% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR013W.t2k-100-30-dssp-ebghstl Host: farm09.cse.ucsc.edu Sun Mar 19 21:38:48 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-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 621 nodes, 1034.96 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(=1.3451) * Reverse)^tau(=0.7988))) % 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 1uuqA 440 -26.36 -13.43 4.56e-01 1twfA 1733 -29.41 -13.33 4.84e-01 1m6yA 301 -27.58 -13.26 5.05e-01 1i50A 1733 -29.19 -13.06 5.69e-01 1j0hA 588 -27.34 -12.43 8.33e-01 1fgs 428 -24.54 -12.26 9.29e-01 1jbwA 428 -24.30 -12.17 9.77e-01 1gvfA 286 -24.63 -11.83 1.20e+00 1mp1A 111 -23.58 -11.73 1.28e+00 1k28A 584 -25.21 -11.37 1.60e+00 1l8qA 324 -26.75 -11.24 1.74e+00 2az4A 429 -24.43 -10.90 2.14e+00 1b9hA 388 -25.88 -10.87 2.19e+00 1clxA 347 -22.96 -10.59 2.61e+00 1wxcA 281 -25.03 -10.36 3.02e+00 1keiA 316 -26.23 -10.33 3.08e+00 2bneA 241 -22.38 -10.31 3.12e+00 1zb1A 392 -29.41 -10.30 3.14e+00 2tmnE 316 -25.72 -10.11 3.53e+00 2bidA 197 -25.84 -10.11 3.53e+00 1qdbA 473 -27.24 -9.96 3.88e+00 1zkiA 133 -21.77 -9.92 4.00e+00 1de4C 640 -25.01 -9.90 4.04e+00 8tlnE 316 -25.72 -9.85 4.16e+00 6tmnE 316 -25.72 -9.85 4.16e+00 1hyt 316 -25.69 -9.82 4.25e+00 1f6dA 376 -23.00 -9.80 4.30e+00 1vgvA 384 -22.96 -9.64 4.78e+00 1ekeA 230 -24.37 -9.59 4.92e+00 1oc7A 364 -24.08 -9.56 5.02e+00 1ocnA 362 -23.84 -9.47 5.33e+00 1bvwA 360 -23.92 -9.41 5.53e+00 2fkcA 247 -22.25 -9.38 5.64e+00 2bvwA 362 -23.76 -9.33 5.82e+00 2b61A 377 -23.05 -9.31 5.91e+00 2d7vA 162 -22.40 -9.29 5.97e+00 1wa5C 960 -31.08 -9.28 6.00e+00 2ao9A 155 -22.94 -9.27 6.06e+00 1vjvA 415 -25.18 -9.22 6.24e+00 1hm2A 700 -24.22 -9.19 6.37e+00 1vlmA 219 -21.53 -9.18 6.40e+00 1qbkB 890 -29.06 -9.18 6.42e+00 1lf6A 684 -22.76 -9.13 6.64e+00 2cq2A 114 -19.42 -9.09 6.78e+00 1jgcA 161 -25.88 -9.04 7.01e+00 1sqc 631 -25.27 -9.02 7.12e+00 1w32A 348 -21.35 -8.99 7.26e+00 1lzlA 323 -20.85 -8.98 7.31e+00 1lwjA 441 -21.27 -8.95 7.46e+00 2cvxA 888 -22.25 -8.72 8.63e+00 1gmlA 178 -21.99 -8.58 9.46e+00 2sqcA 631 -24.75 -8.57 9.54e+00 1mv8A 436 -21.97 -8.57 9.54e+00 1e6qM 501 -23.53 -8.56 9.60e+00 2awdA 323 -20.96 -8.56 9.62e+00 1cb8A 678 -22.77 -8.55 9.69e+00 2f02A 323 -20.97 -8.53 9.82e+00 1ynmA 247 -21.83 -8.47 1.02e+01 2ts1 419 -25.63 -8.47 1.02e+01 16vpA 366 -26.84 -8.36 1.10e+01 2nmbA 160 -19.82 -8.24 1.18e+01 1e70M 501 -23.25 -8.21 1.21e+01 1e4mM 501 -23.25 -8.21 1.21e+01 2d1eA 248 -21.54 -8.13 1.28e+01 1kfwA 435 -21.06 -8.12 1.28e+01 1in6A 334 -23.76 -8.11 1.30e+01 1lmzA 187 -20.94 -8.06 1.34e+01 1ntyA 311 -24.90 -8.01 1.38e+01 1bob 320 -20.44 -8.01 1.39e+01 2acvA 463 -21.64 -7.96 1.43e+01 1eexA 554 -21.39 -7.96 1.43e+01 2ao0A 324 -18.96 -7.94 1.45e+01 1kwfA 363 -24.30 -7.92 1.47e+01 1ht6A 405 -20.95 -7.85 1.54e+01 1wovA 250 -23.65 -7.84 1.55e+01 1pgjA 478 -21.64 -7.83 1.56e+01 2es4D 332 -25.18 -7.80 1.59e+01 1b31A 302 -22.04 -7.79 1.60e+01 1bg4 302 -22.04 -7.79 1.61e+01 2bcgY 206 -19.98 -7.78 1.61e+01 2fflA 756 -26.67 -7.77 1.62e+01 1nq6A 302 -19.47 -7.74 1.65e+01 1tq4A 413 -22.79 -7.73 1.66e+01 1sfkA 76 -19.58 -7.70 1.69e+01 1x8yA 86 -23.54 -7.70 1.70e+01 1j6uA 469 -20.68 -7.69 1.71e+01 1arzC 273 -20.15 -7.69 1.71e+01 1uruA 244 -25.73 -7.65 1.76e+01 1y2mA 716 -21.47 -7.61 1.81e+01 1v58A 241 -19.02 -7.57 1.86e+01 1rzuA 485 -19.70 -7.55 1.88e+01 1m16A 146 -17.83 -7.54 1.89e+01 1nal1 297 -21.96 -7.54 1.90e+01 1qwnA 1045 -22.18 -7.51 1.93e+01 1a04A 215 -20.08 -7.49 1.96e+01 1tmxA 293 -23.56 -7.49 1.96e+01 1e5rA 290 -19.65 -7.47 1.99e+01 1o7fA 469 -21.10 -7.44 2.02e+01 1hxkA 1015 -22.01 -7.44 2.03e+01 1htyA 1015 -22.00 -7.44 2.03e+01 2c5uA 375 -21.44 -7.44 2.03e+01 1fdyA 297 -21.75 -7.40 2.08e+01 1jqzA 146 -17.60 -7.40 2.08e+01 1qjwA 365 -22.32 -7.38 2.11e+01 1szhA 161 -22.88 -7.36 2.13e+01 1v9dA 340 -28.53 -7.32 2.19e+01 1dih 273 -19.91 -7.32 2.19e+01 1qgrA 876 -29.24 -7.32 2.20e+01 1hwwA 1015 -21.74 -7.32 2.20e+01 1iv8A 720 -23.56 -7.32 2.20e+01 2cujA 108 -20.36 -7.30 2.22e+01 1rkeA 262 -23.51 -7.28 2.26e+01 1xyfA 436 -21.22 -7.26 2.28e+01 2myr 501 -22.41 -7.26 2.28e+01 2bvlA 543 -26.94 -7.25 2.31e+01 1s8fA 177 -19.40 -7.19 2.39e+01 1hx0A 496 -20.10 -7.18 2.42e+01 1rg8A 146 -17.37 -7.16 2.44e+01 1e6yA 569 -21.05 -7.16 2.45e+01 1b1yA 500 -23.80 -7.14 2.49e+01 1ek6A 348 -20.17 -7.12 2.51e+01 1rh9A 373 -20.48 -7.12 2.52e+01 2bmhA 455 -24.75 -7.11 2.52e+01 1lc5A 364 -18.96 -7.10 2.55e+01 2basA 431 -20.60 -7.10 2.55e+01 1cem 363 -23.41 -7.10 2.56e+01 1chkA 238 -19.06 -7.09 2.57e+01 1lkcA 364 -18.85 -7.09 2.57e+01 1ofcX 304 -25.14 -7.07 2.60e+01 1y6iA 233 -20.50 -7.04 2.66e+01 1r8iA 213 -21.64 -7.04 2.66e+01 1xw8A 252 -18.49 -7.04 2.67e+01 1htoA 477 -19.56 -7.03 2.67e+01 1jt7A 146 -17.34 -7.03 2.67e+01 1hl2A 297 -21.27 -7.02 2.69e+01 5eau 548 -23.21 -7.02 2.70e+01 1drw 273 -19.88 -7.00 2.73e+01 1cb2A 365 -22.09 -7.00 2.73e+01 137lA 164 -19.54 -6.97 2.79e+01 1y0gA 191 -16.92 -6.97 2.79e+01 1p63A 144 -17.19 -6.96 2.81e+01 1cx8A 639 -21.97 -6.94 2.84e+01 1jr3A 373 -22.67 -6.94 2.85e+01 1d9tA 289 -19.34 -6.92 2.88e+01 1bu7A 455 -24.87 -6.92 2.89e+01 1ukvY 206 -18.98 -6.90 2.92e+01 1f6yA 262 -19.40 -6.90 2.92e+01 1m0kA 262 -20.80 -6.90 2.92e+01 1o7xD 377 -20.89 -6.89 2.94e+01 1o9rA 162 -21.72 -6.89 2.94e+01 1tzvA 142 -22.39 -6.88 2.96e+01 1nd7A 374 -20.13 -6.83 3.07e+01 1fkoB 440 -21.46 -6.83 3.07e+01 1ywfA 296 -20.34 -6.83 3.07e+01 1t6jA 714 -21.08 -6.82 3.08e+01 1ne7A 289 -19.24 -6.82 3.08e+01 5eat 548 -22.79 -6.82 3.09e+01 1eumA 165 -24.77 -6.80 3.12e+01 1sqsA 242 -20.40 -6.80 3.13e+01 1jpzA 473 -24.35 -6.79 3.16e+01 1xxqA 161 -17.49 -6.78 3.18e+01 1qvzA 237 -18.62 -6.78 3.18e+01 1vi0A 206 -24.49 -6.78 3.18e+01 1p4xA 250 -21.55 -6.77 3.19e+01 1nal3 297 -21.19 -6.77 3.19e+01 1gqyA 475 -18.82 -6.74 3.25e+01 1sxrA 183 -19.07 -6.73 3.29e+01 2b8tA 223 -20.19 -6.69 3.37e+01 1dioA 554 -20.10 -6.69 3.38e+01 1ydiA 263 -23.37 -6.68 3.40e+01 1dg3A 592 -26.42 -6.68 3.41e+01 2cybA 323 -21.03 -6.65 3.47e+01 3cbh 365 -21.49 -6.65 3.48e+01 2at9 247 -19.33 -6.64 3.49e+01 2bnfB 241 -18.58 -6.64 3.50e+01 1zvzA 279 -23.36 -6.62 3.54e+01 2f6uA 234 -19.01 -6.61 3.56e+01 2avyM 117 -17.75 -6.52 3.81e+01 1f5nA 592 -26.40 -6.51 3.83e+01 1eu1A 780 -20.33 -6.51 3.83e+01 1e0wA 313 -18.40 -6.49 3.88e+01 1i6lA 328 -23.91 -6.49 3.88e+01 1cx8B 639 -21.78 -6.49 3.88e+01 1i6kA 328 -23.83 -6.49 3.88e+01 1r1hA 696 -21.68 -6.49 3.89e+01 1yzhA 214 -19.78 -6.48 3.90e+01 1hl8A 449 -20.87 -6.48 3.91e+01 1jqiA 388 -19.18 -6.47 3.94e+01 139l 164 -19.22 -6.47 3.94e+01 180lA 164 -19.13 -6.45 3.99e+01