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
More filters
Posted ContentDOI
Finding CRISPR's Niche: Oxygen and Temperature Shape the Incidence of Adaptive Immunity
TL;DR: A strong but hitherto-unknown negative interaction between CRISPR and aerobicity is discovered, which it is hypothesize may result from interference betweenCRISPR associated proteins and DNA repair due to oxidative stress.
Journal ArticleDOI
The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145
TL;DR: In this paper , the authors reported the cytosine methylome of S. coelicolor A(3)2 M145 in solid sporulating and liquid non-sporulating complex media.
Journal ArticleDOI
Bci528I, a new isoschizomer of EcoRI isolated from Bacillus circulans 528.
Sung-Ryong Ra,Myong-Suk Kim,Chon-Il Paek,Yong-Chol Pak,Song-Hui Pak,Hyong-Bom Pak,Kum-Chol Ri +6 more
TL;DR: Bacillus circulans 528 produces a restriction endonuclease, Bci528I which is an isoschizomer of EcoRI which cleaves between G and A of the recognition sequence, producing a symmetric four base 5′overhang.
Posted ContentDOI
The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori
Iratxe Estibariz,Annemarie Overmann,Florent Ailloud,Juliane Krebes,Christine Josenhans,Sebastian Suerbaum +5 more
TL;DR: It is demonstrated that motifs overlapping the promoter influence the expression of genes directly, while methylation of other motifs might cause secondary effects, affecting important phenotypic traits that include adherence to host cells, natural competence for DNA uptake, bacterial cell shape, and susceptibility to copper.
References
More filters
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Journal ArticleDOI
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
Journal ArticleDOI
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
Journal ArticleDOI
The Universal Protein Resource (UniProt)
Amos Marc Bairoch,Rolf Apweiler,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; the UniProt keyword list got augmented by additional keywords; the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications.
Related Papers (5)
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
Richard J. Roberts,Marlene Belfort,Timothy H. Bestor,Ashok S. Bhagwat,Thomas A. Bickle,Jurate Bitinaite,Robert Blumenthal,Sergey Kh. Degtyarev,David T. F. Dryden,Kevin Dybvig,Keith Firman,Elizaveta S. Gromova,Richard I. Gumport,Stephen E. Halford,Stanley Hattman,Joseph Heitman,David P. Hornby,Arvydas Janulaitis,Albert Jeltsch,Jytte Josephsen,Antal Kiss,Todd R. Klaenhammer,Ichizo Kobayashi,Huimin Kong,Detlev H. Krüger,Sanford A. Lacks,Martin G. Marinus,Michiko Miyahara,Richard D. Morgan,Noreen E. Murray,Valakunja Nagaraja,Andrzej Piekarowicz,Alfred Pingoud,Elisabeth A. Raleigh,Desirazu N. Rao,Norbert O. Reich,Repin Vladimir E,Eric U. Selker,Pang-Chui Shaw,Daniel C. Stein,Barry L. Stoddard,Waclaw Szybalski,Thomas A. Trautner,James L. Van Etten,Jorge M. B. Vítor,Geoffrey G. Wilson,Shuang Yong Xu +46 more
N6-methyl-adenine: an epigenetic signal for DNA-protein interactions.
Didier Wion,Josep Casadesús +1 more