# List of top-scoring protein chains for t04-100-40-40-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 2a2pA 129 8.55e-03 2f4qA 346 4.43e-02 1vq2A 193 1.25e-01 1zkdA 387 3.33e-01 1yaxA 153 3.74e-01 2cr5A 109 5.60e-01 1jv4A 162 5.64e-01 b.60.1.1 67343 1m93C 41 5.88e-01 1i06A 180 5.89e-01 1mup b.60.1.1 27131 1i05A 180 6.91e-01 1mup b.60.1.1 27130 1qy1A 174 7.66e-01 b.60.1.1 96568 1m7xA 617 8.83e-01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 1zndA 174 9.95e-01 2bjfA 329 1.01e+00 1mup 166 1.08e+00 1mup b.60.1.1 27133 1u6mA 199 1.10e+00 1ttzA 87 1.25e+00 c.47.1.1 107309 1lktA 104 1.35e+00 1lktA b.90.1.1 28398 2fa8A 105 1.37e+00 1rvkA 382 1.59e+00 c.1.11.2,d.54.1.1 97928,97929 1xvqA 175 1.64e+00 1skoA 143 1.95e+00 d.110.7.1 105676 1zynA 202 2.51e+00 1pm1X 180 2.55e+00 b.60.1.1 104189 1sqeA 109 2.87e+00 d.58.4.5 105908 1uhvA 500 2.91e+00 b.71.1.2,c.1.8.3 99402,99403 1yj7A 171 3.65e+00 2fq9A 225 3.72e+00 1q0qA 406 3.79e+00 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1u0tA 307 4.03e+00 e.52.1.1 107567 1k55A 246 4.10e+00 e.3.1.1 68156 1vetA 124 4.22e+00 d.110.7.1 108553 1u7pA 164 4.29e+00 1lf7A 182 4.35e+00 b.60.1.1 73878 1jvsA 400 4.45e+00 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1nqcA 217 4.53e+00 d.3.1.1 86024 1mp9A 198 4.69e+00 d.129.1.1,d.129.1.1 91385,91386 1vjfA 180 4.70e+00 d.116.1.1 100809 2bs9A 503 4.88e+00 1wdvA 152 4.99e+00 1tp6A 128 5.02e+00 d.17.4.12 107184 1lq9A 112 5.16e+00 d.58.4.3 78129 2b95A 106 5.18e+00 1e3uA 246 5.23e+00 1fofA e.3.1.1 42755 1n3gA 113 5.27e+00 d.204.1.1 79962 2c3vA 102 5.31e+00 1v74A 107 5.73e+00 d.243.1.1 100442 2bfgA 503 5.75e+00 1ztcA 221 5.79e+00 1wi1A 126 5.82e+00 1t0qC 86 6.10e+00 d.15.12.1 106222 1peeA 180 6.15e+00 b.60.1.1 104126 1cdq 77 6.73e+00 1cds g.7.1.3 44459 1wm3A 72 6.86e+00 1vr9A 213 6.93e+00 1ywlA 96 6.98e+00 1wn5A 130 7.05e+00 1twfK 120 7.13e+00 1qhoA 686 7.27e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 2bryA 497 7.56e+00 1xc3A 302 7.69e+00 1euoA 180 7.80e+00 1np1A b.60.1.1 27163 1iujA 106 7.91e+00 d.58.4.5 90701 1llnA 262 7.93e+00 d.165.1.1 84625 1kllA 130 8.11e+00 d.32.1.2 72720 1cqyA 99 8.12e+00 1b9zA b.3.1.1 22527 1qauA 112 8.62e+00 1qauA b.36.1.1 24779 1iscA 192 8.67e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 2fhxA 246 8.93e+00 1mtpB 43 8.96e+00 1obr 326 9.00e+00 1aye c.56.5.2 33828 1zhvA 134 9.24e+00 2gdqA 382 9.25e+00 1voqa 90 9.50e+00 1khbA 625 9.67e+00 c.91.1.1,c.109.1.1 68606,68607 1q32A 544 1.01e+01 d.136.1.3,d.136.1.3 104507,104508 1yx1A 264 1.03e+01 1whzA 70 1.05e+01 1ayaA 101 1.05e+01 1qadA d.93.1.1 40460 1itbB 315 1.05e+01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1l6rA 227 1.07e+01 c.108.1.10 77768 2ghrA 302 1.07e+01 1y88A 199 1.10e+01 1th8A 145 1.10e+01 d.122.1.3 106908 2cx5A 158 1.11e+01 1xfsA 178 1.18e+01 d.129.3.5 109589 1gmuA 143 1.19e+01 b.107.1.1,d.58.38.1 65335,65336 1tqzA 133 1.21e+01 2dg5A 366 1.23e+01 1x6oA 174 1.24e+01 b.34.5.2,b.40.4.5 109493,109494 1bywA 110 1.25e+01 1bywA d.110.3.6 40912 1r6fA 310 1.25e+01 e.46.1.1 97149 1zyeA 220 1.25e+01 1cv8 174 1.27e+01 1cv8 d.3.1.1 37089 1icxA 155 1.31e+01 d.129.3.1 71191 1x54A 434 1.35e+01 1rewC 135 1.36e+01 g.7.1.3 97336 8acn 754 1.36e+01 1amj c.8.2.1,c.83.1.1 30724,35400 2a5hA 416 1.37e+01 1e2wA 251 1.38e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1b24A 188 1.38e+01 1b24A d.95.2.1,d.95.2.1 40573,40574 1c96A 753 1.40e+01 1amj c.8.2.1,c.83.1.1 30727,35403 1aisA 182 1.40e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1ka9H 200 1.40e+01 c.23.16.1 77308 3nul 130 1.42e+01 3nul d.110.1.1 40891 1havA 217 1.43e+01 1havA b.47.1.4 26423 1cliA 345 1.43e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1hw6A 278 1.45e+01 1frb c.1.7.1 61296 1i50K 120 1.48e+01 d.74.3.2 61765 1lgpA 116 1.50e+01 b.26.1.2 73890 1fecA 490 1.52e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1hyuA 521 1.54e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1pvmA 184 1.63e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1xqaA 113 1.63e+01 1xt9A 212 1.64e+01 2gu3A 136 1.65e+01 1q87A 221 1.68e+01 e.47.1.1 96192 1rkd 309 1.75e+01 1rkd c.72.1.1 34928 1w9hA 427 1.75e+01 1h6hA 143 1.76e+01 d.189.1.1 65681 1r0kA 388 1.77e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1dcjA 81 1.82e+01 1dcjA d.68.3.3 59115 1u9tA 354 1.84e+01 1jbbA 153 1.84e+01 1u9aA d.20.1.1 62842 1x74A 360 1.89e+01 1opd 85 1.91e+01 1ptf d.94.1.1 40560 1kngA 156 1.91e+01 c.47.1.10 72777 2gfoA 396 1.94e+01 1u3eM 174 1.95e+01 d.4.1.3,d.285.1.1 107640,107641 1hn2A 159 1.96e+01 b.60.1.1 65890 1h9oA 112 2.01e+01 1qadA d.93.1.1 60837 1sgvA 316 2.03e+01 b.122.1.1,d.265.1.2 98858,98859 2fv7A 331 2.05e+01 2akrA 285 2.08e+01 1p6oA 161 2.08e+01 c.97.1.2 94185 1h3qA 140 2.08e+01 d.110.4.3 76652 1z2mA 155 2.09e+01 1ui0A 205 2.09e+01 c.18.1.2 99411 2dg5B 190 2.14e+01 1vjqA 79 2.14e+01 k.43.1.1 100830 1pylA 97 2.14e+01 d.1.1.2 104391 1xd8A 289 2.16e+01 1i7qA 519 2.20e+01 1qdlA d.161.1.1 61901 1xkpC 143 2.20e+01 1gt1A 159 2.25e+01 b.60.1.1 90515 2cfuA 658 2.26e+01 1qmvA 197 2.26e+01 1qq2A c.47.1.10 33066 2a4hA 126 2.27e+01 1oo0B 110 2.29e+01 d.58.7.1 87183 1jtkA 136 2.32e+01 c.97.1.1 71862 1vqoS 85 2.34e+01 1lr0A 129 2.36e+01 d.212.1.1 74213 1bu6O 501 2.37e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1tiyA 164 2.38e+01 c.97.1.2 107012 2fh5A 185 2.40e+01 1lrwA 600 2.40e+01 b.70.1.1 91111 1tyv 542 2.43e+01 1tyv b.80.1.6 28038 2ewcA 126 2.47e+01 1vkcA 158 2.48e+01 3grs 478 2.49e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1lwdA 413 2.51e+01 c.77.1.1 78265 1wfyA 104 2.54e+01 1jofA 365 2.58e+01 b.69.10.1 71775 2a8eA 220 2.59e+01 1y8qB 640 2.60e+01 1dmhA 311 2.61e+01 1dmhA b.3.6.1 22633 1p5hA 428 2.64e+01 c.123.1.1 87802 2pil 159 2.66e+01 2pil d.24.1.1 38376 1b7gO 340 2.66e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1xe7A 203 2.68e+01 2adbA 148 2.69e+01 1whrA 124 2.71e+01 1g5aA 628 2.77e+01 b.71.1.1,c.1.8.1 65152,65153 1xwwA 157 2.81e+01 2gcc 70 2.82e+01 2gcc d.10.1.2 37484 1qxhA 167 2.83e+01 c.47.1.10 96528 1z5lA 285 2.84e+01 1ffyA 917 2.86e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1m6iA 493 2.88e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1ec7A 446 2.89e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 2c2aA 258 2.89e+01 1jj2R 84 2.90e+01 1ffkP d.12.1.1 63103 2a15A 139 2.93e+01 1j5pA 253 2.98e+01 d.81.1.3,c.2.1.3 71577,83092 1tzaA 134 2.98e+01 b.1.23.1 107468 1w41A 101 2.99e+01 2gaiA 633 2.99e+01 2b18A 164 3.00e+01 1oo0A 147 3.08e+01 d.232.1.1 87182 1nrjA 158 3.09e+01 d.110.4.4 86124 1xvsA 126 3.09e+01 1txkA 498 3.17e+01 b.1.18.2,b.30.5.9 107425,107426 1wrvA 308 3.17e+01 1vcc 77 3.19e+01 1vcc d.121.1.1 41092 1v6tA 255 3.20e+01 1gtkA 313 3.21e+01 c.94.1.1,d.50.2.1 76346,76347 1byrA 155 3.22e+01 1byrA d.136.1.1 41450 2db1A 118 3.27e+01 1d4tA 104 3.27e+01 1d4tA d.93.1.1 40537 1ro5A 201 3.27e+01 d.108.1.3 105023 1zfpE 98 3.28e+01 1griA d.93.1.1 40465 1tt8A 164 3.29e+01 1r6wA 322 3.29e+01 c.1.11.2,d.54.1.1 97165,97166 1nbfD 76 3.30e+01 d.15.1.1 80390 1d8hA 311 3.31e+01 1d8iA d.63.1.1 39544 1lfdA 87 3.32e+01 1lfdA d.15.1.5 37622 1dg9A 157 3.32e+01 1dg9A c.44.1.1 32637 1yvoA 172 3.36e+01 1sur 215 3.38e+01 1sur c.26.2.2 31620 1zg2A 107 3.41e+01 1hkkA 364 3.41e+01 c.1.8.5,d.26.3.1 90634,90635 1xgyH 219 3.44e+01 1b9wA 89 3.45e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 1kb0A 677 3.46e+01 a.3.1.6,b.70.1.1 68378,68379 1xkiA 162 3.47e+01 1kv9A 668 3.50e+01 a.3.1.6,b.70.1.1 73056,73057 1n13B 113 3.51e+01 1c0eA 157 3.53e+01 1dg9A c.44.1.1 32638 1f2aA 215 3.54e+01 1cs8A d.3.1.1 37040 1s72S 85 3.56e+01 d.12.1.1 105338 1v30A 124 3.62e+01 1earA 147 3.65e+01 b.107.1.1,d.58.38.1 64875,64876 1ze3D 125 3.70e+01 1f0xA 571 3.71e+01 1f0xA d.58.32.2,d.145.1.1 39483,41746 1obpA 159 3.71e+01 1obpA b.60.1.1 27092 1fw9A 164 3.71e+01 1fw9A d.190.1.1 60059 1jpmA 366 3.74e+01 c.1.11.2,d.54.1.1 67031,67032 1erxA 184 3.76e+01 1np1A b.60.1.1 27164 1a0rP 245 3.77e+01 1b9yC c.47.1.6 33054 1regX 122 3.79e+01 1regX d.58.27.1 39406 1iow 306 3.81e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1tkkA 366 3.82e+01 c.1.11.2,d.54.1.1 107089,107090 1s9jA 341 3.85e+01 2d2mD 145 3.86e+01 1xrkA 124 3.89e+01 1wejH 223 3.89e+01 1igtB b.1.1.1,b.1.1.2 20361,21353 1ed5A 444 3.90e+01 1nseA d.174.1.1 42530 1u00A 227 3.92e+01 1fjgP 88 3.93e+01 1emwA d.27.1.1 38444 1g72A 573 3.94e+01 4aahA b.70.1.1 27680 1wb0A 445 3.95e+01 2ge3A 170 3.98e+01 1d1vA 444 3.98e+01 1nseA d.174.1.1 59101 1ir21 140 4.00e+01 1qnaA 200 4.00e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 2fauA 341 4.02e+01 2cxvA 219 4.06e+01 1i0cA 60 4.11e+01 1aojA b.34.2.1 61485 2h3jA 75 4.16e+01 1njkA 156 4.19e+01 d.38.1.1 85818 1yghA 164 4.19e+01 1yghA d.108.1.1 40802 1oe8A 211 4.19e+01 a.45.1.1,c.47.1.5 86905,86906 1itcA 516 4.20e+01 b.3.1.1,c.1.8.1 83705,83706 1um5H 217 4.22e+01 1lrzA 426 4.23e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1qa7A 217 4.24e+01 1havA b.47.1.4 26425 2bzpA 226 4.25e+01 1fh0A 221 4.26e+01 1cs8A d.3.1.1 59832 1k7jA 206 4.29e+01 d.115.1.1 72103 1x0rA 249 4.29e+01 1p2hA 571 4.30e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1me4A 215 4.32e+01 d.3.1.1 79023 1fnd 314 4.33e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1k07A 263 4.34e+01 d.157.1.1 77218 1ispA 181 4.35e+01 c.69.1.18 76778 1h7mA 102 4.40e+01 d.79.3.1 83485 1p57A 114 4.41e+01 d.170.1.2 94125 1s9aA 257 4.43e+01 b.3.6.1 105379 1gnkA 112 4.46e+01 2pii d.58.5.1 39073 1omiA 248 4.50e+01 b.82.3.3,a.4.5.4 87079,87080 2bylA 439 4.51e+01 1d0cA 444 4.52e+01 d.174.1.1 64769 1o0wA 252 4.52e+01 a.149.1.1,d.50.1.1 80751,80752 1v4vA 376 4.54e+01 c.87.1.3 100313 1bx1A 314 4.57e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1q9iA 571 4.58e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1y0pA 571 4.58e+01 1i6wA 181 4.59e+01 1i6wA c.69.1.18 61859 1o6aA 96 4.72e+01 b.139.1.1 92562 1xipA 388 4.74e+01 1ryaA 160 4.77e+01 d.113.1.5 105122 1z47A 355 4.80e+01 2b3wA 168 4.80e+01 1xkgA 312 4.80e+01 1u58A 253 4.83e+01 1koiA 184 4.85e+01 b.60.1.1 68725 2bgiA 272 4.85e+01 1gmyA 261 4.87e+01 d.3.1.1 76236 2fafA 608 4.88e+01 2comA 124 4.90e+01 1a0i 348 4.90e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1o7nA 449 4.91e+01 b.33.1.2,d.129.3.3 81162,81163 1oatA 439 4.94e+01 2dkb c.67.1.4 34461 1wlsA 328 4.94e+01 1r77A 103 4.95e+01 1eg9A 449 4.97e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1theA 260 5.00e+01 1theB d.3.1.1 37056 1e39A 571 5.01e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 2byjA 439 5.02e+01 1vemA 516 5.05e+01 1gk8I 140 5.10e+01 d.73.1.1 65242 1j5wA 298 5.10e+01 d.104.1.1 71589 1x9mA 698 5.13e+01 2bsjA 133 5.15e+01 2g5dA 422 5.18e+01 1jdlA 121 5.25e+01 a.3.1.1 66557 1kq1A 77 5.26e+01 b.38.1.2 72848 1ukuA 102 5.33e+01 d.58.5.2 99533 1pc6A 146 5.36e+01 d.262.1.1 94430 1es7B 89 5.37e+01 1es7B g.7.1.3 44465 1ctt 294 5.39e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1xyiA 66 5.39e+01 2a25A 193 5.39e+01 1gqzA 274 5.40e+01 d.21.1.1,d.21.1.1 83311,83312 1s4iA 175 5.41e+01 1sdjA 310 5.48e+01 d.21.1.2,d.21.1.2 98807,98808 2oatA 439 5.49e+01 2dkb c.67.1.4 34452 2aq2B 237 5.55e+01 1uwzA 136 5.56e+01 c.97.1.1 108081 1jbwA 428 5.61e+01 c.59.1.2,c.72.2.2 62860,62861 1gv3A 248 5.62e+01 a.2.11.1,d.44.1.1 70585,70586 1azpA 66 5.63e+01 1azpA b.34.13.1 37467 1v2yA 105 5.71e+01 d.15.1.1 100275 1vybA 238 5.73e+01 d.151.1.1 108897 1a79A 171 5.73e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1uouA 474 5.81e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1d4oA 184 5.84e+01 1d4oA c.31.1.4 31748 1q59A 172 5.86e+01 f.1.4.1 95881 1u2fA 90 5.87e+01 1u2fA d.58.7.1 39168 1q4uA 151 5.92e+01 d.38.1.5 95828 1je0A 236 5.92e+01 c.56.2.1 66581 1fhuA 320 5.93e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1npsA 88 5.94e+01 1prs b.11.1.1 23622 1mmvB 419 5.95e+01 d.174.1.1 91318 1d7cA 190 6.03e+01 1d7bA b.1.9.1 22309 1qhvA 195 6.04e+01 1qhvA b.21.1.1 23842 1rkqA 282 6.04e+01 c.108.1.10 97621 1ifqA 138 6.07e+01 1ifqA d.110.4.1 62350 1qveA 126 6.12e+01 d.24.1.1 104594 1r13A 148 6.14e+01 d.169.1.1,h.1.1.1 96782,96783 1pl3A 186 6.16e+01 b.1.9.1 88158 1kssA 571 6.17e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1dceB 331 6.17e+01 1dceB a.102.4.3 18872 2a9sA 171 6.20e+01 2ap1A 327 6.20e+01 1ukfA 188 6.21e+01 d.3.1.10 99488 1h8dH 260 6.23e+01 5ptp 1t5hX 504 6.34e+01 e.23.1.1 106449 1qx4A 274 6.42e+01 b.43.4.2,c.25.1.1 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