PFRMAT AL 
TARGET T0053 
AUTHOR 5827-4749-3439 
METHOD T0053 structure prediction 
METHOD 
METHOD As usual, we employed a two-pronged approach: (1) We scored the  
METHOD target against all the HMMs and threading models in our libraries,  
METHOD and (2) we  
METHOD gathered homologs to the target using PsiBLAST, constructed an  
METHOD HMM for the target and homologs (using UCSC's HMM software), and  
METHOD scored PDB. This yielded two sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD 
METHOD This match was predicted based on a combination of threading 
METHOD analysis (which highlighted TIM barrels as the most likely structure) 
METHOD and stage 1 (scoring the HMM library).  
METHOD The HMM for d1ctn_2, a SCOP domain, 
METHOD gave a very strong score for one of the target homologs. 
METHOD The alignment submitted was created by aligning the target and structure  
METHOD to an HMM constructed as follows: (1) we gathered homologs to 
METHOD 1ctn_2 using FASTA, 
METHOD (2) aligned these sequences using Gotoh's PRRP program, 
METHOD (3) ran Sjolander's Bete program on the alignment to identify subfamilies, 
METHOD (4) constructed subfamily HMMs for each subfamily, 
METHOD (4) aligned the target and structure to the subfamily  
METHOD giving the target the highest probability. In fact, this 
METHOD subfamily HMM scored the target above all non-homologs 
METHOD in a non-redundant dataset of sequences from PDB40. 
METHOD  
METHOD This alignment has not been edited in any way. 
MODEL 1 
PARENT 1ctn 
M    1    T    133 
K    2    K    142 
K    3    E    143 
A    4    P    144 
L    5    L    145 
L    6    L    146 
V    7    E    147 
G    11    K    148 
T    12    N    149 
S    13    K    150 
Y    14    P    151 
H    15    Y    152 
D    16    K    153 
T    17    Q    154 
C    18    N    155 
E    19    S    156 
K    20    G    157 
N    21    K    158 
I    22    V    159 
V    23    V    160 
A    24    G    161 
C    25    S    162 
E    26    G    171 
R    27    R    172 
D    28    N    173 
L    29    F    174 
A    30    T    175 
D    35    P    180 
R    36    A    181 
D    37    Q    182 
L    38    N    183 
F    39    L    184 
R    40    T    185 
A    41    H    186 
F    42    L    187 
T    43    L    188 
S    44    Y    189 
G    45    G    190 
M    46    F    191 
I    47    I    192 
I    48    P    193 
R    49    I    194 
K    50    C    195 
L    51    G    196 
R    52    G    197 
Q    53    N    198 
R    54    N    201 
D    55    D    202 
G    56    S    203 
I    57    L    204 
D    58    K    205 
I    59    I    207 
D    60    E    208 
T    61    G    209 
P    62    S    210 
L    63    F    211 
Q    64    Q    212 
A    65    A    213 
L    66    L    214 
Q    67    Q    215 
K    68    D    247 
L    69    P    248 
A    70    Y    249 
A    71    K    250 
Q    72    G    251 
G    73    N    252 
Y    74    F    253 
Q    75    G    254 
D    76    Q    255 
V    77    L    256 
A    78    M    257 
I    79    A    258 
Q    80    L    259 
S    81    D    265 
L    82    L    266 
H    83    K    267 
I    84    I    268 
I    85    L    269 
N    86    P    270 
G    87    S    278 
D    88    D    279 
E    89    P    280 
Y    90    F    281 
E    91    F    282 
K    92    F    283 
I    93    M    284 
V    94    G    285 
R    95    D    286 
E    96    K    287 
V    97    V    288 
Q    98    K    289 
R    106    L    301 
L    107    Q    302 
T    108    T    303 
L    109    W    304 
G    110    K    305 
V    111    F    316 
P    112    P    317 
L    113    G    318 
L    114    G    319 
S    115    Q    330 
S    116    D    331 
H    117    G    332 
N    118    E    333 
D    119    T    334 
Y    120    Y    335 
V    121    V    336 
Q    122    L    337 
L    123    L    338 
M    124    M    339 
Q    125    K    340 
A    126    E    341 
L    127    L    342 
R    128    R    343 
Q    129    A    344 
Q    130    M    345 
M    131    L    346 
P    132    D    347 
S    133    Q    348 
L    134    L    349 
R    135    R    355 
Q    136    K    356 
T    137    Y    357 
E    138    E    358 
K    139    L    359 
V    140    T    360 
V    141    S    361 
F    142    A    362 
M    143    I    363 
G    144    S    364 
H    145    A    365 
G    146    G    366 
A    147    K    367 
S    148    D    368 
H    149    K    369 
H    150    I    370 
A    151    D    371 
F    152    N    376 
A    153    V    377 
A    154    A    378 
Y    155    Q    379 
A    156    N    380 
C    157    S    381 
L    158    M    382 
D    159    D    383 
H    160    H    384 
M    161    I    385 
M    162    Q    404 
T    163    T    405 
A    164    A    406 
Q    165    L    407 
R    166    N    408 
F    167    A    409 
P    168    P    410 
A    169    A    411 
R    170    W    412 
V    171    K    413 
G    172    P    414 
E    175    D    415 
S    176    T    416 
Y    177    A    417 
P    178    Y    418 
E    179    T    419 
V    180    T    420 
D    181    V    421 
I    182    N    422 
L    183    G    423 
I    184    V    424 
D    185    N    425 
S    186    A    426 
L    187    L    427 
R    188    L    428 
D    189    A    429 
E    190    Q    430 
G    191    G    431 
V    192    V    432 
T    193    K    433 
G    194    P    434 
V    195    G    435 
H    196    K    436 
P    199    I    437 
L    200    V    438 
M    201    V    439 
L    202    G    440 
V    203    T    441 
TER 
END 
