MEROPS: the peptidase database
Reads0
Chats0
TLDR
The MEROPS database has added an analysis tool to the relevant species pages to show significant gains and losses of peptidase genes relative to related species, and has collected over 39 000 known cleavage sites in proteins, peptides and synthetic substrates.Abstract:
Peptidases (proteolytic enzymes) are of great relevance to biology, medicine and biotechnology. This practical importance creates a need for an integrated source of information about them, and also about their natural inhibitors. The MEROPS database (http://merops.sanger.ac.uk) aims to fill this need. The organizational principle of the database is a hierarchical classification in which homologous sets of the proteins of interest are grouped in families and the homologous families are grouped in clans. Each peptidase, family and clan has a unique identifier. The database has recently been expanded to include the protein inhibitors of peptidases, and these are classified in much the same way as the peptidases. Forms of information recently added include new links to other databases, summary alignments for peptidase clans, displays to show the distribution of peptidases and inhibitors among organisms, substrate cleavage sites and indexes for expressed sequence tag libraries containing peptidases. A new way of making hyperlinks to the database has been devised and a BlastP search of our library of peptidase and inhibitor sequences has been added.read more
Citations
More filters
Journal ArticleDOI
The Human Protease Inhibitor Cystatin C Is an Activating Cofactor for the Streptococcal Cysteine Protease IdeS.
TL;DR: An unexpected function of cystatin C is presented, which acts as a facultative, endogenous cofactor for the papain-like IgG-cleaving enzyme IdeS of the human pathogen Streptococcus pyogenes.
Journal ArticleDOI
Electron microscopy encounters with unusual thermophiles helps direct genomic analysis of Aciduliprofundum boonei
TL;DR: Terry Beveridge's enthusiasm about the ingenuity of microorganisms has stimulated many new avenues of microbial research, and the analysis of the draft genome of the thermoacidophilic archaeum, Aciduliprofundum boonei, found that it possesses a unique organization to its flagellum genes and may represent a third organizational type within the Archaea.
Journal ArticleDOI
Biochemical and Structural Characterization of SplD Protease from Staphylococcus aureus.
Michal Zdzalik,Magdalena Kalinska,Magdalena Wysocka,Justyna Stec-Niemczyk,Przemyslaw Cichon,Natalia Stach,Natalia Gruba,Henning R. Stennicke,Abeer Jabaiah,Michal Markiewicz,Sylwia Kedracka-Krok,Benedykt Wladyka,Patrick S. Daugherty,Adam Lesner,Krzysztof Rolka,Adam Dubin,Jan Potempa,Jan Potempa,Grzegorz Dubin +18 more
TL;DR: The biochemical and structural characteristics of the SplD protease are described and a surprisingly narrow specificity of the protease is revealed, which recognized five consecutive residues with a consensus motif of R-(Y/W)-(P/L)-(T/L/I/V)↓S.
Journal ArticleDOI
Therapeutic and biotechnological applications of substrate specific microbial aminopeptidases.
TL;DR: Aminopeptidases are widely used for the synthesis of biopeptides and amino acids, and found to be efficient than chemical synthesis, thus having biological as well as environmental significance.
Journal ArticleDOI
Genome resequencing and transcriptome profiling reveal structural diversity and expression patterns of constitutive disease resistance genes in Huanglongbing-tolerant Poncirus trifoliata and its hybrids.
Nidhi Rawat,Brajendra Kumar,Ute Albrecht,Dongliang Du,Ming Huang,Qibin Yu,Yi Zhang,Yongping Duan,Kim D. Bowman,Frederick G. Gmitter,Zhanao Deng +10 more
TL;DR: It is revealed that the expansion of the CDR family in Citrus seems to be due to segmental and tandem duplication events, and these two CDR genes seem to be good candidate genes for future studies of their role in citrus-CLas interactions.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
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.