# List of top-scoring protein chains for t2k-100-30-alpha 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 4.81e-13 1nox d.90.1.1 40242 1bkjA 240 1.50e-10 1bkjA d.90.1.1 40243 1f5vA 240 9.01e-10 1bkjA d.90.1.1 40255 1icrA 217 6.59e-08 1vfrA d.90.1.1 62274 1necA 216 1.08e-07 1vfrA d.90.1.1 40249 1vfrA 218 4.76e-07 1vfrA d.90.1.1 40247 1jeoA 180 2.05e-02 c.80.1.3 66611 1khvA 516 1.61e-01 e.8.1.4 68627 1vimA 200 2.29e-01 1n81A 186 6.02e-01 a.185.1.1 85388 1kblA 873 6.32e-01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1nf2A 268 6.34e-01 1m3sA 186 6.35e-01 c.80.1.3 78573 1f48A 589 6.40e-01 1f48A c.37.1.10 32280 c.37.1.10 32281 1ihuA 589 7.72e-01 c.37.1.10 62394 c.37.1.10 62395 1a9xA 1058 1.06e+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 1dik 874 1.20e+00 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1d8dB 437 1.23e+00 1ft1B a.102.4.3 18866 1ld8B 437 1.28e+00 a.102.4.3 73839 1jcrB 437 1.32e+00 a.102.4.3 66507 1m1nA 491 1.33e+00 c.92.2.3 78417 1keeG 1073 1.42e+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 1ro2A 216 1.44e+00 1keeA 1073 1.68e+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 1ft1B 437 1.71e+00 1ft1B a.102.4.3 18867 1fts 295 1.73e+00 1ng1 a.24.13.1 16968 c.37.1.10 32279 1keeC 1073 1.81e+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 1c3oG 1073 1.84e+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 1c3oC 1073 1.86e+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 1.93e+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 1uw4B 248 1.94e+00 1keeE 1073 2.06e+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 2minA 491 2.11e+00 1qguA c.92.2.3 35609 3minC 491 2.13e+00 1qguA c.92.2.3 35607 1j6rA 214 2.15e+00 d.173.1.2 71598 1c3oE 1073 2.15e+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 1gqeA 365 2.33e+00 e.38.1.1 70351 1fp4A 492 2.35e+00 c.92.2.3 76187 1c3oA 1073 2.35e+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 1jdbB 1073 2.50e+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 1cs0C 1073 2.53e+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 1fsfA 266 2.60e+00 c.35.1.1 65047 1amuA 563 2.85e+00 1amuA e.23.1.1 43351 1t35A 191 2.92e+00 1eb7A 323 2.92e+00 1eb7A a.3.1.5 59404 a.3.1.5 59405 1ig8A 486 2.95e+00 2yhx c.55.1.3 64746 c.55.1.3 64747 1o5zA 442 3.12e+00 1fs5A 266 3.36e+00 c.35.1.1 65044 1r6uA 437 3.40e+00 1ro0A 216 3.59e+00 1rztA 331 3.67e+00 1uswA 260 3.69e+00 1sdsA 117 3.72e+00 1s3eA 520 3.77e+00 2lbp 346 3.93e+00 2liv c.93.1.1 35709 1m2oA 768 4.13e+00 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 1vaoA 560 4.28e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 1deaA 266 4.39e+00 1deaA c.35.1.1 31760 1b8fA 509 4.71e+00 1b8fA a.127.1.2 19434 1ghsA 306 4.74e+00 1aq0A c.1.8.3 28840 1psdA 409 4.92e+00 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1mx3A 347 4.97e+00 c.2.1.4 79638 c.23.12.1 79639 1gkmA 509 5.02e+00 a.127.1.2 70228 1d2iA 223 5.04e+00 1d2iA c.52.1.5 33297 1qh8A 478 5.25e+00 1qguA c.92.2.3 35633 1kbjA 412 5.26e+00 c.1.4.1 72280 1ojaA 520 5.28e+00 1oi0A 124 5.46e+00 1g61A 228 6.21e+00 1g61A d.126.1.1 41126 1l6rA 227 6.47e+00 c.108.1.10 77768 1ftrA 296 6.62e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1qguA 478 6.67e+00 1qguA c.92.2.3 35625 1qo7A 394 6.68e+00 1qo7A c.69.1.11 34697 1ei6A 406 6.86e+00 1e8gA 560 7.16e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1dfmA 223 7.43e+00 1d2iA c.52.1.5 33295 1qm4A 396 7.53e+00 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1i1dA 161 7.64e+00 1i21A d.108.1.1 61526 1i7xB 151 7.71e+00 1i7xB j.71.1.1 61914 1h1lA 481 7.72e+00 c.92.2.3 70851 1p65A 73 7.99e+00 1v4vA 376 8.07e+00 1gesA 450 8.36e+00 3grs c.3.1.5 30473 c.3.1.5 30474 d.87.1.1 40168 1qltA 560 8.49e+00 1qltA d.58.32.1 39457 d.145.1.1 41720 1i12A 160 8.50e+00 1i21A d.108.1.1 61515 1pixA 587 8.61e+00 1czaN 917 8.88e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1i21A 159 9.11e+00 1i21A d.108.1.1 61549 1jfiB 179 9.29e+00 1jfiB a.22.1.3 62937 1hkcA 917 9.38e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1oz9A 150 9.48e+00 1nvvS 481 9.68e+00 a.117.1.1 86279 1es4A 262 9.74e+00 1skf e.3.1.1 42683 1jkmA 358 9.89e+00 1jkmA c.69.1.2 34633 1ab4 477 9.97e+00 1ab4 e.11.1.1 43251 1jkmB 361 1.01e+01 1jkmA c.69.1.2 34634 1esiA 262 1.02e+01 1skf e.3.1.1 42682 1f76A 336 1.03e+01 c.1.4.1 76160 1jnyA 435 1.05e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1igs 248 1.05e+01 1a53 c.1.2.4 28565 1ltdA 506 1.06e+01 1gox c.1.4.1 28618 d.120.1.1 41086 1juk 248 1.07e+01 1a53 c.1.2.4 28567 1gqiA 708 1.08e+01 c.1.8.10 76279 d.92.2.2 76280 2ccyA 128 1.08e+01 2ccyA a.24.3.2 16544 1a53 247 1.10e+01 1a53 c.1.2.4 28564 1tafB 70 1.12e+01 1tafB a.22.1.3 16482 1dgkN 917 1.15e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1ec7A 446 1.17e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1qcwA 410 1.19e+01 1gox c.1.4.1 28622 1uwcA 261 1.24e+01 1iv0A 98 1.26e+01 1o0sA 605 1.27e+01 c.2.1.7 86540 c.58.1.3 86541 1g6hA 257 1.31e+01 1gajA c.37.1.12 60318 1rtxA 123 1.33e+01 1envA 123 1.38e+01 1envA h.3.2.1 45726 1hkbA 917 1.38e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1usgA 346 1.40e+01 1kl7A 514 1.40e+01 c.79.1.1 72678 1go3F 107 1.41e+01 a.60.8.2 65407 1gajA 257 1.44e+01 1gajA c.37.1.12 60416 2hgsA 474 1.45e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1q7lA 198 1.47e+01 1hr6A 475 1.51e+01 1hr6A d.185.1.1 61164 d.185.1.1 61165 2fokA 579 1.53e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1pah 308 1.55e+01 4pah d.178.1.1 42578 1skf 262 1.58e+01 1skf e.3.1.1 42684 8pchA 220 1.61e+01 1cs8A 1aihA 170 1.62e+01 1aihA d.163.1.1 42149 1r89A 437 1.64e+01 1wdcC 156 1.64e+01 1wdcC a.39.1.5 17317 1dmwA 307 1.67e+01 4pah d.178.1.1 42580 1qhaA 917 1.71e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 2minB 522 1.73e+01 1qguB c.92.2.3 35610 1pdz 434 1.78e+01 4enl c.1.11.1 29215 d.54.1.1 38859 1eps 427 1.81e+01 1eps d.68.2.2 39586 1pxwA 128 1.82e+01 1mjoA 104 1.84e+01 1cmbA a.43.1.2 17466 1h6zA 913 1.85e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1hfeL 421 1.86e+01 1fehA c.96.1.1 36018 d.58.1.5 39001 1mzgA 146 1.90e+01 d.224.1.1 79696 1un8A 552 1.90e+01 1i4tB 224 1.90e+01 h.4.7.1 61730 1gvnB 287 1.91e+01 c.37.1.21 76354 1uetA 437 1.92e+01 1q9uA 130 1.92e+01 1kqfB 294 1.96e+01 d.58.1.5 75900 f.23.22.1 75901 4pah 308 1.96e+01 4pah d.178.1.1 42576 1es2A 262 2.00e+01 1skf e.3.1.1 42680 1n1jA 93 2.03e+01 a.22.1.3 79813 4bcl 366 2.03e+01 4bcl b.75.1.1 27968 1preA 470 2.07e+01 1preA d.169.1.2 42437 f.8.1.1 43824 1rg9A 383 2.08e+01 1r9dA 787 2.11e+01 1rreA 200 2.12e+01 1scmB 145 2.12e+01 1wdcB a.39.1.5 17304 1es5A 262 2.14e+01 1skf e.3.1.1 42679 1hyuA 521 2.19e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1aocA 175 2.21e+01 1aocA g.17.1.5 44817 1bqcA 302 2.22e+01 1bqcA c.1.8.3 28831 1c9kB 180 2.22e+01 1c9kB c.37.1.11 32364 1mxa 383 2.25e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1h6gA 256 2.28e+01 1h6gA a.24.9.1 60669 a.24.9.1 60670 1nlnA 204 2.28e+01 1fcbA 511 2.28e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1igwA 434 2.32e+01 c.1.12.7 62370 1q7zA 566 2.33e+01 1m6sA 347 2.33e+01 c.67.1.1 78701 1jg8A 347 2.34e+01 1jg8A c.67.1.1 62946 1uanA 227 2.36e+01 1g6sA 427 2.37e+01 1eps d.68.2.2 39584 1n6jG 35 2.39e+01 1ks8A 433 2.41e+01 a.102.1.2 77519 1r6fA 310 2.43e+01 1j8uA 325 2.43e+01 d.178.1.1 71611 1q0bA 367 2.45e+01 1bzsA 165 2.47e+01 1hfc d.92.1.11 40348 1yagA 375 2.48e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 1gosA 520 2.51e+01 c.3.1.2 65425 d.16.1.5 65426 1jdfA 447 2.51e+01 c.1.11.2 62897 d.54.1.1 62898 1jplA 171 2.52e+01 a.118.9.2 67027 1hkhA 279 2.53e+01 1aj8A 371 2.58e+01 1aj8A a.103.1.1 18900 1geeA 261 2.60e+01 1p9bA 442 2.61e+01 1hdiA 413 2.64e+01 16pk c.86.1.1 60964 1k8uA 90 2.67e+01 a.39.1.2 72181 1sviA 195 2.68e+01 1rr9A 200 2.73e+01 1geqA 248 2.76e+01 2tysA c.1.2.4 28589 1nkiA 135 2.78e+01 1iso 416 2.78e+01 1iso c.77.1.1 35065 1cmbA 104 2.78e+01 1cmbA a.43.1.2 17460 5reqA 727 2.79e+01 1reqA c.1.19.1 29632 c.23.6.1 31259 1j6oA 268 2.79e+01 c.1.9.12 77088 1v7oA 165 2.80e+01 1i76A 163 2.81e+01 1hfc d.92.1.11 61877 1cdzA 96 2.81e+01 1cdzA c.15.1.1 30925 1bs0A 384 2.81e+01 1bs0A c.67.1.4 34490 1mxb 383 2.85e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1a79A 171 2.86e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1lqpA 135 2.87e+01 d.32.1.2 78151 1d3gA 367 2.88e+01 1d3gA c.1.4.1 28600 1i49A 224 2.88e+01 1i49A h.4.7.1 61679 1uc7A 125 2.90e+01 1rk6A 496 2.91e+01 1r5tA 142 2.94e+01 1r30A 369 2.97e+01 1gcoA 261 3.01e+01 1ybvA c.2.1.2 29884 1e7uA 961 3.01e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1p2fA 220 3.04e+01 a.4.6.1 87720 c.23.1.1 87721 1qo3C 137 3.09e+01 1qo3C d.169.1.1 42350 3minB 522 3.12e+01 1qguB c.92.2.3 35606 1m7jA 484 3.14e+01 b.92.1.6 78732 b.92.1.6 78733 c.1.9.11 78734 1ew6A 137 3.17e+01 1ewaA a.1.1.2 15637 1zpdA 568 3.19e+01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1h3oB 76 3.19e+01 a.22.1.3 76645 1a3k 137 3.22e+01 1a3k b.29.1.3 24218 1ewaA 137 3.24e+01 1ewaA a.1.1.2 15639 1ew6B 137 3.25e+01 1ewaA a.1.1.2 15638 1cmaA 104 3.25e+01 1cmbA a.43.1.2 17486 1qr0A 228 3.30e+01 1qr0A d.150.1.1 59038 d.150.1.1 59039 1oksA 56 3.31e+01 1a31A 538 3.39e+01 1a36A d.163.1.2 42170 e.15.1.1 43263 1l5jA 865 3.41e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1iqzA 81 3.44e+01 d.58.1.4 66281 4blmA 265 3.47e+01 1btl e.3.1.1 42721 1vh7A 265 3.47e+01 1b6a 478 3.49e+01 1bn5 a.4.5.25 16223 d.127.1.1 41160 7reqA 727 3.49e+01 1reqA c.1.19.1 29616 c.23.6.1 31243 1t5yA 190 3.51e+01 1qtfA 246 3.52e+01 1agjA b.47.1.1 25830 1i4lA 224 3.54e+01 1i49A h.4.7.1 61718 1cmcA 104 3.54e+01 1cmbA a.43.1.2 17462 1obbA 480 3.59e+01 c.2.1.5 86760 d.162.1.2 86761 1dar 691 3.66e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1pv9A 348 3.69e+01 1bgc 174 3.70e+01 1bgc a.26.1.1 16822 1rfzA 168 3.70e+01 1de6A 426 3.75e+01 1de5A c.1.15.2 29398 1qvaA 223 3.75e+01 1qvaA c.37.1.19 32411 1s9pA 227 3.79e+01 1vddA 228 3.79e+01 1ku2A 241 3.81e+01 a.4.13.1 83096 a.177.1.1 83097 1cb7B 483 3.82e+01 1cb7B c.1.19.2 29648 1reqA 727 3.83e+01 1reqA c.1.19.1 29620 c.23.6.1 31247 1i45A 248 3.86e+01 1amk c.1.1.1 61665 1o7bT 98 3.88e+01 1m1nB 522 3.89e+01 c.92.2.3 78418 1atiA 505 3.92e+01 1atiA c.51.1.1 33196 d.104.1.1 40745 1q7sA 117 3.94e+01 1q1aA 289 3.98e+01