AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons002_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944236946 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0033 53 conserved hypothetical protein #1 HI0034 124 conserved hypothetical protein #2 HI0035 205 conserved hypothetical protein #3 HI0121 300 conserved hypothetical protein #4 HI0266 82 conserved hypothetical protein #5 HI0267 41 nitrate/nitrite sensor protein (narQ) #6 HI0908 79 H. influenzae predicted coding region HI0908 #7 HI0909 124 preprotein translocase SecA subunit (secA) #8 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #9 HI1129 201 conserved hypothetical protein #10 HI1130 30 conserved hypothetical protein #11 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #12 HI1137 21 cell division protein (ftsW) #13 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #14 HI1140 71 D-alanine--D-alanine ligase (ddlB) #15 HI1143 83 cell division protein (ftsZ) #16 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #17 HI1716 196 undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase (rfe), putative #18 HI1717 133 H. influenzae predicted coding region HI1717 #19 HI1718 56 H. influenzae predicted coding region HI1718 #20 HI1719 61 uridylyl transferase (glnD) Motif 1 GTTATTTTTTACCGCACTTTACTAAAAT 0 7 0 GTAAAAAATAACCGCACTTTTTAGATAAGGA 0 26 1 CGCGAAATTAACCGCGCTTTTTATGTCTAAA 1 25 0 ATGATAGAATTCCGCACCTTTATTGCTAAGT 1 94 1 GTTATTTTTCACCGCACTTTTATCTCGGATG 2 18 0 GTGAAAAATAACCGCACTTTTTGTAAAAGGG 2 37 1 AAATTTTACCGCACTTTTCTAAATTTCC 5 7 1 AACAATTCAAACGGCTTTTTTCATAAAATTT 9 16 0 GTTTATTCAAACGGCTTTTTTATTTTGATAA 9 44 1 GCGAATTTTAACCGCACTTTTAGTTGAGTTT 13 90 1 GTCAAAATTGACCGCACTTTTACGCCTATCT 17 61 0 GTCAATTTTGACCGCATTTTTTATAAAAATA 17 80 1 GTTCTCCTTGTCCGCCTTGTTCGCCTTGTTC 18 38 0 ATACGCCCTTTTTGTTTTTCTT 20 1 1 ***** ***** MAP Score: 46.6118 Motif 2 CCCTTTTTGTTTTTCTTTATAATAAAACGACTT 20 15 1 TATGATGGTCTTTTCTTTTGAAAGTTCATAGAA 3 230 1 CGGCTGATTATTTTCTTTGTAAATAGTGAGCCA 3 94 1 AATGTAGTACTTTTATCTTAAATTT 10 15 1 TTCGCAACGTTTTTATTTCTAATATTAGCACTT 13 62 0 CATAAGTATTTTTTATATCCAAAAGTGCTAATA 13 40 1 TAACCGCGCTTTTTATGTCTAAATTGAAATTAT 1 15 0 AATTTCTCTTTTTAAATATATAAGTT 7 108 0 AGCGGCTGTATTCTATTTCAAATTACGTCAAAT 8 124 0 AAGGTTTCCTCTAAAATTATTGTAGGC 4 4 1 ATATCTCTATTTTATTAAAAATATAAAACAAC 19 9 1 ACGCCCGTATTTTTATAAAAAATGCGGTCAAAA 17 85 0 TCAATAAAATTTTATGAAAAAAGCCGTTTGAA 9 9 1 TATTTTAATTTTTCATCTACAATAAAGGGAATT 15 11 1 CAAACGGCTTTTTTATTTTGATAAAAATCAGTT 9 51 1 TCGTCACATTTTTTCTTGCGAAATTGAGCATAG 2 93 0 AATCAGTTGCTTTAATGTGGAATTACTTGCAAG 9 76 1 CAAAACAAAGGTTTCTTTTTAATGA 19 41 1 TTCACCGCACTTTTATCTCGGATGGAATATTT 2 9 0 TGTATTTCTCTGTTGATTAAGGAAAACG 3 282 0 GGTTCGCTCTTTCACTTTTGAAAGAGCGACCTT 11 22 1 TTTTTAGAGATTTTCTAAAAATAAGTTCAATTT 9 166 1 TCGTCTCGTTGTTTATTATGAAAATTGCGTGTA 6 56 0 ****** * *** MAP Score: 21.0755 Motif 3 TTTTGACCCTTTTACAAAAAGTGCGGTTATTTT 2 41 0 TCAATAAAATTTTATGAAAAAAGCCGTTTGAAT 9 10 1 CGCCCGTATTTTTATAAAAAATGCGGTCAAAAT 17 84 0 GCTCTTTCACTTTTGAAAGAGCGACCTTTTTTA 11 27 1 TGCATTACAATTTGGAAAAAGTATTCAAGTCGA 3 41 0 TTGGTTAAGGTTTTCAAAAAACAACTTGGATAT 2 144 1 AACTTATATATTTAAAAAGAGAAATT 7 108 1 TTTTCTGTTTTTTGTGAAGAATATTGCTATTGA 7 11 1 TGGCTCACTATTTACAAAGAAAATAATCAGCCG 3 94 0 TTCTATGAACTTTCAAAAGAAAAGACCATCATA 3 230 0 ATTTTAGTAAAGTGCGGTAAAAAA 0 1 1 ACCCTAAAATTTTTTGTAAAGGATAACATAAGG 17 167 0 AAGTCATCCTTATCTAAAAAGTGCGGTTATTTT 0 30 0 TGTTTTATATTTTTAATAAAATAGAGATAT 19 7 0 TGCTATCAATTTTGGGTAGAATAACGAACAGTT 4 40 1 AAAATCTTAGTATTAGAAAAGTATCATCAGTAA 14 28 1 TCCAGTGGAAATTTAGAAAAGTGCGGTAAAATT 5 11 0 ATTTATAGCAATTAAGAAGAAAGAAA 11 106 1 AAGTCGTTTTATTATAAAGAAAAACAAAAAGGG 20 15 0 CTATGCTCAATTTCGCAAGAAAAAATGTGACGA 2 93 1 TTTTAGAGATTTTCTAAAAATAAGTTCAATTTT 9 167 1 AATAGCGATATTTTAAAAAATTATTGTGCATGA 7 44 1 TGACTGAGGCTATTTATAAAACGCCACAACCC 13 9 0 CTCGTTGTTTATTATGAAAATTGCGTGTATTGT 6 52 0 *** ****** * MAP Score: 20.0716 Motif 4 AAGTGCGGTAAAAAATAACCGCACTTTTTAGATAA 0 19 1 TAAAAATAATTTCAATTTAGACATAA 1 1 1 TTTAGACATAAAAAGCGCGGTTAATTTCGCGCTTA 1 25 1 AATCCACGCAAAAAATAAGCGCGAAATTAACCGCG 1 40 0 CATCCGAGATAAAAGTGCGGTGAAAAATAACCGCA 2 18 1 CCCTTTTACAAAAAGTGCGGTTATTTTTCACCGCA 2 33 0 AAAAGGGTCAAAAATTTTCGGTATTGTAGAGGCTA 2 61 1 TCTATGTAGCAAATCTTCCTGCATTACAATTTGGA 3 58 0 TATTCTACCCAAAATTGATAGCATACGCCTACAAT 4 28 0 TCCAGCAAGAAAAACTGTTCGTTATTCTACCCAAA 4 50 0 AAATTTTACCGCACTTTTCTAAATT 5 0 1 AACGGAAATCTAAACTAATGTCATTTACTGGGGGC 6 17 0 GTTTATTATGAAAATTGCGTGTATTGTAACGGAAA 6 44 0 CGATATTTTAAAAAATTATTGTGCATGAAATAAAG 7 49 1 ACGTCAAATCAAAATTGAATTTAAAGATTTTTATA 8 98 0 AAAATAAAGTAAAAGTATTTATATGCCCT 8 162 0 GAGATTTTCTAAAAATAAGTTCAATTTTTAAGGCG 9 172 1 GATGGAAATATAAATTTCCTTTACTAACGTAAAAA 11 54 0 CTATAAATTTTAAAATTATATCATTGATGGAAATA 11 79 0 TTTTATATCCAAAAGTGCTAATATTAGAAATAAAA 13 50 1 AAACTCAACTAAAAGTGCGGTTAAAATTCGCAACG 13 86 0 TTAGTATTAGAAAAGTATCATCAGTAAGAAGAAAA 14 34 1 ATATAAAATATAAATTCCCTTTATTGTAGATGAAA 15 21 0 AGATAGGCGTAAAAGTGCGGTCAATTTTGACCGCA 17 61 1 TATTTTTATAAAAAATGCGGTCAAAATTGACCGCA 17 76 0 CATTTTTTATAAAAATACGGGCGTTGAAGTGAAAA 17 94 1 GTGTGACCCTAAAATTTTTTGTAAAGGATAACATA 17 170 0 **** * * *** * MAP Score: 19.8277 Motif 5 GGTATGATGGTCTTTTCTTTTGAAAGTTCAT 3 228 1 TTTTATCATATTTTTCGTTTTCCTTAATCAA 3 267 1 TTTTTCTGTTTTTTGTGAAGA 7 0 1 AATTTCTCTTTTTAAATATATAA 7 111 0 TTCAAACGGCTTTTTTATTTTGATAAAAATC 9 49 1 CTAGGTTCGCTCTTTCACTTTTGAAAGAGCG 11 19 1 TTTCTTTCTTCTTAATTGCTATA 11 109 0 TTATTTTTCCTTTTCTCCCAATGA 13 123 0 TTCTATCCTGTTTTTCTTCTTACTGATGATA 14 49 0 TTATTTTAATTTTTCATCTACAATAAAGGG 15 9 1 TTTACGCCTATCTTTTATTTTACCAGTGGTA 17 43 0 CGAAGCCCTATTTTTCACTTCAACGCCCGTA 17 109 0 CTTGTTCGCCTTGTTCGCCTTTTAAT 18 5 0 CTTGTCCGCCTTGTTCGCCTTGTTCGCCTTG 18 32 0 CAGATTTTCCTCGTTCTCCTTGTCCGCCTTG 18 50 0 TACGCCCTTTTTGTTTTTCTTTATAATAAAA 20 11 1 ****** **** MAP Score: 15.4439 Motif 6 TAAAGTGCGGTAAAAAATAACCGCACTTTT 0 17 1 AAAAGTGCGGTGAAAAATAACCGCACTTTT 2 28 1 CCCTTAAAAATGAAATTTAACTCCTTCGGA 2 179 0 GAATAAACAATGAAATTTAAGCGATAAAGC 3 143 0 TGTTGATTAAGGAAAACGAAAAATATGATA 3 270 0 AAACTCCAGTGGAAATTTAGAAAAGTGCGG 5 18 0 GTATTGTAACGGAAATCTAAACTAATGTCA 6 29 0 ATCACATTTGTAAAATCTAAAACATCCATT 8 53 0 TGACGTAATTTGAAATAGAATACAGCCGCT 8 127 1 TATCATTGATGGAAATATAAATTTCCTTTA 11 66 0 TGGGAGAAAAGGAAAAATAA 13 127 1 TATTGTAGATGAAAAATTAAAATAA 15 5 0 ACTAAATATATAAAATATAAATTCCCTTTA 15 33 0 GGATACCACTGGTAAAATAAAAGATAGGCG 17 40 1 GGCGTTGAAGTGAAAAATAGGGCTTCGTTA 17 113 1 ********** MAP Score: 11.2024 Motif 7 ATTTTAGTAAAGTGCGGTAAAAAA 0 4 1 CCGCACTTTTTAGATAAGGATGACTT 0 37 1 TTCCATCCGAGATAAAAGTGCGGTGAAAAA 2 15 1 AGTGGAAATTTAGAAAAGTGCGGTAAAATT 5 11 0 GCCAGAAGTGGAGAAAAGTGGTGTTTTGTG 9 132 1 AAATTTAAGATAAAAGTACTACATTATT 10 12 0 TTTTTTACGTTAGTAAAGGAAATTTATATT 11 53 1 TTGTCATTGGGAGAAAAGGAAAAATAA 13 120 1 ATCTTAGTATTAGAAAAGTATCATCAGTAA 14 31 1 ********** MAP Score: 7.46812 Motif 8 ATTTTAGTAAAGTGCGGTAAAAAATAACCGC 0 8 1 CCTTATCTAAAAAGTGCGGTTATTTTTTACCGC 0 23 0 ACTTAGCAATAAAGGTGCGGAATTCTATCATTG 1 92 0 ATCCGAGATAAAAGTGCGGTGAAAAATAACCGC 2 19 1 CCTTTTACAAAAAGTGCGGTTATTTTTCACCGC 2 34 0 ACTTTTTGTAAAAGGGTCAAAAATTTTCGGTAT 2 52 1 TTGTGCTTCTGAAATTGCTTTATCGCTTAAATT 3 127 1 TATTCCTATTGAAGTGGTTAAATAATAGTTCAG 3 168 1 TTTTCTTTTGAAAGTTCATAGAAGTTGTTTTAT 3 240 1 AACTCCAGTGGAAATTTAGAAAAGTGCGGTAAA 5 14 0 TATTCTTCACAAAAAACAGAAAAA 7 1 0 TATTGCTATTGAAATAGCGATATTTTAAAAAAT 7 32 1 AACATCCATTAAAATGCTAATAAATAAGTAATT 8 30 0 AAATCTTATAAAAATCTTTAAATTCAATTTTGA 8 92 1 AAATAAAGTAAAAGTATTTATATGCCCTAAACA 8 157 0 AAACTTGCCAGAAGTGGAGAAAAGTGGTGTTTT 9 126 1 TTTATATCCAAAAGTGCTAATATTAGAAATAAA 13 51 1 AACTCAACTAAAAGTGCGGTTAAAATTCGCAAC 13 87 0 GGATTGATTGAAAATCTTAGTATTAGAAAAGTA 14 18 1 CCGAAGTGATGTGAATGGGGGGGGA 17 2 1 GATAGGCGTAAAAGTGCGGTCAATTTTGACCGC 17 62 1 ATTAAAAGGCGAACAAGGCGAACAAG 18 3 1 TATTTTTAATAAAATAGAGATAT 19 0 0 TTGTTAGATCGAAGTCGTTTTATTATAAAGAAA 20 26 0 ***** * ** ** MAP Score: 0.39479