# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-scores 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 1r5qA 102 5.74e-02 unknown_sccs -965 1moh 142 6.63e-02 1flp a.1.1.2 15012 1flp 142 9.69e-02 1flp a.1.1.2 15011 3sdhA 146 1.22e-01 3sdhA a.1.1.2 14984 1sctB 151 1.41e-01 3sdhA a.1.1.2 15003 1sxjE 354 1.52e-01 1b0b 142 3.29e-01 2fal a.1.1.2 15010 1jfiB 179 3.30e-01 1jfiB a.22.1.3 62937 1hz4A 373 3.43e-01 a.118.8.2 65960 1v9dA 340 4.68e-01 unknown_sccs -1762 1hiwA 133 4.75e-01 1hiwA a.61.1.1 18122 1iuqA 367 5.24e-01 c.112.1.1 -8440 1k30A 368 7.31e-01 c.112.1.1 68067 1or7A 194 7.41e-01 a.4.13.2 87332 a.177.1.1 87333 1mba 147 1.03e+00 2fal a.1.1.2 15149 1hekA 131 1.49e+00 a.61.1.5 65818 1v2zA 111 1.49e+00 2fal 147 1.83e+00 2fal a.1.1.2 15150 1m6nA 802 1.97e+00 a.162.1.1 78697 a.172.1.1 78698 c.37.1.19 78699 c.37.1.19 78700 1dvpA 220 1.99e+00 1dvpA a.118.9.2 19216 g.50.1.1 45358 1vom 762 2.07e+00 1lvk b.34.3.1 24577 c.37.1.9 32174 1iatA 557 2.28e+00 1dqrA c.80.1.2 62123 1abv 134 2.31e+00 1abv a.70.1.1 18317 1h97A 147 2.56e+00 1h97A a.1.1.2 60812 1fnmA 691 2.87e+00 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1l6nA 289 2.90e+00 a.61.1.1 73624 a.73.1.1 73625 1knvA 293 2.90e+00 c.52.1.7 68707 1dar 691 2.93e+00 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1na6A 404 2.95e+00 unknown_sccs -4715 unknown_sccs -7564 1fgjA 546 3.17e+00 1fgjA a.138.1.3 19679 1aj8A 371 3.35e+00 1aj8A a.103.1.1 18900 1mnd 762 3.35e+00 1lvk b.34.3.1 24591 c.37.1.9 32188 1q6aA 107 3.66e+00 unknown_sccs -960 1lvk 762 4.18e+00 1lvk b.34.3.1 24576 c.37.1.9 32173 1fqvJ 149 4.38e+00 1fqvD a.157.1.1 19266 d.42.1.1 38670 1i3dA 146 4.55e+00 a.1.1.2 61587 1okrA 123 4.83e+00 unknown_sccs -235 1hu4A 288 5.17e+00 1hu4A 1n5dA 288 5.17e+00 c.2.1.2 80030 2ezh 75 5.36e+00 2ezh a.4.1.2 16029 1hm5A 558 5.61e+00 c.80.1.2 76717 1g8eA 116 5.81e+00 1g8eA a.145.1.1 60346 1hlb 158 6.06e+00 1hlb a.1.1.2 15625 1iwhA 141 6.59e+00 a.1.1.2 76882 1giqA 413 6.60e+00 d.166.1.1 76224 d.166.1.1 76225 1fqvD 149 6.76e+00 1fqvD a.157.1.1 19263 d.42.1.1 38667 1mijA 152 6.79e+00 a.4.1.1 79150 2occE 109 6.90e+00 2occE a.118.11.1 19224 1dm1A 146 7.11e+00 2fal a.1.1.2 15153 2ezi 75 7.24e+00 2ezh a.4.1.2 16028 1pb6A 212 7.38e+00 a.4.1.9 88017 a.121.1.1 88018 1v54E 109 7.43e+00 a.118.11.1 -1652 1k8tA 510 7.60e+00 e.41.1.1 68316 1hy5A 136 7.71e+00 a.24.11.1 65955 1iawA 317 8.06e+00 c.52.1.9 62126 1adt 356 8.29e+00 1anv a.54.1.1 17887 g.51.1.1 45362 g.51.1.1 45368 1iznB 277 8.32e+00 e.43.1.2 83848 1ng6A 148 8.38e+00 a.182.1.1 85670 3adk 195 8.42e+00 1zin c.37.1.1 31885 1l5zA 155 8.57e+00 c.23.1.1 77722 1tlqA 189 8.59e+00 1jfgA 374 8.75e+00 a.128.1.5 66636 2sas 185 8.93e+00 2sas a.39.1.5 17258 1e3mA 800 9.49e+00 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1k28A 584 9.71e+00 b.40.8.1 68049 b.108.1.2 68050 d.2.1.3 68051 5eat 548 9.75e+00 5eat a.102.4.1 18853 a.128.1.3 19445 1qagA 226 9.91e+00 1qagA a.40.1.1 17400 a.40.1.1 17401 1g4yB 101 1.02e+01 1g4yB f.15.1.1 60251 1uurA 473 1.03e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1gk4C 84 1.03e+01 h.1.20.1 70205 1ev7B 317 1.03e+01 1ev7B c.52.1.9 33316 1abwA 283 1.05e+01 1abwA a.1.1.2 15288 a.1.1.2 15289 1ggzA 148 1.07e+01 a.39.1.5 70176 1d0yA 761 1.08e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1g59A 468 1.15e+01 a.97.1.1 60257 c.26.1.1 60258 1i5rA 327 1.15e+01 c.2.1.2 83668 1i50K 120 1.16e+01 d.74.3.2 61765 1na3A 91 1.19e+01 k.38.1.1 85481 1dqrA 557 1.21e+01 1dqrA c.80.1.2 35305 1ux5A 411 1.22e+01 unknown_sccs -1768 1yub 245 1.24e+01 2ercA c.66.1.24 34219 1rfmA 344 1.24e+01 c.122.1.1 -8032 1jb0L 154 1.25e+01 1jb0L f.31.1.1 62829 1mc0A 368 1.25e+01 d.110.2.1 78937 d.110.2.1 78938 1spgA 144 1.25e+01 1abwA a.1.1.2 15409 1ltlA 279 1.26e+01 b.40.4.11 84701 1gk4A 84 1.30e+01 h.1.20.1 70203 1on0A 158 1.33e+01 d.108.1.1 87095 5eau 548 1.33e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1kpsB 171 1.33e+01 a.118.12.1 68787 1pbwA 216 1.34e+01 1pbwA a.116.1.1 19103 2lfb 100 1.40e+01 1lfb a.4.1.1 15990 1kw4A 89 1.45e+01 a.60.1.2 73077 1gk4D 84 1.46e+01 h.1.20.1 70206 1cg5B 141 1.48e+01 1cg5B a.1.1.2 15585 1anv 356 1.49e+01 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 1vkmA 297 1.49e+01 1kn1A 160 1.49e+01 a.1.1.3 77455 1em9A 154 1.51e+01 1d1dA a.73.1.1 18333 1jplA 171 1.54e+01 a.118.9.2 67027 1mu5A 471 1.55e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1a6m 151 1.56e+01 1a6m a.1.1.2 15018 1g5yA 238 1.64e+01 1lbd a.123.1.1 60294 1o0uA 429 1.65e+01 c.118.1.1 80743 1uedA 406 1.65e+01 a.104.1.1 -1459 1a26 361 1.65e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1dwkA 156 1.67e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1go3F 107 1.69e+01 a.60.8.2 65407 1pjr 724 1.70e+01 1pjr c.37.1.19 32391 c.37.1.19 32392 1um8A 376 1.72e+01 c.37.1.20 -7251 1iomA 377 1.74e+01 a.103.1.1 83698 1j77A 209 1.79e+01 1j77A a.132.1.2 62674 1s7oA 113 1.79e+01 1fpoA 171 1.81e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 1lfjA 119 1.83e+01 1rypJ 204 1.84e+01 d.153.1.4 41878 1g0uI 205 1.84e+01 d.153.1.4 41891 1ufhA 180 1.84e+01 d.108.1.1 88485 1mi1A 414 1.85e+01 a.169.1.1 79137 b.55.1.6 79138 1fds 327 1.86e+01 1fds c.2.1.2 29838 1ax8 146 1.89e+01 1ax8 a.26.1.1 16844 1lfkA 398 1.89e+01 a.104.1.1 77926 1nbmG 272 1.91e+01 1e1qG c.49.2.1 33161 1rh2F 165 1.94e+01 1rh2F a.26.1.3 16898 2mysB 166 1.96e+01 1wdcB a.39.1.5 17308 1e1qG 272 2.00e+01 1e1qG c.49.2.1 33162 1po5A 476 2.00e+01 a.104.1.1 -1467 1fhjB 146 2.03e+01 1abwA a.1.1.2 59838 1allA 160 2.04e+01 1qgwC a.1.1.3 15647 1i4sA 147 2.07e+01 a.149.1.1 66026 1cg5A 141 2.07e+01 1abwA a.1.1.2 15406 1iwhB 146 2.09e+01 a.1.1.2 76883 1bmfG 272 2.10e+01 1e1qG c.49.2.1 33160 1rjdA 334 2.10e+01 unknown_sccs -8079 1dxtB 147 2.12e+01 1abwA a.1.1.2 15450 1gkxA 388 2.15e+01 a.29.5.1 65266 d.122.1.4 65267 1lw1A 177 2.16e+01 a.152.1.1 74290 1a27 289 2.18e+01 1fds c.2.1.2 29839 1efvA 315 2.20e+01 1efvA c.26.2.3 31633 c.31.1.2 31728 1omwA 689 2.20e+01 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 4icb 76 2.21e+01 4icb a.39.1.1 17145 1gkzA 388 2.21e+01 a.29.5.1 65268 d.122.1.4 65269 1dcnD 436 2.23e+01 1auwA a.127.1.1 19423 1v4xA 144 2.24e+01 1l0iA 78 2.24e+01 a.28.1.1 77643 1kcfA 258 2.25e+01 a.140.2.1 68434 c.55.3.7 68435 1i27A 73 2.26e+01 1i27A a.4.5.30 61555 1l7mA 211 2.27e+01 c.108.1.4 73664 1otvA 259 2.30e+01 unknown_sccs -1915 1k9uA 78 2.37e+01 a.39.1.10 84348 1fgs 428 2.38e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1a1z 91 2.40e+01 1a1z a.77.1.4 18427 2spo 154 2.41e+01 1a6m a.1.1.2 15053 1f5sA 211 2.42e+01 1f5sA c.108.1.4 59656 1eh2 106 2.50e+01 1eh2 a.39.1.6 17339 1f5xA 208 2.51e+01 1f5xA a.87.1.1 18516 1bo4B 168 2.52e+01 1bo4A d.108.1.1 40799 1hqvA 191 2.55e+01 1hqvA a.39.1.8 61160 1r5zA 323 2.57e+01 unknown_sccs -12289 1ht9A 76 2.58e+01 4icb a.39.1.1 61252 1ev7A 317 2.60e+01 1ev7B c.52.1.9 33315 1tbmA 326 2.64e+01 1be3F 110 2.64e+01 1be3F f.27.1.1 43668 1o1yA 239 2.65e+01 c.23.16.1 86554 1nnwA 252 2.71e+01 d.159.1.5 80674 1dcnA 424 2.75e+01 1auwA a.127.1.1 19420 1babA 143 2.77e+01 1abwA a.1.1.2 15235 1f5mB 180 2.77e+01 1f5mB d.110.2.1 40896 1q08A 99 2.78e+01 a.6.1.3 -381 1irdB 146 2.79e+01 a.1.1.2 66287 1lk9A 448 2.84e+01 c.67.1.1 78057 1dciA 275 2.89e+01 1dciA c.14.1.3 30918 1jbwA 428 2.95e+01 c.59.1.2 62860 c.72.2.2 62861 1ugpB 226 2.96e+01 1ireB 228 2.97e+01 b.34.4.4 76770 1qjtA 99 2.97e+01 1eh2 a.39.1.6 17335 1e4iA 447 3.00e+01 1e70M c.1.8.4 59225 1owcA 427 3.00e+01 1pi1A 185 3.02e+01 unknown_sccs -762 1jfaA 374 3.03e+01 a.128.1.5 66622 1eco 136 3.06e+01 1flp a.1.1.2 15208 1rdzA 337 3.09e+01 1frpA e.7.1.1 42882 1jtvA 327 3.09e+01 c.2.1.2 84230 1qcrF 103 3.10e+01 1be3F f.27.1.1 43676 1n3kA 130 3.13e+01 a.77.1.4 79965 1efyA 350 3.18e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1j7yA 141 3.21e+01 a.1.1.2 66426 1isaA 192 3.22e+01 1avmA a.2.11.1 15731 d.44.1.1 38724 1dc1A 323 3.29e+01 1dc1A c.52.1.11 33321 1mbd 153 3.30e+01 1a6m a.1.1.2 15033 1j09A 468 3.31e+01 a.97.1.1 77025 c.26.1.1 77026 1babB 146 3.33e+01 1abwA a.1.1.2 15414 1d1dA 262 3.33e+01 1d1dA a.28.3.1 16958 a.73.1.1 18335 1gu9A 177 3.34e+01 a.152.1.1 65540 1ujpA 271 3.38e+01 c.1.2.4 -5177 1cnt1 187 3.42e+01 1cnt3 1irdA 141 3.46e+01 a.1.1.2 66286 1dlyA 164 3.47e+01 1dlyA a.1.1.1 14983 1pp7U 131 3.48e+01 unknown_sccs -304 1tr1A 447 3.49e+01 1e70M c.1.8.4 28957 1qryA 80 3.49e+01 2hddA a.4.1.1 16016 1exrA 148 3.50e+01 1cll a.39.1.5 17299 1j97A 211 3.55e+01 1f5sA c.108.1.4 62753 1kv9A 668 3.55e+01 a.3.1.6 73056 b.70.1.1 73057 1m5iA 125 3.55e+01 h.4.13.1 78648 1qkkA 155 3.57e+01 1dbwA c.23.1.1 31104 1bzpA 153 3.60e+01 1a6m a.1.1.2 15020 1n1jA 93 3.64e+01 a.22.1.3 79813 1hy0A 466 3.64e+01 1auwA a.127.1.1 61392 1o5zA 442 3.65e+01 c.59.1.2 -7939 c.72.2.2 -8418 1eca 136 3.65e+01 1flp a.1.1.2 15209 1gln 468 3.66e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1mx3A 347 3.69e+01 c.2.1.4 79638 c.23.12.1 79639 1ncx 162 3.69e+01 1ncx a.39.1.5 17222 1qhaA 917 3.70e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1r8iA 213 3.71e+01 unknown_sccs -411 1uptB 60 3.73e+01 unknown_sccs -1163 1iexA 605 3.77e+01 c.1.8.7 66127 c.23.11.1 66128 1ntyA 311 3.81e+01 1ej3A 191 3.81e+01 1ej3A a.39.1.5 17259 1top 162 3.85e+01 1ncx a.39.1.5 17223 1ecd 136 3.88e+01 1flp a.1.1.2 15211 1a8o 70 3.90e+01 1a8o a.28.3.1 16953 1d9cA 121 3.91e+01 1d9cA a.26.1.3 16901 1kncA 177 3.98e+01 a.152.1.1 68703 1umdA 367 3.98e+01 c.36.1.11 -6969 1kiyA 374 3.98e+01 a.128.1.5 72555 1ad6 185 3.99e+01 1guxA a.74.1.3 18390 2hfh 109 4.00e+01 2hfh a.4.5.14 16145