# List of top-scoring protein chains for T0398.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. # #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 SCOP_domain SCOP_suid 5S 5N 12S 12S 10N 2dbqA 334 1.31e-14 2eezA 369 1.85e-14 2rirA 300 3.65e-14 1pjcA 361 3.95e-14 c.2.1.4,c.23.12.2 30101,31361 1wwkA 307 4.67e-14 2vhxA 377 1.10e-13 2vojA 371 1.10e-13 2gcgA 330 1.27e-13 2q50A 328 1.27e-13 2vhvA 377 1.42e-13 1a7aA 432 1.99e-13 c.2.1.4,c.23.12.3 30104,31364 1li4A 432 2.12e-13 c.2.1.4,c.23.12.3 84616,84617 1b3rA 431 2.51e-13 c.2.1.4,c.23.12.3 30106,31366 2cukA 311 3.08e-13 1d4fA 431 3.37e-13 c.2.1.4,c.23.12.3 30110,31370 1xwfA 431 3.82e-13 c.2.1.4,c.23.12.3 122392,122393 1ygyA 529 1.33e-12 c.2.1.4,c.23.12.1,d.58.18.1,d.81.2.2 123150,123151,123152,123153 2g76A 335 1.17e-11 1v8bA 479 1.34e-11 c.2.1.4,c.23.12.3 113564,113565 1x13A 401 2.12e-11 2d0iA 333 2.15e-11 2pi1A 334 4.25e-11 2gsdA 402 1.04e-10 2fssA 365 1.36e-10 2j6iA 364 1.51e-10 1gdhA 320 1.60e-10 c.2.1.4,c.23.12.1 30095,31355 1hkuA 358 2.82e-10 c.2.1.4,c.23.12.1 83557,83558 2omeA 336 3.14e-10 1mx3A 347 3.34e-10 c.2.1.4,c.23.12.1 79638,79639 2nacA 393 4.23e-10 c.2.1.4,c.23.12.1 30088,31348 2go1A 401 4.23e-10 1dxyA 333 6.92e-10 c.2.1.4,c.23.12.1 30094,31354 1xdwA 331 2.42e-09 2eklA 313 3.13e-09 1j4aA 333 6.65e-09 c.2.1.4,c.23.12.1 71502,71503 1j49A 333 6.69e-09 c.2.1.4,c.23.12.1 71498,71499 1ybaA 410 6.83e-09 c.2.1.4,c.23.12.1,d.58.18.1 122872,122873,122874 1psdA 409 6.84e-09 c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 2p9cA 410 1.02e-08 c.2.1.4,c.23.12.1,d.58.18.1 139556,139557,139558 2p9gA 410 1.03e-08 c.2.1.4,c.23.12.1,d.58.18.1 139574,139575,139576 2fsvA 384 1.10e-08 c.2.1.4,c.23.12.2 134037,134038 1ptjA 381 1.32e-08 c.2.1.4,c.23.12.2 95099,95100 1l7dA 384 1.33e-08 c.2.1.4,c.23.12.2 77774,77775 2frdA 384 1.43e-08 c.2.1.4,c.23.12.2 133980,133981 2fr8A 384 1.45e-08 c.2.1.4,c.23.12.2 133973,133974 1sc6A 404 1.45e-08 c.2.1.4,c.23.12.1,d.58.18.1 118932,118933,118934 1nm5A 384 1.94e-08 c.2.1.4,c.23.12.2 91968,91969 2dldA 337 2.26e-08 c.2.1.4,c.23.12.1 30099,31359 2o4cA 380 1.02e-07 1qp8A 303 5.45e-07 c.2.1.4,c.23.12.1 30092,31352 1uufA 369 1.16e-06 b.35.1.2,c.2.1.1 100006,100007 1yqdA 366 2.85e-06 2cf5A 357 5.81e-06 1piwA 360 8.49e-05 b.35.1.2,c.2.1.1 104156,104157 1hdyA 374 0.000160 b.35.1.2,c.2.1.1 24723,29739 1htbA 374 0.000161 b.35.1.2,c.2.1.1 24715,29731 1u3uA 374 0.000161 b.35.1.2,c.2.1.1 113005,113006 1hdzA 374 0.000164 b.35.1.2,c.2.1.1 24725,29741 1ju9A 374 0.000183 b.35.1.2,c.2.1.1 63293,63294 1n8kA 374 0.000184 b.35.1.2,c.2.1.1 80298,80299 2jhfA 374 0.000184 b.35.1.2,c.2.1.1 138314,138315 1qv6A 374 0.000187 b.35.1.2,c.2.1.1 96348,96349 1qlhA 374 0.000187 b.35.1.2,c.2.1.1 24685,29701 1axeA 374 0.000209 b.35.1.2,c.2.1.1 24681,29697 1mgoA 374 0.000217 b.35.1.2,c.2.1.1 79094,79095 1u3wA 374 0.000253 b.35.1.2,c.2.1.1 113013,113014 1ee2A 373 0.000256 b.35.1.2,c.2.1.1 24663,29679 1axgA 374 0.000269 b.35.1.2,c.2.1.1 24691,29707 3cosA 381 0.000284 1a71A 374 0.000305 b.35.1.2,c.2.1.1 24673,29689 1d1tA 373 0.000311 b.35.1.2,c.2.1.1 24719,29735 1d1sA 373 0.000318 b.35.1.2,c.2.1.1 24727,29743 2fzwA 373 0.000326 b.35.1.2,c.2.1.1 134482,134483 1mc5A 374 0.000354 b.35.1.2,c.2.1.1 84929,84930 2fzeA 373 0.000354 b.35.1.2,c.2.1.1 134433,134434 1u3tA 374 0.000463 b.35.1.2,c.2.1.1 113001,113002 1kolA 398 0.000630 b.35.1.2,c.2.1.1 77474,77475 1cdoA 374 0.001507 b.35.1.2,c.2.1.1 24747,29763 1e3lA 376 0.003749 b.35.1.2,c.2.1.1 24745,29761 1e3iA 376 0.003887 b.35.1.2,c.2.1.1 24741,29757 1rjwA 339 0.004265 b.35.1.2,c.2.1.1 97582,97583 1p0fA 373 0.004727 b.35.1.2,c.2.1.1 87642,87643 1vpdA 299 0.005024 a.100.1.1,c.2.1.6 113951,113952 2dphA 398 0.007136 1gpjA 404 0.008714 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1lluA 342 0.01247 b.35.1.2,c.2.1.1 91064,91065 1e3jA 352 0.02842 b.35.1.2,c.2.1.1 24765,29781 1jvbA 347 0.03782 b.35.1.2,c.2.1.1 77181,77182 2eerA 347 0.03808 2d8aA 348 0.04054 2dfvA 347 0.04055 2i9pA 319 0.04100 1ntoA 347 0.04129 b.35.1.2,c.2.1.1 92137,92138 1vj0A 380 0.05493 b.35.1.2,c.2.1.1 100786,100787 2gf2A 296 0.05795 2nvbA 352 0.06622 1ykfA 352 0.06971 b.35.1.2,c.2.1.1 24757,29773 2hcyA 347 0.07865 1jqbA 351 0.08714 b.35.1.2,c.2.1.1 77151,77152 2b83A 351 0.09916 b.35.1.2,c.2.1.1 128059,128060 2dq4A 343 0.1234 1kevA 351 0.1304 b.35.1.2,c.2.1.1 24749,29765 2vdcG 456 0.1320 2o7sA 523 0.1431 1y9aA 360 0.1874 2cdcA 366 0.2521 2cd9A 366 0.2530 1np3A 338 0.2819 a.100.1.2,c.2.1.6 85946,85947 1bw9B 356 0.2856 c.2.1.7,c.58.1.1 30275,33923 1bxgA 356 0.2856 c.2.1.7,c.58.1.1 30276,33924 1bxgB 356 0.2856 c.2.1.7,c.58.1.1 30277,33925 1c1dB 355 0.2857 c.2.1.7,c.58.1.1 30271,33919 1c1xB 355 0.2857 c.2.1.7,c.58.1.1 30273,33921 1c1dA 355 0.2875 c.2.1.7,c.58.1.1 30270,33918 1bw9A 356 0.2876 c.2.1.7,c.58.1.1 30274,33922 1vl6A 388 0.2877 c.2.1.7,c.58.1.3 108724,108725 1c1xA 355 0.2877 c.2.1.7,c.58.1.1 30272,33920 1pl8A 356 0.2879 b.35.1.2,c.2.1.1 94878,94879 2haeA 386 0.2884 c.2.1.7,c.58.1.3 136278,136279 2ouiA 360 0.3159 2d5cA 263 0.3681 2uyyA 316 0.3961 1nhsA 447 0.4763 c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1v9lA 421 0.4807 c.2.1.7,c.58.1.1 113583,113584 2a9fA 398 0.5795 2hk9A 275 0.6569 2hk8A 269 0.6613 1nhpA 447 0.7323 c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 1nhrA 447 0.7755 c.3.1.5,c.3.1.5,d.87.1.1 30553,30554,40198 1nhqA 447 0.8727 c.3.1.5,c.3.1.5,d.87.1.1 30551,30552,40197 1f8wA 447 0.8866 c.3.1.5,c.3.1.5,d.87.1.1 30561,30562,40202 1npxA 447 0.9042 c.3.1.5,c.3.1.5,d.87.1.1 30557,30558,40200 1yb5A 351 0.9686 b.35.1.2,c.2.1.1 116601,116602 1lsuA 147 0.9888 c.2.1.9 74250 1jayA 212 1.044 c.2.1.6 66478 2vn8A 375 1.057 2hmvA 144 1.113 c.2.1.9 136615 1iz0A 302 1.217 b.35.1.2,c.2.1.1 83821,83822 1luaA 287 1.376 c.2.1.7,c.58.1.4 78216,78217 2belA 283 1.915 c.2.1.2 116694 2at2A 300 1.948 c.78.1.1,c.78.1.1 35196,35197 1o89A 345 2.019 b.35.1.2,c.2.1.1 92644,92645 2r9zA 463 2.212 2pv7A 298 2.375 1nytA 271 2.438 c.2.1.7,c.58.1.5 86417,86418 1bg6A 359 2.450 a.100.1.5,c.2.1.6 18810,30214 2eggA 297 2.626 2cf2D 295 2.681 2dvmA 439 3.023 1xseA 295 3.032 c.2.1.2 115925 2g5cA 281 3.038 a.100.1.12,c.2.1.6 134646,134647 1nvmB 312 3.233 c.2.1.3,d.81.1.1 86251,86252 1zcjA 463 3.445 1nvtA 287 3.499 c.2.1.7,c.58.1.5 86270,86271 2iltA 275 3.537 1ps9A 671 3.595 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1xu9A 286 3.690 c.2.1.2 116052 3c24A 286 3.696 2rbeA 275 4.092 1nr1A 496 4.336 c.2.1.7,c.58.1.1 86080,86081 1l1fA 505 4.348 c.2.1.7,c.58.1.1 73456,73457 1nr7A 496 4.364 c.2.1.7,c.58.1.1 86095,86096 2irwA 264 4.594 c.2.1.2 137593 2g1uA 155 4.684 1c0pA 363 4.741 c.4.1.2,d.16.1.3 30647,37934 1xhlA 297 4.881 c.2.1.2 109591 1b0aA 288 5.056 c.2.1.7,c.58.1.2 30286,33934 1pr9A 244 5.124 c.2.1.2 95060 2d1yA 256 5.145 c.2.1.2 131151 2dpoA 319 5.174 2c2xA 281 5.178 1z82A 335 5.292 1yrlA 491 5.315 1q1rA 431 5.702 c.3.1.5,c.3.1.5,d.87.1.1 95600,95601,95602 2iidA 498 5.834 c.3.1.2,d.16.1.5 137426,137427 2v6bA 304 6.000 2hqmA 479 6.292 1ydeA 270 6.367 c.2.1.2 122980 1o5iA 249 6.905 c.2.1.2 92499 2ignA 623 6.968 c.3.1.2,d.16.1.1 137369,137370 1tt0A 623 7.043 2igmA 623 7.120 3cgbA 480 7.173 1tzlA 622 7.183 c.3.1.2,d.16.1.1 112876,112877 2cf2E 226 7.451 i.26.1.1 130363 1q7cA 244 8.054 c.2.1.2 96030 1q7bA 244 8.104 c.2.1.2 96026 1euzA 419 8.206 c.2.1.7,c.58.1.1 59513,59514 2cvzA 289 8.280 a.100.1.1,c.2.1.6 130890,130891 2bcpA 490 8.637 1npyA 271 8.721 c.2.1.7,c.58.1.5 85995,85996 2ag5A 246 8.944 c.2.1.2 126719 1zfnA 253 8.993 1cf2O 337 9.197 c.2.1.3,d.81.1.1 29994,39909 1zud1 251 9.441 1hwxA 501 9.705 c.2.1.7,c.58.1.1 30250,33898 1pqwA 198 10.69 c.2.1.1 88278 2gqwA 408 10.83 1hyhA 309 10.87 c.2.1.5,d.162.1.1 30150,42117 1y5mA 276 10.90 c.2.1.2 122645 2ekpA 239 11.40 2jfgA 445 11.60 c.5.1.1,c.59.1.1,c.72.2.1 138306,138307,138308 1vl8A 267 11.64 c.2.1.2 108733 4uagA 437 11.72 c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 2f5vA 595 12.21 c.3.1.2,d.16.1.1 133010,133011 2f6cA 595 12.27 c.3.1.2,d.16.1.1 133037,133038 1yvvA 336 12.34 1xg5A 279 12.86 c.2.1.2 115277 1xkqA 280 13.49 c.2.1.2 115417 1f8fA 371 13.66 b.35.1.2,c.2.1.1 83246,83247 2eihA 343 13.76 2h6eA 344 13.98 2gqfA 401 14.12 3cumA 302 14.32 1yb4A 295 14.80 1aupA 449 15.12 c.2.1.7,c.58.1.1 30222,33870 1bgvA 449 15.33 c.2.1.7,c.58.1.1 30217,33865 2czcA 334 15.44 d.81.1.1 131044 2gr3A 408 15.97 2dm6A 333 16.06 b.35.1.2,c.2.1.1 131567,131568 2braA 484 16.10 2eq6A 464 16.13 2nvkX 488 16.33 2et6A 604 16.44 2bryA 497 16.60 1b3bA 415 16.67 c.2.1.7,c.58.1.1 30244,33892 1mv8A 436 16.70 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 2b4qA 276 16.83 1k89A 449 16.87 c.2.1.7,c.58.1.1 30218,33866 1a5zA 319 16.96 c.2.1.5,d.162.1.1 30181,42148 2hkoA 664 17.21 2iw5A 666 17.27 2h94A 664 17.33 2z3yA 662 17.35 2dw4A 660 17.37 2qa1A 500 17.38 1b26A 416 17.64 c.2.1.7,c.58.1.1 30232,33880 1lehA 364 18.45 c.2.1.7,c.58.1.1 30268,33916 1eyzA 392 18.52 b.84.2.1,c.30.1.1,d.142.1.2 28246,31653,41498 2z5lA 511 18.70 1i36A 264 18.90 a.100.1.8,c.2.1.6 71108,71109 1fmcA 255 19.11 c.2.1.2 29856 1kjqA 391 19.42 b.84.2.1,c.30.1.1,d.142.1.2 72616,72617,72618 1reoA 486 19.59 c.3.1.2,d.16.1.5 97325,97326 2v1dA 730 19.73 2tmgA 415 20.34 c.2.1.7,c.58.1.1 30238,33886 2dwcA 433 21.18 2qa2A 499 22.58 2hsdA 253 22.75 c.2.1.2 29866 2jahA 247 23.31 2bgkA 278 23.98 c.2.1.2 128480 1zjyA 251 24.60 c.2.1.2 125163 1hdcA 254 25.18 c.2.1.2 29862 3bioA 304 25.30 1ldnA 316 27.46 c.2.1.5,d.162.1.1 30166,42133 1ldbA 317 27.57 c.2.1.5,d.162.1.1 30174,42141 1qydA 313 28.02 c.2.1.2 96583 1x31A 964 28.34 2pnfA 248 28.60 1x0vA 354 29.73 1b7gO 340 30.47 c.2.1.3,d.81.1.1 29992,39907 1zk7A 467 31.38 1sezA 504 31.52 c.3.1.2,d.16.1.5 98822,98823 2c07A 285 33.66 c.2.1.2 129577 1m75A 302 35.54 a.100.1.3,c.2.1.6 91212,91213 3c85A 183 35.88 1tt7A 330 36.18 b.35.1.2,c.2.1.1 112623,112624 1djqA 729 39.46 c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 2fr1A 486 39.50 c.2.1.2,c.2.1.2 133961,133962 1ae1A 273 39.70 c.2.1.2 29943 2yyyA 343 40.64 1o94A 729 40.75 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 2yquA 455 43.33 1v59A 478 43.57 c.3.1.5,c.3.1.5,d.87.1.1 119838,119839,119840 2qrlA 394 44.95 1hxhA 253 44.97 c.2.1.2 76725 2q99A 381 45.38 1yxmA 303 46.10 c.2.1.2 124192 1kyqA 274 46.21 c.2.1.11,e.37.1.1 73281,73282 1lvlA 458 47.55 c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1bdbA 277 47.63 c.2.1.2 29874 1wpqA 349 47.94 1vj1A 363 48.42 b.35.1.2,c.2.1.1 100794,100795 2ntnA 267 49.25 2fwmX 250 50.29 1w0mA 226 50.92 c.1.1.1 109027 2ywlA 180 51.37 1wlyA 333 52.02 2cduA 452 54.51 1bvuA 418 54.61 c.2.1.7,c.58.1.1 30226,33874 2r2gA 318 55.00 1zejA 293 55.72 3hadA 308 56.73 a.100.1.3,c.2.1.6 18799,30203 1lldA 319 57.06 c.2.1.5,d.162.1.1 30177,42144 2r6jA 318 57.65 1uzmA 247 57.71 c.2.1.2 119811 1npdA 288 57.78 c.2.1.7,c.58.1.5 80681,80682 3hdhA 302 57.94 a.100.1.3,c.2.1.6 18805,30209 1vknA 351 58.05 c.2.1.3,d.81.1.1 108676,108677 1vc2A 331 59.76 c.2.1.3,d.81.1.1 100555,100556 2hjrA 328 60.58 1qycA 308 61.25 c.2.1.2 96581 2axqA 467 61.39 1a4iA 301 61.77 c.2.1.7,c.58.1.2 30278,33926 1digA 306 62.07 c.2.1.7,c.58.1.2 30282,33930 2gagA 965 62.74 2q2vA 255 62.77 2ew8A 249 62.90 c.2.1.2 132447 2q1sA 377 63.02 1jw9B 249 63.22 c.111.1.1 67377 1lsjA 302 64.53 a.100.1.3,c.2.1.6 91116,91117 1pgjA 478 65.38 a.100.1.1,c.2.1.6 18783,30195 1zk4A 251 65.43 c.2.1.2 125176 1f0yA 302 65.47 a.100.1.3,c.2.1.6 18793,30197 1f17A 310 65.51 a.100.1.3,c.2.1.6 18797,30201 1m76A 302 65.56 a.100.1.3,c.2.1.6 91216,91217 1lsoA 302 65.59 a.100.1.3,c.2.1.6 91120,91121 1d4dA 572 66.65 a.138.1.3,c.3.1.4,d.168.1.1 19702,30439,42322 1il0A 302 67.11 a.100.1.3,c.2.1.6 66189,66190 1d4cA 572 67.12 a.138.1.3,c.3.1.4,d.168.1.1 19698,30435,42318 2jaeA 489 67.13 2gdzA 267 67.54 c.2.1.2 135043 2v7pA 310 67.91 2bc0A 490 67.96 1vi2A 300 68.98 c.2.1.7,c.58.1.5 100726,100727 1zsvA 349 69.96 1cydA 244 70.48 c.2.1.2 29825 1y7pA 223 71.92 c.23.1.7,d.58.18.12 122708,122709 2rafA 209 72.19 2hdhA 293 72.98 a.100.1.3,c.2.1.6 18795,30199 1uzlA 247 73.00 c.2.1.2 119809 1k2wA 256 73.40 c.2.1.2 90927 1mxhA 276 74.09 c.2.1.2 91490 2i0zA 447 75.06 2g82A 331 75.12 c.2.1.3,d.81.1.1 134746,134747 1hyuA 521 76.56 c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 2ehdA 234 76.67 2nm0A 253 79.41 1ybvA 283 81.66 c.2.1.2 29948 2exxA 306 81.74 1g0oA 283 82.41 c.2.1.2 60181 1uayA 242 84.93 c.2.1.2 88390 1w4xA 542 87.27 c.3.1.5,c.3.1.5 109171,109172 1mg5A 255 88.57 c.2.1.2 91264 2nloA 302 89.98