% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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.YDL103C.t2k-100-30-str2 Host: farm02 Sat Nov 13 01:33:15 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL1/YDL103C % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YDL103C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL103C.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10735 sequences, 2539893 residues, 478 nodes, 508.55 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.2930) * Reverse)^tau(=0.7822))) % 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 1vm8A 534 -493.80 -479.28 4.67e-63 1jv1A 505 -486.52 -472.22 2.72e-62 1g97A 459 -59.06 -44.91 4.14e-07 1hm9A 468 -57.53 -42.97 9.34e-07 1fxjA 331 -46.68 -32.44 9.04e-05 1hv9A 456 -46.91 -31.93 1.14e-04 1fwyA 331 -44.25 -29.87 2.89e-04 1jykA 254 -37.42 -24.31 3.86e-03 1i52A 236 -36.32 -22.77 8.09e-03 1q7zA 566 -38.35 -20.29 2.73e-02 1whtB 153 -30.98 -19.48 4.08e-02 1whsB 153 -30.98 -19.48 4.09e-02 1bcsB 160 -30.93 -19.30 4.46e-02 1e5kA 201 -29.59 -19.21 4.67e-02 1r6xA 395 -30.53 -18.44 6.89e-02 1tzfA 259 -30.41 -17.41 1.17e-01 1g8fA 511 -30.33 -17.17 1.32e-01 1f60A 458 -35.38 -16.49 1.88e-01 1h5rA 293 -31.45 -16.30 2.08e-01 1o04A 500 -33.28 -15.96 2.48e-01 1g0rA 293 -30.63 -15.83 2.64e-01 1fxoA 293 -30.95 -15.78 2.72e-01 2reb 352 -29.79 -15.37 3.37e-01 1nhp 447 -29.89 -15.24 3.62e-01 1mc3A 296 -29.20 -15.11 3.87e-01 1gq2A 555 -31.27 -14.91 4.30e-01 1joa 447 -29.23 -14.82 4.53e-01 1mp4A 292 -29.53 -14.71 4.80e-01 1nhs 447 -29.63 -14.60 5.07e-01 1wndA 495 -28.54 -14.06 6.80e-01 1f7uA 607 -30.00 -13.97 7.10e-01 1gqoQ 143 -24.40 -13.94 7.22e-01 1gqoG 143 -24.37 -13.93 7.28e-01 1gqoB 143 -24.64 -13.88 7.49e-01 1gqoL 143 -24.23 -13.85 7.60e-01 1gthA 1025 -40.05 -13.78 7.90e-01 1gqoE 143 -24.32 -13.77 7.91e-01 1gqoM 143 -24.22 -13.73 8.11e-01 1u94A 356 -27.74 -13.65 8.45e-01 1gqoR 143 -24.36 -13.60 8.67e-01 1eudB 396 -28.14 -13.55 8.91e-01 1k7kA 221 -24.41 -13.51 9.13e-01 1gqoF 143 -24.23 -13.51 9.14e-01 1vgwA 231 -27.12 -13.47 9.33e-01 1gteD 1025 -39.77 -13.39 9.72e-01 1gqoS 143 -23.91 -13.39 9.74e-01 1gteA 1025 -39.15 -13.08 1.16e+00 1h7xD 1025 -39.14 -13.07 1.16e+00 1rzrA 332 -26.74 -13.04 1.18e+00 1gthB 1025 -39.46 -13.02 1.19e+00 1o0sA 605 -28.00 -12.89 1.28e+00 1h7wD 1025 -39.12 -12.78 1.36e+00 1gqoH 143 -23.47 -12.76 1.37e+00 1h7wA 1025 -39.16 -12.75 1.38e+00 1v93A 296 -25.60 -12.75 1.38e+00 1gthC 1025 -38.62 -12.56 1.54e+00 1h7wB 1025 -38.91 -12.47 1.61e+00 1h7xB 1025 -38.49 -12.43 1.65e+00 1eucB 396 -27.17 -12.29 1.78e+00 1fr9A 194 -22.85 -12.27 1.80e+00 1h7xC 1025 -38.25 -12.25 1.82e+00 1bd3A 243 -25.29 -12.25 1.82e+00 1he2A 206 -23.65 -12.08 1.99e+00 1jqnA 883 -29.10 -12.07 2.01e+00 1gqoD 143 -22.50 -12.03 2.06e+00 1gqoU 143 -22.50 -11.92 2.18e+00 1h7xA 1025 -38.05 -11.91 2.20e+00 1qumA 285 -24.20 -11.90 2.21e+00 1j7xA 302 -23.86 -11.82 2.31e+00 1ig3A 263 -23.96 -11.82 2.31e+00 1gqoV 143 -22.36 -11.81 2.32e+00 1gvoA 364 -23.71 -11.75 2.41e+00 1qtwA 285 -24.48 -11.74 2.42e+00 1gqoO 143 -22.37 -11.67 2.52e+00 1tv8A 340 -26.97 -11.61 2.59e+00 1gqoJ 143 -22.05 -11.60 2.61e+00 1gqoC 143 -22.05 -11.55 2.69e+00 1gt8D 1025 -38.47 -11.53 2.72e+00 1tq8A 163 -23.15 -11.53 2.72e+00 1gqoK 143 -22.29 -11.52 2.74e+00 1lt8A 406 -23.92 -11.51 2.76e+00 1h61A 364 -23.48 -11.49 2.78e+00 1vyrA 364 -23.47 -11.49 2.78e+00 1v4sA 455 -26.53 -11.41 2.91e+00 1hyeA 313 -31.28 -11.30 3.09e+00 1gqoY 143 -21.96 -11.27 3.14e+00 1gt8B 1025 -37.65 -11.25 3.18e+00 1vypX 364 -23.14 -11.23 3.22e+00 1gqoN 143 -22.05 -11.22 3.25e+00 1gt8C 1025 -37.28 -11.18 3.32e+00 1ge8A 249 -22.73 -11.16 3.35e+00 1dhs 344 -24.31 -11.09 3.48e+00 1rlzA 369 -24.28 -11.04 3.59e+00 1gqoI 143 -21.67 -10.96 3.76e+00 1hh1A 143 -24.03 -10.95 3.77e+00 1gqoX 143 -21.75 -10.89 3.91e+00 1hdoA 206 -22.34 -10.80 4.12e+00 3bamB 213 -23.22 -10.63 4.53e+00 1jpmA 366 -26.50 -10.59 4.63e+00 1gqoP 143 -21.36 -10.54 4.77e+00 1gqoT 143 -20.88 -10.51 4.84e+00 1tkkA 366 -26.76 -10.48 4.93e+00 1qc7A 101 -24.44 -10.48 4.94e+00 1vjrA 271 -22.36 -10.45 5.01e+00 1mo9A 523 -25.70 -10.33 5.37e+00 1ig0A 319 -22.43 -10.33 5.39e+00 1cf9A 753 -26.14 -10.29 5.51e+00 1dbqA 289 -23.51 -10.28 5.54e+00 1lvwA 295 -28.01 -10.25 5.62e+00 1lbqA 362 -24.74 -10.24 5.68e+00 1s4nA 348 -24.15 -10.23 5.69e+00 1p80A 753 -25.70 -10.23 5.70e+00 3bamA 213 -22.87 -10.22 5.74e+00 1ps9A 671 -28.72 -10.09 6.17e+00 1qwgA 251 -24.36 -10.08 6.20e+00 1iu8A 206 -23.58 -10.02 6.43e+00 1gthD 1025 -36.28 -10.02 6.44e+00 1eulA 994 -35.48 -10.02 6.44e+00 1gt8A 1025 -36.47 -10.01 6.46e+00 1bs2A 607 -26.17 -10.00 6.50e+00 1g19A 350 -25.95 -10.00 6.51e+00 1u2zA 433 -23.86 -9.99 6.52e+00 1c3pA 375 -26.35 -9.99 6.53e+00 1vl1A 232 -26.31 -9.97 6.63e+00 1su4A 994 -34.66 -9.96 6.66e+00 1cqqA 180 -20.55 -9.95 6.70e+00 2gbp 309 -22.44 -9.88 6.96e+00 1hmpA 217 -25.61 -9.87 7.00e+00 1vicA 262 -22.75 -9.85 7.11e+00 1d1gA 168 -21.41 -9.76 7.46e+00 1pwhA 327 -25.07 -9.76 7.47e+00 1gca 309 -21.53 -9.71 7.69e+00 1cz3A 168 -21.25 -9.67 7.86e+00 1qapA 296 -21.21 -9.57 8.37e+00 1qr6A 584 -26.42 -9.53 8.57e+00 1rpjA 288 -23.22 -9.48 8.81e+00 1pbtA 244 -25.99 -9.46 8.90e+00 1rj9A 304 -24.61 -9.44 9.02e+00 1rvv1 154 -24.33 -9.42 9.15e+00 1rvvA 154 -24.33 -9.42 9.15e+00 1geqA 248 -23.43 -9.41 9.15e+00 1ia9A 280 -21.03 -9.39 9.26e+00 1ubeA 349 -24.22 -9.39 9.27e+00 1u9cA 224 -21.36 -9.38 9.36e+00 1qb4A 883 -26.08 -9.37 9.39e+00 1b3qA 379 -24.89 -9.36 9.45e+00 1jmsA 381 -22.33 -9.34 9.56e+00 1lfo 128 -21.07 -9.33 9.63e+00 1j8yF 297 -26.06 -9.26 9.99e+00 1sxgA 280 -23.37 -9.26 1.00e+01 1pfkA 320 -26.67 -9.24 1.02e+01 1npdA 288 -22.20 -9.20 1.03e+01 1bd0A 388 -20.49 -9.16 1.07e+01 1ad3A 452 -24.86 -9.10 1.10e+01 1muwA 386 -22.73 -9.10 1.10e+01 1ur4A 399 -21.72 -9.09 1.11e+01 2scuB 388 -25.16 -9.07 1.12e+01 1iz5A 249 -20.76 -9.05 1.13e+01 1unkA 87 -22.40 -9.04 1.14e+01 1jm1A 204 -20.48 -9.02 1.15e+01 1rpxA 230 -23.40 -9.02 1.15e+01 1j8mF 297 -25.49 -8.99 1.17e+01 1e19A 314 -23.41 -8.98 1.18e+01 2pfkA 320 -25.98 -8.98 1.18e+01 1ayl 541 -22.99 -8.96 1.19e+01 1gw9A 388 -23.19 -8.95 1.20e+01 1rdr 461 -22.91 -8.92 1.22e+01 1fs5A 266 -22.22 -8.90 1.24e+01 1i0lA 221 -22.54 -8.89 1.25e+01 1xdyA 298 -19.41 -8.87 1.26e+01 1uumA 372 -23.97 -8.86 1.27e+01 1fiy 883 -25.84 -8.85 1.28e+01 4xiaA 393 -22.11 -8.85 1.28e+01 1n82A 331 -22.36 -8.83 1.29e+01 1tc1A 220 -22.86 -8.82 1.30e+01 1w3iA 293 -22.84 -8.80 1.31e+01 1l8aA 886 -29.17 -8.79 1.32e+01 1bykA 255 -21.79 -8.79 1.32e+01 1jqeA 292 -24.37 -8.77 1.34e+01 1vjoA 393 -24.53 -8.75 1.35e+01 1php 394 -22.23 -8.75 1.36e+01 1hxxA 340 -21.25 -8.74 1.36e+01 1jx7A 117 -20.33 -8.73 1.37e+01 2omf 340 -21.19 -8.72 1.38e+01 1frb 315 -20.58 -8.72 1.38e+01 1cei 94 -21.97 -8.71 1.39e+01 1vi2A 300 -21.60 -8.70 1.40e+01 1hnjA 317 -21.55 -8.69 1.40e+01 1e43A 483 -20.11 -8.69 1.40e+01 1o20A 427 -22.92 -8.67 1.42e+01 1e5xA 486 -23.76 -8.65 1.43e+01 1sftA 388 -19.84 -8.63 1.45e+01 1odfA 290 -28.67 -8.56 1.52e+01 1v4vA 376 -22.05 -8.56 1.52e+01 1vpwA 340 -22.13 -8.56 1.52e+01 1a27 289 -22.34 -8.52 1.55e+01 1k0sA 151 -22.22 -8.51 1.57e+01 1bzyA 217 -25.32 -8.49 1.58e+01 1sesA 421 -23.12 -8.49 1.58e+01 1jtvA 327 -23.08 -8.48 1.60e+01 1deaA 266 -21.76 -8.47 1.60e+01 1qmvA 197 -22.14 -8.46 1.61e+01 1iuqA 367 -22.59 -8.44 1.63e+01 1juk 248 -19.85 -8.44 1.63e+01 1rljA 139 -18.97 -8.43 1.64e+01 1fmcA 255 -22.94 -8.43 1.64e+01 1qo2A 241 -19.15 -8.42 1.65e+01 1igs 248 -19.62 -8.42 1.65e+01 1a53 247 -19.64 -8.38 1.69e+01 6acn 754 -27.34 -8.37 1.70e+01 1fs0G 230 -21.93 -8.37 1.70e+01 1amj 754 -27.14 -8.37 1.70e+01 1ksiB 642 -24.53 -8.36 1.71e+01 1bdg 451 -23.21 -8.36 1.71e+01 1tyfA 193 -22.67 -8.35 1.72e+01 1ksiA 642 -24.45 -8.34 1.73e+01 1nxiA 132 -21.34 -8.33 1.74e+01 1fds 327 -22.76 -8.33 1.75e+01 1c14A 262 -20.23 -8.29 1.78e+01 1gewA 356 -19.81 -8.24 1.83e+01 1ac5 483 -25.21 -8.23 1.85e+01 1qlmA 316 -22.05 -8.20 1.89e+01 1nu5A 370 -20.75 -8.20 1.89e+01 1fgxA 288 -20.35 -8.18 1.91e+01 1qsgA 265 -20.26 -8.17 1.92e+01 1k30A 368 -22.55 -8.16 1.93e+01 1i3kA 348 -23.05 -8.16 1.93e+01 1fsfA 266 -21.12 -8.15 1.94e+01 1pv9A 348 -22.49 -8.14 1.95e+01 1n99A 166 -19.99 -8.14 1.96e+01 1byrA 155 -20.40 -8.13 1.96e+01 1e6qM 501 -21.96 -8.13 1.96e+01 1qf6A 642 -22.71 -8.13 1.97e+01 1kwaA 88 -19.11 -8.13 1.97e+01 1o0uA 429 -23.31 -8.13 1.97e+01 1tluA 130 -18.76 -8.11 1.99e+01 1p3wA 404 -21.71 -8.10 2.01e+01 1bam 213 -21.41 -8.08 2.03e+01 1e4mM 501 -22.16 -8.04 2.07e+01 1tk1A 260 -20.56 -8.04 2.08e+01 1uurA 473 -22.30 -8.02 2.10e+01 1esgA 213 -20.30 -8.01 2.11e+01 1dpjA 329 -20.67 -8.01 2.11e+01 1ak5 503 -25.85 -8.01 2.12e+01 1fdt 327 -22.02 -8.00 2.13e+01 1gc5A 467 -21.60 -7.99 2.14e+01 1tjyA 316 -20.07 -7.97 2.16e+01 1vkyA 347 -22.03 -7.97 2.17e+01 1hrkA 359 -24.44 -7.96 2.18e+01 1jn8B 273 -20.21 -7.95 2.20e+01 2xis 387 -22.10 -7.94 2.20e+01 3pbgA 468 -22.78 -7.94 2.20e+01 1j8wB 273 -20.17 -7.93 2.21e+01 1e70M 501 -22.04 -7.93 2.22e+01 1i5rA 327 -21.57 -7.92 2.24e+01 1pbgA 468 -22.56 -7.84 2.34e+01 7acn 754 -26.87 -7.84 2.35e+01 1bs0A 384 -21.11 -7.83 2.36e+01 1qf9A 194 -21.59 -7.82 2.37e+01 1st9A 143 -18.85 -7.82 2.37e+01 1kxoA 184 -18.92 -7.82 2.37e+01 1dvoA 152 -19.98 -7.81 2.39e+01 1p5jA 372 -25.07 -7.80 2.40e+01 1ipiA 123 -19.53 -7.78 2.42e+01 8acn 754 -26.54 -7.77 2.45e+01 1vmaA 306 -28.71 -7.77 2.45e+01 1wpgA 994 -32.18 -7.77 2.45e+01 1uw4B 248 -22.66 -7.75 2.48e+01 1ji0A 240 -20.71 -7.73 2.51e+01 1eqcA 394 -21.82 -7.72 2.52e+01 1srrA 124 -22.15 -7.72 2.53e+01 1nf9A 207 -22.49 -7.71 2.54e+01 1k66A 149 -21.63 -7.68 2.58e+01 1be3A 446 -20.32 -7.68 2.58e+01 1f8yA 157 -20.50 -7.68 2.58e+01 1jkfA 533 -21.93 -7.68 2.59e+01 1nktA 922 -26.35 -7.67 2.60e+01 1bfd 528 -20.90 -7.67 2.60e+01 1ii7A 333 -20.78 -7.65 2.64e+01 1amp 291 -20.00 -7.65 2.64e+01 1vybA 238 -20.78 -7.64 2.65e+01 1szoA 257 -22.75 -7.61 2.70e+01 1q8iA 783 -22.65 -7.60 2.71e+01 1qg8A 255 -19.48 -7.59 2.73e+01 1j5vA 351 -19.42 -7.59 2.74e+01 1mnzA 388 -21.73 -7.57 2.76e+01 1httA 423 -21.36 -7.55 2.80e+01 9pap 212 -20.01 -7.55 2.81e+01 1xis 387 -21.70 -7.54 2.81e+01 4xis 387 -21.70 -7.54 2.81e+01 1b0jA 754 -27.15 -7.54 2.81e+01 1e8cA 498 -20.89 -7.54 2.82e+01 1eexB 224 -19.46 -7.54 2.82e+01 1cz1A 394 -21.74 -7.54 2.82e+01 1v95A 130 -18.62 -7.53 2.84e+01 1fdr 248 -19.41 -7.52 2.84e+01 2napA 723 -24.40 -7.51 2.88e+01 1ppjA 446 -21.20 -7.50 2.88e+01 1ewxA 146 -20.53 -7.50 2.89e+01 1wetA 340 -20.86 -7.46 2.95e+01 1kmnD 424 -20.89 -7.43 3.01e+01 1ig8A 486 -24.13 -7.43 3.02e+01 2tmdA 729 -25.82 -7.42 3.04e+01 5ukdA 194 -21.29 -7.41 3.05e+01 1h1nA 305 -20.30 -7.41 3.05e+01 1d5nA 205 -20.85 -7.41 3.06e+01 1m3sA 186 -21.33 -7.40 3.08e+01 1qpzA 340 -20.85 -7.39 3.09e+01 1fg7A 356 -18.96 -7.39 3.09e+01 1jhb 106 -20.67 -7.39 3.09e+01 1gv4A 528 -23.54 -7.38 3.12e+01 1fb6A 105 -18.82 -7.37 3.13e+01 1f8xA 157 -20.45 -7.36 3.16e+01 1h5yA 253 -21.42 -7.35 3.16e+01 1dioB 224 -19.23 -7.35 3.16e+01 1je5A 206 -19.14 -7.35 3.17e+01 1evlA 401 -22.71 -7.35 3.18e+01 1qsmA 152 -19.39 -7.34 3.19e+01 1sxjE 354 -22.20 -7.33 3.21e+01 1cvjB 190 -17.45 -7.30 3.26e+01 1pta 318 -18.84 -7.30 3.26e+01 1v77A 212 -18.75 -7.30 3.27e+01 1o6aA 96 -18.88 -7.28 3.30e+01 1gumA 222 -21.17 -7.26 3.34e+01 1eblA 317 -20.34 -7.24 3.38e+01 1t8qA 336 -18.90 -7.24 3.38e+01 1utyA 187 -19.09 -7.24 3.40e+01 1rhcA 330 -19.97 -7.24 3.40e+01 1qcrA 446 -19.92 -7.23 3.40e+01 1kzlA 208 -17.80 -7.23 3.41e+01 1lokA 291 -19.56 -7.23 3.41e+01 1kvnA 104 -18.25 -7.22 3.44e+01 1oalA 151 -18.76 -7.21 3.45e+01 1o8uA 257 -22.32 -7.20 3.48e+01 1eudA 311 -23.01 -7.20 3.48e+01 1fdyA 297 -24.42 -7.20 3.48e+01 1qg6A 261 -19.47 -7.20 3.48e+01 1d2nA 272 -24.81 -7.19 3.50e+01 1ceo 343 -19.64 -7.18 3.52e+01 1w3jA 468 -21.23 -7.16 3.56e+01 1iqyA 638 -23.21 -7.15 3.59e+01 1dysA 348 -19.37 -7.14 3.61e+01 1hd7A 318 -19.70 -7.13 3.62e+01 1gulA 222 -20.92 -7.13 3.64e+01 1ekxA 311 -19.79 -7.12 3.64e+01 1o5zA 442 -22.04 -7.12 3.65e+01 1e55A 512 -21.85 -7.12 3.65e+01 1hr6A 475 -21.33 -7.11 3.67e+01 1nzhA 282 -19.13 -7.11 3.67e+01 1djnA 729 -25.57 -7.10 3.69e+01 1khqA 212 -19.42 -7.09 3.73e+01 1ppn 212 -19.37 -7.03 3.86e+01 1gefA 123 -18.81 -7.01 3.90e+01 1oaoC 729 -31.53 -7.00 3.92e+01 1nnlA 225 -23.91 -7.00 3.93e+01 1k8kG 151 -22.87 -6.99 3.97e+01 1pujA 282 -21.89 -6.98 3.97e+01 1dik 874 -26.65 -6.98 3.98e+01 1f89A 291 -19.05 -6.98 3.98e+01 1eucA 311 -22.71 -6.98 3.99e+01