% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR218W.t2k-100-30-stride-ebghtl Host: farm16 Mon Jan 31 01:04:06 2005 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR218W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YGR218W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR218W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 11262 sequences, 2668995 residues, 1085 nodes, 1326.66 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 (=11000) sequences: % N / (1 + exp(-(lambda(=1.5677) * Reverse)^tau(=0.7513))) % 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 1qbkB 890 -492.44 -407.70 2.40e-52 1wa5C 960 -382.51 -283.03 5.34e-39 1w9cA 321 -312.13 -258.68 3.12e-36 1qgrA 876 -243.93 -138.94 1.77e-21 1ibrB 462 -174.09 -111.75 9.80e-18 1gw5B 591 -116.54 -43.46 4.85e-07 1b3uA 588 -114.78 -39.72 2.31e-06 1bk6A 422 -84.62 -32.95 4.28e-05 1wa5B 530 -87.71 -32.51 5.19e-05 1ee4A 423 -85.21 -32.36 5.56e-05 1bk5A 422 -83.46 -30.06 1.56e-04 1fiy 883 -90.24 -27.07 6.12e-04 1jqnA 883 -90.93 -26.97 6.41e-04 1gw5A 621 -105.32 -26.57 7.70e-04 1qb4A 883 -89.89 -26.31 8.70e-04 1bj5 585 -86.20 -23.58 3.16e-03 1ha2A 585 -84.89 -22.86 4.47e-03 1ao6A 585 -84.98 -22.34 5.76e-03 1w07A 659 -71.39 -22.18 6.23e-03 1n5uA 585 -86.41 -20.93 1.15e-02 1jdhA 529 -87.70 -20.35 1.54e-02 1e7aA 585 -82.29 -20.02 1.81e-02 1i7wA 538 -87.73 -19.92 1.90e-02 2sqcA 631 -70.37 -19.86 1.96e-02 1ldjA 760 -80.34 -19.34 2.54e-02 1jb0A 755 -71.76 -19.21 2.72e-02 1sqc 631 -70.05 -18.98 3.05e-02 1avc 673 -85.57 -17.81 5.54e-02 1g3jA 532 -86.77 -17.40 6.84e-02 1jk0B 345 -52.63 -17.40 6.86e-02 2btvA 901 -49.79 -16.96 8.62e-02 1kxpD 458 -72.46 -16.84 9.18e-02 1miwA 404 -40.11 -15.67 1.70e-01 1ehkA 562 -71.91 -15.17 2.21e-01 1l7vA 326 -50.78 -14.96 2.48e-01 5eat 548 -72.11 -14.55 3.10e-01 1v54A 514 -72.92 -13.57 5.28e-01 1j78A 458 -64.31 -13.44 5.67e-01 2occA 514 -71.46 -13.27 6.22e-01 1oohA 126 -31.00 -13.23 6.36e-01 1eia 207 -37.14 -12.87 7.79e-01 1jk0A 419 -49.59 -11.85 1.39e+00 1a36A 592 -48.35 -11.82 1.40e+00 1xikA 375 -53.70 -11.80 1.42e+00 1upkA 341 -61.42 -11.67 1.53e+00 1afrA 345 -62.05 -11.59 1.61e+00 1d8cA 723 -47.94 -11.55 1.64e+00 1kgnA 329 -53.22 -11.39 1.80e+00 1oyzA 280 -49.31 -11.36 1.83e+00 1lj8A 493 -40.35 -11.34 1.85e+00 1jqcA 375 -54.53 -11.30 1.89e+00 1k4tA 592 -45.81 -11.28 1.92e+00 1upvA 257 -37.50 -11.25 1.95e+00 1mxrA 375 -54.54 -11.06 2.18e+00 1ribA 375 -54.93 -11.05 2.19e+00 1e2gA 215 -25.72 -10.89 2.40e+00 1nfiC 301 -28.11 -10.81 2.51e+00 1n46A 258 -40.05 -10.81 2.52e+00 1e9cA 215 -25.61 -10.77 2.58e+00 1ezfA 340 -57.74 -10.72 2.65e+00 2eiaB 206 -35.58 -10.72 2.65e+00 1mukA 1267 -52.90 -10.69 2.69e+00 1e2fA 215 -25.53 -10.65 2.75e+00 1bob 320 -27.37 -10.64 2.78e+00 1e9eA 215 -25.40 -10.63 2.79e+00 3bct 457 -70.70 -10.59 2.86e+00 1biqA 375 -55.29 -10.50 3.02e+00 1taq 832 -39.95 -10.44 3.12e+00 1e8yA 966 -58.02 -10.43 3.13e+00 1tzvA 142 -41.04 -10.37 3.26e+00 1ulyA 192 -34.00 -10.34 3.31e+00 1mv8A 436 -34.20 -10.33 3.33e+00 1ash 150 -37.05 -10.32 3.36e+00 1p7tA 731 -45.90 -10.30 3.38e+00 1nn5A 215 -25.51 -10.29 3.41e+00 1nktA 922 -69.16 -10.27 3.45e+00 1oq9A 363 -59.93 -10.23 3.54e+00 1y14A 187 -31.13 -10.16 3.69e+00 1e8xA 961 -56.20 -10.15 3.70e+00 1kktA 511 -41.39 -10.13 3.75e+00 5eau 548 -69.35 -10.13 3.76e+00 1nc5A 373 -42.09 -10.07 3.88e+00 1ft1A 377 -52.45 -10.04 3.96e+00 1fchA 368 -52.67 -10.02 4.00e+00 2kfnA 605 -34.04 -9.94 4.20e+00 1ih7A 903 -57.55 -9.87 4.38e+00 1clqA 903 -57.78 -9.87 4.38e+00 1vnc 609 -52.18 -9.85 4.42e+00 1nfiA 301 -26.48 -9.75 4.71e+00 1sctB 151 -36.92 -9.75 4.72e+00 1dmtA 696 -51.22 -9.57 5.24e+00 1ljrA 244 -35.86 -9.53 5.36e+00 1guxA 218 -43.97 -9.47 5.55e+00 1g5hA 454 -27.60 -9.46 5.59e+00 1t7rA 269 -43.18 -9.45 5.63e+00 1jffA 451 -32.74 -9.44 5.67e+00 1m6nA 802 -64.93 -9.41 5.76e+00 1h3fA 432 -27.64 -9.37 5.92e+00 1dceB 331 -35.62 -9.36 5.92e+00 1n35A 1267 -51.85 -9.36 5.95e+00 1evyA 366 -31.64 -9.31 6.12e+00 1ae1A 273 -25.42 -9.29 6.20e+00 1t6jA 714 -47.92 -9.29 6.20e+00 1w4xA 542 -36.08 -9.28 6.25e+00 1m13A 316 -40.07 -9.25 6.33e+00 1rx0A 393 -42.53 -9.23 6.41e+00 1yfm 488 -41.97 -9.23 6.43e+00 1lshA 1056 -50.27 -9.13 6.81e+00 1lnh 857 -47.51 -9.10 6.96e+00 1ih8A 271 -29.64 -9.09 7.00e+00 1tbmA 326 -53.43 -9.08 7.03e+00 1j5sA 463 -36.69 -9.08 7.06e+00 1gaxA 862 -59.30 -9.02 7.32e+00 1o7nB 194 -21.60 -9.01 7.35e+00 1h12A 405 -30.98 -8.99 7.44e+00 1r1hA 696 -48.42 -8.96 7.59e+00 1jsqA 582 -42.65 -8.92 7.75e+00 1nrlA 316 -39.80 -8.90 7.88e+00 1kpkA 473 -55.00 -8.90 7.88e+00 1wmuA 141 -34.99 -8.88 7.96e+00 1nekC 129 -33.05 -8.86 8.05e+00 1a8i 842 -50.53 -8.85 8.12e+00 1va6A 518 -37.25 -8.83 8.20e+00 1tubA 440 -31.93 -8.83 8.21e+00 1rtwA 220 -45.46 -8.77 8.52e+00 1vns 609 -51.75 -8.75 8.61e+00 1d8dA 377 -52.97 -8.72 8.77e+00 1oywA 523 -30.66 -8.69 8.94e+00 1i4sA 147 -36.18 -8.68 8.99e+00 1vjoA 393 -30.06 -8.61 9.36e+00 1kplA 473 -62.98 -8.59 9.50e+00 1k7wA 468 -40.54 -8.51 9.98e+00 1otsA 465 -64.35 -8.51 9.99e+00 1rec 201 -28.46 -8.51 9.99e+00 1hcuA 503 -38.27 -8.50 1.01e+01 1q6hA 224 -30.42 -8.49 1.01e+01 1spvA 184 -22.96 -8.44 1.04e+01 1tf5A 844 -64.21 -8.43 1.05e+01 1dcnD 436 -39.97 -8.42 1.05e+01 1htjF 210 -37.51 -8.41 1.06e+01 1dn1A 594 -35.32 -8.40 1.07e+01 1kzhA 555 -41.27 -8.40 1.07e+01 1hskA 326 -28.03 -8.31 1.13e+01 1irxA 523 -51.29 -8.29 1.14e+01 1jcqA 382 -52.42 -8.28 1.15e+01 1kv9A 668 -52.22 -8.24 1.18e+01 1c1kA 217 -35.87 -8.23 1.18e+01 1ndoB 194 -21.25 -8.23 1.19e+01 1eg9B 194 -21.20 -8.20 1.21e+01 1ld8A 382 -52.77 -8.17 1.23e+01 1b8fA 509 -36.84 -8.17 1.23e+01 1hy0A 466 -39.60 -8.16 1.24e+01 1riqA 465 -46.93 -8.12 1.27e+01 1tjvA 474 -40.52 -8.11 1.28e+01 1rovA 857 -47.01 -8.08 1.30e+01 1kb9G 125 -24.97 -8.06 1.32e+01 1kyoG 126 -24.82 -8.02 1.36e+01 1vp4A 425 -35.70 -8.01 1.36e+01 1fqvD 149 -28.78 -7.98 1.39e+01 1e3hA 757 -41.07 -7.96 1.41e+01 1aueA 100 -31.47 -7.95 1.42e+01 1ornA 226 -31.57 -7.93 1.43e+01 1up8A 598 -43.04 -7.92 1.44e+01 1vlpA 441 -28.94 -7.90 1.46e+01 1m33A 258 -22.38 -7.90 1.46e+01 1phk 298 -26.77 -7.87 1.49e+01 1r9kA 172 -31.99 -7.85 1.51e+01 1ezvF 125 -24.73 -7.83 1.53e+01 1sh0A 510 -33.31 -7.76 1.59e+01 1jqiA 388 -33.76 -7.75 1.60e+01 1peqA 714 -30.71 -7.74 1.61e+01 1h3nA 878 -64.87 -7.74 1.61e+01 1n93X 375 -31.48 -7.74 1.62e+01 1vh4A 435 -22.27 -7.70 1.66e+01 1clc 639 -45.82 -7.68 1.68e+01 1a6dA 545 -44.72 -7.66 1.70e+01 1sz2A 332 -27.96 -7.65 1.72e+01 1f75A 249 -24.55 -7.64 1.72e+01 1vdkA 466 -41.88 -7.63 1.73e+01 1eco 136 -32.19 -7.62 1.74e+01 1vljA 407 -45.72 -7.62 1.74e+01 1uor 585 -40.81 -7.60 1.77e+01 1tqnA 486 -42.76 -7.57 1.80e+01 1fqvJ 149 -28.31 -7.56 1.82e+01 1j33A 335 -25.36 -7.54 1.83e+01 1lfpA 249 -26.37 -7.51 1.86e+01 1kyqA 274 -29.21 -7.50 1.88e+01 1brwA 433 -35.91 -7.50 1.89e+01 1i37A 260 -40.24 -7.47 1.92e+01 1qhbA 596 -40.69 -7.46 1.93e+01 1ecd 136 -32.12 -7.46 1.93e+01 1h5uA 842 -48.37 -7.45 1.94e+01 1xlyA 234 -42.73 -7.43 1.97e+01 1xfhA 422 -58.80 -7.42 1.98e+01 1itkA 731 -59.19 -7.40 2.00e+01 1eca 136 -32.33 -7.40 2.00e+01 1jfaA 374 -54.32 -7.40 2.01e+01 1jvpP 298 -24.42 -7.36 2.06e+01 1tzjA 338 -28.09 -7.35 2.07e+01 1omrA 201 -29.12 -7.33 2.09e+01 1ucrA 78 -20.40 -7.33 2.10e+01 1qhtA 775 -48.34 -7.33 2.10e+01 3tmkA 216 -29.50 -7.32 2.11e+01 1mpgA 282 -25.68 -7.30 2.14e+01 1dcnA 424 -38.13 -7.29 2.15e+01 1wekA 217 -27.03 -7.29 2.15e+01 1q87A 221 -26.33 -7.29 2.15e+01 1vheA 373 -32.24 -7.29 2.16e+01 1auwA 468 -41.25 -7.28 2.16e+01 1vmeA 410 -32.16 -7.26 2.20e+01 1lw7A 365 -25.99 -7.24 2.22e+01 1fo3A 460 -37.05 -7.24 2.22e+01 1u6mA 199 -22.01 -7.22 2.25e+01 2tmkA 216 -28.87 -7.21 2.26e+01 1iv8A 720 -50.26 -7.20 2.28e+01 1jcrA 377 -52.79 -7.19 2.30e+01 1ks8A 433 -38.49 -7.14 2.37e+01 1mgn 154 -34.90 -7.13 2.39e+01 1aorA 605 -49.81 -7.11 2.41e+01 1tml 286 -22.56 -7.10 2.43e+01 1fqiA 147 -27.75 -7.07 2.48e+01 1j6oA 268 -23.69 -7.06 2.49e+01 1vpqA 273 -22.19 -7.06 2.49e+01 1u5kA 244 -25.38 -7.04 2.52e+01 1bbhA 131 -30.62 -7.04 2.53e+01 1lvk 762 -34.23 -7.03 2.54e+01 1ceo 343 -26.54 -7.02 2.55e+01 1tn6A 382 -51.88 -7.02 2.56e+01 1cb8A 678 -47.85 -7.02 2.56e+01 1kqpA 271 -27.56 -7.01 2.57e+01 3erk 364 -25.36 -7.00 2.59e+01 1exbA 332 -24.61 -7.00 2.60e+01 1lrv 244 -22.94 -6.99 2.61e+01 2nsyA 271 -27.54 -6.99 2.61e+01 1nsyA 271 -27.54 -6.98 2.62e+01 1q18A 332 -27.32 -6.95 2.68e+01 1i1qA 520 -22.41 -6.93 2.70e+01 1cpq 129 -25.53 -6.93 2.71e+01 1pprM 312 -44.28 -6.93 2.71e+01 1nxcA 478 -37.01 -6.93 2.71e+01 1c3cA 429 -47.67 -6.92 2.73e+01 1zymA 258 -29.27 -6.92 2.73e+01 1f0yA 302 -25.90 -6.89 2.79e+01 1mnd 762 -32.56 -6.87 2.83e+01 1h4vB 421 -23.88 -6.86 2.83e+01 1f7uA 607 -55.33 -6.86 2.84e+01 1khoA 370 -35.18 -6.85 2.86e+01 1hm2A 700 -47.73 -6.83 2.89e+01 1a04A 215 -23.18 -6.83 2.90e+01 1j79A 347 -20.81 -6.82 2.91e+01 1bc5A 269 -22.65 -6.82 2.92e+01 1qqfA 277 -38.54 -6.81 2.93e+01 1d2nA 272 -21.23 -6.81 2.94e+01 1xqoA 256 -37.18 -6.80 2.95e+01 2hdhA 293 -25.73 -6.79 2.97e+01 1pme 380 -25.24 -6.78 2.98e+01 1h6pA 203 -38.72 -6.78 3.00e+01 1jfzA 154 -34.59 -6.77 3.02e+01 1r4wA 226 -27.50 -6.76 3.04e+01 1ewfA 456 -25.21 -6.74 3.07e+01 1qpzA 340 -24.63 -6.74 3.08e+01 1vmaA 306 -32.65 -6.73 3.10e+01 1ovnA 248 -26.92 -6.72 3.12e+01 1adjA 421 -23.94 -6.71 3.14e+01 1cec 343 -26.54 -6.71 3.14e+01 1oe9A 795 -40.05 -6.70 3.15e+01 2gsaA 432 -34.54 -6.69 3.18e+01 1f20A 435 -23.95 -6.68 3.19e+01 1qqcA 773 -46.71 -6.68 3.20e+01 1l6nA 289 -35.68 -6.66 3.23e+01 1gvnB 287 -30.71 -6.66 3.24e+01 1e7uA 961 -53.16 -6.66 3.24e+01 1anxA 319 -45.40 -6.64 3.28e+01 1nsgB 94 -29.68 -6.62 3.33e+01 3fapB 94 -29.68 -6.62 3.33e+01 1u3dA 509 -31.51 -6.62 3.33e+01 1af7 274 -22.43 -6.61 3.35e+01 1f5qB 252 -41.28 -6.57 3.43e+01 1uiuA 502 -22.24 -6.56 3.45e+01 1gai 472 -35.96 -6.56 3.46e+01 1qsgA 265 -21.91 -6.55 3.47e+01 1bzpA 153 -33.77 -6.55 3.48e+01 1gpb 842 -50.15 -6.54 3.50e+01 1ohuA 175 -31.81 -6.53 3.51e+01 1qkrA 188 -39.13 -6.50 3.59e+01 1vom 762 -32.71 -6.49 3.61e+01 1dr8B 344 -27.49 -6.49 3.62e+01 1wetA 340 -24.80 -6.48 3.65e+01 1xteA 154 -21.75 -6.46 3.70e+01 1vpwA 340 -24.65 -6.46 3.70e+01 1gggB 226 -21.29 -6.43 3.75e+01 153l 185 -27.13 -6.42 3.79e+01 1omhA 293 -20.20 -6.41 3.80e+01 1qrqA 325 -23.71 -6.39 3.87e+01 1pf4A 582 -35.11 -6.38 3.89e+01 1h6kA 757 -98.35 -6.38 3.90e+01 1bk0 331 -22.28 -6.36 3.94e+01 1odmA 331 -22.27 -6.36 3.94e+01 1cpt 412 -40.30 -6.35 3.96e+01 1d1dA 262 -30.22 -6.35 3.96e+01 1jwhC 215 -27.48 -6.35 3.97e+01 1t0qB 330 -47.50 -6.35 3.97e+01 1pw4A 451 -66.50 -6.35 3.98e+01