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
MAFFT version 5: improvement in accuracy of multiple sequence alignment
TL;DR: Improvement in accuracy was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here, which showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences.
Journal ArticleDOI
Matrix metalloproteinases and the regulation of tissue remodelling
TL;DR: Recent studies in mice and flies point to essential roles of MMPs as mediators of change and physical adaptation in tissues, whether developmentally regulated, environmentally induced or disease associated.
Journal ArticleDOI
InterPro: the integrative protein signature database
Sarah Hunter,Rolf Apweiler,Teresa K. Attwood,Amos Marc Bairoch,Alex Bateman,David Binns,Peer Bork,Ujjwal Das,Louise C. Daugherty,Lauranne Duquenne,Robert D. Finn,Julian Gough,Daniel H. Haft,Nicolas Hulo,Daniel Kahn,Elizabeth Kelly,Aurélie Laugraud,Ivica Letunic,David M. Lonsdale,Rodrigo Lopez,Martin Madera,John Maslen,Craig McAnulla,Jennifer McDowall,Jaina Mistry,Alex L. Mitchell,Nicola Mulder,Darren A. Natale,Christine A. Orengo,Antony F. Quinn,Jeremy D. Selengut,Christian J. A. Sigrist,Manjula Thimma,Paul Thomas,Franck Valentin,Derek Wilson,Cathy H. Wu,Corin Yeats +37 more
TL;DR: The InterPro database integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs.
Journal ArticleDOI
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans
Brian D. Muegge,Justin Kuczynski,Dan Knights,Jose C. Clemente,Antonio Gonzalez,Luigi Fontana,Luigi Fontana,Bernard Henrissat,Rob Knight,Rob Knight,Jeffrey I. Gordon +10 more
TL;DR: The value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level is illustrated by shotgun sequencing of microbial community DNA and targeted sequencing of bacterial 16S ribosomal RNA genes.
Journal ArticleDOI
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors
TL;DR: The MEROPS database has been expanded to include proteolytic enzymes other than peptidases, and the inclusion of small-molecule inhibitors in the tables of peptidase–inhibitor interactions is included.
References
More filters