PFRMAT AL 
TARGET T0044 
AUTHOR 5827-4749-3439 
REMARK HMM prediction for t0044 
METHOD Note: this alignment was generated automatically, and has not 
METHOD been hand-edited. 
METHOD Step 1: Using Psi-BLAST, we identified a set of 16 putative 
METHOD homologs to t0044 (one sequence was rejected because it was 
METHOD a short fragment). 
METHOD 
METHOD Step 2: We constructed an HMM using the UCSC SAM software, 
METHOD as follows. 
METHOD  2.1 We used modelfromalign to create an HMM from the 
METHOD t0044 sequence, treating the sequence as if it were an 
METHOD alignment, to effect a 1-1 correspondence between HMM 
METHOD positions and t0044 sequence positions. 
METHOD  2.2 We reestimated the HMM parameters of the model 
METHOD produced in step 2.1 in two stages. First, we using the 
METHOD training sequences found in iteration 0 of PSI-BLAST, 
METHOD disallowing model surgery (the insertion or deletion of 
METHOD nodes in the HMM), to retain the 1-1 correspondence between 
METHOD the HMM positions and t0044 sequence positions. Then we 
METHOD retrained the HMM using all the sequences, again, 
METHOD disallowing surgery, and employing Dirichlet mixture priors 
METHOD to increase sensitivity. 
METHOD 
METHOD Step 3: We scored a sequence version of PDB with the final 
METHOD HMM, using hmmscore and local-local alignment scoring 
METHOD (-swscore 2). 
METHOD 
METHOD Step 4: We scored each of the training set sequences against 
METHOD an HMM library for a non-redundant set of PDB structures, 
METHOD using the same method as in Step 3. We also ran t0044 
METHOD against the UCSC HMM library using their server, for 
METHOD comparison. 
METHOD 
METHOD Step 5: We identified subfamilies in the t0044 homologs 
METHOD using Bete (Sjolander's phylogenetic tree method, ISMB98 
METHOD proceedings), and constructed subfamily HMMs for each 
METHOD subfamily (unpublished method). The subfamily decomposition 
METHOD produced two subfamilies: subfamily 1 consisted of 
METHOD RTC1_CAEEL, RTC1_DROME, RTC1_SCHPO, and RTC1_YEAST. All 
METHOD other t0044 homologs, including t0044, were in subfamily 0. 
METHOD These subfamily HMMs were used to score PDB sequences. 
METHOD 
METHOD Steps 3-5 yielded a list of potential matches for us to 
METHOD examine. Several of the methods employed (especially the 
METHOD subfamily HMMs, and the use of the UCSC server) gave very 
METHOD strong scores to 1eps. (We also considered matches to other 
METHOD PDB structures, but none of these were convincing, and were 
METHOD not pursued.) 
METHOD 
METHOD We created a new search database with 1eps and t0044 
METHOD homologs added to a non-redundant PDB set. Subfamily HMM 
METHOD scores of these sequences ranked 1eps and several 1eps 
METHOD homologs above all non-t0044 homologs for both subfamilies. 
METHOD 
METHOD We then examined the alignments of t0044 sequences and 1eps 
METHOD sequences to each subfamily model, and the alignments of 
METHOD each family separately. This analysis suggested the pairwise 
METHOD alignment of t0044 and 1eps to the t0044 subfamily 1 model 
METHOD would be more likely from a structural standpoint. 
MODEL  1 
PARENT 1eps 
L   8    L  88 
D   9    E  89 
G  10    L  90 
A  11    F  91 
Q  12    L  92 
G  13    G  93 
E  14    N  94 
G  15    A  95 
G  16    G  96 
G  17    T  97 
Q  18    A  98 
I  19    M  99 
L  20    R 100 
R  21    P 101 
S  22    L 102 
A  23    A 103 
L  24    A 104 
S  25    A 105 
L  26    L 106 
S  27    C 107 
M  28    L 108 
I  29    G 109 
T  30    S 110 
G  31    N 111 
Q  32    D 112 
P  33    I 113 
F  34    V 114 
T  35    L 115 
I  36    T 116 
T  37    G 117 
S  38    E 118 
I  39    P 119 
R  40    R 120 
A  41    M 121 
G  42    K 122 
R  43    E 123 
A  44    R 124 
K  45    P 125 
P  46    I 126 
G  47    G 127 
Q  51    H 128 
H  52    L 129 
L  53    V 130 
T  54    D 131 
A  55    A 132 
V  56    L 133 
K  57    R 134 
A  58    L 135 
A  59    G 137 
T  60    A 138 
E  61    K 139 
I  62    I 140 
C  63    T 141 
G  64    Y 142 
A  65    L 143 
T  66    E 144 
V  67    Q 145 
E  68    E 146 
G  69    N 147 
F  79    Y 148 
R  80    P 149 
P  81    P 150 
G  82    L 151 
T  83    R 152 
V  84    L 153 
R  85    Q 154 
G  86    G 155 
G  87    G 156 
D  88    F 157 
Y  89    T 158 
R  90    N 161 
F  91    V 162 
A  92    D 163 
I  93    V 164 
G  94    D 165 
S  95    G 166 
A  96    S 167 
G  97    V 168 
S  98    S 169 
T 100    S 170 
L 101    Q 171 
V 102    F 172 
L 103    L 173 
Q 104    T 174 
T 105    A 175 
V 106    L 176 
L 107    L 177 
P 108    M 178 
A 109    T 179 
L 110    A 180 
W 111    P 181 
F 112    L 182 
A 113    A 183 
D 114    P 184 
G 115    E 185 
P 116    D 186 
S 117    T 187 
R 118    V 188 
V 119    I 189 
E 120    R 190 
V 121    I 191 
S 122    K 192 
G 123    G 193 
G 124    D 194 
T 125    L 195 
D 126    V 196 
N 127    S 197 
P 128    K 198 
S 129    P 199 
A 130    Y 200 
P 131    I 201 
P 132    D 202 
A 133    I 203 
L 140    T 204 
E 141    L 205 
P 142    N 206 
L 143    L 207 
L 144    M 208 
A 145    K 209 
K 146    T 210 
I 147    F 211 
G 148    G 212 
I 149    V 213 
H 150    E 214 
Q 151    I 215 
Q 152    E 216 
T 153    N 217 
T 154    Q 218 
A 169    H 219 
T 170    Y 220 
E 171    Q 221 
V 172    Q 222 
S 173    F 223 
P 174    V 224 
V 175    V 225 
A 176    K 226 
S 177    G 227 
F 178    G 228 
N 179    Q 229 
T 180    S 230 
L 181    Y 231 
Q 182    Q 232 
L 183    S 233 
G 187    P 234 
N 188    G 235 
I 189    T 236 
V 190    Y 237 
Q 191    L 238 
M 192    V 239 
R 193    E 240 
G 194    G 241 
E 195    D 242 
V 196    A 243 
L 197    S 244 
L 198    S 245 
V 201    A 246 
P 202    S 247 
R 203    Y 248 
H 204    F 249 
V 205    L 250 
A 206    A 251 
E 207    A 252 
R 208    A 253 
E 209    A 254 
I 210    I 255 
A 211    K 256 
T 212    G 257 
L 213    G 258 
A 214    T 259 
G 215    V 260 
S 216    G 264 
F 217    I 265 
S 218    G 266 
L 219    R 267 
H 220    N 268 
E 221    S 269 
Q 222    M 270 
N 223    Q 271 
I 224    G 272 
H 225    D 273 
N 226    I 274 
L 227    R 275 
P 228    F 276 
R 229    A 277 
D 230    D 278 
Q 231    V 279 
G 232    L 280 
P 233    E 281 
G 234    K 282 
N 235    M 283 
T 236    G 284 
V 237    A 285 
S 238    T 286 
L 239    I 287 
E 240    C 288 
E 244    W 289 
N 245    G 290 
I 246    D 291 
T 247    D 292 
E 248    Y 293 
R 249    I 294 
F 250    S 295 
F 251    C 296 
V 252    T 297 
V 253    R 298 
G 254    G 299 
E 255    E 300 
K 272    L 301 
R 273    N 302 
Y 274    A 303 
L 275    I 304 
A 276    D 305 
S 277    M 306 
T 278    D 307 
A 279    M 308 
A 280    N 309 
V 281    H 310 
G 282    I 311 
E 283    P 312 
Y 284    D 313 
L 285    A 314 
A 286    A 315 
D 287    M 316 
Q 288    T 317 
L 289    I 318 
V 290    A 319 
L 291    T 320 
P 292    A 321 
M 293    A 322 
A 294    L 323 
L 295    F 324 
A 296    A 325 
G 297    G 327 
A 298    T 328 
G 299    T 329 
E 300    R 330 
F 301    I 334 
T 302    Y 335 
V 303    N 336 
A 304    W 337 
H 305    R 338 
P 306    V 339 
S 307    K 340 
C 308    E 341 
H 309    T 342 
L 310    D 343 
L 311    R 344 
T 312    L 345 
N 313    F 346 
I 314    A 347 
A 315    M 348 
V 316    A 349 
V 317    T 350 
E 318    E 351 
R 319    L 352 
F 320    R 353 
L 321    K 354 
P 322    V 355 
V 323    G 356 
R 324    A 357 
F 325    E 358 
S 326    V 359 
L 327    E 360 
I 328    E 361 
E 329    G 362 
T 330    H 363 
D 331    D 364 
G 332    Y 365 
V 333    I 366 
T 334    R 367 
R 335    I 368 
V 336    T 369 
S 337    P 370 
I 338    P 371 
E 339    E 372 
G 340    K 373 
S 341    L 374 
H 342    N 375 
H 343    F 376 
H 344    A 377 
H 345    E 378 
H 346    I 379 
H 347    A 380 
TER 
END 
