# List of top-scoring protein chains for t2k-100-30-alpha-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 4.68e-01 1tp6A 128 5.23e-01 d.17.4.12 107184 1yx1A 264 7.42e-01 2c3vA 102 8.50e-01 1lktA 104 9.48e-01 1lktA b.90.1.1 28398 2a2pA 129 9.61e-01 1uasA 362 1.13e+00 b.71.1.1,c.1.8.1 88388,88389 1yaxA 153 1.21e+00 1xfsA 178 1.31e+00 d.129.3.5 109589 1ktbA 405 1.59e+00 b.71.1.1,c.1.8.1 72960,72961 1vjfA 180 1.70e+00 d.116.1.1 100809 1isaA 192 1.72e+00 1avmA a.2.11.1,d.44.1.1 15731,38724 1iscA 192 1.73e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 2b59B 172 1.76e+00 2fafA 608 2.05e+00 1b9wA 89 2.09e+00 1b9wA g.3.11.4,g.3.11.4 44334,44335 1cqyA 99 2.18e+00 1b9zA b.3.1.1 22527 1xqaA 113 2.18e+00 1ebdA 455 2.38e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1u0tA 307 2.43e+00 e.52.1.1 107567 2dg5B 190 2.50e+00 1gv3A 248 2.55e+00 a.2.11.1,d.44.1.1 70585,70586 1e19A 314 2.68e+00 1b7bA c.73.1.1 34967 1lgpA 116 3.01e+00 b.26.1.2 73890 1bj8 109 3.25e+00 1bquA b.1.2.1 22070 1vcdA 126 3.33e+00 1bywA 110 3.52e+00 1bywA d.110.3.6 40912 1ui0A 205 3.61e+00 c.18.1.2 99411 1omiA 248 3.87e+00 b.82.3.3,a.4.5.4 87079,87080 1efaA 333 4.01e+00 1tlfA a.35.1.5,c.93.1.1 17106,35691 2gw6A 123 4.01e+00 1kllA 130 4.08e+00 d.32.1.2 72720 2cfuA 658 4.12e+00 3ezmA 101 4.15e+00 3ezmA b.89.1.1 28395 2go8A 122 4.37e+00 2cvzA 289 4.43e+00 1b8iB 63 4.76e+00 1akhA a.4.1.1 16011 1yqtA 538 4.88e+00 1m93C 41 4.94e+00 1tlfA 301 5.13e+00 1tlfA c.93.1.1 35687 1ijqA 316 5.20e+00 1ijqA b.68.5.1,g.3.11.1 62506,62507 1lwdA 413 5.20e+00 c.77.1.1 78265 1g5aA 628 5.27e+00 b.71.1.1,c.1.8.1 65152,65153 1v74A 107 5.38e+00 d.243.1.1 100442 1b24A 188 5.61e+00 1b24A d.95.2.1,d.95.2.1 40573,40574 2cu3A 64 5.61e+00 1txkA 498 5.99e+00 b.1.18.2,b.30.5.9 107425,107426 1m7xA 617 6.19e+00 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1y9wA 140 6.19e+00 1a8q 274 6.21e+00 1brt c.69.1.12 34702 1k2fA 190 6.34e+00 b.8.1.2 68054 2gk3A 256 6.59e+00 1pufB 73 7.34e+00 a.4.1.1 95132 1uliA 460 7.44e+00 b.33.1.2,d.129.3.3 107921,107922 2fhxA 246 7.61e+00 1b72B 87 7.63e+00 1akhA a.4.1.1 16001 1w41A 101 7.91e+00 1w9hA 427 8.06e+00 1itcA 516 8.09e+00 b.3.1.1,c.1.8.1 83705,83706 1o8uA 257 8.59e+00 c.14.1.3 81194 2a25A 193 8.63e+00 5bcaA 516 8.67e+00 1b9zA b.3.1.1,c.1.8.1 22529,28799 1zkdA 387 8.76e+00 1npeA 267 8.83e+00 b.68.5.1 92032 1qhoA 686 8.89e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1ttzA 87 9.06e+00 c.47.1.1 107309 1r1qA 100 9.09e+00 d.93.1.1 104763 1bpv 112 9.13e+00 1bpv b.1.2.1 22071 1jyeA 349 9.20e+00 c.93.1.1 67455 1vq2A 193 9.55e+00 1xvsA 126 9.74e+00 1l9gA 192 9.83e+00 c.18.1.2 84568 1obr 326 9.85e+00 1aye c.56.5.2 33828 1ur1A 378 9.96e+00 c.1.8.3 99804 2bjbA 462 1.02e+01 1pswA 348 1.05e+01 c.87.1.7 88287 2bzoB 79 1.07e+01 1pylA 97 1.07e+01 d.1.1.2 104391 1vkcA 158 1.07e+01 1qx4A 274 1.08e+01 b.43.4.2,c.25.1.1 104624,104625 1b9zA 516 1.12e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1z0wA 207 1.14e+01 1xhcA 367 1.16e+01 2gclA 261 1.16e+01 1vemA 516 1.17e+01 1cor 82 1.19e+01 451c a.3.1.1 15903 1yb3A 175 1.20e+01 1uhvA 500 1.20e+01 b.71.1.2,c.1.8.3 99402,99403 1p6oA 161 1.21e+01 c.97.1.2 94185 1pk6B 132 1.22e+01 b.22.1.1 94802 1huxA 270 1.25e+01 1huxA c.55.1.5 61278 2azqA 311 1.26e+01 2a5hA 416 1.29e+01 1a79A 171 1.31e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1eal 127 1.32e+01 1hmt b.60.1.2 27227 2fh5A 185 1.32e+01 1xxqA 161 1.33e+01 1skoA 143 1.33e+01 d.110.7.1 105676 1q7fA 286 1.38e+01 b.68.9.1 96036 1szoA 257 1.38e+01 c.14.1.3 106164 2he7A 283 1.39e+01 1m13A 316 1.40e+01 a.123.1.1 84746 1culA 217 1.45e+01 1azsA d.58.29.1 39417 2ga9D 469 1.46e+01 2axwA 134 1.46e+01 1h7mA 102 1.48e+01 d.79.3.1 83485 1i3dA 146 1.48e+01 a.1.1.2 61587 2cw9A 194 1.49e+01 1nrlA 316 1.52e+01 a.123.1.1 92091 1tuhA 156 1.53e+01 d.17.4.11 107345 2aotA 292 1.55e+01 1jqeA 292 1.56e+01 c.66.1.19 71789 1cjtA 217 1.56e+01 1azsA d.58.29.1 39419 1ny1A 240 1.57e+01 c.6.2.3 86395 1d4oA 184 1.57e+01 1d4oA c.31.1.4 31748 2bjfA 329 1.59e+01 1n9lA 109 1.60e+01 d.110.3.6 85468 1zu0A 529 1.61e+01 2cdnA 201 1.61e+01 1va4A 279 1.64e+01 c.69.1.12 108458 1dcjA 81 1.66e+01 1dcjA d.68.3.3 59115 1xrkA 124 1.67e+01 1ffyA 917 1.68e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 1.68e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1s4nA 348 1.69e+01 c.68.1.16 98501 1khbA 625 1.71e+01 c.91.1.1,c.109.1.1 68606,68607 2aop 497 1.72e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 1bi5A 389 1.77e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1ne6A 283 1.77e+01 b.82.3.2,b.82.3.2 91831,91832 1wqsA 173 1.78e+01 1dmhA 311 1.79e+01 1dmhA b.3.6.1 22633 1azsA 220 1.79e+01 1azsA d.58.29.1 39416 1f00I 282 1.81e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1ztcA 221 1.88e+01 1xkiA 162 1.90e+01 1i86A 389 1.90e+01 c.95.1.2,c.95.1.2 66068,66069 2fa8A 105 1.93e+01 1jyrA 96 1.93e+01 d.93.1.1 71969 1ryaA 160 1.93e+01 d.113.1.5 105122 1u7pA 164 1.94e+01 2aobA 99 1.95e+01 1zin 217 1.95e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1jofA 365 1.95e+01 b.69.10.1 71775 1xtmA 175 1.96e+01 1qwlA 505 1.98e+01 e.5.1.1 96483 1uaqA 158 1.98e+01 c.97.1.2 88386 2b5nA 323 1.99e+01 1qnnA 191 2.03e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 2cr5A 109 2.04e+01 1vjqA 79 2.04e+01 k.43.1.1 100830 1z5yE 149 2.04e+01 1zfpE 98 2.06e+01 1griA d.93.1.1 40465 1ct5A 256 2.09e+01 1ct5A c.1.6.2 28663 16pk 415 2.11e+01 16pk c.86.1.1 35454 1lq9A 112 2.14e+01 d.58.4.3 78129 1pvmA 184 2.15e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1ntr 124 2.17e+01 1dbwA c.23.1.1 31092 1uesA 191 2.18e+01 a.2.11.1,d.44.1.1 107798,107799 1konA 249 2.18e+01 e.39.1.1 72823 1wm3A 72 2.19e+01 2bgcA 238 2.23e+01 1cch 82 2.23e+01 451c a.3.1.1 15902 1ughI 82 2.26e+01 1ugiA d.17.5.1 38133 1gt1A 159 2.32e+01 b.60.1.1 90515 1tzeE 98 2.33e+01 1griA d.93.1.1 40468 1i88A 389 2.37e+01 c.95.1.2,c.95.1.2 66070,66071 1ugiA 84 2.39e+01 1ugiA d.17.5.1 38125 1iiyA 101 2.40e+01 b.89.1.1 66152 1whzA 70 2.40e+01 1v0jA 399 2.41e+01 1gtkA 313 2.43e+01 c.94.1.1,d.50.2.1 76346,76347 1otcB 260 2.44e+01 1otcB b.40.4.3 25310 1xf1A 926 2.45e+01 1obpA 159 2.47e+01 1obpA b.60.1.1 27092 1gmwA 143 2.47e+01 b.107.1.1,d.58.38.1 65347,65348 1wxcB 134 2.48e+01 1g59A 468 2.52e+01 a.97.1.1,c.26.1.1 60257,60258 1vetA 124 2.52e+01 d.110.7.1 108553 1h8cA 82 2.52e+01 1h8cA d.15.1.2 37608 2fbmA 291 2.57e+01 1msaA 109 2.57e+01 1b2pA b.78.1.1 27987 1glcG 501 2.58e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 1hn2A 159 2.58e+01 b.60.1.1 65890 1wzcA 249 2.60e+01 1x82A 190 2.61e+01 1jpc 109 2.62e+01 1b2pA b.78.1.1 27986 1pmhX 185 2.64e+01 b.18.1.18 104193 1mpyA 307 2.64e+01 1mpyA d.32.1.3,d.32.1.3 38508,38509 1qlaA 656 2.65e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1phr 157 2.65e+01 1dg9A c.44.1.1 32635 1s4iA 175 2.67e+01 1aop 497 2.70e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1sznA 417 2.73e+01 b.71.1.1,c.1.8.1 106162,106163 1z2mA 155 2.74e+01 1ey4A 149 2.74e+01 1snc b.40.1.1 24815 1qq2A 199 2.76e+01 1qq2A c.47.1.10 33064 1ri9A 102 2.78e+01 b.34.2.1 97506 1gln 468 2.78e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1h3qA 140 2.81e+01 d.110.4.3 76652 1zxuA 217 2.82e+01 1nofA 383 2.83e+01 b.71.1.2,c.1.8.3 92020,92021 1bwzA 274 2.85e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1sty 150 2.86e+01 1snc b.40.1.1 24812 1gqzA 274 2.87e+01 d.21.1.1,d.21.1.1 83311,83312 1b7bA 310 2.90e+01 1b7bA c.73.1.1 34963 2bs9A 503 2.90e+01 1vbiA 344 2.91e+01 1vbvA 105 2.94e+01 1qauA 112 2.95e+01 1qauA b.36.1.1 24779 1nrwA 288 2.99e+01 c.108.1.10 86128 2bfgA 503 2.99e+01 1qhdA 398 2.99e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1gsa 316 2.99e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1gyxA 76 3.00e+01 d.80.1.1 76387 1je5A 206 3.01e+01 1je5A b.40.4.7 62909 1bquA 215 3.04e+01 1bquA b.1.2.1,b.1.2.1 22066,22067 1wgoA 123 3.04e+01 1vhh 162 3.04e+01 1vhh d.65.1.2 39550 1p80A 753 3.05e+01 c.23.16.3,e.5.1.1 94337,94338 1bmbA 123 3.06e+01 1griA d.93.1.1 40466 1zip 217 3.08e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1xuvA 178 3.09e+01 1udiI 83 3.09e+01 1ugiA d.17.5.1 38124 1byrA 155 3.10e+01 1byrA d.136.1.1 41450 2gaiA 633 3.11e+01 1qxrA 189 3.13e+01 b.82.1.7 96552 1e25A 282 3.17e+01 1e25A e.3.1.1 42731 1cf9A 753 3.18e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1xwwA 157 3.18e+01 1bu6O 501 3.20e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1f2tB 148 3.25e+01 1f2tB 1tsp 559 3.27e+01 1tyv b.80.1.6 28044 1htjF 210 3.28e+01 1htjF a.91.1.1 61254 1ndoA 449 3.28e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1s5lB 510 3.29e+01 1cv8 174 3.29e+01 1cv8 d.3.1.1 37089 1w6sA 599 3.32e+01 1kjvA 284 3.37e+01 b.1.1.2,d.19.1.1 77421,77422 1a8h 500 3.40e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 7catA 506 3.40e+01 1cf9A e.5.1.1 42781 2b7kA 200 3.44e+01 1snc 149 3.44e+01 1snc b.40.1.1 24813 1kzfA 230 3.46e+01 d.108.1.3 73354 1j6qA 136 3.48e+01 b.40.9.1 77091 1nzjA 298 3.48e+01 c.26.1.1 92377 1xtlA 175 3.49e+01 1tx9A 151 3.51e+01 1b7fA 168 3.53e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1q7lB 88 3.56e+01 1zo2A 129 3.58e+01 2amyA 246 3.58e+01 1ymqA 261 3.58e+01 1ywlA 96 3.59e+01 1qq1A 559 3.60e+01 1tyv b.80.1.6 28041 1jr2A 286 3.60e+01 c.113.1.1 67111 1qa1A 554 3.64e+01 1tyv b.80.1.6 28047 2fikA 287 3.64e+01 1hdj 77 3.66e+01 1bqz a.2.3.1 15696 1ss9A 311 3.67e+01 c.68.1.4 105978 1kv9A 668 3.69e+01 a.3.1.6,b.70.1.1 73056,73057 1o7nA 449 3.70e+01 b.33.1.2,d.129.3.3 81162,81163 1qhuA 460 3.71e+01 1qhuA b.66.1.1,b.66.1.1 27530,27531 1psdA 409 3.71e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1sc6A 404 3.72e+01 1eg9A 449 3.73e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1mkeA 152 3.73e+01 b.55.1.4 79231 1j09A 468 3.74e+01 a.97.1.1,c.26.1.1 77025,77026 1ef1A 294 3.78e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1b54 257 3.79e+01 1ct5A c.1.6.2 28664 1hkfA 122 3.80e+01 b.1.1.1 83553 1hbzA 498 3.82e+01 1cf9A e.5.1.1 60937 1k9tA 540 3.83e+01 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1b2pA 119 3.84e+01 1b2pA b.78.1.1 27998 1vkiA 181 3.84e+01 d.116.1.1 108664 1b0uA 262 3.85e+01 1b0uA c.37.1.12 32370 1ak4C 145 3.85e+01 1ak4C a.73.1.1 18321 1dc7A 124 3.85e+01 1dbwA c.23.1.1 31093 1u2eA 289 3.85e+01 2akrA 285 3.87e+01 1gweA 503 3.89e+01 e.5.1.1 70667 1iq9A 61 3.89e+01 g.7.1.1 90669 1csn 298 3.90e+01 1csn d.144.1.7 41664 1tksA 204 3.90e+01 d.115.1.2 107114 2jdxA 385 3.97e+01 1jdw d.126.1.2 41139 1l0bA 229 3.97e+01 c.15.1.3,c.15.1.3 73391,73392 1nfiC 301 4.00e+01 b.1.18.1,b.2.5.3 21943,22456 1fecA 490 4.01e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1nfiA 301 4.01e+01 1a3qA b.1.18.1,b.2.5.3 21942,22455 1zq1A 438 4.02e+01 1cd31 152 4.02e+01 1cd31 1qmvA 197 4.02e+01 1qq2A c.47.1.10 33066 1m9xC 146 4.04e+01 a.73.1.1 84907 2ghrA 302 4.05e+01 2gxfA 142 4.06e+01 1onqA 283 4.06e+01 b.1.1.2,d.19.1.1 93365,93366 1vrmA 325 4.07e+01 1iow 306 4.11e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1h0hA 977 4.12e+01 b.52.2.2,c.81.1.1 76435,76436 1vggA 161 4.12e+01 1qavB 115 4.14e+01 1qauA b.36.1.1 24780 1aojA 60 4.14e+01 1aojA b.34.2.1 24555 1tdhA 364 4.20e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1lrwA 600 4.20e+01 b.70.1.1 91111 1dk0A 188 4.21e+01 1b2vA d.35.1.1 38530 3il8 72 4.22e+01 1tvxA d.9.1.1 37356 1ppjD 241 4.23e+01 a.3.1.3,f.23.11.1 104258,104259 2gupA 292 4.25e+01 1j1tA 233 4.26e+01 b.29.1.18 90771 1rdj1 113 4.27e+01 1rtm1 2bs3A 656 4.27e+01 1cquA 56 4.29e+01 d.100.1.1 70073 1woyA 500 4.33e+01 1jj2R 84 4.34e+01 1ffkP d.12.1.1 63103 1senA 164 4.34e+01 c.47.1.1 105465 1s72S 85 4.35e+01 d.12.1.1 105338 1tyv 542 4.36e+01 1tyv b.80.1.6 28038 1tedA 393 4.37e+01 c.95.1.2 106807 1dg9A 157 4.37e+01 1dg9A c.44.1.1 32637 1jnuA 104 4.37e+01 d.110.3.6 71762 1v9yA 167 4.38e+01 d.110.3.2 108454 2cc0A 195 4.40e+01 1bxwA 172 4.42e+01 1bxwA f.4.1.1 43743 1wekA 217 4.43e+01 2dln 306 4.46e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1tqxA 227 4.46e+01 1bvh 157 4.47e+01 1dg9A c.44.1.1 32640 1tyu 543 4.48e+01 1tyv b.80.1.6 28037 2aukA 190 4.50e+01 1vjlA 164 4.50e+01 d.257.1.1 100822 1glaG 501 4.50e+01 1glcG c.55.1.4,c.55.1.4 33507,33508 1ndh 272 4.50e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1h1yA 228 4.55e+01 c.1.2.2 76506 1cdcB 99 4.57e+01 1cdcA b.1.1.1 19747 1acz 108 4.57e+01 1kum b.3.1.1 22524 1to4A 156 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