# List of top-scoring protein chains for t04-100-40-40-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 1ifqA 138 3.05e-01 1ifqA d.110.4.1 62350 2gu3A 136 3.90e-01 1ylxA 103 3.94e-01 d.82.5.1 123677 1n6zA 105 3.99e-01 d.263.1.1 85369 1iuhA 198 4.47e-01 d.61.1.2 83711 2g3aA 152 6.82e-01 d.108.1.1 134557 1vr4A 103 7.59e-01 d.230.5.1 120432 1gw5S 142 7.61e-01 d.110.4.2 70633 2cy5A 140 1.05e+00 b.55.1.2 131018 1mkeA 152 1.23e+00 b.55.1.4 79231 1aqcA 172 1.33e+00 1x11A b.55.1.2 26983 1y9wA 140 1.51e+00 d.108.1.1 122783 2f57A 317 1.52e+00 1v9yA 167 1.74e+00 d.110.3.2 108454 1n9lA 109 1.77e+00 d.110.3.6 85468 1ufzA 83 1.89e+00 a.5.9.1 107821 1ru0A 105 1.95e+00 d.74.1.1 111937 1y13A 181 2.00e+00 d.96.1.2 116319 1dwkA 156 2.19e+00 1dw9A a.35.1.4,d.72.1.1 17075,39606 2fl4A 149 2.59e+00 d.108.1.1 133706 1mszA 86 2.97e+00 d.68.7.1 79428 1uilA 113 2.98e+00 d.50.1.1 113255 1x31D 99 2.99e+00 1wguA 136 3.04e+00 b.55.1.2 114623 1ckv 141 3.19e+00 1ckv 1s3sG 127 3.41e+00 d.15.1.2 98457 1zk7A 467 3.55e+00 1p9qC 256 3.62e+00 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1sh8A 154 3.64e+00 d.38.1.5 105549 1jnuA 104 3.68e+00 d.110.3.6 71762 1ecrA 309 3.87e+00 1ecrA e.2.1.1 42678 1914 232 4.12e+00 1914 1ew4A 106 4.25e+00 1ew4A d.82.2.1 40023 2cwoA 197 4.25e+00 2c1gA 431 4.35e+00 c.6.2.3,d.341.1.1 129632,129633 2cfxA 144 4.37e+00 a.4.5.32,d.58.4.2 130395,130396 1scfA 273 4.44e+00 1exzA a.26.1.2 16873 8rucI 123 4.96e+00 1rboC d.73.1.1 39629 1iujA 106 5.03e+00 d.58.4.5 90701 1ospO 257 5.04e+00 1ospO b.76.1.1 27971 1iicA 422 5.10e+00 1nmtA d.108.1.2,d.108.1.2 62422,62423 1rrpB 134 5.13e+00 1rrpB b.55.1.3 26995 1wveC 80 5.26e+00 a.3.1.1 121335 5csmA 256 5.34e+00 5csmA a.130.1.2 19494 1t4oA 117 5.34e+00 d.50.1.1 106425 1vpkA 378 5.35e+00 d.131.1.1,d.131.1.1,d.131.1.1 113963,113964,113965 1kllA 130 5.62e+00 d.32.1.2 72720 1vk8A 106 5.68e+00 d.58.48.1 108636 1zhhB 242 5.70e+00 1ty9A 222 5.74e+00 b.45.1.1 112827 1ml8A 134 5.75e+00 d.227.1.2 85013 2a74A 643 6.02e+00 1vgjA 184 6.37e+00 1in0A 163 6.67e+00 d.58.49.1,d.58.49.1 83694,83695 2c1iA 431 6.78e+00 c.6.2.3,d.341.1.1 129636,129637 2igd 61 7.34e+00 2igd 1yduA 170 7.53e+00 b.162.1.1 123003 1kveB 77 7.62e+00 1kveB 1orc 71 7.74e+00 1orc 1yzsA 121 7.86e+00 1bywA 110 7.99e+00 1bywA d.110.3.6 40912 1sgoA 139 8.07e+00 d.82.3.1 98857 1v6fA 151 8.31e+00 d.109.1.2 108395 2cx1A 187 8.56e+00 b.122.1.1,d.17.6.4 130967,130968 1huuA 90 8.94e+00 1huuA a.55.1.1 17897 1pvgA 418 8.96e+00 d.14.1.3,d.122.1.2 95161,95162 1nrlA 316 8.96e+00 a.123.1.1 92091 1dcoA 104 8.98e+00 1dcpA d.74.1.1 39680 2gi9A 56 9.28e+00 1v74A 107 9.51e+00 d.243.1.1 100442 1ef1A 294 9.80e+00 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1rewA 114 9.92e+00 g.17.1.2 97334 1eg9B 194 1.01e+01 1ndoB d.17.4.4 38120 3grs 478 1.01e+01 3grs 1zs7A 190 1.02e+01 b.122.1.1,d.17.6.4 125593,125594 1o7nB 194 1.03e+01 d.17.4.4 81164 1ujrA 110 1.03e+01 d.289.1.1 113258 3pyp 125 1.06e+01 3pyp 1vdxA 184 1.10e+01 1o70A 324 1.17e+01 b.118.1.1,b.118.1.1 81115,81116 1ntvA 152 1.17e+01 b.55.1.2 86168 1ldjA 760 1.19e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1vkkA 154 1.21e+01 d.109.1.2 108669 1kgnA 329 1.21e+01 a.25.1.2 68584 1ytfD 121 1.23e+01 1ytfD a.32.1.1,b.56.1.1 16998,27011 1jovA 270 1.23e+01 b.30.5.7 84192 1fsiA 189 1.24e+01 1fsiA d.61.1.1 39536 1t6sA 162 1.28e+01 a.4.5.60,a.4.5.60 112271,112272 2cy2A 174 1.29e+01 d.108.1.1 131016 1trb 320 1.31e+01 1trb 1nwzA 125 1.32e+01 d.110.3.1 86370 1ly1A 181 1.33e+01 c.37.1.1 74334 1tn6B 437 1.38e+01 a.102.4.3 112528 1vqoS 85 1.42e+01 d.12.1.1 120380 2bmoB 194 1.42e+01 d.17.4.4 128806 1wddS 128 1.45e+01 d.73.1.1 114532 1owfB 94 1.49e+01 a.55.1.1 87488 2h4uA 145 1.51e+01 d.38.1.5 136082 1owfA 99 1.51e+01 a.55.1.1 87487 1o5uA 101 1.52e+01 b.82.1.8 92518 1zx2A 147 1.54e+01 2c30A 321 1.54e+01 1b3tA 147 1.55e+01 1b3tA d.58.8.1 39228 1sq5A 308 1.56e+01 c.37.1.6 105882 1y4oA 104 1.58e+01 1th5A 74 1.58e+01 d.52.8.1 119263 1f3iA 481 1.58e+01 1b7eA 1t0hB 224 1.61e+01 c.37.1.1 106208 3rubS 123 1.61e+01 1rboC d.73.1.1 39616 1ln1A 214 1.61e+01 d.129.3.2 74038 1diiC 80 1.61e+01 1diiC a.3.1.1 15925 1kx5A 135 1.63e+01 a.22.1.1 77593 1xw3A 110 1.68e+01 1r7mA 235 1.68e+01 d.95.2.1,d.95.2.1 111713,111714 2evrA 246 1.69e+01 b.34.11.3,d.3.1.16 132440,132441 2cg4A 152 1.71e+01 a.4.5.32,d.58.4.2 130417,130418 2fhzB 108 1.74e+01 d.243.1.2 133506 1ld8B 437 1.79e+01 a.102.4.3 73839 1i1dA 161 1.82e+01 1i21A d.108.1.1 61526 2b4vA 468 1.83e+01 a.160.1.4,d.218.1.10 127864,127865 1vkcA 158 1.89e+01 d.108.1.1 113663 1x47A 98 1.92e+01 d.50.1.1 121680 2fckA 181 1.93e+01 d.108.1.1 133272 1jj2R 84 1.94e+01 1ffkP d.12.1.1 63103 1tyv 542 1.95e+01 1tyv 1lxiA 139 1.95e+01 g.17.1.2 84735 1ojqA 212 1.97e+01 d.166.1.1 93146 2a9kB 223 1.99e+01 d.166.1.1 126443 1ngmB 72 2.05e+01 j.104.1.1 85687 1t95A 240 2.08e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1s72S 85 2.09e+01 d.12.1.1 105338 1s28A 132 2.13e+01 d.198.1.1 105223 2fo3A 125 2.17e+01 d.20.1.1 133868 2phlA 397 2.18e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1qnaA 200 2.18e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1vrtA 560 2.22e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 1g24A 211 2.24e+01 1g24A d.166.1.1 42270 1f3mC 297 2.27e+01 1hcl d.144.1.7 41677 1m4uA 206 2.27e+01 g.17.1.7 78625 1nh2D 121 2.28e+01 a.32.1.1,b.56.1.1 91876,91877 1jj2W 91 2.31e+01 1ffkU d.29.1.1 63108 1ugiA 84 2.33e+01 1ugiA d.17.5.1 38125 1rsy 152 2.37e+01 1rsy 1o08A 221 2.37e+01 c.108.1.6 86525 1zmeC 70 2.44e+01 1zmeC g.38.1.1,h.1.3.1 45081,45514 1u6bA 98 2.46e+01 d.58.7.1 107703 1v54D 147 2.48e+01 f.23.1.1 100325 1r9fA 136 2.48e+01 d.255.1.1 97257 2occD 147 2.49e+01 1ocrD f.23.1.1 43521 2essA 248 2.49e+01 d.38.1.8,d.38.1.8 132346,132347 1t6aA 126 2.52e+01 d.129.8.1 106555 1oa8A 133 2.57e+01 b.145.1.1 92698 1fxxA 482 2.57e+01 1fxxA c.55.3.5 33726 1s72X 92 2.59e+01 d.29.1.1 105343 2apoA 357 2.69e+01 b.122.1.1,d.265.1.2 127133,127134 1xw4X 110 2.72e+01 1rxqA 178 2.72e+01 a.213.1.1 105118 1k0hA 117 2.78e+01 b.106.1.2 71975 1musA 477 2.82e+01 c.55.3.4 79494 1nvpD 108 2.84e+01 a.32.1.1,b.56.1.1 92213,92214 1lfwA 470 2.90e+01 c.56.5.4,d.58.19.1 77942,77943 1yfbA 59 2.91e+01 b.129.1.3 123057 1d0qA 103 2.92e+01 1d0qA g.41.3.2 45208 1ihrA 76 2.92e+01 1ihrA d.212.1.2 62392 1jh6A 189 2.93e+01 d.61.1.1 66707 1np8A 159 2.93e+01 a.39.1.8 92022 1yspA 181 2.94e+01 1q7hA 153 2.96e+01 b.122.1.1,d.17.6.2 96042,96043 1uliB 187 2.96e+01 d.17.4.4 107923 1grj 158 2.99e+01 1grj 2fk4A 75 3.04e+01 1pn2A 280 3.06e+01 d.38.1.4,d.38.1.4 94930,94931 1rk8A 165 3.07e+01 d.58.7.1 97603 1w3oA 216 3.16e+01 b.45.1.1 114142 1ufwA 95 3.17e+01 d.58.7.1 99358 1z5lA 285 3.20e+01 b.1.1.2,d.19.1.1 124480,124481 1e4fT 419 3.23e+01 1e4fT c.55.1.1,c.55.1.1 33453,33454 1k0eA 453 3.25e+01 d.161.1.1 67938 1svdM 110 3.28e+01 d.73.1.1 119059 1jeyB 565 3.31e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 2a8kA 108 3.32e+01 d.243.1.2 126404 3erk 364 3.33e+01 1hcl 1uwvA 433 3.36e+01 b.40.4.12,c.66.1.40 100128,100129 1cdcA 99 3.43e+01 1cdcA b.1.1.1 19746 2dbbA 151 3.44e+01 1sgvA 316 3.44e+01 b.122.1.1,d.265.1.2 98858,98859 1w53A 84 3.46e+01 a.186.1.2 109175 1kgdA 180 3.46e+01 c.37.1.1 68582 2fmr 65 3.47e+01 2fmr 1jlvA 209 3.48e+01 a.45.1.1,c.47.1.5 71729,71730 1u84A 90 3.49e+01 a.230.1.1 113114 1vqoX 92 3.53e+01 d.29.1.1 120385 1usmA 80 3.54e+01 d.74.1.1 99876 1y10A 407 3.55e+01 1t4nA 94 3.58e+01 d.50.1.1 106424 1v3wA 173 3.59e+01 b.81.1.5 100291 1yhvA 297 3.61e+01 2bkyX 89 3.70e+01 d.68.6.1 128717 2cr4A 126 3.71e+01 1xg9A 260 3.74e+01 1zghA 260 3.74e+01 b.46.1.1,c.65.1.1 125028,125029 1nwwA 149 3.75e+01 d.17.4.8 86306 1b7yA 350 3.76e+01 1pysA d.104.1.1 40776 1pz4A 116 3.76e+01 d.106.1.1 95400 2c7hA 86 3.86e+01 1zh5A 195 3.91e+01 a.4.5.46,d.58.7.1 125073,125074 1dqtA 117 3.94e+01 1ah1 b.1.1.1 20653 1mjhA 162 3.99e+01 1mjhA c.26.2.4 31639 1x8dA 104 4.02e+01 2azqA 311 4.06e+01 1b77A 228 4.09e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1xj4A 119 4.12e+01 d.110.3.2 122027 1uv7A 110 4.12e+01 d.67.4.1 100040 1bob 320 4.13e+01 1bob 1i2aA 219 4.14e+01 e.24.1.1 90660 1o26A 232 4.15e+01 d.207.1.1 86566 1ymqA 261 4.19e+01 c.108.1.10 123707 1k5dB 201 4.21e+01 b.55.1.3 68169 1w79A 489 4.25e+01 e.3.1.3 120680 1i3jA 116 4.27e+01 1i3jA d.285.1.1 61594 1g79A 218 4.30e+01 1ci0A b.45.1.1 25752 1y6zA 263 4.34e+01 1fzcA 87 4.35e+01 1fzcA h.1.8.1 45590 2b95A 106 4.38e+01 1ucrA 78 4.40e+01 a.4.5.45 99188 1y96B 85 4.47e+01 1s1eA 224 4.49e+01 a.39.1.5 112007 1iwmA 186 4.53e+01 b.125.1.2 83758 1mm4A 170 4.59e+01 f.4.1.2 79294 1kwaA 88 4.59e+01 1kwaA b.36.1.1 24772 1qk8A 146 4.60e+01 1ewxA c.47.1.10 33061 1vg5A 73 4.61e+01 a.5.2.1 113640 1uk5A 111 4.62e+01 a.7.7.1 99487 1erjA 393 4.62e+01 1erjA b.69.4.1 27660 1gzcA 239 4.68e+01 b.29.1.1 70803 1e2wA 251 4.70e+01 1hcz b.2.6.1,b.84.2.2 22466,28252 1of5B 184 4.73e+01 d.17.4.2 86934 1n91A 108 4.74e+01 d.206.1.1 80326 1zdnA 158 4.78e+01 d.20.1.1 124943 1l0qA 391 4.79e+01 b.1.3.1,b.69.2.3 77644,77645 1vp2A 208 4.81e+01 c.51.4.1 113933 1ylkA 172 4.81e+01 1v9jA 113 4.82e+01 d.52.6.1 100542 1gps 47 4.83e+01 1gpt 1ifc 132 4.84e+01 1twfF 155 4.91e+01 a.143.1.2 112731 1phk 298 4.91e+01 1cdkA 1vfqA 143 4.94e+01 d.109.1.2 120054 1i50F 155 4.94e+01 a.143.1.2 61760 1tqzA 133 4.97e+01 b.55.1.11 119327 2a9uA 144 4.99e+01 a.118.23.1 126450 1obdA 306 4.99e+01 d.143.1.1 86767 1hq3C 136 4.99e+01 1aoiA a.22.1.1 16454 1sseB 86 5.00e+01 1zowA 313 5.01e+01 1r6oC 106 5.06e+01 d.45.1.2 118738 1o8xA 146 5.08e+01 c.47.1.10 86681 2akrA 285 5.10e+01 b.1.1.2,d.19.1.1 126931,126932 2b49A 287 5.17e+01 1vr6A 350 5.23e+01 c.1.10.4 120439 2a3qA 170 5.24e+01 a.204.1.2 126092 1z9bA 135 5.24e+01 1t64A 377 5.26e+01 c.42.1.2 106543 1z4eA 153 5.29e+01 d.108.1.1 124431 1vixA 420 5.36e+01 c.56.5.4,d.58.19.1 100777,100778 1ax0 239 5.41e+01 1led 1jmtA 104 5.41e+01 d.58.7.3 63180 1yoxA 250 5.42e+01 b.82.5.2 123789 2fclA 169 5.53e+01 d.218.1.11 133273 1s31A 273 5.54e+01 1wh5A 80 5.63e+01 a.4.1.1 114633 2fp1A 166 5.67e+01 a.130.1.4 133891 1i12A 160 5.72e+01 1i21A d.108.1.1 61515 2amyA 246 5.72e+01 c.108.1.10 127026 1a32 88 5.73e+01 1a32 2arpA 116 5.73e+01 g.17.1.2 127217 1j3mA 129 5.83e+01 d.129.7.1 103836 2a1vA 144 5.83e+01 d.198.3.1 126019 1tzyC 136 5.90e+01 a.22.1.1 107532 1u3eM 174 5.90e+01 d.4.1.3,d.285.1.1 107640,107641 2b1xB 172 5.91e+01 d.17.4.4 127677 1qx2A 76 5.99e+01 a.39.1.1 104622 1a64A 97 6.11e+01 1cdcA b.1.1.1 19750 1j1jA 240 6.20e+01 a.118.16.1 90762 1s6cA 183 6.22e+01 a.39.1.5 98594 2g6yA 217 6.22e+01 1voqa 90 6.23e+01 1top 162 6.24e+01 1ncx 1u0jA 267 6.25e+01 c.37.1.20 107546 1crzA 403 6.27e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1b9mA 265 6.33e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1ci3M 249 6.34e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 2gx9A 129 6.35e+01 d.299.1.1 135828 1cqmA 101 6.35e+01 1ris d.58.14.1 39321 2ez6A 221 6.37e+01 a.149.1.1,d.50.1.1 132616,132617 1fecA 490 6.42e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1cyj 90 6.43e+01 1ctj 2cq8A 110 6.43e+01 1x3eA 165 6.46e+01 2blkA 122 6.50e+01 1z8uA 102 6.52e+01 a.7.11.1 124724 1mmsA 140 6.55e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 3cox 507 6.55e+01 1b8sA 1ou8A 111 6.61e+01 b.136.1.1 93543 1gz6A 319 6.66e+01 c.2.1.2 76410 1t9mA 214 6.66e+01 b.45.1.1 112364 1r7lA 110 6.67e+01 d.277.1.1 104837 2if1 126 6.68e+01 2if1 1k04A 162 6.69e+01 a.24.14.1 67904 2f0aA 98 6.72e+01 b.36.1.1 132661 1ym5A 300 6.72e+01 1gz8A 299 6.74e+01 d.144.1.7 83405 1js8A 394 6.77e+01 a.86.1.1,b.112.1.1 67219,67220 1yvoA 172 6.80e+01 d.108.1.1 124106 1ohtA 215 6.85e+01 d.118.1.1 87036 1ue1A 164 6.86e+01 b.40.4.3 99243 1u96A 69 6.86e+01 a.17.1.2 113232 2gw6A 123 6.88e+01 1oejA 193 6.91e+01 b.60.1.4 92798 1y0hA 105 6.92e+01 d.58.4.11 116303 1h5wA 309 6.97e+01 e.27.1.1 65635 2f6lA 166 6.99e+01 a.130.1.4 133049 1ash 150 7.02e+01 1ash 2b9hA 353 7.04e+01 1u9yA 284 7.04e+01 c.61.1.2,c.61.1.2 119655,119656 2bj7A 138 7.05e+01 a.43.1.3,d.58.18.4 128608,128609 1l5xA 280 7.05e+01 c.106.1.1 77718 2aeuA 374 7.07e+01 c.67.1.8 126646 1fa0A 537 7.11e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 2atxA 194 7.11e+01 c.37.1.8 127315 1jjiA 311 7.23e+01 c.69.1.2 66766 2a8eA 220 7.23e+01 d.296.1.1 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