# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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.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 1dywA 173 9.82e-27 2cpl b.62.1.1 27505 1awqA 164 1.01e-26 2cpl b.62.1.1 27461 2bitX 165 1.03e-26 1awsA 164 1.12e-26 2cpl b.62.1.1 27431 2rmcA 182 1.19e-26 2cpl b.62.1.1 27491 2cpl 165 1.23e-26 2cpl b.62.1.1 27420 1a58 177 1.37e-26 2cpl b.62.1.1 27495 1qoiA 177 1.54e-26 2cpl b.62.1.1 27490 1cwoA 165 1.97e-26 2cpl b.62.1.1 27445 1yndA 165 2.28e-26 1xo7A 166 3.90e-26 1zcxA 178 6.07e-26 2cfeA 162 6.41e-26 1vdnA 162 1.66e-25 1ihgA 370 3.61e-25 2cpl a.118.8.1,b.62.1.1 62380,62381 1h0pA 182 4.29e-25 b.62.1.1 76450 2a2nA 176 7.14e-24 1zkcA 197 1.16e-23 1xwnA 174 2.26e-23 2fu0A 160 5.71e-23 2b71A 196 1.32e-22 1j2aA 166 3.09e-20 b.62.1.1 90779 1v9tA 166 3.98e-20 b.62.1.1 108451 1lopA 164 2.15e-19 2cpl b.62.1.1 27510 1clh 166 2.45e-18 2cpl b.62.1.1 27512 1zx8A 136 9.37e-01 1zoxA 113 2.05e+00 2aexA 346 2.66e+00 1pbyA 489 2.72e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1nbfA 353 3.01e+00 d.3.1.9 80387 1jjuA 489 3.40e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1adwA 123 5.12e+00 1bqk b.6.1.1 22893 1bqk 124 5.29e+00 1bqk b.6.1.1 22889 2gk3A 256 5.54e+00 1kbvA 327 6.49e+00 b.6.1.3,b.6.1.3 68395,68396 2aynA 404 7.35e+00 1eucB 396 1.04e+01 2scuB c.23.4.1,d.142.1.4 31149,41570 1mxiA 160 1.06e+01 c.116.1.1 79646 1paz 123 1.10e+01 1bqk b.6.1.1 22878 1qlpA 394 1.11e+01 1ovaA e.1.1.1 42628 1xsjA 778 1.23e+01 1pswA 348 1.25e+01 c.87.1.7 88287 1m2oA 768 1.36e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1pmy 123 1.37e+01 1bqk b.6.1.1 22888 1np1A 184 1.41e+01 1np1A b.60.1.1 27155 2arzA 247 1.57e+01 1vr8A 142 1.65e+01 1ew3A 159 1.67e+01 1mup b.60.1.1 27114 1nb8A 353 1.70e+01 d.3.1.9 80385 1em2A 229 1.71e+01 1em2A d.129.3.2 41321 2b7oA 464 1.84e+01 1gsoA 431 2.00e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 2gfoA 396 2.23e+01 1eudB 396 2.43e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1u5uA 374 2.48e+01 1xebA 150 2.55e+01 1o94A 729 2.57e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1d3uA 181 2.57e+01 1ytbA d.129.1.1,d.129.1.1 41290,41291 1ewnA 219 2.66e+01 1bnkA b.46.1.2 25762 1fvuB 125 2.67e+01 1ixxB d.169.1.1 42346 2a7mA 250 2.69e+01 1f6oA 219 2.72e+01 1bnkA b.46.1.2 25763 1q5fA 156 2.73e+01 d.24.1.1 104536 2gf9A 189 3.02e+01 1rtqA 299 3.05e+01 c.56.5.4 97819 1btkA 169 3.13e+01 1btkA b.55.1.1 26959 1gggA 226 3.20e+01 1lst c.94.1.1 35817 1sq2N 113 3.20e+01 b.1.1.1 105881 1vj0A 380 3.21e+01 b.35.1.2,c.2.1.1 100786,100787 1ylnA 252 3.22e+01 1y7wA 291 3.22e+01 1ec7A 446 3.24e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1djqA 729 3.28e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 2prf 125 3.36e+01 3nul d.110.1.1 40887 1djnA 729 3.40e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1at3A 247 3.42e+01 1at3A b.57.1.1 27021 1bqg 451 3.50e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 1ycoA 279 3.69e+01 1vr0A 247 3.71e+01 2gefA 217 3.87e+01 1qh5A 260 3.88e+01 1qh5A d.157.1.2 42057 1xfsA 178 3.90e+01 d.129.3.5 109589 1a54A 321 3.95e+01 1ixh c.94.1.1 35763 1kskA 234 4.06e+01 d.66.1.5,d.265.1.3 72920,90389 2b8mA 117 4.11e+01 1k8kD 300 4.11e+01 d.198.2.1,d.198.2.1 68309,68310 1m5sA 297 4.13e+01 d.58.33.1,d.58.33.1 74511,74512 1ejeA 192 4.20e+01 1ejeA b.45.1.2 25757 1ixh 321 4.26e+01 1ixh c.94.1.1 35761 2tmdA 729 4.49e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 1qh3A 260 4.50e+01 1qh5A d.157.1.2 42059 1oheA 348 4.52e+01 c.45.1.1,c.45.1.1 87013,87014 1mdbA 539 4.66e+01 e.23.1.1 79008 1dc1A 323 4.68e+01 1dc1A c.52.1.11 33321 1aisA 182 4.73e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1z7gA 217 4.75e+01 1vqzA 341 4.76e+01 1cliA 345 4.84e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1n25A 368 4.95e+01 c.37.1.20 85264 1pczA 191 4.97e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1hqsA 423 4.99e+01 1iso c.77.1.1 61154 1jdfA 447 5.00e+01 c.1.11.2,d.54.1.1 62897,62898 1wv3A 238 5.07e+01 2anpA 291 5.18e+01 1a25A 149 5.27e+01 1rsy b.7.1.2 23197 2fp4B 395 5.38e+01 2cy7A 396 5.43e+01 1w99A 558 5.43e+01 1r64A 481 5.58e+01 b.18.1.20,c.41.1.1 97140,97141 1iz1A 294 5.63e+01 a.4.5.37,c.94.1.1 83823,83824 1ey2A 471 5.66e+01 1ey2A b.82.1.4 28116 1d5rA 324 5.68e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 1xnaA 183 5.71e+01 1xnaA b.18.1.8 23773 1iqaA 160 5.76e+01 b.22.1.1 71274 1xm7A 195 5.83e+01 1xm0A 147 5.93e+01 1shcA 195 6.00e+01 1shcA b.55.1.2 26992 1wu7A 434 6.05e+01 1vioA 243 6.07e+01 d.265.1.3,d.66.1.5 100762,100763 1bzyA 217 6.24e+01 1qk3A c.61.1.1 34071 1uovA 159 6.25e+01 b.7.1.2 107974 1z4xA 532 6.26e+01 2coeA 120 6.28e+01 2b25A 336 6.39e+01 1yzgA 179 6.49e+01 1hurA 180 6.54e+01 1hurA c.37.1.8 32052 1t1uA 639 6.54e+01 1p9rA 418 6.64e+01 c.37.1.11 94399 1x36A 237 6.69e+01 1uw0A 117 6.71e+01 g.39.1.12 108063 2f2hA 773 6.75e+01 1ot5A 477 7.17e+01 b.18.1.20,c.41.1.1 87409,87410 1yphC 131 7.24e+01 1ay1H 213 7.26e+01 1igtB b.1.1.1,b.1.1.2 20243,21255 1bs9 207 7.44e+01 1bs9 c.69.1.30 31330 1wdnA 226 7.45e+01 1lst c.94.1.1 35816 2shpA 525 7.47e+01 2shpA c.45.1.2,d.93.1.1,d.93.1.1 32683,40533,40534 1zkoA 136 7.48e+01 1qupA 222 7.48e+01 1qupA b.1.8.1,d.58.17.1 22301,39352 1m1hA 248 7.59e+01 b.114.1.1,d.58.42.1 78415,78416 1td2A 287 7.61e+01 c.72.1.5 106765 1gggB 226 7.73e+01 1lst c.94.1.1 35818 1uscA 178 7.82e+01 b.45.1.2 99860 1lg7A 182 7.82e+01 d.213.1.1 73888 1yoxA 250 7.87e+01 1ww9A 392 7.94e+01 1k0iA 394 7.97e+01 c.3.1.2,d.16.1.2 67942,67943 2a8eA 220 8.03e+01 2bf6A 449 8.06e+01 1wguA 136 8.09e+01 1q5qA 259 8.09e+01 d.153.1.4 95904 1e6mA 128 8.12e+01 3chy c.23.1.1 31039 1a45 173 8.12e+01 1amm b.11.1.1,b.11.1.1 23602,23603 1y791 680 8.18e+01 1svmA 377 8.18e+01 1xe7A 203 8.20e+01 1qmtA 134 8.20e+01 7rsa d.5.1.1 37290 1s55A 156 8.22e+01 1elpA 173 8.31e+01 1amm b.11.1.1,b.11.1.1 23596,23597 1f82A 424 8.34e+01 1f82A d.92.1.7 40307 1amp 291 8.51e+01 1amp c.56.5.4 33837 1wnaA 131 8.66e+01 1vgjA 184 8.70e+01 1f3rB 257 8.71e+01 1f3rB b.1.1.1,b.1.1.1 20416,20417 1x8qA 184 8.85e+01 1o9wA 177 8.91e+01 b.2.3.5 86713 1xb2B 291 8.95e+01 1vqvA 306 8.99e+01 1j5wA 298 8.99e+01 d.104.1.1 71589