PFRMAT AL  
TARGET t0044 
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 2:  
METHOD    We performed ordinary threading and reran the best scoring 
METHOD    targets with sequence shuffling. Since the information  
METHOD    stated the PHD secondary structure prediction to be good, 
METHOD    we also performed a run with higher weight for this. 
METHOD    3rub was the best scorer from threading with "ordinary"     
METHOD    weighting for secondary structure, 1nal (model 2) the best 
METHOD    from increased-SS-weight threading. Many of the good 
METHOD    scorers from the HMM program were also TIM barrels, 
METHOD    further strengthening the prediction. 
MODEL 1 
REMARK The parent-none fields below really just indicate 
REMARK that the corresponding residue(s) are not aligned 
PARENT 3rub_L 
M   1	R 167 
V   2	P 168 
M   5	L 169 
I   6	L 170 
A   7	G 171 
L   8	C 172 
D   9	T 173 
G  10	I 174 
A  11	K 175 
Q  12	P 176 
G  13	K 177 
E  14	L 178 
G  15	G 179 
G  16	L 180 
G  17	K 183 
Q  18	N 184 
I  19	Y 185 
L  20	G 186 
R  21	R 187 
S  22	A 188 
A  23	V 189 
L  24	Y 190 
S  25	E 191 
L  26	C 192 
S  27	L 193 
M  28	R 194 
I  29	G 195 
T  30	G 196 
G  31	L 197 
P  33	D 198 
F  34	F 199 
T  35	T 200 
I  36	K 201 
T  37	D 202 
S  38	D 203 
I  39	E 204 
R  40	N 205 
A  41	V 206 
G  42	N 207 
R  43	S 208 
A  44	Q 209 
K  45	P 210 
P  46	R 215 
G  47	D 216 
L  48	R 217 
L  49	F 218 
R  50	L 219 
Q  51	F 220 
H  52	C 221 
L  53	A 222 
T  54	E 223 
A  55	A 224 
V  56	L 225 
K  57	Y 226 
A  58	K 227 
A  59	A 228 
T  60	Q 229 
E  61	A 230 
I  62	E 231 
C  63	T 232 
G  64	G 233 
A  65	E 234 
T  66	I 235 
V  67	K 236 
S  98	G 237 
C  99	H 238 
T 100	Y 239 
L 101	L 240 
V 102	N 241 
L 103	A 242 
Q 104	E 248 
T 105	E 249 
V 106	M 250 
L 107	I 251 
P 108	K 252 
A 109	R 253 
L 110	A 254 
W 111	V 255 
F 112	F 256 
A 113	A 257 
D 114	R 258 
G 115	E 259 
P 116	L 260 
S 117	G 261 
R 118	V 262 
V 119	P 263 
E 120	I 264 
V 121	V 265 
S 122	M 266 
G 123	H 267 
G 124	D 268 
T 125	Y 269 
D 126	L 270 
N 127	T 271 
P 128	G 272 
S 129	G 273 
A 130	F 274 
P 131	T 275 
P 132	A 276 
A 133	N 277 
D 134	T 278 
F 135	S 279 
I 136	L 280 
R 137	A 281 
R 138	H 282 
V 139	Y 283 
L 140	C 284 
E 141	R 285 
P 142	D 286 
L 143	N 287 
L 144	G 288 
A 145	L 289 
K 146	L 290 
I 147	L 291 
G 148	H 292 
I 149	I 293 
H 150	H 294 
Q 151	R 295 
Q 152	A 296 
T 153	M 297 
R 157	H 298 
H 158	A 299 
G 159	V 300 
F 160	I 301 
Y 161	D 302 
P 162	R 303 
A 163	Q 304 
G 164	K 305 
G 165	N 306 
G 166	H 307 
V 167	H 310 
V 168	F 311 
A 169	R 312 
T 170	V 313 
E 171	L 314 
V 172	A 315 
S 173	K 316 
P 174	A 317 
V 175	L 318 
A 176	R 319 
S 177	M 320 
F 178	S 321 
N 179	G 322 
T 180	G 323 
L 181	D 324 
V 196	H 325 
L 197	I 326 
L 198	H 327 
A 199	S 328 
G 200	G 329 
V 201	T 330 
P 202	V 331 
R 203	V 332 
H 204	G 333 
V 205	K 334 
A 206	L 335 
E 207	E 336 
R 208	G 337 
E 209	E 338 
I 210	R 339 
A 211	D 340 
T 212	I 341 
L 213	T 342 
A 214	L 343 
G 215	G 344 
S 216	F 345 
F 217	V 346 
S 218	D 347 
L 219	L 348 
H 220	L 349 
E 221	R 350 
Q 222	D 351 
N 223	D 352 
N 226	F 353 
L 227	V 354 
P 228	E 355 
R 229	Q 356 
D 230	D 357 
Q 231	R 358 
G 232	S 359 
P 233	R 360 
G 234	G 361 
N 235	I 362 
T 236	Y 363 
V 237	F 364 
S 238	T 365 
L 239	Q 366 
E 240	D 367 
V 241	W 368 
E 242	V 369 
S 243	S 370 
E 244	L 371 
N 245	P 372 
I 246	G 373 
T 247	V 374 
F 250	L 375 
F 251	P 376 
V 252	V 377 
V 253	A 378 
G 254	S 379 
E 255	G 380 
K 256	G 381 
A 260	I 382 
E 261	H 383 
V 262	W 385 
V 263	H 386 
A 264	M 387 
A 265	P 388 
Q 266	A 389 
L 267	L 390 
V 268	T 391 
K 269	E 392 
E 270	I 393 
V 271	F 394 
K 272	G 395 
R 273	D 396 
Y 274	V 399 
L 275	L 400 
A 276	Q 401 
S 277	F 402 
T 278	G 403 
A 279	G 404 
A 280	N 413 
V 281	A 414 
G 282	P 415 
E 283	G 416 
Y 284	A 417 
L 285	V 418 
A 286	A 419 
D 287	N 420 
Q 288	R 421 
L 289	V 422 
V 290	A 423 
L 291	L 424 
P 292	E 425 
M 293	A 426 
A 294	C 427 
L 295	V 428 
A 296	K 429 
G 297	A 430 
A 298	R 431 
G 299	N 432 
E 300	E 433 
F 301	R 435 
T 302	D 436 
V 303	L 437 
A 304	A 438 
H 305	Q 439 
P 306	E 440 
S 307	G 441 
C 308	N 442 
H 309	E 443 
L 310	I 444 
L 311	I 445 
T 312	R 446 
N 313	E 447 
I 314	A 448 
A 315	C 449 
V 316	K 450 
V 317	W 451 
E 318	S 452 
R 319	P 453 
F 320	E 454 
L 321	L 455 
P 322	A 456 
V 323	A 457 
R 324	A 458 
F 325	C 459 
S 326	E 460 
L 327	V 461 
I 328	W 462 
E 329	K 463 
T 330	E 464 
D 331	I 465 
G 332	V 466 
TER 
END 
