# List of top-scoring protein chains for t2k-w0.5 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 1qvcA 145 4.37e-27 3ullA b.40.4.3 25284 1kawA 135 1.05e-26 3ullA b.40.4.3 25288 1eygA 116 1.37e-25 3ullA b.40.4.3 25292 3ullA 132 1.32e-17 3ullA b.40.4.3 25282 1pdr 99 1.46e-01 1pdr b.36.1.1 24771 1be9A 119 2.01e-01 1pdr b.36.1.1 24774 1bfeA 119 2.01e-01 1pdr b.36.1.1 24775 1je5A 206 3.25e-01 1je5A b.40.4.7 62909 1bxcA 387 5.24e-01 4xis c.1.15.3 29539 5mdhA 333 7.28e-01 1bmdA c.2.1.5 30126 d.162.1.1 42093 4mdhA 334 7.29e-01 1bmdA c.2.1.5 30128 d.162.1.1 42095 1mxa 383 8.93e-01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1mxb 383 8.93e-01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1f3wA 530 1.31e+00 b.58.1.1 64934 c.1.12.1 64935 c.49.1.1 64936 1a49A 530 1.31e+00 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1f3xA 530 1.31e+00 b.58.1.1 64958 c.1.12.1 64959 c.49.1.1 64960 1xrb 383 1.52e+00 1mxb d.130.1.1 41335 d.130.1.1 41336 d.130.1.1 41337 1bg6 359 1.98e+00 1bg6 a.100.1.5 18810 c.2.1.6 30214 1pkn 530 2.28e+00 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1k8gC 320 3.11e+00 b.40.4.3 68299 b.40.4.3 68300 1mpaH 225 3.12e+00 1mfa b.1.1.1 20135 b.1.1.2 21165 1a8p 258 3.29e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 1al3 324 3.51e+00 1al3 c.94.1.1 35835 1ir6A 424 3.58e+00 1b8zA 90 3.60e+00 1huuA a.55.1.1 17902 1i94C 238 4.09e+00 1fjfC d.52.3.1 61992 d.53.1.1 61993 1fjgC 239 4.10e+00 1fjfC d.52.3.1 38831 d.53.1.1 38839 1k8iB 191 4.29e+00 b.1.1.2 68303 d.19.1.1 68304 1f2tB 148 4.45e+00 1f2tB 2cnd 270 4.59e+00 1ndh b.43.4.2 25659 c.25.1.1 31549 1ju3A 583 4.61e+00 b.18.1.13 67300 c.69.1.21 67301 1cne 270 4.63e+00 1ndh b.43.4.2 25661 c.25.1.1 31551 1hdmB 193 4.83e+00 1hdmB b.1.1.2 21584 d.19.1.1 38158 1b06A 210 4.84e+00 1avmA a.2.11.1 15740 d.44.1.1 38737 1ii8B 174 4.95e+00 1f2tB 1dosA 358 5.15e+00 1dosA c.1.10.2 29175 1b57A 358 5.19e+00 1dosA c.1.10.2 29177 1k0fA 277 5.27e+00 1em2A 229 5.76e+00 1em2A d.129.3.2 41321 1pklG 499 5.79e+00 1a49A b.58.1.1 27058 c.1.12.1 29286 c.49.1.1 33140 1be1 137 5.86e+00 1be1 c.23.6.1 31237 1exeA 99 6.05e+00 1huuA a.55.1.1 17906 1j87A 172 6.05e+00 2fcbA b.1.1.4 62715 b.1.1.4 62716 1j88A 172 6.05e+00 2fcbA b.1.1.4 62717 b.1.1.4 62718 1jb7A 495 6.05e+00 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1otcA 495 6.05e+00 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1j86A 176 6.06e+00 2fcbA b.1.1.4 62711 b.1.1.4 62712 1toaA 313 6.13e+00 1toaA c.92.2.2 35598 1h6kA 757 7.39e+00 a.118.1.2 60675 a.118.1.2 60676 a.118.1.2 60677 2hvm 273 7.81e+00 1cnv c.1.8.5 28985 1fyjA 57 7.88e+00 1r1bA a.16.1.3 60115 1iqvA 218 8.20e+00 1rss a.75.1.1 62661 1fg4A 149 8.61e+00 1ewxA c.47.1.10 59814 3kinB 117 9.01e+00 3kinB 1bgaA 447 9.12e+00 1e70M c.1.8.4 28961 1bggA 448 9.13e+00 1e70M c.1.8.4 28953 1i5gA 144 9.20e+00 1ewxA c.47.1.10 61784 1j8mF 297 9.25e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1bxbA 387 9.47e+00 4xis c.1.15.3 29543 1sssA 205 9.68e+00 1avmA a.2.11.1 15738 d.44.1.1 38735 1hnnA 282 9.83e+00 c.66.1.15 65895 1d1nA 99 1.07e+01 1d1nA b.43.3.1 25718 1rpmA 278 1.09e+01 2shpA c.45.1.2 32679 1kr1A 273 1.12e+01 c.1.8.5 68846 1j8yF 297 1.14e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1dq3A 454 1.14e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1bev3 242 1.15e+01 1aym3 1wtuA 99 1.16e+01 1huuA a.55.1.1 17904 1pkm 530 1.16e+01 1a49A b.58.1.1 27051 c.1.12.1 29254 c.49.1.1 33108 2kinB 100 1.19e+01 3kinB 1b1yA 500 1.19e+01 1byb c.1.8.2 28796 1i1sA 96 1.21e+01 1bjaA a.4.5.9 16124 1bjaA 95 1.24e+01 1bjaA a.4.5.9 16122 1fa2A 498 1.33e+01 1byb c.1.8.2 28797 1fvcB 120 1.35e+01 1igtB b.1.1.1 19863 1pfo 500 1.37e+01 1pfo f.9.1.1 43826 3crd 100 1.38e+01 3crd a.77.1.1 18429 1bj3A 129 1.41e+01 1ixxB d.169.1.1 42341 1vin 268 1.44e+01 1vin a.74.1.1 18354 a.74.1.1 18355 1j7lA 264 1.44e+01 d.144.1.6 62697 1j7iA 264 1.44e+01 1j7iA d.144.1.6 62694 1kr0A 273 1.45e+01 c.1.8.5 68845 1b8kA 119 1.48e+01 1bndA g.17.1.3 44795 1fnlA 175 1.54e+01 2fcbA b.1.1.4 21783 b.1.1.4 21784 1e4kC 176 1.55e+01 2fcbA b.1.1.4 21787 b.1.1.4 21788 1iisC 176 1.55e+01 2fcbA b.1.1.4 62458 b.1.1.4 62459 1ruxA 951 1.59e+01 1dhx b.13.2.2 59040 b.13.2.2 59041 1iodA 129 1.67e+01 1ixxB d.169.1.1 62622 1i0hA 205 1.71e+01 1avmA a.2.11.1 15760 d.44.1.1 38685 1fveB 223 1.73e+01 1igtB b.1.1.1 19871 b.1.1.2 20967 1kmjA 406 1.79e+01 c.67.1.3 68695 1dt9A 437 1.80e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1jf9A 408 1.81e+01 1c0nA c.67.1.3 62931 1kqyA 273 1.95e+01 c.1.8.5 68843 1ganA 134 1.97e+01 1c1lA b.29.1.3 24214 1kzyA 195 2.04e+01 1gsoA 431 2.05e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1ycsA 199 2.07e+01 1tupA b.2.5.1 22433 1i08A 205 2.07e+01 1avmA a.2.11.1 15770 d.44.1.1 38695 1gy3B 258 2.11e+01 1e9hB 261 2.12e+01 a.74.1.1 64813 a.74.1.1 64814 1qmzB 259 2.12e+01 1vin a.74.1.1 18338 a.74.1.1 18339 1finB 260 2.13e+01 1vin a.74.1.1 18342 a.74.1.1 18343 1en5A 205 2.16e+01 1avmA a.2.11.1 59465 d.44.1.1 59466 1en6A 205 2.16e+01 1avmA a.2.11.1 59473 d.44.1.1 59474 1d5nA 205 2.17e+01 1avmA a.2.11.1 15762 d.44.1.1 38687 1en4A 205 2.17e+01 1avmA a.2.11.1 59457 d.44.1.1 59458 1iyu 79 2.24e+01 1iyu b.84.1.1 28227 1thpB 259 2.30e+01 5ptp 1sltB 135 2.32e+01 1c1lA b.29.1.3 24187 1sltA 136 2.33e+01 1c1lA b.29.1.3 24186 1tupA 219 2.33e+01 1tupA b.2.5.1 22434 1hyeA 313 2.33e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1bthH 259 2.44e+01 5ptp 1b7xB 259 2.47e+01 1ucyE 1a0p 290 2.52e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 2thfB 259 2.52e+01 1ucyE 1aj5A 173 2.56e+01 1alvA a.39.1.7 17367 1ghxH 257 2.56e+01 1eb1H 257 2.56e+01 1gj4H 258 2.58e+01 1gj5H 258 2.58e+01 1c5lH 259 2.59e+01 5ptp 1ahtH 259 2.59e+01 5ptp 8kme2 259 2.59e+01 1ucyE 1faoA 126 2.68e+01 1faoA b.55.1.1 26974 1rfbA 119 2.70e+01 1d9cA a.26.1.3 16905 1d9cA 121 2.72e+01 1d9cA a.26.1.3 16901 1ccwA 137 2.75e+01 1be1 c.23.6.1 31238 1fmmS 132 2.76e+01 1bfg b.42.1.1 59883 1eqkA 102 2.83e+01 1eqkA d.17.1.2 37998 1df0B 184 2.84e+01 1alvA a.39.1.7 17369 1bmg 98 2.90e+01 1agdB b.1.1.2 20667 1bmv2 374 2.91e+01 1bmv2 1lbeA 258 3.00e+01 1lbeA e.4.1.1 42773 1jllB 388 3.07e+01 c.23.4.1 66853 d.142.1.4 66854 1mioB 458 3.09e+01 1qguB c.92.2.3 35602 1jouB 259 3.12e+01 1ucyE 1dm4B 260 3.13e+01 1ucyE 1d6wA 287 3.14e+01 1ucyE b.47.1.2 26098 1d9iA 288 3.16e+01 1ucyE b.47.1.2 26159 1eojA 289 3.17e+01 1ucyE b.47.1.2 26105 2pkaB 152 3.18e+01 5ptp 1jx4A 352 3.19e+01 e.8.1.5 67405 1slaA 134 3.22e+01 1c1lA b.29.1.3 24196 1krs 120 3.24e+01 1krs b.40.4.1 25256 1kvdA 63 3.25e+01 1kveA d.70.1.2 39592 1kveA 63 3.25e+01 1kveA d.70.1.2 39590 1hagE 295 3.27e+01 1ucyE b.47.1.2 26135 1iepA 293 3.28e+01 1fgkA d.144.1.2 62333 1jykA 254 3.29e+01 c.68.1.13 67458 1jwtA 305 3.39e+01 b.47.1.2 67398 1gjwA 637 3.42e+01 b.71.1.1 60582 c.1.8.1 60583 1gjuA 637 3.42e+01 b.71.1.1 60580 c.1.8.1 60581 1flgA 582 3.42e+01 4aahA b.70.1.1 27682 1hueA 90 3.47e+01 1huuA a.55.1.1 17900 1huuA 90 3.47e+01 1huuA a.55.1.1 17897 1hwxA 501 3.47e+01 1hwyA c.2.1.7 30250 c.58.1.1 33898 1hwyA 501 3.47e+01 1hwyA c.2.1.7 30262 c.58.1.1 33910 1bryY 248 3.52e+01 1mrj d.165.1.1 42181 1ep3B 262 3.56e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1ep2B 261 3.57e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1vr1H 261 3.65e+01 5ptp 1dx5M 259 3.72e+01 1ucyE 1bndB 119 3.95e+01 1bndA g.17.1.3 44794