# 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 1eygA 116 1.76e-26 3ullA b.40.4.3 25292 1kawA 135 1.86e-26 3ullA b.40.4.3 25288 1qvcA 145 1.86e-26 3ullA b.40.4.3 25284 3ullA 132 1.86e-19 3ullA b.40.4.3 25282 1pdr 99 1.16e-02 1pdr b.36.1.1 24771 1be9A 119 1.45e-02 1pdr b.36.1.1 24774 1bfeA 119 1.45e-02 1pdr b.36.1.1 24775 1f2tB 148 2.57e-01 1f2tB 1ii8B 174 2.77e-01 1f2tB 1k8gC 320 3.43e-01 b.40.4.3 68299 b.40.4.3 68300 1jb7A 495 6.26e-01 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1otcA 495 6.26e-01 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1a8p 258 6.30e-01 1fdr b.43.4.2 25654 c.25.1.1 31544 1ir6A 424 6.60e-01 1bxcA 387 6.66e-01 4xis c.1.15.3 29539 1dc1A 323 1.01e+00 1dc1A c.52.1.11 33321 1dqwA 267 1.20e+00 1dqwA c.1.2.3 28551 1ju3A 583 1.26e+00 b.18.1.13 67300 c.69.1.21 67301 1b8zA 90 1.46e+00 1huuA a.55.1.1 17902 1sltB 135 2.06e+00 1c1lA b.29.1.3 24187 1sltA 136 2.07e+00 1c1lA b.29.1.3 24186 1g0cA 364 2.34e+00 7a3hA c.1.8.3 60165 1slaA 134 2.75e+00 1c1lA b.29.1.3 24196 1bg6 359 2.75e+00 1bg6 a.100.1.5 18810 c.2.1.6 30214 1al3 324 2.90e+00 1al3 c.94.1.1 35835 1mpaH 225 2.95e+00 1mfa b.1.1.1 20135 b.1.1.2 21165 5mdhA 333 3.06e+00 1bmdA c.2.1.5 30126 d.162.1.1 42093 4mdhA 334 3.07e+00 1bmdA c.2.1.5 30128 d.162.1.1 42095 1a78A 134 3.25e+00 1c1lA b.29.1.3 24212 1j87A 172 3.56e+00 2fcbA b.1.1.4 62715 b.1.1.4 62716 1j88A 172 3.56e+00 2fcbA b.1.1.4 62717 b.1.1.4 62718 1j86A 176 3.60e+00 2fcbA b.1.1.4 62711 b.1.1.4 62712 1je5A 206 4.78e+00 1je5A b.40.4.7 62909 2cnd 270 4.97e+00 1ndh b.43.4.2 25659 c.25.1.1 31549 2hvm 273 4.98e+00 1cnv c.1.8.5 28985 1cne 270 5.00e+00 1ndh b.43.4.2 25661 c.25.1.1 31551 1hueA 90 5.07e+00 1huuA a.55.1.1 17900 1huuA 90 5.07e+00 1huuA a.55.1.1 17897 1k8iB 191 5.44e+00 b.1.1.2 68303 d.19.1.1 68304 4tnc 162 6.49e+00 1ncx a.39.1.5 17228 1kr0A 273 6.60e+00 c.1.8.5 68845 1exeA 99 6.65e+00 1huuA a.55.1.1 17906 1eg9B 194 7.07e+00 1ndoB d.17.4.4 38120 1ndoB 194 7.07e+00 1ndoB d.17.4.4 38121 1kr1A 273 7.08e+00 c.1.8.5 68846 1bjmA 216 7.17e+00 8fabA b.1.1.1 20524 b.1.1.2 21460 1ruxA 951 7.82e+00 1dhx b.13.2.2 59040 b.13.2.2 59041 1fnlA 175 8.09e+00 2fcbA b.1.1.4 21783 b.1.1.4 21784 1kqyA 273 8.09e+00 c.1.8.5 68843 1e4kC 176 8.13e+00 2fcbA b.1.1.4 21787 b.1.1.4 21788 1iisC 176 8.23e+00 2fcbA b.1.1.4 62458 b.1.1.4 62459 1i36A 264 8.38e+00 2aak 152 8.56e+00 1u9aA d.20.1.1 38325 1top 162 8.74e+00 1ncx a.39.1.5 17223 1ncx 162 8.74e+00 1ncx a.39.1.5 17222 1bucA 383 9.13e+00 3mdeA a.29.3.1 16590 e.6.1.1 42851 1d1nA 99 9.20e+00 1d1nA b.43.3.1 25718 1i94C 238 9.47e+00 1fjfC d.52.3.1 61992 d.53.1.1 61993 1fjgC 239 9.49e+00 1fjfC d.52.3.1 38831 d.53.1.1 38839 1hnnA 282 1.00e+01 c.66.1.15 65895 1elyA 449 1.02e+01 1b8jA c.76.1.1 35028 1aw5 326 1.04e+01 1b4kA c.1.10.3 29181 1e3jA 352 1.07e+01 1e3jA b.35.1.2 24765 c.2.1.1 29781 1hdmB 193 1.09e+01 1hdmB b.1.1.2 21584 d.19.1.1 38158 1bxbA 387 1.09e+01 4xis c.1.15.3 29543 1bgaA 447 1.12e+01 1e70M c.1.8.4 28961 1bggA 448 1.12e+01 1e70M c.1.8.4 28953 5tnc 162 1.14e+01 1ncx a.39.1.5 17246 1bmv2 374 1.15e+01 1bmv2 1b8jA 449 1.17e+01 1b8jA c.76.1.1 34992 1hjkA 449 1.17e+01 1b8jA c.76.1.1 35006 1iyu 79 1.18e+01 1iyu b.84.1.1 28227 1be1 137 1.18e+01 1be1 c.23.6.1 31237 1ep3B 262 1.27e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1ep2B 261 1.27e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1j8mF 297 1.31e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1igcH 222 1.33e+01 1igtB b.1.1.1 20047 b.1.1.2 21089 1ewiA 114 1.38e+01 1ewiA b.40.4.3 25302 1bmg 98 1.38e+01 1agdB b.1.1.2 20667 1tnw 162 1.44e+01 1ncx a.39.1.5 17235 1tr1A 447 1.47e+01 1e70M c.1.8.4 28957 1e4iA 447 1.47e+01 1e70M c.1.8.4 59225 1j8yF 297 1.49e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1mioB 458 1.53e+01 1qguB c.92.2.3 35602 1qpmA 69 1.57e+01 1qpmA a.4.5.26 16230 1nbcA 155 1.58e+01 1nbcA b.2.2.2 22390 1ylvA 342 1.58e+01 1b4kA c.1.10.3 29180 1ganA 134 1.65e+01 1c1lA b.29.1.3 24214 1i0hA 205 1.65e+01 1avmA a.2.11.1 15760 d.44.1.1 38685 1dosA 358 1.65e+01 1dosA c.1.10.2 29175 1eb3A 340 1.65e+01 1b4kA c.1.10.3 59403 1h7oA 341 1.66e+01 c.1.10.3 60727 1h7nA 342 1.66e+01 1b4kA c.1.10.3 60726 1wtuA 99 1.70e+01 1huuA a.55.1.1 17904 1b57A 358 1.71e+01 1dosA c.1.10.2 29177 1en6A 205 1.74e+01 1avmA a.2.11.1 59473 d.44.1.1 59474 1en5A 205 1.76e+01 1avmA a.2.11.1 59465 d.44.1.1 59466 1i08A 205 1.76e+01 1avmA a.2.11.1 15770 d.44.1.1 38695 1d5nA 205 1.78e+01 1avmA a.2.11.1 15762 d.44.1.1 38687 1iodA 129 1.79e+01 1ixxB d.169.1.1 62622 1en4A 205 1.80e+01 1avmA a.2.11.1 59457 d.44.1.1 59458 1g4dA 69 1.81e+01 1qpmA a.4.5.26 16227 1bj3A 129 1.81e+01 1ixxB d.169.1.1 42341 1jeyB 565 1.85e+01 1jeqB e.31.1.2 62925 1jeqB 565 1.85e+01 1jeqB e.31.1.2 62922 1b1yA 500 1.90e+01 1byb c.1.8.2 28796 1ihjA 98 2.24e+01 1pdr b.36.1.1 62382 1b06A 210 2.26e+01 1avmA a.2.11.1 15740 d.44.1.1 38737 1pmlA 86 2.31e+01 5hpgA g.14.1.1 44632 1mxa 383 2.33e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1mxb 383 2.33e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1elxA 449 2.34e+01 1b8jA c.76.1.1 35026 1tpkA 88 2.37e+01 5hpgA g.14.1.1 44637 1pk2 90 2.45e+01 5hpgA g.14.1.1 44641 1fvcB 120 2.51e+01 1igtB b.1.1.1 19863 1bthH 259 2.56e+01 5ptp 1mdaH 368 2.69e+01 2bbkH b.69.2.1 27637 1ex9A 285 2.71e+01 1cvl c.69.1.18 34785 1fveB 223 2.72e+01 1igtB b.1.1.1 19871 b.1.1.2 20967 1ewjA 126 2.75e+01 1ecsA d.32.1.2 59526 1d9uA 154 2.93e+01 1am7A d.2.1.4 59111 1b8kA 119 2.96e+01 1bndA g.17.1.3 44795 1vrkB 21 2.99e+01 1gawB 314 3.00e+01 1fnc b.43.4.2 25644 c.25.1.1 31534 1dt9A 437 3.00e+01 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1ecsA 126 3.01e+01 1ecsA d.32.1.2 59407 1rtu 114 3.06e+01 9rnt d.1.1.1 36139 1i5gA 144 3.24e+01 1ewxA c.47.1.10 61784 1euzE 419 3.28e+01 1k89 c.2.1.7 59521 c.58.1.1 59522 1fyjA 57 3.31e+01 1r1bA a.16.1.3 60115 1fg4A 149 3.35e+01 1ewxA c.47.1.10 59814 1i70A 96 3.45e+01 d.1.1.1 61862 2pkaB 152 3.46e+01 5ptp 1f6aA 176 3.52e+01 2fcbA b.1.1.4 21791 b.1.1.4 21792 1ce6B 108 3.68e+01 1agdB b.1.1.2 20820 1fa2A 498 3.71e+01 1byb c.1.8.2 28797 3pdzA 96 3.80e+01 1pdr b.36.1.1 24782 1rgeA 96 3.84e+01 1rgeA d.1.1.1 36028 1rgfB 96 3.84e+01 1rgeA d.1.1.1 36035 3pgk 416 3.84e+01 16pk c.86.1.1 35451 1hqcA 324 3.85e+01 1hqcA a.4.5.11 16127 c.37.1.13 32424 2thfB 259 3.87e+01 1ucyE 1b7xB 259 3.88e+01 1ucyE 1ghxH 257 3.90e+01 1eb1H 257 3.91e+01 1gj4H 258 3.91e+01 1gj5H 258 3.92e+01 1c5lH 259 3.93e+01 5ptp 1ahtH 259 3.93e+01 5ptp 8kme2 259 3.93e+01 1ucyE 1jouB 259 3.93e+01 1ucyE 1lbeA 258 3.95e+01 1lbeA e.4.1.1 42773 1urbA 446 3.95e+01 1b8jA c.76.1.1 35000 1dm4B 260 3.95e+01 1ucyE