Pabio 536
Lab session and Homework
Week 8
Multiple Alignment
1.
Perform a multiple alignment using the
ACBP liver forms and the ACBP brain
forms from this week’s
sequence file
and show the alignment (ALN file) you
obtained (10 points).
2.
Compare the pattern of identical residue
s conserved within the liver forms to
those conserved within the brain forms.
Are there brain or li
ver specific residues
(ie residues conserved in liv
er but not in brain or vice
versa)? Provide a couple of
examples (ie brain: A26, liver: W32)(10 points).
3.
A) Determine a “pattern” of liver-specific amino acid residues, ie those amino
acids conserved in all liver forms but not
in the brain forms. Provide your pattern.
(10 points)
B) Do a PHI-BLAST search using the hum
an ACBP Liver form in the query and
your Liver-specific pattern – limit your
output to salmonids. Did you detect a
putative liver ACBP form in
the salmonid “ atlantic salmon salmo” ? provide the
BLAST hit. If you obtain no putative salm
on ACBP hits try altering your pattern
slightly and redo the PHI-BLAST. If a
ll else fails, do a normal BLAST search
with no pattern and exam the hits to see
if you can detect a putative liver ACBP
form in the salmonid “atlantic salmon salmo”? Provide the BLAST hit. In this
last case, how did the salmo sequence
differ from your patt
ern (10 points)
C) Do a multiple alignment of all of the liver forms in question 2 plus your
putative salmon liver ACBP form – pr
ovide the alignment (10 points).
D) Discuss the alignment with regard to
other liver-specific re
sidues that you did
not include in your PHI-BLAST pattern, ie
are those conserve
d as well? Would
you consider this putative atlantic salmon
ACBP to be a liver form? Discuss (10
points).
4.
A) Determine a “pattern” of amino acid re
sidues that are conserved in the ACBP
brain forms but not in the liver forms.
Provide the pattern (10 points)
B)
Do a PHI-BLAST search using the huma
n ACBP Brain form in the query and
your Brain-specific pattern – limit your
output to salmonids. Did you detect a
putative brain ACBP form in the Atlan
tic salmon (Salmo salar)? If you obtain
no putative salmon ACBP hits try altering your pattern slightly and redo the
PHI-BLAST. If you still get no putativ
e salmon ACBP hit try doing a protein
BLAST without the pattern and look at
the hits by eye to determine whether
there is a brain form in Salmo salar (h
int- you should detect
one) (10 points)
C)
Do a multiple alignment of all of th
e brain forms in question 2 plus your
putative salmon brain ACBP form – pr
ovide the alignment. (10 points)
D)
Discuss the alignment with regard to
the brain-specific residues? Would you
consider this salmon ACBP to be a brai
n form? Discuss in relationship to your
PHI-BLAST pattern and other
“brain form”specific characteristics. (10 points)
5.
EXTRA CREDIT: Do an alignment of a
ll of the liver and brain form ACBP
sequences including the salmon sequences
. Identify the identical residues
conserved within all
the sequences and discuss with
regard to cons
ervation of the
previously characterized “ACBP” motif
s (10 points). Can you make any
conclusion regarding how the brain and th
e liver forms differ from each other –
relying upon what you know of the structur
e of ACBP? (no right answer here –
something to think about). (10 points)
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