PFRMAT AL 
TARGET T0051 
AUTHOR 9070-5088-8627 
METHOD Overview 
METHOD  
METHOD Fold recognition was performed using the Target98 (SAM-T98) method 
METHOD [3] using SAM version 2.1.1 [1], a refinement of the methods developed 
METHOD by this group for CASP2 [2].  This method attempts to find and multiply  
METHOD align a set of homologs to a given sequence, then create an HMM from that  
METHOD multiple alignment. 
METHOD  
METHOD First, a set of sequence weights is determined from the alignment.  Next,  
METHOD Modelfromalign is used to build the model from the alignment and the  
METHOD sequence weights.  Finally, hmmscore performs a local, all-paths scoring  
METHOD of the sequences, using a reversed-sequence normalization feature. 
METHOD  
METHOD The weighting method, detailed in upcoming publications [3,4], 
METHOD combines the Henikoffs' scheme [5], Dirichlet mixtures [6], and an 
METHOD entropy method to set the final weights. 
METHOD  
METHOD Alignment generation 
METHOD  
METHOD The initial step uses BLASTP to search NRP twice: once to produce a set 
METHOD of very close homologs, and once to produce a set of possible homologs. 
METHOD  
METHOD The method then uses multiple iterations of a selection, training, and  
METHOD alignment procedure.  Each iteration involves an initial alignment, a set  
METHOD of search sequences, a threshold value, and a transition regularizer.  
METHOD  
METHOD The first iteration uses a single sequence (or seed alignment) as the  
METHOD initial alignment and the close homologs found by BLASTP are used as the  
METHOD search set.  The threshold is set very strictly, so that only good matches  
METHOD to the sequence are considered.  This iteration uses a transition regularizer  
METHOD that was designed to match the gap costs used by BLASTP. 
METHOD  
METHOD On subsequent iterations the input alignment is the output from the 
METHOD previous iteration, the search set is the larger set of possible 
METHOD homologs found by BLASTP, and the thresholds are gradually loosened. 
METHOD The second through second-from-last iteration use a ``long-match'' 
METHOD transition regularizer, and the final iteration uses a transition regularizer  
METHOD trained on FSSP alignments. 
METHOD  
METHOD References 
METHOD [1] R. Hughey and A. Krogh, CABIOS 12(2): 95-107, 1996. 
METHOD     http://www.cse.ucsc.edu/research/compbio/sam.html.   
METHOD [2] K. Karplus, K. Sjolander, C. Barrett, M. Cline, D. Haussler, R. 
METHOD     Hughey, L. Holm, and C. Sander, Proteins: Structure, Function, and  
METHOD     Genetics, Suppl. 1, 134-9, 1997. 
METHOD [3] K. Karplus, C. Barrett, and R. Hughey, Technical Report UCSC-CRL-98-06, 
METHOD     Department of Computer Engineering, Univ. of California, Santa Cruz, 1998. 
METHOD [4] J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, 
METHOD     and C. Chothia, http://cyrah.med.harvard.edu/~jong/assess_final.html, 1998. 
METHOD [5] S. Henikoff and J. C. Henikoff, JMB, vol 243, pp 574-578, Nov 1994. 
METHOD [6] K. Sjolander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S. 
METHOD    Mian, and D. Haussler, CABIOS 12(4):327-345, 1996. 
METHOD  
METHOD  
METHOD The choice of 1reqA for T0051 came mainly from its co-crystalization 
METHOD with T0050, which had an excellent alignment to 1reqA.  The scores were 
METHOD so low that 1reqA did not appear on the list of possible templates 
METHOD for T0051, but aligning to an HMM built from 1reqA and its structural 
METHOD homologs produced acceptable scores---better than any of the templates 
METHOD that did score well in the library search. 
METHOD  
METHOD We made a chimeric sequence (T0051+T0050) by concatenating the two 
METHOD targets and used it for alignment.  The chimeric sequence scored well 
METHOD with both 1bmtA and 1reqA (because of the homologies for T0050). 
METHOD  
METHOD The alignments from the HMMs still looked terrible, though, so we 
METHOD decided to hand-align T0051 to 1reqA, starting from an alignment of a 
METHOD chimeric sequence.  The hand alignment preserves much of the central 
METHOD binding pocket, and the ends of gaps are mostly close in 3-space. 
METHOD  
METHOD We were not able to get a convincing alignment with 1bmtA, because it 
METHOD is so much shorter than T0051+T0050, and even making two copies 
METHOD (1bmtA+1bmtB) did not produce good alignments. 
METHOD  
METHOD Note: because of the low scores for T0051 and extensive 
METHOD hand-alignment, it is quite likely that the fold predictions here are 
METHOD wrong.   
MODEL 1 
PARENT 1req_A 
L 32 T 34 
Q 33 G 35 
E 34 E 36 
A 35 A 37 
V 36 W 38 
D 37 E 39 
Y 38 T 40 
L 39 A 41 
K 40 E 42 
K 41 Q 43 
I 42 I 44 
P 43 P 45 
A 44 V 46 
E 45 G 47 
K 46 T 48 
N 47 L 49 
F 48 F 50 
A 49 N 51 
E 50 E 52 
K 51 D 53 
L 52 V 54 
V 53 Y 55 
L 54 K 56 
G 59 D 57 
I 60 M 58 
T 61 D 59 
M 62 W 60 
A 63 L 61 
Q 64 D 62 
P 65 T 63 
R 66 Y 64 
A 67 A 65 
G 68 G 66 
V 69 I 67 
A 70 P 68 
L 71 P 69 
L 72 F 70 
D 73 V 71 
E 74 H 72 
H 75 G 73 
I 76 P 74 
E 77 Y 75 
L 78 A 76 
L 79 T 77 
R 80 M 78 
Y 81 Y 79 
L 82 A 80 
F 90 F 81 
L 91 R 82 
P 92 P 83 
S 93 W 84 
T 94 T 85 
I 95 I 86 
D 96 R 87 
A 97 Q 88 
Y 98 Y 89 
T 99 A 90 
R 100 G 91 
Q 101 F 92 
N 102 S 93 
R 103 T 94 
Y 104 A 95 
D 105 K 96 
E 106 E 97 
C 107 S 98 
E 108 N 99 
N 109 A 100 
G 110 F 101 
I 111 Y 102 
K 112 R 103 
E 113 R 104 
S 114 N 105 
E 115 L 106 
K 116 A 107 
A 117 A 108 
G 118 G 109 
R 119 Q 110 
S 120 K 111 
L 121 G 112 
L 122 L 113 
N 123 S 114 
G 124 V 115 
F 125 L 119 
P 126 P 120 
G 127 T 121 
V 128 H 122 
N 129 R 123 
Y 130 G 124 
G 131 Y 125 
V 132 D 126 
K 133 S 127 
G 134 D 128 
C 135 N 129 
R 136 P 130 
K 137 R 131 
V 138 V 132 
L 139 A 133 
E 140 G 134 
A 141 D 135 
V 142 V 136 
N 143 G 137 
L 144 M 138 
P 145 A 139 
L 146 G 140 
Q 147 V 141 
A 148 A 142 
R 149 I 143 
H 150 D 144 
G 151 S 145 
T 152 I 146 
P 153 Y 147 
D 154 D 148 
S 155 M 149 
R 156 R 150 
L 157 E 151 
L 158 L 152 
A 159 F 153 
E 160 A 154 
I 161 G 155 
I 162 I 156 
H 163 P 157 
G 174 L 158 
I 175 D 159 
S 176 Q 160 
Y 177 M 161 
N 178 S 162 
V 179 V 163 
P 180 S 164 
Y 181 M 165 
A 182 T 166 
K 183 M 167 
N 184 N 168 
V 185 G 169 
T 186 A 170 
I 187 V 171 
E 188 L 172 
K 189 P 173 
S 190 I 174 
L 191 L 175 
L 192 A 176 
D 193 L 177 
W 194 Y 178 
Q 195 V 179 
Y 196 V 180 
C 197 T 181 
D 198 A 182 
R 199 E 183 
L 200 E 184 
V 201 Q 185 
G 202 G 186 
F 203 V 187 
Y 204 K 188 
E 205 P 189 
E 206 E 190 
Q 207 Q 191 
G 208 L 192 
V 209 G 194 
H 210 T 195 
I 211 I 196 
N 212 Q 197 
R 213 N 198 
E 214 D 199 
P 215 I 200 
F 216 L 201 
G 217 R 207 
P 218 N 208 
L 219 T 209 
T 220 Y 210 
G 221 I 211 
T 222 Y 212 
L 223 P 213 
V 224 P 214 
P 225 Q 215 
P 226 P 216 
S 227 S 217 
M 228 M 218 
S 229 R 219 
N 230 I 220 
A 231 I 221 
V 232 S 222 
G 233 E 223 
I 234 I 224 
T 235 F 225 
E 236 A 226 
A 237 Y 227 
L 238 T 228 
L 239 S 229 
A 240 A 230 
A 241 N 231 
E 242 M 232 
Q 243 P 233 
G 244 F 280 
V 245 A 281 
K 246 P 282 
N 247 R 283 
I 248 L 284 
T 249 S 285 
V 250 F 286 
G 251 F 287 
Y 252 W 288 
G 253 G 289 
E 254 I 290 
C 255 G 291 
G 256 M 292 
N 257 N 293 
M 258 F 294 
I 259 F 295 
Q 260 M 296 
D 261 E 297 
I 262 V 298 
A 263 A 299 
A 264 K 300 
L 265 L 301 
R 266 R 302 
C 267 A 303 
L 268 A 304 
E 269 R 305 
E 270 M 306 
Q 271 L 307 
T 272 W 308 
N 273 A 309 
E 274 K 310 
Y 275 L 311 
L 276 V 312 
K 277 H 313 
A 278 Q 314 
Y 279 F 315 
G 280 G 316 
Y 281 K 318 
N 282 N 319 
D 283 P 320 
V 284 K 321 
F 285 S 322 
V 286 M 323 
T 287 S 324 
T 288 L 325 
V 289 R 326 
F 290 T 327 
H 291 H 328 
Q 292 S 329 
W 293 Q 330 
M 294 T 331 
G 295 S 332 
G 296 G 333 
F 297 W 334 
P 298 S 335 
Q 299 L 336 
D 300 T 337 
E 301 A 338 
S 302 Q 339 
K 303 Y 342 
A 304 N 343 
F 305 N 344 
G 306 V 345 
V 307 V 346 
I 308 R 347 
V 309 T 348 
T 310 C 349 
A 311 I 350 
T 312 E 351 
T 313 A 352 
I 314 M 353 
A 315 A 354 
A 316 A 355 
L 317 T 356 
A 318 Q 357 
G 319 G 358 
A 320 H 359 
T 321 T 360 
K 322 Q 361 
V 323 S 362 
I 324 L 363 
V 325 H 364 
K 326 T 365 
T 327 N 366 
P 328 S 367 
H 329 D 369 
E 330 E 370 
A 331 A 371 
I 332 I 372 
G 333 A 373 
I 334 L 374 
P 335 P 375 
T 336 T 376 
K 337 D 377 
E 338 F 378 
A 339 S 379 
N 340 A 380 
A 341 R 381 
A 342 I 382 
G 343 A 383 
I 344 R 384 
K 345 N 385 
A 346 T 386 
T 347 Q 387 
K 348 L 388 
M 349 F 389 
A 350 L 390 
L 351 Q 391 
N 352 Q 392 
M 353 E 393 
L 354 S 394 
E 355 G 395 
G 356 T 396 
Q 357 T 397 
R 358 R 398 
M 359 V 399 
P 360 W 403 
M 361 S 404 
S 362 G 405 
K 363 S 406 
E 364 A 407 
L 365 Y 408 
E 366 V 409 
T 367 E 410 
E 368 E 411 
M 369 L 412 
A 370 T 413 
V 371 W 414 
I 372 D 415 
K 373 L 416 
A 374 A 417 
E 375 R 418 
T 376 K 419 
K 377 A 420 
C 378 W 421 
I 379 G 422 
L 380 H 423 
D 381 I 424 
K 382 Q 425 
M 383 E 426 
F 384 V 427 
E 385 E 428 
L 386 K 429 
G 387 V 430 
I 393 G 431 
G 394 G 432 
T 395 M 433 
V 396 A 434 
K 397 K 435 
A 398 A 436 
F 399 I 437 
E 400 E 438 
T 401 K 439 
G 402 G 440 
I 406 I 441 
P 407 P 442 
F 408 K 443 
G 409 M 444 
P 410 R 445 
S 411 I 446 
K 412 E 447 
Y 413 E 448 
N 414 A 449 
A 415 A 450 
G 416 A 451 
K 417 R 452 
M 418 T 453 
M 419 Q 454 
P 420 A 455 
V 421 R 456 
R 422 I 457 
D 423 D 458 
N 424 P 463 
L 425 L 464 
G 426 I 465 
C 427 G 466 
V 428 V 467 
R 429 N 468 
Y 430 K 469 
L 431 L 481 
E 432 K 482 
F 433 V 483 
G 434 D 484 
N 435 N 485 
V 436 S 486 
P 437 T 487 
F 438 V 488 
T 439 L 489 
E 440 A 490 
E 441 E 491 
I 442 Q 492 
K 443 K 493 
N 444 A 494 
Y 445 K 495 
N 446 V 545 
R 447 G 546 
E 448 E 547 
R 449 M 548 
L 450 S 549 
Q 451 D 550 
E 452 A 551 
R 453 L 552 
A 454 E 553 
K 455 K 554 
F 456 V 555 
E 457 F 556 
V 461 G 557 
S 462 R 558 
F 463 Y 559 
Q 464 T 560 
M 465 A 561 
V 466 Q 562 
I 467 I 563 
D 468 R 564 
D 469 T 565 
I 470 I 566 
F 471 S 567 
A 472 G 568 
V 473 V 569 
G 474 Y 570 
K 475 S 571 
G 476 K 572 
R 477 E 573 
L 478 V 574 
I 479 K 575 
G 480 N 576 
R 481 T 577 
P 482 P 578 
E 483 E 579 
TER 
END 
