% 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.T0196.t04-100-30-str2 Host: cheep Tue Jun 15 22:05:56 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0196 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.str2s % % 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 T0196.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0196.t04.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6473 sequences, 1530840 residues, 117 nodes, 39.50 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 (=9907) sequences: % N / (1 + exp(-(lambda(=1.7420) * Reverse)^tau(=0.7820))) % 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 1jnyA 435 -48.59 -35.97 9.03e-08 1g7sA 594 -41.01 -28.28 7.08e-06 1f60A 458 -37.13 -24.58 6.29e-05 1exmA 405 -34.61 -19.55 1.39e-03 1ha3A 405 -33.49 -18.69 2.40e-03 1d2eA 397 -32.25 -17.60 4.81e-03 1h8eA 510 -23.69 -11.78 2.42e-01 1e79A 510 -23.98 -11.63 2.69e-01 1f1gA 154 -22.49 -11.12 3.87e-01 1jcv 153 -22.28 -10.94 4.41e-01 1n0uA 842 -22.62 -10.55 5.82e-01 1tib 269 -20.20 -10.34 6.77e-01 1d1nA 99 -20.84 -9.81 9.98e-01 1gt6A 269 -19.72 -9.71 1.08e+00 1njkA 156 -22.74 -9.27 1.48e+00 1uvqB 198 -21.05 -9.15 1.62e+00 1ogsA 497 -22.37 -9.04 1.77e+00 1mp9A 198 -20.21 -8.88 1.99e+00 1b5fB 87 -17.62 -8.81 2.09e+00 1ly2A 130 -17.98 -8.72 2.24e+00 1hh2P 344 -19.13 -8.61 2.43e+00 1dar 691 -20.86 -8.47 2.71e+00 1uj2A 252 -16.58 -8.43 2.80e+00 1hdmA 201 -20.93 -8.36 2.95e+00 1nb5I 98 -21.47 -8.18 3.37e+00 1fmtA 314 -18.65 -8.16 3.41e+00 1eazA 125 -18.33 -7.93 4.09e+00 1at0 145 -20.86 -7.71 4.85e+00 1qz5A 375 -16.81 -7.65 5.09e+00 1ddwA 120 -20.65 -7.60 5.27e+00 1ghqB 134 -16.49 -7.46 5.88e+00 1bwwA 109 -16.94 -7.41 6.13e+00 1qqgA 264 -17.64 -7.27 6.82e+00 1chuA 540 -15.88 -7.21 7.17e+00 1e1oA 504 -19.08 -7.20 7.20e+00 1j6zA 376 -16.18 -7.17 7.35e+00 1mq7A 154 -20.88 -7.01 8.38e+00 1vhoA 346 -17.43 -7.00 8.44e+00 1kk1A 410 -24.87 -6.99 8.52e+00 1sixA 174 -17.88 -6.90 9.11e+00 1gppA 237 -21.06 -6.87 9.32e+00 1uwcA 261 -16.87 -6.86 9.45e+00 1k4nA 192 -18.13 -6.85 9.49e+00 1iznA 286 -21.15 -6.78 1.00e+01 1uxzA 131 -20.28 -6.74 1.03e+01 1gv9A 260 -21.11 -6.68 1.09e+01 2sli 679 -21.92 -6.67 1.10e+01 1fxjA 331 -14.97 -6.60 1.15e+01 1lvwA 295 -17.32 -6.58 1.18e+01 1st0A 337 -17.60 -6.50 1.25e+01 1psuA 140 -18.47 -6.45 1.31e+01 1iq8A 582 -18.05 -6.44 1.32e+01 1lw6I 64 -14.32 -6.43 1.32e+01 1pyaB 228 -18.60 -6.42 1.33e+01 1ah6 220 -18.10 -6.39 1.37e+01 1h9dB 134 -17.39 -6.35 1.42e+01 1p7tA 731 -22.23 -6.32 1.44e+01 1lylA 504 -18.66 -6.26 1.52e+01 1dq3A 454 -23.91 -6.24 1.55e+01 1ei5A 520 -19.63 -6.22 1.57e+01 1iwdA 215 -17.09 -6.19 1.61e+01 1blxA 326 -17.26 -6.17 1.63e+01 1qwyA 291 -17.50 -6.16 1.65e+01 1rovA 857 -18.36 -6.15 1.66e+01 1ytfC 79 -18.63 -6.15 1.67e+01 1aun 208 -16.56 -6.14 1.68e+01 1ln1A 214 -19.32 -6.10 1.73e+01 1k82A 268 -16.71 -6.02 1.85e+01 1g6eA 87 -15.37 -5.93 1.98e+01 1ogpA 393 -16.40 -5.92 2.01e+01 1kyfA 247 -19.41 -5.91 2.03e+01 1gpr 162 -16.79 -5.87 2.09e+01 1go3E 187 -18.98 -5.86 2.12e+01 1brwA 433 -14.56 -5.83 2.15e+01 1tia 279 -13.78 -5.83 2.15e+01 1pvmA 184 -14.76 -5.83 2.16e+01 1nh2C 79 -18.30 -5.81 2.20e+01 6cel 434 -17.87 -5.73 2.34e+01 1h6lA 353 -19.82 -5.72 2.35e+01 1q5hA 147 -21.19 -5.68 2.44e+01 1aonO 97 -15.53 -5.67 2.46e+01 1ifrA 121 -16.73 -5.65 2.50e+01 1q2bA 434 -18.46 -5.64 2.53e+01 1ewfA 456 -22.41 -5.63 2.54e+01 1lvmA 229 -17.46 -5.57 2.68e+01 1t8hA 277 -15.00 -5.54 2.74e+01 1i9zA 347 -19.54 -5.52 2.79e+01 2hgsA 474 -19.64 -5.51 2.80e+01 3rabA 169 -15.27 -5.50 2.82e+01 1m26A 133 -18.60 -5.50 2.83e+01 1hv9A 456 -13.79 -5.50 2.84e+01 1itwA 741 -16.32 -5.49 2.85e+01 1cq3A 233 -20.32 -5.49 2.86e+01 1egnA 434 -17.73 -5.47 2.90e+01 1f3lA 321 -17.04 -5.46 2.93e+01 1nnxA 109 -20.08 -5.43 3.01e+01 1ae9A 179 -13.36 -5.40 3.09e+01 1cv8 174 -17.07 -5.39 3.10e+01 1pk6B 132 -19.45 -5.36 3.20e+01 1gwyA 175 -19.02 -5.33 3.26e+01 1jyhA 157 -15.92 -5.29 3.37e+01 1jpaA 312 -16.26 -5.27 3.42e+01 1n7vA 555 -18.28 -5.27 3.44e+01 1em2A 229 -18.31 -5.26 3.48e+01 1d5tA 433 -16.91 -5.25 3.48e+01 1qtsA 247 -18.73 -5.24 3.54e+01 1cr1A 296 -15.04 -5.18 3.70e+01 1i8dA 213 -15.91 -5.18 3.70e+01 2sfa 191 -16.41 -5.17 3.73e+01 2bltA 361 -15.79 -5.15 3.81e+01 1cl1A 395 -13.43 -5.15 3.81e+01 1mqeA 207 -16.69 -5.14 3.84e+01