# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7-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 1th8A 145 2.14e+00 1lmiA 131 2.91e+00 b.1.19.1 78098 1mwsA 646 3.37e+00 d.17.4.5 79592 d.175.1.1 79593 e.3.1.1 79594 1jgsA 138 3.55e+00 a.4.5.28 66683 1djxB 624 3.55e+00 1djxB a.39.1.7 17343 b.7.1.1 23160 c.1.18.1 29588 1mwxA 646 4.11e+00 d.17.4.5 79610 d.175.1.1 79611 e.3.1.1 79612 1di0A 158 4.28e+00 1di0A c.16.1.1 30957 1f7wA 144 4.74e+00 1f46A d.129.4.1 59679 1j7iA 264 4.97e+00 1j7iA d.144.1.6 62694 1j7lA 264 5.00e+00 d.144.1.6 62697 1ytbB 180 5.30e+00 1ytbA d.129.1.1 41278 d.129.1.1 41279 1s3jA 155 5.61e+00 a.4.5.28 -227 1aonO 97 6.32e+00 b.35.1.1 24642 1pwaA 162 6.82e+00 b.42.1.1 -4009 1f9fA 83 7.77e+00 1f9fA d.58.8.1 39224 1rg9A 383 7.77e+00 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1n6zA 105 8.04e+00 unknown_sccs 85369 1hssA 124 8.32e+00 1bea a.52.1.2 17819 1nqzA 194 8.79e+00 d.113.1.1 86077 1dzlA 505 8.87e+00 1dzlA b.121.6.1 23586 1fdyA 297 9.34e+00 1nal3 c.1.10.1 29071 1mwrA 646 1.05e+01 d.17.4.5 79586 d.175.1.1 79587 e.3.1.1 79588 1r8hA 87 1.08e+01 d.58.8.1 -10041 1nal1 297 1.09e+01 1nal3 1co4A 42 1.11e+01 1co4A g.47.1.1 45347 1mwqA 101 1.12e+01 unknown_sccs -9962 1sedA 117 1.26e+01 1ytbA 180 1.27e+01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1jf8A 131 1.32e+01 c.44.1.1 66621 1in0A 163 1.32e+01 d.58.49.1 83694 d.58.49.1 83695 1jfvA 131 1.36e+01 c.44.1.1 66654 1lxdA 100 1.40e+01 1lfdA d.15.1.5 37624 1cdwA 179 1.44e+01 1ytbA d.129.1.1 41212 d.129.1.1 41213 1mp9A 198 1.45e+01 a.74.1.2 -1127 a.74.1.2 -1128 1m4uA 206 1.51e+01 g.17.1.7 78625 1gh8A 89 1.58e+01 1gh8A d.58.12.1 39309 1buuA 168 1.59e+01 1rtm1 d.169.1.1 42366 h.1.1.1 45388 3kvt 115 1.61e+01 1t1dA d.42.1.2 38642 1ogoX 574 1.74e+01 unknown_sccs -3237 unknown_sccs -4783 1s5lA 344 1.74e+01 1gppA 237 1.76e+01 b.86.1.2 76262 1olgA 42 1.79e+01 1olgA a.53.1.1 17835 1j27A 102 1.79e+01 unknown_sccs -10116 1cm9A 74 1.82e+01 1b3aA d.9.1.1 37405 1t95A 240 1.82e+01 1gtdA 85 1.88e+01 d.58.45.1 76344 1fj7A 101 1.98e+01 1fj7A d.58.7.1 39209 1l8aA 886 2.04e+01 c.36.1.6 73678 c.36.1.10 73677 c.48.1.1 73679 1who 96 2.11e+01 1who b.7.3.1 23215 1nal3 297 2.13e+01 1nal3 1hl2A 297 2.25e+01 c.1.10.1 83581 1jhb 106 2.26e+01 1kte c.47.1.1 32772 1j0wA 103 2.27e+01 b.55.1.2 -4364 1mw7A 240 2.35e+01 e.39.1.1 79557 1btn 106 2.35e+01 1btn b.55.1.1 26952 1afb1 154 2.38e+01 1rtm1 1obbA 480 2.47e+01 c.2.1.5 86760 d.162.1.2 86761 1mxa 383 2.51e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1qv9A 283 2.55e+01 unknown_sccs -6888 1aba 87 2.75e+01 1aba c.47.1.1 32760 1ofuX 119 2.78e+01 c.37.1.22 86976 1urrA 102 2.90e+01 1lfdA 87 2.92e+01 1lfdA d.15.1.5 37622 1p8kZ 254 2.99e+01 d.95.2.1 -10648 d.95.2.1 -10649 1ht9A 76 3.02e+01 4icb a.39.1.1 61252 1jfkA 134 3.05e+01 a.39.1.5 66639 1lnwA 147 3.05e+01 a.4.5.28 78104 1mxb 383 3.06e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1st9A 143 3.12e+01 c.47.1.10 -7503 1fzgD 87 3.14e+01 1fzgD h.1.8.1 45605 1rtm1 149 3.16e+01 1rtm1 1a8y 367 3.17e+01 1a8y c.47.1.3 32781 c.47.1.3 32782 c.47.1.3 32783 1konA 249 3.18e+01 e.39.1.1 72823 1bak 119 3.20e+01 1bak b.55.1.1 26973 1gmwA 143 3.23e+01 b.107.1.1 65347 d.58.38.1 65348 1nzaA 103 3.24e+01 d.58.5.2 86444 1o0pA 104 3.33e+01 d.58.7.1 86535 1f47B 144 3.34e+01 1f46A d.129.4.1 59645 1jj2R 84 3.35e+01 1ffkP d.12.1.1 63103 1hb5A 394 3.35e+01 i.6.1.1 65752 1hx6A 394 3.35e+01 1cjdA b.121.2.1 58995 b.121.2.1 58996 1xxbA 78 3.40e+01 1xxaA d.74.2.1 39706 1vsgA 364 3.45e+01 1vsgA h.4.1.1 45782 1bfa 134 3.46e+01 1bea a.52.1.2 17827 1oksA 56 3.52e+01 unknown_sccs -426 1gzqA 300 3.53e+01 b.1.1.2 70818 d.19.1.1 70819 1fzqA 181 3.54e+01 1hurA c.37.1.8 32060 1oejA 193 3.54e+01 unknown_sccs -4461 1s72S 85 3.63e+01 1tbaB 180 3.68e+01 1ytbA d.129.1.1 41286 d.129.1.1 41287 1bea 127 3.72e+01 1bea a.52.1.2 17826 1xxaA 78 3.76e+01 1xxaA d.74.2.1 39700 1tdj 514 3.76e+01 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1cf2O 337 3.80e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 1i5hW 50 3.85e+01 1i5hW b.72.1.1 61785 1c9fA 90 3.91e+01 1c9fA d.15.2.1 37639