Homework 4: Fill in the blank – 2.5 points each – capitalization does not matter. Students can take this assignment an unlimited number of times with the best score kept.
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Question 1 of 1
1. Question
For this homework, you first need to acquire the nucleotide and amino acid sequences for two Methanocaldococcus jannaschii DSM 2661proteins, MJ_RS01470 (formerly MJ0277) and MJ_RS03495 (formerly MJ0663), from NCBI Gene and Protein databases. Perform the following for both proteins:
• Use BLASTN to compare the nucleotide sequence between the 2 proteins
• Use BLASTP to compare the protein sequence between the 2 proteins
• Use BLASTP to compare the amino acid sequence for each protein individually to the non-redundant protein sequences (nr) database
• Use PSI-BLAST to compare the amino acid sequence for each protein individually to the non-redundant protein sequences (nr) database-
- 1. From the BLASTN results, what was the query cover as a percentage?
2. From the BLASTN results, what was the E-value?
3. From the BLASTN results, what was the percent identity?
4. From the BLASTP results compare the protein sequence between the 2 proteins, what was the query cover as a percentage?
5. From the BLASTP results compare the protein sequence between the 2 proteins, what was the E-value?
6. From the BLASTP results compare the protein sequence between the 2 proteins, what was the percent identity?
7. From the BLASTP results comparing MJ0277 to the non-redundant protein sequences (nr) database, what is the identity of the protein (HINT: Found in the Description)?
8. From the BLASTP results comparing MJ0277 to the non-redundant protein sequences (nr) database, what was the percent identity of the protein with protein found in Methanocaldococcus bathoardescens?
9. From the BLASTP results comparing MJ0633 to the non-redundant protein sequences (nr) database, what is the identity of the protein (HINT: Found in the Description)?
10. From the first iteration of PSI-BLAST results comparing MJ0277 to the non-redundant protein sequences (nr) database, are the results the same or different from those obtained from BLASTP results?
11. From the second iteration of PSI-BLAST results comparing MJ0277 to the non-redundant protein sequences (nr) database, are the results the same or different from those obtained from BLASTP results?
12. From the second iteration of PSI-BLAST results comparing MJ0633 to the non-redundant protein sequences (nr) database, what was the percent identity of the protein with protein found in Thermincola potens?
- 1. From the BLASTN results, what was the query cover as a percentage?
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