% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YEL012W.t2k-100-40-40-str2+CB_burial_14_7 Host: farm09 Fri Nov 18 20:04:15 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YEL0/YEL012W % --------------------------------------------------------------------- % 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 YEL012W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YEL012W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YEL012W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13048 sequences, 3092733 residues, 219 nodes, 366.52 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(=0.6316) * Reverse)^tau(=0.8784))) % 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 1z2uA 150 -268.39 -242.75 8.43e-33 1x23A 155 -261.96 -237.17 4.54e-32 2ayvA 166 -261.11 -234.72 9.50e-32 1y6lA 149 -252.44 -232.86 1.67e-31 2bepA 159 -243.01 -222.99 3.32e-30 2e2c 156 -234.53 -216.17 2.66e-29 1jatA 155 -240.87 -214.80 4.03e-29 1jbbA 153 -242.22 -214.27 4.75e-29 1yh2A 175 -238.72 -213.70 5.64e-29 2ucz 165 -235.76 -211.18 1.22e-28 1fzyA 149 -237.06 -210.90 1.33e-28 1u9aA 160 -236.73 -209.57 2.00e-28 1i7kA 179 -226.90 -208.52 2.76e-28 1fxtA 149 -219.50 -197.55 8.05e-27 1zdnA 158 -222.24 -195.78 1.39e-26 1yrvA 169 -203.19 -184.78 4.20e-25 1yh6A 179 -208.11 -183.65 5.97e-25 1yf9A 171 -203.77 -180.25 1.72e-24 1wzvA 155 -196.13 -175.95 6.60e-24 2awfA 172 -194.40 -171.29 2.85e-23 2a4dA 160 -180.58 -157.60 2.14e-21 1j7dA 145 -175.76 -151.39 1.54e-20 1jatB 138 -169.34 -150.03 2.37e-20 1zuoA 186 -124.16 -108.28 1.86e-14 1s1qA 145 -62.63 -44.62 7.67e-05 1uzxA 169 -54.46 -35.81 2.08e-03 1kppA 145 -52.32 -33.75 4.56e-03 2es9A 115 -43.79 -26.66 7.12e-02 1ois 223 -38.29 -21.08 6.62e-01 1k3eA 156 -38.89 -20.43 8.61e-01 1qhtA 775 -38.05 -19.64 1.19e+00 1dvpA 220 -36.41 -19.48 1.27e+00 1qqcA 773 -38.08 -19.19 1.43e+00 1j7iA 264 -36.83 -18.30 2.06e+00 1ukxA 137 -47.24 -18.21 2.13e+00 2c1dA 264 -30.37 -17.69 2.65e+00 1us7B 265 -44.22 -17.67 2.67e+00 1vj7A 393 -36.94 -17.48 2.88e+00 1ai7A 209 -37.95 -17.32 3.09e+00 1nzyA 269 -34.20 -17.00 3.53e+00 1fx3A 169 -30.51 -16.82 3.80e+00 1ajqA 209 -37.11 -16.50 4.34e+00 1usuA 260 -36.90 -16.40 4.53e+00 1h6hA 143 -35.75 -16.28 4.76e+00 1jbkA 195 -28.55 -16.13 5.05e+00 1jpzA 473 -40.09 -15.94 5.48e+00 1gk9A 260 -38.31 -15.92 5.53e+00 1fc3A 120 -36.48 -15.86 5.66e+00 1fx3B 169 -31.20 -15.64 6.20e+00 1srqA 341 -30.81 -15.58 6.38e+00 1on2A 142 -36.39 -15.48 6.66e+00 1umkA 275 -28.71 -15.45 6.72e+00 1p32C 209 -35.31 -15.40 6.88e+00 1qv9A 283 -32.56 -15.39 6.90e+00 1upkA 341 -35.45 -15.16 7.60e+00 1vf7A 369 -36.01 -15.11 7.77e+00 1alu 186 -36.15 -14.94 8.33e+00 1q16B 512 -36.22 -14.80 8.85e+00 1y5iB 512 -36.65 -14.76 9.01e+00 1ut1A 148 -33.11 -14.69 9.26e+00 1ks8A 433 -26.15 -14.48 1.01e+01 1hs6A 611 -34.09 -14.47 1.02e+01 1vctA 205 -32.81 -14.38 1.06e+01 1wlmA 151 -40.68 -14.37 1.06e+01 1t5eA 360 -34.17 -14.36 1.07e+01 1v9sA 208 -26.50 -14.35 1.07e+01 1m1eB 81 -34.79 -14.34 1.08e+01 1su0B 159 -29.60 -14.15 1.16e+01 1iynA 295 -27.10 -13.97 1.26e+01 1pszA 303 -29.55 -13.96 1.26e+01 1m9sA 605 -26.88 -13.82 1.34e+01 2ae6A 166 -27.19 -13.77 1.37e+01 1qu1A 155 -43.03 -13.73 1.39e+01 1gakA 141 -32.62 -13.72 1.40e+01 1poiA 317 -27.07 -13.59 1.48e+01 1winA 143 -34.01 -13.51 1.53e+01 1ryc 294 -29.95 -13.50 1.54e+01 2ac3A 316 -37.69 -13.48 1.55e+01 1p0yA 444 -34.07 -13.36 1.63e+01 1mlvA 444 -35.25 -13.33 1.65e+01 1qs0A 407 -31.24 -13.31 1.67e+01 1lj9A 144 -31.85 -13.23 1.73e+01 1hg5A 289 -35.19 -13.19 1.75e+01 1o5oA 221 -28.28 -13.17 1.77e+01 1qhhA 167 -40.13 -13.14 1.79e+01 1h3fA 432 -29.98 -13.08 1.84e+01 2bkkA 264 -29.57 -13.07 1.85e+01 1k94A 165 -32.88 -13.04 1.87e+01 1yqcA 170 -24.86 -13.02 1.89e+01 1dseA 292 -27.51 -13.02 1.89e+01 8prkA 287 -27.43 -13.01 1.89e+01 1htrB 329 -24.96 -12.96 1.94e+01 1wteA 272 -36.09 -12.96 1.94e+01 1tf4A 605 -27.09 -12.88 2.01e+01 1hg2A 289 -34.51 -12.88 2.01e+01 1w94A 156 -26.05 -12.87 2.02e+01 1wgjA 286 -27.34 -12.83 2.05e+01 1ej8A 140 -25.95 -12.79 2.08e+01 2pgd 482 -34.56 -12.72 2.15e+01 1e9gA 286 -26.83 -12.69 2.17e+01 2ac5A 316 -35.90 -12.68 2.19e+01 1b0pA 1231 -47.11 -12.58 2.28e+01 1qc7A 101 -36.29 -12.55 2.31e+01 1jenA 267 -30.94 -12.53 2.33e+01 1gm7A 209 -34.34 -12.51 2.35e+01 1ywmA 200 -31.28 -12.44 2.43e+01 1nnxA 109 -26.07 -12.35 2.52e+01 1j7lA 264 -33.01 -12.33 2.54e+01 1cpt 412 -28.82 -12.32 2.55e+01 1fjgM 126 -34.80 -12.32 2.55e+01 1ufhA 180 -31.30 -12.32 2.55e+01 1il6 185 -33.79 -12.31 2.56e+01 1hf8A 289 -34.23 -12.30 2.58e+01 1kekA 1231 -46.62 -12.29 2.59e+01 1e9gB 286 -25.92 -12.20 2.69e+01 1lnwA 147 -31.29 -12.13 2.77e+01 1q52A 314 -28.59 -12.13 2.77e+01 1i7pA 274 -24.50 -12.11 2.80e+01 1zbyA 294 -26.25 -12.07 2.84e+01 1br0A 120 -42.55 -12.07 2.84e+01 1pyiA 96 -34.91 -12.05 2.86e+01 1y60A 169 -24.32 -12.04 2.88e+01 2arhA 203 -34.95 -11.98 2.95e+01 1kqwA 134 -26.38 -11.98 2.96e+01 1crzA 403 -25.06 -11.96 2.98e+01 2bzuA 181 -29.67 -11.95 2.99e+01 1f5nA 592 -34.89 -11.94 3.00e+01 1wer 334 -38.49 -11.93 3.02e+01 1ds4A 292 -26.64 -11.90 3.05e+01 1dlyA 164 -33.78 -11.89 3.07e+01 1nd4A 264 -29.88 -11.83 3.16e+01 1jdrA 294 -25.92 -11.81 3.18e+01 1dlc 584 -31.06 -11.80 3.19e+01 1se7A 83 -37.20 -11.80 3.20e+01 1on0A 158 -30.93 -11.79 3.21e+01 1fm2A 169 -36.88 -11.77 3.24e+01 1jk0A 419 -38.08 -11.75 3.26e+01 1ku2A 241 -35.06 -11.75 3.27e+01 1jvr 137 -41.39 -11.73 3.30e+01 1ijtA 128 -21.64 -11.72 3.31e+01 1z53A 294 -26.32 -11.70 3.34e+01 1jyhA 157 -26.83 -11.69 3.35e+01 1ccg 291 -28.14 -11.68 3.36e+01 1dg3A 592 -34.60 -11.62 3.45e+01 1w33A 181 -36.77 -11.62 3.45e+01 2tmkA 216 -32.90 -11.60 3.49e+01 1jb0F 164 -38.48 -11.59 3.50e+01 1fjgI 128 -29.57 -11.58 3.51e+01 1senA 164 -25.08 -11.58 3.52e+01 1cp3A 277 -25.33 -11.58 3.52e+01 1lokA 291 -22.55 -11.54 3.57e+01 1molA 94 -25.04 -11.54 3.58e+01 1fqvJ 149 -29.70 -11.53 3.59e+01 1or7A 194 -38.58 -11.51 3.62e+01 1ej5A 107 -34.68 -11.47 3.69e+01 7atjA 308 -26.63 -11.45 3.72e+01 1stfI 98 -26.63 -11.44 3.74e+01 1zeeA 403 -29.47 -11.42 3.76e+01 1dqeA 137 -29.21 -11.38 3.84e+01 1h7wD 1025 -34.14 -11.36 3.87e+01 1fa3A 96 -25.12 -11.35 3.89e+01 1bu7A 455 -38.09 -11.34 3.90e+01 1gt8C 1025 -33.09 -11.32 3.93e+01