# List of top-scoring protein chains for t2k-100-30-near-backbone-11-scores 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.soe.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 1onqA 283 6.72e-01 b.1.1.2,d.19.1.1 93365,93366 3eo6A 106 9.56e-01 1pysB 785 1.36e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,b.153.1.1 16299,16300,25311,39310,40779,41455 2jngA 105 1.45e+00 b.34.9.4 148150 1aihA 170 1.81e+00 1aihA d.163.1.1 42149 2ghfA 102 2.69e+00 g.37.1.1,g.37.1.1 135175,135176 1b7yB 785 3.19e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,b.153.1.1 16301,16302,25312,39311,40780,41456 1i7pA 274 3.32e+00 b.43.4.2,c.25.1.1 66048,66049 2amuA 143 3.76e+00 1umkA 275 4.09e+00 b.43.4.2,c.25.1.1 113312,113313 1ndh 272 4.44e+00 1ndh 3k62A 412 7.14e+00 1qx4A 274 7.84e+00 b.43.4.2,c.25.1.1 104624,104625 1y6kR 214 8.76e+00 b.1.2.1,b.1.2.1 122663,122664 2rdkA 109 1.01e+01 2glzA 153 1.04e+01 d.81.3.1 135348 2hbwA 235 1.13e+01 2vovA 336 1.13e+01 1z47A 355 1.38e+01 2wgoA 98 1.38e+01 2e7aA 157 1.41e+01 3hrpA 409 1.85e+01 2ifeA 100 1.86e+01 1tig d.68.1.1 39567 1tnfA 158 1.92e+01 2tnfA b.22.1.1 23871 1f9rA 70 1.96e+01 d.9.1.1 90484 3l9jT 149 1.96e+01 4tsvA 150 2.06e+01 2tnfA b.22.1.1 23860 1vc3B 97 2.11e+01 1wvvA 265 2.21e+01 2oynA 146 2.31e+01 b.43.5.2 149067 1pdkB 157 2.34e+01 1pdkB b.2.3.2 22427 3ab9A 129 2.36e+01 1k42A 168 2.59e+01 b.18.1.14 72032 2vbuA 136 2.77e+01 b.43.5.2 152911 1t4aA 84 2.86e+01 d.284.1.1 106404 1uz5A 402 2.87e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 2heqA 84 2.90e+01 b.34.20.1 147272 1dxgA 36 2.95e+01 1dxgA g.41.5.2 45247 1a8mA 157 3.13e+01 2tnfA b.22.1.1 23868 1danU 121 3.20e+01 1boy b.1.2.1 21954 2rovA 117 3.26e+01 1n9pA 207 3.33e+01 b.1.18.16 80343 3a7lA 128 3.49e+01 2i24N 121 3.50e+01 1wdxA 69 3.54e+01 3cloA 258 3.58e+01 2fblA 153 3.63e+01 d.63.1.2 133249 3gm8A 801 3.81e+01 3hzhB 172 3.89e+01 2tnfA 156 3.92e+01 2tnfA b.22.1.1 23880 2jjuA 127 4.01e+01 2cx6A 90 4.04e+01 c.9.1.1 130981 1boy 219 4.17e+01 1boy 1x58A 62 4.32e+01 a.4.1.1 121705 2fvgA 340 4.54e+01 b.49.3.1,c.56.5.4 134201,134202 2ckkA 127 4.72e+01 3jxsA 174 4.85e+01 2a6zA 222 4.88e+01 b.29.1.13 126319 3dl3A 119 5.31e+01 b.82.2.13 157762 3ibsA 218 5.31e+01 3cwxA 176 5.52e+01 2jv3A 110 5.65e+01 1jdqA 98 5.67e+01 d.68.3.3 66559 3gxsA 109 5.91e+01 1cojA 212 5.92e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2i2qA 137 5.94e+01 3ersX 118 5.96e+01 1jcfA 344 6.30e+01 c.55.1.1,c.55.1.1 62878,62879 3fppA 341 6.31e+01 3hi0A 508 6.51e+01 1tg0A 68 6.58e+01 2hm2Q 89 6.81e+01 2d4nA 152 6.81e+01 1z8kA 193 6.87e+01 b.159.1.1 124703 3laxA 109 6.88e+01 3eb8A 358 6.95e+01 1wwhA 119 6.95e+01 d.58.7.1 121358 2kdgA 100 7.18e+01 2kddA 76 7.35e+01 2zx2A 195 7.36e+01 1oqeA 144 7.38e+01 b.22.1.1 87286 1q7lA 198 7.70e+01 c.56.5.4 96044 2edmA 161 7.72e+01 b.170.1.1 146804 2zklA 369 7.77e+01 3gxwA 103 7.81e+01 2ds0A 130 7.84e+01 1hwtC 81 7.96e+01 1hwtC g.38.1.1,h.1.3.1 45085,45518 1waaA 93 7.96e+01