# List of top-scoring protein chains for t2k-100-30-str2 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 1mkmA 249 5.75e-04 a.4.5.33 79242 d.110.2.2 79243 1hqcA 324 1.07e-02 1hqcA a.4.5.11 16127 c.37.1.20 32424 1in4A 334 1.23e-01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1vi9A 299 1.71e-01 1in6A 334 1.73e-01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1rvkA 382 1.82e-01 1jdfA 447 1.83e-01 c.1.11.2 62897 d.54.1.1 62898 1ec7A 446 2.39e-01 1bqg c.1.11.2 29218 d.54.1.1 38862 1gqyA 475 5.41e-01 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1llfA 534 5.90e-01 c.69.1.17 78094 1vjpA 394 6.41e-01 1bqg 451 7.24e-01 1bqg c.1.11.2 29217 d.54.1.1 38861 1mdl 359 8.51e-01 2mnr c.1.11.2 29247 d.54.1.1 38891 1crl 534 9.37e-01 1thg c.69.1.17 34765 1cleA 534 9.49e-01 1thg c.69.1.17 34771 1p3dA 475 1.10e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1q48A 134 1.46e+00 1g0oA 283 1.66e+00 1ybvA c.2.1.2 60181 1jq5A 370 1.77e+00 e.22.1.2 67084 2mnr 357 1.94e+00 2mnr c.1.11.2 29245 d.54.1.1 38889 1exqA 154 1.97e+00 1b9dA c.55.3.2 33646 1b0uA 262 2.06e+00 1b0uA c.37.1.12 32370 1tml 286 2.08e+00 1tml c.6.1.1 30656 1j54A 186 2.09e+00 c.55.3.5 77077 1ig8A 486 2.14e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1gg4A 452 2.29e+00 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1lea 84 2.42e+00 1lea a.4.5.2 16085 1a27 289 2.44e+00 1fds c.2.1.2 29839 1xgsA 295 2.45e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1ybvA 283 2.66e+00 1ybvA c.2.1.2 29948 1jhfA 202 2.69e+00 a.4.5.2 63057 b.87.1.1 63058 1j6uA 469 2.74e+00 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1j5yA 187 2.82e+00 a.4.5.1 71592 d.94.2.1 71593 1lshB 319 2.83e+00 f.7.1.1 74245 1ihrA 76 2.91e+00 1ihrA d.212.1.2 62392 1fdt 327 3.05e+00 1fds c.2.1.2 29841 1itg 166 3.20e+00 1b9dA c.55.3.2 33661 1qmhA 347 3.67e+00 1qmhA c.47.2.1 33082 d.68.2.1 39568 1khiA 176 3.73e+00 b.34.5.2 77408 b.40.4.5 77409 1bj7 156 3.75e+00 1bj7 b.60.1.1 27113 1az9 457 3.75e+00 1az9 c.55.2.1 33547 d.127.1.1 41164 1c0pA 363 3.81e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 4xiaA 393 3.88e+00 4xis c.1.15.3 29439 1ad3A 452 3.90e+00 1ad3A c.82.1.1 35335 1i5rA 327 4.03e+00 c.2.1.2 83668 1khdA 345 4.22e+00 a.46.2.1 77400 c.27.1.1 77401 1i6iA 366 4.36e+00 1bg2 c.37.1.9 61844 3xis 387 4.70e+00 4xis c.1.15.3 29423 1qi6A 475 4.72e+00 1euhA c.82.1.1 35373 1bupA 386 5.31e+00 1ba1 c.55.1.1 33377 c.55.1.1 33378 1nu5A 370 5.38e+00 1dkzA 219 5.42e+00 1dkzA e.20.1.1 43314 1jtvA 327 5.45e+00 c.2.1.2 84230 1fds 327 5.47e+00 1fds c.2.1.2 29838 1gw9A 388 5.48e+00 c.1.15.3 70658 2bbvA 363 5.57e+00 2bbvA b.121.4.4 23323 1ubkL 534 5.59e+00 e.18.1.1 88422 1a16 440 5.66e+00 1az9 c.55.2.1 33548 d.127.1.1 41165 2hsdA 253 5.70e+00 1e6wA c.2.1.2 29866 1mnzA 388 5.83e+00 c.1.15.3 79328 1xis 387 5.84e+00 4xis c.1.15.3 29422 4xis 387 5.84e+00 4xis c.1.15.3 29421 1frvB 536 5.92e+00 1h2rL e.18.1.1 43296 1h2rL 534 5.93e+00 1h2rL e.18.1.1 43298 1h2aL 567 5.99e+00 1h2rL e.18.1.1 43299 1ba1 386 6.11e+00 1ba1 c.55.1.1 33387 c.55.1.1 33388 1bl3A 160 6.51e+00 1b9dA c.55.3.2 33655 1i1gA 141 6.59e+00 a.4.5.32 65982 d.58.4.2 65983 1hdcA 253 6.77e+00 1e6wA c.2.1.2 29862 1kczA 413 6.88e+00 c.1.11.2 68451 d.54.1.1 68452 1gpmA 525 6.89e+00 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1okrA 123 7.13e+00 1dkxA 219 7.15e+00 1dkzA e.20.1.1 43315 1lpuA 332 7.30e+00 d.144.1.7 74177 1a8d 452 7.57e+00 1a8d b.29.1.6 24262 b.42.4.2 25607 1diwA 441 7.81e+00 1a8d b.29.1.6 24264 b.42.4.2 25609 1uteA 313 8.03e+00 1uteA d.159.1.1 42078 1nv8A 284 8.04e+00 c.66.1.30 86224 1s1dA 331 8.23e+00 1b9dA 163 8.25e+00 1b9dA c.55.3.2 33649 1nbwA 607 8.64e+00 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1jpmA 366 8.72e+00 c.1.11.2 67031 d.54.1.1 67032 1hyvA 166 8.79e+00 1b9dA c.55.3.2 61424 1om1A 332 8.92e+00 1a8q 274 9.10e+00 1brt c.69.1.12 34702 1geeA 261 9.21e+00 1gcoA 261 9.25e+00 1ybvA c.2.1.2 29884 2bbvC 363 9.26e+00 2bbvA b.121.4.4 23325 1je8A 82 9.31e+00 a.4.6.2 77108 1lp4A 332 9.39e+00 d.144.1.7 74170 1ekeA 230 9.50e+00 1ekeA c.55.3.1 33572 1o5zA 442 9.55e+00 1fkmA 396 9.65e+00 1fkmA a.69.2.1 18315 a.69.2.1 18316 3il8 72 9.75e+00 1tvxA d.9.1.1 37356 2xis 387 9.79e+00 4xis c.1.15.3 29427 1a0cA 438 9.79e+00 1a0cA c.1.15.3 29529 1floA 422 9.90e+00 1floA a.60.9.1 18106 d.163.1.1 42166 1mzbA 136 1.01e+01 1kzhA 555 1.03e+01 c.89.1.1 73361 1jnrB 150 1.05e+01 d.58.1.5 66969 1thg 544 1.06e+01 1thg c.69.1.17 34763 1kay 381 1.06e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1e4fT 419 1.10e+01 1e4fT c.55.1.1 33453 c.55.1.1 33454 1lwyA 324 1.12e+01 a.96.1.3 78285 d.129.1.2 78286 1m2rA 327 1.14e+01 d.144.1.7 84760 1byqA 228 1.22e+01 1yer d.122.1.1 41100 2phlA 397 1.22e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1cqwA 295 1.25e+01 1b6g c.69.1.8 34679 1bn7A 294 1.30e+01 1bn6A c.69.1.8 34677 1m8uA 173 1.31e+01 2ak3A 226 1.33e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1euhA 475 1.35e+01 1euhA c.82.1.1 35369 1o08A 221 1.37e+01 c.108.1.6 86525 1bjaA 95 1.38e+01 1bjaA a.4.5.9 16122 1bn6A 294 1.39e+01 1bn6A c.69.1.8 34678 1gdeA 389 1.41e+01 c.67.1.1 60456 1ojrA 274 1.42e+01 1gln 468 1.44e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1gd9A 389 1.47e+01 c.67.1.1 60454 1m3qA 317 1.48e+01 1fsz 372 1.48e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1moq 368 1.49e+01 1moq c.80.1.1 35302 1pmaA 233 1.52e+01 1pmaA d.153.1.4 41918 1ebmA 317 1.52e+01 1ebmA a.96.1.3 18751 d.129.1.2 41300 1g6oA 330 1.52e+01 1g6oA c.37.1.11 32430 1e3oC 160 1.59e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1n62C 288 1.60e+01 d.87.2.1 80094 d.145.1.3 80095 1hyeA 313 1.60e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1mopA 300 1.63e+01 c.26.1.4 85035 1i7dA 659 1.63e+01 1d6mA e.10.1.1 61886 1l9gA 192 1.64e+01 c.18.1.2 84568 1n2eA 300 1.65e+01 c.26.1.4 85268 1budA 197 1.65e+01 1atlA d.92.1.9 40328 1s3jA 155 1.65e+01 1qj2C 285 1.67e+01 1qj2C 1elpA 173 1.68e+01 1amm b.11.1.1 23596 b.11.1.1 23597 1fgs 428 1.69e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1h61A 364 1.70e+01 1oyc c.1.4.1 60657 2itg 163 1.71e+01 1b9dA c.55.3.2 33669 1k8kA 418 1.72e+01 c.55.1.1 68305 c.55.1.1 68306 1e2xA 243 1.75e+01 1e2xA a.4.5.6 16113 a.78.1.1 18443 1oapA 109 1.76e+01 1rkd 309 1.76e+01 1rkd c.72.1.1 34928 1lv9A 77 1.76e+01 d.9.1.1 78233 1gm5A 780 1.76e+01 a.29.4.1 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1iw0A 215 1.77e+01 a.132.1.1 83720 1uzbA 516 1.78e+01 1gr5A 547 1.79e+01 i.16.1.1 65478 2dpg 485 1.82e+01 1dpgA c.2.1.3 30076 d.81.1.5 39991 1gt7A 274 1.84e+01 c.74.1.1 70398 1e3mA 800 1.86e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1s1pA 331 1.89e+01 1d0hA 469 1.89e+01 1a8d b.29.1.6 24265 b.42.4.2 25610 1obpA 159 1.90e+01 1obpA b.60.1.1 27092 1gvoA 364 1.91e+01 c.1.4.1 76357 1lfwA 470 1.92e+01 c.56.5.4 77942 d.58.19.1 77943 1rlaA 323 1.95e+01 1d3vA c.42.1.1 32561 1tadA 324 1.95e+01 1cipA a.66.1.1 18194 c.37.1.8 32077 1d4xG 126 1.97e+01 1d0nA d.109.1.1 59109 1sbxA 106 1.97e+01 1tag 324 2.01e+01 1cipA a.66.1.1 18197 c.37.1.8 32080 1hxhA 253 2.01e+01 c.2.1.2 76725 1othA 321 2.04e+01 1othA c.78.1.1 35260 c.78.1.1 35261 1hw1A 239 2.04e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1qe5A 266 2.05e+01 1b8oA c.56.2.1 33784 1q1hA 110 2.08e+01 1yagG 125 2.09e+01 1d0nA d.109.1.1 40846 1hn2A 159 2.09e+01 b.60.1.1 65890 1nm1G 125 2.09e+01 d.109.1.1 80653 1gt1A 159 2.09e+01 1ixmB 192 2.10e+01 1ixmA d.123.1.1 41115 1itkA 731 2.11e+01 a.93.1.3 71417 a.93.1.3 71418 1a3yA 149 2.11e+01 1obpA b.60.1.1 27110 1squA 155 2.11e+01 1o7zA 77 2.12e+01 d.9.1.1 86660 1a4iA 301 2.13e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1kvkA 395 2.16e+01 d.14.1.5 73060 d.58.26.3 73061 6paxA 133 2.18e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1vypX 364 2.20e+01 2frvB 536 2.21e+01 1h2rL e.18.1.1 43291 1e2o 233 2.25e+01 1eaf c.43.1.1 32631 1sspE 223 2.27e+01 3eugA c.18.1.1 31009 1f60B 94 2.30e+01 1b64 d.58.12.1 39307 1fd9A 213 2.32e+01 1fd9A d.26.1.1 59771 1r5qA 102 2.32e+01 1ru3A 732 2.34e+01 1diaA 306 2.35e+01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1j7dA 145 2.37e+01 1jatB d.20.1.1 62680 1mwvA 714 2.40e+01 a.93.1.3 85161 a.93.1.3 85162 1bcpC 199 2.41e+01 1bcpB b.40.2.1 25121 d.169.1.2 42430 1knwA 425 2.41e+01 1fiuA 286 2.46e+01 1fiuA c.52.1.10 33317 1aj8A 371 2.48e+01 1aj8A a.103.1.1 18900 1lgyA 269 2.48e+01 3tgl c.69.1.17 34758 1zpdA 568 2.53e+01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1dmgA 225 2.55e+01 1dmgA c.22.1.1 31036 1nf2A 268 2.56e+01 1seiA 130 2.57e+01 1seiA d.140.1.1 41463 1bxeA 113 2.58e+01 1bxeA d.55.1.1 38898 1msc 129 2.58e+01 1msc d.85.1.1 40039 1spxA 278 2.59e+01 1j93A 353 2.60e+01 c.1.22.1 66454 1eyyA 510 2.60e+01 1eyyA c.82.1.1 35389 1axdA 209 2.60e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1g7cB 94 2.64e+01 1b64 d.58.12.1 39308 1ju5A 109 2.66e+01 d.93.1.1 77173 1cnuA 137 2.67e+01 1cof d.109.1.2 40862 1n3lA 372 2.67e+01 c.26.1.1 79966 1hfc 169 2.69e+01 1hfc d.92.1.11 40335 1dpgA 485 2.71e+01 1dpgA c.2.1.3 30074 d.81.1.5 39989 1yer 228 2.72e+01 1yer d.122.1.1 41101 1kyqA 274 2.75e+01 c.2.1.11 73281 e.37.1.1 73282 1htwA 158 2.75e+01 c.37.1.18 71083 1dzkA 157 2.80e+01 1obpA b.60.1.1 27096 1lwdA 413 2.81e+01 c.77.1.1 78265 1jpdX 324 2.83e+01 c.1.11.2 67014 d.54.1.1 67015 1ckiA 317 2.86e+01 1csn d.144.1.7 41660 1mc0A 368 2.87e+01 d.110.2.1 78937 d.110.2.1 78938 1ez0A 510 2.87e+01 1eyyA c.82.1.1 35385 2admA 421 2.91e+01 2admA c.66.1.27 34238 1ja9A 274 2.92e+01 c.2.1.2 62817 1lla 628 2.93e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1derA 547 2.93e+01 1derA 4crxA 322 2.95e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1i4jA 110 3.00e+01 d.55.1.1 76734 1gutA 68 3.01e+01 b.40.6.1 65576 1h8mA 140 3.02e+01 1h8mA d.110.4.1 60782 1ma3A 253 3.02e+01 c.31.1.5 78883 1ow4A 129 3.04e+01 1p9oA 313 3.06e+01 1mwmA 320 3.06e+01 c.55.1.1 79580 c.55.1.1 79581 1aqjA 421 3.10e+01 2admA c.66.1.27 34242 1huxA 270 3.10e+01 1huxA c.55.1.5 61278 3cbh 365 3.11e+01 1bvwA c.6.1.1 30665 1d3vA 323 3.11e+01 1d3vA c.42.1.1 32559 1i1sA 96 3.11e+01 1bjaA a.4.5.9 16124 1ccg 291 3.11e+01 1ryc a.93.1.1 18627 1k3xA 262 3.13e+01 a.156.1.2 77242 b.113.1.1 77243 g.39.1.8 77244 1wdcB 156 3.15e+01 1wdcB a.39.1.5 17302 1lvaA 258 3.16e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1i5sA 367 3.17e+01 1bg2 c.37.1.9 61822 1nffA 260 3.18e+01 c.2.1.2 80457 7odcA 424 3.18e+01 7odcA b.49.2.3 26488 c.1.6.1 28650 1iq8A 582 3.19e+01 b.122.1.1 83074 c.1.20.1 71270 d.17.6.1 83075 1crxA 322 3.20e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1a4iB 301 3.23e+01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1a04A 215 3.24e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1vjzA 341 3.24e+01 1ak1 310 3.24e+01 1ak1 c.92.1.1 35594 1fl9A 161 3.27e+01 c.37.1.18 70137 1faoA 126 3.28e+01 1faoA b.55.1.1 26974 1czaN 917 3.29e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1mw9X 592 3.33e+01 2rmcA 182 3.42e+01 2cpl b.62.1.1 27491 1aa7A 158 3.42e+01 1aa7A a.95.1.1 18741 1e8cA 498 3.44e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1viaA 175 3.50e+01 1jdrA 294 3.52e+01 1ryc a.93.1.1 62908 1sczA 233 3.56e+01 2xat 212 3.56e+01 2xat b.81.1.3 28058 1r71A 178 3.58e+01 1yprA 125 3.58e+01 3nul d.110.1.1 40888 1m0kA 262 3.59e+01 f.13.1.1 78344 1nnhA 294 3.60e+01 1jx4A 352 3.61e+01 e.8.1.5 67405 1xat 212 3.61e+01 2xat b.81.1.3 28059 1ko9A 345 3.63e+01 a.96.1.3 68717 d.129.1.2 68718 1ryc 294 3.64e+01 1ryc a.93.1.1 18601 1iqsA 88 3.69e+01 d.214.1.1 71278 3chbD 104 3.71e+01 3chbD b.40.2.1 24970 1ds4A 292 3.73e+01 1ryc a.93.1.1 59129 1v74A 107 3.73e+01 1qfcA 306 3.74e+01 1uteA d.159.1.1 42077 1bx4A 345 3.75e+01 1bx4A c.72.1.1 34935 1d6mA 653 3.82e+01 1d6mA e.10.1.1 43248 1cliA 345 3.84e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1slvA 142 3.86e+01 1sluA b.16.1.1 23688 1cc1L 498 3.86e+01 1h2rL e.18.1.1 43301 1div 149 3.88e+01 1div d.99.1.1 40692 d.100.1.1 40693 1v64A 108 3.92e+01 1k4mA 213 3.94e+01 c.26.1.3 77258 1f9mA 112 3.96e+01 1erv c.47.1.1 32736