
PFRMAT AL
TARGET T0115
AUTHOR 7770-2312-5826
REMARK GROUP NAME: SHESTOPALOV.
REMARK GROUP LEADER: Shestopalov Boris V. TEAM: NO.
REMARK E-mail: shest@mail.cytspb.rssi.ru
METHOD Secondary structures predicted by DOUBLET CODE METHOD
METHOD (see SHESTOPALOV, ab initio secondary structure category)
METHOD and also various information from protein data bases are used.
METHOD Predicted secondary structure is used for search in PDB
METHOD similar secondary structures. BLAST and FASTA data for target
METHOD sequence are used to restrict this search. For this purpose
METHOD SCOP, CATH, PRODOM, CD-BLAST, SWISSPROT and other databases
METHOD are used also. Fruitful tools for the target are mentioned 
METHOD especially. Alignment is constructed manually, using,
METHOD when it is possible, Yale structural alignments for
METHOD PARENT and its homologues.
METHOD Here BLAST-2 service has been fruitful (Yan P. Yuan, 
METHOD Eulenstein, O., Vingron, M. & Bork, P. 1998. Towards 
METHOD detection of orthologues in sequence databases. Bioinformatics, 
METHOD 14, 285-289), EMBL installation (first PARENT). 
METHOD SCOP server(Reference: Murzin A. G., Brenner S. E., 
METHOD Hubbard T., Chothia C. (1995). SCOP: a structural classification 
METHOD of proteins database for the investigation of sequences and 
METHOD structures. J. Mol. Biol. 247, 536-540) has been fruitful
METHOD for the second domain. 
MODEL  1
PARENT 1a3q_A
R 2 S 226
E 3 N 227
I 4 L 228
M 5 K 229
K 6 I 230
V 7 S 231
R 8 R 232
V 9 M 233
N 17 D 234
L 18 K 235
G 19 T 236
V 20 A 237
G 21 G 238
F 22 S 239
D 23 E 245
V 24 V 246
F 25 Y 247
G 26 L 248
L 27 L 249
C 28 C 250
L 29 D 251
K 30 K 252
E 31 V 253
P 32 Q 254
Y 33 K 255
D 34 D 256
V 35 D 257
I 36 I 258
E 37 E 259
V 38 V 260
E 39 R 261
A 40 F 262
I 41 Y 263
D 42 E 264
D 43 D 265
K 44 D 266
E 45 E 267
I 46 G 269
I 47 W 270
I 48 Q 271
E 49 A 272
V 50 F 273
D 51 G 274
D 52 D 275
K 53 F 276
N 54 S 277
P 56 P 278
T 57 T 279
D 58 D 280
P 59 V 281
D 60 H 282
K 61 K 283
N 62 Q 284
V 63 Y 285
A 64 A 286
G 65 I 287
I 66 V 288
V 67 F 289
A 68 R 290
K 69 H 295
K 70 K 296
M 71 M 297
I 72 I 299
D 73 E 300
D 74 T 304
F 75 V 305
N 76 F 306
I 77 L 307
G 78 S 318
K 79 D 319
G 80 S 320
V 81 K 321
K 82 Q 322
I 83 F 323
T 84 T 324
I 85 Y 325
K 86 Y 326
TER
PARENT 1ah6
A 103 A 2
G 104 S 3
T 105 E 4
A 106 T 5
Y 107 F 6
A 108 E 7
I 109 I 12
N 110 T 13
E 111 Q 14
L 112 L 15
F 113 M 16
K 114 S 17
L 115 L 18
N 116 I 19
L 117 I 20
D 118 S 25
K 119 N 26
L 120 I 29
K 121 F 30
L 122 L 31
V 123 R 32
D 124 E 33
Y 125 L 34
A 126 I 35
S 127 S 36
Y 128 N 37
G 129 A 38
E 130 S 39
L 131 D 40
A 132 A 41
S 133 L 42
S 134 D 43
G 135 K 44
A 136 I 45
K 137 R 46
H 138 Y 47
A 139 K 48
D 140 S 49
N 155 L 50
Y 156 S 51
E 157 D 52
P 158 P 53
L 159 K 54
E 160 Q 55
V 161 L 56
L 162 E 57
H 163 T 58
I 164 E 59
P 165 P 60
I 166 D 61
D 167 L 62
F 168 F 63
K 169 I 64
L 170 R 65
D 171 I 66
I 172 T 67
L 173 P 68
I 174 K 69
A 175 P 70
I 176 E 71
P 177 Q 72
N 178 K 73
I 179 V 74
S 180 L 75
I 181 E 76
N 182 I 77
T 183 R 78
K 184 K 86
E 185 A 87
A 186 E 88
R 187 L 89
E 188 I 90
I 189 N 91
L 190 N 92
P 191 L 93
K 192 G 94
A 193 T 95
V 194 I 96
G 195 A 97
L 196 K 98
K 197 S 99
K 205 G 100
A 206 T 101
C 207 K 102
G 208 A 103
M 209 F 104
V 210 M 105
Y 211 E 106
A 212 A 107
L 213 L 108
Y 214 S 109
N 215 A 110
K 216 G 111
D 217 A 112
K 218 D 113
L 220 V 114
F 221 S 115
G 222 M 116
R 223 I 117
Y 224 G 118
M 225 Q 119
M 226 F 120
I 239 G 121
P 240 V 122
N 241 G 123
Y 242 F 124
F 243 Y 125
K 244 S 126
I 245 L 127
K 246 F 128
E 247 L 129
E 248 V 130
V 249 A 131
K 250 D 132
D 251 R 133
K 252 G 154
V 253 S 155
Y 254 F 156
G 255 T 157
I 256 V 158
T 257 T 159
I 258 L 160
S 259 D 161
G 260 E 162
S 261 V 163
G 262 R 169 
P 263 G 170
S 264 T 171
I 265 I 172
I 266 L 173
A 267 R 174
F 268 L 175
P 269 D 180
K 270 Q 181
E 271 E 187
E 272 K 188
F 273 R 189
I 274 I 190
D 275 K 191
E 276 E 192
V 277 V 193
E 278 I 194
N 279 K 195
I 280 R 196
L 281 H 197
R 282 S 198
D 283 E 199
Y 284 F 200
Y 285 V 201
E 286 A 202
I 289 Y 203
R 290 P 204
T 291 I 205
E 292 Q 206
V 293 L 207
V 297 V 208
E 298 V 209
V 299 T 210
TER
END

