# List of top-scoring protein chains for t04-100-30-alpha-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 2ct7A 86 1.99e-01 1vk6A 269 2.06e-01 d.113.1.4,d.113.1.4 100851,100852 1s72Z 73 2.11e-01 g.41.8.1 105345 1wrvA 308 2.71e-01 1vqoZ 83 2.77e-01 1ww8A 439 2.80e-01 1vckA 115 3.71e-01 1jj2Y 73 5.18e-01 1ffkW g.41.8.1 63110 1odhA 174 5.38e-01 d.239.1.1 86850 1kmtA 141 5.83e-01 b.1.18.8 77442 1qqqA 264 6.26e-01 1bkpA d.117.1.1 40931 1evfA 264 6.36e-01 1bkpA d.117.1.1 40932 1deoA 233 6.49e-01 1deoA c.23.10.4 31345 1k7cA 233 7.19e-01 c.23.10.4 68267 1hvyA 288 7.27e-01 1bkpA d.117.1.1 41049 1ifqA 138 8.78e-01 1ifqA d.110.4.1 62350 1jm1A 204 8.99e-01 b.33.1.1 71745 1fsoA 139 9.82e-01 1rhoA b.1.18.8 60007 1mswD 883 1.11e+00 e.8.1.3 79427 1ypvA 313 1.21e+00 2g2kA 170 1.35e+00 1d0qA 103 1.42e+00 1d0qA g.41.3.2 45208 2g8mA 264 1.43e+00 2g8oA 264 1.44e+00 2cklB 165 1.47e+00 1vd4A 62 1.56e+00 1ji1A 637 1.62e+00 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 2aq6A 147 1.69e+00 1rfs 139 1.79e+00 1rfs b.33.1.1 24434 1ur6B 52 1.79e+00 g.44.1.1 99812 1k3eA 156 1.90e+00 d.198.1.1 68103 1i1kA 309 2.10e+00 1daaA e.17.1.1 61533 1r6lA 239 2.11e+00 d.14.1.4,d.101.1.1 97153,97154 1uh4A 637 2.30e+00 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 3daaA 277 2.49e+00 1daaA e.17.1.1 43272 1x75A 132 2.65e+00 1iyeA 309 2.67e+00 e.17.1.1 83786 1w9aA 147 2.87e+00 1xxoA 147 3.26e+00 1wpkA 146 3.34e+00 1d4xA 375 3.37e+00 1yagA c.55.1.1,c.55.1.1 59107,59108 1u79A 129 3.54e+00 d.26.1.1 107714 1upiA 225 3.74e+00 b.82.1.1 99757 1dgaA 375 3.90e+00 1yagA 2csvA 72 3.96e+00 1nv8A 284 4.03e+00 c.66.1.30 86224 1qz5A 375 4.11e+00 c.55.1.1,c.55.1.1 96614,96615 2fxuA 375 4.18e+00 1u8bA 133 4.20e+00 1o12A 376 4.24e+00 b.92.1.5,c.1.9.10 80758,80759 1e53A 59 4.44e+00 1e53A g.49.1.2 45356 1l8dA 112 4.51e+00 h.4.12.1 73687 1g38A 393 4.66e+00 2admA c.66.1.27 60235 1dl0A 37 4.85e+00 1dl0A g.3.6.2 44112 1exkA 79 4.89e+00 1exkA g.54.1.1 45384 1lm5A 214 5.01e+00 d.211.2.1 74029 1ee8A 266 5.06e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 2ampA 304 5.18e+00 1weoA 93 5.24e+00 1mr1C 99 5.32e+00 d.217.1.2 79420 2g8yA 385 5.62e+00 1inp 400 5.99e+00 1inp e.7.1.1 42972 1wuaA 375 6.02e+00 1g8kB 133 6.08e+00 1g8jB b.33.1.1 24435 1sp1 29 6.10e+00 g.37.1.1 45051 1qvbA 481 6.20e+00 1qvbA c.1.8.4 28983 1qlnA 883 6.28e+00 1cezA e.8.1.3 43111 1vphA 149 6.56e+00 1rb9 53 6.67e+00 1rb9 g.41.5.1 45214 1a4yB 123 6.74e+00 7rsa d.5.1.1 37296 1g6aA 271 7.13e+00 1btl e.3.1.1 42704 1m22A 503 7.14e+00 c.117.1.1 78464 1adn 92 7.21e+00 1adn g.48.1.1 45348 1brfA 53 7.21e+00 1rb9 g.41.5.1 45236 1y3nA 490 7.36e+00 830cA 168 7.63e+00 1ck7A d.92.1.11 40400 1bq9A 54 7.64e+00 1rb9 g.41.5.1 45238 1ptq 50 7.67e+00 1ptq g.49.1.1 45349 1l1oC 181 8.02e+00 b.40.4.3 73480 1un3A 123 8.06e+00 d.5.1.1 99646 1theA 260 8.10e+00 1theB d.3.1.1 37056 1pfvA 551 8.14e+00 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1jx4A 352 8.72e+00 d.240.1.1,e.8.1.7 90378,90379 1mea 28 8.75e+00 g.41.1.1 45176 1o7iA 119 8.80e+00 b.40.4.3 86642 1fp0A 88 8.90e+00 1fp0A g.50.1.2 45361 1yk4A 52 9.00e+00 1rmd 116 9.06e+00 1rmd g.37.1.1,g.44.1.1 45025,45322 1rdg 53 9.21e+00 1rb9 g.41.5.1 45221 1nykA 165 9.23e+00 b.33.1.1 86408 1o5uA 101 9.24e+00 b.82.1.8 92518 1f4lA 551 9.25e+00 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 2bwkA 121 9.30e+00 2aujD 309 9.30e+00 1k8kA 418 9.43e+00 c.55.1.1,c.55.1.1 68305,68306 2cklA 108 9.45e+00 2fqpA 97 9.47e+00 1zgwA 139 9.71e+00 2bx9A 53 9.78e+00 1r5mA 425 9.86e+00 1afp 51 9.88e+00 1afp g.26.1.1 44947 2a1rA 430 1.01e+01 1zd9A 188 1.01e+01 1ywmA 200 1.02e+01 1w2lA 99 1.03e+01 2dasA 62 1.04e+01 1wd2A 60 1.04e+01 g.44.1.1 109232 1lvoA 302 1.06e+01 b.47.1.4 74284 2aaa 484 1.09e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1sefA 274 1.09e+01 b.82.1.11 105452 2an1A 292 1.10e+01 1hl9A 449 1.12e+01 b.71.1.3,c.1.8.11 90650,90651 1zkkA 167 1.14e+01 2bwfA 77 1.15e+01 7taa 478 1.16e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1dl6A 58 1.17e+01 1dl6A g.41.3.1 45207 6rxn 46 1.17e+01 1rb9 g.41.5.1 45222 2sak 121 1.18e+01 2sak d.15.5.1 37711 1m2tB 263 1.22e+01 b.42.2.1,b.42.2.1 84762,84763 1wfeA 86 1.24e+01 2a20A 62 1.24e+01 1ywzA 175 1.25e+01 1tr9A 341 1.27e+01 1a78A 134 1.27e+01 1c1lA b.29.1.3 24212 1kdj 102 1.28e+01 1plc b.6.1.1 22864 1zxzA 197 1.30e+01 1ew4A 106 1.31e+01 1ew4A d.82.2.1 40023 1v87A 114 1.33e+01 g.44.1.1 108422 1sz6B 263 1.34e+01 1zs7A 190 1.34e+01 1ty9A 222 1.36e+01 1a7cA 379 1.41e+01 1sek e.1.1.1 42660 1iro 54 1.41e+01 1rb9 g.41.5.1 45223 2a8mA 420 1.43e+01 1j6zA 376 1.48e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 2aq4A 434 1.49e+01 2bhvA 246 1.50e+01 1i6pA 220 1.52e+01 1ddzA c.53.2.1 61848 2aaiB 262 1.52e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 1z60A 59 1.53e+01 1o7eA 276 1.54e+01 e.3.1.1 92622 1s1dA 331 1.56e+01 b.67.3.1 98344 1vq0A 302 1.56e+01 1rutX 188 1.62e+01 1u00A 227 1.62e+01 1lj5A 379 1.68e+01 e.1.1.1 73928 1c3hA 137 1.70e+01 b.22.1.1 90405 1yhfA 115 1.74e+01 1iugA 352 1.78e+01 c.67.1.3 90699 2cjsC 62 1.79e+01 1ab4 477 1.79e+01 1ab4 e.11.1.1 43251 1i76A 163 1.83e+01 1hfc d.92.1.11 61877 1nepA 130 1.84e+01 b.1.18.7 80440 1dgfA 497 1.89e+01 1cf9A e.5.1.1 42782 1ww9A 392 1.89e+01 1n9dA 199 1.89e+01 a.26.1.1 85464 1lv3A 68 1.90e+01 g.39.1.9 78231 1p32A 209 1.90e+01 1p32A d.25.1.1 38379 1q35A 320 1.93e+01 c.94.1.1 95661 1s7jA 262 1.93e+01 d.21.1.2 98647 1yl35 60 1.93e+01 2fiyA 309 1.95e+01 2fclA 169 2.01e+01 1xakA 83 2.06e+01 1nigA 152 2.08e+01 a.25.2.1 85740 1fl2A 310 2.11e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1vekA 84 2.13e+01 1yp8A 33 2.13e+01 1z6uA 150 2.14e+01 1dgwA 178 2.19e+01 1dgwA b.82.1.2 28090 1guiA 155 2.23e+01 b.18.1.14 76351 1e7lA 157 2.23e+01 1en7A a.140.4.1,d.4.1.5 64728,64729 2eifA 136 2.24e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1oxdA 227 2.27e+01 d.22.1.1 93687 2cx1A 187 2.30e+01 2ewrA 170 2.30e+01 1dxgA 36 2.31e+01 1dxgA g.41.5.2 45247 1utyA 187 2.31e+01 b.147.1.1 108036 1nx8A 273 2.33e+01 b.82.2.8 86374 1yc5A 246 2.37e+01 1o7sA 127 2.38e+01 b.1.1.1 86644 1pszA 303 2.40e+01 1toaA c.92.2.2 35600 1ayoA 130 2.40e+01 1ayoA b.2.4.1 22431 1z90A 469 2.43e+01 1f1zA 273 2.44e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1c28A 135 2.45e+01 1c28A b.22.1.1 23857 1ile 821 2.46e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 2fgtA 417 2.47e+01 1zu1A 127 2.48e+01 1ema 236 2.52e+01 1ema d.22.1.1 38339 1twfI 122 2.52e+01 2f6eA 127 2.59e+01 1p6pA 125 2.60e+01 b.60.1.2 87839 1xlqA 106 2.62e+01 1pk6C 129 2.66e+01 b.22.1.1 94803 1hw5A 210 2.69e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1ukkA 142 2.69e+01 d.227.1.1 99491 1cv8 174 2.71e+01 1cv8 d.3.1.1 37089 1q33A 292 2.71e+01 d.113.1.1 95657 1k0mA 241 2.72e+01 a.45.1.1,c.47.1.5 67949,67950 1rlyA 60 2.77e+01 g.41.3.1 104988 1t0fA 276 2.77e+01 1i50I 122 2.77e+01 g.41.3.1,g.41.3.1 61762,61763 2cy2A 174 2.79e+01 2bmoA 447 2.82e+01 2ct0A 74 2.87e+01 1erjA 393 2.92e+01 1erjA b.69.4.1 27660 1k7hA 476 2.93e+01 c.76.1.1 72101 1kypA 237 2.93e+01 d.22.1.1 73280 1ogdA 131 2.93e+01 c.133.1.1 92893 2cohA 202 2.95e+01 2cyeA 133 2.98e+01 1h3nA 878 3.02e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1vrmA 325 3.04e+01 1oqqA 106 3.06e+01 d.15.4.1 93422 1qtwA 285 3.10e+01 1qumA c.1.15.1 29392 1erd 40 3.11e+01 1erd a.10.1.1 16362 1x31D 99 3.17e+01 2a8jA 420 3.18e+01 1bc8C 93 3.21e+01 1awcA a.4.5.21 16168 1nkoA 132 3.22e+01 b.1.1.1 85829 1ldjB 90 3.22e+01 g.44.1.1 73850 1twfL 70 3.22e+01 1xgsA 295 3.27e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 2awkA 228 3.27e+01 1q68B 29 3.29e+01 j.108.1.1 95963 1e19A 314 3.29e+01 1b7bA c.73.1.1 34967 1th8A 145 3.30e+01 d.122.1.3 106908 2cszA 76 3.32e+01 1l7bA 92 3.32e+01 c.15.1.2 91053 1i6aA 219 3.33e+01 c.94.1.1 61827 1dxsA 80 3.34e+01 1cokA a.60.1.2 17944 1fjgS 93 3.35e+01 1qkfA d.28.1.1 38451 1qxfA 66 3.35e+01 g.41.8.4 96527 2gpyA 233 3.36e+01 2fs3A 282 3.37e+01 1a8h 500 3.38e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1m1qA 91 3.38e+01 a.138.1.3 74419 1jkvA 266 3.38e+01 a.25.1.3 71719 2fe5A 94 3.41e+01 1vor2 58 3.52e+01 4eugA 229 3.52e+01 3eugA c.18.1.1 31019 1gvjA 146 3.55e+01 a.4.5.21 90525 1f0xA 571 3.56e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1xkwA 665 3.56e+01 1qd1A 325 3.57e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1wflA 74 3.59e+01 1i50L 70 3.60e+01 g.41.9.2 61766 1wjpA 107 3.62e+01 1m07A 111 3.65e+01 d.5.1.1 78328 1abrA 251 3.67e+01 1mrj d.165.1.1 42196 2eng 210 3.75e+01 2eng b.52.1.1 26895 1o9iA 266 3.80e+01 a.25.1.3 92671 1zy1B 197 3.80e+01 2axcA 264 3.81e+01 2frnA 278 3.94e+01 1lp9E 194 3.96e+01 b.1.1.1,b.1.1.2 91086,91087 1r61A 207 3.96e+01 c.8.8.1 97138 1g9pA 45 4.02e+01 g.3.6.2 65171 1ap6A 198 4.04e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1vm9A 111 4.04e+01 b.33.1.1 108886 2adoA 196 4.08e+01 1e8rA 50 4.09e+01 1e8rA g.29.1.1 44960 1cqmA 101 4.11e+01 1ris d.58.14.1 39321 1woyA 500 4.12e+01 1y9uA 323 4.20e+01 2btfA 375 4.25e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 2g1lA 104 4.28e+01 1fgs 428 4.29e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 2c1xA 456 4.34e+01 1jb0F 164 4.39e+01 1jb0F f.23.16.1 62825 1x4sA 59 4.40e+01 1qwtA 255 4.43e+01 b.26.1.3 96501 1w6sB 74 4.48e+01 1n0nA 199 4.48e+01 a.2.11.1,d.44.1.1 79750,79751 1mldA 314 4.48e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1m2kA 249 4.48e+01 c.31.1.5 84754 1ohgA 282 4.51e+01 d.183.1.1 93018 1wgeA 83 4.51e+01 1eaxA 241 4.52e+01 b.47.1.2 64889 1qjpA 171 4.53e+01 1bxwA f.4.1.1 43742 1pl4A 198 4.55e+01 a.2.11.1,d.44.1.1 94854,94855 1lw7A 365 4.57e+01 c.26.1.3,c.37.1.1 74295,74296 1ykdA 398 4.62e+01 2f4pA 147 4.68e+01 1xebA 150 4.68e+01 2etxA 209 4.69e+01 2apoB 60 4.70e+01 1wxiA 275 4.71e+01 2fn4A 181 4.75e+01 1gqpA 221 4.77e+01 b.18.1.9 70372 1am2 199 4.86e+01 1am2 b.86.1.2 28381 1ej1A 190 4.89e+01 1ejhA d.86.1.1 40144 1e6eB 128 4.90e+01 1ayfA d.15.4.1 59300 1ubkS 267 4.91e+01 e.19.1.1 88423 2bf6A 449 4.95e+01 2kfnA 605 4.95e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1wuiS 267 4.96e+01 1juvA 193 4.96e+01 c.71.1.1 90912 1txoA 237 4.98e+01 2cwsA 237 5.05e+01 1fn9A 365 5.07e+01 1fn9A d.196.1.1 59894 1iupA 282 5.12e+01 c.69.1.10 76815 1shuX 182 5.14e+01 c.62.1.1 98882 1uk8A 282 5.16e+01 c.69.1.10 107907 1yovA 537 5.17e+01 2d8vA 67 5.26e+01 1c9kA 180 5.27e+01 1c9kB c.37.1.11 32363 1ku1A 230 5.29e+01 a.118.3.1 72996 2awpA 198 5.31e+01 1pu6A 218 5.32e+01 a.96.1.5 95123 1s9rA 410 5.39e+01 d.126.1.4 98758 1h2rS 267 5.43e+01 2frvA e.19.1.1 43310 1r4pB 70 5.45e+01 b.40.2.1 97026 1a1iA 90 5.45e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 44998,44999,45000 1xk5A 204 5.47e+01 1u24A 337 5.49e+01 1wr8A 231 5.53e+01 1h4rA 314 5.54e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1vl2A 421 5.55e+01 c.26.2.1,d.210.1.1 108708,108709 2c3vA 102 5.55e+01 1qqhA 144 5.55e+01 1dtoA b.91.1.1 28404 1ift 263 5.55e+01 1mrj d.165.1.1 42211 2dg5B 190 5.56e+01 1u3eM 174 5.60e+01 d.4.1.3,d.285.1.1 107640,107641 1agi 125 5.63e+01 7rsa d.5.1.1 37303 1cojA 212 5.64e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1tpm 50 5.67e+01 1tpg g.27.1.1 44957 1bueA 265 5.67e+01 1btl e.3.1.1 42727 1qmyA 167 5.68e+01 1qmyA d.3.1.2 37094 1yyaA 250 5.69e+01 1uq5A 263 5.70e+01 d.165.1.1 99778 2as9A 210 5.71e+01 1tl2A 236 5.75e+01 1tl2A b.67.1.1 27541 1hyeA 313 5.75e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1io1A 398 5.76e+01 1io1A e.32.1.1 62611 1vqoU 66 5.77e+01 1t71A 281 5.84e+01 2bngA 149 5.89e+01 1vhqA 232 5.89e+01 c.23.16.2 100696 1rfeA 162 5.91e+01 1t64A 377 5.93e+01 c.42.1.2 106543 1bfg 146 5.94e+01 1bfg b.42.1.1 25485 2ctoA 93 5.97e+01 1cr1A 296 6.00e+01 1cr1A c.37.1.11 32286 1tuaA 191 6.00e+01 d.51.1.1,d.51.1.1 107321,107322 1rsy 152 6.01e+01 1rsy b.7.1.2 23192 1rgyA 360 6.03e+01 e.3.1.1 97456 1e0gA 48 6.03e+01 1e01A d.7.1.1 37325 1srkA 35 6.03e+01 g.37.1.1 105966 1sur 215 6.04e+01 1sur c.26.2.2 31620 1i6xA 209 6.05e+01 a.4.5.4,b.82.3.2 83673,83674 1i5pA 633 6.07e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1llmC 88 6.08e+01 g.37.1.1,g.37.1.1 91059,91060 1ri6A 343 6.12e+01 b.69.11.1 97503 1f97A 212 6.12e+01 1f97A b.1.1.1,b.1.1.4 19763,21764 1z4rA 168 6.12e+01 1pz7A 204 6.15e+01 b.29.1.4 95405 1tmxA 293 6.18e+01 1hyuA 521 6.19e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1nwwA 149 6.29e+01 d.17.4.8 86306 1dtoA 221 6.29e+01 1dtoA b.91.1.1 28405 2iv2X 715 6.31e+01 1pk6A 133 6.35e+01 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