% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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.YGR212W.t2k-100-40-40-str2+CB_burial_14_7 Host: cc50 Sun Oct 12 01:55:16 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR212W % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR212W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR212W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR212W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 469 nodes, 473.53 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(=0.7444) * Reverse)^tau(=0.8910))) % 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 1l5aA 436 -64.12 -33.66 1.78e-04 1o7fA 469 -49.44 -20.27 1.09e-01 1jn5A 140 -50.74 -18.21 3.02e-01 1jkgA 140 -50.99 -17.68 3.93e-01 1je5A 206 -50.21 -17.58 4.14e-01 1foeA 377 -49.98 -16.91 5.79e-01 1ryp2 233 -47.10 -16.83 6.03e-01 1ki1B 352 -53.73 -16.82 6.06e-01 1b7yA 350 -44.66 -16.44 7.37e-01 1pysA 350 -46.17 -15.94 9.49e-01 1icxA 155 -53.66 -15.43 1.23e+00 1g0u1 266 -45.71 -15.29 1.31e+00 1oejA 193 -48.60 -15.29 1.32e+00 1f1sA 814 -47.01 -15.08 1.46e+00 1f5aA 513 -45.51 -15.06 1.48e+00 1e7uA 961 -50.81 -14.61 1.86e+00 1k8kA 418 -43.88 -14.15 2.36e+00 1hjp 203 -45.70 -14.08 2.45e+00 1jhnA 424 -64.17 -13.54 3.23e+00 1a15A 67 -41.72 -13.48 3.32e+00 1fa0B 537 -43.99 -13.17 3.90e+00 1rgs 288 -39.94 -13.10 4.04e+00 1qgvA 142 -37.83 -13.05 4.16e+00 1nhs 447 -41.70 -13.04 4.19e+00 1o0iA 138 -41.42 -13.01 4.24e+00 1nhp 447 -41.85 -12.98 4.32e+00 1regX 122 -41.42 -12.84 4.63e+00 1lenA 181 -45.92 -12.75 4.87e+00 1qg7A 67 -41.36 -12.73 4.91e+00 1joa 447 -40.94 -12.71 4.96e+00 1g4mA 393 -47.05 -12.61 5.22e+00 1o57A 291 -40.25 -12.57 5.32e+00 1p41A 291 -40.25 -12.57 5.32e+00 1ffyA 917 -40.22 -12.41 5.79e+00 1qu2A 917 -40.22 -12.41 5.79e+00 1f3rB 257 -43.45 -12.39 5.85e+00 1hcz 252 -43.32 -12.24 6.33e+00 1i1iP 681 -43.86 -12.13 6.71e+00 1qf6A 642 -41.29 -12.13 6.72e+00 1f4qA 165 -40.34 -12.02 7.09e+00 1bgp 309 -35.29 -11.97 7.27e+00 1fxlA 167 -47.82 -11.96 7.34e+00 1bh5A 183 -47.61 -11.94 7.38e+00 1jjoC 261 -51.93 -11.84 7.78e+00 1ar0A 127 -44.33 -11.70 8.40e+00 1rhi3 236 -45.62 -11.67 8.54e+00 2pcfB 250 -43.00 -11.65 8.61e+00 1f2nA 238 -39.76 -11.58 8.92e+00 1qddA 144 -36.03 -11.50 9.33e+00 1e2wA 251 -42.28 -11.47 9.48e+00 1dmuA 299 -39.32 -11.41 9.76e+00 1qqp3 220 -49.65 -11.37 9.97e+00 2pvaA 345 -43.42 -11.37 9.97e+00 1ounA 127 -43.82 -11.36 1.00e+01 1b12A 248 -41.30 -11.32 1.02e+01 1cqxA 403 -41.58 -11.31 1.03e+01 1bbt3 220 -47.78 -11.29 1.04e+01 1hh2P 344 -48.80 -11.21 1.09e+01 1k4jA 230 -39.28 -11.10 1.15e+01 1qipA 183 -46.87 -11.10 1.15e+01 1qk3A 233 -36.82 -11.09 1.16e+01 1fh6A 282 -40.76 -11.08 1.16e+01 1m5yA 408 -51.29 -11.02 1.20e+01 1a8h 500 -39.72 -10.94 1.25e+01 1amj 754 -39.02 -10.89 1.28e+01 1cx4A 305 -41.35 -10.86 1.30e+01 1kzfA 230 -40.19 -10.86 1.30e+01 3dapA 320 -39.10 -10.85 1.31e+01 1a4kA 217 -47.03 -10.83 1.32e+01 1jmuB 666 -48.06 -10.80 1.35e+01 1i58A 189 -44.33 -10.77 1.37e+01 1ge8A 249 -56.34 -10.76 1.38e+01 8acn 754 -38.87 -10.75 1.38e+01 4rhv3 236 -44.56 -10.73 1.40e+01 1gwmA 153 -39.68 -10.71 1.41e+01 7icd 416 -39.32 -10.71 1.42e+01 1j6wA 175 -38.76 -10.69 1.43e+01 1gy6A 127 -43.18 -10.58 1.51e+01 1k94A 165 -39.09 -10.57 1.52e+01 1qqgA 264 -38.81 -10.57 1.52e+01 1hq8A 123 -33.85 -10.55 1.54e+01 1guqA 348 -36.41 -10.54 1.55e+01 1k8wA 327 -42.42 -10.52 1.56e+01 1e8xA 961 -48.77 -10.50 1.58e+01 1njkA 156 -44.11 -10.47 1.61e+01 1ekrA 161 -35.27 -10.44 1.63e+01 1dttA 560 -53.98 -10.44 1.63e+01 1gg3A 279 -40.47 -10.42 1.65e+01 1h6dA 433 -37.40 -10.37 1.69e+01 1gupA 348 -36.28 -10.37 1.69e+01 2ltnA 181 -43.54 -10.28 1.77e+01 1vfrA 218 -38.56 -10.26 1.79e+01 2bpa1 426 -42.49 -10.25 1.80e+01 1lnh 857 -42.86 -10.24 1.81e+01 1f06A 320 -38.46 -10.23 1.82e+01 1b0jA 754 -39.09 -10.20 1.85e+01 1dapA 320 -38.99 -10.16 1.88e+01 3pcgA 200 -38.27 -10.14 1.91e+01 1lvl 458 -38.22 -10.12 1.93e+01 1gztA 115 -40.16 -10.12 1.93e+01 1gw5M 435 -46.79 -10.12 1.93e+01 1lkvX 232 -44.16 -10.12 1.93e+01 1i4nA 251 -32.79 -10.08 1.97e+01 1iso 416 -38.25 -10.04 2.02e+01 1jk0B 345 -37.19 -10.03 2.03e+01 1iz5A 249 -55.12 -10.00 2.06e+01 3pvaA 335 -40.67 -10.00 2.06e+01 7acn 754 -38.96 -9.97 2.09e+01 1c96A 753 -38.82 -9.97 2.09e+01 6acn 754 -39.03 -9.96 2.10e+01 1gqeA 365 -43.55 -9.95 2.11e+01 1el6B 219 -54.43 -9.89 2.18e+01 3pchA 200 -37.86 -9.88 2.20e+01 1o0pA 104 -41.95 -9.87 2.20e+01 2pcdA 200 -38.76 -9.86 2.22e+01 1e43A 483 -34.38 -9.85 2.22e+01 1azo 232 -37.95 -9.84 2.25e+01 1epaA 164 -42.21 -9.83 2.25e+01 1l1qA 186 -34.43 -9.83 2.25e+01 1hw7A 255 -55.64 -9.82 2.26e+01 1o5hA 214 -34.73 -9.79 2.30e+01 1oxcA 114 -40.55 -9.76 2.34e+01 1fv0A 121 -34.70 -9.75 2.36e+01 2fnbA 95 -38.94 -9.71 2.40e+01 3pmgA 561 -43.74 -9.70 2.41e+01 1ggwA 140 -40.51 -9.70 2.42e+01 1drmA 131 -38.90 -9.68 2.43e+01 1qj8A 148 -41.08 -9.65 2.48e+01 1c5cL 214 -45.57 -9.61 2.53e+01 1kpmA 121 -34.41 -9.53 2.64e+01 1aipE 405 -41.03 -9.52 2.66e+01 1jb2A 127 -41.50 -9.48 2.71e+01 1dgsA 667 -41.38 -9.44 2.77e+01 1cjcA 460 -36.47 -9.43 2.78e+01 1b6rA 355 -44.03 -9.42 2.80e+01 1mmiA 366 -43.65 -9.38 2.87e+01 1brwA 433 -34.56 -9.36 2.89e+01 1lswA 131 -38.36 -9.36 2.89e+01 1l7iL 214 -43.53 -9.35 2.91e+01 3cla 213 -37.39 -9.33 2.93e+01 2hmiA 558 -48.20 -9.33 2.94e+01 1avqA 228 -36.89 -9.33 2.94e+01 1a6wL 109 -36.15 -9.26 3.05e+01 1cuk 203 -42.21 -9.26 3.05e+01 1kb9B 352 -36.02 -9.26 3.05e+01 1pb1A 416 -37.54 -9.26 3.06e+01 1aisA 182 -45.36 -9.25 3.06e+01 1iicA 422 -45.30 -9.23 3.10e+01 1m22A 503 -34.01 -9.21 3.14e+01 1hbyA 123 -35.92 -9.20 3.15e+01 1of4A 179 -40.67 -9.20 3.15e+01 1rthA 560 -52.97 -9.15 3.24e+01 1go3E 187 -42.18 -9.09 3.34e+01 1a36A 592 -44.06 -9.09 3.35e+01 1mfa 247 -37.27 -9.08 3.37e+01 1jvwA 167 -35.32 -9.04 3.42e+01 1epbA 164 -41.87 -9.03 3.46e+01 1as4A 341 -50.02 -9.00 3.50e+01 1gvzA 237 -33.39 -9.00 3.52e+01 1hxpA 348 -36.10 -8.97 3.56e+01 1b35A 260 -42.79 -8.97 3.56e+01 1n99A 166 -41.06 -8.93 3.64e+01 1drqA 131 -38.47 -8.93 3.64e+01 1rbp 182 -40.78 -8.93 3.64e+01 1b6sA 355 -41.90 -8.93 3.64e+01 1mkiA 330 -34.73 -8.91 3.68e+01 1a6uL 108 -35.06 -8.91 3.69e+01 1a6vL 110 -36.29 -8.90 3.70e+01 1et9A 204 -36.37 -8.87 3.76e+01 1j7iA 264 -43.09 -8.86 3.79e+01 1nvvS 481 -42.49 -8.86 3.79e+01 1hdmB 193 -50.66 -8.85 3.79e+01 1zin 217 -35.66 -8.85 3.80e+01 1awcA 110 -35.09 -8.79 3.92e+01 1i69A 219 -37.16 -8.78 3.94e+01 1mv3A 213 -51.42 -8.78 3.94e+01 1iuz 98 -33.30 -8.78 3.95e+01 1h9oA 112 -33.94 -8.78 3.96e+01 1ezvB 352 -35.95 -8.77 3.97e+01 1fwxA 595 -35.06 -8.76 3.99e+01