Glycan Structures
KEGG GLYCAN is a collection of glycan structures, first created in 2003 by taking unique structures from CarbBank. Since then it has been expanded with other structures based on published materials, especially those structures present in KEGG pathways. Each structure is identified by the G number, such as G00242 for sialyl Lewis x, and displayed with predefined monosaccharide codes shown below. The structure may also be converted to the SNFG (Symbol Nomenclature for Glycans) representation by clicking on the SNFG button.
Glycan Biosynthesis and Metabolism
KEGG GLYCAN is tightly integrated with other KEGG resources, including KEGG PATHWAY, KEGG MODULE, KEGG NETWORK and KEGG DISEASE.
In the KEGG PATHWAY database the section of:
contains metabolic pathway maps for glycans. In addition to the regular pathway map representation, a different representation of glycan biosynthesis or degradation is sometimes presented. It is called the "glycan structure map", showing genes (or KOs) responsible for bond formation or breakage are shown. For example, N-glycan biosynthesis is shown both as a regular pathway map and a structure map in map00510.
The following datasets indicate relationships among pathways, structures and biosynthetic genes.
The following datasets indicate relationships among pathways, structures and biosynthetic genes.
- br08020
- Nucleotide sugars
- map01250
- Biosynthesis of nucleotide sugars
- map00520
- Amino sugar and nucleotide sugar metaboddsm
- map00541
- O-Antigen nucleotide sugar biosynthesis
- ko01003
- Glycosyltransferases
- ko01005
- Lipopolysaccharide biosynthesis proteins
- map00540
- Lipopolysaccharide biosynthesis
- map00542
- O-Antigen repeat unit biosynthesis
- br08120
- O-Antigens
Glycans in Other Pathways
The roles of glycans in various cellular processes may be examined with other types of pathway maps in the KEGG PATHWAY database, such as in Signaling molecules and interaction, Cell communication and Immune system.
Different types of glycans and glycan binding proteins are classified in:
Different types of glycans and glycan binding proteins are classified in:
- ko00535
- Proteoglycans
- ko00536
- Glycosaminoglycan binding proteins
- ko00537
- Glycosylphosphatidylinositol (GPI)-anchored proteins
- ko04091
- Lectins
Glycans and Diseases
Human diseases associated with glycan biosynthesis and metabolism are being accumulated in the KEGG NETWORK database.
For example, the network variation map nt06015 for N-Glycan biosynthesis contains gene variants associated with congenital disorders of glycosylation, H00118 and H00119.
The network variation maps are the basis for developing a KEGG original disease classification system. The roles of glycans in cancers are represented in the following datasets.
The network variation maps are the basis for developing a KEGG original disease classification system. The roles of glycans in cancers are represented in the following datasets.
- hsa05205
- Proteoglycans in cancer
- br08441
- Cancer-associated carbohydrates
KCaM Search Tool
KCaM is a database search program for similar glycan structures. It can be used to search against KEGG GLYCAN or CarbBank. A query glycan structure may be entered with the KegDraw tool.
References
- Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., and Kanehisa, M.; KEGG as a glycome informatics resource. Glycobiology 16, 63R-70R (2006). [pubmed] [pdf]
- Kanehisa, M.; KEGG GLYCAN. In "A Practical Guide to Using Glycomics Databases" (Aoki-Kinoshita, K.F., ed.), pp. 177-193, Springer (2017).
- Hashimoto, K., Kawano, S., Goto, S., Aoki-Kinoshita, K., Kawashima, M., and Kanehisa, M.; A global representation of the carbohydrate structures: a tool for the analysis of glycan. Genome Informatics 16(1), 214-222 (2005). [pubmed]
- Hashimoto, K., Tokimatsu, T., Kawano, S., Yoshizawa, A.C., Okuda, S., Goto, S., and Kanehisa, M.; Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr. Res. 344, 881-887 (2009). [pubmed]
- Aoki, K.F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S., and Kanehisa, M.; KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32, W267-W272 (2004). [pubmed] [pdf]
Last updated: Septermber 8, 2023