PFRMAT AL 
TARGET T0082 
AUTHOR 5827-4749-3439 
METHOD T0082 prediction method 
METHOD 
METHOD For this prediction, we were given the correct homologous 
METHOD structure, and constructing an alignment between the 
METHOD structure and target was achieved as follows: 
METHOD (1) gathering homologs to the target using BLAST; 
METHOD (2) aligning the target and homologs using CLUSTALW; 
METHOD (3) identifying subfamilies in the homolog set using 
METHOD Sjolander's Bayesian evolutionary tree estimation 
METHOD method, and constructing subfamily HMMs for each 
METHOD subfamily found; 
METHOD (4) identifying a subfamily that assigned high 
METHOD probability to both the target and the structure; 
METHOD (5) re-estimating the parameters of that subfamily HMM 
METHOD using a selected subset of target and structure homologs; 
METHOD (6) aligning the target and structure to the re-estimated HMM. 
METHOD 
METHOD As usual, the alignment has not been edited in any way. 
MODEL 1 
PARENT 1bol 
F    1    S    1 
D    2    G    25 
S    3    L    26 
F    4    V    27 
W    5    V    28 
F    6    L    29 
V    7    N    30 
Q    8    M    31 
Q    9    Q    32 
W    10    W    33 
P    11    A    34 
P    12    P    35 
A    13    G    36 
V    14    Y    37 
C    23    G    38 
P    24    P    39 
G    25    D    40 
S    26    N    41 
T    30    A    42 
F    31    F    43 
T    32    T    44 
I    33    L    45 
H    34    H    46 
G    35    G    47 
L    36    L    48 
W    37    W    49 
P    38    P    50 
Q    39    D    51 
Q    40    K    52 
S    41    S    54 
G    42    G    55 
T    43    A    56 
S    44    Y    57 
L    45    A    58 
T    46    P    59 
N    47    S    60 
C    48    C    63 
P    49    D    64 
G    50    S    65 
S    51    N    66 
P    52    R    67 
F    53    V    75 
D    54    I    76 
I    55    K    77 
T    56    S    78 
K    57    K    79 
I    58    D    80 
S    59    S    81 
H    60    S    82 
L    61    L    83 
Q    62    Y    84 
S    63    N    85 
Q    64    S    86 
L    65    M    87 
N    66    L    88 
T    67    T    89 
L    68    Y    90 
W    69    W    91 
P    70    P    92 
N    71    S    93 
V    72    N    94 
R    74    Q    95 
A    75    G    96 
N    76    N    97 
N    77    N    98 
Q    78    N    99 
Q    79    V    100 
F    80    F    101 
W    81    W    102 
S    82    S    103 
H    83    H    104 
E    84    E    105 
W    85    W    106 
T    86    S    107 
K    87    K    108 
H    88    H    109 
G    89    G    110 
T    90    T    111 
C    91    C    112 
S    92    Y    124 
E    93    E    125 
S    94    E    126 
T    95    G    127 
F    96    E    128 
N    97    D    129 
Q    98    I    130 
A    99    V    131 
A    100    D    132 
Y    101    Y    133 
F    102    F    134 
K    103    Q    135 
L    104    K    136 
A    105    A    137 
V    106    M    138 
D    107    D    139 
M    108    L    140 
R    109    R    141 
N    110    S    142 
N    111    Q    143 
Y    112    Y    144 
D    113    N    145 
I    114    V    146 
I    115    Y    147 
G    116    K    148 
A    117    A    149 
L    118    F    150 
R    119    S    151 
P    120    S    152 
H    121    N    153 
A    122    G    154 
A    123    I    155 
G    124    T    156 
P    125    P    157 
G    127    G    158 
R    128    G    159 
T    129    T    160 
K    130    Y    161 
S    131    T    162 
R    132    A    163 
Q    133    T    164 
A    134    E    165 
I    135    M    166 
K    136    Q    167 
G    137    S    168 
F    138    A    169 
L    139    I    170 
K    140    E    171 
A    141    S    172 
K    142    Y    173 
F    143    F    174 
G    144    G    175 
K    145    A    176 
F    146    K    177 
P    147    A    178 
G    148    K    179 
L    149    I    180 
R    150    D    181 
C    151    C    182 
P    155    S    183 
Q    156    S    184 
K    158    G    185 
V    159    T    186 
S    160    L    187 
Y    161    S    188 
L    162    D    189 
V    163    V    190 
Q    164    A    191 
V    165    L    192 
V    166    Y    193 
A    167    F    194 
C    168    Y    195 
F    169    V    196 
A    170    R    197 
Q    171    G    198 
D    172    R    199 
G    173    D    200 
S    174    T    201 
T    175    Y    202 
L    176    V    203 
I    177    I    204 
D    178    T    205 
T    180    D    206 
R    181    A    207 
D    182    L    208 
T    183    S    209 
C    184    T    210 
G    185    G    211 
A    186    E    218 
N    187    Y    219 
F    188    P    220 
I    189    T    221 
F    190    K    222 
TER 
END 
