% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 07/18/04_06:53:46 % (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.T0252.t04-100-30-dssp-ehl2 Host: crow Tue Jul 27 12:35:47 2004 % ggshack Dir: /projects/compbio/experiments/protein-predict/casp6/T0252 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.dssps % % 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 T0252.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0252.t04.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6648 sequences, 1569757 residues, 311 nodes, 72.14 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 (=10083) sequences: % N / (1 + exp(-(lambda(=1.3350) * Reverse)^tau(=0.7665))) % 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 1mkiA 330 -303.33 -288.79 2.05e-38 1i2sA 282 -38.33 -26.44 2.15e-03 4blmA 265 -35.93 -24.27 5.71e-03 1ghpA 258 -33.19 -21.19 2.36e-02 1iysA 262 -31.59 -20.64 3.06e-02 1bza 262 -30.91 -20.01 4.13e-02 1hzoA 271 -26.90 -14.15 7.45e-01 1bsg 266 -25.04 -14.14 7.48e-01 1e25A 282 -27.31 -13.78 9.05e-01 1qq5A 253 -24.97 -13.74 9.22e-01 1qq7A 253 -24.98 -13.67 9.54e-01 1pjjA 271 -25.58 -13.37 1.12e+00 1fw9A 164 -22.95 -13.23 1.20e+00 1bueA 265 -26.49 -13.04 1.33e+00 1g6aA 271 -24.99 -12.72 1.58e+00 1fcyA 236 -25.22 -12.58 1.69e+00 2sqcA 631 -26.13 -12.51 1.76e+00 1ouvA 273 -26.84 -11.79 2.58e+00 1pd21 199 -23.78 -11.60 2.86e+00 1klxA 138 -30.57 -11.46 3.08e+00 1odoA 408 -25.15 -11.46 3.08e+00 1nnjA 271 -25.76 -11.37 3.23e+00 1top 162 -25.24 -11.33 3.31e+00 1n9bA 265 -24.45 -11.02 3.92e+00 1keaA 221 -22.68 -10.70 4.68e+00 1j1jA 240 -24.31 -10.51 5.17e+00 1uw4B 248 -24.95 -10.36 5.64e+00 1eguA 731 -25.30 -10.25 5.99e+00 1qwlA 505 -21.65 -10.17 6.26e+00 1auiB 169 -26.10 -10.08 6.58e+00 1ad4A 266 -21.06 -9.86 7.46e+00 16pk 415 -23.38 -9.64 8.44e+00 1qmeA 702 -21.35 -9.63 8.47e+00 1dgfA 497 -21.01 -9.56 8.82e+00 1uocA 289 -21.58 -9.54 8.93e+00 1nq7A 244 -22.76 -9.43 9.49e+00 1q2wA 308 -20.52 -9.42 9.52e+00 1oshA 232 -27.60 -9.41 9.57e+00 1m7sA 484 -20.66 -9.34 9.95e+00 1n7oA 721 -24.15 -9.32 1.01e+01 1gpr 162 -20.08 -9.18 1.09e+01 1ei5A 520 -22.31 -9.13 1.12e+01 1k8kD 300 -22.73 -9.08 1.16e+01 1is1A 185 -22.44 -9.06 1.17e+01 1iyhA 198 -22.54 -9.06 1.17e+01 1cqqA 180 -21.66 -9.06 1.17e+01 1mtyD 512 -24.05 -9.00 1.21e+01 1ad1A 266 -20.51 -8.89 1.29e+01 1k38A 254 -20.12 -8.79 1.37e+01 1fm9D 272 -23.69 -8.78 1.38e+01 1ezvD 245 -20.86 -8.77 1.38e+01 1euvA 221 -21.18 -8.77 1.38e+01 1ermA 263 -23.07 -8.75 1.40e+01 1m40A 263 -22.99 -8.68 1.45e+01 1k82A 268 -19.55 -8.68 1.46e+01 1o7eA 276 -19.33 -8.66 1.47e+01 1el4A 195 -20.65 -8.64 1.49e+01 1b8dA 164 -23.27 -8.62 1.50e+01 1btl 263 -22.92 -8.60 1.53e+01 1kktA 511 -22.02 -8.46 1.65e+01 1uch 230 -24.97 -8.38 1.73e+01 1dxrL 273 -22.29 -8.22 1.90e+01 1d5rA 324 -20.12 -8.16 1.97e+01 1qv1A 195 -20.41 -8.13 2.00e+01 1bu7A 455 -22.89 -8.06 2.09e+01 1mwxA 646 -21.24 -8.04 2.11e+01 1np3A 338 -23.45 -8.01 2.15e+01 1kkhA 317 -21.30 -8.00 2.17e+01 1gal 583 -19.17 -7.94 2.24e+01 1uwzA 136 -19.16 -7.90 2.30e+01 1kb9D 246 -20.29 -7.81 2.41e+01 1q5dA 419 -23.16 -7.80 2.43e+01 1d7uA 433 -20.57 -7.78 2.46e+01 1omhA 293 -18.38 -7.78 2.46e+01 1ek8A 185 -20.87 -7.67 2.62e+01 1mp1A 111 -19.18 -7.66 2.64e+01 1o4sA 389 -22.75 -7.59 2.75e+01 4crxA 322 -19.86 -7.59 2.75e+01 1k0dA 260 -20.76 -7.55 2.82e+01 1r31A 428 -19.28 -7.52 2.86e+01 1e7uA 961 -25.99 -7.50 2.91e+01 1dfoA 417 -19.05 -7.49 2.93e+01 1spgA 144 -20.63 -7.37 3.13e+01 1cf9A 753 -18.43 -7.32 3.24e+01 1jf2A 195 -20.53 -7.31 3.25e+01 1dceB 331 -18.40 -7.29 3.29e+01 2dkb 433 -20.33 -7.24 3.39e+01 1jpzA 473 -21.34 -7.21 3.45e+01 1qazA 351 -19.70 -7.00 3.92e+01 2bltA 361 -18.21 -6.98 3.97e+01