Rv3832c Family assigned · medium auto-curated
H37Rv Rv3832c · MTBC0 mtbc0_004061 ·
191 aa · 4330346–4330921 (-) ·
RefSeq NP_218349.1
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), RrnaAD (PF00398.27), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13), 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 |
P96246
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Ribosomal RNA adenine dimethylase |
| 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 | 0.721 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 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 | 2.9e-07 | 33–136 | Methyltransferase domain |
RrnaAD | PF00398.27 | 5.7e-07 | 38–121 | Ribosomal RNA adenine dimethylase |
Methyltransf_11 | PF08241.19 | 2.9e-18 | 39–133 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 7.7e-16 | 39–130 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 1.2e-11 | 39–132 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3833 (AraC family transcriptional regulator), medium confidence from genomic context alone (score 691 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) |
|---|---|---|---|---|
Rv3833 |
AraC family transcriptional regulator | 702 | 691 ctx | neighborhood:573 |
Rv2590 fadD9 |
fatty-acid--CoA ligase FadD9 | 575 | 576 ctx | cooccurence:564 |
Rv2695 hyp |
hypothetical protein | 525 | 526 ctx | cooccurence:517 |
Rv3415c hyp |
hypothetical protein | 400 | 401 |
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=3e-07), RrnaAD PF00398.27 (E=6e-07), Methyltransf_11 PF08241.19 (E=3e-18), Methyltransf_25 PF13649.13 (E=8e-16), Methyltransf_12 PF08242.19 (E=1e-11)
- (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_218349.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), RrnaAD (PF00398.27), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13), 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 P96246 (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 —
4 functional partner(s); context anchor
Rv3833 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004061|Rv3832c| MAMNLLHRRHCSSAGWEKAVANQLLPWALQHVELGPRTLEIGPGYGATLQALLGLTASLTAVEVDNSMVERLNRRYGQRARIIRGDGTQTGLPDDHFTSVVCFTMLHHVASAQLQDQLFAEAYRVLQPGGVFAGSDGVPSLPFRLIHIADTYTPIAPADLPGRLRAVGFTDIHVDVAGARLRWRATKPVAA