What is the gap-existence penalty

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Reference no: EM133255953

Goal: Perform pairwise alignment on two seemingly different proteins. Answer some questions about the alignment and the proteins.
Given: BLASTP pairwise alignment, default values.
Given: The following two sequences:
>NP_476761.3 abnormal wing discs, isoform C [Drosophila melanogaster]

>CAA35621.1 Nm23 protein, partial [Homo sapiens]

Question 1: Based on the bits and the E value, are these two proteins homologous? Briefly explain what led you to that conclusion.

Question 2: List the % identity and the % positives and briefly explain the difference between identity and similarity.

Question 3: What is the gap-existence penalty? The gap extension penalty?

Question 4: Look at the last (C-terminal) 10 amino acids in the alignment. Using the BLOSUM62 matrix (see lecture notes or use R) to evaluate the matches and mismatches, score the last 10 amino acids in the alignment. Show your work (or the R command and output).

Question 5: Go to the human protein record and find the reference by Rosengard et al. What is the name of the human protein?

Question 6: What does awd (the name of the fly protein) stand for?

Question 7: On the surface, it might seem surprising that two such proteins would align. According to the abstract, how are tumor metastases related to abnormal wing disc development in flies?

Reference no: EM133255953

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