PFRMAT AL 
TARGET T0052 
AUTHOR 4139-4764-1095 
METHOD 1) Secondary structure was predicted with PHD and 
METHOD Predator.  
METHOD 2) Medline search: 
METHOD From the publiced abstracts and ss prediction it was  
METHOD assumed that the protein had atleast two helixes 
METHOD and a significant number of disulfide bonds. 
METHOD We guessed that this should be a phospholipas A2 fold 
METHOD Pfam*, ssHMM and THREADER were used with with this 
METHOD predicted structure, default parameters. 
METHOD ssHMM and Pfam* - no significant hits 
METHOD 3) An hmm from all phospholipase_a2 structures was 
METHOD created. T0052 was aligned to this HMM, showing a good but 
METHOD not significant match. 
METHOD 4) THREADER: 
METHOD The first couple of good-scoring alignments with 
METHOD energies no lower than the native stucture was 
METHOD then threaded again with sequence shuffling. 
METHOD The best scorer was 1ppa00, a phospholipase A2. 
METHOD 5) Sequenca alignments 
METHOD We also experienced semi-good sequence alignments 
METHOD with several other phospholipases, and therefor 
METHOD constructed a consensus-sequence for those. 
METHOD 1bunA was judged to be one of the structures 
METHOD closest to this consensus sequence (25% identity), and we have 
METHOD thus aligned the target with this structure. 
METHOD * ALIGNMENTS * 
METHOD Sequence alignments were made in different ways: 
METHOD Model 1 and 2 from manual judgement after alignment  
METHOD to the consensus sequence. 
METHOD model 3 is the alignment to the consensus sequence 
METHOD model 4 is a clustalw alignment of t0052 1bunA and 1ppa 
METHOD model 5 is from threader 
METHOD REMARKS: 
METHOD Alignment are pasted manually dueto lack of time. 
MODEL 2 
REMARK The parent-none fields below really just indicate 
REMARK that the corresponding residue(s) are not aligned 
REMARK  
REMARK PARENT NONE [1 4] 
REMARK PARENT NONE [41 48] 
REMARK PARENT NONE [59 ] 
REMARK  
PARENT 1bun_A 
S  5         N    1 
Q  6         L    2 
T  7         I    3 
C  8         N    4 
Y  9      A    31    
N   10    G    32    
S   11    G    33    
A   12    S    34    
I   13    G    35    
Q   14    R    36    
G   15    P    37    
S   16    I    38    
V   17    D    39    
L   18    A    40    
T   19    L    41    
S   20    D    42    
T   21    R    43    
C   22    C    44    
E   23    C    45    
R   24    Y    46    
T   25    V    47    
N   26    H    48    
G   27    D    49    
G   28    N    50    
Y   29    C    51    
N   30    Y    52    
T   31    G    53    
S   32    D    54    
S   33    A    55  
I   34    E    56  
D   35    K    57  
L   36    K    58  
N   37    H    59  
S   38    K    60  
V   39    C    61  
I   40    N    62  
W   49    P    63   
Q   50      K    64 
P   51      T    65 
S   52      Q    66 
N   53      S    67 
F   54      Y    68 
I   55      S    69 
E   56      Y    70 
T   57      K    71 
C   58      L    72 
N   60      T    73 
T   61      K    74 
N   62      R    75 
L   63      T    76 
A   64      I    77 
G   65      I    78 
S   66      C    79 
S   67      Y    80 
E   68      G    81 
L   69      A    82 
A   70      A    83 
A   71      G    84 
E   72      T    85 
C   73      C    86 
K   74      A    87 
T   75      R    88 
R   76      I    89 
A   77      V    90 
Q   78      C    91 
Q   79      D    92 
F   80      C    93 
V   81      D    94 
S   82      R    95 
T   83      T    96 
K   84      A    97 
I   85      A    98 
N   86      L    99 
L   87      C    100 
D   88      F    101 
D   89      G    102 
H   90      N    103 
I   91      S    104 
A   92      E    105 
N   93      Y    106 
I   94      I    107 
D   95      E    108 
G   96      G    109 
T   97      H    110 
L   98      K    111 
K   99      N    112 
Y  100      I    113 
E  101      D    114 
TER 
END 
