Rv3348 Resolved · high auto-curated
H37Rv Rv3348 · MTBC0 - ·
163 aa · 3753765–3754256 (+) ·
RefSeq NP_217865.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transposase. Pfam: DEDD_Tnp_IS110 (PF01548.24). |
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 |
P96234
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible transposase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | from Streptomyces clavuligerus (399 aa), FASTA scores opt 146, E() |
| Orthologous group | 2DW6Q |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
DEDD_Tnp_IS110 | PF01548.24 | 1.9e-15 | 14–160 | Transposase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3844 |
transposase | 836 | 836 | coexpression:836 |
Rv3475 |
Possible transposase for insertion element IS6110 [second part]; Rv3475, (MTCY13E12.28), len: 328 aa. Probable transposase subunit for IS611 | 818 | 107 | textmining:804 |
Rv0796 |
Putative transposase for insertion sequence element IS6110; Involved in the transposition of the insertion sequence. | 419 | 107 | |
Rv3474 |
Possible transposase for insertion element IS6110 (fragment); Rv3474, (MTCY13E12.27), len: 108 aa. Probable transposase subunit for IS6110. | 808 | 61 | textmining:804 |
Rv0795 |
Rv0795, (MTV042.05), len: 108 aa. Putative transposase for IS6110 (fragment), identical to Q50686 insertion element IS6110 (108 aa), FASTA s | 555 | 61 | textmining:546 |
Rv2354 |
Rv2354, (MTCY98.23), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase sub | 520 | 59 | textmining:511 |
Rv3349c |
transposase | 863 | 54 | textmining:862 |
Rv3346c |
transmembrane protein | 652 | 41 | textmining:652 |
Rv1396c PE_PGRS25 |
PE-PGRS family protein PE_PGRS25 | 627 | 41 | textmining:627 |
Rv3345c PE_PGRS50 |
PE-PGRS family protein PE_PGRS50 | 520 | 41 | textmining:520 |
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): DEDD_Tnp_IS110 PF01548.24 (E=2e-15)
- (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_217865.1)
- Domains: Pfam-A via hmmscan --cut_ga — DEDD_Tnp_IS110 (PF01548.24)
- 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
2DW6Q - Curated reference: UniProt P96234 (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 — 10 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3348| MTAENPGRSRRTLVGIDAAITACHHIAIRDDVGARSIRFSVEPTLAGLRTLTDKLSGYDDIDATVEPTSMTWLPLTIAVENAGDTMHMAGARHCARLRGAIVGKSKSDVIDAEVLTRASEVFDLTPLTLPTPAQLALRRSVIRRAGAVIDANRSWRRLMSLAR