# List of top-scoring protein chains for t06-80-60-80-str2+near-backbone-11-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 2essA 248 8.77e-03 1xv2A 237 1.41e-02 1qlpA 394 5.16e-02 1ovaA e.1.1.1 42628 1m1hA 248 6.71e-02 b.114.1.1,d.58.42.1 78415,78416 1gy6A 127 1.11e-01 d.17.4.2 70736 2bvcA 486 2.48e-01 1t0bA 252 2.57e-01 c.23.16.6 106199 1vdwA 254 2.91e-01 e.7.1.1 100569 1feuA 206 3.66e-01 1feuA b.53.1.1 59801 1yloA 348 4.08e-01 1cr1A 296 5.08e-01 1cr1A c.37.1.11 32286 1wznA 252 5.13e-01 2gq1A 332 5.34e-01 2f69A 261 5.40e-01 1j5wA 298 5.51e-01 d.104.1.1 71589 1uteA 313 5.95e-01 1uteA d.159.1.1 42078 1wrvA 308 6.02e-01 1y08A 323 6.29e-01 1uxy 340 6.97e-01 2mbr d.145.1.2,d.146.1.1 41748,41761 1n6aA 259 7.61e-01 b.76.2.1,b.85.7.1 80121,80122 1v25A 541 7.81e-01 e.23.1.1 108275 3gcb 470 8.17e-01 3gcb d.3.1.1 37032 1f89A 291 1.04e+00 d.160.1.1 64988 3cla 213 1.05e+00 3cla c.43.1.1 32610 1gwyA 175 1.16e+00 b.97.1.1 83356 1jcfA 344 1.19e+00 c.55.1.1,c.55.1.1 62878,62879 1v9kA 228 1.34e+00 d.265.1.3 108449 1dl5A 317 1.37e+00 1dl5A c.66.1.7,d.197.1.1 64720,64721 1f1xA 322 1.44e+00 d.32.1.3,d.32.1.3 83208,83209 1nd6A 354 1.47e+00 c.60.1.2 80407 2al3A 90 1.59e+00 1wdjA 187 1.65e+00 1suwA 249 1.81e+00 e.52.1.1 106027 1nuyA 337 1.83e+00 e.7.1.1 86213 1ugjA 141 1.98e+00 b.41.1.3 107826 2f06A 144 2.14e+00 1s98A 107 2.21e+00 b.124.1.1 105377 1whnA 128 2.35e+00 1wyuB 474 2.37e+00 1zo2A 129 2.65e+00 1pgl1 185 2.77e+00 1c1yB 77 2.77e+00 1c1yB d.15.1.5 37618 1xe7A 203 2.78e+00 1m6kA 251 2.99e+00 e.3.1.1 78695 1fukA 165 3.07e+00 1fukA c.37.1.19 32409 1vcoA 550 3.08e+00 c.23.16.1,c.37.1.10 108508,108509 1c3mA 147 3.13e+00 1jotA b.77.3.1 27983 1cv8 174 3.16e+00 1cv8 d.3.1.1 37089 1z0sA 278 3.20e+00 1bw0A 416 3.21e+00 1bw0A c.67.1.1 34385 2fug7 129 3.21e+00 1w41A 101 3.22e+00 1te0A 318 3.25e+00 2hgsA 474 3.34e+00 2hgsA c.30.1.4,d.142.1.6 31722,75997 1jnyA 435 3.37e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1xkzA 255 3.38e+00 1yx1A 264 3.41e+00 2aukA 190 3.41e+00 1jk7A 323 3.53e+00 1auiA d.159.1.3 63144 1pmmA 466 3.62e+00 c.67.1.6 94901 1ys7A 233 3.64e+00 2f7fA 494 3.67e+00 1y4hA 188 3.74e+00 1sdjA 310 3.77e+00 d.21.1.2,d.21.1.2 98807,98808 1sv6A 269 3.81e+00 d.177.1.1 106043 1qtqA 553 3.92e+00 1gtrA b.53.1.2,c.26.1.1 26940,31579 1uhgA 385 4.17e+00 e.1.1.1 88491 1iyeA 309 4.20e+00 e.17.1.1 83786 1vr9A 213 4.24e+00 1qqrA 138 4.25e+00 1bmlC d.15.5.1 37721 1jmsA 381 4.27e+00 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1r4pA 297 4.32e+00 d.165.1.2 97025 1erjA 393 4.48e+00 1erjA b.69.4.1 27660 1uirA 314 4.71e+00 c.66.1.17 99429 1nbcA 155 4.73e+00 1nbcA b.2.2.2 22390 1x3lA 440 4.80e+00 2aneA 125 4.82e+00 1b77A 228 4.93e+00 1b77A d.131.1.2,d.131.1.2 41362,41363 1jg1A 235 4.95e+00 c.66.1.7 66661 1wduA 245 4.99e+00 d.151.1.1 109286 1wosA 364 5.02e+00 b.44.2.1,d.250.1.1 109468,109469 2bl9A 238 5.05e+00 1qveA 126 5.06e+00 d.24.1.1 104594 1r5mA 425 5.08e+00 1jyhA 157 5.12e+00 d.60.1.3 71956 1om4A 422 5.27e+00 d.174.1.1 87067 1lbvA 252 5.29e+00 e.7.1.1 73813 2bh1A 250 5.62e+00 2gk3A 256 5.65e+00 2bjiA 277 5.69e+00 1cvl 319 5.90e+00 1cvl c.69.1.18 34786 2bj7A 138 5.98e+00 1qhqA 140 5.99e+00 1qhqA b.6.1.1 63326 1kv7A 488 5.99e+00 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1uf5A 303 6.03e+00 d.160.1.2 107808 1y12A 165 6.12e+00 1kbvA 327 6.14e+00 b.6.1.3,b.6.1.3 68395,68396 1zpvA 91 6.18e+00 2gjgA 248 6.23e+00 1pxvA 183 6.24e+00 d.3.1.1 95301 1xjcA 169 6.28e+00 1wz9A 375 6.37e+00 1jm1A 204 6.39e+00 b.33.1.1 71745 2bcqA 335 6.51e+00 1n26A 325 6.56e+00 b.1.1.4,b.1.2.1,b.1.2.1 79850,79851,79852 1m7vA 363 6.64e+00 d.174.1.1 78748 1xeeA 91 6.69e+00 1d4tA 104 6.71e+00 1d4tA d.93.1.1 40537 1yljA 263 6.74e+00 1g6aA 271 6.86e+00 1btl e.3.1.1 42704 1n5nA 180 6.87e+00 d.167.1.1 85336 2bs3A 656 6.93e+00 1rtu 114 6.98e+00 9rnt d.1.1.4 36139 1gd7A 109 7.12e+00 b.40.4.4 60441 1z2lA 423 7.17e+00 1b8oA 284 7.24e+00 1b8oA c.56.2.1 33762 1gs5A 258 7.28e+00 c.73.1.2 70395 2amhA 207 7.32e+00 1k20A 310 7.36e+00 c.107.1.1 68027 1tp9A 162 7.59e+00 1vyrA 364 7.74e+00 c.1.4.1 108906 1xm7A 195 7.89e+00 1ispA 181 7.90e+00 c.69.1.18 76778 1vr3A 191 7.98e+00 1q7sA 117 7.98e+00 c.131.1.1 96055 1wn2A 121 8.02e+00 1zmdA 474 8.31e+00 1sek 378 8.31e+00 1sek e.1.1.1 42675 1o69A 394 8.32e+00 c.67.1.4 92560 1vheA 373 8.32e+00 b.49.3.1,c.56.5.4 100669,100670 1y0yA 353 8.34e+00 1hq0A 295 8.35e+00 1hzgA d.194.1.1 61122 1ecsA 126 8.37e+00 1ecsA d.32.1.2 59407 1m65A 245 8.50e+00 c.6.3.1 84847 1xc3A 302 8.52e+00 1tmxA 293 8.60e+00 1ed8A 449 8.72e+00 1b8jA c.76.1.1 34988 1qmvA 197 8.77e+00 1qq2A c.47.1.10 33066 2cy5A 140 8.81e+00 1gefA 123 8.85e+00 1gefA c.52.1.18 60465 1h09A 338 8.97e+00 b.109.1.1,c.1.8.8 83420,83421 1vqqA 646 9.11e+00 1tl9A 339 9.55e+00 1ls1A 295 9.61e+00 a.24.13.1,c.37.1.10 78170,78171 1dzfA 215 9.62e+00 1dzfA c.52.3.1,d.78.1.1 33344,39753 1ys1X 320 9.62e+00 1u8sA 192 9.67e+00 d.58.18.5,d.58.18.5 107737,107738 1zgzA 122 9.79e+00 1im8A 244 9.90e+00 c.66.1.14 66212 1vf7A 369 1.00e+01 f.46.1.1 108557 1umdA 367 1.01e+01 c.36.1.11 99599 1qexA 288 1.01e+01 1qexA b.32.1.1 24425 1gskA 513 1.02e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 2c7pA 327 1.03e+01 1g60A 260 1.04e+01 c.66.1.11 70151 2gnxA 365 1.05e+01 2bwvA 440 1.05e+01 2bcjB 340 1.05e+01 1xvqA 175 1.06e+01 1amuA 563 1.06e+01 1amuA e.23.1.1 43351 1womA 271 1.07e+01 1ri6A 343 1.08e+01 b.69.11.1 97503 1ohvA 472 1.10e+01 c.67.1.4 93031 2fpoA 202 1.11e+01 1bn7A 294 1.11e+01 1bn6A c.69.1.8 34677 1ztpA 251 1.12e+01 1siqA 392 1.12e+01 a.29.3.1,e.6.1.1 105585,105586 1y8aA 332 1.13e+01 1n9eA 787 1.14e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 1g291 372 1.15e+01 1g291 1byfA 125 1.16e+01 1byfA d.169.1.1 42419 1d0cA 444 1.18e+01 d.174.1.1 64769 1oz9A 150 1.18e+01 d.92.1.15 93808 1ghpA 258 1.21e+01 1btl e.3.1.1 60520 1pkhA 204 1.22e+01 b.85.4.1 94832 1w4vA 119 1.22e+01 1gy7A 125 1.25e+01 d.17.4.2 70738 1zn6A 227 1.25e+01 1s5uA 138 1.28e+01 d.38.1.1 98573 1ttuA 477 1.31e+01 b.1.18.1,b.2.5.8,b.42.7.1 107305,107306,107307 1ojrA 274 1.32e+01 c.74.1.1 93147 2fbwA 621 1.36e+01 1qj4A 257 1.36e+01 1qj4A c.69.1.20 34796 1qh5A 260 1.36e+01 1qh5A d.157.1.2 42057 2fnuA 375 1.38e+01 3bamA 213 1.39e+01 1bam c.52.1.3 33288 1ugxA 133 1.39e+01 1r17A 343 1.40e+01 b.2.3.4,b.2.3.4 96796,96797 2aq2B 237 1.41e+01 2cwpA 112 1.41e+01 1h65A 270 1.42e+01 c.37.1.8 65640 1hm9A 468 1.42e+01 b.81.1.4,c.68.1.5 65866,65867 1kb0A 677 1.43e+01 a.3.1.6,b.70.1.1 68378,68379 1m4lA 307 1.45e+01 c.56.5.1 78604 1v5eA 590 1.45e+01 1zx8A 136 1.45e+01 2cwkA 160 1.46e+01 1cby 259 1.47e+01 1cby d.103.1.1 40705 1nr0A 611 1.48e+01 b.69.4.1,b.69.4.1 86078,86079 1g2oA 268 1.49e+01 1b8oA c.56.2.1 60228 2f1fA 164 1.50e+01 1hzoA 271 1.51e+01 e.3.1.1 71092 1v9fA 325 1.51e+01 d.265.1.3 108448 1fus 106 1.53e+01 9rnt d.1.1.4 36050 1aop 497 1.53e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1xngA 268 1.53e+01 1k2eA 156 1.54e+01 d.113.1.1 72010 2bkyX 89 1.57e+01 1cr5A 189 1.58e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1g3qA 237 1.61e+01 1hyqA c.37.1.10 60237 2bmoB 194 1.61e+01 1bupA 386 1.61e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 1wmzA 140 1.62e+01 d.169.1.1 109422 2axoA 270 1.62e+01 1qgvA 142 1.62e+01 1qgvA c.47.1.8 33056 1n9lA 109 1.64e+01 d.110.3.6 85468 1jhfA 202 1.64e+01 a.4.5.2,b.87.1.1 63057,63058 1crzA 403 1.65e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1fjgE 162 1.68e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1usmA 80 1.68e+01 d.74.1.1 99876 1fc6A 388 1.69e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1ji6A 589 1.69e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1zhhB 242 1.71e+01 2bzlA 325 1.72e+01 1uk8A 282 1.73e+01 c.69.1.10 107907 1qyaA 307 1.73e+01 d.21.1.2,d.21.1.2 104653,104654 2f71A 298 1.74e+01 2c5aA 379 1.77e+01 1xffA 240 1.77e+01 d.153.1.1 109580 1dmhA 311 1.77e+01 1dmhA b.3.6.1 22633 1jmcA 246 1.79e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1ftrA 296 1.79e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1vgjA 184 1.80e+01 1lj5A 379 1.81e+01 e.1.1.1 73928 1rds 105 1.81e+01 9rnt d.1.1.4 36236 1rl0A 255 1.82e+01 3seb 238 1.82e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1xtzA 264 1.82e+01 1vloA 381 1.82e+01 b.44.2.1,d.250.1.1 108838,108839 2bt9A 90 1.83e+01 1a8s 273 1.85e+01 1brt c.69.1.12 34710 1eluA 390 1.88e+01 1elqA c.67.1.3 34434 2cwsA 237 1.89e+01 2f5tX 233 1.89e+01 1uwvA 433 1.90e+01 b.40.4.12,c.66.1.40 100128,100129 3daaA 277 1.91e+01 1daaA e.17.1.1 43272 1xruA 282 1.91e+01 2a74B 188 1.92e+01 1ty9A 222 1.92e+01 1wchA 315 1.93e+01 1e8cA 498 1.94e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1oh0A 131 1.97e+01 d.17.4.3 87004 1mngA 203 1.98e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1xtaA 221 1.98e+01 1w1hA 151 1.99e+01 1ufyA 122 1.99e+01 d.79.1.2 88489 1wz8A 264 2.01e+01 1wstA 417 2.03e+01 1i5pA 633 2.04e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1rdqE 350 2.05e+01 d.144.1.7 97314 1tcvA 287 2.09e+01 1kqpA 271 2.09e+01 c.26.2.1 72883 1n57A 291 2.09e+01 c.23.16.2 85328 1s4bP 674 2.09e+01 d.92.1.5 105252 1kmtA 141 2.10e+01 b.1.18.8 77442 1qmyA 167 2.10e+01 1qmyA d.3.1.2 37094 1gouA 116 2.11e+01 d.1.1.2 65429 1e44B 96 2.13e+01 1e44B b.101.1.1 59220 2gd9A 189 2.15e+01 1f46A 140 2.15e+01 1f46A d.129.4.1 59643 1o75A 415 2.17e+01 b.1.20.1,b.1.20.1,b.120.1.1 81117,81118,81119 1mugA 168 2.17e+01 1mugA c.18.1.2 31030 1wh0A 134 2.18e+01 1tif 78 2.20e+01 1tif d.15.8.1 37836 1gotB 340 2.20e+01 1tbgA b.69.4.1 27648 1q45A 391 2.21e+01 c.1.4.1 95780 2f15A 96 2.23e+01 1ojjA 402 2.24e+01 b.29.1.10 93130 1v37A 177 2.25e+01 2aa4A 289 2.25e+01 1z47A 355 2.25e+01 1p1jA 533 2.25e+01 c.2.1.3,d.81.1.3 87687,87688 1ktgA 138 2.26e+01 d.113.1.1 72972 2f57A 317 2.26e+01 1so7A 382 2.27e+01 1w07A 659 2.28e+01 1lnsA 763 2.28e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1htwA 158 2.29e+01 c.37.1.18 71083 1n8jA 186 2.30e+01 c.47.1.10 85401 1nepA 130 2.30e+01 b.1.18.7 80440 1l4dB 122 2.31e+01 d.15.5.1 77684 1o7eA 276 2.32e+01 e.3.1.1 92622 1vybA 238 2.33e+01 d.151.1.1 108897 1vc1A 110 2.33e+01 c.13.2.1 108493 1gvzA 237 2.33e+01 b.47.1.2 76360 1lk2A 274 2.33e+01 b.1.1.2,d.19.1.1 91056,91057 1je5A 206 2.37e+01 1je5A b.40.4.7 62909 1chuA 540 2.41e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1ve6A 582 2.41e+01 1j2rA 199 2.41e+01 c.33.1.3 90788 2fdiA 211 2.41e+01 1m98A 317 2.42e+01 a.175.1.1,d.17.4.6 78866,78867 1h6lA 353 2.42e+01 b.68.3.1 60687 1wtjA 343 2.43e+01 1xwwA 157 2.46e+01 1ym5A 300 2.46e+01 1ub0A 258 2.49e+01 c.72.1.2 88394 2ch4A 320 2.49e+01 1s57A 153 2.50e+01 1hl9A 449 2.51e+01 b.71.1.3,c.1.8.11 90650,90651 1vkkA 154 2.53e+01 d.109.1.2 108669 1ekjA 221 2.57e+01 1ekjB c.53.2.1 33364 8abp 306 2.58e+01 8abp c.93.1.1 35647 2fiqA 420 2.60e+01 1mrg 263 2.61e+01 1mrj d.165.1.1 42183 1ospO 257 2.61e+01 1ospO b.76.1.1 27971 1wvqA 167 2.61e+01 1w96A 554 2.62e+01 1dbhA 354 2.65e+01 1awe a.87.1.1,b.55.1.1 18514,26967 1mpp 361 2.69e+01 2rmpA b.50.1.2 26856 1ek6A 348 2.69e+01 1xel c.2.1.2 29800 2fhqA 141 2.70e+01 1fobA 334 2.75e+01 c.1.8.3 83255 2a8jA 420 2.76e+01 1vhoA 346 2.78e+01 b.49.3.1,c.56.5.4 100694,100695 1ur4A 399 2.78e+01 1w1oA 534 2.79e+01 d.58.32.4,d.145.1.1 109071,109072 2bibA 547 2.82e+01 1pvmA 184 2.82e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1xeoA 168 2.82e+01 1vrmA 325 2.83e+01 2bi0A 337 2.84e+01 1chmA 401 2.84e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1pwbA 177 2.85e+01 d.169.1.1,h.1.1.1 95212,95213 1dtdA 303 2.86e+01 1aye c.56.5.1 33823 1z5rA 306 2.87e+01 2f1lA 187 2.87e+01 1xo7A 166 2.87e+01 2aifA 135 2.88e+01 1qu9A 128 2.91e+01 1qu9A d.79.1.1 39755 1h2wA 710 2.91e+01 b.69.7.1,c.69.1.4 76596,76597 2fvgA 340 2.92e+01 1e25A 282 2.92e+01 1e25A e.3.1.1 42731 1eybA 471 2.95e+01 1ey2A b.82.1.4 28115 1rm6A 769 3.00e+01 1s1hC 192 3.00e+01 i.1.1.1 105156 1uf3A 228 3.00e+01 d.159.1.6 99317 1ry9A 145 3.00e+01 d.198.1.1 98094 1k8wA 327 3.02e+01 b.122.1.1,d.265.1.2 83094,90388 1p35A 299 3.03e+01 1p35A b.28.1.1 23925 1s1pA 331 3.03e+01 c.1.7.1 98350 1xr4A 509 3.05e+01 1vicA 262 3.07e+01 c.68.1.13 100756 1yphC 131 3.08e+01 1l9kA 305 3.10e+01 c.66.1.25 84569 1xm8A 254 3.13e+01 1vr4A 103 3.14e+01 1v0wA 506 3.14e+01 d.136.1.2,d.136.1.2 108220,108221 2c4bA 143 3.16e+01 1i9gA 280 3.17e+01 c.66.1.13 62090 1sgvA 316 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