# 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 1sur 215 2.79e-23 1sur c.26.2.2 31620 1gpmA 525 2.00e-05 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1xngA 268 8.94e-04 1q15A 503 2.97e-03 c.26.2.1,d.153.1.1 95538,95539 1wy5A 317 4.99e-03 1ni5A 433 1.41e-02 c.26.2.5,d.229.1.1 80533,80534 1korA 400 4.22e-02 c.26.2.1,d.210.1.1 72824,72825 1vl2A 421 9.21e-02 c.26.2.1,d.210.1.1 108708,108709 1jgtA 513 1.10e-01 c.26.2.1,d.153.1.1 66684,66685 1k92A 455 1.40e-01 c.26.2.1,d.210.1.1 68325,68326 2d13A 227 1.50e-01 1m1zA 513 3.20e-01 c.26.2.1,d.153.1.1 78457,78458 1kw4A 89 7.65e-01 a.60.1.2 73077 1v7lA 163 1.54e+00 1ru8A 232 1.66e+00 c.26.2.1 97849 2er7E 330 2.29e+00 2er7E b.50.1.2 26779 1oewA 329 2.70e+00 b.50.1.2 86924 1pk1B 89 2.75e+00 1gvuA 329 2.77e+00 b.50.1.2 70619 1g8pA 350 2.78e+00 1g8pA c.37.1.20 60376 5er2E 330 3.15e+00 2er7E b.50.1.2 26783 1epnE 330 3.28e+00 2er7E b.50.1.2 26780 1wvfA 520 3.43e+00 1xrtA 467 3.95e+00 2dri 271 4.29e+00 2dri c.93.1.1 35637 1vmaA 306 5.07e+00 a.24.13.1,c.37.1.10 108887,108888 1gt6A 269 5.19e+00 c.69.1.17 76342 1wxiA 275 5.20e+00 1tib 269 5.33e+00 3tgl c.69.1.17 34738 1pl8A 356 5.34e+00 b.35.1.2,c.2.1.1 94878,94879 1pvmA 184 6.17e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1kqpA 271 6.28e+00 c.26.2.1 72883 1ih8A 271 6.31e+00 2nsyA c.26.2.1 62377 1fp4A 492 6.42e+00 c.92.2.3 76187 1nsyA 271 6.47e+00 2nsyA c.26.2.1 31614 1w41A 101 6.53e+00 2ah5A 210 7.14e+00 1cf2O 337 7.28e+00 1b7gO c.2.1.3,d.81.1.1 29994,39909 1ipaA 274 7.70e+00 c.116.1.1,d.79.3.3 71254,71255 1sv0C 82 7.76e+00 a.60.1.1 106037 2nsyA 271 8.21e+00 2nsyA c.26.2.1 31612 2minA 491 8.25e+00 1qguA c.92.2.3 35609 1uouA 474 8.60e+00 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1nar 290 9.18e+00 1nar c.1.8.5 28988 1ox6A 555 9.40e+00 c.1.2.1,c.23.16.1 87505,87506 3minC 491 9.62e+00 1qguA c.92.2.3 35607 1k0wA 231 1.03e+01 c.74.1.1 77220 1jvnA 555 1.03e+01 c.1.2.1,c.23.16.1 67355,67356 1jdiA 231 1.04e+01 c.74.1.1 66551 1zjjA 263 1.11e+01 1crzA 403 1.14e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 1u7pA 164 1.16e+01 1h7mA 102 1.20e+01 d.79.3.1 83485 1lk5A 229 1.24e+01 c.124.1.4,d.58.40.1 73960,73961 1m1nA 491 1.25e+01 c.92.2.3 78417 1vbiA 344 1.26e+01 1wkvA 389 1.31e+01 1wqaA 455 1.38e+01 1jk7A 323 1.46e+01 1auiA d.159.1.3 63144 1fjmA 330 1.47e+01 1auiA d.159.1.3 42082 1mioA 534 1.48e+01 1qguA c.92.2.3 35601 2fm8A 135 1.53e+01 1xqiA 195 1.54e+01 2cy7A 396 1.60e+01 1br2A 791 1.60e+01 1lvk b.34.3.1,c.37.1.9 24558,32155 1rcuA 195 1.62e+01 c.129.1.1 97295 1u32A 293 1.63e+01 d.159.1.3 107631 1iloA 77 1.63e+01 c.47.1.1 66205 1ufoA 238 1.64e+01 c.69.1.27 99344 1w8iA 156 1.71e+01 1ehyA 294 1.75e+01 1ehyA c.69.1.11 34693 1vgvA 384 1.76e+01 c.87.1.3 100608 2b4zA 104 1.80e+01 1ct9A 553 1.81e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1kicA 339 1.81e+01 c.70.1.1 72510 1h1yA 228 1.82e+01 c.1.2.2 76506 1wzlA 585 1.82e+01 1ic8A 194 1.84e+01 a.4.1.1,a.35.1.1 76740,76741 1fsu 492 1.88e+01 1auk c.76.1.2 35032 2adbA 148 1.91e+01 1uohA 226 2.12e+01 d.211.1.1 99690 1do6A 124 2.13e+01 1do6A b.1.13.1 22361 1nmoA 247 2.15e+01 c.135.1.1 91980 1f6dA 376 2.16e+01 1f6dA c.87.1.3 35467 1j0hA 588 2.17e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1nnjA 271 2.26e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1j8yF 297 2.26e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 2arkA 188 2.28e+01 1jdlA 121 2.28e+01 a.3.1.1 66557 2cx6A 90 2.32e+01 1wstA 417 2.32e+01 1y8aA 332 2.33e+01 1zdyA 307 2.39e+01 2fhzA 109 2.40e+01 1ebdC 41 2.46e+01 1ebdC a.9.1.1 16355 1hp0A 339 2.46e+01 c.70.1.1 65900 1tyyA 339 2.47e+01 1vecA 206 2.50e+01 c.37.1.19 100575 1o1zA 234 2.53e+01 c.1.18.3 86555 2aqwA 332 2.54e+01 2cvhA 220 2.55e+01 1tdzA 272 2.59e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1fts 295 2.65e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1sviA 195 2.66e+01 c.37.1.8 106048 1c9kA 180 2.66e+01 1c9kB c.37.1.11 32363 1deuA 277 2.66e+01 1theB d.3.1.1 37085 1xrjA 261 2.67e+01 1c5kA 439 2.71e+01 1crzA b.68.4.1,c.51.2.1 27630,33212 1r0mA 375 2.79e+01 c.1.11.2,d.54.1.1 104747,104748 1eaxA 241 2.81e+01 b.47.1.2 64889 2d0oA 610 2.96e+01 1v1aA 309 3.02e+01 c.72.1.1 100249 1n0wA 243 3.05e+01 c.37.1.11 79772 1ydxA 406 3.08e+01 1vp8A 201 3.14e+01 2fdsA 352 3.17e+01 1i2sA 282 3.19e+01 e.3.1.1 71104 1dz3A 130 3.25e+01 1dz3A c.23.1.1 31105 2ddrA 306 3.41e+01 1xm3A 264 3.41e+01 1r13A 148 3.46e+01 d.169.1.1,h.1.1.1 96782,96783 1ma3A 253 3.50e+01 c.31.1.5 78883 1enxA 190 3.50e+01 1axkA b.29.1.11 24325 1ubeA 349 3.53e+01 c.37.1.11,d.48.1.1 88412,88413 1j8mF 297 3.53e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1mnd 762 3.77e+01 1lvk b.34.3.1,c.37.1.9 24591,32188 1he2A 206 3.85e+01 1he2A c.2.1.2 60966 1f76A 336 3.88e+01 c.1.4.1 76160 1dqiA 124 3.88e+01 1do6A b.1.13.1 22357 2c4xA 260 3.89e+01 2c5uA 375 3.93e+01 2ucz 165 3.95e+01 1u9aA d.20.1.1 38330 1uj2A 252 3.98e+01 c.37.1.6 99452 1o0vA 327 4.08e+01 b.1.1.2,b.1.1.2,b.1.1.2 80745,80746,80747 1o58A 303 4.09e+01 c.79.1.1 92491 1jx6A 342 4.10e+01 c.93.1.1 67406 2ffcA 353 4.11e+01 1rzrA 332 4.19e+01 1y4jA 284 4.25e+01 2gn4A 344 4.33e+01 2f6kA 307 4.34e+01 1h30A 422 4.45e+01 b.29.1.4,b.29.1.4 76604,76605 1tk9A 188 4.46e+01 c.80.1.3 107082 1lkyA 77 4.48e+01 a.60.1.1 73985 1nj3A 31 4.54e+01 g.41.12.1 85761 1vplA 256 4.66e+01 1vpjA 192 4.68e+01 1ppjA 446 4.73e+01 d.185.1.1,d.185.1.1 104252,104253 1brwA 433 4.82e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1hdoA 206 4.82e+01 1he2A c.2.1.2 60965 1b3oA 514 4.83e+01 1ak5 c.1.5.1 28640 1c2n 137 4.84e+01 1ycc a.3.1.1 15889 1c2rA 116 4.85e+01 1ycc a.3.1.1 15887 2c26A 260 4.85e+01 1nbwB 117 4.96e+01 c.51.3.2 80396 1vydA 116 5.03e+01 a.3.1.1 108900 1ybxA 143 5.07e+01 1gqyA 475 5.10e+01 c.5.1.1,c.59.1.1,c.72.2.1 83305,83306,83307 1zghA 260 5.10e+01 2gcuA 245 5.11e+01 1ek6A 348 5.16e+01 1xel c.2.1.2 29800 1xg9A 260 5.23e+01 1a2oA 349 5.26e+01 1chd c.23.1.1,c.40.1.1 31120,32479 2fz4A 237 5.30e+01 1httA 423 5.36e+01 1adjA c.51.1.1,d.104.1.1 33178,40727 1db3A 372 5.39e+01 1db3A c.2.1.2 29813 1mh1 186 5.44e+01 1eesA c.37.1.8 32002 1v9mA 323 5.44e+01 f.40.1.1 100543 1q3eA 207 5.49e+01 b.82.3.2 95669 1ltdA 506 5.50e+01 1gox c.1.4.1,d.120.1.1 28618,41086 1d02A 202 5.50e+01 1d02A c.52.1.8 33313 1wddS 128 5.56e+01 1u0sY 118 5.56e+01 c.23.1.1 107566 1g61A 228 5.58e+01 1g61A d.126.1.1 41126 1bvzA 585 5.73e+01 1bvzA b.1.18.2,b.71.1.1,c.1.8.1 21856,27783,28770 2masA 314 5.84e+01 2masA c.70.1.1 34810 1r5zA 323 5.92e+01 f.40.1.1 97135 2b10B 108 5.94e+01 1ly1A 181 5.96e+01 c.37.1.1 74334 1ipiA 123 5.97e+01 c.52.1.18 66255 2es9A 115 6.24e+01 1r8gA 372 6.24e+01 d.128.1.3 104845 2a8mA 420 6.24e+01 1uc7A 125 6.43e+01 c.47.1.1 99163 1fcdA 401 6.53e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1lplA 95 6.55e+01 b.34.10.1 74173 1eucB 396 6.57e+01 2scuB c.23.4.1,d.142.1.4 31149,41570 1ww9A 392 6.58e+01 1xkyA 301 6.66e+01 1qv9A 283 6.69e+01 c.127.1.1 96356 1gmyA 261 6.72e+01 d.3.1.1 76236 1z70X 311 6.75e+01 1p3dA 475 6.78e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2akaA 776 6.79e+01 1u9jA 358 6.81e+01 1hozA 339 6.82e+01 c.70.1.1 65898 1al8 359 6.82e+01 1gox c.1.4.1 28608 1ji2A 585 6.84e+01 b.1.18.2,b.71.1.1,c.1.8.1 71672,71673,71674 1oghA 204 6.86e+01 b.85.4.1 86994 1j8dA 180 6.92e+01 c.108.1.5 66433 1xm7A 195 6.96e+01 2aq4A 434 7.01e+01 1vb5A 276 7.03e+01 1g84A 105 7.04e+01 1g84A b.1.1.2 60345 1g71A 347 7.05e+01 1g71A d.264.1.1 43268 1b2rA 304 7.06e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1l5oA 356 7.14e+01 c.39.1.1 77711 1vbkA 307 7.15e+01 1ltqA 301 7.19e+01 c.108.1.9,c.37.1.1 78208,78209 1ku0A 388 7.23e+01 c.69.1.18 72994 1dg6A 191 7.33e+01 1d4vB b.22.1.1 23883 1tovA 98 7.33e+01 b.34.10.1 107179 1zjcA 418 7.37e+01 1vljA 407 7.46e+01 e.22.1.2 108832 1ogiA 303 7.48e+01 b.43.4.2,c.25.1.1 92914,92915 1k1eA 180 7.48e+01 c.108.1.5 67995 1go2A 304 7.58e+01 b.43.4.2,c.25.1.1 76243,76244 1a4jB 219 7.69e+01 1igtB b.1.1.1,b.1.1.2 20233,21245 1rwrA 301 7.71e+01 b.80.1.11 97990 1q1aA 289 7.74e+01 c.31.1.5 95561 1y89A 238 7.77e+01 1que 303 7.93e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1eudB 396 7.95e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 2a3nA 355 7.97e+01 1h67A 108 7.98e+01 a.40.1.1 65643 1okgA 373 8.02e+01 c.46.1.2,c.46.1.2,d.26.1.3 93250,93251,93252 2bllA 345 8.13e+01 1ycc 108 8.13e+01 1ycc a.3.1.1 15834 1gcpA 70 8.13e+01 1gcpA b.34.2.1 60430 1s6cA 183 8.16e+01 a.39.1.5 98594 2pgd 482 8.26e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 2g42A 79 8.26e+01 1svb 395 8.31e+01 1svb b.1.18.4,f.10.1.1 21814,43827 2fztA 79 8.33e+01 1um5H 217 8.35e+01 1z2nX 324 8.41e+01 1xwyA 264 8.50e+01 1h3gA 601 8.53e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1hrkA 359 8.58e+01 1hrkA c.92.1.1 61228 1l0lA 446 8.64e+01 d.185.1.1,d.185.1.1 84482,84483 1gm6A 175 8.65e+01 b.60.1.1 70272 1td2A 287 8.69e+01 c.72.1.5 106765 1va0A 239 8.76e+01 1ex2A 189 8.76e+01 1ex2A c.51.4.2 33225 1qh0A 295 8.79e+01 b.43.4.2,c.25.1.1 68891,68892 1pyfA 312 8.82e+01 c.1.7.1 95334 1jh8A 356 8.84e+01 c.39.1.1 63052 1k0dA 260 8.89e+01 a.45.1.1,c.47.1.5 67930,67931 2acvA 463 8.89e+01 1v8eA 224 8.93e+01 1rzfH 235 8.98e+01 b.1.1.1,b.1.1.2 98150,98151