PFRMAT SS 
TARGET T0054 
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 t54.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 33.2209 
METHOD 
METHOD There is a nice alignment of T0054 to 1hma that 
METHOD conflicts with this prediction of secondary structure: 
METHOD  T0054	RPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKG 
METHOD		CCCHHHHHHHHEEECCCCCCCCCCCCCCCHHHHHCECC 
METHOD	1HMA	KPKRPLSAYMLWLNSARESIKREN--PGIKVTEVAKRG 
METHOD		SLLLLLLHHHHHHHHHHHHHHHHT--TSLLHHHHHHHH 
METHOD We don't have particulary high confidence in either prediction of 
METHOD secondary structure. 
METHOD  
MODEL 1 
M C 0.88 
E C 0.81 
I C 0.79 
G C 0.64 
F E 0.57 
T E 0.60 
F E 0.53 
L C 0.40 
D H 0.55 
E H 0.65 
I H 0.49 
V C 0.75 
H C 0.85 
G C 0.82 
V C 0.60 
R E 0.49 
W E 0.53 
D E 0.53 
A E 0.50 
K E 0.51 
Y E 0.51 
A E 0.46 
T C 0.44 
W C 0.60 
D C 0.77 
N C 0.80 
F C 0.82 
T C 0.82 
G C 0.79 
K C 0.68 
P C 0.49 
V C 0.46 
D C 0.57 
G C 0.74 
Y C 0.73 
E C 0.56 
V C 0.45 
N H 0.51 
R H 0.49 
I H 0.46 
V H 0.46 
G C 0.49 
T H 0.70 
Y H 0.94 
E H 0.97 
L H 0.97 
A H 0.98 
E H 0.99 
S H 0.98 
L H 0.98 
L H 0.99 
K H 0.99 
A H 0.99 
K H 0.99 
E H 0.98 
L H 0.98 
A H 0.97 
A H 0.94 
T H 0.82 
Q C 0.51 
G C 0.77 
Y C 0.66 
G E 0.70 
L E 0.88 
L E 0.91 
L E 0.85 
W E 0.61 
D C 0.62 
G C 0.82 
Y C 0.87 
R C 0.92 
P C 0.83 
K H 0.57 
R H 0.80 
A H 0.83 
V H 0.86 
N H 0.84 
C H 0.74 
F H 0.58 
M H 0.44 
Q E 0.40 
W E 0.43 
A E 0.40 
A C 0.52 
Q C 0.83 
P C 0.89 
E C 0.92 
N C 0.93 
N C 0.84 
L C 0.65 
T C 0.59 
K C 0.65 
E C 0.64 
S C 0.64 
Y C 0.76 
Y C 0.82 
P C 0.81 
N C 0.55 
I H 0.75 
D H 0.79 
R H 0.76 
T H 0.66 
E H 0.51 
M C 0.36 
I E 0.42 
S C 0.45 
K C 0.51 
G C 0.67 
Y C 0.57 
V C 0.48 
A C 0.51 
S C 0.60 
K C 0.78 
S C 0.84 
S C 0.77 
H C 0.81 
S C 0.85 
R C 0.81 
G C 0.87 
S C 0.78 
A E 0.50 
I E 0.66 
D E 0.73 
L E 0.75 
T E 0.72 
L E 0.63 
Y E 0.47 
R C 0.54 
L C 0.69 
D C 0.69 
T C 0.61 
G C 0.56 
E E 0.54 
L E 0.72 
V E 0.72 
P E 0.58 
M C 0.67 
G C 0.89 
S C 0.83 
R C 0.68 
F C 0.57 
D H 0.51 
F H 0.65 
M H 0.69 
D H 0.76 
E H 0.82 
R H 0.77 
S H 0.75 
H H 0.69 
H H 0.58 
A H 0.53 
A H 0.45 
N C 0.52 
G C 0.61 
I C 0.68 
S C 0.67 
C H 0.55 
N H 0.79 
E H 0.89 
A H 0.92 
Q H 0.90 
N H 0.90 
R H 0.95 
R H 0.97 
R H 0.96 
L H 0.97 
R H 0.97 
S H 0.96 
I H 0.91 
M H 0.82 
E H 0.63 
N C 0.59 
S C 0.85 
G C 0.89 
F C 0.85 
E C 0.67 
A C 0.58 
Y C 0.50 
S C 0.47 
L C 0.44 
E E 0.51 
W E 0.60 
W E 0.67 
H E 0.73 
Y E 0.66 
V E 0.52 
L C 0.59 
R C 0.74 
D C 0.86 
E C 0.88 
P C 0.87 
Y C 0.88 
P C 0.80 
N C 0.57 
S E 0.56 
Y E 0.64 
F E 0.63 
D E 0.62 
F E 0.56 
P E 0.52 
V C 0.53 
K C 0.70 
END 
