% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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.YGR217W.t2k-100-30-str2 Host: cc85 Thu Feb 26 18:14:42 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR217W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR217W.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 9381 sequences, 2218509 residues, 2040 nodes, 2963.49 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(=1.4437) * Reverse)^tau(=0.7657))) % 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 1ggzA 148 -48.86 -24.65 1.65e-03 3cln 148 -46.84 -24.18 2.07e-03 1ncx 162 -47.76 -23.99 2.27e-03 1top 162 -47.72 -23.91 2.36e-03 1t1dA 100 -35.57 -22.63 4.39e-03 1jvmA 125 -39.12 -22.58 4.51e-03 1j95A 125 -38.98 -21.92 6.22e-03 1g4yR 148 -42.26 -21.60 7.29e-03 1k4cC 124 -39.26 -21.38 8.13e-03 1r3jC 124 -39.26 -21.38 8.13e-03 1cll 148 -48.65 -21.12 9.22e-03 1bl8A 97 -37.19 -20.80 1.08e-02 1avsA 90 -36.53 -20.56 1.22e-02 1jb0A 755 -51.49 -19.94 1.67e-02 1a68 95 -31.68 -19.84 1.75e-02 2mysB 166 -37.72 -18.84 2.90e-02 1zac 90 -35.52 -18.32 3.79e-02 1exrA 148 -46.89 -17.84 4.85e-02 1dsxA 87 -29.58 -17.76 5.05e-02 1lnh 857 -60.07 -16.56 9.47e-02 1be3C 379 -47.53 -16.50 9.76e-02 1iwgA 1053 -57.40 -16.32 1.08e-01 1osa 148 -46.37 -16.15 1.18e-01 1j7rA 86 -30.89 -16.07 1.22e-01 1m46A 148 -31.04 -15.97 1.29e-01 1byyA 53 -27.95 -15.89 1.34e-01 1kb9C 385 -51.80 -15.39 1.76e-01 1ezvC 385 -51.81 -15.39 1.76e-01 1wdcC 156 -33.52 -15.17 1.97e-01 1ehkA 562 -58.04 -14.76 2.46e-01 1m45A 148 -29.37 -14.68 2.58e-01 1kyoC 385 -50.58 -13.82 4.10e-01 1o1fC 147 -31.01 -13.70 4.39e-01 1wdcB 156 -31.80 -13.56 4.75e-01 1nn7A 105 -28.03 -13.43 5.09e-01 9wgaA 171 -39.60 -13.43 5.10e-01 1ezfA 340 -36.99 -13.36 5.31e-01 1dceA 567 -39.68 -13.30 5.46e-01 1ho2A 20 -24.38 -13.29 5.52e-01 1wgtA 186 -40.45 -13.07 6.23e-01 1qg9A 21 -24.11 -12.29 9.61e-01 1dqeA 137 -28.47 -11.77 1.29e+00 1ggwA 140 -27.55 -11.46 1.55e+00 1k9uA 78 -26.04 -10.79 2.27e+00 1orsC 132 -38.91 -10.76 2.30e+00 1jbaA 204 -29.73 -10.74 2.34e+00 1bf2 750 -40.96 -10.63 2.48e+00 1o86A 589 -36.62 -10.62 2.50e+00 1qlaA 656 -47.22 -10.53 2.63e+00 1oyeA 1049 -52.52 -10.50 2.68e+00 1upkA 341 -32.52 -10.38 2.89e+00 1ulmA 82 -28.18 -10.13 3.33e+00 1oahA 519 -47.78 -10.03 3.53e+00 3kvt 115 -23.08 -9.98 3.66e+00 1dhx 967 -56.88 -9.82 4.01e+00 2frvB 536 -35.03 -9.82 4.02e+00 1q9bA 43 -22.86 -9.77 4.14e+00 1aijL 281 -39.27 -9.77 4.14e+00 1dceB 331 -30.31 -9.72 4.26e+00 1hev 43 -22.60 -9.60 4.58e+00 1n9dA 199 -29.93 -9.43 5.07e+00 1nr6A 473 -39.39 -9.42 5.09e+00 1g8iA 190 -28.95 -9.39 5.18e+00 1br1B 150 -26.79 -9.38 5.21e+00 1k94A 165 -31.58 -9.34 5.33e+00 1o26A 232 -24.43 -9.23 5.70e+00 1ctaA 36 -21.14 -9.23 5.71e+00 2scpA 174 -26.70 -9.22 5.76e+00 1gntA 553 -41.73 -9.18 5.89e+00 1e2uA 553 -41.74 -9.10 6.18e+00 1f6fA 199 -31.02 -9.09 6.20e+00 1jpaA 312 -27.24 -9.06 6.34e+00 1kq4A 232 -23.89 -9.03 6.45e+00 1irxA 523 -38.38 -9.00 6.55e+00 1mwvA 714 -42.87 -9.00 6.57e+00 1e1dA 553 -41.33 -8.98 6.64e+00 1q0sA 259 -28.09 -8.97 6.68e+00 1pal 108 -22.07 -8.81 7.36e+00 1n6bA 473 -37.32 -8.79 7.43e+00 1e6fA 143 -22.96 -8.79 7.47e+00 1dlc 584 -30.65 -8.71 7.82e+00 1c3wA 222 -32.02 -8.70 7.88e+00 1f4qA 165 -27.64 -8.68 7.99e+00 1gp0A 143 -23.05 -8.66 8.06e+00 1dt6A 473 -37.91 -8.66 8.06e+00 1i50A 1733 -81.74 -8.65 8.11e+00 1h2aL 567 -35.75 -8.61 8.30e+00 1dcnD 436 -29.94 -8.61 8.31e+00 1kgbA 231 -32.71 -8.58 8.46e+00 1n93X 375 -28.14 -8.57 8.53e+00 1f5aA 513 -32.86 -8.50 8.89e+00 1otsA 465 -43.46 -8.49 8.94e+00 1gupA 348 -28.27 -8.45 9.17e+00 1rec 201 -25.75 -8.44 9.22e+00 5pal 109 -22.25 -8.35 9.78e+00 1guqA 348 -28.20 -8.34 9.82e+00 1dugA 234 -31.57 -8.30 1.01e+01 2lbp 346 -28.98 -8.27 1.02e+01 1ponA 36 -19.74 -8.23 1.05e+01 1ulkA 126 -30.60 -8.22 1.06e+01 1b6a 478 -35.84 -8.19 1.08e+01 1j7dA 145 -22.76 -8.18 1.09e+01 1m1jA 491 -43.80 -8.11 1.13e+01 1m48A 133 -23.07 -8.07 1.16e+01 1c3cA 429 -29.55 -8.04 1.18e+01 1ctdA 36 -20.16 -7.99 1.22e+01 1bn5 478 -35.86 -7.97 1.23e+01 1dxrM 323 -35.99 -7.92 1.27e+01 2btvA 901 -34.80 -7.89 1.30e+01 1n1cA 217 -25.15 -7.88 1.31e+01 1omrA 201 -28.71 -7.85 1.33e+01 1kpkA 473 -37.61 -7.83 1.34e+01 1mmc 30 -19.71 -7.83 1.35e+01 1bi0 226 -22.89 -7.83 1.35e+01 1mtyD 512 -38.85 -7.81 1.36e+01 1nv8A 284 -24.06 -7.80 1.37e+01 1h2rL 534 -37.21 -7.73 1.43e+01 1a28A 256 -26.99 -7.73 1.43e+01 1f5sA 211 -24.74 -7.71 1.45e+01 6prcM 323 -35.42 -7.70 1.46e+01 1j97A 211 -24.74 -7.70 1.46e+01 1keyA 235 -29.44 -7.68 1.48e+01 2liv 344 -28.73 -7.64 1.52e+01 1m0kA 262 -32.41 -7.62 1.54e+01 1txb 73 -24.14 -7.60 1.55e+01 6gsvA 217 -28.19 -7.55 1.61e+01 1l7mA 211 -24.43 -7.55 1.61e+01 1e19A 314 -28.35 -7.54 1.62e+01 1ubkL 534 -36.35 -7.53 1.62e+01 2pvbA 107 -21.73 -7.53 1.63e+01 1pv5A 264 -28.64 -7.51 1.65e+01 1cdp 109 -20.85 -7.50 1.66e+01 1q41A 424 -27.61 -7.48 1.68e+01 1phnA 162 -22.75 -7.42 1.74e+01 1gweA 503 -36.57 -7.41 1.75e+01 1hcuA 503 -26.25 -7.37 1.80e+01 1auwA 468 -29.96 -7.31 1.87e+01 1dcnA 424 -28.12 -7.27 1.92e+01 1h21A 247 -31.01 -7.25 1.95e+01 1lufA 343 -25.68 -7.20 2.01e+01 1rvgA 305 -23.59 -7.20 2.01e+01 1egdA 396 -33.50 -7.16 2.05e+01 1pvaA 110 -21.36 -7.14 2.08e+01 1i1iP 681 -38.20 -7.10 2.14e+01 1el4A 195 -29.10 -7.07 2.18e+01 1fa0A 537 -32.99 -7.03 2.23e+01 1p49A 562 -35.40 -7.03 2.24e+01 1bolA 222 -23.15 -6.95 2.35e+01 1hyp 80 -20.72 -6.94 2.36e+01 1en2A 89 -23.09 -6.91 2.42e+01 1dguA 183 -27.36 -6.89 2.45e+01 1usgA 346 -30.60 -6.88 2.46e+01 1hbzA 498 -35.71 -6.86 2.50e+01 1n4qB 377 -30.59 -6.82 2.56e+01 1fa0B 537 -29.97 -6.81 2.58e+01 1iqbB 89 -22.45 -6.80 2.59e+01 2dtr 226 -22.11 -6.79 2.60e+01 1alvA 173 -30.34 -6.78 2.62e+01 1wer 334 -27.91 -6.74 2.70e+01 1gx5A 536 -27.40 -6.71 2.74e+01 1jchA 551 -51.46 -6.66 2.84e+01 1jchC 551 -51.46 -6.66 2.84e+01 1nw3A 416 -28.17 -6.64 2.88e+01 1csh 435 -26.80 -6.64 2.88e+01 1j1jA 240 -28.47 -6.59 2.98e+01 1htjF 210 -27.47 -6.58 2.99e+01 4cpv 109 -20.66 -6.51 3.12e+01 1qhbA 596 -38.98 -6.47 3.21e+01 1jf2A 195 -29.33 -6.46 3.22e+01 1jf0A 195 -28.24 -6.46 3.24e+01 1drs 59 -21.73 -6.45 3.25e+01 1kfuS 184 -30.02 -6.45 3.25e+01 1k7wA 468 -28.80 -6.41 3.33e+01 1npoC 95 -21.34 -6.41 3.34e+01 1rxwA 336 -27.88 -6.41 3.34e+01 1eo9A 209 -23.96 -6.40 3.36e+01 1o20A 427 -32.11 -6.38 3.40e+01 1r89A 437 -26.61 -6.38 3.41e+01 1a4iA 301 -25.18 -6.37 3.42e+01 1allA 160 -23.58 -6.37 3.43e+01 1phnB 172 -24.57 -6.34 3.48e+01 1qcrC 378 -34.34 -6.29 3.61e+01 1hrdA 449 -34.17 -6.28 3.63e+01 1bgvA 449 -34.16 -6.28 3.63e+01 1diaA 306 -25.47 -6.27 3.66e+01 1nr3A 122 -20.39 -6.26 3.68e+01 1cb0A 283 -21.25 -6.25 3.71e+01 1htxA 32 -19.01 -6.22 3.78e+01 1k89 449 -33.58 -6.21 3.80e+01 1mg7A 417 -24.89 -6.21 3.82e+01 1kn1A 160 -24.23 -6.19 3.87e+01 1qqfA 277 -26.18 -6.18 3.89e+01 1mpuA 138 -19.29 -6.17 3.91e+01 1quvA 578 -26.67 -6.16 3.93e+01 1mh1 186 -18.75 -6.15 3.97e+01