# List of top-scoring protein chains for t04-100-30-n_notor2-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 1s5uA 138 9.31e-08 d.38.1.1 98573 1z54A 132 1.11e-07 2av9A 147 2.07e-07 2cyeA 133 3.65e-07 1njkA 156 1.09e-06 d.38.1.1 85818 2aliA 158 1.63e-06 1yliA 153 4.83e-06 1lo7A 141 9.23e-06 d.38.1.1 74144 1vpmA 169 9.57e-06 1bvqA 141 1.68e-05 1bvqA d.38.1.1 38542 2gf6A 135 2.63e-05 2essA 248 3.29e-05 2gvhA 288 5.16e-04 2h4uA 145 1.09e-03 1wluA 136 4.85e-03 1j1yA 136 5.14e-03 d.38.1.5 90776 1zkiA 133 5.70e-03 1psuA 140 1.23e-02 d.38.1.5 88285 2fs2A 151 1.44e-02 2cwzA 141 1.60e-02 1q4uA 151 5.88e-02 d.38.1.5 95828 1vh5A 148 6.42e-02 d.38.1.5 100642 2b6eA 146 1.42e-01 1ixlA 131 1.52e-01 d.38.1.5 90717 1o0iA 138 1.70e-01 d.38.1.5 86532 1c8uA 285 2.73e-01 1c8uA d.38.1.3,d.38.1.3 38547,38548 2b3nA 159 2.82e-01 1t82A 155 3.72e-01 d.38.1.5 106639 1iq6A 134 3.74e-01 d.38.1.4 76755 1u1zA 168 4.41e-01 d.38.1.6 107602 1e39A 571 6.14e-01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1c0pA 363 1.03e+00 1an9A c.4.1.2,d.16.1.3 30647,37934 1z6bA 154 1.53e+00 1r6vA 671 1.73e+00 1yocA 147 1.82e+00 1sh8A 154 1.84e+00 d.38.1.5 105549 1e8yA 966 2.67e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1dfmA 223 3.17e+00 1d2iA c.52.1.5 33295 1ojrA 274 3.24e+00 c.74.1.1 93147 1ukvG 453 4.08e+00 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 2bcgG 453 4.71e+00 1bsg 266 4.82e+00 1btl e.3.1.1 42729 1b0uA 262 4.99e+00 1b0uA c.37.1.12 32370 1el4A 195 5.12e+00 1ej3A a.39.1.5 59453 1nbaA 264 5.79e+00 1nbaA c.33.1.3 31753 2bdvA 231 6.08e+00 2gdnA 267 6.15e+00 1hg8A 349 6.28e+00 b.80.1.3 65830 1mwvA 714 6.59e+00 a.93.1.3,a.93.1.3 85161,85162 1hq0A 295 6.79e+00 1hzgA d.194.1.1 61122 2bcfA 276 7.86e+00 1nnwA 252 8.26e+00 d.159.1.5 80674 1d2kA 392 9.06e+00 1d2kA c.1.8.5,d.26.3.1 29008,38442 2aaa 484 9.18e+00 7taa b.71.1.1,c.1.8.1 27777,28764 1h09A 338 9.57e+00 b.109.1.1,c.1.8.8 83420,83421 2ew0A 192 1.01e+01 1bag 425 1.02e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1ga6A 372 1.04e+01 1ga1A c.41.1.2 32556 1bu6O 501 1.06e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1moq 368 1.10e+01 1moq c.80.1.1 35302 1bs4A 168 1.12e+01 1bs4A d.167.1.1 42287 1y0pA 571 1.12e+01 1wdeA 294 1.14e+01 1jndA 420 1.17e+01 c.1.8.5,d.26.3.1 71757,71758 1edzA 320 1.18e+01 1ee9A c.2.1.7,c.58.1.2 30287,33935 1ghpA 258 1.18e+01 1btl e.3.1.1 60520 1nofA 383 1.19e+01 b.71.1.2,c.1.8.3 92020,92021 1u94A 356 1.26e+01 c.37.1.11,d.48.1.1 107743,107744 2bshA 125 1.26e+01 1ixh 321 1.28e+01 1ixh c.94.1.1 35761 1uedA 406 1.30e+01 a.104.1.1 99256 2fh7A 595 1.34e+01 1xeoA 168 1.34e+01 1f8vA 355 1.37e+01 2bbvA b.121.4.4 23329 1r0mA 375 1.39e+01 c.1.11.2,d.54.1.1 104747,104748 1gowA 489 1.43e+01 1qvbA c.1.8.4 28981 1xovA 326 1.47e+01 1ve5A 311 1.48e+01 1fo4A 1332 1.48e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 1wy2A 351 1.49e+01 1hx0A 496 1.50e+01 b.71.1.1,c.1.8.1 61346,61347 1r2jA 366 1.52e+01 a.29.3.1,e.6.1.1 96869,96870 1xc1A 309 1.55e+01 c.94.1.1 109543 2mprA 421 1.56e+01 2mprA f.4.3.2 43788 2bb6A 414 1.59e+01 1pkp 150 1.59e+01 1pkp d.14.1.1,d.50.1.2 37551,38787 1smlA 269 1.65e+01 1smlA d.157.1.1 42053 1koiA 184 1.65e+01 b.60.1.1 68725 1d2eA 397 1.76e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1pn0A 665 1.80e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1wyuA 438 1.81e+01 1w7lA 422 1.84e+01 c.67.1.1 109226 2bwvA 440 1.88e+01 2azqA 311 1.91e+01 1s4bP 674 1.98e+01 d.92.1.5 105252 3csuA 310 2.01e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 1vemA 516 2.05e+01 1k32A 1045 2.09e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1lldA 319 2.10e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1mplA 349 2.10e+01 e.3.1.1 79387 1v5dA 386 2.10e+01 1g9mG 321 2.10e+01 1gc1G d.172.1.1 42492 1vcoA 550 2.11e+01 c.23.16.1,c.37.1.10 108508,108509 1vl2A 421 2.12e+01 c.26.2.1,d.210.1.1 108708,108709 1g2aA 168 2.15e+01 d.167.1.1 65109 1ed8A 449 2.16e+01 1b8jA c.76.1.1 34988 1lla 628 2.25e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1s95A 333 2.25e+01 d.159.1.3 105375 1ylxA 103 2.27e+01 1fzoA 274 2.28e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1tbuA 118 2.29e+01 1qwoA 442 2.32e+01 c.60.1.2 104620 1nr0A 611 2.33e+01 b.69.4.1,b.69.4.1 86078,86079 1jsdA 319 2.34e+01 b.19.1.2 63258 1u0fA 564 2.42e+01 1g6aA 271 2.44e+01 1btl e.3.1.1 42704 1xf1A 926 2.44e+01 1zowA 313 2.51e+01 1pguA 615 2.57e+01 b.69.4.1,b.69.4.1 88069,88070 1f1xA 322 2.61e+01 d.32.1.3,d.32.1.3 83208,83209 1f1uA 323 2.62e+01 d.32.1.3,d.32.1.3 83200,83201 1f6yA 262 2.63e+01 1f6yA c.1.21.2 29673 2bsjA 133 2.70e+01 1th0A 226 2.71e+01 d.3.1.7 106903 2d0oA 610 2.72e+01 1ep0A 185 2.74e+01 1dzrA b.82.1.1 28080 1uylA 236 2.87e+01 d.122.1.1 108147 1k7kA 221 2.88e+01 c.51.4.1 72104 1iysA 262 2.91e+01 e.3.1.1 90723 1te5A 257 2.92e+01 d.153.1.1 106795 1o26A 232 2.94e+01 d.207.1.1 86566 1ntyA 311 3.01e+01 a.87.1.1,b.55.1.1 103873,103874 2fnuA 375 3.01e+01 1w66A 232 3.17e+01 2bvlA 543 3.20e+01 1nu5A 370 3.21e+01 c.1.11.2,d.54.1.1 92183,92184 1eg7A 557 3.21e+01 1eg7A c.37.1.10 32241 1gnd 447 3.24e+01 1gnd c.3.1.3,d.16.1.6 30423,37987 2b5eA 504 3.25e+01 1kt6A 183 3.25e+01 b.60.1.1 84466 8prn 289 3.26e+01 3prn f.4.3.1 43767 1wl4A 397 3.31e+01 1yifA 533 3.32e+01 1zruA 264 3.34e+01 1vr5A 547 3.37e+01 1c7sA 858 3.38e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1fmtA 314 3.39e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1wkyA 464 3.41e+01 2a9dA 372 3.44e+01 1fsu 492 3.44e+01 1auk c.76.1.2 35032 1n7vA 555 3.46e+01 b.126.1.1 85377 2bf6A 449 3.46e+01 1itcA 516 3.46e+01 b.3.1.1,c.1.8.1 83705,83706 1o0xA 262 3.57e+01 d.127.1.1 80755 1y4wA 518 3.60e+01 1ks8A 433 3.65e+01 a.102.1.2 77519 1qf6A 642 3.68e+01 1qf6A c.51.1.1,d.15.10.1,d.67.1.1,d.104.1.1 33210,39551,39562,40759 1yljA 263 3.68e+01 1m15A 357 3.68e+01 a.83.1.1,d.128.1.2 78368,78369 1zxxA 319 3.70e+01 1aym1 285 3.76e+01 1aym1 1heiA 451 3.86e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1wqaA 455 3.88e+01 1oz2A 331 3.96e+01 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1oq1A 223 4.05e+01 b.29.1.17 93408 1erjA 393 4.06e+01 1erjA b.69.4.1 27660 1d5tA 433 4.09e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1x7dA 350 4.11e+01 1qxyA 252 4.12e+01 d.127.1.1 96565 2c2xA 281 4.13e+01 1zxkA 98 4.16e+01 1mxgA 435 4.21e+01 b.71.1.1,c.1.8.1 85193,85194 1xnzA 264 4.27e+01 1qhxA 178 4.29e+01 1qhsA c.37.1.3 31936 1dxrL 273 4.31e+01 6prcL f.26.1.1 43431 1wkbA 810 4.38e+01 1k2xB 143 4.40e+01 1q33A 292 4.41e+01 d.113.1.1 95657 1hm9A 468 4.41e+01 b.81.1.4,c.68.1.5 65866,65867 1qi9A 556 4.46e+01 1qhbA a.111.1.2 19053 2b6nA 278 4.50e+01 1wleA 501 4.50e+01 1pj5A 830 4.51e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1oyjA 231 4.52e+01 a.45.1.1,c.47.1.5 87597,87598 1u04A 771 4.63e+01 b.34.14.1,c.55.3.10 107539,107540 1zz1A 369 4.65e+01 1zxiF 288 4.67e+01 1wl9A 440 4.67e+01 1gc0A 398 4.67e+01 c.67.1.3 70168 1jeoA 180 4.70e+01 c.80.1.3 66611 1kqfA 1015 4.75e+01 b.52.2.2,c.81.1.1 72871,72872 1nkxA 348 4.77e+01 c.94.1.2 91943 2csgA 424 4.77e+01 1lj8A 493 4.80e+01 a.100.1.9,c.2.1.6 90392,90393 1w2wB 191 4.82e+01 1htqA 477 4.84e+01 d.15.9.1,d.128.1.1 71035,71036 1ylhA 560 4.91e+01 2aysA 348 4.92e+01 1txqA 93 5.05e+01 2ddfA 257 5.07e+01 1ktbA 405 5.12e+01 b.71.1.1,c.1.8.1 72960,72961 1djxA 624 5.18e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17342,23159,29587 1vlbA 907 5.24e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1hlrA 907 5.29e+01 2f3yA 148 5.30e+01 1sg0A 230 5.32e+01 2ar0A 541 5.33e+01 1mdbA 539 5.38e+01 e.23.1.1 79008 1y6hA 177 5.39e+01 1ycsB 239 5.42e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 1ytvA 366 5.49e+01 1v9nA 360 5.51e+01 2bzsA 236 5.53e+01 2g9zA 348 5.60e+01 1tqyA 424 5.60e+01 c.95.1.1,c.95.1.1 107245,107246 2ffcA 353 5.62e+01 2abqA 306 5.63e+01 1aohA 147 5.69e+01 1aohA b.2.2.2 22401 1iv8A 720 5.74e+01 b.71.1.1,c.1.8.1 76842,76843 1ja1A 622 5.75e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 2gl5A 410 5.78e+01 1p3dA 475 5.80e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1d8dB 437 5.81e+01 1ft1B a.102.4.3 18866 1uteA 313 5.86e+01 1uteA d.159.1.1 42078 2fgtA 417 5.95e+01 1iyeA 309 5.97e+01 e.17.1.1 83786 2myr 501 5.97e+01 1f4lA 551 5.98e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 3chy 128 5.99e+01 3chy c.23.1.1 31038 2bitX 165 6.00e+01 1atg 231 6.02e+01 1atg c.94.1.1 35834 1gln 468 6.03e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1mkfA 382 6.08e+01 b.116.1.1 79232 1w9yA 319 6.13e+01 1wdyA 285 6.15e+01 1hv9A 456 6.22e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1hxxA 340 6.22e+01 2omf f.4.3.1 61385 1m98A 317 6.28e+01 a.175.1.1,d.17.4.6 78866,78867 1jmmA 377 6.29e+01 b.30.6.1 71749 2cfeA 162 6.33e+01 1gjwA 637 6.41e+01 b.71.1.1,c.1.8.1 60582,60583 1sw5A 275 6.44e+01 c.94.1.1 106069 1rwrA 301 6.46e+01 b.80.1.11 97990 1i1iP 681 6.48e+01 1i1iP d.92.1.5 40297 2bwnA 401 6.48e+01 2rmcA 182 6.50e+01 2cpl b.62.1.1 27491 1qy5A 269 6.51e+01 d.122.1.1 96573 1vyfA 135 6.57e+01 b.60.1.2 108902 1qhdA 398 6.57e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 3tdt 274 6.58e+01 3tdt b.81.1.2 28053 1goiA 499 6.58e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1p3cA 215 6.60e+01 b.47.1.1 93996 1cghA 224 6.61e+01 1a7s b.47.1.2 26290 1v97A 1332 6.63e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 1w3jA 468 6.66e+01 c.1.8.4 109156 2aioA 269 6.66e+01 1qmeA 702 6.71e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1y8aA 332 6.73e+01 1y8qB 640 6.78e+01 2bg1A 494 6.78e+01 1l6sA 323 6.80e+01 c.1.10.3 73627 2as0A 396 6.86e+01 1x8qA 184 6.86e+01 2ch4A 320 6.87e+01 1ll7A 392 6.94e+01 c.1.8.5,d.26.3.1 78085,78086 2bi0A 337 7.00e+01 1j5uA 136 7.03e+01 d.208.1.1 71584 1jmsA 381 7.09e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1zvdA 380 7.15e+01 1jqgA 433 7.18e+01 c.56.5.1,d.58.3.1 71791,71792 1ohlA 342 7.21e+01 c.1.10.3 87035 2fdsA 352 7.23e+01 1rcqA 357 7.26e+01 b.49.2.2,c.1.6.1 104882,104883 1ctn 540 7.28e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1a4iA 301 7.30e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1bg6 359 7.31e+01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1q0qA 406 7.38e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 2h3jA 75 7.46e+01 1ymtA 246 7.46e+01 1mrzA 293 7.47e+01 b.43.5.1,c.26.1.3 91452,91453 1foeA 377 7.49e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1hn0A 1021 7.52e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1i9zA 347 7.54e+01 1i9yA d.151.1.2 62102 2eifA 136 7.55e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1qh4A 380 7.57e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1qx4A 274 7.59e+01 b.43.4.2,c.25.1.1 104624,104625 1tltA 319 7.60e+01 c.2.1.3,d.81.1.5 107135,107136 1yfsA 465 7.63e+01 1htyA 1015 7.64e+01 a.8.3.1,b.30.5.6,c.6.2.1 83064,83065,83066 3bamA 213 7.65e+01 1bam c.52.1.3 33288 1sw5B 275 7.67e+01 c.94.1.1 106070 2f96A 224 7.69e+01 1auiA 521 7.71e+01 1auiA d.159.1.3 42085 1mdc 133 7.77e+01 1hmt b.60.1.2 27198 2auaA 224 7.83e+01 1hf2A 210 7.84e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1mp4A 292 7.94e+01 c.68.1.6 79376 1e7uA 961 8.00e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1k3bB 164 8.00e+01 d.3.1.1 72015 1y42X 392 8.00e+01 2a74A 643 8.02e+01 1bk1 184 8.10e+01 1axkA b.29.1.11 24340 1ohfA 644 8.15e+01 b.121.4.8 93014 1d2nA 272 8.16e+01 1d2nA c.37.1.20 32428 2viuA 328 8.17e+01 1hgeA b.19.1.2 23797 2aaoA 166 8.21e+01 1flcA 432 8.24e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 1bquA 215 8.30e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1xikA 375 8.41e+01 1xikA a.25.1.2 16784 1x38A 602 8.42e+01 1td2A 287 8.47e+01 c.72.1.5 106765 1juvA 193 8.49e+01 c.71.1.1 90912 1yqgA 263 8.55e+01 1rl4A 188 8.60e+01 d.167.1.1 97636 1o7eA 276 8.61e+01 e.3.1.1 92622 1y7wA 291 8.63e+01 1rtu 114 8.66e+01 9rnt d.1.1.4 36139 1qe3A 489 8.66e+01 2bce c.69.1.1 34630 1u69A 163 8.68e+01 d.32.1.7 107699 1syyA 346 8.69e+01 a.25.1.2 106126 1rerA 391 8.71e+01 b.1.18.4,f.10.1.1 97327,97328 1i2sA 282 8.71e+01 e.3.1.1 71104 2bhoA 130 8.80e+01 1bv1 159 8.87e+01 1bv1 d.129.3.1 41313 1qniA 581 8.94e+01 1qniA b.6.1.4,b.69.3.1 23042,27642 1p2xA 159 8.95e+01 a.40.1.1 104062 1xocA 520 8.95e+01 1pn2A 280 8.95e+01 d.38.1.4,d.38.1.4 94930,94931 1jbeA 128 8.97e+01 3chy c.23.1.1 62845 1rhs 296 9.00e+01 1rhs c.46.1.2,c.46.1.2 32703,32704