Rv3387 Resolved · high auto-curated
H37Rv Rv3387 · MTBC0 - ·
225 aa · 3800786–3801463 (+) ·
RefSeq NP_217904.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transposase. Pfam: DDE_Tnp_1 (PF01609.28). |
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 |
O50414
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible transposase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Transposase DDE domain |
| Orthologous group | COG3039 |
| KEGG orthology |
K07481
|
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 | 1.363 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 |
|---|---|---|---|---|
DDE_Tnp_1 | PF01609.28 | 2.9e-07 | 73–217 | Transposase DDE domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3386 (transposase), high confidence from genomic context alone (score 986 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3386 |
transposase | 985 | 986 ctx | neighborhood:882 fusion:494 cooccurence:774 |
Rv1495 mazF4 |
mRNA interferase MazF4 | 629 | 630 ctx | cooccurence:628 |
Rv0790c hyp |
hypothetical protein | 587 | 587 ctx | cooccurence:585 |
Rv0582 vapC26 |
ribonuclease VapC26 | 577 | 577 ctx | cooccurence:577 |
Rv1036c |
Rv1036c, (MTCY10G2.13), len: 112 aa. Probable IS1560 transposase fragment, similar to part of Rv3386|E1202304|MTV004.44 (234 aa) (82.8% iden | 543 | 543 ctx | fusion:540 |
Rv3385c vapB46 |
antitoxin VapB46 | 542 | 542 ctx | neighborhood:542 |
Rv3384c vapC46 |
ribonuclease VapC46 | 524 | 524 ctx | neighborhood:524 |
Rv2086 hyp |
hypothetical protein | 518 | 518 ctx | cooccurence:515 |
Rv0741 |
Probable transposase (fragment); Rv0741, (MTV041.15), len: 104 aa. Probable truncated transposase for IS1557, showing similarity to transpos | 458 | 459 ctx | cooccurence:458 |
Rv3388 PE_PGRS52 |
PE-PGRS family protein PE_PGRS52 | 452 | 452 ctx | neighborhood:452 |
Rv1246c relE |
toxin RelE | 439 | 440 ctx | cooccurence:436 |
Rv2549c vapC20 |
ribonuclease VapC20 | 439 | 439 ctx | cooccurence:439 |
Rv2014 |
Transposase; Rv2014, (MTCY39.03c), len: 196 aa. Transposase,similar to insertion elements; possibly made by frameshifting with respect to Rv | 430 | 430 ctx | cooccurence:418 |
Rv0071 |
maturase | 423 | 423 ctx | cooccurence:413 |
Rv2590 fadD9 |
fatty-acid--CoA ligase FadD9 | 415 | 416 ctx | cooccurence:415 |
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_1 PF01609.28 (E=3e-07)
- (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_217904.1)
- Domains: Pfam-A via hmmscan --cut_ga — DDE_Tnp_1 (PF01609.28)
- 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
COG3039 - Curated reference: UniProt O50414 (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 —
16 functional partner(s); context anchor
Rv3386 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3387| MVRNAQRAVRRASGRRKAWLRQAINHLEKLIGRTERVVDQARSRLAGVMPDSSSRLVSLHDADARPIRKGRLGKPVEFGYKAQVVDNADGVILDHSVELGNPADAPQLAPAIERISRRTGRPPRAVTADRGCGDASVEDDLHQLGVRNVAIPRKSKPSATRRAFEHRRAFRDKIKWRTGSEGRINHLKRSYGWNRTELTGITGARTWCGHGVFAHNLVKISTLAA