Choline Oxidase: Difference between revisions

The Basic Local Alignment Search Tool (BLAST) is a web program that aligns a protein with other proteins to find areas of similarities in terms of similar residues.  It was used to first find the closest possible sequences to choline oxidase from Arthrobacter globiformis and then to compare the sequence of choline oxidase to caritine acetyltransferase (CRAT) from Mus musculus. Using the National Center for Biotechnology Information (NCBI) website, accession numbers were obtained for the both proteins. The NCBI website also showed a taxonomic tree for choline oxidase. The only protein from a mammal on that tree was CRAT. For this reason CRAT was chosen for comparison. A protein BLAST was run on just choline oxidase alone. The amino acids sequences near the FAD ligand were noted. Then the accession numbers for both choline oxidase and CRAT were aligned in the protein BLAST for comparison. The E-value predicts the likelihood that two genes are truly similar by random chance. E-values close to zero represent that the correspondence between the two sequences must have arose from similar ancestry and not by random chance.  The query in the alignment represents choline oxidase and the subject represents CRAT. The composition of choline oxidase from residues 460 to 483 was of interest since it was close to the flavin group. This is not indicative of the whole structure being similar, but just key amino acids. The BLAST was able to compute the identities, positive and gap scores. Identities represent the number of amino acids were purely conserved between the two sequences. There are seven amino acids evolutionarily preserved within the vicinity of the flavin group. Similar but non-identical residues along with matches were counted for positives. The gap score was zero since neither sequence was shifted by adding a gap in order to align.