For Introduction to NCBI, explore the hemoglobin protein sequence using BLAST.

Go to NCBI home page (Welcome to NCBI). Use this link:https://www.ncbi.nlm.nih.gov/

In the search window, type the RefSeq accession number for the human beta hemoglobin protein chain, NP_000509. Click the search button. There is only one search result because this is a unique accession number.

Click on the link. Explore the beta hemoglobin NP_000509 file.

Find the link to the BLAST on the right side at the top of the page (Run BLAST). Click on the link. Explore the BLAST page.

1. What is the suggested database for the search?

Select the Reference proteins (Refseq_proteins) database. Scroll all the way down.

2. In the Program Selection section, what is the suggested program (algorithm)?

Click the BLAST button at the bottom of the screen.

The processing of your request for the sequence alignment may take a few minutes. You need to wait without any additional attempts to speed it up. After the results page opened, scroll down, click the Alignments button and explore the alignment page.

Scroll down all the way to the actual alignments. Each of them has three lines of letters. The top line is the original sequence (Query). The bottom line is another sequence from the database, calledsubject(Sbjct). The middle line shows which amino acids are identical in both sequences and where the alignment hasmismatchesandgaps.

Find the alignment of the human and the gorilla beta hemoglobin protein sequences. It is among the top few alignments. The name of the source (species) follows the title of each alignment.

3. How many mismatches does this alignment has? How many gaps does this alignment has?

4. What is the specific difference between the two sequences in the alignment? Give the one letter code and full names for the amino acid substitution(s).

5. Is this substitution conservative or nonconservative? Please explain.

6. What is theidentity percentagefor this alignment? Define identity percentage for sequence alignment.

7. What is the percentage forpositives? What are positives in the context of BLAST alignment? Use the NCBI glossary page:https://www.ncbi.nlm.nih.gov/Class/FieldGuide/glossary.html#P