# List of top-scoring protein chains for t06-100-40-40-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 1xb4A 202 1.74e-02 1y0nA 78 2.91e-02 2fwhA 134 3.38e-01 1bjt 793 4.04e-01 1bjt e.11.1.1 43249 1w85A 368 4.18e-01 1uc7A 125 6.45e-01 c.47.1.1 99163 1wkaA 147 9.36e-01 2fdbM 164 1.05e+00 1ne7A 289 1.25e+00 c.124.1.1 91833 1zs9A 261 1.30e+00 1bif 469 1.45e+00 1bif c.37.1.7,c.60.1.4 31961,34003 1x7yA 400 1.47e+00 1zz1A 369 1.48e+00 1p2fA 220 1.56e+00 a.4.6.1,c.23.1.1 87720,87721 1vyiA 112 1.64e+00 1umdA 367 1.70e+00 c.36.1.11 99599 1ro0A 216 1.80e+00 d.264.1.2 97664 1p4oA 322 1.88e+00 d.144.1.7 87775 1zelA 298 1.88e+00 1npiA 61 1.88e+00 g.3.7.1 80685 1exqA 154 1.95e+00 1b9dA c.55.3.2 33646 1mngA 203 2.03e+00 1avmA a.2.11.1,d.44.1.1 15776,38701 1ro2A 216 2.17e+00 d.264.1.2 97665 1w23A 360 2.36e+00 2bjfA 329 2.39e+00 1whzA 70 2.53e+00 1m70A 190 2.54e+00 a.3.1.4,a.3.1.4 91200,91201 1z1lA 345 2.60e+00 2abqA 306 2.71e+00 2c0rA 362 2.74e+00 1xvxA 312 2.87e+00 1jpaA 312 2.98e+00 d.144.1.7 67011 2bfdA 400 3.06e+00 1iwmA 186 3.08e+00 b.125.1.2 83758 1ignA 246 3.16e+00 1ignA a.4.1.6,a.4.1.6 16048,16049 2f3yA 148 3.34e+00 1jsf 130 3.34e+00 3lzt d.2.1.2 36410 1b4pA 217 3.48e+00 a.45.1.1,c.47.1.5 83158,83159 1a6m 151 3.71e+00 1a6m a.1.1.2 15018 1zcbA 362 3.91e+00 1u3eM 174 4.10e+00 d.4.1.3,d.285.1.1 107640,107641 1ustA 93 4.41e+00 a.4.5.13 99884 1exrA 148 4.47e+00 1cll a.39.1.5 17299 1xyiA 66 4.57e+00 1st9A 143 4.82e+00 c.47.1.10 98987 1qznA 173 4.83e+00 b.2.2.2 104669 1obdA 306 5.40e+00 d.143.1.1 86767 1dk8A 147 5.46e+00 1agrE a.91.1.1 18548 1u1sA 82 5.51e+00 2daqA 110 5.52e+00 1y81A 138 5.54e+00 1vyrA 364 5.65e+00 c.1.4.1 108906 1gjnA 153 5.67e+00 a.1.1.2 70191 1vr9A 213 5.74e+00 1u1tA 82 5.84e+00 1qd9A 124 6.00e+00 1qu9A d.79.1.1 39758 1z3xA 238 6.00e+00 1uwmA 106 6.30e+00 1sauA 115 6.41e+00 2btdA 210 6.56e+00 1augA 215 6.63e+00 1a2zA c.56.4.1 33798 1rypL 212 6.85e+00 d.153.1.4 41880 1gqzA 274 6.87e+00 d.21.1.1,d.21.1.1 83311,83312 2f9sA 151 6.88e+00 2ch0A 133 7.05e+00 1n2aA 201 7.14e+00 a.45.1.1,c.47.1.5 91553,91554 1zv9A 172 7.18e+00 1pvmA 184 7.32e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1t95A 240 7.42e+00 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1vr0A 247 7.51e+00 2bbrA 195 7.86e+00 1u46A 291 7.99e+00 d.144.1.7 107656 2cnqA 306 8.46e+00 1xlqA 106 8.52e+00 1m32A 366 8.59e+00 c.67.1.3 78508 1umwA 237 8.72e+00 d.223.1.2,d.223.1.2 99631,99632 1ijtA 128 8.88e+00 1bfg b.42.1.1 62510 1zpdA 568 8.95e+00 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31741,31785,31786 1tn6A 382 9.02e+00 2frfA 153 9.06e+00 1kxvC 121 9.14e+00 b.1.1.1 73190 1toaA 313 9.28e+00 1toaA c.92.2.2 35598 2bs3A 656 9.44e+00 2fafA 608 9.56e+00 1ib2A 349 9.61e+00 1ib2A a.118.1.8 62141 1hdoA 206 9.86e+00 1he2A c.2.1.2 60965 2b0tA 738 9.87e+00 2b49A 287 9.88e+00 1anf 370 1.01e+01 4mbp c.94.1.1 35776 1u04A 771 1.03e+01 b.34.14.1,c.55.3.10 107539,107540 1nzjA 298 1.03e+01 c.26.1.1 92377 2bjbA 462 1.05e+01 2f9zC 159 1.05e+01 1yzxA 226 1.05e+01 1e8gA 560 1.05e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1q1uA 144 1.11e+01 b.42.1.1 95608 1t3tA 1303 1.11e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1hw7A 255 1.13e+01 1i7fA d.193.1.1 61297 1gqvA 135 1.16e+01 d.5.1.1 70376 1xqrA 296 1.18e+01 1dptA 117 1.24e+01 1dptA d.80.1.3 39862 1v25A 541 1.25e+01 e.23.1.1 108275 1urjA 1136 1.30e+01 1wzoA 246 1.34e+01 1dekA 241 1.37e+01 1dekA c.37.1.1 31842 1w2lA 99 1.38e+01 1oe4A 247 1.38e+01 c.18.1.3 86895 1gwiA 411 1.39e+01 a.104.1.1 76364 1vr5A 547 1.39e+01 1eljA 381 1.41e+01 4mbp c.94.1.1 35791 1eaiC 61 1.43e+01 1eaiC g.22.1.1 44894 2erfA 209 1.45e+01 1vcc 77 1.46e+01 1vcc d.121.1.1 41092 1yovA 537 1.46e+01 1fd3A 41 1.47e+01 1fd3A g.9.1.1 44572 1qh8A 478 1.47e+01 1qguA c.92.2.3 35633 1tns 76 1.49e+01 1qpmA a.6.1.7 16228 1wtaA 275 1.54e+01 1snrA 341 1.56e+01 b.6.1.3,b.6.1.3 105823,105824 1ttzA 87 1.58e+01 c.47.1.1 107309 1uw4A 91 1.60e+01 d.58.7.4 100071 1ae9A 179 1.62e+01 1ae9A d.163.1.1 42153 1e7wA 291 1.62e+01 c.2.1.2 59373 1yfnA 118 1.64e+01 2bt6A 108 1.65e+01 1i60A 278 1.67e+01 c.1.15.4 71118 1lngA 87 1.76e+01 d.201.1.1 74045 1oc2A 348 1.79e+01 c.2.1.2 92765 1ex7A 186 1.79e+01 1gky c.37.1.1 59537 1pv5A 264 1.80e+01 d.251.1.1 95150 1yj7A 171 1.80e+01 1oqqA 106 1.82e+01 d.15.4.1 93422 1a2yB 116 1.83e+01 1gc1H b.1.1.1 19927 1ggzA 148 1.88e+01 a.39.1.5 70176 1ihkA 174 1.90e+01 1bfg b.42.1.1 62384 1iybA 208 1.93e+01 d.124.1.1 90720 1ois 223 1.99e+01 1a36A e.15.1.1 43267 1avsA 90 2.04e+01 1cll a.39.1.5 17226 1v7rA 186 2.04e+01 c.51.4.1 100482 2bw3A 534 2.08e+01 1xkpA 246 2.11e+01 1fzqA 181 2.12e+01 1hurA c.37.1.8 32060 1e6iA 121 2.13e+01 1b91A a.29.2.1 16969 2czrA 226 2.19e+01 1nu7D 282 2.23e+01 a.8.6.1,a.8.6.1 92191,92192 1o50A 157 2.24e+01 d.37.1.1,d.37.1.1 92478,92479 1tyjA 170 2.26e+01 2b95A 106 2.26e+01 1sglA 209 2.28e+01 d.124.1.1 105536 2a2rA 210 2.29e+01 1xhcA 367 2.30e+01 1dm9A 133 2.30e+01 1dm9A d.66.1.3 39560 1dzkA 157 2.31e+01 1obpA b.60.1.1 27096 1oe1A 336 2.32e+01 b.6.1.3,b.6.1.3 86891,86892 1tueA 212 2.36e+01 c.37.1.20 107323 1gxmA 332 2.37e+01 a.102.5.1 76371 1m55A 197 2.39e+01 d.89.1.3 74469 1vp4A 425 2.39e+01 1b43A 340 2.40e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1gky 187 2.42e+01 1gky c.37.1.1 31839 1lm8C 96 2.46e+01 d.42.1.1 74034 1xzoA 174 2.49e+01 1zvtA 256 2.49e+01 1vj1A 363 2.51e+01 b.35.1.2,c.2.1.1 100794,100795 2f2hA 773 2.57e+01 1nuuA 252 2.58e+01 c.26.1.3 86209 2f02A 323 2.58e+01 2dgkA 452 2.63e+01 1yw5A 177 2.64e+01 2bk9A 153 2.64e+01 1brfA 53 2.67e+01 1rb9 g.41.5.1 45236 1e5rA 290 2.70e+01 1e5rA b.82.2.4 59276 1yk4A 52 2.71e+01 1rhs 296 2.72e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1k0eA 453 2.74e+01 d.161.1.1 67938 1ff9A 450 2.74e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1khbA 625 2.77e+01 c.91.1.1,c.109.1.1 68606,68607 1ug7A 128 2.77e+01 a.24.24.1 107824 2b5lC 222 2.80e+01 1zm0A 114 2.80e+01 1np7A 489 2.80e+01 a.99.1.1,c.28.1.1 80677,80678 2aieP 203 2.82e+01 1fqiA 147 2.82e+01 1agrE a.91.1.1 18542 1xbbA 291 2.85e+01 1rp0A 284 2.90e+01 1zrn 232 2.90e+01 1qq5A c.108.1.1 43323 1a2zA 220 2.91e+01 1a2zA c.56.4.1 33794 2ew2A 316 2.91e+01 1ztdA 133 2.92e+01 1bkrA 109 2.93e+01 1bkrA a.40.1.1 17394 1rwhA 757 3.00e+01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1ktbA 405 3.01e+01 b.71.1.1,c.1.8.1 72960,72961 2cvbA 188 3.03e+01 2f62A 161 3.05e+01 1afp 51 3.09e+01 1afp g.26.1.1 44947 2fx0A 201 3.09e+01 1ui5A 215 3.10e+01 a.4.1.9,a.121.1.1 107856,107857 1m65A 245 3.14e+01 c.6.3.1 84847 1n3kA 130 3.17e+01 a.77.1.4 79965 1khcA 147 3.19e+01 b.34.9.2 68608 2fj6A 82 3.19e+01 1c52 131 3.22e+01 1c52 a.3.1.1 15810 1nykA 165 3.24e+01 b.33.1.1 86408 1d3bA 75 3.24e+01 1d3bA b.38.1.1 24798 1aua 296 3.25e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1lm8V 160 3.28e+01 b.3.3.1 74035 1hw5A 210 3.29e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1wzzA 334 3.30e+01 1f74A 293 3.32e+01 1nal3 c.1.10.1 29079 1l4dB 122 3.33e+01 d.15.5.1 77684 1iugA 352 3.33e+01 c.67.1.3 90699 1eca 136 3.35e+01 1flp a.1.1.2 15209 1kq1A 77 3.36e+01 b.38.1.2 72848 1wn5A 130 3.36e+01 1ncwH 222 3.36e+01 b.1.1.1,b.1.1.2 85555,85556 1jlvA 209 3.37e+01 a.45.1.1,c.47.1.5 71729,71730 2a5dA 175 3.38e+01 1vs0A 310 3.39e+01 1lmq 129 3.41e+01 3lzt d.2.1.2 36588 1mqkH 127 3.41e+01 b.1.1.1 85053 2gh1A 301 3.42e+01 1pf5A 131 3.43e+01 d.79.1.1 94604 1ou8A 111 3.43e+01 b.136.1.1 93543 1jgsA 138 3.45e+01 a.4.5.28 66683 1lbkA 208 3.49e+01 a.45.1.1,c.47.1.5 73809,73810 1o9iA 266 3.52e+01 a.25.1.3 92671 1k3yA 221 3.53e+01 a.45.1.1,c.47.1.5 77245,77246 1efpB 252 3.55e+01 1efvB c.26.2.3 31636 1pgtA 210 3.58e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1ckeA 227 3.61e+01 1ckeA c.37.1.1 31846 1hywA 68 3.62e+01 1hywA d.186.1.1 61425 2bw4A 340 3.68e+01 2asfA 137 3.72e+01 1bzkA 43 3.72e+01 1bzkA j.35.1.1 46250 6rxn 46 3.72e+01 1rb9 g.41.5.1 45222 1v3vA 333 3.78e+01 b.35.1.2,c.2.1.1 108345,108346 1uvjA 664 3.79e+01 e.8.1.6 100045 1wnyA 186 3.81e+01 1wlmA 151 3.81e+01 1ycdA 243 3.83e+01 1iv3A 152 3.83e+01 d.79.5.1 76828 3htsB 102 3.86e+01 2hts a.4.5.22 16175 1opjA 293 3.93e+01 d.144.1.7 87230 1tfzA 424 3.97e+01 d.32.1.3,d.32.1.3 106886,106887 1rybA 212 3.98e+01 c.56.3.1 98098 1vns 609 3.98e+01 1vns a.111.1.3 19061 2h1tA 188 3.98e+01 1fobA 334 4.05e+01 c.1.8.3 83255 1cby 259 4.05e+01 1cby d.103.1.1 40705 1wi9A 72 4.07e+01 1tdhA 364 4.07e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 2al3A 90 4.07e+01 1mhnA 59 4.12e+01 b.34.9.1 84964 1th0A 226 4.13e+01 d.3.1.7 106903 1fjgK 129 4.17e+01 1fjfK c.55.4.1 33733 1chuA 540 4.18e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 2ae6A 166 4.18e+01 1ta3A 274 4.19e+01 c.1.8.5 106731 1winA 143 4.21e+01 2bf6A 449 4.24e+01 2b7kA 200 4.25e+01 1qpcA 279 4.25e+01 1fgkA d.144.1.7 41685 1t4wA 196 4.26e+01 b.2.5.2 106427 2gkeA 274 4.27e+01 1lr5A 163 4.27e+01 b.82.1.2 74215 1xqsA 280 4.30e+01 1pbwA 216 4.32e+01 1pbwA a.116.1.1 19103 1kb0A 677 4.36e+01 a.3.1.6,b.70.1.1 68378,68379 1kqpA 271 4.42e+01 c.26.2.1 72883 1sqiA 393 4.46e+01 d.32.1.3,d.32.1.3 105914,105915 1eemA 241 4.47e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1xffA 240 4.48e+01 d.153.1.1 109580 1ydyA 356 4.49e+01 1kjyB 36 4.49e+01 1orc 71 4.50e+01 1orc a.35.1.2 17054 1ucnA 152 4.50e+01 d.58.6.1 99183 1vqoI 162 4.51e+01 1csh 435 4.52e+01 1csh a.103.1.1 18880 1iro 54 4.55e+01 1rb9 g.41.5.1 45223 1seiA 130 4.56e+01 1seiA d.140.1.1 41463 2aa4A 289 4.58e+01 1h7cA 108 4.59e+01 a.7.5.1 70914 1pyoB 105 4.60e+01 1sv0C 82 4.60e+01 a.60.1.1 106037 1vf1A 229 4.61e+01 1tu7A 208 4.61e+01 1jogA 146 4.63e+01 a.24.16.2 77142 1ikpA 613 4.70e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 1tzpA 255 4.71e+01 d.65.1.3 107520 1zxfA 155 4.72e+01 2c4jA 218 4.73e+01 2pspA 106 4.75e+01 2pspA g.16.1.1,g.16.1.1 44730,44731 1vpmA 169 4.76e+01 1feuA 206 4.80e+01 1feuA b.53.1.1 59801 1kafA 108 4.82e+01 d.199.1.1 68372 1g6sA 427 4.84e+01 1eps d.68.2.2 39584 1x6oA 174 4.87e+01 b.34.5.2,b.40.4.5 109493,109494 1e4cP 215 4.88e+01 2fua c.74.1.1 34969 2aukA 190 4.89e+01 2cwcA 303 4.93e+01 1lmzA 187 4.95e+01 a.96.1.4 74037 1qe3A 489 4.95e+01 2bce c.69.1.1 34630 1nrjA 158 4.97e+01 d.110.4.4 86124 1mbmA 198 5.00e+01 b.47.1.3 78916 1mi8A 158 5.03e+01 b.86.1.2 91279 1e5mA 416 5.03e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1erd 40 5.04e+01 1erd a.10.1.1 16362 2f06A 144 5.04e+01 1fp3A 402 5.06e+01 1fp3A a.102.1.3 18842 1swxA 209 5.07e+01 a.224.1.1 106075 2bm3A 166 5.10e+01 2gs5A 198 5.11e+01 1gtzA 156 5.11e+01 c.23.13.1 70539 2f6rA 281 5.13e+01 2ex0A 399 5.18e+01 1oa8A 133 5.18e+01 b.145.1.1 92698 1wbeA 209 5.21e+01 1gkmA 509 5.21e+01 a.127.1.2 70228 1xkpC 143 5.21e+01 1w7jA 795 5.23e+01 2ga9A 297 5.23e+01 2ah5A 210 5.24e+01 2g09A 297 5.24e+01 2freA 200 5.25e+01 1keaA 221 5.26e+01 a.96.1.2 68491 1gpmA 525 5.30e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1e6bA 221 5.30e+01 1e6bA a.45.1.1,c.47.1.5 59294,59295 1wm3A 72 5.30e+01 1xu9A 286 5.36e+01 1rb9 53 5.38e+01 1rb9 g.41.5.1 45214 1on2A 142 5.46e+01 a.4.5.24,a.76.1.1 87103,87104 1noyA 388 5.47e+01 1clqA c.55.3.5 33713 1q7fA 286 5.48e+01 b.68.9.1 96036 1j57A 143 5.50e+01 d.221.1.1 77079 1rzhH 260 5.51e+01 b.41.1.1,f.23.10.1 98162,98163 1m1hA 248 5.52e+01 b.114.1.1,d.58.42.1 78415,78416 1y4tA 322 5.52e+01 1v76A 96 5.59e+01 1sg5A 86 5.60e+01 2cmwA 310 5.62e+01 1i7nA 309 5.66e+01 c.30.1.5,d.142.1.3 83681,83682 1o97C 264 5.68e+01 c.26.2.3 81232 1wpuA 147 5.68e+01 1q33A 292 5.71e+01 d.113.1.1 95657 2csoA 127 5.71e+01 1uacH 114 5.72e+01 b.1.1.1 99132 2c1iA 431 5.73e+01 1uasA 362 5.76e+01 b.71.1.1,c.1.8.1 88388,88389 1jeyB 565 5.80e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 1yseA 141 5.81e+01 1wu3I 161 5.81e+01 1rdg 53 5.85e+01 1rb9 g.41.5.1 45221 1oz2A 331 5.87e+01 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1qzzA 374 5.87e+01 a.4.5.29,c.66.1.12 96719,96720 2a38A 194 5.88e+01 1wgzA 510 5.89e+01 1xg7A 250 5.89e+01 1dmgA 225 5.91e+01 1dmgA c.22.1.1 31036 2dd8S 202 5.95e+01 2gsfA 373 5.97e+01 1us0A 316 6.03e+01 c.1.7.1 99850 1nz0A 118 6.05e+01 d.14.1.2 86433 1i40A 175 6.07e+01 b.40.5.1 66024 1e85A 127 6.09e+01 1bbhA a.24.3.2 16549 1px5A 349 6.15e+01 a.160.1.2,d.218.1.6 95277,95278 1mxiA 160 6.16e+01 c.116.1.1 79646 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