# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1konA 249 1.86e-01 e.39.1.1 72823 1jenA 267 2.77e-01 1jenA 2cq2A 114 4.26e-01 1hbyA 123 4.34e-01 7rsa d.5.1.1 60936 1b1eA 123 4.74e-01 7rsa d.5.1.1 37300 1un3A 123 4.87e-01 d.5.1.1 99646 2gfaA 119 4.94e-01 2a2pA 129 5.19e-01 1fx3B 169 5.35e-01 1fx3B d.33.1.1 38525 1k59A 123 5.43e-01 d.5.1.1 72073 1jqlB 140 6.26e-01 c.37.1.20 63234 1b1iA 123 6.71e-01 7rsa d.5.1.1 37295 1csbB 205 8.27e-01 1theB 1zg2A 107 8.34e-01 1a4yB 123 8.46e-01 7rsa d.5.1.1 37296 1id3B 102 8.76e-01 a.22.1.1 66113 1gio 125 1.04e+00 7rsa d.5.1.1 37304 1jl0A 334 1.05e+00 1jenA d.156.1.1 63155 1aoiB 87 1.06e+00 1aoiB a.22.1.1 16470 1o13A 136 1.06e+00 c.55.5.1 80762 1theB 260 1.17e+00 1theB d.3.1.1 37057 1eonA 245 1.18e+00 1rvaA c.52.1.2 33238 1theA 260 1.18e+00 1theB d.3.1.1 37056 1ru8A 232 1.19e+00 c.26.2.1 97849 1sx5A 244 1.20e+00 c.52.1.2 99023 1lfpA 249 1.29e+00 e.39.1.1 73885 1aoiF 87 1.37e+00 1aoiB a.22.1.1 16471 1mc3A 296 1.43e+00 c.68.1.6 78943 1hq3D 103 1.44e+00 1aoiB a.22.1.1 16464 1gxuA 91 1.62e+00 d.58.10.1 76378 1fjgP 88 1.63e+00 1emwA d.27.1.1 38444 1spiA 358 1.64e+00 1frpA e.7.1.1 42939 1b94A 244 1.74e+00 1rvaA c.52.1.2 33250 1qynA 153 1.75e+00 d.33.1.1 96597 1rvaA 244 1.75e+00 1rvaA c.52.1.2 33240 1b97A 244 1.79e+00 1rvaA c.52.1.2 33252 1tzyD 103 1.79e+00 a.22.1.1 107533 1agi 125 1.81e+00 7rsa d.5.1.1 37303 2gu3A 136 1.83e+00 1kx5B 102 1.83e+00 a.22.1.1 77594 1emwA 88 1.85e+00 1emwA d.27.1.1 38448 2cokA 113 1.88e+00 1wdcC 156 1.98e+00 1wdcC a.39.1.5 17317 2nef 136 2.04e+00 1efnB d.102.1.1 40704 1e69B 322 2.11e+00 1e69B c.37.1.12 32377 1widA 130 2.22e+00 1kn0A 212 2.37e+00 d.50.1.3 77444 1louA 101 2.38e+00 1ris d.58.14.1 39323 1twfH 146 2.50e+00 1b1jA 123 2.69e+00 7rsa d.5.1.1 37298 2ghpA 292 2.74e+00 2d1uA 104 2.75e+00 1vr5A 547 2.76e+00 1idsA 207 2.82e+00 1avmA a.2.11.1,d.44.1.1 15722,38730 2ca6A 386 2.87e+00 1qsgA 265 2.89e+00 1eny c.2.1.2 29935 1tif 78 2.94e+00 1tif d.15.8.1 37836 1iloA 77 2.98e+00 c.47.1.1 66205 1vixA 420 3.02e+00 c.56.5.4,d.58.19.1 100777,100778 1gmyA 261 3.10e+00 d.3.1.1 76236 2d4pA 141 3.37e+00 1rewC 135 3.38e+00 g.7.1.3 97336 1eqnA 321 3.43e+00 1dd9A e.13.1.1 43256 1l0bA 229 3.52e+00 c.15.1.3,c.15.1.3 73391,73392 1j8rA 196 3.80e+00 1j8rA b.2.3.3 62745 1zc6A 305 3.97e+00 2a6cA 83 3.98e+00 1e44A 85 4.05e+00 3eipA d.26.2.1 59219 1yrgA 385 4.08e+00 1yrgA c.10.1.2 30854 1vdxA 184 4.10e+00 1rz1A 161 4.11e+00 b.45.1.2 98124 1i50H 146 4.16e+00 b.40.4.8 61761 1u6zA 513 4.35e+00 1p5hA 428 4.44e+00 c.123.1.1 87802 1rz4A 226 4.47e+00 a.4.5.53,a.118.1.18 105131,105132 2ewcA 126 4.47e+00 1n0uA 842 4.50e+00 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 1h2vZ 156 4.56e+00 d.58.7.1 76595 1xk7A 408 4.57e+00 2scuB 388 4.60e+00 2scuB c.23.4.1,d.142.1.4 31141,41562 2cc0A 195 4.66e+00 1fnoA 417 4.71e+00 d.58.19.1,c.56.5.4 70145,75841 2f1lA 187 4.87e+00 1s3cA 141 4.90e+00 1c14A 262 5.12e+00 1eny c.2.1.2 29927 1j9bA 141 5.14e+00 c.47.1.12 66459 1qg6A 261 5.28e+00 1eny c.2.1.2 29919 1h6kX 97 5.32e+00 d.58.7.1 60684 1s31A 273 5.80e+00 1kijA 390 6.34e+00 d.14.1.3,d.122.1.2 72514,72515 1mp9A 198 6.45e+00 d.129.1.1,d.129.1.1 91385,91386 1x74A 360 6.56e+00 1b96A 244 6.58e+00 1rvaA c.52.1.2 33268 1vgjA 184 6.69e+00 1apyA 162 6.82e+00 1apyA d.153.1.5 42004 1wznA 252 6.83e+00 1hjrA 158 6.86e+00 1hjrA c.55.3.6 33727 1buuA 168 7.09e+00 1rtm1 d.169.1.1,h.1.1.1 42366,45388 2a1vA 144 7.49e+00 1lb2B 84 7.53e+00 a.60.3.1 77871 1l7bA 92 7.56e+00 c.15.1.2 91053 1yioA 208 7.59e+00 1yezA 68 7.61e+00 1kppA 145 7.67e+00 d.20.1.2 72846 1b5eA 246 7.73e+00 1b5eA d.117.1.1 41056 1xngA 268 7.74e+00 1pysA 350 7.78e+00 1pysA d.104.1.1 40775 1ris 101 7.82e+00 1ris d.58.14.1 39314 2bwkA 121 7.85e+00 1xfxO 149 8.01e+00 1xer 103 8.09e+00 1xer d.58.1.3 38990 2bibA 547 8.16e+00 1whzA 70 8.24e+00 1yvoA 172 8.26e+00 1zdyA 307 8.30e+00 2d13A 227 8.40e+00 2prd 174 8.44e+00 2prd b.40.5.1 25435 2axcA 264 8.45e+00 1cqmA 101 8.62e+00 1ris d.58.14.1 39321 1exqA 154 8.70e+00 1b9dA c.55.3.2 33646 2cy2A 174 8.70e+00 1ew3A 159 8.85e+00 1mup b.60.1.1 27114 1tygB 87 8.98e+00 d.15.3.2 107455 1b7yA 350 9.17e+00 1pysA d.104.1.1 40776 1nxiA 132 9.20e+00 d.58.47.1 86381 1am1 213 9.23e+00 1yer d.122.1.1 41095 1zrjA 50 9.35e+00 1yrgB 385 9.35e+00 1yrgA c.10.1.2 30855 1zo0A 126 9.38e+00 1aazA 87 9.42e+00 1aba c.47.1.1 32761 1aba 87 9.43e+00 1aba c.47.1.1 32760 2msbB 115 9.57e+00 1rtm1 d.169.1.1 42356 1jn5B 250 1.03e+01 d.17.4.2 66922 1d3uA 181 1.03e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1t6cA 315 1.05e+01 c.55.1.8,c.55.1.8 106558,106559 1fvgA 199 1.06e+01 1fvaA d.58.28.1 39408 1df3A 162 1.06e+01 1mup b.60.1.1 27134 1pmzA 86 1.08e+01 a.39.1.10 104195 2gfgA 193 1.08e+01 1rznA 205 1.09e+01 1bh5A 183 1.10e+01 1qipA d.32.1.1 38476 1scmB 145 1.11e+01 1wdcB a.39.1.5 17304 2f96A 224 1.11e+01 1fu1A 203 1.11e+01 1fu1B b.59.1.1,h.1.11.1 27076,45630 1hup 141 1.11e+01 1rtm1 d.169.1.1,h.1.1.1 42354,45422 1jbeA 128 1.13e+01 3chy c.23.1.1 62845 1zljA 78 1.14e+01 1a4pA 96 1.14e+01 1b4cA a.39.1.2 17176 1ig3A 263 1.17e+01 1ig3A b.82.6.1,c.100.1.1 62358,62359 1vlmA 219 1.17e+01 c.66.1.41 108836 1bssA 244 1.18e+01 1rvaA c.52.1.2 33256 1rifA 282 1.18e+01 c.37.1.23 97507 2erxA 172 1.18e+01 1jjoC 261 1.20e+01 1itg 166 1.21e+01 1b9dA c.55.3.2 33661 1xa3A 437 1.21e+01 1lvwA 295 1.22e+01 c.68.1.6 84723 1mup 166 1.22e+01 1mup b.60.1.1 27133 1ab6A 125 1.22e+01 3chy c.23.1.1 31054 1rtm1 149 1.23e+01 1rtm1 2btfA 375 1.24e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1dqeA 137 1.25e+01 1dqeA a.39.2.1 17388 1xi1A 575 1.25e+01 2g76A 335 1.26e+01 1go3E 187 1.27e+01 b.40.4.5,d.230.1.1 83054,83055 1gm6A 175 1.27e+01 b.60.1.1 70272 2fl4A 149 1.29e+01 1pvyA 227 1.29e+01 d.115.1.2 95195 1i06A 180 1.31e+01 1mup b.60.1.1 27131 1sglA 209 1.31e+01 d.124.1.1 105536 1sk7A 198 1.31e+01 a.132.1.2 105671 1eggA 147 1.32e+01 1eggA d.169.1.1 42333 1a3yA 149 1.35e+01 1obpA b.60.1.1 27110 1cll 148 1.35e+01 1cll a.39.1.5 17263 2mysB 166 1.38e+01 1wdcB a.39.1.5 17308 1i05A 180 1.38e+01 1mup b.60.1.1 27130 1jjrA 151 1.42e+01 a.140.2.1 66772 1k8tA 510 1.42e+01 e.41.1.1 68316 1h7mA 102 1.43e+01 d.79.3.1 83485 1e87A 118 1.45e+01 1b6e d.169.1.1 42327 1rthA 560 1.46e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 1p9yA 121 1.48e+01 d.241.2.1 94402 1jv4A 162 1.49e+01 b.60.1.1 67343 1e6mA 128 1.49e+01 3chy c.23.1.1 31039 1lrzA 426 1.49e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1iukA 140 1.49e+01 c.2.1.8 83712 1m45A 148 1.51e+01 a.39.1.5 78598 1xzoA 174 1.57e+01 1itwA 741 1.58e+01 c.77.1.2 76793 1p9qC 256 1.59e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1vr9A 213 1.59e+01 1uirA 314 1.60e+01 c.66.1.17 99429 2gclA 261 1.64e+01 1j6zA 376 1.65e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1jkgB 250 1.67e+01 d.17.4.2 66796 2msbA 115 1.67e+01 1rtm1 d.169.1.1 42355 2bl0C 142 1.68e+01 1djxB 624 1.69e+01 1djxB a.39.1.7,b.7.1.1,c.1.18.1 17343,23160,29588 1yh3A 256 1.69e+01 2coeA 120 1.70e+01 1oj5A 132 1.70e+01 d.110.3.8 93087 1g4yR 148 1.73e+01 1cll a.39.1.5 60252 1wmqA 147 1.79e+01 1rwsA 77 1.79e+01 d.15.3.2 97991 2fyxA 143 1.79e+01 1hztA 190 1.80e+01 1i9aA d.113.1.2 61459 1wf3A 301 1.80e+01 1jqeA 292 1.82e+01 c.66.1.19 71789 1ni5A 433 1.85e+01 c.26.2.5,d.229.1.1 80533,80534 1osa 148 1.87e+01 1cll a.39.1.5 17300 1dzkA 157 1.87e+01 1obpA b.60.1.1 27096 3cln 148 1.89e+01 1cll a.39.1.5 17286 1b74A 254 1.89e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1u8sA 192 1.90e+01 d.58.18.5,d.58.18.5 107737,107738 1mr4A 47 1.90e+01 g.3.7.5 91429 1wuaA 375 1.92e+01 1yvcA 70 1.92e+01 1snnA 227 1.94e+01 d.115.1.2 105821 1fvaA 217 1.95e+01 1fvaA d.58.28.1 39409 1aisA 182 1.95e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 2bcqA 335 1.98e+01 1v8hA 107 1.99e+01 1exrA 148 1.99e+01 1cll a.39.1.5 17299 1u6tA 121 2.00e+01 1a26 361 2.02e+01 1a26 a.41.1.1,d.166.1.2 17412,42274 1fwp 139 2.03e+01 1eayC d.58.24.1 39396 1h6kZ 98 2.03e+01 d.58.7.1 60686 1aop 497 2.04e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1t4hA 290 2.05e+01 d.144.1.7 106420 1dy2A 180 2.09e+01 1koe d.169.1.5 42451 1nm1G 125 2.10e+01 d.109.1.1 80653 1k5dC 386 2.10e+01 c.10.1.2 68170 1r5jA 337 2.13e+01 c.77.1.5 97097 1r13A 148 2.17e+01 d.169.1.1,h.1.1.1 96782,96783 1vl5A 260 2.20e+01 c.66.1.41 108720 1h05A 146 2.22e+01 c.23.13.1 76433 1z5bA 469 2.22e+01 2d27A 149 2.23e+01 1dcuA 357 2.23e+01 1frpA e.7.1.1 42943 1g0rA 293 2.23e+01 1g0rA c.68.1.6 34532 1xewX 182 2.24e+01 1cb1 78 2.24e+01 4icb a.39.1.1 17156 1qwdA 177 2.25e+01 b.60.1.1 96471 2a19B 284 2.26e+01 1efyA 350 2.27e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1fp0A 88 2.27e+01 1fp0A g.50.1.2 45361 1wdcB 156 2.29e+01 1wdcB a.39.1.5 17302 1d1qA 161 2.32e+01 1dg9A c.44.1.1 32642 1w41A 101 2.32e+01 1mp4A 292 2.35e+01 c.68.1.6 79376 1oeyA 83 2.35e+01 d.15.2.2 92800 1coo 98 2.35e+01 1coo a.60.3.1 17967 1xl3C 92 2.36e+01 1gudA 288 2.36e+01 c.93.1.1 83326 1bb8 71 2.36e+01 2bb8 d.10.1.1 37478 2fz4A 237 2.36e+01 1zybA 232 2.37e+01 1ktbA 405 2.38e+01 b.71.1.1,c.1.8.1 72960,72961 1fm5A 199 2.38e+01 1fm5A d.169.1.1 42330 1omhA 293 2.39e+01 d.89.1.5 93348 1ls8A 142 2.41e+01 a.39.2.1 78176 2cxcA 144 2.41e+01 1j7qA 86 2.44e+01 1j7rA a.39.1.5 62700 2f5gA 133 2.46e+01 1zp7A 206 2.48e+01 1ut7A 171 2.48e+01 b.143.1.1 99906 2bl0B 145 2.48e+01 1kk8B 139 2.49e+01 a.39.1.5 77430 1nkiA 135 2.50e+01 d.32.1.2 91941 2brcA 214 2.53e+01 1qz5A 375 2.54e+01 c.55.1.1,c.55.1.1 96614,96615 1h1jS 51 2.55e+01 a.140.2.1 70850 2bm5A 186 2.57e+01 1sfe 180 2.57e+01 1sfe a.4.2.1,c.55.7.1 16073,33748 1fxoA 293 2.58e+01 1g0rA c.68.1.6 34524 1zy4A 303 2.58e+01 1yruB 74 2.60e+01 1s6lA 212 2.61e+01 1d4xG 126 2.61e+01 1d0nA d.109.1.1 59109 1h9eA 56 2.63e+01 1h9eA a.140.1.1 60825 1top 162 2.64e+01 1ncx a.39.1.5 17223 1cye 129 2.67e+01 3chy c.23.1.1 31077 1wpuA 147 2.68e+01 1a1d 146 2.68e+01 1a1d b.40.4.8 25394 1y81A 138 2.69e+01 1fu1B 203 2.71e+01 1fu1B b.59.1.1,h.1.11.1 27077,45631 1wd7A 261 2.71e+01 2gcuA 245 2.73e+01 1ayyA 151 2.74e+01 1apyA d.153.1.5 42016 1st9A 143 2.74e+01 c.47.1.10 98987 1sz2A 332 2.75e+01 1vhsA 175 2.78e+01 d.108.1.1 100698 1bap 306 2.82e+01 8abp c.93.1.1 35654 2bbeA 108 2.83e+01 1x0pA 143 2.84e+01 1o4wA 147 2.84e+01 c.120.1.1 86629 1abe 306 2.88e+01 8abp c.93.1.1 35648 1o1xA 155 2.91e+01 c.121.1.1 86553 2aexA 346 2.94e+01 1o50A 157 2.94e+01 d.37.1.1,d.37.1.1 92478,92479 1noa 113 2.95e+01 2mcm b.1.7.1 22208 1lqc 56 2.97e+01 1pru a.35.1.5 17109 1v6tA 255 2.97e+01 1jr5A 90 2.98e+01 a.150.1.1 67113 2phlA 397 2.99e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1g6nA 210 3.01e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1w2wB 191 3.04e+01 3eipA 84 3.05e+01 3eipA d.26.2.1 38434 1mkzA 172 3.07e+01 c.57.1.1 84998 1sazA 381 3.08e+01 1ik9A 213 3.08e+01 b.59.1.1,h.1.11.1 66176,66177 1wcwA 261 3.10e+01 1j2gA 319 3.10e+01 d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4 103824,103825,103826,103827,103828 2cgpA 210 3.18e+01 2cgpA a.4.5.4,b.82.3.2 16102,28141 1ky9B 448 3.19e+01 b.36.1.4,b.36.1.4,b.47.1.1 73200,73201,73202 1amw 214 3.20e+01 1yer d.122.1.1 41093 1mszA 86 3.22e+01 d.68.7.1 79428 2ch4A 320 3.23e+01 8abp 306 3.25e+01 8abp c.93.1.1 35647 1ebdC 41 3.26e+01 1ebdC a.9.1.1 16355 1l8aA 886 3.28e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1a5p 124 3.28e+01 7rsa d.5.1.1 37201 1a4h 230 3.28e+01 1yer d.122.1.1 41099 1ospH 218 3.31e+01 1igtB b.1.1.1,b.1.1.2 20117,21147 1xp3A 307 3.33e+01 1wsrA 375 3.34e+01 1banA 110 3.34e+01 1b20A d.1.1.2 36197 1ntyA 311 3.35e+01 a.87.1.1,b.55.1.1 103873,103874 1hdhA 536 3.35e+01 c.76.1.2 65805 1wmwA 330 3.36e+01 1gkuB 1054 3.39e+01 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 1z0jA 170 3.40e+01 2breA 219 3.40e+01 2acaA 189 3.43e+01 2sxl 88 3.43e+01 1b7fA d.58.7.1 39179 1lqpA 135 3.43e+01 d.32.1.2 78151 2gx9A 129 3.45e+01 1a6dB 543 3.45e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1u7lA 392 3.46e+01 1g61A 228 3.48e+01 1g61A d.126.1.1 41126 1flmA 122 3.50e+01 1axj b.45.1.1 25747 1bx4A 345 3.53e+01 1bx4A c.72.1.1 34935 1kp9B 287 3.55e+01 c.66.1.18 68734 1qo3C 137 3.55e+01 1qo3C d.169.1.1 42350 1qhaA 917 3.55e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 1sh8A 154 3.56e+01 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