# 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 1xngA 268 2.36e-02 1kijA 390 2.23e-01 d.14.1.3,d.122.1.2 72514,72515 2a2pA 129 2.69e-01 1gpmA 525 3.48e-01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2cokA 113 8.02e-01 1id3B 102 9.37e-01 a.22.1.1 66113 1zg2A 107 1.01e+00 1aoiF 87 1.05e+00 1aoiB a.22.1.1 16471 1aoiB 87 1.07e+00 1aoiB a.22.1.1 16470 1hq3D 103 1.12e+00 1aoiB a.22.1.1 16464 1tzyD 103 1.12e+00 a.22.1.1 107533 1kx5B 102 1.24e+00 a.22.1.1 77594 1ih8A 271 1.26e+00 2nsyA c.26.2.1 62377 1kvlA 358 1.30e+00 e.3.1.1 73062 1qwdA 177 1.50e+00 b.60.1.1 96471 1qmeA 702 1.58e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1pmzA 86 1.66e+00 a.39.1.10 104195 1pi4A 358 1.69e+00 e.3.1.1 94700 1xzoA 174 1.80e+00 1l0gA 358 1.83e+00 e.3.1.1 73400 1ni5A 433 1.84e+00 c.26.2.5,d.229.1.1 80533,80534 1s31A 273 1.94e+00 1rewC 135 1.95e+00 g.7.1.3 97336 1qtfA 246 2.01e+00 1agjA b.47.1.1 25830 1u6zA 513 2.05e+00 1fsyA 358 2.06e+00 1gceA e.3.1.1 60016 2nsyA 271 2.35e+00 2nsyA c.26.2.1 31612 1kqpA 271 2.39e+00 c.26.2.1 72883 1theB 260 2.46e+00 1theB d.3.1.1 37057 1ru8A 232 2.48e+00 c.26.2.1 97849 2blsA 358 2.55e+00 1gceA e.3.1.1 42747 1nsyA 271 2.59e+00 2nsyA c.26.2.1 31614 1csbB 205 2.64e+00 1theB 1theA 260 3.00e+00 1theB d.3.1.1 37056 1emwA 88 3.02e+00 1emwA d.27.1.1 38448 2ffyA 358 3.09e+00 2cc0A 195 3.16e+00 1xl3C 92 3.20e+00 1yezA 68 3.23e+00 1widA 130 3.34e+00 1o50A 157 3.38e+00 d.37.1.1,d.37.1.1 92478,92479 1xer 103 3.39e+00 1xer d.58.1.3 38990 1fxoA 293 3.59e+00 1g0rA c.68.1.6 34524 1ew3A 159 3.82e+00 1mup b.60.1.1 27114 1e69B 322 3.83e+00 1e69B c.37.1.12 32377 1kppA 145 3.90e+00 d.20.1.2 72846 1ga0A 364 3.90e+00 1gceA e.3.1.1 60410 1rgzA 363 4.76e+00 e.3.1.1 97457 1onhA 364 4.88e+00 e.3.1.1 93357 1iloA 77 5.07e+00 c.47.1.1 66205 2bltA 361 5.10e+00 1gceA e.3.1.1 42739 1g0rA 293 5.10e+00 1g0rA c.68.1.6 34532 1q8iA 783 5.27e+00 c.55.3.5,e.8.1.1 96208,96209 1ecfA 504 5.42e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1s5jA 847 6.28e+00 1wy5A 317 6.32e+00 1jenA 267 6.34e+00 1jenA 1vquA 374 6.37e+00 1ecfB 504 6.55e+00 1ecfB c.61.1.1,d.153.1.1 34054,41821 1gmyA 261 6.90e+00 d.3.1.1 76236 1lvl 458 7.35e+00 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30567,30568,40205 1k3iA 656 7.36e+00 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1fjgP 88 7.59e+00 1emwA d.27.1.1 38444 1f89A 291 7.67e+00 d.160.1.1 64988 1xtmA 175 7.81e+00 1vlmA 219 7.96e+00 c.66.1.41 108836 1o4sA 389 8.35e+00 c.67.1.1 86620 1gof 639 8.65e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 1whzA 70 9.13e+00 1cqqA 180 9.25e+00 1cqqA b.47.1.4 26422 2axcA 264 9.31e+00 1wucA 250 9.31e+00 1ud9A 245 9.75e+00 d.131.1.2,d.131.1.2 107768,107769 2fomB 185 9.87e+00 1tif 78 9.92e+00 1tif d.15.8.1 37836 1goh 639 1.02e+01 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 1jqeA 292 1.02e+01 c.66.1.19 71789 2aotA 292 1.03e+01 1iow 306 1.03e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1xi1A 575 1.12e+01 1c14A 262 1.21e+01 1eny c.2.1.2 29927 1ibvB 229 1.21e+01 1qsgA 265 1.24e+01 1eny c.2.1.2 29935 1xtlA 175 1.24e+01 1lcyA 325 1.26e+01 b.36.1.4,b.47.1.1 73834,73835 1lvwA 295 1.26e+01 c.68.1.6 84723 1pyaB 228 1.27e+01 1pyaB 2fd6U 276 1.31e+01 1gceA 364 1.31e+01 1gceA e.3.1.1 42738 1zkpA 268 1.35e+01 1rypI 222 1.37e+01 d.153.1.4 41877 1d5tA 433 1.39e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1oixA 191 1.41e+01 2dln 306 1.42e+01 1iow c.30.1.2,d.142.1.1 31715,41483 1s4iA 175 1.43e+01 1s3cA 141 1.44e+01 1j9bA 141 1.45e+01 c.47.1.12 66459 1oxsC 353 1.48e+01 b.40.6.3,c.37.1.12 87519,87520 1zczA 464 1.48e+01 1itwA 741 1.55e+01 c.77.1.2 76793 1oxxK 353 1.59e+01 b.40.6.3,c.37.1.12 93715,93716 1idsA 207 1.61e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1hjrA 158 1.64e+01 1hjrA c.55.3.6 33727 1qg6A 261 1.65e+01 1eny c.2.1.2 29919 1yrgA 385 1.65e+01 1yrgA c.10.1.2 30854 2fp7B 172 1.67e+01 2a1vA 144 1.72e+01 1jqlB 140 1.75e+01 c.37.1.20 63234 1wdcC 156 1.75e+01 1wdcC a.39.1.5 17317 1ycoA 279 1.76e+01 2g6tA 306 1.76e+01 2ca6A 386 1.77e+01 2alp 198 1.78e+01 1qq4A b.47.1.1 25772 1zljA 78 1.79e+01 1ssxA 198 1.81e+01 b.47.1.1 98978 1bu6O 501 1.82e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 2g76A 335 1.83e+01 2ew2A 316 1.87e+01 1fnoA 417 1.89e+01 d.58.19.1,c.56.5.4 70145,75841 1uvzA 119 1.89e+01 1r9gA 216 1.89e+01 c.23.16.1 97258 1dy9A 187 1.90e+01 1jxpA b.47.1.3 26400 1fr1A 361 1.93e+01 1gceA e.3.1.1 42734 1a64A 97 1.94e+01 1cdcA b.1.1.1 19750 1kxvC 121 1.95e+01 b.1.1.1 73190 1r26A 125 1.95e+01 c.47.1.1 96847 1bgj 394 1.96e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1cdcA 99 1.99e+01 1cdcA b.1.1.1 19746 1sk7A 198 2.00e+01 a.132.1.2 105671 1ris 101 2.00e+01 1ris d.58.14.1 39314 1fc4A 401 2.03e+01 1bs0A c.67.1.4 59760 2scuB 388 2.06e+01 2scuB c.23.4.1,d.142.1.4 31141,41562 1rgyA 360 2.07e+01 e.3.1.1 97456 1bb8 71 2.08e+01 2bb8 d.10.1.1 37478 1lrzA 426 2.08e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1zp7A 206 2.08e+01 1qr4A 186 2.11e+01 1qr4B b.1.2.1,b.1.2.1 21986,21987 1o4wA 147 2.11e+01 c.120.1.1 86629 1w6tA 444 2.11e+01 2fuvA 549 2.11e+01 2f9lA 199 2.14e+01 1iyeA 309 2.17e+01 e.17.1.1 83786 1l0bA 229 2.17e+01 c.15.1.3,c.15.1.3 73391,73392 1i1kA 309 2.17e+01 1daaA e.17.1.1 61533 1befA 181 2.19e+01 1befA b.47.1.3 26419 1vixA 420 2.19e+01 c.56.5.4,d.58.19.1 100777,100778 1jvnA 555 2.20e+01 c.1.2.1,c.23.16.1 67355,67356 1ebdC 41 2.20e+01 1ebdC a.9.1.1 16355 1df9A 191 2.23e+01 1befA b.47.1.3 26420 1ywhA 313 2.24e+01 1cdcB 99 2.24e+01 1cdcA b.1.1.1 19747 1z5yE 149 2.25e+01 1mpgA 282 2.36e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1iueA 98 2.37e+01 d.15.4.1 90697 1h5rA 293 2.43e+01 c.68.1.6 65623 1pbe 394 2.43e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1jl0A 334 2.43e+01 1jenA d.156.1.1 63155 1k38A 254 2.45e+01 e.3.1.1 84303 1ab6A 125 2.46e+01 3chy c.23.1.1 31054 1mr4A 47 2.47e+01 g.3.7.5 91429 1jbeA 128 2.48e+01 3chy c.23.1.1 62845 1cll 148 2.48e+01 1cll a.39.1.5 17263 2bbeA 108 2.50e+01 1oivA 191 2.54e+01 c.37.1.8 93076 1rznA 205 2.55e+01 1w4vA 119 2.56e+01 1p5hA 428 2.58e+01 c.123.1.1 87802 1a26 361 2.60e+01 1a26 a.41.1.1,d.166.1.2 17412,42274 1qy6A 274 2.61e+01 b.47.1.1 96574 1g6nA 210 2.66e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1zrjA 50 2.66e+01 1yrgB 385 2.69e+01 1yrgA c.10.1.2 30855 1cj3A 392 2.73e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1rifA 282 2.77e+01 c.37.1.23 97507 1qq4A 198 2.77e+01 1qq4A b.47.1.1 25768 2cq2A 114 2.78e+01 3cln 148 2.80e+01 1cll a.39.1.5 17286 1uluA 261 2.82e+01 2gcuA 245 2.83e+01 1sb2A 133 2.84e+01 1st9A 143 2.84e+01 c.47.1.10 98987 1d7yA 408 2.87e+01 1d7yA c.3.1.5,c.3.1.5,d.87.1.1 30565,30566,40204 1jmmA 377 2.88e+01 b.30.6.1 71749 1b97A 244 2.89e+01 1rvaA c.52.1.2 33252 1kagA 173 2.89e+01 c.37.1.2 72249 1jlwA 219 2.89e+01 a.45.1.1,c.47.1.5 71741,71742 1v6tA 255 2.90e+01 1y1oA 203 2.93e+01 2cgpA 210 2.96e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1louA 101 2.97e+01 1ris d.58.14.1 39323 2gfaA 119 2.97e+01 1yvcA 70 2.98e+01 1iyxA 432 3.00e+01 c.1.11.1,d.54.1.1 83815,83816 1n4kA 381 3.00e+01 a.118.22.1,b.42.6.1 79992,79993 1cye 129 3.00e+01 3chy c.23.1.1 31077 1x0pA 143 3.01e+01 2pcdA 200 3.01e+01 3pchA b.3.6.1 22665 1k0iA 394 3.05e+01 c.3.1.2,d.16.1.2 67942,67943 1yb3A 175 3.06e+01 1esc 306 3.07e+01 1esc c.23.10.1 31334 1sh0A 510 3.07e+01 e.8.1.4 98876 1efyA 350 3.07e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1zkdA 387 3.09e+01 3pcnA 200 3.11e+01 3pchA b.3.6.1 22725 1o1xA 155 3.11e+01 c.121.1.1 86553 2b43A 526 3.13e+01 1l7bA 92 3.16e+01 c.15.1.2 91053 1c8zA 265 3.18e+01 1c8zA d.23.1.1 38375 1h6kX 97 3.18e+01 d.58.7.1 60684 1rz1A 161 3.20e+01 b.45.1.2 98124 1exrA 148 3.20e+01 1cll a.39.1.5 17299 1w85I 49 3.21e+01 1osa 148 3.22e+01 1cll a.39.1.5 17300 1rc9A 221 3.23e+01 1xewX 182 3.23e+01 3pchA 200 3.29e+01 3pchA b.3.6.1 22653 1apj 74 3.29e+01 1apj g.23.1.1 44899 1m65A 245 3.30e+01 c.6.3.1 84847 1x1rA 178 3.32e+01 1z2lA 423 3.32e+01 1ut7A 171 3.39e+01 b.143.1.1 99906 1wdcB 156 3.42e+01 1wdcB a.39.1.5 17302 1jalA 363 3.44e+01 c.37.1.8,d.15.10.2 84138,84139 1asx 159 3.47e+01 1a6dA c.8.5.2 30821 1d3bB 91 3.50e+01 1d3bB b.38.1.1 24804 1yruB 74 3.50e+01 1kwkA 645 3.50e+01 b.71.1.1,c.1.8.1,c.23.16.5 77565,77566,77567 1kwgA 645 3.51e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1zkjA 359 3.53e+01 1dgrM 93 3.54e+01 1caxB b.82.1.2 28101 2atxA 194 3.57e+01 3pcgA 200 3.59e+01 3pchA b.3.6.1 22647 1eonA 245 3.59e+01 1rvaA c.52.1.2 33238 2b0tA 738 3.59e+01 1scmB 145 3.69e+01 1wdcB a.39.1.5 17304 1wpoB 256 3.73e+01 1lay b.57.1.1 27013 1lfpA 249 3.74e+01 e.39.1.1 73885 1ig3A 263 3.75e+01 1ig3A b.82.6.1,c.100.1.1 62358,62359 1n3yA 198 3.77e+01 c.62.1.1 79976 1prgA 270 3.77e+01 2prgA a.123.1.1 19314 1lj5A 379 3.81e+01 e.1.1.1 73928 1p27B 106 3.81e+01 d.58.7.1 93908 1mvuB 121 3.84e+01 b.1.1.1 91475 1ox6A 555 3.86e+01 c.1.2.1,c.23.16.1 87505,87506 1xfpA 142 3.86e+01 b.1.1.1 109587 1sx5A 244 3.86e+01 c.52.1.2 99023 1xfxO 149 3.96e+01 1gm6A 175 3.97e+01 b.60.1.1 70272 1hw5A 210 3.98e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1knlA 130 3.98e+01 b.42.2.1 72780 1knmA 130 3.99e+01 b.42.2.1 72781 1lucB 324 4.00e+01 1lucA c.1.16.1 29548 1e6mA 128 4.15e+01 3chy c.23.1.1 31039 2d13A 227 4.15e+01 2nef 136 4.19e+01 1efnB d.102.1.1 40704 1wlyA 333 4.24e+01 1wpoA 256 4.29e+01 1lay b.57.1.1 27012 2mysB 166 4.29e+01 1wdcB a.39.1.5 17308 1mkzA 172 4.29e+01 c.57.1.1 84998 1dofA 403 4.29e+01 1c3cA a.127.1.1 19429 2d28C 149 4.34e+01 1i7nA 309 4.36e+01 c.30.1.5,d.142.1.3 83681,83682 1cqmA 101 4.38e+01 1ris d.58.14.1 39321 1jtdB 273 4.44e+01 b.69.5.2 67265 1t5jA 313 4.47e+01 a.209.1.1 99125 1rvaA 244 4.48e+01 1rvaA c.52.1.2 33240 1g0sA 209 4.50e+01 1g0sA d.113.1.1 60187 1b94A 244 4.53e+01 1rvaA c.52.1.2 33250 1mylA 53 4.56e+01 1bazA a.43.1.1 17427 1z5bA 469 4.61e+01 1mp4A 292 4.63e+01 c.68.1.6 79376 1a6pA 94 4.64e+01 1cdcA b.1.1.1 19748 2erxA 172 4.73e+01 1uf5A 303 4.76e+01 d.160.1.2 107808 1rz4A 226 4.78e+01 a.4.5.53,a.118.1.18 105131,105132 1dctA 324 4.78e+01 6mhtA c.66.1.26 34244 2c46A 241 4.82e+01 1u1iA 392 4.83e+01 c.2.1.3,d.81.1.3 107582,107583 1ass 159 4.83e+01 1a6dA c.8.5.2 30818 1brlB 324 4.84e+01 1lucA c.1.16.1 29554 1b96A 244 4.86e+01 1rvaA c.52.1.2 33268 2awpA 198 4.87e+01 2g84A 197 4.88e+01 1odkA 235 4.88e+01 c.56.2.1 86863 1zdyA 307 4.90e+01 1kn0A 212 4.94e+01 d.50.1.3 77444 1vetA 124 4.96e+01 d.110.7.1 108553 1wr2A 238 5.02e+01 2d4pA 141 5.04e+01 1yucA 255 5.12e+01 1m6yA 301 5.14e+01 a.60.13.1,c.66.1.23 78716,78717 1nxiA 132 5.18e+01 d.58.47.1 86381 1r5jA 337 5.19e+01 c.77.1.5 97097 1g4yR 148 5.21e+01 1cll a.39.1.5 60252 1erzA 303 5.22e+01 1erzA d.160.1.2 59498 2pdd 43 5.30e+01 1ebdC a.9.1.1 16358 1j5xA 342 5.30e+01 c.80.1.1 71591 1z0jA 170 5.31e+01 1gv3A 248 5.31e+01 a.2.11.1,d.44.1.1 70585,70586 2a7oA 112 5.32e+01 1a7cA 379 5.32e+01 1sek e.1.1.1 42660 1yhtA 367 5.35e+01 1ysjA 404 5.36e+01 1uteA 313 5.36e+01 1uteA d.159.1.1 42078 1a6dB 543 5.37e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1wmqA 147 5.37e+01 1l1eA 287 5.38e+01 c.66.1.18 73454 1wpuA 147 5.39e+01 1p04A 198 5.46e+01 1qq4A b.47.1.1 25805 2fp4B 395 5.58e+01 1ysqA 193 5.67e+01 2f3yA 148 5.76e+01 1r7mA 235 5.77e+01 1viaA 175 5.78e+01 c.37.1.2 100754 1gkuB 1054 5.81e+01 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 2a19B 284 5.85e+01 1f6oA 219 5.88e+01 1bnkA b.46.1.2 25763 1k2yX 463 5.89e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1kk8B 139 5.92e+01 a.39.1.5 77430 1b2pA 119 5.94e+01 1b2pA b.78.1.1 27998 1a3gA 308 5.98e+01 1daaA e.17.1.1 43286 1y2tA 142 6.00e+01 1oeyA 83 6.01e+01 d.15.2.2 92800 3chy 128 6.02e+01 3chy c.23.1.1 31038 1cb8A 678 6.10e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1eziA 228 6.10e+01 1eyrA c.68.1.13 34512 1bteA 97 6.12e+01 1bteA g.7.1.3 44463 1dqeA 137 6.15e+01 1dqeA a.39.2.1 17388 1fmtB 314 6.18e+01 1fmtA b.46.1.1,c.65.1.1 25759,34175 2al1A 436 6.20e+01 1txb 73 6.23e+01 1txb g.7.1.1 44455 1onjA 61 6.26e+01 g.7.1.1 93358 1um8A 376 6.28e+01 c.37.1.20 99580 1h05A 146 6.34e+01 c.23.13.1 76433 1sglA 209 6.44e+01 d.124.1.1 105536 1nw3A 416 6.49e+01 c.66.1.31 86288 2al2A 436 6.50e+01 1vhnA 318 6.51e+01 c.1.4.1 100693 2bb8 71 6.52e+01 2bb8 d.10.1.1 37480 1lgpA 116 6.61e+01 b.26.1.2 73890 1es7B 89 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