Based only on the jackhmmer iteration two results

Assignment Help Biology

Reference no: EM133255957

Goal: Use JACKHMMER to find matches and then assess homology.

Given: Everyone will be assigned a query protein, a database and a taxonomy limit. You will be looking for your target protein on Iteration 2 of JACKHMMER. You will also be looking for matches that match your assigned domain pattern.

Query Protein: WP_104828400; Database: Uniprot; Taxonomy Limit: Archaea;

Domain in sequence: Hemerythrin, Hemerythrin; Target Protein: Q8ZUP5_PYRAE

Question 1: Start with a few sentences about your particular query protein and your target protein. If you can find their functions, focus on that.

Question 2: What is the E value for your target protein in the iteration two results?

Question 3: Based ONLY on the JACKHMMER iteration two results. can you definitively conclude homology between your query and your target? Briefly explain.

Question 4: After iteration two of JACKHMMER, how many sequences have the domain pattern to which you were assigned? List the identifiers for two of those matches (if there are two).

Question 5: Using only BLAST and/or pairwise BLAST, assess homology between your query sequence and your target sequence. You can use a series of blastp searches. Describe your strategy and your conclusion.

Question 6: List the domains are shared between your query protein and your target protein. Based on domain sharing, do you think that provides further evidence of homology between your query and target? Briefly explain.

Reference no: EM133255957

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