# 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 7.35e-01 1lktA b.90.1.1 28398 1m93C 41 8.67e-01 1yx1A 264 2.43e+00 1vjfA 180 2.45e+00 d.116.1.1 100809 1tp6A 128 2.66e+00 d.17.4.12 107184 1iscA 192 2.78e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1isaA 192 2.80e+00 1avmA a.2.11.1,d.44.1.1 15731,38724 2f4qA 346 3.11e+00 1qauA 112 3.15e+00 1qauA b.36.1.1 24779 1gpeA 587 3.30e+00 1gpeA c.3.1.2,d.16.1.1 30387,37951 1qavB 115 3.57e+00 1qauA b.36.1.1 24780 1v74A 107 4.24e+00 d.243.1.1 100442 1cds 77 4.46e+00 1cds g.7.1.3 44461 1zkdA 387 4.69e+00 1xqaA 113 4.86e+00 2go8A 122 5.10e+00 1lq9A 112 5.18e+00 d.58.4.3 78129 1cdq 77 5.29e+00 1cds g.7.1.3 44459 1n9lA 109 5.30e+00 d.110.3.6 85468 2cfuA 658 5.49e+00 2c3vA 102 5.98e+00 1yaxA 153 6.30e+00 1obr 326 6.58e+00 1aye c.56.5.2 33828 1eagA 342 7.01e+00 1eagA b.50.1.2 26826 1xewY 172 7.18e+00 2a2pA 129 7.53e+00 1m7xA 617 7.60e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1wm3A 72 7.64e+00 1bxwA 172 8.30e+00 1bxwA f.4.1.1 43743 1dcjA 81 8.35e+00 1dcjA d.68.3.3 59115 1cqyA 99 8.38e+00 1b9zA b.3.1.1 22527 1tqzA 133 8.72e+00 1ijqA 316 9.04e+00 1ijqA b.68.5.1,g.3.11.1 62506,62507 1huxA 270 9.43e+00 1huxA c.55.1.5 61278 1yqtA 538 9.61e+00 1vr9A 213 1.01e+01 1nzjA 298 1.02e+01 c.26.1.1 92377 2cvzA 289 1.05e+01 1qhoA 686 1.05e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1u0tA 307 1.06e+01 e.52.1.1 107567 1vq2A 193 1.16e+01 1cv8 174 1.23e+01 1cv8 d.3.1.1 37089 2bzoB 79 1.24e+01 1txkA 498 1.26e+01 b.1.18.2,b.30.5.9 107425,107426 1iow 306 1.27e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1tyyA 339 1.30e+01 1byrA 155 1.36e+01 1byrA d.136.1.1 41450 1qq2A 199 1.38e+01 1qq2A c.47.1.10 33064 1ui0A 205 1.39e+01 c.18.1.2 99411 1nrlA 316 1.40e+01 a.123.1.1 92091 1ryaA 160 1.42e+01 d.113.1.5 105122 1ndoA 449 1.45e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1lwdA 413 1.46e+01 c.77.1.1 78265 1kllA 130 1.46e+01 d.32.1.2 72720 3ezmA 101 1.46e+01 3ezmA b.89.1.1 28395 1eg9A 449 1.51e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1o7nA 449 1.53e+01 b.33.1.2,d.129.3.3 81162,81163 2fh5A 185 1.71e+01 1lv9A 77 1.73e+01 d.9.1.1 78233 1omiA 248 1.76e+01 b.82.3.3,a.4.5.4 87079,87080 1h8eG 272 1.77e+01 1e79G c.49.2.1 60756 2dln 306 1.81e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1bpv 112 1.85e+01 1bpv b.1.2.1 22071 1bywA 110 1.92e+01 1bywA d.110.3.6 40912 2cr5A 109 1.94e+01 1yprA 125 1.98e+01 3nul d.110.1.1 40888 1qjpA 171 2.01e+01 1bxwA f.4.1.1 43742 1f2tB 148 2.07e+01 1f2tB 2f9zC 159 2.08e+01 2bjbA 462 2.10e+01 1psdA 409 2.12e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1vetA 124 2.18e+01 d.110.7.1 108553 2akrA 285 2.30e+01 1iiyA 101 2.40e+01 b.89.1.1 66152 2dg5B 190 2.43e+01 1dvfD 120 2.47e+01 1mfa b.1.1.1 20107 1te7A 103 2.48e+01 2bzuA 181 2.48e+01 1m13A 316 2.48e+01 a.123.1.1 84746 1jofA 365 2.49e+01 b.69.10.1 71775 1u9aA 160 2.49e+01 1u9aA d.20.1.1 38333 1w9hA 427 2.50e+01 2grrA 161 2.53e+01 1emwA 88 2.59e+01 1emwA d.27.1.1 38448 1kjvA 284 2.61e+01 b.1.1.2,d.19.1.1 77421,77422 2fikA 287 2.63e+01 2he7A 283 2.65e+01 1xkiA 162 2.65e+01 1ne9A 335 2.74e+01 d.108.1.4,d.108.1.4 91839,91840 1u58A 253 2.76e+01 1a5r 103 2.79e+01 1a5r d.15.1.1 37597 3nul 130 2.80e+01 3nul d.110.1.1 40891 2fhxA 246 2.89e+01 1fjgP 88 2.93e+01 1emwA d.27.1.1 38444 1th8A 145 2.95e+01 d.122.1.3 106908 1npeA 267 3.02e+01 b.68.5.1 92032 2gjdA 157 3.08e+01 1h8cA 82 3.15e+01 1h8cA d.15.1.2 37608 1a0k 131 3.19e+01 3nul d.110.1.1 40892 1uasA 362 3.22e+01 b.71.1.1,c.1.8.1 88388,88389 2bgiA 272 3.24e+01 1d4oA 184 3.26e+01 1d4oA c.31.1.4 31748 1zip 217 3.29e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1pm1X 180 3.31e+01 b.60.1.1 104189 1ay2 159 3.33e+01 2pil d.24.1.1 38377 1z5lA 285 3.34e+01 1itcA 516 3.35e+01 b.3.1.1,c.1.8.1 83705,83706 2pil 159 3.36e+01 2pil d.24.1.1 38376 1jnuA 104 3.39e+01 d.110.3.6 71762 1vemA 516 3.40e+01 1l0oA 150 3.42e+01 d.122.1.3 73403 1e39A 571 3.44e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1b9zA 516 3.45e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 2dchX 216 3.48e+01 1nofA 383 3.51e+01 b.71.1.2,c.1.8.3 92020,92021 1uhvA 500 3.54e+01 b.71.1.2,c.1.8.3 99402,99403 1cd1A 315 3.54e+01 1cd1A b.1.1.2,d.19.1.1 21579,38155 1m64A 571 3.54e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1u14A 172 3.60e+01 c.51.4.3 107579 1xc3A 302 3.61e+01 1jic 62 3.62e+01 1azpA b.34.13.1 37462 1kssA 571 3.66e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1e19A 314 3.71e+01 1b7bA c.73.1.1 34967 1qjdA 571 3.75e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1qmvA 197 3.77e+01 1qq2A c.47.1.10 33066 1b9wA 89 3.77e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1ffyA 917 3.79e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 3.79e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1mtpB 43 3.81e+01 1y9wA 140 3.86e+01 1mkeA 152 3.90e+01 b.55.1.4 79231 1gyxA 76 3.94e+01 d.80.1.1 76387 1ap8 213 3.94e+01 1ap8 d.86.1.1 40151 2db9A 149 3.96e+01 1xvqA 175 4.01e+01 1jssA 224 4.05e+01 d.129.3.2 71844 1pczA 191 4.05e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1ynmA 247 4.06e+01 1h4rA 314 4.11e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1gln 468 4.15e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1ln1A 214 4.16e+01 d.129.3.2 74038 1pqzA 238 4.17e+01 b.1.1.2,d.19.1.1 104297,104298 1p2hA 571 4.22e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1e25A 282 4.24e+01 1e25A e.3.1.1 42731 12e8H 221 4.30e+01 1igtB b.1.1.1,b.1.1.2 20269,21269 1bvh 157 4.30e+01 1dg9A c.44.1.1 32640 1y0pA 571 4.31e+01 1o5xA 248 4.32e+01 c.1.1.1 92528 1o50A 157 4.32e+01 d.37.1.1,d.37.1.1 92478,92479 1lj1A 571 4.35e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1q9iA 571 4.36e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1l9gA 192 4.40e+01 c.18.1.2 84568 5bcaA 516 4.40e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 2bfgA 503 4.44e+01 1p6oA 161 4.46e+01 c.97.1.2 94185 1lgpA 116 4.47e+01 b.26.1.2 73890 1skoA 143 4.48e+01 d.110.7.1 105676 2gaiA 633 4.49e+01 1wgoA 123 4.56e+01 2gk3A 256 4.68e+01 1zu0A 529 4.70e+01 1j09A 468 4.70e+01 a.97.1.1,c.26.1.1 77025,77026 1uaqA 158 4.77e+01 c.97.1.2 88386 1gmuA 143 4.80e+01 b.107.1.1,d.58.38.1 65335,65336 1zin 217 4.86e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1phr 157 4.91e+01 1dg9A c.44.1.1 32635 1gv3A 248 4.99e+01 a.2.11.1,d.44.1.1 70585,70586 2hglA 136 5.08e+01 1dg9A 157 5.09e+01 1dg9A c.44.1.1 32637 1edqA 540 5.13e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1vhvA 268 5.28e+01 c.90.1.1 100704 2gcc 70 5.29e+01 2gcc d.10.1.2 37484 1khbA 625 5.30e+01 c.91.1.1,c.109.1.1 68606,68607 1jyeA 349 5.31e+01 c.93.1.1 67455 2bs9A 503 5.33e+01 2evrA 246 5.36e+01 1yp2A 451 5.36e+01 1nqcA 217 5.37e+01 d.3.1.1 86024 1b8qA 127 5.45e+01 1qauA b.36.1.1 24781 1vcdA 126 5.51e+01 2fq9A 225 5.52e+01 1t0qC 86 5.53e+01 d.15.12.1 106222 1gmwA 143 5.54e+01 b.107.1.1,d.58.38.1 65347,65348 1a5j 110 5.59e+01 1a5j a.4.1.3,a.4.1.3 16043,16044 1iujA 106 5.62e+01 d.58.4.5 90701 1ctn 540 5.64e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1x6oA 174 5.67e+01 b.34.5.2,b.40.4.5 109493,109494 1voqa 90 5.68e+01 1ttwA 138 5.68e+01 d.198.1.1 107308 1gqiA 708 5.84e+01 c.1.8.10,d.92.2.2 76279,76280 1iwdA 215 5.87e+01 d.3.1.1 83756 1ct5A 256 5.89e+01 1ct5A c.1.6.2 28663 6acn 754 5.94e+01 1amj c.8.2.1,c.83.1.1 30721,35397 1ka9H 200 5.96e+01 c.23.16.1 77308 1qx4A 274 6.11e+01 b.43.4.2,c.25.1.1 104624,104625 1dmhA 311 6.21e+01 1dmhA b.3.6.1 22633 1tm0A 350 6.24e+01 d.21.1.3 107147 1s0yA 76 6.24e+01 d.80.1.1 98314 1xwwA 157 6.26e+01 1sc6A 404 6.28e+01 1c0eA 157 6.32e+01 1dg9A c.44.1.1 32638 1b7bA 310 6.34e+01 1b7bA c.73.1.1 34963 1mi0A 65 6.36e+01 d.15.7.1 79135 1htjF 210 6.41e+01 1htjF a.91.1.1 61254 1g59A 468 6.43e+01 a.97.1.1,c.26.1.1 60257,60258 1cr5A 189 6.46e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1cch 82 6.50e+01 451c a.3.1.1 15902 1jtdB 273 6.51e+01 b.69.5.2 67265 1l6rA 227 6.54e+01 c.108.1.10 77768 1pylA 97 6.57e+01 d.1.1.2 104391 1xfsA 178 6.59e+01 d.129.3.5 109589 1i0cA 60 6.64e+01 1aojA b.34.2.1 61485 1aisA 182 6.76e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1sqeA 109 6.79e+01 d.58.4.5 105908 1c4zA 358 6.84e+01 1c4zA d.148.1.1 41766 1am2 199 6.84e+01 1am2 b.86.1.2 28381 7acn 754 6.85e+01 1amj c.8.2.1,c.83.1.1 30717,35393 2gw6A 123 6.89e+01 1tiiD 99 6.90e+01 1tiiD b.40.2.1 24965 1qb5D 99 6.90e+01 b.40.2.1 88357 1u6mA 199 6.91e+01 1c96A 753 6.91e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1ospO 257 6.98e+01 1ospO b.76.1.1 27971 1lyxA 248 6.99e+01 c.1.1.1 78304 1cor 82 7.06e+01 451c a.3.1.1 15903 1ebdA 455 7.10e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1k9tA 540 7.23e+01 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1d3uA 181 7.25e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1m9sA 605 7.25e+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 7.27e+01 d.204.1.1 77693 1d4tA 104 7.27e+01 1d4tA d.93.1.1 40537 1ef1A 294 7.27e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 2czrA 226 7.30e+01 2cu3A 64 7.32e+01 1yuzA 202 7.33e+01 1gtkA 313 7.45e+01 c.94.1.1,d.50.2.1 76346,76347 2ge3A 170 7.49e+01 2c26A 260 7.55e+01 1azqA 66 7.55e+01 1azpA b.34.13.1 37469 1rewC 135 7.60e+01 g.7.1.3 97336 1efaA 333 7.61e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1e4eA 343 7.62e+01 1iow c.30.1.2,d.142.1.1 59221,59222 1kb0A 677 7.64e+01 a.3.1.6,b.70.1.1 68378,68379 2bmoA 447 7.67e+01 1xgyH 219 7.67e+01 1pot 325 7.68e+01 1pot c.94.1.1 35807 1b0jA 754 7.69e+01 1amj c.8.2.1,c.83.1.1 30719,35395 1hd2A 161 7.70e+01 c.47.1.10 60962 1wrvA 308 7.79e+01 1z2mA 155 7.79e+01 1dujA 187 7.80e+01 1dujA d.135.1.1 41449 2atfA 200 7.82e+01 2b5hA 200 7.88e+01 1uesA 191 7.89e+01 a.2.11.1,d.44.1.1 107798,107799 1e0bA 68 7.89e+01 1e0bA b.34.13.2 37476 2ga9D 469 7.95e+01 1wzcA 249 8.05e+01 1b54 257 8.07e+01 1ct5A c.1.6.2 28664 1azpA 66 8.09e+01 1azpA b.34.13.1 37467 1k75A 434 8.12e+01 c.82.1.2 68253 1sso 62 8.12e+01 1azpA b.34.13.1 37463 1c75A 71 8.14e+01 451c a.3.1.1 15796 1jtkA 136 8.15e+01 c.97.1.1 71862 1qnnA 191 8.15e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1xyiA 66 8.18e+01 1tiyA 164 8.19e+01 c.97.1.2 107012 1z0wA 207 8.21e+01 1d0iA 156 8.22e+01 2dhqA c.23.13.1 31383 1uh6A 100 8.28e+01 d.15.1.1 99394 1wn5A 130 8.33e+01 1a79A 171 8.42e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 2ghrA 302 8.47e+01 1jjgA 102 8.47e+01 b.40.4.5 71696 1b8iB 63 8.48e+01 1akhA a.4.1.1 16011 1jj2R 84 8.52e+01 1ffkP d.12.1.1 63103 1s72S 85 8.53e+01 d.12.1.1 105338 1zyeA 220 8.53e+01 1n3gA 113 8.63e+01 d.204.1.1 79962 1m65A 245 8.71e+01 c.6.3.1 84847 1pmhX 185 8.73e+01 b.18.1.18 104193 1ny1A 240 8.79e+01 c.6.2.3 86395 1upsA 420 8.80e+01 1e79G 272 8.86e+01 1e79G c.49.2.1 33158 1cuk 203 8.87e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1wkqA 164 8.93e+01 c.97.1.2 109393 1aojA 60 8.94e+01 1aojA b.34.2.1 24555 1bnzA 64 8.95e+01 1azpA b.34.13.1 37468