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 4 
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 [ ] 
REMARK PARENT NONE [ ] 
REMARK PARENT NONE [ ] 
REMARK PARENT NONE [ ] 
REMARK  
PARENT 1bun_A 
L  1        M    8      
G  2        I    9    
K  3        R    10   
F  4        Y    11 
S  5        T    12 
Q  6        I    13 
T  7        P    14 
C  8        C    15 
Y  9        E    16 
N   10      K    17  
S   11      T    18  
A   12      W    19  
I   13      G    20   
Q   14      E    21   
G   15      Y    22   
S   16      A    23   
V   17      D    24   
L   18      Y    25   
T   19      G    26   
S   20      C    27   
T   21      Y    28   
C   22      C    29  
E   23      G    30   
R   24      A    31   
T   25      G    32   
N   26      G    33   
G   27      S    34   
G   28      G    35   
Y   29      R    36   
N   30      P    37   
T   31      I    38   
S   32      D    39  
S   33      A    40   
I   34      L    41   
D   35      D    42   
L   36      R    43   
N   37      C    44   
S   38      C    45   
V   39      Y    46   
I   40      V    47   
E   41      H    48   
N   42      D    49  
V   43      N    50   
D   44      C    51   
G   45      Y    52   
S   46      K    60   
L   47      C    61 
K   48      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 
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      T    85   
E   68      C    86   
L   69      A    87   
A   70      R    88   
A   71      I    89  
E   72      V    90  
C   73      C    91  
K   74      D    92  
T   75      C    93  
R   76      D    94  
A   77      R    95  
Q   78      T    96  
Q   79      A    97  
F   80      A    98  
V   81      L    99  
S   82      C    100 
T   83      F    101 
K   84      G    102 
I   85      N    103 
REMARK N   86       
REMARK L   87       
D   88      S    104 
D   89      E    105 
H   90      Y    106 
I   91      I    107 
A   92      E    108 
N   93      G    109 
I   94      H	 110 
D   95      K  	 111 
G   96      N  	 112 
T   97      I    113 
L   98      D  	 114 
K   99      T    115 
Y  100      A    116 
E  101      R    117 
TER 
END 
