# List of top-scoring protein chains for t04-100-30-bys-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 1tmxA 293 3.70e-02 3cbnA 151 9.78e-02 2uxyA 341 3.62e-01 1n9lA 109 5.20e-01 d.110.3.6 85468 1ikpA 613 9.70e-01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 2f4wA 187 1.12e+00 d.20.1.1 132958 2aukA 190 1.12e+00 1x6oA 174 1.15e+00 b.34.5.2,b.40.4.5 109493,109494 2dg1A 333 1.25e+00 b.68.6.1 131493 2ftwA 521 1.33e+00 b.92.1.3,c.1.9.6 134083,134084 2ie2A 222 1.75e+00 1mkeA 152 1.86e+00 b.55.1.4 79231 1wcqA 601 2.07e+00 b.1.18.2,b.18.1.1,b.68.1.1 120894,120895,120896 2dyuA 334 2.14e+00 2b79A 144 2.42e+00 1w8oA 601 2.91e+00 b.1.18.2,b.18.1.1,b.68.1.1 114374,114375,114376 1xssA 225 3.63e+00 1pm4A 119 3.90e+00 b.135.1.1 94891 2f69A 261 3.95e+00 b.76.2.1,b.85.7.1 133035,133036 1n6aA 259 3.99e+00 b.76.2.1,b.85.7.1 80121,80122 2gysA 419 4.26e+00 b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 135865,135866,135867,135868 2dddA 225 4.30e+00 1o5uA 101 4.87e+00 b.82.1.8 92518 2aydA 76 4.96e+00 1z4vA 532 5.26e+00 2co7B 221 5.29e+00 1iz6A 138 5.42e+00 b.34.5.2,b.40.4.5 76976,76977 1thjA 214 5.46e+00 1qreA b.81.1.5 28072 1w6tA 444 5.67e+00 c.1.11.1,d.54.1.1 120670,120671 2ib5A 233 6.00e+00 1qu1A 155 6.24e+00 1qu1A h.3.1.1 45670 1cdy 178 6.25e+00 1cdy 2j69A 695 6.38e+00 1g8kB 133 6.75e+00 1g8jB b.33.1.1 24435 2yyoA 171 6.75e+00 1qreA 247 7.07e+00 1qreA b.81.1.5 28066 2gw3A 225 7.15e+00 2gw4B 162 7.24e+00 2d7nA 93 7.66e+00 b.1.18.10 131322 1vlgA 176 8.14e+00 a.25.1.1 108816 2i4iA 417 9.19e+00 2v6oA 596 9.62e+00 3bxpA 277 1.02e+01 1bkb 136 1.03e+01 1bkb 1bkbA 136 1.03e+01 b.34.5.2,b.40.4.5 24609,25341 2iw0A 254 1.05e+01 c.6.2.3 137737 1hdoA 206 1.05e+01 1he2A c.2.1.2 60965 1dmhA 311 1.06e+01 1dmhA b.3.6.1 22633 1wzvA 155 1.10e+01 d.20.1.1 121529 3cnqP 80 1.15e+01 1b35A 260 1.22e+01 1b35A b.121.4.1 23333 1xaoA 121 1.26e+01 2ywnA 157 1.26e+01 2ux0A 143 1.28e+01 1tupA 219 1.30e+01 1tupA b.2.5.2 22434 1pfsA 78 1.31e+01 1pfsA b.40.4.7 25391 1zuxA 224 1.36e+01 1yg9A 330 1.38e+01 3c26A 266 1.39e+01 2qmqA 286 1.49e+01 1ybdA 239 1.55e+01 c.73.1.3 122884 2a13A 166 1.56e+01 b.60.1.8 125971 1q7fA 286 1.58e+01 b.68.9.1 96036 2d1kC 32 1.65e+01 1i6pA 220 1.70e+01 1ddzA c.53.2.1 61848 1jsdB 176 1.74e+01 h.3.1.1 63259 1gmuA 143 1.77e+01 b.107.1.1,d.58.38.1 65335,65336 1ifrA 121 1.78e+01 b.1.16.1 71203 1jjfA 268 1.82e+01 c.69.1.2 66765 2q4nA 166 1.85e+01 b.60.1.8 139871 1aipA 405 1.91e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1ex2A 189 1.92e+01 1ex2A c.51.4.2 33225 1o7dC 159 1.94e+01 b.30.5.6 86640 2ew0A 192 1.94e+01 d.310.1.1 132445 2azwA 148 2.01e+01 d.113.1.1 127615 1vlwA 217 2.02e+01 c.1.10.1 108868 2o4cA 380 2.02e+01 3bxoA 239 2.03e+01 1j1nA 492 2.04e+01 c.94.1.1 83978 1x3cA 73 2.04e+01 g.37.1.1 121660 1eybA 471 2.06e+01 1ey2A b.82.1.4 28115 1xf1A 926 2.09e+01 1iicA 422 2.11e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1v6sA 390 2.12e+01 c.86.1.1 100424 1ok7A 366 2.13e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1wa3A 205 2.15e+01 c.1.10.1 120802 2fliA 220 2.18e+01 c.1.2.2 133714 1x1oA 286 2.22e+01 2awfA 172 2.23e+01 d.20.1.1 127432 1rd5A 262 2.23e+01 c.1.2.4 111772 2j8gA 339 2.23e+01 1i1nA 226 2.24e+01 c.66.1.7 71102 1nepA 130 2.24e+01 b.1.18.7 80440 1z2uA 150 2.28e+01 d.20.1.1 124389 2ac0A 200 2.29e+01 b.2.5.2 126539 2gciA 360 2.30e+01 c.123.1.1 134983 2j21A 219 2.31e+01 2furA 209 2.31e+01 b.45.1.1 134185 1edqA 540 2.34e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1dpjA 329 2.35e+01 1smrA b.50.1.2 26828 1hbq 183 2.35e+01 1aqb 1x74A 360 2.36e+01 c.123.1.1 121771 1gvp 87 2.38e+01 1gvp 1gvpA 87 2.38e+01 b.40.4.7 25369 1ctn 540 2.39e+01 1ctn 2fo3A 125 2.43e+01 d.20.1.1 133868 2pa6A 427 2.53e+01 1lqyA 184 2.54e+01 d.167.1.1 74212 2gnqA 336 2.55e+01 2vl7A 540 2.57e+01 1l3aA 228 2.57e+01 d.18.1.2 73531 1z7uA 112 2.58e+01 a.4.5.69 124672 2cx4A 164 2.58e+01 c.47.1.10 130973 1uolA 219 2.60e+01 b.2.5.2 99695 1prxA 224 2.63e+01 1prxA c.47.1.10 33076 2ef7A 133 2.70e+01 1cqyA 99 2.71e+01 1b9zA b.3.1.1 22527 2trcP 217 2.73e+01 1b9yC c.47.1.6 33051 1oohA 126 2.77e+01 a.39.2.1 93383 1wb4A 297 2.82e+01 c.69.1.2 120827 2ahnA 222 2.84e+01 1ois 223 2.86e+01 1a36A 1oisA 223 2.86e+01 e.15.1.1 43267 3bjsA 428 2.92e+01 1uzxA 169 2.96e+01 d.20.1.2 100238 2pcxA 220 3.01e+01 2b4rO 345 3.02e+01 c.2.1.3,d.81.1.1 127845,127846 1b9xC 246 3.05e+01 1b9yC c.47.1.6 33053 2pi2E 142 3.07e+01 1o4rA 108 3.13e+01 d.93.1.1 92469 2c78A 405 3.34e+01 b.43.3.1,b.44.1.1,c.37.1.8 130037,130038,130039 3czbA 351 3.34e+01 2pkhA 148 3.44e+01 2z0mA 337 3.49e+01 3c3dA 311 3.49e+01 3dahA 319 3.50e+01 1dqpA 230 3.54e+01 1dqnA c.61.1.1 34069 1o12A 376 3.55e+01 b.92.1.5,c.1.9.10 80758,80759 2pt7A 330 3.58e+01 2biqA 219 3.58e+01 1iyxA 432 3.60e+01 c.1.11.1,d.54.1.1 83815,83816 2db9A 149 3.60e+01 1ymzA 43 3.61e+01 2r78A 117 3.66e+01 1yf9A 171 3.70e+01 d.20.1.1 123054 1utcA 363 3.74e+01 a.118.1.4,b.69.6.1 99914,99915 1usrA 454 3.76e+01 b.68.1.1 99881 1dqnA 230 3.81e+01 1dqnA c.61.1.1 34067 1itcA 516 3.86e+01 b.3.1.1,c.1.8.1 83705,83706 1o20A 427 3.89e+01 c.82.1.1 86556 2yzuA 109 3.93e+01 1vmoA 163 3.98e+01 1vmoA b.77.1.1 27974 1vlqA 337 3.98e+01 c.69.1.25 108848 1lf2A 331 4.03e+01 b.50.1.2 77914 2p4mA 219 4.06e+01 3c0fB 91 4.09e+01 1wj2A 78 4.11e+01 g.79.1.1 114689 2dknA 255 4.12e+01 1iwmA 186 4.16e+01 b.125.1.2 83758 2oklA 185 4.19e+01 2dvkA 188 4.21e+01 1z6rA 406 4.21e+01 a.4.5.63,c.55.1.10,c.55.1.10 124557,124558,124559 2nvwA 479 4.22e+01 c.2.1.3,d.81.1.5 138665,138666 2ek8A 421 4.23e+01 1x23A 155 4.26e+01 d.20.1.1 121615 1scjB 71 4.28e+01 1scjB d.58.3.2 39069 2a50B 168 4.28e+01 2r0hA 164 4.30e+01 1fzyA 149 4.35e+01 d.20.1.1 65072 1iu8A 206 4.38e+01 c.56.4.1 71436 1j6wA 175 4.38e+01 1j98A d.185.1.2 62663 2fyqA 194 4.40e+01 2p6yA 142 4.43e+01 2ogrA 229 4.44e+01 1b3bA 415 4.47e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1bhe 376 4.49e+01 1bhe 1bheA 376 4.49e+01 b.80.1.3 28030 1dtoA 221 4.52e+01 1dtoA b.91.1.1 28405 2pgeA 377 4.54e+01 2fymA 431 4.54e+01 c.1.11.1,d.54.1.1 134379,134380 2v2gA 233 4.59e+01 3bnwA 181 4.62e+01 2o5nA 319 4.64e+01 2biwA 490 4.64e+01 1hkxA 147 4.71e+01 d.17.4.7 83567 1b26A 416 4.74e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1h9oA 112 4.75e+01 1qadA d.93.1.1 60837 2ifsA 169 4.75e+01 2oznA 165 4.78e+01 1bmv1 198 4.90e+01 1bmv1 1vemA 516 4.96e+01 b.3.1.1,c.1.8.1 120021,120022 2qguA 211 4.97e+01 2hf2A 283 5.02e+01 1nif 340 5.05e+01 1nif 1xe7A 203 5.07e+01 b.82.1.16 115213 1h3fA 432 5.12e+01 c.26.1.1,d.66.1.4 76631,76632 1tzaA 134 5.17e+01 b.1.23.1 107468 1xzoA 174 5.23e+01 c.47.1.10 122474 2d0eA 407 5.31e+01 1ir6A 424 5.33e+01 c.107.1.2 71342 1dymA 402 5.36e+01 1celA b.29.1.10 24304 2brjA 188 5.37e+01 1g0cA 364 5.41e+01 7a3hA c.1.8.3 60165 2v0uA 146 5.45e+01 1u3dA 509 5.50e+01 a.99.1.1,c.28.1.1 107638,107639 2qzjA 136 5.55e+01 2g2cA 167 5.58e+01 c.57.1.1 134535 1vkyA 347 5.62e+01 e.53.1.1 108696 2uwnA 187 5.62e+01 1wba 175 5.66e+01 1wba 1wbaA 175 5.66e+01 b.42.4.1 25591 1d2eA 397 5.68e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1s1fA 406 5.68e+01 a.104.1.1 112008 1erzA 303 5.75e+01 1erzA d.160.1.2 59498 1huuA 90 5.77e+01 1huuA a.55.1.1 17897 1ryp2 233 5.78e+01 1ryp2 2jh2A 148 5.79e+01 2polA 366 5.81e+01 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1y3nA 490 5.82e+01 c.94.1.1 122597 2fauA 341 5.82e+01 1xmiA 291 5.83e+01 c.37.1.12 115489 2i7vA 459 5.84e+01 2e4tA 519 5.86e+01 2pg9A 337 5.87e+01 1qhoA 686 5.88e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1tk9A 188 5.89e+01 c.80.1.3 107082 1uf5A 303 5.89e+01 d.160.1.2 107808 1bpoA 494 5.91e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1o5iA 249 5.93e+01 c.2.1.2 92499 1kcxA 518 6.00e+01 b.92.1.3,c.1.9.6 90953,90954 3bmzA 199 6.04e+01 1quqB 121 6.04e+01 1quqB b.40.4.3 25305 2bpa1 426 6.04e+01 2bpa1 3cniA 156 6.04e+01 1qwgA 251 6.08e+01 c.1.27.1 96473 2p9rA 102 6.20e+01 3c5xA 402 6.23e+01 1vyoA 128 6.37e+01 1a04A 215 6.40e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1ush 550 6.40e+01 1ush 2nycA 144 6.45e+01 d.37.1.1 138812 1pgl1 185 6.48e+01 2f86B 143 6.49e+01 2okjA 504 6.50e+01 2yvpA 182 6.56e+01 1vr3A 191 6.56e+01 b.82.1.6 120431 1iirA 415 6.57e+01 1iirA c.87.1.5 62453 2htdA 140 6.68e+01 2nptB 100 6.75e+01 d.15.2.2 138449 2jcbA 200 6.83e+01 1k47A 337 6.86e+01 d.14.1.5,d.58.26.4 72040,72041 1p0zA 131 6.89e+01 d.110.6.1 93882 1i8lC 126 6.94e+01 1ah1 b.1.1.1 61974 1z8kA 193 6.96e+01 b.159.1.1 124703 2ph3A 245 7.02e+01 2ol1A 147 7.02e+01 1nqnA 122 7.03e+01 b.61.1.1 86042 1hqlA 257 7.03e+01 b.29.1.1 65907 1h09A 338 7.09e+01 b.109.1.1,c.1.8.8 83420,83421 1j3lA 164 7.11e+01 c.8.7.1 90813 2k0qA 74 7.11e+01 2d7eA 105 7.16e+01 1oe1A 336 7.19e+01 b.6.1.3,b.6.1.3 86891,86892 3b47A 134 7.20e+01 1aohA 147 7.21e+01 1aohA b.2.2.2 22401 2p11A 231 7.21e+01 1hl9A 449 7.24e+01 b.71.1.3,c.1.8.11 90650,90651 2hq9A 149 7.27e+01 b.45.1.1 136659 2gj3A 120 7.32e+01 1seiA 130 7.34e+01 1seiA d.140.1.1 41463 2cc1A 262 7.38e+01 e.3.1.1 130211 1ituA 369 7.38e+01 c.1.9.7 71423 2bghA 421 7.41e+01 1a7cA 379 7.50e+01 1sek e.1.1.1 42660 1k3iA 656 7.53e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 2fcfA 103 7.54e+01 b.36.1.1 133267 1v9yA 167 7.57e+01 d.110.3.2 108454 2h14A 317 7.62e+01 1f0iA 504 7.69e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1sjyA 159 7.75e+01 d.113.1.1 98900 2q8kA 401 7.78e+01 1mvfD 82 7.79e+01 b.129.1.1 85143 1lj5A 379 7.80e+01 e.1.1.1 73928 2fxqA 264 7.81e+01 2d4gA 171 7.81e+01 1gypA 358 7.83e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 2pdrA 149 7.83e+01 2bw4A 340 7.85e+01 b.6.1.3,b.6.1.3 129320,129321 2b3yA 888 7.87e+01 c.8.2.1,c.83.1.1 127803,127804 1rlmA 271 7.90e+01 c.108.1.10 111860 2hxdA 204 7.95e+01