
PFRMAT AL
TARGET T0127
AUTHOR 6305-9733-7289
REMARK similar to 1doo.
METHOD PSI-BLAST (Altschul et al., Nucl. Acids Res. 25, 3389-3402, 1997)
METHOD (-h 0.0005 -j 20) and iterative SCANPS
METHOD (Barton et al., 2000, http://barton.ebi.ac.uk/scanps/)
METHOD were run against a combined search set comprising the SWALL, PDB and ENSEMBL
METHOD sequence databases.
METHOD Sequences hit from these runs with an E-value of less than 0.0005 were collected.
METHOD These sequences were then aligned all-against-all using AMPS
METHOD (Barton, G. J., Methods in Enzymology 183, 403-428, 1990)
METHOD and one sequence was removed from any pair sharing greater than 75%
METHOD identity. Each of the remaining sequences was then used as queries
METHOD in a second round of psiblast runs. From these runs, 1doo (chain F)
METHOD was identified as a possible homologue. A multiple alignment was
METHOD constructed from target t0127, the intermediate query sequences,
METHOD and 1doo_F by CLUSTALW (Higgins et al., Methods in Enz.266,383-402,1996.)
METHOD The alignment between t0127 and 1doo_F was extracted,
METHOD edited and corrected by hand in the Jalview alignment editor
METHOD (M. Clamp, URL: http://www2.ebi.ac.uk/~michele/jalview/contents.html).
METHOD Secondary structure information predicted for t0127 by (JPRED2, Cuff and
METHOD Barton, 2000, Proteins 40, 502-511,2000) was incorporated.
MODEL  1
PARENT 1doo_F
A 4 I F9
V 5 V F10
A 6 S F11
R 7 E F12
L 8 L F13
Q 9 D F14
P 10 K F15
S 11 H F16
A 12 I F17
S 13 I F18
K 16 N F22
T 17 A F23
R 18 K F24
P 19 R F25
V 20 S F26
F 21 V F27
P 22 A F28
F 23 I F29
S 24 A F30
A 25 L F31
I 26 R F32
V 27 N F33
G 28 R F34
Q 29 W F35
L 34 N F41
A 35 E F42
L 36 E F43
L 37 L F44
L 38 R F45
T 39 H F46
A 40 E F47
V 41 V F48
D 42 T F49
P 43 P F50
G 44 K F51
G 47 N F52
V 48 I F53
L 49 L F54
V 50 M F55
F 51 I F56
G 52 G F57
D 53 P F58
R 54 T F59
G 55 G F60
T 56 V F61
G 57 G F62
K 58 K F63
S 59 T F64
T 60 E F65
A 61 I F66
V 62 A F67
R 63 R F68
A 64 R F69
L 65 L F70
A 66 A F71
L 69 F F78
P 70 I F79
E 71 K F80
I 72 V F81
E 73 E F82
A 74 A F83
V 75 T F84
P 83 K F94
N 84 E F95
V 85 V F96
E 86 D F97
M 87 S F98
I 88 I F99
P 89 I F100
D 90 R F101
W 91 D F102
A 92 L F103
T 93 T F104
V 94 D F105
L 95 A F106
S 96 A F107
T 97 V F108
N 98 K F109
V 99 M F110
I 100 V F111
R 101 R F112
K 102 V F113
P 103 Q F114
T 104 A F115
P 105 I F116
V 107 Y F121
D 108 R F122
L 109 A F123
P 110 E F124
L 111 E F125
G 112 L F126
V 113 A F127
S 114 E F128
E 115 E F129
D 116 R F130
R 117 I F131
V 118 L F132
V 119 D F133
G 120 V F134
A 121 L F135
L 122 I F136
D 123 P F137
E 136 E F151
P 137 P F152
G 138 S F153
L 139 A F154
L 140 A F155
A 141 R F156
R 142 Q F157
A 143 A F158
N 144 F F159
R 145 R F160
G 146 K F161
Y 147 K F162
L 148 L F163
N 154 D F220
L 155 A F221
L 156 M F222
E 157 K F223
D 158 L F224
H 159 L F225
I 160 I F226
V 161 E F227
D 162 E F228
L 163 E F229
L 164 A F230
L 165 A F231
D 166 K F232
V 167 L F233
A 168 V F234
Q 169 N F235
S 170 P F236
G 171 E F237
E 172 E F238
N 173 L F239
V 174 K F240
V 175 Q F241
E 176 D F242
R 177 A F243
D 178 I F244
G 179 D F245
L 180 A F246
S 181 V F247
I 182 E F248
R 183 Q F249
H 184 H F250
P 185 G F251
A 186 I F252
R 187 V F253
F 188 F F254
V 189 I F255
L 190 D F256
V 191 E F257
G 192 I F258
S 193 D F259
G 194 K F260
N 195 I F261
P 196 C F262
E 197 K F263
E 198 R F264
G 199 G F265
D 200 E F266
L 201 S F267
R 202 S F268
P 203 G F269
Q 204 P F270
L 205 D F271
L 206 V F272
D 207 S F273
R 208 R F274
F 209 E F275
G 210 G F276
L 211 V F277
S 212 Q F278
V 213 R F279
E 214 D F280
V 215 L F281
L 216 L F282
S 217 P F283
P 218 L F284
R 219 V F285
D 220 E F286
V 221 G F287
E 222 C F288
T 223 T F289
R 224 V F290
V 225 S F291
I 228 M F296
R 229 V F297
R 230 K F298
R 231 T F299
D 232 D F300
T 233 H F301
Y 234 I F302
D 235 L F303
A 236 F F304
D 237 I F305
P 238 A F306
K 239 S F307
A 240 G F308
F 241 A F309
R 260 R F329
E 261 V F330
R 262 E F331
L 263 L F332
P 264 Q F333
K 265 A F334
V 266 L F335
E 267 T F336
A 268 T F337
P 269 S F338
N 270 D F339
T 271 F F340
A 272 I F351
L 273 T F352
Y 274 V F353
D 275 Q F354
C 276 Y F355
A 277 K F356
A 278 A F357
L 279 L F358
C 280 M F359
I 281 A F360
A 282 T F361
L 283 E F362
G 284 G F363
S 285 V F364
D 286 N F365
G 287 I F366
L 288 E F367
R 289 F F368
G 290 T F369
E 291 D F370
L 292 S F371
T 293 G F372
L 294 I F373
L 295 K F374
R 296 R F375
S 297 I F376
A 298 A F377
R 299 E F378
A 300 A F379
L 301 A F380
A 302 Q F382
A 303 V F383
L 304 N F384
E 305 E F385
G 306 S F386
A 307 T F387
H 314 I F390
L 315 G F391
K 316 A F392
R 317 R F393
V 318 R F394
A 319 L F395
T 320 H F396
M 321 T F397
A 322 V F398
L 323 L F399
S 324 E F400
H 325 R F401
R 326 L F402
L 327 M F403
R 328 E F404
R 329 E F405
D 330 I F406
P 331 S F407
L 332 Y F408
D 333 D F409
E 334 A F410
A 335 S F411
G 336 D F412
S 337 L F413
T 338 S F414
A 339 G F415
R 340 Q F416
V 341 N F417
A 342 I F418
R 343 T F419
T 344 I F420
V 345 D F421
E 346 A F422
E 347 D F423
T 348 Y F424
L 349 V F425
P 350 S F426
TER
END


