istB Family assigned · medium auto-curated
H37Rv Rv3427c · MTBC0 mtbc0_003642 ·
251 aa · 3869323–3870078 (-) ·
RefSeq NP_217944.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transposase |
|---|---|
| MTBC0 PGAP re-annotation | IS21-like element ISMt2 family helper ATPase IstB |
| Revised (this work) | IS21-like element ISMt2 family helper ATPase IstB. Pfam: IstB_IS21 (PF01695.24), Bac_DnaA (PF00308.25), AAA (PF00004.36). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q50701
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative ATP-binding protein Rv3427c in insertion sequence |
UniProt still lists this protein as Putative ATP-binding protein Rv3427c in insertion sequence; 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 | IstB-like ATP binding protein |
| Orthologous group | COG1484 |
| Gene Ontology (35) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006139, GO:0006259, GO:0006260, GO:0006261, GO:0006271, GO:0006725, GO:0006807 +23 more
|
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, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (181) · clonal |
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 |
|---|---|---|---|---|
IstB_IS21 | PF01695.24 | 3.3e-50 | 12–245 | IstB-like ATP binding protein |
Bac_DnaA | PF00308.25 | 1.2e-07 | 71–208 | Bacterial DnaA ATPAse domain |
AAA | PF00004.36 | 3.2e-04 | 104–204 | ATPase family associated with various cellular activities (AAA) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3428c (transposase), high confidence from genomic context alone (score 900 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3428c |
transposase | 986 | 900 ctx | neighborhood:547 cooccurence:774 textmining:875 |
Rv0058 dnaB |
replicative DNA helicase | 815 | 798 | experimental:773 |
Rv2943 |
insertion sequence element IS1533 transposase | 790 | 783 ctx | cooccurence:762 |
Rv2943A |
transposase | 773 | 773 ctx | cooccurence:772 |
Rv0071 |
maturase | 590 | 587 ctx | cooccurence:585 |
Rv3637 |
Possible transposase; Rv3637, (MTCY15C10.15c), len: 166 aa. Possible transposase. C-terminal end highly similar to Q9RLQ9|ISTA putative tran | 600 | 585 ctx | cooccurence:546 |
Rv3127 hyp |
hypothetical protein | 663 | 71 | textmining:653 |
Rv1756c |
Putative transposase; Rv1756c, (MTCY28.22c), len: 328 aa. Putative Transposase subunit for IS6110. Identical to many other M. tuberculosis I | 452 | 65 | textmining:439 |
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 804 | 49 | textmining:803 |
Rv3193c |
transmembrane protein | 658 | 47 | textmining:656 |
Rv3231c hyp |
hypothetical protein | 536 | 47 | textmining:534 |
Rv3128c |
Rv3128c, (MTCY164.38c), len: 337 aa. Conserved hypothetical protein, similar to other conserved hypothetical proteins. This ORF corresponds | 870 | 46 | 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
- Legacy H37Rv annotation: transposase
- MTBC0 PGAP product: IS21-like element ISMt2 family helper ATPase IstB
- Pfam (hmmscan --cut_ga): IstB_IS21 PF01695.24 (E=3e-50), Bac_DnaA PF00308.25 (E=1e-07), AAA PF00004.36 (E=3e-04)
- (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_217944.1)
- Domains: Pfam-A via hmmscan --cut_ga — IstB_IS21 (PF01695.24), Bac_DnaA (PF00308.25), AAA (PF00004.36)
- 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 Q50701 (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 —
12 functional partner(s); context anchor
Rv3428c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003642|Rv3427c|istB MSICDPALRNALRTLKLSGMLDTLDARLAQTRNGDLGHLEFLQALREDEIARRESAALTRRLRRAKFEAQATFEDFDFTANPKLPGAMLRDLAALRWLDAGESVILHGPVGVGKTHVAQALVHAVARRGGDVRFAKTSRMLSDLAGGHADRSWGQRIREYTKPLVLILDDFAMREHTAMHADDLYELISDRAITGKPLILTSNRAPNNWYGLFPNPVVAESLLDRLINTSHQILMDGPSYRPRKRPGRTTS