% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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.T0226.t04-100-30-alpha Host: peep Tue Jul 6 14:13:08 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0226 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.alphas % % 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 T0226.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0226.t04.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6593 sequences, 1557114 residues, 291 nodes, 57.57 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 (=10028) sequences: % N / (1 + exp(-(lambda(=1.7853) * Reverse)^tau(=0.7216))) % 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 1c7qA 445 -227.57 -210.44 4.75e-28 1iatA 557 -58.28 -45.80 3.79e-07 1j5xA 342 -29.55 -18.69 3.49e-02 1moq 368 -28.35 -17.30 6.89e-02 1e8cA 498 -25.24 -13.88 3.97e-01 1vimA 200 -25.92 -12.25 9.46e-01 1o58A 303 -24.71 -12.22 9.63e-01 1hq0A 295 -24.65 -11.99 1.09e+00 1bupA 386 -22.70 -11.65 1.32e+00 1hyeA 313 -24.01 -11.61 1.35e+00 1ad2 228 -22.39 -11.46 1.47e+00 1kay 381 -22.43 -11.43 1.49e+00 1lqtA 456 -23.19 -11.40 1.52e+00 1ur5A 309 -22.91 -11.38 1.54e+00 1m6jA 261 -23.28 -11.25 1.65e+00 1qv9A 283 -24.24 -11.23 1.67e+00 1iz6A 138 -21.23 -11.05 1.84e+00 1mtzA 293 -22.20 -11.03 1.86e+00 1nksA 194 -23.29 -11.03 1.86e+00 1t35A 191 -22.61 -10.67 2.29e+00 1jeoA 180 -23.29 -10.60 2.38e+00 1sxjE 354 -22.23 -10.54 2.46e+00 1kyqA 274 -21.54 -10.53 2.48e+00 1b0uA 262 -21.68 -10.47 2.56e+00 1eziA 228 -22.08 -10.18 3.03e+00 1iv8A 720 -21.60 -9.55 4.37e+00 1hvyA 288 -19.84 -9.54 4.37e+00 1eljA 381 -21.59 -9.50 4.49e+00 1uypA 432 -21.88 -9.47 4.57e+00 1uouA 474 -20.24 -9.36 4.86e+00 1r3eA 309 -19.50 -9.29 5.06e+00 1m6yA 301 -20.09 -9.08 5.74e+00 1ghj 79 -19.21 -9.01 6.00e+00 1us5A 314 -18.78 -8.97 6.11e+00 1pkhA 204 -20.02 -8.92 6.29e+00 4pfk 319 -21.39 -8.72 7.12e+00 1hxhA 253 -19.40 -8.66 7.37e+00 1o22A 170 -20.33 -8.65 7.42e+00 1dxeA 256 -20.88 -8.60 7.65e+00 1rwzA 245 -20.73 -8.55 7.90e+00 1f0xA 571 -21.33 -8.55 7.90e+00 1gpmA 525 -20.98 -8.52 8.03e+00 1dkuA 317 -20.79 -8.49 8.19e+00 1hmt 132 -20.89 -8.43 8.47e+00 1rqpA 299 -18.53 -8.40 8.64e+00 1o5uA 101 -18.40 -8.38 8.73e+00 1rg9A 383 -18.90 -8.34 8.94e+00 1udxA 416 -19.58 -8.34 8.97e+00 1qh8A 478 -20.23 -8.15 1.01e+01 1iw7C 1119 -19.46 -8.08 1.05e+01 1b0pA 1231 -20.61 -7.96 1.13e+01 1q1gA 276 -18.89 -7.91 1.16e+01 1nytA 271 -19.10 -7.81 1.23e+01 1tml 286 -18.58 -7.79 1.25e+01 1ni9A 338 -18.79 -7.70 1.33e+01 1d2fA 390 -18.65 -7.56 1.45e+01 1iq6A 134 -17.03 -7.52 1.48e+01 1lh0A 213 -19.33 -7.45 1.55e+01 1p5fA 189 -18.74 -7.41 1.59e+01 1c8bA 371 -18.99 -7.40 1.60e+01 1l3iA 192 -20.10 -7.37 1.62e+01 1e79A 510 -20.55 -7.32 1.68e+01 1h65A 270 -19.62 -7.19 1.82e+01 1bv1 159 -18.57 -7.18 1.83e+01 1fm4A 159 -18.35 -7.16 1.85e+01 1lylA 504 -18.01 -7.16 1.86e+01 1oroA 213 -19.24 -7.09 1.94e+01 1m2tB 263 -18.01 -7.08 1.95e+01 1sig 339 -18.99 -7.06 1.98e+01 1q9uA 130 -17.80 -7.02 2.02e+01 1od5A 492 -19.71 -6.95 2.12e+01 1bkb 136 -16.66 -6.95 2.12e+01 1eajA 126 -18.89 -6.85 2.26e+01 1oi7A 288 -19.52 -6.83 2.30e+01 1rc6A 261 -17.85 -6.82 2.30e+01 1pbgA 468 -17.74 -6.80 2.34e+01 1a8l 226 -18.91 -6.78 2.36e+01 1mnaA 298 -19.16 -6.76 2.40e+01 1i7pA 274 -18.14 -6.75 2.41e+01 1h8eA 510 -19.60 -6.75 2.41e+01 1mv8A 436 -18.68 -6.71 2.48e+01 1sf8A 126 -17.13 -6.71 2.48e+01 1jjvA 206 -17.18 -6.69 2.50e+01 1f0kA 364 -21.70 -6.69 2.52e+01 1vjrA 271 -17.31 -6.67 2.54e+01 1g7nA 131 -20.17 -6.67 2.54e+01 8fabA 212 -16.37 -6.66 2.56e+01 1oxxK 353 -18.23 -6.65 2.57e+01 1e1oA 504 -17.63 -6.65 2.57e+01 1agi 125 -16.47 -6.62 2.62e+01 1o4wA 147 -17.31 -6.61 2.65e+01 1p0hA 318 -18.20 -6.60 2.66e+01 1dp4A 435 -19.22 -6.50 2.84e+01 6ldh 330 -18.17 -6.49 2.86e+01 1gsa 316 -16.93 -6.47 2.90e+01 1oxsC 353 -17.87 -6.44 2.95e+01 1jbiA 100 -16.66 -6.44 2.96e+01 1k2yX 463 -18.23 -6.43 2.98e+01 1p5dX 463 -18.62 -6.42 2.98e+01 1cydA 244 -17.31 -6.40 3.03e+01 1q7hA 153 -15.96 -6.40 3.04e+01 1tlk 154 -17.42 -6.38 3.06e+01 1lid 131 -20.28 -6.38 3.07e+01 1a12A 413 -18.32 -6.36 3.10e+01 1j08A 226 -19.48 -6.35 3.12e+01 2cmd 312 -19.75 -6.35 3.13e+01 1nrlA 316 -17.71 -6.35 3.13e+01 1paqA 189 -18.07 -6.32 3.19e+01 1qs1A 462 -18.52 -6.31 3.21e+01 1fhgA 154 -17.20 -6.28 3.28e+01 1jayA 212 -16.42 -6.28 3.28e+01 1je0A 236 -16.15 -6.27 3.30e+01 1cnzA 363 -17.47 -6.26 3.31e+01 1dofA 403 -18.90 -6.26 3.31e+01 1kwgA 645 -16.59 -6.21 3.42e+01 1gqpA 221 -18.45 -6.21 3.44e+01 2masA 314 -16.88 -6.21 3.44e+01 1f20A 435 -18.00 -6.20 3.45e+01 1mk0A 97 -16.10 -6.20 3.46e+01 3daaA 277 -19.10 -6.19 3.46e+01 1rybA 212 -16.46 -6.17 3.51e+01 1nxzA 246 -17.22 -6.15 3.57e+01 1q15A 503 -17.11 -6.12 3.64e+01 1pjxA 314 -17.70 -6.11 3.65e+01 1rx0A 393 -19.08 -6.11 3.66e+01 1gnuA 117 -17.63 -6.10 3.68e+01 1e1aA 314 -17.70 -6.10 3.69e+01 1nogA 177 -18.39 -6.10 3.69e+01 1ptvA 321 -16.47 -6.09 3.71e+01 1fohA 664 -17.99 -6.07 3.75e+01 1o50A 157 -16.71 -6.07 3.76e+01 1st9A 143 -16.54 -6.06 3.79e+01 1p77A 272 -16.29 -6.06 3.79e+01 1afwA 393 -16.16 -6.01 3.91e+01 1n57A 291 -16.39 -5.99 3.97e+01 1kekA 1231 -18.83 -5.98 3.99e+01