# 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 1d2zA 108 1.69e-01 1d2zA a.77.1.1 18437 1frqA 314 8.73e-01 1fnc b.43.4.2 25632 c.25.1.1 31522 1fnc 314 8.73e-01 1fnc b.43.4.2 25627 c.25.1.1 31517 1fnd 314 8.73e-01 1fnc b.43.4.2 25626 c.25.1.1 31516 1bx0A 314 8.73e-01 1fnc b.43.4.2 25630 c.25.1.1 31520 1bx1A 314 8.73e-01 1fnc b.43.4.2 25629 c.25.1.1 31519 1f6dA 376 1.03e+00 1f6dA c.87.1.3 35467 1fohA 664 1.26e+00 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1frn 314 1.47e+00 1fnc b.43.4.2 25631 c.25.1.1 31521 1bqk 124 2.08e+00 1bqk b.6.1.1 22889 1b1zA 219 2.17e+00 3seb b.40.2.2 25216 d.15.6.1 37805 1l0yD 221 2.21e+00 1fnuA 221 2.24e+00 3seb b.40.2.2 25212 d.15.6.1 37801 1ha5A 218 2.34e+00 1b47A 304 2.51e+00 2cblA a.39.1.7 17381 a.48.1.1 17775 d.93.1.1 40529 2cblA 305 2.51e+00 2cblA a.39.1.7 17380 a.48.1.1 17774 d.93.1.1 40528 1c5dB 215 2.59e+00 1igtB b.1.1.1 20415 b.1.1.2 21387 1fbvA 388 3.21e+00 2cblA a.39.1.7 17384 a.48.1.1 17778 d.93.1.1 40532 g.44.1.1 45321 1fryA 29 3.43e+00 1pls 113 3.71e+00 1pls b.55.1.1 26965 1g2nA 264 4.35e+00 1lbd a.123.1.1 60227 1jhgA 101 4.41e+00 1jhgA a.107.1.1 19009 1rcsA 105 4.88e+00 1jhgA a.107.1.1 19025 2wrpR 107 5.01e+00 1jhgA a.107.1.1 19010 1trrA 107 5.16e+00 1jhgA a.107.1.1 19017 3wrp 108 5.26e+00 1jhgA a.107.1.1 19015 1a3gA 308 5.40e+00 1daaA e.17.1.1 43286 1i1kA 309 5.41e+00 1daaA e.17.1.1 61533 1troA 108 5.52e+00 1jhgA a.107.1.1 19011 1c4oA 664 5.55e+00 1d2mA c.37.1.13 32415 c.37.1.13 32416 1d2mA 665 5.56e+00 1d2mA c.37.1.13 32417 c.37.1.13 32418 1qfzA 308 5.73e+00 1fnc b.43.4.2 25633 c.25.1.1 31523 1qg0A 308 5.73e+00 1fnc b.43.4.2 25639 c.25.1.1 31529 1qgaA 308 5.73e+00 1fnc b.43.4.2 25637 c.25.1.1 31527 1bvkB 117 6.02e+00 1gc1H b.1.1.1 20279 1g3fA 117 6.43e+00 1g3fA g.52.1.1 45378 1g73C 121 6.58e+00 1g3fA g.52.1.1 45375 1ql0A 241 6.69e+00 1qaeA d.4.1.2 37139 1f9xA 120 6.76e+00 1g3fA g.52.1.1 59748 1g8tA 245 6.82e+00 1qaeA d.4.1.2 37137 1smnA 245 6.82e+00 1qaeA d.4.1.2 37143 1qaeA 245 6.82e+00 1qaeA d.4.1.2 37141 1d9xA 658 7.03e+00 1d2mA c.37.1.13 32419 c.37.1.13 32420 1kiqB 116 7.21e+00 1gc1H b.1.1.1 19939 1a2yB 116 7.24e+00 1gc1H b.1.1.1 19927 1vfaB 116 7.24e+00 1gc1H b.1.1.1 19929 1g7jB 116 7.24e+00 1f3rB b.1.1.1 19933 1a7nH 116 7.25e+00 1gc1H b.1.1.1 19941 1kipB 116 7.38e+00 1gc1H b.1.1.1 19957 1cz8V 94 8.25e+00 1vpfA g.17.1.1 44765 1c05A 159 8.44e+00 1c05A d.66.1.2 39559 1pmy 123 8.48e+00 1bqk b.6.1.1 22888 1a1x 108 8.66e+00 1a1x b.63.1.1 27514 1fltV 98 8.79e+00 1vpfA g.17.1.1 44751 1qpkA 418 8.85e+00 1jdc b.71.1.1 27793 c.1.8.1 28780 1qttA 117 9.20e+00 1a1x b.63.1.1 27516 1vpfA 102 9.54e+00 1vpfA g.17.1.1 44767 1emtH 213 1.07e+01 1igtB b.1.1.1 20483 b.1.1.2 21447 1dqiA 124 1.17e+01 1do6A b.1.13.1 22357 1do6A 124 1.17e+01 1do6A b.1.13.1 22361 2amg 415 1.35e+01 1jdc b.71.1.1 27796 c.1.8.1 28783 1ntp 223 1.37e+01 5ptp b.47.1.2 25858 1cqyA 99 1.37e+01 1b9zA b.3.1.1 22527 1cf4B 44 1.37e+01 1cf4B 2rig 144 1.40e+01 1d9cA a.26.1.3 16921 2tldE 220 1.41e+01 5ptp b.47.1.2 25881 1jglH 218 1.42e+01 b.1.1.1 66679 b.1.1.2 66680 1j8aA 223 1.46e+01 b.47.1.2 62737 1c5sA 223 1.46e+01 5ptp b.47.1.2 25903 5ptp 223 1.49e+01 5ptp b.47.1.2 25831 1ggwA 140 1.50e+01 1ggwA a.39.1.5 60490 1fdlH 218 1.51e+01 1igtB b.1.1.1 19961 b.1.1.2 21021 1hj9A 223 1.51e+01 b.47.1.2 65845 1i7pA 274 1.52e+01 b.43.4.2 66048 c.25.1.1 66049 1agjA 242 1.54e+01 1agjA b.47.1.1 25827 1fxwF 229 1.57e+01 c.23.10.3 65058 1jdc 429 1.59e+01 1jdc b.71.1.1 27789 c.1.8.1 28776 1qi4A 429 1.60e+01 1jdc b.71.1.1 27791 c.1.8.1 28778 1qi5A 429 1.61e+01 1jdc b.71.1.1 27792 c.1.8.1 28779 1qi3A 429 1.68e+01 1jdc b.71.1.1 27794 c.1.8.1 28781 1m6pA 152 1.70e+01 1m6pA b.64.1.1 27519 1g3cA 228 1.70e+01 5ptp b.47.1.2 25921 1ibgH 217 1.71e+01 1igtB b.1.1.1 20049 b.1.1.2 21091 1keoA 154 1.72e+01 b.64.1.1 68534 1b28A 53 1.76e+01 1bazA a.43.1.1 17445 1phm 310 1.77e+01 1phm b.13.1.2 59015 b.13.1.2 59016 1tgsZ 229 1.86e+01 5ptp b.47.1.2 25850 1tgb 229 1.87e+01 5ptp b.47.1.2 25875 1eiwA 111 1.87e+01 1eiwA c.23.3.1 31130 1gsoA 431 1.88e+01 1gsoA b.84.2.1 28240 c.30.1.1 31647 d.142.1.2 41492 1nddA 76 1.88e+01 1ubi d.15.1.1 37599 1nddD 76 1.88e+01 1ubi d.15.1.1 37602 1fb3A 296 1.93e+01 1fnc b.43.4.2 25641 c.25.1.1 31531 1gcyA 527 1.95e+01 1jdc b.71.1.1 27788 c.1.8.1 28775 1eoeA 100 1.95e+01 1t1dA d.42.1.2 38638 1eptC 98 2.05e+01 5ptp 1oakH 223 2.11e+01 1igtB b.1.1.1 20291 b.1.1.2 21283 1fnsH 225 2.12e+01 1igtB b.1.1.1 20289 b.1.1.2 21281 1ncs 47 2.15e+01 1ncs g.37.1.1 45040 1fmhB 33 2.16e+01 1fmhB k.6.1.1 46410 1dl7H 112 2.21e+01 1f3rB b.1.1.1 20499 1jn6B 218 2.24e+01 b.1.1.1 66925 b.1.1.2 66926 1adwA 123 2.27e+01 1bqk b.6.1.1 22893 1c3tA 76 2.39e+01 1ubi d.15.1.1 37594 1qqyA 130 2.40e+01 3lzt d.2.1.2 36586 1rvfH 119 2.42e+01 1mfa b.1.1.1 19991 1el1A 130 2.42e+01 3lzt d.2.1.2 59451 1k5rA 41 2.49e+01 b.72.1.1 68206 1zzzA 237 2.55e+01 5ptp b.47.1.2 25892 1gawB 314 2.61e+01 1fnc b.43.4.2 25644 c.25.1.1 31534 1tawA 223 2.63e+01 5ptp b.47.1.2 25860 1f0tA 243 2.81e+01 5ptp b.47.1.2 25937 1xlmA 394 2.86e+01 4xis c.1.15.3 29441 1xlaA 394 2.92e+01 4xis c.1.15.3 29445 1cwpA 190 2.93e+01 1cwpA b.10.1.2 23305 4xiaA 393 2.94e+01 4xis c.1.15.3 29439 1cynA 178 3.02e+01 2cpl b.62.1.1 27489 1qurI 20 3.09e+01 1jljA 189 3.27e+01 c.57.1.1 63169 1k9qA 40 3.29e+01 b.72.1.1 68357 1ffsB 134 3.30e+01 1eayC d.58.24.1 39388 1gq8A 319 3.31e+01 1ihcA 188 3.38e+01 1di6A c.57.1.1 62379 1e63A 304 3.44e+01 1fnc b.43.4.2 59287 c.25.1.1 59288 1ekfA 365 3.44e+01 1ekfA e.17.1.1 59445 1g6uA 48 3.47e+01 1g6uA k.9.1.1 46425 1i3gH 121 3.52e+01 b.1.1.1 66018 1trnA 224 3.54e+01 5ptp b.47.1.2 26000 1fshA 105 3.57e+01 1fshA a.4.5.31 60006 2gsaA 432 3.60e+01 2gsaA c.67.1.4 34446 1l5jA 865 3.68e+01 1bqeA 295 3.72e+01 b.43.4.2 64760 c.25.1.1 64761 1e64A 304 3.74e+01 1fnc b.43.4.2 59289 c.25.1.1 59290 1ewiA 114 3.78e+01 1ewiA b.40.4.3 25302 1coi 31 3.83e+01 k.5.1.1 46408 1mfbH 219 3.86e+01 1mfa b.1.1.1 19891 b.1.1.2 20985 1h85A 295 3.88e+01 b.43.4.2 65716 c.25.1.1 65717 1qfwH 117 3.95e+01 1gc1H b.1.1.1 20435 1bjk 295 3.95e+01 1fnc b.43.4.2 25649 c.25.1.1 31539