% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR224W.t2k-100-40-40-str2+CB_burial_14_7 Host: farm11-10.kilokluster.ucsc.edu Fri Oct 6 09:19:43 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.str2s,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 0.400 File YGR224W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR224W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 614 nodes, 1508.37 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(=0.6091) * Reverse)^tau(=0.8556))) % 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 -295.99 -186.84 1.24e-21 2gfpA 375 -225.03 -150.54 2.01e-17 1pv6A 417 -195.84 -127.47 1.13e-14 2cfqA 417 -148.74 -96.62 7.09e-11 2a65A 519 -117.25 -34.00 1.72e-02 1otsA 465 -122.46 -31.79 3.63e-02 1kpkA 473 -112.41 -30.58 5.48e-02 1wpgA 994 -155.18 -27.30 1.70e-01 1sesA 421 -68.92 -25.10 3.65e-01 1o7xC 377 -83.47 -25.02 3.76e-01 1o7xD 377 -78.65 -24.90 3.92e-01 1a59 378 -76.45 -24.78 4.09e-01 1o7xB 377 -79.41 -24.72 4.18e-01 1wa5B 530 -90.57 -24.67 4.25e-01 1eulA 994 -146.70 -23.64 6.11e-01 1hkbA 917 -142.96 -23.59 6.22e-01 1t9xA 1049 -100.58 -23.42 6.62e-01 1o0wA 252 -66.27 -23.11 7.38e-01 1wgzA 510 -77.81 -22.58 8.91e-01 1vgmA 378 -78.56 -22.32 9.79e-01 1uzeA 589 -88.87 -22.26 1.00e+00 1o86A 589 -90.21 -22.20 1.02e+00 1dgkN 917 -138.74 -22.02 1.09e+00 1y1uA 585 -92.73 -21.82 1.17e+00 1czaN 917 -140.31 -21.56 1.28e+00 1sly 618 -80.22 -21.35 1.39e+00 1hkcA 917 -140.31 -21.24 1.44e+00 1jpnA 296 -50.53 -21.09 1.52e+00 1qsaA 618 -80.26 -21.02 1.56e+00 1qhaA 917 -140.73 -20.92 1.62e+00 2ng1 293 -50.54 -20.92 1.62e+00 1gqeA 365 -85.41 -20.41 1.94e+00 1be3C 379 -71.41 -19.88 2.36e+00 2ac4A 309 -68.16 -19.67 2.54e+00 1fa0B 537 -85.20 -19.60 2.62e+00 1fa0A 537 -89.07 -19.60 2.62e+00 1ruxA 951 -110.97 -19.41 2.80e+00 1su4A 994 -145.86 -19.40 2.81e+00 1f76A 336 -54.05 -19.39 2.82e+00 2ajfA 597 -94.36 -19.32 2.89e+00 1p30A 952 -111.29 -19.14 3.09e+00 1p2zA 968 -105.75 -19.12 3.11e+00 2ac2A 309 -68.29 -19.05 3.19e+00 1ak1 310 -68.55 -19.02 3.22e+00 1ka2A 499 -91.81 -18.98 3.28e+00 1dozA 309 -67.93 -18.76 3.55e+00 1jb0A 755 -83.22 -18.65 3.70e+00 1u7gA 385 -88.08 -18.64 3.71e+00 3vtk 343 -42.31 -18.42 4.02e+00 1ls1A 295 -46.82 -18.40 4.05e+00 1ffh 294 -47.31 -18.24 4.29e+00 1k3pA 426 -78.59 -18.13 4.47e+00 1jmoA 480 -74.89 -18.07 4.57e+00 1ng1 294 -47.72 -18.05 4.61e+00 1mroA 548 -81.73 -18.03 4.64e+00 2gnxA 365 -50.11 -18.03 4.65e+00 1up8A 598 -82.03 -17.83 4.99e+00 1qhbA 596 -72.01 -17.80 5.06e+00 2f2bA 246 -59.07 -17.71 5.22e+00 2c2aA 258 -68.18 -17.71 5.23e+00 1vqrA 297 -67.54 -17.70 5.25e+00 1uetA 437 -84.52 -17.63 5.39e+00 1hbnA 549 -81.15 -17.61 5.41e+00 1h38C 883 -113.14 -17.61 5.43e+00 1ibrB 462 -91.80 -17.57 5.50e+00 1h38D 883 -112.88 -17.53 5.59e+00 1qazA 351 -71.01 -17.49 5.67e+00 1ubkL 534 -70.81 -17.40 5.86e+00 1jqnA 883 -120.64 -17.31 6.07e+00 1h2rL 534 -70.02 -17.25 6.20e+00 1txuA 273 -74.48 -17.19 6.33e+00 1r89A 437 -84.28 -17.11 6.53e+00 1h38B 883 -112.49 -16.92 7.01e+00 1wuiL 534 -70.34 -16.77 7.41e+00 1hw8A 467 -54.90 -16.75 7.45e+00 1fkmA 396 -77.94 -16.38 8.55e+00 1qcrC 378 -55.50 -16.38 8.56e+00 1u0jA 267 -48.92 -16.37 8.60e+00 2h4vA 320 -56.13 -16.30 8.82e+00 1is2A 661 -100.08 -16.28 8.90e+00 1gkmA 509 -65.29 -16.26 8.96e+00 2csgA 424 -56.58 -16.23 9.05e+00 1qb4A 883 -119.93 -16.19 9.21e+00 1larA 575 -77.88 -16.13 9.41e+00 1fiy 883 -120.07 -16.11 9.46e+00 1iomA 377 -76.70 -16.08 9.56e+00 1owcA 427 -77.70 -16.01 9.82e+00 1ar1B 298 -60.66 -16.01 9.84e+00 1w98B 283 -54.25 -15.86 1.04e+01 1jk0A 419 -89.63 -15.77 1.07e+01 1dqaA 467 -50.80 -15.71 1.10e+01 2gakA 391 -63.41 -15.66 1.12e+01 1k89 449 -64.25 -15.64 1.13e+01 1hrdA 449 -65.75 -15.51 1.19e+01 2b2hA 399 -85.94 -15.45 1.21e+01 1l5wA 796 -113.04 -15.29 1.29e+01 2cm2A 304 -59.97 -15.13 1.37e+01 2g9mA 133 -40.68 -15.01 1.44e+01 1s35A 214 -72.56 -14.99 1.45e+01 1keyA 235 -64.16 -14.83 1.54e+01 1d8iA 311 -61.24 -14.81 1.54e+01 1j1jA 240 -65.40 -14.76 1.58e+01 1b8fA 509 -63.15 -14.75 1.58e+01 1d8hA 311 -60.65 -14.70 1.61e+01 1dqaC 467 -49.26 -14.70 1.61e+01 1zb1A 392 -77.10 -14.65 1.64e+01 1fs0G 230 -43.27 -14.63 1.65e+01 1rqjA 299 -60.34 -14.60 1.67e+01 2h8oA 335 -64.64 -14.59 1.68e+01 1bgc 174 -38.03 -14.59 1.68e+01 1bgvA 449 -64.37 -14.59 1.68e+01 1h2aL 567 -69.02 -14.55 1.70e+01 2bynA 227 -39.27 -14.55 1.71e+01 1kinA 366 -38.17 -14.52 1.72e+01 2a84A 300 -31.13 -14.46 1.76e+01 1y82A 157 -40.31 -14.44 1.78e+01 1e1oA 504 -74.19 -14.44 1.78e+01 1k7yA 577 -87.44 -14.43 1.79e+01 1kb9C 385 -59.84 -14.41 1.80e+01 1a5y 330 -57.31 -14.35 1.84e+01 2bcjB 340 -43.86 -14.34 1.84e+01 1rzrA 332 -52.35 -14.33 1.85e+01 1j8mF 297 -51.40 -14.33 1.86e+01 1pa1A 310 -61.84 -14.30 1.87e+01 1ig8A 486 -78.12 -14.23 1.93e+01 1j8yF 297 -50.92 -14.21 1.94e+01 1ouvA 273 -64.99 -14.20 1.95e+01 1ap8 213 -52.50 -14.17 1.97e+01 1b5sA 242 -46.19 -14.10 2.03e+01 1gotB 340 -43.37 -14.10 2.03e+01 1hm6A 346 -71.49 -14.09 2.03e+01 1pii 452 -51.16 -14.06 2.05e+01 1s9uA 207 -44.89 -13.97 2.12e+01 2gdnA 267 -37.68 -13.97 2.13e+01 1ezvC 385 -59.32 -13.97 2.13e+01 1rj9A 304 -47.77 -13.96 2.14e+01 1cii 602 -118.80 -13.96 2.14e+01 1lkvX 232 -59.77 -13.96 2.14e+01 1m5yA 408 -62.57 -13.93 2.16e+01 1rp4A 389 -84.18 -13.89 2.20e+01 1esxA 96 -65.44 -13.88 2.20e+01 1nf1A 333 -40.52 -13.88 2.20e+01 1iwgA 1053 -122.16 -13.85 2.22e+01 1tbgA 340 -43.01 -13.85 2.23e+01 2azqA 311 -54.17 -13.83 2.25e+01 1bu2A 229 -44.21 -13.80 2.27e+01 2j4oA 401 -52.57 -13.72 2.34e+01 1kimA 366 -37.36 -13.69 2.37e+01 1hx1B 114 -52.98 -13.64 2.42e+01 1g7fA 298 -58.58 -13.61 2.44e+01 1a0rB 340 -42.93 -13.58 2.47e+01 2dpmA 284 -50.61 -13.58 2.47e+01 1ahpA 797 -108.27 -13.57 2.48e+01 1i21A 159 -33.81 -13.55 2.49e+01 3crxA 343 -59.18 -13.52 2.52e+01 1oq9A 363 -75.78 -13.52 2.53e+01 1wkbA 810 -148.94 -13.51 2.54e+01 1yqyA 523 -112.45 -13.50 2.55e+01 1oheA 348 -52.62 -13.50 2.55e+01 1cqxA 403 -54.34 -13.49 2.55e+01 2f71A 298 -58.40 -13.45 2.60e+01 169lA 164 -37.98 -13.43 2.61e+01 1fc4A 401 -46.93 -13.43 2.62e+01 1ciy 590 -47.96 -13.43 2.62e+01 2fh7A 595 -80.02 -13.37 2.68e+01 2bvaA 292 -43.77 -13.36 2.69e+01 1buyA 166 -41.57 -13.35 2.70e+01 1qkrA 188 -47.69 -13.33 2.72e+01 1v96A 149 -39.55 -13.30 2.75e+01 2d5xB 146 -44.10 -13.26 2.79e+01 1gxyA 226 -44.84 -13.26 2.79e+01 1wloA 136 -32.68 -13.24 2.82e+01 2ax3A 502 -67.12 -13.20 2.86e+01 1b04A 318 -51.82 -13.18 2.88e+01 1k7hA 476 -79.02 -13.11 2.95e+01 2hnp 321 -55.58 -13.09 2.98e+01 1mmoG 162 -47.89 -13.07 3.00e+01 1zs9A 261 -44.86 -13.06 3.01e+01 1mkmA 249 -54.67 -13.06 3.02e+01 2db0A 253 -57.30 -13.04 3.04e+01 2ghcX 261 -43.38 -13.04 3.04e+01 1h7cA 108 -59.59 -13.03 3.05e+01 1b33B 161 -36.71 -13.03 3.05e+01 1j33A 335 -31.45 -13.03 3.05e+01 1y9iA 178 -39.35 -13.03 3.05e+01 1bgeA 175 -35.78 -13.01 3.08e+01 1b3qA 379 -64.13 -12.99 3.10e+01 2d7vA 162 -35.96 -12.98 3.11e+01 1b8dA 164 -41.17 -12.98 3.12e+01 1i1dA 161 -33.44 -12.95 3.15e+01 1a8i 842 -118.86 -12.92 3.18e+01 1q79A 514 -70.10 -12.91 3.20e+01 1qhiA 366 -36.39 -12.87 3.25e+01 1iwhB 146 -42.93 -12.86 3.25e+01 1jjyA 636 -63.75 -12.86 3.26e+01 1v54E 109 -40.51 -12.83 3.30e+01 1i12A 160 -33.30 -12.81 3.33e+01 1lylA 504 -73.45 -12.80 3.34e+01 1oyeA 1049 -111.47 -12.79 3.35e+01 1reqD 637 -83.31 -12.73 3.42e+01 1f5aA 513 -66.96 -12.72 3.44e+01 1r5jA 337 -49.41 -12.71 3.45e+01 5eat 548 -77.07 -12.71 3.46e+01 1xo0A 324 -56.64 -12.70 3.47e+01 1wetA 340 -43.05 -12.69 3.48e+01 2bzlA 325 -51.20 -12.68 3.49e+01 1wyuB 474 -79.16 -12.68 3.50e+01 1lfpA 249 -52.71 -12.61 3.59e+01 1px5A 349 -56.40 -12.60 3.60e+01 1bf5A 545 -88.18 -12.56 3.65e+01 1mtyG 162 -47.67 -12.53 3.70e+01 1wchA 315 -50.53 -12.53 3.70e+01 1a53 247 -43.26 -12.53 3.71e+01 1vpwA 340 -42.90 -12.50 3.74e+01 1bd3A 243 -37.64 -12.50 3.75e+01 1oafA 261 -42.71 -12.49 3.76e+01 2cchB 260 -57.40 -12.48 3.77e+01 177l 164 -37.65 -12.47 3.78e+01 1tbfA 347 -63.62 -12.46 3.80e+01 2ki5A 366 -36.39 -12.46 3.80e+01 2j0wA 449 -35.96 -12.45 3.81e+01 1nv8A 284 -43.85 -12.44 3.83e+01 2azjA 289 -74.59 -12.41 3.87e+01 1m1cA 680 -65.58 -12.41 3.88e+01 1qpzA 340 -43.07 -12.40 3.89e+01 1bs2A 607 -104.63 -12.39 3.91e+01 1jftA 340 -43.38 -12.38 3.93e+01