% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YDL010W.t2k-100-30-CB_burial_14_7 Host: farm08 Sun Jan 2 17:46:09 2005 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL0/YDL010W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/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 YDL010W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL010W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 11126 sequences, 2638630 residues, 232 nodes, 255.88 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(=1.4854) * Reverse)^tau(=0.8688))) % 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 1kte 105 -115.41 -103.35 3.99e-31 1jhb 106 -113.67 -103.08 4.78e-31 3grx 82 -100.54 -88.11 1.15e-26 1ego 85 -67.59 -53.05 5.56e-16 1qfnA 85 -67.43 -53.02 5.69e-16 1egr 85 -68.48 -52.34 9.36e-16 1grx 85 -67.13 -51.06 2.38e-15 1t1vA 93 -47.44 -34.64 5.20e-10 1j0fA 100 -47.54 -34.53 5.69e-10 1aba 87 -45.14 -29.78 2.28e-08 1t3bA 211 -30.90 -19.08 1.27e-04 1fo5A 85 -30.38 -16.97 7.45e-04 1h75A 81 -29.76 -16.55 1.07e-03 1eejA 216 -26.08 -15.76 2.09e-03 1a8l 226 -24.76 -14.63 5.50e-03 1j08A 226 -23.98 -14.27 7.53e-03 1erv 105 -26.70 -14.05 9.05e-03 1thx 115 -24.15 -13.36 1.65e-02 1v58A 241 -26.01 -13.26 1.81e-02 1eemA 241 -23.28 -12.81 2.68e-02 1aiu 105 -25.05 -12.69 2.98e-02 1lu4A 136 -20.88 -11.74 6.89e-02 1wouA 123 -22.48 -11.51 8.42e-02 1w0bA 102 -27.99 -10.30 2.49e-01 1v9wA 130 -20.40 -10.28 2.53e-01 1gh2A 107 -20.15 -10.14 2.87e-01 1faaA 124 -21.01 -9.97 3.36e-01 1e6bA 221 -20.52 -9.84 3.77e-01 1mdiA 105 -19.75 -9.69 4.33e-01 1t5iA 172 -22.14 -9.66 4.46e-01 1vj5A 555 -20.95 -9.40 5.62e-01 1tof 112 -20.15 -9.36 5.85e-01 1w8xP 117 -31.59 -9.35 5.88e-01 1kagA 173 -20.41 -9.30 6.16e-01 1i3kA 348 -17.69 -8.94 8.56e-01 1senA 164 -19.88 -8.85 9.29e-01 2trxA 108 -19.26 -8.74 1.03e+00 1kebA 108 -20.16 -8.69 1.09e+00 1kk9A 221 -19.31 -8.60 1.18e+00 1jr2A 286 -18.23 -8.53 1.25e+00 1nw2A 105 -19.40 -8.52 1.27e+00 1ozhA 566 -18.12 -8.39 1.43e+00 1t0iA 191 -20.00 -8.27 1.59e+00 1hv8A 367 -17.59 -8.19 1.72e+00 1k0nA 241 -19.18 -8.14 1.80e+00 2dhqA 146 -18.28 -8.11 1.85e+00 1r5jA 337 -17.80 -8.04 1.97e+00 1rttA 193 -17.48 -8.02 2.02e+00 1k0mA 241 -19.95 -7.85 2.36e+00 1q44A 326 -19.42 -7.75 2.58e+00 1xg8A 111 -20.07 -7.73 2.63e+00 1uqrA 154 -20.12 -7.72 2.67e+00 1ek6A 348 -16.78 -7.66 2.81e+00 1ao0A 459 -18.19 -7.65 2.84e+00 1vpfA 102 -29.30 -7.64 2.87e+00 1ttzA 87 -19.70 -7.64 2.88e+00 1dbuA 158 -17.47 -7.58 3.03e+00 1f9mA 112 -18.26 -7.58 3.03e+00 1k7jA 206 -18.32 -7.54 3.16e+00 1vppV 102 -29.06 -7.47 3.35e+00 1xtnA 120 -21.55 -7.40 3.59e+00 1jeoA 180 -18.74 -7.27 4.05e+00 1uptC 170 -16.92 -7.23 4.21e+00 1kmdA 117 -23.77 -7.14 4.58e+00 1r4aA 165 -16.15 -7.01 5.18e+00 1hyuA 521 -16.40 -7.01 5.22e+00 1fltV 98 -29.08 -6.99 5.27e+00 1xmxA 385 -17.10 -6.88 5.86e+00 2cevA 299 -15.58 -6.84 6.13e+00 1pszA 303 -16.70 -6.83 6.18e+00 1jbkA 195 -15.82 -6.72 6.88e+00 1g7oA 215 -17.63 -6.66 7.22e+00 1t6lA 290 -18.03 -6.66 7.28e+00 1vljA 407 -16.21 -6.63 7.49e+00 2fx2 147 -16.27 -6.56 7.97e+00 1g8eA 116 -26.40 -6.55 8.04e+00 1eo1A 124 -18.43 -6.55 8.07e+00 1m1jA 491 -43.59 -6.53 8.25e+00 1rw1A 114 -18.77 -6.50 8.44e+00 1vmeA 410 -15.75 -6.50 8.45e+00 2dpmA 284 -18.34 -6.43 9.01e+00 1e19A 314 -17.75 -6.43 9.06e+00 1exeA 99 -29.96 -6.37 9.58e+00 1j6oA 268 -14.98 -6.37 9.59e+00 1h05A 146 -15.90 -6.29 1.03e+01 1mxmA 254 -22.62 -6.21 1.12e+01 1lnqA 336 -23.26 -6.16 1.17e+01 1qr6A 584 -16.52 -6.13 1.21e+01 1gqoX 143 -16.61 -6.13 1.21e+01 1fb6A 105 -16.87 -6.12 1.22e+01 1jbgA 109 -25.84 -6.12 1.22e+01 1od5A 492 -20.93 -6.11 1.24e+01 1vgyA 393 -16.82 -6.02 1.34e+01 1lxyA 409 -15.40 -6.02 1.35e+01 1fp4A 492 -16.37 -5.99 1.38e+01 3minC 491 -16.54 -5.99 1.38e+01 1m1nA 491 -16.43 -5.98 1.40e+01 2minA 491 -16.41 -5.97 1.40e+01 1gqoV 143 -16.33 -5.97 1.41e+01 1lw7A 365 -18.12 -5.96 1.42e+01 1ft8E 271 -21.90 -5.96 1.42e+01 1gqoM 143 -17.09 -5.96 1.43e+01 1xteA 154 -19.86 -5.94 1.45e+01 1cf2O 337 -15.71 -5.94 1.45e+01 1o6jA 150 -15.80 -5.93 1.46e+01 1v5wA 343 -18.36 -5.92 1.48e+01 1qydA 313 -16.91 -5.89 1.52e+01 1khtA 192 -17.18 -5.87 1.56e+01 1it2A 146 -19.99 -5.84 1.60e+01 1jj2F 119 -15.67 -5.83 1.62e+01 2wrpR 107 -26.85 -5.82 1.63e+01 1y01A 102 -22.39 -5.79 1.68e+01 1a23 189 -15.52 -5.78 1.69e+01 2fox 138 -18.61 -5.78 1.69e+01 1s9rA 410 -15.22 -5.77 1.70e+01 1dsbA 189 -15.90 -5.75 1.74e+01 1bu5A 147 -15.54 -5.74 1.77e+01 1eysH 259 -30.40 -5.72 1.80e+01 1usjA 384 -15.93 -5.72 1.80e+01 1iloA 77 -17.68 -5.72 1.80e+01 1v37A 177 -16.15 -5.68 1.86e+01 1gqoL 143 -16.56 -5.68 1.87e+01 1t6nA 220 -15.56 -5.67 1.89e+01 1r26A 125 -19.13 -5.66 1.90e+01 1erw 105 -16.36 -5.65 1.91e+01 1krhA 338 -14.32 -5.64 1.94e+01 1adjA 421 -15.33 -5.63 1.96e+01 1dxy 333 -15.97 -5.62 1.97e+01 1h1lA 481 -15.30 -5.62 1.97e+01 1gqoQ 143 -16.64 -5.60 2.01e+01 3nll 138 -18.66 -5.60 2.02e+01 1te6A 439 -14.06 -5.60 2.02e+01 2fvx 138 -18.56 -5.59 2.03e+01 1qguA 478 -15.20 -5.59 2.05e+01 1fvkA 189 -15.92 -5.58 2.06e+01 1txgA 335 -14.62 -5.56 2.10e+01 1hcnB 145 -25.72 -5.55 2.12e+01 1gqoN 143 -15.79 -5.54 2.15e+01 1n8vA 112 -19.11 -5.53 2.16e+01 1uptA 171 -14.34 -5.50 2.22e+01 1qh8A 478 -15.07 -5.49 2.25e+01 1j8iA 93 -21.12 -5.47 2.29e+01 1fxkA 107 -26.74 -5.46 2.32e+01 1h4vB 421 -15.61 -5.45 2.34e+01 1j4aA 333 -16.10 -5.44 2.35e+01 1pnkA 209 -29.11 -5.42 2.41e+01 5nul 138 -18.69 -5.41 2.43e+01 1cw0A 155 -18.30 -5.40 2.45e+01 1jhgA 101 -26.59 -5.39 2.47e+01 1kigL 51 -20.65 -5.39 2.48e+01 1dbxA 158 -14.96 -5.36 2.54e+01 1izmA 184 -18.58 -5.36 2.55e+01 1h03P 125 -23.09 -5.36 2.55e+01 1v5mA 136 -18.16 -5.35 2.57e+01 1acvA 189 -15.73 -5.31 2.68e+01 1s5lE 84 -28.87 -5.26 2.81e+01 1gqoK 143 -15.28 -5.23 2.89e+01 1m2kA 249 -16.72 -5.21 2.95e+01 1jjiA 311 -16.24 -5.20 2.98e+01 1ffkE 119 -14.32 -5.18 3.03e+01 1dbdA 100 -21.58 -5.18 3.04e+01 1mkkA 96 -26.64 -5.15 3.14e+01 1tocR 120 -21.96 -5.14 3.16e+01 1izcA 339 -17.50 -5.13 3.20e+01 1qk8A 146 -15.35 -5.11 3.27e+01 1xkcA 179 -18.82 -5.10 3.31e+01 1jdpA 441 -14.43 -5.09 3.33e+01 3hsf 92 -22.54 -5.03 3.52e+01 1lv9A 77 -16.35 -5.02 3.58e+01 1lmeA 176 -16.29 -4.99 3.68e+01 1lw6E 281 -12.35 -4.91 3.96e+01