Module 5 Assignment

Open the SKP1A nucleotide sequence

1. Translate the CDS into a protein sequence. (Note: there are no introns/exons in this ORF).
2. Paste that sequence into the results.
3. BLAST the whole protein sequnce against the nr database.
(Note you can either do this in vectorNTI or a web browser).
1. What is the accession number of the best hit?
2. What is the E value for the best hit?
3. What is the percent identity?
Hint:   Make sure that you use the nr database.

Open the protein sequence in BioAnnoatator.

4. Set the plot to display the following:
   1. Display Hydrophobicity indices at pH 3.4 determined by HPLC to be red lines. Set the window size to be 11 characters.
   2. Display Hydropathicity as solid blue bars. Set the window size to be 11 characters.
   3. Overlay the Hydrophobicity (red lines) on top of the Hydropathicity (blue bars)
5. Use the camera to take a photo of that image and paste it into a word document
6. Align the following protein sequences:
   • AAC50407
   • AAC50408
   Generate a pairwise dotplot between them. Paste that dotplot into your results. Does the dot plot suggest anything about the similarity of the two proteins?

Paste the results into a microsoft word file. When you save the file, please include your name in the title. Email it to Rob