Task 6: Sequence-based mutation analysis
Contents
Task description
A detailed task description can be found here.
Mutation selection
We selected the following ten mutations:
- I65T
- R71H
- R158Q
- R261Q
- T266A
- P275S
- T278N
- P281L
- G312D
- R408W
5 of these mutations are associated with our disease phenylketonuria the other 5 not. The 5 disease causing mutations are the most frequent missense/nonsense mutations of people who suffer from phenylketonuria. These numbers were taken from pahDB. However, at this point we are not going to tell which of these are the associated and which are not. We are going to lift this "secret" after our sequence based mutation analysis in order to validate our in silico generated predictions.
To keep our association secret we encrypted the file which contains the disease association for each mutation with the following linux command: "vim -x selected_mutations_and_association.txt"
The encrypted output is as follows:
The decryption can be only performed with the correct password.
Physicochemical properties and changes
I65T
I: aliphatic, hydrophob, large, unpolar, neutral
T: small, hydrophob, polar, neutral
R71H
R: polar, aliphatic, positive charged, hydrophob, large, neutral
H: positive charged, polar, aromatic, hydrophob, basic
R158Q
R261Q
R: polar, aliphatic, positive charged, hydrophob, large, neutral
Q: polar, neutral, unpolar
T266A
P275S
T278N
P281L
G312D
G: very small, unpolar, neutral
D: polar, small, negative charged, acidic
R408W
R: polar, aliphatic, positive charged, hydrophob, large, neutral
W: polar, aromatic, large, hydrophob, neutral
Mutations compared to BLOSUM62, PAM(1/250), PSSM and conservation of MSA with all mammalian homologous
BLOSUM 62 matrix
| BLOSUM 62 Matrix |
|---|
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| The BLOSUM 62 was calculated from blocks of clusters with a sequence identity of 62%. A positive score is given to the more likely substitutions while a negative score is given to the less likely substitutions. Source: [1] Disclaimer: This file is redistributed from Wikimedia and copyrighted under the Creative Commons licence. |
PAM 1/250 matrix
PAM1 Matrix
| A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V | |
| A | 9867 | 2 | 9 | 10 | 3 | 8 | 17 | 21 | 2 | 6 | 4 | 2 | 6 | 2 | 22 | 35 | 32 | 0 | 2 | 18 |
| R | 1 | 9913 | 1 | 0 | 1 | 10 | 0 | 0 | 10 | 3 | 1 | 19 | 4 | 1 | 4 | 6 | 1 | 8 | 0 | 1 |
| N | 4 | 1 | 9822 | 36 | 0 | 4 | 6 | 6 | 21 | 3 | 1 | 13 | 0 | 1 | 2 | 20 | 9 | 1 | 4 | 1 |
| D | 6 | 0 | 42 | 9859 | 0 | 6 | 53 | 6 | 4 | 1 | 0 | 3 | 0 | 0 | 1 | 5 | 3 | 0 | 0 | 1 |
| C | 1 | 1 | 0 | 0 | 9973 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 5 | 1 | 0 | 3 | 2 |
| Q | 3 | 9 | 4 | 5 | 0 | 9876 | 27 | 1 | 23 | 1 | 3 | 6 | 4 | 0 | 6 | 2 | 2 | 0 | 0 | 1 |
| E | 10 | 0 | 7 | 56 | 0 | 35 | 9865 | 4 | 2 | 3 | 1 | 4 | 1 | 0 | 3 | 4 | 2 | 0 | 1 | 2 |
| G | 21 | 1 | 12 | 11 | 1 | 3 | 7 | 9935 | 1 | 0 | 1 | 2 | 1 | 1 | 3 | 21 | 3 | 0 | 0 | 5 |
| H | 1 | 8 | 18 | 3 | 1 | 20 | 1 | 0 | 9912 | 0 | 1 | 1 | 0 | 2 | 3 | 1 | 1 | 1 | 4 | 1 |
| I | 2 | 2 | 3 | 1 | 2 | 1 | 2 | 0 | 0 | 9872 | 9 | 2 | 12 | 7 | 0 | 1 | 7 | 0 | 1 | 33 |
| L | 3 | 1 | 3 | 0 | 0 | 6 | 1 | 1 | 4 | 22 | 9947 | 2 | 45 | 13 | 3 | 1 | 3 | 4 | 2 | 15 |
| K | 2 | 37 | 25 | 6 | 0 | 12 | 7 | 2 | 2 | 4 | 1 | 9926 | 20 | 0 | 3 | 8 | 11 | 0 | 1 | 1 |
| M | 1 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 5 | 8 | 4 | 9874 | 1 | 0 | 1 | 2 | 0 | 0 | 4 |
| F | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 2 | 8 | 6 | 0 | 4 | 9946 | 0 | 2 | 1 | 3 | 28 | 0 |
| P | 13 | 5 | 2 | 1 | 1 | 8 | 3 | 2 | 5 | 1 | 2 | 2 | 1 | 1 | 9926 | 12 | 4 | 0 | 0 | 2 |
| S | 28 | 11 | 34 | 7 | 11 | 4 | 6 | 16 | 2 | 2 | 1 | 7 | 4 | 3 | 17 | 9840 | 38 | 5 | 2 | 2 |
| T | 22 | 2 | 13 | 4 | 1 | 3 | 2 | 2 | 1 | 11 | 2 | 8 | 6 | 1 | 5 | 32 | 9871 | 0 | 2 | 9 |
| W | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 9976 | 1 | 0 |
| Y | 1 | 0 | 3 | 0 | 3 | 0 | 1 | 0 | 4 | 1 | 1 | 0 | 0 | 21 | 0 | 1 | 1 | 2 | 9945 | 1 |
| V | 13 | 2 | 1 | 1 | 3 | 2 | 2 | 3 | 3 | 57 | 11 | 1 | 17 | 1 | 3 | 2 | 10 | 0 | 2 | 9901 |
PAM250 Matrix
| A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V | |
| A | 13 | 6 | 9 | 9 | 5 | 8 | 9 | 12 | 6 | 8 | 6 | 7 | 7 | 4 | 11 | 11 | 11 | 2 | 4 | 9 |
| R | 3 | 17 | 4 | 3 | 2 | 5 | 3 | 2 | 6 | 3 | 2 | 9 | 4 | 1 | 4 | 4 | 3 | 7 | 2 | 2 |
| N | 4 | 4 | 6 | 7 | 2 | 5 | 6 | 4 | 6 | 3 | 2 | 5 | 3 | 2 | 4 | 5 | 4 | 2 | 3 | 3 |
| D | 5 | 4 | 8 | 11 | 1 | 7 | 10 | 5 | 6 | 3 | 2 | 5 | 3 | 1 | 4 | 5 | 5 | 1 | 2 | 3 |
| C | 2 | 1 | 1 | 1 | 52 | 1 | 1 | 2 | 2 | 2 | 1 | 1 | 1 | 1 | 2 | 3 | 2 | 1 | 4 | 2 |
| Q | 3 | 5 | 5 | 6 | 1 | 10 | 7 | 3 | 7 | 2 | 3 | 5 | 3 | 1 | 4 | 3 | 3 | 1 | 2 | 3 |
| E | 5 | 4 | 7 | 11 | 1 | 9 | 12 | 5 | 6 | 3 | 2 | 5 | 3 | 1 | 4 | 5 | 5 | 1 | 2 | 3 |
| G | 12 | 5 | 10 | 10 | 4 | 7 | 9 | 27 | 5 | 5 | 4 | 6 | 5 | 3 | 8 | 11 | 9 | 2 | 3 | 7 |
| H | 2 | 5 | 5 | 4 | 2 | 7 | 4 | 2 | 15 | 2 | 2 | 3 | 2 | 2 | 3 | 3 | 2 | 2 | 3 | 2 |
| I | 3 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 10 | 6 | 2 | 6 | 5 | 2 | 3 | 4 | 1 | 3 | 9 |
| L | 6 | 4 | 4 | 3 | 2 | 6 | 4 | 3 | 5 | 15 | 34 | 4 | 20 | 13 | 5 | 4 | 6 | 6 | 7 | 13 |
| K | 6 | 18 | 10 | 8 | 2 | 10 | 8 | 5 | 8 | 5 | 4 | 24 | 9 | 2 | 6 | 8 | 8 | 4 | 3 | 5 |
| M | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 2 | 3 | 2 | 6 | 2 | 1 | 1 | 1 | 1 | 1 | 2 |
| F | 2 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 3 | 5 | 6 | 1 | 4 | 32 | 1 | 2 | 2 | 4 | 20 | 3 |
| P | 7 | 5 | 5 | 4 | 3 | 5 | 4 | 5 | 5 | 3 | 3 | 4 | 3 | 2 | 20 | 6 | 5 | 1 | 2 | 4 |
| S | 9 | 6 | 8 | 7 | 7 | 6 | 7 | 9 | 6 | 5 | 4 | 7 | 5 | 3 | 9 | 10 | 9 | 4 | 4 | 6 |
| T | 8 | 5 | 6 | 6 | 4 | 5 | 5 | 6 | 4 | 6 | 4 | 6 | 5 | 3 | 6 | 8 | 11 | 2 | 3 | 6 |
| W | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 55 | 1 | 0 |
| Y | 1 | 1 | 2 | 1 | 3 | 1 | 1 | 1 | 3 | 2 | 2 | 1 | 2 | 15 | 1 | 2 | 2 | 3 | 31 | 2 |
| V | 7 | 4 | 4 | 4 | 4 | 4 | 4 | 4 | 5 | 4 | 15 | 10 | 4 | 10 | 5 | 5 | 5 | 72 | 4 | 17 |
