The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
Brandi L. Cantarel,Pedro M. Coutinho,Corinne Rancurel,Thomas Bernard,Vincent Lombard,Bernard Henrissat +5 more
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TLDR
The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates and has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation.Abstract:
The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates. As of September 2008, the database describes the present knowledge on 113 glycoside hydrolase, 91 glycosyltransferase, 19 polysaccharide lyase, 15 carbohydrate esterase and 52 carbohydrate-binding module families. These families are created based on experimentally characterized proteins and are populated by sequences from public databases with significant similarity. Protein biochemical information is continuously curated based on the available literature and structural information. Over 6400 proteins have assigned EC numbers and 700 proteins have a PDB structure. The classification (i) reflects the structural features of these enzymes better than their sole substrate specificity, (ii) helps to reveal the evolutionary relationships between these enzymes and (iii) provides a convenient framework to understand mechanistic properties. This resource has been available for over 10 years to the scientific community, contributing to information dissemination and providing a transversal nomenclature to glycobiologists. More recently, this resource has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation. The CAZy resource resides at URL: http://www.cazy.org/.read more
Citations
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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.
Journal ArticleDOI
The carbohydrate-active enzymes database (CAZy) in 2013
TL;DR: The changes that have occurred in CAZy during the past 5 years are outlined and a novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes is presented.
Journal ArticleDOI
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Vanessa K. Ridaura,Jeremiah J. Faith,Federico E. Rey,Jiye Cheng,Alexis E. Duncan,Andrew L. Kau,Nicholas W. Griffin,Vincent Lombard,Bernard Henrissat,Bernard Henrissat,James R. Bain,Michael J. Muehlbauer,Olga Ilkayeva,Clay F. Semenkovich,Katsuhiko Funai,David K. Hayashi,Barbara J. Lyle,Margaret C. Martini,Luke K. Ursell,Jose C. Clemente,Will Van Treuren,William A. Walters,Rob Knight,Rob Knight,Christopher B. Newgard,Andrew C. Heath,Jeffrey I. Gordon +26 more
TL;DR: The results reveal that transmissible and modifiable interactions between diet and microbiota influence host biology and that adiposity is transmissible from human to mouse and that it was associated with changes in serum levels of branched-chain amino acids.
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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Peter J. Turnbaugh,Vanessa K. Ridaura,Jeremiah J. Faith,Federico E. Rey,Rob Knight,Jeffrey I. Gordon +5 more
TL;DR: A translational medicine pipeline is described where human gut microbial communities and diets are re-created in gnotobiotic mice and the impact on microbe and host is defined using metagenomics, creating a well-defined, representative animal model of the human gut ecosystem.
Journal ArticleDOI
Genome sequencing and analysis of the model grass Brachypodium distachyon
John P. Vogel,David F. Garvin,Todd C. Mockler,Jeremy Schmutz,Daniel S. Rokhsar,Michael W. Bevan,Kerrie Barry,Susan Lucas,Miranda Harmon-Smith,Kathleen Lail,Hope Tice,Jane Grimwood,Neil McKenzie,Naxin Huo,Yong Q. Gu,Gerard R. Lazo,Olin D. Anderson,Frank M. You,Ming-Cheng Luo,Jan Dvorak,Jonathan M. Wright,Melanie Febrer,Dominika Idziak,Robert Hasterok,Erika Lindquist,Mei Wang,Samuel E. Fox,Henry D. Priest,Sergei A. Filichkin,Scott A. Givan,Douglas W. Bryant,Jeff H. Chang,Haiyan Wu,Wei Wu,An-Ping Hsia,Patrick S. Schnable,Anantharaman Kalyanaraman,Brad Barbazuk,Todd P. Michael,Samuel P. Hazen,Jennifer N. Bragg,Debbie Laudencia-Chingcuanco,Yiqun Weng,Georg Haberer,Manuel Spannagl,Klaus F. X. Mayer,Thomas Rattei,Therese Mitros,Sang-Jik Lee,Jocelyn K. C. Rose,Lukas A. Mueller,Thomas L. York,Thomas Wicker,Jan P. Buchmann,Jaakko Tanskanen,Alan H. Schulman,Heidrun Gundlach,Michael W. Bevan,Antonio Costa de Oliveira,Luciano da C. Maia,William R. Belknap,Ning Jiang,Jinsheng Lai,Liucun Zhu,Jianxin Ma,Cheng Sun,Ellen J. Pritham,Jérôme Salse,Florent Murat,Michael Abrouk,Rémy Bruggmann,Joachim Messing,Noah Fahlgren,Christopher M. Sullivan,James C. Carrington,Elisabeth J. Chapman,Greg D. May,Jixian Zhai,Matthias Ganssmann,Sai Guna Ranjan Gurazada,Marcelo A German,Blake C. Meyers,Pamela J. Green,Ludmila Tyler,Jiajie Wu,James A. Thomson,Shan Chen,Henrik Vibe Scheller,Jesper Harholt,Peter Ulvskov,Jeffrey A. Kimbrel,Laura E. Bartley,Peijian Cao,Ki-Hong Jung,Manoj Sharma,Miguel E. Vega-Sánchez,Pamela C. Ronald,Chris Dardick,Stefanie De Bodt,Wim Verelst,Dirk Inzé,Maren Heese,Arp Schnittger,Xiaohan Yang,Udaya C. Kalluri,Gerald A. Tuskan,Zhihua Hua,Richard D. Vierstra,Yu Cui,Shuhong Ouyang,Qixin Sun,Zhiyong Liu,Alper Yilmaz,Erich Grotewold,Richard Sibout,Kian Hématy,Grégory Mouille,Herman Höfte,Todd P. Michael,Jérôme Pelloux,Devin O'Connor,James C. Schnable,Scott C. Rowe,Frank G. Harmon,Cynthia L. Cass,John C. Sedbrook,Mary E. Byrne,Sean Walsh,Janet Higgins,Pinghua Li,Thomas P. Brutnell,Turgay Unver,Hikmet Budak,Harry Belcram,Mathieu Charles,Boulos Chalhoub,Ivan Baxter +136 more
TL;DR: The high-quality genome sequence will help Brachypodium reach its potential as an important model system for developing new energy and food crops and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat.
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Journal ArticleDOI
New families in the classification of glycosyl hydrolases based on amino acid sequence similarities.
TL;DR: On the basis of a comparison of 482 sequences corresponding to 52 EC entries, 45 families, out of which 22 are polyspecific, can now be defined and has been implemented in the SWISS-PROT protein sequence data bank.