AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 mog 114 required for the efficient incorporation of molybdate into molybdoproteins #2 moaA 300 molybdopterin biosynthesis, protein A #3 moaB 21 molybdopterin biosynthesis, protein B #4 moeA 203 molybdopterin biosynthesis #5 HI0329 37 conserved hypothetical protein #6 HI0330 98 opacity associated protein (oapA) #7 HI0331 59 opacity associated protein (oapB) #8 HI0334 77 GTP pyrophosphokinase (relA) #9 HI0336 82 molybdopeterin biosynthesis protein (mog) #10 HI1448 137 molybdopterin biosynthesis protein (moeA) #11 HI1675 91 molybdenum cofactor biosynthesis protein C (moaC) #12 HI1676 300 molybdenum cofactor biosynthesis protein A (moaA) Motif number 1 CAAAGTAAAACCGCCATTTTCCCTTATTCT 2 59 1 CCGCCATTTT 0.963034 -242 CTGATCTCTCCTTTTGACGTT 3 6 0 TCTCCTTTTG 0.778809 -16 TAAGGGTGGTTCGCCACTTTTGCTATAAAT 4 24 1 TCGCCACTTT 0.889833 -180 TCAAACCATCTCTCATTTTTAGGATATTTC 5 15 0 TCTCATTTTT 0.932595 -23 AATTTTTTCGCCGCACTTTTGAGCTTCTCA 6 30 1 CCGCACTTTT 0.985857 -69 CTTTTGAGCTTCTCAATTTTGTGGCTAATT 6 45 1 TCTCAATTTT 0.932595 -54 GGGCGAGTAATCGCCCCTTTTTCTTTTTAA 7 17 1 TCGCCCCTTT 0.94072 -43 TAAAAACTTACCGCACTTTTGGAGGG 9 7 0 CCGCACTTTT 0.985857 -76 TAAGTTTTTACCGCATTTTTGATTTATCCA 9 27 1 CCGCATTTTT 0.972587 -56 TTGCAATTTTTCTCATTTTACCATCCTATT 10 55 0 TCTCATTTTA 0.637414 -83 TCATTCAAATTTGCAATTTTTCTCATTTTA 10 65 0 TTGCAATTTT 0.69635 -73 TTACCATTCATCTCACTTTGCTTT 11 5 0 TCTCACTTTG 0.904038 -87 AATATTTTAACCGCACTTTTATTATATT 11 74 1 CCGCACTTTT 0.985857 -18 ********** Masking position 8 Map Score: 17.6617 Number of sites scoring better than the average of aligned sites = 719 Number in coding regions = 604 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 GCGGTTTTACTTTGATATACATCATCAGGGAG 2 41 0 TTTATAACAT 0.844379 -260 GTTCGCCACTTTTGCTATAAATATCAGAATTT 4 32 1 TTTCTAAAAT 0.834311 -172 TGAATGAGTAATTCATAAAAATTCTGATATTT 4 50 0 ATTATAAAAT 0.871059 -154 TTTGTGGCTAATTAATATAAATAAGAACAAGC 6 62 1 ATTATAAAAT 0.644131 -37 CGTCAAAATCATTTATAAAAATAAGGAAAAAT 9 61 1 ATTATAAAAT 0.533849 -22 CTAAAGCCTAATTCATTCAAATTTGCAATTTT 10 75 0 ATTATTAAAT 0.846704 -63 AAAATCCTTATTTGATAAAATTTGTCAGCTAT 10 114 0 TTTATAAATT 0.87667 -24 TTTATGGTTATTAATATAAATAGGATTAATT 12 10 1 ATTATAAAAT 0.644131 -291 TTATGTATTTTTTTATATAATTGATTTTTAAG 12 69 1 TTTATAAATT 0.853808 -232 ATTTTCCTAAATTCTTAAAAATCAATTATATA 12 82 0 ATTTTAAAAT 0.756587 -219 AATCAATAATATTGATGAAAATCAGTATTTTC 12 108 0 ATTATGAAAT 0.888551 -193 TTAGCCTAAGTTTCATAGAAATACGGTGGCAA 12 206 1 TTTATAAAAT 0.964457 -95 *** *** **** Masking position 9 Map Score: 16.6509 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 27 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 ACATCATCAGGGAGGCATAGCGTGCATCGT 2 25 0 GGAGGCATAG 0.958469 -276 CCTTCGCCCTGGTGGCAATCTTTACGAGCA 2 243 0 GGTGGCAATC 0.984621 -58 TCCAGATACGGGAGGCGAAGTCATTTCTTC 2 272 0 GGAGGCGAAG 0.97275 -29 TTATAGCAAAAGTGGCGAACCACCCTTAAT 4 22 0 AGTGGCGAAC 0.950855 -182 CTACGCCCGAGGTGGCATACAGTCTGTGGC 4 132 1 GGTGGCATAC 0.981819 -72 ACACTCCTGCGGAGGCAAAATCGAATTTGC 4 180 0 GGAGGCAAAA 0.958527 -24 AACAAGCATCAGAGGCAATCCA 6 87 1 AGAGGCAATC 0.93697 -12 ATAGAAATACGGTGGCAAGCCAATAACGCG 12 220 1 GGTGGCAAGC 0.981798 -81 ********** Masking position 5 Map Score: 10.1101 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 442 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 TTTCGCTACAGAATAAGGGAAAATGGCGGT 2 68 0 GAATAAGGGA 0.971345 -233 ATATTGTACCGAATAACCGAG 8 2 0 GAATAACCGA 0.989525 -76 TCCTTTGCTAGAATAGCCGATTATTTTTTT 10 24 0 GAATAGCCGA 0.987393 -114 TTTAGATATAGAATAGCTGACAAATTTTAT 10 102 1 GAATAGCTGA 0.95172 -36 TGAATGTTTTAAATAAGCGACAAAAGGAAG 11 45 0 AAATAAGCGA 0.884242 -47 GCGTATCCCTGAATAACGTAGCGCGTTATT 12 241 0 GAATAACGTA 0.909365 -60 ********** Masking position 5 Map Score: 3.10937 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 55 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 GAAGCTCAAAAGTGCGGCGAAAAAATTATGT 6 26 0 AGTGCGGCAA 0.989062 -73 CCCTCCAAAAGTGCGGTAAGTTTTTACCGC 9 10 1 AGTGCGGTAG 0.989063 -73 ATAAATCAAAAATGCGGTAAAAACTTACCGC 9 23 0 AATGCGGTAA 0.974664 -60 AAAGCAAAGTGAGATGAATGGTAATATT 11 8 1 AGTGAGATAA 0.880557 -84 ATATAATAAAAGTGCGGTTAAAATATTGAAT 11 70 0 AGTGCGGTAA 0.995044 -22 ******** ** Masking position 3 Map Score: 3.05188 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 90 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 6 TCATTCTTAGCGTGACCGGGAAGTCGGT 1 8 1 TAGCGTGACG 0.988085 -107 TCAGAAGAGGTAGCGTGACCGACTTCCCGGT 1 25 0 TAGCGTGACG 0.988085 -90 TCATTCTGTTTAACGAGACTGTTTAAACGGA 1 85 1 TAACGAGACG 0.967168 -30 CCTTATTCTGTAGCGAAATAGCACGATCATG 2 80 1 TAGCGAAATG 0.958687 -221 CATGATTACATAGCGAAAGTGTGGATGGTAA 2 121 1 TAGCGAAAGG 0.972896 -180 CTGATATTTATAGCAAAAGTGGCGAACCACC 4 28 0 TAGCAAAAGG 0.823192 -176 TAAATGATTTTGACGTGATTGGATAAATCAA 9 45 0 TGACGTGATG 0.755473 -38 ********* * Masking position 8 Map Score: 3.32141 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 183 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TGACAGACAGGCTTCAGAAGAGGTAGCGTG 1 39 0 GCTTCAGAAG 0.88193 -76 ATGATACACTGCGAAGGGAGTGACAGACAG 1 59 0 GCGAAGGGAG 0.969914 -56 GTGCTATTTCGCTACAGAATAAGGGAAAAT 2 74 0 GCTACAGAAT 0.915524 -227 TGCCACCAGGGCGAAGGAAGAAATGACTTC 2 256 1 GCGAAGGAAG 0.975052 -45 CACCTTTCCAGATACGGGAGGCGAAGTCAT 2 278 0 GATACGGGAG 0.759638 -23 CAAAAGTGCGGCGAAAAAATTATGTGTATT 6 21 0 GCGAAAAAAT 0.712549 -78 CAAAATAAAAGCGACAGGAAGTTGCTTGCT 8 37 1 GCGACAGGAA 0.90876 -41 TTTTAAATAAGCGACAAAAGGAAGCAGATG 11 39 0 GCGACAAAAG 0.955143 -53 TGAAACTTAGGCTAAACAAGCTCGGAGTTA 12 191 0 GCTAAACAAG 0.822582 -110 ********** Masking position 9 Map Score: 2.59214 Number of sites scoring better than the average of aligned sites = 1201 Number in coding regions = 1128 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 8 CGCCTCCCGTATCTGGAAAGGTGTAC 2 285 1 ATTGAAAGGA 0.976016 -16 CTATATTCAAAAATTGAATGAGTAATTCATAAAAA 4 61 0 AATGAATGTA 0.937761 -143 CAATTTTTGAATATAGAAAGATGGATATGGCATGT 4 80 1 ATTGAAAGGA 0.976016 -124 AAAAATTGCAAATTTGAATGAATTAGGCTTTAGAT 10 74 1 AATGAATGTA 0.937761 -64 TAGGCTTTAGATATAGAATAGCTGACAAATTTTAT 10 97 1 ATTGAATATA 0.821302 -41 TGCGGTTAAAATATTGAATGTTTTAAATAAGCGAC 11 54 0 ATTGAATGTA 0.976279 -38 GAGTGAAATCTTTTAGAATGACGAAAAATCAAATT 12 149 1 TTTGAATGGA 0.921253 -152 TCCTCTCCGTATTTAGAAAGGTGTAAA 12 284 1 ATTGAAAGGA 0.976016 -17 ** * ***** * * Masking position 8 Map Score: 5.78701 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 38 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 GTGGATGGTAAAAATCTCATTTACACGCTAGT 2 141 1 AAAATCATTT 0.942243 -160 TTTTGCTATAAATATCAGAATTTTTATGAATT 4 41 1 AATATCAATT 0.711851 -163 CTGCGGAGGCAAAATCGAATTTGCCTATTATG 4 172 0 AAAATCATTT 0.742324 -32 CGTGATTGGATAAATCAAAAATGCGGTAAAAA 9 31 0 TAAATCAAAT 0.675302 -52 CAATCACGTCAAAATCATTTATAAAAATAAGG 9 55 1 AAAATCTTAT 0.919759 -28 TAAAATGAGAAAAATTGCAAATTTGAATGAAT 10 65 1 AAAATTAAAT 0.563245 -73 AGAAAATCCTTATTTGATAAAATT 10 124 0 AAAATCTATT 0.941583 -14 TAAATTCTTAAAAATCAATTATATAAAAAAAT 12 75 0 AAAATCTTAT 0.892454 -226 AATATTGATGAAAATCAGTATTTTCCTAAATT 12 101 0 AAAATCTATT 0.93889 -200 CTCCATAAACACAATCAATAATATTGATGAAA 12 120 0 ACAATCTAAT 0.721612 -181 AGAATGACGAAAAATCAAATTTAACGCATAAC 12 163 1 AAAATCATTT 0.916009 -138 ****** **** Masking position 4 Map Score: 8.72886 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 128 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 10 ********** No masking Map Score: 3.20698e-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 11 ********** No masking Map Score: 3.20698e-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 12 ********** No masking Map Score: 3.20698e-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