PFRMAT AL 
TARGET T0057 
AUTHOR 9070-5088-8627 
METHOD Overview 
METHOD  
METHOD Fold recognition was performed using the Target98 (SAM-T98) method 
METHOD [3] using SAM version 2.1.1 [1], a refinement of the methods developed 
METHOD by this group for CASP2 [2].  This method attempts to find and multiply  
METHOD align a set of homologs to a given sequence, then create an HMM from that  
METHOD multiple alignment. 
METHOD  
METHOD First, a set of sequence weights is determined from the alignment.  Next,  
METHOD Modelfromalign is used to build the model from the alignment and the  
METHOD sequence weights.  Finally, hmmscore performs a local, all-paths scoring  
METHOD of the sequences, using a reversed-sequence normalization feature. 
METHOD  
METHOD The weighting method, detailed in upcoming publications [3,4], 
METHOD combines the Henikoffs' scheme [5], Dirichlet mixtures [6], and an 
METHOD entropy method to set the final weights. 
METHOD  
METHOD Alignment generation 
METHOD  
METHOD The initial step uses BLASTP to search NRP twice: once to produce a set 
METHOD of very close homologs, and once to produce a set of possible homologs. 
METHOD  
METHOD The method then uses multiple iterations of a selection, training, and  
METHOD alignment procedure.  Each iteration involves an initial alignment, a set  
METHOD of search sequences, a threshold value, and a transition regularizer.  
METHOD  
METHOD The first iteration uses a single sequence (or seed alignment) as the  
METHOD initial alignment and the close homologs found by BLASTP are used as the  
METHOD search set.  The threshold is set very strictly, so that only good matches  
METHOD to the sequence are considered.  This iteration uses a transition regularizer  
METHOD that was designed to match the gap costs used by BLASTP. 
METHOD  
METHOD On subsequent iterations the input alignment is the output from the 
METHOD previous iteration, the search set is the larger set of possible 
METHOD homologs found by BLASTP, and the thresholds are gradually loosened. 
METHOD The second through second-from-last iteration use a ``long-match'' 
METHOD transition regularizer, and the final iteration uses a transition regularizer  
METHOD trained on FSSP alignments. 
METHOD  
METHOD References 
METHOD [1] R. Hughey and A. Krogh, CABIOS 12(2): 95-107, 1996. 
METHOD     http://www.cse.ucsc.edu/research/compbio/sam.html.   
METHOD [2] K. Karplus, K. Sjolander, C. Barrett, M. Cline, D. Haussler, R. 
METHOD     Hughey, L. Holm, and C. Sander, Proteins: Structure, Function, and  
METHOD     Genetics, Suppl. 1, 134-9, 1997. 
METHOD [3] K. Karplus, C. Barrett, and R. Hughey, Technical Report UCSC-CRL-98-06, 
METHOD     Department of Computer Engineering, Univ. of California, Santa Cruz, 1998. 
METHOD [4] J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, 
METHOD     and C. Chothia, http://cyrah.med.harvard.edu/~jong/assess_final.html, 1998. 
METHOD [5] S. Henikoff and J. C. Henikoff, JMB, vol 243, pp 574-578, Nov 1994. 
METHOD [6] K. Sjolander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S. 
METHOD    Mian, and D. Haussler, CABIOS 12(4):327-345, 1996. 
METHOD  
METHOD  
METHOD Wu-blast found 1dapA as a reasonably close homolog, but double-blast 
METHOD found 1gadP (with intermediate sequence G3P_METBR from Swissprot) to 
METHOD be a better match.  Our target HMM scored 1gadP best, but the library 
METHOD HMM scored 1dapA best.  The 1gadP sequence does not have a model in 
METHOD our library, though 1gypA (the FSSP representative for 1gadP) scored 
METHOD fairly well.  Summing both ways, the top hits were 1gd1O, 1dapA, and 
METHOD 1gadP, all with scores well into the region where we had fewer than 1% 
METHOD false positives in our superfamily-recognition tests. 
METHOD  
METHOD The 1gd1O and 1gadP alignments looked OK, but needed extensive hand 
METHOD editing.  We finally chose a 1gd1O alignment as having the most 
METHOD reasonable gaps.  The binding site for NAD is well preserved in both, 
METHOD as is the beta sheet for the dimerization site. 
MODEL 1 
PARENT 1gd1_O 
M 1 A 0 
I 2 V 1 
N 3 K 2 
V 4 V 3 
A 5 G 4 
V 6 I 5 
N 7 N 6 
G 8 G 7 
Y 9 F 8 
G 10 G 9 
T 11 R 10 
I 12 I 11 
G 13 G 12 
K 14 R 13 
R 15 N 14 
V 16 V 15 
A 17 F 16 
D 18 R 17 
A 19 A 18 
I 20 A 19 
I 21 L 20 
K 22 K 21 
Q 23 N 22 
P 24 P 23 
D 25 D 24 
M 26 I 25 
K 27 E 26 
L 28 V 27 
V 29 V 28 
G 30 A 29 
V 31 V 30 
A 32 N 31 
K 33 D 32 
T 34 T 34 
S 35 D 36 
P 36 A 37 
N 37 N 38 
Y 38 T 39 
E 39 L 40 
A 40 A 41 
F 41 H 42 
I 42 L 43 
A 43 L 44 
H 44 K 45 
R 45 Y 46 
R 46 L 53 
G 47 D 54 
I 48 A 55 
R 49 E 56 
I 50 V 57 
Y 51 S 58 
V 52 V 59 
P 53 N 60 
Q 54 G 61 
Q 55 N 62 
S 56 N 63 
I 57 L 64 
K 58 V 65 
K 59 V 66 
F 60 N 67 
E 61 G 68 
E 62 K 69 
S 63 E 70 
G 64 I 71 
I 65 I 72 
P 66 V 73 
V 67 K 74 
A 68 A 75 
G 69 E 76 
T 70 R 77 
V 71 D 78 
E 72 P 79 
D 73 E 80 
L 74 N 81 
I 75 L 82 
K 76 A 83 
T 77 W 84 
S 78 G 85 
D 79 E 86 
I 80 I 87 
V 81 G 88 
V 82 V 89 
D 83 D 90 
T 84 I 91 
T 85 V 92 
P 86 V 93 
N 87 E 94 
G 88 S 95 
V 89 T 96 
G 90 G 97 
A 91 R 98 
Q 92 F 99 
Y 93 T 100 
K 94 K 101 
P 95 R 102 
I 96 E 103 
Y 97 D 104 
L 98 A 105 
Q 99 A 106 
L 100 K 107 
Q 101 H 108 
R 102 K 114 
N 103 K 115 
A 104 V 116 
I 105 I 117 
F 106 I 118 
Q 107 S 119 
G 108 A 120 
G 109 P 121 
E 110 A 122 
K 111 K 122A 
A 112 N 123 
E 113 E 124 
V 114 D 125 
A 115 I 126 
D 116 T 127 
I 117 I 128 
S 118 V 129 
F 119 M 130 
S 120 G 131 
A 121 V 132 
L 122 N 133 
C 123 Q 134 
N 124 D 135 
Y 125 K 136 
N 126 Y 137 
E 127 D 138 
A 128 P 138A 
L 129 K 139 
G 130 A 140 
K 131 H 141 
K 132 H 142 
Y 133 V 143 
I 134 I 144 
R 135 S 145 
V 136 N 146 
V 137 A 147 
S 138 S 148 
C 139 C 149 
N 140 T 150 
T 141 T 151 
T 142 N 152 
A 143 C 153 
L 144 L 154 
L 145 A 155 
R 146 P 156 
T 147 F 157 
I 148 A 158 
C 149 K 159 
T 150 V 160 
V 151 L 161 
N 152 H 162 
K 153 E 163 
V 154 Q 164 
S 155 F 165 
K 156 G 166 
V 157 I 167 
E 158 V 168 
K 159 R 169 
V 160 G 170 
R 161 M 171 
A 162 M 172 
T 163 T 173 
I 164 T 174 
V 165 V 175 
R 166 H 176 
R 167 S 177 
A 168 T 179 
A 169 N 180 
D 170 D 181 
Q 171 Q 182 
K 172 R 183 
E 173 I 184 
V 174 L 185 
K 175 D 186 
G 177 L 187 
P 178 P 188 
I 179 H 190 
N 180 K 191 
S 181 D 192 
L 182 L 193 
V 183 R 194 
P 184 R 195 
D 185 A 196 
P 186 R 197 
A 187 A 198 
T 188 A 199 
V 189 A 200 
P 190 E 201 
S 191 S 202 
H 192 G 209 
H 193 A 210 
A 194 A 211 
K 195 K 212 
D 196 A 213 
V 197 V 214 
N 198 A 215 
S 199 L 216 
V 200 V 217 
I 201 L 218 
R 202 P 219 
N 203 E 220 
L 204 L 221 
D 205 K 222 
I 206 L 225 
A 207 N 226 
T 208 G 227 
M 209 M 228 
A 210 A 229 
V 211 M 230 
I 212 R 231 
A 213 V 232 
P 214 P 233 
T 215 T 234 
T 216 P 235 
L 217 N 236 
M 218 V 237 
H 219 S 238 
M 220 V 239 
H 221 V 240 
F 222 D 241 
I 223 L 242 
N 224 V 243 
I 225 A 244 
T 226 E 245 
L 227 L 246 
K 228 E 247 
D 229 K 248 
K 230 E 249 
V 231 V 250 
E 232 T 251 
K 233 V 252 
K 234 E 253 
D 235 E 254 
I 236 V 255 
L 237 N 256 
S 238 A 257 
V 239 A 258 
L 240 L 259 
E 241 K 260 
N 242 A 261 
T 243 A 262 
P 244 A 263 
R 245 E 264 
S 250 G 265 
S 251 E 266 
K 252 L 267 
Y 253 K 268 
D 254 G 269 
A 255 I 270 
E 256 L 271 
A 257 A 272 
T 258 Y 273 
A 259 S 274 
E 260 E 275 
L 261 E 276 
V 262 P 277 
E 263 L 278 
V 264 V 279 
A 265 S 280 
R 266 R 281 
D 267 D 282 
L 268 Y 283 
K 269 N 284 
R 270 G 285 
D 271 S 286 
R 272 T 287 
N 273 V 288 
D 274 S 289 
I 275 S 290 
P 276 T 291 
E 277 I 292 
V 278 D 293 
M 279 A 294 
I 280 L 295 
F 281 S 296 
S 282 T 297 
D 283 M 298 
S 284 V 299 
I 285 I 300 
Y 286 D 301 
V 287 G 302 
K 288 K 303 
D 289 M 304 
D 290 V 305 
E 291 K 306 
V 292 V 307 
M 293 V 308 
L 294 S 309 
M 295 W 310 
Y 296 Y 311 
A 297 D 312 
V 298 N 313 
H 299 E 314 
Q 300 T 315 
E 301 G 316 
S 302 Y 317 
I 303 S 318 
V 304 H 319 
V 305 R 320 
P 306 V 321 
E 307 V 322 
N 308 D 323 
I 309 L 324 
D 310 A 325 
A 311 A 326 
I 312 Y 327 
R 313 I 328 
A 314 A 329 
S 315 S 330 
M 316 K 331 
K 317 G 332 
L 318 L 333 
TER 
END 
