# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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.soe.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 2g2uB 165 5.31e-07 d.98.1.1 134541 1jtgB 165 6.85e-07 d.98.1.1 67267 2h36X 112 3.24e-02 2joyA 96 7.14e-02 2iorA 235 1.12e-01 2pbiB 354 1.80e-01 1pufB 73 3.67e-01 a.4.1.1 95132 1b72B 87 5.99e-01 1akhA a.4.1.1 16001 1gq6A 313 8.41e-01 c.42.1.1 70341 1plqA 258 1.05e+00 d.131.1.2,d.131.1.2 41388,41389 1plq 258 1.11e+00 1plq 1ucrA 78 1.17e+00 a.4.5.45 99188 1b1gA 75 1.34e+00 1psrA a.39.1.1 17151 2p3hA 101 1.37e+00 1b8iB 63 1.47e+00 1akhA a.4.1.1 16011 1squA 155 1.51e+00 d.252.1.1 98971 1eb7A 323 1.52e+00 1eb7A a.3.1.5,a.3.1.5 59404,59405 1du6A 64 1.91e+00 1akhA a.4.1.1 16002 1hz4A 373 1.94e+00 a.118.8.2 65960 1b74A 254 2.05e+00 1b74A c.78.2.1,c.78.2.1 35264,35265 1oheA 348 2.91e+00 c.45.1.1,c.45.1.1 87013,87014 2dekA 265 3.12e+00 c.90.1.1 131430 2i10A 202 3.20e+00 a.4.1.9,a.121.1.1 136960,136961 2h27A 73 3.22e+00 a.4.13.2 135993 1br1B 150 3.81e+00 1wdcC a.39.1.5 17309 2g17A 337 4.16e+00 c.2.1.3,d.81.1.1 134512,134513 1j7jA 178 4.30e+00 c.61.1.1 84131 2i0xA 85 4.55e+00 2dhqA 146 4.57e+00 2dhqA c.23.13.1 31382 1zckA 154 4.93e+00 2vjvA 159 5.04e+00 2amyA 246 5.35e+00 c.108.1.10 127026 2dkoA 146 5.61e+00 1eq3A 96 5.68e+00 1eq3A d.26.1.1 59486 2e50A 225 5.85e+00 1v5sA 126 6.00e+00 d.129.6.1 108384 1lmb3 92 6.01e+00 1lmb3 2ns9A 157 6.04e+00 1a6dA 545 6.05e+00 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 1mvwC 147 6.19e+00 i.15.1.1 79525 2hl7A 84 6.19e+00 2eqaA 352 6.72e+00 2p10A 286 6.87e+00 2bjfA 329 7.11e+00 2yvyA 278 7.11e+00 2nvmA 126 7.17e+00 d.326.1.1 138631 2jejA 358 7.46e+00 d.240.1.1,e.8.1.7 138284,138285 1z00B 84 7.47e+00 a.60.2.5 124295 1w78A 422 7.50e+00 1rxdA 159 7.71e+00 c.45.1.1 111959 1vhvA 268 7.83e+00 c.90.1.1 100704 2phcB 225 8.09e+00 2yy3A 91 8.40e+00 1vz0A 230 8.60e+00 a.4.14.1,d.268.1.1 108929,108930 1r6jA 82 8.78e+00 b.36.1.1 97151 1jofA 365 8.91e+00 b.69.10.1 71775 2pjoA 268 9.31e+00 2ofyA 86 9.47e+00 2vc4A 267 9.64e+00 2a1jA 63 1.02e+01 a.60.2.5 126000 1a99A 344 1.02e+01 1pot c.94.1.1 35812 1wh8A 111 1.03e+01 a.35.1.7 114636 2f9dA 125 1.05e+01 d.58.7.1 133159 2o8xA 70 1.06e+01 1jx4A 352 1.06e+01 d.240.1.1,e.8.1.7 90378,90379 2b5aA 77 1.08e+01 a.35.1.3 127882 2dj5A 133 1.08e+01 c.92.1.3 131536 1fxlA 167 1.16e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1e3oC 160 1.16e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1vpvA 300 1.19e+01 c.119.1.1 113975 1vlaA 150 1.19e+01 d.227.1.2 108735 2rldA 121 1.23e+01 1jpdX 324 1.23e+01 c.1.11.2,d.54.1.1 67014,67015 1x24A 180 1.24e+01 2a6mA 155 1.26e+01 d.58.57.1 126287 1w6nA 134 1.28e+01 b.29.1.3 114275 1aoeA 192 1.28e+01 1aoeA c.71.1.1 34923 2iwxA 214 1.30e+01 d.122.1.1 137758 1lliA 92 1.31e+01 1lmb3 a.35.1.2 17025 1e0bA 68 1.33e+01 1e0bA b.34.13.2 37476 2od5A 116 1.33e+01 2iskA 230 1.34e+01 2bcjB 340 1.34e+01 b.69.4.1 128289 1zclA 180 1.38e+01 1h05A 146 1.38e+01 c.23.13.1 76433 1sltA 134 1.39e+01 1c1lA b.29.1.3 24186 1igwA 434 1.41e+01 c.1.12.7 62370 1paqA 189 1.41e+01 a.118.1.14 94413 1jvwA 167 1.52e+01 d.26.1.1 71907 2fueA 262 1.57e+01 c.108.1.10 134119 3bw8A 217 1.57e+01 1or7A 194 1.58e+01 a.4.13.2,a.177.1.1 87332,87333 2breA 219 1.60e+01 d.122.1.1 128994 2v75A 104 1.65e+01 1mgpA 313 1.66e+01 c.119.1.1 79098 2j7tA 302 1.71e+01 1xnb 185 1.72e+01 1axkA 2pliA 91 1.75e+01 2gqpA 236 1.80e+01 d.122.1.1 135513 1hlcA 129 1.80e+01 1c1lA b.29.1.3 24208 1dd3A 128 1.83e+01 1dd3C a.108.1.1,d.45.1.1 19031,38760 2hd1A 326 1.84e+01 a.211.1.2 136338 1g55A 343 1.88e+01 1g55A c.66.1.26 34247 1t95A 240 1.89e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 2gu3A 136 1.96e+01 2jw5A 106 1.98e+01 2fziA 206 2.01e+01 c.71.1.1 134448 2a9dA 372 2.05e+01 b.1.18.6,d.176.1.1 126431,126432 2fkcA 247 2.07e+01 1miwA 404 2.08e+01 a.173.1.1,d.218.1.4 79162,79163 2nqwA 93 2.12e+01 1sfeA 180 2.13e+01 a.4.2.1,c.55.7.1 16073,33748 2ze0A 555 2.15e+01 2ip2A 334 2.18e+01 1r6uA 437 2.18e+01 c.26.1.1 97163 1gzwA 134 2.19e+01 b.29.1.3 90535 1bqnA 558 2.20e+01 1rthA c.55.3.1,e.8.1.2 33599,43064 1oeyA 83 2.22e+01 d.15.2.2 92800 1whzA 70 2.23e+01 d.50.3.2 114656 2gx9A 129 2.25e+01 d.299.1.1 135828 1rthA 560 2.29e+01 1rthA c.55.3.1,e.8.1.2 33576,43028 2q3pA 112 2.30e+01 d.58.4.4 139798 1fkoA 543 2.35e+01 1rthA c.55.3.1,e.8.1.2 33612,43094 1trrA 107 2.36e+01 1jhgA a.4.12.1 19017 1byqA 228 2.38e+01 1yer d.122.1.1 41100 1ybvA 283 2.39e+01 1ybvA c.2.1.2 29948 1yueA 427 2.46e+01 1a3yA 149 2.47e+01 1obpA b.60.1.1 27110 1mzgA 146 2.47e+01 d.224.1.1 79696 1lp8A 254 2.56e+01 d.165.1.1 91082 1rl0A 255 2.60e+01 d.165.1.1 111859 1r4vA 171 2.60e+01 a.22.1.4 97049 2qv6A 268 2.61e+01 1vdwA 254 2.65e+01 e.7.1.1 100569 1jkeA 145 2.66e+01 c.110.1.1 66791 1dzkA 157 2.67e+01 1obpA b.60.1.1 27096 2hnlA 225 2.77e+01 1ecfB 504 2.84e+01 1ecfB c.61.1.1,d.153.1.1 34054,41821 1slqA 278 2.88e+01 f.47.1.1 105719 1octC 156 2.91e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 1i6pA 220 2.91e+01 1ddzA c.53.2.1 61848 1ggwA 140 2.94e+01 1ggwA a.39.1.5 60490 1jhgA 101 2.97e+01 1jhgA a.4.12.1 19009 2h8gA 267 2.97e+01 1xfdA 723 3.08e+01 b.70.3.1,c.69.1.24 115251,115252 1b8aA 438 3.09e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ft9A 222 3.10e+01 1ft9A a.4.5.4,b.82.3.1 16107,28131 1r69 69 3.13e+01 1r69 1r69A 69 3.13e+01 a.35.1.2 17028 1p9qC 256 3.14e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 2i7cA 283 3.16e+01 1wosA 364 3.21e+01 b.44.2.1,d.250.1.1 109468,109469 1ds6B 180 3.22e+01 1rhoA b.1.18.8 21898 3sxlA 184 3.27e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 2iakA 224 3.27e+01 1g0oA 283 3.30e+01 1ybvA c.2.1.2 60181 1ustA 93 3.30e+01 a.4.5.13 99884 1ecfA 504 3.31e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1giqA 413 3.34e+01 d.166.1.1,d.166.1.1 76224,76225 1fk9A 543 3.39e+01 1rthA c.55.3.1,e.8.1.2 33607,43080 1shkA 173 3.39e+01 1shkA c.37.1.2 31932 2bf5A 98 3.44e+01 d.137.1.1 128405 2iv2X 715 3.55e+01 b.52.2.2,c.81.1.1 137714,137715 1y89A 238 3.57e+01 1uylA 236 3.60e+01 d.122.1.1 108147 1j99A 293 3.63e+01 c.37.1.5 71618 1im4A 221 3.66e+01 e.8.1.7 62581 1vrtA 560 3.71e+01 1rthA c.55.3.1,e.8.1.2 33574,43023 2qe6A 274 3.76e+01 2qpqA 301 3.81e+01 1fkoB 440 3.83e+01 1rthA e.8.1.2 43095 2c60A 111 3.83e+01 d.15.2.2 129966 1eetA 557 3.84e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1zuhA 168 3.85e+01 2f02A 323 3.88e+01 c.72.1.1 132649 2z79A 185 3.97e+01 1zfjA 491 4.03e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 2gmqA 118 4.03e+01 1vkmA 297 4.06e+01 c.138.1.1 108670 1h6vA 499 4.06e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 60693,60694,60695 1d0qA 103 4.07e+01 1d0qA g.41.3.2 45208 1k8kD 300 4.07e+01 d.198.2.1,d.198.2.1 68309,68310 1k8kG 151 4.12e+01 a.118.13.1 68313 2j6pA 152 4.16e+01 1vdhA 249 4.16e+01 d.58.4.10 108523 1tbgA 340 4.17e+01 1tbgA b.69.4.1 27649 2yv4A 105 4.21e+01 1gqvA 135 4.24e+01 d.5.1.1 70376 1soxA 466 4.27e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1js8A 394 4.27e+01 a.86.1.1,b.112.1.1 67219,67220 1btmA 252 4.36e+01 1amk c.1.1.1 28513 2fgtA 417 4.38e+01 1k8uA 90 4.39e+01 a.39.1.2 72181 2outA 131 4.44e+01 1m2oB 190 4.48e+01 c.37.1.8 78485 1irp 153 4.50e+01 1irp 1zx8A 136 4.52e+01 b.62.1.3 125764 2o35A 105 4.52e+01 3bduA 62 4.54e+01 1qy5A 269 4.55e+01 d.122.1.1 96573 2zhgA 154 4.56e+01 1wlsA 328 4.60e+01 1l6pA 125 4.62e+01 b.1.17.1 73626 1keyA 235 4.63e+01 a.118.16.1 72389 2dvyA 226 4.70e+01 1e8aA 91 4.70e+01 1b4cA a.39.1.2 17188 2o2kA 355 4.80e+01 1l0iA 78 4.81e+01 a.28.1.1 77643 1j1jA 240 4.82e+01 a.118.16.1 90762 2dcyA 185 4.83e+01 b.29.1.11 131388 1xmxA 385 4.92e+01 c.52.1.26 115568 1dpsA 167 5.05e+01 1dpsA a.25.1.1 16716 2qtdA 105 5.11e+01 1j3kA 280 5.11e+01 c.71.1.1 84070 3cerA 343 5.14e+01 2va8A 715 5.15e+01 1agdA 276 5.23e+01 1agdA b.1.1.2,d.19.1.1 20741,38260 1sf8A 126 5.25e+01 d.271.1.1 105472 2prsA 284 5.27e+01 1wdvA 152 5.30e+01 d.116.1.1 114539 1d7qA 143 5.45e+01 1d7qA b.40.4.5 25331 1r4aA 165 5.46e+01 c.37.1.8 96986 1b9yC 246 5.48e+01 1b9yC c.47.1.6 33052 1zavA 180 5.49e+01 1a4pA 96 5.52e+01 1b4cA a.39.1.2 17176 1w7jB 151 5.53e+01 a.39.1.5 120690 2d4uA 176 5.59e+01 1k5nA 276 5.83e+01 b.1.1.2,d.19.1.1 77266,77267 1xh3A 276 5.87e+01 b.1.1.2,d.19.1.1 115287,115288 1xfsA 178 5.87e+01 d.129.3.5 109589 1j8mF 297 5.88e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1gotB 340 5.90e+01 1tbgA b.69.4.1 27648 1j8yF 297 5.91e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1anxA 319 5.97e+01 1avc a.65.1.1 18161 2j0nA 200 6.00e+01 a.250.1.1 137899 3b4dA 96 6.04e+01 2d0sA 79 6.06e+01 2bvpA 276 6.10e+01 b.1.1.2,d.19.1.1 129291,129292 2rn7A 108 6.10e+01 2ix2B 245 6.29e+01 1hniA 558 6.31e+01 1rthA c.55.3.1,e.8.1.2 33586,43044 2c0dA 221 6.32e+01 2g50A 530 6.36e+01 b.58.1.1,c.1.12.1,c.49.1.1 134618,134619,134620 1rzsA 61 6.40e+01 a.35.1.2 105139 2gauA 232 6.41e+01 a.4.5.4,b.82.3.2 134894,134895 2q7nA 488 6.44e+01 1r6xA 395 6.45e+01 b.122.1.3,c.26.1.5 97167,97168 1dpeA 507 6.46e+01 c.94.1.1 35799 1a4mA 349 6.48e+01 1a4mA c.1.9.1 29014 1a1nA 276 6.50e+01 1agdA b.1.1.2,d.19.1.1 20755,38267 1fliA 98 6.50e+01 1awcA a.4.5.21 16160 1i7kA 179 6.52e+01 1u9aA d.20.1.1 61889 1ospO 257 6.56e+01 1ospO b.76.1.1 27971 3cnwA 148 6.73e+01 1zmaA 118 6.75e+01 c.47.1.1 125354 1ugiA 84 6.75e+01 1ugiA d.17.5.1 38125 1ae9A 179 6.82e+01 1ae9A d.163.1.1 42153 1msk 331 6.89e+01 1msk 1b00A 127 6.91e+01 3chy c.23.1.1 31122 1zh5A 195 6.97e+01 a.4.5.46,d.58.7.1 125073,125074 1l8dA 112 7.06e+01 h.4.12.1 73687 1fecA 490 7.07e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 2bsyA 278 7.07e+01 b.85.4.1,b.85.4.1 129129,129130 2yugA 155 7.08e+01 1imjA 210 7.10e+01 c.69.1.23 71246 2hyjA 200 7.20e+01 1yer 228 7.20e+01 1yer 1t8kA 77 7.32e+01 a.28.1.1 106666 1a0rB 340 7.32e+01 1tbgA b.69.4.1 27658 1du0A 57 7.38e+01 2hddA a.4.1.1 15974 2hkjA 469 7.42e+01 a.156.1.3,d.14.1.3,d.122.1.2 136553,136554,136555 1y0uA 96 7.42e+01 a.4.5.5 116310 1pdnC 128 7.46e+01 6paxA a.4.1.5 16047 3bwaA 276 7.56e+01 1g6eA 87 7.57e+01 1g6eA b.11.1.6 60317 1ef4A 55 7.61e+01 1ef4A a.4.11.1 16272 2d9rA 104 7.62e+01 b.129.2.1 131350 1uq5A 263 7.63e+01 d.165.1.1 99778 2qdfA 335 7.67e+01 2jbaA 127 7.68e+01 1pl3A 186 7.76e+01 b.1.9.1 88158 1yi8A 351 7.82e+01 3buvA 326 7.87e+01 1b9xC 246 7.94e+01 1b9yC c.47.1.6 33053