# 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.soe.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 1mkmA 249 5.88e-24 a.4.5.33,d.110.2.2 79242,79243 1yspA 181 7.16e-24 1td5A 202 2.69e-22 d.110.2.2 106767 2o99A 182 1.22e-21 d.110.2.2 138952 1tf1A 198 2.02e-21 d.110.2.2 106826 2ia2A 265 1.77e-20 1ysqA 193 2.59e-20 2g7uA 257 2.73e-19 3bjnA 165 1.52e-17 2o0yA 260 1.68e-17 2iyeA 263 2.70e-01 3rubS 123 1.59e+00 1rboC d.73.1.1 39616 2odiA 238 1.96e+00 2o28A 184 2.28e+00 1svdM 110 2.51e+00 d.73.1.1 119059 1fmjA 351 2.89e+00 c.37.1.5 59879 3bkbA 377 3.09e+00 2i5uA 83 3.47e+00 3cblA 377 3.49e+00 2g76A 335 3.56e+00 8rucI 123 3.76e+00 1rboC d.73.1.1 39629 1qtqA 553 3.81e+00 1gtrA b.53.1.2,c.26.1.1 26940,31579 1k6kA 143 3.91e+00 a.174.1.1 77274 2ou6A 190 4.20e+00 2jj7A 186 4.41e+00 1wstA 417 4.63e+00 c.67.1.1 121244 2fgoA 82 4.77e+00 2zc2A 78 4.88e+00 2v79A 135 5.03e+00 1m1hA 248 5.35e+00 b.114.1.1,d.58.42.1 78415,78416 1gtrA 553 5.64e+00 1gtrA b.53.1.2,c.26.1.1 26939,31578 1wdcB 156 5.88e+00 1wdcB a.39.1.5 17302 2ciwA 299 5.96e+00 a.39.3.1,a.39.3.1 130502,130503 1mvwB 145 6.37e+00 i.15.1.1 79524 2iutA 574 6.92e+00 1vemA 516 7.15e+00 b.3.1.1,c.1.8.1 120021,120022 1ir21 140 7.19e+00 1ys7A 233 7.37e+00 a.4.6.1,c.23.1.1 123961,123962 1zunA 325 7.38e+00 c.26.2.2 125676 1j4aA 333 7.45e+00 c.2.1.4,c.23.12.1 71502,71503 1mc0A 368 7.50e+00 d.110.2.1,d.110.2.1 78937,78938 1yo5C 97 7.70e+00 a.4.5.21 123768 2gjlA 328 7.72e+00 1r5jA 337 8.00e+00 c.77.1.5 97097 2g2qA 124 8.23e+00 2dt8A 280 8.29e+00 1itcA 516 8.53e+00 b.3.1.1,c.1.8.1 83705,83706 1twdA 256 8.63e+00 c.1.30.1 107397 1sknP 92 9.04e+00 1sknP a.37.1.1 17127 2i6eA 301 9.24e+00 1wddS 128 9.55e+00 d.73.1.1 114532 1l2tA 235 9.63e+00 c.37.1.12 73514 2j13A 247 9.69e+00 c.6.2.3 137934 1fc4A 401 9.85e+00 1bs0A c.67.1.4 59760 1gk8I 140 9.97e+00 d.73.1.1 65242 2a6aA 218 1.01e+01 c.55.1.9,c.55.1.9 126231,126232 1cpo 299 1.03e+01 1cpo 2jfrA 234 1.03e+01 1rscI 111 1.07e+01 d.73.1.1 118620 3cgvA 397 1.08e+01 2uytA 489 1.09e+01 1vi9A 299 1.10e+01 c.72.1.5 100750 1mgpA 313 1.11e+01 c.119.1.1 79098 1td2A 287 1.11e+01 c.72.1.5 106765 1fgxA 288 1.12e+01 1fgxA c.68.1.2 34508 1vpvA 300 1.13e+01 c.119.1.1 113975 1yg2A 179 1.16e+01 a.4.5.61 116681 1u55A 188 1.16e+01 d.278.1.1 107677 1rhcA 330 1.16e+01 c.1.16.3 97468 1x42A 232 1.17e+01 c.108.1.1 121677 1b1gA 75 1.18e+01 1psrA a.39.1.1 17151 2fx0A 201 1.21e+01 a.4.1.9,a.121.1.1 134269,134270 1rblI 109 1.22e+01 d.73.1.1 118599 1vbuA 328 1.23e+01 c.1.8.3 119963 2pjhB 193 1.25e+01 2fcoA 200 1.29e+01 2aexA 346 1.29e+01 1ns5A 155 1.30e+01 c.116.1.3 80705 2ps2A 371 1.31e+01 2hgcA 102 1.31e+01 2nq2C 253 1.31e+01 2hjmA 103 1.35e+01 3cklA 298 1.35e+01 1xtlA 175 1.37e+01 1v5iB 76 1.40e+01 1wqgA 185 1.43e+01 2oqgA 114 1.44e+01 1b9zA 516 1.46e+01 1b9zA b.3.1.1,c.1.8.1 22528,28798 2ofkA 183 1.47e+01 2abyA 146 1.53e+01 1ovnA 248 1.53e+01 a.71.1.1,c.47.1.7 93602,93603 1pueE 89 1.56e+01 1awcA a.4.5.21 16165 2c0gA 248 1.61e+01 a.71.1.1,c.47.1.7 129590,129591 1srvA 145 1.62e+01 1derA c.8.5.1 30817 1pztA 286 1.63e+01 c.68.1.2 95470 2oqzA 223 1.63e+01 b.100.1.1 139255 2ha8A 184 1.65e+01 1z47A 355 1.66e+01 1eexG 173 1.69e+01 1dioG a.23.2.1 16490 1b0jA 754 1.73e+01 1amj c.8.2.1,c.83.1.1 30719,35395 3c19A 186 1.73e+01 1qwgA 251 1.79e+01 c.1.27.1 96473 1nmmB 286 1.87e+01 c.68.1.2 80662 1r0kA 388 1.87e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1yvkA 163 1.89e+01 d.108.1.1 124101 1mqeA 207 1.94e+01 d.113.1.1 91394 1dceB 331 1.94e+01 1dceB a.102.4.3 18872 1bg2 325 1.97e+01 1bg2 1bg2A 325 1.97e+01 c.37.1.9 32189 1q1hA 110 1.97e+01 a.4.5.41 95580 1o6eA 235 1.98e+01 b.57.1.1 81083 2b6cA 220 1.99e+01 a.118.1.17 127983 1vlrA 350 2.00e+01 d.13.1.3,d.246.1.1 108860,108861 1iurA 88 2.06e+01 a.2.3.1 90704 1mzhA 225 2.09e+01 c.1.10.1 79698 1nf5B 286 2.11e+01 c.68.1.2 80454 2e85A 159 2.12e+01 1yw5A 177 2.14e+01 1w7jB 151 2.14e+01 a.39.1.5 120690 2jdxA 385 2.15e+01 1jdw d.126.1.2 41139 2e7jA 371 2.18e+01 1yrtA 364 2.20e+01 1sv6A 269 2.21e+01 d.177.1.1 106043 1y1oA 203 2.25e+01 c.52.1.28 116345 2mysB 166 2.26e+01 1wdcB a.39.1.5 17308 3cnhA 200 2.27e+01 1fb6A 105 2.28e+01 1thx c.47.1.1 32739 1v3hA 495 2.29e+01 c.1.8.1 108303 2o37A 92 2.30e+01 2pbqA 178 2.32e+01 1zxxA 319 2.34e+01 1avsA 90 2.34e+01 1cll a.39.1.5 17226 1e32A 458 2.35e+01 1e32A b.52.2.3,c.37.1.20,d.31.1.1 59183,59184,59185 1rz2A 254 2.35e+01 b.100.1.1 105130 2nn4A 72 2.36e+01 1fwkA 296 2.37e+01 1fwkA d.14.1.5,d.58.26.1 37576,39398 2hf2A 283 2.40e+01 1g0hA 252 2.40e+01 1dk4A e.7.1.1 60171 5rubA 490 2.40e+01 1burA c.1.14.1,d.58.9.1 29382,39288 2qr6A 393 2.41e+01 1t3yA 141 2.42e+01 d.109.1.2 119141 2debA 653 2.42e+01 1byb 495 2.47e+01 1byb 1s4iA 175 2.48e+01 2fe3A 145 2.49e+01 2hw2A 143 2.54e+01 2do5A 58 2.54e+01 1p3y1 194 2.55e+01 1lkvX 232 2.56e+01 a.118.14.1 73980 1sedA 117 2.58e+01 a.219.1.1 105449 1rlmA 271 2.58e+01 c.108.1.10 111860 1udmA 149 2.62e+01 d.109.1.2 107780 1vr4A 103 2.62e+01 d.230.5.1 120432 1w4tA 299 2.67e+01 d.3.1.5 120639 1xtmA 175 2.68e+01 1hybA 181 2.71e+01 1f9aA c.26.1.3 61399 2qddA 378 2.73e+01 1f9aA 168 2.75e+01 1f9aA c.26.1.3 31602 1ct9A 553 2.76e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1ctf 74 2.78e+01 1ctf 1k8kF 168 2.80e+01 d.198.2.1 68312 2h4tA 626 2.80e+01 1itpA 77 2.81e+01 d.58.3.2 66371 1hr6B 443 2.83e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1j6wA 175 2.84e+01 1j98A d.185.1.2 62663 1cr1A 296 2.85e+01 1cr1A c.37.1.11 32286 2nv0A 196 2.87e+01 c.23.16.1 138625 1dk4A 252 2.87e+01 1dk4A e.7.1.1 42970 1a0i 348 2.90e+01 1a0i 1a0iA 348 2.90e+01 b.40.4.6,d.142.2.1 25363,41577 2obpA 96 2.90e+01 1ctfA 74 2.92e+01 d.45.1.1 38759 1b0uA 262 2.95e+01 1b0uA c.37.1.12 32370 1qdlA 422 3.00e+01 1qdlA d.161.1.1 42088 3canA 182 3.01e+01 1c96A 753 3.02e+01 1amj c.8.2.1,c.83.1.1 30727,35403 2axpA 173 3.02e+01 c.37.1.1 127497 1gkuB 1054 3.02e+01 c.37.1.16,c.37.1.16,e.10.1.1 65257,65258,65259 1p0zA 131 3.03e+01 d.110.6.1 93882 1jdw 423 3.06e+01 1jdw 1jdwA 423 3.06e+01 d.126.1.2 41129 2cyyA 151 3.14e+01 a.4.5.32,d.58.4.2 131028,131029 1jc4A 148 3.14e+01 1jc4A d.32.1.4 62863 2gzsA 278 3.15e+01 1duxC 94 3.15e+01 1awcA a.4.5.21 16170 1sgjA 284 3.15e+01 c.1.12.5 105535 1h72C 296 3.16e+01 d.14.1.5,d.58.26.1 60712,60713 1wdpA 495 3.22e+01 c.1.8.1 120907 9gafA 295 3.25e+01 1apyA d.153.1.5 42008 1ks9A 291 3.26e+01 a.100.1.7,c.2.1.6 68857,68858 3bddA 142 3.30e+01 1i27A 73 3.31e+01 1i27A a.4.5.30 61555 1dowA 205 3.34e+01 1dovA a.24.9.1 16626 1vfqA 143 3.35e+01 d.109.1.2 120054 2qx5A 661 3.37e+01 1p4kA 295 3.45e+01 d.153.1.5 87772 1yroB 286 3.47e+01 c.68.1.2 123932 1t3qB 788 3.47e+01 d.41.1.1,d.133.1.1 106369,106370 2a8lA 420 3.51e+01 2g64A 140 3.51e+01 d.96.1.2 134694 1tx2A 297 3.60e+01 c.1.21.1 107420 2dcfA 392 3.61e+01 1unkA 87 3.62e+01 1cei a.28.2.1 16935 1q7zA 566 3.63e+01 c.1.21.2,c.1.26.1 96090,96091 1qd1A 325 3.64e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 2yzuA 109 3.66e+01 1j1nA 492 3.70e+01 c.94.1.1 83978 1wdcC 156 3.70e+01 1wdcC a.39.1.5 17317 1g5aA 628 3.72e+01 b.71.1.1,c.1.8.1 65152,65153 2d4gA 171 3.73e+01 1g8tA 245 3.77e+01 1qaeA d.4.1.2 37137 2gscA 128 3.78e+01 1uuqA 440 3.81e+01 c.1.8.3 100015 2pmzA 880 3.83e+01 2vluA 122 3.84e+01 1z0jB 59 3.84e+01 a.2.19.1 124320 1wueA 386 3.87e+01 c.1.11.2,d.54.1.1 114892,114893 2v78A 313 3.88e+01 1kdoA 227 3.88e+01 c.37.1.1 68478 1ko7A 314 3.91e+01 c.98.2.1,c.91.1.2 72797,72798 2j66A 428 3.91e+01 1a79A 171 3.92e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 2cvkA 110 3.99e+01 2r2iA 198 4.02e+01 2pn0A 141 4.08e+01 2ewfA 610 4.21e+01 1ornA 226 4.25e+01 a.96.1.1 87342 1o4uA 285 4.26e+01 c.1.17.1,d.41.2.1 86624,86625 1f5mA 180 4.29e+01 1f5mB d.110.2.1 40895 2fa5A 162 4.30e+01 2iwbA 246 4.35e+01 2hq4A 161 4.35e+01 1r9gA 216 4.39e+01 c.23.16.1 97258 2pa8D 265 4.39e+01 1jjhA 86 4.46e+01 2bopA d.58.8.1 63119 2fy7A 287 4.48e+01 1hzfA 367 4.48e+01 a.102.4.4 76731 1auiB 169 4.50e+01 1auiB a.39.1.5 17325 2v9kA 530 4.54e+01 1gdhA 320 4.54e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 2pe3A 354 4.56e+01 1utuA 108 4.60e+01 1r1dA 247 4.61e+01 c.69.1.29 96813 1q7rA 219 4.64e+01 c.23.16.1 96054 3bfxA 296 4.70e+01 1scmB 145 4.70e+01 1wdcB a.39.1.5 17304 2os0A 188 4.73e+01 1lrzA 426 4.74e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1z00B 84 4.77e+01 a.60.2.5 124295 1a8pA 258 4.80e+01 b.43.4.2,c.25.1.1 25654,31544 2qmoA 220 4.84e+01 1nzjA 298 4.86e+01 c.26.1.1 92377 1adeA 431 4.91e+01 1adeA c.37.1.10 32213 1h67A 108 5.06e+01 a.40.1.1 65643 1puzA 82 5.10e+01 a.218.1.1 104320 1ykdA 398 5.14e+01 2fhpA 187 5.16e+01 c.66.1.46 133495 2p90A 319 5.18e+01 2bayA 61 5.21e+01 g.44.1.2 128251 2o5gA 148 5.21e+01 2kinA 238 5.22e+01 1bg2 c.37.1.9 32190 1ggzA 148 5.25e+01 a.39.1.5 70176 2i8lA 156 5.26e+01 1gln 468 5.26e+01 1gln 2f3yA 148 5.32e+01 2q02A 272 5.34e+01 1rqjA 299 5.36e+01 a.128.1.1 97744 1to3A 304 5.36e+01 c.1.10.1 107161 1oxxK 353 5.39e+01 b.40.6.3,c.37.1.12 93715,93716 1id0A 152 5.45e+01 d.122.1.3 66111 1ji7A 89 5.46e+01 a.60.1.1 71682 3pfk 319 5.47e+01 3pfk 1wybA 392 5.51e+01 1q35A 320 5.58e+01 c.94.1.1 95661 1topA 162 5.59e+01 a.39.1.5 17223 3borA 237 5.60e+01 1wycA 392 5.62e+01 3bwvA 180 5.63e+01 1dmaA 214 5.64e+01 1aerA d.166.1.1 42251 1umwA 237 5.64e+01 d.223.1.2,d.223.1.2 99631,99632 1wzuA 300 5.66e+01 c.145.1.1 121528 2e58A 308 5.72e+01 1aerA 205 5.73e+01 1aerA d.166.1.1 42249 1kl7A 514 5.74e+01 c.79.1.1 72678 1iioA 84 5.74e+01 a.39.4.1 66150 1rkbA 173 5.75e+01 c.37.1.1 111854 1qf5A 431 5.79e+01 1adeA c.37.1.10 32212 2ddzA 190 5.79e+01 1ae9A 179 5.82e+01 1ae9A d.163.1.1 42153 1wndA 495 5.83e+01 c.82.1.1 114751 1bj4A 470 5.92e+01 1bj4A c.67.1.4 34479 2dgdA 223 5.98e+01 1vliA 385 6.05e+01 b.85.1.1,c.1.10.6 108830,108831 1gh8A 89 6.07e+01 1gh8A d.58.12.1 39309 1lddA 74 6.09e+01 a.4.5.34 73841 2a2pA 129 6.13e+01 c.47.1.23 126051 1yfoA 302 6.23e+01 2shpA c.45.1.2 32681 1vizA 240 6.24e+01 c.1.4.1 100784 2c4eA 302 6.24e+01 2f5gA 133 6.26e+01 d.58.57.1 132991 2pkfA 334 6.30e+01 2bopA 85 6.32e+01 2bopA d.58.8.1 39217 1dmzA 158 6.34e+01 1qu5A b.26.1.2 23921 1jqgA 433 6.36e+01 c.56.5.1,d.58.3.1 71791,71792 2au5A 139 6.37e+01 a.244.1.1 127322 1ispA 181 6.40e+01 c.69.1.18 76778 1mzeA 351 6.41e+01 b.82.2.6 79694 1ql0A 241 6.42e+01 1qaeA d.4.1.2 37139 1lmzA 187 6.42e+01 a.96.1.4 74037 1mfgA 95 6.44e+01 b.36.1.1 79043 6pfkA 319 6.46e+01 3pfk c.89.1.1 35583 2c2xA 281 6.47e+01 1wfxA 186 6.47e+01 d.166.1.5 114596 1ncx 162 6.48e+01 1ncx 2gx5A 170 6.49e+01 1bc8C 93 6.50e+01 1awcA a.4.5.21 16168 1s4nA 348 6.52e+01 c.68.1.16 98501 2a1jA 63 6.53e+01 a.60.2.5 126000 1jr3A 373 6.58e+01 a.80.1.1,c.37.1.20 63245,63246 3bofA 566 6.60e+01 1j09A 468 6.65e+01 a.97.1.1,c.26.1.1 77025,77026 2qdxA 257 6.70e+01 2yxtA 312 6.71e+01 2hzmB 317 6.72e+01 1oxsC 353 6.73e+01 b.40.6.3,c.37.1.12 87519,87520 3b6hA 498 6.74e+01 1tw3A 360 6.91e+01 a.4.5.29,c.66.1.12 107373,107374 1e2xA 243 6.91e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 2fgeA 995 6.91e+01 d.185.1.1,d.185.1.1,d.185.1.1,d.185.1.1 133430,133431,133432,133433 1zg2A 107 6.94e+01 1xkpA 246 6.96e+01 a.243.1.3 122086 2eaqA 90 6.96e+01 1nmsA 249 7.00e+01 c.17.1.1 85879 2ogxA 276 7.00e+01 2jigA 224 7.01e+01 1e7uA 961 7.11e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1uptB 60 7.13e+01 a.193.1.1 99768 1rgs 288 7.14e+01 1rgs 2pc1A 201 7.15e+01 1qauA 112 7.19e+01 1qauA b.36.1.1 24779 2cxiA 348 7.19e+01 1br1B 150 7.19e+01 1wdcC a.39.1.5 17309 1s6cA 183 7.21e+01 a.39.1.5 98594 1suuA 312 7.23e+01 b.68.10.1 99006 1ojxA 263 7.25e+01 c.1.10.1 93164 1b5tA 275 7.27e+01 1b5tA c.1.23.1 29676 1twfB 1224 7.28e+01 e.29.1.1 112726 2yvyA 278 7.29e+01 2dknA 255 7.29e+01 1w8sA 263 7.30e+01 c.1.10.1 120744 1ne6A 283 7.32e+01 b.82.3.2,b.82.3.2 91831,91832 1t5oA 351 7.34e+01 c.124.1.5 106459 1zotA 358 7.40e+01 2e62A 61 7.40e+01 1ockA 412 7.43e+01 c.117.1.1 86802 1tqhA 247 7.43e+01 c.69.1.29 107225 2esrA 177 7.47e+01 c.66.1.46 132344 2o3fA 111 7.49e+01 1t1iA 364 7.53e+01 c.41.1.2 106248 2obhA 143 7.56e+01 2fdrA 229 7.57e+01 c.108.1.6 133319 1y9uA 323 7.61e+01 c.94.1.1 116594 2trxA 108 7.62e+01 1thx c.47.1.1 32719 2r98A 456 7.65e+01 1o9rA 162 7.68e+01 a.25.1.1 86706 1zxtA 76 7.75e+01 1wn0A 145 7.76e+01 a.24.10.2 121070 1fn8A 224 7.77e+01 5ptp b.47.1.2 26012 1i6wA 181 7.78e+01 1i6wA c.69.1.18 61859 3b5mA 205 7.78e+01 2ditA 112 7.80e+01 d.58.7.1 131533 1mvuB 121 7.81e+01 b.1.1.1 91475 3bxoA 239 7.86e+01 1try 224 7.87e+01 5ptp 2h3lA 103 7.88e+01 b.36.1.1 136046 1qavB 115 7.92e+01 1qauA b.36.1.1 24780 1zdsA 336 7.92e+01 b.6.1.3,b.6.1.3 124952,124953 2owrA 218 7.92e+01 2ogiA 196 7.94e+01 2b2aA 199 7.94e+01 1eyuA 157 7.99e+01 3pviA c.52.1.6 33304