PFRMAT SS 
TARGET T0043 
AUTHOR 1751-3146-3362 
METHOD Using neural net fssp-12345-IDaa13-9-6-11-9-3-8-7-ehl-seeded2-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 ( EHC ) 
METHOD The input amino acid frequencies were determined from 
METHOD alignment t43.remote_2.a2m.gz 
METHOD with weighted counts, using HenikoffWeight(1.3 bits/column, 0.6) 
METHOD The weighting was determined by the posterior distribution 
METHOD after regularizing with recode2.20comp. 
METHOD Counts were regularized to probabilities using 
METHOD /projects/compbio/lib/recode2.20comp 
METHOD Total sequence weight for alignment was 30.9529 
METHOD 
METHOD Based on alignments to 1gcmA and 2end, we expect the 
METHOD helices at APEELLNHTQRIELQQGRVRKAER to be a single helix. 
METHOD (Note: an alignment to 1ris contradicts this, and 
METHOD suggests a very different secondary structure from what the 
METHOD neural net predicts: 
METHOD T0043	NHTQRIELQQGRVRKAERWGPRTLDLDI 
METHOD		HHHHHHHHTTLEEEEEEEEEEEEEEEEE 
METHOD 1ris	IIQRALENYGARVEKVEELGLRRLAYPI 
METHOD 
MODEL 1 
T C 0.83 
V E 0.62 
A E 0.90 
Y E 0.95 
I E 0.95 
A E 0.92 
I E 0.77 
G C 0.56 
S C 0.77 
N C 0.78 
L C 0.76 
A C 0.70 
S C 0.49 
P H 0.78 
L H 0.94 
E H 0.98 
Q H 0.98 
V H 0.99 
N H 0.99 
A H 1.00 
A H 0.99 
L H 0.99 
K H 0.99 
A H 0.98 
L H 0.96 
G H 0.90 
D H 0.79 
I C 0.52 
P C 0.80 
E C 0.82 
S C 0.60 
H E 0.68 
I E 0.81 
L E 0.80 
T E 0.71 
V E 0.55 
S C 0.50 
S C 0.43 
F C 0.39 
Y C 0.44 
R C 0.54 
T C 0.75 
P C 0.91 
P C 0.89 
L C 0.77 
G C 0.75 
P C 0.73 
Q C 0.70 
D C 0.80 
Q C 0.83 
P C 0.71 
D C 0.53 
Y C 0.48 
L C 0.38 
N C 0.37 
A E 0.50 
A E 0.69 
V E 0.74 
A E 0.78 
L E 0.70 
E C 0.46 
T C 0.67 
S C 0.68 
L C 0.69 
A C 0.85 
P H 0.64 
E H 0.93 
E H 0.98 
L H 0.97 
L H 0.98 
N H 0.99 
H H 0.98 
T H 0.98 
Q H 0.97 
R H 0.93 
I H 0.92 
E H 0.93 
L H 0.90 
Q H 0.80 
Q H 0.57 
G C 0.58 
R C 0.46 
V H 0.48 
R H 0.62 
K H 0.72 
A H 0.72 
E H 0.59 
R C 0.52 
W C 0.79 
G C 0.92 
P C 0.93 
R C 0.79 
T C 0.66 
L C 0.56 
D C 0.49 
L E 0.43 
D E 0.49 
I E 0.50 
M E 0.48 
L E 0.45 
F C 0.59 
G C 0.77 
N C 0.64 
E C 0.48 
V C 0.45 
I C 0.49 
N C 0.61 
T C 0.68 
E C 0.70 
R C 0.63 
L C 0.52 
T C 0.52 
V C 0.69 
P C 0.84 
H C 0.70 
Y C 0.51 
D H 0.46 
M H 0.48 
K C 0.44 
N C 0.57 
R C 0.55 
G C 0.50 
F C 0.49 
M E 0.39 
L E 0.35 
W H 0.38 
P H 0.44 
L H 0.82 
F H 0.89 
E H 0.88 
I H 0.55 
A C 0.76 
P C 0.73 
E C 0.56 
L C 0.56 
V C 0.61 
F C 0.71 
P C 0.85 
D C 0.84 
G H 0.56 
E H 0.84 
M H 0.80 
L H 0.92 
R H 0.97 
Q H 0.98 
I H 0.97 
L H 0.96 
H H 0.95 
T H 0.92 
R H 0.74 
A C 0.54 
F C 0.64 
D C 0.70 
K C 0.71 
L C 0.69 
N C 0.73 
K C 0.76 
W C 0.79 
END 
