# 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 1qwgA 251 1.78e-02 1k1xA 659 7.55e-02 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1ii7A 333 9.04e-02 1ii7A d.159.1.4 62415 1ad1A 266 1.12e-01 1aj2 c.1.21.1 29668 1qo2A 241 1.37e-01 1qo2A c.1.2.1 28533 1btmA 252 6.81e-01 1amk c.1.1.1 28513 1n7kA 234 6.93e-01 c.1.10.1 85374 1geqA 248 7.43e-01 2tysA c.1.2.4 28589 1frb 315 7.46e-01 1frb c.1.7.1 28665 1mi3A 322 7.56e-01 1k8cA 322 8.16e-01 c.1.7.1 72172 1j96A 323 8.78e-01 c.1.7.1 71616 1oltA 457 1.03e+00 1thfD 253 1.11e+00 1thfD c.1.2.1 28535 1gs5A 258 1.53e+00 c.73.1.2 70395 1g2qA 187 1.72e+00 c.61.1.1 65117 1zpdA 568 2.06e+00 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1juk 248 2.09e+00 1a53 c.1.2.4 28567 1km4A 247 2.09e+00 c.1.2.3 72740 1gvfA 286 2.21e+00 c.1.10.2 70599 1j5sA 463 2.24e+00 c.1.9.8 71580 1ujpA 271 2.32e+00 1vh7A 265 2.33e+00 1un8A 552 2.34e+00 1j6oA 268 2.36e+00 c.1.9.12 77088 1edg 380 2.70e+00 1edg c.1.8.3 28807 1j8mF 297 2.81e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1us0A 316 2.81e+00 1j8yF 297 2.89e+00 1ng1 a.24.13.1 62747 c.37.1.10 62748 1el3A 316 3.02e+00 1frb c.1.7.1 28672 1m6jA 261 3.28e+00 c.1.1.1 78693 1pwmA 316 3.49e+00 1igs 248 3.62e+00 1a53 c.1.2.4 28565 1qnrA 344 3.62e+00 1qnoA c.1.8.3 28834 1f89A 291 3.69e+00 d.160.1.1 64988 1s1pA 331 3.79e+00 1ads 315 3.98e+00 1frb c.1.7.1 28671 1a53 247 4.05e+00 1a53 c.1.2.4 28564 1aw1A 256 4.20e+00 1amk c.1.1.1 28515 2acr 315 4.32e+00 1frb c.1.7.1 28674 1dvjC 246 4.42e+00 1dvjA c.1.2.3 28548 1g60A 260 4.49e+00 c.66.1.11 70151 1hw6A 278 4.55e+00 1frb c.1.7.1 61296 1qs1A 462 4.86e+00 1qs1A d.166.1.1 42260 d.166.1.1 42261 1e69B 322 5.37e+00 1e69B c.37.1.12 32377 1neyA 247 5.49e+00 c.1.1.1 80449 1qv9A 283 5.50e+00 7timA 247 5.57e+00 1amk c.1.1.1 28457 1tph1 247 5.68e+00 1amk 1qnoA 344 5.85e+00 1qnoA c.1.8.3 28838 1uumA 372 5.98e+00 1ayaA 101 6.02e+00 1qadA d.93.1.1 40460 2wsyA 268 6.15e+00 2tysA c.1.2.4 28588 1i60A 278 6.25e+00 c.1.15.4 71118 1dvjA 246 6.26e+00 1dvjA c.1.2.3 28546 1ou0A 207 6.28e+00 1qopA 268 6.52e+00 2tysA c.1.2.4 28570 1qpbA 563 6.84e+00 1zpdA c.31.1.3 31739 c.36.1.5 31781 c.36.1.9 31782 1hg3A 225 6.92e+00 1hg3A c.1.1.1 61025 1fmcA 255 6.95e+00 1cydA c.2.1.2 29856 1g7vA 284 6.95e+00 1d9eA c.1.10.4 60335 1zid 268 7.11e+00 1eny c.2.1.2 29911 1rpxA 230 7.17e+00 1rpxA c.1.2.2 28536 1vjrA 271 7.31e+00 1ht6A 405 7.37e+00 b.71.1.1 83629 c.1.8.1 83630 1bvyF 191 7.42e+00 1bvyF c.23.5.1 31207 1e0cA 271 7.47e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 2ptd 298 7.63e+00 2plc c.1.18.2 29605 1i45A 248 7.67e+00 1amk c.1.1.1 61665 1kp0A 402 7.79e+00 c.55.2.1 72834 d.127.1.1 72835 1qg8A 255 8.09e+00 1qg8A c.68.1.1 34505 1ouvA 273 8.39e+00 1r30A 369 8.39e+00 1o5kA 306 8.58e+00 1o60A 292 8.68e+00 1qcwA 410 8.74e+00 1gox c.1.4.1 28622 1pydA 556 8.81e+00 1zpdA c.31.1.3 31735 c.36.1.5 31773 c.36.1.9 31774 1eny 268 9.16e+00 1eny c.2.1.2 29910 1bqcA 302 9.25e+00 1bqcA c.1.8.3 28831 1pvdA 537 9.29e+00 1zpdA c.31.1.3 31737 c.36.1.5 31777 c.36.1.9 31778 1h5yA 253 9.43e+00 c.1.2.1 65638 1d9eA 284 9.99e+00 1d9eA c.1.10.4 29195 1rj9A 304 1.00e+01 1ur3M 319 1.03e+01 1cbuA 180 1.05e+01 1c9kB c.37.1.11 32360 1a05A 358 1.07e+01 1cnzA c.77.1.1 35059 1ho1A 242 1.07e+01 1ho1A c.1.24.1 61097 1m5wA 243 1.08e+01 c.1.24.1 84836 1og6A 298 1.09e+01 c.1.7.1 86984 1cfyA 143 1.10e+01 1cof d.109.1.2 40858 1c9kB 180 1.10e+01 1c9kB c.37.1.11 32364 1h1nA 305 1.13e+01 c.1.8.3 70855 1e0tA 470 1.14e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1cof 143 1.14e+01 1cof d.109.1.2 40860 1jeoA 180 1.14e+01 c.80.1.3 66611 1qs2A 401 1.15e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1a80 277 1.19e+01 1frb c.1.7.1 28700 1r2rA 248 1.26e+01 1pz1A 333 1.27e+01 1nu5A 370 1.29e+01 1gt8B 1025 1.32e+01 a.1.2.2 70423 c.1.4.1 70424 c.3.1.1 70425 c.4.1.1 70426 d.58.1.5 70427 1eudA 311 1.38e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1q7bA 244 1.39e+01 1mo0A 275 1.40e+01 c.1.1.1 79329 1p1mA 406 1.41e+01 b.92.1.4 87696 c.1.9.9 87697 1n0wA 243 1.41e+01 c.37.1.11 79772 1jljA 189 1.41e+01 c.57.1.1 63169 2tysA 268 1.41e+01 2tysA c.1.2.4 28572 1bksA 268 1.42e+01 2tysA c.1.2.4 28585 1b93A 152 1.43e+01 1b93A c.24.1.2 31507 1eyeA 280 1.47e+01 1aj2 c.1.21.1 29672 1sviA 195 1.47e+01 1h7wB 1025 1.51e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1vhnA 318 1.56e+01 1fcqA 350 1.57e+01 c.1.8.9 65006 1d7kA 421 1.59e+01 7odcA b.49.2.3 26486 c.1.6.1 28648 1gteD 1025 1.61e+01 a.1.2.2 70455 c.1.4.1 70456 c.3.1.1 70457 c.4.1.1 70458 d.58.1.5 70459 1b93B 152 1.61e+01 1b93A c.24.1.2 31508 1gt8D 1025 1.62e+01 a.1.2.2 70433 c.1.4.1 70434 c.3.1.1 70435 c.4.1.1 70436 d.58.1.5 70437 1h7wD 1025 1.62e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1kbjA 412 1.62e+01 c.1.4.1 72280 1eucA 311 1.64e+01 2scuA c.2.1.8 30311 c.23.4.1 31139 1rvkA 382 1.65e+01 1nf2A 268 1.65e+01 1bfd 528 1.67e+01 1bfd c.31.1.3 31745 c.36.1.5 31801 c.36.1.9 31802 1ojxA 263 1.67e+01 1jlm 192 1.69e+01 1ido c.62.1.1 34140 1gt8A 1025 1.69e+01 a.1.2.2 70418 c.1.4.1 70419 c.3.1.1 70420 c.4.1.1 70421 d.58.1.5 70422 1h7xD 1025 1.71e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1avaA 403 1.73e+01 1jdc b.71.1.1 27797 c.1.8.1 28784 1h7wA 1025 1.77e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1gteA 1025 1.77e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1gthD 1025 1.79e+01 a.1.2.2 70498 c.1.4.1 70499 c.3.1.1 70500 c.4.1.1 70501 d.58.1.5 70502 1mwmA 320 1.80e+01 c.55.1.1 79580 c.55.1.1 79581 1c0aA 585 1.81e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1k8kA 418 1.81e+01 c.55.1.1 68305 c.55.1.1 68306 2aaa 484 1.82e+01 7taa b.71.1.1 27777 c.1.8.1 28764 1h7xC 1025 1.83e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1gthC 1025 1.86e+01 a.1.2.2 70493 c.1.4.1 70494 c.3.1.1 70495 c.4.1.1 70496 d.58.1.5 70497 1oe1A 336 1.87e+01 b.6.1.3 86891 b.6.1.3 86892 1ihcA 188 1.88e+01 1di6A c.57.1.1 62379 1pea 385 1.91e+01 1pea c.93.1.1 35662 1j6pA 418 1.92e+01 b.92.1.4 77089 c.1.9.9 77090 1qdlA 422 1.94e+01 1qdlA d.161.1.1 42088 1gthB 1025 1.94e+01 a.1.2.2 70488 c.1.4.1 70489 c.3.1.1 70490 c.4.1.1 70491 d.58.1.5 70492 1gg3A 279 1.96e+01 1ef1A a.11.2.1 16372 b.55.1.5 27007 d.15.1.4 37615 1gthA 1025 1.97e+01 a.1.2.2 70483 c.1.4.1 70484 c.3.1.1 70485 c.4.1.1 70486 d.58.1.5 70487 1c9kA 180 1.98e+01 1c9kB c.37.1.11 32363 1fbtA 190 1.99e+01 1bif c.60.1.4 34004 1onwA 390 1.99e+01 b.92.1.7 87172 c.1.9.13 87173 1gt8C 1025 1.99e+01 a.1.2.2 70428 c.1.4.1 70429 c.3.1.1 70430 c.4.1.1 70431 d.58.1.5 70432 1p3jA 217 2.00e+01 1onxA 390 2.02e+01 b.92.1.7 87176 c.1.9.13 87177 1fts 295 2.03e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1dvh 79 2.05e+01 1c53 a.3.1.1 15802 1h7xB 1025 2.05e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1esc 306 2.05e+01 1esc c.23.10.1 31334 1b8oA 284 2.07e+01 1b8oA c.56.2.1 33762 1knwA 425 2.16e+01 1h7xA 1025 2.16e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1n3oA 252 2.17e+01 b.29.1.1 79967 1t2dA 322 2.20e+01 1pymA 295 2.20e+01 1pymA c.1.12.7 29308 1cnuA 137 2.20e+01 1cof d.109.1.2 40862 1mxiA 160 2.21e+01 c.116.1.1 79646 1gklA 297 2.21e+01 c.69.1.2 65250 1pwxA 254 2.22e+01 1gkkA 297 2.33e+01 c.69.1.2 65248 1k0fA 277 2.34e+01 c.92.2.2 71974 1ohlA 342 2.34e+01 c.1.10.3 87035 1ae1A 273 2.36e+01 1bdb c.2.1.2 29943 1aw5 326 2.36e+01 1b4kA c.1.10.3 29181 1aj0 282 2.37e+01 1aj2 c.1.21.1 29667 1qgoA 264 2.37e+01 1qgoA c.92.1.2 35596 1pbn 289 2.38e+01 1b8oA c.56.2.1 33771 1ukgA 252 2.39e+01 1kqyA 273 2.40e+01 c.1.8.5 68843 1jwqA 179 2.41e+01 2tpsA 227 2.45e+01 2tpsA c.1.3.1 28591 1fcbA 511 2.47e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1xvaA 292 2.48e+01 1xvaA c.66.1.5 34183 1dlwA 116 2.49e+01 1dlyA a.1.1.1 14982 1fgyA 127 2.50e+01 1faoA b.55.1.1 26976 4xis 387 2.54e+01 4xis c.1.15.3 29421 1muwA 386 2.62e+01 c.1.15.3 79495 1m9sA 605 2.62e+01 b.1.18.15 78874 b.34.11.1 78875 b.34.11.1 78876 b.34.11.1 78877 c.10.2.1 78878 1kv5A 250 2.62e+01 c.1.1.1 73052 1jqaA 370 2.62e+01 e.22.1.2 67085 2hvm 273 2.63e+01 1cnv c.1.8.5 28985 1kqzA 273 2.65e+01 c.1.8.5 68844 1bg4 302 2.66e+01 1taxA c.1.8.3 28806 1edqA 540 2.71e+01 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1toaA 313 2.76e+01 1toaA c.92.2.2 35598 1qumA 285 2.77e+01 1qumA c.1.15.1 29393 3timA 250 2.77e+01 1amk c.1.1.1 28483 1j5xA 342 2.80e+01 c.80.1.1 71591 1lyxA 248 2.80e+01 c.1.1.1 78304 1h7eA 245 2.81e+01 c.68.1.13 60717 1ghr 306 2.81e+01 1aq0A c.1.8.3 28844 1ivnA 190 2.82e+01 c.23.10.5 83719 1l9vA 317 2.82e+01 d.13.2.1 73760 d.216.1.1 73761 1e87A 118 2.87e+01 1b6e d.169.1.1 42327 1l6wA 220 2.88e+01 c.1.10.1 73632 1m4jA 142 2.91e+01 d.109.1.2 78602 1o6dA 163 2.93e+01 1su4A 994 2.93e+01 1bhjA 292 2.96e+01 1xvaA c.66.1.5 34189 3xis 387 2.97e+01 4xis c.1.15.3 29423 1gqnA 252 3.06e+01 1r89A 437 3.07e+01 1ggvA 232 3.08e+01 1din c.69.1.9 34683 1uetA 437 3.09e+01 1fnnA 389 3.10e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1qvbA 481 3.12e+01 1qvbA c.1.8.4 28983 1keaA 221 3.12e+01 a.96.1.2 68491 1pnsB 234 3.12e+01 i.1.1.1 88169 1j5eB 256 3.14e+01 c.23.15.1 71543 1eywA 331 3.17e+01 1pscA c.1.9.3 29057 1din 236 3.18e+01 1din c.69.1.9 34682 1hkvA 453 3.19e+01 b.49.2.3 83559 c.1.6.1 83560 1ldg 316 3.22e+01 1ceqA c.2.1.5 30165 d.162.1.1 42132 2plc 274 3.25e+01 2plc c.1.18.2 29614 1j4aA 333 3.25e+01 c.2.1.4 71502 c.23.12.1 71503 1ru8A 232 3.25e+01 1aj2 282 3.25e+01 1aj2 c.1.21.1 29665 1pbtA 244 3.27e+01 1eqcA 394 3.28e+01 1cz1A c.1.8.3 28811 1n8nA 212 3.30e+01 1fjgB 256 3.30e+01 1fjfB c.23.15.1 31400 1vizA 240 3.32e+01 1bf6A 291 3.33e+01 1pscA c.1.9.3 29065 1jpmA 366 3.34e+01 c.1.11.2 67031 d.54.1.1 67032 3pnp 289 3.35e+01 1b8oA c.56.2.1 33763 1ido 192 3.40e+01 1ido c.62.1.1 34139 1tpfA 250 3.45e+01 1amk c.1.1.1 28467 1mf7A 194 3.48e+01 c.62.1.1 84937 1vjzA 341 3.50e+01 1hgxA 183 3.52e+01 1tc1A c.61.1.1 34027 1nsyA 271 3.52e+01 2nsyA c.26.2.1 31614 1b31A 302 3.55e+01 1taxA c.1.8.3 28892 1ylvA 342 3.66e+01 1b4kA c.1.10.3 29180 1qtwA 285 3.68e+01 1qumA c.1.15.1 29392 2nsyA 271 3.71e+01 2nsyA c.26.2.1 31612 1uf3A 228 3.73e+01 1agrE 205 3.74e+01 1agrE a.91.1.1 18538 1moq 368 3.74e+01 1moq c.80.1.1 35302 1nal1 297 3.74e+01 1nal3 1kqpA 271 3.75e+01 c.26.2.1 72883 1cz1A 394 3.80e+01 1cz1A c.1.8.3 28839 1lqaA 346 3.81e+01 c.1.7.1 84674 1fdyA 297 3.81e+01 1nal3 c.1.10.1 29071 1eazA 125 3.82e+01 b.55.1.1 70113 7icd 416 3.83e+01 1iso c.77.1.1 35072 1eemA 241 3.83e+01 1eemA a.45.1.1 17717 c.47.1.5 33011 2mhr 118 3.85e+01 2mhr a.24.4.1 16581 1h1yA 228 3.87e+01 c.1.2.2 76506 2pth 193 3.87e+01 2pth c.56.3.1 33793 1pzgA 331 3.89e+01 1hv8A 367 3.93e+01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1eulA 994 3.99e+01 1eulA b.82.7.1 75829 c.108.1.7 75830 d.220.1.1 75831 f.33.1.1 75832