Figure 1

Gene Composer software, Alignment View. Comparative sequence alignments and corresponding structural information are organized by the Alignment Viewer of Gene Composer, shown here with PDB file sequences for human renal dipeptidase (1ITU), and the amino acid sequences of full length human renal dipeptidase plus selected vertebrate homologues (FASTA files read from a BLAST search using the amino acid sequence file of PDB file 1ITU). The sequence alignments are produced by the popular ClustalW algorithm [6, 7]. The conserved consensus sequence is also shown. Solvent accessible surface area is represented in purple shading levels (light is low and dark is high) calculated according to Connolly [9]. Thermal B-factors from the PDB file are normalized and represented in red shading levels (light is low and dark is high). Residues that contain atoms within 3.5 Angstroms (or other user defined setting) of an oxygen atom of water molecules are illustrated with a blue dot. Residues that contain atoms within 4.0 Angstrom (or other user defined setting) of a non-hydrogen atom of a small molecule ligand are illustrated with colored circles or dots (excluding blue dots for water contacts). Residues that contain non-hydrogen atoms within 4.0 Angstroms (or other user defined setting) of any non-hydrogen atom in a neighboring protein chain are illustrated with a green diamond when space group symmetry operators are applied to build crystallographic neighbor molecules, or a red diamond when the contact is between non-crystallographic symmetrically related polypeptide chains. Protein secondary structural regions are represented by red helices for alpha helical regions, blue arrows for beta-sheet regions, and green squiggles for turns, as defined the respective PDB file format.