Protein Alignment

This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009

T-Coffee protein sequence alignment 

This protein sequence alignment was done using T-Coffee (2) against the orgaism Mus musculus, Danio rerio, Gallus gallus, Rattus norvegicus, Pan troglodytes, Drosophila melanogaster and Homo sapiens.  The results of this analysis are seen in the file below. 

alignment.pdf
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ClustalW2 protein alignment  

Here I did another  Protein sequence aligment of SIRT6 this time using ClustalW2 (1), this analysis was done using all standard setting and all the same species were used as before. I performed this alignment to see if different sequence alignment programs would effect the results I would obtain.  

untitled.bmp
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Protein alignment results

The results I found with my protein alignment where some what supprising, how they where supprising was due to the fact that the proteins where much more similar compared to the DNA sequences.  For example human had a score of 88 and 87 for rat and mouse which was alot higher of a score compared to my DNA sequence alingment. And even Gallus had higher scores to human, mouse and rat.  Some possible reasons for these high protein alignment scores could be due to some of the DNA sequences where mRNA products, so they werent taken directly from the DNA and contained poly a tail.  But this still dosent explain this even though I did a extra analysis of the DNA with the poly a tail removed and didnt get any better results.

Sirtuin Family alignment

Using ClustalW I did a search to compare the Sirtuin family of protein in humans to determine how similar they could be to each other.  From this one can draw some very interesting conclusions, for one SIRT2 and SIRT3 are most closely related is surprising because SIRT3 is mitochondrial protein  while SIRT2 locates only to the cytoplasm.  Also the very close relation with SIRT6 and SIRT7 is not surprising because of the fact that these two proteins are both nuclear proteins.   I think this tree shows how distinct each protein is compared to the other sirtuin family members. 

Sequence alignment

This is an amino acid alignment of all the siturin family members, I did this to see at the actual protein sequence level how similar each of these proteins is to one and another.  As one can clearly see most of the family is not similar to each other, but there are some interesting relationships.  For one how closely SIRT3 and SIRT2 are 42 is again as I said above very interesting due to there different location in the cell. But what really shocked me was how SIRT7 and SIRT6 have one hundred similarity to each other.  This makes me wonder if they could interact with some of the same proteins found in the nucleus. 

References

1. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007). ClustalW and ClustalX version 2. Bioinformatics, 23(21): 2947-2948. doi:10.1093/bioinformatics/btm404.


2. Notredame, E., Higgins, D.G., and Heringa, J. (2000). T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1):205-217. doi:10.1006/jmbi.2000.4042.

Mark Devries
Email [email protected]
last updated 1/22/09
http://www.gen677.weebly.com