# List of top-scoring protein chains for t2k-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.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 1v7lA 163 2.16e-04 2gp4A 628 1.81e-02 1fx2A 235 1.37e-01 1fx2A d.58.29.1 39430 1fx4A 231 1.65e-01 1fx2A d.58.29.1 39431 1dl5A 317 2.82e-01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1ivyA 452 4.55e-01 1ivyA c.69.1.5 34654 1amx 180 4.76e-01 1amx b.2.3.1 22410 1kqfA 1015 5.76e-01 b.52.2.2,c.81.1.1 72871,72872 1q7hA 153 8.62e-01 b.122.1.1,d.17.6.2 96042,96043 1ndh 272 9.35e-01 1ndh b.43.4.2,c.25.1.1 25662,31552 2bf5A 98 1.20e+00 1eu3A 210 1.27e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1kk9A 221 1.46e+00 d.115.1.1 77432 1kblA 873 1.48e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1dmr 823 1.58e+00 1dmr b.52.2.2,c.81.1.1 26904,35312 1owfA 99 1.68e+00 a.55.1.1 87487 1k7jA 206 1.72e+00 d.115.1.1 72103 1a88A 275 1.72e+00 1brt c.69.1.12 34707 1g8fA 511 1.81e+00 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1vpjA 192 2.00e+00 1huuA 90 2.10e+00 1huuA a.55.1.1 17897 1sb8A 352 2.12e+00 c.2.1.2 105410 1vjlA 164 2.22e+00 d.257.1.1 100822 1i1dA 161 2.40e+00 1i21A d.108.1.1 61526 1uebA 184 2.62e+00 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1ihfA 99 2.78e+00 1huuA a.55.1.1 17893 1iz6A 138 2.95e+00 b.34.5.2,b.40.4.5 76976,76977 1z85A 234 3.02e+00 1tuaA 191 3.06e+00 d.51.1.1,d.51.1.1 107321,107322 1r6xA 395 3.23e+00 b.122.1.3,c.26.1.5 97167,97168 1t0hB 224 3.28e+00 c.37.1.1 106208 1wmmA 145 3.40e+00 1hueA 90 3.62e+00 1huuA a.55.1.1 17900 1e58A 249 3.94e+00 1qhfA c.60.1.1 59262 1napA 70 4.16e+00 1tvxA d.9.1.1 37445 1e19A 314 4.39e+00 1b7bA c.73.1.1 34967 1ihfB 94 4.62e+00 1huuA a.55.1.1 17894 1knwA 425 4.82e+00 b.49.2.3,c.1.6.1 90969,90970 1o60A 292 4.82e+00 c.1.10.4 92532 1df7A 159 4.86e+00 3dfr c.71.1.1 34885 1x13A 401 4.90e+00 1ju3A 583 5.15e+00 b.18.1.13,c.69.1.21 67300,67301 1dv2A 452 5.26e+00 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1kl9A 182 5.35e+00 b.40.4.5 72681 1tvxB 75 5.54e+00 1tvxA d.9.1.1 37442 2bnfB 241 5.61e+00 2bneA 241 5.65e+00 1luzA 88 5.70e+00 b.40.4.5 74271 1viuA 203 5.74e+00 d.113.1.1 100771 1qfgA 725 5.78e+00 1by5A f.4.3.3 43803 1yb5A 351 5.81e+00 3ullA 132 6.15e+00 3ullA b.40.4.3 25282 1b8qA 127 6.35e+00 1qauA b.36.1.1 24781 1w41A 101 6.41e+00 1uv4A 293 6.44e+00 1zoiA 276 6.91e+00 1owfB 94 7.11e+00 a.55.1.1 87488 1cruA 454 7.19e+00 1c9uA b.68.2.1 27617 1uae 419 7.28e+00 1uae d.68.2.2 39574 1httA 423 7.37e+00 1adjA c.51.1.1,d.104.1.1 33178,40727 1gm0A 142 7.44e+00 a.39.2.1 65297 1jb9A 316 7.58e+00 1fnc b.43.4.2,c.25.1.1 62840,62841 1b7bA 310 7.64e+00 1b7bA c.73.1.1 34963 1b34B 118 7.75e+00 1b34B b.38.1.1 24797 1ii2A 524 7.82e+00 c.91.1.1,c.109.1.1 66146,66147 1zvyA 136 7.89e+00 1v74A 107 8.09e+00 d.243.1.1 100442 2gfaA 119 8.11e+00 1tvxA 75 8.11e+00 1tvxA d.9.1.1 37441 1k28A 584 8.12e+00 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 6paxA 133 8.37e+00 6paxA a.4.1.5,a.4.1.5 64758,64759 1fltX 95 8.43e+00 1fltX b.1.1.4 21765 2napA 723 8.44e+00 2napA b.52.2.2,c.81.1.1 26926,35334 1qbiA 454 8.63e+00 1c9uA b.68.2.1 27619 1qg0A 308 8.64e+00 1fnc b.43.4.2,c.25.1.1 25639,31529 1i12A 160 9.10e+00 1i21A d.108.1.1 61515 1umkA 275 9.21e+00 1tk9A 188 9.30e+00 c.80.1.3 107082 1lgpA 116 9.42e+00 b.26.1.2 73890 1nqcA 217 9.42e+00 d.3.1.1 86024 1aquA 297 9.82e+00 1aquA c.37.1.5 31942 2ccjA 205 9.85e+00 1jsdA 319 1.01e+01 b.19.1.2 63258 1akp 114 1.02e+01 2mcm b.1.7.1 22212 2f1rA 171 1.03e+01 1juvA 193 1.04e+01 c.71.1.1 90912 1x7dA 350 1.05e+01 2f2eA 146 1.06e+01 1zpsA 138 1.07e+01 1yr2A 741 1.09e+01 1jf9A 408 1.11e+01 1c0nA c.67.1.3 62931 1fokA 568 1.14e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 1ti6A 875 1.15e+01 b.52.2.2,c.81.1.1 106974,106975 2f23A 156 1.16e+01 1k78A 149 1.16e+01 a.4.1.5,a.4.1.5 68255,68256 1d9eA 284 1.17e+01 1d9eA c.1.10.4 29195 1ddgA 374 1.20e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1afp 51 1.22e+01 1afp g.26.1.1 44947 2bikB 313 1.22e+01 2a8kA 108 1.23e+01 1zx8A 136 1.23e+01 1okgA 373 1.29e+01 c.46.1.2,c.46.1.2,d.26.1.3 93250,93251,93252 1i7pA 274 1.30e+01 b.43.4.2,c.25.1.1 66048,66049 1pdnC 128 1.30e+01 6paxA a.4.1.5 16047 1p57A 114 1.31e+01 d.170.1.2 94125 4aahA 571 1.32e+01 4aahA b.70.1.1 27678 1k8wA 327 1.36e+01 b.122.1.1,d.265.1.2 83094,90388 1wn0A 145 1.36e+01 1i21A 159 1.37e+01 1i21A d.108.1.1 61549 2fb6A 117 1.37e+01 2a19A 175 1.38e+01 1ybdA 239 1.39e+01 1g72A 573 1.39e+01 4aahA b.70.1.1 27680 1ym0A 238 1.40e+01 1xovA 326 1.40e+01 1a5z 319 1.42e+01 1ceqA c.2.1.5,d.162.1.1 30181,42148 1wn5A 130 1.43e+01 1plfA 72 1.43e+01 1tvxA d.9.1.1 37373 1q7fA 286 1.44e+01 b.68.9.1 96036 1fltY 95 1.46e+01 1fltX b.1.1.4 21766 1fnd 314 1.46e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 2cmkA 227 1.48e+01 1ckeA c.37.1.1 31847 1fnc 314 1.48e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1fnb 314 1.48e+01 1fnc b.43.4.2,c.25.1.1 25628,31518 1qx4A 274 1.49e+01 b.43.4.2,c.25.1.1 104624,104625 1lrwA 600 1.53e+01 b.70.1.1 91111 1go2A 304 1.53e+01 b.43.4.2,c.25.1.1 76243,76244 1kjkA 64 1.55e+01 d.10.1.4 72613 1bx1A 314 1.55e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1o4sA 389 1.58e+01 c.67.1.1 86620 1b2rA 304 1.62e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 2fq9A 225 1.62e+01 2g76A 335 1.63e+01 1iwdA 215 1.63e+01 d.3.1.1 83756 1fseA 74 1.64e+01 1fseA a.4.6.2 60000 1ejdA 419 1.65e+01 1uae d.68.2.2 39576 2bsaA 303 1.69e+01 1o54A 277 1.70e+01 c.66.1.13 92482 1w34A 304 1.70e+01 1t3lA 337 1.72e+01 b.34.2.1,c.37.1.1 106358,106359 1qh0A 295 1.78e+01 b.43.4.2,c.25.1.1 68891,68892 1p65A 73 1.80e+01 d.254.1.1 94156 1lucB 324 1.81e+01 1lucA c.1.16.1 29548 1a8p 258 1.82e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 2bmwA 304 1.84e+01 2b59B 172 1.86e+01 7ahlA 293 1.86e+01 7ahlA f.6.1.1 43812 1ogiA 303 1.87e+01 b.43.4.2,c.25.1.1 92914,92915 1ir6A 424 1.88e+01 c.107.1.2 71342 1sbp 310 1.88e+01 1sbp c.94.1.1 35760 1l7dA 384 1.90e+01 c.2.1.4,c.23.12.2 77774,77775 1vs0A 310 1.93e+01 1v8yA 170 1.94e+01 1d3bA 75 1.96e+01 1d3bA b.38.1.1 24798 1hruA 188 1.98e+01 1hruA d.115.1.1 40926 2fokA 579 2.00e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 2bklA 695 2.00e+01 1zeqX 84 2.01e+01 1que 303 2.06e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1i1nA 226 2.07e+01 c.66.1.7 71102 1qvzA 237 2.09e+01 c.23.16.2 96453 1yn3A 98 2.09e+01 1uj6A 227 2.13e+01 c.124.1.4,d.58.40.1 107898,107899 1se8A 301 2.15e+01 b.40.4.3 105448 1ep2B 261 2.15e+01 1ep2B b.43.4.2,c.25.1.3 25666,31556 1h7mA 102 2.17e+01 d.79.3.1 83485 1uheA 97 2.17e+01 1mvfA 135 2.18e+01 b.1.1.1 85141 3il8 72 2.18e+01 1tvxA d.9.1.1 37356 1pueE 89 2.19e+01 1awcA a.4.5.21 16165 1kl7A 514 2.24e+01 c.79.1.1 72678 1xwsA 313 2.24e+01 1zaiA 363 2.24e+01 1o20A 427 2.25e+01 c.82.1.1 86556 1pv9A 348 2.28e+01 c.55.2.1,d.127.1.1 95157,95158 1kzlA 208 2.33e+01 b.43.4.3,b.43.4.3 77635,77636 1qauA 112 2.34e+01 1qauA b.36.1.1 24779 2ffeA 311 2.34e+01 2myo 118 2.35e+01 2myo d.211.1.1 19175 1kv9A 668 2.35e+01 a.3.1.6,b.70.1.1 73056,73057 1aorA 605 2.35e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1b8zA 90 2.37e+01 1huuA a.55.1.1 17902 1vajA 214 2.37e+01 1adoA 363 2.39e+01 1fbaA c.1.10.1 29124 2fivA 116 2.39e+01 1fmb b.50.1.1 26766 1ep3B 262 2.41e+01 1ep2B b.43.4.2,c.25.1.3 25664,31554 1lf2A 331 2.42e+01 b.50.1.2 77914 1t46A 313 2.43e+01 d.144.1.7 106397 2a6qA 86 2.46e+01 1f8gA 384 2.47e+01 1sayA c.2.1.4,c.23.12.2 59695,59696 1c30B 382 2.54e+01 c.8.3.1,c.23.16.1 30736,31413 1abe 306 2.56e+01 8abp c.93.1.1 35648 1w0uA 55 2.60e+01 1oahA 519 2.61e+01 a.138.1.3 86736 1hbzA 498 2.63e+01 1cf9A e.5.1.1 60937 2es9A 115 2.65e+01 1qavB 115 2.67e+01 1qauA b.36.1.1 24780 1k4iA 233 2.68e+01 d.115.1.2 72056 1t3iA 420 2.74e+01 c.67.1.3 106354 1pguA 615 2.75e+01 b.69.4.1,b.69.4.1 88069,88070 1ppo 216 2.77e+01 1cs8A d.3.1.1 37020 5abp 306 2.77e+01 8abp c.93.1.1 35651 1ywnA 316 2.77e+01 1snnA 227 2.78e+01 d.115.1.2 105821 1g10A 102 2.78e+01 1g10A d.137.1.1 60191 1io1A 398 2.79e+01 1io1A e.32.1.1 62611 1c9uA 454 2.80e+01 1c9uA b.68.2.1 27623 1wr4A 36 2.82e+01 1a9xB 379 2.85e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1c3oB 382 2.87e+01 1c3oB c.8.3.1,c.23.16.1 30744,31421 1xtoA 311 2.91e+01 1zmdA 474 2.92e+01 1esfA 233 2.93e+01 3seb b.40.2.2,d.15.6.1 25146,37735 1v9kA 228 2.94e+01 d.265.1.3 108449 1qvcA 145 2.98e+01 3ullA b.40.4.3 25284 1vkmA 297 3.00e+01 c.138.1.1 108670 1dqeA 137 3.01e+01 1dqeA a.39.2.1 17388 1pvyA 227 3.01e+01 d.115.1.2 95195 1rw7A 243 3.01e+01 c.23.16.2 97963 1qu9A 128 3.02e+01 1qu9A d.79.1.1 39755 1qu9C 128 3.02e+01 1qu9A d.79.1.1 39757 1brlB 324 3.02e+01 1lucA c.1.16.1 29554 1k6dA 220 3.07e+01 c.124.1.2 72082 1bjx 110 3.08e+01 1bjx c.47.1.2 32774 2bjxA 110 3.08e+01 1bjx c.47.1.2 32776 1em8A 147 3.13e+01 c.128.1.1 90457 1bkb 136 3.15e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 2hntE 81 3.17e+01 1ucyH 1a63 130 3.17e+01 1a62 a.140.3.1,b.40.4.5 64710,64711 2gjgA 248 3.24e+01 1oyzA 280 3.26e+01 a.118.1.16 93775 2aorA 223 3.26e+01 1cs0B 382 3.28e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 1ws0A 156 3.29e+01 1e3jA 352 3.29e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1tig 94 3.29e+01 1tig d.68.1.1 39566 1fdr 248 3.31e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1sxvA 172 3.33e+01 1dv1A 449 3.33e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1vdmA 153 3.35e+01 1cne 270 3.35e+01 1ndh b.43.4.2,c.25.1.1 25661,31551 1kjnA 157 3.35e+01 c.115.1.1 72614 1hn2A 159 3.37e+01 b.60.1.1 65890 2bbkH 355 3.38e+01 2bbkH b.69.2.1 27634 2cb5A 453 3.39e+01 3gcb d.3.1.1 37035 1gt1A 159 3.40e+01 b.60.1.1 90515 1xu9A 286 3.43e+01 3ladA 476 3.44e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1fivA 113 3.45e+01 1fmb b.50.1.1 26764 1v76A 96 3.46e+01 1nfp 228 3.46e+01 1nfp c.1.16.2 29555 1qw1A 121 3.52e+01 1iw7C 1119 3.52e+01 e.29.1.1 71474 1i6cA 39 3.53e+01 1i6cA b.72.1.1 61828 1vchA 175 3.58e+01 1ne9A 335 3.59e+01 d.108.1.4,d.108.1.4 91839,91840 1tksA 204 3.62e+01 d.115.1.2 107114 2bz8A 58 3.64e+01 1konA 249 3.67e+01 e.39.1.1 72823 1h0hA 977 3.68e+01 b.52.2.2,c.81.1.1 76435,76436 1brt 277 3.68e+01 1brt c.69.1.12 34699 1pch 88 3.69e+01 1ptf d.94.1.1 40564 1oe8A 211 3.70e+01 a.45.1.1,c.47.1.5 86905,86906 1fvrA 327 3.74e+01 d.144.1.7 60047 1alq 266 3.75e+01 1btl e.3.1.1 42707 1rkxA 357 3.77e+01 c.2.1.2 97631 1wocA 103 3.77e+01 1wthD 391 3.79e+01 2fbyA 205 3.91e+01 1ve6A 582 3.91e+01 2hcuA 213 3.92e+01 2cz1B 212 3.94e+01 1cqxA 403 3.96e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1gweA 503 3.98e+01 e.5.1.1 70667 1smrA 335 4.00e+01 1smrA b.50.1.2 26878 1pedA 351 4.02e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1xneA 113 4.05e+01 1xdwA 331 4.05e+01 1qxrA 189 4.07e+01 b.82.1.7 96552 1ghpA 258 4.08e+01 1btl e.3.1.1 60520 2viuA 328 4.08e+01 1hgeA b.19.1.2 23797 1kr5A 226 4.17e+01 c.66.1.7 68847 1lywA 97 4.19e+01 1lywA b.50.1.2 26861 1obpA 159 4.21e+01 1obpA b.60.1.1 27092 1iqzA 81 4.25e+01 d.58.1.4 66281 1qtyT 101 4.27e+01 1fltX b.1.1.4 21769 1wdjA 187 4.28e+01 1a2n 419 4.28e+01 1uae d.68.2.2 39575 1i18A 97 4.30e+01 b.43.4.3 61520 1nmoA 247 4.30e+01 c.135.1.1 91980 1g7vA 284 4.31e+01 1d9eA c.1.10.4 60335 1mpyA 307 4.33e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1dzfA 215 4.34e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1lroA 267 4.34e+01 c.1.10.4 78161 1kb0A 677 4.35e+01 a.3.1.6,b.70.1.1 68378,68379 1a8s 273 4.36e+01 1brt c.69.1.12 34710 1jcxA 267 4.37e+01 c.1.10.4 66510 3hmgA 328 4.40e+01 1hgeA b.19.1.2 23825 1b7gO 340 4.41e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1hqz9 141 4.44e+01 1nzyA 269 4.45e+01 1nzyA c.14.1.3 30903 1vkfA 188 4.46e+01 c.1.29.1 108656 1e2gA 215 4.47e+01 3tmkA c.37.1.1 59165 1e9eA 215 4.51e+01 c.37.1.1 64810 1e9cA 215 4.53e+01 c.37.1.1 64808 1z08A 170 4.55e+01 1xmbA 418 4.56e+01 1fxpA 267 4.61e+01 1d9eA c.1.10.4 60106 2be1A 339 4.61e+01 1e2fA 215 4.63e+01 3tmkA c.37.1.1 59164 1r5mA 425 4.65e+01 1rl6A 177 4.68e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1a62 130 4.69e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1nn5A 215 4.70e+01 c.37.1.1 85892 1a8vA 121 4.75e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1myo 118 4.76e+01 2myo d.211.1.1 19174 2ha8A 184 4.79e+01 1fxqA 267 4.83e+01 1d9eA c.1.10.4 60108 3hmgB 175 4.84e+01 1hgeB h.3.1.1 45704 1jx7A 117 4.84e+01 c.114.1.1 77195 1ewxA 146 4.89e+01 1ewxA c.47.1.10 33062 1pkm 530 4.90e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27051,29254,33108 1fwsA 267 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