# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1gdgA 293 7.06e-05 1kw3B 292 2.10e-04 d.32.1.3 77549 d.32.1.3 77550 1dhy 292 2.70e-04 1han d.32.1.3 38504 d.32.1.3 38505 1han 297 1.03e-03 1han d.32.1.3 38506 d.32.1.3 38507 1lkdA 297 1.39e-03 d.32.1.3 78059 d.32.1.3 78060 1lgtA 297 5.44e-03 d.32.1.3 77956 d.32.1.3 77957 1fa8A 135 1.61e-02 1qipA d.32.1.1 38486 1f9zA 135 1.73e-02 1qipA d.32.1.1 38484 1kllA 130 2.91e-02 d.32.1.2 72720 1jc4A 148 6.72e-02 1jc4A d.32.1.4 62863 1i9gA 280 7.65e-01 c.66.1.13 62090 7aatA 401 9.68e-01 1ajsA c.67.1.1 34250 1q1gA 276 1.10e+00 c.56.2.1 -7846 1skyE 473 1.86e+00 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1obpA 159 2.07e+00 1obpA b.60.1.1 27092 1gt1A 159 2.08e+00 b.60.1.1 -4436 1hn2A 159 2.08e+00 b.60.1.1 65890 2dynA 122 2.17e+00 1dynA b.55.1.1 26957 1bh5A 183 2.20e+00 1qipA d.32.1.1 38476 1dynA 125 2.24e+00 1dynA b.55.1.1 26955 1h8eD 482 2.38e+00 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1qqgA 264 2.73e+00 1qqgA b.55.1.2 26987 b.55.1.2 26988 1q16B 512 3.13e+00 d.58.1.5 -9938 1gkuB 1054 3.28e+00 c.37.1.16 65257 c.37.1.16 65258 e.10.1.1 65259 1f1uA 323 3.76e+00 d.32.1.3 83200 d.32.1.3 83201 1kyqA 274 4.03e+00 c.2.1.11 73281 e.37.1.1 73282 1k0gA 453 4.25e+00 d.161.1.1 67940 1vk3A 615 4.54e+00 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1e79D 482 4.65e+00 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1a8a 318 4.77e+00 1avc a.65.1.1 18169 1k0eA 453 4.79e+00 d.161.1.1 67938 1dxeA 256 4.90e+00 1dxeA c.1.12.5 29310 2ran 316 4.97e+00 1avc a.65.1.1 18170 1a8b 318 5.12e+00 1avc a.65.1.1 18171 1eg7A 557 5.17e+00 1eg7A c.37.1.10 32241 8ohm 435 5.22e+00 1heiA c.37.1.14 32469 c.37.1.14 32470 3fruA 269 5.42e+00 1agdA b.1.1.2 20657 d.19.1.1 38150 1h6zA 913 6.01e+00 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 1a8p 258 6.20e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 1eazA 125 6.39e+00 b.55.1.1 70113 1bykA 255 6.58e+00 1bykA c.93.1.1 35706 1v61A 132 6.63e+00 1anxA 319 6.68e+00 1avc a.65.1.1 18161 1o0wA 252 7.03e+00 a.149.1.1 80751 d.50.1.1 80752 1dkuA 317 7.24e+00 1dkuA c.61.1.2 34118 c.61.1.2 34119 1qipA 183 8.38e+00 1qipA d.32.1.1 38470 1ibsA 317 8.39e+00 c.61.1.2 66107 c.61.1.2 66108 1ftrA 296 8.51e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1brmA 367 8.65e+00 1brmA c.2.1.3 30030 d.81.1.1 39945 1tmcA 175 9.09e+00 1agdA d.19.1.1 38258 1dkrA 317 9.09e+00 1dkuA c.61.1.2 34114 c.61.1.2 34115 1j5pA 253 9.37e+00 c.2.1.3 83092 d.81.1.3 71577 1j5yA 187 9.70e+00 a.4.5.1 71592 d.94.2.1 71593 1lrzA 426 9.87e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1jr3A 373 9.97e+00 a.80.1.1 63245 c.37.1.20 63246 1q9uA 130 1.02e+01 unknown_sccs -11025 1hsbA 270 1.10e+01 1agdA b.1.1.2 20736 d.19.1.1 38257 1faoA 126 1.14e+01 1faoA b.55.1.1 26974 1nxzA 246 1.18e+01 b.122.1.2 86391 c.116.1.5 86392 1jotA 133 1.22e+01 1jotA 1eggA 147 1.22e+01 1eggA d.169.1.1 42333 1ge9A 184 1.23e+01 1dd5A d.67.3.1 60463 1kjvA 284 1.26e+01 b.1.1.2 77421 d.19.1.1 77422 1f6bA 198 1.27e+01 c.37.1.8 64986 1pbn 289 1.37e+01 1b8oA c.56.2.1 33771 1ogiA 303 1.38e+01 b.43.4.2 -4042 c.25.1.1 -6587 1uwzA 136 1.40e+01 1egiA 147 1.43e+01 1eggA d.169.1.1 42331 1btn 106 1.44e+01 1btn b.55.1.1 26952 1jtkA 136 1.47e+01 c.97.1.1 71862 1nzoA 363 1.47e+01 b.105.1.1 -2933 e.3.1.1 -11784 1i9yA 347 1.49e+01 1i9yA d.151.1.2 62101 1t4bA 367 1.50e+01 1i9zA 347 1.51e+01 1i9yA d.151.1.2 62102 1mpyA 307 1.54e+01 1mpyA d.32.1.3 38508 d.32.1.3 38509 1kwnA 207 1.56e+01 b.25.1.1 77568 1af5 126 1.57e+01 1bp7A d.95.2.1 40572 1vknA 351 1.57e+01 1amoA 615 1.58e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1f1xA 322 1.58e+01 d.32.1.3 83208 d.32.1.3 83209 1uxy 340 1.58e+01 2mbr d.145.1.2 41748 d.146.1.1 41761 1q7bA 244 1.63e+01 c.2.1.2 -5826 1go2A 304 1.64e+01 b.43.4.2 76243 c.25.1.1 76244 1em8A 147 1.67e+01 unknown_sccs -7272 1b2rA 304 1.68e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1b4bA 71 1.69e+01 1b4aA d.74.2.1 39718 1oboA 169 1.70e+01 c.23.5.1 86776 1skyB 502 1.72e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1f0iA 504 1.73e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 1jn5A 140 1.77e+01 d.17.4.2 66921 1rqwA 207 1.77e+01 b.25.1.1 -3313 2mbr 340 1.77e+01 2mbr d.145.1.2 41749 d.146.1.1 41762 1s96A 219 1.77e+01 c.37.1.1 -6972 1thw 207 1.78e+01 1thv b.25.1.1 23903 1v0wA 506 1.80e+01 1dc1A 323 1.82e+01 1dc1A c.52.1.11 33321 1v9kA 228 1.82e+01 1hd8A 363 1.82e+01 b.105.1.1 65803 e.3.1.1 65804 1nj4A 363 1.85e+01 b.105.1.1 80545 e.3.1.1 80546 1lqpA 135 1.86e+01 d.32.1.2 78151 1nkiA 135 1.86e+01 d.32.1.2 -9544 1iv0A 98 1.89e+01 unknown_sccs -7667 1heiA 451 1.94e+01 1heiA c.37.1.14 32463 c.37.1.14 32464 1rcf 169 1.96e+01 1rcf c.23.5.1 31170 1ihkA 174 1.97e+01 1bfg b.42.1.1 62384 1dik 874 1.99e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1que 303 2.05e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 3pnp 289 2.06e+01 1b8oA c.56.2.1 33763 1g9zA 152 2.11e+01 1bp7A d.95.2.1 60408 1cwwA 102 2.11e+01 1cy5A a.77.1.3 18434 1ltqA 301 2.14e+01 c.108.1.9 78208 c.37.1.1 78209 1draA 159 2.15e+01 1vdrA c.71.1.1 34831 1mi0A 65 2.18e+01 d.15.7.1 79135 1b8oA 284 2.18e+01 1b8oA c.56.2.1 33762 1thv 207 2.19e+01 1thv b.25.1.1 23904 1fxoA 293 2.21e+01 1g0rA c.68.1.6 34524 1qgvA 142 2.26e+01 1qgvA c.47.1.8 33056 1tml 286 2.29e+01 1tml c.6.1.1 30656 1jacA 133 2.30e+01 1jotA 1fukA 165 2.34e+01 1fukA c.37.1.19 32409 1jacC 133 2.38e+01 1jotA 1m26A 133 2.38e+01 1awqA 164 2.38e+01 2cpl b.62.1.1 27461 1q8iA 783 2.38e+01 c.55.3.5 -7635 e.8.1.1 -11885 1ugxA 133 2.40e+01 1b4aA 149 2.42e+01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1ku8A 133 2.46e+01 1hvd 319 2.51e+01 1avc a.65.1.1 18154 1vhyA 257 2.51e+01 b.122.1.2 -5129 c.116.1.5 -6705 1cwoA 165 2.52e+01 2cpl b.62.1.1 27445 1khdA 345 2.55e+01 a.46.2.1 77400 c.27.1.1 77401 1bp7A 152 2.56e+01 1bp7A d.95.2.1 40568 1nnmA 652 2.56e+01 1pg4A 652 2.56e+01 e.23.1.1 88067 1t6uA 117 2.57e+01 1ckv 141 2.57e+01 1ckv d.137.1.1 41452 1jy1A 464 2.59e+01 d.136.1.3 67438 d.136.1.3 67439 1ja1A 622 2.62e+01 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 2cpl 165 2.64e+01 2cpl b.62.1.1 27420 1sty 150 2.66e+01 1snc b.40.1.1 24812 1vmoA 163 2.68e+01 1vmoA b.77.1.1 27974 1agdA 276 2.84e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 1qh0A 295 2.84e+01 b.43.4.2 68891 c.25.1.1 68892 2wsyA 268 2.87e+01 2tysA c.1.2.4 28588 1havA 217 2.94e+01 1havA b.47.1.4 26423 1hkeA 137 2.97e+01 1qd9A 124 2.99e+01 1qu9A d.79.1.1 39758 1mu7A 485 3.06e+01 d.136.1.3 79475 d.136.1.3 79476 1uuzA 137 3.09e+01 d.233.1.1 -9478 1uw4A 91 3.11e+01 unknown_sccs -10038 1a6dA 545 3.11e+01 1a6dA a.129.1.2 19488 c.8.5.2 30819 d.56.1.2 38936 1b5tA 275 3.13e+01 1b5tA c.1.23.1 29676 1pz7A 204 3.14e+01 b.29.1.4 -3439 1p1lA 102 3.15e+01 d.58.5.2 87695 1lc0A 294 3.18e+01 c.2.1.3 73823 d.81.1.4 73824 1pms 136 3.18e+01 1awe b.55.1.1 26966 1snc 149 3.19e+01 1snc b.40.1.1 24813 1bak 119 3.23e+01 1bak b.55.1.1 26973 1pj5A 830 3.30e+01 unknown_sccs -4066 c.3.1.2 -6031 d.16.1.5 -9251 unknown_sccs -10171 6dfr 159 3.31e+01 1vdrA c.71.1.1 34874 1duzA 275 3.33e+01 1agdA b.1.1.2 20670 d.19.1.1 38224 1i4fA 275 3.33e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1ii6A 368 3.33e+01 1bg2 c.37.1.9 62413 1k3bA 119 3.34e+01 b.61.5.1 72016 1jkgA 140 3.36e+01 d.17.4.2 66795 1r9cA 139 3.50e+01 d.32.1.2 -9557 2ygsA 92 3.50e+01 1cy5A a.77.1.3 18431 1ue1A 164 3.52e+01 b.40.4.3 -3905 1go3F 107 3.52e+01 a.60.8.2 65407 1fxlA 167 3.59e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1ex2A 189 3.60e+01 1ex2A c.51.4.2 33225 1nkqA 259 3.61e+01 1uslA 170 3.62e+01 c.121.1.1 -6682 1aisA 182 3.64e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1kblA 873 3.64e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1mu5A 471 3.75e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1jmoA 480 3.76e+01 e.1.1.1 77138 1p27B 106 3.78e+01 d.58.7.1 -10020 1k66A 149 3.78e+01 c.23.1.1 -6406 1g2iA 166 3.79e+01 1g2iA c.23.16.2 31438 1uch 230 3.79e+01 1uch d.3.1.6 37129 1dat 174 3.80e+01 2fha a.25.1.1 16677 1rxxA 421 3.80e+01 unknown_sccs -10982 1hyvA 166 3.81e+01 1b9dA c.55.3.2 61424 1yagA 375 3.84e+01 1yagA c.55.1.1 33449 c.55.1.1 33450 1ur3M 319 3.86e+01 c.1.7.1 -5248 1dssG 333 3.89e+01 1dssG c.2.1.3 30022 d.81.1.1 39937 1utwA 432 3.91e+01 1uypA 432 3.92e+01 unknown_sccs -3480 unknown_sccs -4554 1k5nA 276 3.97e+01 b.1.1.2 77266 d.19.1.1 77267 1p5hA 428 3.99e+01 c.123.1.1 87802 1oywA 523 3.99e+01 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210