PFRMAT AL 
TARGET T0048 
AUTHOR 5827-4749-3439 
REMARK Threading alignment for T0048 
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 This alignment scored significantly higher than any other structure 
METHOD matches. 
METHOD 
METHOD Note that the threading alignment differs from the HMM alignment 
METHOD (in MODEL 1), in only a short region.  The HMM chooses to make 
METHOD 3 indels in favor of aligning 5 more identical residues.  The 
METHOD threading parameters, on the other hand, penalize these gaps 
METHOD quite highly, since two of them occur in secondary structure 
METHOD elements.  As a result, the threading parameters favor this 
METHOD ungapped alignment. 
MODEL 2 
PARENT 1dco_A 
P    17    H    6 
H    18    R    7 
V    19    L    8 
S    20    S    9 
D    21    A    10 
E    22    E    11 
E    23    E    12 
L    24    R    13 
P    25    D    14 
V    26    Q    15 
L    27    L    16 
L    28    L    17 
R    29    P    18 
Q    30    N    19 
I    31    L    20 
P    32    R    21 
D    33    A    22 
W    34    V    23 
N    35    G    24 
I    36    W    25 
E    37    N    26 
V    38    E    27 
R    39    L    28 
D    40    E    29 
G    41    G    30 
I    42    R    31 
M    43    D    32 
Q    44    A    33 
L    45    I    34 
E    46    F    35 
K    47    K    36 
V    48    Q    37 
Y    49    F    38 
L    50    H    39 
F    51    F    40 
K    52    K    41 
N    53    D    42 
F    54    F    43 
K    55    N    44 
H    56    R    45 
A    57    A    46 
L    58    F    47 
A    59    G    48 
F    60    F    49 
T    61    M    50 
N    62    T    51 
A    63    R    52 
V    64    V    53 
G    65    A    54 
E    66    L    55 
I    67    Q    56 
S    68    A    57 
E    69    E    58 
A    70    K    59 
E    71    L    60 
G    72    D    61 
H    73    H    62 
H    74    H    63 
P    75    P    64 
G    76    E    65 
L    77    W    66 
L    78    F    67 
T    79    N    68 
E    80    V    69 
W    81    Y    70 
G    82    N    71 
K    83    K    72 
V    84    V    73 
T    85    H    74 
V    86    I    75 
T    87    T    76 
W    88    L    77 
W    89    S    78 
S    90    T    79 
H    91    H    80 
S    92    E    81 
I    93    C    82 
K    94    A    83 
G    95    G    84 
L    96    L    85 
H    97    S    86 
R    98    E    87 
N    99    R    88 
D    100    D    89 
F    101    I    90 
I    102    N    91 
M    103    L    92 
A    104    A    93 
A    105    S    94 
R    106    F    95 
T    107    I    96 
D    108    E    97 
E    109    Q    98 
V    110    V    99 
A    111    A    100 
K    112    V    101 
T    113    S    102 
A    114    M    103 
E    115    T    104 
TER 
END   
