Bioinformatics: Multiple Sequence Alignment Lab, science homework help

Science

Assignment: 

In this lab, we are comparing sequences of phosphoglycerate kinase amongst different organisms. 

Procedure:

1. Visit http://www.ebi.ac.uk/Tools/msa/clustalo/

2. Copy & Paste alignment sequences into input box (You will find this attached as “4NG4 Multisequence”)

3. Click Submit

4. Right Click “Download Alignment File” –> “Download Linked File”

5. Visit http://consurf.tau.ac.il

6. Click Amino Acids –> Is there a protein structure ? Yes –> PDB ID: 4NG4 –> Click “Next” –> Chain A –> MSA to upload ? Yes –> Choose File: Upload the file you downloaded from Clustal Omega –> Query Sequence Name: sp|P0A799|PGK_ECOLI –> Tree file to upload ? No –> Uncheck send link to email –> Click “Submit” & wait for results

After getting results from Consurf, use Jmol or Chimera to: 

1) produce the overall 3D structure (capture/screenshot this image)

2) produce an image of least conserved regions and most conserved regions (capture/screenshot this image)

***NOTE: The molecule will be in space filling mode color coded by conservation with the most conserved regions in maroon and the least conserved regions in blue. ***

ALSO, If Jmol doesn’t work you may have to download Chimera !