# 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 2bkqA 212 3.77e-01 1euvA 221 5.79e-01 1euvA d.3.1.7 37133 1udxA 416 8.40e-01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 1fhuA 320 9.59e-01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1fhvA 323 9.90e-01 1fhuA c.1.11.2,d.54.1.1 29235,38879 1r6wA 322 1.07e+00 c.1.11.2,d.54.1.1 97165,97166 1dc1A 323 1.30e+00 1dc1A c.52.1.11 33321 1mkp 144 1.81e+00 1vhrA c.45.1.1 32654 1nfiC 301 1.95e+00 b.1.18.1,b.2.5.3 21943,22456 1nfiA 301 1.97e+00 1a3qA b.1.18.1,b.2.5.3 21942,22455 2bkrA 212 2.00e+00 1iknA 286 2.13e+00 1a3qA b.1.18.1,b.2.5.3 21936,22449 1ih7A 903 2.46e+00 1clqA c.55.3.5,e.8.1.1 62375,62376 1uwzA 136 3.15e+00 c.97.1.1 108081 1fchA 368 3.16e+00 1fchA a.118.8.1 19212 1wa3A 205 3.36e+00 1rjdA 334 3.63e+00 c.66.1.37 97558 1xt9A 212 3.64e+00 1jx4A 352 3.87e+00 d.240.1.1,e.8.1.7 90378,90379 1t0iA 191 3.93e+00 c.23.5.4 106209 1wsrA 375 4.30e+00 1vlwA 217 4.45e+00 c.1.10.1 108868 1bh6A 274 4.59e+00 1gci c.41.1.1 32487 1iv0A 98 4.71e+00 c.55.3.8 90706 2g6bA 180 4.72e+00 1y74A 57 4.77e+00 2b49A 287 4.83e+00 1tiiD 99 5.05e+00 1tiiD b.40.2.1 24965 1pysB 785 5.29e+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 16299,16300,25311,39310,40779,41455 1qb5D 99 5.43e+00 b.40.2.1 88357 1ah2 269 5.52e+00 1gci c.41.1.1 32542 1jrkA 156 5.57e+00 d.113.1.1 71827 1vicA 262 5.82e+00 c.68.1.13 100756 1qaxA 428 6.06e+00 1qaxA d.58.20.1,d.179.1.1 39376,42597 1nozA 388 6.13e+00 1clqA c.55.3.5 33715 1s01 283 6.15e+00 1gci c.41.1.1 32511 2a7kA 250 6.57e+00 1avt 274 6.62e+00 1gci c.41.1.1 32488 1i88A 389 6.66e+00 c.95.1.2,c.95.1.2 66070,66071 1a2q 275 6.69e+00 1gci c.41.1.1 32512 1aqn 275 6.87e+00 1gci c.41.1.1 32514 1ak9 275 6.92e+00 1gci c.41.1.1 32517 1hnoA 280 7.26e+00 1hnoA c.14.1.3 61095 2fm8A 135 7.33e+00 5nul 138 7.87e+00 5nul c.23.5.1 31191 3nll 138 7.88e+00 5nul c.23.5.1 31206 1qhtA 775 7.89e+00 1tgoA c.55.3.5,e.8.1.1 33722,43011 1clqA 903 8.05e+00 1clqA c.55.3.5,e.8.1.1 33717,43006 1sup 275 8.27e+00 1gci c.41.1.1 32510 1wbpA 397 8.45e+00 1r31A 428 8.47e+00 d.58.20.1,d.179.1.1 96897,96898 1x6oA 174 8.61e+00 b.34.5.2,b.40.4.5 109493,109494 2fvx 138 8.68e+00 5nul c.23.5.1 31200 1tuoA 464 8.69e+00 1nnwA 252 8.99e+00 d.159.1.5 80674 1im4A 221 9.02e+00 e.8.1.7 62581 2wsyA 268 9.20e+00 2tysA c.1.2.4 28588 2aynA 404 9.22e+00 1hq0A 295 9.39e+00 1hzgA d.194.1.1 61122 1p90A 145 9.51e+00 c.55.5.2 94377 1zclA 180 9.66e+00 1lw6E 281 9.93e+00 c.41.1.1 74293 1gci 269 9.93e+00 1gci c.41.1.1 32503 1hzgA 295 9.95e+00 1hzgA d.194.1.1 61436 1to2E 281 9.99e+00 1cseE 274 1.02e+01 1gci c.41.1.1 32481 2ap1A 327 1.04e+01 1q8yA 373 1.06e+01 d.144.1.7 96234 1gg1A 350 1.07e+01 1qr7A c.1.10.4 29187 1ltdA 506 1.10e+01 1gox c.1.4.1,d.120.1.1 28618,41086 2eu9A 355 1.12e+01 1zxfA 155 1.17e+01 1noyA 388 1.18e+01 1clqA c.55.3.5 33713 2g8yA 385 1.21e+01 1ufhA 180 1.24e+01 d.108.1.1 88485 1zrzA 364 1.30e+01 1y88A 199 1.30e+01 1yzbA 182 1.33e+01 1uptC 170 1.34e+01 c.37.1.8 99769 1x24A 180 1.35e+01 1ii6A 368 1.35e+01 1bg2 c.37.1.9 62413 1ayoA 130 1.35e+01 1ayoA b.2.4.1 22431 1yu6A 275 1.36e+01 1vkxA 273 1.37e+01 1a3qA b.1.18.1,b.2.5.3 21941,22454 1qayA 428 1.40e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 2dg5B 190 1.42e+01 1jtkA 136 1.43e+01 c.97.1.1 71862 1oltA 457 1.44e+01 c.1.28.2 93334 1gc5A 467 1.44e+01 1gc5A c.72.1.3 60429 1zo0A 126 1.48e+01 2fpmA 322 1.49e+01 1r0rE 274 1.52e+01 c.41.1.1 96735 1qcwA 410 1.56e+01 1gox c.1.4.1 28622 1hnuA 280 1.57e+01 1hnoA c.14.1.3 61096 1zckA 154 1.59e+01 1jm1A 204 1.60e+01 b.33.1.1 71745 1rxdA 159 1.62e+01 1yw5A 177 1.64e+01 1z08A 170 1.67e+01 1svdM 110 1.70e+01 1fcbA 511 1.75e+01 1gox c.1.4.1,d.120.1.1 28620,41087 2h1tA 188 1.76e+01 1qqcA 773 1.77e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1o2dA 371 1.80e+01 e.22.1.2 86591 1g6oA 330 1.81e+01 1g6oA c.37.1.11 32430 1wrmA 165 1.81e+01 1bv8A 138 1.81e+01 1ayoA b.2.4.1 22430 2kinA 238 1.83e+01 1bg2 c.37.1.9 32190 1k2eA 156 1.84e+01 d.113.1.1 72010 1n8fA 350 1.86e+01 c.1.10.4 85397 1u5tC 202 1.86e+01 a.4.5.54,a.4.5.54 107688,107689 1k26A 156 1.86e+01 d.113.1.1 72003 1on0A 158 1.89e+01 d.108.1.1 87095 2az4A 429 1.93e+01 1howA 373 2.02e+01 1hcl d.144.1.7 41679 1vpqA 273 2.12e+01 1qfjA 232 2.18e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1qr7A 350 2.22e+01 1qr7A c.1.10.4 29191 1tum 129 2.24e+01 1tum d.113.1.1 40922 1lehA 364 2.24e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1xsjA 778 2.27e+01 1q52A 314 2.36e+01 c.14.1.3 95846 1odzA 386 2.36e+01 c.1.8.3 86889 2agaA 190 2.43e+01 3cla 213 2.47e+01 3cla c.43.1.1 32610 2cxxA 190 2.50e+01 2f2hA 773 2.53e+01 2tysA 268 2.57e+01 2tysA c.1.2.4 28572 1p8xA 344 2.64e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1o1yA 239 2.65e+01 c.23.16.1 86554 1bdfA 235 2.66e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1b07A 59 2.68e+01 1ckaA b.34.2.1 24461 1xrtA 467 2.69e+01 1ckaA 57 2.71e+01 1ckaA b.34.2.1 24459 1i82A 189 2.75e+01 1i82A b.1.9.2 61937 1i8aA 189 2.75e+01 1i82A b.1.9.2 61951 1bksA 268 2.78e+01 2tysA c.1.2.4 28585 1ek9A 428 2.78e+01 1ek9A f.5.1.1 43809 1u7zA 226 2.79e+01 1vdrA 162 2.90e+01 1vdrA c.71.1.1 34893 1x88A 359 2.91e+01 1j9yA 385 2.96e+01 1j9yA c.1.8.3 62791 1em8A 147 3.00e+01 c.128.1.1 90457 2a10A 125 3.06e+01 1yadA 221 3.09e+01 1gw1A 376 3.12e+01 c.1.8.3 76361 1pjhA 280 3.17e+01 c.14.1.3 94761 2f7fA 494 3.41e+01 2fox 138 3.42e+01 5nul c.23.5.1 31197 1lzlA 323 3.42e+01 c.69.1.2 78306 1kbjA 412 3.44e+01 c.1.4.1 72280 2d00A 109 3.51e+01 1z6nA 167 3.55e+01 1qopA 268 3.55e+01 2tysA c.1.2.4 28570 1jhgA 101 3.56e+01 1jhgA a.4.12.1 19009 2aq4A 434 3.64e+01 2fn0A 437 3.64e+01 1lam 484 3.66e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1rybA 212 3.67e+01 c.56.3.1 98098 1bcpC 199 3.71e+01 1bcpB b.40.2.1,d.169.1.2 25121,42430 1a05A 358 3.81e+01 1cnzA c.77.1.1 35059 1vbkA 307 3.85e+01 1vl4A 447 3.87e+01 d.283.1.1 108718 1ofuX 119 3.95e+01 c.37.1.22 86976 2ag9A 164 4.00e+01 1mo2A 294 4.03e+01 c.69.1.22 79331 2gf9A 189 4.04e+01 1vlaA 150 4.05e+01 d.227.1.2 108735 1gw5S 142 4.08e+01 d.110.4.2 70633 1pgs 314 4.09e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 1kfcA 268 4.09e+01 c.1.2.4 77371 1hywA 68 4.13e+01 1hywA d.186.1.1 61425 1lap 488 4.16e+01 1lam c.50.1.1,c.56.5.3 33171,33834 1bllE 488 4.17e+01 1lam c.50.1.1,c.56.5.3 33170,33833 1xb4A 202 4.22e+01 1j0dA 341 4.30e+01 c.79.1.1 83902 1iuqA 367 4.30e+01 c.112.1.1 90703 2b0aA 186 4.35e+01 1poiB 260 4.35e+01 1poiB c.124.1.3 34155 1rj9A 304 4.55e+01 a.24.13.1,c.37.1.10 97553,97554 1u9cA 224 4.64e+01 1k1gA 131 4.65e+01 d.51.1.1 68015 1cskA 71 4.68e+01 1ckaA b.34.2.1 24513 1ooeA 236 4.82e+01 c.2.1.2 87196 1lnsA 763 4.84e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1u0mA 382 4.86e+01 c.95.1.2,c.95.1.2 107557,107558 1ox0A 430 4.88e+01 c.95.1.1,c.95.1.1 87495,87496 1yh3A 256 4.92e+01 1k30A 368 4.99e+01 c.112.1.1 68067 1wosA 364 5.01e+01 b.44.2.1,d.250.1.1 109468,109469 1eeoA 321 5.09e+01 1pty c.45.1.2 32655 1bqcA 302 5.09e+01 1bqcA c.1.8.3 28831 2gtrA 261 5.10e+01 1sh7A 284 5.10e+01 1aax 321 5.10e+01 1pty c.45.1.2 32657 1mpxA 615 5.11e+01 b.18.1.13,c.69.1.21 85041,85042 1ptvA 321 5.12e+01 1pty c.45.1.2 32665 1bg2 325 5.13e+01 1bg2 c.37.1.9 32189 1v54J 59 5.13e+01 f.23.4.1 100331 2occJ 59 5.13e+01 2occJ f.23.4.1 43524 1nrjB 218 5.13e+01 c.37.1.8 86125 1ar61 302 5.15e+01 1pov1 1eo1A 124 5.17e+01 1eo1A c.55.5.1 33739 1z9zA 60 5.17e+01 1al21 302 5.18e+01 1pov1 1uj0A 62 5.25e+01 b.34.2.1 99449 1taq 832 5.26e+01 1taq a.60.7.1,c.120.1.2,c.55.3.5,e.8.1.1 18082,33352,33698,42991 2cu1A 103 5.26e+01 1e6fA 143 5.27e+01 1e6fA b.64.1.1 59304 1g13A 162 5.27e+01 1g13A b.95.1.1 60194 1vljA 407 5.33e+01 e.22.1.2 108832 2hnp 321 5.34e+01 1pty c.45.1.2 32678 1uptA 171 5.34e+01 c.37.1.8 99767 1a5y 330 5.34e+01 1pty c.45.1.2 32673 1dkgD 383 5.37e+01 1ba1 c.55.1.1,c.55.1.1 33427,33428 1jegA 83 5.38e+01 b.34.2.1 66610 1w15A 153 5.48e+01 b.7.1.2 109041 1aj2 282 5.52e+01 1aj2 c.1.21.1 29665 1pty 321 5.53e+01 1pty c.45.1.2 32656 2f57A 317 5.60e+01 2gx9A 129 5.71e+01 1pme 380 5.71e+01 1hcl d.144.1.7 41653 1wthD 391 5.78e+01 1zkrA 153 5.79e+01 1acf 125 5.79e+01 3nul d.110.1.1 40882 1trrA 107 5.84e+01 1jhgA a.4.12.1 19017 1f2dA 341 5.84e+01 1f2dA c.79.1.1 35298 1id1A 153 5.85e+01 1id1A c.2.1.9 62286 1xviA 275 5.85e+01 1qcrA 446 5.85e+01 1be3A d.185.1.1,d.185.1.1 59025,59026 2wrpR 107 5.90e+01 1jhgA a.4.12.1 19010 1wnaA 131 5.91e+01 1txoA 237 6.10e+01 1imjA 210 6.13e+01 c.69.1.23 71246 1fztA 211 6.15e+01 1qhfA c.60.1.1 60158 2adzA 178 6.17e+01 1m4jA 142 6.20e+01 d.109.1.2 78602 4tmkA 213 6.25e+01 5tmpA c.37.1.1 31930 1pu5A 164 6.26e+01 b.95.1.1 104310 1ep3A 311 6.32e+01 2dorA c.1.4.1 28597 1fbtA 190 6.32e+01 1bif c.60.1.4 34004 1jl0A 334 6.40e+01 1jenA d.156.1.1 63155 1vloA 381 6.45e+01 b.44.2.1,d.250.1.1 108838,108839 1gpmA 525 6.46e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 5tmpA 213 6.50e+01 5tmpA c.37.1.1 31931 1zxuA 217 6.52e+01 1aj0 282 6.65e+01 1aj2 c.1.21.1 29667 1h8gA 95 6.69e+01 b.109.1.1 65735 1zpyA 95 6.75e+01 2c71A 216 6.77e+01 2b7aA 293 6.80e+01 2b81A 323 6.82e+01 1whsB 153 6.83e+01 1whtB 1whtB 153 6.83e+01 1whtB 1xp8A 366 6.84e+01 1wy5A 317 6.91e+01 1q0bA 367 6.95e+01 c.37.1.9 95502 1b7yB 785 6.97e+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 16301,16302,25312,39311,40780,41456 1kcqA 104 6.97e+01 d.109.1.1 68449 1xa1A 255 7.07e+01 e.3.1.1 109529 1i7qB 193 7.10e+01 1qdlB c.23.16.1 61902 2cfuA 658 7.12e+01 2f7tA 227 7.13e+01 1g19A 350 7.16e+01 2reb c.37.1.11,d.48.1.1 32284,38770 1qqtA 551 7.19e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 1hxs1 302 7.23e+01 2a0kA 161 7.23e+01 2f2tA 161 7.23e+01 1u02A 239 7.24e+01 c.108.1.15 107538 1mi3A 322 7.25e+01 c.1.7.1 91274 1k8cA 322 7.26e+01 c.1.7.1 72172 1xkzA 255 7.29e+01 2f62A 161 7.38e+01 1oxkB 134 7.44e+01 c.23.1.1 93691 2aplA 157 7.49e+01 2cayA 145 7.59e+01 1p57A 114 7.63e+01 d.170.1.2 94125 1lba 146 7.66e+01 1lba d.118.1.1 41062 1i7qA 519 7.67e+01 1qdlA d.161.1.1 61901 1wguA 136 7.70e+01 1be3A 446 7.70e+01 1be3A d.185.1.1,d.185.1.1 58950,58951 1hh1A 143 7.74e+01 1gefA c.52.1.18 61036 2gqrA 237 7.77e+01 1dpjA 329 7.78e+01 1smrA b.50.1.2 26828 1f4lA 551 7.82e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1xm7A 195 7.86e+01 1d5cA 162 7.86e+01 1ctqA c.37.1.8 32021 1pfvA 551 7.88e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1yloA 348 7.92e+01 1vjzA 341 7.93e+01 c.1.8.3 100838 1ar71 302 7.95e+01 1pov1 1yr2A 741 7.99e+01 1k0fA 277 8.18e+01 c.92.2.2 71974 1sqhA 312 8.23e+01 d.108.1.5 98966 1yqeA 282 8.26e+01 2ag4A 164 8.30e+01 1aoxA 203 8.32e+01 1aoxA c.62.1.1 34151 1pprM 312 8.33e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1t95A 240 8.37e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1cz6A 25 8.41e+01 j.3.1.3 46072 1iyxA 432 8.41e+01 c.1.11.1,d.54.1.1 83815,83816 1vraB 215 8.46e+01 1yz4A 160 8.46e+01 1huuA 90 8.47e+01 1huuA a.55.1.1 17897 1uwdA 103 8.69e+01 1ad4A 266 8.71e+01 1aj2 c.1.21.1 29670 1i86A 389 8.74e+01 c.95.1.2,c.95.1.2 66068,66069 1ad1A 266 8.75e+01 1aj2 c.1.21.1 29668 1toaA 313 8.79e+01 1toaA c.92.2.2 35598 2b6nA 278 8.79e+01 1tgoA 773 8.81e+01 1tgoA c.55.3.5,e.8.1.1 33721,43010 1hcxA 127 8.84e+01 b.109.1.1 65800 1bcsB 160 8.84e+01 1whtB 1pov1 302 8.86e+01 1pov1 1aroL 151 8.87e+01 1lba d.118.1.1 41063 1qz9A 416 8.88e+01 c.67.1.3 96621 1e2tA 284 8.97e+01 1e2tA d.3.1.5 37121