PFRMAT AL 
TARGET T0074 
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: 1fliA, which is a non bundle small helical protein 
REMARK  with a helix-loop-helix motif which resembles the motif of 
REMARK  calcium binding proteins. 1fliA is a DNA binding protein. 
REMARK  The sec. structure prediction used for the alignment is a 
REMARK  SIMPA prediction w/o homologues. 
MODEL   1 
PARENT  1fli_A 
E       127     Q    282 
D       128     L    283 
K       129     W    284 
A       130     Q    285 
K       131     F    286 
Y       132     L    287 
D       133     L    288 
A       134     E    289 
I       135     L    290 
F       136     L    291 
D       137     S    292 
S       138     D    293 
G       144     C    299 
F       145     I    300 
L       146     T    301 
S       147     W    302 
G       148     E    303 
D       149     G    304 
K       150     T    305 
V       151     N    306 
K       152     G    307 
P       153     E    308 
V       154     F    309 
L       155     K    310 
L       156     M    311 
N       157     T    312 
L       160     D    313 
P       161     P    314 
V       162     D    315 
D       163     E    316 
I       164     V    317 
L       165     A    318 
G       166     R    319 
R       167     R    320 
V       168     W    321 
W       169     G    322 
E       170     E    323 
L       171     R    324 
S       172     K    325 
D       173     S    326 
L       180     M    330 
D       181     N    331 
R       182     Y    332 
D       183     D    333 
E       184     K    334 
F       185     L    335 
A       186     S    336 
V       187     R    337 
A       188     A    338 
M       189     L    339 
F       190     R    340 
L       191     Y    341 
V       192     Y    342 
Y       193     Y    343 
C       194     D    344 
A       195     K    345 
L       196     N    346 
E       197     I    347 
TER 
END 
