# List of top-scoring protein chains for t2k-100-30-str2 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 1wosA 364 4.84e-45 b.44.2.1 109468 d.250.1.1 109469 1wsrA 375 5.49e-43 1v5vA 401 8.46e-43 1vloA 381 6.71e-42 b.44.2.1 108838 d.250.1.1 108839 1pj5A 830 1.78e-39 b.44.2.1 94742 c.3.1.2 94743 d.16.1.5 94744 d.250.1.1 94745 1vlyA 338 7.66e-17 b.44.2.1 108871 d.250.1.1 108872 1nrkA 328 9.84e-17 b.44.2.1 92089 d.250.1.1 92090 1x31C 206 6.45e-08 1xzpB 150 8.17e-03 1efcA 393 2.96e-02 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1jdw 423 9.13e-02 1jdw d.126.1.2 41129 1d2eA 397 1.90e-01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1ha3A 405 1.90e-01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1exmA 405 2.26e-01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1nmtA 392 5.14e-01 1nmtA d.108.1.2 40823 d.108.1.2 40824 1g7tA 594 5.60e-01 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1j6wA 175 5.78e-01 1j98A d.185.1.2 62663 1g7rA 594 6.08e-01 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1a7tA 232 6.25e-01 1a7tA d.157.1.1 42041 1ko3A 230 6.45e-01 d.157.1.1 90974 1s95A 333 6.70e-01 d.159.1.3 105375 1g0cA 364 6.74e-01 7a3hA c.1.8.3 60165 2coiA 386 7.93e-01 1aipE 405 9.93e-01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1g01A 364 1.18e+00 7a3hA c.1.8.3 60161 1dd6A 228 1.19e+00 1a7tA d.157.1.1 42054 1rlw 126 1.23e+00 1rlw b.7.1.1 23177 1dkgD 383 1.24e+00 1ba1 c.55.1.1 33427 c.55.1.1 33428 1nd7A 374 1.24e+00 d.148.1.1 91817 1jjeA 222 1.26e+00 1a7tA d.157.1.1 63117 1ur4A 399 1.28e+00 1g7sA 594 1.44e+00 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1jjtA 228 1.48e+00 1a7tA d.157.1.1 63139 2cunA 410 1.53e+00 1b6sA 355 1.55e+00 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1ceqA 316 1.62e+00 1ceqA c.2.1.5 30163 d.162.1.1 42130 1b6rA 355 1.62e+00 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1jw3A 140 1.73e+00 d.208.1.1 67373 1jl3A 139 1.75e+00 c.44.1.1 66826 1tdj 514 1.86e+00 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1pv9A 348 1.90e+00 c.55.2.1 95157 d.127.1.1 95158 1hrhA 136 1.95e+00 1rthA c.55.3.1 33577 1ja1A 622 1.96e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1pz1A 333 2.23e+00 c.1.7.1 95390 1ecxA 384 2.27e+00 1ecxA c.67.1.3 34431 1b1cA 181 2.43e+00 1amoA c.23.5.2 31212 1xfsA 178 2.48e+00 d.129.3.5 109589 1t2dA 322 2.56e+00 c.2.1.5 99084 d.162.1.1 99085 1geeA 261 2.83e+00 c.2.1.2 90509 1gcoA 261 2.84e+00 1ybvA c.2.1.2 29884 1io1A 398 2.87e+00 1io1A e.32.1.1 62611 1m2xA 223 2.88e+00 d.157.1.1 84764 1xsjA 778 2.94e+00 2boqA 331 3.56e+00 1sotA 320 3.56e+00 b.36.1.4 105852 b.47.1.1 105853 2fcr 173 3.66e+00 1rcf c.23.5.1 31151 1vjeA 166 3.73e+00 d.185.1.2 100807 1jnyA 435 3.74e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1cnuA 137 3.81e+00 1cof d.109.1.2 40862 1b93A 152 4.13e+00 1b93A c.24.1.2 31507 1at0 145 4.24e+00 1at0 b.86.1.1 28374 1txdA 385 4.33e+00 a.87.1.1 107422 b.55.1.1 107423 1smlA 269 4.33e+00 1smlA d.157.1.1 42053 1zc1A 208 4.35e+00 1sviA 195 4.50e+00 c.37.1.8 106048 1rp0A 284 4.50e+00 1zejA 293 4.73e+00 1yf5L 254 4.97e+00 1r9cA 139 5.00e+00 d.32.1.2 97255 1ldg 316 5.01e+00 1ceqA c.2.1.5 30165 d.162.1.1 42132 2aioA 269 5.01e+00 1vk1A 242 5.03e+00 d.268.1.2 108634 1rvkA 382 5.06e+00 c.1.11.2 97928 d.54.1.1 97929 1fvuA 133 5.14e+00 1ixxB d.169.1.1 42345 1f06A 320 5.25e+00 1dapA c.2.1.3 59556 d.81.1.3 59557 1d0nA 729 5.44e+00 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 2asbA 251 5.52e+00 1eg5A 384 5.55e+00 1ecxA c.67.1.3 34429 1dapA 320 5.73e+00 1dapA c.2.1.3 30053 d.81.1.3 39968 1eysH 259 5.80e+00 6prcH b.41.1.1 25484 f.23.10.1 43517 1ofuA 320 5.84e+00 c.32.1.1 86972 d.79.2.1 86973 1on0A 158 6.02e+00 d.108.1.1 87095 1innA 166 6.07e+00 1j98A d.185.1.2 62608 1jf8A 131 6.16e+00 c.44.1.1 66621 1ockA 412 6.30e+00 c.117.1.1 86802 1k0rA 366 6.65e+00 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1inlA 296 6.65e+00 c.66.1.17 66220 1ufhA 180 6.70e+00 d.108.1.1 88485 1dbxA 158 6.72e+00 1dbuA d.116.1.1 40928 1ekfA 365 6.77e+00 1ekfA e.17.1.1 59445 1vpqA 273 6.79e+00 3dapA 320 6.84e+00 1dapA c.2.1.3 30051 d.81.1.3 39966 1f60A 458 6.86e+00 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1qydA 313 7.00e+00 c.2.1.2 96583 1b93B 152 7.13e+00 1b93A c.24.1.2 31508 1n8fA 350 7.37e+00 c.1.10.4 85397 2bghA 421 7.38e+00 1gsa 316 7.45e+00 1gsa c.30.1.3 31718 d.142.1.1 41477 1vlbA 907 7.52e+00 a.56.1.1 108739 d.15.4.2 108740 d.41.1.1 108741 d.133.1.1 108742 1b0pA 1231 7.58e+00 c.36.1.8 31831 c.36.1.12 31832 c.48.1.3 33104 c.64.1.1 34157 d.58.1.5 39003 1hlrA 907 7.62e+00 1mt6A 280 7.71e+00 b.76.2.1 79446 b.85.7.1 79447 1jfvA 131 7.84e+00 c.44.1.1 66654 1ewqA 765 7.92e+00 1ewqA a.113.1.1 19069 c.37.1.12 32383 c.55.6.1 33740 d.75.2.1 39743 1ydwA 362 8.13e+00 1pyfA 312 8.18e+00 c.1.7.1 95334 1efdN 266 8.24e+00 1efdN c.92.2.1 35597 1kt8A 365 8.49e+00 e.17.1.1 77531 1kfiA 572 8.56e+00 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1ukfA 188 8.84e+00 d.3.1.10 99488 1n6aA 259 9.14e+00 b.76.2.1 80121 b.85.7.1 80122 1mgtA 174 9.20e+00 1mgtA a.4.2.1 16078 c.55.7.1 33753 1dleA 298 9.21e+00 1dleA b.47.1.2 26312 1j7nB 776 9.30e+00 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1nytA 271 9.44e+00 c.2.1.7 86417 c.58.1.5 86418 1f0cA 305 9.45e+00 1c8oA e.1.1.1 42676 2hrvA 142 9.94e+00 2hrvA b.47.1.4 26429 2a1hA 365 1.01e+01 1lk9A 448 1.02e+01 c.67.1.1 78057 2bvfA 459 1.03e+01 1ktaA 365 1.03e+01 e.17.1.1 77533 2hgsA 474 1.05e+01 2hgsA c.30.1.4 31722 d.142.1.6 75997 1ss4A 153 1.06e+01 d.32.1.6 105976 1t2wA 145 1.06e+01 b.100.1.1 106289 1zhvA 134 1.06e+01 1f5jA 199 1.08e+01 1axkA b.29.1.11 24342 1hdmB 193 1.08e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 1j7nA 776 1.10e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1cliA 345 1.10e+01 1cliA d.79.4.1 39816 d.139.1.1 41459 1g61A 228 1.11e+01 1g61A d.126.1.1 41126 1wy2A 351 1.15e+01 7acn 754 1.16e+01 1amj c.8.2.1 30717 c.83.1.1 35393 1dbuA 158 1.17e+01 1dbuA d.116.1.1 40930 1b24A 188 1.18e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1dgsA 667 1.19e+01 1dgsA a.60.2.2 17963 b.40.4.6 25365 d.142.2.2 41581 1k07A 263 1.19e+01 d.157.1.1 77218 1j4aA 333 1.19e+01 c.2.1.4 71502 c.23.12.1 71503 1szwA 379 1.21e+01 d.265.1.4 99047 1pcfA 66 1.24e+01 1pcfA d.18.1.1 38142 1taq 832 1.24e+01 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1dmhA 311 1.25e+01 1dmhA b.3.6.1 22633 1zdzA 302 1.28e+01 1e1dA 553 1.29e+01 1e1dA e.26.1.1 43363 1dnlA 199 1.30e+01 1ci0A b.45.1.1 25753 1tuaA 191 1.30e+01 d.51.1.1 107321 d.51.1.1 107322 1hdiA 413 1.30e+01 16pk c.86.1.1 60964 1d2iA 223 1.30e+01 1d2iA c.52.1.5 33297 1r5pA 108 1.31e+01 c.47.1.15 97101 1y81A 138 1.31e+01 1uw4A 91 1.31e+01 d.58.7.4 100071 1dkgA 197 1.33e+01 1dkgA b.73.1.1 27812 h.1.9.1 45626 1xqiA 195 1.36e+01 1j9eA 147 1.36e+01 c.23.5.1 62756 1j0aA 325 1.36e+01 c.79.1.1 83871 1y7pA 223 1.37e+01 1oj4A 283 1.37e+01 d.14.1.5 93083 d.58.26.5 93084 1g79A 218 1.37e+01 1ci0A b.45.1.1 25752 1rloA 271 1.38e+01 1olmA 403 1.40e+01 a.5.3.1 104008 b.132.1.1 104009 c.13.1.1 104010 1m98A 317 1.40e+01 a.175.1.1 78866 d.17.4.6 78867 1lxjA 104 1.41e+01 d.58.48.1 84736 1dxrH 258 1.41e+01 6prcH b.41.1.1 25456 f.23.10.1 43433 6prcH 258 1.41e+01 6prcH b.41.1.1 25457 f.23.10.1 43436 1kekA 1231 1.42e+01 c.36.1.8 68524 c.36.1.12 68525 c.48.1.3 68526 c.64.1.1 68527 d.58.1.5 68528 1mqoA 227 1.43e+01 d.157.1.1 103846 1ul7A 102 1.43e+01 d.129.6.1 99540 1nnwA 252 1.43e+01 d.159.1.5 80674 1rlmB 271 1.45e+01 3minB 522 1.45e+01 1qguB c.92.2.3 35606 1eudA 311 1.46e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1wwjA 105 1.47e+01 1kk1A 410 1.47e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1ffkQ 119 1.48e+01 1ffkQ b.34.5.1 24605 1amoA 615 1.49e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1vr6A 350 1.49e+01 1eucA 311 1.51e+01 2scuA c.2.1.8 30311 c.23.4.1 31139 1ezvE 185 1.56e+01 1rie b.33.1.1 59548 f.23.12.1 59549 1vl7A 157 1.57e+01 b.45.1.1 108732 1zj8A 566 1.57e+01 2bi7A 384 1.58e+01 1agdA 276 1.58e+01 1agdA b.1.1.2 20741 d.19.1.1 38260 2minB 522 1.59e+01 1qguB c.92.2.3 35610 1rlmA 271 1.59e+01 1mw7A 240 1.60e+01 e.39.1.1 79557 1c96A 753 1.61e+01 1amj c.8.2.1 30727 c.83.1.1 35403 1jmxA 494 1.62e+01 a.3.1.7 66901 a.3.1.7 66902 b.1.18.14 66903 b.1.18.14 66904 b.61.4.1 66905 1vgvA 384 1.63e+01 c.87.1.3 100608 1glv 303 1.63e+01 1gsa c.30.1.3 31721 d.142.1.1 41480 2fx2 147 1.63e+01 1rcf c.23.5.1 31158 2aebA 322 1.64e+01 1h65A 270 1.64e+01 c.37.1.8 65640 1qhtA 775 1.65e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1m93B 245 1.67e+01 1wvfA 520 1.68e+01 8acn 754 1.68e+01 1amj c.8.2.1 30724 c.83.1.1 35400 1fnoA 417 1.69e+01 c.56.5.4 75841 d.58.19.1 70145 1amj 754 1.69e+01 1amj c.8.2.1 30725 c.83.1.1 35401 1h6oA 204 1.70e+01 a.146.1.1 60689 2ai4A 119 1.70e+01 1bq3B 246 1.70e+01 1qhfA c.60.1.1 33979 1rcqA 357 1.70e+01 b.49.2.2 104882 c.1.6.1 104883 1dar 691 1.71e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1auvA 311 1.72e+01 1auvA c.30.1.5 31723 d.142.1.3 41558 1fp2A 352 1.74e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 6acn 754 1.75e+01 1amj c.8.2.1 30721 c.83.1.1 35397 1vrbA 342 1.76e+01 1y7rA 133 1.77e+01 1ox6A 555 1.78e+01 c.1.2.1 87505 c.23.16.1 87506 1te0A 318 1.80e+01 1w9hA 427 1.81e+01 1v8bA 479 1.82e+01 2c1lA 358 1.82e+01 1h8lA 380 1.82e+01 b.3.2.1 65737 c.56.5.1 65738 1xq6A 253 1.83e+01 1c0pA 363 1.85e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 1bu5A 147 1.87e+01 5nul c.23.5.1 31155 1vkyA 347 1.90e+01 e.53.1.1 108696 1konA 249 1.93e+01 e.39.1.1 72823 1itwA 741 1.95e+01 c.77.1.2 76793 1vkcA 158 1.96e+01 7timA 247 1.98e+01 1amk c.1.1.1 28457 1q44A 326 1.99e+01 c.37.1.5 95779 1vb5A 276 2.00e+01 1b3nA 412 2.04e+01 1dd8A c.95.1.1 35966 c.95.1.1 35967 1vr8A 142 2.05e+01 1hyqA 263 2.05e+01 1hyqA c.37.1.10 61412 1tx2A 297 2.05e+01 c.1.21.1 107420 1g0oA 283 2.06e+01 1ybvA c.2.1.2 60181 1nbwA 607 2.06e+01 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1dfmA 223 2.07e+01 1d2iA c.52.1.5 33295 1o6uA 403 2.07e+01 a.5.3.1 92589 b.132.1.1 92590 c.13.1.1 92591 1devC 196 2.08e+01 1ygs b.26.1.1 23915 1wdtA 665 2.10e+01 1vbiA 344 2.11e+01 1b5fA 239 2.11e+01 1smrA b.50.1.2 26836 1iwmA 186 2.16e+01 b.125.1.2 83758 1vliA 385 2.18e+01 b.85.1.1 108830 c.1.10.6 108831 1uj6A 227 2.20e+01 c.124.1.4 107898 d.58.40.1 107899 1gs5A 258 2.21e+01 c.73.1.2 70395 2bv9A 290 2.21e+01 1o1yA 239 2.24e+01 c.23.16.1 86554 2bc2B 227 2.24e+01 1a7tA d.157.1.1 42032 3bamA 213 2.25e+01 1bam c.52.1.3 33288 1fpxA 352 2.26e+01 1fpxA a.4.5.29 59950 c.66.1.12 59951 1tv8A 340 2.26e+01 c.1.28.3 107352 1j34A 129 2.27e+01 d.169.1.1 84048 1p9eA 331 2.29e+01 d.157.1.5 104088 1vhoA 346 2.29e+01 b.49.3.1 100694 c.56.5.4 100695 1iy8A 267 2.29e+01 c.2.1.2 83774 1s72H 171 2.30e+01 d.41.4.1 105327 1nhp 447 2.30e+01 1nhp c.3.1.5 30549 c.3.1.5 30550 d.87.1.1 40196 1xmzA 241 2.31e+01 2bh1A 250 2.34e+01 2a50B 168 2.36e+01 1wjgA 137 2.37e+01 1h3iA 293 2.38e+01 b.76.2.1 76635 b.85.7.1 76636 1aye 401 2.38e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1vjtA 483 2.38e+01 c.2.1.5 100833 d.162.1.2 100834 1iq4A 179 2.40e+01 1iq4A d.77.1.1 62641 1m1nB 522 2.44e+01 c.92.2.3 78418 1ysjA 404 2.45e+01 2ax3A 502 2.46e+01 2bc2A 227 2.46e+01 1a7tA d.157.1.1 42031 1gqeA 365 2.47e+01 e.38.1.1 70351 1um8A 376 2.47e+01 c.37.1.20 99580 1nhs 447 2.47e+01 1nhp c.3.1.5 30555 c.3.1.5 30556 d.87.1.1 40199 1u0tA 307 2.48e+01 e.52.1.1 107567 1s48A 609 2.49e+01 e.8.1.4 98475 1sheA 103 2.51e+01 d.274.1.1 105551 1t8sA 484 2.51e+01 c.56.2.1 106679 3bamB 213 2.53e+01 1bam c.52.1.3 33289 1usjA 384 2.53e+01 1neyA 247 2.54e+01 c.1.1.1 80449 1v5sA 126 2.54e+01 d.129.6.1 108384 1oboA 169 2.55e+01 c.23.5.1 86776 2acy 98 2.57e+01 2acy d.58.10.1 39298 1qgvA 142 2.57e+01 1qgvA c.47.1.8 33056 1z4rA 168 2.58e+01 1mkp 144 2.59e+01 1vhrA c.45.1.1 32654 1ayl 541 2.61e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1esgA 213 2.62e+01 1bam c.52.1.3 33286 1xkcA 179 2.62e+01 1mh3A 421 2.62e+01 a.4.1.1 79112 c.94.1.1 79113 1jroB 777 2.63e+01 d.41.1.1 67141 d.133.1.1 67142 1k66A 149 2.65e+01 c.23.1.1 90941 1xwfA 431 2.68e+01 9gafA 295 2.72e+01 1apyA d.153.1.5 42008 1t7pA 698 2.75e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1naqA 112 2.75e+01 d.58.5.2 91761 1qstA 160 2.77e+01 1yghA d.108.1.1 40804 1r8oB 71 2.78e+01 1z0wA 207 2.78e+01 1ej1A 190 2.79e+01 1ejhA d.86.1.1 40144 1y9wA 140 2.80e+01 1ky9B 448 2.80e+01 b.36.1.4 73200 b.36.1.4 73201 b.47.1.1 73202 1b4bA 71 2.81e+01 1b4aA d.74.2.1 39718 2a46A 238 2.82e+01 1f4pA 147 2.83e+01 5nul c.23.5.1 59651 1qguB 519 2.84e+01 1qguB c.92.2.3 35626 1li4A 432 2.84e+01 c.2.1.4 84616 c.23.12.3 84617 1w24A 182 2.84e+01 1rz1A 161 2.85e+01 b.45.1.2 98124 1nktA 922 2.85e+01 a.162.1.1 85830 a.172.1.1 85831 c.37.1.19 85832 c.37.1.19 85833 1ak7 174 2.87e+01 1cof d.109.1.2 40864 1nofA 383 2.89e+01 b.71.1.2 92020 c.1.8.3 92021 1lqpA 135 2.94e+01 d.32.1.2 78151 1nkiA 135 2.94e+01 d.32.1.2 91941 1pu5A 164 2.94e+01 b.95.1.1 104310 1jb2A 127 2.94e+01 d.17.4.2 71624 1uouA 474 2.95e+01 a.46.2.1 99706 c.27.1.1 99707 d.41.3.1 99708 1qf6A 642 3.03e+01 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 1ybvA 283 3.04e+01 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