# 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 1y14B 171 1.18e-01 1ihjA 98 2.13e-01 1pdr b.36.1.1 62382 1dhn 121 2.97e-01 1dhn d.96.1.3 40663 1kqqA 139 4.94e-01 a.4.3.1 72885 1w6uA 302 6.63e-01 2d9rA 104 7.99e-01 1ts9A 102 8.50e-01 2basA 431 8.58e-01 2h6lA 146 1.15e+00 1jmxA 494 1.25e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 2c78A 405 1.26e+00 1g0oA 283 1.42e+00 1ybvA c.2.1.2 60181 1wjnA 97 1.67e+00 1qd5A 275 1.74e+00 1qd5A f.4.2.1 43748 1c9oA 66 2.14e+00 1mjc b.40.4.5 25325 1a62 130 2.33e+00 1a62 a.140.3.1,b.40.4.5 64708,64709 1yo8A 634 2.40e+00 1exmA 405 2.48e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1fr3A 67 2.67e+00 1fr3A b.40.6.1 25436 1ha3A 405 2.76e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1qd6C 240 2.78e+00 1qd5A 1u04A 771 2.86e+00 b.34.14.1,c.55.3.10 107539,107540 2f9nA 245 3.09e+00 1yezA 68 3.18e+00 1wqaA 455 3.20e+00 1z0wA 207 3.29e+00 2bszA 278 3.67e+00 1bjt 793 3.73e+00 1bjt e.11.1.1 43249 1l6pA 125 3.76e+00 b.1.17.1 73626 1zq1A 438 3.80e+00 1hk9A 74 3.91e+00 b.38.1.2 83541 2cqsA 842 4.06e+00 1a8vA 121 4.20e+00 1a62 a.140.3.1,b.40.4.5 64712,64713 2gk9A 426 4.22e+00 1ux6A 350 4.31e+00 b.29.1.16,g.75.1.1 100145,100146 1qx4A 274 4.77e+00 b.43.4.2,c.25.1.1 104624,104625 1q7hA 153 4.79e+00 b.122.1.1,d.17.6.2 96042,96043 1kq1A 77 5.32e+00 b.38.1.2 72848 1cleA 534 5.63e+00 1thg c.69.1.17 34771 1llfA 534 5.93e+00 c.69.1.17 78094 1ltoA 245 6.03e+00 b.47.1.2 84707 1khoA 370 6.12e+00 a.124.1.1,b.12.1.3 72489,72490 1lf6A 684 6.24e+00 a.102.1.5,b.30.5.5 77918,77919 1rznA 205 6.70e+00 2f2lX 167 6.79e+00 1xneA 113 6.84e+00 1mgqA 83 7.40e+00 b.38.1.1 79099 1em8B 112 7.81e+00 c.126.1.1 90458 1j5wA 298 7.88e+00 d.104.1.1 71589 1z1yA 186 7.88e+00 1u1sA 82 8.22e+00 1p4kA 295 8.29e+00 d.153.1.5 87772 1wdiA 345 8.73e+00 1k2yX 463 9.27e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 2ew2A 316 9.36e+00 2g9zA 348 9.61e+00 1u0mA 382 9.64e+00 c.95.1.2,c.95.1.2 107557,107558 1o0xA 262 9.77e+00 d.127.1.1 80755 1u1tA 82 1.01e+01 8abp 306 1.02e+01 8abp c.93.1.1 35647 1s5aA 150 1.04e+01 d.17.4.10 98525 1j1lA 290 1.05e+01 b.82.1.12 90766 1xw4X 110 1.10e+01 9gafA 295 1.11e+01 1apyA d.153.1.5 42008 1bia 321 1.18e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1yfuA 174 1.20e+01 1ug6A 431 1.25e+01 c.1.8.4 88490 1p5dX 463 1.29e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1rwiA 270 1.31e+01 b.68.9.1 97987 1cbf 285 1.33e+01 1cbf c.90.1.1 35587 1vl6A 388 1.35e+01 c.2.1.7,c.58.1.3 108724,108725 1a12A 413 1.36e+01 1a12A b.69.5.1 27663 1q6hA 224 1.36e+01 d.26.1.1 95975 1jtkA 136 1.36e+01 c.97.1.1 71862 1zp7A 206 1.36e+01 1uwzA 136 1.40e+01 c.97.1.1 108081 2fcfA 103 1.44e+01 1wzoA 246 1.46e+01 1o6uA 403 1.47e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1a7tA 232 1.48e+01 1a7tA d.157.1.1 42041 1e3dB 542 1.52e+01 1h2rL e.18.1.1 59189 1ejbA 168 1.53e+01 1rvv1 c.16.1.1 59417 1mfgA 95 1.54e+01 b.36.1.1 79043 2h3lA 103 1.57e+01 1pdkB 157 1.58e+01 1pdkB b.2.3.2 22427 1i6pA 220 1.58e+01 1ddzA c.53.2.1 61848 1v5iB 76 1.58e+01 1am2 199 1.62e+01 1am2 b.86.1.2 28381 1sxrA 183 1.63e+01 d.118.1.1 106101 1vjnA 220 1.74e+01 d.157.1.4 100825 1pl8A 356 1.85e+01 b.35.1.2,c.2.1.1 94878,94879 1lqsR 214 1.87e+01 b.1.2.1,b.1.2.1 74194,74195 1k3yA 221 1.89e+01 a.45.1.1,c.47.1.5 77245,77246 1kzlA 208 1.93e+01 b.43.4.3,b.43.4.3 77635,77636 1h2kA 349 1.93e+01 b.82.2.6 76572 1rkd 309 1.94e+01 1rkd c.72.1.1 34928 1g6sA 427 1.95e+01 1eps d.68.2.2 39584 1tzpA 255 2.00e+01 d.65.1.3 107520 1y1oA 203 2.02e+01 1ccwA 137 2.05e+01 1be1 c.23.6.1 31238 1h09A 338 2.06e+01 b.109.1.1,c.1.8.8 83420,83421 1c30B 382 2.10e+01 c.8.3.1,c.23.16.1 30736,31413 1iktA 120 2.11e+01 d.106.1.1 66188 1d3bB 91 2.16e+01 1d3bB b.38.1.1 24804 1e3jA 352 2.17e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1vpjA 192 2.17e+01 1zx8A 136 2.22e+01 1nykA 165 2.22e+01 b.33.1.1 86408 2cwpA 112 2.24e+01 1vj0A 380 2.27e+01 b.35.1.2,c.2.1.1 100786,100787 1iirA 415 2.29e+01 1iirA c.87.1.5 62453 1m26A 133 2.29e+01 1fl0A 171 2.29e+01 1eujA b.40.4.4 25315 1ci3M 249 2.30e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 1olmA 403 2.35e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1xclA 235 2.37e+01 5abp 306 2.38e+01 8abp c.93.1.1 35651 1vr3A 191 2.44e+01 1gyzA 60 2.46e+01 a.144.2.1 70793 1w9pA 433 2.62e+01 1kwgA 645 2.64e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1gefA 123 2.66e+01 1gefA c.52.1.18 60465 1vjrA 271 2.69e+01 c.108.1.14 100832 1qw9A 502 2.70e+01 b.71.1.2,c.1.8.3 96466,96467 1xw3A 110 2.74e+01 2bi7A 384 2.76e+01 1sefA 274 2.80e+01 b.82.1.11 105452 2abqA 306 2.80e+01 1q6uA 245 2.82e+01 d.26.1.1 95998 1el6A 219 2.83e+01 1el6B d.182.1.1 42606 2b30A 301 2.83e+01 2fwkA 121 2.88e+01 2b5rC 165 2.88e+01 1ndh 272 2.90e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1xnzA 264 2.94e+01 1p1cA 199 2.95e+01 c.66.1.16 87669 2fwmX 250 3.00e+01 2arcA 164 3.00e+01 2arcA b.82.4.1 28148 1umkA 275 3.06e+01 1l3iA 192 3.07e+01 c.66.1.22 77676 1mjc 69 3.09e+01 1mjc b.40.4.5 25319 1kqpA 271 3.11e+01 c.26.2.1 72883 1z4eA 153 3.22e+01 1h8gA 95 3.25e+01 b.109.1.1 65735 1b8aA 438 3.27e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1gutA 68 3.29e+01 b.40.6.1 65576 1a9xB 379 3.31e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1ugxA 133 3.33e+01 2gdjA 264 3.34e+01 1dzaA 129 3.34e+01 7rsa d.5.1.1 37275 1uekA 275 3.42e+01 d.14.1.5,d.58.26.5 88483,88484 1zg2A 107 3.42e+01 1fdr 248 3.44e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1dl5A 317 3.48e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1zgsA 447 3.55e+01 1v1hA 103 3.55e+01 b.83.1.1,h.1.17.1 108243,108244 1zkdA 387 3.62e+01 1n0qA 93 3.62e+01 k.37.1.1 79754 1a8p 258 3.66e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 2ew8A 249 3.70e+01 1xxqA 161 3.71e+01 1zx0A 236 3.76e+01 2h7bA 105 3.77e+01 1db3A 372 3.78e+01 1db3A c.2.1.2 29813 1widA 130 3.78e+01 1nz6A 101 3.79e+01 a.2.3.1 86441 2a9fA 398 3.83e+01 1xh9A 350 3.83e+01 1wcv1 257 3.92e+01 1mq4A 272 3.94e+01 d.144.1.7 91391 2ak5A 64 3.95e+01 1c24A 263 3.97e+01 1c24A d.127.1.1 41148 1uufA 369 4.04e+01 b.35.1.2,c.2.1.1 100006,100007 1jtgB 165 4.13e+01 d.98.1.1 67267 1vz6A 393 4.14e+01 d.154.1.2 108949 1yavA 159 4.18e+01 1p97A 114 4.18e+01 d.110.3.7 94382 1yloA 348 4.24e+01 1vkwA 218 4.26e+01 d.90.1.2 108695 1fthA 122 4.26e+01 d.150.1.2 60028 2ggcA 263 4.28e+01 1apmE 350 4.33e+01 1cdkA d.144.1.7 41628 1gz6A 319 4.37e+01 c.2.1.2 76410 1yphE 97 4.39e+01 1l7dA 384 4.39e+01 c.2.1.4,c.23.12.2 77774,77775 1oqvA 192 4.40e+01 d.24.1.2 87320 5nul 138 4.42e+01 5nul c.23.5.1 31191 1yqdA 366 4.46e+01 1tkiA 321 4.47e+01 1tkiA d.144.1.7 41638 1yn9A 169 4.50e+01 1u4nA 310 4.51e+01 1eq9A 222 4.64e+01 5ptp b.47.1.2 26068 1xm8A 254 4.64e+01 1f8gA 384 4.65e+01 1sayA c.2.1.4,c.23.12.2 59695,59696 1vk1A 242 4.66e+01 d.268.1.2 108634 1jqbA 351 4.67e+01 b.35.1.2,c.2.1.1 77151,77152 1ef8A 261 4.74e+01 1ef8A c.14.1.3 30921 1vjkA 98 4.78e+01 d.15.3.1 108631 2g6fX 59 4.79e+01 2eveA 157 4.85e+01 2c2xA 281 4.98e+01 1yzsA 121 5.03e+01 1iz0A 302 5.10e+01 b.35.1.2,c.2.1.1 83821,83822 1eljA 381 5.14e+01 4mbp c.94.1.1 35791 1ksiA 642 5.17e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 1prtF 98 5.19e+01 1prtF b.40.2.1 25140 1lba 146 5.22e+01 1lba d.118.1.1 41062 1vmfA 145 5.24e+01 2f1kA 279 5.26e+01 1s98A 107 5.27e+01 b.124.1.1 105377 1q7eA 428 5.27e+01 c.123.1.1 96035 1chuA 540 5.28e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 2gwdA 449 5.32e+01 3ygsP 97 5.42e+01 3ygsP a.77.1.3 18435 1o98A 511 5.42e+01 c.105.1.1,c.76.1.3 86684,86685 1gvkB 240 5.45e+01 b.47.1.2 70610 1wr2A 238 5.45e+01 1g38A 393 5.62e+01 2admA c.66.1.27 60235 1qorA 327 5.64e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 2bfxA 284 5.72e+01 1jl3A 139 5.73e+01 c.44.1.1 66826 1bcpF 99 5.76e+01 1prtF b.40.2.1 25142 1ass 159 5.77e+01 1a6dA c.8.5.2 30818 1nnwA 252 5.79e+01 d.159.1.5 80674 1sk4A 163 5.87e+01 d.118.1.1 105664 1m5q1 130 5.88e+01 2bdeA 470 5.88e+01 1qwrA 319 5.92e+01 b.82.1.3 96491 1eqjA 511 5.94e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 2gwnA 452 5.94e+01 1sotA 320 5.95e+01 b.36.1.4,b.47.1.1 105852,105853 2g2uB 165 6.03e+01 1nscA 390 6.07e+01 2qwc b.68.1.1 27591 1dciA 275 6.07e+01 1dciA c.14.1.3 30918 1kafA 108 6.07e+01 d.199.1.1 68372 1vr0A 247 6.09e+01 1cg2A 393 6.10e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1qnjA 240 6.11e+01 5ptp b.47.1.2 26238 1pt7A 437 6.15e+01 c.123.1.1 95093 1y2qA 143 6.22e+01 2b6nA 278 6.25e+01 1paz 123 6.26e+01 1bqk b.6.1.1 22878 1ecsA 126 6.31e+01 1ecsA d.32.1.2 59407 1dnlA 199 6.38e+01 1ci0A b.45.1.1 25753 2azeB 106 6.38e+01 1jmtB 28 6.40e+01 1edg 380 6.42e+01 1edg c.1.8.3 28807 3ezmA 101 6.48e+01 3ezmA b.89.1.1 28395 1lk5A 229 6.49e+01 c.124.1.4,d.58.40.1 73960,73961 1d0qA 103 6.53e+01 1d0qA g.41.3.2 45208 1vggA 161 6.58e+01 2fjbA 643 6.61e+01 1kevA 351 6.61e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1kdj 102 6.71e+01 1plc b.6.1.1 22864 1xe0A 114 6.80e+01 1fehA 574 6.82e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1ih8A 271 6.86e+01 2nsyA c.26.2.1 62377 1cdy 178 6.97e+01 1cdy b.1.1.1,b.1.1.3 19719,21658 2affA 120 7.05e+01 1o6lA 337 7.08e+01 d.144.1.7 81092 2ghjA 118 7.08e+01 1wsrA 375 7.11e+01 2czqA 205 7.12e+01 1z7gA 217 7.21e+01 1ha1 184 7.24e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1v54B 227 7.24e+01 b.6.1.2,f.17.2.1 100322,100323 1fo1A 271 7.24e+01 1fo1A c.10.2.3,d.58.7.2 30869,39213 1jnrA 643 7.32e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1ivyA 452 7.34e+01 1ivyA c.69.1.5 34654 1b65A 375 7.37e+01 1b65A d.154.1.1 42020 1e0tA 470 7.39e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1i27A 73 7.41e+01 1i27A a.4.5.30 61555 1eyqA 222 7.43e+01 1eypA d.36.1.1 38534 2bibA 547 7.44e+01 1vc3B 97 7.46e+01 1rxxA 421 7.46e+01 d.126.1.4 98061 1jsmA 325 7.47e+01 b.19.1.2 63264 1z02A 446 7.47e+01 1zd7A 159 7.50e+01 1k0hA 117 7.51e+01 b.106.1.2 71975 1pmy 123 7.51e+01 1bqk b.6.1.1 22888 2bc4A 211 7.53e+01 1g6xA 58 7.53e+01 1bpi g.8.1.1 60320 1b78A 193 7.59e+01 1b78A c.51.4.1 33221 1jg1A 235 7.61e+01 c.66.1.7 66661 1chmA 401 7.65e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 2bdwA 362 7.72e+01 1ve4A 206 7.75e+01 2dekA 265 7.76e+01 1ca1 370 7.92e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1kfwA 435 7.97e+01 c.1.8.5,d.26.3.1 77376,77377 1r5yA 386 8.02e+01 c.1.20.1 97134 1gg6C 97 8.02e+01 5ptp 1jihA 531 8.07e+01 d.240.1.1,e.8.1.7 90374,90375 1wdyA 285 8.09e+01 1sv6A 269 8.09e+01 d.177.1.1 106043 1ml8A 134 8.10e+01 d.227.1.2 85013 1f3uB 171 8.18e+01 1f3uB b.65.1.1 27525 3pviA 157 8.20e+01 3pviA c.52.1.6 33300 1i8aA 189 8.22e+01 1i82A b.1.9.2 61951 1efdN 266 8.24e+01 1efdN c.92.2.1 35597 1s3iA 310 8.28e+01 b.46.1.1,c.65.1.1 98435,98436 2f4nA 273 8.28e+01 2f20A 240 8.28e+01 1eybA 471 8.31e+01 1ey2A b.82.1.4 28115 2a5zA 262 8.38e+01 1tuhA 156 8.44e+01 d.17.4.11 107345 1h6wA 312 8.46e+01 d.231.1.1,b.108.1.1 83059,83060 1vmeA 410 8.52e+01 c.23.5.1,d.157.1.3 108893,108894 1vkyA 347 8.65e+01 e.53.1.1 108696 1j5yA 187 8.67e+01 a.4.5.1,d.94.2.1 71592,71593 1rlhA 173 8.70e+01 d.256.1.1 97646 1kutA 230 8.78e+01 d.143.1.1 73017 2ex4A 241 8.81e+01 2akrA 285 8.83e+01 1zbqA 327 8.84e+01 1vkkA 154 8.88e+01 d.109.1.2 108669 1hw5A 210 8.88e+01 2cgpA a.4.5.4,b.82.3.2 16098,28137 1brwA 433 8.90e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2fy6A 143 8.94e+01 1bqk 124 8.94e+01 1bqk b.6.1.1 22889