Practical 1: Exercise 2

Introduction

From the previous exercise you should already know the assignment of your gene to an enzyme, either through its name or EC number. This remaining exercise is to recover information about the enzyme's function from the relevant databases.

Links

The various databases you need are these:

• Kyoto Encyclopaedia of Genes and Genomes (KEGG): http://www.genome.jp/kegg/

• BioCyc: http://biocyc.org/

• IntEnz at http://www.ebi.ac.uk/intenz/

• ENZYME database at http://www.expasy.org/enzyme/

• Brenda: http://www.brenda-enzymes.info/

Much of the information is duplicated between these, though presented in different formats, often with cross-links to the other databases. Brenda is the only one that contains enzyme kinetic information though.

Exercise

• Use IntEnz and/or Enzyme to detail the reaction catalyzed by your enzyme.

• Use Kegg or BioCyc to find the metabolic function of the enzyme and its position in the metabolic network (e.g. from a pathway diagram).

• See what other information about the enzyme you can find from Brenda. It is doubtful that Brenda will contain any information specifically about the enzyme from the species you are studying, but you can attempt to see whether there is information about enzymes from related species (or maybe just the same phylum!).