% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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. % --------------------------------------------------------------------- % str2foo.1.YGR212W.t2k-100-30-str2 Host: cc50 Sun Oct 12 00:34:58 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR212W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR212W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR212W.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 469 nodes, 428.91 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 (0.00) % E-value on N (=8162) sequences: % N / (1 + exp(-(lambda(=1.6268) * Reverse)^tau(=0.7494))) % 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 1l5aA 436 -40.79 -16.98 4.89e-02 8acn 754 -35.50 -11.06 1.34e+00 1amj 754 -35.50 -11.05 1.34e+00 1c96A 753 -35.51 -10.52 1.83e+00 1bgp 309 -32.98 -10.43 1.93e+00 1b0jA 754 -35.45 -10.41 1.96e+00 7acn 754 -35.52 -10.39 1.98e+00 6acn 754 -35.26 -10.38 2.00e+00 1jkgA 140 -32.88 -10.31 2.08e+00 1a15A 67 -30.49 -10.01 2.49e+00 1icxA 155 -35.77 -9.86 2.73e+00 1gk8A 475 -33.68 -9.79 2.86e+00 1jn5A 140 -32.02 -9.58 3.24e+00 1keiA 316 -32.23 -9.56 3.28e+00 1i19A 561 -34.04 -9.34 3.75e+00 6tmnE 316 -31.90 -9.19 4.12e+00 2tmnE 316 -31.90 -9.18 4.15e+00 8tlnE 316 -31.90 -9.18 4.15e+00 1hyt 316 -31.90 -9.18 4.16e+00 1bk1 184 -32.42 -9.17 4.18e+00 1lnsA 763 -35.26 -9.12 4.32e+00 1n99A 166 -30.53 -8.87 5.04e+00 1jvpP 298 -32.74 -8.84 5.14e+00 1h2aL 567 -33.74 -8.80 5.26e+00 1qg7A 67 -30.39 -8.76 5.37e+00 8pchA 220 -30.92 -8.76 5.40e+00 1f1sA 814 -36.19 -8.64 5.81e+00 1dmuA 299 -31.83 -8.39 6.78e+00 1f5mB 180 -31.96 -8.39 6.81e+00 1f5mA 180 -31.96 -8.39 6.82e+00 1hcl 298 -32.09 -8.33 7.05e+00 1mwxA 646 -34.28 -8.32 7.13e+00 1gz8A 299 -31.82 -8.08 8.30e+00 1mwsA 646 -34.24 -8.07 8.33e+00 1e1xA 299 -31.75 -8.04 8.52e+00 1eaxA 241 -31.33 -7.87 9.51e+00 1cx4A 305 -31.15 -7.82 9.79e+00 1uc8A 280 -30.50 -7.28 1.39e+01 1mkiA 330 -31.19 -7.27 1.40e+01 1ubkL 534 -33.04 -7.14 1.53e+01 1o0iA 138 -28.38 -7.08 1.59e+01 1cxqA 162 -27.90 -6.93 1.75e+01 1h3gA 601 -31.86 -6.88 1.81e+01 1qusA 322 -29.70 -6.81 1.89e+01 1vsd 152 -27.78 -6.81 1.90e+01 1mu5A 471 -32.19 -6.80 1.91e+01 1oe4A 247 -29.14 -6.78 1.93e+01 1dkxA 219 -31.91 -6.74 1.98e+01 1gtkA 313 -28.88 -6.73 2.01e+01 1f4qA 165 -28.12 -6.69 2.05e+01 1e2wA 251 -30.09 -6.68 2.07e+01 1h2rL 534 -32.84 -6.68 2.07e+01 1mwrA 646 -32.76 -6.67 2.08e+01 1ltm 320 -29.48 -6.66 2.10e+01 1asu 162 -27.91 -6.64 2.12e+01 1bn5 478 -30.93 -6.59 2.19e+01 1el6A 219 -30.33 -6.59 2.20e+01 1b6a 478 -30.93 -6.58 2.22e+01 1k94A 165 -28.20 -6.56 2.24e+01 1nf3C 128 -27.59 -6.55 2.26e+01 1hcz 252 -30.32 -6.52 2.31e+01 1qgvA 142 -27.25 -6.51 2.31e+01 1azo 232 -28.28 -6.50 2.34e+01 1bpr 191 -29.05 -6.50 2.34e+01 1bowA 159 -30.68 -6.47 2.38e+01 1joa 447 -29.97 -6.46 2.39e+01 1el6B 219 -30.53 -6.44 2.43e+01 1jqpA 438 -31.47 -6.44 2.43e+01 1nhs 447 -29.97 -6.43 2.44e+01 1a6wL 109 -27.36 -6.43 2.45e+01 1nhp 447 -29.97 -6.37 2.54e+01 1bxnA 485 -30.02 -6.37 2.55e+01 1j6wA 175 -28.87 -6.35 2.58e+01 1lbvA 252 -29.26 -6.31 2.65e+01 1parA 53 -24.87 -6.29 2.69e+01 1fm4A 159 -31.48 -6.26 2.74e+01 1ku8A 133 -29.41 -6.23 2.80e+01 2dri 271 -26.97 -6.19 2.89e+01 1ayyA 151 -26.70 -6.18 2.91e+01 1a6uL 108 -26.93 -6.16 2.93e+01 1gqeA 365 -31.10 -6.12 3.02e+01 1g7tA 594 -30.74 -6.10 3.05e+01 1mykA 53 -24.86 -6.09 3.07e+01 1a6vL 110 -27.33 -6.09 3.08e+01 1jacA 133 -28.97 -6.08 3.10e+01 1m26A 133 -29.05 -6.08 3.11e+01 1smd 496 -30.71 -6.07 3.13e+01 1dim 381 -31.51 -6.05 3.16e+01 1bdtA 53 -24.57 -6.03 3.20e+01 1ge8A 249 -33.50 -6.03 3.21e+01 1erjA 393 -31.21 -6.02 3.22e+01 1f60A 458 -30.19 -5.99 3.29e+01 1g7rA 594 -30.66 -5.98 3.31e+01 1bf8 205 -29.81 -5.96 3.36e+01 2fnbA 95 -28.90 -5.96 3.36e+01 1o7fA 469 -30.02 -5.96 3.37e+01 1jhnA 424 -32.29 -5.94 3.42e+01 1cq3A 233 -28.85 -5.90 3.50e+01 1pda 315 -28.00 -5.90 3.52e+01 1e3dB 542 -30.10 -5.89 3.54e+01 3sil 379 -31.18 -5.86 3.60e+01 1fxlA 167 -28.24 -5.86 3.61e+01 1fzvA 132 -27.65 -5.81 3.73e+01 1f8rA 498 -30.36 -5.79 3.79e+01 1dkzA 219 -31.75 -5.78 3.82e+01 1a6q 382 -30.80 -5.77 3.84e+01 1mo9A 523 -29.32 -5.77 3.84e+01 1m1nB 522 -29.21 -5.75 3.90e+01 1ffyA 917 -30.91 -5.73 3.95e+01 1qu2A 917 -30.91 -5.73 3.95e+01