Rv1313c Family assigned · medium auto-curated
H37Rv Rv1313c · MTBC0 mtbc0_000786 ·
107 aa · 836720–837043 (+) ·
RefSeq NP_215829.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | insertion sequence element IS1557 transposase |
|---|---|
| MTBC0 PGAP re-annotation | transposase |
| Revised (this work) | ISL3-like element IS1557 family transposase. Pfam: Zn_ribbon_ISL3 (PF14690.12), HTH_Tnp_ISL3 (PF13542.13), DDE_Tnp_ISL3 (PF01610.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKH7
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Transposase for insertion sequence element IS1557 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Transposase |
| Orthologous group | COG3464 |
| KEGG orthology |
K07485
|
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 | 0.687 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
Zn_ribbon_ISL3 | PF14690.12 | 8.4e-12 | 47–92 | zinc-finger of transposase IS204/IS1001/IS1096/IS1165 |
HTH_Tnp_ISL3 | PF13542.13 | 2.3e-12 | 98–147 | Helix-turn-helix domain of transposase family ISL3 |
DDE_Tnp_ISL3 | PF01610.24 | 6.3e-05 | 163–193 | Transposase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3428c (transposase), medium confidence from genomic context alone (score 476 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3798 |
insertion sequence element IS1557 transposase | 739 | 739 | coexpression:738 |
Rv3428c |
transposase | 475 | 476 ctx | cooccurence:464 |
Rv1314c |
cob(I)yrinic acid a,c-diamide adenosyltransferase | 469 | 469 ctx | neighborhood:467 |
Rv2737A |
Rv2737A, len: 57 aa. Conserved hypothetical cys-rich protein (possibly gene fragment), similar to central part of AJ243803_1|glgA from Strep | 425 | 426 ctx | cooccurence:419 |
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: insertion sequence element IS1557 transposase
- MTBC0 PGAP product: ISL3-like element IS1557 family transposase
- Pfam (hmmscan --cut_ga): Zn_ribbon_ISL3 PF14690.12 (E=8e-12), HTH_Tnp_ISL3 PF13542.13 (E=2e-12), DDE_Tnp_ISL3 PF01610.24 (E=6e-05)
- (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_215829.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zn_ribbon_ISL3 (PF14690.12), HTH_Tnp_ISL3 (PF13542.13), DDE_Tnp_ISL3 (PF01610.24)
- 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
COG3464 - Curated reference: UniProt P9WKH7 (SwissProt, reviewed; 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 —
4 functional partner(s); context anchor
Rv3428c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000786|Rv1313c| MRQVFSVKGEEGKQALDRWISWARRCRIPVFVELAGGIVRHRQAIDAALDHGLWQGLIESTNTKIRLLTRIAFGFRSPEALIALAMLALGGRRPALPGRTKHPRISQ