PFRMAT AL 
TARGET T0068 
AUTHOR 5827-4749-3439 
REMARK HMM prediction for t0068 
METHOD Note: this alignment was generated automatically, and has not 
METHOD been hand-edited, except to unalign a total of 14 residues that 
METHOD were in segments that were clearly poorly gapped (indicated by 
METHOD '*' above the residues of t0068): 
METHOD 
METHOD >T0068, 767 bases, C82FE547 checksum. 
METHOD ---------------------------------------SDSRTVSEPKT 
METHOD                          *** 
METHOD PSSCTTLKADSSTATSTIQ------KAL---------------------- 
METHOD --------------------NNCDQGKAVRLSAGSTSVFL--SGPLSLPS 
METHOD GVSLLIDKgVTLRAvNNAKSFENAPSSCGVVDKNGKGCDAFITAV--STT 
METHOD         **  * 
METHOD N-------SGIYG-PGTIDGQGGVKLQDKkvswwELAADAKVKKLKQNTP 
METHOD RLIQINK--SKNFTLYNVSLINSPNFHVVFSDGDGFTAWKTTIKTPSTA- 
METHOD ---RNTDGIDPMSSKNITIAYSNIATGDDNVAIkayKGRAETRNISILHN 
METHOD DFGTGHGM-SIGSETMGV---YNVTVDDLKMNGTT--------------- 
METHOD --NGLRIKSDKS-------------AAGVVNGVRYSNVVMKNVAKPIVID 
METHOD                               **   * 
METHOD TVYEK--KEGSNVP----DWSDITFKDV--TS---ETKGVVVLNGENAKK 
METHOD PIEVTMKNVKLTSDS----------------------------------- 
METHOD                                       ***** 
METHOD --------------------------------------TWQIK------- 
METHOD -------------------------------------------------- 
METHOD -------------------------------------------------- 
METHOD -------------------------------------------------- 
METHOD -----------NVNVKK 
METHOD >gi|2981975|pdb|1RMG|, 767 bases, 209A77F3 checksum. 
METHOD -----------------------------------------------QLS 
METHOD GSVGPLTSASTKGATKTCNILSYGAVAD---------------------- 
METHOD --------------------NSTDVG-PAITSAWAACKSG---GLVYIPS 
METHOD GNYALNTW.VTLTG.----GSATAIQLDGIIYRTGTASGNMIAVT--DTT 
METHOD DFELFSSTSK--G---AVQGFGYVYHAEG.....------------TYGA 
METHOD RILRLTD--VTHFSVHDIILVDAPAFHFTMDTCSDGEVYNMAIRGGNEG- 
METHOD ----GLDGIDVWG-SNIWVHDVEVTNKDECVTV...KSPANNILVESIYC 
METHOD NWSGGCAMGSLGADTDVT----DIVYRNVYTWSSN--------------- 
METHOD --QMYMIKSNGG--------------SGTVSNVLLENFIGHGNAYSLDID 
METHOD GYWSS----MTAVAGDGVQLNNITVKNWKGTEANGATRPPIRVVCSDTAP 
METHOD CTDLTLEDIAIWTESG-------------------------------S-- 
METHOD -------SELYLCRSAYGSGYCLK-DSSSHTSY-TTTSTVTAAPSGYSAT 
METHOD TMAADLATAFGLTASIPIPTIPTSFYPGLTPYSALAG------------- 
METHOD -------------------------------------------------- 
METHOD -------------------------------------------------- 
METHOD ----------------- 
METHOD 
METHOD As usual, we employed a two-pronged approach: (1) We scored the 
METHOD target against all the HMMs in our HMM library, and (2) we 
METHOD gathered homologs to the target using PsiBLAST, constructed an 
METHOD HMM for the target and homologs (using UCSC's HMM software), and 
METHOD scored PDB. This yielded two sets of scores, which we then used 
METHOD to find a target-structure match. 
METHOD 
METHOD Both PsiBLAST and hmmscores against PDB gave 1RMG strong scores. 
METHOD The subsequent mailing from CASP organizers confirmed this match. 
METHOD (We didn't have an HMM for 1RMG in our library.) 
METHOD 
METHOD The alignment submitted was created by aligning the target and structure 
METHOD to an HMM constructed as follows: (1) converting a Clustal 
METHOD alignment  of 1RMG and BLAST-identified homologs into an HMM using 
METHOD modelfromalign from the UCSC SAM software suite, (2) phylogenetic 
METHOD analysis and subfamily-HMM construction for 1RMG subfamilies 
METHOD based on this alignment; 
METHOD (3) scoring t0068 against each subfamily HMM; 
METHOD (4) aligning t0068 and 1RMG to the subfamily HMM which gave 
METHOD both the target and structure high probability. 
MODEL  1 
PARENT 1rmg 
P   9    Q   1 
K  10    L   2 
T  11    S   3 
P  12    G   4 
S  13    S   5 
S  14    V   6 
C  15    G   7 
T  16    P   8 
T  17    L   9 
L  18    T  10 
K  19    S  11 
A  20    A  12 
D  21    S  13 
S  22    T  14 
S  23    K  15 
T  24    G  16 
A  25    A  17 
T  26    T  18 
S  27    K  19 
T  28    T  20 
I  29    C  21 
Q  30    N  22 
N  34    N  32 
N  35    S  33 
C  36    T  34 
D  37    D  35 
Q  38    V  36 
G  39    G  37 
A  41    P  38 
V  42    A  39 
R  43    I  40 
L  44    T  41 
S  45    S  42 
A  46    A  43 
G  47    W  44 
S  48    A  45 
T  49    A  46 
S  50    C  47 
V  51    K  48 
F  52    S  49 
L  53    G  50 
G  55    G  51 
P  56    L  52 
L  57    V  53 
S  58    Y  54 
L  59    I  55 
P  60    P  56 
S  61    S  57 
G  62    G  58 
V  63    N  59 
S  64    Y  60 
L  65    A  61 
L  66    L  62 
I  67    N  63 
D  68    T  64 
K  69    W  65 
V  71    V  66 
T  72    T  67 
L  73    L  68 
R  74    T  69 
A  75    G  70 
S  81    G  71 
F  82    S  72 
E  83    A  73 
N  84    T  74 
A  85    A  75 
P  86    I  76 
S  87    Q  77 
S  88    L  78 
C  89    D  79 
G  90    G  80 
V  91    I  81 
V  92    I  82 
D  93    Y  83 
K  94    R  84 
N  95    T  85 
G  96    G  86 
K  97    T  87 
G  98    A  88 
C  99    S  89 
D 100    G  90 
A 101    N  91 
F 102    M  92 
I 103    I  93 
T 104    A  94 
A 105    V  95 
V 106    T  96 
S 107    D  97 
T 108    T  98 
T 109    T  99 
N 110    D 100 
T 118    A 111 
I 119    V 112 
D 120    Q 113 
G 121    G 114 
Q 122    F 115 
G 123    G 116 
G 124    Y 117 
V 125    V 118 
K 126    Y 119 
L 127    H 120 
Q 128    A 121 
D 129    E 122 
K 130    G 123 
Q 148    T 124 
N 149    Y 125 
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 
S 196    N 172 
T 197    E 173 
A 198    G 174 
N 200    G 175 
T 201    L 176 
D 202    D 177 
G 203    G 178 
I 204    I 179 
D 205    D 180 
P 206    V 181 
M 207    W 182 
S 208    G 183 
K 210    S 184 
N 211    N 185 
I 212    I 186 
T 213    W 187 
I 214    V 188 
A 215    H 189 
Y 216    D 190 
S 217    V 191 
N 218    E 192 
I 219    V 193 
A 220    T 194 
T 221    N 195 
G 222    K 196 
D 223    D 197 
D 224    E 198 
N 225    C 199 
V 226    V 200 
A 227    T 201 
I 228    V 202 
K 232    K 203 
G 233    S 204 
R 234    P 205 
A 235    A 206 
E 236    N 207 
T 237    N 208 
R 238    I 209 
N 239    L 210 
I 240    V 211 
S 241    E 212 
I 242    S 213 
L 243    I 214 
H 244    Y 215 
N 245    C 216 
D 246    N 217 
F 247    W 218 
G 248    S 219 
T 249    G 220 
G 250    G 221 
H 251    C 222 
G 252    A 223 
M 253    M 224 
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 
N 264    D 235 
V 265    I 236 
T 266    V 237 
V 267    Y 238 
D 268    R 239 
D 269    N 240 
L 270    V 241 
K 271    Y 242 
M 272    T 243 
N 273    W 244 
G 274    S 245 
T 275    S 246 
T 276    N 247 
N 277    Q 248 
G 278    M 249 
L 279    Y 250 
R 280    M 251 
I 281    I 252 
K 282    K 253 
S 283    S 254 
D 284    N 255 
K 285    G 256 
S 286    G 257 
A 288    S 258 
G 289    G 259 
V 290    T 260 
V 291    V 261 
N 292    S 262 
G 293    N 263 
V 294    V 264 
R 295    L 265 
Y 296    L 266 
S 297    E 267 
N 298    N 268 
V 299    F 269 
V 300    I 270 
M 301    G 271 
K 302    H 272 
N 303    G 273 
V 304    N 274 
A 305    A 275 
K 306    Y 276 
P 307    S 277 
I 308    L 278 
V 309    D 279 
I 310    I 280 
D 311    D 281 
T 312    G 282 
V 313    Y 283 
Y 314    W 284 
E 315    S 285 
K 316    S 286 
G 319    M 287 
S 320    T 288 
N 321    A 289 
V 322    V 290 
P 323    A 291 
D 324    Q 296 
W 325    L 297 
S 326    N 298 
D 327    N 299 
I 328    I 300 
T 329    T 301 
F 330    V 302 
K 331    K 303 
D 332    N 304 
V 333    W 305 
T 337    T 314 
K 338    R 315 
G 339    P 316 
V 340    P 317 
V 341    I 318 
V 342    R 319 
L 343    V 320 
N 344    V 321 
G 345    C 322 
E 346    S 323 
N 347    D 324 
A 348    T 325 
K 349    A 326 
K 350    P 327 
P 351    C 328 
I 352    T 329 
E 353    D 330 
V 354    L 331 
T 355    T 332 
M 356    L 333 
K 357    E 334 
N 358    D 335 
V 359    I 336 
K 360    A 337 
L 361    I 338 
T 362    W 339 
S 363    T 340 
D 364    E 341 
S 365    S 342 
TER 
END 
