# List of top-scoring protein chains for t2k-100-30-CB_burial_14_7 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 1cnzA 363 5.96e-49 1cnzA c.77.1.1 35061 1cm7A 363 5.16e-48 1cnzA c.77.1.1 35063 1a05A 358 1.73e-47 1cnzA c.77.1.1 35059 1dr8B 344 1.64e-46 1cnzA c.77.1.1 35052 1ipd 345 2.02e-46 1cnzA c.77.1.1 35038 1idm 343 2.07e-46 1cnzA c.77.1.1 35035 1iso 416 1.56e-44 1iso c.77.1.1 35065 1pb1A 416 3.56e-44 c.77.1.1 88014 7icd 416 6.01e-44 1iso c.77.1.1 35072 1hqsA 423 1.67e-43 1iso c.77.1.1 61154 1lwdA 413 2.14e-37 c.77.1.1 78265 1itwA 741 9.71e-06 c.77.1.2 76793 1h5vA 304 3.82e-02 c.1.8.3 70898 7a3hA 303 4.36e-02 7a3hA c.1.8.3 28817 1a3h 300 5.42e-02 7a3hA c.1.8.3 28819 1lkcA 364 1.31e-01 c.67.1.1 73978 1lc5A 364 1.85e-01 c.67.1.1 73827 1hizA 379 5.05e-01 c.1.8.3 65841 1tikA 213 5.11e-01 1ceo 343 5.40e-01 1ceo c.1.8.3 28808 1t0iA 191 5.60e-01 1b66A 140 6.12e-01 1b66A d.96.1.2 40657 1gtqA 140 8.61e-01 1b66A d.96.1.2 40661 1nr6A 473 8.63e-01 a.104.1.1 -1464 1n6bA 473 9.12e-01 a.104.1.1 85359 1cec 343 9.54e-01 1ceo c.1.8.3 28809 1xyzA 347 9.84e-01 1taxA c.1.8.3 28804 1do0A 442 1.16e+00 1do0A c.37.1.20 32432 1j1iA 296 1.18e+00 c.69.1.10 83977 1q7zA 566 1.25e+00 c.1.21.2 -5638 c.1.26.1 -5666 1kmqA 184 1.36e+00 c.37.1.8 84412 1dt6A 473 1.53e+00 1dt6A a.104.1.1 18977 1kc0A 299 1.79e+00 1clxA 347 2.05e+00 1taxA c.1.8.3 28899 1vicA 262 2.13e+00 c.68.1.13 -8252 1joa 447 2.17e+00 1nhp c.3.1.5 30563 c.3.1.5 30564 d.87.1.1 40203 1fjhA 257 2.21e+00 1fjhB c.2.1.2 29870 1n2sA 299 2.26e+00 c.2.1.2 79857 1bqcA 302 2.49e+00 1bqcA c.1.8.3 28831 1n5dA 288 2.67e+00 c.2.1.2 80030 1hu4A 288 2.69e+00 1hu4A 1fjhB 257 2.80e+00 1fjhB c.2.1.2 29871 1aw5 326 2.85e+00 1b4kA c.1.10.3 29181 1nhp 447 2.99e+00 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1og6A 298 3.01e+00 c.1.7.1 86984 1nkqA 259 3.03e+00 1fts 295 3.10e+00 1ng1 a.24.13.1 16968 c.37.1.10 32279 1i24A 404 3.10e+00 c.2.1.2 83663 1j6oA 268 3.23e+00 c.1.9.12 77088 1pj5A 830 3.28e+00 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 1d2gA 292 3.35e+00 1xvaA c.66.1.5 34187 2fcr 173 3.59e+00 1rcf c.23.5.1 31151 1kk9A 221 3.75e+00 d.115.1.1 77432 1nhs 447 3.84e+00 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1nq6A 302 3.86e+00 c.1.8.3 -5332 1xvaA 292 3.88e+00 1xvaA c.66.1.5 34183 1kid 203 3.93e+00 1derA c.8.5.1 30771 1bg4 302 3.97e+00 1taxA c.1.8.3 28806 1pwxA 254 4.05e+00 c.2.1.2 -5858 1bhjA 292 4.09e+00 1xvaA c.66.1.5 34189 1ur3M 319 4.21e+00 c.1.7.1 -5248 1qdlA 422 4.34e+00 1qdlA d.161.1.1 42088 1l8aA 886 4.47e+00 c.36.1.6 73678 c.36.1.10 73677 c.48.1.1 73679 3thiA 371 4.61e+00 2thiA c.94.1.1 35792 1gz6A 319 4.86e+00 c.2.1.2 76410 1od8A 313 5.03e+00 c.1.8.3 86838 1g0oA 283 5.07e+00 1ybvA c.2.1.2 60181 1ybvA 283 5.11e+00 1ybvA c.2.1.2 29948 1qrrA 394 5.35e+00 1qrrA c.2.1.2 29824 1k7jA 206 5.44e+00 d.115.1.1 72103 1b31A 302 5.48e+00 1taxA c.1.8.3 28892 1ohlA 342 5.77e+00 c.1.10.3 87035 1b73A 254 5.79e+00 1b74A c.78.2.1 35266 c.78.2.1 35267 1jykA 254 5.85e+00 c.68.1.13 67458 1e0wA 313 5.90e+00 1taxA c.1.8.3 59150 1cnv 299 5.99e+00 1cnv c.1.8.5 28989 1n82A 331 6.12e+00 c.1.8.3 -5306 1lst 239 6.49e+00 1lst c.94.1.1 35755 1h7nA 342 6.92e+00 1b4kA c.1.10.3 60726 1cb0A 283 7.15e+00 1cb0A c.56.2.1 33790 1o4sA 389 7.22e+00 c.67.1.1 86620 1ylvA 342 7.56e+00 1b4kA c.1.10.3 29180 1umdB 324 7.58e+00 c.36.1.7 -6929 c.48.1.2 -7539 1o5iA 249 7.96e+00 c.2.1.2 -5833 1dkrA 317 7.99e+00 1dkuA c.61.1.2 34114 c.61.1.2 34115 1d2kA 392 8.10e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1j9yA 385 8.13e+00 1j9yA c.1.8.3 62791 1mg2D 155 8.21e+00 a.3.1.1 79062 1cydA 244 8.38e+00 1cydA c.2.1.2 29825 1b74A 254 8.39e+00 1b74A c.78.2.1 35264 c.78.2.1 35265 1p6oA 161 8.50e+00 c.97.1.2 -8774 1o4vA 183 8.68e+00 c.23.8.1 86628 1qcwA 410 8.86e+00 1gox c.1.4.1 28622 1dtyA 429 9.59e+00 1dtyA c.67.1.4 34495 1c4xA 285 9.83e+00 1c4xA c.69.1.10 34684 1qp8A 303 1.10e+01 1qp8A c.2.1.4 30092 c.23.12.1 31352 1tx4B 178 1.11e+01 1ctqA c.37.1.8 32045 1odzA 386 1.13e+01 c.1.8.3 86889 1fjxA 327 1.14e+01 6mhtA c.66.1.26 34228 1sayA 361 1.20e+01 1sayA c.2.1.4 30102 c.23.12.2 31362 1jj2L 194 1.20e+01 1ffkI d.12.1.2 63097 1crl 534 1.23e+01 1thg c.69.1.17 34765 1fjgB 256 1.24e+01 1fjfB c.23.15.1 31400 1ll7A 392 1.26e+01 c.1.8.5 78085 d.26.3.1 78086 1kfuS 184 1.27e+01 a.39.1.8 68574 1di0A 158 1.30e+01 1di0A c.16.1.1 30957 1v6sA 390 1.34e+01 c.86.1.1 -8567 1sxjE 354 1.35e+01 1hskA 326 1.36e+01 2mbr d.145.1.2 61241 d.146.1.1 61242 1fp2A 352 1.36e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 1lfwA 470 1.38e+01 c.56.5.4 77942 d.58.19.1 77943 1xyfA 436 1.43e+01 1taxA b.42.2.1 25577 c.1.8.3 28909 1uaqA 158 1.45e+01 c.97.1.2 88386 1dmhA 311 1.47e+01 1dmhA b.3.6.1 22633 1ryp1 222 1.48e+01 1ryp1 1dkuA 317 1.48e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 2mtaC 147 1.53e+01 2mtaC a.3.1.1 15908 1srvA 145 1.55e+01 1derA c.8.5.1 30817 1qj5A 429 1.57e+01 1dtyA c.67.1.4 34493 1fpxA 352 1.59e+01 1fpxA a.4.5.29 59950 c.66.1.12 59951 2thiA 379 1.61e+01 2thiA c.94.1.1 35794 1fpkA 335 1.62e+01 1frpA e.7.1.1 42930 1jdbB 1073 1.66e+01 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1eqcA 394 1.67e+01 1cz1A c.1.8.3 28811 1bc5A 269 1.68e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 1h1yA 228 1.74e+01 c.1.2.2 76506 16pk 415 1.77e+01 16pk c.86.1.1 35454 1ni4A 365 1.80e+01 c.36.1.7 85728 1kewA 361 1.82e+01 c.2.1.2 68544 1rm8A 169 1.83e+01 d.92.1.11 -10584 1s0aA 429 1.91e+01 c.67.1.4 -8201 1qxyA 252 1.93e+01 d.127.1.1 -10993 1mu7A 485 1.93e+01 d.136.1.3 79475 d.136.1.3 79476 1gr0A 367 1.94e+01 c.2.1.3 70379 d.81.1.3 70380 1af7 274 2.00e+01 1af7 a.58.1.1 17928 c.66.1.8 34203 1nni1 174 2.01e+01 1k6wA 426 2.03e+01 b.92.1.2 68236 c.1.9.5 68237 1fc3A 120 2.05e+01 1fc3A a.4.6.3 16237 1k07A 263 2.05e+01 d.157.1.1 77218 1cz1A 394 2.05e+01 1cz1A c.1.8.3 28839 1b8pA 329 2.10e+01 1bmdA c.2.1.5 30147 d.162.1.1 42114 5fbpA 335 2.10e+01 1frpA e.7.1.1 42873 1wdnA 226 2.11e+01 1lst c.94.1.1 35816 1gokA 303 2.13e+01 c.1.8.3 65420 2acr 315 2.14e+01 1frb c.1.7.1 28674 1e9eA 215 2.18e+01 c.37.1.1 64810 1q1rA 431 2.20e+01 c.3.1.5 -6048 c.3.1.5 -6049 d.87.1.1 -10502 2frvA 264 2.20e+01 2frvA e.19.1.1 43303 1etu 394 2.21e+01 1efcA c.37.1.8 64737 1a99A 344 2.24e+01 1pot c.94.1.1 35812 1g01A 364 2.24e+01 7a3hA c.1.8.3 60161 1dtwB 342 2.26e+01 1qs0B c.36.1.7 31828 c.48.1.2 33102 1g0uL 241 2.26e+01 d.153.1.4 41894 1h49A 512 2.26e+01 c.1.8.4 83477 1k6aA 303 2.26e+01 c.1.8.3 72081 1fxmA 302 2.27e+01 1taxA 1a4uA 254 2.27e+01 1b16A c.2.1.2 29878 1pjcA 361 2.30e+01 1sayA c.2.1.4 30101 c.23.12.2 31361 1hu3A 260 2.43e+01 1hu3A unknown_sccs 19137 1e4mM 501 2.44e+01 1e70M c.1.8.4 59226 1olsB 342 2.48e+01 c.36.1.7 -6919 c.48.1.2 -7529 1d6zA 727 2.50e+01 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1jy1A 464 2.50e+01 d.136.1.3 67438 d.136.1.3 67439 1vgvA 384 2.51e+01 c.87.1.3 -8575 2nacA 393 2.55e+01 2nadA c.2.1.4 30088 c.23.12.1 31348 1thg 544 2.55e+01 1thg c.69.1.17 34763 1cs0C 1073 2.57e+01 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1frpA 335 2.57e+01 1frpA e.7.1.1 42875 1bxrA 1073 2.59e+01 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1g0cA 364 2.61e+01 7a3hA c.1.8.3 60165 1gw1A 376 2.61e+01 c.1.8.3 76361 1pjbA 361 2.66e+01 1sayA c.2.1.4 30103 c.23.12.2 31363 1hslA 238 2.69e+01 1lst c.94.1.1 35804 1pwmA 316 2.70e+01 c.1.7.1 -5232 1spuB 727 2.72e+01 1oacA b.30.2.1 24399 d.17.2.1 38025 d.17.2.1 38026 d.82.1.1 40012 1bglA 1023 2.72e+01 1bglA b.1.4.1 22097 b.1.4.1 22098 b.18.1.5 23734 b.30.5.1 24358 c.1.8.3 28857 1ads 315 2.74e+01 1frb c.1.7.1 28671 1qoxN 449 2.75e+01 1qoxN c.1.8.4 28978 1qwnA 1045 2.80e+01 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 2nadA 393 2.81e+01 2nadA c.2.1.4 30090 c.23.12.1 31350 1e70M 501 2.83e+01 1e70M c.1.8.4 28926 1svsA 353 2.83e+01 1iciA 256 2.84e+01 1iciA c.31.1.5 62266 1lj5A 379 2.84e+01 e.1.1.1 73928 1el3A 316 2.85e+01 1frb c.1.7.1 28672 1ik6A 369 2.85e+01 c.36.1.7 66174 c.48.1.2 66175 1ak1 310 2.86e+01 1ak1 c.92.1.1 35594 3mhtA 327 2.86e+01 6mhtA c.66.1.26 34234 1qo2A 241 2.88e+01 1qo2A c.1.2.1 28533 1kz8A 337 2.89e+01 e.7.1.1 77633 1i56A 130 2.91e+01 d.2.1.2 66033 1nuyA 337 2.94e+01 e.7.1.1 86213 1ka2A 499 2.96e+01 d.92.1.5 77305 1rkd 309 2.97e+01 1rkd c.72.1.1 34928 1f6dA 376 2.97e+01 1f6dA c.87.1.3 35467 1m2kA 249 3.02e+01 c.31.1.5 84754 1e6qM 501 3.06e+01 1e70M c.1.8.4 28920 1qc5A 192 3.08e+01 1aoxA c.62.1.1 34147 1riqA 465 3.14e+01 unknown_sccs -1295 d.104.1.1 -10769 1pt6A 213 3.17e+01 c.62.1.1 -7975 1l9vA 317 3.22e+01 d.13.2.1 73760 d.216.1.1 73761 1ni3A 392 3.23e+01 c.37.1.8 80531 d.15.10.2 80532 1cc1S 283 3.26e+01 2frvA e.19.1.1 43313 1tux 301 3.26e+01 1taxA c.1.8.3 28907 1geeA 261 3.27e+01 c.2.1.2 -5814 1zpdA 568 3.27e+01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1skyE 473 3.28e+01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1c3oE 1073 3.29e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1c3oA 1073 3.32e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1gcoA 261 3.36e+01 1ybvA c.2.1.2 29884 1c3oC 1073 3.38e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1b16A 254 3.44e+01 1b16A c.2.1.2 29875 1e2fA 215 3.46e+01 3tmkA c.37.1.1 59164 1e55A 512 3.47e+01 1e70M c.1.8.4 28934 1j96A 323 3.47e+01 c.1.7.1 71616 1j31A 262 3.49e+01 d.160.1.2 -11473 1cipA 353 3.50e+01 1cipA a.66.1.1 18210 c.37.1.8 32093 1gegA 256 3.54e+01 1ybvA c.2.1.2 29888 1edg 380 3.55e+01 1edg c.1.8.3 28807 1pnsB 234 3.56e+01 i.1.1.1 88169 1j5eB 256 3.59e+01 c.23.15.1 71543 1jqgA 433 3.61e+01 c.56.5.1 71791 d.58.3.1 71792 1f61A 429 3.63e+01 1dquA c.1.12.7 29319 1g2iA 166 3.68e+01 1g2iA c.23.16.2 31438 1i5sA 367 3.70e+01 1bg2 c.37.1.9 61822 1i6iA 366 3.71e+01 1bg2 c.37.1.9 61844 1kwkA 645 3.71e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1e3dA 266 3.74e+01 2frvA e.19.1.1 59188 1qdeA 224 3.77e+01 1qvaA c.37.1.19 32410 1fh9A 312 3.82e+01 1taxA c.1.8.3 28913 1v02A 565 3.89e+01 1pe0A 197 3.93e+01 c.23.16.2 88045 1nmoA 247 3.98e+01 unknown_sccs -8746 1i1wA 303 3.98e+01 c.1.8.3 76732