PFRMAT AL 
TARGET T0070 
AUTHOR 5827-4749-3439 
METHOD T0070 target prediction method 
METHOD 
METHOD As usual, we employed a two-pronged approach: (1) We scored the target  
METHOD against all the HMMs and threading models in our libraries, and (2) we  
METHOD gathered homologs to the target using one or more tools 
METHOD (such as iterated FASTA or PsiBLAST), constructed an  
METHOD HMM for the target and homologs (using UCSC's HMM software), and  
METHOD scored PDB. This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD Since the documentation provided for the target said 
METHOD the target was a porin, we restricted our analysis to the 
METHOD porin structures at the top of our list. The structure chosen, 
METHOD 1opf, had the highest score of all pdb structures for the target 
METHOD hmms (subfamily and general). The alignment was constructed 
METHOD by aligning the structure and target to the target subfamily hmm 
METHOD giving 1opf the highest score. 
METHOD  
METHOD As usual, the alignment has not been edited in any way. 
MODEL 1 
PARENT 1opf 
S    2    A    1 
S    3    E    2 
V    4    V    11 
T    5    D    12 
L    6    L    13 
F    7    Y    14 
G    8    G    15 
V    10    K    16 
D    11    A    17 
T    12    V    18 
N    13    G    19 
V    14    L    20 
A    15    H    21 
Y    16    Y    22 
V    17    F    23 
N    18    S    24 
K    19    K    25 
D    20    G    26 
A    21    N    27 
A    22    G    28 
G    23    E    29 
S    25    N    30 
R    26    S    31 
Y    27    Y    32 
G    28    G    33 
L    29    G    34 
G    30    N    35 
T    31    G    36 
S    32    D    37 
G    33    M    38 
A    34    T    39 
S    35    Y    40 
S    37    A    41 
R    38    R    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    Q    76 
S    69    T    77 
G    70    G    78 
F    71    N    79 
N    72    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    Y    90 
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 
Q    99    V    105 
K    100    Y    106 
L    101    D    107 
T    102    A    108 
Y    104    L    109 
D    105    G    110 
L    106    Y    111 
F    107    T    112 
S    108    D    113 
A    109    M    114 
T    110    L    115 
G    111    P    116 
I    112    E    117 
G    113    F    118 
P    114    G    119 
F    115    G    120 
M    116    D    121 
G    117    T    122 
R    119    A    123 
N    120    Y    124 
W    121    S    125 
A    122    D    126 
A    123    D    127 
G    124    F    128 
Q    125    F    129 
G    126    V    130 
A    127    G    131 
D    128    R    132 
D    129    V    133 
N    130    G    134 
G    131    G    135 
I    132    V    136 
R    133    A    137 
S    139    T    138 
Y    140    Y    139 
Y    141    R    140 
T    142    N    141 
P    143    S    142 
N    144    N    143 
F    145    F    144 
G    146    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 
T    164    A    166 
A    165    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    L    205 
A    195    G    206 
L    199    N    207 
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    I    240 
K    229    T    241 
R    230    N    242 
D    231    K    243 
I    232    F    244 
G    233    T    245 
G    234    N    246 
D    235    T    247 
I    236    S    248 
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    V    283 
D    268    E    284 
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 
G    309    G    325 
V    310    V    326 
Y    311    G    327 
A    312    S    328 
G    313    D    329 
G    314    D    330 
T    322    T    331 
G    323    V    332 
V    324    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 
