Step 7: Where Does Your Protein Fit In?
Now you know a lot about your specific protein, but you might need to know more about how it's integrated into your cell's webwork of biological machinery. For this you can turn to the KEGG Database, which is a graphical repository of common pathways as well as the site for numerical nomenclature of enzymes. We'll check out Bradyrhizobium japonicum ATP synthase and see what we find.
- Open the KEGG page.
- Select "KEGG Genes".
- Where it says "Search KEGG organism", put "bja" (for Bradyrhizobium japonicum) in the short text box and "ATP synthase" in the long one.
- Click "Go".
- Our protein is the ATP synthase alpha chain, so select the entry for atpA.
You now have quite a lot of information available to you about this protein. You have all of the following:
- The abbreviated four letter name for the gene
- The EC number, which is the standard numerical nomenclature for this specific enzyme
- Clickable links to the specific pathways into which this enzyme is integrated
- Clickable links to entries for the gene in other databases, including GenBank and Swiss-PROT
- Another rendition of the sequence for this enzyme for comparative analysis
It is worth clicking on the two Pathway links to see how KEGG can show you linkages. For instance, clicking on the ATP Synthesis will give you the following information on the quarternary structure of the synthase:
