# 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 1iq7A 345 1.01e+00 c.94.1.2 66261 1ovtA 686 1.26e+00 c.94.1.2 35882 c.94.1.2 35883 2d3iA 686 1.27e+00 c.94.1.2 131208 c.94.1.2 131209 1bf4A 63 1.70e+00 1azpA b.34.13.1 37461 1bnzA 64 1.80e+00 1azpA b.34.13.1 37468 1gsoA 431 1.89e+00 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1jicA 62 2.04e+00 b.34.13.1 37462 1bbxC 63 2.05e+00 1azpA b.34.13.1 37465 1dxhA 335 2.15e+00 1othA c.78.1.1 35202 c.78.1.1 35203 1ortA 335 2.18e+00 1othA c.78.1.1 35204 c.78.1.1 35205 2cgfA 225 2.39e+00 1c8cA 64 2.47e+00 1azpA b.34.13.1 59084 2akpA 186 2.62e+00 1am1A 213 2.83e+00 d.122.1.1 41095 2iwxA 214 2.84e+00 d.122.1.1 137758 2breA 219 2.90e+00 d.122.1.1 128994 1ah6A 220 2.91e+00 d.122.1.1 41094 1bgqA 225 2.91e+00 d.122.1.1 41098 1a4hA 230 2.96e+00 d.122.1.1 41099 1zwhA 240 3.00e+00 d.122.1.1 125739 1b69A 69 3.29e+00 2bb8 d.10.1.1 37479 2heoA 67 3.30e+00 1b4oA 62 3.34e+00 b.34.13.1 37464 2gs3A 185 3.41e+00 2obiA 183 3.42e+00 2qcuA 501 4.57e+00 1wzcA 249 4.69e+00 c.108.1.10 121491 1bb8A 71 4.82e+00 d.10.1.1 37478 1wtqA 66 5.26e+00 1wtoA 66 6.03e+00 1vdmA 153 7.11e+00 c.61.1.1 119994 2nutA 769 7.31e+00 3bjkA 153 7.69e+00 1yliA 153 7.73e+00 d.38.1.1 123651 1wtxA 66 8.28e+00 1uliA 460 8.62e+00 b.33.1.2 107921 d.129.3.3 107922 1bprA 191 9.25e+00 b.130.1.1 118433 1gydB 315 9.35e+00 b.67.2.1 70751 2aieP 203 9.37e+00 2aiaA 203 9.38e+00 1gyhA 318 9.43e+00 b.67.2.1 70757 1dkzA 219 9.50e+00 1dkzA a.8.4.1 90345 b.130.1.1 90346 1lm6A 215 9.79e+00 d.167.1.1 84628 2cg9A 677 9.95e+00 1dkxA 219 1.03e+01 1dkzA a.8.4.1 90339 b.130.1.1 90340 2cvrA 62 1.06e+01 b.34.13.1 130889 1f2eA 201 1.07e+01 1a0fA a.45.1.1 17745 c.47.1.5 33039 1azpA 66 1.11e+01 1azpA b.34.13.1 37467 1lqyA 184 1.12e+01 d.167.1.1 74212 1gyeB 315 1.16e+01 b.67.2.1 70752 2c0kA 151 1.20e+01 1wvlA 80 1.22e+01 b.34.13.1 121343 1bgjA 394 1.28e+01 c.3.1.2 30352 d.16.1.2 37883 2qeuA 141 1.45e+01 1ixzA 254 1.46e+01 c.37.1.20 76938 1x5xA 109 1.46e+01 b.1.2.1 121724 3bf5A 306 1.54e+01 1iy2A 278 1.54e+01 c.37.1.20 76941 1zswA 338 1.65e+01 d.32.1.10 125620 d.32.1.10 125621 1rh9A 373 1.65e+01 c.1.8.3 118773 1xx8A 66 1.69e+01 2os3A 205 1.74e+01 1xyiA 66 1.75e+01 1j75A 67 1.80e+01 a.4.5.19 62673 2fnjC 96 1.87e+01 d.42.1.1 133820 1lm8C 96 1.87e+01 d.42.1.1 74034 2dytA 312 1.91e+01 2c9wC 97 1.94e+01 d.42.1.1 130146 2rb6A 61 1.95e+01 1x10A 208 2.01e+01 1z8xA 208 2.02e+01 1z8wA 208 2.02e+01 1z8tA 208 2.02e+01 1x12A 208 2.03e+01 1ioiA 208 2.03e+01 1a2zA c.56.4.1 62629 2higA 487 2.04e+01 1a88A 275 2.05e+01 1brt c.69.1.12 34707 1yd7A 395 2.05e+01 1suuA 312 2.07e+01 b.68.10.1 99006 2eo8A 208 2.09e+01 1iofA 208 2.24e+01 1a2zA c.56.4.1 62625 2df5A 213 2.25e+01 1wtvA 66 2.26e+01 2pi4A 878 2.27e+01 e.8.1.3 139700 1igmH 129 2.28e+01 1igtB b.1.1.1 19827 1mswD 883 2.28e+01 e.8.1.3 79427 1cezA 883 2.28e+01 1cezA e.8.1.3 43110 1zmyA 142 2.32e+01 1aroP 883 2.33e+01 1cezA e.8.1.3 43112 1keqA 248 2.34e+01 b.74.1.1 72387 2gu9A 113 2.34e+01 2ilbA 114 2.35e+01 1vp4A 425 2.44e+01 c.67.1.1 113935 1mjdA 113 2.47e+01 d.15.11.1 84977 2osaA 202 2.53e+01 1mdbA 539 2.60e+01 e.23.1.1 79008 1n5bA 132 2.61e+01 d.198.1.1 80026 1fnhA 271 2.62e+01 1fnhA b.1.2.1 21976 b.1.2.1 21977 b.1.2.1 21978 1dmxA 248 2.68e+01 2cba b.74.1.1 27959 2sqcA 631 2.75e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 3sqcA 631 2.77e+01 2sqcA a.102.4.2 18860 a.102.4.2 18861 2dhrA 499 2.81e+01 1umpA 631 2.81e+01 a.102.4.2 99619 a.102.4.2 99620 1nb8A 353 2.83e+01 d.3.1.9 80385 1cj3A 392 2.87e+01 1pbe c.3.1.2 30347 d.16.1.2 37878 2h36X 112 2.88e+01 1cj2A 391 2.88e+01 1pbe c.3.1.2 30351 d.16.1.2 37882 1cj4A 392 2.89e+01 1pbe c.3.1.2 30345 d.16.1.2 37876 1pbfA 394 2.91e+01 c.3.1.2 30349 d.16.1.2 37880 1bf3A 394 2.93e+01 c.3.1.2 30346 d.16.1.2 37877 1pbdA 394 2.93e+01 c.3.1.2 30342 d.16.1.2 37873 1bkwA 394 2.93e+01 1pbe c.3.1.2 30343 d.16.1.2 37874 2mltA 26 2.94e+01 j.19.1.1 46171 1bgnA 394 2.95e+01 c.3.1.2 30339 d.16.1.2 37870 1xfpA 142 3.02e+01 b.1.1.1 109587 2jesA 503 3.06e+01 1pbeA 394 3.22e+01 c.3.1.2 30338 d.16.1.2 37869 2atzA 180 3.24e+01 d.264.1.3 127317 1zt2B 212 3.29e+01 a.262.1.1 125625 1wwbX 103 3.29e+01 1wwcA b.1.1.4 21777 2apcA 342 3.31e+01 c.68.1.10 127125 1dobA 394 3.31e+01 c.3.1.2 30362 d.16.1.2 37893 1pxcA 394 3.32e+01 c.3.1.2 30361 d.16.1.2 37892 1fo8A 343 3.32e+01 1foaA c.68.1.10 59927 1k0iA 394 3.33e+01 c.3.1.2 67942 d.16.1.2 67943 1pxaA 394 3.33e+01 c.3.1.2 30366 d.16.1.2 37897 1pxbA 394 3.33e+01 c.3.1.2 30367 d.16.1.2 37898 1iutA 394 3.33e+01 c.3.1.2 30355 d.16.1.2 37886 1l2wA 123 3.34e+01 d.198.1.1 73518 1hcfX 101 3.36e+01 b.1.1.4 65790 1ykjA 394 3.38e+01 1jyaA 130 3.41e+01 d.198.1.1 67453 1k2yX 463 3.43e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1k6zA 141 3.54e+01 d.198.1.1 68247 2fkfA 462 3.54e+01 c.84.1.1 133653 c.84.1.1 133654 c.84.1.1 133655 d.129.2.1 133656 1p5dX 463 3.55e+01 c.84.1.1 94138 c.84.1.1 94139 c.84.1.1 94140 d.129.2.1 94141 2h5aX 463 3.55e+01 c.84.1.1 136141 c.84.1.1 136142 c.84.1.1 136143 d.129.2.1 136144 2hwjA 205 3.56e+01 2fkmX 462 3.63e+01 c.84.1.1 133660 c.84.1.1 133661 c.84.1.1 133662 d.129.2.1 133663 2bmoA 447 3.63e+01 b.33.1.2 128804 d.129.3.3 128805 2dgdA 223 3.75e+01 1x88A 359 3.77e+01 c.37.1.9 121797 1tkbA 678 3.80e+01 1trkA c.36.1.6 31808 c.36.1.10 31807 c.48.1.1 33092 1q0bA 367 3.80e+01 c.37.1.9 95502 1gpuA 680 3.80e+01 c.36.1.6 65455 c.36.1.10 65454 c.48.1.1 65456 1trkA 680 3.80e+01 1trkA c.36.1.6 31804 c.36.1.10 31803 c.48.1.1 33090 2pg2A 368 3.81e+01 c.37.1.9 139688 1fo9A 348 3.81e+01 1foaA c.68.1.10 59928 1foaA 348 3.81e+01 1foaA c.68.1.10 59929 1o6cA 388 3.90e+01 c.87.1.3 92565 2f1zA 522 3.90e+01 2i5vO 251 3.91e+01 1o7nA 449 3.92e+01 b.33.1.2 81162 d.129.3.3 81163 1eg9A 449 3.92e+01 1ndoA b.33.1.2 24443 d.129.3.3 41322 1ndoA 449 3.92e+01 1ndoA b.33.1.2 24444 d.129.3.3 41323 2bqqA 113 3.94e+01 1jtoA 148 3.96e+01 b.1.1.1 67274 1ne3A 68 3.98e+01 b.40.4.5 91828