# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1uqrA 154 3.75e-01 c.23.13.1 99779 1mjhB 162 4.86e-01 1mjhA c.26.2.4 31640 1vjgA 218 6.12e-01 c.23.10.6 100810 2fnaA 357 9.16e-01 1mjhA 162 9.49e-01 1mjhA c.26.2.4 31639 2anuA 255 1.05e+00 1kkoA 413 1.40e+00 c.1.11.2,d.54.1.1 68675,68676 1i60A 278 2.23e+00 c.1.15.4 71118 1to3A 304 2.52e+00 c.1.10.1 107161 1vpgA 192 3.08e+00 1p0kA 349 3.29e+00 c.1.4.1 87648 1mzhA 225 3.32e+00 c.1.10.1 79698 1f89A 291 3.48e+00 d.160.1.1 64988 3pga1 337 3.49e+00 4pgaA 1d0iA 156 3.75e+00 2dhqA c.23.13.1 31383 1z41A 338 3.78e+00 1php 394 4.37e+00 16pk c.86.1.1 35452 2cbiA 594 4.39e+00 1o20A 427 4.46e+00 c.82.1.1 86556 1w0mA 226 4.50e+00 c.1.1.1 109027 1wc9A 169 4.62e+00 1edt 271 5.05e+00 2ebn c.1.8.5 28993 1gtzA 156 5.15e+00 c.23.13.1 70539 2b6hA 192 5.21e+00 1o9iA 266 5.24e+00 a.25.1.3 92671 1ispA 181 5.27e+00 c.69.1.18 76778 1qumA 285 5.66e+00 1qumA c.1.15.1 29393 1tv8A 340 5.82e+00 c.1.28.3 107352 1rdfA 267 6.18e+00 c.108.1.3 104884 1hg3A 225 6.21e+00 1hg3A c.1.1.1 61025 1lfpA 249 6.27e+00 e.39.1.1 73885 1xzoA 174 6.39e+00 1jkvA 266 6.51e+00 a.25.1.3 71719 1fezA 256 6.61e+00 1fezA c.108.1.3 43343 1i6wA 181 6.63e+00 1i6wA c.69.1.18 61859 1bw0A 416 6.68e+00 1bw0A c.67.1.1 34385 1fzqA 181 7.09e+00 1hurA c.37.1.8 32060 2f5xA 312 7.09e+00 4pgaA 337 7.34e+00 4pgaA c.88.1.1 35565 1ak2 233 7.43e+00 1zin c.37.1.1,g.41.2.1 31894,45195 1e8gA 560 7.73e+00 1qltA d.58.32.1,d.145.1.1 39455,41718 1o5oA 221 7.95e+00 c.61.1.1 92509 1c93A 265 7.98e+00 2ebn c.1.8.5 28998 1vaoA 560 8.36e+00 1qltA d.58.32.1,d.145.1.1 39461,41724 1vjtA 483 8.43e+00 c.2.1.5,d.162.1.2 100833,100834 1a4iB 301 8.70e+00 1a4iA c.2.1.7,c.58.1.2 30279,33927 1qtwA 285 8.90e+00 1qumA c.1.15.1 29392 2fyxA 143 9.21e+00 1a4iA 301 9.45e+00 1a4iA c.2.1.7,c.58.1.2 30278,33926 1ufoA 238 9.46e+00 c.69.1.27 99344 1diaA 306 9.67e+00 1a4iA c.2.1.7,c.58.1.2 30280,33928 1bpb 248 9.87e+00 1bpyA a.60.12.1,d.218.1.2 75811,75812 1lh0A 213 9.89e+00 c.61.1.1 73896 1erzA 303 1.02e+01 1erzA d.160.1.2 59498 1b3uA 588 1.02e+01 1b3uA a.118.1.2 19135 1e6yB 433 1.03e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 1qltA 560 1.03e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1u02A 239 1.05e+01 c.108.1.15 107538 1sz7A 200 1.05e+01 1kczA 413 1.06e+01 c.1.11.2,d.54.1.1 68451,68452 1w1kA 560 1.08e+01 d.58.32.1,d.145.1.1 109059,109060 1k1xA 659 1.13e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1wpoA 256 1.14e+01 1lay b.57.1.1 27012 1uf5A 303 1.16e+01 d.160.1.2 107808 1e3oC 160 1.17e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1eswA 500 1.18e+01 1cwyA c.1.8.1 59500 2dhqA 146 1.19e+01 2dhqA c.23.13.1 31382 1glqA 209 1.32e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 2bwfA 77 1.33e+01 1yzfA 195 1.36e+01 1ezwA 349 1.36e+01 1ezwA c.1.16.3 29558 1q1gA 276 1.37e+01 c.56.2.1 95574 1kfd 605 1.51e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1cwyA 500 1.53e+01 1cwyA c.1.8.1 28789 1pdo 135 1.55e+01 1pdo c.54.1.1 33376 7odcA 424 1.58e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1h5qA 265 1.58e+01 1cydA c.2.1.2 60643 1e4yA 214 1.61e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1xnaA 183 1.66e+01 1xnaA b.18.1.8 23773 1khyA 148 1.70e+01 a.174.1.1 77410 1c0pA 363 1.72e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1rqlA 267 1.78e+01 c.108.1.3 97750 1mdwA 328 1.80e+01 d.3.1.3 84934 1vl8A 267 1.81e+01 c.2.1.2 108733 1swvA 267 1.84e+01 1mr3F 181 1.85e+01 c.37.1.8 79422 1i8tA 367 1.94e+01 c.4.1.3,d.16.1.7 66094,66095 1uk8A 282 1.94e+01 c.69.1.10 107907 1wd5A 208 1.96e+01 2tpsA 227 1.97e+01 2tpsA c.1.3.1 28591 1nfp 228 1.98e+01 1nfp c.1.16.2 29555 1uptC 170 2.00e+01 c.37.1.8 99769 2g76A 335 2.00e+01 1yb0A 159 2.00e+01 1jmvA 141 2.02e+01 c.26.2.4 66897 1nom 248 2.02e+01 1bpyA a.60.12.1,d.218.1.2 75929,75930 1h05A 146 2.03e+01 c.23.13.1 76433 1izcA 339 2.08e+01 c.1.12.5 83838 2bsxA 253 2.08e+01 1rpl 251 2.08e+01 1bpyA a.60.12.1,d.218.1.2 75933,75934 1thfD 253 2.14e+01 1thfD c.1.2.1 28535 2minA 491 2.16e+01 1qguA c.92.2.3 35609 1iupA 282 2.24e+01 c.69.1.10 76815 1hurA 180 2.24e+01 1hurA c.37.1.8 32052 1s95A 333 2.26e+01 d.159.1.3 105375 1ydyA 356 2.27e+01 1tqgA 105 2.30e+01 a.24.10.3 107224 1o3yA 166 2.30e+01 c.37.1.8 86618 1nt2B 258 2.30e+01 a.183.1.1 86150 2d13A 227 2.31e+01 1y2qA 143 2.33e+01 2b18A 164 2.33e+01 1r85A 379 2.34e+01 c.1.8.3 104839 3minC 491 2.34e+01 1qguA c.92.2.3 35607 1xi3A 215 2.35e+01 c.1.3.1 109601 1k6dA 220 2.36e+01 c.124.1.2 72082 1uptA 171 2.41e+01 c.37.1.8 99767 1gudA 288 2.41e+01 c.93.1.1 83326 1w8kA 447 2.42e+01 1zbqA 327 2.43e+01 1deoA 233 2.44e+01 1deoA c.23.10.4 31345 1yzgA 179 2.44e+01 1opr 213 2.47e+01 1opr c.61.1.1 34091 1u9yA 284 2.48e+01 1b68A 191 2.49e+01 1nfn a.24.1.1 59076 1oasA 322 2.52e+01 1oasA c.79.1.1 35293 1k7cA 233 2.53e+01 c.23.10.4 68267 1bt0A 76 2.59e+01 1ubi d.15.1.1 37607 1r8sA 164 2.63e+01 c.37.1.8 97247 1deaA 266 2.67e+01 1deaA c.124.1.1 31760 1ywfA 296 2.68e+01 1lehA 364 2.68e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 2bznA 351 2.70e+01 1p0iA 529 2.70e+01 c.69.1.1 93867 1ypfA 336 2.72e+01 1nbaA 264 2.73e+01 1nbaA c.33.1.3 31753 1ko9A 345 2.74e+01 a.96.1.3,d.129.1.2 68717,68718 1fsfA 266 2.76e+01 c.124.1.1 65047 1mjgM 729 2.77e+01 e.26.1.3 79204 1ljrA 244 2.85e+01 1ljrA a.45.1.1,c.47.1.5 17707,33001 1i6pA 220 2.89e+01 1ddzA c.53.2.1 61848 1akeA 214 2.91e+01 1zin c.37.1.1,g.41.2.1 31905,45185 1meoA 209 2.92e+01 c.65.1.1 79035 1bxkA 355 3.09e+01 1bxkA c.2.1.2 29803 1dad 224 3.11e+01 1byi c.37.1.10 32204 2c6qA 351 3.17e+01 1ct5A 256 3.20e+01 1ct5A c.1.6.2 28663 1r4aA 165 3.23e+01 c.37.1.8 96986 1oaoC 729 3.25e+01 e.26.1.3 86746 1dugA 234 3.26e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1mv8A 436 3.29e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 2a33A 215 3.33e+01 1fs5A 266 3.34e+01 c.124.1.1 65044 1es9A 232 3.35e+01 1wab c.23.10.3 31340 1nlfA 279 3.35e+01 c.37.1.11 85850 1m1nA 491 3.39e+01 c.92.2.3 78417 1aqwA 209 3.39e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 1fp4A 492 3.40e+01 c.92.2.3 76187 1hizA 379 3.40e+01 c.1.8.3 65841 1gz6A 319 3.43e+01 c.2.1.2 76410 1octC 156 3.44e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 1vh7A 265 3.44e+01 c.1.2.1 100646 1b8xA 280 3.45e+01 1b8xA a.45.1.1,c.47.1.5 17739,33033 1dn1B 267 3.46e+01 1dn1B a.47.2.1 17771 1nddD 76 3.47e+01 1ubi d.15.1.1 37602 1zj6A 187 3.50e+01 1vdkA 466 3.59e+01 a.127.1.1 100561 1dts 221 3.63e+01 1byi c.37.1.10 32200 1gzqA 300 3.63e+01 b.1.1.2,d.19.1.1 70818,70819 1jqnA 883 3.66e+01 c.1.12.3 77159 1p32A 209 3.69e+01 1p32A d.25.1.1 38379 1xszA 356 3.69e+01 1xvxA 312 3.72e+01 1lucA 355 3.74e+01 1lucA c.1.16.1 29547 1fcjA 322 3.76e+01 1oasA c.79.1.1 35289 1wpoB 256 3.84e+01 1lay b.57.1.1 27013 1wab 232 3.84e+01 1wab c.23.10.3 31341 1unnC 115 3.88e+01 d.240.1.1 99680 1oyjA 231 3.89e+01 a.45.1.1,c.47.1.5 87597,87598 2g45A 129 3.96e+01 1aoa 275 4.04e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1w6uA 302 4.08e+01 1othA 321 4.15e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1hyuA 521 4.18e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1qd1A 325 4.20e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1vplA 256 4.22e+01 1gdhA 320 4.23e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1pou 71 4.24e+01 1au7A a.35.1.1 17020 1knwA 425 4.27e+01 b.49.2.3,c.1.6.1 90969,90970 1lbkA 208 4.30e+01 a.45.1.1,c.47.1.5 73809,73810 2bvlA 543 4.33e+01 1lw7A 365 4.33e+01 c.26.1.3,c.37.1.1 74295,74296 1cwwA 102 4.36e+01 1cy5A a.77.1.3 18434 1bolA 222 4.36e+01 1bolA d.124.1.1 41120 1byuA 216 4.37e+01 1byuA c.37.1.8 32032 1k4nA 192 4.41e+01 d.32.1.5 72059 2bleA 367 4.45e+01 1lwyA 324 4.45e+01 a.96.1.3,d.129.1.2 78285,78286 1rljA 139 4.49e+01 c.23.5.7 104983 2b7kA 200 4.50e+01 2b4gA 317 4.54e+01 1g5hA 454 4.54e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1byi 224 4.54e+01 1byi c.37.1.10 32199 1ru8A 232 4.56e+01 c.26.2.1 97849 1eh9A 558 4.59e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1mejA 223 4.60e+01 c.65.1.1 79029 2cw6A 298 4.63e+01 1pgtA 210 4.69e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1g8yA 279 4.69e+01 1g8yA c.37.1.11 32302 17gsA 210 4.79e+01 1pgtA a.45.1.1,c.47.1.5 17524,32818 1rypJ 204 4.82e+01 d.153.1.4 41878 1t8qA 336 4.82e+01 c.1.18.3 106669 1nddA 76 4.83e+01 1ubi d.15.1.1 37599 1b7fA 168 4.86e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 12asA 330 4.88e+01 12asA d.104.1.1 40783 1m7yA 435 4.97e+01 c.67.1.4 78761 1sflA 238 4.97e+01 2aexA 346 5.00e+01 1tdpA 111 5.00e+01 a.29.8.1 106781 1uuqA 440 5.15e+01 c.1.8.3 100015 1sfjA 238 5.16e+01 2dfkA 402 5.18e+01 2dg5A 366 5.19e+01 1r1mA 164 5.22e+01 d.79.7.1 96820 18gsA 210 5.25e+01 1pgtA a.45.1.1,c.47.1.5 17528,32822 1rztA 331 5.25e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1sz9A 144 5.34e+01 a.118.9.4 106139 1vbuA 328 5.41e+01 2bkrB 77 5.48e+01 1v6tA 255 5.54e+01 1vykA 149 5.57e+01 1ynuA 473 5.60e+01 1tzjA 338 5.70e+01 1j7nB 776 5.74e+01 d.92.1.14,d.92.1.14,d.166.1.1 66412,66413,66414 1yspA 181 5.77e+01 1qoxN 449 5.82e+01 1qoxN c.1.8.4 28978 2rslA 140 5.82e+01 2rslA c.53.1.1 33345 1b8gA 429 5.84e+01 1b8gA c.67.1.4 34499 1obdA 306 5.86e+01 d.143.1.1 86767 1xfhA 422 5.87e+01 1dbs 224 5.91e+01 1byi c.37.1.10 32209 1ja1A 622 5.95e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1ebmA 317 5.98e+01 1ebmA a.96.1.3,d.129.1.2 18751,41300 1yarA 233 6.03e+01 1cr1A 296 6.04e+01 1cr1A c.37.1.11 32286 1bc9 200 6.13e+01 1pbv a.118.3.1 19180 1o60A 292 6.15e+01 c.1.10.4 92532 1efvB 255 6.16e+01 1efvB c.26.2.3 31634 1xqiA 195 6.18e+01 1m3qA 317 6.32e+01 a.96.1.3,d.129.1.2 91184,91185 1x1nA 524 6.32e+01 2bijA 305 6.35e+01 1s1iG 119 6.36e+01 i.1.1.1 105181 1sazA 381 6.50e+01 1kgnA 329 6.51e+01 a.25.1.2 68584 1gnlA 544 6.52e+01 e.26.1.1 70287 1brlB 324 6.66e+01 1lucA c.1.16.1 29554 1u8sA 192 6.66e+01 d.58.18.5,d.58.18.5 107737,107738 1k0wA 231 6.68e+01 c.74.1.1 77220 2dpg 485 6.69e+01 1dpgA c.2.1.3,d.81.1.5 30076,39991 1w3iA 293 6.70e+01 c.1.10.1 109152 1fc4A 401 6.80e+01 1bs0A c.67.1.4 59760 1cr0A 296 6.81e+01 1cr1A c.37.1.11 32287 2f5gA 133 6.88e+01 1jmeA 455 6.90e+01 a.104.1.1 66885 1kshA 186 6.93e+01 c.37.1.8 72914 1vl2A 421 7.11e+01 c.26.2.1,d.210.1.1 108708,108709 1jdiA 231 7.11e+01 c.74.1.1 66551 1jetA 517 7.12e+01 1jevA c.94.1.1 35718 1qsdA 106 7.17e+01 1qsdA a.7.5.1 16335 1ru0A 105 7.23e+01 1vhwA 253 7.24e+01 c.56.2.1 100706 1vizA 240 7.28e+01 c.1.4.1 100784 1nfn 191 7.31e+01 1nfn a.24.1.1 16523 1ysqA 193 7.32e+01 1mjfA 281 7.33e+01 c.66.1.17 79198 3pcgM 238 7.35e+01 3pchM b.3.6.1 22742 1xesA 413 7.41e+01 1xkyA 301 7.42e+01 1jndA 420 7.42e+01 c.1.8.5,d.26.3.1 71757,71758 1a48 306 7.44e+01 1a48 d.143.1.1 41590 1eguA 731 7.46e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1g0uI 205 7.55e+01 d.153.1.4 41891 1nr6A 473 7.55e+01 a.104.1.1 92085 1ehaA 558 7.65e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1sumB 235 7.68e+01 a.7.12.1 106025 1pa7A 130 7.75e+01 a.40.1.1 94410 1ub3A 220 7.76e+01 c.1.10.1 88395 1rzmA 338 7.78e+01 c.1.10.4 105137 2bodX 286 7.78e+01 1j4wA 174 7.79e+01 d.51.1.1,d.51.1.1 71529,71530 1o0wA 252 7.81e+01 a.149.1.1,d.50.1.1 80751,80752 1pz1A 333 7.83e+01 c.1.7.1 95390 1onqA 283 7.85e+01 b.1.1.2,d.19.1.1 93365,93366 1uf3A 228 7.87e+01 d.159.1.6 99317 1be1 137 7.89e+01 1be1 c.23.6.1 31237 1b43A 340 7.90e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1km4A 247 7.93e+01 c.1.2.3 72740 1dpgA 485 7.93e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1hv8A 367 7.95e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1mun 225 8.00e+01 1mun a.96.1.2 18744 1zroA 602 8.06e+01 1lwdA 413 8.08e+01 c.77.1.1 78265 1ez3A 127 8.09e+01 1dn1B a.47.2.1 17768 1lxnA 99 8.12e+01 d.58.48.1 84737 1mkmA 249 8.14e+01 a.4.5.33,d.110.2.2 79242,79243 1o0xA 262 8.16e+01 d.127.1.1 80755 2pcdM 238 8.16e+01 3pchM b.3.6.1 22760 1o4vA 183 8.17e+01 c.23.8.1 86628 1h5yA 253 8.20e+01 c.1.2.1 65638 1usmA 80 8.22e+01 d.74.1.1 99876 1pj5A 830 8.32e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1s8nA 205 8.33e+01 c.23.1.1 105374 1pv5A 264 8.39e+01 d.251.1.1 95150 1xfiA 367 8.41e+01 e.50.1.1 109584 2g8lA 299 8.47e+01 1hjsA 332 8.48e+01 c.1.8.3 83492 1uuyA 167 8.51e+01 c.57.1.1 108059 1cnt2 187 8.52e+01 1cnt3 1b54 257 8.58e+01 1ct5A c.1.6.2 28664 1y8aA 332 8.60e+01 2bogX 286 8.64e+01 1sczA 233 8.73e+01 c.43.1.1 98802 1vr6A 350 8.73e+01 1m12A 84 8.74e+01 a.64.1.1 84745 1lucB 324 8.75e+01 1lucA c.1.16.1 29548 1jevA 517 8.82e+01 1jevA c.94.1.1 35720 2b99A 156 8.83e+01 1lpe 144 8.85e+01 1nfn a.24.1.1 16524 1sxgA 280 8.86e+01 1zx4A 192 8.88e+01 1muyA 225 8.98e+01 1mun a.96.1.2 18745