% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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. % --------------------------------------------------------------------- % alphafoo.1.YGR236C.t2k-100-30-alpha Host: farm16.cse.ucsc.edu Fri Mar 3 08:55:41 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR236C % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR236C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR236C.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 96 nodes, 158.78 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=3.6876) * Reverse)^tau(=0.6979))) % Calculated when Simple < simple_threshold (10000.00) % 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 1nt4A 391 -16.63 -8.46 1.77e-01 1zvdA 380 -14.52 -6.49 1.15e+00 1sgg 75 -14.05 -6.17 1.57e+00 1s5lX 50 -14.93 -5.84 2.18e+00 1qmzB 259 -15.47 -5.76 2.39e+00 1m3yA 413 -13.23 -5.75 2.40e+00 1j5qA 437 -13.28 -5.73 2.44e+00 1t7pA 698 -14.40 -5.66 2.63e+00 1r5zA 323 -13.47 -5.39 3.49e+00 1zk7A 467 -13.13 -5.37 3.55e+00 1dfoA 417 -13.58 -5.32 3.76e+00 1k0nA 241 -13.50 -5.30 3.83e+00 1x9mA 698 -14.04 -5.29 3.87e+00 1zsxA 347 -13.31 -5.26 4.02e+00 2cohA 202 -13.15 -5.22 4.15e+00 1urqA 63 -13.17 -5.15 4.50e+00 1vk9A 151 -13.14 -5.15 4.50e+00 1m6dA 214 -13.10 -5.14 4.54e+00 1k9tA 540 -13.31 -5.09 4.80e+00 1yaxA 153 -13.05 -5.07 4.86e+00 1eni 138 -13.04 -5.03 5.11e+00 1yw0A 276 -13.55 -5.00 5.23e+00 1edqA 540 -13.22 -4.99 5.32e+00 2end 138 -13.01 -4.98 5.37e+00 1n2sA 299 -12.79 -4.96 5.49e+00 1k0mA 241 -13.49 -4.95 5.57e+00 1f07A 321 -13.33 -4.93 5.69e+00 1exbA 332 -12.94 -4.91 5.77e+00 1ctn 540 -13.13 -4.83 6.31e+00 1qrqA 325 -12.84 -4.82 6.35e+00 1bx4A 345 -13.03 -4.81 6.42e+00 1ffkV 143 -12.92 -4.78 6.69e+00 2lbp 346 -13.01 -4.56 8.43e+00 1ze3H 122 -11.56 -4.56 8.47e+00 1lvmA 229 -12.02 -4.50 9.02e+00 1vasA 137 -12.60 -4.49 9.16e+00 1b4fG 82 -12.32 -4.46 9.44e+00 1rylA 167 -12.43 -4.44 9.67e+00 2a6qA 86 -12.44 -4.43 9.74e+00 1r12A 258 -12.66 -4.43 9.80e+00 1vin 268 -14.56 -4.41 9.97e+00 1f0mA 82 -12.21 -4.39 1.02e+01 1rwtA 232 -12.66 -4.38 1.03e+01 1b4fA 82 -12.19 -4.38 1.03e+01 1uelB 48 -11.44 -4.38 1.04e+01 1wpgA 994 -13.85 -4.35 1.06e+01 1m2eA 135 -11.75 -4.34 1.07e+01 2afwA 329 -12.41 -4.33 1.09e+01 1enk 138 -12.49 -4.32 1.10e+01 1ou8A 111 -11.85 -4.32 1.10e+01 1nfiA 301 -11.84 -4.30 1.13e+01 1h2eA 207 -12.13 -4.30 1.13e+01 1lj8A 493 -12.38 -4.29 1.15e+01 1qhtA 775 -12.94 -4.28 1.16e+01 2aefA 234 -13.18 -4.20 1.27e+01 1k8mA 93 -11.74 -4.19 1.27e+01 1h8lA 380 -12.41 -4.19 1.28e+01 1hnnA 282 -12.37 -4.15 1.34e+01 1nfiC 301 -11.68 -4.13 1.36e+01 1t0qA 498 -12.60 -4.12 1.38e+01 1klpA 115 -12.47 -4.06 1.48e+01 1p9cA 45 -11.37 -4.06 1.49e+01 1vflA 356 -12.72 -4.05 1.50e+01 1qmuA 380 -12.29 -4.04 1.51e+01 1ebbA 202 -11.91 -4.03 1.53e+01 1ll2A 333 -12.46 -4.02 1.55e+01 1aa7A 158 -13.00 -4.01 1.57e+01 1xc0A 33 -11.64 -4.00 1.58e+01 1vp6A 138 -11.45 -3.96 1.65e+01 1yydA 357 -12.39 -3.95 1.67e+01 1jtdB 273 -11.69 -3.95 1.67e+01 1ovnA 248 -11.98 -3.95 1.68e+01 1vqoY 241 -12.57 -3.93 1.71e+01 1enj 138 -11.98 -3.88 1.82e+01 1u5tA 233 -12.37 -3.87 1.83e+01 1zsyA 357 -12.19 -3.87 1.84e+01 1yfnA 118 -11.30 -3.85 1.88e+01 1usgA 346 -12.17 -3.85 1.89e+01 1ea3A 164 -13.11 -3.84 1.90e+01 1pgs 314 -11.37 -3.81 1.97e+01 1ash 150 -12.32 -3.80 1.99e+01 1jeyB 565 -12.19 -3.79 2.02e+01 1dv2A 452 -11.44 -3.78 2.05e+01 1lbeA 258 -11.99 -3.76 2.08e+01 1tueB 218 -11.43 -3.75 2.10e+01 1o51A 114 -11.36 -3.75 2.11e+01 1w9yA 319 -11.72 -3.75 2.11e+01 1dv1A 449 -11.43 -3.74 2.14e+01 1jud 232 -11.56 -3.73 2.15e+01 2cz1A 206 -11.70 -3.73 2.16e+01 1bncB 449 -11.52 -3.73 2.16e+01 1zrn 232 -11.57 -3.72 2.18e+01 1pbgA 468 -12.16 -3.71 2.22e+01 1ll0A 339 -12.13 -3.71 2.22e+01 2c3vA 102 -10.92 -3.70 2.24e+01 3pflA 759 -12.76 -3.70 2.24e+01 1mn1 357 -12.10 -3.69 2.26e+01 1crkA 380 -12.12 -3.69 2.27e+01 1mnp 357 -12.11 -3.68 2.28e+01 1a17 166 -11.65 -3.65 2.36e+01 1z83A 196 -11.66 -3.65 2.37e+01 2aamA 309 -12.27 -3.64 2.40e+01 3adk 195 -11.76 -3.63 2.42e+01 1oyb 400 -12.16 -3.62 2.44e+01 1oyc 400 -12.02 -3.62 2.46e+01 1ds6B 180 -11.33 -3.61 2.50e+01 2lhb 149 -11.71 -3.60 2.50e+01 1bpyA 335 -11.75 -3.60 2.51e+01 1quqB 121 -11.30 -3.60 2.52e+01 2f96A 224 -11.52 -3.59 2.56e+01 1cm5A 759 -12.62 -3.55 2.65e+01 2ahjA 206 -11.44 -3.55 2.66e+01 1yp5A 58 -11.18 -3.55 2.68e+01 1mioA 534 -11.94 -3.54 2.71e+01 1tgoA 773 -12.41 -3.53 2.73e+01 1ahjA 207 -11.48 -3.53 2.74e+01 1jeqB 565 -11.96 -3.52 2.76e+01 2pflA 759 -12.60 -3.52 2.77e+01 3pbgA 468 -11.73 -3.51 2.79e+01 1y0hA 105 -11.71 -3.51 2.81e+01 1jj2X 240 -12.08 -3.49 2.86e+01 1g4yR 148 -11.74 -3.49 2.87e+01 1xfxO 149 -12.14 -3.47 2.93e+01 1zpvA 91 -10.86 -3.47 2.94e+01 1s72Y 241 -12.06 -3.47 2.95e+01 1h8eI 50 -11.47 -3.46 2.96e+01 1c0pA 363 -11.60 -3.46 2.97e+01 1s1iD 361 -12.14 -3.43 3.08e+01 1tv9A 335 -11.53 -3.42 3.10e+01 1h16A 759 -12.49 -3.41 3.16e+01 1lqtA 456 -11.78 -3.39 3.21e+01 1f88A 348 -12.43 -3.39 3.21e+01 1kfuS 184 -11.64 -3.39 3.23e+01 1bncA 449 -11.11 -3.38 3.25e+01 1a3aC 148 -11.72 -3.37 3.30e+01 1a3aA 148 -11.75 -3.37 3.31e+01 2aw4Q 117 -12.91 -3.37 3.31e+01 1am4A 199 -11.59 -3.36 3.35e+01 1lbvA 252 -11.12 -3.36 3.36e+01 1b22A 114 -11.65 -3.35 3.38e+01 1yruB 74 -11.27 -3.34 3.44e+01 1hqsA 423 -11.66 -3.32 3.51e+01 1nekC 129 -12.52 -3.32 3.51e+01 1fsu 492 -11.76 -3.32 3.53e+01 1ox8A 107 -10.75 -3.30 3.60e+01 3thiA 371 -11.43 -3.29 3.63e+01 1ds1A 324 -10.80 -3.28 3.69e+01 1y0vH 146 -11.97 -3.28 3.70e+01 1u04A 771 -12.30 -3.28 3.70e+01 1ruwA 69 -10.56 -3.27 3.71e+01 2ahjC 206 -11.22 -3.27 3.72e+01 1v9mA 323 -11.43 -3.27 3.75e+01 2c5uA 375 -11.40 -3.26 3.76e+01 2thiA 379 -11.52 -3.25 3.80e+01 1qqhA 144 -10.59 -3.25 3.81e+01 2d00A 109 -11.12 -3.25 3.84e+01 1oya 400 -11.74 -3.24 3.87e+01 1ko3A 230 -10.61 -3.24 3.87e+01 1xkwA 665 -10.74 -3.24 3.88e+01 1irxA 523 -12.22 -3.23 3.90e+01