% 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.YGR017W.t2k-100-30-alpha Host: farm03-10.kilokluster.ucsc.edu Fri Oct 6 04:27:32 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR017W % --------------------------------------------------------------------- % 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 YGR017W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR017W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 298 nodes, 456.61 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(=2.8084) * Reverse)^tau(=0.7191))) % 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 2i51A 195 -234.73 -223.74 2.43e-41 1t9mA 214 -72.84 -63.02 1.22e-14 1ty9A 222 -64.27 -54.60 7.01e-13 1nrgA 261 -52.62 -40.98 7.34e-10 1dnlA 199 -47.89 -36.39 8.80e-09 1g79A 218 -47.47 -36.09 1.03e-08 2a2jA 246 -38.82 -28.42 8.21e-07 1ci0A 228 -36.82 -25.69 4.20e-06 2i02A 148 -24.75 -15.08 4.18e-03 1rfeA 162 -24.55 -14.27 7.43e-03 2aq6A 147 -21.26 -11.70 4.90e-02 1d8hA 311 -19.72 -9.81 2.14e-01 1d8iA 311 -18.52 -8.88 4.49e-01 1ursA 402 -19.06 -8.49 6.20e-01 1e1hA 287 -18.89 -8.28 7.42e-01 1egxA 115 -17.58 -8.27 7.48e-01 1a2vA 655 -18.58 -8.20 7.91e-01 2fhqA 141 -18.65 -8.19 7.97e-01 2dafA 118 -17.52 -8.16 8.18e-01 1waaA 93 -18.24 -8.12 8.49e-01 1ywnA 316 -17.59 -8.11 8.54e-01 2thiA 379 -18.18 -7.98 9.54e-01 3thiA 371 -17.73 -7.94 9.88e-01 1wgzA 510 -18.08 -7.84 1.07e+00 1w9aA 147 -17.22 -7.70 1.20e+00 2asfA 137 -17.13 -7.69 1.21e+00 2hhzA 150 -16.77 -7.61 1.30e+00 1ag9A 175 -18.33 -7.43 1.51e+00 1hocA 272 -17.58 -7.39 1.57e+00 2fg9A 178 -16.74 -7.28 1.72e+00 1tit 98 -17.70 -7.26 1.75e+00 1vkxA 273 -17.61 -7.20 1.85e+00 1xxoA 147 -16.67 -7.20 1.86e+00 1l1eA 287 -18.05 -7.17 1.91e+00 2iutA 574 -18.72 -7.06 2.09e+00 2bcjB 340 -17.12 -7.02 2.16e+00 1tbgA 340 -17.01 -6.98 2.24e+00 2b5lC 222 -16.89 -6.82 2.59e+00 1gotB 340 -16.86 -6.81 2.62e+00 2ew2A 316 -16.58 -6.57 3.21e+00 1ew3A 159 -17.44 -6.55 3.27e+00 1dbgA 506 -17.40 -6.54 3.31e+00 1l7dA 384 -15.95 -6.51 3.39e+00 1iknA 286 -17.11 -6.51 3.40e+00 1dboA 506 -17.38 -6.50 3.42e+00 2hq9A 149 -16.05 -6.48 3.50e+00 1f8gA 384 -15.51 -6.42 3.70e+00 2i3dA 249 -16.36 -6.38 3.82e+00 1a0rB 340 -16.48 -6.29 4.15e+00 1hfuA 503 -17.51 -6.26 4.25e+00 1vjoA 393 -15.79 -6.25 4.30e+00 1esfA 233 -16.33 -6.25 4.31e+00 1o65A 246 -16.14 -6.24 4.33e+00 1ra0A 430 -16.13 -6.17 4.63e+00 1tmcA 175 -15.46 -6.12 4.81e+00 1apa 266 -15.91 -6.10 4.94e+00 1k6wA 426 -15.94 -6.09 4.95e+00 1t46A 313 -16.30 -6.08 5.01e+00 2hq7A 146 -16.17 -6.07 5.05e+00 1dyqA 234 -16.04 -6.06 5.09e+00 1rfa 79 -14.58 -6.03 5.26e+00 1duzA 275 -15.77 -5.97 5.53e+00 1j8uA 325 -15.80 -5.97 5.55e+00 1sesA 421 -15.53 -5.91 5.86e+00 1gpb 842 -16.02 -5.91 5.87e+00 2hmhA 152 -15.09 -5.90 5.93e+00 1eyzA 392 -15.79 -5.89 5.95e+00 1larA 575 -16.18 -5.88 6.00e+00 2b25A 336 -16.63 -5.84 6.22e+00 1y7bA 542 -16.08 -5.81 6.41e+00 1a65A 504 -17.06 -5.80 6.45e+00 1tiu 98 -16.47 -5.80 6.47e+00 2mtaC 147 -15.90 -5.79 6.56e+00 1wzlA 585 -17.39 -5.78 6.61e+00 2cnqA 306 -17.64 -5.76 6.74e+00 1qbhA 101 -16.29 -5.75 6.76e+00 1toh 343 -15.14 -5.73 6.90e+00 1jbwA 428 -15.87 -5.69 7.15e+00 1i4fA 275 -15.74 -5.69 7.15e+00 2htdA 140 -14.99 -5.67 7.33e+00 1oflA 481 -16.44 -5.65 7.43e+00 1o59A 355 -16.46 -5.64 7.53e+00 1jalA 363 -14.99 -5.55 8.18e+00 2av1A 275 -15.31 -5.51 8.45e+00 1kv9A 668 -15.40 -5.49 8.66e+00 1anf 370 -15.81 -5.46 8.89e+00 1b9kA 238 -15.38 -5.41 9.30e+00 1cto 109 -15.09 -5.39 9.47e+00 1k5nA 276 -15.42 -5.38 9.55e+00 1ji2A 585 -17.09 -5.38 9.58e+00 1bvzA 585 -16.76 -5.38 9.59e+00 1bk0 331 -15.29 -5.38 9.59e+00 1am2 199 -15.40 -5.37 9.63e+00 1iwmA 186 -15.69 -5.37 9.64e+00 1odmA 331 -15.25 -5.35 9.83e+00 1fneA 192 -15.79 -5.35 9.84e+00 1agdA 276 -15.29 -5.33 1.01e+01 1zkoA 136 -14.76 -5.31 1.02e+01 1x1fA 149 -15.32 -5.30 1.03e+01 1uv7A 110 -16.57 -5.30 1.04e+01 1gcf 109 -15.74 -5.29 1.04e+01 1omp 370 -15.67 -5.29 1.04e+01 1u07A 90 -14.35 -5.29 1.04e+01 2av7A 275 -15.05 -5.28 1.05e+01 1fr2B 134 -15.93 -5.27 1.06e+01 1fgs 428 -15.45 -5.27 1.06e+01 1mpb 370 -15.82 -5.27 1.06e+01 1xh3A 276 -15.24 -5.27 1.06e+01 1ur1A 378 -14.78 -5.24 1.09e+01 2fujA 137 -14.79 -5.22 1.12e+01 1fngA 192 -15.60 -5.22 1.12e+01 1ez1A 392 -15.08 -5.20 1.14e+01 1a48 306 -17.31 -5.19 1.14e+01 1gcoA 261 -15.37 -5.18 1.16e+01 1zc1A 208 -14.86 -5.17 1.17e+01 1c1yB 77 -13.78 -5.16 1.18e+01 1c8kA 842 -15.28 -5.15 1.19e+01 1yifA 533 -15.79 -5.14 1.20e+01 1hmcA 148 -14.12 -5.14 1.20e+01 1gikA 261 -15.51 -5.13 1.21e+01 1pex 207 -16.93 -5.13 1.22e+01 1guaB 81 -13.73 -5.11 1.24e+01 2gj8A 172 -14.43 -5.09 1.26e+01 1kopA 223 -14.72 -5.06 1.29e+01 1geeA 261 -15.19 -5.04 1.32e+01 1jffB 445 -15.65 -5.03 1.34e+01 1q67A 231 -19.02 -5.02 1.34e+01 1a9eA 277 -15.03 -5.02 1.35e+01 1obdA 306 -17.27 -5.02 1.35e+01 1z02A 446 -15.59 -5.01 1.36e+01 1qtsA 247 -15.00 -5.01 1.36e+01 2hd5A 359 -14.79 -4.99 1.39e+01 1kyfA 247 -14.95 -4.97 1.42e+01 1kjqA 391 -14.86 -4.96 1.43e+01 1o5uA 101 -14.27 -4.95 1.45e+01 1jixA 351 -14.87 -4.93 1.47e+01 1b76A 442 -15.77 -4.93 1.47e+01 2bvpA 276 -14.98 -4.93 1.48e+01 2f6eA 127 -15.25 -4.92 1.48e+01 1bxiB 134 -15.14 -4.91 1.49e+01 7ahlA 293 -14.92 -4.90 1.52e+01 1ae3 86 -14.78 -4.89 1.53e+01 1sqnA 261 -13.89 -4.87 1.56e+01 1qawF 74 -15.09 -4.87 1.56e+01 1q7zA 566 -14.61 -4.85 1.58e+01 2freA 200 -15.47 -4.85 1.59e+01 1h5uA 842 -14.93 -4.85 1.59e+01 1xhnA 184 -14.67 -4.84 1.60e+01 4mbp 370 -15.12 -4.84 1.60e+01 4pah 308 -14.55 -4.83 1.62e+01 1a1nA 276 -14.81 -4.82 1.63e+01 1gweA 503 -14.57 -4.82 1.63e+01 1hbzA 498 -14.58 -4.82 1.63e+01 1cd9B 215 -15.61 -4.82 1.64e+01 1zm8A 259 -15.03 -4.80 1.66e+01 2cr4A 126 -14.43 -4.79 1.68e+01 1sr7A 259 -13.81 -4.79 1.69e+01 1abbA 828 -14.91 -4.79 1.69e+01 1g5yA 238 -13.94 -4.78 1.71e+01 1a1mA 278 -14.68 -4.77 1.72e+01 1u69A 163 -14.81 -4.75 1.75e+01 1emvB 134 -15.02 -4.74 1.76e+01 1iugA 352 -13.83 -4.74 1.77e+01 1gw0A 559 -15.64 -4.74 1.77e+01 2dnjA 260 -14.46 -4.74 1.77e+01 2hzgA 401 -14.13 -4.73 1.79e+01 1azo 232 -15.25 -4.71 1.81e+01 2apoA 357 -14.98 -4.68 1.88e+01 2ag5A 246 -13.67 -4.68 1.88e+01 1vqb 87 -14.69 -4.67 1.89e+01 1vpkA 378 -14.91 -4.67 1.89e+01 1z94A 147 -14.28 -4.66 1.90e+01 1dxsA 80 -13.37 -4.65 1.93e+01 2prd 174 -15.19 -4.64 1.95e+01 1b8bA 605 -14.44 -4.63 1.97e+01 1ef8A 261 -13.84 -4.62 1.98e+01 1f6bA 198 -14.11 -4.61 2.00e+01 1vhh 162 -14.41 -4.61 2.01e+01 1ste 239 -14.21 -4.61 2.01e+01 1mh3A 421 -14.55 -4.59 2.05e+01 1mxiA 160 -13.78 -4.58 2.06e+01 1qydA 313 -14.19 -4.58 2.06e+01 1wkoA 180 -15.50 -4.58 2.07e+01 1fviA 297 -14.91 -4.58 2.07e+01 1g6q2 328 -15.59 -4.58 2.07e+01 1gvp 87 -14.59 -4.57 2.08e+01 1jh6A 189 -13.55 -4.57 2.09e+01 1jg7A 351 -14.50 -4.56 2.10e+01 1a1oA 276 -14.53 -4.56 2.11e+01 1pah 308 -14.32 -4.56 2.11e+01 1zbqA 327 -14.15 -4.54 2.14e+01 2gzqA 200 -14.63 -4.54 2.15e+01 3dni 260 -14.26 -4.54 2.15e+01 2cglA 489 -14.00 -4.52 2.19e+01 1mznA 240 -13.80 -4.50 2.22e+01 1gcb 454 -14.16 -4.50 2.23e+01 1k07A 263 -14.16 -4.49 2.25e+01 1fsiA 189 -13.50 -4.49 2.25e+01 1vjpA 394 -14.35 -4.49 2.26e+01 2tgf 50 -13.36 -4.48 2.28e+01 1oj5A 132 -13.70 -4.48 2.28e+01 2b3hA 329 -14.47 -4.48 2.28e+01 1nhkL 144 -13.53 -4.48 2.28e+01 2b30A 301 -13.97 -4.48 2.29e+01 3caoA 103 -13.48 -4.47 2.30e+01 1hmcB 148 -13.45 -4.46 2.32e+01 3gcb 470 -14.09 -4.45 2.35e+01 1ia9A 280 -14.55 -4.45 2.35e+01 1uebA 184 -14.22 -4.45 2.36e+01 1moxC 50 -13.35 -4.44 2.37e+01 2fg1A 158 -13.64 -4.43 2.40e+01 1znbA 232 -13.87 -4.43 2.40e+01 1muhA 481 -14.58 -4.42 2.42e+01 1zdnA 158 -14.13 -4.39 2.48e+01 1kyqA 274 -14.30 -4.39 2.49e+01 1mvcA 240 -13.81 -4.39 2.49e+01 2acoA 173 -13.70 -4.39 2.50e+01 1hsbA 270 -14.55 -4.38 2.51e+01 1ytvA 366 -14.62 -4.38 2.53e+01 1lqtA 456 -15.32 -4.37 2.54e+01 2a40B 260 -14.29 -4.35 2.60e+01 1rr7A 129 -13.62 -4.34 2.63e+01 1dmwA 307 -14.12 -4.32 2.66e+01 1j1qA 261 -14.73 -4.32 2.66e+01 1nlbH 218 -14.37 -4.31 2.69e+01 1bak 119 -16.52 -4.31 2.71e+01 1msk 331 -13.97 -4.30 2.72e+01 2fh7A 595 -14.92 -4.30 2.72e+01 1pc6A 146 -13.75 -4.29 2.74e+01 1ck7A 631 -14.83 -4.29 2.75e+01 1a7lA 389 -14.97 -4.29 2.76e+01 2bydA 323 -14.65 -4.29 2.76e+01 1vkdA 338 -15.93 -4.28 2.79e+01 1ieaA 192 -14.62 -4.26 2.84e+01 1zmoA 244 -13.26 -4.25 2.86e+01 1sz7A 200 -13.77 -4.25 2.87e+01 1cznA 169 -14.54 -4.24 2.88e+01 1j0aA 325 -14.36 -4.24 2.88e+01 1k32A 1045 -15.30 -4.24 2.89e+01 1bxkA 355 -14.72 -4.24 2.90e+01 1omrA 201 -13.72 -4.24 2.91e+01 1ofv 169 -14.62 -4.23 2.92e+01 1mg2D 155 -14.14 -4.21 2.98e+01 1b57A 358 -13.89 -4.20 3.01e+01 1ihrA 76 -13.26 -4.20 3.02e+01 1n6eA 1071 -15.34 -4.20 3.02e+01 1jlnA 297 -13.63 -4.20 3.03e+01 1htrB 329 -13.72 -4.19 3.03e+01 1k7iA 479 -14.91 -4.17 3.11e+01 1dosA 358 -14.16 -4.17 3.11e+01 2htiA 185 -14.45 -4.16 3.14e+01 1rec 201 -13.52 -4.16 3.14e+01 2extA 77 -14.46 -4.16 3.14e+01 1oyeA 1049 -14.03 -4.15 3.15e+01 1fmcA 255 -13.34 -4.15 3.16e+01 2d3jA 157 -14.38 -4.15 3.19e+01 1mlwA 301 -13.44 -4.14 3.21e+01 1laxA 370 -14.38 -4.13 3.24e+01 1uscA 178 -15.80 -4.12 3.27e+01 1m4uA 206 -14.43 -4.12 3.27e+01 1a28A 256 -13.11 -4.11 3.28e+01 1ecfA 504 -14.10 -4.11 3.29e+01 1f3iA 481 -14.30 -4.11 3.29e+01 1bhgA 613 -14.81 -4.10 3.32e+01 1qk4A 233 -14.11 -4.09 3.36e+01 1nxcA 478 -13.66 -4.09 3.37e+01 1lrwA 600 -14.61 -4.09 3.38e+01 2fgtA 417 -14.54 -4.08 3.40e+01 1y8oA 419 -13.62 -4.08 3.40e+01 1mz5A 638 -14.99 -4.08 3.41e+01 1dkfA 233 -13.50 -4.07 3.44e+01 1atnD 260 -13.83 -4.07 3.45e+01 2gvaA 87 -14.22 -4.06 3.46e+01 1dquA 538 -13.93 -4.06 3.46e+01 1qwdA 177 -13.35 -4.06 3.47e+01 1a6r 471 -13.73 -4.06 3.48e+01 1koqA 253 -14.78 -4.06 3.48e+01 1yruA 364 -13.55 -4.05 3.50e+01 1l3kA 196 -13.36 -4.05 3.50e+01 2ganA 190 -13.93 -4.05 3.52e+01 1e5uI 187 -13.20 -4.04 3.54e+01 1yarH 217 -12.87 -4.03 3.58e+01 1z47A 355 -13.34 -4.03 3.59e+01 1aqdA 192 -14.84 -4.03 3.60e+01 1hx0A 496 -14.14 -4.02 3.62e+01 2b81A 323 -14.61 -4.01 3.64e+01 2gp5A 349 -14.15 -4.01 3.66e+01 1co4A 42 -12.47 -4.01 3.67e+01 1zthA 258 -13.61 -4.00 3.69e+01 2gn5 87 -13.78 -3.99 3.72e+01 1ha1 184 -13.15 -3.98 3.76e+01 1jj2R 84 -12.84 -3.98 3.76e+01 1umkA 275 -15.19 -3.98 3.76e+01 1zotA 358 -13.54 -3.97 3.80e+01 1s72S 85 -12.83 -3.97 3.80e+01 1kyaA 499 -14.79 -3.97 3.82e+01 1ox8A 107 -12.88 -3.97 3.82e+01 2izpA 303 -13.53 -3.96 3.83e+01 1bx7 55 -12.47 -3.96 3.85e+01 1yuf 50 -13.38 -3.96 3.85e+01 1yfnA 118 -12.81 -3.95 3.87e+01 2fb7A 95 -13.56 -3.95 3.88e+01 1fnnA 389 -13.74 -3.95 3.88e+01 1kk6A 209 -14.57 -3.95 3.89e+01 1a7tA 232 -13.23 -3.93 3.97e+01 1ezoA 370 -14.33 -3.92 3.99e+01