# List of top-scoring protein chains for T0325.t2k-w0.5 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 1uzeA 589 3.74e-01 d.92.1.5 108174 1ry8A 323 3.90e-01 1s1pA 331 4.13e-01 c.1.7.1 98350 2c6nA 612 1.15e+00 1oafA 261 1.20e+00 a.93.1.1 86734 1vl4A 447 1.22e+00 d.283.1.1 108718 1en7A 157 1.49e+00 1en7A a.140.4.1,d.4.1.5 64733,64734 1mrqA 323 1.75e+00 c.1.7.1 91445 1ihiA 323 1.88e+00 c.1.7.1 66142 1rrvA 416 1.88e+00 c.87.1.5 105083 1j96A 323 1.88e+00 c.1.7.1 71616 1xjbA 325 1.89e+00 1e7lA 157 1.90e+00 1en7A a.140.4.1,d.4.1.5 64728,64729 1x7fA 385 1.96e+00 b.62.1.2,c.1.8.12 109498,109499 1xzpB 150 1.98e+00 1l9vA 317 1.98e+00 d.13.2.1,d.216.1.1 73760,73761 1xzqB 149 2.01e+00 1ku1A 230 2.20e+00 a.118.3.1 72996 1q9jA 422 2.77e+00 c.43.1.2,c.43.1.2 104590,104591 2gp0A 309 3.07e+00 1lurA 339 3.09e+00 b.30.5.4 84717 1lluA 342 3.13e+00 b.35.1.2,c.2.1.1 91064,91065 1tz9A 367 3.39e+00 c.1.15.6 107466 1zc0A 309 3.46e+00 1c0aA 585 3.66e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1il2A 590 3.69e+00 b.40.4.1,d.74.4.1,d.104.1.1 66193,66194,66195 1w0hA 204 3.85e+00 1q5mA 322 4.47e+00 c.1.7.1 104539 1q13A 323 4.49e+00 1s2oA 244 4.80e+00 2ewrA 170 5.16e+00 1c7nA 399 5.17e+00 1d2fA c.67.1.3 34413 2fclA 169 5.18e+00 2ah5A 210 5.27e+00 1apxA 249 6.22e+00 1ryc a.93.1.1 18669 1z7dA 433 6.91e+00 1vf1A 229 6.91e+00 2fauA 341 7.78e+00 2ffiA 288 8.24e+00 1tyyA 339 8.35e+00 1wzuA 300 8.41e+00 1zbdB 134 8.46e+00 1zbdB g.50.1.1 45359 1v1gA 222 8.59e+00 1vlmA 219 8.66e+00 c.66.1.41 108836 1sm9A 322 9.91e+00 1z9aA 321 9.98e+00 1ye6A 322 9.99e+00 2b0jA 358 9.99e+00 1y4oA 104 1.00e+01 1mi3A 322 1.01e+01 c.1.7.1 91274 2gzqA 200 1.03e+01 1fduA 327 1.15e+01 1fds c.2.1.2 29848 2acu 315 1.17e+01 1frb c.1.7.1 28676 1ffyA 917 1.21e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1c9wA 315 1.21e+01 1frb c.1.7.1 28699 1az1 315 1.26e+01 1frb c.1.7.1 28677 1fdw 327 1.27e+01 1fds c.2.1.2 29845 1iol 327 1.28e+01 1fds c.2.1.2 29842 1fds 327 1.29e+01 1fds c.2.1.2 29838 1xgdA 315 1.31e+01 1jtvA 327 1.31e+01 c.2.1.2 84230 2c7fA 513 1.32e+01 1abn 315 1.33e+01 1frb c.1.7.1 28683 1ads 315 1.33e+01 1frb c.1.7.1 28671 1el3A 316 1.34e+01 1frb c.1.7.1 28672 1us0A 316 1.34e+01 c.1.7.1 99850 1z3nA 319 1.36e+01 2agtA 319 1.37e+01 1r38A 322 1.39e+01 1j7xA 302 1.58e+01 c.14.1.2 66425 2fvlA 324 1.60e+01 1ee8A 266 1.62e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1dqwA 267 1.64e+01 1dqwA c.1.2.3 28551 1frb 315 1.70e+01 1frb c.1.7.1 28665 2fhnX 126 1.72e+01 1ulzA 451 1.73e+01 b.84.2.1,c.30.1.1,d.142.1.2 99575,99576,99577 1j36A 607 1.76e+01 d.92.1.5 84054 1xzpA 482 1.89e+01 1yh6A 179 2.17e+01 1dy2A 180 2.25e+01 1koe d.169.1.5 42451 1oizA 278 2.41e+01 a.5.3.1,c.13.1.1 93079,93080 1r5lA 262 2.41e+01 a.5.3.1,c.13.1.1 97099,97100 1a27 289 2.52e+01 1fds c.2.1.2 29839 1xi6A 262 2.56e+01 1vm7A 311 2.60e+01 c.72.1.1 108884 1b35A 260 2.60e+01 1b35A b.121.4.1 23333 1ubpB 122 2.61e+01 1ubpB b.85.3.1 28346 4ubpB 126 2.61e+01 1ubpB b.85.3.1 28345 1jr2A 286 2.81e+01 c.113.1.1 67111 2f4pA 147 2.97e+01 1x9jA 375 3.14e+01 1zzmA 259 3.17e+01 2b95A 106 3.17e+01 1ux8A 132 3.34e+01 1ebvA 551 3.36e+01 1cqeA a.93.1.2,g.3.11.1 18709,44252 1kf0A 416 3.47e+01 c.86.1.1 72393 1vjdA 416 3.52e+01 c.86.1.1 100806 1vppX 20 3.58e+01 1vljA 407 3.63e+01 e.22.1.2 108832 2glzA 153 3.65e+01 1fr4A 260 3.75e+01 2cba b.74.1.1 27842 1u67A 600 3.84e+01 a.93.1.2,g.3.11.1 107697,107698 1skoB 130 3.92e+01 d.110.7.1 105677 1ngr 85 4.06e+01 1ngr a.77.1.2 18422 1nfiE 213 4.07e+01 1iknD d.211.1.1 19172 1ht8A 551 4.07e+01 1cqeA a.93.1.2,g.3.11.1 61248,61249 1q4gA 553 4.08e+01 a.93.1.2,g.3.11.1 95789,95790 2bs3B 239 4.08e+01 1xm8A 254 4.10e+01 1prhA 554 4.11e+01 1cqeA a.93.1.2,g.3.11.1 18710,44253 1iknD 236 4.12e+01 1iknD d.211.1.1 19171 1glv 303 4.14e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 1mswD 883 4.19e+01 e.8.1.3 79427 1qo8A 566 4.20e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19696,30433,42316 1igzA 576 4.29e+01 a.93.1.2,g.3.11.1 66138,66139 1tu5A 746 4.32e+01 1indH 226 4.34e+01 1igtB b.1.1.1,b.1.1.2 19839,20943 1eqgA 580 4.37e+01 1cqeA a.93.1.2,g.3.11.1 59487,59488 1qwkA 317 4.43e+01 c.1.7.1 96482 1h3nA 878 4.44e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2ajfA 597 4.56e+01 1wbiA 129 4.56e+01 1r42A 615 4.57e+01 d.92.1.5 96968 1sr4C 166 4.57e+01 b.42.2.1 105950 1umkA 275 4.68e+01 2adbA 148 4.69e+01 1n11A 437 4.73e+01 d.211.1.1 79778 1zr9A 124 4.75e+01 1m65A 245 4.86e+01 c.6.3.1 84847 1j5yA 187 4.98e+01 a.4.5.1,d.94.2.1 71592,71593 2f2fC 186 5.01e+01 1o0wA 252 5.13e+01 a.149.1.1,d.50.1.1 80751,80752 1dlaA 314 5.20e+01 1frb c.1.7.1 28690 1g8oA 310 5.28e+01 1g8oA c.68.1.9 60375 2blkA 122 5.29e+01 1s0uA 408 5.49e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1ah4 315 5.50e+01 1frb c.1.7.1 28684 1pfkA 320 5.52e+01 3pfk c.89.1.1 35575 2pfkC 320 5.53e+01 3pfk c.89.1.1 35579 2g3mA 693 5.56e+01 1go7P 462 5.64e+01 b.80.7.1,d.92.1.6 76245,76246 1ub1A 133 5.67e+01 d.10.1.3 99140 1jykA 254 5.75e+01 c.68.1.13 67458 1ah0 316 5.82e+01 1frb c.1.7.1 28685 1r6uA 437 5.90e+01 c.26.1.1 97163 1xxlA 239 5.92e+01 1koe 172 5.94e+01 1koe d.169.1.5 42448 1u1zA 168 6.00e+01 d.38.1.6 107602 1gsa 316 6.08e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1dy1A 188 6.24e+01 1koe d.169.1.5 42450 1nfgA 457 6.25e+01 b.92.1.3,c.1.9.6 85632,85633 1zin 217 6.34e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1yiiA 320 6.41e+01 1ndh 272 6.47e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1w77A 228 6.53e+01 3gbp 307 6.58e+01 1gca c.93.1.1 35661 1gca 309 6.64e+01 1gca c.93.1.1 35659 1tr1A 447 6.65e+01 1e70M c.1.8.4 28957 1a6zA 275 6.70e+01 1agdA b.1.1.2,d.19.1.1 20781,38280 2d2mD 145 6.76e+01 2fhlA 122 6.76e+01 1qw9A 502 6.78e+01 b.71.1.2,c.1.8.3 96466,96467 1ghtA 105 6.82e+01 2rslA c.53.1.1 60526 1pz3A 502 6.89e+01 b.71.1.2,c.1.8.3 95396,95397 1vqsA 116 6.89e+01 1bgaA 447 6.94e+01 1e70M c.1.8.4 28961 1bggA 448 6.95e+01 1e70M c.1.8.4 28953 2b30A 301 7.02e+01 1cnh 259 7.02e+01 2cba b.74.1.1 27880 2fp4B 395 7.06e+01 1eudB 396 7.06e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1q4rA 112 7.12e+01 d.58.4.4 95823 1r0pA 312 7.29e+01 d.144.1.7 96734 1y55X 126 7.34e+01 1p8lA 304 7.43e+01 b.40.4.6,d.142.2.1 94363,94364 1flcA 432 7.49e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1ecsA 126 7.58e+01 1ecsA d.32.1.2 59407 1rajA 393 7.62e+01 e.8.1.4 104881 2gbp 309 7.77e+01 1gca c.93.1.1 35657 1ulhA 390 7.86e+01 c.26.1.1 99557 1r6tA 477 7.87e+01 a.16.1.3,c.26.1.1 97160,97161 1a6q 382 7.90e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 2alr 324 7.95e+01 1frb c.1.7.1 28679 2aeuA 374 7.96e+01 1k7jA 206 8.01e+01 d.115.1.1 72103 1pq2A 476 8.01e+01 a.104.1.1 94987 2bnlA 136 8.02e+01 1go8P 462 8.29e+01 b.80.7.1,d.92.1.6 76247,76248 1s6yA 450 8.36e+01 c.2.1.5,d.162.1.2 105314,105315 2c57A 180 8.51e+01 1sf8A 126 8.64e+01 d.271.1.1 105472 1kk9A 221 8.64e+01 d.115.1.1 77432 1imjA 210 8.65e+01 c.69.1.23 71246 1a5j 110 8.69e+01 1a5j a.4.1.3,a.4.1.3 16043,16044 1ig8A 486 8.72e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1eq2A 310 8.73e+01 1eq2A c.2.1.2 29814 2g15A 318 8.81e+01 1o5tA 378 8.83e+01 c.26.1.1 103891 1e4iA 447 8.93e+01 1e70M c.1.8.4 59225