# List of top-scoring protein chains for t2k-100-30-bys 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 1abmA 198 5.97e-01 1avmA 1psdA 409 6.10e-01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1pl4A 198 7.35e-01 a.2.11.1 -132 d.44.1.1 -9733 1ap6A 198 7.81e-01 1avmA a.2.11.1 15746 d.44.1.1 38705 1n0nA 199 8.58e-01 a.2.11.1 79750 d.44.1.1 79751 1vmoA 163 1.34e+00 1vmoA b.77.1.1 27974 1tocR 120 2.59e+00 1tocR g.8.1.2 44558 g.8.1.2 44559 1ohtA 215 2.96e+00 d.118.1.1 87036 1v33A 366 3.92e+00 unknown_sccs -11384 1pmaA 233 5.66e+00 1pmaA d.153.1.4 41918 1kf6D 119 6.01e+00 f.21.2.2 72400 1idsA 207 6.34e+00 1avmA a.2.11.1 15722 d.44.1.1 38730 1josA 128 6.42e+00 d.52.7.1 84191 1d8bA 81 6.86e+00 1d8bA a.60.8.1 18094 1qw9A 502 7.06e+00 b.71.1.2 -4677 c.1.8.3 -5348 1mk0A 97 7.24e+00 d.226.1.1 79216 1h09A 338 7.42e+00 b.109.1.1 83420 c.1.8.8 83421 1jwiB 125 7.55e+00 d.169.1.1 67384 1ud0A 113 8.82e+00 unknown_sccs -450 1nb8A 353 1.09e+01 d.3.1.9 80385 1i85A 110 1.12e+01 1i85A b.1.1.1 61946 1ej0A 180 1.15e+01 1ej0A c.66.1.2 34179 1nbfA 353 1.32e+01 d.3.1.9 80387 1qe3A 489 1.36e+01 2bce c.69.1.1 34630 1lkxA 697 1.41e+01 c.37.1.9 73981 1lfaA 187 1.43e+01 1ido c.62.1.1 34122 1mjnA 179 1.46e+01 c.62.1.1 79210 1dgqA 188 1.47e+01 1ido c.62.1.1 34131 1k9jA 139 1.67e+01 d.169.1.1 68353 1viuA 203 1.77e+01 d.113.1.1 -10889 1sl4A 155 1.79e+01 1icxA 155 1.95e+01 d.129.3.1 71191 1g71A 347 1.97e+01 1g71A unknown_sccs 43268 1ut0A 190 2.02e+01 1qz8A 113 2.06e+01 unknown_sccs -4264 2ccyA 128 2.12e+01 2ccyA a.24.3.2 16544 1eu8A 409 2.24e+01 1eu8A c.94.1.1 59502 1igqA 62 2.26e+01 b.34.1.3 66130 1kagA 173 2.38e+01 c.37.1.2 72249 1shsA 147 2.43e+01 1shsA b.15.1.1 23675 1e2o 233 2.56e+01 1eaf c.43.1.1 32631 1h10A 125 2.56e+01 b.55.1.1 83446 1ly2A 130 2.59e+01 g.18.1.1 74335 g.18.1.1 74336 1sxjE 354 2.61e+01 1shp 55 2.72e+01 1bpi g.8.1.1 44553 1rwhA 757 2.89e+01 a.102.3.2 -1340 b.24.1.1 -3300 b.30.5.2 -3508 2nef 136 2.91e+01 1efnB d.102.1.1 40704 3mspA 126 2.91e+01 1mspA b.1.11.2 22343 1t7sA 137 2.91e+01 1ghqB 134 2.93e+01 1ghqB g.18.1.1 60522 g.18.1.1 60523 1grwA 126 2.94e+01 b.1.11.2 70391 1qo3C 137 3.03e+01 1qo3C d.169.1.1 42350 1dik 874 3.04e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 1ovlA 271 3.12e+01 a.123.1.1 87455 1jdc 429 3.19e+01 1jdc b.71.1.1 27789 c.1.8.1 28776 2hgf 97 3.23e+01 1bhtA g.10.1.1 44607 1q87A 221 3.26e+01 unknown_sccs -12028 1jb7B 260 3.39e+01 1otcB b.40.4.3 62839 1kblA 873 3.44e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1i86A 389 3.46e+01 c.95.1.2 66068 c.95.1.2 66069 1tn3 137 3.48e+01 1htn d.169.1.1 42423 1slvA 142 3.49e+01 1sluA b.16.1.1 23688 1mc3A 296 3.50e+01 c.68.1.6 78943 1otcB 260 3.51e+01 1otcB b.40.4.3 25310 1e5rA 290 3.54e+01 1e5rA b.82.2.4 59276 1rypC 244 3.56e+01 1rypC d.153.1.4 41934 1fezA 256 3.67e+01 1fezA c.108.1.3 43343 1euu 605 3.70e+01 1eut b.1.18.2 21892 b.18.1.1 23713 b.68.1.1 27610 1lugA 259 3.75e+01 b.74.1.1 -4726 1n7zA 334 3.78e+01 b.127.1.1 85380 1mooA 260 3.79e+01 b.74.1.1 79359 1ip0A 50 3.86e+01 g.3.11.1 71253 1bkjA 240 3.94e+01 1bkjA d.90.1.1 40243 1bdc 60 3.96e+01 1fc2C a.8.1.1 16350 1g72A 573 3.96e+01 4aahA b.70.1.1 27680