PFRMAT AL 
TARGET T0057 
AUTHOR 2234-4819-7150 
METHOD Identification of PDB sequences related by evolution to the target 
METHOD (query) sequence was performed by PSI-BLAST run locally.   
METHOD The first search is performed with the CASP3 sequence against  
METHOD the non-redundant protein database ("nr").  Four runs of PSI-BLAST were 
METHOD run with an E-value cutoff of 0.001.  The final matrix (checkpoint file) was 
METHOD used to search the PDB.   
METHOD This search results in the following homologous chains: 
METHOD 
METHOD gi|1421424|pdb|1GAD|O Escherichia coli >gi|1421425|pdb|1GAD|P E...   442  e-125 
METHOD gi|1421428|pdb|1GAE|O Escherichia coli >gi|1421429|pdb|1GAE|P E...   438  e-124 
METHOD gi|230867|pdb|3GPD|R Homo sapiens >gi|230868|pdb|3GPD|G Homo sa...   432  e-122 
METHOD gi|231017|pdb|4GPD|1 Homarus americanus >gi|231018|pdb|4GPD|2 H...   429  e-121 
METHOD gi|229953|pdb|1GPD|G Homarus americanus >gi|229954|pdb|1GPD|R H...   429  e-121 
METHOD gi|229937|pdb|1GD1|O Bacillus stearothermophilus >gi|229938|pdb...   403  e-113 
METHOD gi|2392744|pdb|3DBV|O Bacillus stearothermophilus >gi|2392745|p...   401  e-113 
METHOD gi|2392251|pdb|1DBV|O Bacillus stearothermophilus >gi|2392252|p...   401  e-113 
METHOD gi|3318907|pdb|1A7K|A Chain A, Glycosomal Glyceraldehyde-3-Phos...   376  e-105 
METHOD gi|1311019|pdb|1GYP|A Leishmania mexicana >gi|1311020|pdb|1GYP|...   375  e-105 
METHOD gi|494037|pdb|1GGA|O Trypanosoma brucei brucei >gi|494038|pdb|1...   371  e-104 
METHOD gi|1421448|pdb|1CER|O Thermus aquaticus >gi|1421449|pdb|1CER|P ...   359  e-100 
METHOD gi|999601|pdb|1HDG|O Thermotoga maritima >gi|999602|pdb|1HDG|Q ...   355  2e-99 
METHOD 
METHOD Chain 1gd1_O had an alignment that placed insertions and deletions in loops 
METHOD so this chain was used for modeling.  The alignment is presented below. 
MODEL  1 
PARENT 1gd1_O 
M   1    A    0 
I   2    V    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    N   14 
V  16    V   15 
A  17    F   16 
D  18    R   17 
A  19    A   18 
I  20    A   19 
I  21    L   20 
K  22    K   21 
Q  23    N   22 
P  24    P   23 
D  25    D   24 
M  26    I   25 
K  27    E   26 
L  28    V   27 
V  29    V   28 
G  30    A   29 
V  31    V   30 
A  32    N   31 
K  33    D   32 
T  34    L   33 
S  35    T   34 
N  37    D   36 
Y  38    A   37 
E  39    N   38 
A  40    T   39 
F  41    L   40 
I  42    A   41 
A  43    H   42 
H  44    L   43 
R  45    L   44 
R  46    K   45 
G  47    Y   46 
I  48    D   47 
R  49    S   48 
I  50    V   49 
Y  51    H   50 
V  52    G   51 
P  53    R   52 
Q  54    L   53 
Q  55    D   54 
S  56    A   55 
I  57    E   56 
K  58    V   57 
K  59    S   58 
F  60    V   59 
E  61    N   60 
E  62    G   61 
S  63    N   62 
G  64    N   63 
I  65    L   64 
P  66    V   65 
V  67    V   66 
A  68    N   67 
G  69    G   68 
T  70    K   69 
V  71    E   70 
E  72    I   71 
D  73    W   84 
L  74    G   85 
I  75    E   86 
K  76    I   87 
T  77    G   88 
S  78    V   89 
D  79    D   90 
I  80    I   91 
V  81    V   92 
V  82    V   93 
D  83    E   94 
T  84    S   95 
T  85    T   96 
P  86    G   97 
N  87    R   98 
G  88    F   99 
V  89    T  100 
G  90    K  101 
A  91    R  102 
Q  92    E  103 
Y  93    D  104 
K  94    A  105 
P  95    A  106 
I  96    K  107 
Y  97    H  108 
L  98    L  109 
Q  99    E  110 
L 100    A  111 
Q 101    G  112 
R 102    A  113 
N 103    K  114 
A 104    K  115 
I 105    V  116 
F 106    I  117 
Q 107    I  118 
G 108    S  119 
G 109    A  120 
E 110    P  121 
K 111    A  122 
A 112    K 122A 
E 113    E  124 
V 114    D  125 
A 115    I  126 
D 116    T  127 
I 117    I  128 
S 118    V  129 
F 119    M  130 
S 120    G  131 
A 121    V  132 
L 122    N  133 
C 123    Q  134 
N 124    D  135 
Y 125    K  136 
N 126    Y  137 
E 127    D  138 
A 128    P 138A 
L 129    K  139 
G 130    A  140 
K 131    H  141 
K 132    H  142 
Y 133    V  143 
I 134    I  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    F  157 
I 148    A  158 
C 149    K  159 
T 150    V  160 
V 151    L  161 
N 152    H  162 
K 153    E  163 
V 154    Q  164 
S 155    F  165 
K 156    G  166 
V 157    I  167 
E 158    V  168 
K 159    R  169 
V 160    G  170 
R 161    M  171 
A 162    M  172 
T 163    T  173 
I 164    T  174 
V 165    V  175 
R 166    H  176 
R 167    S  177 
A 168    Y  178 
A 169    T  179 
D 170    N  180 
Q 171    D  181 
K 172    Q  182 
E 173    R  183 
V 174    I  184 
K 175    L  185 
K 176    D  186 
G 177    L  187 
P 178    P  188 
I 179    H  190 
N 180    R  195 
S 181    A  196 
L 182    R  197 
V 183    A  198 
P 184    A  199 
D 185    A  200 
P 186    E  201 
A 187    S  202 
T 188    I  203 
V 189    I  204 
P 190    P  205 
S 191    T  206 
H 192    T  207 
H 193    A  210 
A 194    A  211 
K 195    K  212 
D 196    A  213 
V 197    V  214 
N 198    A  215 
S 199    L  216 
V 200    V  217 
I 201    L  218 
R 202    P  219 
N 203    E  220 
L 204    L  221 
D 205    K  224 
I 206    L  225 
A 207    N  226 
T 208    G  227 
M 209    M  228 
A 210    A  229 
V 211    M  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    V  243 
I 225    A  244 
T 226    E  245 
L 227    L  246 
K 228    E  247 
D 229    K  248 
K 230    E  249 
V 231    V  250 
E 232    T  251 
K 233    V  252 
K 234    E  253 
D 235    E  254 
I 236    V  255 
L 237    N  256 
S 238    A  257 
V 239    A  258 
L 240    L  259 
E 241    K  260 
N 242    A  261 
T 243    A  262 
P 244    A  263 
R 245    E  264 
I 246    G  265 
V 247    E  266 
L 248    L  267 
I 249    K  268 
S 250    G  269 
S 251    I  270 
K 252    L  271 
Y 253    A  272 
D 254    Y  273 
A 255    S  274 
E 256    E  275 
A 257    E  276 
T 258    P  277 
A 259    L  278 
E 260    V  279 
L 261    S  280 
V 262    R  281 
E 263    D  282 
V 264    Y  283 
A 265    N  284 
R 266    G  285 
D 267    S  286 
L 268    T  287 
K 269    V  288 
R 270    S  289 
D 271    S  290 
R 272    T  291 
N 273    I  292 
D 274    D  293 
I 275    A  294 
P 276    L  295 
E 277    S  296 
V 278    T  297 
M 279    M  298 
I 280    V  299 
F 281    I  300 
K 288    D  301 
D 289    G  302 
D 290    K  303 
E 291    M  304 
V 292    V  305 
M 293    K  306 
L 294    V  307 
M 295    V  308 
Y 296    S  309 
A 297    W  310 
V 298    Y  311 
H 299    D  312 
Q 300    N  313 
E 301    E  314 
S 302    T  315 
I 303    G  316 
V 304    Y  317 
V 305    S  318 
P 306    H  319 
E 307    R  320 
N 308    V  321 
I 309    V  322 
D 310    D  323 
A 311    L  324 
I 312    A  325 
R 313    A  326 
A 314    Y  327 
S 315    I  328 
M 316    A  329 
K 317    S  330 
L 318    K  331 
M 319    G  332 
S 320    L  333 
TER 
END 
