Rv3023c Resolved · high auto-curated
H37Rv Rv3023c · MTBC0 - ·
415 aa · 3381375–3382622 (-) ·
RefSeq NP_217539.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 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.
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 |
P96354
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 | 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 |
|---|---|---|---|---|
Transposase_mut | PF00872.25 | 1.2e-156 | 1–379 | Transposase, Mutator family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: iscS (cysteine desulfurase), medium confidence from genomic context alone (score 475 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1047 |
transposase | 852 | 853 | coexpression:852 |
Rv2512c |
insertion sequence element IS1081 transposase | 845 | 846 | coexpression:845 |
Rv1199c |
insertion sequence element IS1081 transposase | 841 | 842 | coexpression:841 |
Rv3115 |
transposase | 839 | 840 | coexpression:839 |
Rv2666 |
Probable transposase for insertion sequence element IS1081 (fragment); Required for the transposition of the insertion element. | 818 | 818 | coexpression:817 |
Rv3025c iscS |
cysteine desulfurase | 475 | 475 ctx | neighborhood:468 |
Rv3024c trmU |
tRNA-specific 2-thiouridylase | 473 | 473 ctx | neighborhood:468 |
Rv0277c vapC25 |
ribonuclease VapC25 | 553 | 54 | textmining:547 |
Rv0617 vapC29 |
ribonuclease VapC29 | 517 | 47 | textmining:514 |
Rv3531c hyp |
hypothetical protein | 870 | 44 | textmining:870 |
Rv3530c |
oxidoreductase | 870 | 41 | textmining:870 |
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): Transposase_mut PF00872.25 (E=1e-156)
- (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_217539.1)
- 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 P96354 (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 —
11 functional partner(s); context anchor
iscS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3023c| MTSSHLIDAEQLLADQLAQASPDLLRGLLSTFIAALMGAEADALCGAGYRERSDERSNQRNGYRHRDFDTRAATIDVAIPKLRQGSYFPDWLLQRRKRAERALTSVVATCYLLGVSTRRMERLVETLGVTKLSKSQVSIMAKELDEAVEAFRTRPLDAGPYTFLAADALVLKVREAGRVVGVHTLIATGVNAEGYREILGIQVTSAEDGAGWLAFFRDLVARGLSGVALVTSDAHAGLVAAIGATLPAAAWQRCRTHYAANLMAATPKPSWPWVRTLLHSIYDQPDAESVVAQYDRVLDALTDKLPAVAEHLDTARTDLLAFTAFPKQIWRQIWSNNPQERLNREVRRRTDVVGIFPDRASIIRLVGAVLAEQHDEWIEGRRYLGLEVLTRARAALTSTEEPAKQQTTNTPALTT