Rv3115 Resolved · high auto-curated
H37Rv Rv3115 · MTBC0 - ·
415 aa · 3481451–3482698 (+) ·
RefSeq NP_217631.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transposase. Pfam: Transposase_mut (PF00872.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P96354
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Mutator family transposase |
| Curated function | Required for the transposition of the insertion element. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Transposase, mutator |
| Orthologous group | COG3328 |
| KEGG orthology |
K07493
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
Transposase_mut | PF00872.25 | 1.2e-156 | 1–379 | Transposase, Mutator family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moeB2 (molybdenum cofactor biosynthesis protein MoeB), medium confidence from genomic context alone (score 558 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2512c |
insertion sequence element IS1081 transposase | 860 | 861 | coexpression:860 |
Rv1199c |
insertion sequence element IS1081 transposase | 860 | 861 | coexpression:860 |
Rv1047 |
transposase | 860 | 861 | coexpression:860 |
Rv3023c |
transposase | 839 | 840 | coexpression:839 |
Rv2666 |
Probable transposase for insertion sequence element IS1081 (fragment); Required for the transposition of the insertion element. | 803 | 803 | coexpression:802 |
Rv3116 moeB2 |
molybdenum cofactor biosynthesis protein MoeB | 558 | 558 ctx | neighborhood:558 |
Rv3118 sseC1 hyp |
hypothetical protein | 499 | 500 ctx | neighborhood:495 |
Rv3117 cysA3 |
thiosulfate sulfurtransferase | 498 | 498 ctx | neighborhood:495 |
Rv3114 hyp |
hypothetical protein | 467 | 467 ctx | neighborhood:467 |
Rv3120 hyp |
hypothetical protein | 460 | 461 ctx | neighborhood:459 |
Rv3119 moaE1 |
molybdopterin synthase catalytic subunit 1 | 459 | 459 ctx | neighborhood:459 |
Rv3113 |
phosphatase | 443 | 443 ctx | neighborhood:443 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transposase
- Pfam (hmmscan --cut_ga): Transposase_mut PF00872.25 (E=1e-156)
- (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_217631.1)
- Domains: Pfam-A via hmmscan --cut_ga — Transposase_mut (PF00872.25)
- 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
COG3328 - Curated reference: UniProt P96354 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
12 functional partner(s); context anchor
moeB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3115| MTSSHLIDAEQLLADQLAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERSNQRNGYRHRDFDTRAATIDVAIPKLRQGSYFPDWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGVTKLSKSQVSIMAKELDEAVEAFRTRPLDAGPYTFLAADALVLKVREAGRVVGVHTLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARGLSGVALVTSDAHAGLVAAIGATLPAAAWQRCRTHYAANLMAATPKPSWPWVRTLLHSIYDQPDAESVVAQYDRVLDALTDKLPAVAEHLDTARTDLLAFTAFPKQIWRQIWSNNPQERLNREVRRRTDVVGIFPDRASIIRLVGAVLAEQHDEWIEGRRYLGLEVLTRARAALTSTEEPAKQQTTNTPALTT