# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1oqcA 125 7.62e-24 a.24.15.1 87264 1jraA 117 3.88e-21 a.24.15.1 67117 1jr8A 117 4.34e-21 a.24.15.1 67115 1iwhA 141 8.14e-02 a.1.1.2 76882 1euvA 221 8.62e-02 1euvA d.3.1.7 37133 1ku1A 230 9.15e-02 a.118.3.1 72996 1myf 153 9.61e-02 1a6m a.1.1.2 15147 1fxxA 482 2.00e-01 1fxxA c.55.3.5 33726 1pbwA 216 2.45e-01 1pbwA a.116.1.1 19103 1dwtA 153 3.16e-01 1a6m a.1.1.2 15190 1cviA 342 3.71e-01 1cviA c.60.1.2 33989 1mbd 153 3.80e-01 1a6m a.1.1.2 15033 1irdA 141 3.93e-01 a.1.1.2 66286 1eyvA 156 3.99e-01 1eyvA a.79.1.1 18446 1nd6A 354 4.14e-01 c.60.1.2 80407 1rpa 342 4.15e-01 1cviA c.60.1.2 33983 2hpaA 342 4.17e-01 1cviA c.60.1.2 33985 1gjnA 153 4.26e-01 a.1.1.2 70191 1cg5B 141 4.76e-01 1cg5B a.1.1.2 15585 2spo 154 4.87e-01 1a6m a.1.1.2 15053 1babA 143 5.59e-01 1abwA a.1.1.2 15235 1ngvA 534 5.60e-01 c.111.1.2 85698 1ciy 590 5.77e-01 1ciy b.18.1.3 23720 b.77.2.1 27977 f.1.3.1 43392 1mgn 154 5.91e-01 1a6m a.1.1.2 15097 1p8cA 145 5.95e-01 1abwA 283 6.81e-01 1abwA a.1.1.2 15288 a.1.1.2 15289 1bzpA 153 6.93e-01 1a6m a.1.1.2 15020 3erdA 261 7.23e-01 3erdA a.123.1.1 19293 1g8lA 411 7.37e-01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1mlwA 301 8.58e-01 d.178.1.1 79289 1gkxA 388 8.76e-01 a.29.5.1 65266 d.122.1.4 65267 1j7yA 141 8.94e-01 a.1.1.2 66426 1a6m 151 9.55e-01 1a6m a.1.1.2 15018 1b9dA 163 1.01e+00 1b9dA c.55.3.2 33649 1rcb 129 1.01e+00 1rcb a.26.1.2 16854 1hyvA 166 1.07e+00 1b9dA c.55.3.2 61424 1hziA 129 1.13e+00 1rcb a.26.1.2 61449 1b75A 94 1.15e+00 1dfuP b.53.1.1 26937 1l2iA 261 1.18e+00 a.123.1.1 73503 1fgyA 127 1.45e+00 1faoA b.55.1.1 26976 1g4yR 148 1.52e+00 1cll a.39.1.5 60252 1c4zA 358 1.75e+00 1c4zA d.148.1.1 41766 2int 129 1.95e+00 1rcb a.26.1.2 16855 1hzfA 367 1.98e+00 a.102.4.4 76731 1jf3A 147 2.14e+00 a.1.1.2 71642 1it2A 146 2.22e+00 a.1.1.2 66365 1nubA 229 2.81e+00 1sra a.39.1.3 17191 g.3.11.3 44330 g.15.1.1 44715 1spgA 144 3.00e+00 1abwA a.1.1.2 15409 1vreA 147 3.01e+00 2hbg a.1.1.2 15017 1ll7A 392 3.04e+00 c.1.8.5 78085 d.26.3.1 78086 1d2kA 392 3.17e+00 1d2kA c.1.8.5 29008 d.26.3.1 38442 1g8iA 190 3.23e+00 1rec a.39.1.5 60363 1jf8A 131 3.24e+00 c.44.1.1 66621 1bl3A 160 3.32e+00 1b9dA c.55.3.2 33655 1lriA 98 3.39e+00 a.134.1.1 74223 1itm 130 3.43e+00 1rcb a.26.1.2 16858 1bxm 99 3.57e+00 1bxm a.134.1.1 19618 1kb9C 385 3.84e+00 f.32.1.1 77315 f.21.1.2 77316 1bbn 133 4.03e+00 1rcb a.26.1.2 16861 1jf4A 147 4.13e+00 a.1.1.2 71643 1l7vC 249 4.16e+00 c.37.1.12 73674 1ld8B 437 4.19e+00 a.102.4.3 73839 1ft1B 437 4.35e+00 1ft1B a.102.4.3 18867 1itg 166 4.44e+00 1b9dA c.55.3.2 33661 1o1fC 147 4.55e+00 i.15.1.1 80997 1ezvC 385 4.59e+00 1be3C f.32.1.1 75833 f.21.1.2 75834 1isaA 192 5.07e+00 1avmA a.2.11.1 15731 d.44.1.1 38724 1pn1A 176 5.17e+00 1jwgA 147 5.34e+00 a.118.9.2 71911 1cc8A 73 5.59e+00 1cc8A d.58.17.1 39343 1bp7A 152 5.63e+00 1bp7A d.95.2.1 40568 1iscA 192 5.66e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 2sas 185 5.79e+00 2sas a.39.1.5 17258 1dgnA 89 5.99e+00 1dgnA a.77.1.3 18436 1fd8A 73 6.03e+00 1cc8A d.58.17.1 59770 1jcrB 437 6.26e+00 a.102.4.3 66507 2hbg 147 6.29e+00 2hbg a.1.1.2 15014 1gkzA 388 6.37e+00 a.29.5.1 65268 d.122.1.4 65269 1je8A 82 6.40e+00 a.4.6.2 77108 1beg 98 6.53e+00 1bxm a.134.1.1 19620 1fjgD 209 6.80e+00 1c05A d.66.1.2 39553 1gcvB 136 7.33e+00 1cg5B a.1.1.2 15589 1auiB 169 7.74e+00 1auiB a.39.1.5 17325 1khbA 625 7.98e+00 c.91.1.1 68606 c.109.1.1 68607 1n40A 396 8.12e+00 a.104.1.1 79977 1qm9A 198 8.37e+00 1qm9A d.58.7.1 39207 d.58.7.1 39208 1ljrA 244 8.87e+00 1ljrA a.45.1.1 17707 c.47.1.5 33001 1jfvA 131 9.30e+00 c.44.1.1 66654 1k4wA 252 9.55e+00 a.123.1.1 72068 1qghA 156 9.90e+00 1qghA a.25.1.1 16728 1ile 821 1.00e+01 1ile a.27.1.1 16924 b.51.1.1 26889 c.26.1.1 31591 1fazA 122 1.01e+01 1fazA a.133.1.3 59757 1lm8B 118 1.01e+01 d.15.1.1 74033 1nv8A 284 1.01e+01 c.66.1.30 86224 1beo 98 1.01e+01 1bxm a.134.1.1 19619 1hbg 147 1.03e+01 2hbg a.1.1.2 15015 2pvaA 345 1.03e+01 3pvaA d.153.1.3 41850 1i5nA 146 1.03e+01 1i5nA a.24.10.3 61805 1mznA 240 1.05e+01 a.123.1.1 79704 3ertA 261 1.07e+01 3erdA a.123.1.1 19292 1kncA 177 1.07e+01 a.152.1.1 68703 1iygA 133 1.07e+01 a.118.8.1 76947 1d8dB 437 1.12e+01 1ft1B a.102.4.3 18866 1j78A 458 1.12e+01 a.126.1.1 66397 a.126.1.1 66398 a.126.1.1 66399 1gu9A 177 1.14e+01 a.152.1.1 65540 1em2A 229 1.21e+01 1em2A d.129.3.2 41321 1kv9A 668 1.22e+01 a.3.1.6 73056 b.70.1.1 73057 1dceA 567 1.22e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 2cblA 305 1.28e+01 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1aueA 100 1.29e+01 1nsgB a.24.7.1 16615 3nodB 423 1.29e+01 1nseA d.174.1.1 42513 1bbhA 131 1.34e+01 1bbhA a.24.3.2 16546 1gs9A 165 1.40e+01 a.24.1.1 83313 1kyoD 248 1.40e+01 a.3.1.3 73254 f.23.11.1 73255 1hqvA 191 1.41e+01 1hqvA a.39.1.8 61160 1lwbA 122 1.43e+01 a.133.1.3 84728 1r2fA 319 1.44e+01 1r2fA a.25.1.2 16800 1dxrC 336 1.46e+01 6prcC a.138.1.2 19670 1j0mA 752 1.51e+01 a.102.3.2 83910 b.24.1.1 83911 b.30.5.2 83912 1fm2A 169 1.52e+01 1fm2A d.153.1.2 59877 1toh 343 1.52e+01 4pah d.178.1.1 42573 3crd 100 1.52e+01 3crd a.77.1.3 18429 1a8s 273 1.52e+01 1brt c.69.1.12 34710 1i3dA 146 1.56e+01 a.1.1.2 61587 3lynA 136 1.57e+01 1lis a.19.1.1 16413 1jr3A 373 1.60e+01 a.80.1.1 63245 c.37.1.20 63246 1a0fA 201 1.63e+01 1a0fA a.45.1.1 17737 c.47.1.5 33031 1prcC 336 1.65e+01 6prcC a.138.1.2 19674 1lpe 144 1.65e+01 1nfn a.24.1.1 16524 1oxjA 173 1.66e+01 a.60.1.2 87517 a.118.1.13 87518 1iapA 211 1.66e+01 a.91.1.1 62119 1lc0A 294 1.67e+01 c.2.1.3 73823 d.81.1.4 73824 1osa 148 1.71e+01 1cll a.39.1.5 17300 6prcC 336 1.75e+01 6prcC a.138.1.2 19671 1j77A 209 1.75e+01 1j77A a.132.1.2 62674 1kwgA 645 1.76e+01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1en7A 157 1.77e+01 1en7A a.140.4.1 64733 d.4.1.5 64734 1lki 180 1.78e+01 1lki a.26.1.1 16829 1e7lA 157 1.78e+01 1en7A a.140.4.1 64728 d.4.1.5 64729 1qsdA 106 1.81e+01 1qsdA a.7.5.1 16335 1ezvD 245 1.82e+01 1be3D a.3.1.3 59546 f.23.11.1 59547 1eh8A 207 1.82e+01 1sfe a.4.2.1 16077 c.55.7.1 33752 1f0lA 535 1.84e+01 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1kwkA 645 1.84e+01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1gotG 73 1.85e+01 1tbgE a.137.3.1 19629 1ggzA 148 1.86e+01 a.39.1.5 70176 1pov1 302 1.91e+01 1pov1 1rec 201 1.93e+01 1rec a.39.1.5 17326 1mhqA 148 1.95e+01 a.118.9.2 84973 1f2rI 100 1.95e+01 1c9fA d.15.2.1 37641 1b3uA 588 1.95e+01 1b3uA a.118.1.2 19135 1fit 147 2.02e+01 1fit d.13.1.1 37499 1gcuA 295 2.03e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1pa1A 310 2.03e+01 1pq9A 253 2.04e+01 1kxpD 458 2.06e+01 a.126.1.1 73160 a.126.1.1 73161 a.126.1.1 73162 1qgtA 149 2.09e+01 1qgtA a.62.1.1 18135 1mai 131 2.09e+01 1mai b.55.1.1 26951 1om4A 422 2.12e+01 d.174.1.1 87067 1n1fA 159 2.16e+01 a.26.1.3 79803 3pvaA 335 2.23e+01 3pvaA d.153.1.3 41854 1kvkA 395 2.24e+01 d.14.1.5 73060 d.58.26.3 73061 2itg 163 2.26e+01 1b9dA c.55.3.2 33669 1kb9D 246 2.29e+01 a.3.1.3 77317 f.23.11.1 77318 1ijgA 309 2.30e+01 1fouA e.27.1.1 62493 1tbgE 68 2.33e+01 1tbgE a.137.3.1 19630 1mvcA 240 2.36e+01 a.123.1.1 79499 1cqxA 403 2.37e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1d8hA 311 2.38e+01 1d8iA d.63.1.1 39544 7catA 506 2.40e+01 1cf9A e.5.1.1 42781 1jtkA 136 2.44e+01 c.97.1.1 71862 1kf6D 119 2.45e+01 f.21.2.2 72400 1jwiB 125 2.46e+01 d.169.1.1 67384 1exqA 154 2.46e+01 1b9dA c.55.3.2 33646 1i4yA 114 2.48e+01 2mhr a.24.4.1 61738 1ltzA 297 2.52e+01 d.178.1.1 74254 1j5sA 463 2.53e+01 c.1.9.8 71580 1dfuP 94 2.53e+01 1dfuP b.53.1.1 26936 1dghB 498 2.54e+01 1cf9A e.5.1.1 42791 1b47A 304 2.56e+01 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 1mzm 93 2.56e+01 1rzl a.52.1.1 17814 1ft1A 377 2.60e+01 1ft1A a.118.6.1 19186 1nrlA 316 2.61e+01 1aa7A 158 2.65e+01 1aa7A a.95.1.1 18741 1jcrA 377 2.65e+01 a.118.6.1 66506 1ed5A 444 2.66e+01 1nseA d.174.1.1 42530 1iloA 77 2.68e+01 c.47.1.1 66205 1gh9A 71 2.70e+01 1gh9A g.41.6.1 45266 1q8yA 373 2.73e+01 1n9lA 109 2.73e+01 d.110.3.6 85468 1kyoC 385 2.76e+01 f.32.1.1 75904 f.21.1.2 75905 1l5xA 280 2.79e+01 c.106.1.1 77718 1dc1A 323 2.80e+01 1dc1A c.52.1.11 33321 3cyr 107 2.83e+01 3cyr a.138.1.1 19648 2lhb 149 2.85e+01 2fal a.1.1.2 15597 1e4uA 78 2.86e+01 1e4uA g.44.1.1 59231 1g291 372 2.90e+01 1g291 1f16A 192 2.92e+01 1f16A f.1.4.1 43400 1fehA 574 2.95e+01 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1jkmA 358 2.99e+01 1jkmA c.69.1.2 34633 1cqeA 580 3.00e+01 1cqeA a.93.1.2 18703 g.3.11.1 44246 1dguA 183 3.02e+01 1dguA a.39.1.5 17333 1is2A 661 3.05e+01 a.29.3.2 71382 a.29.3.2 71383 e.6.1.2 71384 1ge9A 184 3.06e+01 1dd5A d.67.3.1 60463 1ddt 535 3.08e+01 1ddt b.2.1.1 22379 d.166.1.1 42241 f.1.2.1 43384 1dn1B 267 3.13e+01 1dn1B a.47.2.1 17771 1f83A 425 3.17e+01 1f82A d.92.1.7 40306 1qovH 260 3.19e+01 6prcH b.41.1.1 25464 f.23.10.1 43457 1ak1 310 3.19e+01 1ak1 c.92.1.1 35594 1kyqA 274 3.19e+01 c.2.1.11 73281 e.37.1.1 73282 1cg5A 141 3.20e+01 1abwA a.1.1.2 15406 1mat 264 3.22e+01 1c24A d.127.1.1 41152 1g4wR 383 3.23e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1hn0A 1021 3.24e+01 a.102.3.2 83616 b.18.1.17 83617 b.24.1.1 83618 b.30.5.2 83619 3caoA 103 3.24e+01 3caoA a.138.1.1 19661 1b68A 191 3.28e+01 1nfn a.24.1.1 59076 1jjfA 268 3.31e+01 c.69.1.2 66765 1nxmA 197 3.34e+01 b.82.1.1 86385 1dliA 402 3.39e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1sw6A 327 3.46e+01 1sw6A d.211.1.1 19176 1jpc 109 3.47e+01 1b2pA b.78.1.1 27986 1idrA 136 3.48e+01 1dlyA a.1.1.1 62301 1co6A 107 3.49e+01 1ycc a.3.1.1 15894 2hts 88 3.49e+01 2hts a.4.5.22 16174 1ay2 159 3.50e+01 2pil d.24.1.1 38377 1fk5A 93 3.56e+01 1rzl a.52.1.1 59866 1bk7A 190 3.59e+01 1bk7A d.124.1.1 41121 1dxrL 273 3.63e+01 6prcL f.26.1.1 43431 1hs7A 97 3.67e+01 1hs7A a.47.2.1 61236 1dgfA 497 3.67e+01 1cf9A e.5.1.1 42782 1msaA 109 3.71e+01 1b2pA b.78.1.1 27987 1i4wA 353 3.72e+01 c.66.1.24 66028 1oqvA 192 3.75e+01 d.24.1.2 87320 1nstA 325 3.76e+01 1nstA c.37.1.5 31951 1l3lA 234 3.77e+01 a.4.6.2 73541 d.110.5.1 73542 1j8uA 325 3.77e+01 d.178.1.1 71611 1kkhA 317 3.78e+01 d.14.1.5 72645 d.58.26.3 72646 1j3bA 529 3.78e+01 c.91.1.1 77071 c.109.1.1 77072 1bz4A 144 3.79e+01 1nfn a.24.1.1 16521 1cll 148 3.81e+01 1cll a.39.1.5 17263 1q59A 172 3.83e+01 1ntcA 91 3.83e+01 1ntcA a.105.1.1 19004 4rxn 54 3.83e+01 1rb9 g.41.5.1 45226 1d1vA 444 3.83e+01 1nseA d.174.1.1 59101 1howA 373 3.83e+01 1hcl d.144.1.7 41679 1ngkA 128 3.90e+01 a.1.1.1 85673 1f82A 424 3.90e+01 1f82A d.92.1.7 40307 1d8iA 311 3.91e+01 1d8iA d.63.1.1 39541 1aipE 405 3.95e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1dozA 309 3.95e+01 1ak1 c.92.1.1 35592