# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1ihoA 283 8.58e-66 1ihoA c.26.1.4 62390 1cozA 129 5.76e-02 1cozA c.26.1.2 31598 1fwkA 296 5.92e-02 1fwkA d.14.1.5 37576 d.58.26.1 39398 1dar 691 6.78e-02 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1h72C 296 9.62e-02 d.14.1.5 60712 d.58.26.1 60713 1qjcA 158 1.40e-01 1b6tA c.26.1.3 63328 1b6tA 159 1.43e-01 1b6tA c.26.1.3 31600 1bwsA 321 1.73e-01 1bsvA c.2.1.2 29812 1e6uA 321 3.40e-01 1bsvA c.2.1.2 29805 1vjs 483 5.20e-01 1bli b.71.1.1 27714 c.1.8.1 28701 1fd9A 213 5.97e-01 1fd9A d.26.1.1 59771 1cz1A 394 6.01e-01 1cz1A c.1.8.3 28839 1cec 343 6.02e-01 1ceo c.1.8.3 28809 1eqcA 394 6.03e-01 1cz1A c.1.8.3 28811 1ceo 343 6.22e-01 1ceo c.1.8.3 28808 1c0dA 358 7.49e-01 1eceA c.1.8.3 28815 1ej2A 181 7.68e-01 1f9aA c.26.1.3 59414 1bli 483 7.89e-01 1bli b.71.1.1 27715 c.1.8.1 28702 1dctA 324 8.37e-01 6mhtA c.66.1.10 34244 1bdmB 327 8.66e-01 1bmdA c.2.1.5 30138 d.162.1.1 42105 1bmdA 327 8.68e-01 1bmdA c.2.1.5 30139 d.162.1.1 42106 1i58A 189 9.02e-01 1b3qA d.122.1.3 61773 1bdmA 327 9.05e-01 1bmdA c.2.1.5 30137 d.162.1.1 42104 1g8jA 825 9.07e-01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1kk1A 410 9.99e-01 1eceA 358 1.06e+00 1eceA c.1.8.3 28813 1ll1 590 1.08e+00 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.1.5 21864 1gfsA 321 1.18e+00 c.2.1.2 29811 1bsvA 321 1.35e+00 1bsvA c.2.1.2 29809 1g8kA 825 1.63e+00 1g8jA b.52.2.2 26920 c.81.1.1 35328 1tr1A 447 1.77e+00 1e70M c.1.8.4 28957 1dpe 507 1.83e+00 1dpe c.94.1.1 35799 1dyqA 234 1.94e+00 3seb b.40.2.2 59140 d.15.6.1 59141 2cbf 234 2.38e+00 1cbf c.90.1.1 35588 1e43A 483 2.58e+00 1bli b.71.1.1 59217 c.1.8.1 59218 1dppA 507 2.72e+00 1dpe c.94.1.1 35800 1c4oA 664 2.81e+00 1d2mA c.37.1.13 32415 c.37.1.13 32416 1qoxN 449 3.03e+00 1qoxN c.1.8.4 28978 1d3hA 367 3.25e+00 1d3gA c.1.4.1 28601 1f9aA 168 3.31e+00 1f9aA c.26.1.3 31602 1fds 327 3.33e+00 1fds c.2.1.2 29838 1ff9A 450 3.39e+00 1ff9A c.2.1.3 30039 d.81.1.2 39954 1d3gA 367 3.51e+00 1d3gA c.1.4.1 28600 1b3qA 379 3.54e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1f20A 435 3.59e+00 b.43.4.1 64932 c.25.1.4 64933 1iciA 256 3.59e+00 1iciA c.31.1.5 62266 1b8pA 329 3.82e+00 1bmdA c.2.1.5 30147 d.162.1.1 42114 1iqrA 420 4.29e+00 a.99.1.1 66275 c.28.1.1 66276 1fwcA 100 4.58e+00 1ubpA d.8.1.1 37331 2kauA 100 4.58e+00 1ubpA d.8.1.1 37335 2nmbA 160 5.27e+00 2nmbA b.55.1.2 26994 1pdz 434 5.49e+00 4enl c.1.11.1 29215 d.54.1.1 38859 1a27 289 5.92e+00 1fds c.2.1.2 29839 1cbf 285 6.02e+00 1cbf c.90.1.1 35587 2oneA 436 6.07e+00 4enl c.1.11.1 29203 d.54.1.1 38847 1dkrA 317 6.65e+00 1dkuA c.61.1.2 34114 c.61.1.2 34115 1esfA 233 6.79e+00 3seb b.40.2.2 25146 d.15.6.1 37735 1fp1D 372 6.87e+00 1fpqA a.4.5.29 59939 c.66.1.12 59940 1pinA 163 7.02e+00 1pinA b.72.1.1 27802 d.26.1.1 38431 1har 216 7.54e+00 1rthA e.8.1.2 43025 1ubpA 101 7.55e+00 1ubpA d.8.1.1 37353 4ubpA 101 7.55e+00 1ubpA d.8.1.1 37352 1b9yC 246 8.26e+00 1b9yC c.47.1.6 33052 1lla 628 8.47e+00 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.1.5 21861 1fpzA 212 8.87e+00 1fpzA c.45.1.1 59976 3aig 202 9.16e+00 1atlA d.92.1.9 40321 1ex2A 189 9.18e+00 1ex2A c.51.4.2 33225 1qciA 262 9.55e+00 1qi7A d.165.1.1 42201 1g8fA 511 9.61e+00 1g8fA b.58.1.2 60348 c.26.1.5 60349 c.37.1.15 60350 1ihnA 113 1.01e+01 1ihnA c.103.1.1 62388 1e4iA 447 1.06e+01 1e70M c.1.8.4 59225 1iqvA 218 1.09e+01 1rss a.75.1.1 62661 1jhdA 396 1.11e+01 b.58.1.2 66712 c.26.1.5 66713 1fdt 327 1.13e+01 1fds c.2.1.2 29841 1cmiA 85 1.14e+01 1cmiA d.39.1.1 38551 1ig8A 486 1.14e+01 2yhx c.55.1.3 64746 c.55.1.3 64747 1lldA 319 1.16e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 1gegA 256 1.20e+01 1ybvA c.2.1.2 29888 1qgvA 142 1.20e+01 1qgvA c.47.1.8 33056 1sur 215 1.22e+01 1sur c.26.2.2 31620 1atlA 202 1.22e+01 1atlA d.92.1.9 40322 1bykA 255 1.26e+01 1bykA c.93.1.1 35706 2pvaA 345 1.29e+01 3pvaA d.153.1.3 41850 1hg3A 225 1.35e+01 1hg3A c.1.1.1 61025 1zfjA 491 1.36e+01 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1i1kA 309 1.37e+01 1daaA e.17.1.1 61533 1huvA 380 1.38e+01 c.1.4.1 61277 1dhn 121 1.43e+01 1dhn d.96.1.3 40663 1gw9A 388 1.44e+01 1clxA 347 1.45e+01 1taxA c.1.8.3 28899 1udb 338 1.47e+01 1xel c.2.1.2 29787 1f8yA 157 1.59e+01 1f8xA c.23.14.1 31395 1geqA 248 1.59e+01 2tysA c.1.2.4 28589 1d6aB 262 1.63e+01 1qi7A d.165.1.1 42198 1iirA 415 1.71e+01 1iirA c.87.1.5 62453 1e6qM 501 1.73e+01 1e70M c.1.8.4 28920 1gq6A 313 1.77e+01 4xis 387 1.77e+01 4xis c.1.15.3 29421 1nsf 273 1.78e+01 1d2nA c.37.1.13 32429 1a3gA 308 1.80e+01 1daaA e.17.1.1 43286 1e70M 501 1.83e+01 1e70M c.1.8.4 28926 1pea 385 1.83e+01 1pea c.93.1.1 35662 1dkuA 317 1.83e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1jn5A 140 1.86e+01 d.17.4.2 66921 2xis 387 1.93e+01 4xis c.1.15.3 29427 3xis 387 1.94e+01 4xis c.1.15.3 29423 1jkgA 140 1.99e+01 d.17.4.2 66795 1qipA 183 1.99e+01 1qipA d.32.1.1 38470 1ckmA 330 2.00e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1tap 60 2.04e+01 1kigI g.8.1.2 44569 1f74A 293 2.06e+01 1nal3 c.1.10.1 29079 1ehyA 294 2.08e+01 1ehyA c.69.1.11 34693 1bg1A 722 2.15e+01 1bg1A a.47.1.1 17767 b.2.5.1 22461 d.93.1.1 40527 1fpqA 372 2.18e+01 1fpqA a.4.5.29 59947 c.66.1.12 59948 1qnf 484 2.21e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 2trcP 217 2.22e+01 1b9yC c.47.1.6 33051 1f75A 249 2.25e+01 1f75A c.101.1.1 59662 1derA 547 2.29e+01 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1d0dA 60 2.32e+01 1kigI g.8.1.2 44566 1uok 558 2.34e+01 1uok b.71.1.1 27801 c.1.8.1 28788 1ihuA 589 2.36e+01 c.37.1.10 62394 c.37.1.10 62395 1brmA 367 2.36e+01 1brmA c.2.1.3 30030 d.81.1.1 39945 1efyA 350 2.37e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 2spo 154 2.38e+01 1a6m a.1.1.2 15053 1din 236 2.44e+01 1din c.69.1.9 34682 1aoiD 99 2.51e+01 1aoiD a.22.1.1 16452 4enl 436 2.52e+01 4enl c.1.11.1 29202 d.54.1.1 38846 1gcoA 261 2.53e+01 1ybvA c.2.1.2 29884 7odcA 424 2.57e+01 7odcA b.49.2.1 26488 c.1.6.1 28650 1a26 361 2.59e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1pbgA 468 2.61e+01 1e70M c.1.8.4 28946 1bh5A 183 2.63e+01 1qipA d.32.1.1 38476 1k77A 260 2.70e+01 1bfd 528 2.73e+01 1bfd c.31.1.3 31745 c.36.1.1 31801 c.36.1.1 31802 1h61A 364 2.75e+01 1oyc c.1.4.1 60657 1emsA 440 2.90e+01 1emsA d.13.1.1 37520 d.160.1.1 42086 1aw5 326 2.90e+01 1b4kA c.1.10.3 29181 9ldtA 332 2.91e+01 3ldh c.2.1.5 30154 d.162.1.1 42121 1oneA 436 2.92e+01 4enl c.1.11.1 29200 d.54.1.1 38844 1e2tA 284 2.94e+01 1e2tA d.3.1.5 37121 1f2tB 148 2.96e+01 1f2tB 3pbgA 468 2.97e+01 1e70M c.1.8.4 28951 1mgn 154 3.07e+01 1a6m a.1.1.2 15097 1d0iA 156 3.07e+01 2dhqA c.23.13.1 31383 1h4rA 314 3.14e+01 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1qj5A 429 3.16e+01 1dtyA c.67.1.4 34493 1fo5A 85 3.22e+01 1fo5A c.47.1.1 59922 2dtr 226 3.23e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1qo7A 394 3.26e+01 1qo7A c.69.1.11 34697 1rss 151 3.27e+01 1rss a.75.1.1 18392 1kvs 338 3.40e+01 1xel c.2.1.2 29799 1l1sA 113 3.41e+01 1xel 338 3.42e+01 1xel c.2.1.2 29786 1jd0A 263 3.49e+01 2cba b.74.1.1 62888 1lylA 504 3.51e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1bec 238 3.56e+01 1bec b.1.1.1 20627 b.1.1.2 21561 1mldA 314 3.59e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1cydA 244 3.62e+01 1cydA c.2.1.2 29825 1sqc 631 3.69e+01 2sqcA a.102.4.2 18858 a.102.4.2 18859 1e55A 512 3.70e+01 1e70M c.1.8.4 28934 1akeA 214 3.76e+01 1zin c.37.1.1 31905 g.41.2.1 45185 1enfA 212 3.85e+01 3seb b.40.2.2 25198 d.15.6.1 37787 2cmd 312 3.88e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1qcwA 410 3.88e+01 1gox c.1.4.1 28622 1g24A 211 3.89e+01 1g24A d.166.1.1 42270 1qqvA 67 3.91e+01 1qqvA a.14.1.1 16379 1a9xB 379 3.92e+01 1c3oB c.8.3.1 30732 c.23.16.1 31409