Figure 1. Largest open reading frame (ORF) of Saccharomyces cerevisiae Pyruvate kinase. MacDNAsis was used to produce this analysis of the different reading frames of  Pyruvate kinase cDNA from the Saccharomyces cerevisiae gene. The blue segment is the largest ORF and begins with the start codon marked by a red triangle at nucleotide 1 and continues until nucleotide 1503 where a green line marks the stop codon.

Figure 2. The amino acid content of Saccharomyces cerevisiae Pyruvate kinase. MacDNAsis was used to determine the amino acid content encoded by the above largest ORF from Saccharomyces cerevisiae Pyruvate kinase (see figure 1) sequence. Saccharomyces cerevisiae Pyruvate kinase contains 501 amino acid residues, and has a molecular weight of 54541.71 Daltons.

Figure 3. Kyte and Doolittle hydropathy plot of Saccharomyces cerevisiae Pyruvate kinase. MacDNAsis was used to produce a hydropathy plot of Saccharomyces cerevisiae Pyruvate kinase based on the hydrophobicity of the amino acid residues. The X-axis represents the number of the amino acid within the protein sequence, and the Y-axis represents the hydrophobicity of the amino acid being analyzed. The regions where the hydrophobicity is greater than 2.00 indicate integral membrane domains. Saccharomyces cerevisiae Pyruvate kinase is likely an integral membrane protein, as suggested by the numerous regions above the threshold line at 2.00.

Figure 4. Hopp and Woods antigenicity plot of Saccharomyces cerevisiae Pyruvate kinase. MacDNAsis was used to produce an antigenicity plot of Saccharomyces cerevisiae Pyruvate kinase by demonstrating regions of hydrophilicity.  The X-axis represents the number of the corresponding amino acids within the protein sequence, and the Y-axis represents hydrophilic (positive Y-values) and hydrophobic (negative Y-values) regions of the protein sequence being analyzed. This portion of the plot shows the most hydrophilic region that indicates a potential epitope location which can be used in generating a monoclonal antibody. The hydrophilic portion of the protein around amino acid 193 could be used to generate a peptide and a monoclonal antibody against the peptide which could recognize the epitope, while the protein is in its native conformation.

Figure 5. Chou, Fasman, and Rose prediction of Saccharomyces cerevisiae Pyruvate kinase secondary structure. The secondary structure of Saccharomyces cerevisiae Pyruvate kinase was predicted by MacDNAsis. The predicted secondary structures (helix, sheet, turn, and coil) are displayed using different colors and patterns as shown in the legend.

Figure 6. Multiple sequence Alignment of Pyruvate kinase. MacDNAsis was used to perform a multiple sequence analysis (Higgins method) of the following species: Homo sapiens, Mus musculus, Caenorhabditis elegans, Saccharomyces cerevisiae, and Arabidopsis thaliana. This multiple sequence analysis highlights the amino acid residues which are common to more than one species. Only the amino acid residues from 1 to 400 are shown. A phylogenic tree of the species according to Pyruvate kinase (Figure 7) was predicted by comparing these residues.

Figure 7. Phylogenic Tree illustrating the percentage of homology between the amino acid sequences of five different species: Homo sapiens, Mus musculus, Caenorhabditis elegans, Saccharomyces cerevisiae, and Arabidopsis thaliana. MacDNAsis was used to predict the phylogenic tree of the five different species (above) according to Pyruvate kinase. The two mammalian species, Homo sapiens and Mus musculus, have the most highly conserved amino acid sequences. Arabidopsis thaliana shows the least homology to the other protein sequences of the other species.

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