# List of top-scoring protein chains for t04-100-30-dssp-ebghstl 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 1qwgA 251 2.03e-03 1r89A 437 7.05e-03 1j8mF 297 8.42e-03 1ng1 a.24.13.1 62742 c.37.1.10 62743 1j8yF 297 1.04e-02 1ng1 a.24.13.1 62747 c.37.1.10 62748 1m5wA 243 1.20e-02 c.1.24.1 84836 1pea 385 1.31e-02 1pea c.93.1.1 35662 1j96A 323 1.36e-02 c.1.7.1 71616 1fts 295 1.56e-02 1ng1 a.24.13.1 16968 c.37.1.10 32279 1s1pA 331 1.60e-02 1ads 315 1.70e-02 1frb c.1.7.1 28671 1k7jA 206 1.85e-02 d.115.1.1 72103 1oltA 457 1.95e-02 1ho1A 242 2.08e-02 1ho1A c.1.24.1 61097 1pwmA 316 2.20e-02 1k1xA 659 2.30e-02 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1n7kA 234 2.45e-02 c.1.10.1 85374 1us0A 316 2.54e-02 1frb 315 2.54e-02 1frb c.1.7.1 28665 1mi3A 322 3.03e-02 1cs1A 386 3.07e-02 1ibjA c.67.1.3 34399 1qw9A 502 3.28e-02 1uuqA 440 3.77e-02 1ii7A 333 3.81e-02 1ii7A d.159.1.4 62415 1ru8A 232 3.92e-02 1mkp 144 4.12e-02 1vhrA c.45.1.1 32654 1m3uA 264 4.62e-02 c.1.12.8 84784 1vi2A 300 4.62e-02 1rpxA 230 4.70e-02 1rpxA c.1.2.2 28536 1rj9A 304 5.19e-02 1jq5A 370 5.39e-02 e.22.1.2 67084 1o60A 292 6.34e-02 1o66A 275 7.23e-02 1pz1A 333 7.80e-02 1brt 277 8.02e-02 1brt c.69.1.12 34699 1vhnA 318 8.86e-02 5reqA 727 1.07e-01 1reqA c.1.19.1 29632 c.23.6.1 31259 1reqA 727 1.32e-01 1reqA c.1.19.1 29620 c.23.6.1 31247 3dni 260 1.39e-01 3dni d.151.1.1 41791 1ek6A 348 1.41e-01 1xel c.2.1.2 29800 1d3gA 367 1.56e-01 1d3gA c.1.4.1 28600 1gefA 123 1.72e-01 1gefA c.52.1.18 60465 1rvkA 382 1.72e-01 1vjzA 341 1.74e-01 1kl1A 419 1.74e-01 c.67.1.4 72663 1j31A 262 1.81e-01 1hh1A 143 1.82e-01 1gefA c.52.1.18 61036 2dnjA 260 1.85e-01 3dni d.151.1.1 41790 1hw6A 278 1.87e-01 1frb c.1.7.1 61296 1uumA 372 2.04e-01 1hkhA 279 2.06e-01 1broA 277 2.14e-01 1brt c.69.1.12 34700 1h1nA 305 2.32e-01 c.1.8.3 70855 1kepA 348 2.34e-01 c.2.1.2 68536 1zpdA 568 2.35e-01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1scfA 273 2.36e-01 1exzA a.26.1.2 16873 1q7zA 566 2.65e-01 1ogiA 303 2.67e-01 1o5kA 306 2.77e-01 1xel 338 2.90e-01 1xel c.2.1.2 29786 1go2A 304 3.04e-01 b.43.4.2 76243 c.25.1.1 76244 1thfD 253 3.08e-01 1thfD c.1.2.1 28535 1udc 338 3.10e-01 1xel c.2.1.2 29785 1oc2A 348 3.17e-01 1e0tA 470 3.20e-01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1r6xA 395 3.20e-01 1qvbA 481 3.22e-01 1qvbA c.1.8.4 28983 1a4iA 301 3.34e-01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1qtwA 285 3.38e-01 1qumA c.1.15.1 29392 1j08A 226 3.49e-01 c.47.1.2 83855 c.47.1.2 83856 1iyxA 432 3.65e-01 c.1.11.1 83815 d.54.1.1 83816 1ls1A 295 3.85e-01 a.24.13.1 78170 c.37.1.10 78171 1g94A 448 3.91e-01 b.71.1.1 65169 c.1.8.1 65170 1que 303 3.99e-01 1fnc b.43.4.2 25647 c.25.1.1 31537 1fcqA 350 4.00e-01 c.1.8.9 65006 1ad1A 266 4.10e-01 1aj2 c.1.21.1 29668 2ts1 419 4.11e-01 2ts1 c.26.1.1 31564 1ehyA 294 4.13e-01 1ehyA c.69.1.11 34693 1kkoA 413 4.32e-01 c.1.11.2 68675 d.54.1.1 68676 2dri 271 4.32e-01 2dri c.93.1.1 35637 1geqA 248 4.41e-01 2tysA c.1.2.4 28589 1v8gA 329 4.52e-01 1pymA 295 4.61e-01 1pymA c.1.12.7 29308 1dozA 309 4.70e-01 1ak1 c.92.1.1 35592 1jb9A 316 4.92e-01 1fnc b.43.4.2 62840 c.25.1.1 62841 1ixkA 315 5.04e-01 1rf6A 427 5.10e-01 2cb5A 453 5.11e-01 3gcb d.3.1.1 37035 1a53 247 5.33e-01 1a53 c.1.2.4 28564 1k8kA 418 5.35e-01 c.55.1.1 68305 c.55.1.1 68306 4pfk 319 5.35e-01 3pfk c.89.1.1 35582 1eyeA 280 5.44e-01 1aj2 c.1.21.1 29672 1edg 380 5.52e-01 1edg c.1.8.3 28807 1ug6A 431 5.59e-01 c.1.8.4 88490 1jvnA 555 5.59e-01 c.1.2.1 67355 c.23.16.1 67356 1lwjA 441 5.71e-01 b.71.1.1 74303 c.1.8.1 74304 1igs 248 5.72e-01 1a53 c.1.2.4 28565 1un8A 552 5.84e-01 1dusA 194 5.93e-01 1dusA c.66.1.4 34182 3tmkA 216 5.96e-01 3tmkA c.37.1.1 31920 1jl0A 334 5.98e-01 1jenA d.156.1.1 63155 1aqm 453 6.04e-01 1smd b.71.1.1 27717 c.1.8.1 28704 1o69A 394 6.45e-01 1ohlA 342 6.52e-01 c.1.10.3 87035 1ht6A 405 6.55e-01 b.71.1.1 83629 c.1.8.1 83630 1pswA 348 6.65e-01 c.87.1.7 88287 1b5tA 275 6.70e-01 1b5tA c.1.23.1 29676 1ceo 343 6.76e-01 1ceo c.1.8.3 28808 1pyfA 312 6.90e-01 1i9sA 210 6.94e-01 1i9sA c.45.1.1 62099 1gt91 357 6.96e-01 2ng1 293 7.35e-01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1bqcA 302 7.65e-01 1bqcA c.1.8.3 28831 1vizA 240 7.79e-01 1h7nA 342 7.82e-01 1b4kA c.1.10.3 60726 1s2wA 295 7.88e-01 1sviA 195 7.94e-01 1ua4A 455 8.26e-01 1kwgA 645 8.29e-01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1ewqA 765 8.47e-01 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1e4iA 447 8.49e-01 1e70M c.1.8.4 59225 1qgvA 142 8.73e-01 1qgvA c.47.1.8 33056 1m7jA 484 8.76e-01 b.92.1.6 78732 b.92.1.6 78733 c.1.9.11 78734 1rk6A 496 8.86e-01 1fnc 314 9.02e-01 1fnc b.43.4.2 25627 c.25.1.1 31517 1jz8A 1023 9.16e-01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1g0oA 283 9.24e-01 1ybvA c.2.1.2 60181 1h4pA 408 9.34e-01 1dp0A 1023 9.37e-01 b.1.4.1 22073 b.1.4.1 22074 b.18.1.5 23722 b.30.5.1 24346 c.1.8.3 28845 1a05A 358 9.40e-01 1cnzA c.77.1.1 35059 1a8s 273 9.62e-01 1brt c.69.1.12 34710 1jpmA 366 9.68e-01 c.1.11.2 67031 d.54.1.1 67032 1d8wA 426 9.75e-01 1de5A c.1.15.2 29394 1lnsA 763 9.82e-01 a.40.2.1 78101 b.18.1.13 78102 c.69.1.21 78103 1yasA 257 9.86e-01 1qj4A c.69.1.20 34801 1ewkA 490 1.04e+00 1ewkA c.93.1.1 35712 1in6A 334 1.08e+00 1hqcA a.4.5.11 62601 c.37.1.20 62602 1ad4A 266 1.08e+00 1aj2 c.1.21.1 29670 1hwxA 501 1.11e+00 1hwyA c.2.1.7 30250 c.58.1.1 33898 1h49A 512 1.11e+00 c.1.8.4 83477 1v02A 565 1.11e+00 1r6wA 322 1.12e+00 1qwkA 317 1.12e+00 1ohvA 472 1.14e+00 1c7sA 858 1.14e+00 1qba b.1.18.2 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1cv2A 296 1.20e+00 1bn6A c.69.1.8 34680 1o6dA 163 1.20e+00 1f5mA 180 1.20e+00 1f5mB d.110.2.1 40895 1c96A 753 1.22e+00 1amj c.8.2.1 30727 c.83.1.1 35403 1exbA 332 1.24e+00 1qrqA c.1.7.1 28666 1fnd 314 1.28e+00 1fnc b.43.4.2 25626 c.25.1.1 31516 1gadO 330 1.30e+00 1dssG c.2.1.3 29950 d.81.1.1 39865 1rlhA 173 1.36e+00 1g60A 260 1.40e+00 c.66.1.11 70151 1qo2A 241 1.41e+00 1qo2A c.1.2.1 28533 1e55A 512 1.43e+00 1e70M c.1.8.4 28934 1g8fA 511 1.43e+00 1g8fA b.122.1.3 60348 c.26.1.5 60349 c.37.1.15 60350 1gpmA 525 1.43e+00 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 1o7jA 327 1.47e+00 c.88.1.1 81140 1gs5A 258 1.47e+00 c.73.1.2 70395 1fkx 349 1.47e+00 1a4mA c.1.9.1 29018 8acn 754 1.49e+00 1amj c.8.2.1 30724 c.83.1.1 35400 1in4A 334 1.54e+00 1hqcA a.4.5.11 62597 c.37.1.20 62598 2pfkA 320 1.55e+00 3pfk c.89.1.1 35577 1b93A 152 1.55e+00 1b93A c.24.1.2 31507 2lbp 346 1.56e+00 2liv c.93.1.1 35709 1h61A 364 1.56e+00 1oyc c.1.4.1 60657 1gvoA 364 1.57e+00 c.1.4.1 76357 1qj4A 257 1.62e+00 1qj4A c.69.1.20 34796 1j24A 143 1.63e+00 c.52.1.20 84008 1eq2A 310 1.63e+00 1eq2A c.2.1.2 29814 1vypX 364 1.67e+00 1q0sA 259 1.72e+00 1c3pA 375 1.81e+00 1c3pA c.42.1.2 32606 1r3sA 367 1.84e+00 1adoA 363 1.85e+00 1fbaA c.1.10.1 29124 1uroA 367 1.85e+00 1uroA c.1.22.1 29675 1qnrA 344 1.95e+00 1qnoA c.1.8.3 28834 2liv 344 1.96e+00 2liv c.93.1.1 35708 1amy 403 1.97e+00 1jdc b.71.1.1 27799 c.1.8.1 28786 1ejxC 567 1.98e+00 b.92.1.1 83184 c.1.9.2 83185 1tml 286 1.99e+00 1tml c.6.1.1 30656 1o1yA 239 2.00e+00 c.23.16.1 86554 1icpA 376 2.04e+00 1oyc c.1.4.1 62270 1sjdA 368 2.04e+00 1p3jA 217 2.07e+00 1cr1A 296 2.09e+00 1cr1A c.37.1.11 32286 1fpzA 212 2.10e+00 1fpzA c.45.1.1 59976 1svy 114 2.12e+00 1svy d.109.1.1 40831 1j9yA 385 2.13e+00 1j9yA c.1.8.3 62791 1d4xA 375 2.19e+00 1yagA c.55.1.1 59107 c.55.1.1 59108 1lv7A 257 2.20e+00 c.37.1.20 78232 1p3wA 404 2.24e+00 c.67.1.3 87752 2tmdA 729 2.27e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1d2fA 390 2.28e+00 1d2fA c.67.1.3 34411 1f52A 468 2.31e+00 1lgr d.15.9.1 37839 d.128.1.1 41169 1mj5A 302 2.33e+00 1fsz 372 2.39e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1djnA 729 2.44e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1obfO 335 2.44e+00 c.2.1.3 86768 d.81.1.1 86769 1k6wA 426 2.46e+00 b.92.1.2 68236 c.1.9.5 68237 1cl1A 395 2.49e+00 1cl2A c.67.1.3 34395 1p0kA 349 2.52e+00 c.1.4.1 87648 1gqnA 252 2.53e+00 1pg4A 652 2.54e+00 e.23.1.1 88067 1avaA 403 2.58e+00 1jdc b.71.1.1 27797 c.1.8.1 28784 1odzA 386 2.59e+00 c.1.8.3 86889 1ihoA 283 2.59e+00 1ihoA c.26.1.4 62390 1ay7B 89 2.68e+00 1ay7B c.9.1.1 30836 1a8l 226 2.68e+00 1a8l c.47.1.2 32777 c.47.1.2 32778 1dbwA 126 2.72e+00 1dbwA c.23.1.1 31095 1ne9A 335 2.76e+00 1bn7A 294 2.77e+00 1bn6A c.69.1.8 34677 1qfeA 252 2.80e+00 1qfeA c.1.10.1 29167 1eg7A 557 2.80e+00 1eg7A c.37.1.10 32241 1f74A 293 2.82e+00 1nal3 c.1.10.1 29079 1q0rA 298 2.84e+00 1i60A 278 2.88e+00 c.1.15.4 71118 1aa6 715 2.90e+00 2napA b.52.2.2 26916 c.81.1.1 35324 1ursA 402 2.90e+00 1nar 290 3.02e+00 1nar c.1.8.5 28988 1edt 271 3.04e+00 2ebn c.1.8.5 28993 1g5aA 628 3.06e+00 b.71.1.1 65152 c.1.8.1 65153 1o98A 511 3.10e+00 c.105.1.1 86684 c.76.1.3 86685 1h0hA 977 3.12e+00 b.52.2.2 76435 c.81.1.1 76436 1pvyA 227 3.13e+00 1gc0A 398 3.15e+00 c.67.1.3 70168 1a4mA 349 3.24e+00 1a4mA c.1.9.1 29014 1hnuA 280 3.25e+00 1hnoA c.14.1.3 61096 1vhcA 224 3.26e+00 1gcoA 261 3.28e+00 1ybvA c.2.1.2 29884 1geeA 261 3.28e+00 1v7zA 260 3.30e+00 1fhuA 320 3.35e+00 1fhuA c.1.11.2 29234 d.54.1.1 38878 1cg2A 393 3.36e+00 1cg2A c.56.5.4 33844 d.58.19.1 39360 1dgaA 375 3.46e+00 1yagA 1aj2 282 3.50e+00 1aj2 c.1.21.1 29665 1iupA 282 3.51e+00 c.69.1.10 76815 1gqiA 708 3.52e+00 c.1.8.10 76279 d.92.2.2 76280 1uwsA 489 3.52e+00 1zin 217 3.53e+00 1zin c.37.1.1 31915 g.41.2.1 45178 1dhpA 292 3.55e+00 1dhpA c.1.10.1 29097 1n2eA 300 3.58e+00 c.26.1.4 85268 1bfd 528 3.60e+00 1bfd c.31.1.3 31745 c.36.1.5 31801 c.36.1.9 31802 1g3qA 237 3.66e+00 1hyqA c.37.1.10 60237 1zfjA 491 3.69e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1ro7A 259 3.74e+00 1l5oA 356 3.76e+00 c.39.1.1 77711 1eqcA 394 3.77e+00 1cz1A c.1.8.3 28811 1a6q 382 3.77e+00 1a6q a.159.1.1 75801 d.219.1.1 75802 1brwA 433 3.80e+00 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 3csuA 310 3.87e+00 3csuA c.78.1.1 35094 c.78.1.1 35095 1o4sA 389 3.89e+00 c.67.1.1 86620 1e9lA 377 3.91e+00 1e9lA c.1.8.5 59395 d.26.3.1 59396 1qcwA 410 3.92e+00 1gox c.1.4.1 28622 1ep3A 311 3.93e+00 2dorA c.1.4.1 28597 1mdbA 539 4.01e+00 e.23.1.1 79008 1kbjA 412 4.04e+00 c.1.4.1 72280 1j7xA 302 4.08e+00 c.14.1.2 66425 1nal1 297 4.14e+00 1nal3 1o0sA 605 4.15e+00 c.2.1.7 86540 c.58.1.3 86541 1gvfA 286 4.20e+00 c.1.10.2 70599 1gd1O 334 4.22e+00 1dssG c.2.1.3 29962 d.81.1.1 39877 1a76 326 4.24e+00 1a76 a.60.7.1 18091 c.120.1.2 33361 1kgdA 180 4.29e+00 c.37.1.1 68582 1a7tA 232 4.36e+00 1a7tA d.157.1.1 42041 1j0hA 588 4.37e+00 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1vc4A 254 4.37e+00 2mnr 357 4.38e+00 2mnr c.1.11.2 29245 d.54.1.1 38889 1g38A 393 4.40e+00 2admA c.66.1.27 60235 1mtzA 293 4.43e+00 c.69.1.7 79467 1vhxA 150 4.50e+00 1oatA 439 4.55e+00 2dkb c.67.1.4 34461 1epxA 370 4.56e+00 1fbaA c.1.10.1 29150 1v2xA 194 4.61e+00 1fnnA 389 4.62e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 2arcA 164 4.63e+00 2arcA b.82.4.1 28148 1p9qC 256 4.64e+00 1gdeA 389 4.67e+00 c.67.1.1 60456 1vjgA 218 4.69e+00 1jj2M 186 4.73e+00 1ffkK c.55.4.1 63098 1go4A 205 4.74e+00 d.135.1.1 70292 1ek1A 554 4.78e+00 1cr6B c.108.1.2 43335 c.69.1.11 34685 1ub3A 220 4.84e+00 c.1.10.1 88395 1f1zA 273 4.85e+00 1f1zA a.4.5.27 16081 c.52.1.16 33334 1j6zA 376 4.89e+00 1yagA c.55.1.1 62667 c.55.1.1 62668 1kq3A 376 4.95e+00 e.22.1.2 68790 1pqnA 127 5.00e+00 1ofuA 320 5.04e+00 c.32.1.1 86972 d.79.2.1 86973 1i3zA 103 5.04e+00 d.93.1.1 83667 1jenA 267 5.08e+00 1jenA 1mumA 295 5.13e+00 c.1.12.7 85108 1p4cA 380 5.15e+00 1o94A 729 5.16e+00 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1b8oA 284 5.17e+00 1b8oA c.56.2.1 33762 1i74A 309 5.24e+00 1i74A c.107.1.1 61867 1hrkA 359 5.26e+00 1hrkA c.92.1.1 61228 1usgA 346 5.26e+00 1ro0A 216 5.28e+00 1ozhA 566 5.29e+00 1v6fA 151 5.29e+00 1htqA 477 5.30e+00 d.15.9.1 71035 d.128.1.1 71036 2btfA 375 5.32e+00 1yagA c.55.1.1 33429 c.55.1.1 33430 1g0cA 364 5.35e+00 7a3hA c.1.8.3 60165 1d1gA 168 5.40e+00 1d1gA c.71.1.1 34889 1v7rA 186 5.41e+00 1l6rA 227 5.43e+00 c.108.1.10 77768 1jk7A 323 5.55e+00 1auiA d.159.1.3 63144 1a8q 274 5.63e+00 1brt c.69.1.12 34702 1gjwA 637 5.66e+00 b.71.1.1 60582 c.1.8.1 60583 1ukmB 128 5.68e+00 1e8yA 966 5.75e+00 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 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1din 236 3.94e+01 1din c.69.1.9 34682 1rcuA 195 3.97e+01 1iirA 415 3.98e+01 1iirA c.87.1.5 62453 1nrvA 105 3.98e+01 d.93.1.1 86126 1uteA 313 3.99e+01 1uteA d.159.1.1 42078 2nacA 393 4.00e+01 2nadA c.2.1.4 30088 c.23.12.1 31348