# List of top-scoring protein chains for t2k-100-30-str2-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 1rypB 250 1.02e+00 1rypB d.153.1.4 41933 1vpkA 378 1.32e+00 1z9lA 128 1.34e+00 1qwtA 255 1.95e+00 b.26.1.3 96501 1on0A 158 2.32e+00 d.108.1.1 87095 1ufhA 180 2.34e+00 d.108.1.1 88485 1qxrA 189 2.63e+00 b.82.1.7 96552 1gumA 222 2.80e+00 1pgtA a.45.1.1,c.47.1.5 17683,32977 1hn9A 317 2.95e+00 1hn9A c.95.1.2,c.95.1.2 35977,35978 1hnjA 317 2.95e+00 1hn9A c.95.1.2,c.95.1.2 35969,35970 1eblB 317 3.02e+00 1hn9A c.95.1.2,c.95.1.2 35975,35976 2gaiA 633 3.04e+00 1gulA 222 3.41e+00 1pgtA a.45.1.1,c.47.1.5 17675,32969 1bbzE 58 3.55e+00 1bbzA b.34.2.1 24479 1bbzA 58 3.59e+00 1bbzA b.34.2.1 24477 1eblA 317 4.04e+00 1hn9A c.95.1.2,c.95.1.2 35973,35974 1awo 62 4.24e+00 1bbzA b.34.2.1 24482 1x82A 190 4.70e+00 1plfA 72 4.79e+00 1tvxA d.9.1.1 37373 1aboA 62 4.81e+00 1bbzA b.34.2.1 24474 1gzqA 300 4.93e+00 b.1.1.2,d.19.1.1 70818,70819 1jjgA 102 5.09e+00 b.40.4.5 71696 1k3bA 119 5.22e+00 b.61.5.1 72016 1go4E 100 5.46e+00 h.1.22.1 70296 2a5jA 191 5.49e+00 1rypC 244 6.75e+00 1rypC d.153.1.4 41934 1zowA 313 6.80e+00 1womA 271 7.25e+00 3thiA 371 7.66e+00 2thiA c.94.1.1 35792 1ho8A 480 8.27e+00 1ho8A a.118.1.9 61107 2c0cA 362 8.27e+00 1a7qH 116 1.07e+01 1gc1H b.1.1.1 19955 1i1qA 520 1.07e+01 1qdlA d.161.1.1 61543 1fqvA 336 1.20e+01 1fqvA a.158.1.1,c.10.1.3 19254,30856 5p21 166 1.24e+01 1ctqA c.37.1.8 31966 1k3yA 221 1.24e+01 a.45.1.1,c.47.1.5 77245,77246 1kaeA 434 1.25e+01 c.82.1.2 72247 1k75A 434 1.27e+01 c.82.1.2 68253 1lwjA 441 1.28e+01 b.71.1.1,c.1.8.1 74303,74304 1xeeA 91 1.31e+01 1gseA 221 1.36e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1k3lA 221 1.39e+01 a.45.1.1,c.47.1.5 77229,77230 1agp 166 1.42e+01 1ctqA c.37.1.8 31985 1x47A 98 1.50e+01 1otgA 125 1.53e+01 1otgA d.80.1.2 39831 1e1hA 287 1.54e+01 d.92.1.7 83167 1ctqA 166 1.57e+01 1ctqA c.37.1.8 31965 2aabH 243 1.58e+01 821p 166 1.68e+01 1ctqA c.37.1.8 31969 1phk 298 1.71e+01 1cdkA d.144.1.7 41635 1u20A 212 1.75e+01 2gf9A 189 1.81e+01 1rybA 212 1.86e+01 c.56.3.1 98098 1t9mA 214 1.87e+01 1pmaA 233 1.91e+01 1pmaA d.153.1.4 41918 2f9lA 199 1.96e+01 1r77A 103 1.96e+01 1x3sA 195 2.07e+01 1wqgA 185 2.10e+01 1cf4B 44 2.31e+01 1cf4B 1vprA 374 2.31e+01 1rgxA 114 2.31e+01 g.77.1.1 104932 1b5sA 242 2.34e+01 1eaf c.43.1.1 32626 1hzpA 335 2.38e+01 1hn9A c.95.1.2,c.95.1.2 61455,61456 2a9mH 126 2.47e+01 1jmtA 104 2.50e+01 d.58.7.3 63180 1k4nA 192 2.56e+01 d.32.1.5 72059 2gw6A 123 2.56e+01 1cojA 212 2.60e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1yarA 233 2.68e+01 1vkcA 158 2.80e+01 8fabB 224 2.82e+01 1igtB b.1.1.1,b.1.1.2 19773,20883 1y74A 57 2.99e+01 2bmeA 186 3.06e+01 1rw2A 152 3.07e+01 a.118.19.1 97961 1ic7H 114 3.11e+01 1f3rB b.1.1.1 62258 1omwA 689 3.11e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 2adgB 222 3.12e+01 1ze3D 125 3.28e+01 1n13B 113 3.32e+01 1vd3A 217 3.33e+01 1nt2A 210 3.43e+01 c.66.1.3 86149 1l3lA 234 3.45e+01 a.4.6.2,d.110.5.1 73541,73542 1avv 151 3.62e+01 1efnB d.102.1.1 40703 1px5A 349 3.71e+01 a.160.1.2,d.218.1.6 95277,95278 1a2yB 116 3.77e+01 1gc1H b.1.1.1 19927 1z6oM 191 3.77e+01 1fvrA 327 3.78e+01 d.144.1.7 60047 1ppo 216 3.84e+01 1cs8A d.3.1.1 37020 2a9nH 126 3.86e+01 1k6zA 141 4.08e+01 d.198.1.1 68247 1f3aA 222 4.10e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1c6vX 81 4.15e+01 1ihvA b.34.7.1 24641 1u6eA 335 4.17e+01 1uacH 114 4.25e+01 b.1.1.1 99132 1a7oH 116 4.35e+01 1gc1H b.1.1.1 19943 1fnnA 389 4.42e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1j1xH 114 4.43e+01 b.1.1.1 77063 1vf1A 229 4.44e+01 1m4jA 142 4.49e+01 d.109.1.2 78602 1p6xA 334 4.55e+01 c.37.1.1 94195 1khoA 370 4.56e+01 a.124.1.1,b.12.1.3 72489,72490 1vfaB 116 4.62e+01 1gc1H b.1.1.1 19929 2mspA 126 4.65e+01 1mspA b.1.11.2 22335 1wwpA 119 4.68e+01 2ddrA 306 4.70e+01 1mzjA 339 4.75e+01 c.95.1.2,c.95.1.2 79700,79701 1z8gA 372 4.85e+01 1xrkA 124 4.94e+01 1wucA 250 4.94e+01 1s8fA 177 5.06e+01 c.37.1.8 105370 2thiA 379 5.10e+01 2thiA c.94.1.1 35794 1v7cA 351 5.10e+01 c.79.1.1 100446 1wgrA 100 5.14e+01 1sfxA 109 5.23e+01 a.4.5.50 105505 1kcxA 518 5.24e+01 b.92.1.3,c.1.9.6 90953,90954 3rabA 169 5.24e+01 1ctqA c.37.1.8 32018 1eyuA 157 5.38e+01 3pviA c.52.1.6 33304 2msbA 115 5.38e+01 1rtm1 d.169.1.1 42355 1p57B 255 5.63e+01 b.47.1.2 94126 1m1nA 491 5.66e+01 c.92.2.3 78417 1ifqA 138 5.76e+01 1ifqA d.110.4.1 62350 1ksyA 154 5.76e+01 d.89.1.2 72948 2fd5A 180 5.82e+01 2pviA 157 5.84e+01 3pviA c.52.1.6 33302 1u69A 163 5.87e+01 d.32.1.7 107699 1wcuA 153 5.90e+01 1mkyA 439 5.91e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1qhqA 140 5.91e+01 1qhqA b.6.1.1 63326 1avoA 60 5.97e+01 1avoA a.24.8.1 16619 2minA 491 5.98e+01 1qguA c.92.2.3 35609 1meoA 209 6.05e+01 c.65.1.1 79035 2f62A 161 6.05e+01 1bylA 125 6.10e+01 1bylA d.32.1.2 38495 3minC 491 6.11e+01 1qguA c.92.2.3 35607 1j8rA 196 6.12e+01 1j8rA b.2.3.3 62745 1yw5A 177 6.16e+01 1aec 218 6.26e+01 1cs8A d.3.1.1 37003 1lj2A 110 6.33e+01 h.1.13.2 73926 1fdlH 218 6.33e+01 1igtB b.1.1.1,b.1.1.2 19961,21021 1fp4A 492 6.35e+01 c.92.2.3 76187 1rypE 242 6.37e+01 1rypE d.153.1.4 41936 1efuB 282 6.41e+01 1efuB d.43.1.1,a.5.2.2,d.43.1.1 38677,58975,58976 2b33A 140 6.51e+01 1e3dB 542 6.53e+01 1h2rL e.18.1.1 59189 2a0kA 161 6.57e+01 2f2tA 161 6.57e+01 1qlaB 239 6.59e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1eq1A 166 6.60e+01 a.63.1.1 64910 3pviA 157 6.62e+01 3pviA c.52.1.6 33300 1rktA 205 6.71e+01 a.4.1.9,a.121.1.1 97623,97624 1e0zA 128 6.82e+01 1awd d.15.4.1 59153 1jjyA 636 6.88e+01 1jjyA 1y08A 323 6.90e+01 1nseA 444 6.91e+01 1nseA d.174.1.1 42534 2xat 212 6.96e+01 2xat b.81.1.3 28058 1ihfB 94 6.97e+01 1huuA a.55.1.1 17894 1gw9A 388 7.03e+01 c.1.15.3 70658 1q02A 52 7.06e+01 a.5.2.1 95490 1gg4A 452 7.14e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 6gsvA 217 7.17e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1f5qB 252 7.20e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 1s6bA 119 7.20e+01 a.133.1.2 98592 1mejA 223 7.21e+01 c.65.1.1 79029 1u0mA 382 7.21e+01 c.95.1.2,c.95.1.2 107557,107558 5nseA 444 7.23e+01 d.174.1.1 74644 2bw8A 227 7.26e+01 1iyu 79 7.32e+01 1iyu b.84.1.1 28227 1su8A 636 7.38e+01 e.26.1.2 98999 1d1vA 444 7.39e+01 1nseA d.174.1.1 59101 1cbs 137 7.43e+01 1hmt b.60.1.2 27201 1p9eA 331 7.52e+01 d.157.1.5 104088 1ek8A 185 7.59e+01 1ek8A d.67.3.1 59444 1vkjA 285 7.63e+01 c.37.1.5 108666 1b8aA 438 7.65e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1n9eA 787 7.66e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 2b8eA 273 7.70e+01 1pvuA 154 7.79e+01 3pviA c.52.1.6 33306 1xat 212 7.80e+01 2xat b.81.1.3 28059 1mw7A 240 7.90e+01 e.39.1.1 79557 3hhrB 203 7.90e+01 1axiB b.1.2.1,b.1.2.1 22005,22006 2fikA 287 7.90e+01 1xd7A 145 7.91e+01 a.4.5.55 109566 2g3aA 152 7.92e+01 1hilB 220 7.97e+01 1igtB b.1.1.1,b.1.1.2 19787,20897 1iseA 185 7.97e+01 d.67.3.1 90691 1u0tA 307 8.12e+01 e.52.1.1 107567 1ixmB 192 8.16e+01 1ixmA d.123.1.1 41115 1d0cA 444 8.27e+01 d.174.1.1 64769 1ufaA 520 8.29e+01 a.8.3.3,c.6.2.4 99329,99330 1o70A 324 8.29e+01 b.118.1.1,b.118.1.1 81115,81116 2occA 514 8.50e+01 2occA f.24.1.1 43518 2b0lA 102 8.52e+01 1zkcA 197 8.54e+01 1kxlA 199 8.57e+01 b.40.4.3 73155 1v32A 101 8.58e+01 a.42.1.1 100277 1go3E 187 8.58e+01 b.40.4.5,d.230.1.1 83054,83055 2ae6A 166 8.66e+01 1vh5A 148 8.68e+01 d.38.1.5 100642 1y8oA 419 8.69e+01 2occB 227 8.84e+01 2occB b.6.1.2,f.17.2.1 23027,43519 1b1cA 181 8.85e+01 1amoA c.23.5.2 31212 1h0bA 256 8.85e+01 b.29.1.11 83422 1x4rA 99 8.89e+01 1jguH 217 8.93e+01 b.1.1.1,b.1.1.2 66688,66689 1h65A 270 8.96e+01 c.37.1.8 65640 1h1lA 481 8.96e+01 c.92.2.3 70851 1tu7A 208 8.97e+01