PFRMAT AL 
TARGET t0079 
AUTHOR 4139-4764-1095 
METHOD 1) Secondary structure was predicted with PHD and Predator. 
METHOD 2) We used a hidden markov model that predicts SCOP 
METHOD    classification based on sequence and secondary structure. 
METHOD 3) We also performed threading, using THREADER2 and taking 
METHOD    secondary structure into account. The best hits were 
METHOD    rethreaded using sequence shuffling.  
METHOD    The results from both methods were at least in part 
METHOD    compatible - we are submitting the HMM hit as model1 
METHOD    and the threader one as model2. 
MODEL 2 
PARENT 1ann 
N   7	P  85 
T   8	T  86 
D   9	V  87 
A  10	L  88 
I  11	Y  89 
T  12	D  90 
I  13	V  91 
H  14	Q  92 
S  15	E  93 
I  16	L  94 
L  17	R  95 
D  18	K  96 
W  19	A  97 
I  20	M  98 
E  21	K  99 
D  22	G 100 
N  23	A 101 
G  38	G 102 
Y  39	T 103 
S  40	D 104 
K  41	E 105 
W  42	G 106 
H  43	C 107 
L  44	L 108 
Q  45	I 109 
R  46	E 110 
M  47	I 111 
F  48	L 112 
K  49	A 113 
K  50	S 114 
E  51	R 115 
R  61	T 116 
S  62	P 117 
R  63	E 118 
K  64	E 119 
M  65	I 120 
T  66	R 121 
E  67	R 122 
I  68	I 123 
A  69	N 124 
Q  70	Q 125 
K  71	T 126 
L  72	Y 127 
K  73	Q 128 
E  74	L 129 
S  75	Q 130 
N  76	Y 131 
E  77	G 132 
P  78	R 133 
I  79	L 135 
L  80	E 136 
Y  81	D 137 
L  82	D 138 
A  83	I 139 
E  84	R 140 
R  85	S 141 
Y  86	D 142 
G  87	T 143 
Q  91	S 144 
Q  92	F 145 
T  93	M 146 
L  94	F 147 
T  95	Q 148 
R  96	R 149 
T  97	V 150 
F  98	L 151 
K  99	V 152 
N 100	S 153 
Y 101	L 154 
F 102	S 155 
D 103	A 156 
V 104	G 157 
P 105	G 158 
TER 
END 
