PFRMAT AL 
TARGET T0084 
AUTHOR 5827-4749-3439 
METHOD HMM alignment for T0084  
METHOD 
METHOD As usual, we employed a two-pronged approach: (1) We scored the target  
METHOD against all the HMMs and threading models in our libraries, and (2) we  
METHOD gathered homologs to the target using one or more tools 
METHOD (such as iterated FASTA or PsiBLAST), constructed an  
METHOD HMM for the target and homologs (using UCSC's HMM software), and  
METHOD scored PDB. This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD Not surprisingly, given that the target is an artificial 
METHOD construct, BLAST produced no homologs to the target.  
METHOD However, when we scored all the HMMs in our library, 
METHOD one structure had a weak but significant score: d2ztaa. 
METHOD When we examined the alignment of the target and  
METHOD structure we discovered the two sequences were perfect 
METHOD reversals of each other.  
METHOD The HMM alignment in this submission shows several 
METHOD identities. Normally, we would have more confidence 
METHOD in an alignment that maximized identities between 
METHOD two proteins that are related by evolution. 
METHOD Since, however, these two proteins are not thus related, 
METHOD we decided to make the threading alignment model 1, 
METHOD and the HMM alignment model 2, under the presumption 
METHOD that the threading alignment may be closer to  
METHOD a physically plausible structure. 
METHOD  
METHOD This alignment was generated by aligning the target 
METHOD and structure to an HMM trained on the structure 
METHOD and its close homologs. As usual, the alignment 
METHOD has not been edited in any way from the automatic  
METHOD alignment produced. 
METHOD 
MODEL 2 
PARENT 2zta_A 
C    1    R    1 
G    2    M    2 
G    3    K    3 
R    4    Q    4 
E    5    E    10 
G    6    E    11 
V    7    L    12 
L    8    L    13 
K    9    S    14 
K    10    K    15 
L    11    N    16 
R    12    Y    17 
A    13    H    18 
V    14    L    19 
E    15    E    20 
N    16    N    21 
E    17    E    22 
L    18    V    23 
H    19    A    24 
Y    20    R    25 
N    21    L    26 
K    22    K    27 
S    23    K    28 
L    24    L    29 
L    25    V    30 
TER 
END 
