# 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 2f4qA 346 8.34e-02 2a2pA 129 8.69e-02 1yaxA 153 1.84e-01 2fa8A 105 1.97e-01 1vq2A 193 2.21e-01 1m7xA 617 3.89e-01 b.1.18.2,b.71.1.1,c.1.8.1 78749,78750,78751 2cr5A 109 4.65e-01 1m93C 41 7.60e-01 2fhxA 246 1.15e+00 1lktA 104 1.39e+00 1lktA b.90.1.1 28398 2bjfA 329 1.40e+00 1vjfA 180 1.41e+00 d.116.1.1 100809 1ttzA 87 1.63e+00 c.47.1.1 107309 1kllA 130 1.86e+00 d.32.1.2 72720 1zkdA 387 2.44e+00 1rvkA 382 2.44e+00 c.1.11.2,d.54.1.1 97928,97929 1wi1A 126 2.64e+00 1uhvA 500 2.74e+00 b.71.1.2,c.1.8.3 99402,99403 1u0tA 307 2.87e+00 e.52.1.1 107567 1jv4A 162 2.88e+00 b.60.1.1 67343 2fv7A 331 2.93e+00 2fq9A 225 3.04e+00 1iscA 192 3.39e+00 1avmA a.2.11.1,d.44.1.1 15733,38726 1i06A 180 3.64e+00 1mup b.60.1.1 27131 1i05A 180 4.07e+00 1mup b.60.1.1 27130 1nqcA 217 4.09e+00 d.3.1.1 86024 1r6wA 322 4.10e+00 c.1.11.2,d.54.1.1 97165,97166 1qy1A 174 4.22e+00 b.60.1.1 96568 1rkd 309 4.35e+00 1rkd c.72.1.1 34928 1zndA 174 4.42e+00 1v74A 107 4.46e+00 d.243.1.1 100442 1q32A 544 4.51e+00 d.136.1.3,d.136.1.3 104507,104508 1q0qA 406 4.55e+00 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1khbA 625 4.57e+00 c.91.1.1,c.109.1.1 68606,68607 2c3vA 102 4.66e+00 8acn 754 4.66e+00 1amj c.8.2.1,c.83.1.1 30724,35400 1kyfA 247 4.80e+00 b.1.10.1,d.105.1.1 73220,73221 1gqzA 274 4.81e+00 d.21.1.1,d.21.1.1 83311,83312 1c96A 753 5.06e+00 1amj c.8.2.1,c.83.1.1 30727,35403 1e2wA 251 5.18e+00 1hcz b.2.6.1,b.84.2.2 22466,28252 1ztcA 221 5.20e+00 1qtsA 247 5.38e+00 1qtsA b.1.10.1,d.105.1.1 22313,40789 1oe8A 211 5.39e+00 a.45.1.1,c.47.1.5 86905,86906 1tp6A 128 5.39e+00 d.17.4.12 107184 1uh6A 100 5.53e+00 d.15.1.1 99394 1k55A 246 5.59e+00 e.3.1.1 68156 1jvsA 400 6.10e+00 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1wdvA 152 6.10e+00 1tqzA 133 6.11e+00 1zynA 202 6.11e+00 1lq9A 112 6.23e+00 d.58.4.3 78129 1mup 166 6.33e+00 1mup b.60.1.1 27133 1itbB 315 6.38e+00 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1voqa 90 6.39e+00 1je0A 236 6.41e+00 c.56.2.1 66581 1qhoA 686 6.42e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1y88A 199 6.60e+00 1vkcA 158 6.64e+00 1u7pA 164 7.00e+00 1vr9A 213 7.03e+00 1xfsA 178 7.12e+00 d.129.3.5 109589 1cqyA 99 7.25e+00 1b9zA b.3.1.1 22527 1fhuA 320 7.29e+00 1fhuA c.1.11.2,d.54.1.1 29234,38878 1wm3A 72 7.33e+00 1xvqA 175 7.43e+00 1u6mA 199 7.47e+00 1tyv 542 7.61e+00 1tyv b.80.1.6 28038 1yvoA 172 7.61e+00 1h9oA 112 7.84e+00 1qadA d.93.1.1 60837 1bywA 110 7.90e+00 1bywA d.110.3.6 40912 1llnA 262 8.02e+00 d.165.1.1 84625 1lfdA 87 8.39e+00 1lfdA d.15.1.5 37622 2bs9A 503 8.48e+00 1iow 306 8.57e+00 1iow c.30.1.2,d.142.1.1 31713,41481 1aisA 182 8.70e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 1pylA 97 8.82e+00 d.1.1.2 104391 1qauA 112 9.04e+00 1qauA b.36.1.1 24779 1t0qC 86 9.10e+00 d.15.12.1 106222 1e3uA 246 9.10e+00 1fofA e.3.1.1 42755 1r0kA 388 9.49e+00 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 3nul 130 9.67e+00 3nul d.110.1.1 40891 2ghrA 302 9.72e+00 1havA 217 9.81e+00 1havA b.47.1.4 26423 2bfgA 503 9.94e+00 1x6oA 174 9.98e+00 b.34.5.2,b.40.4.5 109493,109494 1jtkA 136 1.02e+01 c.97.1.1 71862 1n3gA 113 1.04e+01 d.204.1.1 79962 1skoA 143 1.08e+01 d.110.7.1 105676 1vqoS 85 1.09e+01 1cdq 77 1.10e+01 1cds g.7.1.3 44459 1pm1X 180 1.11e+01 b.60.1.1 104189 1ui0A 205 1.13e+01 c.18.1.2 99411 1g5aA 628 1.16e+01 b.71.1.1,c.1.8.1 65152,65153 1xc3A 302 1.19e+01 1mtpB 43 1.22e+01 1ka9H 200 1.24e+01 c.23.16.1 77308 1qnnA 191 1.27e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1sgvA 316 1.29e+01 b.122.1.1,d.265.1.2 98858,98859 1nytA 271 1.31e+01 c.2.1.7,c.58.1.5 86417,86418 1vetA 124 1.33e+01 d.110.7.1 108553 2pil 159 1.34e+01 2pil d.24.1.1 38376 1ywlA 96 1.34e+01 1y9wA 140 1.39e+01 1l6rA 227 1.39e+01 c.108.1.10 77768 1jj2R 84 1.39e+01 1ffkP d.12.1.1 63103 1hyuA 521 1.39e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 2dg5B 190 1.41e+01 1zyeA 220 1.41e+01 1mp9A 198 1.42e+01 d.129.1.1,d.129.1.1 91385,91386 2b3yA 888 1.43e+01 1wkqA 164 1.44e+01 c.97.1.2 109393 1fecA 490 1.45e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1cliA 345 1.45e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1tt8A 164 1.47e+01 1wrvA 308 1.47e+01 1qnaA 200 1.48e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1gv3A 248 1.50e+01 a.2.11.1,d.44.1.1 70585,70586 1bu6O 501 1.53e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1hkkA 364 1.55e+01 c.1.8.5,d.26.3.1 90634,90635 1ir21 140 1.55e+01 1uesA 191 1.61e+01 a.2.11.1,d.44.1.1 107798,107799 1w9hA 427 1.63e+01 2gaiA 633 1.64e+01 1b7gO 340 1.65e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1xt9A 212 1.65e+01 1vybA 238 1.67e+01 d.151.1.1 108897 1icxA 155 1.68e+01 d.129.3.1 71191 1wn5A 130 1.69e+01 2fh5A 185 1.69e+01 2gdqA 382 1.70e+01 1s72S 85 1.71e+01 d.12.1.1 105338 1tzzA 392 1.71e+01 1rkqA 282 1.73e+01 c.108.1.10 97621 1gk8I 140 1.74e+01 d.73.1.1 65242 1ayaA 101 1.75e+01 1qadA d.93.1.1 40460 1wb0A 445 1.76e+01 1fw9A 164 1.77e+01 1fw9A d.190.1.1 60059 1s9aA 257 1.79e+01 b.3.6.1 105379 1fnd 314 1.79e+01 1fnc b.43.4.2,c.25.1.1 25626,31516 1lrwA 600 1.80e+01 b.70.1.1 91111 1sqeA 109 1.80e+01 d.58.4.5 105908 1ec7A 446 1.81e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1z2mA 155 1.82e+01 1ro5A 201 1.83e+01 d.108.1.3 105023 1gmuA 143 1.83e+01 b.107.1.1,d.58.38.1 65335,65336 1jbbA 153 1.84e+01 1u9aA d.20.1.1 62842 1p6oA 161 1.87e+01 c.97.1.2 94185 1tiyA 164 1.88e+01 c.97.1.2 107012 1xipA 388 1.89e+01 1e39A 571 1.92e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 2dchX 216 1.93e+01 1p2hA 571 1.95e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1pqzA 238 1.99e+01 b.1.1.2,d.19.1.1 104297,104298 1svdM 110 1.99e+01 1l2mA 118 2.05e+01 d.89.1.4 77657 2hayA 224 2.06e+01 1wduA 245 2.08e+01 d.151.1.1 109286 1bx1A 314 2.09e+01 1fnc b.43.4.2,c.25.1.1 25629,31519 1npyA 271 2.12e+01 c.2.1.7,c.58.1.5 85995,85996 1dcjA 81 2.17e+01 1dcjA d.68.3.3 59115 1q9iA 571 2.17e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1whrA 124 2.18e+01 1kssA 571 2.18e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 2db1A 118 2.19e+01 1ne9A 335 2.22e+01 d.108.1.4,d.108.1.4 91839,91840 1yx1A 264 2.24e+01 1p57A 114 2.28e+01 d.170.1.2 94125 1xqaA 113 2.29e+01 2fkcA 247 2.35e+01 1th8A 145 2.36e+01 d.122.1.3 106908 2h3bA 494 2.37e+01 1y0pA 571 2.37e+01 2hglA 136 2.42e+01 1kngA 156 2.44e+01 c.47.1.10 72777 1qxhA 167 2.44e+01 c.47.1.10 96528 1hw6A 278 2.49e+01 1frb c.1.7.1 61296 1f2aA 215 2.50e+01 1cs8A d.3.1.1 37040 1xm8A 254 2.50e+01 1m6iA 493 2.51e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1bwzA 274 2.53e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 2atfA 200 2.53e+01 1obr 326 2.57e+01 1aye c.56.5.2 33828 2gfoA 396 2.57e+01 1ffyA 917 2.57e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 3grs 478 2.60e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 2gcc 70 2.61e+01 2gcc d.10.1.2 37484 1ukfA 188 2.62e+01 d.3.1.10 99488 1yghA 164 2.63e+01 1yghA d.108.1.1 40802 2ge3A 170 2.65e+01 2dg5A 366 2.69e+01 3bamA 213 2.69e+01 1bam c.52.1.3 33288 1x54A 434 2.73e+01 2fafA 608 2.77e+01 2c82A 413 2.78e+01 2bylA 439 2.81e+01 2bs3A 656 2.85e+01 1a79A 171 2.91e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1qhvA 195 2.93e+01 1qhvA b.21.1.1 23842 1jofA 365 2.94e+01 b.69.10.1 71775 1i7qA 519 2.96e+01 1qdlA d.161.1.1 61901 2b5hA 200 2.97e+01 1lrzA 426 3.00e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 3pyp 125 3.02e+01 3pyp d.110.3.1 40897 1cv8 174 3.02e+01 1cv8 d.3.1.1 37089 1x31C 206 3.03e+01 1w4tA 299 3.07e+01 1dmhA 311 3.08e+01 1dmhA b.3.6.1 22633 1ed5A 444 3.08e+01 1nseA d.174.1.1 42530 2byjA 439 3.09e+01 1byrA 155 3.12e+01 1byrA d.136.1.1 41450 1huxA 270 3.15e+01 1huxA c.55.1.5 61278 1kv9A 668 3.15e+01 a.3.1.6,b.70.1.1 73056,73057 1h3qA 140 3.16e+01 d.110.4.3 76652 1c44A 123 3.22e+01 1qndA d.106.1.1 40795 2bgiA 272 3.24e+01 1peeA 180 3.25e+01 b.60.1.1 104126 2cfuA 658 3.26e+01 1ko3A 230 3.27e+01 d.157.1.1 90974 1vg0A 650 3.28e+01 c.3.1.3,d.16.1.6 108596,108597 1psdA 409 3.35e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1fnc 314 3.36e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 2bl1A 172 3.36e+01 1y6lA 149 3.42e+01 1pysA 350 3.43e+01 1pysA d.104.1.1 40775 1xvsA 126 3.45e+01 1d0cA 444 3.46e+01 d.174.1.1 64769 1jjeA 222 3.47e+01 1a7tA d.157.1.1 63117 1rewC 135 3.48e+01 g.7.1.3 97336 1thtA 305 3.50e+01 1thtA c.69.1.13 34711 1d1vA 444 3.52e+01 1nseA d.174.1.1 59101 1qmvA 197 3.54e+01 1qq2A c.47.1.10 33066 1k0sA 151 3.55e+01 b.40.7.1 67969 1cuk 203 3.55e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 2c7xA 436 3.56e+01 1yqzA 438 3.57e+01 1f5vA 240 3.59e+01 1bkjA d.90.1.1 40255 1q4uA 151 3.61e+01 d.38.1.5 95828 1uwzA 136 3.63e+01 c.97.1.1 108081 1oatA 439 3.63e+01 2dkb c.67.1.4 34461 1fsz 372 3.63e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1o0wA 252 3.64e+01 a.149.1.1,d.50.1.1 80751,80752 1gw5S 142 3.65e+01 d.110.4.2 70633 2cxvA 219 3.67e+01 1qa7A 217 3.69e+01 1havA b.47.1.4 26425 1me4A 215 3.69e+01 d.3.1.1 79023 1jndA 420 3.70e+01 c.1.8.5,d.26.3.1 71757,71758 1ryaA 160 3.70e+01 d.113.1.5 105122 1k7jA 206 3.72e+01 d.115.1.1 72103 1twfK 120 3.73e+01 1g72A 573 3.76e+01 4aahA b.70.1.1 27680 2c6cA 707 3.76e+01 1nwzA 125 3.77e+01 d.110.3.1 86370 1b9wA 89 3.81e+01 1b9wA g.3.11.4,g.3.11.4 44334,44335 2gu3A 136 3.84e+01 1jjtA 228 3.84e+01 1a7tA d.157.1.1 63139 1um5H 217 3.87e+01 1itcA 516 3.88e+01 b.3.1.1,c.1.8.1 83705,83706 2b95A 106 3.96e+01 2cy0A 263 4.03e+01 1tkkA 366 4.03e+01 c.1.11.2,d.54.1.1 107089,107090 1wxdA 263 4.04e+01 2d5cA 263 4.09e+01 2ew0A 192 4.10e+01 1zdnA 158 4.13e+01 1qlaA 656 4.18e+01 1qlaA a.7.3.1,c.3.1.4,d.168.1.1 16328,30427,42310 1xkgA 312 4.18e+01 1u9tA 354 4.21e+01 1hynP 379 4.23e+01 1hynP d.112.1.2 61408 1s3sG 127 4.24e+01 d.15.1.2 98457 1jpmA 366 4.24e+01 c.1.11.2,d.54.1.1 67031,67032 1sr9A 644 4.28e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1xrkA 124 4.35e+01 1zsxA 347 4.36e+01 1pvmA 184 4.37e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1kb5B 117 4.46e+01 1kb5B b.1.1.1 20632 1v6tA 255 4.51e+01 1sc6A 404 4.52e+01 1theA 260 4.54e+01 1theB d.3.1.1 37056 1jlwA 219 4.54e+01 a.45.1.1,c.47.1.5 71741,71742 1ei5A 520 4.56e+01 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1kb0A 677 4.58e+01 a.3.1.6,b.70.1.1 68378,68379 1iujA 106 4.59e+01 d.58.4.5 90701 1wmhB 86 4.59e+01 1o6aA 96 4.62e+01 b.139.1.1 92562 1o7nA 449 4.63e+01 b.33.1.2,d.129.3.3 81162,81163 1vemA 516 4.63e+01 1z4vA 532 4.68e+01 1r13A 148 4.69e+01 d.169.1.1,h.1.1.1 96782,96783 1euoA 180 4.70e+01 1np1A b.60.1.1 27163 1uliB 187 4.70e+01 d.17.4.4 107923 2oatA 439 4.72e+01 2dkb c.67.1.4 34452 1gmyA 261 4.72e+01 d.3.1.1 76236 1xa1A 255 4.74e+01 e.3.1.1 109529 1wddS 128 4.75e+01 1x8hA 228 4.76e+01 1npsA 88 4.80e+01 1prs b.11.1.1 23622 1vcc 77 4.86e+01 1vcc d.121.1.1 41092 1ri5A 298 4.87e+01 c.66.1.34 97502 2aioA 269 4.88e+01 1vhwA 253 4.92e+01 c.56.2.1 100706 1u58A 253 4.95e+01 1mai 131 5.01e+01 1mai b.55.1.1 26951 1z4xA 532 5.01e+01 1smlA 269 5.02e+01 1smlA d.157.1.1 42053 1ctt 294 5.04e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1d4tA 104 5.07e+01 1d4tA d.93.1.1 40537 1tmxA 293 5.07e+01 1r6fA 310 5.07e+01 e.46.1.1 97149 2dcnA 311 5.08e+01 2a4vA 159 5.15e+01 1eg9A 449 5.15e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1h9dB 134 5.17e+01 2jhbA b.54.1.1 60822 2gjsA 176 5.18e+01 1xuvA 178 5.19e+01 1m9sA 605 5.19e+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 2c9wA 169 5.20e+01 1fo0B 112 5.20e+01 1kb5B b.1.1.1 20631 1j5pA 253 5.22e+01 d.81.1.3,c.2.1.3 71577,83092 1b7yA 350 5.26e+01 1pysA d.104.1.1 40776 1n13A 52 5.33e+01 d.155.1.2 85248 1yreA 197 5.33e+01 1ju2A 536 5.36e+01 c.3.1.2,d.16.1.1 77169,77170 8rucI 123 5.36e+01 1rboC d.73.1.1 39629 1w4sA 174 5.38e+01 1mmvB 419 5.39e+01 d.174.1.1 91318 1ri9A 102 5.41e+01 b.34.2.1 97506 2cb5A 453 5.43e+01 3gcb d.3.1.1 37035 1j5wA 298 5.47e+01 d.104.1.1 71589 1k07A 263 5.47e+01 d.157.1.1 77218 1wteA 272 5.50e+01 1op3H 225 5.51e+01 b.1.1.1,b.1.1.2 87208,87209 1vjqA 79 5.62e+01 k.43.1.1 100830 1lr0A 129 5.66e+01 d.212.1.1 74213 1lgpA 116 5.71e+01 b.26.1.2 73890 2akrA 285 5.75e+01 1x8gA 227 5.76e+01 1rmg 422 5.79e+01 1rmg b.80.1.3 28029 1cdcA 99 5.82e+01 1cdcA b.1.1.1 19746 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