Protein Structures - CDD

Since you found that there are few similarities in the amino acid sequences for alpha amylase in the three organisms, how do we account for them being functionally similar?  We need to take one more step and examine the three dimensional structure of the enzymes.  You can use tools on the NCBI website for this as well.

Open the NCBI main page. Click on Domains and Structure on the left hand menu bar, and then select Conserved Domain Database (CDD) under the resource tab.

http://abacus.bates.edu/bioinformatics1/screenshots/NCBI-13-Structure-1.webp

Protein Structures - CDD

There are many ways to search for structure information on conserved domains. We will use the FASTA sequences. Click on "Search Methods"' as shown below:

http://abacus.bates.edu/bioinformatics1/screenshots/NCBI-14-Structure-2.webp

 

Protein Structures - CDD

Type the accession number for human alpha amylase into the big center search window.  Select the CDD database from the pull-down menu.  Click on SUBMIT QUERY.

http://abacus.bates.edu/bioinformatics1/screenshots/NCBI-15-Structure-3.webp

The results window should confirm that this sequence is for alpha amylase.  Click on SEARCH FOR SIMILAR DOMAIN ARCHETECTURE.

http://abacus.bates.edu/bioinformatics1/screenshots/NCBI-16-Structure-4.webp

At the CDART page (Conserved Domain Architecture Retrieval Tool), scroll down and select the alpha amylase catalytic domain (pfam000128).

http://abacus.bates.edu/bioinformatics1/screenshots/NCBI-17-Structure-5.webp

Expand the "[+]Structure" menu, which is collapsed by default. Then click on SHOW STRUCTURE:

http://abacus.bates.edu/bioinformatics1/screenshots/NCBI-18-Structure-6.webp