# List of top-scoring protein chains for t04-100-30-o_notor2-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 1dhn 121 9.87e-02 1dhn d.96.1.3 40663 1zq1A 438 1.15e-01 1y14B 171 2.39e-01 1khoA 370 3.69e-01 a.124.1.1,b.12.1.3 72489,72490 1a62 130 3.76e-01 1a62 a.140.3.1,b.40.4.5 64708,64709 2c78A 405 4.91e-01 1ha3A 405 5.26e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 2h6lA 146 6.23e-01 1c9oA 66 7.03e-01 1mjc b.40.4.5 25325 1a8vA 121 8.20e-01 1a62 a.140.3.1,b.40.4.5 64712,64713 1u4nA 310 8.77e-01 1s5aA 150 1.12e+00 d.17.4.10 98525 1exmA 405 1.13e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 2d9rA 104 1.24e+00 1ig0A 319 1.40e+00 1ig0A b.82.6.1,c.100.1.1 62354,62355 1fr3A 67 1.97e+00 1fr3A b.40.6.1 25436 2fcfA 103 2.07e+00 1ts9A 102 2.45e+00 1iz0A 302 2.87e+00 b.35.1.2,c.2.1.1 83821,83822 2a5zA 262 3.03e+00 1xzpB 150 3.06e+00 1xg9A 260 3.07e+00 1zghA 260 3.09e+00 2f4nA 273 3.21e+00 1l6pA 125 3.60e+00 b.1.17.1 73626 1ofdA 1520 3.67e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1ugxA 133 3.72e+00 1vkkA 154 3.91e+00 d.109.1.2 108669 1h2kA 349 3.98e+00 b.82.2.6 76572 1m26A 133 4.15e+00 2basA 431 4.43e+00 1rznA 205 4.47e+00 1yezA 68 4.54e+00 1kngA 156 4.55e+00 c.47.1.10 72777 1kqqA 139 4.56e+00 a.4.3.1 72885 2cqsA 842 5.25e+00 1i6pA 220 5.34e+00 1ddzA c.53.2.1 61848 1wqaA 455 5.38e+00 1jmxA 494 5.81e+00 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 1vphA 149 6.13e+00 1vjnA 220 6.40e+00 d.157.1.4 100825 1s4cA 155 6.56e+00 1unqA 125 6.72e+00 b.55.1.1 107968 1vrbA 342 7.09e+00 1ihjA 98 7.14e+00 1pdr b.36.1.1 62382 1ift 263 7.45e+00 1mrj d.165.1.1 42211 1wjnA 97 7.49e+00 1h10A 125 7.58e+00 b.55.1.1 83446 1zd7A 159 7.63e+00 1cleA 534 8.06e+00 1thg c.69.1.17 34771 1ca1 370 8.11e+00 1ca1 a.124.1.1,b.12.1.3 19340,23648 2fb7A 95 8.11e+00 2fdiA 211 8.21e+00 2fwkA 121 8.36e+00 1qzgA 187 8.50e+00 b.40.4.3 96643 1krhA 338 8.55e+00 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1zp7A 206 8.63e+00 2aj6A 159 9.00e+00 1a8p 258 9.28e+00 1fdr b.43.4.2,c.25.1.1 25654,31544 1mfgA 95 9.53e+00 b.36.1.1 79043 1llfA 534 9.54e+00 c.69.1.17 78094 1x74A 360 9.59e+00 1v54B 227 9.64e+00 b.6.1.2,f.17.2.1 100322,100323 1yo8A 634 9.69e+00 1a8i 842 9.75e+00 1a8i c.87.1.4 35490 1mgqA 83 9.76e+00 b.38.1.1 79099 1d3bB 91 9.93e+00 1d3bB b.38.1.1 24804 1fdr 248 1.01e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 4ubpC 570 1.04e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1h8gA 95 1.07e+01 b.109.1.1 65735 2h3lA 103 1.08e+01 1yloA 348 1.08e+01 1xw4X 110 1.12e+01 1usuA 260 1.13e+01 d.14.1.8 99885 1jopA 155 1.15e+01 b.82.2.7 84187 1dl2A 511 1.15e+01 1dl2A a.102.2.1 18844 1kv7A 488 1.17e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1avaC 181 1.22e+01 1avaC b.42.4.1 25604 1e0gA 48 1.31e+01 1e01A d.7.1.1 37325 1ukmB 128 1.31e+01 d.169.1.1 99500 1ux6A 350 1.31e+01 b.29.1.16,g.75.1.1 100145,100146 1lba 146 1.36e+01 1lba d.118.1.1 41062 1qd5A 275 1.37e+01 1qd5A f.4.2.1 43748 2cwpA 112 1.39e+01 1qx4A 274 1.41e+01 b.43.4.2,c.25.1.1 104624,104625 1uq5A 263 1.43e+01 d.165.1.1 99778 2gzvA 114 1.47e+01 2g9zA 348 1.48e+01 1v5iB 76 1.50e+01 2ci9A 102 1.53e+01 1sefA 274 1.53e+01 b.82.1.11 105452 1gutA 68 1.54e+01 b.40.6.1 65576 1qlaA 656 1.54e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1xpiA 231 1.58e+01 1t3cA 421 1.59e+01 d.92.1.7 106343 1b77A 228 1.59e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1vmfA 145 1.59e+01 1yavA 159 1.62e+01 2bs3A 656 1.70e+01 1o0xA 262 1.74e+01 d.127.1.1 80755 1xxqA 161 1.85e+01 1pl8A 356 1.89e+01 b.35.1.2,c.2.1.1 94878,94879 1tuhA 156 1.90e+01 d.17.4.11 107345 1l2mA 118 1.95e+01 d.89.1.4 77657 1smvA 260 1.97e+01 1smvA b.121.4.7 23288 2cxaA 256 1.97e+01 1m5q1 130 1.98e+01 1zg2A 107 1.99e+01 1cbf 285 2.00e+01 1cbf c.90.1.1 35587 1v9kA 228 2.06e+01 d.265.1.3 108449 1x1oA 286 2.08e+01 1v7pB 128 2.11e+01 d.169.1.1 108407 1rkd 309 2.11e+01 1rkd c.72.1.1 34928 1yfuA 174 2.12e+01 1r4pB 70 2.12e+01 b.40.2.1 97026 1ml8A 134 2.13e+01 d.227.1.2 85013 1iz5A 249 2.14e+01 d.131.1.2,d.131.1.2 83834,83835 2f2lX 167 2.14e+01 2b1xA 470 2.16e+01 1vjrA 271 2.17e+01 c.108.1.14 100832 1efdN 266 2.22e+01 1efdN c.92.2.1 35597 1db3A 372 2.23e+01 1db3A c.2.1.2 29813 1g0hA 252 2.27e+01 1dk4A e.7.1.1 60171 1qd6C 240 2.30e+01 1qd5A 2bibA 547 2.31e+01 1bia 321 2.31e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1l5wA 796 2.33e+01 c.87.1.4 73605 1k8tA 510 2.34e+01 e.41.1.1 68316 1ns5A 155 2.37e+01 c.116.1.3 80705 1wzoA 246 2.38e+01 1sacA 204 2.38e+01 1sacA b.29.1.5 24237 1vj0A 380 2.40e+01 b.35.1.2,c.2.1.1 100786,100787 1xneA 113 2.41e+01 1eq9A 222 2.48e+01 5ptp b.47.1.2 26068 1iktA 120 2.51e+01 d.106.1.1 66188 1bjt 793 2.54e+01 1bjt e.11.1.1 43249 1s4iA 175 2.57e+01 1rgyA 360 2.57e+01 e.3.1.1 97456 1ms9A 648 2.59e+01 b.29.1.15,b.68.1.1 85088,85089 2bjkA 516 2.59e+01 1sk4A 163 2.62e+01 d.118.1.1 105664 1n1tA 641 2.70e+01 b.29.1.15,b.68.1.1 79821,79822 1h5uA 842 2.70e+01 1a8i c.87.1.4 60655 1hw5A 210 2.70e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1dbhA 354 2.72e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1dleA 298 2.76e+01 1dleA b.47.1.2 26312 1odfA 290 2.76e+01 c.37.1.6 92782 1sxrA 183 2.79e+01 d.118.1.1 106101 1lk5A 229 2.83e+01 c.124.1.4,d.58.40.1 73960,73961 1z1yA 186 2.84e+01 2ew0A 192 2.90e+01 1uwzA 136 2.93e+01 c.97.1.1 108081 1sotA 320 2.94e+01 b.36.1.4,b.47.1.1 105852,105853 1uzbA 516 2.98e+01 c.82.1.1 100220 2b30A 301 3.01e+01 1jtkA 136 3.04e+01 c.97.1.1 71862 1yb3A 175 3.05e+01 1vmeA 410 3.05e+01 c.23.5.1,d.157.1.3 108893,108894 1dmhA 311 3.10e+01 1dmhA b.3.6.1 22633 1gyzA 60 3.11e+01 a.144.2.1 70793 1e3jA 352 3.12e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 2czqA 205 3.13e+01 1p4kA 295 3.16e+01 d.153.1.5 87772 1i27A 73 3.19e+01 1i27A a.4.5.30 61555 2akrA 285 3.23e+01 1a7tA 232 3.26e+01 1a7tA d.157.1.1 42041 1am2 199 3.27e+01 1am2 b.86.1.2 28381 1qxoA 388 3.28e+01 d.258.1.1 96539 1f3uB 171 3.33e+01 1f3uB b.65.1.1 27525 1ndh 272 3.37e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1oa4A 222 3.38e+01 b.29.1.11 86731 1t3kA 152 3.43e+01 c.46.1.1 106357 9gafA 295 3.55e+01 1apyA d.153.1.5 42008 1m2eA 135 3.61e+01 c.23.1.5 78478 1wraA 308 3.63e+01 1dqaA 467 3.64e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 2ajtA 500 3.68e+01 1gefA 123 3.72e+01 1gefA c.52.1.18 60465 1qftA 175 3.72e+01 1qftA b.60.1.1 27151 4tmkA 213 3.73e+01 5tmpA c.37.1.1 31930 1gdoA 240 3.74e+01 1gdoA 1cyw 205 3.79e+01 1cyx b.6.1.2 23024 1o5uA 101 3.81e+01 b.82.1.8 92518 1j1lA 290 3.82e+01 b.82.1.12 90766 1xtqA 177 3.82e+01 1ecsA 126 3.82e+01 1ecsA d.32.1.2 59407 1whi 122 3.82e+01 1whi b.39.1.1 24810 1ss4A 153 3.84e+01 d.32.1.6 105976 1e3dB 542 3.85e+01 1h2rL e.18.1.1 59189 1l5aA 436 3.95e+01 c.43.1.2,c.43.1.2 75923,75924 1fsyA 358 3.96e+01 1gceA e.3.1.1 60016 1g291 372 3.99e+01 1g291 2cu3A 64 4.00e+01 1pi4A 358 4.04e+01 e.3.1.1 94700 1gx1A 160 4.08e+01 d.79.5.1 70675 1z5yE 149 4.08e+01 1vk4A 298 4.10e+01 c.72.1.1 100850 1xw3A 110 4.11e+01 1rc6A 261 4.15e+01 b.82.1.11 97287 2h7bA 105 4.15e+01 1u0mA 382 4.15e+01 c.95.1.2,c.95.1.2 107557,107558 1h9mA 145 4.19e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 1m1hA 248 4.20e+01 b.114.1.1,d.58.42.1 78415,78416 1q7hA 153 4.21e+01 b.122.1.1,d.17.6.2 96042,96043 1c30B 382 4.24e+01 c.8.3.1,c.23.16.1 30736,31413 1f56A 91 4.25e+01 2cbp b.6.1.1 22896 2cjaA 522 4.30e+01 1zjjA 263 4.30e+01 1ibyA 112 4.34e+01 1ibzA b.6.1.4 62233 1u7bA 261 4.37e+01 1opbA 135 4.42e+01 1hmt b.60.1.2 27216 1iirA 415 4.43e+01 1iirA c.87.1.5 62453 1nz6A 101 4.45e+01 a.2.3.1 86441 1j5wA 298 4.47e+01 d.104.1.1 71589 1u04A 771 4.47e+01 b.34.14.1,c.55.3.10 107539,107540 1va6A 518 4.48e+01 1fi2A 201 4.50e+01 1fi2A b.82.1.2 59845 1mqoA 227 4.54e+01 d.157.1.1 103846 2bbhA 269 4.65e+01 1z85A 234 4.66e+01 1wsrA 375 4.68e+01 1k0iA 394 4.68e+01 c.3.1.2,d.16.1.2 67942,67943 1eqjA 511 4.70e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1nnwA 252 4.74e+01 d.159.1.5 80674 2gwnA 452 4.74e+01 1q6hA 224 4.77e+01 d.26.1.1 95975 1o98A 511 4.79e+01 c.105.1.1,c.76.1.3 86684,86685 1g6sA 427 4.79e+01 1eps d.68.2.2 39584 1nr4A 71 4.82e+01 d.9.1.1 92077 1xm8A 254 4.84e+01 1dgwA 178 4.85e+01 1dgwA b.82.1.2 28090 1i0lA 221 4.88e+01 c.61.1.1 71096 1g0oA 283 4.90e+01 1ybvA c.2.1.2 60181 2frnA 278 4.96e+01 2bszA 278 4.98e+01 1q6uA 245 5.00e+01 d.26.1.1 95998 1xtmA 175 5.10e+01 1nz0A 118 5.11e+01 d.14.1.2 86433 1ym0A 238 5.15e+01 2f6eA 127 5.22e+01 1reoA 486 5.23e+01 c.3.1.2,d.16.1.5 97325,97326 1z4eA 153 5.23e+01 1hdmA 201 5.23e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 2gn4A 344 5.31e+01 1t6aA 126 5.32e+01 d.129.8.1 106555 8abp 306 5.35e+01 8abp c.93.1.1 35647 1t9mA 214 5.35e+01 1j6wA 175 5.37e+01 1j98A d.185.1.2 62663 2bjfA 329 5.39e+01 2fhfA 1083 5.45e+01 1zkoA 136 5.45e+01 1ctt 294 5.45e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1o6uA 403 5.45e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 5abp 306 5.49e+01 8abp c.93.1.1 35651 1ois 223 5.56e+01 1a36A e.15.1.1 43267 1ro5A 201 5.56e+01 d.108.1.3 105023 1zjcA 418 5.57e+01 1kqwA 134 5.58e+01 b.60.1.2 72887 2a2fX 325 5.61e+01 1wi5A 119 5.63e+01 1djrD 103 5.64e+01 3chbD b.40.2.1 24865 1b8aA 438 5.65e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1rwiA 270 5.71e+01 b.68.9.1 97987 1nykA 165 5.79e+01 b.33.1.1 86408 1aonO 97 5.80e+01 b.35.1.1 24642 1euaA 213 5.80e+01 1fwrA c.1.10.1 29155 2f5yA 91 5.89e+01 1dl5A 317 5.89e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1lqsR 214 5.89e+01 b.1.2.1,b.1.2.1 74194,74195 1ido 192 5.91e+01 1ido c.62.1.1 34139 1o7nB 194 5.91e+01 d.17.4.4 81164 1yz1A 174 5.93e+01 1rl6A 177 5.96e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1te0A 318 5.98e+01 1x35A 268 6.00e+01 2et1A 201 6.02e+01 1jmtB 28 6.07e+01 2czrA 226 6.09e+01 2hciA 69 6.13e+01 1y1oA 203 6.20e+01 1eceA 358 6.22e+01 1eceA c.1.8.3 28813 1tl0D 103 6.22e+01 1rdqE 350 6.24e+01 d.144.1.7 97314 1jihA 531 6.27e+01 d.240.1.1,e.8.1.7 90374,90375 2ak5A 64 6.27e+01 1lt5D 103 6.28e+01 3chbD b.40.2.1 24875 2h0uA 217 6.31e+01 1c5yB 253 6.34e+01 5ptp 1ni9A 338 6.38e+01 e.7.1.2 85739 1pjxA 314 6.40e+01 b.68.6.1 104167 1x47A 98 6.40e+01 2g76A 335 6.40e+01 1uspA 139 6.40e+01 d.227.1.1 99879 1brwA 433 6.41e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1eg9B 194 6.45e+01 1ndoB d.17.4.4 38120 2arcA 164 6.47e+01 2arcA b.82.4.1 28148 1ou8A 111 6.50e+01 b.136.1.1 93543 2bw8A 227 6.50e+01 2ggcA 263 6.51e+01 1olmA 403 6.52e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1vr9A 213 6.54e+01 1zx5A 300 6.63e+01 1o6lA 337 6.64e+01 d.144.1.7 81092 2cbiA 594 6.65e+01 2cvjA 180 6.66e+01 1ltoA 245 6.68e+01 b.47.1.2 84707 1wnyA 186 6.73e+01 1zybA 232 6.75e+01 1l0gA 358 6.76e+01 e.3.1.1 73400 1zupA 315 6.76e+01 1i6xA 209 6.77e+01 a.4.5.4,b.82.3.2 83673,83674 1lf6A 684 6.78e+01 a.102.1.5,b.30.5.5 77918,77919 2fy6A 143 6.78e+01 1ve0A 134 6.78e+01 1yvcA 70 6.80e+01 1dzaA 129 6.86e+01 7rsa d.5.1.1 37275 1ykjA 394 6.88e+01 1vizA 240 6.89e+01 c.1.4.1 100784 1xffA 240 6.90e+01 d.153.1.1 109580 1p5dX 463 6.91e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1w0uA 55 6.92e+01 1xebA 150 6.93e+01 1zpvA 91 7.02e+01 1k2fA 190 7.03e+01 b.8.1.2 68054 2bgiA 272 7.04e+01 2fikA 287 7.07e+01 1xk5A 204 7.18e+01 2gu2A 312 7.22e+01 1f5mA 180 7.22e+01 1f5mB d.110.2.1 40895 2b6nA 278 7.24e+01 1xh9A 350 7.26e+01 2ciaA 102 7.29e+01 2cs7A 55 7.36e+01 1fftB 315 7.42e+01 1cyx b.6.1.2,f.17.2.1 23025,43628 2f9nA 245 7.44e+01 1wapA 75 7.46e+01 1wapA b.82.5.1 28153 1ucyH 150 7.49e+01 1ucyH 1gg6C 97 7.50e+01 5ptp 1tq5A 242 7.57e+01 2gimA 106 7.59e+01 1u1wA 298 7.62e+01 2gf9A 189 7.67e+01 1u2xA 474 7.71e+01 c.72.1.3 107622 2g6fX 59 7.71e+01 1d7qA 143 7.75e+01 1d7qA b.40.4.5 25331 1m8aA 70 7.82e+01 d.9.1.1 74579 1i45A 248 7.91e+01 1amk c.1.1.1 61665 1c24A 263 7.91e+01 1c24A d.127.1.1 41148 1fjgL 135 7.92e+01 1fjfL b.40.4.5 25346 1vz6A 393 7.96e+01 d.154.1.2 108949 1umkA 275 7.97e+01 8rucA 475 7.97e+01 1burA c.1.14.1,d.58.9.1 29339,39245 1cqkA 101 7.97e+01 1cqkA b.1.1.2 21547 1xklA 273 7.98e+01 1udzA 182 7.98e+01 b.51.1.1 99239 2f1kA 279 8.05e+01 1xubA 298 8.07e+01 1e1aA 314 8.21e+01 1e1aA b.68.6.1 59155 1mc0A 368 8.24e+01 d.110.2.1,d.110.2.1 78937,78938 1x36A 237 8.24e+01 1vm6A 228 8.29e+01 c.2.1.3,d.81.1.3 108876,108877 2bokA 241 8.32e+01 1hq1A 105 8.34e+01 1dulA a.36.1.1 17120 1dfcA 493 8.37e+01 1dfcA 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