PFRMAT AL 
TARGET T0064 
AUTHOR 5827-4749-3439 
METHOD T0064 structure prediction 
METHOD 
METHOD As usual, we employed a three-pronged approach: (1) We scored the  
METHOD target against all the HMMs and threading models in our libraries,  
METHOD and (2) we gathered homologs to the target using PsiBLAST,  
METHOD constructed an HMM for the target and homologs (using UCSC's HMM  
METHOD software), and scored PDB.  
METHOD This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD The highest-scoring HMM in the first stage of the analysis  
METHOD was constructed for the scop domain d1r69 and homologs. 
METHOD The HMM constructed for the target and homologs in the 
METHOD second stage also scored this structure in first place. 
METHOD A threading model for a superfamily member (d1llia) was  
METHOD also very high scoring, helping confirm the prediction. 
METHOD The threading hit included a greater portion of the target, 
METHOD and we used threading to align the portion of 
METHOD the target that was not covered by 1r69. 
METHOD 
METHOD The alignment submitted was created by aligning the target and structure  
METHOD to the HMM constructed for the target and homologs as follows: (1)  
METHOD constructing an HMM for T0064 alone using modelfromalign 
METHOD and the target sequence as the template alignment,  
METHOD (2) reestimating the HMM using sequences found using BLAST, 
METHOD (3) then reestimating that HMM using sequence weighting, 
METHOD to allow the HMM to generalize. The weighting method 
METHOD used Henikoff weighting to set relative weights and 
METHOD our own method of estimating the number of independent 
METHOD observations to set the total weight allotted 
METHOD the sequences. This alignment submitted was not edited in any way 
METHOD from the automatic alignment. 
MODEL 1 
PARENT 1r69 
M A1    S   1 
I A2    I   2 
G A3    S   3 
Q A4    S   4 
R A5    R   5 
I A6    V   6 
K A7    K   7 
Q A8    S   8 
Y A9    K   9 
R A10    R  10 
K A11    I  11 
E A12    Q  12 
K A13    L  13 
G A14    G  14 
Y A15    L  15 
S A16    N  16 
L A17    Q  17 
S A18    A  18 
E A19    E  19 
L A20    L  20 
A A21    A  21 
E A22    Q  22 
K A23    K  23 
A A24    V  24 
G A25    G  25 
V A26    T  26 
A A27    T  27 
K A28    Q  28 
S A29    Q  29 
Y A30    S  30 
L A31    I  31 
S A32    E  32 
S A33    Q  33 
I A34    L  34 
E A35    E  35 
R A36    N  36 
N A37    G  37 
L A38    K  38 
Q A39    T  39 
T A40    K  40 
N A41    R  41 
P A42    P  42 
Q A45    R  43 
F A46    F  44 
L A47    L  45 
E A48    P  46 
K A49    E  47 
V A50    L  48 
S A51    A  49 
A A52    S  50 
V A53    A  51 
L A54    L  52 
D A55    G  53 
V A56    V  54 
S A57    S  55 
V A58    V  56 
H A59    D  57 
T A60    W  58 
L A61    L  59 
L A62    L  60 
D A63    N  61 
E A64    G  62 
K A65    T  63 
TER 
END 
