% 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.T0231.t04-100-30-dssp-ehl2 Host: cheep Thu Jul 8 10:32:32 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0231 % --------------------------------------------------------------------- % 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 T0231.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0231.t04.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6593 sequences, 1557114 residues, 143 nodes, 54.25 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(=1.1887) * Reverse)^tau(=0.8542))) % 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 1v6fA 151 -142.05 -122.21 2.97e-27 1f7sA 139 -140.99 -121.47 4.26e-27 1hqz1 141 -107.35 -89.96 3.18e-20 1m4jA 142 -113.45 -89.79 3.46e-20 1udmA 149 -76.79 -64.07 2.60e-14 1p1cA 199 -23.22 -12.67 3.96e-01 1gtmA 419 -24.74 -12.44 4.63e-01 1jkgA 140 -24.13 -11.88 6.78e-01 1hjrA 158 -22.62 -11.74 7.51e-01 1qcxA 359 -22.79 -11.44 9.25e-01 1svy 114 -22.41 -11.31 1.01e+00 1qy5A 269 -22.60 -10.94 1.31e+00 1ex2A 189 -20.73 -10.90 1.34e+00 1nmeA 146 -23.25 -10.75 1.49e+00 1mai 131 -21.55 -10.27 2.10e+00 1a88A 275 -20.10 -10.10 2.35e+00 1p8xA 344 -24.72 -9.83 2.85e+00 1odzA 386 -19.91 -9.67 3.20e+00 1j7lA 264 -20.96 -9.58 3.40e+00 1h2wA 710 -24.10 -9.35 4.01e+00 1qfmA 710 -24.10 -9.35 4.01e+00 1gnd 447 -20.07 -9.31 4.14e+00 1fe0A 68 -20.83 -9.30 4.15e+00 1a99A 344 -19.45 -9.28 4.22e+00 1qd1A 325 -22.67 -9.22 4.41e+00 1qo7A 394 -21.47 -9.10 4.78e+00 1o6sB 105 -21.22 -9.10 4.79e+00 1acc 735 -20.08 -9.09 4.84e+00 1ixmA 192 -20.59 -9.07 4.89e+00 1pvgA 418 -21.55 -9.05 4.97e+00 1o2dA 371 -21.93 -9.04 5.02e+00 1j9yA 385 -19.81 -9.00 5.17e+00 1r6uA 437 -19.41 -8.99 5.20e+00 1l2tA 235 -22.75 -8.78 6.02e+00 1lci 550 -23.12 -8.78 6.04e+00 1xgsA 295 -20.48 -8.63 6.75e+00 1lhpA 312 -19.60 -8.56 7.06e+00 1f9aA 168 -20.04 -8.56 7.11e+00 1idk 359 -20.26 -8.49 7.43e+00 1h1aA 191 -20.08 -8.42 7.82e+00 1nm1G 125 -23.88 -8.42 7.82e+00 1d4xG 126 -23.87 -8.42 7.83e+00 1qqqA 264 -22.31 -8.31 8.48e+00 1uayA 242 -19.28 -8.22 9.08e+00 1evfA 264 -21.97 -8.17 9.38e+00 1a8s 273 -18.09 -8.05 1.03e+01 1ddmA 135 -19.07 -8.03 1.04e+01 1ho1A 242 -17.95 -8.02 1.05e+01 1ivnA 190 -18.90 -7.92 1.12e+01 1pg4A 652 -21.28 -7.86 1.18e+01 1mdbA 539 -20.43 -7.79 1.24e+01 1dz3A 130 -21.32 -7.76 1.27e+01 1hnnA 282 -16.91 -7.64 1.38e+01 1ufoA 238 -18.25 -7.60 1.42e+01 1mu5A 471 -19.45 -7.53 1.50e+01 1r0wA 286 -19.73 -7.46 1.59e+01 1jd0A 263 -19.51 -7.43 1.62e+01 1ujxA 119 -16.92 -7.39 1.67e+01 1p2fA 220 -20.40 -7.34 1.73e+01 1k32A 1045 -21.87 -7.28 1.80e+01 1o5oA 221 -21.14 -7.25 1.85e+01 1qmpA 130 -20.74 -7.15 1.98e+01 1pytA 94 -16.42 -7.14 2.00e+01 1qqp2 218 -20.52 -7.12 2.04e+01 1fgkA 310 -19.63 -7.02 2.19e+01 1i58A 189 -20.73 -6.99 2.24e+01 1owqA 361 -16.79 -6.97 2.27e+01 1i4wA 353 -17.92 -6.97 2.27e+01 1b0pA 1231 -18.47 -6.94 2.33e+01 1j0aA 325 -20.34 -6.93 2.35e+01 1burS 123 -20.99 -6.91 2.38e+01 1o8xA 146 -18.21 -6.90 2.40e+01 1cvrA 435 -19.13 -6.87 2.44e+01 1p9qC 256 -19.18 -6.86 2.47e+01 1hjxA 362 -16.62 -6.83 2.52e+01 1cc8A 73 -17.91 -6.80 2.58e+01 1ucaA 190 -16.15 -6.71 2.76e+01 1ucdA 190 -16.15 -6.71 2.77e+01 1s3zA 165 -16.78 -6.71 2.77e+01 1bk7A 190 -16.15 -6.69 2.80e+01 1sviA 195 -17.83 -6.69 2.80e+01 1d5tA 433 -19.14 -6.67 2.84e+01 1kekA 1231 -18.48 -6.65 2.89e+01 1n8jA 186 -19.38 -6.65 2.89e+01 1jenA 267 -21.40 -6.63 2.92e+01 1ohvA 472 -17.65 -6.61 2.97e+01 1mml 265 -17.36 -6.59 3.01e+01 1j1bA 420 -20.08 -6.57 3.06e+01 1j3wA 163 -18.85 -6.57 3.06e+01 1crzA 403 -20.23 -6.57 3.07e+01 1byqA 228 -18.58 -6.55 3.10e+01 4uagA 437 -17.09 -6.54 3.14e+01 1ecfA 504 -18.86 -6.52 3.18e+01 1kepA 348 -19.27 -6.52 3.18e+01 1oc2A 348 -19.27 -6.52 3.18e+01 1jzuA 157 -18.25 -6.52 3.19e+01 1fvuA 133 -16.32 -6.51 3.22e+01 1f0xA 571 -18.81 -6.49 3.26e+01 1b00A 127 -18.01 -6.46 3.34e+01 1pxgA 382 -16.55 -6.44 3.38e+01 1r5yA 386 -16.51 -6.43 3.41e+01 1skoB 130 -21.75 -6.40 3.49e+01 1qk8A 146 -18.14 -6.38 3.54e+01 1e4yA 214 -15.54 -6.37 3.56e+01 1bbt1 213 -16.91 -6.37 3.56e+01 1l3aA 228 -17.65 -6.37 3.57e+01 1jj2H 167 -19.10 -6.36 3.58e+01 1l3kA 196 -19.05 -6.35 3.62e+01 1n7oA 721 -19.47 -6.34 3.63e+01 1b7yA 350 -18.26 -6.33 3.68e+01 1jl0A 334 -20.52 -6.32 3.69e+01 1kjwA 295 -16.81 -6.30 3.75e+01 1elt 236 -16.52 -6.30 3.76e+01 1qtnA 164 -21.65 -6.29 3.77e+01 1bo4A 168 -17.84 -6.28 3.81e+01 1ako 268 -17.06 -6.26 3.88e+01 1t95A 240 -17.73 -6.25 3.90e+01 1kjnA 157 -17.81 -6.23 3.97e+01