# List of top-scoring protein chains for t2k-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 1.15e-01 1dhn 121 1.98e-01 1dhn d.96.1.3 40663 1ihjA 98 2.01e-01 1pdr b.36.1.1 62382 1kqqA 139 5.55e-01 a.4.3.1 72885 1w6uA 302 6.62e-01 1c20A 128 6.88e-01 1c20A a.4.3.1 16079 2d9rA 104 7.94e-01 1ts9A 102 8.99e-01 1crl 534 1.01e+00 1thg c.69.1.17 34765 2basA 431 1.07e+00 2h6lA 146 1.16e+00 2c78A 405 1.19e+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 1g0oA 283 1.57e+00 1ybvA c.2.1.2 60181 1qd5A 275 1.94e+00 1qd5A f.4.2.1 43748 1wjnA 97 1.97e+00 1exmA 405 2.46e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1aipA 405 2.57e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1yo8A 634 2.58e+00 1fr3A 67 2.74e+00 1fr3A b.40.6.1 25436 1ha3A 405 2.77e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1a63 130 2.87e+00 1a62 a.140.3.1,b.40.4.5 64710,64711 1qd6C 240 3.15e+00 1qd5A 2f9nA 245 3.25e+00 1eft 405 3.35e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1jpeA 151 3.47e+00 b.1.17.1 77146 1yezA 68 3.74e+00 1aipE 405 3.84e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1a62 130 4.14e+00 1a62 a.140.3.1,b.40.4.5 64708,64709 1l6pA 125 4.35e+00 b.1.17.1 73626 1c9oA 66 4.43e+00 1mjc b.40.4.5 25325 2gk9A 426 4.64e+00 1ux6A 350 4.74e+00 b.29.1.16,g.75.1.1 100145,100146 2cqsA 842 4.79e+00 2bszA 278 4.84e+00 2occB 227 5.30e+00 2occB b.6.1.2,f.17.2.1 23027,43519 1bjt 793 5.31e+00 1bjt e.11.1.1 43249 1xw4X 110 5.53e+00 1u04A 771 5.74e+00 b.34.14.1,c.55.3.10 107539,107540 1wqaA 455 5.84e+00 1mgqA 83 5.84e+00 b.38.1.1 79099 1kq1A 77 5.85e+00 b.38.1.2 72848 1zq1A 438 6.09e+00 1z0wA 207 6.17e+00 1khoA 370 6.29e+00 a.124.1.1,b.12.1.3 72489,72490 1hk9A 74 6.34e+00 b.38.1.2 83541 1cleA 534 6.48e+00 1thg c.69.1.17 34771 1a8vA 121 6.53e+00 1a62 a.140.3.1,b.40.4.5 64712,64713 1a0lA 244 6.63e+00 5ptp b.47.1.2 26286 1ltoA 245 6.65e+00 b.47.1.2 84707 1llfA 534 6.76e+00 c.69.1.17 78094 1lf6A 684 6.92e+00 a.102.1.5,b.30.5.5 77918,77919 1qx4A 274 6.99e+00 b.43.4.2,c.25.1.1 104624,104625 1rznA 205 7.49e+00 1i81A 83 7.70e+00 1d3bB b.38.1.1 61930 1bia 321 8.42e+00 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1xneA 113 8.61e+00 1em8B 112 9.04e+00 c.126.1.1 90458 1z1yA 186 9.08e+00 2pcfB 250 9.28e+00 1hcz i.4.1.1 45911 1hcz 252 9.98e+00 1hcz b.2.6.1,b.84.2.2 22464,28250 2ew2A 316 1.08e+01 1u0mA 382 1.10e+01 c.95.1.2,c.95.1.2 107557,107558 1o0xA 262 1.11e+01 d.127.1.1 80755 1q6hA 224 1.11e+01 d.26.1.1 95975 1p4kA 295 1.12e+01 d.153.1.5 87772 1e3dB 542 1.14e+01 1h2rL e.18.1.1 59189 1cmkE 350 1.18e+01 1cdkA d.144.1.7 41623 2g9zA 348 1.19e+01 1wdiA 345 1.21e+01 1ug6A 431 1.23e+01 c.1.8.4 88490 1pdkB 157 1.30e+01 1pdkB b.2.3.2 22427 1q7hA 153 1.31e+01 b.122.1.1,d.17.6.2 96042,96043 1bib 321 1.34e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16084,24448,40788 1s5aA 150 1.35e+01 d.17.4.10 98525 1u1sA 82 1.36e+01 2f2lX 167 1.36e+01 1xw3A 110 1.38e+01 1eujA 166 1.38e+01 1eujA b.40.4.4 25316 2fcfA 103 1.38e+01 9gafA 295 1.40e+01 1apyA d.153.1.5 42008 1pc0A 61 1.41e+01 b.137.1.1 94426 1rwiA 270 1.53e+01 b.68.9.1 97987 2cbf 234 1.53e+01 1cbf c.90.1.1 35588 1yfuA 174 1.54e+01 2arcB 164 1.55e+01 2arcA b.82.4.1 28149 1h2kA 349 1.55e+01 b.82.2.6 76572 1ykfA 352 1.55e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 1a12A 413 1.56e+01 1a12A b.69.5.1 27663 1jtkA 136 1.56e+01 c.97.1.1 71862 1zp7A 206 1.58e+01 1uwzA 136 1.60e+01 c.97.1.1 108081 1dctA 324 1.63e+01 6mhtA c.66.1.26 34244 1vl6A 388 1.65e+01 c.2.1.7,c.58.1.3 108724,108725 1jacC 133 1.65e+01 1jotA 1k2yX 463 1.69e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1j5wA 298 1.71e+01 d.104.1.1 71589 1b6fA 159 1.72e+01 1bv1 d.129.3.1 41316 1wzoA 246 1.73e+01 1u1tA 82 1.74e+01 1j1lA 290 1.75e+01 b.82.1.12 90766 1o6uA 403 1.76e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 2h3lA 103 1.84e+01 1mfgA 95 1.86e+01 b.36.1.1 79043 1v5iB 76 1.88e+01 1khhA 198 1.94e+01 c.66.1.16 68615 1gvmA 136 1.94e+01 b.109.1.1 70612 2admA 421 2.00e+01 2admA c.66.1.27 34238 1vjnA 220 2.03e+01 d.157.1.4 100825 1g6nA 210 2.06e+01 2cgpA a.4.5.4,b.82.3.2 16100,28139 1csp 67 2.08e+01 1mjc b.40.4.5 25321 1cs0B 382 2.08e+01 1c3oB c.8.3.1,c.23.16.1 30740,31417 1i6pA 220 2.11e+01 1ddzA c.53.2.1 61848 1lqsR 214 2.15e+01 b.1.2.1,b.1.2.1 74194,74195 1xclA 235 2.15e+01 2cwpA 112 2.17e+01 1tzpA 255 2.20e+01 d.65.1.3 107520 1d3bB 91 2.22e+01 1d3bB b.38.1.1 24804 1p5dX 463 2.27e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1iktA 120 2.28e+01 d.106.1.1 66188 1ccwA 137 2.31e+01 1be1 c.23.6.1 31238 1am2 199 2.32e+01 1am2 b.86.1.2 28381 1aqjA 421 2.32e+01 2admA c.66.1.27 34242 1ejbA 168 2.34e+01 1rvv1 c.16.1.1 59417 1q6uA 245 2.35e+01 d.26.1.1 95998 1b1a 137 2.39e+01 1be1 c.23.6.1 31242 1rkd 309 2.39e+01 1rkd c.72.1.1 34928 1vpjA 192 2.41e+01 2aacA 177 2.41e+01 2arcA b.82.4.1 28150 1y1oA 203 2.43e+01 1q8uA 350 2.48e+01 d.144.1.7 96230 1hcxA 127 2.48e+01 b.109.1.1 65800 1c30B 382 2.54e+01 c.8.3.1,c.23.16.1 30736,31413 1nykA 165 2.59e+01 b.33.1.1 86408 1yzsA 121 2.59e+01 1kzlA 208 2.62e+01 b.43.4.3,b.43.4.3 77635,77636 1cbf 285 2.63e+01 1cbf c.90.1.1 35587 1iirA 415 2.63e+01 1iirA c.87.1.5 62453 8abp 306 2.63e+01 8abp c.93.1.1 35647 1p1cA 199 2.68e+01 c.66.1.16 87669 1h09A 338 2.69e+01 b.109.1.1,c.1.8.8 83420,83421 1jacA 133 2.73e+01 1jotA 1fl0A 171 2.75e+01 1eujA b.40.4.4 25315 1olmA 403 2.77e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1m26A 133 2.78e+01 1pl8A 356 2.81e+01 b.35.1.2,c.2.1.1 94878,94879 1bmlC 362 2.87e+01 1bmlC d.15.5.1,d.15.5.1,d.15.5.1 37729,37730,37731 1gefA 123 2.87e+01 1gefA c.52.1.18 60465 1g6sA 427 2.88e+01 1eps d.68.2.2 39584 1ci3M 249 2.91e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 2arcA 164 2.93e+01 2arcA b.82.4.1 28148 1sefA 274 2.95e+01 b.82.1.11 105452 1zx8A 136 2.96e+01 1vr3A 191 2.97e+01 1sxrA 183 2.97e+01 d.118.1.1 106101 2abqA 306 2.99e+01 1qw9A 502 3.03e+01 b.71.1.2,c.1.8.3 96466,96467 1vj0A 380 3.06e+01 b.35.1.2,c.2.1.1 100786,100787 1jotA 133 3.13e+01 1jotA 2b30A 301 3.16e+01 1el6A 219 3.19e+01 1el6B d.182.1.1 42606 1k3yA 221 3.22e+01 a.45.1.1,c.47.1.5 77245,77246 2bi7A 384 3.26e+01 2fwkA 121 3.28e+01 1zx0A 236 3.38e+01 1v54B 227 3.46e+01 b.6.1.2,f.17.2.1 100322,100323 2gdjA 264 3.47e+01 1h8gA 95 3.48e+01 b.109.1.1 65735 1a7tA 232 3.48e+01 1a7tA d.157.1.1 42041 2fwmX 250 3.51e+01 2b5rC 165 3.52e+01 1c3oB 382 3.52e+01 1c3oB c.8.3.1,c.23.16.1 30744,31421 1fdr 248 3.58e+01 1fdr b.43.4.2,c.25.1.1 25653,31543 1el6B 219 3.59e+01 1el6B d.182.1.1 42607 1e3jA 352 3.67e+01 1e3jA b.35.1.2,c.2.1.1 24765,29781 1w9pA 433 3.67e+01 1gutA 68 3.73e+01 b.40.6.1 65576 1ybvA 283 3.76e+01 1ybvA c.2.1.2 29948 1dzaA 129 3.81e+01 7rsa d.5.1.1 37275 1yn9A 169 3.85e+01 2h7bA 105 3.89e+01 2matA 264 3.90e+01 1c24A d.127.1.1 41146 1bvsB 203 3.93e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16281,17956,25275 1m8nA 121 3.94e+01 b.81.2.1 78771 1bpi 58 3.96e+01 1bpi g.8.1.1 44468 1ugxA 133 4.02e+01 1a9xB 379 4.06e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1kqpA 271 4.06e+01 c.26.2.1 72883 1mjc 69 4.09e+01 1mjc b.40.4.5 25319 1b8aA 438 4.11e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1xnzA 264 4.11e+01 1zg2A 107 4.13e+01 1vjkA 98 4.18e+01 d.15.3.1 108631 1p97A 114 4.20e+01 d.110.3.7 94382 1yphE 97 4.21e+01 3nll 138 4.28e+01 5nul c.23.5.1 31206 1wr2A 238 4.32e+01 1btu 240 4.34e+01 5ptp b.47.1.2 26241 1mq4A 272 4.35e+01 d.144.1.7 91391 1l4zB 136 4.40e+01 d.15.5.1 77704 1xh9A 350 4.44e+01 1zgsA 447 4.44e+01 1db3A 372 4.49e+01 1db3A c.2.1.2 29813 1abe 306 4.54e+01 8abp c.93.1.1 35648 1dl5A 317 4.56e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1g38A 393 4.57e+01 2admA c.66.1.27 60235 2ew8A 249 4.59e+01 1l7dA 384 4.64e+01 c.2.1.4,c.23.12.2 77774,77775 2ak5A 64 4.67e+01 1ndh 272 4.70e+01 1ndh b.43.4.2,c.25.1.1 25662,31552 1m5zA 91 4.70e+01 b.36.1.1 78676 1nz6A 101 4.74e+01 a.2.3.1 86441 1gyzA 60 4.79e+01 a.144.2.1 70793 1vjrA 271 4.79e+01 c.108.1.14 100832 1wcv1 257 4.80e+01 1edg 380 4.85e+01 1edg c.1.8.3 28807 1tkiA 321 4.85e+01 1tkiA d.144.1.7 41638 1vkwA 218 4.96e+01 d.90.1.2 108695 1f8gA 384 4.98e+01 1sayA c.2.1.4,c.23.12.2 59695,59696 1widA 130 5.00e+01 1v1hA 103 5.01e+01 b.83.1.1,h.1.17.1 108243,108244 1zkdA 387 5.01e+01 1ipiA 123 5.01e+01 c.52.1.18 66255 1jtgB 165 5.03e+01 d.98.1.1 67267 1vz6A 393 5.03e+01 d.154.1.2 108949 2a9fA 398 5.07e+01 1xm8A 254 5.08e+01 1b9bA 255 5.08e+01 1amk c.1.1.1 28531 1jqbA 351 5.12e+01 b.35.1.2,c.2.1.1 77151,77152 1adwA 123 5.14e+01 1bqk b.6.1.1 22893 1eq9A 222 5.15e+01 5ptp b.47.1.2 26068 1bap 306 5.18e+01 8abp c.93.1.1 35654 1iz0A 302 5.22e+01 b.35.1.2,c.2.1.1 83821,83822 1umkA 275 5.22e+01 1cdkA 350 5.30e+01 1cdkA d.144.1.7 41620 1oqvA 192 5.32e+01 d.24.1.2 87320 1ku8A 133 5.33e+01 1z4eA 153 5.39e+01 2gwdA 449 5.39e+01 1c24A 263 5.41e+01 1c24A d.127.1.1 41148 1a8p 258 5.45e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1apmE 350 5.47e+01 1cdkA d.144.1.7 41628 1uufA 369 5.50e+01 b.35.1.2,c.2.1.1 100006,100007 1vmfA 145 5.60e+01 2g6fX 59 5.61e+01 1xxqA 161 5.61e+01 1gz6A 319 5.63e+01 c.2.1.2 76410 1u4nA 310 5.64e+01 2ggcA 263 5.68e+01 1gvkB 240 5.69e+01 b.47.1.2 70610 1yqdA 366 5.72e+01 1zd7A 159 5.76e+01 1a6dB 543 5.82e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1jpyB 137 5.89e+01 g.17.1.6 67066 1ef8A 261 6.00e+01 1ef8A c.14.1.3 30921 1pcs 98 6.03e+01 1plc b.6.1.1 22871 1vk1A 242 6.05e+01 d.268.1.2 108634 2f1kA 279 6.10e+01 1prtF 98 6.11e+01 1prtF b.40.2.1 25140 2fvx 138 6.19e+01 5nul c.23.5.1 31200 1q7eA 428 6.20e+01 c.123.1.1 96035 2eveA 157 6.22e+01 1pedA 351 6.22e+01 1pedA b.35.1.2,c.2.1.1 24753,29769 1yloA 348 6.23e+01 1uekA 275 6.27e+01 d.14.1.5,d.58.26.5 88483,88484 1m5q1 130 6.32e+01 1paz 123 6.34e+01 1bqk b.6.1.1 22878 1qwrA 319 6.43e+01 b.82.1.3 96491 1d4bA 122 6.47e+01 1d4bA d.15.2.1 37638 5abp 306 6.52e+01 8abp c.93.1.1 35651 1qnjA 240 6.53e+01 5ptp b.47.1.2 26238 1o98A 511 6.61e+01 c.105.1.1,c.76.1.3 86684,86685 1jihA 531 6.61e+01 d.240.1.1,e.8.1.7 90374,90375 1l3iA 192 6.69e+01 c.66.1.22 77676 1kfwA 435 6.78e+01 c.1.8.5,d.26.3.1 77376,77377 2bfxA 284 6.80e+01 1yavA 159 6.83e+01 1sotA 320 6.90e+01 b.36.1.4,b.47.1.1 105852,105853 1eqjA 511 6.92e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1i27A 73 6.93e+01 1i27A a.4.5.30 61555 1nscA 390 6.94e+01 2qwc b.68.1.1 27591 1qorA 327 6.96e+01 1qorA b.35.1.2,c.2.1.1 24766,29782 1n0qA 93 6.96e+01 k.37.1.1 79754 1bcpF 99 6.98e+01 1prtF b.40.2.1 25142 1b34A 119 7.07e+01 1d3bA b.38.1.1 24796 1xe0A 114 7.09e+01 1cr8A 42 7.13e+01 1ajj g.12.1.1 44613 1fthA 122 7.17e+01 d.150.1.2 60028 2affA 120 7.21e+01 1mzeA 351 7.27e+01 b.82.2.6 79694 1ass 159 7.28e+01 1a6dA c.8.5.2 30818 4matA 278 7.37e+01 1c24A d.127.1.1 41150 1bihA 395 7.38e+01 1bihA b.1.1.4,b.1.1.4,b.1.1.4,b.1.1.4 21752,21753,21754,21755 5nul 138 7.42e+01 5nul c.23.5.1 31191 2g2uB 165 7.43e+01 1sk4A 163 7.43e+01 d.118.1.1 105664 1opaA 135 7.45e+01 1hmt b.60.1.2 27214 1pt7A 437 7.47e+01 c.123.1.1 95093 2gwnA 452 7.51e+01 2bdeA 470 7.51e+01 1kevA 351 7.52e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1kwkA 645 7.58e+01 b.71.1.1,c.1.8.1,c.23.16.5 77565,77566,77567 1vc3B 97 7.59e+01 1s98A 107 7.61e+01 b.124.1.1 105377 1kwgA 645 7.62e+01 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1kdj 102 7.69e+01 1plc b.6.1.1 22864 1lba 146 7.76e+01 1lba d.118.1.1 41062 1pmy 123 7.78e+01 1bqk b.6.1.1 22888 3ezmA 101 7.89e+01 3ezmA b.89.1.1 28395 1gg6C 97 7.91e+01 5ptp 1aroL 151 7.92e+01 1lba d.118.1.1 41063 1jmtB 28 7.98e+01 2azeB 106 8.06e+01 1d0qA 103 8.07e+01 1d0qA g.41.3.2 45208 1b65A 375 8.09e+01 1b65A d.154.1.1 42020 1ha1 184 8.12e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 5pti 58 8.19e+01 1bpi g.8.1.1 44467 1vggA 161 8.25e+01 1fehA 574 8.29e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1bqk 124 8.31e+01 1bqk b.6.1.1 22889 1lk5A 229 8.32e+01 c.124.1.4,d.58.40.1 73960,73961 2b6nA 278 8.40e+01 3ygsP 97 8.41e+01 3ygsP a.77.1.3 18435 1qxoA 388 8.46e+01 d.258.1.1 96539 2f20A 240 8.49e+01 1cdy 178 8.49e+01 1cdy b.1.1.1,b.1.1.3 19719,21658 1vkkA 154 8.63e+01 d.109.1.2 108669 1k3lA 221 8.64e+01 a.45.1.1,c.47.1.5 77229,77230 2czqA 205 8.65e+01 1nnwA 252 8.68e+01 d.159.1.5 80674 1o6lA 337 8.69e+01 d.144.1.7 81092 1ejjA 511 8.70e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1e0tA 470 8.80e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 2nsyA 271 8.80e+01 2nsyA c.26.2.1 31612 1fo1A 271 8.81e+01 1fo1A c.10.2.3,d.58.7.2 30869,39213 1dnlA 199 8.82e+01 1ci0A b.45.1.1 25753 2bibA 547 8.87e+01 1f3aA 222 8.89e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1ivyA 452 8.89e+01 1ivyA c.69.1.5 34654 1a3yA 149 8.90e+01 1obpA b.60.1.1 27110 1ecsA 126 8.94e+01 1ecsA d.32.1.2 59407 2fox 138 8.97e+01 5nul c.23.5.1 31197