# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1u9yA 284 1.25e-01 1uqrA 154 5.75e-01 c.23.13.1 99779 1vqoO 116 1.27e+00 1ps9A 671 1.30e+00 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1xr4A 509 1.43e+00 1jj2N 115 1.83e+00 1ffkL c.12.1.1 63099 1o9rA 162 1.84e+00 a.25.1.1 86706 1o94A 729 1.99e+00 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 2dhqA 146 2.02e+00 2dhqA c.23.13.1 31382 1s72O 116 2.07e+00 c.12.1.1 105334 1vaoA 560 2.51e+00 1qltA d.58.32.1,d.145.1.1 39461,41724 1h05A 146 2.72e+00 c.23.13.1 76433 1q7rA 219 2.79e+00 c.23.16.1 96054 1i5nA 146 2.87e+00 1i5nA a.24.10.3 61805 1djnA 729 3.07e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1nfp 228 3.19e+00 1nfp c.1.16.2 29555 1w1kA 560 3.25e+00 d.58.32.1,d.145.1.1 109059,109060 1djqA 729 3.38e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1to3A 304 3.79e+00 c.1.10.1 107161 3pga1 337 3.80e+00 4pgaA 1qltA 560 4.15e+00 1qltA d.58.32.1,d.145.1.1 39457,41720 2tmdA 729 4.26e+00 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1wc9A 169 4.43e+00 1l4uA 176 5.05e+00 c.37.1.2 73568 1fzqA 181 5.18e+00 1hurA c.37.1.8 32060 1i8tA 367 5.78e+00 c.4.1.3,d.16.1.7 66094,66095 1e8gA 560 6.51e+00 1qltA d.58.32.1,d.145.1.1 39455,41718 2a0b 125 6.69e+00 2a0b a.24.10.1 16630 1vpgA 192 7.20e+00 1f89A 291 7.73e+00 d.160.1.1 64988 1eh9A 558 8.38e+00 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 4pgaA 337 8.40e+00 4pgaA c.88.1.1 35565 1qksA 567 9.09e+00 1qksA a.3.1.2,b.70.2.1 15951,27710 1i60A 278 9.13e+00 c.1.15.4 71118 1aoqA 567 9.31e+00 1qksA a.3.1.2,b.70.2.1 15934,27692 1jndA 420 9.39e+00 c.1.8.5,d.26.3.1 71757,71758 1dorA 311 9.87e+00 2dorA c.1.4.1 28595 1ypfA 336 1.11e+01 2dorA 311 1.11e+01 2dorA c.1.4.1 28593 1q1gA 276 1.14e+01 c.56.2.1 95574 1ex1A 605 1.15e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1vjgA 218 1.16e+01 c.23.10.6 100810 1khyA 148 1.20e+01 a.174.1.1 77410 1r4vA 171 1.22e+01 a.197.1.1 97049 1gjwA 637 1.26e+01 b.71.1.1,c.1.8.1 60582,60583 1r5rA 119 1.31e+01 a.39.2.1 97104 1x38A 602 1.32e+01 1n7oA 721 1.32e+01 a.102.3.2,b.24.1.1,b.30.5.2 80259,80260,80261 1sz7A 200 1.40e+01 1bpb 248 1.48e+01 1bpyA a.60.12.1,d.218.1.2 75811,75812 1glqA 209 1.49e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 1tzjA 338 1.50e+01 1im5A 180 1.51e+01 c.33.1.3 66211 1iexA 605 1.52e+01 c.1.8.7,c.23.11.1 66127,66128 1mdwA 328 1.53e+01 d.3.1.3 84934 1w77A 228 1.55e+01 1wwiA 148 1.55e+01 1jubA 311 1.63e+01 c.1.4.1 90908 1vdeA 454 1.65e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 2bsxA 253 1.69e+01 2g8lA 299 1.76e+01 1pa7A 130 1.80e+01 a.40.1.1 94410 1ehaA 558 1.86e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21859,27786,28773 1bxkA 355 1.90e+01 1bxkA c.2.1.2 29803 1nftA 329 1.98e+01 1nnt c.94.1.2 35881 1meoA 209 1.98e+01 c.65.1.1 79035 1tv9A 335 1.98e+01 1sazA 381 1.99e+01 1vixA 420 2.00e+01 c.56.5.4,d.58.19.1 100777,100778 1php 394 2.05e+01 16pk c.86.1.1 35452 1uk8A 282 2.09e+01 c.69.1.10 107907 1w0mA 226 2.12e+01 c.1.1.1 109027 1mejA 223 2.12e+01 c.65.1.1 79029 1dpsD 167 2.12e+01 1dpsA a.25.1.1 16719 1ezwA 349 2.15e+01 1ezwA c.1.16.3 29558 1oj6A 151 2.16e+01 a.1.1.2 93088 2fji1 399 2.22e+01 1gjuA 637 2.26e+01 b.71.1.1,c.1.8.1 60580,60581 1yarA 233 2.33e+01 1aomA 567 2.35e+01 1qksA b.70.2.1 27694 1t3gA 159 2.36e+01 1ispA 181 2.39e+01 c.69.1.18 76778 1hyeA 313 2.41e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 2bijA 305 2.42e+01 1oxxK 353 2.50e+01 b.40.6.3,c.37.1.12 93715,93716 2bvlA 543 2.51e+01 1b57A 358 2.52e+01 1dosA c.1.10.2 29177 1fnoA 417 2.54e+01 d.58.19.1,c.56.5.4 70145,75841 1iupA 282 2.57e+01 c.69.1.10 76815 1vdxA 184 2.61e+01 1kagA 173 2.67e+01 c.37.1.2 72249 1bpyA 335 2.67e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1qd1A 325 2.79e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1dpsA 167 2.83e+01 1dpsA a.25.1.1 16716 1yacA 208 2.87e+01 1yacA c.33.1.3 31757 1i6wA 181 2.90e+01 1i6wA c.69.1.18 61859 1wy1A 172 2.90e+01 1gudA 288 2.93e+01 c.93.1.1 83326 1tfaA 329 2.95e+01 1nnt c.94.1.2 35880 1u2zA 433 3.01e+01 c.66.1.31 107626 1edt 271 3.02e+01 2ebn c.1.8.5 28993 1oxsC 353 3.06e+01 b.40.6.3,c.37.1.12 87519,87520 1xyzA 347 3.08e+01 1taxA c.1.8.3 28804 1q1fA 151 3.09e+01 a.1.1.2 104476 1hjxA 362 3.15e+01 c.1.8.5,d.26.3.1 83512,83513 2bneA 241 3.18e+01 1n1mA 728 3.19e+01 b.70.3.1,c.69.1.24 79815,79816 1pbe 394 3.21e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1e15A 499 3.21e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 27810,29006,38440 2phh 394 3.22e+01 1pbe c.3.1.2,d.16.1.2 30353,37884 1xsvA 113 3.23e+01 1h0oA 390 3.24e+01 a.25.1.2 70845 1ej1A 190 3.27e+01 1ejhA d.86.1.1 40144 1bgj 394 3.29e+01 1pbe c.3.1.2,d.16.1.2 30352,37883 1dosA 358 3.33e+01 1dosA c.1.10.2 29175 1c93A 265 3.35e+01 2ebn c.1.8.5 28998 2c07A 285 3.36e+01 1sg6A 393 3.42e+01 e.22.1.1 105522 2f6hX 419 3.44e+01 1txvB 440 3.45e+01 1pnbB 75 3.55e+01 1pnbB 1fxpA 267 3.56e+01 1d9eA c.1.10.4 60106 1rpl 251 3.57e+01 1bpyA a.60.12.1,d.218.1.2 75933,75934 1a54A 321 3.61e+01 1ixh c.94.1.1 35763 1fxqA 267 3.65e+01 1d9eA c.1.10.4 60108 1x3lA 440 3.70e+01 1llnA 262 3.72e+01 d.165.1.1 84625 1o70A 324 3.82e+01 b.118.1.1,b.118.1.1 81115,81116 1j0aA 325 3.88e+01 c.79.1.1 83871 1ib2A 349 3.89e+01 1ib2A a.118.1.8 62141 1dqrA 557 3.91e+01 1dqrA c.80.1.2 35305 1jfvA 131 3.92e+01 c.44.1.1 66654 1lxkA 721 3.93e+01 a.102.3.2,b.24.1.1,b.30.5.2 74331,74332,74333 1lucA 355 3.97e+01 1lucA c.1.16.1 29547 2b6cA 220 3.98e+01 1goiA 499 4.02e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1zuwA 272 4.05e+01 1k0wA 231 4.13e+01 c.74.1.1 77220 1lroA 267 4.17e+01 c.1.10.4 78161 1mioB 458 4.17e+01 1qguB c.92.2.3 35602 1vgjA 184 4.24e+01 1izcA 339 4.25e+01 c.1.12.5 83838 1aqwA 209 4.26e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 1ykjA 394 4.29e+01 1eguA 731 4.35e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1zhaA 267 4.39e+01 1t0iA 191 4.40e+01 c.23.5.4 106209 1ixh 321 4.44e+01 1ixh c.94.1.1 35761 1x42A 232 4.50e+01 1wpoA 256 4.51e+01 1lay b.57.1.1 27012 1e6pA 499 4.52e+01 1e15A b.72.2.1,c.1.8.5,d.26.3.1 59314,59315,59316 1dpgA 485 4.53e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 2dpg 485 4.54e+01 1dpgA c.2.1.3,d.81.1.5 30076,39991 1jcxA 267 4.56e+01 c.1.10.4 66510 1qghA 156 4.63e+01 1qghA a.25.1.1 16728 2cbuA 468 4.65e+01 1dkrA 317 4.68e+01 1dkuA c.61.1.2,c.61.1.2 34114,34115 1gqoQ 143 4.72e+01 c.23.13.1 76311 1l8bA 190 4.78e+01 d.86.1.1 73683 1aurA 218 4.83e+01 1auoA c.69.1.14 34718 1v1rB 342 4.88e+01 c.36.1.7,c.48.1.2 108273,108274 1a4uA 254 4.91e+01 1b16A c.2.1.2 29878 1olsB 342 4.93e+01 c.36.1.7,c.48.1.2 93332,93333 1viwB 198 4.93e+01 1led b.29.1.1 24170 1w9yA 319 4.97e+01 1mkmA 249 5.03e+01 a.4.5.33,d.110.2.2 79242,79243 1wwkA 307 5.05e+01 1x7yB 342 5.07e+01 1ycoA 279 5.07e+01 1on0A 158 5.08e+01 d.108.1.1 87095 1knqA 175 5.13e+01 c.37.1.17 72786 1a59 378 5.22e+01 1aj8A a.103.1.1 18902 1hrhA 136 5.25e+01 1rthA c.55.3.1 33577 1nom 248 5.25e+01 1bpyA a.60.12.1,d.218.1.2 75929,75930 1uz1A 468 5.27e+01 1b73A 254 5.28e+01 1b74A c.78.2.1,c.78.2.1 35266,35267 1amuA 563 5.29e+01 1amuA e.23.1.1 43351 1fiy 883 5.33e+01 1fiy c.1.12.3 29307 2fmpA 335 5.35e+01 1pe1A 267 5.52e+01 c.1.10.4 94591 1uuqA 440 5.58e+01 c.1.8.3 100015 1qs0B 338 5.61e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 1qspA 165 5.65e+01 1qspA a.24.10.2 16639 1fwsA 267 5.67e+01 1d9eA c.1.10.4 60063 1fezA 256 5.73e+01 1fezA c.108.1.3 43343 1gqoM 143 5.75e+01 c.23.13.1 76307 1ufhA 180 5.76e+01 d.108.1.1 88485 1skyB 502 5.77e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1uf3A 228 5.78e+01 d.159.1.6 99317 1frb 315 5.90e+01 1frb c.1.7.1 28665 1uf5A 303 5.98e+01 d.160.1.2 107808 1s7hA 200 5.98e+01 d.58.48.2 105349 1lqwA 183 6.00e+01 d.167.1.1 74210 1c02A 166 6.00e+01 1qspA a.24.10.2 16633 1shkA 173 6.03e+01 1shkA c.37.1.2 31932 1y0kA 209 6.07e+01 1ubeA 349 6.10e+01 c.37.1.11,d.48.1.1 88412,88413 1lxnA 99 6.10e+01 d.58.48.1 84737 1xesA 413 6.14e+01 1hm5A 558 6.16e+01 c.80.1.2 76717 1bxeA 113 6.21e+01 1bxeA d.55.1.1 38898 1erzA 303 6.22e+01 1erzA d.160.1.2 59498 1n2aA 201 6.22e+01 a.45.1.1,c.47.1.5 91553,91554 1shuX 182 6.23e+01 c.62.1.1 98882 1vdkA 466 6.25e+01 a.127.1.1 100561 1gqoS 143 6.27e+01 c.23.13.1 76313 1kewA 361 6.29e+01 c.2.1.2 68544 2fiuA 99 6.32e+01 1ejhA 190 6.33e+01 1ejhA d.86.1.1 40147 1b74A 254 6.41e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1gqoO 143 6.42e+01 c.23.13.1 76309 1fr0A 125 6.47e+01 2a0b a.24.10.1 59996 1gqoF 143 6.48e+01 c.23.13.1 76300 1zy9A 564 6.51e+01 1pnsC 206 6.51e+01 i.1.1.1 88170 1dbuA 158 6.54e+01 1dbuA d.116.1.1 40930 2cw6A 298 6.56e+01 1t8xA 267 6.61e+01 2c5uA 375 6.65e+01 1gqoU 143 6.73e+01 c.23.13.1 76315 2bfdB 345 6.74e+01 2aexA 346 6.75e+01 1e3oC 160 6.79e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 2d1sA 548 6.79e+01 1zzmA 259 6.79e+01 1brlA 355 6.79e+01 1lucA c.1.16.1 29553 1g5hA 454 6.81e+01 1g5hA c.51.1.1,d.104.1.1 60270,60271 1jclA 260 6.91e+01 c.1.10.1 66501 1dtwB 342 6.91e+01 1qs0B c.36.1.7,c.48.1.2 31828,33102 1sfjA 238 6.94e+01 1mmsA 140 6.94e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 1lm4A 194 6.96e+01 d.167.1.1 84626 1j5eC 239 6.97e+01 d.52.3.1,d.53.1.1 71544,71545 1vquA 374 6.98e+01 2f51A 118 7.00e+01 2gp5A 349 7.05e+01 1sedA 117 7.09e+01 a.219.1.1 105449 1gqoL 143 7.10e+01 c.23.13.1 76306 1gy8A 397 7.18e+01 c.2.1.2 83376 1a0fA 201 7.19e+01 1a0fA a.45.1.1,c.47.1.5 17737,33031 1e3dB 542 7.20e+01 1h2rL e.18.1.1 59189 1fjgC 239 7.26e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 2b6hA 192 7.28e+01 1q9uA 130 7.29e+01 d.129.7.1 96314 1ibsA 317 7.37e+01 c.61.1.2,c.61.1.2 66107,66108 2chnA 716 7.45e+01 2bnfB 241 7.45e+01 2shkA 173 7.50e+01 1shkA c.37.1.2 31934 1btmA 252 7.51e+01 1amk c.1.1.1 28513 1jdiA 231 7.51e+01 c.74.1.1 66551 2b7oA 464 7.58e+01 1ljrA 244 7.62e+01 1ljrA a.45.1.1,c.47.1.5 17707,33001 1s99A 200 7.67e+01 1gqoG 143 7.70e+01 c.23.13.1 76301 1auoA 218 7.82e+01 1auoA c.69.1.14 34716 2sli 679 7.83e+01 2sli b.29.1.9,b.68.1.1 24274,27611 1a3yA 149 7.83e+01 1obpA b.60.1.1 27110 1swxA 209 7.84e+01 a.224.1.1 106075 1vp8A 201 7.87e+01 1tfjA 219 7.87e+01 1rdfA 267 7.89e+01 c.108.1.3 104884 1nbaA 264 7.91e+01 1nbaA c.33.1.3 31753 1gqoK 143 7.96e+01 c.23.13.1 76305 1zu4A 320 8.01e+01 2g62A 325 8.02e+01 1pgtA 210 8.03e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1aoa 275 8.04e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1qb4A 883 8.06e+01 c.1.12.3 74640 1d9eA 284 8.07e+01 1d9eA c.1.10.4 29195 1gqoT 143 8.13e+01 c.23.13.1 76314 1wyzA 242 8.15e+01 1lvaA 258 8.20e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1agx 331 8.23e+01 4pgaA c.88.1.1 35564 1gqoD 143 8.24e+01 c.23.13.1 76298 1a40 321 8.29e+01 1ixh c.94.1.1 35767 1p1xA 260 8.30e+01 c.1.10.1 104060 1cliA 345 8.38e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2gwgA 350 8.41e+01 1cj3A 392 8.43e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1fmjA 351 8.50e+01 c.37.1.5 59879 1swvA 267 8.52e+01 1lyxA 248 8.57e+01 c.1.1.1 78304 2bv5A 282 8.58e+01 1dkuA 317 8.58e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1gqoX 143 8.67e+01 c.23.13.1 76317 1rztA 331 8.71e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1wi6A 88 8.73e+01 1j96A 323 8.75e+01 c.1.7.1 71616 1jcjA 260 8.80e+01 c.1.10.1 66499 1lbkA 208 8.80e+01 a.45.1.1,c.47.1.5 73809,73810 1m6eX 359 8.89e+01 c.66.1.35 91188 1ywfA 296 8.93e+01 1lehA 364 8.99e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1a6l 106 8.99e+01 1a6l d.58.1.2 38966