AlignACE 3.0 10/20/99 AlignACE2 -i AA/AA_operons014_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944235464 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 kdsA 264 3-deoxy-d-manno-octulosonic acid 8-phosphate synthase #1 aq_087 122 putative protein #2 aq_090 27 putative protein #3 hth 63 transcriptional regulator (H-T-H) #4 folK 300 folate biosynthesis 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase #5 rpsO 58 ribosomal protein S15 #6 aldH2_ntrC3 413 aldH2: aldehyde dehydrogenase, ntrC3: transcriptional regulator (NtrC family) #7 hksP4 161 histidine kinase sensor protein #8 hksP2_phoB 284 hksP2: histidine kinase sensor protein, phoB: transcriptional regulator (PhoB-like) #9 aq_1111 216 hypothetical protein #10 aq_1791 40 putative protein #11 ntrC2 209 transcriptional regulator (NtrC family) Motif 1 GAGTAAACCCGGAAAGGTAGAA 3 51 1 GGGAAAAATAGGAAAGGTAGACATCTCGGC 9 63 0 TGCTTTCGTTGTAAAGGAAACCGCTTAAAA 0 57 0 CAGGGTGAAGGTAAAGGAAAAGGAACCCCA 9 15 0 AAGGGCAGAAGTAGAGGGAGTGGATCTAGG 9 117 0 AGTGGTAAAGAGAAAGGAAAAGAGA 2 5 0 TTTAAACAGTGAAAAGGTAAGGCGCTTCGT 11 152 1 ATCAGGTGCAATAAAGGAAAGTTCAAGT 4 282 1 TTCCATTTCTGGAAAGGATAAC 0 2 0 GATATTCTAAGGAGAGGTTAGTATGAACTT 4 201 0 AAACCTCACGGGAAAGGTTACTATGGGATT 0 113 0 GAACCCTTCAAAAGAGGAAATAGTAAGTGT 6 378 1 GGGTAATAAGGGAGAGGTTGAGACTTACCG 6 107 1 AGAAGAGCCAAAAAAGGGAAAAATCCCATA 0 92 1 GGTTTTTGAAAAAGAGGAAGGTTGTAGCGG 8 70 0 TCAGTACCCAGTCAAGGAAGCGGAATGAAA 6 213 1 CAAGAACGCTGAGGAGGAAAAACCTCACGG 0 132 0 AGAGGCAGAAAGAGAGGGTAATTAGTAGGT 8 97 0 GTTCGGATGCGGTAAGGGAATATGCGGTTC 6 144 1 AATAATAACCATCGAGGGAATTCCCGAAGA 6 246 1 TTAAGTTTCGGTTAAGGAAATGTTTTAAAT 8 189 1 ACGAACAAAAATGGAGGTAAGAGT 7 4 0 TTTAAAACTTATGGAGGTAGGAATGCTTTT 6 21 1 CTTTGGCTACAACAAGGGAGCTTTTACAGG 3 12 1 TCTTTTTTAGAGTAAGGTTAAATTAGTAGT 0 243 1 ********** MAP Score: 23.5459 Motif 2 GCTTTTTAAGCGGTTTCCTTTACAACGAAAG 0 54 1 TACTATGGGATTTTTCCCTTTTTTGGCTCTT 0 94 0 CTCAGCGTTCTTGTTTTCTTTATCGTTTACT 0 149 1 GTTTTCTTTATCGTTTACTTTTACAAGGCTG 0 161 1 GCTGAAGGGGCTATTCTCTTTACGATTTCCC 0 188 1 CCGTGCCAAACTTTTCCCTTTGATTTTCAAC 1 57 0 CTTCACACCTCCTTTTGGTTTTCACATTTTT 1 100 0 TCTCTTTTCCTTTCTCTTTACCACTTT 2 8 1 GTACATTTTTCCGTTTACTTTTAAAAGCATT 6 42 0 ATTACAACATCCGCTTTCTTTAAAATATCGT 8 12 1 ACCGCTACAACCTTCCTCTTTTTCAAAAACC 8 69 1 TCTTGGGGTTCCTTTTCCTTTACCTTCACCC 9 12 1 AATCTTAGCTTTTTTTACTTTGCTTTTACTC 9 161 0 TTCCGAACCTCCGTTTCGTGTGGTGGACTAA 10 19 0 CCGTCAAGCCCCTTTTTCATTCCTGCGCTCT 11 81 1 ATTCCTGCGCTCTTTTGCTTTTACAAAGCCT 11 99 1 AGCGCCTTACCTTTTCACTGTTTAAAACCTT 11 147 0 ****** **** MAP Score: 19.7181 Motif 3 TTGCTGGACGTTCCATTTCTGGAAAGGATAA 0 11 0 TATGGGATTTTTCCCTTTTTTGGCTCTTCTG 0 91 0 TCTCTTTTCCTTTCTCTTTACCACTTT 2 6 1 ACTTCAATCCTTCCAATTTTTAGCTTTGGTA 4 171 1 ACTTGAACTTTCCTTTATTGCACCTGATAA 4 280 0 TCGTACATTTTTCCGTTTACTTTTAAAAGCA 6 44 0 GAACCGCATATTCCCTTACCGCATCCGAACT 6 143 0 TTTCTTTTCATTCCGCTTCCTTGACTGGGTA 6 217 0 GTGCATAGGCTTCCACTATTTGTCCGGGCTG 6 331 0 CACTTACTATTTCCTCTTTTGAAGGGTTCGG 6 376 0 GCAATTTTCGTGCCAATTTCTGGACACTGAA 7 44 1 AAATTACAACATCCGCTTTCTTTAAAATATC 8 10 1 CGCTACAACCTTCCTCTTTTTCAAAAACCTA 8 71 1 CCTCTCTTTCTGCCTCTTATTCCTGACTGCT 8 110 1 ACTCTTGGGGTTCCTTTTCCTTTACCTTCAC 9 10 1 ATGTCTACCTTTCCTATTTTTCCCACGGCAG 9 69 1 AAAGGCCTAGATCCACTCCCTCTACTTCTGC 9 112 1 AATTCCGTCAAGCCCCTTTTTCATTCCTGCG 11 77 1 **** ****** MAP Score: 17.9772 Motif 4 GTAAAGAGAATAGCCCCTTCAGCCTTGTAAAA 0 179 0 CTTTACGATTTCCCACCTTCTCGGGCGTTTCT 0 205 1 TGCAACACTGCAACACCTTCCTGAAACGCCCT 1 24 1 GCTTCACACCTCCTTTTGGTTTTCA 1 107 0 ACGACACCAATAGCACCTTCTCTTGCAACGCT 4 78 1 TTAAAAGCATTCCTACCTCCATAAGTTTTAAA 6 21 0 CCTTACCGCATCCGAACTTCGTCCCGGTAAGT 6 129 0 ACTCTTACCTCCATTTTTGTTCGT 7 2 1 TCACAACCGCTACAACCTTCCTCTTTTTCAAA 8 64 1 TCCTGACTGCTAAGACCTTCATCTCACACCTC 8 130 1 GACCTTCATCTCACACCTCCTTACTTAAGGTT 8 143 1 TTACCTTCACCCTGACCTTCGGACACATAACA 9 31 1 CTTTGTCTTATAGCACCTGCCGTGGGAAAAAT 9 84 0 TTCCGAACCTCCGTTTCGTGTGGT 10 26 0 ** ******* * MAP Score: 15.0023 Motif 5 AAAAACCTCACGGGAAAGGTTACTATGGGATT 0 113 0 AGCCTTGTAAAAGTAAACGATAAAGAAAACAA 0 159 0 TTACTCTAAAAAAGAGCTGGAAGAAACGCCCG 0 226 0 GCTCTTTTTTAGAGTAAGGTTAAATTAGTAGT 0 241 1 TGAAAATCAAAGGGAAAAGTTTGGCACGGAGT 1 59 1 TGAAAACCAAAAGGAGGTGTGAAGC 1 107 1 GGTAAAGAGAAAGGAAAAGAGA 2 0 0 AAGATATTCTAAGGAGAGGTTAGTATGAACTT 4 201 0 AGGTGCAATAAAGGAAAGTTCAAGT 4 285 1 ATGCTTTTAAAAGTAAACGGAAAAATGTACGA 6 43 1 AAAATGTACGAAGTAAATGTAAGTCCTGATAC 6 64 1 CTGGGTAATAAGGGAGAGGTTGAGACTTACCG 6 105 1 GTACCCAGTCAAGGAAGCGGAATGAAAAGAAA 6 216 1 CTGAAATTCTAAGGAACTTGAAAAGAATCAGG 7 70 1 TAAGAGGCAGAAAGAGAGGGTAATTAGTAGGT 8 97 0 AACCTTAAGTAAGGAGGTGTGAGATGAAGGTC 8 143 0 AGTTTCGGTTAAGGAAATGTTTTAAATTAATG 8 192 1 GGTGAAGGTAAAGGAAAAGGAACCCCAAGAGT 9 10 0 TCCGAAGGTCAGGGTGAAGGTAAAGGAAAAGG 9 22 0 AAAAGGGCAGAAGTAGAGGGAGTGGATCTAGG 9 117 0 GGTTTTAAACAGTGAAAAGGTAAGGCGCTTCG 11 149 1 ******* ** * MAP Score: 14.5086 Motif 6 AAAGTGGTAAAGAGAAAGGAAAAGAGA 2 3 0 GTCAGGGTGAAGGTAAAGGAAAAGGAACCCCAAG 9 13 0 TGAAATTCTAAGGAACTTGAAAAGAATCAGGTGT 7 71 1 GTTCCGAAGAAAGTTCTTGAAAAGCTAAATTAAA 11 180 1 AAGTTCGGATAGGCTTTGTAAAAGCAAAAGAGCG 11 106 0 GGTGTTGGTATATCCTGGGAAAAGCTCGCCGGAA 4 109 0 CAGTCAAGGAAGCGGAATGAAAAGAAATAATAAC 6 221 1 ATAGCCCCTTCAGCCTTGTAAAAGTAAACGATAA 0 168 0 TGGAGGTAGGAATGCTTTTAAAAGTAAACGGAAA 6 32 1 AAAAAGGTTTTAAACAGTGAAAAGGTAAGGCGCT 11 144 1 CTGCCGTGGGAAAAATAGGAAAGGTAGACATCTC 9 66 0 CAGAAGAGCCAAAAAAGGGAAAAATCCCATAGTA 0 91 1 CTGGACGTTCCATTTCTGGAAAGGATAAC 0 5 0 CTTGTTGAAAATCAAAGGGAAAAGTTTGGCACGG 1 54 1 TTTACCCGAGCAGGAGAGTAAAAGCAAAGTAAAA 9 146 1 TACTCGCAATTGCTCCTGTAAAAGCTCCCTTGTT 3 22 0 TCCCGAAGAACACCCTGTTAAAAGGGCATGGATT 6 267 1 CCTATAATTCCGAATATTGAAAGGATAACTCCGC 11 28 0 GGTAATTAGTAGGTTTTTGAAAAAGAGGAAGGTT 8 77 0 AGCCTATCCGAACTTTGTGAAAAAGGTTTTAAAC 11 125 1 CAAAAGAGCGCAGGAATGAAAAAGGGGCTTGACG 11 82 0 TTGTAAAGGAAACCGCTTAAAAAGCCTATAATAC 0 45 0 TTATTTGCTCAATTCTAAGAAAAGACGGAGGTAT 5 26 1 ** ******** MAP Score: 13.7271 Motif 7 CTCTCCTCTGGGTAATAAGGGAGAGGTTGAGA 6 98 1 AGCGCAGGAATGAAAAAGGGGCTTGACGGAAT 11 78 0 CATAATTCAAGGCGGAATGGGTGTTGGTATAT 4 130 0 TCGTTTCCGCTGTGGAACAGGCTACAGATATC 4 50 0 TTAGCAGTCAGGAATAAGAGGCAGAAAGAGAG 8 111 0 ACCTGCCGTGGGAAAAATAGGAAAGGTAGACA 9 70 0 ACTTTTACAAGGCTGAAGGGGCTATTCTCTTT 0 177 1 GAAGTTCGGATGCGGTAAGGGAATATGCGGTT 6 141 1 TCTCCTGCTCGGGTAAAAGGGCAGAAGTAGAG 9 131 0 AGTAGGTTTTTGAAAAAGAGGAAGGTTGTAGC 8 72 0 TCCAGCAATATGTATTATAGGCTTTTTAAGCG 0 34 1 CTTTATCAGGTGCAATAAAGGAAAGTTCAAGT 4 278 1 AAGAACACCCTGTTAAAAGGGCATGGATTGAA 6 272 1 TTCAATATTCGGAATTATAGGTCTTATACTAC 11 41 1 ATCCGAACTTTGTGAAAAAGGTTTTAAACAGT 11 130 1 CATTCCGCCTTGAATTATGGGTATATCTACTT 4 143 1 GAACAAAAATGGAGGTAAGAGT 7 0 0 ** **** **** MAP Score: 13.1186 Motif 8 AACCAAAAGGAGGTGTGAAGC 1 111 1 AGGTGTGAAGACATGACACT 6 403 0 ACGCCCGAGAAGGTGGGAAATCGTAAAGAG 0 203 0 GAAAAGAATCAGGTGTCAAAAATGACACCT 7 89 1 TCCTTACTTAAGGTTTTAAACCCCAAATTT 8 160 1 TTTGTGAAAAAGGTTTTAAACAGTGAAAAG 11 138 1 AAGAATTTTTAAGTGTCAAGTTTGTCACTA 7 119 0 CTACCTCCATAAGTTTTAAATTTAATTGAT 6 11 0 TGCAATTAAAAAATGTGAAAACCAAAAGGA 1 92 1 AAAGTGGTAAAGAGAAAGGAA 2 16 0 TATTAGTATAAGATTTCAAGACTTATTAAT 8 243 1 TTTAAACCCCAAATTTTAAGTTTCGGTTAA 8 174 1 ATCTTAAAACAAATTTTAAGATAGAATTAT 4 228 1 TTAAGTAAGGAGGTGTGAGATGAAGGTCTT 8 141 0 GGTTAAGGAAATGTTTTAAATTAATGTTAA 8 198 1 CCAAAGCTAAAAATTGGAAGGATTGAAGTA 4 170 0 AGACGGAGGTATATGGGAAG 5 48 1 CTGAAGAACGATATTTTAAAGAAAGCGGAT 8 20 0 TATAAAACTTAGATGGTAGGGTTAATCTTA 9 185 0 ********** MAP Score: 13.0719 Motif 9 TCCCTCTTTACTAGATGGGGATATCTGTAGCCTGTTC 4 31 1 AAGCGTTGCAAGAGAAGGTGCTATTGGTGTCGTTTCC 4 74 0 AATTCTAAGAAAAGACGGAGGTATATGGGAAG 5 36 1 AGTTCGGATGCGGTAAGGGAATATGCGGTTCCTGCAC 6 143 1 GACGGAAATCCTGTGAGGAGCTGTCAGTACCCAGTCA 6 190 1 ACTATTTGTCCGGGCTGGCAGTATCCGCACTGGGGAA 6 311 0 TTAAAACCTTAAGTAAGGAGGTGTGAGATGAAGGTCT 8 142 0 TATTTTTCCCACGGCAGGTGCTATAAGACAAAGGCCT 9 83 1 TATCCTTTCAATATTCGGAATTATAGGTCTTATACTA 11 35 1 GAAAAAGGGGCTTGACGGAATTATCGGTAGTATAAGA 11 62 0 * ** ** * *** * MAP Score: 11.9235 Motif 10 GTAACCTTTCCCGTGAGGTTTTTCCTCCTCAGCGTTC 0 122 1 GGGGCTATTCTCTTTACGATTTCCCACCTTCTCGGGC 0 194 1 CGCAATTGCTCCTGTAAAAGCTCCCTTGTTGTAGCCA 3 15 0 CCTATCGGTCTTCCGAACTTGTCCCTCTTTACTAGAT 4 10 1 GATGGGGATATCTGTAGCCTGTTCCACAGCGGAAACG 4 44 1 AGCACCTTCTCTTGCAACGCTTCCGGCGAGCTTTTCC 4 89 1 CCAGGATATACCAACACCCATTCCGCCTTGAATTATG 4 125 1 CTGACAGCTCCTCACAGGATTTCCGTCTATTAAAACG 6 180 0 AACAGGGTGTTCTTCGGGAATTCCCTCGATGGTTATT 6 249 0 TTGTTCACAACCGCTACAACCTTCCTCTTTTTCAAAA 8 60 1 GATGTCTACCTTTCCTATTTTTCCCACGGCAGGTGCT 9 68 1 AAGACAAAGGCCTAGATCCACTCCCTCTACTTCTGCC 9 107 1 CCATCTAAGTTTTATAATATTTCCCGC 9 199 1 AGGTCTTATACTACCGATAATTCCGTCAAGCCCCTTT 11 59 1 ** ** ***** * MAP Score: 5.74738 Motif 11 AAGAGCCAAAAAAGGGAAAAATCCCATAGT 0 94 1 GTTGAAAATCAAAGGGAAAAGTTTGGCACG 1 57 1 GCAATTAAAAAATGTGAAAACCAAAAGGAG 1 93 1 TTTTAAAAGTAAACGGAAAAATGTACGAAG 6 47 1 TCGGATGCGGTAAGGGAATATGCGGTTCCT 6 146 1 AAGGTTTTAAACAGTGAAAAGGTAAGGCGC 11 147 1 ********** MAP Score: 1.22524