AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_operons007_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944251875 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0278 300 sugar ABC transporter, permease protein #1 TM0280 188 hypothetical protein #2 TM0281 21 alpha-L-arabinofuranosidase #3 TM0282 28 aldose 1-epimerase #4 TM0511 109 conserved hypothetical protein #5 TM0571 113 heat shock serine protease, periplasmic #6 TM0572 96 lipopolysaccharide biosynthesis protein, putative #7 TM0579 243 conserved hypothetical protein #8 TM0607 144 hypothetical protein #9 TM0619 116 conserved hypothetical protein #10 TM0620 300 lipopolysaccharide biosynthesis protein #11 TM0622 88 lipopolysaccharide biosynthesis protein, putative #12 TM0623 205 hypothetical protein #13 TM0624 109 N-acetylglucosaminyl-phosphatidylinositol biosynthesis-related protein #14 TM0627 28 lipopolysaccharide biosynthesis protein #15 TM0632 26 extracellular polysaccharide biosynthesis-related protein #16 TM0633 40 flagellar-related protein #17 TM0636 82 hypothetical protein #18 TM0637 202 hypothetical protein #19 TM0667 163 conserved hypothetical protein #20 TM0751 168 uridine kinase-related protein #21 TM0752 89 alpha-glucosidase, putative #22 TM0755 111 conserved hypothetical protein #23 TM0757 107 hypothetical protein #24 TM0758 159 flagellin #25 TM0862 82 glucose-1-phosphate thymidylyltransferase #26 TM0888 55 conserved hypothetical protein #27 TM0889 64 conserved hypothetical protein #28 TM1034 40 UDP-N-acetylglucosamine 2-epimerase #29 TM1196 21 oligopeptide ABC transporter, ATP-binding protein #30 TM1198 69 oligopeptide ABC transporter, permease protein #31 TM1199 154 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #32 TM1203 60 maltose ABC transporter, permease protein #33 TM1204 300 maltose ABC transporter, periplasmic maltose-binding protein #34 TM1403 135 antibiotic ABC transporter, ATP-binding protein, putative #35 TM1405 79 lipopolysaccharide biosynthesis protein-related protein #36 TM1547 78 conserved hypothetical protein Motif 1 CAAAAAATTCACAGGAGGTGTTATC 18 187 1 TACAATTTTAACAGGAGGTGGAGGAC 28 24 1 GAATCTTTTTACAGGAGGAGATT 13 96 1 GTATATTAACACAGGAGGAGGGATATTTCA 19 143 1 TATCTACCCGCAAGGAGGTGAAGGTGGT 33 282 1 GGAAAAATTTTCAGGAGGTGATTTGTT 25 7 0 AATCTTGAAAAGAGGAGGTGTGAAGT 25 66 1 AAAACTGTTGCCAGGAGGAGAAAGAA 3 12 1 TATAATTCTATCAGGAGGCG 26 0 0 AAATTGTACACGAGGAGGTGAA 28 2 0 TCTTGGAAAATAAGGAGGTGAAGAGGGGGC 0 262 1 ATCCCCCTCCACCGGAGGGGGAAAGATCAC 6 45 0 CAATAACGGAGGTGTTATTGC 29 4 1 TTTTCAAGTTAAGGGAGGGGGAACCCCTCC 30 25 0 AAACCTTTCGAAGGGAGGGGTAAGAG 5 97 1 CGAAACCATATGAGGAGGTGAAGTGGT 17 65 1 AGAATACTCACACGGAGGTGAGTAGGTC 24 141 1 CACAAAAATAAAAGGGGGCGTATGCCCCCT 23 29 0 CTTTTAATTAAGGGGAGGCGAATGTT 15 10 1 AGTCGGGAAACCAGGAGGTAGAAAGG 5 6 0 TCCCTAATTTAATGGAGGTGTCTCTGT 22 94 1 AAGGAGGTGAAGAGGGGGCGCTCTGCCCCC 0 273 1 ATGGAACTTTCGGGGAGGGGTTCCCCCTCC 30 12 1 CCGCTTTCTTTCTGGAGGTGATATC 16 25 1 AATCAAACGATCTGGAGGTGGTGGATATGG 19 17 0 ATTTCTTTTTAATGGAGGGGTGTGAAGCAT 7 174 1 AGTTTTTTGTCAAGGAGGTTTTTATT 8 6 0 AAATGTATGAAAAGGAGGAATATCGTTT 1 170 1 TGAAAAGAACAAAGGAGGAAAAGATCGAAC 30 49 1 CTTTTGACTCTATGGAGGTGTCAGAG 34 119 1 TCCAAAAAGACCGGGAGGGAAGATC 7 5 0 AGAAGTGAAGAAGGGAGGTTTGATCTACTT 27 41 1 CACCGTCAATCCAGGGGGCATACGCCCCCT 23 17 1 GAAAAGACGAAGAGGAGGGTTCGAG 18 5 0 CCTTGAACGAGAAGGAGGAGTAGAAATCC 26 36 1 GACTCGATCTTCGGGAGGTTCTGAAACCGT 8 99 1 GGCAAAAGGGGGCAGAGCGCCCCC 0 286 0 TCCATACGTTCAGGGAGGGAAAACA 32 45 1 AAGCTCCTTCAAGGGAGGAAGCCAGC 20 152 1 CAATACCAAGCAAGGAGGATCCCT 10 286 1 ATTAACATTGAGGGGAGGTTCT 6 2 0 GATATCATTGAGACGAGGTGATATCG 6 80 1 TTTACCAGAATCCGGGGGAGAAAGGC 4 93 1 CCAGAAAGAAAGCGGGGGAGACCCCCGCCT 16 10 0 AAAGATCACCAAAGGGGGCTGTATTAACAT 6 24 0 GAGATGAGGAGGGAAAAGAGT 2 4 1 ATTATACAACCCAGGAGGTCTTGAAAATTC 7 36 1 GGTAAGGAAAACGCGAGGAGAAAACCTAAA 10 88 0 TGACACCAGTAGAGGGGGGATTTTC 31 139 1 AGAAATATACAACCGAGGTGAGAAA 23 92 1 AAGCCCCCGGTCAGGGGGCTTTGTTCTT 20 8 0 GAATTTAACATAAGGGGGCAGGATC 21 74 1 CACTCCAGGATCCCGAGGTGAGGGCCGCTG 0 57 1 AAAGCTGCGTGCAGGAGGCTTATAAAAAAA 10 142 1 ATTAGGAACTTCTGGGGGTACTTCAC 9 100 1 TCAAGCGACATCCCGAGGAGATTTTCAACG 33 213 0 GATAATCCGAGAGGGAGGCTGGATT 24 5 0 TACTACCATTTGTGGAGGATAAAATCAAGT 8 49 1 ********** MAP Score: 87.2321 Motif 2 TCCCCCGGATTCTGGTAAAATATTTCTGGAA 4 81 0 TCCTCCACCTCCTGTTAAAATTGTACACGAG 28 18 0 TTCCTGTGCGGCTGGTAAAATAGAAACCAGA 7 63 1 TTCACACAAATCTGGTAGAATACTTTAAAGT 9 48 1 CACTCGAAAATATGGTAAAATTACTAAAAAA 36 28 0 CGCCTCCTGATAGAATTATATCAGGG 26 5 1 ATACCTTACGTCTGAAAAAAGACCGAACCAG 18 46 1 AAGGATAGTTTGTGAAAAAATGAGAAACCAT 1 10 1 CTTTTATTTTTGTGCAAAAATATATGAGGAA 23 45 1 ACCTGCAAAAGCTGATAGAATTTTCTCAGGT 21 23 1 TAACGACATGGGTGGTAAAATCTTTCCAGAT 24 32 0 ATTACAATATATGAAAAAATTCACATAGTT 22 9 1 AATCTCCTCCTGTAAAAAGATTCCAATCA 13 90 0 TTTCATTATACCTGCAAAAAGGCAGGGAAAT 35 39 0 ATTTATAGTGGATGATAAAATTAAGTAAGGT 4 41 1 TCACCACCCTTCTGTTAAATTGTATCACTCG 36 53 0 CAAAGGCTTTTGTGAAAAAAGTGAAGAGGTT 19 108 0 ATCAATCAAGCATGATAGAATAGATAAGGAA 25 33 0 CCTTACATTTTCTGCTATAATCACTTTGGAA 22 63 1 CAATAAGATTTTTGGAAAAATTTATAGTGGA 4 22 1 CCTGCCCCCTTATGTTAAATTCGTTTCTGAG 21 65 0 CAACCCTTTCCGTGCTATAATTTTACCACTG 20 116 1 **** ****** MAP Score: 14.8619 Motif 3 GGTTCTGATAATTTCCAGAAATATTTTACCA 4 69 1 GGGTTGTATAATATCCAAAAAGACCGGGAGG 7 17 0 CATGCAATATTTGTCCAGAAATATACTTGAT 1 88 1 CACTATAAATTTTTCCAAAAATCTTATTGGG 4 20 0 GATATCACCTCCAGAAAGAAAGCGGGG 16 23 0 ATCGACTTTTACGTCCAGAAAACGAATATTT 33 159 0 CCTTTTATTTTTGTGCAAAAATATATGAGGA 23 44 1 ATTTCATTATACCTGCAAAAAGGCAGGGAAA 35 40 0 CGTCTCAATGATATCAAAAAATCCCCCTCCA 6 64 0 AGAGCGGGAGTTCTCCAGAGAGGATCTTGGA 0 188 0 AAATCTTTCTATTTCCAGATAATCACCTGTA 31 24 0 TTTCAACGTTATTTCCAAATAATTTCCTGGA 33 190 0 TTTCCGACGAATTTGAAGAAAGATTTCTGAG 7 203 1 GCCGGTGTGGTCTTCCAAAGACTCGATCTTC 8 80 1 ATTACAATATATGAAAAAATTCACATAGT 22 8 1 ACAAAGGCTTTTGTGAAAAAAGTGAAGAGGT 19 109 0 AAGGATAGTTTGTGAAAAAATGAGAAACCA 1 9 1 CTTGATTTTATCCTCCACAAATGGTAGTATT 8 47 0 CACTTCATTAATTTCAAGATAAAGAACTTTT 13 28 1 CCCTCCCTTAACTTGAAAAGAACAAAGGAGG 30 36 1 ATTGATATAATCTTGAAAAGAGGAGGTGTGA 25 58 1 ** ******** MAP Score: 13.1548 Motif 4 TCTCTGGAGAACTCCCGCTCTCCATGGAAACG 0 198 1 CCCCTCTTCACCTCCTTATTTTCCAAGAATCT 0 258 0 GGGGGCAGAGCGCCCCCTCTTCACCTCCTTAT 0 271 0 ACTCTTTTCCCTCCTCATCTC 2 0 0 TTCTTTCTCCTCCTGGCAACAGTTTTT 3 11 0 GCCTTTCTCCCCCGGATTCTGGTAAAATA 4 90 0 CTCTTACCCCTCCCTTCGAAAGGTTTC 5 96 0 AGAACCTCCCCTCAATGTTAATACAGCC 6 6 1 AATGTTAATACAGCCCCCTTTGGTGATCTTTC 6 23 1 TGGTGATCTTTCCCCCTCCGGTGGAGGGGGAT 6 43 1 CGATATCACCTCGTCTCAATGATATCA 6 79 0 GATCTTCCCTCCCGGTCTTTTTGGATATT 7 7 1 GCTACGCTGGCCTCCCTCTGGTTTCTATTTTA 7 78 0 GTTTAGGTTTTCTCCTCGCGTTTTCCTTACCA 10 87 1 GTTTTCCTTACCATCTGGCTTCATCTTTCAAG 10 106 1 AGGGATCCTCCTTGCTTGGTATTGAAAT 10 282 0 AATTCAGTTTTCACCTTCCTTTCTAGCTCTAT 11 66 0 AATCTCCTCCTGTAAAAAGATTCC 13 95 0 AACATTCGCCTCCCCTTAATTAAAAG 15 9 0 AGGCGGGGGTCTCCCCCGCTTTCTTTCTGGA 16 9 1 CACTTACGTTTCCGCTCAGCTCGTCACGTACG 17 35 1 ACCACTTCACCTCCTCATATGGT 17 69 0 CTCGAACCCTCCTCTTCGTCTTTTCTGTT 18 7 1 GATAACACCTCCTGTGAATTTTTTGT 18 186 0 GAAAGGTGAACCTCTTCACTTTTTTCACAAAA 19 100 1 TGAAATATCCCTCCTCCTGTGTTAATATACT 19 142 0 AAGAACAAAGCCCCCTGACCGGGGGCTTTTCT 20 10 1 CCAAAGTCCGCCGCCTTACCGCTTGGCCACGC 20 82 1 GCTGGCTTCCTCCCTTGAAGGAGCTTT 20 151 0 GATCCTGCCCCCTTATGTTAAATTCGTTT 21 70 0 CAGGGGGCATACGCCCCCTTTTATTTTTGTGC 23 28 1 AATCCAGCCTCCCTCTCGGATTATCTGGA 24 7 1 GACCTACTCACCTCCGTGTGAGTATTCTT 24 140 0 ACTTCACACCTCCTCTTTTCAAGATTATAT 25 62 0 GATTTCTACTCCTCCTTCTCGTTCAAGGCCCT 26 32 0 GTAGATCAAACCTCCCTTCTTCACTTCTATCG 27 37 0 GTCCTCCACCTCCTGTTAAAATTGTAC 28 23 0 GGGGAGGGGTTCCCCCTCCCTTAACTTGAAAA 30 23 1 TCGATCTTTTCCTCCTTTGTTCTTTTCAAGTT 30 45 0 TTCTTTTTTTCAACCTTTTCTTATTCTTGATT 31 77 1 GAAAATCCCCCCTCTACTGGTGTCATAGT 31 135 0 TGTTTTCCCTCCCTGAACGTATGGA 32 45 0 ACGTTGAAAATCTCCTCGGGATGTCGCTTGAC 33 212 1 ACCACCTTCACCTCCTTGCGGGTAGATATTAC 33 278 0 GGCAGGGAAATCCCCTGCCTTCGTTTTTGCTG 35 18 0 CCTCCGCTTCTCCTTTTCTTTT 36 0 1 GCTATCACCACCCTTCTGTTAAATTGTATC 36 58 0 ** **** **** MAP Score: 10.5199 Motif 5 AGCTTTTAAACGGAAATATTTGTATCTATTA 1 49 1 ATAAGATTTTTGGAAAAATTTATAGTGGATG 4 24 1 TGATAATTTCCAGAAATATTTTACCAGAATC 4 74 1 TCTAAGAAACCGGAAACCTTTCGAAGGGAGG 5 84 1 TCAAAAAGCTCAGAAATCTTTCTTCAAATTC 7 211 0 AAGACCGAACCAGAAATAATTCGCTTAGCGA 18 64 1 GTTAAAACCAAAGAAACCTTTTCATCACAGA 19 71 1 TCGGATTATCTGGAAAGATTTTACCACCCAT 24 25 1 AGAATAGATAAGGAAAAATTTTCAGGAGGTG 25 17 0 TATCTGGAAATAGAAAGATTTATTTGTGGTT 31 34 1 AAACGAAACACAGAAATATTCGTTTTCTGGA 33 146 1 ****** **** MAP Score: 8.51871 Motif 6 CCGCTGATCCGAGAGTTCCCGCCCTCGAGGTA 0 81 1 CATCACCGTTGAGACCTTCTCCAAGATCCTCT 0 169 1 CCTTCTCCAAGATCCTCTCTGGAGAACTCCCG 0 183 1 CCTCTCTGGAGAACTCCCGCTCTCCATGGAAA 0 196 1 AAAGGGGGCAGAGCGCCCCCTCTTCACCTCCT 0 274 0 AGAACCTCCCCTCAATGTTAATA 6 1 1 CCCCTTTGGTGATCTTTCCCCCTCCGGTGGAG 6 37 1 ATGATATCAAAAAATCCCCCTCCACCGGAGGG 6 56 0 CGATATCACCTCGTCTCAATGAT 6 83 0 GATCTTCCCTCCCGGTCTTTTT 7 0 1 AGGAGGTCTTGAAAATTCCTGTGCGGCTGGTA 7 48 1 AGGGATCCTCCTTGCTTGGTATTGA 10 285 0 TAGTTACTGATATCTCTCCCGCGAACTCATTT 12 56 0 GAAAGCGGGGGAGACCCCCGCCT 16 1 0 GATATCACCTCCAGAAAGAAAG 16 28 0 TTTGTGGACTGCGCAGCCCCTCCAATAAATAA 18 159 0 GATAACACCTCCTGTGAATTTT 18 190 0 TGAAATATCCCTCCTCCTGTGTTAATA 19 146 0 TCCCTTGAAGGAGCTTTCCTACAGTGGTAAAA 20 136 0 GATCCTGCCCCCTTATGTTAAA 21 77 0 TTAAAATCCCTAAAGCCTCTTCCGATTAAAGA 24 76 1 ACTTCACACCTCCTCTTTTCAAGAT 25 67 0 GAAGTAGATCAAACCTCCCTTCTTCACTTCTA 27 40 0 GCAATAACACCTCCGTTATTG 29 7 0 AAGGGAGGGGGAACCCCTCCCCGAAAGTTCCA 30 13 0 GTTCGATCTTTTCCTCCTTTGTTCTT 30 53 0 GAAAATCCCCCCTCTACTGGTG 31 142 0 AAATAACGTTGAAAATCTCCTCGGGATGTCGC 33 207 1 AAAAGGCAGGGAAATCCCCTGCCTTCGTTTTT 35 22 0 ** * ******* MAP Score: 5.78627 Motif 7 GCCCCCTCTTCACCTCCTTATTTTCCAAGAATCT 0 258 0 AACGATATTCCTCCTTTTCATACATTTAGGTACG 1 163 0 ACTCTTTTCCCTCCTCATCTC 2 0 0 TTCTTTCTCCTCCTGGCAACAGTTTTT 3 11 0 AGAACCTCCCCTCAATGTTAATACAG 6 2 1 CGATATCACCTCGTCTCAATGATATCAAAA 6 76 0 GATCTTCCCTCCCGGTCTTTTTGGATATT 7 5 1 TTGTTTAGGTTTTCTCCTCGCGTTTTCCTTACCA 10 85 1 CAACCAGAAGACTCTTTTGCTCTTAGAACAACCG 12 11 0 AACATTCGCCTCCCCTTAATTAAAAG 15 6 0 ACCACTTCACCTCCTCATATGGTTTCGTACG 17 61 0 CTCGAACCCTCCTCTTCGTCTTTTCTGTT 18 5 1 AAACCAAAGAAACCTTTTCATCACAGAAAGGTGA 19 75 1 CAGAAAGGTGAACCTCTTCACTTTTTTCACAAAA 19 98 1 GGGCATACGCCCCCTTTTATTTTTGTGCAAAAAT 23 32 1 TCCTGTTCTTTCCTTCCTCATATATTTTTGCACA 23 55 0 AATCCAGCCTCCCTCTCGGATTATCTGGAAAG 24 8 1 AAATCCCTAAAGCCTCTTCCGATTAAAGATAATG 24 79 1 ACTTCACACCTCCTCTTTTCAAGATTATAT 25 62 0 ATTTCTACTCCTCCTTCTCGTTCAAGGCCCTGAT 26 29 0 GATCAAACCTCCCTTCTTCACTTCTATCGTGACT 27 32 0 TTCACCTCCTCGTGTACAATTTTAAC 28 2 1 GTCCTCCACCTCCTGTTAAAATTGTAC 28 23 0 GGGAGGGGTTCCCCCTCCCTTAACTTGAAAAGAA 30 24 1 ATTTGTGGTTAATCTTTTCTTTTTCTTTTTTTCA 31 55 1 TCTTTTTTTCAACCTTTTCTTATTCTTGATTTTA 31 78 1 GGTCTAAATTTCCCTCTTCGTTCTCTTCGAAACT 33 93 0 TAACGTTGAAAATCTCCTCGGGATGTCGCTTGAC 33 210 1 AAATTAATAGATCCTTTTCTCTGTCTTCAAGTTC 34 22 1 CCTCCGCTTCTCCTTTTCTTTTTTAGTAATTTT 36 9 1 GCTATCACCACCCTTCTGTTAAATTGTATCACT 36 55 0 * ******* * * MAP Score: 4.16976 Motif 8 TTCCAAGAATCTCTTCCCATTTCTTTGCGA 0 240 0 AAACGATATTCCTCCTTTTCATACATTTA 1 169 0 ACTCTTTTCCCTCCTCATCTC 2 3 0 TTCTTTCTCCTCCTGGCAACAGTT 3 14 0 GCCTTTCTCCCCCGGATTCTG 4 98 0 CTCTTACCCCTCCCTTCGAAAGGTTTC 5 96 0 CTTTGGTGATCTTTCCCCCTCCGGTGGAGG 6 40 1 GATCTTCCCTCCCGGTCTTTTT 7 2 1 AGCTACGCTGGCCTCCCTCTGGTTTCTATT 7 81 0 CCTTTCTTCCTTCAAAAAGC 7 233 0 CATTGTTTAGGTTTTCTCCTCGCGTTTTCC 10 83 1 TCAGTTTTCACCTTCCTTTCTAGCTCTATC 11 65 0 CCAGAAGACTCTTTTGCTCTTAGAACAACC 12 12 0 ATCCAACACTTCCTTCTTCTCTTTAGTTAC 12 81 0 GGTCTCCCCCGCTTTCTTTCTGGAGGTGAT 16 17 1 CTCGAACCCTCCTCTTCGTCTTTTCT 18 6 1 TGAAATATCCCTCCTCCTGTGTTAATAT 19 145 0 TGACCGGGGGCTTTTCTTTTGGCTGGGGCG 20 25 1 GCTGGCTTCCTCCCTTGAAGGAGC 20 154 0 GATCCTGCCCCCTTATGTTAAAT 21 76 0 TTTGAAACCGCTTTCCTTACATTTTCTGCT 22 49 1 CCTGTTCTTTCCTTCCTCATATATTTTTGC 23 58 0 AATCCAGCCTCCCTCTCGGATTATCT 24 6 1 TCCTGAAAATTTTTCCTTATCTATTCTATC 25 21 1 GGATTTCTACTCCTCCTTCTCGTTCAAGGC 26 35 0 GGGGAGGGGTTCCCCCTCCCTTAACTTGAA 30 23 1 ATCTTTTCCTCCTTTGTTCTTTTCAAGTTA 30 44 0 TTTTTTCAACCTTTTCTTATTCTTGATTTT 31 81 1 TGTTTTCCCTCCCTGAACGTAT 32 48 0 ACCACCTTCACCTCCTTGCGGGTA 33 286 0 GTTTTCCCCTCCAAATTAAT 34 0 1 AAATCCCCTGCCTTCGTTTTTGCTGTTGAT 35 13 0 AGGGGATTTCCCTGCCTTTTTGCAGGTATA 35 34 1 GCTATCACCACCCTTCTGTTAAATTGTATC 36 58 0 ********** MAP Score: 2.5531 Motif 9 GGAGTGTTGAGATTCTGGCAGGAGCGACGGCG 0 31 0 ACAGGCCAAGGATTCCAGAGGAACCAAGACTC 0 132 1 TATTTTACCAGAATCCGGGGGAGAAAGGC 4 90 1 TATTAGTCGGGAAACCAGGAGGTAGAAAGG 5 8 0 GTGTGTCTAAGAAACCGGAAACCTTTCGAAGG 5 79 1 AATATCCAAAAAGACCGGGAGGGAAGATC 7 7 0 GGATATTATACAACCCAGGAGGTCTTGAAAAT 7 32 1 TGGTAAAATAGAAACCAGAGGGAGGCCAGCGT 7 75 1 GGGAGGTTCTGAAACCGTGGAAATAAAGCGTC 8 111 1 CCTCCAGAAAGAAAGCGGGGGAGACCCCCGCC 16 11 0 CGTCACGTACGAAACCATATGAGGAGGTGAAG 17 56 1 TGAACACCGTCAATCCAGGGGGCATACGCCCC 23 13 1 CATTTACTATGACACCAGTAGAGGGGGGATTT 31 130 1 ATTATTTTATAATCCCAGAGGATATATCTATC 34 80 1 CAGCAAAAACGAAGGCAGGGGATTTCCCTGCC 35 18 1 ** ******** MAP Score: 1.62586