# List of top-scoring protein chains for t06-100-30-n_sep-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1mugA 168 3.17e-02 1mugA c.18.1.2 31030 1qynA 153 3.92e-02 d.33.1.1 96597 1z54A 132 2.64e-01 1oshA 232 3.94e-01 a.123.1.1 93496 1fcyA 236 4.02e-01 2lbd a.123.1.1 19282 1ijbA 202 4.49e-01 c.62.1.1 71229 1qysA 106 4.74e-01 k.41.1.1 96603 1rz1A 161 5.21e-01 b.45.1.2 98124 1yvoA 172 5.74e-01 1u6zA 513 6.43e-01 2ggcA 263 6.91e-01 1ttuA 477 7.34e-01 b.1.18.1,b.2.5.8,b.42.7.1 107305,107306,107307 1yqtA 538 8.06e-01 1zsoA 164 8.61e-01 1oxxK 353 9.61e-01 b.40.6.3,c.37.1.12 93715,93716 1xnzA 264 1.01e+00 1zcbA 362 1.19e+00 1dqiA 124 1.36e+00 1do6A b.1.13.1 22357 7odcA 424 1.38e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 1oqjA 97 1.42e+00 d.217.1.1 93417 1y9wA 140 1.58e+00 1gtmA 419 1.66e+00 1hwyA c.2.1.7,c.58.1.1 30223,33871 1o0xA 262 1.83e+00 d.127.1.1 80755 1wywA 230 1.85e+00 1k3xA 262 1.93e+00 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1fl1A 230 2.01e+00 1at3A b.57.1.1 27023 2g6yA 217 2.13e+00 1tf1A 198 2.21e+00 d.110.2.2 106826 1oj4A 283 2.34e+00 d.14.1.5,d.58.26.5 93083,93084 1jp4A 308 2.37e+00 1jp4A e.7.1.1 63223 1ryp2 233 2.48e+00 1ryp2 1z4rA 168 2.51e+00 2c43A 323 2.58e+00 1o69A 394 2.68e+00 c.67.1.4 92560 1jk7A 323 2.73e+00 1auiA d.159.1.3 63144 2gx9A 129 2.75e+00 1jhdA 396 2.79e+00 b.122.1.3,c.26.1.5 66712,66713 1sr9A 644 2.81e+00 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 2fvvA 194 3.02e+00 1uyjA 296 3.07e+00 f.8.1.2 108143 1x8qA 184 3.28e+00 1m4iA 181 3.41e+00 d.108.1.1 74457 1pv5A 264 3.48e+00 d.251.1.1 95150 1kopA 223 3.51e+00 2cba b.74.1.1 27966 1ex2A 189 3.62e+00 1ex2A c.51.4.2 33225 1vkhA 273 3.69e+00 c.69.1.32 108662 1lssA 140 3.69e+00 c.2.1.9 74246 1fs7A 485 3.74e+00 1qdbA a.138.1.3 19691 1vjlA 164 3.79e+00 d.257.1.1 100822 2fxqA 264 3.85e+00 1bh9A 45 3.89e+00 1bh9A a.22.1.3 16483 2d9rA 104 3.90e+00 1mkyA 439 4.03e+00 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1jjtA 228 4.07e+00 1a7tA d.157.1.1 63139 1q77A 138 4.15e+00 c.26.2.4 96023 2gf6A 135 4.21e+00 1f2tA 149 4.40e+00 1f2tA c.37.1.12 32373 2giyA 191 4.43e+00 1rypL 212 5.49e+00 d.153.1.4 41880 1mkmA 249 5.53e+00 a.4.5.33,d.110.2.2 79242,79243 2bmoB 194 5.60e+00 1vcoA 550 5.64e+00 c.23.16.1,c.37.1.10 108508,108509 1vjnA 220 5.75e+00 d.157.1.4 100825 2c4nA 250 5.78e+00 1t1jA 125 5.81e+00 c.137.1.1 106249 1h75A 81 5.83e+00 1h75A c.47.1.1 60716 1y8qB 640 5.83e+00 2mcm 112 5.84e+00 2mcm b.1.7.1 22207 1i39A 225 6.40e+00 1ekeA c.55.3.1 61585 1g6hA 257 6.55e+00 1gajA c.37.1.12 60318 1h7sA 365 6.74e+00 d.14.1.3,d.122.1.2 65705,65706 2gpiA 91 6.76e+00 1ctj 89 6.80e+00 1ctj a.3.1.1 15798 2bj0A 203 6.91e+00 2d37A 176 7.04e+00 1uliB 187 7.08e+00 d.17.4.4 107923 1dqpA 230 7.12e+00 1dqnA c.61.1.1 34069 1zgoA 223 7.26e+00 1zpyA 95 7.32e+00 1w07A 659 7.47e+00 1ukfA 188 7.71e+00 d.3.1.10 99488 1uujA 88 7.73e+00 a.221.1.1 108046 2fvgA 340 7.73e+00 2b8eA 273 7.78e+00 1s3zA 165 8.07e+00 d.108.1.1 105250 1tuhA 156 8.14e+00 d.17.4.11 107345 1wzcA 249 8.23e+00 1hf2A 210 8.38e+00 1hf2A b.80.3.1,c.102.1.1 60992,60993 1e9gA 286 8.59e+00 1wgjA b.40.5.1 59393 1uq5A 263 8.61e+00 d.165.1.1 99778 1ylxA 103 8.62e+00 1qxyA 252 8.69e+00 d.127.1.1 96565 1qmeA 702 9.04e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1itxA 419 9.56e+00 c.1.8.5,d.26.3.1 71425,71426 2h4uA 145 9.66e+00 2c6cA 707 9.72e+00 1eceA 358 9.82e+00 1eceA c.1.8.3 28813 1fit 147 9.89e+00 1fit d.13.1.1 37499 1vp4A 425 1.01e+01 1snzA 344 1.01e+01 b.30.5.4 98930 1p7tA 731 1.03e+01 c.1.13.1 94319 1imjA 210 1.04e+01 c.69.1.23 71246 1rypJ 204 1.06e+01 d.153.1.4 41878 1yckA 175 1.08e+01 2fkbA 180 1.09e+01 1vhcA 224 1.09e+01 c.1.10.1 100661 1svsA 353 1.10e+01 c.37.1.8 106051 1zupA 315 1.11e+01 2d8aA 348 1.11e+01 1c52 131 1.12e+01 1c52 a.3.1.1 15810 1dzkA 157 1.12e+01 1obpA b.60.1.1 27096 1lyvA 306 1.12e+01 c.45.1.2 74348 1s7kA 182 1.14e+01 1khdA 345 1.15e+01 a.46.2.1,c.27.1.1 77400,77401 1gyxA 76 1.15e+01 d.80.1.1 76387 2d7vA 162 1.19e+01 1pg4A 652 1.20e+01 e.23.1.1 88067 1s0yA 76 1.29e+01 d.80.1.1 98314 1faaA 124 1.29e+01 1erv c.47.1.1 32738 1vqzA 341 1.30e+01 1gpqA 135 1.30e+01 d.233.1.1 83295 1mnnA 340 1.32e+01 b.2.5.7 79324 1thqA 170 1.33e+01 f.4.1.2 106920 1vr5A 547 1.36e+01 1b7yA 350 1.36e+01 1pysA d.104.1.1 40776 1vqoE 178 1.36e+01 1xauA 122 1.37e+01 1wpoA 256 1.38e+01 1lay b.57.1.1 27012 2dddA 225 1.38e+01 2d5cA 263 1.39e+01 1cqqA 180 1.41e+01 1cqqA b.47.1.4 26422 1fiwA 290 1.42e+01 5ptp 1mml 265 1.43e+01 1mml e.8.1.2 43015 1i1qA 520 1.44e+01 1qdlA d.161.1.1 61543 1ekrA 161 1.44e+01 1ekrA d.58.21.1 39380 1g5aA 628 1.44e+01 b.71.1.1,c.1.8.1 65152,65153 1zy9A 564 1.45e+01 1yb2A 275 1.48e+01 1vkyA 347 1.51e+01 e.53.1.1 108696 2etjA 250 1.52e+01 1pguA 615 1.52e+01 b.69.4.1,b.69.4.1 88069,88070 1sviA 195 1.53e+01 c.37.1.8 106048 2c78A 405 1.54e+01 1fepA 724 1.54e+01 1fepA f.4.3.3 43808 2f51A 118 1.55e+01 2b4lA 268 1.57e+01 1xvsA 126 1.58e+01 1xodA 118 1.60e+01 1t1dA 100 1.60e+01 1t1dA d.42.1.2 38637 1d7uA 433 1.62e+01 2dkb c.67.1.4 34439 1m98A 317 1.63e+01 a.175.1.1,d.17.4.6 78866,78867 1bdmA 327 1.64e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1x13A 401 1.65e+01 1gy7A 125 1.65e+01 d.17.4.2 70738 1qwiA 143 1.67e+01 d.227.1.1 96474 1j1bA 420 1.68e+01 d.144.1.7 90758 1fm4A 159 1.70e+01 1bv1 d.129.3.1 76186 2c2xA 281 1.72e+01 1wocA 103 1.73e+01 1z5yE 149 1.74e+01 2trcP 217 1.75e+01 1b9yC c.47.1.6 33051 1vq0A 302 1.75e+01 1edg 380 1.78e+01 1edg c.1.8.3 28807 1e5pA 151 1.79e+01 1bj7 b.60.1.1 59272 1ospO 257 1.81e+01 1ospO b.76.1.1 27971 1r3dA 264 1.83e+01 1r2zA 274 1.84e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1j27A 102 1.87e+01 d.58.50.1 90778 1uekA 275 1.87e+01 d.14.1.5,d.58.26.5 88483,88484 1u9iA 519 1.89e+01 1sauA 115 1.93e+01 1tbfA 347 1.93e+01 a.211.1.2 106743 1di2A 69 1.94e+01 1di2A d.50.1.1 38780 1ym5A 300 1.95e+01 2aneA 125 1.96e+01 2ajuL 216 1.97e+01 2bjrA 368 1.97e+01 1q9rA 219 1.99e+01 b.1.1.1,b.1.1.2 96305,96306 2dd8S 202 2.05e+01 2bhmA 164 2.06e+01 1iqcA 308 2.07e+01 a.3.1.5,a.3.1.5 66266,66267 3pmgA 561 2.07e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1rurL 217 2.08e+01 b.1.1.1,b.1.1.2 97881,97882 1g87A 614 2.09e+01 a.102.1.2,b.2.2.2 83275,83276 1tadA 324 2.10e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1gcvB 136 2.11e+01 1cg5B a.1.1.2 15589 1n1jA 93 2.12e+01 a.22.1.3 79813 1t64A 377 2.13e+01 c.42.1.2 106543 2g38B 198 2.15e+01 1ew0A 130 2.15e+01 1drmA d.110.3.2 40905 2bolA 314 2.16e+01 1brwA 433 2.16e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1wb0A 445 2.17e+01 1x88A 359 2.18e+01 2acvA 463 2.19e+01 1j5wA 298 2.19e+01 d.104.1.1 71589 1i8aA 189 2.19e+01 1i82A b.1.9.2 61951 1w44A 331 2.20e+01 1e6bA 221 2.20e+01 1e6bA a.45.1.1,c.47.1.5 59294,59295 2czrA 226 2.21e+01 1mjuL 219 2.23e+01 b.1.1.1,b.1.1.2 91304,91305 1rtqA 299 2.24e+01 c.56.5.4 97819 1xkyA 301 2.25e+01 1wzlA 585 2.28e+01 1am9A 82 2.28e+01 1am9A a.38.1.1 17140 1jfmA 174 2.30e+01 d.19.1.1 66640 1sk4A 163 2.31e+01 d.118.1.1 105664 1xklA 273 2.33e+01 1yqvL 211 2.33e+01 1iu4A 331 2.33e+01 d.3.1.8 71430 2gnqA 336 2.34e+01 5rubA 490 2.36e+01 1burA c.1.14.1,d.58.9.1 29382,39288 1msk 331 2.36e+01 1msk d.173.1.1 42495 1xjvA 294 2.36e+01 1sqgA 429 2.37e+01 a.79.1.3,c.66.1.38 105912,105913 1a5t 334 2.38e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 2ethA 154 2.39e+01 1ysqA 193 2.39e+01 2bg9A 370 2.40e+01 1hxxA 340 2.41e+01 2omf f.4.3.1 61385 1lk2B 99 2.42e+01 b.1.1.2 91058 2d83A 363 2.42e+01 1wubA 178 2.45e+01 1uluA 261 2.46e+01 2bfdA 400 2.47e+01 1onwA 390 2.48e+01 b.92.1.7,c.1.9.13 87172,87173 3daaA 277 2.48e+01 1daaA e.17.1.1 43272 1bdb 277 2.51e+01 1bdb c.2.1.2 29874 1qtqA 553 2.53e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1kjvB 100 2.53e+01 b.1.1.2 77423 1io2A 213 2.55e+01 1ekeA c.55.3.1 62612 1sgwA 214 2.58e+01 c.37.1.12 105541 2aqlA 173 2.59e+01 1tkiA 321 2.62e+01 1tkiA d.144.1.7 41638 1p4kA 295 2.62e+01 d.153.1.5 87772 1l0wA 580 2.62e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1acf 125 2.64e+01 3nul d.110.1.1 40882 1winA 143 2.68e+01 1w9pA 433 2.68e+01 1d7pM 159 2.72e+01 1cztA b.18.1.2 23718 1gl4A 285 2.72e+01 d.22.1.2,g.3.11.5 65286,65287 1xkzA 255 2.72e+01 1qftA 175 2.75e+01 1qftA b.60.1.1 27151 1vr4A 103 2.75e+01 1xgsA 295 2.77e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1o5kA 306 2.79e+01 c.1.10.1 92504 1tlyA 278 2.80e+01 f.4.6.1 107143 1mkaA 171 2.80e+01 1mkaA d.38.1.2 38543 1f1xA 322 2.82e+01 d.32.1.3,d.32.1.3 83208,83209 1z8uA 102 2.83e+01 1cipA 353 2.84e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1g0cA 364 2.85e+01 7a3hA c.1.8.3 60165 1t1uA 639 2.87e+01 1t3qC 288 2.89e+01 d.87.2.1,d.145.1.3 106371,106372 1mexL 213 2.90e+01 b.1.1.1,b.1.1.2 91259,91260 1ta0A 197 2.91e+01 c.108.1.16 106729 1xk4C 113 2.97e+01 1whsA 255 2.97e+01 1ivyA c.69.1.5 34649 1x31D 99 3.00e+01 1ztdA 133 3.00e+01 2bhoA 130 3.02e+01 1pz4A 116 3.02e+01 d.106.1.1 95400 1v7rA 186 3.03e+01 c.51.4.1 100482 1vf6A 83 3.03e+01 a.194.1.1 100600 1w4tA 299 3.05e+01 1yrbA 262 3.11e+01 2b1xB 172 3.13e+01 1vkfA 188 3.13e+01 c.1.29.1 108656 1n67A 359 3.14e+01 b.2.3.4,b.2.3.4 85354,85355 1yliA 153 3.15e+01 1f1uA 323 3.15e+01 d.32.1.3,d.32.1.3 83200,83201 1kk1A 410 3.16e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 2gviA 204 3.16e+01 1xuvA 178 3.17e+01 1mw7A 240 3.18e+01 e.39.1.1 79557 1ceo 343 3.19e+01 1ceo c.1.8.3 28808 1ozjA 144 3.20e+01 d.164.1.1 93846 1g0oA 283 3.22e+01 1ybvA c.2.1.2 60181 1zklA 353 3.22e+01 1vl4A 447 3.23e+01 d.283.1.1 108718 1bkb 136 3.28e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 1molA 94 3.30e+01 1molA d.17.1.1 37988 2bbsA 290 3.31e+01 1tovA 98 3.32e+01 b.34.10.1 107179 1w7jA 795 3.32e+01 1ncwL 219 3.32e+01 b.1.1.1,b.1.1.2 85557,85558 1fmb 104 3.34e+01 1fmb b.50.1.1 26777 1vf1A 229 3.36e+01 1iicA 422 3.38e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1y7wA 291 3.39e+01 1nmoA 247 3.40e+01 c.135.1.1 91980 1jb3A 131 3.40e+01 1jc7A b.40.3.2 62833 2gs8A 317 3.42e+01 1hyeA 313 3.43e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 2blnA 305 3.45e+01 1olrA 224 3.48e+01 b.29.1.11 93330 1kutA 230 3.51e+01 d.143.1.1 73017 1i12A 160 3.52e+01 1i21A d.108.1.1 61515 1s69A 124 3.54e+01 a.1.1.1 105305 1ugxA 133 3.58e+01 1qlmA 316 3.61e+01 1qlmA d.147.1.1 41765 3fruA 269 3.66e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 1p32A 209 3.66e+01 1p32A d.25.1.1 38379 2cohA 202 3.67e+01 2aexA 346 3.67e+01 2gi3A 476 3.70e+01 1vpqA 273 3.71e+01 1jmxB 349 3.75e+01 b.69.2.2 66906 1i1jA 108 3.76e+01 1i1jA b.34.2.1 61531 1owfA 99 3.76e+01 a.55.1.1 87487 2a15A 139 3.81e+01 1kvkA 395 3.84e+01 d.14.1.5,d.58.26.3 73060,73061 1uzeA 589 3.85e+01 d.92.1.5 108174 1x7yA 400 3.87e+01 2c31A 568 3.90e+01 2d13A 227 3.91e+01 1j7gA 144 3.92e+01 c.110.1.1 84130 2d4rA 147 3.94e+01 1upvA 257 3.95e+01 2g09A 297 3.95e+01 1dsxA 87 3.96e+01 1t1dA d.42.1.2 38644 2bf6A 449 3.96e+01 2fhzA 109 3.96e+01 1vkkA 154 3.99e+01 d.109.1.2 108669 2aeeA 211 4.00e+01 1wrvA 308 4.01e+01 1bywA 110 4.01e+01 1bywA d.110.3.6 40912 1vajA 214 4.02e+01 1earA 147 4.02e+01 b.107.1.1,d.58.38.1 64875,64876 2b1eA 564 4.03e+01 2gjgA 248 4.03e+01 1u55A 188 4.05e+01 d.278.1.1 107677 1cb0A 283 4.06e+01 1cb0A c.56.2.1 33790 2a3qA 170 4.07e+01 2guhA 214 4.10e+01 1erjA 393 4.11e+01 1erjA b.69.4.1 27660 1uylA 236 4.12e+01 d.122.1.1 108147 1o57A 291 4.13e+01 a.4.5.40,c.61.1.1 92483,92484 1upaA 573 4.14e+01 c.31.1.3,c.36.1.5,c.36.1.9 99714,99715,99716 1yhvA 297 4.14e+01 1k4nA 192 4.18e+01 d.32.1.5 72059 2g8oA 264 4.22e+01 1v9yA 167 4.25e+01 d.110.3.2 108454 1qj4A 257 4.25e+01 1qj4A c.69.1.20 34796 1k3yA 221 4.27e+01 a.45.1.1,c.47.1.5 77245,77246 1txjA 171 4.28e+01 b.88.1.2 107424 1g291 372 4.28e+01 1g291 2c30A 321 4.29e+01 1jmvA 141 4.29e+01 c.26.2.4 66897 1x75A 132 4.33e+01 1ucdA 190 4.34e+01 d.124.1.1 107767 2brcA 214 4.34e+01 1sb0A 87 4.35e+01 a.12.1.1 98789 1nqeA 594 4.40e+01 f.4.3.3 86027 1fxoA 293 4.40e+01 1g0rA c.68.1.6 34524 2cw5A 255 4.45e+01 1oh4A 179 4.46e+01 b.18.1.18 92978 2cwzA 141 4.48e+01 1vheA 373 4.49e+01 b.49.3.1,c.56.5.4 100669,100670 1izcA 339 4.51e+01 c.1.12.5 83838 1u8fO 335 4.52e+01 1pgs 314 4.52e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 1va4A 279 4.55e+01 c.69.1.12 108458 1dpjA 329 4.55e+01 1smrA b.50.1.2 26828 2dbqA 334 4.55e+01 1lm4A 194 4.58e+01 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