% 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. % --------------------------------------------------------------------- % str2foo.1.YGR034W.t2k-100-30-str2 Host: farm20 Wed Nov 17 18:47:02 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 % % 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 0.300 File YGR034W.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 130 nodes, 140.36 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(=2.0759) * Reverse)^tau(=0.7256))) % 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 -114.49 -102.46 6.48e-18 1jj2S 119 -114.00 -101.97 7.69e-18 1ffkQ 119 -103.70 -92.82 1.90e-16 1az9 457 -23.15 -14.18 9.46e-02 1a16 440 -23.19 -14.17 9.51e-02 1e32A 458 -23.62 -13.66 1.29e-01 1txlA 215 -22.53 -11.35 5.36e-01 1qa7B 217 -22.25 -11.32 5.48e-01 1bmfA 510 -19.97 -11.11 6.27e-01 1oejA 193 -22.08 -10.95 6.93e-01 1v76A 96 -23.67 -10.64 8.44e-01 1jj2A 239 -20.01 -10.40 9.90e-01 1nxzA 246 -18.79 -10.39 9.91e-01 1bbzA 58 -18.64 -10.18 1.14e+00 1bbzE 58 -18.62 -10.17 1.15e+00 1kbvA 327 -20.39 -10.07 1.22e+00 1aboA 62 -18.60 -10.06 1.23e+00 1vhyA 257 -18.27 -10.06 1.23e+00 1e79A 510 -18.57 -9.88 1.39e+00 1kypA 237 -19.38 -9.80 1.46e+00 1utwA 432 -23.67 -9.72 1.54e+00 1qa7A 217 -20.51 -9.69 1.57e+00 1irp 153 -19.47 -9.69 1.57e+00 1ts9A 102 -21.14 -9.59 1.67e+00 1tuc 63 -19.07 -9.59 1.68e+00 1sfdA 105 -18.20 -9.49 1.79e+00 1uypA 432 -23.67 -9.47 1.82e+00 1jotA 133 -21.80 -9.46 1.82e+00 1mxgA 435 -19.49 -9.45 1.84e+00 1nwwA 149 -20.56 -9.42 1.88e+00 1aac 105 -18.20 -9.34 1.98e+00 1mvfD 82 -20.19 -9.34 1.98e+00 1havA 217 -21.37 -9.34 1.98e+00 1imvA 398 -18.63 -9.33 1.99e+00 1nhp 447 -18.31 -9.25 2.10e+00 1a49A 530 -19.20 -9.19 2.19e+00 1bxvA 91 -18.37 -9.13 2.28e+00 1gutA 68 -19.32 -9.11 2.31e+00 1aaj 105 -17.80 -9.10 2.33e+00 1bxaA 105 -17.85 -9.08 2.36e+00 1qniA 581 -21.20 -9.03 2.45e+00 1nngA 153 -23.93 -9.00 2.49e+00 1dj7B 75 -18.87 -9.00 2.49e+00 1nls 237 -19.97 -8.93 2.61e+00 1g291 372 -19.21 -8.82 2.80e+00 1lvoA 302 -18.61 -8.79 2.87e+00 1hdkA 141 -18.70 -8.78 2.88e+00 1nhs 447 -17.77 -8.72 3.01e+00 1h8eA 510 -17.46 -8.70 3.05e+00 2mcm 112 -19.93 -8.70 3.06e+00 1eysH 259 -24.46 -8.67 3.10e+00 1jnyA 435 -21.49 -8.64 3.17e+00 1vif 62 -17.72 -8.64 3.17e+00 1scs 237 -19.67 -8.62 3.23e+00 1joa 447 -17.64 -8.57 3.33e+00 1h7xD 1025 -19.27 -8.55 3.37e+00 9apiA 347 -18.25 -8.54 3.40e+00 1jacA 133 -20.74 -8.52 3.45e+00 1g86A 142 -18.55 -8.50 3.50e+00 1lcl 142 -18.55 -8.50 3.50e+00 1gteD 1025 -19.05 -8.48 3.55e+00 1h7wB 1025 -19.01 -8.45 3.61e+00 1ku8A 133 -20.80 -8.41 3.71e+00 1h7xB 1025 -19.00 -8.40 3.76e+00 1h7xC 1025 -19.00 -8.39 3.77e+00 1gteA 1025 -18.98 -8.39 3.77e+00 1h7wD 1025 -18.99 -8.39 3.78e+00 2emo 237 -18.26 -8.38 3.80e+00 1gthC 1025 -18.81 -8.35 3.88e+00 1h7xA 1025 -18.77 -8.34 3.90e+00 1h7wA 1025 -18.78 -8.32 3.96e+00 1gthA 1025 -18.67 -8.30 4.01e+00 1cbs 137 -18.19 -8.27 4.10e+00 1t3qB 788 -17.57 -8.26 4.13e+00 1ugxA 133 -20.72 -8.26 4.14e+00 1vie 62 -17.29 -8.22 4.25e+00 1p9uA 302 -17.95 -8.13 4.52e+00 1m26A 133 -20.68 -8.06 4.75e+00 1rovA 857 -17.31 -8.05 4.79e+00 7ahlA 293 -19.06 -7.99 4.99e+00 1d7qA 143 -17.55 -7.96 5.06e+00 1lplA 95 -19.95 -7.95 5.11e+00 1gt8C 1025 -18.58 -7.95 5.11e+00 2cuaA 135 -19.31 -7.93 5.18e+00 1xm8A 254 -17.23 -7.92 5.24e+00 1dynA 125 -16.91 -7.89 5.32e+00 1exmA 405 -18.39 -7.83 5.56e+00 1ov3A 138 -18.70 -7.80 5.68e+00 1hlcA 129 -18.78 -7.78 5.76e+00 1kcw 1046 -18.29 -7.76 5.84e+00 1tuaA 191 -16.94 -7.75 5.87e+00 1mqeA 207 -18.23 -7.74 5.92e+00 1ema 236 -17.79 -7.73 5.95e+00 1gthB 1025 -17.52 -7.69 6.14e+00 1csp 67 -17.90 -7.66 6.26e+00 1qlyA 58 -15.80 -7.66 6.27e+00 1smxA 96 -16.58 -7.65 6.33e+00 1ah9 71 -15.86 -7.64 6.33e+00 1pse 69 -17.80 -7.64 6.36e+00 1o97D 320 -16.43 -7.63 6.39e+00 1aipE 405 -18.42 -7.63 6.39e+00 1x6oA 174 -17.58 -7.59 6.58e+00 1gpr 162 -17.58 -7.57 6.66e+00 1pbp 321 -16.00 -7.57 6.69e+00 1ixh 321 -16.00 -7.56 6.71e+00 1tovA 98 -19.51 -7.54 6.81e+00 1jacC 133 -19.92 -7.54 6.82e+00 1ejfA 125 -19.14 -7.53 6.87e+00 1iraX 152 -17.71 -7.49 7.08e+00 1trb 320 -16.24 -7.45 7.26e+00 1m5q1 130 -19.80 -7.45 7.28e+00 1pwt 61 -16.54 -7.43 7.39e+00 1avaA 403 -16.42 -7.42 7.42e+00 1ilr1 152 -18.14 -7.41 7.46e+00 1shg 62 -16.49 -7.38 7.64e+00 1jb0E 75 -16.79 -7.37 7.68e+00 2dynA 122 -16.56 -7.37 7.70e+00 1ehkB 168 -18.41 -7.35 7.79e+00 1qmyA 167 -18.45 -7.34 7.85e+00 1luzA 88 -19.17 -7.32 8.00e+00 1jegA 83 -16.05 -7.27 8.28e+00 1c9oA 66 -18.68 -7.26 8.35e+00 1b56 135 -20.02 -7.24 8.46e+00 1jdqA 98 -16.09 -7.22 8.55e+00 1jxmA 301 -15.77 -7.22 8.56e+00 1vhqA 232 -14.85 -7.22 8.56e+00 1jksA 294 -16.09 -7.19 8.78e+00 1ckaA 57 -15.87 -7.17 8.85e+00 1vkkA 154 -16.82 -7.17 8.87e+00 1g2oA 268 -15.60 -7.17 8.90e+00 1fwxA 595 -19.62 -7.16 8.94e+00 1qs1A 462 -19.07 -7.15 8.99e+00 1c3mA 147 -19.68 -7.15 9.04e+00 1o59A 355 -19.37 -7.14 9.08e+00 1gt8D 1025 -16.92 -7.12 9.21e+00 1i0cA 60 -15.94 -7.09 9.42e+00 1uw6A 211 -16.75 -7.08 9.49e+00 1mhnA 59 -16.43 -7.07 9.50e+00 2ms2A 129 -19.52 -7.07 9.52e+00 1vk3A 615 -16.94 -7.06 9.63e+00 1cskA 71 -15.83 -7.05 9.68e+00 1kpuA 274 -17.49 -7.03 9.85e+00 1j48A 110 -16.75 -7.02 9.92e+00 1oxdA 227 -16.42 -7.01 9.95e+00 1gt8A 1025 -17.10 -7.01 9.96e+00 1se8A 301 -18.95 -7.01 9.98e+00 1fr3A 67 -17.57 -7.00 1.00e+01 1qhoA 686 -17.61 -6.98 1.02e+01 1gt8B 1025 -16.66 -6.96 1.03e+01 1rqpA 299 -15.96 -6.96 1.03e+01 1pkn 530 -16.88 -6.96 1.03e+01 1wosA 364 -16.80 -6.96 1.03e+01 1f7sA 139 -15.96 -6.94 1.05e+01 1tie 172 -17.40 -6.93 1.05e+01 1rl6A 177 -20.61 -6.93 1.06e+01 1g7pA 274 -17.38 -6.92 1.07e+01 1fzkA 274 -17.36 -6.92 1.07e+01 1omiA 248 -15.32 -6.91 1.07e+01 1lk2A 274 -17.36 -6.91 1.07e+01 1oy1A 228 -14.67 -6.90 1.08e+01 1id2A 106 -16.02 -6.86 1.11e+01 1pm4A 119 -19.23 -6.85 1.12e+01 1fzoA 274 -17.16 -6.83 1.13e+01 1ng2A 193 -18.23 -6.82 1.15e+01 1t9hA 307 -15.46 -6.79 1.17e+01 1l5jA 865 -15.02 -6.76 1.19e+01 1b34B 118 -17.17 -6.75 1.20e+01 1gcqA 61 -18.11 -6.74 1.21e+01 1ha3A 405 -18.03 -6.73 1.22e+01 1j7nB 776 -16.50 -6.71 1.24e+01 1mqoA 227 -16.94 -6.67 1.28e+01 1jdiA 231 -16.64 -6.65 1.29e+01 1skyB 502 -16.95 -6.65 1.29e+01 1ktbA 405 -16.77 -6.64 1.31e+01 1kafA 108 -15.15 -6.62 1.32e+01 1i60A 278 -13.91 -6.58 1.36e+01 1k0wA 231 -16.54 -6.58 1.36e+01 1qr4A 186 -18.02 -6.56 1.38e+01 1fdr 248 -15.93 -6.54 1.41e+01 1j7nA 776 -16.65 -6.50 1.45e+01 1eerB 227 -15.65 -6.50 1.45e+01 1h4rA 314 -15.33 -6.49 1.45e+01 1o0xA 262 -16.24 -6.49 1.46e+01 1kk1A 410 -19.74 -6.48 1.46e+01 1ny4A 82 -19.03 -6.48 1.46e+01 1sro 76 -15.91 -6.48 1.46e+01 1pjxA 314 -19.13 -6.47 1.47e+01 1e1aA 314 -19.14 -6.47 1.48e+01 1kjwA 295 -15.09 -6.44 1.51e+01 1j1lA 290 -16.92 -6.44 1.51e+01 1qr4B 186 -18.19 -6.43 1.52e+01 1liuA 528 -18.87 -6.43 1.52e+01 1hjdA 101 -16.10 -6.43 1.52e+01 1wkt 88 -16.07 -6.43 1.52e+01 7taa 478 -17.58 -6.42 1.53e+01 1qksA 567 -19.68 -6.41 1.54e+01 1ootA 60 -18.76 -6.41 1.55e+01 1q1lA 401 -16.29 -6.39 1.57e+01 1iv8A 720 -16.34 -6.35 1.61e+01 1ncwH 222 -15.88 -6.32 1.65e+01 1ksiB 642 -18.72 -6.31 1.66e+01 1ciy 590 -15.89 -6.30 1.67e+01 1lfo 128 -20.06 -6.29 1.69e+01 1qz8A 113 -15.89 -6.29 1.69e+01 1ksiA 642 -18.86 -6.22 1.77e+01 1d6mA 653 -14.78 -6.20 1.80e+01 1qbiA 454 -17.46 -6.19 1.81e+01 1uasA 362 -14.69 -6.18 1.83e+01 1gr3A 160 -17.24 -6.18 1.83e+01 1g5vA 88 -16.14 -6.17 1.85e+01 1m5dA 263 -14.53 -6.16 1.86e+01 1mqiA 263 -14.54 -6.16 1.86e+01 1mqdA 261 -14.54 -6.16 1.86e+01 1k2eA 156 -16.94 -6.14 1.88e+01 1c9uA 454 -17.28 -6.14 1.89e+01 1bjt 793 -14.78 -6.12 1.91e+01 1h9jA 145 -16.59 -6.11 1.93e+01 1i78A 297 -16.39 -6.08 1.97e+01 1h9mA 145 -16.45 -6.02 2.06e+01 1uebA 184 -16.62 -6.01 2.09e+01 1ebaA 215 -14.92 -6.00 2.09e+01 1pu5A 164 -16.83 -5.99 2.12e+01 1qxmA 300 -15.88 -5.98 2.12e+01 1azeA 56 -14.19 -5.97 2.15e+01 1njhA 119 -17.37 -5.97 2.15e+01 1lnh 857 -15.25 -5.95 2.18e+01 1axiB 236 -16.75 -5.94 2.19e+01 1i1jA 108 -15.13 -5.94 2.19e+01 1jztA 246 -13.59 -5.93 2.21e+01 1dgsA 667 -15.21 -5.92 2.22e+01 1u69A 163 -13.99 -5.92 2.23e+01 1m5eA 263 -14.44 -5.90 2.27e+01 1m2tA 254 -14.18 -5.89 2.28e+01 1preB 470 -17.21 -5.89 2.28e+01 1nqjA 119 -17.07 -5.89 2.28e+01 1s72E 178 -17.55 -5.88 2.29e+01 1pcs 98 -14.84 -5.85 2.35e+01 1kawA 135 -15.49 -5.85 2.35e+01 1bawA 105 -15.11 -5.84 2.36e+01 1sv6A 269 -15.25 -5.84 2.36e+01 1tbgA 340 -15.71 -5.84 2.37e+01 1gttA 429 -15.76 -5.83 2.38e+01 2plc 274 -13.42 -5.82 2.40e+01 1ft9A 222 -19.31 -5.82 2.40e+01 1g2bA 62 -14.42 -5.81 2.42e+01 1qqjA 419 -15.23 -5.79 2.46e+01 1fhoA 119 -15.36 -5.78 2.47e+01 1ystH 260 -16.42 -5.77 2.49e+01 1evhA 112 -15.60 -5.77 2.50e+01 1u4cA 349 -17.05 -5.76 2.51e+01 1jr7A 311 -14.22 -5.75 2.52e+01 1hyoA 421 -15.23 -5.75 2.53e+01 1bvp1 349 -14.21 -5.75 2.54e+01 1c9qA 117 -13.72 -5.75 2.54e+01 1qcnA 421 -15.22 -5.74 2.55e+01 1cl2A 395 -13.94 -5.73 2.56e+01 1gd7A 109 -16.66 -5.73 2.56e+01 1hr0W 71 -13.80 -5.73 2.56e+01 1jh2A 99 -16.45 -5.72 2.58e+01 1gr2A 279 -13.75 -5.69 2.65e+01 1qs2A 401 -18.36 -5.68 2.66e+01 1rrpB 134 -17.57 -5.65 2.73e+01 1iz6A 138 -20.44 -5.64 2.75e+01 1d8hA 311 -14.79 -5.64 2.75e+01 1awo 62 -14.14 -5.64 2.75e+01 1vlyA 338 -16.07 -5.63 2.77e+01 1i7oA 429 -15.58 -5.63 2.77e+01 1ggxA 223 -16.24 -5.63 2.78e+01 1tud 62 -14.15 -5.62 2.80e+01 1ebpA 211 -15.51 -5.62 2.80e+01 1dfx 125 -18.04 -5.61 2.81e+01 1ftkA 279 -13.75 -5.61 2.81e+01 1i9bA 217 -15.43 -5.61 2.81e+01 1fa4A 105 -13.89 -5.60 2.83e+01 1x9zA 188 -14.27 -5.60 2.84e+01 1t6aA 126 -17.92 -5.60 2.85e+01 1fvrA 327 -14.42 -5.59 2.85e+01 1k26A 156 -16.98 -5.59 2.87e+01 1hjp 203 -15.41 -5.56 2.93e+01 1crzA 403 -15.63 -5.55 2.94e+01 1s0uA 408 -17.52 -5.53 2.99e+01 1n67A 359 -16.63 -5.53 2.99e+01 1dzfA 215 -14.03 -5.52 3.02e+01 1griA 217 -15.99 -5.52 3.02e+01 1h0hA 977 -14.58 -5.51 3.03e+01 1g13A 162 -15.99 -5.51 3.04e+01 4tsvA 150 -14.99 -5.50 3.08e+01 1c5kA 439 -15.54 -5.49 3.08e+01 1cruA 454 -16.58 -5.49 3.10e+01 1jj2E 177 -17.11 -5.48 3.11e+01 1o5zA 442 -13.94 -5.48 3.11e+01 1l3aA 228 -14.91 -5.48 3.11e+01 1h9sA 140 -15.88 -5.47 3.14e+01 1ollA 188 -16.73 -5.47 3.14e+01 1rss 151 -14.35 -5.47 3.15e+01 1e5mA 416 -14.28 -5.46 3.15e+01 1cl1A 395 -13.74 -5.45 3.18e+01 1e9pA 151 -16.68 -5.45 3.19e+01 1semA 58 -15.33 -5.44 3.20e+01 1sgoA 139 -14.16 -5.43 3.24e+01 1p32A 209 -17.09 -5.38 3.36e+01 1oqkA 97 -16.63 -5.37 3.39e+01 1q0sA 259 -14.53 -5.37 3.40e+01 1egxA 115 -14.00 -5.35 3.43e+01 1gotB 340 -15.21 -5.35 3.44e+01 1mo9A 523 -14.22 -5.34 3.46e+01 1nkqA 259 -14.29 -5.34 3.47e+01 1bt0A 76 -13.45 -5.34 3.48e+01 1wba 175 -15.29 -5.33 3.48e+01 1gpjA 404 -13.60 -5.33 3.50e+01 3hhrB 203 -16.35 -5.32 3.52e+01 1dhkB 223 -15.09 -5.31 3.55e+01 1c3kA 147 -18.48 -5.30 3.57e+01 1qcoA 423 -14.80 -5.30 3.59e+01 1feuA 206 -15.47 -5.29 3.61e+01 2dpmA 284 -14.66 -5.28 3.63e+01 2std 172 -13.98 -5.27 3.67e+01 1ufkA 254 -14.07 -5.26 3.68e+01 1an8 208 -14.31 -5.26 3.68e+01 1x8mA 288 -17.43 -5.26 3.69e+01 1nddD 76 -13.28 -5.22 3.79e+01 1h6rA 236 -15.04 -5.22 3.80e+01 1b2vA 188 -14.34 -5.22 3.81e+01 1mwxA 646 -15.65 -5.21 3.84e+01 1oxxK 353 -17.49 -5.20 3.86e+01 1vhrA 184 -12.94 -5.20 3.87e+01 1dk0A 188 -14.33 -5.20 3.88e+01 1oxsC 353 -17.37 -5.18 3.93e+01 1b9mA 265 -14.78 -5.17 3.96e+01