# 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 1v6fA 151 3.43e-01 1k6zA 141 5.75e-01 d.198.1.1 68247 1szwA 379 9.81e-01 unknown_sccs -10164 1si7A 369 1.16e+00 unknown_sccs -10163 1r4xA 275 1.62e+00 unknown_sccs -2846 unknown_sccs -10776 1jyaA 130 2.25e+00 d.198.1.1 67453 1pzdA 322 2.34e+00 unknown_sccs -2848 unknown_sccs -10778 1pmaA 233 2.89e+00 1pmaA d.153.1.4 41918 1fu1B 203 4.27e+00 1fu1B b.59.1.1 27077 h.1.11.1 45631 1v74A 107 4.60e+00 unknown_sccs -9319 1omiA 248 4.75e+00 a.4.5.4 87079 b.82.3.3 87080 1lr0A 129 4.85e+00 d.212.1.1 74213 1d1gA 168 4.99e+00 1d1gA c.71.1.1 34889 1bgvA 449 5.02e+00 1k89 c.2.1.7 30217 c.58.1.1 33865 1bsmA 201 5.25e+00 1avmA a.2.11.1 15780 d.44.1.1 38743 1mn8A 100 5.29e+00 a.61.1.6 79318 1fu1A 203 5.41e+00 1fu1B b.59.1.1 27076 h.1.11.1 45630 1f35A 162 5.44e+00 1f35A b.94.1.1 59628 1g6oA 330 5.97e+00 1g6oA c.37.1.11 32430 1hrdA 449 6.19e+00 1k89 c.2.1.7 30219 c.58.1.1 33867 1cz3A 168 6.48e+00 1d1gA c.71.1.1 34891 1jm7B 117 6.66e+00 g.44.1.1 66881 1ci0A 228 6.90e+00 1ci0A b.45.1.1 25750 1bxeA 113 8.19e+00 1bxeA d.55.1.1 38898 1s98A 107 8.28e+00 1jobA 162 8.46e+00 1f35A b.94.1.1 63207 1n6zA 105 8.56e+00 unknown_sccs 85369 1ui8A 638 1.02e+01 b.30.2.1 -3525 d.17.2.1 -9272 d.17.2.1 -9273 1lvk 762 1.03e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1k89 449 1.04e+01 1k89 c.2.1.7 30218 c.58.1.1 33866 1f48A 589 1.08e+01 1f48A c.37.1.10 32280 c.37.1.10 32281 1eijA 80 1.15e+01 1eijA a.5.6.1 16298 1ivwA 638 1.16e+01 b.30.2.1 71456 d.17.2.1 71457 d.17.2.1 71458 1d0yA 761 1.21e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1iqyA 638 1.23e+01 b.30.2.1 76763 d.17.2.1 76764 d.17.2.1 76765 1ui7A 638 1.25e+01 b.30.2.1 -3523 d.17.2.1 -9268 d.17.2.1 -9269 155c 135 1.30e+01 1ycc a.3.1.1 15900 1g0uI 205 1.40e+01 d.153.1.4 41891 7ceiB 206 1.42e+01 1bxiB d.4.1.1 37134 1avmA 201 1.43e+01 1avmA a.2.11.1 15782 d.44.1.1 38745 1g0uL 241 1.47e+01 d.153.1.4 41894 1vjlA 164 1.47e+01 unknown_sccs -11117 1m56B 264 1.48e+01 b.6.1.2 74472 f.17.2.1 74473 1o5yA 193 1.50e+01 1iknA 286 1.50e+01 1a3qA b.1.18.1 21936 b.2.5.3 22449 1a17 166 1.58e+01 1a17 a.118.8.1 19206 1lqtA 456 1.58e+01 c.3.1.1 74198 c.4.1.1 74199 1c0pA 363 1.60e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1um8A 376 1.61e+01 c.37.1.20 -7251 1dynA 125 1.64e+01 1dynA b.55.1.1 26955 1hcl 298 1.64e+01 1hcl d.144.1.7 41593 2dynA 122 1.66e+01 1dynA b.55.1.1 26957 1r94A 118 1.72e+01 b.124.1.1 -4402 1ryp1 222 1.73e+01 1ryp1 1oq1A 223 1.83e+01 unknown_sccs -3455 1e1xA 299 1.84e+01 1hcl d.144.1.7 59157 1uxxX 133 1.85e+01 b.18.1.10 -3107 1q0uA 219 1.85e+01 c.37.1.19 -7205 1avk 638 1.88e+01 1a2vA b.30.2.1 24410 d.17.2.1 38047 d.17.2.1 38048 1lkxA 697 1.88e+01 c.37.1.9 73981 1mveA 243 1.96e+01 b.29.1.2 85140 1p7gA 222 1.98e+01 a.2.11.1 -108 d.44.1.1 -9742 1aipE 405 2.00e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1jvpP 298 2.02e+01 d.144.1.7 67371 1rypJ 204 2.03e+01 d.153.1.4 41878 1aohB 147 2.17e+01 1aohA b.2.2.2 22402 3dni 260 2.24e+01 3dni d.151.1.1 41791 1ry9A 145 2.26e+01 d.198.1.1 -9020 2btvA 901 2.30e+01 2btvA e.28.1.1 43376 1vi9A 299 2.32e+01 c.72.1.5 -8393 1d8cA 723 2.33e+01 1d8cA c.1.13.1 29325 1prtD 110 2.37e+01 1bcpD b.40.2.1 25128 1gz8A 299 2.52e+01 d.144.1.7 83405 1rypE 242 2.60e+01 1rypE d.153.1.4 41936 1ffkR 66 2.66e+01 1ffkR g.39.1.6 45152 1i19A 561 2.70e+01 1i19A d.58.32.3 61522 d.145.1.1 61523 1nt2B 258 2.72e+01 a.183.1.1 86150 1uwsA 489 2.74e+01 1rypF 233 2.76e+01 1rypF d.153.1.4 41937 1ik9A 213 2.92e+01 b.59.1.1 66176 h.1.11.1 66177 1h6fA 193 2.93e+01 b.2.5.4 70901 1i4jA 110 3.16e+01 d.55.1.1 76734 1mixA 206 3.20e+01 a.11.2.1 79166 b.55.1.5 79167 1bcpD 110 3.29e+01 1bcpD b.40.2.1 25132 1b04A 318 3.33e+01 1b04A d.142.2.2 41579 1o5oA 221 3.46e+01 c.61.1.1 -7954 1fonA 240 3.46e+01 5ptp b.47.1.2 26231 1nrgA 261 3.50e+01 b.45.1.1 80694 1ia9A 280 3.50e+01 1ia9A d.144.1.5 62113 1cqkA 101 3.62e+01 1cqkA b.1.1.2 21547 1o26A 232 3.65e+01 d.207.1.1 86566 1aohA 147 3.68e+01 1aohA b.2.2.2 22401 1p90A 145 3.68e+01 unknown_sccs -7684 1j6rA 214 3.70e+01 d.173.1.2 71598 1rlhA 173 3.71e+01 unknown_sccs -10786 2nllB 103 3.74e+01 2nllB g.39.1.2 45115 1nxzA 246 3.77e+01 b.122.1.2 86391 c.116.1.5 86392 1kkcA 221 3.77e+01 a.2.11.1 68660 d.44.1.1 68661 1p9eA 331 3.85e+01 1vhyA 257 3.88e+01 b.122.1.2 -5129 c.116.1.5 -6705 1j2gA 319 3.90e+01 1kw4A 89 3.93e+01 a.60.1.2 73077 1kq4A 232 3.96e+01 d.207.1.1 68791 1p7tA 731 3.96e+01 c.1.13.1 -5600