Assignment 3
1. Do a BLAST search with the human (Homo sapiens) protein oncostatin M (Seq ID: AAX29842.1)
a. Does your BLAST search identify OSM orthologs in other species that are present in the protein database? List the names, species of origin, E-values and accession numbers of potential orthologs.
b. Does BLAST identify any obvious paralog of the oncostatin M? If you detect a paralog provide the data and reasoning for your conclusion. If you don't detect a paralog describe the basis of your conclusion.
2. Use PSIPRED with GenTHREADER or Phyre2 to identify protein folds within the human (Homo sapiens) protein oncostatin M.
a. Do either of these programs identify a protein with similar folds?
b. Would you consider one of these to be a paralog of oncostatin M? Provide your reasoning
3. Take the most probable paralog of oncostatin M and do a protein-protein alignment. Discuss the similarity identified in your alignment
4. Go to the PDB database and look at the Oncostatin M record - view the structure. In your own words briefly describe the structure
5. Go to the Conserved domain database and search with the oncostatin M sequence.
a. Is a conserved domain identified? If so, which domain?
b. List the names and species origin of the sequences that were used to define the domain (hint-link to one of the PSSMs and click on the accession number of the sequence)
c. Are any of the sequences used to define the domain potential paralogs of OSM? Describe briefly.
d. Can you identify amino acid residues in the PSSMs that are conserved in all of the sequences that would substantiate the classification of this as a conserved domain? Very briefly describe.
e. Are there conserved cysteines that could contribute to structural conservation?
Format your assignment according to the following formatting requirements:
1. The answer should be typed, double spaced, using Times New Roman font (size 12), with one-inch margins on all sides.
2. The response also include a cover page containing the title of the assignment, the student's name, the course title, and the date. The cover page is not included in the required page length.
3. Also Include a reference page. The Citations and references should follow APA format. The reference page is not included in the required page length.