% 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.YDL013W.t2k-100-30-alpha Host: cc65 Mon Nov 11 16:47:28 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL0/YDL013W % --------------------------------------------------------------------- % 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 YDL013W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL013W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 620 nodes, 437.33 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(=1.5073) * Reverse)^tau(=0.8158))) % 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 1bpoA 494 -35.08 -10.46 5.55e-01 1gd1O 334 -33.19 -10.15 6.99e-01 1rdg 53 -28.01 -9.90 8.43e-01 1ffkN 95 -30.86 -9.84 8.80e-01 1plr 258 -33.24 -9.80 9.07e-01 2gd1O 334 -32.30 -9.76 9.36e-01 1plq 258 -33.17 -9.62 1.04e+00 1jj2P 95 -30.96 -9.49 1.15e+00 1ezvC 385 -36.13 -9.31 1.31e+00 1f4tA 368 -33.93 -9.22 1.41e+00 1kyoC 385 -36.14 -9.11 1.53e+00 1jm7A 112 -29.30 -9.08 1.56e+00 1j5vA 351 -32.07 -8.86 1.84e+00 1ygs 234 -31.50 -8.54 2.36e+00 1knyA 253 -31.47 -8.50 2.44e+00 1jk0A 419 -35.59 -8.47 2.49e+00 1dvpA 220 -32.21 -8.41 2.61e+00 1h9dB 134 -28.69 -8.36 2.72e+00 1g5aA 628 -34.92 -8.25 2.95e+00 1e6yA 569 -32.22 -8.17 3.13e+00 1e50B 134 -28.25 -8.06 3.42e+00 1gkuB 1054 -36.19 -8.00 3.57e+00 1lmzA 187 -30.03 -7.98 3.64e+00 1kanA 253 -30.56 -7.91 3.85e+00 1h9jA 145 -28.73 -7.85 4.01e+00 1jdc 429 -32.34 -7.74 4.38e+00 1zin 217 -30.91 -7.71 4.49e+00 1qtsA 247 -29.74 -7.67 4.62e+00 1f16A 192 -32.12 -7.58 4.98e+00 1kyfA 247 -29.57 -7.54 5.12e+00 1h9mA 145 -28.58 -7.53 5.15e+00 1j8fA 323 -30.47 -7.45 5.50e+00 1kum 108 -27.62 -7.41 5.68e+00 2jhbA 143 -27.45 -7.28 6.27e+00 1c4rA 182 -29.84 -7.20 6.68e+00 3pflA 759 -33.29 -7.17 6.85e+00 2pflA 759 -33.26 -7.10 7.24e+00 1i4lA 224 -35.87 -7.06 7.51e+00 1k8kG 151 -27.83 -7.01 7.77e+00 1chc 68 -26.19 -7.01 7.80e+00 1i7wA 538 -33.92 -6.95 8.15e+00 1g25A 65 -25.19 -6.94 8.21e+00 1g3jA 532 -33.35 -6.93 8.33e+00 1hulA 108 -28.83 -6.85 8.85e+00 2kfnA 605 -32.98 -6.85 8.88e+00 1jdhA 529 -33.25 -6.75 9.62e+00 1eu8A 409 -31.56 -6.74 9.65e+00 1opbA 135 -28.66 -6.70 1.00e+01 1ebaA 215 -28.05 -6.66 1.03e+01 1li1A 229 -28.38 -6.62 1.07e+01 1cm5A 759 -32.78 -6.61 1.07e+01 1be3A 446 -32.12 -6.57 1.11e+01 1ebpA 211 -27.87 -6.52 1.16e+01 1opaA 135 -28.49 -6.51 1.16e+01 1c1lA 136 -27.54 -6.46 1.21e+01 1gpjA 404 -36.05 -6.46 1.21e+01 1hdhA 536 -31.01 -6.45 1.22e+01 1pyp 285 -30.09 -6.43 1.24e+01 1qjvA 342 -29.80 -6.42 1.25e+01 1h9sA 140 -26.96 -6.32 1.36e+01 1ewqA 765 -34.56 -6.31 1.37e+01 1h8vA 218 -28.58 -6.30 1.38e+01 1b3uA 588 -37.95 -6.29 1.39e+01 1bupA 386 -31.57 -6.27 1.41e+01 1k32A 1045 -34.67 -6.26 1.42e+01 1c53 79 -26.03 -6.24 1.45e+01 1ba1 386 -31.48 -6.22 1.46e+01 1b77A 228 -28.52 -6.18 1.52e+01 1f6fA 199 -32.29 -6.18 1.52e+01 1qcrA 446 -32.01 -6.13 1.58e+01 1preB 470 -30.76 -6.13 1.58e+01 1dkgD 383 -29.95 -6.07 1.66e+01 1a1iA 90 -25.30 -6.03 1.71e+01 1e5rA 290 -30.39 -6.02 1.73e+01 1fxkB 109 -30.09 -6.02 1.73e+01 1phnB 172 -29.79 -5.99 1.77e+01 1hxn 219 -27.77 -5.99 1.78e+01 1gaxA 862 -33.91 -5.97 1.80e+01 1in4A 334 -29.13 -5.97 1.81e+01 1hr6B 443 -31.06 -5.95 1.83e+01 1zaaC 87 -25.13 -5.95 1.84e+01 1jsmB 176 -29.50 -5.94 1.85e+01 1h54A 754 -31.53 -5.94 1.85e+01 1fxiA 96 -25.72 -5.92 1.87e+01 1aayA 90 -25.37 -5.90 1.90e+01 1qcrC 378 -31.44 -5.89 1.92e+01 1rb9 53 -24.12 -5.87 1.95e+01 8rxnA 52 -24.05 -5.87 1.96e+01 1g41A 444 -32.48 -5.87 1.96e+01 1erd 40 -23.54 -5.87 1.96e+01 1bdmB 327 -30.18 -5.84 2.00e+01 1h99A 224 -31.28 -5.84 2.00e+01 1kay 381 -31.15 -5.83 2.03e+01 1gs5A 258 -28.68 -5.82 2.04e+01 1im2A 444 -31.42 -5.81 2.05e+01 1ey2A 471 -29.76 -5.80 2.07e+01 1d2rB 326 -30.46 -5.78 2.11e+01 1d2rA 326 -30.46 -5.78 2.11e+01 1fn8A 224 -29.80 -5.76 2.14e+01 1in6A 334 -28.84 -5.75 2.17e+01 1i36A 264 -30.98 -5.74 2.18e+01 1dk8A 147 -27.79 -5.73 2.19e+01 1eybA 471 -29.76 -5.72 2.21e+01 1hfuA 503 -30.44 -5.71 2.23e+01 1d2sA 170 -28.38 -5.70 2.25e+01 1e9gA 286 -29.17 -5.69 2.27e+01 1gnd 447 -29.41 -5.69 2.28e+01 1gg3A 279 -28.87 -5.69 2.28e+01 1gy6A 127 -26.44 -5.67 2.30e+01 1wgjA 286 -29.10 -5.67 2.31e+01 1akp 114 -25.34 -5.66 2.32e+01 1pmt 203 -29.31 -5.64 2.37e+01 1f5aA 513 -32.10 -5.62 2.40e+01 1f5fA 205 -28.84 -5.59 2.47e+01 1esmA 316 -30.17 -5.57 2.50e+01 1ezvB 352 -28.73 -5.57 2.51e+01 1bj7 156 -27.30 -5.56 2.52e+01 1bdmA 327 -30.06 -5.56 2.52e+01 1hp1A 516 -29.01 -5.56 2.54e+01 1kcvH 217 -27.22 -5.54 2.56e+01 1kgnA 329 -34.01 -5.53 2.58e+01 1bq8A 54 -23.13 -5.52 2.62e+01 1kdkA 177 -28.45 -5.51 2.63e+01 1ihgA 370 -30.26 -5.51 2.63e+01 1pbwA 216 -28.75 -5.51 2.63e+01 1rmd 116 -25.84 -5.50 2.66e+01 1jb1A 205 -27.85 -5.50 2.66e+01 1qfcA 306 -28.59 -5.49 2.67e+01 1bmdA 327 -29.88 -5.48 2.69e+01 1fxkA 107 -29.87 -5.48 2.69e+01 1ac0 108 -25.65 -5.44 2.78e+01 1brwA 433 -29.09 -5.44 2.79e+01 1preA 470 -30.56 -5.44 2.79e+01 1acz 108 -25.13 -5.42 2.83e+01 1e1oA 504 -30.31 -5.41 2.86e+01 1qj4A 257 -26.98 -5.38 2.95e+01 1l9xA 315 -27.63 -5.36 2.98e+01 1a65A 504 -30.19 -5.35 3.01e+01 1fkmA 396 -34.09 -5.34 3.03e+01 1hyiA 65 -24.46 -5.33 3.05e+01 1efvB 255 -27.82 -5.32 3.09e+01 1jb2A 127 -26.17 -5.32 3.10e+01 1try 224 -29.61 -5.31 3.12e+01 1f0xA 571 -29.45 -5.30 3.13e+01 2ahjA 206 -26.94 -5.30 3.13e+01 1gcyA 527 -31.87 -5.29 3.16e+01 1e9gB 286 -29.06 -5.29 3.17e+01 1ar0A 127 -26.03 -5.27 3.20e+01 1j7iA 264 -27.72 -5.27 3.21e+01 1ounA 127 -26.04 -5.26 3.24e+01 1d5tA 433 -28.82 -5.25 3.28e+01 1brfA 53 -22.77 -5.24 3.29e+01 1j7lA 264 -27.58 -5.23 3.34e+01 8prkB 287 -28.66 -5.22 3.34e+01 1i6kA 328 -30.44 -5.22 3.36e+01 1jksA 294 -27.85 -5.21 3.38e+01 8prkA 287 -28.64 -5.21 3.39e+01 1be3C 379 -32.08 -5.19 3.44e+01 1thv 207 -27.23 -5.18 3.47e+01 1kzhA 555 -29.51 -5.15 3.56e+01 1dqsA 393 -32.21 -5.14 3.58e+01 1alvA 173 -27.05 -5.11 3.68e+01 1m26A 133 -26.84 -5.10 3.72e+01 5eat 548 -35.80 -5.06 3.83e+01 1oyb 400 -28.37 -5.05 3.86e+01 1qgtA 149 -30.50 -5.05 3.86e+01 1thw 207 -26.87 -5.05 3.88e+01 1i6lA 328 -30.19 -5.04 3.89e+01 1cp3A 277 -28.53 -5.03 3.94e+01 1glaF 168 -25.94 -5.03 3.94e+01