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With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5.
About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data.
Collectively designated as Carbohydrate-Active en Zymes (CAZymes), these enzymes build and breakdown complex carbohydrates and glycoconjugates for a large body of biological roles (collectively studied under the term of Glycobiology).
Descriptions of the microbial communities that live on and in the human body have progressed at a spectacular rate over the past 5 years, fuelled primarily by highly parallel DNA-sequencing technologies and associated advances in bioinformatics, and by the expectation that understanding how to manipulate the structure and functions of our microbiota will allow us to affect health and prevent or treat diseases.
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.
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.
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Among the myriad of genes that have been identified in the human gut microbiome, those that encode carbohydrate-active enzymes (CAZymes) are of particular interest, as these enzymes are required to digest most of our complex repertoire of dietary polysaccharides.