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