# List of top-scoring protein chains for t06-100-30-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 1xv2A 237 5.93e-04 1wrvA 308 1.87e-01 2al3A 90 1.98e-01 1ys7A 233 3.60e-01 1kv0A 66 5.29e-01 g.3.7.1 91040 1upiA 225 7.06e-01 b.82.1.1 99757 2ffyA 358 8.28e-01 1wm3A 72 8.71e-01 2aukA 190 8.76e-01 1kgsA 225 9.04e-01 a.4.6.1,c.23.1.1 68596,68597 1rlhA 173 9.44e-01 d.256.1.1 97646 1xxlA 239 9.56e-01 1c1yB 77 1.09e+00 1c1yB d.15.1.5 37618 2cvjA 180 1.13e+00 1i8fA 81 1.24e+00 1i8fA b.38.1.1 61959 1ub0A 258 1.33e+00 c.72.1.2 88394 1wn2A 121 1.40e+00 1z4rA 168 1.40e+00 1gox 370 1.45e+00 1gox c.1.4.1 28607 1iyeA 309 1.46e+00 e.17.1.1 83786 2c6cA 707 1.76e+00 1hf2A 210 1.81e+00 1hf2A b.80.3.1,c.102.1.1 60992,60993 1vl4A 447 2.08e+00 d.283.1.1 108718 1bolA 222 2.09e+00 1bolA d.124.1.1 41120 2gnxA 365 2.40e+00 1euvB 86 2.69e+00 1a5r d.15.1.1 37598 1rfs 139 2.75e+00 1rfs b.33.1.1 24434 1q33A 292 2.79e+00 d.113.1.1 95657 3tdt 274 2.85e+00 3tdt b.81.1.2 28053 1cr1A 296 2.88e+00 1cr1A c.37.1.11 32286 1wfyA 104 3.18e+00 1a6cA 513 3.31e+00 1a6cA b.121.4.2,b.121.4.2,b.121.4.2 23296,23297,23298 2absA 383 3.43e+00 2f1rA 171 3.43e+00 1sn4A 64 3.57e+00 1aho g.3.7.1 44136 1pt6A 213 3.61e+00 c.62.1.1 95091 1dceA 567 3.82e+00 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1zjjA 263 3.99e+00 1aym3 238 4.09e+00 1aym3 1omyA 65 4.18e+00 g.3.7.1 93354 1idk 359 4.37e+00 1qcxA b.80.1.2 28025 1rkd 309 4.39e+00 1rkd c.72.1.1 34928 1oa2A 218 4.58e+00 b.29.1.11 86721 1vjoA 393 4.60e+00 c.67.1.3 100827 2bgcA 238 4.61e+00 1qhqA 140 4.62e+00 1qhqA b.6.1.1 63326 1dmhA 311 4.64e+00 1dmhA b.3.6.1 22633 1fukA 165 4.74e+00 1fukA c.37.1.19 32409 1p5fA 189 4.77e+00 c.23.16.2 94142 1j1lA 290 4.92e+00 b.82.1.12 90766 1w41A 101 4.98e+00 1vl5A 260 5.14e+00 c.66.1.41 108720 2aq5A 402 5.14e+00 1moq 368 5.17e+00 1moq c.80.1.1 35302 1k2eA 156 5.20e+00 d.113.1.1 72010 1jmcA 246 5.47e+00 1jmcA b.40.4.3,b.40.4.3 25300,25301 1jnyA 435 5.69e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2cpgA 45 5.88e+00 2cpgA a.43.1.3 17455 2c0zA 216 5.90e+00 1vizA 240 5.97e+00 c.1.4.1 100784 1i5pA 633 5.98e+00 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1zo2A 129 6.03e+00 1naqA 112 6.08e+00 d.58.5.2 91761 1y8qA 346 6.35e+00 1chmA 401 6.37e+00 1chmA c.55.2.1,d.127.1.1 33545,41142 1xrtA 467 6.43e+00 1vjqA 79 6.44e+00 k.43.1.1 100830 1yfuA 174 6.72e+00 1p90A 145 6.84e+00 c.55.5.2 94377 1vjkA 98 6.84e+00 d.15.3.1 108631 1vloA 381 7.10e+00 b.44.2.1,d.250.1.1 108838,108839 1xeuA 263 7.20e+00 1zud1 251 7.34e+00 1q7sA 117 7.36e+00 c.131.1.1 96055 1s5uA 138 7.41e+00 d.38.1.1 98573 1ze3H 122 7.44e+00 2fp7B 172 7.46e+00 1vr6A 350 7.51e+00 1m1hA 248 7.55e+00 b.114.1.1,d.58.42.1 78415,78416 1vcoA 550 7.82e+00 c.23.16.1,c.37.1.10 108508,108509 1wcdJ 441 8.02e+00 1siqA 392 8.29e+00 a.29.3.1,e.6.1.1 105585,105586 1s3sG 127 8.35e+00 d.15.1.2 98457 1z9lA 128 8.72e+00 2eifA 136 8.99e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 2bm5A 186 9.08e+00 1qkkA 155 9.17e+00 1dbwA c.23.1.1 31104 1js8A 394 9.34e+00 a.86.1.1,b.112.1.1 67219,67220 1e1oA 504 9.36e+00 1lylA b.40.4.1,d.104.1.1 25258,40714 1uv7A 110 9.41e+00 d.67.4.1 100040 1gwmA 153 9.69e+00 b.18.1.19 83348 2bh8A 101 9.72e+00 1rz3A 201 9.73e+00 c.37.1.6 98132 2dexX 671 9.80e+00 2c78A 405 9.82e+00 1sc6A 404 9.87e+00 1vgyA 393 9.92e+00 c.56.5.4,d.58.19.1 100620,100621 1g291 372 1.02e+01 1g291 1pm4A 119 1.02e+01 b.135.1.1 94891 1uk8A 282 1.02e+01 c.69.1.10 107907 1zboA 210 1.02e+01 1kn6A 90 1.04e+01 d.58.3.3 72770 1yllA 200 1.05e+01 1vkmA 297 1.07e+01 c.138.1.1 108670 2f1fA 164 1.07e+01 1i8dA 213 1.07e+01 b.43.4.3,b.43.4.3 61953,61954 1ny4A 82 1.08e+01 b.40.4.5 92316 1g0oA 283 1.08e+01 1ybvA c.2.1.2 60181 1ejxC 567 1.08e+01 b.92.1.1,c.1.9.2 83184,83185 1tmxA 293 1.10e+01 1qcxA 359 1.12e+01 1qcxA b.80.1.2 28028 1or0B 528 1.13e+01 1pwgA 349 1.13e+01 e.3.1.1 104340 2c4xA 260 1.14e+01 2azpA 318 1.15e+01 1ej0A 180 1.19e+01 1ej0A c.66.1.2 34179 1xjcA 169 1.21e+01 1ohvA 472 1.21e+01 c.67.1.4 93031 1kzfA 230 1.22e+01 d.108.1.3 73354 1pvmA 184 1.23e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1zpwX 90 1.23e+01 1y9wA 140 1.24e+01 2f06A 144 1.26e+01 1wzoA 246 1.28e+01 2bx6A 350 1.29e+01 1xsoA 150 1.29e+01 1mfmA b.1.8.1 22273 2f96A 224 1.29e+01 1m4vA 204 1.30e+01 b.40.2.2,d.15.6.1 74459,74460 1uzmA 247 1.32e+01 1s1qA 145 1.32e+01 d.20.1.2 98351 1j3wA 163 1.33e+01 d.110.7.1 90833 1o69A 394 1.33e+01 c.67.1.4 92560 1b56 135 1.35e+01 1hmt b.60.1.2 27183 1ivg 388 1.36e+01 2qwc b.68.1.1 27578 1onwA 390 1.38e+01 b.92.1.7,c.1.9.13 87172,87173 1f5jA 199 1.40e+01 1axkA b.29.1.11 24342 1bkb 136 1.41e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 2f91A 237 1.42e+01 1nzaA 103 1.44e+01 d.58.5.2 86444 1w2wB 191 1.46e+01 1nv8A 284 1.47e+01 c.66.1.30 86224 1vhoA 346 1.50e+01 b.49.3.1,c.56.5.4 100694,100695 1xzoA 174 1.51e+01 1yqsA 349 1.51e+01 1ogwA 76 1.55e+01 d.15.1.1 87001 1m1nB 522 1.58e+01 c.92.2.3 78418 1b2pA 119 1.59e+01 1b2pA b.78.1.1 27998 1i60A 278 1.59e+01 c.1.15.4 71118 1gs5A 258 1.60e+01 c.73.1.2 70395 1vybA 238 1.61e+01 d.151.1.1 108897 1iz6A 138 1.63e+01 b.34.5.2,b.40.4.5 76976,76977 1ln1A 214 1.63e+01 d.129.3.2 74038 1wl4A 397 1.64e+01 1eybA 471 1.65e+01 1ey2A b.82.1.4 28115 1kjnA 157 1.67e+01 c.115.1.1 72614 1k3iA 656 1.68e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1pg4A 652 1.76e+01 e.23.1.1 88067 1gsmA 210 1.77e+01 b.1.1.4,b.1.1.4 65535,65536 1s1hC 192 1.77e+01 i.1.1.1 105156 2b99A 156 1.77e+01 2gc9A 179 1.78e+01 1bqsA 209 1.80e+01 1bqsA b.1.1.4,b.1.1.4 21704,21705 1yhfA 115 1.83e+01 1gutA 68 1.84e+01 b.40.6.1 65576 1xubA 298 1.84e+01 1bykA 255 1.85e+01 1bykA c.93.1.1 35706 1wosA 364 1.87e+01 b.44.2.1,d.250.1.1 109468,109469 1zuoA 186 1.87e+01 1wy2A 351 1.87e+01 8abp 306 1.88e+01 8abp c.93.1.1 35647 1wduA 245 1.89e+01 d.151.1.1 109286 2b8eA 273 1.91e+01 1gteA 1025 1.91e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1ryiA 382 1.94e+01 1nbcA 155 1.95e+01 1nbcA b.2.2.2 22390 1u9tA 354 1.96e+01 1egwA 77 2.05e+01 1mnmA d.88.1.1 40234 1qexA 288 2.07e+01 1qexA b.32.1.1 24425 1mvoA 136 2.09e+01 c.23.1.1 79513 1zdrA 164 2.10e+01 1zmdA 474 2.11e+01 1uvqB 198 2.11e+01 b.1.1.2,d.19.1.1 100064,100065 2fqxA 318 2.13e+01 2gaxA 135 2.15e+01 1kv7A 488 2.16e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1n6zA 105 2.17e+01 d.263.1.1 85369 1r6fA 310 2.20e+01 e.46.1.1 97149 1mgqA 83 2.21e+01 b.38.1.1 79099 1k92A 455 2.22e+01 c.26.2.1,d.210.1.1 68325,68326 1w2xA 758 2.23e+01 c.14.1.4,c.14.1.4 109134,109135 1sjwA 144 2.24e+01 d.17.4.9 98899 2fwuA 157 2.25e+01 2fikA 287 2.26e+01 1e44B 96 2.26e+01 1e44B b.101.1.1 59220 1o5uA 101 2.28e+01 b.82.1.8 92518 1k66A 149 2.29e+01 c.23.1.1 90941 1khdA 345 2.31e+01 a.46.2.1,c.27.1.1 77400,77401 2yhx 457 2.31e+01 2yhx i.12.1.1 46024 1vrmA 325 2.32e+01 1vf8A 377 2.33e+01 1djtA 64 2.33e+01 1aho g.3.7.1 44132 2bi0A 337 2.36e+01 1c3mA 147 2.37e+01 1jotA b.77.3.1 27983 1bupA 386 2.43e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 2beiA 170 2.44e+01 1gskA 513 2.45e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1rm6A 769 2.45e+01 1g2oA 268 2.53e+01 1b8oA c.56.2.1 60228 1xhcA 367 2.54e+01 1olrA 224 2.55e+01 b.29.1.11 93330 1zjkA 403 2.58e+01 1xm8A 254 2.60e+01 1ru3A 732 2.61e+01 e.26.1.3 97835 7ahlA 293 2.68e+01 7ahlA f.6.1.1 43812 2b9eA 303 2.69e+01 1ep0A 185 2.69e+01 1dzrA b.82.1.1 28080 1f89A 291 2.70e+01 d.160.1.1 64988 1gx3A 284 2.71e+01 d.3.1.5 70678 1ugnA 198 2.72e+01 b.1.1.4,b.1.1.4 107828,107829 1dosA 358 2.72e+01 1dosA c.1.10.2 29175 1oa4A 222 2.73e+01 b.29.1.11 86731 1aym1 285 2.73e+01 1aym1 1oltA 457 2.76e+01 c.1.28.2 93334 1gr0A 367 2.76e+01 c.2.1.3,d.81.1.3 70379,70380 1qzgA 187 2.77e+01 b.40.4.3 96643 1qstA 160 2.77e+01 1yghA d.108.1.1 40804 1xjvA 294 2.79e+01 1cs1A 386 2.80e+01 1ibjA c.67.1.3 34399 1pytA 94 2.81e+01 1pytA d.58.3.1 39064 1j31A 262 2.82e+01 d.160.1.2 90808 1tg7A 971 2.83e+01 2ch4A 320 2.84e+01 2ahuA 531 2.85e+01 1u8sA 192 2.87e+01 d.58.18.5,d.58.18.5 107737,107738 1md6A 154 2.88e+01 b.42.1.2 91242 2a2cA 478 2.88e+01 1ekqA 272 2.88e+01 1c3qA c.72.1.2 34941 1ymqA 261 2.90e+01 1icpA 376 2.92e+01 1oyc c.1.4.1 62270 1sefA 274 2.93e+01 b.82.1.11 105452 1ktgA 138 2.95e+01 d.113.1.1 72972 1wmmA 145 2.98e+01 1ydyA 356 2.99e+01 1ms9A 648 3.00e+01 b.29.1.15,b.68.1.1 85088,85089 1sqiA 393 3.00e+01 d.32.1.3,d.32.1.3 105914,105915 1swvA 267 3.00e+01 2bngA 149 3.01e+01 1fhgA 154 3.02e+01 1tlk b.1.1.4 21706 1upqA 123 3.02e+01 2axwA 134 3.08e+01 1qh8B 519 3.13e+01 1qguB c.92.2.3 35634 1usuB 170 3.16e+01 d.83.2.1 99886 1k3bA 119 3.16e+01 b.61.5.1 72016 2erfA 209 3.20e+01 1gy6A 127 3.21e+01 d.17.4.2 70736 1yvoA 172 3.22e+01 1zgzA 122 3.29e+01 2fdsA 352 3.29e+01 1yj1A 76 3.31e+01 1r75A 141 3.33e+01 b.134.1.1 97189 1vjpA 394 3.35e+01 c.2.1.3,d.81.1.3 100828,100829 2hlcA 230 3.35e+01 5ptp b.47.1.2 26074 1nrvA 105 3.38e+01 d.93.1.1 86126 1gpmA 525 3.41e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1np6A 174 3.41e+01 c.37.1.10 85954 1r85A 379 3.43e+01 c.1.8.3 104839 1p94A 76 3.44e+01 a.43.1.3 94380 1rowA 109 3.45e+01 b.1.11.2 97676 1uyrA 737 3.46e+01 c.14.1.4,c.14.1.4 100188,100189 1ve3A 227 3.47e+01 1gvfA 286 3.49e+01 c.1.10.2 70599 1nwwA 149 3.49e+01 d.17.4.8 86306 2ae5B 528 3.50e+01 1zdnA 158 3.50e+01 1fehA 574 3.53e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1im8A 244 3.53e+01 c.66.1.14 66212 1vd4A 62 3.53e+01 1qo0D 196 3.56e+01 1qo0D c.23.1.3 31125 1n7kA 234 3.58e+01 c.1.10.1 85374 1a8s 273 3.58e+01 1brt c.69.1.12 34710 1uqrA 154 3.59e+01 c.23.13.1 99779 1vjjA 692 3.60e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1vmfA 145 3.62e+01 1h03P 125 3.66e+01 g.18.1.1,g.18.1.1 83411,83412 1gsa 316 3.69e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1o5zA 442 3.69e+01 c.59.1.2,c.72.2.2 92530,92531 1jmvA 141 3.70e+01 c.26.2.4 66897 1zrn 232 3.71e+01 1qq5A c.108.1.1 43323 2fxuA 375 3.72e+01 1jm1A 204 3.76e+01 b.33.1.1 71745 1tl2A 236 3.77e+01 1tl2A b.67.1.1 27541 1erjA 393 3.78e+01 1erjA b.69.4.1 27660 1vphA 149 3.78e+01 1vkcA 158 3.79e+01 1yzyA 413 3.83e+01 1xipA 388 3.83e+01 1ewfA 456 3.85e+01 1bp1 d.83.1.1,d.83.1.1 40024,40025 1ut1A 148 3.85e+01 b.2.3.6 108014 2fwkA 121 3.88e+01 1ec7A 446 3.89e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1wzaA 488 3.91e+01 2c3mA 1231 3.92e+01 1w8oA 601 3.93e+01 1bqcA 302 3.93e+01 1bqcA c.1.8.3 28831 1z4vA 532 3.93e+01 1f60A 458 3.96e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1h4gA 207 3.98e+01 b.29.1.11 70863 1pm1X 180 3.99e+01 b.60.1.1 104189 2ftbA 125 4.04e+01 1utyA 187 4.05e+01 b.147.1.1 108036 1ssqA 267 4.05e+01 b.81.1.6 105993 1gheA 177 4.06e+01 d.108.1.1 76222 1ydmA 187 4.09e+01 1ve6A 582 4.09e+01 1uehA 253 4.10e+01 c.101.1.1 99259 1ezwA 349 4.12e+01 1ezwA c.1.16.3 29558 1zx5A 300 4.13e+01 1p5tA 127 4.16e+01 b.55.1.2 94148 2ftwA 521 4.16e+01 1ig8A 486 4.17e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 1lk2A 274 4.17e+01 b.1.1.2,d.19.1.1 91056,91057 1iktA 120 4.18e+01 d.106.1.1 66188 1jx6A 342 4.19e+01 c.93.1.1 67406 1gps 47 4.23e+01 1gpt g.3.7.5 44176 1pbyA 489 4.26e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 2cxxA 190 4.28e+01 1te0A 318 4.29e+01 2basA 431 4.33e+01 1tiqA 180 4.34e+01 d.108.1.1 107010 1g8kA 825 4.40e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1e0tA 470 4.41e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1wguA 136 4.46e+01 2b0vA 153 4.48e+01 1cg2A 393 4.48e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1o7iA 119 4.49e+01 b.40.4.3 86642 1uufA 369 4.49e+01 b.35.1.2,c.2.1.1 100006,100007 1y2qA 143 4.51e+01 1ee6A 197 4.52e+01 1ee6A b.80.1.1 28024 1epfA 191 4.53e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 2a2lA 145 4.54e+01 1d0cA 444 4.56e+01 d.174.1.1 64769 1z2lA 423 4.56e+01 1dbwA 126 4.59e+01 1dbwA c.23.1.1 31095 2cwsA 237 4.63e+01 1y4hA 188 4.66e+01 1r77A 103 4.66e+01 1t4wA 196 4.71e+01 b.2.5.2 106427 2db3A 434 4.71e+01 1l4dB 122 4.73e+01 d.15.5.1 77684 1zruA 264 4.74e+01 1pgl2 370 4.79e+01 2bpsA 81 4.81e+01 1edqA 540 4.85e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1xtmA 175 4.85e+01 1v8yA 170 4.88e+01 2fomB 185 4.89e+01 1jbwA 428 5.00e+01 c.59.1.2,c.72.2.2 62860,62861 1gt1A 159 5.01e+01 b.60.1.1 90515 1vkkA 154 5.05e+01 d.109.1.2 108669 1twuA 139 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