Rv3349c Resolved · high auto-curated
H37Rv Rv3349c · MTBC0 - ·
314 aa · 3754293–3755237 (-) ·
RefSeq NP_217866.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transposase. Pfam: DDE_Tnp_ISL3 (PF01610.24). |
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 |
V5QQS8
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable transposase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Transposase |
| Orthologous group | COG3464 |
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) pseudogene candidate
| pN/pS | 0.733 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 10.07% of strains (14626) · 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 |
|---|---|---|---|---|
DDE_Tnp_ISL3 | PF01610.24 | 2.4e-18 | 67–180 | Transposase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2810c (Probable transposase; Rv2810c, (MTCY16B7.33), len: 133 aa. Probable transposase for IS1555, similar to C-terminal domain of transposases for), high confidence from genomic context alone (score 750 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2810c |
Probable transposase; Rv2810c, (MTCY16B7.33), len: 133 aa. Probable transposase for IS1555, similar to C-terminal domain of transposases for | 750 | 750 ctx | cooccurence:747 |
Rv1978 hyp |
hypothetical protein | 628 | 629 ctx | cooccurence:627 |
Rv2086 hyp |
hypothetical protein | 622 | 623 ctx | cooccurence:617 |
Rv3786c hyp |
hypothetical protein | 611 | 611 ctx | cooccurence:608 |
Rv1435c hyp |
hypothetical protein | 598 | 598 ctx | cooccurence:597 |
Rv2311 hyp |
hypothetical protein | 593 | 594 ctx | cooccurence:589 |
Rv2812 |
transposase | 587 | 587 ctx | cooccurence:581 |
Rv2082 hyp |
hypothetical protein | 582 | 582 ctx | cooccurence:576 |
Rv3899c hyp |
hypothetical protein | 567 | 567 ctx | cooccurence:563 |
Rv3896c hyp |
hypothetical protein | 544 | 545 ctx | cooccurence:542 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 516 | 516 ctx | cooccurence:513 |
Rv0837c hyp |
hypothetical protein | 508 | 508 ctx | cooccurence:502 |
Rv0804 hyp |
hypothetical protein | 496 | 497 ctx | cooccurence:495 |
Rv2633c hyp |
hypothetical protein | 495 | 495 ctx | cooccurence:492 |
Rv2529 hyp |
hypothetical protein | 485 | 486 ctx | cooccurence:465 |
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): DDE_Tnp_ISL3 PF01610.24 (E=2e-18)
- (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_217866.2)
- Domains: Pfam-A via hmmscan --cut_ga — DDE_Tnp_ISL3 (PF01610.24)
- 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
COG3464 - Curated reference: UniProt V5QQS8 (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 —
40 functional partner(s); context anchor
Rv2810c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3349c| MTRHGEENPDGSAAPRLAGGYGSTRGIPGSSTWPVIRGLWGSMKAAAARRCWHGCKRAHRSSGRASSTVAIDPAAAYASAIRTPGLLPNAKLVVDHFHVTTLANDALTAVRRRVTWAFHDRRGRKIDPQWANRRRLLTARERLSDKSFAKMRNRINAVDPRAQILSAWIAKEELRTLLSTVRTGGDPHLARHHLHRFLPGASTRRSPNCSPWPPPLTSHPRSTPSWSPASPTRASVVGEVAEMLGDIDGQCVQVEVPVPERGPAGCGGLDGLGRAGVSATPRVCAAMTAVNVAGRCAGQQADVGPTPQHRCRGR