% 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.YGL227W.t2k-100-30-alpha Host: farm15.cse.ucsc.edu Sun Mar 19 22:11:54 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGL2/YGL227W % --------------------------------------------------------------------- % 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 YGL227W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGL227W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 959 nodes, 1709.75 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(=1.5808) * Reverse)^tau(=0.8015))) % 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 1uujA 88 -32.15 -20.70 8.51e-04 2fbeA 201 -32.09 -18.60 3.27e-03 1ag8A 499 -31.35 -17.40 7.14e-03 1o04A 500 -28.89 -13.87 7.61e-02 1syyA 346 -27.79 -13.82 7.89e-02 1ly1A 181 -26.40 -13.48 1.00e-01 1od3A 168 -25.48 -13.43 1.03e-01 1ltqA 301 -26.64 -12.57 1.88e-01 1xgwA 176 -23.79 -11.56 3.83e-01 1k1xA 659 -24.92 -11.30 4.60e-01 1ukz 203 -24.01 -11.20 4.96e-01 1ki9A 192 -23.01 -11.08 5.40e-01 1iqpA 327 -24.35 -11.02 5.63e-01 1q1lA 401 -25.92 -10.99 5.74e-01 1lkvX 232 -23.80 -10.62 7.53e-01 1vhmA 195 -22.60 -10.50 8.21e-01 1yo8A 634 -28.14 -10.45 8.51e-01 2viuB 175 -21.82 -10.38 8.95e-01 1ykhA 108 -24.40 -10.38 8.97e-01 1zb1A 392 -23.29 -10.35 9.15e-01 1gr3A 160 -21.91 -10.25 9.80e-01 1hgeB 175 -21.78 -10.16 1.05e+00 1r5qA 102 -27.92 -10.13 1.07e+00 1jnyA 435 -22.90 -10.11 1.09e+00 1azsC 388 -23.37 -9.97 1.21e+00 1lv7A 257 -23.09 -9.95 1.22e+00 1w3iA 293 -21.80 -9.87 1.29e+00 1tlfA 301 -20.87 -9.85 1.31e+00 1sv6A 269 -21.58 -9.80 1.37e+00 1efaA 333 -20.85 -9.70 1.48e+00 1qfcA 306 -22.01 -9.66 1.51e+00 3hmgB 175 -21.13 -9.53 1.67e+00 1rj1A 151 -20.22 -9.36 1.89e+00 1ej6B 1275 -35.93 -9.27 2.02e+00 2mspA 126 -20.68 -9.27 2.03e+00 1hl2A 297 -22.02 -9.21 2.11e+00 1e1oA 504 -21.93 -9.18 2.16e+00 1ji0A 240 -21.16 -9.16 2.19e+00 1tdpA 111 -20.19 -9.14 2.22e+00 1su4A 994 -37.17 -9.03 2.43e+00 2fbjL 213 -20.40 -8.99 2.50e+00 1bn5 478 -24.74 -8.77 2.93e+00 1fdyA 297 -21.70 -8.72 3.04e+00 1qu1A 155 -24.19 -8.71 3.07e+00 1lylA 504 -21.36 -8.69 3.12e+00 1eulA 994 -36.89 -8.68 3.15e+00 1b6a 478 -24.66 -8.65 3.22e+00 1ei7B 158 -20.23 -8.61 3.33e+00 1r75A 141 -19.86 -8.59 3.37e+00 1b59A 370 -22.53 -8.54 3.51e+00 1kdj 102 -19.50 -8.52 3.54e+00 2cavA 445 -21.68 -8.51 3.58e+00 1mi3A 322 -23.09 -8.49 3.64e+00 1q5dA 419 -20.38 -8.45 3.74e+00 1tg7A 971 -23.13 -8.44 3.77e+00 2cbp 96 -19.46 -8.43 3.81e+00 2f6eA 127 -23.00 -8.38 3.96e+00 1lk9A 448 -20.14 -8.36 4.02e+00 1f5jA 199 -20.49 -8.34 4.07e+00 2c4jA 218 -21.05 -8.32 4.13e+00 1y01A 102 -20.65 -8.26 4.34e+00 1nnxA 109 -22.37 -8.24 4.38e+00 1xw5A 217 -20.69 -8.16 4.68e+00 1hqz1 141 -19.07 -8.12 4.81e+00 2gsq 202 -21.78 -8.09 4.91e+00 1r3eA 309 -21.40 -8.07 5.00e+00 1hqz9 141 -18.98 -8.04 5.10e+00 1ii6A 368 -21.29 -7.98 5.35e+00 1b2pA 119 -20.60 -7.98 5.35e+00 1qhdA 398 -22.60 -7.96 5.46e+00 1kl1A 419 -20.65 -7.95 5.48e+00 1dc1A 323 -22.43 -7.91 5.64e+00 1q7sA 117 -19.10 -7.91 5.65e+00 1ay1L 210 -19.32 -7.87 5.83e+00 1dhkB 223 -21.66 -7.87 5.84e+00 1o0sA 605 -22.34 -7.85 5.90e+00 1chmA 401 -20.84 -7.85 5.91e+00 1mcpL 220 -19.58 -7.81 6.10e+00 1kkjA 419 -20.45 -7.72 6.55e+00 1xmrA 243 -21.87 -7.71 6.61e+00 1x9zA 188 -18.67 -7.68 6.75e+00 1zbqA 327 -22.06 -7.66 6.85e+00 1k4wA 252 -20.56 -7.63 6.98e+00 5ukdA 194 -20.52 -7.62 7.09e+00 1w0bA 102 -20.36 -7.61 7.14e+00 1wjtA 103 -18.94 -7.59 7.22e+00 1qf9A 194 -20.53 -7.53 7.55e+00 1jhjA 171 -18.64 -7.52 7.62e+00 3mspA 126 -19.20 -7.51 7.69e+00 1guxA 218 -21.60 -7.50 7.72e+00 1khtA 192 -19.11 -7.50 7.74e+00 1ixmA 192 -19.39 -7.46 7.99e+00 1nal3 297 -20.47 -7.44 8.09e+00 1wyuA 438 -19.43 -7.42 8.25e+00 1j8mF 297 -21.38 -7.42 8.27e+00 2bmfA 451 -20.19 -7.39 8.45e+00 1yjsA 419 -20.08 -7.39 8.46e+00 1xr4A 509 -20.41 -7.38 8.48e+00 1mspA 126 -18.79 -7.38 8.51e+00 1ootA 60 -18.92 -7.37 8.58e+00 1t0bA 252 -20.67 -7.34 8.77e+00 1z8uA 102 -19.85 -7.31 8.95e+00 1iweA 457 -23.37 -7.31 9.01e+00 1l4uA 176 -18.32 -7.29 9.14e+00 2a6hD 1524 -24.53 -7.29 9.15e+00 1y63A 184 -18.73 -7.28 9.17e+00 1f9aA 168 -19.71 -7.25 9.43e+00 1nlbL 220 -18.65 -7.22 9.65e+00 1cr6B 554 -22.06 -7.21 9.67e+00 1nal1 297 -20.03 -7.20 9.76e+00 1fh0A 221 -19.26 -7.18 9.97e+00 1kblA 873 -21.28 -7.18 9.98e+00 3aprE 325 -21.34 -7.15 1.02e+01 1p30A 952 -20.87 -7.12 1.04e+01 1forL 210 -19.63 -7.12 1.04e+01 2tmvP 158 -18.89 -7.11 1.05e+01 1jwhC 215 -19.72 -7.10 1.06e+01 1jpzA 473 -20.53 -7.10 1.06e+01 2bjqA 345 -19.59 -7.05 1.10e+01 1wusA 180 -18.36 -7.05 1.10e+01 1oe8A 211 -19.76 -7.04 1.11e+01 1mkyA 439 -22.25 -7.01 1.14e+01 2apr 325 -21.26 -7.00 1.15e+01 1kmtA 141 -18.01 -6.93 1.21e+01 1jbkA 195 -18.77 -6.93 1.21e+01 1omwA 689 -21.13 -6.92 1.22e+01 1v5xA 203 -18.40 -6.91 1.22e+01 1rxwA 336 -18.96 -6.87 1.27e+01 1jyeA 349 -19.51 -6.86 1.28e+01 1qbqA 333 -19.31 -6.86 1.28e+01 1nq7A 244 -19.59 -6.84 1.30e+01 1k8cA 322 -21.44 -6.80 1.33e+01 1a8l 226 -19.05 -6.80 1.34e+01 1j71A 334 -18.62 -6.80 1.34e+01 1clqA 903 -24.24 -6.78 1.36e+01 1zd3A 555 -20.78 -6.78 1.36e+01 1vjnA 220 -19.17 -6.77 1.37e+01 1lshA 1056 -20.59 -6.75 1.39e+01 1o0xA 262 -20.24 -6.73 1.41e+01 1a2oA 349 -18.84 -6.73 1.42e+01 1ie7C 570 -24.70 -6.73 1.42e+01 1dik 874 -20.57 -6.72 1.43e+01 1yc7A 124 -18.41 -6.67 1.48e+01 1am5 324 -19.16 -6.67 1.49e+01 1jmeA 455 -20.38 -6.66 1.50e+01 1mmq 170 -18.63 -6.65 1.51e+01 1y1nA 291 -22.32 -6.64 1.51e+01 1ypxA 375 -19.59 -6.63 1.53e+01 2bmhA 455 -20.14 -6.63 1.53e+01 1lenB 52 -16.63 -6.63 1.54e+01 2ax4A 198 -19.44 -6.62 1.55e+01 1ubpC 570 -24.47 -6.59 1.59e+01 1dvoA 152 -17.54 -6.58 1.60e+01 1ixmB 192 -18.68 -6.58 1.60e+01 1e8yA 966 -29.59 -6.58 1.60e+01 1iyhA 198 -18.01 -6.57 1.60e+01 1nksA 194 -17.78 -6.56 1.62e+01 1r89A 437 -19.28 -6.55 1.63e+01 4ubpC 570 -24.35 -6.54 1.65e+01 1l7vA 326 -24.99 -6.52 1.68e+01 2ayh 214 -22.23 -6.49 1.71e+01 1l9kA 305 -18.79 -6.49 1.71e+01 3adk 195 -17.98 -6.49 1.71e+01 1na3A 91 -17.96 -6.49 1.72e+01 1d9uA 154 -17.67 -6.48 1.72e+01 1b8dB 177 -17.46 -6.48 1.73e+01 1wgkA 114 -17.93 -6.47 1.74e+01 1zsoA 164 -18.46 -6.46 1.76e+01 1htmB 138 -21.19 -6.45 1.76e+01 1a8q 274 -18.98 -6.45 1.77e+01 1gppA 237 -18.29 -6.43 1.80e+01 1fchA 368 -19.33 -6.42 1.81e+01 1uteA 313 -18.27 -6.41 1.82e+01 1rdr 461 -21.26 -6.41 1.83e+01 2g5cA 281 -18.34 -6.40 1.84e+01 1fnnA 389 -20.29 -6.40 1.84e+01 1vjkA 98 -18.48 -6.40 1.85e+01 2a8jA 420 -21.08 -6.39 1.86e+01 1z6fA 363 -18.05 -6.38 1.86e+01 1wxrA 1048 -19.69 -6.38 1.88e+01 1xf1A 926 -18.56 -6.36 1.90e+01 1gg3A 279 -19.19 -6.35 1.91e+01 1ek1A 554 -22.00 -6.35 1.92e+01 1dvkA 173 -18.59 -6.34 1.94e+01 1bu7A 455 -19.78 -6.33 1.95e+01 1iwlA 182 -17.85 -6.32 1.96e+01 1v9yA 167 -18.07 -6.32 1.97e+01 4kbpA 432 -18.95 -6.31 1.98e+01 1qdlA 422 -20.53 -6.31 1.98e+01 1ux6A 350 -25.04 -6.31 1.98e+01 1cqzA 554 -21.85 -6.30 1.99e+01 1yrgB 385 -19.97 -6.30 2.00e+01 1senA 164 -18.24 -6.28 2.03e+01 1cjbA 231 -20.78 -6.28 2.03e+01 1r77A 103 -17.78 -6.27 2.04e+01 1ck7A 631 -20.20 -6.27 2.05e+01 1fxzA 476 -19.97 -6.25 2.07e+01 1x6vA 630 -19.38 -6.25 2.08e+01 1izoA 417 -18.80 -6.25 2.08e+01 1e15A 499 -18.04 -6.22 2.13e+01 1fjgT 106 -19.01 -6.21 2.14e+01 1qatB 622 -18.66 -6.21 2.15e+01 1qz9A 416 -18.53 -6.21 2.15e+01 1uwwA 191 -18.24 -6.20 2.16e+01 1nzoA 363 -17.86 -6.20 2.17e+01 1qasA 622 -18.60 -6.19 2.18e+01 1djxA 624 -18.52 -6.19 2.18e+01 1vj5A 555 -20.33 -6.18 2.20e+01 821p 166 -17.78 -6.17 2.21e+01 1hv9A 456 -21.58 -6.17 2.22e+01 1chd 203 -17.97 -6.16 2.23e+01 1tm0A 350 -19.99 -6.16 2.24e+01 1gv4A 528 -19.54 -6.15 2.26e+01 1k5dC 386 -20.10 -6.14 2.27e+01 2a8lA 420 -20.81 -6.13 2.28e+01 1yrgA 385 -19.74 -6.13 2.29e+01 2d2sA 235 -21.60 -6.12 2.31e+01 1xeuA 263 -17.85 -6.11 2.32e+01 1m12A 84 -19.59 -6.11 2.32e+01 1in4A 334 -19.14 -6.10 2.33e+01 1jcrA 377 -18.78 -6.08 2.38e+01 1goiA 499 -17.83 -6.08 2.39e+01 1jcqA 382 -18.50 -6.05 2.43e+01 1pzxA 289 -19.29 -6.05 2.43e+01 1v10A 521 -22.63 -6.05 2.44e+01 2a9kA 187 -17.63 -6.04 2.46e+01 1epuA 591 -18.67 -6.04 2.46e+01 1cnt2 187 -23.39 -6.04 2.46e+01 1gveA 327 -18.04 -6.03 2.48e+01 1z83A 196 -17.82 -6.03 2.49e+01 1am7A 158 -17.35 -6.02 2.51e+01 2fdiA 211 -19.14 -6.01 2.51e+01 1wy2A 351 -19.09 -6.01 2.52e+01 2a8mA 420 -20.27 -5.99 2.55e+01 1p42A 270 -21.15 -5.99 2.56e+01 2fxqA 264 -18.08 -5.99 2.57e+01 1qppA 218 -18.08 -5.98 2.57e+01 1nijA 318 -19.33 -5.98 2.59e+01 1tn6A 382 -18.68 -5.97 2.61e+01 1i85A 110 -17.82 -5.97 2.61e+01 1e6pA 499 -17.68 -5.94 2.66e+01 1ft1A 377 -18.49 -5.93 2.68e+01 1fts 295 -18.30 -5.93 2.70e+01 1ld8A 382 -18.65 -5.92 2.71e+01 1ztxL 212 -17.40 -5.92 2.72e+01 1q0bA 367 -19.21 -5.90 2.75e+01 1yueA 427 -19.64 -5.90 2.76e+01 1fcqA 350 -19.21 -5.90 2.76e+01 1d8dA 377 -18.57 -5.89 2.78e+01 1gqyA 475 -19.23 -5.87 2.81e+01 1ulyA 192 -19.82 -5.85 2.87e+01 1ei1A 391 -18.17 -5.85 2.88e+01 1bif 469 -21.40 -5.84 2.90e+01 1iznB 277 -18.69 -5.83 2.91e+01 1a5fL 220 -17.58 -5.83 2.92e+01 1o7fA 469 -19.68 -5.82 2.94e+01 1tuhA 156 -17.28 -5.82 2.95e+01 1oh0A 131 -18.37 -5.82 2.95e+01 1h6lA 353 -17.92 -5.81 2.95e+01 1qpxA 218 -17.79 -5.81 2.96e+01 1n0lA 224 -17.75 -5.81 2.97e+01 1bxeA 113 -17.37 -5.80 2.99e+01 1js3A 486 -20.41 -5.78 3.03e+01 2a4nA 182 -17.35 -5.78 3.03e+01 2act 220 -18.24 -5.78 3.04e+01 1xfhA 422 -30.00 -5.77 3.05e+01 1nj4A 363 -17.69 -5.77 3.05e+01 1b89A 449 -19.81 -5.77 3.07e+01 1kk1A 410 -20.74 -5.77 3.07e+01 1q7rA 219 -18.36 -5.76 3.10e+01 1fb6A 105 -17.91 -5.75 3.11e+01 1ei7A 158 -19.43 -5.73 3.15e+01 1u8zA 168 -16.92 -5.73 3.16e+01 1iazA 179 -17.85 -5.73 3.18e+01 1ye8A 178 -20.46 -5.72 3.18e+01 1h09A 338 -21.77 -5.72 3.19e+01 1r0pA 312 -18.14 -5.71 3.20e+01 1ea2A 131 -18.18 -5.71 3.21e+01 2ca6A 386 -19.38 -5.70 3.24e+01 1sacA 204 -17.72 -5.69 3.27e+01 1zk8A 183 -17.13 -5.67 3.32e+01 1btgA 110 -17.98 -5.67 3.32e+01 2c2nA 339 -17.18 -5.67 3.33e+01 1wpgA 994 -33.89 -5.67 3.33e+01 1efuA 385 -20.05 -5.67 3.33e+01 2cygA 312 -16.92 -5.66 3.35e+01 1jsdB 176 -20.31 -5.65 3.38e+01 1fx3B 169 -17.52 -5.63 3.43e+01 1kn9A 249 -17.35 -5.63 3.43e+01 1n71A 180 -17.17 -5.63 3.45e+01 1kbpA 432 -18.29 -5.62 3.45e+01 1aroP 883 -20.57 -5.62 3.45e+01 1m4uA 206 -18.76 -5.62 3.46e+01 1y88A 199 -17.10 -5.62 3.46e+01 1v9sA 208 -17.25 -5.61 3.50e+01 1kz7A 353 -19.29 -5.60 3.52e+01 3bifA 468 -21.28 -5.60 3.53e+01 1k28A 584 -18.45 -5.60 3.53e+01 1zbpA 273 -17.18 -5.60 3.53e+01 1tzvA 142 -17.43 -5.59 3.53e+01 1cpcA 162 -15.89 -5.59 3.55e+01 1lvaA 258 -17.27 -5.59 3.56e+01 1x3mA 415 -18.73 -5.57 3.60e+01 1hkxA 147 -17.08 -5.57 3.61e+01 1bnr 110 -16.68 -5.55 3.68e+01 1rkbA 173 -18.00 -5.54 3.69e+01 2ng1 293 -17.22 -5.54 3.69e+01 2c6cA 707 -24.34 -5.54 3.70e+01 1z3eA 132 -17.62 -5.53 3.71e+01 2pooA 355 -17.42 -5.53 3.73e+01 1mrzA 293 -18.82 -5.53 3.73e+01 1fx3A 169 -17.39 -5.53 3.73e+01 1i4jA 110 -16.44 -5.52 3.75e+01 1p3qQ 54 -16.47 -5.51 3.78e+01 1otgA 125 -16.95 -5.51 3.80e+01 2a1rA 430 -19.96 -5.51 3.80e+01 1egaA 301 -17.28 -5.50 3.80e+01 1jjtA 228 -18.42 -5.49 3.83e+01 1wp5A 323 -18.06 -5.49 3.83e+01 1pxgA 382 -18.32 -5.49 3.84e+01 1hyhA 309 -16.95 -5.49 3.84e+01 1k3sA 113 -17.54 -5.49 3.85e+01 1bykA 255 -18.81 -5.48 3.87e+01 1cawB 184 -17.67 -5.48 3.87e+01 1mxa 383 -17.98 -5.47 3.90e+01 2aqjA 538 -18.03 -5.47 3.92e+01 12e8L 214 -17.23 -5.47 3.93e+01 1ruxA 951 -19.09 -5.46 3.93e+01 1bxsA 501 -20.97 -5.46 3.93e+01 1jalA 363 -20.75 -5.46 3.94e+01 2d0tA 406 -17.91 -5.46 3.94e+01 1nn5A 215 -16.88 -5.46 3.95e+01 1w61A 414 -20.97 -5.46 3.96e+01 1hv8A 367 -18.55 -5.45 3.97e+01 1t6nA 220 -16.83 -5.45 3.98e+01