% 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.YGR236C.t2k-100-40-40-str2+CB_burial_14_7 Host: farm16.cse.ucsc.edu Fri Mar 3 09:13:23 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR236C % --------------------------------------------------------------------- % 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 YGR236C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR236C.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR236C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 96 nodes, 172.36 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(=1.1374) * Reverse)^tau(=0.8911))) % 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 1eni 138 -30.44 -15.59 2.57e-02 1enk 138 -29.93 -15.36 3.05e-02 1vasA 137 -29.26 -15.18 3.50e-02 1enj 138 -28.52 -14.03 8.26e-02 2end 138 -28.39 -13.46 1.27e-01 1yx4A 132 -36.07 -11.73 4.71e-01 1urqA 63 -31.95 -11.30 6.52e-01 1su4A 994 -23.69 -10.86 9.14e-01 1mml 265 -21.84 -10.62 1.10e+00 1ny9A 143 -23.54 -10.11 1.63e+00 1ufbA 127 -20.82 -10.10 1.65e+00 1b43A 340 -21.62 -10.04 1.73e+00 2hfh 109 -24.88 -9.86 1.99e+00 1ijyA 130 -21.61 -9.84 2.02e+00 1rwtA 232 -27.12 -9.52 2.59e+00 1im4A 221 -24.91 -9.41 2.83e+00 1mroC 247 -25.68 -9.38 2.89e+00 1ovnA 248 -20.71 -9.37 2.91e+00 1hbnC 248 -25.39 -9.28 3.12e+00 1jb0D 138 -26.84 -9.23 3.24e+00 1ijxA 127 -19.77 -9.20 3.33e+00 1f07A 321 -19.45 -9.15 3.45e+00 1cokA 68 -21.15 -9.05 3.76e+00 1w6uA 302 -22.03 -8.92 4.16e+00 1zsxA 347 -19.17 -8.91 4.18e+00 1r5zA 323 -19.39 -8.88 4.27e+00 1bpe 335 -25.18 -8.87 4.31e+00 1iyjB 817 -24.67 -8.87 4.31e+00 1qs0A 407 -21.20 -8.81 4.51e+00 1nt4A 391 -18.17 -8.74 4.78e+00 1a8rA 221 -23.47 -8.71 4.89e+00 1sfkA 76 -23.73 -8.71 4.91e+00 1unlD 208 -20.64 -8.62 5.28e+00 1h4lD 147 -19.71 -8.59 5.37e+00 1x9mA 698 -24.99 -8.53 5.66e+00 1o51A 114 -19.32 -8.52 5.68e+00 1v1rA 400 -26.00 -8.49 5.82e+00 1x7yA 400 -26.12 -8.34 6.55e+00 1wwpA 119 -19.16 -8.33 6.61e+00 2astA 159 -24.42 -8.22 7.19e+00 1fqvJ 149 -24.63 -8.22 7.22e+00 1t7pA 698 -24.21 -8.18 7.42e+00 1qb2A 109 -27.26 -8.13 7.78e+00 2fpmA 322 -19.03 -8.12 7.82e+00 1uelB 48 -25.89 -8.06 8.18e+00 1yewB 247 -26.05 -8.04 8.32e+00 1tv9A 335 -19.22 -8.03 8.40e+00 1e0fI 57 -21.90 -8.02 8.44e+00 1olsA 400 -25.56 -8.00 8.60e+00 1v9mA 323 -18.26 -7.99 8.66e+00 1exbA 332 -18.12 -7.95 8.97e+00 1ztsA 139 -26.10 -7.88 9.49e+00 1xo3A 101 -17.75 -7.80 1.00e+01 1fqvD 149 -24.52 -7.77 1.03e+01 1g8eA 116 -26.55 -7.74 1.06e+01 1gfsA 321 -17.74 -7.71 1.08e+01 1bsvA 321 -17.80 -7.70 1.09e+01 1vk9A 151 -19.70 -7.70 1.09e+01 1aa7A 158 -21.84 -7.70 1.10e+01 1yaxA 153 -22.06 -7.69 1.10e+01 1m5yA 408 -23.02 -7.67 1.12e+01 1umgA 362 -17.96 -7.64 1.15e+01 1jgsA 138 -21.28 -7.58 1.20e+01 1alvA 173 -20.06 -7.57 1.21e+01 1cfi 47 -22.40 -7.56 1.22e+01 1t4gA 322 -18.57 -7.48 1.31e+01 1xfxO 149 -24.44 -7.45 1.33e+01 1bpyA 335 -18.24 -7.41 1.38e+01 1sk4A 163 -18.49 -7.32 1.48e+01 1or7A 194 -25.03 -7.32 1.48e+01 1w7jB 151 -23.59 -7.28 1.53e+01 2beqD 48 -25.15 -7.27 1.54e+01 1a00B 146 -19.51 -7.27 1.54e+01 1zsyA 357 -16.85 -7.27 1.54e+01 1ubi 76 -19.49 -7.25 1.56e+01 1wywA 230 -23.28 -7.24 1.58e+01 1h7sA 365 -16.60 -7.22 1.61e+01 1ubq 76 -19.76 -7.21 1.62e+01 1ea3A 164 -21.66 -7.20 1.63e+01 1p9cA 45 -26.39 -7.11 1.75e+01 2aalA 131 -18.16 -7.10 1.77e+01 1xn8A 131 -22.96 -7.10 1.77e+01 2c43A 323 -18.07 -7.09 1.78e+01 1aj5A 173 -20.78 -7.09 1.78e+01 1cg5B 141 -18.84 -7.09 1.78e+01 1vl2A 421 -24.46 -7.08 1.79e+01 1ogwA 76 -20.63 -7.06 1.82e+01 1jj2L 194 -22.14 -7.05 1.84e+01 1b4cA 92 -27.53 -7.04 1.85e+01 1l8cA 95 -20.91 -7.01 1.90e+01 1h6oA 204 -20.44 -7.01 1.90e+01 2a4hA 126 -21.52 -7.00 1.92e+01 2lbp 346 -16.11 -6.97 1.97e+01 1oj6A 151 -19.83 -6.96 1.98e+01 2au3A 407 -17.53 -6.91 2.06e+01 1af7 274 -16.81 -6.91 2.06e+01 1qbgA 272 -20.15 -6.89 2.09e+01 1h32B 138 -19.61 -6.89 2.10e+01 1ash 150 -19.34 -6.88 2.10e+01 1hbyA 123 -16.10 -6.87 2.13e+01 1q1fA 151 -18.42 -6.85 2.17e+01 1tbrR 103 -24.37 -6.84 2.19e+01 1to6A 371 -15.68 -6.81 2.24e+01 1ajyA 71 -24.70 -6.78 2.29e+01 1e7rA 321 -16.95 -6.78 2.29e+01 1d4aA 273 -19.81 -6.78 2.29e+01 1d3zA 76 -19.80 -6.77 2.30e+01 1whtA 256 -17.96 -6.76 2.32e+01 1wpgA 994 -23.14 -6.75 2.35e+01 1fdyA 297 -16.13 -6.75 2.35e+01 1nbfD 76 -18.77 -6.75 2.35e+01 1a79A 171 -18.32 -6.74 2.36e+01 1wehA 171 -17.18 -6.74 2.36e+01 1b1eA 123 -15.89 -6.73 2.39e+01 1m2eA 135 -16.04 -6.73 2.39e+01 1whsA 255 -18.04 -6.72 2.41e+01 1bwsA 321 -16.82 -6.70 2.44e+01 1abmA 198 -17.68 -6.70 2.44e+01 2fe7A 166 -19.67 -6.67 2.50e+01 1a17 166 -23.98 -6.66 2.52e+01 1nal1 297 -16.07 -6.65 2.53e+01 1qhdA 398 -17.16 -6.65 2.53e+01 1njkA 156 -16.07 -6.65 2.54e+01 1qrqA 325 -17.06 -6.64 2.56e+01 4rxn 54 -24.66 -6.63 2.58e+01 1hgeB 175 -27.90 -6.62 2.59e+01 2viuB 175 -27.78 -6.60 2.66e+01 1u5kA 244 -16.90 -6.60 2.66e+01 1zzaA 90 -23.65 -6.59 2.66e+01 3hmgB 175 -27.78 -6.59 2.68e+01 1ezjA 115 -29.71 -6.58 2.69e+01 1pv6A 417 -17.87 -6.58 2.70e+01 5rxn 54 -24.42 -6.57 2.72e+01 1k8tA 510 -23.74 -6.56 2.73e+01 1vflA 356 -16.84 -6.55 2.77e+01 1yruB 74 -23.31 -6.54 2.78e+01 1e6uA 321 -16.75 -6.53 2.80e+01 1kbqA 273 -19.59 -6.53 2.81e+01 1nal3 297 -15.89 -6.53 2.81e+01 1vqsA 116 -18.97 -6.52 2.82e+01 1r1mA 164 -17.92 -6.51 2.84e+01 1wolA 122 -17.65 -6.47 2.93e+01 1sfxA 109 -21.03 -6.47 2.94e+01 1b1iA 123 -16.10 -6.46 2.96e+01 1jy3P 48 -23.87 -6.45 2.99e+01 1avgL 41 -25.99 -6.44 3.02e+01 1uf5A 303 -17.11 -6.43 3.03e+01 1ap6A 198 -17.11 -6.42 3.07e+01 1wu3I 161 -19.49 -6.38 3.17e+01 2a73B 991 -23.55 -6.37 3.18e+01 1s4bP 674 -18.32 -6.34 3.28e+01 1u9lA 70 -20.07 -6.32 3.32e+01 1kekA 1231 -24.94 -6.31 3.36e+01 1n0nA 199 -17.29 -6.30 3.37e+01 1aipC 196 -21.00 -6.30 3.38e+01 2aamA 309 -15.81 -6.28 3.44e+01 1on2A 142 -24.39 -6.27 3.45e+01 1mqeA 207 -16.65 -6.27 3.46e+01 1wspA 84 -17.33 -6.26 3.48e+01 1k59A 123 -16.06 -6.24 3.53e+01 1kxqE 120 -13.77 -6.23 3.58e+01 2b9hA 353 -18.83 -6.22 3.60e+01 1erzA 303 -17.19 -6.22 3.60e+01 1g72B 69 -26.62 -6.22 3.61e+01 1bc5A 269 -15.70 -6.21 3.65e+01 2ae6A 166 -15.86 -6.20 3.66e+01 1llp 343 -15.52 -6.20 3.66e+01 1zmbA 290 -19.93 -6.20 3.68e+01 1vicA 262 -17.14 -6.20 3.68e+01 1yydA 357 -15.52 -6.19 3.70e+01 1hcc 59 -18.57 -6.17 3.75e+01 1b2jA 54 -23.19 -6.17 3.77e+01 1ru4A 400 -14.50 -6.16 3.79e+01 1f0mA 82 -17.47 -6.14 3.84e+01 1mn1 357 -15.54 -6.14 3.85e+01 1pl4A 198 -17.15 -6.12 3.90e+01 1j34C 46 -21.81 -6.10 3.96e+01 2fb6A 117 -14.54 -6.10 3.97e+01