# List of top-scoring protein chains for t06-100-30-o_sep-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 1vemA 516 3.68e-01 1k0wA 231 6.54e-01 c.74.1.1 77220 1din 236 6.68e-01 1din c.69.1.9 34682 1kshA 186 8.06e-01 c.37.1.8 72914 2agyA 361 8.23e-01 1zi8A 236 1.12e+00 1pl4A 198 1.66e+00 a.2.11.1,d.44.1.1 94854,94855 1yyaA 250 2.27e+00 1io1A 398 2.49e+00 1io1A e.32.1.1 62611 1wjxA 122 2.60e+00 1nar 290 2.89e+00 1nar c.1.8.5 28988 2gnqA 336 3.00e+00 1q15A 503 3.22e+00 c.26.2.1,d.153.1.1 95538,95539 2gu3A 136 3.73e+00 1sfxA 109 3.86e+00 a.4.5.50 105505 1sh0A 510 3.88e+00 e.8.1.4 98876 1obdA 306 4.49e+00 d.143.1.1 86767 1nmoA 247 4.54e+00 c.135.1.1 91980 1q0xH 221 5.05e+00 b.1.1.1,b.1.1.2 95517,95518 2a5dA 175 5.18e+00 1ig5A 75 5.34e+00 4icb a.39.1.1 62363 1iicA 422 5.35e+00 1nmtA d.108.1.2,d.108.1.2 62422,62423 1uw4A 91 5.68e+00 d.58.7.4 100071 1g5bA 221 6.17e+00 1g5bA d.159.1.3 60261 2cnqA 306 6.25e+00 1zkjA 359 6.28e+00 1yvhA 329 6.66e+00 1rypL 212 6.70e+00 d.153.1.4 41880 1wmhA 89 6.97e+00 1rypJ 204 7.01e+00 d.153.1.4 41878 1mr3F 181 7.01e+00 c.37.1.8 79422 1o50A 157 7.14e+00 d.37.1.1,d.37.1.1 92478,92479 2bkdN 134 7.17e+00 2acaA 189 7.86e+00 1v02A 565 7.92e+00 c.1.8.4 108194 1f9zA 135 8.16e+00 1qipA d.32.1.1 38484 1ghpA 258 8.39e+00 1btl e.3.1.1 60520 1mg4A 113 8.59e+00 d.15.11.1 84953 1h4rA 314 8.86e+00 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1yumA 242 9.15e+00 1zd9A 188 9.33e+00 1oo0A 147 9.61e+00 d.232.1.1 87182 1ywnA 316 9.90e+00 1jlyA 304 9.97e+00 1jlyA b.42.3.1,b.42.3.1 25587,25588 1exbA 332 1.01e+01 1qrqA c.1.7.1 28666 1bb8 71 1.06e+01 2bb8 d.10.1.1 37478 1gx5A 536 1.07e+01 e.8.1.4 70682 1q42A 201 1.08e+01 d.17.4.2 95776 2fsrA 195 1.13e+01 1mg7A 417 1.13e+01 d.14.1.6,d.58.26.6 84954,84955 1zx8A 136 1.13e+01 2brcA 214 1.14e+01 1o3yA 166 1.20e+01 c.37.1.8 86618 1zarA 282 1.22e+01 1wdyA 285 1.24e+01 1a8y 367 1.25e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2f9dA 125 1.26e+01 2fckA 181 1.27e+01 1ikpA 613 1.29e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 2cz1A 206 1.30e+01 2cfaA 217 1.32e+01 2cbuA 468 1.32e+01 2btvA 901 1.42e+01 2btvA e.28.1.1 43376 1jkxA 212 1.43e+01 c.65.1.1 66813 1o4rA 108 1.43e+01 d.93.1.1 92469 1b35B 255 1.43e+01 1b35B b.121.4.1 23334 1cojA 212 1.45e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2b7kA 200 1.47e+01 1f6bA 198 1.52e+01 c.37.1.8 64986 1khiA 176 1.53e+01 b.34.5.2,b.40.4.5 77408,77409 1xahA 354 1.57e+01 1f35A 162 1.57e+01 1f35A b.94.1.1 59628 2ajgA 196 1.58e+01 1vjeA 166 1.58e+01 d.185.1.2 100807 1r29A 127 1.59e+01 d.42.1.1 96856 2fz4A 237 1.67e+01 2f1kA 279 1.68e+01 1uwcA 261 1.72e+01 c.69.1.17 100101 2fg9A 178 1.82e+01 1p4kA 295 1.82e+01 d.153.1.5 87772 1th0A 226 1.83e+01 d.3.1.7 106903 2c1iA 431 1.84e+01 1zsxA 347 1.85e+01 1tib 269 1.86e+01 3tgl c.69.1.17 34738 1osdA 72 1.88e+01 d.58.17.1 104022 1h6lA 353 1.92e+01 b.68.3.1 60687 1zhvA 134 1.94e+01 1zm8A 259 1.95e+01 2ftbA 125 1.95e+01 1j55A 95 1.96e+01 a.39.1.2 77078 1v58A 241 1.99e+01 c.47.1.9,d.17.3.1 108371,108372 1wwzA 159 2.00e+01 1ylhA 560 2.02e+01 1yw4A 341 2.03e+01 1n0qA 93 2.07e+01 k.37.1.1 79754 1lv7A 257 2.11e+01 c.37.1.20 78232 1e44B 96 2.15e+01 1e44B b.101.1.1 59220 1mml 265 2.17e+01 1mml e.8.1.2 43015 1krs 120 2.17e+01 1krs b.40.4.1 25256 2aieP 203 2.21e+01 2cn3A 737 2.23e+01 1ri6A 343 2.23e+01 b.69.11.1 97503 1ru0A 105 2.24e+01 2basA 431 2.28e+01 2f0aA 98 2.28e+01 1r8sA 164 2.29e+01 c.37.1.8 97247 1yfnA 118 2.31e+01 1qfxA 460 2.32e+01 1qfxA c.60.1.2 33994 1t2jA 116 2.33e+01 1vqoS 85 2.35e+01 1xs1A 193 2.35e+01 1fj2A 232 2.36e+01 1auoA c.69.1.14 34720 2b20A 403 2.37e+01 1nrjA 158 2.38e+01 d.110.4.4 86124 1ufwA 95 2.40e+01 d.58.7.1 99358 1xcbA 211 2.41e+01 a.4.5.38,c.2.1.12 109552,109553 1wzvA 155 2.41e+01 1seiA 130 2.44e+01 1seiA d.140.1.1 41463 2agaA 190 2.44e+01 1bf5A 545 2.47e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 2cw8A 537 2.49e+01 1xkzA 255 2.50e+01 1azo 232 2.51e+01 1azo c.52.1.14 33329 1zj6A 187 2.56e+01 1zy9A 564 2.56e+01 1a4pA 96 2.57e+01 1b4cA a.39.1.2 17176 1sqsA 242 2.57e+01 c.23.5.5 98968 1zyiA 171 2.58e+01 1rcqA 357 2.61e+01 b.49.2.2,c.1.6.1 104882,104883 1kveB 77 2.62e+01 1kveB 1sxrA 183 2.62e+01 d.118.1.1 106101 1i2sA 282 2.62e+01 e.3.1.1 71104 2gwnA 452 2.68e+01 1nzjA 298 2.71e+01 c.26.1.1 92377 1wrvA 308 2.71e+01 1fdr 248 2.74e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 2ervA 150 2.76e+01 1q33A 292 2.77e+01 d.113.1.1 95657 4pgaA 337 2.77e+01 4pgaA c.88.1.1 35565 1yc9A 442 2.80e+01 1nnsA 326 2.80e+01 c.88.1.1 85910 1to4A 156 2.82e+01 b.1.8.1 107162 1r6jA 82 2.84e+01 b.36.1.1 97151 1ycdA 243 2.85e+01 1y8qA 346 2.85e+01 1i3zA 103 2.91e+01 d.93.1.1 83667 1w2fA 276 2.95e+01 d.143.1.3 109125 2bkyA 97 2.95e+01 1smoA 119 2.98e+01 b.1.1.1 105764 2cb2A 318 2.99e+01 1rypF 233 3.00e+01 1rypF d.153.1.4 41937 1txdA 385 3.00e+01 a.87.1.1,b.55.1.1 107422,107423 1jiwI 106 3.01e+01 1smpI b.61.2.1 63078 1m22A 503 3.02e+01 c.117.1.1 78464 1zt2B 212 3.02e+01 2ex0A 399 3.03e+01 1vmbA 140 3.05e+01 2aexA 346 3.12e+01 1oa8A 133 3.14e+01 b.145.1.1 92698 1zelA 298 3.15e+01 2czrA 226 3.16e+01 2bkkA 264 3.21e+01 1g2iA 166 3.21e+01 1g2iA c.23.16.2 31438 1nlfA 279 3.22e+01 c.37.1.11 85850 1s5jA 847 3.27e+01 2ag4A 164 3.30e+01 1o17A 345 3.32e+01 a.46.2.1,c.27.1.1 80765,80766 1k5dB 201 3.33e+01 b.55.1.3 68169 1rxdA 159 3.33e+01 2dg5B 190 3.34e+01 2b7eA 59 3.36e+01 1g2yA 32 3.37e+01 a.34.2.1 17003 1tfzA 424 3.38e+01 d.32.1.3,d.32.1.3 106886,106887 1h9oA 112 3.38e+01 1qadA d.93.1.1 60837 1m40A 263 3.41e+01 e.3.1.1 74437 1pcfA 66 3.42e+01 1pcfA d.18.1.1 38142 1nqkA 381 3.44e+01 c.1.16.4 92050 1uylA 236 3.45e+01 d.122.1.1 108147 1sqrA 95 3.47e+01 1kqpA 271 3.47e+01 c.26.2.1 72883 1s99A 200 3.48e+01 1deuA 277 3.50e+01 1theB d.3.1.1 37085 2gaiA 633 3.51e+01 2bvfA 459 3.51e+01 2gkpA 167 3.53e+01 1g291 372 3.54e+01 1g291 2fa8A 105 3.54e+01 1t92A 116 3.55e+01 1gxuA 91 3.56e+01 d.58.10.1 76378 2b3yA 888 3.56e+01 1jltA 122 3.57e+01 a.133.1.2 66867 1crzA 403 3.57e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1d8wA 426 3.59e+01 1de5A c.1.15.2 29394 1qmeA 702 3.64e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1x0vA 354 3.73e+01 1xniA 118 3.76e+01 1ru3A 732 3.77e+01 e.26.1.3 97835 1q4rA 112 3.78e+01 d.58.4.4 95823 2bbkL 125 3.79e+01 2bbkL g.21.1.1 44882 2atrA 138 3.81e+01 2h17A 181 3.82e+01 1kolA 398 3.82e+01 b.35.1.2,c.2.1.1 77474,77475 2bngA 149 3.83e+01 1t1gA 364 3.92e+01 c.41.1.2 106246 1htwA 158 3.95e+01 c.37.1.18 71083 1kutA 230 3.96e+01 d.143.1.1 73017 1em8A 147 3.98e+01 c.128.1.1 90457 1c4rA 182 4.02e+01 1c4rA b.29.1.4 24229 1uv4A 293 4.03e+01 1zl0A 311 4.04e+01 1k1aA 241 4.05e+01 d.211.1.1 67992 1r0vA 305 4.06e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 2fpoA 202 4.08e+01 1dbqA 289 4.08e+01 1qpzA c.93.1.1 35666 2gfaA 119 4.09e+01 1fxoA 293 4.10e+01 1g0rA c.68.1.6 34524 1kv0A 66 4.11e+01 g.3.7.1 91040 1cczA 171 4.12e+01 1cczA b.1.1.1,b.1.1.3 19758,21683 1yua 122 4.13e+01 1yua g.41.3.3,g.41.3.3 45210,45211 1y80A 210 4.17e+01 2dbsA 90 4.22e+01 1ignA 246 4.25e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1iwdA 215 4.25e+01 d.3.1.1 83756 1yarA 233 4.26e+01 2gnrA 145 4.28e+01 2be1A 339 4.29e+01 1m2kA 249 4.31e+01 c.31.1.5 84754 1wdvA 152 4.32e+01 1qd9A 124 4.33e+01 1qu9A d.79.1.1 39758 2fbaA 492 4.33e+01 1dzfA 215 4.33e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1b77A 228 4.34e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 2cr4A 126 4.34e+01 1guuA 52 4.37e+01 a.4.1.3 83332 1i4yA 114 4.37e+01 2mhr a.24.4.1 61738 1hz6A 72 4.38e+01 2ptl d.15.7.1 61429 2fb5A 205 4.40e+01 1suuA 312 4.40e+01 b.68.10.1 99006 1wrjA 156 4.40e+01 2gqrA 237 4.40e+01 1t8hA 277 4.43e+01 d.194.1.2 106664 2cx5A 158 4.45e+01 1rypI 222 4.46e+01 d.153.1.4 41877 1v04A 355 4.47e+01 b.68.6.2 100240 2chnA 716 4.53e+01 1on2A 142 4.55e+01 a.4.5.24,a.76.1.1 87103,87104 1sgoA 139 4.58e+01 d.82.3.1 98857 1jnrA 643 4.63e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 2ch8A 201 4.66e+01 1mwwA 128 4.69e+01 d.80.1.4 91483 1m5q1 130 4.71e+01 1cipA 353 4.71e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 2czvC 120 4.72e+01 2sak 121 4.74e+01 2sak d.15.5.1 37711 1zbpA 273 4.75e+01 1wpiA 133 4.79e+01 2fjbA 643 4.81e+01 2f57A 317 4.81e+01 1vjqA 79 4.85e+01 k.43.1.1 100830 1t0qC 86 4.93e+01 d.15.12.1 106222 1dzkA 157 4.93e+01 1obpA b.60.1.1 27096 1e19A 314 4.96e+01 1b7bA c.73.1.1 34967 2h03A 291 4.98e+01 1qy6A 274 4.99e+01 b.47.1.1 96574 1tqhA 247 5.01e+01 c.69.1.29 107225 1z57A 339 5.01e+01 2cxcA 144 5.03e+01 1lkkA 105 5.06e+01 1lckA d.93.1.1 40412 2dp5A 332 5.06e+01 1x47A 98 5.12e+01 1k4mA 213 5.19e+01 c.26.1.3 77258 1qzgA 187 5.23e+01 b.40.4.3 96643 1x75A 132 5.29e+01 2f9zC 159 5.29e+01 1syxB 86 5.35e+01 1vizA 240 5.36e+01 c.1.4.1 100784 2choA 716 5.42e+01 1ixcA 294 5.43e+01 a.4.5.37,c.94.1.1 83764,83765 1hf8A 289 5.47e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 2gtrA 261 5.48e+01 1jmxB 349 5.52e+01 b.69.2.2 66906 2cxxA 190 5.53e+01 2cdqA 510 5.54e+01 2bj0A 203 5.58e+01 1jmcA 246 5.60e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1vzoA 355 5.64e+01 d.144.1.7 108971 1txgA 335 5.68e+01 1wnaA 131 5.69e+01 1ylxA 103 5.73e+01 1x74A 360 5.75e+01 1qahA 136 5.76e+01 d.79.1.1 96338 1jftA 340 5.77e+01 a.35.1.5,c.93.1.1 66652,66653 2fswA 107 5.81e+01 1xkgA 312 5.82e+01 1h5rA 293 5.82e+01 c.68.1.6 65623 1vd3A 217 5.83e+01 1ufkA 254 5.86e+01 c.66.1.39 99340 1y93A 159 5.90e+01 1cixA 44 5.96e+01 g.3.6.2 70066 2dkaA 544 5.96e+01 1m1hA 248 6.01e+01 b.114.1.1,d.58.42.1 78415,78416 2a1rA 430 6.01e+01 1w0pA 781 6.01e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 2aj6A 159 6.06e+01 1nw1A 429 6.14e+01 d.144.1.8 86286 1jykA 254 6.16e+01 c.68.1.13 67458 1f3uA 118 6.17e+01 1f3uA b.65.1.1 27521 1wp5A 323 6.22e+01 1f32A 149 6.25e+01 1f32A d.62.1.1 39539 1ul7A 102 6.27e+01 d.129.6.1 99540 1n2sA 299 6.30e+01 c.2.1.2 79857 2fcjA 119 6.31e+01 1sddA 306 6.31e+01 b.6.1.3,b.6.1.3 105431,105432 1vqoX 92 6.34e+01 1e1hA 287 6.35e+01 d.92.1.7 83167 1rgyA 360 6.46e+01 e.3.1.1 97456 1y6uA 70 6.50e+01 1y7bA 542 6.55e+01 2ey4C 82 6.55e+01 1m0wA 491 6.56e+01 c.30.1.4,d.142.1.6 78363,78364 1tr8A 102 6.63e+01 1sqhA 312 6.65e+01 d.108.1.5 98966 1ii5A 233 6.65e+01 c.94.1.1 62412 1r7lA 110 6.67e+01 d.277.1.1 104837 1w2xA 758 6.68e+01 c.14.1.4,c.14.1.4 109134,109135 1jli 112 6.74e+01 1jli a.26.1.2 16884 1rqwA 207 6.76e+01 b.25.1.1 97781 2cxaA 256 6.77e+01 1d4tA 104 6.77e+01 1d4tA d.93.1.1 40537 1jr7A 311 6.78e+01 b.82.2.3 63255 2dbnA 461 6.79e+01 1enfA 212 6.80e+01 3seb b.40.2.2,d.15.6.1 25198,37787 2trxA 108 6.80e+01 1thx c.47.1.1 32719 1zzmA 259 6.81e+01 1gudA 288 6.81e+01 c.93.1.1 83326 2czlA 272 6.87e+01 1z1lA 345 6.89e+01 1r1qA 100 6.94e+01 d.93.1.1 104763 2a26A 50 6.95e+01 1oo2A 119 6.97e+01 b.3.4.1 93372 1q3lA 69 6.98e+01 1rlzA 369 6.99e+01 c.31.1.1 104989 1nvmA 345 7.02e+01 a.5.7.1,c.1.10.5 86249,86250 1p5dX 463 7.02e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1vkcA 158 7.02e+01 1q5hA 147 7.04e+01 b.85.4.1 95893 1omhA 293 7.13e+01 d.89.1.5 93348 1zbxB 141 7.16e+01 1j1tA 233 7.16e+01 b.29.1.18 90771 1ykhB 132 7.20e+01 2bsjA 133 7.20e+01 1xypA 190 7.22e+01 1axkA b.29.1.11 24327 1oh0A 131 7.28e+01 d.17.4.3 87004 1g2oA 268 7.31e+01 1b8oA c.56.2.1 60228 1djtA 64 7.32e+01 1aho g.3.7.1 44132 1wohA 305 7.39e+01 c.42.1.1 109446 1awd 94 7.39e+01 1awd d.15.4.1 37673 2av5A 120 7.42e+01 1pv0A 46 7.49e+01 a.2.12.1 95141 1voqa 90 7.53e+01 1jyrA 96 7.56e+01 d.93.1.1 71969 1xg5A 279 7.56e+01 1puc 105 7.63e+01 1puc d.97.1.1 40675 1zxfA 155 7.66e+01 1csn 298 7.70e+01 1csn d.144.1.7 41664 2g03A 194 7.72e+01 1yreA 197 7.74e+01 1utcA 363 7.75e+01 a.118.1.4,b.69.6.1 99914,99915 1snzA 344 7.80e+01 b.30.5.4 98930 2g1uA 155 7.80e+01 1va0A 239 7.82e+01 1knwA 425 7.82e+01 b.49.2.3,c.1.6.1 90969,90970 1z4eA 153 7.85e+01 1nfp 228 7.85e+01 1nfp c.1.16.2 29555 2faoA 309 7.86e+01 1o5xA 248 7.87e+01 c.1.1.1 92528 2gh1A 301 7.88e+01 1l6rA 227 7.96e+01 c.108.1.10 77768 1c1dA 355 7.96e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1t95A 240 7.98e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1ir21 140 7.99e+01 1qzmA 94 8.00e+01 c.37.1.20 96651 2fhzA 109 8.00e+01 1iv3A 152 8.01e+01 d.79.5.1 76828 2ca6A 386 8.02e+01 1g8aA 227 8.05e+01 c.66.1.3 90506 1zw8A 64 8.07e+01 1wraA 308 8.07e+01 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