PFRMAT AL 
TARGET T0067 
AUTHOR 5529-3140-9255 
REMARK Prediction team BENNER-COHEN has two group leaders, 
REMARK but we will consistently use Steven Benner's predictor 
REMARK number to avoid confusion concerning a second team 
REMARK connected with Fred Cohen (called Cohen, Fred). 
REMARK (Fred Cohen's number as a group leader is 6140-7890-6093). 
REMARK Prediction team members: D.L.Gerloff, G.Cannarozzi, 
REMARK M.Joachimiak, F.E.Cohen & S.A.Benner. 
METHOD 
METHOD This submission is a threading alignment for T0067 
METHOD (Phosphatidylethanolamine binding protein), with a parent 
METHOD structure suggested at a significant score by one the fold 
METHOD recognition programs by D. Fischer and D. Eisenberg, UCLA,  
METHOD as available through the UCLA-DOE fold recognition server.  
METHOD (Ref. D.Fischer & D. Eisenberg (1996). Protein Sci. 5:947-55), 
METHOD A different program in the suite returned a significant match 
METHOD with 1an3_B. Structural and functional arguments compelled us 
METHOD to chose 1mdc as a parent structure (member of the fatty acid 
METHOD binding protein family). It should be noted that ProCyon 
METHOD (H. Floeckner & M. Sippl) did not return any members of this 
METHOD fold family in its default output. However, the program found 
METHOD two possible matches with members of a closely related fold 
METHOD family, the lipocalins. 
METHOD 
METHOD OUR INTENTION WITH SUBMITTING THIS MANUAL THREADING ALIGNMENT 
METHOD IS TO ASSIST IN IMPROVING THE QUALITY OF AUTOMATED THREADING 
METHOD ALIGNMENTS BY UNCOVERING WHICH OF THE CLUES COMMONLY USED BY 
METHOD EXPERTS ALIGNING MANUALLY ARE MOST USEFUL AND COULD BE 
METHOD EXPLORED SYSTEMATICALLY. 
METHOD  
METHOD The proposed threading alignment was generated manually and 
METHOD takes into account sequence similarity between a T0067 align- 
METHOD ment of 11 sequences from SwissProt and an well-populated 
METHOD alignment for the template structure, 
METHOD predicted secondary structures (an automated prediction  
METHOD by the program SAINT (Benner et al.), server-generated PHD  
METHOD predictions, the prediction by Chandonia&Cohen, and our manual  
METHOD predictions), predicted Surface/Interior positions (DARWIN &  
METHOD manual), but also strong consideration of which residues may be  
METHOD part of the functional sites. 
METHOD  
METHOD In this case, however, the functional clues were sparse, and the 
METHOD local solvent-accessibility in the target structure is likely to 
METHOD be different in many places due to large insertions into the core 
METHOD fold. Interestingly, local sequence similarity in a few locations 
METHOD (D.R. Flower, A.C.T. North and T.K.Attwood) appears to suggest a  
METHOD sequence-structure alignment with multiple insertions inbetween the 
METHOD core secondary structures, instead of an inserted domain. We are 
METHOD not certain whether the large insertions at the *top* of the  
METHOD beta-barrel could be placed without seriously rearranging the  
METHOD two helices near the N-terminus.  
METHOD 
METHOD Due to these inconsistencies, we predict this alignment at low 
METHOD resolution (lower than we would estimate for our predictions 
METHOD for targets T0044 and T0077) 
METHOD 
MODEL 1 
PARENT 1mdc 
S   13   V   6 
L   14   Y   7 
Q   15   S   8 
E   16   L   9 
V   17   V   10 
D   18   K   11 
E   19   Q   12 
Q   22   D   16 
H   23   G   17 
P   24   F   18 
L   25   L   19 
H   26   K   20 
V   27   S   21 
T   28   A   22 
Y   29   G   23 
A   30   L   24 
G   31   S   25 
A   32   D   26 
A   33   D   27 
V   34   K   28 
D   35   I   29 
E   36   Q   30 
L   37   A   31 
G   38   L   32 
K   39   V   33 
V   40   S   34 
L   41   D   35 
T   42   K   36 
P   43   P   37 
T   44   T   38 
Q   45   Q   39 
V   46   K   40 
K   47   M   41 
N   48   E   42 
R   49   A   43 
P   50   N   44 
T   51   D   46 
S   52   S   47 
I   53   Y   48 
S   54   S   49 
W   55   N   50 
D   56   T   51 
G   57   S   52 
L   58   T   53 
D   59   G   54 
S   60   G   57 
G   61   A   58 
K   62   K   59 
L   63   T   60 
Y   64   V   61 
T   65   S   62 
L   66   F   63 
V   67   K   64 
L   68   S   65 
H   86   E   68 
F   87   F   69 
L   88   D   70 
V   89   D   71 
V   90   V   72 
N   91   I   73 
G  100   D   77 
T  101   S   78 
V  102   V   79 
L  103   K   80 
S  104   S   81 
D  105   M   82 
Y  106   Y   83 
V  107   T   84 
G  108   V   85 
S  109   D   86 
R  119   N   88 
Y  120   V   89 
V  121   V   90 
W  122   T   91 
L  123   H   92 
V  124   V   93 
Y  125   V   94 
E  126   K   95 
F  149   A   98 
K  150   G   99 
V  151   V   100 
A  152   A   101 
S  153   T   102 
F  154   F   103 
R  155   K   104 
K  156   K   105 
K  157   E   106 
Y  158   Y   107 
E  159   N   108 
P  163   D   111 
V  164   L   112 
A  165   V   113 
G  166   V   114 
T  167   T   115 
C  168   I   116 
Y  169   T   117 
Q  170   S   118 
A  171   S   119 
E  172   N   120 
W  173   W   121 
D  174   D   122 
D  175   G   123 
V  177   V   124 
P  178   A   125 
K  179   R   126 
L  180   R   127 
Y  181   Y   128 
E  182   Y   129 
Q  183   K   130 
L  184   A   131 
TER 
END 
