# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 1lktA 104 3.15e-01 1lktA b.90.1.1 28398 1m93C 41 3.45e-01 2f4qA 346 8.43e-01 1tp6A 128 1.08e+00 d.17.4.12 107184 1vjfA 180 1.13e+00 d.116.1.1 100809 1yx1A 264 1.18e+00 1qauA 112 1.60e+00 1qauA b.36.1.1 24779 2go8A 122 1.62e+00 1qavB 115 1.82e+00 1qauA b.36.1.1 24780 1iscA 192 1.93e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1isaA 192 1.94e+00 1avmA a.2.11.1,d.44.1.1 15731,38724 1v74A 107 2.11e+00 d.243.1.1 100442 1cds 77 2.51e+00 1cds g.7.1.3 44461 1xqaA 113 2.54e+00 1m7xA 617 2.89e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1cdq 77 2.97e+00 1cds g.7.1.3 44459 2c3vA 102 3.18e+00 1lq9A 112 3.37e+00 d.58.4.3 78129 1zkdA 387 3.39e+00 1obr 326 3.44e+00 1aye c.56.5.2 33828 1gpeA 587 4.40e+00 1gpeA c.3.1.2,d.16.1.1 30387,37951 1dcjA 81 4.40e+00 1dcjA d.68.3.3 59115 1yaxA 153 4.43e+00 2cfuA 658 4.52e+00 1cqyA 99 5.08e+00 1b9zA b.3.1.1 22527 1bxwA 172 5.36e+00 1bxwA f.4.1.1 43743 2cvzA 289 5.37e+00 1vq2A 193 5.51e+00 1n9lA 109 5.75e+00 d.110.3.6 85468 1eagA 342 5.76e+00 1eagA b.50.1.2 26826 2a2pA 129 5.82e+00 1vr9A 213 5.84e+00 1tqzA 133 5.93e+00 1byrA 155 6.48e+00 1byrA d.136.1.1 41450 1xewY 172 6.61e+00 1ijqA 316 6.78e+00 1ijqA b.68.5.1,g.3.11.1 62506,62507 1omiA 248 6.78e+00 b.82.3.3,a.4.5.4 87079,87080 1yqtA 538 6.80e+00 1wm3A 72 7.03e+00 1nzjA 298 7.11e+00 c.26.1.1 92377 1kllA 130 7.17e+00 d.32.1.2 72720 1qhoA 686 7.31e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1qq2A 199 8.14e+00 1qq2A c.47.1.10 33064 1uasA 362 8.65e+00 b.71.1.1,c.1.8.1 88388,88389 1u0tA 307 8.90e+00 e.52.1.1 107567 1lwdA 413 9.00e+00 c.77.1.1 78265 1huxA 270 9.22e+00 1huxA c.55.1.5 61278 2bzoB 79 9.26e+00 1ui0A 205 9.36e+00 c.18.1.2 99411 1tyyA 339 9.74e+00 1d4oA 184 1.02e+01 1d4oA c.31.1.4 31748 2bjbA 462 1.02e+01 1txkA 498 1.05e+01 b.1.18.2,b.30.5.9 107425,107426 1bywA 110 1.09e+01 1bywA d.110.3.6 40912 3ezmA 101 1.14e+01 3ezmA b.89.1.1 28395 1j09A 468 1.20e+01 a.97.1.1,c.26.1.1 77025,77026 1ryaA 160 1.21e+01 d.113.1.5 105122 1jofA 365 1.22e+01 b.69.10.1 71775 1cv8 174 1.25e+01 1cv8 d.3.1.1 37089 1qjpA 171 1.28e+01 1bxwA f.4.1.1 43742 1dvfD 120 1.30e+01 1mfa b.1.1.1 20107 1vetA 124 1.34e+01 d.110.7.1 108553 1te7A 103 1.35e+01 1emwA 88 1.42e+01 1emwA d.27.1.1 38448 1ndoA 449 1.44e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1h8cA 82 1.45e+01 1h8cA d.15.1.2 37608 1ne9A 335 1.45e+01 d.108.1.4,d.108.1.4 91839,91840 1lv9A 77 1.45e+01 d.9.1.1 78233 2bzuA 181 1.46e+01 1nrlA 316 1.49e+01 a.123.1.1 92091 1mkeA 152 1.51e+01 b.55.1.4 79231 1eg9A 449 1.52e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1o7nA 449 1.52e+01 b.33.1.2,d.129.3.3 81162,81163 1psdA 409 1.59e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1iow 306 1.60e+01 1iow c.30.1.2,d.142.1.1 31713,41481 2dg5B 190 1.63e+01 1h8eG 272 1.63e+01 1e79G c.49.2.1 60756 1l6rA 227 1.65e+01 c.108.1.10 77768 1m13A 316 1.71e+01 a.123.1.1 84746 1w9hA 427 1.74e+01 1bpv 112 1.74e+01 1bpv b.1.2.1 22071 1ffyA 917 1.78e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 1.78e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 2fhxA 246 1.81e+01 1ebdA 455 1.87e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1fjgP 88 1.89e+01 1emwA d.27.1.1 38444 1kjvA 284 1.91e+01 b.1.1.2,d.19.1.1 77421,77422 1gln 468 1.94e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1xkiA 162 1.95e+01 1iiyA 101 1.95e+01 b.89.1.1 66152 1f2tB 148 1.96e+01 1f2tB 2akrA 285 1.98e+01 3nul 130 2.00e+01 3nul d.110.1.1 40891 2cr5A 109 2.12e+01 2dln 306 2.12e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1u58A 253 2.17e+01 1ka9H 200 2.18e+01 c.23.16.1 77308 1cuk 203 2.21e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1skoA 143 2.22e+01 d.110.7.1 105676 1a5r 103 2.24e+01 1a5r d.15.1.1 37597 1a0k 131 2.26e+01 3nul d.110.1.1 40892 1b9wA 89 2.33e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 2fh5A 185 2.35e+01 1uhvA 500 2.37e+01 b.71.1.2,c.1.8.3 99402,99403 1zip 217 2.42e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1yprA 125 2.44e+01 3nul d.110.1.1 40888 2fikA 287 2.45e+01 1y9wA 140 2.51e+01 1npeA 267 2.57e+01 b.68.5.1 92032 1pm1X 180 2.59e+01 b.60.1.1 104189 1pczA 191 2.66e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1b8iB 63 2.73e+01 1akhA a.4.1.1 16011 1m65A 245 2.81e+01 c.6.3.1 84847 1hjp 203 2.85e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1b8qA 127 2.85e+01 1qauA b.36.1.1 24781 12e8H 221 2.86e+01 1igtB b.1.1.1,b.1.1.2 20269,21269 1jyeA 349 2.87e+01 c.93.1.1 67455 1h4rA 314 2.87e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1v30A 124 2.88e+01 1xvqA 175 2.91e+01 2ghrA 302 2.92e+01 1itcA 516 2.92e+01 b.3.1.1,c.1.8.1 83705,83706 1wgoA 123 2.99e+01 1vemA 516 3.03e+01 1pqzA 238 3.04e+01 b.1.1.2,d.19.1.1 104297,104298 1gqzA 274 3.07e+01 d.21.1.1,d.21.1.1 83311,83312 1b9zA 516 3.12e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1yp2A 451 3.17e+01 1iwdA 215 3.18e+01 d.3.1.1 83756 1qmvA 197 3.21e+01 1qq2A c.47.1.10 33066 2gcc 70 3.21e+01 2gcc d.10.1.2 37484 1o50A 157 3.23e+01 d.37.1.1,d.37.1.1 92478,92479 1th8A 145 3.24e+01 d.122.1.3 106908 2f9zC 159 3.34e+01 1cd1A 315 3.34e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 1e25A 282 3.37e+01 1e25A e.3.1.1 42731 1l0oA 150 3.41e+01 d.122.1.3 73403 2db9A 149 3.42e+01 1p6oA 161 3.43e+01 c.97.1.2 94185 1z5lA 285 3.43e+01 1nofA 383 3.43e+01 b.71.1.2,c.1.8.3 92020,92021 1uaqA 158 3.49e+01 c.97.1.2 88386 1b72B 87 3.50e+01 1akhA a.4.1.1 16001 1xfsA 178 3.51e+01 d.129.3.5 109589 1ku1A 230 3.53e+01 a.118.3.1 72996 1l9gA 192 3.55e+01 c.18.1.2 84568 2d1uA 104 3.55e+01 1jssA 224 3.56e+01 d.129.3.2 71844 2atfA 200 3.59e+01 1xc3A 302 3.60e+01 2b5hA 200 3.61e+01 1efaA 333 3.67e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1qx4A 274 3.68e+01 b.43.4.2,c.25.1.1 104624,104625 1e39A 571 3.73e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1zu0A 529 3.74e+01 2gk3A 256 3.75e+01 1u9aA 160 3.76e+01 1u9aA d.20.1.1 38333 1mtpB 43 3.76e+01 2grrA 161 3.78e+01 1dmhA 311 3.79e+01 1dmhA b.3.6.1 22633 1b7bA 310 3.79e+01 1b7bA c.73.1.1 34963 1m64A 571 3.79e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1vcdA 126 3.83e+01 5bcaA 516 3.85e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1e19A 314 3.86e+01 1b7bA c.73.1.1 34967 1ay2 159 3.89e+01 2pil d.24.1.1 38377 1kssA 571 3.92e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 2pil 159 3.93e+01 2pil d.24.1.1 38376 1qjdA 571 3.97e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1tzaA 134 4.00e+01 b.1.23.1 107468 1ln1A 214 4.01e+01 d.129.3.2 74038 1zin 217 4.09e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1z0wA 207 4.10e+01 1hd2A 161 4.17e+01 c.47.1.10 60962 2fafA 608 4.18e+01 1cr5A 189 4.21e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1wrvA 308 4.33e+01 1sc6A 404 4.33e+01 1cor 82 4.34e+01 451c a.3.1.1 15903 2bfgA 503 4.34e+01 1htjF 210 4.35e+01 1htjF a.91.1.1 61254 1ny1A 240 4.37e+01 c.6.2.3 86395 1k75A 434 4.44e+01 c.82.1.2 68253 2bgiA 272 4.45e+01 1gmuA 143 4.46e+01 b.107.1.1,d.58.38.1 65335,65336 1gmwA 143 4.49e+01 b.107.1.1,d.58.38.1 65347,65348 1jic 62 4.49e+01 1azpA b.34.13.1 37462 1dpgA 485 4.50e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1gtkA 313 4.57e+01 c.94.1.1,d.50.2.1 76346,76347 2dpg 485 4.66e+01 1dpgA c.2.1.3,d.81.1.5 30076,39991 1p2hA 571 4.69e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1y0pA 571 4.72e+01 1x6oA 174 4.75e+01 b.34.5.2,b.40.4.5 109493,109494 1q9iA 571 4.76e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1pufB 73 4.78e+01 a.4.1.1 95132 1lj1A 571 4.83e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1a79A 171 4.86e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1g59A 468 4.90e+01 a.97.1.1,c.26.1.1 60257,60258 1ap8 213 4.95e+01 1ap8 d.86.1.1 40151 1edqA 540 4.96e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 2gaiA 633 4.96e+01 2evrA 246 4.97e+01 1a15A 67 4.98e+01 1a15A d.9.1.1 37451 1o5xA 248 4.99e+01 c.1.1.1 92528 1gv3A 248 5.00e+01 a.2.11.1,d.44.1.1 70585,70586 2bs9A 503 5.02e+01 1lgpA 116 5.02e+01 b.26.1.2 73890 1g5aA 628 5.08e+01 b.71.1.1,c.1.8.1 65152,65153 1ctn 540 5.13e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 2ga9D 469 5.20e+01 1u14A 172 5.22e+01 c.51.4.3 107579 1aisA 182 5.24e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1gyxA 76 5.26e+01 d.80.1.1 76387 1wzcA 249 5.28e+01 1qhdA 398 5.30e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1t0qC 86 5.42e+01 d.15.12.1 106222 1pylA 97 5.44e+01 d.1.1.2 104391 1jj2R 84 5.48e+01 1ffkP d.12.1.1 63103 1iujA 106 5.48e+01 d.58.4.5 90701 1kaeA 434 5.49e+01 c.82.1.2 72247 1s72S 85 5.49e+01 d.12.1.1 105338 1jjgA 102 5.50e+01 b.40.4.5 71696 1ttzA 87 5.52e+01 c.47.1.1 107309 1pot 325 5.55e+01 1pot c.94.1.1 35807 1wn5A 130 5.58e+01 1d3uA 181 5.66e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1jnuA 104 5.78e+01 d.110.3.6 71762 1b24A 188 5.84e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1wejH 223 5.84e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 1voqa 90 5.84e+01 2bjfA 329 5.89e+01 1btn 106 5.91e+01 1btn b.55.1.1 26952 1cch 82 5.93e+01 451c a.3.1.1 15902 1ct5A 256 5.94e+01 1ct5A c.1.6.2 28663 1ynmA 247 6.01e+01 1jidA 128 6.04e+01 d.201.1.1 66735 1l0bA 229 6.05e+01 c.15.1.3,c.15.1.3 73391,73392 2czrA 226 6.09e+01 1lrwA 600 6.11e+01 b.70.1.1 91111 1k9tA 540 6.15e+01 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1pvmA 184 6.21e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1sqeA 109 6.25e+01 d.58.4.5 105908 1ri9A 102 6.26e+01 b.34.2.1 97506 1khbA 625 6.32e+01 c.91.1.1,c.109.1.1 68606,68607 1w41A 101 6.36e+01 1nqcA 217 6.46e+01 d.3.1.1 86024 1xgyH 219 6.47e+01 1x54A 434 6.51e+01 2cu3A 64 6.56e+01 2fa8A 105 6.57e+01 1m9sA 605 6.68e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1l4sA 112 6.71e+01 d.204.1.1 77693 1c75A 71 6.72e+01 451c a.3.1.1 15796 1oshA 232 6.73e+01 a.123.1.1 93496 2fq9A 225 6.76e+01 1h7mA 102 6.78e+01 d.79.3.1 83485 1e4eA 343 6.86e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1a3rH 218 6.90e+01 1igtB b.1.1.1,b.1.1.2 19781,20891 1ntr 124 6.93e+01 1dbwA c.23.1.1 31092 1k2fA 190 6.94e+01 b.8.1.2 68054 1evsA 187 7.00e+01 1evsA a.26.1.1 16845 1gqiA 708 7.07e+01 c.1.8.10,d.92.2.2 76279,76280 1am2 199 7.07e+01 1am2 b.86.1.2 28381 1vqoS 85 7.12e+01 2c26A 260 7.18e+01 1s9aA 257 7.19e+01 b.3.6.1 105379 2azqA 311 7.24e+01 1u6mA 199 7.25e+01 1bu6O 501 7.26e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1vjvA 415 7.27e+01 d.3.1.9 108632 1t0fC 54 7.28e+01 6acn 754 7.28e+01 1amj c.8.2.1,c.83.1.1 30721,35397 1dppA 507 7.31e+01 1dpe c.94.1.1 35800 1a5j 110 7.33e+01 1a5j a.4.1.3,a.4.1.3 16043,16044 1d0iA 156 7.35e+01 2dhqA c.23.13.1 31383 1ktbA 405 7.37e+01 b.71.1.1,c.1.8.1 72960,72961 1jb7B 260 7.41e+01 1otcB b.40.4.3 62839 1k8kE 178 7.41e+01 a.148.1.1 68311 1i0cA 60 7.46e+01 1aojA b.34.2.1 61485 1to4A 156 7.48e+01 b.1.8.1 107162 1kb0A 677 7.52e+01 a.3.1.6,b.70.1.1 68378,68379 1d4tA 104 7.52e+01 1d4tA d.93.1.1 40537 1rewC 135 7.62e+01 g.7.1.3 97336 2crvA 120 7.66e+01 1tm0A 350 7.69e+01 d.21.1.3 107147 1bwzA 274 7.72e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1yw5A 177 7.76e+01 1b54 257 7.84e+01 1ct5A c.1.6.2 28664 1im4A 221 7.86e+01 e.8.1.7 62581 1w6sA 599 7.89e+01 1wdvA 152 7.93e+01 1uocA 289 7.94e+01 c.55.3.9 99686 2bmoA 447 7.96e+01 1mi0A 65 7.96e+01 d.15.7.1 79135 2amyA 246 7.97e+01 16pk 415 7.99e+01 16pk c.86.1.1 35454 1lyxA 248 8.01e+01 c.1.1.1 78304 1ef1A 294 8.06e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 2db1A 118 8.10e+01 7acn 754 8.11e+01 1amj c.8.2.1,c.83.1.1 30717,35393 1jtdB 273 8.16e+01 b.69.5.2 67265 1ospO 257 8.18e+01 1ospO b.76.1.1 27971 1konA 249 8.30e+01 e.39.1.1 72823 1n3gA 113 8.34e+01 d.204.1.1 79962 1azqA 66 8.39e+01 1azpA b.34.13.1 37469 1bt3A 345 8.51e+01 1bt3A a.86.1.2 18507 1ttwA 138 8.55e+01 d.198.1.1 107308 1e0bA 68 8.57e+01 1e0bA b.34.13.2 37476 1rgs 288 8.58e+01 1rgs b.82.3.2,b.82.3.2 28146,28147 1ppjD 241 8.62e+01 a.3.1.3,f.23.11.1 104258,104259 1rpyA 114 8.63e+01 d.93.1.1 97718 1jqeA 292 8.66e+01 c.66.1.19 71789 1tlfA 301 8.69e+01 1tlfA c.93.1.1 35687 1c96A 753 8.71e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1ka6A 128 8.74e+01 d.93.1.1 68370 1ffkP 84 8.75e+01 1ffkP d.12.1.1 37493 1y8qB 640 8.76e+01 1b9kA 238 8.79e+01 1qtsA b.1.10.1,d.105.1.1 22315,40791 2bgcA 238 8.81e+01 1dujA 187 8.82e+01 1dujA d.135.1.1 41449 1xyiA 66 8.83e+01 2dg5A 366 8.84e+01 2ciaA 102 8.86e+01 1pda 315 8.87e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1xkgA 312 8.89e+01 1ejdA 419 8.90e+01 1uae d.68.2.2 39576 1kq1A 77 8.94e+01 b.38.1.2 72848