tnpB Family assigned · medium auto-curated
H37Rv Rv0922 · MTBC0 mtbc0_000980 ·
550 aa · 1030900–1032552 (+) ·
RefSeq NP_215437.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | IS607 family element RNA-guided endonuclease TnpB |
| Revised (this work) | IS607 family element RNA-guided endonuclease TnpB. Pfam: OrfB_IS605 (PF01385.26), Cas12f1-like_TNB (PF07282.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y560
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Possible transposase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Transposase |
| Orthologous group | COG0675 |
| KEGG orthology |
K07496
|
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 | 2.839 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (223) · 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 |
|---|---|---|---|---|
OrfB_IS605 | PF01385.26 | 6.2e-28 | 271–396 | Probable transposase |
Cas12f1-like_TNB | PF07282.19 | 1.4e-06 | 417–484 | Cas12f1-like, TNB domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0921 (resolvase), high confidence from genomic context alone (score 958 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0921 |
resolvase | 959 | 958 ctx | neighborhood:801 cooccurence:772 |
Rv2792c |
resolvase | 795 | 789 ctx | cooccurence:772 |
Rv0605 |
IS1536 family serine type transposase | 791 | 786 ctx | cooccurence:772 |
Rv3828c |
resolvase | 791 | 786 ctx | cooccurence:772 |
Rv2979c |
resolvase | 791 | 786 ctx | cooccurence:772 |
Rv2886c |
resolvase | 786 | 781 ctx | cooccurence:772 |
Rv0920c |
transposase | 440 | 437 ctx | neighborhood:434 |
Rv2308 hyp |
hypothetical protein | 422 | 422 | experimental:417 |
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: transposase
- MTBC0 PGAP product: IS607 family element RNA-guided endonuclease TnpB
- Pfam (hmmscan --cut_ga): OrfB_IS605 PF01385.26 (E=6e-28), Cas12f1-like_TNB PF07282.19 (E=1e-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_215437.1)
- Domains: Pfam-A via hmmscan --cut_ga — OrfB_IS605 (PF01385.26), Cas12f1-like_TNB (PF07282.19)
- 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
COG0675 - Curated reference: UniProt I6Y560 (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 —
8 functional partner(s); context anchor
Rv0921 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000980|Rv0922|tnpB MIVRMRSCAQAAKVAEATGGVQLAGKPKPDGTPTFSRYVEIGVDFEAHRPVVESVSVLFELYDGDANSYAATGGPGAQLPSGWMVTAAKFEVEWPADPQRAGLVRSHFGARRKAFNWGLAQVKADLDAKAADPAHESVDWDLKSLRWAWNRAKDDVAPWWAENSKECYSSGLADLAQGLANWKAGKNGTRKGRRVGFPRFKSGRRDPGRVRFTTGTMRIEDDRRTITVPVIGPLRAKENTRRVQRHLVSGRAQILNMTLSQRWGRLFVAVCYALRTPTTRSPLTQPTVRAGMDLGVRTLATVATLDTATGEQTIIEYPNPAPLKATLVARRRAGRELSRRIPGSHGHRAVKAKLARLDRRCVHLRREAAHQLTTELAGTYGQVVIEDLDVAAMKRSMRRRAFRRSVSDAAMGLVAPQLAYKTAKCSGVLTVADRWFASSQIHHGCTSPDGTPCRLQGKGRIDKHLLCPVTGEVVDRDRNAALNLRDWPDNASRGPVGTTAPSAPGPTTTVGTGHGADTGSSGAGGASVRPRPRRAGRGEAKTQTPQGDAA