% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR223C.t2k-100-30-dssp-ehl2 Host: cc74 Tue Nov 12 18:32:42 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR223C % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR223C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR223C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 449 nodes, 317.85 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.4175) * Reverse)^tau(=0.7333))) % 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 1erjA 393 -284.36 -214.92 1.19e-25 1gotB 340 -265.14 -205.99 9.09e-25 1tbgA 340 -264.68 -204.88 1.17e-24 1gxrA 337 -207.97 -149.70 6.06e-19 1k8kC 372 -169.79 -108.50 2.66e-14 1crzA 403 -96.92 -49.79 1.03e-06 1c5kA 439 -100.20 -48.95 1.37e-06 1aomA 567 -109.76 -41.45 1.79e-05 1aoqA 567 -108.66 -40.35 2.63e-05 1k32A 1045 -145.17 -39.84 3.16e-05 1qksA 567 -108.65 -38.37 5.33e-05 1jjuB 337 -83.78 -37.49 7.33e-05 1jofA 365 -86.62 -31.96 5.59e-04 1jmxB 349 -80.86 -28.91 1.79e-03 1kb0A 677 -79.57 -24.20 1.15e-02 1e1aA 314 -80.85 -23.75 1.38e-02 4aahA 571 -76.46 -22.36 2.44e-02 1g72A 573 -76.49 -22.31 2.49e-02 1qbiA 454 -84.43 -22.20 2.61e-02 1c9uA 454 -82.95 -21.80 3.08e-02 2bbkH 355 -83.74 -21.12 4.09e-02 1kv9A 668 -73.17 -21.04 4.23e-02 1cruA 454 -82.32 -20.79 4.71e-02 1k3iA 656 -67.96 -20.65 4.99e-02 1goh 639 -67.99 -20.16 6.14e-02 1gof 639 -68.27 -20.11 6.27e-02 1dfcA 493 -62.08 -18.65 1.17e-01 1a12A 413 -71.57 -18.05 1.53e-01 2sil 381 -57.45 -17.87 1.66e-01 3sil 379 -57.79 -17.85 1.67e-01 1lenA 181 -44.78 -17.56 1.90e-01 1dim 381 -56.92 -17.48 1.96e-01 1qfmA 710 -86.64 -17.39 2.04e-01 1e8nA 710 -86.85 -17.16 2.26e-01 1ijqA 316 -63.28 -16.59 2.91e-01 2aaiB 262 -44.69 -16.51 3.01e-01 2ltnA 181 -43.99 -15.85 4.06e-01 1bpoA 494 -83.54 -14.53 7.44e-01 1wba 175 -51.85 -14.25 8.49e-01 1b6e 128 -36.87 -14.09 9.15e-01 1lkfA 299 -50.03 -13.94 9.80e-01 5nn9 388 -55.87 -13.41 1.26e+00 1eur 365 -55.65 -13.29 1.33e+00 1f8eA 388 -55.22 -13.13 1.44e+00 3nn9 388 -55.47 -13.11 1.46e+00 1qba 858 -86.24 -12.97 1.55e+00 1yaiA 151 -40.37 -12.88 1.62e+00 2qwc 388 -55.67 -12.77 1.70e+00 1gnyA 153 -41.47 -12.39 2.06e+00 1at0 145 -45.14 -12.06 2.41e+00 1c7sA 858 -84.36 -12.05 2.42e+00 1ospO 257 -53.08 -11.64 2.95e+00 1pvl 301 -48.34 -11.59 3.03e+00 1ilr1 152 -43.52 -11.26 3.56e+00 1abrB 267 -41.43 -11.20 3.68e+00 1qniA 581 -76.71 -10.95 4.16e+00 1irp 153 -48.34 -10.70 4.72e+00 1h8eA 510 -55.60 -10.59 4.99e+00 1jlyA 304 -55.49 -10.41 5.46e+00 2sli 679 -68.58 -10.41 5.48e+00 4sli 679 -68.58 -10.41 5.48e+00 1kit 757 -86.88 -10.40 5.51e+00 1mrg 263 -37.39 -10.32 5.71e+00 1jlxA 304 -54.37 -10.17 6.17e+00 1fnhA 271 -51.82 -10.15 6.23e+00 1ksiA 642 -62.76 -10.11 6.37e+00 1e79A 510 -55.08 -10.08 6.47e+00 1bmfA 510 -55.28 -9.96 6.89e+00 1ksiB 642 -63.03 -9.86 7.22e+00 1fwxA 595 -80.37 -9.75 7.66e+00 1aj6 219 -36.64 -9.74 7.71e+00 1qexA 288 -46.34 -9.62 8.20e+00 2snv 151 -38.82 -9.60 8.29e+00 1hxs3 237 -43.60 -9.57 8.41e+00 1h6lA 353 -65.35 -9.47 8.85e+00 1d0nA 729 -67.49 -9.39 9.21e+00 1qhoA 686 -59.23 -9.37 9.33e+00 1ijtA 128 -33.94 -9.34 9.48e+00 1jj2A 239 -43.29 -9.24 9.98e+00 1ft9A 222 -40.88 -9.12 1.06e+01 1yna 194 -43.65 -9.03 1.11e+01 2pooA 355 -62.70 -8.99 1.14e+01 1zxq 192 -39.45 -8.81 1.25e+01 2hft 218 -38.93 -8.77 1.28e+01 1qcsA 211 -39.54 -8.73 1.30e+01 1iq8A 582 -67.74 -8.68 1.34e+01 1xnb 185 -42.04 -8.61 1.39e+01 1rypI 222 -35.94 -8.60 1.40e+01 1iraX 152 -39.69 -8.58 1.41e+01 1g24A 211 -35.00 -8.53 1.45e+01 1ax0 239 -40.28 -8.46 1.51e+01 2mllB 255 -41.28 -8.45 1.52e+01 1je6A 275 -36.89 -8.39 1.57e+01 1cknA 330 -53.88 -8.33 1.62e+01 1cvmA 353 -65.43 -8.29 1.65e+01 1rmg 422 -62.49 -8.25 1.69e+01 1gcyA 527 -53.96 -8.24 1.70e+01 1hms 132 -38.20 -8.23 1.71e+01 1hmr 132 -38.20 -8.23 1.71e+01 1hmt 132 -38.14 -8.21 1.72e+01 1ee8A 266 -39.35 -8.18 1.76e+01 1tl2A 236 -40.17 -8.16 1.77e+01 1svpA 161 -38.37 -8.12 1.81e+01 1dlc 584 -48.01 -8.10 1.83e+01 1epwA 1290 -121.87 -8.10 1.83e+01 2nlrA 234 -37.88 -8.08 1.85e+01 1dceA 567 -43.18 -7.97 1.97e+01 1ckmA 330 -54.01 -7.94 2.00e+01 1nlr 234 -37.97 -7.92 2.02e+01 1b7yB 785 -76.69 -7.90 2.04e+01 1pvxA 194 -40.83 -7.84 2.10e+01 1fnf 368 -59.95 -7.78 2.18e+01 1f89A 291 -37.87 -7.75 2.22e+01 1g4mA 393 -49.84 -7.66 2.33e+01 1dq3A 454 -62.19 -7.63 2.37e+01 1k4nA 192 -33.40 -7.61 2.39e+01 1dzkA 157 -37.30 -7.61 2.39e+01 1bev1 281 -33.70 -7.55 2.47e+01 1iam 185 -38.65 -7.50 2.53e+01 1a3yA 149 -37.56 -7.43 2.64e+01 1lnrI 134 -33.22 -7.36 2.74e+01 1qlgA 355 -63.84 -7.29 2.85e+01 1ga1A 372 -32.92 -7.25 2.91e+01 1ga6A 372 -32.86 -7.21 2.98e+01 1i31A 314 -49.99 -7.21 2.98e+01 1rypH 205 -33.42 -7.20 3.00e+01 1eut 605 -57.22 -7.17 3.05e+01 1euu 605 -58.61 -7.07 3.23e+01 1pysB 785 -76.60 -7.04 3.28e+01 1svb 395 -53.45 -7.03 3.30e+01 1l9xA 315 -36.82 -7.03 3.30e+01 1i82A 189 -39.40 -7.02 3.33e+01 1i8aA 189 -39.40 -7.02 3.33e+01 1dgaA 375 -42.22 -6.98 3.39e+01 1g3gA 164 -36.43 -6.96 3.42e+01 1bj4A 470 -37.54 -6.94 3.46e+01 1hdhA 536 -52.50 -6.94 3.46e+01 1aun 208 -39.41 -6.92 3.51e+01 1dmhA 311 -38.54 -6.88 3.58e+01 1sltA 134 -40.91 -6.83 3.68e+01 1rypK 198 -35.05 -6.83 3.69e+01 1sltB 134 -41.92 -6.80 3.76e+01 1xyn 178 -36.50 -6.78 3.79e+01 1f5mB 180 -31.87 -6.77 3.81e+01 1f5mA 180 -31.87 -6.77 3.81e+01 1lo7A 141 -34.50 -6.75 3.86e+01 1httA 423 -42.21 -6.72 3.92e+01 1bvqA 141 -33.79 -6.72 3.93e+01 1b2pA 119 -44.50 -6.70 3.96e+01 1bkb 136 -40.18 -6.69 3.99e+01