% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR029W.t2k-100-40-40-str2+CB_burial_14_7 Host: cc57 Sat Oct 11 21:56:17 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR029W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 YGR029W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR029W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR029W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 190 nodes, 197.48 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(=1.1331) * Reverse)^tau(=0.8073))) % 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 1oqcA 125 -181.47 -147.27 7.62e-24 1jraA 117 -156.14 -129.22 3.88e-21 1jr8A 117 -156.96 -128.90 4.34e-21 1iwhA 141 -42.67 -18.21 8.14e-02 1euvA 221 -40.89 -18.10 8.62e-02 1ku1A 230 -46.16 -17.98 9.15e-02 1myf 153 -40.90 -17.89 9.61e-02 1fxxA 482 -43.48 -16.47 2.00e-01 1pbwA 216 -42.38 -16.08 2.45e-01 1dwtA 153 -39.59 -15.59 3.16e-01 1cviA 342 -39.92 -15.29 3.71e-01 1mbd 153 -38.33 -15.25 3.80e-01 1irdA 141 -40.36 -15.18 3.93e-01 1eyvA 156 -39.46 -15.15 3.99e-01 1nd6A 354 -39.57 -15.08 4.14e-01 1rpa 342 -40.89 -15.08 4.15e-01 2hpaA 342 -40.11 -15.07 4.17e-01 1gjnA 153 -39.46 -15.03 4.26e-01 1cg5B 141 -37.25 -14.82 4.76e-01 2spo 154 -38.34 -14.78 4.87e-01 1babA 143 -39.70 -14.52 5.59e-01 1ngvA 534 -43.45 -14.51 5.60e-01 1ciy 590 -44.39 -14.46 5.77e-01 1mgn 154 -38.22 -14.41 5.91e-01 1p8cA 145 -39.77 -14.40 5.95e-01 1abwA 283 -40.24 -14.15 6.81e-01 1bzpA 153 -38.64 -14.12 6.93e-01 3erdA 261 -39.13 -14.04 7.23e-01 1g8lA 411 -37.05 -14.00 7.37e-01 1mlwA 301 -38.64 -13.72 8.58e-01 1gkxA 388 -38.29 -13.68 8.76e-01 1j7yA 141 -39.33 -13.64 8.94e-01 1a6m 151 -36.28 -13.52 9.55e-01 1b9dA 163 -35.35 -13.42 1.01e+00 1rcb 129 -36.18 -13.41 1.01e+00 1hyvA 166 -35.63 -13.31 1.07e+00 1hziA 129 -36.16 -13.20 1.13e+00 1b75A 94 -36.35 -13.18 1.15e+00 1l2iA 261 -38.28 -13.14 1.18e+00 1fgyA 127 -33.20 -12.75 1.45e+00 1g4yR 148 -43.41 -12.67 1.52e+00 1c4zA 358 -41.92 -12.41 1.75e+00 2int 129 -35.26 -12.21 1.95e+00 1hzfA 367 -35.21 -12.18 1.98e+00 1jf3A 147 -35.74 -12.04 2.14e+00 1it2A 146 -38.26 -11.98 2.22e+00 1nubA 229 -39.23 -11.55 2.81e+00 1spgA 144 -38.26 -11.43 3.00e+00 1vreA 147 -34.57 -11.43 3.01e+00 1ll7A 392 -33.98 -11.41 3.04e+00 1d2kA 392 -34.03 -11.34 3.17e+00 1g8iA 190 -36.54 -11.30 3.23e+00 1jf8A 131 -32.67 -11.30 3.24e+00 1bl3A 160 -34.15 -11.25 3.32e+00 1lriA 98 -33.14 -11.22 3.39e+00 1itm 130 -35.29 -11.19 3.43e+00 1bxm 99 -33.08 -11.13 3.57e+00 1kb9C 385 -38.78 -10.99 3.84e+00 1bbn 133 -34.72 -10.91 4.03e+00 1jf4A 147 -34.04 -10.86 4.13e+00 1l7vC 249 -33.01 -10.85 4.16e+00 1ld8B 437 -40.87 -10.84 4.19e+00 1ft1B 437 -38.43 -10.77 4.35e+00 1itg 166 -33.71 -10.74 4.44e+00 1o1fC 147 -40.49 -10.69 4.55e+00 1ezvC 385 -38.58 -10.68 4.59e+00 1isaA 192 -34.13 -10.50 5.07e+00 1pn1A 176 -32.86 -10.47 5.17e+00 1jwgA 147 -32.05 -10.41 5.34e+00 1cc8A 73 -28.82 -10.33 5.59e+00 1bp7A 152 -32.19 -10.32 5.63e+00 1iscA 192 -33.85 -10.31 5.66e+00 2sas 185 -34.19 -10.27 5.79e+00 1dgnA 89 -32.31 -10.21 5.99e+00 1fd8A 73 -29.67 -10.20 6.03e+00 1jcrB 437 -39.08 -10.13 6.26e+00 2hbg 147 -33.81 -10.12 6.29e+00 1gkzA 388 -35.96 -10.10 6.37e+00 1je8A 82 -32.76 -10.09 6.40e+00 1beg 98 -32.44 -10.06 6.53e+00 1fjgD 209 -37.59 -9.99 6.80e+00 1gcvB 136 -34.32 -9.86 7.33e+00 1auiB 169 -35.78 -9.76 7.74e+00 1khbA 625 -35.18 -9.71 7.98e+00 1n40A 396 -34.20 -9.68 8.12e+00 1qm9A 198 -42.44 -9.63 8.37e+00 1ljrA 244 -35.30 -9.52 8.87e+00 1jfvA 131 -32.24 -9.44 9.30e+00 1k4wA 252 -33.17 -9.40 9.55e+00 1qghA 156 -35.02 -9.34 9.90e+00 1ile 821 -36.77 -9.32 1.00e+01 1fazA 122 -35.27 -9.31 1.01e+01 1lm8B 118 -37.34 -9.31 1.01e+01 1nv8A 284 -34.86 -9.30 1.01e+01 1beo 98 -30.21 -9.30 1.01e+01 1hbg 147 -33.22 -9.27 1.03e+01 2pvaA 345 -38.61 -9.27 1.03e+01 1i5nA 146 -33.56 -9.26 1.03e+01 1mznA 240 -33.19 -9.23 1.05e+01 3ertA 261 -36.63 -9.21 1.07e+01 1kncA 177 -38.82 -9.20 1.07e+01 1iygA 133 -32.65 -9.19 1.07e+01 1d8dB 437 -38.74 -9.13 1.12e+01 1j78A 458 -37.14 -9.12 1.12e+01 1gu9A 177 -38.40 -9.08 1.14e+01 1em2A 229 -32.16 -8.98 1.21e+01 1kv9A 668 -35.78 -8.98 1.22e+01 1dceA 567 -38.63 -8.98 1.22e+01 2cblA 305 -34.57 -8.90 1.28e+01 1aueA 100 -33.49 -8.88 1.29e+01 3nodB 423 -38.49 -8.88 1.29e+01 1bbhA 131 -36.00 -8.82 1.34e+01 1gs9A 165 -33.24 -8.74 1.40e+01 1kyoD 248 -38.58 -8.74 1.40e+01 1hqvA 191 -35.42 -8.74 1.41e+01 1lwbA 122 -34.43 -8.71 1.43e+01 1r2fA 319 -34.52 -8.69 1.44e+01 1dxrC 336 -37.66 -8.66 1.46e+01 1j0mA 752 -32.92 -8.62 1.51e+01 1fm2A 169 -30.65 -8.61 1.52e+01 1toh 343 -33.44 -8.60 1.52e+01 3crd 100 -29.10 -8.60 1.52e+01 1a8s 273 -30.70 -8.60 1.52e+01 1i3dA 146 -32.23 -8.56 1.56e+01 3lynA 136 -36.12 -8.55 1.57e+01 1jr3A 373 -36.48 -8.52 1.60e+01 1a0fA 201 -34.43 -8.48 1.63e+01 1prcC 336 -39.48 -8.46 1.65e+01 1lpe 144 -32.79 -8.46 1.65e+01 1oxjA 173 -35.01 -8.45 1.66e+01 1iapA 211 -35.33 -8.45 1.66e+01 1lc0A 294 -31.53 -8.44 1.67e+01 1osa 148 -37.78 -8.40 1.71e+01 6prcC 336 -37.55 -8.37 1.75e+01 1j77A 209 -31.18 -8.36 1.75e+01 1kwgA 645 -33.13 -8.35 1.76e+01 1en7A 157 -40.34 -8.35 1.77e+01 1lki 180 -34.02 -8.34 1.78e+01 1e7lA 157 -40.06 -8.33 1.78e+01 1qsdA 106 -32.40 -8.31 1.81e+01 1ezvD 245 -39.02 -8.30 1.82e+01 1eh8A 207 -32.29 -8.29 1.82e+01 1f0lA 535 -32.88 -8.28 1.84e+01 1kwkA 645 -33.13 -8.28 1.84e+01 1gotG 73 -35.89 -8.27 1.85e+01 1ggzA 148 -36.16 -8.26 1.86e+01 1pov1 302 -39.82 -8.21 1.91e+01 1rec 201 -31.98 -8.20 1.93e+01 1mhqA 148 -33.66 -8.18 1.95e+01 1f2rI 100 -31.02 -8.18 1.95e+01 1b3uA 588 -32.83 -8.18 1.95e+01 1fit 147 -30.01 -8.12 2.02e+01 1gcuA 295 -30.73 -8.11 2.03e+01 1pa1A 310 -33.18 -8.11 2.03e+01 1pq9A 253 -33.37 -8.10 2.04e+01 1kxpD 458 -35.12 -8.09 2.06e+01 1qgtA 149 -34.36 -8.06 2.09e+01 1mai 131 -30.04 -8.06 2.09e+01 1om4A 422 -34.32 -8.04 2.12e+01 1n1fA 159 -35.29 -8.01 2.16e+01 3pvaA 335 -37.39 -7.96 2.23e+01 1kvkA 395 -31.97 -7.95 2.24e+01 2itg 163 -34.85 -7.93 2.26e+01 1kb9D 246 -39.19 -7.91 2.29e+01 1ijgA 309 -38.60 -7.90 2.30e+01 1tbgE 68 -37.98 -7.88 2.33e+01 1mvcA 240 -32.08 -7.86 2.36e+01 1cqxA 403 -37.58 -7.85 2.37e+01 1d8hA 311 -34.50 -7.84 2.38e+01 7catA 506 -45.74 -7.83 2.40e+01 1jtkA 136 -28.23 -7.80 2.44e+01 1kf6D 119 -33.45 -7.79 2.45e+01 1jwiB 125 -31.53 -7.79 2.46e+01 1exqA 154 -33.26 -7.79 2.46e+01 1i4yA 114 -30.76 -7.77 2.48e+01 1ltzA 297 -34.66 -7.75 2.52e+01 1j5sA 463 -34.68 -7.75 2.53e+01 1dfuP 94 -28.12 -7.74 2.53e+01 1dghB 498 -44.54 -7.74 2.54e+01 1b47A 304 -34.17 -7.73 2.56e+01 1mzm 93 -30.12 -7.73 2.56e+01 1ft1A 377 -38.55 -7.70 2.60e+01 1nrlA 316 -33.71 -7.69 2.61e+01 1aa7A 158 -32.83 -7.67 2.65e+01 1jcrA 377 -38.58 -7.67 2.65e+01 1ed5A 444 -37.59 -7.66 2.66e+01 1iloA 77 -26.05 -7.65 2.68e+01 1gh9A 71 -32.79 -7.64 2.70e+01 1q8yA 373 -32.00 -7.62 2.73e+01 1n9lA 109 -30.70 -7.62 2.73e+01 1kyoC 385 -37.31 -7.60 2.76e+01 1l5xA 280 -31.73 -7.58 2.79e+01 1dc1A 323 -31.49 -7.58 2.80e+01 3cyr 107 -36.16 -7.56 2.83e+01 2lhb 149 -30.24 -7.54 2.85e+01 1e4uA 78 -42.34 -7.54 2.86e+01 1g291 372 -30.33 -7.52 2.90e+01 1f16A 192 -36.89 -7.51 2.92e+01 1fehA 574 -31.88 -7.49 2.95e+01 1jkmA 358 -30.13 -7.47 2.99e+01 1cqeA 580 -32.37 -7.46 3.00e+01 1dguA 183 -33.02 -7.45 3.02e+01 1is2A 661 -35.21 -7.44 3.05e+01 1ge9A 184 -30.72 -7.43 3.06e+01 1ddt 535 -32.69 -7.42 3.08e+01 1dn1B 267 -35.18 -7.39 3.13e+01 1f83A 425 -33.02 -7.37 3.17e+01 1qovH 260 -43.34 -7.36 3.19e+01 1ak1 310 -30.35 -7.36 3.19e+01 1kyqA 274 -35.33 -7.36 3.19e+01 1cg5A 141 -33.66 -7.36 3.20e+01 1mat 264 -28.27 -7.34 3.22e+01 1g4wR 383 -30.81 -7.34 3.23e+01 1hn0A 1021 -33.51 -7.34 3.24e+01 3caoA 103 -40.68 -7.34 3.24e+01 1b68A 191 -32.37 -7.31 3.28e+01 1jjfA 268 -30.85 -7.30 3.31e+01 1nxmA 197 -30.35 -7.28 3.34e+01 1dliA 402 -33.82 -7.26 3.39e+01 1sw6A 327 -32.69 -7.22 3.46e+01 1jpc 109 -28.79 -7.22 3.47e+01 1idrA 136 -30.98 -7.21 3.48e+01 1co6A 107 -33.18 -7.21 3.49e+01 2hts 88 -30.45 -7.21 3.49e+01 1ay2 159 -27.35 -7.20 3.50e+01 1fk5A 93 -29.93 -7.18 3.56e+01 1bk7A 190 -31.44 -7.17 3.59e+01 1dxrL 273 -35.82 -7.15 3.63e+01 1hs7A 97 -32.13 -7.13 3.67e+01 1dgfA 497 -43.05 -7.13 3.67e+01 1msaA 109 -27.34 -7.11 3.71e+01 1i4wA 353 -33.00 -7.10 3.72e+01 1oqvA 192 -27.72 -7.09 3.75e+01 1nstA 325 -32.13 -7.09 3.76e+01 1l3lA 234 -30.79 -7.08 3.77e+01 1j8uA 325 -35.02 -7.08 3.77e+01 1kkhA 317 -30.23 -7.08 3.78e+01 1j3bA 529 -30.29 -7.08 3.78e+01 1bz4A 144 -32.09 -7.08 3.79e+01 1cll 148 -35.98 -7.07 3.81e+01 1q59A 172 -32.38 -7.06 3.83e+01 1ntcA 91 -37.32 -7.06 3.83e+01 4rxn 54 -35.38 -7.06 3.83e+01 1d1vA 444 -38.54 -7.06 3.83e+01 1howA 373 -30.59 -7.06 3.83e+01 1ngkA 128 -38.87 -7.03 3.90e+01 1f82A 424 -33.12 -7.03 3.90e+01 1d8iA 311 -34.04 -7.02 3.91e+01 1aipE 405 -31.99 -7.01 3.95e+01 1dozA 309 -29.67 -7.01 3.95e+01