% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YDR030C.t2k-100-30-dssp-ehl2 Host: farm15 Sat Nov 13 20:37:48 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR0/YDR030C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.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 YDR030C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDR030C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10735 sequences, 2539893 residues, 507 nodes, 548.90 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.6884) * Reverse)^tau(=0.6835))) % 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 1tbgA 340 -296.66 -249.43 1.02e-23 1gotB 340 -295.45 -248.55 1.18e-23 1erjA 393 -288.89 -239.51 5.58e-23 1nr0A 611 -277.25 -201.09 5.10e-20 1gxrA 337 -224.28 -174.74 6.96e-18 1pguA 615 -222.62 -148.86 1.10e-15 1k8kC 372 -185.73 -133.58 2.49e-14 1u4cA 349 -149.70 -107.70 6.45e-12 1sq9A 397 -153.52 -106.11 9.21e-12 1l0qA 391 -118.18 -56.03 1.96e-06 1k32A 1045 -144.25 -51.70 6.52e-06 1n6eA 1071 -145.13 -51.64 6.61e-06 1jofA 365 -90.50 -49.54 1.20e-05 1crzA 403 -82.15 -42.37 9.68e-05 1c5kA 439 -85.37 -42.05 1.06e-04 1aomA 567 -104.11 -41.45 1.27e-04 1aoqA 567 -104.71 -39.86 2.06e-04 1qksA 567 -104.94 -39.54 2.27e-04 1q7fA 286 -80.66 -38.94 2.74e-04 1jjuB 337 -73.11 -37.16 4.74e-04 1pbyB 337 -72.70 -36.91 5.13e-04 1pjxA 314 -76.95 -35.66 7.59e-04 1e1aA 314 -76.85 -35.53 7.90e-04 1utcA 363 -74.93 -35.41 8.21e-04 1bpoA 494 -78.33 -34.67 1.04e-03 1kb0A 677 -87.57 -34.40 1.13e-03 1jmxB 349 -72.96 -33.66 1.43e-03 1lrwA 600 -89.53 -33.44 1.54e-03 1ri6A 343 -99.97 -32.44 2.12e-03 1kv9A 668 -86.15 -32.33 2.21e-03 1npeA 267 -61.08 -31.22 3.17e-03 1g72A 573 -76.41 -30.94 3.48e-03 4aahA 571 -75.94 -30.60 3.89e-03 1suuA 312 -67.79 -29.76 5.14e-03 1wp5A 323 -64.24 -28.62 7.54e-03 1qbiA 454 -68.98 -27.28 1.19e-02 1v04A 355 -62.64 -27.13 1.26e-02 1c9uA 454 -67.89 -25.65 2.09e-02 1ijqA 316 -55.65 -25.31 2.36e-02 1cruA 454 -66.56 -25.14 2.51e-02 1rwiA 270 -62.26 -23.58 4.37e-02 2bbkH 355 -69.21 -22.92 5.55e-02 1orvA 728 -68.92 -21.84 8.25e-02 1n1mA 728 -69.47 -19.57 1.93e-01 1u6dX 308 -45.67 -18.58 2.82e-01 1goh 639 -58.48 -17.28 4.69e-01 1a12A 413 -63.62 -16.97 5.32e-01 1xfdA 723 -74.63 -16.92 5.44e-01 1gof 639 -57.78 -16.73 5.85e-01 1k3iA 656 -57.26 -16.53 6.34e-01 1s1dA 331 -53.14 -16.44 6.57e-01 2ltnA 181 -31.23 -13.02 2.75e+00 1lenA 181 -31.67 -12.94 2.84e+00 1wba 175 -36.84 -12.75 3.08e+00 1yaiA 151 -31.09 -12.70 3.15e+00 1o75A 415 -44.38 -12.64 3.24e+00 1r17A 343 -42.95 -12.62 3.27e+00 1at0 145 -35.74 -12.61 3.28e+00 1dfcA 493 -47.98 -11.86 4.58e+00 1tl2A 236 -31.26 -11.81 4.68e+00 1ukfA 188 -24.12 -11.41 5.61e+00 1oalA 151 -30.52 -11.39 5.66e+00 1snzA 344 -43.97 -11.30 5.87e+00 1cvmA 353 -55.76 -11.28 5.95e+00 1ckmA 330 -48.32 -11.14 6.32e+00 1cknA 330 -48.26 -11.08 6.50e+00 1sqjA 789 -87.92 -10.78 7.47e+00 2mllB 255 -30.75 -10.68 7.82e+00 1h30A 422 -42.65 -10.65 7.93e+00 1od5A 492 -50.42 -10.61 8.10e+00 1oq1A 223 -35.41 -10.54 8.35e+00 2pooA 355 -52.54 -10.40 8.92e+00 1gskA 513 -55.96 -10.22 9.68e+00 1qlgA 355 -53.68 -10.15 1.00e+01 1p57A 114 -22.54 -10.15 1.00e+01 1b6e 128 -22.68 -9.73 1.22e+01 1ofzA 312 -42.63 -9.64 1.27e+01 1fnuA 221 -28.89 -9.63 1.28e+01 1fnhA 271 -38.87 -9.55 1.33e+01 1gqzA 274 -35.02 -9.42 1.42e+01 1m2tB 263 -27.43 -9.24 1.54e+01 1jlyA 304 -42.06 -9.21 1.57e+01 1bu8A 452 -42.01 -9.21 1.57e+01 1ax0 239 -30.39 -9.17 1.60e+01 1pvl 301 -32.76 -9.12 1.63e+01 1vclA 432 -40.65 -9.10 1.65e+01 1abrB 267 -26.37 -9.07 1.68e+01 1ojqA 212 -23.52 -8.97 1.76e+01 1v3eA 431 -40.81 -8.85 1.87e+01 1o0vA 327 -27.44 -8.77 1.94e+01 1n67A 359 -38.08 -8.72 1.99e+01 1l9xA 315 -28.07 -8.70 2.01e+01 1xsjA 778 -75.77 -8.69 2.02e+01 1vh5A 148 -22.85 -8.57 2.14e+01 1jlxA 304 -41.02 -8.50 2.21e+01 1nqeA 594 -49.15 -8.37 2.37e+01 1luqA 127 -25.89 -8.28 2.48e+01 1sriA 121 -24.84 -8.23 2.54e+01 1dq3A 454 -48.47 -8.17 2.62e+01 1khiA 176 -27.07 -8.09 2.73e+01 3sil 379 -37.75 -8.08 2.73e+01 1jsdA 319 -27.04 -8.08 2.73e+01 1qhdA 398 -30.89 -8.06 2.77e+01 1jdc 429 -44.07 -8.02 2.82e+01 1h6lA 353 -53.15 -8.01 2.84e+01 1eut 605 -56.98 -7.98 2.87e+01 1xakA 83 -22.15 -7.98 2.88e+01 1swuA 127 -25.44 -7.96 2.90e+01 1dim 381 -37.22 -7.94 2.93e+01 1h0bA 256 -29.05 -7.92 2.97e+01 1d7pM 159 -25.73 -7.91 2.98e+01 1h4rA 314 -38.26 -7.88 3.03e+01 1cqyA 99 -26.22 -7.80 3.15e+01 1hmr 132 -26.95 -7.77 3.20e+01 1hms 132 -26.96 -7.75 3.23e+01 1hmt 132 -26.81 -7.73 3.27e+01 1jpc 109 -36.01 -7.66 3.38e+01 1q47A 495 -54.86 -7.55 3.58e+01 1rocA 155 -25.25 -7.54 3.60e+01 1mkfA 382 -30.71 -7.53 3.61e+01 1ga1A 372 -25.85 -7.41 3.85e+01 1ga6A 372 -25.83 -7.40 3.87e+01 1shyB 551 -47.06 -7.39 3.89e+01 1qniA 581 -64.72 -7.38 3.91e+01 2izgB 123 -24.50 -7.36 3.94e+01 2izhB 123 -24.50 -7.36 3.95e+01 1j98A 157 -20.80 -7.36 3.95e+01