
PFRMAT AL
TARGET T0109
AUTHOR 4216-9015-4014
REMARK Predictor remarks
METHOD CASP4 submission
METHOD 
METHOD Work by Kelley LA, MacCallum RM & Sternberg MJE
METHOD Biomolecular Modelling Laboratory
METHOD Imperial Cancer Research Fund
METHOD 44 Lincoln's Inn Fields
METHOD London WC2A 3PX, England 
METHOD Tel +44-(0)20-7269-3565 / 3242
METHOD FAX +44-(0)20-7269-3534
METHOD
METHOD Using the results from the 3D-PSSM server:
METHOD see http://cafasp.bioinfo.pl/server/3dpssm.html
METHOD and Kelley LA, MacCallum RM & Sternberg MJE (2000).
METHOD     Enhanced Genome Annotation using Structural Profiles
METHOD     in the Program 3D-PSSM. J. Mol. Biol. 299(2), 501-522.
METHOD
METHOD The template was found at rank 1 with 80% confidence.
METHOD This was achieved using a global alignment algorithm
METHOD as opposed to the global-local algorithm used in CAFASP. 
METHOD A good SAWTED text description score between target and template
METHOD also improved the score substantially (keyword exonuclease and others)
METHOD The alignment was slightly manually adjusted to preserve the
METHOD integrity of secondary structural elements. 

MODEL 1
PARENT 1kfs_A
M    1 I 343
S    2 K 345
F    3 L 346
D    4 E 347
K    5 K 348
Q    6 A 349
N    7 P 350
L    8 V 351
I    9 F 352
W   10 A 353
I   11 F 354
D   12 D 355
L   13 T 356
E   14 E 357
M   15 T 358
T   16 D 359
G   17 S 360
L   18 L 361
D   19 D 362
P   20 N 363
E   21 I 364
K   22 S 365
E   23 A 366
R   24 N 367
I   25 L 368
I   26 V 369
E   27 G 370
I   28 L 371
A   29 S 372
T   30 F 373
I   31 A 374
V   32 I 375
T   33 E 376
D   34 P 377
G   43 G 378
P   44 V 379
V   45 A 380
L   46 A 381
A   47 Y 382
V   48 I 383
H   49 P 384
Q   50 V 385
S   51 A 386
D   52 H 387
E   53 D 388
L   54 Y 389
L   55 L 390
N   56 D 391
K   57 A 392
M   58 P 393
N   59 D 394
D   60 Q 395
W   61 I 396
A   85 S 397
E   86 R 398
L   87 E 399
Q   88 R 400
T   89 A 401
L   90 L 402
D   91 E 403
F   92 L 404
L   93 L 405
K   94 K 406
K   95 P 407
W   96 L 408
V   97 L 409
P   98 E 410
K   99 D 411
G  100 E 412
A  101 K 413
S  102 A 414
P  103 L 415
I  104 K 416
C  105 V 417
G  106 G 418
N  107 Q 419
S  108 N 420
I  109 L 421
A  110 K 422
Q  111 Y 423
D  112 D 424
K  113 R 425
R  114 G 426
F  115 I 427
L  116 L 428
V  117 A 429
K  118 N 430
Y  119 Y 431
M  120 G 432
P  121 I 433
D  122 E 434
L  123 L 435
H  128 R 436
Y  129 G 437
R  130 I 438
H  131 A 439
L  132 F 440
D  133 D 441
V  134 T 442
S  135 M 443
T  136 L 444
L  137 L 461
K  138 A 462
E  139 E 463
L  140 R 464
A  141 W 465
A  142 L 466
R  143 K 467
W  144 H 468
K  145 T 472
P  146 F 473
E  147 E 474
I  148 E 475
L  149 I 476
E  150 A 477
G  151 N 482
F  152 Q 483
K  153 L 484
K  154 T 485
E  155 F 486
N  156 N 487
T  157 Q 488
H  158 I 489
L  159 A 490
A  160 L 491
L  161 E 492
D  162 E 493
D  163 A 494
I  164 G 495
R  165 R 496
E  166 Y 497
S  167 A 498
I  168 A 499
K  169 E 500
E  170 D 501
L  171 A 502
A  172 D 503
Y  173 V 504
Y  174 T 505
R  175 L 506
E  176 Q 507
H  177 L 508
F  178 H 509
M  179 L 510
K  180 K 511
L  181 M 512
D  182 W 513
TER
END

