PFRMAT AL 
TARGET T0069 
AUTHOR 5827-4749-3439 
METHOD T0069 structure prediction 
METHOD 
METHOD 
METHOD As usual, we employed a two-pronged approach: (1) We scored the  
METHOD target against all the HMMs in our HMM library, and (2) we  
METHOD gathered homologs to the target using PsiBLAST, constructed an  
METHOD HMM for the target and homologs (using UCSC's HMM software), and  
METHOD scored PDB. This yielded two sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD 
METHOD HMM methods showed 1rtm1 to be the obvious choice; 
METHOD stage 2 scoring of the target hmm against PDB produced the top  
METHOD NLL-NULL score of -277 for 1rtm1. Stage 1 analysis confirmed 
METHOD this assignment. 
METHOD  
METHOD The alignment submitted was created by aligning the target and structure  
METHOD to the HMM constructed for the target and homologs. 
METHOD The alignment has not been edited in any way. 
MODEL 1 
PARENT 1rtm_1 
A    1    K    77 
E    2    L    78 
A    3    A    79 
N    4    N    80 
A    5    M    81 
L    6    E    82 
K    7    A    83 
Q    8    E    84 
R    9    I    85 
V    10    N    86 
T    11    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 
S    73    A    141 
A    74    E    142 
E    75    E    143 
N    76    N    144 
E    77    K    145 
A    78    A    146 
V    79    I    147 
Q    81    Q    148 
M    82    E    149 
V    83    V    150 
R    84    A    151 
A    85    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 
A    117    K    182 
D    118    K    183 
G    119    D    184 
E    120    E    185 
P    121    P    186 
N    122    N    187 
N    123    D    188 
S    124    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 
