# List of top-scoring protein chains for t2k-100-30-CB_burial_14_7-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 1xv2A 237 2.15e-01 1ym3A 215 5.22e-01 2boqA 331 7.21e-01 1mioB 458 1.08e+00 1qguB c.92.2.3 35602 2a5vA 213 1.71e+00 1pi4A 358 2.60e+00 e.3.1.1 94700 2ffyA 358 2.85e+00 1xyzA 347 2.94e+00 1taxA c.1.8.3 28804 1fsyA 358 3.10e+00 1gceA e.3.1.1 60016 2blsA 358 3.10e+00 1gceA e.3.1.1 42747 1c7iA 489 3.18e+00 1thg c.69.1.1 34632 1l0gA 358 3.25e+00 e.3.1.1 73400 1m65A 245 3.55e+00 c.6.3.1 84847 2pgd 482 3.69e+00 2pgd a.100.1.1,c.2.1.6 18778,30190 1kvlA 358 4.29e+00 e.3.1.1 73062 1vcoA 550 4.38e+00 c.23.16.1,c.37.1.10 108508,108509 1h2eA 207 5.11e+00 c.60.1.1 70857 1p5tA 127 5.34e+00 b.55.1.2 94148 1bif 469 5.36e+00 1bif c.37.1.7,c.60.1.4 31961,34003 1ebbA 202 7.03e+00 c.60.1.1 64900 2bifA 469 7.03e+00 1bif c.37.1.7,c.60.1.4 31963,34009 2f6rA 281 7.46e+00 3bifA 468 7.88e+00 1bif c.37.1.7,c.60.1.4 31962,34008 1hqkA 154 8.17e+00 c.16.1.1 65902 2gnxA 365 8.54e+00 1iyeA 309 8.90e+00 e.17.1.1 83786 2f96A 224 9.28e+00 1kolA 398 9.37e+00 b.35.1.2,c.2.1.1 77474,77475 2czlA 272 9.64e+00 1gveA 327 1.01e+01 c.1.7.1 70597 1xebA 150 1.04e+01 1hl9A 449 1.04e+01 b.71.1.3,c.1.8.11 90650,90651 2bneA 241 1.07e+01 1vjzA 341 1.09e+01 c.1.8.3 100838 1hl8A 449 1.09e+01 b.71.1.3,c.1.8.11 90646,90647 1awsA 164 1.11e+01 2cpl b.62.1.1 27431 1awqA 164 1.12e+01 2cpl b.62.1.1 27461 1y4tA 322 1.13e+01 1gqoC 143 1.13e+01 c.23.13.1 76297 1zkiA 133 1.20e+01 1gqoJ 143 1.22e+01 c.23.13.1 76304 1cwoA 165 1.22e+01 2cpl b.62.1.1 27445 1cs1A 386 1.23e+01 1ibjA c.67.1.3 34399 2g9iA 249 1.25e+01 1vphA 149 1.26e+01 1gqoG 143 1.29e+01 c.23.13.1 76301 1uanA 227 1.32e+01 c.134.1.1 99135 1yndA 165 1.33e+01 1vkmA 297 1.38e+01 c.138.1.1 108670 2cpl 165 1.38e+01 2cpl b.62.1.1 27420 1gqoV 143 1.39e+01 c.23.13.1 76316 1qpaA 345 1.40e+01 1arv a.93.1.1 18585 1jqnA 883 1.42e+01 c.1.12.3 77159 1gqoR 143 1.42e+01 c.23.13.1 76312 1gqoE 143 1.44e+01 c.23.13.1 76299 1gqoO 143 1.45e+01 c.23.13.1 76309 1cs1C 386 1.46e+01 1ibjA c.67.1.3 34401 1gqoN 143 1.49e+01 c.23.13.1 76308 1gqoB 143 1.51e+01 c.23.13.1 76296 1gqoI 143 1.51e+01 c.23.13.1 76303 1gqoH 143 1.52e+01 c.23.13.1 76302 1llp 343 1.53e+01 1arv a.93.1.1 18578 1vqrA 297 1.54e+01 2bduA 297 1.54e+01 1b59A 370 1.56e+01 1bn5 a.4.5.25,d.127.1.1 16225,41162 1gqoQ 143 1.63e+01 c.23.13.1 76311 1gqoF 143 1.63e+01 c.23.13.1 76300 2g09A 297 1.65e+01 1fiy 883 1.69e+01 1fiy c.1.12.3 29307 1pmt 203 1.72e+01 1a0fA a.45.1.1,c.47.1.5 17740,33034 2d0oB 125 1.75e+01 1gqoU 143 1.81e+01 c.23.13.1 76315 1gqoD 143 1.84e+01 c.23.13.1 76298 1gqoX 143 1.86e+01 c.23.13.1 76317 2fug7 129 1.86e+01 1qb4A 883 1.87e+01 c.1.12.3 74640 1gqoT 143 1.89e+01 c.23.13.1 76314 1sr2A 116 1.91e+01 1bn7A 294 1.94e+01 1bn6A c.69.1.8 34677 1rfa 79 1.94e+01 1c1yB d.15.1.5 37620 1gqoS 143 1.98e+01 c.23.13.1 76313 1qe3A 489 2.04e+01 2bce c.69.1.1 34630 1gqoP 143 2.05e+01 c.23.13.1 76310 1pta 318 2.05e+01 1pscA c.1.9.3 29064 2aq8A 269 2.08e+01 1i1kA 309 2.10e+01 1daaA e.17.1.1 61533 1f89A 291 2.18e+01 d.160.1.1 64988 2d2jA 329 2.21e+01 1pt6A 213 2.22e+01 c.62.1.1 95091 1b80A 351 2.24e+01 1arv a.93.1.1 18579 2cvjA 180 2.24e+01 1w1iE 357 2.25e+01 c.1.9.1 109051 1gqoY 143 2.26e+01 c.23.13.1 76318 1gqoK 143 2.31e+01 c.23.13.1 76305 1b85A 351 2.34e+01 1arv a.93.1.1 18581 1oyzA 280 2.35e+01 a.118.1.16 93775 1ak1 310 2.36e+01 1ak1 c.92.1.1 35594 1p1xA 260 2.41e+01 c.1.10.1 104060 1h67A 108 2.42e+01 a.40.1.1 65643 1gqoM 143 2.47e+01 c.23.13.1 76307 1uzmA 247 2.47e+01 1zjjA 263 2.50e+01 1a3gA 308 2.61e+01 1daaA e.17.1.1 43286 1r6fA 310 2.69e+01 e.46.1.1 97149 1bn5 478 2.69e+01 1bn5 a.4.5.25,d.127.1.1 16224,41161 1hjsA 332 2.71e+01 c.1.8.3 83492 1cx4A 305 2.72e+01 b.82.3.2,b.82.3.2 59099,59100 1zxxA 319 2.73e+01 1c3kA 147 2.75e+01 1jotA b.77.3.1 27984 1wvhA 134 2.75e+01 1ub0A 258 2.76e+01 c.72.1.2 88394 1b6a 478 2.76e+01 1bn5 a.4.5.25,d.127.1.1 16223,41160 1ekjA 221 2.80e+01 1ekjB c.53.2.1 33364 1gqoL 143 2.89e+01 c.23.13.1 76306 1u9cA 224 2.93e+01 1h05A 146 2.95e+01 c.23.13.1 76433 2ac4A 309 2.97e+01 1dozA 309 3.08e+01 1ak1 c.92.1.1 35592 1gskA 513 3.09e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 1pv9A 348 3.17e+01 c.55.2.1,d.127.1.1 95157,95158 1jclA 260 3.17e+01 c.1.10.1 66501 2bnfB 241 3.20e+01 1bn6A 294 3.21e+01 1bn6A c.69.1.8 34678 1jcjA 260 3.22e+01 c.1.10.1 66499 1wrvA 308 3.22e+01 1xqsA 280 3.36e+01 3pfk 319 3.37e+01 3pfk c.89.1.1 35581 1xp8A 366 3.37e+01 1bf6A 291 3.45e+01 1pscA c.1.9.3 29065 1b1yA 500 3.46e+01 1byb c.1.8.1 28796 1qc5A 192 3.46e+01 1aoxA c.62.1.1 34147 1dv8A 128 3.53e+01 1ixxB d.169.1.1 42352 1tz9A 367 3.53e+01 c.1.15.6 107466 2b99A 156 3.54e+01 1bvoA 175 3.63e+01 1a3qA b.2.5.3 22457 1xqrA 296 3.64e+01 4pfk 319 3.66e+01 3pfk c.89.1.1 35582 1nrwA 288 3.69e+01 c.108.1.10 86128 1kr5A 226 3.75e+01 c.66.1.7 68847 1k3fA 253 3.76e+01 c.56.2.1 68105 1vkxA 273 3.90e+01 1a3qA b.1.18.1,b.2.5.3 21941,22454 2ac2A 309 3.96e+01 1r85A 379 4.06e+01 c.1.8.3 104839 1zcxA 178 4.09e+01 1c3mA 147 4.22e+01 1jotA b.77.3.1 27983 1thx 115 4.24e+01 1thx c.47.1.1 32732 1dywA 173 4.28e+01 2cpl b.62.1.1 27505 1qstA 160 4.36e+01 1yghA d.108.1.1 40804 2pfkA 320 4.39e+01 3pfk c.89.1.1 35577 1lay 256 4.40e+01 1lay b.57.1.1 27014 1e25A 282 4.58e+01 1e25A e.3.1.1 42731 1c1yB 77 4.65e+01 1c1yB d.15.1.5 37618 1oaa 259 4.70e+01 1oaa c.2.1.2 29829 1vdwA 254 4.71e+01 e.7.1.1 100569 1zbmA 280 4.71e+01 1dfmA 223 4.72e+01 1d2iA c.52.1.5 33295 2mev2 256 4.72e+01 1aym2 1u5uA 374 4.77e+01 1b12A 248 4.79e+01 1b12A b.87.1.2 28388 1d9nA 75 4.79e+01 1d9nA d.10.1.3 37486 2dabA 282 4.89e+01 1daaA e.17.1.1 43274 1ln1A 214 4.92e+01 d.129.3.2 74038 1s5pA 235 4.95e+01 c.31.1.5 98569 1wl9A 440 4.95e+01 1ox0A 430 4.99e+01 c.95.1.1,c.95.1.1 87495,87496 1a0gA 282 4.99e+01 1daaA e.17.1.1 43276 1mqeA 207 5.01e+01 d.113.1.1 91394 1xklA 273 5.10e+01 1kn9A 249 5.13e+01 b.87.1.2 68699 2bpa1 426 5.14e+01 2bpa1 2bwvA 440 5.16e+01 1w41A 101 5.17e+01 2cxxA 190 5.18e+01 1ydwA 362 5.23e+01 1nv8A 284 5.27e+01 c.66.1.30 86224 1jk7A 323 5.36e+01 1auiA d.159.1.3 63144 1d2iA 223 5.39e+01 1d2iA c.52.1.5 33297 6pfkA 319 5.40e+01 3pfk c.89.1.1 35583 1i1nA 226 5.42e+01 c.66.1.7 71102 1jmvA 141 5.46e+01 c.26.2.4 66897 1a78A 134 5.47e+01 1c1lA b.29.1.3 24212 1sep 261 5.56e+01 1oaa c.2.1.2 29830 1i0dA 332 5.62e+01 1pscA c.1.9.3 61487 2al3A 90 5.74e+01 1ea9C 583 5.76e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1kf6A 602 5.82e+01 a.7.3.1,c.3.1.4,d.168.1.1 72394,72395,72396 1eywA 331 5.89e+01 1pscA c.1.9.3 29057 1i60A 278 5.91e+01 c.1.15.4 71118 1umzA 278 5.94e+01 b.29.1.2 99639 1oz9A 150 5.98e+01 d.92.1.15 93808 3daaA 277 6.01e+01 1daaA e.17.1.1 43272 1guaB 81 6.04e+01 1c1yB d.15.1.5 37619 1y63A 184 6.05e+01 1c9uA 454 6.05e+01 1c9uA b.68.2.1 27623 1yghA 164 6.13e+01 1yghA d.108.1.1 40802 1yqzA 438 6.25e+01 1s1pA 331 6.26e+01 c.1.7.1 98350 1ekjB 221 6.31e+01 1ekjB c.53.2.1 33365 1hzyA 332 6.32e+01 1pscA c.1.9.3 61468 1j6oA 268 6.35e+01 c.1.9.12 77088 1lnzA 342 6.41e+01 b.117.1.1,c.37.1.8 78112,78113 1gwmA 153 6.45e+01 b.18.1.19 83348 1rxyA 253 6.47e+01 c.56.2.1 98065 2bitX 165 6.51e+01 1dysA 348 6.53e+01 1bvwA c.6.1.1 30669 1ycoA 279 6.53e+01 2aukA 190 6.57e+01 1k20A 310 6.58e+01 c.107.1.1 68027 1c24A 263 6.65e+01 1c24A d.127.1.1 41148 1qtfA 246 6.68e+01 1agjA b.47.1.1 25830 1ak2 233 6.94e+01 1zin c.37.1.1,g.41.2.1 31894,45195 1fl2A 310 6.94e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1vjoA 393 7.00e+01 c.67.1.3 100827 1chmA 401 7.19e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1a16 440 7.27e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 1sc6A 404 7.31e+01 2matA 264 7.33e+01 1c24A d.127.1.1 41146 1oz7A 131 7.34e+01 d.169.1.1 93806 1h1yA 228 7.39e+01 c.1.2.2 76506 1sltB 134 7.44e+01 1c1lA b.29.1.3 24187 1cr1A 296 7.45e+01 1cr1A c.37.1.11 32286 1fukA 165 7.49e+01 1fukA c.37.1.19 32409 1mb3A 124 7.55e+01 c.23.1.1 78907 1f5mA 180 7.57e+01 1f5mB d.110.2.1 40895 1m5tA 124 7.59e+01 c.23.1.1 78660 1r6uA 437 7.63e+01 c.26.1.1 97163 1iqrA 420 7.65e+01 a.99.1.1,c.28.1.1 66275,66276 1k1xA 659 7.74e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1b0lA 691 7.76e+01 1cb6A c.94.1.2,c.94.1.2 35847,35848 1j3bA 529 7.80e+01 c.91.1.1,c.109.1.1 77071,77072 1slaA 134 7.80e+01 1c1lA b.29.1.3 24196 1a6zA 275 7.80e+01 1agdA b.1.1.2,d.19.1.1 20781,38280 1ih8A 271 7.82e+01 2nsyA c.26.2.1 62377 1v6tA 255 7.83e+01 1un7A 400 7.85e+01 b.92.1.5,c.1.9.10 99657,99658 1k4jA 230 7.89e+01 d.108.1.3 72057 1z4rA 168 7.91e+01 1ys7A 233 7.96e+01 1pfkA 320 7.96e+01 3pfk c.89.1.1 35575 1hizA 379 7.99e+01 c.1.8.3 65841 1yhtA 367 8.00e+01 1cktA 71 8.02e+01 1cktA a.21.1.1 16417 1kz1A 159 8.05e+01 c.16.1.1 73318 1vflA 356 8.10e+01 1a3qA 285 8.12e+01 1a3qA b.1.18.1,b.2.5.3 21932,22447 1daaA 282 8.20e+01 1daaA e.17.1.1 43270 1c7jA 489 8.23e+01 2bce c.69.1.1 34631 1vmjA 151 8.24e+01 1u7zA 226 8.29e+01 1sznA 417 8.35e+01 b.71.1.1,c.1.8.1 106162,106163 1wn2A 121 8.47e+01 1wzoA 246 8.51e+01 1xngA 268 8.51e+01 1qbiA 454 8.57e+01 1c9uA b.68.2.1 27619 1a1nA 276 8.74e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 2bs9A 503 8.82e+01 1fjmA 330 8.84e+01 1auiA d.159.1.3 42082 1k07A 263 8.87e+01 d.157.1.1 77218 2gokA 429 8.93e+01