% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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. % --------------------------------------------------------------------- % str2foo.1.YGR032W.t2k-100-30-str2 Host: farm08 Wed Nov 17 20:33:20 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR032W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % 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 YGR032W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR032W.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 1896 nodes, 2608.04 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.4698) * Reverse)^tau(=0.7637))) % 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 1qbkB 890 -52.57 -19.07 3.11e-02 1mhyB 395 -43.24 -17.84 5.84e-02 1e8yA 966 -43.14 -16.54 1.15e-01 1cjaA 342 -32.27 -16.10 1.46e-01 1e7uA 961 -43.30 -14.87 2.82e-01 1u19A 349 -48.92 -14.31 3.81e-01 1fkmA 396 -43.34 -14.02 4.48e-01 6cts 433 -39.42 -13.92 4.74e-01 1t7pA 698 -42.28 -13.77 5.14e-01 1fz1C 389 -39.40 -13.56 5.76e-01 1l9hA 349 -47.41 -13.36 6.44e-01 1gw5B 591 -37.29 -12.45 1.07e+00 1hzxA 349 -46.58 -12.35 1.13e+00 1pu6A 218 -29.49 -12.35 1.14e+00 1j0mA 752 -31.28 -11.86 1.50e+00 1r9dA 787 -46.05 -11.82 1.54e+00 1eguA 731 -36.27 -11.81 1.54e+00 1x9mA 698 -41.19 -11.79 1.56e+00 1h2vC 771 -43.92 -11.71 1.63e+00 1rmi 160 -30.85 -11.65 1.70e+00 1t64A 377 -30.54 -11.49 1.85e+00 1n7oA 721 -35.83 -11.33 2.04e+00 1eupA 403 -32.65 -11.26 2.12e+00 1amoA 615 -27.50 -11.10 2.33e+00 1dnpA 471 -30.48 -11.03 2.43e+00 1mhyG 169 -26.66 -10.91 2.59e+00 1iapA 211 -28.91 -10.73 2.88e+00 1csc 433 -37.36 -10.68 2.97e+00 1lxkA 721 -35.06 -10.64 3.04e+00 1v4aA 440 -34.41 -10.62 3.08e+00 1so2A 420 -35.95 -10.60 3.11e+00 1lrv 244 -27.80 -10.55 3.21e+00 1g71A 347 -24.80 -10.22 3.88e+00 1iqrA 420 -27.12 -10.05 4.29e+00 1e8xA 961 -39.12 -10.04 4.33e+00 1f88A 348 -45.52 -9.95 4.58e+00 1csmA 256 -31.74 -9.93 4.62e+00 1itcA 516 -28.60 -9.92 4.65e+00 1jipA 403 -30.87 -9.91 4.68e+00 1r0vA 305 -22.89 -9.87 4.79e+00 1s9uA 207 -28.07 -9.86 4.82e+00 1ndk 155 -22.22 -9.74 5.17e+00 1ja1A 622 -28.08 -9.72 5.23e+00 1npk 154 -22.18 -9.69 5.34e+00 1gaxA 862 -33.82 -9.68 5.37e+00 1ihgA 370 -34.24 -9.64 5.49e+00 1ppjC 379 -43.55 -9.63 5.54e+00 2xis 387 -27.89 -9.62 5.56e+00 1b9zA 516 -28.25 -9.59 5.66e+00 1mxmA 254 -30.44 -9.56 5.76e+00 1kqfC 217 -40.42 -9.54 5.83e+00 1tn6A 382 -35.89 -9.48 6.04e+00 1jb0A 755 -44.01 -9.47 6.10e+00 1s2xA 206 -35.56 -9.46 6.13e+00 1qjaA 245 -33.50 -9.38 6.41e+00 1hmcB 148 -24.75 -9.37 6.47e+00 1f3fA 155 -21.90 -9.36 6.52e+00 1ayx 492 -35.12 -9.34 6.59e+00 1qjbA 245 -34.10 -9.32 6.65e+00 1nhkL 144 -20.97 -9.30 6.77e+00 4xis 387 -27.50 -9.28 6.84e+00 1xis 387 -27.49 -9.27 6.86e+00 1dofA 403 -34.10 -9.27 6.87e+00 1mnzA 388 -27.46 -9.25 6.97e+00 2pflA 759 -33.35 -9.24 6.98e+00 1amz 435 -39.32 -9.24 6.99e+00 1be3C 379 -43.08 -9.21 7.14e+00 2bidA 197 -27.69 -9.18 7.28e+00 1jcqA 382 -36.22 -9.16 7.36e+00 1ld8A 382 -36.25 -9.13 7.48e+00 1pw4A 451 -50.91 -9.12 7.54e+00 1rr7A 129 -27.40 -9.06 7.80e+00 1jk0B 345 -31.03 -9.02 8.00e+00 1oxa 403 -29.43 -8.87 8.77e+00 1rt8A 513 -34.47 -8.86 8.83e+00 1hmcA 148 -25.60 -8.83 9.00e+00 1gw9A 388 -27.54 -8.78 9.25e+00 1ft1A 377 -35.69 -8.76 9.35e+00 1mmoG 162 -25.03 -8.74 9.51e+00 1csh 435 -38.89 -8.72 9.61e+00 1tbfA 347 -33.35 -8.67 9.92e+00 1ir6A 424 -24.99 -8.66 9.94e+00 1fuoA 467 -36.34 -8.64 1.01e+01 1mtyG 162 -24.86 -8.59 1.04e+01 1sig 339 -31.75 -8.57 1.06e+01 1h6kA 757 -42.93 -8.54 1.07e+01 1uddA 226 -31.73 -8.47 1.12e+01 1o86A 589 -36.03 -8.41 1.16e+01 1cpt 412 -28.61 -8.41 1.16e+01 5csmA 256 -32.28 -8.39 1.18e+01 2ran 316 -28.37 -8.39 1.18e+01 1a8b 318 -28.42 -8.37 1.19e+01 3xis 387 -26.49 -8.32 1.23e+01 1aw9 216 -23.60 -8.27 1.27e+01 1a76 326 -24.80 -8.26 1.27e+01 1u7gA 385 -45.92 -8.23 1.30e+01 1l7vA 326 -45.69 -8.23 1.30e+01 1j4nA 271 -34.13 -8.21 1.32e+01 1b43A 340 -24.18 -8.20 1.33e+01 1ea3A 164 -25.05 -8.16 1.35e+01 1n97A 389 -27.00 -8.13 1.39e+01 1cnsA 243 -24.83 -8.12 1.39e+01 1d8dA 377 -34.91 -8.12 1.40e+01 1pot 325 -23.75 -8.08 1.42e+01 1j78A 458 -32.57 -8.08 1.43e+01 1qmzB 259 -27.65 -8.05 1.45e+01 1aa7A 158 -24.58 -8.03 1.48e+01 1fyhA 258 -31.92 -8.01 1.49e+01 1h16A 759 -31.04 -7.93 1.56e+01 4crxA 322 -27.86 -7.92 1.58e+01 1qhbA 596 -31.65 -7.91 1.59e+01 1pv6A 417 -49.37 -7.84 1.66e+01 1n1bA 549 -45.50 -7.82 1.68e+01 1gcvA 140 -24.35 -7.82 1.68e+01 3crxA 343 -29.73 -7.78 1.72e+01 1h7eA 245 -20.30 -7.77 1.73e+01 1f4tA 368 -26.15 -7.72 1.79e+01 1a8a 318 -27.55 -7.62 1.91e+01 1mmoB 384 -35.62 -7.61 1.92e+01 1r1mA 164 -20.19 -7.57 1.96e+01 1dxjA 242 -25.82 -7.57 1.97e+01 1muwA 386 -24.71 -7.55 1.99e+01 1uzeA 589 -34.56 -7.51 2.04e+01 1qlaC 256 -38.53 -7.51 2.05e+01 1j99A 293 -22.78 -7.49 2.06e+01 1jcrA 377 -34.67 -7.49 2.08e+01 1mtyB 384 -36.62 -7.48 2.09e+01 1ofcX 304 -30.21 -7.47 2.09e+01 1pzlA 237 -27.60 -7.43 2.16e+01 1b79A 119 -22.03 -7.40 2.19e+01 1cm5A 759 -30.96 -7.40 2.20e+01 1va6A 518 -28.63 -7.36 2.25e+01 1fjgD 209 -21.91 -7.35 2.26e+01 1up8A 598 -33.00 -7.35 2.27e+01 1hvd 319 -28.24 -7.27 2.38e+01 2baa 243 -23.36 -7.25 2.41e+01 1taq 832 -31.17 -7.24 2.43e+01 1avc 673 -35.39 -7.22 2.46e+01 1v33A 366 -21.71 -7.21 2.48e+01 1ecrA 309 -20.49 -7.19 2.50e+01 1i6lA 328 -27.82 -7.18 2.52e+01 1kbuA 349 -29.48 -7.16 2.56e+01 1f76A 336 -24.64 -7.15 2.56e+01 1ifa 158 -24.27 -7.15 2.57e+01 1rpa 342 -24.00 -7.12 2.62e+01 3pflA 759 -30.21 -7.09 2.67e+01 1lshA 1056 -30.58 -7.07 2.70e+01 1lla 628 -27.00 -7.07 2.71e+01 1swxA 209 -28.44 -7.07 2.71e+01 1br2A 791 -27.11 -7.07 2.71e+01 1fnnA 389 -24.70 -7.04 2.76e+01 1vin 268 -26.50 -7.03 2.79e+01 1aisB 200 -23.02 -7.01 2.81e+01 1by2 119 -18.86 -7.00 2.83e+01 1uf2A 1019 -24.38 -6.99 2.86e+01 1ovlA 271 -31.26 -6.93 2.97e+01 1q8iA 783 -28.08 -6.89 3.05e+01 1crxA 322 -27.45 -6.88 3.06e+01 1pah 308 -23.24 -6.85 3.13e+01 1nu7D 282 -37.33 -6.82 3.17e+01 1i6kA 328 -27.59 -6.81 3.20e+01 1i36A 264 -23.85 -6.79 3.24e+01 1q52A 314 -21.86 -6.79 3.24e+01 1j8uA 325 -23.52 -6.79 3.25e+01 1nrfA 262 -22.54 -6.77 3.29e+01 1rkpA 326 -28.37 -6.76 3.31e+01 1lfkA 398 -30.33 -6.74 3.36e+01 1a0jA 223 -19.37 -6.73 3.38e+01 1lkxA 697 -29.16 -6.71 3.41e+01 1t8qA 336 -20.87 -6.70 3.43e+01 1tubA 440 -23.58 -6.68 3.49e+01 1furA 467 -34.62 -6.67 3.50e+01 1gnlA 544 -30.36 -6.66 3.52e+01 1qi9A 556 -29.98 -6.66 3.53e+01 1io7A 368 -25.88 -6.66 3.53e+01 5bcaA 516 -28.02 -6.65 3.55e+01 1d5yA 292 -20.98 -6.61 3.66e+01 1jm7B 117 -20.51 -6.59 3.69e+01 1fpoA 171 -26.79 -6.58 3.72e+01 1etu 394 -25.26 -6.58 3.73e+01 1ddbA 195 -25.49 -6.54 3.83e+01 1w68A 390 -31.04 -6.54 3.83e+01 1l5wA 796 -31.40 -6.53 3.86e+01 1h1yA 228 -18.12 -6.52 3.87e+01 1j1jA 240 -31.53 -6.52 3.88e+01 1ht6A 405 -26.59 -6.52 3.88e+01 1rgqC 22 -15.93 -6.52 3.88e+01 1uumA 372 -21.70 -6.50 3.92e+01