# List of top-scoring protein chains for t2k-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.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 1rz3A 201 5.74e-02 c.37.1.6 98132 1v6tA 255 1.74e-01 1wy7A 207 1.79e-01 1vdxA 184 2.51e-01 1pczA 191 4.80e-01 1ytbA d.129.1.1,d.129.1.1 41292,41293 2ci1A 275 4.86e-01 1pvgA 418 4.89e-01 d.14.1.3,d.122.1.2 95161,95162 2lbp 346 4.93e-01 2liv c.93.1.1 35709 1y2qA 143 5.23e-01 1usgA 346 5.33e-01 c.93.1.1 99864 1js3A 486 5.47e-01 c.67.1.6 67215 1vgjA 184 5.56e-01 1jdqA 98 6.65e-01 d.68.3.3 66559 1yz7A 188 7.20e-01 1zxmA 400 7.48e-01 1s2oA 244 8.01e-01 1b5eA 246 8.88e-01 1b5eA d.117.1.1 41056 1zip 217 1.02e+00 1zin c.37.1.1,g.41.2.1 31916,45179 1tidB 119 1.07e+00 c.13.2.1 107000 1rpjA 288 1.12e+00 2dri c.93.1.1 35656 1r5jA 337 1.27e+00 c.77.1.5 97097 1gudA 288 1.38e+00 c.93.1.1 83326 1wjgA 137 1.46e+00 1aroL 151 1.51e+00 1lba d.118.1.1 41063 1mp9A 198 1.54e+00 d.129.1.1,d.129.1.1 91385,91386 1zin 217 1.58e+00 1zin c.37.1.1,g.41.2.1 31915,45178 1ufkA 254 1.63e+00 c.66.1.39 99340 1z15A 344 1.82e+00 2liv 344 1.85e+00 2liv c.93.1.1 35708 1f1xA 322 1.86e+00 d.32.1.3,d.32.1.3 83208,83209 2a2kA 175 1.93e+00 1q7rA 219 1.93e+00 c.23.16.1 96054 2dri 271 2.03e+00 2dri c.93.1.1 35637 1v5vA 401 2.08e+00 1tqjA 230 2.22e+00 c.1.2.2 107228 1ve3A 227 2.36e+00 1ymkA 175 2.38e+00 1w25A 459 2.40e+00 1jqlB 140 2.41e+00 c.37.1.20 63234 1fnoA 417 2.68e+00 d.58.19.1,c.56.5.4 70145,75841 1hniB 427 2.75e+00 1rthA e.8.1.2 43045 1on0A 158 2.96e+00 d.108.1.1 87095 1r9gA 216 2.97e+00 c.23.16.1 97258 1vhiA 142 3.03e+00 1b3tA d.58.8.1 39230 2d4pA 141 3.14e+00 1aisA 182 3.16e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 1lba 146 3.20e+00 1lba d.118.1.1 41062 1qb0A 211 3.41e+00 1c25 c.46.1.1 32699 1hruA 188 3.47e+00 1hruA d.115.1.1 40926 1ezwA 349 3.57e+00 1ezwA c.1.16.3 29558 1vm6A 228 3.59e+00 c.2.1.3,d.81.1.3 108876,108877 2cdnA 201 3.63e+00 1vmbA 140 3.64e+00 1mai 131 3.67e+00 1mai b.55.1.1 26951 2cdqA 510 3.77e+00 2fx2 147 3.78e+00 1rcf c.23.5.1 31158 1ecsA 126 3.97e+00 1ecsA d.32.1.2 59407 1w96A 554 4.07e+00 1wetA 340 4.10e+00 1qpzA a.35.1.5,c.93.1.1 17093,35670 1ne2A 200 4.16e+00 c.66.1.32 85586 1eetB 427 4.16e+00 1rthA e.8.1.2 43079 1rpxA 230 4.18e+00 1rpxA c.1.2.2 28536 1a8p 258 4.42e+00 1fdr b.43.4.2,c.25.1.1 25654,31544 1e6yB 433 4.47e+00 1mroB a.89.1.1,d.58.31.2 18535,39453 1j34B 123 4.55e+00 d.169.1.1 84049 1ufhA 180 4.56e+00 d.108.1.1 88485 1d3uA 181 4.60e+00 1ytbA d.129.1.1,d.129.1.1 41290,41291 1p3jA 217 4.83e+00 c.37.1.1,g.41.2.1 94022,94023 2atxA 194 4.85e+00 1snnA 227 4.90e+00 d.115.1.2 105821 1pvyA 227 4.98e+00 d.115.1.2 95195 1b3tA 147 5.06e+00 1b3tA d.58.8.1 39228 2bh1A 250 5.11e+00 1l3iA 192 5.14e+00 c.66.1.22 77676 1c9bB 180 5.16e+00 1ytbA d.129.1.1,d.129.1.1 41216,41217 1fj7A 101 5.35e+00 1fj7A d.58.7.1 39209 1qysA 106 5.69e+00 k.41.1.1 96603 1jftA 340 5.73e+00 a.35.1.5,c.93.1.1 66652,66653 1ionA 243 5.74e+00 c.37.1.10 62633 1jr3D 343 5.77e+00 a.80.1.1,c.37.1.20 63251,63252 1y8cA 246 5.78e+00 1j98A 157 5.86e+00 1j98A d.185.1.2 62755 1hyhA 309 6.16e+00 1hyhA c.2.1.5,d.162.1.1 30150,42117 1c1bB 440 6.18e+00 1rthA e.8.1.2 43077 1in0A 163 6.31e+00 d.58.49.1,d.58.49.1 83694,83695 1jg1A 235 6.31e+00 c.66.1.7 66661 1l0wA 580 6.36e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1ka1A 357 6.62e+00 e.7.1.1 68369 1auz 116 6.80e+00 1auz c.13.2.1 30883 1bvyF 191 6.82e+00 1bvyF c.23.5.1 31207 1d4aA 273 6.90e+00 1d4aA c.23.5.3 31219 1f4pA 147 6.97e+00 5nul c.23.5.1 59651 1vixA 420 7.05e+00 c.56.5.4,d.58.19.1 100777,100778 1ixxB 123 7.10e+00 1ixxB d.169.1.1 42336 1qbgA 272 7.35e+00 1d4aA c.23.5.3 31227 1qrdA 273 7.38e+00 1d4aA c.23.5.3 31217 1kk1A 410 7.63e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1k0fA 277 7.64e+00 c.92.2.2 71974 1kx5C 128 7.67e+00 a.22.1.1 77595 2gukA 120 7.80e+00 2ethA 154 7.87e+00 2atzA 180 7.91e+00 1hyeA 313 7.95e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 2aexA 346 8.02e+00 1bu5A 147 8.06e+00 5nul c.23.5.1 31155 1efuB 282 8.10e+00 1efuB d.43.1.1,a.5.2.2,d.43.1.1 38677,58975,58976 1qgxA 357 8.36e+00 1qgxA e.7.1.1 42973 1jaxA 212 8.40e+00 c.2.1.6 66476 1ois 223 8.48e+00 1a36A e.15.1.1 43267 1g57A 217 8.54e+00 1g57A d.115.1.2 60253 1lxjA 104 8.56e+00 d.58.48.1 84736 1eudB 396 8.89e+00 2scuB c.23.4.1,d.142.1.4 31150,41571 2fm8A 135 9.03e+00 1f1uA 323 9.10e+00 d.32.1.3,d.32.1.3 83200,83201 1akq 147 9.20e+00 5nul c.23.5.1 31159 1tzfA 259 9.22e+00 c.68.1.13 107476 1cdwA 179 9.26e+00 1ytbA d.129.1.1,d.129.1.1 41212,41213 1mo9A 523 9.26e+00 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1y10A 407 9.27e+00 1fvaA 217 9.34e+00 1fvaA d.58.28.1 39409 2ch4A 320 9.61e+00 1i9sA 210 9.71e+00 1i9sA c.45.1.1 62099 1azl 147 9.79e+00 5nul c.23.5.1 31154 1aoiC 116 9.79e+00 1aoiC a.22.1.1 16440 1vljA 407 9.83e+00 e.22.1.2 108832 1qzzA 374 9.89e+00 a.4.5.29,c.66.1.12 96719,96720 1lbqA 362 1.01e+01 c.92.1.1 77877 1gesA 450 1.04e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1akt 147 1.04e+01 5nul c.23.5.1 31157 1gnlA 544 1.05e+01 e.26.1.1 70287 1jayA 212 1.06e+01 c.2.1.6 66478 1jqjC 343 1.06e+01 a.80.1.1,c.37.1.20 67097,67098 1cc8A 73 1.07e+01 1cc8A d.58.17.1 39343 1qpzA 340 1.07e+01 1qpzA a.35.1.5,c.93.1.1 17097,35673 1akw 147 1.09e+01 5nul c.23.5.1 31153 1vmeA 410 1.09e+01 c.23.5.1,d.157.1.3 108893,108894 1u7nA 336 1.11e+01 c.77.1.4 107726 1jg5A 83 1.13e+01 d.205.1.1 66666 2g5cA 281 1.14e+01 1bmtA 246 1.14e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 1is8K 84 1.16e+01 d.205.1.1 66331 1hmvA 560 1.17e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 1ccwA 137 1.17e+01 1be1 c.23.6.1 31238 2av4A 162 1.18e+01 1sxgA 280 1.18e+01 1et0A 269 1.19e+01 1et0A e.17.1.1 43289 1kevA 351 1.19e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1dcjA 81 1.20e+01 1dcjA d.68.3.3 59115 1u6mA 199 1.21e+01 1m2oA 768 1.21e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1eucB 396 1.25e+01 2scuB c.23.4.1,d.142.1.4 31149,41570 1vpjA 192 1.25e+01 1ewjA 126 1.26e+01 1ecsA d.32.1.2 59526 1qupA 222 1.27e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 1vpwA 340 1.28e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1hq3A 129 1.28e+01 1aoiC a.22.1.1 16434 1vokA 200 1.30e+01 1ytbA d.129.1.1,d.129.1.1 41242,41243 1jyhA 157 1.31e+01 d.60.1.3 71956 1pvtA 238 1.32e+01 c.74.1.1 95189 1nfp 228 1.33e+01 1nfp c.1.16.2 29555 1kafA 108 1.34e+01 d.199.1.1 68372 1wznA 252 1.35e+01 1ursA 402 1.35e+01 c.94.1.1 99833 1cnt3 187 1.36e+01 1cnt3 2bjiA 277 1.36e+01 1gefA 123 1.40e+01 1gefA c.52.1.18 60465 1fvgA 199 1.41e+01 1fvaA d.58.28.1 39408 1xsnA 335 1.41e+01 1vzsA 76 1.42e+01 f.45.1.1 108972 1dl5A 317 1.45e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1c25 161 1.50e+01 1c25 c.46.1.1 32698 2bcqA 335 1.50e+01 2fhxA 246 1.51e+01 1cnt1 187 1.51e+01 1cnt3 1bqnB 430 1.52e+01 1rthA e.8.1.2 43065 1lqpA 135 1.55e+01 d.32.1.2 78151 2f9zC 159 1.60e+01 1wqaA 455 1.62e+01 1bxdA 161 1.62e+01 1bxdA d.122.1.3 41111 1nkiA 135 1.62e+01 d.32.1.2 91941 1lsuA 147 1.63e+01 c.2.1.9 74250 1crkA 380 1.63e+01 1qh4A a.83.1.1,d.128.1.2 18458,41193 1qaxA 428 1.66e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 2fcr 173 1.67e+01 1rcf c.23.5.1 31151 2abwA 227 1.67e+01 1tiqA 180 1.71e+01 d.108.1.1 107010 1lldA 319 1.73e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1e1dA 553 1.74e+01 1e1dA e.26.1.1 43363 1t6t1 118 1.77e+01 2b4gA 317 1.77e+01 1w50A 411 1.78e+01 b.50.1.2 109173 1w6tA 444 1.79e+01 1lnqA 336 1.79e+01 c.2.1.9,f.14.1.1 74049,74050 1r31A 428 1.80e+01 d.58.20.1,d.179.1.1 96897,96898 1wvcA 259 1.82e+01 1an0A 190 1.82e+01 1ctqA c.37.1.8 32066 1fwyA 331 1.83e+01 1fwyA b.81.1.4,c.68.1.5 28064,34522 1ro0A 216 1.85e+01 d.264.1.2 97664 1rliA 184 1.85e+01 c.23.5.6 97647 1brlA 355 1.86e+01 1lucA c.1.16.1 29553 1ykfA 352 1.87e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1xqaA 113 1.89e+01 1sqiA 393 1.96e+01 d.32.1.3,d.32.1.3 105914,105915 1toaA 313 1.96e+01 1toaA c.92.2.2 35598 1f07A 321 1.97e+01 1ezwA c.1.16.3 59560 1vetB 125 1.98e+01 d.110.7.1 108554 1sgzA 389 2.01e+01 b.50.1.2 98872 2f1rA 171 2.01e+01 1akr 147 2.04e+01 1rcf c.23.5.1 31152 1fjeB 175 2.06e+01 1fj7A d.58.7.1,d.58.7.1 39210,39211 1veaA 148 2.07e+01 d.275.1.1 108529 1tzyA 129 2.10e+01 a.22.1.1 107530 1j9eA 147 2.12e+01 c.23.5.1 62756 2aefA 234 2.14e+01 1q2lA 939 2.15e+01 1fy2A 229 2.20e+01 1fyeA c.23.16.4 31478 1qnf 484 2.22e+01 1qnf a.99.1.1,c.28.1.1 18777,31632 2iu4A 336 2.26e+01 1pedA 351 2.37e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1gdeA 389 2.39e+01 c.67.1.1 60456 1vi9A 299 2.39e+01 c.72.1.5 100750 1fxjA 331 2.41e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1u35C 120 2.42e+01 2b4aA 138 2.42e+01 2gfgA 193 2.43e+01 1cipA 353 2.50e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1ldnA 316 2.51e+01 1hyhA c.2.1.5,d.162.1.1 30166,42133 1gd9A 389 2.52e+01 c.67.1.1 60454 1yx0A 159 2.53e+01 2f4nA 273 2.53e+01 1xtqA 177 2.54e+01 1y4oA 104 2.55e+01 1dlyA 164 2.55e+01 1dlyA a.1.1.1 14983 1ka9H 200 2.60e+01 c.23.16.1 77308 1b8aA 438 2.61e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1fk9A 543 2.63e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 1owlA 484 2.64e+01 a.99.1.1,c.28.1.1 93647,93648 1qayA 428 2.65e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 1bh5A 183 2.68e+01 1qipA d.32.1.1 38476 1aoiG 116 2.70e+01 1aoiC a.22.1.1 16441 1qnaA 200 2.70e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1fkoB 440 2.70e+01 1rthA e.8.1.2 43095 1cnt2 187 2.74e+01 1cnt3 1o51A 114 2.76e+01 d.58.5.4 92480 1sr4B 261 2.76e+01 d.151.1.1 105949 1hv9A 456 2.76e+01 1fwyA b.81.1.4,c.68.1.5 28060,34518 1gntA 553 2.77e+01 e.26.1.1 70290 1vimA 200 2.83e+01 c.80.1.3 100758 2c1iA 431 2.84e+01 1g8aA 227 2.85e+01 c.66.1.3 90506 1fohA 664 2.86e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1xl3C 92 2.87e+01 1h3qA 140 2.87e+01 d.110.4.3 76652 1p1lA 102 2.88e+01 d.58.5.2 87695 1uetA 437 2.92e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1whsA 255 2.94e+01 1ivyA c.69.1.5 34649 1yf5L 254 2.95e+01 1vrtA 560 2.95e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1lj1A 571 2.98e+01 a.138.1.3,c.3.1.4,d.168.1.1 78023,78024,78025 1k9vF 201 2.98e+01 c.23.16.1 68365 1e2uA 553 3.00e+01 1e1dA e.26.1.1 43362 1xo1A 291 3.01e+01 1exnA a.60.7.1,c.120.1.2 18086,33356 1oapA 109 3.02e+01 d.79.7.1 92706 1atiB 505 3.02e+01 1atiA c.51.1.1,d.104.1.1 33197,40746 1jwwA 80 3.03e+01 d.58.17.1 71919 1s69A 124 3.03e+01 a.1.1.1 105305 1td2A 287 3.03e+01 c.72.1.5 106765 1wkcA 184 3.08e+01 1rtxA 123 3.13e+01 a.1.1.1 97827 1pszA 303 3.14e+01 1toaA c.92.2.2 35600 2aotA 292 3.14e+01 1nh9A 87 3.15e+01 d.68.6.1 91878 1nxiA 132 3.15e+01 d.58.47.1 86381 2bjvA 265 3.17e+01 2frnA 278 3.17e+01 1q9iA 571 3.19e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1ytbB 180 3.22e+01 1ytbA d.129.1.1,d.129.1.1 41278,41279 1atiA 505 3.24e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1r29A 127 3.24e+01 d.42.1.1 96856 1qq9A 284 3.27e+01 1xjo c.56.5.4 33841 1wjtA 103 3.27e+01 1rztA 331 3.28e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1iyxA 432 3.30e+01 c.1.11.1,d.54.1.1 83815,83816 1fyeA 229 3.30e+01 1fyeA c.23.16.4 31477 2a10A 125 3.30e+01 1aky 221 3.31e+01 1zin c.37.1.1,g.41.2.1 31896,45197 8ohm 435 3.31e+01 1heiA c.37.1.14,c.37.1.14 32469,32470 1qdlB 195 3.33e+01 1qdlB c.23.16.1 31437 2b95A 106 3.36e+01 1m64A 571 3.37e+01 a.138.1.3,c.3.1.4,d.168.1.1 78683,78684,78685 1djqA 729 3.37e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1wwhA 119 3.38e+01 1rvaA 244 3.42e+01 1rvaA c.52.1.2 33240 1w3uA 362 3.43e+01 1aa8A 347 3.46e+01 1an9A 1i6wA 181 3.46e+01 1i6wA c.69.1.18 61859 1kbqA 273 3.51e+01 c.23.5.3 68391 1b94A 244 3.53e+01 1rvaA c.52.1.2 33250 1tbaB 180 3.54e+01 1ytbA d.129.1.1,d.129.1.1 41286,41287 1r89A 437 3.54e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1hmpA 217 3.55e+01 1qk3A c.61.1.1 34075 1rp4A 389 3.56e+01 a.227.1.1 105027 1ofcX 304 3.57e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1mgtA 174 3.58e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1p9qC 256 3.59e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1tx4B 178 3.60e+01 1ctqA c.37.1.8 32045 1f9aA 168 3.60e+01 1f9aA c.26.1.3 31602 1e9iA 431 3.60e+01 c.1.11.1,d.54.1.1 64818,64819 1fx2A 235 3.62e+01 1fx2A d.58.29.1 39430 1ok8A 394 3.62e+01 b.1.18.4,f.10.1.1 93236,93237 1mjhB 162 3.65e+01 1mjhA c.26.2.4 31640 2cy7A 396 3.65e+01 1b1cA 181 3.66e+01 1amoA c.23.5.2 31212 1o6jA 150 3.68e+01 c.47.1.10 81089 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