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 a tendency 
METHOD among the top hits in all the HMM methods favoring the SCOP  
METHOD fold class containing the domain d1fna. As d1fna also gave 
METHOD fairly good scores for some of the target homologs, we  
METHOD ran phylogenetic analysis on the d1fna family (using 
METHOD Sjolander's Bayesian evolutionary tree estimation software) 
METHOD to identify subfamilies for d1fna and homologs, and 
METHOD construct subfamily HMMs (unpublished method).  
METHOD When we scored the target homologs 
METHOD using the subfamily HMMs, one subfamily showed a very strong 
METHOD preference for certain homologs, giving them scores 
METHOD above all non-superfamily members in a non-redundant set 
METHOD of pdb domains. This HMM was used as the basis for the 
METHOD alignment shown here (the target and d1fna were aligned 
METHOD to the HMM using the SAM program align2model).  
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 3 
PARENT 1fna 
M    1    G    6 
P    2    S    7 
V    3    L    8 
D    4    E    9 
L    5    V    10 
S    6    V    11 
K    7    A    12 
W    8    A    13 
S    9    T    14 
P    11    P    15 
L    12    T    16 
S    13    S    17 
L    14    L    18 
Q    15    L    19 
E    16    I    20 
V    17    S    21 
D    18    W    22 
E    19    D    23 
Q    20    A    24 
P    21    P    25 
Q    22    V    27 
H    23    T    28 
P    24    V    29 
L    25    R    30 
H    26    Y    31 
V    27    Y    32 
T    28    R    33 
Y    29    I    34 
A    30    T    35 
G    31    Y    36 
A    32    G    37 
A    33    E    38 
V    34    T    39 
D    35    G    40 
E    36    G    41 
L    37    N    42 
G    38    S    43 
K    39    P    44 
V    40    V    45 
L    41    Q    46 
T    42    E    47 
P    43    F    48 
Q    45    T    49 
V    46    V    50 
K    47    P    51 
N    48    G    52 
R    49    S    53 
P    50    K    54 
T    51    S    55 
S    52    T    56 
I    53    A    57 
S    54    T    58 
W    55    I    59 
D    56    S    60 
G    57    G    61 
L    58    L    62 
D    59    K    63 
S    60    P    64 
G    61    G    65 
K    62    V    66 
L    63    D    67 
Y    64    Y    68 
T    65    T    69 
L    66    I    70 
V    67    T    71 
L    68    V    72 
T    69    Y    73 
D    70    A    74 
P    71    V    75 
D    72    T    76 
P    74    G    77 
S    75    R    78 
R    76    G    79 
K    77    D    80 
D    78    S    81 
P    79    P    82 
F    87    A    83 
L    88    S    84 
V    89    S    85 
V    90    K    86 
N    91    P    87 
M    92    I    88 
K    93    S    89 
G    94    I    90 
G    100    N    91 
T    101    Y    92 
V    102    R    93 
L    103    T    94 
S    104    E    95 
TER 
END 
