KEGG Web Querying Examples

Posted Tue, 03/31/2009 - 06:37

KEGG is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE). KEGG provides a reference knowledge base for linking genomes to biological systems and also to environments by the processes of PATHWAY mapping and BRITE mapping. The reference knowledge is stored in KEGG, Kyoto Encyclopedia of Genes and Genomes, and associated bioinformatics technologies are being developed both for basic research and practical applications. [1]

Finding a standard metabolic pathway

Go to KEGG

Click on the link Pathway in the above window. A list with all pathways will be available. To find the pathway link for 'Lysine biosynthesis', scroll down on the browser to the group of pathways called 'amino acid metabolism' and click on its link.

We now see the standard pathway MAP00300 for lysine biosynthesis. Each box represents an enzyme with EC number inside and a circle is a metabolic compound.

Finding species specific pathway maps

Select the species name (Escherichia coli) in the 'Go To' window and click on Go.

We see the same pathway, but the species name is indicated in the window (Escherichia coli K-12 MG1655). All known E.coli enzymes for which a database entry exists are labelled in green.

Finding a chemical structure, metabolite information from a pathway map

Click on the on the small circle next to the compound name to get the structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2, 6-diaminopimelotl-D-alanyl-D-alanine which is the immediate precursor of L-lysine. You will see an information page for KEGG entry C04882.

The preceding problem gives an example of how to find information about a metabolite, namely its chemical structure, formula, KEGG entry number, and pathway map numbers for which it is an intermediate. Clicking on a substrate name (or its circle) on a pathway map page is the easiest way to find relevant chemical information about a substrate and its shared pathways.

Click on the box marked 'Lysine degradation' indicated in a roundish shaped box in the lysine biosynthesis map to view the corresponding catabolic processes (intersecting pathways).

Finding a chemical structure, metabolite information by keyword search

To find a pathway metabolite or enzyme, the table of contents offers a direct link to the DBGET Ligand database at KEGG.

Click on the link called 'Ligand' to access a generic search mode that allows a keyword entry; type 'lysine' and hit the return (enter) key.

You will receive a return list with 159 hits. The search returned all KEGG entries that contained the word 'lysine' anywhere in the enzyme or compound name. The list contains 45 enzyme links (ec: x.x.x.xx) and 51 compound links (cpd: Cxxxxx), one being L-lysine (cpd:C00047) and all others derivatives thereof.

Clicking on the cpd number will bring you to the chemical structure information sheet. This sheet lists compound entry number for L-lysine common name(s), formula, structure, all pathway maps that contain L-lysine as metabolite (5 maps for L-lysine including synthesis and degradation, biotin metabolism, alkaloid biosynthesis II, and Aminoacyl-tRNA biosynthesis), and finally a list of all known enzymes that use L-lysine as a substrate.