# List of top-scoring protein chains for t2k-100-40-40-str2+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 1qqcA 773 5.55e-01 1tgoA c.55.3.5,e.8.1.1 33724,43013 2bkqA 212 7.47e-01 2ap1A 327 8.19e-01 1qhtA 775 8.25e-01 1tgoA c.55.3.5,e.8.1.1 33722,43011 2bkrA 212 1.03e+00 1wnaA 131 1.58e+00 1xt9A 212 1.84e+00 1u6dX 308 2.67e+00 1zgkA 308 2.69e+00 1ufhA 180 2.92e+00 d.108.1.1 88485 1wbpA 397 3.08e+00 1v4sA 455 3.90e+00 c.55.1.3,c.55.1.3 100309,100310 1jx4A 352 3.92e+00 d.240.1.1,e.8.1.7 90378,90379 1j5pA 253 4.15e+00 d.81.1.3,c.2.1.3 71577,83092 1hrhA 136 5.16e+00 1rthA c.55.3.1 33577 1tgoA 773 5.37e+00 1tgoA c.55.3.5,e.8.1.1 33721,43010 1rch 155 5.70e+00 2rn2 c.55.3.1 33570 1eo1A 124 5.73e+00 1eo1A c.55.5.1 33739 1on0A 158 6.07e+00 d.108.1.1 87095 1x9mA 698 6.27e+00 1poiB 260 6.40e+00 1poiB c.124.1.3 34155 1euvA 221 6.48e+00 1euvA d.3.1.7 37133 1x3mA 415 7.50e+00 1k2eA 156 7.64e+00 d.113.1.1 72010 1t7pA 698 8.20e+00 1t7pA c.55.3.5,e.8.1.1 33712,43005 1k26A 156 8.62e+00 d.113.1.1 72003 3nul 130 9.54e+00 3nul d.110.1.1 40891 2al6A 375 9.59e+00 2beiA 170 1.02e+01 1j5eK 129 1.04e+01 c.55.4.1 71554 1a05A 358 1.05e+01 1cnzA c.77.1.1 35059 1uwzA 136 1.06e+01 c.97.1.1 108081 1jrkA 156 1.06e+01 d.113.1.1 71827 2aehA 369 1.11e+01 1p90A 145 1.15e+01 c.55.5.2 94377 1yw5A 177 1.16e+01 1fchA 368 1.19e+01 1fchA a.118.8.1 19212 1zc6A 305 1.23e+01 2bl1A 172 1.27e+01 1howA 373 1.32e+01 1hcl d.144.1.7 41679 1a0k 131 1.34e+01 3nul d.110.1.1 40892 1lwdA 413 1.35e+01 c.77.1.1 78265 1u5tC 202 1.37e+01 a.4.5.54,a.4.5.54 107688,107689 1jtkA 136 1.38e+01 c.97.1.1 71862 1ovqA 138 1.39e+01 c.55.3.8 93607 1nrvA 105 1.45e+01 d.93.1.1 86126 2b49A 287 1.54e+01 1a8y 367 1.63e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 2gx9A 129 1.64e+01 1yuwA 554 1.69e+01 1ovnA 248 1.70e+01 a.71.1.1,c.47.1.7 93602,93603 2b33A 140 1.72e+01 1m2kA 249 1.84e+01 c.31.1.5 84754 1dkxA 219 1.87e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 1zg2A 107 1.89e+01 1hw6A 278 1.90e+01 1frb c.1.7.1 61296 1ymiA 334 1.91e+01 1yr0A 175 1.92e+01 1q8yA 373 1.93e+01 d.144.1.7 96234 1k8cA 322 1.96e+01 c.1.7.1 72172 1t46A 313 1.97e+01 d.144.1.7 106397 1jwqA 179 2.07e+01 c.56.5.6 90921 2dcnA 311 2.12e+01 2rn2 155 2.18e+01 2rn2 c.55.3.1 33551 1lehA 364 2.19e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1x6oA 174 2.20e+01 b.34.5.2,b.40.4.5 109493,109494 1zin 217 2.20e+01 1zin c.37.1.1,g.41.2.1 31915,45178 2cn3A 737 2.21e+01 1vsd 152 2.23e+01 1cxqA c.55.3.2 33625 1zo0A 126 2.28e+01 1iciA 256 2.32e+01 1iciA c.31.1.5 62266 1dkzA 219 2.35e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1kf6B 243 2.41e+01 a.1.2.1,d.15.4.2 72397,72398 1ukz 203 2.46e+01 1zin c.37.1.1 31840 2a9sA 171 2.48e+01 1zip 217 2.55e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1z83A 196 2.59e+01 1jhdA 396 2.73e+01 b.122.1.3,c.26.1.5 66712,66713 1yvoA 172 2.77e+01 1fqvA 336 2.77e+01 1fqvA a.158.1.1,c.10.1.3 19254,30856 1svr 114 2.81e+01 1svy d.109.1.1 40833 1q8iA 783 2.86e+01 c.55.3.5,e.8.1.1 96208,96209 1g99A 408 2.92e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 1gvnB 287 2.93e+01 c.37.1.21 76354 1mi3A 322 2.97e+01 c.1.7.1 91274 1vhoA 346 3.03e+01 b.49.3.1,c.56.5.4 100694,100695 2b5gA 171 3.04e+01 1fjgK 129 3.14e+01 1fjfK c.55.4.1 33733 1cxqA 162 3.14e+01 1cxqA c.55.3.2 33621 1xs0A 136 3.14e+01 1pbyB 337 3.18e+01 b.69.2.2 94422 1w1wA 430 3.29e+01 1svdM 110 3.29e+01 1ofuX 119 3.36e+01 c.37.1.22 86976 1f1zA 273 3.40e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1mkeA 152 3.40e+01 b.55.1.4 79231 3adk 195 3.46e+01 1zin c.37.1.1 31885 2fr1A 486 3.53e+01 1woqA 267 3.53e+01 c.55.1.10,c.55.1.10 109462,109463 1rxxA 421 3.59e+01 d.126.1.4 98061 1nfiA 301 3.62e+01 1a3qA b.1.18.1,b.2.5.3 21942,22455 1a5v 162 3.67e+01 1cxqA c.55.3.2 33629 1z6gA 218 3.67e+01 1o13A 136 3.78e+01 c.55.5.1 80762 1tiiD 99 3.78e+01 1tiiD b.40.2.1 24965 1gpl 432 3.90e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1lvwA 295 3.94e+01 c.68.1.6 84723 1u00A 227 3.95e+01 1qb5D 99 3.99e+01 b.40.2.1 88357 1jpc 109 4.09e+01 1b2pA b.78.1.1 27986 1k07A 263 4.12e+01 d.157.1.1 77218 2a1kA 233 4.29e+01 1mejA 223 4.31e+01 c.65.1.1 79029 1zy9A 564 4.41e+01 1yd0A 96 4.46e+01 1nfiC 301 4.47e+01 b.1.18.1,b.2.5.3 21943,22456 1ilyA 90 4.57e+01 c.55.4.1 71245 2c6cA 707 4.60e+01 1h32A 261 4.77e+01 a.3.1.8,a.3.1.8 76618,76619 1n8fA 350 4.78e+01 c.1.10.4 85397 2b7aA 293 4.81e+01 1jjuB 337 4.83e+01 b.69.2.2 66779 1r1mA 164 4.88e+01 d.79.7.1 96820 1frb 315 4.90e+01 1frb c.1.7.1 28665 1gg1A 350 4.99e+01 1qr7A c.1.10.4 29187 1yf5L 254 5.00e+01 1xx1A 285 5.03e+01 1hv8A 367 5.03e+01 1hv8A c.37.1.19,c.37.1.19 32405,32406 1z3iX 644 5.07e+01 2adzA 178 5.08e+01 1xviA 275 5.13e+01 1svq 114 5.15e+01 1svy d.109.1.1 40832 1e3sA 261 5.20e+01 1e6wA c.2.1.2 59201 1qmvA 197 5.25e+01 1qq2A c.47.1.10 33066 1zdrA 164 5.35e+01 1frpA 335 5.42e+01 1frpA e.7.1.1 42875 1xd5A 112 5.42e+01 1rfeA 162 5.49e+01 1nuyA 337 5.54e+01 e.7.1.1 86213 1lba 146 5.56e+01 1lba d.118.1.1 41062 1zr5A 214 5.61e+01 1qlaB 239 5.62e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1lktA 104 5.66e+01 1lktA b.90.1.1 28398 2gtrA 261 5.74e+01 1gw5S 142 5.76e+01 d.110.4.2 70633 2eu9A 355 5.79e+01 1o4sA 389 5.83e+01 c.67.1.1 86620 1em8A 147 5.84e+01 c.128.1.1 90457 1wrjA 156 5.90e+01 1lpuA 332 5.98e+01 d.144.1.7 74177 1j08A 226 6.00e+01 c.47.1.2,c.47.1.2 83855,83856 1n0uA 842 6.04e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 2a4hA 126 6.10e+01 2ci9A 102 6.13e+01 1rdzA 337 6.19e+01 1frpA e.7.1.1 42882 1dhs 344 6.19e+01 1dhs c.31.1.1 31727 1a8l 226 6.27e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 1hr6B 443 6.29e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1j8dA 180 6.43e+01 c.108.1.5 66433 2vik 126 6.54e+01 2vil d.109.1.1 40829 1jfuA 186 6.54e+01 c.47.1.10 62940 2b06A 155 6.57e+01 1x31D 99 6.59e+01 2f7fA 494 6.61e+01 2ex0A 399 6.66e+01 1pzxA 289 6.67e+01 c.119.1.1 95484 1nvmB 312 6.69e+01 c.2.1.3,d.81.1.1 86251,86252 1f46A 140 6.74e+01 1f46A d.129.4.1 59643 1pg4A 652 6.77e+01 e.23.1.1 88067 1iznA 286 6.79e+01 e.43.1.1 83847 1f21A 155 6.79e+01 2rn2 c.55.3.1 33550 1bpr 191 6.79e+01 1dkzA b.130.1.1 43319 1x1fA 149 6.81e+01 2fcjA 119 6.83e+01 1y71A 130 6.86e+01 1w97L 246 6.91e+01 1kz8A 337 7.07e+01 e.7.1.1 77633 1qhiA 366 7.09e+01 1qhiA c.37.1.1 31860 1f8aB 167 7.11e+01 1pinA b.72.1.1,d.26.1.1 27803,38432 1s01 283 7.13e+01 1gci c.41.1.1 32511 1hh1A 143 7.13e+01 1gefA c.52.1.18 61036 1gc5A 467 7.14e+01 1gc5A c.72.1.3 60429 2f8lA 344 7.17e+01 1aqn 275 7.27e+01 1gci c.41.1.1 32514 1cqa 133 7.30e+01 3nul d.110.1.1 40890 1f7wA 144 7.34e+01 1f46A d.129.4.1 59679 1jzxK 205 7.34e+01 i.1.1.2 67885 1wryA 121 7.35e+01 1u04A 771 7.54e+01 b.34.14.1,c.55.3.10 107539,107540 1hqz9 141 7.54e+01 1vl4A 447 7.61e+01 d.283.1.1 108718 1nz0A 118 7.61e+01 d.14.1.2 86433 1sup 275 7.64e+01 1gci c.41.1.1 32510 1pinA 163 7.73e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1nslA 184 7.74e+01 d.108.1.1 86137 1u9cA 224 7.79e+01 1cf2O 337 7.80e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 1tuaA 191 7.84e+01 d.51.1.1,d.51.1.1 107321,107322 1a6o 332 7.85e+01 1a6o 1ak2 233 7.90e+01 1zin c.37.1.1,g.41.2.1 31894,45195 1lw6E 281 7.93e+01 c.41.1.1 74293 1l9kA 305 7.93e+01 c.66.1.25 84569 2cr9A 139 7.93e+01 1vheA 373 7.94e+01 b.49.3.1,c.56.5.4 100669,100670 2fqxA 318 7.95e+01 1za0A 275 7.97e+01 1ak9 275 7.97e+01 1gci c.41.1.1 32517 1s3aA 102 8.09e+01 2a6hE 99 8.10e+01 1lcjA 109 8.13e+01 1qadA d.93.1.1 40414 2f7tA 227 8.13e+01 1m2rA 327 8.15e+01 d.144.1.7 84760 1sbzA 197 8.18e+01 1qr7A 350 8.20e+01 1qr7A c.1.10.4 29191 1y2qA 143 8.20e+01 1uilA 113 8.23e+01 2bkfA 87 8.25e+01 1k8kC 372 8.27e+01 b.69.4.1 68308 1vk4A 298 8.32e+01 c.72.1.1 100850 1tt0A 623 8.38e+01 1fj2A 232 8.43e+01 1auoA c.69.1.14 34720 1a2q 275 8.45e+01 1gci c.41.1.1 32512 1kimA 366 8.59e+01 1qhiA c.37.1.1 31864 1iknA 286 8.59e+01 1a3qA b.1.18.1,b.2.5.3 21936,22449 1jqaA 370 8.61e+01 e.22.1.2 67085 1k1eA 180 8.63e+01 c.108.1.5 67995 1gpc 218 8.66e+01 1gpc b.40.4.7 25393 1pkoA 139 8.76e+01 b.1.1.1 88147 1jl2A 156 8.82e+01 c.55.3.1 66822 1k28D 391 8.84e+01 b.106.1.1,b.106.1.1 68052,68053 1x1gA 129 8.97e+01 1f1sA 814 9.00e+01 a.102.3.2,b.1.18.2,b.24.1.1,b.30.5.2 64928,64929,64930,64931