Rv3827c Resolved · high auto-curated
H37Rv Rv3827c · MTBC0 - ·
408 aa · 4301563–4302789 (-) ·
RefSeq NP_218344.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transposase. 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.
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 |
O07796
TrEMBL · unreviewed
· Predicted
|
|---|---|
| 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 | 0.725 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 9 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (164) · 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 | 2.3e-10 | 14–50 | Helix-turn-helix domain |
OrfB_IS605 | PF01385.26 | 3.6e-32 | 204–322 | Probable transposase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3828c (resolvase), high confidence from genomic context alone (score 978 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3828c |
resolvase | 978 | 978 ctx | neighborhood:882 cooccurence:761 |
Rv0605 |
IS1536 family serine type transposase | 952 | 952 ctx | cooccurence:762 coexpression:798 |
Rv2979c |
resolvase | 937 | 936 ctx | cooccurence:762 coexpression:732 |
Rv2792c |
resolvase | 866 | 862 ctx | cooccurence:763 coexpression:423 |
Rv2885c |
transposase | 801 | 801 | coexpression:799 |
Rv2978c tnpB |
transposase | 801 | 801 | coexpression:799 |
Rv2886c |
resolvase | 780 | 775 ctx | cooccurence:760 |
Rv3829c |
dehydrogenase | 775 | 774 ctx | neighborhood:773 |
Rv0921 |
resolvase | 778 | 773 ctx | cooccurence:762 |
Rv0606 |
Possible transposase (fragment); Rv0606, (MTCY19H5.16c), len: 247 aa. Possible truncated transposase for IS_1536 element, highly similar to | 769 | 769 | coexpression:767 |
Rv2791c tnpB |
transposase | 746 | 746 | coexpression:744 |
Rv3830c |
TetR family transcriptional regulator | 628 | 627 ctx | neighborhood:625 |
Rv1006 hyp |
hypothetical protein | 505 | 505 ctx | cooccurence:500 |
Rv3831 hyp |
hypothetical protein | 459 | 459 ctx | neighborhood:457 |
Rv1868 hyp |
hypothetical protein | 447 | 447 ctx | cooccurence:447 |
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): HTH_OrfB_IS605 PF12323.15 (E=2e-10), OrfB_IS605 PF01385.26 (E=4e-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_218344.1)
- 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 O07796 (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 —
17 functional partner(s); context anchor
Rv3828c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3827c| MMARFEVPEGWCVQAFRFTLDPTEDQARALARHFGARRKAYNWAVATLKADIEAWRVTGIGTVKPSLRVLRKRWNTVKDEVCVNAETGAVWWPECSKEAYADGIGGAVDAYWNWQNSRSGKREGKTMGFPRFKKKGRDQDRVTFTTGAMRVEPDRRHLTLPVVGTVRTHENTRRIERLIATGRARVLAISVRRNGTRLDASVRVLVQRPQQPNVAQPGSRVGVDVGVRRLATVANEAGAVLEEVPNPRPLDTALKELRYASRARSRCTKGSRRYRERTTEISRLHRRVNDVRTHHLHVLTTRLAQTHGHIVVEGLDAAGMLRQKGLPGARARRRGLSDSALGTPRRHLSYKTGWYGSALVVADRWFPSLSVEPTVRPGLARLVAVKRGREAAAWLPNNPETGCKSRDH