# List of top-scoring protein chains for 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.soe.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 2eezA 369 6.55e-39 1pjcA 361 9.35e-37 1sayA c.2.1.4 30101 c.23.12.2 31361 1sayA 361 9.35e-37 1sayA c.2.1.4 30102 c.23.12.2 31362 2vojA 371 1.05e-36 2vhxA 377 1.05e-36 2vhvA 377 1.40e-36 2rirA 300 1.82e-34 1li4A 432 9.74e-33 c.2.1.4 84616 c.23.12.3 84617 1a7aA 432 1.17e-32 1b3rA c.2.1.4 30104 c.23.12.3 31364 1x13A 401 1.41e-32 1b3rA 431 2.37e-32 1b3rA c.2.1.4 30106 c.23.12.3 31366 1d4fA 431 4.12e-32 1b3rA c.2.1.4 30110 c.23.12.3 31370 1xwfA 431 6.28e-32 c.2.1.4 122392 c.23.12.3 122393 2dbqA 334 5.34e-31 2fsvA 384 3.03e-28 c.2.1.4 134037 c.23.12.2 134038 1v8bA 479 3.30e-28 c.2.1.4 113564 c.23.12.3 113565 1ptjA 381 4.01e-28 c.2.1.4 95099 c.23.12.2 95100 1l7dA 384 4.05e-28 c.2.1.4 77774 c.23.12.2 77775 2frdA 384 4.33e-28 c.2.1.4 133980 c.23.12.2 133981 2fr8A 384 4.91e-28 c.2.1.4 133973 c.23.12.2 133974 1wwkA 307 6.75e-28 1nm5A 384 8.05e-28 c.2.1.4 91968 c.23.12.2 91969 2q50A 328 3.00e-27 2gcgA 330 3.00e-27 2cukA 311 9.31e-26 1ygyA 529 2.18e-25 c.2.1.4 123150 c.23.12.1 123151 d.58.18.1 123152 d.81.2.2 123153 2pi1A 334 2.72e-24 2g76A 335 1.83e-23 2d0iA 333 5.31e-23 1gdhA 320 1.50e-22 1gdhA c.2.1.4 30095 c.23.12.1 31355 1xdwA 331 3.19e-22 1dxyA 333 4.47e-22 c.2.1.4 30094 c.23.12.1 31354 1hkuA 358 1.74e-21 c.2.1.4 83557 c.23.12.1 83558 1mx3A 347 1.95e-21 c.2.1.4 79638 c.23.12.1 79639 2omeA 336 3.65e-21 1j49A 333 2.83e-20 c.2.1.4 71498 c.23.12.1 71499 1j4aA 333 2.88e-20 c.2.1.4 71502 c.23.12.1 71503 2j6iA 364 3.54e-20 2fssA 365 4.05e-20 1psdA 409 1.23e-19 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1ybaA 410 1.23e-19 c.2.1.4 122872 c.23.12.1 122873 d.58.18.1 122874 2p9gA 410 1.81e-19 c.2.1.4 139574 c.23.12.1 139575 d.58.18.1 139576 2p9cA 410 1.81e-19 c.2.1.4 139556 c.23.12.1 139557 d.58.18.1 139558 1qp8A 303 2.65e-19 1qp8A c.2.1.4 30092 c.23.12.1 31352 1sc6A 404 3.17e-19 c.2.1.4 118932 c.23.12.1 118933 d.58.18.1 118934 2dldA 337 3.39e-19 1dxy c.2.1.4 30099 c.23.12.1 31359 2eklA 313 6.98e-19 2gsdA 402 6.69e-18 2nacA 393 2.98e-17 2nadA c.2.1.4 30088 c.23.12.1 31348 2nadA 393 2.98e-17 2nadA c.2.1.4 30090 c.23.12.1 31350 2go1A 401 2.99e-17 2o4cA 380 1.03e-14 1yqdA 366 4.31e-10 2cf5A 357 9.27e-09 1uufA 369 1.15e-08 b.35.1.2 100006 c.2.1.1 100007 1piwA 360 4.93e-08 b.35.1.2 104156 c.2.1.1 104157 1vpdA 299 8.44e-08 a.100.1.1 113951 c.2.1.6 113952 1kolA 398 4.23e-07 b.35.1.2 77474 c.2.1.1 77475 1u3wA 374 6.67e-07 b.35.1.2 113013 c.2.1.1 113014 1d1tA 373 7.42e-07 2ohxA b.35.1.2 24719 c.2.1.1 29735 2haeA 386 8.26e-07 c.2.1.7 136278 c.58.1.3 136279 1vl6A 388 8.27e-07 c.2.1.7 108724 c.58.1.3 108725 2fzeA 373 8.27e-07 b.35.1.2 134433 c.2.1.1 134434 1mc5A 374 8.27e-07 b.35.1.2 84929 c.2.1.1 84930 1d1sA 373 9.66e-07 2ohxA b.35.1.2 24727 c.2.1.1 29743 2fzwA 373 1.23e-06 b.35.1.2 134482 c.2.1.1 134483 1u3uA 374 1.38e-06 b.35.1.2 113005 c.2.1.1 113006 1htbA 374 1.38e-06 2ohxA b.35.1.2 24715 c.2.1.1 29731 1hdyA 374 1.38e-06 2ohxA b.35.1.2 24723 c.2.1.1 29739 1hdzA 374 1.40e-06 2ohxA b.35.1.2 24725 c.2.1.1 29741 1u3tA 374 1.41e-06 b.35.1.2 113001 c.2.1.1 113002 1gpjA 404 1.64e-06 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 2dphA 398 1.69e-06 1vj0A 380 1.93e-06 b.35.1.2 100786 c.2.1.1 100787 3cosA 381 2.57e-06 1e3jA 352 3.07e-06 1e3jA b.35.1.2 24765 c.2.1.1 29781 1rjwA 339 3.09e-06 b.35.1.2 97582 c.2.1.1 97583 2a9fA 398 3.77e-06 2vdcG 456 5.38e-06 1ju9A 374 5.79e-06 b.35.1.2 63293 c.2.1.1 63294 1qv6A 374 5.81e-06 b.35.1.2 96348 c.2.1.1 96349 1n8kA 374 5.95e-06 b.35.1.2 80298 c.2.1.1 80299 1mgoA 374 5.98e-06 b.35.1.2 79094 c.2.1.1 79095 1axeA 374 6.04e-06 2ohxA b.35.1.2 24681 c.2.1.1 29697 2jhfA 374 6.05e-06 b.35.1.2 138314 c.2.1.1 138315 2ohxA 374 6.05e-06 2ohxA b.35.1.2 24669 c.2.1.1 29685 1qlhA 374 6.99e-06 2ohxA b.35.1.2 24685 c.2.1.1 29701 1cdoA 374 7.55e-06 2ohxA b.35.1.2 24747 c.2.1.1 29763 2hcyA 347 9.32e-06 1ee2A 373 1.02e-05 2ohxA b.35.1.2 24663 c.2.1.1 29679 1euzA 419 1.06e-05 1k89 c.2.1.7 59513 c.58.1.1 59514 2i9pA 319 1.12e-05 1a71A 374 1.37e-05 2ohxA b.35.1.2 24673 c.2.1.1 29689 1axgA 374 1.38e-05 2ohxA b.35.1.2 24691 c.2.1.1 29707 1v9lA 421 1.54e-05 c.2.1.7 113583 c.58.1.1 113584 2d5cA 263 1.72e-05 1c1dA 355 1.92e-05 1bw9A c.2.1.7 30270 c.58.1.1 33918 1bxgB 356 1.92e-05 1bw9A c.2.1.7 30277 c.58.1.1 33925 1bxgA 356 1.92e-05 1bw9A c.2.1.7 30276 c.58.1.1 33924 1c1xB 355 1.92e-05 1bw9A c.2.1.7 30273 c.58.1.1 33921 1bw9B 356 1.92e-05 1bw9A c.2.1.7 30275 c.58.1.1 33923 1c1xA 355 1.92e-05 1bw9A c.2.1.7 30272 c.58.1.1 33920 1c1dB 355 1.92e-05 1bw9A c.2.1.7 30271 c.58.1.1 33919 1bw9A 356 1.92e-05 1bw9A c.2.1.7 30274 c.58.1.1 33922 2o7sA 523 1.93e-05 2gptA 523 1.93e-05 2uyyA 316 1.98e-05 2gf2A 296 2.84e-05 1lluA 342 4.36e-05 b.35.1.2 91064 c.2.1.1 91065 2q99A 381 4.81e-05 2qrlA 394 4.83e-05 2r9zA 463 5.26e-05 1e3iA 376 5.40e-05 2ohxA b.35.1.2 24741 c.2.1.1 29757 1e3lA 376 5.42e-05 2ohxA b.35.1.2 24745 c.2.1.1 29761 1f8wA 447 8.10e-05 1nhp c.3.1.5 30561 c.3.1.5 30562 d.87.1.1 40202 1luaA 287 8.94e-05 c.2.1.7 78216 c.58.1.4 78217 1nhsA 447 8.98e-05 c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1nhrA 447 9.08e-05 c.3.1.5 30553 c.3.1.5 30554 d.87.1.1 40198 1npxA 447 9.40e-05 c.3.1.5 30557 c.3.1.5 30558 d.87.1.1 40200 2dvmA 439 9.55e-05 1nhqA 447 9.86e-05 c.3.1.5 30551 c.3.1.5 30552 d.87.1.1 40197 1p0fA 373 1.03e-04 b.35.1.2 87642 c.2.1.1 87643 1nhpA 447 1.08e-04 c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 2dfvA 347 1.11e-04 2d8aA 348 1.11e-04 1pl8A 356 1.18e-04 b.35.1.2 94878 c.2.1.1 94879 2belA 283 1.44e-04 c.2.1.2 116694 2eerA 347 1.94e-04 2dq4A 343 3.11e-04 1bvuA 418 3.24e-04 1hwyA c.2.1.7 30226 c.58.1.1 33874 1lsuA 147 3.24e-04 c.2.1.9 74250 1ydeA 270 3.64e-04 c.2.1.2 122980 2hqmA 479 3.64e-04 1ihxA 333 3.85e-04 c.2.1.3 71211 d.81.1.1 71212 2hmvA 144 3.95e-04 c.2.1.9 136615 2gqwA 408 4.58e-04 1d7yA 408 4.58e-04 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1nr1A 496 4.66e-04 c.2.1.7 86080 c.58.1.1 86081 1xu9A 286 5.15e-04 c.2.1.2 116052 1l1fA 505 5.17e-04 c.2.1.7 73456 c.58.1.1 73457 1nr7A 496 5.19e-04 c.2.1.7 86095 c.58.1.1 86096 2iltA 275 5.48e-04 1y9aA 360 5.64e-04 1xseA 295 6.20e-04 c.2.1.2 115925 1gtmA 419 6.53e-04 1hwyA c.2.1.7 30223 c.58.1.1 33871 1dssG 333 6.57e-04 1dssG c.2.1.3 30022 d.81.1.1 39937 1crwG 333 6.63e-04 1dssG c.2.1.3 30026 d.81.1.1 39941 2gr3A 408 6.95e-04 3cgbA 480 7.24e-04 2nvkX 488 7.27e-04 1ntoA 347 8.26e-04 b.35.1.2 92137 c.2.1.1 92138 2rbeA 275 8.59e-04 1jvbA 347 8.60e-04 b.35.1.2 77181 c.2.1.1 77182 2nvbA 352 8.73e-04 1q1rA 431 9.00e-04 c.3.1.5 95600 c.3.1.5 95601 d.87.1.1 95602 2ouiA 360 9.63e-04 2hk8A 269 9.76e-04 2hk9A 275 9.80e-04 1ykfA 352 9.94e-04 1pedA b.35.1.2 24757 c.2.1.1 29773 1lehA 364 1.07e-03 1bw9A c.2.1.7 30268 c.58.1.1 33916 2irwA 264 1.13e-03 c.2.1.2 137593 2z5lA 511 1.33e-03 4gpd1 333 1.47e-03 1dssG 1np3A 338 1.63e-03 a.100.1.2 85946 c.2.1.6 85947 1pr9A 244 1.89e-03 c.2.1.2 95060 2tmgA 415 1.96e-03 1hwyA c.2.1.7 30238 c.58.1.1 33886 1zcjA 463 1.99e-03 1b3bA 415 2.13e-03 1hwyA c.2.1.7 30244 c.58.1.1 33892 1b26A 416 2.14e-03 1hwyA c.2.1.7 30232 c.58.1.1 33880 2iidA 498 2.18e-03 c.3.1.2 137426 d.16.1.5 137427 1f8rA 498 2.18e-03 1f8rA c.3.1.2 30410 d.16.1.5 37974 2g1uA 155 2.26e-03 2eq6A 464 2.36e-03 1o89A 345 3.02e-03 b.35.1.2 92644 c.2.1.1 92645 1hwxA 501 3.13e-03 1hwyA c.2.1.7 30250 c.58.1.1 33898 1hwyA 501 3.13e-03 1hwyA c.2.1.7 30262 c.58.1.1 33910 1jqbA 351 3.16e-03 b.35.1.2 77151 c.2.1.1 77152 2cvzA 289 3.22e-03 a.100.1.1 130890 c.2.1.6 130891 2bcpA 490 3.22e-03 1k89A 449 3.27e-03 c.2.1.7 30218 c.58.1.1 33866 1iz0A 302 3.30e-03 b.35.1.2 83821 c.2.1.1 83822 1aupA 449 3.33e-03 c.2.1.7 30222 c.58.1.1 33870 1yb5A 351 3.49e-03 b.35.1.2 116601 c.2.1.1 116602 1kevA 351 3.60e-03 1pedA b.35.1.2 24749 c.2.1.1 29765 1pedA 351 3.60e-03 1pedA b.35.1.2 24753 c.2.1.1 29769 1bgvA 449 3.66e-03 1k89 c.2.1.7 30217 c.58.1.1 33865 1hrdA 449 3.66e-03 1k89 c.2.1.7 30219 c.58.1.1 33867 2ekpA 239 3.78e-03 1x1eA 239 3.78e-03 2b83A 351 3.87e-03 b.35.1.2 128059 c.2.1.1 128060 2vn8A 375 3.90e-03 1c0pA 363 5.54e-03 1an9A c.4.1.2 30647 d.16.1.3 37934 1jayA 212 5.56e-03 c.2.1.6 66478 2d1yA 256 5.68e-03 c.2.1.2 131151 1x31A 964 5.93e-03 2gqfA 401 6.05e-03 2bc0A 490 6.13e-03 2jfgA 445 6.16e-03 c.5.1.1 138306 c.59.1.1 138307 c.72.2.1 138308 4uagA 437 6.32e-03 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 2dpoA 319 7.46e-03 1zfnA 253 7.79e-03 2qa1A 500 8.65e-03 1zud1 251 8.83e-03 1pqwA 198 8.92e-03 c.2.1.1 88278 2cf2D 295 8.95e-03 3hdhA 302 9.31e-03 2hdhA a.100.1.3 18805 c.2.1.6 30209 1m75A 302 9.34e-03 a.100.1.3 91212 c.2.1.6 91213 1lvlA 458 9.41e-03 c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1reoA 486 9.77e-03 c.3.1.2 97325 d.16.1.5 97326 1yb4A 295 9.85e-03 1f0yA 302 1.10e-02 2hdhA a.100.1.3 18793 c.2.1.6 30197 1il0A 302 1.10e-02 a.100.1.3 66189 c.2.1.6 66190 1m76A 302 1.11e-02 a.100.1.3 91216 c.2.1.6 91217 1lsoA 302 1.11e-02 a.100.1.3 91120 c.2.1.6 91121 1f17A 310 1.13e-02 2hdhA a.100.1.3 18797 c.2.1.6 30201 2bgkA 278 1.13e-02 c.2.1.2 128480 1nytA 271 1.14e-02 c.2.1.7 86417 c.58.1.5 86418 1y5mA 276 1.14e-02 c.2.1.2 122645 2bryA 497 1.25e-02 2braA 484 1.26e-02 1lsjA 302 1.34e-02 a.100.1.3 91116 c.2.1.6 91117 2cdcA 366 1.37e-02 2cd9A 366 1.39e-02 3hadA 308 1.43e-02 2hdhA a.100.1.3 18799 c.2.1.6 30203 1eyzA 392 1.63e-02 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1ez1A 392 1.63e-02 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1xkqA 280 1.65e-02 c.2.1.2 115417 1mv8A 436 1.66e-02 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1tt0A 623 1.69e-02 1tzlA 622 1.70e-02 c.3.1.2 112876 d.16.1.1 112877 2igmA 623 1.71e-02 1yvvA 336 1.72e-02 2ignA 623 1.72e-02 c.3.1.2 137369 d.16.1.1 137370 2eggA 297 1.73e-02 2dwcA 433 1.73e-02 1kjqA 391 1.76e-02 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 2hdhA 293 1.85e-02 2hdhA a.100.1.3 18795 c.2.1.6 30199 3c85A 183 2.14e-02 1bdbA 277 2.19e-02 c.2.1.2 29874 2v6bA 304 2.22e-02 1xhlA 297 2.40e-02 c.2.1.2 109591 3ladA 476 2.48e-02 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 2g82A 331 2.49e-02 c.2.1.3 134746 d.81.1.1 134747 1sezA 504 2.52e-02 c.3.1.2 98822 d.16.1.5 98823 1a4iA 301 2.61e-02 1a4iA c.2.1.7 30278 c.58.1.2 33926 1digA 306 2.64e-02 1a4iA c.2.1.7 30282 c.58.1.2 33930 1d4dA 572 2.94e-02 1qjdA a.138.1.3 19702 c.3.1.4 30439 d.168.1.1 42322 2f6cA 595 3.23e-02 c.3.1.2 133037 d.16.1.1 133038 2f5vA 595 3.25e-02 c.3.1.2 133010 d.16.1.1 133011 1yxmA 303 3.28e-02 c.2.1.2 124192 2c2xA 281 3.31e-02 1bg6A 359 3.48e-02 a.100.1.5 18810 c.2.1.6 30214 1v59A 478 3.72e-02 c.3.1.5 119838 c.3.1.5 119839 d.87.1.1 119840 2jaeA 489 3.73e-02 1ae1A 273 3.91e-02 1bdb c.2.1.2 29943 2gagA 965 3.92e-02 1ps9A 671 3.96e-02 c.1.4.1 95076 c.3.1.1 95077 c.4.1.1 95078 1lssA 140 4.07e-02 c.2.1.9 74246 2yquA 455 4.13e-02 1d4cA 572 4.16e-02 1qjdA a.138.1.3 19698 c.3.1.4 30435 d.168.1.1 42318 2pv7A 298 4.32e-02 1h2bA 359 4.60e-02 b.35.1.2 90543 c.2.1.1 90544 2et6A 604 4.65e-02 2g5cA 281 4.69e-02 a.100.1.12 134646 c.2.1.6 134647 1fmcA 255 4.71e-02 1cydA c.2.1.2 29856 1lpfA 477 5.03e-02 1lvl c.3.1.5 30569 c.3.1.5 30570 d.87.1.1 40206 2qa2A 499 5.38e-02 2fwmX 250 5.79e-02 2v1dA 730 5.94e-02 1zjyA 251 5.96e-02 c.2.1.2 125163 1vc2A 331 6.33e-02 c.2.1.3 100555 d.81.1.1 100556 2iw5A 666 6.52e-02 2dw4A 660 6.61e-02 2hkoA 664 6.61e-02 2h94A 664 6.61e-02 2z3yA 662 6.61e-02 1i36A 264 6.75e-02 a.100.1.8 71108 c.2.1.6 71109 1o5iA 249 6.81e-02 c.2.1.2 92499 1nvtA 287 7.25e-02 c.2.1.7 86270 c.58.1.5 86271 1hxhA 253 7.35e-02 c.2.1.2 76725 1g0oA 283 7.54e-02 1ybvA c.2.1.2 60181 1ybvA 283 7.59e-02 1ybvA c.2.1.2 29948 3c24A 286 7.84e-02 1zk7A 467 7.93e-02 2fr1A 486 8.34e-02 c.2.1.2 133961 c.2.1.2 133962 2cf2E 226 8.62e-02 i.26.1.1 130363 1fl2A 310 8.83e-02 1hyuA c.3.1.5 59869 c.3.1.5 59870 2c72A 520 8.84e-02 c.3.1.2 130018 d.16.1.5 130019 2ag5A 246 8.86e-02 c.2.1.2 126719 2c76A 520 8.86e-02 c.3.1.2 130030 d.16.1.5 130031 2c75A 520 8.87e-02 c.3.1.2 130026 d.16.1.5 130027 2bk5A 520 8.87e-02 c.3.1.2 128656 d.16.1.5 128657 2c73A 520 8.91e-02 c.3.1.2 130022 d.16.1.5 130023 1s3eA 520 8.93e-02 c.3.1.2 98426 d.16.1.5 98427 1q7cA 244 9.36e-02 c.2.1.2 96030 1q7bA 244 9.38e-02 c.2.1.2 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