# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 2bcoA 350 1.73e-22 1yw4A 341 2.46e-21 1h8lA 380 8.69e-05 b.3.2.1,c.56.5.1 65737,65738 1qmuA 380 1.31e-04 1qmuA b.3.2.1,c.56.5.1 22534,33827 2bo9A 308 7.89e-04 2c1cA 312 3.69e-03 1jqgA 433 5.66e-03 c.56.5.1,d.58.3.1 71791,71792 1aye 401 1.30e-02 1aye c.56.5.1,d.58.3.1 33824,39065 1dtdA 303 1.58e-02 1aye c.56.5.1 33823 1m4lA 307 1.22e-01 c.56.5.1 78604 1yme 309 1.24e-01 1aye c.56.5.1 33804 2ctb 307 1.29e-01 1aye c.56.5.1 33803 2ctc 307 1.83e-01 1aye c.56.5.1 33802 6cpa 307 1.97e-01 1aye c.56.5.1 33816 1kwmA 402 2.28e-01 c.56.5.1,d.58.3.1 73079,73080 1bavA 309 3.09e-01 1aye c.56.5.1 33806 1z5rA 306 5.89e-01 1o0wA 252 9.11e-01 a.149.1.1,d.50.1.1 80751,80752 1obr 326 9.65e-01 1aye c.56.5.2 33828 1f47B 144 1.86e+00 1f46A d.129.4.1 59645 1f7wA 144 2.76e+00 1f46A d.129.4.1 59679 2axpA 173 3.65e+00 1cy9A 264 3.89e+00 1ecl e.10.1.1 43236 1cz1A 394 4.65e+00 1cz1A c.1.8.3 28839 2aqjA 538 4.79e+00 1eqcA 394 4.99e+00 1cz1A c.1.8.3 28811 1jvbA 347 5.05e+00 b.35.1.2,c.2.1.1 77181,77182 1klnA 605 5.21e+00 1xwl c.55.3.5,e.8.1.1 33693,42986 1mjc 69 5.55e+00 1mjc b.40.4.5 25319 1ne2A 200 5.79e+00 c.66.1.32 85586 1vhoA 346 6.12e+00 b.49.3.1,c.56.5.4 100694,100695 1d8yA 605 6.74e+00 1xwl c.55.3.5,e.8.1.1 33684,42977 2kfnA 605 6.80e+00 1xwl c.55.3.5,e.8.1.1 33682,42975 1ab5A 125 6.86e+00 3chy c.23.1.1 31056 1f1sA 814 6.92e+00 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1hyvA 166 6.94e+00 1b9dA c.55.3.2 61424 1jbeA 128 7.18e+00 3chy c.23.1.1 62845 1cye 129 7.63e+00 3chy c.23.1.1 31077 1nt4A 391 7.80e+00 c.60.1.2 92102 1f46A 140 7.96e+00 1f46A d.129.4.1 59643 1d4xG 126 8.29e+00 1d0nA d.109.1.1 59109 1yagG 125 8.88e+00 1d0nA d.109.1.1 40846 1zm7A 230 8.89e+00 1tlfA 301 9.13e+00 1tlfA c.93.1.1 35687 1nm1G 125 9.25e+00 d.109.1.1 80653 1bl3A 160 9.38e+00 1b9dA c.55.3.2 33655 1h1nA 305 9.41e+00 c.1.8.3 70855 1xx1A 285 9.64e+00 2b81A 323 9.84e+00 1kfd 605 1.03e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 2gl5A 410 1.05e+01 1r62A 160 1.07e+01 d.122.1.3 104816 1ki9A 192 1.19e+01 c.37.1.1 84404 1e6mA 128 1.20e+01 3chy c.23.1.1 31039 1f0nA 285 1.26e+01 1dqyA c.69.1.3 34636 1m2rA 327 1.26e+01 d.144.1.7 84760 1lpuA 332 1.26e+01 d.144.1.7 74177 1j90A 230 1.26e+01 c.37.1.1 66448 1pa2A 306 1.27e+01 1bgp a.93.1.1 18693 1jbkA 195 1.28e+01 c.37.1.20 71631 3chy 128 1.28e+01 3chy c.23.1.1 31038 2bklA 695 1.31e+01 1oe0A 230 1.33e+01 c.37.1.1 92788 1xfkA 336 1.33e+01 1jwqA 179 1.35e+01 c.56.5.6 90921 1vp4A 425 1.38e+01 1a6o 332 1.39e+01 1a6o 1qasA 622 1.41e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17340,23157,29585 1pv1A 299 1.43e+01 1qatB 622 1.46e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17355,23172,29600 1t0bA 252 1.47e+01 c.23.16.6 106199 1fxqA 267 1.47e+01 1d9eA c.1.10.4 60108 1ab6A 125 1.48e+01 3chy c.23.1.1 31054 1c0dA 358 1.50e+01 1eceA c.1.8.3 28815 1fxpA 267 1.56e+01 1d9eA c.1.10.4 60106 1d6mA 653 1.60e+01 1d6mA e.10.1.1 43248 1om1A 332 1.61e+01 d.144.1.7 93347 1lp4A 332 1.62e+01 d.144.1.7 74170 1b9dA 163 1.62e+01 1b9dA c.55.3.2 33649 1lw6E 281 1.64e+01 c.41.1.1 74293 1ye8A 178 1.65e+01 1qd1A 325 1.77e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1to2E 281 1.79e+01 1p2fA 220 1.83e+01 a.4.6.1,c.23.1.1 87720,87721 1eceA 358 1.84e+01 1eceA c.1.8.3 28813 1f8yA 157 1.86e+01 1f8xA c.23.14.1 31395 1g0cA 364 1.92e+01 7a3hA c.1.8.3 60165 2lbp 346 1.95e+01 2liv c.93.1.1 35709 1i7dA 659 1.95e+01 1d6mA e.10.1.1 61886 1usgA 346 1.97e+01 c.93.1.1 99864 1g01A 364 2.11e+01 7a3hA c.1.8.3 60161 1xovA 326 2.12e+01 1jcxA 267 2.13e+01 c.1.10.4 66510 1wzcA 249 2.17e+01 1sup 275 2.19e+01 1gci c.41.1.1 32510 1kl7A 514 2.24e+01 c.79.1.1 72678 1o26A 232 2.29e+01 d.207.1.1 86566 1s1pA 331 2.31e+01 c.1.7.1 98350 1xwyA 264 2.32e+01 1h6kZ 98 2.34e+01 d.58.7.1 60686 1vih 71 2.34e+01 1vih d.51.1.1 38807 1vig 71 2.35e+01 1vih d.51.1.1 38806 1pe1A 267 2.40e+01 c.1.10.4 94591 1yaxA 153 2.43e+01 2cybA 323 2.45e+01 1t8xA 267 2.50e+01 1zhaA 267 2.54e+01 1ecl 597 2.55e+01 1ecl e.10.1.1 43238 1lroA 267 2.56e+01 c.1.10.4 78161 1xfjA 261 2.61e+01 d.194.1.2 109585 1yj7A 171 2.62e+01 1w61A 414 2.67e+01 1rk8A 165 2.69e+01 d.58.7.1 97603 3mefA 69 2.71e+01 1mjc b.40.4.5 25320 1gnxA 479 2.72e+01 c.1.8.4 76241 1djxB 624 2.79e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1fwsA 267 2.80e+01 1d9eA c.1.10.4 60063 1y8qB 640 2.80e+01 1fo8A 343 2.82e+01 1foaA c.68.1.10 59927 1k66A 149 2.93e+01 c.23.1.1 90941 2ebn 289 2.93e+01 2ebn c.1.8.5 28990 1fo9A 348 2.94e+01 1foaA c.68.1.10 59928 1e2uA 553 2.94e+01 1e1dA e.26.1.1 43362 1gntA 553 2.96e+01 e.26.1.1 70290 1ifa 158 2.98e+01 1ifa a.26.1.3 16892 1lcyA 325 3.04e+01 b.36.1.4,b.47.1.1 73834,73835 1e1dA 553 3.15e+01 1e1dA e.26.1.1 43363 1f8xA 157 3.15e+01 1f8xA c.23.14.1 31397 2d4qA 257 3.23e+01 1ii2A 524 3.26e+01 c.91.1.1,c.109.1.1 66146,66147 1pf5A 131 3.27e+01 d.79.1.1 94604 1hgxA 183 3.28e+01 1tc1A c.61.1.1 34027 1vpbA 451 3.42e+01 1a0rP 245 3.46e+01 1b9yC c.47.1.6 33054 1yfnA 118 3.48e+01 2freA 200 3.63e+01 1e9iA 431 3.68e+01 c.1.11.1,d.54.1.1 64818,64819 1a2q 275 3.81e+01 1gci c.41.1.1 32512 1zgdA 312 3.85e+01 1gehA 444 3.95e+01 c.1.14.1,d.58.9.1 65181,65182 1aqn 275 3.97e+01 1gci c.41.1.1 32514 1hh2P 344 3.99e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1fp3A 402 4.07e+01 1fp3A a.102.1.3 18842 1foaA 348 4.08e+01 1foaA c.68.1.10 59929 1ak9 275 4.09e+01 1gci c.41.1.1 32517 1h2vZ 156 4.18e+01 d.58.7.1 76595 1ltqA 301 4.20e+01 c.108.1.9,c.37.1.1 78208,78209 1gu7A 364 4.28e+01 b.35.1.2,c.2.1.1 83321,83322 1hjsA 332 4.29e+01 c.1.8.3 83492 2bfdA 400 4.31e+01 1x7yA 400 4.37e+01 1iugA 352 4.40e+01 c.67.1.3 90699 1j7lA 264 4.47e+01 d.144.1.6 62697 1jyeA 349 4.47e+01 c.93.1.1 67455 1mk4A 157 4.56e+01 d.108.1.1 84979 1v1rA 400 4.59e+01 c.36.1.11 108272 1d0nA 729 4.60e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 1ou0A 207 4.60e+01 c.23.17.1 93536 2fymA 431 4.74e+01 1f6yA 262 4.78e+01 1f6yA c.1.21.2 29673 1ox8A 107 4.78e+01 b.136.1.1 93671 1grvB 182 4.79e+01 c.61.1.1 76322 1hs6A 611 4.96e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 2acvA 463 5.05e+01 1p27B 106 5.17e+01 d.58.7.1 93908 1gd9A 389 5.21e+01 c.67.1.1 60454 1sdjA 310 5.23e+01 d.21.1.2,d.21.1.2 98807,98808 1gdeA 389 5.28e+01 c.67.1.1 60456 1dusA 194 5.31e+01 1dusA c.66.1.4 34182 1keeG 1073 5.32e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68516,68517,68518,68519,68520,68521 1a80 277 5.34e+01 1frb c.1.7.1 28700 1b7gO 340 5.40e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1vkwA 218 5.50e+01 d.90.1.2 108695 1hw6A 278 5.53e+01 1frb c.1.7.1 61296 2cunA 410 5.83e+01 1olsA 400 5.85e+01 c.36.1.11 93331 1laxA 370 5.88e+01 c.94.1.1 84576 1c3oC 1073 5.92e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18563,31492,31683,31684,41528,41529 1hfoA 113 5.93e+01 d.80.1.3 61006 2chnA 716 5.97e+01 1z15A 344 5.97e+01 1yyaA 250 6.02e+01 1ou8A 111 6.06e+01 b.136.1.1 93543 2ccjA 205 6.12e+01 1cs0A 1073 6.15e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1jdbB 1073 6.16e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18574,31503,31705,31706,41550,41551 1keeE 1073 6.20e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68508,68509,68510,68511,68512,68513 2akaB 299 6.21e+01 1wstA 417 6.26e+01 1d5wC 126 6.26e+01 1dbwA c.23.1.1 31101 2liv 344 6.34e+01 2liv c.93.1.1 35708 1c3oE 1073 6.36e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18564,31493,31685,31686,41530,41531 1t3tA 1303 6.43e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1oo0B 110 6.58e+01 d.58.7.1 87183 2ashA 381 6.66e+01 1wolA 122 6.69e+01 2cvlA 124 6.72e+01 1ii7A 333 6.74e+01 1ii7A d.159.1.4 62415 1hp0A 339 6.81e+01 c.70.1.1 65900 1xfsA 178 6.88e+01 d.129.3.5 109589 1c3oG 1073 6.89e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18565,31494,31687,31688,41532,41533 2conA 79 6.95e+01 1p9bA 442 6.96e+01 c.37.1.10 94385 2b33A 140 6.97e+01 1cec 343 6.98e+01 1ceo c.1.8.3 28809 1awd 94 7.01e+01 1awd d.15.4.1 37673 1rliA 184 7.02e+01 c.23.5.6 97647 1itg 166 7.02e+01 1b9dA c.55.3.2 33661 1rkxA 357 7.03e+01 c.2.1.2 97631 2evaA 307 7.08e+01 1keeC 1073 7.10e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 68500,68501,68502,68503,68504,68505 2cq2A 114 7.24e+01 1nd4A 264 7.27e+01 d.144.1.6 91815 1kkoA 413 7.27e+01 c.1.11.2,d.54.1.1 68675,68676 1ihnA 113 7.32e+01 1ihnA c.103.1.1 62388 1ceo 343 7.38e+01 1ceo c.1.8.3 28808 2b9wA 424 7.38e+01 1in0A 163 7.44e+01 d.58.49.1,d.58.49.1 83694,83695 1j3bA 529 7.44e+01 c.91.1.1,c.109.1.1 77071,77072 1nqkA 381 7.46e+01 c.1.16.4 92050 1kicA 339 7.48e+01 c.70.1.1 72510 1v7cA 351 7.54e+01 c.79.1.1 100446 1ex2A 189 7.56e+01 1ex2A c.51.4.2 33225 1j7iA 264 7.58e+01 1j7iA d.144.1.6 62694 1cs0C 1073 7.64e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18559,31488,31675,31676,41520,41521 1qyaA 307 7.67e+01 d.21.1.2,d.21.1.2 104653,104654 1hozA 339 7.68e+01 c.70.1.1 65898 1avt 274 7.69e+01 1gci c.41.1.1 32488 1yh1A 359 7.71e+01 1qzmA 94 7.72e+01 c.37.1.20 96651 2a14A 263 7.75e+01 1dp4A 435 7.76e+01 1dp4A c.93.1.1 35710 1djxA 624 7.78e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17342,23159,29587 1qo2A 241 7.83e+01 1qo2A c.1.2.1 28533 3bifA 468 7.86e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1rlzA 369 7.91e+01 c.31.1.1 104989 1xwiA 322 7.97e+01 1vq0A 302 8.06e+01 1wm1A 317 8.06e+01 c.69.1.7 109405 1fbaA 361 8.22e+01 1fbaA c.1.10.1 29120 1wy5A 317 8.22e+01 1lox 662 8.24e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1s6yA 450 8.40e+01 c.2.1.5,d.162.1.2 105314,105315 2itg 163 8.42e+01 1b9dA c.55.3.2 33669 1nrzA 164 8.44e+01 c.38.1.1 86131 1uch 230 8.47e+01 1uch d.3.1.6 37129 1uqrA 154 8.48e+01 c.23.13.1 99779 1cjcA 460 8.48e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1yvvA 336 8.59e+01 1z7aA 308 8.67e+01 1d3yA 301 8.68e+01 1d3yA e.12.1.1 43252 1y8oA 419 8.70e+01 2d13A 227 8.96e+01