# List of top-scoring protein chains for t2k-100-30-dssp-ehl2-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 1hw5A 210 1.19e-23 2cgpA a.4.5.4,b.82.3.2 16098,28137 1g6nA 210 2.26e-23 2cgpA a.4.5.4,b.82.3.2 16100,28139 2cgpA 210 2.47e-23 2cgpA a.4.5.4,b.82.3.2 16102,28141 1i6xA 209 7.31e-23 a.4.5.4,b.82.3.2 83673,83674 2gauA 232 1.75e-16 a.4.5.4,b.82.3.2 134894,134895 2pqqA 149 1.95e-16 2fmyA 220 5.45e-16 2z69A 154 2.04e-14 2cohA 202 3.62e-14 a.4.5.4,b.82.3.2 130677,130678 2zcwA 202 3.62e-14 1o5lA 213 2.79e-13 b.82.3.2 92506 1ft9A 222 7.09e-13 1ft9A a.4.5.4,b.82.3.1 16107,28131 2h6bA 250 9.18e-13 1zybA 232 1.06e-12 a.4.5.4,b.82.3.2 125815,125816 3bpzA 202 2.04e-12 1q3eA 207 2.79e-12 b.82.3.2 95669 1vp6A 138 3.53e-12 b.82.3.2 113939 1cx4A 305 6.27e-12 b.82.3.2,b.82.3.2 59099,59100 1rgs 288 1.70e-11 1rgs 1ne6A 283 2.65e-11 b.82.3.2,b.82.3.2 91831,91832 1rl3A 288 8.29e-11 b.82.3.2,b.82.3.2 104975,104976 1u7eB 154 9.75e-11 2ptmA 198 1.25e-10 2bgcA 238 6.30e-10 a.4.5.4,b.82.3.3 128458,128459 1omiA 248 1.58e-09 b.82.3.3,a.4.5.4 87079,87080 1o7fA 469 7.15e-09 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 2d93A 134 5.30e-05 1lccA 51 1.19e-01 1pru a.35.1.5 17110 1cjgA 62 1.40e-01 1pru a.35.1.5 17112 1vj2A 126 1.46e-01 b.82.1.10 100796 1yhfA 115 1.73e-01 b.82.1.9 123176 1j58A 385 2.29e-01 b.82.1.2 71531 2bjcA 62 2.95e-01 a.35.1.5 128620 1efaA 333 7.48e-01 1tlfA a.35.1.5,c.93.1.1 17106,35691 2fbhA 146 7.68e-01 a.4.5.28 133245 2dbbA 151 7.68e-01 3ctaA 230 8.93e-01 2bkkA 264 8.96e-01 1j7iA 264 9.87e-01 1j7iA d.144.1.6 62694 1j7lA 264 1.03e+00 d.144.1.6 62697 2j59M 168 1.13e+00 1trrA 107 1.34e+00 1jhgA a.4.12.1 19017 3deuA 166 1.45e+00 2uuqA 414 1.52e+00 1jhgA 101 1.59e+00 1jhgA a.4.12.1 19009 3cloA 258 1.89e+00 1h8eH 146 2.03e+00 1e79H b.93.1.1 60757 1a0rB 340 2.18e+00 1tbgA b.69.4.1 27658 1m6kA 251 2.23e+00 e.3.1.1 78695 3bj6A 152 2.36e+00 1tbgA 340 2.47e+00 1tbgA b.69.4.1 27649 1yioA 208 2.57e+00 a.4.6.2,c.23.1.1 123326,123327 1rp3A 239 2.61e+00 a.4.13.1,a.4.13.2,a.177.1.1 97678,97679,97680 2h09A 155 2.63e+00 2bcjB 340 2.90e+00 b.69.4.1 128289 1gotB 340 3.65e+00 1tbgA b.69.4.1 27648 1hq1A 105 3.80e+00 1dulA a.36.1.1 17120 1e79H 146 3.81e+00 1e79H a.2.10.1,b.93.1.1 15721,28438 1qbjA 81 3.90e+00 1qbjA a.4.5.19 16155 1jjgA 102 3.99e+00 b.40.4.5 71696 1mgtA 174 4.08e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1cr6B 554 4.11e+00 1cr6B c.69.1.11,c.108.1.2 34688,43338 2d40A 354 4.18e+00 3bghA 236 4.30e+00 1rcsA 105 4.37e+00 1jhgA a.4.12.1 19025 1qgpA 77 4.93e+00 1qbjA a.4.5.19 16158 1a8d 452 5.04e+00 1a8d 1a8dA 452 5.04e+00 b.29.1.6,b.42.4.2 24262,25607 2cxkA 95 5.31e+00 b.1.18.1 131006 2o3fA 111 5.47e+00 2d5fA 493 5.68e+00 1od5A 492 5.80e+00 b.82.1.2,b.82.1.2 86832,86833 1bw6A 56 6.00e+00 1bw6A a.4.1.7 16052 1dgwA 178 6.05e+00 1dgwA b.82.1.2 28090 1diwA 441 6.38e+00 1a8d b.29.1.6,b.42.4.2 24264,25609 2jn6A 97 6.43e+00 1dulA 69 6.63e+00 1dulA a.36.1.1 17121 1u8bA 133 6.75e+00 2p4oA 306 6.76e+00 2b0lA 102 7.28e+00 a.4.5.66 127641 1je8A 82 8.40e+00 a.4.6.2 77108 1l0oC 243 8.53e+00 a.4.13.2 73405 2d1hA 109 8.60e+00 a.4.5.50 131125 1d0hA 469 8.62e+00 1a8d b.29.1.6,b.42.4.2 24265,25610 1i1gA 141 8.64e+00 a.4.5.32,d.58.4.2 65982,65983 2dg7A 195 9.35e+00 1danT 80 9.41e+00 1boy b.1.2.1 21953 1khxA 227 9.52e+00 b.26.1.1 68631 2dx0A 138 9.89e+00 3bpvA 138 1.04e+01 1b1bA 140 1.05e+01 1bi0 a.4.5.24,a.76.1.1 16215,18421 3cjnA 162 1.06e+01 2b9uA 176 1.11e+01 3bkbA 377 1.12e+01 1k3sA 113 1.12e+01 d.198.1.1 68120 2cavA 445 1.15e+01 1dgwA b.82.1.2,b.82.1.2 28094,28095 1wpkA 146 1.16e+01 2rn7A 108 1.17e+01 2phlA 397 1.18e+01 1dgwA b.82.1.2,b.82.1.2 28082,28083 1hlvA 131 1.18e+01 a.4.1.7,a.4.1.7 65854,65855 1viuA 203 1.22e+01 d.113.1.1 100771 1sur 215 1.24e+01 1sur 1surA 215 1.24e+01 c.26.2.2 31620 1ku3A 73 1.26e+01 a.4.13.2 73000 2ddhA 661 1.26e+01 a.29.3.2,a.29.3.2,e.6.1.2 131394,131395,131396 1utxA 66 1.30e+01 a.35.1.3 108034 1ukkA 142 1.31e+01 d.227.1.1 99491 1zgwA 139 1.31e+01 1xahA 354 1.32e+01 2yvdA 431 1.34e+01 1v30A 124 1.35e+01 d.269.1.1 113496 1cauA 181 1.36e+01 1dgwA b.82.1.2 28102 2qjvA 270 1.43e+01 1kzfA 230 1.47e+01 d.108.1.3 73354 1q7fA 286 1.57e+01 b.68.9.1 96036 1xkzA 255 1.60e+01 e.3.1.1 115426 1a04A 215 1.61e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 1lj9A 144 1.64e+01 a.4.5.28 78035 3bruA 222 1.67e+01 1xd7A 145 1.68e+01 a.4.5.55 109566 1kvkA 395 1.72e+01 d.14.1.5,d.58.26.3 73060,73061 2rckA 225 1.74e+01 3bqxA 150 1.75e+01 1ez3A 127 1.79e+01 1dn1B a.47.2.1 17768 1c3hA 137 1.80e+01 b.22.1.1 90405 2dkfA 431 1.83e+01 2o38A 120 1.88e+01 2z15A 130 1.89e+01 2bnmA 198 1.96e+01 a.35.1.3,b.82.1.10 128835,128836 2e18A 257 1.99e+01 2f4iA 197 2.12e+01 b.40.11.1 132923 2ay1A 394 2.20e+01 1ajsA c.67.1.1 34357 2g5fA 450 2.23e+01 d.161.1.1 134654 1fx7A 230 2.24e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 2h0bA 184 2.25e+01 2j7tA 302 2.35e+01 2ea7A 434 2.37e+01 2ch9A 131 2.39e+01 2p4eA 692 2.41e+01 1jkoC 52 2.46e+01 a.4.1.2 66809 2om6A 235 2.50e+01 2e9qA 459 2.52e+01 1u7zA 226 2.57e+01 c.72.3.1 113107 2aalA 131 2.58e+01 d.80.1.6 126483 3c0dA 119 2.59e+01 2i8gA 151 2.66e+01 1hcrA 52 2.75e+01 1hcrA a.4.1.2 16020 1h8vA 218 2.82e+01 2nlrA b.29.1.11 60795 1oa2A 218 2.86e+01 b.29.1.11 86721 2uwqA 86 2.89e+01 1fxzA 476 2.93e+01 b.82.1.2,b.82.1.2 65059,65060 1r69 69 2.96e+01 1r69 1r69A 69 2.96e+01 a.35.1.2 17028 1rwiA 270 2.98e+01 b.68.9.1 97987 1bi0 226 2.98e+01 1bi0 2nyxA 168 3.04e+01 2dtr 226 3.14e+01 1bi0 1de4C 640 3.20e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1r8mE 203 3.26e+01 a.118.3.1 97242 2d0oA 610 3.28e+01 c.8.6.1,c.55.1.6,c.55.1.6 131075,131076,131077 2pia 321 3.29e+01 2pia 2piaA 321 3.29e+01 b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1znpA 154 3.31e+01 b.82.1.16 125394 1wljA 189 3.32e+01 c.55.3.5 114734 1u2wA 122 3.32e+01 a.4.5.5 119487 2i7pA 362 3.34e+01 1gwiA 411 3.40e+01 a.104.1.1 76364 1awe 130 3.41e+01 1awe 1pbv 195 3.46e+01 1pbv 1pbvA 195 3.46e+01 a.118.3.1 19179 2b67A 204 3.46e+01 d.90.1.1 127970 1in4A 334 3.59e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 3bnwA 181 3.60e+01 1eyqA 222 3.62e+01 1eypA d.36.1.1 38534 2ethA 154 3.68e+01 a.4.5.28 132358 1h30A 422 3.70e+01 b.29.1.4,b.29.1.4 76604,76605 1r8sE 203 3.77e+01 a.118.3.1 97248 2np5A 203 3.78e+01 a.4.1.9,a.121.1.1 138424,138425 3cqyA 370 3.80e+01 2v9cA 215 3.90e+01 2o7iA 592 3.97e+01 2ajgA 196 3.98e+01 1ic8A 194 3.99e+01 a.4.1.1,a.35.1.1 76740,76741 2dtrA 226 3.99e+01 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 2qgnA 322 3.99e+01 1orvA 728 4.01e+01 b.70.3.1,c.69.1.24 87354,87355 1ugjA 141 4.08e+01 b.41.1.3 107826 1j6qA 136 4.09e+01 b.40.9.1 77091 3dczA 207 4.11e+01 1zpsA 138 4.11e+01 b.168.1.1 125473 2gpiA 91 4.12e+01 1i7fA 292 4.14e+01 1i7fA d.193.1.1 61888 1qadA 111 4.20e+01 1qadA d.93.1.1 40498 2fnaA 357 4.23e+01 a.4.5.11,c.37.1.20 133809,133810 2ictA 94 4.26e+01 1pp7U 131 4.28e+01 a.4.5.44 94973 1gdtA 183 4.31e+01 2rslA a.4.1.2,c.53.1.1 16021,33348 1qzzA 374 4.31e+01 a.4.5.29,c.66.1.12 96719,96720 1br0A 120 4.32e+01 a.47.2.1 17772 1umqA 81 4.34e+01 a.4.1.12 99625 3bddA 142 4.37e+01 2ao9A 155 4.40e+01 a.4.1.17 127069 1mt6A 280 4.43e+01 b.76.2.1,b.85.7.1 79446,79447 1r1uA 106 4.51e+01 a.4.5.5 104771 1gvmA 136 4.52e+01 b.109.1.1 70612 1f00I 282 4.57e+01 1f00I b.1.14.1,b.1.14.1,d.169.1.3 22368,22369,42439 1f5tA 121 4.59e+01 1bi0 a.4.5.24,a.76.1.1 16203,18409 2h3gX 268 4.77e+01 1hw7A 255 4.79e+01 1i7fA d.193.1.1 61297 1khiA 176 4.82e+01 b.34.5.2,b.40.4.5 77408,77409 2cro 71 4.82e+01 1r69 2croA 71 4.82e+01 a.35.1.2 17038 2ofyA 86 4.82e+01 1kpgA 287 4.85e+01 c.66.1.18 68735 1h3iA 293 4.85e+01 b.76.2.1,b.85.7.1 76635,76636 2p8gA 162 4.88e+01 2g7uA 257 4.89e+01 2e52A 300 4.94e+01 1t16A 427 5.00e+01 f.4.3.4 106242 1lvoA 302 5.07e+01 b.47.1.4 74284 2r1jL 68 5.07e+01 1dn1B 267 5.08e+01 1dn1B a.47.2.1 17771 1hi9A 274 5.12e+01 1hi9A c.99.1.1 61063 1smtA 122 5.17e+01 1smtA a.4.5.5 16109 1in6A 334 5.19e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 3bexA 249 5.21e+01 1hs7A 97 5.26e+01 1hs7A a.47.2.1 61236 2qf2A 624 5.26e+01 1qd1A 325 5.27e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 2gtdA 251 5.30e+01 c.55.1.13,c.55.1.13 135634,135635 1qfoA 119 5.32e+01 1qfoA b.1.1.1 19708 1p35A 299 5.35e+01 1p35A b.28.1.1 23925 1lkvX 232 5.36e+01 a.118.14.1 73980 1aqt 138 5.44e+01 1aqt 1nf3C 128 5.44e+01 b.36.1.1 85596 1rzsA 61 5.45e+01 a.35.1.2 105139 2ampA 304 5.50e+01 b.47.1.4 127021 1qrzA 246 5.52e+01 5ptp b.47.1.2 26366 1adrA 76 5.55e+01 a.35.1.2 17042 1a12A 413 5.61e+01 1a12A b.69.5.1 27663 1eqnA 321 5.62e+01 1dd9A e.13.1.1 43256 1fxkC 133 5.72e+01 1fxkC a.2.5.1 15702 2ja9A 175 5.73e+01 2ftwA 521 5.80e+01 b.92.1.3,c.1.9.6 134083,134084 1mdc 133 5.82e+01 1hmt 1h8gA 95 5.88e+01 b.109.1.1 65735 1cnuA 137 5.90e+01 1cof d.109.1.2 40862 1j3mA 129 5.94e+01 d.129.7.1 103836 2q1zB 195 6.14e+01 2infA 359 6.15e+01 2hyxA 352 6.15e+01 1c0wA 225 6.23e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 1q1hA 110 6.23e+01 a.4.5.41 95580 1r1tA 122 6.26e+01 a.4.5.5 104769 2yskA 145 6.26e+01 1nkqA 259 6.27e+01 d.177.1.1 103862 2fqpA 97 6.28e+01 2b5aA 77 6.29e+01 a.35.1.3 127882 1on2A 142 6.32e+01 a.4.5.24,a.76.1.1 87103,87104 1hw1A 239 6.33e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1x8hA 228 6.34e+01 d.157.1.1 114961 1ulyA 192 6.38e+01 a.4.5.58 113297 1e2xA 243 6.39e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1ahsA 126 6.42e+01 1ahsA b.19.1.1 23794 1mdcA 131 6.51e+01 b.60.1.2 27198 2hc5A 117 6.73e+01 1qs1A 462 6.76e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 2b5tI 432 6.78e+01 e.1.1.1 127905 1h9oA 112 6.83e+01 1qadA d.93.1.1 60837 2pa7A 141 6.87e+01 1xoyA 161 6.92e+01 b.18.1.26 115718 1fseA 74 6.94e+01 1fseA a.4.6.2 60000 1fs0E 138 6.95e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1boy 219 6.97e+01 1boy 1aeiA 315 6.97e+01 1avc a.65.1.1 18180 2pw4A 188 6.99e+01 1vpbA 451 7.10e+01 d.283.1.1 113950 1b8iB 63 7.11e+01 1akhA a.4.1.1 16011 2ho9A 167 7.12e+01 2ev0A 142 7.19e+01 a.4.5.24,a.76.1.1 132413,132414 1lh0A 213 7.20e+01 c.61.1.1 73896 2genA 197 7.20e+01 a.4.1.9,a.121.1.1 135062,135063 1dm5A 315 7.34e+01 1avc a.65.1.1 18186 1du6A 64 7.35e+01 1akhA a.4.1.1 16002 2qm0A 275 7.35e+01 1td6A 306 7.40e+01 a.234.1.1 112390 2bf6A 449 7.42e+01 2z0lA 318 7.47e+01 2qenA 350 7.54e+01 1s99A 200 7.63e+01 d.58.48.2 112046 2i6hA 207 7.63e+01 2qikA 285 7.65e+01 2zdiC 151 7.70e+01 2ef8A 84 7.72e+01 2a0jA 149 7.77e+01 2oerA 214 7.78e+01 2qtwB 546 7.81e+01