% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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. % --------------------------------------------------------------------- % alphafoo.1.YGR217W.t2k-100-30-alpha Host: cc85 Thu Feb 26 20:47:24 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR217W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.alphas % % 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 YGR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR217W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 9381 sequences, 2218509 residues, 2040 nodes, 2732.70 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(=1.8390) * Reverse)^tau(=0.7557))) % 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 1ncx 162 -42.66 -24.08 1.97e-04 1top 162 -42.23 -23.63 2.52e-04 1t1dA 100 -35.06 -22.67 4.32e-04 1jvmA 125 -37.07 -22.02 6.21e-04 1r3jC 124 -36.86 -21.34 9.09e-04 1k4cC 124 -36.67 -21.17 1.00e-03 1j95A 125 -34.76 -20.27 1.67e-03 1g4yR 148 -37.19 -20.15 1.80e-03 1a68 95 -31.67 -19.80 2.20e-03 1bl8A 97 -34.10 -19.34 2.86e-03 1zac 90 -32.98 -19.27 2.99e-03 1kyoC 385 -40.09 -19.14 3.23e-03 3cln 148 -37.72 -19.08 3.34e-03 1ggzA 148 -38.64 -18.78 3.98e-03 1dsxA 87 -30.17 -18.77 4.01e-03 1avsA 90 -32.51 -18.67 4.23e-03 1kb9C 385 -39.93 -18.64 4.31e-03 1cll 148 -38.25 -18.62 4.37e-03 1ezvC 385 -38.85 -17.56 8.17e-03 1exrA 148 -38.01 -16.38 1.65e-02 1osa 148 -37.71 -16.35 1.68e-02 1ho2A 20 -26.00 -15.55 2.75e-02 1qg9A 21 -25.98 -14.57 5.03e-02 1nn7A 105 -27.47 -14.18 6.40e-02 1j7rA 86 -25.70 -13.50 9.81e-02 1byyA 53 -24.51 -13.28 1.13e-01 2mysB 166 -26.80 -13.19 1.20e-01 1wdcC 156 -26.97 -12.44 1.94e-01 1oyeA 1049 -42.06 -12.27 2.16e-01 1iwgA 1053 -42.97 -11.76 3.03e-01 1wdcB 156 -25.12 -11.24 4.26e-01 1m46A 148 -24.77 -11.02 4.93e-01 9wgaA 171 -31.17 -10.86 5.46e-01 1o1fC 147 -25.21 -10.74 5.94e-01 1ggwA 140 -23.40 -10.71 6.06e-01 1wgtA 186 -32.29 -10.38 7.57e-01 1nr6A 473 -28.56 -10.37 7.60e-01 1br1B 150 -23.51 -10.08 9.29e-01 1m45A 148 -22.96 -10.07 9.36e-01 1ezfA 340 -28.11 -10.03 9.60e-01 3kvt 115 -21.61 -9.85 1.08e+00 1ehkA 562 -37.11 -9.68 1.22e+00 1orsC 132 -33.15 -9.60 1.29e+00 1alvA 173 -25.03 -9.53 1.35e+00 1n6bA 473 -27.71 -9.46 1.42e+00 1k94A 165 -26.52 -9.42 1.45e+00 1dt6A 473 -27.99 -9.29 1.60e+00 1scmB 145 -22.89 -9.24 1.66e+00 1be3C 379 -28.77 -9.15 1.75e+00 1gtxA 472 -31.66 -9.11 1.81e+00 1f4qA 165 -24.23 -9.05 1.88e+00 1ohvA 472 -31.56 -9.03 1.91e+00 1ctdA 36 -19.64 -8.74 2.34e+00 1kfuS 184 -24.15 -8.67 2.46e+00 1nr3A 122 -20.48 -8.65 2.49e+00 1mmoD 512 -28.78 -8.60 2.59e+00 1j97A 211 -25.68 -8.60 2.59e+00 1brd 248 -33.36 -8.54 2.70e+00 1k9uA 78 -21.54 -8.51 2.77e+00 1o86A 589 -25.61 -8.33 3.15e+00 1f5sA 211 -25.36 -8.25 3.33e+00 1upkA 341 -24.41 -8.22 3.39e+00 1fp3A 402 -23.87 -8.12 3.65e+00 1q9bA 43 -20.42 -8.10 3.69e+00 1otsA 465 -27.94 -8.00 3.97e+00 1lufA 343 -22.15 -8.00 3.97e+00 1ldfA 281 -25.04 -7.99 4.01e+00 1l7mA 211 -24.89 -7.94 4.14e+00 1aijL 281 -25.97 -7.91 4.23e+00 1c3wA 222 -23.88 -7.90 4.28e+00 1o20A 427 -30.44 -7.88 4.35e+00 1e6fA 143 -21.25 -7.85 4.42e+00 2liv 344 -27.91 -7.84 4.44e+00 1gp0A 143 -20.98 -7.82 4.51e+00 1hqvA 191 -24.25 -7.76 4.73e+00 1b6a 478 -34.05 -7.75 4.75e+00 1e12A 253 -24.74 -7.74 4.81e+00 1dguA 183 -21.29 -7.66 5.07e+00 1fx8A 281 -24.85 -7.57 5.44e+00 1e2uA 553 -35.46 -7.45 5.93e+00 1e1dA 553 -34.92 -7.44 5.98e+00 1mtyD 512 -27.83 -7.39 6.20e+00 1gntA 553 -35.24 -7.38 6.25e+00 1dceA 567 -25.50 -7.34 6.43e+00 1kcxA 518 -33.06 -7.33 6.47e+00 1bn5 478 -33.59 -7.18 7.25e+00 1kktA 511 -29.88 -7.16 7.32e+00 1hev 43 -19.25 -7.15 7.41e+00 6prcM 323 -24.57 -7.15 7.41e+00 1o9gA 250 -19.87 -7.07 7.85e+00 1h38C 883 -39.72 -7.01 8.18e+00 1em2A 229 -20.46 -6.98 8.40e+00 1a87 321 -29.74 -6.95 8.55e+00 1e19A 314 -26.64 -6.95 8.56e+00 1jb0A 755 -30.22 -6.94 8.65e+00 1ulmA 82 -22.86 -6.94 8.67e+00 1ctaA 36 -18.32 -6.91 8.84e+00 1m0kA 262 -24.24 -6.90 8.92e+00 1jbaA 204 -20.60 -6.89 8.96e+00 1g8iA 190 -22.91 -6.81 9.52e+00 1jk0A 419 -24.77 -6.80 9.62e+00 1btkA 169 -20.80 -6.79 9.62e+00 1h38B 883 -39.65 -6.78 9.76e+00 1keyA 235 -24.85 -6.77 9.80e+00 1dxrM 323 -24.25 -6.73 1.01e+01 1kgbA 231 -23.76 -6.69 1.04e+01 2lbp 346 -27.54 -6.68 1.05e+01 2scpA 174 -21.66 -6.67 1.06e+01 1phnA 162 -19.18 -6.62 1.10e+01 1giqA 413 -31.82 -6.58 1.13e+01 1od5A 492 -26.48 -6.58 1.13e+01 1j1jA 240 -24.24 -6.55 1.16e+01 1kf6C 130 -24.52 -6.49 1.21e+01 1dmuA 299 -22.74 -6.47 1.23e+01 1mswD 883 -39.56 -6.46 1.24e+01 1jpzA 473 -28.52 -6.42 1.28e+01 1m1jA 491 -32.76 -6.42 1.28e+01 1dqeA 137 -19.93 -6.39 1.31e+01 1ulkA 126 -26.94 -6.34 1.35e+01 1ponA 36 -17.47 -6.32 1.38e+01 1qcrC 378 -26.90 -6.32 1.38e+01 1btkB 169 -21.55 -6.32 1.38e+01 1ivhA 394 -25.84 -6.25 1.46e+01 1pal 108 -17.79 -6.24 1.46e+01 1fa0B 537 -24.91 -6.23 1.47e+01 1p49A 562 -28.55 -6.21 1.50e+01 1h38D 883 -39.02 -6.18 1.53e+01 1jpaA 312 -21.75 -6.18 1.53e+01 1a28A 256 -20.18 -6.13 1.59e+01 1uhnA 189 -20.33 -6.11 1.61e+01 1mmc 30 -17.74 -6.11 1.62e+01 1lnqA 336 -27.44 -6.10 1.63e+01 1omrA 201 -21.34 -6.09 1.65e+01 1ca1 370 -28.94 -6.07 1.67e+01 1mxgA 435 -26.59 -6.03 1.73e+01 1sesA 421 -24.14 -6.02 1.73e+01 1dlc 584 -23.79 -5.93 1.86e+01 1a4iA 301 -23.50 -5.89 1.92e+01 1colA 204 -21.32 -5.88 1.94e+01 2bn2A 95 -20.95 -5.87 1.95e+01 2pvbA 107 -17.44 -5.85 1.97e+01 1rec 201 -20.35 -5.83 2.00e+01 1a4iB 301 -24.92 -5.83 2.01e+01 1k8kG 151 -20.53 -5.83 2.01e+01 1npoC 95 -20.34 -5.83 2.01e+01 1fa0A 537 -26.77 -5.80 2.06e+01 1as4A 341 -18.36 -5.79 2.07e+01 1cii 602 -37.44 -5.78 2.09e+01 1diaA 306 -23.85 -5.78 2.09e+01 1pvaA 110 -17.76 -5.74 2.15e+01 1ng5A 215 -21.74 -5.74 2.15e+01 1phnB 172 -19.82 -5.74 2.15e+01 1ffkB 338 -33.42 -5.74 2.16e+01 1cdp 109 -17.35 -5.71 2.20e+01 1pixA 587 -36.29 -5.67 2.27e+01 4cpv 109 -17.31 -5.67 2.27e+01 1oshA 232 -21.45 -5.62 2.37e+01 1usgA 346 -27.06 -5.62 2.37e+01 1clvI 32 -17.33 -5.61 2.38e+01 1q0sA 259 -21.28 -5.57 2.46e+01 1bd3A 243 -19.08 -5.57 2.47e+01 1o0xA 262 -22.00 -5.56 2.48e+01 1gm9B 557 -26.78 -5.55 2.49e+01 1gk9B 557 -26.69 -5.55 2.50e+01 1hyp 80 -17.44 -5.51 2.58e+01 1jk4A 89 -20.12 -5.51 2.59e+01 1dro 122 -20.63 -5.40 2.81e+01 1prxA 224 -18.31 -5.39 2.83e+01 1n83A 270 -21.88 -5.37 2.88e+01 2bmhA 455 -26.44 -5.36 2.91e+01 1bbn 133 -18.27 -5.35 2.93e+01 1lngA 87 -18.86 -5.34 2.95e+01 1iqbB 89 -21.57 -5.30 3.05e+01 1i37A 260 -19.42 -5.28 3.09e+01 2aaiB 262 -20.31 -5.28 3.09e+01 1jogA 146 -19.09 -5.28 3.10e+01 1uaaA 673 -23.26 -5.27 3.12e+01 1en2A 89 -21.10 -5.22 3.25e+01 1ki1B 352 -26.13 -5.21 3.27e+01 1dx5I 118 -20.19 -5.18 3.34e+01 1eulA 994 -52.29 -5.17 3.38e+01 1oohA 126 -17.76 -5.17 3.38e+01 1epwA 1290 -68.02 -5.16 3.39e+01 1sva1 361 -25.62 -5.16 3.40e+01 1tf4A 605 -34.01 -5.16 3.40e+01 1r9cA 139 -18.17 -5.15 3.43e+01 1nijA 318 -20.57 -5.15 3.44e+01 1n9dA 199 -18.58 -5.13 3.48e+01 1e3aB 560 -26.39 -5.12 3.51e+01 1abv 134 -18.61 -5.12 3.53e+01 1gotG 73 -19.32 -5.11 3.55e+01 1ad3A 452 -25.65 -5.08 3.62e+01 1q33A 292 -25.95 -5.02 3.81e+01 1ii7A 333 -22.76 -5.01 3.83e+01 1htxA 32 -17.00 -5.01 3.85e+01 1nd7A 374 -21.49 -5.01 3.85e+01 1gm7B 557 -26.13 -4.99 3.90e+01 2bpa1 426 -20.82 -4.98 3.94e+01 1npoA 95 -19.59 -4.96 3.99e+01