# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1dbuA 158 8.24e-28 1dbuA d.116.1.1 40930 1dbxA 158 9.83e-28 1dbuA d.116.1.1 40928 1vkiA 181 1.63e-17 1vjfA 180 3.93e-17 d.116.1.1 -10941 1izcA 339 7.55e-02 c.1.12.5 83838 1d7kA 421 7.88e-02 7odcA b.49.2.3 26486 c.1.6.1 28648 1d4oA 184 9.25e-02 1d4oA c.31.1.4 31748 1o4vA 183 1.32e-01 c.23.8.1 86628 7odcA 424 2.38e-01 7odcA b.49.2.3 26488 c.1.6.1 28650 1oniA 137 3.22e-01 d.79.1.1 87144 1kt9A 138 4.16e-01 d.113.1.1 72959 1qahA 136 5.17e-01 d.79.1.1 -10377 1nnlA 225 5.33e-01 c.108.1.4 85906 1dc1A 323 5.70e-01 1dc1A c.52.1.11 33321 3grx 82 7.36e-01 1aba c.47.1.1 32769 2fsp 124 8.82e-01 1dz3A c.23.1.1 31119 1n97A 389 9.10e-01 a.104.1.1 80335 1aba 87 9.24e-01 1aba c.47.1.1 32760 1dv2A 452 1.10e+00 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1j0fA 100 1.15e+00 unknown_sccs -7483 1qu9A 128 1.25e+00 1qu9A d.79.1.1 39755 1qu9C 128 1.25e+00 1qu9A d.79.1.1 39757 1pyoA 167 1.44e+00 c.17.1.1 -7932 1g01A 364 1.54e+00 7a3hA c.1.8.3 60161 1e44A 85 1.67e+00 3eipA d.26.2.1 59219 1gv4A 528 1.78e+00 c.3.1.5 70589 c.3.1.5 70590 d.87.1.1 70591 2tpsA 227 2.04e+00 2tpsA c.1.3.1 28591 1st9A 143 2.39e+00 c.47.1.10 -7503 1delA 241 2.48e+00 1dekA c.37.1.1 31844 1dekA 241 2.63e+00 1dekA c.37.1.1 31842 1qczA 169 2.66e+00 1qczA c.23.8.1 31276 1j9bA 141 2.72e+00 c.47.1.12 66459 1aw9 216 2.76e+00 1gnwA a.45.1.1 17736 c.47.1.5 33030 1q7hA 153 3.04e+00 b.122.1.1 -5124 unknown_sccs -9313 1vkfA 188 3.05e+00 1l1qA 186 3.12e+00 c.61.1.1 77653 1bgj 394 3.37e+00 1pbe c.3.1.2 30352 d.16.1.2 37883 1bh5A 183 3.40e+00 1qipA d.32.1.1 38476 1g0cA 364 3.64e+00 7a3hA c.1.8.3 60165 1nv8A 284 3.87e+00 c.66.1.30 86224 1lucB 324 4.00e+00 1lucA c.1.16.1 29548 1brlB 324 4.13e+00 1lucA c.1.16.1 29554 1axdA 209 4.18e+00 1gnwA a.45.1.1 17730 c.47.1.5 33024 1j5rA 371 4.19e+00 1o2dA 371 4.19e+00 e.22.1.2 86591 3sxlA 184 4.32e+00 1b7fA d.58.7.1 39173 d.58.7.1 39174 1k0dA 260 4.38e+00 a.45.1.1 67930 c.47.1.5 67931 1jykA 254 4.49e+00 c.68.1.13 67458 1t1vA 93 4.54e+00 1l7mA 211 4.59e+00 c.108.1.4 73664 1of5B 184 4.83e+00 d.17.4.2 86934 1egzA 291 4.96e+00 7a3hA c.1.8.3 28828 1regX 122 5.20e+00 1regX d.58.27.1 39406 2sxl 88 5.38e+00 1b7fA d.58.7.1 39179 1i5pA 633 5.48e+00 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1914 232 6.02e+00 1914 d.49.1.1 83028 d.49.1.1 83029 1ktgA 138 6.17e+00 d.113.1.1 72972 2prd 174 6.47e+00 2prd b.40.5.1 25435 1nd7A 374 6.53e+00 d.148.1.1 -11394 1kngA 156 6.68e+00 c.47.1.10 72777 1h75A 81 6.99e+00 1h75A c.47.1.1 60716 1hqoA 258 7.04e+00 1hqoA a.45.1.1 17749 c.47.1.5 33043 1qd9A 124 7.06e+00 1qu9A d.79.1.1 39758 1wdaA 670 7.16e+00 1k1xA 659 7.33e+00 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1f5sA 211 7.53e+00 1f5sA c.108.1.4 59656 1j97A 211 7.53e+00 1f5sA c.108.1.4 62753 1rhcA 330 7.64e+00 c.1.16.3 -5606 1bmqA 167 7.64e+00 1pauA c.17.1.1 30998 1e8oB 106 7.72e+00 1914 d.49.1.1 38775 1k1eA 180 7.76e+00 c.108.1.5 67995 1p4kA 295 7.98e+00 d.153.1.5 87772 1ibcA 194 8.12e+00 1pauA c.17.1.1 30997 9gafA 295 8.22e+00 1apyA d.153.1.5 42008 1vgyA 393 8.80e+00 c.56.5.4 -7882 d.58.19.1 -10106 1cj3A 392 9.21e+00 1pbe c.3.1.2 30347 d.16.1.2 37878 1crn 46 9.31e+00 1cbn g.13.1.1 44622 1nrjA 158 9.36e+00 d.110.4.4 86124 1gq2A 555 9.67e+00 c.2.1.7 70308 c.58.1.3 70309 1k0iA 394 9.75e+00 c.3.1.2 67942 d.16.1.2 67943 1p57B 255 9.85e+00 b.47.1.2 -4248 1ubi 76 1.01e+01 1ubi d.15.1.1 37584 1ubq 76 1.01e+01 1ubi d.15.1.1 37585 1d3zA 76 1.04e+01 1ubi d.15.1.1 37592 1ibsA 317 1.05e+01 c.61.1.2 66107 c.61.1.2 66108 2phh 394 1.06e+01 1pbe c.3.1.2 30353 d.16.1.2 37884 1j8fA 323 1.08e+01 1j8fA c.31.1.5 62738 1cbn 46 1.08e+01 1cbn g.13.1.1 44619 1cnr 46 1.08e+01 1cbn g.13.1.1 44621 1ejgA 46 1.08e+01 1cbn g.13.1.1 44618 1ahxA 396 1.09e+01 1ajsA c.67.1.1 34293 1qipA 183 1.09e+01 1qipA d.32.1.1 38470 1pbe 394 1.10e+01 1pbe c.3.1.2 30338 d.16.1.2 37869 1pv9A 348 1.12e+01 c.55.2.1 -7610 d.127.1.1 -11000 1f07A 321 1.16e+01 1ezwA c.1.16.3 59560 1b7gO 340 1.16e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 1ogwA 76 1.18e+01 d.15.1.1 87001 1i2aA 219 1.19e+01 e.24.1.1 -12012 1g33A 73 1.20e+01 a.39.1.4 65121 1djrD 103 1.22e+01 3chbD b.40.2.1 24865 1jd1A 129 1.22e+01 1qu9A d.79.1.1 62890 1ltsD 103 1.22e+01 3chbD b.40.2.1 24900 1qisA 396 1.22e+01 1ajsA c.67.1.1 34284 1gu7A 364 1.22e+01 b.35.1.2 83321 c.2.1.1 83322 1vi2A 300 1.26e+01 c.2.1.7 -5960 c.58.1.5 -6366 1npdA 288 1.29e+01 c.2.1.7 80681 c.58.1.5 80682 1ars 396 1.31e+01 1ajsA c.67.1.1 34287 1e4iA 447 1.33e+01 1e70M c.1.8.4 59225 4tmkA 213 1.34e+01 5tmpA c.37.1.1 31930 1ijgA 309 1.34e+01 1fouA e.27.1.1 62493 1onxA 390 1.35e+01 b.92.1.7 87176 c.1.9.13 87177 1q5yA 85 1.35e+01 unknown_sccs -10081 1kqwA 134 1.36e+01 b.60.1.2 72887 1efiD 103 1.36e+01 3chbD b.40.2.1 24870 1ccm 46 1.42e+01 1cbn g.13.1.1 44623 1np6A 174 1.45e+01 c.37.1.10 85954 1vicA 262 1.45e+01 c.68.1.13 -8252 5tmpA 213 1.45e+01 5tmpA c.37.1.1 31931 1onwA 390 1.47e+01 b.92.1.7 87172 c.1.9.13 87173 1gudA 288 1.48e+01 c.93.1.1 83326 1f89A 291 1.50e+01 d.160.1.1 64988 1o5oA 221 1.51e+01 c.61.1.1 -7954 1uroA 367 1.54e+01 1uroA c.1.22.1 29675 1qmhA 347 1.55e+01 1qmhA c.47.2.1 33082 d.68.2.1 39568 1uthA 315 1.60e+01 1v02A 565 1.61e+01 1vjqA 79 1.62e+01 unknown_sccs -13478 1e6yC 247 1.63e+01 1mroC d.58.31.1 39441 1peqA 714 1.65e+01 1k6zA 141 1.66e+01 d.198.1.1 68247 1id1A 153 1.67e+01 1id1A c.2.1.9 62286 1uhgA 385 1.68e+01 e.1.1.1 88491 1hu4A 288 1.68e+01 1hu4A 1gnwA 211 1.70e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1n5dA 288 1.70e+01 c.2.1.2 80030 2tct 207 1.76e+01 2tct a.4.1.9 16063 a.121.1.1 19240 2gbp 309 1.79e+01 1gca c.93.1.1 35657 1eemA 241 1.81e+01 1eemA a.45.1.1 17717 c.47.1.5 33011 1j8dA 180 1.81e+01 c.108.1.5 66433 1omwA 689 1.81e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1rpjA 288 1.82e+01 2dri c.93.1.1 35656 1yveI 524 1.84e+01 1qmgA a.100.1.2 18789 c.2.1.6 30186 1qmgA 524 1.85e+01 1qmgA a.100.1.2 18785 c.2.1.6 30182 1gggB 226 1.86e+01 1lst c.94.1.1 35818 1tz9A 367 1.86e+01 1dkuA 317 1.86e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1a8rA 221 1.87e+01 1a8rA d.96.1.1 40587 1rthA 560 1.87e+01 1rthA c.55.3.1 33576 e.8.1.2 43028 1lc5A 364 1.88e+01 c.67.1.1 73827 1ako 268 1.91e+01 1ako d.151.1.1 41779 1bjz 207 1.92e+01 2tct a.4.1.9 16065 a.121.1.1 19242 2sas 185 1.93e+01 2sas a.39.1.5 17258 3kvt 115 1.94e+01 1t1dA d.42.1.2 38642 1art 396 1.95e+01 1ajsA c.67.1.1 34285 1cjsA 219 1.97e+01 1cjsA e.24.1.1 43354 1bif 469 2.02e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1dkrA 317 2.02e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1qmvA 197 2.04e+01 1qq2A c.47.1.10 33066 1tr1A 447 2.05e+01 1e70M c.1.8.4 28957 1cozA 129 2.05e+01 1cozA c.26.1.2 31598 1d2mA 665 2.06e+01 1d2mA c.37.1.19 32417 c.37.1.19 32418 1lkcA 364 2.08e+01 c.67.1.1 73978 1m3uA 264 2.11e+01 c.1.12.8 84784 1spa 396 2.12e+01 1ajsA c.67.1.1 34291 3bifA 468 2.13e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1j3wA 163 2.14e+01 unknown_sccs -10870 1bc5A 269 2.17e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 1pg5A 299 2.18e+01 1qq7A 253 2.18e+01 1qq5A c.108.1.1 43329 1lssA 140 2.19e+01 c.2.1.9 74246 1qq5A 253 2.22e+01 1qq5A c.108.1.1 43327 3ldh 330 2.23e+01 3ldh i.12.1.1 46015 1jqeA 292 2.25e+01 c.66.1.19 71789 1nbwB 117 2.25e+01 c.51.3.2 80396 1o6dA 163 2.26e+01 c.116.1.3 -6689 1bncB 449 2.27e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1ovaA 386 2.31e+01 1ovaA e.1.1.1 42619 2bifA 469 2.32e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1r3sA 367 2.34e+01 c.1.22.1 -5648 2aop 497 2.36e+01 2aop d.58.36.1 39503 d.58.36.1 39504 d.134.1.1 41427 d.134.1.1 41428 1aop 497 2.36e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1nq6A 302 2.37e+01 c.1.8.3 -5332 1t3uA 104 2.37e+01 unknown_sccs -9325 1s9uA 207 2.37e+01 1g6hA 257 2.37e+01 1gajA c.37.1.12 60318 1qfoA 119 2.41e+01 1qfoA b.1.1.1 19708 1gtvA 214 2.41e+01 c.37.1.1 70537 1q1aA 289 2.41e+01 c.31.1.5 -6781 1bvsB 203 2.42e+01 1hjp a.5.1.1 16281 a.60.2.1 17956 b.40.4.2 25275 1onrA 316 2.42e+01 1onrA c.1.10.1 29169 1v32A 101 2.45e+01 a.42.1.1 -912 1ev0A 58 2.45e+01 1ev0A d.71.1.1 39594 1qq2A 199 2.46e+01 1qq2A c.47.1.10 33064 1jruA 89 2.46e+01 1jruA d.15.1.2 63257 1nddA 76 2.47e+01 1ubi d.15.1.1 37599 1okhA 46 2.47e+01 g.13.1.1 -12554 1nddD 76 2.48e+01 1ubi d.15.1.1 37602 1ih7A 903 2.51e+01 1clqA c.55.3.5 62375 e.8.1.1 62376 1pytA 94 2.51e+01 1pytA d.58.3.1 39064 1fc6A 388 2.53e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 5pal 109 2.56e+01 1a75A a.39.1.4 17215 1qysA 106 2.57e+01 unknown_sccs -13432 1kq6A 141 2.57e+01 d.189.1.1 -9926 1hcl 298 2.59e+01 1hcl d.144.1.7 41593 1gca 309 2.59e+01 1gca c.93.1.1 35659 1q44A 326 2.60e+01 c.37.1.5 -7037 1srrA 124 2.66e+01 1dz3A c.23.1.1 31110 1j08A 226 2.69e+01 c.47.1.2 83855 c.47.1.2 83856 1e32A 458 2.69e+01 1e32A b.52.2.3 59183 c.37.1.20 59184 d.31.1.1 59185 1q3kA 259 2.70e+01 unknown_sccs -6335 1mxa 383 2.73e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1auk 489 2.73e+01 1auk c.76.1.2 35030 1g55A 343 2.74e+01 1g55A c.66.1.26 34247 1fw1A 216 2.75e+01 a.45.1.1 60051 c.47.1.5 60052 1h6kZ 98 2.75e+01 d.58.7.1 60686 1sfe 180 2.76e+01 1sfe a.4.2.1 16073 c.55.7.1 33748 1bak 119 2.77e+01 1bak b.55.1.1 26973 1mxb 383 2.77e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1bebA 162 2.82e+01 1bebA b.60.1.1 27115 1s6yA 450 2.83e+01 1fxlA 167 2.84e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1m6iA 493 2.88e+01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1o7kA 131 2.94e+01 d.189.1.1 81144 1vjoA 393 2.96e+01 c.67.1.3 -8173 1vrtA 560 2.96e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 3tgl 269 2.99e+01 3tgl c.69.1.17 34733 1jqaA 370 3.00e+01 e.22.1.2 67085 1hyqA 263 3.00e+01 1hyqA c.37.1.10 61412 1jqlB 140 3.01e+01 c.37.1.20 63234 1o6zA 303 3.03e+01 c.2.1.5 81107 d.162.1.1 81108 1g6wA 261 3.04e+01 1hqoA a.45.1.1 17751 c.47.1.5 33045 1nrjB 218 3.11e+01 c.37.1.8 86125 1f6bA 198 3.12e+01 c.37.1.8 64986 1rg9A 383 3.13e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1h70A 255 3.14e+01 1h70A d.126.1.3 60711 1ofgA 381 3.15e+01 1ofgA c.2.1.3 30064 d.81.1.5 39979 1gr0A 367 3.15e+01 c.2.1.3 70379 d.81.1.3 70380 1pymA 295 3.16e+01 1pymA c.1.12.7 29308 1pauA 147 3.17e+01 1pauA c.17.1.1 30994 1qfoC 119 3.17e+01 1qfoA b.1.1.1 19710 1fzaB 328 3.17e+01 3fib d.171.1.1 42480 h.1.8.1 45621 1knwA 425 3.18e+01 b.49.2.3 -4274 c.1.6.1 -5229 1yveJ 524 3.23e+01 1qmgA a.100.1.2 18790 c.2.1.6 30187 8abp 306 3.25e+01 8abp c.93.1.1 35647 1g99A 408 3.26e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1h2vZ 156 3.28e+01 d.58.7.1 76595 1mzeA 351 3.29e+01 b.82.2.6 79694 1nf2A 268 3.29e+01 c.108.1.10 -6842 1s3sG 127 3.30e+01 d.15.1.2 -9152 1gnd 447 3.34e+01 1gnd c.3.1.3 30423 d.16.1.6 37987 1eq2A 310 3.36e+01 1eq2A c.2.1.2 29814 1cj5A 162 3.40e+01 1bebA b.60.1.1 27124 1upaA 573 3.42e+01 c.31.1.3 -6745 c.36.1.5 -6903 c.36.1.9 -6943 1j5vA 351 3.43e+01 c.72.1.1 71585 1nox 205 3.45e+01 1nox d.90.1.1 40242 1em8B 112 3.47e+01 unknown_sccs -6364 1itxA 419 3.54e+01 c.1.8.5 71425 d.26.3.1 71426 3eipA 84 3.57e+01 3eipA d.26.2.1 38434 1whsB 153 3.58e+01 1whtB 1qgwA 76 3.59e+01 1qgwA d.184.1.1 42616 1i42A 89 3.59e+01 1jruA d.15.1.2 61651 1obbA 480 3.60e+01 c.2.1.5 86760 d.162.1.2 86761 1nh8A 304 3.62e+01 c.94.1.1 80507 d.58.5.3 80508 1b93A 152 3.64e+01 1b93A c.24.1.2 31507 1iz7A 295 3.67e+01 c.69.1.8 76982 1dugA 234 3.68e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1gwcA 230 3.69e+01 a.45.1.1 70660 c.47.1.5 70661 1mx3A 347 3.70e+01 c.2.1.4 79638 c.23.12.1 79639 1t5jA 313 3.71e+01 unknown_sccs -1951 1i2oA 316 3.72e+01 1onrA c.1.10.1 61574 1nvmA 345 3.73e+01 a.5.7.1 86249 c.1.10.5 86250 1be1 137 3.75e+01 1be1 c.23.6.1 31237 1dxeA 256 3.88e+01 1dxeA c.1.12.5 29310 1v2yA 105 3.94e+01 d.15.1.1 -9148 1v7rA 186 3.94e+01 c.51.4.1 -7546 1eg5A 384 3.97e+01 1ecxA c.67.1.3 34429 1dkgD 383 3.98e+01 1ba1 c.55.1.1 33427 c.55.1.1 33428 1hfeL 421 3.98e+01 1fehA c.96.1.1 36018 d.58.1.5 39001 2hmiA 558 3.99e+01 1rthA c.55.3.1 33604 e.8.1.2 43106