% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 04/28/03_14:00:53 % (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.YGR014W.t2k-100-30-str Host: cc47 Sun Jun 8 23:33:23 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR014W % --------------------------------------------------------------------- % 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 YGR014W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR014W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8223 sequences, 1949748 residues, 1307 nodes, 1693.78 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 (=8162) sequences: % N / (1 + exp(-(lambda(=1.3268) * Reverse)^tau(=0.7968))) % 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 1c9uA 454 -60.22 -14.36 2.31e-01 1k3iA 656 -73.00 -13.65 3.52e-01 1h2xA 710 -54.30 -13.26 4.42e-01 1h2wA 710 -53.89 -12.98 5.20e-01 1qfmA 710 -54.07 -12.81 5.77e-01 1goh 639 -71.49 -12.68 6.22e-01 2bbkH 355 -48.80 -12.65 6.33e-01 1e8nA 710 -53.82 -12.58 6.61e-01 1knvA 293 -36.86 -12.32 7.71e-01 2sli 679 -65.92 -12.29 7.89e-01 1gof 639 -70.96 -12.27 7.97e-01 1aoqA 567 -49.79 -12.24 8.11e-01 4sli 679 -65.73 -12.07 8.97e-01 1cruA 454 -57.52 -12.04 9.13e-01 1qksA 567 -49.81 -11.80 1.06e+00 1nbwA 607 -40.18 -11.66 1.15e+00 1g72A 573 -56.42 -11.56 1.22e+00 1gk1B 522 -42.19 -11.56 1.22e+00 1qbiA 454 -57.89 -11.27 1.46e+00 1oaoC 729 -53.73 -11.17 1.55e+00 2sqcA 631 -41.82 -10.92 1.81e+00 1dqiA 124 -36.68 -10.89 1.84e+00 1jj2B 337 -40.94 -10.76 2.00e+00 4aahA 571 -55.84 -10.75 2.00e+00 1gxrA 337 -45.52 -10.43 2.44e+00 1clc 639 -41.07 -10.43 2.45e+00 1h6lA 353 -46.83 -10.40 2.49e+00 1phb 414 -35.72 -10.24 2.75e+00 1axkA 394 -42.05 -10.23 2.76e+00 1acc 735 -55.89 -10.12 2.96e+00 1dszA 86 -30.38 -10.08 3.03e+00 1jb7A 495 -41.72 -10.02 3.15e+00 1n7vA 555 -50.25 -10.01 3.17e+00 1sqc 631 -40.80 -9.83 3.56e+00 1mjgM 729 -52.26 -9.81 3.60e+00 1aomA 567 -49.58 -9.75 3.72e+00 1dghB 498 -40.20 -9.64 4.01e+00 1jv2A 957 -68.35 -9.63 4.02e+00 1igtD 444 -54.22 -9.55 4.23e+00 1ema 236 -38.18 -9.46 4.48e+00 1qlgA 355 -45.77 -9.45 4.51e+00 1dgfA 497 -40.05 -9.42 4.61e+00 1mxtA 504 -41.59 -9.38 4.70e+00 1fm2B 520 -40.46 -9.36 4.77e+00 1msaA 109 -33.72 -9.33 4.85e+00 1euu 605 -58.86 -9.28 5.01e+00 1ddlA 188 -41.14 -9.27 5.06e+00 1djnA 729 -37.84 -9.13 5.54e+00 2tmdA 729 -37.84 -9.13 5.54e+00 1pd21 199 -31.03 -9.10 5.64e+00 1h54A 754 -43.57 -9.02 5.93e+00 1ehkA 562 -45.29 -9.01 5.98e+00 1mmoD 512 -36.60 -9.00 6.00e+00 1ihmA 530 -57.86 -8.99 6.03e+00 1kypA 237 -37.96 -8.96 6.17e+00 1pvc3 238 -41.95 -8.94 6.26e+00 1f3uB 171 -35.55 -8.91 6.34e+00 1do6A 124 -36.53 -8.91 6.38e+00 1ijhA 504 -40.87 -8.85 6.62e+00 1jpc 109 -33.22 -8.78 6.91e+00 1cvmA 353 -44.71 -8.76 7.00e+00 1n1mA 728 -52.93 -8.68 7.39e+00 1o94A 729 -37.71 -8.67 7.40e+00 1g97A 459 -33.30 -8.66 7.45e+00 1ll7A 392 -35.77 -8.59 7.83e+00 1d2kA 392 -35.62 -8.54 8.06e+00 1fc6A 388 -35.15 -8.54 8.07e+00 1igtB 444 -53.66 -8.53 8.14e+00 1h54B 754 -43.26 -8.46 8.51e+00 1jfpA 348 -38.21 -8.44 8.62e+00 1b8sA 504 -40.34 -8.40 8.84e+00 1b4vA 504 -40.35 -8.39 8.88e+00 1mtyD 512 -35.99 -8.30 9.43e+00 1e1aA 314 -43.14 -8.28 9.57e+00 2pooA 355 -44.98 -8.27 9.63e+00 1eut 605 -58.13 -8.23 9.84e+00 1lf2A 331 -38.15 -8.21 1.00e+01 1k32A 1045 -71.04 -8.21 1.00e+01 1phg 414 -33.59 -8.14 1.04e+01 1mpxA 615 -47.28 -8.08 1.09e+01 1i8dA 213 -33.97 -8.00 1.14e+01 1ivwA 638 -45.36 -7.98 1.16e+01 1b2pA 119 -34.07 -7.97 1.17e+01 1jlxA 304 -40.00 -7.96 1.17e+01 1f83A 425 -44.97 -7.95 1.18e+01 5cpp 414 -33.52 -7.95 1.18e+01 2shpA 525 -37.42 -7.91 1.21e+01 1erjA 393 -49.85 -7.87 1.24e+01 1phd 414 -33.30 -7.86 1.26e+01 1otcA 495 -40.02 -7.85 1.26e+01 1qmqA 414 -32.76 -7.84 1.27e+01 1liuA 528 -35.55 -7.82 1.29e+01 1n6eA 1071 -72.11 -7.78 1.32e+01 1bdfA 235 -36.82 -7.73 1.36e+01 1hra 81 -28.77 -7.70 1.39e+01 1efm 393 -38.04 -7.68 1.41e+01 1dz4A 414 -32.65 -7.68 1.41e+01 1iyhA 198 -29.22 -7.66 1.43e+01 1fwyA 331 -32.26 -7.61 1.48e+01 1bpoA 494 -48.98 -7.57 1.52e+01 1iw7C 1119 -52.06 -7.56 1.53e+01 1j0mA 752 -40.82 -7.47 1.62e+01 1kmnD 424 -33.57 -7.37 1.73e+01 1hm9A 468 -32.91 -7.37 1.74e+01 1n1bA 549 -42.48 -7.27 1.85e+01 1onwA 390 -37.25 -7.26 1.87e+01 1ig8A 486 -37.14 -7.23 1.90e+01 1nn6A 228 -40.04 -7.14 2.02e+01 1hxs3 237 -39.19 -7.13 2.04e+01 1h6rA 236 -38.87 -7.05 2.14e+01 7catA 506 -39.74 -7.04 2.16e+01 1gvzA 237 -36.93 -7.03 2.18e+01 1qvbA 481 -40.07 -7.00 2.22e+01 1jhfA 202 -34.34 -7.00 2.22e+01 1a7s 221 -41.07 -6.97 2.26e+01 1fxjA 331 -31.42 -6.97 2.27e+01 1pjpA 226 -40.91 -6.95 2.29e+01 1mkmA 249 -32.40 -6.95 2.30e+01 1orvA 728 -49.38 -6.92 2.34e+01 1ju3A 583 -46.79 -6.90 2.37e+01 1l8nA 679 -42.25 -6.90 2.38e+01 1rmvA 157 -29.58 -6.88 2.41e+01 1ton 235 -39.89 -6.87 2.42e+01 2emo 237 -37.91 -6.86 2.44e+01 1ej2A 181 -28.26 -6.85 2.45e+01 1eemA 241 -30.70 -6.80 2.54e+01 1mhyD 521 -32.88 -6.77 2.60e+01 1klt 226 -40.87 -6.73 2.67e+01 1epwA 1290 -88.19 -6.70 2.71e+01 1bbzA 58 -27.61 -6.68 2.74e+01 1bd2D 204 -34.54 -6.67 2.77e+01 1bbzE 58 -27.55 -6.66 2.80e+01 1by5A 714 -38.97 -6.63 2.85e+01 1g4mA 393 -41.49 -6.60 2.90e+01 1go3E 187 -33.07 -6.59 2.93e+01 1k9dA 679 -42.26 -6.56 2.98e+01 1jz8A 1023 -47.00 -6.56 2.99e+01 1aboA 62 -28.01 -6.54 3.03e+01 1httA 423 -32.40 -6.53 3.04e+01 1befA 181 -34.07 -6.52 3.07e+01 1f6fB 210 -36.31 -6.49 3.13e+01 1kzhA 555 -43.97 -6.48 3.15e+01 1bglA 1023 -47.96 -6.43 3.26e+01 1jlvA 209 -28.22 -6.42 3.28e+01 1df9A 191 -33.89 -6.38 3.38e+01 1qi6A 475 -32.01 -6.37 3.39e+01 1mn1 357 -35.85 -6.34 3.47e+01 1gpmA 525 -39.58 -6.33 3.48e+01 1ewqA 765 -35.51 -6.33 3.48e+01 1awo 62 -27.60 -6.33 3.50e+01 1f3eA 386 -31.46 -6.31 3.53e+01 1cqxA 403 -35.23 -6.31 3.53e+01 1a8y 367 -33.16 -6.28 3.62e+01 1qa7A 217 -36.88 -6.28 3.62e+01 1lw9A 164 -27.30 -6.25 3.68e+01 1qovH 260 -38.26 -6.22 3.76e+01 1fbnA 230 -31.00 -6.20 3.81e+01 1aocA 175 -33.68 -6.19 3.84e+01 2msbA 115 -28.58 -6.18 3.88e+01 3pgk 416 -32.04 -6.16 3.93e+01 1ffkB 338 -39.46 -6.14 3.98e+01