% 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. % --------------------------------------------------------------------- % dsspfoo.1.YCR023C.t2k-100-30-dssp-ebghstl Host: cc72 Sun Nov 10 20:45:51 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCR0/YCR023C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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 YCR023C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YCR023C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 612 nodes, 422.66 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(=1.4743) * Reverse)^tau(=0.7656))) % 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 1qgrA 876 -135.35 -15.18 1.49e-01 1dxrM 323 -59.52 -14.53 2.13e-01 6prcM 323 -59.60 -14.19 2.57e-01 1kplA 473 -75.44 -13.18 4.52e-01 1rlr 761 -112.02 -12.73 5.82e-01 1f16A 192 -47.79 -11.72 1.04e+00 1is2A 661 -87.86 -11.61 1.11e+00 2occA 514 -75.29 -11.18 1.42e+00 2sqcA 631 -90.77 -10.54 2.07e+00 1jb0A 755 -69.80 -10.52 2.10e+00 1sqc 631 -91.68 -9.86 3.11e+00 1kpkA 473 -76.04 -9.47 3.93e+00 1jli 112 -38.33 -9.39 4.13e+00 1g2nA 264 -49.21 -9.28 4.42e+00 16vpA 366 -54.37 -9.18 4.71e+00 1eza 259 -56.00 -8.94 5.45e+00 2tct 207 -45.92 -8.92 5.52e+00 1h8aC 128 -48.31 -8.87 5.70e+00 1ldfA 281 -62.76 -8.86 5.73e+00 1c20A 128 -39.89 -8.75 6.12e+00 1iwgA 1053 -102.35 -8.74 6.17e+00 1bmfG 272 -45.38 -8.66 6.49e+00 1k3kA 158 -38.10 -8.61 6.67e+00 1mroA 548 -80.49 -8.51 7.12e+00 1hbnA 549 -80.47 -8.45 7.37e+00 1bxlA 181 -48.14 -8.45 7.39e+00 1ee4A 423 -67.59 -8.37 7.75e+00 1l58 164 -42.56 -8.34 7.89e+00 1bk6A 422 -66.71 -8.31 8.05e+00 1ktpA 162 -34.58 -8.28 8.23e+00 1ck7A 631 -110.68 -8.26 8.31e+00 1nbmG 272 -44.95 -8.19 8.68e+00 1mtyB 384 -69.76 -8.09 9.26e+00 1as4A 341 -53.58 -8.09 9.27e+00 1hwyA 501 -83.07 -8.04 9.53e+00 1h4lD 147 -38.10 -8.04 9.59e+00 256bA 106 -44.10 -8.03 9.59e+00 1af3 196 -39.85 -8.02 9.70e+00 1gqeA 365 -86.04 -7.93 1.02e+01 1dchA 104 -33.13 -7.92 1.03e+01 1kqqA 139 -42.19 -7.87 1.06e+01 1i0hA 205 -42.78 -7.87 1.06e+01 1hzfA 367 -45.83 -7.87 1.06e+01 1maz 221 -41.02 -7.85 1.08e+01 1e1qG 272 -45.07 -7.83 1.09e+01 1bk5A 422 -66.60 -7.80 1.11e+01 1c2pA 576 -75.79 -7.79 1.12e+01 1c3d 294 -50.16 -7.76 1.14e+01 1d5nA 205 -42.73 -7.74 1.16e+01 1zymA 258 -53.20 -7.68 1.20e+01 1hw8A 467 -58.45 -7.66 1.22e+01 1aa7A 158 -39.16 -7.60 1.26e+01 119l 164 -41.83 -7.59 1.27e+01 1fx8A 281 -60.92 -7.58 1.28e+01 1i9sA 210 -47.30 -7.54 1.31e+01 1mmoB 384 -66.72 -7.48 1.36e+01 1dcoA 104 -32.11 -7.47 1.38e+01 1l92 164 -41.61 -7.45 1.39e+01 1cznA 169 -42.71 -7.41 1.42e+01 1qasA 622 -73.71 -7.38 1.45e+01 1sesA 421 -63.67 -7.36 1.47e+01 1hwxA 501 -82.85 -7.33 1.50e+01 1dcpA 104 -31.97 -7.32 1.51e+01 1bjz 207 -46.12 -7.32 1.51e+01 1aoa 275 -56.96 -7.32 1.51e+01 1ofv 169 -42.42 -7.29 1.54e+01 1f93A 104 -31.81 -7.26 1.57e+01 1k4wA 252 -48.47 -7.23 1.60e+01 3vtk 343 -39.41 -7.22 1.61e+01 1floA 422 -60.66 -7.17 1.66e+01 1g5aA 628 -83.95 -7.12 1.72e+01 1ki1B 352 -70.54 -7.04 1.81e+01 1jb0L 154 -45.60 -7.03 1.83e+01 1jfbA 404 -69.21 -6.98 1.89e+01 1k30A 368 -61.58 -6.89 2.00e+01 1aueA 100 -38.11 -6.83 2.08e+01 1mat 264 -53.52 -6.78 2.15e+01 1f24A 402 -68.77 -6.75 2.19e+01 1djxA 624 -76.01 -6.75 2.19e+01 2ng1 293 -50.09 -6.65 2.33e+01 1lkyA 77 -33.24 -6.65 2.34e+01 1bxsA 501 -71.39 -6.63 2.38e+01 1e1dA 553 -76.89 -6.60 2.42e+01 1dcnD 436 -56.49 -6.59 2.44e+01 2matA 264 -53.40 -6.57 2.47e+01 1ji7A 89 -34.23 -6.56 2.48e+01 3nodB 423 -62.47 -6.56 2.48e+01 1gnlA 544 -71.62 -6.55 2.50e+01 1c24A 263 -53.33 -6.54 2.52e+01 1d2fA 390 -50.12 -6.54 2.52e+01 3fapB 94 -37.55 -6.53 2.53e+01 1qo7A 394 -45.12 -6.53 2.54e+01 1fa0A 537 -87.41 -6.51 2.57e+01 1qmzB 259 -49.21 -6.49 2.61e+01 3ygsP 97 -36.30 -6.46 2.65e+01 1nox 205 -36.68 -6.42 2.72e+01 1fezA 256 -47.57 -6.39 2.78e+01 1ksfX 758 -104.29 -6.38 2.80e+01 1sly 618 -84.49 -6.37 2.82e+01 1g1eB 89 -35.25 -6.37 2.82e+01 1gcvB 136 -43.72 -6.35 2.85e+01 1a59 378 -57.49 -6.34 2.87e+01 1jpnA 296 -49.50 -6.33 2.90e+01 1dcnA 424 -55.30 -6.32 2.91e+01 1efyA 350 -60.64 -6.32 2.91e+01 1ibrB 462 -81.11 -6.29 2.98e+01 1is8A 230 -41.04 -6.28 2.99e+01 1bgc 174 -34.56 -6.27 3.01e+01 6cts 433 -48.06 -6.27 3.01e+01 1gxyA 226 -45.99 -6.27 3.02e+01 1b2vA 188 -28.65 -6.26 3.04e+01 1dk0A 188 -28.65 -6.26 3.04e+01 1hdj 77 -40.44 -6.24 3.08e+01 1ew6A 137 -42.31 -6.20 3.15e+01 1ewaA 137 -42.31 -6.20 3.15e+01 1qsaA 618 -84.43 -6.18 3.21e+01 1nsgB 94 -37.34 -6.18 3.21e+01 1mngA 203 -40.07 -6.15 3.26e+01 4matA 278 -55.95 -6.15 3.27e+01 1kblA 873 -137.10 -6.15 3.27e+01 1ng1 294 -49.38 -6.12 3.34e+01 1ea3A 164 -39.00 -6.09 3.39e+01 1ak4C 145 -34.77 -6.09 3.40e+01 1dik 874 -135.30 -6.08 3.42e+01 2occD 147 -44.81 -6.02 3.56e+01 1eztA 166 -46.12 -5.97 3.67e+01 1ocrD 147 -44.72 -5.92 3.81e+01 1l7vA 326 -65.81 -5.91 3.85e+01 1dc1A 323 -64.52 -5.90 3.86e+01 1lxkA 721 -125.85 -5.89 3.90e+01 1qatB 622 -73.74 -5.88 3.91e+01 1ctt 294 -34.82 -5.88 3.92e+01 2at2A 300 -54.19 -5.87 3.93e+01 1qcrC 378 -53.16 -5.86 3.96e+01 1eijA 80 -31.55 -5.85 3.99e+01