% 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. % --------------------------------------------------------------------- % alphafoo.1.YGR024C.t2k-100-30-alpha Host: cc69 Fri Nov 8 18:01:04 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.alphas % % 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.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 238 nodes, 161.84 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(=2.2164) * Reverse)^tau(=0.7474))) % 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 1c1dA 355 -30.23 -9.08 5.90e-01 1qkmA 255 -31.09 -9.06 5.98e-01 1qgwC 177 -28.74 -8.89 6.83e-01 1aqb 183 -28.42 -8.62 8.41e-01 1hbq 183 -28.26 -8.61 8.48e-01 1hbp 183 -28.17 -8.56 8.85e-01 1bw9A 356 -29.79 -8.48 9.42e-01 1ezm 301 -30.31 -8.34 1.05e+00 1qo0D 196 -28.77 -8.27 1.11e+00 1a8y 367 -30.16 -8.20 1.18e+00 1d0qA 103 -25.39 -7.72 1.73e+00 1go4A 205 -30.68 -7.46 2.13e+00 1ihfA 99 -25.43 -7.27 2.49e+00 1f2tB 148 -27.09 -7.08 2.90e+00 1hjp 203 -27.69 -6.95 3.25e+00 1crxA 322 -29.10 -6.90 3.38e+00 1pyaB 228 -27.81 -6.90 3.38e+00 1cnt2 187 -28.55 -6.76 3.80e+00 2dri 271 -27.03 -6.70 4.00e+00 1g24A 211 -26.09 -6.57 4.47e+00 1jf0A 195 -27.08 -6.50 4.73e+00 1cec 343 -28.94 -6.49 4.78e+00 1yuiA 54 -22.06 -6.42 5.04e+00 1bouA 139 -24.80 -6.33 5.45e+00 1f44A 324 -28.39 -6.27 5.72e+00 1b4uA 139 -24.69 -6.24 5.88e+00 1rbp 182 -25.87 -6.21 6.04e+00 1pydA 556 -28.00 -6.18 6.21e+00 1lox 662 -28.47 -6.17 6.24e+00 4crxA 322 -28.71 -6.13 6.45e+00 1pvdA 537 -27.88 -6.13 6.47e+00 3ertA 261 -27.12 -6.13 6.48e+00 1ceo 343 -28.45 -6.12 6.53e+00 2kinA 238 -26.65 -6.08 6.78e+00 1ej3A 191 -26.69 -6.07 6.82e+00 1kbuA 349 -29.46 -6.07 6.82e+00 1l2iA 261 -27.75 -6.06 6.87e+00 1ps1A 337 -27.89 -6.04 7.00e+00 1qlaC 256 -27.51 -6.03 7.04e+00 1tfe 145 -25.33 -6.02 7.13e+00 1hu4A 288 -26.78 -5.97 7.41e+00 1dt6A 473 -28.37 -5.93 7.70e+00 3aig 202 -25.54 -5.92 7.79e+00 3crxA 343 -29.03 -5.90 7.91e+00 1avqA 228 -26.21 -5.89 7.95e+00 1qlpA 394 -27.03 -5.87 8.11e+00 3erdA 261 -27.10 -5.83 8.38e+00 1ip9A 85 -22.93 -5.83 8.39e+00 1aw5 326 -27.84 -5.82 8.47e+00 1qpbA 563 -27.63 -5.81 8.56e+00 1k2yX 463 -27.93 -5.80 8.58e+00 1qu6A 179 -25.01 -5.78 8.76e+00 1ekeA 230 -26.55 -5.71 9.28e+00 1i3dA 146 -25.28 -5.70 9.36e+00 1fxjA 331 -26.42 -5.70 9.40e+00 1cuk 203 -25.83 -5.62 1.00e+01 1b77A 228 -25.27 -5.57 1.05e+01 1fwyA 331 -26.27 -5.49 1.13e+01 1k8eA 345 -26.20 -5.44 1.18e+01 1a0p 290 -26.49 -5.41 1.20e+01 1auwA 468 -28.27 -5.39 1.23e+01 1f61A 429 -26.89 -5.39 1.23e+01 1ax0 239 -25.06 -5.39 1.23e+01 1de4C 640 -28.09 -5.36 1.26e+01 2bdpA 580 -28.30 -5.30 1.33e+01 1g8kA 825 -28.48 -5.30 1.33e+01 1bcsA 263 -25.26 -5.26 1.38e+01 1kskA 234 -24.51 -5.24 1.41e+01 1gzcA 239 -24.98 -5.23 1.42e+01 1hv9A 456 -26.48 -5.21 1.45e+01 1pfkA 320 -26.82 -5.21 1.45e+01 1hy0A 466 -27.79 -5.19 1.47e+01 1k7wA 468 -28.14 -5.16 1.50e+01 1gzgA 337 -26.24 -5.16 1.51e+01 1hn2A 159 -24.13 -5.15 1.52e+01 1gaxA 862 -28.96 -5.15 1.52e+01 1f8mA 429 -26.75 -5.14 1.54e+01 1bg2 325 -26.12 -5.09 1.60e+01 1ltm 320 -26.06 -5.09 1.61e+01 3bifA 468 -27.48 -5.06 1.65e+01 1obpA 159 -24.04 -5.05 1.67e+01 1qusA 322 -26.06 -5.05 1.67e+01 1eljA 381 -26.76 -5.03 1.69e+01 1bif 469 -27.64 -5.03 1.70e+01 1hueA 90 -23.72 -5.03 1.70e+01 1xwl 580 -28.19 -5.02 1.71e+01 1vid 221 -24.98 -5.02 1.71e+01 1g8jA 825 -28.19 -5.00 1.75e+01 1b4kA 337 -26.01 -4.97 1.79e+01 1io2A 213 -25.45 -4.97 1.80e+01 1qfeA 252 -25.16 -4.96 1.80e+01 1hv8A 367 -26.66 -4.96 1.81e+01 1imvA 398 -26.92 -4.95 1.82e+01 1nom 248 -25.57 -4.94 1.84e+01 3bdpA 580 -27.93 -4.93 1.85e+01 1jp3A 253 -26.03 -4.90 1.90e+01 1whtA 256 -24.87 -4.90 1.92e+01 2pfkA 320 -26.51 -4.88 1.94e+01 1efuB 282 -26.46 -4.81 2.06e+01 1aua 296 -25.44 -4.81 2.08e+01 1k3fA 253 -24.92 -4.80 2.08e+01 9apiA 347 -25.69 -4.80 2.09e+01 1floA 422 -26.73 -4.76 2.18e+01 1qr6A 584 -27.17 -4.74 2.21e+01 1nf1A 333 -27.79 -4.74 2.21e+01 1eucB 396 -26.37 -4.73 2.22e+01 1eudB 396 -26.36 -4.72 2.25e+01 1whsA 255 -24.71 -4.71 2.26e+01 1kq4A 232 -27.12 -4.70 2.30e+01 1b71A 191 -26.68 -4.65 2.40e+01 9gafA 295 -25.47 -4.64 2.42e+01 1dzfA 215 -24.89 -4.64 2.42e+01 1ncs 47 -20.21 -4.63 2.44e+01 1hm6A 346 -25.70 -4.61 2.49e+01 1rpl 251 -25.47 -4.61 2.50e+01 1bed 181 -24.92 -4.60 2.51e+01 1bcfA 158 -26.06 -4.56 2.61e+01 1dvbA 191 -26.44 -4.53 2.68e+01 1exnB 290 -26.61 -4.51 2.72e+01 1ryt 190 -26.67 -4.50 2.75e+01 1jygA 69 -23.03 -4.50 2.76e+01 1pch 88 -21.76 -4.50 2.76e+01 1nmtA 392 -25.69 -4.45 2.89e+01 1hg5A 289 -25.65 -4.42 2.95e+01 1lrzA 426 -27.01 -4.42 2.97e+01 1eu8A 409 -25.73 -4.36 3.13e+01 1dnlA 199 -23.60 -4.35 3.15e+01 1d8dA 377 -26.75 -4.35 3.15e+01 1hg2A 289 -25.56 -4.34 3.18e+01 1jcrA 377 -26.72 -4.33 3.22e+01 1jsbA 73 -21.82 -4.33 3.23e+01 1dofA 403 -27.44 -4.31 3.27e+01 1huuA 90 -23.25 -4.31 3.27e+01 1ylvA 342 -26.36 -4.31 3.29e+01 1gkuB 1054 -28.40 -4.30 3.31e+01 1g0uE 234 -24.93 -4.29 3.33e+01 1qbqA 333 -25.57 -4.29 3.35e+01 1trkA 680 -27.69 -4.26 3.44e+01 1dcnD 436 -26.99 -4.26 3.45e+01 1b3jA 274 -24.91 -4.26 3.45e+01 1hf8A 289 -25.46 -4.25 3.48e+01 1e0eA 55 -20.49 -4.25 3.48e+01 1p35A 299 -25.14 -4.24 3.51e+01 1kn6A 90 -21.37 -4.23 3.53e+01 1a48 306 -25.71 -4.22 3.58e+01 1qbjA 81 -21.77 -4.21 3.61e+01 1d6jA 211 -24.29 -4.20 3.64e+01 1gky 187 -24.23 -4.19 3.67e+01 1f7wA 144 -24.28 -4.18 3.71e+01 1qgpA 77 -21.54 -4.18 3.72e+01 1lucB 324 -25.85 -4.17 3.73e+01 1ji0A 240 -24.28 -4.17 3.73e+01 1bpb 248 -25.09 -4.15 3.81e+01 1bvsB 203 -24.29 -4.14 3.85e+01 2abk 211 -25.44 -4.14 3.86e+01 1ebfA 358 -25.36 -4.13 3.90e+01 1kqqA 139 -23.01 -4.12 3.90e+01 1dl5A 317 -26.20 -4.12 3.92e+01 3proC 166 -23.40 -4.12 3.93e+01 1h7nA 342 -26.30 -4.11 3.96e+01 1anv 356 -25.24 -4.11 3.97e+01 3proD 166 -23.40 -4.10 3.98e+01 1m4zA 238 -24.07 -4.10 3.98e+01