# 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 2.69e-25 1yw4A 341 2.17e-24 1h8lA 380 1.19e-05 b.3.2.1,c.56.5.1 65737,65738 1qmuA 380 1.54e-05 1qmuA b.3.2.1,c.56.5.1 22534,33827 2bo9A 308 8.93e-04 1jqgA 433 4.04e-03 c.56.5.1,d.58.3.1 71791,71792 2c1cA 312 4.44e-03 1aye 401 1.10e-02 1aye c.56.5.1,d.58.3.1 33824,39065 1dtdA 303 1.57e-02 1aye c.56.5.1 33823 1kwmA 402 6.97e-02 c.56.5.1,d.58.3.1 73079,73080 1yme 309 1.37e-01 1aye c.56.5.1 33804 1z5rA 306 1.50e-01 1m4lA 307 1.71e-01 c.56.5.1 78604 2ctb 307 1.84e-01 1aye c.56.5.1 33803 6cpa 307 2.60e-01 1aye c.56.5.1 33816 2ctc 307 2.72e-01 1aye c.56.5.1 33802 1bavA 309 3.38e-01 1aye c.56.5.1 33806 1o0wA 252 6.47e-01 a.149.1.1,d.50.1.1 80751,80752 1ysc 421 1.96e+00 1ivyA c.69.1.5 34652 1obr 326 2.07e+00 1aye c.56.5.2 33828 1cpy 421 2.19e+00 1ivyA c.69.1.5 34651 1fp3A 402 2.57e+00 1fp3A a.102.1.3 18842 1hyvA 166 2.58e+00 1b9dA c.55.3.2 61424 1bl3A 160 2.72e+00 1b9dA c.55.3.2 33655 1b9dA 163 3.96e+00 1b9dA c.55.3.2 33649 1jvbA 347 4.21e+00 b.35.1.2,c.2.1.1 77181,77182 1mjc 69 4.50e+00 1mjc b.40.4.5 25319 1eqcA 394 4.62e+00 1cz1A c.1.8.3 28811 1ne2A 200 4.79e+00 c.66.1.32 85586 1cz1A 394 5.41e+00 1cz1A c.1.8.3 28839 1tlfA 301 5.71e+00 1tlfA c.93.1.1 35687 1jbkA 195 5.91e+00 c.37.1.20 71631 1f7wA 144 6.18e+00 1f46A d.129.4.1 59679 1qasA 622 6.19e+00 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17340,23157,29585 1yloA 348 6.22e+00 1f47B 144 6.52e+00 1f46A d.129.4.1 59645 1vp4A 425 6.63e+00 1ki9A 192 7.04e+00 c.37.1.1 84404 1a2zA 220 7.34e+00 1a2zA c.56.4.1 33794 1qatB 622 7.63e+00 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17355,23172,29600 1s1pA 331 7.64e+00 c.1.7.1 98350 1nt4A 391 7.91e+00 c.60.1.2 92102 1f1sA 814 8.21e+00 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931 1ads 315 8.26e+00 1frb c.1.7.1 28671 1qd1A 325 8.31e+00 1qd1A d.58.34.1,d.58.34.1 39493,39494 1wzcA 249 8.90e+00 1r62A 160 8.92e+00 d.122.1.3 104816 1f0nA 285 9.03e+00 1dqyA c.69.1.3 34636 2b81A 323 9.41e+00 1w6tA 444 9.69e+00 6ldh 330 9.96e+00 3ldh c.2.1.5,d.162.1.1 30161,42128 1iyxA 432 1.01e+01 c.1.11.1,d.54.1.1 83815,83816 2cvlA 124 1.04e+01 1cy9A 264 1.07e+01 1ecl e.10.1.1 43236 2acr 315 1.08e+01 1frb c.1.7.1 28674 1laxA 370 1.09e+01 c.94.1.1 84576 1az1 315 1.13e+01 1frb c.1.7.1 28677 1gdhA 320 1.14e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1d4xG 126 1.14e+01 1d0nA d.109.1.1 59109 1k66A 149 1.15e+01 c.23.1.1 90941 2aqjA 538 1.16e+01 2agtA 319 1.17e+01 1pwmA 316 1.17e+01 c.1.7.1 95231 1e9iA 431 1.20e+01 c.1.11.1,d.54.1.1 64818,64819 1vggA 161 1.23e+01 2fymA 431 1.29e+01 1c0dA 358 1.31e+01 1eceA c.1.8.3 28815 1djxB 624 1.32e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1nm1G 125 1.32e+01 d.109.1.1 80653 1yagG 125 1.35e+01 1d0nA d.109.1.1 40846 1f8yA 157 1.35e+01 1f8xA c.23.14.1 31395 1yvvA 336 1.47e+01 2lbp 346 1.48e+01 2liv c.93.1.1 35709 1usgA 346 1.49e+01 c.93.1.1 99864 7aatA 401 1.52e+01 1ajsA c.67.1.1 34250 1klnA 605 1.53e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1el3A 316 1.54e+01 1frb c.1.7.1 28672 2gl5A 410 1.54e+01 2ashA 381 1.56e+01 2axpA 173 1.57e+01 1eceA 358 1.64e+01 1eceA c.1.8.3 28813 1z1zA 131 1.66e+01 1spvA 184 1.67e+01 c.50.1.2 98957 1h2vZ 156 1.67e+01 d.58.7.1 76595 1m2rA 327 1.72e+01 d.144.1.7 84760 1lpuA 332 1.72e+01 d.144.1.7 74177 1xwyA 264 1.73e+01 1gu7A 364 1.73e+01 b.35.1.2,c.2.1.1 83321,83322 1us0A 316 1.74e+01 c.1.7.1 99850 1f46A 140 1.78e+01 1f46A d.129.4.1 59643 3mefA 69 1.80e+01 1mjc b.40.4.5 25320 1wyuB 474 1.83e+01 1uqrA 154 1.85e+01 c.23.13.1 99779 1a6o 332 1.89e+01 1a6o 1vq0A 302 1.90e+01 1lw6E 281 1.92e+01 c.41.1.1 74293 1jwqA 179 1.92e+01 c.56.5.6 90921 1f8xA 157 2.03e+01 1f8xA c.23.14.1 31397 1kyqA 274 2.04e+01 c.2.1.11,e.37.1.1 73281,73282 1pa2A 306 2.08e+01 1bgp a.93.1.1 18693 1d8yA 605 2.09e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1xx1A 285 2.09e+01 1xovA 326 2.10e+01 1akaA 401 2.10e+01 1ajsA c.67.1.1 34258 1xfjA 261 2.11e+01 d.194.1.2 109585 1to2E 281 2.11e+01 1ydgA 211 2.14e+01 1ezoA 370 2.16e+01 4mbp c.94.1.1 59539 1wohA 305 2.18e+01 c.42.1.1 109446 2kfnA 605 2.18e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1lldA 319 2.21e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1lp4A 332 2.23e+01 d.144.1.7 74170 1om1A 332 2.23e+01 d.144.1.7 93347 1gnxA 479 2.33e+01 c.1.8.4 76241 1h6kZ 98 2.33e+01 d.58.7.1 60686 1vixA 420 2.39e+01 c.56.5.4,d.58.19.1 100777,100778 1xfkA 336 2.42e+01 1k3sA 113 2.47e+01 d.198.1.1 68120 1yfnA 118 2.49e+01 1s5lH 66 2.54e+01 1lv3A 68 2.55e+01 g.39.1.9 78231 1pf5A 131 2.56e+01 d.79.1.1 94604 1w8sA 263 2.57e+01 1h1nA 305 2.64e+01 c.1.8.3 70855 1itg 166 2.70e+01 1b9dA c.55.3.2 33661 1g01A 364 2.72e+01 7a3hA c.1.8.3 60161 1rk8A 165 2.73e+01 d.58.7.1 97603 1yhtA 367 2.73e+01 1w61A 414 2.73e+01 1g0cA 364 2.75e+01 7a3hA c.1.8.3 60165 2g8lA 299 2.88e+01 2ebn 289 2.90e+01 2ebn c.1.8.5 28990 1b8pA 329 2.94e+01 1bmdA c.2.1.5,d.162.1.1 30147,42114 1jyeA 349 2.96e+01 c.93.1.1 67455 1mq4A 272 2.98e+01 d.144.1.7 91391 2cunA 410 3.01e+01 2bklA 695 3.02e+01 2freA 200 3.05e+01 1cec 343 3.08e+01 1ceo c.1.8.3 28809 1ox8A 107 3.08e+01 b.136.1.1 93671 1yt8A 539 3.14e+01 1ywnA 316 3.17e+01 1sup 275 3.18e+01 1gci c.41.1.1 32510 1rpxA 230 3.21e+01 1rpxA c.1.2.2 28536 1iba 101 3.22e+01 1iba d.95.1.1 40567 1a80 277 3.24e+01 1frb c.1.7.1 28700 2d4qA 257 3.28e+01 1hd7A 318 3.30e+01 1bix d.151.1.1 41780 1avt 274 3.33e+01 1gci c.41.1.1 32488 1awd 94 3.34e+01 1awd d.15.4.1 37673 1hw6A 278 3.37e+01 1frb c.1.7.1 61296 1sdjA 310 3.41e+01 d.21.1.2,d.21.1.2 98807,98808 1zm7A 230 3.43e+01 1vkwA 218 3.45e+01 d.90.1.2 108695 1y8qB 640 3.46e+01 1qh4A 380 3.46e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1bix 287 3.47e+01 1bix d.151.1.1 41781 1ah4 315 3.49e+01 1frb c.1.7.1 28684 1ceo 343 3.50e+01 1ceo c.1.8.3 28808 1rpyA 114 3.57e+01 d.93.1.1 97718 1yj7A 171 3.58e+01 1blxA 326 3.64e+01 1hcl d.144.1.7 41596 1rq2A 382 3.67e+01 c.32.1.1,d.79.2.1 105048,105049 1sflA 238 3.69e+01 1ou8A 111 3.71e+01 b.136.1.1 93543 1fo9A 348 3.72e+01 1foaA c.68.1.10 59928 1kfd 605 3.74e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1fo8A 343 3.74e+01 1foaA c.68.1.10 59927 1r3dA 264 3.78e+01 1sfjA 238 3.79e+01 1djxA 624 3.85e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17342,23159,29587 1vpbA 451 3.88e+01 1o26A 232 3.91e+01 d.207.1.1 86566 1ldm 329 3.92e+01 3ldh c.2.1.5,d.162.1.1 30160,42127 1t0bA 252 3.92e+01 c.23.16.6 106199 2bfxA 284 3.97e+01 2axtH 66 3.98e+01 2d2eA 250 4.02e+01 1amp 291 4.12e+01 1amp c.56.5.4 33837 2as0A 396 4.14e+01 1a0rP 245 4.29e+01 1b9yC c.47.1.6 33054 1ald 363 4.31e+01 1fbaA c.1.10.1 29100 2acvA 463 4.34e+01 1ab5A 125 4.43e+01 3chy c.23.1.1 31056 1vhoA 346 4.50e+01 b.49.3.1,c.56.5.4 100694,100695 2cmd 312 4.52e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1yaxA 153 4.57e+01 2itg 163 4.60e+01 1b9dA c.55.3.2 33669 1j90A 230 4.64e+01 c.37.1.1 66448 1lcyA 325 4.67e+01 b.36.1.4,b.47.1.1 73834,73835 1f6yA 262 4.79e+01 1f6yA c.1.21.2 29673 1lokA 291 4.81e+01 c.56.5.4 78122 1a7j 290 4.83e+01 1a7j c.37.1.6 31952 9ldtA 332 4.92e+01 3ldh c.2.1.5,d.162.1.1 30154,42121 1c9bB 180 4.94e+01 1ytbA d.129.1.1,d.129.1.1 41216,41217 1xfsA 178 4.96e+01 d.129.3.5 109589 1yu6A 275 4.97e+01 1oe0A 230 5.05e+01 c.37.1.1 92788 1cjcA 460 5.05e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 12asA 330 5.06e+01 12asA d.104.1.1 40783 1foaA 348 5.10e+01 1foaA c.68.1.10 59929 1c9kB 180 5.11e+01 1c9kB c.37.1.11 32364 1opr 213 5.15e+01 1opr c.61.1.1 34091 1es9A 232 5.15e+01 1wab c.23.10.3 31340 1qyaA 307 5.16e+01 d.21.1.2,d.21.1.2 104653,104654 1w5fA 353 5.17e+01 1m2eA 135 5.17e+01 c.23.1.5 78478 1vih 71 5.19e+01 1vih d.51.1.1 38807 1zgdA 312 5.32e+01 1q5yA 85 5.34e+01 d.58.18.4 95950 1ihnA 113 5.38e+01 1ihnA c.103.1.1 62388 1wm1A 317 5.47e+01 c.69.1.7 109405 1gehA 444 5.51e+01 c.1.14.1,d.58.9.1 65181,65182 1vig 71 5.55e+01 1vih d.51.1.1 38806 2cybA 323 5.56e+01 1f1uA 323 5.58e+01 d.32.1.3,d.32.1.3 83200,83201 1ecl 597 5.59e+01 1ecl e.10.1.1 43238 1g8lA 411 5.66e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1hs6A 611 5.73e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1wab 232 5.77e+01 1wab c.23.10.3 31341 1a2q 275 5.80e+01 1gci c.41.1.1 32512 1cseE 274 5.81e+01 1gci c.41.1.1 32481 1s6yA 450 5.85e+01 c.2.1.5,d.162.1.2 105314,105315 1bg0 356 5.89e+01 1qh4A a.83.1.1,d.128.1.2 18476,41211 1xwiA 322 5.96e+01 3bifA 468 5.98e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1x7yA 400 5.99e+01 1r0rE 274 6.06e+01 c.41.1.1 96735 1kczA 413 6.17e+01 c.1.11.2,d.54.1.1 68451,68452 1aqn 275 6.19e+01 1gci c.41.1.1 32514 1ou0A 207 6.21e+01 c.23.17.1 93536 1iugA 352 6.22e+01 c.67.1.3 90699 1mk4A 157 6.24e+01 d.108.1.1 84979 2ccjA 205 6.27e+01 1ak9 275 6.29e+01 1gci c.41.1.1 32517 1m15A 357 6.29e+01 a.83.1.1,d.128.1.2 78368,78369 1h4pA 408 6.32e+01 c.1.8.3 90617 2ez6A 221 6.39e+01 1z7aA 308 6.46e+01 3pgk 416 6.54e+01 16pk c.86.1.1 35451 2bfdA 400 6.66e+01 1uirA 314 6.66e+01 c.66.1.17 99429 1v1rA 400 6.69e+01 c.36.1.11 108272 1pv1A 299 6.72e+01 1hh2P 344 6.73e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1ii2A 524 6.78e+01 c.91.1.1,c.109.1.1 66146,66147 2a14A 263 6.80e+01 1efaA 333 6.86e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1o5zA 442 6.92e+01 c.59.1.2,c.72.2.2 92530,92531 1yn9A 169 6.98e+01 1t4hA 290 7.05e+01 d.144.1.7 106420 1p27B 106 7.05e+01 d.58.7.1 93908 1wstA 417 7.13e+01 1lap 488 7.26e+01 1lam c.50.1.1,c.56.5.3 33171,33834 1t6cA 315 7.29e+01 c.55.1.8,c.55.1.8 106558,106559 1s48A 609 7.45e+01 e.8.1.4 98475 1lox 662 7.52e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1bllE 488 7.60e+01 1lam c.50.1.1,c.56.5.3 33170,33833 1fbaA 361 7.67e+01 1fbaA c.1.10.1 29120 1rtqA 299 7.73e+01 c.56.5.4 97819 1wolA 122 7.73e+01 1lam 484 7.75e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1u2fA 90 7.78e+01 1u2fA d.58.7.1 39168 1htyA 1015 7.79e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 1rkxA 357 7.79e+01 c.2.1.2 97631 1bqg 451 7.82e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 1hxkA 1015 7.83e+01 a.8.3.1,b.30.5.6,c.6.2.1 83070,83071,83072 1hjsA 332 7.86e+01 c.1.8.3 83492 1qwnA 1045 7.90e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1cye 129 7.91e+01 3chy c.23.1.1 31077 1tf9A 284 7.92e+01 1ah0 316 7.93e+01 1frb c.1.7.1 28685 1cdwA 179 7.93e+01 1ytbA d.129.1.1,d.129.1.1 41212,41213 2anpA 291 7.95e+01 1kamA 194 7.96e+01 c.26.1.3 72254 1oo0B 110 7.99e+01 d.58.7.1 87183 1t3tA 1303 7.99e+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 1keeG 1073 8.00e+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 1hfoA 113 8.00e+01 d.80.1.3 61006 1uvzA 119 8.03e+01 1nxiA 132 8.07e+01 d.58.47.1 86381 1pvtA 238 8.14e+01 c.74.1.1 95189 1guzA 310 8.14e+01 c.2.1.5,d.162.1.1 65586,65587 1qq9A 284 8.16e+01 1xjo c.56.5.4 33841 2evaA 307 8.16e+01 2conA 79 8.18e+01 1iciA 256 8.24e+01 1iciA c.31.1.5 62266 1se7A 83 8.24e+01 1xjo 284 8.33e+01 1xjo c.56.5.4 33843 1tkjA 284 8.35e+01 1jbeA 128 8.36e+01 3chy c.23.1.1 62845 4kbpA 432 8.37e+01 4kbpA b.1.12.1,d.159.1.1 22345,42064 1dg9A 157 8.37e+01 1dg9A c.44.1.1 32637 1olsA 400 8.48e+01 c.36.1.11 93331 1ymiA 334 8.49e+01 1kbpA 432 8.49e+01 4kbpA b.1.12.1,d.159.1.1 22349,42068 1ihuA 589 8.50e+01 c.37.1.10,c.37.1.10 62394,62395 1l2tA 235 8.53e+01 c.37.1.12 73514 1txpA 28 8.64e+01 1j3bA 529 8.66e+01 c.91.1.1,c.109.1.1 77071,77072 1c3oC 1073 8.72e+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 1d3yA 301 8.72e+01 1d3yA e.12.1.1 43252 1ldnA 316 8.76e+01 1hyhA c.2.1.5,d.162.1.1 30166,42133 1j7lA 264 8.82e+01 d.144.1.6 62697 1kt9A 138 8.91e+01 d.113.1.1 72959 4xiaA 393 8.97e+01 4xis c.1.15.3 29439 2govA 195 8.99e+01