# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1exmA 405 6.98e-21 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1aipE 405 1.08e-20 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1ha3A 405 1.19e-20 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1jnyA 435 6.77e-20 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1efcA 393 7.40e-20 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1f60A 458 1.04e-18 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1d2eA 397 2.40e-18 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1kk1A 410 3.30e-09 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1s0uA 408 1.36e-07 1g7sA 594 3.50e-04 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1g7rA 594 3.56e-04 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1g7tA 594 4.42e-04 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1n0uA 842 5.55e-04 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1d1nA 99 1.34e-03 1d1nA b.43.3.1 25718 1bzyA 217 2.39e-01 1qk3A c.61.1.1 34071 1fnmA 691 2.84e-01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1dar 691 3.84e-01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1qk4A 233 7.12e-01 1qk3A c.61.1.1 34037 1fsgA 233 8.93e-01 1qk3A c.61.1.1 34029 1cjbA 231 9.18e-01 1qk3A c.61.1.1 34079 1kmoA 774 1.03e+00 f.4.3.3 72753 1po0A 751 1.43e+00 1qfgA 725 1.99e+00 1by5A f.4.3.3 43803 1qk3A 233 2.02e+00 1qk3A c.61.1.1 34031 1dlc 584 2.94e+00 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1hmpA 217 3.35e+00 1qk3A c.61.1.1 34075 2fcpA 723 3.95e+00 1by5A f.4.3.3 43802 1bb9 115 4.52e+00 1bb9 b.34.2.1 24554 1cyu 98 4.93e+00 1stfI d.17.1.2 38004 1ten 90 4.96e+00 1ten b.1.2.1 21990 1etu 394 5.36e+00 1efcA c.37.1.8 64737 1iraX 152 5.81e+00 1irp b.42.1.2 25556 1h6yA 170 6.38e+00 b.18.1.7 70904 1by3A 714 6.39e+00 1by5A f.4.3.3 43801 1ilr1 152 6.82e+00 1irp 1pkoA 139 7.28e+00 b.1.1.1 88147 1g2aA 168 7.32e+00 d.167.1.1 65109 1g3p 217 8.19e+00 1g3p b.37.1.1 24788 b.37.1.1 24789 1ga1A 372 8.34e+00 1ga1A c.41.1.2 32557 1ga6A 372 8.34e+00 1ga1A c.41.1.2 32556 1bkb 136 8.39e+00 1bkb b.34.5.2 24609 b.40.4.5 25341 1bsjA 168 8.95e+00 1bs4A d.167.1.1 42302 1by5A 714 9.14e+00 1by5A f.4.3.3 43800 1irp 153 9.28e+00 1irp b.42.1.2 25559 1nb5I 98 9.62e+00 d.17.1.2 80381 1idk 359 1.01e+01 1qcxA b.80.1.2 28025 1go3E 187 1.05e+01 b.40.4.5 83054 d.230.1.1 83055 1is8A 230 1.19e+01 d.96.1.1 66321 1f1xA 322 1.32e+01 d.32.1.3 83208 d.32.1.3 83209 1jhfA 202 1.39e+01 a.4.5.2 63057 b.87.1.1 63058 1sro 76 1.39e+01 1sro b.40.4.5 25327 1mq7A 154 1.48e+01 b.85.4.1 79404 1vjnA 220 1.53e+01 1ixlA 131 1.56e+01 1fiwA 290 1.58e+01 5ptp 1pmy 123 1.63e+01 1bqk b.6.1.1 22888 1m56B 264 1.64e+01 b.6.1.2 74472 f.17.2.1 74473 1j7lA 264 1.73e+01 d.144.1.6 62697 1l7vC 249 1.82e+01 c.37.1.12 73674 1jw3A 140 1.86e+01 d.208.1.1 67373 1mv3A 213 1.94e+01 1kzlA 208 1.98e+01 b.43.4.3 77635 b.43.4.3 77636 1kn9A 249 2.00e+01 b.87.1.2 68699 1soxA 466 2.02e+01 1soxA b.1.18.6 21947 d.120.1.1 41090 d.176.1.1 42563 1ew0A 130 2.04e+01 1drmA d.110.3.2 40905 1b12A 248 2.08e+01 1b12A b.87.1.2 28388 1jj2A 239 2.09e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085 1n7fA 97 2.09e+01 1f1uA 323 2.11e+01 d.32.1.3 83200 d.32.1.3 83201 1gztA 115 2.12e+01 b.115.1.1 76428 2eifA 136 2.20e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1oi1A 221 2.20e+01 b.34.9.3 87037 b.34.9.3 87038 1uebA 184 2.23e+01 1pm4A 119 2.23e+01 1bs4A 168 2.24e+01 1bs4A d.167.1.1 42287 1icjA 168 2.24e+01 1bs4A d.167.1.1 42284 1c3hA 137 2.26e+01 1jp4A 308 2.26e+01 1jp4A e.7.1.1 63223 1umwA 237 2.27e+01 1d06A 130 2.28e+01 1drmA d.110.3.2 40906 1vhzA 198 2.30e+01 1bjt 793 2.32e+01 1bjt e.11.1.1 43249 1n7eA 97 2.36e+01 1vgyA 393 2.37e+01 1iknA 286 2.39e+01 1a3qA b.1.18.1 21936 b.2.5.3 22449 1h6tA 291 2.62e+01 b.1.18.15 65686 c.10.2.1 65687 3prn 289 2.73e+01 3prn f.4.3.1 43761 1ni9A 338 2.73e+01 e.7.1.2 85739 1oxcA 114 2.77e+01 1k0hA 117 2.80e+01 b.106.1.2 71975 8prn 289 2.91e+01 3prn f.4.3.1 43767 1npuA 117 3.09e+01 1bdo 80 3.12e+01 1bdo b.84.1.1 28214 1sixA 174 3.18e+01 1earA 147 3.26e+01 b.107.1.1 64875 d.58.38.1 64876 1dpjA 329 3.26e+01 1smrA b.50.1.2 26828 1js8A 394 3.26e+01 a.86.1.1 67219 b.112.1.1 67220 2kauB 106 3.34e+01 1ubpB b.85.3.1 28328 1gvhA 396 3.45e+01 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1bh3 289 3.51e+01 3prn f.4.3.1 43766 1prn 289 3.51e+01 3prn f.4.3.1 43762 1ui0A 205 3.53e+01 1l6oA 95 3.59e+01 b.36.1.1 84534 1lp8A 254 3.59e+01 1fwcB 106 3.65e+01 1ubpB b.85.3.1 28324 1h0hA 977 3.70e+01 b.52.2.2 76435 c.81.1.1 76436 1fm0E 150 3.86e+01 1fmaE d.41.5.1 38629 1g8lA 411 3.87e+01 1g8lA b.85.6.1 60365 b.103.1.1 60366 c.57.1.2 60367 1llwA 1520 4.00e+01 b.80.4.1 74017 c.1.4.1 74018 d.153.1.1 74019