PFRMAT AL 
TARGET T0084 
AUTHOR 5827-4749-3439 
METHOD Threading alignment for T0084 
METHOD 
METHOD Note: this alignment was obtained automatically, and has not been 
METHOD hand-edited. 
METHOD 
METHOD This alignment was created by aligning the target sequence to a 
METHOD library of 3D-1D type threading models.  Matching and gap scores 
METHOD were optimized for discriminating remote homolog sequence-structure 
METHOD alignments from alignments on incorrect folds. 
METHOD 
METHOD For this structure template, as well as for other proteins which 
METHOD show significant intermolecular interactions in the PDB file, we 
METHOD calculated two threading models-- one with solvent accessibilities 
METHOD calculated for the domain/chain in isolation, and the other in 
METHOD complex with other domains/chains.  For this target, the top- 
METHOD scoring match was 2zta_A in complex with 2zta_B, while the  
METHOD fifth best match was 2zta_A in isolation. 
METHOD 
METHOD Once we had identified the hit, it was obvious that the target 
METHOD sequence was exactly the reverse of 2zta_A.  Either this target 
METHOD is a red-herring, or it is an academic exercise-- an interesting 
METHOD one given the symmetry of the structure and the polarity of the 
METHOD alpha-helix.  Because there are no evolutionary constraints on 
METHOD function, we don't stake much on this prediction. Packing 
METHOD details, which are presumably critical for zipper formation,  
METHOD are ignored by our threading algorithm.  However, in keeping  
METHOD with our desire to submit only automated alignments, we have 
METHOD avoided the temptation to examine the resulting 3D model to 
METHOD check for steric (or electrostatic) clashes which would prevent  
METHOD the interactions that stabilize the wild-type dimer. 
MODEL 1 
PARENT 2zta_A 
G    3    R    1 
R    4    M    2 
E    5    K    3 
G    6    Q    4 
V    7    L    5 
L    8    E    6 
K    9    D    7 
K    10    K    8 
L    11    V    9 
R    12    E    10 
A    13    E    11 
V    14    L    12 
E    15    L    13 
N    16    S    14 
E    17    K    15 
L    18    N    16 
H    19    Y    17 
Y    20    H    18 
N    21    L    19 
K    22    E    20 
S    23    N    21 
L    24    E    22 
L    25    V    23 
E    26    A    24 
E    27    R    25 
V    28    L    26 
K    29    K    27 
D    30    K    28 
E    31    L    29 
L    32    V    30 
Q    33    G    31 
TER 
END 
