Rv2944 Resolved · high auto-curated
H37Rv Rv2944 · MTBC0 - ·
238 aa · 3289790–3290506 (+) ·
RefSeq NP_217460.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | insertion sequence element IS1533 transposase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Insertion sequence element IS1533 transposase. Pfam: Bac_DnaA (PF00308.25), IstB_IS21 (PF01695.24). |
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 |
P96287
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible transposase for insertion sequence element IS1533 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | PFAM IstB-like ATP binding protein |
| Orthologous group | COG1484 |
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 | 0.344 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
Bac_DnaA | PF00308.25 | 5.8e-06 | 86–181 | Bacterial DnaA ATPAse domain |
IstB_IS21 | PF01695.24 | 4.8e-51 | 88–225 | IstB-like ATP binding protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2943A (transposase), high confidence from genomic context alone (score 982 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2943A |
transposase | 982 | 982 ctx | fusion:596 cooccurence:774 coexpression:822 |
Rv2943 |
insertion sequence element IS1533 transposase | 940 | 806 ctx | cooccurence:772 textmining:707 |
Rv0058 dnaB |
replicative DNA helicase | 815 | 799 | experimental:773 |
Rv3428c |
transposase | 804 | 797 ctx | cooccurence:772 |
Rv3637 |
Possible transposase; Rv3637, (MTCY15C10.15c), len: 166 aa. Possible transposase. C-terminal end highly similar to Q9RLQ9|ISTA putative tran | 746 | 737 ctx | cooccurence:712 |
Rv3636 |
Possible transposase; Rv3636, (MTCY15C10.16c), len: 115 aa. Possible transposase, weakly similar to others e.g. O69924|SC3C8.12 putative tra | 538 | 521 ctx | cooccurence:466 |
Rv0071 |
maturase | 445 | 440 ctx | cooccurence:436 |
Rv2948c fadD22 |
p-hydroxybenzoyl--AMP ligase | 516 | 51 | textmining:511 |
Rv2949c |
chorismate pyruvate-lyase | 655 | 47 | textmining:653 |
Rv2950c fadD29 |
long-chain-fatty-acid--AMP ligase FadD29 | 514 | 47 | textmining:511 |
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): insertion sequence element IS1533 transposase
- Pfam (hmmscan --cut_ga): Bac_DnaA PF00308.25 (E=6e-06), IstB_IS21 PF01695.24 (E=5e-51)
- (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_217460.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_DnaA (PF00308.25), IstB_IS21 (PF01695.24)
- 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
COG1484 - Curated reference: UniProt P96287 (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); context anchor
Rv2943A - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2944| MSQCPGWPIAPAPRTGATKNTWPPACSGKCQPGSPMVVRAASAPPASRLGSRWKSSTLSMLVASNATPSHIWAPWISSPPAITSCFWAPPGTGKTHLAVGLAIRACQAGHRVLFATAAEWVARLAEAHHAGRIYAELTRLCRYPLLVVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKAFGRWGEVFGGDDVVAAAMIDRLVHHAEVVALKGDSYRLKDRDLGRVPPAGTTEE