# List of top-scoring protein chains for t2k-100-30-str 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 1kyfA 247 6.35e-03 1b9kA 238 6.71e-03 1qtsA b.1.10.1 22315 d.105.1.1 40791 1e42A 258 6.84e-03 1e42A b.1.10.1 22316 d.105.1.1 40792 1qtsA 247 1.13e-02 1qtsA b.1.10.1 22313 d.105.1.1 40789 1fzyA 149 4.07e-01 d.20.1.1 65072 1fit 147 1.02e+00 1fit d.13.1.1 37499 1kpf 126 1.31e+00 1kpf d.13.1.1 37507 1plr 258 2.34e+00 1plq d.131.1.2 41390 d.131.1.2 41391 1uch 230 2.64e+00 1uch d.3.1.6 37129 1kpeA 126 2.68e+00 1kpf d.13.1.1 37508 1g4mA 393 2.71e+00 b.1.1.5 65143 b.1.1.5 65144 2arcB 164 3.00e+00 2arcA b.82.4.1 28149 1plq 258 3.16e+00 1plq d.131.1.2 41388 d.131.1.2 41389 2arcA 164 3.42e+00 2arcA b.82.4.1 28148 2ms2A 129 3.76e+00 1msc d.85.1.1 40049 2sfa 191 4.33e+00 1qq4A b.47.1.1 25815 1f5jA 199 4.83e+00 1axkA b.29.1.11 24342 1mcpL 220 4.92e+00 8fabA b.1.1.1 19858 b.1.1.2 20958 1l6xA 207 5.13e+00 1etb1 127 5.30e+00 1etb1 1bhgA 613 5.49e+00 1bhgA b.1.4.1 22161 b.18.1.5 23766 c.1.8.3 28889 1emsA 440 5.62e+00 1emsA d.13.1.1 37520 d.160.1.1 42086 1rl6A 177 5.69e+00 1rl6A d.141.1.1 41473 d.141.1.1 41474 1fc1A 224 6.19e+00 1igtB b.1.1.2 21520 b.1.1.2 21521 1cgt 684 6.41e+00 1cxlA b.1.1.5 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 1ev2E 220 6.71e+00 1cvsC b.1.1.4 21738 b.1.1.4 21739 1smlA 269 6.72e+00 1smlA d.157.1.1 42053 1dykA 394 7.00e+00 1dykA b.29.1.4 24223 b.29.1.4 24224 1eajA 126 7.12e+00 1f5wA b.1.1.1 59401 1f5wA 126 7.12e+00 1f5wA b.1.1.1 19705 1f1sA 814 7.17e+00 a.102.3.2 64928 b.1.1.5 64929 b.24.1.1 64930 b.30.3.1 64931 1cdwA 179 7.26e+00 1ytbA d.129.1.1 41212 d.129.1.1 41213 2stv 195 7.38e+00 2stv b.10.1.2 23287 1hbp 183 7.80e+00 1aqb b.60.1.1 27079 1hdkA 141 7.92e+00 b.29.1.3 65807 1f86A 115 8.02e+00 1etb1 b.3.4.1 59689 1mypA 108 8.20e+00 1d2vA a.93.1.2 18701 1f41A 127 8.30e+00 1etb1 b.3.4.1 22539 1eta1 127 8.69e+00 1etb1 1lcl 142 8.97e+00 1lcl b.29.1.3 24216 1gh9A 71 9.05e+00 1gh9A g.41.6.1 45266 1mypB 108 9.62e+00 1mypB a.93.1.2 18702 1lox 662 9.82e+00 1lox a.119.1.2 19238 b.12.1.1 23638 1ema 236 9.91e+00 1ema d.22.1.1 38339 1bmv2 374 1.01e+01 1bmv2 1ttbA 127 1.04e+01 1etb1 b.3.4.1 22543 1earA 147 1.05e+01 b.107.1.1 64875 d.58.38.1 64876 1cxpA 104 1.06e+01 1d2vA a.93.1.2 18695 1d2vA 104 1.06e+01 1d2vA a.93.1.2 18697 1fc2D 224 1.06e+01 1igtB b.1.1.2 21516 b.1.1.2 21517 1mhlA 108 1.07e+01 1d2vA a.93.1.2 18699 1obpA 159 1.08e+01 1obpA b.60.1.1 27092 1cqkA 101 1.08e+01 1cqkA b.1.1.2 21547 1hn2A 159 1.08e+01 b.60.1.1 65890 2madH 373 1.09e+01 2bbkH b.69.2.1 27639 1cvsC 225 1.13e+01 1cvsC b.1.1.4 21726 b.1.1.4 21727 1ejhA 190 1.24e+01 1ejhA d.86.1.1 40147 1gefA 123 1.25e+01 1gefA c.52.1.18 60465 1skyB 502 1.26e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1cf1A 404 1.27e+01 1cf1A b.1.1.5 21907 b.1.1.5 21908 1gpc 218 1.36e+01 1gpc b.40.4.7 25393 1ap8 213 1.38e+01 1ap8 d.86.1.1 40151 1yge 839 1.40e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1gg6B 131 1.44e+01 5ptp 1auvA 311 1.48e+01 1auvA c.30.1.5 31723 d.142.1.3 41558 1b3qA 379 1.54e+01 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1gctA 245 1.57e+01 5ptp b.47.1.2 26021 1eb0A 147 1.61e+01 b.107.1.1 64890 d.58.38.1 64891 12e8L 214 1.61e+01 8fabA b.1.1.1 20268 b.1.1.2 21268 1qorA 327 1.63e+01 1qorA b.35.1.2 24766 c.2.1.1 29782 3grx 82 1.63e+01 1aba c.47.1.1 32769 1dkxA 219 1.64e+01 1dkzA e.20.1.1 43315 2pabA 127 1.70e+01 1etb1 b.3.4.1 22597 1hbq 183 1.72e+01 1aqb b.60.1.1 27078 1e6oL 212 1.74e+01 32c2A b.1.1.1 20494 b.1.1.2 21452 1hfuA 503 1.74e+01 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1a65A 504 1.76e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1thx 115 1.80e+01 1thx c.47.1.1 32732 2fbjL 213 1.81e+01 8fabA b.1.1.1 19850 b.1.1.2 20954 1qpoA 284 1.82e+01 1qpoA c.1.17.1 29561 d.41.2.1 38597 1ebuA 358 1.88e+01 1ebuA c.2.1.3 30035 d.81.1.2 39950 1xypA 190 1.93e+01 1axkA b.29.1.11 24327 1a1w 91 1.95e+01 1a1z a.77.1.1 18425 1bjx 110 1.98e+01 1bjx c.47.1.2 32774 2bjxA 110 1.98e+01 1bjx c.47.1.2 32776 1bpoA 494 2.03e+01 1bpoA a.118.1.4 19143 b.69.6.1 27670 2pth 193 2.04e+01 2pth c.56.3.1 33793 1kid 203 2.08e+01 1derA c.8.5.1 30771 1lc0A 294 2.10e+01 1qdbA 473 2.11e+01 1qdbA a.138.1.3 19688 1ospL 214 2.15e+01 32c2A b.1.1.1 20116 b.1.1.2 21146 1efuB 282 2.17e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1gw5S 142 2.18e+01 1je5A 206 2.22e+01 1je5A b.40.4.7 62909 1eagA 342 2.23e+01 1eagA b.50.1.2 26826 2bc2A 227 2.27e+01 1a7tA d.157.1.1 42031 1qi7A 253 2.34e+01 1qi7A d.165.1.1 42210 1dqwA 267 2.36e+01 1dqwA c.1.2.3 28551 1c5cL 214 2.41e+01 32c2A b.1.1.1 20474 b.1.1.2 21438 1ftrA 296 2.45e+01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1j98A 157 2.48e+01 1j98A d.185.1.2 62755 1jdfA 447 2.52e+01 c.1.11.2 62897 d.54.1.1 62898 1aqb 183 2.53e+01 1aqb b.60.1.1 27084 1forL 210 2.55e+01 8fabA b.1.1.1 19988 b.1.1.2 21044 1ec7A 446 2.56e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1l8bA 190 2.61e+01 1g96A 120 2.68e+01 1g96A d.17.1.2 60393 1jj2A 239 2.70e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085 1f3uA 118 2.71e+01 1f3uA b.65.1.1 27521 2tbd 134 2.74e+01 2tbd d.89.1.1 40241 1gcuA 295 2.76e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1wwbX 103 2.78e+01 1wwcA b.1.1.4 21777 1fb6A 105 2.78e+01 1thx c.47.1.1 32739 1eguA 731 2.83e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.3.1 24423 1e9lA 377 2.83e+01 1e9lA c.1.8.5 59395 d.26.3.1 59396 1k6dA 220 2.83e+01 1hynP 379 2.88e+01 1hynP d.112.1.2 61408 1svy 114 2.94e+01 1svy d.109.1.1 40831 2trxA 108 2.95e+01 1thx c.47.1.1 32719 1el5A 389 2.97e+01 1b3mA c.3.1.2 30369 d.16.1.3 37937 1ebfA 358 3.00e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1e69B 322 3.03e+01 1e69B c.37.1.12 32377 1sltA 134 3.04e+01 1c1lA b.29.1.3 24186 1mlbA 214 3.04e+01 8fabA b.1.1.1 20050 b.1.1.2 21092 1a8y 367 3.13e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1cwvA 492 3.16e+01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1axkA 394 3.17e+01 1axkA b.29.1.2 24181 b.29.1.11 24315 1rrpB 134 3.26e+01 1rrpB b.55.1.3 26995 1ytbA 180 3.30e+01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1rbp 182 3.31e+01 1aqb b.60.1.1 27085 1i40A 175 3.34e+01 b.40.5.1 66024 1semA 58 3.35e+01 1ckaA b.34.2.1 24544 1jsxA 207 3.36e+01 1l9fA 389 3.41e+01 1j5wA 298 3.42e+01 1a78A 134 3.43e+01 1c1lA b.29.1.3 24212 1sltB 134 3.46e+01 1c1lA b.29.1.3 24187 1soxA 466 3.47e+01 1soxA b.1.1.5 21947 d.120.1.1 41090 d.176.1.1 42563 1ay2 159 3.53e+01 2pil d.24.1.1 38377 1jeqB 565 3.57e+01 1jeqB e.31.1.2 62922 2pil 159 3.59e+01 2pil d.24.1.1 38376 2bc2B 227 3.60e+01 1a7tA d.157.1.1 42032 1j58A 385 3.62e+01 1tif 78 3.65e+01 1tif d.15.8.1 37836 1qqfA 277 3.67e+01 1c3d a.102.4.4 18875 1vokA 200 3.71e+01 1ytbA d.129.1.1 41242 d.129.1.1 41243 1c9fA 90 3.74e+01 1c9fA d.15.2.1 37639 1pne 140 3.82e+01 1pne d.110.1.1 40866 1ej1A 190 3.86e+01 1ejhA d.86.1.1 40144 1jiwI 106 3.86e+01 1smpI b.61.2.1 63078 1fl2A 310 3.88e+01 1hyuA c.3.1.5 59869 c.3.1.5 59870 1acx 108 3.92e+01 2mcm b.1.7.1 22211 1dkzA 219 3.92e+01 1dkzA e.20.1.1 43314 1ipcA 217 3.94e+01 1f97A 212 4.00e+01 1f97A b.1.1.1 19763 b.1.1.4 21764