PFRMAT AL 
TARGET T0079 
REMARK ======================================================================= 
AUTHOR 2738-1421-4442 
REMARK This prediction was prepared by Anna Panchenko, Aron Marchler-Bauer, and 
REMARK 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 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 has been identifed based on the presence 
METHOD of the repeated helix-turn-helix motif in the target and based on 
METHOD sequence similarity searches (BLAST). No threading database search 
METHOD seemed necessary. Attempts to align the target sequence to the dimer 
METHOD of the template (and to account for the repeated motif in this way) 
METHOD have been unsuccessful - the target sequence seems to short. Instead 
METHOD we list alignments for two separate regions of the target sequence, 
METHOD residues 1-64 and residues 65-129. Both of them have been aligned to 
METHOD the same template, and we do NOT specify the overall topological 
METHOD arrangement of the two "domains" with respect to each other.  
REMARK ======================================================================= 
MODEL  2 
PARENT 1smt_A 
M   65    R   48   
T   66    L   49   
E   67    R   50   
I   68    L   51   
A   69    L   52   
Q   70    S   53   
K   71    L   54   
L   72    L   55   
I   79    V   62   
L   80    G   63   
Y   81    D   64   
L   82    L   65   
A   83    A   66   
E   84    Q   67   
R   85    A   68   
Y   86    I   69   
G   87    G   70   
F   88    V   71   
S   90    S   72   
Q   91    E   73   
Q   92    S   74   
T   93    A   75   
L   94    V   76   
T   95    S   77   
R   96    H   78   
T   97    Q   79   
F   98    L   80   
K   99    R   81   
N  100    S   82   
Y  101    L   83   
F  102    R   84   
D  103    N   85   
V  104    L   86   
P  105    R   87   
P  106    L   88   
H  107    V   89   
Y  109    Y  100   
R  110    Q  101   
M  111    L  102   
T  112    Q  103   
N  113    D  104   
M  114    H  105   
Q  115    H  106   
G  116    I  107   
E  117    V  108   
S  118    A  109   
R  119    L  110   
F  120    Y  111   
L  121    Q  112   
H  122    N  113   
P  123    A  114   
TER 
END 
