% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR208W.t2k-100-30-CB_burial_14_7 Host: cc61 Mon Apr 26 00:00:26 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR208W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 YGR208W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR208W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 9673 sequences, 2287462 residues, 310 nodes, 323.04 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(=2.2924) * Reverse)^tau(=0.7044))) % 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 1f5sA 211 -206.56 -191.84 2.05e-28 1j97A 211 -206.50 -191.52 2.24e-28 1l7mA 211 -205.03 -189.91 3.44e-28 1nnlA 225 -142.40 -129.26 9.64e-21 1eulA 994 -156.98 -128.18 1.33e-20 1rkqA 282 -127.25 -116.57 4.61e-19 1nrwA 288 -126.51 -114.75 8.12e-19 1nf2A 268 -116.27 -98.19 1.57e-16 1rkuA 206 -103.31 -90.51 1.98e-15 1l6rA 227 -92.30 -78.65 1.12e-13 1j8dA 180 -82.37 -72.53 9.66e-13 1k1eA 180 -81.22 -71.43 1.43e-12 1vjrA 271 -71.57 -57.42 2.53e-10 1zrn 232 -67.25 -56.13 4.12e-10 1o08A 221 -68.01 -55.55 5.16e-10 1lvhA 221 -68.46 -55.47 5.34e-10 1qq5A 253 -58.93 -48.56 8.04e-09 1qq7A 253 -58.76 -48.36 8.72e-09 1aq6A 253 -58.13 -47.69 1.14e-08 1qyiA 384 -58.40 -41.16 1.68e-07 1rqlA 267 -53.00 -38.62 4.94e-07 1fezA 256 -52.60 -38.49 5.23e-07 1n8nA 212 -50.90 -37.77 7.13e-07 1ltqA 301 -39.58 -22.33 9.25e-04 1cqzA 554 -41.86 -19.33 4.33e-03 1ek1A 554 -41.02 -18.25 7.70e-03 1cr6B 554 -40.52 -18.23 7.77e-03 1rkd 309 -27.81 -17.37 1.24e-02 1mh9A 197 -29.88 -15.50 3.47e-02 1q92A 197 -29.79 -15.47 3.54e-02 1hg3A 225 -25.60 -15.00 4.60e-02 1p9rA 418 -27.03 -14.53 6.01e-02 1o58A 303 -26.68 -13.73 9.59e-02 1j6nA 303 -26.64 -13.71 9.68e-02 1q3kA 259 -24.74 -12.92 1.54e-01 1lhpA 312 -29.76 -12.69 1.77e-01 1fkx 349 -26.94 -12.45 2.04e-01 1r30A 369 -25.67 -12.26 2.28e-01 1a4mA 349 -27.16 -12.05 2.59e-01 1add 349 -26.98 -11.89 2.85e-01 1ox0A 430 -25.54 -11.86 2.91e-01 1uekA 275 -23.30 -11.63 3.35e-01 1n7kA 234 -21.34 -11.53 3.56e-01 1v7zA 260 -22.69 -10.93 5.15e-01 1kagA 173 -22.12 -10.85 5.42e-01 8abp 306 -26.02 -10.80 5.61e-01 1cbuA 180 -21.34 -10.61 6.30e-01 1o0uA 429 -25.72 -10.50 6.76e-01 1o69A 394 -27.05 -10.48 6.83e-01 1lwjA 441 -32.24 -10.40 7.19e-01 1c9kB 180 -21.09 -10.37 7.34e-01 1udb 338 -25.31 -10.26 7.86e-01 1g6hA 257 -23.85 -10.20 8.18e-01 1c9kA 180 -20.13 -10.18 8.26e-01 1xel 338 -24.90 -10.10 8.68e-01 1n45A 233 -20.32 -9.93 9.73e-01 1ek6A 348 -24.20 -9.90 9.90e-01 1php 394 -25.72 -9.77 1.07e+00 1qq8A 214 -19.90 -9.71 1.12e+00 1d3hA 367 -22.08 -9.68 1.14e+00 1gajA 257 -23.35 -9.59 1.21e+00 1k1xA 659 -37.39 -9.59 1.21e+00 1rypE 242 -20.23 -9.57 1.23e+00 1ub0A 258 -19.20 -9.51 1.27e+00 1udc 338 -24.21 -9.39 1.37e+00 2udpA 338 -24.07 -9.31 1.45e+00 1amoA 615 -28.59 -9.30 1.46e+00 1ibsA 317 -23.28 -9.28 1.47e+00 1top 162 -25.05 -9.25 1.51e+00 1i3kA 348 -23.75 -9.19 1.57e+00 1owlA 484 -22.33 -9.14 1.62e+00 1kvs 338 -24.35 -9.13 1.63e+00 1dkrA 317 -23.08 -9.02 1.75e+00 1d3gA 367 -21.86 -8.94 1.85e+00 1qvbA 481 -29.30 -8.93 1.87e+00 1zfjA 491 -21.34 -8.78 2.05e+00 1mq4A 272 -20.90 -8.76 2.08e+00 2dpmA 284 -25.80 -8.76 2.09e+00 1vhvA 268 -20.06 -8.75 2.10e+00 1j9aA 184 -20.08 -8.75 2.10e+00 1dkuA 317 -22.30 -8.68 2.20e+00 1krhA 338 -22.94 -8.67 2.21e+00 1qnf 484 -21.65 -8.67 2.21e+00 1iso 416 -25.47 -8.55 2.39e+00 1npyA 271 -20.15 -8.55 2.39e+00 1ncx 162 -24.92 -8.54 2.42e+00 1gs5A 258 -19.40 -8.53 2.42e+00 1ur1A 378 -23.08 -8.39 2.67e+00 1go3F 107 -20.68 -8.38 2.68e+00 1fts 295 -19.92 -8.38 2.69e+00 1cf7B 95 -18.56 -8.35 2.74e+00 7icd 416 -25.93 -8.34 2.76e+00 1l9wA 252 -18.08 -8.34 2.76e+00 1kh5A 449 -18.97 -8.32 2.79e+00 1cnv 299 -22.43 -8.29 2.86e+00 1ii7A 333 -25.43 -8.20 3.03e+00 1kwkA 645 -19.98 -8.19 3.05e+00 1onxA 390 -22.47 -8.14 3.15e+00 1ja1A 622 -27.94 -8.13 3.18e+00 1fnnA 389 -21.94 -8.11 3.22e+00 1j96A 323 -21.55 -8.11 3.22e+00 1l6wA 220 -17.81 -8.06 3.33e+00 1m65A 245 -18.85 -7.99 3.50e+00 1nrzA 164 -17.99 -7.98 3.53e+00 1kwgA 645 -19.87 -7.97 3.55e+00 3chy 128 -19.98 -7.96 3.56e+00 1aisB 200 -19.68 -7.96 3.58e+00 1d3uB 201 -20.35 -7.95 3.59e+00 1e19A 314 -23.01 -7.95 3.60e+00 1v4vA 376 -20.19 -7.85 3.84e+00 1ad1A 266 -18.74 -7.84 3.87e+00 1jg1A 235 -22.50 -7.83 3.89e+00 1s9rA 410 -23.83 -7.78 4.05e+00 1lxyA 409 -23.74 -7.69 4.30e+00 1onwA 390 -21.30 -7.67 4.37e+00 1e8cA 498 -18.80 -7.66 4.39e+00 1qfeA 252 -17.27 -7.64 4.44e+00 1m41A 380 -21.42 -7.61 4.54e+00 1d3yA 301 -22.09 -7.60 4.59e+00 1pb1A 416 -25.10 -7.58 4.64e+00 1ceqA 316 -22.00 -7.57 4.68e+00 1iz0A 302 -17.85 -7.47 5.00e+00 1gkkA 297 -21.45 -7.46 5.04e+00 1cll 148 -19.52 -7.44 5.13e+00 6pfkA 319 -21.96 -7.43 5.14e+00 1deoA 233 -17.72 -7.41 5.23e+00 1ma3A 253 -19.47 -7.39 5.29e+00 1hdoA 206 -17.65 -7.36 5.41e+00 1q6oA 216 -18.98 -7.34 5.47e+00 1he2A 206 -17.66 -7.33 5.51e+00 1np7A 489 -29.14 -7.30 5.63e+00 1ho1A 242 -19.42 -7.30 5.63e+00 4pfk 319 -21.76 -7.30 5.66e+00 1pscA 365 -18.66 -7.27 5.75e+00 3cln 148 -19.22 -7.23 5.91e+00 1b8jA 449 -17.87 -7.22 5.98e+00 1gklA 297 -21.03 -7.21 6.01e+00 1s1pA 331 -20.58 -7.20 6.05e+00 1n82A 331 -20.20 -7.18 6.15e+00 3pfk 319 -21.67 -7.17 6.16e+00 1uyrA 737 -33.38 -7.17 6.19e+00 1jmkC 230 -18.70 -7.16 6.23e+00 1gqnA 252 -16.78 -7.15 6.27e+00 1geqA 248 -18.79 -7.15 6.28e+00 1rhcA 330 -18.89 -7.11 6.44e+00 1im5A 180 -20.42 -7.11 6.45e+00 1alkA 449 -17.76 -7.07 6.65e+00 1pujA 282 -21.91 -7.07 6.65e+00 1hdhA 536 -19.30 -7.04 6.80e+00 1uasA 362 -23.17 -7.02 6.88e+00 1ae1A 273 -18.63 -7.01 6.91e+00 1pta 318 -18.38 -7.00 6.97e+00 1g4yR 148 -19.21 -6.99 7.03e+00 1l8bA 190 -20.84 -6.98 7.09e+00 1j31A 262 -18.41 -6.96 7.18e+00 1viaA 175 -19.79 -6.89 7.55e+00 1jljA 189 -18.50 -6.88 7.59e+00 1pyfA 312 -22.39 -6.88 7.62e+00 1kv8A 216 -18.24 -6.86 7.68e+00 1upaA 573 -20.73 -6.86 7.69e+00 1evyA 366 -18.36 -6.84 7.79e+00 2anhA 446 -17.58 -6.84 7.81e+00 1e4fT 419 -24.48 -6.83 7.89e+00 1g99A 408 -21.92 -6.81 7.97e+00 1n8jA 186 -17.54 -6.81 8.01e+00 1m6sA 347 -18.66 -6.80 8.01e+00 1xjo 284 -17.91 -6.79 8.09e+00 1eyeA 280 -16.82 -6.79 8.10e+00 1ru8A 232 -18.71 -6.76 8.28e+00 1eq2A 310 -21.11 -6.75 8.35e+00 1eucA 311 -21.09 -6.74 8.38e+00 1khbA 625 -33.09 -6.71 8.57e+00 1q67A 231 -21.42 -6.67 8.80e+00 1ed8A 449 -17.29 -6.67 8.85e+00 1kkhA 317 -26.55 -6.66 8.87e+00 1nqkA 381 -21.45 -6.66 8.90e+00 1exrA 148 -19.46 -6.65 8.94e+00 1k7cA 233 -16.87 -6.63 9.09e+00 1uumA 372 -18.56 -6.61 9.23e+00 7reqA 727 -22.53 -6.57 9.51e+00 1qq9A 284 -17.93 -6.55 9.60e+00 1g5aA 628 -27.02 -6.55 9.62e+00 1hqsA 423 -24.20 -6.54 9.73e+00 1e6mA 128 -18.63 -6.53 9.80e+00 1osa 148 -19.28 -6.52 9.85e+00 1ji0A 240 -19.21 -6.51 9.88e+00 1jg8A 347 -18.36 -6.51 9.93e+00 1ihcA 188 -18.38 -6.50 9.98e+00 1reqA 727 -22.32 -6.49 1.01e+01 2fsp 124 -17.88 -6.43 1.05e+01 1aquA 297 -22.81 -6.43 1.05e+01 1elyA 449 -17.14 -6.42 1.06e+01 1n0uA 842 -34.56 -6.42 1.06e+01 1l8qA 324 -22.83 -6.42 1.06e+01 1fcqA 350 -20.70 -6.41 1.06e+01 1cb6A 691 -33.85 -6.41 1.07e+01 1mp9A 198 -18.12 -6.40 1.08e+01 1ji2A 585 -26.16 -6.40 1.08e+01 5reqA 727 -22.35 -6.39 1.08e+01 1eywA 331 -17.83 -6.39 1.08e+01 1m5wA 243 -18.69 -6.39 1.08e+01 1b1cA 181 -19.51 -6.39 1.08e+01 1cye 129 -18.34 -6.35 1.11e+01 1jykA 254 -23.02 -6.30 1.15e+01 1lvl 458 -17.31 -6.24 1.21e+01 1v93A 296 -19.27 -6.20 1.24e+01 1eudA 311 -20.73 -6.18 1.26e+01 1h1yA 228 -16.82 -6.17 1.27e+01 1oi7A 288 -17.49 -6.17 1.27e+01 1ak1 310 -21.84 -6.16 1.28e+01 1frvB 536 -19.35 -6.14 1.30e+01 1srrA 124 -17.59 -6.11 1.33e+01 1ipcA 217 -20.20 -6.04 1.39e+01 1vh7A 265 -20.48 -6.02 1.42e+01 1uayA 242 -18.52 -6.01 1.43e+01 1vjzA 341 -25.23 -5.99 1.45e+01 1cjaA 342 -19.17 -5.99 1.46e+01 1kay 381 -19.73 -5.98 1.46e+01 1nstA 325 -19.48 -5.94 1.51e+01 1qhtA 775 -34.79 -5.92 1.53e+01 1ktbA 405 -23.84 -5.91 1.55e+01 1dp4A 435 -20.48 -5.89 1.56e+01 1ryc 294 -23.79 -5.86 1.60e+01 1ble 163 -15.61 -5.85 1.61e+01 1tr1A 447 -23.90 -5.84 1.62e+01 1s5pA 235 -17.03 -5.83 1.64e+01 1g5rA 196 -16.06 -5.78 1.69e+01 1ejjA 511 -24.26 -5.77 1.71e+01 1rjdA 334 -18.26 -5.74 1.75e+01 1iejA 332 -20.14 -5.73 1.76e+01 1dhpA 292 -16.76 -5.73 1.76e+01 1iqzA 81 -16.28 -5.73 1.76e+01 1ba1 386 -19.61 -5.72 1.77e+01 1frb 315 -20.24 -5.72 1.78e+01 1mzhA 225 -16.83 -5.71 1.79e+01 1bupA 386 -19.67 -5.70 1.80e+01 1mooA 260 -19.89 -5.70 1.81e+01 1fr7A 260 -19.64 -5.67 1.84e+01 1ggzA 148 -17.92 -5.67 1.85e+01 1n5dA 288 -18.00 -5.66 1.85e+01 1hu4A 288 -18.00 -5.66 1.86e+01 1mwmA 320 -21.12 -5.65 1.87e+01 1lfpA 249 -19.74 -5.62 1.92e+01 1m2oB 190 -16.42 -5.62 1.92e+01 2cba 260 -20.14 -5.61 1.94e+01 1bf6A 291 -16.10 -5.60 1.95e+01 1mszA 86 -15.35 -5.58 1.97e+01 1jqhA 308 -19.32 -5.57 2.00e+01 1m7gA 211 -16.54 -5.56 2.00e+01 1o1yA 239 -20.16 -5.54 2.04e+01 1caj 260 -20.24 -5.54 2.04e+01 1gosA 520 -23.55 -5.53 2.04e+01 1s3eA 520 -23.46 -5.53 2.04e+01 1ge9A 184 -19.32 -5.53 2.05e+01 1ojaA 520 -23.46 -5.52 2.07e+01 1lvk 762 -34.24 -5.50 2.09e+01 1thfD 253 -19.85 -5.49 2.11e+01 1bvzA 585 -25.21 -5.47 2.15e+01 1p4xA 250 -19.22 -5.47 2.16e+01 1fgs 428 -16.90 -5.46 2.16e+01 1p9oA 313 -16.34 -5.46 2.17e+01 1lroA 267 -17.63 -5.45 2.19e+01 1taq 832 -21.86 -5.44 2.20e+01 1r6wA 322 -19.46 -5.43 2.21e+01 3pgk 416 -19.37 -5.43 2.22e+01 1qo2A 241 -18.04 -5.42 2.23e+01 1ccg 291 -23.21 -5.42 2.23e+01 1bmtA 246 -17.81 -5.42 2.23e+01 1ff9A 450 -20.89 -5.42 2.24e+01 1wdnA 226 -18.22 -5.40 2.26e+01 1vi9A 299 -15.59 -5.38 2.29e+01 1f76A 336 -21.42 -5.36 2.34e+01 1r2rA 248 -16.39 -5.35 2.36e+01 1e8eA 124 -15.84 -5.34 2.37e+01 1o5oA 221 -16.31 -5.33 2.39e+01 1nzjA 298 -17.04 -5.32 2.40e+01 1liuA 528 -19.71 -5.32 2.40e+01 1i0dA 332 -17.02 -5.31 2.43e+01 2frvB 536 -18.81 -5.31 2.43e+01 1am7A 158 -15.76 -5.30 2.44e+01 1d0yA 761 -33.85 -5.29 2.46e+01 1vizA 240 -16.80 -5.27 2.51e+01 1fyhA 258 -22.60 -5.26 2.52e+01 1pswA 348 -17.30 -5.25 2.54e+01 1o98A 511 -23.75 -5.25 2.55e+01 1lugA 259 -19.42 -5.25 2.55e+01 1pwmA 316 -19.94 -5.24 2.57e+01 1f07A 321 -17.17 -5.22 2.59e+01 1oc2A 348 -20.39 -5.22 2.60e+01 1ads 315 -19.94 -5.21 2.61e+01 1hzyA 332 -16.92 -5.21 2.63e+01 1ni9A 338 -18.10 -5.20 2.63e+01 1nni1 174 -15.32 -5.20 2.64e+01 1eqjA 511 -23.66 -5.18 2.69e+01 1vjgA 218 -17.24 -5.17 2.69e+01 1edg 380 -25.23 -5.17 2.70e+01 1iqpA 327 -18.51 -5.17 2.71e+01 1puiA 210 -17.22 -5.16 2.72e+01 1b74A 254 -19.25 -5.15 2.74e+01 1gqyA 475 -18.48 -5.14 2.76e+01 1fy2A 229 -15.48 -5.13 2.78e+01 1mkp 144 -17.24 -5.13 2.80e+01 1om1A 332 -22.84 -5.12 2.81e+01 1mua 256 -19.17 -5.11 2.82e+01 1fztA 211 -17.82 -5.11 2.83e+01 2acr 315 -19.78 -5.11 2.83e+01 1d9uA 154 -15.32 -5.10 2.85e+01 1ej1A 190 -19.00 -5.09 2.88e+01 1bfd 528 -16.89 -5.09 2.88e+01 1hrkA 359 -19.41 -5.08 2.89e+01 1e4iA 447 -23.14 -5.08 2.90e+01 1h6gA 256 -18.35 -5.07 2.93e+01 1zac 90 -17.35 -5.06 2.94e+01 1f8fA 371 -18.89 -5.06 2.94e+01 1npdA 288 -16.89 -5.06 2.95e+01 1d6jA 211 -16.49 -5.05 2.96e+01 1dozA 309 -20.57 -5.05 2.98e+01 1oapA 109 -14.78 -5.04 3.00e+01 1fc4A 401 -20.72 -5.03 3.00e+01 1fyeA 229 -15.26 -5.03 3.01e+01 4aahA 571 -28.98 -5.02 3.05e+01 1ah2 269 -15.41 -5.00 3.08e+01 1ccwB 483 -24.61 -5.00 3.09e+01 1om0A 274 -16.25 -4.99 3.11e+01 1knqA 175 -16.14 -4.99 3.12e+01 1gq6A 313 -17.21 -4.99 3.12e+01 1nddA 76 -16.63 -4.98 3.14e+01 1p8kZ 254 -20.39 -4.97 3.17e+01 1jbeA 128 -17.06 -4.97 3.17e+01 1miwA 404 -16.53 -4.96 3.18e+01 1ejhA 190 -18.41 -4.95 3.22e+01 1oen 540 -23.11 -4.95 3.22e+01 1gu2A 124 -15.51 -4.95 3.22e+01 1o5iA 249 -16.37 -4.93 3.25e+01 1fm9D 272 -19.61 -4.93 3.26e+01 1edt 271 -15.38 -4.91 3.31e+01 1mw9X 592 -18.89 -4.91 3.31e+01 1lssA 140 -15.77 -4.91 3.32e+01 1orrA 347 -20.72 -4.90 3.33e+01 1aw1A 256 -14.62 -4.90 3.34e+01 1a36A 592 -31.45 -4.89 3.35e+01 1b73A 254 -19.09 -4.89 3.35e+01 1pnsC 206 -16.63 -4.89 3.36e+01 1dw0A 112 -14.02 -4.89 3.37e+01 1mxgA 435 -27.16 -4.88 3.38e+01 1eo1A 124 -15.78 -4.88 3.39e+01 1wba 175 -17.54 -4.88 3.41e+01 1j54A 186 -15.60 -4.87 3.41e+01 1g5tA 196 -15.12 -4.87 3.41e+01 1oafA 261 -17.58 -4.87 3.42e+01 1c7nA 399 -28.83 -4.87 3.43e+01 1ir6A 424 -16.07 -4.86 3.43e+01 1g72A 573 -28.79 -4.85 3.47e+01 1j98A 157 -15.65 -4.85 3.48e+01 1j2rA 199 -15.29 -4.85 3.48e+01 1hgxA 183 -18.21 -4.82 3.56e+01 1ocvA 125 -14.54 -4.82 3.56e+01 2acy 98 -14.75 -4.79 3.65e+01 1jdrA 294 -22.86 -4.79 3.66e+01 1ass 159 -17.70 -4.78 3.66e+01 1ayl 541 -25.09 -4.78 3.68e+01 1lct 333 -20.79 -4.77 3.69e+01 1o5kA 306 -20.24 -4.75 3.75e+01 1q6hA 224 -18.57 -4.74 3.78e+01 1pixA 587 -27.45 -4.74 3.79e+01 1nxqA 251 -17.42 -4.74 3.79e+01 1jvpP 298 -16.49 -4.74 3.80e+01 1m0kA 262 -14.67 -4.72 3.84e+01 1rdr 461 -21.16 -4.68 3.97e+01 2dnjA 260 -15.26 -4.67 3.99e+01 1paqA 189 -16.75 -4.67 4.00e+01 1iiwA 232 -14.74 -4.67 4.00e+01