% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 07/27/04_17:11:35 % (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.T0263.t04-100-30-dssp-ehl2 Host: crow Wed Aug 4 16:18:20 2004 % ggshack Dir: /projects/compbio/experiments/protein-predict/casp6/T0263 % --------------------------------------------------------------------- % 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 T0263.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0263.t04.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6717 sequences, 1583500 residues, 102 nodes, 27.96 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 (=6717) sequences: % N / (1 + exp(-(lambda(=1.9440) * Reverse)^tau(=0.7317))) % 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 1iujA 106 -31.81 -21.72 1.29e-03 1lq9A 112 -30.41 -21.09 1.79e-03 1edt 271 -28.53 -18.24 8.26e-03 1q4rA 112 -23.96 -13.09 1.55e-01 1qysA 106 -23.99 -11.48 4.12e-01 1bm9A 122 -20.22 -10.35 8.33e-01 1jmtA 104 -20.64 -10.02 1.03e+00 1g0cA 364 -22.76 -10.00 1.04e+00 1shdA 107 -18.18 -9.81 1.18e+00 1cnt1 187 -18.60 -9.81 1.18e+00 1af7 274 -18.38 -9.45 1.49e+00 1o4rA 108 -17.49 -9.44 1.50e+00 1a4iA 301 -19.69 -9.20 1.75e+00 1v02A 565 -19.84 -9.18 1.78e+00 1j5yA 187 -18.21 -9.16 1.80e+00 1shbA 104 -17.25 -9.15 1.82e+00 1o0uA 429 -19.70 -8.90 2.14e+00 1q8bA 105 -22.85 -8.11 3.64e+00 1j27A 102 -21.35 -8.10 3.65e+00 1fxlA 167 -17.82 -8.08 3.70e+00 1qb0A 211 -17.25 -8.03 3.83e+00 1h09A 338 -18.20 -7.86 4.30e+00 1nu0A 138 -20.39 -7.82 4.44e+00 1e44B 96 -15.34 -7.81 4.46e+00 1sb8A 352 -19.54 -7.75 4.63e+00 1ro2A 216 -16.83 -7.75 4.63e+00 1ro0A 216 -16.73 -7.73 4.71e+00 1e55A 512 -18.11 -7.72 4.73e+00 1h49A 512 -18.11 -7.71 4.77e+00 1dtdA 303 -18.44 -7.60 5.15e+00 1eceA 358 -17.32 -7.59 5.17e+00 1m15A 357 -17.45 -7.56 5.29e+00 1ftkA 279 -17.33 -7.47 5.62e+00 1khbA 625 -17.64 -7.42 5.84e+00 1g60A 260 -16.30 -7.40 5.90e+00 1j9yA 385 -17.60 -7.28 6.40e+00 1d2kA 392 -17.04 -7.22 6.68e+00 1urrA 102 -16.43 -7.05 7.54e+00 1ll7A 392 -16.91 -7.04 7.62e+00 1umhA 184 -15.94 -6.98 7.92e+00 1odzA 386 -17.42 -6.95 8.10e+00 1fi4A 416 -15.87 -6.90 8.38e+00 1vkbA 161 -16.20 -6.86 8.66e+00 1bag 425 -15.64 -6.83 8.79e+00 1thfD 253 -18.61 -6.78 9.11e+00 1n13B 113 -15.37 -6.78 9.17e+00 7a3hA 303 -18.92 -6.72 9.55e+00 1mml 265 -15.85 -6.55 1.07e+01 1iibA 106 -15.80 -6.44 1.17e+01 1tidB 119 -16.63 -6.37 1.23e+01 1bg0 356 -16.21 -6.35 1.25e+01 1on0A 158 -16.13 -6.23 1.36e+01 1h9dB 134 -14.96 -6.22 1.37e+01 1gy8A 397 -16.03 -6.20 1.38e+01 1whtA 256 -16.93 -6.20 1.39e+01 1v1aA 309 -17.78 -6.16 1.43e+01 1goiA 499 -16.20 -6.13 1.46e+01 1bjx 110 -15.52 -6.10 1.49e+01 1im8A 244 -15.85 -6.10 1.50e+01 2ebn 289 -15.97 -6.09 1.50e+01 1e6pA 499 -16.07 -5.98 1.63e+01 1whsA 255 -16.39 -5.93 1.69e+01 1fiqB 350 -15.55 -5.91 1.71e+01 1o0pA 104 -15.73 -5.88 1.75e+01 1dpe 507 -15.19 -5.86 1.79e+01 1a0cA 438 -15.78 -5.85 1.79e+01 1mqiA 263 -15.89 -5.79 1.88e+01 2igd 61 -14.90 -5.77 1.90e+01 1nox 205 -14.80 -5.76 1.92e+01 2myr 501 -15.40 -5.75 1.93e+01 1nv8A 284 -15.03 -5.75 1.94e+01 1e4mM 501 -15.44 -5.74 1.94e+01 1jwqA 179 -16.15 -5.70 2.01e+01 1sr9A 644 -16.20 -5.68 2.04e+01 1ppjB 439 -15.91 -5.63 2.11e+01 1l0lB 439 -15.91 -5.63 2.11e+01 1e4iA 447 -14.82 -5.62 2.13e+01 1s2dA 167 -15.71 -5.57 2.21e+01 1prxA 224 -14.93 -5.55 2.24e+01 1itxA 419 -14.52 -5.51 2.32e+01 1mkeA 152 -14.44 -5.49 2.34e+01 1qgvA 142 -18.54 -5.48 2.36e+01 1kpgA 287 -14.72 -5.45 2.41e+01 1ta3B 303 -16.61 -5.45 2.41e+01 1oflA 481 -13.87 -5.44 2.44e+01 1ubeA 349 -15.78 -5.43 2.44e+01 1b5tA 275 -17.44 -5.43 2.45e+01 1oapA 109 -14.73 -5.41 2.49e+01 1c4kA 730 -15.22 -5.40 2.51e+01 1dboA 506 -13.83 -5.39 2.54e+01 1evhA 112 -13.88 -5.38 2.54e+01 1dbgA 506 -13.83 -5.38 2.55e+01 1vjzA 341 -15.88 -5.31 2.69e+01 1l8nA 679 -15.79 -5.30 2.70e+01 1forL 210 -13.25 -5.26 2.79e+01 1sacA 204 -13.89 -5.25 2.82e+01 1c25 161 -14.77 -5.24 2.84e+01 2ptd 298 -18.03 -5.22 2.87e+01 1b3tA 147 -15.10 -5.20 2.93e+01 1btkA 169 -15.14 -5.19 2.94e+01 1g8kA 825 -14.45 -5.18 2.98e+01 1k77A 260 -14.16 -5.17 2.98e+01 1jae 471 -14.82 -5.17 2.99e+01 1omzA 293 -14.91 -5.14 3.05e+01 1pqnA 127 -15.04 -5.14 3.06e+01 1lvmA 229 -15.40 -5.13 3.07e+01 3pviA 157 -14.42 -5.11 3.13e+01 1vid 221 -14.96 -5.07 3.21e+01 1bjt 793 -15.25 -5.07 3.23e+01 1mwqA 101 -17.27 -5.05 3.27e+01 1v84A 253 -15.74 -5.04 3.29e+01 1eg2A 319 -14.04 -5.04 3.30e+01 1luzA 88 -13.86 -5.02 3.35e+01 1jr8A 117 -14.32 -5.01 3.38e+01 1urnA 97 -15.36 -5.01 3.39e+01 1g71A 347 -14.18 -4.99 3.43e+01 1t3uA 104 -14.96 -4.99 3.44e+01 1vhiA 142 -14.79 -4.98 3.44e+01 1n82A 331 -15.08 -4.98 3.44e+01 1i1wA 303 -14.40 -4.98 3.46e+01 1va4A 279 -14.03 -4.97 3.49e+01 1mjfA 281 -16.19 -4.96 3.50e+01 1nmeB 92 -13.38 -4.95 3.53e+01 1iv3A 152 -13.79 -4.94 3.56e+01 1hvyA 288 -13.86 -4.93 3.59e+01 1h10A 125 -13.95 -4.92 3.61e+01 1m7xA 617 -15.89 -4.90 3.67e+01 1n7hA 381 -14.75 -4.89 3.70e+01 1pbgA 468 -15.55 -4.88 3.73e+01 5nul 138 -14.28 -4.88 3.73e+01 1js3A 486 -15.26 -4.88 3.73e+01 1tz9A 367 -14.57 -4.88 3.75e+01 1r1dA 247 -14.76 -4.87 3.77e+01 1k28D 391 -13.50 -4.86 3.80e+01 1l3kA 196 -14.41 -4.84 3.84e+01 1uu1A 335 -13.88 -4.84 3.85e+01 1ur3M 319 -14.69 -4.84 3.86e+01 1nlnA 204 -14.79 -4.83 3.86e+01 1lzlA 323 -15.99 -4.82 3.90e+01 1pyaB 228 -14.90 -4.81 3.94e+01 1cb0A 283 -14.10 -4.81 3.95e+01 1uroA 367 -14.77 -4.80 3.97e+01 1r3sA 367 -14.77 -4.79 4.00e+01