# 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.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 1dnyA 91 1.94e-13 1dnyA a.28.1.2 16934 1l0iA 78 4.67e-12 a.28.1.1 77643 1f80D 81 1.11e-10 1acp a.28.1.1 59686 1klpA 115 2.26e-10 a.28.1.1 72721 2af8 86 2.22e-08 2af8 a.28.1.1 16933 1af8 86 4.70e-07 2af8 a.28.1.1 16932 1acp 77 8.09e-07 1acp a.28.1.1 16931 1dv5A 80 1.84e-03 1dv5A a.28.1.3 59139 1h72C 296 2.83e-01 d.14.1.5 60712 d.58.26.1 60713 1ffkU 91 3.47e-01 1ffkU d.29.1.1 38458 1fwkA 296 3.52e-01 1fwkA d.14.1.5 37576 d.58.26.1 39398 1j0aA 325 3.69e-01 c.79.1.1 83871 1jj2W 91 3.76e-01 1ffkU d.29.1.1 63108 1gd0A 122 3.86e-01 1dptA d.80.1.3 39834 1oj4A 283 4.19e-01 1ecxA 384 4.19e-01 1ecxA c.67.1.3 34431 1dptA 117 4.24e-01 1dptA d.80.1.3 39862 1eg5A 384 4.26e-01 1ecxA c.67.1.3 34429 1cxpA 104 6.33e-01 1d2vA a.93.1.2 18695 1d2vA 104 6.33e-01 1d2vA a.93.1.2 18697 1mhlA 108 7.10e-01 1d2vA a.93.1.2 18699 1otfA 62 7.97e-01 1otfA d.80.1.1 39820 1nw3A 416 8.57e-01 c.66.1.31 86288 1ytfB 53 8.63e-01 1ytfB a.32.1.1 16997 1nvpB 57 8.96e-01 1mlvA 444 1.04e+00 a.166.1.1 79283 b.85.7.3 79284 1eluB 390 1.13e+00 1elqA c.67.1.3 34435 1ku1A 230 1.19e+00 a.118.3.1 72996 1eluA 390 1.19e+00 1elqA c.67.1.3 34434 1elqA 390 1.19e+00 1elqA c.67.1.3 34436 1h05A 146 1.23e+00 c.23.13.1 76433 1pdz 434 1.31e+00 4enl c.1.11.1 29215 d.54.1.1 38859 1mfiA 114 1.34e+00 1dptA d.80.1.3 39856 1rmvA 157 1.34e+00 1rmvA a.24.5.1 16589 1rqtA 37 1.48e+00 1l0oC 243 1.61e+00 a.4.13.2 73405 1qhhA 167 1.81e+00 1pjr c.37.1.19 32393 1m4tA 392 2.01e+00 c.95.1.1 78617 c.95.1.1 78618 1m3kA 392 2.01e+00 c.95.1.1 78565 c.95.1.1 78566 1nh2B 53 2.04e+00 1c0aA 585 2.06e+00 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1lm8B 118 2.15e+00 d.15.1.1 74033 1iomA 377 2.41e+00 a.103.1.1 83698 1o4vA 183 2.43e+00 c.23.8.1 86628 1qflA 389 2.55e+00 1afwA c.95.1.1 35908 c.95.1.1 35909 1uekA 275 2.58e+00 d.14.1.5 88483 d.58.26.5 88484 1ks9A 291 2.61e+00 a.100.1.7 68857 c.2.1.6 68858 1h5wA 309 2.62e+00 e.27.1.1 65635 3pbgA 468 2.88e+00 1e70M c.1.8.4 28951 1pbgA 468 2.93e+00 1e70M c.1.8.4 28946 5reqA 727 2.93e+00 1reqA c.1.19.1 29632 c.23.6.1 31259 1fiqB 350 2.98e+00 1fiqB d.87.2.1 40229 d.145.1.3 41760 1cby 259 3.04e+00 1cby d.103.1.1 40705 2rslA 140 3.24e+00 2rslA c.53.1.1 33345 1s0yB 71 3.28e+00 1afwA 393 3.30e+00 1afwA c.95.1.1 35900 c.95.1.1 35901 1nbwA 607 3.34e+00 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 2dhqA 146 3.37e+00 2dhqA c.23.13.1 31382 1jbaA 204 3.91e+00 1rec a.39.1.5 17330 1ijgA 309 3.97e+00 1fouA e.27.1.1 62493 1vom 762 4.00e+00 1lvk b.34.3.1 24577 c.37.1.9 32174 1jidA 128 4.07e+00 d.201.1.1 66735 1js3A 486 4.11e+00 c.67.1.6 67215 1k47A 337 4.42e+00 d.14.1.5 72040 d.58.26.4 72041 1mpgA 282 4.47e+00 1mpgA a.96.1.3 18747 d.129.1.2 41296 1jr2A 286 4.52e+00 c.113.1.1 67111 1uc2A 481 4.64e+00 1jroB 777 4.89e+00 d.41.1.1 67141 d.133.1.1 67142 1qk9A 92 4.89e+00 1qk9A d.10.1.3 37485 1o22A 170 4.92e+00 d.238.1.1 86557 1p3wA 404 5.21e+00 c.67.1.3 87752 1g8mA 593 5.27e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1hyhA 309 5.29e+00 1hyhA c.2.1.5 30150 d.162.1.1 42117 1e5xA 486 5.32e+00 c.79.1.1 59283 1lm6A 215 5.47e+00 d.167.1.1 84628 1n97A 389 5.55e+00 a.104.1.1 80335 1prcC 336 5.68e+00 6prcC a.138.1.2 19674 1b5tA 275 5.92e+00 1b5tA c.1.23.1 29676 1b25A 619 6.10e+00 1b25A a.110.1.1 19044 d.152.1.1 41796 1s0yA 76 6.11e+00 2occE 109 6.45e+00 2occE a.118.11.1 19224 1m9nA 613 6.49e+00 c.24.1.3 78870 c.97.2.1 78871 1htjF 210 6.49e+00 1htjF a.91.1.1 61254 1oj6A 151 6.54e+00 1h67A 108 6.55e+00 a.40.1.1 65643 1oeyA 83 6.67e+00 1n62B 809 6.79e+00 d.41.1.1 80092 d.133.1.1 80093 1fm0D 81 6.83e+00 1fmaD d.15.3.1 37642 1qj2B 809 6.84e+00 1qj2B 1bu8A 452 6.87e+00 1gpl b.12.1.2 23647 c.69.1.19 34795 1e1oA 504 6.89e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 1ofgA 381 6.92e+00 1ofgA c.2.1.3 30064 d.81.1.5 39979 1p0yA 444 7.02e+00 a.166.1.1 87654 b.85.7.3 87655 1fmaD 81 7.05e+00 1fmaD d.15.3.1 37643 1mwwA 128 7.07e+00 1vcbA 118 7.27e+00 1vcbA d.15.1.1 37603 1lngA 87 7.31e+00 d.201.1.1 74045 3kvt 115 7.48e+00 1t1dA d.42.1.2 38642 1lc5A 364 7.56e+00 c.67.1.1 73827 1rw2A 152 7.57e+00 3minB 522 7.57e+00 1qguB c.92.2.3 35606 1rkqA 282 7.62e+00 1qgdA 662 7.63e+00 c.36.1.6 88367 c.36.1.10 88368 c.48.1.1 88369 1g99A 408 7.78e+00 1g99A c.55.1.2 33457 c.55.1.2 33458 1nw1A 429 7.82e+00 d.144.1.8 86286 2vsgA 358 7.88e+00 2vsgA h.4.1.1 45780 1m1nB 522 7.89e+00 c.92.2.3 78418 1ng4A 390 7.92e+00 c.3.1.2 85666 d.16.1.3 85667 1lkcA 364 8.04e+00 c.67.1.1 73978 1f0mA 82 8.05e+00 1b4fA a.60.1.2 17942 1ev0A 58 8.24e+00 1ev0A d.71.1.1 39594 1e4iA 447 8.25e+00 1e70M c.1.8.4 59225 1tr1A 447 8.37e+00 1e70M c.1.8.4 28957 1neq 74 8.59e+00 1neq a.35.1.2 17063 1h2rL 534 9.01e+00 1h2rL e.18.1.1 43298 1h2aL 567 9.09e+00 1h2rL e.18.1.1 43299 1sedA 117 9.51e+00 1cjtA 217 9.73e+00 1azsA d.58.29.1 39419 1jhfA 202 9.81e+00 a.4.5.2 63057 b.87.1.1 63058 1hlrA 907 1.01e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1lmeA 176 1.02e+01 d.167.1.1 84629 1o4sA 389 1.04e+01 c.67.1.1 86620 1qgrA 876 1.04e+01 1qgrA a.118.1.1 19119 1hzpA 335 1.05e+01 1hn9A c.95.1.1 61455 c.95.1.1 61456 7reqA 727 1.07e+01 1reqA c.1.19.1 29616 c.23.6.1 31243 1reqA 727 1.07e+01 1reqA c.1.19.1 29620 c.23.6.1 31247 1gpl 432 1.09e+01 1gpl b.12.1.2 23645 c.69.1.19 34793 1jdfA 447 1.09e+01 c.1.11.2 62897 d.54.1.1 62898 1eblA 317 1.09e+01 1hn9A c.95.1.1 35973 c.95.1.1 35974 1dd9A 338 1.10e+01 1dd9A e.13.1.1 43254 1hn9A 317 1.14e+01 1hn9A c.95.1.1 35977 c.95.1.1 35978 1ddeA 338 1.15e+01 1dd9A e.13.1.1 43255 1j6wA 175 1.16e+01 1j98A d.185.1.2 62663 1div 149 1.18e+01 1div d.99.1.1 40692 d.100.1.1 40693 1dlwA 116 1.19e+01 1dlyA a.1.1.1 14982 1nubA 229 1.20e+01 1sra a.39.1.3 17191 g.3.11.3 44330 g.15.1.1 44715 1fo4A 1332 1.23e+01 a.56.1.1 17910 d.15.4.2 37695 d.41.1.1 38586 d.87.2.1 40227 d.133.1.1 41416 d.145.1.3 41758 1gdtA 183 1.27e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1eblB 317 1.28e+01 1hn9A c.95.1.1 35975 c.95.1.1 35976 1sra 151 1.28e+01 1sra a.39.1.3 17190 1gu2A 124 1.28e+01 a.3.1.1 76348 2minB 522 1.31e+01 1qguB c.92.2.3 35610 1pb6A 212 1.33e+01 a.4.1.9 88017 a.121.1.1 88018 1hnjA 317 1.33e+01 1hn9A c.95.1.1 35969 c.95.1.1 35970 1gyxA 76 1.35e+01 d.80.1.1 76387 1qr0A 228 1.35e+01 1qr0A d.150.1.1 59038 d.150.1.1 59039 1qlmA 316 1.38e+01 1qlmA d.147.1.1 41765 1azsA 220 1.39e+01 1azsA d.58.29.1 39416 1ubkL 534 1.39e+01 e.18.1.1 88422 1n9lA 109 1.40e+01 d.110.3.6 85468 1lylA 504 1.40e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1p2xA 159 1.40e+01 1fgjA 546 1.41e+01 1fgjA a.138.1.3 19679 1rl4A 188 1.42e+01 1t8hA 277 1.43e+01 1lmb3 92 1.45e+01 1lmb3 1tc5A 194 1.48e+01 1j6oA 268 1.49e+01 c.1.9.12 77088 1pieA 419 1.50e+01 1cc1S 283 1.51e+01 2frvA e.19.1.1 43313 1ebfA 358 1.53e+01 1ebuA c.2.1.3 30033 d.81.1.2 39948 1lliA 92 1.54e+01 1lmb3 a.35.1.2 17025 1nu0A 138 1.57e+01 1dgjA 907 1.58e+01 1alo a.56.1.1 17909 d.15.4.2 37694 d.41.1.1 38585 d.133.1.1 41415 1ne2A 200 1.61e+01 c.66.1.32 85586 1ebuA 358 1.62e+01 1ebuA c.2.1.3 30035 d.81.1.2 39950 1h99A 224 1.63e+01 a.142.1.1 60814 a.142.1.1 60815 1dxrC 336 1.65e+01 6prcC a.138.1.2 19670 6prcC 336 1.66e+01 6prcC a.138.1.2 19671 1miwA 404 1.67e+01 a.173.1.1 79162 d.218.1.4 79163 1e5pA 151 1.68e+01 1bj7 b.60.1.1 59272 1i27A 73 1.72e+01 1i27A a.4.5.30 61555 1i8tA 367 1.72e+01 c.4.1.3 66094 d.16.1.7 66095 1hn4A 131 1.76e+01 a.133.1.2 65893 1d5wC 126 1.77e+01 1dbwA c.23.1.1 31101 1nv8A 284 1.80e+01 c.66.1.30 86224 1dbuA 158 1.80e+01 1dbuA d.116.1.1 40930 1gjsA 65 1.81e+01 1gab a.8.1.2 60578 1q7rA 219 1.83e+01 1pbyA 489 1.85e+01 1ow4A 129 1.87e+01 1gq6A 313 1.92e+01 c.42.1.1 70341 1o75A 415 1.94e+01 b.1.20.1 81117 b.1.20.1 81118 b.120.1.1 81119 1ireA 204 2.02e+01 d.149.1.1 76769 1n9eA 787 2.04e+01 1v54E 109 2.05e+01 1e0gA 48 2.07e+01 1e01A d.7.1.1 37325 1lssA 140 2.08e+01 c.2.1.9 74246 1pujA 282 2.10e+01 c.37.1.8 88294 1iw0A 215 2.12e+01 a.132.1.1 83720 1gu7A 364 2.13e+01 b.35.1.2 83321 c.2.1.1 83322 1io7A 368 2.14e+01 1f4tA a.104.1.1 18971 1n91A 108 2.17e+01 d.206.1.1 80326 1vjrA 271 2.19e+01 1guxB 152 2.19e+01 1guxB a.74.1.3 18389 1pjr 724 2.19e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1ksyA 154 2.20e+01 d.89.1.2 72948 1e01A 48 2.20e+01 1e01A d.7.1.1 37326 1f83A 425 2.21e+01 1f82A d.92.1.7 40306 1go3F 107 2.22e+01 a.60.8.2 65407 1reoA 486 2.25e+01 8rxnA 52 2.25e+01 1rb9 g.41.5.1 45215 1gosA 520 2.26e+01 c.3.1.2 65425 d.16.1.5 65426 1f08A 148 2.27e+01 1f08A d.89.1.2 59564 1rb9 53 2.27e+01 1rb9 g.41.5.1 45214 1c3cA 429 2.27e+01 1c3cA a.127.1.1 19425 1p5sA 203 2.29e+01 1gx3A 284 2.29e+01 d.3.1.5 70678 1jjuA 489 2.31e+01 a.3.1.7 66774 a.3.1.7 66775 b.1.18.14 66776 b.1.18.14 66777 b.61.4.1 66778 1n3kA 130 2.32e+01 a.77.1.4 79965 1q1fA 151 2.33e+01 1j54A 186 2.37e+01 c.55.3.5 77077 1br2A 791 2.37e+01 1lvk b.34.3.1 24558 c.37.1.9 32155 1mzjA 339 2.37e+01 c.95.1.1 79700 c.95.1.1 79701 1ec7A 446 2.38e+01 1bqg c.1.11.2 29218 d.54.1.1 38862 1h8eD 482 2.44e+01 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1ct5A 256 2.49e+01 1ct5A c.1.6.2 28663 1dckA 126 2.51e+01 1dbwA c.23.1.1 31097 1a41 234 2.52e+01 1a41 d.163.1.2 42174 1lfpA 249 2.52e+01 e.39.1.1 73885 1lea 84 2.55e+01 1lea a.4.5.2 16085 1iapA 211 2.55e+01 a.91.1.1 62119 1k8kA 418 2.64e+01 c.55.1.1 68305 c.55.1.1 68306 1guzA 310 2.64e+01 c.2.1.5 65586 d.162.1.1 65587 1jh8A 356 2.67e+01 c.39.1.1 63052 1jnyA 435 2.70e+01 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1p3jA 217 2.71e+01 1d0qA 103 2.71e+01 1d0qA g.41.3.2 45208 1d0vA 356 2.72e+01 1d0vA c.39.1.1 32476 1d0sA 356 2.72e+01 1d0vA c.39.1.1 32477 1l5oA 356 2.74e+01 c.39.1.1 77711 1bolA 222 2.76e+01 1bolA d.124.1.1 41120 1mldA 314 2.81e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1e0eA 55 2.81e+01 1wjcA a.4.10.1 59147 1dbwA 126 2.81e+01 1dbwA c.23.1.1 31095 1iuhA 198 2.84e+01 d.61.1.2 83711 1id1A 153 2.86e+01 1id1A c.2.1.9 62286 1rypE 242 2.86e+01 1rypE d.153.1.4 41936 2frvB 536 2.86e+01 1h2rL e.18.1.1 43291 4rxn 54 2.87e+01 1rb9 g.41.5.1 45226 1vjs 483 2.95e+01 1bli b.71.1.1 27714 c.1.8.1 28701 1bhjA 292 2.96e+01 1xvaA c.66.1.5 34189 1j0lA 98 2.96e+01 1as4A 341 2.97e+01 1sek e.1.1.1 42623 1i1iP 681 3.00e+01 1i1iP d.92.1.5 40297 1e79D 482 3.02e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1ogwA 76 3.03e+01 d.15.1.1 87001 1b4fA 82 3.03e+01 1b4fA a.60.1.2 17934 1v5sA 126 3.04e+01 1d3zA 76 3.04e+01 1ubi d.15.1.1 37592 1ubi 76 3.04e+01 1ubi d.15.1.1 37584 1ubq 76 3.04e+01 1ubi d.15.1.1 37585 1iwdA 215 3.12e+01 d.3.1.1 83756 1dx8A 70 3.14e+01 1rb9 g.41.5.1 45243 1b4fG 82 3.16e+01 1b4fA a.60.1.2 17940 1e08A 371 3.18e+01 i.4.1.1 45914 1viaA 175 3.22e+01 1mnaA 298 3.29e+01 c.69.1.22 79322 1nstA 325 3.29e+01 1nstA c.37.1.5 31951 1g7vA 284 3.31e+01 1d9eA c.1.10.4 60335 1tsp 559 3.32e+01 1tyv b.80.1.6 28044 1qq1A 559 3.35e+01 1tyv b.80.1.6 28041 1hr6B 443 3.40e+01 1be3A d.185.1.1 61166 d.185.1.1 61167 1lqxA 82 3.46e+01 d.120.1.1 78153 1qmyA 167 3.47e+01 1qmyA d.3.1.2 37094 1aj8A 371 3.50e+01 1aj8A a.103.1.1 18900 1obdA 306 3.50e+01 d.143.1.1 86767 1d9eA 284 3.52e+01 1d9eA c.1.10.4 29195 1q45A 391 3.53e+01 1b1a 137 3.57e+01 1be1 c.23.6.1 31242 1mli 96 3.57e+01 1mli d.58.4.1 39070 1rdg 53 3.57e+01 1rb9 g.41.5.1 45221 1mswD 883 3.59e+01 e.8.1.3 79427 1b54 257 3.61e+01 1ct5A c.1.6.2 28664 1v9dA 340 3.63e+01 1usuA 260 3.67e+01 1h5qA 265 3.69e+01 1cydA c.2.1.2 60643 1su8A 636 3.70e+01 1dbxA 158 3.73e+01 1dbuA d.116.1.1 40928 1a48 306 3.83e+01 1a48 d.143.1.1 41590 1j5vA 351 3.85e+01 c.72.1.1 71585 1tyv 542 3.85e+01 1tyv b.80.1.6 28038 1tyu 543 3.85e+01 1tyv b.80.1.6 28037 1jp3A 253 3.93e+01 1f75A c.101.1.1 63221 1frvB 536 3.94e+01 1h2rL e.18.1.1 43296 1bc5A 269 3.95e+01 1af7 a.58.1.1 17929 c.66.1.8 34204 1d3uB 201 3.96e+01 1aisB a.74.1.2 18386 a.74.1.2 18387 1rmi 160 3.98e+01 1ifa a.26.1.3 16891 1it2A 146 3.98e+01 a.1.1.2 66365