# 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 1atg 231 5.84e-02 1atg c.94.1.1 35834 1qlmA 316 5.58e-01 1qlmA d.147.1.1 41765 1i6wA 181 6.85e-01 1i6wA c.69.1.18 61859 1ap8 213 8.94e-01 1ap8 d.86.1.1 40151 1ispA 181 9.52e-01 c.69.1.18 76778 1wod 233 1.52e+00 1wod c.94.1.1 35832 1amf 233 1.98e+00 1wod c.94.1.1 35833 2f9sA 151 2.12e+00 1tib 269 2.79e+00 3tgl c.69.1.17 34738 1qapA 296 2.79e+00 1qpoA c.1.17.1,d.41.2.1 29559,38595 1iugA 352 2.95e+00 c.67.1.3 90699 1t5hX 504 3.52e+00 e.23.1.1 106449 1st9A 143 3.80e+00 c.47.1.10 98987 1xocA 520 4.17e+00 1v72A 356 4.29e+00 1jevA 517 4.44e+00 1jevA c.94.1.1 35720 1zr6A 503 4.54e+00 1jetA 517 4.65e+00 1jevA c.94.1.1 35718 1im4A 221 4.95e+00 e.8.1.7 62581 1yqgA 263 4.95e+00 1fjeB 175 5.33e+00 1fj7A d.58.7.1,d.58.7.1 39210,39211 2olbA 517 5.40e+00 1jevA c.94.1.1 35721 1fbtA 190 5.68e+00 1bif c.60.1.4 34004 1zavA 180 6.13e+00 2dcnA 311 6.46e+00 1rg9A 383 6.95e+00 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1tzbA 302 7.29e+00 c.80.1.1 107470 1x9iA 302 7.31e+00 1cydA 244 7.49e+00 1cydA c.2.1.2 29825 1rhs 296 8.35e+00 1rhs c.46.1.2,c.46.1.2 32703,32704 1k68A 140 8.66e+00 c.23.1.1 90943 1qtqA 553 9.41e+00 1gtrA b.53.1.2,c.26.1.1 26940,31579 1ys7A 233 1.04e+01 1jq5A 370 1.05e+01 e.22.1.2 67084 1wmaA 276 1.09e+01 1q35A 320 1.14e+01 c.94.1.1 95661 1w0mA 226 1.16e+01 c.1.1.1 109027 1uhnA 189 1.21e+01 a.39.1.5 99399 2a10A 125 1.21e+01 1gt6A 269 1.27e+01 c.69.1.17 76342 1p9qC 256 1.28e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2ajrA 331 1.28e+01 1zn6A 227 1.33e+01 2a2dA 478 1.38e+01 1i4nA 251 1.45e+01 c.1.2.4 71114 1o4sA 389 1.56e+01 c.67.1.1 86620 1c7gA 456 1.59e+01 c.67.1.2 90415 1r89A 437 1.63e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1vetB 125 1.65e+01 d.110.7.1 108554 2bvfA 459 1.76e+01 1uarA 285 1.77e+01 c.46.1.2,c.46.1.2 107762,107763 1xygD 359 1.78e+01 1cznA 169 1.80e+01 1rcf c.23.5.1 31181 1b3mA 389 1.80e+01 1b3mA 3dapA 320 1.85e+01 1dapA c.2.1.3,d.81.1.3 30051,39966 1l9fA 389 1.85e+01 c.3.1.2,d.16.1.3 73716,73717 1i3cA 149 1.86e+01 c.23.1.1 71112 2a2cA 478 1.90e+01 1f06A 320 1.91e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1yt8A 539 1.92e+01 1el5A 389 1.93e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1t95A 240 1.99e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1khbA 625 2.00e+01 c.91.1.1,c.109.1.1 68606,68607 1fp1D 372 2.06e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1wdcB 156 2.10e+01 1wdcB a.39.1.5 17302 2bgkA 278 2.15e+01 1sc3A 178 2.16e+01 c.17.1.1 105416 1x6mA 196 2.17e+01 1eqnA 321 2.17e+01 1dd9A e.13.1.1 43256 1neeA 138 2.18e+01 d.241.1.1,g.59.1.1 91841,91842 1usyA 275 2.20e+01 1ofv 169 2.21e+01 1rcf c.23.5.1 31184 1js3A 486 2.21e+01 c.67.1.6 67215 1ws6A 171 2.21e+01 1rwxA 178 2.22e+01 1ad4A 266 2.27e+01 1aj2 c.1.21.1 29670 1dd9A 338 2.29e+01 1dd9A e.13.1.1 43254 1dapA 320 2.32e+01 1dapA c.2.1.3,d.81.1.3 30053,39968 1prxA 224 2.33e+01 1prxA c.47.1.10 33076 1zghA 260 2.34e+01 1ywqA 200 2.35e+01 1skoB 130 2.49e+01 d.110.7.1 105677 1kq3A 376 2.51e+01 e.22.1.2 68790 1xg9A 260 2.58e+01 1uetA 437 2.64e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1j0aA 325 2.69e+01 c.79.1.1 83871 1aisA 182 2.75e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1b1a 137 2.81e+01 1be1 c.23.6.1 31242 1t6nA 220 2.84e+01 c.37.1.19 106576 1r5jA 337 2.86e+01 c.77.1.5 97097 1mvwB 145 2.88e+01 i.15.1.1 79524 1mb3A 124 2.89e+01 c.23.1.1 78907 1bmqA 167 2.89e+01 1pauA c.17.1.1 30998 2g40A 224 2.93e+01 1f6kA 293 3.00e+01 1nal3 c.1.10.1 29081 1j3mA 129 3.03e+01 d.129.7.1 103836 1i19A 561 3.06e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1ywfA 296 3.09e+01 1ub3A 220 3.12e+01 c.1.10.1 88395 2f5gA 133 3.16e+01 1kafA 108 3.17e+01 d.199.1.1 68372 1wy9A 147 3.19e+01 1d3uA 181 3.20e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1prxB 224 3.21e+01 1prxA c.47.1.10 33077 1xmrA 243 3.23e+01 1z63A 500 3.25e+01 1yw3A 208 3.28e+01 1vqoX 92 3.29e+01 1kk8B 139 3.31e+01 a.39.1.5 77430 1osa 148 3.34e+01 1cll a.39.1.5 17300 1skyE 473 3.35e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 1mho 88 3.38e+01 1b4cA a.39.1.2 17171 1exrA 148 3.42e+01 1cll a.39.1.5 17299 1wdjA 187 3.42e+01 1eluA 390 3.43e+01 1elqA c.67.1.3 34434 1ibcA 194 3.44e+01 1pauA c.17.1.1 30997 1bx4A 345 3.47e+01 1bx4A c.72.1.1 34935 1k9uA 78 3.47e+01 a.39.1.10 84348 1bpwA 503 3.47e+01 1bpwA c.82.1.1 35365 1nonA 179 3.49e+01 c.61.1.1 103868 1vjvA 415 3.51e+01 d.3.1.9 108632 1ddeA 338 3.55e+01 1dd9A e.13.1.1 43255 2g9iA 249 3.55e+01 1tplA 426 3.62e+01 1ax4A c.67.1.2 34387 1zetA 388 3.68e+01 1whvA 100 3.75e+01 1fj7A 101 3.79e+01 1fj7A d.58.7.1 39209 1ve3A 227 3.79e+01 1eiwA 111 3.79e+01 1eiwA c.23.3.1 31130 1vkpA 383 3.94e+01 d.126.1.6 108686 1elqA 390 3.98e+01 1elqA c.67.1.3 34436 1z5nA 242 4.06e+01 1j6oA 268 4.07e+01 c.1.9.12 77088 1xu9A 286 4.09e+01 1jqaA 370 4.13e+01 e.22.1.2 67085 1dcfA 136 4.13e+01 1dcfA c.23.1.2 31124 1f4qA 165 4.14e+01 1alvA a.39.1.8 17360 1mugA 168 4.24e+01 1mugA c.18.1.2 31030 1bq3B 246 4.31e+01 1qhfA c.60.1.1 33979 1z5oA 242 4.33e+01 1gtrA 553 4.35e+01 1gtrA b.53.1.2,c.26.1.1 26939,31578 1lq9A 112 4.36e+01 d.58.4.3 78129 1s72X 92 4.40e+01 d.29.1.1 105343 1fokA 568 4.48e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16137,16138,16139,33325 1pczA 191 4.52e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1jj2W 91 4.54e+01 1ffkU d.29.1.1 63108 2av5A 120 4.56e+01 1wviA 257 4.60e+01 1l0wA 580 4.61e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1dguA 183 4.63e+01 1dguA a.39.1.5 17333 2g8lA 299 4.67e+01 1cll 148 4.96e+01 1cll a.39.1.5 17263 1eudA 311 4.96e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1j08A 226 4.98e+01 c.47.1.2,c.47.1.2 83855,83856 1n8jA 186 5.02e+01 c.47.1.10 85401 1cqmA 101 5.02e+01 1ris d.58.14.1 39321 2fokA 579 5.07e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1eluB 390 5.08e+01 1elqA c.67.1.3 34435 2g0wA 296 5.17e+01 1y4tA 322 5.18e+01 1k94A 165 5.26e+01 a.39.1.8 68333 1z5zA 271 5.27e+01 1zdrA 164 5.27e+01 2c3zA 222 5.34e+01 1mxb 383 5.40e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41329,41330,41331 1mxa 383 5.46e+01 1mxb d.130.1.1,d.130.1.1,d.130.1.1 41326,41327,41328 1fx4A 231 5.47e+01 1fx2A d.58.29.1 39431 3cln 148 5.49e+01 1cll a.39.1.5 17286 1xvxA 312 5.51e+01 1fo5A 85 5.60e+01 1fo5A c.47.1.1 59922 1a4sA 503 5.68e+01 1bpwA c.82.1.1 35361 1foeA 377 5.73e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1qx2A 76 5.74e+01 a.39.1.1 104622 2f3yA 148 5.88e+01 1dciA 275 5.89e+01 1dciA c.14.1.3 30918 1edzA 320 5.91e+01 1ee9A c.2.1.7,c.58.1.2 30287,33935 1frb 315 5.91e+01 1frb c.1.7.1 28665 1cjcA 460 6.11e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 2alzA 390 6.12e+01 1kllA 130 6.17e+01 d.32.1.2 72720 1hg3A 225 6.19e+01 1hg3A c.1.1.1 61025 1b26A 416 6.20e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1iiwA 232 6.26e+01 c.94.1.1 62461 2aop 497 6.26e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39503,39504,41427,41428 1yruB 74 6.27e+01 1j5xA 342 6.27e+01 c.80.1.1 71591 1aop 497 6.28e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1j98A 157 6.33e+01 1j98A d.185.1.2 62755 1ucaA 190 6.42e+01 d.124.1.1 88462 1es9A 232 6.43e+01 1wab c.23.10.3 31340 1pbp 321 6.45e+01 1ixh c.94.1.1 35768 2ck3D 482 6.45e+01 1t8qA 336 6.47e+01 c.1.18.3 106669 1f74A 293 6.48e+01 1nal3 c.1.10.1 29079 1atnA 373 6.49e+01 1yagA c.55.1.1,c.55.1.1 33437,33438 1tk1A 260 6.50e+01 d.248.1.1 107066 1bk7A 190 6.50e+01 1bk7A d.124.1.1 41121 1xfxO 149 6.51e+01 1ixh 321 6.63e+01 1ixh c.94.1.1 35761 1a54A 321 6.64e+01 1ixh c.94.1.1 35763 1scmB 145 6.65e+01 1wdcB a.39.1.5 17304 1ykhB 132 6.67e+01 1cb1 78 6.73e+01 4icb a.39.1.1 17156 2fdrA 229 6.73e+01 1xzoA 174 6.77e+01 1tqyB 415 6.77e+01 c.95.1.1,c.95.1.1 107247,107248 1jg8A 347 6.80e+01 1jg8A c.67.1.1 62946 1m6sA 347 6.80e+01 c.67.1.1 78701 1a40 321 6.83e+01 1ixh c.94.1.1 35767 2af6A 258 6.83e+01 1x9zA 188 6.92e+01 2cveA 191 6.92e+01 2u1a 88 7.01e+01 2u1a d.58.7.1 39164 1eybA 471 7.06e+01 1ey2A b.82.1.4 28115 1xznA 179 7.11e+01 1xc1A 309 7.14e+01 c.94.1.1 109543 2amlA 373 7.14e+01 1juk 248 7.17e+01 1a53 c.1.2.4 28567 1igs 248 7.17e+01 1a53 c.1.2.4 28565 1xkqA 280 7.17e+01 1ab6A 125 7.24e+01 3chy c.23.1.1 31054 1rcuA 195 7.35e+01 c.129.1.1 97295 1o12A 376 7.35e+01 b.92.1.5,c.1.9.10 80758,80759 1tca 317 7.55e+01 1tca c.69.1.17 34726 1cvl 319 7.55e+01 1cvl c.69.1.18 34786 1oi7A 288 7.57e+01 c.2.1.8,c.23.4.1 87049,87050 2cvdA 198 7.60e+01 1jztA 246 7.69e+01 c.104.1.1 63319 1ej5A 107 7.70e+01 1ej5A a.68.1.1 18268 1vlwA 217 7.70e+01 c.1.10.1 108868 1v4pA 157 7.77e+01 1e0cA 271 7.81e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1lwjA 441 7.81e+01 b.71.1.1,c.1.8.1 74303,74304 1g57A 217 7.82e+01 1g57A d.115.1.2 60253 1zsyA 357 7.85e+01 1yliA 153 7.86e+01 2arkA 188 7.96e+01 1ea0A 1479 8.03e+01 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 1ey2A 471 8.08e+01 1ey2A b.82.1.4 28116 1t35A 191 8.10e+01 c.129.1.1 99108 1iyhA 198 8.14e+01 a.45.1.1,c.47.1.5 83790,83791 2d13A 227 8.17e+01 1sd4A 126 8.20e+01 a.4.5.39 105428 1ggzA 148 8.24e+01 a.39.1.5 70176 1yw5A 177 8.26e+01 1u0sA 86 8.35e+01 d.58.24.1 107565 1q0pA 223 8.38e+01 c.62.1.1 95507 1bgvA 449 8.38e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 2fxuA 375 8.41e+01 1vzyA 291 8.47e+01 1tikA 213 8.59e+01 c.23.5.3 107003 1ucdA 190 8.66e+01 d.124.1.1 107767 1zzmA 259 8.67e+01 1z6aA 500 8.71e+01 1a53 247 8.82e+01 1a53 c.1.2.4 28564 1h4vB 421 8.84e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1jfkA 134 8.93e+01 a.39.1.5 66639 1j6zA 376 8.96e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1pbjA 125 8.98e+01 d.37.1.1,d.37.1.1 94414,94415