% 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. % --------------------------------------------------------------------- % strfoo.1.YGR010W.t2k-100-30-str Host: cc50 Fri Nov 8 16:27:12 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR010W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YGR010W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR010W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 396 nodes, 273.96 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(=2.0828) * Reverse)^tau(=0.6750))) % 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 1kkuA 279 -290.24 -264.15 1.35e-27 1kamA 194 -244.87 -215.03 1.30e-23 1k4mA 213 -232.90 -204.56 1.00e-22 1b6tA 159 -132.89 -108.12 1.12e-13 1qjcA 158 -131.79 -107.05 1.44e-13 1f9aA 168 -93.69 -69.77 2.25e-09 1ej2A 181 -82.95 -55.01 1.61e-07 1cozA 129 -58.79 -33.26 1.89e-04 1jhdA 396 -47.02 -20.71 2.25e-02 1d2fA 390 -43.23 -19.82 3.26e-02 1g8fA 511 -51.38 -19.60 3.58e-02 1bksA 268 -37.42 -15.01 2.69e-01 1d4oA 184 -38.25 -14.42 3.53e-01 1d3yA 301 -39.15 -14.36 3.62e-01 2tysA 268 -36.30 -14.20 3.91e-01 1qfjA 232 -37.38 -12.80 7.59e-01 1qamA 244 -35.72 -12.56 8.53e-01 1gz0A 253 -36.52 -12.40 9.25e-01 1f6kA 293 -37.11 -12.38 9.32e-01 1qopA 268 -34.48 -12.34 9.51e-01 1jilA 420 -40.86 -12.02 1.11e+00 1hv8A 367 -38.59 -11.91 1.18e+00 1pfkA 320 -36.71 -11.86 1.20e+00 2wsyA 268 -33.79 -11.79 1.25e+00 1gpmA 525 -39.05 -11.67 1.32e+00 1gewA 356 -34.85 -11.59 1.38e+00 1eqjA 511 -39.09 -11.48 1.45e+00 1ejjA 511 -39.21 -11.45 1.47e+00 1es9A 232 -35.88 -11.20 1.67e+00 1wab 232 -35.85 -11.16 1.71e+00 1fts 295 -35.12 -10.88 1.97e+00 1fkx 349 -33.54 -10.78 2.07e+00 3csuA 310 -36.93 -10.70 2.16e+00 1fg7A 356 -34.98 -10.66 2.21e+00 2ercA 244 -32.25 -10.66 2.21e+00 2pfkA 320 -35.36 -10.62 2.25e+00 1k77A 260 -32.23 -10.54 2.34e+00 1be1 137 -34.70 -10.49 2.41e+00 1e79D 482 -36.05 -10.46 2.45e+00 1dliA 402 -34.81 -10.41 2.51e+00 1a4mA 349 -33.26 -10.35 2.59e+00 1at1A 310 -36.72 -10.31 2.64e+00 1dekA 241 -33.95 -10.26 2.72e+00 1hyuA 521 -35.51 -10.24 2.75e+00 1fsz 372 -36.67 -10.17 2.84e+00 1f74A 293 -34.78 -10.17 2.85e+00 1jr3A 373 -32.84 -10.15 2.87e+00 1add 349 -32.75 -9.98 3.13e+00 1dljA 402 -34.36 -9.98 3.14e+00 1e79A 510 -35.01 -9.93 3.22e+00 1h8eD 482 -35.41 -9.91 3.25e+00 1c7nA 399 -37.39 -9.89 3.28e+00 1fdyA 297 -32.90 -9.83 3.40e+00 1nal1 297 -32.90 -9.83 3.40e+00 1hnjA 317 -31.72 -9.75 3.54e+00 1h8eA 510 -34.71 -9.64 3.76e+00 1nal3 297 -32.60 -9.54 3.97e+00 1i1qB 192 -35.93 -9.52 4.01e+00 1delA 241 -33.06 -9.49 4.07e+00 1b8oA 284 -32.25 -9.40 4.26e+00 1qmpA 130 -33.15 -9.38 4.31e+00 1ltqA 301 -33.65 -9.37 4.34e+00 1kqfA 1015 -42.37 -9.36 4.37e+00 1dz3A 130 -34.04 -9.28 4.55e+00 1pbn 289 -31.75 -9.12 4.95e+00 1bmfA 510 -34.17 -9.11 4.99e+00 1efvB 255 -31.75 -9.10 5.00e+00 3pnp 289 -31.97 -9.04 5.17e+00 1gajA 257 -32.82 -8.89 5.62e+00 1jb9A 316 -34.44 -8.86 5.71e+00 1f8mA 429 -32.85 -8.85 5.75e+00 1ewqA 765 -32.95 -8.81 5.88e+00 1hg3A 225 -31.36 -8.67 6.34e+00 4pfk 319 -34.80 -8.61 6.55e+00 7aatA 401 -34.08 -8.57 6.69e+00 6pfkA 319 -34.87 -8.53 6.83e+00 1hkbA 917 -36.29 -8.45 7.17e+00 1f61A 429 -32.22 -8.40 7.34e+00 1j9yA 385 -34.23 -8.37 7.47e+00 1hkcA 917 -36.27 -8.34 7.60e+00 1eblA 317 -30.04 -8.30 7.75e+00 1cf2O 337 -32.14 -8.30 7.76e+00 1g2qA 187 -30.79 -8.29 7.80e+00 1bu6O 501 -31.16 -8.25 7.98e+00 3pfk 319 -34.45 -8.19 8.27e+00 1h61A 364 -32.02 -8.18 8.30e+00 1glcG 501 -31.27 -8.17 8.34e+00 1qisA 396 -33.41 -8.14 8.48e+00 1go2A 304 -32.70 -8.13 8.53e+00 1egr 85 -27.39 -8.12 8.60e+00 1i86A 389 -33.85 -8.08 8.81e+00 1i88A 389 -33.85 -8.08 8.81e+00 1bi5A 389 -33.85 -8.07 8.83e+00 16pk 415 -33.61 -8.06 8.88e+00 1bw0A 416 -32.60 -8.06 8.88e+00 2ts1 419 -34.22 -8.05 8.94e+00 1f89A 291 -30.48 -8.04 8.97e+00 2tmdA 729 -34.81 -8.00 9.17e+00 1dgkN 917 -35.51 -8.00 9.21e+00 1taq 832 -36.64 -7.90 9.71e+00 1auq 208 -32.68 -7.86 9.95e+00 1mldA 314 -33.27 -7.84 1.01e+01 1b2rA 304 -32.36 -7.82 1.02e+01 1c7qA 445 -32.70 -7.77 1.05e+01 1ekxA 311 -34.37 -7.75 1.06e+01 1ahxA 396 -33.59 -7.69 1.10e+01 1i7qB 193 -33.86 -7.67 1.11e+01 1icpA 376 -32.11 -7.66 1.11e+01 4ts1A 319 -32.95 -7.66 1.11e+01 1dckA 126 -32.08 -7.64 1.13e+01 1b0zA 445 -32.60 -7.62 1.14e+01 2pgi 445 -32.60 -7.62 1.14e+01 1art 396 -33.36 -7.59 1.16e+01 1dbwA 126 -32.50 -7.59 1.16e+01 1a8p 258 -30.97 -7.58 1.17e+01 1bzyA 217 -32.00 -7.57 1.18e+01 1ukz 203 -33.36 -7.54 1.19e+01 1bf6A 291 -29.72 -7.54 1.19e+01 1czaN 917 -35.06 -7.52 1.21e+01 1ars 396 -33.44 -7.49 1.23e+01 1ibcA 194 -29.99 -7.47 1.24e+01 3tgl 269 -29.00 -7.45 1.25e+01 1ccwA 137 -31.97 -7.44 1.26e+01 1ijbA 202 -32.16 -7.44 1.26e+01 1e32A 458 -32.95 -7.43 1.27e+01 1fzqA 181 -31.21 -7.37 1.31e+01 1fehA 574 -32.15 -7.30 1.37e+01 1f0kA 364 -33.86 -7.25 1.41e+01 1pdz 434 -31.06 -7.24 1.42e+01 1k9vF 201 -30.21 -7.20 1.45e+01 1brt 277 -31.87 -7.16 1.49e+01 1d02A 202 -28.90 -7.14 1.50e+01 1broA 277 -31.86 -7.14 1.50e+01 1djnA 729 -33.85 -7.13 1.51e+01 1qhaA 917 -34.86 -7.13 1.51e+01 1gkuB 1054 -34.74 -7.13 1.51e+01 1eokA 290 -33.84 -7.10 1.54e+01 1fl2A 310 -31.94 -7.08 1.56e+01 1ctn 540 -32.62 -7.08 1.56e+01 1spa 396 -33.21 -7.06 1.58e+01 1bmqA 167 -29.16 -7.05 1.58e+01 1hn9A 317 -28.59 -7.03 1.61e+01 1cl2A 395 -30.44 -7.01 1.62e+01 1im2A 444 -34.30 -7.00 1.64e+01 1krhA 338 -32.70 -6.98 1.66e+01 1cl1A 395 -30.35 -6.95 1.68e+01 1oakA 196 -31.65 -6.91 1.73e+01 1erzA 303 -30.20 -6.85 1.79e+01 1e3sA 261 -32.30 -6.82 1.81e+01 1crl 534 -32.14 -6.82 1.82e+01 1yrgA 385 -29.66 -6.81 1.83e+01 1yub 245 -28.83 -6.79 1.84e+01 1pbp 321 -30.03 -6.78 1.85e+01 1f6dA 376 -32.41 -6.74 1.91e+01 1g55A 343 -33.77 -6.72 1.92e+01 1nulA 152 -30.02 -6.70 1.95e+01 1qfnA 85 -26.01 -6.70 1.95e+01 1jq5A 370 -31.70 -6.68 1.97e+01 1pjcA 361 -30.25 -6.68 1.98e+01 1qtrA 317 -30.45 -6.67 1.98e+01 1qatB 622 -31.10 -6.66 1.99e+01 1scuA 288 -31.94 -6.65 2.01e+01 1bkjA 240 -27.21 -6.64 2.02e+01 1qk4A 233 -30.29 -6.63 2.03e+01 1bjwA 382 -31.71 -6.62 2.04e+01 1sayA 361 -30.39 -6.62 2.04e+01 1l6wA 220 -26.99 -6.59 2.09e+01 1cne 270 -29.13 -6.54 2.14e+01 1jk7A 323 -31.12 -6.54 2.15e+01 2kfnA 605 -30.49 -6.53 2.16e+01 1qk3A 233 -30.32 -6.52 2.17e+01 1thjA 214 -28.03 -6.48 2.22e+01 1lv7A 257 -31.59 -6.47 2.24e+01 1edqA 540 -31.73 -6.46 2.25e+01 1dmgA 225 -30.46 -6.44 2.28e+01 1dl5A 317 -32.08 -6.44 2.28e+01 1hnuA 280 -29.23 -6.42 2.30e+01 1tpt 440 -34.92 -6.41 2.32e+01 1qh0A 295 -31.72 -6.40 2.33e+01 1efpB 252 -29.84 -6.28 2.50e+01 1fnnA 389 -33.47 -6.28 2.51e+01 1k9sA 237 -29.02 -6.28 2.52e+01 1que 303 -31.53 -6.28 2.52e+01 1evlA 401 -30.33 -6.26 2.54e+01 1eblB 317 -27.73 -6.26 2.54e+01 1qdeA 224 -30.02 -6.21 2.62e+01 1dapA 320 -30.36 -6.20 2.64e+01 1yveJ 524 -31.65 -6.19 2.64e+01 1ihoA 283 -30.81 -6.19 2.66e+01 1kshA 186 -29.98 -6.18 2.67e+01 1pjbA 361 -29.70 -6.17 2.68e+01 1d1qA 161 -27.55 -6.16 2.70e+01 1i4wA 353 -31.19 -6.16 2.71e+01 1jndA 420 -30.37 -6.15 2.72e+01 1jqaA 370 -31.32 -6.14 2.73e+01 1djxA 624 -30.83 -6.10 2.80e+01 1fnsA 196 -31.39 -6.08 2.84e+01 1hmpA 217 -30.82 -6.06 2.88e+01 1g5rA 196 -31.26 -6.04 2.90e+01 1g5tA 196 -31.26 -6.04 2.90e+01 1pfzA 380 -28.58 -6.03 2.92e+01 1a5t 334 -28.68 -6.01 2.97e+01 3dapA 320 -30.08 -5.96 3.06e+01 1fjmA 330 -30.77 -5.96 3.06e+01 2rusB 490 -29.70 -5.95 3.06e+01 1yrgB 385 -29.63 -5.95 3.07e+01 1d2nA 272 -31.77 -5.95 3.08e+01 1g3qA 237 -29.70 -5.94 3.08e+01 1gpwB 201 -29.46 -5.93 3.11e+01 1igwA 434 -31.80 -5.92 3.13e+01 1ahjB 212 -28.72 -5.92 3.13e+01 1hnoA 280 -28.55 -5.90 3.16e+01 5rubA 490 -29.67 -5.90 3.17e+01 1qklA 127 -29.26 -5.88 3.20e+01 1cleA 534 -31.21 -5.88 3.21e+01 1yveI 524 -31.32 -5.88 3.21e+01 1qmgA 524 -31.32 -5.87 3.23e+01 2ahjB 212 -28.71 -5.87 3.23e+01 1a8s 273 -30.65 -5.85 3.27e+01 1ibsA 317 -31.86 -5.85 3.27e+01 1eh9A 558 -33.07 -5.84 3.30e+01 1smeA 329 -28.22 -5.80 3.37e+01 1fgxA 288 -30.77 -5.79 3.39e+01 1eluB 390 -28.78 -5.77 3.43e+01 1skyE 473 -35.82 -5.77 3.44e+01 1e7kA 128 -26.19 -5.76 3.45e+01 1f06A 320 -29.94 -5.76 3.46e+01 1g41A 444 -32.99 -5.73 3.52e+01 1ecpA 238 -28.90 -5.71 3.56e+01 1fsgA 233 -29.63 -5.70 3.59e+01 1a1s 314 -31.36 -5.68 3.63e+01 1kzhA 555 -33.51 -5.68 3.64e+01 1esmA 316 -30.11 -5.67 3.65e+01 1eluA 390 -28.78 -5.67 3.66e+01 1elqA 390 -28.78 -5.67 3.66e+01 1qczA 169 -30.47 -5.66 3.67e+01 2tpsA 227 -27.48 -5.65 3.71e+01 1ofgA 381 -29.68 -5.63 3.76e+01 1fdr 248 -29.11 -5.62 3.76e+01 1bh6A 274 -28.56 -5.59 3.85e+01 1gfsA 321 -30.46 -5.58 3.87e+01 1kv8A 216 -31.90 -5.55 3.95e+01