Explicit Example

Explicit Example for Sequence Analysis Using Algorithms

You will see how the optimal alignment of two proteins stored in a database can be performed over the Internet. We will use concanavalin A, a lectin, as the protein under analysis and try to find another protein that has a similar sequence.
In the end you will see that the best sequence comparison of the concanavalin amino acid sequence with the other protein, soybean agglutinin, will be achieved by a shift of the second sequence by 123 positions. Thus, if we had looked for a protein that had a similar amino acid sequence to concanavalin A, we would have had a hard time to look for such a sequence manually. This example also demonstrates how fast and relatively easy existing databases can be searched. The biggest advantage of these databases is of course, that they are accessible over the Internet using the World Wide Web as graphical user interface. All the programs for your search are usable over the Internet.

Let's start with a new browser window and connect to the

Connect to Entrez	The Entrez browser allows you to retrieve files from the Protein Data Bank in a format suitable for further analysis. This is done by a search in a protein database.
A search in a protein database.	Type in concanavalin in the Enter Terms field and Search.
	Let the browser then retrieve 102 documents for you.
	Look for the 3CNA entry on page 5 of 6.
	Choose the FASTA Report.
Display Sequence in FASTA Format	This will display the sequence in FASTA format.

Below is the sequence in FASTA format which can be used to run the BLASTp program.

>gi|230826|pdb|3CNA| Concanavalin A ADTIVAVELDTYPNTDIGDPSYPHIGIDIKSVRSKKTAKWNMQDGKVGTAHIIYNSVDKRLSAVVSYPNA DATSVSYDVDLNDVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTHQTDALHFMFNQFSKDQKDL ILQGDATTGTDGNLELTRVSSNGSPEGSSVGRALFYAPVHIWESSAATVSFEATFAFLIKSPDSHPADGI AFFISNIDSSIPSGSTGRLLGLFPDAN

Connect to BLAST site To analyse this sequence using the BLAST algorithm, which stands for Basic Local Alignment Search Tool, connect to the BLAST site http://www.ncbi.nlm.nih.gov/BLAST/

Advanced Blast Search Choose the Advanced BLASTsearch option.

Set the program to blastp and the database to pdb

Copy and paste the derived sequence into the FASTA format field and Submit Query to the server.

Look for the Soybean Agglutinin (sba) (PDB code: 1SBA) in the output and click on the number on the right.

Here is the result: Sequence Alignment

Result of the alignment of parts of the amino acid sequences of Concanavalin A lectin and Soybean agglutinin using the Blastp program

Using the data that we have just retrieved it is possible to 'feed' them into a molecule viewer to find out what the molecule might actually look like. We did this and here is the output: Have a look for yourself and you will see how similar the 3D structure of these two molecules is.

Image of concanavalin A lectin (Data retrieved from the Protein Data Bank, ID-code 3CNA, Image constructed with the help of the program Rasmol.)
The grey/blue strands symbolize the amino acid backbone, while the yellow and red cartoons symbolize different foldings of the amino acid sequence; yellow: beta-sheet, red: alpha helix.

Soybean agglutinin

Image of soybean lectin (Data retrieved from the Protein Data Bank, ID-code 1SBA.)

Connect to BLAST site	To analyse this sequence using the BLAST algorithm, which stands for Basic Local Alignment Search Tool, connect to the BLAST site http://www.ncbi.nlm.nih.gov/BLAST/
Advanced Blast Search	Choose the Advanced BLASTsearch option.
	Set the program to *blastp* and the database to *pdb*
	Copy and paste the derived sequence into the FASTA format field and *Submit Query* to the server.
	Look for the Soybean Agglutinin (sba) (PDB code: 1SBA) in the output and click on the number on the right.