# List of top-scoring protein chains for t06-100-30-alpha-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 1yndA 165 1.29e-44 2bitX 165 9.18e-44 1ihgA 370 1.01e-43 2cpl a.118.8.1,b.62.1.1 62380,62381 1dywA 173 2.38e-43 2cpl b.62.1.1 27505 1xo7A 166 4.82e-43 1zcxA 178 1.01e-42 2rmcA 182 2.17e-42 2cpl b.62.1.1 27491 2cfeA 162 2.96e-42 1h0pA 182 5.11e-42 b.62.1.1 76450 1vdnA 162 1.07e-41 2a2nA 176 2.52e-39 1zkcA 197 5.69e-39 2fu0A 160 1.15e-36 1v9tA 166 6.14e-34 b.62.1.1 108451 1lopA 164 2.26e-33 2cpl b.62.1.1 27510 1zx8A 136 1.54e-03 1vr0A 247 1.22e-01 1mxiA 160 1.23e-01 c.116.1.1 79646 2ex4A 241 2.83e-01 1rx0A 393 4.29e-01 a.29.3.1,e.6.1.1 98007,98008 1qcsA 211 4.35e-01 1qcsA b.52.2.3,d.31.1.1 26927,38461 3sil 379 5.05e-01 3sil b.68.1.1 27542 1gteA 1025 6.52e-01 a.1.2.2,c.1.4.1,c.3.1.1,c.4.1.1,d.58.1.5 70440,70441,70442,70443,70444 1vi2A 300 7.50e-01 c.2.1.7,c.58.1.5 100726,100727 1wi1A 126 8.28e-01 1dz3A 130 8.55e-01 1dz3A c.23.1.1 31105 1x3lA 440 9.35e-01 1dl5A 317 9.52e-01 1dl5A c.66.1.7,d.197.1.1 64720,64721 2b8mA 117 1.06e+00 1us5A 314 1.10e+00 c.94.1.1 99856 2azpA 318 1.14e+00 1vl4A 447 1.24e+00 d.283.1.1 108718 1yymG 313 1.29e+00 2cy7A 396 1.34e+00 1t2bA 397 1.63e+00 2bvfA 459 1.68e+00 1lehA 364 1.68e+00 1bw9A c.2.1.7,c.58.1.1 30268,33916 2bm5A 186 1.84e+00 2bx6A 350 1.89e+00 1thfD 253 1.91e+00 1thfD c.1.2.1 28535 1oflA 481 2.20e+00 b.80.1.4 103934 2b8tA 223 2.22e+00 1h4xA 117 2.29e+00 1auz c.13.2.1 60626 1cr5A 189 2.52e+00 1cr5A b.52.2.3,d.31.1.1 26931,38465 1icpA 376 2.81e+00 1oyc c.1.4.1 62270 1tyv 542 2.85e+00 1tyv b.80.1.6 28038 2bdrA 175 3.01e+00 1y1nA 291 3.14e+00 2a46A 238 3.18e+00 1fsgA 233 3.44e+00 1qk3A c.61.1.1 34029 1ezwA 349 3.59e+00 1ezwA c.1.16.3 29558 1tmy 120 3.59e+00 1dbwA c.23.1.1 31083 1svpA 161 3.97e+00 1svpA b.47.1.3 26384 1fnlA 175 4.01e+00 2fcbA b.1.1.4,b.1.1.4 21783,21784 1wdnA 226 4.23e+00 1lst c.94.1.1 35816 1v9sA 208 4.26e+00 1q45A 391 4.27e+00 c.1.4.1 95780 1vfjA 116 4.43e+00 4ubpC 570 4.58e+00 1ubpC b.92.1.1,c.1.9.2 28431,29053 2bm3A 166 4.74e+00 1qwyA 291 4.75e+00 b.84.3.2 96509 1fjgE 162 4.83e+00 1pkp d.14.1.1,d.50.1.2 37553,38789 1o7iA 119 4.85e+00 b.40.4.3 86642 1j71A 334 4.92e+00 1eagA b.50.1.2 62669 1oxxK 353 4.93e+00 b.40.6.3,c.37.1.12 93715,93716 2atpB 115 4.94e+00 1m1cA 680 4.99e+00 e.42.1.1 78395 2aq2B 237 5.09e+00 1ejxC 567 5.16e+00 b.92.1.1,c.1.9.2 83184,83185 1llnA 262 5.30e+00 d.165.1.1 84625 1kbvA 327 5.48e+00 b.6.1.3,b.6.1.3 68395,68396 1u0sY 118 5.63e+00 c.23.1.1 107566 2bolA 314 5.68e+00 1n35A 1267 6.04e+00 e.8.1.4 79935 1w9zA 283 6.06e+00 1c96A 753 6.10e+00 1amj c.8.2.1,c.83.1.1 30727,35403 1pa1A 310 6.27e+00 c.45.1.2 94404 2as9A 210 6.33e+00 1z4vA 532 6.46e+00 1dqiA 124 6.47e+00 1do6A b.1.13.1 22357 1sr4B 261 6.49e+00 d.151.1.1 105949 1sq2N 113 6.50e+00 b.1.1.1 105881 1v7wA 807 6.66e+00 a.102.1.4,b.30.5.3 108411,108412 2fdiA 211 6.77e+00 1ve2A 235 6.81e+00 2f71A 298 6.87e+00 1oalA 151 6.91e+00 b.1.8.1 86739 1vqvA 306 6.97e+00 1fs0E 138 7.08e+00 1aqt a.2.10.1,b.93.1.1 59997,59998 2bf6A 449 7.16e+00 1z2kA 109 7.23e+00 1vyrA 364 7.31e+00 c.1.4.1 108906 1dzlA 505 7.34e+00 1dzlA b.121.6.1 23586 1stzA 338 7.34e+00 a.4.5.51,d.110.2.3 106009,106010 1x9uA 116 7.35e+00 1xwwA 157 7.92e+00 2fomB 185 7.92e+00 1i6aA 219 8.07e+00 c.94.1.1 61827 1zxfA 155 8.17e+00 2g3aA 152 8.28e+00 1dg9A 157 8.32e+00 1dg9A c.44.1.1 32637 1t5rA 284 8.46e+00 f.6.1.1 106465 1vqzA 341 8.48e+00 1xxaA 78 8.56e+00 1xxaA d.74.2.1 39700 1yoaA 159 8.57e+00 1pguA 615 8.66e+00 b.69.4.1,b.69.4.1 88069,88070 1wchA 315 8.76e+00 1wisA 124 8.79e+00 1xewX 182 8.88e+00 1ww9A 392 8.95e+00 1wriA 93 9.07e+00 1f39A 101 9.13e+00 1umuA b.87.1.1 28386 1q1oA 98 9.17e+00 d.15.2.2 95596 830cA 168 9.52e+00 1ck7A d.92.1.11 40400 1a0tP 413 9.96e+00 1a0tP f.4.3.2 43794 2dexX 671 9.99e+00 1czfA 362 1.06e+01 1czfA b.80.1.3 28031 1i3cA 149 1.07e+01 c.23.1.1 71112 2f6eA 127 1.07e+01 1guiA 155 1.09e+01 b.18.1.14 76351 1o04A 500 1.09e+01 c.82.1.1 86508 1vqoD 177 1.10e+01 1vq2A 193 1.12e+01 1cliA 345 1.13e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 2b59B 172 1.14e+01 1h5rA 293 1.14e+01 c.68.1.6 65623 2cqsA 842 1.17e+01 1uwsA 489 1.19e+01 c.1.8.4 108073 1d3gA 367 1.22e+01 1d3gA c.1.4.1 28600 1w2wB 191 1.25e+01 1khbA 625 1.27e+01 c.91.1.1,c.109.1.1 68606,68607 1u2cA 246 1.28e+01 b.1.6.2,d.272.1.1 107610,107611 2ltnA 181 1.30e+01 1led b.29.1.1 24024 2cbzA 237 1.32e+01 1vjvA 415 1.32e+01 d.3.1.9 108632 1xqbA 247 1.33e+01 1eybA 471 1.33e+01 1ey2A b.82.1.4 28115 1gmuA 143 1.35e+01 b.107.1.1,d.58.38.1 65335,65336 1usuB 170 1.35e+01 d.83.2.1 99886 1zjjA 263 1.35e+01 1g291 372 1.37e+01 1g291 1b77A 228 1.38e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1v6sA 390 1.39e+01 c.86.1.1 100424 1k66A 149 1.43e+01 c.23.1.1 90941 1nddA 76 1.44e+01 1ubi d.15.1.1 37599 1xe1A 116 1.44e+01 b.43.3.1 109571 1vj2A 126 1.45e+01 b.82.1.10 100796 2gk3A 256 1.48e+01 1g6hA 257 1.49e+01 1gajA c.37.1.12 60318 1mw5A 187 1.49e+01 d.259.1.1 91477 2c12A 439 1.53e+01 1zm8A 259 1.55e+01 1y7mA 164 1.57e+01 1xxqA 161 1.59e+01 1woqA 267 1.59e+01 c.55.1.10,c.55.1.10 109462,109463 1vkdA 338 1.59e+01 b.67.2.4 108644 1y89A 238 1.59e+01 1r64A 481 1.60e+01 b.18.1.20,c.41.1.1 97140,97141 1u69A 163 1.64e+01 d.32.1.7 107699 1lq9A 112 1.64e+01 d.58.4.3 78129 1juhA 350 1.65e+01 b.82.1.5 71884 1sqkB 25 1.66e+01 j.86.1.1 105924 1ru3A 732 1.67e+01 e.26.1.3 97835 2f9nA 245 1.67e+01 1vr8A 142 1.67e+01 1rypK 198 1.67e+01 d.153.1.4 41879 1w5fA 353 1.69e+01 1p77A 272 1.70e+01 c.2.1.7,c.58.1.5 94214,94215 1jfbA 404 1.71e+01 a.104.1.1 66624 2g0cA 76 1.78e+01 1gotG 73 1.79e+01 1tbgE a.137.3.1 19629 1yzxA 226 1.80e+01 1o9wA 177 1.81e+01 b.2.3.5 86713 1a73A 163 1.83e+01 1a73A d.4.1.3 37145 1idpA 172 1.86e+01 d.17.4.1 83685 1yi9A 309 1.90e+01 1ewnA 219 1.91e+01 1bnkA b.46.1.2 25762 1wraA 308 1.93e+01 1z5bA 469 1.99e+01 1pfo 500 2.03e+01 1pfo f.9.1.1 43826 2bibA 547 2.08e+01 1lvwA 295 2.13e+01 c.68.1.6 84723 1e1oA 504 2.15e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1hy7A 173 2.15e+01 d.92.1.11 65957 1k87A 669 2.16e+01 a.176.1.1,c.1.23.2 77286,77287 1vclA 432 2.17e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1y0mA 61 2.18e+01 1rzhH 260 2.19e+01 b.41.1.1,f.23.10.1 98162,98163 2bjqA 345 2.19e+01 1ux6A 350 2.21e+01 b.29.1.16,g.75.1.1 100145,100146 1e9pA 151 2.34e+01 1mfmA b.1.8.1 22215 1b6g 310 2.34e+01 1b6g c.69.1.8 34661 1qlmA 316 2.36e+01 1qlmA d.147.1.1 41765 3il8 72 2.36e+01 1tvxA d.9.1.1 37356 1mqoA 227 2.37e+01 d.157.1.1 103846 2cfuA 658 2.40e+01 2aiqA 231 2.41e+01 1ufbA 127 2.42e+01 a.24.16.3 99331 1t64A 377 2.58e+01 c.42.1.2 106543 1zpvA 91 2.60e+01 2pii 112 2.60e+01 2pii d.58.5.1 39071 1hdoA 206 2.61e+01 1he2A c.2.1.2 60965 1nhcA 336 2.63e+01 b.80.1.3 91879 1lv7A 257 2.63e+01 c.37.1.20 78232 1e9rA 437 2.66e+01 c.37.1.11 64827 1pcfA 66 2.68e+01 1pcfA d.18.1.1 38142 1s8nA 205 2.69e+01 c.23.1.1 105374 1tiqA 180 2.75e+01 d.108.1.1 107010 1tuwA 109 2.76e+01 d.58.4.8 107346 2bdeA 470 2.78e+01 1llfA 534 2.79e+01 c.69.1.17 78094 3seb 238 2.79e+01 3seb b.40.2.2,d.15.6.1 25184,37773 2fiqA 420 2.81e+01 1acf 125 2.84e+01 3nul d.110.1.1 40882 1fonA 240 2.84e+01 5ptp b.47.1.2 26231 1tq5A 242 2.86e+01 1vlaA 150 2.88e+01 d.227.1.2 108735 1wguA 136 2.88e+01 1cb0A 283 2.90e+01 1cb0A c.56.2.1 33790 1lam 484 2.90e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1vhuA 211 2.90e+01 c.50.1.2 100703 1u9lA 70 2.91e+01 a.60.4.2 107751 2gaxA 135 2.93e+01 1vkpA 383 2.95e+01 d.126.1.6 108686 1jbeA 128 2.97e+01 3chy c.23.1.1 62845 1byrA 155 3.00e+01 1byrA d.136.1.1 41450 1rlmA 271 3.01e+01 1xubA 298 3.01e+01 1fxoA 293 3.03e+01 1g0rA c.68.1.6 34524 1ys7A 233 3.06e+01 2gwgA 350 3.07e+01 1g8sA 230 3.08e+01 c.66.1.3 90507 1z41A 338 3.10e+01 1o26A 232 3.12e+01 d.207.1.1 86566 1e5kA 201 3.12e+01 1fr9A c.68.1.8 34578 1pz7A 204 3.12e+01 b.29.1.4 95405 1c4rA 182 3.15e+01 1c4rA b.29.1.4 24229 1qe3A 489 3.16e+01 2bce c.69.1.1 34630 2b7kA 200 3.16e+01 1h7sA 365 3.20e+01 d.14.1.3,d.122.1.2 65705,65706 1gd0A 122 3.21e+01 1dptA d.80.1.3 39834 1ooyA 481 3.22e+01 c.124.1.3,c.124.1.2 93388,93389 1xiwA 105 3.27e+01 1ve4A 206 3.27e+01 1mpgA 282 3.31e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 2ftwA 521 3.36e+01 1q0eA 152 3.38e+01 b.1.8.1 95504 2fug5 207 3.40e+01 1h30A 422 3.42e+01 b.29.1.4,b.29.1.4 76604,76605 1x1iA 752 3.42e+01 1xknA 355 3.46e+01 1d5tA 433 3.53e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 4dpvZ 584 3.54e+01 2cas b.121.5.2 23377 1kugA 203 3.55e+01 d.92.1.9 73008 2fh7A 595 3.55e+01 1v54G 85 3.56e+01 f.23.2.1 100328 1eylA 186 3.59e+01 1wba b.42.4.1 25593 1k12A 158 3.60e+01 b.18.1.15 71978 1m1lA 236 3.61e+01 d.260.1.1 91166 2ew0A 192 3.61e+01 1vloA 381 3.63e+01 b.44.2.1,d.250.1.1 108838,108839 1ogwA 76 3.65e+01 d.15.1.1 87001 1ee6A 197 3.65e+01 1ee6A b.80.1.1 28024 1pbyA 489 3.70e+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 1vkbA 161 3.71e+01 d.269.1.1 108643 1n40A 396 3.71e+01 a.104.1.1 79977 1xzwA 426 3.73e+01 1sxvA 172 3.76e+01 1xsqA 168 3.77e+01 1i3jA 116 3.77e+01 1i3jA d.285.1.1 61594 1pg4A 652 3.79e+01 e.23.1.1 88067 2b49A 287 3.80e+01 1zjcA 418 3.80e+01 1gesA 450 3.92e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1gr0A 367 3.96e+01 c.2.1.3,d.81.1.3 70379,70380 1a8s 273 3.99e+01 1brt c.69.1.12 34710 1p42A 270 4.00e+01 d.14.1.7,d.14.1.7 87754,87755 2bgiA 272 4.01e+01 1mkyA 439 4.02e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1kufA 203 4.03e+01 d.92.1.9 73007 1mveA 243 4.07e+01 b.29.1.2 85140 2coeA 120 4.10e+01 1w0nA 131 4.10e+01 1hxn 219 4.11e+01 1hxn b.66.1.1 27529 2b3hA 329 4.12e+01 1p5vA 235 4.13e+01 b.1.11.1,b.7.2.1 87812,87813 1g6gA 127 4.15e+01 1g6gA b.26.1.2 23916 1el6A 219 4.15e+01 1el6B d.182.1.1 42606 1uok 558 4.21e+01 1uok b.71.1.1,c.1.8.1 27801,28788 2d5cA 263 4.25e+01 1zq9A 285 4.35e+01 2bb3A 221 4.38e+01 1xhnA 184 4.39e+01 1ti6B 274 4.41e+01 b.3.5.1,d.58.1.5 106976,106977 1isiA 265 4.44e+01 e.4.1.1 71394 1tt8A 164 4.44e+01 1o4tA 133 4.45e+01 b.82.1.9 86622 1ww8A 439 4.45e+01 1v8hA 107 4.45e+01 1molA 94 4.47e+01 1molA d.17.1.1 37988 2bsxA 253 4.56e+01 1nrzA 164 4.58e+01 c.38.1.1 86131 1xfcA 384 4.58e+01 1a70 97 4.60e+01 1awd d.15.4.1 37678 1z2uA 150 4.62e+01 2bi0A 337 4.62e+01 1yleA 342 4.65e+01 1vr3A 191 4.67e+01 1g3p 217 4.69e+01 1g3p b.37.1.1,b.37.1.1 24788,24789 1zd9A 188 4.72e+01 1wl8A 189 4.72e+01 1xnzA 264 4.75e+01 2fbyA 205 4.76e+01 2aqlA 173 4.77e+01 2gdm 153 4.87e+01 2gdm a.1.1.2 15212 1o69A 394 4.94e+01 c.67.1.4 92560 1dgwX 79 5.06e+01 1caxB b.82.1.2 28091 1qreA 247 5.11e+01 1qreA b.81.1.5 28066 1sgwA 214 5.14e+01 c.37.1.12 105541 1qwlA 505 5.19e+01 e.5.1.1 96483 1nkgA 508 5.21e+01 b.3.1.2,b.18.1.25,b.30.5.10 103859,103860,103861 2fgtA 417 5.21e+01 1kqrA 179 5.30e+01 b.29.1.14 72886 1nszA 347 5.33e+01 b.30.5.4 80724 1xvxA 312 5.36e+01 1fqtA 112 5.41e+01 1fqtA b.33.1.1 24441 1lqtA 456 5.44e+01 c.3.1.1,c.4.1.1 74198,74199 1z02A 446 5.45e+01 1bfg 146 5.47e+01 1bfg b.42.1.1 25485 1z3qA 200 5.47e+01 1uozA 315 5.50e+01 1ogiA 303 5.52e+01 b.43.4.2,c.25.1.1 92914,92915 1vkcA 158 5.55e+01 1f0lA 535 5.55e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1xrtA 467 5.55e+01 1ixcA 294 5.57e+01 a.4.5.37,c.94.1.1 83764,83765 1hqz1 141 5.57e+01 1tvdA 116 5.60e+01 1tvdA b.1.1.1 20650 1rqwA 207 5.62e+01 b.25.1.1 97781 1j7gA 144 5.65e+01 c.110.1.1 84130 2b4wA 315 5.67e+01 1jovA 270 5.73e+01 b.30.5.7 84192 1vqtA 213 5.79e+01 1a2yB 116 5.80e+01 1gc1H b.1.1.1 19927 1z52A 470 5.80e+01 1g0sA 209 5.82e+01 1g0sA d.113.1.1 60187 1yyaA 250 5.83e+01 1b9hA 388 5.88e+01 1b9hA c.67.1.4 34488 1dzfA 215 5.90e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1thx 115 5.99e+01 1thx c.47.1.1 32732 2f8yA 223 6.00e+01 1q3eA 207 6.01e+01 b.82.3.2 95669 1nykA 165 6.04e+01 b.33.1.1 86408 1pmhX 185 6.08e+01 b.18.1.18 104193 1amm 174 6.10e+01 1amm b.11.1.1,b.11.1.1 23587,23588 1ylxA 103 6.10e+01 1lf7A 182 6.26e+01 b.60.1.1 73878 1khoA 370 6.27e+01 a.124.1.1,b.12.1.3 72489,72490 1kgsA 225 6.29e+01 a.4.6.1,c.23.1.1 68596,68597 1j58A 385 6.30e+01 b.82.1.2 71531 1pmi 440 6.30e+01 1pmi b.82.1.3 28114 1r89A 437 6.32e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1ieaB 228 6.40e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 2f9cA 334 6.40e+01 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