# List of top-scoring protein chains for t2k-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 1wqaA 455 1.39e-01 1wb9A 800 3.28e-01 2bvfA 459 3.34e-01 1fts 295 3.62e-01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1ex1A 605 5.51e-01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1e3mA 800 5.93e-01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19075,32389,33746,39747 1uohA 226 6.42e-01 d.211.1.1 99690 1jfaA 374 7.25e-01 a.128.1.5 66622 2aelA 374 7.82e-01 1wdkC 390 9.74e-01 c.95.1.1,c.95.1.1 109258,109259 2aorA 223 1.17e+00 1szqA 483 1.35e+00 e.44.1.1 99045 1jevA 517 1.38e+00 1jevA c.94.1.1 35720 1fcjA 322 1.48e+00 1oasA c.79.1.1 35289 1kiyA 374 1.52e+00 a.128.1.5 72555 2cevA 299 1.62e+00 1d3vA c.42.1.1 32576 1t7lA 766 1.81e+00 1f83A 425 1.87e+00 1f82A d.92.1.7 40306 1j4aA 333 1.90e+00 c.2.1.4,c.23.12.1 71502,71503 1dik 874 1.93e+00 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 6prcL 273 2.04e+00 6prcL f.26.1.1 43434 1iexA 605 2.05e+00 c.1.8.7,c.23.11.1 66127,66128 1i8tA 367 2.10e+00 c.4.1.3,d.16.1.7 66094,66095 1ydnA 295 2.17e+00 1e39A 571 2.24e+00 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1r1hA 696 2.24e+00 d.92.1.4 104756 1sr7A 259 2.34e+00 a.123.1.1 105957 1w5fA 353 2.40e+00 1fiy 883 2.53e+00 1fiy c.1.12.3 29307 1eiyB 785 2.59e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16305,16306,25314,39313,40782,41458 1c7sA 858 3.02e+00 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1cs0A 1073 3.24e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1kssA 571 3.38e+00 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1c0aA 585 3.39e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1f45B 197 3.45e+00 1f45B a.26.1.1 59642 1dxrL 273 3.71e+00 6prcL f.26.1.1 43431 180lA 164 3.76e+00 1l92 d.2.1.3 36867 7odcA 424 3.83e+00 7odcA b.49.2.3,c.1.6.1 26488,28650 147l 164 3.92e+00 1l92 d.2.1.3 36864 1aosA 464 4.00e+00 1auwA a.127.1.1 19414 1fwrA 213 4.11e+00 1fwrA c.1.10.1 29164 1aszB 490 4.45e+00 1b8aA b.40.4.1,d.104.1.1 25241,40762 1cc1L 498 4.49e+00 1h2rL e.18.1.1 43301 1jvsA 400 4.53e+00 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1pioA 257 4.69e+00 1btl e.3.1.1 42719 175lA 164 4.73e+00 1l92 d.2.1.3 36924 1riqA 465 4.91e+00 a.203.1.1,d.104.1.1 97516,97517 5reqA 727 4.92e+00 1reqA c.1.19.1,c.23.6.1 29632,31259 1hkbA 917 5.08e+00 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33479,33480,33481,33482 2ez6A 221 5.12e+00 1ry6A 360 5.38e+00 c.37.1.9 98090 1ald 363 5.52e+00 1fbaA c.1.10.1 29100 2gsfA 373 5.68e+00 1qjdA 571 5.76e+00 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1w33A 181 5.84e+00 1a0eA 443 6.12e+00 1a0cA c.1.15.3 29537 146l 164 6.29e+00 1l92 d.2.1.3 36763 2dldA 337 6.42e+00 1dxy c.2.1.4,c.23.12.1 30099,31359 115l 164 6.50e+00 1l92 d.2.1.3 36700 1jlwA 219 6.56e+00 a.45.1.1,c.47.1.5 71741,71742 1gcb 454 6.74e+00 3gcb d.3.1.1 37034 1a5mC 566 6.90e+00 1ubpC b.92.1.1,c.1.9.2 28423,29045 7icd 416 7.44e+00 1iso c.77.1.1 35072 1ti6A 875 7.71e+00 b.52.2.2,c.81.1.1 106974,106975 1g87A 614 7.89e+00 a.102.1.2,b.2.2.2 83275,83276 1mo9A 523 7.89e+00 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1xwl 580 7.96e+00 1xwl c.55.3.5,e.8.1.1 33708,43001 196l 164 8.28e+00 1l92 d.2.1.3 36927 1epwA 1290 8.77e+00 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2bryA 497 8.93e+00 108l 164 8.93e+00 1l92 d.2.1.3 36669 1yzxA 226 9.17e+00 1tzzA 392 9.56e+00 1oasA 322 9.59e+00 1oasA c.79.1.1 35293 1qba 858 9.61e+00 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21810,22406,29009,40408 1k6dA 220 9.71e+00 c.124.1.2 72082 1cii 602 9.75e+00 1cii f.1.1.1,h.4.3.1 43381,45787 1cs1C 386 9.83e+00 1ibjA c.67.1.3 34401 1poiA 317 9.84e+00 1poiA c.124.1.2 34153 1l1lA 739 1.00e+01 c.7.1.4 73470 1xrtA 467 1.02e+01 1ojrA 274 1.04e+01 c.74.1.1 93147 1nu5A 370 1.04e+01 c.1.11.2,d.54.1.1 92183,92184 1f5nA 592 1.05e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1dg3A 592 1.06e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 1x38A 602 1.06e+01 1otkA 249 1.07e+01 a.25.1.2 93521 1wkyA 464 1.08e+01 112l 164 1.09e+01 1l92 d.2.1.3 36677 1bqg 451 1.10e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 1ordA 730 1.11e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1xwfA 431 1.12e+01 1zcjA 463 1.14e+01 1jdfA 447 1.14e+01 c.1.11.2,d.54.1.1 62897,62898 1sx7A 164 1.14e+01 1n8fA 350 1.15e+01 c.1.10.4 85397 1uok 558 1.17e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1alq 266 1.17e+01 1btl e.3.1.1 42707 1ejrC 567 1.18e+01 1ubpC b.92.1.1,c.1.9.2 28420,29042 1htjF 210 1.20e+01 1htjF a.91.1.1 61254 1bx4A 345 1.20e+01 1bx4A c.72.1.1 34935 1wn0A 145 1.21e+01 1ibcA 194 1.25e+01 1pauA c.17.1.1 30997 1swyA 164 1.26e+01 1l5wA 796 1.29e+01 c.87.1.4 73605 1tf4A 605 1.31e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1xpmA 396 1.31e+01 1b7yB 785 1.32e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 2aaa 484 1.32e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1d4fA 431 1.33e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1a5kC 566 1.34e+01 1ubpC b.92.1.1,c.1.9.2 28425,29047 2akaA 776 1.35e+01 1fwcC 567 1.35e+01 1ubpC b.92.1.1,c.1.9.2 28410,29032 1eejA 216 1.36e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1uasA 362 1.36e+01 b.71.1.1,c.1.8.1 88388,88389 2a8lA 420 1.36e+01 1vloA 381 1.41e+01 b.44.2.1,d.250.1.1 108838,108839 1lycA 343 1.41e+01 a.93.1.1 74344 110l 164 1.44e+01 1l92 d.2.1.3 36684 1ofgA 381 1.48e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1l58 164 1.48e+01 1l92 d.2.1.3 36635 1my6A 199 1.48e+01 a.2.11.1,d.44.1.1 85232,85233 128l 164 1.50e+01 1l92 d.2.1.3 36634 1jbgA 109 1.51e+01 a.6.1.3 66480 1m46A 148 1.51e+01 a.39.1.5 78599 1qv1A 195 1.54e+01 a.39.1.5 96347 1a28A 256 1.55e+01 1a28A a.123.1.1 19290 1a0fA 201 1.55e+01 1a0fA a.45.1.1,c.47.1.5 17737,33031 1daaA 282 1.57e+01 1daaA e.17.1.1 43270 1z5lA 285 1.57e+01 125l 164 1.60e+01 1l92 d.2.1.3 36672 195l 164 1.61e+01 1l92 d.2.1.3 36841 2napA 723 1.61e+01 2napA b.52.2.2,c.81.1.1 26926,35334 123l 164 1.61e+01 1l92 d.2.1.3 36697 1b0uA 262 1.62e+01 1b0uA c.37.1.12 32370 1tie 172 1.66e+01 1wba b.42.4.1 25592 2b8nA 429 1.66e+01 144l 164 1.67e+01 1l92 d.2.1.3 36893 145l 164 1.69e+01 1l92 d.2.1.3 36860 1ji2A 585 1.72e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 129l 164 1.73e+01 1l92 d.2.1.3 36660 1yadA 221 1.73e+01 1pe0A 197 1.75e+01 c.23.16.2 88045 1gteD 1025 1.75e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70455,70456,70457,70458,70459 1dzlA 505 1.76e+01 1dzlA b.121.6.1 23586 138l 164 1.77e+01 1l92 d.2.1.3 36679 1csh 435 1.81e+01 1csh a.103.1.1 18880 1qwnA 1045 1.81e+01 a.8.3.1,b.30.5.6,c.6.2.1 96487,96488,96489 1lvk 762 1.82e+01 1lvk b.34.3.1,c.37.1.9 24576,32173 1ra0A 430 1.82e+01 1a7aA 432 1.83e+01 1b3rA c.2.1.4,c.23.12.3 30104,31364 1muwA 386 1.84e+01 c.1.15.3 79495 1cezA 883 1.85e+01 1cezA e.8.1.3 43110 1ynfA 458 1.87e+01 131l 164 1.87e+01 1l92 d.2.1.3 36685 1n7oA 721 1.88e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 199l 164 1.91e+01 1l92 d.2.1.3 36855 1ih8A 271 1.93e+01 2nsyA c.26.2.1 62377 1y1xA 191 1.93e+01 1zb1A 392 1.93e+01 1cf2O 337 1.98e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 2c6cA 707 1.98e+01 1oyb 400 1.98e+01 1oyc c.1.4.1 28602 122l 164 1.99e+01 1l92 d.2.1.3 36667 1txdA 385 1.99e+01 a.87.1.1,b.55.1.1 107422,107423 1jjyA 636 2.01e+01 1jjyA 1tvzA 388 2.01e+01 c.95.1.2,c.95.1.2 107367,107368 1vzyA 291 2.02e+01 1fuqA 472 2.02e+01 1furA a.127.1.1 19405 1hqsA 423 2.05e+01 1iso c.77.1.1 61154 141l 164 2.05e+01 1l92 d.2.1.3 36863 1cm5A 759 2.07e+01 1cm5A c.7.1.1 30671 2grrB 170 2.07e+01 1ejxC 567 2.08e+01 b.92.1.1,c.1.9.2 83184,83185 1k5hA 398 2.08e+01 a.69.3.1,c.2.1.3,d.81.1.3 68192,68193,68194 1i7fA 292 2.08e+01 1i7fA d.193.1.1 61888 1zs3A 182 2.10e+01 1fy7A 278 2.11e+01 1fy7A d.108.1.1 40817 152l 164 2.12e+01 1l92 d.2.1.3 36904 1iqcA 308 2.13e+01 a.3.1.5,a.3.1.5 66266,66267 1ebdA 455 2.13e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1eguA 731 2.13e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1gteA 1025 2.15e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 2b34A 199 2.15e+01 192l 164 2.15e+01 1l92 d.2.1.3 36815 1a5cA 368 2.16e+01 1fbaA c.1.10.1 29148 1h7wB 1025 2.16e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15684,28629,30325,30610,39008 1ej3A 191 2.17e+01 1ej3A a.39.1.5 17259 2wsyB 396 2.19e+01 2tysB c.79.1.1 35288 2br9A 234 2.19e+01 1l2uA 245 2.21e+01 c.1.2.3 73516 114l 164 2.25e+01 1l92 d.2.1.3 36663 1mhlC 466 2.25e+01 1mhlC 118l 164 2.26e+01 1l92 d.2.1.3 36642 137lA 164 2.28e+01 1l92 d.2.1.3 36791 1d2vC 466 2.29e+01 1mhlC 1n4qB 377 2.31e+01 a.102.4.3 91636 1g7oA 215 2.33e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 2fbyA 205 2.34e+01 1mvwB 145 2.35e+01 i.15.1.1 79524 2cwsA 237 2.36e+01 1euaA 213 2.37e+01 1fwrA c.1.10.1 29155 130l 164 2.37e+01 1l92 d.2.1.3 36638 1liuA 528 2.38e+01 b.58.1.1,c.1.12.1,c.49.1.1 77970,77971,77972 1n4kA 381 2.39e+01 a.118.22.1,b.42.6.1 79992,79993 139l 164 2.42e+01 1l92 d.2.1.3 36643 1kqpA 271 2.43e+01 c.26.2.1 72883 126l 164 2.44e+01 1l92 d.2.1.3 36699 1ju2A 536 2.47e+01 c.3.1.2,d.16.1.1 77169,77170 1gt7A 274 2.47e+01 c.74.1.1 70398 1vkmA 297 2.50e+01 c.138.1.1 108670 1h7wA 1025 2.50e+01 1h7wA a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15683,28628,30324,30609,39007 2nsyA 271 2.51e+01 2nsyA c.26.2.1 31612 1lw9A 164 2.51e+01 d.2.1.3 84727 1erjA 393 2.53e+01 1erjA b.69.4.1 27660 1a9xA 1058 2.54e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1qhlA 227 2.55e+01 1qhlA c.37.1.12 32382 1emy 153 2.56e+01 1a6m a.1.1.2 15204 120l 164 2.56e+01 1l92 d.2.1.3 36720 1xpkC 388 2.56e+01 198l 164 2.57e+01 1l92 d.2.1.3 36785 1h7xC 1025 2.57e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15689,28634,30330,30615,39013 1fw1A 216 2.58e+01 a.45.1.1,c.47.1.5 60051,60052 1bg0 356 2.62e+01 1qh4A a.83.1.1,d.128.1.2 18476,41211 109l 164 2.63e+01 1l92 d.2.1.3 36781 102l 165 2.65e+01 1l92 d.2.1.3 36724 1o26A 232 2.65e+01 d.207.1.1 86566 1clqA 903 2.65e+01 1clqA c.55.3.5,e.8.1.1 33717,43006 1l92 164 2.66e+01 1l92 d.2.1.3 36629 1oy3D 282 2.66e+01 d.211.1.1 87554 119l 164 2.67e+01 1l92 d.2.1.3 36622 1h7wD 1025 2.68e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 15686,28631,30327,30612,39010 1djxB 624 2.70e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1fehA 574 2.74e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1ox6A 555 2.74e+01 c.1.2.1,c.23.16.1 87505,87506 1amz 435 2.74e+01 1csh a.103.1.1 18884 1h7nA 342 2.74e+01 1b4kA c.1.10.3 60726 1dciA 275 2.75e+01 1dciA c.14.1.3 30918 1wl9A 440 2.75e+01 113l 164 2.76e+01 1l92 d.2.1.3 36678 142l 164 2.79e+01 1l92 d.2.1.3 36874 172l 164 2.80e+01 1l92 d.2.1.3 36905 1fs1B 141 2.88e+01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1rp0A 284 2.88e+01 164l 164 2.89e+01 1l92 d.2.1.3 36714 1lxkA 721 2.91e+01 a.102.3.2,b.24.1.1,b.30.5.2 74331,74332,74333 1fm2B 520 2.92e+01 1fm2B 140l 164 2.93e+01 1l92 d.2.1.3 36891 1arv 344 2.94e+01 1arv a.93.1.1 18590 156l 164 2.95e+01 1l92 d.2.1.3 36709 1p36A 164 2.96e+01 d.2.1.3 93978 1jf0A 195 2.97e+01 1ej3A a.39.1.5 62926 1y7lA 316 2.97e+01 2sqcA 631 3.03e+01 2sqcA a.102.4.2,a.102.4.2 18854,18855 1eu8A 409 3.03e+01 1eu8A c.94.1.1 59502 1cktA 71 3.07e+01 1cktA a.21.1.1 16417 1w3jA 468 3.09e+01 c.1.8.4 109156 1evyA 366 3.09e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 143l 164 3.10e+01 1l92 d.2.1.3 36857 1ynpA 317 3.11e+01 166l 164 3.12e+01 1l92 d.2.1.3 36681 160l 164 3.16e+01 1l92 d.2.1.3 36748 127l 164 3.19e+01 d.2.1.3 36745 1vhuA 211 3.23e+01 c.50.1.2 100703 1aab 83 3.26e+01 1cktA a.21.1.1 16420 1csn 298 3.27e+01 1csn d.144.1.7 41664 1gpeA 587 3.29e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1x0rA 249 3.32e+01 190l 164 3.35e+01 1l92 d.2.1.3 36892 111l 164 3.36e+01 1l92 d.2.1.3 36661 1w27A 714 3.37e+01 1cs1A 386 3.39e+01 1ibjA c.67.1.3 34399 1ox0A 430 3.39e+01 c.95.1.1,c.95.1.1 87495,87496 1whsA 255 3.40e+01 1ivyA c.69.1.5 34649 155l 164 3.43e+01 1l92 d.2.1.3 36762 2fflA 756 3.44e+01 1oyeA 1049 3.45e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1x42A 232 3.50e+01 107l 164 3.55e+01 1l92 d.2.1.3 36690 177l 164 3.57e+01 1l92 d.2.1.3 36958 1fpkA 335 3.58e+01 1frpA e.7.1.1 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