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
Citations
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Genomic and secretomic analyses reveal unique features of the lignocellulolytic enzyme system of Penicillium decumbens.
Guodong Liu,Lei Zhang,Xiaomin Wei,Gen Zou,Yuqi Qin,Liang Ma,Jie Li,Huajun Zheng,Shengyue Wang,Chengshu Wang,Luying Xun,Luying Xun,Guoping Zhao,Guoping Zhao,Zhihua Zhou,Yinbo Qu +15 more
TL;DR: Comparative genomics analysis with the phylogenetically most similar species Penicillium chrysogenum and proteomic analysis of secretomes revealed that P. decumbens has evolved with more genes involved in plant cell wall degradation, but fewer genes in cellular metabolism and regulation.
Journal ArticleDOI
Metalloprotease-mediated OPA1 processing is modulated by the mitochondrial membrane potential
Olwenn Guillery,Florence Malka,Florence Malka,Thomas Landes,Emmanuelle Guillou,Craig Blackstone,Anne Lombès,Anne Lombès,Pascale Belenguer,Damien Arnoult,Damien Arnoult,Manuel Rojo,Manuel Rojo +12 more
TL;DR: This work focuses on protease processing of OPA1, a dynamin‐related protein of the mitochondrial IMS involved in membrane fusion and remodelling that exists in various isoforms generated by alternative splicing and processing.
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SWISS-PROT: connecting biomolecular knowledge via a protein database.
TL;DR: The effort in connecting biological information as demonstrated in the SWISS-PROT protein database is highlighted.
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Towards specific functions of lysosomal cysteine peptidases: phenotypes of mice deficient for cathepsin B or cathepsin L.
TL;DR: The finding that cathepsin L appears to be critically involved in epidermal homeostasis, regulation of the hair cycle, and MHC class IImediated antigen presentation in cortical epithelial cells of the thymus is discussed.
Journal ArticleDOI
Cysteine peptidases of mammals: their biological roles and potential effects in the oral cavity and other tissues in health and disease
TL;DR: Although these proteins are presumed to serve a protective function, their in vivo targets are unknown, and it remains to be discovered whether they serve to control any human CP activity.
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.