% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53 % (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-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. % --------------------------------------------------------------------- % alphafoo.1.YGR224W.t2k-100-30-alpha Host: farm11-10.kilokluster.ucsc.edu Fri Oct 6 07:38:02 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR224W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR224W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR224W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 614 nodes, 986.51 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(=1.7107) * Reverse)^tau(=0.8055))) % 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 1pw4A 451 -215.20 -166.40 7.31e-38 2gfpA 375 -173.03 -153.61 2.71e-35 1pv6A 417 -144.10 -107.04 1.51e-25 2cfqA 417 -134.85 -100.70 3.67e-24 1kplA 473 -52.56 -19.32 5.92e-04 2a65A 519 -54.79 -16.01 6.22e-03 1otsA 465 -54.87 -15.37 9.90e-03 1wpgA 994 -122.64 -14.04 2.64e-02 1qlaC 256 -46.19 -12.41 8.95e-02 1kpkA 473 -49.88 -12.10 1.14e-01 2bs3C 256 -46.98 -11.78 1.45e-01 1i4lA 224 -37.40 -11.07 2.51e-01 1c3wA 222 -33.58 -10.90 2.87e-01 1i4tB 224 -37.31 -10.72 3.30e-01 1i4dA 224 -36.59 -10.27 4.70e-01 1t9xA 1049 -65.76 -9.94 6.10e-01 2at9 247 -28.07 -9.85 6.54e-01 1i49A 224 -37.46 -9.78 6.95e-01 1kyoC 385 -36.34 -9.76 7.04e-01 2h8fB 146 -24.94 -9.60 7.99e-01 1o7xB 377 -50.33 -9.59 8.09e-01 1o7xC 377 -49.92 -9.41 9.34e-01 1qkrA 188 -34.05 -9.28 1.04e+00 1kb9C 385 -36.43 -9.19 1.11e+00 1m0kA 262 -35.19 -9.17 1.13e+00 2h79A 269 -40.36 -9.13 1.17e+00 1iwhB 146 -29.03 -9.04 1.26e+00 2gnxA 365 -33.59 -8.97 1.33e+00 1b5sA 242 -31.19 -8.81 1.52e+00 1o7xD 377 -49.34 -8.73 1.61e+00 2axtB 510 -46.52 -8.73 1.62e+00 1vgmA 378 -42.44 -8.64 1.73e+00 1h2sA 225 -39.34 -8.64 1.74e+00 2gifA 1057 -78.14 -8.62 1.77e+00 1kxpD 458 -77.30 -8.61 1.78e+00 2avpA 70 -25.11 -8.58 1.83e+00 1ezvC 385 -36.11 -8.57 1.85e+00 1iwgA 1053 -67.53 -8.51 1.94e+00 1myo 118 -24.38 -8.38 2.15e+00 1hx1B 114 -31.53 -8.36 2.19e+00 1nz6A 101 -23.57 -8.33 2.23e+00 2d5xB 146 -27.94 -8.29 2.31e+00 1zs3A 182 -34.08 -8.24 2.41e+00 1oyeA 1049 -65.81 -8.23 2.44e+00 2f6hX 419 -45.13 -8.14 2.62e+00 1h68A 239 -38.65 -8.10 2.70e+00 1kgbA 231 -33.70 -8.10 2.71e+00 1uetA 437 -75.19 -8.07 2.77e+00 1h4lD 147 -21.97 -8.04 2.84e+00 1s35A 214 -50.44 -8.01 2.91e+00 1xiuA 230 -32.59 -7.99 2.96e+00 1dm5A 315 -42.11 -7.99 2.98e+00 2c5kT 95 -34.42 -7.97 3.02e+00 1mznA 240 -31.65 -7.97 3.02e+00 1aeiA 315 -42.33 -7.96 3.04e+00 1aijM 307 -26.98 -7.92 3.15e+00 1paqA 189 -33.26 -7.88 3.25e+00 1wekA 217 -21.42 -7.84 3.35e+00 2j0wA 449 -26.35 -7.77 3.57e+00 1iomA 377 -40.11 -7.72 3.72e+00 1qzzA 374 -24.37 -7.68 3.83e+00 1j7yB 146 -25.18 -7.64 3.95e+00 1aijS 301 -26.56 -7.60 4.09e+00 1nw3A 416 -56.16 -7.57 4.19e+00 2gmyA 153 -24.48 -7.57 4.22e+00 1i3dA 146 -24.64 -7.56 4.26e+00 1u7gA 385 -40.45 -7.55 4.29e+00 1irdB 146 -25.71 -7.53 4.34e+00 1rxqA 178 -31.71 -7.51 4.42e+00 2fb5A 205 -24.29 -7.47 4.57e+00 2myo 118 -23.52 -7.46 4.61e+00 1mvcA 240 -29.32 -7.46 4.63e+00 1r89A 437 -74.71 -7.36 5.01e+00 1babB 146 -26.12 -7.36 5.02e+00 1a0p 290 -28.92 -7.35 5.05e+00 1n46A 258 -32.99 -7.33 5.16e+00 2fm9A 215 -31.58 -7.27 5.43e+00 1v96A 149 -25.64 -7.18 5.83e+00 1ls1A 295 -33.93 -7.17 5.90e+00 1ar1A 558 -48.74 -7.16 5.95e+00 1y01A 102 -24.19 -7.15 5.97e+00 1eztA 166 -33.05 -7.13 6.08e+00 1jb0L 154 -27.52 -7.13 6.09e+00 2ax3A 502 -53.51 -7.13 6.11e+00 1ibrB 462 -63.96 -7.09 6.31e+00 1yewB 247 -26.28 -7.08 6.35e+00 1rzhM 307 -26.27 -7.08 6.37e+00 1agrE 205 -36.06 -7.06 6.48e+00 1z8uA 102 -24.49 -7.02 6.69e+00 2csgA 424 -45.24 -6.97 6.97e+00 1rh5A 436 -33.27 -6.94 7.18e+00 1jli 112 -22.94 -6.93 7.19e+00 1bf5A 545 -78.14 -6.90 7.38e+00 2tct 207 -26.03 -6.90 7.43e+00 1fx8A 281 -38.10 -6.90 7.44e+00 2cwyA 94 -25.02 -6.88 7.53e+00 2ghcX 261 -34.54 -6.85 7.71e+00 1no1A 126 -23.13 -6.79 8.14e+00 1yeyA 444 -36.94 -6.78 8.19e+00 2c2aA 258 -42.79 -6.76 8.34e+00 2g9pA 26 -18.54 -6.74 8.47e+00 1g5yA 238 -29.28 -6.74 8.51e+00 1qq8A 214 -28.66 -6.72 8.61e+00 1agrH 205 -33.28 -6.72 8.62e+00 2iu1A 208 -45.68 -6.69 8.88e+00 1czaN 917 -117.59 -6.65 9.19e+00 1jgjA 217 -37.81 -6.64 9.22e+00 1rfzA 168 -32.14 -6.64 9.24e+00 3mag 307 -35.95 -6.64 9.28e+00 1j1jA 240 -35.66 -6.63 9.29e+00 2cwcA 303 -27.06 -6.63 9.35e+00 1dxtB 147 -25.31 -6.60 9.57e+00 1a01B 146 -24.86 -6.59 9.67e+00 1o57A 291 -24.42 -6.58 9.71e+00 1av6A 289 -34.87 -6.58 9.72e+00 2at2A 300 -42.26 -6.56 9.93e+00 1ykdA 398 -49.72 -6.54 1.00e+01 1ann 318 -46.84 -6.54 1.01e+01 1oafA 261 -34.21 -6.53 1.02e+01 1su4A 994 -113.61 -6.53 1.02e+01 1eulA 994 -113.23 -6.51 1.04e+01 1mla 309 -23.76 -6.51 1.04e+01 1o17A 345 -39.48 -6.49 1.05e+01 1nf1A 333 -27.14 -6.48 1.06e+01 1euvA 221 -39.82 -6.46 1.08e+01 1keyA 235 -37.03 -6.44 1.10e+01 3bct 457 -30.54 -6.43 1.11e+01 1hkcA 917 -118.42 -6.42 1.12e+01 1e1qG 272 -28.61 -6.39 1.15e+01 1hz4A 373 -37.70 -6.38 1.15e+01 1zn8A 180 -18.22 -6.38 1.16e+01 1pk5A 248 -36.15 -6.38 1.16e+01 1ffh 294 -33.58 -6.37 1.17e+01 2fupA 168 -27.82 -6.36 1.18e+01 1u19A 349 -40.27 -6.34 1.20e+01 1xjzA 233 -30.45 -6.29 1.26e+01 1bmfG 272 -27.56 -6.28 1.26e+01 1lfpA 249 -43.84 -6.28 1.26e+01 1ldfA 281 -36.86 -6.25 1.29e+01 1egpA 45 -16.90 -6.24 1.31e+01 2ng1 293 -35.13 -6.20 1.35e+01 1g2nA 264 -27.33 -6.20 1.35e+01 1wgzA 510 -59.92 -6.19 1.36e+01 1cseI 71 -17.51 -6.18 1.37e+01 1aii 323 -49.86 -6.18 1.37e+01 1v4xB 146 -23.89 -6.15 1.41e+01 1oglA 283 -38.65 -6.13 1.44e+01 1z57A 339 -51.11 -6.11 1.47e+01 1dgkN 917 -116.84 -6.10 1.48e+01 2azeA 155 -29.11 -6.10 1.48e+01 1jpnA 296 -34.99 -6.09 1.49e+01 1a00B 146 -24.57 -6.09 1.49e+01 1adt 356 -34.63 -6.09 1.50e+01 1avhA 320 -42.38 -6.08 1.50e+01 1bgc 174 -19.46 -6.08 1.50e+01 1ewaA 137 -23.84 -6.08 1.51e+01 1v74B 87 -21.94 -6.07 1.51e+01 1myt 146 -23.09 -6.05 1.54e+01 1qhiA 366 -23.56 -6.03 1.57e+01 1x42A 232 -43.48 -6.02 1.59e+01 1nbmG 272 -27.70 -6.01 1.59e+01 1g3jA 532 -36.13 -6.00 1.62e+01 2scpA 174 -27.71 -5.99 1.62e+01 1s5lB 510 -45.46 -5.99 1.62e+01 1a8rA 221 -24.80 -5.98 1.64e+01 1ng1 294 -34.68 -5.97 1.65e+01 1ew6A 137 -23.79 -5.95 1.68e+01 1y1uA 585 -73.45 -5.94 1.69e+01 1yucA 255 -33.03 -5.93 1.72e+01 1dkfA 233 -27.03 -5.91 1.75e+01 1a59 378 -38.26 -5.90 1.75e+01 1jdhA 529 -34.86 -5.90 1.75e+01 1c20A 128 -22.04 -5.87 1.81e+01 1anxA 319 -42.51 -5.86 1.81e+01 1axn 323 -49.63 -5.84 1.86e+01 1q1vA 70 -25.35 -5.83 1.87e+01 1jb0A 755 -35.75 -5.83 1.87e+01 174lA 164 -20.25 -5.83 1.88e+01 1th0A 226 -36.27 -5.81 1.90e+01 1i7wA 538 -35.20 -5.81 1.91e+01 1kqqA 139 -23.31 -5.80 1.91e+01 1n0qA 93 -17.61 -5.80 1.92e+01 1eijA 80 -21.19 -5.80 1.92e+01 1y82A 157 -23.74 -5.79 1.93e+01 1sdiA 213 -21.64 -5.79 1.94e+01 2i7aA 174 -19.58 -5.79 1.94e+01 2ga9A 297 -34.22 -5.79 1.94e+01 2azjA 289 -42.37 -5.77 1.96e+01 1i1gA 141 -25.45 -5.77 1.97e+01 2fbwC 141 -22.49 -5.77 1.97e+01 2bt2A 161 -26.00 -5.77 1.97e+01 1fp3A 402 -45.47 -5.77 1.97e+01 1to2I 64 -17.67 -5.75 2.00e+01 1my6A 199 -22.26 -5.74 2.02e+01 1wr2A 238 -38.57 -5.73 2.04e+01 2dfaA 250 -21.12 -5.71 2.07e+01 1n45A 233 -30.24 -5.71 2.08e+01 1a9cA 221 -24.66 -5.66 2.18e+01 1bccE 196 -29.35 -5.64 2.20e+01 1l7mA 211 -44.33 -5.64 2.21e+01 1foeA 377 -56.77 -5.63 2.22e+01 2gpyA 233 -24.30 -5.63 2.23e+01 1go4E 100 -26.60 -5.63 2.24e+01 1ew6B 137 -23.56 -5.62 2.24e+01 1f5sA 211 -44.54 -5.62 2.25e+01 1j97A 211 -44.54 -5.62 2.26e+01 1xgsA 295 -34.67 -5.59 2.32e+01 1cis 66 -19.34 -5.58 2.32e+01 1anv 356 -36.42 -5.57 2.35e+01 1x46A 150 -19.60 -5.56 2.37e+01 2b5aA 77 -20.59 -5.56 2.38e+01 1f93A 104 -19.45 -5.55 2.40e+01 1h3oB 76 -25.29 -5.54 2.42e+01 1z21A 112 -20.79 -5.54 2.42e+01 2dgzA 113 -22.26 -5.53 2.44e+01 1nsyA 271 -46.28 -5.52 2.46e+01 1aow 309 -45.98 -5.52 2.47e+01 1ithA 141 -18.44 -5.51 2.47e+01 1unlD 208 -20.95 -5.51 2.47e+01 1dquA 538 -67.19 -5.51 2.48e+01 1j55A 95 -20.98 -5.51 2.48e+01 1apxA 249 -33.46 -5.49 2.52e+01 1spgA 144 -23.37 -5.48 2.55e+01 1cxzB 86 -26.42 -5.47 2.57e+01 1pii 452 -42.17 -5.47 2.58e+01 1y74B 50 -20.00 -5.44 2.63e+01 1lw6I 64 -17.07 -5.44 2.64e+01 2f23A 156 -27.22 -5.44 2.64e+01 2avkA 136 -29.76 -5.42 2.69e+01 1qz4A 213 -21.47 -5.42 2.69e+01 1ala 321 -42.73 -5.40 2.74e+01 1h3fA 432 -47.59 -5.39 2.77e+01 1xe0A 114 -20.96 -5.37 2.81e+01 2h88C 140 -22.50 -5.36 2.84e+01 1zs4A 83 -19.52 -5.35 2.85e+01 1m5iA 125 -31.11 -5.35 2.87e+01 2hneA 436 -34.22 -5.35 2.87e+01 2ki5A 366 -22.96 -5.34 2.89e+01 2b2hA 399 -39.75 -5.34 2.90e+01 1lbd 282 -32.47 -5.33 2.91e+01 1hvd 319 -41.77 -5.33 2.91e+01 1v4xA 144 -22.81 -5.33 2.92e+01 1spgB 147 -23.44 -5.32 2.94e+01 1yiiA 320 -43.69 -5.32 2.94e+01 2d1sA 548 -57.11 -5.28 3.04e+01 1h7cA 108 -35.38 -5.28 3.05e+01 1x3zB 72 -16.22 -5.26 3.10e+01 1kimA 366 -23.32 -5.26 3.10e+01 1evhA 112 -17.50 -5.26 3.10e+01 1crl 534 -34.38 -5.25 3.13e+01 169lA 164 -20.71 -5.24 3.14e+01 2fd5A 180 -22.38 -5.24 3.16e+01 1x91A 153 -24.02 -5.24 3.16e+01 1hkbA 917 -118.01 -5.23 3.18e+01 2d1hA 109 -21.87 -5.23 3.19e+01 2bc4B 211 -21.61 -5.22 3.21e+01 1g3nC 257 -19.37 -5.21 3.25e+01 2fcwB 80 -24.58 -5.19 3.30e+01 1dkgB 197 -30.60 -5.18 3.32e+01 168lA 164 -20.93 -5.18 3.34e+01 2eulA 156 -26.93 -5.17 3.35e+01 1nfvA 179 -32.65 -5.16 3.38e+01 1z98A 281 -27.86 -5.16 3.39e+01 1aa7A 158 -20.81 -5.15 3.42e+01 1i5rA 327 -21.93 -5.15 3.43e+01 1glm 470 -31.84 -5.14 3.45e+01 1e2o 233 -26.93 -5.13 3.48e+01 1k87A 669 -54.08 -5.13 3.49e+01 1wjtA 103 -20.62 -5.12 3.52e+01 1vpt 348 -36.95 -5.12 3.53e+01 1ih8A 271 -46.01 -5.12 3.53e+01 1xwrA 97 -19.88 -5.09 3.62e+01 2cfuA 658 -54.41 -5.08 3.65e+01 1wyuA 438 -21.51 -5.08 3.66e+01 1jtvA 327 -22.15 -5.07 3.68e+01 1kinA 366 -22.46 -5.07 3.69e+01 2d7vA 162 -18.73 -5.06 3.72e+01 1shuX 182 -20.71 -5.01 3.87e+01 1coaI 64 -17.74 -5.01 3.88e+01 1lvmA 229 -24.37 -5.01 3.88e+01 1fdt 327 -21.38 -5.01 3.89e+01 1a32 88 -27.09 -5.00 3.91e+01 1ll2A 333 -28.28 -5.00 3.93e+01 1u0mA 382 -29.57 -4.99 3.94e+01 2d8dA 90 -27.91 -4.99 3.94e+01 1bxeA 113 -18.64 -4.99 3.94e+01 1v8gA 329 -19.76 -4.99 3.95e+01 1ucpA 91 -17.14 -4.99 3.95e+01 2bzpA 226 -37.96 -4.98 3.99e+01