Using the cDNA and amino acid sequences generated from the GenBank search of Alcohol Dehydrogenase in Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana MacDNAsis was able to determine the following: the largest open reading frame (ORF) in the cDNA, the sequence and molecular weight of the protein (Alcohol Dehydrogenase) encoded by this cDNA, hydropathy and antigenicty plots of the protein, a predicted secondary structure of the protein, and a multiple sequence allignment of the protein from all five organsims.
Homo sapiens Alcohol Dehydrogenase cDNA Open Reading Frame
MacDNAsis produced this analysis of the different reading frames of human Alcohol Dehydrogenase cDNA. The black segment in Figure 1 is the largest ORF and begins with the start codon marked by a red triangle at nucleotide 73 and continues until nucleotide 1200 where a green line marks the stop codon. The amino acid sequence encoded by this ORF from the Homo sapiens cDNA sequence contains 376 residues and forms a protein with a weight of 39,823 Daltons (D).
Hydropathy Plot of Alcohol Dehydrogenase
MacDNAsis produced a hydropathy plot of Alcohol Dehydrogenase based on the hydrophobicity of the amino acid residues. Regions where the hydrophobicity is greater than 2.00 suggest integral membrane domains. With the numerous regions above the line at 2.00, it is likely that Alcohol Dehydrogenase is an integral membrane protein.
Antigenecity Plot of Alcohol Dehydrogenase
This antigenecity plot from MacDNAsis shows regions of hydrophilicity. The regions with the highest values are the most hydrophilic and indicate potential epitope locations for antigens.
Secondary Structure of Alcohol Dehydrogenase
The secondary structure of Alcohol Dehydrogenase was predicted by MacDNAsis using the Chou, Fasman, and Rose guidelines to produce the above structure. The different possible secondary structures, helix, sheet, turn, and coil, are demonstrated using different colors and patterns as shown in the legend. A Rasmol image of Alcohol Dehydrogenase is also available to help visualize the structure of Alcohol Dehydrogenase.
Our knowledge of the different amino acid sequences encoding Alcohol Dehydrogenase in the five different species mentioned above allows MacDNAsis to perform a multiple sequence analysis on Alcohol Dehydrogenase. This analysis points out similarities and differences in the amino acid structure of Alcohol Dehydrogenase among the species and even predicts the evolutionary history of the protein.
Multiple Sequence Allignment of Alcohol Dehydrogenase
This multiple sequence analysis highlights the residues that are common to more than one species. Only the residues from 150 to 250 are shown above. This comparison of residues allows MacDNAsis to predict the phylogenetic tree of the species according to Alcohol Dehydrogenase.
Phylogenetic Tree of the Species According to Alcohol Dehydrogenase
The above figure shows the phylogenetic relationship among species and determines the percent allignment between two species according to Alcohol Dehydrogenase residue similarity. It is not surprising that the two mammalian species, mice and humans, have highly conserved amino acid sequences. Mice, humans, and C. elegans differ greatly from Arabidopsis and fruit flies suggesting a divergent evolution in regards to Alcohol Dehydrogense.
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