PFRMAT AL 
TARGET T0054 
REMARK ======================================================================= 
AUTHOR 2738-1421-4442 
REMARK This prediction was prepared by Anna Panchenko and 
REMARK Aron Marchler-Bauer, 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 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 (and with alignment constraints derived from sequence comparison, 
METHOD based on manually generated alignments, if PSSMs were not used to 
METHOD score alignments, Models 3 and 5). Initally the templates were 
METHOD identified by a literature search using PubMed focusing on 
METHOD apparently well-conserved active-site motifs. Template structures 
METHOD were identified using Entrez. No threading database-search seemed 
METHOD necessary. 
REMARK ======================================================================= 
MODEL  3 
PARENT 1lbu 
W   17    Y   88   
D   18    A   89   
A   19    E   90   
K   20    L   91   
Y   21    N   92   
A   22    R   93   
T   23    C   94   
W   24    N   95   
D   25    S   96   
N   26    D   97   
F   27    W   98   
T   28    S   99   
G   29    G  100   
K   30    G  101   
P   31    K  102   
V   32    V  103   
D   33    S  104   
G   34    A  105   
Y   35    A  106   
E   36    T  107   
V   37    A  108   
N   38    R  109   
R   39    A  110   
I   40    N  111   
V   41    A  112   
G   42    L  113   
T   43    V  114   
Y   44    T  115   
E   45    M  116   
L   46    W  117   
A   47    K  118   
E   48    L  119   
S   49    Q  120   
L   50    A  121   
L   51    M  122   
K   52    R  123   
A   53    H  124   
K   54    A  125   
Y   62    K  129   
G   63    P  130   
L   64    I  131   
L   65    T  132   
L   66    V  133   
W   67    N  134   
D   68    G  135   
G   69    G  136   
Y   70    F  137   
R   71    R  138   
P   72    S  139   
K   73    V  140   
R   74    T  141   
A   75    C  142   
V   76    N  143   
Y  109    G  147   
V  110    G  148   
A  111    A  149   
S  112    S  150   
K  113    N  151   
S  114    S  152   
S  115    R  153   
H  116    H  154   
S  117    M  155   
R  118    Y  156   
G  119    G  157   
S  120    H  158   
A  121    A  159   
I  122    A  160   
D  123    D  161   
L  124    L  162   
T  125    G  163   
L  126    A  164   
Y  127    G  165   
R  128    S  166   
L  129    Q  167   
D  130    G  168   
T  131    F  169   
G  132    C  170   
E  133    A  171   
L  134    L  172   
V  135    A  173   
P  136    Q  174   
M  137    A  175   
G  138    A  176   
R  140    G  180   
F  141    F  181   
D  142    T  182   
F  143    E  183   
M  144    I  184   
D  145    L  185   
E  146    G  186   
R  147    P  187   
S  148    G  188   
H  149    Y  189   
H  150    P  190   
A  151    G  191   
L  180    N  193   
E  181    D  194   
W  182    H  195   
W  183    T  196   
H  184    H  197   
Y  185    V  198   
V  186    A  199   
L  187    G  200   
S  195    R  204   
Y  196    F  205   
F  197    W  206   
D  198    S  207   
F  199    A  208   
P  200    P  209   
V  201    S  210   
K  202    C  211   
TER 
END 
