AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipdhR_ecoli_bsub_300.orf -g0.5 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pdhR 300 transcriptional regulator for pyruvate dehydrogenase complex #2 aceE 160 pyruvate dehydrogenase (decarboxylase component) #3 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #4 metA 156 homoserine transsuccinylase #5 aceB 268 malate synthase A #6 aceA 29 isocitrate lyase #7 aceK 182 isocitrate dehydrogenase kinase/phosphatase #8 yfjN 300 similar to hypothetical proteins #9 yfjM 195 yfjM #10 yfjL 29 alternate gene name: yztA #11 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #12 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #13 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #14 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #15 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #16 yqiS 124 similar to phosphate butyryltransferase #17 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) Motif number 1 AAGCGCATATAAAAGCGCGGCAACTAAACG 2 52 1 AAAAGCGCGG 0.81352 -109 GGAAAGCTCAATAAGACAGGTTCTACGTTT 2 77 0 ATAAGACAGG 0.89933 -84 CAAAAAGTTCAAAAGCAAGGCCACTAAGAA 8 87 1 AAAAGCAAGG 0.941053 -214 AAAGGCTAACAAAATAAAGGGATTTTTACA 9 30 1 AAAATAAAGG 0.923426 -166 GGATTTACCGAAAATCCAGGTTTATTTTAG 9 70 0 AAAATCCAGG 0.855207 -126 TAAATTAGAGAAAAGACAGGCTGAGTAAAA 9 120 0 AAAAGACAGG 0.977648 -76 TTATTGTAAGAAAATAATGGTATATTTAGT 9 147 1 AAAATAATGG 0.848089 -49 ACATATGAGGAAAAGAGTGGGAAC 10 16 1 AAAAGAGTGG 0.925627 -14 GCATGCAAAAAAAAGACCGGATATCACCCG 11 54 0 AAAAGACCGG 0.943779 -178 TTACGGGCTCAAAAGACTGGCACACTTCTT 11 170 1 AAAAGACTGG 0.952938 -62 ATGACTGTTTAAAAGAAAGGAAGAGGTGAC 12 276 1 AAAAGAAAGG 0.974199 -25 AAACAGATATATAATAGAGGGAAAACGTTC 13 38 0 ATAATAGAGG 0.636852 -77 ATGCTTTTAAAAATGAATGGCTTTGCCATC 15 39 0 AAATGAATGG 0.615412 -35 CGGAGTCGAAACAAGAAAGGTGGTAACAG 16 106 1 ACAAGAAAGG 0.922654 -19 TTTCCGCTGGACAATAAAGGAAATGAAAAG 17 30 0 ACAATAAAGG 0.792095 -123 ********** Masking position 3 Map Score: 17.8303 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 175 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 ACCACCGGGTCGTTCTATCCGTCGGTATTTTAC 3 103 0 CGTATCCGTC 0.964398 -198 GCGGCGTGAACGCCTTATCCGGCCTACAGTCAG 7 27 0 CGCATCCGGC 0.99834 -156 AAGGCGTTCACGCCGCATCCGGCAATCGGTGCA 7 44 1 CGCATCCGGC 0.99834 -139 GACGCGCAAGCGTCGCATCAGGCATCGTGCACC 7 71 0 CGCATCAGGC 0.994952 -112 GACGCTTGCGCGTCTTATCATGCCTACAGCCGT 7 90 1 CGCATCATGC 0.956544 -93 GCGGCGTAAACGCCTTATCCAGCCTACGTTCGG 7 125 0 CGCATCCAGC 0.985329 -58 AAGGCGTTTACGCCGCATCCGGCAATTCTCTGC 7 142 1 CGCATCCGGC 0.99834 -41 CCTGGATTTTCGGTAAATCCGGGTCTTTTTTGT 9 80 1 CGTATCCGGG 0.952353 -116 CTTTTGAGCCCGTAAAATCAGTCTTCTCATCTT 11 152 0 CGAATCAGTC 0.83429 -80 ** * ******* Masking position 7 Map Score: 17.8234 Number of sites scoring better than the average of aligned sites = 1051 Number in coding regions = 417 Number in noncoding regions = 634 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 ATACCCGTCGTCTTTCAGGCCGCAGCGGCGTTA 3 247 0 TCTTCAGCGC 0.960967 -54 GCCTTATCCGGCCTACAGTCAGCAACGGTTGTT 7 16 0 GCTACATCGC 0.981904 -167 GCCGGATAAGGCGTTCACGCCGCATCCGGCAAT 7 37 1 GCTTCAGCGC 0.994757 -146 GCCTTATCCAGCCTACGTTCGGCAACGGCTGTA 7 114 0 GCTACGTCGC 0.954464 -69 GCTGGATAAGGCGTTTACGCCGCATCCGGCAAT 7 135 1 GCTTTAGCGC 0.989234 -48 TTTGTACGCAGCTTTTACTCAGCCTGTCTTTTC 9 108 1 GCTTTATCGC 0.987018 -88 GCAGATGTTTGCGTTTATTCTGCAAA 16 4 0 GCTTTATCGC 0.987018 -121 ** **** ** ** Masking position 4 Map Score: 6.90487 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 134 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TGGATAATTTTTACCAGAAAAATCA 2 5 0 TTACCAGAAA 0.982202 -156 TGGTAAAAATTATCCAGAAGATGTTGTAAAT 2 20 1 TATCCAGAAA 0.97019 -141 AATGGGACAGGTTCCAGAAAACTCAACGTTA 2 118 1 GTTCCAGAAA 0.929057 -43 ATTCATGAGATTACCAGAAAAAAGC 3 5 0 TTACCAGAAA 0.982202 -296 TAGCTGAAGATAACCAGAAAATTTGCCAATG 4 90 0 TAACCAGAAA 0.976978 -67 CAGCGCCAGTTAACCAGAATATAAAAAATAG 8 127 1 TAACCAGAAA 0.977 -174 TTTGCAGAATAAACGCAAACA 16 1 1 TTTGCAGAAA 0.889625 -124 ********* * Masking position 6 Map Score: 6.66632 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 78 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 AAACAACAAACGGCAACCGATTTGTCTATTCG 3 52 0 CGGCAACGTT 0.991171 -249 GATAGTCGATCGTTAAGCGATTCAGCACCTTA 5 19 1 CGTTAACGTT 0.798899 -250 GGCCTACAGTCAGCAACGGTTGTTGTTGC 7 8 0 CAGCAAGGTG 0.926895 -175 ACGCCGCATCCGGCAATCGGTGCACGATGCCT 7 53 1 CGGCAACGTG 0.995622 -130 AGCCTACGTTCGGCAACGGCTGTAGGCATGAT 7 106 0 CGGCAAGGTG 0.989787 -77 AAAGAAGAACCGTCAATCGTTTTCATCGCTGA 12 47 0 CGTCAACGTT 0.968379 -254 TTGCCATCTGCGGCAAGCGCAGCTTCTCCAAT 15 15 0 CGGCAACGAG 0.979627 -59 ****** ** ** Masking position 6 Map Score: 5.67097 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 356 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 TCATGAAACTGTGCACATTTTAACAACTTGA 1 169 0 GTGCACATTT 0.955864 -132 CGTGCAGCTCCTCGTCATGGAT 5 257 0 GTGCAGCTCT 0.983077 -12 GTGCAGATGCTCCATAGTTAT 6 19 0 GTGCAGATCT 0.978318 -11 ATCAGGCATCGTGCACCGATTGCCGGATGCG 7 57 0 GTGCACCGTT 0.866926 -126 TTTGTGCGCCTCCTTCTATTTAGG 11 218 0 GTGCGCCTCT 0.911763 -14 TCTGCGGCAAGCGCAGCTTCTCCAATTGCT 15 10 0 GCGCAGCTCT 0.931377 -64 CGAAACATTCGTGCAGATGTTTGCGTTTATT 16 18 0 GTGCAGATTT 0.96604 -107 ACATAGGGTTGTGCAAATTATTGCAACGGAA 17 91 1 GTGCAAATAT 0.744999 -62 ATAAATAGGTGTGCAAATTTTTTCATACAAA 17 121 1 GTGCAAATTT 0.905768 -32 ******** ** Masking position 11 Map Score: 5.62769 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 85 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TCGTTAAAAAACTCCTTTCCTACGTAAAGT 1 98 1 ACTCCTTTCC 0.825307 -203 TTGTGTAAAAATCCCTTTATTTTGTTAGCC 9 33 0 ATCCCTTTAT 0.874341 -163 TTTCCTCTCCCCCTTTATATGATATCTC 9 178 0 CCCCCTTTAT 0.979696 -18 TAAGTCACCTCTTCCTTTCTTTTAAACAGT 12 279 0 CTTCCTTTCT 0.865826 -22 TCAAGCCCCTCCTTTATGCTTTTAAAA 15 57 0 CCTCCTTTAT 0.958954 -17 CTGTTACCACCTTTCTTGTTTCGACT 16 109 0 CCACCTTTCT 0.917803 -16 CTTCAGAAAACCCCTTTATCTTTTCATTT 17 10 1 ACCCCTTTAT 0.968174 -143 CCCGATACCCCTTTGTATGAAAAAAT 17 137 0 ACCCCTTTGT 0.931992 -16 ********** Masking position 6 Map Score: 4.26781 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 70 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 ATCGTTAAGCGATTCAGCACCTTACCTCAGGCA 5 27 1 GATTAGCATT 0.976288 -242 AATTGTTTTTGATTTTGCATTTTAAATGAGTAG 5 162 1 GATTTGCATT 0.98715 -107 CTTCCCTCTCGATTATGCAGTTTGA 13 3 0 GATTTGCATT 0.98715 -112 CTCCTAGTTTGATTAAGCAATTTTAAAGTTTAC 13 82 0 GATTAGCATT 0.976288 -33 CTCCGCCTTTTATTATGCAAGTTCCATGCCAGC 16 78 0 TATTTGCATT 0.922384 -47 GGTAACATAGGGTTGTGCAAATTATTGCAACGG 17 87 1 GGTTTGCATT 0.965622 -66 **** **** ** Masking position 9 Map Score: 3.83934 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 26 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 CATGTCTGTGACGCTAAAGTAACAAAGTAT 1 232 0 ACGCTAAAGT 0.810343 -69 TACTTCACATACCCTATGGATTTCTGGGTG 3 147 1 ACCCTATGGA 0.926276 -154 TAAAAAAGGCACCCGAAGGTGCCTGAGGTA 5 49 0 ACCCGAAGGT 0.914357 -220 ATGATTATCTACCCTATTTTTTATATTCTG 8 141 0 ACCCTATTTT 0.704734 -160 ATAATGGTGAACCCTAAATAGAAGGAGGCG 11 206 1 ACCCTAAATA 0.887047 -26 AACTTAGGGTACCCTAAAGTATCAGCAGTA 12 219 0 ACCCTAAAGT 0.966059 -82 ACTTTAGGGTACCCTAAGTTTGTATGTATA 12 229 1 ACCCTAAGTT 0.958652 -72 GTATGACAGCACCCTTAAGAGCTGGCATGG 16 58 1 ACCCTTAAGA 0.708651 -67 AATTTGCACAACCCTATGTTACCACGTTTT 17 80 0 ACCCTATGTT 0.924781 -73 ********** Masking position 1 Map Score: 3.66285 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 37 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TGATAACAATATGAATAAAATTTATTCACCTGCTGAGG 5 92 0 ATGAAAATCA 0.974955 -177 TTTGAACTTTTTGGATAAAAAGGATTCCAACCTAAATA 8 62 0 TTGAAAATCC 0.939748 -239 TTTTTTTTGCATGCTGTAAAACGAGACAAATGAATCAG 11 70 1 ATGAAAAGCA 0.922948 -162 GTGTCTCGTTTTGTCTCAAACTGATTCATTTGTCTCGT 11 90 0 TTGAAAATCA 0.980654 -142 TCTTCTTTATTTGGTGTAAACTAATCCATGTTAAGCGG 12 71 1 TTGAAAATCA 0.980653 -230 TATTTCGAAGTTGTAAAAAACTAATACAACACCGCTTA 12 102 0 TTGAAAATCA 0.980654 -199 CTAAGTTTGTATGTATAAAAGGAATGCACGTCTAATGA 12 242 1 ATGAAAATCA 0.974955 -59 *** *** ** ** Masking position 9 Map Score: 2.53611 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 13 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ACTATAAAAATCCGAATTGAACCGATTCACT 1 60 0 TCCAATTGAA 0.863497 -241 AAAACTCCTTTCCTACGTAAAGTCTACATTT 1 105 1 TCCACGTAAA 0.970604 -196 TAAAAAGGATTCCAACCTAAATAGAATATCA 8 54 0 TCCACCTAAA 0.924909 -247 TAGATAATCATCCCACGTGAAATCTTCAAAA 8 160 1 TCCACGTGAA 0.981102 -141 TGAACCTTTATCCCAAATTAAAAACTGACCA 8 245 0 TCCAAATTAA 0.737406 -56 TCAAACTGTCTCCAAAGTGAAGATGAGAAGA 11 133 1 TCCAAGTGAA 0.961715 -99 AGTGTAACTATCCTACATAAAAGGTTTTGGC 12 156 1 TCCACATAAA 0.936121 -145 *** ******* Masking position 5 Map Score: 1.64305 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 25 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 TATGACCGCCGGAGATAAATATATAGAGGTC 3 277 1 GGAATAAATA 0.823241 -24 GACTACGTTAGAATATAAGAATGACTAAAAG 4 19 0 GAAATAAGAA 0.904238 -138 CCTGCATGTTGAAGGTGAGAAAGTTTCAAGG 4 54 0 GAAGTGAGAA 0.739608 -103 GGTACGTTTCGGAAATAAAAAAGGCACCCGA 5 63 0 GGAATAAAAA 0.936461 -206 CAGTTAACCAGAATATAAAAAATAGGGTAGA 8 133 1 GAAATAAAAA 0.919665 -168 AGATTTCCAAGGAAATAAATACGTCGATCAT 11 13 1 GGAATAAATA 0.823241 -219 TCTCCAAAGTGAAGATGAGAAGACTGATTTT 11 141 1 GAAATGAGAA 0.923994 -91 TTGATGAAAATGTAAAGCGAATACAT 12 6 1 GAAATGTAAA 0.699102 -295 GGACAATAAAGGAAATGAAAAGATAAAGGGG 17 21 0 GGAATGAAAA 0.949937 -132 *** ******* Masking position 6 Map Score: 2.0327 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 109 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 13 ********** No masking Map Score: -2.30683e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ACCGATTCACTTACCAATTTTGTGATTTTT 1 41 0 TTACCAATTT 0.904169 -260 TTGTGCATAGTTACAACTTTGAAACGTTAT 1 134 1 TTACAACTTT 0.938338 -167 TCAATTGGTCTTACCAATTTCATGTCTGTG 1 252 0 TTACCAATTT 0.904169 -49 TGCGCTTGATTTACAACATCTTCTGGATAA 2 29 0 TTACAACATC 0.822017 -132 CGTCGGTATTTTACAAAATTGTTAACAATT 3 87 0 TTACAAAATT 0.761228 -214 TATTAGTTTTTTACAACTTCGAAATAATAC 12 114 1 TTACAACTTC 0.89602 -187 CTGTTACCACCTTTCTTGTTTCG 16 112 0 TTACCACCTT 0.915778 -13 CAACCCTATGTTACCACGTTTTCTTCTCTT 17 72 0 TTACCACGTT 0.915778 -81 ********** Masking position 6 Map Score: 2.7131 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 88 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 15 GGTAATCTCATGAATGTATTGAGGTTATTAGCGA 3 21 1 TGTGATTAGG 0.925115 -280 TAGAACGACCCGGTGGTGGTTAGGGTATTACTTC 3 119 1 CGGGGGTAGG 0.974401 -182 TATGGATTTCTGGGTGCAGCAAGGTAGCAAGCGC 3 161 1 TGTGAGCAGG 0.966886 -140 CATAAGTAAGTGACTGGGGTGAGGGCGTGAAGCT 3 214 1 TGTGGGTAGG 0.992099 -87 AACGTATAAGCGTATGTAGTGAGGTAATCAGGTT 4 133 1 CGTGAGTAGG 0.98512 -24 CACCCGAAGGTGCCTGAGGTAAGGTGCTGAATCG 5 36 0 TGTGGGTAGG 0.992099 -233 ** ** *** *** Masking position 12 Map Score: 1.1899 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 34 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467