AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_operons006_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944251808 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0050 100 iron(II) transport protein A #1 TM0100 50 DNA ligase #2 TM0258 300 DNA topoisomerase #3 TM0266 180 DNA-binding protein, HU #4 TM0270 64 conserved hypothetical protein #5 TM0445 120 conserved hypothetical protein #6 TM0524 209 conserved hypothetical protein #7 TM0526 30 host factor I #8 TM0667 163 conserved hypothetical protein #9 TM0826 127 hypothetical protein #10 TM0828 29 sugar kinase, pfkB family #11 TM0839 54 rod shape-determining protein RodA #12 TM0840 39 hypothetical protein #13 TM0842 37 response regulator #14 TM0926 125 chromosomal replication initiator protein #15 TM1085 60 methionyl-tRNA synthetase #16 TM1095 300 adenylosuccinate lyase #17 TM1241 181 hypothetical protein #18 TM1243 43 phosphoribosylaminoimidazole-succinocarboxamide synthase #19 TM1375 166 spermidine/putrescine ABC transporter, periplasmic spermidine/putrescine-binding protein #20 TM1379 27 seryl-tRNA synthetase #21 TM1440 299 translation initiation factor, eIF-2B alpha subunit-related #22 TM1446 300 conserved hypothetical protein #23 TM1458 125 ribosomal protein L21 #24 TM1463 183 ribonuclease P protein component #25 TM1466 49 conserved hypothetical protein #26 TM1546 78 single stranded DNA-specific exonuclease, putative Motif 1 GAGAGAATAGACACTGTTGAGGAGGAGGTCAGGCAGGA 24 25 1 ATTGAATCAAACGATCTGGAGGTGGTGGATATGGTATC 8 13 0 CTATTTTGAAATCACATCGAGGGGGGAG 7 12 1 GTGCTTTACAACCCTAGAAAGGAGGGGGTTTC 3 158 1 AAAAAGACCGTTCCACCTGAGGTGGAGGGCACCCGACA 5 30 1 GTGTAGCCTGGCTCTCTGGAGGCGGCGGTGGGATTCGA 19 102 0 ACTTATGATAACACAGGAAAGGAGGTAGCACG 4 42 1 ACTGAGGCCAAGAAGGCGGAAGCATTTCAGAG 6 4 1 GGCGTAGCCAAGCGGTCAAAGGCGGGGGTCTGCAAAAT 19 50 1 ATTTTCAAAAAGGGCGGGGAGGCGAGCGT 18 24 1 TTAGGGTAGAATACTATAGAGGTGGGGTT 21 280 1 ATAGATAGGGAAAACAAGGAGGTGACACT 15 41 1 GAAGAAGAATCTTTTTAAGAGGTGGAGGAACTG 2 277 1 TAGAATTGTGATAAGGGGAGGGATAAG 20 4 1 GAGGAGTACAAAAAAATGGTGGAGAAGGAGAGCTCTCA 22 229 1 CTTAGAATAGATCCCGACGAGGTGTTCGGTGGAAGAAT 22 151 1 TTCGAACCCCTCGAGGACGAGGAGAAAGATCAGACTCA 16 31 0 TGGAGGGCACCCGACACCGAGGGGGAACTCACCCCTTC 5 52 1 CTGAACGAGAAGCTCTTAGAGGTGATAGAGA 6 188 1 GAGAATCATTCTCAAAAAAAGGGGGCAGAGCC 0 78 1 CTCCTCACTTTTGACTTCGAGGTGATCGT 10 10 1 AAGAAGAGTTCTCAAGAACAGGAGAAGGAAAGGACGCT 24 142 1 GTGAGCTATCACAACTATCAGGTGGCACTGGAGAAGCA 6 92 1 AAAATTACTAAAAAAGAAAAGGAGAAGCGGAGG 26 55 1 GGGGTTAGAATCAAAAACGAGGTGATGCCTC 9 106 1 CAATGATACCACACACCGGAGGTGAGATTT 15 2 0 TGGCACGCAAGAGAACACCAGGTGGAAGAAGAGTTCTC 24 117 1 ATACAATTTAACAGAAGGGTGGTGATAGC 26 1 0 AAACCTTTTCATCACAGAAAGGTGAACCTCTTCACTTT 8 84 1 GGGGGGCGAAATCATGAAGAGGAGAAGAGATACTGAAG 21 85 0 TTTTAAAACGAAGATTAACTGGGGGGCGAAATCATGAA 21 105 0 TCATGCTAACATACGAGTAAGGAGGGATGCAAG 25 5 0 TGTAGTATATTAACACAGGAGGAGGGATATTTCA 8 139 1 GAGCGCCAGAATCGGGATCTGGAGGTCGCGGGT 17 5 0 TAAAATTAGTGATAAAGGGAGGAGTTCGCA 13 17 1 AATGGAGGACCCCCAAACGAGGAGTGACTGGATTAATT 14 97 0 GTGGAAGTCGAAGAGTACGATGTGGAGGGTTTCGTGCC 22 58 1 * * **** ** ** MAP Score: 42.9807 Motif 2 CTCCTCACTTTTGACTTCGAG 10 0 1 TGCGAACTCCTCCCTTTATCACTAATT 13 20 0 ACGCTCGCCTCCCCGCCCTTTTTGAAAAT 18 24 0 CAATACCTCCCTTCTTCCAATATAAAA 19 149 0 AAAGGTGAACCTCTTCACTTTTTTCACAAAA 8 101 1 AATCCAGTCACTCCTCGTTTGGGGGTCCTCC 14 101 1 CTCCCCCCTCGATGTGATTTC 7 19 0 ACTTCAGTATCTCTTCTCCTCTTCATGATTT 21 84 1 CGTGCTACCTCCTTTCCTGTGTTATCATA 4 45 0 AGTGTCACCTCCTTGTTTTCCCTATCTAT 15 41 0 GTTCAGAACCTCCTTCTTTTTTCTTCACCA 4 9 1 CCTCCGCTTCTCCTTTTCTTTTTTAGTAAT 26 58 0 GAAACCCCCTCCTTTCTAGGGTTGT 3 165 0 GAACTCTCTTCTTTACTTGAAAGT 12 3 1 TCTGATCTTTCTCCTCGTCCTCGAGGGGTTC 16 35 1 TTTCTGAGAGCTCTCCTTCTCCACCATTTTT 22 240 0 CGTCTCAACTCCCCATTCGGGATTATACT 1 8 1 CGAGGGGGAACTCACCCCTTCGGTCGTGCGA 5 69 1 CAGTTCCTCCACCTCTTAAAAAGATTC 2 283 0 GTGTCGGGTGCCCTCCACCTCAGGTGGAACG 5 38 0 TGAAATATCCCTCCTCCTGTGTTAATATA 8 144 0 GGCTCTGCCCCCTTTTTTTGAGAATGAT 0 82 0 ATTTCACTCTCCATTCTTTTTGAGAAGGT 22 281 0 GCTCTTCACTCCCCTGAGAAAT 17 169 0 ATTTTCTCACCCTTTTTCATGCTAAC 25 33 0 CTTGCATCCCTCCTTACTCGTATGTTAGCA 25 9 1 GGGTGGAAAACCCCACCCCTTACC 14 3 0 TATTTTACTACTCTTTCTTTTCGGATATTTT 23 19 0 TCCGTGTGTTCTCTTTCTCTTCCTTCTAGAA 24 82 0 AAGCACTCTTCTCACTGCTTGTAAATATACC 3 133 0 TTTTGTACTCCTCTATGTTTTTCCTTTCTTC 22 211 0 CTTTCTGTTCCTCTATCTTTGTCTTCAATTC 6 155 0 ****** **** MAP Score: 36.6565 Motif 3 TTTTTTGAGAATCATTCTCAAAAAAAGGGGGCAGAGCC 0 72 1 ATTCGGGATTATACTATAGACAAGGGGTGATCAAGA 1 24 1 TTTGGGAAGAAGAATCTTTTTAAGAGGTGGAGGAACTG 2 272 1 TGAAAGTTCTAAAATCCCCATAAAAAGCGGGATTTCGAAA 3 44 0 TTGTAAATATACCATTTTACAGCGGGGTGTTGCAAGTCCC 3 106 0 AGAGTGCTTTACAACCCTAGAAAGGAGGGGGTTTC 3 155 1 TGAGGTGGAGGGCACCCGACACCGAGGGGGAACTCACCCC 5 47 1 CAGGAATTGAAGACAAAGATAGAGGAACAGAAAGCGCTGA 6 152 1 TTCTATTTTGAAATCACATCGAGGGGGGAG 7 9 1 ATTCCATTGAATCAAACGATCTGGAGGTGGTGGATATGGT 8 16 0 CTCCAGGGTTAAAATCTATCCTGGAGGTGATTGG 9 4 0 TCGATGTTAAAATTAGTGATAAAGGGAGGAGTTCGCA 13 8 1 AACAGATCTGAAAAATTTCTAAAGGGGTGGAAAACCCCAC 14 18 0 AATGGAGGACCCCCAAACGAGGAGTGACTGGATTAAT 14 98 0 ATTCAATGATACCACACACCGGAGGTGAGATTT 15 3 0 AAATATTCGAACCCCTCGAGGACGAGGAGAAAGATCAGAC 16 34 0 CGTGTTCACGAGAGATCTGTTTGGGAGGGAAAAAG 16 275 1 CGAAGAGCGTAAAAAAATTTCTCAGGGGAGTGAAGAGC 17 153 1 ATTGAAGTATAGAATTTTCAAAAAGGGCGGGGAGGCGAGC 18 11 1 ATGGCGGCGTAGCCAAGCGGTCAAAGGCGGGGGTCTGCAA 19 45 1 TAGAATTGTGATAAGGGGAGGGATAAG 20 1 1 GGGGGGCGAAATCATGAAGAGGAGAAGAGATACTGAAGTG 21 83 0 AGTTTAGGGTAGAATACTATAGAGGTGGGGTT 21 277 1 ATACTGAGCGAAAAGCGGTATGAAGAAAGGAAAAACATAG 22 190 1 TAGAGGAGTACAAAAAAATGGTGGAGAAGGAGAGCTCTCA 22 227 1 TTCTTTTTTAAAATATCCGAAAAGAAAGAGTAGTAAAAT 23 9 1 GCACTTGTATACCATGTGATTGGGAGGTGAAG 23 103 1 ATGAGAGAATAGACACTGTTGAGGAGGAGGTCAGGCAGGA 24 23 1 AAAAGAACGTACCAGCCTTCTAGAAGGAAGAGAAAGAGAA 24 65 1 GGCACGCAAGAGAACACCAGGTGGAAGAAGAGTTCTCAAG 24 118 1 TTTTCATGCTAACATACGAGTAAGGAGGGATGCAAG 25 6 0 TTCGAGTGATACAATTTAACAGAAGGGTGGTGATAGC 26 7 0 GGTAAAATTACTAAAAAAGAAAAGGAGAAGCGGAGG 26 52 1 * ** ***** ** MAP Score: 13.3307 Motif 4 AATCATTCTCAAAAAAAGGGGGCAGAGCC 0 81 1 CGTGGTTCCAAAGACGATAGAGGCTTTAATAGTTC 2 143 1 GTATATTTACAAGCAGTGAGAAGAGTGCTTTACAA 3 134 1 AGTGCTTTACAACCCTAGAAAGGAGGGGGTTTC 3 157 1 TTGGTGAAGAAAAAAGAAGGAGGTTCTGAAC 4 6 0 AACTTATGATAACACAGGAAAGGAGGTAGCACG 4 41 1 GAGGGCACCCGACACCGAGGGGGAACTCACCCCTT 5 54 1 ACTGAGGCCAAGAAGGCGGAAGCATTTCAGAGTT 6 9 1 GATAGCTCACGAGAAAAACAAAGATCATAAAGAAA 6 67 0 GGAATTGAAGACAAAGATAGAGGAACAGAAAGCGC 6 154 1 TCTATTTTGAAATCACATCGAGGGGGGAG 7 11 1 AGGCTTTTGTGAAAAAAGTGAAGAGGTTCACCTTT 8 101 0 TGTGTAGTATATTAACACAGGAGGAGGGATATTTC 8 137 1 TCACCTCGAAGTCAAAAGTGAGGAG 10 0 0 AATAGATAGGGAAAACAAGGAGGTGACACT 15 40 1 ATCGCAACGAGAAACCAGAAAAGCGATTTGAGAGG 16 171 0 TAGCCAAGCGGTCAAAGGCGGGGGTCTGCAAAATC 19 54 1 TAGAATTGTGATAAGGGGAGGGATAAG 20 9 1 TGGGGGGCGAAATCATGAAGAGGAGAAGAGATACT 21 89 0 TTTAGGGTAGAATACTATAGAGGTGGGGTT 21 279 1 TCGTGAGTGGAACCATAAAGAAGATCGTGAACTCG 22 14 1 GATCTATTCTAAGAACGACGAGGTTTAAAGCTTTT 22 129 0 TCTTAGAATAGATCCCGACGAGGTGTTCGGTGGAA 22 150 1 TGAAGAAAGGAAAAACATAGAGGAGTACAAAAAAA 22 210 1 AGGAGTACAAAAAAATGGTGGAGAAGGAGAGCTCT 22 230 1 AGACCTTCTCAAAAAGAATGGAGAGTGAAAT 22 279 1 TGAGAGAATAGACACTGTTGAGGAGGAGGTCAGGC 24 24 1 GAGTTCTCAAGAACAGGAGAAGGAAAGGACGCTGG 24 147 1 TAAAATTACTAAAAAAGAAAAGGAGAAGCGGAGG 26 54 1 ** ** * **** * MAP Score: 13.2289 Motif 5 TCTCAAAAAATTCAGATTAATTGTATCATCATCACATG 0 44 0 AATCCCGCTTTTTATGGGGATTTTAGAACTTTCAGACT 3 50 1 AACGGTCTTTTTCATGTTAATTTTATCACAAT 5 4 0 GATCGTTTGATTCAATGGAATTATATCAACCTAATTGT 8 35 1 ACAAAAGCCTTTGTGTAGTATATTAACACAGGAGGAGG 8 126 1 AGGCATCACCTCGTTTTTGATTCTAACCCCAAACCTTT 9 98 0 ACTCCTCCCTTTATCACTAATTTTAACATCGA 13 4 0 CGGTGCAAAATCATATGTTATAATACCAGAGGCTACGG 17 62 0 CTCCCCGCCCTTTTTGAAAATTCTATACTTCAATC 18 7 0 TTAATCTTCGTTTTAAAAAATTATAACACAGATGGATT 21 125 1 AACCCCACCTCTATAGTATTCTACCCTAAACTCTTT 21 273 0 CTACTCTTTCTTTTCGGATATTTTAAAAAAGAA 23 5 0 ATCACCACCCTTCTGTTAAATTGTATCACTCGAAAATA 26 13 1 CTCCTTTTCTTTTTTAGTAATTTTACCATATTTTCGAG 26 41 0 ** * *** ** ** MAP Score: 10.9688 Motif 6 TCGTGGGTTCGAATCCCACCGCCGCCTCCAGAGAGCCAGGCTA 19 94 1 ACCTGAGGTGGAGGGCACCCGACACCGAGGGGGAACTCACCCC 5 44 1 TCGAATATTTGAAAGGGACAGATTACGATCGAGCCGAGTTGTT 16 64 1 TGAGGGATTTGAAACGCACCCCACGCACCAGCGAAGAGTATTT 23 45 0 CCTCTATAAAGAAAAATCCCCTTCGCACGACCGAAGGGGTGAG 5 79 0 GTTTCGCAAAGAAAAAAACCGTGAACATACCTCTCAAATCGCT 16 142 1 GAGAAAAGACCCTGTTTCATGTGAGTCTGATCTTT 16 2 1 AGGATGAAAAGAACGTACCAGCCTTCTAGAAGGAAGAGAAAGA 24 59 1 AAATTAACATGAAAAAGACCGTTCCACCTGAGGTGGAGGGCAC 5 19 1 TCTTATGGCTGAAAACAACCGATTACAATTATCGAATCCAGAA 21 228 1 TGGCACGCAAGAGAACACCAGGTGGAAGAAGAGTTCTCAAGAA 24 117 1 TTCGGTGGAAGAATGATACTGAGCGAAAAGCGGTATGAAGAAA 22 175 1 AGGCTACGGGGAGTAGCTCAGACGGCCAGAGCGCCAGAATCGG 17 28 0 ACCCGCGACCTCCAGATCCCGATTCTGGCGCTCTGGC 17 4 1 *** **** * * * MAP Score: 3.70046 Motif 7 ATACTATAGACAAGGGGTGATCAAGA 1 34 1 TCTTTCGCACCACGGAGAGCTCGAATGGGGTT 2 107 1 CGTTCCACCTGAGGTGGAGGGCACCCGACACC 5 38 1 TATATTAACACAGGAGGAGGGATATTTCA 8 144 1 TTAGTGATAAAGGGAGGAGTTCGCA 13 22 1 TCTCCTCGTCCTCGAGGGGTTCGAATATTTGA 16 44 1 CAAGCGGTCAAAGGCGGGGGTCTGCAAAATCC 19 58 1 AATAGATCCCGACGAGGTGTTCGGTGGAAGAA 22 156 1 AAGGAAAAACATAGAGGAGTACAAAAAAATGG 22 216 1 AAATGGTGGAGAAGGAGAGCTCTCAGAAATCC 22 242 1 AGACACTGTTGAGGAGGAGGTCAGGCAGGATG 24 33 1 ACACCAGGTGGAAGAAGAGTTCTCAAGAACAG 24 131 1 **** **** ** MAP Score: 1.77925 Motif 8 GGCTCTGCCCCCTTTTTTTGAGAATGATT 0 81 0 GAAACCCCCTCCTTTCTAGGGTTGTA 3 164 0 GTTCAGAACCTCCTTCTTTTTTCTTCA 4 7 1 CGTGCTACCTCCTTTCCTGTGTTATC 4 48 0 TGAAATATCCCTCCTCCTGTGTTAATAT 8 145 0 GGTGGGGTTTTCCACCCCTTTAGAAATTTT 14 17 1 TCTGGTGCTGTCCTTCTTTCCTCTGATCGC 16 107 1 TGACTTTTAAAACTTCTCCTGTATAATTCG 17 125 1 CAATACCTCCCTTCTTCCAATATAAAAA 19 148 0 CTTATCCCTCCCCTTATCACAATTC 20 12 0 ACTTCAGTATCTCTTCTCCTCTTCATGATT 21 84 1 TATTTTACTACTCTTTCTTTTCGGATATTT 23 20 0 ATCCTGCCTGACCTCCTCCTCAACAGTGTC 24 34 0 GTTCTCTTTCTCTTCCTTCTAGAAGGCTGG 24 76 0 CAGCGTCCTTTCCTTCTCCTGTTCTTGAGA 24 151 0 CTTGCATCCCTCCTTACTCGTATGTTA 25 7 1 CCTCCGCTTCTCCTTTTCTTTTTTAGT 26 61 0 ********** MAP Score: 1.53115 Motif 9 GAAATTGTCTATTCCAGAGCACAAGATCCTCGAG 2 59 1 TCTTTCGCACCACGGAGAGCTCGAATGGGGTTCA 2 107 1 GCACGACCGAAGGGGTGAGTTCCCCCTCGGTGTC 5 64 0 TTAGTGATAAAGGGAGGAGTTCGCA 13 22 1 TCTCCTCGTCCTCGAGGGGTTCGAATATTTGAAA 16 44 1 GATCTCTCGTGAACACGAGCGCAACAACAGGAAA 16 258 0 GTAGCTCAGACGGCCAGAGCGCCAGAATCGGGAT 17 25 0 AAGTTTTAAAAGTCAAGGGTTCGATCGGTAAACG 17 106 0 CAAAATCCCTATTCGTGGGTTCGAATCCCACCGC 19 82 1 CCCACCGCCGCCTCCAGAGAGCCAGGCTACACGG 19 108 1 AAATCCAAGTATTCAGGAGCTCAAAAAATTCGCC 21 40 0 TTCCACTACCACTCCCGAGTTCACGATCTTCTTT 22 30 0 GGTAGTGGAAGTCGAAGAGTACGATGTGGAGGGT 22 54 1 AAATGGTGGAGAAGGAGAGCTCTCAGAAATCCAT 22 242 1 GATTTCTGGCACGCAAGAGAACACCAGGTGGAAG 24 111 1 ACACCAGGTGGAAGAAGAGTTCTCAAGAACAGGA 24 131 1 * ** ****** * MAP Score: 0.616438