# List of top-scoring protein chains for t2k.100-30-stride-ebghtl 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 2vojA 371 7.28e-32 2vhxA 377 1.50e-31 1sayA 361 2.80e-31 1sayA c.2.1.4 30102 c.23.12.2 31362 1pjcA 361 3.48e-31 1sayA c.2.1.4 30101 c.23.12.2 31361 1x13A 401 6.75e-29 2dbqA 334 1.95e-26 1li4A 432 4.59e-26 c.2.1.4 84616 c.23.12.3 84617 1a7aA 432 6.03e-26 1b3rA c.2.1.4 30104 c.23.12.3 31364 1b3rA 431 8.27e-26 1b3rA c.2.1.4 30106 c.23.12.3 31366 1xwfA 431 1.51e-25 c.2.1.4 122392 c.23.12.3 122393 1d4fA 431 2.84e-25 1b3rA c.2.1.4 30110 c.23.12.3 31370 1wwkA 307 1.26e-24 1l7dA 384 1.81e-24 c.2.1.4 77774 c.23.12.2 77775 2gcgA 330 5.74e-24 1v8bA 479 2.03e-23 c.2.1.4 113564 c.23.12.3 113565 2cukA 311 1.16e-22 1ygyA 529 2.51e-22 c.2.1.4 123150 c.23.12.1 123151 d.58.18.1 123152 d.81.2.2 123153 2g76A 335 9.67e-22 2pi1A 334 5.16e-21 1gdhA 320 1.07e-20 1gdhA c.2.1.4 30095 c.23.12.1 31355 2d0iA 333 1.72e-20 1mx3A 347 2.55e-20 c.2.1.4 79638 c.23.12.1 79639 1dxy 333 4.63e-20 1dxy 1dxyA 333 4.63e-20 c.2.1.4 30094 c.23.12.1 31354 1xdwA 331 4.59e-19 2eklA 313 7.10e-19 2j6iA 364 9.21e-19 2fssA 365 1.03e-18 1j4aA 333 2.14e-18 c.2.1.4 71502 c.23.12.1 71503 1psdA 409 6.48e-18 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1sc6A 404 1.69e-17 c.2.1.4 118932 c.23.12.1 118933 d.58.18.1 118934 2dldA 337 1.76e-17 1dxy c.2.1.4 30099 c.23.12.1 31359 2nadA 393 3.76e-17 2nadA c.2.1.4 30090 c.23.12.1 31350 2nacA 393 4.41e-17 2nadA c.2.1.4 30088 c.23.12.1 31348 1qp8A 303 5.73e-17 1qp8A c.2.1.4 30092 c.23.12.1 31352 2o4cA 380 1.69e-14 1yqdA 366 5.25e-10 1uufA 369 2.57e-09 b.35.1.2 100006 c.2.1.1 100007 2cf5A 357 1.01e-08 1bw9A 356 1.15e-08 1bw9A c.2.1.7 30274 c.58.1.1 33922 1vl6A 388 1.90e-08 c.2.1.7 108724 c.58.1.3 108725 1gpjA 404 4.27e-08 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1c1dA 355 4.60e-08 1bw9A c.2.1.7 30270 c.58.1.1 33918 1vpdA 299 1.12e-07 a.100.1.1 113951 c.2.1.6 113952 1u3wA 374 1.41e-07 b.35.1.2 113013 c.2.1.1 113014 1e3jA 352 2.09e-07 1e3jA b.35.1.2 24765 c.2.1.1 29781 2dvmA 439 3.11e-07 1kolA 398 4.92e-07 b.35.1.2 77474 c.2.1.1 77475 2d5cA 263 5.25e-07 2jhfA 374 5.57e-07 b.35.1.2 138314 c.2.1.1 138315 1axeA 374 7.13e-07 2ohxA b.35.1.2 24681 c.2.1.1 29697 2ohxA 374 7.44e-07 2ohxA b.35.1.2 24669 c.2.1.1 29685 2a9fA 398 7.91e-07 1ee2A 373 8.65e-07 2ohxA b.35.1.2 24663 c.2.1.1 29679 1pl8A 356 8.88e-07 b.35.1.2 94878 c.2.1.1 94879 1n8kA 374 1.01e-06 b.35.1.2 80298 c.2.1.1 80299 1vj0A 380 1.43e-06 b.35.1.2 100786 c.2.1.1 100787 1axgA 374 1.54e-06 2ohxA b.35.1.2 24691 c.2.1.1 29707 1a71A 374 1.65e-06 2ohxA b.35.1.2 24673 c.2.1.1 29689 2gptA 523 1.81e-06 2o7sA 523 1.94e-06 1lluA 342 2.79e-06 b.35.1.2 91064 c.2.1.1 91065 1p0fA 373 7.27e-06 b.35.1.2 87642 c.2.1.1 87643 2hcyA 347 8.41e-06 1yb5A 351 8.56e-06 b.35.1.2 116601 c.2.1.1 116602 2qrlA 394 9.34e-06 1luaA 287 1.54e-05 c.2.1.7 78216 c.58.1.4 78217 2hk9A 275 1.59e-05 2eggA 297 2.36e-05 1h2bA 359 2.55e-05 b.35.1.2 90543 c.2.1.1 90544 2g5cA 281 2.70e-05 a.100.1.12 134646 c.2.1.6 134647 1lehA 364 2.71e-05 1bw9A c.2.1.7 30268 c.58.1.1 33916 1hwxA 501 3.75e-05 1hwyA c.2.1.7 30250 c.58.1.1 33898 2f1kA 279 4.10e-05 a.100.1.12 132772 c.2.1.6 132773 1hwyA 501 4.22e-05 1hwyA c.2.1.7 30262 c.58.1.1 33910 2cvzA 289 5.24e-05 a.100.1.1 130890 c.2.1.6 130891 1zcjA 463 5.40e-05 1gtmA 419 5.50e-05 1hwyA c.2.1.7 30223 c.58.1.1 33871 2d8aA 348 5.57e-05 1crwG 333 6.55e-05 1dssG c.2.1.3 30026 d.81.1.1 39941 2r9zA 463 6.60e-05 1nytA 271 6.78e-05 c.2.1.7 86417 c.58.1.5 86418 1bgvA 449 1.02e-04 1k89 c.2.1.7 30217 c.58.1.1 33865 1hrdA 449 1.03e-04 1k89 c.2.1.7 30219 c.58.1.1 33867 1dssG 333 1.21e-04 1dssG c.2.1.3 30022 d.81.1.1 39937 2d1yA 256 1.27e-04 c.2.1.2 131151 1b0aA 288 1.30e-04 1a4iA c.2.1.7 30286 c.58.1.2 33934 1nhsA 447 1.50e-04 c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1o89A 345 1.85e-04 b.35.1.2 92644 c.2.1.1 92645 1nhp 447 1.93e-04 1nhp 1nhpA 447 1.93e-04 c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 2ouiA 360 2.11e-04 1lsuA 147 2.13e-04 c.2.1.9 74250 2g1uA 155 2.30e-04 1k89 449 2.31e-04 1k89 1ykfA 352 2.42e-04 1pedA b.35.1.2 24757 c.2.1.1 29773 1y9aA 360 2.60e-04 1f8rA 498 2.61e-04 1f8rA c.3.1.2 30410 d.16.1.5 37974 2iidA 498 2.61e-04 c.3.1.2 137426 d.16.1.5 137427 1mv8A 436 2.65e-04 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1np3A 338 3.08e-04 a.100.1.2 85946 c.2.1.6 85947 1iz0A 302 3.13e-04 b.35.1.2 83821 c.2.1.1 83822 1c0pA 363 3.64e-04 1an9A c.4.1.2 30647 d.16.1.3 37934 2cdcA 366 3.64e-04 2hmvA 144 3.79e-04 c.2.1.9 136615 1reoA 486 4.25e-04 c.3.1.2 97325 d.16.1.5 97326 1d7yA 408 4.92e-04 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1b26A 416 5.14e-04 1hwyA c.2.1.7 30232 c.58.1.1 33880 1kevA 351 5.15e-04 1pedA b.35.1.2 24749 c.2.1.1 29765 2gqwA 408 5.23e-04 1ydeA 270 5.68e-04 c.2.1.2 122980 1xhlA 297 5.77e-04 c.2.1.2 109591 1x1eA 239 6.19e-04 3c24A 286 6.61e-04 1pedA 351 7.94e-04 1pedA b.35.1.2 24753 c.2.1.1 29769 1z82A 335 8.19e-04 1b3bA 415 8.27e-04 1hwyA c.2.1.7 30244 c.58.1.1 33892 2dwcA 433 8.36e-04 1q1rA 431 8.47e-04 c.3.1.5 95600 c.3.1.5 95601 d.87.1.1 95602 2ekpA 239 8.63e-04 1xseA 295 8.69e-04 c.2.1.2 115925 3c85A 183 9.38e-04 1jqbA 351 9.69e-04 b.35.1.2 77151 c.2.1.1 77152 2g82A 331 9.79e-04 c.2.1.3 134746 d.81.1.1 134747 2z3yA 662 1.00e-03 1p77A 272 1.01e-03 c.2.1.7 94214 c.58.1.5 94215 1f0yA 302 1.02e-03 2hdhA a.100.1.3 18793 c.2.1.6 30197 2dpoA 319 1.04e-03 2bgkA 278 1.04e-03 c.2.1.2 128480 1o5iA 249 1.05e-03 c.2.1.2 92499 1bg6 359 1.07e-03 1bg6 1bg6A 359 1.07e-03 a.100.1.5 18810 c.2.1.6 30214 2o8nA 265 1.23e-03 2hdhA 293 1.26e-03 2hdhA a.100.1.3 18795 c.2.1.6 30199 2jfgA 445 1.26e-03 c.5.1.1 138306 c.59.1.1 138307 c.72.2.1 138308 1xu9A 286 1.42e-03 c.2.1.2 116052 4uagA 437 1.64e-03 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 2czcA 334 1.75e-03 d.81.1.1 131044 1jayA 212 1.84e-03 c.2.1.6 66478 1cydA 244 1.85e-03 1cydA c.2.1.2 29825 1nvtA 287 1.90e-03 c.2.1.7 86270 c.58.1.5 86271 1f8fA 371 1.92e-03 b.35.1.2 83246 c.2.1.1 83247 1bdb 277 1.95e-03 1bdb 1npyA 271 1.99e-03 c.2.1.7 85995 c.58.1.5 85996 2bmaA 470 2.32e-03 1ae1A 273 2.41e-03 1bdb c.2.1.2 29943 2gagA 965 2.44e-03 1a4iA 301 2.46e-03 1a4iA c.2.1.7 30278 c.58.1.2 33926 2eihA 343 2.55e-03 2eq6A 464 2.58e-03 1yvvA 336 2.64e-03 2pv7A 298 2.76e-03 2jaeA 489 2.90e-03 2yyyA 343 3.13e-03 1tt7A 330 3.24e-03 b.35.1.2 112623 c.2.1.1 112624 1jvbA 347 3.29e-03 b.35.1.2 77181 c.2.1.1 77182 1nvmB 312 3.32e-03 c.2.1.3 86251 d.81.1.1 86252 2h6eA 344 3.85e-03 1vl8A 267 3.90e-03 c.2.1.2 108733 1pjqA 457 4.00e-03 c.2.1.11 94766 c.90.1.1 94767 e.37.1.1 94768 1tzlA 622 4.07e-03 c.3.1.2 112876 d.16.1.1 112877 1y5mA 276 4.14e-03 c.2.1.2 122645 1lssA 140 4.16e-03 c.2.1.9 74246 1xkqA 280 4.97e-03 c.2.1.2 115417 1ldnA 316 5.23e-03 1hyhA c.2.1.5 30166 d.162.1.1 42133 2a4kA 263 5.60e-03 c.2.1.2 126156 1tt0A 623 5.65e-03 1qo8A 566 5.66e-03 1qjdA a.138.1.3 19696 c.3.1.4 30433 d.168.1.1 42316 2e57A 637 5.67e-03 1zejA 293 5.70e-03 1vi2A 300 6.57e-03 c.2.1.7 100726 c.58.1.5 100727 1y56B 382 7.05e-03 2f5vA 595 7.19e-03 c.3.1.2 133010 d.16.1.1 133011 2dm6A 333 7.22e-03 b.35.1.2 131567 c.2.1.1 131568 1npdA 288 7.51e-03 c.2.1.7 80681 c.58.1.5 80682 1hyhA 309 7.84e-03 1hyhA c.2.1.5 30150 d.162.1.1 42117 1fmcA 255 7.98e-03 1cydA c.2.1.2 29856 3cggA 195 7.99e-03 1hxhA 253 8.10e-03 c.2.1.2 76725 1eyzA 392 8.17e-03 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1wlyA 333 8.21e-03 1xg5A 279 8.26e-03 c.2.1.2 115277 1ez1A 392 8.31e-03 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1kjqA 391 8.54e-03 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1gesA 450 8.54e-03 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1i36A 264 8.54e-03 a.100.1.8 71108 c.2.1.6 71109 1xa0A 328 8.62e-03 b.35.1.2 115021 c.2.1.1 115022 1s3eA 520 8.97e-03 c.3.1.2 98426 d.16.1.5 98427 3bioA 304 9.86e-03 1zud1 251 9.99e-03 1w0mA 226 1.03e-02 c.1.1.1 109027 1yb4A 295 1.04e-02 1kyqA 274 1.14e-02 c.2.1.11 73281 e.37.1.1 73282 2fr1A 486 1.15e-02 c.2.1.2 133961 c.2.1.2 133962 1lldA 319 1.17e-02 3ldh c.2.1.5 30177 d.162.1.1 42144 1y1pA 342 1.23e-02 c.2.1.2 122550 2ae2A 260 1.24e-02 1bdb c.2.1.2 29945 1a5zA 319 1.29e-02 c.2.1.5 30181 d.162.1.1 42148 1k3tA 359 1.30e-02 c.2.1.3 72022 d.81.1.1 72023 1djqA 729 1.36e-02 2tmdA c.1.4.1 28614 c.3.1.1 30315 c.4.1.1 30600 1ybvA 283 1.40e-02 1ybvA c.2.1.2 29948 2ew2A 316 1.41e-02 1o94A 729 1.44e-02 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 2tmdA 729 1.44e-02 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1cf2O 337 1.49e-02 1b7gO c.2.1.3 29994 d.81.1.1 39909 2c5aA 379 1.65e-02 c.2.1.2 129894 2ax3A 502 1.69e-02 c.72.1.4 127477 c.104.1.1 127478 2q1sA 377 1.69e-02 1pvvA 315 1.70e-02 c.78.1.1 95190 c.78.1.1 95191 1yqgA 263 1.78e-02 2ag5A 246 1.83e-02 c.2.1.2 126719 1jztA 246 1.89e-02 c.104.1.1 63319 1g0oA 283 1.98e-02 1ybvA c.2.1.2 60181 2ew8A 249 1.99e-02 c.2.1.2 132447 1zsyA 357 2.00e-02 3cgvA 397 2.05e-02 2ahrA 259 2.07e-02 a.100.1.10 126775 c.2.1.6 126776 2olnA 397 2.15e-02 2fwmX 250 2.16e-02 1yxmA 303 2.21e-02 c.2.1.2 124192 1i24A 404 2.24e-02 c.2.1.2 83663 1lqtA 456 2.30e-02 c.3.1.1 74198 c.4.1.1 74199 2pd6A 264 2.30e-02 2qa1A 500 2.35e-02 1i2cA 404 2.37e-02 c.2.1.2 83666 3ladA 476 2.38e-02 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1qorA 327 2.45e-02 1qorA b.35.1.2 24766 c.2.1.1 29782 2c2xA 281 2.52e-02 2v7pA 310 2.54e-02 2cduA 452 2.58e-02 2c0cA 362 2.65e-02 2gdzA 267 2.70e-02 c.2.1.2 135043 1lvl 458 2.87e-02 1lvl 1lvlA 458 2.87e-02 c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1gypA 358 2.88e-02 1dssG c.2.1.3 30004 d.81.1.1 39919 2yquA 455 2.88e-02 1w4xA 542 2.90e-02 c.3.1.5 109171 c.3.1.5 109172 1qydA 313 2.92e-02 c.2.1.2 96583 1yrlA 491 3.00e-02 1fl2A 310 3.01e-02 1hyuA c.3.1.5 59869 c.3.1.5 59870 2bi7A 384 3.25e-02 1s3iA 310 3.37e-02 b.46.1.1 98435 c.65.1.1 98436 2pnfA 248 3.49e-02 1hg3A 225 3.51e-02 1hg3A c.1.1.1 61025 1iy8A 267 3.72e-02 c.2.1.2 83774 1w6uA 302 3.77e-02 c.2.1.2 114288 1k2wA 256 3.86e-02 c.2.1.2 90927 2ewdA 317 3.93e-02 2bw0A 329 3.95e-02 b.46.1.1 129303 c.65.1.1 129304 1dljA 402 4.05e-02 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1q7bA 244 4.06e-02 c.2.1.2 96026 1zemA 262 4.08e-02 c.2.1.2 124984 2h7mA 269 4.08e-02 c.2.1.2 136219 1dliA 402 4.13e-02 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1zk4A 251 4.20e-02 c.2.1.2 125176 2cvjA 180 4.36e-02 2ywlA 180 4.48e-02 1h7xA 1025 4.55e-02 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 2b69A 343 4.75e-02 c.2.1.2 127974 1spxA 278 4.76e-02 c.2.1.2 98958 1geeA 261 5.05e-02 c.2.1.2 90509 1h7wA 1025 5.09e-02 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1x7gA 261 5.14e-02 c.2.1.2 114929 2jahA 247 5.26e-02 1gcoA 261 5.65e-02 1ybvA c.2.1.2 29884 1u8fO 335 5.65e-02 c.2.1.3 119626 d.81.1.1 119627 2axqA 467 5.71e-02 1jw9B 249 5.89e-02 c.111.1.1 67377 1xhcA 367 6.01e-02 c.3.1.5 115292 c.3.1.5 115293 d.87.1.1 115294 2pqmA 343 6.32e-02 1eny 268 6.65e-02 1eny 1gteA 1025 6.66e-02 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1ebdA 455 7.08e-02 1lvl c.3.1.5 30577 c.3.1.5 30578 d.87.1.1 40210 1ee9A 320 7.26e-02 1ee9A c.2.1.7 30288 c.58.1.2 33936 1zk7A 467 8.01e-02 2p4qA 497 8.08e-02 1vknA 351 8.51e-02 c.2.1.3 108676 d.81.1.1 108677 2c07A 285 8.56e-02 c.2.1.2 129577 1pj5A 830 8.81e-02 b.44.2.1 94742 c.3.1.2 94743 d.16.1.5 94744 d.250.1.1 94745 3ceaA 346 9.64e-02 2bryA 497 9.74e-02 1xa3A 437 9.76e-02 c.123.1.1 115025 2nloA 302 9.85e-02 1j5pA 253 1.00e-01 c.2.1.3 83092 d.81.1.3 71577 1e39A 571 1.00e-01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 2j3hA 345 1.04e-01 1jeoA 180 1.04e-01 c.80.1.3 66611 1edzA 320 1.04e-01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1qrrA 394 1.09e-01 1qrrA c.2.1.2 29824 1y7lA 316 1.10e-01 c.79.1.1 122695 2at2A 300 1.11e-01 3csuA c.78.1.1 35196 c.78.1.1 35197 1q9iA 571 1.12e-01 a.138.1.3 96273 c.3.1.4 96274 d.168.1.1 96275 1y0pA 571 1.12e-01 a.138.1.3 122507 c.3.1.4 122508 d.168.1.1 122509 1hdcA 253 1.14e-01 1e6wA c.2.1.2 29862 1gz6A 319 1.20e-01 c.2.1.2 76410 1yb1A 272 1.23e-01 c.2.1.2 116599 1dapA 320 1.23e-01 1dapA c.2.1.3 30053 d.81.1.3 39968 1h6vA 499 1.28e-01 3grs c.3.1.5 60693 c.3.1.5 60694 d.87.1.1 60695 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