PFRMAT AL 
TARGET T0070 
AUTHOR 2234-4819-7150 
REMARK Unrefined prediction (no energy minimization) 
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  
METHOD (checkpoint file) was used to search the PDB.   
METHOD This search results in the following homologous chains: 
METHOD 
METHOD Chain                                                               Bits Evalue 
METHOD gi|999982|pdb|1OPF|  Matrix Porin (Ompf) >gi|1310953|pdb|2OMF| ...   225  3e-60 
METHOD gi|1943073|pdb|1GFM|  Ompf Porin (Mutant D113g) Outer Membrane,...   225  4e-60 
METHOD gi|1943075|pdb|1GFO|  Ompf Porin (Mutant R132p) Outer Membrane,...   224  7e-60 
METHOD gi|1943076|pdb|1GFP|  Ompf Porin (Mutant R42c) Outer Membrane, ...   223  9e-60 
METHOD gi|999673|pdb|1MPF|  Matrix Porin (Ompf) Mutant With Gly 119 Re...   223  2e-59 
METHOD gi|1943077|pdb|1GFQ|  Ompf Porin (Mutant R82c) Outer Membrane, ...   223  2e-59 
METHOD gi|1943074|pdb|1GFN|  Ompf Porin Deletion (Mutant Delta 109-114...   214  5e-57 
METHOD gi|443180|pdb|1PHO|  Phosphoporin (Phoe)                             200  8e-53 
METHOD gi|443427|pdb|2POR|  Porin (Crystal Form B) >gi|443479|pdb|3POR...   111  7e-26 
METHOD gi|640363|pdb|1PRN|  Porin                                            35  0.007 
METHOD 
METHOD  
METHOD The alignments were checked against the structures.   
METHOD Chain 1GFP had the best resolution (2.7 A) and was chosen for the model. 
METHOD The alignment was adjusted manually to move gaps to loop regions.   
METHOD 
MODEL 1 
PARENT 1gfp 
Q   1    G    8 
S   2    N    9 
S   3    K   10 
V   4    V   11 
T   5    D   12 
L   6    L   13 
F   7    Y   14 
G   8    G   15 
I   9    K   16 
V  10    A   17 
D  11    V   18 
T  12    G   19 
N  13    L   20 
V  14    H   21 
A  15    Y   22 
Y  16    F   23 
V  17    S   24 
N  18    K   25 
K  19    G   26 
D  20    N   27 
G  23    G   28 
D  24    E   29 
S  25    N   30 
R  26    S   31 
Y  27    Y   32 
G  28    G   33 
G  30    G   34 
T  31    N   35 
S  32    G   36 
G  33    D   37 
A  34    M   38 
S  35    T   39 
T  36    Y   40 
S  37    A   41 
R  38    C   42 
L  39    L   43 
G  40    G   44 
L  41    F   45 
R  42    K   46 
G  43    G   47 
T  44    E   48 
E  45    T   49 
D  46    Q   50 
L  47    I   51 
G  48    N   52 
G  49    S   53 
G  50    D   54 
L  51    L   55 
K  52    T   56 
A  53    G   57 
G  54    Y   58 
F  55    G   59 
W  56    Q   60 
L  57    W   61 
E  58    E   62 
G  59    Y   63 
E  60    N   64 
I  61    F   65 
F  62    Q   66 
G  63    G   67 
D  64    N   68 
D  65    N   69 
G  66    S   70 
N  67    E   71 
A  68    A   75 
S  69    Q   76 
G  70    T   77 
F  71    G   78 
N  72    N   79 
F  73    K   80 
K  74    T   81 
R  75    R   82 
R  76    L   83 
S  77    A   84 
T  78    F   85 
V  79    A   86 
S  80    G   87 
L  81    L   88 
S  82    K   89 
G  83    A   91 
N  84    D   92 
F  85    V   93 
G  86    G   94 
E  87    S   95 
V  88    F   96 
R  89    D   97 
L  90    Y   98 
G  91    G   99 
R  92    R  100 
D  93    N  101 
L  94    Y  102 
V  95    G  103 
P  96    V  104 
T  97    V  105 
S  98    Y  106 
Q  99    D  107 
K 100    A  108 
L 101    L  109 
T 102    G  110 
S 103    Y  111 
Y 104    T  112 
D 105    D  113 
L 106    M  114 
F 107    L  115 
S 108    P  116 
A 109    E  117 
T 110    F  118 
G 111    G  119 
G 113    G  120 
P 114    D  121 
F 115    T  122 
M 116    A  123 
G 117    Y  124 
F 118    S  125 
R 119    D  126 
N 120    D  127 
W 121    F  128 
A 122    F  129 
A 123    V  130 
G 124    G  131 
Q 125    R  132 
G 126    V  133 
A 127    G  134 
D 128    G  135 
D 129    V  136 
N 130    A  137 
G 131    T  138 
I 132    Y  139 
R 133    R  140 
A 134    N  141 
N 135    S  142 
N 136    N  143 
L 137    F  144 
I 138    F  145 
S 139    G  146 
Y 140    L  147 
Y 141    V  148 
T 142    D  149 
G 147    G  150 
F 148    L  151 
N 149    N  152 
A 150    F  153 
G 151    A  154 
F 152    V  155 
G 153    Q  156 
Y 154    Y  157 
A 155    L  158 
F 156    G  159 
D 157    K  160 
E 158    N  161 
K 159    E  162 
Q 160    R  163 
T 161    D  164 
I 162    T  165 
G 163    A  166 
T 164    R  167 
D 166    R  168 
S 167    S  169 
V 168    N  170 
G 169    G  171 
R 170    D  172 
Y 171    G  173 
I 172    V  174 
G 173    G  175 
G 174    G  176 
Y 175    S  177 
V 176    I  178 
A 177    S  179 
Y 178    Y  180 
D 179    E  181 
N 180    Y  182 
G 181    E  183 
P 182    G  184 
L 183    F  185 
S 184    G  186 
A 185    I  187 
S 186    V  188 
L 187    G  189 
G 188    A  190 
L 189    Y  191 
A 190    G  192 
Q 191    A  193 
Q 192    A  194 
K 193    D  195 
T 194    R  196 
A 195    T  197 
V 196    N  198 
G 197    L  199 
G 198    Q  200 
L 199    E  201 
A 200    G  208 
T 201    K  209 
D 202    K  210 
R 203    A  211 
D 204    E  212 
E 205    Q  213 
I 206    W  214 
T 207    A  215 
L 208    T  216 
G 209    G  217 
A 210    L  218 
S 211    K  219 
Y 212    Y  220 
N 213    D  221 
F 214    A  222 
G 215    N  223 
V 216    N  224 
A 217    I  225 
K 218    Y  226 
L 219    L  227 
S 220    A  228 
G 221    A  229 
L 222    N  230 
L 223    Y  231 
Q 224    G  232 
Q 225    E  233 
T 226    T  234 
K 227    R  235 
F 228    N  236 
K 229    A  237 
R 230    T  238 
D 231    P  239 
I 232    I  240 
G 233    G  249 
G 234    F  250 
D 235    A  251 
I 236    N  252 
K 237    K  253 
T 238    T  254 
N 239    Q  255 
S 240    D  256 
Y 241    V  257 
M 242    L  258 
L 243    L  259 
G 244    V  260 
A 245    A  261 
S 246    Q  262 
A 247    Y  263 
P 248    Q  264 
V 249    F  265 
G 250    D  266 
G 251    F  267 
V 252    G  268 
G 253    L  269 
E 254    R  270 
V 255    P  271 
K 256    S  272 
L 257    I  273 
Q 258    A  274 
Y 259    Y  275 
A 260    T  276 
L 261    K  277 
Y 262    S  278 
D 263    K  279 
Q 264    A  280 
K 265    K  281 
A 266    D  282 
I 267    D  288 
D 268    V  289 
S 269    D  290 
K 270    L  291 
A 271    V  292 
H 272    N  293 
Q 273    Y  294 
I 274    F  295 
T 275    E  296 
L 276    V  297 
G 277    G  298 
Y 278    A  299 
V 279    T  300 
H 280    Y  301 
N 281    Y  302 
L 282    F  303 
S 283    N  304 
K 284    K  305 
R 285    N  306 
T 286    M  307 
A 287    S  308 
L 288    T  309 
Y 289    Y  310 
G 290    V  311 
N 291    D  312 
L 292    Y  313 
A 293    I  314 
F 294    I  315 
L 295    N  316 
K 296    Q  317 
N 297    I  318 
K 298    D  319 
D 299    S  320 
A 300    D  321 
S 301    N  322 
T 302    K  323 
L 303    L  324 
A 317    G  325 
G 318    V  326 
E 319    G  327 
S 320    S  328 
Q 321    D  329 
T 322    D  330 
G 323    T  331 
V 324    V  332 
Q 325    A  333 
V 326    V  334 
G 327    G  335 
I 328    I  336 
R 329    V  337 
H 330    Y  338 
A 331    Q  339 
F 332    F  340 
TER 
END 
