Identifying Conserved Regions in Genes and Proteins

  • Enter your email address in the blank space in the top left corner of the search screen. Change the "Color Alignment" option to "yes." Be sure to leave the other search options on their default settings. Then, scroll down the page to the large search box.

  • Click on the link below to access the sequences you will be comparing. When the screen opens, first select the "Select All" and then "Copy" commands under the Edit menu. Then use your browsers back button to return to the Clustal W search page. Use the "Paste" option under the edit menu to paste the beta-globin sequences into the search box.

    ClustalW Sequences

  • Click on "Run ClustalW" to begin the alignment. This may take a few minutes, the webpage will automatically refresh until the results are displayed.

  • Interpreting Your Search Results:
  • The alignment results will be displayed in color. You can use the following key to determine what each color represents:
    Red=Small (small+ hydrophobic (incl.aromatic -Y)) amino acids (AVFPMILW)

    Blue=Acidic amino acids (DE)

    Magenta=Basic amino acids (RHK)

    Green=Hydroxyl + Amine + Basic - Q amino acids (STYHCNGQ)


  • ClustalW also uses symbols to represent sequence conservation.

    "*" = identical or conserved in all sequences in the alignment

    ":" = conserved substitutions

    "." = semi-conserved substitutions
  • Use the ClustalW alignment to answer the following questions:

    1. What amino acid residues appear to be conserved among all of the beta-globin gene family members? (Record amino acid and position)

    2. Why do you think that some areas exhibit greater sequence conservation than other areas?

    3. Using the sequence homology data given at the top of the screen, does the percent homology between beta-globin gene family members given by ClustalW match the evolutionary path you previously predicted based on exon size (see Entrez Nucleotide question #6)? Why or why not?

    4. Does the homology data given by Clustal W help to explain why the Blast N search did not recognize sequence homology of beta-globin with epsilon or delta globin?

    When you are finished, return to the Beta-thalessemia Menu Page to move on to the next section of the laboratory.

    Beta-thalessemia Menu Page