Rv3428c Resolved · high auto-curated
H37Rv Rv3428c · MTBC0 - ·
410 aa · 3844738–3845970 (-) ·
RefSeq NP_217945.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transposase. Pfam: rve (PF00665.33), Mu-transpos_C_2 (PF22483.3). |
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 |
Q50700
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative transposase Rv3428c |
UniProt still lists this protein as Putative transposase Rv3428c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | Integrase core domain |
| Orthologous group | COG4584 |
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.893 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 67.23% of strains (97630) · reference-fixed |
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 |
|---|---|---|---|---|
rve | PF00665.33 | 9.1e-12 | 61–158 | Integrase core domain |
Mu-transpos_C_2 | PF22483.3 | 1.5e-13 | 227–290 | Mu transposase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: istB (transposase), high confidence from genomic context alone (score 900 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3427c istB |
transposase | 986 | 900 ctx | neighborhood:547 cooccurence:774 textmining:875 |
Rv3638 |
transposase | 833 | 827 ctx | cooccurence:771 |
Rv2944 |
insertion sequence element IS1533 transposase | 804 | 797 ctx | cooccurence:772 |
Rv2943A |
transposase | 773 | 765 ctx | cooccurence:737 |
Rv2943 |
insertion sequence element IS1533 transposase | 710 | 711 ctx | cooccurence:708 |
Rv0071 |
maturase | 670 | 670 ctx | cooccurence:657 |
Rv3798 |
insertion sequence element IS1557 transposase | 477 | 477 ctx | cooccurence:464 |
Rv1313c |
insertion sequence element IS1557 transposase | 475 | 476 ctx | cooccurence:464 |
Rv2424c |
transposase | 463 | 464 ctx | cooccurence:454 |
Rv2177c |
transposase | 430 | 430 ctx | cooccurence:422 |
Rv1756c |
Putative transposase; Rv1756c, (MTCY28.22c), len: 328 aa. Putative Transposase subunit for IS6110. Identical to many other M. tuberculosis I | 519 | 55 | textmining:512 |
Rv3128c |
Rv3128c, (MTCY164.38c), len: 337 aa. Conserved hypothetical protein, similar to other conserved hypothetical proteins. This ORF corresponds | 697 | 54 | textmining:693 |
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 808 | 47 | textmining:807 |
Rv3127 hyp |
hypothetical protein | 659 | 46 | textmining:658 |
Rv3231c hyp |
hypothetical protein | 593 | 46 | textmining:591 |
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): rve PF00665.33 (E=9e-12), Mu-transpos_C_2 PF22483.3 (E=1e-13)
- (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_217945.1)
- Domains: Pfam-A via hmmscan --cut_ga — rve (PF00665.33), Mu-transpos_C_2 (PF22483.3)
- 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
COG4584 - Curated reference: UniProt Q50700 (SwissProt, reviewed; 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
istB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3428c| MATIAQRLRDDHGVAASESSVRRWIATHFAEEVARERVTVPRGPVDAGSEAQIDYGRLGMWFDPATARRVAVWAFVMVLAFSRHLFVRPVIRMDQTAWCACHVAAFEFFDGVPARLVCDNLRTGVDKPDLYDPQINRSYAELASHYATLVDPARARKPKDKPRVERPMTYVRDSFWKGREFDSLAQMQQAAVTWSTEVAGLRYLRALEGAQPLRMFEAVEQQALIALPPRAFELTSWSIGTVGVDTHLKVGKALYSVPWRLIGQRLHARTAGDVVQIFAGNDVVATHVRRPSGRSTDFSHYPPEKIAFHMRTPTWCRHTAELVGPASQQVIAEFMRDNAIHHLRSAQGVLGLRDKHGCDRLEAACARAIEVGDPSYRTIKGILVAGTEHAANEPTTSSPASTAGGVPARP