PFRMAT AL 
TARGET T0063 
AUTHOR 7278-7379-8158 
METHOD	The method is based on a combination of hidden Markov models and 	 
METHOD	secondary structure prediction. Each HMM represents a structural family  
METHOD	of proteins and it is trained from known secondary structure sequences  
METHOD	of proteins belonging to the structural family. 
METHOD	Secondary structure prediction is performed for the target sequence  
METHOD	using several types of prediction algorithms (GOR, QL, PHD, etc.). The  
METHOD	predicted fold of the target protein is the fold described by the HMM  
METHOD	that fits one (or most) of the predicted secondary structure sequences  
METHOD	the best. 
METHOD	At present the library consists of about 300 HMMs 
METHOD	Di Francesco et al. JMB (1997) 267, 446-463 
METHOD	Di Francesco et al. Proteins, Supplement 1 (1997) 123-128 
REMARK	Chosen model: 1fnd, dom 1 (residues 19 - 151). Nitrate reductase 
REMARK	SIMPA with alignment of homologues prediction used for the alignment 
MODEL  1 
PARENT 1fnd 
G       20      P     37 
S       21      Y     38 
Y       22      V     39 
V       23      G     40 
V       24      R     41 
I       25      C     42 
D       26      L     43 
G       27      P     54 
E       28      G     55 
P       29      E     56 
C       30      T     57 
R       31      W     58 
V       32      H     59 
V       33      M     60 
E       34      V     61 
I       35      F     62 
E       36      S     63 
K       37      H     64 
S       38      E     65 
K       39      G     66 
T       40      E     67 
G       41      I     68 
K       42      P     69 
H       43      Y     70 
G       44      R     71 
S       45      E     72 
A       46      G     73 
K       47      Q     74 
A       48      S     75 
R       49      V     76 
I       50      G     77 
V       51      V     78 
A       52      I     79 
V       53      P     80 
G       54      D     81 
K       60      L     92 
R       61      R     93 
T       62      L     94 
L       63      Y     95 
S       64      S     96 
L       65      I     97 
P       66      A     98 
F       79      D    107 
T       80      A    108 
A       81      K    109 
Q       82      S    110 
I       83      V    111 
L       84      S    112 
S       85      L    113 
V       86      C    114 
S       87      V    115 
G       88      K    116 
D       89      R    117 
Y       108     G    130 
V       109     V    131 
E       110     C    132 
E       111     S    133 
E       112     N    134 
A       113     F    135 
K       114     L    136 
G       115     C    137 
R       116     D    138 
L       117     L    139 
A       118     K    140 
Y       132     V    145 
K       133     K    146 
I       134     L    147 
I       135     T    148 
R       136     G    149 
V       137     P    150 
K       138     V    151 
TER 
END 
