# List of top-scoring protein chains for t04-100-30-bys 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 1top 162 6.93e-05 1ncx a.39.1.5 17223 1ggzA 148 4.75e-03 a.39.1.5 70176 1s29A 92 1.03e-02 unknown_sccs -315 2sas 185 2.18e-02 2sas a.39.1.5 17258 1nhkL 144 3.05e-02 1npk d.58.6.1 39142 1oi7A 288 4.29e-02 c.2.1.8 87049 c.23.4.1 87050 1kgdA 180 5.96e-02 c.37.1.1 68582 1e0cA 271 5.99e-02 1e0cA c.46.1.2 32717 c.46.1.2 32718 1dqeA 137 6.23e-02 1dqeA a.39.2.1 17388 1auiB 169 6.43e-02 1auiB a.39.1.5 17325 1avsA 90 7.08e-02 1cll a.39.1.5 17226 1k94A 165 7.09e-02 a.39.1.8 68333 1k4iA 233 9.19e-02 d.115.1.2 72056 1efyA 350 9.61e-02 1a26 a.41.1.1 17413 d.166.1.2 42275 1f4qA 165 9.62e-02 1alvA a.39.1.8 17360 1cbf 285 9.65e-02 1cbf c.90.1.1 35587 1wdcB 156 1.06e-01 1wdcB a.39.1.5 17302 1nt4A 391 1.11e-01 c.60.1.2 -7942 1on2A 142 1.86e-01 a.4.5.24 87103 a.76.1.1 87104 1g57A 217 2.11e-01 1g57A d.115.1.2 60253 1aerA 205 2.13e-01 1aerA d.166.1.1 42249 1a4iA 301 2.30e-01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1exrA 148 2.70e-01 1cll a.39.1.5 17299 1gnlA 544 2.73e-01 e.26.1.1 70287 1f6yA 262 3.29e-01 1f6yA c.1.21.2 29673 1n0wA 243 3.35e-01 c.37.1.11 79772 1kk8B 139 3.36e-01 a.39.1.5 77430 1wdcC 156 4.04e-01 1wdcC a.39.1.5 17317 1s96A 219 4.15e-01 c.37.1.1 -6972 1eg5A 384 4.32e-01 1ecxA c.67.1.3 34429 1wm1A 317 4.51e-01 1g4yR 148 4.63e-01 1cll a.39.1.5 60252 1qtrA 317 5.59e-01 1qtrA c.69.1.7 34660 1m45A 148 5.78e-01 a.39.1.5 78598 1k9uA 78 7.15e-01 a.39.1.10 84348 1din 236 7.38e-01 1din c.69.1.9 34682 1g8iA 190 7.70e-01 1rec a.39.1.5 60363 4icb 76 8.36e-01 4icb a.39.1.1 17145 1dfmA 223 1.11e+00 1d2iA c.52.1.5 33295 1tm0A 350 1.13e+00 1f46A 140 1.17e+00 1f46A d.129.4.1 59643 1bt0A 76 1.49e+00 1ubi d.15.1.1 37607 1dfoA 417 1.52e+00 1bj4A c.67.1.4 34480 1t3cA 421 1.69e+00 1kbvA 327 1.72e+00 b.6.1.3 68395 b.6.1.3 68396 1gky 187 1.81e+00 1gky c.37.1.1 31839 1lvwA 295 1.83e+00 c.68.1.6 84723 1s6cA 183 1.90e+00 a.39.1.5 -858 1twdA 256 2.09e+00 1ig5A 75 2.13e+00 4icb a.39.1.1 62363 1jl3A 139 2.23e+00 c.44.1.1 66826 1ex7A 186 2.56e+00 1gky c.37.1.1 59537 2pvbA 107 2.68e+00 1a75A a.39.1.4 17205 1augA 215 2.94e+00 1a2zA c.56.4.1 33798 1rv3A 483 3.23e+00 1g8mA 593 3.32e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1ly1A 181 3.37e+00 c.37.1.1 74334 1a4mA 349 3.38e+00 1a4mA c.1.9.1 29014 1fkx 349 3.68e+00 1a4mA c.1.9.1 29018 1uhnA 189 3.69e+00 a.39.1.5 -853 1k6dA 220 3.71e+00 unknown_sccs 72082 1i60A 278 3.76e+00 c.1.15.4 71118 1nmeA 146 3.79e+00 c.17.1.1 85874 1cy5A 97 3.80e+00 1cy5A a.77.1.3 18430 1j3wA 163 3.91e+00 unknown_sccs -10870 1iyeA 309 4.02e+00 e.17.1.1 83786 1pvc1 301 4.20e+00 1pov1 1nmeB 92 4.38e+00 1mdc 133 4.41e+00 1hmt b.60.1.2 27198 1rl6A 177 4.42e+00 1rl6A d.141.1.1 41473 d.141.1.1 41474 1k6kA 143 4.52e+00 a.174.1.1 77274 1czaN 917 4.60e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1n25A 368 4.64e+00 c.37.1.20 85264 1b5fA 239 4.66e+00 1smrA b.50.1.2 26836 1j9bA 141 4.71e+00 c.47.1.12 66459 1nvmA 345 4.86e+00 a.5.7.1 86249 c.1.10.5 86250 1a7w 69 4.87e+00 1a7w a.22.1.2 16477 1bmqB 88 4.93e+00 1pauB 1npyA 271 5.04e+00 c.2.1.7 85995 c.58.1.5 85996 1vi2A 300 5.31e+00 c.2.1.7 -5960 c.58.1.5 -6366 1br1B 150 5.42e+00 1wdcC a.39.1.5 17309 1p3wA 404 5.81e+00 c.67.1.3 87752 1np6A 174 5.93e+00 c.37.1.10 85954 1rwyA 109 5.96e+00 a.39.1.4 -825 1gvp 87 6.03e+00 1gvp b.40.4.7 25369 1i6pA 220 6.28e+00 1ddzA c.53.2.1 61848 1q9jA 422 6.28e+00 1i4mA 108 6.34e+00 d.6.1.1 66025 1vqb 87 6.36e+00 1gvp b.40.4.7 25370 4cpv 109 6.49e+00 1a75A a.39.1.4 17198 1fnnA 389 6.57e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1qwoA 442 6.78e+00 1c7gA 456 6.79e+00 c.67.1.2 -8153 1mmiA 366 7.02e+00 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1q0sA 259 7.07e+00 c.66.1.28 -8110 1ixkA 315 7.11e+00 unknown_sccs -8099 1paz 123 7.18e+00 1bqk b.6.1.1 22878 1cr5A 189 7.18e+00 1cr5A b.52.2.3 26931 d.31.1.1 38465 1sc3B 88 7.29e+00 1lam 484 7.38e+00 1lam c.56.5.3 33829 c.50.1.1 33166 1i2kA 269 7.46e+00 e.17.1.1 -11995 1j75A 67 7.52e+00 a.4.5.19 62673 1kjwA 295 7.53e+00 b.34.2.1 68643 c.37.1.1 68644 2fokA 579 7.63e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1mxgA 435 7.73e+00 b.71.1.1 85193 c.1.8.1 85194 1et0A 269 7.90e+00 1et0A e.17.1.1 43289 1rypG 244 8.06e+00 d.153.1.4 41938 1a99A 344 8.21e+00 1pot c.94.1.1 35812 1i2aA 219 8.24e+00 e.24.1.1 -12012 1nbfD 76 8.64e+00 d.15.1.1 80390 1smlA 269 8.74e+00 1smlA d.157.1.1 42053 5pal 109 8.79e+00 1a75A a.39.1.4 17215 3cla 213 8.89e+00 3cla c.43.1.1 32610 1kl9A 182 9.28e+00 b.40.4.5 72681 1a8vA 121 9.52e+00 1a62 a.140.3.1 64712 b.40.4.5 64713 1ok7A 366 9.57e+00 1ec7A 446 9.62e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1nddA 76 9.63e+00 1ubi d.15.1.1 37599 1jd0A 263 9.78e+00 2cba b.74.1.1 62888 1ubi 76 9.82e+00 1ubi d.15.1.1 37584 1gmxA 108 9.85e+00 c.46.1.3 65355 1j9lA 247 9.87e+00 c.106.1.1 62762 1knwA 425 1.00e+01 b.49.2.3 -4274 c.1.6.1 -5229 1bx7 55 1.00e+01 1bx7 g.3.15.1 44355 1sznA 417 1.04e+01 1sedA 117 1.08e+01 1lf6A 684 1.09e+01 a.102.1.5 77918 b.30.5.5 77919 1bgp 309 1.15e+01 1bgp a.93.1.1 18690 1n3bA 216 1.15e+01 c.37.1.1 79959 1gs5A 258 1.16e+01 c.73.1.2 70395 1f5jA 199 1.16e+01 1axkA b.29.1.11 24342 5ukdA 194 1.16e+01 1zin c.37.1.1 31851 1mzbA 136 1.17e+01 unknown_sccs -266 1p57B 255 1.18e+01 b.47.1.2 -4248 1nxiA 132 1.20e+01 d.58.47.1 86381 1k28D 391 1.21e+01 b.106.1.1 68052 b.106.1.1 68053 1pixA 587 1.22e+01 c.14.1.4 -6282 1vhtA 218 1.24e+01 c.37.1.1 -7004 1gggA 226 1.26e+01 1lst c.94.1.1 35817 1jf9A 408 1.28e+01 1c0nA c.67.1.3 62931 1mbxC 106 1.29e+01 d.45.1.2 78929 1ks9A 291 1.31e+01 a.100.1.7 68857 c.2.1.6 68858 1el4A 195 1.31e+01 1ej3A a.39.1.5 59453 1uesA 191 1.32e+01 1lvfA 110 1.32e+01 a.47.2.1 74280 1g5bA 221 1.33e+01 1g5bA d.159.1.3 60261 1sw6A 327 1.35e+01 1sw6A d.211.1.1 19176 1qv1A 195 1.36e+01 a.39.1.5 -830 1bj4A 470 1.37e+01 1bj4A c.67.1.4 34479 1qnnA 191 1.39e+01 1avmA a.2.11.1 15792 d.44.1.1 38755 4pep 326 1.41e+01 1smrA b.50.1.2 26843 1gln 468 1.42e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1ri5A 298 1.43e+01 unknown_sccs -8063 1rtxA 123 1.46e+01 a.1.1.1 -3 1lla 628 1.49e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.18.3 21861 1wdnA 226 1.53e+01 1lst c.94.1.1 35816 1qf9A 194 1.59e+01 1zin c.37.1.1 31848 1ogwA 76 1.60e+01 d.15.1.1 87001 1rvgA 305 1.62e+01 c.1.10.2 -5500 1evyA 366 1.64e+01 1evyA a.100.1.6 18811 c.2.1.6 30215 1f66C 128 1.66e+01 1aoiC a.22.1.1 16442 1d3vA 323 1.69e+01 1d3vA c.42.1.1 32559 1g2iA 166 1.72e+01 1g2iA c.23.16.2 31438 1k77A 260 1.73e+01 c.1.15.5 72096 1jf2A 195 1.74e+01 1ej3A a.39.1.5 62930 1rqlA 267 1.74e+01 c.108.1.3 -6814 1otgA 125 1.75e+01 1otgA d.80.1.2 39831 1apyB 141 1.76e+01 1apyB 1jk7A 323 1.76e+01 1auiA d.159.1.3 63144 1p9gA 41 1.81e+01 1dfaA 454 1.82e+01 1vdeA b.86.1.2 28375 d.95.2.2 40575 d.95.2.2 40576 1d1gA 168 1.82e+01 1d1gA c.71.1.1 34889 1lu4A 136 1.85e+01 c.47.1.10 -7509 1nrvA 105 1.87e+01 d.93.1.1 86126 1j1bA 420 1.87e+01 d.144.1.7 -11312 2liv 344 1.88e+01 2liv c.93.1.1 35708 1gvnA 90 1.88e+01 a.8.2.1 76353 1lfwA 470 1.89e+01 c.56.5.4 77942 d.58.19.1 77943 1b67A 68 1.91e+01 1a7w a.22.1.2 16474 1i7dA 659 1.92e+01 1d6mA e.10.1.1 61886 1ayl 541 1.93e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1nu5A 370 1.94e+01 c.1.11.2 -5565 d.54.1.1 -9823 1j09A 468 1.98e+01 a.97.1.1 77025 c.26.1.1 77026 1alvA 173 1.99e+01 1alvA a.39.1.8 17370 1b4kA 337 2.03e+01 1b4kA c.1.10.3 29184 1lktA 104 2.05e+01 1lktA b.90.1.1 28398 1g2yA 32 2.05e+01 unknown_sccs 17003 1ugmA 125 2.08e+01 1f74A 293 2.08e+01 1nal3 c.1.10.1 29079 1pvaA 110 2.09e+01 1a75A a.39.1.4 17207 3ladA 476 2.09e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1a62 130 2.10e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1vk1A 242 2.17e+01 1j30A 144 2.17e+01 a.25.1.1 -650 1jv4A 162 2.18e+01 b.60.1.1 67343 1fdr 248 2.19e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1s1pA 331 2.20e+01 c.1.7.1 -5240 1m1nA 491 2.21e+01 c.92.2.3 78417 1fmjA 351 2.26e+01 c.37.1.5 59879 1ursA 402 2.31e+01 c.94.1.1 -8651 1uzxA 169 2.32e+01 d.20.1.2 -9409 1ss4A 153 2.34e+01 1o1zA 234 2.37e+01 c.1.18.3 86555 1nc5A 373 2.39e+01 a.102.1.6 85548 1kzyC 259 2.40e+01 c.15.1.4 73383 c.15.1.4 73384 1kdj 102 2.45e+01 1plc b.6.1.1 22864 1pkoA 139 2.46e+01 b.1.1.1 88147 1scuA 288 2.46e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1jipA 403 2.47e+01 a.104.1.1 66748 1qjtA 99 2.64e+01 1eh2 a.39.1.6 17335 1k9sA 237 2.64e+01 c.56.2.1 68359 1htyA 1015 2.66e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 4ubpA 101 2.68e+01 1ubpA d.8.1.1 37352 1q6hA 224 2.68e+01 d.26.1.1 -9487 1fezA 256 2.69e+01 1fezA c.108.1.3 43343 1i1kA 309 2.69e+01 1daaA e.17.1.1 61533 1ir6A 424 2.69e+01 c.107.1.2 71342 1qwnA 1045 2.73e+01 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1qycA 308 2.79e+01 c.2.1.2 -5782 1ayoA 130 2.80e+01 1ayoA b.2.4.1 22431 1n46A 258 2.80e+01 a.123.1.1 85315 1l2lA 457 2.81e+01 c.72.1.3 77656 1lucB 324 2.83e+01 1lucA c.1.16.1 29548 1oi2A 366 2.84e+01 c.32.1.2 87039 d.79.2.2 87040 1l3iA 192 2.84e+01 c.66.1.22 77676 1cot 129 2.85e+01 1ycc a.3.1.1 15899 1j2gA 319 2.89e+01 1e8aA 91 2.90e+01 1b4cA a.39.1.2 17188 1iirA 415 2.92e+01 1iirA c.87.1.5 62453 1ukfA 188 2.94e+01 unknown_sccs -8886 1q9bA 43 2.97e+01 g.3.1.1 -12392 1uasA 362 3.02e+01 b.71.1.1 88388 c.1.8.1 88389 1omrA 201 3.03e+01 a.39.1.5 -854 1u08A 386 3.15e+01 1cwpA 190 3.17e+01 1cwpA b.121.4.5 23305 1pg4A 652 3.17e+01 e.23.1.1 88067 1v2xA 194 3.23e+01 c.116.1.1 -6704 1gadO 330 3.27e+01 1dssG c.2.1.3 29950 d.81.1.1 39865 3psg 370 3.29e+01 1smrA b.50.1.2 26841 1bxyA 60 3.30e+01 1bxyA d.59.1.1 39525 1vh7A 265 3.34e+01 c.1.2.1 -5159 1kx5C 128 3.34e+01 a.22.1.1 77595 1gzgA 337 3.37e+01 c.1.10.3 70805 1ecpA 238 3.39e+01 1ecpA c.56.2.1 33775 1m65A 245 3.40e+01 c.6.3.1 84847 1fjmA 330 3.41e+01 1auiA d.159.1.3 42082 1mr8A 93 3.41e+01 1b4cA a.39.1.2 17186 1qtnA 164 3.43e+01 1pauA c.17.1.1 30999 1sn4A 64 3.43e+01 1aho g.3.7.1 44136 1vkmA 297 3.43e+01 1qhxA 178 3.43e+01 1qhsA c.37.1.3 31936 1iloA 77 3.48e+01 c.47.1.1 66205 1vicA 262 3.51e+01 c.68.1.13 -8252 1o0xA 262 3.51e+01 d.127.1.1 80755 1kx5B 102 3.52e+01 a.22.1.1 77594 1brwA 433 3.53e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1fxoA 293 3.54e+01 1g0rA c.68.1.6 34524 3htsB 102 3.56e+01 2hts a.4.5.22 16175 1gjjA 168 3.57e+01 a.140.1.1 83291 a.140.1.1 83292 1dqgA 135 3.59e+01 1dqgA b.42.2.2 25579 1i1nA 226 3.59e+01 c.66.1.7 71102 1qtqA 553 3.59e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1s3jA 155 3.60e+01 a.4.5.28 -227 1gowA 489 3.61e+01 1qvbA c.1.8.4 28981 1v7cA 351 3.62e+01 c.79.1.1 -8512 1euaA 213 3.64e+01 1fwrA c.1.10.1 29155 1ekfA 365 3.66e+01 1ekfA e.17.1.1 59445 1tvlA 454 3.68e+01 1t5hX 504 3.76e+01 1nbwB 117 3.77e+01 c.51.3.2 80396 1hfoA 113 3.77e+01 d.80.1.3 61006 1nowA 507 3.78e+01 c.1.8.6 85936 d.92.2.1 85937 1sc3A 178 3.80e+01 1qh8A 478 3.81e+01 1qguA c.92.2.3 35633 1ryt 190 3.81e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 2scpA 174 3.82e+01 2scpA a.39.1.5 17256 1rro 108 3.82e+01 1a75A a.39.1.4 17195 1s9aA 257 3.87e+01 1qyaA 307 3.89e+01 1ku1A 230 3.89e+01 a.118.3.1 72996 1m2xA 223 3.93e+01 d.157.1.1 84764