% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR034W.t2k-100-40-40-str2+CB_burial_14_7 Host: farm20 Wed Nov 17 19:01:23 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR034W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 YGR034W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR034W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR034W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 130 nodes, 154.01 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(=0.8915) * Reverse)^tau(=0.8457))) % 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 1s72T 120 -145.86 -126.69 2.35e-20 1jj2S 119 -145.24 -126.07 2.95e-20 1ffkQ 119 -128.37 -111.28 6.73e-18 1omiA 248 -33.09 -22.53 3.44e-02 1bbzE 58 -32.88 -20.26 1.02e-01 1bbzA 58 -33.15 -20.15 1.08e-01 1hjdA 101 -33.26 -19.01 1.88e-01 1aboA 62 -32.12 -18.71 2.17e-01 1t6aA 126 -43.75 -18.41 2.52e-01 1s72Q 96 -42.15 -18.13 2.88e-01 1jj2P 95 -41.05 -17.39 4.15e-01 1i0cA 60 -29.46 -17.37 4.19e-01 1jj2A 239 -32.85 -17.27 4.41e-01 1bxvA 91 -27.58 -16.78 5.60e-01 1tuc 63 -36.39 -16.46 6.57e-01 1ljoA 77 -33.82 -16.36 6.91e-01 1ugpB 226 -38.95 -16.32 7.04e-01 2cuaA 135 -30.91 -16.23 7.40e-01 2phlA 397 -34.79 -16.10 7.88e-01 1jegA 83 -29.44 -16.00 8.30e-01 1uw6A 211 -29.23 -15.95 8.50e-01 1lplA 95 -32.03 -15.73 9.49e-01 1d3bA 75 -33.35 -15.69 9.66e-01 1gmeA 151 -36.27 -15.63 9.98e-01 1gcqA 61 -29.32 -15.59 1.02e+00 1eikA 77 -29.89 -15.55 1.04e+00 1jotA 133 -33.87 -15.41 1.11e+00 1i8fA 81 -29.39 -15.38 1.13e+00 1mtnC 97 -29.80 -15.37 1.13e+00 1cskA 71 -28.63 -15.28 1.19e+00 1ab9C 97 -29.96 -15.27 1.20e+00 1kvdB 77 -34.43 -15.14 1.28e+00 1d2pA 373 -30.99 -15.11 1.29e+00 1tovA 98 -31.38 -15.07 1.32e+00 1ireB 228 -37.58 -14.97 1.39e+00 1luzA 88 -31.71 -14.93 1.42e+00 1ckaA 57 -27.82 -14.80 1.51e+00 1jacA 133 -33.11 -14.79 1.52e+00 1txlA 215 -27.83 -14.58 1.70e+00 1nhp 447 -26.11 -14.55 1.72e+00 1qlyA 58 -23.77 -14.50 1.76e+00 1o97D 320 -27.92 -14.49 1.77e+00 1kveB 77 -33.66 -14.41 1.85e+00 1sfdA 105 -23.55 -14.40 1.86e+00 1qniA 581 -25.36 -14.37 1.89e+00 1oejA 193 -26.95 -14.29 1.96e+00 1ou8A 111 -30.99 -14.28 1.97e+00 1lfo 128 -37.15 -14.19 2.07e+00 1shfA 59 -26.21 -14.16 2.10e+00 1trb 320 -26.10 -14.08 2.18e+00 1pwt 61 -30.39 -14.01 2.26e+00 1noa 113 -28.33 -13.97 2.31e+00 1jpyB 137 -36.17 -13.96 2.32e+00 1hdkA 141 -27.42 -13.89 2.41e+00 1gg6C 97 -28.63 -13.88 2.42e+00 1dwkA 156 -32.72 -13.85 2.46e+00 1dw9A 156 -32.96 -13.77 2.56e+00 1aac 105 -22.89 -13.75 2.58e+00 1jyoA 130 -29.37 -13.71 2.64e+00 1v76A 96 -32.94 -13.69 2.67e+00 1i9bA 217 -27.62 -13.46 3.00e+00 1nhs 447 -25.02 -13.40 3.09e+00 1ebaA 215 -26.07 -13.40 3.10e+00 1lckA 175 -24.79 -13.33 3.21e+00 1ku8A 133 -31.25 -13.26 3.32e+00 1mgqA 83 -31.08 -13.24 3.37e+00 1ycsB 239 -24.31 -13.21 3.42e+00 1m5q1 130 -32.31 -13.18 3.47e+00 1smxA 96 -26.13 -13.16 3.50e+00 1uj0A 62 -25.94 -13.07 3.66e+00 1awo 62 -27.10 -13.04 3.72e+00 1shg 62 -29.88 -13.01 3.79e+00 1d7qA 143 -38.44 -13.00 3.81e+00 1ejfA 125 -27.66 -12.99 3.82e+00 1kkeA 210 -43.52 -12.92 3.96e+00 1oebA 62 -24.85 -12.92 3.97e+00 1bxaA 105 -22.05 -12.91 3.98e+00 2mcm 112 -30.54 -12.89 4.02e+00 1irp 153 -30.41 -12.88 4.05e+00 1hw5A 210 -27.24 -12.88 4.05e+00 1gd7A 109 -29.96 -12.80 4.22e+00 1aaj 105 -21.90 -12.76 4.30e+00 1jh2A 99 -29.40 -12.75 4.33e+00 1gcqC 70 -23.76 -12.71 4.42e+00 1cuk 203 -25.85 -12.69 4.48e+00 1a62 130 -22.51 -12.65 4.56e+00 1nwwA 149 -31.35 -12.58 4.73e+00 1a49A 530 -22.84 -12.55 4.80e+00 1gjuA 637 -25.54 -12.54 4.82e+00 1wkt 88 -26.42 -12.49 4.95e+00 1joa 447 -23.94 -12.45 5.05e+00 1rqpA 299 -24.14 -12.44 5.08e+00 1j48A 110 -25.21 -12.39 5.21e+00 1jpyA 137 -34.71 -12.35 5.32e+00 1umuA 116 -31.35 -12.33 5.39e+00 1jacC 133 -30.92 -12.30 5.46e+00 1ox8A 107 -25.76 -12.30 5.48e+00 1aipE 405 -27.06 -12.30 5.48e+00 1lcl 142 -26.74 -12.30 5.48e+00 1oqkA 97 -30.55 -12.28 5.52e+00 1ehkB 168 -30.83 -12.24 5.63e+00 1m26A 133 -31.89 -12.23 5.67e+00 1ootA 60 -30.53 -12.18 5.81e+00 1bmfA 510 -23.77 -12.13 5.97e+00 1c3mA 147 -27.78 -12.11 6.04e+00 1vif 62 -26.08 -12.08 6.13e+00 1g86A 142 -26.66 -12.06 6.21e+00 1nycA 111 -27.49 -11.99 6.43e+00 1ef1A 294 -25.72 -11.97 6.48e+00 1pm4A 119 -28.32 -11.94 6.61e+00 1aizA 129 -20.43 -11.92 6.65e+00 1my7A 114 -23.57 -11.91 6.70e+00 1ffkN 95 -32.00 -11.90 6.73e+00 1f3uB 171 -39.01 -11.89 6.78e+00 1jdqA 98 -30.85 -11.88 6.81e+00 1b12A 248 -26.58 -11.88 6.81e+00 1ihfA 99 -34.23 -11.80 7.09e+00 1ospL 214 -21.69 -11.74 7.34e+00 1x6oA 174 -29.34 -11.69 7.51e+00 1id2A 106 -21.33 -11.68 7.54e+00 1ekrA 161 -24.37 -11.68 7.55e+00 1g291 372 -27.76 -11.68 7.58e+00 1d6mA 653 -22.73 -11.68 7.58e+00 1csp 67 -28.23 -11.63 7.78e+00 1jztA 246 -20.17 -11.62 7.81e+00 1i1jA 108 -24.17 -11.57 8.01e+00 1ul7A 102 -23.65 -11.56 8.03e+00 1mkeA 152 -33.22 -11.54 8.13e+00 1utiA 58 -24.62 -11.54 8.15e+00 1mhnA 59 -29.39 -11.51 8.26e+00 1stmA 157 -22.88 -11.49 8.35e+00 1iz6A 138 -33.19 -11.47 8.45e+00 1nnxA 109 -26.10 -11.40 8.77e+00 1dnlA 199 -26.80 -11.39 8.82e+00 1e2wA 251 -26.24 -11.38 8.84e+00 1fneA 192 -34.98 -11.36 8.94e+00 1h9mA 145 -28.85 -11.35 9.02e+00 1bdyA 123 -27.43 -11.35 9.02e+00 1qq1A 559 -27.96 -11.34 9.03e+00 1dj7B 75 -28.41 -11.34 9.05e+00 1nxzA 246 -23.38 -11.33 9.10e+00 1c3kA 147 -25.50 -11.30 9.26e+00 1m4zA 238 -28.97 -11.28 9.31e+00 1ft9A 222 -32.79 -11.28 9.35e+00 1hr0W 71 -21.34 -11.24 9.51e+00 2pcfB 250 -26.22 -11.24 9.51e+00 1ipiA 123 -25.79 -11.24 9.55e+00 1d2oA 187 -28.76 -11.22 9.62e+00 1g79A 218 -27.76 -11.22 9.64e+00 1umuB 116 -31.08 -11.18 9.82e+00 2dtr 226 -24.77 -11.16 9.92e+00 1ri9A 102 -27.72 -11.15 9.98e+00 1g2bA 62 -26.70 -11.14 1.00e+01 1hjp 203 -23.50 -11.10 1.02e+01 1ugxA 133 -32.25 -11.08 1.04e+01 1a3qA 285 -24.01 -11.07 1.05e+01 1fngA 192 -34.41 -10.99 1.09e+01 1vie 62 -25.07 -10.98 1.09e+01 1iq6A 134 -24.84 -10.97 1.10e+01 1ktbA 405 -25.06 -10.95 1.11e+01 2azaA 129 -19.25 -10.91 1.13e+01 1k3bA 119 -28.16 -10.91 1.14e+01 1owfA 99 -32.94 -10.91 1.14e+01 1qa1A 554 -27.88 -10.87 1.16e+01 1azeA 56 -25.57 -10.86 1.17e+01 1tud 62 -25.87 -10.86 1.17e+01 1rgxA 114 -31.52 -10.84 1.18e+01 1ieaA 192 -33.84 -10.80 1.20e+01 1tyv 542 -27.77 -10.77 1.22e+01 1ov3A 138 -41.57 -10.75 1.23e+01 1kn9A 249 -26.39 -10.72 1.25e+01 1my5A 114 -22.69 -10.69 1.28e+01 1kbvA 327 -20.41 -10.69 1.28e+01 1c9oA 66 -30.80 -10.63 1.32e+01 1qz8A 113 -26.55 -10.59 1.34e+01 1div 149 -24.48 -10.57 1.36e+01 1exmA 405 -22.81 -10.54 1.38e+01 1nngA 153 -37.26 -10.54 1.38e+01 1vhyA 257 -22.36 -10.53 1.39e+01 1h4rA 314 -22.38 -10.48 1.43e+01 1jmtA 104 -28.03 -10.44 1.45e+01 1h9jA 145 -28.67 -10.43 1.47e+01 1h9dA 134 -23.07 -10.40 1.49e+01 2eifA 136 -36.84 -10.37 1.51e+01 3stdA 165 -23.81 -10.36 1.52e+01 1fwxA 595 -21.68 -10.35 1.53e+01 1qmyA 167 -23.01 -10.33 1.54e+01 1n6aA 259 -22.71 -10.33 1.55e+01 1b34B 118 -25.97 -10.32 1.55e+01 1a63 130 -21.08 -10.32 1.56e+01 1bymA 97 -27.72 -10.24 1.62e+01 2std 172 -22.11 -10.20 1.66e+01 1i81A 83 -29.99 -10.20 1.66e+01 1meyC 87 -29.20 -10.13 1.72e+01 1tyu 543 -27.61 -10.13 1.72e+01 1fhoA 119 -25.27 -10.12 1.73e+01 1bal 51 -34.04 -10.12 1.73e+01 1lvl 458 -22.80 -10.12 1.73e+01 1shwA 138 -22.01 -10.11 1.74e+01 1m4uA 206 -29.91 -10.09 1.76e+01 1cvsC 225 -25.43 -10.08 1.76e+01 1mxmA 254 -26.11 -10.08 1.77e+01 1uvqA 197 -29.64 -10.08 1.77e+01 1ujrA 110 -32.42 -10.07 1.78e+01 1vkkA 154 -23.00 -10.06 1.79e+01 1g4mA 393 -22.28 -10.02 1.83e+01 1jjgA 102 -37.46 -9.96 1.88e+01 1u96A 69 -31.29 -9.96 1.88e+01 1tlk 154 -24.23 -9.95 1.89e+01 1hk9A 74 -22.82 -9.95 1.89e+01 1b56 135 -28.64 -9.90 1.94e+01 1semA 58 -27.15 -9.89 1.96e+01 1vrtA 560 -21.42 -9.89 1.96e+01 1qexA 288 -29.14 -9.88 1.96e+01 1fdr 248 -20.10 -9.88 1.97e+01 1ektA 53 -24.79 -9.87 1.98e+01 1bwwA 109 -20.78 -9.86 1.99e+01 1ds6B 180 -30.19 -9.85 2.00e+01 1dynA 125 -23.50 -9.85 2.00e+01 1i7dA 659 -20.23 -9.79 2.06e+01 1tsp 559 -27.31 -9.77 2.09e+01 1pcs 98 -21.04 -9.76 2.09e+01 1preB 470 -26.63 -9.72 2.14e+01 1fl2A 310 -20.10 -9.70 2.17e+01 1pwaA 162 -22.09 -9.69 2.18e+01 1usmA 80 -22.70 -9.67 2.20e+01 1r0pA 312 -21.08 -9.67 2.20e+01 1eerB 227 -24.18 -9.61 2.27e+01 1i7nA 309 -21.87 -9.61 2.27e+01 1lcyA 325 -21.16 -9.59 2.30e+01 1guiA 155 -26.45 -9.58 2.31e+01 1gcpA 70 -20.87 -9.58 2.31e+01 1vhqA 232 -18.00 -9.56 2.34e+01 1ecrA 309 -29.57 -9.56 2.34e+01 1fa4A 105 -19.17 -9.54 2.36e+01 1jxmA 301 -22.40 -9.54 2.36e+01 1ibzA 112 -30.97 -9.53 2.37e+01 1v5mA 136 -23.56 -9.53 2.38e+01 1ha3A 405 -22.14 -9.50 2.41e+01 1o5zA 442 -17.88 -9.49 2.43e+01 1uliB 187 -31.04 -9.49 2.43e+01 2dynA 122 -24.81 -9.48 2.44e+01 2bpa1 426 -24.90 -9.46 2.47e+01 1xfsA 178 -31.61 -9.44 2.49e+01 1q0sA 259 -20.01 -9.44 2.49e+01 1b9mA 265 -22.16 -9.43 2.51e+01 1si2A 149 -20.52 -9.42 2.52e+01 1ogiA 303 -19.72 -9.41 2.53e+01 1dyzA 129 -17.82 -9.41 2.54e+01 1wdaA 670 -21.13 -9.40 2.56e+01 1pkn 530 -20.24 -9.38 2.57e+01 1mt6A 280 -22.82 -9.36 2.60e+01 1cx4A 305 -27.57 -9.34 2.63e+01 7pcy 98 -20.47 -9.34 2.64e+01 1i12A 160 -22.97 -9.30 2.70e+01 1hcz 252 -24.41 -9.29 2.70e+01 1hl6A 165 -28.18 -9.26 2.75e+01 1jy3P 48 -28.83 -9.26 2.76e+01 1ge8A 249 -27.85 -9.26 2.76e+01 1g87A 614 -18.23 -9.24 2.77e+01 1uurA 473 -23.00 -9.21 2.82e+01 1i3uA 127 -19.69 -9.15 2.92e+01 1fr3A 67 -31.82 -9.14 2.93e+01 2hntE 81 -38.88 -9.14 2.94e+01 1i1dA 161 -24.97 -9.12 2.97e+01 1u1zA 168 -24.77 -9.11 2.99e+01 1iraX 152 -27.06 -9.09 3.01e+01 1dzfA 215 -21.53 -9.09 3.02e+01 1j1tA 233 -21.42 -9.09 3.03e+01 1be9A 119 -23.41 -9.07 3.05e+01 1ci3M 249 -26.09 -9.06 3.07e+01 1bawA 105 -22.93 -9.05 3.08e+01 1nnvA 110 -22.39 -9.03 3.11e+01 1k2fA 190 -24.89 -9.03 3.11e+01 1ibyA 112 -30.63 -9.03 3.12e+01 2pcdM 238 -26.98 -8.99 3.19e+01 1jxcA 68 -21.06 -8.98 3.21e+01 1bgyE 196 -29.25 -8.93 3.29e+01 1hyxL 216 -19.63 -8.92 3.32e+01 1gjwA 637 -21.61 -8.91 3.32e+01 1e79A 510 -20.10 -8.91 3.33e+01 1r13A 148 -22.22 -8.90 3.34e+01 1skyE 473 -22.01 -8.88 3.38e+01 1lvk 762 -21.02 -8.87 3.39e+01 1fzkA 274 -24.48 -8.86 3.41e+01 1p32A 209 -27.41 -8.85 3.43e+01 1gfc 59 -19.82 -8.85 3.45e+01 1p32C 209 -27.37 -8.84 3.45e+01 1ff4A 65 -22.40 -8.83 3.47e+01 1dqqA 214 -19.53 -8.81 3.52e+01 1aqb 183 -23.76 -8.80 3.52e+01 1e1oA 504 -22.44 -8.77 3.60e+01 1ebpA 211 -25.74 -8.77 3.60e+01 1mwsA 646 -25.33 -8.75 3.62e+01 1sy7A 715 -29.80 -8.73 3.67e+01 12e8L 214 -19.61 -8.71 3.71e+01 1n67A 359 -21.58 -8.71 3.71e+01 1nepA 130 -27.71 -8.71 3.72e+01 1l7iL 214 -19.40 -8.71 3.72e+01 1d0yA 761 -20.11 -8.70 3.73e+01 1sro 76 -22.87 -8.70 3.74e+01 1i21A 159 -22.51 -8.69 3.76e+01 1nrgA 261 -27.42 -8.67 3.79e+01 1s5lO 246 -22.46 -8.67 3.80e+01 1iuz 98 -19.29 -8.66 3.82e+01 1evhA 112 -25.53 -8.65 3.83e+01 1jkgA 140 -27.17 -8.65 3.84e+01 1eg9B 194 -24.38 -8.65 3.84e+01 1ntyA 311 -24.15 -8.64 3.85e+01 1k8bA 52 -20.30 -8.64 3.86e+01 1gefA 123 -21.42 -8.62 3.91e+01 1ollA 188 -23.08 -8.61 3.92e+01 1cb8A 678 -19.94 -8.61 3.93e+01 1b2rA 304 -18.91 -8.58 3.99e+01 1k1zA 78 -23.68 -8.58 3.99e+01