# List of top-scoring protein chains for t2k-100-30-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 2fnaA 357 6.50e-03 1o20A 427 3.17e-01 c.82.1.1 86556 1i6pA 220 4.62e-01 1ddzA c.53.2.1 61848 1o5oA 221 4.94e-01 c.61.1.1 92509 1z41A 338 4.96e-01 1jmeA 455 5.40e-01 a.104.1.1 66885 1qumA 285 5.50e-01 1qumA c.1.15.1 29393 2fqxA 318 6.18e-01 1kkoA 413 6.90e-01 c.1.11.2,d.54.1.1 68675,68676 1qtwA 285 7.01e-01 1qumA c.1.15.1 29392 1eguA 731 1.25e+00 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 2a33A 215 1.59e+00 1lfwA 470 1.72e+00 c.56.5.4,d.58.19.1 77942,77943 1kczA 413 1.89e+00 c.1.11.2,d.54.1.1 68451,68452 1i60A 278 1.95e+00 c.1.15.4 71118 1ep3A 311 1.98e+00 2dorA c.1.4.1 28597 1wpoA 256 2.01e+00 1lay b.57.1.1 27012 3pga1 337 2.04e+00 4pgaA 1p0kA 349 2.04e+00 c.1.4.1 87648 1to3A 304 2.71e+00 c.1.10.1 107161 1oa4A 222 2.90e+00 b.29.1.11 86731 1rcuA 195 3.21e+00 c.129.1.1 97295 1n7oA 721 3.36e+00 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1vjgA 218 3.46e+00 c.23.10.6 100810 1lxkA 721 3.57e+00 a.102.3.2,b.24.1.1,b.30.5.2 74331,74332,74333 4pgaA 337 3.62e+00 4pgaA c.88.1.1 35565 12asA 330 4.47e+00 12asA d.104.1.1 40783 1pz1A 333 4.51e+00 c.1.7.1 95390 2cbiA 594 4.62e+00 1w8kA 447 4.98e+00 1o58A 303 5.14e+00 c.79.1.1 92491 1pv1A 299 5.26e+00 1ispA 181 5.37e+00 c.69.1.18 76778 1yw4A 341 5.48e+00 1dr8B 344 5.89e+00 1cnzA c.77.1.1 35052 1zbqA 327 6.81e+00 1thfD 253 6.88e+00 1thfD c.1.2.1 28535 1xyzA 347 6.93e+00 1taxA c.1.8.3 28804 1lfpA 249 7.32e+00 e.39.1.1 73885 1xzoA 174 8.13e+00 1lay 256 8.35e+00 1lay b.57.1.1 27014 1tv8A 340 8.45e+00 c.1.28.3 107352 1b0zA 445 8.80e+00 2pgi c.80.1.2 35309 2pgi 445 8.80e+00 2pgi c.80.1.2 35308 1sfjA 238 9.44e+00 1w0mA 226 9.67e+00 c.1.1.1 109027 1tml 286 9.80e+00 1tml c.6.1.1 30656 2bs9A 503 1.03e+01 1c7qA 445 1.04e+01 2pgi c.80.1.2 35307 1svvA 359 1.04e+01 c.67.1.1 106054 2bwfA 77 1.08e+01 1j0aA 325 1.10e+01 c.79.1.1 83871 1hfbA 370 1.14e+01 c.1.10.4 76706 2c6qA 351 1.17e+01 2bodX 286 1.22e+01 1bw0A 416 1.29e+01 1bw0A c.67.1.1 34385 2bznA 351 1.31e+01 1aj8A 371 1.32e+01 1aj8A a.103.1.1 18900 1wpoB 256 1.32e+01 1lay b.57.1.1 27013 1qqcA 773 1.38e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1lrzA 426 1.38e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1m1zA 513 1.43e+01 c.26.2.1,d.153.1.1 78457,78458 1of8A 370 1.56e+01 c.1.10.4 92819 1hqkA 154 1.67e+01 c.16.1.1 65902 2a5vA 213 1.67e+01 1i6wA 181 1.69e+01 1i6wA c.69.1.18 61859 1k1xA 659 1.71e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1vaoA 560 1.71e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 1ipd 345 1.72e+01 1cnzA c.77.1.1 35038 1wh5A 80 1.74e+01 2bogX 286 1.75e+01 1j6oA 268 1.76e+01 c.1.9.12 77088 1lqtA 456 1.79e+01 c.3.1.1,c.4.1.1 74198,74199 1uhvA 500 1.81e+01 b.71.1.2,c.1.8.3 99402,99403 1gz6A 319 1.82e+01 c.2.1.2 76410 1fehA 574 1.83e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1goiA 499 1.83e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1bpe 335 1.87e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 18076,75815,75816 1ydhA 216 1.91e+01 1qltA 560 1.91e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1tahB 318 1.93e+01 1cvl c.69.1.18 34774 1wznA 252 1.98e+01 1cwyA 500 1.98e+01 1cwyA c.1.8.1 28789 1e6pA 499 2.02e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1lxtA 561 2.05e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35432,35433,35434,41309 1u4nA 310 2.07e+01 1uqrA 154 2.12e+01 c.23.13.1 99779 1fds 327 2.19e+01 1fds c.2.1.2 29838 1de4C 640 2.22e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1w1kA 560 2.24e+01 d.58.32.1,d.145.1.1 109059,109060 1w3iA 293 2.36e+01 c.1.10.1 109152 1sayA 361 2.40e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 1ym3A 215 2.41e+01 1h5qA 265 2.45e+01 1cydA c.2.1.2 60643 1cx8A 639 2.49e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17782,30763,33851 2b5dX 528 2.52e+01 1idm 343 2.59e+01 1cnzA c.77.1.1 35035 1jykA 254 2.60e+01 c.68.1.13 67458 1k7cA 233 2.62e+01 c.23.10.4 68267 3pmgA 561 2.64e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1o89A 345 2.65e+01 b.35.1.2,c.2.1.1 92644,92645 1jplA 171 2.66e+01 a.118.9.2 67027 1k47A 337 2.67e+01 d.14.1.5,d.58.26.4 72040,72041 1yb0A 159 2.72e+01 1bz4A 144 2.72e+01 1nfn a.24.1.1 16521 1mv8A 436 2.77e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 2bfgA 503 2.79e+01 1nfn 191 2.82e+01 1nfn a.24.1.1 16523 1vheA 373 2.84e+01 b.49.3.1,c.56.5.4 100669,100670 1tahA 318 2.85e+01 1cvl c.69.1.18 34775 1tt7A 330 2.87e+01 1sflA 238 2.90e+01 1e8gA 560 2.91e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 2acr 315 2.94e+01 1frb c.1.7.1 28674 1a27 289 2.96e+01 1fds c.2.1.2 29839 1zsqA 528 2.97e+01 1gpeA 587 3.01e+01 1gpeA c.3.1.2,d.16.1.1 30387,37951 1pjbA 361 3.01e+01 1sayA c.2.1.4,c.23.12.2 30103,31363 1eswA 500 3.04e+01 1cwyA c.1.8.1 59500 1f1eA 154 3.07e+01 a.22.1.2 64927 1az1 315 3.11e+01 1frb c.1.7.1 28677 2fyxA 143 3.15e+01 1fdt 327 3.16e+01 1fds c.2.1.2 29841 1yxyA 234 3.18e+01 1xp3A 307 3.19e+01 1b0aA 288 3.26e+01 1a4iA c.2.1.7,c.58.1.2 30286,33934 1mjhB 162 3.29e+01 1mjhA c.26.2.4 31640 1el3A 316 3.33e+01 1frb c.1.7.1 28672 1lw3A 657 3.37e+01 b.55.1.8,c.45.1.3 91152,91153 1xaa 345 3.40e+01 1cnzA c.77.1.1 35033 1vh7A 265 3.41e+01 c.1.2.1 100646 1yarA 233 3.41e+01 1ads 315 3.43e+01 1frb c.1.7.1 28671 1ufoA 238 3.45e+01 c.69.1.27 99344 1lpe 144 3.51e+01 1nfn a.24.1.1 16524 1y10A 407 3.52e+01 1pjcA 361 3.55e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1v5vA 401 3.55e+01 1hg3A 225 3.69e+01 1hg3A c.1.1.1 61025 1f89A 291 3.69e+01 d.160.1.1 64988 1deoA 233 3.73e+01 1deoA c.23.10.4 31345 1uroA 367 3.74e+01 1uroA c.1.22.1 29675 1kgnA 329 3.79e+01 a.25.1.2 68584 2bijA 305 3.79e+01 2akzA 439 3.82e+01 1r3sA 367 3.91e+01 c.1.22.1 96963 1poxA 585 3.92e+01 1poxA c.31.1.3,c.36.1.5,c.36.1.9 31731,31793,31794 1us0A 316 3.93e+01 c.1.7.1 99850 1gzgA 337 4.03e+01 c.1.10.3 70805 1c8bA 371 4.14e+01 1c8bA c.56.1.2 59082 1mucA 373 4.16e+01 1mucA c.1.11.2,d.54.1.1 29236,38880 1bu7A 455 4.21e+01 1bu7A a.104.1.1 18937 1mqdA 261 4.22e+01 c.94.1.1 85049 1oglA 283 4.25e+01 a.204.1.1 92922 1xszA 356 4.28e+01 1nddD 76 4.34e+01 1ubi d.15.1.1 37602 1lt8A 406 4.35e+01 c.1.26.1 78186 1cx8B 639 4.36e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17783,30764,33852 1j0dA 341 4.40e+01 c.79.1.1 83902 1ki9A 192 4.40e+01 c.37.1.1 84404 2f5gA 133 4.44e+01 2b18A 164 4.50e+01 1b9zA 516 4.62e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 1e15A 499 4.63e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 27810,29006,38440 1pdo 135 4.67e+01 1pdo c.54.1.1 33376 1vypX 364 4.67e+01 c.1.4.1 108905 1umkA 275 4.71e+01 1luaA 287 4.75e+01 c.2.1.7,c.58.1.4 78216,78217 1agx 331 4.79e+01 4pgaA c.88.1.1 35564 2bkrB 77 4.80e+01 1bt0A 76 4.82e+01 1ubi d.15.1.1 37607 2f5xA 312 4.88e+01 1mqiA 263 4.88e+01 c.94.1.1 91398 1ys1X 320 4.89e+01 2ez9A 603 4.90e+01 1te6A 439 4.98e+01 c.1.11.1,d.54.1.1 106797,106798 1tzjA 338 4.99e+01 1m5eA 263 5.03e+01 c.94.1.1 78642 1nr6A 473 5.09e+01 a.104.1.1 92085 1uxy 340 5.14e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1jgtA 513 5.16e+01 c.26.2.1,d.153.1.1 66684,66685 1u6bA 98 5.17e+01 d.58.7.1 107703 1fcjA 322 5.23e+01 1oasA c.79.1.1 35289 1vekA 84 5.25e+01 5bcaA 516 5.25e+01 1b9zA b.3.1.1,c.1.8.1 22529,28799 2bl1A 172 5.29e+01 1nddA 76 5.31e+01 1ubi d.15.1.1 37599 2bynA 227 5.33e+01 1o9iA 266 5.36e+01 a.25.1.3 92671 1mzhA 225 5.36e+01 c.1.10.1 79698 1xkyA 301 5.52e+01 1jtvA 327 5.58e+01 c.2.1.2 84230 1r8gA 372 5.60e+01 d.128.1.3 104845 2bmhA 455 5.60e+01 1bu7A a.104.1.1 18941 1b33A 160 5.60e+01 1qgwC a.1.1.3 15649 2bvyA 475 5.62e+01 1n1fA 159 5.63e+01 a.26.1.3 79803 1sb8A 352 5.63e+01 c.2.1.2 105410 1audA 101 5.70e+01 1urnA d.58.7.1 39156 1nbaA 264 5.81e+01 1nbaA c.33.1.3 31753 2agtA 319 5.82e+01 1c0pA 363 5.86e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2ciaA 102 5.93e+01 1ynuA 473 5.94e+01 7a3hA 303 5.96e+01 7a3hA c.1.8.3 28817 2anuA 255 6.03e+01 1eq1A 166 6.06e+01 a.63.1.1 64910 1b4kA 337 6.10e+01 1b4kA c.1.10.3 29184 1brlA 355 6.21e+01 1lucA c.1.16.1 29553 2bleA 367 6.22e+01 1uuyA 167 6.26e+01 c.57.1.1 108059 3pchM 238 6.26e+01 3pchM b.3.6.1 22748 1xvxA 312 6.30e+01 2f20A 240 6.35e+01 1f2dA 341 6.41e+01 1f2dA c.79.1.1 35298 1othA 321 6.44e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1rhcA 330 6.50e+01 c.1.16.3 97468 1m5dA 263 6.54e+01 c.94.1.1 78641 1km4A 247 6.59e+01 c.1.2.3 72740 1jkvA 266 6.76e+01 a.25.1.3 71719 1vhwA 253 6.77e+01 c.56.2.1 100706 3pcgM 238 6.80e+01 3pchM b.3.6.1 22742 1hkvA 453 6.80e+01 b.49.2.3,c.1.6.1 83559,83560 2b7kA 200 6.82e+01 2bypA 214 6.89e+01 2b8nA 429 7.05e+01 1pwmA 316 7.07e+01 c.1.7.1 95231 1d0iA 156 7.14e+01 2dhqA c.23.13.1 31383 1tdpA 111 7.24e+01 a.29.8.1 106781 1pj5A 830 7.27e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1inp 400 7.28e+01 1inp e.7.1.1 42972 1hyeA 313 7.29e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1dt6A 473 7.31e+01 1dt6A a.104.1.1 18977 1uf5A 303 7.34e+01 d.160.1.2 107808 2bghA 421 7.35e+01 1ra0A 430 7.37e+01 1cvl 319 7.44e+01 1cvl c.69.1.18 34786 1itcA 516 7.49e+01 b.3.1.1,c.1.8.1 83705,83706 1tz9A 367 7.66e+01 c.1.15.6 107466 1r3nA 462 7.67e+01 c.56.5.4,d.58.19.1 96945,96946 1hf8A 289 7.69e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1vjtA 483 7.71e+01 c.2.1.5,d.162.1.2 100833,100834 1hg5A 289 7.87e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1erzA 303 7.88e+01 1erzA d.160.1.2 59498 1i2oA 316 7.91e+01 1onrA c.1.10.1 61574 1z2lA 423 7.92e+01 1b8gA 429 7.92e+01 1b8gA c.67.1.4 34499 1n6bA 473 8.08e+01 a.104.1.1 85359 1odzA 386 8.11e+01 c.1.8.3 86889 1vemA 516 8.14e+01 1o0uA 429 8.14e+01 c.118.1.1 80743 1wa8A 99 8.16e+01 1ax4A 467 8.25e+01 1ax4A c.67.1.2 34391 1or3A 165 8.25e+01 1nfn a.24.1.1 16522 1yzfA 195 8.26e+01 1vbuA 328 8.29e+01 1kkeA 210 8.29e+01 b.21.1.2,b.83.1.2 68669,68670 2aexA 346 8.31e+01 1nu4A 97 8.34e+01 d.58.7.1 80731 1x1nA 524 8.36e+01 2scuA 288 8.38e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1c93A 265 8.46e+01 2ebn c.1.8.5 28998 1nxuA 333 8.47e+01 c.122.1.1 86389 2ahqA 76 8.61e+01 1cx0A 95 8.61e+01 1urnA d.58.7.1 39158 1lu9A 287 8.67e+01 c.2.1.7,c.58.1.4 78210,78211 1tgoA 773 8.74e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1pmaA 233 8.81e+01 1pmaA d.153.1.4 41918 1ndh 272 8.88e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1afwA 393 8.90e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 1a5z 319 8.91e+01 1ceqA c.2.1.5,d.162.1.1 30181,42148 1v9nA 360 8.94e+01