REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
TLDR
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems that contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data.Abstract:
REBASE is a comprehensive and fully curated database of information about the components of restriction-modification (RM) systems. It contains fully referenced information about recognition and cleavage sites for both restriction enzymes and methyltransferases as well as commercial availability, methylation sensitivity, crystal and sequence data. All genomes that are completely sequenced are analyzed for RM system components, and with the advent of PacBio sequencing, the recognition sequences of DNA methyltransferases (MTases) are appearing rapidly. Thus, Type I and Type III systems can now be characterized in terms of recognition specificity merely by DNA sequencing. The contents of REBASE may be browsed from the web http://rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.read more
Citations
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Journal ArticleDOI
Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing.
Daniel Wibberg,Andreas Bremges,Tanja Dammann-Kalinowski,Irena Maus,María Isabel Igeño,Ralph Vogelsang,Christoph König,Víctor M. Luque-Almagro,María Dolores Roldán,Alexander Sczyrba,Conrado Moreno-Vivián,Rafael Blasco,Alfred Pühler,Andreas Schlüter +13 more
TL;DR: The complete genome sequence of the strain CECT5344 now provides the basis for exploitation of genetic features for biotechnological purposes and the methylome of P. pseudoalcaligenes was established.
Journal ArticleDOI
Developing Clostridium diolis as a biorefinery chassis by genetic manipulation.
TL;DR: The strain was engineered to improve productions of diol (1,3-propanediol) and n-alcohol (butanol), and to enable butyl acetate synthesis in vivo, respectively under different culture conditions, and represented a milestone of breeding C. diolis using metabolic engineering, and paved the way for studying C.diolis on the molecular level.
Journal ArticleDOI
Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix.
TL;DR: In this article, the authors characterized CamA kinetic parameters and determined its structure bound to DNA containing the recognition sequence, and found that major and minor groove DNA contacts in the recognition site involve base-specific hydrogen bonds, van der Waals contacts and the Watson-Crick pairing of a rearranged A:T base pair.
Journal ArticleDOI
Correction: A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen.
Michael C. Chao,Shijia Zhu,Satoshi Kimura,Brigid M. Davis,Eric E. Schadt,Gang Fang,Matthew K. Waldor +6 more
TL;DR: This research presents a novel probabilistic approach to estimating the response of the immune system to laser-spot assisted, 3D image analysis of central nervous system injury.
Journal ArticleDOI
Whole genome sequencing provides possible explanations for the difference in phage susceptibility among two Salmonella Typhimurium phage types (DT8 and DT30) associated with a single foodborne outbreak
Manal Mohammed,Martin Cormican +1 more
TL;DR: Differences in phage susceptibility between DT8 and DT30 may be related to acquisition of ICE in DT30 and loss of pSLT like plasmid that might be associated with DT30 resistance to almost all phages used in the typing scheme.
References
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