# List of top-scoring protein chains for T0235.t2k-w0.5 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 1nb8A 353 4.96e-37 d.3.1.9 80385 1v86A 95 5.67e-02 1v5tA 90 9.15e-02 1hbxG 157 7.69e-01 1awcA a.4.5.21 60934 1omiA 248 7.90e-01 a.4.5.4 87079 b.82.3.3 87080 1ng7A 60 9.41e-01 a.178.1.1 85671 1ud7A 76 4.11e+00 1ubi d.15.1.1 37593 1g55A 343 5.24e+00 1g55A c.66.1.26 34247 1gveA 327 6.45e+00 c.1.7.1 70597 1hyuA 521 6.96e+00 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1cd9A 175 7.19e+00 1bgc a.26.1.1 16815 1rhgA 174 7.22e+00 1bgc a.26.1.1 16812 1bgeA 175 7.35e+00 1bgc a.26.1.1 16823 1ffyA 917 7.83e+00 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1hkfA 122 7.96e+00 b.1.1.1 83553 1mdaH 368 8.81e+00 2bbkH b.69.2.1 27637 1gnc 178 1.05e+01 1bgc a.26.1.1 16821 1bgc 174 1.15e+01 1bgc a.26.1.1 16822 1pq2A 476 1.18e+01 a.104.1.1 -1470 1rdg 53 1.29e+01 1rb9 g.41.5.1 45221 1mkhA 107 1.33e+01 b.40.4.4 79238 1c3tA 76 1.33e+01 1ubi d.15.1.1 37594 1e8jA 52 1.42e+01 g.41.5.1 64796 1hc7A 477 1.43e+01 1hc7A c.51.1.1 60938 d.68.5.1 60940 d.104.1.1 60939 3hohA 104 1.46e+01 9rnt d.1.1.4 36085 1fipA 98 1.54e+01 1fipA unknown_sccs 18980 1p3qU 76 1.58e+01 d.15.1.1 87750 1cmxB 75 1.71e+01 1ubi d.15.1.1 37595 1rqgA 722 1.74e+01 1gveB 327 1.89e+01 c.1.7.1 70598 1i3iA 104 1.89e+01 9rnt d.1.1.4 61593 1hfx 123 1.93e+01 3lzt d.2.1.2 36600 1s96A 219 2.15e+01 c.37.1.1 -6972 1fqiA 147 2.20e+01 1agrE a.91.1.1 18542 1fzuA 104 2.25e+01 9rnt d.1.1.4 36071 1ezvD 245 2.31e+01 1be3D a.3.1.3 59546 f.23.11.1 59547 1ni3A 392 2.34e+01 c.37.1.8 80531 d.15.10.2 80532 1kb9D 246 2.35e+01 a.3.1.3 77317 f.23.11.1 77318 1kenH 221 2.39e+01 b.1.1.1 72379 b.1.1.2 72380 1kyoD 248 2.42e+01 a.3.1.3 73254 f.23.11.1 73255 1q9eA 104 2.42e+01 d.1.1.4 -8810 1pwjA 89 2.47e+01 d.39.1.1 -9707 1bcw 319 2.48e+01 1avc a.65.1.1 18176 2hohA 104 2.49e+01 9rnt d.1.1.4 36077 1m6bA 621 2.51e+01 c.10.2.5 74521 c.10.2.5 74522 g.3.9.1 74523 g.3.9.1 74524 1bg5 254 2.51e+01 1b8xA a.45.1.1 17723 c.47.1.5 33017 1fysA 104 2.53e+01 9rnt d.1.1.4 36104 1clm 148 2.55e+01 1cll a.39.1.5 17301 1nexB 464 2.56e+01 a.158.1.1 80443 b.69.4.1 80444 1exrA 148 2.56e+01 1cll a.39.1.5 17299 1rhlA 104 2.56e+01 9rnt d.1.1.4 36082 1mqtB 261 2.58e+01 1birA 104 2.60e+01 9rnt d.1.1.4 36083 1n42A 319 2.60e+01 a.65.1.1 79979 1i0vA 104 2.64e+01 9rnt d.1.1.4 36054 1lowA 104 2.64e+01 d.1.1.4 74167 7rnt 104 2.64e+01 9rnt d.1.1.4 36105 1hyfA 104 2.66e+01 9rnt d.1.1.4 36065 1g02A 104 2.67e+01 9rnt d.1.1.4 36076 2birA 104 2.68e+01 9rnt d.1.1.4 36133 1i2gA 104 2.69e+01 9rnt d.1.1.4 61567 2aae 104 2.69e+01 9rnt d.1.1.4 36066 1re6A 94 2.71e+01 d.39.1.1 -9712 1det 104 2.74e+01 9rnt d.1.1.4 36101 1gaxA 862 2.79e+01 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1gm5A 780 2.80e+01 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1dugA 234 2.81e+01 1b8xA a.45.1.1 17718 c.47.1.5 33012 1r13A 148 2.82e+01 d.169.1.1 -11646 h.1.1.1 -12895 1loyA 104 2.83e+01 d.1.1.4 74168 1rhwA 89 2.83e+01 d.39.1.1 -9709 1kngA 156 2.84e+01 c.47.1.10 72777 1gne 232 2.84e+01 1b8xA a.45.1.1 17721 c.47.1.5 33015 1lovA 104 2.93e+01 d.1.1.4 74166 1bc0 319 2.93e+01 1avc a.65.1.1 18174 1a8b 318 2.97e+01 1avc a.65.1.1 18171 1rgk 104 2.98e+01 9rnt d.1.1.4 36067 1f3cA 89 2.99e+01 1cmiA d.39.1.1 38557 1ch0A 104 3.05e+01 9rnt d.1.1.4 36129 2ran 316 3.13e+01 1avc a.65.1.1 18170 1cmiA 85 3.17e+01 1cmiA d.39.1.1 38551 1trqA 104 3.22e+01 9rnt d.1.1.4 36127 5hohA 104 3.26e+01 9rnt d.1.1.4 36096 1qz8A 113 3.26e+01 unknown_sccs -4264 1trpA 104 3.28e+01 9rnt d.1.1.4 36134 1bcy 319 3.28e+01 1avc a.65.1.1 18172 1oedE 260 3.32e+01 f.36.1.1 86915 1q9cA 191 3.33e+01 a.22.1.3 -567 1jv2B 692 3.41e+01 b.1.15.1 67338 c.62.1.1 67339 d.200.1.1 67340 g.3.11.6 67341 g.3.11.6 67342 1q90C 127 3.44e+01 b.33.1.1 -3544 4hohA 104 3.45e+01 9rnt d.1.1.4 36118 1bcz 319 3.49e+01 1avc a.65.1.1 18177 1extA 162 3.54e+01 1extA g.24.1.1 44900 g.24.1.1 44901 g.24.1.1 44902 1ktaA 365 3.61e+01 e.17.1.1 77533 1shyA 234 3.68e+01 1q6xA 644 3.69e+01 1ntyA 311 3.73e+01 1ffvA 163 3.73e+01 1qj2A a.56.1.1 17915 d.15.4.2 37700 1m9aA 218 3.75e+01 a.45.1.1 84882 c.47.1.5 84883 1b8xA 280 3.78e+01 1b8xA a.45.1.1 17739 c.47.1.5 33033 1rf6A 427 3.81e+01 d.68.2.2 -10314 1s72G 348 3.82e+01 1og5A 475 3.83e+01 a.104.1.1 86982 1ujqA 305 3.84e+01 c.1.12.7 -5581 1neeA 138 3.87e+01 unknown_sccs -9002 g.59.1.1 -12824 1ujvA 96 3.93e+01 b.36.1.1 -3753 1g87A 614 4.00e+01 a.102.1.2 83275 b.2.2.2 83276