# List of top-scoring protein chains for T0216.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.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 1m6yA 301 1.50e+00 a.60.13.1 78716 c.66.1.23 78717 1f2dA 341 2.33e+00 1f2dA c.79.1.1 35298 1j0dA 341 2.33e+00 c.79.1.1 83902 1j0eA 341 2.41e+00 c.79.1.1 83906 1emsA 440 2.73e+00 1emsA d.13.1.1 37520 d.160.1.1 42086 1danL 152 4.39e+00 1edmB g.3.11.1 44209 g.3.11.1 44210 g.32.1.1 44965 1sdmA 369 4.70e+00 1bqyA 234 5.02e+00 5ptp b.47.1.2 26332 1qq2A 199 5.58e+00 1qq2A c.47.1.10 33064 1h4pA 408 7.06e+00 c.1.8.3 -5314 1hqmA 313 7.85e+00 i.8.1.1 45972 1l9uA 314 8.17e+00 i.8.1.1 73748 1v7rA 186 8.92e+00 c.51.4.1 -7546 1fvuB 125 9.53e+00 1ixxB d.169.1.1 42346 1fmtA 314 1.03e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1koa 491 1.21e+01 1tkiA b.1.1.4 21712 d.144.1.7 41642 1qibA 161 1.24e+01 1ck7A d.92.1.11 40359 1hwmB 266 1.33e+01 1abrB b.42.2.1 25569 b.42.2.1 25570 1eodA 100 1.37e+01 1t1dA d.42.1.2 38641 1gfq 340 1.45e+01 2omf f.4.3.1 43751 1q92A 197 1.57e+01 c.108.1.8 -6819 1i6vA 314 1.62e+01 d.74.3.1 61852 d.181.1.1 61853 1lmeA 176 1.67e+01 d.167.1.1 84629 1eakA 421 1.71e+01 a.20.1.2 70093 d.92.1.11 70094 g.14.1.2 70095 g.14.1.2 70096 g.14.1.2 70097 1im8A 244 1.78e+01 c.66.1.14 66212 1p9bA 442 1.81e+01 c.37.1.10 -7115 1ck7A 631 1.88e+01 1ck7A a.20.1.2 58969 b.66.1.1 27538 d.92.1.11 58970 g.14.1.2 44674 g.14.1.2 44675 g.14.1.2 44676 1hovA 163 2.00e+01 d.92.1.11 65897 1knmA 130 2.02e+01 b.42.2.1 72781 1on4A 174 2.11e+01 c.47.1.10 -7512 1nuiA 255 2.20e+01 e.13.1.2 86194 g.41.3.2 86195 1eofA 100 2.29e+01 1t1dA d.42.1.2 38640 1k8kB 394 2.30e+01 c.55.1.1 68307 1it2A 146 2.30e+01 a.1.1.2 66365 1jt8A 102 2.44e+01 b.40.4.5 63279 1yal 218 2.49e+01 1cs8A d.3.1.1 37025 1iw7A 315 2.51e+01 d.74.3.1 71470 d.181.1.1 71471 1op2A 234 2.51e+01 1e94A 175 2.61e+01 1nedA d.153.1.4 41977 1op0A 234 2.68e+01 1hxxA 340 2.69e+01 2omf f.4.3.1 61385 1nedA 183 2.77e+01 1nedA d.153.1.4 41974 1lkdA 297 2.78e+01 d.32.1.3 78059 d.32.1.3 78060 1kkoA 413 2.82e+01 c.1.11.2 68675 d.54.1.1 68676 1eoeA 100 2.88e+01 1t1dA d.42.1.2 38638 1exbE 103 2.96e+01 1t1dA d.42.1.2 38643 1a68 95 2.98e+01 1t1dA d.42.1.2 38639 1mkmA 249 2.98e+01 a.4.5.33 79242 d.110.2.2 79243 1su4A 994 3.04e+01 b.82.7.1 -4927 c.108.1.7 -6854 d.220.1.1 -11668 f.33.1.1 -12333 1gfp 340 3.06e+01 2omf f.4.3.1 43750 1t1dA 100 3.07e+01 1t1dA d.42.1.2 38637 1oe0A 230 3.23e+01 c.37.1.1 -6976 1ho1A 242 3.30e+01 1ho1A c.1.24.1 61097 1h2rL 534 3.30e+01 1h2rL e.18.1.1 43298 1m5wA 243 3.30e+01 c.1.24.1 84836 1ubkL 534 3.31e+01 e.18.1.1 88422 1ot3A 250 3.34e+01 c.37.1.1 87400 1k3pA 426 3.35e+01 a.103.1.1 77237 1owcA 427 3.35e+01 1bgp 309 3.39e+01 1bgp a.93.1.1 18690 1pn5A 159 3.41e+01 unknown_sccs -1196 1okiA 210 3.42e+01 b.11.1.1 -3030 b.11.1.1 -3031 1h2aL 567 3.49e+01 1h2rL e.18.1.1 43299 1nxeA 427 3.69e+01 a.103.1.1 86377 1ci0A 228 3.73e+01 1ci0A b.45.1.1 25750 1d7dA 186 3.78e+01 1d7bA b.1.9.1 22311 1pl3A 186 3.79e+01 b.1.9.1 88158 1d7cA 190 3.81e+01 1d7bA b.1.9.1 22309 1q57A 503 3.86e+01 c.37.1.11 -7131 e.13.1.2 -11987 1iakB 185 3.88e+01 1iakB b.1.1.2 21626 d.19.1.1 38200 1ow1A 195 3.89e+01 unknown_sccs -4422 1d9kD 188 3.89e+01 1iakB b.1.1.2 21628 d.19.1.1 38202 2omf 340 3.93e+01 2omf f.4.3.1 43749 1gfo 340 3.98e+01 2omf f.4.3.1 43753