% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 07/18/04_06:53:46 % (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.T0249.t04-100-30-dssp-ebghstl Host: coo Mon Jul 26 12:37:30 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0249 % --------------------------------------------------------------------- % 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 T0249.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0249.t04.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6648 sequences, 1569757 residues, 210 nodes, 41.08 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 (=10083) sequences: % N / (1 + exp(-(lambda(=2.8083) * Reverse)^tau(=0.6116))) % 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 1lvaA 258 -34.98 -21.43 4.82e-02 1smtA 122 -27.54 -17.67 1.88e-01 1lj9A 144 -27.07 -17.15 2.30e-01 1bjaA 95 -25.84 -16.55 2.89e-01 1hw5A 210 -27.34 -16.47 2.98e-01 1j5yA 187 -27.45 -16.30 3.18e-01 1r1tA 122 -25.64 -15.71 4.00e-01 1aisB 200 -26.81 -15.38 4.57e-01 1fp2A 352 -25.36 -15.00 5.31e-01 1o57A 291 -24.35 -14.67 6.08e-01 1in4A 334 -25.04 -14.25 7.21e-01 1in6A 334 -25.04 -14.10 7.65e-01 1jhfA 202 -24.04 -14.07 7.74e-01 1lnwA 147 -23.38 -13.34 1.05e+00 1oyiA 82 -23.62 -13.20 1.12e+00 1p2fA 220 -23.21 -12.84 1.30e+00 1mkmA 249 -23.74 -12.80 1.32e+00 1j75A 67 -24.08 -12.70 1.38e+00 1okrA 123 -23.62 -12.54 1.47e+00 1bia 321 -23.40 -12.48 1.52e+00 1q1hA 110 -22.03 -12.25 1.67e+00 1hw1A 239 -22.49 -12.06 1.82e+00 1opc 110 -20.59 -11.53 2.30e+00 1res 43 -19.55 -11.42 2.41e+00 1rypE 242 -20.54 -11.23 2.63e+00 1rwyA 109 -20.86 -11.21 2.64e+00 1khyA 148 -20.73 -10.92 3.01e+00 1l9vA 317 -20.66 -10.84 3.13e+00 1gvjA 146 -20.61 -10.77 3.23e+00 1cuk 203 -23.04 -10.76 3.24e+00 1s3jA 155 -24.02 -10.74 3.27e+00 1p4xA 250 -20.78 -10.59 3.51e+00 1on2A 142 -22.84 -10.51 3.65e+00 1fy7A 278 -22.99 -10.31 3.99e+00 1mjnA 179 -20.52 -9.94 4.75e+00 1xwl 580 -21.85 -9.84 4.99e+00 1j2rA 199 -18.69 -9.79 5.09e+00 1l3lA 234 -19.40 -9.75 5.19e+00 1je8A 82 -18.97 -9.74 5.22e+00 1np7A 489 -19.90 -9.70 5.31e+00 1byi 224 -18.49 -9.59 5.62e+00 1nxiA 132 -20.49 -9.48 5.90e+00 1kgsA 225 -20.06 -9.44 6.03e+00 1pu6A 218 -19.41 -9.39 6.18e+00 1i27A 73 -19.56 -9.37 6.23e+00 1ng6A 148 -20.81 -9.34 6.32e+00 1cbs 137 -19.37 -9.32 6.40e+00 1fi2A 201 -18.16 -9.21 6.75e+00 1qbjA 81 -19.95 -9.17 6.85e+00 1azsA 220 -19.75 -9.16 6.92e+00 1rypL 212 -19.19 -9.14 6.97e+00 8rucI 123 -19.06 -9.06 7.24e+00 1burS 123 -18.82 -9.01 7.43e+00 1no4A 97 -19.21 -9.00 7.45e+00 1pylA 97 -17.10 -8.89 7.87e+00 1pi1A 185 -19.81 -8.87 7.97e+00 1nk4A 580 -20.42 -8.84 8.08e+00 1c7gA 456 -18.84 -8.82 8.17e+00 1k47A 337 -20.81 -8.79 8.27e+00 1g71A 347 -18.55 -8.77 8.37e+00 1tlqA 189 -19.79 -8.76 8.39e+00 1keaA 221 -20.58 -8.75 8.43e+00 1l3sA 580 -20.41 -8.71 8.62e+00 1qc7A 101 -19.21 -8.65 8.87e+00 1ku3A 73 -18.24 -8.64 8.91e+00 1te5A 257 -19.99 -8.62 8.98e+00 1j3mA 129 -18.12 -8.45 9.82e+00 1a5t 334 -21.72 -8.42 9.93e+00 1nnvA 110 -17.84 -8.42 9.94e+00 1hr6B 443 -19.92 -8.29 1.06e+01 1ub9A 100 -19.39 -8.28 1.07e+01 1mw9X 592 -19.46 -8.22 1.10e+01 1fnnA 389 -21.67 -8.22 1.10e+01 1fx2A 235 -19.82 -8.16 1.14e+01 1v33A 366 -19.44 -8.06 1.19e+01 1lfaA 187 -19.10 -8.05 1.20e+01 1nqkA 381 -17.88 -8.03 1.21e+01 4kbpA 432 -16.85 -8.03 1.21e+01 1dlwA 116 -17.87 -8.00 1.23e+01 1ctt 294 -16.76 -7.98 1.24e+01 1or7A 194 -18.97 -7.98 1.25e+01 1k7jA 206 -19.85 -7.96 1.26e+01 1vjzA 341 -19.08 -7.88 1.31e+01 1a8h 500 -18.22 -7.86 1.32e+01 2dtr 226 -17.01 -7.85 1.33e+01 1ufmA 84 -17.44 -7.82 1.35e+01 1f1zA 273 -17.89 -7.79 1.37e+01 1nigA 152 -17.91 -7.78 1.38e+01 1gxqA 106 -17.39 -7.77 1.39e+01 1mf7A 194 -18.48 -7.76 1.39e+01 1o08A 221 -17.44 -7.76 1.39e+01 1ezvA 430 -18.90 -7.75 1.40e+01 1kk8B 139 -18.23 -7.73 1.42e+01 1kb9A 431 -18.90 -7.72 1.42e+01 1regX 122 -16.72 -7.67 1.46e+01 1teaA 299 -18.46 -7.64 1.48e+01 1rypI 222 -17.44 -7.56 1.54e+01 1rypG 244 -17.96 -7.55 1.55e+01 1fpzA 212 -18.04 -7.55 1.55e+01 1v38A 78 -16.39 -7.54 1.56e+01 1abv 134 -18.63 -7.53 1.57e+01 1gy8A 397 -17.83 -7.49 1.61e+01 1kbpA 432 -16.24 -7.48 1.61e+01 1jx4A 352 -18.97 -7.48 1.61e+01 1rypC 244 -20.42 -7.46 1.63e+01 1r1uA 106 -18.75 -7.46 1.63e+01 1csn 298 -17.87 -7.41 1.67e+01 5eau 548 -21.00 -7.39 1.69e+01 1ckiA 317 -17.44 -7.29 1.78e+01 1p4wA 99 -17.68 -7.27 1.80e+01 1qo7A 394 -18.18 -7.25 1.82e+01 1iw7C 1119 -16.96 -7.25 1.82e+01 1rec 201 -17.65 -7.24 1.83e+01 1n3yA 198 -17.74 -7.23 1.84e+01 1s7oA 113 -17.94 -7.19 1.87e+01 1bjt 793 -17.58 -7.17 1.90e+01 1gnxA 479 -17.06 -7.16 1.91e+01 1hg4A 279 -18.61 -7.14 1.93e+01 1octC 156 -18.22 -7.12 1.95e+01 1mi3A 322 -16.79 -7.12 1.95e+01 4crxA 322 -17.11 -7.12 1.96e+01 1q5qA 259 -17.93 -7.07 2.01e+01 1r1mA 164 -17.23 -7.03 2.05e+01 1pvmA 184 -15.68 -7.01 2.07e+01 1b79A 119 -17.65 -7.00 2.08e+01 1a04A 215 -17.54 -6.99 2.09e+01 1k8uA 90 -18.08 -6.98 2.10e+01 1tml 286 -16.48 -6.98 2.10e+01 1ucrA 78 -17.91 -6.97 2.12e+01 1r6rA 100 -17.69 -6.91 2.18e+01 1ido 192 -18.07 -6.88 2.22e+01 1b24A 188 -19.32 -6.88 2.22e+01 1pxvA 183 -15.63 -6.88 2.23e+01 1f44A 324 -16.85 -6.82 2.29e+01 1rypH 205 -16.67 -6.81 2.31e+01 1fjgD 209 -18.07 -6.79 2.34e+01 1nb8A 353 -16.79 -6.78 2.34e+01 1frb 315 -16.02 -6.70 2.45e+01 1apyB 141 -15.16 -6.70 2.45e+01 1tiqA 180 -16.53 -6.70 2.45e+01 1fobA 334 -16.43 -6.67 2.49e+01 1foeA 377 -19.87 -6.65 2.52e+01 1omrA 201 -16.91 -6.65 2.52e+01 1rqtA 37 -16.09 -6.62 2.56e+01 1qlpA 394 -19.89 -6.57 2.64e+01 1edg 380 -17.65 -6.56 2.65e+01 1pueE 89 -16.05 -6.54 2.68e+01 1phnA 162 -16.62 -6.53 2.68e+01 1vkeA 133 -16.86 -6.53 2.69e+01 1guxA 218 -17.41 -6.51 2.72e+01 1hbnB 442 -17.04 -6.49 2.75e+01 1mroB 442 -16.96 -6.45 2.80e+01 6paxA 133 -15.90 -6.45 2.82e+01 1rypD 241 -17.22 -6.44 2.82e+01 1p9bA 442 -16.94 -6.43 2.84e+01 1j8uA 325 -16.56 -6.43 2.85e+01 1d0vA 356 -17.95 -6.42 2.86e+01 4pah 308 -16.60 -6.41 2.88e+01 5pal 109 -16.42 -6.39 2.91e+01 1l5oA 356 -17.90 -6.38 2.93e+01 1vin 268 -17.10 -6.37 2.93e+01 1nthA 458 -15.99 -6.37 2.94e+01 1iqrA 420 -16.21 -6.35 2.97e+01 1i7dA 659 -17.19 -6.35 2.97e+01 1aj8A 371 -18.40 -6.34 2.98e+01 1owlA 484 -16.62 -6.34 2.99e+01 1qnf 484 -16.60 -6.33 3.01e+01 1r0vA 305 -19.40 -6.31 3.03e+01 1scfA 273 -18.06 -6.29 3.07e+01 1bed 181 -16.74 -6.29 3.08e+01 1jzgA 128 -14.04 -6.26 3.13e+01 1k78A 149 -15.86 -6.25 3.14e+01 3rubS 123 -15.92 -6.25 3.15e+01 1ii7A 333 -16.32 -6.25 3.15e+01 1rcwA 231 -16.98 -6.25 3.15e+01 1om0A 274 -16.93 -6.23 3.18e+01 1nfp 228 -16.58 -6.18 3.27e+01 1q7bA 244 -15.85 -6.17 3.28e+01 1oeyJ 107 -15.58 -6.16 3.30e+01 1hrhA 136 -18.91 -6.15 3.32e+01 1obwA 175 -15.48 -6.13 3.37e+01 1gntA 553 -17.18 -6.12 3.38e+01 1cpcA 162 -16.29 -6.12 3.39e+01 2ahjB 212 -15.32 -6.11 3.40e+01 1jclA 260 -15.50 -6.09 3.45e+01 1p1xA 260 -15.52 -6.07 3.48e+01 1r5qA 102 -19.28 -6.06 3.50e+01 1gk8I 140 -16.08 -6.02 3.59e+01 1i40A 175 -15.45 -6.01 3.60e+01 1uheA 97 -14.25 -5.98 3.67e+01 1rypA 243 -15.61 -5.97 3.68e+01 1a9xA 1058 -16.68 -5.95 3.73e+01 1e3oC 160 -17.71 -5.94 3.76e+01 1p0zA 131 -15.90 -5.93 3.76e+01 1pyfA 312 -16.87 -5.93 3.78e+01 1k1vA 41 -14.78 -5.92 3.79e+01 1s9pA 227 -17.15 -5.91 3.82e+01 1g0oA 283 -15.75 -5.87 3.90e+01 1f2aA 215 -15.37 -5.86 3.91e+01 1heiA 451 -15.56 -5.86 3.92e+01 1it2A 146 -16.84 -5.86 3.93e+01 1bby 69 -18.23 -5.83 3.99e+01