Rv0839 Family assigned · medium auto-curated
H37Rv Rv0839 · MTBC0 mtbc0_000894 ·
270 aa · 938728–939540 (+) ·
RefSeq NP_215354.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | methyltransferase domain-containing protein |
| Revised (this work) | Methyltransferase domain-containing protein. Pfam: Methyltransf_23 (PF13489.13), PCMT (PF01135.26), MetW (PF07021.19), Methyltransf_31 (PF13847.13), Ubie_methyltran (PF01209.25), MTS (PF05175.21), NodS (PF05401.17), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X9X6
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methyltransferase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Methionine biosynthesis protein MetW |
| Orthologous group | COG0500 |
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 | 0.356 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Methyltransf_23 | PF13489.13 | 9.5e-20 | 19–195 | Methyltransferase domain |
PCMT | PF01135.26 | 5.5e-04 | 33–112 | Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) |
MetW | PF07021.19 | 8.6e-08 | 36–135 | Methionine biosynthesis protein MetW |
Methyltransf_31 | PF13847.13 | 2.7e-28 | 39–146 | Methyltransferase domain |
Ubie_methyltran | PF01209.25 | 9.7e-15 | 39–141 | ubiE/COQ5 methyltransferase family |
MTS | PF05175.21 | 2.0e-06 | 42–111 | Methyltransferase small domain |
NodS | PF05401.17 | 1.7e-05 | 42–128 | Nodulation protein S (NodS) |
Methyltransf_25 | PF13649.13 | 1.7e-23 | 43–138 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 1.6e-24 | 44–141 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 9.4e-19 | 44–140 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqR (lipoprotein LpqR), high confidence from genomic context alone (score 781 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0838 lpqR |
lipoprotein LpqR | 781 | 781 ctx | neighborhood:780 |
Rv1832 gcvB |
glycine dehydrogenase | 738 | 725 ctx | fusion:716 |
Rv1405c |
methyltransferase | 415 | 416 ctx | cooccurence:415 |
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: hypothetical protein
- MTBC0 PGAP product: methyltransferase domain-containing protein
- Pfam (hmmscan --cut_ga): Methyltransf_23 PF13489.13 (E=1e-19), PCMT PF01135.26 (E=6e-04), MetW PF07021.19 (E=9e-08), Methyltransf_31 PF13847.13 (E=3e-28), Ubie_methyltran PF01209.25 (E=1e-14), MTS PF05175.21 (E=2e-06), NodS PF05401.17 (E=2e-05), Methyltransf_25 PF13649.13 (E=2e-23), Methyltransf_11 PF08241.19 (E=2e-24), Methyltransf_12 PF08242.19 (E=9e-19)
- (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_215354.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), PCMT (PF01135.26), MetW (PF07021.19), Methyltransf_31 (PF13847.13), Ubie_methyltran (PF01209.25), MTS (PF05175.21), NodS (PF05401.17), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19)
- 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
COG0500 - Curated reference: UniProt I6X9X6 (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 —
3 functional partner(s); context anchor
lpqR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000894|Rv0839| MNDKRRAIYTHGYHESVLRSHRRRTAENSAGYLLPYLVPGLSVLDVGCGPGTITVDLAARVVPGSVTGVEPTDDALSLARAEAQLHRLSNISFTTSDVHKLDFPDDAFDVVHAHQVLQHVADPVRALQEMRRVCTPGGIVAARDADYSGFIWFPKLPALDRWLDLYERAARANGGEPDAGRRLLSWARAAGFDDVTPTASVWCFATASAREWWGLVWADRILQSDLAHQLVDSGLATAAQLEEISTAWREWAAAPDGWLAIPHGEILCRA