AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_fusions003_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944250990 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 TM0122 247 ferric uptake regulation protein #1 TM0143 93 response regulator #2 TM0399 300 response regulator #3 TM0703 42 competence-damage inducible protein, putative #4 TM0957 73 hypothetical protein #5 TM0958 57 ribose ABC transporter, periplasmic ribose-binding protein #6 TM0960 207 ribokinase #7 TM0972 221 conserved hypothetical protein, GGDEF domain #8 TM1162 207 conserved hypothetical protein #9 TM1263 49 phosphate ABC transporter, permease protein #10 TM1264 224 phosphate ABC transporter, periplasmic phosphate-binding protein #11 TM1596 49 purine nucleoside phosphorylase #12 TM1788 215 conserved hypothetical protein, GGDEF domain Motif 1 GCTTTGCATTTGCAGGTGAGAGT 0 234 1 CTCAGGGATAGGGTGGAGATTG 1 81 1 CTTTCTGGCTGGGAGGGGAGGACTCGAACC 2 122 1 CTGGATCCGCTGGTGGAGGTTCGAGTCCTC 2 139 0 AAAGGCCGTTGGGAGGTCGTCTAACGGTAG 2 180 0 ATAGTTCAAGGGGTGGTGTTTCACGTTTTT 2 233 1 AATTTCCTTAGGGAGGTGGGTTTT 5 43 1 AAGCGGTCCGAGGAGGTGTGAAA 8 3 0 ATGCTTTTTCGGGAGGTGATTTCTAAGTGG 8 58 0 AATCTAAAATGGGAGGTGGTAAC 8 194 1 AATCCTGATGTGGAGGTGTCTCTT 10 210 1 CTACTATAAAGTGAGGTGTTG 11 1 0 AATAGTTACGTGGAGGTGATCACAAGTT 11 31 1 ********** MAP Score: 20.9176 Motif 2 GGTTCAACTCGTTTTTTTCTCTGATAATATA 1 38 1 GGTGTTTCACGTTTTTTTCACGTTCAAGCTG 2 247 1 AGAAAATACTGTTTTTACCTCAAATTTCCTT 5 21 1 GAGATTCTTTGTTTTTCTCTCGTTGACTTTT 6 117 1 GCATGTACCTGCTTTTTTCACTCCAGAATTA 7 160 0 TCCACATCAGGATTTTACCACTTCTTAGTTT 10 193 0 AGGTGATTTTCCCTCTGATATCACA 12 4 1 TTATTGTCTGAATTTTATCACAGTATTCTTT 12 62 0 CCTGTAATTGGTTTTGTTCTCCTGGAAAGCG 12 171 1 ****** **** MAP Score: 12.5018 Motif 3 ACTCTCACCTGCAAATGCAAAGCA 0 233 0 AGGTTCGAGTCCTCCCCTCCCAGCCAGAAAGG 2 121 0 TACCGTTAGACGACCTCCCAACGGCCTTTCAA 2 181 1 ACGTGAAACACCACCCCTTGAACTATCCCTGT 2 227 0 ACGATCCCTCCTCAGTGATATGATAACA 3 24 0 ATTCCATCCTCCTTTCTAAAAGGGGGCAC 4 54 0 AAAACCCACCTCCCTAAGGAAATTTGA 5 40 0 ACACCAAAGTCTTCCTCCCAAAAATATAAATC 7 79 0 TTTCACACCTCCTCGGACCGCTTTTTTAC 8 7 1 AAGCACCAGTCTTCCTCCGTAAAAAAGCGGTC 8 25 0 CACTTAGAAATCACCTCCCGAAAAAGCATCTG 8 59 1 CCCTGGCGAATTTCCTCAGAAAACTG 9 33 1 AGTATGCACCTCCTCTGGAACGAATTATAG 10 8 1 AGAGACACCTCCACATCAGGATTTTACCACTT 10 201 0 ******* * ** MAP Score: 11.2459 Motif 4 AGATTTATATTTTTGGGAGGAAGACTTTGGTGTCGT 7 78 1 TATTTGGTCATTTTTGAAAGAATACTGTGATAAAAT 12 46 1 AATCGTTCTCTTTCAGAACGAAGAGTCGGCTTAACA 10 116 1 GGGTGCCCCCTTTTAGAAAGGAGGATGGAAT 4 52 1 CTGGAACGAATTATAGCACAAAACGTTCTCAAAAAG 10 24 1 ATTATTCCAGTTATGGCATAAAAATTAATTTGGTCT 2 53 1 TTTATAATTTTTATTGTAAGGAATCTCAAGGGGGA 7 9 0 TCAACGTTAATTTCCGAAAAGAGTATAATCTAAAAT 8 168 1 TCATTCTGAATTATTGAAAAAAGTGCTTTATTCTTT 12 131 1 ACACCTCACTTTATAGTAGAATAGTTACGTGGAGGT 11 12 1 CAGTTTTCTGAGGAAATTCGCCAGGGTTC 9 30 0 CGGCTTAACATTTCTTAACAAACCATGTGAAATCAC 10 142 1 TTTAAGGGGTTTATTTTAGAAAATATAACTTTGTTA 0 26 0 GGACCGCTTTTTTACGGAGGAAGACTGGTGCTTTCC 8 24 1 ATAAATGAATTTTTTGGATAATATCCATGAACGAGA 6 47 0 TTCCGTTCTGTTATAGAACGATAGTCTCACAAAATC 10 84 1 TTCGAAATCGTTTTCACAAGAATGGTAACACGAAGG 6 154 0 TACACGGATGTTTCATAACAGACTTTTACTTTTCTC 2 17 0 ATCCCTGAGTTTTCATAATAATATATTATCAGAGAA 1 54 0 ATTCAACTTTTTATTGTCTGAATTTTATCACAGTAT 12 67 0 **** * * *** * MAP Score: 10.9241 Motif 5 TTCATCGTGCTCTCCGATTATACCGTATTATGGTAT 0 115 0 TTTTAAATGATACCATTAATCTGTCA 1 0 1 CGTTTTTTTCTCTGATAATATATTATTATGAAAACT 1 47 1 TACACGGATGTTTCATAACAGACTTTTACTTTTCTC 2 17 0 CCCAACGGCCTTTCAAATTATACATCAAGAACAGGG 2 197 1 GGGTGCCCCCTTTTAGAAAGGAGGATGGAAT 4 52 1 GAACGAGAATTTTCATAATATAGAATTTCATGGTAA 6 19 0 AAGAAAAATTTTTCAACGAACACATTCCTTCTTCAA 8 136 1 CCACCTCCCATTTTAGATTATACTCTTTTCGGAAAT 8 177 0 CACAAAACGTTCTCAAAAAGAACGATTTTTCGTAGA 10 40 1 TATTTTCCGTTCTGTTATAGAACGATAGTCTCACAA 10 80 1 GACTCTTCGTTCTGAAAGAGAACGATTTTGTGAGAC 10 107 0 CGGCTTAACATTTCTTAACAAACCATGTGAAATCAC 10 142 1 TGATTTTCCCTCTGATATCACACCATCGAAAATTAT 12 13 1 TTTGGTCATTTTTGAAAGAATACTGTGATAAAATTC 12 48 1 GCTATCACCCTTTGAGATTCAACTTTTTATTGTCTG 12 83 0 ***** * * ** * MAP Score: 10.8688 Motif 6 GTTTATTTTAGAAAATATAACTTTGTTAAAACAAAAATC 0 15 0 TTATATTTTCTAAAATAAACCCCTTAAAAAAATCGAAGA 0 34 1 TTTTTTCTCTGATAATATATTATTATGAAAACTCAGGGA 1 50 1 TCTATATTATGAAAATTCTCGTTCATGGATATTATCCAA 6 31 1 ATTAATCGATGATAAATGAATTTTTTGGATAATATCCAT 6 55 0 GTCAACGAGAGAAAAACAAAGAATCTCGATCATAAAACC 6 105 0 TAACACGAAGGAAAATGAAAAGTCAACGAGAGAAAAACA 6 126 0 AAACGATTTCGAAAACGATTTCATCAAGACACAAGGGAG 6 177 1 TTCCTTACAATAAAAATTATAAATGATGATTTGCTAAAT 7 22 1 CGCGGTGTCGTAAAATTGACATTTTACGACACCAAAGTC 7 100 0 ATCACCTCCCGAAAAAGCATCTGCGTAGAACTATTCTAA 8 68 1 GTTAATTTCCGAAAAGAGTATAATCTAAAATGGGAGGTG 8 173 1 AGAATTCTACGAAAAATCGTTCTTTTTGAGAACGTTTTG 10 42 0 ATCACACAAAGAAAACCTGGAAACTAAGAAGTGGTAAAA 10 173 1 AGAATACTGTGATAAAATTCAGACAATAAAAAGTTGAAT 12 64 1 ***** * * * ** MAP Score: 8.35448 Motif 7 ACCAGTACAGAAAGAAAAATTTTTCAACGAACA 8 125 1 ACGTTCTCAAAAAGAACGATTTTTCGTAGAATT 10 46 1 TTGTTTTAACAAAGTTATATTTTCTAAAATAAA 0 20 1 CACATTTAGCAAATCATCATTTATAATTTTTAT 7 31 0 TGGTGTCGTAAAATGTCAATTTTACGACACCGC 7 105 1 CGTAAAGAATAAAGCACTTTTTTCAATAATTCA 12 137 0 AATCGATGATAAATGAATTTTTTGGATAATATC 6 58 0 ATGATTTGCTAAATGTGAATTTAGTAAATTCAG 7 47 1 CCAAAAATATAAATCTGAATTTACTAAATTCAC 7 61 0 TCGTTCTGAAAGAGAACGATTTTGTGAGACTAT 10 104 0 ATTTGAGGTAAAAACAGTATTTTCTTCTTTTCA 5 13 0 AGACACCTCCACATCAGGATTTTACCACTTCTT 10 198 0 TCCACAGACCAAATTAATTTTTATGCCATAACT 2 61 0 GATTTTTCGTAGAATTCTATTTTCCGTTCTGTT 10 63 1 **** * ***** MAP Score: 8.2756 Motif 8 CTCCTGATTTTTGTTTTAACAAAGTTA 0 5 1 ATCTGCCATCCATTTTCATTATACCATAATAC 0 95 1 CCTATCCCTGAGTTTTCATAATAATATATTAT 1 61 0 AATGCATCCCCTTTTTCTTTATCCACAGACCA 2 83 0 CATGAACGAGAATTTTCATAATATAGAATTTC 6 26 0 TATGATCGAGATTCTTTGTTTTTCTCTCGTTG 6 110 1 TCTCTCGTTGACTTTTCATTTTCCTTCGTGTT 6 132 1 CATCATTTATAATTTTTATTGTAAGGAATCTC 7 18 0 TCGTTGAAAAATTTTTCTTTCTGTACTGGTGT 8 123 0 GTAGAATTCTATTTTCCGTTCTGTTATAGAAC 10 71 1 TGTTAAGCCGACTCTTCGTTCTGAAAGAGAAC 10 120 0 TTAGTTTCCAGGTTTTCTTTGTGTGATTTCAC 10 168 0 TTGAGATTCAACTTTTTATTGTCTGAATTTTA 12 76 0 AAATAGTTTCTCATTTTCACTGTCGCT 12 198 0 * ******** * MAP Score: 7.8254 Motif 9 TTTAAGGGGTTTATTTTAGAAAATATAACTT 0 31 0 TTCGTTTGAGAAAAGTAAAAGT 2 1 1 AGCGGGTGCCCCCTTTTAGAAAGGAGGATGG 4 49 1 TCCCCCTTGAGATTCCTTACAAT 7 2 1 TACGACACCGCGATTTGAGAAACATCTACCG 7 127 1 TTACCACCTCCCATTTTAGATTATACTCTTT 8 185 0 AAAAATCGTTCTTTTTGAGAACGTTTTGTGC 10 39 0 ATTTTCCGTTCTGTTATAGAACGATAGTCTC 10 81 1 CAAAATCGTTCTCTTTCAGAACGAAGAGTCG 10 113 1 ACGGCTATCACCCTTTGAGATTCAACTTTTT 12 91 0 ** ******** MAP Score: 7.46453 Motif 10 CAATCTCCACCCTATCCCTGAGTTTTCA 1 75 0 ATGCAATGCATCCCCTTTTTCTTTATCCACA 2 88 0 ATGCATTGCATCCCCTTTCTGGCTGGGAGGG 2 108 1 GTTCGAGTCCTCCCCTCCCAGCCAGAAAGGG 2 120 0 AACATCCCCCTGTGTGTTATCATATC 3 5 1 ACGATCCCTCCTCAGTGATATGATA 3 27 0 GGTCGCGGGTCCCCCTGTCTAGATTAGCTCA 4 14 0 TGAGCGGGTGCCCCCTTTTAGAAAGGAGGAT 4 47 1 CCTCCCTTGTGTCTTGATGAAAT 6 194 0 TCCCCCTTGAGATTCCTTACA 7 0 1 AGTATGCACCTCCTCTGGAACGAATTA 10 6 1 TCACGGCTATCACCCTTTGAGATTCAACTTT 12 93 0 ****** **** MAP Score: 6.61771 Motif 11 GTTTTAACAAAGTTATATTTTCTAAAATAAACCCCTTAAAAAAA 0 22 1 TTTCATAATAATATATTATCAGAGAAAAAAACGAGTTGAACCGA 1 36 0 AGAAGAAAATACTGTTTTTACCTCAAATTTCCTTAGGGAGGTGG 5 18 1 TTACTCATGTTACCATGAAATTCTATATTATGAAAA 6 2 1 ATTCTCGTTCATGGATATTATCCAAAAAATTCATTTATCATCGA 6 45 1 TCGTTTTCACAAGAATGGTAACACGAAGGAAAATGAAAAGTCAA 6 139 0 AAAAATTATAAATGATGATTTGCTAAATGTGAATTTAGTAAATT 7 33 1 ACGACACCAAAGTCTTCCTCCCAAAAATATAAATCTGAATTTAC 7 70 0 GGAAAGCACCAGTCTTCCTCCGTAAAAAAGCGGTCCGAGGAGGT 8 16 0 CTTTCCACTTAGAAATCACCTCCCGAAAAAGCATCTGCGTAGAA 8 54 1 TTCCTTCTTCAACGTTAATTTCCGAAAAGAGTATAATCTAAAAT 8 160 1 CTCCTCTGGAACGAATTATAGCACAAAACGTTCTCAAAAAGAAC 10 19 1 TCTCAAAAAGAACGATTTTTCGTAGAATTCTATTTTCCGTTCTG 10 50 1 TCTGTTATAGAACGATAGTCTCACAAAATCGTTCTCTTTCAGAA 10 90 1 TCATTTTTGAAAGAATACTGTGATAAAATTCAGACAATAAAAAG 12 53 1 * ** * * **** * MAP Score: 6.16872 Motif 12 TTTTAAATGATACCATTAATCTGTC 1 2 1 CTCAGTGATATGATAACACACAGGGGGATGTT 3 9 0 AAAATTGACATTTTACGACACCAAAGTCTTCCT 7 95 0 AAAATGTCAATTTTACGACACCGCGATTTGAGA 7 114 1 AGAACTATTCTAACATCACACCGGAAGAAACAC 8 94 1 CTGGAACGAATTATAGCACAAAACGTTCTCAAA 10 24 1 GCTTAACATTTCTTAACAAACCATGTGAAATCA 10 144 1 ACAAACCATGTGAAATCACACAAAGAAAACCTG 10 159 1 ATTTTCCCTCTGATATCACACCATCGAAAATTA 12 15 1 * * * ******* MAP Score: 4.53471 Motif 13 GGATGCAATGCATCCCCTTTTTCTTTATCCA 2 90 0 GGGATGCATTGCATCCCCTTTCTGGCTGGGA 2 105 1 GCGGACTCTGGATCCGCTGGTGGAGGTTCGA 2 145 0 ACCCCTTGAACTATCCCTGTTCTTGATGTAT 2 216 0 ACGTGAAACACCACCCCTTGAACTATCCCTG 2 228 0 AACATCCCCCTGTGTGTTATCAT 3 2 1 ATAGGTCGCGGGTCCCCCTGTCTAGATTAGC 4 17 0 CTATGAGCGGGTGCCCCCTTTTAGAAAGGAG 4 44 1 ATTCCATCCTCCTTTCTAAAAGGGG 4 58 0 CATGGTGAGAGGACCGCATGTACCTGCTTTT 7 175 0 ACACCTCCTCGGACCGCTTTTTTACGGAGGA 8 14 1 AAGCACCAGTCTTCCTCCGTAAAAAAGCGGT 8 26 0 GTTACCACCTCCCATTTTAGATTATACT 8 189 0 AGTATGCACCTCCTCTGGAACGAATTATA 10 8 1 * ********* MAP Score: 4.25305 Motif 14 CTCCTGATTTTTGTTTTAACAAAGT 0 5 1 TAATTACACGGATGTTTCATAACAGACTTT 2 27 0 TTCAAGGGGTGGTGTTTCACGTTTTTTTCA 2 237 1 CACCCCGATTTTTGACCTTGATCAAA 2 284 0 TTCTCTCGTTGACTTTTCATTTTCCTTCGT 6 131 1 TTAAACGGTAGATGTTTCTCAAATCGCGGT 7 133 0 TTTCTGTACTGGTGTTTCTTCCGGTGTGAT 8 108 0 TTCGTTGAAAAATTTTTCTTTCTGTACTGG 8 126 0 CAAAAAGAACGATTTTTCGTAGAATTCTAT 10 53 1 ********** MAP Score: 1.84875 Motif 15 CATTAATCTGTCATCGGTTCAACTCGTTTTTTTCTCTGA 1 23 1 AGGGGTGGTGTTTCACGTTTTTTTCACGTTCAAGCTGAT 2 241 1 AAGAAGAAAATACTGTTTTTACCTCAAATTTCCTTAGGG 5 17 1 ATGATCGAGATTCTTTGTTTTTCTCTCGTTGACTTTTCA 6 111 1 TCTCGTTGACTTTTCATTTTCCTTCGTGTTACCATTCTT 6 134 1 TTTCTTTCTGTACTGGTGTTTCTTCCGGTGTGATGTTAG 8 103 0 TTTCGTAGAATTCTATTTTCCGTTCTGTTATAGAACGAT 10 67 1 AGGTGATTTTCCCTCTGATATCACACCAT 12 0 1 TTACGACCTGTAATTGGTTTTGTTCTCCTGGAAAGCGAC 12 165 1 * * **** *** * MAP Score: 0.553067 Motif 16 CTCCTGATTTTTGTTTTAACAAAG 0 2 1 AGTCCGCCGTCCTACCGTTAGACGACCTCCCA 2 169 1 CTTGAACTATCCCTGTTCTTGATGTATAATTT 2 211 0 CACCCCGATTTTTGACCTTGATCAA 2 285 0 AACATCCCCCTGTGTGTTATCATATCA 3 5 1 TGAGCGGGTGCCCCCTTTTAGAAAGGAGGATG 4 47 1 CTTCGTGTTACCATTCTTGTGAAAACGATTTC 6 155 1 CCTCCCTTGTGTCTTGATGAAA 6 195 0 TTTACGACACCGCGATTTGAGAAACATCTACC 7 125 1 GTTACCACCTCCCATTTTAGATTATACTCTT 8 186 0 TACGAAAAATCGTTCTTTTTGAGAACGTTTTG 10 42 0 TCACGGCTATCACCCTTTGAGATTCAACTTTT 12 92 0 *** ******* MAP Score: 0.345755