% 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.YEL012W.t2k-100-30-alpha Host: farm09 Fri Nov 18 19:28:36 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YEL0/YEL012W % --------------------------------------------------------------------- % 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 YEL012W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL012W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13048 sequences, 3092733 residues, 219 nodes, 339.57 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(=2.0674) * Reverse)^tau(=0.7781))) % 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 1x23A 155 -194.85 -184.79 4.94e-41 1z2uA 150 -198.24 -183.43 8.90e-41 2ayvA 166 -192.65 -181.16 2.36e-40 1y6lA 149 -184.56 -175.08 3.29e-39 1jbbA 153 -173.60 -160.77 1.77e-36 2bepA 159 -170.60 -159.11 3.70e-36 1u9aA 160 -171.60 -159.10 3.72e-36 1jatA 155 -170.34 -157.99 6.10e-36 2ucz 165 -171.53 -157.65 7.10e-36 1yh2A 175 -167.22 -157.38 8.00e-36 1fzyA 149 -166.93 -157.11 9.00e-36 2e2c 156 -167.20 -156.68 1.09e-35 1fxtA 149 -163.09 -152.38 7.49e-35 1i7kA 179 -159.71 -150.10 2.08e-34 1zdnA 158 -156.85 -146.11 1.26e-33 1yh6A 179 -151.88 -141.88 8.61e-33 1yrvA 169 -145.19 -135.57 1.55e-31 1yf9A 171 -142.33 -133.19 4.67e-31 2awfA 172 -140.50 -129.38 2.73e-30 1wzvA 155 -140.24 -128.11 4.93e-30 2a4dA 160 -120.54 -111.03 1.61e-26 1j7dA 145 -117.74 -106.51 1.43e-25 1jatB 138 -113.69 -104.48 3.85e-25 1zuoA 186 -79.81 -69.54 2.05e-17 1s1qA 145 -35.62 -24.34 7.60e-06 1kppA 145 -35.47 -23.72 1.16e-05 1uzxA 169 -32.79 -22.77 2.21e-05 1tgoA 773 -24.71 -12.62 3.52e-02 1ywzA 175 -22.97 -11.83 6.53e-02 1qhtA 775 -22.61 -10.56 1.82e-01 1qqcA 773 -21.99 -10.52 1.88e-01 2ac5A 316 -19.96 -10.40 2.07e-01 1ukxA 137 -20.09 -10.35 2.16e-01 2ac3A 316 -19.79 -10.23 2.38e-01 1ks8A 433 -21.22 -10.23 2.38e-01 1eyvA 156 -20.31 -9.72 3.61e-01 2es9A 115 -21.19 -9.57 4.10e-01 2biiA 424 -18.19 -9.35 4.89e-01 1who 96 -18.22 -9.02 6.47e-01 2auaA 224 -19.90 -8.97 6.76e-01 1bihA 395 -18.30 -8.96 6.79e-01 1h3oB 76 -19.74 -8.68 8.60e-01 1jpzA 473 -20.28 -8.63 9.00e-01 1xaoA 121 -18.38 -8.62 9.03e-01 1nekC 129 -19.12 -8.37 1.12e+00 6gsvA 217 -18.70 -8.28 1.21e+00 1winA 143 -19.60 -8.23 1.27e+00 1eqfA 280 -19.75 -8.09 1.42e+00 1gaxA 862 -20.95 -8.03 1.50e+00 1iynA 295 -17.68 -7.77 1.88e+00 1srqA 341 -17.61 -7.63 2.13e+00 1c3cA 429 -20.28 -7.43 2.53e+00 1kbhB 59 -16.59 -7.36 2.69e+00 2bnxA 386 -18.95 -7.34 2.73e+00 1x8vA 455 -18.09 -7.33 2.76e+00 1d8hA 311 -16.81 -7.23 3.02e+00 1ccg 291 -18.44 -7.20 3.11e+00 1bu7A 455 -18.75 -7.15 3.24e+00 1b2pA 119 -15.79 -7.09 3.41e+00 2cyp 294 -18.41 -7.06 3.51e+00 1ryc 294 -18.44 -7.04 3.56e+00 1vj7A 393 -18.38 -7.03 3.59e+00 2bzvA 181 -16.17 -6.96 3.81e+00 2bzuA 181 -15.94 -6.95 3.86e+00 1wloA 136 -17.52 -6.92 3.96e+00 1kb9F 74 -18.25 -6.90 4.05e+00 1dseA 292 -18.12 -6.89 4.08e+00 1kb9D 246 -17.29 -6.88 4.11e+00 1y4wA 518 -15.95 -6.87 4.16e+00 1mkrA 294 -18.09 -6.83 4.29e+00 1xx1A 285 -16.49 -6.82 4.33e+00 1kyoD 248 -17.31 -6.82 4.34e+00 1ny9A 143 -17.97 -6.82 4.35e+00 1ezvD 245 -17.08 -6.77 4.52e+00 1ds4A 292 -18.10 -6.77 4.56e+00 1zbyA 294 -18.15 -6.68 4.90e+00 1z53A 294 -18.15 -6.67 4.95e+00 1jdrA 294 -17.97 -6.62 5.21e+00 1cdy 178 -16.22 -6.61 5.24e+00 1vfaB 116 -15.05 -6.60 5.30e+00 1d8iA 311 -16.00 -6.58 5.40e+00 1ffyA 917 -18.32 -6.55 5.55e+00 1qu2A 917 -18.32 -6.55 5.55e+00 1nu5A 370 -16.21 -6.52 5.68e+00 1i8kB 124 -14.80 -6.49 5.82e+00 2b1yA 104 -14.99 -6.43 6.16e+00 1s5jA 847 -19.87 -6.42 6.19e+00 1f6fB 210 -15.37 -6.42 6.21e+00 1h5zA 455 -17.16 -6.38 6.44e+00 1bp3B 211 -16.33 -6.38 6.48e+00 2bmhA 455 -18.02 -6.37 6.51e+00 1g7jB 116 -14.79 -6.34 6.67e+00 1a2yB 116 -14.74 -6.32 6.78e+00 1go3E 187 -15.52 -6.24 7.32e+00 1uu1A 335 -17.64 -6.23 7.40e+00 1g9mC 185 -15.67 -6.23 7.41e+00 1otkA 249 -17.31 -6.22 7.44e+00 1u13A 455 -16.84 -6.16 7.87e+00 1htrB 329 -14.70 -6.14 8.04e+00 1vhzA 198 -15.27 -6.14 8.04e+00 1ezvH 74 -17.69 -6.13 8.12e+00 1z2cB 383 -17.11 -6.09 8.38e+00 1h3fA 432 -16.46 -5.95 9.53e+00 1rtwA 220 -19.98 -5.93 9.71e+00 1kkjA 419 -16.88 -5.92 9.80e+00 1chrA 370 -15.45 -5.91 9.87e+00 1lvmA 229 -15.15 -5.90 1.00e+01 1itkA 731 -17.23 -5.84 1.06e+01 1fm2A 169 -17.98 -5.84 1.06e+01 1o5oA 221 -15.28 -5.82 1.07e+01 1iapA 211 -16.50 -5.81 1.09e+01 1kl1A 419 -16.82 -5.80 1.10e+01 1xszA 356 -17.03 -5.80 1.10e+01 1qnrA 344 -15.61 -5.75 1.15e+01 1jk0A 419 -18.84 -5.75 1.15e+01 1fg7A 356 -16.09 -5.74 1.16e+01 2a4nA 182 -14.61 -5.72 1.18e+01 1v54A 514 -17.96 -5.70 1.20e+01 1ykhA 108 -18.23 -5.68 1.22e+01 1b87A 181 -14.64 -5.68 1.23e+01 1ezfA 340 -17.03 -5.67 1.24e+01 3cd4 182 -15.40 -5.66 1.25e+01 1keyA 235 -18.87 -5.65 1.26e+01 1j0tA 78 -16.99 -5.65 1.26e+01 1td6A 306 -17.83 -5.64 1.27e+01 1ibrB 462 -17.75 -5.63 1.28e+01 1eal 127 -14.59 -5.62 1.29e+01 1w4xA 542 -15.91 -5.62 1.29e+01 2bnfB 241 -15.04 -5.61 1.31e+01 1ea1A 455 -16.34 -5.59 1.34e+01 2bneA 241 -15.04 -5.58 1.35e+01 1rt8A 513 -16.74 -5.54 1.40e+01 1qnoA 344 -15.47 -5.54 1.40e+01 1j1jA 240 -18.52 -5.52 1.42e+01 1im2A 444 -17.60 -5.50 1.45e+01 1c1kA 217 -16.20 -5.48 1.47e+01 1snrA 341 -15.27 -5.48 1.48e+01 1bd3A 243 -16.08 -5.47 1.50e+01 1fdlH 218 -14.42 -5.44 1.53e+01 1yjsA 419 -16.45 -5.44 1.53e+01 1fo8A 343 -15.53 -5.43 1.55e+01 1xo1A 291 -15.97 -5.42 1.56e+01 1gewA 356 -15.72 -5.42 1.56e+01 2occA 514 -17.78 -5.41 1.57e+01 1t7sA 137 -17.93 -5.41 1.57e+01 1ornA 226 -15.71 -5.41 1.58e+01 1lm8V 160 -16.76 -5.41 1.59e+01 1isaA 192 -15.05 -5.40 1.59e+01 1fjgB 256 -17.92 -5.40 1.59e+01 1jpmA 366 -15.46 -5.40 1.59e+01 1fm4A 159 -16.41 -5.39 1.60e+01 1fo9A 348 -15.47 -5.39 1.61e+01 1iscA 192 -15.04 -5.38 1.63e+01 1n71A 180 -14.33 -5.37 1.63e+01 1vljA 407 -16.18 -5.37 1.64e+01 1um0A 365 -15.60 -5.36 1.65e+01 2c1dA 264 -15.23 -5.34 1.68e+01 1cdi 179 -14.49 -5.33 1.71e+01 1xkrA 206 -14.83 -5.32 1.72e+01 1zgsA 447 -14.28 -5.32 1.72e+01 1tkkA 366 -15.77 -5.31 1.74e+01 1wgzA 510 -16.92 -5.30 1.75e+01 1q8bA 105 -16.30 -5.29 1.76e+01 1ev0A 58 -15.35 -5.28 1.78e+01 1senA 164 -15.77 -5.26 1.82e+01 1qfhA 212 -15.40 -5.26 1.83e+01 1bw0A 416 -18.11 -5.24 1.86e+01 1y60A 169 -15.13 -5.23 1.87e+01 1oivA 191 -14.47 -5.23 1.87e+01 1mla 309 -15.42 -5.23 1.88e+01 1u08A 386 -14.82 -5.22 1.88e+01 1u1jA 765 -16.30 -5.21 1.91e+01 2aq4A 434 -15.54 -5.20 1.92e+01 1oxsC 353 -14.99 -5.20 1.93e+01 1cd9C 175 -16.01 -5.18 1.96e+01 1bea 127 -14.22 -5.18 1.97e+01 1qkrA 188 -17.74 -5.18 1.97e+01 1bfa 134 -14.27 -5.17 1.99e+01 1mqsA 671 -16.78 -5.16 2.00e+01 1j9qA 341 -15.07 -5.16 2.00e+01 1v9sA 208 -14.52 -5.14 2.05e+01 1q8cA 151 -16.15 -5.12 2.07e+01 1ldjA 760 -17.06 -5.12 2.08e+01 1c4kA 730 -17.06 -5.11 2.09e+01 1kewA 361 -15.46 -5.11 2.09e+01 1ut8A 291 -15.66 -5.11 2.09e+01 1oxxK 353 -15.12 -5.11 2.10e+01 1mxrA 375 -17.45 -5.11 2.10e+01 1uxtA 501 -16.62 -5.10 2.11e+01 1br0A 120 -18.44 -5.08 2.16e+01 1e9xA 455 -15.80 -5.07 2.19e+01 1exnB 290 -15.56 -5.07 2.19e+01 1oixA 191 -14.47 -5.06 2.19e+01 1bs0A 384 -14.84 -5.05 2.22e+01 1tqgA 105 -16.53 -5.05 2.22e+01 1foaA 348 -15.05 -5.03 2.27e+01 1deeG 54 -13.94 -5.02 2.29e+01 1vb5A 276 -16.46 -4.99 2.35e+01 1j7vR 214 -13.92 -4.99 2.35e+01 1i0lA 221 -16.21 -4.98 2.38e+01 1xp3A 307 -15.08 -4.96 2.43e+01 2ar9A 278 -15.58 -4.94 2.46e+01 1et7A 341 -14.84 -4.92 2.52e+01 2a5jA 191 -14.86 -4.90 2.56e+01 2bwnA 401 -15.08 -4.88 2.61e+01 1t7lA 766 -17.61 -4.87 2.65e+01 2abk 211 -14.51 -4.86 2.67e+01 1m98A 317 -14.66 -4.84 2.70e+01 1iomA 377 -16.11 -4.84 2.72e+01 1pszA 303 -18.79 -4.83 2.74e+01 1e1aA 314 -13.68 -4.82 2.76e+01 1ha2A 585 -16.71 -4.82 2.77e+01 1pufB 73 -14.04 -4.81 2.78e+01 1b72B 87 -14.10 -4.81 2.79e+01 1lqsR 214 -13.70 -4.81 2.80e+01 1or0A 160 -17.78 -4.80 2.81e+01 1w9hA 427 -17.88 -4.80 2.82e+01 1qgrA 876 -17.18 -4.77 2.91e+01 1xauA 122 -14.18 -4.76 2.94e+01 1n5uA 585 -16.57 -4.75 2.96e+01 1exnA 290 -15.19 -4.74 3.00e+01 1h6qA 168 -16.45 -4.74 3.00e+01 1lqbC 162 -16.62 -4.73 3.01e+01 1tc1A 220 -15.73 -4.73 3.01e+01 1bg1A 722 -18.11 -4.73 3.02e+01 1o4tA 133 -13.52 -4.72 3.05e+01 1dh3A 55 -16.55 -4.72 3.05e+01 1sxjE 354 -15.08 -4.72 3.05e+01 1m41A 380 -16.55 -4.71 3.06e+01 1humA 69 -12.94 -4.71 3.08e+01 1wpaA 114 -17.82 -4.71 3.09e+01 1xsrA 168 -14.11 -4.69 3.13e+01 2d2eA 250 -15.40 -4.69 3.14e+01 1as8A 343 -14.69 -4.68 3.17e+01 1t4hA 290 -14.47 -4.68 3.17e+01 1w2wB 191 -14.84 -4.68 3.17e+01 1v63A 101 -15.17 -4.68 3.17e+01 1r3sA 367 -14.84 -4.67 3.19e+01 1biqA 375 -17.82 -4.67 3.19e+01 1dypA 271 -13.12 -4.67 3.20e+01 1iruK 201 -14.87 -4.67 3.21e+01 1iq0A 592 -16.34 -4.66 3.22e+01 1nt0A 286 -13.98 -4.66 3.24e+01 1l4uA 176 -14.35 -4.63 3.32e+01 2bxkA 585 -16.74 -4.62 3.35e+01 1dd5A 185 -18.76 -4.61 3.40e+01 1ksr 100 -14.25 -4.61 3.40e+01 1rcd 173 -17.45 -4.60 3.42e+01 1v0aA 178 -13.42 -4.59 3.46e+01 1djtA 64 -12.96 -4.59 3.47e+01 1uroA 367 -14.76 -4.58 3.48e+01 1hjxA 362 -15.04 -4.58 3.48e+01 1ir6A 424 -15.28 -4.58 3.50e+01 1ej8A 140 -13.45 -4.56 3.58e+01 1imvA 398 -14.09 -4.55 3.58e+01 1vi0A 206 -15.60 -4.53 3.66e+01 1mwvA 714 -16.38 -4.53 3.67e+01 1fo5A 85 -13.77 -4.52 3.72e+01 1rj1A 151 -14.75 -4.52 3.72e+01 1i5nA 146 -16.43 -4.51 3.75e+01 1j5vA 351 -15.96 -4.48 3.83e+01 1ospH 218 -13.26 -4.48 3.85e+01 2bi7A 384 -14.37 -4.48 3.86e+01 1k6kA 143 -14.60 -4.47 3.90e+01 6acn 754 -14.70 -4.45 3.96e+01 1gtkA 313 -14.28 -4.45 3.96e+01 1qupA 222 -13.20 -4.45 3.98e+01 1dvpA 220 -14.32 -4.44 3.99e+01