% 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. % --------------------------------------------------------------------- % dsspfoo.1.YEL023C.t2k-100-30-dssp-ebghstl Host: cc32 Mon Nov 11 05:29:03 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL023C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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 YEL023C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL023C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 683 nodes, 486.49 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(=1.4416) * Reverse)^tau(=0.8157))) % 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 1jeoA 180 -38.56 -15.99 1.78e-02 1im8A 244 -37.34 -14.13 6.13e-02 1adeA 431 -39.82 -13.87 7.34e-02 1qf5A 431 -38.81 -13.22 1.13e-01 1kezA 300 -38.66 -12.65 1.68e-01 1kxu 333 -39.29 -12.51 1.85e-01 1b8gA 429 -36.23 -12.01 2.62e-01 1dseA 292 -37.37 -11.90 2.84e-01 1ji2A 585 -39.64 -11.68 3.29e-01 1kpsB 171 -33.50 -11.44 3.91e-01 1bh9B 89 -32.88 -11.25 4.46e-01 1mxb 383 -35.05 -10.65 6.81e-01 1mxa 383 -34.92 -10.56 7.24e-01 1eps 427 -34.95 -10.54 7.39e-01 1jmkC 230 -35.29 -10.37 8.33e-01 1eh9A 558 -42.75 -10.31 8.69e-01 1ehaA 558 -41.81 -10.23 9.19e-01 1kwkA 645 -37.11 -10.22 9.26e-01 1gox 370 -34.80 -10.12 9.98e-01 1tpt 440 -35.34 -9.93 1.14e+00 1gjuA 637 -42.91 -9.93 1.14e+00 1ryc 294 -35.86 -9.80 1.25e+00 1ccg 291 -35.60 -9.75 1.30e+00 1ds4A 292 -35.78 -9.74 1.31e+00 1gg3A 279 -35.53 -9.73 1.32e+00 1fezA 256 -33.90 -9.66 1.39e+00 1ej6B 1275 -42.61 -9.62 1.43e+00 1e6yB 433 -37.67 -9.49 1.57e+00 1gjwA 637 -42.20 -9.31 1.79e+00 1e9iA 431 -37.01 -9.21 1.92e+00 1qm4A 396 -34.49 -9.21 1.92e+00 1lbeA 258 -32.77 -9.19 1.96e+00 1jkw 323 -35.32 -9.18 1.97e+00 1i50A 1733 -51.30 -9.16 1.99e+00 1c4zA 358 -35.57 -9.15 2.01e+00 1ijbA 202 -31.89 -9.09 2.10e+00 1hekA 131 -33.32 -9.08 2.11e+00 1zpdA 568 -34.13 -9.01 2.23e+00 1auq 208 -32.08 -8.86 2.49e+00 1qc5A 192 -31.02 -8.80 2.59e+00 2cyp 294 -34.48 -8.74 2.71e+00 1edqA 540 -34.55 -8.71 2.78e+00 1btmA 252 -31.28 -8.67 2.86e+00 1crl 534 -36.10 -8.59 3.03e+00 1a3gA 308 -32.30 -8.57 3.08e+00 1cb0A 283 -32.44 -8.53 3.17e+00 1jdrA 294 -34.14 -8.49 3.27e+00 4uagA 437 -32.15 -8.43 3.41e+00 1ctn 540 -34.15 -8.41 3.47e+00 1uag 437 -32.15 -8.39 3.52e+00 1jae 471 -34.55 -8.38 3.55e+00 1ir6A 424 -34.22 -8.32 3.71e+00 1azwA 313 -32.11 -8.30 3.76e+00 1gklA 297 -31.83 -8.29 3.80e+00 1g6sA 427 -32.42 -8.26 3.86e+00 1gpjA 404 -38.53 -8.25 3.90e+00 5eat 548 -38.52 -8.22 3.98e+00 1oakA 196 -30.75 -8.20 4.07e+00 3uagA 437 -31.81 -8.17 4.15e+00 1lwjA 441 -34.85 -8.15 4.20e+00 1gylA 369 -34.20 -8.08 4.44e+00 1f82A 424 -38.10 -8.02 4.63e+00 1dvjC 246 -30.41 -8.02 4.65e+00 1chuA 540 -34.17 -7.98 4.76e+00 1qbkB 890 -43.05 -7.94 4.91e+00 1k7qA 479 -37.01 -7.93 4.96e+00 1j5eB 256 -35.18 -7.92 4.98e+00 1awd 94 -27.15 -7.91 5.02e+00 1bvzA 585 -37.66 -7.89 5.11e+00 1fnsA 196 -30.69 -7.87 5.17e+00 1jdw 423 -32.63 -7.84 5.31e+00 1cex 214 -31.13 -7.79 5.49e+00 2liv 344 -31.25 -7.77 5.57e+00 1cus 200 -30.92 -7.74 5.70e+00 1dvjA 246 -30.16 -7.73 5.74e+00 1guqA 348 -32.13 -7.72 5.80e+00 1tib 269 -32.04 -7.71 5.87e+00 1opc 110 -28.76 -7.69 5.95e+00 1tpfA 250 -29.69 -7.66 6.09e+00 1agy 200 -30.76 -7.60 6.35e+00 1qlaA 656 -35.94 -7.60 6.36e+00 1gupA 348 -32.05 -7.60 6.37e+00 1gkkA 297 -31.12 -7.60 6.37e+00 1e0wA 313 -30.75 -7.59 6.39e+00 1km4A 247 -29.96 -7.57 6.48e+00 1kv5A 250 -29.63 -7.56 6.56e+00 5eau 548 -38.56 -7.52 6.73e+00 1aw5 326 -32.03 -7.50 6.83e+00 1fdi 715 -37.10 -7.49 6.88e+00 1kblA 873 -38.18 -7.49 6.93e+00 1bolA 222 -31.38 -7.45 7.10e+00 1fj2A 232 -30.83 -7.45 7.10e+00 1esc 306 -32.65 -7.44 7.19e+00 1jqjC 343 -33.30 -7.43 7.21e+00 1g6hA 257 -31.17 -7.43 7.25e+00 1fi2A 201 -29.21 -7.39 7.43e+00 1h7nA 342 -31.80 -7.37 7.55e+00 1h6zA 913 -37.80 -7.37 7.58e+00 1augA 215 -32.43 -7.37 7.59e+00 1eyeA 280 -31.35 -7.36 7.64e+00 1l1sA 113 -28.50 -7.35 7.69e+00 1itkA 731 -41.12 -7.35 7.69e+00 1qr6A 584 -34.55 -7.34 7.72e+00 1odd 118 -28.84 -7.34 7.74e+00 1jvnA 555 -32.86 -7.32 7.84e+00 1iw7C 1119 -37.03 -7.31 7.92e+00 1dik 874 -37.07 -7.21 8.52e+00 1hd8A 363 -30.68 -7.17 8.78e+00 1jeyB 565 -33.64 -7.17 8.82e+00 1azo 232 -29.78 -7.17 8.84e+00 3timA 250 -29.32 -7.16 8.86e+00 1pbwA 216 -33.41 -7.13 9.08e+00 1smd 496 -35.92 -7.12 9.14e+00 1f83A 425 -36.91 -7.12 9.19e+00 1gosA 520 -32.51 -7.07 9.50e+00 1f52A 468 -34.20 -7.06 9.60e+00 1qgtA 149 -30.57 -7.05 9.62e+00 1bf2 750 -35.69 -7.03 9.83e+00 1bdb 277 -30.78 -7.01 9.93e+00 1ebfA 358 -32.13 -6.95 1.04e+01 1gp4A 356 -32.14 -6.93 1.06e+01 1i39A 225 -30.27 -6.92 1.07e+01 1mnd 762 -35.68 -6.91 1.08e+01 1yge 839 -37.02 -6.90 1.08e+01 1cleA 534 -33.36 -6.90 1.09e+01 1k7iA 479 -36.09 -6.89 1.09e+01 1akr 147 -28.94 -6.87 1.11e+01 1ewqA 765 -33.45 -6.84 1.14e+01 1hxpA 348 -31.30 -6.82 1.15e+01 2bgu 351 -31.99 -6.79 1.18e+01 1f8nA 839 -36.94 -6.79 1.18e+01 1ahpA 797 -39.16 -6.78 1.18e+01 1aoa 275 -32.76 -6.78 1.19e+01 1xyzA 347 -31.88 -6.77 1.20e+01 1k7gA 479 -36.12 -6.75 1.21e+01 1gp6A 356 -31.90 -6.73 1.24e+01 1lxa 262 -30.42 -6.70 1.26e+01 1irxA 523 -34.65 -6.70 1.27e+01 1fgqA 839 -36.93 -6.67 1.29e+01 1jpaA 312 -31.99 -6.65 1.32e+01 1amoA 615 -32.29 -6.64 1.33e+01 1ebuA 358 -31.69 -6.61 1.35e+01 1go7P 462 -35.47 -6.59 1.38e+01 1eudB 396 -30.33 -6.58 1.38e+01 1fvzA 271 -30.86 -6.55 1.42e+01 1f0iA 504 -32.21 -6.55 1.42e+01 1ay7B 89 -26.60 -6.55 1.42e+01 1fdo 715 -36.06 -6.54 1.44e+01 1erzA 303 -29.13 -6.53 1.45e+01 1c3jA 351 -31.70 -6.52 1.46e+01 1eucB 396 -30.27 -6.50 1.48e+01 1b2sD 90 -26.50 -6.48 1.49e+01 1e08A 371 -33.60 -6.46 1.53e+01 2hnp 321 -31.81 -6.45 1.53e+01 1go8P 462 -35.75 -6.45 1.54e+01 1i1kA 309 -29.57 -6.44 1.54e+01 1huuA 90 -25.66 -6.44 1.55e+01 1auoA 218 -28.21 -6.43 1.56e+01 1kvs 338 -30.64 -6.42 1.57e+01 2gsq 202 -31.36 -6.41 1.58e+01 1jf9A 408 -30.75 -6.38 1.62e+01 1ejjA 511 -32.36 -6.38 1.62e+01 1fmk 452 -32.17 -6.35 1.65e+01 1a16 440 -32.00 -6.34 1.67e+01 1ebmA 317 -31.03 -6.32 1.70e+01 1h2aL 567 -32.90 -6.31 1.72e+01 1ipaA 274 -28.54 -6.28 1.75e+01 1gs5A 258 -28.89 -6.26 1.77e+01 1xsm 390 -32.96 -6.26 1.79e+01 1aurA 218 -28.20 -6.24 1.80e+01 1jkvA 266 -31.49 -6.21 1.85e+01 1ylvA 342 -30.83 -6.21 1.85e+01 1hx0A 496 -35.60 -6.18 1.89e+01 1byb 495 -35.12 -6.16 1.92e+01 1jeqB 565 -32.42 -6.15 1.94e+01 1bj4A 470 -29.74 -6.11 2.00e+01 1knzA 164 -27.89 -6.09 2.03e+01 1i4nA 251 -29.61 -6.03 2.13e+01 1jr3D 343 -30.82 -6.03 2.14e+01 1qq7A 253 -29.20 -6.03 2.14e+01 1bcpB 199 -27.46 -6.02 2.15e+01 1fwcC 567 -32.07 -6.02 2.15e+01 1hkbA 917 -39.66 -6.01 2.17e+01 1lox 662 -35.57 -6.00 2.17e+01 1cwxA 44 -25.62 -5.99 2.20e+01 1xel 338 -30.22 -5.99 2.21e+01 1ep3B 262 -28.56 -5.97 2.23e+01 1gw9A 388 -33.03 -5.97 2.23e+01 1az9 457 -32.18 -5.97 2.24e+01 1ltqA 301 -31.46 -5.96 2.25e+01 1h6gA 256 -30.57 -5.96 2.25e+01 1ee8A 266 -29.50 -5.95 2.26e+01 1hfeL 421 -33.24 -5.94 2.29e+01 1a26 361 -31.99 -5.94 2.29e+01 1sra 151 -31.68 -5.93 2.30e+01 1efyA 350 -31.93 -5.93 2.31e+01 1alkA 449 -30.37 -5.93 2.32e+01 2aaa 484 -32.97 -5.92 2.32e+01 1jilA 420 -34.42 -5.92 2.33e+01 1gouA 116 -25.80 -5.91 2.34e+01 1gefA 123 -26.44 -5.91 2.35e+01 1ed8A 449 -30.08 -5.89 2.37e+01 1l3eB 101 -27.73 -5.88 2.39e+01 1b8jA 449 -30.32 -5.88 2.40e+01 1xyfA 436 -30.74 -5.87 2.41e+01 1adjA 421 -32.21 -5.87 2.43e+01 1jakA 512 -35.48 -5.85 2.45e+01 1ipiA 123 -26.39 -5.85 2.45e+01 1aq6A 253 -28.98 -5.84 2.47e+01 1udc 338 -30.04 -5.84 2.48e+01 2mysB 166 -29.43 -5.83 2.49e+01 1ml9A 302 -30.07 -5.82 2.51e+01 1k4cC 124 -27.75 -5.82 2.52e+01 1jwhA 337 -31.83 -5.82 2.52e+01 1gx1A 160 -27.90 -5.82 2.53e+01 1qnoA 344 -30.98 -5.81 2.54e+01 1ilk 151 -29.97 -5.80 2.55e+01 8adh 374 -29.92 -5.80 2.55e+01 2or1L 69 -25.25 -5.79 2.57e+01 1kbuA 349 -33.71 -5.79 2.58e+01 2udpA 338 -30.03 -5.79 2.58e+01 1kvoA 124 -28.74 -5.78 2.59e+01 1keeG 1073 -35.02 -5.77 2.61e+01 1eceA 358 -32.33 -5.76 2.64e+01 1kfiA 572 -35.86 -5.76 2.65e+01 2ohxA 374 -29.82 -5.75 2.65e+01 1hp5A 512 -35.52 -5.74 2.69e+01 1qq5A 253 -28.83 -5.72 2.71e+01 1c3pA 375 -33.08 -5.72 2.71e+01 1xis 387 -32.40 -5.72 2.73e+01 4xis 387 -32.40 -5.72 2.73e+01 1k8cA 322 -31.50 -5.71 2.74e+01 1h4vB 421 -31.54 -5.71 2.74e+01 1hzfA 367 -32.37 -5.69 2.79e+01 1ldjA 760 -34.91 -5.68 2.80e+01 2fx2 147 -27.14 -5.68 2.81e+01 1gyzA 60 -24.49 -5.68 2.81e+01 1ko9A 345 -31.59 -5.68 2.81e+01 2pflA 759 -33.56 -5.67 2.83e+01 2frvB 536 -32.54 -5.67 2.84e+01 1kcmA 270 -29.63 -5.67 2.84e+01 1aca 86 -27.68 -5.66 2.85e+01 7timA 247 -28.52 -5.65 2.89e+01 5bcaA 516 -33.61 -5.64 2.91e+01 1i3kA 348 -29.93 -5.63 2.92e+01 1egpB 25 -21.41 -5.63 2.92e+01 1c4oA 664 -34.65 -5.63 2.93e+01 1i45A 248 -28.48 -5.61 2.97e+01 1hizA 379 -33.01 -5.61 2.97e+01 1ybvA 283 -30.71 -5.61 2.98e+01 1g7fA 298 -29.93 -5.60 2.99e+01 1ejrC 567 -31.75 -5.60 3.00e+01 1fo4A 1332 -37.63 -5.59 3.03e+01 1eqjA 511 -31.27 -5.58 3.04e+01 1jwyB 315 -31.08 -5.58 3.04e+01 1udb 338 -29.83 -5.58 3.06e+01 1jv2B 692 -37.64 -5.57 3.08e+01 1f4pA 147 -26.99 -5.56 3.08e+01 1aa7A 158 -28.44 -5.54 3.13e+01 1elyA 449 -30.79 -5.54 3.16e+01 1xbl 107 -27.27 -5.53 3.16e+01 1l0wA 580 -33.79 -5.53 3.18e+01 1jq2A 34 -22.85 -5.52 3.19e+01 1l0oA 150 -28.18 -5.52 3.19e+01 1h0oA 390 -32.43 -5.52 3.20e+01 1f1mA 164 -28.93 -5.51 3.23e+01 2anhA 446 -29.89 -5.50 3.24e+01 1f75A 249 -29.94 -5.50 3.26e+01 1hqvA 191 -31.28 -5.49 3.26e+01 1eeoA 321 -30.49 -5.48 3.29e+01 1keeC 1073 -35.18 -5.45 3.37e+01 1qhaA 917 -39.26 -5.43 3.42e+01 3xis 387 -32.28 -5.42 3.46e+01 1spa 396 -30.47 -5.42 3.47e+01 1frd 98 -25.38 -5.41 3.48e+01 2xis 387 -32.34 -5.40 3.50e+01 1c3oC 1073 -34.77 -5.39 3.54e+01 1czaN 917 -39.05 -5.39 3.54e+01 1bw0A 416 -31.34 -5.38 3.56e+01 1bs9 207 -27.05 -5.38 3.58e+01 1jslA 327 -28.64 -5.37 3.59e+01 1jsrA 327 -28.79 -5.37 3.60e+01 1lla 628 -33.73 -5.36 3.63e+01 1l1zA 274 -29.14 -5.35 3.65e+01 1bu5A 147 -26.69 -5.35 3.65e+01 1hkcA 917 -39.15 -5.35 3.67e+01 1aw1A 256 -27.89 -5.34 3.69e+01 1gajA 257 -29.81 -5.32 3.76e+01 1g0oA 283 -30.87 -5.31 3.77e+01 1korA 400 -37.25 -5.30 3.80e+01 1d02A 202 -29.10 -5.29 3.83e+01 1g66A 207 -26.99 -5.29 3.83e+01 1pfkA 320 -30.41 -5.28 3.87e+01 1d8cA 723 -32.96 -5.28 3.88e+01 1ksgB 152 -25.76 -5.27 3.89e+01 1hynP 379 -28.72 -5.27 3.90e+01 1ireA 204 -29.69 -5.27 3.91e+01 1ptvA 321 -30.04 -5.27 3.91e+01 1uor 585 -35.29 -5.26 3.92e+01 1j9eA 147 -26.70 -5.26 3.92e+01 1cezA 883 -34.34 -5.25 3.97e+01 1j5sA 463 -32.50 -5.25 3.97e+01