# List of top-scoring protein chains for t2k-100-30-str2 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 2.79e-03 1ncx a.39.1.5 17223 1ncx 162 4.67e-03 1ncx a.39.1.5 17222 1s29A 92 1.66e-02 unknown_sccs -315 1gnlA 544 1.24e-01 e.26.1.1 70287 1ggzA 148 2.14e-01 a.39.1.5 70176 2sas 185 2.47e-01 2sas a.39.1.5 17258 1f4qA 165 5.57e-01 1alvA a.39.1.8 17360 1wdcC 156 5.93e-01 1wdcC a.39.1.5 17317 1ctdA 36 6.02e-01 1ctdA a.39.1.5 17230 1rqlA 267 8.80e-01 c.108.1.3 -6814 1fezA 256 9.31e-01 1fezA c.108.1.3 43343 1ecxA 384 9.96e-01 1ecxA c.67.1.3 34431 1eg5A 384 1.07e+00 1ecxA c.67.1.3 34429 1q0uA 219 1.08e+00 c.37.1.19 -7205 1auiB 169 1.11e+00 1auiB a.39.1.5 17325 1avsA 90 1.15e+00 1cll a.39.1.5 17226 1i2aA 219 1.33e+00 e.24.1.1 -12012 1mdc 133 1.45e+00 1hmt b.60.1.2 27198 1nxiA 132 1.60e+00 d.58.47.1 86381 1nt4A 391 1.66e+00 c.60.1.2 -7942 1a26 361 1.85e+00 1a26 a.41.1.1 17412 d.166.1.2 42274 2mysB 166 1.86e+00 1wdcB a.39.1.5 17308 3cla 213 1.91e+00 3cla c.43.1.1 32610 1dqeA 137 1.95e+00 1dqeA a.39.2.1 17388 1auiA 521 1.97e+00 1auiA d.159.1.3 42085 1cjsA 219 2.15e+00 1cjsA e.24.1.1 43354 1k94A 165 2.25e+00 a.39.1.8 68333 1scmB 145 2.59e+00 1wdcB a.39.1.5 17304 1m45A 148 2.76e+00 a.39.1.5 78598 1efyA 350 2.81e+00 1a26 a.41.1.1 17413 d.166.1.2 42275 1smlA 269 2.82e+00 1smlA d.157.1.1 42053 1vi2A 300 2.89e+00 c.2.1.7 -5960 c.58.1.5 -6366 1npdA 288 2.92e+00 c.2.1.7 80681 c.58.1.5 80682 1ponA 36 2.92e+00 1ponA a.39.1.5 17239 1ddgA 374 3.19e+00 1amoA b.43.4.1 25671 c.25.1.4 31559 1cll 148 3.28e+00 1cll a.39.1.5 17263 1e0cA 271 3.45e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 1g4yR 148 3.66e+00 1cll a.39.1.5 60252 1gc0A 398 3.89e+00 c.67.1.3 70168 3cln 148 4.04e+00 1cll a.39.1.5 17286 1k4iA 233 4.06e+00 d.115.1.2 72056 1q15A 503 4.41e+00 c.26.2.1 -6625 d.153.1.1 -11400 1gntA 553 4.54e+00 e.26.1.1 70290 1fp4A 492 4.58e+00 c.92.2.3 76187 1e2uA 553 4.59e+00 1e1dA e.26.1.1 43362 1s3eA 520 4.77e+00 c.3.1.2 -6022 d.16.1.5 -9242 1kk8B 139 5.04e+00 a.39.1.5 77430 1ojaA 520 5.05e+00 c.3.1.2 -6000 d.16.1.5 -9220 1din 236 5.09e+00 1din c.69.1.9 34682 1a4iA 301 5.22e+00 1a4iA c.2.1.7 30278 c.58.1.2 33926 1rwyA 109 5.24e+00 a.39.1.4 -825 1p9kA 79 5.30e+00 unknown_sccs -10238 1k9uA 78 5.34e+00 a.39.1.10 84348 1e1dA 553 5.39e+00 1e1dA e.26.1.1 43363 1ibcB 88 5.44e+00 1pauB 1ls8A 142 5.46e+00 a.39.2.1 78176 1bmqB 88 5.50e+00 1pauB 1ggvA 232 5.54e+00 1din c.69.1.9 34683 1ok7A 366 5.64e+00 1g57A 217 5.65e+00 1g57A d.115.1.2 60253 1a4iB 301 5.76e+00 1a4iA c.2.1.7 30279 c.58.1.2 33927 1dgkN 917 5.98e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1czaN 917 6.12e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1brlB 324 6.12e+00 1lucA c.1.16.1 29554 2polA 366 6.18e+00 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 2pna 104 6.45e+00 1qadA d.93.1.1 40501 1a7w 69 6.92e+00 1a7w a.22.1.2 16477 1n25A 368 6.95e+00 c.37.1.20 85264 1m46A 148 6.97e+00 a.39.1.5 78599 1lucB 324 7.05e+00 1lucA c.1.16.1 29548 1npyA 271 7.05e+00 c.2.1.7 85995 c.58.1.5 85996 1sc3B 88 7.09e+00 1mmiA 366 7.09e+00 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1hkcA 917 7.10e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1aerA 205 7.29e+00 1aerA d.166.1.1 42249 1cr5A 189 7.30e+00 1cr5A b.52.2.3 26931 d.31.1.1 38465 1qo7A 394 7.40e+00 1qo7A c.69.1.11 34697 1qfjA 232 7.62e+00 1qfjA b.43.4.2 25655 c.25.1.1 31545 1gosA 520 7.63e+00 c.3.1.2 65425 d.16.1.5 65426 1o1fC 147 7.76e+00 i.15.1.1 80997 1iybA 208 7.97e+00 d.124.1.1 -10977 1ctaA 36 7.97e+00 1ctdA a.39.1.5 17232 1m9nA 613 8.53e+00 c.24.1.3 78870 c.97.2.1 78871 2fokA 579 8.94e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1jdfA 447 8.96e+00 c.1.11.2 62897 d.54.1.1 62898 1fgs 428 9.00e+00 1fgs c.59.1.2 33959 c.72.2.2 34962 1g33A 73 9.04e+00 a.39.1.4 65121 1kgdA 180 9.18e+00 c.37.1.1 68582 1a99A 344 9.24e+00 1pot c.94.1.1 35812 1wdcB 156 9.75e+00 1wdcB a.39.1.5 17302 1qcsA 211 9.79e+00 1qcsA b.52.2.3 26927 d.31.1.1 38461 1ej3A 191 1.03e+01 1ej3A a.39.1.5 17259 1m1nA 491 1.03e+01 c.92.2.3 78417 1qwnA 1045 1.08e+01 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1j2gA 319 1.09e+01 1diaA 306 1.10e+01 1a4iA c.2.1.7 30280 c.58.1.2 33928 1on2A 142 1.10e+01 a.4.5.24 87103 a.76.1.1 87104 1hwwA 1015 1.17e+01 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1g8mA 593 1.18e+01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1htyA 1015 1.19e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1hxkA 1015 1.19e+01 a.8.3.1 83070 b.30.5.6 83071 c.6.2.1 83072 1kas 412 1.26e+01 1dd8A c.95.1.1 35964 c.95.1.1 35965 1bfmA 69 1.27e+01 1a7w a.22.1.2 16479 1k07A 263 1.28e+01 d.157.1.1 77218 1bj4A 470 1.28e+01 1bj4A c.67.1.4 34479 1jv4A 162 1.30e+01 b.60.1.1 67343 1wdkC 390 1.31e+01 1qhaA 917 1.34e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1el4A 195 1.37e+01 1ej3A a.39.1.5 59453 1sedA 117 1.37e+01 1rv3A 483 1.38e+01 1b3nA 412 1.40e+01 1dd8A c.95.1.1 35966 c.95.1.1 35967 1ge8A 249 1.43e+01 1plq d.131.1.2 41398 d.131.1.2 41399 1i05A 180 1.48e+01 1mup b.60.1.1 27130 1cqxA 403 1.50e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1ku1A 230 1.52e+01 a.118.3.1 72996 2minA 491 1.57e+01 1qguA c.92.2.3 35609 1nrzA 164 1.57e+01 c.38.1.1 86131 5gcnA 166 1.61e+01 1yghA d.108.1.1 40807 1osa 148 1.63e+01 1cll a.39.1.5 17300 1fe0A 68 1.63e+01 1cc8A d.58.17.1 39345 1e5mA 416 1.65e+01 1dd8A c.95.1.1 58973 c.95.1.1 58974 1ig5A 75 1.65e+01 4icb a.39.1.1 62363 1gypA 358 1.68e+01 1dssG c.2.1.3 30004 d.81.1.1 39919 1d7yA 408 1.73e+01 1d7yA c.3.1.5 30565 c.3.1.5 30566 d.87.1.1 40204 1s6cA 183 1.75e+01 a.39.1.5 -858 1cbs 137 1.75e+01 1hmt b.60.1.2 27201 1i06A 180 1.77e+01 1mup b.60.1.1 27131 1nuuA 252 1.77e+01 c.26.1.3 86209 1br1B 150 1.81e+01 1wdcC a.39.1.5 17309 1jh3A 107 1.82e+01 d.66.1.4 71661 1i6pA 220 1.82e+01 1ddzA c.53.2.1 61848 1exrA 148 1.87e+01 1cll a.39.1.5 17299 2liv 344 1.90e+01 2liv c.93.1.1 35708 3minC 491 1.92e+01 1qguA c.92.2.3 35607 1qy1A 174 1.96e+01 b.60.1.1 -4445 1mzbA 136 1.98e+01 unknown_sccs -266 1df3A 162 2.07e+01 1mup b.60.1.1 27134 1tedA 393 2.07e+01 1l1qA 186 2.09e+01 c.61.1.1 77653 1dqgA 135 2.11e+01 1dqgA b.42.2.2 25579 1larA 575 2.12e+01 1larA c.45.1.2 32693 c.45.1.2 32694 1tljA 213 2.13e+01 5pal 109 2.15e+01 1a75A a.39.1.4 17215 2hnp 321 2.16e+01 1pty c.45.1.2 32678 1ltqA 301 2.17e+01 c.108.1.9 78208 c.37.1.1 78209 1zac 90 2.20e+01 1ncx a.39.1.5 17236 1fsz 372 2.20e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1fdr 248 2.21e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1hqvA 191 2.25e+01 1hqvA a.39.1.8 61160 1dmaA 214 2.26e+01 1aerA d.166.1.1 42251 1h1lA 481 2.28e+01 c.92.2.3 70851 1mg7A 417 2.30e+01 d.14.1.6 84954 d.58.26.6 84955 1eh2 106 2.30e+01 1eh2 a.39.1.6 17339 1r9cA 139 2.31e+01 d.32.1.2 -9557 1g7fA 298 2.34e+01 1pty c.45.1.2 60330 1gvp 87 2.36e+01 1gvp b.40.4.7 25369 1vqb 87 2.36e+01 1gvp b.40.4.7 25370 1ggwA 140 2.40e+01 1ggwA a.39.1.5 60490 1ht9A 76 2.41e+01 4icb a.39.1.1 61252 1wdnA 226 2.43e+01 1lst c.94.1.1 35816 1hkbA 917 2.43e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1dt9A 437 2.58e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1qstA 160 2.62e+01 1yghA d.108.1.1 40804 1seiA 130 2.62e+01 1seiA d.140.1.1 41463 1brt 277 2.69e+01 1brt c.69.1.12 34699 1a3gA 308 2.79e+01 1daaA e.17.1.1 43286 1djnA 729 2.80e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 3htsB 102 2.87e+01 2hts a.4.5.22 16175 1pm1X 180 2.89e+01 1s5uA 138 2.90e+01 d.38.1.1 -9626 1bllE 488 2.93e+01 1lam c.56.5.3 33833 c.50.1.1 33170 1rfzA 168 2.96e+01 unknown_sccs -1206 1fwuA 134 2.99e+01 1dqgA b.42.2.2 25580 1iynA 295 3.08e+01 a.93.1.1 -1244 1hfoA 113 3.17e+01 d.80.1.3 61006 1g8iA 190 3.18e+01 1rec a.39.1.5 60363 1broA 277 3.18e+01 1brt c.69.1.12 34700 1csgA 127 3.18e+01 2gmfA a.26.1.2 16851 1pal 108 3.18e+01 1a75A a.39.1.4 17209 1hqkA 154 3.19e+01 c.16.1.1 65902 1t3cA 421 3.20e+01 1jf2A 195 3.24e+01 1ej3A a.39.1.5 62930 1fokA 568 3.25e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1hztA 190 3.27e+01 1i9aA d.113.1.2 61459 1uzxA 169 3.32e+01 d.20.1.2 -9409 1s1qA 145 3.37e+01 d.20.1.2 -9405 1ii7A 333 3.40e+01 1ii7A d.159.1.4 62415 1qguA 478 3.40e+01 1qguA c.92.2.3 35625 1rpmA 278 3.41e+01 2shpA c.45.1.2 32679 1qh8A 478 3.44e+01 1qguA c.92.2.3 35633 1f60B 94 3.44e+01 1b64 d.58.12.1 39307 1wm1A 317 3.46e+01 1bt0A 76 3.46e+01 1ubi d.15.1.1 37607 1itzA 675 3.49e+01 c.36.1.6 76798 c.36.1.10 76797 c.48.1.1 76799 1bd3A 243 3.57e+01 1bd3A c.61.1.1 34098 1mcvI 28 3.58e+01 g.3.2.1 78951 1dd6A 228 3.62e+01 1a7tA d.157.1.1 42054 2tmdA 729 3.63e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1iq3A 110 3.64e+01 1iq3A a.39.1.6 62640 1m6yA 301 3.71e+01 a.60.13.1 78716 c.66.1.23 78717 1qv1A 195 3.71e+01 a.39.1.5 -830 1cf9A 753 3.74e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1rl6A 177 3.75e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1pqhA 143 3.79e+01 b.52.2.1 -4318 1e08A 371 3.85e+01 i.4.1.1 45914 1i9aA 182 3.85e+01 1i9aA d.113.1.2 62082 1ir6A 424 3.88e+01 c.107.1.2 71342 1oi7A 288 3.92e+01 c.2.1.8 87049 c.23.4.1 87050 1hozA 339 3.94e+01 c.70.1.1 65898 1j75A 67 3.94e+01 a.4.5.19 62673 1c7gA 456 3.97e+01 c.67.1.2 -8153 1nnmA 652 3.98e+01 1pg4A 652 3.98e+01 e.23.1.1 88067 1gggB 226 4.00e+01 1lst c.94.1.1 35818