# List of top-scoring protein chains for t06-100-40-40-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 2d4pA 141 4.63e-02 1vhsA 175 5.39e-02 d.108.1.1 100698 2bswA 146 7.29e-02 1mk4A 157 7.89e-02 d.108.1.1 84979 1z4rA 168 9.69e-02 1rxyA 253 1.26e-01 c.56.2.1 98065 1on0A 158 1.28e-01 d.108.1.1 87095 1q2yA 140 3.21e-01 d.108.1.1 95655 1xt8A 292 3.63e-01 2ewcA 126 3.67e-01 1d4xG 126 3.99e-01 1d0nA d.109.1.1 59109 1zbfA 142 4.07e-01 2fl4A 149 4.93e-01 1xviA 275 4.98e-01 2g3aA 152 5.00e-01 1t44G 147 5.36e-01 d.109.1.1 106395 1vc1A 110 5.58e-01 c.13.2.1 108493 1xm7A 195 7.36e-01 1lssA 140 7.40e-01 c.2.1.9 74246 1ec7A 446 8.10e-01 1bqg c.1.11.2,d.54.1.1 29218,38862 1akz 223 8.16e-01 3eugA c.18.1.1 31007 2gx9A 129 8.85e-01 2beiA 170 9.18e-01 2gcuA 245 9.50e-01 3nul 130 9.78e-01 3nul d.110.1.1 40891 1wnaA 131 1.00e+00 1wsrA 375 1.01e+00 1bn7A 294 1.03e+00 1bn6A c.69.1.8 34677 1u04A 771 1.05e+00 b.34.14.1,c.55.3.10 107539,107540 2d28C 149 1.07e+00 1jykA 254 1.12e+00 c.68.1.13 67458 2bhuA 602 1.26e+00 1qh5A 260 1.27e+00 1qh5A d.157.1.2 42057 1u02A 239 1.29e+00 c.108.1.15 107538 1jysA 242 1.31e+00 c.56.2.1 77216 1xc3A 302 1.61e+00 2a1vA 144 1.62e+00 2a7mA 250 1.63e+00 1yqzA 438 1.72e+00 1i12A 160 1.85e+00 1i21A d.108.1.1 61515 1jjtA 228 1.88e+00 1a7tA d.157.1.1 63139 1xm8A 254 1.94e+00 1id1A 153 1.97e+00 1id1A c.2.1.9 62286 1pvgA 418 2.00e+00 d.14.1.3,d.122.1.2 95161,95162 1rz3A 201 2.26e+00 c.37.1.6 98132 1vybA 238 2.27e+00 d.151.1.1 108897 1l6rA 227 2.31e+00 c.108.1.10 77768 1yvoA 172 2.39e+00 1xdpA 687 2.45e+00 1x8hA 228 2.46e+00 1wzcA 249 2.52e+00 1wstA 417 2.55e+00 1t4oA 117 2.64e+00 d.50.1.1 106425 1wosA 364 2.69e+00 b.44.2.1,d.250.1.1 109468,109469 1t6cA 315 2.86e+00 c.55.1.8,c.55.1.8 106558,106559 1jubA 311 2.94e+00 c.1.4.1 90908 1tiqA 180 3.03e+00 d.108.1.1 107010 2b5gA 171 3.03e+00 2fz4A 237 3.15e+00 1ixcA 294 3.16e+00 a.4.5.37,c.94.1.1 83764,83765 1zxxA 319 3.20e+00 1wduA 245 3.21e+00 d.151.1.1 109286 2fg9A 178 3.23e+00 1vd6A 224 3.27e+00 1zo0A 126 3.44e+00 1rloA 271 3.45e+00 1qstA 160 3.57e+00 1yghA d.108.1.1 40804 1fo8A 343 3.63e+00 1foaA c.68.1.10 59927 1je0A 236 3.64e+00 c.56.2.1 66581 1stzA 338 3.74e+00 a.4.5.51,d.110.2.3 106009,106010 1r6wA 322 3.97e+00 c.1.11.2,d.54.1.1 97165,97166 1zczA 464 4.26e+00 1xo7A 166 4.27e+00 2cy2A 174 4.28e+00 1q77A 138 4.29e+00 c.26.2.4 96023 1ycoA 279 4.30e+00 1tp9A 162 4.31e+00 2a1hA 365 4.39e+00 1x8gA 227 4.44e+00 1wekA 217 4.62e+00 1e87A 118 4.70e+00 1b6e d.169.1.1 42327 1nv8A 284 4.77e+00 c.66.1.30 86224 1xtoA 311 4.83e+00 1h4xA 117 4.93e+00 1auz c.13.2.1 60626 1qo3C 137 5.01e+00 1qo3C d.169.1.1 42350 1d1qA 161 5.02e+00 1dg9A c.44.1.1 32642 1mk0A 97 5.14e+00 d.226.1.1 79216 1khtA 192 5.50e+00 c.37.1.1 84401 1y13A 181 5.69e+00 1yt3A 375 5.83e+00 1k8kB 394 5.89e+00 c.55.1.1 68307 1gw5S 142 6.01e+00 d.110.4.2 70633 1yirA 408 6.22e+00 1ki9A 192 6.40e+00 c.37.1.1 84404 1bjt 793 6.40e+00 1bjt e.11.1.1 43249 1vkhA 273 6.54e+00 c.69.1.32 108662 1fecA 490 6.69e+00 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1z9tA 255 6.73e+00 2bkrA 212 6.85e+00 2bmfA 451 6.89e+00 1t0fA 276 7.11e+00 1pjcA 361 7.19e+00 1sayA c.2.1.4,c.23.12.2 30101,31361 1q67A 231 7.35e+00 b.55.1.7 95960 1zccA 248 7.46e+00 2bkyX 89 7.51e+00 1x9zA 188 7.63e+00 2fp4B 395 7.76e+00 2aeuA 374 7.79e+00 1xkrA 206 7.97e+00 2c4wA 176 8.09e+00 1vkcA 158 8.17e+00 1spvA 184 8.79e+00 c.50.1.2 98957 1fvuB 125 8.83e+00 1ixxB d.169.1.1 42346 1wcv1 257 8.86e+00 2fymA 431 8.94e+00 1gmxA 108 9.28e+00 c.46.1.3 65355 1ta9A 450 9.44e+00 1khyA 148 9.50e+00 a.174.1.1 77410 2fhxA 246 9.55e+00 1vjlA 164 9.60e+00 d.257.1.1 100822 1xmtA 103 9.69e+00 2cohA 202 9.92e+00 1ypqA 135 9.98e+00 1mqoA 227 1.00e+01 d.157.1.1 103846 1rlmA 271 1.01e+01 1g5tA 196 1.01e+01 1g5rA c.37.1.11 32366 2c5qA 240 1.02e+01 1u0mA 382 1.02e+01 c.95.1.2,c.95.1.2 107557,107558 1n62B 809 1.02e+01 d.41.1.1,d.133.1.1 80092,80093 1jc4A 148 1.02e+01 1jc4A d.32.1.4 62863 1y2qA 143 1.02e+01 1h1dA 221 1.02e+01 c.66.1.1 83452 1m2xA 223 1.03e+01 d.157.1.1 84764 1odkA 235 1.03e+01 c.56.2.1 86863 1es5A 262 1.05e+01 1skf e.3.1.1 42679 1gvjA 146 1.06e+01 a.4.5.21 90525 1zc6A 305 1.08e+01 1o5zA 442 1.09e+01 c.59.1.2,c.72.2.2 92530,92531 2f9zC 159 1.10e+01 1i9zA 347 1.10e+01 1i9yA d.151.1.2 62102 1t3tA 1303 1.12e+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 2c5uA 375 1.13e+01 1hgxA 183 1.13e+01 1tc1A c.61.1.1 34027 1cnv 299 1.16e+01 1cnv c.1.8.5 28989 1zzoA 136 1.17e+01 1vp2A 208 1.17e+01 1r77A 103 1.18e+01 1zosA 230 1.18e+01 1yksA 440 1.22e+01 1uuyA 167 1.22e+01 c.57.1.1 108059 1jznA 135 1.23e+01 d.169.1.1 84262 1kkoA 413 1.23e+01 c.1.11.2,d.54.1.1 68675,68676 1mai 131 1.23e+01 1mai b.55.1.1 26951 1vi6A 208 1.23e+01 c.23.15.1 100736 1vloA 381 1.24e+01 b.44.2.1,d.250.1.1 108838,108839 1zjjA 263 1.25e+01 1kg0C 136 1.26e+01 d.169.1.1 72445 1prxA 224 1.27e+01 1prxA c.47.1.10 33076 1jl0A 334 1.28e+01 1jenA d.156.1.1 63155 1yx0A 159 1.29e+01 2fg1A 158 1.34e+01 1udh 244 1.34e+01 3eugA c.18.1.1 31015 1ydyA 356 1.34e+01 2booA 247 1.34e+01 2czrA 226 1.35e+01 2g7zA 282 1.36e+01 2g1uA 155 1.38e+01 1o20A 427 1.39e+01 c.82.1.1 86556 1ny1A 240 1.39e+01 c.6.2.3 86395 1vhwA 253 1.41e+01 c.56.2.1 100706 1yymG 313 1.42e+01 1iibA 106 1.42e+01 1iibA c.44.2.1 32648 1h70A 255 1.43e+01 1h70A d.126.1.3 60711 1qx4A 274 1.43e+01 b.43.4.2,c.25.1.1 104624,104625 1vk1A 242 1.44e+01 d.268.1.2 108634 1oj4A 283 1.46e+01 d.14.1.5,d.58.26.5 93083,93084 1cl1A 395 1.50e+01 1cl2A c.67.1.3 34395 2f8aA 208 1.50e+01 1ey4A 149 1.50e+01 1snc b.40.1.1 24815 2bv5A 282 1.50e+01 1dzkA 157 1.52e+01 1obpA b.60.1.1 27096 1tzpA 255 1.54e+01 d.65.1.3 107520 2ae6A 166 1.55e+01 1ko3A 230 1.56e+01 d.157.1.1 90974 1qmhA 347 1.56e+01 1qmhA c.47.2.1,d.68.2.1 33082,39568 1vlmA 219 1.56e+01 c.66.1.41 108836 2aefA 234 1.57e+01 4eugA 229 1.57e+01 3eugA c.18.1.1 31019 1o13A 136 1.57e+01 c.55.5.1 80762 1qz5A 375 1.58e+01 c.55.1.1,c.55.1.1 96614,96615 1ni9A 338 1.61e+01 e.7.1.2 85739 1o98A 511 1.63e+01 c.105.1.1,c.76.1.3 86684,86685 1x7oA 287 1.65e+01 1lrzA 426 1.67e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 2bjkA 516 1.68e+01 1ve3A 227 1.68e+01 1uwzA 136 1.68e+01 c.97.1.1 108081 1ukfA 188 1.73e+01 d.3.1.10 99488 2es7A 142 1.78e+01 1jyeA 349 1.78e+01 c.93.1.1 67455 1huxA 270 1.81e+01 1huxA c.55.1.5 61278 1ceo 343 1.82e+01 1ceo c.1.8.3 28808 2g0qA 173 1.82e+01 1e4yA 214 1.83e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1wu7A 434 1.83e+01 1hw5A 210 1.85e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1f8mA 429 1.85e+01 1dquA c.1.12.7 29315 1l3iA 192 1.88e+01 c.66.1.22 77676 2fe7A 166 1.90e+01 1xkpC 143 1.91e+01 2bszA 278 1.93e+01 1s12A 94 1.94e+01 1poiB 260 1.95e+01 1poiB c.124.1.3 34155 2bsxA 253 1.96e+01 1mw7A 240 1.98e+01 e.39.1.1 79557 1g2rA 100 2.00e+01 1g2rA d.192.1.1 60231 1o0xA 262 2.00e+01 d.127.1.1 80755 1yb2A 275 2.00e+01 1rvkA 382 2.03e+01 c.1.11.2,d.54.1.1 97928,97929 1uxy 340 2.03e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1wn5A 130 2.04e+01 1ujcA 161 2.04e+01 1qamA 244 2.04e+01 2ercA c.66.1.24 34220 1yarH 217 2.10e+01 2f5xA 312 2.11e+01 1cxqA 162 2.13e+01 1cxqA c.55.3.2 33621 1umkA 275 2.15e+01 1vrvA 101 2.15e+01 2bkyA 97 2.19e+01 7odcA 424 2.21e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1tkkA 366 2.22e+01 c.1.11.2,d.54.1.1 107089,107090 1xebA 150 2.24e+01 1ryp2 233 2.24e+01 1ryp2 1pne 140 2.27e+01 1pne d.110.1.1 40866 1u6tA 121 2.28e+01 1x9mA 698 2.30e+01 3thiA 371 2.31e+01 2thiA c.94.1.1 35792 1x3mA 415 2.32e+01 1vkpA 383 2.32e+01 d.126.1.6 108686 3bamA 213 2.32e+01 1bam c.52.1.3 33288 1ef8A 261 2.34e+01 1ef8A c.14.1.3 30921 1a7tA 232 2.36e+01 1a7tA d.157.1.1 42041 1p99A 295 2.36e+01 c.94.1.1 94384 1vs0A 310 2.38e+01 1voqa 90 2.40e+01 1uhvA 500 2.42e+01 b.71.1.2,c.1.8.3 99402,99403 1epuA 591 2.43e+01 1dn1A e.25.1.1 43358 1wzuA 300 2.43e+01 1y9wA 140 2.44e+01 2cvlA 124 2.44e+01 1euvA 221 2.45e+01 1euvA d.3.1.7 37133 1xvwA 160 2.45e+01 3cla 213 2.45e+01 3cla c.43.1.1 32610 1f0kA 364 2.46e+01 1f0kA c.87.1.2 35465 1th0A 226 2.47e+01 d.3.1.7 106903 1ne2A 200 2.47e+01 c.66.1.32 85586 2irfG 113 2.48e+01 2irfG a.4.5.23 16185 1sr8A 298 2.48e+01 e.54.1.1 105959 1nn5A 215 2.50e+01 c.37.1.1 85892 2a2nA 176 2.51e+01 1vk8A 106 2.55e+01 d.58.48.1 108636 1bdfA 235 2.57e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1dqaA 467 2.63e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 1xfjA 261 2.63e+01 d.194.1.2 109585 1ct5A 256 2.66e+01 1ct5A c.1.6.2 28663 2gu3A 136 2.66e+01 1tjxA 159 2.67e+01 2akzA 439 2.67e+01 1ne9A 335 2.68e+01 d.108.1.4,d.108.1.4 91839,91840 1rv9A 259 2.68e+01 d.194.1.2 105105 1kzfA 230 2.69e+01 d.108.1.3 73354 2dg5A 366 2.70e+01 1zx0A 236 2.70e+01 1reqA 727 2.72e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1a53 247 2.72e+01 1a53 c.1.2.4 28564 2plc 274 2.73e+01 2plc c.1.18.2 29614 1k8kA 418 2.78e+01 c.55.1.1,c.55.1.1 68305,68306 1o7nA 449 2.79e+01 b.33.1.2,d.129.3.3 81162,81163 1bcpB 199 2.80e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 1vdmA 153 2.82e+01 1d5rA 324 2.82e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 2cxcA 144 2.86e+01 1y5eA 169 2.89e+01 1o1xA 155 2.92e+01 c.121.1.1 86553 2fcjA 119 2.93e+01 1pz1A 333 2.95e+01 c.1.7.1 95390 2bmoA 447 2.99e+01 1k6iA 352 2.99e+01 c.2.1.2 68223 1kqpA 271 2.99e+01 c.26.2.1 72883 1i39A 225 3.06e+01 1ekeA c.55.3.1 61585 1ylqA 96 3.08e+01 1muwA 386 3.10e+01 c.1.15.3 79495 1yemA 179 3.11e+01 1xkzA 255 3.14e+01 1vqoB 338 3.17e+01 1vmeA 410 3.20e+01 c.23.5.1,d.157.1.3 108893,108894 1pzxA 289 3.21e+01 c.119.1.1 95484 1yrkA 126 3.22e+01 1mrzA 293 3.26e+01 b.43.5.1,c.26.1.3 91452,91453 1ub3A 220 3.26e+01 c.1.10.1 88395 1f28A 297 3.26e+01 1bkpA d.117.1.1 59608 1hh1A 143 3.28e+01 1gefA c.52.1.18 61036 1jb0D 138 3.29e+01 1jb0D d.187.1.1 62823 1k0fA 277 3.30e+01 c.92.2.2 71974 1ktgA 138 3.30e+01 d.113.1.1 72972 1bo4A 168 3.31e+01 1bo4A d.108.1.1 40798 1up7A 417 3.33e+01 1uzbA 516 3.33e+01 c.82.1.1 100220 1e8gA 560 3.33e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1zavA 180 3.36e+01 1xgkA 352 3.36e+01 1wg8A 285 3.37e+01 1n7oA 721 3.37e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 2biiA 424 3.39e+01 1m6yA 301 3.40e+01 a.60.13.1,c.66.1.23 78716,78717 1n1xA 124 3.44e+01 d.5.1.1 91548 2fxuA 375 3.45e+01 1w4tA 299 3.51e+01 2az4A 429 3.54e+01 1p5dX 463 3.55e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1iv3A 152 3.57e+01 d.79.5.1 76828 1wv2A 265 3.57e+01 1j6wA 175 3.58e+01 1j98A d.185.1.2 62663 2cy5A 140 3.60e+01 1zmdA 474 3.66e+01 1rkqA 282 3.68e+01 c.108.1.10 97621 1hs6A 611 3.69e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1gx1A 160 3.71e+01 d.79.5.1 70675 1q0uA 219 3.74e+01 c.37.1.19 95512 2fs3A 282 3.75e+01 1njrA 284 3.79e+01 c.50.1.2 103858 2fyxA 143 3.79e+01 1toaA 313 3.81e+01 1toaA c.92.2.2 35598 1ypfA 336 3.82e+01 2fueA 262 3.84e+01 1rwhA 757 3.85e+01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1nf2A 268 3.86e+01 c.108.1.10 91849 2cxxA 190 3.88e+01 1vhuA 211 3.90e+01 c.50.1.2 100703 1e4fT 419 3.90e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1gx5A 536 3.90e+01 e.8.1.4 70682 1wozA 177 3.91e+01 1zk7A 467 3.94e+01 2gdqA 382 3.95e+01 1squA 155 3.95e+01 d.252.1.1 98971 1vlpA 441 3.95e+01 d.41.2.2,d.41.2.3 108840,108841 1wguA 136 3.96e+01 1p5tA 127 3.96e+01 b.55.1.2 94148 1kamA 194 3.97e+01 c.26.1.3 72254 1xs5A 241 3.98e+01 1dmlA 319 3.99e+01 1dmlA d.131.1.2,d.131.1.2 41380,41381 1bykA 255 3.99e+01 1bykA c.93.1.1 35706 1vjzA 341 4.00e+01 c.1.8.3 100838 1g3p 217 4.01e+01 1g3p b.37.1.1,b.37.1.1 24788,24789 1ga8A 311 4.02e+01 1ga8A c.68.1.4 34516 1pjhA 280 4.03e+01 c.14.1.3 94761 1wlqC 201 4.03e+01 a.4.5.52 109400 2as9A 210 4.04e+01 1gxuA 91 4.06e+01 d.58.10.1 76378 1pq4A 291 4.09e+01 c.92.2.2 94995 1t8hA 277 4.09e+01 d.194.1.2 106664 1wd5A 208 4.09e+01 1grj 158 4.10e+01 1grj a.2.1.1,d.26.1.2 15691,38433 2cx1A 187 4.12e+01 2dg5B 190 4.13e+01 1l0qA 391 4.13e+01 b.1.3.1,b.69.2.3 77644,77645 1v5vA 401 4.14e+01 1wy7A 207 4.15e+01 1jftA 340 4.16e+01 a.35.1.5,c.93.1.1 66652,66653 1tzfA 259 4.17e+01 c.68.1.13 107476 1ztcA 221 4.19e+01 1qddA 144 4.20e+01 1qddA d.169.1.1 42324 1vqoL 165 4.20e+01 1y7rA 133 4.21e+01 1t6sA 162 4.22e+01 1jr2A 286 4.22e+01 c.113.1.1 67111 1v37A 177 4.25e+01 1u7nA 336 4.29e+01 c.77.1.4 107726 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