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Posted: February 20th, 2023
Bioinformatics: Multiple Sequence Alignment Lab, science homework help
Question 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 Submit4. Right Click "Download Alignment File" --> "Download Linked File"5. Visit http://consurf.tau.ac.il6. 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 resultsAfter 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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