This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009.
Profile Structure Homology Phylogeny
The Phylogeny.fr tree above is somewhat different than the genetic phylogenetic tree previously presented using the same program. This seems a little strange, but could be possibly due to two things. First, I've already shown that the DNA sequences are much less similar in comparison to the protein sequences of these organisms. This would certainly have an affect on the tree. Also this tree contains the sequence for Arabidopsis. Previously I did not use it and Danio rerio ended up being the out group of the tree.
The above seed tree shows the relationships of the steroid-dh family(from PFAM, see below). Again notice the outbranching of the Arabidopsis gene(DET2 at the top). It is also very interesting SRD5A1, the other isoform of SRD5A2) is related more closely to the rat SRD5A1 than to the human SRD5A2. I know they are both different isoforms, but I would expect them to still more related within a single species. To see the entire phylogenetic relationship of all the steroid-dh domains, click here.
References
1. Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed) *: joint first authors
2. The Pfam protein families database: Nucleic Acids Research (2008) Database Issue 36:D281-D288
