PFRMAT AL 
TARGET T0057 
AUTHOR 5827-4749-3439 
METHOD T0057 structure prediction 
METHOD 
METHOD As usual, we employed a three-pronged approach: (1) and (2) 
METHOD  We scored the target against all the HMMs and threading models  
METHOD in our libraries,  
METHOD and (3) we gathered homologs to the target using PsiBLAST,  
METHOD constructed an HMM for the target and homologs (using UCSC's HMM  
METHOD software), and scored PDB.  
METHOD This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD Structural matches for this target were easy to identify 
METHOD using PsiBLAST--1gaeO came up in the second iteration. 
METHOD 1gaeO was also the highest-scoring threading model. 
METHOD In the HMM analysis, 1dapA actually scored higher, and 
METHOD had some areas of definitively higher pairwise residue 
METHOD identity than the match to 1gaeO. When we examined the 
METHOD alignments however, we decided the match was somewhat 
METHOD superior to 1gaeO, especially in the binding site. 
METHOD 
METHOD The alignment submitted was created by aligning the target and structure  
METHOD to the HMM constructed for the target and homologs as follows: (1)  
METHOD constructing an HMM for T0057 alone using modelfromalign 
METHOD and the target sequence as the template alignment,  
METHOD (2) reestimating the HMM using sequences found using BLAST, 
METHOD (3) then reestimating that HMM using sequence weighting, 
METHOD to allow the HMM to generalize. The weighting method 
METHOD used Henikoff weighting to set relative weights and 
METHOD our own method of estimating the number of independent 
METHOD observations to set the total weight allotted 
METHOD the sequences. This alignment submitted was not edited in any way 
METHOD from the automatic alignment. 
MODEL 1 
PARENT 1gae_O 
M   1    T   0 
I   2    I   1 
N   3    K   2 
V   4    V   3 
A   5    G   4 
V   6    I   5 
N   7    N   6 
G   8    G   7 
Y   9    F   8 
G  10    G   9 
T  11    R  10 
I  12    I  11 
G  13    G  12 
K  14    R  13 
R  15    I  14 
V  16    V  15 
A  17    F  16 
D  18    R  17 
A  19    A  18 
I  20    A  19 
I  21    Q  20 
K  22    K  21 
Q  23    R  22 
P  24    S  23 
D  25    D  24 
M  26    I  25 
K  27    E  26 
L  28    I  27 
V  29    V  28 
G  30    A  29 
V  31    I  30 
A  32    N  31 
K  33    D  32 
T  34    L  34 
S  35    D  36 
P  36    A  37 
N  37    D  38 
Y  38    Y  39 
E  39    M  40 
A  40    A  41 
F  41    Y  42 
I  42    M  43 
A  43    S  48 
H  44    T  49 
R  45    H  50 
R  46    G  51 
G  47    R  52 
I  48    F  53 
R  49    D  54 
I  50    G  55 
Y  51    T  56 
V  52    V  57 
P  53    E  58 
Q  54    V  59 
Q  55    K  60 
S  56    D  61 
I  57    G  62 
K  58    H  63 
K  59    L  64 
F  60    I  65 
E  61    V  66 
E  62    N  67 
G  64    G  68 
I  65    K  69 
P  66    K  70 
V  67    I  71 
A  68    R  72 
G  69    V  73 
T  70    T  74 
V  71    A  75 
E  72    E  76 
D  73    R  77 
L  74    N  81 
I  75    L  82 
K  76    K  83 
T  77    W  84 
S  78    D  85 
D  79    E  86 
I  80    V  87 
V  81    G  88 
V  82    V  89 
D  83    D  90 
T  84    V  91 
T  85    V  92 
P  86    A  93 
N  87    E  94 
G  88    A  95 
V  89    T  96 
G  90    G  97 
K  94    L  98 
P  95    F  99 
I  96    L 100 
Y  97    T 101 
L  98    D 102 
Q  99    E 103 
L 100    T 104 
Q 101    A 105 
R 102    R 106 
N 103    K 107 
A 104    H 108 
I 105    I 109 
F 106    T 110 
Q 107    A 111 
G 108    G 112 
G 109    A 113 
E 110    K 114 
K 111    K 115 
A 112    V 116 
E 113    V 117 
V 114    M 118 
A 115    T 119 
D 116    G 120 
I 117    P 121 
S 118    S 122 
F 119    F 128 
S 120    V 129 
A 121    K 130 
L 122    G 131 
C 123    A 132 
N 124    N 133 
Y 125    F 134 
N 126    D 135 
E 127    K 136 
A 128    Y 137 
L 129    A 138 
G 130    G 138A 
K 131    Q 141 
K 132    D 142 
Y 133    I 143 
I 134    V 144 
R 135    S 145 
V 136    N 146 
V 137    A 147 
S 138    S 148 
C 139    C 149 
N 140    T 150 
T 141    T 151 
T 142    N 152 
A 143    C 153 
L 144    L 154 
L 145    A 155 
R 146    P 156 
T 147    L 157 
I 148    A 158 
C 149    K 159 
T 150    V 160 
V 151    I 161 
N 152    N 162 
K 153    D 163 
V 154    N 164 
S 155    F 165 
K 156    G 166 
V 157    I 167 
E 158    I 168 
K 159    E 169 
V 160    G 170 
R 161    L 171 
A 162    M 172 
T 163    T 173 
I 164    T 174 
V 165    V 175 
R 166    Q 182 
R 167    K 183 
A 168    T 184 
A 169    V 185 
D 170    D 186 
Q 171    G 187 
K 172    P 188 
E 173    S 189 
V 174    H 190 
K 175    K 191 
K 176    R 197 
G 177    G 198 
P 178    A 199 
I 179    S 200 
N 180    Q 201 
S 181    N 202 
L 182    I 203 
V 183    I 204 
P 184    P 205 
D 185    S 206 
P 186    S 207 
A 187    T 208 
T 188    G 209 
V 189    A 210 
A 194    A 211 
K 195    K 212 
D 196    A 213 
V 197    V 214 
N 198    G 215 
S 199    K 216 
V 200    V 217 
I 201    L 218 
R 202    P 219 
N 203    E 220 
L 204    L 221 
D 205    N 222 
I 206    L 225 
A 207    T 226 
T 208    G 227 
M 209    M 228 
A 210    A 229 
V 211    F 230 
I 212    R 231 
A 213    V 232 
P 214    P 233 
T 215    T 234 
T 216    P 235 
L 217    N 236 
M 218    V 237 
H 219    S 238 
M 220    V 239 
H 221    V 240 
F 222    D 241 
I 223    L 242 
N 224    T 243 
I 225    V 244 
T 226    R 245 
L 227    L 246 
K 228    E 247 
D 229    K 248 
K 230    A 249 
V 231    A 250 
E 232    T 251 
K 233    Y 252 
K 234    E 253 
D 235    Q 254 
I 236    I 255 
L 237    K 256 
S 238    A 257 
V 239    A 258 
L 240    V 259 
E 241    E 264 
N 242    G 265 
T 243    E 266 
P 244    M 267 
R 245    K 268 
I 246    G 269 
V 247    V 270 
L 248    L 271 
I 249    G 272 
S 250    Y 273 
S 251    T 274 
K 252    E 275 
Y 253    D 276 
D 254    D 277 
A 255    V 278 
E 256    V 279 
A 257    S 280 
T 258    T 281 
E 263    D 282 
V 264    F 283 
A 265    N 284 
R 266    G 285 
D 267    E 286 
L 268    V 287 
K 269    C 288 
R 270    T 289 
D 271    S 290 
R 272    V 291 
N 273    F 292 
D 274    D 293 
I 275    A 294 
S 282    K 295 
D 283    A 296 
S 284    G 297 
I 285    I 298 
Y 286    A 299 
V 287    L 300 
K 288    N 301 
D 289    D 302 
D 290    N 303 
S 315    F 304 
M 316    V 305 
K 317    K 306 
L 318    L 307 
M 319    V 308 
S 320    S 309 
A 321    W 310 
E 322    Y 311 
D 323    D 312 
S 324    T 313 
M 325    E 314 
R 326    T 315 
I 327    G 316 
T 328    Y 317 
N 329    S 318 
E 330    N 319 
S 331    K 320 
L 332    V 321 
G 333    L 322 
I 334    D 323 
L 335    L 324 
K 336    I 325 
G 337    A 326 
Y 338    H 327 
L 339    I 328 
I 340    S 329 
TER 
END 
