# List of top-scoring protein chains for t2k-100-30-bys-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 1vi3A 170 2.15e-02 b.17.1.2 100730 1fjjA 159 2.55e-02 1fjjA b.17.1.2 59852 2qpwA 149 1.10e+00 2gfaA 119 1.10e+00 b.34.9.1,b.34.9.1 135089,135090 1ew3A 159 1.26e+00 1mup b.60.1.1 27114 1fuxA 166 1.40e+00 1fjjA b.17.1.2 60034 2eifA 136 1.68e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1qwdA 177 2.06e+00 b.60.1.1 96471 3cddA 361 2.23e+00 2hbwA 235 3.05e+00 2acoA 173 3.16e+00 2cbpA 96 3.20e+00 b.6.1.1 22895 1f8fA 371 3.25e+00 b.35.1.2,c.2.1.1 83246,83247 1xuvA 178 3.31e+00 d.129.3.5 116069 2p18A 311 3.60e+00 1isiA 265 3.68e+00 c.23.14.3 71394 1aonO 97 4.31e+00 b.35.1.1 24642 1bkb 136 4.76e+00 1bkb 1bkbA 136 4.76e+00 b.34.5.2,b.40.4.5 24609,25341 1ws8A 109 4.80e+00 b.6.1.1 114843 2qqrA 118 4.94e+00 1ktjA 129 4.96e+00 b.1.18.7 72974 1x6oA 174 5.47e+00 b.34.5.2,b.40.4.5 109493,109494 2hc8A 113 5.92e+00 1gpl 432 6.15e+00 1gpl 2qtpA 194 6.20e+00 1jjtA 228 6.43e+00 1a7tA d.157.1.1 63139 1kdkA 177 6.53e+00 b.29.1.4 72351 1ux6A 350 7.11e+00 b.29.1.16,g.75.1.1 100145,100146 2bkdN 134 7.46e+00 1jjeA 222 7.58e+00 1a7tA d.157.1.1 63117 1hgeA 328 7.58e+00 1hgeA b.19.1.2 23816 1d2sA 170 7.69e+00 1d2sA b.29.1.4 24221 2q7nA 488 8.27e+00 1cr5A 189 8.47e+00 1cr5A b.52.2.3,d.31.1.1 26931,38465 2d9rA 104 8.70e+00 b.129.2.1 131350 2ak5A 64 8.81e+00 1a0nB 69 9.02e+00 1bbzA b.34.2.1 24469 2g6fX 59 9.38e+00 1f5fA 205 9.69e+00 1d2sA b.29.1.4 24222 1c3hA 137 9.99e+00 b.22.1.1 90405 1zxiC 288 1.04e+01 d.87.2.1,d.145.1.3 125776,125777 1z85A 234 1.07e+01 1p9yA 121 1.10e+01 d.241.2.1 94402 2p0wA 324 1.12e+01 1n62C 288 1.12e+01 d.87.2.1,d.145.1.3 80094,80095 1e0tA 470 1.14e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2bmjA 178 1.16e+01 c.37.1.8 128797 3hmgA 328 1.16e+01 1hgeA b.19.1.2 23825 1aozA 552 1.17e+01 1aozA b.6.1.3,b.6.1.3,b.6.1.3 23124,23125,23126 2g3rA 123 1.18e+01 b.34.9.1,b.34.9.1 134570,134571 2q3zA 687 1.23e+01 2hf0A 316 1.24e+01 3bxoA 239 1.27e+01 1yz4A 160 1.28e+01 1yezA 68 1.30e+01 b.40.4.12 123026 3besR 250 1.31e+01 1s0uA 408 1.32e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1dl5A 317 1.33e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1w4sA 174 1.34e+01 2qf4A 172 1.35e+01 1wn1A 356 1.36e+01 1o7sA 127 1.36e+01 b.1.1.1 86644 2e3hA 90 1.36e+01 2oqkA 117 1.39e+01 1z9lA 128 1.39e+01 1epaA 164 1.40e+01 1epaA b.60.1.1 27128 2viuA 328 1.40e+01 1hgeA b.19.1.2 23797 1rl2A 137 1.52e+01 1rl2A b.34.5.3,b.40.4.5 24610,25342 1on0A 158 1.55e+01 d.108.1.1 87095 1ufhA 180 1.55e+01 d.108.1.1 88485 2ptfA 233 1.59e+01 1iznB 277 1.65e+01 e.43.1.2 83848 1gzcA 239 1.66e+01 b.29.1.1 70803 1gmiA 136 1.67e+01 b.7.1.1 65309 1ssfA 156 1.67e+01 b.34.9.1,b.34.9.1 105982,105983 1gmlA 178 1.68e+01 c.8.5.2 70273 2euiA 153 1.69e+01 d.108.1.1 132387 2bgiA 272 1.71e+01 1ao7D 204 1.72e+01 1tcrA b.1.1.1 20623 1yqhA 109 1.76e+01 d.58.48.1 123886 2r99A 173 1.77e+01 2qg5A 294 1.79e+01 1wthD 391 1.83e+01 b.106.1.1,b.106.1.1 121268,121269 1e8yA 966 1.85e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 2in0A 139 1.86e+01 1mh1 186 1.87e+01 1eesA 1mh1A 186 1.87e+01 c.37.1.8 32002 1qubA 319 1.99e+01 1qubA g.18.1.1,g.18.1.1,g.18.1.1,g.18.1.1,g.18.1.1 44863,44864,44865,44866,44867 2re9A 181 2.02e+01 2bz8A 58 2.03e+01 2oseA 234 2.07e+01 2qikA 285 2.09e+01 1c28A 135 2.12e+01 1c28A b.22.1.1 23857 1l6xA 207 2.24e+01 b.1.1.2,b.1.1.2 73642,73643 1zc1A 208 2.31e+01 2gw2A 198 2.31e+01 1shfA 59 2.36e+01 1bbzA b.34.2.1 24462 3tssA 194 2.37e+01 b.40.2.2,d.15.6.1 25160,37749 1dleA 298 2.39e+01 1dleA b.47.1.2 26312 1mwsA 646 2.40e+01 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1avaC 181 2.52e+01 1avaC b.42.4.1 25604 2f5kA 102 2.52e+01 b.34.13.3 132995 1nykA 165 2.53e+01 b.33.1.1 86408 2c9oA 456 2.55e+01 2qk0A 74 2.55e+01 1vqoD 177 2.57e+01 d.77.1.1 120365 1nkoA 132 2.59e+01 b.1.1.1 85829 1u2hA 99 2.61e+01 1lgpA 116 2.82e+01 b.26.1.2 73890 2rc5A 314 2.83e+01 2bgzA 299 2.84e+01 1pieA 419 2.85e+01 d.14.1.5,d.58.26.7 94706,94707 1xhkA 187 2.89e+01 d.14.1.10 115299 1g5vA 88 2.92e+01 1g5vA b.34.9.1 60292 1jhfA 202 2.94e+01 a.4.5.2,b.87.1.1 63057,63058 2it1A 362 2.99e+01 1efyA 350 3.00e+01 1a26 a.41.1.1,d.166.1.2 17413,42275 1pk6A 133 3.08e+01 b.22.1.1 94801 1avbA 226 3.09e+01 1led b.29.1.1 24158 2cy2A 174 3.10e+01 d.108.1.1 131016 1yo8A 634 3.10e+01 2q4zA 312 3.11e+01 2ftsA 419 3.12e+01 b.85.6.1,b.103.1.1,c.57.1.2 134079,134080,134081 1oebA 62 3.13e+01 b.34.2.1 86909 2z14A 133 3.16e+01 1xniA 118 3.17e+01 b.34.9.1,b.34.9.1 115582,115583 2rmcA 182 3.20e+01 2cpl b.62.1.1 27491 1c4qA 69 3.21e+01 2bosA b.40.2.1 25010 1ezvB 352 3.22e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 2cmtA 172 3.24e+01 1bb9 115 3.24e+01 1bb9 1bb9A 115 3.24e+01 b.34.2.1 24554 1vc3B 97 3.31e+01 2nykA 285 3.34e+01 2jrmA 65 3.37e+01 1utiA 58 3.40e+01 b.34.2.1 99962 1n9lA 109 3.42e+01 d.110.3.6 85468 1wk8A 194 3.52e+01 1mxgA 435 3.53e+01 b.71.1.1,c.1.8.1 85193,85194 1zn8A 180 3.55e+01 c.61.1.1 125376 2cksA 306 3.55e+01 1v7lA 163 3.58e+01 c.8.2.1 113562 1uebA 184 3.65e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1udzA 182 3.66e+01 b.51.1.1 99239 1q2yA 140 3.72e+01 d.108.1.1 95655 2dtqA 223 3.73e+01 b.1.1.2,b.1.1.2 131725,131726 2cw9A 194 3.77e+01 d.17.4.13 130920 1iq6A 134 3.84e+01 d.38.1.4 76755 1coaI 64 3.84e+01 2sniI d.40.1.1 38574 2qxlA 658 3.93e+01 1mhnA 59 3.99e+01 b.34.9.1 84964 1axsA 211 4.06e+01 8fabA b.1.1.1,b.1.1.2 20200,21216 3byvA 377 4.07e+01 1a98A 152 4.08e+01 1nulA c.61.1.1 34021 1dg6A 191 4.10e+01 1d4vB b.22.1.1 23883 1ggxA 223 4.10e+01 1ggxA d.22.1.1 38367 1i8dA 213 4.11e+01 b.43.4.3,b.43.4.3 61953,61954 2h4pA 394 4.13e+01 1h6kX 97 4.13e+01 d.58.7.1 60684 2dy0A 190 4.13e+01 1x2kA 68 4.16e+01 2r3uA 211 4.24e+01 1ibyA 112 4.27e+01 1ibzA b.6.1.4 62233 2ii1A 301 4.29e+01 3b9eA 584 4.29e+01 2iwrA 178 4.29e+01 1el5A 389 4.32e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 2qfeA 148 4.34e+01 2gf3A 389 4.37e+01 c.3.1.2,d.16.1.3 135070,135071 1fdr 248 4.43e+01 1fdr 1fdrA 248 4.43e+01 b.43.4.2,c.25.1.1 25653,31543 1yewA 382 4.45e+01 1b9vA 390 4.56e+01 2qwc b.68.1.1 27603 2b9uA 176 4.57e+01 1l9cA 389 4.59e+01 c.3.1.2,d.16.1.3 77815,77816 1bywA 110 4.63e+01 1bywA d.110.3.6 40912 1ahxA 396 4.64e+01 1ajsA c.67.1.1 34293 1lw6I 64 4.64e+01 d.40.1.1 74294 2oynA 146 4.70e+01 2bzlA 325 4.70e+01 1dr9A 201 4.72e+01 1dr9A b.1.1.1,b.1.1.3 19762,21684 1avzC 57 4.77e+01 1bbzA b.34.2.1 24467 1wpgA 994 4.81e+01 b.82.7.1,c.108.1.7,d.220.1.1,f.33.1.1 114806,114807,114808,114809 1yvcA 70 4.82e+01 b.40.4.12 124094 1arhA 396 4.82e+01 1ajsA c.67.1.1 34321 1ehsA 48 4.83e+01 g.2.1.1 43998 1p97A 114 4.84e+01 d.110.3.7 94382 1at0 145 4.86e+01 1at0 1at0A 145 4.86e+01 b.86.1.1 28374 2qecA 204 4.88e+01 2rdeA 251 4.90e+01 1wlgA 299 4.95e+01 b.152.1.1 114726 2hhcA 330 4.95e+01 3c2qA 345 4.95e+01 1wnyA 186 5.03e+01 1g1sA 162 5.06e+01 d.169.1.1,g.3.11.1 65100,65101 2zaiA 497 5.15e+01 2fhxA 246 5.16e+01 2ouxA 286 5.17e+01 1yr0A 175 5.19e+01 d.108.1.1 123905 1vz0A 230 5.20e+01 a.4.14.1,d.268.1.1 108929,108930 2bwjA 199 5.25e+01 1qjwA 365 5.27e+01 1bvwA c.6.1.1 30657 1ypcI 64 5.31e+01 2sniI d.40.1.1 38570 2bjqA 345 5.32e+01 b.169.1.1,b.169.1.1 128626,128627 2oiwA 136 5.40e+01 2g1uA 155 5.41e+01 2b1kA 168 5.41e+01 1rzfH 235 5.46e+01 b.1.1.1,b.1.1.2 98150,98151 2nnwA 376 5.46e+01 1o91A 178 5.53e+01 b.22.1.1 92656 1kfuL 699 5.54e+01 a.39.1.8,b.14.1.1,d.3.1.3 68571,68572,68573 1xo3A 101 5.56e+01 d.15.3.3 115678 1ariA 396 5.61e+01 1ajsA c.67.1.1 34331 2oh5A 248 5.66e+01 1zgoA 223 5.78e+01 1kb9B 352 5.82e+01 d.185.1.1,d.185.1.1 77313,77314 1jvnA 555 5.85e+01 c.1.2.1,c.23.16.1 67355,67356 1jpzA 473 5.87e+01 a.104.1.1 67069 1y8xA 160 5.88e+01 d.20.1.1 122769 1zpwX 90 5.88e+01 d.58.58.1 125478 2gu2A 312 5.93e+01 2bpsA 81 5.96e+01 1y8tA 324 5.98e+01 b.36.1.4,b.47.1.1 122763,122764 1tovA 98 5.99e+01 b.34.10.1 107179 2im9A 333 6.04e+01 d.3.1.13 137508 2jixB 225 6.06e+01 1ht6A 405 6.08e+01 b.71.1.1,c.1.8.1 83629,83630 1vqqA 646 6.11e+01 d.17.4.5,d.175.1.1,e.3.1.1 114009,114010,114011 1ile 821 6.13e+01 1ile 2msbA 115 6.16e+01 1rtm1 d.169.1.1 42355 2vnfA 60 6.16e+01 2bzsA 236 6.17e+01 c.23.5.3 129560 1f60A 458 6.23e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1jnyA 435 6.23e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2iiiA 135 6.24e+01 2jodA 106 6.24e+01 1wznA 252 6.29e+01 c.66.1.43 121525 1gcqA 61 6.34e+01 1ckaA b.34.2.1 60434 1ylnA 252 6.37e+01 b.45.2.1,b.45.2.2 123657,123658 2oaaA 249 6.42e+01 1g2oA 268 6.52e+01 1b8oA c.56.2.1 60228 2hqxA 246 6.58e+01 b.34.9.1 136675 1ako 268 6.58e+01 1ako 1akoA 268 6.58e+01 d.151.1.1 41779 3b77A 193 6.61e+01 1msoB 30 6.63e+01 g.1.1.1 85092 1rtm1 149 6.66e+01 1rtm1 2bzyA 67 6.72e+01 1uheA 97 6.78e+01 1o54A 277 6.79e+01 c.66.1.13 92482 1xwvA 129 6.80e+01 b.1.18.7 116134 1b9eB 30 6.81e+01 g.1.1.1 43885 1b08A 158 6.82e+01 1rtm1 d.169.1.1,h.1.1.1 42416,45423 2yzjA 169 6.87e+01 2pbnA 313 6.96e+01 1azgB 67 6.98e+01 1bbzA b.34.2.1 24471 1lplA 95 7.03e+01 b.34.10.1 74173 2j59M 168 7.04e+01 2f1cX 286 7.06e+01 1rkiA 102 7.07e+01 d.308.1.2 118776 1a6dB 543 7.12e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 2rieA 160 7.12e+01 2q7sA 290 7.13e+01 3cb0A 173 7.13e+01 1btn 106 7.14e+01 1btn 1btnA 106 7.14e+01 b.55.1.1 26952 1dciA 275 7.16e+01 1dciA c.14.1.3 30918 2imlA 199 7.19e+01 1bu7A 455 7.20e+01 1bu7A a.104.1.1 18937 2arhA 203 7.22e+01 d.108.1.9 127197 1l1dA 152 7.22e+01 b.88.1.3 73452 2ovlA 371 7.27e+01 2hr0A 645 7.28e+01 1e8xA 961 7.34e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1yjmA 110 7.38e+01 b.26.1.2 123427 1rwiA 270 7.40e+01 b.68.9.1 97987 1a58A 177 7.43e+01 b.62.1.1 27495 2ijaA 295 7.50e+01 1oapA 109 7.51e+01 d.79.7.1 92706 1yn8A 59 7.51e+01 2o8qA 134 7.51e+01 1sotA 320 7.52e+01 b.36.1.4,b.47.1.1 105852,105853 1vjjA 692 7.53e+01 b.1.18.9,b.1.5.1,b.1.5.1,d.3.1.4 100814,100815,100816,100817 1onxA 390 7.59e+01 b.92.1.7,c.1.9.13 87176,87177 1b94A 244 7.62e+01 1rvaA c.52.1.2 33250 2ar1A 172 7.62e+01 b.122.1.8 127187 2h2tB 175 7.62e+01 1m7sA 484 7.62e+01 e.5.1.1 74574 1vprA 374 7.68e+01 b.60.1.7 120066 2pfrA 294 7.77e+01 3caxA 369 7.78e+01 2qntA 141 7.80e+01 1xe0A 114 7.80e+01 b.121.3.1 115197 1xo7A 166 7.83e+01 b.62.1.1 115694 1b97A 244 7.85e+01 1rvaA c.52.1.2 33252 1smoA 119 7.91e+01 b.1.1.1 105764 1fhgA 154 7.93e+01 1tlk b.1.1.4 21706 1wgvA 124 7.95e+01 b.15.1.4 114624 1f6fB 210 7.98e+01 1axiB b.1.2.1,b.1.2.1 22033,22034 2hdaA 64 7.98e+01