# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1zq9A 285 3.08e-23 1p4xA 250 4.15e-01 a.4.5.28,a.4.5.28 87784,87785 1a5v 162 4.62e-01 1cxqA c.55.3.2 33629 1i4wA 353 6.18e-01 c.66.1.24 66028 1cxqA 162 6.20e-01 1cxqA c.55.3.2 33621 1jb0F 164 6.64e-01 1jb0F f.23.16.1 62825 1vsd 152 9.29e-01 1cxqA c.55.3.2 33625 1ap4 89 1.18e+00 1ncx a.39.1.5 17253 1yf3A 259 1.22e+00 1xr4A 509 1.38e+00 1cwwA 102 1.45e+00 1cy5A a.77.1.3 18434 1i58A 189 1.47e+00 1b3qA d.122.1.3 61773 1qyrA 252 1.53e+00 c.66.1.24 104657 1ox0A 430 1.53e+00 c.95.1.1,c.95.1.1 87495,87496 1uiuA 502 1.69e+00 c.94.1.1 99434 1lw7A 365 1.92e+00 c.26.1.3,c.37.1.1 74295,74296 1zd3A 555 1.98e+00 1asu 162 2.26e+00 1cxqA c.55.3.2 33626 1vj5A 555 2.27e+00 c.108.1.2,c.69.1.11 100799,100800 2ygsA 92 2.30e+00 1cy5A a.77.1.3 18431 1cy5A 97 2.31e+00 1cy5A a.77.1.3 18430 1eejA 216 2.32e+00 1eejA c.47.1.9,d.17.3.1 33057,38071 1y1xA 191 2.35e+00 1i17A 107 2.41e+00 1i17A d.6.1.1 61519 1z7mA 344 2.48e+00 1ynuA 473 2.68e+00 1v0dA 329 2.88e+00 d.4.1.7 108204 1hqvA 191 3.02e+00 1hqvA a.39.1.8 61160 1m7vA 363 3.39e+00 d.174.1.1 78748 1m1nB 522 3.46e+00 c.92.2.3 78418 1b5tA 275 3.78e+00 1b5tA c.1.23.1 29676 1m7yA 435 3.79e+00 c.67.1.4 78761 1ukxA 137 4.03e+00 d.20.1.3 107919 1vj1A 363 4.11e+00 b.35.1.2,c.2.1.1 100794,100795 1f76A 336 4.14e+00 c.1.4.1 76160 1ggzA 148 4.23e+00 a.39.1.5 70176 1zlqA 502 4.23e+00 1dc1A 323 4.34e+00 1dc1A c.52.1.11 33321 1huw 166 4.97e+00 1huw a.26.1.1 16831 1l2iA 261 5.06e+00 a.123.1.1 73503 1b8gA 429 5.07e+00 1b8gA c.67.1.4 34499 1ahpA 797 5.15e+00 1a8i c.87.1.4 35544 1p35A 299 5.15e+00 1p35A b.28.1.1 23925 1qgrA 876 5.42e+00 1qgrA a.118.1.1 19119 1reqB 637 5.55e+00 1reqB c.1.19.1,c.23.6.1 29621,31248 1q0sA 259 5.62e+00 c.66.1.28 95509 2be4A 272 6.10e+00 1gtmA 419 6.17e+00 1hwyA c.2.1.7,c.58.1.1 30223,33871 7reqB 637 6.22e+00 1reqB c.1.19.1,c.23.6.1 29617,31244 2a0kA 161 6.37e+00 2f2tA 161 6.54e+00 1rktA 205 6.59e+00 a.4.1.9,a.121.1.1 97623,97624 1dk0A 188 6.61e+00 1b2vA d.35.1.1 38530 1b2vA 188 6.75e+00 1b2vA d.35.1.1 38532 1txnA 328 6.87e+00 1i7fA 292 7.28e+00 1i7fA d.193.1.1 61888 1jb9A 316 7.31e+00 1fnc b.43.4.2,c.25.1.1 62840,62841 1cfpA 92 7.38e+00 1b4cA a.39.1.2 17172 1z72A 225 7.57e+00 1fzrA 138 7.57e+00 1fzrA c.52.1.17 33336 1m65A 245 7.64e+00 c.6.3.1 84847 1elvA 333 7.65e+00 5ptp b.47.1.2,g.18.1.1 59454,59455 1gajA 257 7.70e+00 1gajA c.37.1.12 60416 1vqzA 341 7.71e+00 2fnaA 357 7.91e+00 1g6hA 257 7.93e+00 1gajA c.37.1.12 60318 1mvwC 147 8.01e+00 i.15.1.1 79525 1o1fC 147 8.01e+00 i.15.1.1 80997 2f62A 161 8.43e+00 1g8jA 825 8.73e+00 1g8jA b.52.2.2,c.81.1.1 26924,35332 1z21A 112 8.75e+00 1cnzA 363 8.94e+00 1cnzA c.77.1.1 35061 1kezA 300 9.18e+00 c.69.1.22 68546 1whzA 70 1.01e+01 1onqA 283 1.03e+01 b.1.1.2,d.19.1.1 93365,93366 1twfA 1733 1.03e+01 1reqD 637 1.04e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1k9dA 679 1.09e+01 c.1.8.10,d.92.2.2 77292,77293 1gdvA 85 1.10e+01 1ctj a.3.1.1 60458 1qovH 260 1.10e+01 6prcH b.41.1.1,f.23.10.1 25464,43457 1m0dA 138 1.11e+01 c.52.1.17 74354 1hw7A 255 1.14e+01 1i7fA d.193.1.1 61297 1g8kA 825 1.16e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1mioB 458 1.20e+01 1qguB c.92.2.3 35602 1a7s 221 1.22e+01 1a7s b.47.1.2 26284 2ethA 154 1.23e+01 1bmtA 246 1.24e+01 1bmtA a.46.1.1,c.23.6.1 17757,31235 3erdA 261 1.25e+01 3erdA a.123.1.1 19293 2ercA 244 1.25e+01 2ercA c.66.1.24 34224 1qwgA 251 1.25e+01 c.1.27.1 96473 1fyvA 161 1.30e+01 1fyvA c.23.2.1 31127 3minB 522 1.32e+01 1qguB c.92.2.3 35606 2minB 522 1.41e+01 1qguB c.92.2.3 35610 1itkA 731 1.45e+01 a.93.1.3,a.93.1.3 71417,71418 1bpoA 494 1.46e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1p57B 255 1.46e+01 b.47.1.2 94126 1prcC 336 1.47e+01 6prcC a.138.1.2 19674 2ch4A 320 1.47e+01 1yemA 179 1.48e+01 1irxA 523 1.49e+01 a.97.1.2,c.26.1.1 71378,71379 1kjvA 284 1.53e+01 b.1.1.2,d.19.1.1 77421,77422 1fs1B 141 1.53e+01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1jk7A 323 1.54e+01 1auiA d.159.1.3 63144 1ao5A 237 1.54e+01 5ptp b.47.1.2 26334 1soxA 466 1.59e+01 1soxA b.1.18.6,d.120.1.1,d.176.1.1 21947,41090,42563 1uwsA 489 1.60e+01 c.1.8.4 108073 1wstA 417 1.62e+01 1u32A 293 1.63e+01 d.159.1.3 107631 2cujA 108 1.63e+01 1rj1A 151 1.63e+01 a.29.6.1 97526 1fc4A 401 1.64e+01 1bs0A c.67.1.4 59760 2b9lA 394 1.65e+01 2ba2A 85 1.68e+01 1he2A 206 1.68e+01 1he2A c.2.1.2 60966 1rylA 167 1.68e+01 d.276.1.1 105124 1pczA 191 1.68e+01 1ytbA d.129.1.1,d.129.1.1 41292,41293 1h3nA 878 1.68e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1rypK 198 1.72e+01 d.153.1.4 41879 1zk8A 183 1.73e+01 1w0mA 226 1.74e+01 c.1.1.1 109027 1riqA 465 1.75e+01 a.203.1.1,d.104.1.1 97516,97517 1qamA 244 1.77e+01 2ercA c.66.1.24 34220 1w7jB 151 1.77e+01 2prd 174 1.78e+01 2prd b.40.5.1 25435 1yovA 537 1.78e+01 1qgpA 77 1.78e+01 1qbjA a.4.5.19 16158 1mfqC 129 1.79e+01 a.36.1.1 79046 1dxrC 336 1.79e+01 6prcC a.138.1.2 19670 1zwwA 256 1.86e+01 1mo2A 294 1.86e+01 c.69.1.22 79331 1kb9B 352 1.87e+01 d.185.1.1,d.185.1.1 77313,77314 6prcC 336 1.89e+01 6prcC a.138.1.2 19671 1zthA 258 1.94e+01 1qguB 519 1.99e+01 1qguB c.92.2.3 35626 1cot 129 2.02e+01 1ycc a.3.1.1 15899 1oxjA 173 2.04e+01 a.60.1.2,a.118.1.13 87517,87518 1rzhH 260 2.04e+01 b.41.1.1,f.23.10.1 98162,98163 1ne9A 335 2.04e+01 d.108.1.4,d.108.1.4 91839,91840 1l8nA 679 2.07e+01 c.1.8.10,d.92.2.2 84564,84565 1cf9A 753 2.07e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1gowA 489 2.09e+01 1qvbA c.1.8.4 28981 1k5nA 276 2.14e+01 b.1.1.2,d.19.1.1 77266,77267 2bw3A 534 2.15e+01 1uwoA 92 2.23e+01 4icb a.39.1.2 17174 1ahr 146 2.26e+01 1cll a.39.1.5 17287 2f3yA 148 2.34e+01 2aj2A 208 2.38e+01 2bvpA 276 2.42e+01 1lkvX 232 2.42e+01 a.118.14.1 73980 1y0vH 146 2.43e+01 1vqtA 213 2.43e+01 1o6dA 163 2.44e+01 c.116.1.3 92567 1orvA 728 2.48e+01 b.70.3.1,c.69.1.24 87354,87355 1br1B 150 2.48e+01 1wdcC a.39.1.5 17309 1b4cA 92 2.48e+01 1b4cA a.39.1.2 17169 1it2A 146 2.48e+01 a.1.1.2 66365 1aijH 260 2.60e+01 6prcH b.41.1.1,f.23.10.1 25466,43463 1ibcA 194 2.62e+01 1pauA c.17.1.1 30997 1ls9A 91 2.62e+01 a.3.1.1 78177 1lvaA 258 2.64e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1yzqA 170 2.65e+01 1dqaC 467 2.68e+01 1dqaA d.58.20.1,d.179.1.1 39366,42587 2fhpA 187 2.72e+01 1cpcA 162 2.72e+01 1cpcA a.1.1.3 15643 1o8bA 219 2.73e+01 c.124.1.4,d.58.40.1 81180,81181 1z57A 339 2.78e+01 1q5qA 259 2.81e+01 d.153.1.4 95904 1y82A 157 2.82e+01 1e4mM 501 2.82e+01 1e70M c.1.8.4 59226 1ab6A 125 2.85e+01 3chy c.23.1.1 31054 1ekzA 76 2.86e+01 1di2A d.50.1.1 38783 1e3oC 160 2.87e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1z8gA 372 2.89e+01 2myr 501 2.91e+01 1jzxK 205 2.94e+01 i.1.1.2 67885 1mwyA 73 2.96e+01 d.58.17.1 79616 1itwA 741 2.97e+01 c.77.1.2 76793 1lk9A 448 2.98e+01 c.67.1.1 78057 1ea9C 583 2.98e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1dp3A 55 2.99e+01 1dp3A a.55.1.2 59128 1m9nA 613 2.99e+01 c.24.1.3,c.97.2.1 78870,78871 2a5sA 284 2.99e+01 2cevA 299 3.01e+01 1d3vA c.42.1.1 32576 1e6qM 501 3.03e+01 1e70M c.1.8.4 28920 2fxaA 207 3.03e+01 1b3jA 274 3.04e+01 1agdA b.1.1.2,d.19.1.1 20855,38319 2fp4B 395 3.04e+01 2fo3A 125 3.05e+01 1rypL 212 3.06e+01 d.153.1.4 41880 1jdlA 121 3.07e+01 a.3.1.1 66557 1z77A 200 3.10e+01 1sr8A 298 3.10e+01 e.54.1.1 105959 1c4kA 730 3.12e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1k8tA 510 3.15e+01 e.41.1.1 68316 1xfxA 777 3.17e+01 2ax3A 502 3.18e+01 1fipA 98 3.24e+01 1fipA a.4.1.12 18980 1xfuA 747 3.24e+01 1vkeA 133 3.26e+01 a.152.1.2 108650 1lwjA 441 3.26e+01 b.71.1.1,c.1.8.1 74303,74304 1h0hB 214 3.27e+01 d.58.1.5 76437 1ncx 162 3.30e+01 1ncx a.39.1.5 17222 1swvA 267 3.31e+01 1t4oA 117 3.31e+01 d.50.1.1 106425 1top 162 3.31e+01 1ncx a.39.1.5 17223 3bifA 468 3.31e+01 1bif c.37.1.7,c.60.1.4 31962,34008 2b2yA 187 3.33e+01 1hl6A 165 3.36e+01 d.58.7.1 83609 1fiqC 763 3.38e+01 1fiqC d.41.1.1,d.133.1.1 38588,41418 1aii 323 3.39e+01 1avc a.65.1.1 18150 1ru3A 732 3.40e+01 e.26.1.3 97835 1ql3A 99 3.42e+01 1ycc a.3.1.1 15822 1h8dH 260 3.42e+01 5ptp 2cj4A 150 3.42e+01 1p8cA 145 3.43e+01 a.152.1.2 94354 1vlbA 907 3.43e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1hlrA 907 3.43e+01 2bifA 469 3.48e+01 1bif c.37.1.7,c.60.1.4 31963,34009 1wmaA 276 3.48e+01 1stu 68 3.49e+01 1di2A d.50.1.1 38782 1whtB 153 3.53e+01 1whtB 1rlmB 271 3.56e+01 1xb4A 202 3.60e+01 1wy1A 172 3.62e+01 1e70M 501 3.62e+01 1e70M c.1.8.4 28926 1n9dA 199 3.63e+01 a.26.1.1 85464 1xclA 235 3.64e+01 1b47A 304 3.66e+01 2cblA a.39.1.7,a.48.1.1,d.93.1.1 17381,17775,40529 1aisA 182 3.69e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1gaxA 862 3.74e+01 1gaxA b.51.1.1,c.26.1.1,a.2.7.3,a.27.1.1 26893,31595,75842,75843 1eyhA 144 3.82e+01 1eduA a.118.9.1 19214 1yfsA 465 3.92e+01 1b4aA 149 3.94e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1b3bA 415 3.95e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 1y9iA 178 3.96e+01 1g8mA 593 3.96e+01 1g8mA c.24.1.3,c.97.2.1 60371,60372 1hdoA 206 3.97e+01 1he2A c.2.1.2 60965 1wf3A 301 4.01e+01 1oe0A 230 4.02e+01 c.37.1.1 92788 1l2tA 235 4.04e+01 c.37.1.12 73514 2f05A 105 4.05e+01 1vbuA 328 4.05e+01 2gsaA 432 4.06e+01 2gsaA c.67.1.4 34446 1qlzA 210 4.06e+01 1b10A d.6.1.1 37309 1qh8B 519 4.06e+01 1qguB c.92.2.3 35634 3lck 271 4.07e+01 1fmk d.144.1.7 41686 1que 303 4.09e+01 1fnc b.43.4.2,c.25.1.1 25647,31537 1ac5 483 4.12e+01 1ac5 c.69.1.5 34653 1yaxA 153 4.12e+01 1oixA 191 4.13e+01 1wijA 140 4.13e+01 1dcs 311 4.14e+01 1dcs b.82.2.1 28124 1ebdC 41 4.15e+01 1ebdC a.9.1.1 16355 1z5lA 285 4.16e+01 1qpcA 279 4.18e+01 1fgkA d.144.1.7 41685 1a3yA 149 4.20e+01 1obpA b.60.1.1 27110 1ak8 76 4.22e+01 1cll a.39.1.5 17281 1qm3A 112 4.22e+01 1b10A d.6.1.1 37313 1cm7A 363 4.22e+01 1cnzA c.77.1.1 35063 1p80A 753 4.29e+01 c.23.16.3,e.5.1.1 94337,94338 1aj4 161 4.31e+01 1ncx a.39.1.5 17244 2u1a 88 4.33e+01 2u1a d.58.7.1 39164 1pmaA 233 4.34e+01 1pmaA d.153.1.4 41918 1bcsB 160 4.35e+01 1whtB 1eh2 106 4.35e+01 1eh2 a.39.1.6 17339 2bsaA 303 4.36e+01 1ggwA 140 4.44e+01 1ggwA a.39.1.5 60490 2bjcA 62 4.46e+01 1c5lH 259 4.49e+01 5ptp 1vkiA 181 4.50e+01 d.116.1.1 108664 1rmvA 157 4.53e+01 1rmvA a.24.5.1 16589 1uf2C 421 4.57e+01 a.115.1.3,b.19.1.1 99291,99292 1ogiA 303 4.59e+01 b.43.4.2,c.25.1.1 92914,92915 1hlvA 131 4.60e+01 a.4.1.7,a.4.1.7 65854,65855 3fisA 98 4.62e+01 1fipA a.4.1.12 18994 1gc0A 398 4.65e+01 c.67.1.3 70168 1ahtH 259 4.65e+01 5ptp 1bqyA 234 4.66e+01 5ptp b.47.1.2 26332 2fflA 756 4.66e+01 1nwmX 142 4.67e+01 a.7.8.1 86301 1uj8A 77 4.69e+01 1mb1 130 4.75e+01 1bm8 d.34.1.1 38529 1j0hA 588 4.80e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1wudA 89 4.84e+01 1a8s 273 4.87e+01 1brt c.69.1.12 34710 1jmoA 480 4.89e+01 e.1.1.1 77138 1dpe 507 4.90e+01 1dpe c.94.1.1 35799 1bmqA 167 4.93e+01 1pauA c.17.1.1 30998 1rloA 271 4.96e+01 1lqc 56 5.05e+01 1pru a.35.1.5 17109 1qh0A 295 5.05e+01 b.43.4.2,c.25.1.1 68891,68892 1az3A 244 5.06e+01 1rvaA c.52.1.2 33276 1sbxA 106 5.08e+01 a.6.1.4 105414 1x9mA 698 5.10e+01 1j90A 230 5.14e+01 c.37.1.1 66448 1ab5A 125 5.17e+01 3chy c.23.1.1 31056 1cr6B 554 5.18e+01 1cr6B c.69.1.11,c.108.1.2 34688,43338 1jalA 363 5.23e+01 c.37.1.8,d.15.10.2 84138,84139 1mk0A 97 5.24e+01 d.226.1.1 79216 2reb 352 5.26e+01 2reb c.37.1.11,d.48.1.1 32282,38767 1eduA 149 5.26e+01 1eduA a.118.9.1 19215 1ks2A 219 5.27e+01 c.124.1.4,d.58.40.1 72908,72909 1kncA 177 5.28e+01 a.152.1.1 68703 1b26A 416 5.31e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1e6mA 128 5.32e+01 3chy c.23.1.1 31039 3chy 128 5.35e+01 3chy c.23.1.1 31038 2aw5A 541 5.35e+01 1fchA 368 5.35e+01 1fchA a.118.8.1 19212 1vjqA 79 5.39e+01 k.43.1.1 100830 1ton 235 5.42e+01 5ptp b.47.1.2 26307 1pyoB 105 5.46e+01 1dik 874 5.47e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1yadA 221 5.48e+01 1eucB 396 5.49e+01 2scuB c.23.4.1,d.142.1.4 31149,41570 1bif 469 5.57e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1rqlA 267 5.58e+01 c.108.1.3 97750 2c1lA 358 5.58e+01 1q7zA 566 5.61e+01 c.1.21.2,c.1.26.1 96090,96091 1b2rA 304 5.62e+01 1fnc b.43.4.2,c.25.1.1 25648,31538 1cx4A 305 5.63e+01 b.82.3.2,b.82.3.2 59099,59100 1nekA 588 5.65e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1xocA 520 5.67e+01 1ezoA 370 5.69e+01 4mbp 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