The protein sequence for the SDR family member 1 protein being investigated was downloaded from the PDB site, using the accession code 2qq5. This was then iteratively searched in blastp using an offline, non redundant copy of the database produced on the 28th of April 2008.
MULTIPLE SEQUENCE ALIGNMENT
The results from the blast search were then screened and a selection was of these results were used for a multiple sequence alignment using ClustalX. This result was boostrapped using 1000 simulations and these values checked and more sequences were added to improve the resolution of specific branches. A bootstrapped phylogram was produced.
The results from ClustalX were imported into treeview and a phylogenetic tree was produced, with bootstrapping values attached, and then split into bacteria and anamalia kingdoms.
The protien sequence from PDB (2qq5) was aligned aginst other known sequences for structural similarity using the Dali web server. The structure of the most structurally related protien (Oxoacyl-(Acyl-carrier-protien) reductase) was alighned against DHRS1 in 3D using Pymol.