# 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 2zwmA 130 2.70e-18 3f6pA 120 4.09e-18 1mvoA 136 5.00e-18 c.23.1.1 79513 1zesA 125 7.57e-18 c.23.1.1 124994 2a9oA 120 1.05e-17 c.23.1.1 126444 1b00A 127 1.41e-17 3chy c.23.1.1 31122 2jbaA 127 1.01e-16 1w25A 459 3.04e-16 c.23.1.1,c.23.1.1,d.58.29.2 114090,114091,114092 1zh2A 121 4.46e-16 c.23.1.1 125069 1kgsA 225 4.70e-16 a.4.6.1,c.23.1.1 68596,68597 1xhfA 123 5.92e-16 c.23.1.1 122003 3dgfC 122 6.59e-16 3gt7A 154 7.14e-16 1ys7A 233 1.07e-15 a.4.6.1,c.23.1.1 123961,123962 3gl9A 122 1.09e-15 2pl1A 121 1.55e-15 c.23.1.1 149610 1zgzA 122 5.65e-15 c.23.1.1 125065 2oqrA 230 1.63e-14 2qzjA 136 1.83e-14 1srrA 124 2.44e-14 1dz3A c.23.1.1 31110 1mb3A 124 3.65e-14 c.23.1.1 78907 1ab5A 125 3.90e-14 3chy c.23.1.1 31056 3h1gA 129 4.84e-14 1ab6A 125 5.55e-14 3chy c.23.1.1 31054 3a10A 116 6.68e-14 3gwgA 129 7.75e-14 3chy 128 7.83e-14 3chy 1dc7A 124 9.36e-14 1dbwA c.23.1.1 31093 3jteA 143 1.05e-13 3crnA 132 1.10e-13 1jbeA 128 1.46e-13 3chy c.23.1.1 62845 3cg4A 142 1.65e-13 3i5aA 334 1.87e-13 3breA 358 2.00e-13 3h1fA 129 2.06e-13 1tmyA 120 2.22e-13 c.23.1.1 31083 1p2fA 220 2.28e-13 a.4.6.1,c.23.1.1 87720,87721 3c3mA 138 2.76e-13 1u8tA 129 3.30e-13 c.23.1.1 113192 1e6mA 128 3.60e-13 3chy c.23.1.1 31039 1s8nA 205 3.69e-13 c.23.1.1 105374 3cfyA 137 3.79e-13 1u0sY 118 3.86e-13 c.23.1.1 107566 3lteA 132 5.84e-13 2zayA 147 8.62e-13 3hdgA 137 9.63e-13 3cnbA 143 1.93e-12 1qkkA 155 1.94e-12 1dbwA c.23.1.1 31104 1l5zA 155 2.31e-12 c.23.1.1 77722 1yioA 208 2.41e-12 a.4.6.2,c.23.1.1 123326,123327 1dbwA 126 2.67e-12 1dbwA c.23.1.1 31095 2qxyA 142 3.03e-12 1a04A 215 5.98e-12 1a04A a.4.6.2,c.23.1.1 16234,31089 1k68A 140 7.13e-12 c.23.1.1 90943 1k66A 149 1.11e-11 c.23.1.1 90941 3hdvA 136 1.34e-11 3eodA 130 1.42e-11 1i3cA 149 1.56e-11 c.23.1.1 71112 3lufA 259 1.59e-11 2jk1A 139 2.42e-11 1oxkB 134 2.49e-11 c.23.1.1 93691 2vuhB 139 2.58e-11 3hzhA 157 3.02e-11 2gkgA 127 3.10e-11 2r25B 133 3.61e-11 c.23.1.1 151530 3h5iA 140 4.17e-11 3cu5A 141 5.06e-11 3cz5A 153 5.13e-11 3grcA 140 6.47e-11 3hv2A 153 7.12e-11 3hebA 152 7.82e-11 3eulA 152 7.84e-11 1dz3A 130 8.48e-11 1dz3A c.23.1.1 31105 3khtA 144 1.07e-10 3kcnA 151 1.07e-10 3b2nA 133 1.18e-10 2qr3A 140 3.45e-10 2rjnA 154 3.58e-10 3f6cA 134 4.29e-10 3luaA 140 4.70e-10 2qvgA 143 6.63e-10 2plnA 137 1.18e-09 1a2oA 349 2.18e-09 1chd c.23.1.1,c.40.1.1 31120,32479 2qsjA 154 2.22e-09 3cg0A 140 2.84e-09 2qv0A 143 5.52e-09 3i42A 127 5.86e-09 1dcfA 136 1.88e-08 1dcfA c.23.1.2 31124 3kyjB 145 1.92e-08 2rdmA 132 1.96e-08 3eqzA 135 2.63e-08 3c97A 140 5.48e-08 3ilhA 146 2.49e-07 3ktoA 136 4.27e-07 2b4aA 138 1.52e-06 c.23.1.1 127817 3kyiB 145 3.41e-06 1m2eA 135 3.62e-03 c.23.1.5 78478 2vycA 755 1.17e-02 2yxbA 161 1.91e-02 2ekcA 262 8.39e-02 2pyyA 228 1.63e-01 1qo0D 196 1.79e-01 1qo0D c.23.1.3 31125 1xm3A 264 2.22e-01 c.1.31.1 115461 1y80A 210 2.37e-01 3c3pA 210 2.45e-01 2jgnA 185 2.54e-01 3labA 217 2.55e-01 1h5yA 253 2.93e-01 c.1.2.1 65638 1qv9A 283 3.09e-01 c.127.1.1 96356 3jr2A 218 3.11e-01 1wv9A 94 3.14e-01 1jvsA 400 3.28e-01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 3iebA 218 3.47e-01 1ls1A 295 3.78e-01 a.24.13.1,c.37.1.10 78170,78171 2c3zA 222 3.95e-01 1mwyA 73 4.38e-01 d.58.17.1 79616 1q0qA 406 5.57e-01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1ng1 294 5.74e-01 1ng1 1jpnA 296 6.14e-01 a.24.13.1,c.37.1.10 67039,67040 2a1iA 146 7.42e-01 c.52.1.20 125999 2h6rA 219 7.52e-01 1xuuA 349 8.15e-01 b.85.1.1,c.1.10.6 116067,116068 2zdrA 349 8.82e-01 b.85.1.1,c.1.10.6 154398,154399 1i7qB 193 9.16e-01 1qdlB c.23.16.1 61902 3n4fA 392 9.55e-01 2a0nA 265 1.10e+00 c.1.2.1 125961 2wqpA 349 1.10e+00 2jbmA 299 1.13e+00 1vh7A 265 1.20e+00 c.1.2.1 100646 1thfD 253 1.23e+00 1thfD c.1.2.1 28535 1izcA 339 1.27e+00 c.1.12.5 83838 3fzqA 274 1.32e+00 3llvA 141 1.35e+00 3iivA 263 1.52e+00 3iioA 262 1.60e+00 1yadA 221 1.66e+00 3iipA 256 1.72e+00 3igsA 232 1.75e+00 2gjlA 328 1.77e+00 3hutA 358 1.79e+00 2iksA 293 1.80e+00 2qorA 204 2.11e+00 2v3aA 384 2.18e+00 3g1yA 228 2.31e+00 1i1qB 192 2.40e+00 1qdlB c.23.16.1 61544 1wrvA 308 2.41e+00 3af5A 651 2.53e+00 1ccwA 137 2.53e+00 1be1 c.23.6.1 31238 1eudB 396 2.63e+00 2scuB c.23.4.1,d.142.1.4 31150,41571 2cjwA 192 2.64e+00 1wl8A 189 2.72e+00 c.23.16.1 120997 2eiyA 308 2.81e+00 3gr7A 340 2.87e+00 2yw3A 207 2.88e+00 1vhcA 224 2.97e+00 c.1.10.1 100661 3g1pA 258 2.99e+00 2czdA 208 3.11e+00 c.1.2.3 131045 2q88A 257 3.16e+00 1o4uA 285 3.17e+00 c.1.17.1,d.41.2.1 86624,86625 3i6vA 232 3.22e+00 1x1oA 286 3.23e+00 3e61A 277 3.25e+00 1ii5A 233 3.35e+00 c.94.1.1 62412 3ciwA 348 3.36e+00 1nv8A 284 3.38e+00 c.66.1.30 86224 3iixA 348 3.46e+00 3muqA 237 3.48e+00 3k13A 300 3.52e+00 1zjjA 263 3.68e+00 3g8rA 350 3.82e+00 1ep3A 311 3.84e+00 2dorA c.1.4.1 28597 1a53 247 3.85e+00 1a53 1a53A 247 3.86e+00 c.1.2.4 28564 1geqA 248 3.88e+00 2tysA c.1.2.4 28589 1bj4A 470 3.95e+00 1bj4A c.67.1.4 34479 2dzxA 248 3.96e+00 1tif 78 3.99e+00 1tif 1tifA 78 3.99e+00 d.15.8.1 37836 3gm8A 801 4.40e+00 3i6eA 385 4.51e+00 3cs3A 277 4.54e+00 1igs 248 4.59e+00 1a53 2nyuA 196 4.59e+00 2qx2A 344 4.59e+00 1z15A 344 4.65e+00 2rbcA 343 4.65e+00 2dkjA 407 4.72e+00 3cniA 156 4.74e+00 2gjsA 176 4.77e+00 c.37.1.8 135287 3gybA 280 4.84e+00 2dpxA 174 4.96e+00 2xdqA 460 5.06e+00 2krcA 99 5.09e+00 2fp4B 395 5.20e+00 c.23.4.1,d.142.1.4 133897,133898 2avnA 260 5.21e+00 c.66.1.41 127380 3aekB 525 5.22e+00 3ia7A 402 5.28e+00 2zz5A 252 5.39e+00 2plwA 201 5.42e+00 1v82A 253 5.43e+00 c.68.1.7 108415 3bppA 230 5.57e+00 3hv1A 268 5.65e+00 3d1pA 139 5.75e+00 2dm6A 333 5.88e+00 b.35.1.2,c.2.1.1 131567,131568 1v84A 253 5.90e+00 c.68.1.7 108419 3hojA 248 5.91e+00 2deoA 230 5.94e+00 1usgA 346 6.07e+00 c.93.1.1 99864 3ic5A 118 6.11e+00 3m47A 228 6.12e+00 3ms5A 388 6.20e+00 3giyA 380 6.27e+00 2nmlA 104 6.28e+00 d.330.1.1 138371 3f4wA 211 6.35e+00 3jvvA 356 6.37e+00 1p4cA 380 6.59e+00 c.1.4.1 94100 1w5qA 337 6.64e+00 3c1oA 321 6.65e+00 1x7gA 261 6.71e+00 c.2.1.2 114929 3lhdA 253 6.72e+00 1pea 385 6.74e+00 1pea 1peaA 385 6.88e+00 c.93.1.1 35662 2ayyA 121 7.03e+00 c.23.1.6 127576 2liv 344 7.11e+00 2liv 3g1vA 228 7.23e+00 1rv3A 483 7.27e+00 c.67.1.4 105101 1km3A 247 7.29e+00 c.1.2.3 72739 3ez2A 398 7.51e+00 2og2A 359 7.53e+00 3bilA 348 7.56e+00 1gzgA 337 7.62e+00 c.1.10.3 70805 1w5nA 337 7.65e+00 3lp8A 442 7.70e+00 1qtwA 285 7.76e+00 1qumA c.1.15.1 29392 1qumA 285 7.83e+00 1qumA c.1.15.1 29393 1b74A 254 7.88e+00 1b74A c.78.2.1,c.78.2.1 35264,35265 3ll7A 410 7.88e+00 1km4A 247 7.97e+00 c.1.2.3 72740 1b4kA 337 8.00e+00 1b4kA c.1.10.3 29184 1zu4A 320 8.22e+00 3bi8A 291 8.39e+00 1hdhA 536 8.55e+00 c.76.1.2 65805 1s2oA 244 8.59e+00 c.108.1.10 118846 2iw1A 374 8.62e+00 c.87.1.8 137738 3g1aA 228 8.67e+00 2r5fA 264 8.71e+00 c.124.1.8 151590 1dvjA 246 8.73e+00 1dvjA c.1.2.3 28546 2dztA 248 8.88e+00 1qapA 296 8.97e+00 1qpoA c.1.17.1,d.41.2.1 29559,38595 1q1vA 70 9.04e+00 a.159.4.1 104479 2hqbA 296 9.15e+00 1bmtA 246 9.32e+00 1bmtA a.46.1.1,c.23.6.1 17757,31235 3dsdA 349 9.44e+00 3daqA 292 9.48e+00 1qq9A 284 9.60e+00 1xjo c.56.5.4 33841 3e70C 328 9.81e+00 1wz7A 111 1.01e+01 d.330.1.1 121480 1ka9H 200 1.01e+01 c.23.16.1 77308 1tkjA 284 1.02e+01 c.56.5.4 119296 1g67A 225 1.02e+01 c.1.3.1 60311 2nu8B 388 1.02e+01 c.23.4.1,d.142.1.4 148414,148415 1itxA 419 1.05e+01 c.1.8.5,d.26.3.1 71425,71426 1uc8A 280 1.05e+01 c.30.1.6,d.142.1.7 99165,99166 2scuB 388 1.07e+01 2scuB c.23.4.1,d.142.1.4 31141,41562 2zz3A 252 1.08e+01 1ii7A 333 1.09e+01 1ii7A d.159.1.4 62415 2qi2A 347 1.10e+01 b.38.4.1,c.55.4.2,d.79.3.2 150800,150801,150802 1k7yA 577 1.10e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1zd9A 188 1.10e+01 c.37.1.8 124938 3dlcA 219 1.11e+01 1twdA 256 1.11e+01 c.1.30.1 107397 2wjiA 165 1.12e+01 2h18A 193 1.12e+01 3dzzA 391 1.12e+01 2a9kA 187 1.13e+01 c.37.1.8 126442 3eh7A 434 1.14e+01 2i6xA 211 1.14e+01 1a0rP 245 1.15e+01 1b9yC c.47.1.6 33054 2eo0A 147 1.15e+01 1z0jA 170 1.15e+01 c.37.1.8 124319 2iojA 139 1.17e+01 c.98.2.2 147745 3a5fA 291 1.18e+01 2zz2A 252 1.18e+01 1wddS 128 1.18e+01 d.73.1.1 114532 1iukA 140 1.18e+01 c.2.1.8 83712 1mzhA 225 1.19e+01 c.1.10.1 79698 2gwfA 157 1.19e+01 c.46.1.4 135802 1j9eA 147 1.19e+01 c.23.5.1 62756 3bghA 236 1.22e+01 2tpsA 227 1.22e+01 2tpsA c.1.3.1 28591 2trcP 217 1.24e+01 1b9yC c.47.1.6 33051 3irsA 291 1.25e+01 1z6gA 218 1.27e+01 3c4uA 307 1.31e+01 1u8zA 168 1.34e+01 c.37.1.8 113212 2zz4A 252 1.37e+01 3hbmA 282 1.39e+01 3dscA 349 1.42e+01 d.159.1.4 157840 1f4pA 147 1.42e+01 5nul c.23.5.1 59651 3cnhA 200 1.42e+01 1x1zA 252 1.43e+01 c.1.2.3 121613 3kl4A 433 1.43e+01 3k4oA 266 1.46e+01 1g59A 468 1.46e+01 a.97.1.1,c.26.1.1 60257,60258 3dd7A 135 1.47e+01 1guaA 167 1.48e+01 1ctqA c.37.1.8 32013 2amlA 373 1.48e+01 1hkkA 364 1.48e+01 c.1.8.5,d.26.3.1 90634,90635 2z1dA 372 1.48e+01 1y0eA 223 1.50e+01 c.1.2.5 116297 1zxxA 319 1.50e+01 2bf5A 98 1.50e+01 d.137.1.1 128405 1a79A 171 1.50e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 3b9qA 302 1.51e+01 3n0lA 417 1.52e+01 1nsj 205 1.53e+01 1nsj 1nsjA 205 1.53e+01 c.1.2.4 28560 2p6pA 384 1.55e+01 1vlwA 217 1.56e+01 c.1.10.1 108868 1wv2A 265 1.57e+01 c.1.31.1 114910 1gggA 226 1.57e+01 1lst c.94.1.1 35817 2nv2A 294 1.58e+01 2dp9A 124 1.58e+01 b.122.1.5 131609 1vf8A 377 1.59e+01 c.1.8.5,d.26.3.1 120029,120030 1fggA 261 1.61e+01 1fggA c.68.1.7 34576 3mizA 301 1.61e+01 1b1xA 689 1.61e+01 1cb6A c.94.1.2,c.94.1.2 35865,35866 2hi1A 330 1.63e+01 1o5oA 221 1.65e+01 c.61.1.1 92509 1kwsA 261 1.66e+01 c.68.1.7 73083 2pk8A 103 1.68e+01 d.274.1.1 139707 1b0lA 691 1.69e+01 1cb6A c.94.1.2,c.94.1.2 35847,35848 2aeeA 211 1.69e+01 c.61.1.1 126620 2qhbA 86 1.72e+01 a.4.1.3 150786 2qs9A 194 1.73e+01 1cb6A 691 1.74e+01 1cb6A c.94.1.2,c.94.1.2 35840,35841 2f02A 323 1.74e+01 c.72.1.1 132649 2ggsA 273 1.74e+01 1a9xA 1058 1.75e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 3hz7A 87 1.76e+01 1b9xC 246 1.78e+01 1b9yC c.47.1.6 33053 1gsoA 431 1.80e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1b9yC 246 1.80e+01 1b9yC c.47.1.6 33052 1c3oA 1073 1.80e+01 1c3oA a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18562,31491,31681,31682,41526,41527 2d00A 109 1.82e+01 c.149.1.1 146441 3jyhA 469 1.84e+01 1zmbA 290 1.84e+01 c.23.10.7 125355 3bfkA 181 1.84e+01 2rfmA 192 1.86e+01 3icaA 213 1.86e+01 3h16A 154 1.88e+01 2z6iA 332 1.90e+01 1y81A 138 1.90e+01 c.2.1.8 122731 3kruA 343 1.91e+01 1u6mA 199 1.91e+01 d.108.1.1 113069 1s8eA 333 1.93e+01 d.159.1.4 105368 1lg2A 365 1.93e+01 c.1.8.5,d.26.3.1 77950,77951 1nvmA 345 1.95e+01 a.5.7.1,c.1.10.5 86249,86250 3b5vA 248 1.95e+01 2pt2A 334 1.98e+01 2yr1A 257 2.00e+01 1f6bA 198 2.00e+01 c.37.1.8 64986 1cs0A 1073 2.00e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 3hn0A 283 2.01e+01 3kbrA 239 2.02e+01 3drnA 161 2.03e+01 1w77A 228 2.04e+01 c.68.1.13 120679 1mjfA 281 2.04e+01 c.66.1.17 79198 3lhsA 296 2.07e+01 3ie2A 431 2.07e+01 3e21A 45 2.07e+01 1jqoA 970 2.08e+01 c.1.12.3 77160 3cu0A 281 2.10e+01 c.68.1.7 156986 1efvB 255 2.11e+01 1efvB c.26.2.3 31634 2yxlA 450 2.12e+01 1sjiA 350 2.16e+01 2nv1A 305 2.16e+01 2gmnA 274 2.17e+01 d.157.1.1 147132 1og6A 298 2.18e+01 c.1.7.1 86984 1wzcA 249 2.20e+01 c.108.1.10 121491 2an1A 292 2.22e+01 2iyaA 424 2.24e+01 1f0kA 364 2.27e+01 1f0kA c.87.1.2 35465 3e8xA 236 2.27e+01 1bu5A 147 2.28e+01 5nul c.23.5.1 31155 3kn6A 325 2.28e+01 2iyfA 430 2.28e+01 2wjjA 168 2.29e+01 1b0aA 288 2.33e+01 1a4iA c.2.1.7,c.58.1.2 30286,33934 1cs1A 386 2.33e+01 1ibjA c.67.1.3 34399 2ahoA 414 2.34e+01 b.43.3.1,b.44.1.1,c.37.1.8 126767,126768,126769 3kc2A 352 2.34e+01 2w00A 1038 2.35e+01 1dcjA 81 2.36e+01 1dcjA d.68.3.3 59115 1xjo 284 2.39e+01 1xjo 3h7eA 237 2.39e+01 1qpoA 284 2.42e+01 1qpoA c.1.17.1,d.41.2.1 29561,38597 2dwcA 433 2.42e+01 2w7qA 204 2.44e+01 3kucA 167 2.44e+01 1qdlB 195 2.47e+01 1qdlB c.23.16.1 31437 1r44A 202 2.47e+01 d.65.1.4 104787 1hh1A 143 2.47e+01 1gefA c.52.1.18 61036 3ecdA 425 2.49e+01 1ur3M 319 2.51e+01 c.1.7.1 99806 2du2A 374 2.52e+01 2on8A 56 2.52e+01 1szoA 257 2.53e+01 c.14.1.3 106164 2zosA 249 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