
PFRMAT AL
TARGET T0125
AUTHOR 9794-5632-1504
METHOD Fold recognition and structure generation are based on
METHOD alignment with a template.  When available, functional
METHOD information about the protein is used to help select
METHOD templates and validate alignments.   In order to find
METHOD templates, alignments are constructed using a variant of the
METHOD Smith-Waterman algorithm which incorporates position specific
METHOD scoring information.  If sequence identity is very low,  then
METHOD alignments are also attempted using predicted secondary 
METHOD structure information with various weights.  Secondary
METHOD structure is predicted using the consensus of three
METHOD methods: PHd (Rost et al.), Preditor (Frishman & Argos), and
METHOD PSIPRED (Jones).   The alignment the target to the template 
METHOD which is submitted is based on aligning the target with the
METHOD core of the template.  The core is identified by structural
METHOD alignments using the CE program (Shindyalov & Bourne).   The
METHOD core alignment algorithm is a position specific dynamic
METHOD programming algorithm which does not permit gaps within the 
METHOD core.
MODEL 1
PARENT 3LYN_B
S   12    V   17
Y   13    T   18
V   14    M   19
Q   15    K   20
R   16    I   21
G   17    Q   22
M   18    I   23
V   19    I   24
N   20    S   25
F   21    G   26
L   22    F   27
D   23    D   28
E   24    R   29
E   25    Q   30
M   26    L   31
H   27    T   32
K   28    A   33
L   29    W   34
V   30    L   35
K   31    R   36
R   32    V   37
F   33    H   38
R   37    G   39
W   38    R   40
N   39    R   41
L   40    L   42
G   41    T   43
P   42    N   44
G   43    N   45
F   44    Q   46
V   45    K   47
F   46    K   48
L   47    T   49
L   48    L   50
K   49    F   51
K   50    F   52
V   51    V   53
N   52    N   54
R   53    R   55
E   54    R   56
R   55    Y   57
M   56    M   58
M   57    Q   59
R   58    T   60
Y   59    H   61
C   60    W   62
M   61    Q   63
D   62    N   64
Y   63    Y   65
A   64    M   66
R   65    L   67
Y   66    W   68
S   67    V   69
K   68    K   70
K   69    R   71
I   70    K   72
L   71    I   73
Q   72    K   74
L   73    A   75
K   74    L   76
H   75    G   77
L   76    R   78
P   77    P   79
V   78    A   80
N   79    A   81
K   80    V   82
K   81    G   83
T   82    D   84
L   83    Y   85
T   84    T   86
K   85    R   87
M   86    L   88
G   87    G   89
R   88    A   90
F   89    E   91
V   90    I   92
G   91    G   93
Y   92    R   94
R   93    R   95
N   94    V   96
Y   95    D   97
G   96    M   98
V   97    V   99
I   98    F  100
R   99    F  101
E  100    Y  102
L  101    N  103
Y  102    F  104
A  103    L  105
D  104    S  106
V  105    G  107
G  111    R  108
F  112    K  109
R  113    M  110
G  114    I  111
P  115    P  112
K  116    P  113
M  117    Y  114
T  118    S  115
A  119    A  116
A  120    Y  117
M  121    M  118
R  122    A  119
K  123    K  120
Y  124    L  121
S  125    N  122
S  126    A  123
K  127    L  124
D  128    R  125
P  129    P  126
G  130    A  127
T  131    D  128
F  132    V  129
P  133    P  130
C  134    V  131
K  135    K  132
N  136    N  133
TER
END

