AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons011_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944237563 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #1 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #2 HI0205 292 H. influenzae predicted coding region HI0205 #3 HI0206 22 5'-nucleotidase, putative #4 HI0207 284 shikimic acid kinase I (aroK) #5 HI0604 300 adenylate cyclase (cyaA) #6 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #7 HI0658 160 ABC transporter, ATP-binding protein #8 HI0660 269 H. influenzae predicted coding region HI0660 #9 HI0661 300 hemoglobin-binding protein #10 HI0949 300 aminotransferase #11 HI1019 300 thiamin ABC transporter, periplasmic-binding protein (tbpA) #12 HI1022 112 biotin synthetase (bioB) #13 HI1445 102 dethiobiotin synthase (bioD-1) #14 HI1447 137 GTP cyclohydrolase I (folE) #15 HI1556 59 2-hydroxyacid dehydrogenase #16 HI1560 22 H. influenzae predicted coding region HI1560 #17 HI1561 106 peptide chain release factor 1 (prfA) #18 HI1562 252 H. influenzae predicted coding region HI1562 #19 HI1563 32 conserved hypothetical protein #20 HI1564 32 H. influenzae predicted coding region HI1564 #21 HI1564.1 284 H. influenzae predicted coding region HI1564.1 #22 HI1587 300 DNA-binding protein H-NS (hns) #23 HI1588 69 formyltetrahydrofolate deformylase (purU) Motif 1 TCAAATTTGCAATTTTTCTCATTTTACCATCCTAT 14 67 1 ATTTACAATGAGTTATCTTCATTTTTATAGACTAG 11 30 1 AAATGATCGAATTTTATTTCACTTTTAATTTAATT 4 247 1 GTGCGGTAAAAATTTACCGCACTTTTGATTTTAGA 8 15 0 GTGCGGTCAAAATTAACCGCACTTTTGATGAAAT 15 9 0 AAATGTAGAAAGTTTATTTCTTTTTAAAAAGCCGT 11 105 1 AAGTGATCAAAATTGCTCACTTTTTTCAGTCTTAA 18 17 1 GTGCGGTTTGTTTTTATTTCATTTTACGAGCTTAA 0 12 0 TTCTATGCGTACTTCTTTTTATTTTAGGAGTAATC 9 42 0 TGATAGGTAAAATTTATAGTATTTTTCGAAAAATT 5 190 1 TATGTTTGAGAATTATTATTATTTTTTTTATAGGA 21 74 0 ATTTGAGGCTATTTTGCAATATTTTTTCTTTTCTC 7 117 0 AGATATCTATACTTATTTCCTCTTTTACTAGATAA 6 39 1 TGAGTAAGGTATTTTATAATACTTTGCGTTGATAA 5 29 1 TTTATGTCACATTTTTTTGCATTTATACTCCCTAA 5 229 1 AGCGTGGTGTTTTTAACCGCACTTTCAAAGGAAAA 12 85 1 TATTAAATAAATTTTCCCACATTTAATGTTATTTA 22 263 1 TTTCGGCAACTATTCCTTTCTTTTTTCTTCTTCGT 22 19 1 TAATTGCTCCTTTTTTATATACAAAG 15 43 0 TTATTGCGATAATCTACCCCATTTTTTGGGAGATC 4 172 1 AAATAAAAACTATTCTTATTATTTTCTGTATTTAA 21 168 1 TTTGTGTTTATTTTCTTTATATTTTTATTAAAGTT 22 163 0 AGATAACGCAAATTTTCACTTTTTTTATCTTATAA 13 19 0 AAAATCAAGCTATTTTCGCTATTTTTGCGATCTAG 8 132 1 AAAAATATACAATTGTCCCCGTTTTGACGTAACCC 10 88 1 AGGATCTATCTTTTACTCTCTCTTTCAAAGCCAAT 8 63 1 ATTCCTTTAAAATCCACCGCACTTTTTAAAGGAGA 13 72 1 CCGACTTATTTTTTTTCACCTCTTTTAGAAGGTTT 10 266 1 TTTAATCTAAAATTGGTCATATTTAGTCCTATAAA 21 48 1 AATTTATCCTATTTATCTACTTATT 8 254 0 GAGATCTTTCTATCTTCTGCATTTTTACGCAGTTT 4 201 1 TTTTTATTAAAGTTTATAAAATTTTTATAAAATCT 22 142 0 ATTCTTCTTTAATTGCTTCAATTTTTTCTTGAAGA 18 225 0 TATCATTCACAATTTATTTTGTTTTACGATATAAT 2 182 1 TTTTCGTCATTATTGCTGCCTTTTAATCATAAATA 11 264 1 AATAGTTTTTATTTCTTGATTTTTATCAAAAATCA 21 147 0 CTATTCTCATTATTTGCTGTATTTAAACGTGCTTG 9 204 0 AAAATACCTTACTCAATATCACTTATTAAGGAAT 5 9 0 * ** * ****** MAP Score: 37.4461 Motif 2 TTTAAGCTCGTAAAATGAAATAAAAACAAACCGCAC 0 11 1 ACAATCGAGGTAAAAGTGCTATAAAAGTGCGGTTTG 0 37 0 TATACAGAGAAAAAAGTAAGCTATATTCTCAAATCA 2 61 0 ATATATAGACAAAAAGCCTGCGAATTTTATACTTTT 2 94 1 GCTATACGCGTAAATTTGACCTAAAACAGCTGGATG 2 223 0 TTAGCTTGATAAAATATCAGTTAAATGAGGTTTATA 2 265 1 AATTGAAAAATAGGCTAAAAATAGCGCGTAT 4 5 1 ATAGAGGTTGAAAAATAGGGTGATTTATTGCGATAA 4 148 1 GATCTCCCAAAAAATGGGGTAGATTATCGCAATAAA 4 171 0 CTAATTAAATTAAAAGTGAAATAAAATTCGATCATT 4 248 0 CAATTTTTCGAAAAATACTATAAATTTTACCTATCA 5 190 0 TATAAATGCAAAAAAATGTGACATAAATCACAATTT 5 220 0 TTTCTAGTCAAAAAAGCCACGTATAATAAGACGCAA 7 54 0 CCGAGAAAAGAAAAAATATTGCAAAATAGCCTCAAA 7 115 1 CTTTCTTAAGAAAAAGTGCGGTAAAAATTTACCGCA 8 29 0 GCATTTGTGCAAAATCTCCTTGAAAATCAAGCTATT 8 110 1 TCTAGATCGCAAAAATAGCGAAAATAGCTTGATTTT 8 132 0 TGTGTAATCATAAATAGAAACTAAAAATTTGGCGAG 8 189 0 TAAAACCTTCTAAAAGAGGTGAAAAAAAATAAGTCG 10 267 0 TATTTATGATTAAAAGGCAGCAATAATGACGAAAAG 11 263 0 TTTATAAGATAAAAAAAGTGAAAATTTGCGTTATCT 13 18 1 TTATTAAATAAAAAATTCCTTTAAAATCCACCGCAC 13 58 1 CTTTGTATATAAAAAAGGAGCAATTA 15 43 1 AATTTTCCCTAAAATCGGCTAGAATACGCCGATTTT 17 62 1 TTAAGACTGAAAAAAGTGAGCAATTTTGATCACTTT 18 16 0 TGAAATGATTAAAAATTGAACTATTTAATTAGGAGG 18 64 0 ATCTTCAAGAAAAAATTGAAGCAATTAAAGAAGAAT 18 224 1 TCGACTCCTAAAAAACCGCAAGATTATA 19 2 0 CGTTTAATCTAAAATTGGTCATATTTAGTCCTATAA 21 46 1 TTAGTCCTATAAAAAAAATAATAATAATTCTCAAAC 21 70 1 TGATTTTTGATAAAAATCAAGAAATAAAAACTATTC 21 147 1 CAAGCAGGTTTAAATACAGAAAATAATAAGAATAGT 21 176 0 AACGAAGAAGAAAAAAGAAAGGAATAGTTGCCGAAA 22 19 0 TCCACTCTGAAAAAATACTTATAATAATTGCGCCTC 22 56 1 AAATATAAAGAAAATAAACACAAAAAAATATATCTG 22 174 1 AAATTTATTGTAAATATCTATTATTAAATAAATGGT 22 215 0 TTTAGATAAAAAAATAGAACCCATAAAATAGGTTCT 23 27 0 ***** * **** MAP Score: 30.9081 Motif 3 TAAGCTCGTAAAATGAAATAAAAACAAACCG 0 13 1 TTATATCGTAAAACAAAATAAATTGTGAATG 2 185 0 TAGGGAGTATAAATGCAAAAAAATGTGACAT 5 232 0 CCTATCAACCACAGGAAAATA 6 0 0 ATCTAGTAAAAGAGGAAATAAGTATAGATAT 6 41 0 ACGTATAATAAGACGCAATAAAAACTATTTA 7 41 0 CTGTTCCGAGAAAAGAAAAAATATTGCAAAA 7 110 1 ACGTTTAAATACAGCAAATAATGAGAATAGT 9 209 1 TTGATCAAAATCAAGAAATAAAAACTATTCT 9 232 0 AACTAGGGTAAAAACAAAAAAGCTGAAACGC 10 164 1 AAAAGAGGTGAAAAAAAATAAGTCGGGTGCC 10 261 0 CTACATTTTCTGAAAAAATAAAGGGGCTGAC 11 82 0 CGGCTTTTTAAAAAGAAATAAACTTTCTACA 11 108 0 ATAATGACGAAAAGGAGATAAGGTTATATTC 11 246 0 TCTATTTATAAGATAAAAAAAGTGAAAATTT 13 14 1 CGCACTTTTTAAAGGAGAAAAAA 13 89 1 TAGGATGGTAAAATGAGAAAAATTGCAAATT 14 70 0 TAGTCTTTCCTAAAAAAATAATCGGCTATTC 14 114 0 TTGACAGCGAAAAGGAAATTAAGAATCTCAG 17 33 0 AGCCTGATCTTCAAGAAAAAATTGAAGCAAT 18 218 1 TTAGTCCTATAAAAAAAATAATAATAATTCT 21 70 1 TTGATAAAAATCAAGAAATAAAAACTATTCT 21 153 1 AGGTTTAAATACAGAAAATAATAAGAATAGT 21 176 0 ATAGTTGCCGAAATCAAATAAA 22 1 0 TGGATAACGAAGAAGAAAAAAGAAAGGAATA 22 29 0 ATAAAAATATAAAGAAAATAAACACAAAAAA 22 170 1 AAGAAAATAAACACAAAAAAATATATCTGTT 22 181 1 ATTTAATAATAGAGAAAATAAAATTTATTGT 22 240 0 TGCTATGTTTAGATAAAAAAATAGAACCCAT 23 39 0 *** ******* MAP Score: 30.5055 Motif 4 AAAGTGCGGTTTGTTTTTATTTCATTTTACGA 0 18 0 AATACAACCCTTAATTTTTTAGAGGGAAAACA 0 78 1 ACAAAACTTGCAATTTTGCTTGAAAAGTATAA 2 120 0 CATTCACAATTTATTTTGTTTTACGATATAAT 2 185 1 TTTAACGCGCTATTTTTGTTATTAGTCCTAGG 4 40 1 TAGAAATGATCGAATTTTATTTCACTTTTAAT 4 244 1 TATAAAAATCTATATTTTCTATTATTAGTGGA 5 80 0 GGTAAAAAAGTCATTTTGATTGTTGATAGGTA 5 167 1 TGATTTATGTCACATTTTTTTGCATTTATACT 5 226 1 ATATTATAAATAGTTTTTATTGCGTCTTATTA 7 35 1 TCCGATTTTATCGATTTTCTAGTCAAAAAAGC 7 73 0 TATTTTGCAATATTTTTTCTTTTCTCGGAACA 7 111 0 AAATTTACCGCACTTTTGATTTTAGATAGGT 8 9 0 CTATGCGTACTTCTTTTTATTTTAGGAGTAAT 9 43 0 ATAATGAGAATAGTTTTTATTTCTTGATTTTG 9 226 1 TAGAAACGTTTGCTTTTTATTTAGCCGTTTGA 10 20 1 GGGACAATTGTATATTTTTTTTGCAATATGAA 10 75 0 AGCGTTTCAGCTTTTTTGTTTTTACCCTAGTT 10 164 0 AGGCACCCGACTTATTTTTTTTCACCTCTTTT 10 260 1 TGAGTTATCTTCATTTTTATAGACTAGTGCAC 11 38 1 CGCAAATTTTCACTTTTTTTATCTTATAAATA 13 16 0 GAATAGCCGATTATTTTTTTAGGAAAGACTAT 14 114 1 TAATTGCTCCTTTTTTATATACAAAGTGCG 15 39 0 CTAGAATACGCCGATTTTATTTTCGGTGACTT 17 80 1 TGTTTTAGTGTGTTTTTGATTTGCCAAAACAG 18 188 1 ATTATTATTATTTTTTTTATAGGACTAAATAT 21 66 0 ATAATAAGAATAGTTTTTATTTCTTGATTTTT 21 158 0 TTTATTTGATTTCGGCAACTAT 22 0 1 TTTTTTTGTGTTTATTTTCTTTATATTTTTAT 22 170 0 TCGAAACAGATATATTTTTTTGTGTTTATTTT 22 184 0 ATATTTACAATAAATTTTATTTTCTCTATTAT 22 234 1 TTTATGGGTTCTATTTTTTTATCTAAACATAG 23 36 1 * ********* MAP Score: 29.1443 Motif 5 AAGTGCTATAAAAGTGCGGTTTGTTTTTAT 0 30 0 TCTAAAATCAAAAGTGCGGTAAATTTTTAC 8 15 1 TTCTTAAGAAAAAGTGCGGTAAAAATTTAC 8 33 0 GAAAGTATAAAAAGCGTGGTGTTTTTAACC 12 73 1 TTTTCCTTTGAAAGTGCGGTTAAAAACACC 12 90 0 TCTCCTTTAAAAAGTGCGGTGGATTTTAAA 13 77 0 ATTTCATCAAAAGTGCGGTTAATTTTGAC 15 9 1 TTTTATATACAAAGTGCGGTCAAAATTAAC 15 27 0 ********** MAP Score: 29.1174 Motif 6 TGCGGTTTGTTTTTATTTCATTTTACGAGCTTAAA 0 11 0 CAAACCGCACTTTTATAGCACTTTTACCTCGATTG 0 37 1 CAACCCTTAATTTTTTAGAGGGAAAACAAA 0 82 1 AAAAGTAAGCTATATTCTCAAATCACTTTCGAATT 2 51 0 TATAGCTTACTTTTTTCTCTGTATATATAGACAAA 2 72 1 GGATGCCTCGTATTATATCGTAAAACAAAATAAAT 2 193 0 CGTATAGCGGTATTTTAGCTTGATAAAATATCAGT 2 251 1 TTTTACGCAGTTTATTTTCATTAGAAATGATCGAA 4 223 1 AATGATCGAATTTTATTTCACTTTTAATTTAATTA 4 248 1 TGTTCTTTATCTAATTAAATTAAAAGT 4 267 0 TATAAAAATCTATATTTTCTATTATTAGTGGATAG 5 77 0 AAATATAGATTTTTATATCGGCAGAATTAAGCTAT 5 95 1 TAGTACCTAGTTTTATTGCGTAAATAGCTTAATTC 5 118 0 TTATGTCACATTTTTTTGCATTTATACTCCCTAAG 5 230 1 TATACGTGGCTTTTTTGACTAGAAAATCGATAAAA 7 65 1 TATTTTGCAATATTTTTTCTTTTCTCGGAACAGTC 7 108 0 AAAATCAAGCTATTTTCGCTATTTTTGCGATCTAG 8 132 1 TGAGAATAGTTTTTATTTCTTGATTTTGATCAAAA 9 230 1 ACCCGACTTATTTTTTTTCACCTCTTTTAGAAGGT 10 264 1 TCAGCCCCTTTATTTTTTCAGAAAATGTAGAAAGT 11 83 1 AATTTTCACTTTTTTTATCTTATAAATAGACAAA 13 9 0 TTTTTTCTCCTTTAAAAAGTGCGGT 13 87 0 ATAGCTGACAAATTTTATCAAATAAGGATTTTCT 14 9 0 CAAATTTGCAATTTTTCTCATTTTACCATCCTATT 14 68 1 TAATTGCTCCTTTTTTATATACAAAGTGCGGTCAA 15 34 0 TGAAGAAAGGTATTTTCTCACAACAATAAAGATTG 21 114 1 TAAGAATAGTTTTTATTTCTTGATTTTTATCAAAA 21 151 0 TTTTTTTGTGTTTATTTTCTTTATATTTTTATTAA 22 167 0 TACAATAAATTTTATTTTCTCTATTATTAAATAAA 22 239 1 AACTAGAACCTATTTTATGGGTTCTATTTTTTTAT 23 23 1 TGGGTTCTATTTTTTTATCTAAACATAGCACACAA 23 40 1 ****** ** * * MAP Score: 16.6959 Motif 7 AAATGAAATAAAAACAAACCGCACTTTTATAGCACTTT 0 23 1 GTGATTTGAGAATATAGCTTACTTTTTTCTCTGTATAT 2 60 1 TATATAGACAAAAAGCCTGCGAATTTTATACTTTTCAA 2 95 1 TAGAGGTTGAAAAATAGGGTGATTTATTGCGATAATCT 4 149 1 TATTTTCATTAGAAATGATCGAATTTTATTTCACTTTT 4 235 1 CACTAATAATAGAAAATATAGATTTTTATATCGGCAGA 5 82 1 AATTTTTCGAAAAATACTATAAATTTTACCTATCAACA 5 187 0 AAGTGCGGTAAAAATTTACCGCACTTTTGATTTTAGAT 8 14 0 AAAAATAGCGAAAATAGCTTGATTTTCAAGGAGATTTT 8 120 0 ACGCATAGAAAGAATTATGCGTACTTAATGTAGGGTGG 9 67 1 TCAGCCCACCAAAATATCTTACGATTGTTTGATGGTGG 9 108 1 ATCAAAATCAAGAAATAAAAACTATTCTCATTATTTGC 9 222 0 TGTTCTTATTAGAAACGTTTGCTTTTTATTTAGCCGTT 10 11 1 TCATATTGCAAAAAAAATATACAATTGTCCCCGTTTTG 10 76 1 GTAAAAACAAAAAAGCTGAAACGCTTTTTTTAATAAGT 10 171 1 ATTTTTTCAGAAAATGTAGAAAGTTTATTTCTTTTTAA 11 94 1 CTAGTGTATTAAAATTTACTAAGATTGCCAACGGCTTT 11 132 0 AGTGCGGTTAAAAACACCACGCTTTTTATACTTTCTTA 12 70 0 TTATAAGATAAAAAAAGTGAAAATTTGCGTTATCTCAA 13 19 1 AAATTCCTTTAAAATCCACCGCACTTTTTAAAGGAGAA 13 70 1 CTTTCCTAAAAAAATAATCGGCTATTCTAGCAAAGGAT 14 103 0 AAGTGCGGTCAAAATTAACCGCACTTTTGATGAAAT 15 8 0 AAGGAAATTAAGAATCTCAGACGCTTTATTTGTGATTT 17 15 0 AAAATCGGCTAGAATACGCCGATTTTATTTTCGGTGAC 17 72 1 TAAGACTGAAAAAAGTGAGCAATTTTGATCACTTTCTG 18 13 0 TTGATTTGCCAAAACAGCCTGATCTTCAAGAAAAAATT 18 203 1 ATCTTCAAGAAAAAATTGAAGCAATTAAAGAAGAATTG 18 224 1 ATAAAAATCAAGAAATAAAAACTATTCTTATTATTTTC 21 156 1 AGATTTTATAAAAATTTTATAAACTTTAATAAAAATAT 22 142 1 ATTTAATAATAGAGAAAATAAAATTTATTGTAAATATC 22 233 0 TGTTTAGATAAAAAAATAGAACCCATAAAATAGGTTCT 23 27 0 **** ** *** * MAP Score: 14.7081 Motif 8 TTTGTTTTCCCTCTAAAAAATTAAGGGTTGTATTAT 0 76 0 TTTGAGAATATTCTTTTAGTAATTAAACATTTAGAGGAA 2 14 0 ACTTGCAATTTTGCTTGAAAAGTATAAAATTCGCAGGCT 2 108 0 ATGCCTCGTATTATATCGTAAAACAAAATAAATTGTGAA 2 187 0 CTTCAAACCTAGGACTAATAACAAAAATAGCGCGTTAAA 4 40 0 CTTTATCTAATTAAATTAAAAGTGAAATAAAATTCGATC 4 251 0 TATAATACTTTGCGTTGATAAGAAAAATATCAAGCTATC 5 43 1 TATCAAGCTATCCACTAATAATAGAAAATATAGATTTTT 5 70 1 CGGAATAGACTGTTCCGAGAAAAGAAAAAATATTGCAAA 7 101 1 TATTGGTTATTGAAATAAGTAGATAAATAGGATAAATT 8 241 1 TCATAATGATTACTCCTAAAATAAAAAGAAGTACGCATA 9 35 1 GGAGAAAGTATTCTCTCACAATACTAAAAGTGTATTTTT 9 261 0 TTCTTACGAGTCAAACGGCTAAATAAAAAGCAAACGTTT 10 23 0 AATTTACTTTTCATATTGCAAAAAAAATATACAATTGTC 10 66 1 ATGGGCAAACTAGGGTAAAAACAAAAAAGCTGAAACGCT 10 157 1 ACTTTCTACATTTTCTGAAAAAATAAAGGGGCTGACGTA 11 79 0 TTTGTCTATTTATAAGATAAAAAAAGTGAAAAT 13 4 1 TTGCGTTATCTCAAATTATTAAATAAAAAATTCCTTTAA 13 43 1 AAGATCAGGCTGTTTTGGCAAATCAAAAACACACTAAAA 18 190 0 TGGTCATATTTAGTCCTATAAAAAAAATAATAATAATTC 21 61 1 AAGAAAGGTATTTTCTCACAACAATAAAGATTGATTTTT 21 116 1 TTTTATAAACTTTAATAAAAATATAAAGAAAATAAACAC 22 156 1 GTGGGAAAATTTATTTAATAATAGAGAAAATAAAATTTA 22 244 0 * * * ** * *** * MAP Score: 14.1842 Motif 9 GTTTTCCCTCTAAAAAATTAAGGGTTGTATT 0 78 0 CACTCTTAGGTAAAAAAGTCATTTTGATTGT 5 159 1 ATTTTACCTATCAACAATCAAAATGACTTTT 5 172 0 ACCTATCTAAAATCAAAAGTGCGGTA 8 5 1 TGATTACACATCAAAAATCAATAACTTATTG 8 215 1 ATTACTAATATCAACAATCAACGGCTCGCAT 9 164 1 TTGATTTTGATCAAAAATACACTTTTAGTAT 9 249 1 AACTAGGGTAAAAACAAAAAAGCTGAAACGC 10 164 1 AAAAGAGGTGAAAAAAAATAAGTCGGGTGCC 10 261 0 GCACTAGTCTATAAAAATGAAGATAACTCAT 11 37 0 CTACATTTTCTGAAAAAATAAAGGGGCTGAC 11 82 0 ATACACTAATTCATCAATTAAGAAAGTATAA 12 52 1 TAGTCTTTCCTAAAAAAATAATCGGCTATTC 14 114 0 TACAGAGAGTACAACAAAGCATAATTGGCAA 18 130 1 TTTTGGCAAATCAAAAACACACTAAAACAAG 18 186 0 TTAGTCCTATAAAAAAAATAATAATAATTCT 21 70 1 GTATTTTCTCACAACAATAAAGATTGATTTT 21 123 1 TTGATTTTTATCAAAAATCAATCTTTATTGT 21 136 0 CAACTACTAATCAACAATCAACGGCTCGCAT 21 221 0 AGCCCACCCTACAACTACTAATCAACAATCA 21 232 0 CTTTAGCCCACCAAAAAACAATCGAGAGATA 21 261 1 AGATTACCGTAAAACAAACAAAATGCCAACA 22 112 1 ******** ** MAP Score: 0.607361