |
| EC number |
EC 2.1.1.34
|
| KEGG orthology |
K00556
|
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 | 0.926 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 | 6.6e-25 | 34–170 | SpoU rRNA Methylase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pyrE (orotate phosphoribosyltransferase), high confidence from genomic context alone (score 776 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0381c hyp |
hypothetical protein | 775 | 776 ctx | neighborhood:776 |
Rv0382c pyrE |
orotate phosphoribosyltransferase | 775 | 776 ctx | neighborhood:765 |
Rv2420c rsfS hyp |
hypothetical protein | 780 | 771 | experimental:763 |
Rv3456c rplQ |
50S ribosomal protein L17 | 764 | 761 | experimental:739 |
Rv2442c rplU |
50S ribosomal protein L21 | 747 | 747 | experimental:739 |
Rv0723 rplO |
50S ribosomal protein L15 | 743 | 743 | experimental:732 |
Rv0383c ttfA hyp |
hypothetical protein | 718 | 719 ctx | neighborhood:706 |
Rv0640 rplK |
50S ribosomal protein L11 | 706 | 706 | experimental:696 |
Rv3443c rplM |
50S ribosomal protein L13 | 715 | 702 | experimental:687 |
Rv0715 rplX |
50S ribosomal protein L24 | 695 | 695 | experimental:676 |
Rv0701 rplC |
50S ribosomal protein L3 | 690 | 675 | experimental:664 |
Rv0384c clpB |
chaperone protein ClpB | 665 | 663 ctx | neighborhood:652 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 675 | 646 ctx | neighborhood:456 |
Rv1023 eno |
enolase | 589 | 590 | database:546 |
Rv3580c cysS1 |
cysteine--tRNA ligase | 585 | 560 | coexpression:414 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): RNA methyltransferase
- Pfam (hmmscan --cut_ga): SpoU_methylase PF00588.25 (E=7e-25)
- (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_214894.1)
- 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 O53715 (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 —
73 functional partner(s); context anchor
pyrE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0380c| MLLRDGDARNVVDAYRYWTREAIIADIDTRRHPLHVAIENFGHDANIGSVVRTANAFAVHTVHIVGRRRWNRRGAMVTDRYQRLCHHDSTTGLLEFAAGAGLTVVAVDNVPGAARLEQTALPRECLLLFGQEGPGITDDARAGAAVTVSIAQFGSTRSINAGVAAGIAMHAWIRQHADLGRAW