Rv1509 Family assigned · medium auto-curated
H37Rv Rv1509 · MTBC0 mtbc0_001615 ·
293 aa · 1710021–1710902 (+) ·
RefSeq NP_216025.1
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_11 (PF08241.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLW3
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv1509 |
UniProt still lists this protein as Uncharacterized protein Rv1509; the revised annotation above is ahead of the current UniProt record.
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 | 0.804 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 5 frameshift |
| Disruption | 5 distinct premature-stop/frameshift site(s); most common in 0.64% of strains (929) · convergent |
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 | 1.0e-08 | 45–160 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 6.8e-07 | 65–160 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1508c (membrane protein), medium confidence from genomic context alone (score 577 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) |
|---|---|---|---|---|
Rv1508A hyp |
hypothetical protein | 971 | 833 ctx | neighborhood:780 textmining:835 |
Rv1508c |
membrane protein | 577 | 577 ctx | neighborhood:572 |
Rv1510 hyp |
hypothetical protein | 811 | 469 ctx | neighborhood:461 textmining:660 |
Rv1507c hyp |
hypothetical protein | 708 | 200 | textmining:651 |
Rv1503c |
Rv1503c, (MTCY277.25c), len: 182 aa. Conserved hypothetical protein, similar to C-terminal region of P27833|RFFA_ECOLI lipopolysaccharide bi | 497 | 114 | textmining:456 |
Rv1511 gmdA |
GDP-D-mannose dehydratase GmdA | 870 | 82 | textmining:865 |
Rv3915 cwlM |
peptidoglycan hydrolase | 460 | 82 | textmining:437 |
Rv3717 hyp |
hypothetical protein | 456 | 69 | textmining:440 |
Rv1493 mutB |
methylmalonyl-CoA mutase large subunit | 443 | 55 | textmining:435 |
Rv3594 hyp |
hypothetical protein | 659 | 50 | textmining:656 |
Rv1521 fadD25 |
fatty-acid--CoA ligase FadD25 | 870 | 49 | textmining:869 |
Rv1495 mazF4 |
mRNA interferase MazF4 | 549 | 46 | textmining:547 |
Rv1494 mazE4 |
antitoxin MazE4 | 631 | 45 | textmining:630 |
Rv3679 |
anion transporter ATPase | 870 | 44 | textmining:870 |
Rv2370c hyp |
hypothetical protein | 870 | 44 | textmining:870 |
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-08), Methyltransf_11 PF08241.19 (E=7e-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_216025.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), Methyltransf_11 (PF08241.19)
- 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
COG2227 - Curated reference: UniProt P9WLW3 (SwissProt, reviewed; Predicted)
- 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 —
17 functional partner(s); context anchor
Rv1508c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001615|Rv1509| MFALSNNLNRVNACMDGFLARIRSHVDAHAPELRSLFDTMAAEARFARDWLSEDLARLPVGAALLEVGGGVLLLSCQLAAEGFDITAIEPTGEGFGKFRQLGDIVLELAAARPTIAPCKAEDFISEKRFDFAFSLNVMEHIDLPDEAVRRVSEVLKPGASYHFLCPNYVFPYEPHFNIPTFFTKELTCRVMRHRIEGNTGMDDPKGVWRSLNWITVPKVKRFAAKDATLTLRFHRAMLVWMLERALTDKEFAGRRAQWMVAAIRSAVKLRVHHLAGYVPATLQPIMDVRLTKR