# List of top-scoring protein chains for t04-100-40-40-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 1pb6A 212 2.62e-02 a.4.1.9,a.121.1.1 88017,88018 2b1eA 564 8.71e-02 2g8yA 385 9.44e-02 1j8bA 112 1.49e-01 d.222.1.1 77101 1ybxA 143 1.56e-01 1kxu 333 1.97e-01 1jkw a.74.1.1,a.74.1.1 18358,18359 1debA 54 2.71e-01 1debA h.1.18.1 45660 1sedA 117 3.96e-01 a.219.1.1 105449 1yg2A 179 4.21e-01 1ad1A 266 4.41e-01 1aj2 c.1.21.1 29668 2a3qA 170 5.51e-01 2a6cA 83 5.84e-01 2aucA 126 7.68e-01 4tmkA 213 8.53e-01 5tmpA c.37.1.1 31930 1r0wA 286 9.24e-01 c.37.1.12 96754 4ubpA 101 1.00e+00 1ubpA d.8.1.1 37352 1k28A 584 1.18e+00 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1sauA 115 1.22e+00 2bduA 297 1.26e+00 1mbe 53 1.27e+00 1mbe a.4.1.3 16038 2cruA 118 1.32e+00 1ku1A 230 1.55e+00 a.118.3.1 72996 451c 82 1.56e+00 451c a.3.1.1 15904 1kmiZ 214 1.57e+00 h.4.11.1 72752 351c 82 1.71e+00 451c a.3.1.1 15905 2g09A 297 1.75e+00 1f45B 197 1.76e+00 1f45B a.26.1.1 59642 1ovnA 248 1.84e+00 a.71.1.1,c.47.1.7 93602,93603 2bpa1 426 1.85e+00 2bpa1 1n1jB 97 1.89e+00 a.22.1.3 79814 2adoA 196 1.90e+00 1rkeA 262 2.16e+00 a.24.9.1,a.24.9.1 97608,97609 2ax9A 256 2.35e+00 1zoyC 140 2.35e+00 1rylA 167 2.51e+00 d.276.1.1 105124 1oohA 126 2.65e+00 a.39.2.1 93383 1ykhB 132 2.68e+00 1x3aA 100 2.70e+00 2fxaA 207 2.74e+00 1yviA 149 2.87e+00 1v9nA 360 2.90e+00 1lj2A 110 2.97e+00 h.1.13.2 73926 2ax8A 256 2.98e+00 2etxA 209 2.99e+00 1ejxA 100 3.22e+00 d.8.1.1 83182 1wrdA 103 3.24e+00 1mvwC 147 3.27e+00 i.15.1.1 79525 1bouA 139 3.56e+00 1bouA a.88.1.1 18521 1kx5C 128 3.69e+00 a.22.1.1 77595 2cz1A 206 4.11e+00 1pulA 125 4.15e+00 2ax6A 256 4.16e+00 1r5jA 337 4.17e+00 c.77.1.5 97097 1t7rA 269 4.26e+00 a.123.1.1 106635 1y8qB 640 4.27e+00 1z2iA 358 4.28e+00 1r9dA 787 4.51e+00 c.7.1.1 104865 1pbwA 216 4.53e+00 1pbwA a.116.1.1 19103 1bw0A 416 4.70e+00 1bw0A c.67.1.1 34385 1wn0A 145 4.97e+00 1fgkA 310 5.04e+00 1fgkA d.144.1.7 41693 119l 164 5.09e+00 1l92 d.2.1.3 36622 1dceA 567 5.11e+00 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1oneA 436 5.32e+00 4enl c.1.11.1,d.54.1.1 29200,38844 1i7qA 519 5.35e+00 1qdlA d.161.1.1 61901 2cybA 323 5.50e+00 1nxhA 126 5.61e+00 a.200.1.1 92300 1ohuA 175 5.63e+00 f.1.4.1 93029 1i37A 260 5.69e+00 1a28A a.123.1.1 61583 1on2A 142 5.74e+00 a.4.5.24,a.76.1.1 87103,87104 2fbwC 141 5.77e+00 1guuA 52 5.92e+00 a.4.1.3 83332 1swyA 164 5.96e+00 1lw9A 164 6.01e+00 d.2.1.3 84727 1yzbA 182 6.09e+00 1n2fA 142 6.32e+00 d.227.1.1 79853 1yz8P 68 6.43e+00 1v9dA 340 6.50e+00 a.207.1.1 100535 1sx7A 164 6.51e+00 1l8dA 112 6.71e+00 h.4.12.1 73687 1m45A 148 6.94e+00 a.39.1.5 78598 1is2A 661 7.03e+00 a.29.3.2,a.29.3.2,e.6.1.2 71382,71383,71384 1pzlA 237 7.21e+00 a.123.1.1 104393 1vk5A 157 7.29e+00 a.220.1.1 108635 1q1vA 70 7.41e+00 a.159.4.1 104479 1dxrH 258 7.49e+00 6prcH b.41.1.1,f.23.10.1 25456,43433 1div 149 7.56e+00 1div d.99.1.1,d.100.1.1 40692,40693 2bbsA 290 7.58e+00 1a0rP 245 7.60e+00 1b9yC c.47.1.6 33054 1w4xA 542 7.63e+00 c.3.1.5,c.3.1.5 109171,109172 1uj8A 77 7.73e+00 1n8vA 112 7.73e+00 a.118.21.1 85457 1tzyA 129 7.73e+00 a.22.1.1 107530 1j1iA 296 7.84e+00 c.69.1.10 83977 2cujA 108 8.17e+00 1a4pA 96 8.19e+00 1b4cA a.39.1.2 17176 2al1A 436 8.34e+00 2fvhA 120 8.45e+00 1p36A 164 8.46e+00 d.2.1.3 93978 1m12A 84 8.48e+00 a.64.1.1 84745 1wlzA 105 8.55e+00 2awiA 317 8.56e+00 1qo7A 394 8.62e+00 1qo7A c.69.1.11 34697 1yqyA 523 8.63e+00 1jb0L 154 8.68e+00 1jb0L f.31.1.1 62829 1nxiA 132 8.71e+00 d.58.47.1 86381 1a28A 256 8.72e+00 1a28A a.123.1.1 19290 1p4wA 99 8.74e+00 a.4.6.2 87783 1rxqA 178 8.74e+00 a.213.1.1 105118 2al2A 436 8.96e+00 2aaxA 275 8.97e+00 1jl2A 156 9.04e+00 c.55.3.1 66822 4enl 436 9.29e+00 4enl c.1.11.1,d.54.1.1 29202,38846 1nh1A 330 9.56e+00 e.45.1.1 91871 1t01A 255 9.65e+00 a.24.9.1,a.24.9.1 106188,106189 1kx5B 102 9.65e+00 a.22.1.1 77594 1ithA 141 9.83e+00 1ithA a.1.1.2 15623 1fiqB 350 1.01e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1te6A 439 1.01e+01 c.1.11.1,d.54.1.1 106797,106798 1otsA 465 1.02e+01 f.20.1.1 87415 2akzA 439 1.03e+01 1efnB 152 1.04e+01 1efnB d.102.1.1 40699 1ixcA 294 1.08e+01 a.4.5.37,c.94.1.1 83764,83765 2bl0B 145 1.08e+01 1wt4A 73 1.08e+01 1nznA 126 1.10e+01 a.118.8.1 92382 2fbhA 146 1.12e+01 1aky 221 1.14e+01 1zin c.37.1.1,g.41.2.1 31896,45197 1flcB 175 1.14e+01 1flcB h.3.1.1 45716 1f0nA 285 1.18e+01 1dqyA c.69.1.3 34636 1r4vA 171 1.19e+01 a.197.1.1 97049 1b67A 68 1.21e+01 1a7w a.22.1.2 16474 1o7kA 131 1.22e+01 d.189.1.1 81144 1ogdA 131 1.22e+01 c.133.1.1 92893 1a7w 69 1.24e+01 1a7w a.22.1.2 16477 1kdxA 81 1.25e+01 1kdxA a.12.1.1 16375 1lml 478 1.26e+01 1lml d.92.1.3 40295 2g3bA 208 1.28e+01 1ofwA 296 1.29e+01 a.138.1.1 92850 1a3aA 148 1.29e+01 1a3aA d.112.1.1 40917 1w1oA 534 1.29e+01 d.58.32.4,d.145.1.1 109071,109072 2ahjA 206 1.31e+01 2ahjA d.149.1.1 41772 1zt2B 212 1.35e+01 2aioA 269 1.35e+01 1dpgA 485 1.40e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1fjmA 330 1.41e+01 1auiA d.159.1.3 42082 1sesA 421 1.41e+01 1sesA a.2.7.1,d.104.1.1 15710,40710 2audA 257 1.42e+01 1ja1A 622 1.43e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1kbjA 412 1.43e+01 c.1.4.1 72280 1nekD 115 1.45e+01 f.21.2.2 80432 1uc7A 125 1.48e+01 c.47.1.1 99163 1xmiA 291 1.49e+01 1xwyA 264 1.49e+01 1sqnA 261 1.49e+01 a.123.1.1 105944 1ad4A 266 1.50e+01 1aj2 c.1.21.1 29670 1fmhB 33 1.54e+01 1fmhB k.6.1.1 46410 2bolA 314 1.56e+01 1y10A 407 1.57e+01 1jgsA 138 1.57e+01 a.4.5.28 66683 1sxvA 172 1.58e+01 1hw7A 255 1.59e+01 1i7fA d.193.1.1 61297 1ydiA 263 1.59e+01 1smlA 269 1.60e+01 1smlA d.157.1.1 42053 1u3eM 174 1.60e+01 d.4.1.3,d.285.1.1 107640,107641 1ryp2 233 1.62e+01 1ryp2 1wijA 140 1.63e+01 1uspA 139 1.63e+01 d.227.1.1 99879 1k87A 669 1.64e+01 a.176.1.1,c.1.23.2 77286,77287 1a4iA 301 1.68e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1ldjA 760 1.69e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1sr2A 116 1.69e+01 1s9rA 410 1.70e+01 d.126.1.4 98758 1whtB 153 1.72e+01 1whtB 2a1dD 329 1.73e+01 1enh 54 1.74e+01 2hddA a.4.1.1 15973 1g73A 162 1.75e+01 1fewA a.7.4.1 16332 1gcvB 136 1.78e+01 1cg5B a.1.1.2 15589 1jfxA 217 1.78e+01 c.1.8.8 62943 2cb5A 453 1.79e+01 3gcb d.3.1.1 37035 1jk7A 323 1.82e+01 1auiA d.159.1.3 63144 2bsaA 303 1.82e+01 1miwA 404 1.83e+01 a.173.1.1,d.218.1.4 79162,79163 1vp4A 425 1.84e+01 1qb2A 109 1.84e+01 1qb2A a.36.1.1 17125 1bmqA 167 1.84e+01 1pauA c.17.1.1 30998 1hq3A 129 1.84e+01 1aoiC a.22.1.1 16434 1v7nV 163 1.87e+01 a.26.1.2 100476 1ornA 226 1.87e+01 a.96.1.1 87342 1k2xA 177 1.89e+01 d.153.1.5 90929 1fmhA 33 1.90e+01 1fmhB k.6.1.1 46409 1ihoA 283 1.93e+01 1ihoA c.26.1.4 62390 2cwoA 197 1.93e+01 1vctA 205 1.96e+01 1jj2O 148 1.98e+01 1ffkM a.94.1.1 63100 2ztaA 34 1.98e+01 2ztaA h.1.3.1 45474 1u32A 293 2.01e+01 d.159.1.3 107631 2fq4A 192 2.02e+01 1upvA 257 2.04e+01 1y7qA 98 2.04e+01 1cuk 203 2.04e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1jj2U 70 2.05e+01 1ffkS a.2.2.1 63106 1eq1A 166 2.06e+01 a.63.1.1 64910 2gnxA 365 2.06e+01 1y8aA 332 2.07e+01 1ogiA 303 2.07e+01 b.43.4.2,c.25.1.1 92914,92915 1s72V 71 2.08e+01 a.2.2.1 105341 2axpA 173 2.09e+01 1br1B 150 2.10e+01 1wdcC a.39.1.5 17309 1trkA 680 2.10e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1yub 245 2.11e+01 2ercA c.66.1.24 34219 2f6uA 234 2.12e+01 1zchA 255 2.13e+01 1h99A 224 2.13e+01 a.142.1.1,a.142.1.1 60814,60815 1gpuA 680 2.14e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1whsB 153 2.15e+01 1whtB 1zvzA 279 2.15e+01 1zxxA 319 2.17e+01 1wdcC 156 2.18e+01 1wdcC a.39.1.5 17317 1vp7A 100 2.18e+01 2d1eA 248 2.19e+01 1dc1A 323 2.20e+01 1dc1A c.52.1.11 33321 1wmiB 67 2.20e+01 2bk7B 222 2.21e+01 2bo9B 222 2.21e+01 2b1fA 34 2.24e+01 1vj7A 393 2.25e+01 a.211.1.1,d.218.1.8 100801,100802 1que 303 2.25e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1jsxA 207 2.26e+01 c.66.1.20 71846 1sh0A 510 2.27e+01 e.8.1.4 98876 1ihnA 113 2.27e+01 1ihnA c.103.1.1 62388 2ch4A 320 2.31e+01 2eulA 156 2.31e+01 2ethA 154 2.32e+01 1w2lA 99 2.33e+01 1o9gA 250 2.33e+01 c.66.1.29 86692 2fsjA 346 2.37e+01 1vqoV 71 2.39e+01 1tzyD 103 2.41e+01 a.22.1.1 107533 1sr7A 259 2.41e+01 a.123.1.1 105957 1jkeA 145 2.41e+01 c.110.1.1 66791 1zu1A 127 2.43e+01 1y4oA 104 2.43e+01 1go2A 304 2.45e+01 b.43.4.2,c.25.1.1 76243,76244 1sgwA 214 2.46e+01 c.37.1.12 105541 1xbbA 291 2.47e+01 1ltoA 245 2.48e+01 b.47.1.2 84707 2pvbA 107 2.48e+01 1a75A a.39.1.4 17205 1jhdA 396 2.49e+01 b.122.1.3,c.26.1.5 66712,66713 1k8kE 178 2.49e+01 a.148.1.1 68311 1e8aA 91 2.49e+01 1b4cA a.39.1.2 17188 6paxA 133 2.53e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 1nu7D 282 2.57e+01 a.8.6.1,a.8.6.1 92191,92192 1jpaA 312 2.60e+01 d.144.1.7 67011 1qamA 244 2.61e+01 2ercA c.66.1.24 34220 1s95A 333 2.62e+01 d.159.1.3 105375 2f3nA 76 2.62e+01 1vqoP 149 2.63e+01 2a7oA 112 2.64e+01 1pueE 89 2.65e+01 1awcA a.4.5.21 16165 1s62A 106 2.66e+01 1ru0A 105 2.67e+01 1q6uA 245 2.68e+01 d.26.1.1 95998 1s72P 149 2.68e+01 a.94.1.1 105335 1zw0A 66 2.68e+01 1rifA 282 2.69e+01 c.37.1.23 97507 1v60A 123 2.71e+01 2f9nA 245 2.75e+01 1hq3D 103 2.76e+01 1aoiB a.22.1.1 16464 3fapB 94 2.77e+01 1nsgB a.24.7.1 16612 2ac4A 309 2.77e+01 1xeqA 103 2.83e+01 1f1mA 164 2.83e+01 1ggqA a.24.12.1 59598 2b5oA 402 2.84e+01 1h4lD 147 2.88e+01 a.74.1.1 70873 1vsrA 136 2.90e+01 1vsrA c.52.1.15 33332 1u61A 138 2.92e+01 a.149.1.1 107696 1b7gO 340 2.93e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 2gboA 104 2.95e+01 1wouA 123 2.98e+01 c.47.1.16 109471 2a26A 50 3.03e+01 1g4yR 148 3.05e+01 1cll a.39.1.5 60252 1vhiA 142 3.07e+01 1b3tA d.58.8.1 39230 1g8fA 511 3.10e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1xfuA 747 3.15e+01 1tn4 159 3.15e+01 1ncx a.39.1.5 17248 1ylmA 144 3.19e+01 1r3dA 264 3.21e+01 1a04A 215 3.23e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1s7iA 124 3.23e+01 d.58.4.9 105353 1lnwA 147 3.23e+01 a.4.5.28 78104 1qhxA 178 3.27e+01 1qhsA c.37.1.3 31936 1ispA 181 3.29e+01 c.69.1.18 76778 1mvcA 240 3.30e+01 a.123.1.1 79499 2ac2A 309 3.30e+01 1fxxA 482 3.31e+01 1fxxA c.55.3.5 33726 1wpkA 146 3.33e+01 1sig 339 3.33e+01 1sig a.177.1.1 19068 1wv9A 94 3.34e+01 1sflA 238 3.37e+01 1yrnB 83 3.38e+01 1akhB a.4.1.1 15986 1lvaA 258 3.39e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1hc7A 477 3.40e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2bjfA 329 3.41e+01 2a07F 93 3.42e+01 1h5uA 842 3.42e+01 1a8i c.87.1.4 60655 1vqoD 177 3.42e+01 1wmbA 260 3.43e+01 2b61A 377 3.45e+01 1nbaA 264 3.47e+01 1nbaA c.33.1.3 31753 2fkiA 126 3.49e+01 2b3nA 159 3.50e+01 1wzdA 215 3.51e+01 1cq3A 233 3.53e+01 1cq3A b.27.1.1 23923 1xvjA 109 3.54e+01 1ireA 204 3.54e+01 d.149.1.1 76769 1i1qA 520 3.55e+01 1qdlA d.161.1.1 61543 2f6kA 307 3.55e+01 1fa0A 537 3.58e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1e3dB 542 3.59e+01 1h2rL e.18.1.1 59189 1xjdA 345 3.60e+01 1unlD 208 3.61e+01 1q1gA 276 3.61e+01 c.56.2.1 95574 2azeB 106 3.61e+01 1s21A 206 3.62e+01 d.166.1.4 105222 1t5eA 360 3.62e+01 f.46.1.1 106436 1kq6A 141 3.63e+01 d.189.1.1 91020 1np8A 159 3.64e+01 a.39.1.8 92022 1ni5A 433 3.65e+01 c.26.2.5,d.229.1.1 80533,80534 1wddS 128 3.67e+01 1urjA 1136 3.68e+01 1rw6A 210 3.73e+01 a.47.4.1 105113 1v64A 108 3.74e+01 a.21.1.1 108392 1ojrA 274 3.74e+01 c.74.1.1 93147 2fk4A 75 3.74e+01 1qzgA 187 3.75e+01 b.40.4.3 96643 2bw3A 534 3.76e+01 1qydA 313 3.78e+01 c.2.1.2 96583 1mhdA 132 3.78e+01 1mhdA d.164.1.1 42175 1q6hA 224 3.80e+01 d.26.1.1 95975 1foeA 377 3.80e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1vfrA 218 3.81e+01 1vfrA d.90.1.1 40247 1xb2B 291 3.84e+01 1brwA 433 3.84e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1sseB 86 3.85e+01 1dozA 309 3.86e+01 1ak1 c.92.1.1 35592 2b7aA 293 3.89e+01 1w6sB 74 3.90e+01 1ugpA 203 3.96e+01 d.149.1.1 107831 2ng1 293 3.98e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1ixmA 192 3.99e+01 1ixmA d.123.1.1 41114 2fggA 101 4.00e+01 1h5wA 309 4.00e+01 e.27.1.1 65635 1j7nA 776 4.02e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1idrA 136 4.02e+01 1dlyA a.1.1.1 62301 1oy3D 282 4.05e+01 d.211.1.1 87554 2ax3A 502 4.06e+01 1scfA 273 4.07e+01 1exzA a.26.1.2 16873 1q8bA 105 4.08e+01 d.58.4.6 96201 1kgdA 180 4.09e+01 c.37.1.1 68582 1z00B 84 4.14e+01 1qwgA 251 4.16e+01 c.1.27.1 96473 1lldA 319 4.20e+01 3ldh 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