# List of top-scoring protein chains for t2k-100-30-bys 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 1kk8B 139 2.92e-02 a.39.1.5 77430 1rvkA 382 3.57e-02 c.1.11.2 -5568 d.54.1.1 -9826 1q48A 134 7.80e-02 unknown_sccs -9776 1wdcB 156 1.75e-01 1wdcB a.39.1.5 17302 1nlfA 279 2.98e-01 c.37.1.11 85850 1g8yA 279 3.13e-01 1g8yA c.37.1.11 32302 1nt4A 391 3.14e-01 c.60.1.2 -7942 1fqgA 263 6.06e-01 1btl e.3.1.1 42699 1k1vA 41 6.32e-01 a.37.1.1 71999 1r71A 178 7.59e-01 1btl 263 7.74e-01 1btl e.3.1.1 42691 1scmB 145 8.60e-01 1wdcB a.39.1.5 17304 1o08A 221 1.21e+00 c.108.1.6 86525 1exqA 154 1.44e+00 1b9dA c.55.3.2 33646 1uylA 236 1.54e+00 1yer 228 1.80e+00 1yer d.122.1.1 41101 1ermA 263 1.87e+00 1btl e.3.1.1 42690 1ec7A 446 1.97e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1bj7 156 1.97e+00 1bj7 b.60.1.1 27113 1q1hA 110 2.31e+00 unknown_sccs -262 1b0zA 445 2.69e+00 2pgi c.80.1.2 35309 2pgi 445 2.72e+00 2pgi c.80.1.2 35308 1c7qA 445 2.78e+00 2pgi c.80.1.2 35307 1hg5A 289 2.82e+00 1hg5A unknown_sccs -400 unknown_sccs -1629 1hg2A 289 2.84e+00 1hg5A unknown_sccs -401 unknown_sccs -1630 1hf8A 289 2.93e+00 1hg5A unknown_sccs -399 unknown_sccs -1628 1o6dA 163 3.03e+00 c.116.1.3 -6689 1d0nA 729 3.28e+00 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1k4mA 213 3.54e+00 c.26.1.3 77258 1ad3A 452 3.61e+00 1ad3A c.82.1.1 35335 1lshB 319 3.72e+00 f.7.1.1 74245 1e3oC 160 3.79e+00 1au7A a.4.1.1 59197 a.35.1.1 59198 1jdfA 447 3.79e+00 c.1.11.2 62897 d.54.1.1 62898 1n9bA 265 3.94e+00 e.3.1.1 85463 2mnr 357 4.04e+00 2mnr c.1.11.2 29245 d.54.1.1 38889 1byqA 228 4.09e+00 1yer d.122.1.1 41100 1us6A 102 4.17e+00 1ecmA 109 4.28e+00 1ecmA a.130.1.1 19492 1dgrN 79 4.44e+00 1caxB 1mdl 359 4.61e+00 2mnr c.1.11.2 29247 d.54.1.1 38891 1jbgA 109 4.70e+00 a.6.1.3 66480 1gw0A 559 5.02e+00 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1bqg 451 5.17e+00 1bqg c.1.11.2 29217 d.54.1.1 38861 1do6A 124 5.33e+00 1do6A b.1.13.1 22361 1s1dA 331 5.57e+00 unknown_sccs -4566 1yagG 125 5.63e+00 1d0nA d.109.1.1 40846 1g40A 244 5.87e+00 1e5gA g.18.1.1 44823 g.18.1.1 44824 g.18.1.1 44825 g.18.1.1 44826 1r1dA 247 5.93e+00 unknown_sccs -8335 1efiD 103 5.99e+00 3chbD b.40.2.1 24870 1rw2A 152 6.25e+00 unknown_sccs -1645 1tvxA 75 6.64e+00 1tvxA d.9.1.1 37441 1gr0A 367 6.68e+00 c.2.1.3 70379 d.81.1.3 70380 1m40A 263 6.92e+00 e.3.1.1 74437 1ltsD 103 7.03e+00 3chbD b.40.2.1 24900 1gt7A 274 7.29e+00 c.74.1.1 70398 1lvhA 221 7.32e+00 c.108.1.6 74282 1dgwX 79 7.66e+00 1caxB b.82.1.2 28091 1eyvA 156 7.70e+00 1eyvA a.79.1.1 18446 1i6iA 366 7.97e+00 1bg2 c.37.1.9 61844 1hq1A 105 8.16e+00 1dulA a.36.1.1 17120 1h2aL 567 8.38e+00 1h2rL e.18.1.1 43299 1kay 381 8.48e+00 1ba1 c.55.1.1 33385 c.55.1.1 33386 3chbD 104 8.57e+00 3chbD b.40.2.1 24970 1dqiA 124 8.77e+00 1do6A b.1.13.1 22357 1lucA 355 8.90e+00 1lucA c.1.16.1 29547 1rzhM 307 9.04e+00 f.26.1.1 -12227 1fsz 372 9.78e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1t3uA 104 9.90e+00 unknown_sccs -9325 6pfkA 319 9.99e+00 3pfk c.89.1.1 35583 1itkA 731 1.03e+01 a.93.1.3 71417 a.93.1.3 71418 1ba1 386 1.03e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1i5sA 367 1.05e+01 1bg2 c.37.1.9 61822 1brsD 89 1.06e+01 1ay7B c.9.1.1 30825 1fiuA 286 1.08e+01 1fiuA c.52.1.10 33317 1nm1G 125 1.11e+01 d.109.1.1 80653 1nu5A 370 1.12e+01 c.1.11.2 -5565 d.54.1.1 -9823 1b0uA 262 1.12e+01 1b0uA c.37.1.12 32370 1okrA 123 1.13e+01 unknown_sccs -235 1h0pA 182 1.17e+01 b.62.1.1 76450 1viaA 175 1.18e+01 c.37.1.2 -7021 1djrD 103 1.19e+01 3chbD b.40.2.1 24865 1dulA 69 1.23e+01 1dulA a.36.1.1 17121 1bmlC 362 1.25e+01 1bmlC d.15.5.1 37729 d.15.5.1 37730 d.15.5.1 37731 1ekeA 230 1.25e+01 1ekeA c.55.3.1 33572 1qnxA 209 1.26e+01 1qnxA d.111.1.1 40914 1d4xG 126 1.27e+01 1d0nA d.109.1.1 59109 1jx4A 352 1.28e+01 unknown_sccs -10188 unknown_sccs -11898 1h2rL 534 1.34e+01 1h2rL e.18.1.1 43298 3pfk 319 1.37e+01 3pfk c.89.1.1 35581 1ihrA 76 1.38e+01 1ihrA d.212.1.2 62392 1c6vX 81 1.38e+01 1ihvA b.34.7.1 24641 1hm6A 346 1.43e+01 1avc a.65.1.1 18147 1mj5A 302 1.44e+01 c.69.1.8 -8326 1dkxA 219 1.44e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1a73A 163 1.45e+01 1a73A d.4.1.3 37145 1itg 166 1.48e+01 1b9dA c.55.3.2 33661 1dgrV 79 1.49e+01 1caxB b.82.1.2 28099 1jpdX 324 1.50e+01 c.1.11.2 67014 d.54.1.1 67015 1ojrA 274 1.50e+01 c.74.1.1 -8441 6paxA 133 1.56e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1iz6A 138 1.62e+01 b.34.5.2 76976 b.40.4.5 76977 4pfk 319 1.63e+01 3pfk c.89.1.1 35582 1axdA 209 1.66e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1bx4A 345 1.69e+01 1bx4A c.72.1.1 34935 1ubkL 534 1.70e+01 e.18.1.1 88422 1csn 298 1.74e+01 1csn d.144.1.7 41664 1iq4A 179 1.77e+01 1iq4A d.77.1.1 62641 1vmoA 163 1.80e+01 1vmoA b.77.1.1 27974 1scuA 288 1.80e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1dvoA 152 1.83e+01 1dvoA a.136.1.1 19623 1qe5A 266 1.87e+01 1b8oA c.56.2.1 33784 1ay7B 89 1.89e+01 1ay7B c.9.1.1 30836 1l4uA 176 1.92e+01 c.37.1.2 73568 1hrnA 337 1.94e+01 1smrA b.50.1.2 26869 1bupA 386 1.96e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1m2bA 110 1.98e+01 c.47.1.11 78474 1ixxB 123 2.03e+01 1ixxB d.169.1.1 42336 1q6hA 224 2.03e+01 d.26.1.1 -9487 1dmgA 225 2.06e+01 1dmgA c.22.1.1 31036 1a8d 452 2.06e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 2cavA 445 2.07e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1php 394 2.09e+01 16pk c.86.1.1 35452 1a8i 842 2.10e+01 1a8i c.87.1.4 35490 1ht6A 405 2.10e+01 b.71.1.1 83629 c.1.8.1 83630 1napA 70 2.11e+01 1tvxA d.9.1.1 37445 1i4jA 110 2.13e+01 d.55.1.1 76734 1lzlA 323 2.14e+01 c.69.1.2 78306 1tvxB 75 2.14e+01 1tvxA d.9.1.1 37442 1g2oA 268 2.17e+01 1b8oA c.56.2.1 60228 1div 149 2.17e+01 1div d.99.1.1 40692 d.100.1.1 40693 1f44A 324 2.20e+01 a.60.9.1 64982 d.163.1.1 64983 1k78A 149 2.27e+01 a.4.1.5 68255 a.4.1.5 68256 1j54A 186 2.28e+01 c.55.3.5 77077 1gpb 842 2.29e+01 1a8i c.87.1.4 35478 1kit 757 2.29e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1dozA 309 2.29e+01 1ak1 c.92.1.1 35592 1np1A 184 2.29e+01 1np1A b.60.1.1 27155 1amz 435 2.33e+01 1csh a.103.1.1 18884 1kte 105 2.33e+01 1kte c.47.1.1 32771 1caxB 184 2.34e+01 1caxB b.82.1.2 28105 1diwA 441 2.34e+01 1a8d b.29.1.6 24264 b.42.4.2 25609 1cv2A 296 2.51e+01 1bn6A c.69.1.8 34680 1csh 435 2.51e+01 1csh a.103.1.1 18880 1iz7A 295 2.52e+01 c.69.1.8 76982 1jfiB 179 2.53e+01 1jfiB a.22.1.3 62937 1r5zA 323 2.54e+01 unknown_sccs -12289 1drw 273 2.59e+01 1drw c.2.1.3 30057 d.81.1.3 39972 1ak1 310 2.62e+01 1ak1 c.92.1.1 35594 1bynA 128 2.62e+01 1rsy b.7.1.2 23193 1bia 321 2.65e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1hm5A 558 2.66e+01 c.80.1.2 76717 1m2dA 110 2.66e+01 c.47.1.11 78476 1xat 212 2.69e+01 2xat b.81.1.3 28059 1j09A 468 2.69e+01 a.97.1.1 77025 c.26.1.1 77026 1iatA 557 2.75e+01 1dqrA c.80.1.2 62123 1dkzA 219 2.76e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1avaA 403 2.78e+01 1jdc b.71.1.1 27797 c.1.8.1 28784 2xat 212 2.90e+01 2xat b.81.1.3 28058 1jkvA 266 2.95e+01 unknown_sccs 71719 1b9dA 163 2.95e+01 1b9dA c.55.3.2 33649 1o9iA 266 3.02e+01 unknown_sccs -698 1qv9A 283 3.04e+01 unknown_sccs -6888 1hn2A 159 3.06e+01 b.60.1.1 65890 1j34B 123 3.07e+01 d.169.1.1 84049 1sbxA 106 3.08e+01 1j1nA 492 3.08e+01 c.94.1.1 83978 1mldA 314 3.10e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1hdiA 413 3.10e+01 16pk c.86.1.1 60964 1cauB 184 3.12e+01 1caxB b.82.1.2 28103 1ucrA 78 3.12e+01 unknown_sccs -308 1aa7A 158 3.17e+01 1aa7A a.95.1.1 18741 1btmA 252 3.17e+01 1amk c.1.1.1 28513 1bxeA 113 3.24e+01 1bxeA d.55.1.1 38898 1m1nB 522 3.27e+01 c.92.2.3 78418 1edg 380 3.28e+01 1edg c.1.8.3 28807 1h7zA 194 3.32e+01 1qhvA b.21.1.1 60733 1oz9A 150 3.36e+01 unknown_sccs -10588 1ki1B 352 3.37e+01 a.87.1.1 72497 b.55.1.1 72498 1pq9A 253 3.38e+01 a.123.1.1 -1687 1gt1A 159 3.38e+01 b.60.1.1 -4436 1jfgA 374 3.41e+01 a.128.1.5 66636 1gln 468 3.43e+01 1gln a.97.1.1 18752 c.26.1.1 31588 2bdpA 580 3.44e+01 1xwl c.55.3.5 33709 e.8.1.1 43002 1dqrA 557 3.45e+01 1dqrA c.80.1.2 35305 1vi9A 299 3.45e+01 c.72.1.5 -8393 1r6rA 100 3.48e+01 unknown_sccs -1071 1a70 97 3.52e+01 1awd d.15.4.1 37678 1b2sD 90 3.52e+01 1ay7B c.9.1.1 30837 1s72R 155 3.54e+01 1ceo 343 3.54e+01 1ceo c.1.8.3 28808 1tig 94 3.56e+01 1tig d.68.1.1 39566 2minB 522 3.58e+01 1qguB c.92.2.3 35610 1nouA 507 3.58e+01 c.1.8.6 85932 d.92.2.1 85933 1jj2Q 154 3.61e+01 1ffkO d.55.1.1 63102 1vyrA 364 3.66e+01 1m2aA 110 3.68e+01 c.47.1.11 78472 1vypX 364 3.69e+01 1ouwA 152 3.72e+01 b.77.3.1 -4759 1cuj 214 3.72e+01 1cex unknown_sccs 31294 1gox 370 3.72e+01 1gox c.1.4.1 28607 1sw6A 327 3.75e+01 1sw6A d.211.1.1 19176 1n9lA 109 3.83e+01 d.110.3.6 85468 1mfiA 114 3.87e+01 1dptA d.80.1.3 39856 1gzsB 165 3.90e+01 a.168.1.1 76425 1d2nA 272 3.90e+01 1d2nA c.37.1.20 32428 1a0p 290 3.94e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 1ma3A 253 3.96e+01 c.31.1.5 78883 1nowA 507 3.99e+01 c.1.8.6 85936 d.92.2.1 85937