1. Aphrodisin and odorant-binding protein are both examples of lipocalins. First obtain the accession numbers for rodent forms of these proteins, and then perform a pairwise sequence alignment (use pairwise BLAST). Record the percent amino acid identity, the percent similarities, the expected values, and bit scores. Which matrix is most useful in helping you determine relatedness?
2. Is the pol protein of HIV-1 more closely related to the pol protein of HIV-2 or to the pol protein of simian immunodeficiency virus (SIV)? Use the blastp program to decide. Hint: try the Entrez command "NOT hiv-1 [organism]" to focus the search away from HIV-1 matches.
3. You perform a BLAST search and a result has an E value of about 1 x 10-4. What does this E value mean? What are some parameters on which an E value depends?
4. Olfactory receptors are related to the rhodopsin-like G-protein couple receptor (GPCR) superfamily. Use the Integr8 proteome tool at EBI to decide about what percent of the mouse proteome is comprised of these receptors. About what percent of the human proteome is comprised of these receptors?
5. Mutations in the beta chain of hemoglobin (gene symbol HBB; also called bata globin) can cause sickle cell anemia or other diseases. Try to find the PDB accession numbers for both normal hemoglobin and a mutated form. Try the following:
a. The NCBI structure page
b. The PDB
c. CATH or SCOP
d. A blastp search against the PDB at the NCBI website.