# 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.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 2h3jA 75 4.18e-10 2gcxA 75 8.07e-10 1fx7A 230 2.46e-04 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 2dtr 226 2.58e-04 1bi0 1bi0 226 3.74e-04 1bi0 1bymA 97 9.57e-04 1bi0 b.34.1.2 24458 3c0cA 73 6.85e-03 2g6fX 59 1.15e-02 1gcqA 61 1.28e-02 1ckaA b.34.2.1 60434 2drmA 58 1.30e-02 1zx6A 58 1.99e-02 1aboA 62 2.15e-02 1bbzA b.34.2.1 24474 2qq9A 226 2.23e-02 2ak5A 64 2.48e-02 2jngA 105 2.68e-02 1oebA 62 2.94e-02 b.34.2.1 86909 1w70A 60 3.19e-02 2a28A 54 3.27e-02 1bbzA 58 3.30e-02 1bbzA b.34.2.1 24477 2vgeA 229 3.80e-02 1utiA 58 4.15e-02 b.34.2.1 99962 2ggrA 76 4.83e-02 1ylnA 252 4.92e-02 b.45.2.1,b.45.2.2 123657,123658 2a08A 60 7.14e-02 2p19A 149 7.55e-02 1hd3A 62 7.94e-02 b.34.2.1 65802 2o88A 58 8.62e-02 1ootA 60 8.89e-02 b.34.2.1 93386 1ov3A 138 9.05e-02 b.34.2.1,b.34.2.1 87451,87452 2o9sA 67 1.37e-01 2qtxA 71 1.52e-01 1ng2A 193 1.76e-01 b.34.2.1,b.34.2.1 85660,85661 2fa1A 160 1.94e-01 d.190.1.2 133182 2o31A 67 2.01e-01 1tuc 63 2.18e-01 1tuc 2mcm 112 2.54e-01 2mcm 2mcmA 112 2.54e-01 b.1.7.1 22207 1u06A 62 3.06e-01 b.34.2.1 119404 1dj7B 75 3.37e-01 1dj7B b.34.4.3 24598 1griA 217 3.40e-01 1griA b.34.2.1,b.34.2.1,d.93.1.1 24531,24532,40473 1j48A 110 4.04e-01 b.1.7.1 84112 2ealA 148 4.10e-01 1tg0A 68 4.45e-01 2iimA 62 4.83e-01 b.34.2.1 137434 2d1xA 66 4.83e-01 2oq0A 206 4.96e-01 1gcqC 70 5.07e-01 1gcpA b.34.2.1 60436 1semA 58 5.21e-01 1ckaA b.34.2.1 24544 1amy 403 5.43e-01 1jdc 2bz8A 58 5.51e-01 2bzyA 67 5.70e-01 1e0cA 271 5.72e-01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1zlmA 58 6.05e-01 2cwzA 141 6.19e-01 d.38.1.7 130961 1noaA 113 6.31e-01 b.1.7.1 22208 1zq1A 438 6.34e-01 b.38.3.1,c.88.1.1 125489,125490 1q7hA 153 6.52e-01 b.122.1.1,d.17.6.2 96042,96043 3bwgA 239 6.67e-01 2rdeA 251 7.24e-01 1wlpB 138 7.62e-01 b.34.2.1 121010 1z9zA 60 7.78e-01 3cnvA 162 8.08e-01 2j6fA 62 1.02e+00 2d6mA 159 1.08e+00 2i7rA 118 1.12e+00 d.32.1.2 137102 1db3A 372 1.16e+00 1db3A c.2.1.2 29813 1pcaA 95 1.22e+00 d.58.3.1 39063 1eejA 216 1.26e+00 1eejA c.47.1.9,d.17.3.1 33057,38071 1zc1A 208 1.27e+00 1lcl 142 1.27e+00 1lcl 1hk6A 95 1.31e+00 b.1.18.18 83539 2pu9B 74 1.32e+00 1jegA 83 1.33e+00 b.34.2.1 66610 1lq9A 112 1.39e+00 d.58.4.3 78129 1xxaA 78 1.43e+00 1xxaA d.74.2.1 39700 2v1qA 60 1.51e+00 1b0jA 754 1.55e+00 1amj c.8.2.1,c.83.1.1 30719,35395 1vavA 222 1.56e+00 b.29.1.18 108472 1avaA 403 1.60e+00 1jdc b.71.1.1,c.1.8.1 27797,28784 1efnA 59 1.68e+00 1bbzA b.34.2.1 24465 1pytA 94 1.70e+00 1pytA d.58.3.1 39064 1ts9A 102 1.75e+00 b.137.1.1 112618 2fomB 185 1.83e+00 b.47.1.3 133884 1ug1A 92 1.84e+00 b.34.2.1 99360 1shfA 59 1.87e+00 1bbzA b.34.2.1 24462 1cjxA 357 1.89e+00 1cjxA d.32.1.3,d.32.1.3 38516,38517 2ivsA 314 1.92e+00 2i04A 85 1.97e+00 1opd 85 1.97e+00 1ptf 1opdA 85 1.97e+00 d.94.1.1 40560 2ikkA 173 2.01e+00 1hdkA 141 2.06e+00 b.29.1.3 65807 2qr7A 342 2.08e+00 1wdxA 69 2.09e+00 1wyxA 69 2.24e+00 1y14B 171 2.29e+00 b.40.4.5,d.230.1.1 116323,116324 1wjxA 122 2.31e+00 b.111.1.1 114716 1xneA 113 2.40e+00 b.122.1.6 115579 2yxyA 115 2.42e+00 2v1rA 80 2.46e+00 2hhzA 150 2.52e+00 2ba1A 179 2.55e+00 2p0pA 126 2.58e+00 2gncA 60 2.60e+00 1g2bA 62 2.61e+00 1tud b.34.2.1 24488 2qggA 182 2.65e+00 1gcpA 70 2.69e+00 1gcpA b.34.2.1 60430 1z47A 355 2.70e+00 1wexA 104 2.77e+00 d.58.7.1 114568 3cp0A 82 2.78e+00 2dbsA 90 2.78e+00 1bkzA 135 2.81e+00 1a3k b.29.1.3 24202 1dkgA 197 2.84e+00 1dkgA b.73.1.1,h.1.9.1 27812,45626 2de0X 526 2.87e+00 3cjxA 165 2.88e+00 2qf7A 1165 2.97e+00 1b4bA 71 2.97e+00 1b4aA d.74.2.1 39718 1azgB 67 2.99e+00 1bbzA b.34.2.1 24471 1mhnA 59 3.06e+00 b.34.9.1 84964 2hvqA 335 3.11e+00 1eikA 77 3.14e+00 1eikA d.78.1.1 39751 1cskA 71 3.15e+00 1ckaA b.34.2.1 24513 1kjlA 146 3.21e+00 b.29.1.3 118689 1uj0A 62 3.21e+00 b.34.2.1 99449 2r5xA 129 3.27e+00 1ngzA 213 3.28e+00 b.1.1.1,b.1.1.2 80500,80501 1sf9A 128 3.35e+00 b.34.15.1 98831 1zi0A 307 3.44e+00 2f57A 317 3.46e+00 2j05A 65 3.49e+00 2reiA 318 3.51e+00 1aw8B 91 3.57e+00 1aw8B 1jj2S 119 3.62e+00 1ffkQ b.34.5.1 63104 2nn8A 138 3.65e+00 b.29.1.3 138392 2pa1A 87 3.73e+00 1c96A 753 3.76e+00 1amj c.8.2.1,c.83.1.1 30727,35403 1uarA 285 3.80e+00 c.46.1.2,c.46.1.2 107762,107763 2e27L 119 3.85e+00 1zuyA 58 3.86e+00 1ht6A 405 3.87e+00 b.71.1.1,c.1.8.1 83629,83630 1z94A 147 3.91e+00 d.129.3.5 124740 1pn2A 280 3.91e+00 d.38.1.4,d.38.1.4 94930,94931 2hbwA 235 3.97e+00 1yhvA 297 3.97e+00 1b4aA 149 4.01e+00 1b4aA a.4.5.3,d.74.2.1 16088,39721 1c0aA 585 4.09e+00 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1kkhA 317 4.13e+00 d.14.1.5,d.58.26.3 72645,72646 1qw1A 121 4.15e+00 2pn0A 141 4.22e+00 1pbyA 489 4.27e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 2yv8A 164 4.29e+00 1vqoT 120 4.44e+00 b.34.5.1 120381 1xe1A 116 4.44e+00 b.43.3.1 109571 1a78A 134 4.62e+00 1c1lA b.29.1.3 24212 1ir3A 306 4.65e+00 1fmk d.144.1.7 41702 1y8oB 128 4.65e+00 b.84.1.1 122759 2hcuA 213 4.65e+00 1xuvA 178 4.66e+00 d.129.3.5 116069 2jilA 97 4.72e+00 2nwvA 114 4.73e+00 d.326.1.1 138720 1a3k 137 4.77e+00 1a3k 2q20A 109 4.79e+00 1wr2A 238 4.85e+00 1uheA 97 4.87e+00 2dchX 216 5.09e+00 2il5A 171 5.11e+00 1ruwA 69 5.13e+00 2fyqA 194 5.17e+00 2o1qA 145 5.33e+00 2eifA 136 5.38e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1zs7A 190 5.45e+00 b.122.1.1,d.17.6.4 125593,125594 1kafA 108 5.49e+00 d.199.1.1 68372 1b07A 59 5.50e+00 1ckaA b.34.2.1 24461 1k2pA 263 5.54e+00 d.144.1.7 72012 1nglA 179 5.61e+00 1nglA b.60.1.1 27146 1cbfA 285 5.70e+00 c.90.1.1 35587 2egoA 96 5.74e+00 3c4sA 66 5.77e+00 2cx1A 187 5.84e+00 b.122.1.1,d.17.6.4 130967,130968 2jdqD 83 5.88e+00 1n3hA 207 5.90e+00 b.55.1.2 91564 1qcsA 211 6.08e+00 1qcsA b.52.2.3,d.31.1.1 26927,38461 2a7lA 136 6.11e+00 d.20.1.1 126350 1i8dA 213 6.20e+00 b.43.4.3,b.43.4.3 61953,61954 1han 297 6.25e+00 1han 1xppA 115 6.36e+00 d.74.3.2 115768 1gz8A 299 6.48e+00 d.144.1.7 83405 2hpsA 186 6.49e+00 1jnyA 435 6.50e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1fdr 248 6.50e+00 1fdr 1fdrA 248 6.50e+00 b.43.4.2,c.25.1.1 25653,31543 2fcfA 103 6.57e+00 b.36.1.1 133267 1quqA 129 6.59e+00 1quqA b.40.4.3 25303 1d1rA 116 6.63e+00 1d1rA d.64.1.1 39548 2cu2A 337 6.63e+00 1txyA 104 6.65e+00 b.40.4.3 112791 1m9sA 605 6.72e+00 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 2a6mA 155 6.77e+00 d.58.57.1 126287 1fo9A 348 6.84e+00 1foaA c.68.1.10 59928 1f3vA 179 6.85e+00 1f3vA d.58.22.1 39382 1s68A 249 6.89e+00 d.142.2.4 98591 2polA 366 6.90e+00 2polA d.131.1.1,d.131.1.1,d.131.1.1 41356,41357,41358 1lkdA 297 6.90e+00 d.32.1.3,d.32.1.3 78059,78060 1kwaA 88 6.91e+00 1kwaA b.36.1.1 24772 1hcl 298 6.92e+00 1hcl 1yleA 342 7.03e+00 d.108.1.8 123647 2pkhA 148 7.07e+00 1pht 85 7.08e+00 1ckaA 1phtA 85 7.08e+00 b.34.2.1 24483 1wocA 103 7.19e+00 2bpsA 81 7.20e+00 12e8L 214 7.27e+00 8fabA b.1.1.1,b.1.1.2 20268,21268 2evrA 246 7.34e+00 b.34.11.3,d.3.1.16 132440,132441 2he4A 90 7.39e+00 1iz6A 138 7.39e+00 b.34.5.2,b.40.4.5 76976,76977 2bi0A 337 7.67e+00 d.38.1.4,d.38.1.4 128565,128566 2it1A 362 7.69e+00 2brfA 110 7.74e+00 b.26.1.2 128996 1z6bA 154 7.83e+00 d.38.1.6 124510 1fo8A 343 7.87e+00 1foaA c.68.1.10 59927 1whi 122 8.08e+00 1whi 1whiA 122 8.08e+00 b.39.1.1 24810 2hykA 245 8.15e+00 2am1A 454 8.20e+00 2oggA 152 8.21e+00 2hl5C 97 8.26e+00 1uadC 99 8.29e+00 b.1.18.18 88379 1u9kA 114 8.29e+00 b.1.1.1 113244 1pqhA 143 8.36e+00 b.52.2.1 95017 1sphA 88 8.38e+00 1ptf d.94.1.1 40544 2k3aA 155 8.39e+00 3b9cA 144 8.40e+00 2bqxA 173 8.47e+00 1csbB 205 8.47e+00 1theB 1h9sA 140 8.50e+00 1b9mA b.40.6.2,b.40.6.2 60843,60844 1t3tA 1303 8.53e+00 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1cz4A 185 8.57e+00 1cz4A b.52.2.3,d.31.1.1 26934,38468 2qc1B 212 8.60e+00 1widA 130 8.78e+00 b.142.1.2 114667 1jpaA 312 8.90e+00 d.144.1.7 67011 2e7zA 727 9.01e+00 1bkb 136 9.09e+00 1bkb 1bkbA 136 9.09e+00 b.34.5.2,b.40.4.5 24609,25341 1p3hA 99 9.10e+00 b.35.1.1 87734 2nwiA 172 9.21e+00 1ru8A 232 9.22e+00 c.26.2.1 97849 1v1qA 134 9.22e+00 b.40.4.3 113490 1o6yA 299 9.44e+00 d.144.1.7 81106 1z85A 234 9.50e+00 1dcjA 81 9.70e+00 1dcjA d.68.3.3 59115 1b9mA 265 9.71e+00 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1l0wA 580 9.92e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1o6aA 96 9.95e+00 b.139.1.1 92562 2gk6A 624 1.00e+01 2fe5A 94 1.02e+01 b.36.1.1 133323 1dxeA 256 1.02e+01 1dxeA c.1.12.5 29310 1io1A 398 1.04e+01 1io1A e.32.1.1 62611 1je3A 97 1.04e+01 d.68.3.3 71637 1qx4A 274 1.05e+01 b.43.4.2,c.25.1.1 104624,104625 2aanA 139 1.05e+01 2pjsA 119 1.05e+01 1umkA 275 1.06e+01 b.43.4.2,c.25.1.1 113312,113313 1cmcA 104 1.07e+01 1cmbA a.43.1.5 17462 3baeL 218 1.07e+01 2p2uA 171 1.08e+01 3bs2A 148 1.08e+01 2cw5A 255 1.12e+01 1ckaA 57 1.12e+01 1ckaA b.34.2.1 24459 2e5yA 133 1.13e+01 2icsA 379 1.13e+01 b.92.1.8,c.1.9.14 137241,137242 2eueA 279 1.14e+01 1vg5A 73 1.16e+01 a.5.2.1 113640 3csvA 333 1.17e+01 1cmbA 104 1.18e+01 1cmbA a.43.1.5 17460 1o8bA 219 1.18e+01 c.124.1.4,d.58.40.1 81180,81181 1foaA 348 1.18e+01 1foaA c.68.1.10 59929 2pvfA 334 1.19e+01 2q9vA 90 1.19e+01 1ww7A 160 1.20e+01 1hlcA 129 1.21e+01 1c1lA b.29.1.3 24208 1y51A 88 1.23e+01 2eqjA 66 1.24e+01 1vgjA 184 1.24e+01 1vc3B 97 1.24e+01 1wubA 178 1.25e+01 b.61.6.1 114891 2vjvA 159 1.26e+01 1pt1A 143 1.26e+01 b.52.2.1 95084 1r5mA 425 1.28e+01 3blzA 128 1.29e+01 2dtrA 226 1.30e+01 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 2fvgA 340 1.31e+01 b.49.3.1,c.56.5.4 134201,134202 2au7A 175 1.32e+01 1qw2A 102 1.32e+01 d.249.1.1 96456 1kzlA 208 1.32e+01 b.43.4.3,b.43.4.3 77635,77636 1jhfA 202 1.32e+01 a.4.5.2,b.87.1.1 63057,63058 1ycsB 239 1.32e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 1pneA 139 1.33e+01 d.110.1.1 40866 1a7nL 107 1.35e+01 8fabA b.1.1.1 19940 2gciA 360 1.35e+01 c.123.1.1 134983 1pne 140 1.36e+01 1pne 1n0xL 215 1.37e+01 b.1.1.1,b.1.1.2 91532,91533 1zuuA 58 1.37e+01 b.34.2.1 125688 2e2wA 113 1.38e+01 1yjmA 110 1.39e+01 b.26.1.2 123427 1qfwM 108 1.39e+01 32c2A b.1.1.1 20436 1azeA 56 1.40e+01 b.34.2.1 24536 1wmxA 205 1.40e+01 b.18.1.24 109418 1nnxA 109 1.41e+01 b.40.10.1 92013 1f3aA 222 1.41e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 2elcA 329 1.41e+01 1bob 320 1.42e+01 1bob 1bobA 320 1.42e+01 d.108.1.1 40816 1ok7A 366 1.42e+01 d.131.1.1,d.131.1.1,d.131.1.1 103992,103993,103994 1hh2P 344 1.43e+01 b.40.4.5,d.52.3.1,d.52.3.1,d.202.1.1 65835,65836,65837,65838 1dlfL 113 1.43e+01 8fabA b.1.1.1 20382 2d7tL 116 1.45e+01 1i9yA 347 1.48e+01 1i9yA d.151.1.2 62101 1q46A 175 1.50e+01 a.60.14.1,b.40.4.5 111594,111595 1pjqA 457 1.52e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1lckA 175 1.53e+01 1lckA b.34.2.1,d.93.1.1 24552,40421 2glwA 92 1.53e+01 1i7pA 274 1.56e+01 b.43.4.2,c.25.1.1 66048,66049 1y8xB 98 1.56e+01 1jqgA 433 1.58e+01 c.56.5.1,d.58.3.1 71791,71792 2hziA 277 1.59e+01 1k1zA 78 1.59e+01 b.34.2.1 68026 1i9zA 347 1.60e+01 1i9yA d.151.1.2 62102 1rqpA 299 1.60e+01 b.141.1.1,c.132.1.1 97754,97755 2hnfA 133 1.61e+01 1nqbA 256 1.61e+01 1mfa b.1.1.1,b.1.1.1 20042,20043 2e7xA 150 1.61e+01 1g9oA 91 1.62e+01 1pdr b.36.1.1 60400 1nycA 111 1.64e+01 b.61.2.2 92336 1ymiA 334 1.64e+01 1qvbA 481 1.67e+01 1qvbA c.1.8.4 28983 2ftsA 419 1.68e+01 b.85.6.1,b.103.1.1,c.57.1.2 134079,134080,134081 2e7dA 131 1.69e+01 2z14A 133 1.70e+01 2jdiA 510 1.71e+01 2hq7A 146 1.71e+01 b.45.1.1 136657 1ewqA 765 1.73e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 3crkC 87 1.74e+01 2q2bA 179 1.75e+01 2diuA 96 1.75e+01 1jjhA 86 1.75e+01 2bopA d.58.8.1 63119 2grvA 621 1.75e+01 1bxyA 60 1.76e+01 1bxyA d.59.1.1 39525 1wfwA 74 1.76e+01 b.34.2.1 114595 2dxcA 126 1.76e+01 1suuA 312 1.77e+01 b.68.10.1 99006 1vf1A 229 1.77e+01 1a0nB 69 1.77e+01 1bbzA b.34.2.1 24469 2fpeA 62 1.77e+01 2hqhA 93 1.80e+01 1ahjB 212 1.80e+01 2ahjB b.34.4.4 24601 2pn6A 150 1.82e+01 1f2hA 169 1.82e+01 1f3vA d.58.22.1 59612 2jsxA 95 1.83e+01 1ay9A 108 1.85e+01 1umuA b.87.1.1 28384 1jl0A 334 1.85e+01 1jenA d.156.1.1 63155 1bb9 115 1.85e+01 1bb9 1bb9A 115 1.85e+01 b.34.2.1 24554 1hc9B 74 1.86e+01 g.7.1.1 65787 1xs1A 193 1.86e+01 b.85.4.1 115892 1b7yB 785 1.86e+01 1pysB 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