% 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.YGR014W.t2k-100-30-alpha Host: farm17.cse.ucsc.edu Sun Mar 19 20:00:47 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR014W % --------------------------------------------------------------------- % 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 YGR014W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR014W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 1307 nodes, 2456.82 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(=2.5293) * Reverse)^tau(=0.6942))) % 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 1k3iA 656 -41.33 -14.01 7.45e-02 1gof 639 -38.86 -13.94 7.78e-02 1goh 639 -37.67 -12.99 1.37e-01 1wxrA 1048 -39.06 -12.53 1.81e-01 1axkA 394 -32.85 -11.96 2.57e-01 1cwvA 492 -34.08 -11.64 3.14e-01 1phd 414 -23.80 -11.53 3.37e-01 1dz4A 414 -23.82 -11.51 3.40e-01 1qmqA 414 -23.49 -11.50 3.43e-01 5cpp 414 -23.60 -11.36 3.73e-01 1phb 414 -23.62 -11.34 3.79e-01 1re9A 414 -23.28 -11.30 3.88e-01 1s9aA 257 -26.05 -10.86 5.14e-01 1kypA 237 -28.07 -10.77 5.44e-01 2fn0A 437 -22.75 -10.68 5.74e-01 1itbB 315 -28.36 -10.46 6.62e-01 1acc 735 -26.78 -10.42 6.82e-01 1yrcA 414 -22.40 -10.35 7.10e-01 1phg 414 -22.36 -10.28 7.44e-01 1oxdA 227 -27.33 -10.24 7.65e-01 2nlrA 234 -25.34 -9.81 1.01e+00 1b4vA 504 -23.23 -9.68 1.10e+00 1ijhA 504 -23.33 -9.57 1.19e+00 2emo 237 -25.62 -9.48 1.26e+00 1a0qL 212 -27.27 -9.40 1.33e+00 1nlr 234 -24.72 -9.40 1.33e+00 1s7kA 182 -20.84 -9.37 1.35e+00 2d0oA 610 -22.35 -9.31 1.41e+00 1mxtA 504 -23.14 -9.30 1.42e+00 1ema 236 -28.89 -9.29 1.43e+00 2bsyA 278 -24.46 -9.27 1.44e+00 1nt0A 286 -26.28 -9.18 1.54e+00 1n4wA 504 -23.07 -9.18 1.54e+00 1b8sA 504 -22.26 -8.86 1.92e+00 1ogoX 574 -28.67 -8.84 1.93e+00 2axtO 247 -23.98 -8.82 1.97e+00 1n1pA 504 -22.56 -8.76 2.05e+00 1nr0A 611 -29.33 -8.73 2.08e+00 1ju2A 536 -22.94 -8.67 2.18e+00 1m3jA 471 -24.91 -8.66 2.19e+00 1b9cA 236 -26.02 -8.54 2.38e+00 1jpc 109 -23.08 -8.46 2.52e+00 1xgyH 219 -24.36 -8.44 2.54e+00 1msaA 109 -22.73 -8.24 2.92e+00 1pjpA 226 -20.69 -8.19 3.02e+00 1o20A 427 -20.60 -8.19 3.03e+00 1ig3A 263 -20.78 -8.17 3.07e+00 2aamA 309 -21.21 -8.14 3.13e+00 1sgzA 389 -21.93 -8.04 3.35e+00 1s7mA 174 -21.74 -8.02 3.41e+00 1m3iA 471 -24.79 -8.01 3.44e+00 1e4fT 419 -22.92 -8.00 3.45e+00 1w2tA 432 -25.09 -7.96 3.56e+00 1jv2A 957 -34.60 -7.95 3.57e+00 1fknA 391 -21.64 -7.89 3.74e+00 1h6rA 236 -27.63 -7.84 3.87e+00 2bsdA 264 -29.56 -7.82 3.92e+00 2bbkH 355 -24.50 -7.75 4.11e+00 1nhcA 336 -29.77 -7.74 4.15e+00 1qcxA 359 -24.10 -7.60 4.57e+00 1ju3A 583 -23.05 -7.59 4.61e+00 1dmaA 214 -19.87 -7.57 4.67e+00 1z4xA 532 -24.72 -7.57 4.68e+00 1klt 226 -20.57 -7.51 4.88e+00 1czfA 362 -28.12 -7.46 5.05e+00 1yal 218 -20.70 -7.44 5.15e+00 1yp2A 451 -22.34 -7.43 5.17e+00 1z4vA 532 -24.45 -7.43 5.18e+00 1e3uA 246 -19.39 -7.35 5.49e+00 1nnlA 225 -18.06 -7.26 5.84e+00 1uypA 432 -24.08 -7.22 5.99e+00 1aoqA 567 -24.04 -7.19 6.13e+00 1aerA 205 -19.61 -7.19 6.15e+00 1k4fA 248 -19.17 -7.17 6.21e+00 1gv9A 260 -24.59 -7.11 6.50e+00 1knvA 293 -21.48 -7.11 6.53e+00 1xg8A 111 -18.01 -7.07 6.71e+00 1fxzA 476 -23.69 -7.04 6.83e+00 1a3gA 308 -20.13 -7.00 7.06e+00 1fofA 246 -18.71 -6.97 7.20e+00 1k55A 246 -18.86 -6.96 7.27e+00 2bibA 547 -26.08 -6.89 7.66e+00 1gl4A 285 -23.45 -6.87 7.75e+00 1jv2B 692 -23.24 -6.87 7.76e+00 1x1iA 752 -23.03 -6.85 7.84e+00 1bihA 395 -26.25 -6.80 8.18e+00 2bm5A 186 -21.28 -6.76 8.41e+00 1jb7A 495 -20.20 -6.75 8.44e+00 1f5jA 199 -22.22 -6.75 8.50e+00 1t2bA 397 -18.83 -6.73 8.61e+00 1qksA 567 -23.44 -6.72 8.67e+00 1jmmA 377 -24.42 -6.72 8.69e+00 1j0mA 752 -22.46 -6.66 9.05e+00 1nn6A 228 -19.81 -6.66 9.06e+00 1pvc2 271 -19.06 -6.66 9.08e+00 1uacH 114 -21.31 -6.63 9.22e+00 1clc 639 -20.98 -6.63 9.29e+00 1pd21 199 -17.30 -6.62 9.29e+00 1xhcA 367 -22.43 -6.61 9.38e+00 1xipA 388 -24.91 -6.57 9.66e+00 1onwA 390 -20.47 -6.57 9.66e+00 1otcA 495 -19.75 -6.56 9.75e+00 1a0jA 223 -19.36 -6.56 9.77e+00 1pfo 500 -23.01 -6.55 9.80e+00 1vorW 173 -20.34 -6.53 9.94e+00 1fnf 368 -24.51 -6.53 9.96e+00 1ruxA 951 -26.76 -6.53 9.98e+00 1g6sA 427 -19.27 -6.51 1.01e+01 1jxpA 186 -20.67 -6.50 1.02e+01 1jmxB 349 -23.26 -6.50 1.02e+01 1tffA 234 -17.92 -6.48 1.03e+01 3kvt 115 -17.64 -6.48 1.03e+01 1v5vA 401 -24.21 -6.47 1.04e+01 1itvA 195 -22.16 -6.42 1.08e+01 2aujD 309 -20.42 -6.39 1.10e+01 1ve6A 582 -24.11 -6.39 1.11e+01 2pil 159 -19.22 -6.37 1.12e+01 1pfxC 235 -18.10 -6.32 1.17e+01 1gnyA 153 -20.28 -6.30 1.18e+01 1cgt 684 -24.14 -6.28 1.20e+01 1h54A 754 -25.15 -6.27 1.21e+01 1ik6A 369 -19.21 -6.27 1.21e+01 1rzfH 235 -23.71 -6.27 1.21e+01 1t5rA 284 -22.22 -6.26 1.22e+01 1axsB 221 -20.83 -6.25 1.23e+01 2bspA 420 -23.66 -6.22 1.25e+01 1ttuA 477 -22.41 -6.20 1.27e+01 1pz7A 204 -21.92 -6.20 1.28e+01 2blcA 238 -18.77 -6.19 1.28e+01 1wdaA 670 -26.81 -6.19 1.29e+01 1eps 427 -18.82 -6.17 1.30e+01 1dkuA 317 -18.42 -6.17 1.31e+01 1mn4A 282 -22.75 -6.17 1.31e+01 1f3eA 386 -18.01 -6.14 1.34e+01 1x31C 206 -17.86 -6.13 1.35e+01 1z9fA 153 -19.17 -6.10 1.37e+01 1hg8A 349 -26.03 -6.10 1.37e+01 2madH 373 -24.20 -6.10 1.38e+01 1djnA 729 -20.88 -6.10 1.38e+01 1y4wA 518 -24.09 -6.08 1.40e+01 1qa7B 217 -20.21 -6.08 1.40e+01 1a0sP 413 -26.83 -6.06 1.41e+01 3rp2A 224 -19.48 -6.00 1.49e+01 1rxwA 336 -18.17 -6.00 1.49e+01 1ztxH 219 -21.94 -5.98 1.51e+01 1tme1 274 -20.66 -5.97 1.52e+01 1lp3A 519 -22.29 -5.97 1.52e+01 2f6kA 307 -17.76 -5.96 1.54e+01 1qbiA 454 -22.07 -5.95 1.54e+01 16pk 415 -17.39 -5.94 1.55e+01 1rlmA 271 -18.32 -5.93 1.57e+01 1rwhA 757 -20.80 -5.92 1.58e+01 1h4uA 265 -22.00 -5.92 1.58e+01 2b8lA 405 -21.55 -5.91 1.59e+01 1q47A 495 -23.71 -5.91 1.60e+01 1kb0A 677 -23.99 -5.90 1.61e+01 1djqA 729 -20.53 -5.90 1.61e+01 2bjrA 368 -21.71 -5.89 1.62e+01 1oe9A 795 -33.58 -5.87 1.65e+01 1w50A 411 -21.43 -5.86 1.65e+01 12e8H 221 -21.35 -5.85 1.66e+01 1a0tP 413 -26.39 -5.85 1.66e+01 1oa4A 222 -20.81 -5.82 1.70e+01 1ujkA 147 -16.08 -5.81 1.72e+01 1k4gA 386 -17.64 -5.80 1.73e+01 1a1rA 198 -21.67 -5.79 1.75e+01 1ay2 159 -18.49 -5.77 1.77e+01 1iirA 415 -16.74 -5.77 1.77e+01 2a46A 238 -20.20 -5.77 1.78e+01 1p30A 952 -25.75 -5.74 1.81e+01 1yocA 147 -17.73 -5.72 1.85e+01 1w7jA 795 -31.37 -5.69 1.88e+01 1jmaA 290 -19.33 -5.69 1.89e+01 1dj0A 264 -17.12 -5.68 1.90e+01 1kjkA 64 -16.73 -5.67 1.92e+01 2c26A 260 -25.10 -5.66 1.93e+01 1rhi1 288 -19.28 -5.65 1.94e+01 1afoA 40 -21.34 -5.64 1.96e+01 1rypB 250 -19.53 -5.63 1.98e+01 1htyA 1015 -26.99 -5.62 1.99e+01 1j2zA 270 -22.52 -5.62 1.99e+01 1kqaA 203 -21.88 -5.61 2.01e+01 1krrA 203 -21.88 -5.61 2.01e+01 1h3gA 601 -21.74 -5.60 2.02e+01 2fxqA 264 -21.81 -5.60 2.02e+01 1rloA 271 -18.05 -5.60 2.03e+01 1mz5A 638 -22.86 -5.60 2.03e+01 1xnkA 196 -21.35 -5.59 2.04e+01 1h1aA 191 -21.80 -5.55 2.10e+01 1yymG 313 -19.42 -5.54 2.11e+01 1mexL 213 -21.32 -5.54 2.12e+01 1em2A 229 -19.38 -5.54 2.12e+01 1rlmB 271 -18.06 -5.54 2.12e+01 1ibsA 317 -17.89 -5.53 2.13e+01 1xhkA 187 -17.22 -5.53 2.13e+01 1ee6A 197 -22.25 -5.53 2.14e+01 1sr4B 261 -18.56 -5.52 2.14e+01 1scs 237 -22.57 -5.52 2.15e+01 2bw8A 227 -21.67 -5.52 2.15e+01 1lay 256 -17.45 -5.52 2.16e+01 1n1tA 641 -22.09 -5.50 2.19e+01 1j1xH 114 -19.52 -5.50 2.19e+01 1d5bB 221 -21.23 -5.49 2.20e+01 1h0bA 256 -23.33 -5.49 2.21e+01 1pvuA 154 -17.52 -5.48 2.23e+01 1o94A 729 -19.95 -5.46 2.25e+01 1jwgA 147 -15.71 -5.46 2.26e+01 1uf2C 421 -19.73 -5.43 2.31e+01 1go3E 187 -19.00 -5.43 2.31e+01 1o12A 376 -18.38 -5.42 2.33e+01 2ffsA 157 -20.06 -5.42 2.34e+01 1wcqA 601 -28.83 -5.41 2.36e+01 1q4gA 553 -25.90 -5.40 2.36e+01 1zpdA 568 -17.86 -5.39 2.38e+01 1dkrA 317 -17.66 -5.38 2.40e+01 1hzxA 349 -26.26 -5.38 2.40e+01 1y7bA 542 -23.19 -5.38 2.40e+01 1lkvX 232 -16.04 -5.38 2.40e+01 1sw6A 327 -18.69 -5.38 2.40e+01 2c1iA 431 -18.25 -5.37 2.43e+01 1l9hA 349 -27.04 -5.36 2.44e+01 1pw4A 451 -25.03 -5.35 2.46e+01 1xbsA 149 -16.80 -5.35 2.46e+01 1v8yA 170 -17.34 -5.35 2.46e+01 1i1kA 309 -17.63 -5.35 2.47e+01 1bt7 186 -19.61 -5.33 2.49e+01 1prn 289 -23.04 -5.33 2.49e+01 1iweA 457 -21.13 -5.33 2.50e+01 2bl9A 238 -17.62 -5.33 2.51e+01 3prn 289 -22.53 -5.31 2.54e+01 2azeC 46 -15.32 -5.31 2.54e+01 1dowA 205 -18.58 -5.30 2.56e+01 1vm6A 228 -17.54 -5.30 2.57e+01 1do6A 124 -19.01 -5.29 2.58e+01 1ztxL 212 -21.01 -5.29 2.58e+01 1nxjA 183 -18.00 -5.29 2.59e+01 1cf1A 404 -24.54 -5.28 2.60e+01 2cxkA 95 -17.61 -5.28 2.60e+01 2pviA 157 -17.13 -5.28 2.61e+01 1lcyA 325 -20.34 -5.27 2.62e+01 1z02A 446 -21.59 -5.27 2.62e+01 2bnh 457 -16.02 -5.26 2.64e+01 1mvpA 124 -18.48 -5.26 2.64e+01 1ikpA 613 -19.99 -5.25 2.67e+01 1a0nB 69 -16.78 -5.24 2.69e+01 1aerB 195 -18.12 -5.23 2.71e+01 1h1iD 350 -23.60 -5.23 2.71e+01 1wpoB 256 -16.91 -5.21 2.74e+01 1hwwA 1015 -26.81 -5.21 2.75e+01 1cknA 330 -23.05 -5.19 2.79e+01 2tmdA 729 -20.01 -5.18 2.80e+01 1cpn 208 -24.74 -5.18 2.83e+01 1b3oA 514 -19.66 -5.17 2.83e+01 1fkoB 440 -20.23 -5.17 2.83e+01 2c4xA 260 -24.56 -5.16 2.86e+01 2ashA 381 -19.05 -5.16 2.86e+01 1suuA 312 -23.05 -5.16 2.87e+01 1mnnA 340 -21.66 -5.16 2.87e+01 1c7sA 858 -21.72 -5.14 2.90e+01 1xjcA 169 -18.82 -5.12 2.95e+01 3pviA 157 -17.13 -5.11 2.98e+01 1srqA 341 -18.85 -5.10 3.01e+01 1na6A 404 -18.84 -5.09 3.02e+01 1umdB 324 -16.58 -5.09 3.03e+01 1yfsA 465 -26.03 -5.09 3.03e+01 1avbA 226 -21.75 -5.09 3.03e+01 35c8H 217 -20.25 -5.09 3.03e+01 1ohfA 644 -24.12 -5.09 3.03e+01 1zclA 180 -16.83 -5.07 3.08e+01 1ajkA 214 -23.57 -5.05 3.13e+01 2awaA 390 -20.90 -5.04 3.15e+01 1ic7H 114 -19.43 -5.04 3.15e+01 1p2zA 968 -23.26 -5.03 3.18e+01 1jmuB 666 -19.39 -5.03 3.18e+01 1aomA 567 -23.80 -5.02 3.21e+01 1m1nB 522 -21.76 -5.00 3.25e+01 1i7oA 429 -20.30 -5.00 3.25e+01 1a3rH 218 -21.55 -4.99 3.28e+01 2bkdN 134 -17.68 -4.99 3.28e+01 1hxkA 1015 -26.25 -4.99 3.28e+01 1b12A 248 -21.17 -4.99 3.29e+01 1mkmA 249 -17.20 -4.98 3.30e+01 1iyhA 198 -15.65 -4.98 3.30e+01 1s3rA 535 -20.31 -4.98 3.31e+01 1nls 237 -21.66 -4.98 3.31e+01 2a74A 643 -33.77 -4.98 3.31e+01 1mtyD 512 -19.15 -4.95 3.38e+01 1an7A 136 -16.34 -4.95 3.40e+01 2btzA 394 -18.25 -4.94 3.40e+01 1i8dA 213 -17.47 -4.94 3.41e+01 1h1iC 350 -22.99 -4.94 3.41e+01 1sfp 114 -17.84 -4.94 3.41e+01 1by5A 714 -30.01 -4.94 3.42e+01 1kzhA 555 -28.30 -4.94 3.43e+01 1mmoD 512 -19.20 -4.94 3.43e+01 1dovA 181 -18.12 -4.93 3.44e+01 1o75A 415 -22.74 -4.93 3.44e+01 1fi8A 228 -17.53 -4.93 3.44e+01 1dqiA 124 -18.48 -4.92 3.46e+01 1ltoA 245 -18.49 -4.92 3.47e+01 1shfA 59 -16.62 -4.92 3.48e+01 1dxjA 242 -15.93 -4.92 3.48e+01 1bh3 289 -22.67 -4.91 3.50e+01 1ecmA 109 -17.37 -4.91 3.51e+01 1xdyA 298 -16.96 -4.90 3.53e+01 1yq2A 1024 -23.39 -4.89 3.55e+01 1k8tA 510 -23.05 -4.89 3.57e+01 1xfxA 777 -32.13 -4.88 3.58e+01 2apoA 357 -19.79 -4.88 3.59e+01 1f82A 424 -27.74 -4.86 3.63e+01 1pud 386 -16.72 -4.85 3.67e+01 1eemA 241 -16.49 -4.85 3.68e+01 1ev2E 220 -20.97 -4.85 3.69e+01 1qvbA 481 -23.14 -4.84 3.69e+01 1rwrA 301 -23.36 -4.84 3.69e+01 1xfdA 723 -21.39 -4.84 3.71e+01 1oq1A 223 -21.67 -4.83 3.73e+01 1pxgA 382 -16.57 -4.81 3.78e+01 1gv3A 248 -16.11 -4.81 3.79e+01 2be6D 37 -14.96 -4.81 3.80e+01 1x24A 180 -16.09 -4.80 3.82e+01 1ile 821 -26.02 -4.80 3.83e+01 2mprA 421 -25.26 -4.80 3.84e+01 1h4rA 314 -20.40 -4.78 3.89e+01 1azgB 67 -16.07 -4.77 3.92e+01 1kmtA 141 -18.60 -4.76 3.95e+01 1ahtH 259 -17.78 -4.76 3.96e+01 1gttA 429 -20.26 -4.76 3.96e+01 1ckmA 330 -22.58 -4.75 3.98e+01 1oaoC 729 -32.47 -4.75 3.99e+01 1ve9A 347 -18.53 -4.75 3.99e+01 1dqqA 214 -22.00 -4.75 3.99e+01