% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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.YGR032W.t2k-100-30-alpha Host: farm08 Thu Nov 18 00:18:50 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR032W % --------------------------------------------------------------------- % 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 YGR032W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR032W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 1896 nodes, 2625.30 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 (=10700) sequences: % N / (1 + exp(-(lambda(=2.2677) * Reverse)^tau(=0.7355))) % 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 1pw4A 451 -39.09 -13.52 4.41e-02 1hmcA 148 -23.51 -10.82 2.86e-01 1cjaA 342 -22.74 -10.28 4.25e-01 1odoA 408 -25.19 -9.91 5.55e-01 1ah7 245 -25.55 -9.83 5.89e-01 1hmcB 148 -22.35 -9.77 6.14e-01 1fkmA 396 -28.14 -9.06 1.04e+00 1l9hA 349 -36.42 -9.06 1.05e+00 1ppjC 379 -35.01 -8.98 1.11e+00 1u19A 349 -36.58 -8.87 1.20e+00 1hzxA 349 -34.84 -8.52 1.57e+00 1j5sA 463 -23.44 -8.51 1.58e+00 1lkxA 697 -28.55 -8.50 1.59e+00 1h2vC 771 -30.12 -8.50 1.59e+00 1qjbA 245 -27.76 -8.35 1.78e+00 1n1bA 549 -29.77 -8.22 1.97e+00 1g71A 347 -21.26 -8.18 2.04e+00 1mhyB 395 -25.01 -8.03 2.28e+00 1h6kA 757 -30.07 -8.01 2.32e+00 1qcrC 378 -31.98 -8.01 2.32e+00 1kb9C 385 -35.33 -7.95 2.43e+00 1ezvC 385 -34.49 -7.86 2.61e+00 1ezfA 340 -29.48 -7.77 2.78e+00 1f88A 348 -33.57 -7.55 3.33e+00 1mhyG 169 -20.51 -7.51 3.42e+00 1fqiA 147 -20.42 -7.44 3.62e+00 1lla 628 -22.97 -7.43 3.66e+00 1ajqB 557 -21.48 -7.42 3.68e+00 1j4nA 271 -26.40 -7.42 3.69e+00 1gm9B 557 -21.51 -7.42 3.69e+00 1gm7B 557 -21.28 -7.15 4.54e+00 1ifa 158 -20.50 -7.15 4.56e+00 1gk9B 557 -21.23 -7.12 4.68e+00 3crxA 343 -22.79 -7.03 5.03e+00 1ihgA 370 -27.23 -7.02 5.07e+00 1gkfB 557 -21.10 -7.01 5.10e+00 1be3C 379 -34.19 -6.91 5.52e+00 1crxA 322 -20.65 -6.90 5.58e+00 1qbkB 890 -32.36 -6.85 5.78e+00 1e3aB 560 -20.90 -6.75 6.30e+00 1r1mA 164 -18.73 -6.74 6.33e+00 2pgd 482 -28.62 -6.70 6.53e+00 1ouoA 210 -19.24 -6.70 6.55e+00 1uk8A 282 -18.61 -6.67 6.71e+00 1s2xA 206 -25.24 -6.66 6.75e+00 1amz 435 -23.01 -6.66 6.78e+00 1j99A 293 -19.00 -6.60 7.08e+00 1i36A 264 -21.15 -6.60 7.11e+00 1keyA 235 -27.42 -6.57 7.31e+00 1c17M 177 -35.15 -6.54 7.47e+00 1tbmA 326 -22.90 -6.54 7.49e+00 1ku1A 230 -21.82 -6.50 7.70e+00 1pnkB 557 -20.54 -6.48 7.82e+00 1olrA 224 -20.14 -6.46 7.97e+00 1jipA 403 -26.64 -6.46 7.99e+00 1a76 326 -21.06 -6.40 8.33e+00 1iapA 211 -22.11 -6.40 8.34e+00 1ll1 590 -21.36 -6.34 8.79e+00 1kqfC 217 -32.99 -6.33 8.83e+00 1b5l 172 -24.01 -6.25 9.47e+00 2dri 271 -19.05 -6.22 9.73e+00 1kbuA 349 -22.17 -6.20 9.89e+00 1hg4A 279 -22.19 -6.14 1.03e+01 1dugA 234 -20.97 -6.13 1.05e+01 1ichA 112 -18.98 -6.11 1.07e+01 1gw5B 591 -22.39 -6.10 1.08e+01 1fo3A 460 -19.99 -6.07 1.10e+01 1b9zA 516 -21.29 -6.07 1.10e+01 1eupA 403 -24.38 -6.06 1.11e+01 1j1jA 240 -28.17 -6.05 1.11e+01 1csh 435 -22.39 -6.04 1.13e+01 4crxA 322 -20.38 -6.03 1.14e+01 1dq3A 454 -22.20 -6.03 1.14e+01 1gx3A 284 -18.78 -5.99 1.17e+01 1l0lA 446 -18.75 -5.99 1.18e+01 1rr7A 129 -20.62 -5.99 1.18e+01 1qlaC 256 -31.74 -5.97 1.19e+01 1a0rP 245 -18.64 -5.97 1.20e+01 1b43A 340 -19.69 -5.95 1.21e+01 1e9lA 377 -20.84 -5.95 1.22e+01 2ran 316 -19.25 -5.93 1.24e+01 1ea3A 164 -18.57 -5.91 1.25e+01 1a8b 318 -19.37 -5.86 1.31e+01 1xyzA 347 -20.00 -5.86 1.31e+01 2bidA 197 -19.49 -5.86 1.31e+01 1bib 321 -18.66 -5.85 1.32e+01 1iupA 282 -17.82 -5.84 1.33e+01 1a8a 318 -19.19 -5.82 1.35e+01 1ltm 320 -20.05 -5.82 1.36e+01 1tljA 213 -18.67 -5.81 1.36e+01 1mtyG 162 -18.95 -5.81 1.37e+01 1ehkA 562 -37.68 -5.81 1.37e+01 1s7zA 117 -19.57 -5.80 1.38e+01 1ecrA 309 -18.16 -5.80 1.38e+01 1qusA 322 -20.09 -5.80 1.38e+01 1ldfA 281 -27.74 -5.78 1.40e+01 1xsvA 113 -19.13 -5.76 1.42e+01 5bcaA 516 -20.72 -5.75 1.44e+01 1dofA 403 -24.69 -5.75 1.44e+01 1bp3A 191 -20.15 -5.73 1.47e+01 1fjgD 209 -17.32 -5.69 1.51e+01 1jk0B 345 -22.41 -5.69 1.52e+01 1pu6A 218 -18.18 -5.68 1.52e+01 1gnlA 544 -26.81 -5.68 1.52e+01 1anxA 319 -19.14 -5.68 1.53e+01 1ofcX 304 -21.77 -5.67 1.54e+01 1tw9A 206 -22.52 -5.67 1.54e+01 1qjaA 245 -26.79 -5.66 1.55e+01 1nc5A 373 -19.97 -5.63 1.59e+01 1eqfA 280 -20.61 -5.62 1.60e+01 1n83A 270 -22.96 -5.62 1.61e+01 1be3A 446 -18.30 -5.61 1.62e+01 1b77A 228 -17.15 -5.60 1.63e+01 1lvoA 302 -19.64 -5.60 1.63e+01 1uedA 406 -24.59 -5.59 1.64e+01 1qfjA 232 -17.51 -5.56 1.69e+01 1f6bA 198 -16.71 -5.56 1.69e+01 1s6bB 119 -17.76 -5.54 1.72e+01 3fapB 94 -20.14 -5.52 1.75e+01 1h5vA 304 -20.06 -5.50 1.78e+01 1e5rA 290 -18.09 -5.48 1.81e+01 1ib2A 349 -18.92 -5.48 1.81e+01 1t8qA 336 -19.56 -5.47 1.83e+01 1r0vA 305 -18.23 -5.45 1.86e+01 1pme 380 -17.47 -5.44 1.87e+01 1bia 321 -18.58 -5.42 1.91e+01 1so2A 420 -23.04 -5.39 1.95e+01 1tn6A 382 -24.35 -5.39 1.96e+01 1h7eA 245 -16.89 -5.38 1.96e+01 1v33A 366 -18.69 -5.37 1.99e+01 1aa7A 158 -17.71 -5.35 2.03e+01 1ht6A 405 -23.21 -5.33 2.06e+01 1j8rA 196 -18.01 -5.32 2.08e+01 7a3hA 303 -19.72 -5.31 2.09e+01 1tbfA 347 -22.06 -5.31 2.09e+01 1qgrA 876 -32.13 -5.30 2.10e+01 1by2 119 -16.41 -5.28 2.14e+01 1wer 334 -22.81 -5.27 2.17e+01 1h68A 239 -30.38 -5.27 2.17e+01 1q8yA 373 -18.02 -5.26 2.18e+01 1ornA 226 -17.90 -5.26 2.19e+01 1ld8A 382 -24.06 -5.25 2.21e+01 1jetA 517 -18.91 -5.24 2.23e+01 1q5zA 177 -18.54 -5.23 2.25e+01 1utg 70 -17.19 -5.22 2.25e+01 1jcqA 382 -23.77 -5.22 2.26e+01 1u4qA 322 -27.33 -5.21 2.28e+01 1h2kA 349 -19.05 -5.21 2.28e+01 1sftA 388 -16.72 -5.17 2.35e+01 1rkpA 326 -21.71 -5.16 2.38e+01 1rztA 331 -17.50 -5.16 2.38e+01 1gkxA 388 -22.60 -5.16 2.38e+01 1howA 373 -18.14 -5.15 2.39e+01 1hfoA 113 -16.53 -5.15 2.40e+01 1fx8A 281 -27.73 -5.13 2.45e+01 1ppjA 446 -17.92 -5.13 2.45e+01 1hqvA 191 -19.69 -5.11 2.49e+01 1n40A 396 -21.53 -5.08 2.55e+01 2olbA 517 -18.83 -5.06 2.59e+01 3erk 364 -17.12 -5.06 2.60e+01 1h2sA 225 -30.04 -5.05 2.62e+01 1qcrA 446 -18.15 -5.04 2.65e+01 1g2nA 264 -19.64 -5.03 2.66e+01 2at9 247 -23.15 -5.03 2.67e+01 1mjgM 729 -31.19 -5.03 2.67e+01 1bd0A 388 -16.52 -5.02 2.69e+01 1b3qA 379 -22.91 -5.01 2.71e+01 5csmA 256 -21.53 -4.99 2.75e+01 1va6A 518 -22.35 -4.99 2.76e+01 1mmoG 162 -18.01 -4.99 2.77e+01 1u5pA 216 -26.64 -4.98 2.78e+01 1aueA 100 -20.36 -4.98 2.79e+01 1oxa 403 -25.10 -4.98 2.79e+01 1a3h 300 -19.23 -4.97 2.80e+01 1l2tA 235 -16.60 -4.97 2.81e+01 1pxfA 111 -15.26 -4.95 2.86e+01 821p 166 -16.57 -4.95 2.86e+01 1jgjA 217 -29.73 -4.94 2.87e+01 1ofv 169 -19.74 -4.94 2.89e+01 1qceA 123 -21.60 -4.92 2.95e+01 5p21 166 -16.50 -4.91 2.96e+01 1v5xA 203 -16.61 -4.91 2.98e+01 1nsgB 94 -19.40 -4.90 2.98e+01 1ctqA 166 -16.40 -4.89 3.02e+01 1itcA 516 -19.86 -4.87 3.06e+01 2utgA 70 -16.82 -4.87 3.07e+01 1cznA 169 -19.43 -4.87 3.07e+01 1gcvA 140 -17.90 -4.87 3.08e+01 1p9uA 302 -18.72 -4.86 3.11e+01 1brlA 355 -19.85 -4.85 3.11e+01 1ls6A 295 -16.46 -4.83 3.17e+01 1rykA 69 -16.89 -4.83 3.19e+01 1h1yA 228 -16.68 -4.82 3.21e+01 1oa4A 222 -16.71 -4.80 3.27e+01 1elwA 118 -19.37 -4.79 3.29e+01 1oaoC 729 -31.21 -4.78 3.32e+01 1tllA 688 -22.46 -4.76 3.38e+01 1gvhA 396 -20.34 -4.74 3.45e+01 1dnpA 471 -16.99 -4.73 3.47e+01 1hvd 319 -18.33 -4.73 3.48e+01 1csmA 256 -20.55 -4.73 3.48e+01 1kyoC 385 -33.22 -4.72 3.52e+01 1pot 325 -18.94 -4.71 3.54e+01 1jfaA 374 -22.04 -4.69 3.59e+01 1wmuA 141 -19.58 -4.69 3.60e+01 1aisB 200 -17.36 -4.69 3.61e+01 2ts1 419 -19.55 -4.68 3.62e+01 1pzlA 237 -20.31 -4.67 3.65e+01 1iqrA 420 -17.61 -4.67 3.66e+01 1np7A 489 -18.40 -4.67 3.67e+01 1m1hA 248 -19.33 -4.66 3.69e+01 1envA 123 -28.18 -4.65 3.74e+01 1k0iA 394 -18.62 -4.64 3.75e+01 1qpaA 345 -18.12 -4.64 3.76e+01 1rec 201 -17.51 -4.61 3.88e+01 1e3oC 160 -19.39 -4.59 3.93e+01 2phh 394 -18.13 -4.57 4.00e+01