Gene Cloning

L
G
S
236 Gene Cloning
4
3
Bits
2
1
0
N
MEL
1
2
C C GDSGGP
FI AV
D
3
4
G
5
6
7
8
9
10
11
SAS TC
12
13
14
O
15
16
17
18
19
20
21
LV NV
G
22
23
24
weblogo.berkeley.edu
C
Figure 8.15 Sequence logo. This shows the region around the conserved
active site serine of the alignment from Figure 8.14. A sequence logo is a
graphical representation of a multiple alignment, the height of the letter indicates
both the frequency of an amino acid at a particular position and the degree of
conservation at that position. This means that the height of the column where a
single residue is always present is greater than that in less well-conserved
positions.
One such database, Prosite, gives a consensus pattern describing the
conserved region around the active site serine of the trypsin-like serine
proteases in the form of a regular expression as:
1 2 3,4 5 6 7 8 9 10
[DNSTAGC]-[GSTAPIMVQH]-x(2)-G-[DE]-S-G-[GS]-[SAPHV]-
11 12
[LIVMFYWH]-[LIVMFYSTANQH]
In this representation a single letter indicates positions where only one
amino acid is ever found in multiple alignments, such as positions 5, 7 and
8. In this example the serine at position 7, shown here in blue, is the active
site serine. Positions 6 and 9 allow one of two possible residues, namely
aspartate or glutamate at position 6 and glycine or serine at position 9.
Positions 1, 2, 10, 11 and 12 allow any one of the amino acids from the
group in square brackets. Positions 3 and 4 can be occupied by any
residues, as indicated by x(2). If you compare this regular expression to the
consensus pattern derived from our multiple alignment you should see
that it describes the conserved region from our multiple alignment but also
allows for greater variation. This is because it was generated from a much
larger data set that included more distantly related members of the trypsinlike
serine protease family.
Q8.18. Can you locate the sequence described by the following regular
expression on the multiple alignment in Figure 8.14?
[LIVM]-[ST]-A-[STAG]-H-C