% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YGL227W.t2k-100-30-dssp-ehl2 Host: farm15.cse.ucsc.edu Sun Mar 19 22:40:48 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGL2/YGL227W % --------------------------------------------------------------------- % 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 YGL227W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGL227W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 959 nodes, 1707.91 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=0.9515) * Reverse)^tau(=0.8959))) % Calculated when Simple < simple_threshold (10000.00) % 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 2fbeA 201 -39.80 -20.32 7.47e-03 1uujA 88 -32.29 -19.65 1.14e-02 1omwA 689 -35.27 -17.66 4.00e-02 1ag8A 499 -33.82 -16.41 8.85e-02 1eulA 994 -46.06 -15.67 1.43e-01 1od3A 168 -30.45 -15.01 2.18e-01 1q1lA 401 -31.17 -13.78 4.84e-01 1ly1A 181 -26.95 -13.33 6.50e-01 1dhx 967 -35.69 -13.31 6.61e-01 1o04A 500 -31.67 -12.60 1.05e+00 1xw5A 217 -28.19 -12.57 1.07e+00 1su4A 994 -41.83 -12.42 1.18e+00 1dik 874 -28.68 -12.37 1.23e+00 1syyA 346 -30.01 -12.17 1.39e+00 2mspA 126 -25.98 -12.04 1.52e+00 1kblA 873 -28.52 -11.80 1.78e+00 1k8cA 322 -27.29 -11.48 2.20e+00 1mi3A 322 -27.25 -11.45 2.25e+00 2c4jA 218 -27.71 -11.44 2.26e+00 1k1xA 659 -27.40 -11.16 2.73e+00 1dhkB 223 -26.04 -11.08 2.87e+00 1rj1A 151 -22.78 -11.08 2.88e+00 1bn5 478 -29.54 -11.03 2.97e+00 1tdpA 111 -23.32 -10.99 3.04e+00 1b6a 478 -29.37 -10.83 3.39e+00 1kbpA 432 -24.99 -10.58 4.00e+00 4kbpA 432 -24.88 -10.50 4.23e+00 1ig8A 486 -29.09 -10.43 4.43e+00 1p30A 952 -26.98 -10.35 4.70e+00 1xgwA 176 -25.08 -10.21 5.13e+00 1ruxA 951 -26.81 -10.14 5.39e+00 1kkjA 419 -24.04 -10.12 5.48e+00 1kl1A 419 -24.04 -10.12 5.48e+00 1wjtA 103 -22.58 -10.08 5.62e+00 1dc1A 323 -26.57 -9.98 6.01e+00 1yjsA 419 -23.93 -9.93 6.23e+00 1hgeB 175 -23.24 -9.84 6.61e+00 1tm0A 350 -25.70 -9.81 6.75e+00 2tmvP 158 -22.59 -9.57 7.92e+00 1lylA 504 -26.37 -9.50 8.29e+00 1viwB 198 -25.18 -9.49 8.34e+00 1kd6A 179 -27.01 -9.49 8.38e+00 1wpgA 994 -39.27 -9.45 8.61e+00 1fnmA 691 -29.78 -9.44 8.65e+00 1o0xA 262 -25.07 -9.42 8.79e+00 1lv7A 257 -26.01 -9.39 8.97e+00 2a6hD 1524 -30.56 -9.18 1.03e+01 2a8mA 420 -25.85 -9.14 1.06e+01 2a8lA 420 -25.82 -9.13 1.07e+01 1e1oA 504 -25.95 -9.12 1.08e+01 1gr3A 160 -22.84 -9.10 1.09e+01 2a8jA 420 -25.70 -9.04 1.13e+01 1ok8A 394 -24.29 -9.03 1.15e+01 1ltqA 301 -26.67 -8.99 1.17e+01 3hmgB 175 -22.43 -8.94 1.22e+01 2viuB 175 -22.40 -8.93 1.22e+01 1b59A 370 -26.91 -8.91 1.24e+01 1ux6A 350 -37.58 -8.90 1.25e+01 1qu1A 155 -26.89 -8.89 1.26e+01 1b2pA 119 -24.37 -8.85 1.29e+01 1kz7A 353 -24.03 -8.81 1.33e+01 1cnt3 187 -24.05 -8.71 1.42e+01 1kfiA 572 -26.07 -8.71 1.43e+01 1vimA 200 -23.54 -8.69 1.44e+01 1fvuB 125 -22.20 -8.68 1.45e+01 1q5dA 419 -23.78 -8.63 1.51e+01 1exmA 405 -24.70 -8.61 1.52e+01 1ykhA 108 -25.21 -8.58 1.55e+01 1qsaA 618 -22.66 -8.58 1.55e+01 1ukz 203 -24.30 -8.57 1.56e+01 1tlfA 301 -20.87 -8.51 1.63e+01 1x9zA 188 -20.98 -8.50 1.64e+01 1ixmB 192 -20.80 -8.50 1.64e+01 1ypxA 375 -24.25 -8.49 1.65e+01 1lkvX 232 -25.99 -8.46 1.69e+01 1ha3A 405 -24.60 -8.44 1.72e+01 1dar 691 -27.56 -8.42 1.74e+01 1ffyA 917 -28.96 -8.33 1.85e+01 1qu2A 917 -28.96 -8.33 1.85e+01 1hl2A 297 -24.26 -8.28 1.91e+01 1lenB 52 -19.21 -8.23 1.97e+01 1eysH 259 -23.24 -8.23 1.97e+01 1efaA 333 -20.85 -8.23 1.98e+01 1tg7A 971 -27.05 -8.22 1.98e+01 1g5aA 628 -24.78 -8.22 1.99e+01 1h0cA 392 -23.83 -8.21 2.00e+01 1y14B 171 -21.45 -8.20 2.02e+01 1dvkA 173 -24.10 -8.18 2.04e+01 1cnt2 187 -26.93 -8.14 2.10e+01 3mspA 126 -21.93 -8.11 2.15e+01 1v7wA 807 -25.09 -8.07 2.20e+01 1ki9A 192 -23.69 -8.05 2.24e+01 1hqz9 141 -20.71 -8.04 2.25e+01 1ar1B 298 -25.23 -8.04 2.26e+01 1cnt1 187 -23.43 -7.97 2.36e+01 1nznA 126 -20.15 -7.89 2.49e+01 1zbqA 327 -23.78 -7.88 2.51e+01 1cr6B 554 -26.71 -7.87 2.53e+01 1r75A 141 -21.73 -7.86 2.54e+01 1gpiA 431 -23.91 -7.83 2.60e+01 1hqz1 141 -20.65 -7.82 2.62e+01 1gcb 454 -22.88 -7.81 2.64e+01 1epwA 1290 -50.50 -7.81 2.64e+01 1a6r 471 -22.62 -7.80 2.66e+01 1z3iX 644 -25.86 -7.79 2.67e+01 2bmfA 451 -22.36 -7.75 2.74e+01 1tu5A 746 -24.49 -7.73 2.80e+01 1zb1A 392 -22.78 -7.70 2.84e+01 1fftB 315 -21.76 -7.70 2.85e+01 1r77A 103 -21.55 -7.65 2.95e+01 1oq9A 363 -24.65 -7.62 3.01e+01 3gcb 470 -22.62 -7.61 3.04e+01 1ei7B 158 -21.98 -7.61 3.04e+01 1r5qA 102 -27.06 -7.59 3.07e+01 1yspA 181 -21.20 -7.58 3.09e+01 1ek1A 554 -26.33 -7.58 3.10e+01 1ii6A 368 -23.15 -7.57 3.11e+01 1ixmA 192 -20.11 -7.55 3.15e+01 1cqzA 554 -26.35 -7.52 3.23e+01 5nn9 388 -23.68 -7.48 3.32e+01 1iazA 179 -24.29 -7.46 3.37e+01 1qbqA 333 -23.02 -7.45 3.38e+01 1ki0A 253 -25.03 -7.45 3.39e+01 1w0bA 102 -21.10 -7.41 3.49e+01 1jcqA 382 -22.63 -7.39 3.53e+01 1ld8A 382 -22.63 -7.39 3.53e+01 1tn6A 382 -22.62 -7.39 3.53e+01 1uwsA 489 -22.86 -7.37 3.58e+01 2booA 247 -20.57 -7.37 3.58e+01 1mspA 126 -20.60 -7.37 3.58e+01 1vhmA 195 -24.07 -7.36 3.61e+01 1pguA 615 -25.95 -7.35 3.64e+01 1ft1A 377 -23.20 -7.34 3.65e+01 1ixxB 123 -20.34 -7.34 3.66e+01 1xmrA 243 -24.36 -7.33 3.68e+01 1f5jA 199 -21.38 -7.32 3.71e+01 1d8dA 377 -23.02 -7.31 3.72e+01 1m0wA 491 -21.86 -7.31 3.74e+01 1efuA 385 -24.38 -7.30 3.75e+01 1jcrA 377 -23.21 -7.30 3.76e+01 1z8uA 102 -20.50 -7.27 3.82e+01 1xksA 450 -24.72 -7.26 3.85e+01 2act 220 -20.81 -7.25 3.88e+01 1wgkA 114 -20.22 -7.23 3.94e+01 1aipE 405 -24.04 -7.23 3.95e+01 1nnxA 109 -21.88 -7.22 3.98e+01