In this exercise you will explore some of the metabolic pathway sites. We will again use the protein COMT as our guide, but you may wish to choose any protein of interest to you. (Please note that the Kegg links do not always show up in every browser window). Point your browser at this link - http://www.genome.jp/kegg/kegg2.html and navigate to the KEGG Table of Contents - http://www.genome.jp/kegg/kegg2.html
KEGG is probably the best resource for pathway information, which is extensively linked into a comprehensive database of information. Navigating KEGG can be trying, so please follow a few of these links first. Then try your gene, protein, enzyme etc., and find a pathway. Using COMT (and EC 2.1.1.6) you should get this link for the enzyme entry http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.6 (study this entry carefully as it has other useful links within KEGG) and this link for the pathway: http://www.genome.jp/dbget-bin/show_pathway?hsa00350+2.1.1.6 Take some time to explore the pathway map. You should be able to navigate back and forth between the enzyme entry and the pathway map. This website also supports XML (KGML), which we will talk about in our section on XML.
KEGG - GenomeNet at Kyoto University and Kyoto Encyclopedia of Genes and Genomes - http://www.genome.jp/kegg/
KEGG Pathways - http://www.genome.jp/kegg/pathway.html
KEGG Genes - http://www.genome.jp/kegg/genes.html
KEGG Ligands - http://www.genome.jp/kegg/ligand.html
KEGG BRITE - http://www.genome.jp/kegg/brite.html
ExPASy Biochemical Pathways - A resource for finding enzyme entries and pathway information, is a quick way to get enzyme information that's linked into the ExPASy protein database. Try doing a search with COMT. What two results did you get? Follow the link into NiceZyme view. What links are available from their to other bioinformatic sites? Try a search from that page into NCBI PubMed. Report interesting findings. Finally, follow the link to the pathway map for COMT (or your target). Things start to get pretty busy from here on out.
E-Cell System - an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. Check out this site, and if you are interested in XML and systems biology, try CellML and Systems Biology Markup Language - SBML.