Posted: March 21st, 2015
#-Find the conserved Domains for two protein sequences by using these steps:
Go to http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi and paste in your protein sequence.
What conserved domains are present in your sequence?
Go to http://pfam.xfam.org/ and paste in your protein sequence.
What conserved domains are present in your sequence? Do you have both PFAM-A and PFAM –B domains? How do these results compare with the previous?
Protein Secondary Structure
Go to Softberry Proteins secondary structure page http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=propt
There are a number of software tools here. Try these out on your protein sequence.
3-D protein structure
Go to PDB http://www.rcsb.org/pdb/home/home.do#Subcategory-search_sequences , and paste in your protein sequence.
Other tools are available – take a look at CN3D
Exercise – 3D structures
you can find the structure of the two proteins in these two databases.
Look for secondary structure, and 3D structure
Secondary structure prediction
Take the sequence for the protein you just looked at, and run it through 2 or more of the following secondary structure tools. You may also wish to try the test sequences that some of these sites have.
How does the prediction compare to the structure
This is a link to the servers that can predict protein structure. Try running your protein sequence through one of these (note it may not run in the time available, but can be looked later) http://www.predictioncenter.org/index.cgi?page=links
** TMMA – Multiple Sequence Alignment
In this exercise we are going to look at the conservation of sequence in rhodopsin and related sequences. Rhodopsin is the visual pigment in the eye, and is member of the G-Protein Coupled Receptor (GPCR)/seven transmembrane domain (7TM) protein superfamily.
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