# 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.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 3lmmA 583 6.56e-05 1yzgA 179 2.92e-01 c.37.1.8 124276 1oygA 447 5.20e-01 b.67.2.2 93726 2qtfA 364 5.79e-01 1o3yA 166 6.59e-01 c.37.1.8 86618 2w83A 165 8.96e-01 2a5dA 175 9.18e-01 c.37.1.8 126172 2a6tA 271 9.78e-01 a.242.1.1,d.113.1.7 126309,126310 1wcuA 153 9.94e-01 1m2oB 190 1.07e+00 c.37.1.8 78485 2isnA 364 1.58e+00 1uptA 171 1.79e+00 c.37.1.8 99767 1ln1A 214 1.96e+00 d.129.3.2 74038 2a8eA 220 1.98e+00 d.296.1.1 126397 2gcoA 201 2.10e+00 1kshA 186 2.24e+00 c.37.1.8 72914 3hmiA 292 2.61e+00 1x9nA 688 2.83e+00 a.235.1.1,b.40.4.6,d.142.2.1 115002,115003,115004 3lxrA 185 3.11e+00 1m2rA 327 3.24e+00 d.144.1.7 84760 1mkyA 439 3.26e+00 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1kobA 387 3.30e+00 1tkiA d.144.1.7 41640 3fpqA 290 3.41e+00 1ukvY 206 3.48e+00 c.37.1.8 107918 1r8sA 164 4.41e+00 c.37.1.8 97247 2qkmB 266 4.85e+00 2f57A 317 5.07e+00 2h17A 181 5.20e+00 2bcgY 206 5.54e+00 c.37.1.8 128285 2gu3A 136 5.60e+00 d.17.1.6,d.17.1.6 147178,147179 3l2nA 395 5.70e+00 1om1A 332 6.61e+00 d.144.1.7 93347 2dj5A 133 7.11e+00 c.92.1.3 131536 2retA 103 7.18e+00 d.24.1.7 151983 3hx9A 124 7.21e+00 1gtkA 313 7.26e+00 c.94.1.1,d.50.2.1 76346,76347 2uxtA 451 7.30e+00 3c0iA 351 7.36e+00 2dyiA 162 7.41e+00 1z57A 339 7.54e+00 1zc1A 208 8.04e+00 2qm4A 235 8.11e+00 1t4hA 290 8.53e+00 d.144.1.7 106420 3cfzA 292 8.69e+00 3glaA 100 9.47e+00 2h57A 190 9.74e+00 2vjxA 846 1.00e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 153203,153204,153205,153206,153207 1r4aA 165 1.04e+01 c.37.1.8 96986 1rypH 205 1.07e+01 d.153.1.4 41876 2uubE 162 1.08e+01 d.14.1.1,d.50.1.2 139936,139937 2je8A 848 1.09e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 147998,147999,148000,148001,148002 2w02A 620 1.11e+01 1qw2A 102 1.12e+01 d.249.1.1 96456 2wjiA 165 1.13e+01 1fjgE 162 1.15e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1f6bA 198 1.16e+01 c.37.1.8 64986 1ry9A 145 1.16e+01 d.198.1.1 98094 1bvoA 175 1.20e+01 1a3qA b.2.5.3 22457 2fm8A 135 1.26e+01 d.198.1.1 133767 2qpzA 103 1.26e+01 1k20A 310 1.28e+01 c.107.1.1 68027 2f1nA 262 1.29e+01 d.151.1.1 132782 3fucA 284 1.30e+01 2vr4A 846 1.31e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 153495,153496,153497,153498,153499 3c0dA 119 1.32e+01 b.33.1.3 155819 1oixA 191 1.38e+01 c.37.1.8 118710 2p5dA 147 1.39e+01 1kmqA 184 1.41e+01 c.37.1.8 84412 1vkdA 338 1.44e+01 b.67.2.4 108644 2cxcA 144 1.44e+01 2vqeE 162 1.45e+01 i.1.1.3 153429 2a5jA 191 1.45e+01 c.37.1.8 126175 2ce2X 166 1.45e+01 3aazA 229 1.46e+01 2zo4A 317 1.46e+01 3gokA 334 1.46e+01 1htwA 158 1.51e+01 c.37.1.18 71083 3efyA 195 1.54e+01 2k8qA 134 1.54e+01 3lo5A 166 1.55e+01 1xtmA 175 1.56e+01 1a6uL 108 1.62e+01 1mfa b.1.1.1 20254 1e8oB 106 1.63e+01 1914 d.49.1.1 38775 1u55A 188 1.67e+01 d.278.1.1 107677 3fhrA 336 1.69e+01 1waaA 93 1.73e+01 3kg7A 293 1.73e+01 1zj6A 187 1.74e+01 c.37.1.8 125145 2qggA 182 1.76e+01 1a6wL 109 1.76e+01 1mfa b.1.1.1 20252 2j7tA 302 1.79e+01 1mvfD 82 1.79e+01 b.129.1.1 85143 1vmkA 277 1.81e+01 c.56.2.1 113680 2pqvA 154 1.82e+01 2hziA 277 1.82e+01 1ieaA 192 1.82e+01 1iakA b.1.1.2,d.19.1.1 21631,38205 2fkbA 180 1.84e+01 d.113.1.2 133650 3grnA 153 1.87e+01 1ib8A 164 1.89e+01 b.38.2.1,d.52.4.1 71168,71169 2oezA 247 1.95e+01 e.68.1.1 148758 1hw7A 255 2.00e+01 1i7fA d.193.1.1 61297 3lahA 188 2.02e+01 3ckwA 304 2.02e+01 2afcA 168 2.03e+01 c.50.1.2 126676 1vloA 381 2.08e+01 b.44.2.1,d.250.1.1 108838,108839 1kcvH 217 2.12e+01 b.1.1.1,b.1.1.2 72315,72316 3holA 509 2.12e+01 2gxfA 142 2.18e+01 d.17.4.22 147191 2z06A 252 2.22e+01 d.159.1.10 153906 2fg1A 158 2.31e+01 c.50.1.2 133400 1wh0A 134 2.34e+01 b.15.1.3 114628 1wi1A 126 2.36e+01 b.55.1.1 114658 3k9nA 166 2.37e+01 1vs0A 310 2.41e+01 1fngA 192 2.42e+01 1iakA b.1.1.2,d.19.1.1 59904,59905 2dykA 161 2.44e+01 1l0wA 580 2.45e+01 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1z06A 189 2.47e+01 c.37.1.8 124301 1uv4A 293 2.47e+01 b.67.2.1 119705 1xtlA 175 2.48e+01 3bqcA 335 2.48e+01 d.144.1.7 155497 2iwrA 178 2.49e+01 2welA 327 2.50e+01 1qpcA 279 2.55e+01 1fgkA d.144.1.7 41685 1cojA 212 2.57e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1vlmA 219 2.61e+01 c.66.1.41 108836 3kk8A 284 2.62e+01 1an7A 136 2.65e+01 1seiA d.140.1.1 41465 1gydB 315 2.66e+01 b.67.2.1 70751 2gumA 628 2.69e+01 e.76.1.1 147184 1vluA 468 2.72e+01 c.82.1.1 108864 3lk41 286 2.76e+01 3blzA 128 2.76e+01 d.17.4.14 155403 1opjA 293 2.80e+01 d.144.1.7 87230 1cfyA 143 2.82e+01 1cof d.109.1.2 40858 3silA 379 2.82e+01 b.68.1.1 27542 3g12A 128 2.86e+01 2zuvA 759 2.87e+01 1v2bA 177 2.87e+01 d.107.1.2 108279 1gyhA 318 2.92e+01 b.67.2.1 70757 3lmlA 460 2.93e+01 1onqA 283 2.94e+01 b.1.1.2,d.19.1.1 93365,93366 3c5jA 181 2.95e+01 1je6A 275 2.96e+01 b.1.1.2,d.19.1.1 71638,71639 1hh1A 143 2.98e+01 1gefA c.52.1.18 61036 3kfaA 288 2.98e+01 1w6sA 599 2.99e+01 b.70.1.1 114284 1fzqA 181 3.03e+01 1hurA c.37.1.8 32060 2bdwA 362 3.07e+01 1mh1 186 3.11e+01 1eesA 1mh1A 186 3.11e+01 c.37.1.8 32002 3k86A 185 3.19e+01 1iz0A 302 3.19e+01 b.35.1.2,c.2.1.1 83821,83822 1q9rB 222 3.20e+01 b.1.1.1,b.1.1.2 96307,96308 1rdqE 350 3.22e+01 d.144.1.7 97314 1fa0A 537 3.30e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1vfgA 390 3.34e+01 a.173.1.1,d.218.1.4 108570,108571 1hl9A 449 3.37e+01 b.71.1.3,c.1.8.11 90650,90651 1yrzA 528 3.42e+01 b.29.1.23,b.67.2.1 123948,123949 3kymB 227 3.42e+01 1k81A 36 3.45e+01 g.59.1.1 72136 1xtqA 177 3.49e+01 c.37.1.8 122297 1j5yA 187 3.51e+01 a.4.5.1,d.94.2.1 71592,71593 3d79A 179 3.54e+01 2q3hA 201 3.54e+01 3f14A 112 3.55e+01 1zunB 434 3.56e+01 b.43.3.1,b.44.1.1,c.37.1.8 125677,125678,125679 1wsrA 375 3.61e+01 1urjA 1136 3.65e+01 e.58.1.1 113410 1yqzA 438 3.68e+01 2wcwA 139 3.74e+01 3er7A 131 3.76e+01 d.17.4.24 158191 2vgpA 284 3.79e+01 2omdA 154 3.81e+01 2hwzH 227 3.81e+01 2zjrG 174 3.86e+01 c.21.1.1 154560 3bb7A 321 3.87e+01 2gysA 419 3.92e+01 b.1.2.1,b.1.2.1,b.1.2.1,b.1.2.1 135865,135866,135867,135868 2pziA 681 3.93e+01 2q66A 525 3.95e+01 a.160.1.1,d.218.1.3,d.58.16.1 150057,150058,150059 2pvrA 334 3.97e+01 d.144.1.7 149893 2fk6A 320 4.01e+01 d.157.1.7 133646 3dc6A 198 4.04e+01 1n0nA 199 4.08e+01 a.2.11.1,d.44.1.1 79750,79751 3ke7A 134 4.12e+01 2abyA 146 4.12e+01 1sjyA 159 4.12e+01 d.113.1.1 98900 2o09A 189 4.20e+01 2jbwA 386 4.21e+01 c.69.1.41 147962 1y44A 320 4.22e+01 d.157.1.7 122608 3i26A 384 4.22e+01 1skoB 130 4.23e+01 d.110.7.1 105677 3dkuA 153 4.26e+01 2ov7A 137 4.29e+01 1pl4A 198 4.31e+01 a.2.11.1,d.44.1.1 94854,94855 1s9rA 410 4.31e+01 d.126.1.4 98758 1s4iA 175 4.33e+01 1fl9A 161 4.37e+01 c.37.1.18 70137 2eu9A 355 4.39e+01 1lxyA 409 4.40e+01 d.126.1.4 91154 2vavA 444 4.50e+01 c.69.1.40 152844 1n1tA 641 4.52e+01 b.29.1.15,b.68.1.1 79821,79822 2vxsH 225 4.52e+01 1t11A 392 4.53e+01 a.223.1.1,d.241.2.1,d.26.1.1 106236,106237,106238 2vatA 444 4.56e+01 c.69.1.40 152831 1d2gA 292 4.59e+01 1xvaA c.66.1.5 34187 1x3sA 195 4.61e+01 c.37.1.8 121670 3eqeA 171 4.64e+01 1o20A 427 4.68e+01 c.82.1.1 86556 1ml8A 134 4.68e+01 d.227.1.2 85013 2wzpD 123 4.73e+01 3hmmA 303 4.74e+01 1aqdA 192 4.78e+01 1iakA b.1.1.2,d.19.1.1 21585,38159 1pqzA 238 4.87e+01 b.1.1.2,d.19.1.1 104297,104298 3lm2A 226 4.90e+01 2cbnA 306 4.95e+01 d.157.1.7 130191 2z1eA 342 4.98e+01 d.79.4.1,d.139.1.1 153932,153933 2j5zA 221 4.99e+01 2wwxA 175 5.01e+01 2hhpA 530 5.02e+01 a.160.1.1,d.218.1.3,d.58.16.1 136503,136504,136505 3cgxA 242 5.14e+01 2g6bA 180 5.14e+01 c.37.1.8 134701 1wgpA 137 5.16e+01 b.82.3.2 114619 2oxgA 108 5.23e+01 3cyeA 387 5.27e+01 3hr6A 436 5.27e+01 2r3iA 298 5.28e+01 2bkrA 212 5.29e+01 d.3.1.7 128710 2dnrA 91 5.35e+01 1zhsA 113 5.42e+01 3beqA 385 5.43e+01 3e7eA 365 5.45e+01 2covD 104 5.54e+01 2qf2A 624 5.54e+01 2j0iA 303 5.62e+01 3g9xA 299 5.69e+01 3lh5A 251 5.69e+01 2fikA 287 5.75e+01 b.1.1.2,d.19.1.1 133524,133525 2gq0A 303 5.77e+01 3f3zA 277 5.78e+01 1vjyA 303 5.82e+01 d.144.1.7 108633 3b7eA 385 5.90e+01 2bsjA 133 5.92e+01 2kc8A 98 5.93e+01 1i8aA 189 6.04e+01 1i82A b.1.9.2 61951 2ppqA 322 6.05e+01 d.144.1.6 149782 3cptB 131 6.07e+01 1s98A 107 6.10e+01 b.124.1.1 105377 2zxdA 455 6.12e+01 1yztA 184 6.18e+01 c.37.1.8 124288 1bn7A 294 6.20e+01 1bn6A c.69.1.8 34677 1oivA 191 6.21e+01 c.37.1.8 93076 2c43A 323 6.25e+01 3dtbA 624 6.39e+01 1hdfA 102 6.40e+01 1ag4 b.11.1.1 23627 3bp5A 117 6.44e+01 b.1.1.1 155462 2ch0A 133 6.44e+01 3fbwA 299 6.48e+01 3m05A 114 6.49e+01 3fwhA 299 6.53e+01 3bp6A 117 6.59e+01 1oaqL 120 6.60e+01 b.1.1.1 92708 1dpeA 507 6.68e+01 c.94.1.1 35799 2eo0A 147 6.73e+01 2vapA 364 6.78e+01 c.32.1.1,d.79.2.1 152828,152829 1tigA 94 6.80e+01 d.68.1.1 39566 2fafA 608 6.83e+01 1zk7A 467 6.83e+01 1xedA 117 6.84e+01 b.1.1.1 115229 1iznA 286 6.85e+01 e.43.1.1 83847 2b0rA 202 6.87e+01 3i84A 98 6.87e+01 1npuA 117 6.88e+01 b.1.1.1 92038 2bmjA 178 6.89e+01 c.37.1.8 128797 3kpiA 434 6.96e+01 1r7mA 235 6.97e+01 d.95.2.1,d.95.2.1 111713,111714 3eesA 153 6.97e+01 2yxyA 115 7.01e+01 3fnbA 405 7.01e+01 3e8lC 185 7.02e+01 1gmeA 151 7.05e+01 b.15.1.1 65305 2p02A 396 7.09e+01 d.130.1.1,d.130.1.1,d.130.1.1 149132,149133,149134 3d7rA 326 7.11e+01 2dvyA 226 7.13e+01 1ynaA 194 7.16e+01 b.29.1.11 24335 1r2jA 366 7.16e+01 a.29.3.1,e.6.1.1 96869,96870 3k6kA 322 7.17e+01 2cw2A 226 7.25e+01 1khbA 625 7.26e+01 c.91.1.1,c.109.1.1 68606,68607 2oc6A 124 7.27e+01 d.198.4.1 148721 2q83A 346 7.28e+01 1u5xA 140 7.30e+01 b.22.1.1 113055 1u58A 253 7.30e+01 b.1.1.2,d.19.1.1 144387,144388 1o8uA 257 7.33e+01 c.14.1.3 81194 1zpvA 91 7.38e+01 d.58.18.7 125475 3e0lA 455 7.41e+01 1szoA 257 7.42e+01 c.14.1.3 106164 3ec6A 139 7.44e+01 2htuA 390 7.46e+01 1gwmA 153 7.47e+01 b.18.1.19 83348 1ufoA 238 7.47e+01 c.69.1.27 99344 2pr1A 163 7.49e+01 3ib7A 330 7.55e+01 1kvnA 104 7.56e+01 d.201.1.1 73066 2qjvA 270 7.57e+01 2wczA 139 7.59e+01 1xu1A 138 7.60e+01 b.22.1.1 116033 2hy1A 280 7.61e+01 d.159.1.11 147437 2pd1A 104 7.61e+01 d.58.4.11 149387 1mz5A 638 7.63e+01 b.29.1.15,b.68.1.1 79679,79680 2ux0A 143 7.65e+01 d.17.4.7 152231 2bnmA 198 7.66e+01 a.35.1.3,b.82.1.10 128835,128836 1zkkA 167 7.68e+01 2qr7A 342 7.69e+01 1ogoX 574 7.70e+01 b.133.1.1,b.80.1.10 92925,92926 2i8dA 123 7.79e+01 d.198.4.1 147561 1h8gA 95 7.89e+01 b.109.1.1 65735 3m2tA 359 7.91e+01 2inpE 118 7.95e+01 1vk6A 269 7.98e+01 d.113.1.4,d.113.1.4,g.41.14.1 100852,111609,111610 2vzkA 173 7.99e+01 2bshA 125 8.00e+01