Specialized databases

There are many specialized databases covering diverse areas of Biochemistry and Bioinformatics. Examples are:

IMGT - immunogenetics Database
KEGG - pathways database
OMIM - Online Mendelian Inheritance in Man
dbSNP - single nucleotide polymorphisms
HGVBase - single nucleotide polymorphisms and mutations (human)
p53 - mutations in p53 - also many other locus specific mutation databases
PubMed - publications
CATH, SCOP - structural classifications

Practical work

You will look briefly at KEGG, a very powerful database of pathway information including (but not limited to) metabolic pathways.

KEGG - the pathway database

Visit KEGG at: http://www.genome.jp/kegg/

You will find a page which summarizes the function of KEGG.

You will see that Kegg is divided into several main areas which include:

PATHWAY (pathway maps)
BRITE (functional hierarchies)
ORTHOLOGY (KO system and ortholog annotation)
GENES (genomes, genes, and proteins)
LIGAND (chemical substances and reactions)
...

Click KEGG PATHWAY to access the pathway database.

Here you will see pathways listed in 7 groups:

Metabolism
Genetic Information Processing
Environmental Information Processing
Cellular Processes
Organismal Systems
Human Diseases
Drug Development

Scroll down to section 1.1 Metabolism / Carbohydrate Metabolism, click Glycolysis / Gluconeogenesis.

This takes you to http://www.genome.jp/kegg/pathway/map/map00010.html where you will see the reference metabolic pathway map. What you are looking at on this page are all the reactions of these pathways, and the interconnections with other related pathways (which you can also click on to display a new page containing that pathway).

The boxes containing numbers such as 3.1.3.11 are Enzyme Commission (EC) numbers representing reactions carried out by enzymes.

The reference pathway includes enzymes from all organisms. At the top is a menu where you can select a specific organism.

Choose Homo sapiens and click Go. The map changes to one where certain EC number boxes are coloured in green. These are the enzymes present in humans.

Now view the enzymes present in E. coli in the same way. Choose one of the E. coli species (Escherichia coli K-12 MG1655) from the pull-down menu and click Go.

Getting more information

All the boxes containing EC numbers are clickable giving detailed information on the particular enzymes.

Click on the EC number box for phosphofructokinase (EC number: 2.7.1.11)

This takes you to a page which gives you an overview of the enzyme in the currently selected species: in which pathways it appears, its sequence and cross-references to primary sequence database entries.

In the Orthology section, is a link to the generic information for the EC number, 2.7.1.11.

Click on the EC number: 2.7.1.11 in the Orthology section.

You now arrive at a page with complete information on this enzyme and with links to many other pieces of more detailed related information: substrates, products, effectors, inhibitors, pathways, genes, diseases and structures. (Note: Had you selected the enzyme from the reference pathway instead of from the E. coli pathway, you would have been taken straight to this page.)

In 2006, this illustrated an important problem with cross-links between databases. In the Other DBs section is a cross-link to UniProt. In 2006 the the accession code was P06998. This was a dead link as the accession code had expired - UniProt had been updated and P06998 was no longer a valid primary accession, having been replaced by P0A796.

KEGG is a very powerful resource allowing you to explore pathways and compare genomes. You can search on the basis of ligands as well as proteins. It provides links out to many other databases.