% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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. % --------------------------------------------------------------------- % dsspfoo.1.T0196.t04-100-30-alpha Host: cheep Tue Jun 15 22:09:55 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0196 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.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 T0196.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0196.t04.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6473 sequences, 1530840 residues, 117 nodes, 36.51 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 (=9907) sequences: % N / (1 + exp(-(lambda(=3.4750) * Reverse)^tau(=0.6906))) % 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 1jnyA 435 -41.65 -32.15 5.23e-08 1f60A 458 -33.39 -23.81 6.75e-06 1ha3A 405 -29.72 -20.44 5.60e-05 1exmA 405 -28.79 -19.52 1.01e-04 1g7sA 594 -27.58 -18.91 1.51e-04 1d2eA 397 -26.51 -17.88 2.99e-04 1d1nA 99 -23.78 -14.54 2.98e-03 1b5fB 87 -17.90 -9.67 1.20e-01 1h2rL 534 -16.91 -8.32 3.64e-01 1uvqB 198 -17.00 -8.24 3.90e-01 1e79A 510 -16.77 -8.17 4.15e-01 1ubkL 534 -16.55 -7.96 4.97e-01 1f1gA 154 -16.15 -7.89 5.27e-01 1jcv 153 -16.07 -7.79 5.73e-01 1e3dB 542 -16.23 -7.59 6.85e-01 1h8eA 510 -16.12 -7.58 6.86e-01 1ghqB 134 -15.26 -7.56 7.03e-01 1kbvA 327 -18.24 -7.27 9.01e-01 1kxgA 152 -15.88 -6.85 1.32e+00 1ejeA 192 -15.00 -6.81 1.37e+00 1aun 208 -14.53 -6.67 1.55e+00 1aym2 261 -14.78 -6.66 1.57e+00 1be9A 119 -16.93 -6.49 1.83e+00 1ly2A 130 -14.11 -6.33 2.12e+00 1s0uA 408 -16.00 -6.26 2.24e+00 1kjqA 391 -15.52 -6.26 2.25e+00 1kk1A 410 -18.19 -6.11 2.58e+00 1l1qA 186 -14.13 -6.10 2.61e+00 1eyzA 392 -15.44 -6.04 2.77e+00 1ae9A 179 -13.86 -6.03 2.79e+00 1tib 269 -14.17 -5.98 2.93e+00 1k0sA 151 -15.66 -5.87 3.23e+00 1kay 381 -14.82 -5.86 3.26e+00 1p32A 209 -16.06 -5.86 3.28e+00 1gnyA 153 -14.85 -5.85 3.30e+00 1lvwA 295 -14.63 -5.72 3.74e+00 1j0hA 588 -14.60 -5.66 3.95e+00 1yaiA 151 -13.80 -5.66 3.97e+00 1lfo 128 -16.26 -5.63 4.08e+00 1r0uA 148 -15.22 -5.63 4.08e+00 1k4nA 192 -13.48 -5.60 4.20e+00 1n0uA 842 -14.22 -5.59 4.23e+00 1pjxA 314 -14.97 -5.38 5.16e+00 1bupA 386 -14.58 -5.37 5.21e+00 1sdwA 314 -14.22 -5.29 5.63e+00 1hxn 219 -14.15 -5.26 5.85e+00 1lx7A 253 -13.23 -5.23 6.00e+00 1lw6I 64 -12.62 -5.20 6.19e+00 1a7tA 232 -13.68 -5.19 6.21e+00 1pvmA 184 -12.63 -5.19 6.25e+00 1e1aA 314 -14.95 -5.18 6.31e+00 1dar 691 -15.66 -5.17 6.35e+00 1o7iA 119 -15.00 -5.12 6.65e+00 1nd4A 264 -14.29 -5.12 6.66e+00 1i8dA 213 -13.83 -5.05 7.18e+00 1ckmA 330 -15.33 -5.02 7.39e+00 1bio 228 -13.73 -5.01 7.44e+00 1phm 310 -14.09 -4.98 7.70e+00 1gt6A 269 -13.20 -4.93 8.10e+00 1ten 90 -14.79 -4.92 8.11e+00 1rxyA 253 -12.88 -4.89 8.37e+00 1oalA 151 -13.34 -4.87 8.58e+00 1g2qA 187 -12.97 -4.87 8.58e+00 1g9oA 91 -13.11 -4.83 8.91e+00 1k82A 268 -13.47 -4.82 8.97e+00 1oi6A 205 -14.09 -4.80 9.23e+00 1eazA 125 -13.37 -4.76 9.53e+00 1nb5I 98 -14.57 -4.76 9.53e+00 1a3k 137 -14.24 -4.74 9.77e+00 1b65A 375 -13.22 -4.73 9.84e+00 1ip9A 85 -12.79 -4.72 9.98e+00 1bbpA 173 -13.01 -4.71 1.01e+01 1shbA 104 -12.40 -4.71 1.01e+01 1bdo 80 -13.10 -4.64 1.08e+01 1sbxA 106 -12.58 -4.63 1.09e+01 1ecrA 309 -13.21 -4.63 1.09e+01 1crb 134 -13.90 -4.62 1.10e+01 1jy4A 35 -12.45 -4.59 1.14e+01 1k2eA 156 -13.88 -4.58 1.14e+01 1qvbA 481 -12.70 -4.57 1.16e+01 1rwrA 301 -15.15 -4.55 1.18e+01 1hh2P 344 -12.89 -4.54 1.19e+01 1bvqA 141 -12.75 -4.54 1.20e+01 1ofnA 205 -13.81 -4.53 1.21e+01 1ei5A 520 -13.46 -4.50 1.24e+01 1lo7A 141 -12.62 -4.50 1.25e+01 1efvB 255 -13.12 -4.48 1.27e+01 1cl1A 395 -12.37 -4.47 1.28e+01 1mexL 213 -12.57 -4.46 1.29e+01 1nbwA 607 -13.19 -4.46 1.30e+01 4bcl 366 -14.06 -4.44 1.33e+01 8fabA 212 -13.63 -4.42 1.35e+01 1i0cA 60 -12.30 -4.41 1.37e+01 1ogsA 497 -13.48 -4.39 1.39e+01 1j9qA 341 -13.03 -4.38 1.40e+01 1efvA 315 -12.46 -4.36 1.44e+01 1g8lA 411 -12.50 -4.35 1.45e+01 1dseA 292 -12.97 -4.34 1.47e+01 1lvmA 229 -13.12 -4.32 1.50e+01 1am2 199 -13.21 -4.29 1.55e+01 1mp9A 198 -12.91 -4.28 1.55e+01 1qz5A 375 -12.44 -4.27 1.57e+01 1ollA 188 -13.75 -4.27 1.58e+01 1gr3A 160 -13.90 -4.27 1.58e+01 1pwaA 162 -12.53 -4.24 1.63e+01 1oacA 727 -15.42 -4.21 1.67e+01 1e30A 155 -13.37 -4.21 1.68e+01 1cq3A 233 -14.24 -4.18 1.72e+01 1gadO 330 -12.20 -4.18 1.73e+01 1j6zA 376 -12.20 -4.15 1.78e+01 1hr0W 71 -12.14 -4.13 1.83e+01 1xsoA 150 -13.59 -4.12 1.85e+01 1fmtA 314 -12.48 -4.11 1.86e+01 1g99A 408 -12.96 -4.11 1.87e+01 1euvB 86 -12.99 -4.10 1.89e+01 1pbe 394 -12.23 -4.09 1.91e+01 1q5hA 147 -15.37 -4.09 1.91e+01 1kkeA 210 -13.09 -4.07 1.94e+01 1pmi 440 -12.57 -4.07 1.95e+01 1mjuL 219 -12.16 -4.07 1.95e+01 1rurL 217 -12.28 -4.06 1.96e+01 1i07A 60 -11.93 -4.03 2.04e+01 2eng 210 -11.96 -4.03 2.04e+01 1vjnA 220 -14.96 -4.02 2.05e+01 1dun 134 -13.60 -4.01 2.08e+01 1ka1A 357 -12.01 -3.99 2.12e+01 2fmr 65 -12.24 -3.99 2.13e+01 1ugiA 84 -12.29 -3.98 2.14e+01 1paqA 189 -11.78 -3.98 2.15e+01 1pyaB 228 -12.60 -3.97 2.15e+01 1ncwL 219 -12.11 -3.97 2.16e+01 1iznA 286 -12.20 -3.97 2.17e+01 1k0iA 394 -12.15 -3.96 2.19e+01 1cc1L 498 -12.38 -3.96 2.19e+01 1khiA 176 -13.11 -3.90 2.33e+01 1itwA 741 -12.18 -3.90 2.34e+01 1ksiA 642 -14.14 -3.89 2.36e+01 1ifrA 121 -11.91 -3.88 2.38e+01 1kcvL 214 -11.87 -3.88 2.38e+01 1ubeA 349 -13.04 -3.88 2.38e+01 1htp 131 -12.08 -3.88 2.39e+01 1kzkA 99 -15.14 -3.87 2.40e+01 1gcqC 70 -11.58 -3.87 2.40e+01 1rcy 151 -13.22 -3.87 2.40e+01 2phlA 397 -13.78 -3.87 2.41e+01 1iq8A 582 -12.91 -3.86 2.42e+01 1ln1A 214 -12.67 -3.86 2.43e+01 1nkr 201 -12.67 -3.86 2.44e+01 1sacA 204 -13.58 -3.86 2.44e+01 1pbyA 489 -13.76 -3.84 2.47e+01 3nul 130 -13.33 -3.82 2.54e+01 1cdy 178 -12.76 -3.82 2.55e+01 1nu5A 370 -12.99 -3.81 2.55e+01 1j2zA 270 -15.14 -3.80 2.59e+01 1o9gA 250 -11.79 -3.79 2.62e+01 1gjwA 637 -12.69 -3.79 2.63e+01 1pn0A 665 -12.88 -3.79 2.63e+01 1hpcA 131 -12.05 -3.78 2.65e+01 1dtdA 303 -12.20 -3.77 2.68e+01 1usuB 170 -13.02 -3.77 2.69e+01 1difA 99 -15.26 -3.76 2.70e+01 1hdmA 201 -12.07 -3.76 2.71e+01 1dxrH 258 -12.35 -3.76 2.71e+01 1tetL 216 -11.87 -3.76 2.72e+01 1j71A 334 -12.06 -3.75 2.74e+01 1qhdA 398 -12.20 -3.72 2.84e+01 2fbjL 213 -11.97 -3.72 2.84e+01 1forL 210 -11.88 -3.71 2.85e+01 1a41 234 -11.61 -3.71 2.86e+01 1agjA 242 -14.29 -3.70 2.88e+01 1ew4A 106 -13.28 -3.69 2.91e+01 1nnxA 109 -12.53 -3.69 2.93e+01 1mmsA 140 -11.51 -3.67 2.98e+01 1ckaA 57 -12.00 -3.67 2.98e+01 2bpa2 175 -11.78 -3.67 2.99e+01 1pg4A 652 -11.94 -3.67 2.99e+01 1mlbA 214 -12.13 -3.66 3.01e+01 1fo8A 343 -11.59 -3.66 3.01e+01 1njkA 156 -12.39 -3.65 3.07e+01 1iw7C 1119 -12.93 -3.64 3.09e+01 1chmA 401 -11.57 -3.60 3.22e+01 1cyx 205 -12.48 -3.60 3.24e+01 1ihnA 113 -12.54 -3.59 3.25e+01 1fw9A 164 -11.44 -3.58 3.28e+01 1vj1A 363 -12.37 -3.58 3.28e+01 1vybA 238 -11.68 -3.58 3.29e+01 1qwrA 319 -12.85 -3.58 3.29e+01 1opbA 135 -13.00 -3.58 3.31e+01 1ifc 132 -14.52 -3.57 3.32e+01 2sns 149 -11.47 -3.56 3.36e+01 1shdA 107 -11.81 -3.56 3.36e+01 1l8fA 207 -11.48 -3.55 3.40e+01 1g2bA 62 -12.36 -3.55 3.40e+01 1luzA 88 -11.45 -3.55 3.42e+01 1v3wA 173 -14.13 -3.55 3.42e+01 1mdc 133 -16.07 -3.54 3.45e+01 1e6oL 212 -11.64 -3.53 3.47e+01 1kblA 873 -12.24 -3.53 3.47e+01 1j1lA 290 -13.67 -3.52 3.52e+01 1qqgA 264 -12.01 -3.51 3.54e+01 1earA 147 -11.64 -3.51 3.55e+01 1eyqA 222 -11.67 -3.50 3.59e+01 1q9rA 219 -11.91 -3.49 3.63e+01 1od5A 492 -12.93 -3.49 3.65e+01 1jhdA 396 -11.49 -3.48 3.67e+01 1iyhA 198 -11.16 -3.48 3.67e+01 1gpeA 587 -11.76 -3.47 3.70e+01 1f0lA 535 -12.15 -3.46 3.75e+01 1mveA 243 -11.68 -3.46 3.76e+01 1d7cA 190 -12.09 -3.45 3.79e+01 1o5uA 101 -12.03 -3.45 3.79e+01 2sfa 191 -11.83 -3.45 3.80e+01 1nh0A 99 -15.00 -3.44 3.83e+01 1idaA 99 -15.62 -3.44 3.85e+01 1gw0A 559 -13.38 -3.44 3.87e+01 1g8mA 593 -11.25 -3.42 3.91e+01 1sgpE 185 -12.07 -3.42 3.94e+01 1sek 378 -12.01 -3.42 3.95e+01 1qgxA 357 -11.37 -3.41 4.00e+01