# 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 1vk1A 242 1.53e-03 d.268.1.2 108634 1xb4A 202 1.08e-01 1u5tC 202 2.19e-01 a.4.5.54,a.4.5.54 107688,107689 1iuhA 198 1.63e+00 d.61.1.2 83711 1asu 162 1.82e+00 1cxqA c.55.3.2 33626 1vsd 152 2.13e+00 1cxqA c.55.3.2 33625 1dmtA 696 2.29e+00 1dmtA d.92.1.4 40296 1ekxA 311 2.86e+00 3csuA c.78.1.1,c.78.1.1 35088,35089 1r1hA 696 2.92e+00 d.92.1.4 104756 1gz0A 253 3.27e+00 c.116.1.1,d.79.3.3 76391,76392 1a5v 162 3.79e+00 1cxqA c.55.3.2 33629 1m65A 245 3.99e+00 c.6.3.1 84847 3csuA 310 4.43e+00 3csuA c.78.1.1,c.78.1.1 35094,35095 1cxqA 162 4.44e+00 1cxqA c.55.3.2 33621 1acmA 310 4.65e+00 3csuA c.78.1.1,c.78.1.1 35180,35181 8atcA 310 5.31e+00 3csuA c.78.1.1,c.78.1.1 35132,35133 2cohA 202 5.33e+00 1wd5A 208 5.78e+00 1gs5A 258 6.20e+00 c.73.1.2 70395 2bnfB 241 7.17e+00 1ve1A 304 7.30e+00 2bbhA 269 8.00e+00 1y0vH 146 8.79e+00 1xuuA 349 9.06e+00 1at1A 310 9.18e+00 3csuA c.78.1.1,c.78.1.1 35168,35169 1apxA 249 9.39e+00 1ryc a.93.1.1 18669 2bneA 241 9.57e+00 1ecpA 238 1.02e+01 1ecpA c.56.2.1 33775 1pk9A 237 1.02e+01 c.56.2.1 94823 2a0fA 310 1.02e+01 1k9sA 237 1.06e+01 c.56.2.1 68359 2dg5A 366 1.09e+01 3minC 491 1.12e+01 1qguA c.92.2.3 35607 1w85A 368 1.14e+01 1nnwA 252 1.15e+01 d.159.1.5 80674 2rslA 140 1.17e+01 2rslA c.53.1.1 33345 1xfxO 149 1.22e+01 1egwA 77 1.26e+01 1mnmA d.88.1.1 40234 3kvt 115 1.38e+01 1t1dA d.42.1.2 38642 1oc2A 348 1.39e+01 c.2.1.2 92765 1pscA 365 1.40e+01 1pscA c.1.9.3 29058 1fxoA 293 1.40e+01 1g0rA c.68.1.6 34524 1zz1A 369 1.40e+01 1ebdA 455 1.52e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30577,30578,40210 1rboC 123 1.53e+01 1rboC d.73.1.1 39634 2bivA 243 1.54e+01 1yzsA 121 1.55e+01 1kepA 348 1.55e+01 c.2.1.2 68536 1pylA 97 1.56e+01 d.1.1.2 104391 1oz2A 331 1.65e+01 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1tplA 426 1.71e+01 1ax4A c.67.1.2 34387 1m70A 190 1.73e+01 a.3.1.4,a.3.1.4 91200,91201 1jbwA 428 1.78e+01 c.59.1.2,c.72.2.2 62860,62861 1c7gA 456 1.79e+01 c.67.1.2 90415 1i0dA 332 1.79e+01 1pscA c.1.9.3 61487 1eywA 331 1.81e+01 1pscA c.1.9.3 29057 1z0kB 69 1.87e+01 1qqyA 130 1.88e+01 3lzt d.2.1.2 36586 1pwhA 327 1.89e+01 c.79.1.1 95224 1w98B 283 1.92e+01 1pujA 282 1.93e+01 c.37.1.8 88294 1xw3A 110 1.95e+01 1xw4X 110 1.95e+01 1hzyA 332 1.96e+01 1pscA c.1.9.3 61468 1g0rA 293 2.03e+01 1g0rA c.68.1.6 34532 1ufwA 95 2.06e+01 d.58.7.1 99358 8rucI 123 2.18e+01 1rboC d.73.1.1 39629 1e6iA 121 2.24e+01 1b91A a.29.2.1 16969 1e5mA 416 2.24e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1mlvA 444 2.24e+01 a.166.1.1,b.85.7.3 79283,79284 1d9tA 289 2.26e+01 1deaA 1ne7A 289 2.30e+01 c.124.1.1 91833 1x9mA 698 2.32e+01 1u0fA 564 2.40e+01 1ak8 76 2.43e+01 1cll a.39.1.5 17281 1p3dA 475 2.54e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1a6o 332 2.72e+01 1a6o 1o1yA 239 2.75e+01 c.23.16.1 86554 1qycA 308 2.75e+01 c.2.1.2 96581 1ffkC 246 2.81e+01 1ffkC c.22.1.1 31037 1guzA 310 2.86e+01 c.2.1.5,d.162.1.1 65586,65587 1etpA 190 2.89e+01 1etpA a.3.1.4,a.3.1.4 15962,15963 2agtA 319 2.89e+01 1l5wA 796 2.93e+01 c.87.1.4 73605 1gmuA 143 2.99e+01 b.107.1.1,d.58.38.1 65335,65336 1vqtA 213 2.99e+01 1i3kA 348 3.05e+01 1xel c.2.1.2 61595 1qryA 80 3.12e+01 2hddA a.4.1.1 16016 1xx6A 191 3.15e+01 1ll1 590 3.23e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 1hi2A 135 3.24e+01 7rsa d.5.1.1 61057 1gqvA 135 3.25e+01 d.5.1.1 70376 2faoA 309 3.26e+01 1gqyA 475 3.31e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1nnhA 294 3.31e+01 d.104.1.1 92005 1p3wA 404 3.33e+01 c.67.1.3 87752 1cl8A 276 3.35e+01 1ckqA c.52.1.1 33230 1ckqA 276 3.36e+01 1ckqA c.52.1.1 33229 1px5A 349 3.40e+01 a.160.1.2,d.218.1.6 95277,95278 2c2hA 192 3.40e+01 1rvkA 382 3.43e+01 c.1.11.2,d.54.1.1 97928,97929 1gwcA 230 3.43e+01 a.45.1.1,c.47.1.5 70660,70661 1ads 315 3.44e+01 1frb c.1.7.1 28671 1dfoA 417 3.49e+01 1bj4A c.67.1.4 34480 1r6dA 337 3.51e+01 c.2.1.2 97148 1lkoA 191 3.53e+01 a.25.1.1,g.41.5.1 78063,78064 1vhwA 253 3.53e+01 c.56.2.1 100706 1vcbB 112 3.53e+01 1vcbB d.42.1.1 38633 1jmxA 494 3.54e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1wi9A 72 3.57e+01 1pdz 434 3.57e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1lla 628 3.61e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1m2rA 327 3.62e+01 d.144.1.7 84760 2b34A 199 3.63e+01 1bksA 268 3.64e+01 2tysA c.1.2.4 28585 1yrbA 262 3.67e+01 1taq 832 3.73e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 2gp4A 628 3.77e+01 1hywA 68 3.84e+01 1hywA d.186.1.1 61425 2acr 315 3.89e+01 1frb c.1.7.1 28674 1ghtA 105 3.91e+01 2rslA c.53.1.1 60526 2cxnA 557 3.91e+01 1j8dA 180 3.93e+01 c.108.1.5 66433 1ng1 294 3.96e+01 1ng1 a.24.13.1,c.37.1.10 16961,32272 1wrjA 156 4.04e+01 2h21A 440 4.04e+01 1ylkA 172 4.06e+01 1p42A 270 4.09e+01 d.14.1.7,d.14.1.7 87754,87755 1h5rA 293 4.13e+01 c.68.1.6 65623 1g5cA 170 4.20e+01 1g5cA c.53.2.1 60264 1i56A 130 4.26e+01 d.2.1.2 66033 2bbrA 195 4.30e+01 1kgsA 225 4.33e+01 a.4.6.1,c.23.1.1 68596,68597 1wr7A 41 4.36e+01 1yewC 289 4.36e+01 1t5oA 351 4.42e+01 c.124.1.5 106459 1p0yA 444 4.45e+01 a.166.1.1,b.85.7.3 87654,87655 1u1jA 765 4.52e+01 c.1.22.2,c.1.22.2 107590,107591 2tysA 268 4.68e+01 2tysA c.1.2.4 28572 1mlwA 301 4.68e+01 d.178.1.1 79289 1rusA 490 4.71e+01 1burA c.1.14.1,d.58.9.1 29388,39294 1sviA 195 4.76e+01 c.37.1.8 106048 2a1fA 247 4.76e+01 1p6pA 125 4.82e+01 b.60.1.2 87839 1a98A 152 4.83e+01 1nulA c.61.1.1 34021 2bgkA 278 4.90e+01 2fnjC 96 4.97e+01 2b8tA 223 5.08e+01 1ajsA 412 5.12e+01 1ajsA c.67.1.1 34276 2cevA 299 5.12e+01 1d3vA c.42.1.1 32576 1y7lA 316 5.24e+01 1yp2A 451 5.29e+01 1q5dA 419 5.29e+01 a.104.1.1 95891 1kwkA 645 5.32e+01 b.71.1.1,c.1.8.1,c.23.16.5 77565,77566,77567 1kwgA 645 5.33e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1yq2A 1024 5.37e+01 1us0A 316 5.38e+01 c.1.7.1 99850 1btmA 252 5.38e+01 1amk c.1.1.1 28513 1vliA 385 5.44e+01 b.85.1.1,c.1.10.6 108830,108831 1tc5A 194 5.44e+01 c.110.1.1 106752 1az1 315 5.45e+01 1frb c.1.7.1 28677 1iatA 557 5.49e+01 1dqrA c.80.1.2 62123 1r1uA 106 5.52e+01 a.4.5.5 104771 1u2wA 122 5.52e+01 1el3A 316 5.54e+01 1frb c.1.7.1 28672 1pwmA 316 5.54e+01 c.1.7.1 95231 1ymqA 261 5.60e+01 1c7uA 85 5.61e+01 1mnmA d.88.1.1 40238 2atvA 196 5.63e+01 1oi1A 221 5.71e+01 b.34.9.3,b.34.9.3 87037,87038 1v5xA 203 5.77e+01 c.1.2.4 100377 1gwiA 411 5.79e+01 a.104.1.1 76364 1zoyA 622 5.81e+01 1a99A 344 5.82e+01 1pot c.94.1.1 35812 1ejjA 511 5.87e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1mfgA 95 5.95e+01 b.36.1.1 79043 1o98A 511 5.98e+01 c.105.1.1,c.76.1.3 86684,86685 1za0A 275 6.03e+01 1ef8A 261 6.10e+01 1ef8A c.14.1.3 30921 1wj9A 211 6.11e+01 1eqjA 511 6.13e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1lnzA 342 6.15e+01 b.117.1.1,c.37.1.8 78112,78113 1x13A 401 6.24e+01 1wvgA 359 6.26e+01 1aihA 170 6.30e+01 1aihA d.163.1.1 42149 1mgrA 99 6.32e+01 d.1.1.2 79106 1gy8A 397 6.34e+01 c.2.1.2 83376 1qh5A 260 6.35e+01 1qh5A d.157.1.2 42057 1iz6A 138 6.43e+01 b.34.5.2,b.40.4.5 76976,76977 1ex2A 189 6.54e+01 1ex2A c.51.4.2 33225 1wf3A 301 6.54e+01 1ha3A 405 6.55e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1kagA 173 6.57e+01 c.37.1.2 72249 1ryt 190 6.57e+01 1ryt a.25.1.1,g.41.5.1 16646,45245 1z5zA 271 6.69e+01 1he2A 206 6.87e+01 1he2A c.2.1.2 60966 1dd9A 338 6.87e+01 1dd9A e.13.1.1 43254 1zyeA 220 6.89e+01 1id1A 153 6.91e+01 1id1A c.2.1.9 62286 1g4yR 148 6.99e+01 1cll a.39.1.5 60252 1fe8A 196 7.13e+01 1atzA c.62.1.1 59783 1nzjA 298 7.15e+01 c.26.1.1 92377 1fzaB 328 7.22e+01 3fib d.171.1.1,h.1.8.1 42480,45621 1gmwA 143 7.22e+01 b.107.1.1,d.58.38.1 65347,65348 1s14A 194 7.22e+01 d.122.1.2 98329 1gdtA 183 7.25e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 2oatA 439 7.35e+01 2dkb c.67.1.4 34452 1rh5A 436 7.38e+01 f.41.1.1 97464 1ipiA 123 7.39e+01 c.52.1.18 66255 1oafA 261 7.43e+01 a.93.1.1 86734 1vjeA 166 7.44e+01 d.185.1.2 100807 1mvoA 136 7.47e+01 c.23.1.1 79513 3thiA 371 7.52e+01 2thiA c.94.1.1 35792 1w0bA 102 7.52e+01 a.7.11.1 108985 1a0cA 438 7.55e+01 1a0cA c.1.15.3 29529 2byjA 439 7.55e+01 1innA 166 7.62e+01 1j98A d.185.1.2 62608 1jf4A 147 7.64e+01 a.1.1.2 71643 1b7dA 61 7.71e+01 1aho g.3.7.1 44139 1vd5A 377 7.72e+01 a.102.1.7 108518 1jc4A 148 7.80e+01 1jc4A d.32.1.4 62863 1b5zA 130 7.81e+01 3lzt d.2.1.2 36567 1cf2O 337 7.86e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 1ow4A 129 7.87e+01 a.39.2.1 93628 1wzcA 249 7.92e+01 1yvkA 163 7.93e+01 1hn2A 159 8.00e+01 b.60.1.1 65890 1gt1A 159 8.02e+01 b.60.1.1 90515 1a9xB 379 8.03e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1u04A 771 8.07e+01 b.34.14.1,c.55.3.10 107539,107540 1obpA 159 8.09e+01 1obpA b.60.1.1 27092 1i60A 278 8.12e+01 c.1.15.4 71118 1gmpA 96 8.19e+01 1rgeA d.1.1.2 36036 1hbxA 92 8.21e+01 1mnmA d.88.1.1 60930 1zs9A 261 8.29e+01 2bylA 439 8.31e+01 1r6uA 437 8.32e+01 c.26.1.1 97163 1rfeA 162 8.33e+01 1jvpP 298 8.33e+01 d.144.1.7 67371 1xkrA 206 8.35e+01 1kx5B 102 8.43e+01 a.22.1.1 77594 1f28A 297 8.43e+01 1bkpA d.117.1.1 59608 1afrA 345 8.44e+01 1afrA a.25.1.2 16805 1u1hA 765 8.44e+01 c.1.22.2,c.1.22.2 107580,107581 1b7oA 130 8.45e+01 3lzt d.2.1.2 36491 2b49A 287 8.48e+01 2fdbM 164 8.52e+01 1t9kA 347 8.53e+01 c.124.1.5 106721 1ddeA 338 8.58e+01 1dd9A e.13.1.1 43255 2thiA 379 8.60e+01 2thiA c.94.1.1 35794 1ta3B 303 8.61e+01 c.1.8.3 106732 1kfcA 268 8.66e+01 c.1.2.4 77371 1r3sA 367 8.66e+01 c.1.22.1 96963 1nw1A 429 8.67e+01 d.144.1.8 86286 1epwA 1290 8.67e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2a1iA 146 8.78e+01 1iukA 140 8.79e+01 c.2.1.8 83712 1fgs 428 8.82e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1b5uA 130 8.83e+01 3lzt d.2.1.2 36453 1ahpA 797 8.88e+01 1a8i c.87.1.4 35544 1y9kA 157 8.91e+01 1cs0B 382 8.96e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 1ik6A 369 8.97e+01 c.36.1.7,c.48.1.2 66174,66175