# 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 2a9uA 144 3.42e-03 1i1rB 181 9.45e-02 1i1rB a.26.1.1 61548 2c3mA 1231 1.55e-01 2cwyA 94 2.43e-01 1s9pA 227 2.60e-01 a.123.1.1 105384 1hh8A 213 3.42e-01 1e96B a.118.8.1 61042 1dvoA 152 3.74e-01 1dvoA a.136.1.1 19623 1xszA 356 4.96e-01 1oyzA 280 6.18e-01 a.118.1.16 93775 1colA 204 6.59e-01 1a87 f.1.1.1 43378 1vbiA 344 7.05e-01 1zs3A 182 8.00e-01 1lniA 96 9.97e-01 d.1.1.2 74046 1kpsB 171 1.00e+00 a.118.12.1 68787 1mp1A 111 1.07e+00 a.188.1.1 91382 1di1A 300 1.09e+00 1di1A a.128.1.4 19446 1pylA 97 1.09e+00 d.1.1.2 104391 1mgrA 99 1.45e+00 d.1.1.2 79106 1cuk 203 1.46e+00 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1u2wA 122 1.53e+00 1go3F 107 1.66e+00 a.60.8.2 65407 1y0uA 96 1.70e+00 1tfr 305 2.03e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1q87A 221 2.27e+00 e.47.1.1 96192 1x8vA 455 2.92e+00 1r1uA 106 3.10e+00 a.4.5.5 104771 1ew4A 106 3.20e+00 1ew4A d.82.2.1 40023 1zl8B 54 3.27e+00 1tbfA 347 3.28e+00 a.211.1.2 106743 1no1A 126 3.30e+00 a.179.1.1 85913 1gvhA 396 3.31e+00 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1lwbA 122 3.32e+00 a.133.1.3 84728 1vmaA 306 3.83e+00 a.24.13.1,c.37.1.10 108887,108888 1u61A 138 3.94e+00 a.149.1.1 107696 1rzsA 61 4.02e+00 a.35.1.2 105139 1unkA 87 4.20e+00 1cei a.28.2.1 16935 1zroA 602 4.48e+00 1pbwA 216 4.59e+00 1pbwA a.116.1.1 19103 1ujwB 135 4.59e+00 h.4.9.1 99472 1kb9A 431 4.86e+00 d.185.1.1,d.185.1.1 77311,77312 1w07A 659 4.89e+00 1vi0A 206 5.10e+00 a.4.1.9,a.121.1.1 100720,100721 1ll2A 333 5.21e+00 c.68.1.14 74005 2f22A 144 5.32e+00 1w68A 390 5.72e+00 a.25.1.2 109216 1pszA 303 5.94e+00 1toaA c.92.2.2 35600 2c5uA 375 5.95e+00 1yz7A 188 6.24e+00 1utxA 66 6.36e+00 a.35.1.3 108034 1hw5A 210 6.40e+00 2cgpA a.4.5.4,b.82.3.2 16098,28137 1lrv 244 6.55e+00 1lrv a.118.1.5 19146 1f7uA 607 6.58e+00 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1yt3A 375 6.62e+00 1u4bA 580 6.63e+00 c.55.3.5,e.8.1.1 107664,107665 1nznA 126 6.81e+00 a.118.8.1 92382 1xnfA 275 6.86e+00 2b1eA 564 7.15e+00 1gweA 503 7.22e+00 e.5.1.1 70667 1m98A 317 7.41e+00 a.175.1.1,d.17.4.6 78866,78867 1hm6A 346 7.50e+00 1avc a.65.1.1 18147 1fpzA 212 7.53e+00 1fpzA c.45.1.1 59976 1xcbA 211 7.65e+00 a.4.5.38,c.2.1.12 109552,109553 1r9dA 787 7.93e+00 c.7.1.1 104865 1hx1B 114 8.05e+00 1hx1B a.7.7.1 61350 2b4jC 98 8.10e+00 2cruA 118 8.18e+00 2c1xA 456 8.26e+00 1yb3A 175 8.48e+00 1vddA 228 8.48e+00 e.49.1.1 108519 1wa8A 99 8.77e+00 1ng6A 148 9.66e+00 a.182.1.1 85670 1zy4A 303 9.66e+00 1mpgA 282 9.84e+00 1mpgA a.96.1.3,d.129.1.2 18747,41296 2b5aA 77 1.01e+01 1vh4A 435 1.03e+01 b.80.6.1 100640 1ds1A 324 1.04e+01 1drtA b.82.2.2 28127 2gpiA 91 1.05e+01 1z7lA 276 1.06e+01 1sheA 103 1.09e+01 d.274.1.1 105551 1gakA 141 1.10e+01 1gakA a.19.1.1 16415 1zybA 232 1.11e+01 1k7wA 468 1.12e+01 a.127.1.1 72130 1yqyA 523 1.12e+01 1wt4A 73 1.13e+01 1thtA 305 1.17e+01 1thtA c.69.1.13 34711 1zg2A 107 1.24e+01 1y7yA 74 1.27e+01 2d8dA 90 1.27e+01 2fupA 168 1.32e+01 1xk4A 93 1.32e+01 2anxA 146 1.33e+01 1a0cA 438 1.34e+01 1a0cA c.1.15.3 29529 1pzlA 237 1.34e+01 a.123.1.1 104393 2bl0B 145 1.34e+01 1ho8A 480 1.38e+01 1ho8A a.118.1.9 61107 2fug1 438 1.38e+01 1n97A 389 1.43e+01 a.104.1.1 80335 1a5t 334 1.46e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1muwA 386 1.49e+01 c.1.15.3 79495 1kr7A 110 1.51e+01 a.1.1.4 72890 1ehiA 377 1.54e+01 1iow c.30.1.2,d.142.1.1 31716,41484 1j2mA 99 1.56e+01 a.165.1.1 84018 1ka2A 499 1.57e+01 d.92.1.5 77305 1pvaA 110 1.57e+01 1a75A a.39.1.4 17207 1qynA 153 1.57e+01 d.33.1.1 96597 1v7bA 185 1.58e+01 1z5zA 271 1.60e+01 1wz8A 264 1.61e+01 1wa5B 530 1.62e+01 1s9rA 410 1.62e+01 d.126.1.4 98758 1q52A 314 1.64e+01 c.14.1.3 95846 1mv8A 436 1.65e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1tjvA 474 1.66e+01 a.127.1.1 107054 1zthA 258 1.66e+01 1vjxA 157 1.68e+01 a.25.1.1 100837 1vg8A 207 1.73e+01 c.37.1.8 108606 1iq8A 582 1.73e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1y2kA 349 1.74e+01 2c2xA 281 1.79e+01 2d00A 109 1.79e+01 1wy0A 342 1.82e+01 1y8aA 332 1.82e+01 2a1iA 146 1.84e+01 1p7tA 731 1.88e+01 c.1.13.1 94319 2ae0X 345 1.90e+01 1vfgA 390 1.91e+01 a.173.1.1,d.218.1.4 108570,108571 1v38A 78 1.94e+01 a.60.1.2 100280 1sur 215 1.99e+01 1sur c.26.2.2 31620 1dytA 133 2.00e+01 7rsa d.5.1.1 37288 1rxqA 178 2.00e+01 a.213.1.1 105118 1wc3A 219 2.00e+01 1wgzA 510 2.01e+01 2bnmA 198 2.03e+01 1a0p 290 2.03e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1kdxB 28 2.04e+01 2g7sA 194 2.06e+01 1v9nA 360 2.07e+01 2fuqA 747 2.10e+01 1z5hA 780 2.12e+01 1jhfA 202 2.13e+01 a.4.5.2,b.87.1.1 63057,63058 1f0lA 535 2.13e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1dgfA 497 2.19e+01 1cf9A e.5.1.1 42782 1fseA 74 2.21e+01 1fseA a.4.6.2 60000 1x6zA 123 2.26e+01 1bjt 793 2.28e+01 1bjt e.11.1.1 43249 1g2nA 264 2.31e+01 1lbd a.123.1.1 60227 1ufzA 83 2.32e+01 a.5.9.1 107821 2gmyA 153 2.37e+01 2bykA 140 2.37e+01 1b3uA 588 2.39e+01 1b3uA a.118.1.2 19135 1zklA 353 2.41e+01 1mjhA 162 2.41e+01 1mjhA c.26.2.4 31639 1t56A 216 2.42e+01 a.4.1.9,a.121.1.1 106428,106429 1jqnA 883 2.45e+01 c.1.12.3 77159 1pq4A 291 2.49e+01 c.92.2.2 94995 1s6lA 212 2.52e+01 1s8nA 205 2.58e+01 c.23.1.1 105374 1jkoC 52 2.59e+01 a.4.1.2 66809 1x0tA 120 2.60e+01 1zwyA 185 2.63e+01 1r1tA 122 2.65e+01 a.4.5.5 104769 1v54H 85 2.72e+01 a.51.1.1 100329 1y7qA 98 2.75e+01 1keaA 221 2.77e+01 a.96.1.2 68491 1cipA 353 2.77e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1q79A 514 2.80e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1ee4A 423 2.84e+01 1ee4A a.118.1.1 19128 1w2fA 276 2.84e+01 d.143.1.3 109125 1e8yA 966 2.86e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1qbjA 81 2.89e+01 1qbjA a.4.5.19 16155 1w2yA 229 2.90e+01 a.204.1.1 109140 1x6iA 91 2.90e+01 1ls1A 295 2.94e+01 a.24.13.1,c.37.1.10 78170,78171 1bed 181 2.96e+01 1fvkA c.47.1.13 90330 1v63A 101 2.96e+01 a.21.1.1 108391 2cxnA 557 2.97e+01 1wloA 136 2.97e+01 1zarA 282 2.98e+01 1u55A 188 3.02e+01 d.278.1.1 107677 1nd4A 264 3.03e+01 d.144.1.6 91815 1m7kA 99 3.05e+01 a.7.7.1 74573 1k8kD 300 3.05e+01 d.198.2.1,d.198.2.1 68309,68310 1svsA 353 3.06e+01 c.37.1.8 106051 1dlyA 164 3.09e+01 1dlyA a.1.1.1 14983 1dk8A 147 3.09e+01 1agrE a.91.1.1 18548 2gkpA 167 3.10e+01 1m12A 84 3.11e+01 a.64.1.1 84745 3lynA 136 3.12e+01 1lis a.19.1.1 16413 1eh8A 207 3.18e+01 1sfe a.4.2.1,c.55.7.1 16077,33752 2c0rA 362 3.23e+01 1qmyA 167 3.24e+01 1qmyA d.3.1.2 37094 1mkmA 249 3.37e+01 a.4.5.33,d.110.2.2 79242,79243 1xs5A 241 3.38e+01 1hu3A 260 3.38e+01 1hu3A a.118.1.14 19137 1jhgA 101 3.40e+01 1jhgA a.4.12.1 19009 2f05A 105 3.45e+01 1oaa 259 3.47e+01 1oaa c.2.1.2 29829 1nnvA 110 3.51e+01 d.17.7.1 92012 1w8iA 156 3.53e+01 1d2zB 153 3.54e+01 1d2zB a.77.1.2 18439 1f5nA 592 3.55e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1usyA 275 3.59e+01 2cujA 108 3.59e+01 1wzaA 488 3.59e+01 1ztuA 341 3.71e+01 1u5tA 233 3.73e+01 a.4.5.54,a.4.5.54 107684,107685 1qgtA 149 3.78e+01 1qgtA a.62.1.1 18135 1gqiA 708 3.83e+01 c.1.8.10,d.92.2.2 76279,76280 1pi1A 185 3.87e+01 a.29.7.1 94699 2oatA 439 3.88e+01 2dkb c.67.1.4 34452 1ohuA 175 3.89e+01 f.1.4.1 93029 2cp8A 54 3.90e+01 1gl2C 65 3.99e+01 h.1.15.1 65280 1h3nA 878 4.01e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1jx4A 352 4.06e+01 d.240.1.1,e.8.1.7 90378,90379 2dh4A 340 4.08e+01 1xpcA 248 4.15e+01 1p99A 295 4.16e+01 c.94.1.1 94384 1s28A 132 4.18e+01 d.198.1.1 105223 1q3eA 207 4.31e+01 b.82.3.2 95669 1hw7A 255 4.32e+01 1i7fA d.193.1.1 61297 1ajsA 412 4.36e+01 1ajsA c.67.1.1 34276 1iyhA 198 4.39e+01 a.45.1.1,c.47.1.5 83790,83791 1qwtA 255 4.41e+01 b.26.1.3 96501 2fp1A 166 4.41e+01 1tw9A 206 4.49e+01 a.45.1.1,c.47.1.5 107381,107382 1vjvA 415 4.51e+01 d.3.1.9 108632 1k5dB 201 4.56e+01 b.55.1.3 68169 1nekC 129 4.56e+01 f.21.2.2 80431 1gl2D 65 4.57e+01 h.1.15.1 65281 2a6hC 1119 4.62e+01 1jmsA 381 4.62e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1gtkA 313 4.65e+01 c.94.1.1,d.50.2.1 76346,76347 1su8A 636 4.68e+01 e.26.1.2 98999 1vs0A 310 4.69e+01 2ghjA 118 4.73e+01 1srqA 341 4.73e+01 e.55.1.1 105967 1nekD 115 4.76e+01 f.21.2.2 80432 1oxjA 173 4.76e+01 a.60.1.2,a.118.1.13 87517,87518 1aisB 200 4.76e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1kgnA 329 4.78e+01 a.25.1.2 68584 2f6hX 419 4.81e+01 1x75A 132 4.90e+01 1uj6A 227 4.91e+01 c.124.1.4,d.58.40.1 107898,107899 1aocA 175 4.92e+01 1aocA g.17.1.5 44817 1kl9A 182 4.93e+01 b.40.4.5 72681 2b0jA 358 4.97e+01 1utg 70 4.98e+01 1utg a.101.1.1 18813 1zk8A 183 5.02e+01 1lbvA 252 5.03e+01 e.7.1.1 73813 1wm1A 317 5.04e+01 c.69.1.7 109405 1y9qA 192 5.04e+01 2ar0A 541 5.05e+01 1lmb3 92 5.08e+01 1lmb3 1yn9A 169 5.08e+01 1nrzA 164 5.16e+01 c.38.1.1 86131 1zx4A 192 5.16e+01 1erp 38 5.24e+01 2erl a.10.1.1 16363 1qczA 169 5.30e+01 1qczA c.23.8.1 31276 1xo5A 183 5.30e+01 2d1eA 248 5.38e+01 2fji1 399 5.41e+01 1u0fA 564 5.42e+01 1sumB 235 5.44e+01 a.7.12.1 106025 1qh8A 478 5.45e+01 1qguA c.92.2.3 35633 1xu9A 286 5.50e+01 1pjhA 280 5.52e+01 c.14.1.3 94761 1k0fA 277 5.57e+01 c.92.2.2 71974 1sedA 117 5.58e+01 a.219.1.1 105449 1tqxA 227 5.64e+01 1khdA 345 5.66e+01 a.46.2.1,c.27.1.1 77400,77401 1o9iA 266 5.66e+01 a.25.1.3 92671 1jli 112 5.69e+01 1jli a.26.1.2 16884 2erl 40 5.72e+01 2erl a.10.1.1 16360 1x93A 55 5.72e+01 2f3nA 76 5.77e+01 1i36A 264 5.81e+01 a.100.1.8,c.2.1.6 71108,71109 1dk0A 188 5.89e+01 1b2vA d.35.1.1 38530 1mzgA 146 5.93e+01 d.224.1.1 79696 1yloA 348 5.94e+01 1q35A 320 6.04e+01 c.94.1.1 95661 1hfeS 123 6.07e+01 1hfeS a.137.4.1 19640 1ff9A 450 6.18e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1tqnA 486 6.19e+01 a.104.1.1 107238 1uz3A 102 6.24e+01 1wer 334 6.25e+01 1wer a.116.1.2 19108 1hjrA 158 6.25e+01 1hjrA c.55.3.6 33727 1w96A 554 6.31e+01 1ksoA 101 6.33e+01 a.39.1.2 72926 1dgnA 89 6.35e+01 1dgnA a.77.1.3 18436 1uzeA 589 6.56e+01 d.92.1.5 108174 1yemA 179 6.60e+01 2eulA 156 6.64e+01 1us7B 265 6.65e+01 a.205.1.1 99858 1aj8A 371 6.66e+01 1aj8A a.103.1.1 18900 1oe8A 211 6.70e+01 a.45.1.1,c.47.1.5 86905,86906 1kf6D 119 6.72e+01 f.21.2.2 72400 1hynP 379 6.73e+01 1hynP d.112.1.2 61408 2fnaA 357 6.73e+01 1y791 680 6.73e+01 1wwzA 159 6.74e+01 5csmA 256 6.85e+01 5csmA a.130.1.2 19494 1omrA 201 6.97e+01 a.39.1.5 93349 1d2nA 272 6.97e+01 1d2nA c.37.1.20 32428 1xrsA 516 7.04e+01 2bbhA 269 7.07e+01 1fs0G 230 7.07e+01 1fs0G c.49.2.1 59999 1jmuB 666 7.09e+01 1wy9A 147 7.09e+01 2fjrA 189 7.12e+01 1bc5A 269 7.17e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 2a6cA 83 7.17e+01 1o04A 500 7.18e+01 c.82.1.1 86508 1yozA 116 7.18e+01 1g8pA 350 7.28e+01 1g8pA c.37.1.20 60376 1ppjA 446 7.31e+01 d.185.1.1,d.185.1.1 104252,104253 2bcqA 335 7.36e+01 1a6q 382 7.36e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1xqwA 293 7.40e+01 2fb5A 205 7.45e+01 1iznB 277 7.45e+01 e.43.1.2 83848 1ekeA 230 7.46e+01 1ekeA c.55.3.1 33572 2fd5A 180 7.51e+01 1jf9A 408 7.55e+01 1c0nA c.67.1.3 62931 1sh0A 510 7.63e+01 e.8.1.4 98876 1vjgA 218 7.64e+01 c.23.10.6 100810 1jr8A 117 7.70e+01 a.24.15.1 67115 1tqgA 105 7.71e+01 a.24.10.3 107224 1z67A 135 7.71e+01 2es4D 332 7.72e+01 2h1nA 567 7.72e+01 1d8wA 426 7.79e+01 1de5A c.1.15.2 29394 1cqxA 403 7.81e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1ugpA 203 7.82e+01 d.149.1.1 107831 2fhpA 187 7.86e+01 1oz9A 150 7.88e+01 d.92.1.15 93808 1oyjA 231 7.90e+01 a.45.1.1,c.47.1.5 87597,87598 1jpaA 312 7.99e+01 d.144.1.7 67011 1ppjB 439 8.00e+01 d.185.1.1,d.185.1.1 104254,104255 1o26A 232 8.04e+01 d.207.1.1 86566 1xc1A 309 8.06e+01 c.94.1.1 109543 1ixcA 294 8.13e+01 a.4.5.37,c.94.1.1 83764,83765 1uptB 60 8.13e+01 a.193.1.1 99768 1fqiA 147 8.15e+01 1agrE a.91.1.1 18542 1uayA 242 8.18e+01 c.2.1.2 88390 1orjA 130 8.23e+01 a.24.19.1 93456 1ucrA 78 8.24e+01 a.4.5.45 99188 1xqoA 256 8.29e+01 1c52 131 8.30e+01 1c52 a.3.1.1 15810 1ib2A 349 8.31e+01 1ib2A a.118.1.8 62141 1zljA 78 8.33e+01 2csoA 127 8.34e+01 2gaeA 346 8.41e+01 1yzvA 204 8.49e+01 1rktA 205 8.49e+01 a.4.1.9,a.121.1.1 97623,97624 1yrbA 262 8.51e+01 1puiA 210 8.55e+01 c.37.1.8 88292 1izoA 417 8.60e+01 a.104.1.1 83851 1yodA 30 8.61e+01 1mtzA 293 8.61e+01 c.69.1.7 79467 1wljA 189 8.62e+01 1nwaA 203 8.63e+01 d.58.28.1 86295 1l5aA 436 8.63e+01 c.43.1.2,c.43.1.2 75923,75924 1evyA 366 8.64e+01 1evyA a.100.1.6,c.2.1.6 18811,30215 1jbeA 128 8.68e+01 3chy c.23.1.1 62845 1xg8A 111 8.69e+01 1xeoA 168 8.71e+01 2gfsA 372 8.71e+01 2lisA 136 8.72e+01 1lis a.19.1.1 16405 1mswD 883 8.72e+01 e.8.1.3 79427 1u58A 253 8.77e+01 1vctA 205 8.81e+01 1vixA 420 8.82e+01 c.56.5.4,d.58.19.1 100777,100778 2bo4A 397 8.82e+01 2genA 197 8.82e+01 1adr 76 8.83e+01 1r69 a.35.1.2 17042 1f20A 435 8.83e+01 b.43.4.1,c.25.1.4 64932,64933 1spgA 144 8.84e+01 1abwA a.1.1.2 15409 1mw9X 592 8.89e+01 e.10.1.1 91480 1pd3A 58 8.91e+01 a.30.3.1 94512 1r3dA 264 8.99e+01