AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons017_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944237852 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0136 300 GTP-binding protein #1 HI0567 150 DNA gyrase, subunit B (gyrB) #2 HI0568 95 transcription accessory protein (tex) #3 HI0993 191 chromosomal replication initiator protein (dnaA) #4 HI0994 27 transferrin-binding protein 1 precursor (tbp1) #5 HI0995 97 transferrin-binding protein 2 precursor (tbp2) #6 HI0997 300 H. influenzae predicted coding region HI0997 #7 HI0998 180 ribosomal protein L34 (rpL34) #8 HI1225.1 65 conserved hypothetical protein #9 HI1227 104 uracil permease (uraA) #10 HI1228 123 uracil phosphoribosyltransferase (upp) #11 HI1230 147 adenine phosphoribosyltransferase (apt) #12 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #13 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #14 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #15 HI1264 300 DNA gyrase, subunit A (gyrA) #16 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #17 HI1528 73 topoisomerase IV, subunit B (parE) #18 HI1529 66 topoisomerase IV, subunit A (parC) Motif 1 ACAATTTTTACCGCACTTTTCTCTATTACA 3 151 1 GAAAAACTGACCGCACTTTTAAGTTAATTC 9 64 1 TCTTTTTTTACCGCACTTTTGAGCATTATT 11 126 1 AAAATATTGACCGCACTTTTACGGTCTTTA 12 72 0 TCGAATATCACCGCACTTTTTGATAGAATT 17 18 1 AAAAAAATTACCGCACTTTCAAATAATTAT 14 106 1 TGTTTTATGACCGCACTTTAAAAGGAACAA 13 39 1 TGTTTTTTGACCGCAGTTTTCATCAA 13 6 0 GGTAAAATCGCCACAATTTTGGTTATTCAA 16 26 0 CTATAATCCGCCACAATTTTTGATCAAAAA 15 270 1 AACCACATATCCACAATTTTATGCTATAAT 15 247 1 TACAATACTGGCGCATTTTTTTCTGTTCTA 3 48 1 CTATAATCTCGCCCAATTTTTATTTACAAA 1 115 1 CCTACCCCCTGCCCACTTTCTTTTTCCCAA 6 222 0 TAGCCAGGTCCGGCAATTTCCGTTAAGGAA 15 102 1 ATATAATAGTCGCCATTTTTGACAAAATAA 0 270 1 GTAAAATCTCCGACAATTTTTACCGCACTT 3 139 1 AGAAAGGCGACCCTACTTTTCCTTGTTTCC 15 147 0 AATCTATCTGGCGCATTTTAAT 3 2 0 ATCTGCCCATGGCCATTTTTTTTCTACTGA 6 262 0 ATAAAATAGAGCGCAATTCTAGTCATAAAA 7 130 0 ********** MAP Score: 40.3779 Motif 2 CAAACTTGGATTTTTTAGAAGATCTTTTCACGCATT 3 99 1 AAACGTTTCTTTTTTTACCGCACTTTTGAGCATTAT 11 119 1 AACACAATGTTTTTTGACCGCAGTTTTCATCAA 13 7 0 TGGTATTCCTTTTTTGATCAAAAATTGTGGCGGATT 15 274 0 ATCACCGCACTTTTTGATAGAATTTTCTCAAATTTA 17 24 1 TAGGATTAAATTTTTTAAATGATGATAATTTGAATA 6 146 1 CATTTTGTATTTTTTTAATCTAGAATTTGTCAATTT 10 68 1 CTCTTTCTATTTTTTTATGATAGAATGCCAATCTAA 11 83 1 TAAAAGAAAGTTTTTTGAATTATATTTGAGCCATCC 2 18 1 TTTAGAAGATTTTTTGAGATAAAGATAGTGAATTTT 14 171 0 GGATATGTGGTTTTTGATATCAGGATTTCGCCTGAT 15 223 0 TGCTGAGTCCTTTTTGAAAAAAATCTGAAAAAACTT 14 10 1 CCAATTGGGGATTTTTATTTAAGTTTGAATTTACAA 11 31 0 ATCTCCGACAATTTTTACCGCACTTTTCTCTATTAC 3 144 1 AGTGCATATATTTTTTAATATTCGTTTGAAGTTTTT 7 58 1 TATGAAATGATTTTTTACCAATCCTTTAACTTCCGA 0 235 1 AAAACGGCGATTTTTTGCTATAATCTCGCCCAATTT 1 98 1 CAATTATCAATTTTGTATAAGAATATAATTCT 5 75 1 TATCTCATTCTTTTGTAAATAAAAATTGGGCGAGAT 1 120 0 CCAACTACCAATTTTTGTGCCACTTTTTGGAGCGTT 6 181 0 GTGCGGTAATTTTTTTGTGTTTTTTTGTTCGCTAAA 14 86 0 AGAAACGGAAATTTTTAAAAAAAACTTCAAACGAAT 7 77 0 TCCTTAATCTGTTTTGAGTGAATATTAGTTTAGACA 14 267 0 ATGATGAAAAATTTTTAGGTGTTATTGATCAGTATC 6 71 1 GTGGAATTGAATTTGTAGGAAATTTTCGTCTGTTTG 15 62 1 TTATCATTTTTTTTTTGTAATAATGTCAACTTATAA 5 33 0 ******* * ** MAP Score: 30.4438 Motif 3 TATAGAACAGAAAAAAATGCGCCAGTATTGTATA 3 46 0 TTATCAGTAGAAAAAAAATGGCCATGGGCAGATC 6 259 1 GGAAATTTTTAAAAAAAACTTCAAACGAATATTA 7 73 0 ATTCTAGATTAAAAAAATACAAAATGGTAGAGGT 10 60 0 GTCCTTTTTGAAAAAAATCTGAAAAAACTTTAAA 14 16 1 CATTATTACAAAAAAAAAATGATAATGCGAACAA 5 44 1 TTCTCAAATTTAAAAAATTAACGAATAACCTCAC 17 48 1 AGTTTTACTAAAAAAATGATCTGCCCATGGCCA 6 277 0 AGGAAAACGATAAAAAAAGGGCGAATAATTTCGC 1 46 0 TGCACTAAAAAATTGGAAAAAATAACAAG 1 5 1 ATTCTATCATAAAAAAATAGAAAGAGAGGAAAAT 11 75 0 TTCTTTATTATAAAAAAACGAAGATAGAATACTG 2 63 0 TCAAACTTAAATAAAAATCCCCAATTGGGGATTT 11 39 1 AGAGAGGAAAATAAAAATCCCCAATTGGGGATTT 11 53 0 TTTCATAAAGAAAAGAAAAAGCCACAGGATACAA 0 208 0 TTTTATTTACAAAAGAATGAGATAAATT 1 132 1 AATAAAAATAAAAGAAAGTTTTTTG 2 1 1 ATCTTTATCTCAAAAAATCTTCTAAAATTTACAA 14 181 1 TCCATGAACTTAAAAAATTATAAGTTGACATTAT 5 16 1 TTTCTACTGATAAAGAATACCCTACCCCCTGCCC 6 238 0 AAAAGTGCGGTAAAAAAAGAAACGTTTTTAGATT 11 112 0 GTAGAGGTTTATAAAAATATTCTGACTTGAAACG 10 34 0 TTTTAGCGAACAAAAAAACACAAAAAAATTACCG 14 85 1 AAAAAACTTTAAAACAAAGCCCGATGGAATGCAA 14 37 1 TGACTCTTAAAAAACAAATTGACAAATTCTAGAT 10 85 0 CGTTCGTCAAATAAGAAACGGAAATTTTTAAAAA 7 92 0 CAAACGAATATTAAAAAATATATGCACTTTGCTA 7 52 0 AAAAGATCTTCTAAAAAATCCAAGTTTGACCTTT 3 93 0 ******** * * MAP Score: 28.4285 Motif 4 TTTCTTTTCTTTATGAAATGATTTTTTACCAATCCT 0 224 1 ATAACTTGTTATTTTTTCCAATTTTTTAGTGCA 1 7 0 TATGGGGCGAAATTATTCGCCCTTTTTTTATCGTTT 1 40 1 TTTTGCTATAATCTCGCCCAATTTTTATTTACAAAA 1 110 1 AACCAGTATTCTATCTTCGTTTTTTTATAATAAAGA 2 60 1 ACTGGCGCATTTTTTTCTGTTCTATAATCTGCTTAA 3 54 1 AACTTGGATTTTTTAGAAGATCTTTTCACGCATTTA 3 101 1 TCTCCGACAATTTTTACCGCACTTTTCTCTATTACA 3 145 1 TAATTGTTCGCATTATCATTTTTTTTTTGTAATAAT 5 45 0 AACTACCAATTTTTGTGCCACTTTTTGGAGCGTTAT 6 179 0 GGCTGAAAAGTTGTAACCTAACTTTTGAGGTATCTC 7 10 1 ACAAGACGGCATTTAAGCCGTCTTTTTTCCGTGCGT 9 18 1 ACACAAGAAAAACTGACCGCACTTTTAAGTTAATTC 9 58 1 AATCTAGAATTTGTCAATTTGTTTTTTAAGAGTCAA 10 84 1 AACGTTTCTTTTTTTACCGCACTTTTGAGCATTATT 11 120 1 ACGTTAAAAATATTGACCGCACTTTTACGGTCTTTA 12 72 0 ACACAATGTTTTTTGACCGCAGTTTTCATCAA 13 6 0 ACATTGTGTTTTATGACCGCACTTTAAAAGGAACAA 13 33 1 TGTTTTAAAGTTTTTTCAGATTTTTTTCAAAAAGGA 14 17 0 GTGCGGTAATTTTTTTGTGTTTTTTTGTTCGCTAAA 14 86 0 ATCTTGTAAATTTTAGAAGATTTTTTGAGATAAAGA 14 182 0 TTGGGTTCCCTTCTTTTCCACCTTTGTGGAATTGAA 15 37 1 GGTCGCCTTTCTTTTTACTTACTTTTTCTTTGGCGA 15 165 1 GTGCGGTCGAATATCACCGCACTTTTTGATAGAATT 17 12 1 ** * ** ***** MAP Score: 14.6296 Motif 5 AATAGTCGCCATTTTTGACAAAATAAGAGATTTTTT 0 274 1 AGTTTTACTAAAAAAATGATCTGCCC 6 284 0 TAAGAAACGGAAATTTTTAAAAAAAACTTCAAACGA 7 79 0 ATAAGTTGACATTATTACAAAAAAAAAATGATAATG 5 35 1 GAATTTTCTCAAATTTAAAAAATTAACGAATAACCT 17 43 1 AGCAAATCCGAATTTTAATAAATTAAGAATATATCA 18 24 1 TGCACTAAAAAATTGGAAAAAATAACAAGTTATG 1 8 1 TGCTGAGTCCTTTTTGAAAAAAATCTGAAAAAA 14 7 1 AAAATGGTAGAGGTTTATAAAAATATTCTGACTTGA 10 38 0 TCGCCCAATTTTTATTTACAAAAGAATGAGATAAAT 1 123 1 CGCACTTTTCTCTATTACAAAAACAATAAGGATCCT 3 162 1 ACTTCAAACGAATATTAAAAAATATATGCACTTTGC 7 54 0 CGGAAGTTAAAGGATTGGTAAAAAATCATTTCATAA 0 234 0 CTGCCAAAATTCAATTTGAAAAATTACGTACAGAGG 6 32 1 AAGTAGGATTAAATTTTTTAAATGATGATAATTTGA 6 143 1 TGGCTCAAATATAATTCAAAAAACTTTCTTTTATTT 2 15 0 AAAATTTACAAGATTTGTTAAATGTTTGTGAAAAGC 14 204 1 ATCCGCCACAATTTTTGATCAAAAAAGGAATACCA 15 275 1 * *** **** ** MAP Score: 12.4882 Motif 6 AAAGCGAGTGTTGCGCTTTTTCGCAACGTTT 0 100 0 GATTGTATCCTGTGGCTTTTTCTTTTCTTTA 0 206 1 GATATAATAGTCGCCATTTTTGACAAAATAA 0 269 1 TTGTTATTTTTTCCAATTTTTTAGTGCA 1 7 0 GCGAAATTATTCGCCCTTTTTTTATCGTTTT 1 46 1 ATCGCCAAAACGGCGATTTTTTGCTATAATC 1 92 1 GCTATAATCTCGCCCAATTTTTATTTACAAA 1 114 1 TTAATCTATCTGGCGCATTTTAAT 3 3 0 TATACAATACTGGCGCATTTTTTTCTGTTCT 3 46 1 AAAGGTCAAACTTGGATTTTTTAGAAGATCT 3 93 1 CCAATTTTTGTGCCACTTTTTGGAGCGTTAT 6 179 0 GATCTGCCCATGGCCATTTTTTTTCTACTGA 6 262 0 TAATATTCGTTTGAAGTTTTTTTTAAAAATT 7 73 1 AAATAAGAAACGGAAATTTTTAAAAAAAACT 7 87 0 TATTTGACGAACGCGTATTTTATGACTAGAA 7 113 1 CTCTACCATTTTGTATTTTTTTAATCTAGAA 10 62 1 AATCCCCAATTGGGGATTTTTATTTAAGTTT 11 41 0 AATCCCCAATTGGGGATTTTTATTTTCCTCT 11 54 1 CGTTTTTAGATTGGCATTCTATCATAAAAAA 11 93 0 TCTTTTTTTACCGCACTTTTGAGCATTATTT 11 126 1 TCAAAAAACATTGTGTTTTATGACCGCACTT 13 26 1 GGTAATTTTTTTGTGTTTTTTTGTTCGCTAA 14 87 0 TTTGAAAGTGCGGTAATTTTTTTGTGTTTTT 14 98 0 AAAAGTAGGGTCGCCTTTCTTTTTACTTACT 15 157 1 TCAAAAATTGTGGCGGATTATAGCATAAAAT 15 262 0 ACCAAAATTGTGGCGATTTTACCACAACTCA 16 33 1 TCGAATATCACCGCACTTTTTGATAGAATTT 17 18 1 ***** ***** MAP Score: 4.17414