PFRMAT AL 
TARGET t0062 
AUTHOR 4139-4764-1095 
METHOD Secondary structure was predicted with PHD and Predator. 
METHOD We then used threader with weight given to predicted SS. 
METHOD The best scoring alignments were then rethreaded with 
METHOD sequence shuffling. Of the best scoring alignments in the 
METHOD second round, number 2 & 3 had very similar folds.  
METHOD The alignment below is from hit number 2 - hit number3 
METHOD was 1cnd which has been replaced by 2cnd in pdb. 
METHOD Since the folds are quite similiar we chose not to use 1cnd. 
MODEL 1 
PARENT 1fnb 
T   1	W  58 
T   2	H  59 
L   3	M  60 
S   4	V  61 
C   5	F  62 
K   6	S  63 
V   7	H  64 
T   8	E  65 
S   9	G  66 
E  11	E  67 
A  12	I  68 
I  13	P  69 
T  14	Y  70 
D  15	R  71 
T  16	E  72 
V  17	G  73 
Y  18	Q  74 
R  19	S  75 
V  20	V  76 
R  21	G  77 
I  22	V  78 
V  23	I  79 
P  24	P  80 
D  25	D  81 
A  26	G  82 
A  27	E  83 
F  28	D  84 
S  29	P  89 
F  30	H  90 
R  31	K  91 
A  32	L  92 
G  33	R  93 
Q  34	L  94 
Y  35	Y  95 
L  36	S  96 
M  37	I  97 
V  38	A  98 
V  39	S  99 
M  40	S 100 
D  41	A 101 
E  42	L 102 
R  43	F 105 
D  44	G 106 
K  45	D 107 
R  46	A 108 
P  47	K 109 
F  48	S 110 
S  49	V 111 
M  50	S 112 
A  51	L 113 
S  52	C 114 
T  53	V 115 
P  54	K 116 
D  55	R 117 
E  56	L 118 
K  57	I 119 
G  58	Y 120 
F  59	T 121 
I  60	N 122 
E  61	D 123 
L  62	A 124 
H  63	G 125 
G  65	E 126 
A  66	T 127 
S  67	I 128 
E  68	K 129 
I  69	G 130 
N  70	V 131 
L  71	C 132 
Y  72	S 133 
A  73	N 134 
K  74	F 135 
A  75	L 136 
V  76	C 137 
M  77	D 138 
D  78	L 139 
R  79	K 140 
K  82	P 141 
D  83	G 142 
H  84	A 143 
Q  85	E 144 
I  86	V 145 
V  87	K 146 
V  88	L 147 
D  89	T 148 
I  90	G 149 
P  91	P 150 
H  92	V 151 
G  93	G 152 
E  94	K 153 
A  95	M 155 
W  96	L 156 
L  97	M 157 
R  98	P 158 
D  99	K 159 
D 100	D 160 
E 101	P 161 
E 102	N 162 
R 103	A 163 
P 104	T 164 
M 105	I 165 
I 106	I 166 
L 107	M 167 
I 108	L 168 
A 109	G 169 
G 110	T 170 
G 111	G 171 
T 112	T 172 
G 113	G 173 
F 114	I 174 
S 115	A 175 
Y 116	P 176 
A 117	F 177 
R 118	R 178 
S 119	S 179 
I 120	F 180 
L 121	L 181 
L 122	W 182 
T 123	K 183 
A 124	M 184 
L 125	F 185 
A 126	F 186 
R 127	E 187 
N 128	K 188 
P 129	H 189 
N 130	N 195 
R 131	G 196 
D 132	L 197 
I 133	A 198 
T 134	W 199 
I 135	L 200 
Y 136	F 201 
W 137	L 202 
G 138	G 203 
G 139	V 204 
R 140	P 205 
E 141	T 206 
E 142	S 207 
Q 143	S 208 
H 144	S 209 
L 145	L 210 
Y 146	L 211 
D 147	Y 212 
L 148	K 213 
C 149	E 214 
E 150	E 215 
L 151	F 216 
E 152	E 217 
A 153	K 218 
L 154	M 219 
S 155	K 220 
L 156	E 221 
K 157	K 222 
H 158	A 223 
P 159	P 224 
G 160	D 225 
L 161	F 227 
Q 162	R 228 
V 163	L 229 
V 164	D 230 
P 165	F 231 
V 166	A 232 
V 167	V 233 
E 168	S 234 
Q 169	R 235 
P 170	E 236 
E 171	E 240 
A 172	K 241 
G 173	G 242 
W 174	E 243 
R 175	K 244 
G 176	M 245 
R 177	Y 246 
T 178	I 247 
G 179	Q 248 
T 180	T 249 
V 181	R 250 
L 182	M 251 
T 183	A 252 
A 184	Q 253 
V 185	Y 254 
L 186	A 255 
Q 187	V 256 
D 188	E 257 
H 189	L 258 
G 190	W 259 
T 191	E 260 
L 192	M 261 
A 193	L 262 
E 194	K 263 
H 195	Y 268 
D 196	V 269 
I 197	Y 270 
Y 198	M 271 
I 199	C 272 
A 200	G 273 
G 201	L 274 
R 202	E 278 
F 203	K 279 
E 204	G 280 
M 205	I 281 
A 206	D 282 
K 207	D 283 
I 208	I 284 
A 209	M 285 
R 210	V 286 
D 211	S 287 
L 212	L 288 
F 213	A 289 
C 214	A 290 
S 215	A 291 
E 216	I 297 
R 217	E 298 
N 218	Y 299 
A 219	K 300 
R 220	R 301 
E 221	Q 302 
D 222	L 303 
R 223	K 304 
L 224	K 305 
F 225	A 306 
G 226	E 307 
D 227	Q 308 
A 228	W 309 
F 229	N 310 
A 230	V 311 
F 231	E 312 
I 232	V 313 
TER 
END 
