% 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. % --------------------------------------------------------------------- % strfoo.1.YGR217W.t2k-100-30-str Host: cc54 Wed Nov 13 13:56:37 2002 % 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.strs % % 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 YGR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR217W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 2040 nodes, 2025.67 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(=1.3018) * Reverse)^tau(=0.7868))) % 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 -58.51 -24.62 1.66e-03 3cln 148 -55.81 -24.54 1.73e-03 1top 162 -57.20 -24.00 2.25e-03 1ncx 162 -57.17 -23.87 2.40e-03 1g4yR 148 -52.69 -22.64 4.40e-03 1t1dA 100 -43.86 -21.81 6.66e-03 1cll 148 -58.36 -21.75 6.85e-03 1jvmA 125 -46.91 -21.23 8.90e-03 1k4cC 124 -47.66 -21.18 9.13e-03 1j95A 125 -47.12 -21.02 9.91e-03 2mysB 166 -47.99 -20.39 1.37e-02 1bl8A 97 -45.35 -20.31 1.42e-02 1avsA 90 -44.42 -20.10 1.58e-02 1zac 90 -44.61 -18.88 2.97e-02 1a68 95 -39.86 -18.78 3.13e-02 1jb0A 755 -61.66 -18.63 3.37e-02 1exrA 148 -56.51 -18.01 4.65e-02 1osa 148 -56.94 -17.59 5.79e-02 1dsxA 87 -37.85 -17.17 7.24e-02 1byyA 53 -37.15 -17.09 7.55e-02 1iwgA 1053 -70.42 -16.75 9.03e-02 1lnh 857 -73.47 -16.34 1.13e-01 1j7rA 86 -39.32 -16.13 1.26e-01 1ezvC 385 -63.11 -15.24 2.03e-01 1ehkA 562 -68.70 -14.94 2.39e-01 1wdcC 156 -41.51 -14.74 2.66e-01 1wdcB 156 -41.97 -14.51 3.02e-01 1kyoC 385 -62.02 -14.32 3.35e-01 1be3C 379 -58.63 -14.21 3.55e-01 1ho2A 20 -30.91 -13.97 4.07e-01 1qg9A 21 -30.53 -12.80 7.81e-01 1dhx 967 -76.36 -12.70 8.27e-01 1ggwA 140 -38.15 -12.55 9.01e-01 1wgtA 186 -49.85 -12.09 1.17e+00 9wgaA 171 -48.48 -11.83 1.35e+00 1bf2 750 -55.53 -11.53 1.60e+00 1i50A 1733 -97.72 -11.30 1.84e+00 1dceA 567 -46.94 -11.07 2.09e+00 1aijL 281 -50.02 -11.02 2.16e+00 1jbaA 204 -39.70 -10.97 2.22e+00 1dqeA 137 -36.71 -10.86 2.37e+00 1ezfA 340 -44.15 -10.66 2.66e+00 1gntA 553 -54.70 -10.62 2.72e+00 1e2uA 553 -54.73 -10.60 2.75e+00 1mmoD 512 -53.06 -10.34 3.21e+00 2pvbA 107 -33.48 -10.26 3.37e+00 1e1dA 553 -54.06 -10.23 3.42e+00 1gupA 348 -43.42 -10.01 3.91e+00 1dugA 234 -43.14 -9.94 4.07e+00 1mtyD 512 -51.21 -9.93 4.09e+00 1k94A 165 -42.22 -9.91 4.12e+00 3kvt 115 -32.20 -9.88 4.22e+00 1guqA 348 -43.27 -9.80 4.42e+00 1gx5A 536 -42.44 -9.70 4.69e+00 1jk0A 419 -47.15 -9.70 4.69e+00 1ctaA 36 -28.68 -9.67 4.77e+00 1pvaA 110 -33.03 -9.58 5.04e+00 1pal 108 -31.93 -9.57 5.06e+00 1f5aA 513 -45.16 -9.53 5.17e+00 1f4qA 165 -38.00 -8.97 7.27e+00 1gweA 503 -51.90 -8.89 7.61e+00 1g8iA 190 -38.11 -8.86 7.77e+00 4cpv 109 -32.03 -8.82 7.98e+00 1phnA 162 -33.58 -8.78 8.15e+00 1quvA 578 -41.48 -8.74 8.37e+00 1hev 43 -29.05 -8.73 8.40e+00 1c2pA 576 -41.71 -8.72 8.45e+00 2scpA 174 -37.04 -8.71 8.50e+00 1rec 201 -35.49 -8.66 8.76e+00 1kfuS 184 -42.46 -8.57 9.24e+00 1qazA 351 -43.74 -8.57 9.29e+00 2lbp 346 -40.83 -8.51 9.59e+00 1alvA 173 -41.94 -8.39 1.03e+01 1hxpA 348 -40.14 -8.37 1.05e+01 1cdp 109 -30.79 -8.34 1.06e+01 1drs 59 -31.91 -8.26 1.12e+01 1cb0A 283 -34.50 -8.26 1.12e+01 1kq4A 232 -33.99 -8.24 1.13e+01 6gsvA 217 -38.44 -8.24 1.13e+01 1ctdA 36 -27.47 -8.23 1.14e+01 3erk 364 -38.69 -8.23 1.14e+01 1bi0 226 -33.63 -8.19 1.17e+01 5pal 109 -31.07 -8.14 1.21e+01 1dt6A 473 -51.80 -8.08 1.25e+01 1hbzA 498 -50.73 -8.07 1.26e+01 2frvB 536 -46.14 -8.04 1.28e+01 1j7dA 145 -32.62 -8.04 1.29e+01 1b6a 478 -48.46 -7.94 1.37e+01 1m48A 133 -32.81 -7.84 1.45e+01 1auiB 169 -38.71 -7.81 1.48e+01 1e6fA 143 -32.91 -7.80 1.49e+01 1phnB 172 -35.17 -7.80 1.49e+01 1dlc 584 -40.62 -7.79 1.50e+01 1dxrM 323 -45.61 -7.77 1.51e+01 1dcnD 436 -40.15 -7.77 1.52e+01 6prcM 323 -45.36 -7.75 1.53e+01 1mmc 30 -26.59 -7.72 1.57e+01 2liv 344 -40.08 -7.68 1.60e+01 1dttA 560 -49.25 -7.65 1.63e+01 1irxA 523 -49.26 -7.64 1.65e+01 1k75A 434 -37.84 -7.60 1.69e+01 1gp0A 143 -32.98 -7.55 1.74e+01 1jwhA 337 -40.61 -7.49 1.82e+01 1dceB 331 -39.96 -7.47 1.83e+01 1bn5 478 -48.50 -7.47 1.83e+01 1jpaA 312 -37.07 -7.45 1.85e+01 1kaeA 434 -37.72 -7.44 1.87e+01 1fa0B 537 -42.42 -7.39 1.93e+01 1e19A 314 -39.05 -7.36 1.96e+01 1hcuA 503 -37.87 -7.28 2.07e+01 2lbd 267 -38.79 -7.24 2.11e+01 1f6fA 199 -38.62 -7.22 2.15e+01 1mh1 186 -30.31 -7.19 2.18e+01 1csjA 531 -40.18 -7.19 2.18e+01 1g33A 73 -29.46 -7.18 2.19e+01 1h2rL 534 -47.42 -7.13 2.28e+01 2dtr 226 -33.09 -7.09 2.32e+01 1qlaA 656 -56.45 -7.09 2.32e+01 4lbd 267 -38.64 -7.09 2.33e+01 1allA 160 -33.42 -7.01 2.45e+01 1dmuA 299 -38.68 -6.98 2.50e+01 1c3cA 429 -39.88 -6.96 2.53e+01 1ponA 36 -25.53 -6.91 2.62e+01 1f5sA 211 -36.07 -6.89 2.65e+01 1j97A 211 -36.07 -6.88 2.66e+01 1egdA 396 -44.34 -6.85 2.72e+01 1fa0A 537 -44.55 -6.83 2.74e+01 1pme 380 -37.47 -6.82 2.77e+01 1fqyA 269 -35.89 -6.76 2.88e+01 1txb 73 -32.42 -6.74 2.91e+01 1l7mA 211 -35.72 -6.73 2.94e+01 1ezvE 185 -31.23 -6.65 3.08e+01 1a4iA 301 -36.02 -6.59 3.20e+01 1dx5I 118 -31.46 -6.54 3.30e+01 2btvA 901 -45.75 -6.53 3.33e+01 1diaA 306 -36.36 -6.53 3.34e+01 1c3wA 222 -41.43 -6.48 3.45e+01 1h2aL 567 -45.51 -6.46 3.48e+01 1iqbB 89 -30.98 -6.44 3.55e+01 1g5hA 454 -32.80 -6.43 3.55e+01 1htxA 32 -26.01 -6.42 3.58e+01 1en2A 89 -31.44 -6.40 3.63e+01 6prcL 273 -42.53 -6.37 3.70e+01 1apxA 249 -40.08 -6.35 3.75e+01 1jf0A 195 -38.50 -6.32 3.82e+01 1fokA 568 -49.39 -6.32 3.83e+01 1g6q2 328 -32.83 -6.31 3.85e+01 1btkB 169 -33.50 -6.29 3.89e+01 1csh 435 -36.66 -6.28 3.92e+01