#-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?

PFAM

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

http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

Protein Structure

Exercise – 3D structures

you can find the structure of the two proteins in these two databases.

http://www.ncbi.nlm.nih.gov/structure

http://www.pdb.org/pdb/home/home.do

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

http://bioinf.cs.ucl.ac.uk/psipred/

http://www.compbio.dundee.ac.uk/jpred4/index.html

http://expasy.org/resources/search/keywords:secondary%20structure%20prediction

https://www.predictprotein.org/

3D prediction

http://predictioncenter.org/

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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