# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 2u1a 88 5.01e-01 2u1a d.58.7.1 39164 1b44D 129 1.86e+00 3chbD b.40.2.1 24960 1oneA 436 1.93e+00 4enl c.1.11.1,d.54.1.1 29200,38844 4enl 436 2.15e+00 4enl c.1.11.1,d.54.1.1 29202,38846 1d2eA 397 2.17e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 3chbD 104 2.30e+00 3chbD b.40.2.1 24970 1kid 203 2.41e+00 1derA c.8.5.1 30771 2al2A 436 2.45e+00 1tl0D 103 2.95e+00 2al1A 436 3.06e+00 1ww9A 392 3.24e+00 1ksyA 154 4.09e+00 d.89.1.2 72948 2fbiA 142 4.13e+00 1oz9A 150 4.45e+00 d.92.1.15 93808 1ejeA 192 4.53e+00 1ejeA b.45.1.2 25757 2oneA 436 5.03e+00 4enl c.1.11.1,d.54.1.1 29203,38847 1qo0D 196 5.32e+00 1qo0D c.23.1.3 31125 1ymqA 261 5.42e+00 1o2dA 371 5.99e+00 e.22.1.2 86591 1yhpA 212 6.24e+00 2bzlA 325 7.44e+00 1w1wA 430 7.82e+00 2akzA 439 8.50e+00 2gf9A 189 8.53e+00 1te6A 439 8.57e+00 c.1.11.1,d.54.1.1 106797,106798 1rm4A 337 9.16e+00 c.2.1.3,d.81.1.1 105000,105001 1b6rA 355 9.29e+00 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28241,31648,41493 1b6sA 355 9.41e+00 1b6rA b.84.2.1,c.30.1.1,d.142.1.2 28242,31649,41494 1jb7B 260 9.48e+00 1otcB b.40.4.3 62839 2fcr 173 9.62e+00 1rcf c.23.5.1 31151 1vggA 161 9.62e+00 1i8tA 367 1.06e+01 c.4.1.3,d.16.1.7 66094,66095 1e5eA 404 1.08e+01 1ibjA c.67.1.3 59265 1exmA 405 1.10e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1bcpB 199 1.13e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 2c78A 405 1.16e+01 1g3qA 237 1.21e+01 1hyqA c.37.1.10 60237 1eft 405 1.22e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1pdz 434 1.29e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1fmcA 255 1.30e+01 1cydA c.2.1.2 29856 1f08A 148 1.31e+01 1f08A d.89.1.2 59564 1ursA 402 1.45e+01 c.94.1.1 99833 1sviA 195 1.46e+01 c.37.1.8 106048 1q7zA 566 1.50e+01 c.1.21.2,c.1.26.1 96090,96091 1a6q 382 1.56e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1wwiA 148 1.56e+01 1kblA 873 1.57e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2d8dA 90 1.58e+01 1wstA 417 1.60e+01 2f46A 156 1.67e+01 1rzsA 61 1.67e+01 a.35.1.2 105139 1vp4A 425 1.68e+01 1q0pA 223 1.70e+01 c.62.1.1 95507 1gegA 256 1.71e+01 1ybvA c.2.1.2 29888 1kv7A 488 1.73e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1xmxA 385 1.78e+01 1ha3A 405 1.95e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1lvwA 295 2.09e+01 c.68.1.6 84723 1tbd 134 2.10e+01 2tbd d.89.1.1 40240 1ri7A 171 2.11e+01 a.4.5.32,d.58.4.2 97504,97505 1kafA 108 2.12e+01 d.199.1.1 68372 1lr0A 129 2.26e+01 d.212.1.1 74213 1aqzA 149 2.29e+01 1aqzA d.1.1.3 36238 1u1hA 765 2.36e+01 c.1.22.2,c.1.22.2 107580,107581 3rabA 169 2.37e+01 1ctqA c.37.1.8 32018 1vjeA 166 2.40e+01 d.185.1.2 100807 1d3uB 201 2.43e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1nvmA 345 2.46e+01 a.5.7.1,c.1.10.5 86249,86250 1iyeA 309 2.47e+01 e.17.1.1 83786 1innA 166 2.48e+01 1j98A d.185.1.2 62608 1rgyA 360 2.53e+01 e.3.1.1 97456 2cuaA 135 2.53e+01 2cuaA b.6.1.2 23039 1ehkB 168 2.80e+01 2cuaA b.6.1.2,f.17.2.1 23041,43625 3ullA 132 2.81e+01 3ullA b.40.4.3 25282 1xfsA 178 2.83e+01 d.129.3.5 109589 2b0jA 358 2.88e+01 1jmtA 104 2.97e+01 d.58.7.3 63180 1pot 325 2.99e+01 1pot c.94.1.1 35807 1yj7A 171 3.03e+01 1qopA 268 3.05e+01 2tysA c.1.2.4 28570 1a5y 330 3.08e+01 1pty c.45.1.2 32673 1aisB 200 3.10e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1g0rA 293 3.14e+01 1g0rA c.68.1.6 34532 1g7fA 298 3.17e+01 1pty c.45.1.2 60330 1l8aA 886 3.19e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1w5fA 353 3.19e+01 1fsz 372 3.25e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 3bifA 468 3.25e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1x7oA 287 3.29e+01 1tdj 514 3.33e+01 1tdj c.79.1.1,d.58.18.2,d.58.18.2 35297,39356,39357 1fnmA 691 3.37e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 25709,32144,37546,39302,39303 2f96A 224 3.39e+01 1nrjB 218 3.40e+01 c.37.1.8 86125 1wsrA 375 3.42e+01 2a5dA 175 3.48e+01 1eg9A 449 3.50e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1zuhA 168 3.57e+01 1b7eA 420 3.57e+01 1b7eA c.55.3.4 33680 1h8lA 380 3.58e+01 b.3.2.1,c.56.5.1 65737,65738 1aipE 405 3.59e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1zzkA 82 3.69e+01 1qtrA 317 3.69e+01 1qtrA c.69.1.7 34660 1o7nA 449 3.70e+01 b.33.1.2,d.129.3.3 81162,81163 1lci 550 3.77e+01 1lci e.23.1.1 43349 2h2tB 175 3.78e+01 1bksA 268 3.79e+01 2tysA c.1.2.4 28585 1pa1A 310 3.83e+01 c.45.1.2 94404 2tysA 268 3.84e+01 2tysA c.1.2.4 28572 1u1jA 765 3.84e+01 c.1.22.2,c.1.22.2 107590,107591 2bgzA 299 3.95e+01 2wsyA 268 3.96e+01 2tysA c.1.2.4 28588 1ndoA 449 3.97e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 2as9A 210 4.00e+01 1qmuA 380 4.00e+01 1qmuA b.3.2.1,c.56.5.1 22534,33827 1ryiA 382 4.03e+01 1o6yA 299 4.05e+01 d.144.1.7 81106 1dqnA 230 4.11e+01 1dqnA c.61.1.1 34067 1ecl 597 4.14e+01 1ecl e.10.1.1 43238 1eeoA 321 4.15e+01 1pty c.45.1.2 32655 2tbd 134 4.15e+01 2tbd d.89.1.1 40241 1aipA 405 4.20e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1asyA 490 4.21e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1slqA 278 4.22e+01 f.47.1.1 105719 1pt6A 213 4.26e+01 c.62.1.1 95091 1z3eA 132 4.27e+01 1uwvA 433 4.28e+01 b.40.4.12,c.66.1.40 100128,100129 1dqpA 230 4.31e+01 1dqnA c.61.1.1 34069 1ng4A 390 4.33e+01 c.3.1.2,d.16.1.3 85666,85667 1wvqA 167 4.35e+01 2fbmA 291 4.36e+01 2bolA 314 4.37e+01 1p4xA 250 4.37e+01 a.4.5.28,a.4.5.28 87784,87785 1uirA 314 4.39e+01 c.66.1.17 99429 2f71A 298 4.42e+01 1dik 874 4.42e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1nfn 191 4.44e+01 1nfn a.24.1.1 16523 1j5kA 89 4.46e+01 d.51.1.1 71565 2dri 271 4.47e+01 2dri c.93.1.1 35637 1geqA 248 4.52e+01 2tysA c.1.2.4 28589 1xkpC 143 4.53e+01 1wi9A 72 4.55e+01 1wleA 501 4.55e+01 2hnp 321 4.57e+01 1pty c.45.1.2 32678 2a3nA 355 4.64e+01 1gnhA 206 4.67e+01 1sacA b.29.1.5 24252 1q6oA 216 4.73e+01 c.1.2.3 95986 1kv8A 216 4.74e+01 c.1.2.3 73054 1e9rA 437 4.75e+01 c.37.1.11 64827 1cl2A 395 4.79e+01 1cl2A c.67.1.3 34397 2fckA 181 4.80e+01 2fsqA 243 4.95e+01 1g8lA 411 5.00e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1oi7A 288 5.00e+01 c.2.1.8,c.23.4.1 87049,87050 1q9uA 130 5.02e+01 d.129.7.1 96314 1yacA 208 5.04e+01 1yacA c.33.1.3 31757 2ch8A 201 5.04e+01 1l7aA 318 5.05e+01 c.69.1.25 77772 2cu1A 103 5.10e+01 1xn7A 78 5.11e+01 1wlgA 299 5.11e+01 1dar 691 5.13e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1u4cA 349 5.19e+01 b.69.4.2 107666 1nwwA 149 5.20e+01 d.17.4.8 86306 1q77A 138 5.20e+01 c.26.2.4 96023 2bifA 469 5.24e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1f3iA 481 5.28e+01 1b7eA 1fzaB 328 5.28e+01 3fib d.171.1.1,h.1.8.1 42480,45621 2ffuA 501 5.30e+01 1ujnA 348 5.32e+01 e.22.1.1 99460 1fc6A 388 5.36e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1ybvA 283 5.36e+01 1ybvA c.2.1.2 29948 1apxA 249 5.53e+01 1ryc a.93.1.1 18669 1wggA 96 5.53e+01 1f52A 468 5.54e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1jfbA 404 5.65e+01 a.104.1.1 66624 1pty 321 5.66e+01 1pty c.45.1.2 32656 2f5gA 133 5.70e+01 1g0oA 283 5.72e+01 1ybvA c.2.1.2 60181 2cw5A 255 5.82e+01 1f24A 402 5.84e+01 1rom a.104.1.1 18953 2c9aA 259 5.87e+01 1qc5A 192 5.87e+01 1aoxA c.62.1.1 34147 1cmnA 402 5.88e+01 1rom a.104.1.1 18958 1lvaA 258 5.89e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1mhnA 59 5.92e+01 b.34.9.1 84964 1fxoA 293 5.94e+01 1g0rA c.68.1.6 34524 1kk1A 410 5.96e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1m41A 380 6.12e+01 c.1.16.4 78595 1djrD 103 6.21e+01 3chbD b.40.2.1 24865 2fw2A 260 6.23e+01 1yfqA 342 6.24e+01 1ooeA 236 6.25e+01 c.2.1.2 87196 2arhA 203 6.29e+01 1g5vA 88 6.33e+01 1g5vA b.34.9.1 60292 1zejA 293 6.33e+01 1mw9X 592 6.41e+01 e.10.1.1 91480 1fr1A 361 6.42e+01 1gceA e.3.1.1 42734 1edoA 244 6.43e+01 1ybvA c.2.1.2 29896 1vprA 374 6.47e+01 1qu9A 128 6.52e+01 1qu9A d.79.1.1 39755 1qu9C 128 6.52e+01 1qu9A d.79.1.1 39757 1ssn 136 6.57e+01 2sak d.15.5.1 37720 1tin 69 6.60e+01 2sniI d.40.1.1 38580 1k2fA 190 6.61e+01 b.8.1.2 68054 1pj5A 830 6.62e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1udxA 416 6.63e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1eguA 731 6.64e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1frvB 536 6.69e+01 1h2rL e.18.1.1 43296 2fiqA 420 6.74e+01 1wkoA 180 6.78e+01 1ble 163 6.83e+01 1ble c.38.1.1 32475 1nkiA 135 6.85e+01 d.32.1.2 91941 1muhA 481 6.86e+01 c.55.3.4 79485 1c9bA 207 6.94e+01 1tfb a.74.1.2,a.74.1.2 18372,18373 1e2xA 243 7.02e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1xccA 220 7.10e+01 1geeA 261 7.15e+01 c.2.1.2 90509 1a6dA 545 7.16e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 2liv 344 7.17e+01 2liv c.93.1.1 35708 1k0eA 453 7.19e+01 d.161.1.1 67938 1wdiA 345 7.24e+01 1xhbA 472 7.27e+01 1a9nB 96 7.32e+01 1urnA d.58.7.1 39165 1aszB 490 7.36e+01 1b8aA b.40.4.1,d.104.1.1 25241,40762 1lt5D 103 7.36e+01 3chbD b.40.2.1 24875 1pg4A 652 7.36e+01 e.23.1.1 88067 2atzA 180 7.44e+01 1wxaA 116 7.47e+01 1gcoA 261 7.53e+01 1ybvA c.2.1.2 29884 1aqzB 149 7.61e+01 1aqzA d.1.1.3 36239 1bd3A 243 7.69e+01 1bd3A c.61.1.1 34098 1zip 217 7.73e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1w0pA 781 7.73e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1bif 469 7.81e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1ykfA 352 7.84e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1e8cA 498 7.88e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1tc6A 236 7.93e+01 d.122.1.1 106756 1b7gO 340 7.99e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1sg4A 260 8.08e+01 1o5iA 249 8.10e+01 c.2.1.2 92499 1kfcA 268 8.13e+01 c.1.2.4 77371 1wmiB 67 8.16e+01 2anxA 146 8.17e+01 1oq9A 363 8.19e+01 a.25.1.2 87257 1oeyJ 107 8.19e+01 d.15.2.2 92804 1efiD 103 8.22e+01 3chbD b.40.2.1 24870 1musA 477 8.26e+01 c.55.3.4 79494 2bynA 227 8.32e+01 1j27A 102 8.39e+01 d.58.50.1 90778 1aax 321 8.43e+01 1pty c.45.1.2 32657 2ae2A 260 8.46e+01 1bdb c.2.1.2 29945 1c20A 128 8.48e+01 1c20A a.4.3.1 16079 2bhvA 246 8.49e+01 2bz1A 196 8.66e+01 1jzuA 157 8.73e+01 b.60.1.1 84271 1dzlA 505 8.73e+01 1dzlA b.121.6.1 23586 1jflA 228 8.76e+01 c.78.2.1,c.78.2.1 71656,71657 1wi1A 126 8.76e+01 1w78A 422 8.79e+01 1sa3A 262 8.88e+01 c.52.1.23 105400 2cvlA 124 8.93e+01 1taq 832 8.94e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1aoxA 203 8.99e+01 1aoxA c.62.1.1 34151