% 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. % --------------------------------------------------------------------- % alphafoo.1.YGR030C.t2k-100-30-alpha Host: cc50 Fri Nov 8 18:42:20 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR030C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.alphas % % 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 YGR030C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR030C.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 159 nodes, 106.69 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(=2.2051) * Reverse)^tau(=0.7702))) % 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 1qfoC 119 -27.48 -8.90 3.66e-01 1h0xA 100 -27.31 -8.44 5.48e-01 1mldA 314 -29.55 -8.39 5.68e-01 1ig8A 486 -30.18 -7.91 8.66e-01 1qfoA 119 -26.07 -7.48 1.27e+00 1qguB 519 -29.55 -7.08 1.82e+00 1bn7A 294 -27.19 -6.86 2.22e+00 1cqwA 295 -27.19 -6.83 2.27e+00 1bn6A 294 -27.11 -6.78 2.38e+00 1kk1A 410 -27.75 -6.66 2.65e+00 1qh8B 519 -29.04 -6.53 2.98e+00 1kllA 130 -24.74 -6.53 3.01e+00 1k7hA 476 -27.55 -6.39 3.40e+00 1ospH 218 -26.01 -6.34 3.56e+00 1adoA 363 -27.83 -6.29 3.76e+00 1ptf 88 -24.23 -6.28 3.77e+00 1gw0A 559 -28.30 -6.09 4.50e+00 1gt7A 274 -25.81 -6.02 4.80e+00 1ihmA 530 -27.87 -6.02 4.82e+00 1eo6A 117 -23.86 -5.98 4.98e+00 1jkmB 361 -26.71 -5.78 6.00e+00 1a26 361 -26.49 -5.78 6.00e+00 1gk8A 475 -27.05 -5.77 6.07e+00 1tubA 440 -27.88 -5.76 6.13e+00 1jkmA 358 -26.70 -5.72 6.40e+00 1mdl 359 -26.36 -5.68 6.64e+00 1preB 470 -28.58 -5.66 6.73e+00 2mnr 357 -26.15 -5.46 8.20e+00 1preA 470 -28.39 -5.45 8.24e+00 1lu9A 287 -25.93 -5.45 8.28e+00 1qfrA 89 -23.43 -5.44 8.33e+00 1e4fT 419 -27.00 -5.43 8.42e+00 1i4nA 251 -25.68 -5.24 1.01e+01 1efyA 350 -25.82 -5.23 1.02e+01 1nlr 234 -25.03 -5.17 1.08e+01 1add 349 -26.80 -5.15 1.10e+01 1g10A 102 -23.31 -5.14 1.11e+01 1dkrA 317 -27.00 -5.13 1.12e+01 1fkx 349 -26.69 -5.13 1.12e+01 1dfmA 223 -25.25 -5.13 1.13e+01 1jqeA 292 -27.85 -5.08 1.17e+01 8rucA 475 -26.50 -5.08 1.18e+01 1bla 155 -24.04 -5.08 1.18e+01 1j5yA 187 -24.79 -5.08 1.18e+01 2nlrA 234 -24.88 -5.06 1.20e+01 1ezwA 349 -26.42 -5.06 1.20e+01 1ibsA 317 -26.72 -5.02 1.25e+01 1dkuA 317 -26.77 -4.99 1.29e+01 1hstA 90 -22.47 -4.99 1.29e+01 1d2iA 223 -25.03 -4.98 1.30e+01 1cznA 169 -25.62 -4.98 1.31e+01 1hy3A 294 -24.97 -4.95 1.34e+01 1f7cA 231 -24.50 -4.93 1.36e+01 1a4mA 349 -26.54 -4.93 1.37e+01 1fofA 246 -24.87 -4.89 1.42e+01 1ofv 169 -25.63 -4.88 1.44e+01 2bopA 85 -21.84 -4.85 1.48e+01 1e3uA 246 -24.88 -4.81 1.54e+01 1k55A 246 -24.83 -4.77 1.59e+01 1lucA 355 -26.61 -4.69 1.72e+01 1i1qA 520 -26.93 -4.68 1.76e+01 1h77A 605 -27.09 -4.64 1.81e+01 1jkxA 212 -23.97 -4.64 1.82e+01 1cjsA 219 -24.82 -4.60 1.89e+01 1jffA 451 -26.80 -4.55 1.98e+01 1garA 212 -23.90 -4.52 2.05e+01 1btmA 252 -25.13 -4.51 2.06e+01 1k4fA 248 -24.72 -4.51 2.07e+01 1j4aA 333 -26.08 -4.50 2.09e+01 2gar 212 -23.87 -4.43 2.24e+01 1l6pA 125 -22.44 -4.41 2.28e+01 1jjhA 86 -21.41 -4.38 2.36e+01 1uroA 367 -25.42 -4.36 2.41e+01 1ek1A 554 -28.29 -4.35 2.43e+01 1qs2A 401 -25.74 -4.29 2.59e+01 1f3uB 171 -23.32 -4.27 2.64e+01 1hqkA 154 -24.24 -4.26 2.67e+01 1hlvA 131 -23.89 -4.21 2.79e+01 1lnqA 336 -24.85 -4.19 2.85e+01 1j71A 334 -25.14 -4.18 2.88e+01 1qlaA 656 -28.82 -4.13 3.04e+01 1h5rA 293 -25.42 -4.12 3.05e+01 1hueA 90 -21.31 -4.11 3.08e+01 1caj 260 -24.62 -4.11 3.10e+01 1ldg 316 -25.74 -4.10 3.12e+01 2cba 260 -24.51 -4.10 3.14e+01 1b73A 254 -24.16 -4.09 3.16e+01 1qs1A 462 -25.94 -4.07 3.23e+01 1b74A 254 -24.11 -4.06 3.25e+01 1bf4A 63 -20.71 -4.02 3.39e+01 1thg 544 -26.29 -4.02 3.41e+01 1knaA 69 -20.94 -4.01 3.42e+01 1e19A 314 -25.83 -4.00 3.45e+01 1jic 62 -20.74 -3.97 3.56e+01 1dbdA 100 -21.43 -3.97 3.59e+01 1brlA 355 -25.76 -3.97 3.59e+01 1bdg 451 -25.75 -3.96 3.60e+01 1floA 422 -25.60 -3.93 3.72e+01 1ehyA 294 -24.40 -3.92 3.75e+01 1ko7A 314 -24.84 -3.92 3.76e+01 1lzjA 292 -25.14 -3.92 3.77e+01 1hetA 374 -25.31 -3.90 3.86e+01