PFRMAT AL 
TARGET T0053 
REMARK ======================================================================= 
AUTHOR 2738-1421-4442 
REMARK This prediction was prepared by Anna Panchenko, Aron Marchler-Bauer, 
REMARK and Steve Bryant, NCBI. 
REMARK ======================================================================= 
METHOD Predictions were made with the potential and alignment model used in 
METHOD CASP1 and CASP2 predictions, as described by Madej et al. in Proteins 
METHOD 23:356-369, 1995. Convergence control has been added to the Gibbs- 
METHOD Sampling alignment model. In addition to contact-based threading 
METHOD potentials, PSSMs summarizing sequence conservation in the family 
METHOD represented by the template structure are used to score threading 
METHOD alignments. Threading "cores" summarizing the conserved substructure 
METHOD in the templates used for models below may have been based on structure 
METHOD superpositions generated by VAST (Gibrat et al., Curr Opin Struct 
METHOD Biol 1996 Jun;6(3):377-385 ). 
METHOD The alignments have been calculated with the Gibbs Sampling threading 
METHOD engine. The template structure has been identified by threading 
METHOD database searches as the top scoring hit, and by functional similarity 
METHOD as well as the apparent conservation of key functional residues. 
METHOD  Model 1: PSSM, weight 1.0 
METHOD  Model 2: PSSM, weight 0.5 
METHOD  Model 3: contact-based threader 
REMARK ======================================================================= 
 
MODEL  3 
PARENT 1ak1 
K    3    K    5   
A    4    M    6   
L    5    G    7   
L    6    L    8   
V    7    L    9   
V    8    V   10   
S    9    M   11   
F   10    A   12   
G   11    Y   13   
T   12    G   14   
S   13    T   15   
Y   14    P   16   
H   15    Y   17   
D   16    K   18   
T   17    E   19   
I   22    T   60   
V   23    E   61   
A   24    Q   62   
C   25    Q   63   
E   26    A   64   
R   27    H   65   
D   28    N   66   
L   29    L   67   
A   30    E   68   
A   31    Q   69   
S   32    H   70   
C   33    L   71   
P   34    N   72   
D   35    E   73   
R   36    Q   75   
D   37    D   76   
L   38    E   77   
F   39    I   78   
R   40    T   79   
A   41    F   80   
F   42    K   81   
T   43    A   82   
S   44    Y   83   
G   45    I   84   
M   46    G   85   
I   47    L   86   
I   48    K   87   
R   49    H   88   
I   57    P   91   
D   58    F   92   
I   59    I   93   
D   60    E   94   
T   61    D   95   
P   62    A   96   
L   63    V   97   
Q   64    A   98   
A   65    E   99   
L   66    M  100   
Q   67    H  101   
K   68    K  102   
L   69    D  103   
A   70    G  104   
A   71    I  105   
D   76    E  107   
V   77    A  108   
A   78    V  109   
I   79    S  110   
Q   80    I  111   
S   81    V  112   
L   82    L  113   
H   83    A  114   
I   84    P  115   
I   85    H  116   
I   93    S  118   
V   94    T  119   
R   95    F  120   
E   96    S  121   
V   97    V  122   
Q   98    Q  123   
L   99    S  124   
L  100    Y  125   
R  101    N  126   
P  102    K  127   
L  103    R  128   
F  104    A  129   
T  105    K  130   
R  106    E  131   
L  107    E  132   
T  108    A  133   
L  109    L  139   
G  110    T  140   
V  111    I  141   
P  112    T  142   
L  113    S  143   
L  114    V  144   
S  115    E  145   
S  116    S  146   
H  117    W  147   
Y  120    V  154   
V  121    T  155   
Q  122    Y  156   
L  123    W  157   
M  124    V  158   
Q  125    D  159   
A  126    R  160   
L  127    V  161   
R  128    K  162   
Q  129    E  163   
Q  130    T  164   
M  131    Y  165   
R  135    D  171   
Q  136    E  172   
T  137    R  173   
E  138    E  174   
K  139    N  175   
V  140    A  176   
V  141    M  177   
F  142    L  178   
M  143    I  179   
G  144    V  180   
H  145    S  181   
G  146    A  182   
A  147    H  183   
S  148    S  184   
H  149    L  185   
A  153    Q  199   
A  154    L  200   
Y  155    H  201   
A  156    E  202   
C  157    S  203   
L  158    A  204   
D  159    K  205   
H  160    L  206   
M  161    I  207   
M  162    A  208   
T  163    E  209   
A  164    G  210   
Q  165    A  211   
R  166    G  212   
F  167    V  213   
A  169    E  215   
R  170    Y  216   
V  171    A  217   
G  172    V  218   
A  173    G  219   
V  174    W  220   
Y  177    G  232   
P  178    P  233   
E  179    D  234   
V  180    V  235   
D  181    Q  236   
I  182    D  237   
L  183    L  238   
I  184    T  239   
D  185    R  240   
S  186    D  241   
L  187    L  242   
R  188    F  243   
D  189    E  244   
E  190    Q  245   
G  191    G  247   
V  192    Y  248   
T  193    Q  249   
G  194    A  250   
V  195    F  251   
H  196    V  252   
L  197    Y  253   
M  198    V  254   
P  199    P  255   
L  200    V  256   
M  201    G  257   
L  202    F  258   
V  203    V  259   
D  206    L  266   
H  207    Y  267   
A  208    D  268   
I  209    N  269   
N  210    D  270   
D  211    Y  271   
M  212    E  272   
A  213    C  273   
S  214    K  274   
D  215    V  275   
D  216    V  276   
G  217    T  277   
D  218    D  278   
S  219    D  279   
W  220    I  280   
K  221    G  281   
A  227    A  282   
G  228    S  283   
I  229    Y  284   
P  230    Y  285   
A  231    R  286   
T  232    P  287   
P  233    E  288   
W  234    M  289   
L  235    P  290   
A  243    N  291   
I  244    A  292   
R  245    K  293   
A  246    P  294   
M  247    E  295   
F  248    F  296   
V  249    I  297   
A  250    D  298   
H  251    A  299   
L  252    L  300   
H  253    A  301   
Q  254    T  302   
A  255    V  303   
L  256    V  304   
N  257    L  305   
M  258    K  306   
A  259    K  307   
V  260    L  308   
E  261    G  309   
TER 
END 
