PFRMAT AL 
TARGET T0083 
AUTHOR 5827-4749-3439 
METHOD Threading alignment for T0083 
METHOD 
METHOD Note: this alignment was obtained automatically, and has not been 
METHOD hand-edited. 
METHOD 
METHOD This alignment was created by aligning the target sequence to a 
METHOD library of 3D-1D type threading models.  Matching and gap scores 
METHOD were optimized for discriminating remote homolog sequence-structure 
METHOD alignments from alignments on incorrect folds. 
METHOD 
METHOD 1llia did not score the highest when the entire sequence was threaded. 
METHOD However, it scored among the highest per residue aligned.  This alignment 
METHOD was obtained by truncating the target sequence where the alignment 
METHOD ended.  This segment was then threaded against all folds in our library, 
METHOD and 1llia scored higher than any other structure, though by a very 
METHOD small margin (two other all-alpha structures also scored highly). 
METHOD We chose this prediction because of the relatively high sequence  
METHOD similarity of the threading alignment, and because HMMs also 
METHOD scored a similar fold as the top (though weak) hit. 
METHOD 
MODEL 2 
PARENT 1lli_A 
Q    3    K    4 
S    4    K    5 
Q    5    P    6 
I    6    L    7 
N    7    T    8 
R    8    Q    9 
N    9    E    10 
I    10    Q    11 
R    11    L    12 
L    12    E    13 
D    13    D    14 
L    14    A    15 
A    15    R    16 
D    16    R    17 
A    17    L    18 
I    18    K    19 
L    19    A    20 
L    20    I    21 
S    21    Y    22 
K    22    E    23 
A    23    K    24 
K    24    K    25 
K    25    K    26 
D    26    N    27 
L    27    L    31 
S    28    S    32 
F    29    Q    33 
A    30    E    34 
E    31    S    35 
I    32    L    36 
A    33    A    37 
D    34    D    38 
G    35    K    39 
T    36    L    40 
G    37    G    41 
L    38    M    42 
A    39    G    43 
E    40    Q    44 
A    41    S    45 
F    42    G    46 
V    43    I    47 
T    44    G    48 
A    45    A    49 
A    46    L    50 
L    47    F    51 
L    48    N    52 
G    49    G    53 
Q    50    I    54 
Q    51    N    55 
A    52    A    56 
L    53    L    57 
P    54    N    58 
A    55    A    59 
D    56    Y    60 
A    57    N    61 
A    58    A    62 
R    59    A    63 
L    60    L    64 
V    61    L    65 
G    62    A    66 
A    63    K    67 
K    64    I    68 
L    65    L    69 
D    66    K    70 
L    67    V    71 
D    68    S    72 
E    69    V    73 
D    70    E    74 
S    71    E    75 
I    72    F    76 
L    73    S    77 
Q    76    P    78 
M    77    S    79 
I    78    I    80 
P    79    A    81 
L    80    R    82 
R    81    E    83 
I    84    I    84 
D    85    Y    85 
D    86    E    86 
R    87    M    87 
I    88    Y    88 
P    89    E    89 
T    90    A    90 
D    91    V    91 
P    92    S    92 
TER 
END 
