# List of top-scoring protein chains for t2k-100-30-str2 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 1d8iA 311 5.75e-01 1d8iA d.63.1.1 39541 1awcA 110 8.01e-01 1awcA a.4.5.21 16167 1d8hA 311 1.35e+00 1d8iA d.63.1.1 39544 1p4xA 250 1.98e+00 a.4.5.28 87784 a.4.5.28 87785 1g2rA 100 2.28e+00 1g2rA d.192.1.1 60231 1f4tA 368 2.63e+00 1f4tA a.104.1.1 18973 1m4vA 204 4.28e+00 b.40.2.2 74459 d.15.6.1 74460 1io7A 368 4.54e+00 1f4tA a.104.1.1 18971 1jbgA 109 5.37e+00 a.6.1.3 66480 2bifA 469 5.74e+00 1bif c.37.1.7 31963 c.60.1.4 34009 1etc 110 5.99e+00 1awcA a.4.5.21 16162 1lnsA 763 5.99e+00 a.40.2.1 78101 b.18.1.13 78102 c.69.1.21 78103 1j7xA 302 6.50e+00 c.14.1.2 66425 1bif 469 6.55e+00 1bif c.37.1.7 31961 c.60.1.4 34003 1crl 534 6.58e+00 1thg c.69.1.17 34765 1c2aA 120 7.00e+00 1c2aA g.3.13.1 44349 g.3.13.1 44350 1riqA 465 8.19e+00 unknown_sccs -1295 d.104.1.1 -10769 1k8kD 300 8.57e+00 d.198.2.1 68309 d.198.2.1 68310 1vk8A 106 8.63e+00 1o86A 589 8.80e+00 d.92.1.5 81177 1iujA 106 9.00e+00 unknown_sccs -9953 1cds 77 9.16e+00 1cds g.7.1.3 44461 3bifA 468 1.00e+01 1bif c.37.1.7 31962 c.60.1.4 34008 1s7oA 113 1.04e+01 1mk0A 97 1.26e+01 d.226.1.1 79216 1ef1A 294 1.42e+01 1ef1A a.11.2.1 16368 b.55.1.5 27003 d.15.1.4 37611 1booA 323 1.45e+01 1booA c.66.1.11 34248 1jpmA 366 1.70e+01 c.1.11.2 67031 d.54.1.1 67032 1jgjA 217 1.79e+01 1c3wA f.13.1.1 62952 1psdA 409 1.92e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1lfjA 119 1.93e+01 1ly2A 130 2.01e+01 g.18.1.1 74335 g.18.1.1 74336 1pfjA 108 2.16e+01 1imt 80 2.20e+01 1imt g.3.10.1 44201 g.3.10.1 44202 1q6cA 495 2.24e+01 c.1.8.1 -5300 1azsB 212 2.25e+01 1azsA d.58.29.1 39423 1h9oA 112 2.29e+01 1qadA d.93.1.1 60837 1a8vA 121 2.36e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1byb 495 2.37e+01 1byb c.1.8.1 28790 2nacA 393 2.45e+01 2nadA c.2.1.4 30088 c.23.12.1 31348 1o8vA 134 2.46e+01 b.60.1.2 86680 1ekgA 127 2.52e+01 1dlxA d.82.2.1 40021 1gvjA 146 2.63e+01 a.4.5.21 -293 1brlA 355 2.63e+01 1lucA c.1.16.1 29553 1earA 147 2.64e+01 b.107.1.1 64875 d.58.38.1 64876 1dmlA 319 2.64e+01 1dmlA d.131.1.2 41380 d.131.1.2 41381 1jj2S 119 2.65e+01 1ffkQ b.34.5.1 63104 1s72T 120 2.66e+01 3crxA 343 2.67e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1iqzA 81 2.73e+01 d.58.1.4 66281 1evsA 187 2.73e+01 1evsA a.26.1.1 16845 1dfeA 37 2.85e+01 1dfeA g.42.1.1 45318 1hyqA 263 2.98e+01 1hyqA c.37.1.10 61412 1g291 372 2.99e+01 1g291 1j90A 230 3.06e+01 c.37.1.1 66448 1pz4A 116 3.09e+01 d.106.1.1 -10780 1dgzA 37 3.15e+01 1dfeA g.42.1.1 45319 1bw4 125 3.20e+01 1bw4 b.52.1.2 26900 1ab8A 220 3.21e+01 1azsA d.58.29.1 39414 1sqgA 429 3.24e+01 1g3kA 174 3.31e+01 1nedA d.153.1.4 41989 1eb0A 147 3.33e+01 b.107.1.1 64890 d.58.38.1 64891 1dun 134 3.43e+01 1dun b.85.4.1 28371 1qnxA 209 3.44e+01 1qnxA d.111.1.1 40914 1dik 874 3.49e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 4crxA 322 3.64e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1fjsL 52 3.83e+01 1hcgB g.3.11.1 44226 1f9fA 83 3.85e+01 1f9fA d.58.8.1 39224 2nadA 393 3.89e+01 2nadA c.2.1.4 30090 c.23.12.1 31350 1ghqB 134 3.91e+01 1ghqB g.18.1.1 60522 g.18.1.1 60523 1uspA 139 3.95e+01 d.227.1.1 -11179 1m98A 317 3.96e+01 a.175.1.1 78866 d.17.4.6 78867