The carbohydrate-active enzymes database (CAZy) in 2013
Reads0
Chats0
TLDR
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.Abstract:Â
The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3D structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides. Functional and 3D structural information is added and curated on a regular basis based on the available literature. In addition to the use of the database by enzymologists seeking curated information on CAZymes, the dissemination of a stable nomenclature for these enzymes is probably a major contribution of CAZy. The past few years have seen the expansion of the CAZy classification scheme to new families, the development of subfamilies in several families and the power of CAZy for the analysis of genomes and metagenomes. This article outlines the changes that have occurred in CAZy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes.read more
Citations
More filters
Journal ArticleDOI
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life.
Fredrik Bäckhed,Fredrik Bäckhed,Josefine Roswall,Yangqing Peng,Qiang Feng,Huijue Jia,Petia Kovatcheva-Datchary,Yin Li,Yan Xia,Hailiang Xie,Huanzi Zhong,Muhammad Tanweer Khan,Jianfeng Zhang,Junhua Li,Liang Xiao,Jumana Y. Al-Aama,Dongya Zhang,Ying Shiuan Lee,Dorota Ewa Kotowska,Camilla Colding,Valentina Tremaroli,Ye Yin,Stefan Bergman,Xun Xu,Lise Madsen,Lise Madsen,Karsten Kristiansen,Jovanna Dahlgren,Jun Wang +28 more
TL;DR: The gut microbiota of infants delivered by C-section showed significantly less resemblance to their mothers and nutrition had a major impact on early microbiota composition and function, with cessation of breast-feeding, rather than introduction of solid food, being required for maturation into an adult-like microbiota.
Journal ArticleDOI
Biological Roles of Glycans
TL;DR: It is time for the diverse functional roles of glycans to be fully incorporated into the mainstream of biological sciences, as they are no different from other major macromolecular building blocks of life, simply more rapidly evolving and complex.
Journal ArticleDOI
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
Han Zhang,Tanner Yohe,Le Huang,Sarah Entwistle,Peizhi Wu,Zhenglu Yang,Peter Kamp Busk,Ying Xu,Yanbin Yin +8 more
TL;DR: The dbCAN2 (http://cys.bios.niu.edu/dbCAN2) as mentioned in this paper is an updated meta server, which integrates three state-of-the-art tools for CAZome annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against CAZy pre-annotated CAZY sequence database and (iii) Hotpep search against conserved CAZys short peptide database.
Journal ArticleDOI
Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes
Liping Zhao,Liping Zhao,Feng Zhang,Xiaoying Ding,Guojun Wu,Yan Y. Lam,Xuejiao Wang,Huaqing Fu,Xinhe Xue,Chunhua Lu,Jilin Ma,Lihua Yu,Chengmei Xu,Zhongying Ren,Ying Xu,Songmei Xu,Hongli Shen,Xiuli Zhu,Yu Shi,Qingyun Shen,Weiping Dong,Rui Liu,Yunxia Ling,Yue Zeng,Xing-peng Wang,Qianpeng Zhang,Jing Wang,Linghua Wang,Yanqiu Wu,Benhua Zeng,Hong Wei,Menghui Zhang,Yongde Peng,Chenhong Zhang +33 more
TL;DR: It is found that adopting a high-fiber diet promoted the growth of SCFA-producing organisms in diabetic humans and had better improvement in hemoglobin A1c levels, partly via increased glucagon-like peptide-1 production.
Journal ArticleDOI
Diet-induced extinctions in the gut microbiota compound over generations
Erica D. Sonnenburg,Samuel A. Smits,Mikhail Tikhonov,Steven K. Higginbottom,Ned S. Wingreen,Justin L. Sonnenburg +5 more
TL;DR: It is shown that changes in the microbiota of mice consuming a low-MAC diet and harbouring a human microbiota are largely reversible within a single generation, and that taxa driven to low abundance when dietary MACs are scarce are inefficiently transferred to the next generation and are at increased risk of becoming extinct within an isolated population.
References
More filters
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.
Journal ArticleDOI
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
A classification of glycosyl hydrolases based on amino acid sequence similarities.
TL;DR: With the steady increase in sequence and structural data, it is suggested that the enzyme classification system should perhaps be revised.
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.