% 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. % --------------------------------------------------------------------- % alphafoo.1.YGR041W.t2k-100-30-alpha Host: cc42 Tue Nov 12 04:53:05 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR041W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.alphas % % 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 YGR041W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR041W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 548 nodes, 383.94 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(=2.7061) * Reverse)^tau(=0.6828))) % 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 1igtB 444 -37.94 -10.86 3.14e-01 1tgoA 773 -34.84 -10.20 4.77e-01 1jqpA 438 -34.29 -9.86 5.94e-01 1ey2A 471 -36.28 -9.69 6.65e-01 1bn8A 420 -33.59 -9.64 6.87e-01 1eybA 471 -35.97 -9.40 8.07e-01 1qgtA 149 -29.30 -9.33 8.42e-01 1xsoA 150 -30.93 -9.24 8.97e-01 1igtD 444 -35.93 -8.79 1.21e+00 1tyv 542 -35.16 -8.78 1.22e+00 1lqtA 456 -32.20 -8.72 1.27e+00 1hvc 203 -31.74 -8.52 1.46e+00 1ejfA 125 -29.44 -8.45 1.53e+00 1tyu 543 -35.00 -8.32 1.67e+00 1qa1A 554 -35.38 -8.26 1.74e+00 8fabB 224 -32.44 -7.90 2.24e+00 1kv7A 488 -34.85 -7.90 2.24e+00 1thjA 214 -30.54 -7.81 2.37e+00 1qr4B 186 -30.66 -7.68 2.60e+00 1tsp 559 -34.35 -7.45 3.07e+00 1h80A 464 -33.55 -7.40 3.18e+00 1bkb 136 -28.21 -7.30 3.42e+00 1qr4A 186 -30.39 -7.22 3.61e+00 2fcr 173 -28.60 -7.06 4.07e+00 1iatA 557 -31.10 -6.97 4.33e+00 1jhnA 424 -36.27 -6.95 4.41e+00 1cxlA 686 -31.81 -6.85 4.75e+00 1yghA 164 -26.92 -6.82 4.83e+00 1d2pA 373 -31.52 -6.72 5.20e+00 1qq1A 559 -34.01 -6.67 5.40e+00 1kb0A 677 -33.18 -6.64 5.50e+00 1d3cA 686 -31.46 -6.56 5.84e+00 1jgsA 138 -26.76 -6.56 5.86e+00 1cqqA 180 -29.99 -6.48 6.24e+00 1agjA 242 -29.79 -6.44 6.40e+00 1l2tA 235 -27.75 -6.36 6.83e+00 1gof 639 -32.41 -6.35 6.87e+00 1mpp 361 -31.56 -6.34 6.89e+00 1r2fA 319 -28.25 -6.34 6.93e+00 1thv 207 -27.94 -6.27 7.27e+00 1goh 639 -32.14 -6.26 7.33e+00 1hm5A 558 -30.31 -6.23 7.48e+00 1dqrA 557 -30.31 -6.20 7.68e+00 1thw 207 -27.87 -6.15 7.94e+00 2asi 360 -30.06 -6.15 7.95e+00 1sva1 361 -34.75 -6.11 8.19e+00 1k3iA 656 -32.78 -6.10 8.29e+00 1qrzA 246 -28.69 -6.03 8.71e+00 1qreA 247 -30.78 -5.99 8.98e+00 1ddjA 247 -28.65 -5.99 8.98e+00 1jtaA 361 -30.62 -5.94 9.32e+00 1jjuA 489 -30.03 -5.87 9.86e+00 1htyA 1015 -34.64 -5.87 9.88e+00 1lml 478 -29.18 -5.84 1.01e+01 1jb9A 316 -29.15 -5.81 1.04e+01 1hxkA 1015 -34.58 -5.71 1.11e+01 1lktA 104 -25.96 -5.71 1.12e+01 2bbvC 363 -29.32 -5.70 1.12e+01 1kwhA 492 -28.84 -5.68 1.14e+01 1jj2V 154 -25.74 -5.66 1.16e+01 1ffkT 154 -25.74 -5.63 1.19e+01 1hurA 180 -27.29 -5.58 1.24e+01 1cbuA 180 -25.97 -5.50 1.31e+01 1hjp 203 -26.45 -5.49 1.32e+01 1hwwA 1015 -34.48 -5.49 1.33e+01 1k4iA 233 -26.98 -5.46 1.36e+01 1c9kB 180 -25.85 -5.44 1.38e+01 1jbuH 254 -27.30 -5.43 1.39e+01 1h7zA 194 -27.57 -5.42 1.40e+01 1bdmA 327 -27.76 -5.41 1.41e+01 1jc9A 269 -28.15 -5.38 1.44e+01 1eu3A 210 -27.83 -5.37 1.46e+01 1ikoP 178 -27.23 -5.34 1.49e+01 1c9kA 180 -26.17 -5.32 1.51e+01 1h68A 239 -28.33 -5.26 1.58e+01 1hhnA 101 -26.13 -5.26 1.59e+01 1ewqA 765 -29.29 -5.25 1.60e+01 1fzaB 328 -29.35 -5.23 1.63e+01 1f6dA 376 -27.49 -5.20 1.67e+01 1bmdA 327 -27.41 -5.20 1.67e+01 1kwsA 261 -27.53 -5.19 1.68e+01 1gal 583 -29.75 -5.19 1.68e+01 2sodB 152 -29.86 -5.18 1.70e+01 2rmpA 361 -29.05 -5.17 1.70e+01 1m0kA 262 -29.23 -5.16 1.71e+01 1koqA 253 -28.30 -5.16 1.72e+01 1pvl 301 -28.32 -5.16 1.72e+01 1fknA 391 -30.18 -5.10 1.81e+01 1hbp 183 -27.09 -5.05 1.87e+01 1hetA 374 -29.64 -5.05 1.88e+01 1arb 268 -28.81 -5.05 1.88e+01 1fggA 261 -27.36 -5.02 1.92e+01 2at9 247 -27.77 -4.99 1.97e+01 1kopA 223 -28.09 -4.99 1.97e+01 1kzhA 555 -29.34 -4.99 1.98e+01 1c3wA 222 -27.70 -4.97 2.00e+01 1sek 378 -27.60 -4.94 2.05e+01 1qhqA 140 -25.24 -4.88 2.15e+01 1qh4A 380 -27.50 -4.88 2.16e+01 1k4vA 289 -27.02 -4.84 2.23e+01 1qs8A 329 -28.52 -4.83 2.24e+01 1at3A 247 -27.24 -4.82 2.26e+01 1m4iA 181 -26.63 -4.80 2.30e+01 1g8oA 310 -27.53 -4.78 2.33e+01 1iw7C 1119 -31.68 -4.76 2.38e+01 1fjkA 52 -25.00 -4.75 2.39e+01 2bbvA 363 -28.30 -4.73 2.44e+01 1fhoA 119 -25.48 -4.72 2.45e+01 1lxdA 100 -24.06 -4.72 2.47e+01 1danH 254 -26.74 -4.71 2.47e+01 1knb 196 -28.67 -4.69 2.53e+01 1faoA 126 -25.04 -4.68 2.54e+01 1kf6D 119 -28.11 -4.67 2.56e+01 1qbjA 81 -23.62 -4.66 2.58e+01 1g7tA 594 -28.56 -4.65 2.60e+01 1dbuA 158 -25.10 -4.64 2.61e+01 1idk 359 -28.35 -4.64 2.62e+01 1pcl 355 -28.55 -4.64 2.63e+01 1kxlA 199 -26.94 -4.63 2.65e+01 1nls 237 -27.29 -4.62 2.67e+01 1cwvA 492 -30.02 -4.61 2.69e+01 1e8uA 454 -29.60 -4.61 2.69e+01 1pamA 686 -29.56 -4.57 2.78e+01 1dykA 394 -29.39 -4.57 2.79e+01 1heuA 374 -29.56 -4.56 2.80e+01 1eulA 994 -30.54 -4.55 2.82e+01 1preB 470 -29.22 -4.54 2.84e+01 2cb5A 453 -27.63 -4.53 2.87e+01 1iw5A 113 -23.39 -4.51 2.91e+01 1kv9A 668 -30.15 -4.51 2.92e+01 1scs 237 -27.39 -4.51 2.93e+01 1qmeA 702 -30.17 -4.47 3.01e+01 1bdmB 327 -26.64 -4.46 3.03e+01 1i50A 1733 -35.61 -4.46 3.04e+01 1lfdA 87 -23.36 -4.46 3.04e+01 1c5kA 439 -29.39 -4.46 3.04e+01 1e8tA 454 -29.53 -4.42 3.14e+01 1bvoA 175 -27.20 -4.42 3.15e+01 1ebaA 215 -26.74 -4.41 3.16e+01 1hdhA 536 -28.13 -4.38 3.26e+01 1e8cA 498 -27.72 -4.37 3.28e+01 1qba 858 -29.62 -4.32 3.42e+01 1qtfA 246 -28.16 -4.31 3.44e+01 1nfdA 203 -27.25 -4.31 3.44e+01 1omp 370 -27.24 -4.30 3.47e+01 1rthA 560 -28.12 -4.26 3.60e+01 1rcy 151 -25.56 -4.25 3.63e+01 1cf3A 583 -28.26 -4.25 3.63e+01 1clh 166 -25.60 -4.24 3.67e+01 1jeoA 180 -25.82 -4.22 3.74e+01 1dyr 206 -25.77 -4.21 3.75e+01 1qo0D 196 -24.66 -4.21 3.75e+01 1c01A 76 -25.11 -4.21 3.76e+01 1gkxA 388 -26.88 -4.19 3.82e+01 2bnh 457 -26.87 -4.19 3.84e+01 1a3z 155 -25.52 -4.17 3.88e+01 1hbq 183 -26.00 -4.17 3.88e+01 1ahpA 797 -29.61 -4.17 3.90e+01 1l9fA 389 -27.85 -4.17 3.90e+01 1e30A 155 -25.62 -4.16 3.91e+01