% 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.YDR018C.t2k-100-30-str Host: cc60 Mon Nov 11 22:17:19 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR0/YDR018C % --------------------------------------------------------------------- % 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 YDR018C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDR018C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 397 nodes, 277.52 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(=1.6894) * Reverse)^tau(=0.7926))) % 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 1k30A 368 -43.40 -16.04 8.45e-03 1fvaA 217 -38.63 -14.23 2.92e-02 1fvgA 199 -37.42 -13.13 6.28e-02 1e1dA 553 -37.21 -11.89 1.52e-01 1b3qA 379 -35.83 -10.96 2.98e-01 1i58A 189 -32.42 -10.64 3.78e-01 1gntA 553 -36.70 -10.03 5.90e-01 1e2uA 553 -36.70 -10.02 5.95e-01 1f89A 291 -32.32 -9.90 6.51e-01 1gnlA 544 -34.55 -9.78 7.13e-01 3bifA 468 -34.02 -9.73 7.42e-01 1a3aC 148 -30.47 -9.50 8.84e-01 1bjwA 382 -33.25 -9.41 9.40e-01 1gumA 222 -31.98 -9.11 1.18e+00 1vhh 162 -30.19 -8.99 1.30e+00 1cleA 534 -33.93 -8.91 1.37e+00 1a3aA 148 -30.39 -8.89 1.39e+00 1pioA 257 -30.64 -8.89 1.40e+00 1hizA 379 -31.99 -8.65 1.68e+00 1ghpA 258 -30.63 -8.63 1.70e+00 1auiA 521 -34.78 -8.63 1.70e+00 1f0xA 571 -33.39 -8.58 1.77e+00 1iw7C 1119 -35.08 -8.49 1.90e+00 1bif 469 -33.25 -8.47 1.93e+00 1gqeA 365 -34.96 -8.42 2.01e+00 1e6yC 247 -29.54 -8.36 2.10e+00 3blm 257 -29.85 -8.36 2.10e+00 1c3wA 222 -40.10 -8.19 2.40e+00 1kijA 390 -33.11 -8.15 2.47e+00 1dbwA 126 -28.24 -8.10 2.57e+00 1d5wC 126 -29.07 -8.02 2.73e+00 1tdj 514 -32.78 -8.01 2.76e+00 1cg2A 393 -32.35 -7.98 2.83e+00 3minB 522 -31.91 -7.91 2.98e+00 1lc0A 294 -31.71 -7.80 3.24e+00 1jyaA 130 -29.05 -7.80 3.26e+00 1dckA 126 -28.19 -7.74 3.39e+00 1f3mC 297 -30.58 -7.66 3.63e+00 1qkkA 155 -29.48 -7.61 3.76e+00 1ewkA 490 -32.99 -7.58 3.87e+00 1moq 368 -34.10 -7.49 4.16e+00 2minB 522 -31.39 -7.41 4.43e+00 1b3rA 431 -30.09 -7.38 4.52e+00 1a6q 382 -31.14 -7.37 4.56e+00 1gulA 222 -30.60 -7.28 4.89e+00 1k8eA 345 -30.36 -7.21 5.17e+00 1dpb 243 -29.38 -7.19 5.26e+00 1l2tA 235 -32.50 -7.14 5.47e+00 1egaA 301 -32.36 -7.13 5.52e+00 1esmA 316 -31.18 -7.11 5.60e+00 1gcuA 295 -31.00 -7.10 5.64e+00 1iso 416 -32.52 -7.03 5.98e+00 1d02A 202 -28.18 -7.02 6.03e+00 7icd 416 -32.74 -6.99 6.19e+00 1l5zA 155 -29.18 -6.98 6.22e+00 1svy 114 -27.35 -6.97 6.27e+00 1tlfA 301 -28.70 -6.96 6.33e+00 1dfaA 454 -30.70 -6.93 6.46e+00 1f7tA 122 -28.46 -6.91 6.58e+00 1nfp 228 -28.73 -6.86 6.86e+00 1i0lA 221 -28.33 -6.84 6.98e+00 1f75A 249 -28.79 -6.82 7.11e+00 1jztA 246 -28.97 -6.79 7.27e+00 2aop 497 -31.47 -6.77 7.36e+00 7timA 247 -28.71 -6.77 7.37e+00 1k6zA 141 -27.77 -6.73 7.63e+00 1cliA 345 -29.96 -6.64 8.16e+00 1jyeA 349 -28.75 -6.64 8.18e+00 1mdbA 539 -30.71 -6.64 8.20e+00 1aop 497 -31.16 -6.61 8.42e+00 1pty 321 -30.50 -6.59 8.52e+00 1al3 324 -29.00 -6.57 8.68e+00 1f7lA 121 -28.48 -6.53 8.96e+00 1l0bA 229 -27.34 -6.52 9.02e+00 1qlmA 316 -29.61 -6.50 9.16e+00 1crzA 403 -28.50 -6.48 9.31e+00 2hnp 321 -30.32 -6.47 9.38e+00 1a1s 314 -29.04 -6.41 9.91e+00 1e2fA 215 -27.76 -6.38 1.01e+01 1f2eA 201 -28.19 -6.37 1.02e+01 1a4iA 301 -29.15 -6.35 1.04e+01 1h70A 255 -28.18 -6.34 1.05e+01 1jeoA 180 -31.86 -6.31 1.07e+01 1eeoA 321 -30.15 -6.31 1.07e+01 1f1eA 154 -28.91 -6.30 1.08e+01 1azo 232 -28.98 -6.28 1.10e+01 2at9 247 -33.31 -6.27 1.10e+01 1a8y 367 -32.25 -6.27 1.11e+01 1i7dA 659 -31.58 -6.27 1.11e+01 1eaf 243 -28.57 -6.26 1.11e+01 1qtnA 164 -27.51 -6.22 1.16e+01 1h72C 296 -30.65 -6.21 1.17e+01 1d3uB 201 -28.34 -6.18 1.19e+01 1fnoA 417 -32.56 -6.17 1.20e+01 1dceB 331 -28.73 -6.17 1.20e+01 1b67A 68 -25.68 -6.17 1.20e+01 1diaA 306 -29.20 -6.16 1.21e+01 1kgbA 231 -37.51 -6.15 1.22e+01 1pd21 199 -29.49 -6.15 1.22e+01 1d8wA 426 -29.41 -6.14 1.24e+01 1svr 114 -27.01 -6.14 1.24e+01 1e9cA 215 -27.80 -6.13 1.24e+01 1e9eA 215 -27.79 -6.13 1.24e+01 1ptvA 321 -30.10 -6.12 1.25e+01 1bmtA 246 -28.16 -6.12 1.25e+01 1cfzA 162 -27.53 -6.11 1.26e+01 1i45A 248 -27.89 -6.11 1.26e+01 1mmoD 512 -34.81 -6.10 1.27e+01 1m0kA 262 -37.48 -6.09 1.28e+01 1e2gA 215 -27.73 -6.09 1.28e+01 1eudB 396 -29.54 -6.09 1.29e+01 1k7yA 577 -30.60 -6.07 1.30e+01 1fzrA 138 -26.53 -6.07 1.31e+01 1a53 247 -26.91 -6.06 1.32e+01 1igs 248 -26.91 -6.06 1.32e+01 1jvwA 167 -27.54 -6.03 1.34e+01 1biqA 375 -35.11 -5.99 1.40e+01 1jjyA 636 -31.94 -5.98 1.40e+01 1f9aA 168 -27.45 -5.98 1.41e+01 1g7fA 298 -29.42 -5.95 1.44e+01 1m0dA 138 -25.79 -5.91 1.49e+01 1ltqA 301 -29.09 -5.90 1.50e+01 1fthA 122 -25.71 -5.88 1.52e+01 1lu9A 287 -28.39 -5.86 1.55e+01 1mxa 383 -28.29 -5.85 1.56e+01 1e5xA 486 -30.20 -5.83 1.59e+01 1oxa 403 -34.54 -5.82 1.60e+01 2ifeA 100 -25.14 -5.81 1.62e+01 1ly1A 181 -28.06 -5.80 1.63e+01 1i2sA 282 -27.85 -5.79 1.65e+01 1de5A 426 -29.24 -5.78 1.66e+01 1vxrA 537 -30.35 -5.78 1.66e+01 1xyzA 347 -28.08 -5.77 1.67e+01 2tmkA 216 -30.11 -5.76 1.68e+01 1geqA 248 -27.54 -5.76 1.69e+01 1d0nA 729 -31.93 -5.76 1.69e+01 1ea5A 537 -30.09 -5.69 1.79e+01 1eucB 396 -28.98 -5.68 1.80e+01 1aisB 200 -27.79 -5.68 1.81e+01 1js1X 324 -30.03 -5.68 1.81e+01 1c9kA 180 -27.62 -5.67 1.82e+01 1a7aA 432 -28.26 -5.65 1.85e+01 1bvzA 585 -30.35 -5.64 1.87e+01 1kmvA 186 -30.03 -5.64 1.87e+01 1c5kA 439 -28.10 -5.63 1.88e+01 1sesA 421 -30.57 -5.63 1.88e+01 1fts 295 -29.94 -5.63 1.89e+01 1ep3B 262 -28.05 -5.61 1.92e+01 1dar 691 -31.73 -5.59 1.95e+01 1juk 248 -26.43 -5.58 1.97e+01 1hp5A 512 -29.27 -5.57 1.97e+01 1hp4A 512 -29.23 -5.56 1.99e+01 1jipA 403 -33.50 -5.56 2.00e+01 1e66A 543 -30.20 -5.55 2.02e+01 1jakA 512 -29.22 -5.54 2.03e+01 1xikA 375 -34.36 -5.54 2.03e+01 1b9lA 120 -24.83 -5.52 2.07e+01 1jmeA 455 -32.32 -5.50 2.10e+01 1dmuA 299 -28.59 -5.48 2.13e+01 1bj7 156 -29.82 -5.48 2.14e+01 1svq 114 -26.48 -5.47 2.14e+01 1gox 370 -28.70 -5.47 2.15e+01 1crl 534 -31.14 -5.46 2.16e+01 1j5pA 253 -27.80 -5.45 2.18e+01 1a79A 171 -26.59 -5.45 2.19e+01 1eupA 403 -34.17 -5.43 2.22e+01 1bi0 226 -27.94 -5.42 2.24e+01 1pcfA 66 -24.34 -5.42 2.25e+01 1adeA 431 -28.66 -5.40 2.29e+01 1asx 159 -25.65 -5.38 2.31e+01 1php 394 -29.31 -5.35 2.38e+01 2dtr 226 -27.49 -5.33 2.42e+01 1mvoA 136 -25.93 -5.33 2.42e+01 1hta 69 -24.99 -5.33 2.43e+01 1jpnA 296 -27.91 -5.32 2.44e+01 1auoA 218 -26.10 -5.31 2.45e+01 1hyeA 313 -29.10 -5.31 2.47e+01 1psdA 409 -27.85 -5.30 2.49e+01 1amuA 563 -29.79 -5.30 2.49e+01 1jeyB 565 -29.69 -5.29 2.49e+01 1aurA 218 -26.05 -5.29 2.50e+01 1jobA 162 -27.22 -5.29 2.51e+01 1yacA 208 -30.01 -5.28 2.51e+01 1cch 82 -23.63 -5.26 2.57e+01 1i19A 561 -30.21 -5.26 2.58e+01 1rpjA 288 -27.82 -5.25 2.58e+01 1qh8B 519 -32.72 -5.24 2.61e+01 1dt9A 437 -30.15 -5.23 2.63e+01 1bjz 207 -28.53 -5.23 2.64e+01 1jqcA 375 -33.95 -5.20 2.69e+01 1qd9A 124 -25.79 -5.20 2.71e+01 1de6A 426 -28.50 -5.15 2.81e+01 1nhs 447 -28.82 -5.14 2.84e+01 1b35A 260 -25.71 -5.13 2.87e+01 1e3jA 352 -27.27 -5.13 2.87e+01 1fwkA 296 -29.15 -5.12 2.89e+01 1egzA 291 -26.88 -5.12 2.90e+01 1ae7 119 -26.39 -5.12 2.90e+01 1qf5A 431 -28.04 -5.09 2.97e+01 1k75A 434 -28.08 -5.09 2.98e+01 1e3mA 800 -31.89 -5.07 3.01e+01 1thg 544 -30.73 -5.07 3.02e+01 1qguB 519 -32.54 -5.07 3.03e+01 1bfmA 69 -25.18 -5.06 3.06e+01 1eiyB 785 -29.85 -5.04 3.09e+01 1a4iB 301 -27.62 -5.04 3.09e+01 1h3nA 878 -33.02 -5.03 3.11e+01 1cf2O 337 -28.40 -5.03 3.12e+01 8dfr 189 -26.45 -5.02 3.15e+01 1m7bA 184 -26.66 -5.01 3.18e+01 1qidA 537 -29.76 -5.01 3.19e+01 1cbuA 180 -27.20 -4.99 3.24e+01 1k8tA 510 -30.81 -4.99 3.24e+01 1joa 447 -28.57 -4.97 3.27e+01 1j8mF 297 -33.89 -4.97 3.30e+01 1dyr 206 -26.49 -4.96 3.30e+01 1lfwA 470 -30.41 -4.95 3.35e+01 1jlm 192 -28.19 -4.94 3.39e+01 1cb7B 483 -28.74 -4.93 3.39e+01 1pszA 303 -29.25 -4.93 3.40e+01 1g61A 228 -26.26 -4.93 3.40e+01 1qrdA 273 -27.15 -4.93 3.41e+01 2cmkA 227 -27.09 -4.93 3.41e+01 2ng1 293 -27.19 -4.90 3.50e+01 1jj2M 186 -26.71 -4.89 3.51e+01 1fokA 568 -28.68 -4.89 3.52e+01 1ebdC 41 -21.38 -4.89 3.53e+01 1ng1 294 -27.19 -4.86 3.61e+01 1bu7A 455 -32.28 -4.84 3.67e+01 1ga6A 372 -27.69 -4.84 3.68e+01 1h6zA 913 -31.41 -4.83 3.72e+01 1f93A 104 -24.42 -4.83 3.72e+01 1kaeA 434 -27.87 -4.81 3.77e+01 4blmA 265 -26.78 -4.79 3.85e+01 1dcoA 104 -24.40 -4.77 3.90e+01 1jeqB 565 -29.25 -4.77 3.92e+01 1jf9A 408 -28.78 -4.76 3.94e+01 2sqcA 631 -28.99 -4.76 3.94e+01 1lbvA 252 -28.86 -4.76 3.95e+01 1fw9A 164 -24.82 -4.75 3.96e+01 1hv2A 99 -24.76 -4.75 3.97e+01 1en7A 157 -26.05 -4.75 3.98e+01