Bioinformatics: Clustal W and Consurf, science homework help

a) What do the “*” and “:” indicate on the MSA alignment?

b) Why does the secondary structure prediction come back with a higher percentage of random coil then actually exists in the protein?  Is this prediction accurate and/or realistic? Why or why not?  Please explain

c)  What is a conserved sequence motif? 

d)  Is there a relationship between the sequence conservation and the overall 3-D structure? 

e)  The exercise looked at the multiple sequence alignment of a protein. How would you use MSA on a nucleic acid (such as a tRNA) and what information might you obtain from that exercise? Will you always look simply for conservation or are there other factors that might come into play? To answer this question, think about the structure of tRNA. If you don’t know what tRNA looks like, work through this tRNA tutorial before answering the question.