# List of top-scoring protein chains for t2k-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 1m1fA 110 1.83e+00 b.34.6.2 78401 2atrA 138 4.83e+00 1v1rA 400 4.89e+00 c.36.1.11 108272 102l 165 6.52e+00 1l92 d.2.1.3 36724 1j2mA 99 6.73e+00 a.165.1.1 84018 2c1dA 264 7.04e+00 2bfdA 400 8.12e+00 1kn6A 90 8.66e+00 d.58.3.3 72770 1ne8A 117 8.89e+00 b.34.6.2 80424 1vjyA 303 9.39e+00 d.144.1.7 108633 2aegA 268 9.82e+00 1x7yA 400 1.10e+01 1kgcD 206 1.13e+01 b.1.1.1,b.1.1.2 77384,77385 1lm8B 118 1.15e+01 d.15.1.1 74033 1q79A 514 1.17e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1kb9C 385 1.21e+01 f.32.1.1,f.21.1.2 77315,77316 1py5A 326 1.22e+01 d.144.1.7 104389 1jmoA 480 1.25e+01 e.1.1.1 77138 1iml 76 1.26e+01 1iml g.39.1.3,g.39.1.3 45145,45146 1ezvC 385 1.27e+01 1be3C f.32.1.1,f.21.1.2 75833,75834 1zowA 313 1.28e+01 1m5dA 263 1.51e+01 c.94.1.1 78641 1mqiA 263 1.52e+01 c.94.1.1 91398 1f5aA 513 1.52e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1b6cB 342 1.62e+01 1b6cB d.144.1.7 41673 1m5eA 263 1.69e+01 c.94.1.1 78642 1mqdA 261 1.76e+01 c.94.1.1 85049 1ztsA 139 1.87e+01 1hi0P 664 2.06e+01 1hi0P e.8.1.6 61051 104lA 166 2.12e+01 1l92 d.2.1.3 36969 1oghA 204 2.22e+01 b.85.4.1 86994 1h09A 338 2.25e+01 b.109.1.1,c.1.8.8 83420,83421 1bkjA 240 2.28e+01 1bkjA d.90.1.1 40243 1agqD 135 2.37e+01 1agqA g.17.1.2 44792 1kyoC 385 2.40e+01 f.32.1.1,f.21.1.2 75904,75905 1k8kA 418 2.41e+01 c.55.1.1,c.55.1.1 68305,68306 2agmA 167 2.48e+01 2bkaA 242 2.52e+01 1u04A 771 2.59e+01 b.34.14.1,c.55.3.10 107539,107540 1ae3 86 2.61e+01 1gvp b.40.4.7 25381 1esxA 96 2.63e+01 1esxA j.11.1.1 59501 1hcnB 145 2.68e+01 1hcnB g.17.1.4 44810 1olsA 400 2.70e+01 c.36.1.11 93331 131l 164 2.76e+01 1l92 d.2.1.3 36685 1vpsB 289 2.81e+01 1vpsA b.121.6.1 23337 1sj1A 66 2.84e+01 d.58.1.4 105595 1vpsA 289 2.90e+01 1vpsA b.121.6.1 23336 1mg2B 131 2.91e+01 g.21.1.1 79060 1sdeA 347 3.01e+01 1agqA 135 3.08e+01 1agqA g.17.1.2 44789 1ml8A 134 3.23e+01 d.227.1.2 85013 1m2oA 768 3.25e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1hvbA 349 3.44e+01 3pte e.3.1.1 42686 1v8eA 224 3.57e+01 2bbkL 125 3.65e+01 2bbkL g.21.1.1 44882 2ae0X 345 3.67e+01 1k7hA 476 3.69e+01 c.76.1.1 72101 1yqsA 349 3.85e+01 1nnvA 110 3.91e+01 d.17.7.1 92012 1vd6A 224 3.98e+01 1ze3H 122 4.09e+01 2acaA 189 4.12e+01 1mplA 349 4.18e+01 e.3.1.1 79387 3pte 349 4.34e+01 3pte e.3.1.1 42687 1qcrC 378 4.34e+01 1be3C f.32.1.1,f.21.1.2 75931,75932 1iqrA 420 4.34e+01 a.99.1.1,c.28.1.1 66275,66276 1l8aA 886 4.40e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1dr9A 201 4.49e+01 1dr9A b.1.1.1,b.1.1.3 19762,21684 1f28A 297 4.50e+01 1bkpA d.117.1.1 59608 1pkhA 204 4.53e+01 b.85.4.1 94832 1ng0A 253 4.54e+01 b.121.4.7 80475 1xszA 356 4.56e+01 1vcbA 118 4.65e+01 1vcbA d.15.1.1 37603 1ydlA 79 4.67e+01 1ezvD 245 4.74e+01 1be3D a.3.1.3,f.23.11.1 59546,59547 1imoA 88 4.91e+01 1imoA c.15.1.2 62590 1kb9D 246 5.00e+01 a.3.1.3,f.23.11.1 77317,77318 1twfA 1733 5.09e+01 108l 164 5.12e+01 1l92 d.2.1.3 36669 1kyoD 248 5.16e+01 a.3.1.3,f.23.11.1 73254,73255 5lyz 129 5.17e+01 3lzt d.2.1.2 36289 1ppjC 379 5.33e+01 f.32.1.1,f.21.1.2 104256,104257 1o7nA 449 5.34e+01 b.33.1.2,d.129.3.3 81162,81163 199l 164 5.35e+01 1l92 d.2.1.3 36855 1xewY 172 5.43e+01 193l 129 5.48e+01 3lzt d.2.1.2 36247 1abrA 251 5.55e+01 1mrj d.165.1.1 42196 145l 164 5.63e+01 1l92 d.2.1.3 36860 1mtyD 512 5.67e+01 1mhyD a.25.1.2 16742 158l 164 5.71e+01 1l92 d.2.1.3 36747 143l 164 5.78e+01 1l92 d.2.1.3 36857 164l 164 5.80e+01 1l92 d.2.1.3 36714 112l 164 5.85e+01 1l92 d.2.1.3 36677 162l 164 5.87e+01 1l92 d.2.1.3 36749 146l 164 5.91e+01 1l92 d.2.1.3 36763 130l 164 5.91e+01 1l92 d.2.1.3 36638 126l 164 5.92e+01 1l92 d.2.1.3 36699 123l 164 5.95e+01 1l92 d.2.1.3 36697 141l 164 5.97e+01 1l92 d.2.1.3 36863 1pwgA 349 5.98e+01 e.3.1.1 104340 138l 164 5.99e+01 1l92 d.2.1.3 36679 155l 164 5.99e+01 1l92 d.2.1.3 36762 2fclA 169 6.06e+01 114l 164 6.07e+01 1l92 d.2.1.3 36663 1wrjA 156 6.10e+01 115l 164 6.10e+01 1l92 d.2.1.3 36700 128l 164 6.14e+01 1l92 d.2.1.3 36634 1ae2 87 6.15e+01 1gvp b.40.4.7 25382 195l 164 6.17e+01 1l92 d.2.1.3 36841 118l 164 6.17e+01 1l92 d.2.1.3 36642 125l 164 6.18e+01 1l92 d.2.1.3 36672 122l 164 6.19e+01 1l92 d.2.1.3 36667 144l 164 6.19e+01 1l92 d.2.1.3 36893 1l92 164 6.20e+01 1l92 d.2.1.3 36629 129l 164 6.25e+01 1l92 d.2.1.3 36660 163l 164 6.27e+01 1l92 d.2.1.3 36658 170l 164 6.28e+01 1l92 d.2.1.3 36968 1hhsA 664 6.28e+01 1hi0P e.8.1.6 61045 156l 164 6.31e+01 1l92 d.2.1.3 36709 2bmoA 447 6.31e+01 159l 164 6.34e+01 1l92 d.2.1.3 36682 2fnjB 118 6.34e+01 166l 164 6.36e+01 1l92 d.2.1.3 36681 1ogaD 215 6.36e+01 b.1.1.1,b.1.1.2 86990,86991 127l 164 6.39e+01 d.2.1.3 36745 1gvp 87 6.50e+01 1gvp b.40.4.7 25369 1h32A 261 6.54e+01 a.3.1.8,a.3.1.8 76618,76619 1mr1C 99 6.61e+01 d.217.1.2 79420 1broA 277 6.64e+01 1brt c.69.1.12 34700 1ndoA 449 6.69e+01 1ndoA b.33.1.2,d.129.3.3 24444,41323 1nqkA 381 6.78e+01 c.1.16.4 92050 1x9zA 188 6.88e+01 152l 164 6.90e+01 1l92 d.2.1.3 36904 107l 164 6.92e+01 1l92 d.2.1.3 36690 1x4sA 59 6.92e+01 139l 164 6.95e+01 1l92 d.2.1.3 36643 192l 164 7.02e+01 1l92 d.2.1.3 36815 1brt 277 7.10e+01 1brt c.69.1.12 34699 1x1gA 129 7.15e+01 1ofdA 1520 7.30e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1dmmA 131 7.31e+01 1opy d.17.4.3 38114 1l58 164 7.35e+01 1l92 d.2.1.3 36635 147l 164 7.39e+01 1l92 d.2.1.3 36864 1mfqC 129 7.43e+01 a.36.1.1 79046 198l 164 7.46e+01 1l92 d.2.1.3 36785 140l 164 7.58e+01 1l92 d.2.1.3 36891 1vqb 87 7.64e+01 1gvp b.40.4.7 25370 1wyuB 474 7.76e+01 1flcA 432 7.84e+01 1flcA b.19.1.3,c.23.10.2 23837,31337 160l 164 7.94e+01 1l92 d.2.1.3 36748 1ib8A 164 8.00e+01 b.38.2.1,d.52.4.1 71168,71169 1uj8A 77 8.04e+01 1x3eA 165 8.04e+01 1nzaA 103 8.05e+01 d.58.5.2 86444 196l 164 8.10e+01 1l92 d.2.1.3 36927 111l 164 8.15e+01 1l92 d.2.1.3 36661 1eg9A 449 8.18e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1at6 129 8.22e+01 3lzt d.2.1.2 36333 1p36A 164 8.25e+01 d.2.1.3 93978 1hvyA 288 8.25e+01 1bkpA d.117.1.1 41049 142l 164 8.36e+01 1l92 d.2.1.3 36874 1cb6A 691 8.43e+01 1cb6A c.94.1.2,c.94.1.2 35840,35841 1oh0A 131 8.43e+01 d.17.4.3 87004 137lA 164 8.43e+01 1l92 d.2.1.3 36791 1gx5A 536 8.46e+01 e.8.1.4 70682 1oiaA 95 8.48e+01 d.58.7.1 87051 1wdiA 345 8.49e+01 1f13A 731 8.55e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21877,22163,22164,37107 2ar0A 541 8.64e+01 1swyA 164 8.68e+01 1sx7A 164 8.74e+01 1a8uA 277 8.79e+01 1brt c.69.1.12 34703 1evuA 731 8.80e+01 1f13A b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 21883,22175,22176,37113 1go3E 187 8.95e+01 b.40.4.5,d.230.1.1 83054,83055 1uvjA 664 8.97e+01 e.8.1.6 100045 161l 164 8.97e+01 1l92 d.2.1.3 36636 1lw9A 164 8.98e+01 d.2.1.3 84727