HOMEWORK 8 – make sure to answer all three parts of the question (a,b,c)

The phylogenetic alignment of amino acid can be used to infer evolutionary relationships among organisms. In this problem, you will align protein sequences from Genbank website using http://www.phylogeny.fr/simple_phylogeny.cgi.

Align amino sequences of a protein that is not ATP synthase alpha subunit from 6 different organisms. You can use any protein, but Calmodulin, Histone H1, and Sialyltransferase are suggested as they are fairly conserved and align easily. You only need to do the alignment for one protein.

The problem has 3 parts, as noted below.

1. Turn in the alignment result in Clustal format.
2. Turn in a picture of the Phylogenetic tree rendering.
3. Describe briefly the function of your protein and the common names of the organisms in your

tree (for example Gallus gallus is a chicken or red junglefowl).

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The following is an example for how to solve the problem for the protein ATP synthase alpha subunit.

1. Go to the website: http://www.ncbi.nlm.nih.gov/protein
2. In box next to Protein, type in “ATP synthase subunit alpha”. The first result should be for Gallus

gallus.

3. Click on the word FASTA under the organism you choose. (Hint: For this simple alignment, try to

choose amino acid sequences that are of similar length. 450 amino acids and 550 amino acids is

close enough, but 250 vs. 550 might not align well.)

4. In the FASTA page is all the data you need for the alignment. For Gallus gallus we will copy and

paste the following into

>gi|45383566|ref|NP_989617.1| ATP synthase subunit alpha, mitochondrial

[Gallus gallus] MLSVRVAAVFARSLPRQAGLVSRNALGAAFVATRNIHASKMRFQKTGTAEVSSILEERILGADTSAELEE TGRVLSIGDGIARVYGLRNVQAEEMVEFFFGLKGMSLNLEPDNVGVVVFGNDRLIKEGDVVKRTGAIVDV PVGEELLGRVVVALGNPIDGKGPITSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELI IGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATAS DAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLE RAAKMNDSFGGGSLTALPAIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSA AQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYA GVKSHLDKLEPSKITKFESAFLAHVLSQHQALLSTIRTEGKISDQTEAKLKEIFTNFLSTFEA

1. Paste six such sequences into the “Or paste it here” box on the website:

http://www.phylogeny.fr/simple_phylogeny.cgi

2. The six sequences need to contain the “> description” line. You can change the description to something other than “gi|45383566|ref|NP_989617.1| ATP synthase subunit alpha, mitochondrial [Gallus gallus]”. For example I shortened it to “> Gallus gallus”.
3. After pasting six sequences, clikc the “Submit” button. This will directly make your tree (the answer to part b). You simply copy the tree from the webpage and paste it into a word document.

To answer part A, now click “3. Alignment” which is slightly above the tree. At the bottom it says “Outputs”. Click on “Alignment in Clustal format”. Copy and paste the aligned sequences into a word document to answer part a.

In the ATP synthase alpha subunit, the answers to a and b would be: