# List of top-scoring protein chains for t06-100-30-alpha-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 1zkiA 133 7.45e-19 1j1yA 136 3.26e-18 d.38.1.5 90776 1o0iA 138 3.93e-18 d.38.1.5 86532 1wluA 136 7.12e-18 2fs2A 151 7.93e-18 1vh5A 148 5.55e-17 d.38.1.5 100642 1vpmA 169 1.47e-16 1yliA 153 2.59e-16 1ixlA 131 8.07e-15 d.38.1.5 90717 1z6bA 154 1.12e-14 2gvhA 288 1.98e-14 1q4uA 151 3.00e-14 d.38.1.5 95828 1yocA 147 6.64e-14 2cyeA 133 6.91e-14 1t82A 155 3.17e-13 d.38.1.5 106639 1sh8A 154 1.10e-11 d.38.1.5 105549 1s5uA 138 2.13e-11 d.38.1.1 98573 1z54A 132 1.13e-10 2b3nA 159 1.13e-10 2gf6A 135 1.76e-10 2aliA 158 2.94e-09 2cwzA 141 5.76e-09 1iq6A 134 7.47e-08 d.38.1.4 76755 1lo7A 141 2.23e-07 d.38.1.1 74144 1tbuA 118 3.52e-07 1c8uA 285 1.84e-06 1c8uA d.38.1.3,d.38.1.3 38547,38548 2essA 248 7.17e-06 1mkaA 171 3.20e-05 1mkaA d.38.1.2 38543 2bi0A 337 3.49e-04 1pn2A 280 2.17e-03 d.38.1.4,d.38.1.4 94930,94931 1yycA 174 2.72e-02 1s1fA 406 9.11e-02 2bm3A 166 1.01e-01 1te5A 257 1.03e-01 d.153.1.1 106795 1xkpC 143 1.77e-01 1vcaA 202 5.05e-01 1vcaA b.1.1.3,b.1.1.4 21649,21685 2f4lA 297 6.88e-01 1oh0A 131 9.76e-01 d.17.4.3 87004 1ry9A 145 1.03e+00 d.198.1.1 98094 1o9yA 84 1.20e+00 b.139.1.1 92692 1zo2A 129 1.26e+00 1xebA 150 1.37e+00 1d2oA 187 1.43e+00 1d2oA b.3.5.1,b.3.5.1 22625,22626 1o6aA 96 1.43e+00 b.139.1.1 92562 2gr8A 99 1.47e+00 1hmt 132 1.49e+00 1hmt b.60.1.2 27169 1txqA 93 1.62e+00 1f3uA 118 1.62e+00 1f3uA b.65.1.1 27521 1q2yA 140 1.81e+00 d.108.1.1 95655 1u69A 163 2.08e+00 d.32.1.7 107699 1hxvA 113 2.15e+00 d.26.1.1 71089 1l0wA 580 2.15e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1x8qA 184 2.18e+00 1nnxA 109 2.18e+00 b.40.10.1 92013 1lshA 1056 2.37e+00 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1fhgA 154 2.51e+00 1tlk b.1.1.4 21706 2fimA 276 2.60e+00 2cu6A 103 2.63e+00 1g7nA 131 2.76e+00 b.60.1.2 83274 2g8oA 264 2.82e+00 1fqtA 112 2.88e+00 1fqtA b.33.1.1 24441 1b06A 210 2.91e+00 1avmA a.2.11.1,d.44.1.1 15740,38737 1idpA 172 2.95e+00 d.17.4.1 83685 1tyjA 170 2.98e+00 1i76A 163 2.99e+00 1hfc d.92.1.11 61877 1qqqA 264 3.01e+00 1bkpA d.117.1.1 40931 1zthA 258 3.01e+00 1g87A 614 3.01e+00 a.102.1.2,b.2.2.2 83275,83276 1uvqA 197 3.13e+00 b.1.1.2,d.19.1.1 100062,100063 1wteA 272 3.21e+00 1kzfA 230 3.21e+00 d.108.1.3 73354 1r4vA 171 3.29e+00 a.197.1.1 97049 1su8A 636 3.36e+00 e.26.1.2 98999 2ftbA 125 3.63e+00 1r7mA 235 3.72e+00 2g8mA 264 3.72e+00 1fm0D 81 3.78e+00 1fmaD d.15.3.1 37642 1yewA 382 4.23e+00 1cbs 137 4.30e+00 1hmt b.60.1.2 27201 2fm8A 135 4.47e+00 2bmeA 186 4.48e+00 1l2tA 235 4.55e+00 c.37.1.12 73514 1je0A 236 4.58e+00 c.56.2.1 66581 1tiqA 180 4.92e+00 d.108.1.1 107010 1kshB 152 5.41e+00 b.1.18.8 72915 1ny4A 82 5.42e+00 b.40.4.5 92316 2awkA 228 5.58e+00 1j98A 157 5.73e+00 1j98A d.185.1.2 62755 1yirA 408 5.79e+00 1whvA 100 6.01e+00 1a3c 181 6.21e+00 1a3c c.61.1.1 34095 2ffsA 157 6.27e+00 2eifA 136 6.35e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 2bf6A 449 6.83e+00 1sdjA 310 6.93e+00 d.21.1.2,d.21.1.2 98807,98808 1geeA 261 7.55e+00 c.2.1.2 90509 1v8bA 479 7.58e+00 1u94A 356 7.66e+00 c.37.1.11,d.48.1.1 107743,107744 1ej0A 180 7.66e+00 1ej0A c.66.1.2 34179 2c78A 405 7.87e+00 1yq2A 1024 7.91e+00 1hq0A 295 8.13e+00 1hzgA d.194.1.1 61122 1pvtA 238 8.45e+00 c.74.1.1 95189 1wxcB 134 8.63e+00 2a15A 139 8.71e+00 3ullA 132 8.73e+00 3ullA b.40.4.3 25282 1kqwA 134 8.79e+00 b.60.1.2 72887 2g3aA 152 8.96e+00 1thqA 170 9.11e+00 f.4.1.2 106920 1kdgA 546 9.19e+00 c.3.1.2,d.16.1.1 77337,77338 1vq2A 193 9.39e+00 2a74B 188 9.43e+00 1gai 472 9.71e+00 1ayx a.102.1.1 18819 1qyaA 307 9.79e+00 d.21.1.2,d.21.1.2 104653,104654 1wgzA 510 9.89e+00 1tmxA 293 9.94e+00 1e2wA 251 1.00e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1v8hA 107 1.01e+01 1rf6A 427 1.02e+01 d.68.2.2 97366 1f2tB 148 1.02e+01 1f2tB 1y43B 173 1.03e+01 1xgsA 295 1.03e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 1o75A 415 1.03e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 1pyaB 228 1.04e+01 1pyaB 1txlA 215 1.07e+01 b.60.1.4 107429 1t0yA 122 1.07e+01 d.15.1.1 99066 1ww7A 160 1.10e+01 1erjA 393 1.15e+01 1erjA b.69.4.1 27660 1suuA 312 1.16e+01 b.68.10.1 99006 1mzyA 333 1.18e+01 b.6.1.3,b.6.1.3 103848,103849 2cb2A 318 1.19e+01 1m2xA 223 1.20e+01 d.157.1.1 84764 1wmmA 145 1.20e+01 2cx6A 90 1.20e+01 1v2bA 177 1.21e+01 d.107.1.2 108279 1y0yA 353 1.23e+01 1f39A 101 1.23e+01 1umuA b.87.1.1 28386 2fg1A 158 1.24e+01 1fm0E 150 1.25e+01 1fmaE d.41.5.1 38629 1vbvA 105 1.28e+01 1kt6A 183 1.29e+01 b.60.1.1 84466 1tp6A 128 1.31e+01 d.17.4.12 107184 1bupA 386 1.35e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1dabA 539 1.37e+01 1dabA b.80.1.7 28049 1ihjA 98 1.37e+01 1pdr b.36.1.1 62382 1vehA 92 1.39e+01 1j1lA 290 1.39e+01 b.82.1.12 90766 1gutA 68 1.42e+01 b.40.6.1 65576 1wubA 178 1.42e+01 1vrmA 325 1.43e+01 1uacL 107 1.43e+01 b.1.1.1 99133 1ra6A 461 1.43e+01 e.8.1.4 104879 1ufwA 95 1.43e+01 d.58.7.1 99358 1ni4A 365 1.44e+01 c.36.1.11 85728 1tu1A 148 1.45e+01 d.107.1.3 107316 2conA 79 1.45e+01 1vl4A 447 1.46e+01 d.283.1.1 108718 2b3hA 329 1.50e+01 1fvkA 189 1.52e+01 1fvkA c.47.1.13 90351 1n9pA 207 1.54e+01 b.1.18.16 80343 1f0lA 535 1.56e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1ddwA 120 1.58e+01 1evhA b.55.1.4 27001 1k8kD 300 1.61e+01 d.198.2.1,d.198.2.1 68309,68310 1tuoA 464 1.61e+01 1uz5A 402 1.63e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1gl4B 98 1.63e+01 b.1.1.4 65288 2gzqA 200 1.64e+01 1x74A 360 1.65e+01 2c5qA 240 1.65e+01 2bjqA 345 1.68e+01 1wbeA 209 1.69e+01 1swxA 209 1.71e+01 a.224.1.1 106075 2a5jA 191 1.73e+01 1oxxK 353 1.76e+01 b.40.6.3,c.37.1.12 93715,93716 2cxcA 144 1.77e+01 1xp8A 366 1.77e+01 1o8vA 134 1.77e+01 b.60.1.2 86680 1wddS 128 1.77e+01 1x3eA 165 1.82e+01 2bolA 314 1.82e+01 1tt8A 164 1.84e+01 2faoA 309 1.84e+01 2a9dA 372 1.85e+01 1yvoA 172 1.86e+01 1vr4A 103 1.87e+01 1vrbA 342 1.92e+01 1g5cA 170 1.95e+01 1g5cA c.53.2.1 60264 1r9hA 135 1.96e+01 d.26.1.1 97260 2a50B 168 1.97e+01 2ajuL 216 1.99e+01 1tr0A 108 1.99e+01 d.58.4.4 107261 2b69A 343 2.00e+01 1tqhA 247 2.01e+01 c.69.1.29 107225 1b56 135 2.05e+01 1hmt b.60.1.2 27183 1r3eA 309 2.07e+01 b.122.1.1,d.265.1.2 96907,96908 1zanL 214 2.08e+01 1f00I 282 2.08e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 2fcbA 173 2.08e+01 2fcbA b.1.1.4,b.1.1.4 21781,21782 2fvgA 340 2.09e+01 2bc4A 211 2.14e+01 2audA 257 2.19e+01 1ustA 93 2.19e+01 a.4.5.13 99884 1oxdA 227 2.20e+01 d.22.1.1 93687 1qhoA 686 2.20e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1o9gA 250 2.20e+01 c.66.1.29 86692 1bcpF 99 2.21e+01 1prtF b.40.2.1 25142 1jsdA 319 2.21e+01 b.19.1.2 63258 2f62A 161 2.21e+01 1stzA 338 2.23e+01 a.4.5.51,d.110.2.3 106009,106010 1yqfA 203 2.23e+01 1zkpA 268 2.26e+01 1wf3A 301 2.29e+01 1vjzA 341 2.30e+01 c.1.8.3 100838 1b8oA 284 2.31e+01 1b8oA c.56.2.1 33762 1cb0A 283 2.32e+01 1cb0A c.56.2.1 33790 1gz8A 299 2.33e+01 d.144.1.7 83405 1uuyA 167 2.37e+01 c.57.1.1 108059 1ir21 140 2.38e+01 2aq8A 269 2.38e+01 1ka2A 499 2.39e+01 d.92.1.5 77305 1sc3A 178 2.40e+01 c.17.1.1 105416 1q6uA 245 2.40e+01 d.26.1.1 95998 1vjlA 164 2.41e+01 d.257.1.1 100822 1on0A 158 2.43e+01 d.108.1.1 87095 1x82A 190 2.43e+01 1vapA 123 2.44e+01 1poa a.133.1.2 19548 1s14A 194 2.44e+01 d.122.1.2 98329 1n67A 359 2.44e+01 b.2.3.4,b.2.3.4 85354,85355 1pz4A 116 2.50e+01 d.106.1.1 95400 2btoA 473 2.53e+01 1xypA 190 2.54e+01 1axkA b.29.1.11 24327 1pwxA 254 2.56e+01 c.2.1.2 95262 1pm1X 180 2.58e+01 b.60.1.1 104189 1fo0B 112 2.58e+01 1kb5B b.1.1.1 20631 2genA 197 2.61e+01 1e6yB 433 2.62e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 1tcvA 287 2.63e+01 1yj7A 171 2.64e+01 2b4wA 315 2.67e+01 1rj8A 164 2.68e+01 b.22.1.1 97547 1unnC 115 2.70e+01 d.240.1.1 99680 1t4wA 196 2.73e+01 b.2.5.2 106427 1ylxA 103 2.73e+01 1gd0A 122 2.75e+01 1dptA d.80.1.3 39834 1qv1A 195 2.79e+01 a.39.1.5 96347 2d81A 318 2.80e+01 1lurA 339 2.83e+01 b.30.5.4 84717 1bwwA 109 2.83e+01 8fabA b.1.1.1 20518 1amuA 563 2.84e+01 1amuA e.23.1.1 43351 2cwsA 237 2.88e+01 1kkeA 210 2.92e+01 b.21.1.2,b.83.1.2 68669,68670 2d1eA 248 2.93e+01 2hgsA 474 2.94e+01 2hgsA c.30.1.4,d.142.1.6 31722,75997 1b5qA 472 2.99e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1se8A 301 2.99e+01 b.40.4.3 105448 2beiA 170 2.99e+01 1bkb 136 2.99e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 2as9A 210 3.00e+01 1u58A 253 3.01e+01 1zaiA 363 3.01e+01 1k8wA 327 3.01e+01 b.122.1.1,d.265.1.2 83094,90388 1hr0W 71 3.02e+01 1ah9 b.40.4.5 25329 1xmzA 241 3.03e+01 1m3sA 186 3.05e+01 c.80.1.3 78573 1v5rA 97 3.11e+01 2ex0A 399 3.13e+01 1ygaA 342 3.13e+01 1zmtA 254 3.15e+01 1yoaA 159 3.15e+01 1josA 128 3.17e+01 d.52.7.1 84191 2d1sA 548 3.17e+01 1f2tA 149 3.20e+01 1f2tA c.37.1.12 32373 1qysA 106 3.20e+01 k.41.1.1 96603 1jbeA 128 3.23e+01 3chy c.23.1.1 62845 1nkqA 259 3.24e+01 d.177.1.1 103862 2aq4A 434 3.25e+01 1iz6A 138 3.25e+01 b.34.5.2,b.40.4.5 76976,76977 2fyxA 143 3.26e+01 1mqkL 120 3.27e+01 b.1.1.1 85054 1dusA 194 3.28e+01 1dusA c.66.1.4 34182 1wisA 124 3.35e+01 1vhoA 346 3.37e+01 b.49.3.1,c.56.5.4 100694,100695 2fmmA 74 3.37e+01 2b5hA 200 3.40e+01 1uv7A 110 3.42e+01 d.67.4.1 100040 2bv4A 113 3.47e+01 1npyA 271 3.48e+01 c.2.1.7,c.58.1.5 85995,85996 1w2wA 211 3.49e+01 c.124.1.5 109130 1yvrA 538 3.49e+01 1fyhB 229 3.52e+01 1jrhI b.1.2.1,b.1.2.1 22055,22056 1mjuL 219 3.52e+01 b.1.1.1,b.1.1.2 91304,91305 1yhfA 115 3.53e+01 1udxA 416 3.56e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1mj5A 302 3.56e+01 c.69.1.8 91285 1vr5A 547 3.58e+01 1jb7A 495 3.62e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1u7iA 136 3.62e+01 d.32.1.7 107724 1iq4A 179 3.67e+01 1iq4A d.77.1.1 62641 1v1aA 309 3.67e+01 c.72.1.1 100249 2aj6A 159 3.70e+01 1ngzA 213 3.71e+01 b.1.1.1,b.1.1.2 80500,80501 2btiA 63 3.74e+01 2g6yA 217 3.76e+01 1txkA 498 3.78e+01 b.1.18.2,b.30.5.9 107425,107426 2f7tA 227 3.81e+01 1vdmA 153 3.82e+01 1pne 140 3.83e+01 1pne d.110.1.1 40866 1ufkA 254 3.84e+01 c.66.1.39 99340 1tzjA 338 3.84e+01 1umhA 184 3.86e+01 b.18.1.21 99605 2a1vA 144 3.86e+01 1mkkA 96 3.90e+01 g.17.1.1 79240 1ifc 132 3.90e+01 b.60.1.2 27173 3nul 130 3.93e+01 3nul d.110.1.1 40891 1ur1A 378 3.93e+01 c.1.8.3 99804 2fl7A 232 3.93e+01 1ej8A 140 3.96e+01 1qupA b.1.8.1 22300 1iam 185 4.01e+01 1zxq b.1.1.3,b.1.1.4 21653,21689 1ecfA 504 4.03e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 2d37A 176 4.03e+01 2bwrA 401 4.04e+01 1dqeA 137 4.04e+01 1dqeA a.39.2.1 17388 1fxlA 167 4.06e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1f20A 435 4.07e+01 b.43.4.1,c.25.1.4 64932,64933 1yn4A 99 4.11e+01 1fnlA 175 4.12e+01 2fcbA b.1.1.4,b.1.1.4 21783,21784 1li4A 432 4.14e+01 c.2.1.4,c.23.12.3 84616,84617 1jndA 420 4.16e+01 c.1.8.5,d.26.3.1 71757,71758 1ln1A 214 4.17e+01 d.129.3.2 74038 1u7eB 154 4.17e+01 1cseI 71 4.19e+01 1egpA d.40.1.1 38559 1orc 71 4.21e+01 1orc a.35.1.2 17054 1khoA 370 4.23e+01 a.124.1.1,b.12.1.3 72489,72490 4bcl 366 4.24e+01 4bcl b.75.1.1 27968 1mvfD 82 4.26e+01 b.129.1.1 85143 1mdc 133 4.28e+01 1hmt b.60.1.2 27198 1cz4A 185 4.31e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1upiA 225 4.35e+01 b.82.1.1 99757 2c1vA 338 4.41e+01 1gmeA 151 4.41e+01 b.15.1.1 65305 1w32A 348 4.43e+01 1n40A 396 4.43e+01 a.104.1.1 79977 1cr5A 189 4.47e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1gq6A 313 4.49e+01 c.42.1.1 70341 1qi9A 556 4.50e+01 1qhbA a.111.1.2 19053 1dfmA 223 4.51e+01 1d2iA c.52.1.5 33295 1sflA 238 4.51e+01 1x3sA 195 4.53e+01 1iz5A 249 4.55e+01 d.131.1.2,d.131.1.2 83834,83835 2cxhA 217 4.55e+01 1xfrA 128 4.55e+01 1o5uA 101 4.58e+01 b.82.1.8 92518 2aioA 269 4.59e+01 1vp4A 425 4.60e+01 1yqyA 523 4.61e+01 2ai4A 119 4.61e+01 1ex2A 189 4.65e+01 1ex2A c.51.4.2 33225 1q7lA 198 4.66e+01 c.56.5.4 96044 1xkpB 124 4.70e+01 1h4pA 408 4.70e+01 c.1.8.3 90617 2exnA 136 4.73e+01 1mc2A 122 4.75e+01 a.133.1.2 74622 1pmy 123 4.78e+01 1bqk b.6.1.1 22888 1s99A 200 4.83e+01 1ve4A 206 4.84e+01 1rhfA 182 4.86e+01 b.1.1.1,b.1.1.4 97469,97470 1vc3B 97 4.86e+01 1g38A 393 4.88e+01 2admA c.66.1.27 60235 1tz9A 367 4.88e+01 c.1.15.6 107466 1z2nX 324 4.89e+01 1k77A 260 4.89e+01 c.1.15.5 72096 1kqpA 271 4.91e+01 c.26.2.1 72883 1f3lA 321 4.95e+01 1g6q2 c.66.1.6 59630 1c44A 123 5.01e+01 1qndA d.106.1.1 40795 1dceA 567 5.02e+01 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 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