% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53 % (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. % --------------------------------------------------------------------- % T0337.t04-100-30-dssp-ehl2 Host: shaw.cse.ucsc.edu Tue Jun 20 10:39:30 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/casp7/T0337 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.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 T0337.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0337.t04.dssp-ehl2.mod % Average encoding costs (nats) for (tau, lambda) settings: % Original (1.0000, 1.0000): 2.3745 % Calibrated (0.8002, 1.2031): 2.2969 % Lambda fit (1.0000, 0.9094): 2.3516 % Not fitted (1.0000, 1.0000): 2.3745 % Calibration data for 10897 database sequences % 4110 of 10897 scores > calibrate_threshold (0) used. % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10897 sequences, 2566898 residues, 152 nodes, 60.83 seconds % % Sequence scores selected if better than: % E-value (Emax 9.0e+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 (=10897) sequences: % N / (1 + exp(-(lambda(=1.2031) * Reverse)^tau(=0.8002))) % 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 1ri7A 171 -147.03 -130.44 1.63e-21 2cg4A 152 -134.55 -119.60 7.54e-20 2cfxA 144 -124.83 -107.57 5.76e-18 1sfxA 109 -51.56 -35.75 1.68e-05 2a61A 145 -44.53 -32.60 7.11e-05 1s3jA 155 -40.35 -30.50 1.89e-04 1ulyA 192 -40.46 -27.69 7.16e-04 2fbiA 142 -39.58 -26.48 1.28e-03 1xnpA 202 -38.17 -26.08 1.55e-03 1ub9A 100 -37.77 -26.01 1.61e-03 2csbA 519 -37.15 -25.15 2.44e-03 2fbhA 146 -36.02 -24.45 3.43e-03 1je8A 82 -32.70 -24.28 3.74e-03 2g7uA 257 -35.08 -23.97 4.35e-03 1j5yA 187 -41.82 -23.89 4.51e-03 1q1hA 110 -34.20 -23.57 5.30e-03 1lj9A 144 -33.94 -23.40 5.75e-03 1z91A 147 -34.06 -23.31 6.03e-03 2b0lA 102 -33.67 -22.97 7.10e-03 1p4xA 250 -32.07 -22.38 9.55e-03 1mkmA 249 -36.41 -22.08 1.11e-02 1u2wA 122 -32.66 -21.95 1.18e-02 1lnwA 147 -33.24 -21.84 1.25e-02 1r1tA 122 -31.64 -21.77 1.29e-02 1zljA 78 -30.08 -21.32 1.62e-02 1smtA 122 -30.94 -21.12 1.80e-02 1lvaA 258 -32.67 -20.65 2.27e-02 2fxaA 207 -31.75 -20.04 3.11e-02 1i6xA 209 -30.50 -19.98 3.21e-02 1bia 321 -31.64 -19.94 3.27e-02 1jhfA 202 -29.87 -19.82 3.48e-02 1jgsA 138 -30.37 -19.81 3.49e-02 1xd7A 145 -29.93 -19.64 3.82e-02 1on2A 142 -30.08 -19.46 4.19e-02 1hw5A 210 -29.96 -19.42 4.27e-02 1in6A 334 -32.63 -19.15 4.91e-02 6paxA 133 -29.24 -18.52 6.79e-02 1in4A 334 -32.63 -18.36 7.36e-02 2dtr 226 -28.06 -18.19 8.04e-02 1y0uA 96 -27.16 -18.11 8.38e-02 2ethA 154 -33.54 -18.00 8.88e-02 1k78A 149 -27.37 -17.45 1.19e-01 1sd4A 126 -29.76 -17.24 1.32e-01 1qbjA 81 -26.86 -16.40 2.06e-01 1j75A 67 -27.85 -16.39 2.08e-01 1zybA 232 -25.86 -16.25 2.23e-01 1s7oA 113 -26.13 -16.09 2.44e-01 1hw1A 239 -26.68 -15.99 2.56e-01 1fseA 74 -25.65 -15.63 3.10e-01 1yyvA 131 -27.20 -15.40 3.51e-01 1a04A 215 -32.04 -15.37 3.57e-01 1aisB 200 -24.67 -15.33 3.64e-01 2fswA 107 -25.79 -15.33 3.65e-01 2cohA 202 -26.17 -14.99 4.38e-01 1hlvA 131 -25.76 -14.69 5.17e-01 1ufmA 84 -23.55 -14.67 5.22e-01 1wi9A 72 -26.56 -14.66 5.25e-01 1xmaA 145 -26.34 -14.56 5.53e-01 1r1uA 106 -25.49 -14.42 5.98e-01 1r7jA 95 -24.93 -14.12 7.03e-01 1uxtA 501 -25.37 -14.09 7.15e-01 1j3mA 129 -24.46 -14.07 7.23e-01 1g2hA 61 -22.05 -13.85 8.15e-01 1xmkA 79 -23.58 -13.82 8.31e-01 1okrA 123 -27.22 -13.80 8.40e-01 2acjA 66 -22.91 -13.39 1.05e+00 1q2lA 939 -24.53 -12.81 1.45e+00 1ofuA 320 -28.63 -12.63 1.61e+00 1xsvA 113 -23.00 -12.48 1.74e+00 1xviA 275 -25.60 -12.40 1.82e+00 1stzA 338 -23.77 -12.13 2.12e+00 1bm9A 122 -24.89 -12.02 2.26e+00 1ixcA 294 -22.87 -11.97 2.33e+00 2ab5A 269 -26.03 -11.87 2.46e+00 2f2eA 146 -23.77 -11.76 2.62e+00 1jhgA 101 -21.60 -11.75 2.63e+00 2fu4A 83 -23.07 -11.73 2.65e+00 1pbgA 468 -27.49 -11.69 2.72e+00 1rr7A 129 -23.75 -11.69 2.72e+00 1qzzA 374 -22.98 -11.59 2.88e+00 1s6lA 212 -20.54 -11.59 2.89e+00 1fsz 372 -28.44 -11.57 2.92e+00 1t56A 216 -21.10 -11.56 2.93e+00 2bj7A 138 -32.06 -11.32 3.36e+00 2a6cA 83 -21.42 -11.09 3.85e+00 1rkqA 282 -21.10 -10.92 4.23e+00 1mai 131 -20.37 -10.90 4.28e+00 1uj6A 227 -23.48 -10.83 4.44e+00 1mgtA 174 -24.26 -10.65 4.95e+00 1qipA 183 -22.07 -10.64 4.96e+00 1umqA 81 -19.54 -10.64 4.96e+00 1ne2A 200 -22.72 -10.64 4.96e+00 1or7A 194 -23.05 -10.63 5.01e+00 1p4wA 99 -21.75 -10.55 5.23e+00 1bbpA 173 -20.88 -10.44 5.58e+00 1pufB 73 -19.04 -10.38 5.78e+00 1z7uA 112 -23.40 -10.31 6.01e+00 1b72B 87 -18.90 -10.26 6.21e+00 1tbxA 99 -18.91 -10.22 6.35e+00 1o54A 277 -23.66 -10.20 6.40e+00 2cujA 108 -20.95 -10.15 6.62e+00 1jayA 212 -25.47 -10.13 6.67e+00 1utxA 66 -21.33 -10.10 6.80e+00 1wpkA 146 -19.46 -10.02 7.13e+00 1u8bA 133 -19.46 -9.94 7.49e+00 1gvdA 52 -19.47 -9.91 7.58e+00 1xn7A 78 -24.80 -9.85 7.85e+00 1pwmA 316 -20.75 -9.74 8.40e+00 2c5uA 375 -20.67 -9.61 9.06e+00 1etxA 98 -19.60 -9.60 9.10e+00 2afwA 329 -21.21 -9.59 9.20e+00 2fokA 579 -20.30 -9.57 9.27e+00 1p0hA 318 -20.13 -9.57 9.27e+00 1z1dA 103 -19.83 -9.56 9.33e+00 1dpuA 99 -20.15 -9.56 9.37e+00 1m32A 366 -23.26 -9.46 9.88e+00 1tx4B 178 -22.75 -9.35 1.06e+01 2agtA 319 -20.21 -9.34 1.07e+01 1ads 315 -20.21 -9.32 1.08e+01 1zgwA 139 -20.28 -9.28 1.11e+01 1zx4A 192 -21.29 -9.27 1.11e+01 2b9eA 303 -19.34 -9.27 1.11e+01 2g7gA 213 -19.66 -9.24 1.13e+01 1us0A 316 -20.21 -9.22 1.14e+01 1bl0A 129 -18.68 -9.20 1.15e+01 1i7dA 659 -20.03 -9.20 1.16e+01 2esnA 310 -19.58 -9.18 1.17e+01 1fipA 98 -20.60 -9.13 1.21e+01 1shyB 551 -21.04 -9.09 1.23e+01 2bgcA 238 -20.53 -9.08 1.24e+01 1xuuA 349 -21.26 -9.08 1.25e+01 2ao9A 155 -18.07 -9.03 1.28e+01 2ad9A 119 -18.07 -9.03 1.28e+01 1jh6A 189 -23.43 -8.97 1.33e+01 1tc3C 51 -16.93 -8.94 1.35e+01 2adbA 148 -20.17 -8.93 1.36e+01 1u04A 771 -25.03 -8.93 1.36e+01 2axoA 270 -22.73 -8.83 1.44e+01 1kxoA 184 -18.99 -8.82 1.45e+01 1vk1A 242 -24.72 -8.81 1.46e+01 1fnnA 389 -22.60 -8.80 1.47e+01 2ae6A 166 -21.39 -8.75 1.51e+01 2ax3A 502 -22.31 -8.74 1.52e+01 1cjgA 62 -17.46 -8.73 1.53e+01 1wa3A 205 -20.74 -8.70 1.56e+01 1r69 69 -17.11 -8.69 1.57e+01 1fa0A 537 -21.69 -8.67 1.59e+01 1yb2A 275 -20.90 -8.67 1.59e+01 1jc4A 148 -20.05 -8.61 1.65e+01 1r71A 178 -19.77 -8.57 1.69e+01 1jggA 60 -17.17 -8.55 1.71e+01 1mhdA 132 -17.84 -8.54 1.72e+01 2bjcA 62 -17.85 -8.52 1.74e+01 2d27A 149 -19.40 -8.50 1.75e+01 2gmqA 118 -17.27 -8.43 1.84e+01 1b0nA 111 -17.66 -8.41 1.86e+01 1dwkA 156 -18.53 -8.39 1.88e+01 2fq4A 192 -17.72 -8.38 1.89e+01 1pru 56 -17.11 -8.35 1.93e+01 1hr6A 475 -18.22 -8.29 2.00e+01 1neq 74 -16.03 -8.28 2.02e+01 1q79A 514 -19.56 -8.25 2.04e+01 1zh5A 195 -22.34 -8.23 2.07e+01 1hqz1 141 -21.01 -8.23 2.07e+01 1yrlA 491 -18.87 -8.21 2.10e+01 1jd1A 129 -21.10 -8.19 2.12e+01 1bjaA 95 -16.68 -8.17 2.14e+01 2b5aA 77 -18.09 -8.16 2.16e+01 2abqA 306 -20.07 -8.10 2.24e+01 1zarA 282 -23.41 -8.10 2.24e+01 1tqmA 282 -23.44 -8.09 2.26e+01 2cro 71 -16.45 -8.08 2.27e+01 1xgsA 295 -20.62 -8.07 2.29e+01 1adr 76 -16.37 -8.06 2.29e+01 1t0fA 276 -18.77 -8.01 2.37e+01 1p9qC 256 -26.58 -7.98 2.42e+01 1mi3A 322 -20.11 -7.91 2.52e+01 1r5jA 337 -19.13 -7.86 2.60e+01 1res 43 -15.87 -7.84 2.63e+01 1cy9A 264 -17.34 -7.83 2.65e+01 2bnmA 198 -17.31 -7.75 2.78e+01 1u0mA 382 -19.76 -7.73 2.81e+01 1tk9A 188 -20.11 -7.73 2.82e+01 2c27A 315 -18.09 -7.72 2.83e+01 1e2uA 553 -20.23 -7.71 2.85e+01 1gntA 553 -20.23 -7.71 2.85e+01 1sjqA 105 -17.77 -7.67 2.92e+01 1p8kZ 254 -21.03 -7.67 2.92e+01 1vhiA 142 -20.04 -7.63 2.99e+01 1ckiA 317 -18.50 -7.63 3.00e+01 1f5aA 513 -19.39 -7.62 3.01e+01 1kfwA 435 -19.21 -7.62 3.01e+01 2aj0A 71 -21.30 -7.60 3.05e+01 1t95A 240 -25.83 -7.59 3.07e+01 1k4nA 192 -18.95 -7.57 3.10e+01 1zzcA 198 -17.04 -7.57 3.11e+01 1qgoA 264 -22.35 -7.54 3.16e+01 1gnlA 544 -19.55 -7.50 3.25e+01 3pmgA 561 -23.08 -7.49 3.27e+01 1b3tA 147 -19.92 -7.48 3.27e+01 1kqpA 271 -19.92 -7.46 3.33e+01 1gtdA 85 -22.11 -7.43 3.38e+01 1abv 134 -17.38 -7.42 3.41e+01 2f06A 144 -27.02 -7.42 3.41e+01 1y1pA 342 -18.06 -7.42 3.41e+01 2c5rA 67 -17.21 -7.37 3.51e+01 1vqsA 116 -20.45 -7.37 3.52e+01 1pxwA 128 -17.31 -7.36 3.54e+01 1rzsA 61 -15.32 -7.33 3.61e+01 1f1zA 273 -18.76 -7.32 3.62e+01 1kmqA 184 -20.84 -7.31 3.66e+01 1ypfA 336 -19.85 -7.28 3.73e+01 1kqfB 294 -16.92 -7.27 3.73e+01 1qc7A 101 -19.03 -7.27 3.74e+01 1mtpA 323 -17.56 -7.27 3.74e+01 1neeA 138 -18.28 -7.25 3.78e+01 2sga 181 -16.14 -7.24 3.80e+01 1chuA 540 -18.85 -7.23 3.82e+01 1ozjA 144 -16.42 -7.23 3.83e+01 1mzbA 136 -20.77 -7.14 4.04e+01 1ku3A 73 -16.05 -7.13 4.09e+01 2gcfA 73 -16.16 -7.12 4.11e+01 1zkcA 197 -17.90 -7.11 4.13e+01 1vmaA 306 -23.89 -7.08 4.20e+01 1sqeA 109 -18.32 -7.08 4.20e+01 1oz9A 150 -21.13 -7.07 4.25e+01 1azo 232 -16.20 -7.06 4.26e+01 1ta0A 197 -19.84 -7.06 4.26e+01 1q1aA 289 -18.99 -7.05 4.29e+01 1f0xA 571 -21.16 -7.05 4.29e+01 2gefA 217 -17.19 -7.05 4.29e+01 1gxqA 106 -16.42 -7.04 4.30e+01 1fxlA 167 -21.17 -7.04 4.31e+01 1x89A 178 -17.99 -7.01 4.39e+01 1x71A 178 -17.99 -7.01 4.39e+01 1rec 201 -16.96 -7.00 4.41e+01 1wu7A 434 -20.64 -7.00 4.42e+01 1ym5A 300 -18.65 -7.00 4.44e+01 2be4A 272 -17.02 -6.97 4.50e+01 1sdoA 203 -18.52 -6.93 4.63e+01 2b71A 196 -17.80 -6.91 4.68e+01 1uarA 285 -18.34 -6.91 4.69e+01 1akhA 61 -15.72 -6.90 4.71e+01 1qfjA 232 -19.37 -6.89 4.75e+01 1js3A 486 -20.86 -6.89 4.76e+01 1fjlA 81 -16.03 -6.87 4.80e+01 1h5uA 842 -18.70 -6.86 4.83e+01 1omiA 248 -17.88 -6.85 4.86e+01 1ftrA 296 -19.42 -6.85 4.86e+01 1h1dA 221 -17.86 -6.85 4.87e+01 1t9iA 163 -19.42 -6.81 4.98e+01 1omrA 201 -16.78 -6.80 5.01e+01 1sqsA 242 -23.95 -6.79 5.05e+01 1o8bA 219 -18.36 -6.77 5.10e+01 1j8fA 323 -18.65 -6.75 5.17e+01 3rubS 123 -19.01 -6.75 5.17e+01 1g9zA 152 -19.18 -6.74 5.20e+01 1mwqA 101 -17.88 -6.73 5.24e+01 1v95A 130 -19.56 -6.71 5.30e+01 5nul 138 -22.57 -6.71 5.30e+01 1xubA 298 -18.39 -6.71 5.31e+01 1yc5A 246 -17.97 -6.70 5.34e+01 1gkpA 458 -20.11 -6.69 5.37e+01 1rloA 271 -18.67 -6.69 5.39e+01 1onrA 316 -17.24 -6.68 5.42e+01 2c9wA 169 -16.47 -6.67 5.44e+01 1zthA 258 -17.49 -6.66 5.47e+01 2fk8A 318 -18.20 -6.65 5.50e+01 1seiA 130 -18.42 -6.65 5.50e+01 2guhA 214 -16.26 -6.65 5.51e+01 1u1wA 298 -18.29 -6.62 5.64e+01 1p7tA 731 -17.86 -6.61 5.65e+01 1fexA 59 -15.53 -6.58 5.75e+01 1ih8A 271 -19.06 -6.58 5.77e+01 2bnjA 303 -20.26 -6.55 5.87e+01 2arzA 247 -18.93 -6.54 5.90e+01 2etxA 209 -15.56 -6.52 6.00e+01 1hcrA 52 -15.13 -6.52 6.00e+01 1y5mA 276 -19.46 -6.51 6.01e+01 1eyvA 156 -15.55 -6.49 6.08e+01 2gauA 232 -16.61 -6.49 6.12e+01 2bgkA 278 -19.25 -6.49 6.12e+01 1u02A 239 -20.97 -6.48 6.16e+01 1r8hA 87 -16.25 -6.47 6.18e+01 2adoA 196 -15.60 -6.46 6.20e+01 1ujmA 342 -17.30 -6.46 6.21e+01 1u8sA 192 -23.24 -6.42 6.39e+01 1of8A 370 -21.64 -6.42 6.39e+01 2pgd 482 -19.38 -6.42 6.39e+01 1zoiA 276 -18.03 -6.41 6.41e+01 1rlmA 271 -19.67 -6.41 6.41e+01 1xseA 295 -20.47 -6.41 6.41e+01 1uekA 275 -18.98 -6.41 6.44e+01 1fsiA 189 -19.87 -6.39 6.52e+01 1lk5A 229 -20.84 -6.38 6.55e+01 2tct 207 -18.41 -6.37 6.59e+01 1un8A 552 -22.82 -6.37 6.60e+01 2givA 295 -18.15 -6.35 6.67e+01 1csn 298 -16.70 -6.35 6.68e+01 1fy7A 278 -17.82 -6.35 6.69e+01 1i2oA 316 -17.06 -6.34 6.69e+01 1y74A 57 -16.51 -6.32 6.79e+01 1k3eA 156 -17.31 -6.32 6.79e+01 1kpgA 287 -17.33 -6.32 6.81e+01 1v9dA 340 -16.55 -6.32 6.81e+01 2f8mA 244 -20.10 -6.30 6.90e+01 1nxiA 132 -19.91 -6.30 6.91e+01 1uz3A 102 -17.33 -6.29 6.91e+01 1fc3A 120 -15.86 -6.28 6.97e+01 1sfuA 75 -17.58 -6.26 7.06e+01 1oaoC 729 -18.20 -6.25 7.10e+01 1naqA 112 -19.26 -6.25 7.11e+01 1xyzA 347 -24.09 -6.23 7.20e+01 1ppjA 446 -17.76 -6.23 7.20e+01 1wtyA 119 -16.40 -6.22 7.25e+01 1vlwA 217 -17.97 -6.22 7.26e+01 1wa8B 95 -15.86 -6.20 7.37e+01 1zq9A 285 -16.85 -6.18 7.42e+01 2b33A 140 -19.64 -6.17 7.48e+01 1cpcB 172 -16.01 -6.17 7.49e+01 1lopA 164 -17.28 -6.17 7.49e+01 2d0oA 610 -18.12 -6.17 7.50e+01 1ns5A 155 -21.35 -6.16 7.54e+01 1pmzA 86 -17.90 -6.15 7.57e+01 1xy7A 166 -16.29 -6.15 7.57e+01 1hy7A 173 -17.76 -6.14 7.61e+01 1heiA 451 -17.63 -6.13 7.68e+01 1jkoC 52 -14.68 -6.12 7.71e+01 1ej1A 190 -17.29 -6.12 7.73e+01 1wrjA 156 -15.58 -6.12 7.73e+01 1t0tV 248 -19.83 -6.09 7.86e+01 1fxxA 482 -16.84 -6.09 7.90e+01 1tz0A 114 -16.62 -6.06 8.01e+01 1a32 88 -16.14 -6.06 8.02e+01 2bjiA 277 -16.05 -6.05 8.06e+01 1r9wA 145 -17.61 -6.05 8.06e+01 1a6jA 163 -17.15 -6.05 8.11e+01 1ecrA 309 -17.59 -6.04 8.12e+01 1cf2O 337 -23.13 -6.04 8.13e+01 1tkiA 321 -17.47 -6.03 8.20e+01 1a8i 842 -17.83 -6.00 8.33e+01 1np6A 174 -18.13 -6.00 8.34e+01 1j97A 211 -18.94 -6.00 8.34e+01 1oxkB 134 -18.93 -6.00 8.35e+01 2cw8A 537 -18.18 -5.99 8.38e+01 1d2kA 392 -20.36 -5.99 8.41e+01 1fp2A 352 -17.72 -5.97 8.52e+01 2bkaA 242 -19.46 -5.97 8.52e+01 1q16B 512 -14.98 -5.96 8.56e+01 1zhhB 242 -20.90 -5.96 8.57e+01 1e7uA 961 -18.05 -5.95 8.60e+01 1xi1A 575 -17.02 -5.93 8.72e+01 1y5iB 512 -14.98 -5.92 8.76e+01 2g3bA 208 -15.41 -5.92 8.77e+01 1d5yA 292 -16.04 -5.92 8.77e+01 1w9pA 433 -18.33 -5.91 8.82e+01 1d8cA 723 -17.28 -5.91 8.86e+01 1t6kA 278 -17.91 -5.90 8.89e+01 1oyiA 82 -15.51 -5.90 8.89e+01 1lmb3 92 -15.52 -5.89 8.94e+01 1i1wA 303 -19.83 -5.89 8.95e+01 1xzoA 174 -19.80 -5.88 8.99e+01