# List of top-scoring protein chains for t04-100-30-bys-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 1ji8A 111 4.50e-01 d.203.1.1 66733 1ijbA 202 9.18e-01 c.62.1.1 71229 1k3xA 262 1.43e+00 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1oshA 232 1.58e+00 a.123.1.1 93496 1mugA 168 1.58e+00 1mugA c.18.1.2 31030 1xoyA 161 1.70e+00 1qynA 153 2.09e+00 d.33.1.1 96597 1k2eA 156 2.13e+00 d.113.1.1 72010 1fnsA 196 2.37e+00 1auq c.62.1.1 34136 1yqdA 366 2.87e+00 1us8A 147 3.09e+00 c.37.1.12 99859 1sjqA 105 3.15e+00 d.58.7.1 105660 1ysqA 193 3.22e+00 1j93A 353 3.43e+00 c.1.22.1 66454 2kfnA 605 3.56e+00 1xwl c.55.3.5,e.8.1.1 33682,42975 1bh9A 45 3.57e+00 1bh9A a.22.1.3 16483 1jjeA 222 3.87e+00 1a7tA d.157.1.1 63117 1oj4A 283 4.68e+00 d.14.1.5,d.58.26.5 93083,93084 1xnzA 264 5.00e+00 1c24A 263 5.22e+00 1c24A d.127.1.1 41148 1vhmA 195 5.24e+00 d.110.2.1 100691 1v1rA 400 7.03e+00 c.36.1.11 108272 2gi3A 476 7.38e+00 1fcyA 236 7.86e+00 2lbd a.123.1.1 19282 1hwxA 501 7.87e+00 1hwyA c.2.1.7,c.58.1.1 30250,33898 1o0xA 262 8.05e+00 d.127.1.1 80755 1vq0A 302 8.11e+00 2ggcA 263 8.54e+00 1no7A 604 9.15e+00 e.48.1.1 92016 1yvoA 172 9.46e+00 1z54A 132 9.61e+00 1vjpA 394 9.63e+00 c.2.1.3,d.81.1.3 100828,100829 1souA 194 1.10e+01 c.124.1.6 105858 2cy0A 263 1.15e+01 1fit 147 1.16e+01 1fit d.13.1.1 37499 1u6zA 513 1.20e+01 2bfdA 400 1.27e+01 1lssA 140 1.27e+01 c.2.1.9 74246 1s14A 194 1.30e+01 d.122.1.2 98329 2bduA 297 1.32e+01 1mc0A 368 1.40e+01 d.110.2.1,d.110.2.1 78937,78938 1jjtA 228 1.45e+01 1a7tA d.157.1.1 63139 1wxdA 263 1.45e+01 1x7yA 400 1.45e+01 1ryp2 233 1.46e+01 1ryp2 2d5cA 263 1.50e+01 2g09A 297 1.56e+01 1q77A 138 1.57e+01 c.26.2.4 96023 1olsA 400 1.70e+01 c.36.1.11 93331 1wywA 230 1.70e+01 2bl1A 172 1.71e+01 1oqjA 97 1.71e+01 d.217.1.1 93417 2es7A 142 1.77e+01 1mkmA 249 1.78e+01 a.4.5.33,d.110.2.2 79242,79243 1s7kA 182 1.84e+01 1w1kA 560 1.87e+01 d.58.32.1,d.145.1.1 109059,109060 1kopA 223 1.94e+01 2cba b.74.1.1 27966 1gtmA 419 2.00e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1yq2A 1024 2.01e+01 1gz6A 319 2.01e+01 c.2.1.2 76410 1uyjA 296 2.19e+01 f.8.1.2 108143 2c3vA 102 2.19e+01 1ukfA 188 2.24e+01 d.3.1.10 99488 1wgeA 83 2.26e+01 1vrpA 381 2.35e+01 2g38B 198 2.35e+01 1vrmA 325 2.36e+01 1jfmA 174 2.37e+01 d.19.1.1 66640 1ul4A 94 2.40e+01 g.72.1.1 99538 1t1jA 125 2.45e+01 c.137.1.1 106249 1e8gA 560 2.48e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1wl9A 440 2.49e+01 1ohgA 282 2.57e+01 d.183.1.1 93018 1qeyA 31 2.62e+01 1qeyA h.2.1.1 45666 2h4uA 145 2.67e+01 1bia 321 2.70e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1zuhA 168 2.71e+01 1az9 457 2.78e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1h7sA 365 2.87e+01 d.14.1.3,d.122.1.2 65705,65706 1c4kA 730 2.88e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 2h2bA 107 2.99e+01 2fs3A 282 3.00e+01 1rvaA 244 3.04e+01 1rvaA c.52.1.2 33240 1mkyA 439 3.06e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1fzoB 99 3.10e+01 1agdB b.1.1.2 60157 1fzkB 99 3.10e+01 1agdB b.1.1.2 60151 1v7rA 186 3.10e+01 c.51.4.1 100482 1t01B 24 3.12e+01 1dowA 205 3.12e+01 1dovA a.24.9.1 16626 2b8eA 273 3.15e+01 1u3aA 189 3.20e+01 2gz4A 207 3.24e+01 2bwvA 440 3.24e+01 1khbA 625 3.31e+01 c.91.1.1,c.109.1.1 68606,68607 1uujA 88 3.31e+01 a.221.1.1 108046 2ch4A 320 3.38e+01 1p1jA 533 3.38e+01 c.2.1.3,d.81.1.3 87687,87688 2gf6A 135 3.42e+01 1eteA 134 3.42e+01 1eteA a.26.1.2 16869 1xmbA 418 3.45e+01 1lk2B 99 3.45e+01 b.1.1.2 91058 1vjnA 220 3.46e+01 d.157.1.4 100825 1wkoA 180 3.46e+01 1s1eA 224 3.47e+01 1m9sA 605 3.54e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1jj2E 177 3.56e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 2fhi 147 3.60e+01 1fit d.13.1.1 37505 1s72E 178 3.66e+01 d.141.1.1,d.141.1.1 105323,105324 1xm8A 254 3.66e+01 1msk 331 3.68e+01 1msk d.173.1.1 42495 2fxqA 264 3.69e+01 1dzkA 157 3.70e+01 1obpA b.60.1.1 27096 1w6uA 302 3.73e+01 1uuqA 440 3.73e+01 c.1.8.3 100015 2ltnA 181 3.96e+01 1led b.29.1.1 24024 1jk7A 323 3.99e+01 1auiA d.159.1.3 63144 1u32A 293 4.04e+01 d.159.1.3 107631 1kjvB 100 4.05e+01 b.1.1.2 77423 1ax4A 467 4.10e+01 1ax4A c.67.1.2 34391 2ad9A 119 4.21e+01 1njkA 156 4.22e+01 d.38.1.1 85818 1o0pA 104 4.24e+01 d.58.7.1 86535 2f1lA 187 4.26e+01 1phk 298 4.27e+01 1cdkA d.144.1.7 41635 1a5t 334 4.27e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1i58A 189 4.31e+01 1b3qA d.122.1.3 61773 1ex2A 189 4.33e+01 1ex2A c.51.4.2 33225 1q0eA 152 4.33e+01 b.1.8.1 95504 1erjA 393 4.36e+01 1erjA b.69.4.1 27660 1bdmA 327 4.37e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1vqoE 178 4.41e+01 1v8dA 235 4.47e+01 c.140.1.1 108425 1lf7A 182 4.47e+01 b.60.1.1 73878 1wjtA 103 4.52e+01 1vqzA 341 4.53e+01 1bmdA 327 4.59e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 2fa8A 105 4.66e+01 1sx5A 244 4.72e+01 c.52.1.2 99023 1odkA 235 4.72e+01 c.56.2.1 86863 1hdkA 141 4.74e+01 b.29.1.3 65807 1fl1A 230 4.78e+01 1at3A b.57.1.1 27023 1onjA 61 4.81e+01 g.7.1.1 93358 1ijgA 309 4.87e+01 1fouA e.27.1.1 62493 1vb0A 61 4.90e+01 1dysA 348 4.96e+01 1bvwA c.6.1.1 30669 2bhvA 246 5.02e+01 1s69A 124 5.06e+01 a.1.1.1 105305 1pbe 394 5.07e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1hq3B 126 5.09e+01 1aoiD a.22.1.1 16444 1u9iA 519 5.10e+01 1i8fA 81 5.15e+01 1i8fA b.38.1.1 61959 1sdjA 310 5.21e+01 d.21.1.2,d.21.1.2 98807,98808 2c6cA 707 5.31e+01 1dqnA 230 5.33e+01 1dqnA c.61.1.1 34067 1o6zA 303 5.37e+01 c.2.1.5,d.162.1.1 81107,81108 1b04A 318 5.39e+01 1b04A d.142.2.2 41579 1snzA 344 5.41e+01 b.30.5.4 98930 1u8vA 490 5.41e+01 2ethA 154 5.42e+01 1ieaA 192 5.43e+01 1iakA b.1.1.2,d.19.1.1 21631,38205 1g87A 614 5.45e+01 a.102.1.2,b.2.2.2 83275,83276 1gyxA 76 5.46e+01 d.80.1.1 76387 1ttwA 138 5.48e+01 d.198.1.1 107308 1h6tA 291 5.53e+01 b.1.18.15,c.10.2.1 65686,65687 1fvkA 189 5.54e+01 1fvkA c.47.1.13 90351 4icb 76 5.57e+01 4icb a.39.1.1 17145 1wbpA 397 5.58e+01 1zklA 353 5.59e+01 1vf6A 83 5.63e+01 a.194.1.1 100600 1m4jA 142 5.69e+01 d.109.1.2 78602 1vp4A 425 5.80e+01 1tzyB 126 5.80e+01 a.22.1.1 107531 1xvsA 126 5.81e+01 2d8aA 348 5.81e+01 1f2tA 149 5.84e+01 1f2tA c.37.1.12 32373 1rtxA 123 5.85e+01 a.1.1.1 97827 1pc3A 350 5.87e+01 c.94.1.1 104102 1lshA 1056 5.87e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1kjlA 146 5.96e+01 1zpyA 95 5.97e+01 1s0yA 76 5.98e+01 d.80.1.1 98314 2akoA 251 6.01e+01 1mjhA 162 6.04e+01 1mjhA c.26.2.4 31639 1em2A 229 6.07e+01 1em2A d.129.3.2 41321 2f51A 118 6.08e+01 1trkA 680 6.08e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1x0tA 120 6.24e+01 1gpuA 680 6.24e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 1x31D 99 6.31e+01 1lcl 142 6.33e+01 1lcl b.29.1.3 24216 1y7tA 327 6.40e+01 1y7wA 291 6.40e+01 1lwjA 441 6.43e+01 b.71.1.1,c.1.8.1 74303,74304 1eonA 245 6.46e+01 1rvaA c.52.1.2 33238 1nytA 271 6.48e+01 c.2.1.7,c.58.1.5 86417,86418 2a15A 139 6.49e+01 1bdb 277 6.49e+01 1bdb c.2.1.2 29874 1w0bA 102 6.49e+01 a.7.11.1 108985 1tzpA 255 6.51e+01 d.65.1.3 107520 1jy2O 56 6.52e+01 h.1.8.1 67441 2a1dD 329 6.55e+01 1fr2B 134 6.56e+01 d.4.1.1 83257 1fh6A 282 6.57e+01 1fh6A 1r2zA 274 6.60e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1iicA 422 6.60e+01 1nmtA d.108.1.2,d.108.1.2 62422,62423 1vhcA 224 6.67e+01 c.1.10.1 100661 1f9mA 112 6.75e+01 1erv c.47.1.1 32736 1jv4A 162 6.77e+01 b.60.1.1 67343 1n67A 359 6.79e+01 b.2.3.4,b.2.3.4 85354,85355 2b7yA 182 6.83e+01 1qysA 106 6.87e+01 k.41.1.1 96603 1k0iA 394 6.89e+01 c.3.1.2,d.16.1.2 67942,67943 1acvA 189 6.96e+01 1fvkA c.47.1.13 90328 1pf4A 582 7.05e+01 c.37.1.12,f.37.1.1 88052,88053 1dqpA 230 7.07e+01 1dqnA c.61.1.1 34069 1lenA 181 7.20e+01 1led b.29.1.1 24032 1o5iA 249 7.23e+01 c.2.1.2 92499 1y01A 102 7.24e+01 2g30A 258 7.24e+01 1pz4A 116 7.26e+01 d.106.1.1 95400 1de4C 640 7.31e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 2bh8A 101 7.38e+01 1emvB 134 7.40e+01 1bxiB d.4.1.1 37135 1a05A 358 7.41e+01 1cnzA c.77.1.1 35059 1iakB 185 7.41e+01 1iakB b.1.1.2,d.19.1.1 21626,38200 1kq1A 77 7.55e+01 b.38.1.2 72848 1ee8A 266 7.64e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1xkyA 301 7.67e+01 1a3k 137 7.69e+01 1a3k b.29.1.3 24218 1ykjA 394 7.71e+01 1a65A 504 7.75e+01 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1xauA 122 7.76e+01 1mkaA 171 7.78e+01 1mkaA d.38.1.2 38543 1owfA 99 7.79e+01 a.55.1.1 87487 1ery 39 7.82e+01 1ery a.10.1.1 16364 1l1zA 274 7.87e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 2b3hA 329 7.91e+01 1imjA 210 8.02e+01 c.69.1.23 71246 1eybA 471 8.05e+01 1ey2A b.82.1.4 28115 1d4fA 431 8.10e+01 1b3rA c.2.1.4,c.23.12.3 30110,31370 1s0yB 71 8.12e+01 d.80.1.1 98315 1e9pA 151 8.23e+01 1mfmA b.1.8.1 22215 1ermA 263 8.23e+01 1btl e.3.1.1 42690 1sctB 151 8.25e+01 3sdhA a.1.1.2 15003 1vr4A 103 8.28e+01 1g7dA 106 8.28e+01 1g7dA a.71.1.1 18318 1etxA 98 8.53e+01 1fipA a.4.1.12 18978 1ak0 270 8.54e+01 1ak0 a.124.1.2 19345 1qw2A 102 8.54e+01 d.249.1.1 96456 1z8uA 102 8.55e+01 1jj2F 119 8.58e+01 1ffkE d.79.3.1 63091 1fs7A 485 8.61e+01 1qdbA a.138.1.3 19691 1oe1A 336 8.61e+01 b.6.1.3,b.6.1.3 86891,86892 1yw3A 208 8.64e+01 1u35D 126 8.66e+01 1g0cA 364 8.69e+01 7a3hA c.1.8.3 60165 1forL 210 8.72e+01 8fabA b.1.1.1,b.1.1.2 19988,21044 1nbwB 117 8.75e+01 c.51.3.2 80396 1jenB 67 8.76e+01 1jenB d.156.1.1 42029 1cbjA 151 8.78e+01 1mfmA b.1.8.1 22213 1ghj 79 8.87e+01 1ghj b.84.1.1 28232 3daaA 277 8.93e+01 1daaA e.17.1.1 43272 2fh1A 344 8.93e+01 2bc4A 211 8.98e+01