To discover the role of this mysterious sequence, we will search for proteins in a database that show high similarity to a translation of Sequence R.
To do this we will use a sequence search engine, BLAST, to search sequences in the database at the National Center for Biotechnology Information (NCBI).
BLASTX uses the genetic code to translate Sequence R, then compares it with every protein in the sequence database.
The BLASTX search may take a few minutes, during which time “Status” on the Web page is “Searching”.
Results will be shown in a long Web page. Scroll down to see a table of results. The best-matching sequence from the database is listed first.
Question 1
Sequence R has an
excellent match to a known protein, indicated by its low E-value and
high percentage identity. We assume Sequence R codes
for this protein.
What is the name of this protein?
Hint: To find out more about this protein, click the link under “Accession”.
Then you will see the protein name near the top of the page, in bold.
Question 2
In which organism is this protein found?
Hint: Look for the line beginning
“SOURCE”.
Question 3
What is the biological role of the
protein?
Hint: Do a Web search for the name of the
protein (from your answer to Question 1).
We will now perform another BLAST search to see if Sequence
R has a match in the human genome.
This time, we will
use BLASTN, which compares a DNA query with a DNA
sequence database.
1. Copy Sequence R again from our Web page.
2. Go back to the main NCBI BLAST Web page. (You can just search for “NCBI BLAST”.)
3. Under “BLAST Genomes”, click “Human”.
4. Click “blastn” at the top of the page, and paste in Sequence R.
5. Under “Program selection” > “Optimize for”, select “Somewhat similar sequences (blastn)”.
6. Click “BLAST”.
Question 4
On which human chromosome has the best
match been found?
In your results, you will see a good match between Sequence R and the human genomic DNA. However, the mouse (Sequence R) and human sequences differ, due to mutations.
Figure 1 shows evidence of substitution and
frameshift mutations in BLASTN results.
Question 5
In the alignment between Sequence
R and the human genomic DNA, can you see evidence of a
substitution mutation?
If so: sketch the region that includes
the substitution.
Question 6
Can you see evidence of an insertion or
deletion mutation?
If so: sketch the region that includes the
insertion or deletion.
A frameshift mutation is an insertion or deletion which disrupts the reading frame of a protein-coding sequence. From this point on, any protein sequence would be scrambled.
A frameshift mutation is strong evidence that the DNA no longer codes for a functional protein.
Question 7
Do you think the human genome includes a
functional version of Sequence R?
Explain
your answer.
Question 8
Sequence R comes from
the house mouse and codes for L-gulonolactone oxidase, an enzyme that
synthesizes vitamin C.
Vitamin C is vital for both humans and
mice.
Does your answer to Question 7 tell us anything about
how the diet of humans might differ from the diet of mice?
Daniel Barker, Heleen Plaisier, Laura CE Campbell, Stevie A Bain, Richard Fitzpatrick and Chenxi Zhang
4273pi Bioinformatics Education Project
Copyright and related rights waived via
CC0 1.0 Public Domain Dedication.
Version 3.1 (short)