dnaB Resolved · high auto-curated
H37Rv Rv0058 · MTBC0 mtbc0_000063 ·
874 aa · 60504–63128 (+) ·
RefSeq NP_214572.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | replicative DNA helicase |
|---|---|
| MTBC0 PGAP re-annotation | replicative DNA helicase |
| Revised (this work) | Replicative DNA helicase. Pfam: DnaB (PF00772.27), DnaB_C (PF03796.22), AAA_25 (PF13481.13), Intein_splicing (PF14890.12), LAGLIDADG_3 (PF14528.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMR3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Replicative DNA helicase DnaB |
| EC (curated) |
EC 3.1.-.-, EC 5.6.2.3
|
| Curated function | The main replicative DNA helicase, it participates in initiation and elongation during chromosome replication. Travels ahead of the DNA replisome, separating dsDNA into templates for DNA synthesis. A 5'-3' DNA helicase with DNA-dependent ATPase activity; helicase is equally active with ATP and dATP. Requires single-stranded (ss)DNA for helicase activity..; FUNCTION: The intein is an endonuclease. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | dnaB |
| eggNOG description | Participates in initiation and elongation during chromosome replication |
| Orthologous group | COG0305 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K02314
|
| KEGG pathways |
map03030, map04112
|
| Gene Ontology (58) |
GO:0003674, GO:0003678, GO:0003824, GO:0004386, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139, GO:0006259 +46 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 | 0.294 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 7 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 |
|---|---|---|---|---|
DnaB | PF00772.27 | 6.7e-34 | 23–125 | DnaB-like helicase N terminal domain |
DnaB_C | PF03796.22 | 3.3e-94 | 201–871 | DnaB-like helicase C terminal domain |
AAA_25 | PF13481.13 | 8.4e-16 | 201–379 | AAA domain |
Intein_splicing | PF14890.12 | 6.3e-18 | 410–815 | Intein splicing domain |
LAGLIDADG_3 | PF14528.12 | 1.6e-20 | 611–694 | LAGLIDADG-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ssb (single-strand DNA-binding protein), high confidence from genomic context alone (score 856 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2343c dnaG |
DNA primase | 995 | 983 | experimental:916 database:540 textmining:735 |
Rv0057 hyp |
hypothetical protein | 943 | 889 ctx | neighborhood:882 textmining:511 |
Rv0059 darT hyp |
hypothetical protein | 856 | 857 ctx | neighborhood:485 coexpression:733 |
Rv0054 ssb |
single-strand DNA-binding protein | 893 | 856 ctx | neighborhood:554 experimental:621 |
Rv0056 rplI |
50S ribosomal protein L9 | 831 | 803 ctx | neighborhood:738 |
Rv2943A |
transposase | 816 | 799 | experimental:773 |
Rv2944 |
insertion sequence element IS1533 transposase | 815 | 799 | experimental:773 |
Rv3427c istB |
transposase | 815 | 798 | experimental:773 |
Rv3638 |
transposase | 814 | 797 | experimental:773 |
Rv0001 dnaA |
chromosomal replication initiator protein DnaA | 959 | 796 | experimental:785 textmining:812 |
Rv3202c adnA |
ATP-dependent DNA helicase | 841 | 746 | coexpression:415 textmining:403 |
Rv0055 rpsR1 |
30S ribosomal protein S18 | 713 | 701 ctx | neighborhood:637 |
Rv3201c adnB |
ATP-dependent DNA helicase | 753 | 670 | coexpression:406 |
Rv1629 polA |
DNA polymerase I | 932 | 643 ctx | neighborhood:473 textmining:820 |
Rv0685 tuf |
elongation factor Tu | 663 | 629 | experimental:614 |
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: replicative DNA helicase
- MTBC0 PGAP product: replicative DNA helicase
- Pfam (hmmscan --cut_ga): DnaB PF00772.27 (E=7e-34), DnaB_C PF03796.22 (E=3e-94), AAA_25 PF13481.13 (E=8e-16), Intein_splicing PF14890.12 (E=6e-18), LAGLIDADG_3 PF14528.12 (E=2e-20)
- (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_214572.1)
- Domains: Pfam-A via hmmscan --cut_ga — DnaB (PF00772.27), DnaB_C (PF03796.22), AAA_25 (PF13481.13), Intein_splicing (PF14890.12), LAGLIDADG_3 (PF14528.12)
- 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
COG0305 - Curated reference: UniProt P9WMR3 (SwissProt, reviewed; Evidence at protein level)
- 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 —
95 functional partner(s); context anchor
ssb - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000063|Rv0058|dnaB MAVVDDLAPGMDSSPPSEDYGRQPPQDLAAEQSVLGGMLLSKDAIADVLERLRPGDFYRPAHQNVYDAILDLYGRGEPADAVTVAAELDRRGLLRRIGGAPYLHTLISTVPTAANAGYYASIVAEKALLRRLVEAGTRVVQYGYAGAEGADVAEVVDRAQAEIYDVADRRLSEDFVALEDLLQPTMDEIDAIASSGGLARGVATGFTELDEVTNGLHPGQMVIVAARPGVGKSTLGLDFMRSCSIRHRMASVIFSLEMSKSEIVMRLLSAEAKIKLSDMRSGRMSDDDWTRLARRMSEISEAPLFIDDSPNLTMMEIRAKARRLRQKANLKLIVVDYLQLMTSGKKYESRQVEVSEFSRHLKLLAKELEVPVVAISQLNRGPEQRTDKKPMLADLRESGCLTASTRILRADTGAEVAFGELMRSGERPMVWSLDERLRMVARPMINVFPSGRKEVFRLRLASGREVEATGSHPFMKFEGWTPLAQLKVGDRIAAPRRVPEPIDTQRMPESELISLARMIGDGSCLKNQPIRYEPVDEANLAAVTVSAAHSDGAAIRDDYLAARVPSLRPARQRLPRGRCTPIAAWLAGLGLFTKRSHEKCVPEAVFRAPNDQVALFLRHLWSAGGSVRWDPTNGQGRVYYGSTSRRLIDDVAQLLLRVGIFSWITHAPKLGGHDSWRLHIHGAKDQVRFLRHVGVHGAEAVAAQEMLRQLKGPVRNPNLDSAPKKVWAQVRNRLSAKQMMDIQLHEPTMWKHSPSRSRPHRAEARIEDRAIHELARGDAYWDTVVEITSIGDQHVFDGTVSGTHNFVANGISLHNSLEQDADVVILLHRPDAFDRDDPRGGEADFILAKHRNGPTKTVTVAHQLHLSRFANMAR