# List of top-scoring protein chains for t2k-100-30-CB_burial_14_7-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 1xngA 268 1.28e-07 1wy5A 317 8.08e-06 1vl2A 421 6.13e-05 c.26.2.1,d.210.1.1 108708,108709 1ni5A 433 1.63e-04 c.26.2.5,d.229.1.1 80533,80534 1gpmA 525 1.71e-04 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1ct9A 553 4.02e-04 1ct9A c.26.2.1,d.153.1.1 31616,41834 1ru8A 232 2.10e-03 c.26.2.1 97849 1jgtA 513 2.21e-03 c.26.2.1,d.153.1.1 66684,66685 2d13A 227 2.34e-03 1m1zA 513 2.51e-03 c.26.2.1,d.153.1.1 78457,78458 1korA 400 4.82e-03 c.26.2.1,d.210.1.1 72824,72825 1q15A 503 8.86e-03 c.26.2.1,d.153.1.1 95538,95539 1k92A 455 2.03e-02 c.26.2.1,d.210.1.1 68325,68326 1kqpA 271 1.04e-01 c.26.2.1 72883 1o89A 345 1.05e-01 b.35.1.2,c.2.1.1 92644,92645 2nsyA 271 1.42e-01 2nsyA c.26.2.1 31612 1nsyA 271 1.79e-01 2nsyA c.26.2.1 31614 1ih8A 271 2.29e-01 2nsyA c.26.2.1 62377 1ojaA 520 4.15e-01 c.3.1.2,d.16.1.5 93096,93097 1s3eA 520 4.74e-01 c.3.1.2,d.16.1.5 98426,98427 1wxiA 275 5.02e-01 1gosA 520 6.27e-01 c.3.1.2,d.16.1.5 65425,65426 1rpnA 335 7.58e-01 c.2.1.2 97708 2a2pA 129 7.99e-01 1bw0A 416 1.16e+00 1bw0A c.67.1.1 34385 1q8fA 313 1.83e+00 c.70.1.1 96203 3cox 507 1.91e+00 1b8sA c.3.1.2,d.16.1.1 30332,37863 1coy 507 2.01e+00 1b8sA c.3.1.2,d.16.1.1 30333,37864 1c0pA 363 2.21e+00 1an9A c.4.1.2,d.16.1.3 30647,37934 2c0cA 362 2.35e+00 2ax3A 502 2.39e+00 1csbB 205 3.82e+00 1theB 1b8sA 504 3.82e+00 1b8sA c.3.1.2,d.16.1.1 30335,37866 2cvjA 180 3.85e+00 1t2aA 375 3.86e+00 c.2.1.2 99078 1lyxA 248 3.90e+00 c.1.1.1 78304 1b4vA 504 3.92e+00 1b8sA c.3.1.2,d.16.1.1 30334,37865 1mxtA 504 4.29e+00 c.3.1.2,d.16.1.1 79671,79672 1n1pA 504 4.30e+00 c.3.1.2,d.16.1.1 91546,91547 1n4wA 504 4.43e+00 c.3.1.2,d.16.1.1 91676,91677 1tqyB 415 5.21e+00 c.95.1.1,c.95.1.1 107247,107248 1vljA 407 5.36e+00 e.22.1.2 108832 1f2dA 341 5.47e+00 1f2dA c.79.1.1 35298 1xa0A 328 5.85e+00 1zk7A 467 6.01e+00 1o5xA 248 6.19e+00 c.1.1.1 92528 1v52A 133 6.39e+00 1o0uA 429 6.48e+00 c.118.1.1 80743 1xg5A 279 6.54e+00 1fwp 139 6.57e+00 1eayC d.58.24.1 39396 1wqaA 455 6.65e+00 1treA 255 6.80e+00 1amk c.1.1.1 28505 1ijhA 504 7.42e+00 c.3.1.2,d.16.1.1 66161,66162 1wj7A 104 8.58e+00 1tksA 204 9.26e+00 d.115.1.2 107114 1iq4A 179 9.35e+00 1iq4A d.77.1.1 62641 1j0aA 325 9.36e+00 c.79.1.1 83871 2b8nA 429 9.42e+00 1fkd 107 9.65e+00 1fkj d.26.1.1 38383 2c5aA 379 9.99e+00 1dekA 241 1.01e+01 1dekA c.37.1.1 31842 1reoA 486 1.02e+01 c.3.1.2,d.16.1.5 97325,97326 1o2dA 371 1.02e+01 e.22.1.2 86591 1fkf 107 1.05e+01 1fkj d.26.1.1 38386 1udc 338 1.08e+01 1xel c.2.1.2 29785 2cokA 113 1.11e+01 1fkj 107 1.13e+01 1fkj d.26.1.1 38384 1bkf 107 1.16e+01 1fkj d.26.1.1 38382 1oafA 261 1.17e+01 a.93.1.1 86734 1a9z 338 1.17e+01 1xel c.2.1.2 29795 1b9bA 255 1.18e+01 1amk c.1.1.1 28531 1udb 338 1.19e+01 1xel c.2.1.2 29787 1zo0A 126 1.21e+01 2udpA 338 1.23e+01 1xel c.2.1.2 29791 2pfkA 320 1.24e+01 3pfk c.89.1.1 35577 2gl5A 410 1.25e+01 7timA 247 1.26e+01 1amk c.1.1.1 28457 1d06A 130 1.27e+01 1drmA d.110.3.2 40906 1zljA 78 1.31e+01 1yt8A 539 1.32e+01 1mo0A 275 1.35e+01 c.1.1.1 79329 1mkeA 152 1.36e+01 b.55.1.4 79231 1kv5A 250 1.37e+01 c.1.1.1 73052 1po5A 476 1.42e+01 a.104.1.1 94963 1tif 78 1.42e+01 1tif d.15.8.1 37836 1pfkA 320 1.44e+01 3pfk c.89.1.1 35575 1w5fA 353 1.44e+01 1rq2A 382 1.47e+01 c.32.1.1,d.79.2.1 105048,105049 1kvs 338 1.47e+01 1xel c.2.1.2 29799 1apxA 249 1.47e+01 1ryc a.93.1.1 18669 1kq3A 376 1.47e+01 e.22.1.2 68790 2btoA 473 1.49e+01 1mnaA 298 1.50e+01 c.69.1.22 79322 1neyA 247 1.53e+01 c.1.1.1 80449 1cqzA 554 1.53e+01 1cr6B c.69.1.11,c.108.1.2 34689,43339 1xel 338 1.53e+01 1xel c.2.1.2 29786 1tt7A 330 1.56e+01 1ofuA 320 1.57e+01 c.32.1.1,d.79.2.1 86972,86973 1a9y 338 1.57e+01 1xel c.2.1.2 29789 1cr6B 554 1.59e+01 1cr6B c.69.1.11,c.108.1.2 34688,43338 1rzmA 338 1.60e+01 c.1.10.4 105137 1u55A 188 1.65e+01 d.278.1.1 107677 1ew0A 130 1.67e+01 1drmA d.110.3.2 40905 1qtnA 164 1.69e+01 1pauA c.17.1.1 30999 1j0dA 341 1.70e+01 c.79.1.1 83902 1poxA 585 1.70e+01 1poxA c.31.1.3,c.36.1.5,c.36.1.9 31731,31793,31794 1delA 241 1.70e+01 1dekA c.37.1.1 31844 1yb2A 275 1.71e+01 1j6uA 469 1.74e+01 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 2djkA 133 1.77e+01 1a0oD 134 1.81e+01 1eayC d.58.24.1 39391 1lj1A 571 1.81e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1ek1A 554 1.84e+01 1cr6B c.69.1.11,c.108.1.2 34685,43335 1wzdA 215 1.84e+01 1mszA 86 1.91e+01 d.68.7.1 79428 1x3lA 440 1.98e+01 2f5gA 133 2.01e+01 2ez9A 603 2.01e+01 1eal 127 2.02e+01 1hmt b.60.1.2 27227 1yyvA 131 2.02e+01 1kssA 571 2.03e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1r2rA 248 2.04e+01 c.1.1.1 96875 1theA 260 2.05e+01 1theB d.3.1.1 37056 1theB 260 2.06e+01 1theB d.3.1.1 37057 1t3tA 1303 2.08e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1p2hA 571 2.12e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 2bdpA 580 2.13e+01 1xwl c.55.3.5,e.8.1.1 33709,43002 1m64A 571 2.15e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1aisB 200 2.15e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1vr6A 350 2.15e+01 1d3uB 201 2.19e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1i45A 248 2.19e+01 1amk c.1.1.1 61665 7odcA 424 2.20e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1y0pA 571 2.22e+01 1qjdA 571 2.24e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1xmpA 170 2.29e+01 1q9iA 571 2.29e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1nk4A 580 2.30e+01 c.55.3.5,e.8.1.1 91923,91924 1e39A 571 2.30e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1pmzA 86 2.33e+01 a.39.1.10 104195 1b93A 152 2.36e+01 1b93A c.24.1.2 31507 2f05A 105 2.36e+01 1ynpA 317 2.36e+01 2tpsA 227 2.38e+01 2tpsA c.1.3.1 28591 1yb5A 351 2.40e+01 3bdpA 580 2.40e+01 1xwl c.55.3.5,e.8.1.1 33711,43004 1u4bA 580 2.42e+01 c.55.3.5,e.8.1.1 107664,107665 1kezA 300 2.45e+01 c.69.1.22 68546 1tpfA 250 2.46e+01 1amk c.1.1.1 28467 1p5hA 428 2.47e+01 c.123.1.1 87802 1jztA 246 2.52e+01 c.104.1.1 63319 1kjs 74 2.55e+01 1kjs a.50.1.1 17792 1dq3A 454 2.60e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1lswA 131 2.69e+01 d.110.3.2 78181 1b93B 152 2.73e+01 1b93A c.24.1.2 31508 1xj4A 119 2.74e+01 2ait 74 2.82e+01 1hoe b.5.1.1 22837 2masA 314 2.85e+01 2masA c.70.1.1 34810 1x0vA 354 2.90e+01 3ait 74 2.92e+01 1hoe b.5.1.1 22835 1i60A 278 2.95e+01 c.1.15.4 71118 1drmA 131 2.95e+01 1drmA d.110.3.2 40908 1g13A 162 3.03e+01 1g13A b.95.1.1 60194 1a4pA 96 3.04e+01 1b4cA a.39.1.2 17176 1hgxA 183 3.08e+01 1tc1A c.61.1.1 34027 1hozA 339 3.10e+01 c.70.1.1 65898 1s1pA 331 3.12e+01 c.1.7.1 98350 1j96A 323 3.19e+01 c.1.7.1 71616 1q41A 424 3.24e+01 d.144.1.7 95774 1ivhA 394 3.24e+01 3mdeA a.29.3.1,e.6.1.1 16608,42869 1whzA 70 3.26e+01 6mhtA 327 3.31e+01 6mhtA c.66.1.26 34226 1tph1 247 3.33e+01 1amk 1hoe 74 3.35e+01 1hoe b.5.1.1 22833 1fj2A 232 3.39e+01 1auoA c.69.1.14 34720 1j8mF 297 3.41e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1zcoA 262 3.43e+01 1xwl 580 3.45e+01 1xwl c.55.3.5,e.8.1.1 33708,43001 2fyxA 143 3.45e+01 3timA 250 3.49e+01 1amk c.1.1.1 28483 1hyhA 309 3.59e+01 1hyhA c.2.1.5,d.162.1.1 30150,42117 2fp3A 316 3.63e+01 1zczA 464 3.66e+01 1n55A 251 3.68e+01 c.1.1.1 80007 1yxcA 292 3.72e+01 1iw0A 215 3.73e+01 a.132.1.1 83720 1ezvD 245 3.79e+01 1be3D a.3.1.3,f.23.11.1 59546,59547 1p4xA 250 3.81e+01 a.4.5.28,a.4.5.28 87784,87785 2fhzB 108 3.85e+01 1h2bA 359 3.90e+01 b.35.1.2,c.2.1.1 90543,90544 1yyaA 250 3.91e+01 1l3sA 580 3.92e+01 c.55.3.5,e.8.1.1 84521,84522 1g47A 77 3.93e+01 1g47A g.39.1.3,g.39.1.3 45147,45148 1ok0A 74 3.95e+01 b.5.1.1 93191 1sg6A 393 3.95e+01 e.22.1.1 105522 1vi2A 300 4.00e+01 c.2.1.7,c.58.1.5 100726,100727 1dqsA 393 4.03e+01 1dqsA e.22.1.1 43347 1wznA 252 4.07e+01 1wstA 417 4.13e+01 1nkl 78 4.15e+01 1nkl a.64.1.1 18140 1yy6A 155 4.18e+01 1q44A 326 4.18e+01 c.37.1.5 95779 3dapA 320 4.19e+01 1dapA c.2.1.3,d.81.1.3 30051,39966 3mhtA 327 4.20e+01 6mhtA c.66.1.26 34234 2fojA 155 4.22e+01 1tfb 208 4.22e+01 1tfb a.74.1.2,a.74.1.2 18382,18383 1kicA 339 4.26e+01 c.70.1.1 72510 1v71A 323 4.29e+01 1yruB 74 4.35e+01 1sdiA 213 4.36e+01 a.198.1.1 105437 1dhpA 292 4.36e+01 1dhpA c.1.10.1 29097 2a1vA 144 4.37e+01 1goh 639 4.37e+01 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 1o5oA 221 4.41e+01 c.61.1.1 92509 1bf6A 291 4.43e+01 1pscA c.1.9.3 29065 1nvmB 312 4.44e+01 c.2.1.3,d.81.1.1 86251,86252 1k3iA 656 4.48e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1b6tA 159 4.49e+01 1b6tA c.26.1.3 31600 1nmoA 247 4.49e+01 c.135.1.1 91980 1j79A 347 4.59e+01 1j79A c.1.9.4 62675 1i24A 404 4.60e+01 c.2.1.2 83663 1ycrA 109 4.60e+01 1ycqA a.42.1.1 17420 1qz4A 213 4.61e+01 a.198.1.1 96613 1gq6A 313 4.62e+01 c.42.1.1 70341 1dapA 320 4.72e+01 1dapA c.2.1.3,d.81.1.3 30053,39968 1rwjA 82 4.75e+01 a.138.1.1 105114 1ng4A 390 4.81e+01 c.3.1.2,d.16.1.3 85666,85667 1kyoD 248 4.82e+01 a.3.1.3,f.23.11.1 73254,73255 1tx2A 297 4.84e+01 c.1.21.1 107420 1t4fM 110 4.85e+01 1l6rA 227 4.89e+01 c.108.1.10 77768 1s6lA 212 4.90e+01 1kzhA 555 4.92e+01 c.89.1.1 73361 2g7uA 257 4.96e+01 1f06A 320 4.96e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1y2qA 143 5.07e+01 1bfd 528 5.07e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1wu7A 434 5.09e+01 1ugnA 198 5.12e+01 b.1.1.4,b.1.1.4 107828,107829 1qjcA 158 5.14e+01 1b6tA c.26.1.3 63328 1fhdA 312 5.18e+01 1taxA c.1.8.3 28915 1zd3A 555 5.19e+01 1gof 639 5.19e+01 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 1hp0A 339 5.24e+01 c.70.1.1 65900 1w24A 182 5.28e+01 1iloA 77 5.28e+01 c.47.1.1 66205 2cdnA 201 5.30e+01 2cxaA 256 5.32e+01 1ha3A 405 5.33e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 2a6nA 292 5.33e+01 1jmkC 230 5.49e+01 c.69.1.22 71747 1wr2A 238 5.54e+01 1zwwA 256 5.55e+01 1ek6A 348 5.57e+01 1xel c.2.1.2 29800 1hmy 327 5.60e+01 6mhtA c.66.1.26 34229 1o4vA 183 5.63e+01 c.23.8.1 86628 1vjuA 309 5.67e+01 d.248.1.1 100835 1efvA 315 5.70e+01 1efvA c.26.2.3,c.31.1.2 31633,31728 1kb9D 246 5.72e+01 a.3.1.3,f.23.11.1 77317,77318 1eylA 186 5.82e+01 1wba b.42.4.1 25593 2gukA 120 5.87e+01 1gmyA 261 5.88e+01 d.3.1.1 76236 1pjzA 203 5.93e+01 c.66.1.36 94794 2a6lA 292 5.95e+01 2c78A 405 5.98e+01 2azqA 311 6.00e+01 1hlvA 131 6.00e+01 a.4.1.7,a.4.1.7 65854,65855 1vj5A 555 6.03e+01 c.108.1.2,c.69.1.11 100799,100800 1dhx 967 6.04e+01 1dhx 1fh9A 312 6.10e+01 1taxA c.1.8.3 28913 2culA 232 6.12e+01 1gthC 1025 6.12e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70493,70494,70495,70496,70497 1ly7A 121 6.12e+01 d.82.2.1 74339 1vqzA 341 6.13e+01 2b5gA 171 6.16e+01 1vbuA 328 6.21e+01 1rsy 152 6.24e+01 1rsy b.7.1.2 23192 1amk 251 6.25e+01 1amk c.1.1.1 28503 1q1vA 70 6.31e+01 a.159.4.1 104479 2his 312 6.34e+01 1taxA c.1.8.3 28918 1eft 405 6.35e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 2ck3H 146 6.35e+01 1e4yA 214 6.35e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1xcbA 211 6.35e+01 a.4.5.38,c.2.1.12 109552,109553 1fnd 314 6.40e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 2a7oA 112 6.40e+01 1f48A 589 6.44e+01 1f48A c.37.1.10,c.37.1.10 32280,32281 1mvwB 145 6.46e+01 i.15.1.1 79524 1mgpA 313 6.49e+01 c.119.1.1 79098 1pu5A 164 6.49e+01 b.95.1.1 104310 1lvl 458 6.53e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1djqA 729 6.56e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1ug6A 431 6.60e+01 c.1.8.4 88490 1mioA 534 6.63e+01 1qguA c.92.2.3 35601 1j7nA 776 6.74e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1a5y 330 6.78e+01 1pty c.45.1.2 32673 1pjcA 361 6.79e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1ryiA 382 6.79e+01 2bnuA 203 6.82e+01 1drqA 131 6.82e+01 1drmA 1dkuA 317 6.83e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1cjsA 219 6.86e+01 1cjsA e.24.1.1 43354 1qy5A 269 6.88e+01 d.122.1.1 96573 1mo2A 294 6.90e+01 c.69.1.22 79331 1qczA 169 6.90e+01 1qczA c.23.8.1 31276 1j8yF 297 6.90e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1m6jA 261 6.94e+01 c.1.1.1 78693 2g6fX 59 6.98e+01 1fsz 372 7.04e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1n4kA 381 7.04e+01 a.118.22.1,b.42.6.1 79992,79993 1djnA 729 7.06e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1q6zA 528 7.08e+01 1qrrA 394 7.08e+01 1qrrA c.2.1.2 29824 1akeA 214 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