# 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 1mhyG 169 5.92e-02 1mtyG a.23.3.1 16518 1fqvD 149 9.26e-02 1fqvD a.157.1.1 19263 d.42.1.1 38667 1fqvJ 149 1.64e-01 1fqvD a.157.1.1 19266 d.42.1.1 38670 1v2yA 105 1.72e-01 1rtwA 220 2.29e-01 1jchC 551 3.18e-01 b.101.1.1 66495 b.110.1.1 66496 h.4.9.1 66497 1jchA 551 3.21e-01 b.101.1.1 66491 b.110.1.1 66492 h.4.9.1 66493 1or7A 194 3.39e-01 a.4.13.2 87332 a.177.1.1 87333 1i5nA 146 5.41e-01 1i5nA a.24.10.3 61805 1jqjC 343 8.16e-01 a.80.1.1 67097 c.37.1.20 67098 1colA 204 1.10e+00 1a87 f.1.1.1 43378 1n2aA 201 1.10e+00 1f5sA 211 1.29e+00 1f5sA c.108.1.4 59656 1ohuA 175 1.34e+00 1axdA 209 1.35e+00 1gnwA a.45.1.1 17730 c.47.1.5 33024 1o4sA 389 1.42e+00 c.67.1.1 86620 1l7mA 211 1.48e+00 c.108.1.4 73664 1fs1B 141 1.60e+00 1vcbB a.157.1.1 19252 d.42.1.1 38664 1vasA 137 1.71e+00 2end a.18.1.1 16404 1ois 223 1.73e+00 1a36A e.15.1.1 43267 1j97A 211 1.87e+00 1f5sA c.108.1.4 62753 1g59A 468 2.00e+00 a.97.1.1 60257 c.26.1.1 60258 1izcA 339 2.02e+00 c.1.12.5 83838 1ouvA 273 2.21e+00 1xfiA 367 2.27e+00 1vg0A 650 2.33e+00 1klo 162 2.33e+00 1klo g.3.11.2 44326 g.3.11.2 44327 g.3.11.2 44328 1eemA 241 2.67e+00 1eemA a.45.1.1 17717 c.47.1.5 33011 1qgdA 662 2.70e+00 c.36.1.6 88367 c.36.1.10 88368 c.48.1.1 88369 1hlvA 131 3.01e+00 a.4.1.7 65854 a.4.1.7 65855 1ig6A 107 3.29e+00 1ig6A a.4.3.1 62364 1jigA 146 3.59e+00 a.25.1.1 71685 1l8yA 91 3.65e+00 a.21.1.1 73708 2hmx 133 3.77e+00 1hiwA a.61.1.1 18129 1s9pA 227 3.88e+00 2end 138 3.98e+00 2end a.18.1.1 16400 1twfF 155 3.98e+00 1riqA 465 3.99e+00 1eia 207 4.43e+00 1eia a.28.3.1 16951 a.73.1.1 18331 2eiaB 206 4.46e+00 1eia a.28.3.1 16950 a.73.1.1 18330 1rzhL 281 4.66e+00 1i50F 155 4.73e+00 d.78.1.2 61760 1dj8A 89 4.79e+00 1bg8A a.57.1.1 17919 1mtyG 162 4.84e+00 1mtyG a.23.3.1 16498 1h99A 224 4.91e+00 a.142.1.1 60814 a.142.1.1 60815 1abv 134 4.94e+00 1abv a.70.1.1 18317 1w36C 1122 5.00e+00 1mmoG 162 5.15e+00 1mtyG a.23.3.1 16512 1deoA 233 5.30e+00 1deoA c.23.10.4 31345 1pu6A 218 5.48e+00 6paxA 133 6.30e+00 6paxA a.4.1.5 64758 a.4.1.5 64759 1rthA 560 6.67e+00 1rthA c.55.3.1 33576 e.8.1.2 43028 1eysH 259 6.72e+00 6prcH b.41.1.1 25484 f.23.10.1 43517 1ew6A 137 6.98e+00 1ewaA a.1.1.2 15637 1ewaA 137 6.98e+00 1ewaA a.1.1.2 15639 1a87 321 7.09e+00 1a87 f.1.1.1 43380 1alvA 173 7.23e+00 1alvA a.39.1.8 17370 1csn 298 7.37e+00 1csn d.144.1.7 41664 1a0fA 201 7.46e+00 1a0fA a.45.1.1 17737 c.47.1.5 33031 1bed 181 7.59e+00 1fvkA a.44.1.1 17514 c.47.1.4 32808 1f4qA 165 7.72e+00 1alvA a.39.1.8 17360 1oe8A 211 7.73e+00 a.45.1.1 86905 c.47.1.5 86906 1jr3A 373 7.94e+00 a.80.1.1 63245 c.37.1.20 63246 1hiwA 133 8.02e+00 1hiwA a.61.1.1 18122 1r85A 379 8.09e+00 1ib8A 164 8.20e+00 b.38.2.1 71168 d.52.4.1 71169 1hh8A 213 8.21e+00 1e96B a.118.8.1 61042 1j09A 468 8.42e+00 a.97.1.1 77025 c.26.1.1 77026 1v95A 130 8.51e+00 1nnlA 225 8.84e+00 c.108.1.4 85906 1v74B 87 8.96e+00 1va6A 518 9.16e+00 1rh2F 165 9.52e+00 1rh2F a.26.1.3 16898 1hs7A 97 9.69e+00 1hs7A a.47.2.1 61236 1vj5A 555 1.01e+01 1dk8A 147 1.02e+01 1agrE a.91.1.1 18548 1k7cA 233 1.02e+01 c.23.10.4 68267 1dipA 78 1.04e+01 1dipA h.1.12.1 45632 1syyA 346 1.04e+01 1ihoA 283 1.05e+01 1ihoA c.26.1.4 62390 1lea 84 1.07e+01 1lea a.4.5.2 16085 1fseA 74 1.09e+01 1fseA a.4.6.2 60000 1p2xA 159 1.09e+01 1a4pA 96 1.11e+01 1b4cA a.39.1.2 17176 1lxjA 104 1.11e+01 d.58.48.1 84736 1aijL 281 1.13e+01 6prcL f.26.1.1 43461 1tn6A 382 1.15e+01 1mlwA 301 1.18e+01 d.178.1.1 79289 1q0pA 223 1.18e+01 1g8iA 190 1.19e+01 1rec a.39.1.5 60363 1hn4A 131 1.19e+01 a.133.1.2 65893 1om2A 95 1.21e+01 1om2A a.23.4.1 16520 1lnqA 336 1.22e+01 c.2.1.9 74049 f.14.1.1 74050 1cfr 285 1.22e+01 1cfr c.52.1.7 33312 1k94A 165 1.23e+01 a.39.1.8 68333 6prcM 323 1.24e+01 6prcM f.26.1.1 43435 1p8kZ 254 1.25e+01 1m1jA 491 1.25e+01 h.1.8.1 74369 1itf 165 1.25e+01 1b5l a.26.1.3 16899 1ko9A 345 1.28e+01 a.96.1.3 68717 d.129.1.2 68718 1dttA 560 1.29e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1dioA 554 1.29e+01 1dioA c.1.19.3 29656 1g5yA 238 1.30e+01 1lbd a.123.1.1 60294 1cwyA 500 1.31e+01 1cwyA c.1.8.1 28789 1wmuA 141 1.31e+01 1pah 308 1.32e+01 4pah d.178.1.1 42578 1e3oC 160 1.33e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 3icb 75 1.34e+01 4icb a.39.1.1 17147 1fhvA 323 1.37e+01 1fhuA c.1.11.2 29235 d.54.1.1 38879 1jr3D 343 1.38e+01 a.80.1.1 63251 c.37.1.20 63252 1eexA 554 1.39e+01 1dioA c.1.19.3 29650 1s3jA 155 1.42e+01 1bouA 139 1.44e+01 1bouA a.88.1.1 18521 1e44B 96 1.45e+01 1e44B b.101.1.1 59220 1r6wA 322 1.47e+01 2ptd 298 1.47e+01 2plc c.1.18.2 29605 1tbmA 326 1.50e+01 1bccD 241 1.52e+01 1be3D a.3.1.3 15959 f.23.11.1 43698 1e96B 203 1.53e+01 1e96B a.118.8.1 19211 1dxrM 323 1.55e+01 6prcM f.26.1.1 43432 1l6nA 289 1.56e+01 a.61.1.1 73624 a.73.1.1 73625 1hizA 379 1.56e+01 c.1.8.3 65841 1ew6B 137 1.57e+01 1ewaA a.1.1.2 15638 1iu4A 331 1.58e+01 d.3.1.8 71430 1eswA 500 1.58e+01 1cwyA c.1.8.1 59500 1j7yA 141 1.59e+01 a.1.1.2 66426 1k8eA 345 1.59e+01 1o17A 345 1.59e+01 a.46.2.1 80765 c.27.1.1 80766 1p5sA 203 1.61e+01 1wer 334 1.63e+01 1wer a.116.1.2 19108 1ubpA 101 1.77e+01 1ubpA d.8.1.1 37353 1c8gA 548 1.77e+01 2cas b.121.5.2 23380 1ejxA 100 1.80e+01 d.8.1.1 83182 2occE 109 1.84e+01 2occE a.118.11.1 19224 1e1hB 174 1.85e+01 1imuA 107 1.85e+01 d.204.1.1 66218 1ede 310 1.86e+01 1b6g c.69.1.8 34662 1hmcA 148 1.89e+01 1hmcB a.26.1.2 16867 1dmwA 307 1.89e+01 4pah d.178.1.1 42580 1j1qA 261 1.90e+01 4ubpA 101 1.90e+01 1ubpA d.8.1.1 37352 1kzhA 555 1.94e+01 c.89.1.1 73361 1j8uA 325 1.94e+01 d.178.1.1 71611 2hdhA 293 2.03e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1f0yA 302 2.04e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1moh 142 2.06e+01 1flp a.1.1.2 15012 1sr4A 206 2.07e+01 1b31A 302 2.11e+01 1taxA c.1.8.3 28892 1t3wA 148 2.11e+01 1uddA 226 2.13e+01 1w5tA 412 2.15e+01 1g65K 211 2.16e+01 d.153.1.4 41907 1v9mA 323 2.17e+01 1r5zA 323 2.19e+01 1p4dA 330 2.21e+01 1ah6 220 2.30e+01 1yer d.122.1.1 41094 1je8A 82 2.30e+01 a.4.6.2 77108 1s6cA 183 2.30e+01 1tbgE 68 2.31e+01 1tbgE a.137.3.1 19630 1aw9 216 2.37e+01 1gnwA a.45.1.1 17736 c.47.1.5 33030 1tqhA 247 2.40e+01 1rypL 212 2.40e+01 d.153.1.4 41880 2gsq 202 2.40e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1nr3A 122 2.41e+01 d.236.1.1 86092 1b6g 310 2.44e+01 1b6g c.69.1.8 34661 1u08A 386 2.45e+01 1ku3A 73 2.50e+01 a.4.13.2 73000 1bg4 302 2.51e+01 1taxA c.1.8.3 28806 1w53A 84 2.52e+01 1i37A 260 2.52e+01 1a28A a.123.1.1 61583 1n3lA 372 2.53e+01 c.26.1.1 79966 1ppjD 241 2.58e+01 1flp 142 2.61e+01 1flp a.1.1.2 15011 1r5qA 102 2.61e+01 1r9kA 172 2.61e+01 1k5hA 398 2.62e+01 a.69.3.1 68192 c.2.1.3 68193 d.81.1.3 68194 1b4uA 139 2.64e+01 1bouA a.88.1.1 18523 2kauA 100 2.66e+01 1ubpA d.8.1.1 37335 1pvc4 68 2.69e+01 1pvc4 1p0yA 444 2.69e+01 a.166.1.1 87654 b.85.7.3 87655 1jcqA 382 2.73e+01 a.118.6.1 66504 1griA 217 2.73e+01 1griA b.34.2.1 24531 b.34.2.1 24532 d.93.1.1 40473 1tq4A 413 2.75e+01 1jmsA 381 2.79e+01 a.60.6.1 66889 a.60.12.1 75862 d.218.1.2 75863 2bmhA 455 2.79e+01 1bu7A a.104.1.1 18941 1go3F 107 2.80e+01 a.60.8.2 65407 1har 216 2.84e+01 1rthA e.8.1.2 43025 1jj2I 145 2.86e+01 1ffkG c.21.1.1 63094 1mijA 152 2.91e+01 a.4.1.1 79150 2ng1 293 2.94e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1hqvA 191 2.94e+01 1hqvA a.39.1.8 61160 1fhuA 320 2.95e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1ekeA 230 2.95e+01 1ekeA c.55.3.1 33572 1m6yA 301 2.98e+01 a.60.13.1 78716 c.66.1.23 78717 1u5tB 169 3.01e+01 1babA 143 3.03e+01 1abwA a.1.1.2 15235 1gouA 116 3.04e+01 d.1.1.2 65429 1apa 266 3.05e+01 1qi7A d.165.1.1 42205 1qagA 226 3.06e+01 1qagA a.40.1.1 17400 a.40.1.1 17401 1gtmA 419 3.06e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1fftB 315 3.10e+01 1cyx b.6.1.2 23025 f.17.2.1 43628 1v3wA 173 3.10e+01 2abd 86 3.12e+01 1aca a.11.1.1 16366 1qbqA 333 3.12e+01 1ft1A a.118.6.1 19187 1jatB 138 3.17e+01 1jatB d.20.1.1 62819 1fwcA 100 3.18e+01 1ubpA d.8.1.1 37331 2lhb 149 3.18e+01 2fal a.1.1.2 15597 1ajqB 557 3.19e+01 1ajqB 3chy 128 3.19e+01 3chy c.23.1.1 31038 1gehA 444 3.22e+01 c.1.14.1 65181 d.58.9.1 65182 1v10A 521 3.23e+01 1e3pA 757 3.23e+01 1e3hA a.4.9.1 16258 b.40.4.5 25328 d.14.1.4 37574 d.14.1.4 37575 d.52.3.1 38811 d.101.1.1 40697 d.101.1.1 40698 2pgd 482 3.24e+01 2pgd a.100.1.1 18778 c.2.1.6 30190 1lwdA 413 3.30e+01 c.77.1.1 78265 1f46A 140 3.36e+01 1f46A d.129.4.1 59643 1jbeA 128 3.37e+01 3chy c.23.1.1 62845 4icb 76 3.39e+01 4icb a.39.1.1 17145 1qqeA 292 3.39e+01 1qqeA a.118.8.1 19210 1qkkA 155 3.41e+01 1dbwA c.23.1.1 31104 1ig5A 75 3.42e+01 4icb a.39.1.1 62363 1adjA 421 3.44e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1eysL 280 3.44e+01 6prcL f.26.1.1 43515 1ksfX 758 3.44e+01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1ng1 294 3.49e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1vfgA 390 3.49e+01 1a26 361 3.50e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1skyE 473 3.50e+01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1ld8A 382 3.52e+01 a.118.6.1 73838 1dgjA 907 3.55e+01 1alo a.56.1.1 17909 d.15.4.2 37694 d.41.1.1 38585 d.133.1.1 41415 1acf 125 3.56e+01 3nul d.110.1.1 40882 1hmcB 148 3.60e+01 1hmcB a.26.1.2 16868 1v4xA 144 3.61e+01 1ogsA 497 3.63e+01 b.71.1.2 86997 c.1.8.3 86998 1irdA 141 3.65e+01 a.1.1.2 66286 1mlvA 444 3.65e+01 a.166.1.1 79283 b.85.7.3 79284 1pmt 203 3.70e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1gln 468 3.70e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1iuqA 367 3.73e+01 1r1dA 247 3.77e+01 1dlyA 164 3.85e+01 1dlyA a.1.1.1 14983 1ls1A 295 3.90e+01 a.24.13.1 78170 c.37.1.10 78171 1hb6A 86 3.92e+01 a.11.1.1 70959 1qcrA 446 3.94e+01 1be3A d.185.1.1 59025 d.185.1.1 59026