% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR027W-A.t2k-100-40-40-str2+CB_burial_14_7 Host: farm01 Tue Nov 30 00:06:26 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR027W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 YGR027W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR027W-A.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR027W-A.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 441 nodes, 527.91 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 (=10700) sequences: % N / (1 + exp(-(lambda(=0.6833) * Reverse)^tau(=0.8575))) % 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 1mhyG 169 -51.14 -25.40 1.03e-01 1rtwA 220 -49.39 -23.23 2.40e-01 1l8yA 91 -38.58 -21.44 4.90e-01 1jigA 146 -42.82 -20.55 7.00e-01 1vasA 137 -39.10 -20.15 8.20e-01 1fqvD 149 -38.13 -19.94 8.93e-01 2pgd 482 -40.26 -19.31 1.15e+00 1fqvJ 149 -36.99 -19.02 1.30e+00 1izcA 339 -33.67 -18.78 1.43e+00 1xfiA 367 -44.16 -18.65 1.51e+00 2end 138 -37.27 -18.24 1.78e+00 1v2yA 105 -31.98 -18.22 1.80e+00 1ois 223 -37.06 -18.06 1.92e+00 1w53A 84 -36.06 -17.69 2.23e+00 1klo 162 -41.03 -17.31 2.62e+00 1o4sA 389 -31.60 -17.22 2.71e+00 1g59A 468 -35.46 -16.97 3.01e+00 1dttA 560 -36.09 -16.62 3.47e+00 1mtyG 162 -36.91 -16.49 3.67e+00 1riqA 465 -41.56 -16.32 3.94e+00 2lefA 86 -33.80 -16.26 4.03e+00 1mmoG 162 -36.50 -16.14 4.24e+00 1v95A 130 -31.74 -15.98 4.54e+00 1i5nA 146 -40.14 -15.91 4.67e+00 1abv 134 -35.98 -15.80 4.88e+00 1f4qA 165 -42.99 -15.68 5.14e+00 1izlC 473 -48.84 -15.63 5.23e+00 1rthA 560 -33.90 -15.42 5.73e+00 1uvqA 197 -32.05 -15.38 5.82e+00 1be3D 241 -37.02 -15.37 5.84e+00 1qgdA 662 -30.04 -15.37 5.84e+00 2eiaB 206 -37.82 -15.19 6.31e+00 1v74B 87 -35.87 -15.05 6.68e+00 6prcM 323 -39.19 -14.98 6.88e+00 1va6A 518 -34.03 -14.76 7.55e+00 1e3aA 260 -43.80 -14.74 7.63e+00 1uddA 226 -37.02 -14.73 7.64e+00 1r85A 379 -35.61 -14.73 7.66e+00 1s9pA 227 -37.69 -14.72 7.68e+00 1hiwA 133 -35.42 -14.72 7.69e+00 1axdA 209 -37.04 -14.68 7.81e+00 1or7A 194 -43.70 -14.67 7.86e+00 1f5sA 211 -29.29 -14.65 7.89e+00 1ieaA 192 -34.59 -14.60 8.07e+00 2hmx 133 -34.84 -14.59 8.11e+00 2hmiA 558 -31.91 -14.55 8.24e+00 1ohuA 175 -31.11 -14.52 8.36e+00 1n3gA 113 -34.24 -14.38 8.85e+00 1csn 298 -30.59 -14.36 8.95e+00 1ihoA 283 -31.73 -14.34 9.02e+00 1go3F 107 -37.53 -14.33 9.07e+00 1eemA 241 -36.11 -14.28 9.26e+00 1hizA 379 -33.63 -14.26 9.34e+00 1l7mA 211 -28.63 -14.22 9.48e+00 1iznA 286 -33.68 -14.20 9.56e+00 1eia 207 -38.11 -14.09 1.00e+01 1dw9A 156 -36.30 -14.09 1.00e+01 1colA 204 -31.23 -14.09 1.00e+01 1p4dA 330 -28.18 -14.06 1.02e+01 1tbmA 326 -38.30 -13.94 1.07e+01 1jqjC 343 -33.96 -13.94 1.07e+01 1j97A 211 -29.04 -13.86 1.11e+01 6paxA 133 -35.94 -13.81 1.13e+01 1fs1B 141 -32.85 -13.77 1.15e+01 1lnqA 336 -30.66 -13.72 1.17e+01 1hlvA 131 -34.38 -13.71 1.18e+01 1iu4A 331 -33.60 -13.64 1.21e+01 1l6nA 289 -48.98 -13.64 1.21e+01 1bccD 241 -35.20 -13.63 1.22e+01 1pbwA 216 -39.99 -13.63 1.22e+01 1hf8A 289 -40.30 -13.40 1.35e+01 1dwkA 156 -36.76 -13.39 1.35e+01 1ig6A 107 -30.01 -13.38 1.36e+01 1ib8A 164 -29.56 -13.36 1.37e+01 1octC 156 -38.18 -13.34 1.38e+01 1qgtA 149 -37.77 -13.28 1.41e+01 1jchC 551 -35.88 -13.25 1.43e+01 1jchA 551 -35.88 -13.25 1.43e+01 1t3wA 148 -36.02 -13.22 1.45e+01 1bed 181 -34.41 -13.19 1.47e+01 1gm7A 209 -35.58 -13.14 1.50e+01 1okrA 123 -37.75 -13.13 1.51e+01 1e3oC 160 -38.48 -13.12 1.51e+01 1g5yA 238 -33.10 -13.09 1.53e+01 1bouA 139 -29.13 -13.08 1.54e+01 1fngA 192 -34.31 -13.07 1.55e+01 1dxrM 323 -38.95 -13.01 1.59e+01 1f75A 249 -28.63 -13.01 1.59e+01 1iakA 199 -29.56 -13.00 1.59e+01 1gouA 116 -25.27 -13.00 1.59e+01 1ckqA 276 -32.00 -13.00 1.60e+01 1f7cA 231 -35.23 -13.00 1.60e+01 1im4A 221 -29.43 -12.99 1.60e+01 1fneA 192 -34.46 -12.98 1.61e+01 1cfr 285 -31.73 -12.95 1.63e+01 1eysH 259 -43.50 -12.95 1.63e+01 1k94A 165 -41.76 -12.94 1.64e+01 1p8kZ 254 -32.11 -12.89 1.67e+01 1r7jA 95 -34.41 -12.85 1.70e+01 1ko9A 345 -28.52 -12.79 1.74e+01 1ajqA 209 -35.84 -12.79 1.75e+01 1dioA 554 -26.05 -12.76 1.77e+01 1ai7A 209 -35.79 -12.75 1.77e+01 1eexA 554 -26.22 -12.68 1.83e+01 1l4sA 112 -32.66 -12.59 1.90e+01 1brnL 110 -25.30 -12.58 1.91e+01 1vg0A 650 -29.36 -12.57 1.92e+01 1j09A 468 -35.29 -12.51 1.96e+01 1q06A 135 -33.72 -12.50 1.97e+01 1k8eA 345 -29.04 -12.49 1.99e+01 1o17A 345 -29.04 -12.49 1.99e+01 1us7B 265 -40.54 -12.47 2.00e+01 1a2pA 110 -25.35 -12.47 2.00e+01 1hg5A 289 -40.53 -12.40 2.07e+01 1deoA 233 -23.94 -12.37 2.09e+01 1dipA 78 -39.30 -12.35 2.11e+01 1ouvA 273 -28.28 -12.33 2.13e+01 1griA 217 -29.99 -12.32 2.14e+01 3icb 75 -31.88 -12.32 2.14e+01 1ki1B 352 -38.16 -12.32 2.14e+01 1eswA 500 -25.99 -12.22 2.24e+01 1n2aA 201 -35.07 -12.21 2.24e+01 1b4uA 139 -28.77 -12.21 2.24e+01 1gk9A 260 -38.22 -12.19 2.26e+01 1n45A 233 -31.87 -12.19 2.26e+01 1bkb 136 -24.95 -12.17 2.28e+01 1nnlA 225 -26.10 -12.13 2.32e+01 1imuA 107 -28.23 -12.13 2.32e+01 1dj8A 89 -30.36 -12.09 2.36e+01 1eriA 276 -30.73 -12.09 2.36e+01 1bnr 110 -25.78 -12.06 2.39e+01 1pu6A 218 -33.14 -12.05 2.40e+01 1cl8A 276 -30.58 -12.05 2.41e+01 1fseA 74 -29.87 -12.01 2.45e+01 1jj2X 240 -39.93 -12.00 2.46e+01 1cwyA 500 -26.13 -11.99 2.46e+01 1rh2F 165 -32.66 -11.99 2.47e+01 1i37A 260 -36.38 -11.97 2.48e+01 1vetB 125 -26.45 -11.96 2.50e+01 1rnbA 110 -24.62 -11.93 2.53e+01 1itf 165 -31.82 -11.91 2.56e+01 1je5A 206 -33.55 -11.88 2.59e+01 2occF 98 -32.51 -11.86 2.60e+01 1hs6A 611 -26.22 -11.86 2.60e+01 1e1hB 174 -36.53 -11.84 2.63e+01 1har 216 -28.21 -11.84 2.63e+01 1qc9A 276 -31.28 -11.84 2.63e+01 1iuqA 367 -32.24 -11.76 2.73e+01 1qgjA 300 -24.70 -11.75 2.74e+01 1vj5A 555 -27.91 -11.75 2.74e+01 1ljrA 244 -28.74 -11.73 2.76e+01 1mlwA 301 -31.96 -11.72 2.77e+01 1gln 468 -32.89 -11.72 2.78e+01 1jr3A 373 -31.57 -11.69 2.81e+01 1ppjD 241 -32.84 -11.68 2.82e+01 1gpjA 404 -35.95 -11.68 2.82e+01 1s72Y 241 -39.43 -11.65 2.85e+01 1b31A 302 -24.58 -11.62 2.89e+01 1s2wA 295 -27.92 -11.62 2.90e+01 1g3mA 294 -25.50 -11.59 2.93e+01 1m8oB 47 -32.93 -11.56 2.97e+01 1ajqB 557 -33.11 -11.53 3.01e+01 1twfF 155 -33.85 -11.48 3.07e+01 1ew6A 137 -40.00 -11.46 3.11e+01 1ewaA 137 -40.00 -11.46 3.11e+01 1wmuA 141 -38.26 -11.45 3.11e+01 1sxjE 354 -34.12 -11.45 3.12e+01 1hqvA 191 -37.16 -11.41 3.17e+01 1dlhB 188 -27.36 -11.39 3.19e+01 1bd3A 243 -30.39 -11.36 3.25e+01 1je8A 82 -30.14 -11.35 3.26e+01 1r5qA 102 -38.56 -11.31 3.32e+01 1rfzA 168 -33.31 -11.30 3.32e+01 1gkxA 388 -35.61 -11.30 3.33e+01 1i50F 155 -33.81 -11.27 3.37e+01 1wer 334 -38.17 -11.26 3.39e+01 3chy 128 -25.21 -11.21 3.46e+01 1rzhL 281 -32.89 -11.20 3.47e+01 1eo9A 209 -27.12 -11.19 3.49e+01 1jr3D 343 -31.25 -11.17 3.52e+01 1hs7A 97 -37.81 -11.15 3.56e+01 1h99A 224 -46.60 -11.14 3.56e+01 1bg4 302 -24.59 -11.13 3.58e+01 1di0A 158 -26.39 -11.11 3.62e+01 1eysL 280 -33.32 -11.10 3.63e+01 1jbeA 128 -24.70 -11.08 3.66e+01 1aisA 182 -24.93 -11.07 3.67e+01 1np3A 338 -27.73 -11.07 3.68e+01 1otkA 249 -27.93 -11.07 3.69e+01 1s6cA 183 -36.65 -11.06 3.70e+01 1k7cA 233 -22.53 -11.05 3.71e+01 1f4kA 122 -30.86 -11.04 3.73e+01 1a17 166 -32.03 -11.00 3.79e+01 1k30A 368 -32.47 -10.99 3.81e+01 1pdnC 128 -34.44 -10.98 3.83e+01 1v4xA 144 -32.23 -10.91 3.95e+01 1otcB 260 -38.65 -10.91 3.95e+01 1ddf 127 -36.68 -10.90 3.96e+01 1ib2A 349 -28.86 -10.90 3.96e+01 1tbxA 99 -26.44 -10.90 3.97e+01