tnpB Family assigned · medium auto-curated
H37Rv Rv2791c · MTBC0 mtbc0_002970 ·
459 aa · 3122617–3123996 (-) ·
RefSeq NP_217307.1
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). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33333
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 | 2.094 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 12 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 |
|---|---|---|---|---|
HTH_OrfB_IS605 | PF12323.15 | 2.3e-10 | 13–49 | Helix-turn-helix domain |
OrfB_IS605 | PF01385.26 | 2.6e-32 | 203–321 | Probable transposase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2792c (resolvase), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2792c |
resolvase | 995 | 996 ctx | neighborhood:882 cooccurence:761 coexpression:860 |
Rv2789c fadE21 |
acyl-CoA dehydrogenase FadE21 | 949 | 950 ctx | neighborhood:655 coexpression:860 |
Rv2979c |
resolvase | 937 | 935 ctx | cooccurence:761 coexpression:732 |
Rv0605 |
IS1536 family serine type transposase | 926 | 925 ctx | cooccurence:761 coexpression:687 |
Rv2790c ltp1 |
lipid-transfer protein | 921 | 921 ctx | neighborhood:721 coexpression:730 |
Rv2978c tnpB |
transposase | 821 | 821 | coexpression:820 |
Rv3828c |
resolvase | 820 | 815 ctx | cooccurence:759 |
Rv0185 hyp |
hypothetical protein | 791 | 791 | coexpression:791 |
Rv2885c |
transposase | 782 | 782 | coexpression:780 |
Rv0921 |
resolvase | 777 | 771 ctx | cooccurence:761 |
Rv2886c |
resolvase | 775 | 769 ctx | cooccurence:758 |
Rv0336 hyp |
hypothetical protein | 748 | 748 | coexpression:748 |
Rv3827c |
transposase | 746 | 746 | coexpression:744 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 734 | 734 | coexpression:732 |
Rv2977c thiL |
thiamine-monophosphate kinase | 732 | 732 | coexpression:731 |
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=2e-10), OrfB_IS605 PF01385.26 (E=3e-32)
- (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_217307.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_OrfB_IS605 (PF12323.15), OrfB_IS605 (PF01385.26)
- 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 O33333 (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
Rv2792c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002970|Rv2791c|tnpB MAKFEIPEGWMVQAFRFTLDPTAEQARALARHFGARRKAYNWTVATLKADIDAWQATGIQTAKPSLRVLRKRWNTVKNDVCVNIETGVVWWPECSKEAYADGIDGAVDAYWNWQNSRSGKRDGKRMGFPRFKKKGRDPDRVTFTTGAMRVEPDRRHLTLPVIGTVRTHENTRRVERLIAKGRSRVLAITVRRNGTRIDASVRVLVQRPQQPKVTDPGSRVGVDVGVRRLATVATADGAVLERVPNPRPLDAALNELRHVCRARSRCTKGSRRYRERTTEISRLHRRVNDVRTHHLHCLTTHLAKTHGRIVVEGLDAAGMLRQQGLSGARARRRGLSDAALGTPRRHLSYKTGWYGSQLVVADRWFPSSKTCHVCGHVQEIGWAEHWQCDSCSASHQRDDCAAINLARYEDTSSVVGPVGAAVKRGADRKTRPGRAGGREARKGSSRKAAEQPRDGVQVA