# 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.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 9.65e-02 1dhn d.96.1.3 40663 1zq1A 438 1.54e-01 1v54B 227 4.89e-01 b.6.1.2,f.17.2.1 100322,100323 1zkdA 387 5.92e-01 2occB 227 6.48e-01 2occB b.6.1.2,f.17.2.1 23027,43519 1usuA 260 8.76e-01 d.14.1.8 99885 1y14B 171 1.08e+00 1ihjA 98 1.28e+00 1pdr b.36.1.1 62382 1tc1A 220 1.78e+00 1tc1A c.61.1.1 34083 1bia 321 1.84e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 2h6lA 146 1.96e+00 1kqqA 139 2.04e+00 a.4.3.1 72885 2basA 431 2.27e+00 1bib 321 2.47e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 2fwkA 121 2.69e+00 2fb7A 95 2.78e+00 2d9rA 104 2.82e+00 1u0mA 382 2.94e+00 c.95.1.2,c.95.1.2 107557,107558 1llwA 1520 3.22e+00 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 2gzvA 114 3.53e+00 1ea0A 1479 3.85e+00 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 2cqsA 842 3.90e+00 1yavA 159 4.09e+00 1fr3A 67 4.43e+00 1fr3A b.40.6.1 25436 1kwiA 101 4.49e+00 d.17.1.3 77564 2bs3A 656 4.62e+00 4ubpC 570 4.63e+00 1ubpC b.92.1.1,c.1.9.2 28431,29053 1jotA 133 4.67e+00 1jotA 1ubpC 570 4.67e+00 1ubpC b.92.1.1,c.1.9.2 28432,29054 1i81A 83 4.68e+00 1d3bB b.38.1.1 61930 1mgqA 83 4.68e+00 b.38.1.1 79099 2aj6A 159 4.71e+00 1afqC 96 4.89e+00 5ptp 1khoA 370 4.94e+00 a.124.1.1,b.12.1.3 72489,72490 1ie7C 570 4.94e+00 1ubpC b.92.1.1,c.1.9.2 62315,62316 1wjnA 97 4.97e+00 1zd7A 159 4.98e+00 1ofdA 1520 5.34e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1qd6C 240 5.34e+00 1qd5A 1qlaA 656 5.39e+00 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1d3bB 91 5.84e+00 1d3bB b.38.1.1 24804 1ts9A 102 5.99e+00 1a63 130 6.40e+00 1a62 a.140.3.1,b.40.4.5 64710,64711 1vrbA 342 6.98e+00 1vj0A 380 7.17e+00 b.35.1.2,c.2.1.1 100786,100787 1iz0A 302 7.41e+00 b.35.1.2,c.2.1.1 83821,83822 1zybA 232 7.62e+00 1crl 534 8.16e+00 1thg c.69.1.17 34765 1m5zA 91 8.17e+00 b.36.1.1 78676 1jacC 133 8.27e+00 1jotA 1i0lA 221 8.80e+00 c.61.1.1 71096 1jmxA 494 8.83e+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 1l2mA 118 9.24e+00 d.89.1.4 77657 1xxqA 161 9.53e+00 1yzsA 121 9.96e+00 1qd5A 275 1.01e+01 1qd5A f.4.2.1 43748 1wqaA 455 1.02e+01 1z7gA 217 1.03e+01 1dbrA 231 1.06e+01 1qk3A c.61.1.1 34041 1cbf 285 1.06e+01 1cbf c.90.1.1 35587 2cbf 234 1.09e+01 1cbf c.90.1.1 35588 1jacA 133 1.10e+01 1jotA 1dl2A 511 1.11e+01 1dl2A a.102.2.1 18844 1c20A 128 1.13e+01 1c20A a.4.3.1 16079 1qk3A 233 1.14e+01 1qk3A c.61.1.1 34031 1a62 130 1.16e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1ugxA 133 1.17e+01 1qzgA 187 1.21e+01 b.40.4.3 96643 1fsgA 233 1.22e+01 1qk3A c.61.1.1 34029 1a8p 258 1.25e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1ku8A 133 1.26e+01 1m26A 133 1.28e+01 1ab9C 97 1.29e+01 5ptp 1gg6C 97 1.29e+01 5ptp 2cwpA 112 1.30e+01 1c9oA 66 1.40e+01 1mjc b.40.4.5 25325 1pc0A 61 1.51e+01 b.137.1.1 94426 1t3cA 421 1.51e+01 d.92.1.7 106343 2ew0A 192 1.58e+01 8abp 306 1.61e+01 8abp c.93.1.1 35647 1hl8A 449 1.61e+01 b.71.1.3,c.1.8.11 90646,90647 1bap 306 1.62e+01 8abp c.93.1.1 35654 1abe 306 1.65e+01 8abp c.93.1.1 35648 5abp 306 1.65e+01 8abp c.93.1.1 35651 1dk4A 252 1.66e+01 1dk4A e.7.1.1 42970 1a8vA 121 1.78e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1uspA 139 1.80e+01 d.227.1.1 99879 1llfA 534 1.83e+01 c.69.1.17 78094 1xw3A 110 1.87e+01 1xw4X 110 1.87e+01 1cleA 534 1.93e+01 1thg c.69.1.17 34771 1zghA 260 1.94e+01 1xg9A 260 1.95e+01 1hcz 252 1.96e+01 1hcz b.2.6.1,b.84.2.2 22464,28250 1i6pA 220 1.98e+01 1ddzA c.53.2.1 61848 1vkkA 154 2.02e+01 d.109.1.2 108669 1gdoB 240 2.09e+01 1gdoA 1k2i1 245 2.12e+01 1h2kA 349 2.13e+01 b.82.2.6 76572 1mzeA 351 2.14e+01 b.82.2.6 79694 1l6pA 125 2.21e+01 b.1.17.1 73626 1ukmB 128 2.25e+01 d.169.1.1 99500 1m2aA 110 2.26e+01 c.47.1.11 78472 1f37A 110 2.43e+01 1f37A c.47.1.11 33088 1pms 136 2.45e+01 1awe b.55.1.1 26966 1g0hA 252 2.50e+01 1dk4A e.7.1.1 60171 1reoA 486 2.50e+01 c.3.1.2,d.16.1.5 97325,97326 1mtnC 97 2.57e+01 5ptp 1iz5A 249 2.58e+01 d.131.1.2,d.131.1.2 83834,83835 1jpeA 151 2.59e+01 b.1.17.1 77146 1ijbA 202 2.59e+01 c.62.1.1 71229 1x1oA 286 2.59e+01 1hmpA 217 2.63e+01 1qk3A c.61.1.1 34075 1oakA 196 2.79e+01 1auq c.62.1.1 34138 1v7pB 128 2.95e+01 d.169.1.1 108407 1jtkA 136 2.96e+01 c.97.1.1 71862 1uwzA 136 2.98e+01 c.97.1.1 108081 1qavA 90 2.99e+01 1qauA b.36.1.1 24777 1ipiA 123 2.99e+01 c.52.1.18 66255 1yphE 97 3.03e+01 1fnsA 196 3.09e+01 1auq c.62.1.1 34136 1v8gA 329 3.14e+01 a.46.2.1,c.27.1.1 100505,100506 2pcfB 250 3.19e+01 1hcz i.4.1.1 45911 1vl6A 388 3.25e+01 c.2.1.7,c.58.1.3 108724,108725 1m2bA 110 3.34e+01 c.47.1.11 78474 1auyA 189 3.35e+01 1auyA b.121.4.6 23311 1s5aA 150 3.36e+01 d.17.4.10 98525 1o6lA 337 3.38e+01 d.144.1.7 81092 1z1yA 186 3.40e+01 1wsrA 375 3.41e+01 1gvkB 240 3.44e+01 b.47.1.2 70610 1t9mA 214 3.50e+01 1yezA 68 3.51e+01 1hl9A 449 3.53e+01 b.71.1.3,c.1.8.11 90650,90651 1c5yB 253 3.70e+01 5ptp 1gj7B 253 3.70e+01 1fthA 122 3.71e+01 d.150.1.2 60028 2fa8A 105 3.74e+01 1cj3A 392 3.79e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1auq 208 3.82e+01 1auq c.62.1.1 34137 1h10A 125 3.87e+01 b.55.1.1 83446 1unqA 125 3.87e+01 b.55.1.1 107968 1xffA 240 3.91e+01 d.153.1.1 109580 1c9fA 90 3.95e+01 1c9fA d.15.2.1 37639 1zx8A 136 4.02e+01 1qqcA 773 4.04e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1qwrA 319 4.17e+01 b.82.1.3 96491 1kngA 156 4.31e+01 c.47.1.10 72777 2fcfA 103 4.37e+01 1qk4A 233 4.40e+01 1qk3A c.61.1.1 34037 1rkd 309 4.41e+01 1rkd c.72.1.1 34928 1mxmA 254 4.44e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1b34A 119 4.56e+01 1d3bA b.38.1.1 24796 2h7bA 105 4.57e+01 1fehA 574 4.64e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 2ar0A 541 4.65e+01 1o6uA 403 4.83e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1avaC 181 4.85e+01 1avaC b.42.4.1 25604 1j7vR 214 4.93e+01 b.1.2.1,b.1.2.1 62705,62706 2a5zA 262 4.97e+01 1eajA 126 4.98e+01 1f5wA b.1.1.1 59401 1f5wA 126 4.98e+01 1f5wA b.1.1.1 19705 1olmA 403 5.02e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1am2 199 5.03e+01 1am2 b.86.1.2 28381 1m2dA 110 5.22e+01 c.47.1.11 78476 1i8fA 81 5.30e+01 1i8fA b.38.1.1 61959 1vc3B 97 5.47e+01 1nriA 306 5.52e+01 c.80.1.3 86123 1j5wA 298 5.53e+01 d.104.1.1 71589 1x74A 360 5.61e+01 1ef8A 261 5.65e+01 1ef8A c.14.1.3 30921 2gefA 217 5.65e+01 1p4kA 295 5.67e+01 d.153.1.5 87772 1yb3A 175 5.98e+01 1asyA 490 5.98e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 9gafA 295 6.03e+01 1apyA d.153.1.5 42008 1kzlA 208 6.12e+01 b.43.4.3,b.43.4.3 77635,77636 2aa4A 289 6.13e+01 1p97A 114 6.19e+01 d.110.3.7 94382 1rbp 182 6.24e+01 1aqb b.60.1.1 27085 1awe 130 6.33e+01 1awe b.55.1.1 26968 2gu2A 312 6.36e+01 1ah9 71 6.50e+01 1ah9 b.40.4.5 25330 2dekA 265 6.51e+01 2f5yA 91 6.59e+01 2ci9A 102 6.64e+01 1zkoA 136 6.66e+01 1ci3M 249 6.67e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 1lqsR 214 6.72e+01 b.1.2.1,b.1.2.1 74194,74195 2cgaA 245 6.77e+01 5ptp b.47.1.2 26028 1kskA 234 6.99e+01 d.66.1.5,d.265.1.3 72920,90389 1fdr 248 7.00e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 2h88B 252 7.09e+01 1gdoA 240 7.10e+01 1gdoA 1qmrA 159 7.13e+01 1bv1 d.129.3.1 41314 1nf3A 195 7.17e+01 c.37.1.8 85594 1vr9A 213 7.20e+01 1yfuA 174 7.25e+01 1vjrA 271 7.34e+01 c.108.1.14 100832 2h3lA 103 7.36e+01 1b6fA 159 7.46e+01 1bv1 d.129.3.1 41316 1btu 240 7.47e+01 5ptp b.47.1.2 26241 1am4D 177 7.51e+01 1ctqA c.37.1.8 32068 1l4zB 136 7.54e+01 d.15.5.1 77704 1bu1A 57 7.63e+01 1bbzA b.34.2.1 24499 1fm4A 159 7.65e+01 1bv1 d.129.3.1 76186 1r4kA 169 7.67e+01 b.34.14.1 96997 1qnjA 240 7.75e+01 5ptp b.47.1.2 26238 1dzkA 157 7.82e+01 1obpA b.60.1.1 27096 1xwiA 322 7.85e+01 1pbe 394 7.86e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1l0wA 580 7.91e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1bmtA 246 8.00e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1jtaA 361 8.11e+01 b.80.1.1 71859 1f56A 91 8.25e+01 2cbp b.6.1.1 22896 1q6hA 224 8.27e+01 d.26.1.1 95975 1a0lA 244 8.41e+01 5ptp b.47.1.2 26286 1gutA 68 8.42e+01 b.40.6.1 65576 2awfA 172 8.47e+01 1gyzA 60 8.48e+01 a.144.2.1 70793 1jmuB 666 8.52e+01 1st0A 337 8.52e+01 d.13.1.3,d.246.1.1 98979,98980 1vjkA 98 8.60e+01 d.15.3.1 108631 1gx1A 160 8.63e+01 d.79.5.1 70675 1apyB 141 8.77e+01 1apyB 1dm0A 287 8.80e+01 1dm0A d.165.1.2 42227 1a3yA 149 8.81e+01 1obpA b.60.1.1 27110 1mfgA 95 8.93e+01 b.36.1.1 79043 1yloA 348 8.97e+01 1pls 113 8.97e+01 1pls b.55.1.1 26965 1pud 386 8.98e+01 1pud c.1.20.1 29658