% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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. % --------------------------------------------------------------------- % str2foo.1.YBL103C.t2k-100-30-str2 Host: farm12 Wed Dec 29 04:00:35 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YBL1/YBL103C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % 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 YBL103C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YBL103C.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 11147 sequences, 2640567 residues, 487 nodes, 546.25 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.4704) * Reverse)^tau(=0.7547))) % 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 1nkpB 83 -96.36 -82.72 5.78e-13 1nkpA 88 -104.07 -82.57 6.08e-13 1hloA 150 -93.12 -80.49 1.24e-12 1nlwB 76 -92.79 -79.70 1.63e-12 1an2A 86 -93.94 -79.17 1.96e-12 1am9A 82 -93.57 -78.64 2.35e-12 1uklC 61 -67.30 -50.62 6.31e-08 1an4A 65 -62.22 -46.69 2.92e-07 1nlwA 80 -65.55 -46.21 3.51e-07 1a0aA 63 -54.68 -44.71 6.37e-07 1mdyA 68 -56.16 -43.35 1.10e-06 1dh3A 55 -31.71 -14.85 3.80e-01 1kddA 36 -31.13 -13.49 7.76e-01 1m1jA 491 -30.30 -13.31 8.52e-01 1korA 400 -25.94 -13.07 9.72e-01 5csmA 256 -28.89 -11.85 1.89e+00 1b4pA 217 -24.37 -10.91 3.18e+00 1vl2A 421 -22.78 -10.86 3.27e+00 1nfa 178 -25.67 -10.06 5.14e+00 1e6yA 569 -26.39 -10.06 5.14e+00 1lq7A 67 -32.57 -10.03 5.25e+00 1et0A 269 -22.47 -9.94 5.51e+00 1gotG 73 -22.32 -9.91 5.63e+00 1i2kA 269 -22.32 -9.84 5.85e+00 1gu4A 78 -28.74 -9.54 6.97e+00 1a02F 56 -24.76 -9.51 7.08e+00 1bh9A 45 -20.89 -9.49 7.13e+00 1kd9A 36 -29.45 -9.41 7.49e+00 1b9xB 68 -21.97 -9.38 7.65e+00 1rdr 461 -23.00 -9.35 7.79e+00 1u7lA 392 -24.72 -9.30 8.01e+00 1ju2A 536 -26.97 -9.28 8.07e+00 1a93A 34 -28.63 -9.27 8.12e+00 1pb6A 212 -22.34 -9.22 8.39e+00 1csmA 256 -27.61 -9.18 8.58e+00 1ci6B 63 -28.50 -9.17 8.61e+00 1p9iA 31 -24.21 -9.14 8.75e+00 1nwmX 142 -27.78 -9.14 8.76e+00 1ci6A 63 -29.24 -9.09 9.03e+00 1fu1B 203 -26.03 -9.02 9.40e+00 1u2xA 474 -21.71 -8.98 9.64e+00 1ik9A 213 -25.94 -8.98 9.66e+00 1lj2A 110 -26.11 -8.97 9.72e+00 1gd2E 70 -25.82 -8.96 9.77e+00 1kd8A 36 -27.05 -8.94 9.86e+00 1pcxA 810 -28.74 -8.81 1.07e+01 1gd2G 70 -26.62 -8.81 1.07e+01 1hjbA 87 -29.52 -8.78 1.08e+01 1fosE 60 -27.90 -8.64 1.18e+01 1e7tA 59 -26.15 -8.56 1.23e+01 1junA 44 -25.52 -8.55 1.24e+01 1a66A 178 -23.01 -8.55 1.25e+01 1ce9C 34 -24.73 -8.47 1.30e+01 1a93B 34 -21.09 -8.40 1.36e+01 1gk7A 39 -23.19 -8.36 1.39e+01 1dpsA 167 -24.32 -8.34 1.41e+01 1dpsD 167 -24.32 -8.34 1.41e+01 1p7gA 222 -22.20 -8.22 1.52e+01 1m7lA 40 -24.77 -8.20 1.53e+01 1h89A 64 -28.51 -8.16 1.57e+01 1n4qB 377 -22.82 -8.12 1.61e+01 1g40A 244 -34.29 -8.06 1.67e+01 1tzvA 142 -20.86 -8.05 1.68e+01 1ce9A 34 -24.81 -8.02 1.71e+01 1l8nA 679 -22.69 -8.01 1.72e+01 1gtxA 472 -20.72 -7.98 1.75e+01 1k9dA 679 -22.75 -7.96 1.77e+01 1ecmA 109 -23.31 -7.90 1.84e+01 1fu1A 203 -25.37 -7.85 1.90e+01 1q7zA 566 -21.17 -7.79 1.97e+01 1eq7A 56 -18.77 -7.77 1.99e+01 1ziiA 34 -24.30 -7.75 2.01e+01 2ztaA 34 -24.30 -7.75 2.01e+01 1tbgE 68 -19.85 -7.75 2.02e+01 1f7uA 607 -21.83 -7.74 2.03e+01 1coi 31 -22.43 -7.69 2.09e+01 1j0hA 588 -25.38 -7.65 2.14e+01 1cxqA 162 -18.31 -7.55 2.28e+01 1h2vC 771 -32.95 -7.52 2.32e+01 1lslA 113 -25.71 -7.50 2.35e+01 1gtrA 553 -19.44 -7.49 2.36e+01 1j8bA 112 -22.58 -7.46 2.40e+01 1qtqA 553 -19.46 -7.40 2.50e+01 1hwyA 501 -21.41 -7.32 2.62e+01 1h6kA 757 -34.31 -7.31 2.64e+01 1kkoA 413 -19.47 -7.20 2.82e+01 1bd3A 243 -18.65 -7.14 2.93e+01 1fmhA 33 -24.84 -7.14 2.93e+01 1nnwA 252 -21.48 -7.12 2.98e+01 1b9uA 34 -17.90 -7.10 3.01e+01 1kwkA 645 -19.67 -7.07 3.06e+01 1u5tC 202 -20.55 -7.07 3.06e+01 1eia 207 -19.69 -7.05 3.10e+01 1c89A 134 -21.72 -7.05 3.11e+01 1p5dX 463 -19.73 -7.04 3.12e+01 1xlyA 234 -21.59 -7.04 3.12e+01 1kwgA 645 -19.58 -7.04 3.13e+01 1bvzA 585 -22.14 -7.03 3.13e+01 1sqc 631 -26.21 -6.99 3.22e+01 1dipB 78 -23.35 -6.98 3.23e+01 1p4xA 250 -19.81 -6.98 3.24e+01 1alu 186 -21.86 -6.98 3.25e+01 1vsd 152 -17.69 -6.97 3.26e+01 1asu 162 -17.83 -6.97 3.27e+01 1vkuA 100 -20.85 -6.92 3.36e+01 1qb4A 883 -25.90 -6.91 3.37e+01 1crl 534 -23.20 -6.87 3.47e+01 1jkiA 533 -20.71 -6.85 3.52e+01 1e3mA 800 -20.64 -6.82 3.57e+01 1fosF 57 -25.39 -6.78 3.68e+01 1wddS 128 -20.35 -6.74 3.77e+01 3pghA 587 -24.17 -6.72 3.82e+01 1fs1B 141 -19.85 -6.68 3.92e+01 1jkfA 533 -19.45 -6.66 3.95e+01 1e1hA 287 -19.26 -6.66 3.96e+01