% 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.YGR010W.t2k-100-30-str2 Host: cc48 Sat Oct 11 20:17:04 2003 % 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.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 YGR010W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR010W.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 396 nodes, 374.16 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(=2.0320) * Reverse)^tau(=0.6820))) % 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 1kqnA 279 -290.82 -266.25 1.43e-28 1kkuA 279 -289.68 -264.57 1.96e-28 1nuuA 252 -268.25 -245.22 7.72e-27 1kamA 194 -243.13 -214.51 3.21e-24 1k4mA 213 -231.22 -203.07 3.25e-23 1od6A 160 -126.51 -104.70 1.28e-13 1b6tA 159 -129.28 -104.24 1.44e-13 1qjcA 158 -127.44 -102.30 2.35e-13 1f9aA 168 -93.28 -70.10 1.35e-09 1ej2A 181 -81.34 -54.50 1.40e-07 1hybA 181 -75.40 -48.64 8.93e-07 1cozA 129 -54.48 -30.50 4.63e-04 1mrzA 293 -50.05 -26.17 2.42e-03 1jhdA 396 -46.79 -21.40 1.66e-02 1g8fA 511 -52.34 -21.12 1.87e-02 1d2fA 390 -38.52 -15.28 2.45e-01 1o0uA 429 -39.70 -15.19 2.56e-01 1d3yA 301 -39.36 -14.69 3.24e-01 1oe4A 247 -38.25 -14.02 4.43e-01 1d4oA 184 -36.79 -13.79 4.97e-01 1bksA 268 -35.77 -13.61 5.41e-01 1ejjA 511 -41.08 -13.59 5.46e-01 1eqjA 511 -40.41 -13.12 6.86e-01 1hv8A 367 -38.90 -12.90 7.63e-01 2tysA 268 -34.87 -12.87 7.74e-01 1efvB 255 -34.61 -12.44 9.58e-01 1hnjA 317 -34.40 -12.41 9.70e-01 1qamA 244 -34.68 -12.17 1.09e+00 1e79A 510 -36.33 -12.01 1.19e+00 1ltqA 301 -35.73 -11.81 1.31e+00 1jilA 420 -40.76 -11.79 1.32e+00 1pfkA 320 -36.00 -11.72 1.37e+00 1nw3A 416 -37.24 -11.72 1.37e+00 1h8eA 510 -36.27 -11.70 1.39e+00 1gz0A 253 -35.91 -11.68 1.40e+00 1o98A 511 -39.14 -11.49 1.55e+00 1qopA 268 -33.28 -11.24 1.75e+00 1fkx 349 -33.48 -11.23 1.76e+00 1oxxK 353 -34.73 -11.08 1.90e+00 1a4mA 349 -33.38 -11.07 1.92e+00 1m33A 258 -34.67 -11.04 1.94e+00 1oxsC 353 -34.38 -11.04 1.95e+00 1fts 295 -35.04 -10.98 2.01e+00 1o0yA 260 -32.64 -10.91 2.08e+00 1add 349 -33.13 -10.88 2.11e+00 2wsyA 268 -32.69 -10.85 2.15e+00 1dliA 402 -34.39 -10.71 2.31e+00 2pfkA 320 -34.39 -10.65 2.38e+00 1hl2A 297 -33.27 -10.51 2.55e+00 1pdz 434 -34.75 -10.49 2.58e+00 1dekA 241 -33.03 -10.43 2.67e+00 1e79D 482 -35.50 -10.42 2.68e+00 1bmfA 510 -34.85 -10.42 2.68e+00 1hyuA 521 -35.09 -10.37 2.76e+00 1gewA 356 -33.65 -10.36 2.76e+00 1gajA 257 -33.32 -10.34 2.80e+00 1e32A 458 -35.66 -10.32 2.82e+00 1fsz 372 -34.99 -10.28 2.88e+00 1egzA 291 -34.26 -10.28 2.89e+00 1gpmA 525 -36.39 -10.24 2.95e+00 3csuA 310 -36.07 -10.22 2.98e+00 1dljA 402 -33.87 -10.21 2.99e+00 1eblA 317 -32.11 -10.12 3.14e+00 1delA 241 -32.59 -10.09 3.20e+00 1qfjA 232 -33.45 -10.06 3.24e+00 1nbwA 607 -35.60 -9.93 3.47e+00 1h8eD 482 -34.57 -9.92 3.50e+00 1nal1 297 -32.74 -9.83 3.66e+00 1auq 208 -33.63 -9.72 3.90e+00 2ercA 244 -31.22 -9.71 3.91e+00 1at1A 310 -35.07 -9.68 3.97e+00 1nal3 297 -32.48 -9.60 4.15e+00 1be1 137 -33.92 -9.53 4.30e+00 1k77A 260 -31.29 -9.51 4.35e+00 1g55A 343 -34.53 -9.50 4.38e+00 1ibcA 194 -31.66 -9.43 4.54e+00 1fg7A 356 -33.53 -9.40 4.62e+00 1fdyA 297 -32.29 -9.38 4.66e+00 1es9A 232 -33.76 -9.34 4.76e+00 2tmdA 729 -35.92 -9.33 4.79e+00 1ml4A 308 -35.05 -9.30 4.88e+00 1ijbA 202 -33.04 -9.27 4.95e+00 1wab 232 -33.72 -9.21 5.14e+00 1hn9A 317 -30.79 -9.19 5.19e+00 1kqfA 1015 -41.46 -9.15 5.29e+00 1ogiA 303 -33.18 -9.13 5.36e+00 1f89A 291 -31.19 -9.08 5.49e+00 1f6kA 293 -33.39 -9.08 5.50e+00 1bmqA 167 -30.74 -9.00 5.75e+00 1i1qB 192 -33.89 -8.99 5.77e+00 4pfk 319 -34.14 -8.99 5.78e+00 1erzA 303 -32.06 -8.95 5.92e+00 1oakA 196 -32.44 -8.92 6.02e+00 1k1xA 659 -33.95 -8.76 6.54e+00 1hg3A 225 -31.74 -8.71 6.73e+00 1f74A 293 -32.84 -8.69 6.83e+00 1jr3A 373 -30.95 -8.58 7.25e+00 3pfk 319 -33.80 -8.58 7.27e+00 1d2nA 272 -32.46 -8.52 7.50e+00 1f0kA 364 -33.12 -8.52 7.52e+00 1fdo 715 -35.17 -8.42 7.91e+00 1a1s 314 -33.97 -8.42 7.95e+00 1djnA 729 -34.86 -8.40 8.01e+00 1fnnA 389 -33.34 -8.34 8.32e+00 1skyE 473 -35.71 -8.32 8.41e+00 1fnsA 196 -32.38 -8.29 8.53e+00 1ede 310 -31.64 -8.25 8.74e+00 1nsf 273 -32.15 -8.19 9.02e+00 1k9sA 237 -30.06 -8.16 9.19e+00 1jr1A 514 -34.01 -8.14 9.28e+00 6pfkA 319 -33.32 -8.10 9.48e+00 1iukA 140 -29.03 -8.02 9.92e+00 1qmgA 524 -34.30 -7.99 1.01e+01 1qk4A 233 -31.33 -7.99 1.01e+01 1j8yF 297 -33.44 -7.98 1.02e+01 1jclA 260 -29.50 -7.97 1.03e+01 1jcjA 260 -29.51 -7.96 1.03e+01 1yveI 524 -34.27 -7.96 1.03e+01 1eblB 317 -29.69 -7.94 1.04e+01 1i88A 389 -32.89 -7.91 1.06e+01 1i86A 389 -32.89 -7.90 1.06e+01 1bi5A 389 -32.89 -7.90 1.06e+01 1ars 396 -32.99 -7.73 1.17e+01 1qmpA 130 -30.73 -7.72 1.18e+01 1ukz 203 -33.50 -7.72 1.18e+01 1b6g 310 -31.16 -7.71 1.19e+01 1aa6 715 -34.96 -7.66 1.22e+01 1o94A 729 -34.50 -7.66 1.22e+01 1art 396 -33.00 -7.65 1.23e+01 1im2A 444 -34.63 -7.63 1.25e+01 1ahxA 396 -33.29 -7.62 1.25e+01 2ts1 419 -33.76 -7.62 1.25e+01 1qk3A 233 -31.07 -7.61 1.26e+01 1kzhA 555 -34.43 -7.59 1.27e+01 1fsgA 233 -30.92 -7.58 1.28e+01 1ecpA 238 -29.94 -7.54 1.31e+01 1dckA 126 -30.65 -7.53 1.32e+01 1qtrA 317 -30.37 -7.53 1.32e+01 1qisA 396 -32.49 -7.49 1.35e+01 1jndA 420 -31.87 -7.48 1.36e+01 1pbp 321 -30.75 -7.47 1.37e+01 1c7qA 445 -32.28 -7.46 1.37e+01 1ewqA 765 -31.56 -7.45 1.38e+01 1dl5A 317 -33.02 -7.44 1.39e+01 1yub 245 -28.77 -7.40 1.42e+01 1egr 85 -26.78 -7.40 1.42e+01 1b0zA 445 -32.38 -7.40 1.42e+01 2pgi 445 -32.38 -7.40 1.42e+01 1llfA 534 -32.29 -7.39 1.43e+01 1i7qB 193 -32.15 -7.39 1.43e+01 1cleA 534 -32.37 -7.38 1.44e+01 1hkcA 917 -34.94 -7.38 1.44e+01 1yveJ 524 -33.66 -7.35 1.47e+01 1i50C 318 -32.04 -7.32 1.49e+01 1bw0A 416 -31.95 -7.31 1.50e+01 1aj8A 371 -30.16 -7.30 1.51e+01 1fdi 715 -34.59 -7.30 1.51e+01 1krhA 338 -30.85 -7.28 1.53e+01 1kv8A 216 -32.07 -7.28 1.53e+01 4ts1A 319 -32.37 -7.21 1.59e+01 1hkbA 917 -34.87 -7.19 1.61e+01 1ekxA 311 -33.20 -7.18 1.62e+01 1dz3A 130 -30.86 -7.14 1.65e+01 1h3fA 432 -31.99 -7.13 1.66e+01 1f61A 429 -31.31 -7.03 1.77e+01 1spa 396 -32.79 -7.03 1.77e+01 1e3sA 261 -31.72 -7.02 1.78e+01 1glcG 501 -30.22 -7.01 1.79e+01 1dbwA 126 -30.36 -7.01 1.79e+01 1bf6A 291 -29.51 -6.98 1.82e+01 7aatA 401 -32.54 -6.97 1.84e+01 1b2rA 304 -31.00 -6.95 1.86e+01 1oaoA 674 -32.53 -6.91 1.90e+01 1d02A 202 -28.53 -6.89 1.93e+01 1exnB 290 -29.77 -6.87 1.94e+01 1bu6O 501 -29.85 -6.87 1.94e+01 1crl 534 -31.59 -6.84 1.98e+01 1g6hA 257 -30.43 -6.84 1.99e+01 1fl2A 310 -31.00 -6.77 2.06e+01 1skyB 502 -30.86 -6.76 2.07e+01 1qh0A 295 -31.60 -6.76 2.08e+01 1io0A 185 -27.09 -6.76 2.08e+01 1ccwA 137 -31.71 -6.75 2.09e+01 1b8oA 284 -29.44 -6.74 2.11e+01 1evlA 401 -31.34 -6.72 2.13e+01 1cf2O 337 -30.60 -6.71 2.14e+01 1e7wA 291 -30.15 -6.71 2.15e+01 1ofgA 381 -29.28 -6.69 2.17e+01 1uayA 242 -30.13 -6.67 2.20e+01 1taq 832 -36.05 -6.65 2.22e+01 1pbn 289 -29.12 -6.63 2.25e+01 1a98A 152 -30.35 -6.62 2.26e+01 1nnsA 326 -31.28 -6.62 2.27e+01 3pnp 289 -29.22 -6.61 2.28e+01 1j9yA 385 -33.33 -6.60 2.30e+01 1dapA 320 -30.16 -6.59 2.31e+01 1go2A 304 -30.64 -6.58 2.31e+01 1d1qA 161 -27.78 -6.57 2.34e+01 1grvB 182 -28.37 -6.56 2.34e+01 1ixh 321 -30.45 -6.56 2.35e+01 1jb9A 316 -31.88 -6.52 2.40e+01 1mldA 314 -31.20 -6.52 2.40e+01 1dgkN 917 -33.89 -6.49 2.44e+01 1ba1 386 -30.58 -6.47 2.48e+01 1eokA 290 -32.81 -6.44 2.52e+01 1bwzA 274 -28.40 -6.42 2.55e+01 1f8mA 429 -31.45 -6.42 2.55e+01 1esmA 316 -29.73 -6.41 2.56e+01 3dapA 320 -30.18 -6.39 2.60e+01 1h6dA 433 -29.49 -6.38 2.62e+01 1gwyA 175 -27.07 -6.38 2.62e+01 1hmpA 217 -30.47 -6.35 2.67e+01 1o4vA 183 -31.58 -6.33 2.70e+01 1gkuB 1054 -34.12 -6.32 2.71e+01 1jh6A 189 -26.89 -6.32 2.72e+01 1dg9A 157 -26.80 -6.31 2.73e+01 1i4wA 353 -31.24 -6.30 2.74e+01 1czaN 917 -33.74 -6.29 2.77e+01 1jq5A 370 -30.34 -6.29 2.77e+01 1cdzA 96 -25.37 -6.28 2.79e+01 1tpt 440 -35.05 -6.25 2.83e+01 1g5rA 196 -30.98 -6.25 2.84e+01 1g5tA 196 -30.98 -6.25 2.84e+01 1inp 400 -30.52 -6.23 2.86e+01 1fgxA 288 -30.26 -6.22 2.88e+01 2kfnA 605 -30.08 -6.21 2.90e+01 1mumA 295 -30.20 -6.21 2.91e+01 1nykA 165 -27.30 -6.20 2.92e+01 1qfnA 85 -26.03 -6.20 2.92e+01 1vpt 348 -33.18 -6.18 2.96e+01 1h6pA 203 -26.76 -6.17 2.98e+01 1iazA 179 -26.14 -6.15 3.01e+01 1j8mF 297 -31.76 -6.15 3.02e+01 1ortA 335 -29.56 -6.14 3.03e+01 3minB 522 -31.97 -6.13 3.05e+01 1m1nB 522 -31.99 -6.12 3.08e+01 1jqaA 370 -30.10 -6.08 3.15e+01 1f06A 320 -29.64 -6.07 3.18e+01 1ep3B 262 -29.11 -6.06 3.18e+01 1qhaA 917 -33.65 -6.06 3.19e+01 1kq8A 100 -27.23 -6.05 3.20e+01 1klpA 115 -27.14 -6.05 3.20e+01 1nw1A 429 -30.30 -6.05 3.20e+01 1gox 370 -29.11 -6.02 3.26e+01 1yrgA 385 -28.68 -6.01 3.29e+01 1a8p 258 -28.95 -6.01 3.29e+01 1lv7A 257 -31.72 -6.00 3.31e+01 1n2zA 245 -29.54 -5.98 3.35e+01 1v39 322 -33.41 -5.97 3.37e+01 1vp9 322 -33.41 -5.97 3.37e+01 1cd9C 175 -26.33 -5.95 3.41e+01 1o20A 427 -32.31 -5.95 3.42e+01 1kay 381 -30.02 -5.93 3.45e+01 1pztA 286 -29.95 -5.92 3.48e+01 1gqzA 274 -27.80 -5.90 3.52e+01 1ehiA 377 -28.95 -5.89 3.54e+01 1scuA 288 -30.90 -5.89 3.55e+01 1jjfA 268 -29.22 -5.88 3.56e+01 1pjcA 361 -29.09 -5.87 3.59e+01 1dn1A 594 -34.43 -5.84 3.65e+01 1jn8B 273 -29.90 -5.84 3.66e+01 1ltoA 245 -27.69 -5.82 3.70e+01 2napA 723 -33.01 -5.81 3.73e+01 1gnxA 479 -29.11 -5.78 3.81e+01 1nulA 152 -28.88 -5.77 3.82e+01 1reqA 727 -31.64 -5.75 3.86e+01 1nmmB 286 -29.91 -5.74 3.90e+01 1e2uA 553 -30.76 -5.70 3.99e+01