Homework #9
 

1)      Obtain the following protein sequences from any public database you wish and align using CLUSTALW program. The protein sequences are: Human MDM2, Hamster MDM2, Murine MDM2, Xenopus MDM2 and Zebrafish MDM2. The human MDM2 sequences is approximately 490 amino acids in length. Name three areas that are structually conserved amongst these orthologs. According to the Guide Tree, which two sequences have the highest similarity? Perform CLUSTALW just using Human MDM2 and Zebrafish MDM2 sequences. Does the human/zebrafish alignment in this run differ from the human/zebrafish alignment obtained in the first run? Explain why.

2)      4. There exists a paralog of MDM2. Obtain the sequences of the human paralog MDMX and the mouse paralog MDMX and perform multiple sequence alignment again together with the original five MDM2 sequences. Give the domains (in amino acid number ranges) that are highly conserved within sequences of this entire family. Use the human MDM2 amino acid numbers as the reference when explaining the ranges that are conserved.


 
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