PFRMAT AL 
TARGET T0079 
AUTHOR 5827-4749-3439 
METHOD T0079 structure prediction 
METHOD 
METHOD As usual, we employed a two-pronged approach: (1)  
METHOD  We scored the target against all the HMMs and threading models  
METHOD in our libraries,  
METHOD and (2) we gathered homologs to the target using PsiBLAST,  
METHOD constructed an HMM for the target and homologs (using UCSC's HMM  
METHOD software), and scored PDB.  
METHOD This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD The structure 1smtA was the second highest scoring structure 
METHOD for the HMM constructed from the target and homologs, and 
METHOD also showed up (just beyond the cutoff) in the third iteration 
METHOD of PsiBLAST. (The top-scoring structure was 1fosE; this structure 
METHOD was rejected due to a less-than-convincing alignment of the target 
METHOD and structure.) 
METHOD  
METHOD The alignment submitted was created by aligning the target and structure  
METHOD to the HMM constructed for the target and homologs as follows: (1)  
METHOD constructing an HMM for T0079 alone using modelfromalign 
METHOD and the target sequence as the template alignment,  
METHOD (2) reestimating the HMM using sequences found using iterated FASTA 
METHOD (using new sequences as seeds in the search until convergence) 
METHOD (3) then reestimating that HMM using sequence weighting, 
METHOD to allow the HMM to generalize. The weighting method 
METHOD used Henikoff weighting to set relative weights and 
METHOD our own method of estimating the number of independent 
METHOD observations to set the total weight allotted 
METHOD the sequences. This alignment submitted was not edited in any way 
METHOD from the automatic alignment. 
MODEL 1 
PARENT 1smt_A 
S    29    E    24 
L    30    L    25 
E    31    Q    26 
K    32    A    27 
V    33    I    28 
S    34    A    29 
E    35    P    30 
R    36    E    31 
S    37    V    32 
G    38    A    33 
Y    39    Q    34 
S    40    S    35 
L    44    L    36 
Q    45    A    37 
R    46    E    38 
M    47    F    39 
F    48    F    40 
H    54    A    41 
S    55    V    42 
L    56    L    43 
G    57    A    44 
Q    58    D    45 
Y    59    P    46 
I    60    N    47 
R    61    R    48 
S    62    L    49 
R    63    R    50 
K    64    L    51 
M    65    L    52 
T    66    S    53 
E    67    L    54 
I    68    L    55 
A    69    A    56 
Q    70    R    57 
S    75    S    58 
N    76    E    59 
E    77    L    60 
P    78    C    61 
I    79    V    62 
L    80    G    63 
Y    81    D    64 
L    82    L    65 
A    83    A    66 
E    84    Q    67 
R    85    A    68 
Y    86    I    69 
G    87    G    70 
E    89    V    71 
S    90    S    72 
Q    91    E    73 
Q    92    S    74 
T    93    A    75 
L    94    V    76 
T    95    S    77 
R    96    H    78 
T    97    Q    79 
F    98    L    80 
K    99    R    81 
N    100    S    82 
Y    101    L    83 
F    102    R    84 
D    103    N    85 
V    104    L    86 
P    105    R    87 
P    106    L    88 
H    107    V    89 
K    108    S    90 
Y    109    Y    91 
R    110    R    92 
M    111    K    93 
T    112    Q    94 
N    113    G    95 
M    114    R    96 
Q    115    H    97 
G    116    V    98 
E    117    Y    99 
S    118    Y    100 
R    119    Q    101 
F    120    L    102 
L    121    Q    103 
H    122    H    106 
P    123    I    107 
L    124    V    108 
N    125    A    109 
H    126    L    110 
Y    127    Y    111 
N    128    Q    112 
S    129    N    113 
TER 
END 
