PFRMAT AL 
TARGET T0069 
AUTHOR 5827-4749-3439 
METHOD Threading alignment for T0069 
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 Threading against a single-domain library derived from SCOP 
METHOD placed d1esl_1 and d1rtm12 in the top 10 hits, despite the fact 
METHOD that they align to only a portion of the target.  Models of each 
METHOD two-domain protein chain were constructed, and 1rmt1 of course 
METHOD scored significantly higher, since it matches in both domains, 
METHOD while 1esl matches only one. 
MODEL 2 
PARENT 1rtm_1 
A    5    A    73 
L    6    I    74 
K    7    E    75 
Q    8    V    76 
R    9    K    77 
V    10    L    78 
T    11    A    79 
I    12    N    80 
L    13    M    81 
D    14    E    82 
G    15    A    83 
H    16    E    84 
L    17    I    85 
R    18    N    86 
R    19    T    87 
F    20    L    88 
Q    21    K    89 
N    22    S    90 
A    23    K    91 
F    24    L    92 
S    25    E    93 
Q    26    L    94 
Y    27    T    95 
K    28    N    96 
K    29    K    97 
A    30    L    98 
V    31    H    99 
L    32    A    100 
F    33    F    101 
P    34    S    102 
D    35    M    103 
G    36    G    104 
Q    37    K    105 
A    38    K    106 
V    39    S    107 
G    40    G    108 
E    41    K    109 
K    42    K    110 
I    43    F    111 
F    44    F    112 
K    45    V    113 
T    46    T    114 
A    47    N    115 
G    48    H    116 
A    49    E    117 
V    50    R    118 
K    51    M    119 
S    52    P    120 
Y    53    F    121 
S    54    S    122 
D    55    K    123 
A    56    V    124 
E    57    K    125 
Q    58    A    126 
L    59    L    127 
C    60    C    128 
R    61    S    129 
E    62    E    130 
A    63    L    131 
K    64    R    132 
G    65    G    133 
Q    66    T    134 
L    67    V    135 
A    68    A    136 
S    69    I    137 
P    70    P    138 
R    71    R    139 
S    72    N    140 
N    76    A    141 
E    77    E    142 
A    78    E    143 
V    79    N    144 
T    80    K    145 
Q    81    A    146 
M    82    I    147 
V    83    Q    148 
R    84    E    149 
A    85    V    150 
Q    86    A    151 
E    87    K    152 
K    88    T    153 
N    89    S    154 
A    90    A    155 
Y    91    F    156 
L    92    L    157 
S    93    G    158 
M    94    I    159 
N    95    T    160 
D    96    D    161 
I    97    E    162 
S    98    V    163 
T    99    T    164 
E    100    E    165 
G    101    G    166 
R    102    Q    167 
F    103    F    168 
T    104    M    169 
Y    105    Y    170 
P    106    V    171 
T    107    T    172 
G    108    G    173 
E    109    G    174 
I    110    R    175 
L    111    L    176 
V    112    T    177 
Y    113    Y    178 
S    114    S    179 
N    115    N    180 
W    116    W    181 
G    119    K    182 
E    120    K    183 
P    121    D    184 
N    122    E    185 
N    123    P    186 
S    124    N    187 
D    125    D    188 
E    126    H    189 
G    127    G    190 
Q    128    S    191 
P    129    G    192 
E    130    E    193 
N    131    D    194 
C    132    C    195 
V    133    V    196 
E    134    T    197 
I    135    I    198 
F    136    V    199 
P    137    D    200 
D    138    N    201 
G    139    G    202 
K    140    L    203 
W    141    W    204 
N    142    N    205 
D    143    D    206 
V    144    I    207 
P    145    S    208 
C    146    C    209 
S    147    Q    210 
K    148    A    211 
Q    149    S    212 
L    150    H    213 
L    151    T    214 
V    152    A    215 
I    153    V    216 
C    154    C    217 
E    155    E    218 
F    156    F    219 
TER 
END 
