PFRMAT AL 
TARGET T0083 
AUTHOR 5827-4749-3439 
METHOD T0083 prediction method 
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 Scores on all counts unanimously singled out d1lmb4 for 
METHOD the most likely structural match. 
METHOD 
METHOD The alignment was created as follows: 
METHOD (1) gathering homologs to the target using BLAST; 
METHOD (2) aligning the target and homologs using CLUSTALW; 
METHOD (3) identifying subfamilies in the homolog set using 
METHOD Sjolander's Bayesian evolutionary tree estimation 
METHOD method, and constructing subfamily HMMs for each 
METHOD subfamily found; 
METHOD (4) identifying a subfamily that assigned high 
METHOD probability to both the target and the structure; 
METHOD (6) aligning the target and structure to the  HMM. 
METHOD 
METHOD As usual, the alignment has not been edited in any way.        
MODEL 1 
PARENT 1lmb_4 
M    1    S    1 
I    2    T    2 
Q    3    K    3 
S    4    K    4 
Q    5    K    5 
I    6    P    6 
N    7    L    7 
R    8    T    8 
N    9    Q    9 
I    10    E    10 
R    11    Q    11 
L    12    L    12 
D    13    E    13 
L    14    D    14 
A    15    A    15 
D    16    R    16 
A    17    R    17 
I    18    L    18 
L    19    K    19 
L    20    K    24 
S    21    K    25 
K    22    K    26 
A    23    N    27 
K    24    E    28 
K    25    L    29 
D    26    G    30 
L    27    L    31 
S    28    S    32 
F    29    Q    33 
A    30    E    34 
E    31    S    35 
I    32    V    36 
A    33    A    37 
D    34    D    38 
G    35    K    39 
T    36    M    40 
G    37    G    41 
L    38    M    42 
A    39    G    43 
E    40    Q    44 
A    41    S    45 
F    42    G    46 
V    43    V    47 
T    44    G    48 
A    45    A    49 
A    46    L    50 
L    47    F    51 
L    48    N    52 
G    49    G    53 
Q    50    I    54 
Q    51    N    55 
A    52    A    56 
L    53    L    57 
P    54    N    58 
A    55    A    59 
D    56    Y    60 
A    57    N    61 
A    58    A    62 
R    59    A    63 
L    60    L    64 
V    61    L    65 
G    62    A    66 
A    63    K    67 
K    64    I    68 
L    65    L    69 
D    66    K    70 
L    67    V    71 
S    71    S    72 
I    72    V    73 
L    73    E    74 
L    74    E    75 
L    75    F    76 
Q    76    S    77 
M    77    P    78 
I    78    S    79 
P    79    I    80 
L    80    A    81 
R    81    R    82 
G    82    E    83 
M    94    I    84 
Y    95    Y    85 
R    96    E    86 
F    97    M    87 
Y    98    Y    88 
E    99    E    89 
M    100    A    90 
L    101    V    91 
Q    102    S    92 
TER 
END 
