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 1 
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 [47 48] 
REMARK PARENT NONE [59 ] 
REMARK PARENT NONE [ ] 
REMARK PARENT NONE [ ] 
REMARK 
PARENT 1bun_A 
S   5        N    1 
Q   6        L    2 
T   7        I    3 
C   8        N    4 
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       G    35  
S   38       R    36  
V   39       P    37  
I   40       I    38  
E   41      D    39  
N   42      A    40 
V   43      L    41  
D   44      D    42  
G   45      R    43  
S   46      C    44  
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 
