PFRMAT AL 
TARGET T0067 
AUTHOR 5827-4749-3439 
METHOD 
METHOD As usual, we employed a two-pronged approach: (1) We scored the target  
METHOD against all the HMMs and threading models in our libraries, and (2) we  
METHOD gathered homologs to the target using one or more tools 
METHOD (such as iterated FASTA or PsiBLAST), constructed an  
METHOD HMM for the target and homologs (using UCSC's HMM software), and  
METHOD scored PDB. This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD While none of the scores were very strong, there was consistency 
METHOD among the top hits in the target HMM scores of PDB, and 
METHOD a weak consensus among the threading hits for target homologs, 
METHOD favoring flavodoxin folds. We chose the top hit for the 
METHOD target HMM as the model for this prediction. 
METHOD 
METHOD Because the alignment of the target and its homologs 
METHOD and the structure and its homologs did not stay in register 
METHOD within each family separately when aligned to the target HMM, 
METHOD we re-estimated the target HMM using a selected subset of 
METHOD the target and structure homologs. This re-estimated HMM 
METHOD was used to align the target and structure. 
METHOD 
METHOD Also as usual, the alignment has not been edited in any way, 
METHOD and was generated fully automatically by the SAM program 
METHOD align2model. 
MODEL 1 
PARENT 1ag9_A 
M    1    A    2 
P    2    I    3 
V    3    T    4 
S    6    G    5 
K    7    I    6 
W    8    F    7 
S    9    F    8 
G    10    G    9 
P    11    S    10 
L    12    D    11 
S    13    T    12 
L    14    G    13 
Q    15    N    14 
E    16    T    15 
V    17    E    16 
D    18    N    17 
E    19    I    18 
Q    20    A    19 
P    21    K    20 
Q    22    M    21 
H    23    I    22 
P    24    Q    23 
L    25    K    24 
H    26    Q    25 
V    27    L    26 
T    28    G    27 
Y    29    K    28 
A    30    D    29 
G    31    V    30 
A    32    A    31 
A    33    D    32 
V    34    V    33 
D    35    H    34 
E    36    D    35 
L    37    I    36 
G    38    A    37 
K    39    K    38 
V    40    S    39 
L    41    S    40 
T    42    K    41 
P    43    E    42 
T    44    D    43 
Q    45    E    45 
V    46    A    46 
K    47    Y    47 
N    48    D    48 
R    49    I    49 
P    50    L    50 
T    51    L    51 
S    52    L    52 
I    53    G    53 
S    54    I    54 
W    55    P    55 
D    56    T    56 
G    57    W    57 
L    58    Y    58 
D    59    Y    59 
S    60    G    60 
G    61    E    61 
K    62    A    62 
L    63    Q    63 
Y    64    C    64 
T    65    D    65 
L    66    W    66 
V    67    D    67 
L    68    D    68 
T    69    F    69 
D    70    F    70 
P    71    P    71 
D    72    T    72 
A    73    L    73 
P    74    E    74 
S    75    E    75 
R    76    I    76 
K    77    D    77 
D    78    F    78 
P    79    N    79 
K    80    G    80 
Y    81    K    81 
R    82    L    82 
E    83    V    83 
W    84    A    84 
H    85    L    85 
H    86    F    86 
F    87    G    87 
L    88    C    88 
V    89    G    89 
V    90    D    90 
N    91    Q    91 
M    92    E    92 
K    93    D    93 
G    94    Y    94 
N    95    A    95 
D    96    E    96 
I    97    Y    97 
K    113    F    98 
G    114    C    99 
T    115    D    100 
G    116    A    101 
L    117    L    102 
H    118    G    103 
R    119    T    104 
Y    120    I    105 
V    121    R    106 
W    122    D    107 
L    123    I    108 
V    124    I    109 
Y    125    E    110 
E    126    P    111 
Q    127    R    112 
D    128    G    113 
R    129    A    114 
P    130    T    115 
L    131    I    116 
K    132    V    117 
C    133    G    118 
D    134    H    119 
E    135    W    120 
P    136    P    121 
I    137    T    122 
L    138    A    123 
S    139    G    124 
N    140    Y    125 
R    141    H    126 
S    142    F    127 
G    143    E    128 
D    144    A    129 
H    145    S    130 
R    146    K    131 
G    147    G    132 
K    148    L    133 
F    149    A    134 
K    150    D    137 
V    151    H    138 
A    152    F    139 
S    153    V    140 
F    154    G    141 
R    155    L    142 
K    156    A    143 
K    157    I    144 
Y    158    D    145 
E    159    E    146 
L    160    D    147 
R    161    R    148 
A    162    Q    149 
P    163    P    150 
V    164    E    151 
A    165    L    152 
G    166    T    153 
T    167    A    154 
C    168    E    155 
Y    169    R    156 
Q    170    V    157 
A    171    E    158 
E    172    K    159 
W    173    W    160 
D    174    V    161 
D    175    K    162 
Y    176    Q    163 
V    177    I    164 
P    178    S    165 
K    179    E    166 
L    180    E    167 
Y    181    L    168 
E    182    H    169 
Q    183    L    170 
L    184    D    171 
S    185    E    172 
G    186    N    175 
K    187    A    176 
TER 
END 
