AJT+Homology

=F2 protein Homology=

Alignments
Using the MEGA program with the following parameters an alignment was created. Part of that alignment is displayed below: - I also ran an alignment through the Geneious collation system with the folowwing results. The parameters remained the same. This alignment is less detailed than the MEGA but does show the families and super families. The KR Kringle domains are regions of the protein that are thourght to bind to membranes and other phospho lipids - They play a key role throughout the clotting cascade pathway. The GLA domain is the vitamin K dependent GLA region and the TrypSPc is the serine protease that acts as the peptide bond breaking region that turns the prothombin zymogen into the active Thrombin.

Phylogenetic Tree
As this is an investigative study, I decided to run several types of tree parameters and systems. I have included here the Geneious UPGMA consensus tree protein alignment for the selected organisms. The selection parameters were as follows : -

I have included the common name for each organisum in this tree for simplicity. The numbers at each node represent the bootstrap percent reliability of the relationship. The length of the lines between organisms represent the degree of similarity. The MEGA tree below using the same alignment was calculated with the following parameters : - The resultant tree was slightly different to the Geneious tree due to the modelling methodolgy used although the basic relationships were the same.

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