PFRMAT AL 
TARGET t0077 
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) THREADER:  
METHOD    Some of the good scorers were in the same SCOP class as the 
METHOD    best results from the HMM. We picked out these and repeated 
METHOD    the threading with sequence shuffling. 
METHOD    Of the structures with good score in both methods, 1ger 
METHOD    was judged to be the best from Threader, and 1gar the 
METHOD    best from the HMM. Since 1ger seemed to be slightly better 
METHOD    aligned by manual inspection, this was chosen as model 1 
METHOD    below. 1gar is submitted as model2. 
MODEL 1 
PARENT 1gerA 
M   1	V 170 
A   2	A 171 
P   3	V 172 
V   4	V 173 
K   5	G 174 
S   6	A 175 
Q   7	G 176 
E   8	Y 177 
S   9	I 178 
I  10	A 179 
N  11	V 180 
Q  12	E 181 
K  13	L 182 
L  14	A 183 
A  15	G 184 
L  16	V 185 
V  17	I 186 
I  18	N 187 
K  19	G 188 
S  20	L 189 
K  38	G 190 
S  39	A 191 
K  40	K 192 
L  41	T 193 
I  42	H 194 
I  43	L 195 
I  44	F 196 
A  45	V 197 
A  46	R 198 
N  47	K 199 
T  48	H 200 
P  49	A 201 
V  50	P 202 
L  51	L 203 
R  52	P 208 
K  53	M 209 
S  54	I 210 
E  55	S 211 
L  56	E 212 
E  57	T 213 
Y  58	L 214 
Y  59	V 215 
A  60	E 216 
M  61	V 217 
L  62	M 218 
S  63	N 219 
K  64	A 220 
T  65	E 221 
K  66	G 222 
V  67	P 223 
Y  68	Q 224 
Y  69	L 225 
F  70	H 226 
Q  71	T 227 
N  74	N 228 
N  75	A 229 
E  76	I 230 
L  77	P 231 
G  78	K 232 
T  79	A 233 
A  80	V 234 
V  81	V 235 
G  82	K 236 
K  83	N 237 
L  84	T 238 
F  85	D 239 
R  86	G 240 
V  87	S 241 
G  88	L 242 
V  89	T 243 
V  90	L 244 
S  91	E 245 
I  92	L 246 
L  93	E 247 
E  94	D 248 
G  96	G 249 
D  97	R 250 
S  98	S 251 
D  99	E 252 
I 100	T 253 
L 101	V 254 
T 102	D 255 
T 103	C 256 
L 104	L 257 
A 105	I 258 
TER 
END 
