# List of top-scoring protein chains for t2k-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 2.79e-01 1ffyA 917 4.52e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 4.52e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1u0tA 307 1.07e+00 e.52.1.1 107567 2c3vA 102 1.56e+00 1bxwA 172 2.23e+00 1bxwA f.4.1.1 43743 1m7xA 617 2.46e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1qhoA 686 2.57e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1qx4A 274 2.76e+00 b.43.4.2,c.25.1.1 104624,104625 1qjpA 171 2.85e+00 1bxwA f.4.1.1 43742 1lktA 104 3.39e+00 1lktA b.90.1.1 28398 1isaA 192 3.63e+00 1avmA a.2.11.1,d.44.1.1 15731,38724 1iscA 192 3.71e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1e19A 314 3.74e+00 1b7bA c.73.1.1 34967 1k2fA 190 3.75e+00 b.8.1.2 68054 1tp6A 128 3.86e+00 d.17.4.12 107184 1zkdA 387 4.22e+00 1b9wA 89 5.63e+00 1b9wA g.3.11.4,g.3.11.4 44334,44335 1m65A 245 5.94e+00 c.6.3.1 84847 2cu3A 64 6.06e+00 1z0wA 207 6.68e+00 2gwnA 452 6.75e+00 2fh5A 185 7.08e+00 2a25A 193 7.16e+00 1th8A 145 7.24e+00 d.122.1.3 106908 3ezmA 101 7.83e+00 3ezmA b.89.1.1 28395 1i86A 389 7.90e+00 c.95.1.2,c.95.1.2 66068,66069 1bi5A 389 7.97e+00 1bi5A c.95.1.2,c.95.1.2 35985,35986 1gpeA 587 8.07e+00 1gpeA c.3.1.2,d.16.1.1 30387,37951 1qavB 115 8.09e+00 1qauA b.36.1.1 24780 1pz7A 204 8.56e+00 b.29.1.4 95405 1qauA 112 8.61e+00 1qauA b.36.1.1 24779 1ui0A 205 1.05e+01 c.18.1.2 99411 1bywA 110 1.08e+01 1bywA d.110.3.6 40912 1yx1A 264 1.12e+01 2bfgA 503 1.13e+01 1yuzA 202 1.16e+01 1cds 77 1.17e+01 1cds g.7.1.3 44461 1ebdA 455 1.21e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1b8iB 63 1.21e+01 1akhA a.4.1.1 16011 1i7pA 274 1.22e+01 b.43.4.2,c.25.1.1 66048,66049 1gv3A 248 1.28e+01 a.2.11.1,d.44.1.1 70585,70586 1u58A 253 1.36e+01 1y14B 171 1.37e+01 1lkkA 105 1.39e+01 1lckA d.93.1.1 40412 1cqyA 99 1.39e+01 1b9zA b.3.1.1 22527 1i88A 389 1.41e+01 c.95.1.2,c.95.1.2 66070,66071 1xfsA 178 1.41e+01 d.129.3.5 109589 1pufB 73 1.42e+01 a.4.1.1 95132 1m9sA 605 1.48e+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 1vjfA 180 1.51e+01 d.116.1.1 100809 1omiA 248 1.51e+01 b.82.3.3,a.4.5.4 87079,87080 1b72B 87 1.54e+01 1akhA a.4.1.1 16001 1umkA 275 1.55e+01 1b8qA 127 1.57e+01 1qauA b.36.1.1 24781 1v74A 107 1.58e+01 d.243.1.1 100442 16pk 415 1.65e+01 16pk c.86.1.1 35454 1itcA 516 1.68e+01 b.3.1.1,c.1.8.1 83705,83706 1kllA 130 1.72e+01 d.32.1.2 72720 1ny1A 240 1.75e+01 c.6.2.3 86395 1yaxA 153 1.83e+01 1nrlA 316 1.84e+01 a.123.1.1 92091 1lcjA 109 1.88e+01 1qadA d.93.1.1 40414 2ge3A 170 1.88e+01 1b7bA 310 1.89e+01 1b7bA c.73.1.1 34963 2gaiA 633 1.94e+01 1vr9A 213 1.96e+01 1vkcA 158 2.00e+01 1pylA 97 2.06e+01 d.1.1.2 104391 1ijqA 316 2.07e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1gmpA 96 2.07e+01 1rgeA d.1.1.2 36036 1cr5A 189 2.09e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 2bgiA 272 2.14e+01 1m13A 316 2.16e+01 a.123.1.1 84746 1am2 199 2.29e+01 1am2 b.86.1.2 28381 1iow 306 2.33e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1ndh 272 2.34e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1b1xA 689 2.34e+01 1cb6A c.94.1.2,c.94.1.2 35865,35866 1ne6A 283 2.35e+01 b.82.3.2,b.82.3.2 91831,91832 1l0oA 150 2.36e+01 d.122.1.3 73403 1jgtA 513 2.41e+01 c.26.2.1,d.153.1.1 66684,66685 1qnnA 191 2.42e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1xkiA 162 2.46e+01 1ttzA 87 2.48e+01 c.47.1.1 107309 1n9lA 109 2.48e+01 d.110.3.6 85468 1te7A 103 2.49e+01 1iiyA 101 2.50e+01 b.89.1.1 66152 2a2pA 129 2.53e+01 2bjbA 462 2.53e+01 1l9gA 192 2.60e+01 c.18.1.2 84568 1uasA 362 2.62e+01 b.71.1.1,c.1.8.1 88388,88389 1eagA 342 2.65e+01 1eagA b.50.1.2 26826 1jyeA 349 2.77e+01 c.93.1.1 67455 1bj8 109 2.77e+01 1bquA b.1.2.1 22070 1tlfA 301 2.80e+01 1tlfA c.93.1.1 35687 1uhvA 500 2.82e+01 b.71.1.2,c.1.8.3 99402,99403 1o7xD 377 2.87e+01 a.103.1.1 81174 1ro5A 201 2.90e+01 d.108.1.3 105023 2gclA 261 2.93e+01 2bs9A 503 2.93e+01 1m93C 41 3.07e+01 1efaA 333 3.11e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 2gk3A 256 3.12e+01 1fjgP 88 3.13e+01 1emwA d.27.1.1 38444 1e39A 571 3.15e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1p2hA 571 3.20e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1cjtA 217 3.23e+01 1azsA d.58.29.1 39419 1kzfA 230 3.23e+01 d.108.1.3 73354 1azsA 220 3.26e+01 1azsA d.58.29.1 39416 2go8A 122 3.26e+01 1m64A 571 3.27e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1txkA 498 3.29e+01 b.1.18.2,b.30.5.9 107425,107426 1ri9A 102 3.31e+01 b.34.2.1 97506 1b9zA 516 3.41e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1csn 298 3.41e+01 1csn d.144.1.7 41664 1a8h 500 3.42e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1pqzA 238 3.46e+01 b.1.1.2,d.19.1.1 104297,104298 1u4cA 349 3.46e+01 b.69.4.2 107666 1lj1A 571 3.46e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1th7A 81 3.47e+01 1vemA 516 3.51e+01 1m1zA 513 3.56e+01 c.26.2.1,d.153.1.1 78457,78458 2fafA 608 3.56e+01 1jb7B 260 3.60e+01 1otcB b.40.4.3 62839 1uesA 191 3.61e+01 a.2.11.1,d.44.1.1 107798,107799 2fa8A 105 3.77e+01 1ktbA 405 3.78e+01 b.71.1.1,c.1.8.1 72960,72961 1hn2A 159 3.87e+01 b.60.1.1 65890 1ugjA 141 3.89e+01 b.41.1.3 107826 1jmxA 494 3.94e+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 1bquA 215 3.96e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1lniA 96 3.99e+01 d.1.1.2 74046 2bt9A 90 4.06e+01 1s6xA 34 4.11e+01 1uliA 460 4.12e+01 b.33.1.2,d.129.3.3 107921,107922 1tgoA 773 4.18e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1huxA 270 4.20e+01 1huxA c.55.1.5 61278 2ciaA 102 4.25e+01 1cv8 174 4.29e+01 1cv8 d.3.1.1 37089 2bs6A 90 4.30e+01 1b78A 193 4.34e+01 1b78A c.51.4.1 33221 1z02A 446 4.36e+01 1usuA 260 4.40e+01 d.14.1.8 99885 1o7iA 119 4.46e+01 b.40.4.3 86642 2ci9A 102 4.51e+01 1vjvA 415 4.60e+01 d.3.1.9 108632 2jdxA 385 4.60e+01 1jdw d.126.1.2 41139 1vjlA 164 4.61e+01 d.257.1.1 100822 1z2mA 155 4.61e+01 1ay2 159 4.61e+01 2pil d.24.1.1 38377 1xqaA 113 4.64e+01 1dcjA 81 4.66e+01 1dcjA d.68.3.3 59115 1lgpA 116 4.67e+01 b.26.1.2 73890 1kjvA 284 4.72e+01 b.1.1.2,d.19.1.1 77421,77422 2dchX 216 4.73e+01 2aysA 348 4.84e+01 1ospO 257 4.92e+01 1ospO b.76.1.1 27971 1d8hA 311 4.95e+01 1d8iA d.63.1.1 39544 1hd2A 161 4.96e+01 c.47.1.10 60962 1mgqA 83 4.97e+01 b.38.1.1 79099 1q7fA 286 5.01e+01 b.68.9.1 96036 1cch 82 5.01e+01 451c a.3.1.1 15902 2pil 159 5.04e+01 2pil d.24.1.1 38376 1i3dA 146 5.04e+01 a.1.1.2 61587 1woyA 500 5.05e+01 1w9hA 427 5.05e+01 1z47A 355 5.06e+01 1ofzA 312 5.13e+01 b.68.8.1 86978 1culA 217 5.16e+01 1azsA d.58.29.1 39417 1obpA 159 5.19e+01 1obpA b.60.1.1 27092 1e1aA 314 5.28e+01 1e1aA b.68.6.1 59155 1k8kE 178 5.33e+01 a.148.1.1 68311 1qq2A 199 5.35e+01 1qq2A c.47.1.10 33064 1s4iA 175 5.37e+01 1r53A 382 5.39e+01 d.258.1.1 97063 1k38A 254 5.41e+01 e.3.1.1 84303 1zo2A 129 5.43e+01 1xvsA 126 5.50e+01 1xksA 450 5.56e+01 1pjxA 314 5.57e+01 b.68.6.1 104167 1aj2 282 5.58e+01 1aj2 c.1.21.1 29665 2g6yA 217 5.60e+01 1xgyH 219 5.67e+01 2fhxA 246 5.69e+01 1ihrA 76 5.71e+01 1ihrA d.212.1.2 62392 1vggA 161 5.73e+01 2c2aA 258 5.76e+01 1f2tB 148 5.77e+01 1f2tB 1ar0A 127 5.83e+01 1ounA d.17.4.2 38092 1um5H 217 5.84e+01 1m4iA 181 5.88e+01 d.108.1.1 74457 1jtkA 136 5.90e+01 c.97.1.1 71862 1pvmA 184 5.90e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1sf9A 128 5.92e+01 b.34.15.1 98831 1pamA 686 5.93e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1yfqA 342 5.93e+01 2cvzA 289 5.96e+01 1xtlA 175 6.01e+01 1mdwA 328 6.04e+01 d.3.1.3 84934 2cwzA 141 6.08e+01 1h6rA 236 6.09e+01 d.22.1.1 65683 1vq2A 193 6.11e+01 1d8iA 311 6.11e+01 1d8iA d.63.1.1 39541 2b5nA 323 6.17e+01 1uwzA 136 6.19e+01 c.97.1.1 108081 1u14A 172 6.22e+01 c.51.4.3 107579 1wtyA 119 6.24e+01 1h9oA 112 6.24e+01 1qadA d.93.1.1 60837 2nmbA 160 6.29e+01 2nmbA b.55.1.2 26994 2dln 306 6.30e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1nkxA 348 6.44e+01 c.94.1.2 91943 1b24A 188 6.47e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 2arcA 164 6.50e+01 2arcA b.82.4.1 28148 1vbvA 105 6.53e+01 1aj0 282 6.54e+01 1aj2 c.1.21.1 29667 5bcaA 516 6.54e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1emwA 88 6.57e+01 1emwA d.27.1.1 38448 1fvrA 327 6.63e+01 d.144.1.7 60047 1xkgA 312 6.66e+01 2bjfA 329 6.66e+01 1id0A 152 6.73e+01 d.122.1.3 66111 1tkeA 224 6.74e+01 1gt1A 159 6.78e+01 b.60.1.1 90515 1i0cA 60 6.78e+01 1aojA b.34.2.1 61485 1ay9A 108 6.89e+01 1umuA b.87.1.1 28384 1jqeA 292 6.95e+01 c.66.1.19 71789 1pxvA 183 6.95e+01 d.3.1.1 95301 1i81A 83 6.95e+01 1d3bB b.38.1.1 61930 1bhtA 176 6.97e+01 1bhtA g.10.1.1,g.14.1.1 44603,44663 1hxrA 115 7.01e+01 1fwqA b.88.1.1 28392 2cn3A 737 7.04e+01 1o2dA 371 7.10e+01 e.22.1.2 86591 1b77A 228 7.28e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1y4hA 188 7.30e+01 1u07A 90 7.39e+01 1pcfA 66 7.39e+01 1pcfA d.18.1.1 38142 1tuhA 156 7.39e+01 d.17.4.11 107345 1cdq 77 7.40e+01 1cds g.7.1.3 44459 2h3jA 75 7.43e+01 1askA 127 7.44e+01 1ounA d.17.4.2 38094 1vhnA 318 7.46e+01 c.1.4.1 100693 1dgmA 363 7.49e+01 1bx4A c.72.1.1 34936 1qjdA 571 7.51e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 2ct5A 73 7.53e+01 1oxdA 227 7.53e+01 d.22.1.1 93687 1qqp1 213 7.56e+01 1qqp1 1w4tA 299 7.61e+01 1omhA 293 7.64e+01 d.89.1.5 93348 1gy6A 127 7.68e+01 d.17.4.2 70736 1y9wA 140 7.77e+01 1s4nA 348 7.83e+01 c.68.1.16 98501 2b49A 287 7.84e+01 1rgeA 96 7.89e+01 1rgeA d.1.1.2 36028 1vcdA 126 7.93e+01 1rgs 288 7.93e+01 1rgs b.82.3.2,b.82.3.2 28146,28147 1tqxA 227 8.02e+01 1v0jA 399 8.11e+01 1jdw 423 8.12e+01 1jdw d.126.1.2 41129 1ema 236 8.18e+01 1ema d.22.1.1 38339 2czrA 226 8.26e+01 1tzaA 134 8.27e+01 b.1.23.1 107468 1o7xB 377 8.30e+01 a.103.1.1 81172 1opd 85 8.34e+01 1ptf d.94.1.1 40560 1szoA 257 8.39e+01 c.14.1.3 106164 1wleA 501 8.43e+01 1h7mA 102 8.50e+01 d.79.3.1 83485 1op1A 82 8.52e+01 a.13.1.1 93396 1ounA 127 8.57e+01 1ounA d.17.4.2 38090 1yppA 286 8.59e+01 1wgjA b.40.5.1 25407 2aacA 177 8.70e+01 2arcA b.82.4.1 28150 2arcB 164 8.74e+01 2arcA b.82.4.1 28149 1h6hA 143 8.78e+01 d.189.1.1 65681 1fnb 314 8.80e+01 1fnc b.43.4.2,c.25.1.1 25628,31518 1g5aA 628 8.99e+01 b.71.1.1,c.1.8.1 65152,65153