# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1oyc 400 5.86e-01 1oyc c.1.4.1 28603 1oya 400 6.12e-01 1oyc c.1.4.1 28604 1oyb 400 6.55e-01 1oyc c.1.4.1 28602 1a8h 500 7.57e-01 1a8h a.27.1.1,c.26.1.1 16922,31589 1zac 90 8.01e-01 1ncx a.39.1.5 17236 2aexA 346 9.09e-01 1b5sA 242 9.38e-01 1eaf c.43.1.1 32626 1woyA 500 1.38e+00 1b1yA 500 1.48e+00 1byb c.1.8.1 28796 1wdpA 495 1.56e+00 1q6cA 495 1.61e+00 c.1.8.1 95970 1byb 495 1.71e+00 1byb c.1.8.1 28790 1gzqA 300 1.76e+00 b.1.1.2,d.19.1.1 70818,70819 1f7wA 144 2.00e+00 1f46A d.129.4.1 59679 1t95A 240 2.12e+00 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1f47B 144 2.15e+00 1f46A d.129.4.1 59645 1y96B 85 2.20e+00 1v3hA 495 2.21e+00 c.1.8.1 108303 1f46A 140 2.23e+00 1f46A d.129.4.1 59643 1g5pA 289 2.58e+00 1cp2A c.37.1.10 32253 1cvrA 435 2.76e+00 1cvrA b.1.18.12,c.17.1.2 21949,31006 2c5kT 95 2.76e+00 1eco 136 2.85e+00 1flp a.1.1.2 15208 1eca 136 2.92e+00 1flp a.1.1.2 15209 1ecd 136 2.92e+00 1flp a.1.1.2 15211 1p5jA 372 2.94e+00 c.79.1.1 104067 2fbhA 146 3.00e+00 1fp6A 289 3.00e+00 1cp2A c.37.1.10 32243 2adoA 196 3.27e+00 2etxA 209 3.49e+00 2amyA 246 3.63e+00 1xd8A 289 3.73e+00 1p9qC 256 4.47e+00 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1vgoA 253 5.00e+00 1ynfA 458 5.28e+00 1avsA 90 5.55e+00 1cll a.39.1.5 17226 1wdtA 665 6.09e+00 1hwtC 81 6.29e+00 1hwtC g.38.1.1,h.1.3.1 45085,45518 1ap4 89 7.15e+00 1ncx a.39.1.5 17253 1cmcA 104 7.33e+00 1cmbA a.43.1.5 17462 1bbhA 131 7.34e+00 1bbhA a.24.3.2 16546 1tn4 159 7.38e+00 1ncx a.39.1.5 17248 2b1eA 564 7.72e+00 1cmaA 104 7.77e+00 1cmbA a.43.1.5 17486 1jg7A 351 7.83e+00 1c3jA c.87.1.1 62945 1jixA 351 7.88e+00 1c3jA c.87.1.1 63081 1jsxA 207 7.93e+00 c.66.1.20 71846 1lj9A 144 7.93e+00 a.4.5.28 78035 1c3jA 351 8.65e+00 1c3jA c.87.1.1 35459 2bgu 351 8.65e+00 1c3jA c.87.1.1 35460 1aj4 161 8.74e+00 1ncx a.39.1.5 17244 1cmbA 104 8.76e+00 1cmbA a.43.1.5 17460 1xeuA 263 9.11e+00 2a6sA 84 9.25e+00 1pvmA 184 9.28e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1ncx 162 9.69e+00 1ncx a.39.1.5 17222 1top 162 9.69e+00 1ncx a.39.1.5 17223 1wkyA 464 9.91e+00 3tmkA 216 9.97e+00 3tmkA c.37.1.1 31920 1t3wA 148 1.03e+01 1xhdA 173 1.04e+01 1a2xA 159 1.07e+01 1ncx a.39.1.5 17251 2ay1A 394 1.07e+01 1ajsA c.67.1.1 34357 1h6pA 203 1.11e+01 a.146.1.1 60690 1ym3A 215 1.15e+01 2a5vA 213 1.17e+01 1q6aA 107 1.20e+01 a.186.1.1 95966 1wmhA 89 1.21e+01 2tmkA 216 1.27e+01 3tmkA c.37.1.1 31928 1jo0A 98 1.30e+01 d.68.4.1 77140 1omrA 201 1.32e+01 a.39.1.5 93349 1grj 158 1.38e+01 1grj a.2.1.1,d.26.1.2 15691,38433 2agaA 190 1.38e+01 1y7qA 98 1.41e+01 1flp 142 1.41e+01 1flp a.1.1.2 15011 1moh 142 1.41e+01 1flp a.1.1.2 15012 1y9qA 192 1.44e+01 1tw9A 206 1.50e+01 a.45.1.1,c.47.1.5 107381,107382 1ockA 412 1.52e+01 c.117.1.1 86802 1b0b 142 1.53e+01 2fal a.1.1.2 15010 2au5A 139 1.55e+01 1j93A 353 1.61e+01 c.1.22.1 66454 1txnA 328 1.62e+01 2amdA 311 1.64e+01 1ir6A 424 1.65e+01 c.107.1.2 71342 1hnjA 317 1.75e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1y97A 238 1.80e+01 2cvhA 220 1.80e+01 1y1xA 191 1.82e+01 1e5pA 151 1.82e+01 1bj7 b.60.1.1 59272 1c3qA 272 1.88e+01 1c3qA c.72.1.2 34948 2af4C 333 1.91e+01 1p5zB 263 2.03e+01 c.37.1.1 87815 1ekqA 272 2.04e+01 1c3qA c.72.1.2 34941 2a4vA 159 2.05e+01 2b5aA 77 2.06e+01 1qh3A 260 2.07e+01 1qh5A d.157.1.2 42059 1m2dA 110 2.09e+01 c.47.1.11 78476 1ofcX 304 2.12e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 2cxxA 190 2.22e+01 1qh5A 260 2.22e+01 1qh5A d.157.1.2 42057 2aukA 190 2.25e+01 1mjoA 104 2.26e+01 1cmbA a.43.1.5 17466 1bj7 156 2.27e+01 1bj7 b.60.1.1 27113 1ydmA 187 2.29e+01 1delA 241 2.31e+01 1dekA c.37.1.1 31844 1xk5A 204 2.38e+01 1r13A 148 2.41e+01 d.169.1.1,h.1.1.1 96782,96783 2basA 431 2.44e+01 1dekA 241 2.45e+01 1dekA c.37.1.1 31842 1a52A 258 2.45e+01 3erdA a.123.1.1 19296 1taq 832 2.46e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1q2wA 308 2.52e+01 b.47.1.4 88355 1im5A 180 2.54e+01 c.33.1.3 66211 2fu2A 102 2.56e+01 1pwhA 327 2.56e+01 c.79.1.1 95224 1pmzA 86 2.58e+01 a.39.1.10 104195 1b0nA 111 2.59e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1eblB 317 2.63e+01 1hn9A c.95.1.2,c.95.1.2 35975,35976 1pbp 321 2.67e+01 1ixh c.94.1.1 35768 1ddmA 135 2.69e+01 2nmbA b.55.1.2 26993 1m2aA 110 2.70e+01 c.47.1.11 78472 1f37A 110 2.71e+01 1f37A c.47.1.11 33088 1uok 558 2.72e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1tr0A 108 2.73e+01 d.58.4.4 107261 1ap6A 198 2.74e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1hn9A 317 2.76e+01 1hn9A c.95.1.2,c.95.1.2 35977,35978 1y791 680 2.76e+01 1v2zA 111 2.81e+01 a.186.1.1 108300 1m2bA 110 2.83e+01 c.47.1.11 78474 1al0F 426 2.86e+01 2bpa1 b.121.5.1 23274 2a5kA 307 2.87e+01 2bpa1 426 2.88e+01 2bpa1 1foeA 377 2.90e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1a6q 382 2.97e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1o6dA 163 2.98e+01 c.116.1.3 92567 1uw4A 91 2.98e+01 d.58.7.4 100071 2ajrA 331 3.02e+01 2f6mA 65 3.04e+01 1sczA 233 3.13e+01 c.43.1.1 98802 1rec 201 3.14e+01 1rec a.39.1.5 17326 1miwA 404 3.15e+01 a.173.1.1,d.218.1.4 79162,79163 1v1dA 31 3.17e+01 2fueA 262 3.26e+01 1l7yA 94 3.28e+01 d.15.1.6 73676 1r2rA 248 3.28e+01 c.1.1.1 96875 1ylxA 103 3.31e+01 1v3wA 173 3.32e+01 b.81.1.5 100291 1vd2A 89 3.37e+01 d.15.2.2 108517 1pta 318 3.40e+01 1pscA c.1.9.3 29064 1ajsA 412 3.42e+01 1ajsA c.67.1.1 34276 1r0mA 375 3.42e+01 c.1.11.2,d.54.1.1 104747,104748 1q0sA 259 3.49e+01 c.66.1.28 95509 1eblA 317 3.53e+01 1hn9A c.95.1.2,c.95.1.2 35973,35974 1q45A 391 3.57e+01 c.1.4.1 95780 1v77A 212 3.60e+01 c.6.3.2 108402 1ut8A 291 3.64e+01 a.60.7.1,c.120.1.2 99908,99909 1xpcA 248 3.65e+01 1ubdC 124 3.66e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1 45053,45054,45055,45056 1xorA 349 3.69e+01 1cpq 129 3.71e+01 1cpq a.24.3.2 16556 1eijA 80 3.74e+01 1eijA a.5.6.1 16298 1ji6A 589 3.74e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1tbbA 332 3.74e+01 a.211.1.2 106741 1tzzA 392 3.76e+01 1yzbA 182 3.77e+01 1e3hA 757 3.79e+01 1e3hA a.4.9.1,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16257,37572,37573,38810,40695,40696 3ertA 261 3.81e+01 3erdA a.123.1.1 19292 2erbA 125 3.86e+01 1bl3A 160 3.87e+01 1b9dA c.55.3.2 33655 2abbA 364 3.88e+01 1vypX 364 3.93e+01 c.1.4.1 108905 1qhtA 775 3.95e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1vyrA 364 3.96e+01 c.1.4.1 108906 1pkhA 204 3.97e+01 b.85.4.1 94832 2aaoA 166 4.02e+01 2c3nA 247 4.02e+01 1zl8A 53 4.03e+01 2mysB 166 4.07e+01 1wdcB a.39.1.5 17308 2cq2A 114 4.07e+01 2beqD 48 4.12e+01 2bkaA 242 4.18e+01 1innA 166 4.22e+01 1j98A d.185.1.2 62608 1vjeA 166 4.22e+01 d.185.1.2 100807 1npoA 95 4.23e+01 1npoA b.9.1.1 23270 1yirA 408 4.25e+01 1oghA 204 4.29e+01 b.85.4.1 86994 1ek9A 428 4.44e+01 1ek9A f.5.1.1 43809 1lpuA 332 4.44e+01 d.144.1.7 74177 1a54A 321 4.45e+01 1ixh c.94.1.1 35763 1rxdA 159 4.46e+01 2es9A 115 4.48e+01 1y2kA 349 4.51e+01 1n4kA 381 4.62e+01 a.118.22.1,b.42.6.1 79992,79993 1wy1A 172 4.70e+01 2cqsA 842 4.75e+01 1zbsA 291 4.76e+01 1zgmA 248 4.91e+01 2fnoA 248 4.91e+01 1f0jA 377 4.92e+01 1f0jA a.211.1.2 19346 1rhd 293 4.93e+01 1rhs c.46.1.2,c.46.1.2 32715,32716 1id3B 102 4.93e+01 a.22.1.1 66113 2fcwA 109 4.95e+01 1sauA 115 4.95e+01 1y8qA 346 4.96e+01 1v6fA 151 4.96e+01 d.109.1.2 108395 1o50A 157 4.97e+01 d.37.1.1,d.37.1.1 92478,92479 1ekyA 129 5.03e+01 1cpq i.11.1.1 46012 1zckA 154 5.08e+01 1q74A 303 5.11e+01 c.134.1.1 96019 1mvwC 147 5.19e+01 i.15.1.1 79525 1o1fC 147 5.19e+01 i.15.1.1 80997 1o70A 324 5.19e+01 b.118.1.1,b.118.1.1 81115,81116 1jbaA 204 5.22e+01 1rec a.39.1.5 17330 1rkbA 173 5.26e+01 1k2xB 143 5.26e+01 1ql3A 99 5.28e+01 1ycc a.3.1.1 15822 2gokA 429 5.38e+01 1exnA 290 5.41e+01 1exnA a.60.7.1,c.120.1.2 18088,33358 1h5rA 293 5.42e+01 c.68.1.6 65623 1g0cA 364 5.49e+01 7a3hA c.1.8.3 60165 1kamA 194 5.58e+01 c.26.1.3 72254 1czqA 46 5.58e+01 1czqA h.3.2.1 45720 1eh2 106 5.62e+01 1eh2 a.39.1.6 17339 1whzA 70 5.63e+01 1w1iE 357 5.66e+01 c.1.9.1 109051 1o5zA 442 5.66e+01 c.59.1.2,c.72.2.2 92530,92531 1ofdA 1520 5.67e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2czrA 226 5.68e+01 1dk5A 322 5.68e+01 1dk5A a.65.1.1 18192 2cfxA 144 5.78e+01 1icpA 376 5.82e+01 1oyc c.1.4.1 62270 2bn2A 95 5.91e+01 1npoA b.9.1.1 23266 1g01A 364 5.98e+01 7a3hA c.1.8.3 60161 1fosF 57 5.99e+01 h.1.3.1 45538 1pgvA 197 6.04e+01 c.10.1.1 88073 1wi9A 72 6.05e+01 1zljA 78 6.09e+01 2f5xA 312 6.17e+01 1qtqA 553 6.17e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 2fefA 294 6.20e+01 1allB 161 6.20e+01 1qgwC a.1.1.3 15648 1aj8A 371 6.20e+01 1aj8A a.103.1.1 18900 2a15A 139 6.22e+01 1fjmA 330 6.23e+01 1auiA d.159.1.3 42082 1gmlA 178 6.23e+01 c.8.5.2 70273 1a4mA 349 6.23e+01 1a4mA c.1.9.1 29014 1iznB 277 6.23e+01 e.43.1.2 83848 1ii7A 333 6.27e+01 1ii7A d.159.1.4 62415 1ixh 321 6.29e+01 1ixh c.94.1.1 35761 1a40 321 6.34e+01 1ixh c.94.1.1 35767 2bnh 457 6.36e+01 1a4yA c.10.1.1 30850 2ffuA 501 6.40e+01 1tdpA 111 6.42e+01 a.29.8.1 106781 1yf3A 259 6.44e+01 1fexA 59 6.54e+01 a.4.1.3 59803 2b18A 164 6.55e+01 1pl4A 198 6.60e+01 a.2.11.1,d.44.1.1 94854,94855 1a7w 69 6.65e+01 1a7w a.22.1.2 16477 1n9dA 199 6.66e+01 a.26.1.1 85464 1vflA 356 6.71e+01 1dp3A 55 6.74e+01 1dp3A a.55.1.2 59128 1n0wA 243 6.79e+01 c.37.1.11 79772 1lvfA 110 6.84e+01 a.47.2.1 74280 1npoC 95 6.87e+01 1npoA b.9.1.1 23271 1oe4A 247 6.89e+01 c.18.1.3 86895 1keaA 221 6.89e+01 a.96.1.2 68491 1tph1 247 6.90e+01 1amk 1l5cA 92 6.95e+01 b.9.1.1 73577 1x54A 434 7.00e+01 1zboA 210 7.08e+01 1pmd 675 7.16e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1jk4A 89 7.17e+01 b.9.1.1 77130 1yruB 74 7.22e+01 1ka1A 357 7.22e+01 e.7.1.1 68369 1qgxA 357 7.24e+01 1qgxA e.7.1.1 42973 1j0hA 588 7.31e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1ox0A 430 7.32e+01 c.95.1.1,c.95.1.1 87495,87496 1treA 255 7.33e+01 1amk c.1.1.1 28505 2tpsA 227 7.35e+01 2tpsA c.1.3.1 28591 1c1dA 355 7.37e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1yzmA 51 7.43e+01 1yadA 221 7.45e+01 1vlpA 441 7.50e+01 d.41.2.2,d.41.2.3 108840,108841 1e1hB 174 7.53e+01 1c52 131 7.53e+01 1c52 a.3.1.1 15810 1x24A 180 7.54e+01 1z5lA 285 7.58e+01 2bexA 460 7.59e+01 1t3qB 788 7.62e+01 d.41.1.1,d.133.1.1 106369,106370 2ct8A 497 7.67e+01 1imoA 88 7.70e+01 1imoA c.15.1.2 62590 2shkA 173 7.71e+01 1shkA c.37.1.2 31934 1cojA 212 7.71e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1lqwA 183 7.74e+01 d.167.1.1 74210 1lqtA 456 7.75e+01 c.3.1.1,c.4.1.1 74198,74199 1aurA 218 7.80e+01 1auoA c.69.1.14 34718 1bmfA 510 7.88e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18281,26446,32326 1hqoA 258 7.98e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1z0kB 69 7.99e+01 1auoA 218 7.99e+01 1auoA c.69.1.14 34716 1ia8A 289 8.00e+01 1ia8A d.144.1.7 62112 1xfxO 149 8.06e+01 1ak0 270 8.06e+01 1ak0 a.124.1.2 19345 1tikA 213 8.11e+01 c.23.5.3 107003 1b8xA 280 8.14e+01 1b8xA a.45.1.1,c.47.1.5 17739,33033 1eejA 216 8.14e+01 1eejA c.47.1.9,d.17.3.1 33057,38071 1wf9A 107 8.15e+01 1vjuA 309 8.17e+01 d.248.1.1 100835 1b0nB 57 8.18e+01 1b0nB a.34.1.1 17002 1u8xX 472 8.23e+01 c.2.1.5,d.162.1.2 107741,107742 1mfqC 129 8.24e+01 a.36.1.1 79046 2gwgA 350 8.26e+01 2apjA 260 8.26e+01 1o2dA 371 8.27e+01 e.22.1.2 86591 1lm4A 194 8.28e+01 d.167.1.1 84626 1uox 296 8.30e+01 1uox 1icxA 155 8.33e+01 d.129.3.1 71191 1r4uA 301 8.34e+01 d.96.1.4,d.96.1.4 97047,97048 1wrrA 301 8.38e+01 2ax8A 256 8.40e+01 1ji1A 637 8.43e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1zclA 180 8.46e+01 2cxaA 256 8.46e+01 1woqA 267 8.47e+01 c.55.1.10,c.55.1.10 109462,109463 1vqoV 71 8.48e+01 2ch4A 320 8.51e+01 1edg 380 8.51e+01 1edg c.1.8.3 28807 1xfxA 777 8.52e+01 1w7jB 151 8.54e+01 3erdA 261 8.55e+01 3erdA a.123.1.1 19293 2ax9A 256 8.64e+01 1n3lA 372 8.66e+01 c.26.1.1 79966 1fn9A 365 8.67e+01 1fn9A d.196.1.1 59894 1k1vA 41 8.67e+01 a.37.1.1 71999 1upvA 257 8.67e+01 1iwmA 186 8.69e+01 b.125.1.2 83758 3cln 148 8.70e+01 1cll a.39.1.5 17286 1rpo 65 8.73e+01 1nkd a.30.1.1 16975 1dpsD 167 8.74e+01 1dpsA a.25.1.1 16719 1dpsA 167 8.74e+01 1dpsA a.25.1.1 16716 1dugA 234 8.78e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1hta 69 8.91e+01 1a7w a.22.1.2 16476 1s72N 187 8.93e+01 c.55.4.1 105333 1prq 125 8.95e+01 3nul d.110.1.1 40883 1q4rA 112 8.98e+01 d.58.4.4 95823