# List of top-scoring protein chains for t2k-100-30-bys-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 2cirA 297 5.60e-23 2htaA 309 1.86e-21 1snzA 344 4.20e-17 b.30.5.4 98930 1mmuA 347 8.82e-16 b.30.5.4 79303 1nszA 347 1.83e-15 b.30.5.4 80724 1lurA 339 4.16e-15 b.30.5.4 84717 1jovA 270 2.00e-14 b.30.5.7 84192 1z45A 699 1.36e-13 b.30.5.4,c.2.1.2 124427,124428 1ygaA 342 3.83e-11 3bs6A 280 6.96e-02 1dq3A 454 4.11e-01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 2d73A 738 4.72e-01 2h1tA 188 6.71e-01 1kz8A 337 7.10e-01 e.7.1.1 77633 1nuyA 337 8.35e-01 e.7.1.1 86213 1frpA 335 1.23e+00 1frpA e.7.1.1 42875 1rdzA 337 1.43e+00 1frpA e.7.1.1 42882 1fwcB 106 1.71e+00 1ubpB b.85.3.1 28324 1txkA 498 2.20e+00 b.1.18.2,b.30.5.9 107425,107426 1ejxB 101 2.22e+00 b.85.3.1 83183 1zpuA 534 2.25e+00 1xdpA 687 2.40e+00 a.7.15.1,d.322.1.2,d.136.1.4,d.136.1.4 121896,121897,121898,121899 5fbpA 335 2.49e+00 1frpA e.7.1.1 42873 1eonA 245 2.66e+00 1rvaA c.52.1.2 33238 1ubpB 122 2.71e+00 1ubpB b.85.3.1 28346 1h4gA 207 2.85e+00 b.29.1.11 70863 4ubpB 126 2.98e+00 1ubpB b.85.3.1 28345 1yewA 382 3.21e+00 1vcbA 118 3.57e+00 1vcbA d.15.1.1 37603 1bglA 1023 3.71e+00 1bglA b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22097,22098,23734,24358,28857 2pjmA 226 3.84e+00 1kn3A 183 4.25e+00 b.17.1.1 72764 1lm8B 118 4.35e+00 d.15.1.1 74033 1v7rA 186 4.61e+00 c.51.4.1 100482 1c9oA 66 4.61e+00 1mjc b.40.4.5 25325 3blcA 330 4.72e+00 1behA 187 4.99e+00 1a44 b.17.1.1 23700 1fg9C 245 5.25e+00 1jrhI b.1.2.1,b.1.2.1 22060,22061 1mjc 69 5.29e+00 1mjc 1mjcA 69 5.29e+00 b.40.4.5 25319 1gyhA 318 5.37e+00 b.67.2.1 70757 1y14B 171 5.53e+00 b.40.4.5,d.230.1.1 116323,116324 1b97A 244 5.66e+00 1rvaA c.52.1.2 33252 2cavA 445 5.75e+00 1dgwA b.82.1.2,b.82.1.2 28094,28095 1xf1A 926 5.97e+00 1b94A 244 6.05e+00 1rvaA c.52.1.2 33250 2gpjA 252 6.27e+00 1jz8A 1023 6.27e+00 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1v7wA 807 6.39e+00 a.102.1.4,b.30.5.3 108411,108412 2p90A 319 6.54e+00 1iqzA 81 6.67e+00 d.58.1.4 66281 2cqsA 842 6.97e+00 1b96A 244 7.06e+00 1rvaA c.52.1.2 33268 1dp0A 1023 7.38e+00 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 1csp 67 7.76e+00 1mjc 2a8mA 420 7.85e+00 2iqyA 190 7.91e+00 1yjmA 110 8.23e+00 b.26.1.2 123427 1yioA 208 8.31e+00 a.4.6.2,c.23.1.1 123326,123327 1gydB 315 8.38e+00 b.67.2.1 70751 2nv4A 147 8.41e+00 2a8jA 420 8.53e+00 2ho9A 167 8.78e+00 1c3mA 147 8.78e+00 1jotA b.77.3.1 27983 2qjjA 402 8.93e+00 3cfuA 159 9.13e+00 1n0lA 224 9.22e+00 b.1.11.1,b.7.2.1 79744,79745 1l8rA 101 9.24e+00 a.6.1.4 73700 2ai4A 119 9.77e+00 b.6.1.7 126816 2c4xA 260 9.95e+00 1xs1A 193 1.05e+01 b.85.4.1 115892 2hxvA 360 1.06e+01 c.71.1.2,c.97.1.2 136859,136860 1b7aA 186 1.06e+01 1a44 b.17.1.1 23705 1sx5A 244 1.09e+01 c.52.1.2 99023 2j8gA 339 1.11e+01 2pviA 157 1.11e+01 3pviA c.52.1.6 33302 1v54G 85 1.14e+01 f.23.2.1 100328 1g3fA 117 1.15e+01 1g3fA g.52.1.1 45378 2bi7A 384 1.16e+01 2ckkA 127 1.18e+01 1hq8A 123 1.19e+01 1b6e d.169.1.1 61127 2ichA 335 1.21e+01 2a8lA 420 1.22e+01 1svb 395 1.22e+01 1svb 1svbA 395 1.22e+01 b.1.18.4,f.10.1.1 21814,43827 1h09A 338 1.26e+01 b.109.1.1,c.1.8.8 83420,83421 2f7tA 227 1.32e+01 2fp8A 322 1.46e+01 2occG 84 1.47e+01 2occG f.23.2.1 43522 1kopA 223 1.50e+01 2cba b.74.1.1 27966 1oe1A 336 1.50e+01 b.6.1.3,b.6.1.3 86891,86892 1w1wA 430 1.54e+01 c.37.1.12 114080 1euwA 152 1.58e+01 1dupA b.85.4.1 28349 2j2zA 218 1.59e+01 b.1.11.1,b.7.2.1 137974,137975 1gk1B 522 1.63e+01 1fyhB 229 1.66e+01 1jrhI b.1.2.1,b.1.2.1 22055,22056 2vfkA 205 1.67e+01 1xwdC 252 1.67e+01 2ae5B 528 1.73e+01 2v95A 371 1.76e+01 1jmcA 246 1.79e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1or0B 528 1.80e+01 1ao5A 237 1.82e+01 5ptp b.47.1.2 26334 1zvtA 256 1.84e+01 1fm2B 520 1.87e+01 1fm2B 1g73C 121 1.91e+01 1g3fA g.52.1.1 45375 2vdxA 373 2.01e+01 1dt9A 437 2.03e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 2aacA 177 2.03e+01 2arcA b.82.4.1 28150 2geeA 203 2.04e+01 2g1lA 104 2.05e+01 b.26.1.2 134520 2arcA 164 2.07e+01 2arcA b.82.4.1 28148 1pjjA 271 2.11e+01 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 2cw8A 537 2.11e+01 3b2mA 295 2.13e+01 1am2 199 2.16e+01 1am2 1am2A 199 2.16e+01 b.86.1.2 28381 2vsmB 140 2.21e+01 1y0yA 353 2.26e+01 b.49.3.1,c.56.5.4 122514,122515 1vj2A 126 2.32e+01 b.82.1.10 100796 1t5hX 504 2.32e+01 e.23.1.1 106449 2o26U 290 2.34e+01 1i7pA 274 2.35e+01 b.43.4.2,c.25.1.1 66048,66049 1ujxA 119 2.37e+01 b.26.1.2 99473 1wkoA 180 2.40e+01 2ffsA 157 2.42e+01 d.129.3.7 133391 2de6D 115 2.44e+01 1edhA 226 2.44e+01 1edhA b.1.6.1,b.1.6.1 22198,22199 2p0wA 324 2.45e+01 1rwiA 270 2.45e+01 b.68.9.1 97987 1vhzA 198 2.52e+01 d.113.1.1 100718 1n08A 163 2.57e+01 b.43.5.1 79730 1zud1 251 2.62e+01 1z8gA 372 2.67e+01 b.47.1.2,d.170.1.2 124697,124698 3cloA 258 2.68e+01 1ikoP 178 2.70e+01 b.6.1.5 71243 1pdkB 157 2.71e+01 1pdkB b.2.3.2 22427 2vg9A 217 2.72e+01 2j4hA 193 2.76e+01 1m9zA 111 2.79e+01 g.7.1.3 78881 2c8mA 262 2.83e+01 1zoxA 113 2.86e+01 1yg9A 330 2.89e+01 1ka1A 357 2.90e+01 e.7.1.1 68369 1ao0A 459 2.93e+01 1ecfB c.61.1.1,d.153.1.1 34049,41816 1ktzB 122 2.93e+01 g.7.1.3 68868 2brfA 110 2.98e+01 b.26.1.2 128996 2hu5A 582 3.08e+01 b.69.7.2,c.69.1.33 136763,136764 1tdzA 272 3.09e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 2fr2A 172 3.10e+01 b.60.1.8 133963 1uctA 218 3.13e+01 b.1.1.4,b.1.1.4 88467,88468 2bf6A 449 3.19e+01 1pmi 440 3.26e+01 1pmi 1pmiA 440 3.26e+01 b.82.1.3 28114 1bssA 244 3.26e+01 1rvaA c.52.1.2 33256 3pviA 157 3.29e+01 3pviA c.52.1.6 33300 1qpxA 218 3.41e+01 1qpxA b.1.11.1,b.7.2.1 22318,23200 1p63A 144 3.43e+01 b.42.1.1 94153 1jb0A 755 3.48e+01 1jb0A f.29.1.1 62820 2adgA 214 3.50e+01 1kit 757 3.50e+01 1kit 1mpuA 138 3.52e+01 d.169.1.1 85040 1tjxA 159 3.54e+01 b.7.1.2 112465 1hfuA 503 3.55e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1ii7A 333 3.55e+01 1ii7A d.159.1.4 62415 1zh1A 163 3.58e+01 2d6mA 159 3.59e+01 2bg9A 370 3.64e+01 1qx4A 274 3.64e+01 b.43.4.2,c.25.1.1 104624,104625 1a65A 504 3.64e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1zi0A 307 3.67e+01 1fzqA 181 3.72e+01 1hurA c.37.1.8 32060 1xvsA 126 3.73e+01 b.1.23.1 116095 2retB 175 3.76e+01 1cauA 181 3.79e+01 1dgwA b.82.1.2 28102 2pefA 373 3.83e+01 2acoA 173 3.85e+01 2e0jA 129 3.88e+01 2ovgA 66 3.92e+01 1avwB 171 3.93e+01 1wba b.42.4.1 25599 1qgxA 357 3.93e+01 1qgxA e.7.1.1 42973 1umkA 275 3.93e+01 b.43.4.2,c.25.1.1 113312,113313 1guiA 155 3.97e+01 b.18.1.14 76351 1uuqA 440 3.98e+01 c.1.8.3 100015 2ivfC 214 4.04e+01 2iiaA 131 4.10e+01 2dawA 154 4.11e+01 2odjA 428 4.12e+01 2bouA 143 4.12e+01 1bnkA 216 4.13e+01 1bnkA b.46.1.2 25765 2q87A 110 4.17e+01 1so9A 164 4.17e+01 b.146.1.1 105842 1nb9A 147 4.18e+01 b.43.5.1 85515 2bfgA 503 4.22e+01 b.71.1.2,c.1.8.3 128423,128424 1xtqA 177 4.25e+01 c.37.1.8 122297 1um5H 217 4.30e+01 b.1.1.1,b.1.1.2 113302,113303 2pzzA 147 4.32e+01 2gc7A 386 4.32e+01 b.69.2.1 134954 1xkwA 665 4.34e+01 1barA 140 4.34e+01 1bfg b.42.1.1 25504 2ix2B 245 4.39e+01 1pk6C 129 4.40e+01 b.22.1.1 94803 1p57B 255 4.41e+01 b.47.1.2 94126 2ok8A 316 4.43e+01 2ao3A 130 4.45e+01 1qppA 218 4.48e+01 1qpxA b.1.11.1,b.7.2.1 22320,23202 5croA 66 4.52e+01 1orc a.35.1.2 17044 3b9fI 395 4.52e+01 1nqjA 119 4.56e+01 b.23.2.1 86031 1z9lA 128 4.62e+01 3cnuA 116 4.62e+01 1xfoA 357 4.64e+01 b.49.3.1,c.56.5.4 115265,115266 1dzlA 505 4.68e+01 1dzlA b.121.6.1 23586 2o14A 375 4.70e+01 2vktA 289 4.70e+01 1eyuA 157 4.71e+01 3pviA c.52.1.6 33304 8rucI 123 4.72e+01 1rboC d.73.1.1 39629 1z4vA 532 4.77e+01 2hrcA 359 4.77e+01 c.92.1.1 136687 2epgA 487 4.78e+01 1hrkA 359 4.83e+01 1hrkA c.92.1.1 61228 2ns9A 157 4.83e+01 2z2nA 299 4.86e+01 2j6gA 266 4.89e+01 1lnsA 763 4.93e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1aol 228 5.00e+01 1aol 1aolA 228 5.00e+01 b.20.1.1 23840 1erjA 393 5.00e+01 1erjA b.69.4.1 27660 1qwdA 177 5.01e+01 b.60.1.1 96471 1pda 315 5.04e+01 1pda 2fjrA 189 5.07e+01 1iujA 106 5.07e+01 d.58.4.5 90701 1ykjA 394 5.09e+01 1xsqA 168 5.12e+01 b.82.1.14 115999 1vdhA 249 5.13e+01 d.58.4.10 108523 1vr3A 191 5.21e+01 b.82.1.6 120431 1n0xL 215 5.23e+01 b.1.1.1,b.1.1.2 91532,91533 2d9rA 104 5.27e+01 b.129.2.1 131350 1x31D 99 5.29e+01 1t3bA 211 5.45e+01 c.47.1.9,d.17.3.1 106341,106342 1dzaA 129 5.50e+01 7rsa d.5.1.1 37275 2h26A 291 5.50e+01 b.1.1.2,d.19.1.1 135990,135991 2ojhA 297 5.52e+01 2z5aB 420 5.52e+01 1o91A 178 5.55e+01 b.22.1.1 92656 2psbA 320 5.57e+01 1eylA 186 5.59e+01 1wba b.42.4.1 25593 1rm8A 169 5.62e+01 d.92.1.11 97660 1rg8A 146 5.67e+01 b.42.1.1 111801 1w18A 493 5.68e+01 2jg9C 131 5.69e+01 1gtkA 313 5.70e+01 c.94.1.1,d.50.2.1 76346,76347 1bxvA 91 5.75e+01 1aac b.6.1.1 22875 2buwB 241 5.76e+01 1ewjA 126 5.78e+01 1ecsA d.32.1.2 59526 2a9gA 418 5.90e+01 d.126.1.4 126435 1vjlA 164 5.92e+01 d.257.1.1 100822 1gph1 465 5.97e+01 1ecfB 1efcA 393 6.01e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 2ol2A 395 6.01e+01 1ogpA 393 6.09e+01 b.1.18.6,d.176.1.1 92927,92928 1hxn 219 6.12e+01 1hxn 1hxnA 219 6.12e+01 b.66.1.1 27529 1i4uA 181 6.12e+01 b.60.1.1 61732 2occF 98 6.12e+01 2occF g.41.5.3 45256 1s7jA 262 6.16e+01 d.21.1.2 98647 1thjA 214 6.21e+01 1qreA b.81.1.5 28072 2a1iA 146 6.22e+01 c.52.1.20 125999 2bbkH 355 6.24e+01 2bbkH b.69.2.1 27634 2gagD 99 6.25e+01 2bs9A 503 6.28e+01 b.71.1.2,c.1.8.3 129062,129063 3nul 130 6.28e+01 3nul 3nulA 130 6.28e+01 d.110.1.1 40891 1ydxA 406 6.31e+01 d.287.1.2,d.287.1.2 123004,123005 2po1B 277 6.32e+01 1f5jA 199 6.36e+01 1axkA b.29.1.11 24342 1ts3A 194 6.40e+01 1aw7A b.40.2.2,d.15.6.1 25168,37757 1fepA 724 6.42e+01 1fepA f.4.3.3 43808 2f0cA 191 6.53e+01 b.21.1.3,b.108.1.4 132665,132666 2oq8A 160 6.55e+01 1jdqA 98 6.57e+01 d.68.3.3 66559 2fvgA 340 6.64e+01 b.49.3.1,c.56.5.4 134201,134202 2nykA 285 6.66e+01 1qksA 567 6.71e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 2dd7A 216 6.80e+01 2h2zA 306 6.82e+01 1zq1A 438 6.83e+01 b.38.3.1,c.88.1.1 125489,125490 1vd3A 217 6.86e+01 2d49A 53 6.91e+01 2nxcA 254 6.93e+01 c.66.1.39 138739 2gnqA 336 6.93e+01 1jdpA 441 6.96e+01 c.93.1.1 62906 1tzaA 134 6.96e+01 b.1.23.1 107468 2fu5C 183 7.04e+01 c.37.1.8 134104 1jd5A 124 7.06e+01 g.52.1.1 66544 2dcyA 185 7.16e+01 b.29.1.11 131388 1qwzA 235 7.16e+01 b.100.1.1 96510 1s8eA 333 7.17e+01 d.159.1.4 105368 1uc2A 481 7.19e+01 d.261.1.1 99161 1i6lA 328 7.19e+01 c.26.1.1 66041 1skyB 502 7.25e+01 1skyB a.69.1.1,b.49.1.1,c.37.1.11 18313,26478,32358 1k1xA 659 7.25e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 2ghsA 326 7.27e+01 b.68.6.1 135209 2bibA 547 7.28e+01 b.109.1.1,d.157.1.8 128581,128582 2cwrA 103 7.30e+01 1qreA 247 7.35e+01 1qreA b.81.1.5 28066 2c9jA 223 7.41e+01 2pq8A 278 7.41e+01 2cbiA 594 7.42e+01 a.246.1.1,c.1.8.10,d.92.2.3 130179,130180,130181 1x8mA 288 7.42e+01 b.82.1.13 109516 2b5iC 199 7.43e+01 b.1.2.1,b.1.2.1 127898,127899 1wdjA 187 7.45e+01 c.52.1.27 114536 2axcA 264 7.49e+01 2amdA 311 7.52e+01 1cxyA 90 7.53e+01 1cyo d.120.1.1 41085 1fvuA 133 7.56e+01 1ixxB d.169.1.1 42345 1et7A 341 7.64e+01 1nif b.6.1.3,b.6.1.3 23070,23071 1ecsA 126 7.64e+01 1ecsA d.32.1.2 59407 1o12A 376 7.65e+01 b.92.1.5,c.1.9.10 80758,80759 1bkb 136 7.70e+01 1bkb 1bkbA 136 7.70e+01 b.34.5.2,b.40.4.5 24609,25341 2fqpA 97 7.70e+01 1v54F 98 7.70e+01 g.41.5.3 100327 2gh1A 301 7.78e+01 c.66.1.49 135170 2ix2A 249 7.79e+01 1gxrA 337 7.81e+01 b.69.4.1 70722 1ql3A 99 7.82e+01 1ycc a.3.1.1 15822 1qftA 175 7.84e+01 1qftA b.60.1.1 27151 2yz0A 138 7.88e+01 2iutA 574 7.91e+01 2hrgA 496 7.96e+01 1e1aA 314 7.99e+01 1e1aA b.68.6.1 59155