% 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.YGR009C.t2k-100-30-str Host: cc77 Tue Jun 10 05:17:53 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR009C % --------------------------------------------------------------------- % 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 YGR009C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR009C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8223 sequences, 1949748 residues, 652 nodes, 592.42 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(=1.1421) * Reverse)^tau(=0.8097))) % 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 1sfcC 83 -115.03 -86.00 1.25e-14 1n7sC 79 -114.84 -85.96 1.26e-14 1l4aD 87 -110.95 -83.93 2.78e-14 1sfcD 87 -115.61 -82.75 4.38e-14 1jthA 82 -107.73 -77.91 2.92e-13 1n7sD 66 -107.29 -74.77 1.01e-12 1kilD 66 -107.17 -74.63 1.07e-12 1gl2C 65 -73.58 -49.94 2.74e-08 1gl2D 65 -76.11 -46.03 1.48e-07 1n7sB 68 -48.76 -22.41 8.22e-03 1sfcB 83 -49.40 -22.20 9.13e-03 1hvvA 75 -48.79 -22.00 1.01e-02 1jthB 77 -48.93 -21.62 1.22e-02 1jthD 77 -47.19 -21.56 1.26e-02 1gl2B 65 -47.11 -20.75 1.90e-02 1dn1B 267 -50.25 -17.18 1.19e-01 1bt3A 345 -41.70 -13.29 9.64e-01 1xsm 390 -40.02 -13.23 9.97e-01 1ab4 477 -40.01 -12.69 1.34e+00 1h0oA 390 -39.64 -12.50 1.49e+00 1k7wA 468 -40.30 -12.27 1.69e+00 1auwA 468 -41.15 -12.18 1.78e+00 1iyjB 817 -43.70 -12.03 1.94e+00 1hy0A 466 -39.24 -12.02 1.95e+00 1prgA 270 -34.81 -10.77 3.96e+00 1fm9D 272 -35.24 -10.65 4.24e+00 1jadA 251 -43.16 -10.42 4.84e+00 1k42A 168 -35.07 -10.26 5.30e+00 1ads 315 -37.13 -10.19 5.54e+00 1dcnD 436 -36.89 -9.98 6.25e+00 2prgA 271 -34.44 -9.97 6.28e+00 1ih7A 903 -40.04 -9.95 6.38e+00 1dxrL 273 -35.02 -9.85 6.75e+00 1clqA 903 -39.77 -9.79 6.98e+00 1nfiA 301 -37.73 -9.58 7.89e+00 1bywA 110 -31.04 -9.48 8.40e+00 1kv7A 488 -36.13 -9.46 8.46e+00 1aho 64 -29.14 -9.34 9.07e+00 1ic2A 81 -35.97 -9.33 9.13e+00 1d7uA 433 -34.19 -9.26 9.53e+00 2dkb 433 -33.86 -9.20 9.90e+00 1reqA 727 -36.45 -9.19 9.96e+00 1nfiC 301 -37.52 -9.15 1.02e+01 1dcnA 424 -34.99 -9.09 1.05e+01 2acr 315 -36.26 -9.08 1.06e+01 1bli 483 -35.21 -9.02 1.10e+01 1js8A 394 -36.11 -8.99 1.12e+01 1jqiA 388 -34.69 -8.98 1.13e+01 5reqA 727 -36.40 -8.94 1.15e+01 1lrzA 426 -38.46 -8.90 1.18e+01 1as4A 341 -34.57 -8.89 1.19e+01 6prcL 273 -33.86 -8.86 1.20e+01 1uahA 431 -34.00 -8.86 1.21e+01 7reqA 727 -36.26 -8.78 1.27e+01 1jeyB 565 -35.86 -8.68 1.34e+01 1el3A 316 -35.66 -8.64 1.38e+01 1qh7A 207 -31.79 -8.63 1.39e+01 1j7lA 264 -32.98 -8.56 1.45e+01 1kjvA 284 -33.62 -8.54 1.47e+01 1h4gA 207 -31.82 -8.53 1.47e+01 1bg7 176 -34.16 -8.52 1.48e+01 1am2 199 -33.80 -8.50 1.49e+01 1ars 396 -32.24 -8.50 1.50e+01 1spa 396 -32.27 -8.42 1.57e+01 1j7vR 214 -32.76 -8.41 1.58e+01 1keyA 235 -37.69 -8.39 1.60e+01 1sup 275 -32.62 -8.31 1.68e+01 1aozA 552 -37.26 -8.31 1.68e+01 1edqA 540 -36.02 -8.29 1.70e+01 1ahxA 396 -32.34 -8.21 1.78e+01 1cqeA 580 -35.56 -8.15 1.84e+01 1lw6E 281 -32.20 -8.15 1.85e+01 1vcaA 202 -31.76 -8.15 1.85e+01 1art 396 -32.22 -8.13 1.87e+01 1gln 468 -33.31 -8.08 1.93e+01 1qg0A 308 -36.44 -8.03 1.99e+01 1bcfA 158 -33.59 -8.02 2.01e+01 1jeqB 565 -36.09 -8.01 2.01e+01 1p9uA 302 -38.74 -7.99 2.03e+01 1qisA 396 -32.19 -7.97 2.06e+01 1smeA 329 -35.32 -7.96 2.07e+01 1fhoA 119 -35.27 -7.95 2.09e+01 1c5yB 253 -33.21 -7.93 2.11e+01 7catA 506 -37.31 -7.93 2.12e+01 1jatA 155 -32.81 -7.91 2.13e+01 1pfzA 380 -36.36 -7.90 2.15e+01 1lf2A 331 -35.01 -7.90 2.15e+01 1ex7A 186 -30.94 -7.90 2.15e+01 1gj7B 253 -33.21 -7.87 2.20e+01 1rdr 461 -34.13 -7.78 2.31e+01 1j5rA 371 -32.84 -7.78 2.31e+01 1icpA 376 -32.22 -7.76 2.34e+01 1j7iA 264 -32.22 -7.75 2.36e+01 1obbA 480 -35.98 -7.74 2.37e+01 1jbbA 153 -32.51 -7.70 2.43e+01 1g0uL 241 -32.14 -7.69 2.44e+01 2tysB 397 -31.71 -7.68 2.46e+01 1e7uA 961 -36.97 -7.67 2.47e+01 1fr0A 125 -30.06 -7.65 2.51e+01 1gky 187 -30.45 -7.63 2.53e+01 1gy8A 397 -30.49 -7.63 2.53e+01 1mgtA 174 -34.60 -7.63 2.54e+01 1fcqA 350 -32.64 -7.62 2.55e+01 1n8fA 350 -32.00 -7.60 2.59e+01 1chuA 540 -35.71 -7.59 2.60e+01 1lqsR 214 -31.53 -7.58 2.62e+01 2mbr 340 -33.56 -7.57 2.64e+01 1cdi 179 -29.69 -7.56 2.64e+01 1ryp1 222 -31.14 -7.43 2.86e+01 1lnh 857 -37.39 -7.43 2.86e+01 1miuA 738 -40.90 -7.39 2.94e+01 1k9tA 540 -34.90 -7.39 2.94e+01 1m0qA 433 -31.89 -7.37 2.96e+01 1gyhA 318 -35.26 -7.37 2.97e+01 1lvoA 302 -37.82 -7.36 2.99e+01 1j09A 468 -32.68 -7.35 3.01e+01 1eriA 276 -33.00 -7.31 3.08e+01 1vjs 483 -33.75 -7.31 3.09e+01 1k92A 455 -32.74 -7.29 3.11e+01 1jb9A 316 -38.04 -7.29 3.11e+01 1dgsA 667 -37.75 -7.28 3.15e+01 1dlwA 116 -27.37 -7.24 3.22e+01 2a0b 125 -29.57 -7.22 3.26e+01 1ctn 540 -35.04 -7.21 3.29e+01 1gcyA 527 -39.10 -7.20 3.30e+01 1l1yA 678 -38.53 -7.20 3.30e+01 1djtA 64 -26.76 -7.17 3.37e+01 1vaoA 560 -40.46 -7.14 3.42e+01 1e8xA 961 -36.49 -7.14 3.42e+01 2abk 211 -29.99 -7.14 3.43e+01 1k8yB 396 -31.94 -7.12 3.46e+01 1fnc 314 -37.60 -7.10 3.52e+01 1bdmB 327 -30.76 -7.09 3.53e+01 1oq9A 363 -35.46 -7.07 3.58e+01 1qbeA 132 -29.82 -7.05 3.61e+01 1jalA 363 -34.61 -7.04 3.65e+01 1qopB 396 -31.82 -7.03 3.67e+01 1h6gA 256 -33.67 -7.02 3.69e+01 1oyb 400 -32.06 -7.00 3.73e+01 1f45B 197 -30.98 -7.00 3.74e+01 1fnb 314 -37.80 -6.99 3.76e+01 1pinA 163 -31.16 -6.98 3.78e+01 1lr1A 61 -27.43 -6.98 3.79e+01 1oahA 519 -40.13 -6.97 3.80e+01 1uxy 340 -33.23 -6.97 3.81e+01 1jsdB 176 -34.40 -6.96 3.82e+01 1smrA 335 -32.18 -6.94 3.88e+01 1fdr 248 -29.62 -6.93 3.89e+01 1itkA 731 -36.85 -6.93 3.90e+01 1eucB 396 -31.26 -6.91 3.95e+01 1qi9A 556 -35.09 -6.91 3.95e+01 1kqlA 56 -32.21 -6.91 3.96e+01