Methods and Materials

Following the evolution of the protein

The protein sequence was blasted in the NCBI website. The blasted sequence was scanned using a non-redundand database to obtain the most significant sequences. 57 sequences with significant E-values were recovered. 55 of these sequences were used to perform a multiple alignment sequence by using the program ClustalX. When this was completed, a distance matrix calculation was performed on the sequences. The program Phylip was used. The calculations from the matrix distance calculation were transformed by using the subprogram in Phylip, Neighbor. Afterwards, the bootstrap values for the sequences was calculated using Phylip. THe resulting tree with the bootstrap values displayed was opened by using the program Treefile.

Determining the protein structure

A protein search on PDB, NCBI Entrez, Pfam and InterPro databases was performed as the initial step in identifying the structure of the given protein. The given PDB code 2i2o was used in the searches. Next, proteins with similar structures were identified using the DALI server. A CE comparison was performed among the identified structures.