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
A Forward Genetic Strategy Reveals Destabilizing Mutations in the Ebolavirus Glycoprotein That Alter Its Protease Dependence during Cell Entry
TL;DR: Ebolavirus entry into cells requires proteolytic disassembly of the viral glycoprotein, GP, and CatB cleavage is required to facilitate the triggering of viral membrane fusion by destabilizing the prefusion conformation of EBOV GP.
Journal ArticleDOI
Proteolytic activity and cysteine protease expression in wheat leaves under severe soil drought and recovery.
TL;DR: Lower proteolytic activity and decreased expression of certain cysteine protease genes under water deficit during early developmental stage could be regarded as an indicator for drought resistance of winter wheat cultivars.
Journal ArticleDOI
Genes and Related Proteins Involved in Amelogenesis Imperfecta
TL;DR: Current knowledge on the candidate genes involved in amelogenesis imperfecta and the proteins derived from them are reviewed, and current knowledge on their structure, localization within the tissue, and correlation with the various types of this disorder is reviewed.
Journal ArticleDOI
Evolution of apoptosis-like programmed cell death in unicellular protozoan parasites
TL;DR: Bioinformatics analyses suggest that apoptosis mechanisms in protozoan parasites and other taxa have diverged during their evolution, that some apoptosis factors are shared across taxa whilst others have been replaced by proteins with similar biochemical activities.
Journal ArticleDOI
Profiling constitutive proteolytic events in vivo
John C. Timmer,John C. Timmer,Mari Enoksson,Eric Wildfang,Wenhong Zhu,Yoshinobu Igarashi,Jean-Benard Denault,Yuliang Ma,Benjamin Dummitt,Yie-Hwa Chang,Alan E. Mast,Alexey Eroshkin,Jeffrey W. Smith,W. Andy Tao,Guy S. Salvesen,Guy S. Salvesen +15 more
TL;DR: In this article, a method to define proteases that are crucial for constitutive proteolytic events in Escherichia coli to humans is described. But the method is based on specific N-terminal biotinylation of protein samples.
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.