# List of top-scoring protein chains for t04-100-30-stride-ebghtl-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 1p3wA 404 2.22e-50 c.67.1.3 87752 1t3iA 420 8.13e-46 c.67.1.3 106354 1eg5A 384 1.91e-45 1ecxA c.67.1.3 34429 1jf9A 408 3.64e-45 1c0nA c.67.1.3 62931 1eluA 390 4.26e-34 1elqA c.67.1.3 34434 1elqA 390 4.37e-34 1elqA c.67.1.3 34436 1e5eA 404 2.87e-33 1ibjA c.67.1.3 59265 1gc0A 398 7.80e-33 c.67.1.3 70168 1cs1A 386 5.20e-31 1ibjA c.67.1.3 34399 1qz9A 416 1.66e-29 c.67.1.3 96621 1vjoA 393 1.77e-25 c.67.1.3 100827 1cl1A 395 3.35e-22 1cl2A c.67.1.3 34395 1v2dA 381 2.01e-21 c.67.1.1 108281 1m32A 366 5.74e-20 c.67.1.3 78508 1iugA 352 2.21e-18 c.67.1.3 90699 1o4sA 389 2.35e-17 c.67.1.1 86620 1jg8A 347 1.45e-16 1jg8A c.67.1.1 62946 1m6sA 347 1.45e-16 c.67.1.1 78701 1b5pA 385 7.19e-16 c.67.1.1 90403 1bjwA 382 1.54e-15 1bjwA c.67.1.1 34349 1wyuA 438 3.23e-15 1z7dA 433 4.10e-15 1bw0A 416 5.02e-15 1bw0A c.67.1.1 34385 1vefA 395 5.54e-15 1wyuB 474 6.15e-15 1lc5A 364 6.73e-15 c.67.1.1 73827 1kl1A 419 8.99e-15 c.67.1.4 72663 1gdeA 389 1.59e-14 c.67.1.1 60456 1yjsA 419 1.83e-14 1pmmA 466 2.07e-14 c.67.1.6 94901 1w7lA 422 3.00e-14 c.67.1.1 109226 1yiyA 429 3.00e-14 1yizA 429 3.08e-14 2bwnA 401 7.64e-14 1fc4A 401 7.76e-14 1bs0A c.67.1.4 59760 1mdoA 393 1.35e-13 c.67.1.4 79013 1dfoA 417 1.35e-13 1bj4A c.67.1.4 34480 1bs0A 384 2.02e-13 1bs0A c.67.1.4 34490 1w23A 360 2.18e-13 1fg7A 356 3.23e-13 1gewA c.67.1.1 59819 1svvA 359 3.58e-13 c.67.1.1 106054 1u08A 386 4.89e-13 c.67.1.1 107543 1gewA 356 9.07e-13 1gewA c.67.1.1 60470 1b9hA 388 1.79e-12 1b9hA c.67.1.4 34488 2aeuA 374 4.57e-12 2oatA 439 4.60e-12 2dkb c.67.1.4 34452 1b8gA 429 4.96e-12 1b8gA c.67.1.4 34499 1m7yA 435 5.90e-12 c.67.1.4 78761 1w3uA 362 6.55e-12 2byjA 439 7.07e-12 1ynuA 473 7.63e-12 1v72A 356 9.64e-12 2c0rA 362 9.78e-12 1oatA 439 1.04e-11 2dkb c.67.1.4 34461 1js3A 486 1.34e-11 c.67.1.6 67215 1o69A 394 1.76e-11 c.67.1.4 92560 2bylA 439 1.93e-11 1rv3A 483 2.16e-11 c.67.1.4 105101 1sffA 426 2.86e-11 c.67.1.4 105482 1uu1A 335 3.78e-11 c.67.1.1 99993 1ax4A 467 4.49e-11 1ax4A c.67.1.2 34391 1wstA 417 4.52e-11 1c7nA 399 8.31e-11 1d2fA c.67.1.3 34413 1vp4A 425 1.76e-10 1bjnA 360 1.95e-10 1bjnA c.67.1.4 34469 1bj4A 470 2.55e-10 1bj4A c.67.1.4 34479 1d2fA 390 4.49e-10 1d2fA c.67.1.3 34411 2gsaA 432 5.22e-10 2gsaA c.67.1.4 34446 2fnuA 375 2.63e-09 1c7gA 456 5.37e-09 c.67.1.2 90415 1ars 396 9.66e-09 1ajsA c.67.1.1 34287 1d7uA 433 1.16e-08 2dkb c.67.1.4 34439 1qisA 396 1.36e-08 1ajsA c.67.1.1 34284 1ahxA 396 1.76e-08 1ajsA c.67.1.1 34293 2dkb 433 2.92e-08 2dkb c.67.1.4 34438 1ohvA 472 3.54e-07 c.67.1.4 93031 1lk9A 448 4.21e-07 c.67.1.1 78057 1qj5A 429 3.15e-06 1dtyA c.67.1.4 34493 1s0aA 429 5.68e-06 c.67.1.4 98263 1c4kA 730 2.35e-05 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 7aatA 401 3.97e-05 1ajsA c.67.1.1 34250 1ajsA 412 8.18e-05 1ajsA c.67.1.1 34276 1e5dA 402 2.63e-02 1e5dA c.23.5.1,d.157.1.3 31208,42061 1pamA 686 9.88e-02 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 7taa 478 2.65e-01 7taa b.71.1.1,c.1.8.1 27778,28765 2ng1 293 3.54e-01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1uqrA 154 3.64e-01 c.23.13.1 99779 2d13A 227 4.21e-01 1d3cA 686 4.39e-01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1tz9A 367 6.28e-01 c.1.15.6 107466 1ls1A 295 6.35e-01 a.24.13.1,c.37.1.10 78170,78171 1qvbA 481 6.89e-01 1qvbA c.1.8.4 28983 1um0A 365 7.11e-01 d.258.1.1 107942 1hd7A 318 9.83e-01 1bix d.151.1.1 41780 1vmeA 410 9.85e-01 c.23.5.1,d.157.1.3 108893,108894 1y9uA 323 1.08e+00 1f2tB 148 1.19e+00 1f2tB 1pszA 303 1.44e+00 1toaA c.92.2.2 35600 1j8yF 297 1.80e+00 1ng1 a.24.13.1,c.37.1.10 62747,62748 1hl2A 297 1.97e+00 c.1.10.1 83581 1k2eA 156 2.16e+00 d.113.1.1 72010 1vb5A 276 2.18e+00 1cvrA 435 2.22e+00 1cvrA b.1.18.12,c.17.1.2 21949,31006 1zu4A 320 2.35e+00 2bx2L 517 2.39e+00 1pq4A 291 2.47e+00 c.92.2.2 94995 1t7lA 766 2.68e+00 2fhpA 187 2.92e+00 1o5kA 306 2.98e+00 c.1.10.1 92504 1vjtA 483 3.04e+00 c.2.1.5,d.162.1.2 100833,100834 1mvoA 136 3.11e+00 c.23.1.1 79513 1k30A 368 3.55e+00 c.112.1.1 68067 1j8mF 297 3.60e+00 1ng1 a.24.13.1,c.37.1.10 62742,62743 1luaA 287 3.81e+00 c.2.1.7,c.58.1.4 78216,78217 1rd5A 262 3.83e+00 1va0A 239 3.84e+00 1zs9A 261 4.05e+00 1iq8A 582 4.51e+00 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1vid 221 4.57e+00 1vid c.66.1.1 34178 1p0zA 131 4.63e+00 d.110.6.1 93882 1wqaA 455 4.74e+00 1ecfA 504 4.92e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 2ap1A 327 5.04e+00 1geqA 248 5.17e+00 2tysA c.1.2.4 28589 1fts 295 5.18e+00 1ng1 a.24.13.1,c.37.1.10 16968,32279 1o58A 303 5.50e+00 c.79.1.1 92491 1ig8A 486 5.64e+00 2yhx c.55.1.3,c.55.1.3 64746,64747 2aa4A 289 5.69e+00 1qgdA 662 6.26e+00 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1szwA 379 6.43e+00 d.265.1.4 99047 1v8dA 235 6.46e+00 c.140.1.1 108425 1tluA 130 6.57e+00 d.156.1.2 107139 1iatA 557 6.58e+00 1dqrA c.80.1.2 62123 1i1qA 520 6.75e+00 1qdlA d.161.1.1 61543 1oapA 109 6.76e+00 d.79.7.1 92706 1vr7A 142 6.94e+00 1u09A 476 7.00e+00 e.8.1.4 107545 1uvjA 664 7.49e+00 e.8.1.6 100045 1ve1A 304 7.50e+00 1g5aA 628 7.65e+00 b.71.1.1,c.1.8.1 65152,65153 1ko7A 314 7.74e+00 c.98.2.1,c.91.1.2 72797,72798 1jy1A 464 7.84e+00 d.136.1.3,d.136.1.3 67438,67439 1fsz 372 7.87e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 1m1nA 491 7.93e+00 c.92.2.3 78417 2bznA 351 8.20e+00 1o7jA 327 8.58e+00 c.88.1.1 81140 2d1sA 548 8.64e+00 1gt6A 269 8.92e+00 c.69.1.17 76342 1o17A 345 9.04e+00 a.46.2.1,c.27.1.1 80765,80766 1zq4A 693 9.19e+00 1vm7A 311 9.25e+00 c.72.1.1 108884 1tib 269 9.51e+00 3tgl c.69.1.17 34738 1qh8A 478 9.76e+00 1qguA c.92.2.3 35633 1hhsA 664 1.01e+01 1hi0P e.8.1.6 61045 1w6tA 444 1.02e+01 1ujpA 271 1.04e+01 c.1.2.4 99462 2cxnA 557 1.06e+01 1rf6A 427 1.07e+01 d.68.2.2 97366 1rvkA 382 1.07e+01 c.1.11.2,d.54.1.1 97928,97929 1ut9A 609 1.08e+01 a.102.1.2,b.1.18.2 99912,99913 1y80A 210 1.09e+01 1gnlA 544 1.09e+01 e.26.1.1 70287 1nu0A 138 1.11e+01 c.55.3.8 92165 1jdpA 441 1.14e+01 c.93.1.1 62906 2c6qA 351 1.28e+01 1iuqA 367 1.32e+01 c.112.1.1 90703 1h7eA 245 1.35e+01 c.68.1.13 60717 1o8bA 219 1.36e+01 c.124.1.4,d.58.40.1 81180,81181 1u0fA 564 1.37e+01 1c3cA 429 1.39e+01 1c3cA a.127.1.1 19425 1w2fA 276 1.40e+01 d.143.1.3 109125 1eziA 228 1.41e+01 1eyrA c.68.1.13 34512 1q45A 391 1.45e+01 c.1.4.1 95780 1h1dA 221 1.45e+01 c.66.1.1 83452 1q4gA 553 1.46e+01 a.93.1.2,g.3.11.1 95789,95790 2adbA 148 1.46e+01 1pot 325 1.48e+01 1pot c.94.1.1 35807 1vlwA 217 1.51e+01 c.1.10.1 108868 1tt7A 330 1.51e+01 1o1yA 239 1.51e+01 c.23.16.1 86554 2cunA 410 1.55e+01 1tqjA 230 1.56e+01 c.1.2.2 107228 1rpxA 230 1.57e+01 1rpxA c.1.2.2 28536 1qv9A 283 1.62e+01 c.127.1.1 96356 1uwsA 489 1.63e+01 c.1.8.4 108073 1bmtA 246 1.66e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 2c3zA 222 1.67e+01 1zaiA 363 1.68e+01 1adoA 363 1.70e+01 1fbaA c.1.10.1 29124 1frb 315 1.70e+01 1frb c.1.7.1 28665 1jq5A 370 1.76e+01 e.22.1.2 67084 1psdA 409 1.77e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1pjcA 361 1.77e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1qm4A 396 1.81e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41350,41351,41352 1jb9A 316 1.82e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1k32A 1045 1.87e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1jmtA 104 1.88e+01 d.58.7.3 63180 2c5uA 375 1.90e+01 1w78A 422 1.91e+01 1d4fA 431 1.93e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1j27A 102 1.94e+01 d.58.50.1 90778 2tysA 268 1.98e+01 2tysA c.1.2.4 28572 1vmaA 306 2.00e+01 a.24.13.1,c.37.1.10 108887,108888 1uxoA 192 2.00e+01 c.69.1.31 108121 1k20A 310 2.01e+01 c.107.1.1 68027 1xfjA 261 2.01e+01 d.194.1.2 109585 1wr8A 231 2.02e+01 1gtmA 419 2.03e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 2gupA 292 2.06e+01 1jj2W 91 2.07e+01 1ffkU d.29.1.1 63108 1vljA 407 2.08e+01 e.22.1.2 108832 1ju2A 536 2.11e+01 c.3.1.2,d.16.1.1 77169,77170 1cbf 285 2.12e+01 1cbf c.90.1.1 35587 1xx1A 285 2.12e+01 1yt5A 258 2.15e+01 2sas 185 2.15e+01 2sas a.39.1.5 17258 1oxkB 134 2.16e+01 c.23.1.1 93691 1s72X 92 2.18e+01 d.29.1.1 105343 1vqoX 92 2.21e+01 1mwmA 320 2.22e+01 c.55.1.1,c.55.1.1 79580,79581 1bd3A 243 2.23e+01 1bd3A c.61.1.1 34098 1q35A 320 2.26e+01 c.94.1.1 95661 1zupA 315 2.27e+01 2basA 431 2.27e+01 1c30B 382 2.28e+01 c.8.3.1,c.23.16.1 30736,31413 2gtrA 261 2.30e+01 1zj8A 566 2.31e+01 2avnA 260 2.36e+01 1a9xB 379 2.36e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1j5yA 187 2.37e+01 a.4.5.1,d.94.2.1 71592,71593 1obfO 335 2.40e+01 c.2.1.3,d.81.1.1 86768,86769 1vpqA 273 2.40e+01 1gveA 327 2.43e+01 c.1.7.1 70597 1pgvA 197 2.44e+01 c.10.1.1 88073 2fjbA 643 2.46e+01 1jnrA 643 2.46e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1a0cA 438 2.47e+01 1a0cA c.1.15.3 29529 1xs5A 241 2.47e+01 1ff9A 450 2.50e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1l0wA 580 2.51e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1yh1A 359 2.51e+01 1igs 248 2.56e+01 1a53 c.1.2.4 28565 1gqnA 252 2.58e+01 c.1.10.1 90514 1ru8A 232 2.59e+01 c.26.2.1 97849 1a8s 273 2.60e+01 1brt c.69.1.12 34710 1pymA 295 2.60e+01 1pymA c.1.12.7 29308 1xwfA 431 2.62e+01 1ve5A 311 2.65e+01 1bag 425 2.71e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1zq6A 359 2.74e+01 1qwgA 251 2.76e+01 c.1.27.1 96473 1ynpA 317 2.76e+01 1ezwA 349 2.76e+01 1ezwA c.1.16.3 29558 1ua7A 422 2.83e+01 b.71.1.1,c.1.8.1 107759,107760 1xrsA 516 2.90e+01 2gjlA 328 2.90e+01 1dixA 208 2.91e+01 1bk7A d.124.1.1 41122 1c4oA 664 2.95e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 1sz2A 332 2.97e+01 1kfcA 268 2.98e+01 c.1.2.4 77371 1lfpA 249 3.06e+01 e.39.1.1 73885 1rvgA 305 3.07e+01 c.1.10.2 97920 1qhoA 686 3.13e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1xttA 216 3.16e+01 5reqA 727 3.19e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1sur 215 3.20e+01 1sur c.26.2.2 31620 1dssG 333 3.22e+01 1dssG c.2.1.3,d.81.1.1 30022,39937 1qfeA 252 3.25e+01 1qfeA c.1.10.1 29167 1r7lA 110 3.26e+01 d.277.1.1 104837 1y7lA 316 3.28e+01 1g5tA 196 3.31e+01 1g5rA c.37.1.11 32366 1wa3A 205 3.36e+01 1uc2A 481 3.39e+01 d.261.1.1 99161 1yr2A 741 3.46e+01 1l8nA 679 3.46e+01 c.1.8.10,d.92.2.2 84564,84565 1ltqA 301 3.50e+01 c.108.1.9,c.37.1.1 78208,78209 2f2hA 773 3.53e+01 1vr5A 547 3.55e+01 1wolA 122 3.60e+01 1sc3A 178 3.61e+01 c.17.1.1 105416 1lj5A 379 3.61e+01 e.1.1.1 73928 1gudA 288 3.61e+01 c.93.1.1 83326 1kfuL 699 3.62e+01 a.39.1.8,b.14.1.1,d.3.1.3 68571,68572,68573 1s2wA 295 3.63e+01 c.1.12.7 98407 1j0aA 325 3.70e+01 c.79.1.1 83871 2czrA 226 3.71e+01 1reqA 727 3.72e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1hskA 326 3.74e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1ccwA 137 3.74e+01 1be1 c.23.6.1 31238 1wd7A 261 3.77e+01 2fdrA 229 3.83e+01 1mg7A 417 3.84e+01 d.14.1.6,d.58.26.6 84954,84955 1qs0B 338 3.84e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 2fsjA 346 3.85e+01 1xa0A 328 3.88e+01 1v37A 177 3.89e+01 1v7lA 163 3.92e+01 1j09A 468 3.93e+01 a.97.1.1,c.26.1.1 77025,77026 1ww8A 439 3.93e+01 2az4A 429 3.94e+01 1vicA 262 3.98e+01 c.68.1.13 100756 1rwxA 178 3.98e+01 2abqA 306 4.02e+01 1knvA 293 4.04e+01 c.52.1.7 68707 1rpjA 288 4.06e+01 2dri c.93.1.1 35656 1z7wA 322 4.06e+01 1hkhA 279 4.07e+01 c.69.1.12 90628 2fp3A 316 4.08e+01 1lm6A 215 4.09e+01 d.167.1.1 84628 1wzcA 249 4.11e+01 1a53 247 4.12e+01 1a53 c.1.2.4 28564 1jdlA 121 4.12e+01 a.3.1.1 66557 1t3bA 211 4.14e+01 c.47.1.9,d.17.3.1 106341,106342 1v3vA 333 4.15e+01 b.35.1.2,c.2.1.1 108345,108346 1ub9A 100 4.15e+01 a.4.5.28 99159 1b7gO 340 4.16e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1ctqA 166 4.16e+01 1ctqA c.37.1.8 31965 1nm2A 317 4.18e+01 c.19.1.1,d.58.23.1 80654,80655 1rdr 461 4.19e+01 1rdr e.8.1.4 43116 1l3iA 192 4.20e+01 c.66.1.22 77676 1lrzA 426 4.25e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 2ar9A 278 4.25e+01 1im8A 244 4.26e+01 c.66.1.14 66212 1j5vA 351 4.29e+01 c.72.1.1 71585 1xklA 273 4.29e+01 1fljA 260 4.30e+01 2cba b.74.1.1 27954 1u0sY 118 4.30e+01 c.23.1.1 107566 1gpmA 525 4.31e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2cwxA 430 4.32e+01 1qj4A 257 4.36e+01 1qj4A c.69.1.20 34796 1jf8A 131 4.40e+01 c.44.1.1 66621 2f46A 156 4.41e+01 1rybA 212 4.42e+01 c.56.3.1 98098 2c0cA 362 4.44e+01 1a7cA 379 4.47e+01 1sek e.1.1.1 42660 2aeeA 211 4.47e+01 1wmaA 276 4.49e+01 1v4aA 440 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