# List of top-scoring protein chains for t04-100-40-40-str2+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 1vhsA 175 3.69e-02 d.108.1.1 100698 2bswA 146 7.02e-02 1z4rA 168 7.93e-02 1q2yA 140 9.99e-02 d.108.1.1 95655 2d4pA 141 1.59e-01 1mk4A 157 1.69e-01 d.108.1.1 84979 2ewcA 126 1.71e-01 1rxyA 253 1.77e-01 c.56.2.1 98065 1on0A 158 2.81e-01 d.108.1.1 87095 1lx7A 253 4.84e-01 c.56.2.1 74329 2fl4A 149 6.88e-01 1ecpA 238 7.82e-01 1ecpA c.56.2.1 33775 2g3aA 152 9.12e-01 1vc1A 110 9.19e-01 c.13.2.1 108493 1qh5A 260 9.50e-01 1qh5A d.157.1.2 42057 1qh3A 260 9.96e-01 1qh5A d.157.1.2 42059 1d4xG 126 1.15e+00 1d0nA d.109.1.1 59109 4pfk 319 1.16e+00 3pfk c.89.1.1 35582 1bn7A 294 1.20e+00 1bn6A c.69.1.8 34677 1y9kA 157 1.23e+00 1lssA 140 1.24e+00 c.2.1.9 74246 1t44G 147 1.33e+00 d.109.1.1 106395 1z5oA 242 1.47e+00 1ec7A 446 1.61e+00 1bqg c.1.11.2,d.54.1.1 29218,38862 2bzpA 226 1.64e+00 2bl1A 172 1.85e+00 2gcuA 245 1.91e+00 2gx9A 129 1.96e+00 2d28C 149 2.02e+00 1jl0A 334 2.03e+00 1jenA d.156.1.1 63155 3nul 130 2.05e+00 3nul d.110.1.1 40891 1tp9A 162 2.09e+00 1khtA 192 2.10e+00 c.37.1.1 84401 1xt8A 292 2.10e+00 1yvoA 172 2.21e+00 1rz3A 201 2.24e+00 c.37.1.6 98132 1z5nA 242 2.27e+00 1xm7A 195 2.28e+00 1zbfA 142 2.33e+00 1nm1G 125 2.36e+00 d.109.1.1 80653 1wstA 417 2.38e+00 1k9sA 237 2.41e+00 c.56.2.1 68359 1je0A 236 2.43e+00 c.56.2.1 66581 1fhuA 320 2.48e+00 1fhuA c.1.11.2,d.54.1.1 29234,38878 1jysA 242 2.48e+00 c.56.2.1 77216 2a7mA 250 2.74e+00 1r6wA 322 2.79e+00 c.1.11.2,d.54.1.1 97165,97166 1wsrA 375 2.87e+00 1akz 223 2.94e+00 3eugA c.18.1.1 31007 1xm8A 254 3.11e+00 1i12A 160 3.19e+00 1i21A d.108.1.1 61515 1wnaA 131 3.28e+00 2bhuA 602 3.31e+00 1jykA 254 3.41e+00 c.68.1.13 67458 1tiqA 180 3.45e+00 d.108.1.1 107010 2fz4A 237 3.45e+00 1yarH 217 3.77e+00 1xtoA 311 3.77e+00 2a1vA 144 4.24e+00 1pjcA 361 4.26e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 2d27A 149 4.31e+00 1jubA 311 4.49e+00 c.1.4.1 90908 2bmfA 451 4.52e+00 1u04A 771 4.71e+00 b.34.14.1,c.55.3.10 107539,107540 1qstA 160 5.15e+00 1yghA d.108.1.1 40804 1x8hA 228 5.18e+00 2bsxA 253 5.19e+00 1zzoA 136 5.20e+00 1e79G 272 5.27e+00 1e79G c.49.2.1 33158 2g1uA 155 5.43e+00 1zxxA 319 5.45e+00 1pvgA 418 5.50e+00 d.14.1.3,d.122.1.2 95161,95162 2ae6A 166 5.68e+00 1zwxA 301 5.95e+00 2dorA 311 5.99e+00 2dorA c.1.4.1 28593 1xviA 275 6.03e+00 1wosA 364 6.16e+00 b.44.2.1,d.250.1.1 109468,109469 1xdpA 687 6.26e+00 1x8gA 227 6.41e+00 2cy2A 174 6.65e+00 1l6rA 227 6.89e+00 c.108.1.10 77768 1h4xA 117 6.94e+00 1auz c.13.2.1 60626 1o0xA 262 7.03e+00 d.127.1.1 80755 1y2qA 143 7.04e+00 1wduA 245 7.09e+00 d.151.1.1 109286 1vybA 238 7.12e+00 d.151.1.1 108897 1ujcA 161 7.24e+00 1id1A 153 7.43e+00 1id1A c.2.1.9 62286 1k8kB 394 7.45e+00 c.55.1.1 68307 1q77A 138 7.50e+00 c.26.2.4 96023 1q67A 231 7.60e+00 b.55.1.7 95960 1jjtA 228 7.75e+00 1a7tA d.157.1.1 63139 1q1gA 276 7.86e+00 c.56.2.1 95574 1nv8A 284 7.86e+00 c.66.1.30 86224 1vkhA 273 7.91e+00 c.69.1.32 108662 1eqjA 511 8.02e+00 1ejjA c.105.1.1,c.76.1.3 59495,59496 1o98A 511 8.08e+00 c.105.1.1,c.76.1.3 86684,86685 1xc3A 302 8.18e+00 1aa8A 347 8.20e+00 1an9A 1ki9A 192 8.26e+00 c.37.1.1 84404 1gmxA 108 8.38e+00 c.46.1.3 65355 2fymA 431 8.55e+00 1w6tA 444 8.68e+00 1lsuA 147 8.68e+00 c.2.1.9 74250 1odkA 235 8.79e+00 c.56.2.1 86863 1mk0A 97 8.81e+00 d.226.1.1 79216 1nksA 194 8.88e+00 1nksA c.37.1.1 31886 1d1qA 161 8.93e+00 1dg9A c.44.1.1 32642 2kfnA 605 9.02e+00 1xwl c.55.3.5,e.8.1.1 33682,42975 1ta9A 450 9.05e+00 1yvkA 163 9.09e+00 1ve9A 347 9.28e+00 c.4.1.2,d.16.1.3 100571,100572 1vd6A 224 9.55e+00 1k07A 263 9.62e+00 d.157.1.1 77218 1pfkA 320 9.85e+00 3pfk c.89.1.1 35575 1xfjA 261 9.90e+00 d.194.1.2 109585 1jjeA 222 1.02e+01 1a7tA d.157.1.1 63117 1stzA 338 1.02e+01 a.4.5.51,d.110.2.3 106009,106010 2beiA 170 1.03e+01 1uuyA 167 1.04e+01 c.57.1.1 108059 1vhwA 253 1.05e+01 c.56.2.1 100706 2plc 274 1.06e+01 2plc c.1.18.2 29614 1iibA 106 1.06e+01 1iibA c.44.2.1 32648 1gw5S 142 1.07e+01 d.110.4.2 70633 1spvA 184 1.08e+01 c.50.1.2 98957 1v8eA 224 1.10e+01 1yksA 440 1.12e+01 2c4wA 176 1.13e+01 1zo0A 126 1.14e+01 1vqzA 341 1.15e+01 1epaA 164 1.17e+01 1epaA b.60.1.1 27128 1wekA 217 1.17e+01 1dorA 311 1.18e+01 2dorA c.1.4.1 28595 2c5qA 240 1.19e+01 2b5gA 171 1.19e+01 1t6cA 315 1.20e+01 c.55.1.8,c.55.1.8 106558,106559 1zc6A 305 1.22e+01 1udvA 89 1.23e+01 d.68.6.1 99224 1y9wA 140 1.23e+01 1fecA 490 1.24e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1i1dA 161 1.24e+01 1i21A d.108.1.1 61526 1rloA 271 1.26e+01 1tidB 119 1.30e+01 c.13.2.1 107000 1y13A 181 1.30e+01 5ukdA 194 1.32e+01 1zin c.37.1.1 31851 1r5jA 337 1.34e+01 c.77.1.5 97097 1hs6A 611 1.34e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1t3tA 1303 1.37e+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 1vk8A 106 1.39e+01 d.58.48.1 108636 1yqzA 438 1.43e+01 1yx0A 159 1.46e+01 2afcA 168 1.49e+01 2g0qA 173 1.50e+01 1xclA 235 1.50e+01 1vrvA 101 1.51e+01 1an9A 340 1.52e+01 1an9A c.4.1.2,d.16.1.3 30617,37904 1xmtA 103 1.57e+01 1dzkA 157 1.59e+01 1obpA b.60.1.1 27096 2a1hA 365 1.61e+01 1lrzA 426 1.64e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1mqoA 227 1.65e+01 d.157.1.1 103846 1t6sA 162 1.65e+01 1g5tA 196 1.66e+01 1g5rA c.37.1.11 32366 1o20A 427 1.67e+01 c.82.1.1 86556 1sr8A 298 1.68e+01 e.54.1.1 105959 1u0mA 382 1.69e+01 c.95.1.2,c.95.1.2 107557,107558 1wryA 121 1.70e+01 1ztcA 221 1.73e+01 1yirA 408 1.74e+01 2avnA 260 1.74e+01 1m2xA 223 1.74e+01 d.157.1.1 84764 2arzA 247 1.78e+01 1h1dA 221 1.79e+01 c.66.1.1 83452 1t4oA 117 1.81e+01 d.50.1.1 106425 1mdl 359 1.83e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 1uxy 340 1.83e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1swxA 209 1.84e+01 a.224.1.1 106075 1x9zA 188 1.85e+01 1vkrA 125 1.85e+01 c.44.2.1 108689 1o8uA 257 1.88e+01 c.14.1.3 81194 2gk3A 256 1.89e+01 1y5eA 169 1.91e+01 2f9zC 159 1.91e+01 2bc2A 227 1.93e+01 1a7tA d.157.1.1 42031 1mw7A 240 1.93e+01 e.39.1.1 79557 1xo7A 166 1.94e+01 2aefA 234 1.94e+01 1wn5A 130 1.94e+01 1zjjA 263 1.96e+01 1fo8A 343 1.98e+01 1foaA c.68.1.10 59927 1zccA 248 2.00e+01 1udh 244 2.01e+01 3eugA c.18.1.1 31015 2fg9A 178 2.01e+01 2pfkA 320 2.03e+01 3pfk c.89.1.1 35577 1vid 221 2.07e+01 1vid c.66.1.1 34178 1lqtA 456 2.08e+01 c.3.1.1,c.4.1.1 74198,74199 1k2yX 463 2.09e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1szoA 257 2.10e+01 c.14.1.3 106164 1ixcA 294 2.11e+01 a.4.5.37,c.94.1.1 83764,83765 1yr0A 175 2.11e+01 1ekfA 365 2.13e+01 1ekfA e.17.1.1 59445 2cvlA 124 2.14e+01 1ddf 127 2.14e+01 1ddf a.77.1.2 18423 1u6tA 121 2.16e+01 1vsd 152 2.16e+01 1cxqA c.55.3.2 33625 1bykA 255 2.16e+01 1bykA c.93.1.1 35706 1ve3A 227 2.16e+01 1vk1A 242 2.17e+01 d.268.1.2 108634 1i9zA 347 2.18e+01 1i9yA d.151.1.2 62102 2cxcA 144 2.19e+01 2bkyX 89 2.20e+01 1cnv 299 2.25e+01 1cnv c.1.8.5 28989 1qf9A 194 2.25e+01 1zin c.37.1.1 31848 2aujD 309 2.29e+01 2bfgA 503 2.31e+01 1hskA 326 2.33e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1zczA 464 2.42e+01 1jetA 517 2.44e+01 1jevA c.94.1.1 35718 1uh5A 329 2.48e+01 c.2.1.2 107840 1tkkA 366 2.50e+01 c.1.11.2,d.54.1.1 107089,107090 1un8A 552 2.51e+01 c.119.1.2,a.208.1.1 103806,99661 1ktaA 365 2.51e+01 e.17.1.1 77533 2bkqA 212 2.56e+01 1zosA 230 2.56e+01 2cohA 202 2.58e+01 1sxgA 280 2.59e+01 1u02A 239 2.60e+01 c.108.1.15 107538 1ofgA 381 2.60e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1vjlA 164 2.60e+01 d.257.1.1 100822 1itwA 741 2.60e+01 c.77.1.2 76793 2bs9A 503 2.60e+01 1s12A 94 2.61e+01 1esiA 262 2.63e+01 1skf e.3.1.1 42682 1kkoA 413 2.64e+01 c.1.11.2,d.54.1.1 68675,68676 1vloA 381 2.64e+01 b.44.2.1,d.250.1.1 108838,108839 1o1xA 155 2.64e+01 c.121.1.1 86553 1xvwA 160 2.74e+01 1c25 161 2.76e+01 1c25 c.46.1.1 32698 2fe7A 166 2.84e+01 2fcjA 119 2.86e+01 1cl1A 395 2.87e+01 1cl2A c.67.1.3 34395 2bsaA 303 2.91e+01 1wg8A 285 2.92e+01 1ur3M 319 2.92e+01 c.1.7.1 99806 1j5pA 253 2.93e+01 d.81.1.3,c.2.1.3 71577,83092 1uhvA 500 2.93e+01 b.71.1.2,c.1.8.3 99402,99403 1yghA 164 2.98e+01 1yghA d.108.1.1 40802 1yb2A 275 3.00e+01 1que 303 3.03e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1mvoA 136 3.04e+01 c.23.1.1 79513 1ylqA 96 3.06e+01 1d4xA 375 3.06e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 2gvkA 317 3.07e+01 2mnr 357 3.09e+01 2mnr c.1.11.2,d.54.1.1 29245,38889 1od6A 160 3.10e+01 c.26.1.3 86836 1voqa 90 3.10e+01 1skoA 143 3.10e+01 d.110.7.1 105676 1t8qA 336 3.11e+01 c.1.18.3 106669 1n3gA 113 3.13e+01 d.204.1.1 79962 1qmhA 347 3.15e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 1e2gA 215 3.15e+01 3tmkA c.37.1.1 59165 1e2fA 215 3.17e+01 3tmkA c.37.1.1 59164 1lxjA 104 3.18e+01 d.58.48.1 84736 1sh0A 510 3.19e+01 e.8.1.4 98876 1jc4A 148 3.21e+01 1jc4A d.32.1.4 62863 1w34A 304 3.23e+01 7odcA 424 3.24e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 3xis 387 3.25e+01 4xis c.1.15.3 29423 1cydA 244 3.25e+01 1cydA c.2.1.2 29825 1dgaA 375 3.25e+01 1yagA 1yqdA 366 3.26e+01 1vp2A 208 3.26e+01 2bkrA 212 3.26e+01 1tzpA 255 3.30e+01 d.65.1.3 107520 3cla 213 3.30e+01 3cla c.43.1.1 32610 1ryp2 233 3.34e+01 1ryp2 1gvjA 146 3.35e+01 a.4.5.21 90525 1prxA 224 3.36e+01 1prxA c.47.1.10 33076 1nn5A 215 3.36e+01 c.37.1.1 85892 1vefA 395 3.38e+01 1oheA 348 3.40e+01 c.45.1.1,c.45.1.1 87013,87014 1q60A 99 3.40e+01 1o13A 136 3.40e+01 c.55.5.1 80762 1ogiA 303 3.41e+01 b.43.4.2,c.25.1.1 92914,92915 2dri 271 3.41e+01 2dri c.93.1.1 35637 2booA 247 3.44e+01 2gdqA 382 3.48e+01 1eudB 396 3.54e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1ycoA 279 3.56e+01 1dqaA 467 3.56e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 1go2A 304 3.60e+01 b.43.4.2,c.25.1.1 76243,76244 1s4nA 348 3.62e+01 c.68.1.16 98501 2es7A 142 3.62e+01 1sqgA 429 3.67e+01 a.79.1.3,c.66.1.38 105912,105913 1zx0A 236 3.69e+01 1up7A 417 3.71e+01 2faoA 309 3.71e+01 2bkyA 97 3.74e+01 1ne2A 200 3.75e+01 c.66.1.32 85586 1gypA 358 3.75e+01 1dssG c.2.1.3,d.81.1.1 30004,39919 1kqpA 271 3.78e+01 c.26.2.1 72883 1s6yA 450 3.80e+01 c.2.1.5,d.162.1.2 105314,105315 1ukfA 188 3.82e+01 d.3.1.10 99488 4eugA 229 3.84e+01 3eugA c.18.1.1 31019 1tvnA 293 3.85e+01 1qo3C 137 3.86e+01 1qo3C d.169.1.1 42350 1vjpA 394 3.88e+01 c.2.1.3,d.81.1.3 100828,100829 2fg1A 158 3.89e+01 1xkrA 206 3.90e+01 1dmlA 319 3.91e+01 1dmlA d.131.1.2,d.131.1.2 41380,41381 2bszA 278 3.91e+01 1q8iA 783 3.94e+01 c.55.3.5,e.8.1.1 96208,96209 1xkzA 255 3.98e+01 2fhxA 246 4.01e+01 1k8kA 418 4.01e+01 c.55.1.1,c.55.1.1 68305,68306 1f6dA 376 4.02e+01 1f6dA c.87.1.3 35467 2c5uA 375 4.02e+01 1poiB 260 4.05e+01 1poiB c.124.1.3 34155 1mrzA 293 4.06e+01 b.43.5.1,c.26.1.3 91452,91453 1v4pA 157 4.06e+01 1xebA 150 4.08e+01 2bv5A 282 4.08e+01 1oneA 436 4.08e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1kamA 194 4.08e+01 c.26.1.3 72254 1qqgA 264 4.10e+01 1qqgA b.55.1.2,b.55.1.2 26987,26988 1ujmA 342 4.11e+01 1muwA 386 4.12e+01 c.1.15.3 79495 1khyA 148 4.12e+01 a.174.1.1 77410 3dni 260 4.13e+01 3dni d.151.1.1 41791 1k0fA 277 4.16e+01 c.92.2.2 71974 4enl 436 4.19e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1i4wA 353 4.23e+01 c.66.1.24 66028 2b43A 526 4.26e+01 1vmeA 410 4.29e+01 c.23.5.1,d.157.1.3 108893,108894 1yymG 313 4.31e+01 1vdmA 153 4.32e+01 2cxxA 190 4.33e+01 1ih8A 271 4.41e+01 2nsyA c.26.2.1 62377 1x31C 206 4.42e+01 1ypqA 135 4.44e+01 1ydyA 356 4.46e+01 3pmgA 561 4.47e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1jb0D 138 4.50e+01 1jb0D d.187.1.1 62823 1bdfA 235 4.51e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1n1xA 124 4.58e+01 d.5.1.1 91548 1a7tA 232 4.58e+01 1a7tA d.157.1.1 42041 1up6A 416 4.59e+01 c.2.1.5,d.162.1.2 107976,107977 1njrA 284 4.59e+01 c.50.1.2 103858 1iyxA 432 4.60e+01 c.1.11.1,d.54.1.1 83815,83816 2dg5B 190 4.61e+01 2al2A 436 4.62e+01 1ub3A 220 4.64e+01 c.1.10.1 88395 1larA 575 4.66e+01 1larA c.45.1.2,c.45.1.2 32693,32694 1nh8A 304 4.66e+01 c.94.1.1,d.58.5.3 80507,80508 1wzcA 249 4.67e+01 1xs5A 241 4.70e+01 1q6zA 528 4.70e+01 1hjxA 362 4.70e+01 c.1.8.5,d.26.3.1 83512,83513 1te6A 439 4.76e+01 c.1.11.1,d.54.1.1 106797,106798 1jtkA 136 4.77e+01 c.97.1.1 71862 1f61A 429 4.78e+01 1dquA c.1.12.7 29319 1avpA 204 4.80e+01 1avpA d.3.1.7 37132 2cruA 118 4.80e+01 2bjkA 516 4.81e+01 1n8jA 186 4.81e+01 c.47.1.10 85401 1zyeA 220 4.81e+01 1zs7A 190 4.82e+01 1nf2A 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