AlignACE 3.0 10/20/99 AlignACE2 -i HI/HI_operons004_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944237084 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 HI0613 72 fuculokinase (fucK) #1 HI0614 181 L-fucose isomerase (fucI) #2 HI0615_HI0616 197 HI0615: L-fucose operon activator (fucR), HI0616: ATP-dependent helicase (hepA) #3 HI0618 26 glp protein, putative #4 HI0619 29 glycerol-3-phosphate regulon repressor (glpR) #5 HI0685_HI0686 292 HI0685: anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA), HI0686: glycerol-3-phosphatase transporter (glpT) #6 HI0687 99 conserved hypothetical protein #7 HI0688 94 H. influenzae predicted coding region HI0688 #8 HI0690 229 glycerol uptake facilitator protein (glpF) #9 HI1009_HI1010 158 HI1009: glycerol-3-phosphate regulon repressor (glpR), HI1010: 3-hydroxyisobutyrate dehydrogenase, putative #10 HI1014 55 conserved hypothetical protein #11 HI1017 237 glycerol uptake facilitator protein (glpF) #12 HI1024 49 hexulose-6-phosphate synthase, putative #13 HI1027 58 L-xylulose kinase (lyx) #14 HI1028 30 conserved hypothetical protein #15 HI1030 71 conserved hypothetical transmembrane protein #16 HI1031 175 conserved hypothetical protein #17 HI1112 233 xylose isomerase (xylA) Motif 1 ACCATTTTGACCGAAAATTACTAAAAATTGAAAGAAT 1 19 1 CGTTTTATCACTAAAATTAACAAAAAATAACATTTTT 9 99 0 TACTCTTGAAAAGAAACTCACAAAAAATTGACCGCAC 2 66 1 AGTAAAGGGAAGAGAATTTATTAAAAAAGAATACGGA 8 156 0 GTTAGTTTTTCACAAAAATACGAAAAATTTCATCACC 17 190 1 TTTGCGAATCATAAAAGAAAATAAAAAATAAGAAAGT 5 73 1 TACTATATAAAATTAAGAGAGGAAAAA 16 158 1 TATTATTCTTATGATAGTTACAAAAAAGGCGACTAAG 6 39 0 TTCTTTCACACTCTAATTCAATGAAAACACCATTTGT 1 148 1 GGATCTAGATCACAAAATCAGTAAAATTATTTTAACA 16 42 1 AGGTTTCTATATCGTAGAAACTAAAAATCTACTCTAA 8 50 1 AATAGGCTGGATTTTACATAATAAAAATCCAGCCCAT 13 12 1 AATAAAAAATAAGAAAGTAAAAAAAATCAAAAATGTG 5 92 1 AATTCTCTTCCCTTTACTTAGGGAAAACACTCTTCAT 8 175 1 TGCCTTCCTCATATTATTTAAGGAAAAACG 12 29 1 AGTTGCAAATAATCAACATAGAAAAATTAAATAACAT 17 141 1 CCCCCGATTCCCAAAATGTAAGAAAAAATAATATAAA 5 259 0 AAAATTTCATCACCTAGAGAGGAAAATGTT 17 213 1 ACAAAAATTGACTATATTTAAGGAAATGTATATGACC 1 57 0 AGATCTAGATCACAGAATGATAAAAAATGTTATTTTT 9 77 1 AAATTAAATAACATAATTGATGAAAAGTTAGTTTTTC 17 164 1 * ** * * ***** MAP Score: 22.7812 Motif 2 TTTCAATTTTTAGTAATTTTCGGTCAAAAT 1 22 0 CCTTAAATATAGTCAATTTTTGTGATGCTC 1 71 1 TTTGTGATGCTCGCAGTTTTGCAACAAAAT 1 89 1 CTGTTTTCCTTATCATTTTTCTTTCACACT 1 130 1 TTTTTTACTTTCTTATTTTTTATTTTCTTT 5 86 0 CTCAAAATGTTGTTAATTTTGGCCGCACTT 5 210 1 ACACTTTTTATATTATTTTTTCTTACATTT 5 253 1 AAAAGATAAGTATCATTTTTGGGAAAAGTA 6 76 1 GTGATCTAGATCTCAGATTTAATTTATTGT 9 60 0 TGATAAAAAATGTTATTTTTTGTTAATTTT 9 94 1 TGTTATTTTTTGTTAATTTTAGTGATAAAA 9 104 1 ATATTCTTAAATTTAACTGCGGTT 10 4 1 GATCGCTTGGTGGCAATTTTTCGGATTTTC 11 14 0 GACTGAGCTTTCTTATTTTTGTAAATTATG 16 117 1 AAATTATGAAACGTAATTTTACTATATAAA 16 139 1 TTTTTCCTCTCTTAATTTTATATAGTAAA 16 156 0 TTGCTCCAGTTGTTAGTTTTCACACTTTAA 17 45 1 ATTGATGAAAAGTTAGTTTTTCACAAAAAT 17 179 1 ATGAAATTTTTCGTATTTTTGTGAAAAACT 17 193 0 ********** MAP Score: 19.692 Motif 3 CATACTCTTGAAAAGAAACTCACAAAAAATTGACCGCAC 2 64 1 CCCAAAATGTAAGAAAAAATAATATAAAAAGTGTAATCA 5 248 0 CCACAGTTGCAAATAATCAACATAGAAAAATTAAATAAC 17 137 1 GAAAATAAAAAATAAGAAAGTAAAAAAAATCAAAAATGT 5 89 1 TGTTTCCAGTAAAACGCCATAATATAAAACGAATCACAT 15 18 1 TTTTCATTGAATTAGAGTGTGAAAGAAAAATGATAAGGA 1 136 0 TGAGATCTAGATCACAGAATGATAAAAAATGTTATTTTT 9 75 1 GGATTTGCGAATCATAAAAGAAAATAAAAAATAAGAAAG 5 70 1 AATGATAAGGAAAACAGTAAGAAATGAAATTTTGTTGCA 1 108 0 CCCCTAATTTGTTTTTATAAAAAAGTGCGGTCAA 0 5 1 TACGTTTCATAATTTACAAAAATAAGAAAGCTCAGTCAA 16 115 0 AAGTAAAGGGAAGAGAATTTATTAAAAAAGAATACGGAG 8 155 0 ATTTTACTATATAAAATTAAGAGAGGAAAAA 16 154 1 TACATAATAAAAATCCAGCCCATAAAAAACTAAGGAGAA 13 26 1 AATTGATGAAAAGTTAGTTTTTCACAAAAATACGAAAAA 17 178 1 GACACATAATTAAAAAGTTGGAGAAAAAATT 5 2 0 TCTAGATATAAAAAGAGTGCTAGAGATAACCCTAGCACT 11 123 0 AATTAACAACATTTTGAGTGTAAAAGAAAGCGATTTTGT 5 189 0 TTTATTATTCTTATGATAGTTACAAAAAAGGCGACTAAG 6 39 0 TTTGTTGCAAAACTGCGAGCATCACAAAAATTGACTATA 1 78 0 AACGTTTTATCACTAAAATTAACAAAAAATAACATTTTT 9 99 0 ** * * * * **** MAP Score: 16.7595 Motif 4 AAAACTGCGAGCATCACAAAAATTGACTATA 1 78 0 AAAAGTTAGTTTTTCACAAAAATACGAAAAA 17 186 1 AATAGGATCTAGATCACAAAATCAGTAAAAT 16 38 1 ATTGTGATCAATATCACAAAATCGCTTTCTT 5 174 1 GTTTACCCCCGATTCCCAAAATGTAAGAAAA 5 270 0 TTTTACTTTTCCCAAAAATGATACTTA 6 82 0 CTCCAATTGATTATCACAAATGTGATTCGTT 15 45 0 ATATGAAATATTATCACAAGAAAATAGGATC 16 16 1 AATGTGAAGTGTTTCACAAATCTTTACACCG 5 123 1 AGGGATTTGCGAATCATAAAAGAAAATAAAA 5 68 1 TCATAACGTTTTATCACTAAAATTAACAAAA 9 111 0 TCTGAGATCTAGATCACAGAATGATAAAAAA 9 73 1 GTGACGTATATCTTCCTAAAAGTGCGGTCAA 2 93 0 TTTGTGATATTGATCACAATAATTTTCGCAT 5 163 0 CTTGAAAAGAAACTCACAAAAAATTGACCGC 2 70 1 * ********* MAP Score: 11.8021 Motif 5 TCATTATGTTTTTGACCGCACTTTTTTATAAAA 0 22 0 CATAATGATTTTTGACTGCGCTGAGGAGAGTTT 0 47 1 CTCACAAAAAATTGACCGCACTTTTAGGAAGAT 2 82 1 TGTTGTTAATTTTGGCCGCACTTCCCTACAATG 5 217 1 CGTGGGTATGTTTACCCACGGTTGTGAGGGATA 8 10 0 TTTTTAATAAATTCTCTTCCCTTTACTTAGGGA 8 166 1 CACTCTTCATTTCAACCGCACTTCTAAGGAGTG 8 202 1 TATTCTTAAATTTAACTGCGGTTTTAAAAACAC 10 11 1 TTTTACATTTATTGACTGAGCTTTCTTATTTTT 16 104 1 TTTTTCCTCTCTTAATTTTATAT 16 162 0 AACATTTTCCTCTCTAGGTGATGAAA 17 217 0 *** **** *** MAP Score: 10.3848 Motif 6 ATGCTCGCAGTTTTGCAACAAAATTTCATTTCTT 1 95 1 ATCATTTTTCTTTCACACTCTAATTCAATGAAAA 1 141 1 GCCCCCAAGTTTTATCAATGTAAATCAGAAAGAG 2 17 0 AGCGAATCCTTTATCCAAATTAAACGGAC 4 5 0 TTTTGTGATATTGATCACAATAATTTTCGCATTC 5 161 0 AATCGCTTTCTTTTACACTCAAAATGTTGTTAAT 5 193 1 TGAAGAGTGTTTTCCCTAAGTAAAGGGAAGAGAA 8 177 0 CTCATAACGTTTTATCACTAAAATTAACAAAAAA 9 109 0 TTCCCACAAGTTCACCAAGATAAAGGTTGATATT 11 182 0 ATAGGCTGGATTTTACATAATAAAAATCCAGCCC 13 13 1 TGAAACGTAATTTTACTATATAAAATTAAGAGAG 16 145 1 AGTTGTTAGTTTTCACACTTTAAAAAAGGCTTTC 17 52 1 GAAAAGTTAGTTTTTCACAAAAATACGAAAAATT 17 185 1 *** *** **** MAP Score: 8.7659 Motif 7 TTTTGACCGAAAATTACTAAAAATTGAAAGAATC 1 23 1 GATAAGGAAAACAGTAAGAAATGAAATTTTGTTG 1 110 0 GCGAATCATAAAAGAAAATAAAAAATAAGAAAGT 5 76 1 AAAAAATAAGAAAGTAAAAAAAATCAAAAATGTG 5 95 1 GTAAGAAAAAATAATATAAAAAGTGTAATCATTG 5 245 0 ACTAAAATTAACAAAAAATAACATTTTTTATCAT 9 93 0 TACAGAAAATCCGAAAAATTGCCACCAAG 11 5 1 ATAGGAGTGAAGATTATGTAAAATATCAACCTTT 11 161 1 TGCCTTCCTCATATTATTTAAGGAAAAACG 12 29 1 GGCTGGATTTTTATTATGTAAAATCCAGCCTATT 13 12 0 GTAAAACGCCATAATATAAAACGAATCACATTTG 15 26 1 TTCACAATATGAAATATTATCACAAGA 16 3 1 TCTAGATCACAAAATCAGTAAAATTATTTTAACA 16 45 1 CAATAAATGTAAAATAAATAAATTATTTATAAAT 16 84 0 ATAATTTACAAAAATAAGAAAGCTCAGTCAATAA 16 112 0 TTATTTTTGTAAATTATGAAACGTAATTTTACTA 16 129 1 CACAGTTGTGAAAAAACGTAATAATGGAGAAAGA 17 96 0 CAACATAGAAAAATTAAATAACATAATTGATGAA 17 154 1 GTTTTTCACAAAAATACGAAAAATTTCATCACCT 17 194 1 * * ** **** ** MAP Score: 8.35351 Motif 8 ATTTTGACCGAAAATTACTAAAAATTGAAAGAATCGGT 1 22 1 TCTTGAAAAGAAACTCACAAAAAATTGACCGCACTTTT 2 69 1 GGGTAAATTTAGATGACACATAATTAAAAAGTTGGAGA 5 17 0 GCGAATCATAAAAGAAAATAAAAAATAAGAAAGTAAAA 5 76 1 AAAAAATAAGAAAGTAAAAAAAATCAAAAATGTGAAGT 5 95 1 CCGATTCCCAAAATGTAAGAAAAAATAATATAAAAAGT 5 255 0 AACTATCATAAGAATAATAAAAAGATAAGTATCATTTT 6 57 1 TTTTATCACTAAAATTAACAAAAAATAACATTTTTTAT 9 96 0 ATAGGAGTGAAGATTATGTAAAATATCAACCTTTATCT 11 161 1 CGTGGATCACAGTTGTGAAAAAACGTAATAATGGAGAA 17 99 0 ATCAACATAGAAAAATTAAATAACATAATTGATGAAAA 17 152 1 GTTTTTCACAAAAATACGAAAAATTTCATCACCTAGAG 17 194 1 *** **** *** MAP Score: 6.93558 Motif 9 TGCATACTCTTGAAAAGAAACTCACAAAAAATTGAC 2 62 1 TGTAAAGATTTGTGAAACACTTCACATTTTTGATTT 5 115 0 CGAAAATTATTGTGATCAATATCACAAAATCGCTTT 5 166 1 AAATTAAATCTGAGATCTAGATCACAGAATGATAAA 9 65 1 CACAAGAAAATAGGATCTAGATCACAAAATCAGTAA 16 30 1 TTTTCACAACTGTGATCCACGCCACAGTTGCAAATA 17 116 1 ** ** * ***** MAP Score: 5.70355 Motif 10 AAACAAATGACCATTTTGACCGAAAATTACTAAAAATT 1 9 1 GCATACTCTTGAAAAGAAACTCACAAAAAATTGACCGCA 2 63 1 TAAGGGATTTGCGAATCATAAAAGAAAATAAAAAATAAG 5 66 1 AAAGAAAATAAAAAATAAGAAAGTAAAAAAAATCAAAAA 5 86 1 GAAAATTATTGTGATCAATATCACAAAATCGCTTTCTTT 5 167 1 CCAAAATGTAAGAAAAAATAATATAAAAAGTGTAATCAT 5 247 0 ATGTTGGTGGAATAGGTATAGTTAAATATCTGGTTCAAT 7 25 1 ACGTTTTATCACTAAAATTAACAAAAAATAACATTTTTT 9 98 0 TTACATAATAAAAATCCAGCCCATAAAAAACTAAGGAGA 13 25 1 CACAATATGAAATATTATCACAAGAAAATAGGATCTAGA 16 12 1 ACAAGAAAATAGGATCTAGATCACAAAATCAGTAAAATT 16 31 1 TTTACTATATAAAATTAAGAGAGGAAAAA 16 156 1 ACAGTTGCAAATAATCAACATAGAAAAATTAAATAACAT 17 139 1 GAAAAATTTCATCACCTAGAGAGGAAAATGTT 17 211 1 * * * * * ***** MAP Score: 2.05722 Motif 11 ACTGTTTTCCTTATCATTTTTCTTTCACACTCTA 1 129 1 TTCCCTACAATGATTACACTTTTTATATTATTTT 5 238 1 TACACTTTTTATATTATTTTTTCTTACATTTTGG 5 252 1 TTACTTAGGGAAAACACTCTTCATTTCAACCGCA 8 188 1 AATTAACAAAAAATAACATTTTTTATCATTCTGT 9 88 0 GATTATGAGCTCATAACGTTTTATCACTAAAATT 9 118 0 ATTATGTAAAATATCAACCTTTATCTTGGTGAAC 11 173 1 TATTTTCTTGTGATAATATTTCATATTGTGAA 16 8 0 TTATATAGTAAAATTACGTTTCATAATTTACAAA 16 134 0 TCTTTCTCCATTATTACGTTTTTTCACAACTGTG 17 96 1 TTTTGTGAAAAACTAACTTTTCATCAATTATGTT 17 173 0 * ** ** **** * MAP Score: 1.42898 Motif 12 CAGTCAAAAATCATTATGTTTTTGACCGCACTT 0 32 0 CTTACTGTTTTCCTTATCATTTTTCTTTCACAC 1 126 1 AATTATTCTCTTTCTGATTTACATT 2 2 1 ACTTTCTTATTTTTTATTTTCTTTTATGATTCG 5 77 0 TTTTTGATTTTTTTTACTTTCTTATTTTTTATT 5 92 0 ATGATTACACTTTTTATATTATTTTTTCTTACA 5 247 1 CTTTTTATTATTCTTATGATAGTTACAAAAAAG 6 48 0 CCAAAAATGATACTTATCTTTTTATTATTCTTA 6 65 0 AAAATAACATTTTTTATCATTCTGTGATCTAGA 9 80 0 AAAATATCAACCTTTATCTTGGTGAACTTGTGG 11 180 1 GGAACAGCATTTTTTATGGTGTTAGGACTTGGC 11 212 1 ATATTCTCCTTAGTTTTTTATGGGCTGGA 13 39 0 TGACTGAGCTTTCTTATTTTTGTAAATTATGAA 16 116 1 TTTTTCCTCTCTTAATTTTATATAGT 16 159 0 TCTTTCTCCATTATTACGTTTTTTCACAACTGT 17 96 1 GATGAAATTTTTCGTATTTTTGTGAAAAACTAA 17 191 0 ******* ** * MAP Score: 1.05078