PFRMAT AL 
TARGET T0063 
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 model 1 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. Depending on the weight placed on PSSM's in scoring, members 
METHOD of the OB-fold family of DNA/RNA-binding domains have been found on 
METHOD top of several hitlists. We have selected a representative domain, 
METHOD 1JMC A 2 for a template in model 1. 
REMARK ======================================================================= 
MODEL  2 
PARENT 1whi 
L   17    I    2   
K   18    Q    3   
E   19    Q    4   
G   20    E    5   
S   21    S    6   
Y   22    R    7   
V   23    L    8   
V   24    K    9   
I   25    V   10   
D   26    A   11   
P   29    G   15   
C   30    A   16   
R   31    R   17   
V   32    E   18   
V   33    V   19   
E   34    L   20   
I   35    V   21   
A   48    G   36   
R   49    D   37   
I   50    V   38   
V   51    V   39   
A   52    V   40   
V   53    A   41   
G   54    T   42   
V   55    V   43   
F   56    K   44   
D   57    D   45   
G   58    A   46   
G   59    T   47   
K   60    P   48   
R   61    G   49   
T   62    G   50   
L   63    V   51   
V   67    V   52   
D   68    K   53   
A   69    K   54   
Q   70    G   55   
V   71    Q   56   
E   72    V   57   
V   73    V   58   
P   74    K   59   
I   75    A   60   
I   76    V   61   
F   79    V   62   
T   80    V   63   
A   81    R   64   
Q   82    T   65   
I   83    K   66   
L   84    R   67   
V   86    F   79   
S   87    D   80   
G   88    E   81   
D   89    N   82   
V   90    A   83   
I   91    C   84   
Q   92    V   85   
L   93    I   86   
M   94    I   87   
D   95    R   88   
M   96    D   89   
I  102    K   91   
E  103    S   92   
V  104    P   93   
P  105    R   94   
M  106    G   95   
K  107    T   96   
K  114    F   99   
G  115    G  100   
R  116    P  101   
L  117    V  102   
A  118    A  103   
G  120    L  106   
A  121    R  107   
E  122    D  108   
V  123    K  109   
E  124    D  110   
V  125    F  111   
W  126    M  112   
Q  127    K  113   
I  128    I  114   
L  129    I  115   
D  130    S  116   
R  131    L  117   
Y  132    A  118   
K  133    P  119   
TER 
END 
