# 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 1.05e-01 1ffyA 917 2.20e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 2.20e-01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1tzaA 134 5.75e-01 b.1.23.1 107468 1qx4A 274 9.57e-01 b.43.4.2,c.25.1.1 104624,104625 1u0tA 307 9.86e-01 e.52.1.1 107567 2c3vA 102 1.08e+00 1bxwA 172 1.19e+00 1bxwA f.4.1.1 43743 1m7xA 617 1.20e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1qjpA 171 1.52e+00 1bxwA f.4.1.1 43742 1qhoA 686 1.58e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1tp6A 128 1.85e+00 d.17.4.12 107184 1lktA 104 2.22e+00 1lktA b.90.1.1 28398 1k2fA 190 2.26e+00 b.8.1.2 68054 1m65A 245 2.63e+00 c.6.3.1 84847 1zkdA 387 3.22e+00 1isaA 192 3.31e+00 1avmA a.2.11.1,d.44.1.1 15731,38724 1iscA 192 3.37e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1i86A 389 3.53e+00 c.95.1.2,c.95.1.2 66068,66069 2gwnA 452 3.76e+00 1bi5A 389 4.04e+00 1bi5A c.95.1.2,c.95.1.2 35985,35986 2cu3A 64 4.23e+00 1b9wA 89 4.40e+00 1b9wA g.3.11.4,g.3.11.4 44334,44335 2a25A 193 4.68e+00 1z0wA 207 5.15e+00 1e19A 314 5.20e+00 1b7bA c.73.1.1 34967 1i7pA 274 5.51e+00 b.43.4.2,c.25.1.1 66048,66049 1b8iB 63 5.76e+00 1akhA a.4.1.1 16011 3ezmA 101 5.86e+00 3ezmA b.89.1.1 28395 1pufB 73 6.27e+00 a.4.1.1 95132 1pz7A 204 6.35e+00 b.29.1.4 95405 1yx1A 264 6.38e+00 1omiA 248 6.38e+00 b.82.3.3,a.4.5.4 87079,87080 1qavB 115 6.75e+00 1qauA b.36.1.1 24780 1b72B 87 6.85e+00 1akhA a.4.1.1 16001 1ebdA 455 6.95e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1umkA 275 6.97e+00 1ui0A 205 7.36e+00 c.18.1.2 99411 1qauA 112 7.38e+00 1qauA b.36.1.1 24779 1i88A 389 7.63e+00 c.95.1.2,c.95.1.2 66070,66071 1th8A 145 7.63e+00 d.122.1.3 106908 1y14B 171 8.25e+00 2fh5A 185 8.94e+00 1xfsA 178 9.03e+00 d.129.3.5 109589 1cqyA 99 9.22e+00 1b9zA b.3.1.1 22527 1ktbA 405 9.91e+00 b.71.1.1,c.1.8.1 72960,72961 1bywA 110 1.00e+01 1bywA d.110.3.6 40912 1u58A 253 1.07e+01 2bfgA 503 1.08e+01 1ndh 272 1.10e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1gpeA 587 1.12e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1gv3A 248 1.15e+01 a.2.11.1,d.44.1.1 70585,70586 1cds 77 1.17e+01 1cds g.7.1.3 44461 1ny1A 240 1.21e+01 c.6.2.3 86395 1lkkA 105 1.35e+01 1lckA d.93.1.1 40412 1itcA 516 1.37e+01 b.3.1.1,c.1.8.1 83705,83706 1b8qA 127 1.38e+01 1qauA b.36.1.1 24781 1gmpA 96 1.39e+01 1rgeA d.1.1.2 36036 1v74A 107 1.44e+01 d.243.1.1 100442 1vjfA 180 1.46e+01 d.116.1.1 100809 1uasA 362 1.46e+01 b.71.1.1,c.1.8.1 88388,88389 1azsA 220 1.49e+01 1azsA d.58.29.1 39416 1yaxA 153 1.49e+01 16pk 415 1.50e+01 16pk c.86.1.1 35454 2go8A 122 1.53e+01 1nrlA 316 1.53e+01 a.123.1.1 92091 1cr5A 189 1.54e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1cjtA 217 1.57e+01 1azsA d.58.29.1 39419 1m9sA 605 1.59e+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 1b7bA 310 1.66e+01 1b7bA c.73.1.1 34963 1tlfA 301 1.66e+01 1tlfA c.93.1.1 35687 1m13A 316 1.69e+01 a.123.1.1 84746 1m93C 41 1.73e+01 1bj8 109 1.73e+01 1bquA b.1.2.1 22070 2b49A 287 1.74e+01 1pylA 97 1.75e+01 d.1.1.2 104391 1am2 199 1.80e+01 1am2 b.86.1.2 28381 1xkiA 162 1.82e+01 1a8h 500 1.83e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1b1xA 689 1.85e+01 1cb6A c.94.1.2,c.94.1.2 35865,35866 1d4oA 184 1.86e+01 1d4oA c.31.1.4 31748 1lcjA 109 1.88e+01 1qadA d.93.1.1 40414 1ne6A 283 1.91e+01 b.82.3.2,b.82.3.2 91831,91832 1efaA 333 1.92e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1jyeA 349 1.93e+01 c.93.1.1 67455 2gaiA 633 1.93e+01 1csn 298 1.99e+01 1csn d.144.1.7 41664 1vr9A 213 2.00e+01 1ttzA 87 2.04e+01 c.47.1.1 107309 1bquA 215 2.05e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1iiyA 101 2.11e+01 b.89.1.1 66152 1ugjA 141 2.12e+01 b.41.1.3 107826 1uhvA 500 2.13e+01 b.71.1.2,c.1.8.3 99402,99403 1ijqA 316 2.15e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1kllA 130 2.18e+01 d.32.1.2 72720 1yuzA 202 2.25e+01 1jgtA 513 2.26e+01 c.26.2.1,d.153.1.1 66684,66685 1xksA 450 2.38e+01 1kzfA 230 2.40e+01 d.108.1.3 73354 1lniA 96 2.42e+01 d.1.1.2 74046 1te7A 103 2.44e+01 1l9gA 192 2.44e+01 c.18.1.2 84568 1culA 217 2.47e+01 1azsA d.58.29.1 39417 1o7xD 377 2.48e+01 a.103.1.1 81174 1ro5A 201 2.55e+01 d.108.1.3 105023 2fafA 608 2.56e+01 1fvrA 327 2.61e+01 d.144.1.7 60047 1pqzA 238 2.66e+01 b.1.1.2,d.19.1.1 104297,104298 1q7fA 286 2.66e+01 b.68.9.1 96036 2cn3A 737 2.68e+01 2bjbA 462 2.70e+01 1ri9A 102 2.70e+01 b.34.2.1 97506 1xvsA 126 2.71e+01 1woyA 500 2.75e+01 2bs9A 503 2.80e+01 1hn2A 159 2.81e+01 b.60.1.1 65890 1hd2A 161 2.83e+01 c.47.1.10 60962 1e39A 571 2.83e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1l0oA 150 2.87e+01 d.122.1.3 73403 1p2hA 571 2.88e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1b9zA 516 2.93e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1m64A 571 2.97e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 2bt9A 90 2.98e+01 1iow 306 3.01e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1ofzA 312 3.02e+01 b.68.8.1 86978 1jmxA 494 3.02e+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 1vemA 516 3.03e+01 1s6xA 34 3.06e+01 1s4iA 175 3.08e+01 1u4cA 349 3.09e+01 b.69.4.2 107666 1lj1A 571 3.10e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 2bjfA 329 3.11e+01 2gclA 261 3.20e+01 2bs6A 90 3.21e+01 1xtlA 175 3.26e+01 1fjgP 88 3.27e+01 1emwA d.27.1.1 38444 2bgcA 238 3.29e+01 2bgiA 272 3.33e+01 1qnnA 191 3.39e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 2a2pA 129 3.41e+01 1vjvA 415 3.41e+01 d.3.1.9 108632 1txkA 498 3.43e+01 b.1.18.2,b.30.5.9 107425,107426 1vkcA 158 3.47e+01 1tksA 204 3.50e+01 d.115.1.2 107114 2cwzA 141 3.50e+01 2fa8A 105 3.54e+01 1jb7B 260 3.57e+01 1otcB b.40.4.3 62839 2ciaA 102 3.59e+01 1th7A 81 3.64e+01 1z47A 355 3.64e+01 2ci9A 102 3.67e+01 1vjlA 164 3.71e+01 d.257.1.1 100822 1e3uA 246 3.72e+01 1fofA e.3.1.1 42755 1vq2A 193 3.73e+01 1m4iA 181 3.73e+01 d.108.1.1 74457 1b78A 193 3.73e+01 1b78A c.51.4.1 33221 1kjvA 284 3.75e+01 b.1.1.2,d.19.1.1 77421,77422 1omhA 293 3.79e+01 d.89.1.5 93348 1xoyA 161 3.82e+01 2ge3A 170 3.83e+01 1n9lA 109 3.84e+01 d.110.3.6 85468 1k38A 254 3.85e+01 e.3.1.1 84303 1qq2A 199 3.91e+01 1qq2A c.47.1.10 33064 1obpA 159 3.97e+01 1obpA b.60.1.1 27092 2c2aA 258 4.06e+01 1pvmA 184 4.10e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1xqaA 113 4.16e+01 1dcjA 81 4.25e+01 1dcjA d.68.3.3 59115 1m1zA 513 4.26e+01 c.26.2.1,d.153.1.1 78457,78458 1zo2A 129 4.27e+01 1v0jA 399 4.29e+01 1b24A 188 4.30e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1k8kE 178 4.36e+01 a.148.1.1 68311 1jofA 365 4.38e+01 b.69.10.1 71775 1usuA 260 4.44e+01 d.14.1.8 99885 1bhtA 176 4.45e+01 1bhtA g.10.1.1,g.14.1.1 44603,44663 2czrA 226 4.54e+01 1wtyA 119 4.57e+01 1ay9A 108 4.60e+01 1umuA b.87.1.1 28384 1w9hA 427 4.74e+01 1tgoA 773 4.79e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1k55A 246 4.87e+01 e.3.1.1 68156 2gk3A 256 4.92e+01 1tkeA 224 4.98e+01 1h9oA 112 5.03e+01 1qadA d.93.1.1 60837 1cch 82 5.11e+01 451c a.3.1.1 15902 2g6yA 217 5.11e+01 1yppA 286 5.13e+01 1wgjA b.40.5.1 25407 1pdnC 128 5.13e+01 6paxA a.4.1.5 16047 1i3dA 146 5.17e+01 a.1.1.2 61587 1f2tB 148 5.17e+01 1f2tB 2jdxA 385 5.20e+01 1jdw d.126.1.2 41139 1h4rA 314 5.25e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1xt9A 212 5.27e+01 1g8kA 825 5.28e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1z02A 446 5.29e+01 1uesA 191 5.31e+01 a.2.11.1,d.44.1.1 107798,107799 1e1aA 314 5.34e+01 1e1aA b.68.6.1 59155 1uliA 460 5.35e+01 b.33.1.2,d.129.3.3 107921,107922 1va4A 279 5.38e+01 c.69.1.12 108458 5bcaA 516 5.39e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 1gt1A 159 5.43e+01 b.60.1.1 90515 1rgeA 96 5.46e+01 1rgeA d.1.1.2 36028 1ay2 159 5.46e+01 2pil d.24.1.1 38377 1vbvA 105 5.47e+01 1vetA 124 5.50e+01 d.110.7.1 108553 1e25A 282 5.55e+01 1e25A e.3.1.1 42731 1ihrA 76 5.56e+01 1ihrA d.212.1.2 62392 1byrA 155 5.58e+01 1byrA d.136.1.1 41450 1xtmA 175 5.61e+01 1o7iA 119 5.62e+01 b.40.4.3 86642 1pjxA 314 5.63e+01 b.68.6.1 104167 1mgqA 83 5.64e+01 b.38.1.1 79099 2cvzA 289 5.78e+01 1u07A 90 5.78e+01 1yfqA 342 5.86e+01 2pil 159 5.90e+01 2pil d.24.1.1 38376 1z2mA 155 5.92e+01 1eagA 342 5.96e+01 1eagA b.50.1.2 26826 1vcdA 126 5.97e+01 1yifA 533 5.99e+01 1fofA 246 6.04e+01 1fofA e.3.1.1 42763 1b77A 228 6.09e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1i8vA 96 6.09e+01 d.1.1.2 61985 1hxrA 115 6.11e+01 1fwqA b.88.1.1 28392 1g5aA 628 6.13e+01 b.71.1.1,c.1.8.1 65152,65153 1lufA 343 6.18e+01 d.144.1.7 78223 1q7lB 88 6.19e+01 1oshA 232 6.21e+01 a.123.1.1 93496 1vggA 161 6.25e+01 7catA 506 6.28e+01 1cf9A e.5.1.1 42781 1ospO 257 6.28e+01 1ospO b.76.1.1 27971 1b63A 333 6.35e+01 1b63A d.14.1.3,d.122.1.2 37566,41107 1u14A 172 6.36e+01 c.51.4.3 107579 1izmA 184 6.36e+01 a.199.1.1 90725 1xriA 151 6.37e+01 1rgs 288 6.39e+01 1rgs b.82.3.2,b.82.3.2 28146,28147 1cv8 174 6.42e+01 1cv8 d.3.1.1 37089 1fx7A 230 6.43e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1ka9H 200 6.46e+01 c.23.16.1 77308 1h6rA 236 6.46e+01 d.22.1.1 65683 1h6hA 143 6.51e+01 d.189.1.1 65681 1o2dA 371 6.61e+01 e.22.1.2 86591 2fhxA 246 6.63e+01 1k4fA 248 6.72e+01 e.3.1.1 68138 1lgpA 116 6.77e+01 b.26.1.2 73890 1yqtA 538 6.77e+01 1jtkA 136 6.83e+01 c.97.1.1 71862 1who 96 6.84e+01 1who b.7.3.1 23215 1rpyA 114 6.86e+01 d.93.1.1 97718 1t0fC 54 6.94e+01 1qjdA 571 6.97e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19695,30432,42315 1vhnA 318 6.97e+01 c.1.4.1 100693 1korA 400 6.98e+01 c.26.2.1,d.210.1.1 72824,72825 1pda 315 7.01e+01 1pda c.94.1.1,d.50.2.1 35751,38794 1tuhA 156 7.03e+01 d.17.4.11 107345 1r53A 382 7.05e+01 d.258.1.1 97063 2aysA 348 7.06e+01 2h3jA 75 7.06e+01 1htjF 210 7.08e+01 1htjF a.91.1.1 61254 1in4A 334 7.10e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1emwA 88 7.10e+01 1emwA d.27.1.1 38448 1uwzA 136 7.13e+01 c.97.1.1 108081 1iwdA 215 7.18e+01 d.3.1.1 83756 1evsA 187 7.19e+01 1evsA a.26.1.1 16845 1fnb 314 7.21e+01 1fnc b.43.4.2,c.25.1.1 25628,31518 1umuA 116 7.21e+01 1umuA b.87.1.1 28382 1umuB 116 7.28e+01 1umuA b.87.1.1 28383 1d8hA 311 7.31e+01 1d8iA d.63.1.1 39544 1k75A 434 7.34e+01 c.82.1.2 68253 1ar0A 127 7.35e+01 1ounA d.17.4.2 38092 4tsvA 150 7.44e+01 2tnfA b.22.1.1 23860 2b5nA 323 7.50e+01 1h7mA 102 7.62e+01 d.79.3.1 83485 1pamA 686 7.62e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1i0cA 60 7.70e+01 1aojA b.34.2.1 61485 1xgyH 219 7.72e+01 1xkgA 312 7.74e+01 2bkrA 212 7.75e+01 1vefA 395 7.79e+01 2ftwA 521 7.80e+01 1ksiB 642 7.82e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24409,38045,38046 1y9wA 140 7.82e+01 1jqeA 292 7.82e+01 c.66.1.19 71789 2aop 497 7.83e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 1fnd 314 7.86e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1o7xB 377 7.86e+01 a.103.1.1 81172 1y0pA 571 7.87e+01 1fpqA 372 7.88e+01 1fpqA a.4.5.29,c.66.1.12 59947,59948 1qqp1 213 7.88e+01 1qqp1 1i81A 83 7.91e+01 1d3bB b.38.1.1 61930 2abd 86 7.96e+01 1aca a.11.1.1 16366 1szoA 257 8.05e+01 c.14.1.3 106164 1ema 236 8.15e+01 1ema d.22.1.1 38339 1dvfD 120 8.30e+01 1mfa b.1.1.1 20107 1mdwA 328 8.37e+01 d.3.1.3 84934 1qfxA 460 8.43e+01 1qfxA c.60.1.2 33994 2dln 306 8.46e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1ksiA 642 8.46e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1cdq 77 8.47e+01 1cds g.7.1.3 44459 1kfwA 435 8.48e+01 c.1.8.5,d.26.3.1 77376,77377 1a0p 290 8.55e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1e5uI 187 8.58e+01 1f00I b.1.14.1,d.169.1.3 22372,42441 2fb1A 226 8.61e+01 1kssA 571 8.62e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1d7bA 186 8.66e+01 1d7bA b.1.9.1 22307 1aj2 282 8.67e+01 1aj2 c.1.21.1 29665 1oxdA 227 8.70e+01 d.22.1.1 93687 1pcfA 66 8.71e+01 1pcfA d.18.1.1 38142 1utyA 187 8.72e+01 b.147.1.1 108036 1vbiA 344 8.75e+01 2ct5A 73 8.75e+01 1k4jA 230 8.77e+01 d.108.1.3 72057 1yllA 200 8.83e+01 1i2uA 44 8.87e+01 g.3.7.4 65987 1cixA 44 8.90e+01 g.3.6.2 70066 1npeA 267 8.91e+01 b.68.5.1 92032 117eA 286 8.94e+01 1wgjA b.40.5.1 25401