% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR207C.t2k-100-30-dssp-ehl2 Host: cc63 Sun Oct 12 00:35:01 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR207C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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 YGR207C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR207C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 262 nodes, 246.72 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(=1.3431) * Reverse)^tau(=0.8100))) % 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 1efvB 255 -279.58 -255.78 5.32e-46 1efpB 252 -273.38 -245.24 2.37e-44 1o97C 264 -230.13 -203.68 1.03e-37 1o97D 320 -89.37 -62.80 1.39e-12 1efvA 315 -68.88 -44.58 9.21e-09 1mo9A 523 -45.88 -18.98 8.49e-03 1o4vA 183 -41.63 -17.85 1.65e-02 1a8s 273 -39.71 -17.34 2.25e-02 1korA 400 -42.68 -16.99 2.76e-02 1ad1A 266 -38.56 -16.92 2.89e-02 1gthD 1025 -42.98 -15.96 5.16e-02 1brt 277 -37.74 -15.35 7.47e-02 1broA 277 -38.09 -15.20 8.19e-02 1p2fA 220 -38.71 -14.74 1.09e-01 1gteD 1025 -46.02 -14.56 1.22e-01 1gt8D 1025 -45.35 -14.32 1.41e-01 1gt8A 1025 -45.25 -14.24 1.49e-01 1h7xD 1025 -45.62 -14.17 1.55e-01 1gt8B 1025 -45.10 -14.09 1.63e-01 1gthB 1025 -45.11 -14.09 1.63e-01 1h7wD 1025 -45.71 -14.03 1.69e-01 1h7wA 1025 -45.70 -14.03 1.69e-01 1gteA 1025 -45.70 -14.03 1.69e-01 1g5cA 170 -38.39 -13.97 1.75e-01 1gthA 1025 -45.56 -13.88 1.85e-01 1gt8C 1025 -45.55 -13.87 1.86e-01 1gthC 1025 -45.40 -13.73 2.04e-01 1h7xB 1025 -45.31 -13.64 2.15e-01 1h7xC 1025 -45.31 -13.64 2.15e-01 1h7wB 1025 -45.31 -13.64 2.16e-01 1i52A 236 -36.97 -13.53 2.31e-01 1l2lA 457 -37.03 -13.50 2.35e-01 1h7xA 1025 -45.15 -13.49 2.37e-01 1jvsA 400 -36.73 -12.99 3.24e-01 1gkkA 297 -37.30 -12.89 3.46e-01 1dcfA 136 -35.17 -12.84 3.57e-01 1k5hA 398 -35.99 -12.39 4.75e-01 1gklA 297 -36.01 -12.14 5.57e-01 1thfD 253 -33.14 -11.96 6.24e-01 1jvnA 555 -36.38 -11.74 7.19e-01 1jkxA 212 -33.19 -11.61 7.81e-01 1ako 268 -34.09 -11.57 8.05e-01 1fzqA 181 -34.16 -11.45 8.67e-01 1om0A 274 -33.58 -11.07 1.11e+00 1olsA 400 -34.02 -11.05 1.13e+00 2scuA 288 -37.04 -10.91 1.23e+00 1lkcA 364 -33.35 -10.84 1.29e+00 1gn0A 108 -31.26 -10.59 1.52e+00 1gmxA 108 -31.49 -10.54 1.58e+00 1a04A 215 -37.50 -10.34 1.79e+00 1h5yA 253 -32.07 -10.30 1.84e+00 1lc5A 364 -32.62 -10.30 1.84e+00 1jclA 260 -36.00 -10.27 1.87e+00 1jcjA 260 -35.99 -10.25 1.90e+00 1ii7A 333 -36.22 -10.20 1.97e+00 1agx 331 -34.29 -10.07 2.14e+00 1k92A 455 -33.57 -10.04 2.18e+00 1ohtA 215 -31.44 -10.03 2.20e+00 1dgmA 363 -32.77 -9.99 2.26e+00 1jr1A 514 -33.73 -9.97 2.30e+00 1jmvA 141 -32.05 -9.93 2.35e+00 1pamA 686 -34.93 -9.91 2.38e+00 1n7kA 234 -32.62 -9.89 2.41e+00 1qmpA 130 -33.82 -9.89 2.41e+00 2gar 212 -32.09 -9.81 2.55e+00 1ig3A 263 -37.38 -9.75 2.64e+00 1adjA 421 -34.29 -9.70 2.74e+00 1io2A 213 -31.30 -9.67 2.80e+00 1a8q 274 -35.63 -9.65 2.82e+00 1h4vB 421 -34.28 -9.65 2.84e+00 1g5pA 289 -33.69 -9.64 2.85e+00 1ehyA 294 -33.44 -9.61 2.91e+00 1h6zA 913 -34.58 -9.57 2.99e+00 1j6rA 214 -30.94 -9.53 3.07e+00 2ebn 289 -31.68 -9.53 3.08e+00 1k6wA 426 -35.52 -9.52 3.09e+00 1j9jA 247 -31.62 -9.46 3.22e+00 1ivnA 190 -30.07 -9.43 3.28e+00 1a9xB 379 -37.03 -9.41 3.33e+00 1hizA 379 -32.27 -9.39 3.38e+00 1d3cA 686 -34.56 -9.38 3.40e+00 1l5xA 280 -31.98 -9.38 3.40e+00 1scuA 288 -35.53 -9.34 3.49e+00 1j9lA 247 -31.47 -9.32 3.52e+00 1cs0C 1073 -36.43 -9.32 3.53e+00 1oe4A 247 -31.47 -9.30 3.57e+00 1j0aA 325 -36.75 -9.21 3.80e+00 1qczA 169 -30.73 -9.20 3.84e+00 1id1A 153 -30.64 -9.19 3.87e+00 1acf 125 -30.22 -9.06 4.22e+00 2pfkA 320 -36.72 -9.04 4.28e+00 1jg1A 235 -32.39 -9.02 4.33e+00 1cxlA 686 -34.24 -9.00 4.39e+00 1ot1A 686 -34.24 -8.99 4.41e+00 1bykA 255 -34.47 -8.98 4.44e+00 1garA 212 -30.41 -8.95 4.55e+00 2liv 344 -36.83 -8.94 4.58e+00 1a53 247 -31.54 -8.90 4.69e+00 1edt 271 -31.87 -8.89 4.72e+00 1igs 248 -31.55 -8.86 4.83e+00 1pfkA 320 -36.89 -8.84 4.89e+00 1c3oE 1073 -35.65 -8.82 4.95e+00 1fp6A 289 -33.51 -8.78 5.08e+00 1huqA 164 -33.70 -8.77 5.13e+00 1e9iA 431 -34.13 -8.73 5.26e+00 1ujnA 348 -31.47 -8.73 5.29e+00 1b9kA 238 -31.01 -8.72 5.32e+00 1tph1 247 -31.73 -8.67 5.48e+00 1fxoA 293 -34.78 -8.66 5.54e+00 1gesA 450 -33.54 -8.63 5.63e+00 1cec 343 -31.03 -8.61 5.70e+00 1b8gA 429 -32.87 -8.59 5.79e+00 1dkuA 317 -33.37 -8.53 6.03e+00 1huvA 380 -32.18 -8.49 6.23e+00 1mjhA 162 -32.57 -8.46 6.33e+00 1qtsA 247 -30.88 -8.46 6.33e+00 1kyfA 247 -30.88 -8.45 6.37e+00 1c8bA 371 -31.52 -8.44 6.43e+00 1diaA 306 -32.58 -8.35 6.82e+00 1qm9A 198 -29.97 -8.34 6.89e+00 1prq 125 -28.81 -8.28 7.15e+00 1juk 248 -30.96 -8.28 7.16e+00 1cliA 345 -32.84 -8.26 7.27e+00 1f00I 282 -30.96 -8.26 7.29e+00 1dhs 344 -30.70 -8.24 7.38e+00 2his 312 -31.26 -8.22 7.48e+00 1m3kA 392 -31.63 -8.19 7.63e+00 1fh9A 312 -31.18 -8.17 7.74e+00 1qflA 389 -31.57 -8.16 7.78e+00 1m4tA 392 -31.58 -8.16 7.79e+00 1m3sA 186 -29.57 -8.13 7.97e+00 1lehA 364 -37.80 -8.11 8.08e+00 1a4iA 301 -32.59 -8.11 8.08e+00 1a4iB 301 -32.59 -8.11 8.08e+00 1nar 290 -29.68 -8.08 8.25e+00 1oejA 193 -29.09 -8.06 8.33e+00 1mjhB 162 -31.86 -8.04 8.45e+00 1konA 249 -32.33 -8.04 8.48e+00 1btmA 252 -32.32 -8.01 8.65e+00 1keeE 1073 -34.78 -8.00 8.68e+00 1m7yA 435 -32.67 -7.93 9.14e+00 1quqB 121 -30.77 -7.93 9.15e+00 1cp2A 269 -30.38 -7.92 9.21e+00 1e5uI 187 -28.58 -7.91 9.28e+00 1f0kA 364 -31.57 -7.90 9.34e+00 1o0yA 260 -32.67 -7.89 9.38e+00 1o9gA 250 -29.30 -7.89 9.40e+00 1ne2A 200 -30.95 -7.87 9.52e+00 1cs0B 382 -35.50 -7.85 9.63e+00 1nipA 289 -32.84 -7.85 9.66e+00 1c3oA 1073 -34.59 -7.84 9.71e+00 1lbqA 362 -30.40 -7.81 9.92e+00 1htwA 158 -30.80 -7.81 9.95e+00 1bvzA 585 -32.89 -7.80 1.00e+01 1psqA 163 -31.71 -7.75 1.03e+01 1gd9A 389 -31.45 -7.73 1.05e+01 1c3oB 382 -35.16 -7.73 1.05e+01 1draA 159 -28.22 -7.71 1.07e+01 1poxA 585 -32.07 -7.69 1.08e+01 1iz1A 294 -29.17 -7.69 1.08e+01 6dfr 159 -27.93 -7.66 1.10e+01 1gdeA 389 -31.42 -7.65 1.11e+01 1dz3A 130 -31.52 -7.63 1.12e+01 1oi7A 288 -33.34 -7.62 1.13e+01 1h7eA 245 -29.92 -7.62 1.14e+01 1gr8A 412 -30.02 -7.59 1.15e+01 1ockA 412 -30.02 -7.59 1.15e+01 1g0rA 293 -32.79 -7.57 1.17e+01 1clqA 903 -32.49 -7.55 1.19e+01 1ojxA 263 -33.92 -7.54 1.20e+01 1mjfA 281 -35.01 -7.53 1.20e+01 1ibsA 317 -34.34 -7.53 1.21e+01 1fhdA 312 -30.63 -7.52 1.21e+01 1bxrA 1073 -34.75 -7.51 1.23e+01 1kmmA 424 -35.50 -7.50 1.23e+01 1keeA 1073 -34.52 -7.49 1.24e+01 3ladA 476 -32.62 -7.48 1.25e+01 1lc0A 294 -29.97 -7.46 1.26e+01 1lvwA 295 -32.70 -7.46 1.27e+01 1dkrA 317 -34.40 -7.45 1.27e+01 1b73A 254 -29.47 -7.45 1.28e+01 1ra9 159 -27.63 -7.40 1.32e+01 1mc3A 296 -33.59 -7.39 1.33e+01 1mo0A 275 -30.97 -7.37 1.35e+01 1eceA 358 -29.30 -7.36 1.36e+01 1fiy 883 -32.31 -7.36 1.36e+01 1j24A 143 -29.39 -7.34 1.38e+01 1ceo 343 -30.12 -7.34 1.38e+01 1k6dA 220 -30.60 -7.33 1.38e+01 1m93C 41 -25.09 -7.33 1.39e+01 1g71A 347 -29.41 -7.31 1.41e+01 1uteA 313 -29.83 -7.30 1.41e+01 1kmnD 424 -35.50 -7.28 1.44e+01 1eqcA 394 -30.45 -7.28 1.44e+01 1dljA 402 -30.64 -7.27 1.45e+01 1qb7A 236 -29.06 -7.27 1.45e+01 1fiuA 286 -29.76 -7.26 1.45e+01 1uanA 227 -32.12 -7.26 1.46e+01 1dbhA 354 -31.88 -7.21 1.51e+01 1ep3A 311 -29.65 -7.21 1.51e+01 1lrzA 426 -33.13 -7.18 1.54e+01 1l2uA 245 -31.67 -7.18 1.54e+01 1lldA 319 -29.60 -7.16 1.57e+01 1augA 215 -31.21 -7.14 1.59e+01 1c0dA 358 -29.65 -7.13 1.60e+01 1jykA 254 -31.28 -7.13 1.60e+01 1qfcA 306 -29.83 -7.12 1.61e+01 1c3pA 375 -32.29 -7.09 1.65e+01 1qlwA 328 -28.77 -7.08 1.66e+01 1gcuA 295 -29.69 -7.07 1.67e+01 2asi 360 -30.78 -7.07 1.67e+01 1hrhA 136 -32.76 -7.02 1.73e+01 2aaa 484 -30.43 -7.01 1.74e+01 1gu7A 364 -32.28 -7.01 1.74e+01 1kv8A 216 -32.36 -7.01 1.74e+01 1blxA 326 -29.58 -7.01 1.74e+01 1k4mA 213 -27.89 -6.98 1.78e+01 1b74A 254 -29.26 -6.97 1.79e+01 1ih7A 903 -31.92 -6.97 1.80e+01 1a88A 275 -30.59 -6.96 1.80e+01 1fcqA 350 -31.58 -6.95 1.82e+01 1jr3A 373 -29.83 -6.94 1.83e+01 2tysB 397 -31.56 -6.94 1.84e+01 1pszA 303 -29.04 -6.91 1.87e+01 1qopB 396 -31.55 -6.90 1.88e+01 1aw1A 256 -29.42 -6.90 1.88e+01 1adl 131 -31.62 -6.84 1.96e+01 1fcdA 401 -32.30 -6.83 1.98e+01 1fr9A 194 -28.26 -6.82 2.00e+01 6pfkA 319 -36.98 -6.82 2.00e+01 1jxmA 301 -31.52 -6.81 2.01e+01 1keeC 1073 -33.59 -6.80 2.02e+01 1ytfD 121 -27.85 -6.78 2.05e+01 1m2oB 190 -28.60 -6.78 2.05e+01 1cz1A 394 -30.44 -6.75 2.09e+01 1dliA 402 -30.13 -6.73 2.12e+01 1mkeA 152 -27.29 -6.72 2.13e+01 1icrA 217 -28.01 -6.72 2.14e+01 1nw8A 319 -30.23 -6.70 2.16e+01 1ji2A 585 -32.82 -6.70 2.16e+01 1gca 309 -32.05 -6.69 2.18e+01 1jdbB 1073 -33.41 -6.69 2.18e+01 1qqiA 104 -25.24 -6.69 2.19e+01 1qo7A 394 -30.85 -6.67 2.22e+01 1lid 131 -31.61 -6.66 2.23e+01 1f0zA 66 -23.84 -6.64 2.27e+01 1liiA 363 -29.56 -6.63 2.27e+01 1kkhA 317 -30.54 -6.62 2.30e+01 1kdkA 177 -29.54 -6.60 2.32e+01 1b16A 254 -29.01 -6.59 2.34e+01 1g7nA 131 -31.63 -6.59 2.35e+01 1gvnB 287 -32.18 -6.57 2.37e+01 1trb 320 -32.37 -6.57 2.38e+01 1fp4A 492 -30.59 -6.57 2.38e+01 1bdmA 327 -31.48 -6.55 2.41e+01 1mugA 168 -27.70 -6.54 2.43e+01 1n08A 163 -29.04 -6.54 2.43e+01 1ag9A 175 -27.23 -6.52 2.46e+01 1kaeA 434 -34.82 -6.52 2.47e+01 2minB 522 -31.85 -6.52 2.47e+01 3minB 522 -31.85 -6.52 2.47e+01 1m1nB 522 -31.85 -6.51 2.48e+01 1bksB 397 -31.56 -6.51 2.48e+01 1ni4A 365 -31.17 -6.51 2.48e+01 1bksA 268 -32.99 -6.50 2.50e+01 1tyv 542 -30.29 -6.48 2.53e+01 1a4uA 254 -28.76 -6.47 2.56e+01 1k8yB 396 -31.55 -6.47 2.56e+01 1dbqA 289 -31.05 -6.47 2.57e+01 1he2A 206 -27.57 -6.47 2.57e+01 1jpnA 296 -35.13 -6.44 2.61e+01 1di6A 195 -28.14 -6.42 2.64e+01 1jobA 162 -27.55 -6.41 2.66e+01 1httA 423 -35.00 -6.41 2.67e+01 1p3wA 404 -29.83 -6.41 2.67e+01 1ijaA 148 -28.00 -6.41 2.67e+01 2fx2 147 -28.91 -6.41 2.68e+01 1k75A 434 -34.88 -6.39 2.71e+01 3minC 491 -31.12 -6.38 2.74e+01 1k1eA 180 -27.59 -6.34 2.81e+01 3pga1 337 -31.18 -6.33 2.83e+01 1hjzA 192 -28.67 -6.32 2.86e+01 1kz7A 353 -28.88 -6.31 2.88e+01 1xyzA 347 -31.02 -6.31 2.88e+01 1eudA 311 -32.91 -6.29 2.91e+01 1kte 105 -27.58 -6.28 2.93e+01 1nx8A 273 -28.40 -6.27 2.95e+01 1tyu 543 -30.30 -6.27 2.96e+01 1eg2A 319 -29.92 -6.26 2.97e+01 1necA 216 -28.00 -6.25 3.00e+01 1h4wA 224 -28.03 -6.24 3.03e+01 1lvl 458 -30.40 -6.24 3.03e+01 2lbp 346 -33.34 -6.23 3.03e+01 1nwwA 149 -26.35 -6.22 3.06e+01 2gbp 309 -30.72 -6.22 3.07e+01 1qpbA 563 -30.80 -6.21 3.09e+01 1bmdA 327 -30.76 -6.21 3.09e+01 1fwcC 567 -35.86 -6.20 3.11e+01 1e5kA 201 -27.91 -6.20 3.11e+01 1e7kA 128 -26.90 -6.17 3.19e+01 1gs5A 258 -30.25 -6.16 3.19e+01 1f7cA 231 -27.82 -6.16 3.21e+01 1mu5A 471 -31.45 -6.14 3.25e+01 2minA 491 -31.14 -6.14 3.25e+01 1chuA 540 -30.17 -6.14 3.25e+01 1gxqA 106 -25.07 -6.13 3.26e+01 1kblA 873 -31.20 -6.13 3.27e+01 1qorA 327 -30.07 -6.12 3.29e+01 2dpg 485 -30.33 -6.12 3.29e+01 1j9eA 147 -29.24 -6.10 3.34e+01 4pfk 319 -35.89 -6.10 3.34e+01 1l1qA 186 -28.83 -6.10 3.35e+01 3kinB 117 -25.24 -6.09 3.37e+01 1j79A 347 -27.67 -6.09 3.37e+01 3pfk 319 -35.73 -6.08 3.39e+01 1fl9A 161 -28.10 -6.08 3.40e+01 1b5tA 275 -29.74 -6.07 3.42e+01 1kllA 130 -26.50 -6.06 3.44e+01 1qopA 268 -32.47 -6.06 3.44e+01 1eucA 311 -32.51 -6.06 3.45e+01 1gg4A 452 -31.18 -6.04 3.48e+01 1qpzA 340 -30.72 -6.04 3.48e+01 1bvoA 175 -27.08 -6.03 3.53e+01 1gdoA 240 -31.18 -6.02 3.54e+01 1t7pA 698 -33.11 -6.00 3.60e+01 1yua 122 -26.89 -5.99 3.61e+01 1qb4A 883 -31.23 -5.99 3.63e+01 1jw9B 249 -27.65 -5.97 3.68e+01 1kkoA 413 -31.78 -5.96 3.71e+01 1qcsA 211 -28.04 -5.95 3.73e+01 1ejxC 567 -35.84 -5.94 3.75e+01 1gsoA 431 -29.87 -5.94 3.75e+01 1k9sA 237 -27.61 -5.92 3.80e+01 1jqnA 883 -31.16 -5.92 3.81e+01 1mdl 359 -32.36 -5.92 3.81e+01 1c0aA 585 -31.00 -5.91 3.83e+01 1f4pA 147 -29.02 -5.91 3.83e+01 1zrn 232 -31.69 -5.91 3.84e+01 1kgsA 225 -29.60 -5.90 3.87e+01 1kmqA 184 -27.05 -5.89 3.89e+01 1cz3A 168 -29.65 -5.89 3.90e+01 1hmr 132 -29.59 -5.89 3.90e+01 1hms 132 -29.59 -5.88 3.92e+01 1kepA 348 -28.68 -5.88 3.93e+01 1hl2A 297 -28.67 -5.88 3.94e+01