% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % str2foo.1.YGR023W.t2k-100-30-str2 Host: farm19.cse.ucsc.edu Sun Mar 19 10:56:20 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR023W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR023W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR023W.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 552 nodes, 920.18 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.5864) * Reverse)^tau(=0.7748))) % Calculated when Simple < simple_threshold (10000.00) % 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 1jk7A 323 -24.57 -12.84 3.58e-01 1u32A 293 -23.73 -12.75 3.78e-01 1prcH 259 -28.30 -11.63 7.69e-01 6prcH 258 -29.86 -11.58 7.91e-01 1fjmA 330 -23.55 -11.33 9.32e-01 1dxrH 258 -29.22 -11.20 1.01e+00 1bqhG 129 -30.90 -11.02 1.13e+00 1zckA 154 -22.55 -10.66 1.44e+00 1aijH 260 -27.51 -10.61 1.48e+00 1rxdA 159 -22.38 -10.47 1.62e+00 1d0nA 729 -25.26 -10.32 1.79e+00 1x24A 180 -22.15 -10.28 1.84e+00 1azsA 220 -21.32 -10.17 1.97e+00 1culA 217 -20.94 -10.13 2.02e+00 1gqpA 221 -23.95 -9.99 2.23e+00 1qovH 260 -27.49 -9.73 2.64e+00 1q40B 219 -23.81 -9.60 2.87e+00 1dgjA 907 -22.58 -9.56 2.95e+00 1f28A 297 -22.22 -9.23 3.68e+00 1rzhH 260 -26.66 -9.11 3.98e+00 1ciy 590 -31.98 -8.96 4.41e+00 1e2tA 284 -23.34 -8.88 4.67e+00 2bzlA 325 -23.32 -8.85 4.76e+00 3aprE 325 -23.53 -8.73 5.15e+00 2apr 325 -23.53 -8.66 5.42e+00 1xwnA 174 -23.60 -8.65 5.47e+00 1ehkB 168 -23.83 -8.64 5.48e+00 1m2tB 263 -30.25 -8.64 5.48e+00 1ksiB 642 -27.64 -8.56 5.80e+00 1cjtA 217 -19.63 -8.55 5.84e+00 1ot1A 686 -30.37 -8.52 5.95e+00 1cx8B 639 -24.71 -8.48 6.13e+00 2sli 679 -33.95 -8.32 6.84e+00 1to4A 156 -22.05 -8.28 7.04e+00 4sli 679 -33.87 -8.26 7.11e+00 1cxlA 686 -29.93 -8.26 7.13e+00 1khbA 625 -23.42 -8.20 7.42e+00 1qoiA 177 -22.09 -8.18 7.52e+00 1ksiA 642 -27.69 -8.18 7.55e+00 1vjjA 692 -28.21 -8.13 7.78e+00 1eu1A 780 -23.30 -8.07 8.12e+00 1cx8A 639 -24.86 -8.05 8.22e+00 1jmxA 494 -24.17 -8.03 8.35e+00 1d3cA 686 -30.38 -8.03 8.38e+00 1jffB 445 -19.40 -8.00 8.51e+00 1ui7A 638 -28.43 -7.93 8.96e+00 1sz6B 263 -29.04 -7.90 9.11e+00 1fn8A 224 -33.80 -7.89 9.24e+00 1p7gA 222 -18.75 -7.84 9.54e+00 1aomA 567 -29.07 -7.81 9.75e+00 1pq7A 224 -33.73 -7.78 9.94e+00 1e1hA 287 -21.23 -7.74 1.03e+01 1try 224 -33.54 -7.69 1.05e+01 1aoqA 567 -28.46 -7.57 1.15e+01 1spuB 727 -25.14 -7.52 1.19e+01 1l9mA 692 -27.92 -7.51 1.20e+01 1lrzA 426 -18.39 -7.51 1.20e+01 1iqyA 638 -28.00 -7.47 1.23e+01 1eysH 259 -29.31 -7.46 1.24e+01 1avk 638 -28.14 -7.45 1.25e+01 1pujA 282 -18.33 -7.44 1.27e+01 1ivwA 638 -26.01 -7.42 1.28e+01 1qksA 567 -28.33 -7.39 1.31e+01 2rmpA 361 -30.95 -7.38 1.31e+01 1ui8A 638 -26.02 -7.36 1.33e+01 1t6kA 278 -19.47 -7.23 1.46e+01 2aaiB 262 -30.91 -7.23 1.47e+01 1mpxA 615 -25.07 -7.22 1.47e+01 1xubA 298 -19.75 -7.21 1.48e+01 1g87A 614 -21.59 -7.17 1.52e+01 1ollA 188 -23.58 -7.10 1.61e+01 1v87A 114 -19.69 -7.09 1.62e+01 1upiA 225 -25.02 -7.06 1.65e+01 1nkgA 508 -35.41 -7.01 1.71e+01 1ymmE 249 -33.42 -6.96 1.77e+01 1k42A 168 -26.12 -6.96 1.77e+01 1d8hA 311 -20.87 -6.96 1.77e+01 1v0eA 666 -26.95 -6.94 1.80e+01 1ft1B 437 -18.03 -6.89 1.86e+01 1w6gA 646 -25.47 -6.85 1.91e+01 1p8xA 344 -20.80 -6.85 1.91e+01 1opoA 348 -23.44 -6.83 1.94e+01 1rjoA 646 -25.55 -6.83 1.95e+01 1tu5A 746 -25.49 -6.77 2.02e+01 1siiA 646 -25.48 -6.73 2.09e+01 2asi 360 -31.66 -6.70 2.14e+01 1ej6A 1289 -27.73 -6.69 2.15e+01 1d6zA 727 -24.53 -6.69 2.15e+01 1jcrB 437 -17.89 -6.68 2.16e+01 1kawA 135 -18.66 -6.67 2.18e+01 1wkrA 340 -34.01 -6.66 2.20e+01 1s48A 609 -18.72 -6.62 2.27e+01 1fx7A 230 -18.95 -6.61 2.28e+01 1qvcA 145 -20.04 -6.60 2.29e+01 1aozA 552 -29.53 -6.59 2.31e+01 1d8dB 437 -17.84 -6.58 2.32e+01 1l6rA 227 -17.59 -6.56 2.36e+01 2eifA 136 -24.03 -6.56 2.36e+01 1xhbA 472 -19.81 -6.55 2.38e+01 1itkA 731 -20.01 -6.53 2.42e+01 1d8iA 311 -20.30 -6.47 2.52e+01 1pbyB 337 -26.44 -6.47 2.52e+01 1zclA 180 -18.24 -6.46 2.54e+01 1u1wA 298 -18.89 -6.45 2.55e+01 1yx1A 264 -16.31 -6.42 2.62e+01 1oacA 727 -24.30 -6.34 2.77e+01 1suwA 249 -21.45 -6.31 2.83e+01 1vzoA 355 -19.88 -6.30 2.86e+01 1de4C 640 -20.53 -6.29 2.88e+01 1f00I 282 -28.88 -6.28 2.90e+01 1v3eA 431 -29.79 -6.25 2.95e+01 1vrpA 381 -19.23 -6.22 3.03e+01 1kcxA 518 -20.28 -6.19 3.09e+01 1jd0A 263 -22.60 -6.19 3.10e+01 1wrmA 165 -15.86 -6.18 3.11e+01 2bbkH 355 -25.56 -6.18 3.13e+01 1vhrA 184 -16.22 -6.14 3.21e+01 1k6dA 220 -17.28 -6.13 3.24e+01 1snyA 267 -16.81 -6.10 3.31e+01 1gpl 432 -22.53 -6.09 3.32e+01 1dim 381 -27.92 -6.09 3.33e+01 2a9dA 372 -22.38 -6.08 3.34e+01 2fflA 756 -22.91 -6.08 3.35e+01 1je0A 236 -15.94 -6.05 3.43e+01 1jjuB 337 -25.97 -6.04 3.46e+01 1z0sA 278 -21.04 -6.03 3.48e+01 1tn6B 437 -17.57 -6.02 3.51e+01 1gctA 245 -28.76 -6.02 3.51e+01 1ld8B 437 -17.29 -5.95 3.68e+01 2bbdA 350 -22.85 -5.95 3.69e+01 1ypvA 313 -17.80 -5.95 3.69e+01 2sqcA 631 -17.80 -5.93 3.74e+01 1e15A 499 -18.08 -5.92 3.77e+01 1e6pA 499 -18.11 -5.90 3.82e+01 2bvyA 475 -21.20 -5.85 3.98e+01 2a6hA 315 -21.03 -5.84 3.99e+01