# List of top-scoring protein chains for t2k-100-30-bys 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 1s1dA 331 4.52e-02 unknown_sccs -4566 1dv2A 452 1.70e+00 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1difA 99 2.33e+00 1fmb b.50.1.1 26503 1hvc 203 2.70e+00 1hvc b.50.1.1 26614 1bncA 449 2.73e+00 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1obpA 159 2.78e+00 1obpA b.60.1.1 27092 1bncB 449 2.84e+00 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 5hvpA 99 2.95e+00 1fmb b.50.1.1 26605 1b4aA 149 3.03e+00 1b4aA a.4.5.3 16088 d.74.2.1 39721 1jpc 109 3.39e+00 1b2pA b.78.1.1 27986 1gt1A 159 3.47e+00 b.60.1.1 -4436 1mejA 223 3.48e+00 c.65.1.1 79029 1hn2A 159 3.51e+00 b.60.1.1 65890 1meoA 209 3.52e+00 c.65.1.1 79035 1b4bA 71 3.64e+00 1b4aA d.74.2.1 39718 1ukmB 128 3.84e+00 d.169.1.1 -11625 1msaA 109 3.98e+00 1b2pA b.78.1.1 27987 1dv1A 449 4.28e+00 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1r4wA 226 4.31e+00 unknown_sccs -7447 1d3bA 75 4.38e+00 1d3bA b.38.1.1 24798 1nzhA 282 4.75e+00 d.151.1.2 -11398 1kzkA 99 4.95e+00 b.50.1.1 73371 1vheA 373 5.24e+00 unknown_sccs -4280 c.56.5.4 -7890 1f8rA 498 5.71e+00 1f8rA c.3.1.2 30410 d.16.1.5 37974 1ntfA 282 7.05e+00 d.151.1.2 -11397 1htqA 477 7.26e+00 d.15.9.1 71035 d.128.1.1 71036 2tmdA 729 8.52e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1nh0A 99 8.78e+00 b.50.1.1 -4299 1ii7A 333 8.88e+00 1ii7A d.159.1.4 62415 1djnA 729 8.95e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1o12A 376 9.34e+00 b.92.1.5 80758 c.1.9.10 80759 1r53A 382 9.34e+00 unknown_sccs -11177 1ghj 79 9.46e+00 1ghj b.84.1.1 28232 1i5pA 633 9.67e+00 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1h5oA 42 1.02e+01 g.9.1.2 83484 1pysB 785 1.03e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1k6dA 220 1.07e+01 unknown_sccs 72082 1qmyA 167 1.09e+01 1qmyA d.3.1.2 37094 1bveA 99 1.09e+01 1hvc b.50.1.1 26713 1r0vA 305 1.12e+01 c.52.2.1 -7572 c.52.2.1 -7573 d.75.1.1 -10344 1dl5A 317 1.13e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1cklA 126 1.18e+01 1cklB g.18.1.1 44851 g.18.1.1 44852 2aacA 177 1.19e+01 2arcA b.82.4.1 28150 1htoA 477 1.25e+01 d.15.9.1 70987 d.128.1.1 70988 1qx2A 76 1.28e+01 1smlA 269 1.30e+01 1smlA d.157.1.1 42053 1dazC 99 1.32e+01 1hvc b.50.1.1 26501 1kb0A 677 1.33e+01 a.3.1.6 68378 b.70.1.1 68379 1trrA 107 1.41e+01 1jhgA a.4.12.1 19017 3pcnA 200 1.42e+01 3pchA b.3.6.1 22725 2arcB 164 1.49e+01 2arcA b.82.4.1 28149 1cklB 126 1.54e+01 1cklB g.18.1.1 44853 g.18.1.1 44854 3pchA 200 1.57e+01 3pchA b.3.6.1 22653 1k2fA 190 1.61e+01 b.8.1.2 68054 1o94A 729 1.61e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 3pcgA 200 1.62e+01 3pchA b.3.6.1 22647 2dorA 311 1.67e+01 2dorA c.1.4.1 28593 1suuA 312 1.67e+01 unknown_sccs -4610 1ctj 89 1.67e+01 1ctj a.3.1.1 15798 1eiyB 785 1.68e+01 1pysB a.6.1.1 16305 a.6.1.1 16306 b.40.4.4 25314 d.58.13.1 39313 d.104.1.1 40782 d.138.1.1 41458 1dorA 311 1.71e+01 2dorA c.1.4.1 28595 1r62A 160 1.72e+01 1dpjA 329 1.78e+01 1smrA b.50.1.2 26828 1cjdA 394 1.81e+01 1cjdA b.121.2.1 58963 b.121.2.1 58964 2pcdA 200 1.82e+01 3pchA b.3.6.1 22665 1l4dB 122 1.83e+01 d.15.5.1 77684 1orc 71 1.89e+01 1orc a.35.1.2 17054 1itwA 741 1.89e+01 c.77.1.2 76793 1h09A 338 1.90e+01 b.109.1.1 83420 c.1.8.8 83421 1rypB 250 1.95e+01 1rypB d.153.1.4 41933 2arcA 164 1.97e+01 2arcA b.82.4.1 28148 1k1tA 99 1.98e+01 b.50.1.1 71995 1b7yB 785 2.01e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1k4zA 159 2.03e+01 b.80.5.1 72070 1l4zB 136 2.12e+01 d.15.5.1 77704 1td5A 202 2.13e+01 1n9eA 787 2.14e+01 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1reoA 486 2.22e+01 c.3.1.2 -5997 d.16.1.5 -9217 1o50A 157 2.25e+01 d.37.1.1 -9604 d.37.1.1 -9605 1e6wA 260 2.29e+01 1e6wA c.2.1.2 59326 2wrpR 107 2.31e+01 1jhgA a.4.12.1 19010 1jubA 311 2.33e+01 c.1.4.1 -5188 1jhgA 101 2.34e+01 1jhgA a.4.12.1 19009 1ip9A 85 2.36e+01 1ip9A d.15.2.2 62638 1hcd 118 2.36e+01 1hce b.42.5.2 25624 1j3wA 163 2.43e+01 unknown_sccs -10870 1amuA 563 2.52e+01 1amuA e.23.1.1 43351 2gar 212 2.52e+01 2gar c.65.1.1 34161 1hb5A 394 2.56e+01 i.6.1.1 65752 1hx6A 394 2.56e+01 1cjdA b.121.2.1 58995 b.121.2.1 58996 1hcxA 127 2.62e+01 b.109.1.1 65800 1inlA 296 2.62e+01 c.66.1.17 66220 1nmtA 392 2.64e+01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1hce 118 2.65e+01 1hce b.42.5.2 25625 1i81A 83 2.67e+01 1d3bB b.38.1.1 61930 1mk4A 157 2.70e+01 d.108.1.1 84979 1ugpB 226 2.73e+01 1ireB 228 2.75e+01 b.34.4.4 76770 1vif 62 2.77e+01 1vie b.34.4.1 24593 1c3oA 1073 2.81e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1k8kF 168 2.87e+01 d.198.2.1 68312 1e3sA 261 2.93e+01 1e6wA c.2.1.2 59201 1kv8A 216 2.94e+01 c.1.2.3 73054 1keeA 1073 2.96e+01 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1pjxA 314 3.02e+01 1mbyA 88 3.04e+01 d.223.1.1 78931 2mspA 126 3.04e+01 1mspA b.1.11.2 22335 1d3bB 91 3.05e+01 1d3bB b.38.1.1 24804 1bxrA 1073 3.08e+01 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1q6oA 216 3.08e+01 c.1.2.3 -5162 1k8tA 510 3.09e+01 e.41.1.1 68316 1kv9A 668 3.12e+01 a.3.1.6 73056 b.70.1.1 73057 1fnnA 389 3.14e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1jkxA 212 3.19e+01 c.65.1.1 66813 2sak 121 3.21e+01 2sak d.15.5.1 37711 1f07A 321 3.26e+01 1ezwA c.1.16.3 59560 1keeC 1073 3.27e+01 a.92.1.1 68500 c.24.1.1 68501 c.30.1.1 68502 c.30.1.1 68503 d.142.1.2 68504 d.142.1.2 68505 1cnuA 137 3.28e+01 1cof d.109.1.2 40862 1qwyA 291 3.28e+01 unknown_sccs -5023 1aw1A 256 3.34e+01 1amk c.1.1.1 28515 1grwA 126 3.38e+01 b.1.11.2 70391 1h7zA 194 3.40e+01 1qhvA b.21.1.1 60733 1rcsA 105 3.44e+01 1jhgA a.4.12.1 19025 1r8oA 96 3.45e+01 1jenA 267 3.47e+01 1jenA 1nrwA 288 3.50e+01 c.108.1.10 86128 1mxmA 254 3.55e+01 b.38.1.3 79647 d.58.43.1 79648 f.34.1.1 79649 2fua 215 3.60e+01 2fua c.74.1.1 34977 1d2qA 173 3.61e+01 1d4vB b.22.1.1 23894 1qg3A 195 3.63e+01 1qg3A b.1.2.1 21993 b.1.2.1 21994 1glv 303 3.69e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 1g8iA 190 3.74e+01 1rec a.39.1.5 60363 1ffkW 73 3.74e+01 1ffkW g.41.8.1 45315 1cseI 71 3.76e+01 1egpA d.40.1.1 38559 1oeyA 83 3.83e+01 d.15.2.2 -9162 1mgqA 83 3.87e+01 b.38.1.1 79099 5croA 66 3.90e+01 1orc a.35.1.2 17044 1c3oC 1073 3.91e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1ed7A 45 3.93e+01 1ed7A b.72.2.1 27809 1eljA 381 3.94e+01 4mbp c.94.1.1 35791 1c3oG 1073 3.95e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533