AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_operons017_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944252303 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0181 83 hypothetical protein #1 TM0653 72 conserved hypothetical protein #2 TM0655 24 conserved hypothetical protein #3 TM0656 281 conserved hypothetical protein #4 TM0703 42 competence-damage inducible protein, putative #5 TM0770 60 conserved hypothetical protein #6 TM0826 127 hypothetical protein #7 TM0828 29 sugar kinase, pfkB family #8 TM0839 54 rod shape-determining protein RodA #9 TM0840 39 hypothetical protein #10 TM0842 37 response regulator #11 TM0883 135 conserved hypothetical protein #12 TM1095 300 adenylosuccinate lyase #13 TM1528 27 1,4-dihydroxy-2-naphthoate octaprenyltransferase, putative #14 TM1530 101 electron transfer flavoprotein, beta subunit #15 TM1537 57 Mg-protoporphyrin IX monomethyl ester oxidative cyclase-related protein #16 TM1597 49 hypothetical protein #17 TM1598 32 RNA polymerase sigma-E factor #18 TM1864 71 hypothetical protein Motif 1 AAATCTATCCTGGAGGTGATTGG 6 3 0 ATCTCAAATGTGGAGGTGATACTT 11 121 1 AATAGTTACGTGGAGGTGATCACAAGTT 16 8 0 TAATTAGAAGGCGAGGTGAGATC 5 3 0 ACTTTTGACTTCGAGGTGATCGT 7 16 1 ATTTGACCTTTGGAGGAGATATCTGAGGAG 14 72 1 CACGGGGGTCTGGAGGAGATTGTT 18 57 1 ATTTTATCACGGGAGGTGGAGAGA 11 4 0 AAATCACCATGAGAGGTGATTGT 0 70 1 AGAATCAAAAACGAGGTGATGCCTC 6 112 1 TTGGATAGTGAGGAGGTGAAAAT 0 3 0 AGAATACCCACAGAGGTGATTCTC 15 43 1 CTATCCCTCCTGGAGGTGCGCTTG 13 4 0 CATGGAAATAGGGAGGTGCAGGGT 3 4 0 TAGTGATAAAGGGAGGAGTTCGCA 10 23 1 AAAATCAGAACTGAGGTGAAAGG 5 47 1 CTACTATAAAGTGAGGTGTTG 16 38 1 TCAAATGTTTCAGAGGTGTGTAAGAAATAT 11 83 1 CCCCTCGAGGACGAGGAGAAAGATCAGACT 12 33 0 GACAACGAAAGGGGGGTGGGTATAATAATG 3 206 1 AAATTTCAGAGGGGAGGGATTAAC 2 6 1 CTCCTCGTCCTCGAGGGGTTCGAATATTTG 12 45 1 TATCATATCACTGAGGAGGGATCGT 4 27 1 AAGTCTTAATACGAGGAGGAAACGGTT 17 15 1 GAGATATCTGAGGAGGCGAAGAGC 14 87 1 ********** MAP Score: 45.5276 Motif 2 CACTATCCAAATAATAACACTTTGAAATTG 0 23 1 TCTCATGGTGATTTTAACACGCTTTGAGAA 0 54 0 GACTAATTAGATTATACCAGAAAGGAAAAA 1 30 0 TCCTGGATTTATTTTACCACATAATTATAA 3 39 1 TCTCGATTCAATTAGAACAGCCTCATCGTT 3 97 0 CACAGACATTATTATACCCACCCCCCTTTC 3 212 0 CCTCAGTGATATGATAACACACAGGGGGAT 4 13 0 TCGCCTTCTAATTATAACAACCAATGATAA 5 19 1 CTCAGTTCTGATTTTATCATTGGTTGTTAT 5 32 0 TCCAGGATAGATTTTAACCCTGGAGACGTT 6 19 1 GATCATTACAATTAAAACCCGGAGAATGTA 6 53 0 CTCGTTTTTGATTCTAACCCCAAACCTTTA 6 97 0 TTTATCACTAATTTTAACATCGA 10 3 0 ACATCAGAAAATTTTATCACGGGAGGTGGA 11 14 0 CCTTTCAAATATTCGAACCCCTCGAGGACG 12 50 0 CTCTGTGGGTATTCTAACACAGAAAGAAGG 15 28 0 GGCTGAATTTATTTTATCACAGCCGAAAAA 18 14 0 ********** MAP Score: 18.4741 Motif 3 CAAAGCGTGTTAAAATCACCATGAGAGGTGATTGT 0 58 1 ATCTAATTAGTCTGAGCAAACTGGGAGGTCGAAC 1 48 1 TTTTGAATAGTTACATTAAACGATGAGGCTGTTCTAATTG 3 79 1 AAAATTAACCTTGACAACGAAAGGGGGGTGGGTATAATAA 3 194 1 AGTTTGTCAACTATAGTGGACAAAGGGGTTGGGAACTTT 3 252 1 CTCAGTGATATGATAACACACAGGGGGATGTT 4 2 0 CATTGGTTGTTATAATTAGAAGGCGAGGTGAGATC 5 5 0 TCTCCAGGGTTAAAATCTATCCTGGAGGTGATTGG 6 5 0 TAATGATCCATACAAGTCCAATTAAAGGTTTGGGGTTAGA 6 75 1 AGGTTTGGGGTTAGAATCAAAAACGAGGTGATGCCTC 6 100 1 ACGATCACCTCGAAGTCAAAAGTGAGGAG 7 0 0 CCCTTTCAAATATTCGAACCCCTCGAGGACGAGGAGAAAG 12 41 0 TCTTTCTGTGTTAGAATACCCACAGAGGTGATTCTC 15 31 1 CACGTAACTATTCTACTATAAAGTGAGGTGTTG 16 26 1 TTCAGCCTCAGGATACCAGACACGGGGGTCTGGAGGAGAT 18 37 1 * * ** ****** MAP Score: 13.5245 Motif 4 TAAAATCACCATGAGAGGTGATTGT 0 68 1 AGTCTGAGCAAACTGGGAGGTCGAAC 1 56 1 AAATTTCAGAGGGGAGGGATTA 2 2 1 ATACCATGGAAATAGGGAGGTGCAGGGT 3 8 0 AAGGTAACTTATCTTGGAGGAATGATCTAA 3 145 0 ATAAAATCAGAACTGAGGTGAAAGG 5 45 1 TCGAAGTCAAAAGTGAGGAG 7 0 0 AAAGTCTTAGATTTGAGGGG 9 29 1 ATTAGTGATAAAGGGAGGAGTTCGCA 10 21 1 CGTGTCAAATGTTTCAGAGGTGTGTAAGAA 11 79 1 TCACCTCCACATTTGAGATGGTGTAAAATA 11 110 0 GGGTTCGAATATTTGAAAGGGACAGATTAC 12 60 1 CAGAAAAGCGATTTGAGAGGTATGTTCACG 12 161 0 CGAGAGATCTGTTTGGGAGGGAAAAAG 12 283 1 TGGAGGAGATATCTGAGGAGGCGAAGAGC 14 82 1 TTCTACTATAAAGTGAGGTGTTG 16 36 1 ********** MAP Score: 11.4035 Motif 5 TGAAATTGTTTCTCAAAGCGTGTTAAAATC 0 45 1 TTAGATCATTCCTCCAAGATAAGTTACCTT 3 145 1 CCAATCACCTCCAGGATAGATTTTAAC 6 7 1 TAATAAAACGTCTCCAGGGTTAAAATCTAT 6 25 0 TTTTACACCATCTCAAATGTGGAGGTGATA 11 112 1 TTCTCCTCGTCCTCGAGGGGTTCGAATATT 12 43 1 TGAACATACCTCTCAAATCGCTTTTCTGGT 12 163 1 CAAGCGCACCTCCAGGAGGGATAGATA 13 8 1 TCAGATATCTCCTCCAAAGGTCAAATCCCA 14 68 0 ********** MAP Score: 4.89909 Motif 6 TGAAATTGTTTCTCAAAGCGTGTTAAAATC 0 45 1 AAATTTCAGAGGGGAGGGATTAA 2 3 1 CACCTCCCTATTTCCATGGTATTTCCTGGA 3 16 1 TTAGATCATTCCTCCAAGATAAGTTACCTT 3 145 1 ACGATCCCTCCTCAGTGATATGATAACAC 4 23 0 CCTTTCACCTCAGTTCTGATTTTATCA 5 43 0 CCCCTCAAATCTAAGACTTTCA 9 27 0 GTGATAAAATTTTCTGATGTCCTCTTTTAG 11 24 1 GTGTCAAATGTTTCAGAGGTGTGTAAGAAA 11 80 1 TTTTACACCATCTCAAATGTGGAGGTGATA 11 112 1 AATCTGTCCCTTTCAAATATTCGAACCCCT 12 58 0 GTCCTTCTTTCCTCTGATCGCCACCAGTTT 12 116 1 TCACGGTTTTTTTCTTTGCGAAACTGGTGG 12 136 0 TGAACATACCTCTCAAATCGCTTTTCTGGT 12 163 1 CGATTATCAGCTTCAGTGCTTTCAT 14 5 0 CTCTTCGCCTCCTCAGATATCTCCTCCAAA 14 80 0 GAGAATCACCTCTGTGGGTATTCTAACA 15 39 0 ********** MAP Score: 4.13463 Motif 7 ACAATCACCTCTCATGGTGATTTTA 0 68 0 ACAGCCCCGCTTCGGCGGGGTTTT 1 4 1 GTTCGACCTCCCAGTTTGCTCAGACTA 1 55 0 GTTAATCCCTCCCCTCTGAAATTT 2 6 0 ACCCTGCACCTCCCTATTTCCATGGTATT 3 9 1 TTATTATACCCACCCCCCTTTCGTTGTCAA 3 204 0 AAAGTTCCCAACCCCTTTGTCCACTATAG 3 262 0 ACGATCCCTCCTCAGTGATATGATAAC 4 25 0 GATCTCACCTCGCCTTCTAATTATA 5 5 1 CCTTTCACCTCAGTTCTGATTTTAT 5 45 0 GAGGCATCACCTCGTTTTTGATTCTAA 6 110 0 CTCCTCACTTTTGACTTCGA 7 0 1 GAACTCTCTTCTTTACTTGAAAG 9 3 1 TGCGAACTCCTCCCTTTATCACTAAT 10 21 0 ATTTTCTGATGTCCTCTTTTAGATTTAGTA 11 32 1 GAGAAAAGACCCTGTTTCATGTGAGTC 12 7 1 TCTGATCTTTCTCCTCGTCCTCGAGGGGTT 12 35 1 TTCTGGTGCTGTCCTTCTTTCCTCTGATCG 12 106 1 ATATTTAATGCTCGCTACCTTCCACAACGC 12 207 0 GGGGCCGAAGCCCCTTTTTT 15 0 0 GGGGCTTCGGCCCCTTCTTTCTGTGTTAGA 15 16 1 GAGAATCACCTCTGTGGGTATTCTAA 15 41 0 CAACACCTCACTTTATAGTAGAA 16 36 0 AACCGTTTCCTCCTCGTATTAAGACTTTC 17 13 0 TCCTCCAGACCCCCGTGTCTGGTATCCTGA 18 44 0 ********** MAP Score: 4.13145 Motif 8 CGTGTTAAAATCACCATGAGAGGTGATTGT 0 63 1 TGGTAAAATAAATCCAGGAAATACCATGGAA 3 27 0 GTTCTAATTGAATCGAGAAAAGATTGCGATC 3 109 1 TTAGATCATTCCTCCAAGATAAGTTACCTTA 3 145 1 CCAATCACCTCCAGGATAGATTTTAACC 6 7 1 ATTACAATTAAAACCCGGAGAATGTAATAAA 6 48 0 TTAGAATCAAAAACGAGGTGATGCCTC 6 110 1 GGACCATACCACACGAGAACAAACGAATAGA 8 14 1 CTAAAAGAGGACATCAGAAAATTTTATCACG 11 23 0 GAAACATTTGACACGAAGATATAGTAAGGTA 11 63 0 TATTCGAACCCCTCGAGGACGAGGAGAAAGA 12 40 0 TCGCAACGAGAAACCAGAAAAGCGATTTGAG 12 174 0 CACGAGCGCAACAACAGGAAAAACAAGATAA 12 248 0 CAAGCGCACCTCCAGGAGGGATAGATA 13 8 1 AACAGCTGCAGCAACCGGAAACTCGATTATC 14 27 0 AATCCCACGAACATGAGAACAGCTGCAGCAA 14 44 0 CTTGTGATCACCTCCACGTAACTATTCTACT 16 12 1 GAAAGTCTTAATACGAGGAGGAAACGGTT 17 13 1 AATAAATTCAGCCTCAGGATACCAGACACGG 18 31 1 ********* * MAP Score: 1.64862 Motif 9 CGTGTTAAAATCACCATGAGAGGTGATTGT 0 63 1 AAATTTCAGAGGGGAGGGATTAAC 2 3 1 GCTGTTCTAATTGAATCGAGAAAAGATTGCGATCTGC 3 106 1 TGTGTTATCATATCACTGAGGAGGGATCGT 4 22 1 CCAATCACCTCCAGGATAGATTTTAACCCTG 6 4 1 TTACACCATCTCAAATGTGGAGGTGATACTT 11 114 1 GGGTTCGAATATTTGAAAGGGACAGATTACGATCGAG 12 60 1 GTTGTTGCGCTCGTGTTCACGAGAGATCTGTTTGGGA 12 264 1 CAAGCGCACCTCCAGGAGGGATAGATA 13 5 1 TCGTGGGATTTGACCTTTGGAGGAGATATCTGAGGAG 14 65 1 CTGTGTTAGAATACCCACAGAGGTGATTCTC 15 36 1 TACCAGACACGGGGGTCTGGAGGAGATTGTT 18 50 1 * * ***** *** MAP Score: 0.722158