% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR013W.t2k-100-30-dssp-ehl2 Host: farm09.cse.ucsc.edu Sun Mar 19 23:24:08 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR013W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR013W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR013W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 621 nodes, 1023.59 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(=1.3649) * Reverse)^tau(=0.8032))) % 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 1m6yA 301 -27.58 -13.38 3.67e-01 1qgrA 876 -33.13 -12.05 8.41e-01 1wa5C 960 -32.14 -11.77 1.00e+00 1uuqA 440 -24.57 -11.74 1.02e+00 1i50A 1733 -27.77 -11.63 1.10e+00 1gvfA 286 -24.94 -11.51 1.18e+00 1twfA 1733 -27.20 -11.14 1.50e+00 1mp1A 111 -22.68 -10.76 1.92e+00 1hm2A 700 -24.71 -10.15 2.84e+00 1jbwA 428 -22.40 -10.04 3.06e+00 1keiA 316 -25.10 -9.99 3.16e+00 1hyt 316 -25.06 -9.99 3.17e+00 6tmnE 316 -25.06 -9.99 3.17e+00 8tlnE 316 -25.06 -9.99 3.17e+00 2tmnE 316 -25.06 -9.97 3.20e+00 1cb8A 678 -23.85 -9.97 3.20e+00 1fgs 428 -22.37 -9.79 3.61e+00 1zb1A 392 -27.93 -9.73 3.76e+00 1zkiA 133 -20.60 -9.71 3.81e+00 1j0hA 588 -23.61 -9.35 4.81e+00 1k28A 584 -22.44 -9.28 5.05e+00 1b9hA 388 -23.46 -9.28 5.07e+00 1lzlA 323 -21.36 -9.22 5.27e+00 2ts1 419 -26.19 -9.21 5.30e+00 1l8qA 324 -24.29 -8.95 6.30e+00 2cvxA 888 -22.52 -8.83 6.84e+00 1bvwA 360 -22.70 -8.63 7.83e+00 1ocnA 362 -22.71 -8.62 7.88e+00 1oc7A 364 -22.70 -8.61 7.94e+00 2bvwA 362 -22.71 -8.59 8.00e+00 1lwjA 441 -21.21 -8.47 8.72e+00 1clxA 347 -20.23 -8.37 9.33e+00 1pgjA 478 -21.39 -8.33 9.54e+00 1uruA 244 -26.02 -8.30 9.77e+00 1sqc 631 -23.32 -8.29 9.79e+00 1gmlA 178 -21.66 -8.16 1.07e+01 2bneA 241 -20.66 -8.12 1.10e+01 1vgvA 384 -21.52 -8.11 1.11e+01 2d7vA 162 -21.01 -8.03 1.17e+01 1f6dA 376 -21.34 -8.03 1.17e+01 1ynmA 247 -20.82 -7.91 1.27e+01 2fkcA 247 -20.63 -7.91 1.28e+01 1ekeA 230 -24.26 -7.89 1.29e+01 2bidA 197 -23.58 -7.81 1.37e+01 1eia 207 -22.48 -7.78 1.39e+01 1d8cA 723 -22.19 -7.76 1.41e+01 1xyfA 436 -20.64 -7.74 1.43e+01 2es4D 332 -23.79 -7.71 1.46e+01 2bcgY 206 -19.73 -7.69 1.49e+01 2awdA 323 -19.31 -7.68 1.49e+01 1ukvY 206 -19.69 -7.68 1.50e+01 2ao9A 155 -21.36 -7.65 1.52e+01 1w32A 348 -19.61 -7.63 1.55e+01 2f02A 323 -19.23 -7.62 1.56e+01 1sfkA 76 -19.36 -7.61 1.56e+01 1vlmA 219 -20.25 -7.57 1.61e+01 1kfwA 435 -20.26 -7.51 1.68e+01 1arzC 273 -19.77 -7.50 1.69e+01 1uc2A 481 -19.68 -7.47 1.72e+01 2cq2A 114 -18.14 -7.47 1.72e+01 1x8yA 86 -22.36 -7.47 1.73e+01 1jgcA 161 -24.74 -7.46 1.74e+01 1sxrA 183 -19.52 -7.39 1.82e+01 16vpA 366 -24.42 -7.37 1.84e+01 1v58A 241 -18.69 -7.34 1.89e+01 1lehA 364 -20.69 -7.32 1.92e+01 1jeoA 180 -24.10 -7.29 1.95e+01 2b61A 377 -21.17 -7.29 1.95e+01 1e6qM 501 -22.29 -7.27 1.98e+01 2az4A 429 -21.57 -7.26 1.99e+01 1nq6A 302 -18.79 -7.26 2.00e+01 3ldh 330 -19.38 -7.24 2.02e+01 1m16A 146 -17.46 -7.22 2.05e+01 1wovA 250 -21.66 -7.19 2.10e+01 1xo1A 291 -20.69 -7.17 2.12e+01 1t6jA 714 -20.62 -7.17 2.13e+01 1bob 320 -20.25 -7.17 2.13e+01 1nxuA 333 -20.44 -7.11 2.22e+01 1qbkB 890 -28.20 -7.09 2.25e+01 1itcA 516 -21.78 -7.08 2.26e+01 1o7xB 377 -21.43 -7.07 2.28e+01 1qdbA 473 -24.29 -7.06 2.30e+01 1o7fA 469 -20.15 -7.06 2.30e+01 1b1yA 500 -20.79 -7.04 2.32e+01 1e4mM 501 -21.95 -7.01 2.38e+01 1e70M 501 -21.96 -7.01 2.38e+01 1jqzA 146 -17.26 -6.99 2.41e+01 1jt7A 146 -17.22 -6.96 2.46e+01 1rg8A 146 -17.13 -6.88 2.60e+01 1hx0A 496 -19.12 -6.88 2.61e+01 1smd 496 -18.95 -6.86 2.65e+01 1vkfA 188 -17.21 -6.84 2.68e+01 1qhbA 596 -20.38 -6.84 2.68e+01 1v6sA 390 -19.59 -6.84 2.68e+01 1a04A 215 -19.21 -6.81 2.74e+01 1ofcX 304 -24.50 -6.80 2.76e+01 1xxqA 161 -17.90 -6.78 2.79e+01 2bkaA 242 -19.13 -6.72 2.91e+01 2ao0A 324 -17.71 -6.71 2.93e+01 1lmzA 187 -19.36 -6.70 2.95e+01 137lA 164 -19.12 -6.68 2.99e+01 4ts1A 319 -21.14 -6.68 3.01e+01 1m0kA 262 -20.34 -6.67 3.02e+01 2cujA 108 -19.07 -6.67 3.02e+01 1f6yA 262 -19.24 -6.65 3.05e+01 1cqzA 554 -19.27 -6.60 3.17e+01 1v9dA 340 -27.29 -6.58 3.22e+01 139l 164 -19.19 -6.58 3.22e+01 1z23A 163 -20.00 -6.57 3.24e+01 1g9gA 629 -18.33 -6.57 3.25e+01 2basA 431 -19.84 -6.57 3.25e+01 1dih 273 -19.23 -6.57 3.25e+01 1p63A 144 -16.84 -6.55 3.28e+01 2sqcA 631 -21.40 -6.55 3.30e+01 180lA 164 -19.06 -6.53 3.34e+01 1b8bA 605 -19.88 -6.52 3.36e+01 1xhkA 187 -20.46 -6.50 3.42e+01 1dg3A 592 -25.63 -6.49 3.44e+01 5bcaA 516 -20.89 -6.47 3.48e+01 1mv8A 436 -19.70 -6.47 3.49e+01 1eypA 222 -18.21 -6.47 3.49e+01 1exnB 290 -20.05 -6.47 3.49e+01 1jepA 222 -18.18 -6.46 3.50e+01 1eyqA 222 -18.19 -6.46 3.52e+01 1zvzA 279 -23.51 -6.45 3.54e+01 1drw 273 -19.46 -6.43 3.59e+01 1lkcA 364 -18.39 -6.42 3.60e+01 1ntyA 311 -22.95 -6.42 3.62e+01 1f5nA 592 -25.56 -6.41 3.64e+01 1rkeA 262 -22.80 -6.40 3.66e+01 1szhA 161 -20.44 -6.39 3.68e+01 1tmxA 293 -21.69 -6.38 3.71e+01 1y2mA 716 -19.74 -6.38 3.71e+01 1pcxA 810 -19.32 -6.37 3.75e+01 128l 164 -18.84 -6.35 3.81e+01 1m7sA 484 -20.75 -6.34 3.82e+01 1vemA 516 -20.89 -6.33 3.85e+01 1hw8A 467 -18.42 -6.33 3.85e+01 1bmlC 362 -17.04 -6.33 3.86e+01 1o9rA 162 -20.81 -6.31 3.89e+01 2nmbA 160 -17.64 -6.30 3.93e+01 1ldfA 281 -23.01 -6.29 3.96e+01 1chkA 238 -18.07 -6.29 3.97e+01