# List of top-scoring protein chains for t2k-100-30-str 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 1qvcA 145 1.86e-19 3ullA b.40.4.3 25284 1kawA 135 8.19e-17 3ullA b.40.4.3 25288 3ullA 132 1.33e-16 3ullA b.40.4.3 25282 1je5A 206 4.15e-01 1je5A b.40.4.7 62909 1f9zA 135 5.56e-01 1qipA d.32.1.1 38484 1fa8A 135 1.04e+00 1qipA d.32.1.1 38486 1ewjA 126 1.66e+00 1ecsA d.32.1.2 59526 1e54A 332 1.82e+00 1e54A f.4.3.1 59258 1gpeA 587 1.92e+00 1gpeA c.3.1.2 30387 d.16.1.4 37951 1lylA 504 2.31e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1ecsA 126 2.50e+00 1ecsA d.32.1.2 59407 1a8p 258 3.11e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 1ggxA 223 3.42e+00 1ggxA d.22.1.1 38367 1ff9A 450 3.76e+00 1ff9A c.2.1.3 30039 d.81.1.2 39954 1huuA 90 4.12e+00 1huuA a.55.1.1 17897 1c0aA 585 4.55e+00 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1e1oA 504 4.73e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 1gm5A 780 4.73e+00 a.29.4.1 65298 b.40.4.9 65299 c.37.1.13 65300 c.37.1.13 65301 1l9mA 692 5.52e+00 1br9 194 5.60e+00 1br9 b.40.3.1 25235 1qlmA 316 5.65e+00 1qlmA d.147.1.1 41765 1e79A 510 5.67e+00 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1otcA 495 5.92e+00 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1bmfA 510 6.19e+00 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1fm0E 150 7.22e+00 1fmaE d.41.5.1 38629 1fmaE 150 7.47e+00 1fmaE d.41.5.1 38630 1h8eA 510 7.83e+00 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1kxrA 339 7.90e+00 1b8aA 438 9.18e+00 1b8aA b.40.4.1 25244 d.104.1.1 40765 1qdbA 473 9.98e+00 1qdbA a.138.1.3 19688 1ndoB 194 1.03e+01 1ndoB d.17.4.4 38121 1j8rA 196 1.08e+01 1j8rA b.2.3.3 62745 1qbiA 454 1.09e+01 1c9uA b.68.2.1 27619 1fnd 314 1.12e+01 1fnc b.43.4.2 25626 c.25.1.1 31516 1fnb 314 1.12e+01 1fnc b.43.4.2 25628 c.25.1.1 31518 1l0wA 580 1.20e+01 1napA 70 1.21e+01 1tvxA d.9.1.1 37445 1j6wA 175 1.25e+01 1j98A d.185.1.2 62663 1kvdB 77 1.26e+01 1kveB 1kveB 77 1.26e+01 1kveB 1c9uA 454 1.26e+01 1c9uA b.68.2.1 27623 1gotB 340 1.28e+01 1tbgA b.69.4.1 27648 1fnc 314 1.28e+01 1fnc b.43.4.2 25627 c.25.1.1 31517 1qo2A 241 1.29e+01 1qo2A c.1.2.1 28533 1tvxA 75 1.32e+01 1tvxA d.9.1.1 37441 1k8eA 345 1.38e+01 1ep3B 262 1.38e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1bovA 69 1.38e+01 2bosA b.40.2.1 25070 1b8zA 90 1.43e+01 1huuA a.55.1.1 17902 1dy9A 187 1.53e+01 1jxpA b.47.1.3 26400 1jb7A 495 1.58e+01 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1sftA 388 1.61e+01 1bd0A b.49.2.1 26482 c.1.6.1 28644 1bd0A 388 1.62e+01 1bd0A b.49.2.1 26480 c.1.6.1 28642 1fs7A 485 1.63e+01 1qdbA a.138.1.3 19691 1d06A 130 1.67e+01 1drmA d.110.3.2 40906 1ew0A 130 1.68e+01 1drmA d.110.3.2 40905 1i1jA 108 1.70e+01 1i1jA b.34.2.1 61531 1quqB 121 1.73e+01 1quqB b.40.4.3 25305 1hdmB 193 1.74e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 1dar 691 1.83e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1tvxB 75 1.85e+01 1tvxA d.9.1.1 37442 1ijaA 148 1.85e+01 1ijaA b.100.1.1 62484 1dyqA 234 1.91e+01 3seb b.40.2.2 59140 d.15.6.1 59141 1gd5A 130 1.94e+01 1gd5A d.189.1.1 60439 2madH 373 2.01e+01 2bbkH b.69.2.1 27639 1agdA 276 2.11e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 1hjdA 101 2.14e+01 b.34.2.1 65846 1c4qA 69 2.15e+01 2bosA b.40.2.1 25010 1hxmA 229 2.27e+01 1hxmA b.1.1.1 61367 b.1.1.2 61368 1tdtA 259 2.30e+01 3tdt b.81.1.2 28055 1cf1A 404 2.30e+01 1cf1A b.1.1.5 21907 b.1.1.5 21908 1vcc 77 2.31e+01 1vcc d.121.1.1 41092 1iakA 199 2.38e+01 1iakA b.1.1.2 21625 d.19.1.1 38199 1fnhA 271 2.39e+01 1fnhA b.1.2.1 21976 b.1.2.1 21977 b.1.2.1 21978 3cox 507 2.43e+01 1b8sA c.3.1.2 30332 d.16.1.1 37863 2tdt 274 2.47e+01 3tdt b.81.1.2 28054 1a62 130 2.48e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1coy 507 2.49e+01 1b8sA c.3.1.2 30333 d.16.1.1 37864 3tdt 274 2.49e+01 3tdt b.81.1.2 28053 1ep2B 261 2.53e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1awqA 164 2.53e+01 2cpl b.62.1.1 27461 1a8vA 121 2.54e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 3mdeA 385 2.56e+01 3mdeA a.29.3.1 16594 e.6.1.1 42855 2cpl 165 2.60e+01 2cpl b.62.1.1 27420 1wit 93 2.64e+01 1wit b.1.1.4 21714 1yaiA 151 2.66e+01 1yaiA b.1.8.1 22289 1cwoA 165 2.71e+01 2cpl b.62.1.1 27445 1h2vZ 156 2.76e+01 1bo4B 168 2.77e+01 1bo4A d.108.1.1 40799 1g13A 162 2.80e+01 1g13A b.95.1.1 60194 1mal 421 2.98e+01 2mprA f.4.3.2 43784 1qfcA 306 2.99e+01 1uteA d.159.1.1 42077 1plfA 72 2.99e+01 1tvxA d.9.1.1 37373 1emwA 88 3.02e+01 1emwA d.27.1.1 38448 1gjuA 637 3.03e+01 b.71.1.1 60580 c.1.8.1 60581 1af6A 421 3.04e+01 2mprA f.4.3.2 43772 1gjwA 637 3.06e+01 b.71.1.1 60582 c.1.8.1 60583 1cqqA 180 3.08e+01 1cqqA b.47.1.4 26422 1que 303 3.09e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1jxpA 186 3.09e+01 1jxpA b.47.1.3 26402 1e9iA 431 3.10e+01 c.1.11.1 64818 d.54.1.1 64819 1at0 145 3.11e+01 1at0 b.86.1.1 28374 1b2rA 304 3.11e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1bgvA 449 3.12e+01 1k89 c.2.1.7 30217 c.58.1.1 33865 1hrdA 449 3.12e+01 1k89 c.2.1.7 30219 c.58.1.1 33867 1qh0A 295 3.14e+01 b.43.4.2 68891 c.25.1.1 68892 1erjA 393 3.17e+01 1erjA b.69.4.1 27660 1mkaA 171 3.17e+01 1mkaA d.38.1.2 38543 1h5bA 113 3.17e+01 1tvdA b.1.1.1 60638 2rhe 114 3.26e+01 8fabA b.1.1.1 20523 1sro 76 3.27e+01 1sro b.40.4.5 25327 1d1nA 99 3.29e+01 1d1nA b.43.3.1 25718 1k89 449 3.31e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1go2A 304 3.35e+01 1pii 452 3.51e+01 1pii c.1.2.4 28559 c.1.2.4 28563 1bo4A 168 3.66e+01 1bo4A d.108.1.1 40798 1qnf 484 3.66e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 1bykA 255 3.73e+01 1bykA c.93.1.1 35706 1eg9B 194 3.78e+01 1ndoB d.17.4.4 38120 1d2sA 170 3.81e+01 1d2sA b.29.1.4 24221 1kd6A 179 3.84e+01 b.97.1.1 68459 1bf8 205 3.86e+01 1qpxA b.1.11.1 22332 b.7.2.1 23214 1awsA 164 3.86e+01 2cpl b.62.1.1 27431 1io1A 398 3.92e+01 1io1A e.32.1.1 62611 1noyA 388 3.94e+01 1clqA c.55.3.5 33713 1d4vB 163 3.99e+01 1d4vB b.22.1.1 23884