The purpose of this assignment is to help you become more familiar with sequence alignment and molecular visualization. In this assignment, you will perform a sequence alignment of glycoside hydrolase family 1 enzymes. For one of the enzymes, you will generate an informative image using VMD.
Go to the CAZY web site (www.cazy.org). Click on the button labeled GH to get into the glycoside hydrolase families of enzymes. Scroll down to the table in which the various families are enumerated. Click on 1 to go to the family 1 enzymes. Select 10 enzymes from this long list for a sequence alignment. You will probably have the fewest problems if you choose enzymes from only one kingdom (i.e., archaea, eubacteria, and eukaryotes), and I would recommend using enzymes from eukaryotes. Within a given kingdom, you should choose the enzyme from 10 different organisms (their organism names will be different). Also, one of your choices should be an enzyme for which a 3-D crystal structure is available.
Use Biology Workbench to perform a multiple sequence alignment (MSA) of the 10 sequences. I think you will find it easiest if you paste in the sequences using FASTA format. This format should be available for all enzymes, though it is not always apparent when you first enter a web site that has information related to the enzyme. You should be able to do the alignment using the default parameter settings, though you may experiment with these if you wish.
1.Generate a color-coded image of the (MSA) (e.g., Boxshade).
2.Provide a discussion of the alignment (i.e., comment on sequence identity, gaps,conserved residues, etc.).
3.For one of your enzymes for which a 3-D structure is available, prepare informative image(s) using VMD. For example, what are the predominant structural features? What is the SCOP fold of this enzyme and can you illustrate that in a figure? Where are some of the highly conserved residues located in the 3-D structure?
4.Prepare a report in which you describe the methods and results that you obtained. Each figure should have its own figure legend that provides a brief description of the content of the figure. A reader should be able to understand the figure from the figure legend you provide (e.g., if you use colors in defining parts of the 3-D structure, you should provide the color coding in the legend).