% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53 % (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. % --------------------------------------------------------------------- % stridefoo.1.YGR017W.t2k-100-30-stride-ebghtl Host: farm03-10.kilokluster.ucsc.edu Fri Oct 6 04:11:52 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR017W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YGR017W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR017W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 298 nodes, 456.93 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(=1.3469) * Reverse)^tau(=0.8188))) % 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 2i51A 195 -250.38 -235.97 2.85e-45 1t9mA 214 -85.37 -73.91 1.82e-15 1ty9A 222 -75.61 -65.24 1.21e-13 1nrgA 261 -68.54 -53.49 4.24e-11 1dnlA 199 -59.91 -47.47 9.34e-10 1g79A 218 -59.59 -47.30 1.02e-09 1ci0A 228 -54.32 -39.99 4.82e-08 2a2jA 246 -50.37 -38.48 1.08e-07 2i02A 148 -31.90 -21.07 2.09e-03 2aq6A 147 -30.02 -19.57 5.19e-03 1xxoA 147 -27.89 -17.24 2.18e-02 1w9aA 147 -27.88 -17.23 2.20e-02 2fhqA 141 -27.79 -16.76 2.94e-02 2asfA 137 -25.18 -14.73 1.07e-01 1rfeA 162 -26.39 -14.52 1.22e-01 2dafA 118 -24.35 -13.45 2.44e-01 1egxA 115 -22.66 -12.41 4.84e-01 1f6bA 198 -22.32 -11.93 6.67e-01 2hhzA 150 -23.44 -11.92 6.71e-01 1vkxA 273 -23.70 -11.31 1.01e+00 2b25A 336 -22.16 -11.17 1.11e+00 1z9tA 255 -21.52 -11.10 1.16e+00 1tqnA 486 -22.82 -10.83 1.39e+00 1toh 343 -22.59 -10.72 1.50e+00 1i7qA 519 -22.88 -10.56 1.67e+00 1p7gA 222 -25.51 -10.39 1.88e+00 2aysA 348 -21.49 -10.26 2.05e+00 1duzA 275 -20.98 -9.75 2.91e+00 1d8iA 311 -20.50 -9.65 3.12e+00 1mlwA 301 -21.12 -9.65 3.13e+00 1qawF 74 -21.05 -9.57 3.31e+00 1d8hA 311 -20.72 -9.46 3.56e+00 1ywnA 316 -21.18 -9.28 4.05e+00 2extA 77 -20.85 -9.26 4.10e+00 1tmcA 175 -19.81 -9.25 4.12e+00 1lcf 691 -21.18 -9.03 4.81e+00 1e1hA 287 -23.65 -9.02 4.86e+00 1xh3A 276 -20.31 -8.96 5.07e+00 2av7A 275 -20.99 -8.94 5.13e+00 2av1A 275 -20.72 -8.89 5.33e+00 1i4fA 275 -20.65 -8.78 5.72e+00 1vm7A 311 -20.30 -8.77 5.79e+00 1a1nA 276 -20.24 -8.68 6.16e+00 2hq7A 146 -23.78 -8.68 6.17e+00 1a65A 504 -22.73 -8.64 6.31e+00 1jb7A 495 -22.34 -8.60 6.51e+00 1b0lA 691 -21.03 -8.58 6.62e+00 1p9rA 418 -20.57 -8.58 6.63e+00 1mg2D 155 -22.00 -8.58 6.63e+00 1b97A 244 -19.96 -8.44 7.29e+00 1hfuA 503 -22.36 -8.40 7.48e+00 1b1xA 689 -19.65 -8.39 7.56e+00 1hsbA 270 -19.67 -8.36 7.71e+00 2bvpA 276 -19.71 -8.36 7.72e+00 1nkxA 348 -19.38 -8.30 8.05e+00 1j8uA 325 -21.40 -8.28 8.18e+00 1cb6A 691 -20.39 -8.22 8.51e+00 1gtfA 74 -19.16 -8.11 9.21e+00 2bv5A 282 -20.73 -8.08 9.42e+00 1a1oA 276 -19.50 -8.01 9.94e+00 2b6dA 345 -19.21 -8.00 9.96e+00 1k5nA 276 -19.49 -8.00 1.00e+01 1agdA 276 -20.01 -7.96 1.03e+01 1cb8A 678 -21.67 -7.94 1.04e+01 2bfdA 400 -19.79 -7.89 1.08e+01 2i1sA 188 -20.60 -7.88 1.09e+01 1dmwA 307 -20.60 -7.81 1.14e+01 1otcA 495 -20.75 -7.81 1.15e+01 1egiA 147 -18.59 -7.80 1.15e+01 1iknA 286 -19.44 -7.76 1.18e+01 1eggA 147 -18.53 -7.73 1.21e+01 1o59A 355 -21.54 -7.73 1.22e+01 1wapA 75 -18.44 -7.71 1.23e+01 1kqfC 217 -18.31 -7.69 1.24e+01 1zdnA 158 -20.01 -7.68 1.26e+01 1sy7A 715 -20.26 -7.67 1.27e+01 1ecfA 504 -18.24 -7.62 1.31e+01 1kwkA 645 -22.16 -7.61 1.33e+01 1o65A 246 -18.31 -7.60 1.33e+01 1b9kA 238 -18.19 -7.60 1.34e+01 1kwgA 645 -22.16 -7.57 1.36e+01 1hm2A 700 -20.95 -7.57 1.36e+01 2ucz 165 -19.71 -7.56 1.37e+01 1ogpA 393 -18.85 -7.51 1.42e+01 2ciwA 299 -19.85 -7.46 1.47e+01 1cpo 299 -19.86 -7.46 1.47e+01 1gpmA 525 -18.06 -7.42 1.52e+01 1xd3A 230 -18.31 -7.41 1.52e+01 1hbzA 498 -19.79 -7.41 1.53e+01 1a36A 592 -18.30 -7.40 1.54e+01 1kjqA 391 -18.10 -7.38 1.57e+01 1a1mA 278 -19.20 -7.34 1.60e+01 3thiA 371 -19.00 -7.34 1.61e+01 1v4sA 455 -18.14 -7.31 1.65e+01 1qrjB 199 -18.68 -7.29 1.66e+01 2axtO 247 -19.65 -7.28 1.68e+01 1e43A 483 -19.05 -7.28 1.68e+01 1ez1A 392 -18.58 -7.27 1.69e+01 1a9eA 277 -18.79 -7.26 1.70e+01 1x7yA 400 -19.50 -7.26 1.71e+01 1mu5A 471 -20.25 -7.25 1.72e+01 1qu0A 191 -19.01 -7.24 1.72e+01 1eyzA 392 -18.49 -7.24 1.73e+01 2c2pA 199 -17.95 -7.21 1.77e+01 2htdA 140 -17.78 -7.19 1.79e+01 1rewA 114 -17.25 -7.19 1.79e+01 1gweA 503 -19.60 -7.18 1.80e+01 1hocA 272 -19.55 -7.14 1.86e+01 1jbbA 153 -20.21 -7.14 1.86e+01 2mtaC 147 -21.20 -7.12 1.89e+01 1ecfB 504 -17.55 -7.03 2.01e+01 2c2qA 199 -17.79 -7.01 2.04e+01 7ahlA 293 -19.54 -6.97 2.11e+01 1vqoE 178 -17.50 -6.96 2.12e+01 1h3gA 601 -19.16 -6.94 2.16e+01 1kyqA 274 -18.02 -6.88 2.25e+01 1ux6A 350 -31.95 -6.87 2.27e+01 1jj2E 177 -17.35 -6.85 2.29e+01 1s72E 178 -17.35 -6.85 2.30e+01 1jatA 155 -19.50 -6.82 2.35e+01 1sglA 209 -17.92 -6.81 2.37e+01 1gv4A 528 -18.11 -6.79 2.41e+01 1if1A 113 -18.85 -6.79 2.41e+01 1qtsA 247 -17.40 -6.78 2.42e+01 1jw9B 249 -16.95 -6.78 2.43e+01 1gpl 432 -19.98 -6.78 2.43e+01 1ffk1 177 -17.33 -6.77 2.43e+01 1wxcA 281 -23.98 -6.77 2.44e+01 4pah 308 -19.71 -6.75 2.48e+01 1oflA 481 -19.29 -6.75 2.48e+01 1qgxA 357 -20.67 -6.74 2.49e+01 2g9zA 348 -18.16 -6.73 2.51e+01 1gikA 261 -21.08 -6.72 2.53e+01 1larA 575 -19.94 -6.72 2.54e+01 1vjpA 394 -17.51 -6.71 2.55e+01 1pah 308 -19.51 -6.69 2.59e+01 1apa 266 -19.46 -6.69 2.59e+01 1gm7B 557 -20.37 -6.69 2.60e+01 1gk9B 557 -20.36 -6.67 2.63e+01 1qfoA 119 -18.11 -6.66 2.64e+01 2hkjA 469 -19.33 -6.65 2.66e+01 1pnkB 557 -19.49 -6.62 2.73e+01 1a35A 538 -17.73 -6.62 2.74e+01 1sqnA 261 -16.84 -6.60 2.77e+01 2fg9A 178 -17.17 -6.59 2.78e+01 1x1fA 149 -18.68 -6.58 2.80e+01 2thiA 379 -18.88 -6.57 2.83e+01 1kopA 223 -19.26 -6.56 2.85e+01 1a28A 256 -16.92 -6.55 2.88e+01 1l1eA 287 -18.22 -6.54 2.88e+01 2h57A 190 -18.13 -6.53 2.91e+01 2b5lC 222 -17.90 -6.53 2.91e+01 1mz5A 638 -21.39 -6.51 2.96e+01 1avbA 226 -17.55 -6.51 2.97e+01 1gkfB 557 -20.19 -6.50 2.97e+01 1m4uA 206 -19.30 -6.50 2.98e+01 1dboA 506 -18.88 -6.48 3.02e+01 1qydA 313 -17.03 -6.48 3.03e+01 1gm9B 557 -20.19 -6.48 3.03e+01 1ayzA 169 -18.87 -6.46 3.07e+01 1k4tA 592 -17.88 -6.45 3.09e+01 1sr7A 259 -16.68 -6.45 3.09e+01 2gp5A 349 -17.53 -6.41 3.18e+01 1waaA 93 -16.80 -6.40 3.20e+01 2hq9A 149 -16.92 -6.39 3.24e+01 1r1hA 696 -18.49 -6.33 3.38e+01 1ejjA 511 -17.95 -6.33 3.38e+01 1jlnA 297 -18.58 -6.33 3.38e+01 1f82A 424 -19.47 -6.33 3.38e+01 1w3fA 315 -19.89 -6.30 3.45e+01 1g9mG 321 -18.86 -6.29 3.49e+01 1dbgA 506 -18.28 -6.28 3.52e+01 1ej9A 563 -17.73 -6.26 3.56e+01 1ji2A 585 -20.04 -6.26 3.56e+01 1bunB 61 -16.76 -6.24 3.62e+01 1dmtA 696 -18.38 -6.23 3.63e+01 1w5cE 84 -16.44 -6.21 3.71e+01 1ajqB 557 -19.57 -6.19 3.75e+01 1e3aB 560 -19.99 -6.19 3.75e+01 1s5lE 84 -16.35 -6.17 3.81e+01 1dykA 394 -18.17 -6.15 3.86e+01 1zkoA 136 -15.43 -6.15 3.87e+01 2gujA 155 -16.62 -6.14 3.89e+01 1y7bA 542 -18.87 -6.11 3.98e+01