AlignACE 3.0 10/20/99 AlignACE2 -i TP/TP_operons034_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944240097 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TP0319 28 membrane lipoprotein (tmpC) #1 TP0321 75 ribose/galactose ABC transporter, ATP-binding protein (rbsA-2) #2 TP0324 103 T. pallidum predicted coding region TP0324 #3 TP0327 56 cationic outer membrane protein (ompH) #4 TP0328 55 DNA mismatch repair protein (mutS) #5 TP0472 74 excinuclease ABC, subunit C (uvrC) #6 TP0473 64 T. pallidum predicted coding region TP0473 #7 TP0474 140 conserved hypothetical protein #8 TP0475 63 glucose-6-phosphate isomerase (gpi) #9 TP0476 66 acetate kinase (ack) #10 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #11 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #12 TP0479 111 T. pallidum predicted coding region TP0479 Motif 1 TTAGGCGTTTAGCGCGCGCCGTCAAGTTTTT 12 46 1 TGTAGCAAAAAACGCGCCCGGAATACAGAAC 2 71 0 CCGCGGTAATTACGCGGGCCGTGCAATATGC 7 27 1 CTGTGCTTCTTAAGCCCGCGGTAATTACGCG 7 12 1 CCCGTTTTGAAACGGTCCGGGGCTGCGTCCA 3 19 1 TACGTACCGGAACGCGGGCGCCTGATGCTAG 7 91 0 TTCTTTGCAATGAGCACCCGGGTAGGGGGTT 2 43 1 CCGTGCAATATGCGCCAGCGGGACTTGGAGA 7 45 1 ACCGTTTCAAAACGGGCACGGAACG 3 4 0 CTTGGAGAAAAGCGCACACCGTGCTAGCATC 7 68 1 AAATTACCAAAACGGTGGAGGTGTATT 9 49 1 TTTCGCCGTATGCGGTGCCCCG 6 52 1 TCGCCCATCAAAAGTGCGCCGCT 6 2 0 TGCACCGTGAGCACCGCGTCTCCTGCCT 4 7 1 ACCGCGGGTATGCGTTCGCCCATCAAAAGTG 6 17 0 ACGACACTAGAACGTAGCGGGAGAGAGGAGG 10 29 1 GCGTGTATGCTACGGTGTCCGAGAAATTACC 9 26 1 CACCGTTGAAAGAAGGGGCGGTTT 11 58 1 AACAGCCGGCGATATGTCTGT 8 0 1 GTAATGAACTTGAGGGAGGGGCT 1 62 1 GCCTTTAGAAAAAGGAGGAGCTC 12 2 0 TAGAACGATAAAAGGAGAACGCGCA 8 48 1 ***** ***** MAP Score: 26.0185 Motif 2 AGTGGGGCGTGTGTCTCGACCCGCCCGTGGTCAGTGGGTAT 1 5 1 GGTATGGGGACGTCCAGTAATGAACTTGAGGGAGGGGCT 1 46 1 CCCCTACCCGGGTGCTCATTGCAAAGAATAGGTGCCACCCAACTCA 2 25 0 GTATTCCGGGCGCGTTTTTTGCTACACTTAGCGGGCT 2 76 1 CGTTCCGTGCCCGTTTTGAAACGGTCCGGGGCTGCGTCCAC 3 5 1 GTGGACGCTCCTGGGCCAACACGTAGGAGGCAGGAGACGCG 4 24 0 CGGGGCACCGCATACGGCGAAAGATCACCGCGGGTATGCGTTCG 6 30 0 GCGGTAATTACGCGGGCCGTGCAATATGCGCCAGCGGGACTTGGAG 7 29 1 TGGAGAAAAGCGCACACCGTGCTAGCATCAGGCGCCCGCGTTCCGG 7 70 1 CCCTAATGCCCGAAAATGTACGTACCGGAACGCGGGCGCCTGATGC 7 94 0 TACCCCGTAGGGTTTACCTACAGACATATCGCCGGCTGTT 8 4 0 CTACGGTGTCCGAGAAATTACCAAAACGGTGGAGGTGTATT 9 35 1 TTCAACGGTGCGACCTACACCGGATGTGCCGCAGGCAGACTCTCCG 11 22 0 ATAATTGCCTCGCAGCCTTTAGAAAAAGGAGGAGCTC 12 1 0 AAGGCTGCGAGGCAATTATTAGGCGTTTAGCGCGCGCCGTCAAGTT 12 28 1 *** * * ** *** MAP Score: 24.8104 Motif 3 TTTGTCGATAAAGGGGGGAGGATTCTT 0 11 1 ACCCACTGACCACGGGCGGGTCGAGACACAC 1 18 0 AATGAACTTGAGGGAGGGGCT 1 64 1 AATGAGCACCCGGGTAGGGGGTTCTGTATTC 2 51 1 TGTAGCAAAAAACGCGCCCGGAATACAGAAC 2 71 0 ACCGTTTCAAAACGGGCACGGAACG 3 4 0 CCCGTTTTGAAACGGTCCGGGGCTGCGTCCA 3 19 1 CGTAGGAGGCAGGAGACGCGGTGCTCACGGT 4 13 0 CCTGGGCCAACACGTAGGAGGCAGGAGACGC 4 25 0 TCGCCCATCAAAAGTGCGCCGCT 6 2 0 CGGGGCACCGCATACGGCGAAAGATCACC 6 45 0 CCGCGGGCTTAAGAAGCACAGAC 7 2 0 CCGCGGTAATTACGCGGGCCGTGCAATATGC 7 27 1 CTTGGAGAAAAGCGCACACCGTGCTAGCATC 7 68 1 CGTACCGGAACGCGGGCGCCTGATGCTAGCA 7 89 0 AGTGTCGTTCAAGGCTCGGCATTACCG 10 6 0 ACGACACTAGAACGTAGCGGGAGAGAGGAGG 10 29 1 TGCCTTAGGGAGCGGAGAGTCTGCCTG 11 6 1 GCACCGTTGAAAGAAGGGGCGGTTT 11 57 1 CCTTTAGAAAAAGGAGGAGCTC 12 1 0 CCTTTTTCTAAAGGCTGCGAGGCAATTATTA 12 18 1 TTAGGCGTTTAGCGCGCGCCGTCAAGTTTTT 12 46 1 TCCTCTTCGCAAGGAAGGGGGGAGGGC 12 94 1 **** ****** MAP Score: 20.6381 Motif 4 AAGAATCCTCCCCCCTTTATCGACAAAC 0 6 0 ACCCACTGACCACGGGCGGGTCGAGACACACGCCC 1 14 0 AGCCCCTCCCTCAAGTTCATTACTGGA 1 58 0 CTTTGCAATGAGCACCCGGGTAGGGGGTTCTGTAT 2 45 1 TTCTGTATTCCGGGCGCGTTTTTTGCTACACTTAG 2 72 1 CGTTCCGTGCCCGTTTTGAAACGGTCCG 3 3 1 GCCTGGTGGACGCAGCCCCGGACCGTTTCAAAACG 3 21 0 AGCACCGCGTCTCCTGCCTCCTACGTGTTGGCCCA 4 19 1 CACGCGCAGAAGCATGCCGGCTTATTTTGGTT 5 7 0 GGCGAAAGATCACCGCGGGTATGCGTTCGCCCATC 6 24 0 CGGGGCACCGCATACGGCGAAAGATCACCGCGG 6 41 0 GCGCATATTGCACGGCCCGCGTAATTACCGCGGGC 7 25 0 GTGCAATATGCGCCAGCGGGACTTGGAGAAAAGCG 7 47 1 TGGAGAAAAGCGCACACCGTGCTAGCATCAGGCGC 7 70 1 CGTACCGGAACGCGGGCGCCTGATGCTAGCACGGT 7 85 0 AATACACCTCCACCGTTTTGGTAATTTCTCGG 9 44 0 CTGCCTGCGGCACATCCGGTGTAGGTCGCACCGTT 11 30 1 AGGCGTTTAGCGCGCGCCGTCAAGTTTTTCTCACC 12 48 1 GCCCTCCCCCCTTCCTTGCGAAGAGGAG 12 93 0 **** ***** * MAP Score: 12.738 Motif 5 CCCACTGACCACGGGCGGGTCGAGACACAC 1 18 0 TAATGAACTTGAGGGAGGGGCT 1 63 1 TCTTTGCAATGAGCACCCGGGTAGGGGGTT 2 44 1 GTAGCAAAAAACGCGCCCGGAATACAGAAC 2 71 0 CCGTTTTGAAACGGTCCGGGGCTGCGTCCA 3 20 1 TCCTTGCCTGGTGGACGCAGCCCCGGACCG 3 31 0 TGCACCGTGAGCACCGCGTCTCCTGCCT 4 8 1 CAACACGTAGGAGGCAGGAGACGCGGTGCT 4 19 0 AACCAAAATAAGCCGGCATGCTTCT 5 5 1 GTTTTTCCTGTCACGCGCAGAAGCATGCCG 5 23 0 CGCCCATCAAAAGTGCGCCGCT 6 2 0 CCGCGGGTATGCGTTCGCCCATCAAAAGTG 6 17 0 GGGCGAACGCATACCCGCGGTGATCTTTCG 6 27 1 CGGGGCACCGCATACGGCGAAAGATCACC 6 45 0 CTGTGCTTCTTAAGCCCGCGGTAATTACGC 7 12 1 CGCATATTGCACGGCCCGCGTAATTACCGC 7 29 0 CGTGCAATATGCGCCAGCGGGACTTGGAGA 7 46 1 TTGGAGAAAAGCGCACACCGTGCTAGCATC 7 69 1 CACCGTGCTAGCATCAGGCGCCCGCGTTCC 7 84 1 ACATTTTCGGGCATTAGGGGAAAGATCTC 7 121 1 AACAGCCGGCGATATGTCTGT 8 1 1 TGCCTTAGGGAGCGGAGAGTCTGCC 11 5 1 CGCACCGTTGAAAGAAGGGGCGGTTT 11 56 1 GCCTTTAGAAAAAGGAGGAGCTC 12 3 0 ATTAGGCGTTTAGCGCGCGCCGTCAAGTTT 12 45 1 TCCTCTTCGCAAGGAAGGGGGGAGGGC 12 94 1 ********** MAP Score: 9.20098 Motif 6 TTGTCGATAAAGGGGGGAGGATTCTT 0 12 1 AGTGGGGCGTGTGTCTCGACCC 1 2 1 CCCACTGACCACGGGCGGGTCGAGACACAC 1 18 0 AATGAACTTGAGGGAGGGGCT 1 64 1 AGAACCCCCTACCCGGGTGCTCATTGCAAA 2 46 0 GTAGCAAAAAACGCGCCCGGAATACAGAAC 2 71 0 CGTTCCGTGCCCGTTTTGAAACGG 3 4 1 CCGTTTTGAAACGGTCCGGGGCTGCGTCCA 3 20 1 CTGGGCCAACACGTAGGAGGCAGGAGACGC 4 25 0 GTGGACGCTCCTGGGCCAACACGT 4 41 0 TCACGATTCTTGGTGGGGGCATGACCC 5 57 1 CGCCCATCAAAAGTGCGCCGCT 6 2 0 GCGAACGCATACCCGCGGTGATCTTTCGCC 6 29 1 TCGCCGTATGCGGTGCCCCG 6 54 1 CGCGTAATTACCGCGGGCTTAAGAAGCACA 7 13 0 CGCGGTAATTACGCGGGCCGTGCAATATGC 7 28 1 TCTCCAAGTCCCGCTGGCGCATATTGCACG 7 46 0 TGCTAGCATCAGGCGCCCGCGTTCCGGTAC 7 89 1 AATTACCAAAACGGTGGAGGTGTATT 9 50 1 CGACACTAGAACGTAGCGGGAGAGAGGAGG 10 30 1 CGTTGAAAGAAGGGGCGGTTT 11 61 1 ATTAGGCGTTTAGCGCGCGCCGTCAAGTTT 12 45 1 CCTCTTCGCAAGGAAGGGGGGAGGGC 12 95 1 ********** MAP Score: 7.89701 Motif 7 AAGAATCCTCCCCCCTTTATCGACAAA 0 11 0 GTGTGTCTCGACCCGCCCGTGGTCAGTGGGT 1 18 1 TCTTTGCAATGAGCACCCGGGTAGGGGGTTC 2 44 1 GTTCTGTATTCCGGGCGCGTTTTTTGCTACA 2 71 1 CGTTCCGTGCCCGTTTTGAAACGGT 3 4 1 CCGTTTTGAAACGGTCCGGGGCTGCGTCCAC 3 20 1 ATCACTCCTTGCCTGGTGGACGCAGCC 3 39 0 AGGAGACGCGGTGCTCACGGTGCA 4 3 0 GTGGACGCTCCTGGGCCAACACGTA 4 40 0 AACTGTTTTTCCTGTCACGCGCAGAAGCATG 5 26 0 TGTGCTTCTTAAGCCCGCGGTAATTACGCGG 7 13 1 GCGCATATTGCACGGCCCGCGTAATTACCGC 7 29 0 CGTGCAATATGCGCCAGCGGGACTTGGAGAA 7 46 1 TTGGAGAAAAGCGCACACCGTGCTAGCATCA 7 69 1 GTACCGGAACGCGGGCGCCTGATGCTAGCAC 7 88 0 TGGTAATTTCTCGGACACCGTAGCATACACG 9 27 0 AATACACCTCCACCGTTTTGGTAATT 9 50 0 AACATCCTCCTCTCTCCCGCTACGTTCTAGT 10 34 0 CAGGCAGACTCTCCGCTCCCTAAGGCA 11 6 0 AGTCTGCCTGCGGCACATCCGGTGTAGGTCG 11 27 1 ATCCGGTGTAGGTCGCACCGTTGAAAGAAGG 11 43 1 TAGGCGTTTAGCGCGCGCCGTCAAGTTTTTC 12 47 1 GCCCTCCCCCCTTCCTTGCGAAG 12 98 0 **** ****** MAP Score: 6.0719 Motif 8 AAGAATCCTCCCCCCTTTATCGACAAAC 0 8 0 GGGCGTGTGTCTCGACCCGCCCGTGGTCAGTGG 1 14 1 TCAGTGGGTATGGGGACGTCCAGTAATGAACTT 1 40 1 AGCCCCTCCCTCAAGTTCATTACTG 1 60 0 ATACAGAACCCCCTACCCGGGTGCTCATTGCAA 2 47 0 CGTTCCGTGCCCGTTTTGAAACGGTCCG 3 5 1 GGTCCGGGGCTGCGTCCACCAGGCAAGGAGTGA 3 32 1 GGAGACGCGGTGCTCACGGTGCA 4 0 0 AGCACCGCGTCTCCTGCCTCCTACGTGTTGGCC 4 19 1 GGGTCATGCCCCCACCAAGAATCGTGAAA 5 55 0 CGGGTATGCGTTCGCCCATCAAAAGTGCGCCGC 6 11 0 CCGCGGTGATCTTTCGCCGTATGCGGTGCCCCG 6 41 1 GCGGTAATTACGCGGGCCGTGCAATATGCGCCA 7 29 1 GCGCACACCGTGCTAGCATCAGGCGCCCGCGTT 7 79 1 TAGCATCAGGCGCCCGCGTTCCGGTACGTACAT 7 92 1 TACGTACATTTTCGGGCATTAGGGGAAAGATCT 7 116 1 AATACACCTCCACCGTTTTGGTAATTTCTC 9 46 0 ACATCCTCCTCTCTCCCGCTACGTTCTAGTGTC 10 31 0 AGGCAGACTCTCCGCTCCCTAAGGCA 11 3 0 GCGGAGAGTCTGCCTGCGGCACATCCGGTGTAG 11 21 1 AGGCGTTTAGCGCGCGCCGTCAAGTTTTTCTCA 12 48 1 CGTCAAGTTTTTCTCACCGTTTGGCATACTCCT 12 65 1 GCCCTCCCCCCTTCCTTGCGAAGAGG 12 95 0 **** ***** * MAP Score: 5.01714 Motif 9 TTTGTCGATAAAGGGGGGAGGATTCTT 0 11 1 GGGTCGAGACACACGCCCCACT 1 2 0 CGTGTGTCTCGACCCGCCCGTGGTCAGTGG 1 17 1 TAATGAACTTGAGGGAGGGGCT 1 63 1 TTTTTGGAAGAAGGGTGAGTTGGGTGGCA 2 9 1 TGCAATGAGCACCCGGGTAGGGGGTTCTGT 2 48 1 GGTTCTGTATTCCGGGCGCGTTTTTTGCTA 2 70 1 TTCAAAACGGGCACGGAACG 3 0 0 GCCCGTTTTGAAACGGTCCGGGGCTGCGTC 3 18 1 TGCACCGTGAGCACCGCGTCT 4 1 1 CACGTAGGAGGCAGGAGACGCGGTGCTCAC 4 16 0 GTTTTTCCTGTCACGCGCAGAAGCATGCCG 5 23 0 TGTGCTTCTTAAGCCCGCGGTAATTACGCG 7 13 1 CGCGGTAATTACGCGGGCCGTGCAATATGC 7 28 1 CCTGATGCTAGCACGGTGTGCGCTTTTCTC 7 72 0 TACGTACCGGAACGCGGGCGCCTGATGCTA 7 92 0 AACAGCCGGCGATATGTCTGT 8 1 1 GTCTGTAGGTAAACCCTACGGGGTAGAACG 8 25 1 GAAAGTGGCGCATTTTGCGT 9 0 1 GAAATTACCAAAACGGTGGAGGTGTATT 9 48 1 TAGTGTCGTTCAAGGCTCGGCATTACCG 10 8 0 ACACTAGAACGTAGCGGGAGAGAGGAGGAT 10 32 1 TGCCTTAGGGAGCGGAGAGTCTGCCTGCG 11 9 1 CCCCTTCTTTCAACGGTGCGACCTACACCG 11 46 0 ACCGTTGAAAGAAGGGGCGGTTT 11 59 1 TCCTTTTTCTAAAGGCTGCGAGGCAATTAT 12 17 1 TAGGCGTTTAGCGCGCGCCGTCAAGTTTTT 12 47 1 GGAGTATGCCAAACGGTGAGAAAAACTTGA 12 67 0 TCTTCGCAAGGAAGGGGGGAGGGC 12 97 1 ********** MAP Score: 4.84928 Motif 10 TACCCACTGACCACGGGCGGGTCGAGACACACGCCCCACT 1 4 0 TGTATTCCGGGCGCGTTTTTTGCTACACTTAGCGGGCT 2 75 1 CGTTCCGTGCCCGTTTTGAAACGGTCCGGGGCTGCGTCCACCAG 3 8 1 TGCACCGTGAGCACCGCGTCTCCTGCCTCCTACGTGT 4 1 1 GCATGCTTCTGCGCGTGACAGGAAAAACAGTTTCACGATTCTTGGT 5 25 1 GAACGCATACCCGCGGTGATCTTTCGCCGTATGCGGTGCCCCG 6 31 1 GTCTGTGCTTCTTAAGCCCGCGGTAATTACGCGGGCCGTGCA 7 6 1 AGCACGGTGTGCGCTTTTCTCCAAGTCCCGCTGGCGCATATTGCAC 7 47 0 CATCAGGCGCCCGCGTTCCGGTACGTACATTTTCGGGCATTAGGGG 7 95 1 GAAAGTGGCGCATTTTGCGTGTATGCTACGGTGTCCGAGAAATTA 9 9 1 AAACCGCCCCTTCTTTCAACGGTGCGACCTACACCGGATGT 11 41 0 GAGCTCCTCCTTTTTCTAAAGGCTGCGAGGCAATTATTAGG 12 5 1 CAAGTTTTTCTCACCGTTTGGCATACTCCTCTTCGCAAGGAAGGGG 12 68 1 ** **** * * * * MAP Score: 3.91719 Motif 11 CCACTGACCACGGGCGGGTCGAGACACACG 1 17 0 TCAGTGGGTATGGGGACGTCCAGTAATGAA 1 40 1 AATGAACTTGAGGGAGGGGCT 1 64 1 CTTTGCAATGAGCACCCGGGTAGGGGGTTC 2 45 1 TTCTGTATTCCGGGCGCGTTTTTTGCTACA 2 72 1 CGTTCCGTGCCCGTTTTGAAACGGT 3 5 1 GGACGCAGCCCCGGACCGTTTCAAAACGGG 3 19 0 CGTGTTGGCCCAGGAGCGTCCAC 4 42 1 GGCGAACGCATACCCGCGGTGATCTTTCGC 6 28 1 GATCTTTCGCCGTATGCGGTGCCCCG 6 48 1 GTGCTTCTTAAGCCCGCGGTAATTACGCGG 7 14 1 GCGGTAATTACGCGGGCCGTGCAATATGCG 7 29 1 GTGCAATATGCGCCAGCGGGACTTGGAGAA 7 47 1 TGGAGAAAAGCGCACACCGTGCTAGCATCA 7 70 1 TACCGGAACGCGGGCGCCTGATGCTAGCAC 7 88 0 TGCCTTAGGGAGCGGAGAGTCTGCCT 11 6 1 AGGCGTTTAGCGCGCGCCGTCAAGTTTTTC 12 48 1 CCTCTTCGCAAGGAAGGGGGGAGGGC 12 95 1 ********** MAP Score: 3.73178 Motif 12 GTTTGTCGATAAAGGGGGGAGGATTCTT 0 10 1 GTAATGAACTTGAGGGAGGGGCT 1 62 1 GGTTCTGTATTCCGGGCGCGTTTTTTGCTAC 2 70 1 CCGTTTTGAAACGGTCCGGGGCTGCGTCCAC 3 20 1 AACCAAAATAAGCCGGCATGCTTCTGCGC 5 8 1 TTCACGATTCTTGGTGGGGGCATGACCC 5 56 1 ACGGCGAAAGATCACCGCGGGTATGCGTTCG 6 30 0 CTGTGCTTCTTAAGCCCGCGGTAATTACGCG 7 12 1 CCGCGGTAATTACGCGGGCCGTGCAATATGC 7 27 1 CCGTGCAATATGCGCCAGCGGGACTTGGAGA 7 45 1 CGTGCTAGCATCAGGCGCCCGCGTTCCGGTA 7 87 1 AACAGCCGGCGATATGTCTGTA 8 1 1 TGCCTTAGGGAGCGGAGAGTCTGCC 11 4 1 CACCGTTGAAAGAAGGGGCGGTTT 11 58 1 TCCTTTTTCTAAAGGCTGCGAGGCAATTATT 12 17 1 TATTAGGCGTTTAGCGCGCGCCGTCAAGTTT 12 44 1 TCTTCGCAAGGAAGGGGGGAGGGC 12 97 1 * ********* MAP Score: 3.56987