PFRMAT SS 
TARGET T0049 
AUTHOR 1751-3146-3362 
METHOD Using neural net fssp-12345-IDaa1-9-6-11-9-3-8-7-ehl-seeded3-trained.net 
METHOD This is a 4-layer network, with  
METHOD	window	units 
METHOD	    9	    6 
METHOD	   11	    9 
METHOD	    3	    8 
METHOD	    7	    3 (1 EHL ) 
METHOD The input amino acid frequencies were determined from 
METHOD alignment t49.t98_2.a2m.gz 
METHOD with weighted counts, using HenikoffWeight(1 bits/column, 0.5) 
METHOD The weighting was determined by the posterior distribution 
METHOD after regularizing with recode3.20comp. 
METHOD Counts were regularized to probabilities using 
METHOD /projects/compbio/lib/recode3.20comp 
METHOD Total sequence weight for alignment was 11.3139 
METHOD 
METHOD The seconary structure prediction does not agree well with the alignment 
METHOD with 3pte predicted by the UCSC fold-recognition group. 
METHOD We suspect that the alignment is better than the secondary-structure 
METHOD prediction. 
MODEL 1 
M C 0.91 
T C 0.74 
A C 0.50 
A C 0.51 
S C 0.59 
L C 0.71 
D C 0.89 
P C 0.91 
T C 0.71 
A C 0.66 
F C 0.76 
S C 0.73 
L C 0.56 
D H 0.69 
A H 0.80 
A H 0.84 
S H 0.85 
L H 0.83 
A H 0.82 
A H 0.86 
R H 0.82 
L H 0.89 
D H 0.94 
A H 0.96 
V H 0.93 
F H 0.94 
D H 0.95 
Q H 0.95 
A H 0.92 
L H 0.91 
R H 0.86 
E H 0.84 
R H 0.69 
R H 0.52 
L C 0.48 
V C 0.63 
G C 0.76 
A C 0.51 
V E 0.81 
A E 0.93 
I E 0.94 
V E 0.89 
A E 0.71 
R C 0.60 
H C 0.88 
G C 0.93 
E C 0.79 
I E 0.58 
L E 0.77 
Y E 0.79 
R E 0.68 
R E 0.51 
A C 0.57 
Q C 0.74 
G C 0.79 
L C 0.61 
A C 0.56 
D C 0.59 
R C 0.64 
E C 0.80 
A C 0.81 
G C 0.85 
R C 0.89 
P C 0.80 
M C 0.77 
R C 0.81 
E C 0.77 
D C 0.90 
T C 0.79 
L E 0.58 
F E 0.82 
R E 0.90 
L E 0.94 
A E 0.90 
S E 0.79 
V E 0.58 
T C 0.42 
K H 0.56 
P H 0.78 
I H 0.84 
V H 0.85 
A H 0.88 
L H 0.90 
A H 0.93 
V H 0.94 
L H 0.94 
R H 0.92 
L H 0.94 
V H 0.91 
A H 0.81 
R C 0.50 
G C 0.77 
E C 0.64 
L C 0.62 
A C 0.78 
L C 0.75 
D C 0.79 
A C 0.67 
P C 0.60 
V H 0.67 
T H 0.66 
R H 0.55 
W C 0.47 
L C 0.68 
P C 0.85 
E C 0.67 
F C 0.71 
R C 0.73 
P C 0.73 
R C 0.68 
L C 0.74 
A C 0.82 
D C 0.85 
G C 0.90 
S C 0.87 
E C 0.93 
P C 0.87 
L C 0.48 
V E 0.56 
T E 0.54 
I H 0.65 
H H 0.86 
H H 0.90 
L H 0.88 
L H 0.76 
T H 0.50 
H C 0.58 
T C 0.85 
S C 0.89 
G C 0.84 
L C 0.69 
G C 0.57 
Y C 0.55 
W C 0.61 
L C 0.65 
L C 0.68 
E C 0.77 
G C 0.84 
A C 0.70 
G C 0.72 
S C 0.72 
V C 0.70 
Y C 0.75 
D C 0.74 
R C 0.59 
L C 0.64 
G C 0.73 
I C 0.69 
S C 0.81 
D C 0.91 
G C 0.83 
I C 0.62 
D C 0.51 
L H 0.52 
R H 0.69 
D H 0.76 
F H 0.75 
D H 0.60 
L H 0.72 
D H 0.86 
E H 0.87 
N H 0.85 
L H 0.87 
R H 0.84 
R H 0.81 
L H 0.61 
A C 0.59 
S C 0.73 
A C 0.81 
P C 0.86 
L C 0.70 
S C 0.61 
F C 0.71 
A C 0.88 
P C 0.91 
G C 0.93 
S C 0.74 
G E 0.68 
W E 0.84 
Q E 0.87 
Y E 0.76 
S C 0.54 
L C 0.77 
A C 0.72 
L H 0.43 
D H 0.60 
V H 0.69 
L H 0.83 
G H 0.90 
A H 0.93 
V H 0.95 
V H 0.96 
E H 0.93 
R H 0.87 
A H 0.61 
T C 0.77 
G C 0.75 
Q C 0.73 
P C 0.53 
L H 0.87 
A H 0.94 
A H 0.98 
A H 0.97 
V H 0.96 
D H 0.96 
A H 0.96 
L H 0.91 
V H 0.77 
A C 0.53 
Q C 0.82 
P C 0.76 
L C 0.77 
G C 0.79 
M C 0.74 
R C 0.80 
D C 0.78 
C C 0.88 
G C 0.72 
F E 0.52 
V C 0.48 
S C 0.63 
A C 0.58 
E C 0.50 
P H 0.63 
E H 0.80 
R H 0.83 
F H 0.77 
A H 0.65 
V H 0.51 
P C 0.36 
Y C 0.38 
H C 0.52 
D C 0.71 
G C 0.81 
Q C 0.88 
P C 0.93 
E C 0.91 
P C 0.69 
V C 0.49 
R C 0.55 
M C 0.62 
R C 0.77 
D C 0.88 
G C 0.91 
I C 0.75 
E C 0.75 
V C 0.84 
P C 0.88 
L C 0.85 
P C 0.78 
E C 0.73 
G C 0.78 
H C 0.71 
G C 0.72 
A C 0.50 
A H 0.36 
V H 0.41 
R C 0.38 
F C 0.58 
A C 0.86 
P C 0.92 
S C 0.89 
R C 0.74 
V C 0.68 
F C 0.72 
E C 0.88 
P C 0.91 
G C 0.87 
A C 0.71 
Y C 0.64 
P C 0.68 
S C 0.86 
G C 0.86 
G C 0.71 
A C 0.68 
G C 0.67 
M C 0.47 
Y C 0.49 
G C 0.73 
S C 0.79 
A H 0.80 
D H 0.96 
D H 0.97 
V H 0.98 
L H 0.99 
R H 0.99 
A H 0.99 
L H 0.99 
E H 0.98 
A H 0.96 
I H 0.89 
R H 0.56 
A C 0.75 
N C 0.89 
P C 0.86 
G C 0.70 
F C 0.70 
L C 0.72 
P C 0.57 
E H 0.60 
T H 0.49 
L H 0.67 
A H 0.85 
D H 0.93 
A H 0.92 
A H 0.91 
R H 0.86 
R H 0.81 
D H 0.70 
Q H 0.49 
A C 0.53 
G C 0.58 
V C 0.74 
G C 0.82 
A C 0.77 
E C 0.74 
T C 0.67 
R C 0.73 
G C 0.68 
P C 0.69 
G C 0.76 
W C 0.65 
G C 0.55 
F C 0.49 
G C 0.43 
Y E 0.41 
L E 0.45 
S E 0.50 
A E 0.50 
V E 0.47 
L C 0.55 
D C 0.76 
D C 0.90 
P C 0.65 
A H 0.56 
A C 0.50 
A C 0.66 
G C 0.87 
T C 0.94 
P C 0.93 
Q C 0.94 
H C 0.87 
A C 0.66 
G C 0.54 
T E 0.57 
L E 0.60 
Q E 0.49 
W C 0.64 
G C 0.84 
G C 0.72 
V C 0.54 
Y C 0.60 
G C 0.78 
H C 0.63 
S C 0.47 
W C 0.43 
F E 0.44 
V C 0.56 
D C 0.86 
R C 0.85 
A C 0.77 
L C 0.64 
G C 0.47 
L E 0.60 
S E 0.77 
V E 0.81 
L E 0.80 
L E 0.78 
L E 0.52 
T C 0.44 
N C 0.58 
T C 0.62 
A C 0.76 
Y C 0.70 
E C 0.65 
G C 0.76 
M C 0.76 
S C 0.76 
G C 0.85 
P C 0.63 
L C 0.39 
T E 0.52 
I E 0.61 
A E 0.53 
L C 0.55 
R C 0.86 
D C 0.88 
A C 0.70 
V C 0.50 
Y C 0.42 
A C 0.41 
R C 0.54 
END 
