% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % strfoo.1.YDR019C.t2k-100-30-str Host: cc34 Mon Nov 11 22:19:44 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR0/YDR019C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YDR019C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDR019C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 401 nodes, 281.86 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.1755) * Reverse)^tau(=0.7809))) % 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 1jdw 423 -44.01 -20.14 5.31e-02 1g7tA 594 -43.10 -16.28 3.25e-01 1j6wA 175 -40.17 -16.19 3.39e-01 1jw3A 140 -40.66 -15.57 4.57e-01 1g7sA 594 -42.04 -15.27 5.29e-01 1g7rA 594 -42.36 -15.20 5.48e-01 1j7lA 264 -41.63 -15.13 5.67e-01 1b6sA 355 -41.37 -15.08 5.82e-01 1eysH 259 -39.82 -14.97 6.12e-01 1rlw 126 -37.56 -14.07 9.56e-01 1ja1A 622 -38.52 -13.97 1.00e+00 1b6rA 355 -41.40 -13.92 1.03e+00 1efcA 393 -43.23 -13.86 1.06e+00 1a7tA 232 -38.67 -13.62 1.20e+00 1g0cA 364 -36.51 -13.36 1.36e+00 1dd6A 228 -38.04 -13.12 1.53e+00 1io1A 398 -39.08 -13.11 1.54e+00 1crzA 403 -39.72 -13.01 1.63e+00 1dbxA 158 -33.48 -12.89 1.72e+00 1b1cA 181 -34.43 -12.79 1.82e+00 1sek 378 -40.40 -12.76 1.84e+00 2hrvA 142 -38.20 -12.74 1.86e+00 1qhtA 775 -42.16 -12.73 1.87e+00 1f60A 458 -38.82 -12.73 1.87e+00 1innA 166 -36.86 -12.67 1.92e+00 1nmtA 392 -38.03 -12.64 1.95e+00 1jjtA 228 -36.41 -12.30 2.33e+00 1dkgD 383 -40.44 -12.29 2.35e+00 1b24A 188 -36.54 -12.23 2.42e+00 1g01A 364 -35.32 -12.11 2.57e+00 1bob 320 -38.90 -12.09 2.59e+00 1c5kA 439 -39.50 -11.96 2.77e+00 1jceA 344 -38.55 -11.92 2.82e+00 1g61A 228 -33.16 -11.68 3.20e+00 1d2eA 397 -39.57 -11.41 3.69e+00 1jnyA 435 -38.18 -11.40 3.70e+00 1ecxA 384 -37.13 -11.38 3.73e+00 1amoA 615 -35.63 -11.36 3.77e+00 1ky9A 448 -40.56 -11.33 3.84e+00 1jcfA 344 -38.29 -11.21 4.09e+00 1at0 145 -34.83 -11.14 4.25e+00 7timA 247 -32.61 -11.05 4.45e+00 1dbuA 158 -31.49 -10.99 4.60e+00 1efdN 266 -33.86 -10.96 4.66e+00 2hgsA 474 -36.49 -10.89 4.84e+00 1dapA 320 -35.48 -10.86 4.91e+00 2fx2 147 -34.15 -10.85 4.93e+00 1j9eA 147 -34.04 -10.76 5.16e+00 1fzaB 328 -33.79 -10.69 5.36e+00 2fcr 173 -32.51 -10.53 5.84e+00 1bu5A 147 -33.86 -10.52 5.86e+00 1j7iA 264 -36.45 -10.47 6.04e+00 1ewqA 765 -36.29 -10.47 6.05e+00 1l9fA 389 -35.78 -10.46 6.05e+00 2madH 373 -35.86 -10.38 6.32e+00 1ijaA 148 -32.77 -10.34 6.47e+00 3dapA 320 -35.04 -10.28 6.66e+00 1ky9B 448 -37.99 -10.28 6.68e+00 1dgsA 667 -38.14 -10.27 6.69e+00 1el5A 389 -35.80 -10.25 6.77e+00 7acn 754 -35.52 -10.22 6.87e+00 8acn 754 -35.55 -10.18 7.04e+00 1dleA 298 -36.91 -10.16 7.09e+00 1amj 754 -35.55 -10.16 7.12e+00 1f06A 320 -34.98 -10.13 7.22e+00 6acn 754 -35.57 -10.07 7.45e+00 1b93A 152 -31.10 -10.05 7.55e+00 1konA 249 -36.28 -10.00 7.73e+00 1jqgA 433 -33.91 -9.97 7.86e+00 1eg5A 384 -35.73 -9.94 7.99e+00 1qapA 296 -33.80 -9.90 8.16e+00 1eq9A 222 -33.11 -9.89 8.22e+00 2rmcA 182 -33.71 -9.88 8.26e+00 1j7nA 776 -37.79 -9.82 8.51e+00 1b93B 152 -31.11 -9.81 8.58e+00 1gs5A 258 -34.03 -9.78 8.70e+00 2scuA 288 -34.51 -9.77 8.74e+00 1ceqA 316 -34.89 -9.73 8.93e+00 2acy 98 -30.25 -9.71 9.03e+00 9gafA 295 -34.68 -9.68 9.19e+00 1h4wA 224 -32.71 -9.68 9.19e+00 1fxjA 331 -33.92 -9.67 9.27e+00 1i45A 248 -31.23 -9.66 9.31e+00 1hdmB 193 -33.56 -9.65 9.34e+00 1jk7A 323 -33.72 -9.61 9.56e+00 1j7nB 776 -37.18 -9.57 9.74e+00 1mgtA 174 -33.47 -9.55 9.87e+00 1f4pA 147 -33.20 -9.54 9.91e+00 1cnuA 137 -33.69 -9.52 1.00e+01 1c96A 753 -35.11 -9.51 1.01e+01 1jj2S 119 -31.52 -9.49 1.02e+01 1cz4A 185 -32.52 -9.46 1.03e+01 1d2iA 223 -33.91 -9.45 1.04e+01 1fwyA 331 -34.07 -9.38 1.08e+01 1hv9A 456 -34.41 -9.36 1.09e+01 1yuf 50 -26.28 -9.33 1.11e+01 1fniA 223 -32.30 -9.28 1.14e+01 1fp2A 352 -33.72 -9.28 1.14e+01 2acr 315 -31.96 -9.28 1.14e+01 1taq 832 -36.22 -9.26 1.15e+01 1ads 315 -32.00 -9.26 1.15e+01 1el3A 316 -32.01 -9.26 1.15e+01 1fuiA 591 -34.37 -9.22 1.18e+01 1b0pA 1231 -38.84 -9.15 1.23e+01 1hdiA 413 -33.48 -9.12 1.25e+01 6prcH 258 -35.36 -9.01 1.32e+01 1dxrH 258 -35.35 -9.00 1.33e+01 1psdA 409 -33.16 -8.99 1.34e+01 1tgoA 773 -42.65 -8.90 1.40e+01 1fpxA 352 -33.68 -8.83 1.46e+01 1b4aA 149 -33.38 -8.79 1.49e+01 1mctA 223 -32.14 -8.78 1.50e+01 1byrA 155 -31.72 -8.74 1.53e+01 1jl3A 139 -28.75 -8.74 1.54e+01 1ffkQ 119 -30.49 -8.73 1.54e+01 1f0cA 305 -35.32 -8.73 1.55e+01 1agdA 276 -35.10 -8.72 1.55e+01 1mdbA 539 -34.71 -8.70 1.56e+01 1fsz 372 -32.74 -8.67 1.59e+01 1b4bA 71 -31.46 -8.66 1.60e+01 1ckmA 330 -38.29 -8.51 1.74e+01 1js3A 486 -33.01 -8.51 1.74e+01 1h8lA 380 -31.72 -8.50 1.75e+01 1aye 401 -31.89 -8.48 1.77e+01 1b0jA 754 -33.76 -8.46 1.79e+01 1dfmA 223 -32.90 -8.45 1.80e+01 1qu6A 179 -30.20 -8.44 1.81e+01 1kr4A 125 -30.93 -8.42 1.83e+01 1xxaA 78 -32.25 -8.42 1.83e+01 1kekA 1231 -38.99 -8.31 1.94e+01 1hylA 230 -33.06 -8.30 1.96e+01 3ladA 476 -32.37 -8.28 1.97e+01 1gqeA 365 -35.77 -8.24 2.02e+01 1cjaA 342 -33.08 -8.23 2.03e+01 1fggA 261 -31.60 -8.23 2.03e+01 1e6yB 433 -34.23 -8.20 2.07e+01 3tgf 50 -25.70 -8.19 2.08e+01 1tux 301 -30.22 -8.18 2.08e+01 3minB 522 -33.38 -8.16 2.11e+01 1bjmA 216 -34.81 -8.15 2.12e+01 2minB 522 -33.35 -8.14 2.13e+01 1f7zA 233 -32.40 -8.14 2.13e+01 1fvuA 133 -28.85 -8.12 2.16e+01 1kijA 390 -36.04 -8.09 2.19e+01 1bg0 356 -35.27 -8.08 2.21e+01 1k0rA 366 -35.19 -8.08 2.21e+01 1cknA 330 -38.59 -8.07 2.22e+01 1itbB 315 -33.68 -8.06 2.23e+01 1e69B 322 -35.38 -8.06 2.24e+01 1jmoA 480 -34.05 -8.02 2.28e+01 1ppfE 218 -31.76 -8.00 2.31e+01 4tgf 50 -25.85 -8.00 2.32e+01 1devC 196 -32.23 -7.99 2.32e+01 1k8wA 327 -34.74 -7.97 2.35e+01 1kriA 186 -33.72 -7.96 2.36e+01 1kqrA 179 -33.18 -7.94 2.38e+01 1ep3A 311 -30.75 -7.92 2.41e+01 1jg1A 235 -31.61 -7.91 2.43e+01 1aisA 182 -32.08 -7.90 2.44e+01 1hd8A 363 -31.93 -7.83 2.54e+01 1bd3A 243 -29.83 -7.80 2.58e+01 1pysA 350 -31.96 -7.78 2.62e+01 1e3mA 800 -33.63 -7.76 2.65e+01 1qf6A 642 -34.52 -7.75 2.66e+01 1c0pA 363 -32.16 -7.74 2.67e+01 1avpA 204 -30.71 -7.73 2.68e+01 1cjxA 357 -33.95 -7.71 2.72e+01 1e0wA 313 -30.56 -7.70 2.74e+01 1tdj 514 -37.94 -7.68 2.76e+01 1azo 232 -28.91 -7.68 2.77e+01 1j4aA 333 -30.39 -7.68 2.77e+01 2tgf 50 -25.16 -7.62 2.86e+01 1g0uG 252 -32.59 -7.58 2.93e+01 1g79A 218 -35.93 -7.57 2.94e+01 1gokA 303 -29.95 -7.56 2.97e+01 1ej1A 190 -29.79 -7.56 2.97e+01 2napA 723 -35.27 -7.55 2.97e+01 1dnlA 199 -34.79 -7.53 3.01e+01 1cdwA 179 -32.05 -7.52 3.02e+01 1a0oD 134 -28.62 -7.51 3.04e+01 1f5jA 199 -32.61 -7.50 3.06e+01 2tbs 222 -31.36 -7.48 3.10e+01 3tgl 269 -29.68 -7.45 3.15e+01 2hlcA 230 -31.76 -7.44 3.17e+01 1fjmA 330 -31.54 -7.44 3.18e+01 1scuA 288 -32.81 -7.41 3.22e+01 1qmuA 380 -30.70 -7.41 3.23e+01 1whsB 153 -27.59 -7.39 3.27e+01 1a04A 215 -30.23 -7.38 3.28e+01 1hj8A 222 -31.19 -7.38 3.28e+01 1j98A 157 -30.63 -7.37 3.29e+01 1whtB 153 -27.57 -7.37 3.30e+01 1e4fT 419 -33.03 -7.37 3.30e+01 1ab9C 97 -28.17 -7.35 3.33e+01 1lbvA 252 -32.59 -7.32 3.40e+01 1j96A 323 -29.38 -7.30 3.44e+01 1as4A 341 -35.47 -7.28 3.46e+01 1ckv 141 -32.14 -7.26 3.51e+01 1kfiA 572 -37.03 -7.25 3.53e+01 1qftA 175 -33.10 -7.25 3.53e+01 1mkp 144 -28.65 -7.25 3.54e+01 1hrhA 136 -29.55 -7.23 3.58e+01 1bcsB 160 -27.61 -7.22 3.59e+01 1jmxA 494 -34.40 -7.21 3.60e+01 1aipE 405 -37.82 -7.20 3.63e+01 5gcnA 166 -29.49 -7.19 3.65e+01 1frb 315 -29.66 -7.19 3.66e+01 1hlrA 907 -36.09 -7.17 3.70e+01 1shfA 59 -24.98 -7.15 3.73e+01 1mli 96 -28.50 -7.15 3.73e+01 1eq6A 189 -31.93 -7.14 3.75e+01 1a63 130 -29.43 -7.14 3.76e+01 1b3nA 412 -30.11 -7.12 3.79e+01 1g6sA 427 -34.56 -7.11 3.82e+01 1iq4A 179 -31.59 -7.10 3.84e+01 1qstA 160 -30.32 -7.09 3.88e+01 1g4uS 383 -32.97 -7.08 3.88e+01 1bhgA 613 -33.54 -7.08 3.89e+01 1eucA 311 -31.77 -7.06 3.93e+01