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The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
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.
A core gut microbiome in obese and lean twins
TLDR
The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
TLDR
Analyzing the draft genome of the black cottonwood tree, Populus trichocarpa, revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome.
The carbohydrate-active enzymes database (CAZy) in 2013
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.
A classification of glycosyl hydrolases based on amino acid sequence similarities.
TLDR
With the steady increase in sequence and structural data, it is suggested that the enzyme classification system should perhaps be revised.
Glycosyltransferases: structures, functions, and mechanisms.
TLDR
The expected two-step double-displacement mechanism is rendered less likely by the lack of conserved architecture in the region where a catalytic nucleophile would be expected, and a mechanism involving a short-lived oxocarbenium ion intermediate now seems the most likely, with the leaving phosphate serving as the base.
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
TLDR
The sequenced genome of Phanerochaete chrysosporium strain RP78 reveals an impressive array of genes encoding secreted oxidases, peroxidases and hydrolytic enzymes that cooperate in wood decay, and provides a framework for further development of bioprocesses for biomass utilization, organopollutant degradation and fiber bleaching.
Structural and sequence-based classification of glycoside hydrolases.
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
TLDR
This work determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.
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