% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YBR221W-A.t2k-100-40-40-str2+CB_burial_14_7 Host: farm15.cse.ucsc.edu Sun Feb 12 15:17:51 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YBR2/YBR221W-A % --------------------------------------------------------------------- % 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 YBR221W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YBR221W-A.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YBR221W-A.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 35 nodes, 62.06 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.8246) * Reverse)^tau(=0.8175))) % Calculated when Simple < simple_threshold (10000.00) % 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 1jpyB 137 -27.90 -12.83 2.10e-02 1jpyA 137 -28.06 -12.57 2.62e-02 1dgfA 497 -24.41 -8.91 6.26e-01 1dghB 498 -24.02 -8.84 6.68e-01 1ng2A 193 -21.90 -8.38 1.01e+00 1r61A 207 -26.10 -8.19 1.21e+00 1ukmB 128 -22.26 -8.15 1.25e+00 1k81A 36 -19.87 -7.94 1.51e+00 1uh6A 100 -21.46 -7.85 1.64e+00 1p94A 76 -22.16 -7.56 2.14e+00 1tp5A 119 -16.74 -7.56 2.15e+00 1b2tA 77 -17.09 -7.50 2.26e+00 1be9A 119 -16.66 -7.48 2.31e+00 1v7pB 128 -22.33 -7.48 2.31e+00 1y6hA 177 -16.25 -7.46 2.34e+00 1grj 158 -16.29 -7.29 2.75e+00 1q48A 134 -20.67 -7.29 2.76e+00 1pwt 61 -17.59 -7.17 3.06e+00 1dbdA 100 -17.85 -6.98 3.68e+00 2bz8A 58 -16.79 -6.92 3.90e+00 1shg 62 -17.69 -6.88 4.03e+00 2a73B 991 -23.36 -6.86 4.12e+00 2b7yB 51 -26.38 -6.71 4.75e+00 2bh8A 101 -21.01 -6.60 5.27e+00 1tud 62 -18.15 -6.54 5.57e+00 1h4aX 173 -13.85 -6.48 5.87e+00 1vl7A 157 -16.11 -6.48 5.88e+00 1gnwA 211 -15.78 -6.47 5.94e+00 1lw3A 657 -14.81 -6.46 6.02e+00 1g2bA 62 -17.68 -6.45 6.07e+00 1ucyH 150 -17.83 -6.36 6.59e+00 2a74B 188 -21.52 -6.36 6.60e+00 1lenB 52 -22.12 -6.36 6.62e+00 1iw4A 55 -16.67 -6.30 6.99e+00 1c8cA 64 -15.26 -6.28 7.12e+00 1un3A 123 -15.08 -6.27 7.18e+00 1jt8A 102 -19.97 -6.22 7.54e+00 1sqzA 121 -15.06 -6.22 7.56e+00 1m2oB 190 -15.48 -6.22 7.58e+00 1yqbA 100 -16.40 -6.08 8.58e+00 1t7sA 137 -16.55 -6.08 8.59e+00 1sso 62 -15.51 -6.03 9.04e+00 1zsqA 528 -14.04 -6.00 9.34e+00 1hmy 327 -14.95 -5.97 9.54e+00 1ovoA 56 -17.94 -5.96 9.64e+00 1jic 62 -16.23 -5.94 9.84e+00 1s5lL 37 -20.06 -5.89 1.03e+01 1fv0A 121 -14.87 -5.89 1.04e+01 1wisA 124 -16.66 -5.82 1.11e+01 2ct7A 86 -21.38 -5.80 1.13e+01 2axtL 37 -20.18 -5.79 1.14e+01 1vokA 200 -14.72 -5.77 1.17e+01 1tj9A 121 -14.94 -5.72 1.22e+01 2aw2B 108 -16.13 -5.71 1.23e+01 1tk4A 121 -15.05 -5.69 1.26e+01 1j9jA 247 -18.10 -5.67 1.28e+01 1i25A 37 -22.00 -5.67 1.28e+01 1zwpA 121 -14.63 -5.67 1.28e+01 1ars 396 -14.14 -5.67 1.29e+01 1ycyA 71 -14.55 -5.58 1.39e+01 1j9lA 247 -17.96 -5.56 1.42e+01 1pm6A 72 -21.93 -5.56 1.43e+01 1z6fA 363 -13.81 -5.55 1.44e+01 2ltnB 52 -20.18 -5.52 1.49e+01 2ct5A 73 -16.87 -5.52 1.49e+01 3mhtA 327 -14.36 -5.51 1.50e+01 1sqiA 393 -13.30 -5.51 1.50e+01 1xg1A 67 -14.89 -5.50 1.51e+01 2bopA 85 -15.58 -5.47 1.55e+01 1i17A 107 -16.69 -5.46 1.57e+01 2asfA 137 -15.29 -5.44 1.61e+01 1jo6A 45 -19.60 -5.44 1.61e+01 1ov3A 138 -21.43 -5.40 1.67e+01 1oghA 204 -16.48 -5.40 1.67e+01 1bf4A 63 -13.84 -5.38 1.70e+01 1ekzA 76 -15.02 -5.37 1.71e+01 1y3tA 337 -13.54 -5.35 1.75e+01 1pkhA 204 -16.68 -5.31 1.82e+01 1hbyA 123 -13.64 -5.30 1.84e+01 2aat 396 -13.78 -5.29 1.85e+01 1dfnA 30 -16.42 -5.29 1.86e+01 1nvmB 312 -13.50 -5.29 1.87e+01 1fjxA 327 -13.42 -5.27 1.90e+01 1f3iA 481 -17.82 -5.25 1.94e+01 1zmiA 29 -15.78 -5.24 1.95e+01 1txb 73 -16.91 -5.22 1.98e+01 1ju8A 37 -19.52 -5.22 2.00e+01 1xlqA 106 -11.71 -5.19 2.06e+01 1yp5A 58 -14.49 -5.18 2.07e+01 1wwuA 99 -18.41 -5.14 2.16e+01 1fv1C 20 -19.40 -5.13 2.18e+01 2rspA 124 -15.38 -5.13 2.18e+01 1vr5A 547 -13.03 -5.11 2.22e+01 1ugxA 133 -13.99 -5.10 2.25e+01 1v86A 95 -17.24 -5.09 2.25e+01 1amm 174 -11.91 -5.09 2.26e+01 1k59A 123 -13.60 -5.09 2.26e+01 1aym4 68 -19.89 -5.08 2.29e+01 1vgjA 184 -13.21 -5.07 2.31e+01 1l6nA 289 -19.45 -5.06 2.33e+01 1u8zA 168 -12.48 -5.04 2.39e+01 1k1tA 99 -16.01 -5.01 2.45e+01 1o54A 277 -19.19 -5.01 2.45e+01 2c7pA 327 -13.21 -4.98 2.52e+01 1y75A 118 -11.92 -4.96 2.59e+01 5p21 166 -12.54 -4.95 2.60e+01 1eerB 227 -12.96 -4.94 2.64e+01 4gcr 174 -11.82 -4.93 2.66e+01 1qhfA 240 -12.43 -4.93 2.67e+01 1dazC 99 -16.21 -4.92 2.69e+01 821p 166 -12.43 -4.90 2.73e+01 1uquA 482 -11.74 -4.85 2.88e+01 1a4yB 123 -13.90 -4.84 2.90e+01 1bfeA 119 -13.28 -4.84 2.90e+01 1xkpB 124 -13.68 -4.82 2.95e+01 2a74A 643 -18.68 -4.82 2.98e+01 1ubpB 122 -15.56 -4.80 3.02e+01 1bl1 31 -12.89 -4.79 3.07e+01 1moxC 50 -15.61 -4.78 3.09e+01 1h9mA 145 -12.18 -4.76 3.15e+01 1ckaA 57 -15.34 -4.75 3.18e+01 1rw2A 152 -19.58 -4.74 3.21e+01 1afoA 40 -14.40 -4.73 3.24e+01 2camA 127 -17.04 -4.73 3.24e+01 1ukkA 142 -13.19 -4.73 3.25e+01 1kpmA 121 -13.64 -4.71 3.30e+01 1k2eA 156 -16.25 -4.71 3.30e+01 1aqt 138 -12.67 -4.71 3.32e+01 1zkcA 197 -12.15 -4.70 3.35e+01 1irdA 141 -11.82 -4.70 3.35e+01 1h9jA 145 -12.13 -4.69 3.36e+01 1gcqC 70 -14.38 -4.68 3.40e+01 1jotA 133 -13.85 -4.68 3.42e+01 1cskA 71 -15.36 -4.67 3.44e+01 9apiB 36 -17.08 -4.67 3.45e+01 1dwnA 127 -18.75 -4.67 3.45e+01 1mai 131 -14.98 -4.66 3.47e+01 1tw7A 99 -14.37 -4.66 3.48e+01 1oqqA 106 -10.98 -4.66 3.49e+01 1qi6A 475 -13.57 -4.66 3.49e+01 1f3mC 297 -11.79 -4.65 3.53e+01 1k26A 156 -16.04 -4.64 3.55e+01 1p9rA 418 -13.31 -4.62 3.62e+01 1yhvA 297 -13.55 -4.62 3.63e+01 1pf4A 582 -18.54 -4.61 3.66e+01 2a9kA 187 -11.96 -4.61 3.66e+01 4ubpB 126 -15.75 -4.61 3.67e+01 2rspB 124 -14.38 -4.61 3.67e+01 1t61C 227 -16.17 -4.60 3.69e+01 1ytfC 79 -14.69 -4.59 3.73e+01 1abwA 283 -11.59 -4.59 3.75e+01 1zirA 173 -12.49 -4.58 3.78e+01 1vajA 214 -14.24 -4.57 3.81e+01 1fgkA 310 -13.90 -4.57 3.81e+01 1mvpA 124 -13.79 -4.57 3.81e+01 2bwkA 121 -13.13 -4.56 3.85e+01 2f15A 96 -15.22 -4.55 3.88e+01 6mhtA 327 -14.40 -4.54 3.91e+01 1nubA 229 -15.49 -4.54 3.92e+01 1iwhA 141 -11.29 -4.53 3.95e+01