Assignment 4: Protein

evolution
Comparisons between amino acid sequences can be used to
understand which areas of a polypeptide are important for its
function. A large family of proteins in bacteria includes a
transcriptional regulator called the cAMP regulatory or activator
protein (CRP or CAP).
.

(i) Go to the NCBI site at http://www.ncbi.nlm.nih.gov/

(ii) Retrieve the amino acid sequences for the following

CRP/CAP family proteins by selecting the Protein database in
the Search menu and typing the underlined accession number
into the adjacent box:
?E.colicatabolite gene activator (cAMP receptor
protein), P0ACJ8
?Yersiniapestiscyclic AMP receptor protein,
AAM87500

(iii) For each retrieval, select FASTA from the display menu
then copy and paste the amino acid sequence into a Word
document, giving each sequence a recognizable byline in
FASTA format: >byline.

(iv) Remove the numbers from the amino acid sequence

.

.
.

(v) Go to the EMBL Clustal W site

(http://www.ebi.ac.uk/Tools/clustalw/index.html), which
will allow you to compare up to 10 different amino acid
sequences.
(vi) Copy and paste the five sequences in FASTA format
consecutively into the open box and hit RUN.
(vii) In a few moments, you will see an output that shows

all five sequences lined up according to the best matches

between them.
Questions:
.
.

(a) Which parts of this protein show the most amino acid
divergence?
(b) Which parts of this protein appear to be the most
conserved?