% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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. % --------------------------------------------------------------------- % alphafoo.1.YGR035W-A.t2k-100-30-alpha Host: farm09.cse.ucsc.edu Sun Feb 12 22:04:41 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.alphas % % 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 YGR035W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR035W-A.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 74 nodes, 118.15 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=3.2606) * Reverse)^tau(=0.7490))) % Calculated when Simple < simple_threshold (10000.00) % 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 1aayA 90 -14.92 -7.82 1.35e-01 1zaaC 87 -14.90 -7.78 1.41e-01 1a1iA 90 -14.60 -7.44 2.03e-01 1tc5A 194 -15.05 -7.09 2.99e-01 1g2fC 90 -13.72 -6.60 5.19e-01 2aw4Z 70 -14.10 -6.28 7.47e-01 1xaoA 121 -14.03 -6.26 7.65e-01 1tqnA 486 -14.15 -6.18 8.43e-01 2ashA 381 -14.09 -6.16 8.57e-01 1zmbA 290 -14.86 -5.74 1.40e+00 1prcC 336 -13.68 -5.64 1.57e+00 1hn6A 110 -14.78 -5.59 1.67e+00 1wthD 391 -13.22 -5.55 1.74e+00 1qlaB 239 -13.48 -5.50 1.85e+00 1g8oA 310 -12.86 -5.39 2.11e+00 1dxrC 336 -13.37 -5.36 2.19e+00 1wf9A 107 -12.79 -5.20 2.66e+00 1j1bA 420 -13.00 -5.17 2.75e+00 1udh 244 -12.98 -5.15 2.81e+00 1twdA 256 -12.55 -5.14 2.86e+00 1mtnC 97 -12.44 -5.09 3.03e+00 1llmC 88 -11.89 -5.09 3.03e+00 1q41A 424 -12.93 -5.07 3.08e+00 1yc61 154 -12.43 -5.03 3.24e+00 1lzlA 323 -13.25 -4.98 3.46e+00 1udg 244 -12.68 -4.93 3.66e+00 4rxn 54 -12.90 -4.90 3.79e+00 1k28D 391 -13.17 -4.89 3.85e+00 1xxsA 122 -13.20 -4.87 3.94e+00 1jnrB 150 -13.58 -4.84 4.09e+00 2bsdA 264 -13.25 -4.84 4.09e+00 1ia9A 280 -12.45 -4.80 4.31e+00 1uyjA 296 -12.67 -4.78 4.44e+00 2b25A 336 -12.76 -4.74 4.64e+00 1plfA 72 -12.02 -4.71 4.83e+00 1gg6C 97 -12.06 -4.69 4.90e+00 1agy 200 -12.07 -4.62 5.38e+00 2a9mL 110 -11.89 -4.61 5.41e+00 1k1gA 131 -12.59 -4.55 5.85e+00 1g0hA 252 -12.56 -4.54 5.96e+00 1ois 223 -12.70 -4.53 5.97e+00 1ffa 214 -12.05 -4.53 6.04e+00 1lldA 319 -12.09 -4.51 6.13e+00 2cszA 76 -13.01 -4.51 6.18e+00 1ab9C 97 -11.88 -4.49 6.32e+00 1cex 214 -12.00 -4.49 6.35e+00 1vqvA 306 -12.35 -4.45 6.61e+00 1ujnA 348 -12.84 -4.44 6.68e+00 1dk4A 252 -12.43 -4.41 6.95e+00 1zcjA 463 -12.67 -4.38 7.20e+00 1vr7A 142 -11.30 -4.34 7.66e+00 6prcC 336 -12.30 -4.31 7.94e+00 1tfi 50 -11.83 -4.30 7.98e+00 1cc1S 283 -12.70 -4.30 8.04e+00 1yk3A 210 -11.36 -4.29 8.11e+00 1iq0A 592 -12.33 -4.28 8.16e+00 1ny6A 267 -12.04 -4.28 8.19e+00 1cus 200 -11.70 -4.26 8.43e+00 1qydA 313 -12.17 -4.22 8.81e+00 1vggA 161 -12.10 -4.18 9.25e+00 1xauA 122 -12.17 -4.16 9.49e+00 1bn5 478 -12.14 -4.10 1.03e+01 1mfn 185 -11.46 -4.10 1.03e+01 2bl5A 140 -11.44 -4.08 1.05e+01 1i81A 83 -11.58 -4.04 1.11e+01 1iro 54 -12.09 -4.04 1.11e+01 1fonA 240 -12.75 -4.04 1.11e+01 1ui0A 205 -11.54 -4.04 1.12e+01 1de6A 426 -13.22 -4.02 1.14e+01 1y4lA 121 -13.12 -4.01 1.16e+01 1tluA 130 -10.94 -4.00 1.16e+01 1de5A 426 -13.18 -3.99 1.18e+01 1k92A 455 -11.36 -3.98 1.20e+01 1yaiA 151 -12.16 -3.98 1.20e+01 1rlyA 60 -12.76 -3.97 1.21e+01 2cgaA 245 -11.48 -3.94 1.26e+01 1gtdA 85 -10.68 -3.91 1.32e+01 1lwdA 413 -11.32 -3.88 1.37e+01 1elt 236 -12.29 -3.87 1.39e+01 1clc 639 -11.99 -3.86 1.40e+01 1hzdA 272 -11.68 -3.85 1.41e+01 1a0hA 159 -11.55 -3.85 1.43e+01 1ddgA 374 -12.22 -3.83 1.46e+01 1tzpA 255 -11.71 -3.82 1.47e+01 2a3nA 355 -11.47 -3.82 1.48e+01 1nbcA 155 -11.36 -3.81 1.49e+01 1ncg 110 -11.06 -3.81 1.49e+01 1wgeA 83 -12.52 -3.81 1.49e+01 1ff9A 450 -11.78 -3.81 1.50e+01 2cs3A 93 -11.57 -3.80 1.50e+01 1cuj 214 -11.32 -3.80 1.51e+01 1jpdX 324 -11.54 -3.80 1.51e+01 1kjvB 100 -10.93 -3.80 1.52e+01 1b6a 478 -11.83 -3.80 1.52e+01 1atlA 202 -11.63 -3.79 1.52e+01 1k2i1 245 -11.35 -3.79 1.53e+01 1e1oA 504 -11.54 -3.79 1.54e+01 1mgqA 83 -11.28 -3.79 1.54e+01 1dthA 203 -11.71 -3.77 1.57e+01 1dl6A 58 -12.50 -3.77 1.57e+01 1m3sA 186 -11.15 -3.75 1.62e+01 1eia 207 -10.88 -3.73 1.66e+01 1s8iA 121 -12.78 -3.73 1.66e+01 1kyhA 276 -13.49 -3.72 1.69e+01 2f4lA 297 -12.53 -3.70 1.73e+01 1wq8A 110 -11.04 -3.70 1.73e+01 1p9hA 226 -11.92 -3.68 1.77e+01 1oalA 151 -12.08 -3.68 1.78e+01 1kmqA 184 -12.22 -3.67 1.80e+01 1mnnA 340 -11.47 -3.67 1.80e+01 1u3wA 374 -11.43 -3.59 2.00e+01 2a4hA 126 -11.01 -3.58 2.02e+01 2d27A 149 -10.79 -3.58 2.03e+01 1uxtA 501 -11.82 -3.58 2.03e+01 1jndA 420 -11.45 -3.57 2.04e+01 1lylA 504 -11.27 -3.53 2.14e+01 1rzfL 213 -10.82 -3.51 2.23e+01 1nyoA 163 -10.92 -3.50 2.25e+01 2eiaB 206 -10.70 -3.49 2.28e+01 1iznA 286 -11.43 -3.49 2.29e+01 1x8mA 288 -11.66 -3.47 2.33e+01 2a9uA 144 -10.92 -3.47 2.33e+01 1iqyA 638 -11.65 -3.47 2.33e+01 1qq8A 214 -11.27 -3.47 2.34e+01 1mc2A 122 -12.31 -3.47 2.34e+01 1o7qA 289 -10.79 -3.45 2.39e+01 3cyr 107 -10.88 -3.43 2.45e+01 1zfuA 40 -11.01 -3.43 2.46e+01 1up9A 107 -10.90 -3.43 2.47e+01 1n45A 233 -11.21 -3.43 2.47e+01 1avk 638 -11.65 -3.41 2.51e+01 1mn4A 282 -11.13 -3.40 2.55e+01 1t3nA 388 -11.18 -3.40 2.56e+01 1erp 38 -10.99 -3.35 2.72e+01 1siiA 646 -11.60 -3.35 2.73e+01 1ui8A 638 -11.55 -3.33 2.80e+01 1ui7A 638 -11.54 -3.32 2.84e+01 1f20A 435 -11.12 -3.28 3.00e+01 1nciA 110 -10.55 -3.28 3.02e+01 1zroA 602 -10.94 -3.26 3.10e+01 1w6gA 646 -11.52 -3.25 3.14e+01 1y7qA 98 -10.71 -3.24 3.18e+01 1yc5A 246 -10.85 -3.23 3.20e+01 1jtaA 361 -11.33 -3.23 3.22e+01 1zetA 388 -11.18 -3.22 3.24e+01 1m6uA 272 -10.76 -3.21 3.28e+01 1h70A 255 -11.35 -3.21 3.29e+01 2b9hA 353 -10.91 -3.21 3.29e+01 1ivwA 638 -11.41 -3.21 3.29e+01 1tllA 688 -11.18 -3.20 3.33e+01 1ppa 121 -12.46 -3.19 3.38e+01 1rjoA 646 -11.46 -3.19 3.38e+01 1xipA 388 -10.83 -3.19 3.40e+01 1cghA 224 -11.06 -3.17 3.49e+01 1ff4A 65 -10.44 -3.17 3.51e+01 1v0eA 666 -11.04 -3.16 3.52e+01 1gnhA 206 -10.86 -3.13 3.68e+01 1u6rA 380 -11.19 -3.13 3.68e+01 1vm9A 111 -11.35 -3.13 3.69e+01 1qw2A 102 -10.07 -3.12 3.71e+01 1xjzA 233 -10.94 -3.12 3.75e+01 1b6rA 355 -10.89 -3.10 3.81e+01 3pbgA 468 -11.11 -3.10 3.82e+01 1bu8A 452 -12.46 -3.10 3.83e+01 1b5fB 87 -10.52 -3.10 3.83e+01 1pe9A 361 -11.05 -3.09 3.87e+01 1tx4B 178 -11.53 -3.09 3.88e+01 1w36C 1122 -11.66 -3.08 3.94e+01 1owfB 94 -10.22 -3.08 3.95e+01 1h9hE 223 -11.04 -3.08 3.96e+01