% 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.YGR229C.t2k-100-40-40-str2+CB_burial_14_7 Host: cc48 Wed Nov 19 16:18:18 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR229C % --------------------------------------------------------------------- % 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 YGR229C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR229C.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR229C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8940 sequences, 2116673 residues, 506 nodes, 543.98 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(=0.7150) * Reverse)^tau(=0.8204))) % 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 1dg3A 592 -64.30 -26.15 1.29e-01 1h2vC 771 -61.60 -25.04 1.90e-01 1h6kA 757 -60.98 -24.06 2.68e-01 1b8xA 280 -68.82 -23.28 3.54e-01 1hqvA 191 -52.97 -21.82 5.96e-01 1f5nA 592 -60.37 -21.34 7.06e-01 2matA 264 -47.34 -20.90 8.30e-01 1c24A 263 -48.48 -20.16 1.08e+00 1qmyA 167 -48.94 -19.82 1.23e+00 1jffA 451 -47.12 -19.60 1.33e+00 1qqqA 264 -46.88 -19.45 1.41e+00 1pujA 282 -47.07 -19.25 1.51e+00 1ndbA 596 -49.46 -18.74 1.82e+00 1evfA 264 -46.61 -18.67 1.87e+00 1ezvG 93 -62.18 -18.59 1.92e+00 1a0hA 159 -70.81 -18.50 1.99e+00 1mat 264 -46.47 -18.33 2.11e+00 1t7pA 698 -67.70 -18.07 2.33e+00 1kb9H 93 -60.83 -17.87 2.51e+00 4matA 278 -43.97 -17.79 2.59e+00 1o0wA 252 -47.90 -17.44 2.94e+00 1qayA 428 -42.42 -17.33 3.07e+00 1umwA 237 -49.52 -17.29 3.12e+00 1anv 356 -51.31 -17.24 3.17e+00 1adt 356 -50.54 -17.22 3.20e+00 1tys 265 -44.82 -17.17 3.25e+00 1m9nA 613 -53.05 -17.08 3.37e+00 1ig8A 486 -51.36 -16.79 3.76e+00 1yghA 164 -43.96 -16.68 3.92e+00 2tscA 264 -44.38 -16.63 3.99e+00 1alvA 173 -47.82 -16.56 4.10e+00 1iw7C 1119 -59.61 -16.45 4.27e+00 1lfaA 187 -41.75 -16.36 4.41e+00 1o0xA 262 -43.33 -16.23 4.63e+00 1mlvA 444 -47.57 -16.22 4.67e+00 1iqrA 420 -46.70 -16.16 4.76e+00 1eq2A 310 -40.82 -16.03 5.00e+00 1kfuS 184 -49.57 -16.02 5.02e+00 1h2kA 349 -43.55 -16.01 5.05e+00 1vaoA 560 -50.65 -15.97 5.11e+00 1nrjB 218 -48.02 -15.92 5.22e+00 1r31A 428 -41.12 -15.86 5.33e+00 1ah6 220 -40.12 -15.74 5.59e+00 1g8mA 593 -52.54 -15.68 5.71e+00 1eu1A 780 -42.29 -15.67 5.73e+00 1gqeA 365 -51.98 -15.45 6.23e+00 1miuA 738 -65.72 -15.45 6.23e+00 1a2vA 655 -47.45 -15.40 6.35e+00 1p0yA 444 -46.84 -15.36 6.46e+00 1jpnA 296 -44.64 -15.23 6.78e+00 1h99A 224 -46.74 -15.23 6.79e+00 1bia 321 -44.09 -15.22 6.80e+00 1ngvA 534 -51.47 -15.11 7.10e+00 1dmr 823 -42.23 -15.06 7.23e+00 1qaxA 428 -40.20 -14.81 7.97e+00 1eluB 390 -42.29 -14.78 8.04e+00 1qu9A 128 -37.37 -14.72 8.25e+00 1qu9C 128 -37.37 -14.72 8.25e+00 1p4dA 330 -46.20 -14.72 8.25e+00 1msc 129 -45.54 -14.62 8.58e+00 1i2sA 282 -44.81 -14.58 8.70e+00 4blmA 265 -44.95 -14.57 8.72e+00 1oxjA 173 -47.85 -14.38 9.38e+00 1elqA 390 -42.50 -14.33 9.56e+00 1gthD 1025 -52.50 -14.30 9.70e+00 1fadA 99 -42.68 -14.19 1.01e+01 1mjnA 179 -39.01 -14.09 1.05e+01 1eluA 390 -42.33 -14.08 1.06e+01 1gln 468 -49.21 -14.06 1.06e+01 1jl0A 334 -43.48 -14.06 1.06e+01 1qltA 560 -48.95 -13.91 1.12e+01 1gthA 1025 -51.89 -13.88 1.14e+01 1ocyA 198 -79.69 -13.84 1.16e+01 1qtqA 553 -42.04 -13.81 1.17e+01 1hr6B 443 -42.31 -13.81 1.17e+01 1e8gA 560 -49.50 -13.74 1.20e+01 1g59A 468 -47.06 -13.71 1.22e+01 1mhlA 108 -63.12 -13.69 1.23e+01 1mzeA 351 -41.34 -13.67 1.24e+01 1ddf 127 -42.27 -13.63 1.25e+01 1mypB 108 -64.48 -13.62 1.26e+01 1gkxA 388 -45.33 -13.58 1.28e+01 1n4kA 381 -49.21 -13.53 1.31e+01 1nn6A 228 -37.25 -13.48 1.33e+01 3kinB 117 -59.99 -13.45 1.35e+01 1h7xD 1025 -51.30 -13.43 1.36e+01 1e3yA 104 -41.32 -13.27 1.44e+01 1h7xA 1025 -51.42 -13.24 1.46e+01 1mi3A 322 -40.05 -13.23 1.47e+01 1n93X 375 -47.08 -13.16 1.51e+01 1jb0A 755 -49.00 -13.10 1.55e+01 1dofA 403 -46.06 -13.08 1.56e+01 1k8cA 322 -40.11 -13.06 1.57e+01 1h7wD 1025 -50.95 -13.04 1.58e+01 1tx4A 198 -40.83 -13.00 1.61e+01 1jqjC 343 -40.44 -12.96 1.63e+01 1cxpA 104 -61.58 -12.96 1.63e+01 1d2vA 104 -61.58 -12.96 1.63e+01 1fgjA 546 -45.76 -12.93 1.65e+01 1nm8A 616 -42.93 -12.87 1.69e+01 1bpb 248 -39.54 -12.85 1.71e+01 1i7kA 179 -39.29 -12.84 1.71e+01 1f8nA 839 -43.26 -12.70 1.80e+01 1gkzA 388 -44.66 -12.68 1.82e+01 1a41 234 -42.91 -12.63 1.86e+01 1i5rA 327 -39.61 -12.62 1.87e+01 1gthC 1025 -50.42 -12.56 1.91e+01 1h7xC 1025 -50.75 -12.54 1.93e+01 1au7A 146 -42.76 -12.52 1.94e+01 1ddzA 496 -44.94 -12.48 1.97e+01 1gwuA 309 -37.73 -12.45 1.99e+01 1ualA 274 -46.07 -12.45 2.00e+01 1n3kA 130 -55.07 -12.45 2.00e+01 1m56B 264 -56.27 -12.42 2.02e+01 1e3dB 542 -42.79 -12.41 2.02e+01 1c0aA 585 -42.81 -12.39 2.05e+01 2occD 147 -68.36 -12.39 2.05e+01 1h7xB 1025 -50.66 -12.38 2.05e+01 1o6uA 403 -44.33 -12.37 2.06e+01 1fiwA 290 -36.54 -12.32 2.10e+01 1h7wB 1025 -50.52 -12.31 2.11e+01 1ef1C 90 -66.66 -12.29 2.12e+01 1yagA 375 -42.82 -12.26 2.15e+01 1gt8C 1025 -51.29 -12.21 2.19e+01 1pjpA 226 -35.92 -12.20 2.20e+01 1jsqA 582 -54.59 -12.17 2.23e+01 1j09A 468 -47.49 -12.16 2.23e+01 1eudA 311 -37.74 -12.14 2.26e+01 1cmxA 236 -38.95 -12.04 2.35e+01 1jwhC 215 -44.57 -12.02 2.37e+01 1ocrD 147 -68.10 -12.01 2.38e+01 1gtrA 553 -40.37 -11.98 2.41e+01 1h7wA 1025 -50.23 -11.98 2.41e+01 1budA 197 -36.54 -11.95 2.44e+01 1irxA 523 -44.52 -11.93 2.46e+01 1k2eA 156 -38.89 -11.89 2.49e+01 1bib 321 -42.16 -11.88 2.50e+01 1m2oA 768 -45.93 -11.85 2.53e+01 1eza 259 -44.23 -11.83 2.56e+01 1eg2A 319 -50.95 -11.82 2.56e+01 1jnrB 150 -54.17 -11.72 2.67e+01 1j99A 293 -43.03 -11.70 2.69e+01 7atjA 308 -37.84 -11.68 2.71e+01 1pmt 203 -42.31 -11.66 2.74e+01 1ngmB 72 -56.65 -11.64 2.75e+01 1jb1A 205 -42.46 -11.64 2.75e+01 1jatA 155 -37.18 -11.64 2.76e+01 3rp2A 224 -36.49 -11.58 2.82e+01 1nw8A 319 -49.72 -11.47 2.95e+01 1do0A 442 -54.41 -11.46 2.96e+01 1k8tA 510 -52.15 -11.45 2.96e+01 1fds 327 -39.53 -11.45 2.97e+01 1gr8A 412 -38.35 -11.45 2.97e+01 1ockA 412 -38.35 -11.45 2.97e+01 1fbtA 190 -36.39 -11.43 2.99e+01 1m4lA 307 -36.79 -11.43 2.99e+01 1l8qA 324 -41.77 -11.39 3.04e+01 2atjA 308 -37.13 -11.39 3.04e+01 1bxkA 355 -38.40 -11.38 3.06e+01 2ctb 307 -36.47 -11.35 3.10e+01 1qy5A 269 -36.88 -11.34 3.11e+01 1k26A 156 -37.34 -11.27 3.20e+01 3csuA 310 -34.43 -11.26 3.21e+01 1qcrG 70 -48.30 -11.24 3.23e+01 1qpsA 261 -41.26 -11.21 3.27e+01 1n9bA 265 -40.16 -11.19 3.30e+01 1i4mA 108 -56.19 -11.18 3.31e+01 1byqA 228 -36.46 -11.16 3.33e+01 1fr1A 361 -38.40 -11.15 3.35e+01 1hkbA 917 -44.13 -11.14 3.36e+01 1ihgA 370 -41.87 -11.12 3.39e+01 1pme 380 -37.82 -11.11 3.40e+01 1u9aA 160 -38.54 -11.09 3.43e+01 1chmA 401 -36.89 -11.08 3.45e+01 1gt8B 1025 -49.96 -11.06 3.48e+01 1pytA 94 -37.18 -11.05 3.49e+01 1mypA 108 -61.62 -11.04 3.50e+01 1tubA 440 -35.76 -11.01 3.55e+01 1im2A 444 -47.30 -10.98 3.58e+01 1trkA 680 -43.11 -10.96 3.61e+01 2ucz 165 -41.36 -10.94 3.65e+01 1ckmA 330 -38.64 -10.93 3.66e+01 1h38D 883 -46.74 -10.92 3.68e+01 1ls1A 295 -40.61 -10.88 3.74e+01 1fs0E 138 -52.28 -10.86 3.76e+01 1ng1 294 -41.07 -10.82 3.83e+01 1gt8D 1025 -49.59 -10.80 3.86e+01 1tkaA 678 -43.25 -10.80 3.87e+01 1hvyA 288 -37.70 -10.79 3.87e+01 1g6wA 261 -39.05 -10.77 3.90e+01 1dvpA 220 -42.26 -10.76 3.92e+01 1ucyH 150 -42.16 -10.74 3.96e+01 1kjnA 157 -32.46 -10.73 3.97e+01 1gt8A 1025 -50.12 -10.72 3.99e+01 1gthB 1025 -48.94 -10.72 3.99e+01