# List of top-scoring protein chains for t06-100-30-str2-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 1wolA 122 3.61e-16 1ufbA 127 3.81e-15 a.24.16.3 99331 1o3uA 135 9.26e-15 a.24.16.3 86615 1wwpA 119 5.12e-02 1na3A 91 4.33e-01 k.38.1.1 85481 1t0qA 498 4.63e-01 a.25.1.2 106220 1w3iA 293 4.72e-01 c.1.10.1 109152 1n97A 389 4.77e-01 a.104.1.1 80335 1dwkA 156 8.22e-01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1qhdA 398 8.76e-01 1qhdA a.115.1.2,b.19.1.1 63324,63325 16vpA 366 9.27e-01 16vpA d.180.1.1 42601 1gzsB 165 1.27e+00 a.168.1.1 76425 1r71A 178 1.28e+00 a.4.14.1 104823 1nv8A 284 1.30e+00 c.66.1.30 86224 1rrmA 386 1.34e+00 e.22.1.2 105081 1mtyB 384 1.39e+00 1mtyB a.25.1.2 16740 2d29A 387 1.40e+00 1j30A 144 1.75e+00 a.25.1.1 90806 1e7uA 961 2.51e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1xx1A 285 2.96e+00 2bptA 861 3.08e+00 2a61A 145 3.30e+00 1wkbA 810 3.38e+00 1ouvA 273 3.52e+00 a.118.18.1 93570 1tw9A 206 3.53e+00 a.45.1.1,c.47.1.5 107381,107382 1v3wA 173 3.61e+00 b.81.1.5 100291 1wy9A 147 3.74e+00 1tqgA 105 4.02e+00 a.24.10.3 107224 2iu1A 208 4.23e+00 1ci4A 89 4.35e+00 1qckA a.60.5.1 17970 1e8yA 966 4.40e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1khoA 370 4.43e+00 a.124.1.1,b.12.1.3 72489,72490 2gtqA 867 4.77e+00 1ee8A 266 5.02e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 2ftzA 284 5.03e+00 2c1iA 431 5.21e+00 1tffA 234 5.84e+00 d.3.1.11 106854 1rm6A 769 6.01e+00 1lb3A 182 6.38e+00 a.25.1.1 77873 2cfuA 658 6.98e+00 1y88A 199 7.13e+00 1r9kA 172 7.51e+00 a.168.1.1 104869 1vk5A 157 7.78e+00 a.220.1.1 108635 2fmlA 273 8.35e+00 1m0kA 262 8.37e+00 f.13.1.1 78344 2fckA 181 8.45e+00 1ry6A 360 9.04e+00 c.37.1.9 98090 2f4qA 346 9.18e+00 1bm9A 122 9.92e+00 1bm9A a.4.5.7 16116 1zemA 262 1.02e+01 2f42A 179 1.02e+01 1qhtA 775 1.02e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1lj2A 110 1.04e+01 h.1.13.2 73926 1dk0A 188 1.05e+01 1b2vA d.35.1.1 38530 1ohuA 175 1.07e+01 f.1.4.1 93029 1zk8A 183 1.10e+01 1aua 296 1.15e+01 1aua a.5.3.1,c.13.1.1 16290,30882 2bikB 313 1.16e+01 1y2mA 716 1.16e+01 1aun 208 1.18e+01 1thv b.25.1.1 23900 1wzaA 488 1.19e+01 1pujA 282 1.20e+01 c.37.1.8 88294 1jmsA 381 1.23e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1uu3A 310 1.24e+01 d.144.1.7 99999 1bc5A 269 1.26e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1af7 274 1.27e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 1q2lA 939 1.28e+01 1gvnA 90 1.29e+01 a.8.2.1 76353 2a2fX 325 1.30e+01 1uwkA 557 1.30e+01 e.51.1.1 108065 2fp1A 166 1.30e+01 1aky 221 1.31e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1w0hA 204 1.33e+01 1sauA 115 1.33e+01 1f1eA 154 1.36e+01 a.22.1.2 64927 1vqoB 338 1.39e+01 1u6zA 513 1.40e+01 1p5zB 263 1.40e+01 c.37.1.1 87815 1ca1 370 1.41e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1yyaA 250 1.42e+01 1mo9A 523 1.43e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1myt 146 1.44e+01 1a6m a.1.1.2 15207 1t6aA 126 1.44e+01 d.129.8.1 106555 1sa3A 262 1.44e+01 c.52.1.23 105400 1tedA 393 1.45e+01 c.95.1.2 106807 1sz9A 144 1.46e+01 a.118.9.4 106139 1tn6A 382 1.49e+01 1oshA 232 1.49e+01 a.123.1.1 93496 1khyA 148 1.52e+01 a.174.1.1 77410 1y0kA 209 1.57e+01 1dofA 403 1.59e+01 1c3cA a.127.1.1 19429 1fuiA 591 1.60e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1g24A 211 1.61e+01 1g24A d.166.1.1 42270 2gmyA 153 1.62e+01 1rr7A 129 1.63e+01 a.4.1.14 105075 2btzA 394 1.65e+01 1q0qA 406 1.68e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1j5sA 463 1.71e+01 c.1.9.8 71580 2fulA 178 1.73e+01 2bcgG 453 1.75e+01 1b5qA 472 1.76e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1zd8A 227 1.77e+01 1hyeA 313 1.79e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 3grs 478 1.85e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1keaA 221 1.85e+01 a.96.1.2 68491 1mo0A 275 1.88e+01 c.1.1.1 79329 2ak3A 226 1.92e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1zcdA 388 1.92e+01 1azo 232 1.94e+01 1azo c.52.1.14 33329 1reqA 727 1.99e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 2bl8A 103 2.00e+01 1s9uA 207 2.05e+01 a.184.1.1 105390 2db0A 253 2.05e+01 2cdnA 201 2.08e+01 1uc8A 280 2.08e+01 c.30.1.6,d.142.1.7 99165,99166 1qc7A 101 2.10e+01 1qc7A a.118.14.1 18456 1yz7A 188 2.10e+01 2e2aA 105 2.11e+01 a.7.2.1 88499 1w7jA 795 2.19e+01 1dgnA 89 2.21e+01 1dgnA a.77.1.3 18436 2fgeA 995 2.27e+01 1ta9A 450 2.32e+01 1m6jA 261 2.37e+01 c.1.1.1 78693 1kb9B 352 2.40e+01 d.185.1.1,d.185.1.1 77313,77314 1hw5A 210 2.42e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1ryiA 382 2.42e+01 1sbxA 106 2.43e+01 a.6.1.4 105414 1elkA 157 2.43e+01 1dvpA a.118.9.2 19217 2fkzA 155 2.45e+01 1rkbA 173 2.48e+01 1h05A 146 2.49e+01 c.23.13.1 76433 1b0uA 262 2.67e+01 1b0uA c.37.1.12 32370 1b8aA 438 2.69e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1wy5A 317 2.69e+01 1e29A 135 2.71e+01 1e29A a.3.1.1 59161 1lvoA 302 2.73e+01 b.47.1.4 74284 1e4yA 214 2.74e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1lbu 213 2.77e+01 1lbu a.20.1.1,d.65.1.1 16416,39549 2ff4A 388 2.78e+01 1h4rA 314 2.78e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1sflA 238 2.81e+01 1bf5A 545 2.84e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1ydiA 263 2.85e+01 1opjA 293 2.86e+01 d.144.1.7 87230 1u61A 138 2.86e+01 a.149.1.1 107696 1wc3A 219 2.89e+01 1eluA 390 2.89e+01 1elqA c.67.1.3 34434 1cydA 244 2.90e+01 1cydA c.2.1.2 29825 1ah7 245 2.91e+01 1ah7 a.124.1.1 19339 1qq5A 253 2.93e+01 1qq5A c.108.1.1 43327 1r5eA 115 2.94e+01 1jogA 146 2.94e+01 a.24.16.2 77142 1ufiA 64 2.95e+01 a.30.4.1 99336 1kblA 873 2.99e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1ijyA 130 3.04e+01 1ijxA a.141.1.1 62517 1uruA 244 3.07e+01 h.4.14.1 99835 1rxwA 336 3.12e+01 a.60.7.1,c.120.1.2 98059,98060 1fnnA 389 3.12e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1yhtA 367 3.13e+01 1twfB 1224 3.15e+01 1k47A 337 3.17e+01 d.14.1.5,d.58.26.4 72040,72041 1wzuA 300 3.19e+01 1kmiZ 214 3.19e+01 h.4.11.1 72752 1siqA 392 3.19e+01 a.29.3.1,e.6.1.1 105585,105586 1vjvA 415 3.21e+01 d.3.1.9 108632 1fs7A 485 3.22e+01 1qdbA a.138.1.3 19691 1z77A 200 3.24e+01 1vjlA 164 3.24e+01 d.257.1.1 100822 1nthA 458 3.28e+01 c.1.25.1 80730 1mtyD 512 3.33e+01 1mhyD a.25.1.2 16742 1r2rA 248 3.37e+01 c.1.1.1 96875 1co6A 107 3.39e+01 1ycc a.3.1.1 15894 2c71A 216 3.40e+01 1o2dA 371 3.42e+01 e.22.1.2 86591 2blkA 122 3.44e+01 1yviA 149 3.45e+01 1ijxA 127 3.45e+01 1ijxA a.141.1.1 62511 1xg2B 153 3.46e+01 1wpnA 188 3.46e+01 1q44A 326 3.47e+01 c.37.1.5 95779 1x54A 434 3.48e+01 1wlxA 129 3.50e+01 1t5bA 201 3.55e+01 c.23.5.3 106433 1wiwA 290 3.58e+01 2chnA 716 3.62e+01 1mijA 152 3.64e+01 a.4.1.1 79150 1pinA 163 3.68e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1zin 217 3.70e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1ylmA 144 3.74e+01 1ml4A 308 3.76e+01 c.78.1.1,c.78.1.1 79255,79256 1u9lA 70 3.79e+01 a.60.4.2 107751 1wcrA 103 3.81e+01 1eexA 554 3.90e+01 1dioA c.1.19.3 29650 1pb1A 416 3.93e+01 c.77.1.1 88014 1z82A 335 4.00e+01 1v4xB 146 4.01e+01 a.1.1.2 108364 1mxmA 254 4.03e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1l8nA 679 4.04e+01 c.1.8.10,d.92.2.2 84564,84565 1oq9A 363 4.05e+01 a.25.1.2 87257 1pufA 77 4.05e+01 a.4.1.1 95131 1mba 147 4.10e+01 2fal a.1.1.2 15149 1b8oA 284 4.10e+01 1b8oA c.56.2.1 33762 1fecA 490 4.11e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1sfkA 76 4.13e+01 a.190.1.1 105488 1zk7A 467 4.15e+01 1cv8 174 4.18e+01 1cv8 d.3.1.1 37089 1mtpA 323 4.18e+01 e.1.1.1 85107 2b0tA 738 4.22e+01 1j09A 468 4.25e+01 a.97.1.1,c.26.1.1 77025,77026 1grj 158 4.26e+01 1grj a.2.1.1,d.26.1.2 15691,38433 1jihA 531 4.30e+01 d.240.1.1,e.8.1.7 90374,90375 1q5nA 454 4.33e+01 a.127.1.1 95901 1o5kA 306 4.33e+01 c.1.10.1 92504 2ag5A 246 4.33e+01 1x9zA 188 4.36e+01 1qkrA 188 4.36e+01 1qkrA a.24.9.1 16628 1z23A 163 4.37e+01 1z6nA 167 4.37e+01 1yovA 537 4.38e+01 1pl4A 198 4.42e+01 a.2.11.1,d.44.1.1 94854,94855 1lddA 74 4.46e+01 a.4.5.34 73841 1r29A 127 4.51e+01 d.42.1.1 96856 1zzpA 130 4.52e+01 2cxaA 256 4.59e+01 1mlwA 301 4.63e+01 d.178.1.1 79289 1uocA 289 4.65e+01 c.55.3.9 99686 1knvA 293 4.66e+01 c.52.1.7 68707 1k8kE 178 4.67e+01 a.148.1.1 68311 1zv1A 65 4.73e+01 1xzoA 174 4.80e+01 1ng6A 148 4.85e+01 a.182.1.1 85670 1w07A 659 4.89e+01 1h16A 759 4.95e+01 c.7.1.1 76462 1up7A 417 4.97e+01 1fit 147 4.98e+01 1fit d.13.1.1 37499 1vfrA 218 5.02e+01 1vfrA d.90.1.1 40247 2ar0A 541 5.03e+01 1srrA 124 5.06e+01 1dz3A c.23.1.1 31110 2d2sA 235 5.11e+01 3gcb 470 5.19e+01 3gcb d.3.1.1 37032 1y8qB 640 5.20e+01 1nogA 177 5.26e+01 a.25.2.2 85923 1kpsB 171 5.27e+01 a.118.12.1 68787 1ui5A 215 5.39e+01 a.4.1.9,a.121.1.1 107856,107857 2h58A 330 5.39e+01 1q8iA 783 5.41e+01 c.55.3.5,e.8.1.1 96208,96209 1rt8A 513 5.42e+01 a.40.1.1 105095 1m7vA 363 5.43e+01 d.174.1.1 78748 1oapA 109 5.45e+01 d.79.7.1 92706 1jnyA 435 5.46e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1wy7A 207 5.47e+01 1ofdA 1520 5.50e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1wmiB 67 5.52e+01 1yqyA 523 5.54e+01 1i36A 264 5.55e+01 a.100.1.8,c.2.1.6 71108,71109 1f60A 458 5.59e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1o5xA 248 5.61e+01 c.1.1.1 92528 1n93X 375 5.65e+01 a.206.1.1 91707 1eg5A 384 5.66e+01 1ecxA c.67.1.3 34429 1a6m 151 5.67e+01 1a6m a.1.1.2 15018 1gesA 450 5.68e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1c3cA 429 5.68e+01 1c3cA a.127.1.1 19425 1yfsA 465 5.69e+01 1n2zA 245 5.75e+01 c.92.2.2 79865 1gu9A 177 5.79e+01 a.152.1.1 65540 2csbA 519 5.80e+01 2crbA 97 5.81e+01 1gnxA 479 5.84e+01 c.1.8.4 76241 1ktbA 405 5.86e+01 b.71.1.1,c.1.8.1 72960,72961 1d5tA 433 5.87e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1k78A 149 5.90e+01 a.4.1.5,a.4.1.5 68255,68256 1n35A 1267 5.91e+01 e.8.1.4 79935 1i1nA 226 5.94e+01 c.66.1.7 71102 2dh4A 340 5.98e+01 1t46A 313 5.99e+01 d.144.1.7 106397 1pprM 312 6.10e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 2gv8A 447 6.11e+01 1uhnA 189 6.11e+01 a.39.1.5 99399 1z8sA 146 6.15e+01 1eu1A 780 6.18e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1e9rA 437 6.23e+01 c.37.1.11 64827 1amuA 563 6.24e+01 1amuA e.23.1.1 43351 2gboA 104 6.24e+01 1hr6A 475 6.26e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1bouB 302 6.27e+01 1bouB c.56.6.1 33859 1jcdA 52 6.32e+01 h.1.16.1 84157 1gpuA 680 6.33e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1o5zA 442 6.35e+01 c.59.1.2,c.72.2.2 92530,92531 1ct5A 256 6.44e+01 1ct5A c.1.6.2 28663 1pu6A 218 6.53e+01 a.96.1.5 95123 1nt2B 258 6.55e+01 a.183.1.1 86150 1neyA 247 6.56e+01 c.1.1.1 80449 2fnaA 357 6.70e+01 1y8qA 346 6.70e+01 1go3F 107 6.71e+01 a.60.8.2 65407 1spvA 184 6.72e+01 c.50.1.2 98957 1aoy 78 6.73e+01 1aoy a.4.5.3 16087 1qsaA 618 6.75e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1ulyA 192 6.77e+01 1nm8A 616 6.87e+01 c.43.1.3,c.43.1.3 85872,85873 2choA 716 6.87e+01 1zaiA 363 6.89e+01 1nowA 507 6.90e+01 c.1.8.6,d.92.2.1 85936,85937 1y2kA 349 6.91e+01 1ezwA 349 6.92e+01 1ezwA c.1.16.3 29558 1i27A 73 6.92e+01 1i27A a.4.5.30 61555 1dkmA 410 6.94e+01 1dklA c.60.1.2 34000 1u00A 227 7.01e+01 2c2aA 258 7.03e+01 2fvhA 120 7.06e+01 1xg0C 177 7.09e+01 1g0cA 364 7.11e+01 7a3hA c.1.8.3 60165 2f60K 64 7.13e+01 2gk9A 426 7.14e+01 1sx7A 164 7.19e+01 1yxcA 292 7.20e+01 1j7xA 302 7.36e+01 c.14.1.2 66425 1x8vA 455 7.42e+01 1lw1A 177 7.43e+01 a.152.1.1 74290 1oywA 523 7.49e+01 a.4.5.43,c.37.1.19,c.37.1.19 93760,93761,93762 2bcqA 335 7.51e+01 1w2lA 99 7.60e+01 1y0zA 330 7.61e+01 1rw6A 210 7.69e+01 a.47.4.1 105113 1kq3A 376 7.73e+01 e.22.1.2 68790 5eau 548 7.77e+01 5eat a.102.4.1,a.128.1.3 18851,19443 1nn5A 215 7.80e+01 c.37.1.1 85892 1vls 146 7.81e+01 1vls a.24.2.1 16532 1t33A 224 7.83e+01 a.4.1.9,a.121.1.1 106295,106296 1d2tA 231 7.83e+01 1d2tA a.111.1.1 19052 1j8uA 325 7.84e+01 d.178.1.1 71611 1yeyA 444 7.88e+01 2fu2A 102 7.90e+01 1elwA 118 7.98e+01 1a17 a.118.8.1 19207 1xi1A 575 7.98e+01 1wt4A 73 7.99e+01 1q45A 391 8.01e+01 c.1.4.1 95780 2fmpA 335 8.06e+01 1tu9A 134 8.07e+01 a.1.1.2 107320 2f8yA 223 8.09e+01 2bskB 90 8.12e+01 2g3kA 94 8.13e+01 2c5rA 67 8.16e+01 1t6uA 117 8.20e+01 a.24.22.1 106584 1vmaA 306 8.21e+01 a.24.13.1,c.37.1.10 108887,108888 2ceyA 306 8.23e+01 1r5lA 262 8.27e+01 a.5.3.1,c.13.1.1 97099,97100 1z8oA 404 8.32e+01 1uvqA 197 8.53e+01 b.1.1.2,d.19.1.1 100062,100063 2bzlA 325 8.58e+01 1c52 131 8.61e+01 1c52 a.3.1.1 15810 1wtaA 275 8.64e+01 1tt7A 330 8.73e+01 1jx4A 352 8.76e+01 d.240.1.1,e.8.1.7 90378,90379 2bfxA 284 8.78e+01 1go4A 205 8.78e+01 d.135.1.1 70292 1fzcA 87 8.78e+01 1fzcA h.1.8.1 45590 1i5nA 146 8.79e+01 1i5nA a.24.10.3 61805 2a7oA 112 8.79e+01 1eueA 86 8.92e+01 1cyo d.120.1.1 59504 1csh 435 8.97e+01 1csh a.103.1.1 18880 1vq0A 302 8.97e+01