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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Journal ArticleDOI
Emerging challenges in the design of selective substrates, inhibitors and activity-based probes for indistinguishable proteases.
TL;DR: Important concepts and the latest challenges are described, focusing mainly on peptide‐based substrate specificity techniques used to distinguish individual enzymes within major protease families.
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Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis
TL;DR: The results indicate that contrary to the traditional monophyletic view of the origin of vertebrate retroviruses, the Retroviridae class I is a molecular fossil, preserving features that were probably predominant among Ty3/Gypsy ancestors predating the split of plants, fungi and animals.
Journal ArticleDOI
Up-regulation of alveolar macrophage matrix metalloproteinases in HIV1(+) smokers with early emphysema.
TL;DR: HIV1+ smokers develop emphysema at an earlier age and with a higher incidence than HIV1– smokers, and the activities of the up‐regulated AM MMPs include collagenases, gelatinases, matrilysins, and elastase are investigated.
Journal ArticleDOI
Post-transcriptional regulation of fruit ripening and disease resistance in tomato by the vacuolar protease SlVPE3
TL;DR: It is shown that SlVPE3 is required for the cleavage of the serine protease inhibitor KTI4, which contributes to resistance against the fungal pathogen B. cinerea.
Journal ArticleDOI
Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina.
Lida Derevnina,Sebastian Chin-Wo-Reyes,Frank N. Martin,Kelsey J. Wood,Lutz Froenicke,Otmar Spring,Richard W Michelmore +6 more
TL;DR: These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens and extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens.
References
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