
PFRMAT AL
TARGET T0115
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 top ranking marginal hit from 3DPSSM does not fit well
METHOD with the patterns of secondary structure predicted in the 
METHOD target.
METHOD
METHOD The multiple sequence alignment for the target from PSI-Blast 
METHOD hints that there may be a domain break around 130-135
METHOD in the target. Also, this would make each domain begin
METHOD with 3 or 4 betas and a helix, similar to the ribonuclease H
METHOD fold. Also hexokinase and glycerol kinase (possibly similar in
METHOD function to the target which is a homoserine kinase) in the
METHOD SCOP superfamily "Actin-like ATPase domain" are ribonuclease H folds. 
METHOD Rerunning each "domain" through 3DPSSM gives marginal
METHOD hits to ribonuclease H folds. 
METHOD 
METHOD The alignment has been manually adjusted to compensate
METHOD for the large excursions/embellishments to the core ribonuclease
METHOD fold. Also adjustments have been made to preserve the
METHOD hydrophobic core and the continuity of the secondary 
METHOD structure elements.

MODEL 1
PARENT 1bup_A
I    4 G 4
M    5 P 5
K    6 A 6
V    7 V 7
R    8 G 8
V    9 I 9
K   10 D 10
A   11 L 11
P   12 G 12
D   23 S 13
V   24 T 14
F   25 Y 15
G   26 S 16
L   27 C 17
C   28 V 18
L   29 G 19
K   30 V 20
E   31 F 21
P   32 Q 22
Y   33 H 23
D   34 G 24
V   35 K 25
I   36 V 26
E   37 E 27
V   38 I 28
E   39 I 29
A   40 A 30
I   41 N 31
D   42 D 32
D   43 Q 33
K   44 G 34
E   45 N 35
I   46 R 36
I   47 T 37
I   48 T 38
E   49 P 39
V   50 S 40
D   51 Y 41
D   52 V 42
K   53 A 43
N   54 F 44
I   55 T 45
P   56 D 46
T   57 F 114
D   58 Y 115
P   59 P 116
D   60 E 117
K   61 E 118
N   62 V 119
V   63 S 120
A   64 S 121
G   65 M 122
I   66 V 123
V   67 L 124
A   68 T 125
K   69 K 126
K   70 M 127
M   71 K 128
I   72 E 129
D   73 I 130
D   74 A 131
F   75 E 132
N   76 A 133
I   77 T 138
G   78 V 139
K   79 T 140
G   80 N 141
V   81 A 142
K   82 V 143
I   83 V 144
T   84 T 145
I   85 V 146
K   86 P 147
K   87 A 148
G   88 Y 149
G   92 F 150
S   93 N 151
G   94 D 152
L   95 S 153
G   96 Q 154
S   97 R 155
S   98 Q 156
A   99 A 157
A  100 T 158
S  101 K 159
S  102 D 160
A  103 A 161
G  104 G 162
T  105 T 163
A  106 I 164
Y  107 A 165
A  108 G 166
I  109 L 167
N  110 N 168
E  111 V 169
L  112 L 170
F  113 R 171
K  114 I 172
L  115 I 173
N  116 N 174
L  117 E 175
D  118 P 176
K  119 T 177
L  120 A 178
K  121 A 179
L  122 A 180
V  123 I 181
D  124 A 182
Y  125 Y 183
A  126 G 184
S  127 L 185
Y  128 D 186
G  129 K 187
E  130 K 188
K  137 V 189
H  138 G 190
A  139 A 191
D  140 E 192
N  141 R 193
V  142 N 194
A  143 V 195
P  144 L 196
A  145 I 197
I  146 F 198
F  147 D 199
G  148 L 200
G  149 G 201
F  150 G 202
V  153 G 203
T  154 T 204
N  155 F 205
Y  156 D 206
E  157 V 207
P  158 S 208
L  159 I 209
E  160 L 210
V  161 T 211
L  162 I 212
H  163 E 213
I  164 D 214
I  166 G 215
D  167 I 216
F  168 F 217
K  169 E 218
L  170 V 219
D  171 K 220
I  172 S 221
L  173 T 222
I  174 A 223
A  175 G 224
I  176 D 225
P  177 T 226
N  178 H 227
I  179 L 228
S  180 G 229
N  182 G 230
T  183 E 231
K  184 D 232
E  185 F 233
A  186 D 234
R  187 N 235
E  188 R 236
I  189 M 237
L  190 V 238
P  191 N 239
K  192 H 240
A  193 F 241
V  194 I 242
G  195 A 243
L  196 E 244
K  197 K 257
D  198 R 258
L  199 A 259
V  200 V 260
N  201 R 261
N  202 R 262
V  203 L 263
G  204 R 264
K  205 T 265
A  206 A 266
C  207 C 267
G  208 E 268
M  209 R 269
V  210 A 270
Y  211 K 271
A  212 R 272
L  213 T 273
Y  214 L 274
N  215 S 275
K  216 S 276
E  232 R 299
P  233 A 300
V  234 R 301
R  235 F 302
G  236 E 303
K  237 E 304
L  238 L 305
I  239 N 306
P  240 A 307
N  241 D 308
Y  242 L 309
F  243 F 310
K  244 R 311
I  245 G 312
K  246 T 313
E  247 L 314
E  248 D 315
V  249 P 316
K  250 V 317
D  251 E 318
K  252 K 319
V  253 I 331
Y  254 H 332
G  255 D 333
I  256 I 334
T  257 V 335
I  258 L 336
S  259 V 337
G  260 G 338
S  261 G 339
G  262 S 340
P  263 T 341
S  264 R 342
I  274 I 343
D  275 P 344
E  276 K 345
V  277 I 346
E  278 Q 347
N  279 K 348
I  280 L 349
L  281 L 350
R  282 Q 351
D  283 D 352
Y  284 F 353
Y  285 F 354
E  286 N 355
N  287 G 356
T  288 K 357
I  289 E 358
R  290 L 359
T  291 N 360
E  292 K 361
V  293 S 362
G  294 I 363
K  295 N 364
G  296 P 365
V  297 D 366
E  298 E 367
V  299 A 368
V  300 V 369
TER
END


