% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % strfoo.1.YGR203W.t2k-100-30-str Host: cc43 Tue Nov 12 14:43:32 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR203W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR203W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR203W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 149 nodes, 104.35 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.6174) * Reverse)^tau(=0.6827))) % 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 1c25 161 -162.25 -137.11 3.23e-14 1qb0A 211 -161.56 -133.10 7.22e-14 1gn0A 108 -76.04 -57.16 2.06e-06 1gmxA 108 -75.71 -56.82 2.26e-06 1e0cA 271 -70.73 -45.93 4.36e-05 1rhs 296 -68.30 -42.15 1.28e-04 1rhd 293 -63.82 -39.30 2.95e-04 1hzmA 154 -53.51 -32.38 2.43e-03 1d5rA 324 -39.83 -17.17 4.60e-01 1jl3A 139 -37.36 -16.19 6.74e-01 1i9sA 210 -38.41 -14.74 1.20e+00 1yveJ 524 -37.11 -14.13 1.54e+00 1eucA 311 -37.72 -13.70 1.83e+00 1yveI 524 -36.70 -13.35 2.12e+00 1qmgA 524 -36.70 -13.35 2.12e+00 1eudA 311 -38.04 -13.22 2.23e+00 1gpjA 404 -36.21 -12.46 3.09e+00 1d0sA 356 -35.06 -12.08 3.62e+00 1d0vA 356 -34.85 -11.85 4.00e+00 1e5dA 402 -37.94 -11.79 4.11e+00 1l5oA 356 -34.66 -11.77 4.15e+00 1vhrA 184 -34.39 -11.76 4.16e+00 1g5pA 289 -38.09 -11.62 4.43e+00 3adk 195 -35.17 -11.58 4.51e+00 1fp6A 289 -37.95 -11.57 4.51e+00 2scuA 288 -36.91 -11.57 4.52e+00 2fokA 579 -33.71 -11.43 4.80e+00 1scuA 288 -36.35 -11.41 4.84e+00 1ecfB 504 -34.53 -11.37 4.93e+00 2shpA 525 -33.86 -11.36 4.95e+00 1jh8A 356 -34.22 -11.26 5.18e+00 1im5A 180 -35.71 -11.00 5.81e+00 1lgyA 269 -31.34 -10.89 6.10e+00 1io2A 213 -34.74 -10.79 6.38e+00 1ad1A 266 -36.49 -10.61 6.92e+00 1ecfA 504 -33.85 -10.57 7.03e+00 1fnb 314 -34.17 -10.54 7.14e+00 1dtgA 334 -31.44 -10.44 7.44e+00 1i88A 389 -36.27 -10.35 7.77e+00 1i86A 389 -36.24 -10.31 7.91e+00 1bi5A 389 -36.23 -10.31 7.91e+00 1phr 157 -33.76 -10.23 8.20e+00 1qo2A 241 -32.51 -10.09 8.74e+00 1cp2A 269 -37.51 -10.08 8.78e+00 1rpmA 278 -31.09 -10.01 9.04e+00 1eqnA 321 -32.27 -9.92 9.42e+00 1kdoA 227 -31.71 -9.92 9.43e+00 1vpt 348 -36.20 -9.92 9.44e+00 3mag 307 -36.38 -9.89 9.58e+00 1fkx 349 -32.14 -9.88 9.60e+00 1nsj 205 -30.97 -9.88 9.62e+00 1dkuA 317 -39.64 -9.88 9.63e+00 1jqfA 334 -31.09 -9.78 1.00e+01 1jlnA 297 -32.25 -9.77 1.01e+01 2hnp 321 -32.15 -9.69 1.05e+01 1fokA 568 -32.17 -9.64 1.07e+01 1eudB 396 -34.72 -9.62 1.09e+01 1khdA 345 -31.91 -9.61 1.09e+01 1ibsA 317 -39.23 -9.61 1.09e+01 1yptA 305 -30.30 -9.60 1.10e+01 1g7fA 298 -31.90 -9.59 1.10e+01 2cmkA 227 -31.47 -9.57 1.11e+01 1d3kA 329 -30.59 -9.48 1.16e+01 1a8e 329 -30.59 -9.47 1.16e+01 1v39 322 -36.10 -9.42 1.19e+01 1vp9 322 -36.10 -9.42 1.19e+01 1bgp 309 -29.90 -9.35 1.23e+01 1larA 575 -32.16 -9.31 1.25e+01 1dg9A 157 -33.72 -9.29 1.26e+01 1bd3A 243 -30.67 -9.27 1.28e+01 1dkrA 317 -39.15 -9.12 1.37e+01 1ii2A 524 -32.98 -9.10 1.38e+01 1tia 279 -29.52 -9.08 1.40e+01 1bvh 157 -33.67 -9.05 1.41e+01 1ewkA 490 -35.66 -9.04 1.42e+01 1ao0A 459 -33.84 -9.00 1.44e+01 1ee9A 320 -33.97 -8.98 1.46e+01 1brmA 367 -32.06 -8.90 1.52e+01 1fl2A 310 -31.80 -8.85 1.55e+01 1eucB 396 -33.69 -8.81 1.58e+01 1lct 333 -30.48 -8.72 1.66e+01 1bjoA 360 -29.45 -8.71 1.66e+01 1i2oA 316 -31.02 -8.69 1.68e+01 1ytn 306 -29.53 -8.68 1.68e+01 1bglA 1023 -32.31 -8.62 1.73e+01 1e4yA 214 -29.35 -8.61 1.74e+01 1bjnA 360 -29.36 -8.59 1.76e+01 1b3eA 330 -29.83 -8.57 1.77e+01 1djnA 729 -36.16 -8.55 1.79e+01 1thfD 253 -34.87 -8.54 1.80e+01 1brwA 433 -32.22 -8.52 1.81e+01 1ytw 306 -29.40 -8.51 1.83e+01 2tmdA 729 -36.08 -8.50 1.83e+01 1cipA 353 -33.19 -8.50 1.84e+01 1add 349 -31.10 -8.49 1.84e+01 1aky 221 -29.54 -8.49 1.84e+01 1jfvA 131 -30.65 -8.49 1.84e+01 1a4iA 301 -31.95 -8.46 1.87e+01 1gntA 553 -35.04 -8.45 1.88e+01 1ihnA 113 -27.75 -8.44 1.89e+01 1tplA 426 -31.13 -8.44 1.89e+01 1jy1A 464 -30.34 -8.44 1.89e+01 1jw9B 249 -30.17 -8.42 1.90e+01 1i9gA 280 -30.14 -8.37 1.95e+01 1a4iB 301 -31.80 -8.35 1.97e+01 2pec 353 -30.56 -8.30 2.02e+01 1a6dA 545 -32.67 -8.28 2.04e+01 1e1dA 553 -34.85 -8.28 2.04e+01 1gnlA 544 -35.05 -8.25 2.06e+01 1ehyA 294 -30.49 -8.24 2.08e+01 1g8kA 825 -31.95 -8.17 2.15e+01 1edzA 320 -33.08 -8.16 2.16e+01 1fnc 314 -31.79 -8.14 2.19e+01 2scuB 388 -33.78 -8.10 2.22e+01 1kezA 300 -30.82 -8.07 2.26e+01 1g8jA 825 -31.85 -8.05 2.28e+01 1onrA 316 -30.41 -8.05 2.29e+01 1zin 217 -31.16 -8.03 2.30e+01 1dp0A 1023 -31.85 -8.03 2.30e+01 1e2uA 553 -34.87 -7.98 2.35e+01 1qg0A 308 -32.39 -7.97 2.37e+01 1cnpA 90 -25.96 -7.96 2.39e+01 1g6oA 330 -34.46 -7.95 2.39e+01 1a4mA 349 -30.84 -7.95 2.40e+01 1dpgA 485 -32.59 -7.91 2.44e+01 1nar 290 -31.52 -7.89 2.47e+01 2dpg 485 -32.84 -7.86 2.50e+01 1fnd 314 -31.50 -7.85 2.52e+01 1fbtA 190 -29.82 -7.85 2.52e+01 1ckeA 227 -29.55 -7.84 2.53e+01 1kyqA 274 -30.41 -7.84 2.53e+01 1jf8A 131 -30.54 -7.78 2.60e+01 1b37B 472 -33.35 -7.76 2.63e+01 1j9eA 147 -31.04 -7.71 2.69e+01 1jz8A 1023 -31.46 -7.67 2.75e+01 1diaA 306 -31.31 -7.66 2.76e+01 1ksfX 758 -34.30 -7.63 2.80e+01 1pjbA 361 -30.02 -7.58 2.87e+01 1e3hA 757 -32.55 -7.58 2.87e+01 1iejA 332 -28.86 -7.57 2.88e+01 1air 353 -29.73 -7.57 2.88e+01 1hzdA 272 -29.92 -7.57 2.89e+01 8ohm 435 -35.32 -7.53 2.95e+01 1e79A 510 -34.28 -7.53 2.95e+01 1jpnA 296 -36.54 -7.53 2.95e+01 1fdr 248 -32.43 -7.53 2.95e+01 1jscA 630 -33.86 -7.51 2.97e+01 1dd9A 338 -30.60 -7.51 2.98e+01 1eyeA 280 -29.83 -7.49 3.00e+01 1eyyA 510 -34.17 -7.48 3.02e+01 1php 394 -31.10 -7.46 3.06e+01 1ekeA 230 -30.25 -7.44 3.07e+01 1nipA 289 -33.87 -7.44 3.08e+01 1hy3A 294 -31.74 -7.40 3.14e+01 1aquA 297 -31.43 -7.39 3.17e+01 1g4uS 383 -34.76 -7.37 3.20e+01 1ez0A 510 -34.13 -7.34 3.23e+01 1jx4A 352 -28.40 -7.33 3.26e+01 1pjcA 361 -29.66 -7.32 3.27e+01 1b5qA 472 -32.43 -7.28 3.34e+01 1fg7A 356 -32.01 -7.23 3.42e+01 1sayA 361 -29.66 -7.18 3.51e+01 2ng1 293 -36.19 -7.17 3.53e+01 1aj2 282 -31.75 -7.14 3.59e+01 1gmlA 178 -29.56 -7.13 3.59e+01 1aj0 282 -31.75 -7.10 3.66e+01 1gpeA 587 -33.78 -7.05 3.74e+01 1bs9 207 -27.65 -7.00 3.84e+01 1hnuA 280 -29.73 -7.00 3.84e+01 1heiA 451 -34.70 -7.00 3.85e+01 1akeA 214 -29.05 -6.97 3.90e+01 1b37A 472 -32.43 -6.97 3.91e+01 1hyuA 521 -32.50 -6.96 3.93e+01 1h1nA 305 -30.89 -6.95 3.95e+01