AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_operons007_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944251860 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0280 188 hypothetical protein #1 TM0281 21 alpha-L-arabinofuranosidase #2 TM0282 28 aldose 1-epimerase #3 TM0511 109 conserved hypothetical protein #4 TM0571 113 heat shock serine protease, periplasmic #5 TM0572 96 lipopolysaccharide biosynthesis protein, putative #6 TM0579 243 conserved hypothetical protein #7 TM0607 144 hypothetical protein #8 TM0619 116 conserved hypothetical protein #9 TM0622 88 lipopolysaccharide biosynthesis protein, putative #10 TM0623 205 hypothetical protein #11 TM0624 109 N-acetylglucosaminyl-phosphatidylinositol biosynthesis-related protein #12 TM0627 28 lipopolysaccharide biosynthesis protein #13 TM0632 26 extracellular polysaccharide biosynthesis-related protein #14 TM0633 40 flagellar-related protein #15 TM0636 82 hypothetical protein #16 TM0637 202 hypothetical protein #17 TM0667 163 conserved hypothetical protein #18 TM0751 168 uridine kinase-related protein #19 TM0757 107 hypothetical protein #20 TM0862 82 glucose-1-phosphate thymidylyltransferase #21 TM0888 55 conserved hypothetical protein #22 TM0889 64 conserved hypothetical protein #23 TM1034 40 UDP-N-acetylglucosamine 2-epimerase #24 TM1196 21 oligopeptide ABC transporter, ATP-binding protein #25 TM1198 69 oligopeptide ABC transporter, permease protein #26 TM1199 154 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #27 TM1403 135 antibiotic ABC transporter, ATP-binding protein, putative #28 TM1405 79 lipopolysaccharide biosynthesis protein-related protein #29 TM1547 78 conserved hypothetical protein Motif 1 TGAAATATCCCTCCTCCTGTGTTAATATACTAC 17 140 0 GTCCTCCACCTCCTGTTAAAATTGTACAC 23 21 0 AATCTCCTCCTGTAAAAAGATTCCAA 11 93 0 GATAACACCTCCTGTGAATTTTTTGTGG 16 184 0 ACTTCACACCTCCTCTTTTCAAGATTATA 20 63 0 TTCTTTCTCCTCCTGGCAACAGTTTTTC 2 9 0 TTCACCTCCTCGTGTACAATTTTAA 23 2 1 AACAAATCACCTCCTGAAAATTTTTCCTTA 20 7 1 ACCACTTCACCTCCTCATATGGTTTCGTAC 15 62 0 CGCCTCCTGATAGAATTATATCA 21 0 1 AACATTCGCCTCCCCTTAATTAAAAG 13 7 0 CCTTTCTACCTCCTGGTTTCCCGACTAAT 4 6 1 GGAGGGGGAACCCCTCCCCGAAAGTTCCATGA 25 9 0 CTCTTACCCCTCCCTTCGAAAGGTTTCCG 4 94 0 AGGGGGCATACGCCCCCTTTTATTTTTGTGCAA 19 29 1 GTTCGATCTTTTCCTCCTTTGTTCTTTTCAAGT 25 46 0 ACTCTTTTCCCTCCTCATCTC 1 1 0 AAACGATATTCCTCCTTTTCATACATTTAGG 0 167 0 GATCTTCCCTCCCGGTCTTTTTGGATAT 6 5 1 CTCGAACCCTCCTCTTCGTCTTTTCTGT 16 5 1 ATGCTTCACACCCCTCCATTAAAAAGAAATGGA 6 171 0 GATATCACCTCCAGAAAGAAAGCGGGGG 14 22 0 CCATATCCACCACCTCCAGATCGTTTGATTCAA 17 17 1 GAAAATCCCCCCTCTACTGGTGTCATAG 26 136 0 AGGGGGCGTATGCCCCCTGGATTGACGGTGTTC 19 14 0 GGATTTCTACTCCTCCTTCTCGTTCAAGGCCC 21 33 0 AGAACCTCCCCTCAATGTTAATACA 5 2 1 GCTGGCTTCCTCCCTTGAAGGAGCTTTCC 18 149 0 AATAAAAACCTCCTTGACAAAAAACTGGG 7 6 1 GTGATCTTTCCCCCTCCGGTGGAGGGGGATTTT 5 45 1 AAGTAGATCAAACCTCCCTTCTTCACTTCTATC 22 38 0 ACGGTTTCAGAACCTCCCGAAGATCGAGTCTTT 7 96 0 CTCTGACACCTCCATAGAGTCAAAAGATA 27 116 0 ATGTTAATACAGCCCCCTTTGGTGATCTTTCCC 5 24 1 GAATTTTCAAGACCTCCTGGGTTGTATAATATC 6 33 0 GCAATAACACCTCCGTTATTG 24 1 0 AAGAACAAAGCCCCCTGACCGGGGGCTTTTC 18 8 1 ACTTGATTTTATCCTCCACAAATGGTAGTATTT 7 46 0 CGGGGAGGGGTTCCCCCTCCCTTAACTTGAAAA 25 22 1 GTGAAGTACCCCCAGAAGTTCCTAATCTT 8 97 0 GACTGCGCAGCCCCTCCAATAAATAAGTCCTGA 16 152 0 GTTTTCCCCTCCAAATTAATAGATCCTT 27 5 1 * ******** * MAP Score: 75.5085 Motif 2 GTTTAAAAGCTCTTTTCTTATGGTTTCTCA 0 30 0 CGATATTCCTCCTTTTCATACATTTAGGTA 0 165 0 ACTCTTTTCCCTCCTCATCTC 1 2 0 GCCTTTCTCCCCCGGATTCTGGTAAAAT 3 91 0 CCTTTCTACCTCCTGGTTTCCCGACTAA 4 8 1 CTCTTACCCCTCCCTTCGAAAGGTTTC 4 96 0 AGAACCTCCCCTCAATGTTAATAC 5 4 1 TCAAAAAATCCCCCTCCACCGGAGGGGGAA 5 52 0 CGCTGGCCTCCCTCTGGTTTCTATTTTACC 6 76 0 ATGCTTCACACCCCTCCATTAAAAAGAAAT 6 174 0 AACACTTCCTTCTTCTCTTTAGTTACTGAT 10 77 0 ATCAAGAAATACCTTTCATCCGTGATCCGG 10 148 1 AACATTCGCCTCCCCTTAATTAAAAG 13 8 0 GCGGGGGTCTCCCCCGCTTTCTTTCTGGAG 14 12 1 ACCACTTCACCTCCTCATATGGTTTCGTA 15 63 0 CTCGAACCCTCCTCTTCGTCTTTTCTG 16 7 1 ACCAAAGAAACCTTTTCATCACAGAAAGGT 17 77 1 GAAAGGTGAACCTCTTCACTTTTTTCACAA 17 100 1 TGAAATATCCCTCCTCCTGTGTTAATA 17 146 0 CTGACCGGGGGCTTTTCTTTTGGCTGGGGC 18 24 1 ACTTCACACCTCCTCTTTTCAAGATTAT 20 64 0 CGCCTCCTGATAGAATTATATC 21 2 1 AGATCAAACCTCCCTTCTTCACTTCTATCG 22 37 0 GTCCTCCACCTCCTGTTAAAATTGTACA 23 22 0 GCAATAACACCTCCGTTATTG 24 3 0 GAGGGGTTCCCCCTCCCTTAACTTGAAAAG 25 26 1 GATCTTTTCCTCCTTTGTTCTTTTCAAGTT 25 45 0 TTGTGGTTAATCTTTTCTTTTTCTTTTTTT 26 57 1 TTTTTTTCAACCTTTTCTTATTCTTGATTT 26 80 1 GTTTTCCCCTCCAAATTAATAGATC 27 5 1 ATTAATAGATCCTTTTCTCTGTCTTCAAGT 27 24 1 GAAATCCCCTGCCTTCGTTTTTGCTGTTGA 28 14 0 CCTCCGCTTCTCCTTTTCTT 29 0 1 CTCCGCTTCTCCTTTTCTTTTTTAGTAATT 29 11 1 CTATCACCACCCTTCTGTTAAATTGTATCA 29 57 0 ********** MAP Score: 14.8761 Motif 3 AAACCGGAAACCTTTCGAAGGGAGGGGTAAG 4 90 1 GGCTCCATTTCTTTTTAATGGAGGGGTGTGA 6 168 1 GATTTCTGAGCTTTTTGAAGGAAGAAAGG 6 224 1 AAAGACTCGATCTTCGGGAGGTTCTGAAACC 7 96 1 TCGAAACGGTTCTTCCGCAGG 10 194 1 TGATTGGAATCTTTTTACAGGAGGAGATT 11 90 1 AAAAACTAACCTTTTGGGAGG 12 17 1 CCCCCGCTTTCTTTCTGGAGGTGATATC 14 22 1 GGGGGCTTTTCTTTTGGCTGGGGCGGGTGGA 18 30 1 TAAGGAAAAATTTTCAGGAGGTGATTTGTT 20 9 0 TGATATAATTCTATCAGGAGGCG 21 2 0 CTCGTGTACAATTTTAACAGGAGGTGGAGGA 23 18 1 ATTTCCCTGCCTTTTTGCAGGTATAATGAAA 28 39 1 ***** ***** MAP Score: 13.8919 Motif 4 AACTTTCGGGGAGGGGTTCCCCCTCCCTTAACT 25 16 1 TGTGAAAAACGACGGATTCGAACGAAATATGTG 8 21 0 GGCTGGGGCGGGTGGATTCGAACCACCGATCGC 18 45 1 AGGCGGGGGTCTCCCCCGCTTTCTTTC 14 4 1 GCTGGCTTCCTCCCTTGAAGGAG 18 155 0 GGAGCCAGCGGTGGGACTCGAACCCACAACCTG 6 141 0 GTCAATCCAGGGGGCATACGCCCCCTTTTATTT 19 21 1 GTTGAGCTACGCTGGCCTCCCTCTGGTTTCTAT 6 82 0 CTCCCTTGAAGGAGCTTTCCTACAGTGGTAAAA 18 136 0 CGCCATTCGTGTTGGGTACGTTCAAACGTGGGT 9 13 1 CGGGAATTACGAAGCTTACGAACATGCATCCAA 10 105 0 CGCCTTACCGCTTGGCCACGCCCCAACCCTTTC 18 93 1 CCCCCGGTCAGGGGGCTTTGTTCTT 18 2 0 CCGGCAGAGCGGCGCATTCGTAATGCGCAGGTT 6 114 1 CACCTCCTCATATGGTTTCGTACGTGACGAGCT 15 52 0 * ** ******* MAP Score: 11.2615 Motif 5 CAATATTTGTCCAGAAATATACTTGATTTAACA 0 92 1 CTGATAATTTCCAGAAATATTTTACCAGAATCC 3 73 1 GTCTAAGAAACCGGAAACCTTTCGAAGGGAGGG 4 83 1 TTCAAATTCGTCGGAAATGCTTCACACCCCTCC 6 187 0 TTCAAAAAGCTCAGAAATCTTTCTTCAAATTCG 6 210 0 CACTTCACCTCCTCATATGGTTTCGTACGTGAC 15 57 0 AAAGACCGAACCAGAAATAATTCGCTTAGCGAT 16 63 1 GCTGCGCAGTCCACAAAAAATTCACAGGAGGTG 16 174 1 TTCTTTCCTTCCTCATATATTTTTGCACAAAAA 19 51 0 CAAATCACCTCCTGAAAATTTTTCCTTATCTAT 20 12 1 CGTTCAAGGCCCTGATATAATTCTATCAGGAGG 21 12 0 CTTTCTATTTCCAGATAATCACCTGTAATTGTC 26 18 0 AAAAGATTAACCACAAATAAATCTTTCTATTTC 26 40 0 ** ***** *** MAP Score: 8.00729 Motif 6 TGGTTTCTCATTTTTTCACAAACTATCCTT 0 9 0 ACATGCAATATTTGTCCAGAAATATACTTGA 0 87 1 CCACTATAAATTTTTCCAAAAATCTTATTGG 3 21 0 TCCAGAAATATTTTACCAGAATCCGGGGGAG 3 82 1 ATTTCTGAGCTTTTTGAAGGAAGAAAGG 6 225 1 AGCCCAGTTTTTTGTCAAGGAGGTTTTTATT 7 10 0 AATACTACCATTTGTGGAGGATAAAATCAAG 7 47 1 GATTGGAATCTTTTTACAGGAGGAGATT 11 91 1 TGGTTCGGTCTTTTTTCAGACGTAAGGTATA 16 45 0 ACCTCTTCACTTTTTTCACAAAAGCCTTTGT 17 109 1 TCCTCATATATTTTTGCACAAAAATAAAAGG 19 44 0 GATAAGGAAAAATTTTCAGGAGGTGATTTGT 20 11 0 TCCTGTTAAAATTGTACACGAGGAGGTGAA 23 9 0 TTTCCCTGCCTTTTTGCAGGTATAATGAAAT 28 40 1 GAGTGATACAATTTAACAGAAGGGTGGTGAT 29 54 1 ***** ***** MAP Score: 5.71272 Motif 7 TAAATGTATGAAAAGGAGGAATATCGTTT 0 169 1 GAGATGAGGAGGGAAAAGAG 1 0 1 AAACTGTTGCCAGGAGGAGAAAGAA 2 13 1 AAATCTTATTGGGGTGATGATTC 3 3 0 TACCAGAATCCGGGGGAGAAAGGC 3 95 1 TCGGGAAACCAGGAGGTAGAAAGG 4 4 0 AACCTTTCGAAGGGAGGGGTAAGAG 4 98 1 TATTAACATTGAGGGGAGGTTCT 5 3 0 AGATCACCAAAGGGGGCTGTATTAACATTG 5 22 0 CCCTCCACCGGAGGGGGAAAGATCACCAAA 5 41 0 CCCCCTCCGGTGGAGGGGGATTTTTTGATA 5 54 1 AAAAAGACCGGGAGGGAAGATC 6 2 0 AATAGAAACCAGAGGGAGGCCAGCGTAGCT 6 81 1 TCTTTTTAATGGAGGGGTGTGAAGCATTTC 6 177 1 AGAGCTAGAAAGGAAGGTGAAAACTGAATT 9 68 1 AATCTTTTTACAGGAGGAGATT 11 97 1 CTTTTAATTAAGGGGAGGCGAATGTT 13 9 1 AGGCGGGGGTCTCCCCCGCT 14 0 1 TCCAGAAAGAAAGCGGGGGAGACCCCCGCC 14 11 0 GAAACCATATGAGGAGGTGAAGTGGT 15 66 1 AAAGACGAAGAGGAGGGTTCGAG 16 3 0 AAAAATTCACAGGAGGTGTTATC 16 189 1 AACGATCTGGAGGTGGTGGATATGGTATCG 17 12 0 TATTAACACAGGAGGAGGGATATTTCA 17 146 1 GGAAAGGGTTGGGGCGTGGCCAAGCGGTAA 18 97 0 AAAGCTCCTTCAAGGGAGGAAGCCAGC 18 151 1 CCGTCAATCCAGGGGGCATACGCCCCCTTT 19 19 1 GCACAAAAATAAAAGGGGGCGTATGCCCCC 19 30 0 AAAATATATGAGGAAGGAAAGAACAGGACA 19 61 1 TAATCTTGAAAAGAGGAGGTGTGAAGT 20 65 1 GCCTTGAACGAGAAGGAGGAGTAGAAATCC 21 35 1 TAGAAGTGAAGAAGGGAGGTTTGATCTACT 22 40 1 CAATTTTAACAGGAGGTGGAGGAC 23 26 1 TGGAACTTTCGGGGAGGGGTTCCCCCTCCC 25 13 1 TTCAAGTTAAGGGAGGGGGAACCCCTCCCC 25 23 0 TTGAAAAGAACAAAGGAGGAAAAGATCGAA 25 48 1 TGACACCAGTAGAGGGGGGATTTTC 26 139 1 CTATTAATTTGGAGGGGAAAAC 27 2 0 GCAAAAACGAAGGCAGGGGATTTCCCTGCC 28 20 1 CAATTTAACAGAAGGGTGGTGATAGC 29 62 1 ********** MAP Score: 5.27549 Motif 8 AAGGATAGTTTGTGAAAAAATGAGAAACC 0 8 1 CCCAATAAGATTTTTGGAAAAATTTATAGTG 3 20 1 ATTTCTGAGCTTTTTGAAGGAAGAAAGG 6 225 1 AATACTACCATTTGTGGAGGATAAAATCAAG 7 47 1 CCCCGCTTTCTTTCTGGAGGTGATATC 14 23 1 CTCTTCGTCTTTTCTGTTGAAAATTATACCT 16 21 1 CACAAAGGCTTTTGTGAAAAAAGTGAAGAGG 17 110 0 CACAAAAGCCTTTGTGTAGTATATTAACACA 17 125 1 CCCTTTTATTTTTGTGCAAAAATATATGAGG 19 43 1 GAAAGATTTATTTGTGGTTAATCTTTTCTTT 26 46 1 TTTCCCTGCCTTTTTGCAGGTATAATGAAAT 28 40 1 ****** **** MAP Score: 3.59828