# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1vddA 228 4.49e-02 e.49.1.1 108519 1u2zA 433 3.42e-01 c.66.1.31 107626 1yqdA 366 4.97e-01 1oo4A 111 6.79e-01 d.93.1.1 87185 1pjqA 457 7.26e-01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1rlzA 369 7.66e-01 c.31.1.1 104989 1g8aA 227 8.31e-01 c.66.1.3 90506 1dhs 344 1.17e+00 1dhs c.31.1.1 31727 1fhvA 323 1.19e+00 1fhuA c.1.11.2,d.54.1.1 29235,38879 1o6dA 163 1.56e+00 c.116.1.3 92567 2dcnA 311 1.58e+00 1r6wA 322 1.72e+00 c.1.11.2,d.54.1.1 97165,97166 1tqjA 230 2.08e+00 c.1.2.2 107228 1vmeA 410 2.10e+00 c.23.5.1,d.157.1.3 108893,108894 1twuA 139 2.16e+00 d.32.1.8 107413 1zjjA 263 2.65e+00 1z5oA 242 2.70e+00 1eiyB 785 2.75e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16305,16306,25314,39313,40782,41458 1t0hB 224 3.04e+00 c.37.1.1 106208 1rpxA 230 3.23e+00 1rpxA c.1.2.2 28536 1lc5A 364 3.38e+00 c.67.1.1 73827 1mo9A 523 3.41e+00 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1vjrA 271 3.44e+00 c.108.1.14 100832 1fl2A 310 3.58e+00 1hyuA c.3.1.5,c.3.1.5 59869,59870 1xdwA 331 3.72e+00 2pna 104 3.85e+00 1qadA d.93.1.1 40501 2b0cA 206 3.95e+00 1d4oA 184 4.28e+00 1d4oA c.31.1.4 31748 1b7yB 785 4.29e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1scuA 288 4.30e+00 2scuA c.2.1.8,c.23.4.1 30307,31135 1rkd 309 4.31e+00 1rkd c.72.1.1 34928 1pg5A 299 4.32e+00 c.78.1.1,c.78.1.1 104146,104147 2ax3A 502 4.41e+00 1i5sA 367 4.46e+00 1bg2 c.37.1.9 61822 1vquA 374 4.50e+00 1b73A 254 4.90e+00 1b74A c.78.2.1,c.78.2.1 35266,35267 1y80A 210 5.52e+00 1gadO 330 5.71e+00 1dssG c.2.1.3,d.81.1.1 29950,39865 1t3lA 337 6.16e+00 b.34.2.1,c.37.1.1 106358,106359 1paqA 189 6.27e+00 a.118.1.14 94413 1bs9 207 6.74e+00 1bs9 c.69.1.30 31330 1g66A 207 6.74e+00 1bs9 c.69.1.30 31329 1z5nA 242 6.85e+00 1wr2A 238 6.89e+00 1uufA 369 6.90e+00 b.35.1.2,c.2.1.1 100006,100007 5nul 138 6.96e+00 5nul c.23.5.1 31191 2bzpA 226 6.97e+00 1yizA 429 7.01e+00 1jqhA 308 7.16e+00 d.144.1.7 71793 2scuA 288 7.25e+00 2scuA c.2.1.8,c.23.4.1 30303,31131 1f2tB 148 8.44e+00 1f2tB 1ekxA 311 8.53e+00 3csuA c.78.1.1,c.78.1.1 35088,35089 1occG 84 8.70e+00 2occG f.23.2.1 43562 2fox 138 8.89e+00 5nul c.23.5.1 31197 1rd5A 262 8.94e+00 1oi7A 288 8.97e+00 c.2.1.8,c.23.4.1 87049,87050 2fvx 138 9.04e+00 5nul c.23.5.1 31200 2avnA 260 9.06e+00 1rypB 250 9.11e+00 1rypB d.153.1.4 41933 1i4jA 110 9.32e+00 d.55.1.1 76734 1zhaA 267 9.63e+00 1acmA 310 9.67e+00 3csuA c.78.1.1,c.78.1.1 35180,35181 1hxiA 121 9.97e+00 1hxiA a.118.8.1 61366 1hyuA 521 1.00e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1hyeA 313 1.04e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1sjdA 368 1.04e+01 c.1.11.2,d.54.1.1 105632,105633 2a5hA 416 1.04e+01 2cbf 234 1.10e+01 1cbf c.90.1.1 35588 3nll 138 1.10e+01 5nul c.23.5.1 31206 1fp2A 352 1.11e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1bxeA 113 1.12e+01 1bxeA d.55.1.1 38898 1fpxA 352 1.14e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1dmgA 225 1.18e+01 1dmgA c.22.1.1 31036 1a12A 413 1.20e+01 1a12A b.69.5.1 27663 1agrE 205 1.21e+01 1agrE a.91.1.1 18538 1wwkA 307 1.21e+01 1yiyA 429 1.22e+01 1b74A 254 1.22e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1u2eA 289 1.26e+01 1t8xA 267 1.30e+01 1vizA 240 1.32e+01 c.1.4.1 100784 1jr1A 514 1.36e+01 c.1.5.1,d.37.1.1,d.37.1.1 63241,63242,63243 1irk 306 1.39e+01 1fmk d.144.1.7 41703 2gtsA 86 1.39e+01 1ibvB 229 1.43e+01 2nadA 393 1.46e+01 2nadA c.2.1.4,c.23.12.1 30090,31350 1e8xA 961 1.50e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 2dln 306 1.52e+01 1iow c.30.1.2,d.142.1.1 31715,41483 2nacA 393 1.55e+01 2nadA c.2.1.4,c.23.12.1 30088,31348 1bkjA 240 1.59e+01 1bkjA d.90.1.1 40243 1y81A 138 1.60e+01 2fz0A 149 1.67e+01 1ye8A 178 1.68e+01 1e8yA 966 1.70e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1d1gA 168 1.71e+01 1d1gA c.71.1.1 34889 1qjcA 158 1.73e+01 1b6tA c.26.1.3 63328 3csuA 310 1.74e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 1fxqA 267 1.74e+01 1d9eA c.1.10.4 60108 1yobA 179 1.74e+01 1fxpA 267 1.74e+01 1d9eA c.1.10.4 60106 1b6tA 159 1.75e+01 1b6tA c.26.1.3 31600 1fwsA 267 1.76e+01 1d9eA c.1.10.4 60063 1qqcA 773 1.76e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1lroA 267 1.77e+01 c.1.10.4 78161 2g76A 335 1.78e+01 1pswA 348 1.80e+01 c.87.1.7 88287 1jcxA 267 1.81e+01 c.1.10.4 66510 1g99A 408 1.82e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1y60A 169 1.83e+01 1wj9A 211 1.84e+01 1xeaA 323 1.85e+01 c.2.1.3,d.81.1.5 109572,109573 1p4oA 322 1.87e+01 d.144.1.7 87775 1f9vA 347 1.87e+01 1bg2 c.37.1.9 59745 1g6oA 330 1.89e+01 1g6oA c.37.1.11 32430 1pe1A 267 1.90e+01 c.1.10.4 94591 2ffeA 311 1.93e+01 1p0hA 318 1.96e+01 d.108.1.1 93866 2b4wA 315 2.01e+01 1qguA 478 2.01e+01 1qguA c.92.2.3 35625 1h1lA 481 2.02e+01 c.92.2.3 70851 1ju3A 583 2.04e+01 b.18.1.13,c.69.1.21 67300,67301 1pea 385 2.13e+01 1pea c.93.1.1 35662 1cz3A 168 2.13e+01 1d1gA c.71.1.1 34891 1bglA 1023 2.15e+01 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 1itkA 731 2.19e+01 a.93.1.3,a.93.1.3 71417,71418 1xwfA 431 2.22e+01 1gg4A 452 2.23e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 1pysB 785 2.26e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16299,16300,25311,39310,40779,41455 1ggvA 232 2.27e+01 1din c.69.1.9 34683 1wyuB 474 2.28e+01 2c27A 315 2.28e+01 1eudA 311 2.30e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 2f1kA 279 2.32e+01 2g0qA 173 2.32e+01 1dvjA 246 2.33e+01 1dvjA c.1.2.3 28546 1qh8A 478 2.33e+01 1qguA c.92.2.3 35633 1u7lA 392 2.44e+01 1qmpA 130 2.46e+01 1dz3A c.23.1.1 31106 1v8bA 479 2.48e+01 1v54G 85 2.57e+01 f.23.2.1 100328 1pyaB 228 2.63e+01 1pyaB 2au3A 407 2.67e+01 1eucA 311 2.69e+01 2scuA c.2.1.8,c.23.4.1 30311,31139 1mjhA 162 2.71e+01 1mjhA c.26.2.4 31639 1mgtA 174 2.74e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1din 236 2.81e+01 1din c.69.1.9 34682 1x1zA 252 2.83e+01 1jx6A 342 2.84e+01 c.93.1.1 67406 1hkhA 279 2.89e+01 c.69.1.12 90628 1griA 217 2.91e+01 1griA b.34.2.1,b.34.2.1,d.93.1.1 24531,24532,40473 1nj4A 363 2.91e+01 b.105.1.1,e.3.1.1 80545,80546 1jysA 242 2.91e+01 c.56.2.1 77216 1mjhB 162 2.93e+01 1mjhA c.26.2.4 31640 1pz1A 333 2.96e+01 c.1.7.1 95390 1at1A 310 2.98e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 1ir3A 306 3.05e+01 1fmk d.144.1.7 41702 1bvzA 585 3.09e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21856,27783,28770 2gmyA 153 3.09e+01 1kl7A 514 3.12e+01 c.79.1.1 72678 1yqzA 438 3.22e+01 1dp0A 1023 3.24e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 1dvjC 246 3.27e+01 1dvjA c.1.2.3 28548 1zq1A 438 3.28e+01 1jz8A 1023 3.37e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1ji2A 585 3.43e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 1ypxA 375 3.48e+01 1dtyA 429 3.50e+01 1dtyA c.67.1.4 34495 1e94F 449 3.59e+01 1do0A c.37.1.20 32443 1b3oA 514 3.60e+01 1ak5 c.1.5.1 28640 1xuuA 349 3.61e+01 1snyA 267 3.61e+01 c.2.1.2 105833 1i6iA 366 3.64e+01 1bg2 c.37.1.9 61844 1aii 323 3.65e+01 1avc a.65.1.1 18150 1g9lA 144 3.66e+01 1g9lA a.144.1.1 60399 1bgyE 196 3.67e+01 1bgyE f.23.12.1 43683 1gqyA 475 3.71e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1iz0A 302 3.75e+01 b.35.1.2,c.2.1.1 83821,83822 1ynuA 473 3.79e+01 1t5hX 504 3.90e+01 e.23.1.1 106449 1yasA 257 3.91e+01 1qj4A c.69.1.20 34801 1sc6A 404 3.92e+01 1zi8A 236 3.92e+01 1b0vA 106 3.93e+01 1a6l d.58.1.2 38982 1vrbA 342 3.99e+01 1jb9A 316 4.04e+01 1fnc b.43.4.2,c.25.1.1 62840,62841 1vr3A 191 4.06e+01 8atcA 310 4.08e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 1przA 252 4.10e+01 d.265.1.3 95064 1iow 306 4.11e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1juk 248 4.22e+01 1a53 c.1.2.4 28567 1i8tA 367 4.26e+01 c.4.1.3,d.16.1.7 66094,66095 1d4fA 431 4.27e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1w4rA 195 4.31e+01 1y8aA 332 4.33e+01 1tgoA 773 4.33e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1ycyA 71 4.37e+01 1wdtA 665 4.37e+01 1wd5A 208 4.38e+01 1zbsA 291 4.40e+01 1axn 323 4.43e+01 1avc a.65.1.1 18149 1j7iA 264 4.44e+01 1j7iA d.144.1.6 62694 3kar 346 4.48e+01 1bg2 c.37.1.9 32198 1yrlA 491 4.48e+01 1d0qA 103 4.48e+01 1d0qA g.41.3.2 45208 1s0aA 429 4.57e+01 c.67.1.4 98263 1pq4A 291 4.58e+01 c.92.2.2 94995 2awaA 390 4.59e+01 7fd1A 106 4.60e+01 1a6l d.58.1.2 38953 2bs3C 256 4.61e+01 1b04A 318 4.63e+01 1b04A d.142.2.2 41579 1qhtA 775 4.68e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1vhxA 150 4.75e+01 c.55.3.8 100712 1km4A 247 4.78e+01 c.1.2.3 72740 1q0sA 259 4.81e+01 c.66.1.28 95509 1zkiA 133 4.85e+01 1m5yA 408 4.85e+01 a.167.1.1,d.26.1.1,d.26.1.1 78664,78665,78666 1womA 271 4.86e+01 1m7bA 184 4.87e+01 c.37.1.8 74572 1ppjE 196 4.89e+01 b.33.1.1,f.23.12.1 104260,104261 1pinA 163 4.95e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1uheA 97 4.95e+01 1xnpA 202 4.95e+01 1gz8A 299 4.96e+01 d.144.1.7 83405 1aw1A 256 4.97e+01 1amk c.1.1.1 28515 1fdd 106 4.99e+01 1a6l d.58.1.2 38960 2as0A 396 5.02e+01 1v1aA 309 5.04e+01 c.72.1.1 100249 1hruA 188 5.07e+01 1hruA d.115.1.1 40926 1y0eA 223 5.07e+01 1e1xA 299 5.08e+01 1hcl d.144.1.7 59157 2c71A 216 5.14e+01 1xbtA 193 5.17e+01 1v8gA 329 5.20e+01 a.46.2.1,c.27.1.1 100505,100506 1xsnA 335 5.20e+01 1ltzA 297 5.26e+01 d.178.1.1 74254 1m1nA 491 5.28e+01 c.92.2.3 78417 2bfwA 200 5.33e+01 1b8qA 127 5.33e+01 1qauA b.36.1.1 24781 1a53 247 5.33e+01 1a53 c.1.2.4 28564 3minC 491 5.37e+01 1qguA c.92.2.3 35607 1b7fA 168 5.41e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1va4A 279 5.45e+01 c.69.1.12 108458 1p4fA 293 5.46e+01 d.144.1.7 104063 1m56B 264 5.52e+01 b.6.1.2,f.17.2.1 74472,74473 1kxlA 199 5.61e+01 b.40.4.3 73155 1crwG 333 5.61e+01 1dssG c.2.1.3,d.81.1.1 30026,39941 1fp4A 492 5.62e+01 c.92.2.3 76187 1dkrA 317 5.64e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1dapA 320 5.65e+01 1dapA c.2.1.3,d.81.1.3 30053,39968 1p3dA 475 5.66e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2b4aA 138 5.70e+01 1p2xA 159 5.71e+01 a.40.1.1 104062 1qj4A 257 5.73e+01 1qj4A c.69.1.20 34796 1ns5A 155 5.76e+01 c.116.1.3 80705 2occG 84 5.77e+01 2occG f.23.2.1 43522 2d2mD 145 5.79e+01 2apjA 260 5.81e+01 1bjwA 382 5.85e+01 1bjwA c.67.1.1 34349 1rhs 296 5.90e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1eztA 166 5.92e+01 1agrE a.91.1.1 18541 1qlaC 256 5.95e+01 1qlaC f.21.2.1 43722 2afcA 168 6.00e+01 1wab 232 6.11e+01 1wab c.23.10.3 31341 1lkcA 364 6.12e+01 c.67.1.1 73978 2f6uA 234 6.12e+01 1a1s 314 6.12e+01 1othA c.78.1.1,c.78.1.1 35258,35259 1rq2A 382 6.13e+01 c.32.1.1,d.79.2.1 105048,105049 2minA 491 6.17e+01 1qguA c.92.2.3 35609 1u8vA 490 6.18e+01 1xm9A 457 6.22e+01 1yyaA 250 6.22e+01 1es9A 232 6.26e+01 1wab c.23.10.3 31340 1b3rA 431 6.28e+01 1b3rA c.2.1.4,c.23.12.3 30106,31366 1s7zA 117 6.33e+01 a.159.3.1 98715 2bb3A 221 6.38e+01 1awcA 110 6.41e+01 1awcA a.4.5.21 16167 2abqA 306 6.44e+01 1qe5A 266 6.45e+01 1b8oA c.56.2.1 33784 1qj5A 429 6.46e+01 1dtyA c.67.1.4 34493 1ml4A 308 6.49e+01 c.78.1.1,c.78.1.1 79255,79256 1o0iA 138 6.57e+01 d.38.1.5 86532 1qvaA 223 6.59e+01 1qvaA c.37.1.19 32411 1efaA 333 6.60e+01 1tlfA a.35.1.5,c.93.1.1 17106,35691 1sxvA 172 6.61e+01 1vb3A 428 6.63e+01 1o97C 264 6.64e+01 c.26.2.3 81232 1lnsA 763 6.68e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1ewaA 137 6.69e+01 1ewaA a.1.1.2 15639 1wy6A 172 6.71e+01 1m7yA 435 6.79e+01 c.67.1.4 78761 1kmdA 117 6.81e+01 d.189.1.1 72744 1cm7A 363 6.86e+01 1cnzA c.77.1.1 35063 1ly7A 121 6.87e+01 d.82.2.1 74339 1yq2A 1024 6.89e+01 2a0fA 310 6.90e+01 1t0iA 191 7.01e+01 c.23.5.4 106209 1ok7A 366 7.03e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1a04A 215 7.04e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1dgjA 907 7.15e+01 1alo a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 17909,37694,38585,41415 2a11A 242 7.16e+01 1w36D 608 7.19e+01 1g26A 31 7.23e+01 1g26A g.3.16.1 44381 1xqoA 256 7.25e+01 2bcqA 335 7.28e+01 2c2qA 199 7.29e+01 1pu1A 94 7.30e+01 d.266.1.1 104307 1cpcA 162 7.35e+01 1cpcA a.1.1.3 15643 1wzlA 585 7.37e+01 2fg1A 158 7.37e+01 1igs 248 7.37e+01 1a53 c.1.2.4 28565 1jvpP 298 7.38e+01 d.144.1.7 67371 1xklA 273 7.40e+01 1i52A 236 7.43e+01 1i52A c.68.1.13 61767 1xv2A 237 7.45e+01 1h2rS 267 7.52e+01 2frvA e.19.1.1 43310 1ub0A 258 7.52e+01 c.72.1.2 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