% 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. % --------------------------------------------------------------------- % dsspfoo.1.T0277.t04-100-30-str2 Host: caw Fri Aug 13 17:29:21 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0277 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.str2s % % 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 T0277.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0277.t04.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6749 sequences, 1593535 residues, 120 nodes, 28.07 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 (=10183) sequences: % N / (1 + exp(-(lambda(=2.0442) * Reverse)^tau(=0.7908))) % 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 1jogA 146 -128.54 -111.33 1.78e-28 1dk8A 147 -22.95 -11.17 7.13e-02 1aua 296 -22.57 -10.99 8.33e-02 1rx0A 393 -22.12 -10.67 1.09e-01 1i50B 1224 -23.70 -10.58 1.17e-01 1or7A 194 -22.38 -10.14 1.71e-01 1b8dA 164 -21.64 -9.81 2.26e-01 1js8A 394 -19.86 -9.74 2.41e-01 1buoA 121 -20.00 -9.51 2.96e-01 1mojA 182 -24.44 -9.40 3.23e-01 2cxbA 124 -17.65 -9.36 3.35e-01 1cxc 124 -17.65 -9.35 3.38e-01 1h16A 759 -21.07 -9.16 3.99e-01 1mb3A 124 -18.06 -8.96 4.77e-01 1s7zA 117 -22.99 -8.69 6.03e-01 1cm5A 759 -20.52 -8.52 7.01e-01 1n3kA 130 -18.32 -8.37 8.00e-01 1icrA 217 -18.48 -8.35 8.18e-01 1o3uA 135 -21.63 -8.20 9.38e-01 1iw7C 1119 -19.68 -7.99 1.13e+00 1su8A 636 -19.13 -7.66 1.53e+00 1jjyA 636 -19.13 -7.66 1.53e+00 1cxzB 86 -19.15 -7.61 1.60e+00 1pa7A 130 -19.77 -7.55 1.68e+00 1l3lA 234 -16.82 -7.51 1.75e+00 1nksA 194 -16.77 -7.46 1.83e+00 3lynA 136 -18.88 -7.42 1.89e+00 1k04A 162 -21.02 -7.42 1.90e+00 1ir6A 424 -18.22 -7.39 1.95e+00 1q08A 99 -17.93 -7.35 2.03e+00 1mvoA 136 -16.06 -7.32 2.07e+00 1rkeA 262 -22.29 -7.27 2.17e+00 1bhdA 118 -16.91 -7.26 2.20e+00 1ah7 245 -19.24 -7.23 2.25e+00 1e4yA 214 -17.17 -7.22 2.28e+00 1rfzA 168 -20.37 -7.13 2.48e+00 1uzbA 516 -17.89 -7.11 2.51e+00 1nznA 126 -20.79 -7.10 2.53e+00 1rktA 205 -23.89 -7.08 2.59e+00 1fpoA 171 -20.44 -7.08 2.59e+00 1teaA 299 -16.70 -7.01 2.77e+00 1qh8A 478 -17.49 -6.98 2.85e+00 1k4nA 192 -15.94 -6.97 2.88e+00 1miwA 404 -18.54 -6.94 2.94e+00 1amf 233 -15.41 -6.92 3.02e+00 2gdm 153 -18.17 -6.91 3.04e+00 1ockA 412 -17.66 -6.78 3.42e+00 1h6pA 203 -21.72 -6.73 3.58e+00 1nu7D 282 -20.96 -6.70 3.69e+00 1qmyA 167 -15.28 -6.68 3.76e+00 1dcs 311 -16.56 -6.66 3.84e+00 2igd 61 -14.95 -6.65 3.85e+00 1sqsA 242 -16.69 -6.65 3.87e+00 1rkpA 326 -18.94 -6.64 3.90e+00 1qq5A 253 -17.02 -6.63 3.95e+00 1o98A 511 -16.68 -6.62 3.99e+00 1f74A 293 -17.44 -6.62 3.99e+00 1eqjA 511 -16.66 -6.59 4.07e+00 1i58A 189 -16.94 -6.52 4.38e+00 1v4eA 299 -19.83 -6.52 4.38e+00 1m6kA 251 -15.59 -6.49 4.47e+00 1izmA 184 -19.79 -6.46 4.64e+00 1ov2A 99 -18.92 -6.44 4.71e+00 1mp4A 292 -16.04 -6.43 4.74e+00 1wod 233 -14.89 -6.42 4.80e+00 1uqvA 85 -17.48 -6.36 5.09e+00 1q02A 52 -14.95 -6.33 5.21e+00 4crxA 322 -17.17 -6.30 5.36e+00 2nacA 393 -14.86 -6.30 5.38e+00 1i39A 225 -17.64 -6.22 5.81e+00 1ld8A 382 -20.76 -6.21 5.85e+00 1p9bA 442 -16.27 -6.18 6.01e+00 1lvaA 258 -16.24 -6.17 6.08e+00 1pq9A 253 -18.49 -6.16 6.15e+00 1i8jA 323 -15.31 -6.15 6.23e+00 2tct 207 -18.99 -6.09 6.54e+00 1l6sA 323 -15.18 -6.08 6.66e+00 2occE 109 -19.82 -6.06 6.75e+00 1ebmA 317 -16.08 -6.06 6.77e+00 1oxkB 134 -15.46 -6.04 6.87e+00 1lis 136 -19.74 -6.03 6.93e+00 2lisA 136 -19.74 -6.03 6.93e+00 1o5hA 214 -20.24 -6.03 6.96e+00 1ukz 203 -17.34 -5.99 7.21e+00 7a3hA 303 -15.29 -5.97 7.33e+00 1qgtA 149 -21.14 -5.93 7.65e+00 1g60A 260 -15.68 -5.93 7.65e+00 1dgfA 497 -16.83 -5.93 7.65e+00 1jvsA 400 -16.74 -5.92 7.70e+00 1v4vA 376 -15.53 -5.91 7.76e+00 1tmy 120 -14.36 -5.91 7.81e+00 1q0qA 406 -16.69 -5.91 7.81e+00 1at3A 247 -14.40 -5.88 8.00e+00 1jipA 403 -16.67 -5.88 8.00e+00 1v54E 109 -19.66 -5.88 8.02e+00 1qq7A 253 -16.08 -5.87 8.10e+00 1b5tA 275 -16.11 -5.86 8.16e+00 1ki1B 352 -18.34 -5.85 8.25e+00 1p32A 209 -17.86 -5.84 8.35e+00 1sqgA 429 -17.83 -5.84 8.35e+00 1mi3A 322 -14.73 -5.78 8.85e+00 1h8uA 117 -14.14 -5.77 8.93e+00 1mjhA 162 -16.54 -5.76 9.03e+00 1fjgD 209 -16.27 -5.75 9.12e+00 1a0p 290 -17.61 -5.75 9.13e+00 1jj2L 194 -14.21 -5.74 9.19e+00 1o4sA 389 -16.82 -5.74 9.19e+00 1f44A 324 -16.21 -5.74 9.23e+00 1csn 298 -15.08 -5.73 9.30e+00 1au1A 166 -17.13 -5.70 9.53e+00 1cjcA 460 -15.76 -5.69 9.65e+00 1wdgA 94 -17.77 -5.68 9.72e+00 1q0gA 117 -16.98 -5.68 9.77e+00 1q6hA 224 -16.29 -5.67 9.82e+00 1q1aA 289 -15.24 -5.62 1.03e+01 1qgrA 876 -19.31 -5.59 1.07e+01 1ur3M 319 -14.98 -5.57 1.08e+01 1jigA 146 -21.43 -5.56 1.09e+01 1k38A 254 -14.96 -5.52 1.13e+01 1umdA 367 -15.95 -5.48 1.18e+01 1us6A 102 -16.24 -5.48 1.19e+01 2a0b 125 -20.26 -5.47 1.20e+01 1oj7A 408 -17.96 -5.44 1.23e+01 1uzcA 71 -14.24 -5.44 1.23e+01 1ui8A 638 -12.65 -5.43 1.24e+01 1r8iA 213 -16.52 -5.43 1.25e+01 1hlvA 131 -17.24 -5.42 1.26e+01 1knqA 175 -14.14 -5.41 1.27e+01 1j09A 468 -17.59 -5.41 1.27e+01 1ccwA 137 -13.95 -5.40 1.27e+01 1a6m 151 -16.70 -5.40 1.28e+01 1k6wA 426 -14.30 -5.35 1.34e+01 1e7uA 961 -16.03 -5.34 1.35e+01 1p4oA 322 -16.18 -5.34 1.35e+01 1jsxA 207 -14.93 -5.33 1.36e+01 1vkeA 133 -16.56 -5.33 1.37e+01 1ail 73 -17.16 -5.32 1.38e+01 1a32 88 -16.90 -5.31 1.40e+01 1eexA 554 -16.15 -5.26 1.46e+01 1g03A 134 -15.89 -5.26 1.47e+01 1m1nA 491 -18.37 -5.25 1.49e+01 1iqyA 638 -12.07 -5.24 1.50e+01 1r5lA 262 -17.61 -5.24 1.50e+01 1jnyA 435 -16.85 -5.24 1.50e+01 1pvyA 227 -13.51 -5.22 1.52e+01 1hrkA 359 -16.17 -5.22 1.53e+01 1dg9A 157 -15.37 -5.21 1.54e+01 1j4nA 271 -16.81 -5.19 1.57e+01 1t7pA 698 -16.29 -5.17 1.61e+01 1d1qA 161 -15.88 -5.15 1.63e+01 1snnA 227 -13.53 -5.13 1.66e+01 1w2wA 211 -18.08 -5.13 1.66e+01 1bh9B 89 -18.91 -5.13 1.67e+01 1k3yA 221 -16.47 -5.13 1.67e+01 1rxqA 178 -15.07 -5.13 1.67e+01 1hwxA 501 -17.07 -5.12 1.68e+01 1ciy 590 -19.02 -5.12 1.69e+01 1dat 174 -18.43 -5.11 1.70e+01 1ui7A 638 -12.42 -5.10 1.71e+01 1jk0A 419 -20.92 -5.06 1.78e+01 1ihgA 370 -17.55 -5.05 1.81e+01 1qwgA 251 -14.20 -5.03 1.84e+01 2lbp 346 -14.00 -5.02 1.87e+01 1n40A 396 -15.73 -5.01 1.87e+01 1udxA 416 -13.20 -5.01 1.88e+01 1pjr 724 -18.66 -5.00 1.89e+01 1ozjA 144 -14.41 -4.99 1.92e+01 1m3qA 317 -16.08 -4.96 1.96e+01 1rwhA 757 -14.76 -4.96 1.97e+01 1ntyA 311 -17.23 -4.95 1.99e+01 1r6rA 100 -16.07 -4.95 1.99e+01 1go3F 107 -18.09 -4.95 1.99e+01 1eupA 403 -16.77 -4.95 2.00e+01 1jalA 363 -15.47 -4.94 2.01e+01 1rxxA 421 -14.85 -4.93 2.02e+01 1c0eA 157 -14.48 -4.93 2.02e+01 1im8A 244 -15.73 -4.93 2.03e+01 1g4yR 148 -16.33 -4.92 2.06e+01 1q5zA 177 -16.39 -4.91 2.07e+01 1vhnA 318 -17.16 -4.91 2.07e+01 1d8wA 426 -16.15 -4.90 2.09e+01 1bykA 255 -13.51 -4.90 2.09e+01 1a76 326 -18.39 -4.90 2.09e+01 1apyA 162 -13.97 -4.89 2.11e+01 1qgoA 264 -14.39 -4.88 2.13e+01 1tdhA 364 -13.93 -4.88 2.14e+01 1hw1A 239 -19.73 -4.88 2.14e+01 1n1fA 159 -18.16 -4.87 2.15e+01 1gk9B 557 -16.62 -4.85 2.19e+01 2gsq 202 -17.49 -4.85 2.20e+01 1vhzA 198 -12.48 -4.85 2.20e+01 1no7A 604 -14.67 -4.83 2.24e+01 1usgA 346 -14.59 -4.83 2.24e+01 1iybA 208 -13.07 -4.82 2.25e+01 1chkA 238 -14.25 -4.82 2.27e+01 1ls1A 295 -15.45 -4.81 2.29e+01 2sqcA 631 -15.65 -4.80 2.30e+01 1b0b 142 -15.48 -4.79 2.32e+01 1l3pA 102 -15.09 -4.78 2.35e+01 1k20A 310 -15.81 -4.78 2.36e+01 1k0wA 231 -13.95 -4.77 2.39e+01 1qflA 389 -13.29 -4.75 2.43e+01 1e6yB 433 -16.13 -4.75 2.44e+01 1wdcB 156 -17.33 -4.73 2.47e+01 1p3jA 217 -17.22 -4.73 2.48e+01 1m3kA 392 -13.28 -4.72 2.49e+01 1viuA 203 -12.61 -4.72 2.50e+01 1r5zA 323 -15.84 -4.72 2.51e+01 1pu6A 218 -16.41 -4.72 2.51e+01 1hvvA 75 -19.16 -4.72 2.52e+01 1l9lA 74 -15.40 -4.71 2.54e+01 1o9rA 162 -23.01 -4.71 2.54e+01 1m4tA 392 -13.28 -4.69 2.57e+01 1ax4A 467 -14.56 -4.69 2.58e+01 1mh1 186 -12.84 -4.69 2.59e+01 1gxyA 226 -13.86 -4.67 2.64e+01 1f8mA 429 -14.42 -4.66 2.65e+01 1c7gA 456 -14.55 -4.65 2.68e+01 1hq0A 295 -12.24 -4.64 2.71e+01 1t7sA 137 -16.85 -4.63 2.75e+01 1kk8B 139 -16.68 -4.63 2.76e+01 1ojrA 274 -16.21 -4.62 2.77e+01 1lb2B 84 -12.89 -4.61 2.79e+01 1anv 356 -13.96 -4.60 2.82e+01 1oi7A 288 -14.30 -4.60 2.83e+01 1f61A 429 -14.34 -4.59 2.85e+01 1ift 263 -15.28 -4.58 2.88e+01 1v9mA 323 -15.19 -4.57 2.90e+01 1n7sB 68 -18.99 -4.57 2.92e+01 1oniA 137 -13.00 -4.55 2.96e+01 1ej0A 180 -13.74 -4.55 2.98e+01 1k94A 165 -17.24 -4.55 2.98e+01 2abk 211 -18.02 -4.55 2.98e+01 1itcA 516 -14.76 -4.54 3.01e+01 1e8yA 966 -16.03 -4.53 3.03e+01 1jdw 423 -13.40 -4.53 3.03e+01 1s5aA 150 -13.12 -4.52 3.06e+01 1dmhA 311 -14.25 -4.51 3.09e+01 1uxoA 192 -13.65 -4.51 3.10e+01 1n1bA 549 -20.46 -4.48 3.21e+01 1mo0A 275 -12.96 -4.46 3.27e+01 1e3aB 560 -16.09 -4.45 3.28e+01 1ib3A 349 -14.82 -4.45 3.29e+01 1oshA 232 -18.19 -4.45 3.30e+01 1jdpA 441 -13.62 -4.45 3.30e+01 1dceA 567 -16.06 -4.45 3.30e+01 1oi6A 205 -11.34 -4.44 3.33e+01 1ofnA 205 -11.34 -4.44 3.33e+01 1qlaA 656 -14.91 -4.44 3.33e+01 1a9xA 1058 -14.52 -4.43 3.36e+01 1q1fA 151 -15.48 -4.42 3.38e+01 1ee4A 423 -16.83 -4.41 3.41e+01 1d9cA 121 -16.49 -4.40 3.46e+01 1i1nA 226 -13.33 -4.40 3.48e+01 1gzsB 165 -16.25 -4.39 3.48e+01 1m0uA 249 -17.91 -4.39 3.49e+01 1e3mA 800 -16.29 -4.38 3.52e+01 1lj2A 110 -17.68 -4.38 3.53e+01 1fftC 204 -15.56 -4.37 3.56e+01 1fmjA 351 -14.16 -4.36 3.59e+01 1gjnA 153 -15.37 -4.36 3.60e+01 1d8dA 377 -19.04 -4.35 3.63e+01 1dy5A 124 -11.36 -4.35 3.63e+01 1fcjA 322 -13.93 -4.34 3.67e+01 1p9qC 256 -14.52 -4.34 3.69e+01 1isiA 265 -13.44 -4.34 3.69e+01 1dwtA 153 -15.34 -4.34 3.69e+01 1ib2A 349 -14.67 -4.33 3.71e+01 1r5pA 108 -13.49 -4.32 3.75e+01 1avk 638 -11.33 -4.31 3.81e+01 1qahA 136 -13.04 -4.30 3.84e+01 1ks9A 291 -16.65 -4.30 3.84e+01 1pvaA 110 -13.34 -4.29 3.88e+01 1ufyA 122 -12.84 -4.28 3.90e+01 1ehkA 562 -15.91 -4.28 3.91e+01 1dzaA 129 -11.18 -4.28 3.92e+01 1rlr 761 -15.14 -4.28 3.92e+01 1mhdA 132 -14.26 -4.27 3.94e+01 1lssA 140 -12.90 -4.27 3.96e+01 1brwA 433 -14.96 -4.26 3.98e+01