BLASTp Practice Problem

(taken from the middle of a case study...)

Part One

1) Go to the BLASTp (for protein) from this page <http://www.ncbi.nlm.nih.gov/BLAST/> and see if you can diagnose this disease. To assist you, use this sequence which was conserved in all family members:

Try to diagnose what is wrong with the child from this family.

Part Two

Some proteins have no known function, so you will have to make some reasonable conjectures based on amino acid sequence and similarity to proteins with known structures. Let’s look at a couple examples.

1) Perform a conserved domain (CD) web search at this URL <http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi>. Search using accession number (select from the pulldown menu) for the protein “AAC83646” which you type into the large box. You will get a page that has a series of boxes that represent the recognized domains.

2) Mouse over the boxes and find out how many different CDs there are. Don’t just count the number of boxes but find out the types of domains as revealed when you mouse over each box. Some domains are present more than once. The red and blue colors indicate alternatively spliced mRNAs.

3) Click on the “Show” proteins button (top left) and see what hits you get. At what protein have you been looking?

4) Go "back" and click on the link that says next to “ZZ, Zink finger …” from the right-hand column. Read the text at the top of your screen. Given the source of the protein, do you think this domain has an important function? Explain your answer.

BLASTp and Conserved Domain Search

Discovery Questions