# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 6.04e-05 1ncx a.39.1.5 17223 1ncx 162 1.08e-04 1ncx a.39.1.5 17222 1s29A 92 5.03e-03 unknown_sccs -315 1mu5A 471 3.21e-02 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1ggzA 148 4.58e-02 a.39.1.5 70176 1ecxA 384 7.52e-02 1ecxA c.67.1.3 34431 1ctdA 36 8.43e-02 1ctdA a.39.1.5 17230 1eg5A 384 8.43e-02 1ecxA c.67.1.3 34429 1f4qA 165 1.07e-01 1alvA a.39.1.8 17360 1a26 361 1.20e-01 1a26 a.41.1.1 17412 d.166.1.2 42274 2sas 185 1.65e-01 2sas a.39.1.5 17258 1avsA 90 2.10e-01 1cll a.39.1.5 17226 1efyA 350 2.13e-01 1a26 a.41.1.1 17413 d.166.1.2 42275 1a7w 69 2.31e-01 1a7w a.22.1.2 16477 1k94A 165 2.32e-01 a.39.1.8 68333 1n25A 368 2.61e-01 c.37.1.20 85264 1g4yR 148 2.74e-01 1cll a.39.1.5 60252 1auiB 169 2.89e-01 1auiB a.39.1.5 17325 1wdcC 156 2.92e-01 1wdcC a.39.1.5 17317 1f47B 144 3.10e-01 1f46A d.129.4.1 59645 1f46A 140 3.43e-01 1f46A d.129.4.1 59643 1bfmA 69 3.99e-01 1a7w a.22.1.2 16479 1cll 148 4.15e-01 1cll a.39.1.5 17263 1jhfA 202 4.21e-01 a.4.5.2 63057 b.87.1.1 63058 1e0cA 271 4.28e-01 1e0cA c.46.1.2 32717 c.46.1.2 32718 1a4iA 301 4.85e-01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1m9nA 613 4.90e-01 c.24.1.3 78870 c.97.2.1 78871 1f7wA 144 5.26e-01 1f46A d.129.4.1 59679 2mysB 166 5.54e-01 1wdcB a.39.1.5 17308 3cln 148 5.59e-01 1cll a.39.1.5 17286 1g8mA 593 5.95e-01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1gnlA 544 6.51e-01 e.26.1.1 70287 1scmB 145 6.57e-01 1wdcB a.39.1.5 17304 1nf2A 268 6.72e-01 c.108.1.10 -6842 1ponA 36 6.98e-01 1ponA a.39.1.5 17239 1wdcB 156 7.24e-01 1wdcB a.39.1.5 17302 3ullA 132 7.42e-01 3ullA b.40.4.3 25282 1a4iB 301 7.59e-01 1a4iA c.2.1.7 30279 c.58.1.2 33927 1ctaA 36 8.63e-01 1ctdA a.39.1.5 17232 1diaA 306 9.24e-01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1bj4A 470 9.58e-01 1bj4A c.67.1.4 34479 1aerA 205 1.03e+00 1aerA d.166.1.1 42249 1kk8B 139 1.11e+00 a.39.1.5 77430 1a75A 108 1.17e+00 1a75A a.39.1.4 17216 1k9uA 78 1.22e+00 a.39.1.10 84348 1eq9A 222 1.48e+00 5ptp b.47.1.2 26068 1a65A 504 1.52e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1kgdA 180 1.53e+00 c.37.1.1 68582 1rwyA 109 1.56e+00 a.39.1.4 -825 1q0uA 219 1.60e+00 c.37.1.19 -7205 1rv3A 483 1.76e+00 1hfuA 503 1.78e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 2matA 264 1.85e+00 1c24A d.127.1.1 41146 1e32A 458 1.87e+00 1e32A b.52.2.3 59183 c.37.1.20 59184 d.31.1.1 59185 1hzfA 367 1.89e+00 a.102.4.4 76731 1sedA 117 1.92e+00 1nt4A 391 1.93e+00 c.60.1.2 -7942 1osa 148 2.05e+00 1cll a.39.1.5 17300 1c24A 263 2.06e+00 1c24A d.127.1.1 41148 1zac 90 2.08e+00 1ncx a.39.1.5 17236 1nxiA 132 2.08e+00 d.58.47.1 86381 4pep 326 2.11e+00 1smrA b.50.1.2 26843 1i8dA 213 2.13e+00 b.43.4.3 61953 b.43.4.3 61954 1rvv1 154 2.26e+00 1rvv1 1rvvA 154 2.26e+00 1rvv1 c.16.1.1 30927 1ibcB 88 2.34e+00 1pauB 1dqeA 137 2.36e+00 1dqeA a.39.2.1 17388 1exrA 148 2.42e+00 1cll a.39.1.5 17299 4matA 278 2.46e+00 1c24A d.127.1.1 41150 1cbf 285 2.50e+00 1cbf c.90.1.1 35587 1bmqB 88 2.50e+00 1pauB 1ls8A 142 2.54e+00 a.39.2.1 78176 1mat 264 2.66e+00 1c24A d.127.1.1 41152 1a99A 344 2.80e+00 1pot c.94.1.1 35812 1qtrA 317 3.07e+00 1qtrA c.69.1.7 34660 1s96A 219 3.10e+00 c.37.1.1 -6972 1qm4A 396 3.12e+00 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 3psg 370 3.23e+00 1smrA b.50.1.2 26841 1wm1A 317 3.31e+00 1ht9A 76 3.38e+00 4icb a.39.1.1 61252 1gutA 68 3.49e+00 b.40.6.1 65576 1ig5A 75 3.58e+00 4icb a.39.1.1 62363 1tm0A 350 3.77e+00 1b5fA 239 3.80e+00 1smrA b.50.1.2 26836 1p9kA 79 3.80e+00 unknown_sccs -10238 1m45A 148 3.81e+00 a.39.1.5 78598 1fsz 372 3.82e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1dmaA 214 3.93e+00 1aerA d.166.1.1 42251 1h97A 147 4.19e+00 1h97A a.1.1.2 60812 1hwwA 1015 4.32e+00 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1hxkA 1015 4.37e+00 a.8.3.1 83070 b.30.5.6 83071 c.6.2.1 83072 1htyA 1015 4.39e+00 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1p1mA 406 4.57e+00 b.92.1.4 87696 c.1.9.9 87697 1cjsA 219 4.58e+00 1cjsA e.24.1.1 43354 1ku1A 230 4.58e+00 a.118.3.1 72996 1j6pA 418 4.71e+00 b.92.1.4 77089 c.1.9.9 77090 1ogsA 497 4.72e+00 b.71.1.2 86997 c.1.8.3 86998 1g33A 73 5.29e+00 a.39.1.4 65121 2fokA 579 5.36e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1qwnA 1045 5.45e+00 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1mx4A 168 5.48e+00 d.211.1.1 79640 1i2aA 219 5.49e+00 e.24.1.1 -12012 1kyaA 499 5.84e+00 b.6.1.3 73203 b.6.1.3 73204 b.6.1.3 73205 1f9zA 135 5.88e+00 1qipA d.32.1.1 38484 1fezA 256 5.92e+00 1fezA c.108.1.3 43343 1nuuA 252 5.98e+00 c.26.1.3 86209 1m7xA 617 6.08e+00 b.1.18.2 78749 b.71.1.1 78750 c.1.8.1 78751 1tplA 426 6.43e+00 1ax4A c.67.1.2 34387 1rg9A 383 6.84e+00 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1j6uA 469 7.16e+00 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1s6cA 183 7.19e+00 a.39.1.5 -858 2pvbA 107 7.24e+00 1a75A a.39.1.4 17205 1jakA 512 7.47e+00 c.1.8.6 66472 d.92.2.1 66473 1ixmB 192 7.58e+00 1ixmA d.123.1.1 41115 1oi2A 366 7.63e+00 c.32.1.2 87039 d.79.2.2 87040 1hfoA 113 7.67e+00 d.80.1.3 61006 1bllE 488 7.84e+00 1lam c.56.5.3 33833 c.50.1.1 33170 1lfpA 249 7.86e+00 e.39.1.1 73885 1o91A 178 7.93e+00 b.22.1.1 -3282 2cbf 234 7.96e+00 1cbf c.90.1.1 35588 1ggwA 140 7.97e+00 1ggwA a.39.1.5 60490 3htsB 102 8.56e+00 2hts a.4.5.22 16175 1mb3A 124 8.76e+00 c.23.1.1 78907 1m46A 148 9.00e+00 a.39.1.5 78599 1uiqA 351 9.21e+00 1v7cA 351 9.21e+00 c.79.1.1 -8512 1p9qC 256 9.34e+00 1uesA 191 9.65e+00 1kn1A 160 9.71e+00 a.1.1.3 77455 1g57A 217 1.00e+01 1g57A d.115.1.2 60253 1pal 108 1.01e+01 1a75A a.39.1.4 17209 1hztA 190 1.01e+01 1i9aA d.113.1.2 61459 1hp4A 512 1.02e+01 1hp4A c.1.8.6 61111 d.92.2.1 61112 1on2A 142 1.02e+01 a.4.5.24 87103 a.76.1.1 87104 1p57B 255 1.03e+01 b.47.1.2 -4248 1fa8A 135 1.04e+01 1qipA d.32.1.1 38486 1uzxA 169 1.06e+01 d.20.1.2 -9409 1hp5A 512 1.07e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1dcs 311 1.10e+01 1dcs b.82.2.1 28124 1jbgA 109 1.13e+01 a.6.1.3 66480 2hnp 321 1.13e+01 1pty c.45.1.2 32678 1havA 217 1.16e+01 1havA b.47.1.4 26423 1lam 484 1.17e+01 1lam c.56.5.3 33829 c.50.1.1 33166 1g7fA 298 1.17e+01 1pty c.45.1.2 60330 1ta3A 274 1.22e+01 1qa7A 217 1.25e+01 1havA b.47.1.4 26425 1e2fA 215 1.27e+01 3tmkA c.37.1.1 59164 1ten 90 1.27e+01 1ten b.1.2.1 21990 3icb 75 1.27e+01 4icb a.39.1.1 17147 1evhA 112 1.27e+01 1evhA b.55.1.4 26997 1e2gA 215 1.29e+01 3tmkA c.37.1.1 59165 2liv 344 1.32e+01 2liv c.93.1.1 35708 1exzA 141 1.32e+01 1exzA a.26.1.2 16877 1e9eA 215 1.33e+01 c.37.1.1 64810 1klaA 112 1.33e+01 2tgi g.17.1.2 44779 1kwmA 402 1.34e+01 c.56.5.1 73079 d.58.3.1 73080 1vi2A 300 1.35e+01 c.2.1.7 -5960 c.58.1.5 -6366 1b4cA 92 1.37e+01 1b4cA a.39.1.2 17169 1fokA 568 1.38e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1esxA 96 1.38e+01 1esxA j.11.1.1 59501 1rqlA 267 1.39e+01 c.108.1.3 -6814 1n0xL 215 1.40e+01 b.1.1.1 -2063 b.1.1.2 -2429 1e9cA 215 1.40e+01 c.37.1.1 64808 5pal 109 1.40e+01 1a75A a.39.1.4 17215 1mdc 133 1.41e+01 1hmt b.60.1.2 27198 1hta 69 1.42e+01 1a7w a.22.1.2 16476 1nn5A 215 1.44e+01 c.37.1.1 85892 1b6rA 355 1.45e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1i9aA 182 1.47e+01 1i9aA d.113.1.2 62082 1o1fC 147 1.50e+01 i.15.1.1 80997 1om0A 274 1.50e+01 c.1.8.5 87058 1lap 488 1.53e+01 1lam c.56.5.3 33834 c.50.1.1 33171 4cpv 109 1.54e+01 1a75A a.39.1.4 17198 1ihbA 162 1.57e+01 1bd8 d.211.1.1 19161 1k4iA 233 1.58e+01 d.115.1.2 72056 1h65A 270 1.61e+01 c.37.1.8 65640 1jyoA 130 1.63e+01 d.198.1.1 67483 1qnnA 191 1.65e+01 1avmA a.2.11.1 15792 d.44.1.1 38755 1b6sA 355 1.65e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1abrA 251 1.66e+01 1mrj d.165.1.1 42196 1uu1A 335 1.69e+01 c.67.1.1 -8146 1kl9A 182 1.70e+01 b.40.4.5 72681 1fp4A 492 1.73e+01 c.92.2.3 76187 1h6fA 193 1.75e+01 b.2.5.4 70901 1c7gA 456 1.77e+01 c.67.1.2 -8153 1svfB 38 1.79e+01 1svfB h.3.2.1 45764 1jli 112 1.80e+01 1jli a.26.1.2 16884 1rfzA 168 1.84e+01 unknown_sccs -1206 1qtoA 122 1.85e+01 1bylA d.32.1.2 38494 1cdp 109 1.85e+01 1a75A a.39.1.4 17197 1mmiA 366 1.90e+01 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1otgA 125 1.92e+01 1otgA d.80.1.2 39831 1ocyA 198 1.95e+01 d.231.1.1 86817 1npdA 288 2.00e+01 c.2.1.7 80681 c.58.1.5 80682 1f6yA 262 2.03e+01 1f6yA c.1.21.2 29673 1d2iA 223 2.03e+01 1d2iA c.52.1.5 33297 1vjpA 394 2.06e+01 c.2.1.3 -5897 d.81.1.3 -10480 1dfmA 223 2.08e+01 1d2iA c.52.1.5 33295 1nd7A 374 2.08e+01 d.148.1.1 -11394 1pdo 135 2.09e+01 1pdo c.54.1.1 33376 1jug 125 2.10e+01 3lzt d.2.1.2 36587 1el4A 195 2.11e+01 1ej3A a.39.1.5 59453 1jf2A 195 2.14e+01 1ej3A a.39.1.5 62930 2rmpA 361 2.14e+01 2rmpA b.50.1.2 26825 1t3cA 421 2.15e+01 1efm 393 2.18e+01 1efcA c.37.1.8 64732 1npyA 271 2.22e+01 c.2.1.7 85995 c.58.1.5 85996 1bgp 309 2.24e+01 1bgp a.93.1.1 18690 1cc1S 283 2.27e+01 2frvA e.19.1.1 43313 1wdnA 226 2.31e+01 1lst c.94.1.1 35816 3cla 213 2.31e+01 3cla c.43.1.1 32610 1br1B 150 2.33e+01 1wdcC a.39.1.5 17309 2asi 360 2.36e+01 2rmpA b.50.1.2 26824 1rtxA 123 2.37e+01 a.1.1.1 -3 1j75A 67 2.37e+01 a.4.5.19 62673 1d2rB 326 2.39e+01 1d2rB c.26.1.1 31573 1qa7B 217 2.41e+01 1havA b.47.1.4 26426 1m6jA 261 2.42e+01 c.1.1.1 78693 1mxa 383 2.42e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1k0sA 151 2.42e+01 b.40.7.1 67969 1ift 263 2.43e+01 1mrj d.165.1.1 42211 1ewqA 765 2.44e+01 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1gs5A 258 2.45e+01 c.73.1.2 70395 1mg7A 417 2.46e+01 d.14.1.6 84954 d.58.26.6 84955 1qapA 296 2.48e+01 1qpoA c.1.17.1 29559 d.41.2.1 38595 1din 236 2.50e+01 1din c.69.1.9 34682 1mcpL 220 2.51e+01 8fabA b.1.1.1 19858 b.1.1.2 20958 1e5dA 402 2.52e+01 1e5dA c.23.5.1 31208 d.157.1.3 42061 1uq5A 263 2.53e+01 d.165.1.1 -11555 1b4aA 149 2.59e+01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1ggvA 232 2.62e+01 1din c.69.1.9 34683 1j2gA 319 2.64e+01 1d2rA 326 2.67e+01 1d2rB c.26.1.1 31572 1jfiA 98 2.71e+01 1jfiA a.22.1.3 62936 1ok7A 366 2.71e+01 1fgs 428 2.72e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1ixmA 192 2.73e+01 1ixmA d.123.1.1 41114 1pvaA 110 2.76e+01 1a75A a.39.1.4 17207 1hqvA 191 2.81e+01 1hqvA a.39.1.8 61160 1hfx 123 2.81e+01 3lzt d.2.1.2 36600 1ubpA 101 2.83e+01 1ubpA d.8.1.1 37353 1h3gA 601 2.84e+01 b.1.18.2 -2725 b.71.1.1 -4653 c.1.8.1 -5277 1ex7A 186 2.87e+01 1gky c.37.1.1 59537 1hr6A 475 2.87e+01 1hr6A d.185.1.1 61164 d.185.1.1 61165 1iqpA 327 2.87e+01 a.80.1.1 62649 c.37.1.20 62650 1gvjA 146 2.89e+01 a.4.5.21 -293 1iq3A 110 2.92e+01 1iq3A a.39.1.6 62640 4ubpA 101 2.98e+01 1ubpA d.8.1.1 37352 1j2jB 45 2.98e+01 a.7.8.1 84017 1uhnA 189 3.08e+01 a.39.1.5 -853 1rro 108 3.11e+01 1a75A a.39.1.4 17195 1qz9A 416 3.13e+01 c.67.1.3 -8180 1ycsB 239 3.19e+01 1ycsB b.34.2.1 24553 d.211.1.1 19155 1lccA 51 3.19e+01 1pru a.35.1.5 17110 1m2dA 110 3.21e+01 c.47.1.11 78476 1j9jA 247 3.22e+01 c.106.1.1 62758 1ponB 36 3.22e+01 1ponB 1m2aA 110 3.24e+01 c.47.1.11 78472 1by2 119 3.26e+01 1by2 d.170.1.1 42452 1kxqE 120 3.26e+01 b.1.1.1 73171 1nmeB 92 3.29e+01 2polA 366 3.30e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1eh2 106 3.32e+01 1eh2 a.39.1.6 17339 1nhkL 144 3.35e+01 1npk d.58.6.1 39142 1bjmA 216 3.35e+01 8fabA b.1.1.1 20524 b.1.1.2 21460 1i8xA 30 3.36e+01 g.3.16.1 71132 1g8iA 190 3.36e+01 1rec a.39.1.5 60363 1lcdA 51 3.39e+01 1pru a.35.1.5 17111 1mkfA 382 3.41e+01 b.116.1.1 79232 1b9hA 388 3.44e+01 1b9hA c.67.1.4 34488 1m2bA 110 3.45e+01 c.47.1.11 78474 2tmdA 729 3.48e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1mxb 383 3.55e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1lvl 458 3.56e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 1ngr 85 3.57e+01 1ngr a.77.1.2 18422 1xxaA 78 3.59e+01 1xxaA d.74.2.1 39700 1lo7A 141 3.60e+01 d.38.1.1 74144 1snrA 341 3.63e+01 1ej3A 191 3.71e+01 1ej3A a.39.1.5 17259 1gq8A 319 3.74e+01 b.80.1.5 70350 1m1nA 491 3.78e+01 c.92.2.3 78417 1rk8A 165 3.78e+01 d.58.7.1 -10018 1o94A 729 3.83e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1bt0A 76 3.86e+01 1ubi d.15.1.1 37607 1oi7A 288 3.86e+01 c.2.1.8 87049 c.23.4.1 87050 1q1rA 431 3.87e+01 c.3.1.5 -6048 c.3.1.5 -6049 d.87.1.1 -10502 1xxcA 78 3.91e+01 1xxaA d.74.2.1 39712 1gky 187 3.94e+01 1gky c.37.1.1 31839 1t5jA 313 3.94e+01 unknown_sccs -1951 1lvhA 221 3.94e+01 c.108.1.6 74282