% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 07/06/04_09:37:16 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dsspfoo.1.T0198.t04-100-30-bys Host: cheep Thu Jul 15 16:54:18 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0198 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.byss % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File T0198.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0198.t04.bys.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6616 sequences, 1561821 residues, 236 nodes, 50.38 seconds % % Sequence scores selected if better than: % E-value (Emax 4.0e+01) (select_score=4) % % Simple: NLL-NULL using FIM probabilities % Reverse: NLL-NULL for the reverse sequence NULL model % Calculated when Simple < simple_threshold (0.00) % E-value on N (=10050) sequences: % N / (1 + exp(-(lambda(=2.8394) * Reverse)^tau(=0.6487))) % Calculated when Simple < simple_threshold (0.00) % Rescale E-values or use -dbsize for multiple scoring runs. % Scores sorted by E-value, best first % % Sequence ID Length Simple Reverse E-value X count 1q0gA 117 -28.74 -13.91 1.94e-01 1oshA 232 -26.80 -13.13 2.89e-01 1nktA 922 -31.39 -12.39 4.26e-01 1l8dA 112 -29.61 -11.77 5.92e-01 256bA 106 -25.72 -11.65 6.31e-01 1jr8A 117 -23.19 -11.31 7.58e-01 1dat 174 -27.73 -10.86 9.70e-01 1v4xB 146 -22.86 -10.62 1.11e+00 1qmqA 414 -22.01 -9.81 1.75e+00 1fcyA 236 -21.73 -9.36 2.27e+00 1lf6A 684 -20.09 -9.34 2.30e+00 1babA 143 -20.42 -9.24 2.44e+00 1io7A 368 -22.23 -9.20 2.49e+00 1v4eA 299 -24.13 -9.17 2.54e+00 1obbA 480 -21.80 -9.17 2.54e+00 1rj1A 151 -24.39 -9.10 2.65e+00 1irdA 141 -19.86 -9.07 2.69e+00 1orsC 132 -21.83 -9.01 2.79e+00 1dz4A 414 -20.38 -8.93 2.92e+00 1fwkA 296 -19.09 -8.85 3.06e+00 1vjtA 483 -20.69 -8.77 3.20e+00 1nfvA 179 -32.98 -8.57 3.63e+00 1ir6A 424 -18.51 -8.45 3.88e+00 1h72C 296 -18.60 -8.39 4.05e+00 1usuA 260 -22.84 -8.37 4.09e+00 1jogA 146 -22.52 -8.29 4.27e+00 1t5jA 313 -20.61 -8.26 4.35e+00 1n81A 186 -25.68 -8.19 4.56e+00 1mojA 182 -25.42 -7.99 5.14e+00 1j1jA 240 -25.31 -7.97 5.21e+00 1s0pA 176 -26.52 -7.84 5.64e+00 1gakA 141 -25.10 -7.81 5.76e+00 1vh6A 145 -29.84 -7.79 5.84e+00 1r2fA 319 -20.46 -7.77 5.89e+00 1gvnA 90 -19.80 -7.75 5.95e+00 1i3dA 146 -19.00 -7.63 6.41e+00 1j7yA 141 -18.07 -7.53 6.85e+00 1di1A 300 -19.35 -7.22 8.31e+00 1tuhA 156 -16.87 -7.22 8.34e+00 1iwhA 141 -18.39 -7.00 9.58e+00 1dpsA 167 -23.00 -6.98 9.71e+00 1h96A 182 -23.14 -6.78 1.11e+01 1umnA 165 -21.62 -6.69 1.17e+01 1iomA 377 -18.21 -6.65 1.20e+01 1hl2A 297 -20.13 -6.53 1.30e+01 1e2aA 105 -20.94 -6.52 1.31e+01 3ertA 261 -21.04 -6.52 1.31e+01 1f5nA 592 -27.31 -6.51 1.32e+01 1hkxA 147 -16.20 -6.49 1.34e+01 1lb3A 182 -22.12 -6.48 1.35e+01 1fkmA 396 -18.11 -6.47 1.36e+01 2ran 316 -17.15 -6.45 1.37e+01 1rxwA 336 -17.44 -6.40 1.42e+01 1b43A 340 -18.66 -6.38 1.44e+01 2e2aA 105 -21.69 -6.37 1.45e+01 1n7sA 63 -23.61 -6.09 1.75e+01 1m2tA 254 -16.19 -6.08 1.76e+01 1bf5A 545 -28.78 -6.04 1.80e+01 1th8A 145 -15.59 -5.90 1.99e+01 1o0wA 252 -18.82 -5.89 2.01e+01 1db1A 259 -19.24 -5.88 2.02e+01 1n5uA 585 -22.28 -5.78 2.16e+01 1fm9D 272 -21.02 -5.78 2.16e+01 1a8b 318 -16.42 -5.78 2.16e+01 1p36A 164 -16.69 -5.74 2.23e+01 1g87A 614 -17.00 -5.69 2.30e+01 1pq1B 33 -17.47 -5.66 2.35e+01 1ka2A 499 -24.36 -5.63 2.39e+01 1h6gA 256 -32.25 -5.62 2.40e+01 1p3qQ 54 -15.61 -5.61 2.42e+01 1kn1A 160 -19.77 -5.61 2.43e+01 1w0bA 102 -18.99 -5.58 2.48e+01 1oaoA 674 -17.70 -5.57 2.50e+01 1pd21 199 -18.07 -5.56 2.52e+01 1rqjA 299 -18.97 -5.45 2.71e+01 119l 164 -16.54 -5.39 2.83e+01 1q5nA 454 -18.36 -5.37 2.87e+01 1r4uA 301 -14.49 -5.37 2.87e+01 1uox 296 -14.52 -5.36 2.89e+01 1gqeA 365 -26.21 -5.36 2.89e+01 7aatA 401 -16.53 -5.32 2.97e+01 1elkA 157 -18.47 -5.21 3.21e+01 1vf6C 72 -15.91 -5.21 3.23e+01 1hg4A 279 -19.90 -5.18 3.30e+01 1eb6A 177 -14.96 -5.15 3.37e+01 1fh0A 221 -13.09 -5.10 3.48e+01 1e7aA 585 -22.08 -5.10 3.49e+01 1bpoA 494 -15.97 -5.07 3.56e+01 1orjA 130 -27.16 -5.07 3.56e+01 1or4A 178 -20.12 -5.01 3.72e+01 1ie9A 259 -17.67 -5.00 3.75e+01 1gcvA 140 -16.23 -4.99 3.75e+01 1khbA 625 -15.17 -4.99 3.78e+01 1s5aA 150 -14.93 -4.98 3.79e+01 1k32A 1045 -15.71 -4.98 3.81e+01 1xgsA 295 -15.68 -4.97 3.83e+01 1cnt1 187 -19.01 -4.94 3.91e+01 5ukdA 194 -15.57 -4.93 3.94e+01