% 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.YEL012W.t2k-100-30-str2 Host: farm09 Fri Nov 18 18:53:12 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YEL0/YEL012W % --------------------------------------------------------------------- % 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 YEL012W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL012W.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13048 sequences, 3092733 residues, 219 nodes, 340.98 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(=1.2057) * Reverse)^tau(=0.8599))) % 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 1x23A 155 -214.55 -198.05 7.86e-45 1z2uA 150 -217.34 -195.55 2.63e-44 2ayvA 166 -211.46 -194.60 4.15e-44 1y6lA 149 -202.76 -187.87 1.08e-42 2bepA 159 -192.23 -177.17 1.97e-40 1jatA 155 -190.32 -172.08 2.39e-39 1jbbA 153 -190.64 -171.82 2.71e-39 2e2c 156 -185.51 -170.34 5.61e-39 1yh2A 175 -186.67 -169.82 7.24e-39 1u9aA 160 -186.85 -168.96 1.10e-38 1fzyA 149 -185.45 -168.65 1.28e-38 2ucz 165 -191.53 -168.52 1.37e-38 1i7kA 179 -177.88 -165.71 5.48e-38 1fxtA 149 -174.57 -157.97 2.53e-36 1zdnA 158 -174.01 -157.24 3.63e-36 1yrvA 169 -160.06 -148.66 2.63e-34 1yh6A 179 -163.19 -146.96 6.17e-34 2awfA 172 -159.94 -143.66 3.24e-33 1yf9A 171 -157.52 -142.63 5.44e-33 1wzvA 155 -155.79 -138.40 4.60e-32 2a4dA 160 -139.52 -123.51 9.19e-29 1j7dA 145 -133.86 -116.31 3.78e-27 1jatB 138 -128.92 -115.58 5.53e-27 1zuoA 186 -90.94 -76.19 7.37e-18 1s1qA 145 -48.00 -32.07 9.53e-07 1uzxA 169 -42.30 -29.29 5.42e-06 1kppA 145 -39.34 -24.91 8.79e-05 2ac3A 316 -26.07 -14.35 1.00e-01 1h3fA 432 -26.18 -12.90 2.77e-01 1ukxA 137 -25.60 -12.38 4.01e-01 2es9A 115 -26.40 -12.21 4.54e-01 2ac5A 316 -23.23 -11.99 5.29e-01 1jpzA 473 -25.97 -11.81 6.02e-01 1gtkA 313 -21.32 -11.36 8.29e-01 6gsvA 217 -23.09 -11.32 8.55e-01 1ny9A 143 -23.10 -11.19 9.40e-01 1htrB 329 -20.48 -11.13 9.79e-01 1eqfA 280 -25.76 -10.60 1.43e+00 1t5eA 360 -23.33 -10.48 1.57e+00 1bu7A 455 -24.83 -10.20 1.93e+00 1ezvH 74 -22.98 -10.13 2.02e+00 1kb9F 74 -22.80 -10.00 2.23e+00 1pda 315 -19.83 -9.84 2.49e+00 2bi7A 384 -20.93 -9.82 2.53e+00 1nu5A 370 -19.73 -9.73 2.70e+00 1chrA 370 -20.60 -9.52 3.17e+00 1usuA 260 -22.94 -9.49 3.23e+00 1y4wA 518 -20.67 -9.46 3.30e+00 1i8kB 124 -18.15 -9.21 3.99e+00 2bnxA 386 -22.85 -9.11 4.29e+00 1ej8A 140 -17.97 -9.08 4.39e+00 1um0A 365 -20.69 -9.07 4.42e+00 1qupA 222 -18.17 -9.06 4.45e+00 1vfaB 116 -18.26 -9.03 4.55e+00 1a2yB 116 -18.28 -8.98 4.70e+00 1fohA 664 -21.96 -8.95 4.83e+00 1kbhB 59 -19.27 -8.95 4.83e+00 1ugjA 141 -18.63 -8.93 4.90e+00 1eyvA 156 -20.77 -8.90 5.00e+00 1k38A 254 -23.95 -8.81 5.34e+00 1vj7A 393 -20.32 -8.79 5.44e+00 1g7jB 116 -18.27 -8.74 5.63e+00 1jw3A 140 -19.49 -8.72 5.73e+00 1i5nA 146 -22.55 -8.70 5.79e+00 1pn0A 665 -21.66 -8.64 6.09e+00 1tgoA 773 -22.79 -8.61 6.19e+00 1nekC 129 -20.93 -8.61 6.23e+00 2auaA 224 -19.04 -8.58 6.34e+00 1qgiA 259 -19.70 -8.38 7.39e+00 1ks8A 433 -24.20 -8.29 7.89e+00 2bmhA 455 -22.91 -8.26 8.09e+00 2c1dA 264 -19.60 -8.23 8.28e+00 1w27A 714 -21.58 -8.12 8.97e+00 1fz1C 389 -22.27 -8.02 9.69e+00 1winA 143 -21.23 -8.01 9.76e+00 1crzA 403 -17.65 -7.89 1.07e+01 2bzuA 181 -18.69 -7.84 1.11e+01 1fm2A 169 -22.99 -7.83 1.12e+01 1go3E 187 -17.91 -7.82 1.12e+01 1n67A 359 -17.69 -7.76 1.18e+01 1sedA 117 -20.03 -7.73 1.20e+01 1qnrA 344 -19.10 -7.73 1.20e+01 1ordA 730 -19.22 -7.73 1.21e+01 1otkA 249 -21.59 -7.72 1.21e+01 1ezfA 340 -20.59 -7.69 1.24e+01 1wwcA 118 -17.90 -7.69 1.25e+01 1rcd 173 -24.42 -7.67 1.25e+01 2abk 211 -19.07 -7.65 1.28e+01 1h3oB 76 -20.30 -7.61 1.32e+01 1fuxA 166 -17.20 -7.60 1.33e+01 4pep 326 -17.18 -7.58 1.35e+01 1qnoA 344 -19.11 -7.57 1.35e+01 1aa0 113 -18.84 -7.56 1.36e+01 1s12A 94 -18.15 -7.55 1.38e+01 1ywzA 175 -20.94 -7.54 1.39e+01 1qhtA 775 -23.03 -7.44 1.50e+01 1phk 298 -19.60 -7.43 1.51e+01 8prkA 287 -18.07 -7.42 1.52e+01 1ir6A 424 -18.91 -7.40 1.54e+01 1dvfD 120 -15.53 -7.40 1.55e+01 1c1kA 217 -21.70 -7.37 1.58e+01 1c5kA 439 -17.16 -7.31 1.65e+01 1iapA 211 -19.05 -7.26 1.72e+01 1vf7A 369 -20.34 -7.23 1.76e+01 1cd9C 175 -21.87 -7.22 1.77e+01 2bzvA 181 -18.05 -7.22 1.78e+01 1wloA 136 -19.29 -7.19 1.81e+01 1gz2A 142 -16.74 -7.16 1.86e+01 1senA 164 -18.89 -7.04 2.04e+01 1yewA 382 -19.27 -7.03 2.05e+01 1seiA 130 -19.55 -7.01 2.08e+01 1tafA 68 -17.96 -6.97 2.16e+01 2biiA 424 -16.48 -6.96 2.17e+01 1bea 127 -17.51 -6.94 2.20e+01 1oebA 62 -15.77 -6.93 2.21e+01 1utiA 58 -15.80 -6.92 2.23e+01 1yqcA 170 -16.37 -6.92 2.23e+01 1w4xA 542 -19.37 -6.92 2.24e+01 1qfhA 212 -17.58 -6.92 2.24e+01 1c4kA 730 -18.24 -6.91 2.26e+01 1ornA 226 -19.13 -6.86 2.33e+01 1yx4A 132 -20.98 -6.83 2.39e+01 1q08A 99 -18.76 -6.81 2.43e+01 1es2A 262 -16.93 -6.78 2.49e+01 1e9gA 286 -17.38 -6.78 2.49e+01 1dseA 292 -19.58 -6.76 2.53e+01 1bfa 134 -17.49 -6.76 2.53e+01 1wlqC 201 -18.54 -6.76 2.53e+01 1jj2L 194 -19.13 -6.73 2.57e+01 1iu4A 331 -17.60 -6.73 2.58e+01 1brwA 433 -17.90 -6.70 2.65e+01 1a81A 254 -18.73 -6.70 2.65e+01 1q8bA 105 -18.46 -6.59 2.88e+01 1bihA 395 -16.44 -6.58 2.91e+01 1krhA 338 -17.12 -6.58 2.91e+01 1mqkH 127 -14.97 -6.56 2.94e+01 1u0fA 564 -18.42 -6.54 2.99e+01 1srqA 341 -18.63 -6.53 3.02e+01 1oaqH 121 -15.56 -6.51 3.06e+01 3psg 370 -15.90 -6.47 3.17e+01 1l0qA 391 -17.46 -6.46 3.19e+01 1kqwA 134 -16.69 -6.44 3.23e+01 2anpA 291 -17.99 -6.43 3.27e+01 1dmhA 311 -17.94 -6.40 3.33e+01 1j4wA 174 -16.53 -6.40 3.35e+01 1lokA 291 -17.97 -6.39 3.37e+01 1w94A 156 -15.71 -6.38 3.39e+01 1fc3A 120 -20.29 -6.36 3.45e+01 1wgjA 286 -16.84 -6.35 3.48e+01 1iynA 295 -20.68 -6.32 3.55e+01 1nnxA 109 -15.19 -6.31 3.57e+01 1e9gB 286 -16.74 -6.31 3.59e+01 1bs0A 384 -16.90 -6.30 3.60e+01 1es4A 262 -15.79 -6.30 3.61e+01 1e1aA 314 -16.12 -6.29 3.64e+01 1jk0A 419 -23.11 -6.24 3.77e+01 1ayaA 101 -17.82 -6.22 3.84e+01 1or0A 160 -21.48 -6.21 3.88e+01 1z2cB 383 -20.14 -6.19 3.93e+01 2ar9A 278 -18.43 -6.19 3.94e+01 1xszA 356 -18.87 -6.18 3.97e+01 2a4nA 182 -15.76 -6.18 3.97e+01 1molA 94 -15.01 -6.18 3.97e+01 1fy2A 229 -16.18 -6.18 3.97e+01