% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR217W.t2k-100-30-dssp-ebghstl Host: cc85 Thu Feb 26 19:04:08 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.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 YGR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR217W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 9381 sequences, 2218509 residues, 2040 nodes, 2841.68 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(=1.3817) * Reverse)^tau(=0.7654))) % 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 -48.75 -26.21 1.36e-03 3cln 148 -46.42 -26.21 1.36e-03 1top 162 -46.52 -24.19 3.47e-03 1ncx 162 -46.49 -24.15 3.53e-03 1cll 148 -48.38 -23.40 5.00e-03 1g4yR 148 -42.44 -23.17 5.58e-03 1t1dA 100 -35.10 -22.22 8.72e-03 1k4cC 124 -39.06 -21.78 1.07e-02 1r3jC 124 -39.06 -21.78 1.07e-02 1j95A 125 -38.87 -21.75 1.09e-02 1jvmA 125 -38.50 -21.64 1.15e-02 1jb0A 755 -54.97 -20.98 1.57e-02 1bl8A 97 -37.00 -20.70 1.81e-02 1exrA 148 -47.19 -20.46 2.03e-02 1avsA 90 -35.76 -20.43 2.05e-02 2mysB 166 -37.50 -20.19 2.31e-02 1zac 90 -36.25 -19.40 3.38e-02 1lnh 857 -62.78 -19.34 3.49e-02 1a68 95 -31.14 -19.12 3.89e-02 1iwgA 1053 -60.59 -19.07 3.98e-02 1osa 148 -46.56 -18.74 4.68e-02 1m46A 148 -31.50 -17.99 6.77e-02 1dsxA 87 -29.32 -17.30 9.56e-02 1m45A 148 -30.14 -17.19 1.01e-01 1kb9C 385 -52.89 -16.42 1.49e-01 1ezvC 385 -52.89 -16.35 1.55e-01 1j7rA 86 -30.78 -16.10 1.76e-01 1oyeA 1049 -58.33 -16.00 1.86e-01 1ehkA 562 -61.10 -15.72 2.13e-01 1kyoC 385 -52.09 -15.06 3.00e-01 1wdcC 156 -32.08 -14.87 3.32e-01 1byyA 53 -26.76 -14.79 3.47e-01 1o1fC 147 -31.66 -14.69 3.64e-01 1nn7A 105 -28.69 -14.55 3.92e-01 1be3C 379 -49.09 -14.40 4.24e-01 1ho2A 20 -25.29 -14.34 4.38e-01 1wdcB 156 -30.46 -13.74 6.01e-01 1o86A 589 -37.19 -13.29 7.62e-01 1ggwA 140 -27.22 -12.06 1.48e+00 9wgaA 171 -36.82 -11.92 1.61e+00 1qg9A 21 -23.51 -11.84 1.68e+00 1k9uA 78 -26.04 -11.80 1.71e+00 1ezfA 340 -35.72 -11.61 1.90e+00 1dceA 567 -38.31 -11.39 2.14e+00 1bf2 750 -45.28 -11.30 2.25e+00 1wgtA 186 -38.23 -11.21 2.38e+00 1irxA 523 -41.66 -10.87 2.86e+00 1mwvA 714 -43.63 -10.86 2.88e+00 1orsC 132 -38.28 -10.82 2.95e+00 1jbaA 204 -29.53 -10.75 3.06e+00 1k94A 165 -31.77 -10.67 3.21e+00 1aijL 281 -40.73 -10.66 3.23e+00 1oahA 519 -47.37 -10.53 3.47e+00 2scpA 174 -26.70 -10.51 3.51e+00 1nr6A 473 -41.29 -10.30 3.95e+00 1f4qA 165 -27.92 -10.26 4.03e+00 1f5aA 513 -34.63 -10.10 4.42e+00 1auwA 468 -31.81 -10.02 4.62e+00 1q0sA 259 -30.72 -9.81 5.23e+00 1n6bA 473 -38.91 -9.68 5.63e+00 1omrA 201 -28.93 -9.60 5.89e+00 1dhx 967 -55.96 -9.60 5.89e+00 1ctaA 36 -21.40 -9.58 5.97e+00 1jpaA 312 -27.91 -9.54 6.11e+00 1ddt 535 -37.63 -9.47 6.34e+00 1upkA 341 -31.82 -9.46 6.37e+00 1dcnD 436 -30.11 -9.45 6.42e+00 1n9dA 199 -29.96 -9.43 6.50e+00 1dguA 183 -27.32 -9.09 7.90e+00 1q9bA 43 -21.70 -8.99 8.39e+00 2lbp 346 -29.75 -8.98 8.46e+00 1el4A 195 -28.86 -8.92 8.74e+00 1ulmA 82 -26.46 -8.91 8.82e+00 5pal 109 -22.41 -8.88 8.96e+00 1dqeA 137 -25.42 -8.86 9.08e+00 1gntA 553 -40.88 -8.79 9.45e+00 1nv8A 284 -25.56 -8.78 9.50e+00 1rec 201 -25.33 -8.77 9.53e+00 1e2uA 553 -40.96 -8.77 9.57e+00 3kvt 115 -21.67 -8.76 9.60e+00 1hev 43 -21.48 -8.74 9.72e+00 2liv 344 -30.44 -8.68 1.01e+01 1pal 108 -21.81 -8.62 1.04e+01 1e6fA 143 -22.86 -8.58 1.07e+01 1n93X 375 -27.76 -8.57 1.07e+01 1f5sA 211 -25.53 -8.50 1.12e+01 1j97A 211 -25.53 -8.50 1.12e+01 1ponA 36 -19.82 -8.40 1.19e+01 1e1dA 553 -40.40 -8.39 1.19e+01 1gp0A 143 -22.93 -8.37 1.21e+01 1f0lA 535 -35.75 -8.37 1.21e+01 1phnA 162 -23.13 -8.37 1.21e+01 1br1B 150 -25.99 -8.36 1.22e+01 1l7mA 211 -25.20 -8.34 1.23e+01 1mtyD 512 -39.64 -8.28 1.28e+01 1q41A 424 -27.38 -8.25 1.30e+01 1gx5A 536 -28.56 -8.23 1.32e+01 1qhbA 596 -40.81 -8.19 1.35e+01 1g8iA 190 -27.55 -8.18 1.36e+01 1rxwA 336 -29.58 -8.15 1.38e+01 1i50A 1733 -79.78 -8.15 1.38e+01 1m1jA 491 -42.58 -8.10 1.42e+01 1jf2A 195 -28.33 -8.10 1.42e+01 1po5A 476 -40.42 -8.08 1.44e+01 1dcnA 424 -28.24 -8.06 1.46e+01 6gsvA 217 -28.17 -8.03 1.49e+01 1egdA 396 -34.04 -8.02 1.49e+01 1jk0A 419 -35.57 -8.01 1.50e+01 1dt6A 473 -40.17 -8.00 1.51e+01 1dlc 584 -29.97 -7.95 1.56e+01 1auiB 169 -28.51 -7.91 1.59e+01 1pvaA 110 -22.21 -7.87 1.63e+01 1m48A 133 -23.43 -7.84 1.66e+01 1jkw 323 -27.02 -7.83 1.67e+01 2pvbA 107 -21.94 -7.79 1.72e+01 2frvB 536 -31.95 -7.76 1.74e+01 1gweA 503 -38.43 -7.74 1.76e+01 1hy0A 466 -29.67 -7.73 1.78e+01 1ctdA 36 -19.61 -7.68 1.83e+01 1gupA 348 -27.69 -7.65 1.86e+01 1ulkA 126 -29.62 -7.61 1.92e+01 1dceB 331 -28.77 -7.59 1.94e+01 1gv3A 248 -28.55 -7.56 1.97e+01 1f6fA 199 -29.32 -7.55 1.98e+01 1quvA 578 -27.52 -7.51 2.03e+01 1cdp 109 -20.86 -7.49 2.06e+01 6prcL 273 -33.53 -7.44 2.12e+01 1kn1A 160 -24.62 -7.43 2.13e+01 1guqA 348 -27.36 -7.38 2.20e+01 1oohA 126 -23.12 -7.33 2.27e+01 1jf0A 195 -27.86 -7.32 2.28e+01 1alvA 173 -29.62 -7.31 2.29e+01 1frvB 536 -36.60 -7.30 2.31e+01 1allA 160 -23.82 -7.29 2.33e+01 1drs 59 -22.07 -7.27 2.35e+01 1e19A 314 -28.09 -7.23 2.41e+01 1i1iP 681 -39.91 -7.21 2.44e+01 1c2pA 576 -27.55 -7.19 2.47e+01 1kfuS 184 -29.79 -7.18 2.48e+01 1htjF 210 -27.79 -7.18 2.48e+01 1mmc 30 -18.94 -7.13 2.56e+01 1kxu 333 -27.20 -7.10 2.61e+01 1mmoD 512 -39.45 -7.09 2.62e+01 2lbd 267 -28.20 -7.08 2.65e+01 1phnB 172 -24.56 -7.04 2.72e+01 1em2A 229 -20.76 -7.02 2.74e+01 1hbzA 498 -37.37 -6.99 2.80e+01 1i0aA 466 -27.25 -6.91 2.93e+01 1usgA 346 -31.11 -6.88 3.00e+01 2occB 227 -25.41 -6.87 3.01e+01 4lbd 267 -27.98 -6.84 3.07e+01 1qcrC 378 -37.40 -6.83 3.09e+01 1uhnA 189 -26.55 -6.82 3.10e+01 1jeyB 565 -34.86 -6.82 3.11e+01 1bi0 226 -21.38 -6.81 3.13e+01 1b6a 478 -34.91 -6.75 3.25e+01 1zncA 266 -21.41 -6.73 3.28e+01 1dugA 234 -30.52 -6.71 3.32e+01 1qv1A 195 -26.95 -6.68 3.40e+01 1v54B 227 -26.87 -6.67 3.42e+01 1o6dA 163 -20.64 -6.64 3.48e+01 1aky 221 -23.06 -6.63 3.49e+01 4cpv 109 -20.87 -6.61 3.53e+01 1dxrL 273 -32.64 -6.61 3.54e+01 1hcuA 503 -25.51 -6.61 3.55e+01 1txb 73 -22.84 -6.60 3.55e+01 1i3cA 149 -19.51 -6.59 3.58e+01 1k7wA 468 -28.36 -6.56 3.65e+01 1hwxA 501 -35.76 -6.55 3.67e+01 1giqA 413 -32.80 -6.55 3.67e+01 1hwyA 501 -35.68 -6.55 3.68e+01 1an7A 136 -18.81 -6.52 3.74e+01 1n1cA 217 -24.14 -6.51 3.78e+01 1bn5 478 -34.94 -6.46 3.88e+01 1yge 839 -46.59 -6.46 3.90e+01 1ezvE 185 -20.30 -6.45 3.92e+01 1n4qB 377 -30.13 -6.44 3.93e+01 1kvkA 395 -24.94 -6.44 3.94e+01 1f8nA 839 -46.53 -6.43 3.96e+01 1scmB 145 -22.94 -6.43 3.96e+01