% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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.YGR217W.t2k-100-40-40-str2+CB_burial_14_7 Host: cc85 Thu Feb 26 23:05:41 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR217W % --------------------------------------------------------------------- % 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 YGR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR217W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR217W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 9381 sequences, 2218509 residues, 2040 nodes, 3306.18 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 (=8162) sequences: % N / (1 + exp(-(lambda(=0.6880) * Reverse)^tau(=0.8150))) % 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 1ncx 162 -81.10 -34.32 1.58e-02 1k94A 165 -61.07 -34.05 1.72e-02 1top 162 -80.13 -32.80 2.54e-02 1gw5B 591 -89.03 -32.69 2.63e-02 1f4qA 165 -53.25 -30.17 5.87e-02 1lnh 857 -79.86 -26.08 2.21e-01 1qs0A 407 -65.07 -25.69 2.51e-01 1alvA 173 -59.99 -25.19 2.96e-01 1kfuS 184 -58.19 -24.87 3.29e-01 1t1dA 100 -44.56 -23.72 4.83e-01 1zac 90 -51.91 -23.66 4.93e-01 1lla 628 -59.75 -23.21 5.73e-01 1omrA 201 -50.55 -22.46 7.38e-01 1m46A 148 -55.32 -22.00 8.61e-01 1a68 95 -40.74 -21.88 8.99e-01 1dsxA 87 -38.86 -21.79 9.26e-01 1ggwA 140 -55.88 -21.70 9.53e-01 1g8iA 190 -53.21 -21.44 1.04e+00 1knzA 164 -63.40 -20.86 1.27e+00 1g3jA 532 -53.71 -20.73 1.33e+00 1aijL 281 -66.12 -20.39 1.49e+00 1n93X 375 -65.02 -19.95 1.74e+00 1vrtA 560 -58.35 -19.81 1.82e+00 1dqeA 137 -45.46 -19.74 1.87e+00 2mysB 166 -64.10 -19.37 2.12e+00 1j7rA 86 -47.02 -19.29 2.18e+00 7catA 506 -80.69 -19.17 2.28e+00 1qbkB 890 -92.26 -19.12 2.32e+00 1avsA 90 -48.20 -18.93 2.48e+00 1ll1 590 -53.89 -18.93 2.48e+00 1qltA 560 -46.90 -18.81 2.58e+00 1e8gA 560 -48.10 -18.56 2.81e+00 1ggzA 148 -65.87 -18.27 3.12e+00 1v54A 514 -82.64 -18.26 3.13e+00 1cll 148 -69.24 -18.10 3.31e+00 2btfA 375 -41.55 -17.95 3.49e+00 1m45A 148 -48.60 -17.86 3.60e+00 1gm7A 209 -59.36 -17.81 3.67e+00 1o1fC 147 -56.50 -17.78 3.71e+00 1qu1A 155 -68.33 -17.72 3.79e+00 1qcrC 378 -56.52 -17.70 3.81e+00 1iicA 422 -53.05 -17.65 3.88e+00 2lbd 267 -46.33 -17.61 3.94e+00 1hqvA 191 -59.22 -17.57 3.99e+00 3cln 148 -66.02 -17.51 4.07e+00 1dttA 560 -62.64 -17.47 4.14e+00 1ddf 127 -45.12 -17.15 4.62e+00 1gkmA 509 -58.02 -17.12 4.69e+00 1gweA 503 -73.06 -17.08 4.75e+00 1i7gA 287 -47.37 -17.00 4.89e+00 1rxwA 336 -54.21 -16.98 4.91e+00 1hbzA 498 -71.96 -16.91 5.04e+00 4lbd 267 -45.81 -16.85 5.14e+00 1kiyA 374 -58.51 -16.79 5.27e+00 1d4xA 375 -36.66 -16.75 5.33e+00 1jfaA 374 -59.13 -16.73 5.38e+00 1wdcC 156 -52.37 -16.60 5.62e+00 1jdhA 529 -50.31 -16.55 5.74e+00 1rthA 560 -61.12 -16.48 5.87e+00 1jr8A 117 -44.22 -16.45 5.95e+00 1jeqA 609 -78.10 -16.31 6.25e+00 1vaoA 560 -44.27 -16.19 6.52e+00 1ho8A 480 -64.55 -16.09 6.75e+00 1fmjA 351 -49.56 -16.09 6.77e+00 2occA 514 -79.86 -16.07 6.81e+00 1dgaA 375 -35.56 -16.03 6.90e+00 1okrA 123 -49.14 -15.92 7.17e+00 1fps 348 -60.57 -15.88 7.29e+00 1m48A 133 -39.33 -15.87 7.31e+00 1jfkA 134 -49.56 -15.85 7.36e+00 1lufA 343 -38.12 -15.77 7.59e+00 1kk1A 410 -44.78 -15.59 8.10e+00 1dceB 331 -50.42 -15.56 8.18e+00 1a36A 592 -85.40 -15.40 8.66e+00 1fcyA 236 -43.76 -15.40 8.67e+00 1qlnA 883 -80.00 -15.30 8.98e+00 1ai7A 209 -57.37 -15.24 9.20e+00 1jraA 117 -42.53 -15.16 9.46e+00 1ajqA 209 -58.09 -15.12 9.60e+00 1uby 367 -62.09 -15.08 9.75e+00 1vi0A 206 -46.59 -15.00 1.00e+01 1f1sA 814 -57.99 -14.99 1.00e+01 1jfgA 374 -56.81 -14.77 1.09e+01 1bi0 226 -39.57 -14.70 1.12e+01 1ovlA 271 -45.88 -14.69 1.12e+01 1ju3A 583 -39.18 -14.67 1.13e+01 1nrlA 316 -52.15 -14.67 1.13e+01 1wgtA 186 -55.06 -14.67 1.13e+01 1br1B 150 -53.19 -14.65 1.14e+01 1uhnA 189 -44.24 -14.63 1.15e+01 6prcM 323 -67.10 -14.63 1.15e+01 1hy3A 294 -47.59 -14.62 1.15e+01 1mxrA 375 -63.92 -14.62 1.15e+01 1eg7A 557 -44.80 -14.61 1.16e+01 1b8fA 509 -56.36 -14.59 1.16e+01 1n3kA 130 -54.63 -14.55 1.18e+01 1exrA 148 -68.13 -14.55 1.18e+01 1e9lA 377 -36.33 -14.53 1.19e+01 1ngvA 534 -58.60 -14.49 1.21e+01 1g4yR 148 -66.92 -14.33 1.28e+01 1taq 832 -66.05 -14.27 1.31e+01 1biqA 375 -60.31 -14.23 1.33e+01 1l7mA 211 -32.05 -14.19 1.35e+01 1sva1 361 -77.69 -14.17 1.36e+01 1f5sA 211 -32.12 -14.13 1.37e+01 9wgaA 171 -52.32 -14.03 1.43e+01 1fjgM 126 -50.07 -14.00 1.44e+01 1j6zA 376 -36.39 -14.00 1.45e+01 2hmiA 558 -57.14 -13.98 1.46e+01 1gh6A 114 -52.54 -13.92 1.49e+01 1dxrM 323 -67.58 -13.82 1.54e+01 1j97A 211 -32.16 -13.82 1.54e+01 1lg2A 365 -34.79 -13.81 1.55e+01 1ebmA 317 -34.56 -13.70 1.62e+01 1e7uA 961 -80.73 -13.69 1.62e+01 1ivhA 394 -49.26 -13.69 1.62e+01 1h7nA 342 -45.71 -13.68 1.62e+01 1itwA 741 -65.13 -13.66 1.64e+01 1p49A 562 -55.46 -13.63 1.66e+01 1jbaA 204 -56.59 -13.62 1.66e+01 1aoa 275 -47.39 -13.62 1.66e+01 1csmA 256 -55.70 -13.59 1.68e+01 1pw4A 451 -80.28 -13.50 1.74e+01 1m1eB 81 -43.07 -13.49 1.74e+01 1de6A 426 -39.57 -13.45 1.77e+01 1be3C 379 -57.20 -13.37 1.83e+01 1s0uA 408 -43.01 -13.34 1.84e+01 1jb0A 755 -82.54 -13.32 1.86e+01 1jeyA 609 -68.09 -13.20 1.94e+01 1lkxA 697 -51.28 -13.15 1.98e+01 1skyB 502 -45.33 -13.14 1.99e+01 1kl1A 419 -40.97 -13.07 2.04e+01 1i7wA 538 -45.11 -13.01 2.08e+01 1gw5A 621 -73.35 -13.00 2.09e+01 1dghB 498 -70.83 -12.98 2.11e+01 2hdhA 293 -37.37 -12.90 2.17e+01 1ribA 375 -63.40 -12.89 2.18e+01 1alq 266 -33.93 -12.87 2.20e+01 1aroP 883 -70.57 -12.83 2.23e+01 1lwyA 324 -33.92 -12.83 2.23e+01 1m13A 316 -49.44 -12.82 2.24e+01 1de5A 426 -40.07 -12.81 2.24e+01 1jqcA 375 -60.58 -12.80 2.26e+01 1fmk 452 -36.86 -12.77 2.28e+01 1e1dA 553 -57.65 -12.74 2.31e+01 1gntA 553 -57.58 -12.72 2.33e+01 1n7zA 334 -47.56 -12.71 2.33e+01 1f83A 425 -51.46 -12.67 2.36e+01 1mo9A 523 -39.82 -12.65 2.38e+01 1e2uA 553 -57.70 -12.65 2.39e+01 1ylvA 342 -45.22 -12.61 2.42e+01 1fs0G 230 -36.91 -12.59 2.44e+01 1miuA 738 -84.18 -12.58 2.45e+01 1nmtA 392 -37.47 -12.57 2.46e+01 2shpA 525 -44.27 -12.53 2.50e+01 1dceA 567 -67.73 -12.52 2.51e+01 3erk 364 -47.18 -12.50 2.53e+01 1g0oA 283 -38.55 -12.49 2.53e+01 1yagA 375 -35.30 -12.49 2.53e+01 1l2lA 457 -41.61 -12.47 2.55e+01 1cezA 883 -75.99 -12.45 2.57e+01 1uf2A 1019 -43.72 -12.45 2.57e+01 1nstA 325 -38.79 -12.42 2.60e+01 1dgfA 497 -69.22 -12.41 2.61e+01 1kjwA 295 -46.01 -12.34 2.68e+01 1fxxA 482 -57.20 -12.33 2.69e+01 1kkjA 419 -40.31 -12.33 2.69e+01 1jeyB 565 -66.39 -12.27 2.75e+01 1e1hB 174 -48.10 -12.26 2.76e+01 1h77A 605 -46.35 -12.22 2.81e+01 1ci8A 392 -37.98 -12.21 2.81e+01 1phnB 172 -44.86 -12.21 2.82e+01 1keyA 235 -54.89 -12.19 2.83e+01 1vhvA 268 -27.26 -12.18 2.84e+01 5csmA 256 -54.41 -12.14 2.89e+01 1fgkA 310 -40.01 -12.13 2.90e+01 1nvvS 481 -92.57 -12.13 2.90e+01 1ltdA 506 -55.02 -12.13 2.91e+01 1htmB 138 -60.01 -12.09 2.95e+01 1ybvA 283 -37.43 -12.06 2.97e+01 1m1jA 491 -105.07 -12.05 2.99e+01 1ohlA 342 -44.54 -12.03 3.01e+01 1aoiG 116 -38.30 -12.02 3.02e+01 5ldh 334 -42.75 -11.98 3.07e+01 1lshA 1056 -50.66 -11.95 3.10e+01 1hz4A 373 -54.84 -11.94 3.12e+01 1rec 201 -38.75 -11.94 3.12e+01 1pal 108 -32.80 -11.94 3.12e+01 1gk9A 260 -58.22 -11.94 3.12e+01 1pnkA 209 -54.08 -11.92 3.14e+01 1upkA 341 -50.01 -11.92 3.14e+01 1dnpA 471 -45.66 -11.83 3.25e+01 1aipE 405 -35.24 -11.83 3.25e+01 1fgqA 839 -61.65 -11.82 3.27e+01 1efdN 266 -28.41 -11.81 3.27e+01 1m2oA 768 -53.43 -11.81 3.28e+01 1f2dA 341 -33.57 -11.81 3.28e+01 1k0rA 366 -53.99 -11.80 3.28e+01 2dtr 226 -38.02 -11.80 3.29e+01 1yge 839 -64.12 -11.77 3.32e+01 1bla 155 -36.94 -11.74 3.36e+01 1cdp 109 -32.79 -11.72 3.38e+01 1ko9A 345 -34.32 -11.69 3.42e+01 1ci9A 392 -36.68 -11.69 3.43e+01 1uetA 437 -45.81 -11.67 3.45e+01 1f8nA 839 -66.18 -11.66 3.46e+01 3lynA 136 -38.20 -11.66 3.47e+01 1qhtA 775 -63.77 -11.65 3.47e+01 3bct 457 -46.71 -11.63 3.51e+01 1ahpA 797 -55.71 -11.62 3.52e+01 1kzhA 555 -54.20 -11.62 3.53e+01 2dpg 485 -42.57 -11.57 3.58e+01 2pvbA 107 -32.24 -11.57 3.58e+01 1gseA 221 -43.36 -11.56 3.59e+01 1n81A 186 -45.21 -11.56 3.60e+01 1bn7A 294 -31.18 -11.55 3.61e+01 1bn6A 294 -30.53 -11.50 3.68e+01 1d8wA 426 -39.65 -11.49 3.69e+01 1j7nB 776 -71.95 -11.48 3.72e+01 1j5eB 256 -37.82 -11.46 3.73e+01 1osa 148 -68.40 -11.41 3.81e+01 1qapA 296 -36.16 -11.41 3.81e+01 1qz5A 375 -32.68 -11.41 3.81e+01 1rpa 342 -47.51 -11.38 3.86e+01 1sek 378 -34.97 -11.34 3.91e+01 1gpb 842 -51.93 -11.32 3.95e+01 2scpA 174 -35.51 -11.30 3.98e+01 5pal 109 -33.34 -11.29 3.99e+01