Glycosyltransferases
The KEGG Orthology (KO) system is a method to characterize gene/protein functions across organisms.
Experimental evidence in specific organisms is extended to other organisms by defining KO groups (or K number entries) in the KEGG ortholog annotation procedure.
The K number entries for glycosyltransferases are finely classified ortholog groups distinguishing known substrate specificity, such as K01001 for ALG7.
A pathway-based classification [reference] is developed as part of the functional hierarchies in the KEGG BRITE database.
The classification contains glycosidic linkage information, which may be used to convert gene information to chemical structure information, as is done in the CSM and GECS tools described below.
KEGG Pathway Maps
The KEGG PATHWAY database is a collection of manually drawn KEGG pathway maps representing current knowledge on molecular interaction networks, including glycan biosynthesis and metabolism.
The glycan structure map is another representation of glycan biosynthesis or degradation. For example, N-glycan biosynthesis is shown both as a pathway map and a structure map in map00510.
N-glycan biosynthesis (pathway map)
N-glycan biosynthesis (structure map)
The roles of glycans in various cellular processes may be examined with other pathway maps in the KEGG PATHWAY database, such as:
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Glycan Binding Proteins
Different types of glycan binding proteins are organized as K number entries and classified as a functional hierarchy of KEGG BRITE.
KEGG GLYCAN Structure Database
The KEGG GLYCAN structure database is a collection of experimentally determined glycan structures [reference]. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways. Each structure is identified by the G number, such as G00197 for CD65. KEGG GLYCAN is maintained in the KEGG LIGAND relational database.
In contrast to the manually drawn KEGG structure maps, the Composite Structure Map (CSM) is computationally generated to represent all possible structures in the KEGG GLYCAN structure database.
CSM can be used to examine the structural repertoire inferred from the genomic or transcriptomic repertoire.
KCaM Search Tool
KCaM is a database search program for similar glycan structures [reference].
It can be used to search against KEGG GLYCAN or CarbBank.
A query glycan structure may be entered with the KegDraw tool.
KegDraw Tool
KegDraw is a standalone Java application for drawing chemical compound structures and glycan structures in a way similar to ChemDraw and ISIS/Draw.
KegDraw runs on Mac, Windows, and Linux, and is made freely available to both academic and non-academic users.
Gene Microarray to Glycan Structures
GECS (Gene Expression to Chemical Structure) is a software package for linking genomic or transcriptomic contents of genes to chemical structures of biosynthetic substances, expecially glycans [reference].
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