# List of top-scoring protein chains for T0307.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 1a2xA 159 1.20e-01 1ncx a.39.1.5 17251 1tcf 159 1.67e-01 1ncx a.39.1.5 17250 1tnw 162 8.32e-01 1ncx a.39.1.5 17235 1top 162 9.48e-01 1ncx a.39.1.5 17223 4tnc 162 9.72e-01 1ncx a.39.1.5 17228 5tnc 162 1.42e+00 1ncx a.39.1.5 17246 1dgnA 89 1.82e+00 1dgnA a.77.1.3 18436 1xouB 95 2.70e+00 1yvuA 706 3.09e+00 1juoA 198 3.61e+00 a.39.1.8 67312 1aj4 161 3.77e+00 1ncx a.39.1.5 17244 1la0A 161 3.99e+00 a.39.1.5 77864 1w68A 390 4.43e+00 a.25.1.2 109216 1repC 251 4.75e+00 1repC a.4.5.10,a.4.5.10 16125,16126 2czdA 208 6.52e+00 1dtlA 161 7.19e+00 1ncx a.39.1.5 17229 1yxoA 328 7.53e+00 1p4wA 99 8.17e+00 a.4.6.2 87783 1ulyA 192 8.70e+00 1ny1A 240 9.09e+00 c.6.2.3 86395 1jwoA 97 9.58e+00 d.93.1.1 63310 1w1b1 257 9.67e+00 1w17A 263 9.77e+00 1t6oA 51 1.03e+01 a.8.5.1 106578 1lr7A 74 1.06e+01 g.3.11.3,g.68.1.1 84679,84680 1oksA 56 1.20e+01 a.8.5.1 93271 1xf5L 80 1.40e+01 1y4rB 146 1.53e+01 1xctL 80 1.56e+01 1lehA 364 1.58e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1enfA 212 1.61e+01 3seb b.40.2.2,d.15.6.1 25198,37787 1hxyD 213 1.61e+01 b.40.2.2,d.15.6.1 61390,61391 2arpF 152 1.64e+01 1f77A 217 1.65e+01 3seb b.40.2.2,d.15.6.1 25200,37789 1ewcA 214 1.70e+01 3seb b.40.2.2,d.15.6.1 25199,37788 1a79A 171 1.74e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1isnA 323 1.76e+01 a.11.2.1,b.55.1.5,d.15.1.4 71400,71401,71402 1smqA 399 1.78e+01 a.25.1.2 105766 1jk0A 419 1.78e+01 a.25.1.2 63142 1qwgA 251 1.80e+01 c.1.27.1 96473 1avsA 90 1.90e+01 1cll a.39.1.5 17226 1uu1A 335 1.91e+01 c.67.1.1 99993 2f8jA 347 1.96e+01 1h4rA 314 2.06e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1j3nA 408 2.08e+01 c.95.1.1,c.95.1.1 84074,84075 1mvwB 145 2.16e+01 i.15.1.1 79524 1gjyA 167 2.18e+01 a.39.1.8 70199 2fkiA 126 2.22e+01 1agx 331 2.29e+01 4pgaA c.88.1.1 35564 1npqA 90 2.30e+01 a.39.1.5 85983 2mysB 166 2.32e+01 1wdcB a.39.1.5 17308 2amlA 373 2.36e+01 3gwxA 271 2.41e+01 2prgA a.123.1.1 19325 1y0sA 272 2.41e+01 2gwxA 267 2.43e+01 2prgA a.123.1.1 19323 2awhA 268 2.44e+01 2b50A 272 2.45e+01 1b9hA 388 2.47e+01 1b9hA c.67.1.4 34488 1b9iA 388 2.48e+01 1b9hA c.67.1.4 34489 1hezE 61 2.61e+01 2ptl d.15.7.1 60991 1ymhE 65 2.66e+01 1tgsI 56 2.72e+01 1tgsI g.68.1.1 44706 1w8iA 156 2.87e+01 1r8kA 329 2.90e+01 c.77.1.3 97240 1mhhE 63 2.93e+01 d.15.7.1 79127 1ro2A 216 2.94e+01 d.264.1.2 97665 1n7kA 234 2.97e+01 c.1.10.1 85374 2b0uC 288 3.07e+01 2cpxA 115 3.14e+01 3mddA 385 3.15e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1udyA 396 3.27e+01 a.29.3.1,e.6.1.1 99231,99232 1x7aC 235 3.30e+01 1trf 76 3.38e+01 1ncx a.39.1.5 17247 1ub3A 220 3.41e+01 c.1.10.1 88395 1rie 129 3.41e+01 1rie b.33.1.1 24427 1t07A 94 3.60e+01 d.279.1.1 106196 2a87A 335 3.62e+01 1gm1A 94 3.68e+01 b.36.1.1 70271 1oziA 99 3.74e+01 b.36.1.1 93845 1k94A 165 3.78e+01 a.39.1.8 68333 1nynA 131 3.83e+01 d.235.1.1 86410 1vj6A 102 3.83e+01 1f4qA 165 3.85e+01 1alvA a.39.1.8 17360 1dflW 139 3.89e+01 1wdcB a.39.1.5 17306 1smg 90 3.91e+01 1ncx a.39.1.5 17234 1um1A 110 3.96e+01 b.36.1.1 99578 1urhA 280 4.06e+01 c.46.1.2,c.46.1.2 99829,99830 1pxqA 35 4.09e+01 j.5.1.2 104382 1pg5B 168 4.10e+01 d.58.2.1,g.41.7.1 104148,104149 1z8qA 404 4.15e+01 1d5gA 96 4.17e+01 b.36.1.1 70080 1jroA 462 4.17e+01 a.56.1.1,d.15.4.2,d.87.2.1,d.145.1.3 67137,67138,67139,67140 1kk8B 139 4.19e+01 a.39.1.5 77430 5croA 66 4.19e+01 1orc a.35.1.2 17044 1o78A 84 4.24e+01 b.84.1.1 81130 1wdcB 156 4.33e+01 1wdcB a.39.1.5 17302 1v9vA 114 4.34e+01 1qb2A 109 4.41e+01 1qb2A a.36.1.1 17125 1ps6A 328 4.46e+01 c.77.1.3 95070 1ptmA 329 4.47e+01 c.77.1.3 95104 1rniA 216 4.54e+01 d.264.1.2 97663 1w9rA 119 4.55e+01 1q7xA 108 4.58e+01 b.36.1.1 96059 1wh5A 80 4.62e+01 1z7z3 234 4.77e+01 1fi5A 81 4.79e+01 1ncx a.39.1.5 17252 1ih0A 71 4.82e+01 a.39.1.5 66140 1z7s3 240 4.83e+01 1bccE 196 4.89e+01 1rie b.33.1.1,f.23.12.1 24431,43699 1timA 247 4.95e+01 1amk c.1.1.1 28453 1tpb1 247 4.99e+01 1amk 3ctn 76 4.99e+01 1ncx a.39.1.5 17241 1dfkA 830 4.99e+01 1lvk b.34.3.1,c.37.1.9 24573,32170 1dflA 831 5.01e+01 1lvk b.34.3.1,c.37.1.9 24574,32171 1dczA 77 5.01e+01 1iyu b.84.1.1 28219 2fug2 181 5.02e+01 1o97D 320 5.03e+01 c.26.2.3,c.31.1.2 81233,81234 1kk8A 837 5.06e+01 b.34.3.1,c.37.1.9 77428,77429 1b7tA 835 5.06e+01 1lvk b.34.3.1,c.37.1.9 24572,32169 1qviA 840 5.06e+01 b.34.3.1,c.37.1.9 96427,96428 1spqA 247 5.09e+01 c.1.1.1 105878 1tpc1 247 5.10e+01 1amk 1e5pA 151 5.11e+01 1bj7 b.60.1.1 59272 1tph1 247 5.13e+01 1amk 1br2A 791 5.13e+01 1lvk b.34.3.1,c.37.1.9 24558,32155 1su5A 247 5.13e+01 c.1.1.1 106020 1sq7A 247 5.16e+01 c.1.1.1 105886 1ssdA 247 5.21e+01 c.1.1.1 105979 1tpwA 247 5.24e+01 1amk c.1.1.1 28449 1c7vA 81 5.26e+01 1cll a.39.1.5 17262 1sw3A 248 5.28e+01 c.1.1.1 106065 1scmB 145 5.29e+01 1wdcB a.39.1.5 17304 1sw7A 248 5.29e+01 c.1.1.1 106073 3pga1 337 5.29e+01 4pgaA 1sw0A 248 5.31e+01 c.1.1.1 106060 1br1A 820 5.33e+01 1lvk b.34.3.1,c.37.1.9 24564,32161 1jipA 403 5.41e+01 a.104.1.1 66748 1tpuA 247 5.45e+01 1amk c.1.1.1 28441 1z8pA 404 5.46e+01 1ozsA 73 5.47e+01 a.39.1.5 93857 1tpvA 247 5.53e+01 1amk c.1.1.1 28443 1ppjE 196 5.62e+01 b.33.1.1,f.23.12.1 104260,104261 2cp8A 54 5.70e+01 2aw4R 103 5.79e+01 1htiA 248 5.80e+01 1amk c.1.1.1 28455 1wyiA 250 5.82e+01 1bea 127 5.83e+01 1bea a.52.1.2 17826 1po0A 751 5.83e+01 f.4.3.3 94960 1pvaA 110 5.85e+01 1a75A a.39.1.4 17207 1kmoA 774 5.97e+01 f.4.3.3 72753 1ctj 89 5.98e+01 1ctj a.3.1.1 15798 1bfa 134 6.00e+01 1bea a.52.1.2 17827 6croA 60 6.04e+01 1orc a.35.1.2 17047 1mfqC 129 6.07e+01 a.36.1.1 79046 1autC 250 6.13e+01 5ptp b.47.1.2 26348 1lkdA 297 6.17e+01 d.32.1.3,d.32.1.3 78059,78060 2b35A 269 6.18e+01 1bvrA 268 6.23e+01 1eny c.2.1.2 29913 1eny 268 6.23e+01 1eny c.2.1.2 29910 2govA 195 6.26e+01 1jtiA 385 6.35e+01 e.1.1.1 63280 1jfjA 134 6.39e+01 a.39.1.5 66638 1v1gA 222 6.43e+01 1ovaA 386 6.46e+01 1ovaA e.1.1.1 42619 1rqgA 722 6.47e+01 a.27.1.1,c.26.1.1,g.41.1.1 105063,105064,105065 2c1cA 312 6.50e+01 1jioA 403 6.65e+01 a.104.1.1 66747 1enz 268 6.67e+01 1eny c.2.1.2 29912 1uhgA 385 6.70e+01 e.1.1.1 88491 1z8oA 404 6.72e+01 1fjrA 195 6.76e+01 1fjrA b.102.1.1 59855 2ao0A 324 6.85e+01 1xvqA 175 6.94e+01 2fvlA 324 6.96e+01 1rlmA 271 7.00e+01 1y25A 165 7.00e+01 1kkqA 269 7.08e+01 a.123.1.1 68679 1rloA 271 7.13e+01 1d3bB 91 7.16e+01 1d3bB b.38.1.1 24804 1ijqA 316 7.21e+01 1ijqA b.68.5.1,g.3.11.1 62506,62507 1i7gA 287 7.26e+01 a.123.1.1 71121 1ynuA 473 7.32e+01 1k7lA 288 7.32e+01 a.123.1.1 68268 1yfsA 465 7.34e+01 1bjfA 193 7.49e+01 1rec a.39.1.5 17331 1ry8A 323 7.51e+01 1f16A 192 7.54e+01 1f16A f.1.4.1 43400 1egeA 396 7.55e+01 3mdeA a.29.3.1,e.6.1.1 16604,42865 1vkuA 100 7.63e+01 a.28.1.1 108690 1egdA 396 7.67e+01 3mdeA a.29.3.1,e.6.1.1 16596,42857 1kqfB 294 8.02e+01 d.58.1.5,f.23.22.1 75900,75901 1txgA 335 8.16e+01 1eupA 403 8.16e+01 1rom a.104.1.1 18967 2a1tA 421 8.21e+01 1i2sA 282 8.21e+01 e.3.1.1 71104 1a3h 300 8.30e+01 7a3hA c.1.8.3 28819 7a3hA 303 8.36e+01 7a3hA c.1.8.3 28817 1h5vA 304 8.39e+01 c.1.8.3 70898 1qi2A 305 8.39e+01 7a3hA c.1.8.3 28824 1g5bA 221 8.45e+01 1g5bA d.159.1.3 60261 1rwsA 77 8.47e+01 d.15.3.2 97991 1lf1A 308 8.57e+01 c.1.8.3 73877 1s1pA 331 8.74e+01 c.1.7.1 98350 1xnpA 202 8.83e+01 1r2rA 248 8.87e+01 c.1.1.1 96875 2vhbA 146 8.94e+01 2vhbA a.1.1.2 15629