Rv3120 Resolved · high auto-curated
H37Rv Rv3120 · MTBC0 mtbc0_003316 ·
200 aa · 3506937–3507539 (+) ·
RefSeq NP_217636.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | class I SAM-dependent methyltransferase |
| Revised (this work) | Class I SAM-dependent methyltransferase. Pfam: Methyltransf_25 (PF13649.13), 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 |
O05796
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methyltransferase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| eggNOG description | methyltransferase |
| Orthologous group | COG2890 |
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 | 1.816 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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_25 | PF13649.13 | 1.8e-10 | 51–140 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 8.2e-06 | 52–140 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moaE1 (molybdopterin synthase catalytic subunit 1), high confidence from genomic context alone (score 958 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) |
|---|---|---|---|---|
Rv3119 moaE1 |
molybdopterin synthase catalytic subunit 1 | 958 | 958 ctx | neighborhood:801 coexpression:798 |
Rv3118 sseC1 hyp |
hypothetical protein | 722 | 721 ctx | neighborhood:716 |
Rv3117 cysA3 |
thiosulfate sulfurtransferase | 716 | 716 ctx | neighborhood:714 |
Rv3116 moeB2 |
molybdenum cofactor biosynthesis protein MoeB | 671 | 659 ctx | neighborhood:636 |
Rv3115 |
transposase | 460 | 461 ctx | neighborhood:459 |
Rv3718c hyp |
hypothetical protein | 458 | 459 ctx | cooccurence:451 |
Rv3121 cyp141 |
cytochrome P450 Cyp141 | 431 | 431 ctx | neighborhood:406 |
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: class I SAM-dependent methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_25 PF13649.13 (E=2e-10), Methyltransf_11 PF08241.19 (E=8e-06)
- (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_217636.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_25 (PF13649.13), 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
COG2890 - Curated reference: UniProt O05796 (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 —
7 functional partner(s); context anchor
moaE1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003316|Rv3120| MSPSPSALLADHPDRIRWNAKYECADPTEAVFAPISWLGDVLQFGVPEGPVLELACGRSGTALGLAAAGRCVTAIDVSDTALVQLELEATRRELADRLTLVHADLCSWQSGDGRFALVLCRLFWHPPTFRQACEAVAPGGVVAWEAWRRPIDVARDTRRAEWCLKPGQPESELPAGFTVIRVVDTDGSEPSRRIIAQRSL