PFRMAT AL 
TARGET T0059 
AUTHOR 7397-8542-2481 
METHOD Sequences from converged PSI-BLAST search of the nr database were  
METHOD aligned in pileup, adjusted manually, and submitted to the JPRED server. 
METHOD The obtained secondary structure prediction strongly indicated an 
METHOD OB-fold.  This assignment was supported by the occurance of the SMD3 
METHOD domain in a RNA-binding protein.  A superposition of OB-structures 
METHOD from the pdb was compared to the fssp file for staphylococcal nuclease 
METHOD and conserved hydrophobic positions were identified.  The SMD3 domain 
METHOD was fitted to the cold shock protein template by maximum overlap of 
METHOD the conserved hydrophobic positions. 
MODEL  1 
PARENT 1mjc 
K   8    S   2 
V   9    G   3 
L  10    K   4 
H  11    M   5 
E  12    T   6 
A  13    G   7 
E  14    I   8 
G  15    V   9 
H  16    K  10 
I  17    W  11 
V  18    F  12 
T  19    N  13 
V  27    F  18 
Y  28    G  19 
R  29    F  20 
G  30    I  21 
K  31    T  22 
L  32    P  23 
I  33    D  24 
E  34    D  25 
A  35    G  26 
E  36    S  27 
D  37    K  28 
N  38    D  29 
M  39    V  30 
N  40    F  31 
C  41    V  32 
Q  42    H  33 
M  43    F  34 
S  44    S  35 
N  45    A  36 
I  46    I  37 
T  47    Q  38 
L  58    G  48 
E  59    Q  49 
Q  60    K  50 
V  61    V  51 
Y  62    S  52 
I  63    F  53 
R  64    T  54 
G  65    I  55 
F  70    A  63 
L  71    A  64 
I  72    G  65 
L  73    N  66 
P  74    V  67 
D  75    T  68 
TER 
END 
