# List of top-scoring protein chains for t2k.w0.5 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.soe.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 2goyA 275 1.92e-27 2oq2A 261 2.28e-26 2o8vA 252 5.88e-25 1surA 215 1.02e-22 c.26.2.2 31620 1zunA 325 6.96e-22 c.26.2.2 125676 2e18A 257 2.40e-04 1gpmA 525 7.17e-04 1gpmA c.23.16.1 31405 c.26.2.1 31608 d.52.2.1 38826 2ywbA 503 1.01e-03 1wy5A 317 2.84e-02 c.26.2.5 121428 d.229.1.1 121429 2dplA 308 6.06e-02 1ni5A 433 7.25e-02 b.153.1.2 111592 c.26.2.5 80533 d.229.1.1 111593 1xngA 268 1.28e-01 c.26.2.1 122186 2pg3A 232 1.30e-01 1k92A 455 1.31e-01 c.26.2.1 68325 d.210.1.1 68326 1q15A 503 2.61e-01 c.26.2.1 95538 d.153.1.1 95539 1n1cA 217 4.21e-01 a.184.1.1 85254 1vdzA 588 6.46e-01 2hmaA 376 6.55e-01 1d7qA 143 1.06e+00 1d7qA b.40.4.5 25331 2j87A 177 1.07e+00 1yvdA 169 1.10e+00 c.37.1.8 124095 1z0jA 170 1.13e+00 c.37.1.8 124319 2d13A 227 1.44e+00 c.26.2.1 131121 2derA 380 2.44e+00 1pk1A 89 2.92e+00 a.60.1.2 118711 1n7vA 555 2.93e+00 b.126.1.1 85377 1n7uA 554 2.94e+00 b.126.1.1 85376 1kw4A 89 3.42e+00 a.60.1.2 73077 1tlqA 189 3.54e+00 a.195.1.1 107134 2c5sA 413 3.89e+00 c.26.2.6 129950 d.308.1.1 129951 1k0wA 231 3.89e+00 c.74.1.1 77220 1dz3A 130 3.92e+00 1dz3A c.23.1.1 31105 2bs3B 239 3.92e+00 a.1.2.1 129045 d.15.4.2 129046 2bs2B 241 3.92e+00 a.1.2.1 129033 d.15.4.2 129034 1jdiA 231 3.94e+00 c.74.1.1 66551 1xbtA 193 4.03e+00 c.37.1.24 115080 g.39.1.14 115081 1m1zA 513 4.11e+00 c.26.2.1 78457 d.153.1.1 78458 2g6zA 211 4.17e+00 1im5A 180 4.25e+00 c.33.1.3 66211 1w4rA 195 4.36e+00 1vl2A 421 4.38e+00 c.26.2.1 108708 d.210.1.1 108709 1tmiA 130 5.07e+00 d.156.1.2 107151 1attA 429 5.76e+00 1ovaA e.1.1.1 42638 2orvA 234 6.28e+00 c.37.1.24 139274 g.39.1.14 139275 1wp9A 494 6.63e+00 c.37.1.19 121143 c.37.1.19 121144 1wymA 155 6.63e+00 1oewA 329 7.47e+00 b.50.1.2 86924 1od1A 330 7.51e+00 b.50.1.2 86820 2er7E 330 7.51e+00 2er7E b.50.1.2 26779 2gv0A 131 8.27e+00 1j32A 388 8.28e+00 c.67.1.1 77067 2idvA 177 8.54e+00 1lwuB 323 8.60e+00 d.171.1.1 74310 h.1.8.1 74311 1h67A 108 8.70e+00 a.40.1.1 65643 1tluA 130 9.59e+00 d.156.1.2 107139 1fjmA 330 1.01e+01 1auiA d.159.1.3 42082 1vr7A 142 1.02e+01 d.156.1.2 120443 1h6kZ 98 1.03e+01 d.58.7.1 60686 2idrA 177 1.04e+01 1j3sA 104 1.06e+01 a.3.1.1 103838 1u32A 293 1.08e+01 d.159.1.3 107631 1deqB 408 1.12e+01 i.9.1.1 45991 1jk7A 323 1.18e+01 1auiA d.159.1.3 63144 2o8gA 329 1.19e+01 2d5rB 116 1.28e+01 2z15A 130 1.33e+01 1pk3A 89 1.37e+01 a.60.1.2 118715 1uz5A 402 1.39e+01 b.85.6.1 100217 b.103.1.1 100218 c.57.1.2 100219 1fxwF 229 1.39e+01 c.23.10.3 65058 1qoyA 318 1.41e+01 1qoyA h.4.4.1 45788 1pk1B 89 1.42e+01 a.60.1.2 118712 1a3hA 300 1.43e+01 c.1.8.3 28819 7a3hA 303 1.43e+01 7a3hA c.1.8.3 28817 1h5vA 304 1.44e+01 c.1.8.3 70898 1ru8A 232 1.44e+01 c.26.2.1 97849 2v38A 305 1.44e+01 1hqoA 258 1.44e+01 1hqoA a.45.1.1 17749 c.47.1.5 33043 1k0dA 260 1.45e+01 a.45.1.1 67930 c.47.1.5 67931 1g6wA 261 1.45e+01 1hqoA a.45.1.1 17751 c.47.1.5 33045 2b4xL 427 1.57e+01 e.1.1.1 127867 2iosA 150 1.57e+01 a.118.1.14 137576 1jvqI 432 1.57e+01 e.1.1.1 84232 2b4xI 427 1.58e+01 1lf1A 308 1.60e+01 c.1.8.3 73877 2hijI 432 1.61e+01 2z4eB 326 1.63e+01 1dzhI 432 1.63e+01 1ovaA e.1.1.1 42652 1fzcB 328 1.64e+01 3fib d.171.1.1 42460 h.1.8.1 45591 1re3B 313 1.65e+01 d.171.1.1 104892 h.1.8.1 104893 1dzgI 432 1.66e+01 1ovaA e.1.1.1 42656 2oyhB 313 1.70e+01 2b5tI 432 1.74e+01 e.1.1.1 127905 2pbtA 134 1.78e+01 1o7kA 131 1.80e+01 d.189.1.1 81144 2ox7A 155 1.81e+01 2nvpA 435 1.81e+01 2ionA 152 1.81e+01 a.118.1.14 137575 1gd5A 130 1.82e+01 1gd5A d.189.1.1 60439 1vg1A 185 1.88e+01 c.37.1.8 108599 1oyhI 432 1.88e+01 e.1.1.1 93727 2gd4C 443 1.92e+01 1fmvA 761 1.92e+01 1lvk b.34.3.1 24580 c.37.1.9 32177 1kq6A 141 1.93e+01 d.189.1.1 91020 1vomA 762 1.93e+01 b.34.3.1 24577 c.37.1.9 32174 1mmgA 762 1.95e+01 b.34.3.1 24579 c.37.1.9 32176 1mmnA 762 1.96e+01 b.34.3.1 24582 c.37.1.9 32179 2ywiA 196 1.98e+01 1d0yA 761 2.00e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1yv3A 762 2.01e+01 1mmaA 762 2.01e+01 b.34.3.1 24587 c.37.1.9 32184 1w9jA 770 2.02e+01 1lvkA 762 2.02e+01 b.34.3.1 24576 c.37.1.9 32173 1w9iA 770 2.02e+01 1jx2A 776 2.02e+01 b.34.3.1 67402 c.37.1.9 67403 2akaA 776 2.02e+01 1w9lA 770 2.05e+01 1w9kA 770 2.06e+01 2b4zA 104 2.15e+01 2nz2A 413 2.19e+01 1g8xA 1010 2.21e+01 1lvk k.1.1.1 46378 1gegA 256 2.22e+01 1ybvA c.2.1.2 29888 2dk6A 102 2.25e+01 2qbyA 386 2.27e+01 1vg8A 207 2.30e+01 c.37.1.8 108606 2d62A 375 2.36e+01 3cfyA 137 2.41e+01 2i9uA 439 2.41e+01 1ys4A 354 2.43e+01 1s70A 330 2.47e+01 d.159.1.3 105316 2gn4A 344 2.51e+01 1w7dA 137 2.55e+01 2c95A 196 2.58e+01 1wnoA 395 2.60e+01 c.1.8.5 121098 d.26.3.1 121099 1ky3A 182 2.69e+01 c.37.1.8 73193 1t91A 207 2.74e+01 c.37.1.8 119192 1gpwA 253 2.77e+01 c.1.2.1 65460 1w9pA 433 2.80e+01 c.1.8.5 114412 d.26.3.1 114413 1thfD 253 2.82e+01 1thfD c.1.2.1 28535 1ylxA 103 2.87e+01 d.82.5.1 123677 1tibA 269 2.93e+01 c.69.1.17 34738 2rn7A 108 2.93e+01 2a0nA 265 2.93e+01 c.1.2.1 125961 1pbtA 244 2.95e+01 c.124.1.1 94416 1vh7A 265 2.97e+01 c.1.2.1 100646 1g8pA 350 2.98e+01 1g8pA c.37.1.20 60376 1wejF 104 3.01e+01 1ycc a.3.1.1 15865 1oidA 532 3.02e+01 d.114.1.1 103952 d.159.1.2 103953 1wywB 97 3.04e+01 d.15.1.1 121468 2e1zA 415 3.10e+01 1x3mA 415 3.10e+01 c.55.1.2 121664 c.55.1.2 121665 1sv0C 82 3.11e+01 a.60.1.1 106037 1a5rA 103 3.12e+01 d.15.1.1 37597 1r0sA 258 3.14e+01 c.23.14.3 96737 1h6kX 97 3.19e+01 d.58.7.1 60684 2h8lA 252 3.22e+01 1r12A 258 3.26e+01 c.23.14.3 96780 1gt6A 269 3.27e+01 c.69.1.17 76342 3adkA 194 3.31e+01 c.37.1.1 31885 2qpxA 376 3.37e+01 1tiiC 53 3.38e+01 1tiiC 1acvA 189 3.41e+01 1fvkA c.47.1.13 90328 1qvbA 481 3.46e+01 1qvbA c.1.8.4 28983 1b43A 340 3.49e+01 1a76 a.60.7.1 18092 c.120.1.2 33362 1s4kA 120 3.50e+01 a.35.1.6 105254 1f59A 442 3.52e+01 1qgrA a.118.1.1 19123 1fvkA 189 3.58e+01 1fvkA c.47.1.13 90351 1vl1A 232 3.58e+01 c.124.1.1 108707 1ac1A 189 3.62e+01 1fvkA c.47.1.13 90326 1gcjA 460 3.63e+01 1qgrA a.118.1.1 19125 1fvjA 189 3.63e+01 1fvkA c.47.1.13 90349 2c1cA 312 3.64e+01 c.56.5.1 129630 1t0aA 159 3.66e+01 d.79.5.1 112192 1u3aA 189 3.66e+01 c.47.1.13 119504 2b6mA 189 3.67e+01 c.47.1.13 127995 2psyA 227 3.69e+01 2c40A 312 3.75e+01 1ibrB 462 3.77e+01 1qgrA a.118.1.1 19120 1bq7A 189 3.81e+01 1fvkA c.47.1.13 90331 2qvwA 756 3.83e+01 2dxaA 166 3.83e+01 2b3sA 189 3.84e+01 c.47.1.13 127794 1m5nS 485 3.89e+01 a.118.1.1 78653 1zh2A 121 3.92e+01 c.23.1.1 125069 1zvbA 34 3.97e+01 h.3.3.1 125702