
PFRMAT AL
TARGET T0089
AUTHOR 7573-5202-7463
METHOD 
METHOD Database searches were performed using standard search algorithms such
METHOD as fasta and psi-blast.  Because sequence alignment was low to all 
METHOD potential templates, numerous alignments were generated to each template.
METHOD Several template "profiles" were generated containing a sequence 
METHOD alignment based on the structural superposition of the templates, 
METHOD generated using CE.  Each profile contained different numbers of templates
METHOD with varying overall similarity.  The target sequence was aligned to
METHOD each of these template profiles.
METHOD 
METHOD Templates and alignments were assessed by monitoring how closely the
METHOD alignment matched the PHD and PDIPRED secondary structure predictions
METHOD for the target with the actual secondary structure of the template.
METHOD Additional assessment was performed using in-house software to identify
METHOD most preferable templates/alignments based on interactions that are
METHOD seen in the template and their likelihood to occur in the given 
METHOD alignment.
METHOD
METHOD
MODEL 4
PARENT 3hsc
L   4    K   3 
S   5    G   4 
K   6    P   5 
T   7    A   6 
V   8    V   7 
F   9    G   8 
I  13    I   9 
D  14    D  10 
I  15    L  11 
G  16    G  12 
S  17    T  13 
R  18    T  14 
Y  19    Y  15 
I  20    S  16 
K  21    C  17 
G  22    V  18 
L  23    G  19 
V  24    V  20 
L  25    F  21 
G  26    Q  22 
K  27    G  24 
R  28    K  25 
D  29    V  26 
Q  30    E  27 
E  31    I  28 
W  32    I  29 
E  33    A  30 
A  34    N  31 
L  35    D  32 
A  36    T  37 
F  37    T  38 
S  38    P  39 
S  39    S  40 
V  40    Y  41 
K  41    V  42 
S  42    A  43 
R  43    F  44 
G  44    T  45 
L  45    D  46 
D  46    T  47 
E  47    E  48 
G  48    R  49 
E  49    L  50 
I  50    I  51 
K  51    G  52 
D  52    D  53 
A  53    A  54 
I  54    A  55 
A  55    K  56 
F  56    N  57 
K  57    Q  58 
E  58    V  59 
S  59    A  60 
V  60    M  61 
N  61    N  62 
T  62    N  65 
L  63    T  66 
L  64    V  67 
K  65    F  68 
E  66    D  69 
L  67    A  70 
E  69    K  71 
Q  70    R  72 
L  71    L  73 
Q  72    D  80 
K  73    A  81 
S  74    V  82 
L  75    V  83 
R  76    Q  84 
S  77    S  85 
D  78    D  86 
F  79    M  87 
V  80    K  88 
I  81    H  89 
S  82    W  90 
F  83    F  92 
S  84    M  93 
S  85    V  94 
V  86    V  95 
S  87    N  96 
F  88    D  97 
E  89    A  98 
E  91    G  99 
D  92    R 100 
T  93    P 101 
V  94    K 102 
I  95    V 103 
E  96    Q 104 
R  97    V 105 
D  98    E 106 
F  99    K 108 
G 100    T 111 
E 101    K 112 
E 102    S 113 
K 103    P 116 
R 104    E 117 
S 105    E 118 
I 106    V 119 
T 107    S 120 
L 108    S 121 
D 109    M 122 
I 110    V 123 
L 111    L 124 
S 112    T 125 
E 113    K 126 
M 114    M 127 
Q 115    K 128 
S 116    E 129 
E 117    I 130 
A 118    A 131 
L 119    E 132 
E 120    A 133 
K 121    Y 134 
L 122    L 135 
K 123    G 136 
E 124    K 137 
N 125    T 138 
G 126    V 139 
T 128    T 140 
P 129    N 141 
L 130    A 142 
H 131    V 143 
I 132    V 144 
F 133    T 145 
S 134    V 146 
K 135    P 147 
R 136    A 148 
Y 137    Y 149 
L 138    F 150 
L 139    N 151 
D 140    D 152 
D 141    S 153 
E 142    Q 154 
R 143    R 155 
K 152    Q 156 
A 153    A 157 
S 154    T 158 
K 155    K 159 
I 156    D 160 
A 157    A 161 
I 158    G 162 
E 159    T 163 
T 161    I 164 
S 162    A 165 
I 163    G 166 
Y 174    L 167 
N 175    N 168 
F 176    V 169 
L 177    L 170 
Q 178    R 171 
T 180    I 172 
V 181    I 173 
K 182    N 174 
S 183    E 175 
P 184    P 176 
S 190    T 177 
L 191    A 178 
V 192    A 179 
S 193    A 180 
T 194    I 181 
A 195    A 182 
E 196    Y 183 
G 197    G 184 
V 198    L 185 
L 199    D 186 
T 200    K 187 
T 201    K 188 
P 202    V 189 
E 203    G 190 
K 204    A 191 
D 205    E 192 
R 206    R 193 
G 207    N 194 
V 208    V 195 
V 209    L 196 
V 210    I 197 
V 211    F 198 
N 212    D 199 
L 213    L 200 
G 214    G 201 
Y 215    G 202 
N 216    T 204 
F 217    F 205 
T 218    D 206 
G 219    V 207 
L 220    S 208 
I 221    I 209 
A 222    L 210 
Y 223    T 211 
I 231    I 212 
S 232    E 213 
Y 233    D 214 
G 237    G 215 
M 238    I 216 
K 239    F 217 
H 240    E 218 
V 241    V 219 
I 242    K 220 
S 246    S 221 
A 247    T 222 
V 248    A 223 
L 249    G 224 
D 250    D 225 
T 251    T 226 
S 252    H 227 
F 253    L 228 
E 255    G 229 
S 256    G 230 
E 257    E 231 
R 258    D 232 
L 259    F 233 
I 260    D 234 
I 261    N 235 
T 262    R 236 
H 263    M 237 
G 264    V 238 
N 265    N 239 
A 266    H 240 
V 267    F 241 
Y 268    I 242 
N 269    A 243 
D 270    E 244 
L 271    F 245 
K 272    K 246 
Q 277    R 247 
Y 278    K 248 
R 279    H 249 
G 280    K 250 
L 281    K 251 
D 282    D 252 
N 284    I 253 
T 285    S 254 
I 286    E 255 
K 287    N 256 
T 288    K 257 
T 289    R 258 
T 290    A 259 
A 291    V 260 
K 292    R 261 
K 293    R 262 
L 294    L 263 
S 295    R 264 
V 296    T 265 
I 297    A 266 
I 298    C 267 
H 299    E 268 
A 300    R 269 
R 301    A 270 
L 302    K 271 
R 303    R 272 
E 304    T 273 
I 305    L 274 
M 306    S 275 
S 307    S 276 
K 308    S 277 
S 309    T 278 
K 311    Q 279 
R 314    A 280 
E 315    S 281 
V 316    I 282 
E 317    E 283 
A 318    I 284 
K 319    D 285 
I 320    S 286 
V 321    L 287 
E 322    Y 288 
E 323    E 289 
G 324    G 290 
E 325    D 292 
I 326    F 293 
G 327    Y 294 
I 328    T 295 
G 331    S 296 
V 332    I 297 
V 333    T 298 
L 334    R 299 
T 335    A 300 
G 336    R 301 
G 337    F 302 
G 338    E 303 
A 339    E 304 
K 340    L 305 
I 341    N 306 
P 342    A 307 
R 343    D 308 
I 344    L 309 
N 345    F 310 
E 346    R 311 
L 347    G 312 
A 348    T 313 
T 349    L 314 
E 350    D 315 
V 351    P 316 
F 352    V 317 
K 353    E 318 
S 354    K 319 
P 355    A 320 
V 356    L 321 
R 357    R 322 
T 358    D 323 
G 359    A 324 
C 360    K 325 
Y 361    L 326 
A 362    D 327 
N 363    K 328 
S 364    S 329 
D 365    Q 330 
R 366    I 331 
P 367    H 332 
S 368    D 333 
I 369    I 334 
I 370    V 335 
N 371    L 336 
A 372    V 337 
D 373    G 338 
E 374    G 339 
V 375    S 340 
A 376    T 341 
N 377    R 342 
D 378    I 343 
P 379    P 344 
S 380    K 345 
F 381    I 346 
A 382    Q 347 
A 383    K 348 
A 384    L 349 
F 385    L 350 
G 386    Q 351 
N 387    D 352 
V 388    F 353 
F 389    F 354 
A 390    N 355 
E 393    G 356 
N 394    K 357 
P 395    E 358 
Y 396    L 359 
E 397    N 360 
E 398    K 361 
T 399    S 362 
P 400    I 363 
V 401    N 364 
K 402    P 365 
S 403    D 366 
E 404    E 367 
N 405    A 368 
L 407    V 369 
K 408    A 370 
K 409    Y 371 
I 410    G 372 
F 411    A 373 
R 412    A 374 
L 413    V 375 
F 414    Q 376 
K 415    A 377 
E 416    A 378 
L 417    I 379 
M 418    L 380 
E 419    S 381 
TER    
END      


