CD task6 protocol

From Bioinformatikpedia
Revision as of 20:09, 18 June 2012 by Gatzmannf (talk | contribs) (PAM250)

Blosum62

#  Matrix made by matblas from blosum62.iij
#  * column uses minimum score
#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
#  Entropy =   0.6979, Expected =  -0.5209
   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 
R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 
N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 
D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 
C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 
Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 
E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 
H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 
I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 
L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 
K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 
M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 
F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 
S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 
Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 
V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 
B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 
Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1

PAM1

1 PAM evolutionary distance

         Ala  Arg  Asn  Asp  Cys  Gln  Glu  Gly  His  Ile  Leu  Lys  Met  Phe  Pro  Ser  Thr  Trp  Tyr  Val
           A    R    N    D    C    Q    E    G    H    I    L    K    M    F    P    S    T    W    Y    V
Ala A  9867     2    9   10    3    8   17   21    2    6    4    2    6    2   22   35   32    0    2   18
Arg R     1  9913    1    0    1   10    0    0   10    3    1   19    4    1    4    6    1    8    0    1
Asn N     4     1 9822   36    0    4    6    6   21    3    1   13    0    1    2   20    9    1    4    1
Asp D     6     0   42 9859    0    6   53    6    4    1    0    3    0    0    1    5    3    0    0    1
Cys C     1     1    0    0 9973    0    0    0    1    1    0    0    0    0    1    5    1    0    3    2
Gln Q     3     9    4    5    0 9876   27    1   23    1    3    6    4    0    6    2    2    0    0    1
Glu E    10     0    7   56    0   35 9865    4    2    3    1    4    1    0    3    4    2    0    1    2
Gly G    21     1   12   11    1    3    7 9935    1    0    1    2    1    1    3   21    3    0    0    5
His H     1     8   18    3    1   20    1    0 9912    0    1    1    0    2    3    1    1    1    4    1
Ile I     2     2    3    1    2    1    2    0    0 9872    9    2   12    7    0    1    7    0    1   33
Leu L     3     1    3    0    0    6    1    1    4   22 9947    2   45   13    3    1    3    4    2   15
Lys K     2    37   25    6    0   12    7    2    2    4    1 9926   20    0    3    8   11    0    1    1
Met M     1     1    0    0    0    2    0    0    0    5    8    4 9874    1    0    1    2    0    0    4
Phe F     1     1    1    0    0    0    0    1    2    8    6    0    4 9946    0    2    1    3   28    0
Pro P    13     5    2    1    1    8    3    2    5    1    2    2    1    1 9926   12    4    0    0    2
Ser S    28    11   34    7   11    4    6   16    2    2    1    7    4    3   17 9840   38    5    2    2
Thr T    22     2   13    4    1    3    2    2    1   11    2    8    6    1    5   32 9871    0    2    9
Trp W     0     2    0    0    0    0    0    0    0    0    0    0    0    1    0    1    0 9976    1    0
Tyr Y     1     0    3    0    3    0    1    0    4    1    1    0    0   21    0    1    1    2 9945    1
Val V    13     2    1    1    3    2    2    3    3   57   11    1   17    1    3    2   10    0    2 9901

PAM250

250 PAM evolutionary distance

                     ORIGINAL AMINO ACID

        Ala  Arg  Asn  Asp  Cys  Gln  Glu  Gly  His  Ile  Leu  Lys  Met  Phe  Pro  Ser  Thr  Trp  Tyr  Val
         A    R    N    D    C    Q    E    G    H    I    L    K    M    F    P    S    T    W    Y    V
Ala A    13    6    9    9    5    8    9   12    6    8    6    7    7    4   11   11   11    2    4    9
Arg R     3   17    4    3    2    5    3    2    6    3    2    9    4    1    4    4    3    7    2    2
Asn N     4    4    6    7    2    5    6    4    6    3    2    5    3    2    4    5    4    2    3    3
Asp D     5    4    8   11    1    7   10    5    6    3    2    5    3    1    4    5    5    1    2    3
Cys C     2    1    1    1   52    1    1    2    2    2    1    1    1    1    2    3    2    1    4    2
Gln Q     3    5    5    6    1   10    7    3    7    2    3    5    3    1    4    3    3    1    2    3
Glu E     5    4    7   11    1    9   12    5    6    3    2    5    3    1    4    5    5    1    2    3
Gly G    12    5   10   10    4    7    9   27    5    5    4    6    5    3    8   11    9    2    3    7
His H     2    5    5    4    2    7    4    2   15    2    2    3    2    2    3    3    2    2    3    2
Ile I     3    2    2    2    2    2    2    2    2   10    6    2    6    5    2    3    4    1    3    9
Leu L     6    4    4    3    2    6    4    3    5   15   34    4   20   13    5    4    6    6    7   13
Lys K     6   18   10    8    2   10    8    5    8    5    4   24    9    2    6    8    8    4    3    5
Met M     1    1    1    1    0    1    1    1    1    2    3    2    6    2    1    1    1    1    1    2
Phe F     2    1    2    1    1    1    1    1    3    5    6    1    4   32    1    2    2    4   20    3
Pro P     7    5    5    4    3    5    4    5    5    3    3    4    3    2   20    6    5    1    2    4
Ser S     9    6    8    7    7    6    7    9    6    5    4    7    5    3    9   10    9    4    4    6
Thr T     8    5    6    6    4    5    5    6    4    6    4    6    5    3    6    8   11    2    3    6
Trp W     0    2    0    0    0    0    0    0    1    0    1    0    0    1    0    1    0   55    1    0
Tyr Y     1    1    2    1    3    1    1    1    3    2    2    1    2   15    1    2    2    3   31    2
Val V     7    4    4    4    4    4    4    4    5    4   15   10    4   10    5    5    5   72    4   17

Create position specific substitution matrix

blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i p45381_wt.fa -o psiblast_it2_p45381_wt_big80.out -j 5 -Q pssm.out


SIFT mutation table

SIFT_Mutation_table

PSSM

pssm.out