PFRMAT AL 
TARGET T0080 
AUTHOR 5827-4749-3439 
METHOD 
METHOD T0080 prediction  
METHOD  
METHOD Prediction 1 
METHOD For this target we have two predictions -- both appear feasible. 
METHOD Neither has our strong confidence.   
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 No scores were strong. We had to check a large number of 
METHOD potential matches, creating alignments and examining each 
METHOD individually. The structure we chose, SCOP domain d1ktq_1, 
METHOD was chosen because it satisfied the following criteria: 
METHOD (1) the HMM for the structure gave strong scores to most 
METHOD of the target homologs, placing them above all the non-homologs 
METHOD in our non-redundant PDB sequence database in NLL-NULL scores; 
METHOD (2) a structure homolog placed 4th among 1300 proteins in 
METHOD NLL-NULL scores for the subfamily HMM constructed for the target 
METHOD homologs (containing the target itself); 
METHOD (3) an alignment of close homologs to the target and structure 
METHOD to a joint model (estimated on a subset of the training sequences 
METHOD for both the target and structure) appeared reasonable; 
METHOD (4) the functions of the target and structure appear related 
METHOD (the structure chosen is an exonuclease domain in a DNA repair protein). 
METHOD 
METHOD Nevertheless, if we could assign a confidence level for 
METHOD this structure-target match, we would give this a low score. 
METHOD It's simply the most likely match we could find. 
METHOD 
METHOD As usual, the alignment has not been edited in any way 
METHOD from the automatic HMM alignment. 
MODEL 1 
PARENT 1ktq 
K    80    S    290 
G    81    P    291 
H    82    K    292 
G    87    A    293 
L    88    L    294 
E    89    E    295 
F    90    E    296 
F    91    A    297 
D    92    P    298 
Q    93    W    299 
P    94    P    300 
A    95    P    301 
V    96    P    302 
P    97    E    303 
R    100    G    304 
A    101    A    305 
F    102    F    306 
L    103    V    307 
G    104    G    308 
Q    105    F    309 
V    106    V    310 
L    107    L    311 
V    108    S    312 
R    109    R    313 
R    110    K    314 
L    111    E    315 
P    112    P    316 
N    113    M    317 
G    114    W    318 
T    115    A    319 
E    116    D    320 
L    117    L    321 
R    118    L    322 
G    119    A    323 
R    120    L    324 
A    135    A    325 
H    136    A    326 
S    137    A    327 
R    138    R    328 
G    139    G    329 
G    140    G    330 
R    141    R    331 
L    180    V    332 
L    181    H    333 
R    182    R    334 
A    183    A    335 
L    184    P    336 
E    185    E    337 
P    186    P    338 
L    187    Y    339 
E    188    K    340 
G    189    A    341 
L    190    L    342 
E    191    R    343 
T    192    D    344 
M    193    L    345 
R    194    K    346 
Q    195    E    347 
L    196    A    348 
R    197    R    349 
S    198    G    350 
T    199    L    351 
L    200    L    352 
R    201    A    353 
K    202    K    354 
G    203    D    355 
T    204    L    356 
A    205    S    357 
S    206    V    358 
R    207    L    359 
V    208    A    360 
L    209    L    361 
K    210    R    362 
D    211    E    363 
E    213    G    364 
L    214    L    365 
C    215    G    366 
S    216    L    367 
G    217    P    368 
P    218    P    369 
S    219    G    370 
K    220    D    371 
L    221    D    372 
C    222    P    373 
Q    223    M    374 
A    224    L    375 
L    225    L    376 
A    226    A    377 
I    227    Y    378 
N    228    L    379 
K    229    L    380 
S    230    D    381 
F    231    P    382 
D    232    S    383 
Q    233    N    384 
A    237    T    385 
Q    238    T    386 
D    239    P    387 
E    240    E    388 
A    241    G    389 
V    242    V    390 
W    243    A    391 
L    244    R    392 
E    245    R    393 
R    246    Y    394 
G    247    G    395 
P    248    G    396 
L    249    E    397 
E    250    W    398 
P    251    T    399 
S    252    E    400 
E    253    E    401 
P    254    E    404 
A    255    R    405 
V    256    A    406 
V    257    A    407 
A    258    L    408 
A    259    S    409 
A    260    E    410 
R    261    R    411 
V    262    L    412 
G    263    F    413 
V    264    L    416 
G    265    W    417 
H    266    G    418 
A    267    R    419 
G    268    L    420 
E    269    E    421 
W    270    G    422 
A    271    E    423 
R    272    E    424 
K    273    R    425 
P    274    L    426 
L    275    L    427 
R    276    W    428 
F    277    L    429 
Y    278    Y    430 
V    279    R    431 
R    280    E    432 
G    281    V    433 
S    282    E    434 
P    283    R    435 
W    284    P    436 
V    285    L    437 
S    286    S    438 
V    287    A    439 
V    288    V    440 
D    289    L    441 
R    290    A    442 
V    291    H    443 
A    292    M    444 
E    293    E    445 
Q    294    A    446 
T    296    T    447 
Q    297    G    448 
A    298    V    449 
TER 
END 
