MEROPS: the peptidase database
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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
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Journal ArticleDOI
Characterization of Potential Polysaccharide Utilization Systems in the Marine Bacteroidetes Gramella Flava JLT2011 Using a Multi-Omics Approach.
TL;DR: A comparison of polysaccharide decomposition within a genus is presented and current knowledge on the diversity and function of PULs in marine Bacteroidetes is expanded, thereby deepening the authors' understanding of their ecological role in poly Saccharide remineralization in the marine system.
Book ChapterDOI
Cathepsin Proteases in Toxoplasma gondii
Zhicheng Dou,Vern B. Carruthers +1 more
TL;DR: The key features and roles of T. gondii cathepsins are reviewed, the therapeutic potential for specific inhibitor development is discussed and the scientific rationale behind the C1 family of cysteine proteases is explained.
Journal ArticleDOI
Highly Specific Protease-Based Approach for Detection of Porphyromonas gingivalis in Diagnosis of Periodontitis
Wendy E. Kaman,Wendy E. Kaman,Wendy E. Kaman,Fabiano Galassi,Fabiano Galassi,Johannes J. de Soet,Johannes J. de Soet,Sergio Bizzarro,Sergio Bizzarro,Bruno G. Loos,Bruno G. Loos,Enno C. I. Veerman,Enno C. I. Veerman,Alex van Belkum,Alex van Belkum,John P. Hays,Floris J. Bikker,Floris J. Bikker +17 more
TL;DR: The development of a highly specific protease-based diagnostic method for the detection of P. gingivalis in gedival crevicular fluid is described and it is envisaged that these substrates may improve the specificity of the current enzyme-based diagnosis of periodontitis associated with P. GingivalIS.
Journal ArticleDOI
Cathepsin D cleaves aggrecan at unique sites within the interglobular domain and chondroitin sulfate attachment regions that are also cleaved when cartilage is maintained at acid pH.
Christopher J. Handley,Meng Tuck Mok,Mirna Z. Ilic,Clair Adcocks,David J. Buttle,H. Clem Robinson +5 more
TL;DR: It is demonstrated that cathepsin D present within the extracellular matrix of articular cartilage has the potential to contribute to the proteolytic processing of the core protein of aggrecan in this tissue.
Journal ArticleDOI
Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: identification, characterisation and putative role in migration and nutrition.
Jan Dvořák,Melaine Delcroix,Andrea Rossi,Václav Vopálenský,Martin Pospíšek,Miroslava Šedinová,Libor Mikeš,Mohammed Sajid,Andrej Sali,James H. McKerrow,Petr Horák,Conor R. Caffrey +11 more
TL;DR: This work has identified and characterised the major 33 kDa cathepsin B-like cysteine endopeptidase in extracts of migrating schistosomula using fluorogenic peptidyl substrates with high extinction coefficients and irreversible affinity-labels and supported the adaptation of T. regenti gut peptidases to parasitism of host nervous tissue.
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.