# 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.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 1dnlA 199 1.06e-30 1ci0A b.45.1.1 25753 1g79A 218 1.97e-30 1ci0A b.45.1.1 25752 1nrgA 261 1.02e-26 b.45.1.1 80694 1t9mA 214 3.49e-22 1ci0A 228 2.48e-21 1ci0A b.45.1.1 25750 1ty9A 222 1.16e-20 1rfeA 162 1.34e-12 2fhqA 141 5.40e-12 2fg9A 178 2.30e-08 1vl7A 157 5.63e-08 b.45.1.1 108732 2asfA 137 9.79e-07 1w9aA 147 7.27e-06 2aq6A 147 7.47e-06 1xxoA 147 9.33e-06 2furA 209 4.81e-04 1w3oA 216 2.73e-03 2arzA 247 4.17e-03 1ejeA 192 4.72e-03 1ejeA b.45.1.2 25757 1xhnA 184 5.68e-03 1m1hA 248 2.15e-02 b.114.1.1,d.58.42.1 78415,78416 1flmA 122 3.73e-02 1axj b.45.1.1 25747 1ye8A 178 9.56e-02 1axj 122 1.37e-01 1axj b.45.1.1 25749 1j09A 468 2.41e-01 a.97.1.1,c.26.1.1 77025,77026 1gln 468 2.74e-01 1gln a.97.1.1,c.26.1.1 18752,31588 1l1zA 274 2.87e-01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1g59A 468 3.07e-01 a.97.1.1,c.26.1.1 60257,60258 2fcjA 119 4.57e-01 1r2zA 274 5.32e-01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1ha1 184 5.84e-01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1jdqA 98 6.67e-01 d.68.3.3 66559 1l3kA 196 6.72e-01 d.58.7.1,d.58.7.1 73539,73540 1mkmA 249 1.16e+00 a.4.5.33,d.110.2.2 79242,79243 2a6sA 84 1.29e+00 1ip9A 85 1.47e+00 1ip9A d.15.2.2 62638 1wj9A 211 1.60e+00 2f6kA 307 1.75e+00 2gukA 120 1.82e+00 1u09A 476 2.10e+00 e.8.1.4 107545 2f9dA 125 2.20e+00 1fqgA 263 2.44e+00 1btl e.3.1.1 42699 1b94A 244 2.53e+00 1rvaA c.52.1.2 33250 1m40A 263 2.67e+00 e.3.1.1 74437 1yruB 74 2.82e+00 1i24A 404 3.00e+00 c.2.1.2 83663 1b97A 244 3.19e+00 1rvaA c.52.1.2 33252 1eu3A 210 3.33e+00 1an8 b.40.2.2,d.15.6.1 25206,37795 1rvaA 244 3.43e+00 1rvaA c.52.1.2 33240 2ay1A 394 3.76e+00 1ajsA c.67.1.1 34357 1qrrA 394 3.87e+00 1qrrA c.2.1.2 29824 1eonA 245 4.05e+00 1rvaA c.52.1.2 33238 1ermA 263 4.09e+00 1btl e.3.1.1 42690 1lfpA 249 4.24e+00 e.39.1.1 73885 1b96A 244 4.86e+00 1rvaA c.52.1.2 33268 2cfxA 144 5.04e+00 1btl 263 5.16e+00 1btl e.3.1.1 42691 1p27B 106 5.42e+00 d.58.7.1 93908 1npsA 88 5.45e+00 1prs b.11.1.1 23622 1gxuA 91 5.68e+00 d.58.10.1 76378 1prr 173 6.86e+00 1prs b.11.1.1,b.11.1.1 23623,23624 1m70A 190 7.38e+00 a.3.1.4,a.3.1.4 91200,91201 1bssA 244 7.57e+00 1rvaA c.52.1.2 33256 1nnjA 271 7.69e+00 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1prs 173 7.83e+00 1prs b.11.1.1,b.11.1.1 23625,23626 2bgiA 272 7.86e+00 1pjjA 271 8.06e+00 a.156.1.2,b.113.1.1,g.39.1.8 104164,104165,104166 1lrrA 131 8.23e+00 d.228.1.1 78165 1z41A 338 8.26e+00 1nar 290 8.53e+00 1nar c.1.8.5 28988 2rveA 244 8.88e+00 1rvaA c.52.1.2 33283 3hsf 92 8.89e+00 2hts a.4.5.22 16182 1zzkA 82 9.21e+00 1p5tA 127 9.34e+00 b.55.1.2 94148 1a7j 290 9.43e+00 1a7j c.37.1.6 31952 1etpA 190 9.95e+00 1etpA a.3.1.4,a.3.1.4 15962,15963 2f3yA 148 1.00e+01 1ois 223 1.08e+01 1a36A e.15.1.1 43267 1ta8A 332 1.08e+01 1nmeA 146 1.09e+01 c.17.1.1 85874 2etvA 346 1.13e+01 1mkp 144 1.22e+01 1vhrA c.45.1.1 32654 1sx5A 244 1.24e+01 c.52.1.2 99023 2hts 88 1.25e+01 2hts a.4.5.22 16174 1tdzA 272 1.29e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1j5kA 89 1.31e+01 d.51.1.1 71565 1z1zA 131 1.33e+01 1ukgA 252 1.33e+01 b.29.1.1 99489 2u2fA 85 1.34e+01 2u2fA d.58.7.1 39167 1umdB 324 1.38e+01 c.36.1.7,c.48.1.2 99600,99601 1ejjA 511 1.43e+01 1ejjA c.105.1.1,c.76.1.3 59422,59423 1z7lA 276 1.45e+01 1vkkA 154 1.49e+01 d.109.1.2 108669 1n3oA 252 1.50e+01 b.29.1.1 79967 1qycA 308 1.56e+01 c.2.1.2 96581 1wvnA 82 1.57e+01 1o98A 511 1.59e+01 c.105.1.1,c.76.1.3 86684,86685 2cwpA 112 1.60e+01 2gfsA 372 1.61e+01 1zeqX 84 1.63e+01 1f6kA 293 1.65e+01 1nal3 c.1.10.1 29081 1m45A 148 1.74e+01 a.39.1.5 78598 1cll 148 1.75e+01 1cll a.39.1.5 17263 1tu7A 208 1.76e+01 1ahr 146 1.77e+01 1cll a.39.1.5 17287 1pauA 147 1.81e+01 1pauA c.17.1.1 30994 2thiA 379 1.83e+01 2thiA c.94.1.1 35794 2ag5A 246 1.85e+01 1eqjA 511 1.86e+01 1ejjA c.105.1.1,c.76.1.3 59495,59496 1pnbB 75 1.91e+01 1pnbB 1k8vA 40 1.92e+01 j.6.1.1 72182 1jv2B 692 1.97e+01 b.1.15.1,c.62.1.1,d.200.1.1,g.3.11.6,g.3.11.6 67338,67339,67340,67341,67342 1g4yR 148 2.03e+01 1cll a.39.1.5 60252 1wi6A 88 2.20e+01 1uhvA 500 2.21e+01 b.71.1.2,c.1.8.3 99402,99403 2f4mA 295 2.28e+01 1vliA 385 2.32e+01 b.85.1.1,c.1.10.6 108830,108831 1xe1A 116 2.34e+01 b.43.3.1 109571 1cp3A 277 2.35e+01 1pauA c.17.1.1 30992 1f93A 104 2.36e+01 1dcpA d.74.1.1 39688 1dbwA 126 2.48e+01 1dbwA c.23.1.1 31095 1qltA 560 2.51e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 2f31A 233 2.53e+01 1tiqA 180 2.54e+01 d.108.1.1 107010 1zr9A 124 2.54e+01 1aquA 297 2.58e+01 1aquA c.37.1.5 31942 1e6uA 321 2.59e+01 1bsvA c.2.1.2 29805 1o4tA 133 2.61e+01 b.82.1.9 86622 2ebn 289 2.67e+01 2ebn c.1.8.5 28990 1tcoA 375 2.67e+01 1auiA d.159.1.3 42084 2f6rA 281 2.72e+01 1az3A 244 2.73e+01 1rvaA c.52.1.2 33276 1a1aA 107 2.75e+01 1fmk d.93.1.1 40449 1b7fA 168 2.87e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 2itg 163 2.87e+01 1b9dA c.55.3.2 33669 1wlzA 105 2.91e+01 1agrE 205 2.93e+01 1agrE a.91.1.1 18538 3sxlA 184 2.94e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 3cln 148 2.97e+01 1cll a.39.1.5 17286 1b0nB 57 2.98e+01 1b0nB a.34.1.1 17002 1v0wA 506 2.98e+01 d.136.1.2,d.136.1.2 108220,108221 1w1kA 560 3.04e+01 d.58.32.1,d.145.1.1 109059,109060 1tdhA 364 3.15e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1tuaA 191 3.18e+01 d.51.1.1,d.51.1.1 107321,107322 1txdA 385 3.20e+01 a.87.1.1,b.55.1.1 107422,107423 3thiA 371 3.22e+01 2thiA c.94.1.1 35792 1g6q2 328 3.23e+01 1g6q2 2bwrA 401 3.28e+01 2bw3A 534 3.35e+01 1ggzA 148 3.44e+01 a.39.1.5 70176 1f74A 293 3.51e+01 1nal3 c.1.10.1 29079 1pvmA 184 3.52e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1f0iA 504 3.55e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1d2dA 59 3.57e+01 1r1bA a.16.1.3 16397 1r1bA 59 3.69e+01 1r1bA a.16.1.3 16396 1m46A 148 3.74e+01 a.39.1.5 78599 2cdcA 366 3.79e+01 1scjB 71 3.88e+01 1scjB d.58.3.2 39069 1vc1A 110 3.90e+01 c.13.2.1 108493 1z4rA 168 3.95e+01 1xhfA 123 3.98e+01 1jajA 174 4.02e+01 d.218.1.2 66471 1f61A 429 4.08e+01 1dquA c.1.12.7 29319 1g0uE 234 4.08e+01 d.153.1.4 41950 2ahyA 110 4.14e+01 1oz9A 150 4.15e+01 d.92.1.15 93808 1nx8A 273 4.17e+01 b.82.2.8 86374 1shdA 107 4.19e+01 1fmk d.93.1.1 40440 1y0vH 146 4.29e+01 1gg6C 97 4.29e+01 5ptp 2a4vA 159 4.29e+01 1feuA 206 4.35e+01 1feuA b.53.1.1 59801 1kl9A 182 4.37e+01 b.40.4.5 72681 1dt4A 73 4.45e+01 1dt4A d.51.1.1 38799 2g09A 297 4.49e+01 1f8mA 429 4.49e+01 1dquA c.1.12.7 29315 1b04A 318 4.52e+01 1b04A d.142.2.2 41579 1e7rA 321 4.57e+01 1bsvA c.2.1.2 29808 1gfsA 321 4.68e+01 c.2.1.2 29811 2g84A 197 4.76e+01 2fytA 340 4.77e+01 1d8yA 605 4.82e+01 1xwl c.55.3.5,e.8.1.1 33684,42977 1h6fA 193 4.85e+01 b.2.5.4 70901 1gosA 520 4.86e+01 c.3.1.2,d.16.1.5 65425,65426 1exrA 148 4.91e+01 1cll a.39.1.5 17299 1sbyA 254 4.92e+01 1cl4A 60 5.08e+01 1cl4A g.40.1.1 45171 1d5wC 126 5.09e+01 1dbwA c.23.1.1 31101 1k1xA 659 5.10e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1gnwA 211 5.21e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1e8gA 560 5.33e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 2biiA 424 5.36e+01 2bitX 165 5.38e+01 1fmk 452 5.45e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1gl2D 65 5.50e+01 h.1.15.1 65281 2bduA 297 5.50e+01 1aotF 106 5.51e+01 1lckA d.93.1.1 40458 1vaoA 560 5.55e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 1di6A 195 5.55e+01 1di6A c.57.1.1 33863 1vig 71 5.58e+01 1vih d.51.1.1 38806 1ub9A 100 5.61e+01 a.4.5.28 99159 1xfxO 149 5.62e+01 1yrbA 262 5.63e+01 1xkzA 255 5.66e+01 2fk4A 75 5.67e+01 1bsvA 321 5.70e+01 1bsvA c.2.1.2 29809 1zfjA 491 5.72e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1o4rA 108 5.76e+01 d.93.1.1 92469 1g0oA 283 5.78e+01 1ybvA c.2.1.2 60181 1p1mA 406 5.82e+01 b.92.1.4,c.1.9.9 87696,87697 1vhtA 218 5.83e+01 c.37.1.1 100700 1dhn 121 5.93e+01 1dhn d.96.1.3 40663 1ntfA 282 5.94e+01 d.151.1.2 92104 2etjA 250 5.96e+01 1zymA 258 6.01e+01 1zymA a.60.10.1,c.8.1.2 18110,30705 1osa 148 6.19e+01 1cll a.39.1.5 17300 1yliA 153 6.24e+01 1ualA 274 6.27e+01 c.116.1.4 88383 1qvcA 145 6.28e+01 3ullA b.40.4.3 25284 2c4nA 250 6.29e+01 1mrzA 293 6.29e+01 b.43.5.1,c.26.1.3 91452,91453 1bwsA 321 6.39e+01 1bsvA c.2.1.2 29812 1pyaB 228 6.39e+01 1pyaB 1wexA 104 6.43e+01 1r0vA 305 6.45e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1rypD 241 6.54e+01 1rypD d.153.1.4 41935 1spbP 78 6.58e+01 1scjB d.58.3.2 39068 1dckA 126 6.60e+01 1dbwA c.23.1.1 31097 1ln1A 214 6.70e+01 d.129.3.2 74038 1ibcA 194 6.80e+01 1pauA c.17.1.1 30997 1myn 44 6.84e+01 1gpt g.3.7.4 44172 1ewjA 126 6.86e+01 1ecsA d.32.1.2 59526 1qcxA 359 6.88e+01 1qcxA b.80.1.2 28028 1ybvA 283 6.93e+01 1ybvA c.2.1.2 29948 1mtnC 97 6.95e+01 5ptp 3htsB 102 7.01e+01 2hts a.4.5.22 16175 1a4iB 301 7.05e+01 1a4iA c.2.1.7,c.58.1.2 30279,33927 1a4uA 254 7.06e+01 1b16A c.2.1.2 29878 1y5hA 133 7.13e+01 1xa1A 255 7.13e+01 e.3.1.1 109529 1gph1 465 7.16e+01 1ecfB 1kjnA 157 7.26e+01 c.115.1.1 72614 2bv2A 83 7.26e+01 1dgsA 667 7.32e+01 1dgsA a.60.2.2,b.40.4.6,d.142.2.2 17963,25365,41581 1rz3A 201 7.36e+01 c.37.1.6 98132 1o6jA 150 7.40e+01 c.47.1.10 81089 2b0jA 358 7.40e+01 1r2rA 248 7.47e+01 c.1.1.1 96875 1qp8A 303 7.52e+01 1qp8A c.2.1.4,c.23.12.1 30092,31352 1uspA 139 7.52e+01 d.227.1.1 99879 1gmlA 178 7.55e+01 c.8.5.2 70273 1dtjA 76 7.58e+01 1dt4A d.51.1.1 38800 2fbqA 235 7.58e+01 1oaoC 729 7.70e+01 e.26.1.3 86746 1wzuA 300 7.71e+01 1kk8B 139 7.73e+01 a.39.1.5 77430 2g64A 140 7.81e+01 1l2lA 457 7.83e+01 c.72.1.3 77656 1eu1A 780 7.84e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1tz9A 367 8.10e+01 c.1.15.6 107466 1f3lA 321 8.26e+01 1g6q2 c.66.1.6 59630 1nz6A 101 8.28e+01 a.2.3.1 86441 1o8xA 146 8.29e+01 c.47.1.10 86681 1r9jA 673 8.37e+01 1av6A 289 8.39e+01 3mag c.66.1.25 34218 1ja9A 274 8.41e+01 c.2.1.2 62817 1a4fA 141 8.45e+01 1abwA a.1.1.2 15394 1ht9A 76 8.47e+01 4icb a.39.1.1 61252 1jkgA 140 8.48e+01 d.17.4.2 66795 1ryp2 233 8.54e+01 1ryp2 1s6dA 103 8.55e+01 a.52.1.3 105307 1wnhA 225 8.58e+01 1v54E 109 8.63e+01 a.118.11.1 100326 1v8qA 85 8.67e+01 b.84.4.1 108428 1crb 134 8.76e+01 1hmt b.60.1.2 27220 1v54G 85 8.82e+01 f.23.2.1 100328 1omwA 689 8.83e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1lc5A 364 8.89e+01 c.67.1.1 73827 1urqA 63 8.96e+01 h.1.15.1 107994