# List of top-scoring protein chains for t04-100-40-40-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.soe.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 2j9cA 119 1.33e-19 2pii 112 1.33e-19 2pii 2eg2A 112 6.71e-18 2ns1B 116 1.61e-17 2gw8A 114 9.79e-17 1vfjA 116 1.30e-16 d.58.5.1 113637 3bzqA 114 5.97e-16 1gnkA 112 1.89e-15 2pii d.58.5.1 39073 2o66A 135 2.43e-15 1o51A 114 1.01e-03 d.58.5.4 92480 2dclA 127 1.40e-02 2pjmA 226 1.58e-02 1y8cA 246 7.25e-02 c.66.1.43 116563 2npoA 207 9.31e-02 2nxcA 254 9.97e-02 c.66.1.39 138739 1cqmA 101 1.22e-01 1ris d.58.14.1 39321 1wyuA 438 1.28e-01 c.67.1.7 121452 2ay1A 394 1.53e-01 1ajsA c.67.1.1 34357 1jg1A 235 1.63e-01 c.66.1.7 66661 1ulrA 88 1.64e-01 d.58.10.1 113283 1u7iA 136 1.81e-01 d.32.1.7 107724 2cyyA 151 2.00e-01 a.4.5.32,d.58.4.2 131028,131029 2p5mA 83 2.02e-01 2r3sA 335 2.04e-01 1qzzA 374 2.05e-01 a.4.5.29,c.66.1.12 96719,96720 2bjdA 101 2.06e-01 2cdqA 510 2.20e-01 c.73.1.3,d.58.18.10,d.58.18.10 130290,130291,130292 2raqA 97 2.32e-01 1mumA 295 2.65e-01 c.1.12.7 85108 2dtjA 178 2.69e-01 1ri7A 171 3.00e-01 a.4.5.32,d.58.4.2 97504,97505 1o54A 277 3.12e-01 c.66.1.13 92482 2jsxA 95 3.22e-01 1psdA 409 3.30e-01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 2cstA 411 3.50e-01 1ajsA c.67.1.1 34273 1sc6A 404 3.51e-01 c.2.1.4,c.23.12.1,d.58.18.1 118932,118933,118934 1xg4A 295 3.71e-01 2d59A 144 3.90e-01 c.2.1.8 131266 1ahxA 396 3.97e-01 1ajsA c.67.1.1 34293 1kzfA 230 4.47e-01 d.108.1.3 73354 2bm0A 691 4.51e-01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 128748,128749,128750,128751,128752 2nzcA 86 4.55e-01 2f1fA 164 4.58e-01 d.58.18.6,d.58.18.6 132760,132761 2ditA 112 4.65e-01 d.58.7.1 131533 2id1A 130 4.77e-01 1konA 249 5.25e-01 e.39.1.1 72823 1zwyA 185 5.66e-01 c.51.4.3 125753 1louA 101 5.75e-01 1ris d.58.14.1 39323 1sqgA 429 5.82e-01 a.79.1.3,c.66.1.38 105912,105913 1ajsA 412 5.83e-01 1ajsA c.67.1.1 34276 2d0oB 125 5.87e-01 c.51.3.2 131078 1q9uA 130 6.02e-01 d.129.7.1 96314 2nyhA 117 6.04e-01 d.58.55.1 138813 1ixkA 315 6.05e-01 c.66.1.38 90716 2abqA 306 6.38e-01 c.72.1.1 126528 2p8iA 117 6.69e-01 d.58.55.1 139522 1vj7A 393 6.95e-01 a.211.1.1,d.218.1.8 100801,100802 7aatA 401 7.04e-01 1ajsA c.67.1.1 34250 2anrA 178 7.36e-01 1nh8A 304 7.49e-01 c.94.1.1,d.58.5.3 80507,80508 2a1rA 430 8.04e-01 1fp2A 352 8.05e-01 1fpxA a.4.5.29,c.66.1.12 59941,59942 3bwwA 307 8.06e-01 2g3mA 693 8.12e-01 2omkA 231 8.42e-01 3bfpA 194 8.61e-01 2p7oA 133 8.81e-01 2pebA 122 8.83e-01 2o5aA 125 8.95e-01 1vl5A 260 9.29e-01 c.66.1.41 108720 2dr3A 247 9.37e-01 2b9eA 303 9.64e-01 c.66.1.38 128124 3cnyA 301 9.71e-01 1w5fA 353 9.84e-01 c.32.1.1,d.79.2.1 114247,114248 2ax4A 198 1.03e+00 2atzA 180 1.05e+00 d.264.1.3 127317 2dy1A 665 1.08e+00 1mw7A 240 1.16e+00 e.39.1.1 79557 1tw3A 360 1.17e+00 a.4.5.29,c.66.1.12 107373,107374 1q8bA 105 1.20e+00 d.58.4.6 96201 2a10A 125 1.24e+00 d.58.56.1 125965 1u8sA 192 1.26e+00 d.58.18.5,d.58.18.5 107737,107738 1vfsA 386 1.28e+00 b.49.2.2,c.1.6.1 108584,108585 1ve3A 227 1.29e+00 c.66.1.43 120010 1ars 396 1.31e+00 1ajsA 1arsA 396 1.31e+00 c.67.1.1 34287 2i6jA 161 1.31e+00 1zclA 180 1.31e+00 2elcA 329 1.34e+00 1xxlA 239 1.38e+00 c.66.1.41 116203 1pjqA 457 1.39e+00 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1whzA 70 1.53e+00 d.50.3.2 114656 2furA 209 1.53e+00 b.45.1.1 134185 1t95A 240 1.54e+00 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1vpqA 273 1.59e+00 c.1.32.1 113974 1kafA 108 1.61e+00 d.199.1.1 68372 1jilA 420 1.65e+00 c.26.1.1 66745 2ewhA 98 1.66e+00 d.58.56.1 132466 1vdhA 249 1.66e+00 d.58.4.10 108523 1qisA 396 1.69e+00 1ajsA c.67.1.1 34284 1zchA 255 1.74e+00 d.90.1.1 124908 1l3iA 192 1.78e+00 c.66.1.22 77676 2q02A 272 1.80e+00 2qyxA 238 1.84e+00 1p9qC 256 1.85e+00 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2z2mC 125 1.93e+00 1yb1A 272 1.97e+00 c.2.1.2 116599 1iujA 106 1.98e+00 d.58.4.5 90701 2b30A 301 2.00e+00 c.108.1.10 127759 1fmcA 255 2.02e+00 1cydA c.2.1.2 29856 1w6uA 302 2.05e+00 c.2.1.2 114288 2q7wA 396 2.07e+00 1xcbA 211 2.13e+00 a.4.5.38,c.2.1.12 109552,109553 1oltA 457 2.19e+00 c.1.28.2 93334 1tluA 130 2.21e+00 d.156.1.2 107139 2gffA 106 2.21e+00 2cw6A 298 2.25e+00 2pgcA 207 2.27e+00 1vpvA 300 2.28e+00 c.119.1.1 113975 2hfsA 332 2.28e+00 2ivmA 150 2.30e+00 1u69A 163 2.34e+00 d.32.1.7 107699 2zc3C 125 2.40e+00 1yz7A 188 2.41e+00 2p91A 285 2.41e+00 1j27A 102 2.44e+00 d.58.50.1 90778 1xtzA 264 2.49e+00 2pfsA 150 2.50e+00 1o63A 219 2.51e+00 c.94.1.1 92540 1yzhA 214 2.52e+00 c.66.1.53 124277 1f0yA 302 2.56e+00 2hdhA a.100.1.3,c.2.1.6 18793,30197 1wn2A 121 2.61e+00 2djwA 92 2.62e+00 1l0wA 580 2.65e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1rkiA 102 2.73e+00 d.308.1.2 118776 1xx1A 285 2.73e+00 1i6aA 219 2.80e+00 c.94.1.1 61827 2h1rA 299 2.82e+00 2i57A 438 2.84e+00 2yqzA 263 2.94e+00 1xhlA 297 2.95e+00 c.2.1.2 109591 2nuhA 118 2.97e+00 1x7gA 261 2.98e+00 c.2.1.2 114929 1h1dA 221 3.06e+00 c.66.1.1 83452 1nvtA 287 3.17e+00 c.2.1.7,c.58.1.5 86270,86271 3brcA 156 3.18e+00 1ghsA 306 3.23e+00 1aq0A c.1.8.3 28840 2yxeA 215 3.24e+00 1xovA 326 3.25e+00 b.34.11.4,c.56.5.6 122206,122207 1heiA 451 3.26e+00 1heiA c.37.1.14,c.37.1.14 32463,32464 2gb3A 409 3.29e+00 c.67.1.1 134903 2pezA 179 3.35e+00 2iiiA 135 3.35e+00 1vf8A 377 3.36e+00 c.1.8.5,d.26.3.1 120029,120030 2nrqA 159 3.44e+00 1bkjA 240 3.47e+00 1bkjA d.90.1.1 40243 1e9lA 377 3.53e+00 1e9lA c.1.8.5,d.26.3.1 59395,59396 1ygyA 529 3.58e+00 c.2.1.4,c.23.12.1,d.58.18.1,d.81.2.2 123150,123151,123152,123153 2qulA 290 3.62e+00 1wb0A 445 3.71e+00 c.1.8.5,d.26.3.1 120825,120826 1ceo 343 3.75e+00 1ceo 1ceoA 343 3.75e+00 c.1.8.3 28808 1spxA 278 3.82e+00 c.2.1.2 98958 1f75A 249 3.88e+00 1f75A c.101.1.1 59662 1x19A 359 3.89e+00 1f5vA 240 3.91e+00 1bkjA d.90.1.1 40255 2dm6A 333 3.94e+00 b.35.1.2,c.2.1.1 131567,131568 2c0hA 353 4.03e+00 c.1.8.3 129594 1no5A 114 4.11e+00 d.218.1.5 92014 1jmtA 104 4.14e+00 d.58.7.3 63180 1v7rA 186 4.14e+00 c.51.4.1 100482 1b4bA 71 4.16e+00 1b4aA d.74.2.1 39718 2qahA 303 4.18e+00 2z2uA 311 4.20e+00 1r9cA 139 4.23e+00 d.32.1.2 97255 2cz9A 350 4.25e+00 1w2iA 91 4.27e+00 d.58.10.1 109127 2ijmA 281 4.38e+00 1ep3A 311 4.38e+00 2dorA c.1.4.1 28597 3c3mA 138 4.47e+00 1lfpA 249 4.51e+00 e.39.1.1 73885 2hiyA 183 4.60e+00 2dejA 350 4.62e+00 1bif 469 4.68e+00 1bif 1bifA 469 4.68e+00 c.37.1.7,c.60.1.4 31961,34003 1is1A 185 4.69e+00 d.67.3.1 83704 1f6bA 198 4.69e+00 c.37.1.8 64986 2p8jA 209 4.71e+00 2i6lA 320 4.84e+00 2i6gA 199 4.86e+00 c.66.1.44 137096 2oxcA 230 4.91e+00 2cviA 83 4.93e+00 1rxdA 159 4.94e+00 c.45.1.1 111959 1nf2A 268 4.99e+00 c.108.1.10 91849 2qz8A 149 5.01e+00 1hkkA 364 5.07e+00 c.1.8.5,d.26.3.1 90634,90635 1rlmA 271 5.12e+00 c.108.1.10 111860 2q3pA 112 5.12e+00 d.58.4.4 139798 1i0lA 221 5.13e+00 c.61.1.1 71096 1a8pA 258 5.18e+00 b.43.4.2,c.25.1.1 25654,31544 2dt5A 211 5.26e+00 a.4.5.38,c.2.1.12 131708,131709 2ca9A 148 5.31e+00 3borA 237 5.32e+00 1ybtA 184 5.41e+00 1qtwA 285 5.51e+00 1qumA c.1.15.1 29392 1uhvA 500 5.56e+00 b.71.1.2,c.1.8.3 99402,99403 2qn6B 93 5.63e+00 1o8bA 219 5.63e+00 c.124.1.4,d.58.40.1 81180,81181 1zunA 325 5.66e+00 c.26.2.2 125676 1o20A 427 5.69e+00 c.82.1.1 86556 1bo1A 416 5.72e+00 1bo1A d.143.1.2 41591 1nal1 297 5.73e+00 1nal3 1zckA 154 5.91e+00 1mp8A 281 5.94e+00 d.144.1.7 91384 1ukuA 102 5.98e+00 d.58.5.2 99533 1b16A 254 6.16e+00 1b16A c.2.1.2 29875 1iseA 185 6.23e+00 d.67.3.1 90691 1x1nA 524 6.26e+00 c.1.8.1 121593 2f7lA 455 6.34e+00 2f46A 156 6.36e+00 2otnA 308 6.42e+00 2gukA 120 6.42e+00 1dl5A 317 6.47e+00 1dl5A c.66.1.7,d.197.1.1 64720,64721 1ufwA 95 6.48e+00 d.58.7.1 99358 3biqA 467 6.51e+00 1k66A 149 6.55e+00 c.23.1.1 90941 2ok3A 161 6.69e+00 2i82A 217 6.89e+00 2hk9A 275 6.91e+00 1ad4A 266 6.91e+00 1aj2 c.1.21.1 29670 1ln4A 104 6.92e+00 d.68.4.1 74043 1vm7A 311 6.94e+00 c.72.1.1 108884 2zihA 347 7.00e+00 1ek8A 185 7.02e+00 1ek8A d.67.3.1 59444 1o5xA 248 7.06e+00 c.1.1.1 92528 1w1oA 534 7.19e+00 d.58.32.4,d.145.1.1 109071,109072 2q7dA 346 7.24e+00 1ta3A 274 7.28e+00 c.1.8.5 106731 1qo0D 196 7.28e+00 1qo0D c.23.1.3 31125 2qdxA 257 7.29e+00 2dt9A 167 7.33e+00 1x7vA 99 7.41e+00 d.58.4.11 109501 1t1iA 364 7.42e+00 c.41.1.2 106248 1hyeA 313 7.43e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 2ig8A 144 7.54e+00 3b8mA 280 7.55e+00 1x24A 180 7.62e+00 1vjzA 341 7.63e+00 c.1.8.3 100838 2imgA 151 7.66e+00 1g60A 260 7.77e+00 c.66.1.11 70151 2rjzA 147 7.77e+00 1lmeA 176 7.79e+00 d.167.1.1 84629 1qamA 244 7.87e+00 2ercA c.66.1.24 34220 3chy 128 7.91e+00 3chy 2ftrA 108 7.93e+00 d.58.4.15 134077 1tuoA 464 7.96e+00 1zdyA 307 7.96e+00 d.313.1.1 124961 1ydnA 295 8.03e+00 1h1nA 305 8.03e+00 c.1.8.3 70855 2bitX 165 8.05e+00 b.62.1.1 128590 2o7rA 338 8.08e+00 2hf9A 226 8.12e+00 1khdA 345 8.20e+00 a.46.2.1,c.27.1.1 77400,77401 2ivyA 101 8.35e+00 2ox1A 196 8.37e+00 1xdzA 240 8.43e+00 c.66.1.20 115196 1p1lA 102 8.53e+00 d.58.5.2 87695 2bg5A 324 8.55e+00 1xseA 295 8.66e+00 c.2.1.2 115925 1pxgA 382 8.73e+00 c.1.20.1 95287 2fprA 176 8.76e+00 c.108.1.19 133919 2yv7A 260 8.93e+00 1ve4A 206 8.94e+00 c.94.1.1 120012 1ypxA 375 8.95e+00 1v4vA 376 9.04e+00 c.87.1.3 100313 2carA 196 9.11e+00 c.51.4.1 130161 1lufA 343 9.11e+00 d.144.1.7 78223 1tcvA 287 9.15e+00 1ujqA 305 9.18e+00 c.1.12.7 99463 1fcqA 350 9.27e+00 c.1.8.9 65006 1y56A 493 9.32e+00 1wqaA 455 9.47e+00 1zy4A 303 9.56e+00 1q7bA 244 9.71e+00 c.2.1.2 96026 2zbcA 83 9.71e+00 2yvlA 248 9.85e+00 2o57A 297 9.92e+00 3csvA 333 9.93e+00 1xkqA 280 9.95e+00 c.2.1.2 115417 1z1zA 131 9.98e+00 d.323.1.1 124366 1x6vA 630 1.00e+01 b.122.1.3,c.26.1.5,c.37.1.4 121755,121756,121757 1ja9A 274 1.01e+01 c.2.1.2 62817 2yxdA 183 1.02e+01 2eqaA 352 1.03e+01 1roaA 122 1.05e+01 d.17.1.2 105024 1vjqA 79 1.06e+01 k.43.1.1 100830 2gviA 204 1.06e+01 2ghpA 292 1.08e+01 d.58.7.1,d.58.7.1,d.58.7.1 135184,135185,135186 1y81A 138 1.08e+01 c.2.1.8 122731 2f4dA 184 1.09e+01 1y0hA 105 1.10e+01 d.58.4.11 116303 1e4fT 419 1.10e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 2hmaA 376 1.10e+01 1pud 386 1.11e+01 1pud 1qd9A 124 1.12e+01 1qu9A d.79.1.1 39758 2c07A 285 1.12e+01 c.2.1.2 129577 1j4aA 333 1.12e+01 c.2.1.4,c.23.12.1 71502,71503 1rjdA 334 1.13e+01 c.66.1.37 97558 1yf5L 254 1.13e+01 c.55.1.11,c.55.1.11 123049,123050 2bd0A 244 1.13e+01 c.2.1.2 128321 2nwuA 155 1.15e+01 1wvfA 520 1.15e+01 d.58.32.1,d.145.1.1 121337,121338 1ynrA 80 1.16e+01 a.3.1.1 123750 1uroA 367 1.16e+01 1uroA c.1.22.1 29675 1kvkA 395 1.16e+01 d.14.1.5,d.58.26.3 73060,73061 2vgbA 528 1.16e+01 2omdA 154 1.16e+01 1ve2A 235 1.17e+01 c.90.1.1 120008 1x9mA 698 1.17e+01 c.55.3.5,e.8.1.1 114999,115000 1xu9A 286 1.17e+01 c.2.1.2 116052 1jbeA 128 1.18e+01 3chy c.23.1.1 62845 2gpyA 233 1.18e+01 1zpvA 91 1.18e+01 d.58.18.7 125475 1nx8A 273 1.19e+01 b.82.2.8 86374 1pujA 282 1.19e+01 c.37.1.8 88294 2vdvE 246 1.19e+01 1j3mA 129 1.20e+01 d.129.7.1 103836 1o26A 232 1.20e+01 d.207.1.1 86566 2fk8A 318 1.21e+01 c.66.1.18 133648 3bwgA 239 1.21e+01 1jpkA 388 1.21e+01 c.1.22.1 67026 2q71A 356 1.22e+01 451cA 82 1.22e+01 a.3.1.1 15904 2fmpA 335 1.22e+01 a.60.6.1,a.60.12.1,d.218.1.2 133786,133787,133788 1xdwA 331 1.22e+01 2i7rA 118 1.23e+01 d.32.1.2 137102 2v6oA 596 1.23e+01 2bbeA 108 1.23e+01 2aefA 234 1.23e+01 2b33A 140 1.24e+01 d.79.1.1 127765 2dc1A 236 1.24e+01 2d0jA 246 1.24e+01 1ka2A 499 1.25e+01 d.92.1.5 77305 1tz0A 114 1.25e+01 d.58.4.5 107463 3b46A 447 1.26e+01 2o3oA 254 1.26e+01 2z8pA 241 1.26e+01 1qcwA 410 1.27e+01 1gox c.1.4.1 28622 2z1nA 260 1.28e+01 2q4kA 251 1.29e+01 d.86.1.2 139864 1x05A 129 1.30e+01 b.55.1.1 121543 1vr7A 142 1.30e+01 d.156.1.2 120443 1bykA 255 1.30e+01 1bykA c.93.1.1 35706 2rbbA 141 1.31e+01 1v5pA 126 1.32e+01 b.55.1.1 108382 2o56A 407 1.34e+01 2p0dA 129 1.35e+01 1kq3A 376 1.36e+01 e.22.1.2 68790 1kkhA 317 1.36e+01 d.14.1.5,d.58.26.3 72645,72646 1t5iA 172 1.38e+01 c.37.1.19 106450 1oxkB 134 1.39e+01 c.23.1.1 93691 2a35A 215 1.39e+01 c.2.1.2 126072 2g30A 258 1.40e+01 b.1.10.1,d.105.1.1 134546,134547 1r3sA 367 1.40e+01 c.1.22.1 96963 1r5yA 386 1.41e+01 c.1.20.1 97134 3xis 387 1.41e+01 4xis 4xis 387 1.41e+01 4xis 2v1xA 591 1.42e+01 1qdlA 422 1.42e+01 1qdlA d.161.1.1 42088 1i7qA 519 1.42e+01 1qdlA d.161.1.1 61901 1xppA 115 1.43e+01 d.74.3.2 115768 2ogyA 262 1.43e+01 1k2yX 463 1.44e+01 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