% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YGR023W.t2k-100-30-alpha Host: farm19.cse.ucsc.edu Sun Mar 19 12:29:16 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR023W % --------------------------------------------------------------------- % 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 YGR023W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR023W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 552 nodes, 918.59 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(=2.5938) * Reverse)^tau(=0.7008))) % 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 1u32A 293 -22.21 -11.40 2.39e-01 1jk7A 323 -22.62 -11.33 2.51e-01 1fjmA 330 -21.77 -10.50 4.37e-01 1zckA 154 -22.34 -9.86 6.74e-01 1d0nA 729 -22.45 -9.53 8.51e-01 2bzlA 325 -20.70 -9.29 1.00e+00 1rxdA 159 -21.88 -9.27 1.02e+00 1g9uA 454 -22.69 -9.01 1.23e+00 1jl5A 454 -22.31 -8.85 1.37e+00 1x24A 180 -21.17 -8.52 1.73e+00 1bqhG 129 -22.31 -8.51 1.75e+00 1wkrA 340 -28.08 -8.51 1.75e+00 1t5hX 504 -20.48 -8.26 2.10e+00 1q40B 219 -20.23 -8.21 2.17e+00 1xm7A 195 -18.75 -8.19 2.21e+00 1pujA 282 -18.21 -8.08 2.39e+00 1zq1A 438 -21.23 -8.02 2.50e+00 1e1hA 287 -19.86 -7.85 2.84e+00 1adqL 213 -26.98 -7.72 3.11e+00 1f28A 297 -18.80 -7.71 3.14e+00 1xubA 298 -19.59 -7.59 3.44e+00 1lcyA 325 -21.95 -7.57 3.48e+00 1try 224 -24.70 -7.48 3.74e+00 1c0aA 585 -18.19 -7.34 4.16e+00 1v54B 227 -21.06 -7.26 4.39e+00 1k5cA 335 -22.40 -7.24 4.45e+00 1nezG 128 -21.88 -7.17 4.71e+00 2fcr 173 -19.27 -7.16 4.73e+00 1t6kA 278 -18.97 -7.08 5.03e+00 2a5dA 175 -17.50 -7.06 5.11e+00 1e5uI 187 -20.60 -6.92 5.69e+00 2et1A 201 -21.27 -6.87 5.94e+00 1n67A 359 -23.80 -6.80 6.27e+00 1cxlA 686 -21.58 -6.79 6.31e+00 1fi2A 201 -21.08 -6.79 6.31e+00 1lrzA 426 -17.44 -6.78 6.34e+00 1u1wA 298 -18.85 -6.71 6.70e+00 1aszB 490 -17.94 -6.67 6.89e+00 1pq7A 224 -23.11 -6.66 6.93e+00 8fabA 212 -26.25 -6.65 6.99e+00 1fn8A 224 -23.64 -6.64 7.06e+00 2d0oB 125 -16.99 -6.57 7.43e+00 1o88A 353 -20.31 -6.55 7.60e+00 1asyA 490 -17.80 -6.53 7.70e+00 1d3cA 686 -21.03 -6.52 7.73e+00 1z41A 338 -16.99 -6.44 8.23e+00 1ciy 590 -24.81 -6.36 8.83e+00 1dr9A 201 -22.95 -6.34 8.94e+00 1jmxA 494 -20.68 -6.31 9.13e+00 2occB 227 -19.94 -6.27 9.40e+00 1ehkB 168 -19.98 -6.27 9.47e+00 1ot1A 686 -20.82 -6.26 9.52e+00 2pec 353 -19.99 -6.20 9.95e+00 1erjA 393 -25.62 -6.20 9.97e+00 6prcL 273 -18.44 -6.20 9.99e+00 1kepA 348 -16.11 -6.15 1.04e+01 1air 353 -20.14 -6.14 1.05e+01 1tjgH 237 -24.41 -6.09 1.09e+01 1itkA 731 -17.50 -6.08 1.09e+01 1dxrL 273 -18.41 -6.08 1.09e+01 1p8xA 344 -18.37 -6.08 1.10e+01 1ollA 188 -19.98 -6.05 1.13e+01 1oc2A 348 -15.99 -6.05 1.13e+01 1dqnA 230 -16.24 -6.04 1.14e+01 1ah0 316 -16.30 -6.03 1.14e+01 2asi 360 -23.75 -6.01 1.16e+01 1ux6A 350 -22.19 -6.00 1.17e+01 1snyA 267 -16.48 -5.95 1.22e+01 2cxxA 190 -16.41 -5.93 1.24e+01 1i2kA 269 -17.77 -5.90 1.26e+01 1w3uA 362 -17.45 -5.88 1.29e+01 1bjnA 360 -17.09 -5.87 1.29e+01 1g40A 244 -21.71 -5.83 1.34e+01 1gskA 513 -26.36 -5.83 1.34e+01 1ai1H 221 -26.29 -5.78 1.40e+01 1bt4A 362 -16.97 -5.77 1.41e+01 1et0A 269 -18.54 -5.75 1.43e+01 2dhqA 146 -16.13 -5.73 1.46e+01 1k42A 168 -18.33 -5.68 1.51e+01 1f00I 282 -23.22 -5.65 1.55e+01 1q47A 495 -18.62 -5.64 1.56e+01 1n99A 166 -16.96 -5.63 1.57e+01 1uf5A 303 -17.51 -5.63 1.57e+01 1mkfA 382 -21.37 -5.63 1.58e+01 1h05A 146 -16.09 -5.60 1.62e+01 1erzA 303 -17.27 -5.58 1.64e+01 1dqpA 230 -15.69 -5.58 1.64e+01 1lycA 343 -16.54 -5.58 1.65e+01 1tdtA 259 -18.87 -5.54 1.69e+01 1z90A 469 -17.34 -5.54 1.69e+01 1wrjA 156 -16.00 -5.53 1.72e+01 1je0A 236 -15.99 -5.52 1.72e+01 1f15B 218 -19.38 -5.52 1.73e+01 1bjoA 360 -16.89 -5.51 1.73e+01 1igtB 444 -26.66 -5.51 1.73e+01 2rmpA 361 -22.72 -5.49 1.77e+01 1v8bA 479 -15.94 -5.48 1.78e+01 1gmiA 136 -16.81 -5.45 1.82e+01 2polA 366 -18.74 -5.44 1.84e+01 1kawA 135 -17.70 -5.43 1.86e+01 2a6hA 315 -18.05 -5.42 1.86e+01 1jniA 123 -15.58 -5.42 1.87e+01 1b43A 340 -16.10 -5.41 1.89e+01 1rmg 422 -22.70 -5.40 1.91e+01 1xkyA 301 -15.55 -5.39 1.91e+01 1f1sA 814 -22.51 -5.35 1.99e+01 2b8nA 429 -15.45 -5.34 2.00e+01 1uz8B 212 -24.16 -5.32 2.04e+01 1xksA 450 -25.61 -5.30 2.06e+01 1npeA 267 -19.41 -5.30 2.07e+01 1odfA 290 -15.87 -5.27 2.11e+01 1upiA 225 -19.83 -5.25 2.15e+01 1q7fA 286 -18.29 -5.23 2.19e+01 1o0uA 429 -15.33 -5.21 2.22e+01 1h6uA 308 -18.77 -5.21 2.22e+01 1s5lA 344 -15.99 -5.20 2.24e+01 1khbA 625 -17.95 -5.20 2.24e+01 2madH 373 -19.60 -5.20 2.24e+01 1l6rA 227 -15.23 -5.18 2.28e+01 1rt8A 513 -16.83 -5.18 2.28e+01 2affA 120 -18.18 -5.17 2.31e+01 1pmi 440 -19.19 -5.16 2.33e+01 1s48A 609 -15.84 -5.15 2.34e+01 1ej6A 1289 -19.87 -5.14 2.35e+01 3tdt 274 -18.68 -5.14 2.36e+01 1sz7A 200 -15.51 -5.14 2.36e+01 1f76A 336 -16.28 -5.13 2.37e+01 1lvmA 229 -19.54 -5.10 2.43e+01 1kgqA 274 -18.76 -5.10 2.43e+01 1prcH 259 -17.36 -5.10 2.45e+01 1e1hB 174 -15.01 -5.09 2.47e+01 1e2tA 284 -16.67 -5.08 2.47e+01 1sqc 631 -15.69 -5.08 2.49e+01 1arv 344 -15.77 -5.07 2.51e+01 1xuqA 212 -15.42 -5.06 2.53e+01 1aru 344 -15.77 -5.05 2.55e+01 1b3qA 379 -19.35 -5.04 2.56e+01 1xszA 356 -15.70 -5.04 2.57e+01 1k6dA 220 -16.94 -5.03 2.59e+01 1u0mA 382 -15.71 -5.02 2.61e+01 1f0lA 535 -19.06 -5.02 2.61e+01 1j0fA 100 -14.93 -5.00 2.65e+01 1sva1 361 -19.22 -4.99 2.67e+01 1wrmA 165 -14.60 -4.99 2.67e+01 2tdt 274 -18.63 -4.98 2.69e+01 1ijqA 316 -18.78 -4.97 2.73e+01 1ospO 257 -22.76 -4.96 2.74e+01 6prcH 258 -17.13 -4.96 2.75e+01 1d8hA 311 -19.83 -4.95 2.77e+01 1hsr 344 -15.77 -4.95 2.77e+01 2sqcA 631 -15.33 -4.94 2.78e+01 1wlnA 120 -18.60 -4.94 2.80e+01 1iatA 557 -15.76 -4.94 2.80e+01 1jfkA 134 -14.62 -4.93 2.81e+01 1ah4 315 -15.24 -4.91 2.87e+01 1bqyA 234 -17.64 -4.90 2.88e+01 1fnf 368 -25.41 -4.90 2.88e+01 1aomA 567 -20.24 -4.88 2.93e+01 2f5bH 235 -22.92 -4.88 2.94e+01 2alaA 391 -22.32 -4.86 2.98e+01 1plq 258 -18.31 -4.85 3.01e+01 1v3eA 431 -21.34 -4.84 3.03e+01 1xkgA 312 -15.18 -4.84 3.04e+01 1jovA 270 -18.58 -4.84 3.04e+01 1kcvL 214 -26.75 -4.79 3.16e+01 1wnhA 225 -16.19 -4.79 3.16e+01 2etvA 346 -15.34 -4.79 3.18e+01 1h3gA 601 -16.17 -4.78 3.20e+01 1pvxA 194 -20.25 -4.78 3.20e+01 1igtD 444 -26.45 -4.78 3.21e+01 1rerA 391 -22.34 -4.76 3.25e+01 1zj8A 566 -16.85 -4.73 3.33e+01 1jmuB 666 -18.55 -4.69 3.47e+01 1pcl 355 -20.91 -4.67 3.51e+01 1yx1A 264 -14.84 -4.67 3.52e+01 1ee6A 197 -17.95 -4.66 3.54e+01 1nnvA 110 -15.50 -4.63 3.65e+01 1ddt 535 -18.10 -4.60 3.73e+01 2cxcA 144 -14.63 -4.59 3.78e+01 1tueB 218 -15.78 -4.58 3.78e+01 1nkgA 508 -25.78 -4.57 3.83e+01 1svb 395 -16.96 -4.56 3.85e+01 1gtkA 313 -15.46 -4.56 3.86e+01 1tikA 213 -14.74 -4.56 3.88e+01 1mmiA 366 -18.06 -4.55 3.91e+01 1bdfA 235 -18.30 -4.53 3.98e+01 1c3yA 108 -14.27 -4.52 3.99e+01