PFRMAT AL 
TARGET T0060 
AUTHOR 5827-4749-3439 
METHOD T0060 structure prediction 
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 The highest-scoring HMMs in the first stage of the analysis  
METHOD were not at all helpful; we had no HMMs for 1gifA or any close 
METHOD family member. 
METHOD 
METHOD The second stage of the analysis, constructing an HMM for 
METHOD the target and iterated FASTA-identified homologs, 
METHOD and then scoring PDB, clearly identified 1gifA (and family members)  
METHOD as the closest match. 
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 1gif_A 
P    1    P    2 
F    2    M    3 
L    3    F    4 
E    4    I    5 
L    5    V    6 
D    6    N    7 
T    7    T    8 
N    8    N    9 
L    9    V    10 
P    10    P    11 
A    11    R    12 
N    12    A    13 
R    13    S    14 
V    14    V    15 
P    15    P    16 
A    16    D    17 
G    17    G    18 
L    18    F    19 
E    19    L    20 
K    20    S    21 
R    21    E    22 
L    22    L    23 
C    23    T    24 
A    24    Q    25 
A    25    Q    26 
A    26    L    27 
A    27    A    28 
S    28    Q    29 
I    29    A    30 
L    30    T    31 
G    31    G    32 
K    32    K    33 
P    33    P    34 
A    34    P    35 
D    35    Q    36 
R    36    Y    37 
V    37    I    38 
N    38    A    39 
V    39    V    40 
T    40    H    41 
V    41    V    42 
R    42    V    43 
P    43    P    44 
G    44    D    45 
L    45    Q    46 
A    46    L    47 
M    47    M    48 
A    48    A    49 
L    49    F    50 
S    50    G    51 
G    51    G    52 
S    52    S    53 
T    53    S    54 
E    54    E    55 
P    55    P    56 
C    56    C    57 
A    57    A    58 
Q    58    L    59 
L    59    C    60 
S    60    S    61 
I    61    L    62 
S    62    H    63 
S    63    S    64 
I    64    I    65 
G    65    G    66 
V    66    K    67 
V    67    I    68 
G    68    G    69 
T    69    G    70 
A    70    A    71 
D    72    Q    72 
N    73    N    73 
R    74    R    74 
S    75    S    75 
H    76    Y    76 
S    77    S    77 
A    78    K    78 
H    79    L    79 
F    80    L    80 
F    81    C    81 
E    82    G    82 
F    83    L    83 
L    84    L    84 
T    85    A    85 
K    86    E    86 
E    87    R    87 
L    88    L    88 
A    89    R    89 
L    90    I    90 
G    91    S    91 
Q    92    P    92 
D    93    D    93 
R    94    R    94 
I    95    V    95 
L    96    Y    96 
I    97    I    97 
R    98    N    98 
F    99    Y    99 
F    100    Y    100 
P    101    D    101 
L    102    M    102 
E    103    N    103 
S    104    A    104 
W    105    A    105 
Q    106    N    106 
I    107    V    107 
G    108    G    108 
K    109    W    109 
I    110    N    110 
G    111    N    111 
T    112    S    112 
V    113    T    113 
F    116    F    114 
L    117    A    115 
TER 
END 
