% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR218W.t2k-100-30-dssp-ehl2 Host: farm16 Mon Jan 31 01:48:26 2005 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR218W % --------------------------------------------------------------------- % 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 YGR218W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR218W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 11262 sequences, 2668995 residues, 1085 nodes, 1291.63 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 (0.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.7938) * Reverse)^tau(=0.7276))) % Calculated when Simple < simple_threshold (0.00) % 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 1qbkB 890 -523.64 -444.86 7.70e-53 1wa5C 960 -373.74 -285.77 2.22e-37 1w9cA 321 -297.47 -250.21 1.25e-33 1qgrA 876 -232.13 -134.06 3.81e-20 1ibrB 462 -166.27 -107.73 1.07e-16 1gw5B 591 -105.14 -39.93 2.10e-06 1b3uA 588 -98.94 -36.96 7.14e-06 1ee4A 423 -77.25 -31.94 6.02e-05 1bk6A 422 -74.84 -28.99 2.20e-04 1bk5A 422 -76.70 -28.26 3.05e-04 1wa5B 530 -75.23 -27.81 3.73e-04 1fiy 883 -79.07 -22.21 5.00e-03 1qb4A 883 -77.06 -20.47 1.16e-02 1jqnA 883 -75.76 -19.90 1.54e-02 1avc 673 -81.90 -19.72 1.68e-02 1gw5A 621 -91.42 -18.91 2.51e-02 1w07A 659 -63.58 -18.36 3.31e-02 1ao6A 585 -77.37 -18.27 3.46e-02 1bj5 585 -77.04 -18.22 3.55e-02 1ha2A 585 -75.94 -18.13 3.72e-02 1kxpD 458 -65.37 -17.80 4.39e-02 1jdhA 529 -74.69 -17.52 5.06e-02 1e7aA 585 -77.60 -17.50 5.13e-02 1n5uA 585 -77.02 -17.34 5.56e-02 1i7wA 538 -73.15 -17.15 6.13e-02 1g3jA 532 -72.94 -16.29 9.53e-02 1ehkA 562 -59.71 -16.09 1.06e-01 1j78A 458 -57.13 -15.13 1.75e-01 1ldjA 760 -66.42 -14.88 2.01e-01 2btvA 901 -44.20 -14.62 2.31e-01 1miwA 404 -37.29 -14.50 2.46e-01 1jk0B 345 -44.80 -14.12 3.02e-01 1jb0A 755 -59.37 -13.51 4.21e-01 2sqcA 631 -62.27 -12.22 8.59e-01 1iv8A 720 -47.47 -11.50 1.29e+00 1fo3A 460 -36.91 -11.21 1.53e+00 1j5sA 463 -38.67 -11.19 1.55e+00 1nktA 922 -64.95 -11.17 1.56e+00 1v54A 514 -56.19 -11.01 1.72e+00 1sqc 631 -61.89 -10.91 1.82e+00 1ka2A 499 -60.73 -10.74 2.01e+00 1fchA 368 -47.55 -10.70 2.05e+00 2kfnA 605 -30.43 -10.67 2.10e+00 1n46A 258 -35.71 -10.65 2.12e+00 1e8yA 966 -50.71 -10.50 2.31e+00 1eia 207 -35.37 -10.48 2.34e+00 1upkA 341 -51.50 -10.47 2.36e+00 5eat 548 -68.56 -10.40 2.45e+00 1l7vA 326 -40.89 -10.23 2.71e+00 1kktA 511 -39.26 -10.14 2.85e+00 1riqA 465 -44.83 -10.12 2.90e+00 2occA 514 -54.08 -9.94 3.22e+00 1t7rA 269 -41.17 -9.88 3.33e+00 1nfiC 301 -26.25 -9.86 3.37e+00 1y14A 187 -30.27 -9.84 3.41e+00 1tzvA 142 -37.39 -9.83 3.43e+00 1kpkA 473 -50.33 -9.80 3.50e+00 1q6hA 224 -29.59 -9.78 3.54e+00 1h6kA 757 -88.74 -9.75 3.60e+00 1a36A 592 -41.57 -9.73 3.66e+00 1htjF 210 -34.69 -9.60 3.95e+00 1taq 832 -38.60 -9.60 3.95e+00 2eiaB 206 -33.36 -9.58 4.00e+00 1g5hA 454 -25.59 -9.37 4.52e+00 1lp4A 332 -26.68 -9.31 4.69e+00 1lnh 857 -46.21 -9.29 4.77e+00 1r9kA 172 -32.44 -9.28 4.79e+00 1oyzA 280 -44.42 -9.27 4.83e+00 1ih7A 903 -53.99 -9.19 5.04e+00 1ljrA 244 -29.42 -9.17 5.12e+00 1vjoA 393 -29.84 -9.16 5.15e+00 1oohA 126 -27.27 -9.14 5.20e+00 1rtwA 220 -43.04 -9.11 5.30e+00 1h12A 405 -30.03 -9.06 5.47e+00 1upvA 257 -32.03 -9.05 5.50e+00 1guxA 218 -39.43 -9.00 5.68e+00 1ulyA 192 -30.25 -8.96 5.81e+00 1m13A 316 -36.07 -8.93 5.92e+00 1lpuA 332 -26.78 -8.93 5.92e+00 1lshA 1056 -42.09 -8.85 6.21e+00 1e9eA 215 -22.05 -8.80 6.42e+00 1peqA 714 -32.16 -8.79 6.44e+00 1rec 201 -28.50 -8.76 6.58e+00 1e9cA 215 -22.05 -8.76 6.60e+00 1oywA 523 -28.81 -8.75 6.60e+00 1a6dA 545 -43.68 -8.75 6.60e+00 1evyA 366 -29.53 -8.71 6.78e+00 1pw4A 451 -57.37 -8.71 6.80e+00 1omrA 201 -28.74 -8.69 6.89e+00 1cb8A 678 -46.47 -8.64 7.08e+00 1e2gA 215 -21.94 -8.63 7.15e+00 1oq9A 363 -52.78 -8.59 7.31e+00 1spvA 184 -22.01 -8.55 7.50e+00 1afrA 345 -54.59 -8.53 7.59e+00 1p7tA 731 -43.21 -8.47 7.88e+00 1nrlA 316 -35.28 -8.47 7.89e+00 3bct 457 -58.81 -8.46 7.94e+00 1ft1A 377 -48.04 -8.44 8.03e+00 1clqA 903 -53.38 -8.42 8.13e+00 1nn5A 215 -21.96 -8.42 8.14e+00 1anxA 319 -45.04 -8.37 8.36e+00 1hcuA 503 -34.87 -8.37 8.40e+00 1aueA 100 -29.73 -8.33 8.56e+00 1irxA 523 -45.72 -8.30 8.75e+00 1e2fA 215 -21.54 -8.24 9.08e+00 1eco 136 -30.18 -8.24 9.10e+00 1hm2A 700 -47.32 -8.23 9.13e+00 1nfiA 301 -24.31 -8.20 9.29e+00 1bob 320 -23.92 -8.19 9.35e+00 1tqnA 486 -39.19 -8.18 9.41e+00 1vljA 407 -43.84 -8.17 9.49e+00 1sctB 151 -33.01 -8.14 9.66e+00 1ornA 226 -31.44 -8.14 9.68e+00 1mxrA 375 -44.50 -8.13 9.74e+00 1dceB 331 -31.52 -8.12 9.81e+00 1lj8A 493 -35.27 -8.05 1.02e+01 1biqA 375 -45.56 -8.00 1.05e+01 1h3fA 432 -26.19 -7.99 1.06e+01 1jk0A 419 -43.07 -7.98 1.07e+01 1om1A 332 -24.96 -7.98 1.07e+01 1e8xA 961 -49.26 -7.96 1.09e+01 1dm5A 315 -48.27 -7.92 1.11e+01 1eca 136 -30.18 -7.91 1.12e+01 1ecd 136 -30.18 -7.91 1.12e+01 1xikA 375 -44.68 -7.90 1.13e+01 1m6nA 802 -62.13 -7.89 1.13e+01 1fqvJ 149 -26.82 -7.89 1.13e+01 1d2nA 272 -21.61 -7.87 1.15e+01 1o7nB 194 -20.05 -7.85 1.16e+01 1ndoB 194 -20.05 -7.85 1.16e+01 1eg9B 194 -20.05 -7.85 1.16e+01 1dn1A 594 -32.79 -7.81 1.19e+01 1ib2A 349 -42.74 -7.80 1.20e+01 1ash 150 -34.56 -7.78 1.21e+01 1f5qB 252 -38.95 -7.76 1.23e+01 1ezfA 340 -49.13 -7.69 1.28e+01 1aorA 605 -51.07 -7.68 1.30e+01 1vheA 373 -32.94 -7.66 1.31e+01 1d8cA 723 -44.39 -7.65 1.32e+01 1otsA 465 -57.77 -7.63 1.34e+01 1jqcA 375 -44.73 -7.57 1.39e+01 1jfaA 374 -51.00 -7.57 1.39e+01 1rovA 857 -45.40 -7.52 1.43e+01 1ovnA 248 -25.71 -7.52 1.43e+01 1w4xA 542 -33.68 -7.47 1.48e+01 1rh5A 436 -54.33 -7.47 1.48e+01 1mukA 1267 -48.50 -7.45 1.51e+01 1fqvD 149 -26.52 -7.42 1.53e+01 1lrv 244 -23.88 -7.39 1.56e+01 1i37A 260 -36.29 -7.37 1.58e+01 1m2rA 327 -24.48 -7.37 1.58e+01 1wekA 217 -25.60 -7.35 1.61e+01 1jixA 351 -24.22 -7.34 1.61e+01 1jg7A 351 -24.24 -7.29 1.67e+01 1brwA 433 -34.92 -7.28 1.68e+01 1oe9A 795 -37.97 -7.27 1.69e+01 1jfgA 374 -51.00 -7.26 1.69e+01 1cec 343 -26.61 -7.26 1.70e+01 1dn1B 267 -42.20 -7.24 1.72e+01 1t0qB 330 -42.33 -7.24 1.72e+01 1vns 609 -47.91 -7.20 1.76e+01 1rt8A 513 -36.84 -7.19 1.78e+01 1kv9A 668 -50.04 -7.15 1.82e+01 1j6oA 268 -23.35 -7.14 1.83e+01 1kzhA 555 -38.33 -7.12 1.86e+01 1xqoA 256 -33.08 -7.11 1.87e+01 1gaxA 862 -53.19 -7.10 1.88e+01 1lrzA 426 -30.04 -7.10 1.88e+01 1h2vC 771 -84.61 -7.09 1.90e+01 1cpq 129 -23.52 -7.07 1.92e+01 1nv8A 284 -23.62 -7.07 1.92e+01 1vnc 609 -47.66 -7.05 1.94e+01 1kf6C 130 -28.25 -7.05 1.94e+01 1tffA 234 -33.63 -7.02 1.98e+01 5pal 109 -21.76 -6.98 2.03e+01 3tmkA 216 -26.88 -6.98 2.04e+01 1ae1A 273 -22.55 -6.91 2.13e+01 1c1kA 217 -32.51 -6.90 2.15e+01 1hy0A 466 -39.10 -6.88 2.17e+01 1qr6A 584 -38.03 -6.88 2.17e+01 1j79A 347 -21.02 -6.87 2.19e+01 1nekC 129 -28.47 -6.81 2.27e+01 1qhbA 596 -36.47 -6.77 2.33e+01 1va6A 518 -32.84 -6.77 2.33e+01 1vkhA 273 -22.45 -6.77 2.34e+01 1lvk 762 -33.48 -6.75 2.37e+01 1lw7A 365 -24.81 -6.73 2.39e+01 1g59A 468 -36.94 -6.73 2.40e+01 2gsaA 432 -33.85 -6.67 2.49e+01 1pgtA 210 -29.57 -6.66 2.51e+01 1mv8A 436 -29.40 -6.64 2.54e+01 3fapB 94 -28.08 -6.63 2.57e+01 1kyqA 274 -26.98 -6.60 2.62e+01 1ayx 492 -37.80 -6.59 2.63e+01 1dcnD 436 -40.44 -6.59 2.63e+01 1glm 470 -32.30 -6.59 2.64e+01 1chuA 540 -40.55 -6.58 2.64e+01 1po5A 476 -45.14 -6.55 2.70e+01 1k5oA 86 -23.31 -6.55 2.71e+01 1jli 112 -24.64 -6.55 2.71e+01 2ts1 419 -29.57 -6.54 2.72e+01 1tf5A 844 -58.41 -6.52 2.77e+01 1sh0A 510 -32.18 -6.50 2.80e+01 1ribA 375 -44.44 -6.50 2.80e+01 1k4tA 592 -39.22 -6.49 2.82e+01 1sig 339 -35.57 -6.47 2.85e+01 1qrjB 199 -26.71 -6.46 2.87e+01 1pprM 312 -39.37 -6.45 2.89e+01 1nekA 588 -41.67 -6.41 2.96e+01 1xlyA 234 -37.67 -6.41 2.96e+01 1j8uA 325 -30.70 -6.37 3.04e+01 5eau 548 -62.77 -6.37 3.05e+01 1ceo 343 -25.10 -6.36 3.06e+01 1kgnA 329 -43.47 -6.36 3.07e+01 1auwA 468 -40.98 -6.36 3.08e+01 1mpgA 282 -26.75 -6.35 3.09e+01 1vom 762 -32.32 -6.33 3.13e+01 1a8h 500 -40.62 -6.33 3.14e+01 2bgu 351 -23.12 -6.31 3.18e+01 1xnfA 275 -38.05 -6.31 3.18e+01 2tmkA 216 -25.93 -6.30 3.19e+01 1hvd 319 -44.56 -6.30 3.20e+01 1tn6A 382 -47.23 -6.29 3.22e+01 1yfm 488 -35.47 -6.29 3.23e+01 1gvnB 287 -26.52 -6.28 3.23e+01 1jcrA 377 -46.52 -6.27 3.27e+01 1qhtA 775 -45.42 -6.25 3.30e+01 1c3jA 351 -22.65 -6.24 3.32e+01 1tzjA 338 -26.88 -6.24 3.32e+01 1jm6A 407 -33.89 -6.24 3.32e+01 1cch 82 -19.29 -6.23 3.34e+01 1kkhA 317 -25.86 -6.18 3.47e+01 1i1qA 520 -21.49 -6.17 3.48e+01 1tvkA 440 -26.60 -6.16 3.50e+01 1q87A 221 -25.15 -6.15 3.52e+01 1phk 298 -26.10 -6.15 3.54e+01 1hta 69 -21.16 -6.14 3.57e+01 1ucrA 78 -19.47 -6.12 3.61e+01 1j2zA 270 -24.42 -6.11 3.64e+01 1rrmA 386 -36.98 -6.10 3.67e+01 1nsf 273 -20.03 -6.08 3.72e+01 1k7wA 468 -39.19 -6.07 3.74e+01 1j09A 468 -38.99 -6.00 3.91e+01 1gweA 503 -33.98 -5.99 3.94e+01 1orjA 130 -34.60 -5.97 3.98e+01 1tbfA 347 -42.83 -5.97 3.99e+01