# List of top-scoring protein chains for t2k-100-30-str2 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 1nox 205 2.47e-14 1nox d.90.1.1 40242 1bkjA 240 2.98e-11 1bkjA d.90.1.1 40243 1f5vA 240 7.13e-10 1bkjA d.90.1.1 40255 1icrA 217 2.12e-08 1vfrA d.90.1.1 62274 1necA 216 5.34e-08 1vfrA d.90.1.1 40249 1vfrA 218 1.30e-07 1vfrA d.90.1.1 40247 1jeoA 180 4.87e-02 c.80.1.3 66611 1gqeA 365 3.16e-01 e.38.1.1 70351 1dik 874 4.21e-01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1n81A 186 4.90e-01 a.185.1.1 85388 1vimA 200 6.93e-01 1nf2A 268 7.89e-01 1kblA 873 8.02e-01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1qklA 127 1.01e+00 1qklA d.78.1.2 39754 1cs0C 1073 1.06e+00 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1a9xA 1058 1.09e+00 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1keeA 1073 1.14e+00 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1f48A 589 1.20e+00 1f48A c.37.1.10 32280 c.37.1.10 32281 1c3oA 1073 1.22e+00 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1keeC 1073 1.32e+00 a.92.1.1 68500 c.24.1.1 68501 c.30.1.1 68502 c.30.1.1 68503 d.142.1.2 68504 d.142.1.2 68505 1jdbB 1073 1.37e+00 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1keeG 1073 1.39e+00 a.92.1.1 68516 c.24.1.1 68517 c.30.1.1 68518 c.30.1.1 68519 d.142.1.2 68520 d.142.1.2 68521 1r6uA 437 1.40e+00 1c3oC 1073 1.42e+00 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1bxrA 1073 1.43e+00 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1keeE 1073 1.44e+00 a.92.1.1 68508 c.24.1.1 68509 c.30.1.1 68510 c.30.1.1 68511 d.142.1.2 68512 d.142.1.2 68513 1c3oE 1073 1.45e+00 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1ihuA 589 1.45e+00 c.37.1.10 62394 c.37.1.10 62395 1c3oG 1073 1.87e+00 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1khvA 516 2.61e+00 e.8.1.4 68627 1vaoA 560 3.30e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 1qltA 560 3.43e+00 1qltA d.58.32.1 39457 d.145.1.1 41720 2ccyA 128 3.64e+00 2ccyA a.24.3.2 16544 1l5jA 865 3.74e+00 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1i12A 160 3.85e+00 1i21A d.108.1.1 61515 1e8gA 560 4.17e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1d8dB 437 4.17e+00 1ft1B a.102.4.3 18866 1jcrB 437 4.20e+00 a.102.4.3 66507 1ec7A 446 4.28e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1ld8B 437 4.31e+00 a.102.4.3 73839 4blmA 265 4.32e+00 1btl e.3.1.1 42721 1ft1B 437 4.46e+00 1ft1B a.102.4.3 18867 1jfiB 179 4.90e+00 1jfiB a.22.1.3 62937 8pchA 220 4.95e+00 1cs8A 1i1dA 161 4.98e+00 1i21A d.108.1.1 61526 1m3sA 186 5.09e+00 c.80.1.3 78573 1kkcA 221 5.44e+00 a.2.11.1 68660 d.44.1.1 68661 1ftrA 296 5.76e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1gajA 257 5.99e+00 1gajA c.37.1.12 60416 1eb7A 323 6.48e+00 1eb7A a.3.1.5 59404 a.3.1.5 59405 1m1nA 491 6.56e+00 c.92.2.3 78417 1h6gA 256 8.25e+00 1h6gA a.24.9.1 60669 a.24.9.1 60670 1envA 123 8.47e+00 1envA h.3.2.1 45726 1g6hA 257 8.49e+00 1gajA c.37.1.12 60318 1uetA 437 8.59e+00 1ab4 477 8.67e+00 1ab4 e.11.1.1 43251 1obbA 480 9.09e+00 c.2.1.5 86760 d.162.1.2 86761 1es2A 262 9.62e+00 1skf e.3.1.1 42680 1hr6A 475 9.63e+00 1hr6A d.185.1.1 61164 d.185.1.1 61165 1ei6A 406 9.88e+00 1ig8A 486 9.98e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1usgA 346 1.01e+01 2lbp 346 1.03e+01 2liv c.93.1.1 35709 1q0bA 367 1.09e+01 1rfmA 344 1.09e+01 1m2oA 768 1.12e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1i1qA 520 1.12e+01 1qdlA d.161.1.1 61543 1i4dA 224 1.21e+01 h.4.7.1 61682 1i21A 159 1.21e+01 1i21A d.108.1.1 61549 1sviA 195 1.23e+01 1r89A 437 1.24e+01 1fts 295 1.25e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1h6zA 913 1.29e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1o5zA 442 1.33e+01 1preB 470 1.36e+01 1preA d.169.1.2 42438 f.8.1.1 43825 1jdfA 447 1.38e+01 c.1.11.2 62897 d.54.1.1 62898 1i3dA 146 1.40e+01 a.1.1.2 61587 1ojaA 520 1.44e+01 1s3eA 520 1.46e+01 1i4lA 224 1.46e+01 1i49A h.4.7.1 61718 1es5A 262 1.49e+01 1skf e.3.1.1 42679 1sdsA 117 1.49e+01 1kkhA 317 1.51e+01 d.14.1.5 72645 d.58.26.3 72646 1rr9A 200 1.52e+01 1nvvS 481 1.52e+01 a.117.1.1 86279 1q7lA 198 1.55e+01 1qksA 567 1.58e+01 1qksA a.3.1.2 15951 b.70.2.1 27710 1d2mA 665 1.59e+01 1d2mA c.37.1.19 32417 c.37.1.19 32418 1f76A 336 1.64e+01 c.1.4.1 76160 1rreA 200 1.67e+01 1tafB 70 1.74e+01 1tafB a.22.1.3 16482 1es4A 262 1.81e+01 1skf e.3.1.1 42683 1iso 416 1.87e+01 1iso c.77.1.1 35065 1c4oA 664 1.95e+01 1d2mA c.37.1.19 32415 c.37.1.19 32416 1gmyA 261 1.98e+01 d.3.1.1 76236 1b8fA 509 1.98e+01 1b8fA a.127.1.2 19434 1gkmA 509 1.99e+01 a.127.1.2 70228 1aoqA 567 2.02e+01 1qksA a.3.1.2 15934 b.70.2.1 27692 2minA 491 2.04e+01 1qguA c.92.2.3 35609 1n1jA 93 2.05e+01 a.22.1.3 79813 1jnyA 435 2.08e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1d2iA 223 2.10e+01 1d2iA c.52.1.5 33297 1i4tB 224 2.10e+01 h.4.7.1 61730 1dfmA 223 2.10e+01 1d2iA c.52.1.5 33295 1r6fA 310 2.12e+01 1iv0A 98 2.12e+01 1i49A 224 2.13e+01 1i49A h.4.7.1 61679 1mzgA 146 2.19e+01 d.224.1.1 79696 1ii6A 368 2.25e+01 1bg2 c.37.1.9 62413 1jipA 403 2.26e+01 a.104.1.1 66748 1gefA 123 2.30e+01 1gefA c.52.1.18 60465 1ipiA 123 2.34e+01 c.52.1.18 66255 1px5A 349 2.35e+01 1bxdA 161 2.39e+01 1bxdA d.122.1.3 41111 1l2tA 235 2.40e+01 c.37.1.12 73514 1oshA 232 2.42e+01 3minC 491 2.43e+01 1qguA c.92.2.3 35607 1qazA 351 2.44e+01 1qazA a.102.3.1 18848 1p65A 73 2.45e+01 1thfD 253 2.50e+01 1thfD c.1.2.1 28535 1q7zA 566 2.52e+01 1qo3C 137 2.53e+01 1qo3C d.169.1.1 42350 1r30A 369 2.53e+01 1bjz 207 2.54e+01 2tct a.4.1.9 16065 a.121.1.1 19242 1ks8A 433 2.55e+01 a.102.1.2 77519 1pv6A 417 2.60e+01 1m5sA 297 2.67e+01 d.58.33.1 74511 d.58.33.1 74512 1asyA 490 2.68e+01 1b8aA b.40.4.1 25242 d.104.1.1 40763 1lucB 324 2.73e+01 1lucA c.1.16.1 29548 1deaA 266 2.73e+01 1deaA c.35.1.1 31760 3gcb 470 2.73e+01 3gcb d.3.1.1 37032 1ignA 246 2.76e+01 1ignA a.4.1.6 16048 a.4.1.6 16049 1amuA 563 2.78e+01 1amuA e.23.1.1 43351 1n46A 258 2.79e+01 a.123.1.1 85315 1nlnA 204 2.89e+01 1r5tA 142 2.89e+01 1preA 470 2.90e+01 1preA d.169.1.2 42437 f.8.1.1 43824 1oi0A 124 2.95e+01 1rfzA 168 2.95e+01 1i50F 155 2.95e+01 d.78.1.2 61760 1un8A 552 3.04e+01 1h4vB 421 3.10e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1szqA 483 3.10e+01 5fbpA 335 3.15e+01 1frpA e.7.1.1 42873 1n6jG 35 3.16e+01 1mxb 383 3.17e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1tpt 440 3.17e+01 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1skf 262 3.18e+01 1skf e.3.1.1 42684 1gqiA 708 3.20e+01 c.1.8.10 76279 d.92.2.2 76280 1ezvD 245 3.23e+01 1be3D a.3.1.3 59546 f.23.11.1 59547 1a79A 171 3.24e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1k4fA 248 3.26e+01 e.3.1.1 68138 1k55A 246 3.34e+01 e.3.1.1 68156 1nmtA 392 3.37e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1r31A 428 3.37e+01 1bqcA 302 3.39e+01 1bqcA c.1.8.3 28831 1kb9D 246 3.44e+01 a.3.1.3 77317 f.23.11.1 77318 1pv9A 348 3.45e+01 1l1jA 239 3.45e+01 b.47.1.1 84516 1kyoD 248 3.45e+01 a.3.1.3 73254 f.23.11.1 73255 1qaxA 428 3.47e+01 1qaxA d.58.20.1 39376 d.179.1.1 42597 1onrA 316 3.49e+01 1onrA c.1.10.1 29169 1gvnB 287 3.52e+01 c.37.1.21 76354 1uc7A 125 3.53e+01 1eupA 403 3.55e+01 1rom a.104.1.1 18967 1gcb 454 3.55e+01 3gcb d.3.1.1 37034 1esiA 262 3.55e+01 1skf e.3.1.1 42682 1jfgA 374 3.63e+01 a.128.1.5 66636 1j2aA 166 3.66e+01 1ew6A 137 3.66e+01 1ewaA a.1.1.2 15637 1ewaA 137 3.66e+01 1ewaA a.1.1.2 15639 1qm4A 396 3.67e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1jfaA 374 3.68e+01 a.128.1.5 66622 1brlB 324 3.72e+01 1lucA c.1.16.1 29554 1v7oA 165 3.73e+01 1a6r 471 3.73e+01 3gcb d.3.1.1 37033 1ew6B 137 3.77e+01 1ewaA a.1.1.2 15638 1avwB 171 3.77e+01 1wba b.42.4.1 25599 1s7jA 262 3.86e+01 1iakA 199 3.86e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 1bgc 174 3.87e+01 1bgc a.26.1.1 16822 1f6kA 293 3.87e+01 1nal3 c.1.10.1 29081 1hy0A 466 3.96e+01 1auwA a.127.1.1 61392 1kiyA 374 3.98e+01 a.128.1.5 72555