% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53 % (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. % --------------------------------------------------------------------- % dsspfoo.1.YGR017W.t2k-100-30-dssp-ebghstl Host: farm03-10.kilokluster.ucsc.edu Fri Oct 6 03:56:08 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR017W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR017W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR017W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 298 nodes, 458.45 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.4706) * Reverse)^tau(=0.8190))) % Calculated when Simple < simple_threshold (10000.00) % 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 2i51A 195 -245.62 -230.87 4.94e-48 1t9mA 214 -81.95 -71.60 2.27e-16 1ty9A 222 -72.46 -62.56 2.61e-14 1nrgA 261 -67.26 -53.11 4.26e-12 1dnlA 199 -59.67 -47.41 9.96e-11 1g79A 218 -58.76 -47.12 1.17e-10 2a2jA 246 -49.86 -38.30 1.77e-08 1ci0A 228 -50.09 -36.82 4.21e-08 2i02A 148 -32.60 -22.46 2.66e-04 2aq6A 147 -27.70 -18.05 4.73e-03 1rfeA 162 -28.79 -17.76 5.72e-03 1xxoA 147 -27.12 -17.09 8.94e-03 1w9aA 147 -27.01 -16.98 9.65e-03 2fhqA 141 -25.23 -14.71 4.53e-02 2asfA 137 -24.05 -14.21 6.42e-02 1egxA 115 -23.21 -13.19 1.31e-01 2hhzA 150 -23.49 -12.44 2.23e-01 2dafA 118 -21.67 -11.69 3.81e-01 1d8hA 311 -21.43 -11.22 5.32e-01 1d8iA 311 -20.75 -10.50 8.99e-01 2ac1A 541 -24.39 -10.49 9.09e-01 2bfdA 400 -21.38 -10.48 9.18e-01 1olsA 400 -22.13 -10.47 9.25e-01 1ayzA 169 -21.50 -10.41 9.63e-01 1x7yA 400 -21.23 -10.23 1.10e+00 1zdnA 158 -20.79 -10.02 1.29e+00 2ucz 165 -21.35 -9.94 1.36e+00 1tqnA 486 -21.37 -9.76 1.55e+00 1a65A 504 -22.79 -9.39 2.05e+00 1gtfA 74 -20.66 -9.36 2.10e+00 1v1rA 400 -20.67 -9.23 2.31e+00 1qawF 74 -20.50 -9.22 2.34e+00 1e1hA 287 -20.39 -9.22 2.34e+00 2bi7A 384 -18.99 -9.02 2.71e+00 1jbbA 153 -20.41 -9.00 2.76e+00 2extA 77 -20.45 -8.98 2.80e+00 1vkxA 273 -20.43 -8.96 2.83e+00 1ywnA 316 -22.25 -8.94 2.87e+00 2iutA 574 -21.57 -8.90 2.97e+00 1aol 228 -20.84 -8.77 3.27e+00 1jatA 155 -19.86 -8.59 3.75e+00 1toh 343 -20.59 -8.51 3.99e+00 1wapA 75 -19.40 -8.46 4.14e+00 1f6bA 198 -19.10 -8.45 4.17e+00 1mlwA 301 -19.66 -8.42 4.27e+00 1yh2A 175 -20.61 -8.42 4.28e+00 7ceiB 206 -22.64 -8.29 4.72e+00 1hfuA 503 -21.67 -8.24 4.90e+00 1i7qA 519 -20.18 -8.22 4.97e+00 3thiA 371 -19.09 -8.19 5.11e+00 1uk8A 282 -18.30 -8.18 5.14e+00 1jlnA 297 -20.06 -8.18 5.14e+00 1j8uA 325 -20.45 -8.15 5.26e+00 1pah 308 -19.79 -8.12 5.37e+00 1z2uA 150 -19.93 -8.03 5.75e+00 2ayvA 166 -19.64 -8.01 5.88e+00 2av1A 275 -18.51 -8.00 5.90e+00 2b29A 123 -19.13 -8.00 5.90e+00 1iupA 282 -18.15 -7.99 5.96e+00 1tmcA 175 -17.91 -7.98 6.00e+00 1waaA 93 -18.02 -7.98 6.01e+00 1z9tA 255 -18.10 -7.96 6.11e+00 1c4zD 154 -20.29 -7.92 6.28e+00 2av7A 275 -18.41 -7.89 6.42e+00 1pnkB 557 -19.16 -7.88 6.45e+00 1e3aB 560 -19.16 -7.88 6.45e+00 1ajqB 557 -19.21 -7.88 6.47e+00 2htdA 140 -18.21 -7.86 6.60e+00 1r1hA 696 -18.80 -7.85 6.62e+00 1vjpA 394 -18.91 -7.79 6.95e+00 1i4fA 275 -18.23 -7.79 6.95e+00 1gm7B 557 -19.10 -7.77 7.04e+00 1gm9B 557 -19.10 -7.77 7.05e+00 1gkfB 557 -19.10 -7.76 7.08e+00 1gk9B 557 -19.09 -7.75 7.15e+00 1duzA 275 -18.23 -7.73 7.27e+00 1iknA 286 -19.76 -7.72 7.33e+00 1dykA 394 -20.04 -7.70 7.44e+00 1q67A 231 -23.07 -7.67 7.63e+00 1k6wA 426 -18.24 -7.65 7.73e+00 4pah 308 -19.23 -7.59 8.14e+00 1qu0A 191 -19.93 -7.54 8.43e+00 1ox8A 107 -17.66 -7.47 8.91e+00 2thiA 379 -19.02 -7.46 8.94e+00 1o5uA 101 -17.72 -7.42 9.27e+00 2awfA 172 -18.91 -7.41 9.33e+00 1x23A 155 -19.25 -7.39 9.44e+00 1z5bA 469 -18.71 -7.36 9.68e+00 1l1eA 287 -18.35 -7.36 9.69e+00 1dmwA 307 -19.11 -7.32 1.00e+01 2mtaC 147 -19.38 -7.32 1.00e+01 2gvaA 87 -18.24 -7.30 1.01e+01 1f1uA 323 -19.66 -7.29 1.02e+01 1mg2D 155 -19.41 -7.28 1.03e+01 2hkjA 469 -18.70 -7.27 1.04e+01 1fl0A 171 -18.73 -7.26 1.05e+01 1mu5A 471 -18.82 -7.18 1.11e+01 2hb6A 491 -17.80 -7.17 1.12e+01 2hq9A 149 -17.48 -7.13 1.16e+01 2hc9A 491 -17.75 -7.11 1.18e+01 1xjuA 163 -16.48 -7.08 1.21e+01 1agdA 276 -17.66 -7.06 1.23e+01 1llwA 1520 -18.94 -7.03 1.25e+01 1eujA 166 -18.67 -6.99 1.29e+01 2c2pA 199 -17.39 -6.98 1.30e+01 1hsbA 270 -17.48 -6.98 1.31e+01 1t46A 313 -19.49 -6.98 1.31e+01 1dmtA 696 -17.61 -6.96 1.33e+01 2c2qA 199 -17.23 -6.95 1.34e+01 1rypK 198 -16.17 -6.90 1.40e+01 1xd3A 230 -17.80 -6.86 1.43e+01 1otcA 495 -19.51 -6.84 1.46e+01 2gw6A 123 -16.67 -6.80 1.50e+01 2bvpA 276 -17.33 -6.80 1.50e+01 1vm7A 311 -18.84 -6.80 1.51e+01 1x1fA 149 -17.93 -6.77 1.54e+01 1mxiA 160 -16.18 -6.75 1.56e+01 1qtsA 247 -17.10 -6.75 1.57e+01 1yh6A 179 -17.79 -6.73 1.59e+01 1v4sA 455 -17.07 -6.72 1.60e+01 1u69A 163 -16.86 -6.69 1.64e+01 1o65A 246 -17.26 -6.69 1.64e+01 2h57A 190 -18.32 -6.68 1.65e+01 1htoA 477 -18.00 -6.68 1.66e+01 1avbA 226 -17.28 -6.68 1.66e+01 2cxaA 256 -16.14 -6.66 1.68e+01 1xh3A 276 -17.25 -6.65 1.70e+01 2af6A 258 -16.55 -6.64 1.72e+01 1sqnA 261 -16.14 -6.59 1.78e+01 1oflA 481 -20.93 -6.57 1.81e+01 1k5nA 276 -17.15 -6.55 1.84e+01 1r3cA 366 -17.43 -6.55 1.84e+01 2gujA 155 -17.08 -6.53 1.86e+01 1gotB 340 -19.03 -6.53 1.87e+01 1fn9A 365 -17.58 -6.52 1.88e+01 2fg9A 178 -16.29 -6.51 1.90e+01 1gbg 214 -16.88 -6.50 1.91e+01 1guqA 348 -19.03 -6.50 1.92e+01 1b0lA 691 -17.73 -6.50 1.92e+01 1if1A 113 -16.91 -6.48 1.95e+01 1mj5A 302 -19.45 -6.47 1.96e+01 1tt0A 623 -18.45 -6.46 1.98e+01 1pysA 350 -17.84 -6.46 1.98e+01 1a1mA 278 -17.07 -6.46 1.98e+01 1sr7A 259 -15.97 -6.45 1.99e+01 1evhA 112 -17.52 -6.43 2.02e+01 1a1oA 276 -17.08 -6.42 2.04e+01 2f5vA 595 -18.41 -6.39 2.08e+01 1htqA 477 -17.73 -6.39 2.08e+01 1b9kA 238 -16.49 -6.39 2.10e+01 1kyfA 247 -16.74 -6.38 2.10e+01 1z47A 355 -16.61 -6.37 2.12e+01 1gv4A 528 -17.76 -6.36 2.13e+01 1gupA 348 -18.86 -6.34 2.17e+01 1a1nA 276 -16.93 -6.34 2.18e+01 1ekxA 311 -17.64 -6.32 2.22e+01 1jb7A 495 -18.61 -6.31 2.23e+01 2g9zA 348 -17.13 -6.31 2.24e+01 1kfuS 184 -17.75 -6.29 2.26e+01 1zybA 232 -17.23 -6.29 2.27e+01 1b7yA 350 -17.78 -6.28 2.28e+01 1i88A 389 -17.19 -6.27 2.30e+01 1gpmA 525 -16.60 -6.25 2.34e+01 2b1pA 355 -17.79 -6.24 2.35e+01 1ra0A 430 -17.00 -6.23 2.37e+01 1sacA 204 -17.12 -6.23 2.38e+01 1sauA 115 -18.43 -6.23 2.38e+01 1fvzA 271 -19.24 -6.20 2.43e+01 1jhnA 424 -25.58 -6.20 2.43e+01 1tbgA 340 -18.28 -6.17 2.49e+01 7ahlA 293 -16.58 -6.17 2.49e+01 1w3oA 216 -16.32 -6.16 2.52e+01 2bcjB 340 -18.40 -6.14 2.55e+01 1tzlA 622 -18.28 -6.14 2.55e+01 2ganA 190 -16.91 -6.14 2.55e+01 1o59A 355 -21.06 -6.13 2.57e+01 1bxeA 113 -14.77 -6.11 2.62e+01 1sv0C 82 -15.03 -6.06 2.74e+01 1f8gA 384 -15.71 -6.04 2.77e+01 2gfsA 372 -17.23 -6.01 2.84e+01 2bwqA 129 -17.55 -6.01 2.85e+01 1spjA 238 -17.74 -6.00 2.85e+01 2aysA 348 -16.17 -6.00 2.85e+01 1a0rB 340 -18.54 -5.99 2.88e+01 1msk 331 -17.47 -5.99 2.90e+01 1u4cA 349 -16.90 -5.98 2.91e+01 1p7gA 222 -17.64 -5.94 2.99e+01 2arcA 164 -16.63 -5.94 3.00e+01 1ywrA 360 -17.30 -5.94 3.01e+01 2gp5A 349 -16.83 -5.92 3.05e+01 1wguA 136 -17.21 -5.92 3.05e+01 1ds1A 324 -16.66 -5.90 3.09e+01 1l7dA 384 -15.77 -5.89 3.12e+01 2b6dA 345 -15.98 -5.89 3.13e+01 1h32A 261 -15.78 -5.88 3.16e+01 1i6pA 220 -16.19 -5.86 3.20e+01 1qpsA 261 -17.63 -5.86 3.21e+01 1n67A 359 -16.97 -5.85 3.23e+01 1yfnA 118 -16.54 -5.84 3.25e+01 2arcB 164 -16.54 -5.84 3.27e+01 1jalA 363 -15.71 -5.84 3.27e+01 1g0uI 205 -15.53 -5.83 3.28e+01 1r1qA 100 -16.49 -5.82 3.32e+01 1rypJ 204 -15.54 -5.80 3.37e+01 1gvp 87 -16.42 -5.80 3.38e+01 1vqb 87 -16.42 -5.79 3.38e+01 2aacA 177 -16.48 -5.79 3.40e+01 1dyqA 234 -16.76 -5.76 3.47e+01 2amg 415 -20.58 -5.75 3.50e+01 1bx7 55 -16.04 -5.75 3.50e+01 1wkrA 340 -16.01 -5.73 3.56e+01 1qfoA 119 -16.90 -5.73 3.57e+01 1bunB 61 -16.67 -5.72 3.58e+01 1oo0A 147 -16.02 -5.72 3.60e+01 2sak 121 -15.58 -5.72 3.60e+01 1k8kA 418 -15.57 -5.69 3.67e+01 2f4qA 346 -16.16 -5.67 3.74e+01 1ae3 86 -16.49 -5.66 3.77e+01 1a28A 256 -15.22 -5.66 3.78e+01 1abrB 267 -16.87 -5.66 3.79e+01 2gv8A 447 -17.09 -5.63 3.86e+01 1a4eA 488 -17.63 -5.61 3.93e+01 1kcmA 270 -17.23 -5.61 3.94e+01 1a9eA 277 -16.17 -5.61 3.94e+01