PFRMAT AL 
TARGET T0053 
AUTHOR 5827-4749-3439 
METHOD Threading alignment for T0053 
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 only slightly higher than any other structure 
METHOD matches.  The close second was 1yasa, which is also a beta-alpha-beta 
METHOD structure of a similar length. 
METHOD We decided to make this prediction because the HMM for one of the 
METHOD SCOP superfamily members (1ctn, see MODEL 1) was the highest scoring, 
METHOD though weak match to the target. 
METHOD 
MODEL 2 
PARENT 1wsy_A 
M    1    M    1 
K    2    E    2 
K    3    R    3 
A    4    Y    4 
L    5    L    7 
L    6    F    8 
V    7    A    18 
V    8    F    19 
S    9    V    20 
F    10    P    21 
G    11    F    22 
T    12    V    23 
S    13    T    24 
Y    14    L    25 
H    15    G    26 
D    16    D    27 
T    17    P    28 
C    18    G    29 
E    19    I    30 
K    20    E    31 
N    21    Q    32 
I    22    S    33 
V    23    L    34 
A    24    K    35 
C    25    I    36 
E    26    I    37 
R    27    D    38 
D    28    T    39 
L    29    L    40 
A    30    I    41 
A    31    D    42 
S    32    A    43 
C    33    G    44 
P    34    A    45 
D    35    D    46 
R    36    A    47 
D    37    L    48 
L    38    E    49 
F    39    L    50 
R    40    G    51 
A    41    V    52 
F    42    P    53 
T    43    F    54 
S    44    D    60 
G    45    G    61 
M    46    P    62 
I    47    T    63 
I    48    I    64 
R    49    Q    65 
K    50    N    66 
L    51    A    67 
R    52    N    68 
Q    53    L    69 
R    54    R    70 
D    55    A    71 
I    57    F    72 
D    58    A    73 
I    59    A    74 
D    60    G    75 
T    61    V    76 
P    62    T    77 
L    63    P    78 
Q    64    A    79 
A    65    Q    80 
L    66    C    81 
Q    67    F    82 
K    68    E    83 
L    69    M    84 
A    70    L    85 
A    71    A    86 
Q    72    L    87 
G    73    I    88 
Y    74    R    89 
Q    75    E    90 
D    76    K    91 
V    77    H    92 
A    78    P    93 
I    79    I    95 
Q    80    P    96 
S    81    I    97 
L    82    G    98 
H    83    L    99 
I    84    L    100 
I    85    M    101 
N    86    Y    102 
G    87    A    103 
D    88    N    104 
E    89    L    105 
Y    90    V    106 
E    91    F    107 
K    92    N    108 
I    93    N    109 
V    94    G    110 
R    95    I    111 
E    96    D    112 
Q    98    A    113 
L    99    F    114 
L    100    Y    115 
R    101    A    116 
P    102    R    117 
L    103    C    118 
T    105    E    119 
R    106    Q    120 
L    107    V    121 
T    108    G    122 
L    109    V    123 
G    110    D    124 
V    111    S    125 
P    112    V    126 
L    113    L    127 
L    114    V    128 
S    115    A    129 
S    116    D    130 
H    117    V    131 
N    118    P    132 
M    124    V    133 
Q    125    E    134 
A    126    E    135 
L    127    S    136 
R    128    A    137 
Q    129    P    138 
Q    130    F    139 
M    131    R    140 
P    132    Q    141 
S    133    A    142 
L    134    A    143 
R    135    L    144 
Q    136    R    145 
T    137    H    146 
E    138    N    147 
K    139    I    148 
V    140    A    149 
V    141    P    150 
F    142    I    151 
M    143    F    152 
G    144    I    153 
H    145    C    154 
G    146    P    155 
A    147    P    156 
S    148    N    157 
H    149    A    158 
H    150    D    159 
Y    155    D    160 
A    156    D    161 
C    157    L    162 
L    158    L    163 
D    159    R    164 
H    160    Q    165 
M    161    V    166 
M    162    A    167 
T    163    S    168 
A    164    Y    169 
Q    165    G    170 
R    166    R    171 
F    167    G    172 
P    168    Y    173 
A    169    T    174 
R    170    Y    175 
V    171    L    176 
P    178    L    177 
E    179    P    192 
V    180    L    193 
D    181    H    194 
I    182    H    195 
L    183    L    196 
I    184    I    197 
D    185    E    198 
S    186    K    199 
L    187    L    200 
R    188    K    201 
D    189    E    202 
E    190    Y    203 
G    191    H    204 
V    192    A    205 
T    193    A    206 
G    194    P    207 
V    195    A    208 
H    196    L    209 
L    197    Q    210 
M    198    G    211 
P    199    F    212 
L    200    G    213 
V    203    I    214 
A    204    S    215 
G    205    S    216 
D    206    P    217 
H    207    E    218 
A    208    Q    219 
I    209    V    220 
N    210    S    221 
D    211    A    222 
M    212    A    223 
A    213    V    224 
S    214    R    225 
D    215    A    226 
D    216    G    227 
G    217    A    228 
D    218    A    229 
A    226    G    230 
A    227    A    231 
G    228    I    232 
I    229    S    233 
P    230    G    234 
T    232    S    235 
P    233    A    236 
W    234    I    237 
L    235    V    238 
S    236    K    239 
G    237    I    240 
L    238    I    241 
G    239    E    242 
E    240    K    243 
N    241    N    244 
P    242    L    245 
A    243    A    246 
I    244    S    247 
R    245    P    248 
A    246    K    249 
M    247    Q    250 
F    248    M    251 
V    249    L    252 
A    250    A    253 
H    251    E    254 
L    252    L    255 
H    253    R    256 
Q    254    S    257 
A    255    F    258 
L    256    V    259 
N    257    S    260 
M    258    A    261 
A    259    M    262 
V    260    K    263 
E    261    A    264 
E    262    A    265 
TER 
END 
