% 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. % --------------------------------------------------------------------- % str2foo.1.YGR236C.t2k-100-30-str2 Host: farm16.cse.ucsc.edu Fri Mar 3 08:38:22 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR236C % --------------------------------------------------------------------- % 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 YGR236C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR236C.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 96 nodes, 159.50 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(=2.7621) * Reverse)^tau(=0.7395))) % 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 1nt4A 391 -16.98 -8.22 4.67e-01 1t7pA 698 -17.15 -7.96 5.92e-01 1x9mA 698 -17.19 -7.94 6.01e-01 1eni 138 -15.37 -6.89 1.60e+00 1enk 138 -15.30 -6.80 1.75e+00 1vasA 137 -15.27 -6.71 1.90e+00 1xc0A 33 -14.10 -6.64 2.03e+00 1yaxA 153 -14.96 -6.61 2.10e+00 2end 138 -15.07 -6.55 2.21e+00 1enj 138 -14.95 -6.49 2.35e+00 1ovnA 248 -14.68 -6.37 2.64e+00 1ctn 540 -14.32 -6.21 3.07e+00 1wpgA 994 -16.26 -6.21 3.08e+00 1xkwA 665 -13.65 -6.10 3.42e+00 1r5zA 323 -14.72 -6.09 3.46e+00 1m6dA 214 -14.29 -6.06 3.57e+00 1su4A 994 -15.89 -5.98 3.86e+00 1m2eA 135 -13.49 -5.98 3.87e+00 1f07A 321 -14.53 -5.97 3.90e+00 1f88A 348 -15.58 -5.81 4.56e+00 1k9tA 540 -13.84 -5.72 4.99e+00 1ebbA 202 -14.31 -5.72 5.00e+00 1edqA 540 -13.84 -5.70 5.10e+00 1s5lX 50 -15.44 -5.63 5.47e+00 1zvdA 380 -13.98 -5.63 5.47e+00 1zsxA 347 -13.88 -5.63 5.48e+00 1exbA 332 -13.85 -5.60 5.60e+00 2aefA 234 -14.05 -5.48 6.31e+00 1mn1 357 -13.96 -5.36 7.16e+00 1pgs 314 -12.99 -5.36 7.17e+00 1yydA 357 -13.96 -5.35 7.22e+00 1vk9A 151 -13.69 -5.35 7.22e+00 1mnp 357 -13.95 -5.34 7.29e+00 1to6A 371 -13.56 -5.26 7.88e+00 1h2eA 207 -13.93 -5.24 8.11e+00 2c3vA 102 -12.33 -5.21 8.33e+00 2bwvA 440 -13.45 -5.10 9.35e+00 1a3aC 148 -14.28 -5.09 9.39e+00 1bx4A 345 -13.33 -5.07 9.65e+00 1qw9A 502 -13.69 -5.05 9.84e+00 1r12A 258 -13.21 -5.04 9.90e+00 1n2sA 299 -12.87 -4.98 1.06e+01 2aamA 309 -14.14 -4.95 1.09e+01 1k3kA 158 -14.09 -4.95 1.09e+01 1az9 457 -13.32 -4.94 1.10e+01 1iv8A 720 -13.98 -4.92 1.12e+01 1bif 469 -13.87 -4.92 1.12e+01 1wl9A 440 -13.29 -4.92 1.13e+01 1h6hA 143 -12.75 -4.91 1.13e+01 1urqA 63 -13.39 -4.91 1.14e+01 1dv1A 449 -12.90 -4.88 1.17e+01 1zsyA 357 -12.96 -4.84 1.21e+01 1a3aA 148 -14.17 -4.83 1.23e+01 1gen 218 -12.37 -4.79 1.28e+01 1rwtA 232 -13.90 -4.79 1.29e+01 1jeyB 565 -13.44 -4.78 1.29e+01 2bifA 469 -13.81 -4.78 1.30e+01 1a16 440 -13.20 -4.77 1.32e+01 1o51A 114 -12.53 -4.76 1.33e+01 1dv2A 452 -12.69 -4.73 1.37e+01 1l9hA 349 -14.47 -4.72 1.38e+01 1qrqA 325 -12.94 -4.72 1.38e+01 2afwA 329 -13.28 -4.69 1.43e+01 1k8mA 93 -12.08 -4.68 1.44e+01 1jeqB 565 -13.40 -4.64 1.51e+01 1ll0A 339 -13.10 -4.63 1.52e+01 1zk7A 467 -12.72 -4.61 1.55e+01 1jdc 429 -13.18 -4.57 1.62e+01 1aa7A 158 -14.72 -4.57 1.62e+01 1ll2A 333 -12.99 -4.56 1.63e+01 1im4A 221 -12.58 -4.54 1.67e+01 1a17 166 -13.01 -4.54 1.68e+01 1h8eI 50 -12.77 -4.54 1.68e+01 3bifA 468 -13.51 -4.52 1.70e+01 1dfoA 417 -13.70 -4.52 1.71e+01 1xfxO 149 -13.03 -4.50 1.74e+01 2c5uA 375 -12.68 -4.46 1.82e+01 1lbeA 258 -12.90 -4.44 1.85e+01 1kdxB 28 -11.58 -4.44 1.86e+01 1bncA 449 -12.40 -4.39 1.95e+01 1ahr 146 -12.95 -4.36 2.03e+01 1b85A 351 -12.54 -4.33 2.08e+01 1z3xA 238 -13.45 -4.33 2.09e+01 1hzxA 349 -14.05 -4.32 2.12e+01 1hcc 59 -11.56 -4.30 2.14e+01 1b43A 340 -12.95 -4.29 2.17e+01 1b80A 351 -12.48 -4.25 2.28e+01 1gc0A 398 -12.43 -4.24 2.29e+01 1ffkV 143 -12.57 -4.22 2.34e+01 9ldtA 332 -12.69 -4.21 2.38e+01 1v9mA 323 -12.72 -4.20 2.39e+01 1vflA 356 -13.01 -4.17 2.47e+01 1llp 343 -12.40 -4.14 2.57e+01 1tueB 218 -12.36 -4.08 2.72e+01 1q52A 314 -13.04 -4.08 2.74e+01 1b4fA 82 -12.30 -4.06 2.79e+01 1zl8B 54 -12.19 -4.05 2.81e+01 1g4yR 148 -12.78 -4.05 2.81e+01 2ahjA 206 -12.62 -4.05 2.82e+01 1lj8A 493 -12.40 -4.04 2.86e+01 1yruB 74 -12.67 -4.03 2.87e+01 1wwpA 119 -14.15 -4.03 2.88e+01 1w9yA 319 -12.33 -4.03 2.89e+01 1u5kA 244 -12.66 -4.03 2.89e+01 1b4fG 82 -12.18 -4.02 2.91e+01 1kxqE 120 -11.03 -4.00 2.98e+01 2fojA 155 -11.30 -3.99 3.00e+01 1f0mA 82 -12.17 -3.99 3.00e+01 2a3qA 170 -12.88 -3.99 3.00e+01 1eulA 994 -13.80 -3.99 3.01e+01 2cz1A 206 -12.58 -3.99 3.01e+01 2cohA 202 -12.11 -3.99 3.01e+01 1fbtA 190 -12.36 -3.99 3.02e+01 1m3yA 413 -11.60 -3.98 3.03e+01 1yy6A 155 -11.29 -3.98 3.05e+01 1uelB 48 -11.36 -3.96 3.11e+01 2f1wA 158 -11.37 -3.95 3.14e+01 1v8dA 235 -12.11 -3.93 3.20e+01 1bncB 449 -11.94 -3.93 3.21e+01 1ahjA 207 -12.63 -3.92 3.26e+01 1hqkA 154 -12.66 -3.92 3.26e+01 2ahjC 206 -12.59 -3.91 3.28e+01 1r30A 369 -13.18 -3.89 3.34e+01 2amg 415 -12.53 -3.88 3.41e+01 1yrlA 491 -13.24 -3.87 3.41e+01 1yw0A 276 -13.46 -3.87 3.43e+01 1hwxA 501 -13.05 -3.86 3.46e+01 1c52 131 -12.22 -3.86 3.47e+01 1j5qA 437 -11.54 -3.85 3.52e+01 1y74B 50 -12.17 -3.85 3.52e+01 2lbp 346 -12.29 -3.84 3.54e+01 1wyuB 474 -13.09 -3.82 3.61e+01 1oltA 457 -11.94 -3.78 3.78e+01 1t0qA 498 -12.86 -3.78 3.80e+01 1xo3A 101 -11.55 -3.75 3.91e+01 1e79I 50 -11.36 -3.75 3.93e+01 1qbgA 272 -12.13 -3.74 3.95e+01 1kbqA 273 -12.16 -3.74 3.96e+01 3pbgA 468 -12.08 -3.73 3.99e+01