PFRMAT AL 
TARGET T0068 
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: 1rmg, which is a parallel beta helix with fold similar 
REMARK  to the fold of pectate lyases. 
REMARK  The sec. structure prediction used for the alignment is a 
REMARK  consensus prediction of several predicted secondary structure 
REMARK  sequences.  
MODEL   1 
PARENT  1rmg 
T       150     G    126 
P       151     A    127 
R       152     R    128 
L       153     I    129 
I       154     L    130 
Q       155     R    131 
I       156     L    132 
N       157     T    133 
K       158     D    134 
S       159     V    135 
K       160     T    136 
N       161     H    137 
F       162     F    138 
T       163     S    139 
L       164     V    140 
Y       165     H    141 
N       166     D    142 
V       167     I    143 
S       168     I    144 
L       169     L    145 
I       170     V    146 
N       171     D    147 
S       172     A    148 
P       173     P    149 
N       174     A    150 
F       175     F    151 
H       176     H    152 
V       177     F    153 
V       178     T    154 
F       179     M    155 
S       180     D    156 
D       181     T    157 
G       182     C    158 
D       183     S    159 
G       184     D    160 
F       185     G    161 
T       186     E    162 
A       187     V    163 
W       188     Y    164 
K       189     N    165 
T       190     M    166 
T       191     A    167 
I       192     I    168 
K       193     R    169 
T       194     G    170 
P       195     G    171 
D       205     G    178 
P       206     I    179 
M       207     D    180 
S       208     V    181 
S       209     W    182 
K       210     G    183 
N       211     S    184 
I       212     N    185 
T       213     I    186 
I       214     W    187 
A       215     V    188 
Y       216     H    189 
S       217     D    190 
N       218     V    191 
I       219     E    192 
A       220     V    193 
T       221     T    194 
G       222     N    195 
D       223     K    196 
D       224     D    197 
N       225     E    198 
V       226     C    199 
A       227     V    200 
I       228     T    201 
K       229     V    202 
A       230     K    203 
Y       231     S    204 
K       232     P    205 
G       233     A    206 
R       234     N    207 
A       235     N    208 
E       236     I    209 
T       237     L    210 
R       238     V    211 
N       239     E    212 
I       240     S    213 
S       241     I    214 
I       242     Y    215 
L       243     C    216 
H       244     N    217 
N       245     W    218 
G       248     G    220 
T       249     G    221 
G       250     C    222 
H       251     A    223 
G       252     M    224 
M       253     G    225 
S       254     S    226 
I       255     L    227 
G       256     G    228 
S       257     A    229 
E       258     D    230 
T       259     T    231 
M       260     D    232 
G       261     V    233 
V       262     T    234 
Y       263     D    235 
N       264     I    236 
V       265     V    237 
T       266     Y    238 
V       267     R    239 
D       268     N    240 
D       269     V    241 
L       270     Y    242 
K       271     T    243 
M       272     W    244 
N       273     S    245 
G       274     S    246 
T       275     N    247 
T       276     Q    248 
N       277     M    249 
G       278     Y    250 
L       279     M    251 
R       280     I    252 
I       281     K    253 
K       282     S    254 
S       283     N    255 
D       284     G    256 
K       285     G    257 
S       286     S    258 
A       287     G    259 
A       288     T    260 
G       289     V    261 
V       290     S    262 
V       291     N    263 
N       292     V    264 
G       293     L    265 
V       294     L    266 
R       295     E    267 
Y       296     N    268 
S       297     F    269 
N       298     I    270 
V       299     G    271 
V       300     H    272 
M       301     G    273 
K       302     N    274 
N       303     A    275 
V       304     Y    276 
A       305     S    277 
K       306     L    278 
P       307     D    279 
I       308     I    280 
V       309     D    281 
I       310     G    282 
D       311     Y    283 
D       324     V    295 
W       325     Q    296 
S       326     L    297 
D       327     N    298 
I       328     N    299 
T       329     I    300 
F       330     T    301 
K       331     V    302 
D       332     K    303 
G       339     N    304 
V       340     W    305 
V       341     K    306 
V       342     G    307 
L       343     T    308 
N       344     E    309 
G       345     A    310 
E       346     N    311 
N       347     G    312 
A       348     A    313 
K       349     T    314 
K       350     R    315 
P       351     P    316 
I       352     P    317 
E       353     I    318 
V       354     R    319 
T       355     V    320 
M       356     V    321 
K       357     C    322 
TER 
END 
