PFRMAT AL 
TARGET T0078 
AUTHOR 5827-4749-3439 
METHOD Threading alignment for T0078 
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 SCOP d1pnra2, which is also a  
METHOD beta-alpha-beta structure of a similar length. 
METHOD We were made more confident of this prediction by the fact that  
METHOD 1yas_A is in the same SCOP family as a thioesterase. 
METHOD We also performed inverse threading, scoring the top matches 
METHOD against PDB sequences.  All of the relatives of 1pnra2 scored much 
METHOD higher than the target sequence.  For 1yasa, however, there were 
METHOD several family members whose sequences scored in the same range 
METHOD as the target, and with similar gapping patterns. 
METHOD 
METHOD There were no convincing HMM hits for this target. 
METHOD 
MODEL 1 
PARENT 1yas_A 
S    26    A    2 
E    27    F    3 
D    28    A    4 
L    29    H    5 
G    30    F    6 
L    31    V    7 
R    32    L    8 
V    34    I    9 
F    35    H    10 
G    36    T    11 
G    37    I    12 
Q    38    C    13 
V    39    H    14 
V    40    G    15 
G    41    A    16 
Q    42    W    17 
A    43    I    18 
L    44    W    19 
Y    45    H    20 
A    46    K    21 
A    47    L    22 
K    48    K    23 
E    49    P    24 
T    50    L    25 
V    51    L    26 
P    52    E    27 
E    53    A    28 
E    54    L    29 
R    55    G    30 
H    58    H    31 
S    59    K    32 
F    60    V    33 
H    61    T    34 
S    62    A    35 
Y    63    L    36 
F    64    D    37 
L    65    L    38 
R    66    A    39 
P    67    A    40 
G    68    S    41 
D    69    G    42 
S    70    V    43 
K    71    D    44 
K    72    P    45 
P    73    R    46 
I    74    Q    47 
I    75    I    48 
Y    76    E    49 
D    77    E    50 
V    78    I    51 
E    79    G    52 
T    80    S    53 
L    81    F    54 
R    82    D    55 
D    83    E    56 
G    84    Y    57 
N    85    S    58 
S    86    E    59 
F    87    P    60 
S    88    L    61 
A    89    L    62 
R    90    T    63 
R    91    F    64 
V    92    L    65 
A    93    E    66 
A    94    A    67 
I    95    L    68 
Q    96    P    69 
N    97    P    70 
G    98    G    71 
K    99    E    72 
P    100    K    73 
I    101    V    74 
F    102    I    75 
Y    103    L    76 
M    104    V    77 
T    105    G    78 
A    106    E    79 
S    107    S    80 
F    108    C    81 
Q    109    G    82 
A    110    G    83 
P    111    L    84 
E    112    N    85 
A    113    I    86 
G    114    A    87 
F    115    I    88 
E    116    A    89 
H    117    A    90 
Q    118    D    91 
K    119    K    92 
T    120    Y    93 
M    121    C    94 
P    122    E    95 
S    123    K    96 
A    124    I    97 
P    125    A    98 
A    126    A    99 
P    127    A    100 
D    128    V    101 
G    129    F    102 
L    130    H    103 
P    131    N    104 
S    132    S    105 
E    133    V    106 
T    134    L    107 
Q    135    P    108 
I    136    D    109 
A    137    T    110 
Q    138    E    111 
S    139    H    112 
L    140    C    113 
A    141    P    114 
H    142    S    115 
L    143    Y    116 
L    144    V    117 
P    145    V    118 
P    146    D    119 
V    147    K    120 
L    148    L    121 
K    149    M    122 
D    150    E    123 
K    151    V    124 
F    152    F    125 
I    153    P    126 
C    154    D    127 
D    155    W    128 
R    156    K    129 
P    157    D    130 
L    158    T    131 
E    159    T    132 
V    160    Y    133 
R    161    F    134 
P    162    T    135 
V    163    Y    136 
E    164    T    137 
F    165    K    138 
N    167    D    139 
P    168    G    140 
L    169    K    141 
K    170    E    142 
G    171    I    143 
H    172    T    144 
V    173    G    145 
A    174    L    146 
E    175    K    147 
P    176    L    148 
H    177    G    149 
R    178    F    150 
Q    179    T    151 
V    180    L    152 
W    181    L    153 
I    182    R    154 
R    183    E    155 
A    184    N    156 
N    185    L    157 
G    186    Y    158 
S    187    T    159 
P    189    L    160 
D    190    C    161 
D    191    G    162 
L    192    P    163 
R    193    E    164 
V    194    E    165 
H    195    Y    166 
Q    196    E    167 
Y    197    L    168 
L    198    A    169 
L    199    K    170 
G    200    M    171 
Y    201    L    172 
A    202    T    173 
S    203    R    174 
D    204    K    175 
L    205    G    176 
N    206    S    177 
F    207    F    179 
L    208    Q    180 
P    209    N    181 
V    210    I    182 
A    211    L    183 
L    212    A    184 
Q    213    K    185 
P    214    R    186 
H    215    P    187 
G    216    F    188 
I    217    F    189 
G    218    G    193 
F    219    Y    194 
L    220    G    195 
E    221    S    196 
P    222    I    197 
G    223    K    198 
I    224    K    199 
I    226    I    200 
A    227    Y    201 
T    228    V    202 
I    229    W    203 
D    230    T    204 
H    231    D    205 
S    232    Q    206 
M    233    D    207 
W    234    E    208 
F    235    I    209 
H    236    F    210 
P    238    L    211 
F    239    P    212 
N    240    E    213 
L    241    F    214 
N    242    Q    215 
E    243    L    216 
W    244    W    217 
L    245    Q    218 
L    246    I    219 
Y    247    E    220 
S    248    N    221 
V    249    Y    222 
E    250    K    223 
S    251    P    224 
T    252    D    225 
S    253    K    226 
A    254    V    227 
S    255    Y    228 
S    256    K    229 
A    257    V    230 
R    258    E    231 
G    259    G    232 
F    260    G    233 
V    261    D    234 
R    262    H    235 
G    263    K    236 
E    264    L    237 
F    265    Q    238 
Y    266    L    239 
T    267    T    240 
Q    268    K    241 
D    269    T    242 
G    270    K    243 
L    272    E    244 
V    273    I    245 
A    274    A    246 
S    275    E    247 
T    276    I    248 
V    277    L    249 
Q    278    Q    250 
E    279    E    251 
V    281    V    252 
M    282    A    253 
R    283    D    254 
N    284    T    255 
H    285    Y    256 
N    286    N    257 
TER 
END 
