Performing a BLAST

• What are the advantages of performing a BLAST based on the amino acid sequence encoded by the nucleotide sequence? • What is the best candidate gene and organism that BLAST returns now? • Note other BLAST hits in the results and compare with those alternate hits seen in the nucleotide – nucleotide BLAST from earlier. Have any shifted up in score? Down? • Other than similarities between two different amino acid’s structures, give a reason for the shift in score. • As suggested in 12, if two different amino acids are “similar” enough, then sometimes a substitution won’t affect protein function. Scroll through the alignments and list three commonly seen substitutions (illustrated with a “+” symbol between the query and subject line), and give a reason those two amino acids might be interchangeable. • Do you see any high scores that are listed as “hypothetical protein?” Is this BLAST search sufficient to claim that those hypothetical proteins are indeed a functional luxI homolog? Why or why not? Include the species name associated with the hypothetical protein. • If you wanted to verify the function of one of these hypothetical proteins, what would be the next step? • List one interesting result you saw during your searches, and why it was interesting to you. 10,000-letter minimum.                                                                              

Sample Solution