% 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.YDR528W.t2k-100-30-alpha Host: cc54 Sat Dec 7 05:46:11 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR5/YDR528W % --------------------------------------------------------------------- % 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 YDR528W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDR528W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 424 nodes, 293.73 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(=2.6090) * Reverse)^tau(=0.7423))) % 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 1es6A 296 -32.41 -9.74 1.17e-01 2fcr 173 -29.35 -8.73 2.78e-01 1bzyA 217 -31.01 -8.68 2.89e-01 1dx5I 118 -29.31 -8.58 3.15e-01 1f6aB 222 -29.22 -7.84 6.09e-01 1ltqA 301 -30.07 -7.70 6.84e-01 1hmpA 217 -29.53 -7.51 8.17e-01 1i7fA 292 -29.82 -7.47 8.47e-01 1fp5A 222 -28.98 -7.42 8.80e-01 1adx 40 -24.35 -6.88 1.45e+00 1dqbA 83 -25.62 -6.83 1.52e+00 1f37A 110 -26.09 -6.64 1.81e+00 1hw7A 255 -28.18 -6.58 1.91e+00 1m2aA 110 -25.88 -6.41 2.24e+00 2adx 40 -23.66 -6.39 2.28e+00 1o0vA 327 -30.05 -6.34 2.39e+00 1m2dA 110 -25.88 -6.33 2.40e+00 2lgsA 468 -29.30 -6.32 2.43e+00 1d0bA 213 -28.26 -6.30 2.48e+00 1lf2A 331 -30.10 -6.29 2.50e+00 1nddA 76 -24.43 -6.21 2.71e+00 1lgr 468 -29.17 -6.20 2.73e+00 1g2iA 166 -27.30 -6.17 2.82e+00 1jfvA 131 -26.96 -6.07 3.07e+00 1qcsA 211 -28.19 -6.05 3.13e+00 1pfo 500 -29.84 -6.00 3.28e+00 1qovH 260 -28.12 -5.91 3.58e+00 1cozA 129 -27.35 -5.78 4.07e+00 1an9A 340 -28.10 -5.77 4.10e+00 1aa8A 347 -28.66 -5.76 4.13e+00 1nddD 76 -23.83 -5.66 4.55e+00 1a8d 452 -30.54 -5.66 4.58e+00 1diwA 441 -30.18 -5.64 4.65e+00 1mn1 357 -29.48 -5.64 4.66e+00 1a04A 215 -26.07 -5.62 4.75e+00 1rcf 169 -27.29 -5.61 4.79e+00 1hlcA 129 -26.67 -5.52 5.25e+00 1qhoA 686 -29.42 -5.45 5.57e+00 1e50A 134 -25.84 -5.44 5.63e+00 3uagA 437 -27.85 -5.42 5.78e+00 1hi0P 664 -28.92 -5.41 5.82e+00 1cznA 169 -26.22 -5.34 6.23e+00 1ofv 169 -26.34 -5.34 6.26e+00 2glsA 470 -28.44 -5.33 6.32e+00 1j7xA 302 -27.37 -5.29 6.55e+00 1hhsA 664 -28.83 -5.29 6.56e+00 1hr6B 443 -28.98 -5.29 6.56e+00 1iqrA 420 -28.10 -5.28 6.59e+00 1h6tA 291 -27.96 -5.28 6.62e+00 1c96A 753 -29.88 -5.25 6.79e+00 1amj 754 -30.25 -5.23 6.94e+00 1b0jA 754 -30.07 -5.18 7.33e+00 1p35A 299 -28.03 -5.15 7.52e+00 1htrB 329 -28.41 -5.15 7.55e+00 8acn 754 -30.12 -5.10 7.93e+00 1dykA 394 -28.10 -5.09 7.99e+00 4uagA 437 -27.47 -5.08 8.07e+00 7acn 754 -29.95 -5.07 8.10e+00 1aw8E 91 -24.41 -5.06 8.20e+00 1f4pA 147 -25.53 -5.06 8.20e+00 1krhA 338 -30.13 -5.05 8.32e+00 1j6pA 418 -27.55 -5.03 8.44e+00 1ee2A 373 -27.75 -5.02 8.59e+00 1uag 437 -27.42 -5.00 8.72e+00 1ppfE 218 -27.27 -4.98 8.90e+00 1kzhA 555 -28.87 -4.97 9.02e+00 6acn 754 -29.91 -4.94 9.30e+00 1aw8B 91 -23.99 -4.93 9.36e+00 4bcl 366 -27.61 -4.89 9.71e+00 1bu5A 147 -25.05 -4.86 1.01e+01 2fx2 147 -25.08 -4.85 1.01e+01 1f52A 468 -28.79 -4.84 1.02e+01 1j8hD 212 -26.66 -4.84 1.03e+01 1h0oA 390 -27.10 -4.81 1.06e+01 1l8rA 101 -23.51 -4.81 1.06e+01 1hh2P 344 -28.14 -4.78 1.09e+01 1eagA 342 -28.28 -4.77 1.10e+01 1f0lA 535 -27.91 -4.76 1.11e+01 1eh9A 558 -29.30 -4.73 1.14e+01 1j9eA 147 -24.80 -4.72 1.16e+01 1gbg 214 -26.97 -4.72 1.16e+01 1ueaB 184 -25.11 -4.67 1.22e+01 1xsm 390 -26.84 -4.66 1.22e+01 2dorA 311 -26.60 -4.64 1.25e+01 1erjA 393 -32.74 -4.63 1.27e+01 1e87A 118 -24.32 -4.61 1.29e+01 1brt 277 -26.09 -4.61 1.30e+01 1dorA 311 -26.44 -4.56 1.37e+01 1akr 147 -24.44 -4.52 1.42e+01 1epnE 330 -27.78 -4.44 1.54e+01 2tbvA 387 -28.39 -4.40 1.60e+01 1di0A 158 -24.14 -4.37 1.65e+01 1abrB 267 -27.34 -4.37 1.65e+01 1a8s 273 -26.34 -4.37 1.65e+01 1fc6A 388 -27.33 -4.37 1.66e+01 1l1dA 152 -26.02 -4.37 1.66e+01 1mhlC 466 -27.80 -4.35 1.69e+01 1ppt 36 -20.73 -4.34 1.70e+01 1smeA 329 -28.21 -4.32 1.74e+01 1efdN 266 -25.64 -4.32 1.74e+01 1sftA 388 -26.58 -4.31 1.76e+01 1cqqA 180 -25.33 -4.31 1.76e+01 1dr9A 201 -27.10 -4.30 1.77e+01 1jl3A 139 -23.53 -4.28 1.81e+01 1llwA 1520 -30.54 -4.28 1.82e+01 1tgoA 773 -29.18 -4.25 1.88e+01 2af8 86 -22.63 -4.24 1.88e+01 1cxpC 466 -27.87 -4.22 1.93e+01 1d0hA 469 -30.02 -4.20 1.97e+01 1lbvA 252 -26.09 -4.18 2.01e+01 1ddt 535 -27.34 -4.18 2.01e+01 5er2E 330 -27.53 -4.13 2.13e+01 1gk8I 140 -23.96 -4.12 2.15e+01 1gzcA 239 -26.40 -4.11 2.16e+01 1ehaA 558 -28.84 -4.11 2.16e+01 1kshA 186 -24.93 -4.11 2.17e+01 1smvA 260 -26.90 -4.10 2.20e+01 1broA 277 -25.75 -4.09 2.21e+01 1ko6A 187 -25.63 -4.08 2.24e+01 1af8 86 -22.60 -4.08 2.24e+01 1ir6A 424 -26.13 -4.06 2.27e+01 1gvuA 329 -27.45 -4.06 2.28e+01 1air 353 -27.49 -4.06 2.29e+01 1booA 323 -27.01 -4.05 2.31e+01 1d2vC 466 -27.48 -4.03 2.36e+01 2pec 353 -27.34 -4.02 2.38e+01 1jv2A 957 -29.82 -4.01 2.40e+01 1pfzA 380 -28.16 -4.01 2.40e+01 1cq3A 233 -26.00 -4.01 2.41e+01 1b00A 127 -23.06 -4.00 2.44e+01 1jpeA 151 -25.04 -3.99 2.45e+01 2er7E 330 -27.11 -3.98 2.48e+01 1a87 321 -25.34 -3.96 2.54e+01 1tap 60 -22.20 -3.95 2.56e+01 1agnA 373 -26.53 -3.92 2.63e+01 1l6pA 125 -24.37 -3.92 2.66e+01 1ahsA 126 -24.46 -3.90 2.69e+01 1m4iA 181 -24.65 -3.90 2.70e+01 1ezvE 185 -25.40 -3.89 2.75e+01 1ek8A 185 -24.48 -3.88 2.77e+01 1h6kA 757 -27.23 -3.87 2.78e+01 1e8tA 454 -28.14 -3.87 2.78e+01 1c5cL 214 -25.68 -3.87 2.80e+01 1i1iP 681 -27.51 -3.86 2.82e+01 1hyqA 263 -25.22 -3.85 2.85e+01 1fiwA 290 -26.11 -3.83 2.90e+01 1heuA 374 -27.31 -3.82 2.94e+01 1evyA 366 -25.89 -3.79 3.05e+01 2btfA 375 -26.90 -3.78 3.07e+01 1b87A 181 -24.09 -3.78 3.08e+01 1k7hA 476 -27.47 -3.77 3.10e+01 1hetA 374 -27.08 -3.77 3.11e+01 1e8uA 454 -28.03 -3.77 3.11e+01 1gy9A 283 -26.44 -3.77 3.12e+01 1qreA 247 -26.16 -3.76 3.14e+01 1hx2A 60 -21.64 -3.76 3.15e+01 1ik6A 369 -26.09 -3.73 3.23e+01 1kr5A 226 -25.46 -3.72 3.28e+01 1ezwA 349 -25.37 -3.71 3.31e+01 1cmoA 127 -24.19 -3.70 3.36e+01 1b3qA 379 -27.53 -3.70 3.37e+01 1crzA 403 -26.52 -3.69 3.37e+01 1pamA 686 -27.95 -3.69 3.40e+01 1mq7A 154 -24.33 -3.67 3.46e+01 1tit 98 -22.63 -3.67 3.47e+01 1dmzA 158 -24.31 -3.66 3.48e+01 1xel 338 -25.53 -3.66 3.50e+01 1l2mA 118 -23.13 -3.66 3.51e+01 1j8iA 93 -22.81 -3.65 3.53e+01 1qu5A 182 -24.95 -3.63 3.60e+01 1gajA 257 -25.77 -3.63 3.61e+01 1bvp1 349 -25.64 -3.62 3.64e+01 1gqwA 283 -26.51 -3.61 3.69e+01 1h9dA 134 -23.86 -3.61 3.70e+01 1cjbA 231 -25.36 -3.61 3.71e+01 2eifA 136 -24.63 -3.60 3.72e+01 2occJ 59 -21.09 -3.60 3.72e+01 1ffyA 917 -28.60 -3.59 3.76e+01 1qu2A 917 -28.60 -3.59 3.76e+01 2mllB 255 -25.84 -3.59 3.77e+01 1gr2A 279 -25.02 -3.58 3.82e+01 1jf8A 131 -23.24 -3.57 3.84e+01 1aim 215 -24.31 -3.56 3.88e+01 1f6dA 376 -25.32 -3.56 3.91e+01 1kigI 60 -21.58 -3.55 3.92e+01 1ffkG 145 -23.11 -3.55 3.95e+01 1ey2A 471 -27.40 -3.55 3.96e+01