# 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.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 1z6oM 191 5.31e-02 2fha 183 1.09e-01 2fha a.25.1.1 16674 1fha 183 1.31e-01 2fha a.25.1.1 16675 1bjwA 382 1.59e-01 1bjwA c.67.1.1 34349 1b5pA 385 2.13e-01 c.67.1.1 90403 1bcfA 158 3.77e-01 1bcfA a.25.1.1 16648 2fkzA 155 4.31e-01 1bgeB 175 6.39e-01 1bgc a.26.1.1 16824 1bgeA 175 7.08e-01 1bgc a.26.1.1 16823 1jgcA 161 8.20e-01 a.25.1.1 66673 1vjxA 157 9.57e-01 a.25.1.1 100837 1q8iA 783 1.32e+00 c.55.3.5,e.8.1.1 96208,96209 1dchA 104 1.61e+00 1dcpA d.74.1.1 39692 2aplA 157 1.88e+00 1tzvA 142 2.18e+00 a.79.1.1 107526 1v2dA 381 2.41e+00 c.67.1.1 108281 1ux8A 132 2.49e+00 1bg7 176 2.87e+00 2fha a.25.1.1 16686 1r03A 182 2.94e+00 a.25.1.1 104675 2cohA 202 3.08e+00 1kx9A 112 3.32e+00 a.118.21.1 77602 6gsvA 217 3.49e+00 1b8xA a.45.1.1,c.47.1.5 17633,32925 1o4sA 389 3.78e+00 c.67.1.1 86620 1a32 88 3.79e+00 1a32 a.16.1.2 16384 2cb5A 453 3.89e+00 3gcb d.3.1.1 37035 2fp1A 166 3.91e+00 1fkoA 543 3.93e+00 1rthA c.55.3.1,e.8.1.2 33612,43094 1w7lA 422 4.02e+00 c.67.1.1 109226 1xw5A 217 4.17e+00 1dcpA 104 4.21e+00 1dcpA d.74.1.1 39672 1yizA 429 4.30e+00 2f6lA 166 4.48e+00 1tjoA 182 4.50e+00 1mojA 182 4.56e+00 a.25.1.1 91367 1fk9A 543 4.72e+00 1rthA c.55.3.1,e.8.1.2 33607,43080 2c4jA 218 4.88e+00 1ru0A 105 5.19e+00 1kq4A 232 5.86e+00 d.207.1.1 68791 1rfyA 102 5.87e+00 1us6A 102 5.95e+00 a.2.13.1 107999 1vrtA 560 6.01e+00 1rthA c.55.3.1,e.8.1.2 33574,43023 1f93A 104 6.20e+00 1dcpA d.74.1.1 39688 3pbgA 468 6.34e+00 1e70M c.1.8.4 28951 1yiyA 429 6.38e+00 1rthA 560 6.48e+00 1rthA c.55.3.1,e.8.1.2 33576,43028 2dc4A 165 6.49e+00 1w6kA 732 6.72e+00 2aexA 346 7.20e+00 1dcoA 104 7.44e+00 1dcpA d.74.1.1 39680 1n8vA 112 7.86e+00 a.118.21.1 85457 1tk1A 260 8.32e+00 d.248.1.1 107066 1mnzA 388 8.75e+00 c.1.15.3 79328 2awiA 317 9.00e+00 1bgc 174 9.16e+00 1bgc a.26.1.1 16822 1b5l 172 9.83e+00 1b5l a.26.1.3 16900 1ek8A 185 9.91e+00 1ek8A d.67.3.1 59444 1vlgA 176 1.00e+01 a.25.1.1 108816 1z5hA 780 1.03e+01 1eetA 557 1.04e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1o26A 232 1.10e+01 d.207.1.1 86566 1dttA 560 1.12e+01 1rthA c.55.3.1,e.8.1.2 33611,43088 1ciy 590 1.18e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1n1bA 549 1.19e+01 a.102.4.1,a.128.1.3 79799,79800 1hwxA 501 1.20e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1rktA 205 1.21e+01 a.4.1.9,a.121.1.1 97623,97624 1dat 174 1.23e+01 2fha a.25.1.1 16677 2dc5A 231 1.27e+01 2gyqA 175 1.32e+01 1pbgA 468 1.32e+01 1e70M c.1.8.4 28946 1lc5A 364 1.37e+01 c.67.1.1 73827 1gw9A 388 1.43e+01 c.1.15.3 70658 1gdeA 389 1.44e+01 c.67.1.1 60456 1pi1A 185 1.44e+01 a.29.7.1 94699 1rw6A 210 1.57e+01 a.47.4.1 105113 1w3iA 293 1.59e+01 c.1.10.1 109152 1rcd 173 1.59e+01 2fha a.25.1.1 16687 1h96A 182 1.61e+01 2fha a.25.1.1 60811 2g2dA 193 1.64e+01 1gd9A 389 1.68e+01 c.67.1.1 60454 2c3nA 247 1.68e+01 1d3yA 301 1.69e+01 1d3yA e.12.1.1 43252 1aew 174 1.69e+01 2fha a.25.1.1 16676 1lb3A 182 1.72e+01 a.25.1.1 77873 1nkpA 88 1.73e+01 a.38.1.1 80573 2hekA 371 1.74e+01 1lkcA 364 1.74e+01 c.67.1.1 73978 1yrlA 491 1.79e+01 1bia 321 1.82e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1qghA 156 1.86e+01 1qghA a.25.1.1 16728 1wwiA 148 1.88e+01 1jhfA 202 1.90e+01 a.4.5.2,b.87.1.1 63057,63058 1gwcA 230 1.91e+01 a.45.1.1,c.47.1.5 70660,70661 2fymA 431 1.91e+01 1bib 321 1.91e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1xis 387 1.92e+01 4xis c.1.15.3 29422 1z98A 281 1.94e+01 1jt6A 188 2.01e+01 a.4.1.9,a.121.1.1 67247,67248 1knqA 175 2.05e+01 c.37.1.17 72786 4xis 387 2.13e+01 4xis c.1.15.3 29421 1ta3A 274 2.21e+01 c.1.8.5 106731 1hniA 558 2.23e+01 1rthA c.55.3.1,e.8.1.2 33586,43044 1nu7D 282 2.27e+01 a.8.6.1,a.8.6.1 92191,92192 1fmk 452 2.28e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1h0cA 392 2.30e+01 c.67.1.3 83424 1ru3A 732 2.32e+01 e.26.1.3 97835 2hmiA 558 2.34e+01 1rthA c.55.3.1,e.8.1.2 33604,43106 1bqnA 558 2.35e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 1mhyB 395 2.40e+01 1mtyB a.25.1.2 16781 1hwyA 501 2.43e+01 1hwyA c.2.1.7,c.58.1.1 30262,33910 1w68A 390 2.43e+01 a.25.1.2 109216 2ceyA 306 2.44e+01 2a1dD 329 2.46e+01 1w6tA 444 2.52e+01 2ezi 75 2.52e+01 2ezh a.4.1.2 16028 1rkpA 326 2.53e+01 a.211.1.2 97620 2dc3A 193 2.56e+01 3erdA 261 2.60e+01 3erdA a.123.1.1 19293 1bo1A 416 2.64e+01 1bo1A d.143.1.2 41591 1lea 84 2.65e+01 1lea a.4.5.2 16085 1om0A 274 2.67e+01 c.1.8.5 87058 2b05A 246 2.69e+01 1midA 91 2.71e+01 a.52.1.1 91280 1urvA 190 2.73e+01 1ut0A 190 2.73e+01 a.1.1.2 108012 1hmvA 560 2.80e+01 1rthA c.55.3.1,e.8.1.2 33587,43046 1rzl 91 2.80e+01 1rzl a.52.1.1 17817 3xis 387 2.84e+01 4xis c.1.15.3 29423 7aatA 401 2.85e+01 1ajsA c.67.1.1 34250 1cnt3 187 2.88e+01 1cnt3 1gnxA 479 2.93e+01 c.1.8.4 76241 2fh1A 344 3.01e+01 2xis 387 3.02e+01 4xis c.1.15.3 29427 1y60A 169 3.08e+01 1sauA 115 3.12e+01 1mroA 548 3.14e+01 1mroA a.89.1.1,d.58.31.2 18525,39443 1dloA 556 3.14e+01 1rthA c.55.3.1,e.8.1.2 33584,43040 1za0A 275 3.15e+01 1ay0A 680 3.21e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31823,31824,33100 1c1bB 440 3.22e+01 1rthA e.8.1.2 43077 1o5kA 306 3.25e+01 c.1.10.1 92504 2ezh 75 3.29e+01 2ezh a.4.1.2 16029 1hbnA 549 3.31e+01 1mroA a.89.1.1,d.58.31.2 60898,60899 1dugA 234 3.32e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 2f1kA 279 3.34e+01 1sqgA 429 3.35e+01 a.79.1.3,c.66.1.38 105912,105913 1gpuA 680 3.36e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1akaA 401 3.37e+01 1ajsA c.67.1.1 34258 1nxcA 478 3.38e+01 a.102.2.1 92293 1hzfA 367 3.40e+01 a.102.4.4 76731 1l2iA 261 3.42e+01 a.123.1.1 73503 1hdmA 201 3.44e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 1p8xA 344 3.46e+01 d.109.1.1,d.109.1.1,d.109.1.1 94365,94366,94367 1hg2A 289 3.47e+01 1hg5A a.7.8.2,a.118.9.3 90358,90359 1hg5A 289 3.51e+01 1hg5A a.7.8.2,a.118.9.3 90360,90361 1ufyA 122 3.52e+01 d.79.1.2 88489 1n97A 389 3.53e+01 a.104.1.1 80335 1jm0A 50 3.57e+01 k.8.1.1 66870 1vlqA 337 3.58e+01 c.69.1.25 108848 1ug3A 339 3.58e+01 2ag4A 164 3.62e+01 1s3cA 141 3.64e+01 1qjaA 245 3.65e+01 1qjaA a.118.7.1 19204 1muwA 386 3.67e+01 c.1.15.3 79495 1on2A 142 3.71e+01 a.4.5.24,a.76.1.1 87103,87104 1jsmB 176 3.71e+01 h.3.1.1 63265 1iwgA 1053 3.72e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 76874,76875,76876,76877,76878,76879,76880,76881 1mzm 93 3.72e+01 1rzl a.52.1.1 17814 1kb5A 115 3.73e+01 1tvdA b.1.1.1 20611 1fk5A 93 3.83e+01 1rzl a.52.1.1 59866 2af6A 258 3.84e+01 1jqnA 883 3.88e+01 c.1.12.3 77159 1q6aA 107 3.90e+01 a.186.1.1 95966 2afaA 425 3.91e+01 1jigA 146 3.93e+01 a.25.1.1 71685 1tf5A 844 3.94e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1vf7A 369 3.96e+01 f.46.1.1 108557 1xmeA 568 3.97e+01 1ee4A 423 3.99e+01 1ee4A a.118.1.1 19128 1g13A 162 4.03e+01 1g13A b.95.1.1 60194 1kpsB 171 4.09e+01 a.118.12.1 68787 1pmnA 364 4.11e+01 d.144.1.7 94907 1dloB 427 4.17e+01 1rthA e.8.1.2 43041 1pu5A 164 4.17e+01 b.95.1.1 104310 1bax 94 4.17e+01 1bax a.61.1.3 18133 1odeA 122 4.20e+01 d.79.1.2 86846 1wa5B 530 4.24e+01 1e7uA 961 4.25e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1xm9A 457 4.26e+01 1j9bA 141 4.28e+01 c.47.1.12 66459 1iyxA 432 4.38e+01 c.1.11.1,d.54.1.1 83815,83816 1vi0A 206 4.42e+01 a.4.1.9,a.121.1.1 100720,100721 1klpA 115 4.42e+01 a.28.1.1 72721 2genA 197 4.47e+01 1hf8A 289 4.50e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1jtyA 194 4.51e+01 a.4.1.9,a.121.1.1 67292,67293 2comA 124 4.53e+01 1womA 271 4.54e+01 1ufzA 83 4.54e+01 a.5.9.1 107821 1jadA 251 4.61e+01 h.4.10.1 66461 1jgjA 217 4.66e+01 1c3wA f.13.1.1 62952 2fm9A 215 4.68e+01 1trkA 680 4.68e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1gkzA 388 4.76e+01 a.29.5.1,d.122.1.4 65268,65269 1e6qM 501 4.77e+01 1e70M c.1.8.4 28920 1e70M 501 4.78e+01 1e70M c.1.8.4 28926 1e4mM 501 4.78e+01 1e70M c.1.8.4 59226 1or0A 160 4.81e+01 d.153.1.2 93445 1mmoB 384 4.83e+01 1mtyB a.25.1.2 16768 1lylA 504 4.88e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1j77A 209 4.91e+01 1j77A a.132.1.2 62674 1fm2A 169 4.91e+01 1fm2A d.153.1.2 59877 1bqnB 430 4.93e+01 1rthA e.8.1.2 43065 1gkxA 388 4.98e+01 a.29.5.1,d.122.1.4 65266,65267 1k3kA 158 5.01e+01 f.1.4.1 72017 1wryA 121 5.02e+01 2ag9A 164 5.13e+01 1e9iA 431 5.14e+01 c.1.11.1,d.54.1.1 64818,64819 1p65A 73 5.15e+01 d.254.1.1 94156 1jusA 194 5.16e+01 a.4.1.9,a.121.1.1 67326,67327 1vcsA 102 5.17e+01 1h68A 239 5.18e+01 f.13.1.1 60664 1tzyA 129 5.19e+01 a.22.1.1 107530 1t5eA 360 5.20e+01 f.46.1.1 106436 1y2oA 250 5.21e+01 1h2sA 225 5.23e+01 f.13.1.1 76578 1y10A 407 5.25e+01 1d9cA 121 5.26e+01 1d9cA a.26.1.3 16901 1nkl 78 5.33e+01 1nkl a.64.1.1 18140 1yy7A 213 5.34e+01 1sceA 112 5.35e+01 1puc d.97.1.1 40676 1w53A 84 5.36e+01 a.186.1.2 109175 1pzlA 237 5.53e+01 a.123.1.1 104393 1lxnA 99 5.55e+01 d.58.48.1 84737 2cwkA 160 5.57e+01 1fx8A 281 5.57e+01 f.19.1.1 43651 1h0oA 390 5.63e+01 a.25.1.2 70845 2myr 501 5.64e+01 1uf2C 421 5.68e+01 a.115.1.3,b.19.1.1 99291,99292 2gsfA 373 5.74e+01 1ji8A 111 5.75e+01 d.203.1.1 66733 1uu1A 335 5.88e+01 c.67.1.1 99993 1cy5A 97 5.91e+01 1cy5A a.77.1.3 18430 1de6A 426 5.93e+01 1de5A c.1.15.2 29398 1xm3A 264 5.94e+01 1h7cA 108 5.97e+01 a.7.5.1 70914 1zb1A 392 5.99e+01 1de5A 426 6.02e+01 1de5A c.1.15.2 29402 1nekC 129 6.02e+01 f.21.2.2 80431 1xsm 390 6.04e+01 1xsm a.25.1.2 16804 2b3hA 329 6.08e+01 2ygsA 92 6.11e+01 1cy5A a.77.1.3 18431 1ehkC 33 6.13e+01 1ehkC f.23.9.1 43626 2cdqA 510 6.16e+01 1hrhA 136 6.21e+01 1rthA c.55.3.1 33577 1bk6A 422 6.21e+01 1bk5A a.118.1.1 19133 1tkaA 678 6.23e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31815,31816,33096 1qynA 153 6.28e+01 d.33.1.1 96597 1wmwA 330 6.32e+01 1zzgA 415 6.33e+01 2grrB 170 6.33e+01 1nf8A 207 6.35e+01 c.33.1.3 85630 1d8wA 426 6.36e+01 1de5A c.1.15.2 29394 1d8cA 723 6.42e+01 1d8cA c.1.13.1 29325 1bu5A 147 6.46e+01 5nul c.23.5.1 31155 1noyA 388 6.48e+01 1clqA c.55.3.5 33713 1abwA 283 6.50e+01 1abwA a.1.1.2,a.1.1.2 15288,15289 2f6hX 419 6.54e+01 1hq3A 129 6.60e+01 1aoiC a.22.1.1 16434 256bA 106 6.61e+01 256bA a.24.3.1 16539 1ljrA 244 6.61e+01 1ljrA a.45.1.1,c.47.1.5 17707,33001 1oaoC 729 6.68e+01 e.26.1.3 86746 1f3iA 481 6.74e+01 1b7eA 1aua 296 6.77e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1wleA 501 6.95e+01 1xmeC 34 6.98e+01 5eat 548 7.07e+01 5eat a.102.4.1,a.128.1.3 18853,19445 1mjgM 729 7.11e+01 e.26.1.3 79204 1e8yA 966 7.16e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1bk5A 422 7.20e+01 1bk5A a.118.1.1 19130 1akw 147 7.22e+01 5nul c.23.5.1 31153 1afh 93 7.23e+01 1rzl a.52.1.1 17816 1f4pA 147 7.25e+01 5nul c.23.5.1 59651 1e1oA 504 7.25e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1t7pA 698 7.28e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 2blcA 238 7.28e+01 1b3uA 588 7.33e+01 1b3uA a.118.1.2 19135 1cnt2 187 7.34e+01 1cnt3 1zq4A 693 7.35e+01 1iseA 185 7.37e+01 d.67.3.1 90691 2cvhA 220 7.38e+01 5eau 548 7.42e+01 5eat a.102.4.1,a.128.1.3 18851,19443 1nf9A 207 7.48e+01 c.33.1.3 85631 2a2mA 258 7.56e+01 1vjoA 393 7.56e+01 c.67.1.3 100827 3ygsP 97 7.59e+01 3ygsP a.77.1.3 18435 1sfjA 238 7.67e+01 1zemA 262 7.71e+01 1muhA 481 7.75e+01 c.55.3.4 79485 1iv3A 152 7.75e+01 d.79.5.1 76828 2cokA 113 7.82e+01 2cglA 489 7.85e+01 1jthA 82 7.86e+01 h.1.15.1 67270 1u4bA 580 7.91e+01 c.55.3.5,e.8.1.1 107664,107665 1rj1A 151 7.92e+01 a.29.6.1 97526 1t5oA 351 7.95e+01 c.124.1.5 106459 1u7kA 131 8.01e+01 1fp4A 492 8.01e+01 c.92.2.3 76187 1q32A 544 8.06e+01 d.136.1.3,d.136.1.3 104507,104508 1nfvA 179 8.09e+01 a.25.1.1 85642 1qoxN 449 8.10e+01 1qoxN c.1.8.4 28978 2g7lA 243 8.10e+01 2ccyA 128 8.14e+01 2ccyA a.24.3.2 16544 1zboA 210 8.16e+01 1i7dA 659 8.19e+01 1d6mA e.10.1.1 61886 1o9rA 162 8.28e+01 a.25.1.1 86706 1akt 147 8.32e+01 5nul c.23.5.1 31157 1konA 249 8.32e+01 e.39.1.1 72823 1w3jA 468 8.34e+01 c.1.8.4 109156 1d3uB 201 8.35e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1s9pA 227 8.41e+01 a.123.1.1 105384 1oe8A 211 8.42e+01 a.45.1.1,c.47.1.5 86905,86906 1sly 618 8.44e+01 1qsaA a.118.5.1,d.2.1.6 19184,36990 1io2A 213 8.47e+01 1ekeA c.55.3.1 62612 1kjs 74 8.51e+01 1kjs a.50.1.1 17792 1jc4A 148 8.51e+01 1jc4A d.32.1.4 62863 1gxmA 332 8.54e+01 a.102.5.1 76371 1qsdA 106 8.56e+01 1qsdA a.7.5.1 16335 1txnA 328 8.65e+01 1q0gA 117 8.68e+01 a.24.22.1 104428 1uz1A 468 8.79e+01 2fh5A 185 8.95e+01 2a2oA 258 8.98e+01