# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1mjhB 162 3.66e-01 1mjhA c.26.2.4 31640 1mjhA 162 4.57e-01 1mjhA c.26.2.4 31639 2bvyA 475 5.32e-01 1r85A 379 5.60e-01 c.1.8.3 104839 1brwA 433 5.88e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1vdkA 466 6.02e-01 a.127.1.1 100561 1lt8A 406 1.02e+00 c.1.26.1 78186 1hizA 379 1.09e+00 c.1.8.3 65841 2a2fX 325 1.16e+00 1u2zA 433 1.33e+00 c.66.1.31 107626 1ag9A 175 1.86e+00 1rcf c.23.5.1 31178 1pz1A 333 1.88e+00 c.1.7.1 95390 1u02A 239 2.07e+00 c.108.1.15 107538 1qumA 285 2.15e+00 1qumA c.1.15.1 29393 2cevA 299 2.15e+00 1d3vA c.42.1.1 32576 1kewA 361 2.46e+00 c.2.1.2 68544 1nbaA 264 2.72e+00 1nbaA c.33.1.3 31753 1fobA 334 2.79e+00 c.1.8.3 83255 1wa3A 205 2.94e+00 1q1lA 401 2.98e+00 d.258.1.1 95591 1qtwA 285 3.13e+00 1qumA c.1.15.1 29392 1delA 241 3.46e+00 1dekA c.37.1.1 31844 2c6cA 707 3.61e+00 1z41A 338 3.78e+00 3pbgA 468 3.91e+00 1e70M c.1.8.4 28951 1qayA 428 4.11e+00 1qaxA d.58.20.1,d.179.1.1 39378,42599 1b57A 358 4.22e+00 1dosA c.1.10.2 29177 1x9iA 302 4.22e+00 1eg2A 319 4.28e+00 1eg2A c.66.1.11 34249 1tzbA 302 4.46e+00 c.80.1.1 107470 1ur4A 399 4.50e+00 1wz3A 96 4.58e+00 1dosA 358 4.68e+00 1dosA c.1.10.2 29175 1xknA 355 4.80e+00 1f74A 293 5.15e+00 1nal3 c.1.10.1 29079 1nw8A 319 5.18e+00 c.66.1.11 86292 1w0mA 226 5.25e+00 c.1.1.1 109027 1pbgA 468 5.56e+00 1e70M c.1.8.4 28946 1hg3A 225 5.67e+00 1hg3A c.1.1.1 61025 1c93A 265 5.95e+00 2ebn c.1.8.5 28998 1yfm 488 6.10e+00 1furA a.127.1.1 19413 1d9eA 284 6.44e+00 1d9eA c.1.10.4 29195 2pfkA 320 6.54e+00 3pfk c.89.1.1 35577 1ps9A 671 6.55e+00 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 2anuA 255 6.59e+00 1pfkA 320 6.72e+00 3pfk c.89.1.1 35575 1g7eA 122 6.82e+00 1g7eA c.47.1.7 33055 1qxoA 388 6.85e+00 d.258.1.1 96539 1mw9X 592 6.94e+00 e.10.1.1 91480 1j5sA 463 7.08e+00 c.1.9.8 71580 1uanA 227 7.52e+00 c.134.1.1 99135 1bxkA 355 7.61e+00 1bxkA c.2.1.2 29803 1np7A 489 7.71e+00 a.99.1.1,c.28.1.1 80677,80678 1blxA 326 7.85e+00 1hcl d.144.1.7 41596 1geqA 248 7.98e+00 2tysA c.1.2.4 28589 1kv5A 250 8.20e+00 c.1.1.1 73052 7a3hA 303 8.22e+00 7a3hA c.1.8.3 28817 1a3h 300 8.22e+00 7a3hA c.1.8.3 28819 1djnA 729 8.23e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1ecl 597 8.37e+00 1ecl e.10.1.1 43238 1ww8A 439 8.41e+00 2b0tA 738 8.62e+00 1mioB 458 8.65e+00 1qguB c.92.2.3 35602 1dekA 241 8.89e+00 1dekA c.37.1.1 31842 1qaxA 428 9.38e+00 1qaxA d.58.20.1,d.179.1.1 39376,42597 1t0hB 224 9.71e+00 c.37.1.1 106208 1xyzA 347 9.90e+00 1taxA c.1.8.3 28804 1q1gA 276 9.95e+00 c.56.2.1 95574 1i60A 278 1.01e+01 c.1.15.4 71118 1ctqA 166 1.02e+01 1ctqA c.37.1.8 31965 1rm6A 769 1.03e+01 1hybA 181 1.06e+01 1f9aA c.26.1.3 61399 1edt 271 1.08e+01 2ebn c.1.8.5 28993 1gesA 450 1.11e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1fuqA 472 1.13e+01 1furA a.127.1.1 19405 2tmdA 729 1.13e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1furA 467 1.17e+01 1furA a.127.1.1 19403 1fkx 349 1.20e+01 1a4mA c.1.9.1 29018 1ydnA 295 1.21e+01 1ituA 369 1.23e+01 c.1.9.7 71423 1m5q1 130 1.24e+01 1ihoA 283 1.26e+01 1ihoA c.26.1.4 62390 1djqA 729 1.28e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1g3uA 214 1.32e+01 c.37.1.1 65132 1lv7A 257 1.33e+01 c.37.1.20 78232 2bgkA 278 1.37e+01 1pdo 135 1.39e+01 1pdo c.54.1.1 33376 1vf8A 377 1.40e+01 1opr 213 1.42e+01 1opr c.61.1.1 34091 1m6eX 359 1.43e+01 c.66.1.35 91188 2bjvA 265 1.44e+01 1o60A 292 1.45e+01 c.1.10.4 92532 1e9lA 377 1.46e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 2btzA 394 1.46e+01 1noyA 388 1.49e+01 1clqA c.55.3.5 33713 1agp 166 1.50e+01 1ctqA c.37.1.8 31985 1j0aA 325 1.52e+01 c.79.1.1 83871 5abp 306 1.52e+01 8abp c.93.1.1 35651 1vkyA 347 1.52e+01 e.53.1.1 108696 2aq4A 434 1.56e+01 2bsxA 253 1.66e+01 1xpjA 126 1.68e+01 1uqrA 154 1.74e+01 c.23.13.1 99779 1tpfA 250 1.79e+01 1amk c.1.1.1 28467 1rqbA 539 1.80e+01 a.5.7.2,c.1.10.5 105057,105058 1xfiA 367 1.84e+01 e.50.1.1 109584 1l4uA 176 1.85e+01 c.37.1.2 73568 2cybA 323 1.85e+01 1obdA 306 1.88e+01 d.143.1.1 86767 1b3qA 379 1.96e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1r31A 428 1.97e+01 d.58.20.1,d.179.1.1 96897,96898 1j0dA 341 1.99e+01 c.79.1.1 83902 1udxA 416 1.99e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1gtzA 156 2.00e+01 c.23.13.1 70539 3aig 202 2.00e+01 1atlA d.92.1.9 40321 1sg6A 393 2.09e+01 e.22.1.1 105522 1add 349 2.12e+01 1a4mA c.1.9.1 29020 1a48 306 2.18e+01 1a48 d.143.1.1 41590 1oj6A 151 2.18e+01 a.1.1.2 93088 2tpt 440 2.20e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1qoxN 449 2.21e+01 1qoxN c.1.8.4 28978 2d13A 227 2.23e+01 1bap 306 2.23e+01 8abp c.93.1.1 35654 1hjsA 332 2.24e+01 c.1.8.3 83492 1cliA 345 2.29e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1pii 452 2.30e+01 1pii c.1.2.4,c.1.2.4 28559,28563 1to6A 371 2.34e+01 c.141.1.1 107170 1ywfA 296 2.35e+01 1fuoA 467 2.35e+01 1furA a.127.1.1 19411 1f1oA 431 2.35e+01 1f1oA a.127.1.1 19433 1pmaA 233 2.36e+01 1pmaA d.153.1.4 41918 1f6kA 293 2.37e+01 1nal3 c.1.10.1 29081 1tgoA 773 2.37e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 8abp 306 2.39e+01 8abp c.93.1.1 35647 1y8qB 640 2.40e+01 1e4iA 447 2.42e+01 1e70M c.1.8.4 59225 1vl8A 267 2.43e+01 c.2.1.2 108733 1abe 306 2.43e+01 8abp c.93.1.1 35648 3pga1 337 2.45e+01 4pgaA 1uozA 315 2.46e+01 1sflA 238 2.48e+01 1vplA 256 2.52e+01 1rzmA 338 2.54e+01 c.1.10.4 105137 1yhtA 367 2.54e+01 1ohvA 472 2.57e+01 c.67.1.4 93031 1lyxA 248 2.57e+01 c.1.1.1 78304 1sxjE 354 2.59e+01 a.80.1.1,c.37.1.20 106089,106090 2glzA 153 2.59e+01 1d0iA 156 2.64e+01 2dhqA c.23.13.1 31383 821p 166 2.65e+01 1ctqA c.37.1.8 31969 1u9iA 519 2.66e+01 1ff9A 450 2.70e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1jmvA 141 2.70e+01 c.26.2.4 66897 1yzgA 179 2.75e+01 1g60A 260 2.77e+01 c.66.1.11 70151 1dvjA 246 2.79e+01 1dvjA c.1.2.3 28546 1efvB 255 2.79e+01 1efvB c.26.2.3 31634 1kamA 194 2.81e+01 c.26.1.3 72254 1lh0A 213 2.85e+01 c.61.1.1 73896 1a3c 181 2.87e+01 1a3c c.61.1.1 34095 1t3lA 337 2.88e+01 b.34.2.1,c.37.1.1 106358,106359 1ofuA 320 2.91e+01 c.32.1.1,d.79.2.1 86972,86973 4pgaA 337 3.00e+01 4pgaA c.88.1.1 35565 1dvjC 246 3.03e+01 1dvjA c.1.2.3 28548 3timA 250 3.05e+01 1amk c.1.1.1 28483 2gaiA 633 3.05e+01 2b69A 343 3.07e+01 1gdtA 183 3.07e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 1oyeA 1049 3.13e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1mzhA 225 3.14e+01 c.1.10.1 79698 1a4mA 349 3.15e+01 1a4mA c.1.9.1 29014 2d2eA 250 3.15e+01 1jubA 311 3.15e+01 c.1.4.1 90908 1u5tA 233 3.18e+01 a.4.5.54,a.4.5.54 107684,107685 1w3iA 293 3.19e+01 c.1.10.1 109152 1yz7A 188 3.19e+01 1k9dA 679 3.20e+01 c.1.8.10,d.92.2.2 77292,77293 1ib8A 164 3.21e+01 b.38.2.1,d.52.4.1 71168,71169 1aod 289 3.23e+01 2plc c.1.18.2 29615 1h5vA 304 3.24e+01 c.1.8.3 70898 1lzlA 323 3.24e+01 c.69.1.2 78306 2hsdA 253 3.26e+01 1e6wA c.2.1.2 29866 1dqsA 393 3.27e+01 1dqsA e.22.1.1 43347 1yxyA 234 3.31e+01 1rcf 169 3.34e+01 1rcf c.23.5.1 31170 2dorA 311 3.35e+01 2dorA c.1.4.1 28593 1o94A 729 3.39e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1yisA 478 3.40e+01 1iwgA 1053 3.40e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 76874,76875,76876,76877,76878,76879,76880,76881 1ipaA 274 3.46e+01 c.116.1.1,d.79.3.3 71254,71255 1lg2A 365 3.46e+01 c.1.8.5,d.26.3.1 77950,77951 1i39A 225 3.48e+01 1ekeA c.55.3.1 61585 1gtxA 472 3.48e+01 1gtxA 1hdcA 253 3.51e+01 1e6wA c.2.1.2 29862 1ug6A 431 3.53e+01 c.1.8.4 88490 1gnlA 544 3.55e+01 e.26.1.1 70287 1xqiA 195 3.57e+01 1eh9A 558 3.57e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1g7vA 284 3.59e+01 1d9eA c.1.10.4 60335 1o58A 303 3.63e+01 c.79.1.1 92491 1sz9A 144 3.64e+01 a.118.9.4 106139 2d1sA 548 3.65e+01 2c1lA 358 3.66e+01 2citA 282 3.74e+01 1vbuA 328 3.75e+01 1q7bA 244 3.83e+01 c.2.1.2 96026 1w5fA 353 3.84e+01 1of8A 370 3.88e+01 c.1.10.4 92819 1dnpA 471 3.89e+01 1qnf a.99.1.1,c.28.1.1 18775,31630 1wndA 495 3.92e+01 1i8tA 367 3.92e+01 c.4.1.3,d.16.1.7 66094,66095 1b16A 254 3.93e+01 1b16A c.2.1.2 29875 1kjnA 157 3.93e+01 c.115.1.1 72614 1cydA 244 3.94e+01 1cydA c.2.1.2 29825 1kinA 366 3.96e+01 1x1zA 252 3.97e+01 2c5aA 379 3.99e+01 1km4A 247 4.00e+01 c.1.2.3 72740 1php 394 4.01e+01 16pk c.86.1.1 35452 1tg7A 971 4.11e+01 1jksA 294 4.13e+01 d.144.1.7 71710 2tpsA 227 4.15e+01 2tpsA c.1.3.1 28591 1zcoA 262 4.16e+01 2bv9A 290 4.16e+01 1c3cA 429 4.18e+01 1c3cA a.127.1.1 19425 1tdj 514 4.21e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 1dv1A 449 4.23e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 2apjA 260 4.24e+01 5p21 166 4.25e+01 1ctqA c.37.1.8 31966 1fjgR 88 4.29e+01 1fjfR a.4.8.1 16252 2a3nA 355 4.32e+01 1khyA 148 4.34e+01 a.174.1.1 77410 1gzsB 165 4.34e+01 a.168.1.1 76425 1hfbA 370 4.35e+01 c.1.10.4 76706 2gnoA 305 4.41e+01 1d0qA 103 4.43e+01 1d0qA g.41.3.2 45208 1dorA 311 4.44e+01 2dorA c.1.4.1 28595 1guzA 310 4.47e+01 c.2.1.5,d.162.1.1 65586,65587 1oboA 169 4.47e+01 c.23.5.1 86776 1snyA 267 4.48e+01 c.2.1.2 105833 1ko9A 345 4.55e+01 a.96.1.3,d.129.1.2 68717,68718 1sayA 361 4.56e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 1dkgB 197 4.59e+01 1dkgA b.73.1.1,h.1.9.1 27813,45627 1p2xA 159 4.60e+01 a.40.1.1 104062 1tr1A 447 4.69e+01 1e70M c.1.8.4 28957 1yaxA 153 4.71e+01 1p4oA 322 4.73e+01 d.144.1.7 87775 1nozA 388 4.75e+01 1clqA c.55.3.5 33715 1g5aA 628 4.75e+01 b.71.1.1,c.1.8.1 65152,65153 2gokA 429 4.79e+01 1dqnA 230 4.82e+01 1dqnA c.61.1.1 34067 1h3fA 432 4.84e+01 c.26.1.1,d.66.1.4 76631,76632 1amk 251 4.86e+01 1amk c.1.1.1 28503 1yueA 427 4.86e+01 1ej2A 181 4.88e+01 1f9aA c.26.1.3 59414 1uouA 474 4.89e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1z7bA 358 4.90e+01 1m3qA 317 4.90e+01 a.96.1.3,d.129.1.2 91184,91185 1j1uA 306 4.91e+01 c.26.1.1 83980 1u9jA 358 4.92e+01 1fmcA 255 4.95e+01 1cydA c.2.1.2 29856 1e0tA 470 4.95e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1w44A 331 4.97e+01 3ladA 476 5.02e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 1hkkA 364 5.06e+01 c.1.8.5,d.26.3.1 90634,90635 1pjcA 361 5.06e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 2dpmA 284 5.10e+01 2dpmA c.66.1.28 34246 2amxA 376 5.20e+01 1be3B 439 5.29e+01 1be3B d.185.1.1,d.185.1.1 58952,58953 7ceiB 206 5.30e+01 1bxiB d.4.1.1 37134 1fvpA 231 5.39e+01 1nfp c.1.16.2 29556 1ubeA 349 5.43e+01 c.37.1.11,d.48.1.1 88412,88413 1e7rA 321 5.49e+01 1bsvA c.2.1.2 29808 1a0rP 245 5.56e+01 1b9yC c.47.1.6 33054 1l8nA 679 5.56e+01 c.1.8.10,d.92.2.2 84564,84565 1o5iA 249 5.57e+01 c.2.1.2 92499 1iow 306 5.59e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1sc6A 404 5.60e+01 1cl1A 395 5.61e+01 1cl2A c.67.1.3 34395 1mw7A 240 5.64e+01 e.39.1.1 79557 1e32A 458 5.64e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1xm3A 264 5.66e+01 1jilA 420 5.67e+01 c.26.1.1 66745 1ryiA 382 5.68e+01 1e6uA 321 5.70e+01 1bsvA c.2.1.2 29805 1ptmA 329 5.73e+01 c.77.1.3 95104 1gt8C 1025 5.76e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70428,70429,70430,70431,70432 2f6hX 419 5.78e+01 1neyA 247 5.78e+01 c.1.1.1 80449 1wwkA 307 5.79e+01 1dv2A 452 5.81e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1qhtA 775 5.85e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1gthA 1025 5.86e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70483,70484,70485,70486,70487 1q7rA 219 5.87e+01 c.23.16.1 96054 2trcP 217 5.88e+01 1b9yC c.47.1.6 33051 1vjgA 218 5.93e+01 c.23.10.6 100810 1bpe 335 5.94e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 18076,75815,75816 1o57A 291 5.96e+01 a.4.5.40,c.61.1.1 92483,92484 1ve6A 582 6.02e+01 1ehaA 558 6.02e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1vflA 356 6.07e+01 1qqcA 773 6.10e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1dr8B 344 6.11e+01 1cnzA c.77.1.1 35052 1gt8A 1025 6.12e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70418,70419,70420,70421,70422 1b0jA 754 6.15e+01 1amj c.8.2.1,c.83.1.1 30719,35395 1tzjA 338 6.25e+01 1p5sA 203 6.25e+01 a.40.1.1 94147 1e5eA 404 6.27e+01 1ibjA c.67.1.3 59265 1ek9A 428 6.30e+01 1ek9A f.5.1.1 43809 1evsA 187 6.32e+01 1evsA a.26.1.1 16845 1a6dB 543 6.38e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 2be3A 226 6.40e+01 1yqtA 538 6.45e+01 1sfjA 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