# List of top-scoring protein chains for t2k-100-30-str2-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 1cwoA 165 6.92e-34 2cpl b.62.1.1 27445 2cpl 165 7.10e-34 2cpl b.62.1.1 27420 2bitX 165 8.97e-34 1awqA 164 9.79e-34 2cpl b.62.1.1 27461 1yndA 165 1.23e-33 1awsA 164 1.31e-33 2cpl b.62.1.1 27431 1dywA 173 1.32e-33 2cpl b.62.1.1 27505 2rmcA 182 1.59e-33 2cpl b.62.1.1 27491 1ihgA 370 1.70e-33 2cpl a.118.8.1,b.62.1.1 62380,62381 1a58 177 1.81e-33 2cpl b.62.1.1 27495 1zcxA 178 5.67e-33 1qoiA 177 6.85e-33 2cpl b.62.1.1 27490 1xo7A 166 9.20e-33 2cfeA 162 1.24e-32 1vdnA 162 2.20e-32 1h0pA 182 5.20e-32 b.62.1.1 76450 2a2nA 176 2.17e-30 1zkcA 197 3.32e-30 1xwnA 174 1.52e-29 2fu0A 160 2.32e-29 2b71A 196 1.08e-28 1j2aA 166 7.68e-26 b.62.1.1 90779 1v9tA 166 1.44e-25 b.62.1.1 108451 1lopA 164 7.55e-25 2cpl b.62.1.1 27510 1clh 166 2.72e-23 2cpl b.62.1.1 27512 1zx8A 136 1.23e-01 1zoxA 113 1.53e+00 1b77A 228 2.02e+00 1b77A d.131.1.2,d.131.1.2 41362,41363 1mxiA 160 2.18e+00 c.116.1.1 79646 1mdbA 539 2.55e+00 e.23.1.1 79008 1fnhA 271 2.65e+00 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 1oa4A 222 3.16e+00 b.29.1.11 86731 1fa0B 537 3.56e+00 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1qupA 222 4.46e+00 1qupA b.1.8.1,d.58.17.1 22301,39352 2b8mA 117 4.74e+00 1lq9A 112 6.44e+00 d.58.4.3 78129 1o91A 178 6.44e+00 b.22.1.1 92656 1prn 289 8.71e+00 3prn f.4.3.1 43762 1qcsA 211 9.17e+00 1qcsA b.52.2.3,d.31.1.1 26927,38461 1bf8 205 9.25e+00 1qpxA b.1.11.1,b.7.2.1 22332,23214 1sq2N 113 9.49e+00 b.1.1.1 105881 1ffk1 177 9.84e+00 1ffk1 1ciy 590 9.88e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1pbyA 489 1.02e+01 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 1jjuA 489 1.04e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 2pii 112 1.07e+01 2pii d.58.5.1 39071 2gk3A 256 1.09e+01 1bev1 281 1.11e+01 1aym1 1c0eA 157 1.21e+01 1dg9A c.44.1.1 32638 1kv9A 668 1.23e+01 a.3.1.6,b.70.1.1 73056,73057 1sglA 209 1.29e+01 d.124.1.1 105536 1cr5A 189 1.35e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1k2fA 190 1.43e+01 b.8.1.2 68054 2bf6A 449 1.49e+01 1bh3 289 1.50e+01 3prn f.4.3.1 43766 1o7iA 119 1.55e+01 b.40.4.3 86642 1si6X 282 1.68e+01 1ezwA 349 1.71e+01 1ezwA c.1.16.3 29558 1rlhA 173 1.71e+01 d.256.1.1 97646 1rc9A 221 1.75e+01 3prn 289 1.76e+01 3prn f.4.3.1 43761 1ve4A 206 1.95e+01 1f0iA 504 2.04e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1y21A 282 2.05e+01 2gaxA 135 2.07e+01 1a5dA 173 2.15e+01 1amm b.11.1.1,b.11.1.1 23614,23615 1m8uA 173 2.19e+01 b.11.1.1,b.11.1.1 91233,91234 1v0wA 506 2.21e+01 d.136.1.2,d.136.1.2 108220,108221 1phr 157 2.24e+01 1dg9A c.44.1.1 32635 1zk5A 176 2.31e+01 1afcA 140 2.31e+01 1bfg b.42.1.1 25506 1pil 112 2.31e+01 2pii d.58.5.1 39072 3stdA 165 2.33e+01 3stdA d.17.4.1 38073 1fjgE 162 2.33e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 2gvkA 317 2.36e+01 1barA 140 2.41e+01 1bfg b.42.1.1 25504 1wloA 136 2.46e+01 1klnA 605 2.51e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1bvh 157 2.55e+01 1dg9A c.44.1.1 32640 1t5rA 284 2.56e+01 f.6.1.1 106465 2std 172 2.58e+01 3stdA d.17.4.1 38085 2b4wA 315 2.59e+01 1idpA 172 2.62e+01 d.17.4.1 83685 1vqvA 306 2.69e+01 1r4wA 226 2.72e+01 c.47.1.13 97050 1dg9A 157 2.75e+01 1dg9A c.44.1.1 32637 4gcr 174 2.76e+01 1amm b.11.1.1,b.11.1.1 23589,23590 1amm 174 2.80e+01 1amm b.11.1.1,b.11.1.1 23587,23588 8prn 289 2.83e+01 3prn f.4.3.1 43767 1j5eE 161 2.85e+01 d.14.1.1,d.50.1.2 71547,71548 1a45 173 2.92e+01 1amm b.11.1.1,b.11.1.1 23602,23603 1n0uA 842 2.95e+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 1c3hA 137 2.97e+01 b.22.1.1 90405 1vfjA 116 3.08e+01 1vybA 238 3.25e+01 d.151.1.1 108897 1gm6A 175 3.25e+01 b.60.1.1 70272 1gowA 489 3.27e+01 1qvbA c.1.8.4 28981 2c5uA 375 3.34e+01 1ewnA 219 3.41e+01 1bnkA b.46.1.2 25762 1f6oA 219 3.46e+01 1bnkA b.46.1.2 25763 2cwsA 237 3.49e+01 1gc1H 229 3.51e+01 1gc1H b.1.1.1,b.1.1.2 20265,21265 1eysH 259 3.61e+01 6prcH b.41.1.1,f.23.10.1 25484,43517 1xk7A 408 3.62e+01 1ay1H 213 3.63e+01 1igtB b.1.1.1,b.1.1.2 20243,21255 2bm3A 166 3.66e+01 1xwwA 157 3.68e+01 1xa3A 437 3.68e+01 1qmpA 130 3.71e+01 1dz3A c.23.1.1 31106 1zirA 173 3.79e+01 1prq 125 3.88e+01 3nul d.110.1.1 40883 1ntfA 282 3.90e+01 d.151.1.2 92104 1psuA 140 3.90e+01 d.38.1.5 88285 1wggA 96 3.92e+01 1qubA 319 3.97e+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 1mt6A 280 3.99e+01 b.76.2.1,b.85.7.1 79446,79447 2fs2A 151 4.00e+01 1rx0A 393 4.08e+01 a.29.3.1,e.6.1.1 98007,98008 2atpB 115 4.09e+01 1c28A 135 4.12e+01 1c28A b.22.1.1 23857 1yzxA 226 4.18e+01 1fvuB 125 4.20e+01 1ixxB d.169.1.1 42346 1v5sA 126 4.23e+01 d.129.6.1 108384 1o9wA 177 4.24e+01 b.2.3.5 86713 1zvnA 99 4.27e+01 1djnA 729 4.42e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1h4xA 117 4.55e+01 1auz c.13.2.1 60626 1w44A 331 4.70e+01 1tl2A 236 4.89e+01 1tl2A b.67.1.1 27541 1q5fA 156 4.98e+01 d.24.1.1 104536 1ntyA 311 5.00e+01 a.87.1.1,b.55.1.1 103873,103874 2gclA 261 5.28e+01 1b9vA 390 5.29e+01 2qwc b.68.1.1 27603 1aps 98 5.33e+01 2acy d.58.10.1 39299 1yoxA 250 5.34e+01 1lylA 504 5.39e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1b2iA 83 5.41e+01 5hpgA g.14.1.1 44640 1acf 125 5.45e+01 3nul d.110.1.1 40882 1fh0A 221 5.45e+01 1cs8A d.3.1.1 59832 1std 172 5.53e+01 3stdA d.17.4.1 38089 1p63A 144 5.55e+01 b.42.1.1 94153 1byuA 216 5.64e+01 1byuA c.37.1.8 32032 1gggA 226 5.64e+01 1lst c.94.1.1 35817 1kskA 234 5.64e+01 d.66.1.5,d.265.1.3 72920,90389 2b0aA 186 5.68e+01 1iw2A 182 5.72e+01 b.60.1.1 71468 1uscA 178 5.73e+01 b.45.1.2 99860 1btkA 169 5.76e+01 1btkA b.55.1.1 26959 1jmxA 494 5.77e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1a6l 106 5.78e+01 1a6l d.58.1.2 38966 1b0tA 106 5.81e+01 1a6l d.58.1.2 38965 1t4wA 196 5.89e+01 b.2.5.2 106427 1o26A 232 5.90e+01 d.207.1.1 86566 2b59A 187 5.92e+01 2kfnA 605 5.92e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1fr7A 260 5.93e+01 2cba b.74.1.1 27828 1o94A 729 5.94e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1dz3A 130 5.94e+01 1dz3A c.23.1.1 31105 1pm1X 180 6.00e+01 b.60.1.1 104189 1jqzA 146 6.01e+01 b.42.1.1 67109 1mu7A 485 6.01e+01 d.136.1.3,d.136.1.3 79475,79476 1vr0A 247 6.03e+01 2eng 210 6.04e+01 2eng b.52.1.1 26895 1bv8A 138 6.04e+01 1ayoA b.2.4.1 22430 1gpl 432 6.07e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1lf7A 182 6.13e+01 b.60.1.1 73878 1h3iA 293 6.13e+01 b.76.2.1,b.85.7.1 76635,76636 1w0pA 781 6.23e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1b88A 114 6.25e+01 1tcrA b.1.1.1 20608 2ncm 99 6.28e+01 2ncm b.1.1.4 21703 1s4bP 674 6.31e+01 d.92.1.5 105252 1mpgA 282 6.31e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1eqnA 321 6.34e+01 1dd9A e.13.1.1 43256 1jy1A 464 6.35e+01 d.136.1.3,d.136.1.3 67438,67439 1pmd 675 6.37e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37491,37492,42562,42771 1gt8A 1025 6.37e+01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70418,70419,70420,70421,70422 1bqcA 302 6.40e+01 1bqcA c.1.8.3 28831 1peeA 180 6.40e+01 b.60.1.1 104126 1f39A 101 6.42e+01 1umuA b.87.1.1 28386 2fimA 276 6.49e+01 1kfd 605 6.54e+01 1xwl c.55.3.5,e.8.1.1 33694,42987 1gggB 226 6.56e+01 1lst c.94.1.1 35818 1y10A 407 6.57e+01 1djqA 729 6.58e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1kit 757 6.58e+01 1kit b.29.1.8,b.29.1.8,b.68.1.1 24272,24273,27616 1d5rA 324 6.78e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 2fjlA 150 6.84e+01 1yo1A 260 6.96e+01 1m16A 146 7.01e+01 b.42.1.1 91164 1yer 228 7.06e+01 1yer d.122.1.1 41101 1tbgE 68 7.14e+01 1tbgE a.137.3.1 19630 2cy5A 140 7.16e+01 1euoA 180 7.17e+01 1np1A b.60.1.1 27163 1krhA 338 7.28e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1qlpA 394 7.33e+01 1ovaA e.1.1.1 42628 1a8p 258 7.34e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1byqA 228 7.41e+01 1yer d.122.1.1 41100 1rg8A 146 7.49e+01 1aogA 485 7.50e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30517,30518,40190 1qmeA 702 7.53e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1gd1O 334 7.58e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1mooA 260 7.66e+01 b.74.1.1 79359 1z4xA 532 7.67e+01 1xe1A 116 7.69e+01 b.43.3.1 109571 2b06A 155 7.72e+01 1cot 129 7.75e+01 1ycc a.3.1.1 15899 1wn0A 145 7.76e+01 1d8yA 605 7.76e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1vq2A 193 7.77e+01 1tjxA 159 7.87e+01 3monB 50 7.89e+01 1molA d.17.1.1 37992 1a5lC 566 7.93e+01 1ubpC b.92.1.1,c.1.9.2 28426,29048 1do6A 124 7.94e+01 1do6A b.1.13.1 22361 1quqB 121 7.99e+01 1quqB b.40.4.3 25305 1o04A 500 8.01e+01 c.82.1.1 86508 1xtaA 221 8.04e+01 1x9uA 116 8.11e+01 1jhfA 202 8.15e+01 a.4.5.2,b.87.1.1 63057,63058 1a5kC 566 8.15e+01 1ubpC b.92.1.1,c.1.9.2 28425,29047 2bdvA 231 8.16e+01 1fnc 314 8.20e+01 1fnc b.43.4.2,c.25.1.1 25627,31517 2gd1O 334 8.26e+01 1dssG c.2.1.3,d.81.1.1 29978,39893 1sqkB 25 8.30e+01 j.86.1.1 105924 1ejxC 567 8.38e+01 b.92.1.1,c.1.9.2 83184,83185 1ajw 145 8.38e+01 1rhoA b.1.18.8 21905 1yr1A 119 8.43e+01 1wriA 93 8.51e+01 1i2mA 216 8.53e+01 1byuA c.37.1.8 61568 1i39A 225 8.56e+01 1ekeA c.55.3.1 61585 1iz1A 294 8.61e+01 a.4.5.37,c.94.1.1 83823,83824 2bi0A 337 8.63e+01 1s0uA 408 8.68e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1a5mC 566 8.68e+01 1ubpC b.92.1.1,c.1.9.2 28423,29045 1fdd 106 8.70e+01 1a6l d.58.1.2 38960 1wxrA 1048 8.71e+01 1h30A 422 8.74e+01 b.29.1.4,b.29.1.4 76604,76605 1kq4A 232 8.77e+01 d.207.1.1 68791 1z7mA 344 8.88e+01 1nbfA 353 8.90e+01 d.3.1.9 80387 1i7pA 274 8.92e+01 b.43.4.2,c.25.1.1 66048,66049