Assignments #2:

1.              Using entrez download the protein sequence with PID# 2506213.
What type of proteins do you find among the related proteins?

2.              Copy the FASTA format of g2506213 onto your computer’s clipboard (not the clipboard of the ncbi page), go to the NCBI blast page and do a gapped blast search (otherwise default options) .
Do you obtain any different results? 

3.              download gi|2506213, 2493127, 4323566, 2983405, 1303679
Using PRSS determine if there is significant similarity between these proteins

4.              Do the same for an D-Alanin-D-Alanin ligase (gi|145722) and a gluthathione synthetase (gi|121663)

5.              Do a blast the D-Ala D-Ala ligase. Increase the Expect parameter to 1000 and the descriptions to 250

6.              Do a PSI-blast the D-Ala D-Ala ligase. After how many iterations do you pick up the carbamoyl phosphate synthetase.  Which other types of enzyme are included among the hits? (If it is too slow check here for 0 iteration, 1st Iteration, 2nd iteration, 3rd iteration, 4th iteration, 7th iteration)

 
***The following will be continued next Wednesday***
 
Some of the other things available at the NCBI website: 

7.              Go to the taxonomy browser in Entrez.  Can you use this to find the taxonomic position of Pyrococcus and Aeropyrum?
To which kingdoms do they belong?
   

 

8.               Go to the ENTREZ genome section. 
Select the genome from
Aeropyrum pernix.

Explore the different genome views (click and explore the different options).
Select Taxtable or TAXA. 
How many ORFs do you find whose most similar sequence is a eukaryotic one? 
What could be the reason for this? (check out the one but last pink dot for a clue – click on it)
Select one of these ORFs and find out what it might encode.