Description
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 !
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Explanation & Answer
Dear student,I have modelled the proteins according to the default settings in both Clustal Omega and ConSurf with the data file you provided me with their sequences and the instructions provided in the assignment specifications.Please find enclosed a zip file with all the results obtained from the Co...