# List of top-scoring protein chains for t04-100-30-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 4.94e-14 1ufbA 127 2.37e-13 a.24.16.3 99331 1o3uA 135 8.07e-13 a.24.16.3 86615 1wwpA 119 8.42e-02 1t0qA 498 3.65e-01 a.25.1.2 106220 1dwkA 156 9.68e-01 1dw9A a.35.1.4,d.72.1.1 17075,39606 16vpA 366 9.72e-01 16vpA d.180.1.1 42601 1wtyA 119 1.03e+00 1n97A 389 1.16e+00 a.104.1.1 80335 1na3A 91 1.23e+00 k.38.1.1 85481 1qhdA 398 1.55e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1w3iA 293 1.72e+00 c.1.10.1 109152 1nhyA 219 1.85e+00 a.45.1.1,c.47.1.5 80520,80521 1r71A 178 1.91e+00 a.4.14.1 104823 1jm6A 407 2.10e+00 a.29.5.1,d.122.1.4 66876,66877 1tbmA 326 2.11e+00 a.211.1.2 106744 1sauA 115 2.65e+00 2gmyA 153 3.09e+00 1nv8A 284 3.09e+00 c.66.1.30 86224 2ftzA 284 3.25e+00 2avpA 70 4.05e+00 2fmlA 273 4.22e+00 1rrmA 386 4.87e+00 e.22.1.2 105081 1v3wA 173 5.07e+00 b.81.1.5 100291 1wkbA 810 5.08e+00 1mtyB 384 5.23e+00 1mtyB a.25.1.2 16740 1y1uA 585 5.86e+00 1ci4A 89 5.98e+00 1qckA a.60.5.1 17970 1xx1A 285 6.97e+00 1gzsB 165 7.02e+00 a.168.1.1 76425 1tw9A 206 7.29e+00 a.45.1.1,c.47.1.5 107381,107382 2db0A 253 7.51e+00 2fgeA 995 7.55e+00 2f42A 179 7.60e+00 1k8kE 178 7.73e+00 a.148.1.1 68311 2a2fX 325 7.98e+00 2iu1A 208 8.04e+00 1j30A 144 8.40e+00 a.25.1.1 90806 1a17 166 9.40e+00 1a17 a.118.8.1 19206 2bptA 861 1.00e+01 1zemA 262 1.07e+01 2cx9A 387 1.08e+01 1u6zA 513 1.08e+01 1ws9A 387 1.18e+01 1qq7A 253 1.18e+01 1qq5A c.108.1.1 43329 1tffA 234 1.20e+01 d.3.1.11 106854 1sz9A 144 1.20e+01 a.118.9.4 106139 1zk8A 183 1.24e+01 1rr7A 129 1.30e+01 a.4.1.14 105075 1gkzA 388 1.31e+01 a.29.5.1,d.122.1.4 65268,65269 2gtqA 867 1.32e+01 1wzaA 488 1.38e+01 1qq5A 253 1.39e+01 1qq5A c.108.1.1 43327 1riqA 465 1.42e+01 a.203.1.1,d.104.1.1 97516,97517 1fuiA 591 1.43e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1m6jA 261 1.44e+01 c.1.1.1 78693 1w0hA 204 1.44e+01 2c1gA 431 1.46e+01 1e7uA 961 1.47e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 2c1iA 431 1.47e+01 1zq4A 693 1.57e+01 1khdA 345 1.60e+01 a.46.2.1,c.27.1.1 77400,77401 1ca1 370 1.61e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1elqA 390 1.61e+01 1elqA c.67.1.3 34436 1eluA 390 1.62e+01 1elqA c.67.1.3 34434 1khoA 370 1.62e+01 a.124.1.1,b.12.1.3 72489,72490 1i50B 1224 1.62e+01 e.29.1.1 61755 1yyaA 250 1.64e+01 2b0tA 738 1.69e+01 1yfsA 465 1.78e+01 1uruA 244 1.79e+01 h.4.14.1 99835 1mo0A 275 1.82e+01 c.1.1.1 79329 1yoyA 175 1.83e+01 1r2rA 248 1.83e+01 c.1.1.1 96875 1y88A 199 1.88e+01 1p5zB 263 1.89e+01 c.37.1.1 87815 1jj2B 337 1.90e+01 1ffkB b.43.3.2 63086 1s72B 338 1.90e+01 b.43.3.2 105320 1pinA 163 1.91e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1pujA 282 1.93e+01 c.37.1.8 88294 1aky 221 1.95e+01 1zin c.37.1.1,g.41.2.1 31896,45197 2cfuA 658 1.95e+01 1elkA 157 1.96e+01 1dvpA a.118.9.2 19217 1n81A 186 1.99e+01 a.185.1.1 85388 2d29A 387 2.06e+01 1vqoB 338 2.06e+01 1q2lA 939 2.07e+01 2a61A 145 2.07e+01 1dk0A 188 2.17e+01 1b2vA d.35.1.1 38530 1k47A 337 2.18e+01 d.14.1.5,d.58.26.4 72040,72041 1gcb 454 2.19e+01 3gcb d.3.1.1 37034 2ak3A 226 2.20e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1t6aA 126 2.20e+01 d.129.8.1 106555 1hyeA 313 2.27e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1e8yA 966 2.28e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1bc5A 269 2.33e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1h16A 759 2.33e+01 c.7.1.1 76462 1af7 274 2.38e+01 1af7 a.58.1.1,c.66.1.8 17928,34203 3gcb 470 2.42e+01 3gcb d.3.1.1 37032 2fckA 181 2.44e+01 1wpnA 188 2.50e+01 1q44A 326 2.51e+01 c.37.1.5 95779 1q5nA 454 2.52e+01 a.127.1.1 95901 1cm5A 759 2.52e+01 1cm5A c.7.1.1 30671 2cdnA 201 2.55e+01 1ukvG 453 2.58e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1elwA 118 2.61e+01 1a17 a.118.8.1 19207 1y0kA 209 2.61e+01 1aun 208 2.61e+01 1thv b.25.1.1 23900 1dofA 403 2.62e+01 1c3cA a.127.1.1 19429 1ornA 226 2.63e+01 a.96.1.1 87342 2chnA 716 2.65e+01 1twfB 1224 2.69e+01 1b5qA 472 2.69e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1aua 296 2.76e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1bcfA 158 2.78e+01 1bcfA a.25.1.1 16648 1fnnA 389 2.78e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1zcdA 388 2.79e+01 2f4qA 346 2.94e+01 1zip 217 2.97e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1vk5A 157 2.98e+01 a.220.1.1 108635 2cmd 312 2.99e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1ee8A 266 3.01e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1bm9A 122 3.04e+01 1bm9A a.4.5.7 16116 1bf5A 545 3.06e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1ezvB 352 3.14e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 2bcgG 453 3.15e+01 1uocA 289 3.23e+01 c.55.3.9 99686 2a5yA 204 3.25e+01 1s6cA 183 3.26e+01 a.39.1.5 98594 1rm6A 769 3.28e+01 1dgnA 89 3.29e+01 1dgnA a.77.1.3 18436 1tikA 213 3.30e+01 c.23.5.3 107003 1r9kA 172 3.31e+01 a.168.1.1 104869 1zin 217 3.32e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1c3wA 222 3.35e+01 1c3wA f.13.1.1 43405 1tph1 247 3.35e+01 1amk 2e2aA 105 3.38e+01 a.7.2.1 88499 1yw0A 276 3.38e+01 1vjlA 164 3.44e+01 d.257.1.1 100822 1kpsB 171 3.48e+01 a.118.12.1 68787 2dh4A 340 3.58e+01 1khyA 148 3.59e+01 a.174.1.1 77410 1azo 232 3.60e+01 1azo c.52.1.14 33329 1p3jA 217 3.67e+01 c.37.1.1,g.41.2.1 94022,94023 1om2A 95 3.71e+01 1om2A a.23.4.1 16520 1kq3A 376 3.72e+01 e.22.1.2 68790 2fkzA 155 3.73e+01 1t7pA 698 3.78e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 2a19A 175 3.78e+01 1wy5A 317 3.79e+01 1mhyD 521 3.82e+01 1mhyD a.25.1.2 16780 1fit 147 3.85e+01 1fit d.13.1.1 37499 1lo7A 141 3.86e+01 d.38.1.1 74144 2fq4A 192 3.88e+01 2a9kB 223 3.88e+01 1bvqA 141 3.96e+01 1bvqA d.38.1.1 38542 1g0cA 364 3.98e+01 7a3hA c.1.8.3 60165 1kmiZ 214 3.99e+01 h.4.11.1 72752 1gg3A 279 4.09e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 2fhi 147 4.11e+01 1fit d.13.1.1 37505 1nm8A 616 4.12e+01 c.43.1.3,c.43.1.3 85872,85873 1te6A 439 4.13e+01 c.1.11.1,d.54.1.1 106797,106798 1nogA 177 4.14e+01 a.25.2.2 85923 1sa3A 262 4.18e+01 c.52.1.23 105400 1e2aA 105 4.19e+01 1e2aA a.7.2.1 16322 1zd8A 227 4.19e+01 1e29A 135 4.21e+01 1e29A a.3.1.1 59161 1xrhA 351 4.29e+01 1h1wA 289 4.31e+01 d.144.1.7 83460 1qhtA 775 4.34e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1hw5A 210 4.36e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1g24A 211 4.36e+01 1g24A d.166.1.1 42270 1ah7 245 4.36e+01 1ah7 a.124.1.1 19339 1siqA 392 4.37e+01 a.29.3.1,e.6.1.1 105585,105586 1uu3A 310 4.37e+01 d.144.1.7 99999 1o5xA 248 4.39e+01 c.1.1.1 92528 1lyxA 248 4.41e+01 c.1.1.1 78304 1x9mA 698 4.43e+01 1jihA 531 4.45e+01 d.240.1.1,e.8.1.7 90374,90375 1tqgA 105 4.51e+01 a.24.10.3 107224 1om4A 422 4.53e+01 d.174.1.1 87067 1n93X 375 4.56e+01 a.206.1.1 91707 1z8sA 146 4.58e+01 1f1eA 154 4.58e+01 a.22.1.2 64927 1lucA 355 4.60e+01 1lucA c.1.16.1 29547 1ireB 228 4.62e+01 b.34.4.4 76770 1nowA 507 4.62e+01 c.1.8.6,d.92.2.1 85936,85937 1r5eA 115 4.62e+01 1ugpB 226 4.63e+01 b.34.4.4 107832 1u9lA 70 4.65e+01 a.60.4.2 107751 2choA 716 4.70e+01 1pufA 77 4.71e+01 a.4.1.1 95131 1neyA 247 4.72e+01 c.1.1.1 80449 2d2sA 235 4.79e+01 1jmsA 381 4.82e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1m0kA 262 4.84e+01 f.13.1.1 78344 1j09A 468 4.86e+01 a.97.1.1,c.26.1.1 77025,77026 1z8oA 404 4.92e+01 1s9uA 207 4.94e+01 a.184.1.1 105390 1gvnA 90 4.94e+01 a.8.2.1 76353 1s1eA 224 4.95e+01 1ap6A 198 4.96e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1ouvA 273 5.01e+01 a.118.18.1 93570 1kb9B 352 5.02e+01 d.185.1.1,d.185.1.1 77313,77314 1cv8 174 5.03e+01 1cv8 d.3.1.1 37089 2cybA 323 5.03e+01 1jlwA 219 5.04e+01 a.45.1.1,c.47.1.5 71741,71742 1v66A 65 5.07e+01 1bu8A 452 5.09e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 2akzA 439 5.12e+01 1xzoA 174 5.12e+01 1rkbA 173 5.14e+01 1zynA 202 5.15e+01 1ta8A 332 5.17e+01 2a1jB 91 5.17e+01 1ic8A 194 5.20e+01 a.4.1.1,a.35.1.1 76740,76741 1lbu 213 5.20e+01 1lbu a.20.1.1,d.65.1.1 16416,39549 1jipA 403 5.21e+01 a.104.1.1 66748 1qqeA 292 5.30e+01 1qqeA a.118.8.1 19210 1ji7A 89 5.31e+01 a.60.1.1 71682 1bpyA 335 5.37e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1z82A 335 5.37e+01 2ampA 304 5.38e+01 1z23A 163 5.41e+01 1lvoA 302 5.44e+01 b.47.1.4 74284 1h05A 146 5.50e+01 c.23.13.1 76433 1rzrA 332 5.55e+01 1b8oA 284 5.56e+01 1b8oA c.56.2.1 33762 1c02A 166 5.57e+01 1qspA a.24.10.2 16633 1m5yA 408 5.60e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 2b4vA 468 5.62e+01 1jvsA 400 5.74e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1n0nA 199 5.75e+01 a.2.11.1,d.44.1.1 79750,79751 1i45A 248 5.77e+01 1amk c.1.1.1 61665 1h96A 182 5.79e+01 2fha a.25.1.1 60811 1lb3A 182 5.79e+01 a.25.1.1 77873 1sfkA 76 5.83e+01 a.190.1.1 105488 1jcdA 52 5.84e+01 h.1.16.1 84157 1mba 147 5.88e+01 2fal a.1.1.2 15149 1v4xB 146 5.91e+01 a.1.1.2 108364 1pl4A 198 5.91e+01 a.2.11.1,d.44.1.1 94854,94855 1xi1A 575 5.94e+01 1q06A 135 5.95e+01 a.6.1.3 95493 1wt4A 73 5.95e+01 1tazA 365 5.97e+01 a.211.1.2 106734 1mo9A 523 6.00e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1yw5A 177 6.01e+01 1tpfA 250 6.02e+01 1amk c.1.1.1 28467 2ag5A 246 6.03e+01 1ct5A 256 6.04e+01 1ct5A c.1.6.2 28663 1rxwA 336 6.06e+01 a.60.7.1,c.120.1.2 98059,98060 2blkA 122 6.08e+01 1ta9A 450 6.12e+01 1kb9F 74 6.18e+01 f.28.1.1 77321 1kiyA 374 6.20e+01 a.128.1.5 72555 1jogA 146 6.21e+01 a.24.16.2 77142 1vjvA 415 6.23e+01 d.3.1.9 108632 2bikB 313 6.23e+01 1wehA 171 6.24e+01 1qgwC 177 6.30e+01 1qgwC a.1.1.3 15673 1t5bA 201 6.32e+01 c.23.5.3 106433 1y0zA 330 6.40e+01 1hl2A 297 6.41e+01 c.1.10.1 83581 1ji8A 111 6.43e+01 d.203.1.1 66733 3mddA 385 6.44e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1sfjA 238 6.46e+01 1z6nA 167 6.48e+01 1sctB 151 6.48e+01 3sdhA a.1.1.2 15003 2gd5A 179 6.49e+01 5croA 66 6.51e+01 1orc a.35.1.2 17044 1aszB 490 6.56e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 2fymA 431 6.57e+01 1q0qA 406 6.61e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1o5zA 442 6.61e+01 c.59.1.2,c.72.2.2 92530,92531 1sxgA 280 6.62e+01 1lf7A 182 6.62e+01 b.60.1.1 73878 2dhqA 146 6.63e+01 2dhqA c.23.13.1 31382 1yh6A 179 6.65e+01 2eu8A 216 6.65e+01 1reqA 727 6.69e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1mtyD 512 6.71e+01 1mhyD a.25.1.2 16742 1fh0A 221 6.74e+01 1cs8A d.3.1.1 59832 1keaA 221 6.76e+01 a.96.1.2 68491 1yeyA 444 6.82e+01 2f1kA 279 6.82e+01 1fjgD 209 6.93e+01 1c05A d.66.1.2 39553 1tbbA 332 6.93e+01 a.211.1.2 106741 1e9rA 437 6.94e+01 c.37.1.11 64827 2c71A 216 7.02e+01 1tedA 393 7.03e+01 c.95.1.2 106807 1bzpA 153 7.06e+01 1a6m a.1.1.2 15020 1xwsA 313 7.07e+01 1u00A 227 7.08e+01 1ijyA 130 7.10e+01 1ijxA a.141.1.1 62517 1yovA 537 7.13e+01 1ry6A 360 7.22e+01 c.37.1.9 98090 1xg0C 177 7.26e+01 1hyuA 521 7.28e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1kv5A 250 7.34e+01 c.1.1.1 73052 1xorA 349 7.36e+01 1wleA 501 7.36e+01 2a2rA 210 7.37e+01 1kblA 873 7.38e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1ryiA 382 7.39e+01 1xg2B 153 7.41e+01 1up7A 417 7.53e+01 5reqA 727 7.54e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1wy7A 207 7.54e+01 1alvA 173 7.55e+01 1alvA a.39.1.8 17370 1ng4A 390 7.57e+01 c.3.1.2,d.16.1.3 85666,85667 1z77A 200 7.64e+01 1nn7A 105 7.65e+01 d.42.1.2 85894 1ohuA 175 7.65e+01 f.1.4.1 93029 1go4A 205 7.66e+01 d.135.1.1 70292 1guxA 218 7.75e+01 1guxA a.74.1.3 18388 1ezvH 74 7.76e+01 1be3H f.28.1.1 59552 1i36A 264 7.78e+01 a.100.1.8,c.2.1.6 71108,71109 1usyA 275 7.95e+01 1myt 146 8.00e+01 1a6m a.1.1.2 15207 1b8aA 438 8.01e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 2cdqA 510 8.02e+01 1ml4A 308 8.07e+01 c.78.1.1,c.78.1.1 79255,79256 2btzA 394 8.07e+01 1lmzA 187 8.09e+01 a.96.1.4 74037 1mhyB 395 8.10e+01 1mtyB a.25.1.2 16781 1c1dA 355 8.12e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1hl9A 449 8.14e+01 b.71.1.3,c.1.8.11 90650,90651 1oe9A 795 8.16e+01 b.34.3.1,c.37.1.9 92792,92793 2bl8A 103 8.19e+01 1yhtA 367 8.25e+01 1tn6A 382 8.36e+01 1amk 251 8.37e+01 1amk c.1.1.1 28503 1iw8A 231 8.40e+01 a.111.1.1 76866 1j8uA 325 8.43e+01 d.178.1.1 71611 1yyqA 374 8.45e+01 1e1oA 504 8.47e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 2gz4A 207 8.47e+01 1hr6B 443 8.48e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1fecA 490 8.49e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1ii2A 524 8.71e+01 c.91.1.1,c.109.1.1 66146,66147 1a6m 151 8.71e+01 1a6m a.1.1.2 15018 1mmvB 419 8.83e+01 d.174.1.1 91318 1nriA 306 8.84e+01 c.80.1.3 86123 4pah 308 8.89e+01 4pah d.178.1.1 42576 1aihA 170 8.91e+01 1aihA d.163.1.1 42149 2aorA 223 8.92e+01 1fohA 664 8.93e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1hlrA 907 9.00e+01