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 5 
REMARK From threader ? 
REMARK The parent-none fields below really just indicate 
REMARK that the corresponding residue(s) are not aligned 
REMARK  
REMARK PARENT NONE [79] 
REMARK PARENT NONE [89 101] 
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   K  17 
T   7   T  18 
C   8   W  19 
Y   9   G  20 
N  10   E  21 
S  11   Y  22 
A  12   A  23 
I  13   D  24 
Q  14   Y  25 
G  15   G  26 
S  16   C  27 
V  17   Y  28 
L  18   C  29 
T  19   G  30 
S  20   A  31 
T  21   G  32 
C  22   G  33 
E  23   S  34 
R  24   G  35 
T  25   R  36 
N  26   P  37 
G  27   I  38 
G  28   D  39 
Y  29   A  40 
N  30   L  41 
T  31   D  42 
S  32   R  43 
S  33   C  44 
I  34   C  45 
D  35   Y  46 
L  36   V  47 
N  37   E  56 
S  38   K  57 
V  39   K  58 
I  40   H  59 
E  41   K  60 
N  42   C  61 
V  43   N  62 
D  44   T  65 
G  45   Q  66 
S  46   S  67 
K  48 Y    80 
W  49 G    81 
Q  50 A    82 
P  51 A    83 
S  52 G    84 
N  53 T    85 
F  54 C    86 
I  55 A    87 
E  56 R    88 
T  57 I    89 
C  58 V    90 
R  59 C    91 
N  60 D    92 
T  61 C    93 
N  62 D    94 
L  63 R    95 
A  64 T    96 
G  65 A    97 
S  66 A    98 
S  67 L    99 
E  68 C   100 
L  69 F   101 
A  70 G   102 
A  71 N   103 
E  72 S   104 
C  73 E   105 
K  74 Y   106 
T  75 I   107 
R  76 E   108 
A  77 G   109 
Q  78 H   110 
F  80 K   111 
V  81 N   112 
S  82 I   113 
T  83 D   114 
K  84 T   115 
I  85 A   116 
N  86 R   117 
L  87 F   118 
TER 
END 
