AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_fusions005_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944251105 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0030 62 oligopeptide ABC transporter, permease protein #1 TM0031 24 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #2 TM0032 300 transcriptional regulator, XylR-related #3 TM0122 247 ferric uptake regulation protein #4 TM0486 66 conserved hypothetical protein #5 TM0766 117 transcriptional regulator, GntR family #6 TM1132 155 moxR protein, putative #7 TM1135 83 branched chain amino acid ABC transporter, periplasmic amino acid-binding protein #8 TM1136 78 branched chain amino acid ABC transporter, permease protein #9 TM1222 55 oligopeptide ABC transporter, permease protein #10 TM1223 131 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein #11 TM1225 52 conserved hypothetical protein #12 TM1227 158 endo-1,4-beta-mannosidase #13 TM1234 42 sugar ABC transporter, permease protein #14 TM1235 22 conserved hypothetical protein #15 TM1299 150 hypothetical protein #16 TM1300 103 hypothetical protein #17 TM1301 185 astB/chuR-related protein #18 TM1632 62 conserved hypothetical protein Motif 1 ACCCGGCCCCGAAGTGGGGCCGGGAAAAGA 0 6 0 TCCCGGCCCCACTTCGGGGCCGGGTTCCACAAAA 0 15 1 GGGTTCCACAAAAACAGAGTGGGGAGTGAGAATT 0 36 1 TAGAAGAGCCGAATTGAGGAGGTGGAAAA 4 47 1 AAATCATTCTCATGAGGGGAGGGAAGAGAT 7 63 1 TCTTTGATTGAAGAAAGGAAGGTGAAAGA 8 59 1 AAAACCCCGCCCCGAGGGGCGGGGTCATCATT 9 8 0 ATGACCCCGCCCCTCGGGGCGGGGTTTTAAAAAA 9 14 1 ATCTCATACTCTTTTAAGGGGGTGTTCTT 10 112 1 AGAGCCCCACCCAAGAGGGTGGGGGAAAAT 11 6 0 TTTCCCCCACCCTCTTGGGTGGGGCTCTAAATCT 11 12 1 TACCCGGGGTGGGGATCCCCACCC 13 0 1 TGCACCCCCGGAAAAGGGGTGGGGATCCCCACCC 13 16 0 AGCAGTATGTAACAAGTGGTCGTGAGAAGAGAAA 15 115 1 AAGATCTGTTCTAATGAGGAAGGGGG 16 87 1 GTACTCTACAAAAATGGGGTGGTTGT 17 169 1 ** **** **** MAP Score: 20.2037 Motif 2 TTATCCATATACAAAGGAGGT 1 13 1 ATAATTTCTTTCTGAGGAAGATAGATAAGAA 2 263 1 GATAGATAAGAAGCAGGAGGAATATGGA 2 282 1 AGTATAATAGAACCGGGAGGG 4 0 0 GAAGAGCCGAATTGAGGAGGTGGAAAA 4 49 1 AAATCAATTAAATCAGGAGGG 5 0 0 AGAAAAGATATTCCAGGAGGT 6 0 0 CAAATACTTCTATCTGGAGGGATCCTCGG 6 136 1 TAAAAATCATTCTCATGAGGGGAGGGAAGAG 7 60 1 GTTTTAAAAAAAGAAGGAGGTAGGAGTC 9 37 1 AGCCCCACCCAAGAGGGTGGGGGAAAAT 11 7 0 GGGCTCTAAATCTAAGGAGGGAAGCATGG 11 33 1 GTTTACTAATTAACGGGAGGTATCGGT 12 141 1 TACCCGGGGTGGGGATCCCCACC 13 2 1 CACCCCCGGAAAAGGGGTGGGGATCCCCACC 13 17 0 TGAAAAGCTTTATGAGGAGGCTCTCTCAGAA 15 26 0 GGCTTTTCAAAACCAGGAAGATTTGAAAGGT 16 51 1 GATCTGTTCTAATGAGGAAGGGGG 16 89 1 ACTCTACAAAAATGGGGTGGTTGT 17 171 1 ATTGTACAACACTGTGGAGGAACAGAAA 18 44 1 ** ******** MAP Score: 19.3212 Motif 3 ATATTAGAATTTGAACTATAATTCGAAATAATTCCTGTTATT 2 162 1 ATTCCTGTTATTCACTCATAATCATAAAAAATGAGTATTACT 2 192 1 TGTTTGTACTTTTTGAGTCATATCGTTATAATTTCTTTCTGA 2 236 1 TGCTCTCCGATTATACCGTATTATGGTATAATGAAAATGGAT 3 102 0 CCCTCCCGGTTCTATTATACTATGTTATAATTCAAATTAGA 4 9 1 GTCTTGCGTGTTTTGTTGCGTTTTGTTAAAATAGATGATGAA 5 29 0 ATGCAGAAATTTCGCCAGTACTGGTGTATAATTTTTCAGAAG 6 29 0 GATTTTAGATTCTAATCGGAAATAATTGCTCACTTT 12 4 1 ATTGCTCACTTTCACAAATAAAACTCGAAAATCACGAAAAAT 12 34 1 TCATAAAGCTTTTCATGACGGTATTTCAGAAATCTTATGTAA 15 42 1 TCATGGCATGTTTTGAAGCAGTATGTAACAAGTGGTCGTGAG 15 99 1 GAAAAGCCCTTTTTAAAGCGTTCTGCGATAAAGGATTTTCAT 16 17 0 GAATATTTGATTATTAAGTACTCTACAAAAATGGGGTGGTTG 17 152 1 TTTCTGTTCCTCCACAGTGTTGTACAATACATATTGAA 18 34 0 ** ** * * * *** MAP Score: 10.7702 Motif 4 CTTCTCACTTTGAGAATGTCTTGAGCTCCTTG 2 89 1 TCTATCTTCCTCAGAAAGAAATTATAACGATA 2 256 0 CGATGAATACTGAGAAATATATCATCAGTACA 3 144 1 TACACTACTCTCAGAATCAAGTTCTGTCTTGC 5 64 0 TTCGAAAAATTGAGAATTTGATAGAAAAACTG 6 87 1 CCTCCCCTCATGAGAATGATTTTTATAAGTAT 7 53 0 TTGCAAATAATCAGAAATAAATCTTGATAATC 10 20 1 TAGATTCTAATCGGAAATAATTGCTCACTTTC 12 15 1 TCGATGACCCTGATAAATAAGTAAAGTTTACT 12 116 1 GGTGAGAAAGTGGTTGTTTTTC 14 2 1 GGAGGCTCTCTCAGAAATAGATAGCGCAATAG 15 10 0 TAGACTGAGGTTAGAAATTTTTAAAGAAGGCG 17 93 1 ********* * MAP Score: 8.94891 Motif 5 TTTTCTTTGAGTTACAACTGATTTTATTCCCGATGCTCT 2 124 0 ACTATAATTCGAAATAATTCCTGTTATTCACTCATAATC 2 176 1 ATCTTCCTCAGAAAGAAATTATAACGATATGACTCAAAA 2 246 0 CCCTCCTGATTTAATTGATTTCATCATCTATTTTAA 5 7 1 ACTACTCTCAGAATCAAGTTCTGTCTTGCGTGTTTTGTT 5 54 0 TTGAGAATTTGATAGAAAAACTGGTATACTTTGAAGTAT 6 96 1 GATCCCTCCAGATAGAAGTATTTGCATACTTCAAAGTAT 6 121 0 CAAATAATCAGAAATAAATCTTGATAATCCCGGGAGACT 10 23 1 ATTCTAATCGGAAATAATTGCTCACTTTCACAAATAAAA 12 18 1 GACTTCTGCAAAGTCAAGTCCTATTTTTCGTGATTTTCG 12 59 0 CAGGGTCATCGAGAAAAAATGTACCATTCGGACTTCTGC 12 89 0 CTTCCGGAGGGATTCAATATGTATTGTACAACACTGTGG 18 22 1 ** * ** * * * * * MAP Score: 8.19588 Motif 6 GTTATAATTTCTTTCTGAGGAAGATAGATAAGA 2 260 1 GGTGTATAATTTTTCAGAAGAAAAGATATTCCA 6 16 0 TAAAAATCATTCTCATGAGGGGAGGGAAGAGAT 7 60 1 TCTCATACTCTTTTAAGGGGGTGTTCTT 10 113 1 GGGCTCTAAATCTAAGGAGGGAAGCATGG 11 33 1 TCCCCACCCCTTTTCCGGGGGTGCACC 13 25 1 TCATGAAAAGCTTTATGAGGAGGCTCTCTCAGA 15 27 0 TCATAAAGCTTTTCATGACGGTATTTCAGAAAT 15 42 1 AAAGATCTGTTCTAATGAGGAAGGGGG 16 86 1 CATTCTATTCCTTTAGGTGGATGCACTAACAGA 17 33 1 GTTAGAAATTTTTAAAGAAGGCGGCCGCCTTCT 17 102 1 ATATTGAATCCCTCCGGAAGGAGACACAACGA 18 9 0 *** * ***** * MAP Score: 7.29335 Motif 7 CCGGCCCCGAAGTGGGGCCGGGAAAAGA 0 5 0 CCACAAAAACAGAGTGGGGAGTGAGAATTGA 0 41 1 GAAGAGCCGAATTGAGGAGGTGGAAAA 4 49 1 ATAATATTACAGCGAGGTGATAGATC 5 101 1 AAATCATTCTCATGAGGGGAGGGAAGAGAT 7 63 1 CTTTGATTGAAGAAAGGAAGGTGAAAGA 8 60 1 CCCCGCCCCGAGGGGCGGGGTCATCATT 9 5 0 GTTTTAAAAAAAGAAGGAGGTAGGAGTC 9 37 1 AGCCCCACCCAAGAGGGTGGGGGAAAAT 11 5 0 CTCTAAATCTAAGGAGGGAAGCATGG 11 36 1 CACCCCCGGAAAAGGGGTGGGGATCCCCACCCC 13 15 0 GATCTGTTCTAATGAGGAAGGGGG 16 89 1 GAAATTTTTAAAGAAGGCGGCCGCCTTCTCTAT 17 106 1 ACTCTACAAAAATGGGGTGGTTGT 17 171 1 ** **** *** * MAP Score: 7.26066 Motif 8 ACATGGAGTCAATAACTTATGATTTCGATGGATTTTTTGT 2 39 1 TCTCACTTTGAGAATGTCTTGAGCTCCTTGGAAAGAGCAT 2 91 1 AATACTGAGAAATATATCATCAGTACAATGTTTGAATGAT 3 149 1 CAATGTTTGAATGATATCTTGAAATCAGCGACTGTGTGTA 3 174 1 GCAAGACAGAACTTGATTCTGAGAGTAGTGTAATAGTATA 5 64 1 GTAGTGTAATAGTATAATATTACAGCGAGGTGATAGATC 5 88 1 GATTCAAAAGGATTTCTTGACCGTTTCGTGGTGAGCCT 7 8 1 AATAATCAGAAATAAATCTTGATAATCCCGGGAGACTGGA 10 25 1 TTAAAAGAGTATGAGATCGCTATCTCCACGTGTAAATGTA 10 89 0 CACTTTCACAAATAAAACTCGAAAATCACGAAAAATAGGA 12 40 1 AATCACGAAAAATAGGACTTGACTTTGCAGAAGTCCGAAT 12 63 1 CGAATGGTACATTTTTTCTCGATGACCCTGATAAATAAGT 12 98 1 GATGTGCAGTAGTAACTCCTTAGACTGAGGTTAGAAATTT 17 73 1 AGGAATATCTAGGAATATTTGATTATTAAGTACTCTACAA 17 140 1 * ** ** *** * * MAP Score: 5.91082 Motif 9 TCTTTTCCCGGCCCCACTTCGGGGCCGGGTTCCACAA 0 8 1 TTATAAAAATCATTCTCATGAGGGGAGGGAAGAGAT 7 57 1 CAAGCAAAAGCGAGGCCCCTCAGGGGCTTCGCTTTCTTT 8 25 1 AATGATGACCCCGCCCCTCGGGGCGGGGTTTTAAAAA 9 8 1 TAGCGATCTCATACTCTTTTAAGGGGGTGTTCTT 10 107 1 ATTTTCCCCCACCCTCTTGGGTGGGGCTCTAAATC 11 6 1 TGGGGATCCCCACCCCTTTTCCGGGGGTGCACC 13 19 1 CACAAAAGATCTGTTCTAATGAGGAAGGGGG 16 82 1 ATGTATTGTACAACACTGTGGAGGAACAGAAA 18 40 1 * * ** * *** * * MAP Score: 4.78672 Motif 10 TAACTCAAAGAAAATATTAGAATTTGAACTATAATTCGAA 2 149 1 TTTTATGATTATGAGTGAATAACAGGAATTATTTCGAATT 2 181 0 ATTATACCATAATACGGTATAATCGGAGAGCACGATGAAT 3 112 1 TTTGAATTATAACATAGTATAATAGAACCGGGAGGG 4 6 0 GTTATAATTCAAATTAGAAGAGCCGAATTGAGGAGGTGGA 4 33 1 TAGATGATGAAATCAATTAAATCAGGAGGG 5 0 0 AAACGCAACAAAACACGCAAGACAGAACTTGATTCTGAGA 5 48 1 CGTGTATTCGAAAAATTGAGAATTTGATAGAAAAACTGGT 6 81 1 TTTGATAGAAAAACTGGTATACTTTGAAGTATGCAAATAC 6 103 1 TGAAGTATGCAAATACTTCTATCTGGAGGGATCCTCGG 6 127 1 AAAACTCGAAAATCACGAAAAATAGGACTTGACTTTGCAG 12 53 1 TCATCGAGAAAAAATGTACCATTCGGACTTCTGCAAAGTC 12 83 0 GGCTTTTCAAAACCAGGAAGATTTGAAAGGTCACAAAAGA 16 51 1 ** * * * * *** * MAP Score: 4.52949 Motif 11 ATCTGCCATCCATTTTCATTATACCATAATACGGTA 3 95 1 AAGCATTTGCAAGTTATATTGTACTACACACAGTCG 3 202 0 CGGCTCTTCTAATTTGAATTATAACATAGTATAATA 4 22 0 CCCTCCCGGTTCTATTATACTATGTTATAATT 4 6 1 TATCACCTCGCTGTAATATTATACTATTACACTACT 5 87 0 TTCGAATTATAGTTCAAATTCTAATATTTTCTTTGA 2 153 0 ATTCATCGTGCTCTCCGATTATACCGTATTATGGTA 3 116 0 GTATTTGCATACTTCAAAGTATACCAGTTTTTCTAT 6 107 0 TTTCGAATACACGTTGAATTTTAATGCAGAAATTTC 6 58 0 GCTGATTTCAAGATATCATTCAAACATTGTACTGAT 3 167 0 AAACTTCCATTGAAACAAGCAAAAGCG 8 1 1 GATTTTAGATTCTAATCGGAAATAATT 12 1 1 AATTGATTTCATCATCTATTTTAACAAAACGCAACA 5 22 1 * * *** ***** MAP Score: 4.20416 Motif 12 GAAAATATTAGAATTTGAACTATAATTCGAAATAATTCCTGTTA 2 158 1 GTTATTCACTCATAATCATAAAAAATGAGTATTACTCGTGTTTG 2 198 1 AAATTATAACGATATGACTCAAAAAGTACAAACACGAGTAATAC 2 226 0 ATTTCTTTCTGAGGAAGATAGATAAGAAGCAGGAGGAATATGGA 2 266 1 TTTCTAAAATAAACCCCTTAAAAAAATCGAAGAACTCAGCTTCG 3 40 1 TATAATCGGAGAGCACGATGAATACTGAGAAATATATCATCAGT 3 129 1 CAAATTAGAAGAGCCGAATTGAGGAGGTGGAAAA 4 42 1 TTGATTTCATCATCTATTTTAACAAAACGCAACAAAACACGCAA 5 24 1 GAAAAATTGAGAATTTGATAGAAAAACTGGTATACTTTGAAGTA 6 90 1 AAACTTCCATTGAAACAAGCAAAAGCGAGGCCCC 8 0 1 CGCTTTCTTTGATTGAAGAAAGGAAGGTGAAAGA 8 54 1 CGCCCCTCGGGGCGGGGTTTTAAAAAAAGAAGGAGGTAGGAGTC 9 21 1 GATTTTAGATTCTAATCGGAAATAATTGCTCACT 12 0 1 CACTTTCACAAATAAAACTCGAAAATCACGAAAAATAGGACTTG 12 40 1 ACGCTTTAAAAAGGGCTTTTCAAAACCAGGAAGATTTGAAAGGT 16 38 1 TGGATGCACTAACAGAAGTCAAAGATGTGCAGTAGTAACTCCTT 17 50 1 ** * * ** * ** * MAP Score: 2.43943 Motif 13 ATAATTTCTTTCTGAGGAAGATAGATAAGAAGCA 2 263 1 TAAAAATCATTCTCATGAGGGGAGGGAAGAGAT 7 60 1 CTTTCTTTGATTGAAGAAAGGAAGGTGAAAGA 8 56 1 GGGCGGGGTTTTAAAAAAAGAAGGAGGTAGGAGT 9 30 1 TTAGAGCCCCACCCAAGAGGGTGGGGGAAAAT 11 8 0 GGGCTCTAAATCTAAGGAGGGAAGCATGG 11 33 1 AAAGGGCTTTTCAAAACCAGGAAGATTTGAAAGG 16 47 1 AAAGATCTGTTCTAATGAGGAAGGGGG 16 86 1 GTTAGAAATTTTTAAAGAAGGCGGCCGCCTTCTC 17 102 1 ** * ***** ** MAP Score: 2.08488