AlignACE 3.0 10/20/99 AlignACE2 -i AA/AA_operons007_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944235067 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 dmsB2 232 dimethylsulfoxide reductase chain B #1 rpmJ 60 ribosomal protein L36 #2 secY 44 preprotein translocase SecY #3 nirB 120 nitrite reductase (NAD(P)H) large subunit #4 fhp 133 flavohemoprotein #5 trxB 142 thioredoxin reductase #6 aq_503 83 hypothetical protein #7 otnA' 30 polysaccharide biosynthesis protein (fragment) #8 lpdA 85 dihydrolipoamide dehydrogenase #9 nox 43 NADH oxidase #10 aq_1035 149 hypothetical protein #11 aq_1036 97 putative protein #12 aq_1037_lysR2 50 aq_1037: putative protein, lysR2: transcriptional regulator (LysR family) #13 fdoG 212 formate dehydrogenase alpha subunit #14 dmsA 23 DMSO reductase chain A #15 cysM 41 cysteine synthase, O-acetylserine (thiol) lyase B #16 aq_1558 27 putative protein #17 gltB 30 glutamate synthase large subunit #18 gltD 39 glutamate synthase small subunit gltD #19 pepA 26 leucine aminopeptidase Motif 1 ATGAAAGTAAGAAGGATGAGGAGCTGAATG 0 35 0 TTTCCCGAGGTAAGGAGAAGTAAAATTTAC 0 84 1 GGATAAGTATTAAGGGGGAAAAGTCAATGC 0 181 0 ATAGAGAGTATAAGGATAAGTATTAAGGGG 0 194 0 CTGAGTATCCTCAGGAGGATAGAGAGTATA 0 212 0 AGTTCTCTCGGAGGTAGAAGA 2 1 0 TTATACGTATACGGGAGGTAACCT 3 4 0 AAGAGTTTCCTCAGGAGGAGTGAAAG 3 104 1 TGTTAAAACAGAACGGGGAGAATTTGGCAC 4 76 1 TAGTTTGAGTGAAGGAGGTGAAAAG 4 118 1 AGATTTTTTAGAGGTGGGAACTTGGGTTTA 5 23 0 TTATTTAAAGTAGGGAGATGTATTACACCT 6 41 1 GATTATGTTGTAGGGAGAATTCTTAAGAGC 7 10 0 ATTTGCCTTAAAAGGAGGAAGCGA 8 4 0 AAACCCCTTTTCAGGAGGAGCTTC 8 71 1 TAAGTACCTAGAGGGAGGTGGTT 9 3 0 TTTCCCTCGGTAGGGAGGTGTTTCGTGGAT 10 48 0 GTTAAAGAGATAGCGATGAGGATAACCGAA 10 79 1 AAAGGTCTCGGAGGTAGAAA 15 0 0 ********** MAP Score: 21.2094 Motif 2 GTTAAAAGATTTTAATATAATAAAGTTCTCTCGGAG 2 18 0 ATTTTCTATCTTTTAACATATTGATATAGGTTGTAAA 5 86 1 TTGATATAGGTTGTAAAATTTTCAACTGTCGCAAGGA 5 106 1 TTGCCTTTAATTTTAGCATTTTGATATACTAATAATT 8 31 0 TAAGCTTAAATTTTAAAATAAGTACCTAGAGGGAGGT 9 14 0 ATAAATATCTTTTAATAATTTTTATTTTATAAATGTA 11 25 0 AAGAAAAAATTTGGAGAATTTTAAACTTTCGT 11 75 1 TTATGTGATATTTGAATATAAGGAATTTATTAACATG 13 48 1 AAAACAATATTTTAAAAATAGGCATATGAACATTTTT 13 108 0 AAAATATTGTTTTGAAAATTTTGTCTTTTTTTTAAAT 13 132 1 TTTTAAATTTTTTCATGATTTGAAAGGGGAATAAACT 13 161 1 CTCCTTTAAGCATTCTTAGTTTTTAGTTTAT 13 191 0 CCTCCGAGACCTTTAAAATAGTATCATACCGCCCT 15 16 1 ATAAACTCTCCTTTAAGATATTCAAGTT 18 1 0 *** * *** * * * MAP Score: 18.1889 Motif 3 AACTTTATTATATTAAAATCTTTTAAC 2 27 1 ACCCGGAACTTTTTGGCACGTTTTTTGCAAGAGT 3 76 1 TCTTGGAAACTTTTCTCTGATTGTGGAGACGCTT 4 40 0 CCCCGTTCTGTTTTAACAGTTCTTGGAAACTTTT 4 60 0 ACGGGGAGAATTTGGCACGCTTTTTGCAATTAGT 4 88 1 ATTTTCTATCTTTTAACATATTGATATAGGTTGT 5 86 1 TTGCTTTTTTCCTATTTTTAATGCATGT 6 4 1 TTGCCTTTAATTTTAGCATTTTGATATACTAATA 8 34 0 TCTAGGTACTTATTTTAAAATTTAAGCTTAAC 9 21 1 TATAAATATCTTTTAATAATTTTTATTTTATAAA 11 29 0 AAGTTTAAAATTCTCCAAATTTTTTCTTCGAAAC 11 69 0 ATTTGGAGAATTTTAAACTTTCGT 11 83 1 TTTTTCGAACATTTTCATTGAATAA 13 1 1 AAAATAGGCATATGAACATTTTTTTATTGTGTAT 13 97 0 ATATGCCTATTTTTAAAATATTGTTTTGAAAATT 13 118 1 AAAATATTGTTTTGAAAATTTTGTCTTTTTTTTA 13 132 1 ATTTTGTCTTTTTTTTAAATTTTTTCATGATTTG 13 149 1 AGGGCGGTATGATACTATTTTAAAGGTCTCG 15 20 0 **** ** **** MAP Score: 12.0049 Motif 4 GGATAGTGTCTCCCTTTTTAGAGCCGATAA 0 127 1 CATTGACTTTTCCCCCTTAATACTTATCCT 0 182 1 AACCCAAGTTCCCACCTCTAAAAAATCTCT 5 25 1 CTCTAAAAAATCTCTCTTCATCTATATGTT 5 40 1 TTGCTTTTTTCCTATTTTTAATGCATGTGT 6 10 1 AATACATCTCCCTACTTTAAATAATACACA 6 35 0 TCTTAAGAATTCTCCCTACAACATAATC 7 12 1 TCGCTTCCTCCTTTTAAGGCAAATTA 8 6 1 GCAATTAAAACCCCTTTTCAGGAGGAGCTT 8 64 1 AACCACCTCCCTCTAGGTACTTATT 9 5 1 GAACTTGCTCTCTACCTGCAATCCACGAAA 10 28 1 TGTTCATATGCCTATTTTTAAAATATTGTT 13 113 1 TTTAGTTTATTCCCCTTTCAAATCATGAAA 13 171 0 GATGATAAACTCTCCTTTAAGATATTCAAG 18 12 0 ********** MAP Score: 8.99412 Motif 5 GTAAGAAGGATGAGGAGCTGAATGAAGACTTTAAC 0 24 0 TTTCCCGAGGTAAGGAGAAGTAAAATTTACTGGTA 0 84 1 TTAGAGCCGATAAGGAAAGTCGTAAAACCGATTAA 0 144 1 ATAGAGAGTATAAGGATAAGTATTAAGGGGGAAAA 0 189 0 CTGAGTATCCTCAGGAGGATAGAGAGTATAAGGAT 0 207 0 TTCTACCTCCGAGAGAACTTTATTATATTAAAATC 2 12 1 TGTAAGTCCTTACAGAGGTTGTAAAATGAAAGTTA 3 31 0 AAGAGTTTCCTCAGGAGGAGTGAAAG 3 104 1 TAGTTTGAGTGAAGGAGGTGAAAAG 4 118 1 AACTTGGGTTTAAAGAATTTGTTAA 5 0 0 TATAGATGAAGAGAGATTTTTTAGAGGTGGGAACT 5 31 0 GCATAGCTTAGAGGGAACATATAGATGAAGAGAGA 5 50 0 TTATTTAAAGTAGGGAGATGTATTACACCTTTTCG 6 41 1 GATTATGTTGTAGGGAGAATTCTTAAGAGC 7 5 0 AGCAAGTTCCTTAGGAGTTTTAAAATC 10 2 0 TTTCCCTCGGTAGGGAGGTGTTTCGTGGATTGCAG 10 43 0 CCTCCCTACCGAGGGAAAGGTTAAAGAGATAGCGA 10 60 1 GAGGATAACCGAAGGAAAGAAAACACCCATTCAGA 10 96 1 GGTAGTTCACAAAAGAGATGATAAGAGAATATAAG 12 23 1 TATTTGAATATAAGGAATTTATTAACATGCAATAT 13 56 1 CTGCCACCCCTTAAGAGTTTTGAGAGTAT 17 4 0 ******* * * * MAP Score: 7.44915 Motif 6 ATAATTTGCCTTAAAAGGAGGAAGCGA 8 6 0 AAACAATATTTTAAAAATAGGCATATGAACA 13 113 0 TACACATGCATTAAAAATAGGAAAAAAGCAA 6 10 0 ATGTGTATTATTTAAAGTAGGGAGATGTATT 6 34 1 ATGAAAAAATTTAAAAAAAAGACAAAATTTT 13 146 0 CTTGAATATCTTAAAGGAGAGTTTATCATCT 18 12 1 TATCAATATGTTAAAAGATAGAAAATTGCAT 5 81 0 AAGCTTAAATTTTAAAATAAGTACCTAGAGG 9 19 0 GAGAGATTTTTTAGAGGTGGGAACTTGGGTT 5 25 0 AATGCTAAAATTAAAGGCAATTAAAACCCCT 8 48 1 CTCCGAGACCTTTAAAATAGTATCATACCGC 15 17 1 TTTTTCATGATTTGAAAGGGGAATAAACTAA 13 169 1 ATAAAAATTATTAAAAGATATTTATATTTAG 11 37 1 TTATCGGCTCTAAAAAGGGAGACACTATCCA 0 126 0 ******* *** MAP Score: 7.31697 Motif 7 CTTCATTCAGCTCCTCATCCTTCTTACTTTCATT 0 32 1 TGACTTTTCCCCCTTAATACTTATCCTTATACTC 0 185 1 TATCCTTATACTCTCTATCCTCCTGAGGATACTC 0 206 1 CTTTCACTCCTCCTGAGGAAACTC 3 106 0 AAGTTCCCACCTCTAAAAAATCTCTCTTCATCTA 5 30 1 GCTCTTAAGAATTCTCCCTACAACA 7 1 1 TAAGAATTCTCCCTACAACATAATC 7 15 1 TCGCTTCCTCCTTTTAAGGCAAATT 8 1 1 AACCACCTCCCTCTAGGTACTTATTTTAAAATTT 9 10 1 GATTTTAAAACTCCTAAGGAACTTG 10 1 1 TCATCGCTATCTCTTTAACCTTTCCCTCGGTAGG 10 64 0 ATATAAATATCTTTTAATAATTTTTATTTTATAA 11 30 0 CGAAGAAAAAATTTGGAGAATTTTAAACTTTCGT 11 73 1 TAGTTTATTCCCCTTTCAAATCATGAAAAAATTT 13 165 0 CTCCTTTAAGCATTCTTAGTTTTTAG 13 196 0 ATACTCTCAAAACTCTTAAGGGGTGGC 17 3 1 **** * **** * MAP Score: 4.47491 Motif 8 TCTTCTACCTCCGAGAGAACTTTA 2 3 1 AACCCAAGTTCCCACCTCTAAAAAATCTCTC 5 25 1 TCTTAAGAATTCTCCCTACAACATAATC 7 12 1 AACCACCTCCCTCTAGGTACTTATTT 9 5 1 GAACTTGCTCTCTACCTGCAATCCACGAAAC 10 28 1 CCACGAAACACCTCCCTACCGAGGGAAAGGT 10 50 1 TTTCTACCTCCGAGACCTTTAAA 15 2 1 ******* *** MAP Score: 2.93048 Motif 9 TCTTCTACCTCCGAGAGAACTTTA 2 4 1 AGGTTACCTCCCGTATACGTATA 3 3 1 TTTCATTTTACAACCTCTGTAAGGACTTAC 3 35 1 CTTTTCACCTCCTTCACTCAAACT 4 119 0 TTTCGTACCTCCTTGCGACAGTTG 5 128 0 AGCAAACCTGCTGTCTCCGAAAAGGTGTAA 6 63 0 GAAGCTCCTCCTGAAAAGGGGTT 8 72 0 AACCACCTCCCTCTAGGTACTT 9 2 1 AACTTGCTCTCTACCTGCAATCCACGAAAC 10 29 1 AATCCACGAAACACCTCCCTACCGAGGGAA 10 47 1 GAACCTCCCATATTTTACAT 11 0 1 TTTCTACCTCCGAGACCTTTAAA 15 3 1 AAATAGTATCATACCGCCCT 15 31 1 ********** MAP Score: 2.59492 Motif 10 TGGATAGTGTCTCCCTTTTTAGAGCCGATAAGG 0 126 1 AACTTTTTGGCACGTTTTTTGCAAGAGTTTCCT 3 82 1 CTTTCACTCCTCCTGAGGAAACTCTTGCA 3 101 0 TGATTGTGGAGACGCTTTGCGTACAATTTTGTA 4 24 0 GAGAATTTGGCACGCTTTTTGCAATTAGTTTGA 4 93 1 AGATGTATTACACCTTTTCGGAGACAGCAGGTT 6 56 1 GCAATTAAAACCCCTTTTCAGGAGGAGCTTC 8 64 1 AACCACCTCCCTCTAGGTACTTATTTTAA 9 6 1 GGAAAGAAAACACCCATTCAGAAGGCTTGGGCT 10 109 1 CTACCTCCGAGACCTTTAAAATAGTATCATACC 15 13 1 TCTGCCACCCCTTAAGAGTTTTGAGAGT 17 12 0 ******** * * MAP Score: 1.70919 Motif 11 TACTCTCTATCCTCCTGAGGATACTCAG 0 214 1 TCTTCTACCTCCGAGAGAACTTTATTATA 2 4 1 TGTTTTGTAAGTCCTTACAGAGGTTGTAAAATGAA 3 36 0 CTTTCACTCCTCCTGAGGAAACTCTTGCAAAAAA 3 96 0 ACCCAAGTTCCCACCTCTAAAAAATCTCTCTTCAT 5 26 1 CATCTATATGTTCCCTCTAAGCTATGCAATTTTCT 5 58 1 TTTCGTACCTCCTTGCGACAGTTGAAAATTTTA 5 119 0 AAACCTGCTGTCTCCGAAAAGGTGTAATACATCTC 6 55 0 GCTCTTAAGAATTCTCCCTACAACA 7 0 1 TCGCTTCCTCCTTTTAAGGCAAATTATTAGTA 8 7 1 GAAGCTCCTCCTGAAAAGGGGTTTTAATTGCC 8 63 0 AACCACCTCCCTCTAGGTACTTATTTTAAAA 9 6 1 AGAGAGCAAGTTCCTTAGGAGTTTTAAAATC 10 6 0 CTCCAAATTTTTTCTTCGAAACTCTAAATATAAAT 11 56 0 TTAGTTTATTCCCCTTTCAAATCATGAAAAAATTT 13 165 0 TTTCTACCTCCGAGACCTTTAAAATAGT 15 3 1 TCTGCCACCCCTTAAGAGTTTTGAGAGTAT 17 8 0 ATGATAAACTCTCCTTTAAGATATTCAAGTT 18 6 0 ****** *** * MAP Score: 0.038776