% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR014W.t2k-100-30-dssp-ebghstl Host: farm17.cse.ucsc.edu Sun Mar 19 17:26:07 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.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 YGR014W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR014W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 1307 nodes, 2281.85 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(=1.3060) * Reverse)^tau(=0.8151))) % 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 1m6bA 621 -41.92 -17.76 2.57e-02 1axkA 394 -39.49 -14.47 1.89e-01 1o20A 427 -27.58 -14.13 2.33e-01 2f6kA 307 -27.02 -13.75 2.95e-01 1ogoX 574 -48.46 -13.38 3.71e-01 1acc 735 -42.36 -12.96 4.85e-01 2ahxA 617 -37.92 -12.95 4.87e-01 1nr0A 611 -52.82 -12.77 5.47e-01 1c9uA 454 -41.57 -12.75 5.54e-01 1phb 414 -25.98 -12.41 6.87e-01 2nlrA 234 -33.98 -12.20 7.83e-01 1nlr 234 -34.03 -12.13 8.21e-01 1wxrA 1048 -50.53 -12.12 8.25e-01 1yrcA 414 -24.66 -11.85 9.83e-01 1k32A 1045 -57.41 -11.50 1.23e+00 1cpn 208 -31.17 -11.40 1.31e+00 1gof 639 -57.85 -11.32 1.38e+00 1ivyA 452 -27.84 -11.18 1.51e+00 1pguA 615 -42.44 -11.14 1.55e+00 1q47A 495 -39.44 -11.12 1.57e+00 1ajkA 214 -32.35 -10.94 1.76e+00 1jb7A 495 -29.72 -10.57 2.24e+00 1pjpA 226 -32.92 -10.53 2.32e+00 1phg 414 -23.61 -10.31 2.67e+00 1goh 639 -57.83 -10.25 2.78e+00 1qbiA 454 -37.46 -10.20 2.87e+00 1dz4A 414 -22.89 -10.18 2.92e+00 5cpp 414 -23.28 -10.15 2.96e+00 1phd 414 -23.37 -10.07 3.13e+00 1pxgA 382 -23.09 -10.05 3.17e+00 1sotA 320 -31.67 -10.02 3.22e+00 1qmqA 414 -22.65 -9.97 3.33e+00 2sqcA 631 -27.46 -9.97 3.34e+00 1uz5A 402 -30.12 -9.97 3.34e+00 1y7bA 542 -40.47 -9.94 3.40e+00 1s9aA 257 -30.59 -9.92 3.45e+00 1n6eA 1071 -58.23 -9.85 3.62e+00 1a0qL 212 -30.52 -9.83 3.67e+00 1otcA 495 -30.23 -9.82 3.70e+00 1pd21 199 -21.16 -9.68 4.04e+00 1uacH 114 -26.55 -9.63 4.19e+00 1re9A 414 -22.35 -9.58 4.33e+00 1itkA 731 -23.64 -9.46 4.67e+00 1kypA 237 -31.59 -9.41 4.85e+00 1ei5A 520 -29.45 -9.28 5.28e+00 1xhcA 367 -26.36 -9.27 5.31e+00 1dkuA 317 -24.14 -9.21 5.54e+00 1oxdA 227 -31.15 -9.21 5.55e+00 1t6eX 381 -27.20 -9.17 5.68e+00 1cruA 454 -37.52 -9.17 5.71e+00 1gv9A 260 -29.87 -9.16 5.71e+00 2aamA 309 -23.82 -9.14 5.82e+00 1sy7A 715 -28.81 -9.09 6.00e+00 2anyA 241 -29.51 -9.06 6.14e+00 1knvA 293 -23.05 -9.05 6.15e+00 1klt 226 -32.39 -9.02 6.28e+00 1g3qA 237 -21.59 -9.02 6.29e+00 1lqsR 214 -27.16 -9.00 6.37e+00 1n1pA 504 -28.81 -8.98 6.49e+00 1n4wA 504 -28.81 -8.98 6.49e+00 1oaoC 729 -37.57 -8.97 6.50e+00 1b9cA 236 -31.30 -8.97 6.52e+00 2rspA 124 -25.09 -8.96 6.53e+00 1mxtA 504 -28.76 -8.89 6.86e+00 1iyhA 198 -20.45 -8.87 6.98e+00 1sqjA 789 -45.56 -8.79 7.35e+00 2madH 373 -33.82 -8.78 7.39e+00 1f3eA 386 -22.04 -8.76 7.53e+00 1mvpA 124 -25.24 -8.73 7.64e+00 2rspB 124 -24.70 -8.67 7.97e+00 1j7vR 214 -27.92 -8.60 8.34e+00 1rh5A 436 -35.54 -8.57 8.54e+00 1qksA 567 -38.44 -8.56 8.58e+00 1xfxA 777 -36.40 -8.56 8.58e+00 1nn6A 228 -30.88 -8.54 8.73e+00 1sqc 631 -26.07 -8.54 8.74e+00 3ladA 476 -22.79 -8.52 8.81e+00 1aoqA 567 -38.68 -8.48 9.07e+00 1czfA 362 -35.53 -8.45 9.26e+00 1dugA 234 -24.17 -8.44 9.34e+00 1aj5A 173 -21.10 -8.44 9.34e+00 1dkrA 317 -23.90 -8.43 9.38e+00 1xg8A 111 -20.47 -8.43 9.38e+00 1ibsA 317 -24.13 -8.37 9.79e+00 1zejA 293 -24.75 -8.36 9.83e+00 1jfpA 348 -26.44 -8.28 1.04e+01 2d0oA 610 -23.92 -8.25 1.06e+01 1svcP 365 -30.66 -8.24 1.07e+01 1e3aB 560 -24.39 -8.24 1.07e+01 1adjA 421 -20.89 -8.21 1.09e+01 1vi6A 208 -20.80 -8.07 1.20e+01 1h4vB 421 -20.89 -8.04 1.23e+01 1k3iA 656 -56.80 -8.03 1.24e+01 1go3E 187 -24.89 -8.02 1.25e+01 1msaA 109 -24.08 -7.99 1.27e+01 2fo3A 125 -23.28 -7.96 1.30e+01 1h6rA 236 -31.68 -7.95 1.30e+01 1xhkA 187 -22.24 -7.94 1.31e+01 1efm 393 -25.31 -7.92 1.33e+01 1fnnA 389 -22.87 -7.91 1.34e+01 1r5yA 386 -20.56 -7.90 1.35e+01 1gm7B 557 -23.90 -7.89 1.37e+01 1np8A 159 -20.44 -7.88 1.38e+01 1ijhA 504 -27.72 -7.87 1.38e+01 2ajrA 331 -22.16 -7.86 1.39e+01 1x1iA 752 -27.94 -7.85 1.40e+01 1j0mA 752 -28.54 -7.84 1.41e+01 1gkfB 557 -23.83 -7.84 1.41e+01 1jpc 109 -23.74 -7.84 1.41e+01 1i8dA 213 -24.41 -7.80 1.45e+01 1dmlA 319 -29.19 -7.77 1.48e+01 1gm9B 557 -23.81 -7.76 1.49e+01 1ajqB 557 -23.81 -7.75 1.50e+01 1ema 236 -29.77 -7.75 1.50e+01 1uypA 432 -33.64 -7.74 1.51e+01 1gk9B 557 -23.78 -7.73 1.52e+01 2emo 237 -30.90 -7.72 1.53e+01 1gbg 214 -25.55 -7.71 1.54e+01 1cd9B 215 -29.55 -7.69 1.56e+01 1gskA 513 -40.21 -7.67 1.58e+01 1qwlA 505 -24.20 -7.67 1.58e+01 1nls 237 -32.68 -7.65 1.61e+01 1dghB 498 -25.32 -7.65 1.61e+01 1ehkA 562 -32.00 -7.64 1.61e+01 1xfuA 747 -35.13 -7.63 1.63e+01 1qvbA 481 -27.15 -7.62 1.65e+01 1o94A 729 -23.95 -7.56 1.71e+01 1m8jA 181 -19.11 -7.56 1.71e+01 1dgfA 497 -25.19 -7.56 1.71e+01 1azdA 237 -34.47 -7.55 1.73e+01 1djnA 729 -23.83 -7.54 1.73e+01 1djqA 729 -23.82 -7.53 1.75e+01 1w2tA 432 -34.46 -7.51 1.77e+01 1t2bA 397 -20.35 -7.51 1.78e+01 1b4vA 504 -27.35 -7.49 1.80e+01 1b8sA 504 -27.26 -7.45 1.84e+01 2tmdA 729 -23.83 -7.44 1.86e+01 1te0A 318 -32.65 -7.42 1.89e+01 1atiA 505 -22.06 -7.42 1.89e+01 169lA 164 -18.17 -7.41 1.90e+01 3psg 370 -33.85 -7.38 1.95e+01 1etu 394 -23.21 -7.35 1.97e+01 1mjgM 729 -35.80 -7.35 1.99e+01 1cwvA 492 -43.38 -7.34 2.00e+01 1a8y 367 -23.75 -7.30 2.05e+01 7catA 506 -25.47 -7.28 2.08e+01 1cvjA 190 -19.56 -7.28 2.09e+01 1gu3A 149 -27.89 -7.25 2.12e+01 1gvzA 237 -27.07 -7.24 2.13e+01 1ysc 421 -23.36 -7.22 2.16e+01 1mvwA 840 -30.80 -7.22 2.17e+01 1x33A 268 -23.00 -7.21 2.19e+01 1ef1A 294 -22.38 -7.19 2.21e+01 1rlmB 271 -21.08 -7.19 2.22e+01 1m7sA 484 -25.25 -7.19 2.22e+01 1rlmA 271 -21.05 -7.16 2.26e+01 2minB 522 -25.05 -7.15 2.29e+01 1wp5A 323 -29.01 -7.14 2.30e+01 1swyA 164 -17.65 -7.13 2.30e+01 1sx7A 164 -17.65 -7.13 2.30e+01 3minB 522 -25.05 -7.13 2.31e+01 1m1nB 522 -25.01 -7.13 2.31e+01 1olzA 663 -36.21 -7.13 2.32e+01 1atiB 505 -22.00 -7.10 2.37e+01 1alvA 173 -21.46 -7.10 2.37e+01 1t5rA 284 -26.91 -7.06 2.43e+01 1gnyA 153 -23.32 -7.04 2.46e+01 2ashA 381 -22.13 -7.04 2.47e+01 1bqg 451 -21.57 -7.02 2.49e+01 1reqA 727 -19.62 -7.00 2.53e+01 1qgtA 149 -19.31 -7.00 2.53e+01 1w7jA 795 -33.76 -7.00 2.54e+01 16pk 415 -19.96 -6.99 2.55e+01 1scs 237 -32.56 -6.99 2.55e+01 1vorW 173 -28.92 -6.97 2.58e+01 1fib 269 -23.07 -6.96 2.61e+01 1nhcA 336 -33.48 -6.96 2.61e+01 1ej2A 181 -18.35 -6.95 2.62e+01 1oe9A 795 -35.73 -6.95 2.62e+01 1ionA 243 -18.94 -6.92 2.69e+01 1qcxA 359 -31.34 -6.89 2.74e+01 1a8p 258 -21.41 -6.89 2.74e+01 1j1xH 114 -23.76 -6.89 2.74e+01 1k4gA 386 -20.01 -6.88 2.75e+01 1ospH 218 -28.86 -6.86 2.81e+01 1up8A 598 -21.61 -6.85 2.82e+01 2a46A 238 -24.04 -6.85 2.83e+01 198l 164 -17.64 -6.84 2.83e+01 2ajuH 219 -27.61 -6.84 2.83e+01 1rwhA 757 -29.16 -6.83 2.85e+01 1lw9A 164 -17.41 -6.83 2.85e+01 1rloA 271 -21.23 -6.83 2.86e+01 1i3kA 348 -20.80 -6.81 2.90e+01 1p36A 164 -17.41 -6.79 2.93e+01 1a0tP 413 -34.74 -6.79 2.93e+01 1aerA 205 -20.30 -6.78 2.95e+01 1wkrA 340 -28.47 -6.78 2.97e+01 1dmaA 214 -21.02 -6.77 2.99e+01 1c8gA 548 -37.20 -6.76 3.00e+01 1b76A 442 -20.51 -6.75 3.02e+01 2bkdN 134 -24.85 -6.73 3.06e+01 163l 164 -17.43 -6.73 3.06e+01 172l 164 -17.42 -6.72 3.09e+01 4pep 326 -28.24 -6.71 3.12e+01 1x36A 237 -21.52 -6.66 3.22e+01 1l58 164 -17.36 -6.66 3.23e+01 2bbkH 355 -32.62 -6.65 3.23e+01 1bf2 750 -26.40 -6.65 3.25e+01 1smvA 260 -21.96 -6.64 3.27e+01 1gweA 503 -27.26 -6.64 3.27e+01 1ddzA 496 -21.50 -6.63 3.29e+01 2bmaA 470 -24.80 -6.61 3.34e+01 167lA 164 -17.12 -6.61 3.34e+01 1q33A 292 -20.83 -6.59 3.38e+01 175lA 164 -17.17 -6.58 3.40e+01 2cas 548 -37.81 -6.58 3.41e+01 1pnkB 557 -23.32 -6.58 3.42e+01 2gsq 202 -19.27 -6.57 3.44e+01 147l 164 -17.18 -6.56 3.45e+01 197l 164 -17.12 -6.55 3.50e+01 125l 164 -17.12 -6.54 3.50e+01 145l 164 -17.12 -6.53 3.53e+01 173l 164 -17.25 -6.50 3.62e+01 1tqxA 227 -20.47 -6.49 3.63e+01 1ll7A 392 -22.91 -6.49 3.64e+01 1ic7H 114 -23.31 -6.48 3.66e+01 168lA 164 -17.19 -6.48 3.67e+01 1e3pA 757 -21.71 -6.47 3.68e+01 1p7tA 731 -21.97 -6.47 3.68e+01 1m0uA 249 -19.37 -6.47 3.69e+01 191l 164 -17.14 -6.46 3.72e+01 1r8nA 185 -32.33 -6.46 3.73e+01 128l 164 -17.12 -6.45 3.73e+01 1dszA 86 -17.29 -6.45 3.74e+01 1n1bA 549 -28.87 -6.45 3.74e+01 127l 164 -17.11 -6.45 3.74e+01 1x35A 268 -23.51 -6.45 3.75e+01 190l 164 -17.15 -6.44 3.77e+01 1vdc 333 -25.16 -6.44 3.77e+01 129l 164 -17.12 -6.44 3.78e+01 1ndbA 596 -24.39 -6.44 3.78e+01 1orvA 728 -33.82 -6.44 3.78e+01 1i7pA 274 -23.14 -6.44 3.78e+01 162l 164 -17.12 -6.43 3.79e+01 1onwA 390 -26.97 -6.43 3.79e+01 170l 164 -17.12 -6.43 3.80e+01 157l 164 -17.12 -6.43 3.80e+01 159l 164 -17.12 -6.43 3.80e+01 1v8yA 170 -20.19 -6.43 3.81e+01 161l 164 -17.12 -6.42 3.82e+01 142l 164 -17.12 -6.42 3.82e+01 1mkmA 249 -20.11 -6.42 3.82e+01 118l 164 -17.12 -6.42 3.82e+01 126l 164 -17.12 -6.42 3.83e+01 164l 164 -17.12 -6.42 3.83e+01 160l 164 -17.12 -6.42 3.83e+01 130l 164 -17.12 -6.42 3.84e+01 119l 164 -17.12 -6.42 3.84e+01 156l 164 -17.12 -6.41 3.85e+01 122l 164 -17.12 -6.41 3.85e+01 1qwoA 442 -19.91 -6.41 3.85e+01 146l 164 -17.12 -6.41 3.86e+01 166l 164 -17.12 -6.41 3.87e+01 158l 164 -17.12 -6.40 3.87e+01 1diwA 441 -33.27 -6.40 3.87e+01 196l 164 -17.12 -6.40 3.87e+01 195l 164 -17.12 -6.40 3.88e+01 165l 164 -17.12 -6.40 3.89e+01 144l 164 -17.12 -6.40 3.89e+01 1xdyA 298 -20.49 -6.39 3.89e+01 1dih 273 -19.55 -6.39 3.90e+01 139l 164 -17.12 -6.39 3.90e+01 155l 164 -17.12 -6.39 3.91e+01 138l 164 -17.12 -6.39 3.91e+01 141l 164 -17.12 -6.39 3.91e+01 143l 164 -17.12 -6.39 3.91e+01 140l 164 -17.12 -6.39 3.92e+01 1nnlA 225 -18.23 -6.39 3.92e+01 1jflA 228 -18.79 -6.38 3.92e+01 1mkiA 330 -18.61 -6.38 3.93e+01 1pud 386 -19.51 -6.38 3.93e+01 199l 164 -17.12 -6.38 3.94e+01 1a5fH 217 -27.43 -6.37 3.96e+01 1svb 395 -25.38 -6.36 3.99e+01 1php 394 -20.02 -6.36 4.00e+01