Directory of Databases
for Plant Cell Wall-Related Enzymes
 

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The Directory of Databases for Plant Cell Wall-Related Enzymes is a companion database of our review paper "A Survey of Databases for Analysis of Plant Cell Wall-Related Enzymes" submitted to BioEnergy Research. The databases discussed in our review are organized into three sections: general databases, species-specific databases and family-specific databases.

General Databases

CAZy
The Carbohydrate-Active enZymes (CAZy) database is the most comprehensive knowledge-based database specializing in cell wall-related enzymes, and has been available on the web since September 1998. The CAZy database contains information about enzymes that build and breakdown complex carbohydrates and glycoconjugates. (Publication)

Cell Wall Genomics
Cell Wall Genomics is a useful online resource database that supports genetic analyses of cell wall-related genes in Arabidopsis and maize. This database indexes the homozygous T-DNA insertion mutants for more than 1,100 cell wall related genes that are currently being generated at the University of Wisconsin. (Publication)

Cell Wall Navigator
Cell Wall Navigator (CWN) is an integrated database and mining tool used to search for protein families involved in plant cell wall metabolism. The sequences used by CWN are retrieved from three different resources: the completed genome sequences of Arabidopsis and O. sativa spp. Japonica, the UniProt database and the EST division of NCBI. (Publication)

Species-specific Databases

The Rice GT Database
The Rice GT Database is a phylogenomic database that integrates, hosts, and displays functional genomic data in a phylogenetic context, with the goal of facilitating functional analysis of the large GT family of enzymes in the rice reference monocotyledonous species. This database provides information about 617 potential GT genes (loci), corresponding to 793 transcripts (gene models) in rice. (Publication)

MAIZEWALL
The MAIZEWALL database provides a bioinformatic analysis and gene expression data repository of cell wall biosynthesis and assembly in maize. This database contains 735 contigs belonging to 174 putative gene functions that were identified and further classified into 19 functional categories. (Publication)

Wheat GTIdb
The Wheat GlycosylTransferase Inventory database (GTIdb) is a searchable database that can be used to apply an exhaustive candidate gene survey in wheat to a particular biological process . (Publication)

Family-specific Databases

GHDB
The Glycoside Hydrolases Database (GHDB) is a structured database dedicated to the CAZy database family GH16 glycoside hydrolases. The database is composed of 260 proteins and 319 sequences from 128 species. (Publication)

XTH World
XTH World is a database specifically targeted toward the nomenclature and systematic identification of xyloglucan endotransglucosylase-hydrolases (XTH), which are enzymes capable of splitting and reconnecting xyloglucan molecules in rapidly growing plant tissues.

Expansin Database
The Expansin Database is a central database that focuses mainly on plant expansin genes, providing comprehensive information about protein structure, mechanism of action, nomenclature, experimental protocols and literature references for this type of protein.



Last modified: Thursday, 17-Dec-2009 17:54:28 PST
UC Davis Indica Last Update: December 2009