Pick a sequence from the table below:
| 1I6V | 1I09 | 1GEH | 7hvp |
| 2LYZ | 1rvc | 1qf6 | 1PPB |
| 1oco | 1KGD | 1KD0 | 1K3D |
| 1K3A | 1HY1 | 1GRQ | 1JR3 |
Search is against the SWISSPROT database using BLAST with the default settings.
I have set up a local version of the BLAST program. You will find it faster and easier to acess than the NIH BLAST server, but the interface is a little different.
1. What Matrix did you use and what were the gap penalties? The Default word size is 3
2. (optional- only works on NIH BLAST) Did your sequence match one of the conserved domains that show up while you are waiting for your resutls? If so tell me the abbreviations for these domains.
Once you click on "Format!", you should be able to retrieve your
results.
3. How many hits did you get?
4. Look at the top scoring hit, this is likely to be the source of the original
sequence. Copy this top line so I can see what score you got. It will look something
like:
gi|9632801|ref|NP_049702.1|
(NC_000866) orf nrdC.4 [Enterob... 613 e-175
The first part is a link to the genbank file for the protein (we'll look at
that in a minute), the 2nd part is an abbreviated name, the 3rd part is a the
score for the alignment that is also a link to the alignmet. The last column
is the E value.
5. Click on the link to the genabnk file for the top scoring protein. What is its name, what organism is it from?
Look down your list of hits. Find one with a score around 100. Click on the
score to jump to the alignment. (If nothing happens, it is because you got more
than 50 hits with score above 100. Just look at the alignment at the bottom
of the page.)
6. How many identical residues were there? how many similar? How many gaps?
7. Copy and paste this info to send to me
and to save it for yourself. Also copy and paste the actual alignment.
8. Click on the link for the Genbank protein file. Does this protein seem to
have the same function as the top scoring one?
Now repeat the BLAST search using the PAM70 matrix. First try the default settings for this matrix ( Gap-11 Extend-1)
9. Did the score of the top protein change much?
10. How about the protein that scored ~100 before, Did its score change? Did
the alignment change?