# 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 1pd21 199 2.26e-07 1pd21 1oktA 211 5.62e-07 a.45.1.1 -942 c.47.1.5 -7467 1iyhA 198 2.13e-06 a.45.1.1 83790 c.47.1.5 83791 1gumA 222 5.48e-06 1pgtA a.45.1.1 17683 c.47.1.5 32977 1gulA 222 6.77e-06 1pgtA a.45.1.1 17675 c.47.1.5 32969 2gsq 202 3.13e-05 1pd21 a.45.1.1 17715 c.47.1.5 33009 1k3lA 221 3.64e-05 a.45.1.1 77229 c.47.1.5 77230 1k3yA 221 3.98e-05 a.45.1.1 77245 c.47.1.5 77246 1gseA 221 4.40e-05 1pgtA a.45.1.1 17667 c.47.1.5 32961 1oe8A 211 5.15e-05 a.45.1.1 86905 c.47.1.5 86906 1f3aA 222 9.08e-05 1pgtA a.45.1.1 17701 c.47.1.5 32995 1pgtA 210 1.14e-04 1pgtA a.45.1.1 17515 c.47.1.5 32809 6gsvA 217 2.22e-04 1b8xA a.45.1.1 17633 c.47.1.5 32925 1b4pA 217 1.61e-03 a.45.1.1 83158 c.47.1.5 83159 1aw9 216 4.59e-03 1gnwA a.45.1.1 17736 c.47.1.5 33030 1m0uA 249 4.83e-03 a.45.1.1 78359 c.47.1.5 78360 1nhyA 219 6.84e-03 a.45.1.1 80520 c.47.1.5 80521 1dugA 234 1.28e-02 1b8xA a.45.1.1 17718 c.47.1.5 33012 1jlvA 209 1.81e-02 a.45.1.1 71729 c.47.1.5 71730 1b8xA 280 2.00e-02 1b8xA a.45.1.1 17739 c.47.1.5 33033 1e6bA 221 3.18e-02 1e6bA a.45.1.1 59294 c.47.1.5 59295 1bo1A 416 1.61e-01 1bo1A d.143.1.2 41591 1gwcA 230 1.65e-01 a.45.1.1 70660 c.47.1.5 70661 1oatA 439 1.74e-01 2dkb c.67.1.4 34461 1f47B 144 1.91e-01 1f46A d.129.4.1 59645 1f46A 140 2.24e-01 1f46A d.129.4.1 59643 2oatA 439 2.91e-01 2dkb c.67.1.4 34452 1ozhA 566 2.92e-01 c.31.1.3 -6737 c.36.1.5 -6895 c.36.1.9 -6935 1o6zA 303 3.95e-01 c.2.1.5 81107 d.162.1.1 81108 1usuA 260 4.06e-01 unknown_sccs -9045 1o26A 232 4.80e-01 d.207.1.1 86566 1cot 129 4.99e-01 1ycc a.3.1.1 15899 1ljrA 244 5.08e-01 1ljrA a.45.1.1 17707 c.47.1.5 33001 1ky9A 448 6.00e-01 b.36.1.4 73198 b.47.1.1 73199 1f7wA 144 6.99e-01 1f46A d.129.4.1 59679 1i8tA 367 7.29e-01 c.4.1.3 66094 d.16.1.7 66095 1fpxA 352 7.72e-01 1fpxA a.4.5.29 59950 c.66.1.12 59951 1fp2A 352 1.09e+00 1fpxA a.4.5.29 59941 c.66.1.12 59942 1f2eA 201 1.11e+00 1a0fA a.45.1.1 17745 c.47.1.5 33039 1qq2A 199 1.29e+00 1qq2A c.47.1.10 33064 1pmt 203 1.47e+00 1a0fA a.45.1.1 17740 c.47.1.5 33034 1kyqA 274 1.57e+00 c.2.1.11 73281 e.37.1.1 73282 1ge9A 184 1.59e+00 1dd5A d.67.3.1 60463 1ksfX 758 1.62e+00 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1dar 691 1.78e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1n2aA 201 1.80e+00 a.45.1.1 -938 c.47.1.5 -7463 1fxxA 482 1.89e+00 1fxxA c.55.3.5 33726 1pmmA 466 2.10e+00 c.67.1.6 -8159 1fjgB 256 2.11e+00 1fjfB c.23.15.1 31400 1pbuA 162 2.19e+00 d.58.46.1 88030 1fs7A 485 2.50e+00 1qdbA a.138.1.3 19691 1rifA 282 2.85e+00 unknown_sccs -7265 1kq4A 232 2.91e+00 d.207.1.1 68791 1lldA 319 3.39e+00 3ldh c.2.1.5 30177 d.162.1.1 42144 1j5eB 256 3.53e+00 c.23.15.1 71543 1fhvA 323 3.53e+00 1fhuA c.1.11.2 29235 d.54.1.1 38879 1pnsB 234 3.54e+00 i.1.1.1 88169 1l2lA 457 3.88e+00 c.72.1.3 77656 1jbkA 195 3.89e+00 c.37.1.20 71631 1jg5A 83 3.92e+00 d.205.1.1 66666 1augA 215 3.92e+00 1a2zA c.56.4.1 33798 1okrA 123 3.94e+00 unknown_sccs -235 1fnmA 691 4.00e+00 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1h10A 125 4.36e+00 b.55.1.1 83446 1a0fA 201 4.36e+00 1a0fA a.45.1.1 17737 c.47.1.5 33031 1efnB 152 4.56e+00 1efnB d.102.1.1 40699 1miwA 404 4.57e+00 a.173.1.1 79162 d.218.1.4 79163 1h6hA 143 4.91e+00 d.189.1.1 65681 1is8K 84 5.01e+00 d.205.1.1 66331 1r6wA 322 5.07e+00 c.1.11.2 -5563 d.54.1.1 -9821 1uhgA 385 5.29e+00 e.1.1.1 88491 1jdlA 121 6.15e+00 a.3.1.1 66557 1umzA 278 6.64e+00 b.29.1.2 -3398 1ayl 541 6.97e+00 1ayl c.91.1.1 64718 c.109.1.1 64719 1fp1D 372 7.01e+00 1fpqA a.4.5.29 59939 c.66.1.12 59940 1co6A 107 7.18e+00 1ycc a.3.1.1 15894 1kssA 571 7.33e+00 a.138.1.3 72928 c.3.1.4 72929 d.168.1.1 72930 1eemA 241 7.71e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 1j7rA 86 7.78e+00 1j7rA a.39.1.5 62701 1qz9A 416 7.90e+00 c.67.1.3 -8180 1bqv 110 7.97e+00 1bqv a.60.1.1 17932 1k3kA 158 8.46e+00 f.1.4.1 72017 1m64A 571 8.80e+00 a.138.1.3 78683 c.3.1.4 78684 d.168.1.1 78685 1j7iA 264 1.00e+01 1j7iA d.144.1.6 62694 1bjnA 360 1.03e+01 1bjnA c.67.1.4 34469 1b4uA 139 1.04e+01 1bouA a.88.1.1 18523 2gliA 160 1.06e+01 2gliA g.37.1.1 45041 g.37.1.1 45042 g.37.1.1 45043 g.37.1.1 45044 g.37.1.1 45045 1ovaA 386 1.07e+01 1ovaA e.1.1.1 42619 1g7oA 215 1.07e+01 1g7oA a.45.1.1 60332 c.47.1.5 60333 1mfqC 129 1.08e+01 a.36.1.1 79046 1nofA 383 1.09e+01 b.71.1.2 -4668 c.1.8.3 -5339 1bjoA 360 1.14e+01 1bjnA c.67.1.4 34471 1pyfA 312 1.15e+01 c.1.7.1 -5251 1i8oA 114 1.17e+01 1ycc a.3.1.1 61979 1g5aA 628 1.17e+01 b.71.1.1 65152 c.1.8.1 65153 1jhb 106 1.22e+01 1kte c.47.1.1 32772 1ftpA 133 1.25e+01 1hmt b.60.1.2 27199 1a41 234 1.26e+01 1a41 d.163.1.2 42174 1jj2Q 154 1.27e+01 1ffkO d.55.1.1 63102 1l9vA 317 1.29e+01 d.13.2.1 73760 d.216.1.1 73761 1ky9B 448 1.30e+01 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1wdcC 156 1.31e+01 1wdcC a.39.1.5 17317 1jm7B 117 1.35e+01 g.44.1.1 66881 1i50B 1224 1.35e+01 e.29.1.1 61755 1v61A 132 1.39e+01 1nw3A 416 1.40e+01 c.66.1.31 86288 1hh7A 114 1.41e+01 1ycc a.3.1.1 15896 1dttA 560 1.42e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1fs1B 141 1.43e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1pbwA 216 1.45e+01 1pbwA a.116.1.1 19103 1fh6A 282 1.47e+01 1fh6A 1neiA 60 1.49e+01 unknown_sccs -10324 1ppa 121 1.52e+01 1poa a.133.1.2 19550 1gpjA 404 1.57e+01 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1p65A 73 1.58e+01 unknown_sccs -10331 1s72R 155 1.61e+01 1e69B 322 1.62e+01 1e69B c.37.1.12 32377 1sjyA 159 1.63e+01 d.113.1.1 -10908 1axdA 209 1.72e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1o1fC 147 1.79e+01 i.15.1.1 80997 1izcA 339 1.79e+01 c.1.12.5 83838 1o6dA 163 1.80e+01 c.116.1.3 -6689 1g87A 614 1.80e+01 a.102.1.2 83275 b.2.2.2 83276 1szwA 379 1.80e+01 unknown_sccs -10164 1tc1A 220 1.81e+01 1tc1A c.61.1.1 34083 1jkgB 250 1.83e+01 d.17.4.2 66796 1efuB 282 1.84e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1jqgA 433 1.86e+01 c.56.5.1 71791 d.58.3.1 71792 1ny6A 267 1.91e+01 c.37.1.20 -7221 1gikA 261 1.91e+01 d.165.1.1 -11545 1al01 152 1.94e+01 1cd31 1kv8A 216 1.97e+01 c.1.2.3 73054 1oyjA 231 1.97e+01 a.45.1.1 87597 c.47.1.5 87598 1k3eA 156 2.00e+01 d.198.1.1 68103 1ecrA 309 2.00e+01 1ecrA e.2.1.1 42678 1qqtA 551 2.02e+01 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1ebbA 202 2.03e+01 c.60.1.1 64900 1j0mA 752 2.06e+01 a.102.3.2 83910 b.24.1.1 83911 b.30.5.2 83912 1q6oA 216 2.09e+01 c.1.2.3 -5162 1j1qA 261 2.16e+01 d.165.1.1 -11546 1tmcA 175 2.17e+01 1agdA d.19.1.1 38258 1bouA 139 2.17e+01 1bouA a.88.1.1 18521 1dw0A 112 2.19e+01 1dw0A a.3.1.1 15911 1h9mA 145 2.19e+01 1h9jA b.40.6.2 60833 b.40.6.2 60834 1kn1B 161 2.20e+01 a.1.1.3 77456 1aisB 200 2.25e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1qciA 262 2.27e+01 1qi7A d.165.1.1 42201 1a76 326 2.29e+01 1a76 a.60.7.1 18091 c.120.1.2 33361 2bidA 197 2.34e+01 2bidA f.1.4.1 43398 1jm7A 112 2.38e+01 g.44.1.1 66880 1edg 380 2.38e+01 1edg c.1.8.3 28807 1aihA 170 2.38e+01 1aihA d.163.1.1 42149 1gln 468 2.41e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1h9jA 145 2.41e+01 1h9jA b.40.6.2 60829 b.40.6.2 60830 1r53A 382 2.44e+01 unknown_sccs -11177 1k66A 149 2.45e+01 c.23.1.1 -6406 1ohgA 282 2.47e+01 d.183.1.1 -11727 1pqnA 127 2.48e+01 c.47.1.8 -7479 1mlvA 444 2.51e+01 a.166.1.1 79283 b.85.7.3 79284 1huuA 90 2.53e+01 1huuA a.55.1.1 17897 1cd31 152 2.56e+01 1cd31 1l3kA 196 2.56e+01 d.58.7.1 73539 d.58.7.1 73540 1hsbA 270 2.61e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 1iweA 457 2.62e+01 c.37.1.10 71486 1r5zA 323 2.64e+01 unknown_sccs -12289 1qysA 106 2.68e+01 unknown_sccs -13432 1exzA 141 2.68e+01 1exzA a.26.1.2 16877 1pytA 94 2.70e+01 1pytA d.58.3.1 39064 1t62A 166 2.73e+01 3nul 130 2.74e+01 3nul d.110.1.1 40891 1s8iA 121 2.77e+01 a.133.1.2 -1968 1vaoA 560 2.78e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1f7cA 231 2.79e+01 1f7cA a.116.1.1 19107 1fbr 93 2.86e+01 1fbr g.27.1.1 44948 g.27.1.1 44949 1e6iA 121 2.88e+01 1b91A a.29.2.1 16969 1ro2A 216 2.89e+01 unknown_sccs -11391 1g3jA 532 2.93e+01 3bct a.118.1.1 19114 1n4kA 381 2.98e+01 unknown_sccs 79992 b.42.6.1 79993 1ivyA 452 3.00e+01 1ivyA c.69.1.5 34654 1g59A 468 3.04e+01 a.97.1.1 60257 c.26.1.1 60258 1lb6A 160 3.05e+01 b.8.1.1 73798 1jeqA 609 3.05e+01 1jeqA a.140.2.1 64748 unknown_sccs -4427 unknown_sccs -7991 1pfvA 551 3.07e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1iknD 236 3.07e+01 1iknD d.211.1.1 19171 1aijL 281 3.09e+01 6prcL f.26.1.1 43461 1khbA 625 3.12e+01 c.91.1.1 68606 c.109.1.1 68607 1n5dA 288 3.12e+01 c.2.1.2 80030 1hu4A 288 3.12e+01 1hu4A 1d6jA 211 3.15e+01 1d6jA c.37.1.4 31940 1eteA 134 3.15e+01 1eteA a.26.1.2 16869 1i0lA 221 3.15e+01 c.61.1.1 71096 1bjt 793 3.15e+01 1bjt e.11.1.1 43249 1mgtA 174 3.19e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1rzhL 281 3.25e+01 f.26.1.1 -12215 1tc5A 194 3.29e+01 1jwhC 215 3.30e+01 g.41.4.1 71915 1bx4A 345 3.33e+01 1bx4A c.72.1.1 34935 1fqvD 149 3.33e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1awcA 110 3.38e+01 1awcA a.4.5.21 16167 1h2kA 349 3.40e+01 b.82.2.6 76572 1cxc 124 3.44e+01 1ycc a.3.1.1 15890 1f44A 324 3.44e+01 a.60.9.1 64982 d.163.1.1 64983 1h2eA 207 3.48e+01 c.60.1.1 70857 1vioA 243 3.49e+01 unknown_sccs -10154 d.66.1.5 -10240 1fw1A 216 3.50e+01 a.45.1.1 60051 c.47.1.5 60052 1k55A 246 3.52e+01 e.3.1.1 68156 3sxlA 184 3.64e+01 1b7fA d.58.7.1 39173 d.58.7.1 39174 1uf2A 1019 3.66e+01 unknown_sccs -12036 1f9aA 168 3.67e+01 1f9aA c.26.1.3 31602 1jn5B 250 3.68e+01 d.17.4.2 66922 1g7nA 131 3.72e+01 b.60.1.2 83274 1qdbA 473 3.79e+01 1qdbA a.138.1.3 19688 1e8gA 560 3.81e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1mzeA 351 3.82e+01 b.82.2.6 79694 1b0zA 445 3.87e+01 2pgi c.80.1.2 35309 2pgi 445 3.87e+01 2pgi c.80.1.2 35308 1jj2C 246 3.88e+01 1ffkC c.22.1.1 63087 1trkA 680 3.88e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 1kcfA 258 3.99e+01 a.140.2.1 68434 c.55.3.7 68435