% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 04/28/03_14:00:53 % (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-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.YGR029W.t2k-100-30-str Host: cc68 Tue Jun 10 05:10:45 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR029W % --------------------------------------------------------------------- % 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 YGR029W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR029W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8223 sequences, 1949748 residues, 190 nodes, 167.44 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(=2.3116) * Reverse)^tau(=0.7506))) % 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 1oqcA 125 -161.17 -137.24 1.40e-29 1jraA 117 -138.18 -116.31 9.40e-26 1jr8A 117 -137.34 -115.32 1.44e-25 1euvA 221 -33.60 -12.66 2.72e-02 1ku1A 230 -31.63 -11.27 7.82e-02 1eyvA 156 -29.86 -11.04 9.36e-02 1dgjA 907 -35.59 -10.99 9.70e-02 1g8lA 411 -30.61 -9.37 3.49e-01 1jvr 137 -31.78 -9.10 4.35e-01 1ngkA 128 -27.99 -8.61 6.51e-01 1iwhA 141 -27.15 -8.44 7.47e-01 1hlrA 907 -32.16 -7.96 1.11e+00 1je8A 82 -25.41 -7.82 1.25e+00 1fd8A 73 -24.65 -7.70 1.39e+00 2abk 211 -27.78 -7.55 1.57e+00 1ciy 590 -30.79 -7.50 1.64e+00 1agi 125 -25.64 -7.33 1.90e+00 1jjfA 268 -27.94 -7.15 2.21e+00 1mlwA 301 -28.29 -7.14 2.23e+00 1a32 88 -24.78 -6.98 2.57e+00 1g4yR 148 -25.81 -6.98 2.58e+00 1gg3A 279 -28.26 -6.93 2.68e+00 1fxxA 482 -28.62 -6.79 3.02e+00 1cc8A 73 -23.33 -6.75 3.14e+00 1bev1 281 -28.00 -6.71 3.24e+00 1m6bA 621 -32.32 -6.68 3.33e+00 4enl 436 -28.37 -6.64 3.45e+00 1jroB 777 -32.22 -6.53 3.81e+00 1irdA 141 -25.39 -6.45 4.09e+00 1pbwA 216 -27.09 -6.41 4.22e+00 1f7tA 122 -24.73 -6.27 4.80e+00 1abwA 283 -26.67 -6.27 4.80e+00 1j7yA 141 -25.17 -6.25 4.87e+00 1babA 143 -25.18 -6.24 4.92e+00 1g8iA 190 -26.20 -6.13 5.43e+00 1o6eA 235 -26.19 -6.11 5.50e+00 1itg 166 -25.33 -6.08 5.67e+00 1a04A 215 -26.42 -6.05 5.81e+00 1pyp 285 -29.84 -5.91 6.59e+00 1e8nA 710 -28.52 -5.85 6.98e+00 1h2wA 710 -28.52 -5.82 7.16e+00 1h2xA 710 -28.53 -5.82 7.18e+00 1qfmA 710 -28.52 -5.81 7.26e+00 1if1A 113 -24.77 -5.81 7.26e+00 1hyvA 166 -24.43 -5.74 7.70e+00 1eqjA 511 -27.75 -5.70 8.02e+00 1ky9A 448 -27.81 -5.68 8.16e+00 1b9dA 163 -24.41 -5.63 8.50e+00 1ejjA 511 -27.80 -5.61 8.67e+00 1o98A 511 -27.71 -5.58 8.90e+00 1jenB 67 -23.18 -5.52 9.45e+00 1f4tA 368 -26.27 -5.48 9.77e+00 1gio 125 -23.68 -5.47 9.89e+00 1bl3A 160 -24.09 -5.41 1.04e+01 1b9xB 68 -22.64 -5.39 1.06e+01 1vaoA 560 -28.94 -5.39 1.06e+01 1ixh 321 -26.41 -5.37 1.08e+01 1dwtA 153 -24.60 -5.29 1.16e+01 1toh 343 -26.26 -5.28 1.17e+01 2oneA 436 -26.96 -5.27 1.19e+01 1ystH 260 -29.10 -5.25 1.21e+01 4rnpA 883 -29.34 -5.24 1.22e+01 1kw4A 89 -23.04 -5.22 1.25e+01 1qovH 260 -27.41 -5.20 1.26e+01 1gjnA 153 -24.48 -5.20 1.27e+01 1jwwA 80 -22.20 -5.18 1.29e+01 1ltzA 297 -26.18 -5.17 1.30e+01 1itf 165 -25.47 -5.15 1.33e+01 1kgnA 329 -26.33 -5.14 1.34e+01 1iapA 211 -24.90 -5.14 1.34e+01 1b75A 94 -23.01 -5.12 1.37e+01 1oneA 436 -26.71 -5.11 1.38e+01 1tbgE 68 -22.22 -5.10 1.40e+01 1mhqA 148 -26.78 -5.00 1.53e+01 1hxs1 302 -27.44 -4.96 1.59e+01 1gotG 73 -22.31 -4.94 1.62e+01 1myf 153 -24.62 -4.90 1.68e+01 1aw0 72 -21.33 -4.87 1.73e+01 1jflA 228 -24.65 -4.86 1.74e+01 1ysc 421 -26.54 -4.85 1.76e+01 1dszA 86 -23.41 -4.83 1.80e+01 1pov1 302 -27.07 -4.80 1.85e+01 1h0hA 977 -30.78 -4.78 1.89e+01 3cln 148 -23.75 -4.69 2.06e+01 1mkaA 171 -24.14 -4.68 2.07e+01 1auk 489 -27.22 -4.68 2.07e+01 1a0sP 413 -25.76 -4.65 2.14e+01 1ha2A 585 -27.94 -4.61 2.21e+01 1ebmA 317 -26.43 -4.60 2.24e+01 1dxsA 80 -22.62 -4.59 2.25e+01 1ko9A 345 -26.82 -4.57 2.31e+01 1mgn 154 -24.38 -4.56 2.33e+01 1sw6A 327 -25.71 -4.54 2.37e+01 1qhtA 775 -27.17 -4.52 2.41e+01 1cokA 68 -21.92 -4.52 2.42e+01 5pal 109 -22.95 -4.48 2.50e+01 1cjwA 166 -24.13 -4.47 2.52e+01 1lwyA 324 -26.46 -4.47 2.53e+01 1aueA 100 -23.14 -4.47 2.54e+01 4rxn 54 -25.98 -4.45 2.59e+01 1ezvD 245 -26.52 -4.42 2.67e+01 1dw9A 156 -23.53 -4.41 2.68e+01 1iu8A 206 -24.50 -4.41 2.68e+01 1dwkA 156 -23.36 -4.37 2.79e+01 1bba 36 -19.98 -4.36 2.81e+01 1j5sA 463 -26.65 -4.36 2.81e+01 1exqA 154 -24.41 -4.36 2.83e+01 1ka3A 90 -22.28 -4.34 2.87e+01 1cg5B 141 -23.21 -4.33 2.90e+01 2spo 154 -24.14 -4.33 2.92e+01 1kyoD 248 -26.40 -4.32 2.92e+01 3kvt 115 -22.56 -4.32 2.93e+01 1tgoA 773 -27.04 -4.31 2.97e+01 1fe0A 68 -20.79 -4.30 2.99e+01 1kb9D 246 -26.43 -4.30 3.00e+01 1iro 54 -25.52 -4.27 3.07e+01 3lynA 136 -24.59 -4.27 3.07e+01 1ez3A 127 -23.21 -4.26 3.11e+01 1jwgA 147 -23.57 -4.24 3.16e+01 1e9rA 437 -26.21 -4.23 3.21e+01 1j5rA 371 -25.39 -4.22 3.22e+01 1oaa 259 -23.79 -4.22 3.22e+01 1sep 261 -23.80 -4.21 3.26e+01 1vrtA 560 -28.21 -4.21 3.27e+01 1e4uA 78 -24.16 -4.20 3.28e+01 1f3vA 179 -23.38 -4.20 3.28e+01 1hra 81 -23.35 -4.20 3.29e+01 1lpuA 332 -25.29 -4.20 3.31e+01 1dn1B 267 -24.47 -4.19 3.31e+01 1ks2A 219 -23.54 -4.18 3.37e+01 1iweA 457 -25.54 -4.15 3.45e+01 1k59A 123 -23.23 -4.15 3.46e+01 1fl0A 171 -24.35 -4.14 3.48e+01 1qltA 560 -28.00 -4.14 3.51e+01 1c1dA 355 -24.42 -4.13 3.53e+01 1avmA 201 -24.21 -4.12 3.57e+01 1m1eB 81 -21.94 -4.11 3.59e+01 1qsdA 106 -23.07 -4.11 3.59e+01 1isuA 62 -23.03 -4.11 3.59e+01 1kuxA 207 -24.09 -4.11 3.61e+01 1no1A 126 -23.71 -4.11 3.61e+01 2occM 46 -20.81 -4.09 3.66e+01 1hbyA 123 -23.03 -4.07 3.73e+01 2itg 163 -23.38 -4.07 3.76e+01 1mbd 153 -23.88 -4.06 3.76e+01 1hdlA 55 -22.84 -4.05 3.82e+01 1dmhA 311 -24.51 -4.05 3.83e+01 1ee8A 266 -26.10 -4.04 3.85e+01 1sbp 310 -25.28 -4.04 3.85e+01 1bsmA 201 -24.11 -4.03 3.91e+01 1m13A 316 -25.18 -4.02 3.92e+01 1cmkE 350 -27.02 -4.02 3.92e+01 1gzsB 165 -22.99 -4.01 3.97e+01 1a4yB 123 -23.50 -4.01 3.98e+01 1jj2P 95 -25.12 -4.01 3.99e+01