% 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.YGR024C.t2k-100-30-str Host: cc69 Fri Nov 8 17:44:45 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR024C % --------------------------------------------------------------------- % 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 YGR024C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR024C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 238 nodes, 162.38 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(=1.3579) * Reverse)^tau(=0.8551))) % 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 1ezm 301 -35.27 -12.48 9.57e-02 1qgwC 177 -33.01 -12.40 1.01e-01 1hbq 183 -31.85 -11.55 1.97e-01 1hbp 183 -31.87 -11.52 2.01e-01 1aqb 183 -30.31 -10.07 6.30e-01 1k2yX 463 -32.97 -9.84 7.55e-01 1k3eA 156 -31.97 -9.81 7.74e-01 1efuB 282 -32.24 -9.79 7.87e-01 1g24A 211 -30.45 -9.71 8.36e-01 1g6oA 330 -32.87 -9.40 1.07e+00 1cxqA 162 -29.94 -9.28 1.19e+00 1cuk 203 -30.64 -9.20 1.26e+00 1hjp 203 -31.24 -9.18 1.28e+00 1b4uA 139 -28.29 -9.13 1.34e+00 1bouA 139 -27.92 -9.00 1.48e+00 1rbp 182 -29.26 -8.95 1.54e+00 1qlpA 394 -30.95 -8.80 1.74e+00 1ryt 190 -32.05 -8.80 1.75e+00 1kwkA 645 -34.15 -8.69 1.91e+00 1dvbA 191 -31.88 -8.67 1.95e+00 1asu 162 -29.38 -8.64 1.98e+00 1b71A 191 -31.70 -8.54 2.16e+00 1pyaB 228 -29.76 -8.52 2.19e+00 1khvA 516 -33.41 -8.50 2.22e+00 1pvdA 537 -31.42 -8.47 2.28e+00 2hmiA 558 -33.03 -8.42 2.37e+00 1pydA 556 -31.46 -8.38 2.47e+00 1j77A 209 -31.08 -8.32 2.58e+00 1kbuA 349 -32.79 -8.23 2.76e+00 4crxA 322 -32.10 -8.21 2.82e+00 1qpbA 563 -31.22 -8.15 2.95e+00 1crxA 322 -31.87 -8.09 3.10e+00 1f44A 324 -31.63 -8.09 3.11e+00 1bw9A 356 -30.33 -8.04 3.24e+00 3crxA 343 -32.76 -8.04 3.24e+00 1vsd 152 -28.45 -8.01 3.32e+00 1go4A 205 -34.22 -7.92 3.58e+00 1qlaC 256 -31.60 -7.60 4.67e+00 1qkmA 255 -32.71 -7.53 4.94e+00 1jdiA 231 -28.11 -7.50 5.07e+00 1hm6A 346 -29.76 -7.48 5.13e+00 1c1dA 355 -29.77 -7.47 5.18e+00 1tfe 145 -27.43 -7.41 5.47e+00 1cnt2 187 -30.42 -7.39 5.54e+00 1ihfA 99 -26.17 -7.37 5.65e+00 1bif 469 -29.78 -7.31 5.95e+00 1kq4A 232 -29.97 -7.18 6.60e+00 1jf0A 195 -28.85 -7.10 7.06e+00 1jp3A 253 -29.06 -7.06 7.30e+00 1dt6A 473 -31.62 -7.00 7.70e+00 3bifA 468 -29.62 -6.98 7.82e+00 1nmtA 392 -28.89 -6.93 8.12e+00 1jq3A 296 -29.87 -6.93 8.15e+00 1ig0A 319 -29.34 -6.92 8.21e+00 1cc1L 498 -29.58 -6.87 8.53e+00 1inlA 296 -29.87 -6.87 8.54e+00 1cec 343 -30.74 -6.85 8.68e+00 1bg2 325 -29.83 -6.78 9.20e+00 1h99A 224 -28.63 -6.77 9.28e+00 1hg2A 289 -29.00 -6.77 9.30e+00 1aokB 122 -25.66 -6.74 9.52e+00 1ej3A 191 -28.27 -6.74 9.52e+00 1jyoA 130 -26.94 -6.68 1.00e+01 2pfkA 320 -28.78 -6.67 1.01e+01 1pfkA 320 -28.82 -6.66 1.02e+01 1a8y 367 -30.01 -6.65 1.03e+01 1cb6A 691 -29.84 -6.63 1.04e+01 1dd5A 185 -28.73 -6.58 1.09e+01 3ertA 261 -28.38 -6.56 1.11e+01 1io2A 213 -28.61 -6.56 1.11e+01 4xiaA 393 -29.39 -6.56 1.11e+01 1ceo 343 -30.30 -6.56 1.12e+01 1jx4A 352 -31.04 -6.53 1.14e+01 9apiA 347 -28.41 -6.46 1.21e+01 2bdpA 580 -34.12 -6.43 1.24e+01 3bdpA 580 -34.14 -6.39 1.29e+01 1ax4A 467 -28.73 -6.36 1.32e+01 1f46A 140 -26.33 -6.33 1.35e+01 1qu6A 179 -26.61 -6.31 1.37e+01 1lox 662 -30.19 -6.30 1.39e+01 1ax0 239 -27.13 -6.29 1.39e+01 1bed 181 -27.56 -6.29 1.40e+01 1hf8A 289 -28.59 -6.27 1.42e+01 1yuiA 54 -22.29 -6.26 1.44e+01 1gzcA 239 -27.15 -6.26 1.44e+01 1f2tB 148 -27.86 -6.25 1.44e+01 19hcA 292 -26.21 -6.24 1.45e+01 1l2iA 261 -28.94 -6.21 1.50e+01 1f47B 144 -26.35 -6.21 1.50e+01 1pch 88 -24.65 -6.19 1.52e+01 1gaxA 862 -31.55 -6.18 1.54e+01 1prgA 270 -28.56 -6.16 1.57e+01 1dynA 125 -25.24 -6.13 1.60e+01 1axj 122 -27.23 -6.11 1.63e+01 1xwl 580 -33.76 -6.07 1.69e+01 1et9A 204 -25.91 -6.04 1.72e+01 1rypF 233 -29.37 -6.04 1.73e+01 1ayyA 151 -26.20 -6.03 1.74e+01 1qo0D 196 -28.42 -6.02 1.76e+01 1dofA 403 -30.06 -6.02 1.76e+01 1cn4C 166 -27.95 -6.01 1.77e+01 1jlnA 297 -27.86 -6.00 1.78e+01 1ii7A 333 -30.64 -6.00 1.79e+01 3erdA 261 -28.30 -5.94 1.89e+01 1jr8A 117 -28.50 -5.93 1.90e+01 2dynA 122 -24.84 -5.88 1.98e+01 1hv8A 367 -28.50 -5.86 2.01e+01 1de4C 640 -29.19 -5.85 2.03e+01 1ig3A 263 -26.46 -5.79 2.14e+01 1jk0A 419 -30.12 -5.76 2.20e+01 1jltB 122 -24.94 -5.76 2.20e+01 1f7wA 144 -25.64 -5.75 2.22e+01 1fvaA 217 -26.50 -5.75 2.22e+01 1jraA 117 -28.04 -5.72 2.27e+01 1i4uA 181 -27.87 -5.66 2.39e+01 1e85A 127 -25.95 -5.65 2.41e+01 1ii5A 233 -26.50 -5.65 2.42e+01 1lucB 324 -27.80 -5.64 2.43e+01 1h91A 180 -27.69 -5.64 2.44e+01 1fvgA 199 -26.38 -5.63 2.45e+01 1cgo 127 -26.02 -5.62 2.47e+01 1iiwA 232 -26.46 -5.61 2.49e+01 2kinA 238 -29.48 -5.59 2.53e+01 1ft1A 377 -28.22 -5.59 2.54e+01 1flmA 122 -26.74 -5.59 2.55e+01 1bmfG 272 -29.46 -5.57 2.59e+01 1egwA 77 -26.66 -5.55 2.63e+01 1hqvA 191 -26.54 -5.52 2.70e+01 1fzrA 138 -24.35 -5.51 2.71e+01 1a0p 290 -27.18 -5.51 2.71e+01 1f8mA 429 -28.17 -5.50 2.75e+01 2tmdA 729 -28.20 -5.50 2.76e+01 1k1vA 41 -21.49 -5.49 2.77e+01 1i3dA 146 -25.52 -5.49 2.77e+01 1vid 221 -27.31 -5.49 2.78e+01 9gafA 295 -28.54 -5.48 2.80e+01 1c7uA 85 -27.19 -5.47 2.83e+01 1djnA 729 -28.20 -5.46 2.85e+01 1hjrA 158 -26.05 -5.45 2.88e+01 1jcrA 377 -28.03 -5.44 2.91e+01 1ecmA 109 -26.37 -5.42 2.94e+01 1qfeA 252 -26.33 -5.36 3.09e+01 1f61A 429 -28.02 -5.36 3.11e+01 1pea 385 -27.62 -5.35 3.12e+01 1d8dA 377 -27.94 -5.35 3.13e+01 1ktpB 172 -26.53 -5.34 3.14e+01 1erp 38 -20.76 -5.34 3.16e+01 1m0dA 138 -24.23 -5.28 3.32e+01 1pioA 257 -26.35 -5.27 3.35e+01 1ghpA 258 -26.70 -5.27 3.36e+01 1gky 187 -25.55 -5.26 3.37e+01 1lliA 92 -23.82 -5.25 3.40e+01 1gpmA 525 -27.88 -5.25 3.40e+01 1klqA 197 -30.36 -5.22 3.51e+01 1jm6A 407 -29.22 -5.21 3.52e+01 1jksA 294 -27.23 -5.21 3.54e+01 1bvsB 203 -25.34 -5.21 3.54e+01 1kvoA 124 -25.03 -5.21 3.54e+01 1ex7A 186 -25.51 -5.19 3.60e+01 1g57A 217 -24.99 -5.15 3.72e+01 1a23 189 -26.44 -5.15 3.74e+01 1d0qA 103 -23.62 -5.14 3.76e+01 1eu8A 409 -27.86 -5.13 3.78e+01 1hy0A 466 -29.27 -5.13 3.80e+01 1phnB 172 -25.95 -5.11 3.85e+01 1phk 298 -27.04 -5.10 3.90e+01 1ab8A 220 -26.92 -5.08 3.96e+01 1edt 271 -25.80 -5.08 3.97e+01