# List of top-scoring protein chains for t04-100-40-40-str2+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 1mkiA 330 7.78e-51 e.3.1.2 84994 4blmA 265 1.72e-08 1btl e.3.1.1 42721 1i2sA 282 2.10e-08 e.3.1.1 71104 1bueA 265 5.23e-08 1btl e.3.1.1 42727 1bza 262 2.45e-07 1btl e.3.1.1 42701 1iysA 262 3.31e-07 e.3.1.1 -11760 1hzoA 271 4.41e-07 e.3.1.1 71092 1ghpA 258 6.34e-07 1btl e.3.1.1 60520 1n9bA 265 9.98e-07 e.3.1.1 85463 1bsg 266 1.16e-06 1btl e.3.1.1 42729 1g6aA 271 1.19e-06 1btl e.3.1.1 42704 1e25A 282 1.23e-06 1e25A e.3.1.1 42731 1m40A 263 3.82e-06 e.3.1.1 74437 1ermA 263 4.03e-06 1btl e.3.1.1 42690 1ei5A 520 5.04e-06 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1btl 263 9.36e-06 1btl e.3.1.1 42691 1o7eA 276 7.22e-04 e.3.1.1 -11766 1pi4A 358 1.25e-03 e.3.1.1 -11774 1nrfA 262 1.70e-03 e.3.1.1 -11780 1fsyA 358 2.03e-03 1gceA e.3.1.1 60016 1nzoA 363 2.45e-03 b.105.1.1 -2933 e.3.1.1 -11784 1nj4A 363 3.01e-03 b.105.1.1 80545 e.3.1.1 80546 1ga0A 364 3.49e-03 1gceA e.3.1.1 60410 2bltA 361 4.13e-03 1gceA e.3.1.1 42739 1rgzA 363 4.21e-03 e.3.1.1 -11771 1l0gA 358 4.81e-03 e.3.1.1 73400 3pte 349 5.03e-03 3pte e.3.1.1 42687 2sqcA 631 8.17e-03 2sqcA a.102.4.2 18854 a.102.4.2 18855 1ci9A 392 8.63e-03 e.3.1.1 64767 1k38A 254 8.80e-03 e.3.1.1 84303 1mwxA 646 1.04e-02 d.17.4.5 79610 d.175.1.1 79611 e.3.1.1 79612 1pwgA 349 1.38e-02 1mplA 349 1.54e-02 e.3.1.1 79387 1f24A 402 2.19e-02 1rom a.104.1.1 18953 1hvbA 349 2.59e-02 3pte e.3.1.1 42686 1rgyA 360 2.62e-02 e.3.1.1 -11768 1tvfA 369 2.70e-02 1m6kA 251 3.12e-02 e.3.1.1 78695 1jfbA 404 3.26e-02 a.104.1.1 66624 1uw4B 248 3.32e-02 unknown_sccs -1560 1klxA 138 6.22e-02 a.118.18.1 77440 1esiA 262 6.32e-02 1skf e.3.1.1 42682 1eu8A 409 9.62e-02 1eu8A c.94.1.1 59502 1j0aA 325 1.08e-01 c.79.1.1 83871 1ej1A 190 3.15e-01 1ejhA d.86.1.1 40144 1es5A 262 4.03e-01 1skf e.3.1.1 42679 1t7pA 698 4.04e-01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1nnjA 271 4.27e-01 a.156.1.2 80669 b.113.1.1 80670 g.39.1.8 80671 1dceB 331 4.28e-01 1dceB a.102.4.3 18872 1pjjA 271 4.37e-01 1qmeA 702 5.78e-01 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1euhA 475 6.07e-01 1euhA c.82.1.1 35369 1csh 435 6.17e-01 1csh a.103.1.1 18880 1uocA 289 6.36e-01 unknown_sccs -7671 1mp1A 111 6.44e-01 unknown_sccs -996 1qazA 351 6.94e-01 1qazA a.102.3.1 18848 1edzA 320 7.08e-01 1ee9A c.2.1.7 30287 c.58.1.2 33935 1uzbA 516 7.30e-01 c.82.1.1 -8552 1aa7A 158 7.87e-01 1aa7A a.95.1.1 18741 1r31A 428 9.16e-01 d.58.20.1 -10108 d.179.1.1 -11716 1nc5A 373 1.01e+00 a.102.1.6 85548 1np7A 489 1.04e+00 a.99.1.1 80677 c.28.1.1 80678 2hhmA 276 1.08e+00 1imbA e.7.1.1 42955 1knyA 253 1.14e+00 1knyA a.24.16.1 75896 d.218.1.1 75897 1l8bA 190 1.15e+00 d.86.1.1 73683 1top 162 1.19e+00 1ncx a.39.1.5 17223 1k82A 268 1.20e+00 a.156.1.2 75866 b.113.1.1 75867 g.39.1.8 75868 1rz2A 254 1.21e+00 1imbA 277 1.22e+00 1imbA e.7.1.1 42957 1ornA 226 1.25e+00 a.96.1.1 87342 1keaA 221 1.36e+00 a.96.1.2 68491 1l1zA 274 1.42e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1mp8A 281 1.52e+00 d.144.1.7 -11361 1td5A 202 1.62e+00 1r2zA 274 1.72e+00 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1dl2A 511 1.80e+00 1dl2A a.102.2.1 18844 1e3uA 246 1.84e+00 1fofA e.3.1.1 42755 1ee8A 266 1.86e+00 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 1ouvA 273 2.01e+00 a.118.18.1 -1586 1qhtA 775 2.09e+00 1tgoA c.55.3.5 33722 e.8.1.1 43011 1odoA 408 2.22e+00 a.104.1.1 -1463 1ld8B 437 2.38e+00 a.102.4.3 73839 1c3wA 222 2.41e+00 1c3wA f.13.1.1 43405 1vi9A 299 2.41e+00 c.72.1.5 -8393 1t5jA 313 2.51e+00 unknown_sccs -1951 1eupA 403 2.65e+00 1rom a.104.1.1 18967 1m2oA 768 2.71e+00 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1lnsA 763 2.75e+00 a.40.2.1 78101 b.18.1.13 78102 c.69.1.21 78103 1d5rA 324 2.78e+00 1d5rA b.7.1.1 23181 c.45.1.1 32697 1t95A 240 2.93e+00 1f5mA 180 2.94e+00 1f5mB d.110.2.1 40895 1uwzA 136 2.96e+00 1ojrA 274 3.06e+00 c.74.1.1 -8441 1gdoA 240 3.11e+00 1gdoA d.153.1.1 41804 1eca 136 3.22e+00 1flp a.1.1.2 15209 1k55A 246 3.22e+00 e.3.1.1 68156 1jx4A 352 3.29e+00 unknown_sccs -10188 unknown_sccs -11898 1abv 134 3.36e+00 1abv a.70.1.1 18317 1h6kA 757 3.59e+00 unknown_sccs 60675 unknown_sccs 60676 unknown_sccs 60677 1mzgA 146 3.59e+00 d.224.1.1 79696 1di1A 300 3.62e+00 1di1A a.128.1.4 19446 1d8dB 437 3.68e+00 1ft1B a.102.4.3 18866 1oaoC 729 3.82e+00 e.26.1.3 86746 1oyeA 1049 3.82e+00 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1pmi 440 3.82e+00 1pmi b.82.1.3 28114 1j5vA 351 3.90e+00 c.72.1.1 71585 1nrvA 105 4.00e+00 d.93.1.1 86126 1lfkA 398 4.56e+00 a.104.1.1 77926 1qmqA 414 4.61e+00 1phd a.104.1.1 18907 1hz4A 373 4.86e+00 a.118.8.2 65960 1ka1A 357 4.96e+00 e.7.1.1 68369 1hr6A 475 5.15e+00 1hr6A d.185.1.1 61164 d.185.1.1 61165 1qgxA 357 5.34e+00 1qgxA e.7.1.1 42973 1lehA 364 5.45e+00 1bw9A c.2.1.7 30268 c.58.1.1 33916 1fsz 372 5.50e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1qmvA 197 5.91e+00 1qq2A c.47.1.10 33066 1jtkA 136 5.96e+00 c.97.1.1 71862 1ks8A 433 6.26e+00 a.102.1.2 77519 1hs6A 611 6.49e+00 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1rec 201 6.82e+00 1rec a.39.1.5 17326 1rvkA 382 7.01e+00 c.1.11.2 -5568 d.54.1.1 -9826 1pjpA 226 7.17e+00 5ptp b.47.1.2 26301 1on2A 142 7.35e+00 a.4.5.24 87103 a.76.1.1 87104 1f2dA 341 7.64e+00 1f2dA c.79.1.1 35298 5eau 548 7.94e+00 5eat a.102.4.1 18851 a.128.1.3 19443 1ca1 370 8.03e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1furA 467 8.13e+00 1furA a.127.1.1 19403 1jipA 403 8.40e+00 a.104.1.1 66748 1rthA 560 8.53e+00 1rthA c.55.3.1 33576 e.8.1.2 43028 1mun 225 8.95e+00 1mun a.96.1.2 18744 1n4qB 377 9.06e+00 a.102.4.3 -1424 1ezwA 349 9.67e+00 1ezwA c.1.16.3 29558 1ollA 188 9.81e+00 b.1.1.4 -2690 b.1.1.4 -2691 1ne9A 335 9.98e+00 d.108.1.4 -10805 d.108.1.4 -10806 1auvA 311 1.01e+01 1auvA c.30.1.5 31723 d.142.1.3 41558 1omrA 201 1.01e+01 a.39.1.5 -854 1k8tA 510 1.04e+01 e.41.1.1 68316 1hjrA 158 1.05e+01 1hjrA c.55.3.6 33727 1r9gA 216 1.06e+01 c.23.16.1 -6504 1vdkA 466 1.06e+01 a.127.1.1 -1752 1hh8A 213 1.06e+01 1e96B a.118.8.1 61042 1r5tA 142 1.08e+01 2shpA 525 1.09e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1p2fA 220 1.10e+01 a.4.6.1 87720 c.23.1.1 87721 1auiB 169 1.11e+01 1auiB a.39.1.5 17325 1cqqA 180 1.12e+01 1cqqA b.47.1.4 26422 1bhdA 118 1.13e+01 1bkrA a.40.1.1 17398 1aj8A 371 1.15e+01 1aj8A a.103.1.1 18900 1cpt 412 1.16e+01 1cpt a.104.1.1 18968 1f0lA 535 1.20e+01 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1q7fA 286 1.24e+01 unknown_sccs -4599 1m0kA 262 1.29e+01 f.13.1.1 78344 1n40A 396 1.29e+01 a.104.1.1 79977 1br1B 150 1.29e+01 1wdcC a.39.1.5 17309 1cxqA 162 1.31e+01 1cxqA c.55.3.2 33621 1dz4A 414 1.32e+01 1phd a.104.1.1 18903 1uch 230 1.32e+01 1uch d.3.1.6 37129 1sig 339 1.33e+01 1sig a.177.1.1 19068 1oheA 348 1.33e+01 c.45.1.1 87013 c.45.1.1 87014 1bif 469 1.34e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1unnC 115 1.36e+01 unknown_sccs -10216 1oohA 126 1.38e+01 a.39.2.1 -884 1dpjA 329 1.38e+01 1smrA b.50.1.2 26828 1n4kA 381 1.38e+01 unknown_sccs 79992 b.42.6.1 79993 1qnjA 240 1.40e+01 5ptp b.47.1.2 26238 1lt8A 406 1.42e+01 c.1.26.1 78186 1h21A 247 1.44e+01 a.138.1.3 76510 1je6A 275 1.46e+01 b.1.1.2 71638 d.19.1.1 71639 1ggzA 148 1.48e+01 a.39.1.5 70176 1hi9A 274 1.50e+01 1hi9A c.99.1.1 61063 1b25A 619 1.50e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1b04A 318 1.53e+01 1b04A d.142.2.2 41579 1mpxA 615 1.58e+01 b.18.1.13 85041 c.69.1.21 85042 1i2aA 219 1.58e+01 e.24.1.1 -12012 1r9dA 787 1.59e+01 1v9mA 323 1.61e+01 unknown_sccs -12292 1vrtA 560 1.62e+01 1rthA c.55.3.1 33574 e.8.1.2 43023 1euvA 221 1.63e+01 1euvA d.3.1.7 37133 4ubpC 570 1.65e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1vhqA 232 1.65e+01 c.23.16.2 -6514 1q35A 320 1.73e+01 c.94.1.1 -8658 1rvaA 244 1.84e+01 1rvaA c.52.1.2 33240 1fp3A 402 1.85e+01 1fp3A a.102.1.3 18842 1b77A 228 1.85e+01 1b77A d.131.1.2 41362 d.131.1.2 41363 1ojaA 520 1.90e+01 c.3.1.2 -6000 d.16.1.5 -9220 1f0cA 305 1.93e+01 1c8oA e.1.1.1 42676 1khdA 345 1.94e+01 a.46.2.1 77400 c.27.1.1 77401 1f21A 155 1.95e+01 2rn2 c.55.3.1 33550 1mkmA 249 1.95e+01 a.4.5.33 79242 d.110.2.2 79243 1sx5A 244 1.95e+01 c.52.1.2 -7551 1ekeA 230 1.97e+01 1ekeA c.55.3.1 33572 1oalA 151 1.97e+01 b.1.8.1 86739 1m93B 245 1.97e+01 1ex2A 189 2.01e+01 1ex2A c.51.4.2 33225 1klt 226 2.02e+01 5ptp b.47.1.2 26300 1pzxA 289 2.02e+01 c.119.1.1 -8623 1e6yB 433 2.04e+01 1mroB a.89.1.1 18535 d.58.31.2 39453 1iapA 211 2.05e+01 a.91.1.1 62119 1fiy 883 2.05e+01 1fiy c.1.12.3 29307 1ygs 234 2.05e+01 1ygs b.26.1.1 23907 1su8A 636 2.06e+01 e.26.1.2 -12015 1b0b 142 2.06e+01 2fal a.1.1.2 15010 1dlyA 164 2.07e+01 1dlyA a.1.1.1 14983 1gsoA 431 2.07e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 4crxA 322 2.08e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1eonA 245 2.09e+01 1rvaA c.52.1.2 33238 1fkmA 396 2.11e+01 1fkmA a.69.2.1 18315 a.69.2.1 18316 1hrhA 136 2.14e+01 1rthA c.55.3.1 33577 1bu7A 455 2.16e+01 1bu7A a.104.1.1 18937 1ka2A 499 2.16e+01 d.92.1.5 77305 1vduA 172 2.17e+01 unknown_sccs -1651 1j1jA 240 2.19e+01 a.118.16.1 -1637 2rn2 155 2.31e+01 2rn2 c.55.3.1 33551 1f2tB 148 2.32e+01 1f2tB 1lfpA 249 2.33e+01 e.39.1.1 73885 1n5uA 585 2.33e+01 a.126.1.1 85339 a.126.1.1 85340 a.126.1.1 85341 1c44A 123 2.35e+01 1qndA d.106.1.1 40795 1jl1A 155 2.35e+01 c.55.3.1 66821 1v8fA 276 2.38e+01 c.26.1.4 -6618 2kfnA 605 2.41e+01 1xwl c.55.3.5 33682 e.8.1.1 42975 1gvkB 240 2.45e+01 b.47.1.2 70610 1s48A 609 2.48e+01 e.8.1.4 -11955 1p9qC 256 2.48e+01 1vk4A 298 2.48e+01 c.72.1.1 -8414 1nn6A 228 2.57e+01 b.47.1.2 85893 1h8dH 260 2.59e+01 5ptp 1a6o 332 2.59e+01 1a6o 1ukgA 252 2.61e+01 b.29.1.1 -3390 1qgrA 876 2.61e+01 1qgrA a.118.1.1 19119 1mc0A 368 2.63e+01 d.110.2.1 78937 d.110.2.1 78938 1lj8A 493 2.63e+01 a.100.1.9 78033 c.2.1.6 78034 1k1xA 659 2.66e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1g4yR 148 2.67e+01 1cll a.39.1.5 60252 1s3eA 520 2.71e+01 c.3.1.2 -6022 d.16.1.5 -9242 1nkqA 259 2.73e+01 1m2rA 327 2.73e+01 d.144.1.7 84760 1pd21 199 2.73e+01 1pd21 3nul 130 2.74e+01 3nul d.110.1.1 40891 1exrA 148 2.76e+01 1cll a.39.1.5 17299 1qf5A 431 2.76e+01 1adeA c.37.1.10 32212 1qyiA 384 2.79e+01 unknown_sccs -6836 2dnjA 260 2.80e+01 3dni d.151.1.1 41790 1jpmA 366 2.83e+01 c.1.11.2 67031 d.54.1.1 67032 1i50B 1224 2.85e+01 e.29.1.1 61755 1ry9A 145 2.85e+01 d.198.1.1 -9020 1kyqA 274 2.87e+01 c.2.1.11 73281 e.37.1.1 73282 1jqnA 883 2.89e+01 c.1.12.3 77159 1uf2C 421 2.89e+01 unknown_sccs -1522 b.19.1.1 -3155 1k32A 1045 2.91e+01 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1ovnA 248 2.93e+01 a.71.1.1 -1096 c.47.1.7 -7477 2fcbA 173 2.95e+01 2fcbA b.1.1.4 21781 b.1.1.4 21782 12asA 330 2.95e+01 12asA d.104.1.1 40783 1c4kA 730 2.96e+01 1ordA c.23.1.4 31273 c.67.1.5 34502 d.125.1.1 41123 1gal 583 2.99e+01 1gpeA c.3.1.2 30386 d.16.1.1 37950 1fm9D 272 3.03e+01 2prgA a.123.1.1 19313 1squA 155 3.09e+01 unknown_sccs -10229 1p36A 164 3.12e+01 d.2.1.3 -8840 1g6oA 330 3.15e+01 1g6oA c.37.1.11 32430 1ua4A 455 3.16e+01 c.72.1.3 -8416 1nw1A 429 3.22e+01 d.144.1.8 86286 1fthA 122 3.24e+01 d.150.1.2 60028 1hj8A 222 3.24e+01 b.47.1.2 65844 1q6hA 224 3.24e+01 d.26.1.1 -9487 1j8yF 297 3.33e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1gw5S 142 3.34e+01 d.110.4.2 70633 1n3oA 252 3.39e+01 b.29.1.1 79967 1ejxC 567 3.39e+01 b.92.1.1 83184 c.1.9.2 83185 1f44A 324 3.40e+01 a.60.9.1 64982 d.163.1.1 64983 1s1pA 331 3.40e+01 c.1.7.1 -5240 1nb5I 98 3.44e+01 d.17.1.2 80381 1by2 119 3.45e+01 1by2 d.170.1.1 42452 1r6wA 322 3.46e+01 c.1.11.2 -5563 d.54.1.1 -9821 1l4dB 122 3.48e+01 d.15.5.1 77684 1iazA 179 3.48e+01 1iazA b.97.1.1 62131 1rxwA 336 3.48e+01 a.60.7.1 -1041 c.120.1.2 -6680 1umdA 367 3.50e+01 c.36.1.11 -6969 1nq7A 244 3.50e+01 a.123.1.1 -1682 1gw5A 621 3.52e+01 a.118.1.10 70629 1omzA 293 3.54e+01 c.68.1.15 87093 1gwiA 411 3.54e+01 a.104.1.1 76364 1ofuA 320 3.56e+01 c.32.1.1 86972 d.79.2.1 86973 1d5tA 433 3.58e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1jpzA 473 3.76e+01 a.104.1.1 67069 1cliA 345 3.77e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1kqqA 139 3.79e+01 a.4.3.1 72885 1b00A 127 3.81e+01 3chy c.23.1.1 31122 1jetA 517 3.81e+01 1jevA c.94.1.1 35718 1uanA 227 3.82e+01 unknown_sccs -8129 1p7tA 731 3.83e+01 c.1.13.1 -5600 1r5zA 323 3.87e+01 unknown_sccs -12289 1js8A 394 3.89e+01 a.86.1.1 67219 b.112.1.1 67220 1ayx 492 3.90e+01 1ayx a.102.1.1 18825 1wdcC 156 3.90e+01 1wdcC a.39.1.5 17317 1o5hA 214 3.91e+01 unknown_sccs -1078 1gtmA 419 3.91e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 2tbs 222 3.95e+01 5ptp b.47.1.2 26009 1msk 331 3.96e+01 1msk d.173.1.1 42495 1dnlA 199 3.96e+01 1ci0A b.45.1.1 25753 1dcqA 278 3.99e+01 1dcqA d.211.1.1 19178 g.45.1.1 45326