AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_operons018_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944252310 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0143 93 response regulator #1 TM0309 300 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #2 TM0310 43 beta-D-galactosidase #3 TM0311 92 hypothetical protein #4 TM0312 50 conserved hypothetical protein #5 TM0972 221 conserved hypothetical protein, GGDEF domain #6 TM1006 128 oxidoreductase, aldo/keto reductase family #7 TM1009 300 oxidoreductase, aldo/keto reductase family #8 TM1162 207 conserved hypothetical protein #9 TM1182_TM1183 73 TM1182: chromosome segregation SMC protein, putative, TM1183: oxidoreductase, aldo/keto reductase family #10 TM1596 49 purine nucleoside phosphorylase #11 TM1743 84 oxidoreductase, aldo/keto reductase family #12 TM1788 215 conserved hypothetical protein, GGDEF domain #13 TM1832 23 transposase #14 TM1833 82 methyl-accepting chemotaxis-related protein #15 TM1834 134 alpha-glucosidase Motif 1 CGGGGTTTTTTGGAGGTGAACATGG 2 28 1 AGCTTCGTATAGGGGGTGTG 3 82 1 TTTAGCAGAAAGGAGATGAAAGAAATC 6 7 0 TTAGAGCGAAAGGAGGGGGAAGT 6 115 1 ATCCATCTATAGGAGGTGTTAAC 7 287 1 AAGCGGTCCGAGGAGGTGTGAAA 8 3 0 ATGCTTTTTCGGGAGGTGATTTCTAAGTGG 8 58 0 AATCTAAAATGGGAGGTGGTAAC 8 194 1 GATAACTGCAAGGAGGTGAAAAT 9 3 0 TCTAACGTGTGGGAGGGGATCGGT 9 59 1 CTACTATAAAGTGAGGTGTTG 10 1 0 AATAGTTACGTGGAGGTGATCACAAGTT 10 31 1 CAAATCGTGTGGGAGGTGACAGG 11 3 0 TTATTATAACCTGAGGTGTTAAAATTCAAT 11 33 0 AGACTAATTCAGGAGGTGGTTGGA 11 70 1 TATAATTGAATGGGGTGATAGGT 13 9 1 ACGAAATACAGGGAGGTGTTTTT 15 121 1 ********** MAP Score: 35.752 Motif 2 TATATTATCAGAGAAAAAAACGAGTTGAAC 0 39 0 AAAAAGCCTTCAGAAAAGAAACTCGACGTT 1 98 0 GAAAAATCACGTGAAAGAAG 4 40 1 TAATTCTGGAGTGAAAAAAGCAGGTACATG 5 160 1 AAAATTTTAGCAGAAAGGAGATGAAAGAAA 6 12 0 ATGTTTTAGAGCGAAAGGAGGGGGAAGT 6 110 1 AAATATTGCCCAGAAAGAAGGGGTTGAAAG 7 38 0 GAAGCAATACCAGAAAGAAGGACAGCTCCC 7 118 0 AGTATAAAAGCCGAAAGGAGTATGGCGTAC 7 193 0 AAGAAAATCGGAGAAAGAATCAGTATAAAA 7 214 0 AACACCAGTACAGAAAGAAAAATTTTTCAA 8 122 1 ACGTTAATTTCCGAAAAGAGTATAATCTAA 8 171 1 AAATTGATAACTGCAAGGAGGTGAAAAT 9 8 0 AAGGATCTGAAAGGGGCCTGAAAGGC 14 6 1 ********** MAP Score: 21.3103 Motif 3 TGGTATCCGGTTTCAGAGGAATTATTCGAACTCT 1 47 0 CGCCGGGGTTTTTTGGAGGTGAACATGG 2 25 1 CCCTTTTTTGTTCTGGTGTTAGAATTTGTACAAG 3 50 1 GATTTATATTTTTGGGAGGAAGACTTTGGTGTCG 5 79 1 TACCGTTTAATTCTGGAGTGAAAAAAGCAGGTAC 5 153 1 TTTCTAACGTTTGCGGAGTAGATAGCGGTATGTT 6 81 1 GTTTTAGAGCGAAAGGAGGGGGAAGT 6 112 1 GGAGATCTCATTCCGCAGGAACACTTCGAAAAAG 7 68 1 TGGATCCATCTATAGGAGGTGTTAAC 7 284 1 GACCGCTTTTTTACGGAGGAAGACTGGTGCTTTC 8 25 1 CAGATGCTTTTTCGGGAGGTGATTTCTAAGTGGA 8 57 0 GATTTTATCATTGTGGAGTGATAAAATTGATAAC 9 27 0 AAATCTAACGTGTGGGAGGGGATCGGT 9 56 1 ACTAGACTAATTCAGGAGGTGGTTGGA 11 67 1 GATGGTGTGATATCAGAGGGAAAATCACCT 12 6 0 ** ***** * ** MAP Score: 13.1243 Motif 4 ACGATTTCAGATGAGAAAATTGACGGTAAA 1 141 1 TTTTGTTCTGGTGTTAGAATTTGTACAAGC 3 55 1 GTACATTATAGTCTGAAAATGTTTTCATT 4 9 0 AGACTTTGGTGTCGTAAAATGTCAATTTTA 5 99 1 AAATCGCGGTGTCGTAAAATTGACATTTTA 5 113 0 TTTCCATCAAAGGGTAAAATTTTAGCAGAA 6 27 0 TTTACCCTTTGATGGAAAATCAGGCAAATA 6 39 1 TTCCGGTGTGATGTTAGAATAGTTCTACGC 8 90 0 AACTGCAAGGAGGTGAAAAT 9 0 0 TCATTGTGGAGTGATAAAATTGATAACTGC 9 24 0 TCACTCCACAATGATAAAATCTAACGTGTG 9 40 1 ATAACCTGAGGTGTTAAAATTCAATCAAAT 11 28 0 TGTGATATCAGAGGGAAAATCACCT 12 5 0 AAAGAATACTGTGATAAAATTCAGACAATA 12 62 1 AATATAATGTGTTGGAAAATCCAAAGAAGA 14 48 1 ********** MAP Score: 11.5365 Motif 5 ATTATCAGAGAAAAAAACGAGTTGAACCGATGACA 0 31 0 AGCCTTCAGAAAAGAAACTCGACGTTAATCTTCTA 1 89 0 TTCCTAATTTGAAAAAGCCTTCAGAAAAGAAACTC 1 104 0 TTTCAGATGAGAAAATTGACGGTAAAAATCGATAT 1 145 1 GTTCACCTCCAAAAAACCCCGGCGATCGCCGGGGC 2 14 0 ACACCAGAACAAAAAAGGGCGGAAATCCGCCCTTG 3 34 0 ATAATGTACTGAAAAATCACGTGAAAGAAG 4 30 1 TTCTGGAGTGAAAAAAGCAGGTACATGCGGTCCTC 5 163 1 TAAAATTTTAGCAGAAAGGAGATGAAAGAAATC 6 8 0 TATTGCCCAGAAAGAAGGGGTTGAAAGTCTCAGAA 7 30 0 GGAACACTTCGAAAAAGCGAGTAGTATCTACGTGG 7 85 1 GTTCATAATAGAAGAAGCAATACCAGAAAGAAGGA 7 126 0 AAAATCGGAGAAAGAATCAGTATAAAAGCCGAAAG 7 206 0 CTTCCTCCGTAAAAAAGCGGTCCGAGGAGGTGTGA 8 12 0 AATTAACGTTGAAGAAGGAATGTGTTCGTTGAAAA 8 145 0 TTCCAGGAGAACAAAACCAATTACAGGTCGTAAAG 12 163 0 AAAATCCAAAGAAGATAGTGGGGGAAAAG 14 63 1 TGAATTCATGGAAAAAACGTTCGGAAAGTATATAG 15 71 1 ****** * * ** MAP Score: 11.4267 Motif 6 AGAAGATTAACGTCGAGTTTCTTTTCTGAAGGCTTTTT 1 90 1 CGATTTTTACCGTCAATTTTCTCATCTGAAATCGTATT 1 138 0 GGGCGGATTTCCGCCCTTTTTTGTTCTGGTGTTAGAAT 3 37 1 TTTTACGACACCAAAGTCTTCCTCCCAAAAATATAAAT 5 80 0 CCGCATGTACCTGCTTTTTTCACTCCAGAATTAAACGG 5 155 0 GATTTCTTTCATCTCCTTTCTGCTAAAATTTTACCCT 6 9 1 CTAAAACATACCGCTATCTACTCCGCAAACGTTAGAAA 6 81 0 ACTTCCCCCTCCTTTCGCTCTAAAACATACCG 6 106 0 AGACTTTCAACCCCTTCTTTCTGGGCAATATTTGGAGA 7 35 1 CACGTAGATACTACTCGCTTTTTCGAAGTGTTCCTGCG 7 81 0 CGCCATACTCCTTTCGGCTTTTATACTGATTCTTTCTC 7 196 1 CTGATTCTTTCTCCGATTTTCTTCACGGTAGCGGGAAA 7 221 1 CACACCTCCTCGGACCGCTTTTTTACGGAGGAAGACTG 8 13 1 TTTCAACGAACACATTCCTTCTTCAACGTTAATTTCCG 8 146 1 TTGAAGATTCCGGCTGGCTTCCGGCCAGCCTTTTAATT 15 19 1 TATATACTTTCCGAACGTTTTTTCCATGAATTCAAACG 15 67 0 * * ****** * * MAP Score: 8.05039 Motif 7 TAATAATATATTATCAGAGAAAAAAACGAGTTGAA 0 40 0 CTGAAACCGGATACCAGGGAATTATAGAAGATTAA 1 65 1 TTTGAAAAAGCCTTCAGAAAAGAAACTCGACGTTA 1 97 0 AGGAAATACGATTTCAGATGAGAAAATTGACGGTA 1 134 1 ACAAATTCTAACACCAGAACAAAAAAGGGCGGAAA 3 44 0 AATGAAAACATTTTCAGACTATAATGTACTGAAAA 4 10 1 AAAAGTGAATCACAGGAAATTATATCATGGTGA 5 198 0 CTTTGATGGAAAATCAGGCAAATATTCGAGAATAT 6 45 1 AAGAAACACCAGTACAGAAAGAAAAATTTTTCAAC 8 118 1 GAATTTTAACACCTCAGGTTATAATAATAATACTA 11 36 1 CGATGGTGTGATATCAGAGGGAAAATCACCT 12 6 0 ACTGTGATAAAATTCAGACAATAAAAAGTTGAATC 12 69 1 AACAAAACCAATTACAGGTCGTAAAGAATAAAGCA 12 154 0 GAAGCGTTTGAATTCATGGAAAAAACGTTCGGAAA 15 63 1 * ***** * *** MAP Score: 7.64463 Motif 8 GAACTCTGCGTGAAAACAGTTTCATGATAA 1 24 0 CGATTTCAGATGAGAAAATTGACGGTAAAA 1 142 1 TCGCAACTATCGATAAATATCGATTTTTAC 1 166 0 GAACCAAACACGAAAAAATCCGATTTTCTG 1 203 0 AGTATAATAACGAAGAAATTTCTTTAGAGG 1 251 1 ACCCCCTTTGATGAATGTTTTTATTTTT 1 282 0 AATGAAAACATTTTCAGACTAT 4 2 1 AATGATGATTTGCTAAATGTGAATTTAGTA 5 43 1 CCTCTCACCATGATATAATTTCCTGTGATT 5 194 1 ATCTCCTTTCTGCTAAAATTTTACCCTTTG 6 20 1 ATGTGTTCGTTGAAAAATTTTTCTTTCTGT 8 131 0 CATTGTGGAGTGATAAAATTGATAACTGCA 9 23 0 CACTCCACAATGATAAAATCTAACGTGTGG 9 41 1 TAACCTGAGGTGTTAAAATTCAATCAAATC 11 27 0 AAGAATACTGTGATAAAATTCAGACAATAA 12 63 1 TCTGAATTATTGAAAAAAGTGCTTTATTCT 12 135 1 ********** MAP Score: 5.50634 Motif 9 GGTTCAACTCGTTTTTTTCTCTGATAATATA 0 38 1 CAGAAAATCGGATTTTTTCGTGTTTGGTTCT 1 203 1 GAGTTTTGCCAACAGGAGTATGT 3 2 1 GCATGTACCTGCTTTTTTCACTCCAGAATTA 5 160 0 AGGTACATGCGGTCCTCTCACCATGATATAA 5 181 1 ATATTTGCCTGATTTTCCATCAAAGGGTAAA 6 39 0 TGGTGGGGTTCTCCATCCTCTTCTGAG 7 6 1 CTTTTATACTGATTCTTTCTCCGATTTTCTT 7 213 1 CAGAAAGAAAAATTTTTCAACGAACACATTC 8 132 1 AGGTGATTTTCCCTCTGATATCACA 12 4 1 CCTGTAATTGGTTTTGTTCTCCTGGAAAGCG 12 171 1 ATCTTCTTTGGATTTTCCAACACATTATATT 14 48 0 CTTTCCGAACGTTTTTTCCATGAATTCAAAC 15 68 0 * ********* MAP Score: 4.63077 Motif 10 TTGTACAAATTCTAACACCAGAACAAAAAA 3 53 0 ATTGACATTTTACGACACCAAAGTCTTCCT 5 95 0 ATGTCAATTTTACGACACCGCGATTTGAGA 5 117 1 TACCTGCTTTTTTCACTCCAGAATTAAACG 5 156 0 TTCTGAGACTTTCAACCCCTTCTTTCTGGG 7 30 1 TTTCACACCTCCTCGGACCG 8 0 1 ATTTTCACCTCCTTGCAGTTAT 9 2 1 TTATCAATTTTATCACTCCACAATGATAAA 9 28 1 ACCGATCCCCTCCCACACGTTAGATTTTAT 9 53 0 CCTGTCACCTCCCACACGATTTGATTGAA 11 9 1 TTGATTGAATTTTAACACCTCAGGTTATAA 11 30 1 TTCCCTCTGATATCACACCATCGAAAATTA 12 18 1 TATTCACGGCTATCACCCTTTGAGATTCAA 12 97 0 ACCTATCACCCCATTCAATTATA 13 10 0 ********** MAP Score: 3.32995 Motif 11 GGTTTCAGAGGAATTATTCGAACTCTGCGT 1 43 0 CGATTTTCTGGAATTATTCGCAACTATCGA 1 183 0 CATCTGCGTAGAACTATTCTAACATCACAC 8 85 1 CACCTCCACGTAACTATTCTACTATAAAGT 10 19 0 ACCACCTCCTGAATTAGTCTAGTATTATTA 11 60 0 ********** MAP Score: 0.837037 Motif 12 TTATCAGAGAAAAAAACGAGTTGAACCGAT 0 35 0 AATAATTCCTCTGAAACCGGATACCAGGGA 1 55 1 AAAAACATTCATCAAAGGGGGT 1 288 1 ACACCAGAACAAAAAAGGGCGGAAATCCGC 3 39 0 TGTAAGGAATCTCAAGGGGGA 5 1 0 GTAGATGTTTCTCAAATCGCGGTGTCGTAA 5 126 0 TTCTGGAGTGAAAAAAGCAGGTACATGCGG 5 163 1 AAAATTTTAGCAGAAAGGAGATGAAAGAAA 6 12 0 CTGATTTTCCATCAAAGGGTAAAATTTTAG 6 32 0 AGTATAAAAGCCGAAAGGAGTATGGCGTAC 7 193 0 CTTCCTCCGTAAAAAAGCGGTCCGAGGAGG 8 17 0 ACGTTAATTTCCGAAAAGAGTATAATCTAA 8 171 1 AGAGTATAATCTAAAATGGGAGGTGGTAAC 8 187 1 AAATTGATAACTGCAAGGAGGTGAAAAT 9 8 0 AAAGTTGAATCTCAAAGGGTGATAGCCGTG 12 93 1 AAGGATCTGAAAGGGGCCTGAAAGGC 14 6 1 TGAAAGGGGCCTGAAAGGCCCCTTTATGTA 14 17 1 ********** MAP Score: 0.228038