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Journal Article
invertiaDB: a database of inverted repeats across organismal genomes
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf329, https://doi.org/10.1093/nar/gkaf329
Published: 24 April 2025
Journal Article
Archaeal replicative primase mediates DNA double-strand break repair
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf322, https://doi.org/10.1093/nar/gkaf322
Published: 24 April 2025
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Cell-cycle dependence of the expression of priL and the response o...
Published: 24 April 2025
Figure 5.
Cell-cycle dependence of the expression of priL and the response of S. islandicus to DNA damage treatment. ( A ) Cell-cycle analysis. Strain E233S and CHI-ΔX were grown at 75°C with shaking to OD 600 of ∼0.2, and the growth of the cells was arrested in G2 by treatment with acetic acid (6 mM). F
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invertiaDB Homepage, navigation bar, and domain selection. ( A ) invertiaDB...
Published: 24 April 2025
Figure 1.
invertiaDB Homepage, navigation bar, and domain selection. ( A ) invertiaDB Homepage showing domains of life bar chart in decreasing order of IR density, and arm, spacer, and sequence length distribution in line charts. IR densities were calculated as the ratio of the total length of IR sequences to
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Assembly accession analysis page showing IR graphs, raw data tables, and ge...
Published: 24 April 2025
Figure 3.
Assembly accession analysis page showing IR graphs, raw data tables, and gene functionalities. ( A ) Line chart of length distribution of arm, spacer, and sequence along with nucleotide composition of arm, spacer, and sequence. ( B ) Table of IRs contained in the organism’s assembly with the ability
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Domain selection and domain analysis along with the organism search page an...
Published: 24 April 2025
Figure 4.
Domain selection and domain analysis along with the organism search page and aggregated analysis page. ( A ) Analysis of the Archaea domain, where each assembly is aggregated per organism along with metadata and the ability to download. ( B ) Search unique organisms to perform aggregated analysis on
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Motif search capabilities. Example of motif search in the left arm using a ...
Published: 24 April 2025
Figure 5.
Motif search capabilities. Example of motif search in the left arm using a single equality filter.
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The cryo-EM structure of S. coelicolor σShbA -RPo-h...
Published: 24 April 2025
Figure 1.
The cryo-EM structure of S. coelicolor σ ShbA -RPo- hrdB p1. ( A ) In vitro transcription assay verified the transcriptional activities of σ ShbA and σ HrdB on hrdB p1 and SCO1145 p, respectively. Mean fold-change values were compared using Student’s t -test. Error bars represent mean ± st
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Structural basis of σShbAR2 recognizing the −10 DNA element. ( A...
Published: 24 April 2025
Figure 3.
Structural basis of σ ShbA R2 recognizing the −10 DNA element. ( A ) Detailed interactions of σ ShbA R2 with the nontemplate strand at positions “−12” to “−4”. σ ShbA R2 is shown in purple, nontemplate DNA (NT) in green, and template DNA (T) in yellow. Hydrogen bonds are shown as dashed lines. ( B )
Journal Article
Molecular basis of Streptomyces ECF σShbA factors transcribing principal σHrdB genes
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf339, https://doi.org/10.1093/nar/gkaf339
Published: 24 April 2025
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Interactive visualizations of annotation results. Presented are genome anno...
Published: 24 April 2025
Figure 1.
Interactive visualizations of annotation results. Presented are genome annotation results of the Escherichia coli O157:H7 str. Sakai chromosome. ( A ) A circular genome plot, including tracks for CDS on the forward and reverse strand, non-coding features, GC-content percent, and GC-skew from outer
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Effect of MMS, NQO, and IR on the survival and mutation of PriL-kd, PriL-op...
Published: 24 April 2025
Figure 2.
Effect of MMS, NQO, and IR on the survival and mutation of PriL-kd, PriL-op, CHI-ΔX, and the parental strain. ( A ) Effect of MMS or NQO treatment on the survival of PriL-kd, PriL-op, CHI-ΔX, and E233S. Cells were grown with shaking at 75°C to an OD 600 of ∼0.3. After the addition of 2 μM NQO or 2
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Comparison of the activities of PriSLn-Xc, PriSLX, and PriSL. ( A ) PADT. R...
Published: 24 April 2025
Figure 4.
Comparison of the activities of PriSLn-Xc, PriSLX, and PriSL. ( A ) PADT. Reactions were performed by incubating PriSLn-Xc, PriSLX, or PriSL (1 μM) with oligonucleotide dT30dC5 (1 μM) and 10 μM rNTPs (2 μCi [α- 32 P] ATP) at 55°C (left panel) and 75°C (right panel) in the standard assay mixture. ( B
Journal Article
Bakta Web – rapid and standardized genome annotation on scalable infrastructures
Nucleic Acids Research, gkaf335, https://doi.org/10.1093/nar/gkaf335
Published: 24 April 2025
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Response of CHI-ΔX and the parental strain to treatment with DNA damaging a...
Published: 24 April 2025
Figure 1.
Response of CHI-ΔX and the parental strain to treatment with DNA damaging agents. ( A ) Growth curves of the E233S and CHI-ΔX following DNA damage treatment. Strain E233S and CHI-ΔX were grown with shaking at 75°C to an OD 600 of ∼0.25, and 2 μM NQO or 2 mM MMS was added, respectively. During furth
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Error-prone repair of DSBs by PriL in vivo. ( A ) Effect of plasmi...
Published: 24 April 2025
Figure 3.
Error-prone repair of DSBs by PriL in vivo . ( A ) Effect of plasmid-encoded primase subunits on the resistance of S. islandicus to endogenously generated DSBs. E233S cells were transformed by electroporation with plasmid pSe-Rp_DSB_PriS, pSe-Rp_DSB_PriL, pSe-Rp_DSB_PriX, or pSe-Rp_DSB_PriSL, and
