% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % strfoo.1.YGR223C.t2k-100-30-str Host: cc74 Tue Nov 12 17:49:56 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR223C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YGR223C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR223C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 449 nodes, 318.80 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.6957) * Reverse)^tau(=0.7060))) % 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 1erjA 393 -329.84 -252.62 3.44e-28 1gotB 340 -309.99 -237.87 6.91e-27 1tbgA 340 -309.53 -235.45 1.14e-26 1gxrA 337 -248.40 -187.00 3.39e-22 1k8kC 372 -202.23 -130.66 1.57e-16 1c5kA 439 -119.82 -63.77 1.03e-08 1crzA 403 -116.66 -63.46 1.13e-08 1k32A 1045 -173.67 -60.68 2.63e-08 1jjuB 337 -110.69 -58.07 5.88e-08 1aoqA 567 -139.04 -54.50 1.80e-07 1aomA 567 -139.35 -54.42 1.85e-07 1qksA 567 -139.74 -53.85 2.21e-07 1jofA 365 -110.73 -53.66 2.35e-07 1jmxB 349 -102.76 -45.36 3.51e-06 2bbkH 355 -107.09 -42.33 9.77e-06 1kb0A 677 -94.33 -40.38 1.91e-05 1e1aA 314 -97.13 -38.35 3.87e-05 1g72A 573 -91.92 -38.24 4.01e-05 1qbiA 454 -99.83 -38.18 4.10e-05 4aahA 571 -91.38 -37.75 4.76e-05 1kv9A 668 -91.58 -36.65 7.05e-05 1cruA 454 -97.53 -35.51 1.06e-04 1c9uA 454 -94.95 -34.78 1.38e-04 1e8nA 710 -107.09 -34.66 1.44e-04 1gof 639 -76.38 -33.02 2.61e-04 1qfmA 710 -104.73 -33.02 2.61e-04 1goh 639 -76.56 -32.64 3.00e-04 1k3iA 656 -75.68 -31.76 4.15e-04 1bpoA 494 -104.87 -29.28 1.05e-03 1qniA 581 -89.23 -25.10 5.33e-03 1ijqA 316 -72.27 -23.42 1.05e-02 5nn9 388 -64.86 -23.36 1.08e-02 3nn9 388 -64.38 -22.70 1.41e-02 1f8eA 388 -64.00 -22.28 1.67e-02 2qwc 388 -64.20 -21.85 1.99e-02 1fwxA 595 -93.94 -21.31 2.50e-02 1a12A 413 -79.80 -21.24 2.57e-02 1h6lA 353 -81.18 -20.61 3.35e-02 2pooA 355 -79.46 -20.20 3.99e-02 1cvmA 353 -81.05 -19.72 4.87e-02 1tl2A 236 -54.40 -19.14 6.25e-02 2aaiB 262 -50.93 -19.01 6.63e-02 1qlgA 355 -80.64 -18.82 7.19e-02 3sil 379 -59.55 -18.66 7.72e-02 2sil 381 -59.07 -18.43 8.50e-02 1ospO 257 -67.81 -18.26 9.18e-02 1dim 381 -58.57 -17.96 1.05e-01 1dfcA 493 -58.89 -17.75 1.15e-01 1svpA 161 -44.53 -16.85 1.71e-01 1yna 194 -51.11 -16.82 1.73e-01 2snv 151 -43.32 -16.66 1.86e-01 4sli 679 -75.51 -16.44 2.05e-01 2sli 679 -75.51 -16.44 2.06e-01 1jlxA 304 -59.64 -16.43 2.06e-01 2madH 373 -62.02 -15.68 2.90e-01 1ksiB 642 -67.90 -15.36 3.36e-01 1ksiA 642 -67.33 -15.20 3.61e-01 1jlyA 304 -59.21 -15.13 3.73e-01 1eur 365 -59.92 -15.11 3.76e-01 1at0 145 -52.77 -14.97 4.01e-01 1pvxA 194 -49.15 -14.62 4.72e-01 1qba 858 -87.94 -14.61 4.74e-01 1kit 757 -89.67 -14.54 4.91e-01 1b6e 128 -36.55 -14.46 5.09e-01 1c7sA 858 -86.87 -14.42 5.20e-01 1abrB 267 -46.07 -13.52 7.94e-01 1wba 175 -51.30 -12.87 1.09e+00 1lenA 181 -40.53 -12.73 1.16e+00 1iq8A 582 -71.22 -12.67 1.19e+00 1ckmA 330 -57.86 -12.53 1.28e+00 1cknA 330 -57.61 -12.50 1.29e+00 1jceA 344 -53.15 -12.47 1.32e+00 2ltnA 181 -41.65 -12.44 1.33e+00 1jcfA 344 -53.00 -12.39 1.37e+00 1yaiA 151 -41.35 -12.35 1.39e+00 1sltA 134 -45.60 -12.20 1.50e+00 1qexA 288 -46.33 -12.13 1.55e+00 1lkfA 299 -45.52 -12.09 1.59e+00 1ijtA 128 -40.62 -12.08 1.60e+00 1soxA 466 -53.62 -11.60 2.03e+00 1eut 605 -62.20 -11.60 2.03e+00 1dlc 584 -49.41 -11.58 2.04e+00 1f5jA 199 -46.03 -11.48 2.14e+00 1c5lH 259 -44.91 -11.37 2.27e+00 1ilr1 152 -50.04 -11.35 2.29e+00 1euu 605 -62.21 -11.35 2.29e+00 1qhdA 398 -46.18 -11.31 2.34e+00 1aozA 552 -63.44 -11.26 2.40e+00 1mpp 361 -50.12 -11.18 2.50e+00 1ahtH 259 -44.94 -11.15 2.54e+00 1hxmD 242 -47.14 -11.13 2.56e+00 1hxs3 237 -42.06 -11.12 2.57e+00 1qhuA 460 -57.36 -11.12 2.57e+00 1sltB 134 -46.53 -11.05 2.67e+00 1gcyA 527 -54.85 -10.93 2.84e+00 1fnhA 271 -53.42 -10.91 2.86e+00 1d2pA 373 -57.11 -10.84 2.97e+00 1d0nA 729 -70.51 -10.76 3.09e+00 1h8dH 260 -44.14 -10.66 3.26e+00 1i82A 189 -44.30 -10.49 3.54e+00 1f89A 291 -39.46 -10.47 3.59e+00 1slaA 134 -45.24 -10.42 3.67e+00 1gw5M 435 -57.42 -10.39 3.72e+00 2eifA 136 -44.06 -10.39 3.72e+00 1yagG 125 -34.26 -10.31 3.89e+00 1ee8A 266 -41.55 -10.22 4.08e+00 2polA 366 -49.37 -10.14 4.24e+00 1rypI 222 -36.26 -10.13 4.26e+00 1i8aA 189 -44.05 -10.11 4.31e+00 1d4xG 126 -34.14 -10.08 4.39e+00 1l1zA 274 -41.80 -10.05 4.45e+00 1aj6 219 -37.22 -10.05 4.45e+00 1bkb 136 -43.76 -10.05 4.46e+00 1pvl 301 -43.51 -10.01 4.54e+00 1ucyH 150 -38.16 -9.99 4.59e+00 2mllB 255 -45.59 -9.93 4.73e+00 1xyn 178 -41.16 -9.92 4.77e+00 1kv7A 488 -60.62 -9.74 5.22e+00 1mrg 263 -37.07 -9.72 5.28e+00 8kme2 259 -42.85 -9.72 5.28e+00 1xypA 190 -46.83 -9.69 5.36e+00 1t7pA 698 -68.65 -9.65 5.47e+00 1bxxA 285 -48.16 -9.57 5.71e+00 1epwA 1290 -123.50 -9.52 5.87e+00 2hft 218 -39.95 -9.48 5.99e+00 1eaf 243 -34.37 -9.43 6.15e+00 1clc 639 -58.67 -9.43 6.15e+00 1xnb 185 -45.36 -9.37 6.37e+00 1bw8A 321 -49.60 -9.28 6.66e+00 1e50B 134 -33.29 -9.24 6.81e+00 1kshB 152 -37.06 -9.15 7.15e+00 1g7pA 274 -43.51 -9.11 7.30e+00 1nhp 447 -53.53 -9.05 7.53e+00 1g8jB 133 -35.07 -8.95 7.98e+00 1nlr 234 -37.87 -8.91 8.14e+00 1nhs 447 -53.54 -8.91 8.15e+00 1fzkA 274 -43.15 -8.90 8.17e+00 1joa 447 -53.56 -8.90 8.19e+00 1dykA 394 -54.53 -8.89 8.20e+00 1fnf 368 -59.66 -8.89 8.22e+00 1b3jA 274 -38.92 -8.84 8.46e+00 1dpb 243 -33.75 -8.83 8.50e+00 1jl0A 334 -45.82 -8.76 8.84e+00 1b7yB 785 -77.31 -8.67 9.25e+00 1gnyA 153 -41.43 -8.67 9.25e+00 1je6A 275 -37.79 -8.66 9.30e+00 2nlrA 234 -37.53 -8.65 9.34e+00 1io1A 398 -48.29 -8.58 9.71e+00 1ju3A 583 -60.80 -8.55 9.88e+00 1ga6A 372 -33.37 -8.52 1.00e+01 1g24A 211 -33.40 -8.51 1.01e+01 1c3oB 382 -45.63 -8.46 1.04e+01 1fzoA 274 -43.92 -8.45 1.04e+01 1iicA 422 -47.74 -8.41 1.07e+01 4rhv3 236 -36.96 -8.41 1.07e+01 1cwvA 492 -53.49 -8.38 1.08e+01 1hd8A 363 -51.60 -8.36 1.10e+01 1cs0B 382 -45.66 -8.33 1.11e+01 1dzkA 157 -39.08 -8.32 1.12e+01 1enxA 190 -46.26 -8.29 1.14e+01 1gv4A 528 -55.46 -8.25 1.17e+01 1g8kB 133 -34.83 -8.21 1.19e+01 1itvA 195 -40.71 -8.18 1.21e+01 1fmtB 314 -40.76 -8.17 1.22e+01 1iraX 152 -44.33 -8.09 1.27e+01 1jdc 429 -49.09 -8.08 1.28e+01 1irp 153 -46.15 -8.06 1.30e+01 1i31A 314 -46.70 -8.04 1.30e+01 1fmtA 314 -40.91 -8.04 1.31e+01 1jpc 109 -49.60 -7.99 1.34e+01 1jacC 133 -35.29 -7.98 1.35e+01 1dgaA 375 -43.18 -7.97 1.36e+01 1ji1A 637 -56.82 -7.92 1.40e+01 1ga1A 372 -32.76 -7.92 1.40e+01 1m26A 133 -35.17 -7.90 1.41e+01 1nmtA 392 -41.05 -7.90 1.41e+01 1ku8A 133 -35.29 -7.86 1.45e+01 1rhi3 236 -36.86 -7.83 1.47e+01 1am2 199 -45.62 -7.81 1.49e+01 1g6oA 330 -40.41 -7.80 1.49e+01 1jfuA 186 -32.21 -7.79 1.50e+01 1cb8A 678 -60.24 -7.78 1.51e+01 1eyqA 222 -37.22 -7.77 1.52e+01 1k4nA 192 -33.32 -7.77 1.52e+01 1jepA 222 -37.23 -7.77 1.52e+01 1pysB 785 -77.81 -7.75 1.53e+01 1eypA 222 -37.23 -7.75 1.54e+01 2shpA 525 -56.18 -7.74 1.55e+01 1m1cA 680 -55.14 -7.73 1.55e+01 1bxvA 91 -34.76 -7.73 1.55e+01 1iarB 207 -37.91 -7.73 1.55e+01 1b2pA 119 -50.16 -7.71 1.57e+01 1msaA 109 -50.67 -7.69 1.59e+01 1jmcA 246 -44.06 -7.65 1.63e+01 1jacA 133 -34.65 -7.61 1.66e+01 1g99A 408 -54.13 -7.59 1.68e+01 1hlcA 129 -41.16 -7.56 1.71e+01 1aqcA 172 -37.94 -7.52 1.75e+01 1aw8B 91 -30.27 -7.47 1.80e+01 1extA 162 -33.60 -7.46 1.81e+01 1eerB 227 -42.25 -7.44 1.83e+01 1elyA 449 -41.99 -7.42 1.85e+01 1bglA 1023 -79.90 -7.41 1.87e+01 1dceA 567 -44.77 -7.40 1.87e+01 1k28D 391 -46.69 -7.40 1.87e+01 1bco 327 -46.49 -7.40 1.88e+01 1ifrA 121 -38.26 -7.40 1.88e+01 1d5rA 324 -42.79 -7.39 1.89e+01 1aun 208 -40.20 -7.39 1.89e+01 1ixxB 123 -28.18 -7.38 1.90e+01 1b8jA 449 -41.50 -7.36 1.91e+01 1ed8A 449 -41.51 -7.36 1.92e+01 1evhA 112 -34.57 -7.36 1.92e+01 1hm2A 700 -62.81 -7.34 1.93e+01 1ky9A 448 -50.66 -7.34 1.94e+01 1ebaA 215 -41.88 -7.31 1.97e+01 1aw8E 91 -29.64 -7.30 1.98e+01 1a78A 134 -40.41 -7.29 2.00e+01 1viwB 198 -39.57 -7.26 2.02e+01 1b87A 181 -33.25 -7.24 2.05e+01 1dkxA 219 -37.70 -7.23 2.06e+01 2ayh 214 -40.23 -7.23 2.07e+01 1ej6A 1289 -83.72 -7.21 2.09e+01 1i9aA 182 -29.78 -7.20 2.10e+01 1vpsA 289 -41.10 -7.19 2.11e+01 1qcsA 211 -34.69 -7.18 2.12e+01 1kh5A 449 -40.85 -7.10 2.22e+01 1c8uA 285 -40.50 -7.10 2.22e+01 1jtdB 273 -45.11 -7.09 2.23e+01 1jwiB 125 -32.32 -7.09 2.24e+01 1i2hA 168 -37.69 -7.07 2.26e+01 1e79A 510 -53.72 -7.06 2.28e+01 1fvuB 125 -31.19 -7.05 2.28e+01 1bmfA 510 -54.27 -7.04 2.30e+01 1vmoA 163 -35.09 -7.04 2.30e+01 3hhrB 203 -40.02 -7.02 2.32e+01 1k0sA 151 -38.05 -7.01 2.33e+01 1ft9A 222 -40.71 -7.01 2.34e+01 2asi 360 -41.85 -6.99 2.36e+01 1orc 71 -29.35 -6.98 2.38e+01 1j6zA 376 -43.62 -6.95 2.43e+01 1alkA 449 -41.27 -6.93 2.46e+01 1pmaA 233 -36.33 -6.92 2.47e+01 1a2vA 655 -61.42 -6.91 2.48e+01 1el6B 219 -32.09 -6.91 2.48e+01 1yagA 375 -42.96 -6.91 2.49e+01 2anhA 446 -40.72 -6.91 2.49e+01 2btfA 375 -42.79 -6.88 2.52e+01 1jotA 133 -37.20 -6.85 2.57e+01 1bv4A 118 -30.40 -6.85 2.57e+01 1g6gA 127 -34.63 -6.85 2.57e+01 1f5mB 180 -32.01 -6.84 2.58e+01 1ei1A 391 -44.25 -6.82 2.62e+01 1r092 262 -34.21 -6.80 2.64e+01 1avwB 171 -42.44 -6.79 2.66e+01 1h8eA 510 -53.82 -6.78 2.68e+01 1vpsB 289 -40.83 -6.78 2.68e+01 1f5mA 180 -32.33 -6.76 2.70e+01 1ei5A 520 -58.20 -6.74 2.74e+01 1rie 129 -33.78 -6.74 2.74e+01 1f00I 282 -41.45 -6.73 2.75e+01 1jv2A 957 -80.65 -6.69 2.82e+01 1k4jA 230 -31.62 -6.67 2.84e+01 1hdkA 141 -36.50 -6.67 2.85e+01 1h9dB 134 -31.18 -6.67 2.85e+01 1fjgK 129 -30.96 -6.64 2.90e+01 1rl2A 137 -41.19 -6.63 2.91e+01 1dmhA 311 -36.97 -6.57 3.03e+01 1mkaA 171 -34.73 -6.56 3.03e+01 1d4xA 375 -41.70 -6.56 3.04e+01 1dujA 187 -31.64 -6.56 3.04e+01 1aapA 58 -26.98 -6.54 3.07e+01 1bawA 105 -31.70 -6.54 3.08e+01 1hms 132 -42.19 -6.50 3.15e+01 1hmr 132 -42.19 -6.50 3.15e+01 1qi6A 475 -54.18 -6.50 3.16e+01 1euhA 475 -54.18 -6.49 3.16e+01 1zxq 192 -39.20 -6.48 3.18e+01 1b77A 228 -41.81 -6.47 3.21e+01 1g86A 142 -36.27 -6.46 3.22e+01 1lcl 142 -36.27 -6.46 3.22e+01 1iazA 179 -33.67 -6.46 3.24e+01 1httA 423 -40.85 -6.44 3.27e+01 1jhnA 424 -60.44 -6.43 3.29e+01 1bwyA 132 -41.59 -6.41 3.32e+01 1tiiD 99 -29.81 -6.41 3.33e+01 1qnaA 200 -34.24 -6.40 3.35e+01 1hmt 132 -42.04 -6.38 3.38e+01 1bebA 162 -37.57 -6.38 3.39e+01 1svb 395 -53.52 -6.36 3.43e+01 1mspA 126 -34.70 -6.36 3.43e+01 1ermA 263 -36.98 -6.34 3.46e+01 3fruA 269 -45.35 -6.34 3.46e+01 1btl 263 -37.25 -6.34 3.46e+01 1boy 219 -36.90 -6.31 3.51e+01 1m40A 263 -36.74 -6.31 3.52e+01 1h4vB 421 -43.84 -6.31 3.53e+01 1fqgA 263 -36.77 -6.31 3.53e+01 1cfyA 143 -30.39 -6.31 3.54e+01 1bj4A 470 -35.85 -6.29 3.58e+01 1cof 143 -30.33 -6.28 3.60e+01 1p35A 299 -45.44 -6.27 3.60e+01 1fh6A 282 -36.11 -6.27 3.61e+01 1lo7A 141 -33.49 -6.25 3.66e+01 1cv8 174 -35.64 -6.24 3.68e+01 4ubpA 101 -26.80 -6.22 3.73e+01 1el6A 219 -31.23 -6.21 3.74e+01 1ubpA 101 -26.78 -6.20 3.76e+01 1a3yA 149 -36.95 -6.20 3.76e+01 1gbg 214 -39.94 -6.19 3.80e+01 1gnhA 206 -41.28 -6.17 3.83e+01 1agdA 276 -42.68 -6.16 3.85e+01 1bsjA 168 -36.10 -6.14 3.89e+01 2rmpA 361 -41.62 -6.14 3.90e+01 1adjA 421 -44.69 -6.14 3.91e+01 1put 106 -26.06 -6.13 3.91e+01 1k82A 268 -45.62 -6.13 3.92e+01 1umuB 116 -36.77 -6.12 3.95e+01 1f53A 84 -33.55 -6.11 3.98e+01 1vokA 200 -32.48 -6.10 3.99e+01