% 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. % --------------------------------------------------------------------- % alphafoo.1.YAL016C-A.t2k-100-30-alpha Host: farm09.cse.ucsc.edu Sun Feb 12 14:49:00 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YAL0/YAL016C-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.alphas % % 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 YAL016C-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YAL016C-A.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 105 nodes, 165.82 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(=2.6952) * Reverse)^tau(=0.7566))) % 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 1ywhA 313 -17.82 -9.35 1.12e-01 1lh0A 213 -15.76 -7.14 9.37e-01 1vjqA 79 -15.61 -7.05 1.03e+00 1hilB 220 -14.60 -6.86 1.24e+00 1omp 370 -15.18 -6.78 1.35e+00 3nodB 423 -15.47 -6.76 1.38e+00 1opr 213 -15.39 -6.73 1.41e+00 1anf 370 -15.37 -6.65 1.53e+00 1ytvA 366 -15.25 -6.64 1.55e+00 1mpb 370 -15.03 -6.59 1.63e+00 1mh3A 421 -15.07 -6.56 1.68e+00 4mbp 370 -14.99 -6.39 2.00e+00 1laxA 370 -14.97 -6.37 2.03e+00 1wvgA 359 -15.38 -6.29 2.21e+00 1xklA 273 -14.68 -6.21 2.40e+00 1oroA 213 -14.71 -6.15 2.55e+00 1mjuH 227 -13.88 -6.14 2.57e+00 1jguH 217 -14.17 -6.12 2.64e+00 3pflA 759 -14.88 -6.11 2.66e+00 2pflA 759 -14.65 -5.81 3.64e+00 1h16A 759 -14.60 -5.80 3.67e+00 1nn7A 105 -13.82 -5.80 3.67e+00 1nc7A 138 -13.93 -5.79 3.70e+00 1ncwH 222 -13.68 -5.65 4.29e+00 1ezoA 370 -13.99 -5.55 4.78e+00 1apmE 350 -13.85 -5.54 4.80e+00 2bydA 323 -13.74 -5.54 4.81e+00 1tqxA 227 -13.97 -5.54 4.84e+00 1cm5A 759 -14.28 -5.50 5.02e+00 1q9rB 222 -13.22 -5.47 5.20e+00 1icxA 155 -14.27 -5.46 5.22e+00 1fdr 248 -13.44 -5.45 5.30e+00 1jb1A 205 -13.43 -5.39 5.68e+00 1xh9A 350 -13.74 -5.38 5.73e+00 1qs8A 329 -14.36 -5.30 6.19e+00 1jx4A 352 -14.84 -5.30 6.25e+00 1rdqE 350 -13.46 -5.28 6.32e+00 1h9sA 140 -12.92 -5.28 6.33e+00 2c43A 323 -13.43 -5.24 6.62e+00 2a7yA 83 -12.59 -5.22 6.77e+00 1ospH 218 -13.34 -5.18 7.06e+00 1zx5A 300 -13.44 -5.14 7.39e+00 2a1vA 144 -12.98 -5.13 7.45e+00 1cmkE 350 -13.44 -5.12 7.54e+00 1q1aA 289 -13.37 -5.10 7.68e+00 1q8uA 350 -13.38 -5.09 7.82e+00 1dts 221 -14.50 -5.05 8.10e+00 1miqA 375 -14.16 -5.02 8.44e+00 1rurH 218 -12.74 -4.97 8.90e+00 1f8vA 355 -14.18 -4.92 9.36e+00 1cdkA 350 -13.23 -4.89 9.66e+00 1gks 78 -12.68 -4.88 9.72e+00 1x6oA 174 -13.75 -4.82 1.04e+01 1tw0A 157 -13.98 -4.82 1.05e+01 1jbkA 195 -12.73 -4.79 1.08e+01 1gmxA 108 -13.07 -4.78 1.09e+01 1a3lH 218 -12.57 -4.78 1.09e+01 1wtjA 343 -13.52 -4.75 1.13e+01 1gn0A 108 -13.03 -4.75 1.13e+01 1fnhA 271 -12.51 -4.74 1.14e+01 1d0hA 469 -13.10 -4.74 1.14e+01 1k51A 72 -12.65 -4.69 1.20e+01 1agjA 242 -12.61 -4.65 1.25e+01 1ohzB 60 -12.41 -4.62 1.30e+01 1ynlH 219 -12.64 -4.58 1.36e+01 1dbs 224 -14.23 -4.50 1.48e+01 2cx5A 158 -11.97 -4.49 1.50e+01 1byi 224 -14.23 -4.49 1.50e+01 1rzfH 235 -12.38 -4.48 1.52e+01 1tetH 210 -11.99 -4.48 1.53e+01 1dqqB 210 -12.46 -4.47 1.53e+01 1dad 224 -14.14 -4.44 1.59e+01 1o3yA 166 -12.43 -4.42 1.62e+01 1b0uA 262 -12.89 -4.40 1.66e+01 2adgB 222 -12.08 -4.38 1.69e+01 1diwA 441 -12.64 -4.38 1.69e+01 1hkbA 917 -14.18 -4.36 1.74e+01 1g2iA 166 -12.67 -4.35 1.75e+01 1hz6A 72 -12.16 -4.32 1.81e+01 1hkcA 917 -13.93 -4.31 1.83e+01 1xriA 151 -12.83 -4.31 1.84e+01 1p3wA 404 -12.68 -4.28 1.89e+01 1hyxH 224 -12.20 -4.28 1.90e+01 1t0iA 191 -13.81 -4.25 1.96e+01 1wejH 223 -12.03 -4.23 2.00e+01 1oheA 348 -12.93 -4.23 2.02e+01 1vqoS 85 -12.07 -4.22 2.03e+01 1h95A 79 -12.69 -4.20 2.07e+01 1s4zC 30 -12.17 -4.20 2.07e+01 1yna 194 -12.33 -4.20 2.07e+01 1xkgA 312 -12.84 -4.18 2.13e+01 2cyjA 118 -12.33 -4.17 2.15e+01 1ox8A 107 -12.62 -4.12 2.28e+01 1kngA 156 -12.91 -4.12 2.28e+01 1h65A 270 -12.77 -4.10 2.32e+01 1f89A 291 -13.13 -4.10 2.32e+01 1aipE 405 -13.13 -4.06 2.43e+01 1exmA 405 -13.18 -4.06 2.44e+01 1v4sA 455 -12.91 -4.04 2.49e+01 1sw6A 327 -13.01 -4.03 2.52e+01 1yfnA 118 -12.65 -4.02 2.53e+01 1imoA 88 -11.89 -4.02 2.55e+01 2f5xA 312 -12.61 -3.99 2.64e+01 1ukuA 102 -12.07 -3.99 2.65e+01 8fabB 224 -12.05 -3.98 2.66e+01 1wloA 136 -12.12 -3.96 2.72e+01 1ap0 73 -12.27 -3.95 2.75e+01 1jj2R 84 -11.77 -3.94 2.80e+01 1s72S 85 -11.76 -3.93 2.82e+01 1zczA 464 -12.42 -3.93 2.82e+01 1qkkA 155 -12.06 -3.92 2.85e+01 1ryp1 222 -12.55 -3.92 2.87e+01 1l5zA 155 -11.93 -3.90 2.93e+01 1aohB 147 -12.29 -3.89 2.94e+01 1gehA 444 -12.70 -3.89 2.95e+01 1u8xX 472 -12.49 -3.89 2.95e+01 1xbsA 149 -12.32 -3.88 2.98e+01 1np3A 338 -12.97 -3.88 2.99e+01 2b6hA 192 -12.41 -3.87 3.02e+01 1i1gA 141 -11.73 -3.87 3.04e+01 1uumA 372 -12.21 -3.85 3.10e+01 1j24A 143 -12.91 -3.83 3.15e+01 1aohA 147 -12.21 -3.83 3.16e+01 2beiA 170 -11.90 -3.83 3.16e+01 1nni1 174 -12.30 -3.82 3.19e+01 1jlnA 297 -12.12 -3.82 3.21e+01 1a8d 452 -12.17 -3.81 3.23e+01 1czaN 917 -13.38 -3.80 3.26e+01 1qf6A 642 -13.06 -3.80 3.27e+01 1ffkP 84 -11.64 -3.78 3.37e+01 1ln4A 104 -11.60 -3.77 3.38e+01 1k52A 72 -11.57 -3.77 3.38e+01 1dgkN 917 -13.57 -3.77 3.40e+01 1nwbA 124 -12.25 -3.76 3.42e+01 1ufkA 254 -12.08 -3.75 3.46e+01 1v5rA 97 -11.14 -3.75 3.47e+01 1evlA 401 -12.27 -3.75 3.48e+01 1abrA 251 -11.75 -3.74 3.49e+01 1jk7A 323 -12.58 -3.74 3.52e+01 1g0uL 241 -12.47 -3.73 3.54e+01 1qhaA 917 -13.93 -3.72 3.59e+01 1sqeA 109 -12.70 -3.70 3.66e+01 2aabH 243 -11.49 -3.70 3.67e+01 2c46A 241 -12.32 -3.69 3.74e+01 1zsoA 164 -13.31 -3.66 3.85e+01 1yh6A 179 -12.30 -3.66 3.86e+01 1jvpP 298 -12.01 -3.66 3.86e+01 1zceA 155 -11.79 -3.65 3.91e+01 1b9mA 265 -12.59 -3.64 3.96e+01 1r6xA 395 -11.94 -3.64 3.96e+01