% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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.T0274.t04-100-30-bys Host: caw Wed Aug 11 11:28:33 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0274 % --------------------------------------------------------------------- % 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 T0274.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0274.t04.bys.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6749 sequences, 1593535 residues, 160 nodes, 40.42 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 (=10183) sequences: % N / (1 + exp(-(lambda(=2.8249) * Reverse)^tau(=0.7056))) % 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 1rz1A 161 -139.88 -130.33 8.43e-25 1ejeA 192 -122.44 -113.61 3.30e-22 1uscA 178 -114.18 -104.97 8.00e-21 1i0rA 169 -112.67 -104.35 1.01e-20 1i0sA 169 -111.93 -103.38 1.45e-20 1d1gA 168 -22.87 -12.66 3.88e-02 1rxxA 421 -20.43 -11.61 8.14e-02 1fhgA 154 -20.63 -11.13 1.15e-01 1ne2A 200 -20.11 -10.71 1.56e-01 1go3E 187 -17.84 -8.62 7.54e-01 1tlk 154 -17.99 -8.61 7.58e-01 1krhA 338 -18.11 -8.34 9.35e-01 1s9rA 410 -16.74 -8.11 1.12e+00 1p6oA 161 -16.12 -7.85 1.38e+00 1smvA 260 -17.36 -7.71 1.55e+00 1mkyA 439 -19.65 -7.63 1.65e+00 1vcaA 202 -16.49 -7.55 1.76e+00 1ax4A 467 -15.66 -7.26 2.22e+00 1hxs1 302 -16.26 -7.17 2.40e+00 1flmA 122 -16.23 -7.04 2.66e+00 1zpdA 568 -16.08 -7.04 2.67e+00 1i3cA 149 -15.57 -6.96 2.84e+00 1dcfA 136 -15.40 -6.95 2.89e+00 1i58A 189 -15.93 -6.86 3.09e+00 1mngA 203 -15.67 -6.70 3.53e+00 1pjqA 457 -15.30 -6.68 3.60e+00 1c4eA 35 -14.23 -6.58 3.93e+00 1ooeA 236 -15.35 -6.54 4.06e+00 1jb3A 131 -15.02 -6.47 4.28e+00 1ytw 306 -14.83 -6.44 4.41e+00 1cydA 244 -14.74 -6.38 4.63e+00 1o98A 511 -16.03 -6.35 4.75e+00 1gmxA 108 -14.48 -6.34 4.78e+00 1eqjA 511 -15.81 -6.24 5.22e+00 1quqB 121 -16.27 -6.23 5.25e+00 1e19A 314 -15.15 -6.15 5.62e+00 1cuk 203 -14.46 -6.12 5.80e+00 1ekeA 230 -16.82 -6.06 6.12e+00 1jdw 423 -15.47 -6.02 6.29e+00 1f06A 320 -15.26 -5.90 6.99e+00 1nox 205 -13.73 -5.76 7.92e+00 1k9sA 237 -15.01 -5.76 7.94e+00 1iakA 199 -15.43 -5.68 8.47e+00 1zxq 192 -14.98 -5.68 8.51e+00 1devB 41 -13.38 -5.65 8.72e+00 1hywA 68 -13.30 -5.65 8.72e+00 1iscA 192 -14.04 -5.63 8.89e+00 1jnyA 435 -15.11 -5.58 9.26e+00 1fthA 122 -13.91 -5.49 1.01e+01 1kkcA 221 -14.07 -5.48 1.02e+01 2bltA 361 -14.12 -5.43 1.06e+01 1o8vA 134 -14.95 -5.42 1.07e+01 1t0hB 224 -14.01 -5.42 1.07e+01 1pxvA 183 -14.44 -5.38 1.10e+01 1fs7A 485 -13.49 -5.35 1.14e+01 1nx8A 273 -14.26 -5.24 1.25e+01 1my6A 199 -13.25 -5.22 1.28e+01 1h1wA 289 -13.41 -5.19 1.31e+01 1o13A 136 -13.47 -5.18 1.33e+01 3hhrB 203 -13.41 -5.15 1.36e+01 1vjuA 309 -15.92 -5.15 1.37e+01 1gmlA 178 -13.73 -5.07 1.47e+01 1din 236 -13.03 -5.02 1.53e+01 1twiA 434 -13.96 -4.98 1.59e+01 1ecpA 238 -14.02 -4.96 1.63e+01 1ha3A 405 -15.05 -4.94 1.65e+01 1iqoA 88 -13.17 -4.94 1.65e+01 1vhsA 175 -12.99 -4.93 1.67e+01 1r9hA 135 -12.97 -4.92 1.68e+01 1nzhA 282 -14.03 -4.92 1.69e+01 1j9bA 141 -12.86 -4.91 1.69e+01 1kzyC 259 -13.48 -4.89 1.72e+01 1l9xA 315 -13.33 -4.86 1.77e+01 1iq6A 134 -12.97 -4.86 1.77e+01 1ok8A 394 -14.86 -4.84 1.80e+01 1kwmA 402 -13.07 -4.83 1.82e+01 1lyvA 306 -13.32 -4.80 1.87e+01 1ad3A 452 -13.45 -4.80 1.88e+01 1fyxA 149 -13.29 -4.78 1.91e+01 1pswA 348 -13.36 -4.78 1.91e+01 1bg2 325 -14.87 -4.78 1.91e+01 1n5dA 288 -13.18 -4.75 1.96e+01 2bbkH 355 -13.35 -4.71 2.03e+01 1n57A 291 -12.99 -4.71 2.03e+01 1n2zA 245 -13.18 -4.70 2.06e+01 1rgyA 360 -13.92 -4.69 2.07e+01 1hu4A 288 -13.09 -4.67 2.11e+01 1l0wA 580 -13.71 -4.65 2.15e+01 1uzxA 169 -13.81 -4.63 2.19e+01 1sl4A 155 -14.92 -4.62 2.21e+01 1n1bA 549 -13.06 -4.62 2.22e+01 1toaA 313 -13.00 -4.59 2.28e+01 1uj6A 227 -14.69 -4.58 2.30e+01 1eg5A 384 -14.18 -4.57 2.33e+01 1igs 248 -12.83 -4.56 2.35e+01 1a53 247 -12.82 -4.56 2.35e+01 1uu3A 310 -12.96 -4.56 2.36e+01 5ukdA 194 -13.59 -4.54 2.39e+01 1i24A 404 -13.28 -4.53 2.41e+01 1gt1A 159 -13.09 -4.52 2.44e+01 1obpA 159 -13.22 -4.50 2.48e+01 1hn2A 159 -13.07 -4.46 2.57e+01 1e58A 249 -14.34 -4.46 2.59e+01 1pfsA 78 -15.72 -4.45 2.59e+01 1b1cA 181 -12.88 -4.42 2.67e+01 1bdo 80 -12.28 -4.38 2.77e+01 1oaiA 59 -11.72 -4.37 2.80e+01 1a9xB 379 -13.75 -4.37 2.80e+01 1ixlA 131 -13.13 -4.36 2.84e+01 1iirA 415 -13.24 -4.35 2.86e+01 1poiA 317 -13.28 -4.33 2.91e+01 1kk1A 410 -13.34 -4.33 2.91e+01 1lrzA 426 -13.48 -4.25 3.15e+01 1stfI 98 -12.34 -4.24 3.17e+01 1cqqA 180 -13.41 -4.24 3.19e+01 1i36A 264 -12.81 -4.23 3.22e+01 1jcfA 344 -13.30 -4.21 3.28e+01 1i2kA 269 -13.26 -4.21 3.28e+01 1o8uA 257 -12.47 -4.20 3.29e+01 1szoA 257 -12.47 -4.19 3.32e+01 1nn6A 228 -12.49 -4.19 3.32e+01 1gl4A 285 -13.76 -4.19 3.34e+01 1j3mA 129 -12.35 -4.18 3.38e+01 1q8iA 783 -13.34 -4.18 3.38e+01 1mgtA 174 -12.58 -4.15 3.47e+01 1qrrA 394 -12.91 -4.14 3.49e+01 1sviA 195 -12.98 -4.14 3.51e+01 1mh1 186 -13.76 -4.13 3.54e+01 1kzlA 208 -12.61 -4.11 3.59e+01 1gdvA 85 -11.38 -4.11 3.62e+01 1j0sA 157 -12.97 -4.08 3.69e+01 1pwhA 327 -12.66 -4.07 3.73e+01 2pgd 482 -13.33 -4.07 3.75e+01 1a3c 181 -13.96 -4.04 3.84e+01 2dkb 433 -12.62 -4.02 3.92e+01 1qf9A 194 -13.05 -4.01 3.96e+01 1mho 88 -11.91 -4.00 4.00e+01