% 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. % --------------------------------------------------------------------- % w0.5foo.1.YGR039W.t2k-w0.5.mod Host: cc41 Fri Nov 8 19:39:10 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR039W % --------------------------------------------------------------------- % Inserted Files: YGR039W.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % 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)) % Single Track Model: YGR039W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 104 nodes, 103.17 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(=3.4163) * Reverse)^tau(=0.7387))) % 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 1bwfO 501 -29.18 -8.11 6.51e-02 1glcG 501 -29.18 -7.91 8.03e-02 1bu6O 501 -29.18 -7.90 8.14e-02 1pciA 322 -26.22 -5.55 1.11e+00 1f03A 82 -21.76 -4.98 2.18e+00 1bhe 376 -25.67 -4.90 2.42e+00 1i5uA 82 -21.66 -4.88 2.48e+00 1hbnB 442 -25.19 -4.80 2.73e+00 1mroB 442 -25.19 -4.80 2.73e+00 1kezA 300 -24.98 -4.70 3.08e+00 1k8wA 327 -24.16 -4.41 4.42e+00 1havA 217 -23.70 -4.39 4.49e+00 1havB 217 -23.70 -4.38 4.55e+00 1lqxA 82 -21.16 -4.32 4.95e+00 1qa7A 215 -23.60 -4.30 5.04e+00 1tx4A 198 -22.87 -4.29 5.09e+00 1qa7B 219 -23.62 -4.29 5.11e+00 1k33A 68 -21.18 -4.22 5.61e+00 1am4A 199 -22.85 -4.20 5.75e+00 1ehbA 82 -21.05 -4.19 5.79e+00 1cyo 93 -21.28 -4.17 5.91e+00 1qjpA 171 -22.05 -4.16 6.05e+00 1bxwA 172 -22.05 -4.14 6.14e+00 3sil 379 -24.35 -4.14 6.20e+00 1es1A 82 -20.98 -4.13 6.21e+00 1dim 381 -24.36 -4.12 6.32e+00 2sil 381 -24.36 -4.12 6.32e+00 1hdkA 141 -21.89 -4.10 6.51e+00 1g86A 142 -21.89 -4.09 6.56e+00 1lcl 142 -21.89 -4.09 6.56e+00 1grnB 203 -22.87 -4.05 6.91e+00 1tmy 120 -21.51 -4.05 6.92e+00 1g90A 176 -22.27 -4.04 6.99e+00 1wdb 104 -21.42 -4.04 7.05e+00 1i94B 255 -23.54 -3.99 7.45e+00 1fjgB 256 -23.55 -3.99 7.47e+00 1j5eB 256 -23.55 -3.99 7.47e+00 1lr6A 82 -20.86 -3.92 8.12e+00 1i6vB 314 -23.66 -3.91 8.29e+00 2ngrB 234 -23.02 -3.90 8.41e+00 1yppA 286 -23.28 -3.88 8.62e+00 1pyp 285 -23.28 -3.86 8.86e+00 1rgp 242 -23.05 -3.82 9.22e+00 1hujA 281 -23.25 -3.79 9.63e+00 1e9gB 286 -23.27 -3.79 9.68e+00 1hukA 281 -23.25 -3.79 9.68e+00 1wgjA 286 -23.26 -3.77 9.86e+00 1e9gA 286 -23.26 -3.77 9.86e+00 117eA 286 -23.26 -3.77 9.91e+00 8prkB 287 -23.27 -3.77 9.96e+00 8prkA 287 -23.27 -3.77 9.96e+00 1hciA 476 -24.66 -3.72 1.05e+01 1dlyA 164 -21.59 -3.69 1.10e+01 1pdnC 128 -21.42 -3.63 1.18e+01 1e6vB 443 -24.10 -3.54 1.33e+01 1h4wA 224 -22.00 -3.45 1.50e+01 1jymA 183 -22.55 -3.45 1.50e+01 1c1kA 217 -23.86 -3.44 1.52e+01 1fwuA 134 -21.35 -3.44 1.53e+01 1dqgA 135 -21.36 -3.43 1.55e+01 1lwsA 454 -24.79 -3.36 1.70e+01 1hdlA 55 -19.53 -3.36 1.70e+01 1m20A 82 -20.12 -3.33 1.76e+01 1vdeA 454 -24.61 -3.24 1.98e+01 1dfaA 454 -24.61 -3.24 1.98e+01 1i5xA 68 -19.79 -3.22 2.03e+01 1ef0A 462 -24.63 -3.22 2.04e+01 1qr8A 68 -19.79 -3.18 2.16e+01 1lay 256 -22.36 -3.17 2.18e+01 1kiyA 374 -23.74 -3.17 2.20e+01 1bccF 109 -20.23 -3.16 2.20e+01 1jfgA 374 -23.74 -3.16 2.22e+01 1jfaA 374 -23.74 -3.16 2.22e+01 1rmg 422 -23.91 -3.13 2.30e+01 1jvaA 475 -24.66 -3.12 2.33e+01 1dj7B 75 -19.21 -3.12 2.35e+01 1d5rA 324 -23.07 -3.09 2.43e+01 1jqiA 388 -22.92 -3.09 2.45e+01 1szt 68 -19.60 -3.04 2.60e+01 1df4A 68 -19.60 -3.04 2.60e+01 1iwpG 141 -21.75 -3.03 2.66e+01 1dlbA 68 -19.65 -3.03 2.66e+01 1g9rA 311 -23.06 -2.98 2.82e+01 1ga8A 311 -23.06 -2.98 2.82e+01 1ac1A 189 -21.19 -2.98 2.84e+01 1m5hA 297 -22.43 -2.96 2.92e+01 1l9uA 314 -22.63 -2.93 3.02e+01 1gsuA 219 -21.80 -2.92 3.08e+01 1eif 135 -21.14 -2.90 3.15e+01 2eifA 136 -21.14 -2.90 3.16e+01 1a5dA 173 -21.72 -2.88 3.24e+01 1jgcA 161 -22.11 -2.86 3.33e+01 1bvwA 360 -22.71 -2.85 3.38e+01 2bvwA 362 -22.71 -2.85 3.39e+01 1qr9A 68 -19.41 -2.84 3.41e+01 1kr4A 125 -20.66 -2.82 3.54e+01 1f23D 76 -19.79 -2.80 3.63e+01 1k34A 68 -19.13 -2.75 3.89e+01 1gppA 237 -23.21 -2.75 3.90e+01 1c72A 219 -21.81 -2.73 3.98e+01