# 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 1ivhA 394 5.49e-01 3mdeA a.29.3.1 16608 e.6.1.1 42869 1eb6A 177 1.68e+00 d.92.1.12 64895 1j99A 293 3.94e+00 1a26 361 4.69e+00 1a26 a.41.1.1 17412 d.166.1.2 42274 1efyA 350 4.77e+00 1a26 a.41.1.1 17413 d.166.1.2 42275 1furA 467 5.22e+00 1furA a.127.1.1 19403 1fuoA 467 5.23e+00 1furA a.127.1.1 19411 1a80 277 6.05e+00 1frb c.1.7.1 28700 1jceA 344 7.14e+00 c.55.1.1 62876 c.55.1.1 62877 1d2zA 108 7.14e+00 1d2zA a.77.1.1 18437 1jcfA 344 7.15e+00 c.55.1.1 62878 c.55.1.1 62879 1dn1A 594 7.50e+00 1dn1A e.25.1.1 43357 1avsA 90 8.34e+00 1cll a.39.1.5 17226 1bpoA 494 8.36e+00 1bpoA a.118.1.4 19143 b.69.6.1 27670 1derA 547 9.15e+00 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1jlvA 209 9.71e+00 1g33A 73 1.02e+01 a.39.1.4 65121 1gqeA 365 1.04e+01 1f74A 293 1.05e+01 1nal3 c.1.10.1 29079 1orc 71 1.05e+01 1orc a.35.1.2 17054 1e3mA 800 1.10e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1e3hA 757 1.15e+01 1e3hA a.4.9.1 16257 d.14.1.4 37572 d.14.1.4 37573 d.52.3.1 38810 d.101.1.1 40695 d.101.1.1 40696 1ctj 89 1.19e+01 1ctj a.3.1.1 15798 1e3pA 757 1.21e+01 1e3hA a.4.9.1 16258 b.40.4.5 25328 d.14.1.4 37574 d.14.1.4 37575 d.52.3.1 38811 d.101.1.1 40697 d.101.1.1 40698 1d6mA 653 1.23e+01 1d6mA e.10.1.1 43248 1hw6A 278 1.27e+01 1frb c.1.7.1 61296 1jpdX 324 1.29e+01 c.1.11.2 67014 d.54.1.1 67015 1fc6A 388 1.30e+01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1evyA 366 1.31e+01 1evyA a.100.1.6 18811 c.2.1.6 30215 1iq8A 582 1.32e+01 1j8uA 325 1.32e+01 1copD 66 1.42e+01 1orc a.35.1.2 17058 1ef4A 55 1.45e+01 1ef4A a.4.11.1 16272 4pah 308 1.45e+01 4pah d.178.1.1 42576 1pah 308 1.46e+01 4pah d.178.1.1 42578 1fs1B 141 1.60e+01 1vcbB a.122.1.1 19252 d.42.1.2 38664 1f8rA 498 1.61e+01 1f8rA c.3.1.2 30410 d.16.1.5 37974 1k8kC 372 1.65e+01 b.69.4.1 68308 1f1zA 273 1.65e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1cdp 109 1.76e+01 1a75A a.39.1.4 17197 4cpv 109 1.77e+01 1a75A a.39.1.4 17198 1iatA 557 1.85e+01 1dqrA c.80.1.2 62123 1e4yA 214 1.86e+01 1zin c.37.1.1 31901 g.41.2.1 45181 1jjyA 636 1.94e+01 1jjyA e.26.1.2 63141 1a1z 91 1.94e+01 1a1z a.77.1.1 18427 1osa 148 1.97e+01 1cll a.39.1.5 17300 1f61A 429 2.06e+01 1dquA c.1.12.6 29319 1dmwA 307 2.08e+01 4pah d.178.1.1 42580 1k92A 455 2.21e+01 c.26.2.1 68325 d.210.1.1 68326 1znf 27 2.22e+01 g.37.1.1 45036 1bvb 211 2.24e+01 1bvb a.138.1.3 19683 1moq 368 2.24e+01 1moq c.80.1.1 35302 1fmjA 351 2.28e+01 c.37.1.5 59879 1shbA 104 2.28e+01 1fmk d.93.1.1 40425 1l7uA 263 2.29e+01 1m40A 263 2.29e+01 1amuA 563 2.29e+01 1amuA e.23.1.1 43351 1fn9A 365 2.30e+01 1fn9A d.196.1.1 59894 1ib2A 349 2.32e+01 1ib2A a.118.1.8 62141 1btl 263 2.41e+01 1btl e.3.1.1 42691 1ermA 263 2.44e+01 1btl e.3.1.1 42690 1exrA 148 2.44e+01 1cll a.39.1.5 17299 1ft5A 211 2.46e+01 1bvb a.138.1.3 19681 1fqgA 263 2.47e+01 1btl e.3.1.1 42699 1ku2A 241 2.47e+01 5pal 109 2.62e+01 1a75A a.39.1.4 17215 1ib3A 349 2.62e+01 1ib2A a.118.1.8 62142 1qhiA 366 2.62e+01 1qhiA c.37.1.1 31860 1kimA 366 2.63e+01 1qhiA c.37.1.1 31864 1qhlA 227 2.63e+01 1qhlA c.37.1.12 32382 1gwcA 230 2.67e+01 1yghA 164 2.67e+01 1yghA d.108.1.1 40802 1qp6A 35 2.68e+01 1qp6A k.16.1.1 46443 2ak3A 226 2.73e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1fqvD 149 2.86e+01 1fqvD a.122.1.1 19263 d.42.1.2 38667 1tfe 145 2.96e+01 1tfe d.43.1.1 38680 3vtk 343 2.96e+01 1qhiA c.37.1.1 31884 1fqvJ 149 2.97e+01 1fqvD a.122.1.1 19266 d.42.1.2 38670 1hy3A 294 3.03e+01 1cll 148 3.04e+01 1cll a.39.1.5 17263 1kkhA 317 3.09e+01 1epuA 591 3.12e+01 1dn1A e.25.1.1 43358 1ocrD 147 3.13e+01 1ocrD f.2.1.3 43541 3cln 148 3.19e+01 1cll a.39.1.5 17286 1kr7A 110 3.34e+01 1ap6A 198 3.35e+01 1avmA a.2.11.1 15746 d.44.1.1 38705 1din 236 3.41e+01 1din c.69.1.9 34682 1gnlA 544 3.43e+01 1cawB 184 3.47e+01 1caxB b.82.1.2 28113 1abmA 198 3.48e+01 1avmA a.2.11.1 15748 d.44.1.1 38707 1kl9A 182 3.48e+01 1chuA 540 3.59e+01 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1f07A 321 3.64e+01 1ezwA c.1.16.3 59560 1f5sA 211 3.69e+01 1f5sA c.108.1.4 59656 1j97A 211 3.69e+01 1f5sA c.108.1.4 62753 1l7mA 211 3.70e+01 1kl1A 419 3.70e+01 1e2kA 331 3.74e+01 1qhiA c.37.1.1 31854 1hi0P 664 3.77e+01 1hi0P e.8.1.6 61051 1hlvA 131 3.77e+01 a.4.1.7 65854 a.4.1.7 65855 1hhsA 664 3.79e+01 1hi0P e.8.1.6 61045 1f8mA 429 3.81e+01 1dquA c.1.12.6 29315 2occD 147 3.91e+01 1ocrD f.2.1.3 43521 1zymA 258 3.96e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1hcrA 52 3.96e+01 1hcrA a.4.1.2 16020 1ltm 320 3.97e+01 1ltm d.2.1.6 36992