% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dsspfoo.1.YGR024C.t2k-100-30-dssp-ebghstl Host: cc69 Fri Nov 8 17:50:12 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR024C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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 YGR024C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR024C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 238 nodes, 162.11 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.3601) * Reverse)^tau(=0.8290))) % 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 1ezm 301 -35.33 -11.81 3.36e-01 1qgwC 177 -32.23 -11.60 3.89e-01 1kwkA 645 -35.06 -10.44 8.87e-01 1g24A 211 -30.68 -10.02 1.20e+00 1qkmA 255 -33.55 -9.62 1.60e+00 1k3eA 156 -30.25 -9.47 1.78e+00 1k2yX 463 -32.94 -9.38 1.90e+00 1hjp 203 -30.82 -9.23 2.12e+00 1qlpA 394 -31.25 -9.16 2.23e+00 1b4uA 139 -28.12 -9.02 2.47e+00 1ryt 190 -32.40 -8.98 2.55e+00 1hbq 183 -30.16 -8.94 2.63e+00 1dvbA 191 -32.32 -8.93 2.64e+00 1hbp 183 -30.09 -8.84 2.83e+00 1jyoA 130 -28.80 -8.75 3.01e+00 1b71A 191 -32.13 -8.73 3.07e+00 1f44A 324 -32.03 -8.70 3.14e+00 1aqb 183 -29.85 -8.64 3.28e+00 1jp3A 253 -31.09 -8.61 3.35e+00 1bouA 139 -27.50 -8.56 3.48e+00 1crxA 322 -32.27 -8.54 3.52e+00 1kbuA 349 -32.78 -8.53 3.55e+00 1dt6A 473 -32.79 -8.46 3.74e+00 3crxA 343 -32.75 -8.45 3.77e+00 4crxA 322 -32.23 -8.44 3.80e+00 1lx7A 253 -28.96 -8.34 4.10e+00 1cuk 203 -29.51 -8.19 4.59e+00 1bw9A 356 -30.51 -8.18 4.60e+00 1hm6A 346 -30.54 -8.14 4.75e+00 1pyaB 228 -29.28 -8.12 4.81e+00 1j77A 209 -30.68 -8.04 5.12e+00 1io2A 213 -29.64 -7.98 5.34e+00 1fntc 245 -29.53 -7.94 5.51e+00 1kq4A 232 -30.50 -7.86 5.84e+00 1ig0A 319 -29.69 -7.82 6.02e+00 1cnt2 187 -30.66 -7.75 6.35e+00 1hv8A 367 -31.77 -7.74 6.41e+00 1pydA 556 -31.08 -7.73 6.47e+00 1pvdA 537 -31.05 -7.72 6.49e+00 1khvA 516 -33.88 -7.72 6.50e+00 1qpbA 563 -30.85 -7.61 7.06e+00 3cla 213 -28.27 -7.59 7.19e+00 1c1dA 355 -30.11 -7.56 7.33e+00 9apiA 347 -29.32 -7.43 8.11e+00 1exnA 290 -30.18 -7.42 8.15e+00 1aq0A 306 -31.05 -7.37 8.46e+00 1l2iA 261 -30.44 -7.36 8.55e+00 1ppa 121 -26.92 -7.34 8.69e+00 1cxqA 162 -27.79 -7.33 8.76e+00 1jx4A 352 -31.08 -7.31 8.87e+00 1ghr 306 -31.05 -7.26 9.22e+00 1tfe 145 -27.37 -7.26 9.23e+00 1jmsA 381 -29.65 -7.24 9.36e+00 1k3fA 253 -27.86 -7.19 9.74e+00 1bed 181 -28.75 -7.10 1.04e+01 1hg2A 289 -29.38 -6.92 1.20e+01 1jf0A 195 -29.37 -6.87 1.24e+01 1rpl 251 -28.27 -6.78 1.34e+01 1aba 87 -24.63 -6.77 1.34e+01 1dkgD 383 -29.65 -6.77 1.34e+01 1ft1A 377 -29.31 -6.77 1.35e+01 1jcrA 377 -29.29 -6.74 1.37e+01 1asu 162 -27.00 -6.72 1.39e+01 1ej3A 191 -28.22 -6.72 1.39e+01 1ayyA 151 -26.52 -6.69 1.42e+01 1kvoA 124 -26.60 -6.68 1.44e+01 2pfkA 320 -29.27 -6.64 1.48e+01 1nmtA 392 -28.66 -6.60 1.53e+01 1efuB 282 -29.68 -6.56 1.58e+01 1d8dA 377 -29.07 -6.55 1.59e+01 1pfkA 320 -29.16 -6.53 1.62e+01 1cn4C 166 -28.46 -6.53 1.62e+01 1eu8A 409 -29.64 -6.49 1.66e+01 1atzB 189 -26.45 -6.48 1.68e+01 1cec 343 -30.30 -6.48 1.68e+01 1ceo 343 -30.13 -6.47 1.69e+01 1fi4A 416 -30.41 -6.40 1.78e+01 3ertA 261 -28.54 -6.39 1.80e+01 1yuiA 54 -22.36 -6.38 1.82e+01 1ekeA 230 -28.80 -6.35 1.86e+01 1exnB 290 -29.29 -6.34 1.88e+01 1cpcL 172 -26.95 -6.34 1.88e+01 1rbp 182 -27.57 -6.33 1.88e+01 1f47B 144 -26.45 -6.31 1.92e+01 1fe8A 196 -26.21 -6.31 1.92e+01 1lox 662 -29.49 -6.30 1.93e+01 1a8y 367 -29.39 -6.29 1.94e+01 1phnB 172 -27.11 -6.29 1.95e+01 1bpb 248 -28.03 -6.29 1.95e+01 1ktpB 172 -27.51 -6.28 1.96e+01 1f46A 140 -26.39 -6.24 2.03e+01 1vsd 152 -26.27 -6.18 2.11e+01 1cb6A 691 -29.46 -6.18 2.13e+01 1jfzA 154 -31.13 -6.17 2.14e+01 1efnB 152 -25.56 -6.17 2.14e+01 1p35A 299 -27.86 -6.11 2.23e+01 1dd5A 185 -28.33 -6.09 2.28e+01 2abk 211 -29.66 -6.08 2.29e+01 1lucB 324 -28.74 -6.08 2.30e+01 1bmfG 272 -30.00 -6.07 2.31e+01 1bif 469 -28.86 -6.06 2.33e+01 1qlaC 256 -30.38 -6.02 2.40e+01 1atzA 189 -26.04 -6.01 2.42e+01 3bifA 468 -28.79 -5.99 2.46e+01 1l5jA 865 -30.98 -5.97 2.50e+01 1dofA 403 -30.43 -5.94 2.56e+01 19hcA 292 -25.90 -5.91 2.62e+01 1ihfA 99 -24.52 -5.90 2.65e+01 4xiaA 393 -30.64 -5.89 2.66e+01 1f7wA 144 -25.79 -5.85 2.75e+01 1jm6A 407 -30.05 -5.81 2.82e+01 1im8A 244 -28.59 -5.79 2.88e+01 1hy0A 466 -29.85 -5.78 2.91e+01 1mc2A 122 -25.44 -5.78 2.91e+01 1qo0D 196 -28.41 -5.77 2.92e+01 3erdA 261 -28.49 -5.77 2.93e+01 1cpcB 172 -26.38 -5.71 3.07e+01 1gaxA 862 -31.31 -5.71 3.07e+01 1axj 122 -25.31 -5.71 3.08e+01 1whsA 255 -26.28 -5.70 3.08e+01 1hqvA 191 -26.97 -5.70 3.09e+01 1bg2 325 -28.27 -5.67 3.15e+01 1hf8A 289 -28.16 -5.67 3.16e+01 1prgA 270 -28.04 -5.64 3.25e+01 1cgo 127 -26.49 -5.63 3.27e+01 1aokB 122 -24.76 -5.63 3.27e+01 1bcsA 263 -26.15 -5.62 3.30e+01 1jcqA 382 -28.37 -5.61 3.32e+01 1jdiA 231 -27.19 -5.61 3.32e+01 1jr8A 117 -27.34 -5.61 3.33e+01 1whtA 256 -26.25 -5.59 3.38e+01 1ld8A 382 -28.36 -5.58 3.39e+01 1e85A 127 -26.18 -5.53 3.54e+01 1h99A 224 -27.32 -5.52 3.58e+01 1i3dA 146 -25.58 -5.51 3.59e+01 1i4uA 181 -27.16 -5.50 3.62e+01 1cwyA 500 -29.03 -5.50 3.64e+01 1h91A 180 -26.96 -5.49 3.64e+01 1k8eA 345 -26.79 -5.43 3.83e+01 1eswA 500 -28.92 -5.40 3.92e+01 1lliA 92 -23.88 -5.38 3.99e+01