# List of top-scoring protein chains for t04-100-30-str2 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 1ec7A 446 6.28e-02 1bqg c.1.11.2 29218 d.54.1.1 38862 1rvkA 382 6.90e-02 c.1.11.2 -5568 d.54.1.1 -9826 1khdA 345 1.24e-01 a.46.2.1 77400 c.27.1.1 77401 1mdl 359 1.32e-01 2mnr c.1.11.2 29247 d.54.1.1 38891 1jpmA 366 1.70e-01 c.1.11.2 67031 d.54.1.1 67032 1vhxA 150 1.72e-01 unknown_sccs -7663 2mnr 357 1.84e-01 2mnr c.1.11.2 29245 d.54.1.1 38889 1dkzA 219 2.79e-01 1dkzA unknown_sccs -445 unknown_sccs -3060 1fsz 372 2.99e-01 1fsz c.32.1.1 31750 d.79.2.1 39802 1q48A 134 6.58e-01 unknown_sccs -9776 1vi9A 299 7.16e-01 c.72.1.5 -8393 1g0oA 283 7.76e-01 1ybvA c.2.1.2 60181 1bj7 156 8.76e-01 1bj7 b.60.1.1 27113 1hf8A 289 1.13e+00 1hg5A unknown_sccs -399 unknown_sccs -1628 1nu5A 370 1.14e+00 c.1.11.2 -5565 d.54.1.1 -9823 1i6iA 366 1.51e+00 1bg2 c.37.1.9 61844 1ikpA 613 1.84e+00 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1gln 468 1.89e+00 1gln a.97.1.1 18752 c.26.1.1 31588 1bupA 386 2.34e+00 1ba1 c.55.1.1 33377 c.55.1.1 33378 1s1dA 331 2.83e+00 unknown_sccs -4566 1kkoA 413 2.85e+00 c.1.11.2 68675 d.54.1.1 68676 1j54A 186 3.04e+00 c.55.3.5 77077 1k32A 1045 3.14e+00 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1f2tB 148 3.30e+00 1f2tB 1f5mA 180 3.31e+00 1f5mB d.110.2.1 40895 1lshB 319 3.51e+00 f.7.1.1 74245 1p3dA 475 3.96e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1qmhA 347 3.98e+00 1qmhA c.47.2.1 33082 d.68.2.1 39568 1nt4A 391 4.30e+00 c.60.1.2 -7942 1zpdA 568 4.31e+00 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1knwA 425 4.34e+00 b.49.2.3 -4274 c.1.6.1 -5229 1oz9A 150 4.87e+00 unknown_sccs -10588 1o7zA 77 5.14e+00 d.9.1.1 86660 1ezwA 349 5.15e+00 1ezwA c.1.16.3 29558 1m3qA 317 5.28e+00 a.96.1.3 -1288 d.129.1.2 -11006 1dpgA 485 6.01e+00 1dpgA c.2.1.3 30074 d.81.1.5 39989 1ebmA 317 6.16e+00 1ebmA a.96.1.3 18751 d.129.1.2 41300 1j09A 468 6.32e+00 a.97.1.1 77025 c.26.1.1 77026 1dzkA 157 6.32e+00 1obpA b.60.1.1 27096 1wdcB 156 6.44e+00 1wdcB a.39.1.5 17302 1q6hA 224 6.65e+00 d.26.1.1 -9487 1khiA 176 6.91e+00 b.34.5.2 77408 b.40.4.5 77409 1h9oA 112 7.05e+00 1qadA d.93.1.1 60837 3il8 72 7.09e+00 1tvxA d.9.1.1 37356 1on2A 142 7.34e+00 a.4.5.24 87103 a.76.1.1 87104 1r6lA 239 7.46e+00 d.14.1.4 -9057 d.101.1.1 -10747 1p9oA 313 7.51e+00 unknown_sccs -8423 1tvxA 75 7.55e+00 1tvxA d.9.1.1 37441 1kay 381 7.64e+00 1ba1 c.55.1.1 33385 c.55.1.1 33386 1ezfA 340 7.72e+00 1ezfA a.128.1.2 19440 1ctt 294 7.80e+00 1ctt c.97.1.1 36022 c.97.1.1 36023 1jg1A 235 7.89e+00 c.66.1.7 66661 1n9lA 109 7.96e+00 d.110.3.6 85468 1ur5A 309 7.97e+00 c.2.1.5 -5910 d.162.1.1 -11477 1exqA 154 7.99e+00 1b9dA c.55.3.2 33646 1jq5A 370 8.02e+00 e.22.1.2 67084 1vybA 238 8.03e+00 1g2rA 100 8.14e+00 1g2rA d.192.1.1 60231 2phlA 397 8.32e+00 1dgwA b.82.1.2 28082 b.82.1.2 28083 1ofuA 320 8.41e+00 c.32.1.1 86972 d.79.2.1 86973 1pjqA 457 8.48e+00 c.2.1.11 -5904 c.90.1.1 -8611 e.37.1.1 -12004 1oacA 727 9.16e+00 1oacA b.30.2.1 24390 d.17.2.1 38007 d.17.2.1 38008 d.82.1.1 40003 1ci3M 249 9.17e+00 1hcz b.2.6.1 22480 b.84.2.2 28266 1b8dA 164 9.26e+00 1cpcA a.1.1.3 15665 1b0uA 262 9.61e+00 1b0uA c.37.1.12 32370 1d2eA 397 9.64e+00 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1m1nB 522 9.94e+00 c.92.2.3 78418 1eyhA 144 9.97e+00 1eduA a.118.9.1 19214 1mwmA 320 9.97e+00 c.55.1.1 79580 c.55.1.1 79581 1p36A 164 1.01e+01 d.2.1.3 -8840 1h9sA 140 1.01e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1fkmA 396 1.01e+01 1fkmA a.69.2.1 18315 a.69.2.1 18316 5eau 548 1.04e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1itg 166 1.08e+01 1b9dA c.55.3.2 33661 1r71A 178 1.09e+01 1o08A 221 1.09e+01 c.108.1.6 86525 1ad3A 452 1.10e+01 1ad3A c.82.1.1 35335 1dmgA 225 1.16e+01 1dmgA c.22.1.1 31036 1kk8B 139 1.16e+01 a.39.1.5 77430 1ohuA 175 1.18e+01 f.1.4.1 -12058 1rkuA 206 1.19e+01 unknown_sccs -6823 1shuX 182 1.22e+01 c.62.1.1 -7982 1vjlA 164 1.28e+01 unknown_sccs -11117 119l 164 1.28e+01 1l92 d.2.1.3 36622 1n3lA 372 1.29e+01 c.26.1.1 79966 1qg7A 67 1.30e+01 1a15A d.9.1.1 37449 1om1A 332 1.37e+01 d.144.1.7 -11318 1khyA 148 1.39e+01 a.174.1.1 77410 1a9xA 1058 1.39e+01 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 1sluA 142 1.40e+01 1sluA b.16.1.1 23685 6paxA 133 1.42e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1pysA 350 1.43e+01 1pysA d.104.1.1 40775 1nnhA 294 1.43e+01 d.104.1.1 -10772 1lw9A 164 1.43e+01 d.2.1.3 84727 1iyhA 198 1.44e+01 a.45.1.1 83790 c.47.1.5 83791 1oz7A 131 1.45e+01 d.169.1.1 -11622 1eyvA 156 1.46e+01 1eyvA a.79.1.1 18446 1ojrA 274 1.52e+01 c.74.1.1 -8441 1q1hA 110 1.57e+01 unknown_sccs -262 1a8d 452 1.60e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 1fiqC 763 1.61e+01 1fiqC d.41.1.1 38588 d.133.1.1 41418 1m8uA 173 1.63e+01 b.11.1.1 -3027 b.11.1.1 -3028 1bl3A 160 1.63e+01 1b9dA c.55.3.2 33655 1hw7A 255 1.64e+01 1i7fA d.193.1.1 61297 1ns5A 155 1.64e+01 c.116.1.3 80705 1j7nA 776 1.65e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 2ae2A 260 1.67e+01 1bdb c.2.1.2 29945 1gw0A 559 1.67e+01 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1o6dA 163 1.68e+01 c.116.1.3 -6689 1l7mA 211 1.69e+01 c.108.1.4 73664 1f00I 282 1.72e+01 1f00I b.1.14.1 22368 b.1.14.1 22369 d.169.1.3 42439 1allA 160 1.73e+01 1qgwC a.1.1.3 15647 1oeyA 83 1.74e+01 d.15.2.2 -9162 1q15A 503 1.75e+01 c.26.2.1 -6625 d.153.1.1 -11400 1e2uA 553 1.78e+01 1e1dA e.26.1.1 43362 1a8q 274 1.79e+01 1brt c.69.1.12 34702 1qysA 106 1.80e+01 unknown_sccs -13432 1dar 691 1.81e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1l1zA 274 1.82e+01 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1obpA 159 1.84e+01 1obpA b.60.1.1 27092 1n62C 288 1.87e+01 d.87.2.1 80094 d.145.1.3 80095 1f0jA 377 1.96e+01 1f0jA a.125.1.1 19346 1j97A 211 1.96e+01 1f5sA c.108.1.4 62753 1hyvA 166 1.98e+01 1b9dA c.55.3.2 61424 1gt1A 159 2.01e+01 b.60.1.1 -4436 1hn2A 159 2.01e+01 b.60.1.1 65890 1byqA 228 2.03e+01 1yer d.122.1.1 41100 1pkp 150 2.08e+01 1pkp d.14.1.1 37551 d.50.1.2 38787 1lfwA 470 2.12e+01 c.56.5.4 77942 d.58.19.1 77943 1h6hA 143 2.14e+01 d.189.1.1 65681 1v9mA 323 2.14e+01 unknown_sccs -12292 1gntA 553 2.14e+01 e.26.1.1 70290 1r2zA 274 2.16e+01 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1xgsA 295 2.17e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1moq 368 2.19e+01 1moq c.80.1.1 35302 1m2rA 327 2.26e+01 d.144.1.7 84760 1jnrB 150 2.27e+01 d.58.1.5 66969 1uteA 313 2.28e+01 1uteA d.159.1.1 42078 1k1vA 41 2.28e+01 a.37.1.1 71999 1lt5D 103 2.30e+01 3chbD b.40.2.1 24875 1ogwA 76 2.30e+01 d.15.1.1 87001 1q2wA 308 2.35e+01 b.47.1.4 88355 1rg9A 383 2.35e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1hfc 169 2.35e+01 1hfc d.92.1.11 40335 1ltzA 297 2.36e+01 d.178.1.1 74254 1a59 378 2.37e+01 1aj8A a.103.1.1 18902 1hz6A 72 2.38e+01 2ptl d.15.7.1 61429 1a6o 332 2.38e+01 1a6o 1ubi 76 2.39e+01 1ubi d.15.1.1 37584 1dm0A 287 2.39e+01 1dm0A d.165.1.2 42227 1zymA 258 2.40e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1fo4A 1332 2.42e+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 1uf6A 178 2.45e+01 unknown_sccs -4533 1lmb3 92 2.48e+01 1lmb3 1n9bA 265 2.50e+01 e.3.1.1 85463 1v97A 1332 2.54e+01 1ecmA 109 2.58e+01 1ecmA a.130.1.1 19492 1jbkA 195 2.58e+01 c.37.1.20 71631 1h10A 125 2.58e+01 b.55.1.1 83446 1cozA 129 2.60e+01 1cozA c.26.1.2 31598 1j8yF 297 2.61e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1djrD 103 2.62e+01 3chbD b.40.2.1 24865 1cpcA 162 2.64e+01 1cpcA a.1.1.3 15643 1ptmA 329 2.65e+01 unknown_sccs -8456 1f60B 94 2.67e+01 1b64 d.58.12.1 39307 1ukz 203 2.68e+01 1zin c.37.1.1 31840 1shyB 551 2.68e+01 1aop 497 2.70e+01 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1kq3A 376 2.70e+01 e.22.1.2 68790 1dozA 309 2.70e+01 1ak1 c.92.1.1 35592 1yrnB 83 2.73e+01 1akhB a.4.1.1 15986 1pwxA 254 2.73e+01 c.2.1.2 -5858 1huxA 270 2.74e+01 1huxA c.55.1.5 61278 1lldA 319 2.75e+01 3ldh c.2.1.5 30177 d.162.1.1 42144 3chbD 104 2.79e+01 3chbD b.40.2.1 24970 1dosA 358 2.79e+01 1dosA c.1.10.2 29175 1uylA 236 2.82e+01 1vypX 364 2.86e+01 1eu3A 210 2.89e+01 1an8 b.40.2.2 25206 d.15.6.1 37795 1q2yA 140 2.93e+01 d.108.1.1 -10791 1lrzA 426 2.96e+01 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1kyqA 274 2.96e+01 c.2.1.11 73281 e.37.1.1 73282 1qnrA 344 3.01e+01 1qnoA c.1.8.3 28834 1poa 118 3.01e+01 1poa a.133.1.2 19514 1pfjA 108 3.02e+01 1ka2A 499 3.02e+01 d.92.1.5 77305 1fhuA 320 3.04e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1exmA 405 3.09e+01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1h61A 364 3.12e+01 1oyc c.1.4.1 60657 1gvoA 364 3.13e+01 c.1.4.1 76357 3hhrB 203 3.16e+01 1axiB b.1.2.1 22005 b.1.2.1 22006 1e1hA 287 3.17e+01 d.92.1.7 83167 1vyrA 364 3.18e+01 1tfr 305 3.19e+01 1tfr a.60.7.1 18081 c.120.1.2 33351 1ihrA 76 3.27e+01 1ihrA d.212.1.2 62392 1ho8A 480 3.29e+01 1ho8A a.118.1.9 61107 1lmzA 187 3.30e+01 a.96.1.4 74037 1csh 435 3.30e+01 1csh a.103.1.1 18880 1ddgA 374 3.39e+01 1amoA b.43.4.1 25671 c.25.1.4 31559 1j7dA 145 3.40e+01 1jatB d.20.1.1 62680 2rmcA 182 3.42e+01 2cpl b.62.1.1 27491 1ha3A 405 3.43e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1h0pA 182 3.50e+01 b.62.1.1 76450 1p0yA 444 3.59e+01 a.166.1.1 87654 b.85.7.3 87655 1qqrA 138 3.59e+01 1bmlC d.15.5.1 37721 1o04A 500 3.68e+01 c.82.1.1 86508 1ub0A 258 3.68e+01 c.72.1.2 88394 1kit 757 3.70e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1pfvA 551 3.72e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1f4lA 551 3.74e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1nox 205 3.78e+01 1nox d.90.1.1 40242 1io7A 368 3.78e+01 1f4tA a.104.1.1 18971 1ku1A 230 3.81e+01 a.118.3.1 72996 1lb2B 84 3.81e+01 a.60.3.1 77871 1fp2A 352 3.81e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 1ry6A 360 3.83e+01 c.37.1.9 -7111 1ma3A 253 3.88e+01 c.31.1.5 78883 1f8gA 384 3.90e+01 1sayA c.2.1.4 59695 c.23.12.2 59696 1r4vA 171 3.96e+01 unknown_sccs -1221 1h4uA 265 3.98e+01 1h4uA d.22.1.2 60622 g.3.11.5 60623 1gutA 68 3.99e+01 b.40.6.1 65576