% 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.YGR218W.t2k-100-30-str Host: cc70 Tue Nov 12 18:41:44 2002 % 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.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 YGR218W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR218W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 1085 nodes, 823.89 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(=1.8572) * Reverse)^tau(=0.7223))) % 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 -502.55 -412.03 1.97e-49 1qgrA 876 -259.53 -145.49 1.20e-21 1ibrB 462 -190.26 -118.88 2.79e-18 1gw5B 591 -124.65 -45.31 1.56e-07 1b3uA 588 -115.18 -41.77 6.32e-07 1ee4A 423 -91.85 -35.52 8.17e-06 1bk5A 422 -90.89 -30.99 5.66e-05 1bk6A 422 -88.10 -30.21 7.96e-05 1gw5A 621 -110.01 -27.91 2.20e-04 1g3jA 532 -94.15 -25.17 7.68e-04 1i7wA 538 -93.36 -24.31 1.14e-03 1jdhA 529 -93.81 -24.26 1.17e-03 1fiy 883 -92.40 -22.10 3.24e-03 1ao6A 585 -93.54 -20.93 5.69e-03 1kxpD 458 -81.97 -20.48 7.08e-03 1qb4A 883 -91.80 -20.43 7.27e-03 1bj5 585 -93.60 -20.23 8.01e-03 1avc 673 -91.66 -19.66 1.06e-02 1e7aA 585 -94.51 -19.61 1.09e-02 1ha2A 585 -90.01 -19.12 1.38e-02 1ehkA 562 -77.14 -18.80 1.62e-02 2sqcA 631 -80.87 -18.21 2.19e-02 1sqc 631 -81.31 -17.79 2.70e-02 1jb0A 755 -79.42 -17.67 2.88e-02 5eat 548 -82.39 -17.64 2.92e-02 1j78A 458 -71.68 -17.36 3.37e-02 2btvA 901 -60.19 -17.30 3.46e-02 1jk0B 345 -57.07 -16.69 4.75e-02 1ldjA 760 -86.62 -16.22 6.08e-02 3bct 457 -77.75 -15.82 7.46e-02 1e8yA 966 -70.35 -15.02 1.14e-01 1lshA 1056 -60.89 -14.60 1.43e-01 1jqcA 375 -65.17 -14.38 1.61e-01 1biqA 375 -66.75 -14.32 1.66e-01 1l7vA 326 -57.32 -14.29 1.69e-01 1xikA 375 -64.69 -14.26 1.72e-01 1ribA 375 -65.05 -14.12 1.85e-01 1h6kA 757 -102.29 -13.03 3.36e-01 1d8cA 723 -60.57 -12.94 3.53e-01 1kgnA 329 -61.18 -12.63 4.20e-01 5eau 548 -77.60 -12.34 4.95e-01 1jk0A 419 -60.17 -12.19 5.37e-01 1fchA 368 -63.94 -12.10 5.66e-01 1e8xA 961 -68.13 -12.04 5.83e-01 1ljrA 244 -45.12 -11.88 6.39e-01 1eia 207 -47.01 -11.76 6.87e-01 2occA 514 -74.12 -11.67 7.21e-01 1dceB 331 -45.23 -11.62 7.41e-01 1glm 470 -49.20 -11.58 7.60e-01 1kpkA 473 -64.89 -11.41 8.38e-01 1ezfA 340 -62.62 -11.35 8.66e-01 1qsaA 618 -62.42 -11.21 9.37e-01 1fo3A 460 -49.64 -10.93 1.10e+00 1a36A 592 -58.22 -10.92 1.11e+00 1gai 472 -50.00 -10.87 1.14e+00 1h2vC 771 -99.96 -10.86 1.15e+00 1htjF 210 -47.09 -10.83 1.17e+00 1e2gA 215 -35.14 -10.82 1.18e+00 2eiaB 206 -44.81 -10.74 1.23e+00 1qrjB 199 -40.76 -10.71 1.26e+00 1jfaA 374 -66.04 -10.66 1.30e+00 1sctB 151 -45.92 -10.64 1.31e+00 1e9eA 215 -35.07 -10.60 1.34e+00 1e9cA 215 -35.07 -10.55 1.38e+00 1afrA 345 -71.22 -10.48 1.44e+00 1mmoD 512 -65.07 -10.45 1.47e+00 1a6dA 545 -59.19 -10.44 1.47e+00 1bob 320 -37.72 -10.44 1.47e+00 1c3d 294 -52.30 -10.43 1.48e+00 1guxA 218 -52.02 -10.24 1.66e+00 1rec 201 -38.68 -10.22 1.68e+00 1e2fA 215 -34.50 -10.15 1.75e+00 2kfnA 605 -44.42 -10.12 1.78e+00 1irxA 523 -60.21 -10.10 1.80e+00 1fqvJ 149 -39.32 -10.05 1.86e+00 1kktA 511 -52.81 -10.04 1.86e+00 1sly 618 -62.17 -10.04 1.87e+00 1gkmA 509 -47.72 -9.93 1.99e+00 1lnh 857 -63.60 -9.85 2.09e+00 1pprM 312 -53.81 -9.85 2.09e+00 1kiyA 374 -66.82 -9.84 2.10e+00 1j5sA 463 -49.51 -9.78 2.18e+00 1b8fA 509 -47.89 -9.66 2.34e+00 1dcnD 436 -53.98 -9.64 2.37e+00 1jfgA 374 -65.95 -9.54 2.52e+00 1vnc 609 -62.85 -9.52 2.55e+00 1pbwA 216 -43.29 -9.51 2.56e+00 1phk 298 -39.25 -9.49 2.60e+00 1ash 150 -46.37 -9.48 2.60e+00 1hy0A 466 -52.61 -9.44 2.68e+00 1fqvD 149 -38.66 -9.37 2.80e+00 1qhbA 596 -52.93 -9.36 2.81e+00 1vns 609 -62.86 -9.35 2.82e+00 1eco 136 -43.34 -9.30 2.92e+00 1clqA 903 -67.82 -9.23 3.03e+00 1l6nA 289 -46.99 -9.17 3.14e+00 1g59A 468 -49.05 -9.17 3.15e+00 1mhyD 521 -63.09 -9.16 3.16e+00 1f5qB 252 -52.57 -9.09 3.31e+00 1aueA 100 -40.47 -9.02 3.44e+00 1eca 136 -43.35 -9.00 3.49e+00 1ecd 136 -43.35 -9.00 3.49e+00 1kplA 473 -70.42 -8.92 3.66e+00 2gsaA 432 -48.51 -8.90 3.72e+00 1nfiC 301 -37.43 -8.89 3.74e+00 1jm6A 407 -50.11 -8.89 3.74e+00 1ndoB 194 -31.80 -8.83 3.89e+00 1qkrA 188 -48.83 -8.82 3.91e+00 1qqfA 277 -49.67 -8.66 4.32e+00 1eg9B 194 -31.66 -8.63 4.39e+00 1g5hA 454 -37.30 -8.61 4.45e+00 1brwA 433 -49.12 -8.58 4.52e+00 1dm5A 315 -58.99 -8.58 4.53e+00 1f0yA 302 -37.93 -8.57 4.57e+00 1fqiA 147 -36.59 -8.52 4.71e+00 1kzhA 555 -53.00 -8.51 4.73e+00 1jvpP 298 -35.27 -8.48 4.81e+00 1ft1A 377 -62.31 -8.48 4.81e+00 1aj8A 371 -56.42 -8.48 4.82e+00 1jsqA 582 -51.40 -8.42 5.00e+00 1pgtA 210 -43.18 -8.41 5.03e+00 1aisB 200 -42.96 -8.35 5.22e+00 1jffA 451 -43.46 -8.28 5.45e+00 1bu2A 229 -40.15 -8.27 5.51e+00 1k94A 165 -38.55 -8.26 5.53e+00 1qpzA 340 -36.55 -8.26 5.54e+00 1qhtA 775 -61.31 -8.24 5.60e+00 1d2nA 272 -33.59 -8.23 5.63e+00 1h6pA 203 -46.84 -8.23 5.63e+00 1hskA 326 -39.52 -8.20 5.75e+00 1wetA 340 -36.47 -8.20 5.76e+00 1iqrA 420 -42.02 -8.15 5.95e+00 1k7wA 468 -52.27 -8.14 5.96e+00 1kv9A 668 -64.57 -8.10 6.10e+00 1a8h 500 -56.52 -8.04 6.35e+00 1c3cA 429 -58.61 -8.04 6.35e+00 1auwA 468 -53.83 -7.99 6.55e+00 1vom 762 -46.90 -7.98 6.59e+00 3fapB 94 -39.11 -7.97 6.62e+00 1j79A 347 -32.48 -7.92 6.85e+00 1a6m 151 -43.45 -7.90 6.93e+00 1jpzA 473 -60.20 -7.89 7.00e+00 1bzpA 153 -44.07 -7.87 7.07e+00 1dcnA 424 -49.07 -7.87 7.10e+00 1e3mA 800 -46.26 -7.85 7.19e+00 1bp1 456 -37.01 -7.83 7.25e+00 2hdhA 293 -37.47 -7.76 7.61e+00 1taq 832 -50.57 -7.75 7.62e+00 1cb8A 678 -60.12 -7.75 7.63e+00 1mbd 153 -43.43 -7.74 7.70e+00 1is2A 661 -70.76 -7.73 7.71e+00 1i37A 260 -49.68 -7.71 7.82e+00 1mgn 154 -44.12 -7.66 8.11e+00 2tmkA 216 -38.18 -7.65 8.15e+00 1ih8A 271 -38.80 -7.62 8.29e+00 1ewfA 456 -36.84 -7.62 8.29e+00 1mpgA 282 -37.52 -7.62 8.33e+00 1tubA 440 -42.08 -7.58 8.51e+00 1dn1A 594 -45.79 -7.58 8.55e+00 1gln 468 -48.03 -7.55 8.69e+00 1hcuA 503 -48.48 -7.54 8.74e+00 1e1xA 299 -34.66 -7.53 8.78e+00 1kxu 333 -50.70 -7.53 8.80e+00 1egaA 301 -31.94 -7.52 8.88e+00 1clc 639 -54.52 -7.51 8.90e+00 2ts1 419 -41.52 -7.50 8.97e+00 3tmkA 216 -38.97 -7.50 9.00e+00 1ib2A 349 -51.85 -7.48 9.08e+00 1qr6A 584 -50.56 -7.46 9.19e+00 1i4sA 147 -43.96 -7.46 9.22e+00 1kmmA 424 -38.82 -7.44 9.30e+00 1db1A 259 -48.73 -7.44 9.33e+00 1sw6A 327 -40.66 -7.44 9.34e+00 1hm2A 700 -61.30 -7.43 9.40e+00 1k8kG 151 -39.77 -7.43 9.42e+00 1hvd 319 -53.25 -7.40 9.54e+00 1hcl 298 -34.38 -7.35 9.90e+00 1hzfA 367 -46.74 -7.34 9.92e+00 1lkvX 232 -51.41 -7.29 1.03e+01 1gaxA 862 -71.30 -7.27 1.04e+01 1iq0A 592 -51.20 -7.25 1.05e+01 1qazA 351 -47.91 -7.25 1.05e+01 1aorA 605 -63.24 -7.25 1.06e+01 1t7pA 698 -63.44 -7.25 1.06e+01 1sig 339 -49.00 -7.24 1.06e+01 1mtyD 512 -58.53 -7.23 1.07e+01 1ps1A 337 -56.61 -7.22 1.07e+01 1anxA 319 -53.80 -7.20 1.09e+01 1nsgB 94 -38.68 -7.20 1.09e+01 1jx6A 342 -34.26 -7.19 1.10e+01 1zymA 258 -39.55 -7.17 1.11e+01 1i0aA 466 -49.47 -7.15 1.13e+01 1dqaA 467 -41.54 -7.14 1.14e+01 1mrj 247 -32.95 -7.11 1.16e+01 2cblA 305 -48.39 -7.09 1.17e+01 1ezvF 125 -32.00 -7.08 1.18e+01 1chuA 540 -55.64 -7.07 1.19e+01 4pah 308 -42.76 -7.04 1.21e+01 1jg7A 351 -36.04 -7.04 1.21e+01 1gcb 454 -44.08 -7.00 1.24e+01 1hu3A 260 -57.38 -6.98 1.26e+01 1kvkA 395 -39.27 -6.95 1.28e+01 1jixA 351 -35.98 -6.95 1.28e+01 1hta 69 -30.42 -6.93 1.30e+01 1dxtB 147 -39.89 -6.92 1.31e+01 1d1dA 262 -41.61 -6.92 1.31e+01 1axn 323 -51.99 -6.92 1.31e+01 1evyA 366 -38.82 -6.91 1.31e+01 1nfiA 301 -35.00 -6.91 1.32e+01 1pah 308 -42.47 -6.91 1.32e+01 1babB 146 -39.85 -6.90 1.33e+01 1dn1B 267 -53.41 -6.89 1.34e+01 1li5A 461 -46.61 -6.89 1.34e+01 1jplA 171 -45.06 -6.87 1.35e+01 1jfzA 154 -42.84 -6.85 1.37e+01 1qq7A 253 -35.03 -6.84 1.38e+01 1jqiA 388 -44.08 -6.82 1.39e+01 1dbqA 289 -34.55 -6.82 1.40e+01 1h4vB 421 -35.35 -6.81 1.40e+01 1lvk 762 -47.10 -6.80 1.42e+01 1ea3A 164 -37.87 -6.78 1.43e+01 1kyoG 126 -32.16 -6.78 1.44e+01 1mc0A 368 -40.22 -6.75 1.46e+01 1j8uA 325 -42.96 -6.75 1.47e+01 1h3nA 878 -78.86 -6.75 1.47e+01 1a04A 215 -32.13 -6.74 1.47e+01 1qhiA 366 -35.30 -6.74 1.48e+01 1nsf 273 -32.21 -6.74 1.48e+01 1b89A 449 -53.38 -6.73 1.48e+01 1dmwA 307 -42.54 -6.73 1.49e+01 2bmhA 455 -58.88 -6.71 1.50e+01 1dfoA 417 -46.87 -6.70 1.52e+01 1jf2A 195 -41.01 -6.68 1.54e+01 1dlyA 164 -33.27 -6.66 1.55e+01 1b47A 304 -49.39 -6.65 1.56e+01 1bbhA 131 -39.28 -6.63 1.59e+01 1dqaC 467 -40.99 -6.62 1.60e+01 2bgu 351 -34.98 -6.57 1.65e+01 1mnd 762 -45.01 -6.57 1.65e+01 1aq6A 253 -35.03 -6.57 1.65e+01 1c3jA 351 -34.57 -6.50 1.73e+01 1fewA 184 -49.18 -6.50 1.73e+01 3gcb 470 -43.86 -6.49 1.74e+01 3vtk 343 -37.16 -6.49 1.74e+01 1jmeA 455 -58.11 -6.49 1.74e+01 1fxxA 482 -43.00 -6.47 1.77e+01 2spo 154 -43.79 -6.46 1.78e+01 1i1qA 520 -34.73 -6.46 1.78e+01 1itkA 731 -71.13 -6.45 1.79e+01 1vin 268 -47.12 -6.45 1.79e+01 1f16A 192 -46.19 -6.44 1.80e+01 1jwhC 215 -38.34 -6.42 1.83e+01 1qq5A 253 -35.04 -6.38 1.88e+01 1g4yR 148 -33.09 -6.37 1.89e+01 1jygA 69 -30.21 -6.32 1.95e+01 4ts1A 319 -36.67 -6.31 1.97e+01 1a8i 842 -62.66 -6.29 1.99e+01 1jcrA 377 -61.25 -6.28 2.01e+01 1lpuA 332 -35.25 -6.27 2.02e+01 1khvA 516 -41.53 -6.25 2.05e+01 1jnrA 643 -58.97 -6.24 2.06e+01 2ki5A 366 -34.78 -6.24 2.06e+01 153l 185 -36.36 -6.23 2.07e+01 1cec 343 -37.59 -6.23 2.08e+01 1a0fA 201 -36.28 -6.22 2.08e+01 1kimA 366 -35.16 -6.22 2.09e+01 1a0rP 245 -31.98 -6.19 2.14e+01 1g5aA 628 -51.61 -6.18 2.14e+01 1eduA 149 -38.85 -6.18 2.15e+01 1irdB 146 -38.46 -6.18 2.15e+01 1dc1A 323 -44.02 -6.16 2.18e+01 1jwgA 147 -40.02 -6.14 2.21e+01 1nksA 194 -31.44 -6.13 2.22e+01 1a59 378 -48.39 -6.12 2.24e+01 1gveA 327 -34.31 -6.11 2.25e+01 1eyhA 144 -38.70 -6.11 2.26e+01 1elkA 157 -41.65 -6.10 2.26e+01 1tahA 318 -33.86 -6.10 2.26e+01 1ceo 343 -37.11 -6.08 2.30e+01 1gcvA 140 -38.02 -6.08 2.30e+01 1f4qA 165 -35.16 -6.07 2.31e+01 3erk 364 -34.40 -6.07 2.31e+01 1e3hA 757 -52.10 -6.06 2.32e+01 1b67A 68 -28.55 -6.05 2.34e+01 1cpt 412 -48.36 -6.05 2.35e+01 1hqvA 191 -39.90 -6.03 2.38e+01 1tahB 318 -32.70 -6.00 2.43e+01 1lfpA 249 -35.86 -6.00 2.43e+01 1eyvA 156 -40.43 -5.99 2.45e+01 1fioA 196 -45.98 -5.98 2.46e+01 1iioA 84 -26.90 -5.97 2.48e+01 1auvA 311 -32.73 -5.96 2.50e+01 1d2fA 390 -36.35 -5.96 2.50e+01 1qc7A 101 -33.62 -5.95 2.52e+01 1h5uA 842 -62.82 -5.93 2.55e+01 1bi5A 389 -37.88 -5.92 2.57e+01 1gpb 842 -64.76 -5.91 2.57e+01 1a6r 471 -43.33 -5.90 2.59e+01 1kkhA 317 -37.86 -5.90 2.59e+01 1i86A 389 -37.35 -5.90 2.60e+01 1ka3A 90 -32.82 -5.90 2.60e+01 1jr3A 373 -43.16 -5.90 2.61e+01 1furA 467 -51.23 -5.89 2.62e+01 1cnpA 90 -29.80 -5.89 2.63e+01 1wdnA 226 -31.63 -5.88 2.63e+01 2nsyA 271 -37.08 -5.88 2.63e+01 4lbd 267 -48.77 -5.88 2.64e+01 1cch 82 -26.57 -5.88 2.64e+01 1i88A 389 -37.41 -5.87 2.65e+01 1cpq 129 -32.71 -5.87 2.65e+01 1cvl 319 -31.61 -5.86 2.67e+01 1e2kA 331 -35.89 -5.86 2.67e+01 1ks9A 291 -40.39 -5.84 2.70e+01 1fnsA 196 -28.99 -5.84 2.72e+01 1c1kA 217 -42.46 -5.84 2.72e+01 1cnsA 243 -35.81 -5.83 2.74e+01 1g24A 211 -31.43 -5.82 2.75e+01 1gggB 226 -31.56 -5.82 2.75e+01 1bu7A 455 -59.25 -5.81 2.77e+01 1e7uA 961 -64.05 -5.81 2.77e+01 1kmiZ 214 -46.00 -5.81 2.78e+01 1ej0A 180 -29.73 -5.81 2.78e+01 1dxjA 242 -37.27 -5.80 2.78e+01 2lbd 267 -48.69 -5.80 2.79e+01 1qqeA 292 -55.85 -5.75 2.89e+01 1tml 286 -32.55 -5.74 2.91e+01 1abwA 283 -50.75 -5.74 2.91e+01 1amz 435 -55.52 -5.73 2.93e+01 1kqpA 271 -37.03 -5.72 2.94e+01 1yrgA 385 -31.90 -5.72 2.94e+01 1jkw 323 -49.99 -5.72 2.94e+01 1aoa 275 -40.11 -5.71 2.97e+01 1h68A 239 -46.75 -5.69 3.01e+01 1ie9A 259 -48.03 -5.68 3.02e+01 1bk0 331 -34.43 -5.68 3.03e+01 1cjaA 342 -39.44 -5.67 3.04e+01 1jli 112 -32.22 -5.67 3.04e+01 1nox 205 -30.13 -5.67 3.05e+01 2ccyA 128 -33.85 -5.64 3.11e+01 1i0hA 205 -31.00 -5.64 3.12e+01 1cgo 127 -34.63 -5.63 3.12e+01 1e2uA 553 -53.31 -5.63 3.14e+01 1csh 435 -55.02 -5.60 3.20e+01 1bkdS 439 -57.49 -5.58 3.25e+01 1ithA 141 -38.60 -5.57 3.26e+01 1gntA 553 -53.25 -5.57 3.28e+01 1jgjA 217 -46.12 -5.55 3.30e+01 1qh8B 519 -44.00 -5.55 3.32e+01 1dcqA 278 -34.21 -5.53 3.35e+01 1ijbA 202 -29.02 -5.51 3.42e+01 1ehyA 294 -35.49 -5.50 3.42e+01 1go3F 107 -33.10 -5.48 3.48e+01 1iufA 144 -31.75 -5.48 3.49e+01 1fa0A 537 -47.17 -5.47 3.50e+01 1pme 380 -33.55 -5.46 3.52e+01 2nadA 393 -36.24 -5.45 3.55e+01 1mznA 240 -45.33 -5.45 3.56e+01 1qguB 519 -43.90 -5.44 3.58e+01 1lqc 56 -24.20 -5.44 3.58e+01 1dghB 498 -46.42 -5.43 3.60e+01 2a3dA 73 -28.82 -5.42 3.62e+01 1dr8B 344 -37.84 -5.42 3.63e+01 1nsyA 271 -36.74 -5.42 3.63e+01 1kf6C 130 -37.07 -5.39 3.70e+01 1lu9A 287 -39.51 -5.39 3.72e+01 1lrv 244 -31.01 -5.38 3.72e+01 2trcP 217 -33.06 -5.38 3.73e+01 1ee8A 266 -30.11 -5.38 3.74e+01 1h97A 147 -38.76 -5.36 3.79e+01 1e85A 127 -33.79 -5.34 3.84e+01 1a8b 318 -53.05 -5.34 3.84e+01 1a7w 69 -30.60 -5.33 3.86e+01 1rlr 761 -51.80 -5.33 3.87e+01 1h67A 108 -32.55 -5.30 3.94e+01 1f7uA 607 -65.21 -5.30 3.96e+01 1b0uA 262 -30.57 -5.29 3.99e+01