
PFRMAT AL
TARGET T0090
AUTHOR 7573-5202-7463
METHOD 
METHOD A PSI-BLAST search of the PDB identified one structure as a likely
METHOD template for T0090:  1mut (or 1tum, which shares 100% sequence
METHOD identity).  One 30-residue region of the target shares very high 
METHOD sequence identity with the template, but the rest of the sequence
METHOD varies greatly between the two sequences.  In an attempt to identify
METHOD the correct alignment between these two sequences, we used several
METHOD alignment techniques.  A sequence profile for the target was generated
METHOD by running PSI-BLAST on the nr database.  A similar sequence profile
METHOD for the template (1mut) was generated.  The two profiles were aligned
METHOD to each other using CLUSTALW.  Additionally, the target sequence alone
METHOD was aligned to the template profile and the template sequence alone was
METHOD aligned to the target profile using CLUSTALW.  Several gap opening 
METHOD penalty values were used for each alignment described above.   
METHOD 
METHOD Each of these alignments, as well as the initial PSI-BLAST alignment of
METHOD 1mut to T0090, were assessed using in-house software designed to
METHOD evaluate the likelihood that a pair of interacting residues in the
METHOD template will be substituted to an analogous pair in the given sequence
METHOD alignment.  
METHOD  
METHOD 
METHOD
MODEL 3
PARENT 1mut
I  53    M   1 
F  54    K   2 
E  55    K   3 
R  56    L   4 
G  57    Q   5 
H  58    I   6 
A  59    A   7 
A  60    V   8 
V  61    G   9 
L  62    I  10 
L  63    I  11 
P  64    R  12 
F  65    N  13 
D  66    E  14 
R  69    N  15 
D  70    N  16 
E  71    E  17 
V  72    I  18 
V  73    F  19 
L  74    I  20 
I  75    T  21 
E  76    R  22 
Q  77    R  23 
I  78    A  24 
R  79    A  25 
I  80    D  26
A  81    A  27 
A  82    H  28  
Y  83    M  29 
D  84    A  30 
T  85    N  31 
L  91    K  32 
L  92    L  33 
E  93    E  34 
M  94    F  35 
V  95    P  36 
A  96    G  37 
G  97    G  38 
M  98    K  39 
I  99    I  40 
E 100    E  41 
E 101    M  42 
G 102    G  43 
E 103    E  44 
S 104    T  45 
V 105    P  46 
E 106    E  47 
D 107    Q  48 
V 108    A  49 
A 109    V  50 
R 110    V  51 
R 111    R  52 
E 112    E  53 
A 113    L  54 
I 114    Q  55 
E 115    E  56 
E 116    E  57 
A 117    V  58 
G 118    G  59 
L 119    I  60 
I 120    T  61 
V 121    P  62 
K 122    Q  63 
R 123    H  64 
T 124    F  65 
K 125    S  66 
P 126    L  67 
V 127    F  68 
L 128    E  69 
S 129    K  70 
F 130    L  71 
L 131    E  72 
A 132    Y  73 
S 133    E  74 
P 134    F  75 
G 135    D  77 
G 136    R  78 
T 137    H  79 
S 138    I  80 
E 139    T  81 
I 143    L  82 
M 144    W  83 
V 145    F  84 
G 146    W  85 
E 147    L  86 
V 148    V  87 
D 149    E  88 
A 150    R  89 
T 151    W  90 
T 152    E  91 
A 153    G  92 
S 154    E  93 
G 155    P  94 
I 156    W  95 
H 157    G  96 
G 158    K  97 
L 159    Q 100 
A 160    P 101 
D 161    G 102 
E 162    E 103 
N 163    W 104 
E 164    S 106 
D 165    L 107 
I 166    V 108 
R 167    G 109 
V 168    L 110 
H 169    N 111 
E 174    A 112 
Q 175    D 113 
A 176    D 114 
Y 177    F 115 
Q 178    P 116 
W 179    P 117 
V 180    A 118 
E 181    N 119 
E 182    E 120 
G 183    P 121 
K 184    V 122 
I 185    I 123 
D 186    A 124 
N 187    K 125 
A 188    L 126 
A 189    K 127 
S 190    R 128 
V 191    L 129 
TER    
END      


