# 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 1om2A 95 3.28e-01 1om2A a.23.4.1 16520 2d1eA 248 3.40e-01 1n93X 375 5.37e-01 a.206.1.1 91707 1z6nA 167 7.77e-01 2utgA 70 9.36e-01 1utg a.101.1.1 18814 1e6cA 173 1.13e+00 1shkA c.37.1.2 59296 1utg 70 1.33e+00 1utg a.101.1.1 18813 1im4A 221 1.86e+00 e.8.1.7 62581 1f3mA 80 1.90e+00 1f3mA j.66.1.1 46358 1pmzA 86 2.19e+00 a.39.1.10 104195 1fsfA 266 2.26e+00 c.124.1.1 65047 1oaiA 59 3.03e+00 a.5.2.3 81255 1fpoA 171 3.85e+00 1fpoA a.2.3.1,a.23.1.1 15693,16487 1mxiA 160 3.92e+00 c.116.1.1 79646 1i36A 264 4.45e+00 a.100.1.8,c.2.1.6 71108,71109 1kn0A 212 4.50e+00 d.50.1.3 77444 1c3pA 375 4.56e+00 1c3pA c.42.1.2 32606 1hq3D 103 4.97e+00 1aoiB a.22.1.1 16464 1xvjA 109 5.02e+00 2f9fA 177 5.08e+00 2booA 247 5.14e+00 1q3eA 207 5.56e+00 b.82.3.2 95669 2fi9A 128 5.56e+00 1lt3A 240 5.98e+00 1lt3A d.166.1.1 42230 1ciqA 40 6.11e+00 2sniI d.40.1.1 38576 1n1jB 97 6.36e+00 a.22.1.3 79814 1tzyD 103 6.75e+00 a.22.1.1 107533 1deaA 266 7.19e+00 1deaA c.124.1.1 31760 2fvtA 135 7.25e+00 1jqSB 32 7.50e+00 1jqsB 32 7.50e+00 i.1.1.1 63238 1xahA 354 7.52e+00 1rbp 182 8.16e+00 1aqb b.60.1.1 27085 1z85A 234 8.20e+00 1lt4A 247 8.37e+00 1lt3A d.166.1.1 42231 1mhyG 169 8.60e+00 1mtyG a.23.3.1 16518 1q5nA 454 8.70e+00 a.127.1.1 95901 1wdcC 156 8.79e+00 1wdcC a.39.1.5 17317 1n6aA 259 8.93e+00 b.76.2.1,b.85.7.1 80121,80122 1v37A 177 8.99e+00 1svr 114 9.27e+00 1svy d.109.1.1 40833 1g33A 73 9.30e+00 a.39.1.4 65121 1f60A 458 9.52e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1aj8A 371 9.57e+00 1aj8A a.103.1.1 18900 2mysB 166 9.60e+00 1wdcB a.39.1.5 17308 1wz7A 111 9.86e+00 1svy 114 9.99e+00 1svy d.109.1.1 40831 1mvwC 147 1.02e+01 i.15.1.1 79525 1o1fC 147 1.02e+01 i.15.1.1 80997 1mlvA 444 1.03e+01 a.166.1.1,b.85.7.3 79283,79284 2f6hX 419 1.07e+01 1qb7A 236 1.10e+01 1qb7A c.61.1.1 34087 1mvwB 145 1.14e+01 i.15.1.1 79524 1tns 76 1.18e+01 1qpmA a.6.1.7 16228 1f3yA 165 1.20e+01 d.113.1.1 59635 1uekA 275 1.21e+01 d.14.1.5,d.58.26.5 88483,88484 2h21A 440 1.24e+01 1y74A 57 1.32e+01 2bj7A 138 1.35e+01 2tct 207 1.38e+01 2tct a.4.1.9,a.121.1.1 16063,19240 1ucpA 91 1.39e+01 a.77.1.5 99186 1lfo 128 1.45e+01 1hmt b.60.1.2 27223 1p0yA 444 1.47e+01 a.166.1.1,b.85.7.3 87654,87655 1ebdC 41 1.50e+01 1ebdC a.9.1.1 16355 1din 236 1.56e+01 1din c.69.1.9 34682 1gmpA 96 1.59e+01 1rgeA d.1.1.2 36036 1svq 114 1.60e+01 1svy d.109.1.1 40832 1bjz 207 1.64e+01 2tct a.4.1.9,a.121.1.1 16065,19242 1huuA 90 1.65e+01 1huuA a.55.1.1 17897 1jvr 137 1.67e+01 1jvr a.61.1.2 18132 1i8vA 96 1.68e+01 d.1.1.2 61985 1w9gA 104 1.68e+01 1b5m 84 1.69e+01 1cyo d.120.1.1 41073 1ncx 162 1.72e+01 1ncx a.39.1.5 17222 2db1A 118 1.72e+01 1rgeA 96 1.73e+01 1rgeA d.1.1.2 36028 1r8eA 278 1.75e+01 a.6.1.3,d.60.1.1 104843,104844 1a6i 217 1.77e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1rro 108 1.79e+01 1a75A a.39.1.4 17195 1azwA 313 1.79e+01 1qtrA c.69.1.7 34658 1ltaC 49 1.87e+01 1ltaC 1zoqC 47 1.90e+01 2bykB 128 1.91e+01 1a2xA 159 1.94e+01 1ncx a.39.1.5 17251 2beiA 170 1.95e+01 1jfiA 98 1.95e+01 1jfiA a.22.1.3 62936 1tw4A 125 1.95e+01 1aoiB 87 1.97e+01 1aoiB a.22.1.1 16470 1sp2 31 1.98e+01 1bhi g.37.1.1 45050 1a80 277 2.01e+01 1frb c.1.7.1 28700 1kx5B 102 2.04e+01 a.22.1.1 77594 1awpA 92 2.09e+01 1cyo d.120.1.1 41071 1lniA 96 2.10e+01 d.1.1.2 74046 1khtA 192 2.12e+01 c.37.1.1 84401 1y0vH 146 2.12e+01 5pal 109 2.16e+01 1a75A a.39.1.4 17215 1mbyA 88 2.16e+01 d.223.1.1 78931 1aijL 281 2.22e+01 6prcL f.26.1.1 43461 1pvaA 110 2.23e+01 1a75A a.39.1.4 17207 1o4sA 389 2.24e+01 c.67.1.1 86620 1qjtA 99 2.27e+01 1eh2 a.39.1.6 17335 2csvA 72 2.34e+01 1ggvA 232 2.35e+01 1din c.69.1.9 34683 1bxyA 60 2.43e+01 1bxyA d.59.1.1 39525 1qrdA 273 2.44e+01 1d4aA c.23.5.3 31217 1o82A 70 2.44e+01 a.64.2.1 92630 1tn4 159 2.49e+01 1ncx a.39.1.5 17248 1p5zB 263 2.52e+01 c.37.1.1 87815 1n91A 108 2.54e+01 d.206.1.1 80326 1yqgA 263 2.54e+01 1ukuA 102 2.56e+01 d.58.5.2 99533 1p65A 73 2.58e+01 d.254.1.1 94156 1id3B 102 2.63e+01 a.22.1.1 66113 1z1dA 103 2.63e+01 2aq9A 262 2.64e+01 2eboA 74 2.66e+01 2eboA h.3.2.1 45754 1aoiF 87 2.71e+01 1aoiB a.22.1.1 16471 1hueA 90 2.74e+01 1huuA a.55.1.1 17900 2bk7B 222 2.74e+01 2bo9B 222 2.74e+01 2bibA 547 2.78e+01 1pp7U 131 2.85e+01 a.4.5.44 94973 1l8wA 348 2.86e+01 a.154.1.1 73704 1wm1A 317 2.89e+01 c.69.1.7 109405 2bykA 140 2.89e+01 1qtrA 317 2.93e+01 1qtrA c.69.1.7 34660 1n27A 96 2.97e+01 b.34.9.2 91549 1rwyA 109 2.97e+01 a.39.1.4 98002 2ftbA 125 3.04e+01 1r1mA 164 3.05e+01 d.79.7.1 96820 1od2A 805 3.05e+01 c.14.1.4,c.14.1.4 86821,86822 1zi8A 236 3.09e+01 1s4cA 155 3.10e+01 1sc3A 178 3.22e+01 c.17.1.1 105416 1lxa 262 3.26e+01 1lxa b.81.1.1 28052 1kyaA 499 3.28e+01 b.6.1.3,b.6.1.3,b.6.1.3 73203,73204,73205 1br1B 150 3.29e+01 1wdcC a.39.1.5 17309 1h2aL 567 3.32e+01 1h2rL e.18.1.1 43299 1z5sD 83 3.36e+01 1jopA 155 3.39e+01 b.82.2.7 84187 1k6iA 352 3.39e+01 c.2.1.2 68223 2c1mB 46 3.42e+01 2ew2A 316 3.43e+01 1wraA 308 3.43e+01 1top 162 3.44e+01 1ncx a.39.1.5 17223 1f07A 321 3.51e+01 1ezwA c.1.16.3 59560 1yzhA 214 3.65e+01 1j5eN 60 3.70e+01 g.39.1.7 71557 1uf2C 421 3.72e+01 a.115.1.3,b.19.1.1 99291,99292 1a0eA 443 3.76e+01 1a0cA c.1.15.3 29537 1id1A 153 3.77e+01 1id1A c.2.1.9 62286 2d00A 109 3.77e+01 2ahqA 76 3.84e+01 1je8A 82 3.88e+01 a.4.6.2 77108 1dpqA 20 3.89e+01 j.60.1.1 46345 1p6pA 125 3.95e+01 b.60.1.2 87839 2es9A 115 3.97e+01 1h75A 81 3.97e+01 1h75A c.47.1.1 60716 1xwwA 157 4.00e+01 2be3A 226 4.03e+01 1vtp 26 4.11e+01 j.36.2.1 46284 1jvwA 167 4.11e+01 d.26.1.1 71907 3znf 30 4.16e+01 g.37.1.1 45049 1i19A 561 4.21e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1jfvA 131 4.22e+01 c.44.1.1 66654 1lfaA 187 4.24e+01 1ido c.62.1.1 34122 1pylA 97 4.31e+01 d.1.1.2 104391 1dlwA 116 4.32e+01 1dlyA a.1.1.1 14982 1aj4 161 4.32e+01 1ncx a.39.1.5 17244 1ql0A 241 4.33e+01 1qaeA d.4.1.2 37139 1yqyA 523 4.33e+01 2as0A 396 4.36e+01 1uqrA 154 4.44e+01 c.23.13.1 99779 1g8tA 245 4.44e+01 1qaeA d.4.1.2 37137 1ew6A 137 4.45e+01 1ewaA a.1.1.2 15637 1ewaA 137 4.45e+01 1ewaA a.1.1.2 15639 1qaeA 245 4.45e+01 1qaeA d.4.1.2 37141 1b35A 260 4.46e+01 1b35A b.121.4.1 23333 1lfb 99 4.52e+01 1lfb a.4.1.1 15989 1wn4A 28 4.57e+01 j.113.1.1 109426 1eysL 280 4.58e+01 6prcL f.26.1.1 43515 1wmiB 67 4.59e+01 1k3pA 426 4.61e+01 a.103.1.1 77237 1ipaA 274 4.68e+01 c.116.1.1,d.79.3.3 71254,71255 1h2rL 534 4.71e+01 1h2rL e.18.1.1 43298 1nubA 229 4.74e+01 1sra a.39.1.3,g.3.11.3,g.68.1.1 17191,44330,44715 1z4eA 153 4.80e+01 2fu4A 83 4.89e+01 1w53A 84 4.90e+01 a.186.1.2 109175 1r4gA 53 4.93e+01 a.8.5.1 96996 1zgyA 272 4.94e+01 1m46A 148 4.96e+01 a.39.1.5 78599 1wywA 230 5.02e+01 1k6xA 352 5.04e+01 c.2.1.2 68238 5croA 66 5.08e+01 1orc a.35.1.2 17044 1wz8A 264 5.13e+01 1g59A 468 5.15e+01 a.97.1.1,c.26.1.1 60257,60258 1r12A 258 5.21e+01 e.4.1.1 96780 2atjA 308 5.25e+01 1bgp a.93.1.1 18675 1yfbA 59 5.26e+01 1gc0A 398 5.27e+01 c.67.1.3 70168 1i2tA 61 5.31e+01 1i2tA a.144.1.1 61582 1f2hA 169 5.34e+01 1f3vA d.58.22.1 59612 1wuiL 534 5.36e+01 1q52A 314 5.36e+01 c.14.1.3 95846 1ubkL 534 5.36e+01 e.18.1.1 88422 1rwxA 178 5.39e+01 1nigA 152 5.40e+01 a.25.2.1 85740 1jf8A 131 5.40e+01 c.44.1.1 66621 1gwuA 309 5.40e+01 a.93.1.1 83351 1xyiA 66 5.51e+01 1vq3A 94 5.54e+01 1smnA 245 5.54e+01 1qaeA d.4.1.2 37143 2bl0C 142 5.59e+01 1a8q 274 5.60e+01 1brt c.69.1.12 34702 1wn0A 145 5.62e+01 2bo4A 397 5.64e+01 2fh7A 595 5.65e+01 1lfpA 249 5.70e+01 e.39.1.1 73885 1r31A 428 5.71e+01 d.58.20.1,d.179.1.1 96897,96898 1ctt 294 5.72e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1c53 79 5.77e+01 1c53 a.3.1.1 15801 1kbqA 273 5.82e+01 c.23.5.3 68391 1jenB 67 5.83e+01 1jenB d.156.1.1 42029 1lpvA 52 5.83e+01 g.62.1.1 78124 1zcjA 463 5.90e+01 1a75B 109 5.92e+01 1a75A a.39.1.4 17217 1g4yR 148 5.92e+01 1cll a.39.1.5 60252 2pdd 43 5.93e+01 1ebdC a.9.1.1 16358 1lqc 56 6.00e+01 1pru a.35.1.5 17109 1x8dA 104 6.00e+01 1hjp 203 6.05e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16274,17947,25266 1b8zA 90 6.09e+01 1huuA a.55.1.1 17902 1mv4A 37 6.09e+01 h.1.5.1 79496 1pz4A 116 6.10e+01 d.106.1.1 95400 1wveC 80 6.11e+01 1c94A 38 6.11e+01 1c94A k.11.1.1 46428 1rzhL 281 6.12e+01 f.26.1.1 98164 1b0nA 111 6.14e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1x7oA 287 6.20e+01 1xbbA 291 6.24e+01 1pvgA 418 6.27e+01 d.14.1.3,d.122.1.2 95161,95162 1mvoA 136 6.27e+01 c.23.1.1 79513 2c5rA 67 6.27e+01 1y1uA 585 6.28e+01 2mysC 149 6.33e+01 1wdcC a.39.1.5 17323 1hbzA 498 6.35e+01 1cf9A e.5.1.1 60937 1vl2A 421 6.36e+01 c.26.2.1,d.210.1.1 108708,108709 1mslA 109 6.37e+01 1mslA f.16.1.1 43660 7atjA 308 6.40e+01 1bgp a.93.1.1 18673 1gweA 503 6.40e+01 e.5.1.1 70667 2fua 215 6.44e+01 2fua c.74.1.1 34977 4cpv 109 6.48e+01 1a75A a.39.1.4 17198 1qbgA 272 6.51e+01 1d4aA c.23.5.3 31227 1c8cA 64 6.66e+01 1azpA b.34.13.1 59084 1r45A 204 6.66e+01 1mypA 108 6.67e+01 1d2vA a.93.1.2 18701 1ig5A 75 6.70e+01 4icb a.39.1.1 62363 2f69A 261 6.70e+01 1d4aA 273 6.70e+01 1d4aA c.23.5.3 31219 1ur1A 378 6.74e+01 c.1.8.3 99804 1j7xA 302 6.75e+01 c.14.1.2 66425 2b9hA 353 6.80e+01 2blkA 122 6.80e+01 1txqB 86 6.82e+01 1d9tA 289 6.82e+01 1deaA 1o0pA 104 6.85e+01 d.58.7.1 86535 1bpe 335 6.89e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 18076,75815,75816 1no5A 114 6.89e+01 d.218.1.5 92014 1f5vA 240 6.99e+01 1bkjA d.90.1.1 40255 1ne7A 289 7.06e+01 c.124.1.1 91833 1yruB 74 7.07e+01 2bopA 85 7.10e+01 2bopA d.58.8.1 39217 2bapC 56 7.11e+01 1z00B 84 7.18e+01 1vkmA 297 7.20e+01 c.138.1.1 108670 1h3fA 432 7.25e+01 c.26.1.1,d.66.1.4 76631,76632 1zkrA 153 7.27e+01 1azpA 66 7.29e+01 1azpA b.34.13.1 37467 1ay7B 89 7.29e+01 1ay7B c.9.1.1 30836 1v9wA 130 7.36e+01 c.47.1.16 108453 1k8tA 510 7.38e+01 e.41.1.1 68316 1jw2A 72 7.41e+01 a.23.5.1 67372 1jjhA 86 7.53e+01 2bopA d.58.8.1 63119 1k9uA 78 7.54e+01 a.39.1.10 84348 1pl4A 198 7.65e+01 a.2.11.1,d.44.1.1 94854,94855 2ct7A 86 7.68e+01 1ur6B 52 7.70e+01 g.44.1.1 99812 1bouA 139 7.71e+01 1bouA a.88.1.1 18521 1a8s 273 7.76e+01 1brt c.69.1.12 34710 1br2A 791 7.79e+01 1lvk b.34.3.1,c.37.1.9 24558,32155 1knzA 164 7.83e+01 e.34.1.1 68709 1wvcA 259 7.84e+01 1fxjA 331 7.85e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 1fgkA 310 7.85e+01 1fgkA d.144.1.7 41693 1b0zA 445 7.91e+01 2pgi c.80.1.2 35309 2pgi 445 7.91e+01 2pgi c.80.1.2 35308 1owfA 99 7.94e+01 a.55.1.1 87487 1ihfA 99 7.94e+01 1huuA a.55.1.1 17893 2cs2A 134 7.98e+01 1aq0A 306 8.02e+01 1aq0A c.1.8.3 28842 1w6uA 302 8.03e+01 1xgkA 352 8.08e+01 1fua 215 8.19e+01 2fua c.74.1.1 34973 1eueA 86 8.31e+01 1cyo d.120.1.1 59504 1ghr 306 8.35e+01 1aq0A c.1.8.3 28844 1jbgA 109 8.35e+01 a.6.1.3 66480 1jx4A 352 8.39e+01 d.240.1.1,e.8.1.7 90378,90379 1dv0A 47 8.46e+01 1dv0A a.5.2.1 16289 2cyeA 133 8.48e+01 1dg9A 157 8.50e+01 1dg9A c.44.1.1 32637 2cxxA 190 8.51e+01 1ln4A 104 8.55e+01 d.68.4.1 74043 1a48 306 8.60e+01 1a48 d.143.1.1 41590 1c0eA 157 8.61e+01 1dg9A c.44.1.1 32638 2fkiA 126 8.65e+01 1wchA 315 8.71e+01 1y1xA 191 8.72e+01 1whtA 256 8.76e+01 1ivyA c.69.1.5 34646 1obdA 306 8.76e+01 d.143.1.1 86767 1wkqA 164 8.82e+01 c.97.1.2 109393 2bn5A 33 8.86e+01 1qaxA 428 8.86e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1bc6 77 8.87e+01 1a6l d.58.1.2 38986 1rpuA 172 8.89e+01 d.255.1.1 97716 1hucA 47 8.91e+01 1hucA d.3.1.1 37049 1frd 98 8.99e+01 1awd d.15.4.1 37648