# List of top-scoring protein chains for t06-100-30-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.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 1tbxA 99 7.62e-02 a.4.5.48 106748 1bgp 309 7.76e-02 1bgp a.93.1.1 18690 1hl9A 449 8.54e-02 b.71.1.3,c.1.8.11 90650,90651 2asfA 137 1.12e-01 2co5A 99 2.08e-01 2fswA 107 2.17e-01 1mkmA 249 2.81e-01 a.4.5.33,d.110.2.2 79242,79243 1ub9A 100 4.06e-01 a.4.5.28 99159 1vljA 407 5.66e-01 e.22.1.2 108832 1wa3A 205 5.83e-01 2fpqA 444 6.26e-01 1wqaA 455 6.81e-01 1x1iA 752 6.85e-01 2trxA 108 7.75e-01 1thx c.47.1.1 32719 1rwhA 757 7.96e-01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 1y0kA 209 8.39e-01 1bouB 302 9.92e-01 1bouB c.56.6.1 33859 1jetA 517 1.07e+00 1jevA c.94.1.1 35718 1ur4A 399 1.11e+00 1rxwA 336 1.32e+00 a.60.7.1,c.120.1.2 98059,98060 1zhvA 134 1.34e+00 2a2cA 478 1.39e+00 2axpA 173 1.43e+00 1ryp1 222 1.66e+00 1ryp1 2a61A 145 1.68e+00 1zjjA 263 1.70e+00 2c1iA 431 1.80e+00 1y93A 159 1.85e+00 1o5zA 442 2.32e+00 c.59.1.2,c.72.2.2 92530,92531 1rqbA 539 2.36e+00 a.5.7.2,c.1.10.5 105057,105058 2ddrA 306 2.37e+00 2bw2A 140 2.59e+00 1rypA 243 2.71e+00 1pmaA d.153.1.4 41932 2b6nA 278 2.72e+00 2f2eA 146 2.79e+00 1zoiA 276 2.88e+00 3thiA 371 3.02e+00 2thiA c.94.1.1 35792 1flmA 122 3.13e+00 1axj b.45.1.1 25747 2b0cA 206 3.23e+00 1xsqA 168 3.31e+00 1j2gA 319 3.41e+00 d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4,d.96.1.4 103824,103825,103826,103827,103828 1qysA 106 3.46e+00 k.41.1.1 96603 1z7uA 112 3.68e+00 1eejA 216 3.75e+00 1eejA c.47.1.9,d.17.3.1 33057,38071 1x72A 334 3.83e+00 d.126.1.6 109495 1rz2A 254 4.02e+00 b.100.1.1 105130 1xrtA 467 4.06e+00 1v30A 124 4.10e+00 1ws0A 156 4.15e+00 2c71A 216 4.16e+00 1rypI 222 4.34e+00 d.153.1.4 41877 1hq0A 295 4.88e+00 1hzgA d.194.1.1 61122 1x9pA 523 4.97e+00 1tz9A 367 5.03e+00 c.1.15.6 107466 1h6pA 203 5.10e+00 a.146.1.1 60690 1rrmA 386 5.12e+00 e.22.1.2 105081 1j96A 323 5.13e+00 c.1.7.1 71616 1a8s 273 5.18e+00 1brt c.69.1.12 34710 8rucI 123 5.24e+00 1rboC d.73.1.1 39629 1l6rA 227 5.51e+00 c.108.1.10 77768 1rfeA 162 6.08e+00 1q87A 221 6.28e+00 e.47.1.1 96192 2fbiA 142 6.30e+00 2culA 232 6.48e+00 1gmyA 261 6.56e+00 d.3.1.1 76236 2ethA 154 6.67e+00 1wxxA 382 6.70e+00 1woyA 500 6.87e+00 2fbhA 146 7.10e+00 2aj6A 159 7.30e+00 1vbuA 328 7.45e+00 1i0dA 332 7.47e+00 1pscA c.1.9.3 61487 1d8wA 426 7.69e+00 1de5A c.1.15.2 29394 1w9zA 283 7.76e+00 2b8tA 223 7.83e+00 1uz5A 402 7.98e+00 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1p5vA 235 8.75e+00 b.1.11.1,b.7.2.1 87812,87813 1h1yA 228 8.83e+00 c.1.2.2 76506 1q5xA 161 8.95e+00 c.8.7.1 95947 2gqrA 237 8.96e+00 1cruA 454 9.29e+00 1c9uA b.68.2.1 27617 1seiA 130 9.36e+00 1seiA d.140.1.1 41463 1tueB 218 9.71e+00 b.91.1.1 107324 1tzvA 142 9.87e+00 a.79.1.1 107526 5eau 548 1.00e+01 5eat a.102.4.1,a.128.1.3 18851,19443 1v7bA 185 1.02e+01 2au3A 407 1.02e+01 1oe8A 211 1.02e+01 a.45.1.1,c.47.1.5 86905,86906 2as9A 210 1.04e+01 1ixkA 315 1.07e+01 c.66.1.38 90716 1n1jB 97 1.08e+01 a.22.1.3 79814 1dbxA 158 1.09e+01 1dbuA d.116.1.1 40928 2a97A 439 1.10e+01 1avyA 74 1.10e+01 1avyB h.1.17.1 45656 1zfjA 491 1.11e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1e87A 118 1.12e+01 1b6e d.169.1.1 42327 1zejA 293 1.13e+01 1hr6A 475 1.19e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1b35C 282 1.19e+01 1b35C 1p5dX 463 1.23e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1wwrA 171 1.25e+01 1yw5A 177 1.27e+01 1z1dA 103 1.28e+01 1w6kA 732 1.32e+01 1ee8A 266 1.33e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1a0p 290 1.37e+01 1a0p a.60.9.1,d.163.1.1 18105,42165 1sg4A 260 1.39e+01 1ifrA 121 1.41e+01 b.1.16.1 71203 1noyA 388 1.42e+01 1clqA c.55.3.5 33713 1cvrA 435 1.43e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 2cmuA 342 1.45e+01 1uesA 191 1.46e+01 a.2.11.1,d.44.1.1 107798,107799 2dkaA 544 1.49e+01 2fuqA 747 1.50e+01 1mlwA 301 1.51e+01 d.178.1.1 79289 1tfr 305 1.52e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1ok0A 74 1.53e+01 b.5.1.1 93191 1z2iA 358 1.53e+01 1w78A 422 1.54e+01 1xo0A 324 1.55e+01 1p4uA 153 1.63e+01 b.1.10.2 87780 2ghpA 292 1.66e+01 1ic6A 279 1.67e+01 1gci c.41.1.1 62257 1w2xA 758 1.69e+01 c.14.1.4,c.14.1.4 109134,109135 1efdN 266 1.71e+01 1efdN c.92.2.1 35597 1stzA 338 1.75e+01 a.4.5.51,d.110.2.3 106009,106010 1tvnA 293 1.78e+01 1d0cA 444 1.79e+01 d.174.1.1 64769 1zkkA 167 1.81e+01 2czdA 208 1.83e+01 1lt8A 406 1.83e+01 c.1.26.1 78186 1vcvA 226 1.83e+01 1n91A 108 1.89e+01 d.206.1.1 80326 1s95A 333 2.03e+01 d.159.1.3 105375 1hrnA 337 2.06e+01 1smrA b.50.1.2 26869 1d9uA 154 2.07e+01 1am7A d.2.1.4 59111 2gdqA 382 2.08e+01 2exrA 524 2.08e+01 1up8A 598 2.10e+01 a.111.1.2 99710 2b9hA 353 2.11e+01 2dfkA 402 2.14e+01 1xewY 172 2.15e+01 2b81A 323 2.16e+01 1v5iB 76 2.16e+01 2glfA 450 2.18e+01 2iu4A 336 2.18e+01 1z41A 338 2.18e+01 1vq2A 193 2.24e+01 1r85A 379 2.26e+01 c.1.8.3 104839 1gk8I 140 2.28e+01 d.73.1.1 65242 1xuuA 349 2.29e+01 1j8fA 323 2.32e+01 1j8fA c.31.1.5 62738 1i60A 278 2.34e+01 c.1.15.4 71118 1vlyA 338 2.43e+01 b.44.2.1,d.250.1.1 108871,108872 1widA 130 2.45e+01 1xhkA 187 2.51e+01 1fzqA 181 2.52e+01 1hurA c.37.1.8 32060 1h0hA 977 2.52e+01 b.52.2.2,c.81.1.1 76435,76436 1ro5A 201 2.53e+01 d.108.1.3 105023 2ae0X 345 2.53e+01 1wfwA 74 2.54e+01 2b3wA 168 2.63e+01 1rypD 241 2.66e+01 1rypD d.153.1.4 41935 1wlmA 151 2.69e+01 2dlbA 80 2.70e+01 1dv1A 449 2.71e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1uyrA 737 2.72e+01 c.14.1.4,c.14.1.4 100188,100189 2cq2A 114 2.77e+01 1yhtA 367 2.79e+01 2jdxA 385 2.79e+01 1jdw d.126.1.2 41139 1fecA 490 2.81e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1d5tA 433 2.81e+01 1gnd c.3.1.3,d.16.1.6 30422,37986 1gz2A 142 2.81e+01 d.169.1.1 83392 1cmcA 104 2.83e+01 1cmbA a.43.1.5 17462 2daxA 152 2.84e+01 2fymA 431 2.88e+01 1h99A 224 2.88e+01 a.142.1.1,a.142.1.1 60814,60815 1iq4A 179 2.94e+01 1iq4A d.77.1.1 62641 1fo8A 343 2.95e+01 1foaA c.68.1.10 59927 1wrrA 301 2.96e+01 1wcdJ 441 2.96e+01 1ctt 294 2.96e+01 1ctt c.97.1.1,c.97.1.1 36022,36023 1fmtA 314 3.06e+01 1fmtA b.46.1.1,c.65.1.1 25758,34174 1u6tA 121 3.08e+01 1cyo 93 3.10e+01 1cyo d.120.1.1 41065 1meoA 209 3.10e+01 c.65.1.1 79035 1xm3A 264 3.11e+01 1s1pA 331 3.14e+01 c.1.7.1 98350 1v1hA 103 3.24e+01 b.83.1.1,h.1.17.1 108243,108244 1s4nA 348 3.28e+01 c.68.1.16 98501 2bkkA 264 3.33e+01 1dpgA 485 3.36e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1ir21 140 3.39e+01 5nul 138 3.41e+01 5nul c.23.5.1 31191 1wdvA 152 3.44e+01 1iynA 295 3.44e+01 a.93.1.1 90722 1sr4A 206 3.45e+01 b.42.2.1 105948 1jw9B 249 3.51e+01 c.111.1.1 67377 1vlbA 907 3.52e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1zin 217 3.52e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1senA 164 3.56e+01 c.47.1.1 105465 1g8aA 227 3.56e+01 c.66.1.3 90506 1xd8A 289 3.57e+01 1bg4 302 3.59e+01 1taxA c.1.8.3 28806 1rypB 250 3.60e+01 1rypB d.153.1.4 41933 1zy9A 564 3.61e+01 1jatB 138 3.61e+01 1jatB d.20.1.1 62819 2g0uA 92 3.62e+01 1hw1A 239 3.62e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1umwA 237 3.63e+01 d.223.1.2,d.223.1.2 99631,99632 4ubpC 570 3.68e+01 1ubpC b.92.1.1,c.1.9.2 28431,29053 1rsgA 516 3.70e+01 1wdyA 285 3.73e+01 1m55A 197 3.74e+01 d.89.1.3 74469 1iscA 192 3.76e+01 1avmA a.2.11.1,d.44.1.1 15733,38726 1wraA 308 3.78e+01 1z6bA 154 3.81e+01 1rxdA 159 3.85e+01 1s2dA 167 3.85e+01 c.23.14.1 98377 1xeoA 168 3.87e+01 1j8mF 297 3.88e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1o97C 264 3.91e+01 c.26.2.3 81232 1gkpA 458 3.92e+01 b.92.1.3,c.1.9.6 70231,70232 2gaeA 346 3.93e+01 1ny1A 240 3.98e+01 c.6.2.3 86395 1xubA 298 3.98e+01 1ul7A 102 3.98e+01 d.129.6.1 99540 1g0cA 364 4.00e+01 7a3hA c.1.8.3 60165 1okiA 210 4.00e+01 b.11.1.1,b.11.1.1 93255,93256 1qhoA 686 4.00e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1z15A 344 4.01e+01 1rkbA 173 4.02e+01 1a41 234 4.03e+01 1a41 d.163.1.2 42174 2a4dA 160 4.08e+01 1y9aA 360 4.10e+01 2fu4A 83 4.13e+01 1v7cA 351 4.19e+01 c.79.1.1 100446 1zmoA 244 4.24e+01 2fsrA 195 4.26e+01 1wcgA 464 4.28e+01 1vlmA 219 4.28e+01 c.66.1.41 108836 2b2aA 199 4.30e+01 1hzdA 272 4.31e+01 c.14.1.3 65969 2e2aA 105 4.34e+01 a.7.2.1 88499 1me4A 215 4.34e+01 d.3.1.1 79023 1wkbA 810 4.35e+01 1rg9A 383 4.37e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1z0pA 84 4.39e+01 1j1tA 233 4.39e+01 b.29.1.18 90771 1a8y 367 4.39e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1y02A 120 4.41e+01 1lvwA 295 4.41e+01 c.68.1.6 84723 1jdw 423 4.42e+01 1jdw d.126.1.2 41129 1yarH 217 4.45e+01 1kid 203 4.49e+01 1derA c.8.5.1 30771 1gefA 123 4.50e+01 1gefA c.52.1.18 60465 1to2E 281 4.51e+01 1wwiA 148 4.51e+01 1gxrA 337 4.55e+01 b.69.4.1 70722 1o2dA 371 4.60e+01 e.22.1.2 86591 1io2A 213 4.61e+01 1ekeA c.55.3.1 62612 1nowA 507 4.64e+01 c.1.8.6,d.92.2.1 85936,85937 2cujA 108 4.67e+01 1h09A 338 4.77e+01 b.109.1.1,c.1.8.8 83420,83421 1vie 62 4.88e+01 1vie b.34.4.1 24592 2f9dP 43 4.89e+01 1un7A 400 4.92e+01 b.92.1.5,c.1.9.10 99657,99658 1gvnB 287 5.00e+01 c.37.1.21 76354 1xtmA 175 5.05e+01 1rypF 233 5.06e+01 1rypF d.153.1.4 41937 1j6qA 136 5.10e+01 b.40.9.1 77091 1sjiA 350 5.12e+01 1ockA 412 5.17e+01 c.117.1.1 86802 2aamA 309 5.28e+01 1r4xA 275 5.31e+01 b.1.10.3,d.105.1.2 97054,97055 2h3bA 494 5.33e+01 1x8bA 289 5.35e+01 1eyqA 222 5.36e+01 1eypA d.36.1.1 38534 1ve1A 304 5.37e+01 1d7uA 433 5.37e+01 2dkb c.67.1.4 34439 1z7xW 461 5.38e+01 1rloA 271 5.41e+01 1gbs 185 5.45e+01 153l d.2.1.5 36986 1yw0A 276 5.50e+01 1ro0A 216 5.51e+01 d.264.1.2 97664 1yn8A 59 5.55e+01 1j1nA 492 5.56e+01 c.94.1.1 83978 1wy5A 317 5.57e+01 1d02A 202 5.58e+01 1d02A c.52.1.8 33313 1nt2A 210 5.64e+01 c.66.1.3 86149 1y88A 199 5.66e+01 1xedA 117 5.68e+01 1je5A 206 5.71e+01 1je5A b.40.4.7 62909 1y7wA 291 5.71e+01 2g5dA 422 5.74e+01 1yx1A 264 5.76e+01 1jakA 512 5.80e+01 c.1.8.6,d.92.2.1 66472,66473 1aky 221 5.83e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1brwA 433 5.87e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1uj2A 252 5.89e+01 c.37.1.6 99452 1vhcA 224 5.90e+01 c.1.10.1 100661 1ci9A 392 5.97e+01 e.3.1.1 64767 1ou0A 207 5.99e+01 c.23.17.1 93536 1q8dA 108 6.00e+01 a.228.1.1 104554 2gokA 429 6.01e+01 1z5yE 149 6.02e+01 2c0rA 362 6.02e+01 1gai 472 6.10e+01 1ayx a.102.1.1 18819 1h4wA 224 6.10e+01 b.47.1.2 65622 1ydwA 362 6.12e+01 2anuA 255 6.14e+01 1xe7A 203 6.23e+01 1ro2A 216 6.27e+01 d.264.1.2 97665 1v3yA 192 6.29e+01 2anxA 146 6.30e+01 1b65A 375 6.32e+01 1b65A d.154.1.1 42020 1chmA 401 6.33e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 2fb5A 205 6.39e+01 2cbuA 468 6.39e+01 1tkeA 224 6.40e+01 1q59A 172 6.40e+01 f.1.4.1 95881 1uh4A 637 6.44e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1ois 223 6.46e+01 1a36A e.15.1.1 43267 1e7wA 291 6.51e+01 c.2.1.2 59373 1pfvA 551 6.54e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1frb 315 6.58e+01 1frb c.1.7.1 28665 2b9eA 303 6.59e+01 1rypK 198 6.60e+01 d.153.1.4 41879 1ynpA 317 6.60e+01 1yovA 537 6.61e+01 1ag9A 175 6.62e+01 1rcf c.23.5.1 31178 1w0hA 204 6.66e+01 1pu6A 218 6.66e+01 a.96.1.5 95123 1xgsA 295 6.66e+01 1bn5 a.4.5.25,d.127.1.1 16216,41153 2a4aA 281 6.76e+01 2a33A 215 6.77e+01 1x0vA 354 6.77e+01 1vhqA 232 6.84e+01 c.23.16.2 100696 1ss9A 311 6.85e+01 c.68.1.4 105978 1thtA 305 6.87e+01 1thtA c.69.1.13 34711 1vpqA 273 6.87e+01 1p3dA 475 6.89e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1a8q 274 6.95e+01 1brt c.69.1.12 34702 1u6pA 56 6.95e+01 2c8vA 288 6.96e+01 1s4iA 175 7.02e+01 2cxcA 144 7.06e+01 1gppA 237 7.08e+01 b.86.1.2 76262 1cq3A 233 7.10e+01 1cq3A b.27.1.1 23923 1fx2A 235 7.14e+01 1fx2A d.58.29.1 39430 1knwA 425 7.15e+01 b.49.2.3,c.1.6.1 90969,90970 1zirA 173 7.15e+01 1gkmA 509 7.18e+01 a.127.1.2 70228 1cr5A 189 7.23e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 1ltqA 301 7.26e+01 c.108.1.9,c.37.1.1 78208,78209 1x79B 112 7.27e+01 1c6vX 81 7.27e+01 1ihvA b.34.7.1 24641 1hl2A 297 7.28e+01 c.1.10.1 83581 1wzcA 249 7.44e+01 1hfc 169 7.45e+01 1hfc d.92.1.11 40335 2f4nA 273 7.45e+01 1jd1A 129 7.51e+01 1qu9A d.79.1.1 62890 1wdcB 156 7.57e+01 1wdcB a.39.1.5 17302 1ju2A 536 7.67e+01 c.3.1.2,d.16.1.1 77169,77170 1lvaA 258 7.74e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1ut1A 148 7.78e+01 b.2.3.6 108014 1mzgA 146 7.79e+01 d.224.1.1 79696 1vkhA 273 7.86e+01 c.69.1.32 108662 1m5wA 243 7.88e+01 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