Rv1515c Family assigned · medium auto-curated
H37Rv Rv1515c · MTBC0 mtbc0_001622 ·
298 aa · 1716439–1717335 (-) ·
RefSeq NP_216031.1
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), Methyltransf_31 (PF13847.13), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71794
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methyltransferase type 11 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| eggNOG description | Methyltransferase domain |
| Orthologous group | COG2227 |
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 | 0.783 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
Methyltransf_23 | PF13489.13 | 2.6e-07 | 60–264 | Methyltransferase domain |
Methyltransf_31 | PF13847.13 | 8.1e-07 | 68–163 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 5.1e-08 | 75–161 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 1.4e-07 | 75–161 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1516c (sugar transferase), high confidence from genomic context alone (score 976 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) |
|---|---|---|---|---|
Rv1516c |
sugar transferase | 976 | 976 ctx | neighborhood:882 coexpression:806 |
Rv2357c glyS |
glycine--tRNA ligase | 793 | 794 | coexpression:793 |
Rv1514c |
glycosyltransferase | 787 | 787 ctx | neighborhood:712 |
Rv1518 hyp |
hypothetical protein | 404 | 401 ctx | neighborhood:401 |
Rv1432 |
dehydrogenase | 418 | 395 |
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), Methyltransf_31 PF13847.13 (E=8e-07), Methyltransf_11 PF08241.19 (E=5e-08), Methyltransf_25 PF13649.13 (E=1e-07)
- (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_216031.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), Methyltransf_31 (PF13847.13), Methyltransf_11 (PF08241.19), Methyltransf_25 (PF13649.13)
- 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
COG2227 - Curated reference: UniProt P71794 (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 —
5 functional partner(s); context anchor
Rv1516c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001622|Rv1515c| MSTNPGPAEGANQVMAQEHSAGAVQFTAHNVRLDDGTLTIPESSRTLDESSWFISARGILETVFPGDKSHLRLADVGCLEGGYAVGFARMGFQVLGIEVRELNMAACNYIKSKTNLPNLRFVHDNALNIANHGLFDTVFCCGLFYHLENPKQYLETLSSVTNKLLILQTHFSIINRSDKWLRLPTTARQLTDRLLRRPAPVKFMLSAPTEHEGLPGRWFTEFSDDRSFGQRDTAKWASWDNRRSFWIQREHLLQAIKDVGFDLVMEEYDNLEPSIAESLLGGSYAANLRGTFIGIKTR