# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1tbxA 99 5.36e-04 a.4.5.48 106748 1xmaA 145 5.74e-04 2fbiA 142 1.85e-03 1yyvA 131 2.25e-03 1ub9A 100 1.25e-02 a.4.5.28 99159 2eshA 118 1.38e-02 1z7uA 112 1.55e-02 1e2xA 243 4.79e-02 1e2xA a.4.5.6,a.78.1.1 16113,18443 1hw1A 239 5.43e-02 1e2xA a.4.5.6,a.78.1.1 16111,18441 3rubS 123 6.31e-02 1rboC d.73.1.1 39616 2fswA 107 6.73e-02 1f4kA 122 7.16e-02 1bm9A a.4.5.7 59646 1an7A 136 1.13e-01 1seiA d.140.1.1 41465 1r7jA 95 1.16e-01 a.4.5.49 104836 2a61A 145 1.26e-01 1sfxA 109 1.31e-01 a.4.5.50 105505 2f2eA 146 1.31e-01 1mzbA 136 1.40e-01 a.4.5.42 91497 2g7uA 257 1.42e-01 1jgsA 138 1.45e-01 a.4.5.28 66683 1wddS 128 1.67e-01 1sd4A 126 2.26e-01 a.4.5.39 105428 1okrA 123 2.34e-01 a.4.5.39 93269 1bm9A 122 2.34e-01 1bm9A a.4.5.7 16116 1ir21 140 3.35e-01 2fbhA 146 3.79e-01 1f5tA 121 4.12e-01 1bi0 a.4.5.24,a.76.1.1 16203,18409 1seiA 130 4.18e-01 1seiA d.140.1.1 41463 1gk8I 140 5.14e-01 d.73.1.1 65242 1ddnA 226 5.52e-01 1bi0 a.4.5.24,a.76.1.1 16207,18413 2ethA 154 6.31e-01 1rboC 123 6.36e-01 1rboC d.73.1.1 39634 1i6uA 130 7.66e-01 d.140.1.1 61850 1bjaA 95 7.70e-01 1bjaA a.4.5.9 16122 8rucI 123 8.63e-01 1rboC d.73.1.1 39629 1s3jA 155 1.31e+00 a.4.5.28 98437 1mkmA 249 1.32e+00 a.4.5.33,d.110.2.2 79242,79243 1b1bA 140 1.40e+00 1bi0 a.4.5.24,a.76.1.1 16215,18421 1q1hA 110 1.61e+00 a.4.5.41 95580 1wwiA 148 1.96e+00 1pls 113 2.07e+00 1pls b.55.1.1 26965 2gjgA 248 2.21e+00 2g0uA 92 2.46e+00 1p4xA 250 2.59e+00 a.4.5.28,a.4.5.28 87784,87785 2esnA 310 2.76e+00 2fug5 207 2.80e+00 2cq2A 114 2.84e+00 2cohA 202 2.95e+00 2fhzA 109 3.15e+00 1r1uA 106 3.35e+00 a.4.5.5 104771 1u2wA 122 4.06e+00 1ulyA 192 4.36e+00 1lj9A 144 4.39e+00 a.4.5.28 78035 1y88A 199 4.55e+00 1b9mA 265 4.93e+00 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1lnwA 147 5.11e+00 a.4.5.28 78104 1i1sA 96 5.13e+00 1bjaA a.4.5.9 16124 1ft9A 222 5.14e+00 1ft9A a.4.5.4,b.82.3.1 16107,28131 1xgsA 295 5.41e+00 1bn5 a.4.5.25,d.127.1.1 16216,41153 1fzdA 201 5.68e+00 3fib d.171.1.1 42484 1mml 265 5.94e+00 1mml e.8.1.2 43015 1fx7A 230 6.15e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 2atzA 180 6.21e+00 1w7jA 795 6.27e+00 2c5uA 375 6.34e+00 1oi0A 124 6.48e+00 c.97.3.1 93045 1jksA 294 6.51e+00 d.144.1.7 71710 1zhvA 134 7.05e+00 1svdM 110 7.22e+00 2b0lA 102 7.68e+00 1yzbA 182 7.71e+00 1lddA 74 7.73e+00 a.4.5.34 73841 1or7C 90 8.81e+00 a.180.1.1 87336 1cojA 212 9.03e+00 1avmA a.2.11.1,d.44.1.1 15737,38734 1bi0 226 9.14e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16202,18408,24453 2cujA 108 9.53e+00 1c0wA 225 1.01e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 1ywlA 96 1.04e+01 1p4fA 293 1.10e+01 d.144.1.7 104063 1yg2A 179 1.10e+01 1u5tC 202 1.12e+01 a.4.5.54,a.4.5.54 107688,107689 1s1hC 192 1.12e+01 i.1.1.1 105156 1wj5A 120 1.14e+01 1s1fA 406 1.14e+01 1smtA 122 1.22e+01 1smtA a.4.5.5 16109 1gefA 123 1.22e+01 1gefA c.52.1.18 60465 1iz1A 294 1.27e+01 a.4.5.37,c.94.1.1 83823,83824 1jeyB 565 1.29e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 1t6cA 315 1.31e+01 c.55.1.8,c.55.1.8 106558,106559 1z91A 147 1.32e+01 1wv2A 265 1.35e+01 1ikpA 613 1.38e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 2fj6A 82 1.39e+01 1uwzA 136 1.40e+01 c.97.1.1 108081 1ob8A 135 1.41e+01 1jtkA 136 1.44e+01 c.97.1.1 71862 1o97C 264 1.48e+01 c.26.2.3 81232 1twfA 1733 1.54e+01 1xewY 172 1.58e+01 1nrwA 288 1.63e+01 c.108.1.10 86128 1vb3A 428 1.63e+01 1sxrA 183 1.65e+01 d.118.1.1 106101 1htoA 477 1.70e+01 d.15.9.1,d.128.1.1 70987,70988 1bib 321 1.71e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 2d83A 363 1.73e+01 1rpl 251 1.78e+01 1bpyA a.60.12.1,d.218.1.2 75933,75934 1scmA 60 1.78e+01 1wdcA 2ckiA 262 1.79e+01 1u5tA 233 1.79e+01 a.4.5.54,a.4.5.54 107684,107685 1yewA 382 1.86e+01 1wkbA 810 1.87e+01 3il8 72 1.88e+01 1tvxA d.9.1.1 37356 1b66A 140 1.88e+01 1b66A d.96.1.2 40657 1mnmC 87 1.88e+01 1akhB a.4.1.1 15983 1aerA 205 1.92e+01 1aerA d.166.1.1 42249 1pqxA 91 1.92e+01 d.267.1.1 104296 1r5pA 108 1.95e+01 c.47.1.15 97101 1i50A 1733 1.97e+01 e.29.1.2 61754 1htqA 477 2.00e+01 d.15.9.1,d.128.1.1 71035,71036 1ipiA 123 2.04e+01 c.52.1.18 66255 1ufoA 238 2.05e+01 c.69.1.27 99344 1axj 122 2.05e+01 1axj b.45.1.1 25749 2d27A 149 2.07e+01 2cb2A 318 2.08e+01 1duxC 94 2.22e+01 1awcA a.4.5.21 16170 1bpyA 335 2.23e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1qwgA 251 2.26e+01 c.1.27.1 96473 1j1hA 144 2.27e+01 b.111.1.1 77056 1icwA 72 2.31e+01 1tvxA d.9.1.1 37357 1qbjA 81 2.31e+01 1qbjA a.4.5.19 16155 1sfuA 75 2.33e+01 a.4.5.19 105503 1tv9A 335 2.36e+01 2fu4A 83 2.36e+01 1hw5A 210 2.37e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1wdcA 64 2.37e+01 1wdcA 2agaA 190 2.37e+01 1oe9A 795 2.37e+01 b.34.3.1,c.37.1.9 92792,92793 1xg9A 260 2.38e+01 1zghA 260 2.38e+01 1gtqA 140 2.39e+01 1b66A d.96.1.2 40661 2d09A 407 2.40e+01 1ffkM 148 2.40e+01 1ffkM a.94.1.1 18740 2dtr 226 2.40e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1rcqA 357 2.44e+01 b.49.2.2,c.1.6.1 104882,104883 1yspA 181 2.47e+01 1r1tA 122 2.48e+01 a.4.5.5 104769 1cliA 345 2.50e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1xb4A 202 2.50e+01 1wxxA 382 2.53e+01 1ckqA 276 2.60e+01 1ckqA c.52.1.1 33229 1jj2O 148 2.62e+01 1ffkM a.94.1.1 63100 1qzmA 94 2.64e+01 c.37.1.20 96651 2fxaA 207 2.70e+01 1cl8A 276 2.71e+01 1ckqA c.52.1.1 33230 1g57A 217 2.76e+01 1g57A d.115.1.2 60253 1oroA 213 2.76e+01 1opr c.61.1.1 34093 1ubeA 349 2.76e+01 c.37.1.11,d.48.1.1 88412,88413 1r4vA 171 2.76e+01 a.197.1.1 97049 1flmA 122 2.77e+01 1axj b.45.1.1 25747 1a9eA 277 2.78e+01 1agdA b.1.1.2,d.19.1.1 20757,38268 1z5bA 469 2.78e+01 1bpb 248 2.79e+01 1bpyA a.60.12.1,d.218.1.2 75811,75812 1nom 248 2.80e+01 1bpyA a.60.12.1,d.218.1.2 75929,75930 1v9jA 113 2.81e+01 d.52.6.1 100542 1wwhA 119 2.84e+01 2cgpA 210 2.84e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1i1gA 141 2.86e+01 a.4.5.32,d.58.4.2 65982,65983 1cm7A 363 2.89e+01 1cnzA c.77.1.1 35063 1nzjA 298 2.91e+01 c.26.1.1 92377 2awpA 198 2.91e+01 1ka8A 100 2.93e+01 a.4.5.20 72241 1bia 321 2.96e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1iscA 192 2.97e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1fp2A 352 3.02e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1jmsA 381 3.03e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1gd5A 130 3.06e+01 1gd5A d.189.1.1 60439 1f93A 104 3.07e+01 1dcpA d.74.1.1 39688 1ysqA 193 3.07e+01 1isaA 192 3.07e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1tif 78 3.09e+01 1tif d.15.8.1 37836 1og6A 298 3.14e+01 c.1.7.1 86984 1io0A 185 3.15e+01 c.10.1.1 76753 1zthA 258 3.17e+01 1jeqB 565 3.19e+01 1jeqB b.131.1.2,c.62.1.4 90368,90369 1lea 84 3.21e+01 1lea a.4.5.2 16085 1smtB 122 3.23e+01 1smtA a.4.5.5 16110 1zybA 232 3.28e+01 1jqgA 433 3.30e+01 c.56.5.1,d.58.3.1 71791,71792 1tzaA 134 3.32e+01 b.1.23.1 107468 1tljA 213 3.35e+01 d.282.1.1 107126 1pfvA 551 3.37e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1vphA 149 3.38e+01 1wn5A 130 3.44e+01 1quqB 121 3.48e+01 1quqB b.40.4.3 25305 1h7nA 342 3.51e+01 1b4kA c.1.10.3 60726 1dosA 358 3.54e+01 1dosA c.1.10.2 29175 2b7kA 200 3.63e+01 1xriA 151 3.63e+01 9gafA 295 3.64e+01 1apyA d.153.1.5 42008 1o82A 70 3.65e+01 a.64.2.1 92630 1vfqA 143 3.67e+01 1af3 196 3.67e+01 1maz f.1.4.1 43397 1j9jA 247 3.68e+01 c.106.1.1 62758 1xkyA 301 3.69e+01 1ois 223 3.77e+01 1a36A e.15.1.1 43267 2fhqA 141 3.81e+01 1t3yA 141 3.81e+01 1ezeA 38 3.82e+01 1ezeA j.39.1.1 46302 1jhfA 202 3.86e+01 a.4.5.2,b.87.1.1 63057,63058 1opr 213 3.86e+01 1opr c.61.1.1 34091 1yodA 30 3.89e+01 1xsnA 335 3.91e+01 1ohlA 342 3.97e+01 c.1.10.3 87035 1ywqA 200 3.98e+01 1ixcA 294 4.02e+01 a.4.5.37,c.94.1.1 83764,83765 1kcxA 518 4.02e+01 b.92.1.3,c.1.9.6 90953,90954 1cfyA 143 4.05e+01 1cof d.109.1.2 40858 1lh0A 213 4.09e+01 c.61.1.1 73896 1cf9A 753 4.11e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 2cxaA 256 4.12e+01 1qpsA 261 4.14e+01 1ckqA c.52.1.1 33234 1wdjA 187 4.21e+01 2gl5A 410 4.23e+01 1pz7A 204 4.26e+01 b.29.1.4 95405 1jofA 365 4.31e+01 b.69.10.1 71775 2bjkA 516 4.38e+01 1ah0 316 4.39e+01 1frb c.1.7.1 28685 1udmA 149 4.40e+01 d.109.1.2 107780 1f4lA 551 4.41e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1e68A 70 4.42e+01 1e68A a.64.2.1 18144 2gwgA 350 4.50e+01 1lvaA 258 4.51e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1ylvA 342 4.56e+01 1b4kA c.1.10.3 29180 1j9lA 247 4.58e+01 c.106.1.1 62762 2avuE 192 4.69e+01 1kx5B 102 4.70e+01 a.22.1.1 77594 1qqtA 551 4.74e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1i6xA 209 4.77e+01 a.4.5.4,b.82.3.2 83673,83674 1plq 258 4.80e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1whzA 70 4.81e+01 2d13A 227 4.84e+01 1cof 143 4.84e+01 1cof d.109.1.2 40860 1dguA 183 4.85e+01 1dguA a.39.1.5 17333 1g60A 260 4.94e+01 c.66.1.11 70151 1xm3A 264 4.99e+01 1vmfA 145 5.03e+01 1ukkA 142 5.14e+01 d.227.1.1 99491 1twfK 120 5.17e+01 1f7uA 607 5.20e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1p4kA 295 5.22e+01 d.153.1.5 87772 1t2lA 141 5.28e+01 1omzA 293 5.35e+01 c.68.1.15 87093 2cfxA 144 5.41e+01 1s1hM 132 5.41e+01 i.1.1.1 105165 1mla 309 5.42e+01 1mla c.19.1.1,d.58.23.1 31031,39383 2a9mL 110 5.45e+01 1i50K 120 5.48e+01 d.74.3.2 61765 1mp4A 292 5.51e+01 c.68.1.6 79376 1stzA 338 5.51e+01 a.4.5.51,d.110.2.3 106009,106010 2bl1A 172 5.54e+01 1t4nA 94 5.54e+01 d.50.1.1 106424 1oltA 457 5.62e+01 c.1.28.2 93334 1awiA 138 5.67e+01 1pne d.110.1.1 40871 1g6nA 210 5.67e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1uzbA 516 5.68e+01 c.82.1.1 100220 2cc0A 195 5.70e+01 1utg 70 5.73e+01 1utg a.101.1.1 18813 1uarA 285 5.74e+01 c.46.1.2,c.46.1.2 107762,107763 1ggvA 232 5.75e+01 1din c.69.1.9 34683 1il8A 72 5.79e+01 1tvxA d.9.1.1 37365 1ru0A 105 5.87e+01 1te0A 318 5.94e+01 2agtA 319 5.97e+01 1a1nA 276 5.98e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 1o60A 292 6.02e+01 c.1.10.4 92532 1xppA 115 6.04e+01 2d0eA 407 6.06e+01 1i4wA 353 6.07e+01 c.66.1.24 66028 1akn 579 6.08e+01 2bce c.69.1.1 34626 1ayyA 151 6.12e+01 1apyA d.153.1.5 42016 2g0qA 173 6.20e+01 1whxA 111 6.22e+01 1y93A 159 6.26e+01 2fmpA 335 6.27e+01 1fil 139 6.28e+01 1pne d.110.1.1 40869 1hh1A 143 6.33e+01 1gefA c.52.1.18 61036 1a63 130 6.44e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 1on2A 142 6.46e+01 a.4.5.24,a.76.1.1 87103,87104 4enl 436 6.47e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1l5zA 155 6.48e+01 c.23.1.1 77722 1quqA 129 6.57e+01 1quqA b.40.4.3 25303 2dpg 485 6.59e+01 1dpgA c.2.1.3,d.81.1.5 30076,39991 1zkjA 359 6.60e+01 1htyA 1015 6.62e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 2utgA 70 6.64e+01 1utg a.101.1.1 18814 1kwgA 645 6.68e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1a1mA 278 6.69e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 1xh3A 276 6.69e+01 1v4eA 299 6.73e+01 a.128.1.1 100296 1wndA 495 6.74e+01 1bak 119 6.82e+01 1bak b.55.1.1 26973 1nr4A 71 6.85e+01 d.9.1.1 92077 1em8B 112 6.87e+01 c.126.1.1 90458 1kbhB 59 6.88e+01 a.153.1.1 68383 1fbaA 361 6.93e+01 1fbaA c.1.10.1 29120 1x79B 112 6.93e+01 1iz5A 249 6.93e+01 d.131.1.2,d.131.1.2 83834,83835 1sw6A 327 6.94e+01 1sw6A d.211.1.1 19176 1b9hA 388 6.95e+01 1b9hA c.67.1.4 34488 6pfkA 319 6.98e+01 3pfk c.89.1.1 35583 1gtmA 419 6.99e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 2nef 136 6.99e+01 1efnB d.102.1.1 40704 1bxdA 161 7.00e+01 1bxdA d.122.1.3 41111 1tdtA 259 7.00e+01 3tdt b.81.1.2 28055 1yme 309 7.02e+01 1aye c.56.5.1 33804 1hwwA 1015 7.02e+01 a.8.3.1,b.30.5.6,c.6.2.1 83067,83068,83069 1qkkA 155 7.04e+01 1dbwA c.23.1.1 31104 1gkpA 458 7.06e+01 b.92.1.3,c.1.9.6 70231,70232 1bavA 309 7.10e+01 1aye c.56.5.1 33806 1jmcA 246 7.14e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1fpxA 352 7.14e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 9apiA 347 7.15e+01 1ovaA e.1.1.1 42630 1frb 315 7.25e+01 1frb c.1.7.1 28665 1m4lA 307 7.30e+01 c.56.5.1 78604 1ewqA 765 7.30e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1m93B 245 7.33e+01 2fpoA 202 7.45e+01 1k77A 260 7.49e+01 c.1.15.5 72096 1e3mA 800 7.53e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1j6rA 214 7.54e+01 d.173.1.2 71598 2b30A 301 7.56e+01 1g7vA 284 7.56e+01 1d9eA c.1.10.4 60335 1rdzA 337 7.60e+01 1frpA e.7.1.1 42882 1hbxG 157 7.60e+01 1awcA a.4.5.21 60934 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8.84e+01 a.69.3.1,c.2.1.3,d.81.1.3 68192,68193,68194 1mu5A 471 8.86e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1e6yA 569 8.89e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 1wwjA 105 8.89e+01 1eriA 276 8.90e+01 1ckqA c.52.1.1 33231 1cz3A 168 8.92e+01 1d1gA c.71.1.1 34891 1a7oL 106 8.93e+01 8fabA b.1.1.1 19942 1fmjA 351 8.96e+01 c.37.1.5 59879