tnpB Family assigned · medium auto-curated
H37Rv Rv2978c · MTBC0 mtbc0_000636 ·
237 aa · 705568–706278 (+) ·
RefSeq NP_217494.1
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: HTH_OrfB_IS605 (PF12323.15), 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 |
I6Y263
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable 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 | 1.405 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.21% of strains (304) · 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 |
|---|---|---|---|---|
HTH_OrfB_IS605 | PF12323.15 | 3.4e-09 | 13–49 | Helix-turn-helix domain |
OrfB_IS605 | PF01385.26 | 5.4e-28 | 203–321 | Probable transposase |
Cas12f1-like_TNB | PF07282.19 | 2.5e-14 | 344–405 | Cas12f1-like, TNB domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2979c (resolvase), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2979c |
resolvase | 995 | 996 ctx | neighborhood:882 cooccurence:759 coexpression:859 |
Rv2977c thiL |
thiamine-monophosphate kinase | 978 | 978 ctx | neighborhood:882 coexpression:824 |
Rv0605 |
IS1536 family serine type transposase | 956 | 955 ctx | cooccurence:760 coexpression:815 |
Rv2792c |
resolvase | 940 | 939 ctx | cooccurence:760 coexpression:746 |
Rv2885c |
transposase | 861 | 861 | coexpression:860 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 854 | 854 | coexpression:853 |
Rv3828c |
resolvase | 843 | 839 ctx | cooccurence:758 |
Rv2791c tnpB |
transposase | 821 | 821 | coexpression:820 |
Rv3827c |
transposase | 801 | 801 | coexpression:799 |
Rv0185 hyp |
hypothetical protein | 778 | 778 | coexpression:778 |
Rv2886c |
resolvase | 777 | 771 ctx | cooccurence:757 |
Rv0921 |
resolvase | 777 | 771 ctx | cooccurence:760 |
Rv3585 radA |
DNA repair protein RadA | 738 | 738 | coexpression:738 |
Rv2737c recA |
recombinase A | 731 | 731 | coexpression:731 |
Rv2976c ung |
uracil-DNA glycosylase | 730 | 729 ctx | neighborhood:721 |
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): HTH_OrfB_IS605 PF12323.15 (E=3e-09), OrfB_IS605 PF01385.26 (E=5e-28), Cas12f1-like_TNB PF07282.19 (E=3e-14)
- (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_217494.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_OrfB_IS605 (PF12323.15), 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 I6Y263 (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 —
23 functional partner(s); context anchor
Rv2979c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000636|Rv2978c|tnpB MPRLEIPNGWCVQAFRFTLDPTAEQAHALARHFGARRKAYNWTVAQLKADIQAWRATGAQTAKPSLRVLRKRWNTVKDEVCVNAETGTVWWPECSKEAYADGIAGAVDAYWNWQQRRAGKRDGKRMGFPRFKKKGRDADRVSFTTGAMRVEPDRRHLTLPVIGCVRTHENTRRIERLIAKDRARVLAITVRRNGTRLDASVRVLVQRPQQPNVELPESRIGVDVGVRRLATVATADG