Rv2424c Resolved · high auto-curated
H37Rv Rv2424c · MTBC0 - ·
333 aa · 2720776–2721777 (-) ·
RefSeq NP_216940.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transposase. Pfam: Transposase_20 (PF02371.23). |
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 |
P71924
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable transposase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | transposase IS116 IS110 IS902 family |
| Orthologous group | COG3547 |
| KEGG orthology |
K07486
|
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) pseudogene candidate
| pN/pS | 0.797 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 9.91% of strains (14394) · clonal |
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_20 | PF02371.23 | 8.4e-22 | 169–255 | Transposase IS116/IS110/IS902 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0071 (maturase), medium confidence from genomic context alone (score 649 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2177c |
transposase | 775 | 776 | coexpression:774 |
Rv0071 |
maturase | 649 | 649 ctx | cooccurence:639 |
Rv2014 |
Transposase; Rv2014, (MTCY39.03c), len: 196 aa. Transposase,similar to insertion elements; possibly made by frameshifting with respect to Rv | 633 | 633 ctx | cooccurence:632 |
Rv2426c hyp |
hypothetical protein | 566 | 566 ctx | neighborhood:561 |
Rv2425c hyp |
hypothetical protein | 566 | 566 ctx | neighborhood:561 |
Rv2427c proA |
gamma-glutamyl phosphate reductase | 465 | 465 ctx | neighborhood:463 |
Rv3428c |
transposase | 463 | 464 ctx | cooccurence:454 |
Rv2966c rsmD |
methyltransferase | 407 | 407 |
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_20 PF02371.23 (E=8e-22)
- (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_216940.1)
- Domains: Pfam-A via hmmscan --cut_ga — Transposase_20 (PF02371.23)
- 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
COG3547 - Curated reference: UniProt P71924 (TrEMBL, unreviewed; 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 —
8 functional partner(s); context anchor
Rv0071 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2424c| MQCRAREERPGRKTDLLDAEWLVHLLECGLLRGWLIPPADIKAARDVIRYRRKLVEHRTSKLQRLGNVLQDAGIKADSVASSVTPKSVRAMVEALIDGERRPAVLADLARGSMRSKIPDLQRALEGRFDDHHALMCRLHLAHLDQLDAMIGALDEQIEQLMHPFCARRELIASIPGIGVGASATVISEIGADPAAWFPSAEHLASWVRLCPGNHESAGKRHHGARRTGNQHLQPVLVECAWAAVRTDGYLREYYRRQVRKFGGFRSPAANKKAITTVAHKLIVIIWHVLATGRPHQDLGADYFTTRMDPDKERRRLVAKLEAQGLGVTLEPAA