# List of top-scoring protein chains for t04-100-30-near-backbone-11-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 2gcxA 75 1.16e-08 2h3jA 75 1.91e-08 1fx7A 230 1.38e-02 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1qw1A 121 3.70e-02 1e0cA 271 1.02e-01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1bymA 97 1.61e-01 1bi0 b.34.1.2 24458 1y8xB 98 1.63e-01 1t0yA 122 2.16e-01 d.15.1.1 99066 2bpsA 81 2.92e-01 1opd 85 4.00e-01 1ptf 1opdA 85 4.08e-01 d.94.1.1 40560 1sphA 88 5.25e-01 1ptf d.94.1.1 40544 2dchX 216 9.32e-01 2nwvA 114 1.18e+00 d.326.1.1 138720 1zx6A 58 1.27e+00 1whzA 70 1.45e+00 d.50.3.2 114656 1gcqA 61 1.63e+00 1ckaA b.34.2.1 60434 1x1mA 107 1.64e+00 d.15.1.1 121592 1aboA 62 1.78e+00 1bbzA b.34.2.1 24474 1y51A 88 1.81e+00 1y8qB 640 1.83e+00 1oebA 62 1.90e+00 b.34.2.1 86909 1vg5A 73 2.21e+00 a.5.2.1 113640 2drmA 58 2.50e+00 2rcfA 91 2.58e+00 1dv0A 47 2.63e+00 1dv0A a.5.2.1 16289 1z2mA 155 2.77e+00 d.15.1.1,d.15.1.1 124387,124388 1utiA 58 2.90e+00 b.34.2.1 99962 1ootA 60 2.95e+00 b.34.2.1 93386 3c0cA 73 3.08e+00 2o88A 58 3.09e+00 1j6oA 268 3.13e+00 c.1.9.12 77088 1bbzA 58 3.27e+00 1bbzA b.34.2.1 24477 2d1hA 109 3.52e+00 a.4.5.50 131125 2hcuA 213 3.82e+00 1cbfA 285 4.20e+00 c.90.1.1 35587 1kafA 108 4.57e+00 d.199.1.1 68372 2iimA 62 4.62e+00 b.34.2.1 137434 1sz7A 200 4.71e+00 1pgyA 47 5.06e+00 a.5.2.1 94696 1v2yA 105 5.09e+00 d.15.1.1 100275 2qsfX 171 5.11e+00 1pht 85 5.15e+00 1ckaA 1phtA 85 5.15e+00 b.34.2.1 24483 1s68A 249 5.19e+00 d.142.2.4 98591 1knmA 130 5.30e+00 b.42.2.1 72781 2bzyA 67 5.38e+00 2fomB 185 5.40e+00 b.47.1.3 133884 2a28A 54 5.43e+00 2re3A 194 5.46e+00 2hvqA 335 5.58e+00 1vqoK 132 5.78e+00 b.39.1.1 120372 2qq9A 226 5.90e+00 2jg2A 422 5.92e+00 2bwbA 46 5.94e+00 a.5.2.1 129329 2cp8A 54 6.10e+00 a.5.2.1 130695 2z1mA 345 6.19e+00 1uarA 285 6.82e+00 c.46.1.2,c.46.1.2 107762,107763 2bjnA 160 7.03e+00 1ghpA 258 7.27e+00 1btl e.3.1.1 60520 2raqA 97 7.28e+00 3c24A 286 7.36e+00 1f42A 306 7.58e+00 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 1zzmA 259 7.78e+00 c.1.9.12 125911 1pch 88 7.88e+00 1ptf 1vekA 84 7.90e+00 a.5.2.1 113636 1pchA 88 7.92e+00 d.94.1.1 40564 1zuyA 58 8.03e+00 2g5cA 281 8.12e+00 a.100.1.12,c.2.1.6 134646,134647 2jejA 358 8.29e+00 d.240.1.1,e.8.1.7 138284,138285 1yixA 265 8.45e+00 c.1.9.12 123371 1wr1B 58 8.60e+00 a.5.2.1 121185 1rhs 296 8.73e+00 1rhs 1rhsA 296 8.76e+00 c.46.1.2,c.46.1.2 32703,32704 1ptf 88 9.00e+00 1ptf 1ptfA 88 9.00e+00 d.94.1.1 40549 1jx4A 352 9.12e+00 d.240.1.1,e.8.1.7 90378,90379 2iayA 114 9.13e+00 1go3F 107 9.15e+00 a.60.8.2 65407 1genA 218 9.37e+00 b.66.1.1 27536 1vr0A 247 9.48e+00 c.148.1.1 120428 3cjxA 165 9.55e+00 1guiA 155 9.64e+00 b.18.1.14 76351 2o8bA 934 9.73e+00 2if1A 126 9.88e+00 d.64.1.1 39547 1fr3A 67 9.91e+00 1fr3A b.40.6.1 25436 3bn1A 373 9.95e+00 1zjjA 263 1.00e+01 2cr5A 109 1.01e+01 d.15.1.2 130733 1rpnA 335 1.02e+01 c.2.1.2 97708 2f1fA 164 1.03e+01 d.58.18.6,d.58.18.6 132760,132761 1qvbA 481 1.03e+01 1qvbA c.1.8.4 28983 2o31A 67 1.04e+01 2i7rA 118 1.06e+01 d.32.1.2 137102 3d33A 108 1.10e+01 1o2dA 371 1.12e+01 e.22.1.2 86591 1iz6A 138 1.13e+01 b.34.5.2,b.40.4.5 76976,76977 1v30A 124 1.16e+01 d.269.1.1 113496 1e0tA 470 1.18e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2ggrA 76 1.19e+01 2dklA 85 1.20e+01 a.5.2.1 131555 2qpqA 301 1.20e+01 2ak5A 64 1.22e+01 2bjdA 101 1.22e+01 1xfsA 178 1.23e+01 d.129.3.5 109589 1bkb 136 1.25e+01 1bkb 1ywyA 74 1.25e+01 b.55.2.1 124166 1zoiA 276 1.27e+01 2a08A 60 1.31e+01 1ktbA 405 1.32e+01 b.71.1.1,c.1.8.1 72960,72961 1h9sA 140 1.33e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 2imlA 199 1.33e+01 2gatA 66 1.35e+01 1gatA g.39.1.1 45102 2nygA 273 1.37e+01 1ci4A 89 1.40e+01 1qckA a.60.5.1 17970 1bkbA 136 1.40e+01 b.34.5.2,b.40.4.5 24609,25341 1x6mA 196 1.43e+01 b.88.1.4 114920 1ulrA 88 1.45e+01 d.58.10.1 113283 1befA 181 1.46e+01 1befA b.47.1.3 26419 2i6vA 87 1.47e+01 2o9sA 67 1.47e+01 2og5A 357 1.47e+01 2g6fX 59 1.50e+01 1isiA 265 1.54e+01 c.23.14.3 71394 1z3eB 73 1.55e+01 a.60.3.1 124401 1dpeA 507 1.56e+01 c.94.1.1 35799 2qalM 117 1.62e+01 1gutA 68 1.63e+01 b.40.6.1 65576 1z96A 40 1.64e+01 2fyqA 194 1.65e+01 2fbhA 146 1.66e+01 a.4.5.28 133245 2vgeA 229 1.67e+01 3bhdA 234 1.74e+01 1wdiA 345 1.74e+01 e.53.1.1 114535 1oe4A 247 1.77e+01 c.18.1.3 86895 1y0eA 223 1.81e+01 c.1.2.5 116297 1ov3A 138 1.85e+01 b.34.2.1,b.34.2.1 87451,87452 1kpeA 126 1.85e+01 1kpf d.13.1.1 37508 1pqhA 143 1.86e+01 b.52.2.1 95017 1r89A 437 1.87e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1wiwA 290 1.91e+01 c.80.1.1 114681 1s69A 124 1.91e+01 a.1.1.1 105305 1wlpB 138 1.95e+01 b.34.2.1 121010 1h80A 464 2.00e+01 b.80.1.8 65714 1nthA 458 2.04e+01 c.1.25.1 80730 1gcqC 70 2.07e+01 1gcpA b.34.2.1 60436 1luzA 88 2.08e+01 b.40.4.5 74271 2v8iA 543 2.10e+01 1k1eA 180 2.12e+01 c.108.1.5 67995 1fjgI 128 2.13e+01 1fjfI d.14.1.1 37559 1cskA 71 2.15e+01 1ckaA b.34.2.1 24513 2fi0A 81 2.18e+01 a.248.1.1 133507 1xu6A 80 2.19e+01 g.16.3.1 116047 1wc9A 169 2.19e+01 d.278.1.2 114507 1wrbA 253 2.29e+01 c.37.1.19 121192 1s7jA 262 2.29e+01 d.21.1.2 98647 2yyvA 227 2.29e+01 3bhnA 236 2.33e+01 2vqeI 128 2.33e+01 2eo2A 71 2.33e+01 2hjhA 354 2.34e+01 2fu4A 83 2.35e+01 1aw8B 91 2.37e+01 1aw8B 1fjgJ 105 2.40e+01 1fjfJ d.58.15.1 39330 2ogeA 399 2.41e+01 1zpvA 91 2.45e+01 d.58.18.7 125475 1hl9A 449 2.48e+01 b.71.1.3,c.1.8.11 90650,90651 2j3wB 188 2.56e+01 2p2uA 171 2.56e+01 2b0jA 358 2.56e+01 a.100.1.11,c.2.1.6 127639,127640 2hldD 478 2.56e+01 1umuA 116 2.61e+01 1umuA b.87.1.1 28382 1y0nA 78 2.61e+01 d.291.1.1 116305 1pexA 207 2.63e+01 b.66.1.1 27540 3cp0A 82 2.67e+01 2zayA 147 2.69e+01 1pn2A 280 2.69e+01 d.38.1.4,d.38.1.4 94930,94931 1vd6A 224 2.74e+01 c.1.18.3 119991 2cxxA 190 2.76e+01 c.37.1.8 131013 2uubI 128 2.76e+01 1zc1A 208 2.79e+01 2p0pA 126 2.79e+01 2op5A 117 2.84e+01 1noaA 113 2.84e+01 b.1.7.1 22208 2qmmA 197 2.85e+01 1mdoA 393 2.85e+01 c.67.1.4 79013 2qbuA 232 2.88e+01 3bpjA 80 2.91e+01 1kpf 126 2.96e+01 1kpf 2glfA 450 3.02e+01 2mcmA 112 3.04e+01 b.1.7.1 22207 1s5jA 847 3.05e+01 c.55.3.5,e.8.1.1 112040,112041 2hpsA 186 3.08e+01 2okfA 140 3.10e+01 1b7yB 785 3.16e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,b.153.1.1 16301,16302,25312,39311,40780,41456 2o11A 407 3.18e+01 2z14A 133 3.19e+01 1h9mA 145 3.22e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 1mo1A 87 3.33e+01 d.94.1.1 91363 1jxgA 100 3.37e+01 b.6.1.1 67413 2j4oA 401 3.38e+01 1fnoA 417 3.44e+01 d.58.19.1,c.56.5.4 70145,75841 2gh1A 301 3.52e+01 c.66.1.49 135170 1zelA 298 3.52e+01 1ew4A 106 3.52e+01 1ew4A d.82.2.1 40023 2jc4A 256 3.54e+01 1b9hA 388 3.59e+01 1b9hA c.67.1.4 34488 3bpdA 100 3.60e+01 1prs 173 3.66e+01 1prs 1ylhA 560 3.69e+01 1uch 230 3.75e+01 1uch 2prrA 197 3.76e+01 2cw5A 255 3.78e+01 1kpfA 125 3.80e+01 d.13.1.1 37507 1oflA 481 3.81e+01 b.80.1.4 103934 2d1zA 436 3.83e+01 3cpkA 150 3.86e+01 1dzfA 215 3.91e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1npsA 88 3.96e+01 1prs b.11.1.1 23622 1zlmA 58 3.99e+01 2mcm 112 4.00e+01 2mcm 1uheA 97 4.05e+01 2irmA 358 4.20e+01 1yzfA 195 4.29e+01 c.23.10.5 124275 2eifA 136 4.32e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 3bk2A 562 4.36e+01 1yz4A 160 4.36e+01 1fjgM 126 4.36e+01 1fjfM a.156.1.1 16293 1x2kA 68 4.37e+01 1wlfA 179 4.38e+01 d.31.1.1,b.52.2.3 109396,109397 1egiA 147 4.38e+01 1eggA d.169.1.1 42331 1qqyA 130 4.45e+01 3lzt d.2.1.2 36586 3berA 249 4.47e+01 1vjrA 271 4.52e+01 c.108.1.14 100832 1plc 99 4.62e+01 1plc 1dboA 506 4.65e+01 1dbgA b.80.1.4 28034 1cuk 203 4.67e+01 1hjp 1cukA 203 4.67e+01 a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1vixA 420 4.70e+01 c.56.5.4,d.58.19.1 100777,100778 1ok7A 366 4.77e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 3by3A 301 4.78e+01 3d26A 301 4.81e+01 1a0nB 69 4.82e+01 1bbzA b.34.2.1 24469 1xv5A 401 4.88e+01 1d2mA 665 4.88e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1xbyA 216 4.89e+01 c.1.2.3 121846 2nqoB 188 4.93e+01 1d2zB 153 4.94e+01 1d2zB a.77.1.2 18439 1rk8A 165 4.96e+01 d.58.7.1 97603 2glwA 92 4.97e+01 2dclA 127 4.97e+01 1w70A 60 4.99e+01 1b9mA 265 5.03e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 2gw8A 114 5.03e+01 2iqjA 134 5.07e+01 1v38A 78 5.09e+01 a.60.1.2 100280 1plcA 99 5.10e+01 b.6.1.1 22846 2cfxA 144 5.11e+01 a.4.5.32,d.58.4.2 130395,130396 1wyxA 69 5.11e+01 1iq8A 582 5.15e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1yvcA 70 5.15e+01 b.40.4.12 124094 1vchA 175 5.15e+01 c.61.1.1 119980 2qmcB 188 5.15e+01 1qwkA 317 5.20e+01 c.1.7.1 96482 2diuA 96 5.22e+01 1avaC 181 5.23e+01 1avaC b.42.4.1 25604 1db3A 372 5.30e+01 1db3A c.2.1.2 29813 2hi1A 330 5.31e+01 1x2iA 75 5.31e+01 a.60.2.5 121641 2eq6A 464 5.33e+01 1yarH 217 5.34e+01 d.153.1.4 122844 2vknA 70 5.35e+01 2inbA 140 5.39e+01 2bexA 460 5.40e+01 c.10.1.1 128398 2c81A 418 5.40e+01 1dbgA 506 5.41e+01 1dbgA b.80.1.4 28033 1h3oA 75 5.42e+01 a.22.1.3 76644 2ccqA 99 5.46e+01 d.314.1.1 130252 3bpuA 88 5.47e+01 2pg4A 95 5.55e+01 1e5rA 290 5.62e+01 1e5rA b.82.2.4 59276 1peaA 385 5.65e+01 c.93.1.1 35662 2gu2A 312 5.69e+01 1pea 385 5.74e+01 1pea 1q6oA 216 5.77e+01 c.1.2.3 95986 3bi7A 212 5.79e+01 1jeoA 180 5.81e+01 c.80.1.3 66611 2cs2A 134 5.84e+01 1pjqA 457 5.87e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 2vqeM 126 5.88e+01 1yezA 68 5.89e+01 b.40.4.12 123026 2h09A 155 5.90e+01 2polA 366 6.05e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1ujnA 348 6.07e+01 e.22.1.1 99460 1ifyA 49 6.07e+01 a.5.2.1 71207 1kpgA 287 6.19e+01 c.66.1.18 68735 1r1gA 31 6.35e+01 g.3.7.2 96816 1ccwA 137 6.40e+01 1be1 c.23.6.1 31238 2v8tA 302 6.43e+01 2nwaA 88 6.51e+01 2dxcA 126 6.56e+01 1bxyA 60 6.67e+01 1bxyA d.59.1.1 39525 1shfA 59 6.67e+01 1bbzA b.34.2.1 24462 1vl4A 447 6.68e+01 d.283.1.1 108718 1y88A 199 6.76e+01 a.60.4.3,c.52.1.30 116560,116561 2ckwA 515 6.79e+01 2hiyA 183 6.79e+01 2ek1A 95 6.84e+01 2i4iA 417 6.86e+01 1c4qA 69 6.92e+01 2bosA b.40.2.1 25010 3b5hA 184 6.94e+01 1z7xW 461 6.95e+01 c.10.1.1 124675 1a4yA 460 6.95e+01 1a4yA c.10.1.1 30852 1ibyA 112 7.02e+01 1ibzA b.6.1.4 62233 2axqA 467 7.02e+01 2qdfA 335 7.06e+01 1ybiA 288 7.09e+01 1rjdA 334 7.10e+01 c.66.1.37 97558 2gncA 60 7.18e+01 2eixA 243 7.19e+01 1widA 130 7.21e+01 b.142.1.2 114667 1q02A 52 7.27e+01 a.5.2.1 95490 2j00I 128 7.27e+01 d.14.1.1 137847 1cmcA 104 7.28e+01 1cmbA a.43.1.5 17462 1y0mA 61 7.28e+01 1qyiA 384 7.29e+01 c.108.1.13 96595 2dpyA 438 7.31e+01 2vqeQ 105 7.35e+01 1t35A 191 7.36e+01 c.129.1.1 99108 1j48A 110 7.40e+01 b.1.7.1 84112 1jnyA 435 7.41e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2p9jA 162 7.43e+01 2q9vA 90 7.46e+01 1tg0A 68 7.46e+01 1kcvL 214 7.52e+01 b.1.1.1,b.1.1.2 72317,72318 2qdyB 212 7.57e+01 2oo2A 86 7.57e+01 2cwlA 302 7.64e+01 a.25.1.3 130927 2otuA 115 7.64e+01 2dtrA 226 7.64e+01 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1zvtA 256 7.69e+01 2il5A 171 7.72e+01 2pngA 89 7.75e+01 a.28.1.1 139742 2eg4A 230 7.78e+01 1rlkA 117 7.80e+01 c.131.1.1 97651 2qrvB 230 7.82e+01 1cmbA 104 7.86e+01 1cmbA a.43.1.5 17460 1v95A 130 7.90e+01 c.51.1.1 108435 1xd3A 230 7.96e+01 d.3.1.6 115145 1qdeA 224 7.98e+01 1qvaA c.37.1.19 32410 1wn2A 121 7.99e+01