% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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. % --------------------------------------------------------------------- % str2foo.1.YGR027W-A.t2k-100-30-str2 Host: farm01 Mon Nov 29 22:46:03 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR027W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % 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 YGR027W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR027W-A.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 441 nodes, 494.50 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.6019) * Reverse)^tau(=0.7600))) % 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 1o4sA 389 -24.23 -13.34 3.79e-01 1fftC 204 -25.61 -13.28 3.94e-01 1qkkA 155 -22.41 -13.17 4.19e-01 1l5zA 155 -22.49 -13.14 4.27e-01 1peqA 714 -23.14 -12.13 7.74e-01 1s9pA 227 -23.37 -11.21 1.35e+00 1lwdA 413 -22.01 -11.16 1.39e+00 1h3fA 432 -20.75 -10.89 1.64e+00 1eemA 241 -22.45 -10.69 1.85e+00 1i37A 260 -23.73 -10.65 1.90e+00 1hw1A 239 -22.57 -10.62 1.94e+00 1mroA 548 -21.59 -10.55 2.03e+00 1hbnA 549 -21.52 -10.47 2.13e+00 1omrA 201 -22.48 -10.43 2.18e+00 1rtwA 220 -26.51 -10.30 2.37e+00 1paqA 189 -26.01 -10.25 2.43e+00 1iq3A 110 -22.12 -10.24 2.45e+00 1v74B 87 -21.04 -10.23 2.46e+00 1n45A 233 -22.85 -10.23 2.46e+00 1ko9A 345 -21.66 -10.10 2.67e+00 1f7cA 231 -22.30 -9.94 2.96e+00 1m1cA 680 -22.65 -9.85 3.12e+00 1r85A 379 -22.65 -9.80 3.22e+00 1iow 306 -19.67 -9.59 3.69e+00 1hizA 379 -22.30 -9.55 3.77e+00 1k8eA 345 -21.11 -9.49 3.91e+00 1o17A 345 -21.11 -9.49 3.91e+00 1hlvA 131 -20.80 -9.44 4.04e+00 1fonA 240 -22.84 -9.44 4.05e+00 1lwyA 324 -20.62 -9.38 4.20e+00 1lnrI 134 -21.92 -9.38 4.20e+00 1w0hA 204 -20.37 -9.21 4.68e+00 1ebmA 317 -20.34 -9.11 5.00e+00 1t7rA 269 -21.93 -8.88 5.78e+00 1ltm 320 -19.96 -8.86 5.87e+00 1eh2 106 -24.44 -8.83 5.97e+00 1g8iA 190 -24.94 -8.80 6.12e+00 1pbp 321 -18.61 -8.73 6.37e+00 1qusA 322 -19.78 -8.70 6.52e+00 1h67A 108 -20.29 -8.60 6.92e+00 2dln 306 -18.76 -8.59 6.97e+00 7catA 506 -24.92 -8.59 7.00e+00 1uddA 226 -24.50 -8.54 7.21e+00 1rec 201 -20.54 -8.41 7.87e+00 1oshA 232 -21.57 -8.36 8.11e+00 1mhyG 169 -21.00 -8.34 8.23e+00 1m3qA 317 -20.10 -8.30 8.43e+00 1qgjA 300 -19.71 -8.30 8.45e+00 1e2xA 243 -20.65 -8.28 8.56e+00 1odoA 408 -21.06 -8.24 8.76e+00 1mhyB 395 -26.71 -8.17 9.18e+00 1klt 226 -20.39 -8.16 9.27e+00 1fqvD 149 -19.91 -8.09 9.69e+00 1qq8A 214 -20.02 -8.08 9.74e+00 1izcA 339 -18.88 -8.05 9.92e+00 1ka2A 499 -23.94 -8.01 1.02e+01 1w7bA 339 -22.73 -7.99 1.03e+01 1n83A 270 -24.28 -7.94 1.07e+01 1kf6A 602 -19.73 -7.92 1.08e+01 1wmuA 141 -21.36 -7.91 1.09e+01 1fqvJ 149 -19.61 -7.91 1.09e+01 1ljrA 244 -18.48 -7.90 1.09e+01 1gkgA 136 -22.12 -7.90 1.10e+01 1pieA 419 -19.33 -7.87 1.12e+01 1tqgA 105 -22.40 -7.83 1.15e+01 1bed 181 -19.95 -7.83 1.15e+01 1or7A 194 -20.07 -7.82 1.16e+01 1a05A 358 -18.26 -7.80 1.17e+01 1spgA 144 -23.26 -7.77 1.20e+01 1ihoA 283 -20.11 -7.76 1.21e+01 1klo 162 -22.66 -7.71 1.25e+01 1tu3F 79 -19.40 -7.69 1.26e+01 1iqqA 200 -19.20 -7.64 1.30e+01 1syyA 346 -25.78 -7.64 1.31e+01 1rfzA 168 -21.08 -7.62 1.32e+01 1dseA 292 -19.95 -7.59 1.35e+01 1uxtA 501 -18.88 -7.53 1.41e+01 1kqfA 1015 -25.75 -7.52 1.41e+01 1w53A 84 -19.00 -7.45 1.48e+01 2tct 207 -20.54 -7.43 1.50e+01 1cm7A 363 -18.50 -7.43 1.50e+01 5pal 109 -18.25 -7.40 1.53e+01 1h99A 224 -22.97 -7.38 1.55e+01 1ryc 294 -19.94 -7.32 1.61e+01 1aisA 182 -16.99 -7.31 1.62e+01 1r5qA 102 -23.13 -7.31 1.63e+01 1b4aA 149 -18.37 -7.31 1.63e+01 1j4nA 271 -20.99 -7.29 1.65e+01 2cyp 294 -19.94 -7.28 1.66e+01 1go3F 107 -19.63 -7.27 1.67e+01 1qcrA 446 -19.31 -7.26 1.68e+01 1ew6A 137 -21.10 -7.26 1.69e+01 1ewaA 137 -21.10 -7.26 1.69e+01 1cqxA 403 -20.03 -7.24 1.70e+01 1o0wA 252 -22.47 -7.21 1.74e+01 1pv6A 417 -24.93 -7.20 1.75e+01 1ds4A 292 -19.95 -7.20 1.75e+01 1mlwA 301 -19.88 -7.19 1.77e+01 1fs1B 141 -19.47 -7.17 1.79e+01 1myt 146 -20.85 -7.15 1.82e+01 3icb 75 -19.23 -7.15 1.82e+01 1f5sA 211 -17.94 -7.13 1.83e+01 1j97A 211 -17.94 -7.13 1.83e+01 1sr7A 259 -19.35 -7.13 1.84e+01 1e3aB 560 -20.80 -7.13 1.84e+01 1s2xA 206 -22.32 -7.12 1.84e+01 1jk0A 419 -22.08 -7.10 1.87e+01 1q7eA 428 -18.48 -7.08 1.90e+01 1v7wA 807 -18.25 -7.04 1.96e+01 1pu6A 218 -18.59 -7.03 1.97e+01 1ekeA 230 -20.24 -7.03 1.97e+01 1l7mA 211 -17.82 -7.03 1.97e+01 1dgfA 497 -23.38 -7.02 1.98e+01 1octC 156 -20.77 -7.02 1.98e+01 1j30A 144 -19.54 -7.01 2.00e+01 1mkrA 294 -19.14 -7.01 2.00e+01 1ig5A 75 -17.77 -7.00 2.00e+01 1a28A 256 -19.38 -6.99 2.02e+01 1ng1 294 -22.77 -6.98 2.03e+01 1qmhA 347 -17.68 -6.98 2.03e+01 1qqfA 277 -19.55 -6.97 2.04e+01 1dghB 498 -23.38 -6.96 2.07e+01 1ew6B 137 -21.04 -6.94 2.10e+01 1twfF 155 -20.39 -6.93 2.11e+01 1sqnA 261 -19.41 -6.92 2.11e+01 1dmwA 307 -18.63 -6.91 2.13e+01 1guxB 152 -18.11 -6.90 2.16e+01 1qltA 560 -19.20 -6.89 2.16e+01 1i50F 155 -20.37 -6.89 2.17e+01 1ccg 291 -19.58 -6.87 2.20e+01 1ixh 321 -16.93 -6.86 2.21e+01 1fzaB 328 -22.23 -6.86 2.21e+01 1f4qA 165 -21.64 -6.84 2.24e+01 1iuqA 367 -18.82 -6.82 2.27e+01 1gkfB 557 -20.42 -6.82 2.28e+01 1vmaA 306 -20.67 -6.81 2.28e+01 1jpnA 296 -22.49 -6.80 2.29e+01 1np8A 159 -27.27 -6.79 2.31e+01 1ls1A 295 -22.48 -6.79 2.31e+01 1alvA 173 -25.12 -6.79 2.32e+01 1iq0A 592 -19.03 -6.76 2.36e+01 1e8gA 560 -19.02 -6.76 2.36e+01 1ht9A 76 -19.68 -6.74 2.39e+01 1a4pA 96 -17.82 -6.73 2.41e+01 1gk9B 557 -20.34 -6.72 2.42e+01 1xsm 390 -24.01 -6.72 2.42e+01 1pt7A 437 -18.05 -6.71 2.44e+01 1csn 298 -18.68 -6.69 2.49e+01 1pvaA 110 -17.87 -6.67 2.52e+01 1ajqB 557 -20.41 -6.67 2.52e+01 4pah 308 -18.63 -6.65 2.55e+01 1e96B 203 -18.61 -6.64 2.57e+01 1om2A 95 -18.21 -6.63 2.58e+01 1h5uA 842 -20.67 -6.63 2.58e+01 1hv8A 367 -17.62 -6.63 2.59e+01 1k30A 368 -18.46 -6.63 2.59e+01 1ax4A 467 -17.76 -6.60 2.63e+01 1ash 150 -21.78 -6.60 2.63e+01 1jdrA 294 -19.15 -6.60 2.63e+01 1gm9B 557 -20.31 -6.60 2.64e+01 1jgsA 138 -18.49 -6.58 2.68e+01 1kfuS 184 -20.90 -6.57 2.69e+01 1e8aA 91 -19.01 -6.57 2.70e+01 1hh8A 213 -18.62 -6.56 2.71e+01 1mijA 152 -20.51 -6.55 2.73e+01 1pah 308 -18.60 -6.54 2.75e+01 1gulA 222 -21.82 -6.53 2.76e+01 1huw 166 -18.95 -6.53 2.77e+01 1j8uA 325 -19.09 -6.52 2.78e+01 1be3A 446 -18.67 -6.52 2.80e+01 1v3wA 173 -15.32 -6.50 2.84e+01 1am7A 158 -17.55 -6.49 2.85e+01 1w1kA 560 -18.87 -6.48 2.87e+01 1u08A 386 -16.41 -6.47 2.89e+01 1srvA 145 -16.17 -6.47 2.89e+01 1w68A 390 -22.43 -6.46 2.90e+01 1dgsA 667 -19.25 -6.43 2.97e+01 1h6pA 203 -20.81 -6.41 3.01e+01 1lea 84 -16.93 -6.39 3.05e+01 1mxmA 254 -21.01 -6.37 3.10e+01 1bg4 302 -17.58 -6.34 3.15e+01 1jigA 146 -19.48 -6.34 3.15e+01 1b31A 302 -17.58 -6.34 3.16e+01 1ouvA 273 -16.97 -6.32 3.21e+01 1vaoA 560 -18.28 -6.31 3.23e+01 1alq 266 -17.32 -6.26 3.34e+01 1pjpA 226 -18.98 -6.26 3.35e+01 1pioA 257 -17.67 -6.24 3.39e+01 1g5yA 238 -17.43 -6.22 3.43e+01 1e3oC 160 -20.60 -6.20 3.48e+01 1s3jA 155 -16.38 -6.18 3.52e+01 1j8mF 297 -19.41 -6.17 3.55e+01 3blm 257 -17.21 -6.17 3.55e+01 1cmbA 104 -17.19 -6.15 3.61e+01 1k04A 162 -21.12 -6.14 3.62e+01 1ib2A 349 -17.07 -6.14 3.64e+01 1is2A 661 -18.62 -6.14 3.64e+01 1gm7B 557 -20.00 -6.13 3.65e+01 1ppjA 446 -18.97 -6.13 3.65e+01 1pmy 123 -16.27 -6.12 3.67e+01 2abk 211 -18.14 -6.10 3.73e+01 1pp5A 21 -15.64 -6.10 3.74e+01 1yrnB 83 -17.02 -6.10 3.74e+01 1ois 223 -19.63 -6.10 3.74e+01 1kgsA 225 -21.78 -6.10 3.75e+01 1nstA 325 -17.47 -6.10 3.75e+01 1wdcC 156 -17.22 -6.09 3.75e+01 1f5qB 252 -20.82 -6.09 3.77e+01 3erdA 261 -21.06 -6.08 3.78e+01 1pbwA 216 -19.24 -6.08 3.78e+01 1j8yF 297 -19.31 -6.07 3.82e+01 1tlqA 189 -18.42 -6.07 3.82e+01 1l0lA 446 -18.84 -6.07 3.82e+01 3ertA 261 -20.47 -6.06 3.85e+01 1cmaA 104 -17.15 -6.06 3.85e+01 1f3aA 222 -20.06 -6.04 3.89e+01 1i5nA 146 -20.61 -6.03 3.92e+01 1nxcA 478 -18.51 -6.02 3.96e+01 1v4xA 144 -18.99 -6.02 3.96e+01 2ng1 293 -21.82 -6.02 3.96e+01 1oe8A 211 -21.44 -6.02 3.96e+01 1vi0A 206 -23.50 -6.01 3.97e+01 2occE 109 -18.77 -6.01 3.97e+01