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 3 
REMARK The parent-none fields below really just indicate 
REMARK that the corresponding residue(s) are not aligned 
REMARK  
REMARK PARENT NONE [1 5] 
REMARK PARENT NONE [47 48] 
REMARK  
PARENT 1bun_A 
Q  6      N    4 
T  7      F    5 
C  8      M    6 
Y  9      E    7 
N   10       M    8 
S   11       I    9 
A   12       R    10 
I   13       Y    11  
Q   14       T    12  
G   15       I    13  
S   16       P    14  
V   17       C    15  
L   18       E    16  
T   19       K    17  
S   20       T    18  
T   21       W    19  
C   22       G    20 
E   23       E    21  
R   24       Y    22  
T   25       A    23  
N   26       D    24  
G   27       Y    25  
G   28       G    26  
Y   29       C    27  
N   30       Y    28  
T   31       C    29  
S   32       G    30 
S   33       A    31  
I   34       G    32  
D   35       G    33  
L   36       S    34  
N   37       R    43 
S   38       C    44 
V   39       C    45 
I   40       Y    46 
E   41       V    47 
N   42       H    48 
V   43       D    49 
D   44       Y    52 
G   45       G    53 
S   46       D    54 
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 
R   59      T    73    
N   60      K    74    
T   61      R    75    
N   62      T    76    
L   63      I    77    
A   64      I    78    
G   65      C    79    
S   66      Y    80    
S   67      G    81    
E   68      A    82    
L   69      A    83    
A   70      G    84    
A   71      T    85    
E   72      C    86    
C   73      A    87    
K   74      R    88    
T   75      I    89    
R   76      V    90    
A   77      C    91    
Q   78      D    92    
Q   79      C    93    
F   80      D    94    
V   81      R    95    
S   82      T    96    
T   83      A    97    
K   84      A    98    
I   85      L    99    
N   86      C    100   
L   87      F    101   
D   88      G    102   
D   89      N    103   
H   90      S    104   
I   91      E    105   
A   92      Y    106   
N   93      I    107   
I   94      E    108   
D   95      G    109   
G   96      H    110   
T   97      K    111   
L   98      N    112   
K   99      I    113  
Y  100      D    114  
E  101      T   115     
TER 
END 
