# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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.soe.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 2eo0A 147 8.24e-03 1hh1A 143 1.43e-02 1gefA c.52.1.18 61036 1gefA 123 1.86e-02 1gefA c.52.1.18 60465 1y88A 199 8.17e-02 a.60.4.3,c.52.1.30 116560,116561 1cliA 345 1.03e-01 1cliA d.79.4.1,d.139.1.1 39816,41459 1ob8A 135 1.53e-01 c.52.1.18 111627 1dv1A 449 5.82e-01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1lvwA 295 7.88e-01 c.68.1.6 84723 1dv2A 452 8.31e-01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 2nw5A 360 1.37e+00 2scuB 388 1.50e+00 2scuB c.23.4.1,d.142.1.4 31141,41562 2b25A 336 1.81e+00 c.66.1.13 127699 2p4hX 322 1.95e+00 1sw2A 275 2.11e+00 c.94.1.1 106064 2btuA 346 2.26e+00 1e4eA 343 2.29e+00 1iow c.30.1.2,d.142.1.1 59221,59222 2fomB 185 2.31e+00 b.47.1.3 133884 3ladA 476 2.60e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 2ganA 190 2.69e+00 d.108.1.1 134889 2uubD 209 3.13e+00 d.66.1.2 139935 2nu8B 388 3.29e+00 2vqeD 209 3.48e+00 1whzA 70 3.59e+00 d.50.3.2 114656 2pbxA 203 3.67e+00 1j3nA 408 3.67e+00 c.95.1.1,c.95.1.1 84074,84075 2abyA 146 3.86e+00 2b2nA 344 3.90e+00 c.37.1.19 127710 1vr8A 142 3.99e+00 d.312.1.1 120445 1tiiD 99 4.02e+00 1tiiD b.40.2.1 24965 1l1jA 239 4.08e+00 b.47.1.1 84516 1qb5D 99 4.09e+00 b.40.2.1 88357 1iow 306 4.14e+00 1iow 1iowA 306 4.14e+00 c.30.1.2,d.142.1.1 31713,41481 1fjgD 209 4.16e+00 1c05A d.66.1.2 39553 2okfA 140 4.29e+00 1eudB 396 4.40e+00 2scuB c.23.4.1,d.142.1.4 31150,41571 1qxoA 388 4.72e+00 d.258.1.1 96539 2inbA 140 4.89e+00 2j5vA 367 5.11e+00 2i2qA 137 5.18e+00 2v79A 135 5.29e+00 3bs2A 148 5.68e+00 1sjiA 350 6.61e+00 1tz9A 367 6.62e+00 c.1.15.6 107466 2icgA 160 6.75e+00 1dosA 358 6.81e+00 1dosA c.1.10.2 29175 2fp4B 395 7.23e+00 c.23.4.1,d.142.1.4 133897,133898 1ky9A 448 7.54e+00 b.36.1.4,b.47.1.1 73198,73199 2oikA 154 7.62e+00 1hqz1 141 7.80e+00 1suuA 312 7.88e+00 b.68.10.1 99006 1jj2M 186 7.93e+00 1ffkK c.55.4.1 63098 1e9lA 377 7.96e+00 1e9lA c.1.8.5,d.26.3.1 59395,59396 2pb2A 420 8.05e+00 1q7fA 286 8.73e+00 b.68.9.1 96036 1vf8A 377 8.86e+00 c.1.8.5,d.26.3.1 120029,120030 1seiA 130 9.15e+00 1seiA d.140.1.1 41463 1qwoA 442 9.28e+00 c.60.1.2 104620 2bfgA 503 9.84e+00 b.71.1.2,c.1.8.3 128423,128424 2bs9A 503 9.91e+00 b.71.1.2,c.1.8.3 129062,129063 2iruA 303 1.02e+01 1xtoA 311 1.04e+01 d.157.1.6 116030 2pziA 681 1.05e+01 1o0pA 104 1.06e+01 d.58.7.1 86535 1lml 478 1.13e+01 1lml 1lmlA 478 1.13e+01 d.92.1.3 40295 1vqoN 187 1.14e+01 c.55.4.1 120375 1eg9A 449 1.16e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 2yydA 345 1.18e+01 2zodA 345 1.18e+01 1zthA 258 1.18e+01 2pi6A 361 1.19e+01 1jq4A 98 1.21e+01 d.15.4.2 67083 1dctA 324 1.25e+01 6mhtA c.66.1.26 34244 2j7uA 635 1.29e+01 2jerA 389 1.34e+01 1ndoA 449 1.40e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 2oodA 475 1.42e+01 1o7nA 449 1.42e+01 b.33.1.2,d.129.3.3 81162,81163 1g0cA 364 1.42e+01 7a3hA c.1.8.3 60165 1xqwA 293 1.45e+01 1hjxA 362 1.46e+01 c.1.8.5,d.26.3.1 83512,83513 2je6A 277 1.50e+01 1ignA 246 1.51e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1mtzA 293 1.52e+01 c.69.1.7 79467 1yemA 179 1.52e+01 d.63.1.2 116646 1vffA 423 1.52e+01 c.1.8.4 120033 2hz5A 106 1.55e+01 1dgmA 363 1.55e+01 1bx4A c.72.1.1 34936 2v1yA 108 1.61e+01 1sw5A 275 1.64e+01 c.94.1.1 106069 1lenA 181 1.66e+01 1led b.29.1.1 24032 1yr0A 175 1.66e+01 d.108.1.1 123905 2buwB 241 1.68e+01 2o88A 58 1.76e+01 1gvfA 286 1.76e+01 c.1.10.2 70599 2burB 241 1.77e+01 b.3.6.1 129228 2yzkA 178 1.78e+01 3bqxA 150 1.81e+01 2q8zA 342 1.86e+01 2pezA 179 1.88e+01 1ijyA 130 1.88e+01 1ijxA a.141.1.1 62517 1r89A 437 1.89e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 2a2lA 145 1.90e+01 d.110.9.1 126035 1k1fA 72 1.94e+01 a.147.1.1 68007 2ia2A 265 1.95e+01 1y4oA 104 1.95e+01 1zmyA 142 1.95e+01 1wfwA 74 1.97e+01 b.34.2.1 114595 2anuA 255 1.97e+01 c.6.3.1 127058 1ea2A 131 1.97e+01 d.17.4.3 64860 1dmmA 131 1.98e+01 1opy d.17.4.3 38114 2ostA 151 1.98e+01 1i6uA 130 1.99e+01 d.140.1.1 61850 1konA 249 2.00e+01 e.39.1.1 72823 1ukgA 252 2.02e+01 b.29.1.1 99489 1j31A 262 2.04e+01 d.160.1.2 90808 2e52A 300 2.05e+01 1f9yA 158 2.06e+01 d.58.30.1 83249 1ceo 343 2.06e+01 1ceo 1ceoA 343 2.06e+01 c.1.8.3 28808 1fpqA 372 2.08e+01 1fpqA a.4.5.29,c.66.1.12 59947,59948 1zmdA 474 2.11e+01 1wwtA 88 2.13e+01 1d8cA 723 2.19e+01 1d8cA c.1.13.1 29325 1fe0A 68 2.19e+01 1cc8A d.58.17.1 39345 1iukA 140 2.24e+01 c.2.1.8 83712 2zceA 291 2.29e+01 2oz8A 389 2.33e+01 2fhzA 109 2.35e+01 d.311.1.1 133505 1o12A 376 2.36e+01 b.92.1.5,c.1.9.10 80758,80759 1an7A 136 2.39e+01 1seiA d.140.1.1 41465 2yvyA 278 2.48e+01 1zq7A 207 2.49e+01 d.309.1.1 125501 1bssA 244 2.49e+01 1rvaA c.52.1.2 33256 2q7eA 291 2.52e+01 2fe7A 166 2.53e+01 d.108.1.1 133325 2c5uA 375 2.53e+01 1zuuA 58 2.65e+01 b.34.2.1 125688 3rubS 123 2.66e+01 1rboC d.73.1.1 39616 1y0kA 209 2.72e+01 c.52.1.31 122485 3cxjA 165 2.74e+01 2bb3A 221 2.74e+01 c.90.1.1 128257 1fp1D 372 2.78e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 2f91A 237 2.80e+01 b.47.1.2 133150 2gvkA 317 2.81e+01 d.58.4.14 135782 2g45A 129 2.81e+01 2ejaA 338 2.84e+01 1ww7A 160 2.84e+01 2b3yA 888 2.87e+01 c.8.2.1,c.83.1.1 127803,127804 1p7tA 731 2.87e+01 c.1.13.1 94319 2j07A 420 2.88e+01 a.99.1.1,c.28.1.1 137891,137892 2uxtA 451 3.01e+01 1bncA 449 3.02e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 1brfA 53 3.04e+01 1rb9 g.41.5.1 45236 2ffiA 288 3.04e+01 c.1.9.15 133385 1pmmA 466 3.04e+01 c.67.1.6 94901 1te5A 257 3.06e+01 d.153.1.1 106795 1j5yA 187 3.08e+01 a.4.5.1,d.94.2.1 71592,71593 2dgmA 466 3.08e+01 c.67.1.6 131508 1bq8A 54 3.08e+01 1rb9 g.41.5.1 45237 1n8fA 350 3.12e+01 c.1.10.4 85397 1pv9A 348 3.14e+01 c.55.2.1,d.127.1.1 95157,95158 1ov3A 138 3.16e+01 b.34.2.1,b.34.2.1 87451,87452 1gulA 222 3.18e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 1btkA 169 3.20e+01 1btkA b.55.1.1 26959 1mzuA 129 3.21e+01 d.110.3.1 79714 1f9zA 135 3.23e+01 1qipA d.32.1.1 38484 1sskA 158 3.24e+01 b.148.1.1 105986 1bq9A 54 3.32e+01 1rb9 g.41.5.1 45238 2uv4A 152 3.34e+01 2jhnA 295 3.35e+01 2hg7A 110 3.38e+01 2bsxA 253 3.39e+01 c.56.2.1 129128 2qz7A 194 3.40e+01 1gg1A 350 3.44e+01 1qr7A c.1.10.4 29187 1u2cA 246 3.46e+01 b.1.6.2,d.272.1.1 107610,107611 2fnuA 375 3.48e+01 c.67.1.4 133831 2ggoA 401 3.49e+01 2f62A 161 3.52e+01 c.23.14.1 133021 1kshA 186 3.53e+01 c.37.1.8 72914 1of5B 184 3.55e+01 d.17.4.2 86934 1ordA 730 3.65e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1nv8A 284 3.66e+01 c.66.1.30 86224 2ax4A 198 3.69e+01 1b96A 244 3.77e+01 1rvaA c.52.1.2 33268 1qr7A 350 3.78e+01 1qr7A c.1.10.4 29191 1i6wA 181 3.83e+01 1i6wA c.69.1.18 61859 2pvxA 54 3.84e+01 1jmxA 494 3.85e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1ispA 181 3.89e+01 c.69.1.18 76778 1owqA 361 3.89e+01 c.1.8.5,d.26.3.1 104041,104042 2re7A 134 3.91e+01 1xmxA 385 3.95e+01 c.52.1.26 115568 1vqsA 116 3.95e+01 d.58.4.13 114019 2ywvA 244 4.01e+01 6rxnA 45 4.02e+01 g.41.5.1 45222 2iz6A 176 4.03e+01 2ex4A 241 4.04e+01 c.66.1.42 132516 2bzeA 153 4.12e+01 1ka9H 200 4.15e+01 c.23.16.1 77308 1t15A 214 4.21e+01 c.15.1.3,c.15.1.3 99067,99068 1nz0A 118 4.23e+01 d.14.1.2 86433 1xvsA 126 4.23e+01 b.1.23.1 116095 1qydA 313 4.28e+01 c.2.1.2 96583 2rauA 354 4.29e+01 1eonA 245 4.31e+01 1rvaA c.52.1.2 33238 1yqyA 523 4.36e+01 d.92.1.14,d.166.1.1 123903,123904 2p7oA 133 4.39e+01 2fxtA 192 4.40e+01 2ac1A 541 4.56e+01 1b34B 118 4.57e+01 1b34B b.38.1.1 24797 2dc4A 165 4.63e+01 1gsoA 431 4.74e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 2bo9A 308 4.75e+01 c.56.5.1 128897 1aboA 62 4.75e+01 1bbzA b.34.2.1 24474 1oroA 213 4.76e+01 1opr c.61.1.1 34093 1b94A 244 4.80e+01 1rvaA c.52.1.2 33250 1bbzA 58 4.80e+01 1bbzA b.34.2.1 24477 1wy7A 207 4.83e+01 c.66.1.32 121433 2ltnA 181 4.83e+01 1led b.29.1.1 24024 1v74A 107 4.83e+01 d.243.1.1 100442 2vhhA 405 4.84e+01 1b97A 244 4.86e+01 1rvaA c.52.1.2 33252 3bcxA 437 4.87e+01 1vcvA 226 4.90e+01 c.1.10.1 119988 1tqnA 486 4.92e+01 a.104.1.1 107238 2nsfA 261 4.92e+01 1mp4A 292 4.99e+01 c.68.1.6 79376 1x6vA 630 5.01e+01 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 2z2nA 299 5.05e+01 1booA 323 5.06e+01 1booA c.66.1.11 34248 1h5rA 293 5.07e+01 c.68.1.6 65623 2dc3A 193 5.16e+01 2hq6A 185 5.21e+01 1c4kA 730 5.22e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1fa8A 135 5.29e+01 1qipA d.32.1.1 38486 1oc0A 379 5.29e+01 e.1.1.1 86790 1kllA 130 5.35e+01 d.32.1.2 72720 2iy2A 72 5.39e+01 3c3yA 237 5.40e+01 1f75A 249 5.46e+01 1f75A c.101.1.1 59662 1ojrA 274 5.61e+01 c.74.1.1 93147 1sx5A 244 5.64e+01 c.52.1.2 99023 2dgkA 452 5.67e+01 2a4xA 138 5.70e+01 d.32.1.2 126166 1h09A 338 5.72e+01 b.109.1.1,c.1.8.8 83420,83421 2v9lA 274 5.75e+01 1lj5A 379 5.76e+01 e.1.1.1 73928 1j7nA 776 5.84e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 2j8gA 339 5.87e+01 2ovgA 66 5.89e+01 1xttA 216 5.93e+01 c.61.1.1 122300 2dsxA 52 6.07e+01 g.41.5.1 131699 3bhwA 209 6.13e+01 1a9nB 96 6.15e+01 1urnA d.58.7.1 39165 1zkcA 197 6.17e+01 b.62.1.1 125182 1d2gA 292 6.20e+01 1xvaA c.66.1.5 34187 3biyA 380 6.20e+01 1eokA 290 6.24e+01 1eokA c.1.8.5 28991 2avxA 171 6.24e+01 2onuA 152 6.29e+01 1b2oA 54 6.30e+01 1rb9 g.41.5.1 45233 2o4tA 100 6.32e+01 2r76A 152 6.35e+01 1jeqB 565 6.37e+01 1jeqB b.131.1.2,c.62.1.4 90368,90369 2evbA 74 6.46e+01 1ml8A 134 6.51e+01 d.227.1.2 85013 1z08A 170 6.52e+01 c.37.1.8 124303 2jrrA 67 6.52e+01 1cojA 212 6.53e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2do3A 69 6.54e+01 b.34.5.5 131596 2pveA 54 6.61e+01 1gd0A 122 6.64e+01 1dptA d.80.1.3 39834 2gj8A 172 6.65e+01 c.37.1.8 135270 1w8sA 263 6.66e+01 c.1.10.1 120744 3canA 182 6.73e+01 1ysjA 404 6.76e+01 c.56.5.4,d.58.19.1 123975,123976 1qmvA 197 6.78e+01 1qq2A c.47.1.10 33066 1vg0A 650 6.84e+01 c.3.1.3,d.16.1.6 108596,108597 2ao3A 130 6.86e+01 2i6cA 160 6.95e+01 d.108.1.1 137095 1yk4A 52 6.95e+01 1db2A 377 6.97e+01 1sek e.1.1.1 42672 1p3wA 404 6.98e+01 c.67.1.3 87752 2jc9A 555 6.99e+01 2o3bB 136 7.02e+01 d.221.1.1 138902 2pajA 492 7.04e+01 1eyzA 392 7.06e+01 1ez1A b.84.2.1,c.30.1.1,d.142.1.2 28246,31653,41498 1n0wA 243 7.12e+01 c.37.1.11 79772 1s1dA 331 7.13e+01 b.67.3.1 98344 1j3wA 163 7.15e+01 d.110.7.1 90833 1j3mA 129 7.20e+01 d.129.7.1 103836 8rucI 123 7.24e+01 1rboC d.73.1.1 39629 1hg3A 225 7.27e+01 1hg3A c.1.1.1 61025 2iswA 323 7.28e+01 2bivA 243 7.32e+01 b.34.9.3,b.34.9.3 128592,128593 1kjqA 391 7.34e+01 b.84.2.1,c.30.1.1,d.142.1.2 72616,72617,72618 1hg8A 349 7.34e+01 b.80.1.3 65830 1wyuA 438 7.36e+01 c.67.1.7 121452 1xesA 413 7.38e+01 1urvA 190 7.39e+01 a.1.1.2 113414 2o1sA 621 7.39e+01 1zxtA 76 7.39e+01 2iu4A 336 7.39e+01 1l1nA 183 7.43e+01 b.47.1.4 73476 1pbyB 337 7.45e+01 b.69.2.2 94422 2jc5A 259 7.49e+01 1ez1A 392 7.51e+01 1ez1A b.84.2.1,c.30.1.1,d.142.1.2 28248,31655,41500 2fvhA 120 7.51e+01 1pa1A 310 7.60e+01 c.45.1.2 94404 1a9cA 221 7.63e+01 1a8rA d.96.1.1 40602 2dfuA 264 7.64e+01 1a8y 367 7.68e+01 1a8y 1a8yA 367 7.68e+01 c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1iroA 54 7.70e+01 g.41.5.1 45223 1nd4A 264 7.72e+01 d.144.1.6 91815 3clkA 290 7.73e+01 2gs8A 317 7.75e+01 1b2jA 54 7.75e+01 1rb9 g.41.5.1 45231 2zjrG 174 7.78e+01 1zt1A 277 7.81e+01 1df7A 159 7.88e+01 3dfr c.71.1.1 34885 1wj9A 211 7.89e+01 d.58.53.1,d.58.53.1 114694,114695 3caiA 406 7.92e+01