This page was produced as an assignment for an undergraduate course at Davidson College.

How to do a Protein BLAST

Now that you've learned how to do a nucleotide BLAST, you can apply the steps to any type of BLAST to match DNA sequences and amino acid sequences. Why don't we do a protein blast together using the following amino acid sequence?:

1 alqsslkeqq ngfnylsdtv kemakkapse icqkylsefe eieghwkkls sqlvescqkl
61 eehmnklrkf q

Your page should look like this right before you press BLAST:

Protein Page

Your top of your results page should look something like this:

Protein Scores

Now scroll down to the top hit. What protein did we find? You may notice that now the top hit also lists something called "positives". This is because amino acids have characteristics like size, acidity, and polarity, that they can have in common with other amino acids. So the "identities" score tells you how many exact matches your query had with the database's found amino acid sequence, while the "positives" score tells you how many amino acids in your query were at least similar to the database's found amino acid sequence. If you scroll down on the results page, you come across this hit:

Protein Scores

The plus sign between the K and Q, the N and S, the A and S, and the Q and R all denote "positives". According to this amino acid chart, K (lysine) and Q (glutamine) are both polar. N (asparagine) and S (serine) are both neutral and polar...and so on. The idea is that if similar amino acids are substituted for each other, there won't be much of a difference in the ultimate shape of the protein. NCBI uses the BLOSUM62 matrix to decide how similar different amino acids are. To learn more about BLOSUM62, check out the "About BLAST Algorithms" section on the front web page.

You may have also noticed that your top hit was a perfect match, yet somehow it had a lower score than our nucleotide search earlier (147 versus 3323). To learn why this happened, check out the Scores and E-Values section.

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