Rv3640c Family assigned · medium auto-curated
H37Rv Rv3640c · MTBC0 mtbc0_003855 ·
409 aa · 4102225–4103454 (-) ·
RefSeq NP_218157.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | IS256-like element IS1553 family transposase |
| Revised (this work) | IS256-like element IS1553 family transposase. Pfam: Transposase_mut (PF00872.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06367
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Mutator family transposase |
| Curated function | Required for the transposition of the insertion element. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Transposase, mutator |
| Orthologous group | COG3328 |
| KEGG orthology |
K07493
|
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 | 0.665 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (251) · 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 |
|---|---|---|---|---|
Transposase_mut | PF00872.25 | 1.6e-158 | 8–380 | Transposase, Mutator family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fic (cell filamentation protein Fic), medium confidence from genomic context alone (score 490 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3639c hyp |
hypothetical protein | 609 | 610 ctx | neighborhood:599 |
Rv3641c fic |
cell filamentation protein Fic | 490 | 490 ctx | neighborhood:488 |
Rv3642c hyp |
hypothetical protein | 489 | 488 ctx | neighborhood:485 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 429 | 132 | |
Rv1371 |
membrane protein | 569 | 89 | textmining:547 |
Rv2515c hyp |
hypothetical protein | 672 | 79 | textmining:659 |
Rv3842c glpQ1 |
glycerophosphoryl diester phosphodiesterase | 670 | 79 | textmining:657 |
Rv1372 pks18 |
alpha-pyrone synthesis polyketide synthase-like protein | 808 | 68 | textmining:803 |
Rv0795 |
Rv0795, (MTV042.05), len: 108 aa. Putative transposase for IS6110 (fragment), identical to Q50686 insertion element IS6110 (108 aa), FASTA s | 519 | 59 | textmining:510 |
Rv3728 |
membrane protein | 449 | 59 | textmining:439 |
Rv2480c |
Rv2480c, (MTV008.36c), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase s | 806 | 56 | textmining:803 |
Rv3727 |
oxidoreductase | 674 | 54 | textmining:670 |
Rv2265 |
integral membrane protein | 438 | 54 | textmining:431 |
Rv0796 |
Putative transposase for insertion sequence element IS6110; Involved in the transposition of the insertion sequence. | 440 | 52 | textmining:434 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 655 | 49 | textmining:653 |
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: IS256-like element IS1553 family transposase
- Pfam (hmmscan --cut_ga): Transposase_mut PF00872.25 (E=2e-158)
- (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_218157.1)
- Domains: Pfam-A via hmmscan --cut_ga — Transposase_mut (PF00872.25)
- 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
COG3328 - Curated reference: UniProt O06367 (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 —
17 functional partner(s); context anchor
fic - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003855|Rv3640c| MALPQSALSELLDAFRTGDGVDLIRDAVRLVLQELSELEATERIGAARYERSDTRVTDRNGARSRVLSTQAGDVELRIPKLRKGSFFPAILEPRRRIDQALYAVVMEAYVHGISTRAVDDLVEAMGVETGISKSEVSRICAGLDEIVGAFRTRTLGHIEFPYVYLDATYLNVRNGTGQVVSMAVIVASGIAADGSREILGLDVGDSEDETFWRGFLTSLKGRGLGGVRLVISDQHAGLVKALKRCFQGAGHQRCRVHFARNLLAHVPKDKADMVASMFRMIFSAPDAEAVHATWEEVRDRLAASFPKIGPLMDDARAEVLAFTAFPKAHWQKIWSTNPLERINKEIKRRSRVVGIFPNPAAVIRLVGAVLADMHDEWQASERRYLSEASMALLYPDSDNAVVAAISGGQ