% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dsspfoo.1.YGR223C.t2k-100-30-dssp-ebghstl Host: cc74 Tue Nov 12 18:00:34 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR223C % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR223C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR223C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 449 nodes, 324.34 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.5863) * Reverse)^tau(=0.7149))) % 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 1erjA 393 -300.19 -230.03 2.40e-26 1gotB 340 -283.80 -224.86 7.15e-26 1tbgA 340 -281.24 -221.68 1.41e-25 1gxrA 337 -224.22 -167.78 2.16e-20 1k8kC 372 -180.21 -119.03 2.86e-15 1crzA 403 -104.94 -59.13 5.02e-08 1c5kA 439 -107.86 -57.79 7.62e-08 1k32A 1045 -154.26 -50.83 7.00e-07 1aomA 567 -118.80 -48.20 1.65e-06 1aoqA 567 -117.77 -47.72 1.94e-06 1qksA 567 -117.98 -46.24 3.17e-06 1jjuB 337 -88.68 -39.72 2.92e-05 1jofA 365 -91.26 -37.77 5.77e-05 1jmxB 349 -87.39 -35.57 1.27e-04 1qbiA 454 -90.32 -34.07 2.18e-04 1e1aA 314 -87.02 -32.03 4.60e-04 1cruA 454 -88.37 -31.69 5.22e-04 2bbkH 355 -89.44 -31.02 6.68e-04 1c9uA 454 -86.91 -30.86 7.12e-04 1kb0A 677 -82.91 -30.14 9.31e-04 1kv9A 668 -79.19 -28.91 1.48e-03 1k3iA 656 -70.40 -28.55 1.70e-03 1goh 639 -71.12 -28.10 2.02e-03 1gof 639 -71.18 -27.76 2.31e-03 4aahA 571 -76.14 -24.97 6.88e-03 1g72A 573 -76.02 -24.84 7.24e-03 1ijqA 316 -66.16 -24.84 7.24e-03 1bpoA 494 -88.63 -22.48 1.88e-02 1e8nA 710 -91.88 -22.35 1.97e-02 1qfmA 710 -89.54 -20.45 4.36e-02 1dfcA 493 -60.19 -20.16 4.93e-02 1a12A 413 -71.12 -18.79 8.82e-02 1lenA 181 -43.46 -18.03 1.23e-01 1ospO 257 -60.87 -17.70 1.42e-01 3sil 379 -56.34 -17.70 1.42e-01 2sil 381 -55.98 -17.59 1.49e-01 1dim 381 -55.40 -17.13 1.82e-01 2aaiB 262 -47.25 -16.99 1.93e-01 1tl2A 236 -49.30 -16.61 2.30e-01 2ltnA 181 -42.17 -16.03 2.98e-01 1at0 145 -48.21 -16.00 3.01e-01 5nn9 388 -56.19 -15.79 3.32e-01 3nn9 388 -55.90 -15.74 3.40e-01 1f8eA 388 -55.98 -15.63 3.57e-01 1eur 365 -56.53 -15.63 3.57e-01 2qwc 388 -56.63 -15.44 3.89e-01 1b6e 128 -37.75 -15.42 3.93e-01 1abrB 267 -46.36 -15.10 4.54e-01 1d0nA 729 -72.81 -14.36 6.38e-01 1wba 175 -49.87 -14.24 6.75e-01 1qba 858 -88.01 -14.20 6.88e-01 1jlyA 304 -56.93 -14.19 6.92e-01 4sli 679 -69.58 -14.09 7.26e-01 2sli 679 -69.56 -14.08 7.29e-01 1ksiB 642 -65.33 -13.93 7.83e-01 1ksiA 642 -64.67 -13.91 7.91e-01 1h6lA 353 -69.64 -13.77 8.43e-01 1jlxA 304 -56.63 -13.74 8.53e-01 1yaiA 151 -40.20 -13.53 9.44e-01 1c7sA 858 -86.48 -13.35 1.03e+00 1cvmA 353 -69.50 -13.01 1.21e+00 1jtdB 273 -47.85 -12.95 1.24e+00 1qniA 581 -76.37 -12.80 1.34e+00 2pooA 355 -67.64 -12.78 1.35e+00 1svpA 161 -41.48 -12.54 1.52e+00 1qhoA 686 -59.57 -12.42 1.61e+00 1fnhA 271 -50.70 -12.35 1.66e+00 1hxs3 237 -43.49 -12.31 1.69e+00 1qexA 288 -46.40 -12.18 1.81e+00 2snv 151 -40.53 -12.06 1.91e+00 1h8eA 510 -57.40 -12.03 1.95e+00 1qlgA 355 -68.60 -11.98 1.99e+00 1aozA 552 -67.03 -11.85 2.12e+00 1lkfA 299 -45.81 -11.81 2.16e+00 1ilr1 152 -47.99 -11.80 2.17e+00 1ax0 239 -42.16 -11.78 2.20e+00 1eut 605 -59.07 -11.72 2.26e+00 1e79A 510 -56.80 -11.52 2.50e+00 1pvl 301 -44.54 -11.48 2.54e+00 1bmfA 510 -57.21 -11.34 2.72e+00 1fnf 368 -57.35 -10.98 3.27e+00 1euu 605 -59.26 -10.90 3.40e+00 1ijtA 128 -37.14 -10.77 3.63e+00 1gnyA 153 -41.29 -10.56 4.04e+00 1mspA 126 -37.37 -10.17 4.92e+00 1f89A 291 -39.00 -10.13 5.02e+00 1ckmA 330 -54.31 -10.10 5.11e+00 1irp 153 -46.43 -9.99 5.40e+00 1je6A 275 -38.85 -9.96 5.49e+00 2mllB 255 -45.20 -9.92 5.60e+00 1bw8A 321 -50.19 -9.82 5.91e+00 1mrg 263 -37.02 -9.71 6.26e+00 1cknA 330 -54.12 -9.66 6.41e+00 1ee8A 266 -39.83 -9.62 6.55e+00 1aun 208 -41.21 -9.49 7.01e+00 1yna 194 -43.13 -9.44 7.21e+00 1aj6 219 -35.35 -9.40 7.35e+00 1ju3A 583 -60.94 -9.37 7.46e+00 1iq8A 582 -66.83 -9.29 7.79e+00 1gw5M 435 -56.81 -9.29 7.80e+00 1kv7A 488 -61.44 -9.28 7.82e+00 1rypI 222 -35.17 -9.22 8.08e+00 1dzkA 157 -39.07 -9.21 8.12e+00 1bxxA 285 -48.88 -9.12 8.51e+00 1nlr 234 -37.08 -9.08 8.71e+00 1dq3A 454 -63.33 -9.04 8.89e+00 1mpyA 307 -43.29 -9.01 9.02e+00 1i82A 189 -41.12 -8.98 9.16e+00 1i8aA 189 -41.08 -8.97 9.22e+00 1i31A 314 -48.34 -8.91 9.54e+00 1itvA 195 -38.28 -8.84 9.89e+00 2hft 218 -36.66 -8.83 9.92e+00 1kit 757 -81.54 -8.81 1.01e+01 1qcsA 211 -38.12 -8.79 1.02e+01 1eyqA 222 -36.37 -8.78 1.02e+01 1dlc 584 -48.32 -8.77 1.03e+01 1jepA 222 -36.37 -8.76 1.03e+01 1eypA 222 -36.37 -8.73 1.05e+01 1l1zA 274 -38.11 -8.73 1.05e+01 1zxq 192 -39.87 -8.70 1.07e+01 1l9xA 315 -37.87 -8.61 1.12e+01 1dgaA 375 -42.72 -8.56 1.15e+01 1c8uA 285 -40.80 -8.54 1.16e+01 4rhv3 236 -35.47 -8.52 1.17e+01 1rhi3 236 -35.41 -8.48 1.20e+01 1epwA 1290 -120.71 -8.45 1.22e+01 2nlrA 234 -36.33 -8.33 1.30e+01 1hms 132 -38.19 -8.33 1.30e+01 1hmr 132 -38.18 -8.33 1.30e+01 1cwvA 492 -52.33 -8.32 1.30e+01 7ahlA 293 -42.00 -8.31 1.31e+01 1hmt 132 -38.09 -8.28 1.34e+01 1sltA 134 -40.52 -8.26 1.35e+01 1dceA 567 -43.56 -8.21 1.39e+01 1gcyA 527 -53.26 -8.20 1.39e+01 1b2pA 119 -46.54 -8.14 1.44e+01 1e50B 134 -31.65 -8.12 1.46e+01 1iraX 152 -42.37 -8.08 1.49e+01 1sltB 134 -41.27 -8.07 1.50e+01 2eifA 136 -40.66 -8.03 1.53e+01 1thtA 305 -36.64 -7.97 1.58e+01 1dykA 394 -52.89 -7.96 1.59e+01 1soxA 466 -50.72 -7.93 1.62e+01 1f5mB 180 -32.19 -7.80 1.74e+01 1d2pA 373 -51.02 -7.76 1.78e+01 1slaA 134 -40.66 -7.68 1.85e+01 1hxmD 242 -45.48 -7.68 1.86e+01 1xnb 185 -38.91 -7.65 1.89e+01 1bvqA 141 -32.97 -7.63 1.91e+01 1g4mA 393 -48.08 -7.63 1.91e+01 1b8aA 438 -59.43 -7.63 1.91e+01 1yagA 375 -42.54 -7.62 1.92e+01 1f5mA 180 -32.23 -7.54 2.01e+01 1d7qA 143 -38.08 -7.53 2.02e+01 1gv4A 528 -55.15 -7.52 2.03e+01 1viwB 198 -37.47 -7.52 2.03e+01 1k0sA 151 -37.54 -7.48 2.07e+01 1pvxA 194 -40.67 -7.47 2.09e+01 1lo7A 141 -33.39 -7.45 2.11e+01 4ubpA 101 -27.18 -7.44 2.12e+01 1fzqA 181 -33.43 -7.44 2.13e+01 1i9aA 182 -30.50 -7.42 2.15e+01 1qhdA 398 -42.59 -7.41 2.16e+01 1ubpA 101 -27.10 -7.38 2.19e+01 1ifrA 121 -36.04 -7.38 2.19e+01 1a3qA 285 -43.33 -7.34 2.24e+01 1hlcA 129 -41.10 -7.32 2.27e+01 1ga6A 372 -32.47 -7.31 2.29e+01 1j6zA 376 -43.18 -7.29 2.31e+01 1fwxA 595 -80.91 -7.26 2.35e+01 1aw8E 91 -29.91 -7.26 2.35e+01 1f5jA 199 -38.71 -7.23 2.38e+01 1iam 185 -38.64 -7.23 2.39e+01 1b3jA 274 -37.06 -7.23 2.39e+01 1jcfA 344 -46.83 -7.23 2.39e+01 1grwA 126 -33.92 -7.19 2.44e+01 1g24A 211 -34.11 -7.18 2.45e+01 1jceA 344 -46.91 -7.18 2.46e+01 2lgsA 468 -46.57 -7.17 2.47e+01 1xypA 190 -40.55 -7.17 2.48e+01 1ga1A 372 -32.27 -7.16 2.48e+01 1lgr 468 -46.55 -7.16 2.48e+01 1gnhA 206 -39.30 -7.12 2.54e+01 1d4xA 375 -41.12 -7.09 2.58e+01 2btfA 375 -42.20 -7.08 2.60e+01 1bwyA 132 -38.30 -7.07 2.62e+01 2bbvA 363 -37.95 -7.00 2.72e+01 1yagG 125 -31.90 -6.99 2.73e+01 1d4xG 126 -31.91 -6.95 2.80e+01 1cd9B 215 -39.70 -6.94 2.81e+01 1clc 639 -55.87 -6.90 2.88e+01 1ifc 132 -36.72 -6.88 2.91e+01 1aw8B 91 -29.94 -6.84 2.98e+01 1quqB 121 -33.78 -6.83 2.99e+01 1iakA 199 -41.04 -6.82 3.01e+01 1preA 470 -43.51 -6.82 3.02e+01 1a3yA 149 -36.82 -6.81 3.03e+01 1k4nA 192 -31.36 -6.81 3.04e+01 3mspA 126 -35.57 -6.79 3.06e+01 1fxzA 476 -58.52 -6.79 3.07e+01 1elyA 449 -42.14 -6.78 3.09e+01 1k6wA 426 -44.50 -6.74 3.16e+01 1h80A 464 -52.87 -6.72 3.19e+01 1f6fB 210 -37.19 -6.72 3.20e+01 1g8jB 133 -31.93 -6.70 3.22e+01 2shpA 525 -55.52 -6.70 3.23e+01 1l7jA 347 -53.52 -6.69 3.25e+01 1enxA 190 -40.61 -6.66 3.30e+01 1kh5A 449 -41.51 -6.66 3.31e+01 1bv4A 118 -31.34 -6.65 3.32e+01 1ytbA 180 -31.05 -6.61 3.41e+01 1put 106 -27.43 -6.60 3.42e+01 1iarB 207 -34.65 -6.59 3.43e+01 1bsjA 168 -33.25 -6.59 3.44e+01 1bypA 99 -29.22 -6.58 3.46e+01 1b8jA 449 -41.88 -6.56 3.50e+01 1xyn 178 -35.60 -6.56 3.51e+01 1ji1A 637 -53.64 -6.56 3.51e+01 1bawA 105 -32.72 -6.55 3.52e+01 1thm 279 -29.61 -6.53 3.56e+01 1alkA 449 -41.92 -6.53 3.56e+01 1ed8A 449 -41.88 -6.52 3.59e+01 1ieaA 192 -40.30 -6.49 3.66e+01 1qi6A 475 -53.43 -6.48 3.67e+01 1c5lH 259 -39.40 -6.44 3.75e+01 2anhA 446 -41.28 -6.43 3.77e+01 1cseI 71 -26.49 -6.43 3.78e+01 1euhA 475 -53.40 -6.43 3.78e+01 1ft9A 222 -36.71 -6.42 3.81e+01 1f52A 468 -47.58 -6.40 3.84e+01 1bebA 162 -34.68 -6.39 3.87e+01 2ahjA 206 -30.14 -6.39 3.87e+01 1i7dA 659 -57.54 -6.38 3.90e+01 2ahjC 206 -30.07 -6.36 3.93e+01