# List of top-scoring protein chains for t04-100-30-o_notor2-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 2f4qA 346 8.96e-02 1ffyA 917 1.34e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 2c3vA 102 2.50e-01 1qx4A 274 5.06e-01 b.43.4.2,c.25.1.1 104624,104625 1m7xA 617 9.07e-01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1qjpA 171 1.36e+00 1bxwA f.4.1.1 43742 1k2fA 190 1.41e+00 b.8.1.2 68054 1zkdA 387 1.70e+00 1qhoA 686 1.98e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1tp6A 128 2.02e+00 d.17.4.12 107184 1i7pA 274 2.14e+00 b.43.4.2,c.25.1.1 66048,66049 1y14B 171 2.66e+00 1yaxA 153 2.71e+00 2cu3A 64 2.75e+00 1lktA 104 2.88e+00 1lktA b.90.1.1 28398 2a25A 193 3.08e+00 1u0tA 307 3.13e+00 e.52.1.1 107567 1umkA 275 3.24e+00 1cr5A 189 3.31e+00 1cr5A b.52.2.3,d.31.1.1 26931,38465 1iscA 192 3.64e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 2a2pA 129 4.28e+00 1omiA 248 4.36e+00 b.82.3.3,a.4.5.4 87079,87080 1tzaA 134 4.71e+00 b.1.23.1 107468 2h3jA 75 4.92e+00 1m65A 245 5.03e+00 c.6.3.1 84847 1ndh 272 5.59e+00 1ndh b.43.4.2,c.25.1.1 25662,31552 1yx1A 264 5.73e+00 1z02A 446 5.85e+00 3ezmA 101 6.63e+00 3ezmA b.89.1.1 28395 1e19A 314 6.84e+00 1b7bA c.73.1.1 34967 1pylA 97 6.93e+00 d.1.1.2 104391 1a8h 500 7.16e+00 1a8h a.27.1.1,c.26.1.1 16922,31589 1bwzA 274 7.22e+00 1bwzA d.21.1.1,d.21.1.1 38337,38338 1th8A 145 7.40e+00 d.122.1.3 106908 1xfsA 178 7.91e+00 d.129.3.5 109589 1gv3A 248 8.21e+00 a.2.11.1,d.44.1.1 70585,70586 1b24A 188 8.40e+00 1b24A d.95.2.1,d.95.2.1 40573,40574 1xvsA 126 8.44e+00 1cqyA 99 8.72e+00 1b9zA b.3.1.1 22527 1pz7A 204 9.27e+00 b.29.1.4 95405 1gpeA 587 9.41e+00 1gpeA c.3.1.2,d.16.1.1 30387,37951 1e3uA 246 9.45e+00 1fofA e.3.1.1 42755 1who 96 9.58e+00 1who b.7.3.1 23215 1ktbA 405 9.65e+00 b.71.1.1,c.1.8.1 72960,72961 1pufB 73 9.70e+00 a.4.1.1 95132 1vr9A 213 9.77e+00 1b9wA 89 1.00e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1bi5A 389 1.01e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1qauA 112 1.01e+01 1qauA b.36.1.1 24779 1z0wA 207 1.02e+01 1vetA 124 1.05e+01 d.110.7.1 108553 1txkA 498 1.09e+01 b.1.18.2,b.30.5.9 107425,107426 1b72B 87 1.16e+01 1akhA a.4.1.1 16001 1u58A 253 1.17e+01 1gqzA 274 1.17e+01 d.21.1.1,d.21.1.1 83311,83312 1itcA 516 1.20e+01 b.3.1.1,c.1.8.1 83705,83706 1th7A 81 1.23e+01 1nrlA 316 1.25e+01 a.123.1.1 92091 1ui0A 205 1.26e+01 c.18.1.2 99411 2cwzA 141 1.27e+01 1bywA 110 1.31e+01 1bywA d.110.3.6 40912 2bfgA 503 1.32e+01 1woyA 500 1.37e+01 2gwnA 452 1.38e+01 1v74A 107 1.40e+01 d.243.1.1 100442 1k55A 246 1.44e+01 e.3.1.1 68156 1am2 199 1.45e+01 1am2 b.86.1.2 28381 2bgcA 238 1.48e+01 1xkiA 162 1.49e+01 2cr5A 109 1.50e+01 2gkeA 274 1.52e+01 1lkkA 105 1.53e+01 1lckA d.93.1.1 40412 1m9sA 605 1.53e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1m93C 41 1.55e+01 1q7fA 286 1.58e+01 b.68.9.1 96036 1uhvA 500 1.59e+01 b.71.1.2,c.1.8.3 99402,99403 1vjvA 415 1.61e+01 d.3.1.9 108632 1vq2A 193 1.65e+01 2fh5A 185 1.68e+01 1l6sA 323 1.70e+01 c.1.10.3 73627 1ijqA 316 1.72e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1iow 306 1.72e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1gy6A 127 1.73e+01 d.17.4.2 70736 1csn 298 1.74e+01 1csn d.144.1.7 41664 2gaiA 633 1.84e+01 1i88A 389 1.85e+01 c.95.1.2,c.95.1.2 66070,66071 1i8jA 323 1.89e+01 1b4kA c.1.10.3 61968 2jdxA 385 1.98e+01 1jdw d.126.1.2 41139 1z47A 355 2.00e+01 1ro5A 201 2.04e+01 d.108.1.3 105023 1hg8A 349 2.07e+01 b.80.1.3 65830 1rkqA 282 2.15e+01 c.108.1.10 97621 1lniA 96 2.18e+01 d.1.1.2 74046 1ig8A 486 2.21e+01 2yhx c.55.1.3,c.55.1.3 64746,64747 16pk 415 2.21e+01 16pk c.86.1.1 35454 1hxrA 115 2.24e+01 1fwqA b.88.1.1 28392 1jb7B 260 2.29e+01 1otcB b.40.4.3 62839 1e39A 571 2.33e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1p2hA 571 2.34e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1ounA 127 2.34e+01 1ounA d.17.4.2 38090 1s6xA 34 2.44e+01 2gclA 261 2.49e+01 1szoA 257 2.52e+01 c.14.1.3 106164 1pm1X 180 2.59e+01 b.60.1.1 104189 1c0eA 157 2.59e+01 1dg9A c.44.1.1 32638 1vrbA 342 2.62e+01 1vemA 516 2.69e+01 1fjgP 88 2.69e+01 1emwA d.27.1.1 38444 2fafA 608 2.71e+01 1o8uA 257 2.75e+01 c.14.1.3 81194 1dg9A 157 2.76e+01 1dg9A c.44.1.1 32637 2ge3A 170 2.77e+01 1pamA 686 2.84e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 2bgiA 272 2.89e+01 1u4cA 349 2.89e+01 b.69.4.2 107666 1xksA 450 2.97e+01 1oshA 232 2.99e+01 a.123.1.1 93496 1xt9A 212 2.99e+01 1pda 315 3.05e+01 1pda c.94.1.1,d.50.2.1 35751,38794 2arcA 164 3.05e+01 2arcA b.82.4.1 28148 1ttzA 87 3.06e+01 c.47.1.1 107309 1pqzA 238 3.08e+01 b.1.1.2,d.19.1.1 104297,104298 2bjbA 462 3.09e+01 2bs9A 503 3.10e+01 2pil 159 3.11e+01 2pil d.24.1.1 38376 1vkcA 158 3.16e+01 1d8hA 311 3.18e+01 1d8iA d.63.1.1 39544 1hn2A 159 3.21e+01 b.60.1.1 65890 1upiA 225 3.38e+01 b.82.1.1 99757 1fepA 724 3.40e+01 1fepA f.4.3.3 43808 1f00I 282 3.43e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1w9hA 427 3.44e+01 1b8aA 438 3.45e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1jdw 423 3.45e+01 1jdw d.126.1.2 41129 2bt9A 90 3.46e+01 1kzfA 230 3.49e+01 d.108.1.3 73354 2fa8A 105 3.49e+01 2b59B 172 3.58e+01 1kfwA 435 3.62e+01 c.1.8.5,d.26.3.1 77376,77377 1g8kA 825 3.63e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1xvqA 175 3.65e+01 1n5nA 180 3.68e+01 d.167.1.1 85336 1h4rA 314 3.70e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 2bs6A 90 3.78e+01 1b2pA 119 3.95e+01 1b2pA b.78.1.1 27998 1m0dA 138 3.95e+01 c.52.1.17 74354 1uasA 362 4.03e+01 b.71.1.1,c.1.8.1 88388,88389 1h6hA 143 4.08e+01 d.189.1.1 65681 1gmuA 143 4.10e+01 b.107.1.1,d.58.38.1 65335,65336 1mhnA 59 4.13e+01 b.34.9.1 84964 1skoA 143 4.18e+01 d.110.7.1 105676 1umuA 116 4.21e+01 1umuA b.87.1.1 28382 1h7mA 102 4.24e+01 d.79.3.1 83485 1zsyA 357 4.24e+01 1twuA 139 4.24e+01 d.32.1.8 107413 1m4iA 181 4.31e+01 d.108.1.1 74457 1qmvA 197 4.33e+01 1qq2A c.47.1.10 33066 1i0sA 169 4.37e+01 1i0rA b.45.1.2 61491 1jmxA 494 4.51e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1qwlA 505 4.52e+01 e.5.1.1 96483 2a4hA 126 4.57e+01 2cn3A 737 4.62e+01 2go8A 122 4.64e+01 3nul 130 4.65e+01 3nul d.110.1.1 40891 1i0rA 169 4.66e+01 1i0rA b.45.1.2 61489 1vjfA 180 4.68e+01 d.116.1.1 100809 1bquA 215 4.76e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1i2uA 44 4.85e+01 g.3.7.4 65987 1uliA 460 4.88e+01 b.33.1.2,d.129.3.3 107921,107922 1obpA 159 4.90e+01 1obpA b.60.1.1 27092 1cv8 174 4.96e+01 1cv8 d.3.1.1 37089 1wtyA 119 4.96e+01 1wm3A 72 4.99e+01 1epfA 191 5.01e+01 2ncm b.1.1.4,b.1.1.4 21694,21695 1xwwA 157 5.01e+01 1fzrA 138 5.01e+01 1fzrA c.52.1.17 33336 1ecfA 504 5.01e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1k8kA 418 5.06e+01 c.55.1.1,c.55.1.1 68305,68306 1mgqA 83 5.09e+01 b.38.1.1 79099 2bkrA 212 5.11e+01 1y8cA 246 5.17e+01 1va4A 279 5.18e+01 c.69.1.12 108458 1v0jA 399 5.18e+01 1wj9A 211 5.20e+01 1gt1A 159 5.21e+01 b.60.1.1 90515 1kjvA 284 5.22e+01 b.1.1.2,d.19.1.1 77421,77422 1iakA 199 5.23e+01 1iakA b.1.1.2,d.19.1.1 21625,38199 1f39A 101 5.23e+01 1umuA b.87.1.1 28386 1ofzA 312 5.25e+01 b.68.8.1 86978 1cf9A 753 5.27e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 2azqA 311 5.28e+01 1hd2A 161 5.37e+01 c.47.1.10 60962 1ospO 257 5.37e+01 1ospO b.76.1.1 27971 1e1aA 314 5.37e+01 1e1aA b.68.6.1 59155 1omhA 293 5.38e+01 d.89.1.5 93348 1gtkA 313 5.39e+01 c.94.1.1,d.50.2.1 76346,76347 1p80A 753 5.39e+01 c.23.16.3,e.5.1.1 94337,94338 1wywA 230 5.40e+01 1xriA 151 5.47e+01 1s4nA 348 5.53e+01 c.68.1.16 98501 1iq9A 61 5.55e+01 g.7.1.1 90669 1e25A 282 5.57e+01 1e25A e.3.1.1 42731 2aysA 348 5.59e+01 1bhtA 176 5.60e+01 1bhtA g.10.1.1,g.14.1.1 44603,44663 1u00A 227 5.60e+01 1ne6A 283 5.63e+01 b.82.3.2,b.82.3.2 91831,91832 1wvqA 167 5.64e+01 2cfuA 658 5.65e+01 1b71A 191 5.69e+01 1ryt a.25.1.1,g.41.5.1 16647,45246 1f2tB 148 5.72e+01 1f2tB 1ryt 190 5.74e+01 1ryt a.25.1.1,g.41.5.1 16646,45245 1pjxA 314 5.74e+01 b.68.6.1 104167 1uvqA 197 5.79e+01 b.1.1.2,d.19.1.1 100062,100063 1h9oA 112 5.81e+01 1qadA d.93.1.1 60837 1xg9A 260 5.91e+01 1lkoA 191 5.94e+01 a.25.1.1,g.41.5.1 78063,78064 1qqp1 213 5.94e+01 1qqp1 1yifA 533 5.94e+01 1q7lB 88 5.95e+01 1i0cA 60 5.99e+01 1aojA b.34.2.1 61485 1yuzA 202 6.00e+01 2c2aA 258 6.01e+01 1fnd 314 6.04e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1iwdA 215 6.04e+01 d.3.1.1 83756 1zghA 260 6.04e+01 1ne9A 335 6.07e+01 d.108.1.4,d.108.1.4 91839,91840 1vggA 161 6.15e+01 1pcfA 66 6.16e+01 1pcfA d.18.1.1 38142 2fbmA 291 6.19e+01 2fc7A 82 6.19e+01 1whzA 70 6.27e+01 1qfxA 460 6.27e+01 1qfxA c.60.1.2 33994 2ey4C 82 6.34e+01 2afaA 425 6.35e+01 1xkgA 312 6.36e+01 1mxiA 160 6.39e+01 c.116.1.1 79646 1ri9A 102 6.42e+01 b.34.2.1 97506 1xkzA 255 6.42e+01 1xebA 150 6.44e+01 1ayaA 101 6.49e+01 1qadA d.93.1.1 40460 1xhcA 367 6.52e+01 1rgeA 96 6.56e+01 1rgeA d.1.1.2 36028 1ng2A 193 6.57e+01 b.34.2.1,b.34.2.1 85660,85661 1xgyH 219 6.58e+01 1huxA 270 6.60e+01 1huxA c.55.1.5 61278 2b49A 287 6.65e+01 1eo9B 241 6.65e+01 3pchM b.3.6.1 22826 4tsvA 150 6.66e+01 2tnfA b.22.1.1 23860 1vbvA 105 6.67e+01 2esnA 310 6.68e+01 1bx1A 314 6.69e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1xqaA 113 6.73e+01 1b63A 333 6.73e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1htrB 329 6.75e+01 1smrA 1euvB 86 6.77e+01 1a5r d.15.1.1 37598 1yfqA 342 6.90e+01 1lgpA 116 6.92e+01 b.26.1.2 73890 1i3dA 146 6.94e+01 a.1.1.2 61587 1u14A 172 6.98e+01 c.51.4.3 107579 1pvmA 184 6.99e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 2cspA 130 7.02e+01 1r53A 382 7.02e+01 d.258.1.1 97063 1ey4A 149 7.03e+01 1snc b.40.1.1 24815 1bbt1 213 7.04e+01 1qqp1 1r0uA 148 7.07e+01 b.60.1.5 96741 1zo2A 129 7.08e+01 1y0pA 571 7.11e+01 1t9xA 1049 7.15e+01 1a8p 258 7.16e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1ny1A 240 7.18e+01 c.6.2.3 86395 1s72S 85 7.20e+01 d.12.1.1 105338 1w41A 101 7.22e+01 1usuA 260 7.23e+01 d.14.1.8 99885 1lwdA 413 7.28e+01 c.77.1.1 78265 1npsA 88 7.29e+01 1prs b.11.1.1 23622 2sli 679 7.29e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1n9lA 109 7.32e+01 d.110.3.6 85468 1pl3A 186 7.39e+01 b.1.9.1 88158 1y88A 199 7.40e+01 1mdwA 328 7.41e+01 d.3.1.3 84934 1vcdA 126 7.47e+01 1nkxA 348 7.49e+01 c.94.1.2 91943 1ju2A 536 7.51e+01 c.3.1.2,d.16.1.1 77169,77170 1xf1A 926 7.53e+01 1hw6A 278 7.56e+01 1frb c.1.7.1 61296 1kssA 571 7.56e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1tkeA 224 7.66e+01 2bjfA 329 7.72e+01 1z2mA 155 7.76e+01 1m1zA 513 7.79e+01 c.26.2.1,d.153.1.1 78457,78458 1w4tA 299 7.81e+01 1nkiA 135 7.84e+01 d.32.1.2 91941 1xrkA 124 7.88e+01 1jj2R 84 7.97e+01 1ffkP d.12.1.1 63103 1oxdA 227 7.98e+01 d.22.1.1 93687 2ciaA 102 7.98e+01 2bkqA 212 8.08e+01 2sns 149 8.09e+01 1snc b.40.1.1 24860 1kay 381 8.11e+01 1ba1 c.55.1.1,c.55.1.1 33385,33386 2fb1A 226 8.13e+01 1y4hA 188 8.13e+01 1dcjA 81 8.15e+01 1dcjA d.68.3.3 59115 1jofA 365 8.20e+01 b.69.10.1 71775 1s4iA 175 8.24e+01 1hkfA 122 8.24e+01 b.1.1.1 83553 1q9iA 571 8.27e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1e3dA 266 8.27e+01 2frvA e.19.1.1 59188 1wkyA 464 8.28e+01 1cbf 285 8.30e+01 1cbf c.90.1.1 35587 1k1eA 180 8.36e+01 c.108.1.5 67995 1ughI 82 8.37e+01 1ugiA d.17.5.1 38133 1obr 326 8.37e+01 1aye c.56.5.2 33828 1azsA 220 8.42e+01 1azsA d.58.29.1 39416 1qhdA 398 8.44e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1qveA 126 8.46e+01 d.24.1.1 104594 1fvrA 327 8.49e+01 d.144.1.7 60047 1v2yA 105 8.56e+01 d.15.1.1 100275 1vqoS 85 8.56e+01 2bzoB 79 8.60e+01 1jb0E 75 8.64e+01 1pse b.34.4.2 62824 1fnc 314 8.68e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 1ema 236 8.73e+01 1ema d.22.1.1 38339 1tqzA 133 8.77e+01 1id0A 152 8.80e+01 d.122.1.3 66111 1ctn 540 8.89e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1xtlA 175 8.91e+01