# 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 1ck9A 104 4.92e-20 1ck9A d.79.3.1 39806 1jj2F 119 2.18e-16 1ffkE d.79.3.1 63091 1ffkE 119 2.18e-16 1ffkE d.79.3.1 39812 1e7kA 128 5.96e-15 1ffkE d.79.3.1 39813 1dt9A 437 1.04e-02 1dt9A c.55.4.2 33738 d.79.3.2 39815 d.91.1.1 40257 1dbxA 158 1.43e+00 1dbuA d.116.1.1 40928 1dbuA 158 1.43e+00 1dbuA d.116.1.1 40930 1jvwA 167 1.43e+00 1tif 78 1.53e+00 1tif d.15.8.1 37836 1a0rB 340 1.84e+00 1tbgA b.69.4.1 27658 1gotB 340 1.84e+00 1tbgA b.69.4.1 27648 1tbgA 340 1.90e+00 1tbgA b.69.4.1 27649 1eehA 437 2.39e+00 4uagA c.5.1.1 30654 c.59.1.1 33955 c.72.2.1 34958 3uagA 437 2.47e+00 4uagA c.5.1.1 30652 c.59.1.1 33953 c.72.2.1 34956 4uagA 437 2.47e+00 4uagA c.5.1.1 30651 c.59.1.1 33952 c.72.2.1 34955 1uag 437 2.47e+00 4uagA c.5.1.1 30653 c.59.1.1 33954 c.72.2.1 34957 1ll2A 333 7.07e+00 1ll0A 339 7.14e+00 1a76 326 8.94e+00 1a76 a.60.7.1 18091 c.53.1.2 33361 1hrhA 136 9.61e+00 1rthA c.55.3.1 33577 1rdhA 146 1.01e+01 1rthA c.55.3.1 33588 1cs1A 386 1.26e+01 1ibjA c.67.1.3 34399 1cs1C 386 1.26e+01 1ibjA c.67.1.3 34401 2ng1 293 1.29e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 1ffh 294 1.30e+01 1ng1 a.24.13.1 16960 c.37.1.10 32271 1g33A 73 1.33e+01 a.39.1.4 65121 1ng1 294 1.37e+01 1ng1 a.24.13.1 16961 c.37.1.10 32272 1scjB 71 1.37e+01 1scjB d.58.3.2 39069 1jpnA 296 1.37e+01 a.24.13.1 67039 c.37.1.10 67040 1ddf 127 1.40e+01 1ddf a.77.1.1 18423 1b75A 94 1.41e+01 1dfuP b.53.1.1 26937 1dfuP 94 1.41e+01 1dfuP b.53.1.1 26936 487dN 95 1.42e+01 1dfuP i.1.1.2 45841 1dk7A 146 1.48e+01 1derA c.8.5.1 30772 1jon 155 1.55e+01 1derA c.8.5.1 30780 1d6nA 214 1.58e+01 1qk3A c.61.1.1 34077 1bzyA 217 1.62e+01 1qk3A c.61.1.1 34071 1hmpA 217 1.62e+01 1qk3A c.61.1.1 34075 2ffhA 425 1.87e+01 1ng1 a.24.13.1 16965 a.36.1.1 17122 c.37.1.10 32276 1fy9A 193 1.92e+01 1derA c.8.5.1 30779 1fyaA 193 1.97e+01 1derA c.8.5.1 30774 1fs2A 272 1.99e+01 1fs1A a.122.1.1 19270 c.10.1.3 30864 1tceA 107 2.05e+01 1d4tA d.93.1.1 40497 1kid 203 2.05e+01 1derA c.8.5.1 30771 1la1A 192 2.06e+01 1jj2P 95 2.07e+01 1ffkN b.34.5.1 63101 1ffkN 95 2.07e+01 1ffkN b.34.5.1 24606 2liv 344 2.09e+01 2liv c.93.1.1 35708 1uteA 313 2.19e+01 1uteA d.159.1.1 42078 1tkiA 321 2.21e+01 1tkiA d.144.1.1 41638 1fqvA 336 2.21e+01 1fqvA a.122.1.1 19254 c.10.1.3 30856 3mdeA 385 2.30e+01 3mdeA a.29.3.1 16594 e.6.1.1 42855 3mddA 385 2.30e+01 3mdeA a.29.3.1 16592 e.6.1.1 42853 1spbP 78 2.33e+01 1scjB d.58.3.2 39068 1fb1A 196 2.35e+01 1a8rA d.96.1.1 40652 1mdl 359 2.44e+01 2mnr c.1.11.2 29247 d.54.1.1 38891 2mnr 357 2.45e+01 2mnr c.1.11.2 29245 d.54.1.1 38889 1mdr 359 2.47e+01 2mnr c.1.11.2 29248 d.54.1.1 38892 1dhs 344 2.49e+01 1dhs c.31.1.1 31727 1dtn 359 2.52e+01 2mnr c.1.11.2 29249 d.54.1.1 38893 1ilk 151 2.56e+01 2ilk a.26.1.3 16886 1mra 359 2.57e+01 2mnr c.1.11.2 29250 d.54.1.1 38894 2ilk 160 2.63e+01 2ilk a.26.1.3 16885 1j84A 180 2.75e+01 b.18.1.12 66432 1bw0A 416 2.77e+01 1bw0A c.67.1.1 34385 1fljA 260 2.92e+01 2cba b.74.1.1 27954 1jmvA 141 3.11e+01 c.29.1.2 66897 1qc5A 192 3.13e+01 1aoxA c.62.1.1 34147 1qc5B 192 3.20e+01 1aoxA c.62.1.1 34148 1qfcA 306 3.27e+01 1uteA d.159.1.1 42077 1dcjA 81 3.29e+01 1dcjA d.68.3.1 59115 1qhwA 327 3.31e+01 1uteA d.159.1.1 42076 1fkl 107 3.35e+01 1fkj d.26.1.1 38423 1bnb 38 3.52e+01 1bnb g.9.1.1 44592 3dpa 218 3.63e+01 1qpxA b.1.11.1 22323 b.7.2.1 23205 1qppA 218 3.64e+01 1qpxA b.1.11.1 22320 b.7.2.1 23202 1pdkA 218 3.66e+01 1qpxA b.1.11.1 22322 b.7.2.1 23204 1jj2X 240 3.80e+01 1ffkV c.9.2.1 63109 1j8mF 297 3.81e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1krs 120 3.83e+01 1krs b.40.4.1 25256 1g31A 111 3.86e+01 1g31A b.35.1.1 24656 1j8yF 297 3.90e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1qpxA 218 3.91e+01 1qpxA b.1.11.1 22318 b.7.2.1 23200 1hqcA 324 3.97e+01 1hqcA a.4.5.11 16127 c.37.1.13 32424