# List of top-scoring protein chains for t2k.100-30-stride-ebghtl 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.soe.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 3h41A 311 2.20e-32 2hbwA 235 6.70e-22 2evrA 246 7.73e-21 b.34.11.3 132440 d.3.1.16 132441 3gt2A 142 4.16e-11 3m1uA 434 2.89e-08 2krsA 74 6.58e-05 1xovA 326 1.39e-04 b.34.11.4 122206 c.56.5.6 122207 2kt8A 76 1.99e-04 1wlpB 138 1.32e-03 b.34.2.1 121010 b.34.2.1 144558 1ng2A 193 1.85e-03 b.34.2.1 85660 b.34.2.1 85661 1ov3A 138 2.12e-03 b.34.2.1 87451 b.34.2.1 87452 1lckA 175 2.46e-02 1lckA b.34.2.1 24552 d.93.1.1 40421 1a0nB 69 2.34e-01 1bbzA b.34.2.1 24469 3cqtA 79 2.47e-01 1azgB 67 2.93e-01 1bbzA b.34.2.1 24471 1efnA 59 3.48e-01 1bbzA b.34.2.1 24465 1bu1A 57 3.80e-01 1bbzA b.34.2.1 24499 1bbzA 58 4.15e-01 1bbzA b.34.2.1 24477 1aboA 62 4.49e-01 1bbzA b.34.2.1 24474 1l0wA 580 5.14e-01 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1vheA 373 5.55e-01 b.49.3.1 100669 c.56.5.4 100670 3eg3A 63 5.68e-01 2iimA 62 6.12e-01 b.34.2.1 137434 2o88A 58 6.30e-01 1zx6A 58 6.51e-01 3lovA 475 6.84e-01 1shfA 59 8.19e-01 1bbzA b.34.2.1 24462 3f7fA 729 8.72e-01 1avzC 57 9.22e-01 1bbzA b.34.2.1 24467 1hd3A 62 9.73e-01 b.34.2.1 65802 1c0aA 585 1.10e+00 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1tuc 63 1.17e+00 1tuc 2vgeA 229 1.18e+00 2vknA 70 1.24e+00 1ruwA 69 1.31e+00 2i5tA 188 1.35e+00 1qhtA 775 1.40e+00 1tgoA c.55.3.5 33722 e.8.1.1 43011 1g8xA 1010 1.40e+00 1lvk k.1.1.1 46378 1fmk 452 1.46e+00 1fmk 3hxrA 761 1.48e+00 2p1gA 249 1.51e+00 3m4pA 456 1.58e+00 1d0yA 761 1.59e+00 1lvk b.34.3.1 24581 c.37.1.9 32178 1k0iA 394 1.63e+00 c.3.1.2 67942 d.16.1.2 67943 3cryA 188 1.65e+00 2g6fX 59 1.85e+00 2akaA 776 1.86e+00 1z9zA 60 1.88e+00 2v1qA 60 1.88e+00 3h7nA 729 1.90e+00 1u06A 62 1.98e+00 b.34.2.1 119404 1zuyA 58 2.01e+00 1k32A 1045 2.04e+00 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 2vwkA 773 2.04e+00 c.55.3.5 153677 e.8.1.1 153678 1gcqA 61 2.47e+00 1ckaA b.34.2.1 60434 1p9bA 442 2.64e+00 c.37.1.10 94385 1mvwA 840 2.66e+00 i.15.1.1 79523 1tgoA 773 2.66e+00 1tgoA c.55.3.5 33721 e.8.1.1 43010 1lvk 762 2.71e+00 1lvk 3js6A 355 2.81e+00 2ak5A 64 2.85e+00 3i6dA 470 2.86e+00 1sy7A 715 2.94e+00 c.23.16.3 112161 3f2bA 1041 3.08e+00 1qqcA 773 3.15e+00 1tgoA c.55.3.5 33724 e.8.1.1 43013 2va8A 715 3.17e+00 1b8aA 438 3.23e+00 1b8aA b.40.4.1 25244 d.104.1.1 40765 2vvkA 56 3.35e+00 1n6eA 1071 3.38e+00 b.36.1.3 80149 b.68.7.1 80150 b.69.9.1 80151 c.14.1.2 80152 1ykjA 394 3.38e+00 c.3.1.2 145914 d.16.1.2 145915 2a08A 60 3.66e+00 2vugA 389 3.67e+00 2qa1A 500 3.94e+00 2hdaA 64 4.09e+00 3i35A 60 4.15e+00 2vwfA 58 4.42e+00 1p1jA 533 4.45e+00 c.2.1.3 87687 d.81.1.3 87688 3gpuA 256 4.47e+00 1utiA 58 4.67e+00 b.34.2.1 99962 2oajA 902 4.82e+00 1jxmA 301 4.87e+00 b.34.2.1 67420 c.37.1.1 67421 1hh2P 344 5.11e+00 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1cwvA 492 5.17e+00 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1o54A 277 5.20e+00 c.66.1.13 92482 1r2zA 274 5.38e+00 a.156.1.2 96892 b.113.1.1 96893 g.39.1.8 96894 2v1rA 80 5.45e+00 b.34.2.1 152411 1g2bA 62 5.54e+00 1tud b.34.2.1 24488 2j05A 65 5.68e+00 3i99A 357 5.71e+00 1l1zA 274 5.74e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1oebA 62 5.75e+00 b.34.2.1 86909 1vj1A 363 5.85e+00 b.35.1.2 100794 c.2.1.1 100795 2if6A 186 5.85e+00 d.3.1.21 147651 1cj3A 392 5.97e+00 1pbe c.3.1.2 30347 d.16.1.2 37878 1pbe 394 6.00e+00 1pbe 1pbeA 394 6.00e+00 c.3.1.2 30338 d.16.1.2 37869 1q46A 175 6.22e+00 a.60.14.1 111594 b.40.4.5 111595 1pj5A 830 6.28e+00 b.44.2.1 94742 c.3.1.2 94743 d.16.1.5 94744 d.250.1.1 94745 2bz8A 58 6.29e+00 2zb4A 357 6.33e+00 3iqlA 71 6.33e+00 1zlmA 58 6.34e+00 3fg1A 696 6.35e+00 1zq1C 633 6.38e+00 a.182.1.2 125493 d.74.4.1 125494 d.128.1.5 125495 1ootA 60 6.44e+00 b.34.2.1 93386 2x3wD 60 6.46e+00 1i84S 1184 6.59e+00 1lvk i.15.1.1 61940 3fj5A 57 6.63e+00 3lgfA 125 6.72e+00 3fg4A 696 6.91e+00 3gsiA 827 6.94e+00 1j0hA 588 6.96e+00 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1yvvA 336 6.98e+00 2g3rA 123 7.20e+00 b.34.9.1 134570 b.34.9.1 134571 3fg3A 696 7.66e+00 2a2cA 478 7.87e+00 3c0cA 73 8.04e+00 1jo8A 58 8.17e+00 b.34.2.1 71774 2wm1A 336 8.39e+00 1wyxA 69 8.67e+00 2drmA 58 8.73e+00 3kkjA 336 8.79e+00 3e1tA 512 8.88e+00 2de6A 392 8.88e+00 b.33.1.2 131415 d.129.3.3 131416 2gf3A 389 8.93e+00 c.3.1.2 135070 d.16.1.3 135071 2ahoB 266 9.16e+00 a.60.14.1 126770 b.40.4.5 126771 d.58.51.1 126772 1el5A 389 9.27e+00 1b3mA c.3.1.2 30369 d.16.1.3 37937 1gppA 237 9.38e+00 b.86.1.2 76262 2prdA 174 9.46e+00 b.40.5.1 25435 1ahpA 797 9.56e+00 1a8i c.87.1.4 35544 2weuA 511 9.61e+00 1dfaA 454 9.64e+00 1vdeA b.86.1.2 28375 d.95.2.2 40575 d.95.2.2 40576 2qtzA 539 1.01e+01 1w70A 60 1.02e+01 2gncA 60 1.03e+01 3ebhA 889 1.06e+01 1loxA 662 1.09e+01 a.119.1.2 19238 b.12.1.1 23638 1v7wA 807 1.09e+01 a.102.1.4 108411 b.30.5.3 108412 2j3hA 345 1.09e+01 2psdA 318 1.11e+01 2wesA 511 1.16e+01 2hldD 478 1.19e+01 1lox 662 1.21e+01 1lox 3c7aA 404 1.22e+01 1azeA 56 1.23e+01 b.34.2.1 24536 3m0oA 389 1.25e+01 2dejA 350 1.26e+01 1xniA 118 1.27e+01 b.34.9.1 115582 b.34.9.1 115583 2ph0A 174 1.29e+01 1eovA 487 1.29e+01 1b8aA b.40.4.1 25239 d.104.1.1 40760 3fvqA 359 1.29e+01 1twlA 186 1.29e+01 b.40.5.1 112764 1tdzA 272 1.31e+01 a.156.1.2 106787 b.113.1.1 106788 g.39.1.8 106789 1x2kA 68 1.34e+01 1l5wA 796 1.34e+01 c.87.1.4 73605 1a6q 382 1.36e+01 1a6q 1a6qA 382 1.36e+01 a.159.1.1 75801 d.219.1.1 75802 1ltdA 506 1.36e+01 1gox c.1.4.1 28618 d.120.1.1 41086 1ee8A 266 1.38e+01 1ee8A a.156.1.2 75823 b.113.1.1 75824 g.39.1.8 75825 2d1xA 66 1.39e+01 2vu9A 444 1.39e+01 3ehrA 222 1.42e+01 2cz9A 350 1.44e+01 2zadA 345 1.44e+01 1semA 58 1.44e+01 1ckaA b.34.2.1 24544 1p80A 753 1.46e+01 c.23.16.3 94337 e.5.1.1 94338 2p0mA 662 1.46e+01 a.119.1.2 149136 b.12.1.1 149137 2p4vA 158 1.49e+01 1u3oA 82 1.49e+01 3h0lB 478 1.50e+01 2g47A 990 1.51e+01 2fsjA 346 1.51e+01 c.55.1.12 134025 c.55.1.12 134026 2axtO 247 1.56e+01 f.4.1.4 144938 1u5fA 148 1.60e+01 b.55.1.1 119542 1m2xA 223 1.61e+01 d.157.1.1 84764 2b7kA 200 1.65e+01 c.47.1.10 128042 3e4aA 1019 1.65e+01 1pjjA 271 1.66e+01 a.156.1.2 104164 b.113.1.1 104165 g.39.1.8 104166 1lnzA 342 1.66e+01 b.117.1.1 78112 c.37.1.8 78113 1wdaA 670 1.67e+01 b.2.9.1 109243 b.6.1.6 109244 d.126.1.5 109245 1h72C 296 1.68e+01 d.14.1.5 60712 d.58.26.1 60713 2qjtA 352 1.70e+01 3e9hA 493 1.71e+01 2exdA 80 1.71e+01 b.40.12.1 132524 3hwpA 302 1.76e+01 1fwkA 296 1.77e+01 1fwkA d.14.1.5 37576 d.58.26.1 39398 1lm8V 160 1.79e+01 b.3.3.1 74035 1lybB 241 1.79e+01 1smrA 1kkhA 317 1.80e+01 d.14.1.5 72645 d.58.26.3 72646 2fvgA 340 1.80e+01 b.49.3.1 134201 c.56.5.4 134202 1w9iA 770 1.80e+01 2wjsA 608 1.81e+01 2i10A 202 1.82e+01 a.4.1.9 136960 a.121.1.1 136961 1lqbC 162 1.83e+01 b.3.3.1 74186 2j82A 240 1.84e+01 3fgbA 361 1.90e+01 1k5dB 201 1.93e+01 b.55.1.3 68169 1cyx 205 1.94e+01 1cyx 1cyxA 205 1.94e+01 b.6.1.2 23023 1ko3A 230 1.97e+01 d.157.1.1 90974 2jdiA 510 1.97e+01 a.69.1.1 145683 b.49.1.1 145684 c.37.1.11 145685 1vhoA 346 1.98e+01 b.49.3.1 100694 c.56.5.4 100695 1l9cA 389 2.00e+01 c.3.1.2 77815 d.16.1.3 77816 3fwyA 314 2.02e+01 1b5qA 472 2.03e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1cf9A 753 2.04e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1abbA 828 2.05e+01 1a8i c.87.1.4 35536 2pm7A 399 2.06e+01 1ao5A 237 2.07e+01 5ptp b.47.1.2 26334 1ecfB 504 2.09e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1q8kA 308 2.11e+01 a.60.14.1 111596 b.40.4.5 111597 d.58.51.1 104557 3dqyA 106 2.11e+01 3fidA 296 2.13e+01 2bqxA 173 2.13e+01 1ycsB 239 2.15e+01 1ycsB b.34.2.1 24553 d.211.1.1 19155 1w9aA 147 2.15e+01 b.45.1.1 114408 2qddA 378 2.17e+01 1b37B 472 2.18e+01 1b37B c.3.1.2 30390 d.16.1.5 37954 1vcbC 160 2.18e+01 1vcbC b.3.3.1 22535 3go5A 285 2.19e+01 1xfoA 357 2.19e+01 b.49.3.1 115265 c.56.5.4 115266 2zxiA 637 2.20e+01 1aszB 490 2.21e+01 1b8aA b.40.4.1 25241 d.104.1.1 40762 1j1tA 233 2.21e+01 b.29.1.18 90771 2w5aA 279 2.21e+01 2whxA 618 2.24e+01 1s5jA 847 2.25e+01 c.55.3.5 112040 e.8.1.1 112041 1h8eA 510 2.27e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 2vnlA 151 2.29e+01 1ecfA 504 2.30e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 2vvmA 495 2.35e+01 3l56A 222 2.39e+01 2gj4A 824 2.40e+01 c.87.1.4 135256 2p4zA 284 2.41e+01 3ei3A 1158 2.46e+01 1noyA 388 2.46e+01 1clqA c.55.3.5 33713 2bg9E 370 2.46e+01 3i79A 484 2.46e+01 1skyE 473 2.47e+01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 2wbyA 990 2.48e+01 2q4vA 170 2.49e+01 d.108.1.1 139878 2dpyA 438 2.50e+01 2oc3A 303 2.52e+01 1sgwA 214 2.54e+01 c.37.1.12 105541 3lm2A 226 2.54e+01 2dexX 671 2.56e+01 b.2.9.1 131436 b.6.1.6 131437 d.126.1.5 131438 3e4zA 990 2.57e+01 2wzqA 619 2.57e+01 2d69A 430 2.59e+01 c.1.14.1 131292 d.58.9.1 131293 1a8i 842 2.61e+01 1a8i 2vccA 891 2.62e+01 1ckaA 57 2.63e+01 1ckaA b.34.2.1 24459 1qlyA 58 2.64e+01 1bbzA b.34.2.1 24530 1b43A 340 2.65e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1bpoA 494 2.68e+01 1bpoA a.118.1.4 19143 b.69.6.1 27670 1kjwA 295 2.68e+01 b.34.2.1 68643 c.37.1.1 68644 1ri6A 343 2.69e+01 b.69.11.1 97503 1w7jA 795 2.72e+01 b.34.3.1 120688 c.37.1.9 120689 1kfuL 699 2.73e+01 a.39.1.8 68571 b.14.1.1 68572 d.3.1.3 68573 2aq6A 147 2.74e+01 b.45.1.1 127156 1dq3A 454 2.74e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 2obeA 932 2.78e+01 1g79A 218 2.78e+01 1ci0A b.45.1.1 25752 2vvlA 495 2.79e+01 3ip4B 483 2.80e+01 1rxyA 253 2.83e+01 c.56.2.1 98065 2agyA 361 2.86e+01 2oizA 361 2.87e+01 3bz1O 247 2.87e+01 2vjxA 846 2.88e+01 b.1.4.1 153203 b.1.4.1 153204 b.1.4.1 153205 b.18.1.5 153206 c.1.8.3 153207 3dmqA 968 2.90e+01 3hx4A 508 2.94e+01 1zo0A 126 3.00e+01 d.108.1.7 125416 2fp8A 322 3.01e+01 1b07A 59 3.01e+01 1ckaA b.34.2.1 24461 1asyA 490 3.01e+01 1b8aA b.40.4.1 25242 d.104.1.1 40763 2v26A 784 3.02e+01 1y0mA 61 3.03e+01 3hfqA 347 3.04e+01 2bkhA 814 3.04e+01 2o9sA 67 3.06e+01 3g9aB 139 3.08e+01 2yvlA 248 3.08e+01 3pcgM 238 3.09e+01 3pchM b.3.6.1 22742 1ua4A 455 3.09e+01 c.72.1.3 99128 1y0yA 353 3.10e+01 b.49.3.1 122514 c.56.5.4 122515 2rc5A 314 3.19e+01 3goxA 200 3.21e+01 3ecqA 1531 3.24e+01 2a19A 175 3.24e+01 3cddA 361 3.24e+01 b.106.1.1 156500 b.106.1.1 156501 3dkcA 317 3.24e+01 2qgnA 322 3.25e+01 2z1pA 348 3.25e+01 1zq1A 438 3.25e+01 b.38.3.1 125489 c.88.1.1 125490 1uch 230 3.28e+01 1uch 2a28A 54 3.30e+01 3ku3A 327 3.36e+01 3igoA 486 3.36e+01 3i7fA 548 3.36e+01 1dghB 498 3.38e+01 1cf9A e.5.1.1 42791 1qzgA 187 3.39e+01 b.40.4.3 96643 1x1gA 129 3.41e+01 b.55.1.1 121580 1q1uA 144 3.43e+01 b.42.1.1 95608 1dgfA 497 3.45e+01 1cf9A e.5.1.1 42782 1x8bA 289 3.45e+01 1aorA 605 3.52e+01 1b25A a.110.1.1 19042 d.152.1.1 41794 2r0cA 549 3.56e+01 1xd3A 230 3.60e+01 d.3.1.6 115145 1zxiB 809 3.62e+01 d.41.1.1 125774 d.133.1.1 125775 2jdqD 83 3.66e+01 d.361.1.1 147989 3ku2A 507 3.67e+01 2o31A 67 3.73e+01 3e1yA 451 3.76e+01 1bn6A 294 3.76e+01 1bn6A c.69.1.8 34678 1bn7A 294 3.82e+01 1bn6A c.69.1.8 34677 3fc3A 200 3.87e+01 2iaaA 390 3.88e+01 1h5uA 842 3.88e+01 1a8i c.87.1.4 60655 2zq0A 738 3.89e+01 2f41A 121 3.90e+01 d.38.1.5 132904 1gcpA 70 3.91e+01 1gcpA b.34.2.1 60430 2v5cA 594 3.91e+01 1hkbA 917 3.92e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 2zodA 345 3.95e+01 d.79.4.1 154718 d.139.1.1 154719