AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons005_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944237155 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0351 172 UDP-glucose 4-epimerase (galE) #1 HI0352 300 conserved hypothetical protein #2 HI0638 128 conserved hypothetical protein #3 HI0639 22 adenylosuccinate lyase (purB) #4 HI0640 271 ribosomal protein L10 (rpL10) #5 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #6 HI0642 159 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #7 HI0812 21 glucosephosphate uridylyltransferase (galU) #8 HI0813 77 carbon storage regulator (csrA) #9 HI0814 187 alanyl-tRNA synthetase (alaS) #10 HI0815 101 universal stress protein A (uspA) #11 HI0817 170 conserved hypothetical protein #12 HI0819 37 galactokinase (galK) #13 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #14 HI0866 300 H. influenzae predicted coding region HI0866 #15 HI0867 237 lipopolysaccharide biosynthesis protein, putative #16 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #17 HI0873 58 DTDP-glucose 4,6-dehydratase (rffG) #18 HI1010 158 3-hydroxyisobutyrate dehydrogenase, putative #19 HI1014 55 conserved hypothetical protein #20 HI1114 52 ADP-L-glycero-D-mannoheptose-6-epimerase (rfaD) #21 HI1115 110 thioredoxin, putative #22 HI1578 300 glycosyl transferase, putative #23 HI1700 125 lipopolysaccharide biosynthesis protein, putative Motif 1 AATCAATCAATCAATCAATCAA 1 1 1 CAATCAATCAATCAATCAATCAATCAATCAA 1 13 1 CAATCAATCAATCAATCAATCAATCAATCAA 1 25 1 CAATCAATCAATCAATCAATCAATCAATCAA 1 37 1 CAATCAATCAATCAATCAATCAATCAATCAA 1 49 1 CAATCAATCAATCAATCAATCAATCAATCAA 1 61 1 CAATCAATCAATCAATCAATCAATCAATCAA 1 73 1 CAATCAATCAATCAATCAATCAATCAATCAA 1 85 1 CAATCAATCAATCAATCAATCAATCAATCAA 1 97 1 CAATCAATCAATCAATCAAAGTCTGTCATTA 1 109 1 TAGATATCCTATCAATCAAGGAACGGTTGGC 8 30 0 TCATTACAAGATCTATAAATCAGGTTCATTT 11 32 1 CCTTGTTATAATCTATAAATCTTATATTTTG 13 18 1 ********* * MAP Score: 42.5344 Motif 2 AGCAACAGGTTTTTTATTTTATTGAAAATCAC 0 87 1 AAAAATACTTTTTTTATTTTCTTGCCAAGAAA 1 241 0 TTTGCTTATTTTCTTATTTTGTGACAAAGATC 13 116 1 GTAGGGTTTATTATTATTTTGTCCAATATTCT 16 227 1 ATAAGGGATATTTTGATTTTATCTCTCTTATC 16 113 1 TTTTAGTATATTATGATTTTTTCGGGTGGGTA 16 150 1 GGCGACTTAGTTTTTATTTTTATTATGGGTAA 9 150 1 TTACTTTCTTTTTTGATTTTAAGATAAGGGAT 16 90 1 ATGATAAAAAATGTTATTTTTTGTTAATTTTA 18 53 0 AATACTACCTTGTTTATTTTCTCGAATAATCG 22 67 0 AGCTTGTCTATGTTGATTTTGTTAAAATAAGC 23 57 1 ACGGGAGCGGTTATTATCTTTAAAATATTAAC 15 33 1 ATTTTGAAGATCATTATTTTCTTGGCAAGAAA 1 224 1 GCAAAATTTTTTATGATTTAGTTCATACTTAT 13 89 0 TATCTTATCTTATCTTATCTTAT 16 1 1 ATCTTATCTTATCTTATCTTATCTTATCTTAT 16 16 1 ATCTTATCTTATCTTATCTTTTTCATTGTTCT 16 31 1 GTTGCAATCAATTTTATTTTGAAGATCATTAT 1 209 1 TCTACAGAGGTTATGATATTCTTAAGCTATAT 22 111 1 GTGGTAAGAATGGTGATTTTCAATAAAATAAA 0 99 0 TTTATTTATTCCTTATCTTGTTGAGATGATT 21 89 0 AGCGATGGCTTTTTTATTTACAAAGGTTTACA 11 118 1 GCATCTCCTTTTGTTATTTAAATAACGTATAA 22 243 1 AATGTTTAAATTGTGATCTAGTACACAGTTTT 10 14 1 TAATCTATAAATCTTATATTTTGATCATAAAT 13 26 1 ** ******* * MAP Score: 23.9164 Motif 3 AGAACAATTAAAAAATACTTTTTTTATTTTCTTGC 1 248 0 AGAAAAAGGCTATTTTTATCAGTACGG 15 2 1 CAGAAGCAAGAAAAATTCTTATTCTGTTCACCATC 4 168 0 GAGTTTTGGCAAAAAGCCTTTTTATAAATTTCAAA 9 100 1 AAGCTAGGTTAAAAATGCTATATTTAACGGAAACG 2 85 1 CTATTGTAGCAAAAATTCTTTATTTTTGACTATGG 21 38 1 CTGCGGTTTTAAAAACACATATTATCTAAGGAGGA 19 26 1 TCAATAAAATAAAAAACCTGTTGCTAAAAAGTATT 0 77 0 ACAGTGATTTAAAAAAACTCAAATTTCTATTTCAA 22 171 1 TACCCACCCGAAAAAATCATAATATACTAAAATAG 16 147 0 TCGAACATTAAAAAAGCCTAGAGTTTCTGATATGA 2 44 0 CTAAATCATAAAAAATTTTGCTTATTTTCTTATTT 13 100 1 CAGAATGATAAAAAATGTTATTTTTTGTTAATTTT 18 54 0 ACATATATAGAGAAAACCTTTATATAGTTTAAGGT 16 274 0 ACCTGTTGCTAAAAAGTATTGTTGTAGCGAGTGAG 0 62 0 TAAAAAGAATCCTTGTTACCCATAAT 9 171 0 TAAAAATGTTTAAATTGTGATCTAGT 10 1 1 GTTTTTACTTAAAAACTTACCATTTGCTATCTTTC 6 87 1 TGATCCGAAGAAAAAAGATTTAACTGAG 14 282 1 ***** ** ** * MAP Score: 20.2543 Motif 4 AAATTTTCTCTTTATTCATCAATAACAACGGGTAA 6 134 0 GCTTATTACTTTCTTTTTTGATTTTAAGATAAGGGATATTTT 16 85 1 TTAAACTATTTTATACGTTATTTAAATAACAAAAGGAGATGC 22 243 0 AAAATTTTGCTTATTTTCTTATTTTGTGACAAAGATCACGGT 13 111 1 AAAATACTTTTTTTATTTTCTTGCCAAGAAAATAATGATCTT 1 230 0 AATGATTTCCTTGTTAATTATTGAGACTAAAAAATTATATCA 0 140 0 TCTTTATTCCTTACAGATCATAAAAGCATTTAGTT 15 212 0 GATTAAGGCGTTCTTAGCTGGTGAGAATAAAAGGAAAACTAA 15 176 1 AATAAAAAAAGTATTTTTTAATTGTTCTACAATTTTTGAGCA 1 255 1 GTCATAGCTTGTCTATGTTGATTTTGTTAAAATAAGCCCCCT 23 52 1 ACTTTCATAAGTATGAACTAAATCATAAAAAATTTTGCTTAT 13 83 1 AATATAAGATTTATAGATTATAACAAGGAAAAAGTT 13 4 0 TTTTATTTATGTTTTACCTATTGTAGCAAAAATTCTTTATTT 21 21 1 GGCGACTTAGTTTTTATTTTTATTATGGGTAACAAGGATTCT 9 150 1 TAACAAGAAATTGTTTTTTGAATAATCTGAAATAACTTAAAT 9 11 1 TTAACCTAGCTTTTGAACTCGAACATTAAAAAAGCCTAGAGT 2 55 0 GTTTTTTGAATTTTAAAGTGGTTAAAATAGAAA 6 1 0 TGAAGTGCGGTTTTATTTTGGAGTTTTGGCAAAAAGCCTTTT 9 80 1 TTAATTTATTGTATCGGCTAATATACAGATAAATTTAGTTAA 18 106 1 AAAATGTTATTTTTTGTTAATTTTAGTGATAAAACGTTATGA 18 36 0 TTTCGGGTGGGTATAGAGTATTTGTATGAAAATTACTCTAAT 16 169 1 ACGGGTAATATTCTATCTTAGAAAGATAGCAAATGGTAAGTT 6 100 0 TTTGGCTCTTTTTTCAACAATATTCTTTACAAGAACATAGCT 4 13 1 AATGGTAAGTTTTTAAGTAAAAACTATAACAAACTTTTATAT 6 69 0 ** * ** ** * ** MAP Score: 10.8529 Motif 5 TTTCTTGGCAAGAAAATAAAAAAAGTATTTTTTA 1 241 1 AAATTGTAGAACAATTAAAAAATACTTTTTTTAT 1 256 0 TTCGGCGCCCAGAAGCAAGAAAAATTCTTATTCT 4 178 0 TTAACCACTTTAAAATTCAAAAAACCGATGGGAA 6 18 1 TTTTTAAGTAAAAACTATAACAAACTTTTATATA 6 68 0 ATTCTATCTTAGAAAGATAGCAAATGGTAAGTTT 6 99 0 TGTTTTTTGAATAATCTGAAATAACTTAAATTTT 9 22 1 AAGCCTTTTTATAAATTTCAAAAATATGCAAAAA 9 113 1 ACCCATAATAAAAATAAAAACTAAGTCGCCCTAT 9 146 0 TTTATAGATTATAACAAGGAAAAAGTT 13 3 0 AAGTATGAACTAAATCATAAAAAATTTTGCTTAT 13 91 1 TCTTTGTCACAAAATAAGAAAATAAGCAAAATTT 13 112 0 TGGTGAGAATAAAAGGAAAACTAAATGCTTTTAT 15 194 1 ATAAAGCACTAGAACAATGAAAAAGATAAGATAA 16 39 0 ATCCCTTATCTTAAAATCAAAAAAGAAAGTAATA 16 88 0 GATAAGAGAGATAAAATCAAAATATCCCTTATCT 16 111 0 CCCACCCGAAAAAATCATAATATACTAAAATAGC 16 146 0 AATATTGGACAAAATAATAATAAACCCTACCAAA 16 223 0 TTTTATCACTAAAATTAACAAAAAATAACATTTT 18 44 1 TCTAGATCACAGAATGATAAAAAATGTTATTTTT 18 64 0 TACAATAGGTAAAACATAAATAAAAGGAGGAAAA 21 12 0 GCTTATTTTAACAAAATCAACATAGACAAGCTAT 23 55 0 * ** * ****** MAP Score: 9.34986 Motif 6 GTAGCGAGTGAGATAACCTCTCATATTTAGG 0 43 0 TCAATAAAATAAAAAACCTGTTGCTAAAAAG 0 81 0 CTCGAACATTAAAAAAGCCTAGAGTTTCTGA 2 49 0 AAGCTAGGTTAAAAATGCTATATTTAACGGA 2 85 1 AGGATTATAGAGAAAAGCTATGTTCTTGTAA 4 39 0 TTTAAAATTCAAAAAACCGATGGGAAACCAT 6 26 1 TTTATATAAGAAAAAACCGATGGTTTCCCAT 6 45 0 GAGTTTTGGCAAAAAGCCTTTTTATAAATTT 9 100 1 CTTTGTAAATAAAAAAGCCATCGCTTGACCA 11 112 0 TGATCCGAAGAAAAAAGATTTAACTGAG 14 282 1 AGAAAAAGGCTATTTTTATCAGT 15 2 1 ACATATATAGAGAAAACCTTTATATAGTTTA 16 278 0 GCGGTAGAAAATCTATTACAATACGC 20 5 1 GGAGATGCATAGATAACCAATTAAAACTCTC 22 220 0 AAATCAACATAGACAAGCTATGACTAATCAT 23 45 0 ********* * MAP Score: 3.44426 Motif 7 TTGCAATCAATTTTATTTTGAAGATCATTAT 1 210 1 TAACAAGAAATTGTTTTTTGAATAATCTGAA 9 11 1 TGAAGTGCGGTTTTATTTTGGAGTTTTGGCA 9 80 1 GCGACTTAGTTTTTATTTTTATTATGGGTAA 9 151 1 TCTATAAATCTTATATTTTGATCATAAATAA 13 29 1 ATAAGCCCCCTTATTTTTTGATAAACGAACG 23 83 1 ** ******** MAP Score: 1.07845