% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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. % --------------------------------------------------------------------- % str2foo.1.YBR239C.t2k-100-30-str2 Host: cc55 Fri Oct 10 10:49:00 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YBR2/YBR239C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % 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 YBR239C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YBR239C.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 530 nodes, 511.33 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 (=8162) sequences: % N / (1 + exp(-(lambda(=1.2487) * Reverse)^tau(=0.7933))) % 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 1ajyA 71 -75.09 -56.14 1.84e-09 1zmeC 70 -72.61 -53.81 4.82e-09 1hwtC 81 -72.14 -51.80 1.11e-08 1d66A 66 -65.15 -46.27 1.15e-07 1pyc 71 -64.53 -45.15 1.87e-07 1aw6 43 -61.41 -44.04 3.02e-07 1pyiA 96 -62.33 -40.39 1.48e-06 2alcA 65 -47.91 -29.90 1.74e-04 1f4sP 65 -46.56 -28.57 3.25e-04 1jmoA 480 -48.02 -18.19 5.48e-02 1jnuA 104 -33.75 -14.48 3.93e-01 1l9vA 317 -39.76 -13.62 6.30e-01 1iyaA 187 -35.75 -13.24 7.79e-01 1f4tA 368 -40.58 -13.21 7.89e-01 1n81A 186 -40.63 -12.50 1.18e+00 1gvhA 396 -38.83 -12.42 1.23e+00 1d8vA 263 -34.77 -12.13 1.44e+00 1dc1A 323 -37.11 -12.06 1.51e+00 1io7A 368 -39.48 -11.93 1.62e+00 1cwyA 500 -43.12 -11.77 1.78e+00 9atcB 146 -38.23 -11.74 1.81e+00 1iybA 208 -36.23 -11.63 1.92e+00 1eswA 500 -42.90 -11.44 2.14e+00 1bywA 110 -32.30 -11.40 2.19e+00 1drmA 131 -32.31 -11.12 2.57e+00 1itcA 516 -39.34 -11.08 2.64e+00 1a5t 334 -35.08 -11.06 2.67e+00 1f5sA 211 -35.18 -10.98 2.79e+00 1j97A 211 -35.17 -10.98 2.80e+00 1l7mA 211 -34.91 -10.77 3.15e+00 1e5dA 402 -36.82 -10.57 3.54e+00 1n9lA 109 -31.23 -10.46 3.78e+00 1g2nA 264 -35.26 -10.19 4.42e+00 1qr6A 584 -47.25 -10.18 4.44e+00 1b9zA 516 -38.12 -10.08 4.70e+00 1nt2B 258 -36.23 -10.04 4.81e+00 1d2vC 466 -42.02 -9.88 5.28e+00 2phy 125 -30.06 -9.75 5.73e+00 5bcaA 516 -37.76 -9.74 5.74e+00 1hh1A 143 -30.60 -9.71 5.87e+00 1gnd 447 -40.80 -9.69 5.91e+00 1nwzA 125 -29.94 -9.68 5.97e+00 3pyp 125 -29.94 -9.68 5.97e+00 1alu 186 -33.31 -9.62 6.16e+00 1jr3E 334 -32.95 -9.59 6.28e+00 1lswA 131 -30.94 -9.57 6.38e+00 1hw1A 239 -34.06 -9.49 6.67e+00 1d06A 130 -30.09 -9.47 6.75e+00 1il6 185 -33.97 -9.45 6.83e+00 1b6sA 355 -33.91 -9.44 6.89e+00 1jmsA 381 -36.31 -9.41 6.98e+00 1ifa 158 -32.42 -9.38 7.11e+00 1ei5A 520 -37.58 -9.38 7.12e+00 1e2xA 243 -34.07 -9.37 7.16e+00 1drqA 131 -30.74 -9.35 7.25e+00 1oq9A 363 -36.58 -9.34 7.28e+00 1lshA 1056 -37.28 -9.34 7.28e+00 1fxxA 482 -37.13 -9.14 8.20e+00 1gq2A 555 -46.37 -9.02 8.85e+00 1irxA 523 -44.81 -9.00 8.96e+00 1jli 112 -30.55 -8.93 9.33e+00 1afrA 345 -35.66 -8.92 9.39e+00 1ew0A 130 -29.99 -8.81 9.99e+00 1k38A 254 -33.21 -8.80 1.00e+01 1mzuA 129 -28.98 -8.76 1.03e+01 1gnwA 211 -33.59 -8.72 1.06e+01 1jf0A 195 -32.10 -8.64 1.11e+01 1gweA 503 -39.17 -8.64 1.11e+01 1kzkA 99 -28.27 -8.63 1.12e+01 1np7A 489 -38.68 -8.60 1.13e+01 1go4A 205 -31.37 -8.57 1.16e+01 1o0wA 252 -35.46 -8.57 1.16e+01 1f88A 348 -44.60 -8.56 1.16e+01 1qlpA 394 -34.40 -8.54 1.18e+01 1p5hA 428 -38.71 -8.53 1.19e+01 1jpnA 296 -31.17 -8.48 1.22e+01 1iynA 295 -35.75 -8.45 1.25e+01 1i4mA 108 -29.10 -8.42 1.27e+01 1hbzA 498 -38.94 -8.40 1.29e+01 1ng1 294 -30.98 -8.40 1.29e+01 1xvaA 292 -31.35 -8.33 1.34e+01 1qm3A 112 -29.05 -8.32 1.35e+01 1qsaA 618 -34.04 -8.31 1.35e+01 1sly 618 -33.95 -8.30 1.36e+01 1hzxA 349 -45.08 -8.24 1.42e+01 1ll8A 114 -31.26 -8.19 1.46e+01 1bn5 478 -41.60 -8.19 1.46e+01 1f76A 336 -33.64 -8.16 1.48e+01 1ls1A 295 -30.89 -8.16 1.49e+01 1d5tA 433 -40.53 -8.16 1.49e+01 1d2gA 292 -31.33 -8.15 1.50e+01 1b6a 478 -41.47 -8.14 1.50e+01 1dixA 208 -33.05 -8.13 1.51e+01 1qm1A 143 -30.71 -8.11 1.54e+01 1qlzA 210 -31.38 -8.10 1.54e+01 2bidA 197 -33.03 -8.10 1.55e+01 1dbhA 354 -36.62 -8.02 1.62e+01 1qmqA 414 -33.65 -8.00 1.64e+01 1eh2 106 -30.21 -7.99 1.65e+01 1erzA 303 -33.51 -7.98 1.66e+01 1mhlC 466 -40.28 -7.97 1.67e+01 1l9hA 349 -44.87 -7.94 1.70e+01 1fkmA 396 -38.07 -7.90 1.74e+01 1ej0A 180 -31.51 -7.79 1.87e+01 1cxpC 466 -40.08 -7.73 1.94e+01 1qf8A 182 -32.07 -7.73 1.94e+01 2ng1 293 -30.28 -7.66 2.03e+01 1j5yA 187 -32.07 -7.64 2.04e+01 1es6A 296 -31.05 -7.59 2.11e+01 1m1cA 680 -41.38 -7.56 2.16e+01 1kxrA 339 -33.23 -7.55 2.16e+01 1mtpB 43 -23.86 -7.54 2.18e+01 1klqA 197 -31.10 -7.50 2.23e+01 1lpvA 52 -25.52 -7.48 2.26e+01 1iqvA 218 -31.30 -7.41 2.36e+01 2cb5A 453 -35.38 -7.41 2.37e+01 1c7nA 399 -41.49 -7.39 2.39e+01 1i4lA 224 -33.25 -7.34 2.47e+01 1m0wA 491 -32.88 -7.30 2.52e+01 1bhjA 292 -30.40 -7.28 2.56e+01 1agg 48 -25.50 -7.28 2.56e+01 1dx0A 219 -32.40 -7.21 2.68e+01 1d0hA 469 -34.49 -7.17 2.74e+01 1dz4A 414 -33.32 -7.16 2.77e+01 1g9lA 144 -31.17 -7.15 2.79e+01 1bolA 222 -29.80 -7.09 2.90e+01 1b6rA 355 -31.07 -7.06 2.94e+01 2gwxA 267 -34.77 -7.06 2.95e+01 1phg 414 -33.75 -7.01 3.05e+01 1hw5A 210 -32.09 -6.98 3.08e+01 1dujA 187 -29.65 -6.96 3.13e+01 1jpmA 366 -32.70 -6.96 3.13e+01 1or4A 178 -34.30 -6.93 3.20e+01 5cpp 414 -33.74 -6.93 3.20e+01 1jb0A 755 -55.92 -6.93 3.20e+01 1qnf 484 -33.36 -6.91 3.23e+01 1e79G 272 -30.79 -6.90 3.26e+01 1utrA 96 -26.73 -6.89 3.27e+01 1a8d 452 -34.15 -6.85 3.36e+01 1ag2 103 -27.10 -6.85 3.37e+01 1phb 414 -33.71 -6.83 3.39e+01 1f0kA 364 -30.98 -6.81 3.45e+01 1csh 435 -32.88 -6.78 3.51e+01 1o7fA 469 -36.39 -6.77 3.53e+01 1o04A 500 -41.73 -6.76 3.55e+01 1jpzA 473 -33.90 -6.76 3.57e+01 1diwA 441 -33.35 -6.71 3.68e+01 1ckmA 330 -37.21 -6.67 3.77e+01 1rbp 182 -27.48 -6.65 3.81e+01 1m55A 197 -30.05 -6.65 3.83e+01 1on2A 142 -33.92 -6.64 3.83e+01 1phd 414 -33.36 -6.64 3.83e+01 1iznB 277 -30.19 -6.64 3.84e+01 1wdb 104 -27.84 -6.63 3.86e+01 1eeoA 321 -30.52 -6.63 3.87e+01 1qk4A 233 -31.25 -6.62 3.89e+01 1cqeA 580 -41.16 -6.62 3.90e+01 1ois 223 -30.51 -6.61 3.91e+01 1bu7A 455 -33.43 -6.61 3.92e+01 1pbwA 216 -31.72 -6.60 3.92e+01 1epwA 1290 -76.74 -6.60 3.94e+01 1eemA 241 -31.23 -6.60 3.94e+01 1l5jA 865 -48.14 -6.59 3.97e+01