# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1pft 50 1.16e-02 1pft g.41.3.1 45206 1vk6A 269 6.88e-01 d.113.1.4,d.113.1.4 100851,100852 1ffkW 73 8.28e-01 1ffkW g.41.8.1 45315 1s72Z 73 8.39e-01 g.41.8.1 105345 1vqoZ 83 8.56e-01 2ct7A 86 9.27e-01 1ww8A 439 1.07e+00 1odhA 174 2.64e+00 d.239.1.1 86850 1neeA 138 2.93e+00 d.241.1.1,g.59.1.1 91841,91842 1kmtA 141 3.42e+00 b.1.18.8 77442 1jj2Y 73 3.51e+00 1ffkW g.41.8.1 63110 1rhoA 145 3.86e+00 1rhoA b.1.18.8 21899 1fsoA 139 3.88e+00 1rhoA b.1.18.8 60007 1rhoC 145 3.90e+00 1rhoA b.1.18.8 21901 1rlyA 60 3.91e+00 g.41.3.1 104988 1u8bA 133 4.32e+00 1jm7A 112 4.43e+00 g.44.1.1 66880 1jm1A 204 5.05e+00 b.33.1.1 71745 1wpkA 146 5.35e+00 1vckA 115 5.54e+00 1lxyA 409 5.77e+00 d.126.1.4 91154 1s9rA 410 5.87e+00 d.126.1.4 98758 1bc8C 93 6.47e+00 1awcA a.4.5.21 16168 1zgwA 139 6.57e+00 1fp0A 88 7.26e+00 1fp0A g.50.1.2 45361 1wd2A 60 7.27e+00 g.44.1.1 109232 1nykA 165 7.94e+00 b.33.1.1 86408 1x75A 132 8.13e+00 1dl6A 58 8.19e+00 1dl6A g.41.3.1 45207 1qxfA 66 8.26e+00 g.41.8.4 96527 2bydA 323 8.81e+00 1ogdA 131 9.28e+00 c.133.1.1 92893 1j6uA 469 9.39e+00 c.5.1.1,c.59.1.1,c.72.2.1 77094,77095,77096 1vd4A 62 9.43e+00 4rxn 54 9.91e+00 1rb9 g.41.5.1 45226 5rxn 54 9.91e+00 1rb9 g.41.5.1 45225 1exkA 79 1.01e+01 1exkA g.54.1.1 45384 1plr 258 1.13e+01 1plq d.131.1.2,d.131.1.2 41390,41391 1rfs 139 1.14e+01 1rfs b.33.1.1 24434 1yk4A 52 1.22e+01 1etc 110 1.24e+01 1awcA a.4.5.21 16162 1l1oC 181 1.32e+01 b.40.4.3 73480 1wxiA 275 1.35e+01 1bor 56 1.41e+01 1bor g.44.1.1 45324 1g25A 65 1.46e+01 1g25A g.44.1.1 45325 1iro 54 1.49e+01 1rb9 g.41.5.1 45223 2bwfA 77 1.50e+01 1d0qA 103 1.54e+01 1d0qA g.41.3.2 45208 1mr1C 99 1.56e+01 d.217.1.2 79420 1ajw 145 1.56e+01 1rhoA b.1.18.8 21905 1g47A 77 1.57e+01 1g47A g.39.1.3,g.39.1.3 45147,45148 1b2jA 54 1.62e+01 1rb9 g.41.5.1 45231 1i5hW 50 1.62e+01 1i5hW b.72.1.1 61785 1k81A 36 1.80e+01 g.59.1.1 72136 1i69A 219 1.89e+01 c.94.1.1 61825 1ab4 477 1.94e+01 1ab4 e.11.1.1 43251 1oahA 519 1.94e+01 a.138.1.3 86736 1ur6B 52 1.95e+01 g.44.1.1 99812 1k0mA 241 1.96e+01 a.45.1.1,c.47.1.5 67949,67950 1f62A 51 2.00e+01 1f62A g.50.1.2 45360 1ee8A 266 2.17e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1n9dA 199 2.22e+01 a.26.1.1 85464 1pfvA 551 2.30e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1k0nA 241 2.32e+01 a.45.1.1,c.47.1.5 67953,67954 1f4lA 551 2.36e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1a67 108 2.37e+01 1cewI d.17.1.2 38000 1fe8A 196 2.38e+01 1atzA c.62.1.1 59783 1dsvA 31 2.43e+01 1dsvA g.40.1.1 45174 1gvjA 146 2.51e+01 a.4.5.21 90525 1rb9 53 2.53e+01 1rb9 g.41.5.1 45214 8rxnA 52 2.64e+01 1rb9 g.41.5.1 45215 1ao3A 187 2.65e+01 1atzA c.62.1.1 34134 1e53A 59 2.70e+01 1e53A g.49.1.2 45356 1qyp 57 2.71e+01 1qyp g.41.3.1 45205 1qqtA 551 2.87e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1i50L 70 2.96e+01 g.41.9.2 61766 1wijA 140 3.11e+01 1wrvA 308 3.15e+01 1ak2 233 3.16e+01 1zin c.37.1.1,g.41.2.1 31894,45195 1e4uA 78 3.16e+01 1e4uA g.44.1.1 59231 2c43A 323 3.26e+01 1zxzA 197 3.28e+01 1ctl 85 3.30e+01 g.39.1.3,g.39.1.3 45133,45134 1atzB 189 3.36e+01 1atzA c.62.1.1 34133 1pn0A 665 3.37e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1weoA 93 3.39e+01 1a90 108 3.46e+01 1cewI d.17.1.2 38001 1vfyA 73 3.50e+01 1vfyA g.50.1.1 45357 1q35A 320 3.52e+01 c.94.1.1 95661 2btfA 375 3.59e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1uby 367 3.60e+01 1uby a.128.1.1 19435 1xxoA 147 3.60e+01 1w9aA 147 3.62e+01 1dx8A 70 3.65e+01 1rb9 g.41.5.1 45243 1k7hA 476 3.66e+01 c.76.1.1 72101 1frvA 264 3.68e+01 2frvA e.19.1.1 43308 1b13A 54 3.70e+01 1rb9 g.41.5.1 45227 1zbdB 134 3.71e+01 1zbdB g.50.1.1 45359 1adn 92 3.73e+01 1adn g.48.1.1 45348 1dxgA 36 3.73e+01 1dxgA g.41.5.2 45247 1v87A 114 3.80e+01 g.44.1.1 108422 1zzpA 130 3.80e+01 1aky 221 3.81e+01 1zin c.37.1.1,g.41.2.1 31896,45197 2fe5A 94 3.95e+01 1yl35 60 3.95e+01 2bx9A 53 3.97e+01 1upiA 225 3.97e+01 b.82.1.1 99757 1fps 348 3.98e+01 1uby a.128.1.1 19436 1b77A 228 4.08e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1t0bA 252 4.09e+01 c.23.16.6 106199 2a1rA 430 4.22e+01 1qli 113 4.40e+01 1iml g.39.1.3,g.39.1.3 45141,45142 2a20A 62 4.46e+01 1kxiA 62 4.48e+01 1tgxA g.7.1.1 44417 1mswD 883 4.49e+01 e.8.1.3 79427 1c3hA 137 4.57e+01 b.22.1.1 90405 1mea 28 4.62e+01 g.41.1.1 45176 1plq 258 4.77e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1vor2 58 4.77e+01 2aaiB 262 4.85e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 1azzA 226 4.96e+01 5ptp b.47.1.2 26072 1sp1 29 5.02e+01 g.37.1.1 45051 1m1qA 91 5.10e+01 a.138.1.3 74419 1v7oA 165 5.15e+01 d.67.1.2 100480 1vhqA 232 5.24e+01 c.23.16.2 100696 1ka2A 499 5.25e+01 d.92.1.5 77305 1l8dA 112 5.25e+01 h.4.12.1 73687 1rdg 53 5.26e+01 1rb9 g.41.5.1 45221 1ji1A 637 5.33e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1zin 217 5.35e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1uh4A 637 5.40e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1zetA 388 5.44e+01 2aq6A 147 5.50e+01 1faq 52 5.51e+01 1far g.49.1.1 45352 1chc 68 5.56e+01 1chc g.44.1.1 45323 1m2tB 263 5.76e+01 b.42.2.1,b.42.2.1 84762,84763 2awpA 198 5.85e+01 1k3eA 156 5.88e+01 d.198.1.1 68103 1bq8A 54 5.89e+01 1rb9 g.41.5.1 45237 1bq9A 54 5.89e+01 1rb9 g.41.5.1 45238 2aheA 267 5.91e+01 2csvA 72 5.94e+01 1zy1B 197 6.00e+01 1dvpA 220 6.04e+01 1dvpA a.118.9.2,g.50.1.1 19216,45358 1r5mA 425 6.05e+01 1kezA 300 6.05e+01 c.69.1.22 68546 1z6uA 150 6.05e+01 1brfA 53 6.12e+01 1rb9 g.41.5.1 45236 2drpA 66 6.16e+01 2drpA g.37.1.1,g.37.1.1 45026,45027 1ghtA 105 6.31e+01 2rslA c.53.1.1 60526 1h38C 883 6.33e+01 e.8.1.3 76627 1ux6A 350 6.36e+01 b.29.1.16,g.75.1.1 100145,100146 2ch4A 320 6.41e+01 1h38D 883 6.41e+01 e.8.1.3 76628 1qdlA 422 6.43e+01 1qdlA d.161.1.1 42088 1fujA 221 6.44e+01 1a7s b.47.1.2 26349 1dgfA 497 6.45e+01 1cf9A e.5.1.1 42782 1h38B 883 6.47e+01 e.8.1.3 76626 1deoA 233 6.47e+01 1deoA c.23.10.4 31345 1cr8A 42 6.49e+01 1ajj g.12.1.1 44613 1pk6C 129 6.51e+01 b.22.1.1 94803 1pueE 89 6.58e+01 1awcA a.4.5.21 16165 1zip 217 6.63e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1yuf 50 6.67e+01 3tgf g.3.11.1 44295 1b8tA 192 6.68e+01 1b8tA g.39.1.3,g.39.1.3,g.39.1.3,g.39.1.3 45135,45136,45137,45138 6rxn 46 6.82e+01 1rb9 g.41.5.1 45222 1c28A 135 6.83e+01 1c28A b.22.1.1 23857 2aq4A 434 6.97e+01 1a7cA 379 7.04e+01 1sek e.1.1.1 42660 1fjgS 93 7.05e+01 1qkfA d.28.1.1 38451 1xu1R 42 7.08e+01 1yagA 375 7.14e+01 1yagA c.55.1.1,c.55.1.1 33449,33450 1twfL 70 7.15e+01 1dl0A 37 7.17e+01 1dl0A g.3.6.2 44112 2b9dA 52 7.18e+01 1oy1A 228 7.19e+01 c.23.16.2 87548 1vq0A 302 7.19e+01 1twfI 122 7.27e+01 1ywzA 175 7.37e+01 2booA 247 7.41e+01 1afp 51 7.42e+01 1afp g.26.1.1 44947 1hyuA 521 7.46e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1dghB 498 7.48e+01 1cf9A e.5.1.1 42791 1zs7A 190 7.49e+01 2au3A 407 7.52e+01 1far 52 7.52e+01 1far g.49.1.1 45351 1jr7A 311 7.54e+01 b.82.2.3 63255 2sak 121 7.57e+01 2sak d.15.5.1 37711 1ae1A 273 7.59e+01 1bdb c.2.1.2 29943 1rmd 116 7.62e+01 1rmd g.37.1.1,g.44.1.1 45025,45322 1rutX 188 7.66e+01 7catA 506 7.71e+01 1cf9A e.5.1.1 42781 1ww9A 392 7.76e+01 1cokA 68 7.78e+01 1cokA a.60.1.2 17945 2mllB 255 7.86e+01 1abrB b.42.2.1,b.42.2.1 25567,25568 2ct0A 74 7.87e+01 2an1A 292 8.00e+01 1ghr 306 8.10e+01 1aq0A c.1.8.3 28844 1zx2A 147 8.11e+01 1arf 29 8.18e+01 g.37.1.1 45035 1p6pA 125 8.20e+01 b.60.1.2 87839 1atzA 189 8.26e+01 1atzA c.62.1.1 34132 1uayA 242 8.28e+01 c.2.1.2 88390 1eqnA 321 8.30e+01 1dd9A e.13.1.1 43256 1l1dA 152 8.36e+01 b.88.1.3 73452 1tsg 98 8.36e+01 1tsg 1j6zA 376 8.38e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1jzxM 60 8.48e+01 i.1.1.2 67887 1ldjA 760 8.61e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1dxsA 80 8.66e+01 1cokA a.60.1.2 17944 1xm0A 147 8.72e+01 1u79A 129 8.80e+01 d.26.1.1 107714 1are 29 8.80e+01 g.37.1.1 45034 1qz5A 375 8.82e+01 c.55.1.1,c.55.1.1 96614,96615 1z92B 219 8.82e+01 1en7A 157 8.93e+01 1en7A a.140.4.1,d.4.1.5 64733,64734