PFRMAT AL 
TARGET T0083 
AUTHOR 7169-6295-1599 
METHOD T0083, its related sequences and their multiple alignment were threaded on 
METHOD the structural library composed of PDB rel.83 by several method we 
METHOD developed, however the results are not significant. The results of the 
METHOD secondary structure prediction strongly suggest that the fold is mainly 
METHOD alpha-type. Regretfully we could not find the reasonable fold among the 
METHOD structures that appear at relatively higher ranking positions in the 
METHOD compatibility searches. When the structures were sorted by the ranking of 
METHOD the compatibility score normalized by the alignment length, we find that 
METHOD the CRO repressor structures have very good compatibility. This 
METHOD structure is all alpha-type DNA-binding unit, and this is consistent with 
METHOD the results of the secondary structure prediction. The aligned region is the 
METHOD N terminal half. Look at the multiple alignment of the target sequences,  
METHOD Pro rich region is found in the middle (78-92)  and it may form coil structure. 
METHOD We consider this may be the hinge of domains and the former takes CRO 
METHOD repressor fold. This prediction was confirmed by the inverse-folding search 
METHOD with a CRO repressor fold (1r69) against the target sequence plus the 
METHOD sequence database constructed from PDB rel. 83. The results show the N 
METHOD terminal half sequence appear among the higher ranking cluster constituting 
METHOD of CRO repressors and lambda repressors which share the same fold. 
MODEL 1 
PARENT 1r69 
D 13 S 1 
L 14 I 2 
A 15 S 3 
D 16 S 4 
A 17 R 5 
I 18 V 6 
L 19 K 7 
L 20 S 8 
S 21 K 9 
K 22 R 10 
A 23 I 11 
K 24 Q 12 
K 25 L 13 
D 26 G 14 
L 27 L 15 
S 28 N 16 
F 29 Q 17 
A 30 A 18 
E 31 E 19 
I 32 L 20 
A 33 A 21 
D 34 Q 22 
G 35 K 23 
T 36 V 24 
G 37 G 25 
L 38 T 26 
A 39 T 27 
E 40 Q 28 
A 41 Q 29 
F 42 S 30 
V 43 I 31 
T 44 E 32 
A 45 Q 33 
A 46 L 34 
L 47 E 35 
L 48 N 36 
G 49 G 37 
Q 50 K 38 
Q 51 T 39 
A 52 K 40 
L 53 R 41 
P 54 P 42 
A 55 R 43 
D 56 F 44 
A 57 L 45 
A 58 P 46 
R 59 E 47 
L 60 L 48 
V 61 A 49 
A 63 S 50 
K 64 A 51 
L 65 L 52 
D 66 G 53 
L 67 V 54 
D 68 S 55 
E 69 V 56 
D 70 D 57 
S 71 W 58 
I 72 L 59 
L 73 L 60 
L 74 N 61 
L 75 G 62 
Q 76 T 63 
TER 
END 
