% 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. % --------------------------------------------------------------------- % dsspfoo.1.YEL012W.t2k-100-30-dssp-ebghstl Host: farm09 Fri Nov 18 19:05:01 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.dssps % % 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.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13048 sequences, 3092733 residues, 219 nodes, 341.72 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(=1.2368) * Reverse)^tau(=0.8484))) % 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 -209.10 -192.10 1.04e-41 1z2uA 150 -211.99 -190.07 2.63e-41 2ayvA 166 -205.57 -188.30 5.91e-41 1y6lA 149 -196.68 -181.51 1.35e-39 2bepA 159 -185.08 -170.40 2.34e-37 1jatA 155 -186.41 -168.50 5.68e-37 1jbbA 153 -186.90 -167.08 1.10e-36 1yh2A 175 -181.14 -166.17 1.69e-36 2e2c 156 -179.08 -165.03 2.87e-36 1u9aA 160 -181.56 -164.47 3.74e-36 1fzyA 149 -179.26 -163.51 5.86e-36 2ucz 165 -187.08 -162.97 7.55e-36 1i7kA 179 -172.22 -160.02 3.03e-35 1fxtA 149 -172.57 -156.29 1.76e-34 1zdnA 158 -168.91 -151.84 1.45e-33 1yh6A 179 -159.04 -144.82 4.09e-32 1yrvA 169 -154.91 -143.45 7.88e-32 1yf9A 171 -154.58 -141.50 2.01e-31 1wzvA 155 -154.82 -138.78 7.42e-31 2awfA 172 -153.46 -136.07 2.73e-30 2a4dA 160 -133.45 -115.52 6.24e-26 1jatB 138 -123.40 -109.05 1.55e-24 1j7dA 145 -127.86 -108.45 2.09e-24 1zuoA 186 -87.56 -72.90 1.78e-16 1s1qA 145 -43.50 -29.65 6.57e-06 1uzxA 169 -41.19 -27.61 2.28e-05 1kppA 145 -37.77 -23.19 3.56e-04 2ac3A 316 -27.22 -15.39 5.67e-02 1ukxA 137 -24.52 -13.28 2.37e-01 1h3fA 432 -26.43 -12.69 3.55e-01 2ac5A 316 -23.79 -12.22 4.93e-01 2es9A 115 -27.17 -11.99 5.79e-01 1l0qA 391 -21.79 -11.67 7.22e-01 1ny9A 143 -23.75 -11.66 7.29e-01 1eqfA 280 -26.82 -11.40 8.74e-01 1srqA 341 -22.36 -11.17 1.03e+00 6gsvA 217 -23.45 -10.96 1.19e+00 1usuA 260 -24.54 -10.81 1.32e+00 2bi7A 384 -21.66 -10.62 1.51e+00 1kb9F 74 -23.40 -10.45 1.71e+00 2biiA 424 -19.71 -10.18 2.07e+00 1jpzA 473 -24.60 -10.17 2.09e+00 1ezvH 74 -23.18 -10.13 2.16e+00 1tgoA 773 -23.70 -9.25 4.04e+00 1bu7A 455 -24.47 -9.10 4.51e+00 1i8kB 124 -17.55 -8.95 5.04e+00 2bnxA 386 -22.98 -8.81 5.59e+00 1cd9C 175 -23.01 -8.79 5.65e+00 1nu5A 370 -19.08 -8.73 5.91e+00 1h3oB 76 -21.41 -8.67 6.19e+00 1kbhB 59 -19.20 -8.64 6.34e+00 1a2yB 116 -17.60 -8.62 6.40e+00 1vfaB 116 -17.58 -8.59 6.56e+00 1um0A 365 -20.44 -8.58 6.61e+00 1qnrA 344 -20.41 -8.58 6.62e+00 1qnoA 344 -20.45 -8.57 6.67e+00 2bmhA 455 -23.91 -8.54 6.82e+00 1nekC 129 -21.13 -8.49 7.03e+00 1i5nA 146 -23.55 -8.48 7.11e+00 1g7jB 116 -17.61 -8.47 7.13e+00 1aa0 113 -19.91 -8.41 7.49e+00 1eyvA 156 -21.20 -8.35 7.83e+00 1lm8V 160 -20.81 -8.23 8.54e+00 2bzuA 181 -18.73 -8.22 8.62e+00 1w9hA 427 -22.13 -8.20 8.72e+00 1w27A 714 -22.49 -8.12 9.25e+00 1px5A 349 -23.02 -8.12 9.29e+00 1c4kA 730 -19.94 -8.10 9.40e+00 1y4wA 518 -18.64 -8.10 9.41e+00 1mkeA 152 -17.87 -8.05 9.72e+00 1qhtA 775 -23.22 -8.03 9.87e+00 1ks8A 433 -24.38 -8.02 9.96e+00 1xaoA 121 -19.15 -7.98 1.03e+01 1who 96 -18.59 -7.93 1.06e+01 1chrA 370 -19.68 -7.93 1.07e+01 1vcbC 160 -19.15 -7.90 1.09e+01 1c1kA 217 -22.61 -7.87 1.12e+01 1fohA 664 -21.43 -7.79 1.18e+01 1g9mC 185 -18.55 -7.78 1.19e+01 1ugjA 141 -17.33 -7.77 1.20e+01 2auaA 224 -18.21 -7.75 1.22e+01 1brwA 433 -19.19 -7.73 1.24e+01 1oaqH 121 -16.49 -7.71 1.26e+01 1htrB 329 -16.97 -7.62 1.34e+01 1v0jA 399 -20.24 -7.61 1.35e+01 1gtkA 313 -17.74 -7.61 1.35e+01 1bp3B 211 -18.09 -7.59 1.37e+01 1winA 143 -20.63 -7.48 1.49e+01 2c1dA 264 -19.27 -7.47 1.50e+01 1pn0A 665 -21.20 -7.46 1.51e+01 1wteA 272 -20.34 -7.44 1.53e+01 2bzvA 181 -17.95 -7.44 1.54e+01 1y7rA 133 -17.16 -7.42 1.56e+01 1b0pA 1231 -20.84 -7.41 1.57e+01 1t5eA 360 -21.12 -7.39 1.59e+01 3cd4 182 -17.76 -7.37 1.62e+01 1um5H 217 -17.20 -7.36 1.63e+01 1kekA 1231 -20.97 -7.30 1.71e+01 1dvfD 120 -15.56 -7.29 1.71e+01 1wlqC 201 -19.38 -7.29 1.72e+01 1vj7A 393 -19.54 -7.24 1.78e+01 1qgiA 259 -18.86 -7.22 1.81e+01 1ej8A 140 -15.97 -7.21 1.82e+01 1rcd 173 -23.70 -7.14 1.92e+01 1otkA 249 -22.31 -7.10 1.99e+01 1iu4A 331 -18.17 -7.09 1.99e+01 2abk 211 -19.04 -7.08 2.02e+01 1es2A 262 -17.24 -7.07 2.03e+01 1phk 298 -19.10 -7.07 2.03e+01 1qupA 222 -16.00 -7.06 2.05e+01 1fz1C 389 -22.43 -7.04 2.07e+01 1pda 315 -16.88 -7.04 2.08e+01 1dypA 271 -16.80 -7.03 2.08e+01 1ezfA 340 -20.55 -7.00 2.14e+01 1qqcA 773 -21.66 -6.99 2.15e+01 1humA 69 -15.43 -6.98 2.17e+01 1cdi 179 -17.91 -6.97 2.19e+01 1lqbC 162 -20.24 -6.93 2.25e+01 1go3E 187 -16.62 -6.91 2.28e+01 1mqkH 127 -15.30 -6.91 2.30e+01 1a6wH 120 -15.69 -6.86 2.37e+01 2ae6A 166 -16.73 -6.86 2.38e+01 1vixA 420 -19.09 -6.84 2.42e+01 2aqjA 538 -19.31 -6.83 2.43e+01 1tqgA 105 -20.82 -6.83 2.43e+01 1mmq 170 -18.56 -6.80 2.49e+01 1b2pA 119 -16.82 -6.77 2.54e+01 1gz2A 142 -16.63 -6.76 2.56e+01 2ar9A 278 -19.23 -6.76 2.57e+01 1fm2A 169 -22.60 -6.75 2.58e+01 2aq4A 434 -17.75 -6.67 2.74e+01 1q8yA 373 -20.28 -6.67 2.75e+01 1vhnA 318 -19.41 -6.63 2.82e+01 1xkrA 206 -17.28 -6.60 2.91e+01 1iknD 236 -17.83 -6.59 2.91e+01 1fuxA 166 -16.10 -6.58 2.94e+01 1cdy 178 -16.04 -6.58 2.94e+01 1t2jA 116 -15.51 -6.58 2.94e+01 1yx4A 132 -21.30 -6.55 3.02e+01 1yakA 263 -23.46 -6.54 3.03e+01 1w4xA 542 -20.35 -6.54 3.03e+01 1ir6A 424 -18.49 -6.52 3.08e+01 1i8tA 367 -19.71 -6.52 3.09e+01 1sq2N 113 -15.65 -6.51 3.10e+01 1jj2L 194 -17.72 -6.51 3.11e+01 1iapA 211 -19.10 -6.51 3.11e+01 2d2eA 250 -19.63 -6.49 3.14e+01 1dseA 292 -19.48 -6.48 3.17e+01 1xszA 356 -19.77 -6.48 3.17e+01 1ywzA 175 -20.20 -6.47 3.19e+01 1j05B 121 -15.30 -6.47 3.19e+01 1kmiZ 214 -19.69 -6.46 3.21e+01 8prkA 287 -17.68 -6.46 3.22e+01 1yqcA 170 -15.81 -6.46 3.23e+01 1q08A 99 -19.16 -6.43 3.30e+01 1jpnA 296 -19.30 -6.43 3.30e+01 1hs6A 611 -21.54 -6.42 3.33e+01 1pnsB 234 -19.67 -6.41 3.36e+01 1ng1 294 -19.40 -6.40 3.36e+01 1ls1A 295 -19.30 -6.40 3.38e+01 1ejbA 168 -16.64 -6.39 3.40e+01 1qrdA 273 -17.80 -6.37 3.45e+01 1rt8A 513 -21.74 -6.36 3.47e+01 1h0aA 158 -19.29 -6.34 3.54e+01 1wgjA 286 -17.37 -6.32 3.58e+01 1j5eB 256 -19.58 -6.31 3.62e+01 1keyA 235 -24.48 -6.29 3.66e+01 1es4A 262 -15.81 -6.25 3.79e+01 1ju2A 536 -17.88 -6.23 3.84e+01 1ordA 730 -18.21 -6.21 3.89e+01 1wj7A 104 -17.96 -6.21 3.91e+01 1wloA 136 -19.16 -6.20 3.93e+01