AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_operons012_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944252147 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0107 76 conserved hypothetical protein #1 TM0110 107 transcriptional regulator, XylR-related #2 TM0276 300 L-arabinose isomerase #3 TM0278 300 sugar ABC transporter, permease protein #4 TM0280 188 hypothetical protein #5 TM0281 21 alpha-L-arabinofuranosidase #6 TM0282 28 aldose 1-epimerase #7 TM0433 246 pectate lyase #8 TM0434 89 alpha-glucosidase, putative #9 TM0436 55 alcohol dehydrogenase, zinc-containing #10 TM0952 300 glycerol kinase #11 TM1069_TM1070 107 TM1069: transcriptional regulator, DeoR family, TM1070: hypothetical protein #12 TM1420 255 hypothetical protein #13 TM1428 108 methyl-accepting chemotaxis protein #14 TM1429 209 glycerol uptake facilitator protein #15 TM1430 31 glycerol kinase #16 TM1432 80 conserved hypothetical protein #17 TM1437 300 dimethyladenosine transferase #18 TM1667 104 xylose isomerase Motif 1 GAAAATGTGGAGGGAGGATTCG 0 2 0 TGAGATCCAAAAGGAGGAATCGAAG 1 92 1 CGAGAAGATCAACGAGGTGATGATGAGAAA 2 64 1 ATTTTTAGGCAGGGGGGATTTGTATGAAGA 2 111 0 CTTGGAAAATAAGGAGGTGAAGAGGGGGCG 3 263 1 GGCAAAAGGGGGCAGAGCGCCCCCTC 3 284 0 AATGTATGAAAAGGAGGAATATCGTTT 4 171 1 GAGATGAGGAGGGAAAAGAGT 5 5 1 AAACTGTTGCCAGGAGGAGAAAGAA 6 13 1 AATCTTATGTTAGGAGGGGAGAGTT 7 5 0 TAACATTTGGAGGGGGGAGACCCCCTCTTT 8 29 1 CCGGAATTTAGAGGAGGTGCACAC 8 75 1 AGAGTGGTTCAAGGAGGGAAATTAGA 10 284 1 TTCGAAAGGAAAGGAGGTGTTGAT 11 93 1 AACAAAAGCTAAGGAGGTGAAACAT 12 5 0 ATAATGAAAAAAGGGGCTGAACGCCCCTTT 13 30 0 ACATTTCAGCAGGGAGGTTTCAGAC 13 93 1 TGGATACTGCTGGGGGGTTAAATATTTACA 14 170 1 ATTTACATACAAGGAGGATTGGGAAA 14 193 1 CTTATCGCAAAAGGAGGGGTCTTC 15 17 1 CTTTTTGTTTAAGGAGGTGCAAACG 16 65 1 TACTTGAATCTGGGAGGTGTTTTCA 18 5 0 GAAAAAATTTAGGGAGGTGTTTAC 18 90 1 ********** MAP Score: 33.8585 Motif 2 ACAGCCAAAAAAGGAGAAAATAACAGATATCC 1 6 1 TAAAAGGATGAAACCATGAGAAAGGAGGTCGGAGA 2 275 1 AAATGGGAAGAGATTCTTGGAAAATAAGGAGGTGAA 3 248 1 AAGGATAGTTTGTGAAAAAATGAGAAACCA 4 4 1 AAAAAATGAGAAACCATAAGAAAAGAGCTTTTAAAC 4 24 1 TGGACAATGTAGAATTTGCGTAAAGAATAATGTACG 4 129 1 GTACGTACCTAAATGTATGAAAAGGAGGAATATCGT 4 160 1 GAGATGAGGAGGGAAAAGAGT 5 3 1 CCAAATATTGACTTGAATCGAAAAGATGTGGTAACA 7 174 1 AGGAGTAGGTAAATTTTGAGAAAGGAATTCTGCAAC 10 144 0 ATTTGTGATAAAATTTTTCGAAAGGAAAGGAGGTGT 11 77 1 TTTGTTTTTGATATGGAAGGAAAGTAACATGGTAAG 12 29 1 ATAGTGAAAAATATAACGTGAAAAGGTTCACGATTT 12 219 1 GTGAAAAGGTTCACGATTTGAAAGGAACG 12 236 1 AAAACGTCTTGAAAAGAAAAAAAGGGG 13 1 1 TTCTTGAAGGAGAGAGAAAAGAGAGAGCCATA 16 6 1 ATATCCTAAAAAAATATTTGAAATGATACCCCAAGA 18 34 1 * * * ******* MAP Score: 13.537 Motif 3 AGATCCAAAAGGAGGAATCGAAG 1 94 1 CGCGTTGTCTGGAGAACAGAGAACGGAGATTT 2 28 1 CCATGAGAAAGGAGGTCGGAGA 2 288 1 TCGGGATCCTGGAGTGTTGAGATTCTGGCAGG 3 41 0 TCCAGGATCCCGAGGTGAGGGCCGCTGATCCG 3 60 1 TACGTTACCTCGAGGGCGGGAACTCTCGGATC 3 86 0 GGATCTTGGAGAAGGTCTCAACGGTGATGTCT 3 166 0 GGCAAAAGGGGGCAGAGCGCCCCCTC 3 284 0 GAGATGAGGAGGGAAAAGAGT 5 4 1 ACTGTTGCCAGGAGGAGAAAGAA 6 15 1 TCTTATGTTAGGAGGGGAGAGTT 7 1 0 GTTAACATTTGGAGGGGGGAGACCCCCTCTTT 8 27 1 TAGCATTTTTGGAGGTCTCGGTGGAGCGGTTG 10 116 1 TAGAGTGGTTCAAGGAGGGAAATTAGA 10 283 1 ATTTCAGCAGGGAGGTTTCAGAC 13 95 1 TTACATACAAGGAGGATTGGGAAA 14 195 1 TTCTTGAAGGAGAGAGAAAAGAGAGAG 16 5 1 TTTTGTTTAAGGAGGTGCAAACG 16 67 1 ***** * **** MAP Score: 11.7074 Motif 4 ACGTTGAAAATGTGGAGGGAGGATTCG 0 6 0 CCACTATTTTTAGGCAGGGGGGATTTGTATG 2 115 0 GATGAAACCATGAGAAAGGAGGTCGGAGA 2 281 1 GTGTTGAGATTCTGGCAGGAGCGACGGCGAA 3 29 0 AATAAGGAGGTGAAGAGGGGGCGCTCTGCCC 3 270 1 GAGATGAGGAGGGAAAAGAGT 5 4 1 AAAACTGTTGCCAGGAGGAGAAAGAA 6 12 1 AAATCTTATGTTAGGAGGGGAGAGTT 7 5 0 ATCAGATATCTCAGTAGGGAGGG 7 233 1 TCCGTTAACATTTGGAGGGGGGAGACCCCCT 8 24 1 GGTTCAAATACAAAGAGGGGGTCTCCCCCCT 8 39 0 AGGTAAATTTTGAGAAAGGAATTCTGCAACC 10 143 0 TAGAGTGGTTCAAGGAGGGAAATTAGA 10 283 1 AAACAAAAGCTAAGGAGGTGAAACAT 12 5 0 TTGTTTTTGATATGGAAGGAAAGTAACATGG 12 30 1 TTTTCACTATTTTTCAGGAGAAGTCAAGGGA 12 198 0 AGGTTCACGATTTGAAAGGAACG 12 242 1 CAAAAACATTTCAGCAGGGAGGTTTCAGAC 13 88 1 TTCTTGAAGGAGAGAGAAAAGA 16 1 1 * ********* MAP Score: 11.3965 Motif 5 CGAATCCTCCCTCCACATTTTCA 0 3 1 CTGTTATTTTCTCCTTTTTTGGCTGT 1 6 0 CTTCGATTCCTCCTTTTGGATCTCAATAT 1 88 0 CTTCATACAAATCCCCCCTGCCTAAAAATA 2 112 1 TTCTCATGGTTTCATCCTTTTAGTATAACA 2 267 0 TCTCCGACCTCCTTTCTCATGGTTTCAT 2 282 0 CTTCTCCAAGATCCTCTCTGGAGAACTCCC 3 184 1 GGGCAGAGCGCCCCCTCTTCACCTCCTTAT 3 271 0 GGGCGCTCTGCCCCCTTTTGCC 3 288 1 AAACGATATTCCTCCTTTTCATACATTT 4 170 0 ACTCTTTTCCCTCCTCATCTC 5 5 0 TTCTTTCTCCTCCTGGCAACAGTTTT 6 12 0 AACTCTCCCCTCCTAACATAAG 7 2 1 CCCTCCCTACTGAGATATCTGA 7 234 0 AAGAGGGGGTCTCCCCCCTCCAAATGTTAA 8 28 0 GAGGGGGGAGACCCCCTCTTTGTATTTGAA 8 38 1 AAACATATCAATCACCCTTGCACTTATTC 10 9 0 GCTCTGAAAACTGCTTCTTCATCCAGGGGT 10 47 0 GGTTGCAGAATTCCTTTCTCAAAATTTACC 10 143 1 AGTTTTTGCAATCCCCTCTGGCGCAAGGCC 10 249 0 TCTAATTTCCCTCCTTGAACCACTCTA 10 283 0 GGGCTGAACGCCCCTTTTTTTCTTTTCAAG 13 17 0 GGGCGTTCAGCCCCTTTTTTCATTATGGTA 13 34 1 GTCTGAAACCTCCCTGCTGAAATGTTTTT 13 89 0 TTTCCCAATCCTCCTTGTATGTAAATA 14 192 0 GAAGACCCCTCCTTTTGCGATAAGATTA 15 13 0 GGATATGGCTCTCTCTTTTCTCTCTCCTTC 16 15 0 AGAGCCATACCCCACTCTTGTGGGATATGG 16 37 0 ********** MAP Score: 10.2568 Motif 6 CTTGATTTTAAATTATTTCCTGCATATAATTAAT 1 45 1 GGAAACGCTGAACGATCTCGCAAAGAAATGGGAA 3 223 1 GTATCTATTAAGGTATAACATGCAATATTTGTCC 4 70 1 CAAGTTAATCAAACTTGACACGGATGAAAATTCG 7 75 0 TATGAAACCAAATATTGACTTGAATCGAAAAGAT 7 167 1 TTTGTATTTGAACCATTACCCGGAATTTAGAGGA 8 56 1 ATTCATACATAAAGTTATCATAAATTAATCACAA 11 32 1 CCTTTCGAAAAATTTTATCACAAATATCGTTGAC 11 68 0 AAATAGTGAAAAATATAACGTGAAAAGGTTCACG 12 217 1 TGGGGGGTTAAATATTTACATACAAGGAGGATTG 14 180 1 TGCTAATCTTATCGCAAAAGGAGGGGTC 15 4 1 GAAAAGAGAGAGCCATATCCCACAAGAGTGGGGT 16 25 1 ATGCTGAGAGAACTATTTCTCGCACAATCGAGCG 17 137 1 AAACAGAACGAAGCTTCACATAAAGAGGTTTCTG 17 217 1 TCCCAGATTCAAGTATATCCTAAAAAAATATTTG 18 20 1 ** ** ** **** MAP Score: 5.4528 Motif 7 ACAGCCAAAAAAGGAGAAAATAACAGATATCCGACCTTG 1 3 1 TTTAACCGAGAAGATCAACGAGGTGATGATGAGAAAGATCAACAGT 2 58 1 TCAATTAGTTAACATAAATCTCCGCAGAAACGGACATGATACGTAT 2 204 1 CGATCTCGCAAAGAAATGGGAAGAGATTCTTGGAAAATAAGGAGGT 3 235 1 AAGGATAGTTTGTGAAAAAATGAGAAACCATAAGAAA 4 1 1 ACATCAAAATCGAAAATCTTATGTTAGGAGGGGAGAGTT 7 3 0 AAATTCGGTGATAAAATCCCTTTGAAGTATCAGACATCAAAATCGA 7 36 0 ATTTGGTTTCATAAGAACACACACAATAATTGGATATAATTGTTTC 7 134 0 AAGATGTGGTAACATCACTGACGTGAAAATTTGAAACATCAGATAT 7 196 1 CCTTCCATATCAAAAACAAAAGCTAAGGAGGTGAAACAT 12 3 0 TCACTAAAAAGAAAACTATTGGTAAAGCACTTGAAATATATGACTG 12 105 0 CTTCTCCTGAAAAATAGTGAAAAATATAACGTGAAAAGGTTCACGA 12 206 1 CAGAAAATAACAACTTCCACATAAGATGAAACTGCATTGTG 14 5 1 TCATGACTACAAGAACGAGTGTTCAATACGCGGAAAACAGAACGAA 17 183 1 CGTTTCTGGAAGAATAGACGAAGAGATGCTAAGATACTACGA 17 268 1 CCCAGATTCAAGTATATCCTAAAAAAATATTTGAAATGATACCCCA 18 21 1 * *** * * * ** * MAP Score: 5.25872 Motif 8 ACAGCCAAAAAAGGAGAAAATAACAGA 1 7 1 TATTGAGATCCAAAAGGAGGAATCGAAG 1 89 1 AGAAGATCAACGAGGTGATGATGAGAAAGA 2 66 1 TGAAACCATGAGAAAGGAGGTCGGAGA 2 283 1 TCCAGGATCCCGAGGTGAGGGCCGCTGATC 3 60 1 AGAGGATCTTGGAGAAGGTCTCAACGGTGA 3 171 0 GGAGTTCTCCAGAGAGGATCTTGGAGAAGG 3 183 0 AACGATCTCGCAAAGAAATGGGAAGAGATT 3 233 1 AAAATAAGGAGGTGAAGAGGGGGCGCTCTG 3 268 1 GGCAAAAGGGGGCAGAGCGCCCC 3 287 0 TAGTTTGTGAAAAAATGAGAAACCATAAGA 4 15 1 AGAAACCATAAGAAAAGAGCTTTTAAACGG 4 32 1 CTAAATGTATGAAAAGGAGGAATATCGTTT 4 168 1 GAGATGAGGAGGGAAAAGAGT 5 2 1 AAACTGTTGCCAGGAGGAGAAAGAA 6 13 1 TCTTATGTTAGGAGGGGAGAGTT 7 3 0 TGACTTGAATCGAAAAGATGTGGTAACATC 7 182 1 GTTAACATTTGGAGGGGGGAGACCCCCTCT 8 27 1 TCAAATACAAAGAGGGGGTCTCCCCCCTCC 8 37 0 CCCGGAATTTAGAGGAGGTGCACAC 8 74 1 TAGAGTGGTTCAAGGAGGGAAATTAGA 10 283 1 TTTTTCGAAAGGAAAGGAGGTGTTGAT 11 90 1 CTTGAAAAGAAAAAAAGGGGCGTTCAGCCC 13 17 1 ACCATAATGAAAAAAGGGGCTGAACGCCCC 13 33 0 GGGGTTTAGAGAAAAAGAGACCCCCCAGTG 14 128 1 AATCTTATCGCAAAAGGAGGGGTCTTC 15 14 1 TTCTTGAAGGAGAGAGAAAAGAGAG 16 5 1 CCTCCTTAAACAAAAAGAGCCATACCCCAC 16 52 0 TCGATCATCTCGTGGAGATGCCTGTAGATC 17 37 0 CCGATCCACTCGTGGAAAGGGTTTTGAATC 17 105 1 CGAAGCTTCACATAAAGAGGTTTCTGAACC 17 225 1 GAAGAATAGACGAAGAGATGCTAAGATACT 17 276 1 ********** MAP Score: 3.29053 Motif 9 TTTTGATGTCTGATACTTCAAAGGGATTTT 7 40 1 CGTGAAAATTTGAAACATCAGATATCTCAG 7 217 1 AAACTATATCTGAAACATCAAACATCTTAA 9 30 1 CGTAGTGTTTTAAAACTTCATCCTGCGTTC 10 220 0 GTCTGAAACCTCCCTGCTGAAAT 13 95 0 CCACATAAGATGAAACTGCATTGTGATTTT 14 26 1 GTAGTCATGATGAAAGCCCAGTCGCTCGAT 17 163 0 ATATTTGAAATGATACCCCAAGATTTTATA 18 47 1 ********** MAP Score: 1.44145 Motif 10 ATGGTAGTATATCATATCTGTCAACAAAGAATTATCT 2 162 1 ATTTCCGTTTAAAAGCTCTTTTCTTATGGTTTCTCAT 4 29 0 CTTTTAAACGGAAATATTTGTATCTATTAAGGTATAA 4 51 1 GGTATAACATGCAATATTTGTCCAGAAATATACTTGA 4 81 1 ACAATAATTGGATATAATTGTTTCTAATCACTCGTAA 7 121 0 ACAAAAGTCAACGATATTTGTGATAAAATTTTTCGAA 11 62 1 TACCTACTTCACAAGTTTTGTAAACAAACTGATTCAC 12 147 0 ACCTTTTCACGTTATATTTTTCACTATTTTTCAGGAG 12 209 0 CCTCCCTGCTGAAATGTTTTTGAAGATTAACTTAGCA 13 73 0 AAACTGCATTGTGATTTTTGTAACTATATTGACATAA 14 38 1 GACATAAAACAAAAGGTTTGTTATAATTCACATCGAG 14 68 1 TCGAAAGAATGATAGATCTTTCGAAAAAGTACTACAA 17 63 1 * ** ***** ** MAP Score: 0.240869