# 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 1pd21 199 6.23e-04 1pd21 1gumA 222 1.61e-03 1pgtA a.45.1.1 17683 c.47.1.5 32977 1gulA 222 1.77e-03 1pgtA a.45.1.1 17675 c.47.1.5 32969 1iyhA 198 1.99e-03 a.45.1.1 83790 c.47.1.5 83791 1oktA 211 6.26e-03 a.45.1.1 -942 c.47.1.5 -7467 1oe8A 211 7.08e-02 a.45.1.1 86905 c.47.1.5 86906 6gsvA 217 9.36e-02 1b8xA a.45.1.1 17633 c.47.1.5 32925 1f3aA 222 1.18e-01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1k3lA 221 1.23e-01 a.45.1.1 77229 c.47.1.5 77230 1k3yA 221 1.50e-01 a.45.1.1 77245 c.47.1.5 77246 1gseA 221 2.44e-01 1pgtA a.45.1.1 17667 c.47.1.5 32961 2gsq 202 2.98e-01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1pgtA 210 3.28e-01 1pgtA a.45.1.1 17515 c.47.1.5 32809 1b4pA 217 4.16e-01 a.45.1.1 83158 c.47.1.5 83159 1l2lA 457 5.62e-01 c.72.1.3 77656 1b8xA 280 1.13e+00 1b8xA a.45.1.1 17739 c.47.1.5 33033 1dugA 234 1.41e+00 1b8xA a.45.1.1 17718 c.47.1.5 33012 1d5tA 433 2.69e+00 1gnd c.3.1.3 30422 d.16.1.6 37986 1gnd 447 2.82e+00 1gnd c.3.1.3 30423 d.16.1.6 37987 1f47B 144 3.01e+00 1f46A d.129.4.1 59645 1augA 215 3.29e+00 1a2zA c.56.4.1 33798 1cot 129 3.55e+00 1ycc a.3.1.1 15899 1f46A 140 3.75e+00 1f46A d.129.4.1 59643 1m0uA 249 4.09e+00 a.45.1.1 78359 c.47.1.5 78360 1f7wA 144 4.32e+00 1f46A d.129.4.1 59679 1nhyA 219 4.46e+00 a.45.1.1 80520 c.47.1.5 80521 1r2rA 248 4.84e+00 c.1.1.1 -5147 1aw9 216 5.07e+00 1gnwA a.45.1.1 17736 c.47.1.5 33030 1o6zA 303 5.74e+00 c.2.1.5 81107 d.162.1.1 81108 1e6bA 221 6.39e+00 1e6bA a.45.1.1 59294 c.47.1.5 59295 1ezfA 340 7.12e+00 1ezfA a.128.1.2 19440 1qmvA 197 7.89e+00 1qq2A c.47.1.10 33066 1amk 251 8.15e+00 1amk c.1.1.1 28503 1uocA 289 8.70e+00 unknown_sccs -7671 2oatA 439 8.71e+00 2dkb c.67.1.4 34452 1oatA 439 9.02e+00 2dkb c.67.1.4 34461 1qq2A 199 9.61e+00 1qq2A c.47.1.10 33064 1bp3A 191 1.06e+01 1huw a.26.1.1 16838 1n55A 251 1.26e+01 c.1.1.1 80007 1q9iA 571 1.30e+01 a.138.1.3 -2051 c.3.1.4 -6041 d.168.1.1 -11607 1ozhA 566 1.53e+01 c.31.1.3 -6737 c.36.1.5 -6895 c.36.1.9 -6935 1kf6C 130 1.55e+01 f.21.2.2 72399 1ksfX 758 1.57e+01 a.174.1.1 77522 c.37.1.20 77523 c.37.1.20 77524 1dttA 560 1.71e+01 1rthA c.55.3.1 33611 e.8.1.2 43088 1bo1A 416 1.72e+01 1bo1A d.143.1.2 41591 1iu8A 206 1.73e+01 c.56.4.1 71436 1kid 203 1.88e+01 1derA c.8.5.1 30771 1m64A 571 1.89e+01 a.138.1.3 78683 c.3.1.4 78684 d.168.1.1 78685 1jkmA 358 1.90e+01 1jkmA c.69.1.2 34633 1nofA 383 1.97e+01 b.71.1.2 -4668 c.1.8.3 -5339 1hm9A 468 2.00e+01 b.81.1.4 65866 c.68.1.5 65867 1izoA 417 2.02e+01 a.104.1.1 83851 1kssA 571 2.08e+01 a.138.1.3 72928 c.3.1.4 72929 d.168.1.1 72930 1qjdA 571 2.08e+01 1qjdA a.138.1.3 19695 c.3.1.4 30432 d.168.1.1 42315 1ovaA 386 2.08e+01 1ovaA e.1.1.1 42619 1lj1A 571 2.09e+01 a.138.1.3 78023 c.3.1.4 78024 d.168.1.1 78025 1uhgA 385 2.09e+01 e.1.1.1 88491 1e39A 571 2.12e+01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1eu8A 409 2.17e+01 1eu8A c.94.1.1 59502 1jdlA 121 2.47e+01 a.3.1.1 66557 1j1qA 261 2.49e+01 d.165.1.1 -11546 1ky9B 448 2.51e+01 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1do0A 442 2.57e+01 1do0A c.37.1.20 32432 1g97A 459 2.98e+01 1fwyA b.81.1.4 60394 c.68.1.5 60395 1imdA 277 3.10e+01 1imbA e.7.1.1 42968 1v7zA 260 3.16e+01 unknown_sccs -6353 1ig3A 263 3.28e+01 1ig3A b.82.6.1 62358 c.100.1.1 62359 1ky9A 448 3.31e+01 b.36.1.4 73198 b.47.1.1 73199 1ry9A 145 3.35e+01 d.198.1.1 -9020 1gwcA 230 3.36e+01 a.45.1.1 70660 c.47.1.5 70661 1imbA 277 3.38e+01 1imbA e.7.1.1 42957 1i19A 561 3.52e+01 1i19A d.58.32.3 61522 d.145.1.1 61523 1jkmB 361 3.63e+01 1jkmA c.69.1.2 34634 1vaoA 560 3.72e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1bx4A 345 3.89e+01 1bx4A c.72.1.1 34935 1ql3A 99 3.91e+01 1ycc a.3.1.1 15822 1k7kA 221 3.96e+01 c.51.4.1 72104