# List of top-scoring protein chains for t04-100-30-alpha-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 1a48 306 3.56e-02 1a48 1ob8A 135 4.73e-02 c.52.1.18 111627 2cnqA 306 4.83e-02 d.143.1.1 130646 1obdA 306 5.50e-02 d.143.1.1 86767 1v7cA 351 5.93e-02 c.79.1.1 100446 2gu3A 136 1.42e-01 1s5jA 847 1.95e-01 c.55.3.5,e.8.1.1 112040,112041 1v5xA 203 2.25e-01 c.1.2.4 100377 1t6sA 162 2.32e-01 a.4.5.60,a.4.5.60 112271,112272 1go4A 205 3.17e-01 d.135.1.1 70292 1p5dX 463 3.67e-01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1jnyA 435 4.01e-01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1tr0A 108 4.76e-01 d.58.4.4 107261 1w53A 84 5.25e-01 a.186.1.2 109175 1i1iP 681 5.26e-01 1i1iP d.92.1.5 40297 2a2lA 145 5.66e-01 d.110.9.1 126035 1jovA 270 6.21e-01 b.30.5.7 84192 1sh8A 154 6.72e-01 d.38.1.5 105549 1u04A 771 7.16e-01 b.34.14.1,c.55.3.10 107539,107540 1bywA 110 7.17e-01 1bywA d.110.3.6 40912 1k2yX 463 8.33e-01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 3proC 166 8.60e-01 3proC d.52.1.1,d.52.1.1 38812,38813 1cs0A 1073 8.79e-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 2nr1 27 9.35e-01 2g0wA 296 9.65e-01 c.1.15.4 134503 1ud0A 113 9.67e-01 a.8.4.1 99198 1wr2A 238 9.92e-01 1plq 258 1.04e+00 1plq 1nqkA 381 1.07e+00 c.1.16.4 92050 1a9xA 1058 1.12e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1ylxA 103 1.19e+00 d.82.5.1 123677 1l0qA 391 1.27e+00 b.1.3.1,b.69.2.3 77644,77645 1zbfA 142 1.35e+00 c.55.3.1 124850 1hbkA 94 1.36e+00 1aca a.11.1.1 60887 1ykdA 398 1.51e+00 1dhkB 223 1.52e+00 1led b.29.1.1 24157 1aqcA 172 1.59e+00 1x11A b.55.1.2 26983 1o7fA 469 1.62e+00 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 2gnqA 336 1.68e+00 1az9 457 1.68e+00 1az9 1s6cA 183 1.71e+00 a.39.1.5 98594 1mixA 206 1.78e+00 a.11.2.1,b.55.1.5 79166,79167 1u84A 90 1.84e+00 a.230.1.1 113114 2ajrA 331 1.84e+00 c.72.1.1 126892 1vkcA 158 1.93e+00 d.108.1.1 113663 1gzcA 239 1.95e+00 b.29.1.1 70803 1yqtA 538 1.98e+00 1914 232 2.04e+00 1914 1dkzA 219 2.20e+00 1dkzA a.8.4.1,b.130.1.1 90345,90346 1ovnA 248 2.23e+00 a.71.1.1,c.47.1.7 93602,93603 1ohtA 215 2.24e+00 d.118.1.1 87036 2bwqA 129 2.35e+00 b.7.1.2 129380 5csmA 256 2.40e+00 5csmA a.130.1.2 19494 1jc9A 269 2.41e+00 d.171.1.1 66490 1ignA 246 2.42e+00 1ignA a.4.1.6,a.4.1.6 16048,16049 1o08A 221 2.51e+00 c.108.1.6 86525 1q4rA 112 2.56e+00 d.58.4.4 95823 1o8xA 146 2.56e+00 c.47.1.10 86681 1obbA 480 2.70e+00 c.2.1.5,d.162.1.2 86760,86761 1rwiA 270 2.74e+00 b.68.9.1 97987 1r2zA 274 2.77e+00 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1sviA 195 2.91e+00 c.37.1.8 106048 2cyjA 118 2.95e+00 c.103.1.1 131026 1s1eA 224 2.96e+00 a.39.1.5 112007 1l1zA 274 2.98e+00 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1vpkA 378 3.07e+00 d.131.1.1,d.131.1.1,d.131.1.1 113963,113964,113965 1zatA 250 3.10e+00 b.160.1.1,d.335.1.1 124845,124846 1qk8A 146 3.12e+00 1ewxA c.47.1.10 33061 2erfA 209 3.15e+00 b.29.1.4 132287 1o58A 303 3.19e+00 c.79.1.1 92491 1olsA 400 3.35e+00 c.36.1.11 93331 2igd 61 3.43e+00 2igd 1iazA 179 3.44e+00 1iazA b.97.1.1 62131 1j6qA 136 3.77e+00 b.40.9.1 77091 1fit 147 3.85e+00 1fit 1rzmA 338 4.01e+00 c.1.10.4 105137 1ykuA 136 4.11e+00 1dxsA 80 4.29e+00 1cokA a.60.1.2 17944 1qcsA 211 4.50e+00 1qcsA b.52.2.3,d.31.1.1 26927,38461 1ash 150 4.50e+00 1ash 1vk8A 106 4.52e+00 d.58.48.1 108636 1oxsC 353 4.66e+00 b.40.6.3,c.37.1.12 87519,87520 1usyA 275 4.68e+00 d.104.1.1 113422 1vr6A 350 4.68e+00 c.1.10.4 120439 1ex1A 605 4.68e+00 1ex1A c.1.8.7,c.23.11.1 29013,31347 1xqoA 256 4.72e+00 a.96.1.6 115853 1x7yA 400 4.72e+00 c.36.1.11 114944 2fhi 147 4.76e+00 1fit 1v1rA 400 4.80e+00 c.36.1.11 108272 1zq1A 438 4.87e+00 b.38.3.1,c.88.1.1 125489,125490 1oxxK 353 5.08e+00 b.40.6.3,c.37.1.12 93715,93716 1b0b 142 5.20e+00 2fal 1c44A 123 5.32e+00 1qndA d.106.1.1 40795 2bfdA 400 5.36e+00 1cdzA 96 5.41e+00 1cdzA c.15.1.1 30925 1bebA 162 5.41e+00 1bebA b.60.1.1 27115 1w96A 554 5.50e+00 b.84.2.1,c.30.1.1,d.142.1.2 114397,114398,114399 1kufA 203 5.73e+00 d.92.1.9 73007 1utcA 363 5.75e+00 a.118.1.4,b.69.6.1 99914,99915 1j8uA 325 5.82e+00 d.178.1.1 71611 1z7wA 322 5.92e+00 c.79.1.1 124674 1kugA 203 5.98e+00 d.92.1.9 73008 1x38A 602 6.03e+00 c.1.8.7,c.23.11.1 121655,121656 1erjA 393 6.22e+00 1erjA b.69.4.1 27660 2a3qA 170 6.23e+00 a.204.1.2 126092 2b06A 155 6.39e+00 d.113.1.1 127624 1zchA 255 6.43e+00 d.90.1.1 124908 1avbA 226 6.62e+00 1led b.29.1.1 24158 1yuwA 554 6.67e+00 b.130.1.1,c.55.1.1,c.55.1.1 124070,124071,124072 1ax0 239 6.96e+00 1led 1dosA 358 7.51e+00 1dosA c.1.10.2 29175 1p9qC 256 7.51e+00 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1w5fA 353 7.55e+00 c.32.1.1,d.79.2.1 114247,114248 1nlfA 279 7.56e+00 c.37.1.11 85850 1j3bA 529 7.60e+00 c.91.1.1,c.109.1.1 77071,77072 1rypK 198 7.64e+00 d.153.1.4 41879 1atlA 202 7.77e+00 1atlA d.92.1.9 40322 1ykhB 132 7.79e+00 a.252.1.1 123519 1kveB 77 7.80e+00 1kveB 2bbkH 355 7.81e+00 2bbkH b.69.2.1 27634 1pguA 615 7.83e+00 b.69.4.1,b.69.4.1 88069,88070 1wznA 252 7.92e+00 c.66.1.43 121525 2cdnA 201 8.08e+00 c.37.1.1 130289 1o70A 324 8.16e+00 b.118.1.1,b.118.1.1 81115,81116 2fmpA 335 8.20e+00 a.60.6.1,a.60.12.1,d.218.1.2 133786,133787,133788 1zpwX 90 8.22e+00 d.58.58.1 125478 1ig5A 75 8.26e+00 4icb a.39.1.1 62363 1t95A 240 8.30e+00 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1mkeA 152 8.30e+00 b.55.1.4 79231 1ov9A 50 8.53e+00 a.155.1.1 93591 1uv7A 110 8.71e+00 d.67.4.1 100040 1b06A 210 8.77e+00 1avmA a.2.11.1,d.44.1.1 15740,38737 1g8yA 279 8.79e+00 1g8yA c.37.1.11 32302 1rypA 243 8.86e+00 1pmaA d.153.1.4 41932 1oz9A 150 8.86e+00 d.92.1.15 93808 1tv9A 335 9.11e+00 a.60.6.1,a.60.12.1,d.218.1.2 112675,112676,112677 1n91A 108 9.22e+00 d.206.1.1 80326 1vmbA 140 9.29e+00 d.58.14.1 113672 1jtvA 327 9.39e+00 c.2.1.2 84230 1zpsA 138 9.40e+00 b.168.1.1 125473 2ax3A 502 9.50e+00 c.72.1.4,c.104.1.1 127477,127478 1lfb 99 9.50e+00 1lfb 4pah 308 9.72e+00 4pah 1gxrA 337 9.89e+00 b.69.4.1 70722 1crzA 403 9.90e+00 1crzA b.68.4.1,c.51.2.1 27629,33211 1kblA 873 9.91e+00 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1muwA 386 1.01e+01 c.1.15.3 79495 1wvvA 265 1.01e+01 1twfI 122 1.02e+01 g.41.3.1,g.41.3.1 112733,112734 1x3mA 415 1.03e+01 c.55.1.2,c.55.1.2 121664,121665 1hmt 132 1.03e+01 1hmt 1ym5A 300 1.04e+01 1bpoA 494 1.04e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 2gw6A 123 1.04e+01 1z7yA 322 1.05e+01 c.79.1.1 124679 1wq3A 322 1.05e+01 1e2wA 251 1.06e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1z5bA 469 1.06e+01 a.156.1.3,d.14.1.3,d.122.1.2 124464,124465,124466 1zejA 293 1.07e+01 1g0uG 252 1.07e+01 d.153.1.4 41952 1y14A 187 1.07e+01 a.60.8.2 116322 1sflA 238 1.08e+01 c.1.10.1 112077 1h5wA 309 1.08e+01 e.27.1.1 65635 1zxzA 197 1.09e+01 1fds 327 1.11e+01 1fds 1l3sA 580 1.13e+01 c.55.3.5,e.8.1.1 84521,84522 1s1hM 132 1.15e+01 i.1.1.1 105165 2c2aA 258 1.16e+01 a.30.2.1,d.122.1.3 129662,129663 1g291 372 1.17e+01 1g291 2cfuA 658 1.17e+01 2aq5A 402 1.17e+01 1u6zA 513 1.18e+01 a.211.1.5,c.55.1.8,c.55.1.8 119608,119609,119610 1xfkA 336 1.18e+01 c.42.1.1 115264 1inlA 296 1.21e+01 c.66.1.17 66220 2ex3B 264 1.21e+01 a.263.1.1 132500 1u53A 196 1.22e+01 2bklA 695 1.24e+01 1mc0A 368 1.24e+01 d.110.2.1,d.110.2.1 78937,78938 1fcjA 322 1.26e+01 1oasA c.79.1.1 35289 1i50I 122 1.27e+01 g.41.3.1,g.41.3.1 61762,61763 1bpyA 335 1.27e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1obwA 175 1.27e+01 2prd b.40.5.1 25416 1i40A 175 1.29e+01 b.40.5.1 66024 1vin 268 1.32e+01 1vin 1qnxA 209 1.32e+01 1qnxA d.111.1.1 40914 1mswD 883 1.32e+01 e.8.1.3 79427 1qh5A 260 1.32e+01 1qh5A d.157.1.2 42057 2bwvA 440 1.34e+01 c.55.2.1,d.127.1.1 129387,129388 2bf9A 36 1.34e+01 j.6.1.1 116717 1qh3A 260 1.35e+01 1qh5A d.157.1.2 42059 1wy0A 342 1.35e+01 1iq5B 27 1.36e+01 1ifc 132 1.37e+01 1sxrA 183 1.37e+01 d.118.1.1 106101 1kwaA 88 1.38e+01 1kwaA b.36.1.1 24772 1ub9A 100 1.38e+01 a.4.5.28 99159 1wl9A 440 1.41e+01 c.55.2.1,d.127.1.1 120998,120999 1tvoA 368 1.42e+01 1mdc 133 1.43e+01 1hmt 1lrwA 600 1.43e+01 b.70.1.1 91111 2gi9A 56 1.45e+01 1mmsA 140 1.48e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 1j5vA 351 1.50e+01 1i2sA 282 1.50e+01 e.3.1.1 71104 830cA 168 1.51e+01 1ck7A d.92.1.11 40400 2fflA 756 1.53e+01 1ly1A 181 1.53e+01 c.37.1.1 74334 1ujpA 271 1.54e+01 c.1.2.4 99462 1txuA 273 1.54e+01 a.222.1.1 107439 1lgpA 116 1.55e+01 b.26.1.2 73890 1qopB 396 1.57e+01 2tysB c.79.1.1 35270 1sfjA 238 1.60e+01 c.1.10.1 112075 1mu5A 471 1.60e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1xt9A 212 1.61e+01 d.3.1.7 116013 1gwyA 175 1.62e+01 b.97.1.1 83356 1in0A 163 1.67e+01 d.58.49.1,d.58.49.1 83694,83695 1i60A 278 1.67e+01 c.1.15.4 71118 1d4oA 184 1.67e+01 1d4oA c.31.1.4 31748 1hwxA 501 1.68e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1jvbA 347 1.69e+01 b.35.1.2,c.2.1.1 77181,77182 1jcfA 344 1.70e+01 c.55.1.1,c.55.1.1 62878,62879 1u5uA 374 1.70e+01 e.5.1.2 113052 1a8rA 221 1.71e+01 1a8rA d.96.1.1 40587 1ppt 36 1.72e+01 1ppt 1uheA 97 1.73e+01 1z2nX 324 1.78e+01 1e8gA 560 1.79e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1y93A 159 1.80e+01 d.92.1.11 122772 1t07A 94 1.80e+01 d.279.1.1 106196 1vliA 385 1.80e+01 b.85.1.1,c.1.10.6 108830,108831 1wlsA 328 1.80e+01 2bgkA 278 1.80e+01 c.2.1.2 128480 1z47A 355 1.82e+01 1weyA 104 1.82e+01 d.58.7.1 114569 2gqrA 237 1.82e+01 1o5zA 442 1.82e+01 c.59.1.2,c.72.2.2 92530,92531 1j0dA 341 1.82e+01 c.79.1.1 83902 1aisA 182 1.83e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1zhhB 242 1.83e+01 1xmxA 385 1.83e+01 c.52.1.26 115568 2pvaA 345 1.85e+01 3pvaA d.153.1.3 41850 1n4xH 120 1.86e+01 b.1.1.1 85324 1p4kA 295 1.87e+01 d.153.1.5 87772 1xwl 580 1.88e+01 1xwl 1a1x 108 1.88e+01 1a1x 1jk3A 158 1.89e+01 d.92.1.11 66790 1vlaA 150 1.89e+01 d.227.1.2 108735 1iuhA 198 1.89e+01 d.61.1.2 83711 1k3xA 262 1.90e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 2afbA 351 1.90e+01 c.72.1.1 126674 1c8cA 64 1.92e+01 1azpA b.34.13.1 59084 1f60A 458 1.94e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1nrlA 316 1.94e+01 a.123.1.1 92091 1xr4A 509 1.95e+01 c.124.1.2,c.124.1.2 115860,115861 1ujnA 348 1.96e+01 e.22.1.1 99460 1y8cA 246 1.97e+01 c.66.1.43 116563 1iznB 277 1.97e+01 e.43.1.2 83848 1t5yA 190 1.99e+01 b.122.1.1,d.17.6.3 106495,106496 1ihuA 589 1.99e+01 c.37.1.10,c.37.1.10 62394,62395 2h4uA 145 2.00e+01 d.38.1.5 136082 1jlvA 209 2.02e+01 a.45.1.1,c.47.1.5 71729,71730 2agyA 361 2.03e+01 1bazA 53 2.06e+01 1bazA a.43.1.1 17421 1ltqA 301 2.07e+01 c.108.1.9,c.37.1.1 78208,78209 1pot 325 2.07e+01 1pot 1v74A 107 2.08e+01 d.243.1.1 100442 1u00A 227 2.08e+01 a.8.4.1,b.130.1.1 112900,112901 1s5aA 150 2.08e+01 d.17.4.10 98525 1vjzA 341 2.11e+01 c.1.8.3 100838 1bg2 325 2.11e+01 1bg2 2f9zC 159 2.11e+01 1g61A 228 2.13e+01 1g61A d.126.1.1 41126 1tuaA 191 2.15e+01 d.51.1.1,d.51.1.1 107321,107322 1x0oA 119 2.16e+01 1dik 874 2.16e+01 1dik 2be4A 272 2.17e+01 1w1kA 560 2.20e+01 d.58.32.1,d.145.1.1 109059,109060 1ln1A 214 2.21e+01 d.129.3.2 74038 1a99A 344 2.21e+01 1pot c.94.1.1 35812 2bvfA 459 2.22e+01 1vkyA 347 2.27e+01 e.53.1.1 108696 1ukkA 142 2.28e+01 d.227.1.1 99491 1yaiA 151 2.28e+01 1yaiA b.1.8.1 22289 1v5tA 90 2.29e+01 d.15.1.1 108385 2cchB 260 2.29e+01 a.74.1.1,a.74.1.1 130237,130238 1fp1D 372 2.32e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1umgA 362 2.34e+01 d.280.1.1 107956 1h16A 759 2.34e+01 c.7.1.1 76462 1ijgA 309 2.34e+01 1fouA e.27.1.1 62493 1mjhA 162 2.35e+01 1mjhA c.26.2.4 31639 1rsy 152 2.38e+01 1rsy 1scfA 273 2.39e+01 1exzA a.26.1.2 16873 1iqaA 160 2.39e+01 b.22.1.1 71274 1cm5A 759 2.41e+01 1cm5A c.7.1.1 30671 2cunA 410 2.41e+01 1s0uA 408 2.42e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 4blmA 265 2.43e+01 1btl e.3.1.1 42721 1gvfA 286 2.45e+01 c.1.10.2 70599 1k0wA 231 2.48e+01 c.74.1.1 77220 3tdt 274 2.48e+01 3tdt 1ywqA 200 2.51e+01 d.90.1.1 124162 1dd3C 32 2.52e+01 1dd3C a.108.1.1 19033 1r7mA 235 2.52e+01 d.95.2.1,d.95.2.1 111713,111714 1agjA 242 2.52e+01 1agjA b.47.1.1 25827 2fwuA 157 2.53e+01 b.1.27.1 134262 1zj8A 566 2.54e+01 1o04A 500 2.57e+01 c.82.1.1 86508 1dq3A 454 2.58e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 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