AlignACE 3.0 10/20/99 AlignACE2 -i AG/AG_fusions001_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944240935 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #1 AF0439 82 transcriptional regulatory protein, AsnC family #2 AF0442 300 succinoglycan biosynthesis regulator (exsB) #3 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #4 AF0685 140 enoyl-CoA hydratase (fad-2) #5 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #6 AF0970 101 A. fulgidus predicted coding region AF0970 #7 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #8 AF1173 180 A. fulgidus predicted coding region AF1173 #9 AF1174 61 A. fulgidus predicted coding region AF1174 #10 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #11 AF1191 32 dihydroxynaphthoic acid synthase (menB) #12 AF1192 50 conserved hypothetical protein #13 AF1195 27 activator 1, replication factor C, 53 KD subunit #14 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #15 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #16 AF1208 165 conserved hypothetical protein #17 AF1210 108 conserved hypothetical protein #18 AF1641 31 enoyl-CoA hydratase (fad-4) #19 AF1642 50 histidyl-tRNA synthetase (hisS) #20 AF2009 101 heme biosynthesis protein (nirJ-2) #21 AF2010 46 A. fulgidus predicted coding region AF2010 #22 AF2011 175 conserved hypothetical protein #23 AF2013 275 coenzyme F390 synthetase (ftsA-3) #24 AF2014 63 sugar transporter, putative #25 AF2426 85 conserved hypothetical protein #26 AF2429 30 enoyl-CoA hydratase (fad-5) Motif 1 TAGTCGTGTAATATTTAATGTTTTCGTGAAATA 0 47 0 CAAACATAAAATTTTTATATTTTTAGTTTACTT 1 52 1 ATTTTTATTTTTATATTTTTGTTTTTAAC 5 6 1 TTTTAATTTTTATTTTTTCCAACAGATA 14 5 1 GTGCATCCAGATATTTAACCTTTTGGAACTAAA 20 22 1 TTTGCATAAAATTTTTAGCTTTTTAATTCTTTA 24 33 1 ATTGAAGAGTATTTTAATCTTTTGAGATTACAA 9 25 0 GATACTTACACTTTAATTGCAATT 1 1 1 CTCCTTTATAATTCTTACTATTTTTACGAAATT 7 101 0 TTCGTTAATACTTAAATTTTACGTAATGTG 5 185 0 AAATCTGGCAATATAAAGCTTTTGCAGATACAC 6 24 1 ATTTAAATTTTTTCATTTATGAA 6 88 0 ATTGCGAAAGATTTAAAACTTTTCGGTAGGAGT 7 16 0 TAGGTTTGTTATATAAAATCTTTTTTCTCGTGC 3 21 1 CAAAAATAAAAATTTTACTATTTAGGCC 21 5 0 AATACTTGATATATTCAATTTTTACGCGTTTAG 5 106 0 ATTTTATCTCAATTTAAGATTTTGATTTGACAT 7 47 1 AAACATACTTAAATTAACTTTTTTGAAGCTAAA 16 140 1 TAGTACTTGAATTCAAACCATTTAAGCTTTTCC 8 23 1 TCTATTTGTAGTATTTACCTTTTCTTTAACAGA 16 14 1 CGGCAAGGGTGTTTAAAAGGTTTTAGAGTTGAG 19 17 0 ******* *** MAP Score: 19.655 Motif 2 TGAAAAAAGTAGTCGTGTAAT 0 68 0 TTTTTAAAGGAAAGATTTATCTTGCAAGA 4 9 1 GGGGCGACGTGGAAAAATTGGACTCTTGCA 4 32 0 GAGAGCAAATGAAAAATCTAAACGCGTAAA 5 89 1 ATCTAAACGCGTAAAAATTGAATATATCAA 5 104 1 GGCACATTACGTAAAATTTAAGTATTAACG 5 183 1 GTTCATAAATGAAAAAATTTAAAT 6 87 1 ATAAAATTGCGAAAGATTTAAAACTTTTCG 7 24 0 CTTAAATTGAGATAAAATTGCGAAAGATTT 7 35 0 AAATTTATTTGAAAAAATTTCGTAAAAATA 7 86 1 CGTAAAAATAGTAAGAATTATAAAGGAGGA 7 106 1 AGTCAGGTGGGAAAAAATTTTGAGGTGGGC 8 81 1 TCCGGGCAGGGAAAAATGTACTGGAAAATA 11 11 0 ATTTTAATAAGAAAAAAGTGAAGGAGGTGT 15 277 1 TGAACAATTCGAAAAATCTGTTAAAGAAAA 16 33 0 ATTTAAGAGAGAAAAATCTGCCGTTCTCCA 17 10 0 GGCCTAAATAGTAAAATTTTTATTTTTGTT 21 10 1 GGAGGGGCCCGATAGATTTGAACATCGAGG 22 17 1 TACTTCAAGTGTAAAAATTGAGTGCCCCAG 22 76 0 ********** MAP Score: 14.7999 Motif 3 ACAAAAATAAAAATTTTACTATTTAGGCC 21 5 0 AAATTGCGAAAGATTTAAAACTTTTCGGTAGGAG 7 17 0 TAGTCGTGTAATATTTAATGTTTTCGTGAAATAT 0 46 0 GTGCATCCAGATATTTAACCTTTTGGAACTAAAT 20 22 1 AAAAATATAAAAATTTTATGTTTGCCATTAAATG 1 42 0 ATTTAAATTTTTTCATTTATGAACACAA 6 83 0 TTTTATTTTTATATTTTTGTTTTTAACACGCTGT 5 12 1 TATTTGCATAAAATTTTTAGCTTTTTAATTCTTT 24 31 1 GCTAACATTTAAACATTGTAATCTCAAA 9 4 1 TTACGCGTTTAGATTTTTCATTTGCTCTCGTAAT 5 84 0 ACATTACGTAAAATTTAAGTATTAACGAA 5 186 1 TAAAATTTTTATATTTTTAGTTTACTTTCATACT 1 58 1 AATTTTATCTCAATTTAAGATTTTGATTTGACAT 7 46 1 TGAATTCAAACCATTTAAGCTTTTCCATAATTAT 8 30 1 ATGACATGCGATATTTATTCATTACGCCTGAATT 20 73 0 ACATTGAAGAGTATTTTAATCTTTTGAGATTACA 9 26 0 TTTTAATTTTTATTTTTTCCAACAGATA 14 4 1 TGGGGCACTCAATTTTTACACTTGAAGTAAAGAA 22 77 1 TGATTAACATATATATTACTATTTTGCTGTAATT 12 16 0 * ****** *** MAP Score: 14.5601 Motif 4 ACAGAACTAAATGCGGGGGGAGGGATTCGAACCCT 2 131 1 TTTTCATCTGAGCGGGGGTTGCCGAGCGGACAAAG 2 201 0 CACGTCGCCCCCGTGGGGTAGCGGATATCCTGAGG 4 51 1 AGCGGATATCCTGAGGGGCTGCGGACTCCTCGACC 4 70 1 CCGGGAGTTGAACCCGGGTCGAGGAGTCCGCAGCC 4 86 0 GTTCAACTCCCGGCGGGGGCATGGAATTTTTAATG 4 108 1 AAATTATCATCCCGGAGGAAGTCGAGTACACCGAA 15 191 1 AACCACCAACAAGAGAGGAAATCGACACACTTAAA 15 224 1 GATTAAGGGAGGGGCCCGATAGATTTGAA 22 4 1 TAGATTTGAACATCGAGGAGACGGATGAAGGTTAT 22 29 1 GTAGCTCAGGCACTGGGGCACTCAATTTTTACACT 22 64 1 GCTCCCAAAGCCGAGAGGATCACCAGGCTACCCTA 23 127 1 TCTTTCTGTCATGAGGGAGGCAGGATTTAAATACT 23 239 0 * * **** * *** MAP Score: 12.0741 Motif 5 GGGTTCGAATCCCTCCCCCCGCATTTAGTTCTGTT 2 130 0 GGGATTCGAACCCTCGAACCCCTACGGGACAGGAC 2 152 1 CGGGACAGGACCCTCAATCCTGCGCCTTTGTCCGC 2 176 1 CCTTTGTCCGCTCGGCAACCCCCGCTCAGATGAAA 2 200 1 CCAATTTTTCCACGTCGCCCCCGTGGGGTAGCGGA 4 41 1 GTCGAGGAGTCCGCAGCCCCTCAGGATATCCGCTA 4 69 0 GGGCTGCGGACTCCTCGACCCGGGTTCAACTCCCG 4 85 1 ATTAAAAATTCCATGCCCCCGCCGGGAGTTGAACC 4 107 0 TAACCATTGCCGCCTCTGCCTCTTTTGAGCATATT 10 15 0 ACAACTCCCGGATACCTCGACGGTAGCAGAG 15 6 1 AGAGAAAGTTCTGGACTTCCGGAAGGCACTGGCCC 15 37 1 AGCTGTTATTCAACACGTCCTCAACGTTACGTCCT 15 150 0 GTTCGGTGTACTCGACTTCCTCCGGGATGATAATT 15 192 0 ATGTTCAAATCTATCGGGCCCCTCCCTTAATC 22 7 0 AAATTGAGTGCCCCAGTGCCTGAGCTACATAACCT 22 57 0 AAGCTTACGACAAGACTGCCTGCTCCTTTATCCTT 22 109 0 GAGTTCAAATCTCGGCGGCCCCATCATTGAACTGG 23 83 0 GTAGGGTAGCCTGGTGATCCTCTCGGCTTTGGGAG 23 128 0 CACCAGGCTACCCTACGGCCCCTCTGTAATGATTA 23 147 1 GTATTTAAATCCTGCCTCCCTCATGACAGAAAGAT 23 240 1 **** * **** * MAP Score: 9.71674 Motif 6 CGAACCCCTACGGGACAGGACCCTCAATCC 2 166 1 GAGCGGACAAAGGCGCAGGATTGAGGGTCC 2 183 0 GTTCAACTCCCGGCGGGGGCATGGAATTTT 4 108 1 GGAACAAATTCGGTACAGGCGGATTATCTA 5 143 1 TGCTCAAAAGAGGCAGAGGCGGCAATGGTT 10 19 1 GACTTCCGGAAGGCACTGGCCCCTACAGGG 15 50 1 GATTAAGGGAGGGGCCCGATAGATT 22 5 1 TATGTAGCTCAGGCACTGGGGCACTCAATT 22 61 1 AGAAGGATAAAGGAGCAGGCAGTCTTGTCG 22 107 1 TAATGATTAAAGGCAGTGGCTTTTAAAGCC 23 173 1 ********** MAP Score: 9.38706 Motif 7 TAGGGGTTCGAGGGTTCGAATCCCTCCCCCCGCATTTAG 2 137 0 GAGGGATTCGAACCCTCGAACCCCTACGGGACAGGACCC 2 150 1 CCTACGGGACAGGACCCTCAATCCTGCGCCTTTGTCCGC 2 172 1 TGCGCCTTTGTCCGCTCGGCAACCCCCGCTCAGATGAAA 2 196 1 GAGTCCAATTTTTCCACGTCGCCCCCGTGGGGTAGCGGA 4 37 1 TGACATTAAAAATTCCATGCCCCCGCCGGGAGTTGAACC 4 107 0 ATGTTTGTTATGAGCACTATGCCCACCTCAAAATTTTTT 8 92 0 GTATTTTCCAGTACATTTTTCCCTGCCCGGAG 11 9 1 ACAACTCCCGGATACCTCGACGGTAGCAGAG 15 2 1 GGACTTCCGGAAGGCACTGGCCCCTACAGGGTGATAACG 15 49 1 GGTGGTTCGGTGTACTCGACTTCCTCCGGGATGATAATT 15 192 0 GCAGTATTAAAAAACGGTTTTCCCGCCAGTTCAATGATG 23 58 1 GCCGAGAGGATCACCAGGCTACCCTACGGCCCCTCTGTA 23 136 1 TGAAGTATTTAAATCCTGCCTCCCTCATGACAGAAAGAT 23 236 1 GGTTTATACCTCCCCATTCTACCCTGCTC 26 11 1 * * ** *** ** * MAP Score: 8.61129 Motif 8 GCGGGGGGAGGGATTCGAACCCTCGAACCC 2 143 1 AGGGATTAATAGAGTTAAACAAGGTGGTGT 3 124 1 GCCCCCGCCGGGAGTTGAACCCGGGTCGAG 4 98 0 GCTGATATGTAGAGTCGAACCACATTGTAT 16 89 1 AAAAGGTTTTAGAGTTGAGCGAATTT 19 6 0 GGGGCCCGATAGATTTGAACATCGAGGAGA 22 20 1 GGGGCCGCCGAGATTTGAACTCGGGTCACC 23 96 1 ********** MAP Score: 6.79436 Motif 9 GTTATATGAAGTCATCGCCCTTTAAACCACAAT 2 258 0 ATATAACTTTGAAATCCACCTTCTAC 2 284 1 TTAAAAATAGATAATCCGCCTGTACCGAATTTG 5 147 0 ACTCATATTTGGAATCCTCCTTTATAATTCTTA 7 117 0 TAAGTAATGAGAAATCTCCCTGTTGGCT 14 47 1 ACCAATCTGCGTTATCACCCTGTAGGGGCCAGT 15 64 0 TTAAGAGAGAAAAATCTGCCGTTCTCCA 17 5 0 AGAATCAACCTGTCAGCTTTTCT 23 0 1 * **** ***** MAP Score: 5.84123 Motif 10 CAGAACTAAATGCGGGGGGAGGGATTCGAACCCTC 2 132 1 GAGGGTCCTGTCCCGTAGGGGTTCGAGGGTTCGAA 2 156 0 ATCCGCTACCCCACGGGGGCGACGTGGAAAAATTG 4 42 0 GGGAGTTGAACCCGGGTCGAGGAGTCCGCAGCCCC 4 84 0 CGGGTTCAACTCCCGGCGGGGGCATGGAATTTTTA 4 105 1 GAAAAAATTTTGAGGTGGGCATAGTGCTCATAACA 8 91 1 GTTCTGGACTTCCGGAAGGCACTGGCCCCTACAGG 15 44 1 GAAATTATCATCCCGGAGGAAGTCGAGTACACCGA 15 190 1 AAGAATTGGACCCGGATGGTATTTTAATAAGAAAA 15 257 1 AAGAAAAAAGTGAAGGAGGTGTATT 15 285 1 GATTAAGGGAGGGGCCCGATAGATTTGA 22 3 1 CATTCGTTTTTCAGGATGGTGAAGTATTTAAATCC 23 217 1 CTTTCTGTCATGAGGGAGGCAGGATTTAAATACTT 23 238 0 ****** ** * * MAP Score: 4.9725 Motif 11 TCGAGGGTTCGAATCCCTCCCCCCGCATTTAGTTCTG 2 132 0 AGTTGAACCCGGGTCGAGGAGTCCGCAGCCCCTCAGG 4 79 0 TGACATTAAAAATTCCATGCCCCCGCCGGGAGTTGAA 4 109 0 AATTGGAACAAATTCGGTACAGGCGGATTATCTATTT 5 139 1 CCCACCTCAAAATTTTTTCCCACCTGACTATATAACG 8 73 0 TCAAATCCAGTCGTCCAAAGGAGTATA 13 8 0 ACAACTCCCGGATACCTCGACGGTAGCAG 15 2 1 TAGCAGAGAAAGTTCTGGACTTCCGGAAGGCACTGGC 15 33 1 ATCCCGGAGGAAGTCGAGTACACCGAACCACCAACAA 15 199 1 TCTGAGCTGCAGTTCCAGAAAAGCTGACAGGTTGATT 23 12 0 ACCCGAGTTCAAATCTCGGCGGCCCCATCATTGAACT 23 85 0 TGAAGTATTTAAATCCTGCCTCCCTCATGACAGAAAG 23 236 1 AGGTTTATACCTCCCCATTCTACCCTG 26 0 1 ** ** * * ** ** MAP Score: 4.74513 Motif 12 AAGAAGATTTACACGTCCACTTTCAATCCC 2 42 0 GAGGGTTCGAATCCCTCCCCCCGCATTTAG 2 137 0 TACACCACCTTGTTTAACTCT 3 134 0 TTTTACCACCACTCATATTTGG 7 138 0 AATACCACCTTGTTAGTACTT 8 1 1 CAACTCCCGGATACCTCGACGGTAGCAGAG 15 11 1 GTCCTCAACGTTACGTCCTTCATGAAGCGC 15 139 0 CTGTTATTCAACACGTCCTCAACGTTACGT 15 153 0 AATACACCTCCTTCACTTTTTTC 15 287 0 CATATCAGCCACACCTCGTTTAAACGAGCT 16 68 0 AGGTTTATACCTCCCCATTCTACCCT 26 6 1 ********** MAP Score: 4.30692 Motif 13 TCCTATGCAGAATTTTTCATCTGAGCGGGG 2 219 0 GGGGGCATGGAATTTTTAATGTCAATAA 4 122 1 TACGCGTTTAGATTTTTCATTTGCTCTCGT 5 87 0 CCTGTACCGAATTTGTTCCAATTAATACTT 5 132 0 ATATTGCCAGATTTGTTAATTATAAAAA 6 8 0 ATTTAAATTTTTTCATTTATGAACAC 6 85 0 TTTTTACGAAATTTTTTCAAATAAATTTCA 7 84 0 ATTTTGCTGTAATTTTTAAT 12 0 0 TTTTAATTTTTATTTTTTCCAACA 14 4 1 AGATTTTTCGAATTGTTCAAGCGAAGCTCG 16 44 1 GTTTTTTAATTAATCATAAC 18 0 1 TTTGGAACTAAATAGTTCATACATAGGAAC 20 43 1 ATTACGCCTGAATTGTTCCTATGTATGAAC 20 57 0 TGGGGCACTCAATTTTTACACTTGAAGTAA 22 77 1 CGGGAAAACCGTTTTTTAATACTGCCAGAT 23 53 0 ********** MAP Score: 3.54003 Motif 14 CAGGATTGAGGGTCCTGTCCCGTAGGGGTTCGAGGGT 2 161 0 TCAATCCTGCGCCTTTGTCCGCTCGGCAACCCCCGCT 2 189 1 CCAATTTTTCCACGTCGCCCCCGTGGGGTAGCGGATA 4 41 1 CCGTGGGGTAGCGGATATCCTGAGGGGCTGCGGACTC 4 61 1 TCGACCCGGGTTCAACTCCCGGCGGGGGCATGGAATT 4 99 1 TTTTCCAGTACATTTTTCCCTGCCCGGAG 11 13 1 TAAGTAATGAGAAATCTCCCTGTTGGCT 14 47 1 AGAGAAAGTTCTGGACTTCCGGAAGGCACTGGCCCCT 15 37 1 ACCAATCTGCGTTATCACCCTGTAGGGGCCAGTGCCT 15 60 0 GTTCGGTGTACTCGACTTCCTCCGGGATGATAATTTC 15 190 0 GTAGGGTAGCCTGGTGATCCTCTCGGCTTTGGGAGCC 23 126 0 GTATTTAAATCCTGCCTCCCTCATGACAGAAAGATAC 23 240 1 * * ***** *** MAP Score: 2.67801 Motif 15 GATACTTACACTTTAATTGCAATTAAAATTGCCATT 1 5 1 TAAGTTGAAATCAGACCAAAATGGGATTGAAAGTGGACGTG 2 20 1 AAGATTTTGATTTGACATACTTTGAAATTTATTTGAAAAAA 7 62 1 AATACCACCTTGTTAGTACTTGAATTCAAACCA 8 2 1 TTCTCGGGCCTCAGGCCCATGTTGTACTGCATGTATGTCCC 10 60 0 ATTAAAAATTACAGCAAAATAGTAATATATATGTTAATC 12 8 1 ACGTGTTGAATAACAGCTCTTTTGAAATTATCATCCCGGAG 15 167 1 ACTTAAAGAATTGGACCCGGATGGTATTTTAATAAGAAAAA 15 252 1 ACCTTTTCTTTAACAGATTTTTCGAATTGTTCAAGCGAAGC 16 30 1 GGAGCTATTTCAGCAATCTGCTATTTGACGTTTCCCAT 25 57 0 * **** * * * * * MAP Score: 1.21982