# 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 4.90e-01 1oyc c.1.4.1 28603 1oya 400 5.20e-01 1oyc c.1.4.1 28604 2aexA 346 5.59e-01 1oyb 400 5.74e-01 1oyc c.1.4.1 28602 1b5sA 242 9.31e-01 1eaf c.43.1.1 32626 1zac 90 9.76e-01 1ncx a.39.1.5 17236 1f7wA 144 9.93e-01 1f46A d.129.4.1 59679 1f47B 144 1.11e+00 1f46A d.129.4.1 59645 1f46A 140 1.14e+00 1f46A d.129.4.1 59643 1b1yA 500 1.77e+00 1byb c.1.8.1 28796 1wdpA 495 1.81e+00 1q6cA 495 1.82e+00 c.1.8.1 95970 1byb 495 1.88e+00 1byb c.1.8.1 28790 1gzqA 300 1.98e+00 b.1.1.2,d.19.1.1 70818,70819 1y96B 85 1.99e+00 1a8h 500 2.01e+00 1a8h a.27.1.1,c.26.1.1 16922,31589 2c5kT 95 2.15e+00 1v3hA 495 2.68e+00 c.1.8.1 108303 1eco 136 2.80e+00 1flp a.1.1.2 15208 1eca 136 2.87e+00 1flp a.1.1.2 15209 1ecd 136 2.87e+00 1flp a.1.1.2 15211 1g5pA 289 3.12e+00 1cp2A c.37.1.10 32253 2amyA 246 3.26e+00 1cvrA 435 3.27e+00 1cvrA b.1.18.12,c.17.1.2 21949,31006 2fbhA 146 3.46e+00 1hwtC 81 3.50e+00 1hwtC g.38.1.1,h.1.3.1 45085,45518 1woyA 500 3.75e+00 1ynfA 458 3.87e+00 1wdtA 665 3.87e+00 1fp6A 289 4.11e+00 1cp2A c.37.1.10 32243 2h0uA 217 4.22e+00 1vgoA 253 4.55e+00 1xd8A 289 4.81e+00 2amdA 311 4.91e+00 1xeuA 263 5.37e+00 1p5jA 372 5.43e+00 c.79.1.1 104067 1lj9A 144 5.63e+00 a.4.5.28 78035 1pvmA 184 5.98e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1wkyA 464 6.37e+00 1jixA 351 6.64e+00 1c3jA c.87.1.1 63081 1jg7A 351 6.68e+00 1c3jA c.87.1.1 62945 2a5vA 213 7.11e+00 1ym3A 215 7.19e+00 2adoA 196 7.21e+00 1c3jA 351 7.39e+00 1c3jA c.87.1.1 35459 2bgu 351 7.41e+00 1c3jA c.87.1.1 35460 2etxA 209 7.47e+00 1y7qA 98 7.53e+00 2b1eA 564 7.54e+00 1omrA 201 7.60e+00 a.39.1.5 93349 1grj 158 7.94e+00 1grj a.2.1.1,d.26.1.2 15691,38433 1avsA 90 8.06e+00 1cll a.39.1.5 17226 1q2wA 308 8.34e+00 b.47.1.4 88355 1jsxA 207 8.70e+00 c.66.1.20 71846 1bbhA 131 8.70e+00 1bbhA a.24.3.2 16546 2a5kA 307 9.20e+00 1j93A 353 9.54e+00 c.1.22.1 66454 1xhdA 173 9.54e+00 1jo0A 98 9.79e+00 d.68.4.1 77140 1q6aA 107 9.92e+00 a.186.1.1 95966 1y9qA 192 1.03e+01 1t3wA 148 1.08e+01 1flp 142 1.09e+01 1flp a.1.1.2 15011 1moh 142 1.09e+01 1flp a.1.1.2 15012 2a6sA 84 1.12e+01 1ir6A 424 1.12e+01 c.107.1.2 71342 1tw9A 206 1.14e+01 a.45.1.1,c.47.1.5 107381,107382 2au5A 139 1.15e+01 1tn4 159 1.16e+01 1ncx a.39.1.5 17248 1ap4 89 1.19e+01 1ncx a.39.1.5 17253 1b0b 142 1.21e+01 2fal a.1.1.2 15010 2basA 431 1.21e+01 1txnA 328 1.21e+01 1ofcX 304 1.28e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1y1xA 191 1.31e+01 1aj4 161 1.32e+01 1ncx a.39.1.5 17244 1e5pA 151 1.33e+01 1bj7 b.60.1.1 59272 1c3qA 272 1.38e+01 1c3qA c.72.1.2 34948 1ockA 412 1.39e+01 c.117.1.1 86802 3tmkA 216 1.39e+01 3tmkA c.37.1.1 31920 1t95A 240 1.43e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 2b5aA 77 1.47e+01 1b0nA 111 1.48e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 2agaA 190 1.49e+01 1a2xA 159 1.56e+01 1ncx a.39.1.5 17251 2af4C 333 1.57e+01 2a4vA 159 1.58e+01 1ekqA 272 1.61e+01 1c3qA c.72.1.2 34941 1ncx 162 1.67e+01 1ncx a.39.1.5 17222 1top 162 1.67e+01 1ncx a.39.1.5 17223 2tmkA 216 1.67e+01 3tmkA c.37.1.1 31928 1wmhA 89 1.69e+01 2aukA 190 1.71e+01 1p9qC 256 1.73e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1a52A 258 1.74e+01 3erdA a.123.1.1 19296 1v1dA 31 1.75e+01 1p5zB 263 1.81e+01 c.37.1.1 87815 2beqD 48 1.84e+01 1uw4A 91 1.84e+01 d.58.7.4 100071 2cxxA 190 1.86e+01 1rec 201 1.88e+01 1rec a.39.1.5 17326 1tr0A 108 1.93e+01 d.58.4.4 107261 2c3nA 247 1.98e+01 1delA 241 2.03e+01 1dekA c.37.1.1 31844 1yirA 408 2.05e+01 1dekA 241 2.14e+01 1dekA c.37.1.1 31842 1eh2 106 2.17e+01 1eh2 a.39.1.6 17339 2ajrA 331 2.17e+01 1a6q 382 2.20e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 2fu2A 102 2.21e+01 1y791 680 2.24e+01 2f6mA 65 2.24e+01 1ajsA 412 2.24e+01 1ajsA c.67.1.1 34276 1miwA 404 2.25e+01 a.173.1.1,d.218.1.4 79162,79163 1h6pA 203 2.29e+01 a.146.1.1 60690 2cq2A 114 2.36e+01 1ap6A 198 2.36e+01 1avmA a.2.11.1,d.44.1.1 15746,38705 1xpcA 248 2.40e+01 3ertA 261 2.41e+01 3erdA a.123.1.1 19292 1wy1A 172 2.43e+01 1lpuA 332 2.44e+01 d.144.1.7 74177 1ylxA 103 2.47e+01 1im5A 180 2.48e+01 c.33.1.3 66211 1allB 161 2.54e+01 1qgwC a.1.1.3 15648 2cvhA 220 2.64e+01 1wi9A 72 2.64e+01 1zgmA 248 2.72e+01 2fnoA 248 2.72e+01 1ut8A 291 2.75e+01 a.60.7.1,c.120.1.2 99908,99909 1v2zA 111 2.76e+01 a.186.1.1 108300 1bj7 156 2.84e+01 1bj7 b.60.1.1 27113 1o6dA 163 2.90e+01 c.116.1.3 92567 1ydmA 187 2.93e+01 2chgA 226 2.95e+01 1k2xB 143 2.97e+01 1v3wA 173 2.98e+01 b.81.1.5 100291 1sczA 233 3.11e+01 c.43.1.1 98802 2fueA 262 3.13e+01 1zl8A 53 3.16e+01 1q0sA 259 3.20e+01 c.66.1.28 95509 1r0mA 375 3.24e+01 c.1.11.2,d.54.1.1 104747,104748 1n4kA 381 3.25e+01 a.118.22.1,b.42.6.1 79992,79993 1jbaA 204 3.30e+01 1rec a.39.1.5 17330 1uok 558 3.30e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1o50A 157 3.31e+01 d.37.1.1,d.37.1.1 92478,92479 1aurA 218 3.44e+01 1auoA c.69.1.14 34718 1e3hA 757 3.46e+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 1q74A 303 3.49e+01 c.134.1.1 96019 2a15A 139 3.50e+01 1yzbA 182 3.54e+01 1cmaA 104 3.54e+01 1cmbA a.43.1.5 17486 1ddmA 135 3.54e+01 2nmbA b.55.1.2 26993 1ubdC 124 3.55e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1,g.37.1.1 45053,45054,45055,45056 2erbA 125 3.55e+01 1auoA 218 3.57e+01 1auoA c.69.1.14 34716 2cqsA 842 3.72e+01 2czrA 226 3.73e+01 1mjoA 104 3.74e+01 1cmbA a.43.1.5 17466 1qhtA 775 3.74e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1r2rA 248 3.74e+01 c.1.1.1 96875 1cmcA 104 3.79e+01 1cmbA a.43.1.5 17462 2mysB 166 3.83e+01 1wdcB a.39.1.5 17308 1foeA 377 3.87e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1taq 832 3.92e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 1b8xA 280 3.93e+01 1b8xA a.45.1.1,c.47.1.5 17739,33033 1vjuA 309 3.93e+01 d.248.1.1 100835 2c8vA 288 3.96e+01 1isaA 192 4.02e+01 1avmA a.2.11.1,d.44.1.1 15731,38724 1ji6A 589 4.02e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1iscA 192 4.02e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1sauA 115 4.06e+01 1n9dA 199 4.17e+01 a.26.1.1 85464 1eijA 80 4.18e+01 1eijA a.5.6.1 16298 1tzzA 392 4.21e+01 1oe4A 247 4.31e+01 c.18.1.3 86895 1fw1A 216 4.33e+01 a.45.1.1,c.47.1.5 60051,60052 1exnA 290 4.36e+01 1exnA a.60.7.1,c.120.1.2 18088,33358 1dugA 234 4.39e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 2abbA 364 4.43e+01 1aj8A 371 4.47e+01 1aj8A a.103.1.1 18900 2bkaA 242 4.48e+01 1ek9A 428 4.50e+01 1ek9A f.5.1.1 43809 1vypX 364 4.55e+01 c.1.4.1 108905 1h5rA 293 4.57e+01 c.68.1.6 65623 1vyrA 364 4.60e+01 c.1.4.1 108906 2ffuA 501 4.61e+01 1ql3A 99 4.64e+01 1ycc a.3.1.1 15822 1l7yA 94 4.68e+01 d.15.1.6 73676 1y8qA 346 4.69e+01 1cmbA 104 4.71e+01 1cmbA a.43.1.5 17460 1izmA 184 4.75e+01 a.199.1.1 90725 1upvA 257 4.77e+01 2bskB 90 4.78e+01 1m2dA 110 4.79e+01 c.47.1.11 78476 2ay1A 394 4.90e+01 1ajsA c.67.1.1 34357 1m2aA 110 4.90e+01 c.47.1.11 78472 1g0cA 364 4.94e+01 7a3hA c.1.8.3 60165 2gokA 429 4.96e+01 1xfxA 777 4.98e+01 1fosF 57 5.00e+01 h.1.3.1 45538 1m2bA 110 5.00e+01 c.47.1.11 78474 1qh3A 260 5.02e+01 1qh5A d.157.1.2 42059 1a7w 69 5.03e+01 1a7w a.22.1.2 16477 1pwhA 327 5.06e+01 c.79.1.1 95224 1t3qB 788 5.09e+01 d.41.1.1,d.133.1.1 106369,106370 1cpq 129 5.12e+01 1cpq a.24.3.2 16556 2fcwA 109 5.15e+01 2b18A 164 5.21e+01 1f37A 110 5.22e+01 1f37A c.47.1.11 33088 2di4A 238 5.25e+01 1qh5A 260 5.31e+01 1qh5A d.157.1.2 42057 2cfxA 144 5.39e+01 1vd2A 89 5.41e+01 d.15.2.2 108517 2cybA 323 5.44e+01 1g01A 364 5.52e+01 7a3hA c.1.8.3 60161 1y7yA 74 5.57e+01 1iznB 277 5.58e+01 e.43.1.2 83848 1pta 318 5.59e+01 1pscA c.1.9.3 29064 1yf3A 259 5.60e+01 1flzA 228 5.67e+01 3eugA c.18.1.1 31027 1o70A 324 5.68e+01 b.118.1.1,b.118.1.1 81115,81116 1pl4A 198 5.86e+01 a.2.11.1,d.44.1.1 94854,94855 1o5zA 442 5.91e+01 c.59.1.2,c.72.2.2 92530,92531 1zbsA 291 5.93e+01 1icpA 376 5.95e+01 1oyc c.1.4.1 62270 1lvfA 110 6.00e+01 a.47.2.1 74280 1woqA 267 6.01e+01 c.55.1.10,c.55.1.10 109462,109463 1b33B 161 6.08e+01 1qgwC a.1.1.3 15650 1hta 69 6.10e+01 1a7w a.22.1.2 16476 1ii7A 333 6.11e+01 1ii7A d.159.1.4 62415 1id3B 102 6.12e+01 a.22.1.1 66113 1xorA 349 6.13e+01 2es9A 115 6.16e+01 1dk5A 322 6.23e+01 1dk5A a.65.1.1 18192 1c52 131 6.23e+01 1c52 a.3.1.1 15810 1tbbA 332 6.25e+01 a.211.1.2 106741 2gwgA 350 6.27e+01 1bl3A 160 6.27e+01 1b9dA c.55.3.2 33655 2aaoA 166 6.30e+01 1v6fA 151 6.39e+01 d.109.1.2 108395 1lkcA 364 6.41e+01 c.67.1.1 73978 1fexA 59 6.43e+01 a.4.1.3 59803 1j0hA 588 6.44e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1czqA 46 6.46e+01 1czqA h.3.2.1 45720 1zuhA 168 6.46e+01 3erdA 261 6.47e+01 3erdA a.123.1.1 19293 1pmzA 86 6.48e+01 a.39.1.10 104195 1eluB 390 6.51e+01 1elqA c.67.1.3 34435 1xteA 154 6.54e+01 2shkA 173 6.60e+01 1shkA c.37.1.2 31934 2ax8A 256 6.61e+01 1a32 88 6.63e+01 1a32 a.16.1.2 16384 2f5xA 312 6.63e+01 1pgvA 197 6.64e+01 c.10.1.1 88073 1imoA 88 6.64e+01 1imoA c.15.1.2 62590 1y0eA 223 6.67e+01 1iwmA 186 6.72e+01 b.125.1.2 83758 1kamA 194 6.83e+01 c.26.1.3 72254 1rkbA 173 6.86e+01 2ax9A 256 6.89e+01 1pq9A 253 6.92e+01 a.123.1.1 95004 1innA 166 6.93e+01 1j98A d.185.1.2 62608 1vjeA 166 6.93e+01 d.185.1.2 100807 1z5lA 285 6.93e+01 1sjdA 368 7.03e+01 c.1.11.2,d.54.1.1 105632,105633 1ak0 270 7.03e+01 1ak0 a.124.1.2 19345 1pkhA 204 7.07e+01 b.85.4.1 94832 1mfqC 129 7.09e+01 a.36.1.1 79046 1y97A 238 7.11e+01 1xfuA 747 7.15e+01 1b0nB 57 7.19e+01 1b0nB a.34.1.1 17002 1gmlA 178 7.24e+01 c.8.5.2 70273 1elqA 390 7.25e+01 1elqA c.67.1.3 34436 1eluA 390 7.25e+01 1elqA c.67.1.3 34434 1whzA 70 7.26e+01 2fefA 294 7.26e+01 1r13A 148 7.27e+01 d.169.1.1,h.1.1.1 96782,96783 2c4jA 218 7.29e+01 1ektA 53 7.29e+01 1ektA b.129.1.3 38764 1zboA 210 7.36e+01 1mvwC 147 7.43e+01 i.15.1.1 79525 1o1fC 147 7.43e+01 i.15.1.1 80997 1be3B 439 7.58e+01 1be3B d.185.1.1,d.185.1.1 58952,58953 1lqtA 456 7.59e+01 c.3.1.1,c.4.1.1 74198,74199 1ak5 503 7.61e+01 1ak5 c.1.5.1 28639 1yzmA 51 7.62e+01 1oghA 204 7.66e+01 b.85.4.1 86994 1gv4A 528 7.67e+01 c.3.1.5,c.3.1.5,d.87.1.1 70589,70590,70591 1ji1A 637 7.70e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1tph1 247 7.79e+01 1amk 1v77A 212 7.79e+01 c.6.3.2 108402 1zckA 154 7.80e+01 1oq9A 363 7.82e+01 a.25.1.2 87257 1ka1A 357 7.85e+01 e.7.1.1 68369 1qgxA 357 7.88e+01 1qgxA e.7.1.1 42973 1uox 296 7.94e+01 1uox 1ojxA 263 7.96e+01 c.1.10.1 93164 1zljA 78 7.96e+01 1r4uA 301 7.97e+01 d.96.1.4,d.96.1.4 97047,97048 1o2dA 371 7.98e+01 e.22.1.2 86591 1treA 255 7.99e+01 1amk c.1.1.1 28505 1wrrA 301 8.01e+01 1bba 36 8.06e+01 1bba j.6.1.1 46088 1hqoA 258 8.07e+01 1hqoA a.45.1.1,c.47.1.5 17749,33043 1z0kB 69 8.10e+01 1w1iE 357 8.14e+01 c.1.9.1 109051 1y2kA 349 8.15e+01 1yozA 116 8.19e+01 2akrA 285 8.21e+01 1rxdA 159 8.23e+01 1q45A 391 8.27e+01 c.1.4.1 95780 1exnB 290 8.27e+01 1exnA a.60.7.1,c.120.1.2 18089,33359 1edg 380 8.27e+01 1edg c.1.8.3 28807 2bm3A 166 8.29e+01 1lqwA 183 8.36e+01 d.167.1.1 74210 1n0wA 243 8.40e+01 c.37.1.11 79772 2fikA 287 8.42e+01 1z0xA 220 8.49e+01 1cc5 83 8.58e+01 1cc5 a.3.1.1 15901 1r1dA 247 8.61e+01 c.69.1.29 96813 2b59A 187 8.62e+01 1k1vA 41 8.62e+01 a.37.1.1 71999 1lm4A 194 8.63e+01 d.167.1.1 84626 2ar0A 541 8.68e+01 1cojA 212 8.72e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1ezvB 352 8.77e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 1ofdA 1520 8.77e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1a4mA 349 8.85e+01 1a4mA c.1.9.1 29014 1rhd 293 8.93e+01 1rhs c.46.1.2,c.46.1.2 32715,32716 2a0kA 161 8.95e+01 2f2tA 161 8.95e+01 2f62A 161 8.99e+01