# List of top-scoring protein chains for T0335.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 1r2uA 89 3.20e-01 a.39.1.5 104783 2amyA 246 7.88e-01 2d2jA 329 1.01e+00 1ap4 89 1.09e+00 1ncx a.39.1.5 17253 2fzfA 175 1.65e+00 1pta 327 1.66e+00 1pscA c.1.9.3 29064 1dpmA 329 1.67e+00 1pscA c.1.9.3 29062 1eywA 331 1.67e+00 1pscA c.1.9.3 29057 1i0dA 332 1.67e+00 1pscA c.1.9.3 61487 1jgmA 336 1.73e+00 1pscA c.1.9.3 62953 1qw7A 336 1.86e+00 1pscA 365 1.96e+00 1pscA c.1.9.3 29058 1la0A 161 2.29e+00 a.39.1.5 77864 1y96B 85 2.37e+00 1q6gA 495 2.69e+00 c.1.8.1 95974 1v3iA 495 2.69e+00 c.1.8.1 108304 1wdqA 495 2.70e+00 1wdpA 495 2.70e+00 1wdsA 495 2.70e+00 1wdrA 495 2.70e+00 1ukpA 495 2.74e+00 c.1.8.1 99505 1v3hA 495 2.75e+00 c.1.8.1 108303 1btc 491 2.76e+00 1byb c.1.8.1 28791 1ukoA 495 2.76e+00 c.1.8.1 99501 1byb 495 2.77e+00 1byb c.1.8.1 28790 1q6dA 495 2.79e+00 c.1.8.1 95971 1wrkA 88 2.98e+00 2ctn 89 3.06e+00 1ncx a.39.1.5 17242 1b5sA 242 3.65e+00 1eaf c.43.1.1 32626 1il1A 219 3.68e+00 1igtB b.1.1.1,b.1.1.2 62539,62540 1qokA 282 3.70e+00 1f3rB b.1.1.1,b.1.1.1 20492,20493 1r59O 505 3.78e+00 1q6eA 495 3.85e+00 c.1.8.1 95972 1xupO 487 3.87e+00 1b1yA 500 4.24e+00 1byb c.1.8.1 28796 2aepH 217 5.65e+00 1v9kA 228 6.10e+00 d.265.1.3 108449 1xpiA 231 6.28e+00 1dtlA 161 7.02e+00 1ncx a.39.1.5 17229 2bk6A 156 7.05e+00 1aj4 161 7.06e+00 1ncx a.39.1.5 17244 1qghA 156 7.11e+00 1qghA a.25.1.1 16728 1ifvA 155 7.54e+00 d.129.3.1 71204 1mvwC 147 8.09e+00 i.15.1.1 79525 2mysC 149 8.16e+00 1wdcC a.39.1.5 17323 2bkcA 156 8.26e+00 2bjyA 156 8.26e+00 1fgnH 214 9.35e+00 1igtB b.1.1.1,b.1.1.2 20217,21229 1pv5A 264 9.62e+00 d.251.1.1 95150 1oe4A 247 9.69e+00 c.18.1.3 86895 1p6bA 336 9.79e+00 c.1.9.3 94163 1cfvH 119 1.01e+01 1igtB b.1.1.1 20161 1wmhA 89 1.07e+01 1fa2A 498 1.16e+01 1byb c.1.8.1 28797 1v11A 400 1.26e+01 c.36.1.11 108227 2bfeA 400 1.27e+01 1x7wA 400 1.27e+01 1x7yA 400 1.27e+01 1v1rA 400 1.27e+01 c.36.1.11 108272 2bfbA 400 1.27e+01 2bewA 400 1.27e+01 2bffA 400 1.27e+01 1v16A 400 1.27e+01 c.36.1.11 108240 1x7zA 400 1.27e+01 1x7xA 400 1.27e+01 2bfdA 400 1.28e+01 2bfcA 400 1.28e+01 1cpq 129 1.45e+01 1cpq a.24.3.2 16556 1cpr 129 1.45e+01 1cpq a.24.3.2 16559 1behA 187 1.45e+01 1a44 b.17.1.1 23700 1h6zA 913 1.47e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 2gm3A 175 1.58e+01 1vh5A 148 1.58e+01 d.38.1.5 100642 1br1B 150 1.80e+01 1wdcC a.39.1.5 17309 1zxfA 155 1.81e+01 2b5xA 148 1.83e+01 1n67A 359 1.84e+01 b.2.3.4,b.2.3.4 85354,85355 1x48A 88 1.84e+01 1pg7H 217 1.86e+01 b.1.1.1,b.1.1.2 94674,94675 1atnD 260 1.88e+01 3dni d.151.1.1 41793 1jptH 225 1.90e+01 b.1.1.1,b.1.1.2 67051,67052 1iqpA 327 1.95e+01 a.80.1.1,c.37.1.20 62649,62650 1zd3A 555 1.96e+01 1npqA 90 2.12e+01 a.39.1.5 85983 1icxA 155 2.18e+01 d.129.3.1 71191 1p5jA 372 2.20e+01 c.79.1.1 104067 1cr9H 217 2.21e+01 8fabA b.1.1.1,b.1.1.2 20431,21401 1jsxA 207 2.22e+01 c.66.1.20 71846 2fzlA 219 2.30e+01 1zboA 210 2.33e+01 1wxpA 110 2.33e+01 1avsA 90 2.51e+01 1cll a.39.1.5 17226 1qvbA 481 2.54e+01 1qvbA c.1.8.4 28983 1xhkA 187 2.66e+01 1o6dA 163 2.69e+01 c.116.1.3 92567 1m0sA 219 2.69e+01 c.124.1.4,d.58.40.1 78351,78352 1smg 90 2.77e+01 1ncx a.39.1.5 17234 1ad9B 219 2.96e+01 1gc1H b.1.1.1,b.1.1.2 20215,21227 1ddmA 135 3.00e+01 2nmbA b.55.1.2 26993 1b0nA 111 3.31e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 2nmbA 160 3.44e+01 2nmbA b.55.1.2 26994 1kn3A 183 3.55e+01 b.17.1.1 72764 1yn5A 103 3.58e+01 1ri8A 134 3.90e+01 1ikfH 228 4.03e+01 1igtB b.1.1.1,b.1.1.2 20033,21087 1ofcX 304 4.08e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1umwA 237 4.11e+01 d.223.1.2,d.223.1.2 99631,99632 1k6qH 216 4.16e+01 b.1.1.1,b.1.1.2 72092,72093 1k03A 399 4.36e+01 c.1.4.1 63322 1oyc 400 4.49e+01 1oyc c.1.4.1 28603 1v59A 478 4.69e+01 1uedA 406 4.77e+01 a.104.1.1 99256 1q4kA 259 4.81e+01 d.223.1.2,d.223.1.2 95797,95798 1djsA 216 4.94e+01 1cvsC b.1.1.4,b.1.1.4 21746,21747 1e0oB 219 4.99e+01 1cvsC b.1.1.4,b.1.1.4 21748,21749 1ev2E 220 5.00e+01 1cvsC b.1.1.4,b.1.1.4 21738,21739 1iilE 220 5.02e+01 1cvsC b.1.1.4,b.1.1.4 62437,62438 1ii4E 220 5.03e+01 1cvsC b.1.1.4,b.1.1.4 62404,62405 2fdbP 220 5.05e+01 2c5kT 95 5.08e+01 1sczA 233 5.08e+01 c.43.1.1 98802 2crjA 92 5.19e+01 1oj5A 132 5.23e+01 d.110.3.8 93087 1v6fA 151 5.35e+01 d.109.1.2 108395 2ajfE 180 5.35e+01 2cycA 375 5.38e+01 2fkfA 462 5.43e+01 2fkmX 462 5.44e+01 1k2yX 463 5.45e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1p5dX 463 5.45e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1sbkA 144 5.53e+01 d.38.1.5 98791 1zbsA 291 5.69e+01 1doi 128 5.80e+01 1awd d.15.4.1 37676 2b5aA 77 5.90e+01 1cvsC 225 5.99e+01 1cvsC b.1.1.4,b.1.1.4 21726,21727 1evtC 225 6.04e+01 1cvsC b.1.1.4,b.1.1.4 21730,21731 2c5iT 101 6.16e+01 2a6sA 84 6.27e+01 1khdA 345 6.27e+01 a.46.2.1,c.27.1.1 77400,77401 1uacH 114 6.38e+01 b.1.1.1 99132 1dtp 190 6.39e+01 1ddt d.166.1.1 42248 2dd8S 202 6.45e+01 1ic5H 114 6.58e+01 1f3rB b.1.1.1 62254 1j1xH 114 6.66e+01 b.1.1.1 77063 1fexA 59 6.67e+01 a.4.1.3 59803 1ic7H 114 6.67e+01 1f3rB b.1.1.1 62258 1nunB 230 6.71e+01 b.1.1.4,b.1.1.4 80735,80736 1ic4H 114 6.77e+01 1f3rB b.1.1.1 62251 1vluA 468 6.80e+01 c.82.1.1 108864 3rabA 169 6.82e+01 1ctqA c.37.1.8 32018 2fueA 262 7.15e+01 1zvhA 134 7.18e+01 1pvmA 184 7.21e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1nwy4 37 7.49e+01 1yc61 154 7.56e+01 1ha9A 34 7.59e+01 1ha9A g.3.2.1 60876 1ndgB 210 7.59e+01 b.1.1.1,b.1.1.2 85578,85579 12e8H 221 7.64e+01 1igtB b.1.1.1,b.1.1.2 20269,21269 2erbA 125 7.68e+01 1yl39 36 7.70e+01 1n0rA 126 7.81e+01 k.37.1.1 79756 1dsfH 119 7.94e+01 1igtB b.1.1.1 20247 1th8B 116 7.98e+01 c.13.2.1 106909 1bwkA 399 8.05e+01 1oyc c.1.4.1 28605 1a7w 69 8.06e+01 1a7w a.22.1.2 16477 1ql3A 99 8.11e+01 1ycc a.3.1.1 15822 2h1pH 220 8.11e+01 1igtB b.1.1.1,b.1.1.2 20191,21207 1vor6 35 8.21e+01 1c7mA 100 8.21e+01 1ycc a.3.1.1 15830 1rkbA 173 8.35e+01 1js9A 189 8.37e+01 b.121.4.5 71840 1a44 185 8.44e+01 1a44 b.17.1.1 23704 1b7aA 186 8.58e+01 1a44 b.17.1.1 23705 1rz7H 219 8.61e+01 b.1.1.1,b.1.1.2 98133,98134 1eca 136 8.65e+01 1flp a.1.1.2 15209 1oy1A 228 8.71e+01 c.23.16.2 87548 1nz0A 118 8.72e+01 d.14.1.2 86433 1n0qA 93 8.72e+01 k.37.1.1 79754 1vhqA 232 8.73e+01 c.23.16.2 100696 1ek9A 428 8.74e+01 1ek9A f.5.1.1 43809 2aaoA 166 8.75e+01 2a40B 260 8.96e+01