# List of top-scoring protein chains for t2k-100-30-near-backbone-11 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 1tqnA 486 2.65e-58 1nr6A 473 2.38e-55 a.104.1.1 -1464 1n6bA 473 4.11e-55 a.104.1.1 85359 1dt6A 473 1.45e-54 1dt6A a.104.1.1 18977 1po5A 476 1.65e-53 a.104.1.1 -1467 2bmhA 455 6.79e-48 1bu7A a.104.1.1 18941 1bu7A 455 1.22e-47 1bu7A a.104.1.1 18937 1jmeA 455 1.52e-47 a.104.1.1 66885 1jpzA 473 1.57e-46 a.104.1.1 67069 1n97A 389 1.76e-44 a.104.1.1 80335 1jipA 403 2.74e-44 a.104.1.1 66748 1eupA 403 8.58e-44 1rom a.104.1.1 18967 1ea1A 455 9.81e-44 1ea1A a.104.1.1 18970 1oxa 403 1.13e-43 1f4tA a.104.1.1 18965 1e9xA 455 1.17e-43 1ea1A a.104.1.1 18969 1h5zA 455 2.14e-43 a.104.1.1 -1456 1u13A 455 3.60e-43 1odoA 408 1.66e-41 a.104.1.1 -1463 1gwiA 411 2.23e-41 a.104.1.1 76364 1cmnA 402 2.99e-41 1rom a.104.1.1 18958 1rom 403 6.26e-41 1rom a.104.1.1 18963 1jfbA 404 6.43e-41 a.104.1.1 66624 1cpt 412 1.06e-40 1cpt a.104.1.1 18968 1f24A 402 1.50e-40 1rom a.104.1.1 18953 1q5dA 419 1.39e-39 a.104.1.1 -1454 1uedA 406 5.66e-39 a.104.1.1 -1459 1lfkA 398 4.74e-37 a.104.1.1 77926 1io7A 368 3.45e-35 1f4tA a.104.1.1 18971 1f4tA 368 6.12e-35 1f4tA a.104.1.1 18973 1qmqA 414 2.68e-34 1phd a.104.1.1 18907 1phd 414 1.36e-33 1phd a.104.1.1 18913 5cpp 414 1.72e-33 1phd a.104.1.1 18935 1phb 414 2.32e-33 1phd a.104.1.1 18906 1phg 414 3.02e-33 1phd a.104.1.1 18910 1dz4A 414 3.27e-33 1phd a.104.1.1 18903 1izoA 417 5.60e-33 a.104.1.1 83851 1n40A 396 1.51e-30 a.104.1.1 79977 1jf0A 195 3.61e-01 1ej3A a.39.1.5 62926 1ru3A 732 8.78e-01 e.26.1.3 -12021 2cb5A 453 1.08e+00 3gcb d.3.1.1 37035 1d2eA 397 1.11e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1vduA 172 1.38e+00 unknown_sccs -1651 2scpA 174 1.61e+00 2scpA a.39.1.5 17256 1g0oA 283 1.77e+00 1ybvA c.2.1.2 60181 1odfA 290 1.93e+00 c.37.1.6 -7045 1qlnA 883 2.03e+00 1cezA e.8.1.3 43111 1o1zA 234 2.17e+00 c.1.18.3 86555 1rpa 342 2.24e+00 1cviA c.60.1.2 33983 1jf2A 195 2.29e+00 1ej3A a.39.1.5 62930 1ofcX 304 2.38e+00 a.4.1.3 -195 unknown_sccs -199 unknown_sccs -978 1oaoC 729 2.49e+00 e.26.1.3 86746 1914 232 2.62e+00 1914 d.49.1.1 83028 d.49.1.1 83029 1g0cA 364 3.15e+00 7a3hA c.1.8.3 60165 1ej3A 191 3.27e+00 1ej3A a.39.1.5 17259 1ybvA 283 3.40e+00 1ybvA c.2.1.2 29948 1g01A 364 3.44e+00 7a3hA c.1.8.3 60161 1exrA 148 3.84e+00 1cll a.39.1.5 17299 1jpnA 296 3.94e+00 a.24.13.1 67039 c.37.1.10 67040 1fp3A 402 4.14e+00 1fp3A a.102.1.3 18842 1rkeA 262 4.32e+00 a.24.9.1 -582 a.24.9.1 -583 1lci 550 4.43e+00 1lci e.23.1.1 43349 1o7xB 377 4.61e+00 a.103.1.1 81172 1nxcA 478 4.67e+00 a.102.2.1 -1333 1o7xD 377 4.68e+00 a.103.1.1 81174 1el4A 195 4.82e+00 1ej3A a.39.1.5 59453 1o7xC 377 5.00e+00 a.103.1.1 81173 1ncx 162 5.04e+00 1ncx a.39.1.5 17222 1d0cA 444 5.04e+00 d.174.1.1 64769 1osa 148 5.20e+00 1cll a.39.1.5 17300 1ckmA 330 5.25e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1cezA 883 5.28e+00 1cezA e.8.1.3 43110 1cb8A 678 5.30e+00 1cb8A a.102.3.2 18849 b.24.1.1 23898 b.30.5.2 24422 1l8qA 324 5.37e+00 a.4.12.2 77809 c.37.1.20 77810 1fnmA 691 5.41e+00 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1ntyA 311 5.55e+00 5nseA 444 5.61e+00 d.174.1.1 74644 1ub3A 220 5.64e+00 c.1.10.1 88395 1lvhA 221 5.72e+00 c.108.1.6 74282 1gr0A 367 5.83e+00 c.2.1.3 70379 d.81.1.3 70380 1jztA 246 5.93e+00 c.104.1.1 63319 1j8mF 297 5.95e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1i2aA 219 6.06e+00 e.24.1.1 -12012 1d1vA 444 6.21e+00 1nseA d.174.1.1 59101 1ed5A 444 6.29e+00 1nseA d.174.1.1 42530 1irdB 146 6.34e+00 a.1.1.2 66287 1mswD 883 6.35e+00 e.8.1.3 79427 1kktA 511 6.36e+00 a.102.2.1 68687 1qv1A 195 6.39e+00 a.39.1.5 -830 1h38D 883 6.42e+00 e.8.1.3 76628 1gnlA 544 6.50e+00 e.26.1.1 70287 1omrA 201 6.69e+00 a.39.1.5 -854 1j8yF 297 6.83e+00 1ng1 a.24.13.1 62747 c.37.1.10 62748 1jbaA 204 6.91e+00 1rec a.39.1.5 17330 1tml 286 7.22e+00 1tml c.6.1.1 30656 1mkeA 152 7.50e+00 b.55.1.4 79231 1cknA 330 7.51e+00 1ckmA b.40.4.6 25360 d.142.2.3 41587 1top 162 7.53e+00 1ncx a.39.1.5 17223 1i3dA 146 7.54e+00 a.1.1.2 61587 1nseA 444 7.72e+00 1nseA d.174.1.1 42534 1h38C 883 8.05e+00 e.8.1.3 76627 1ur3M 319 8.28e+00 c.1.7.1 -5248 1nnvA 110 8.29e+00 unknown_sccs -9309 1keeC 1073 8.37e+00 a.92.1.1 68500 c.24.1.1 68501 c.30.1.1 68502 c.30.1.1 68503 d.142.1.2 68504 d.142.1.2 68505 1h38B 883 8.40e+00 e.8.1.3 76626 1qwgA 251 8.43e+00 unknown_sccs -5678 1cjsA 219 8.46e+00 1cjsA e.24.1.1 43354 1mjgM 729 8.47e+00 e.26.1.3 79204 1knqA 175 8.54e+00 c.37.1.17 72786 1o0xA 262 8.77e+00 d.127.1.1 80755 1s9rA 410 8.81e+00 unknown_sccs -10989 1iciA 256 8.94e+00 1iciA c.31.1.5 62266 1lwjA 441 9.17e+00 b.71.1.1 74303 c.1.8.1 74304 1i1iP 681 9.18e+00 1i1iP d.92.1.5 40297 1ls1A 295 9.34e+00 a.24.13.1 78170 c.37.1.10 78171 1rec 201 9.35e+00 1rec a.39.1.5 17326 2sqcA 631 9.38e+00 2sqcA a.102.4.2 18854 a.102.4.2 18855 1jdbB 1073 9.73e+00 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1c3oG 1073 9.86e+00 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1e8xA 961 9.98e+00 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1phk 298 1.06e+01 1cdkA d.144.1.7 41635 4xiaA 393 1.08e+01 4xis c.1.15.3 29439 1o0yA 260 1.08e+01 c.1.10.1 80756 1og6A 298 1.09e+01 c.1.7.1 86984 1e8yA 966 1.09e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1cs0C 1073 1.11e+01 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1iqpA 327 1.20e+01 a.80.1.1 62649 c.37.1.20 62650 1fhjB 146 1.21e+01 1abwA a.1.1.2 59838 1j7yB 146 1.21e+01 a.1.1.2 66427 1ii7A 333 1.22e+01 1ii7A d.159.1.4 62415 1iexA 605 1.24e+01 c.1.8.7 66127 c.23.11.1 66128 1fs7A 485 1.25e+01 1qdbA a.138.1.3 19691 1gqeA 365 1.30e+01 e.38.1.1 70351 1cm5A 759 1.33e+01 1cm5A c.7.1.1 30671 1gw5B 591 1.35e+01 a.118.1.10 70630 1keeE 1073 1.36e+01 a.92.1.1 68508 c.24.1.1 68509 c.30.1.1 68510 c.30.1.1 68511 d.142.1.2 68512 d.142.1.2 68513 1jadA 251 1.36e+01 h.4.10.1 66461 1sqc 631 1.38e+01 2sqcA a.102.4.2 18858 a.102.4.2 18859 1o20A 427 1.39e+01 c.82.1.1 86556 1gw9A 388 1.42e+01 c.1.15.3 70658 1c7nA 399 1.42e+01 1d2fA c.67.1.3 34413 1ufwA 95 1.42e+01 d.58.7.1 -10034 1g8iA 190 1.45e+01 1rec a.39.1.5 60363 1ggzA 148 1.50e+01 a.39.1.5 70176 1dorA 311 1.51e+01 2dorA c.1.4.1 28595 1hm2A 700 1.53e+01 1cb8A a.102.3.2 61083 b.24.1.1 61084 b.30.5.2 61085 1nal1 297 1.53e+01 1nal3 1ll1 590 1.54e+01 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.18.3 21864 2iadB 205 1.55e+01 1iakB b.1.1.2 21640 d.19.1.1 38214 1a26 361 1.57e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1uzbA 516 1.61e+01 c.82.1.1 -8552 1muwA 386 1.64e+01 c.1.15.3 79495 1nw1A 429 1.69e+01 d.144.1.8 86286 1ng1 294 1.71e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1mnzA 388 1.72e+01 c.1.15.3 79328 1fxxA 482 1.73e+01 1fxxA c.55.3.5 33726 4blmA 265 1.74e+01 1btl e.3.1.1 42721 1nxuA 333 1.75e+01 c.122.1.1 86389 1fcqA 350 1.75e+01 c.1.8.9 65006 1eqcA 394 1.75e+01 1cz1A c.1.8.3 28811 2xis 387 1.79e+01 4xis c.1.15.3 29427 1c3oC 1073 1.80e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1r5jA 337 1.81e+01 unknown_sccs -8471 1keeG 1073 1.82e+01 a.92.1.1 68516 c.24.1.1 68517 c.30.1.1 68518 c.30.1.1 68519 d.142.1.2 68520 d.142.1.2 68521 1lhpA 312 1.82e+01 c.72.1.5 77960 2dorA 311 1.83e+01 2dorA c.1.4.1 28593 1cll 148 1.83e+01 1cll a.39.1.5 17263 1xo1A 291 1.89e+01 1exnA a.60.7.1 18086 c.120.1.2 33356 3pflA 759 1.94e+01 1cm5A c.7.1.1 30673 1xis 387 1.94e+01 4xis c.1.15.3 29422 1ex1A 605 1.95e+01 1ex1A c.1.8.7 29013 c.23.11.1 31347 1oshA 232 1.99e+01 a.123.1.1 -1697 1ho8A 480 2.00e+01 1ho8A a.118.1.9 61107 1c3oA 1073 2.00e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1gudA 288 2.01e+01 c.93.1.1 83326 1t0qA 498 2.02e+01 1c3oE 1073 2.04e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1ucdA 190 2.09e+01 4xis 387 2.11e+01 4xis c.1.15.3 29421 1m2kA 249 2.13e+01 c.31.1.5 84754 1cz1A 394 2.13e+01 1cz1A c.1.8.3 28839 1g60A 260 2.16e+01 c.66.1.11 70151 3xis 387 2.18e+01 4xis c.1.15.3 29423 2sas 185 2.18e+01 2sas a.39.1.5 17258 1iq0A 592 2.19e+01 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 1ib8A 164 2.20e+01 b.38.2.1 71168 d.52.4.1 71169 1n2aA 201 2.22e+01 a.45.1.1 -938 c.47.1.5 -7463 1booA 323 2.23e+01 1booA c.66.1.11 34248 1keeA 1073 2.24e+01 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1iupA 282 2.26e+01 c.69.1.10 76815 1babB 146 2.27e+01 1abwA a.1.1.2 15414 1fsgA 233 2.28e+01 1qk3A c.61.1.1 34029 1dxtB 147 2.31e+01 1abwA a.1.1.2 15450 1cdp 109 2.31e+01 1a75A a.39.1.4 17197 2pflA 759 2.32e+01 1cm5A c.7.1.1 30675 1t0qB 330 2.33e+01 1mjnA 179 2.34e+01 c.62.1.1 79210 1dar 691 2.35e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1efyA 350 2.35e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1umnA 165 2.41e+01 a.25.1.1 -656 2chsA 127 2.44e+01 2chsA d.79.1.2 39764 1k4nA 192 2.52e+01 d.32.1.5 72059 1a75A 108 2.54e+01 1a75A a.39.1.4 17216 1a4mA 349 2.54e+01 1a4mA c.1.9.1 29014 1e7uA 961 2.57e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1lxyA 409 2.58e+01 unknown_sccs -10987 1i4nA 251 2.60e+01 c.1.2.4 71114 3cln 148 2.65e+01 1cll a.39.1.5 17286 1lla 628 2.65e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1tikA 213 2.74e+01 1c2pA 576 2.75e+01 1quvA e.8.1.4 43117 1pvaA 110 2.75e+01 1a75A a.39.1.4 17207 1thjA 214 2.78e+01 1qreA b.81.1.5 28072 1auiB 169 2.81e+01 1auiB a.39.1.5 17325 1bdfA 235 2.81e+01 1bdfA d.74.3.1 39727 d.181.1.1 42602 2gwxA 267 2.84e+01 2prgA a.123.1.1 19323 1iomA 377 2.84e+01 a.103.1.1 83698 1jfxA 217 2.88e+01 c.1.8.8 62943 1pa1A 310 2.88e+01 c.45.1.2 -7332 2ng1 293 2.91e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1a3qA 285 2.92e+01 1a3qA b.1.18.1 21932 b.2.5.3 22447 1yptA 305 2.93e+01 1ytw c.45.1.2 32686 1nktA 922 2.94e+01 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1fy7A 278 2.96e+01 1fy7A d.108.1.1 40817 1g2qA 187 3.00e+01 c.61.1.1 65117 3bct 457 3.01e+01 3bct a.118.1.1 19112 1g4yR 148 3.04e+01 1cll a.39.1.5 60252 2pvbA 107 3.07e+01 1a75A a.39.1.4 17205 1h16A 759 3.11e+01 c.7.1.1 76462 1ituA 369 3.15e+01 c.1.9.7 71423 1gp6A 356 3.16e+01 b.82.2.1 65441 1ytw 306 3.17e+01 1ytw c.45.1.2 32689 1irxA 523 3.19e+01 a.97.1.2 71378 c.26.1.1 71379 1dbfA 127 3.22e+01 2chsA d.79.1.2 39761 1pal 108 3.24e+01 1a75A a.39.1.4 17209 1l2lA 457 3.24e+01 c.72.1.3 77656 1ayx 492 3.33e+01 1ayx a.102.1.1 18825 1tufA 434 3.33e+01 1iwhB 146 3.35e+01 a.1.1.2 76883 1uddA 226 3.36e+01 1sw6A 327 3.37e+01 1sw6A d.211.1.1 19176 4cpv 109 3.37e+01 1a75A a.39.1.4 17198 1v93A 296 3.41e+01 c.1.23.1 -5654 1knvA 293 3.41e+01 c.52.1.7 68707 1ois 223 3.44e+01 1a36A e.15.1.1 43267 1ucaA 190 3.47e+01 d.124.1.1 88462 1mz4A 137 3.49e+01 a.3.1.1 -150 1rwyA 109 3.57e+01 a.39.1.4 -825 1bmlC 362 3.58e+01 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1ytn 306 3.58e+01 1ytw c.45.1.2 32688 1sdoA 203 3.61e+01 unknown_sccs -7558 1lyvA 306 3.63e+01 c.45.1.2 74348 1dlc 584 3.66e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1bk7A 190 3.67e+01 1bk7A d.124.1.1 41121 1kz1A 159 3.68e+01 c.16.1.1 73318 1a7cA 379 3.70e+01 1sek e.1.1.1 42660 1qb4A 883 3.70e+01 c.1.12.3 74640 1m2eA 135 3.75e+01 c.23.1.5 78478 1rypI 222 3.82e+01 d.153.1.4 41877 1nal3 297 3.82e+01 1nal3 1fiy 883 3.84e+01 1fiy c.1.12.3 29307 1erv 105 3.86e+01 1erv c.47.1.1 32743 1jubA 311 3.88e+01 c.1.4.1 -5188 1esiA 262 3.89e+01 1skf e.3.1.1 42682 1lyxA 248 3.90e+01 c.1.1.1 78304 1dkqA 410 3.95e+01 1dklA c.60.1.2 33998 1hqz9 141 3.97e+01 1d2tA 231 3.99e+01 1d2tA a.111.1.1 19052 1je8A 82 3.99e+01 a.4.6.2 77108