AlignACE 3.0 10/20/99 AlignACE2 -i TM/TM_fusions003_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944251023 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 #13 TM1790 100 hypothetical protein #14 TM1791 300 conserved hypothetical protein Motif 1 AAAAGCGGTCCGAGGAGGTGTGAAA 8 5 0 CAAATTTCCTTAGGGAGGTGGGTTTT 5 41 1 GGATAGTTCAAGGGGTGGTGTTTCACGTTT 2 231 1 AATTCGTTCCAGAGGAGGTGCATACT 10 6 0 TGATAACACACAGGGGGATGTT 3 2 0 AGAATAGTTACGTGGAGGTGATCACAAGTT 11 29 1 ATAATCTAAAATGGGAGGTGGTAAC 8 192 1 TTTGTATTCAAGGGGGGATGGAT 13 87 1 ATGATTACCTCAGGGATGTGAAGGGTCTTG 14 46 1 AAGGAAAAAACAAGGTGGTGGATCACCTTG 14 130 1 CCCTTTCTGGCTGGGAGGGGAGGACTCGAA 2 120 1 AGATGCTTTTTCGGGAGGTGATTTCTAAGT 8 60 0 TTCTACTATAAAGTGAGGTGTTG 11 3 0 AAAATCCTGATGTGGAGGTGTCTCTT 10 208 1 GGATAAAGAAAAAGGGGATGCATTGCATCC 2 91 1 TCCCAGCCAGAAAGGGGATGCAATGCATCC 2 106 0 GTGTTTCTTCCGGTGTGATGTTAGAATAGT 8 97 0 TATGAAAACTCAGGGATAGGGTGGAGATTG 1 73 1 GATCCCTCCTCAGTGATATGATAACACACA 3 20 0 AATTATATCATGGTGAGAGGACCGCATGTA 7 184 0 AAATAATTTTCGATGGTGTGATATCAGAGG 12 21 0 ********** MAP Score: 23.7558 Motif 2 AGTATGCACCTCCTCTGGAACGAATTATAG 10 8 1 AAAACCCACCTCCCTAAGGAAATTTGA 5 40 0 ACGATCCCTCCTCAGTGATATGATAACA 3 24 0 AAGCACCAGTCTTCCTCCGTAAAAAAGCGGTC 8 25 0 ACACCAAAGTCTTCCTCCCAAAAATATAAATC 7 79 0 AGGTTCGAGTCCTCCCCTCCCAGCCAGAAAGG 2 121 0 CACTTAGAAATCACCTCCCGAAAAAGCATCTG 8 59 1 TTTCACACCTCCTCGGACCGCTTTTTTAC 8 7 1 CCCTGGCGAATTTCCTCAGAAAACTG 9 33 1 ATTCCATCCTCCTTTCTAAAAGGGGGCAC 4 54 0 ACGTGAAACACCACCCCTTGAACTATCCCTGT 2 227 0 AAAGAGATGATTACCTCAGGGATGTGAAGGGT 14 40 1 AGGTGGTGGATCACCTTGGAAAGATGATCGAA 14 142 1 TCTTTCTCAACTTCCTCAACCAAATTCA 14 6 0 ******* * ** MAP Score: 13.028 Motif 3 TAATATATTATTATGAAAACTCAGGGATAGGGTGGAGATT 1 62 1 TAAAAGTCTGTTATGAAACATCCGTGTAATTATTCCAGTT 2 25 1 GGTCTGTGGATAAAGAAAAAGGGGATGCATTGCATCCCCT 2 84 1 GGTGCCCCCTTTTAGAAAGGAGGATGGAAT 4 53 1 CCCACCTCCCTAAGGAAATTTGAGGTAAAAACAGTATTTT 5 23 0 AAATTCTATATTATGAAAATTCTCGTTCATGGATATTATC 6 27 1 TAAATGTGAATTTAGTAAATTCAGATTTATATTTTTGGGA 7 56 1 TTATACTCTTTTCGGAAATTAACGTTGAAGAAGGAATGTG 8 156 0 ATCGTTCTTTTTGAGAACGTTTTGTGCTATAATTCGTTCC 10 26 0 GAGAACGATTTTGTGAGACTATCGTTCTATAACAGAACGG 10 86 0 ATTTGGTCATTTTTGAAAGAATACTGTGATAAAATTCAGA 12 47 1 CATTCTGAATTATTGAAAAAAGTGCTTTATTCTTTACGAC 12 132 1 GCTGTAGAGTCTTGAAATTCAAAAGATATCAGTGAGCCC 13 9 1 CTTATACATTTTATGAAATTTGTATTCAAGGGGGGATGGA 13 69 1 GTTGAGGAAGTTGAGAAAGACAAAAGAGATGATTACCTCA 14 18 1 ACAATTCTCTTTCTGAAAAAGAAAGGAAAAAACAAGGTGG 14 108 1 ** **** * * ** MAP Score: 10.925 Motif 4 AACACCAGTACAGAAAGAAAAATTTTTCAAC 8 122 1 CTTTCTTTTTCAGAAAGAGAATTGTTCCCAT 14 102 0 TGAGGAAGTTGAGAAAGACAAAAGAGATGAT 14 20 1 ACTCTTCGTTCTGAAAGAGAACGATTTTGTG 10 111 0 AAGTCAACGAGAGAAAAACAAAGAATCTCGA 6 115 0 CGTTCTATAACAGAACGGAAAATAGAATTCT 10 73 0 TATATTATCAGAGAAAAAAACGAGTTGAACC 1 38 0 TTCGTTTGAGAAAAGTAAAAGTCTGTTA 2 7 1 CAGCTTGAACGTGAAAAAAACGTGAAACACC 2 247 0 CGCTTTCCAGGAGAACAAAACCAATTACAGG 12 171 0 CCCTCCCAGCCAGAAAGGGGATGCAATGCAT 2 108 0 TGTGAAATCACACAAAGAAAACCTGGAAACT 10 167 1 CTTTCTGAAAAAGAAAGGAAAAAACAAGGTG 14 116 1 GGGATCGAAGCTGAACAGAACCCTGGCGAAT 9 13 1 GATAATATCCATGAACGAGAATTTTCATAAT 6 36 0 ACAAAACGTTCTCAAAAAGAACGATTTTTCG 10 41 1 TAATTCTGGAGTGAAAAAAGCAGGTACATGC 7 160 1 TTGGTCTGTGGATAAAGAAAAAGGGGATGCA 2 82 1 ******** ** MAP Score: 10.8874 Motif 5 AGCGGGTGCCCCCTTTTAGAAAGGAGGATGGA 4 49 1 TTCGTTTGAGAAAAGTAAAAGTC 2 1 1 TTTTTCCTTTCTTTTTCAGAAAGAGAATTGTT 14 107 0 TTTAAGGGGTTTATTTTAGAAAATATAACTTT 0 30 0 CTTGATGAAATCGTTTTCGAAATCGTTTTCAC 6 173 0 AATTATTTGGTCATTTTTGAAAGAATACTGTG 12 43 1 TACGACACCGCGATTTGAGAAACATCTACCGT 7 127 1 CAAAATCGTTCTCTTTCAGAACGAAGAGTCGG 10 113 1 AAAAATCGTTCTTTTTGAGAACGTTTTGTGCT 10 38 0 TTTCACATGGTTTGTTAAGAAATGTTAAGCCG 10 142 0 AAAGTAAAAGTCTGTTATGAAACATCCGTGTA 2 21 1 TTTTCTTATACATTTTATGAAATTTGTATTCA 13 65 1 TCTTCAACGTTAATTTCCGAAAAGAGTATAAT 8 165 1 GGAAGAAACACCAGTACAGAAAGAAAAATTTT 8 116 1 ATTTTCCGTTCTGTTATAGAACGATAGTCTCA 10 81 1 ** *** ***** MAP Score: 9.90876 Motif 6 TTTGTTAAAACAAAAATCAGGAG 0 2 0 ATTATCAGAGAAAAAAACGAGTTGAACCGAT 1 35 0 ATATTATTATGAAAACTCAGGGATAGGGTGG 1 66 1 GTCTGTGGATAAAGAAAAAGGGGATGCATTG 2 85 1 AATTATACATCAAGAACAGGGATAGTTCAAG 2 212 1 TGATCAAGGTCAAAAATCGGGGTG 2 286 1 GTCAACGAGAGAAAAACAAAGAATCTCGATC 6 113 0 ACGATTTCATCAAGACACAAGGGAGG 6 191 1 TTCTGGAGTGAAAAAAGCAGGTACATGCGGT 7 163 1 AAAACGTTCTCAAAAAGAACGATTTTTCGTA 10 43 1 TACAGGTCGTAAAGAATAAAGCACTTTTTTC 12 146 0 GGAAGTTGAGAAAGACAAAAGAGATGATTAC 14 23 1 TTCTCTTTCTGAAAAAGAAAGGAAAAAACAA 14 112 1 AAAAAGAAAGGAAAAAACAAGGTGGTGGATC 14 123 1 ****** **** MAP Score: 9.63059 Motif 7 CAATCTCCACCCTATCCCTGAG 1 81 0 GGGATGCAATGCATCCCCTTTTTCTTTATC 2 92 0 GGGATGCATTGCATCCCCTTTCTGGCTGGG 2 105 1 TCGAGTCCTCCCCTCCCAGCCAGAAAGGGG 2 119 0 GAGGACTCGAACCTCCACCAGCGGATCCAG 2 139 1 CTACCGTTAGACGACCTCCCAACGGCCTTT 2 180 1 AACGTGAAACACCACCCCTTGAACTATCCC 2 230 0 AACATCCCCCTGTGTGTTATC 3 1 1 ATTCCATCCTCCTTTCTAAAAGG 4 60 0 AAAACCCACCTCCCTAAGGAAATT 5 43 0 GACACCAAAGTCTTCCTCCCAAAAATATAA 7 82 0 TTTCACACCTCCTCGGACCGCTTTTT 8 6 1 CCACTTAGAAATCACCTCCCGAAAAAGCAT 8 58 1 GTTACCACCTCCCATTTTAGATTATA 8 191 0 AGTATGCACCTCCTCTGGAACGAATTA 10 7 1 AAGAGACACCTCCACATCAGGATTTTA 10 207 0 ACTTGTGATCACCTCCACGTAACTATTCTA 11 28 0 ATCCATCCCCCCTTGAATACAA 13 88 0 TCCAAGGTGATCCACCACCTTGTTTTTTCC 14 132 0 CCAGGAGAACCTCTCCGCATCTTTTGAG 14 282 0 ********** MAP Score: 6.09247 Motif 8 TATGGTATAATGAAAATGGATGGCAGATGTC 0 92 0 TTTGGTCTGTGGATAAAGAAAAAGGGGATGC 2 81 1 ATCATATCACTGAGGAGGGATCGT 3 28 1 CTTTTAGAAAGGAGGATGGAAT 4 61 1 GTAACACGAAGGAAAATGAAAAGTCAACGAG 6 135 0 ACCATTCTTGTGAAAACGATTTCGAAAACGA 6 164 1 AAAACGATTTCGAAAACGATTTCATCAAGAC 6 176 1 TATATTTTTGGGAGGAAGACTTTGGTGTCGT 7 83 1 GCTTTTTTACGGAGGAAGACTGGTGCTTTCC 8 29 1 ATGCTTTTTCGGGAGGTGATTTCTAAGTGGA 8 57 0 AAATTAACGTTGAAGAAGGAATGTGTTCGTT 8 150 0 TCGTTCTTTTTGAGAACGTTTTGTGCTATAA 10 34 0 TCGTTCTGAAAGAGAACGATTTTGTGAGACT 10 106 0 TTGTTCTCCTGGAAAGCGACAGTGAAAATGA 12 184 1 AAAGCGACAGTGAAAATGAGAAACTATTT 12 196 1 TGTATTCAAGGGGGGATGGAT 13 89 1 TTGAGGAAGTTGAGAAAGACAAAAGAGATGA 14 19 1 ATTCTCTTTCTGAAAAAGAAAGGAAAAAACA 14 111 1 ACCTGACACTGGAAGATGGTATCGTCGAAAG 14 175 1 AAAGACTGATGGAAAACGAGTTTTTGGATGC 14 202 1 ********* * MAP Score: 3.42662 Motif 9 GGATGCATTGCATCCCCTTTCTGGCTGGGA 2 106 1 AGGTTCGAGTCCTCCCCTCCCAGCCAGAAA 2 123 0 CGTTAGACGACCTCCCAACGGCCTTTCAAA 2 184 1 ACGTGAAACACCACCCCTTGAACTATCCCT 2 229 0 AAAACCCACCTCCCTAAGGAAAT 5 44 0 GGTAGATGTTTCTCAAATCGCGGTGTCGTA 7 127 0 CATGCGGTCCTCTCACCATGATATAATTTC 7 186 1 TTTCACACCTCCTCGGACCGCT 8 2 1 TCCACTTAGAAATCACCTCCCGAAAAAGCA 8 57 1 GTTACCACCTCCCATTTTAGAT 8 195 0 AAGAGACACCTCCACATCAGGATTTTAC 10 206 0 AACTTGTGATCACCTCCACGTAACTAT 11 32 0 CCCTCTGATATCACACCATCGAAAATTATT 12 20 1 ATCCATCCCCCCTTGAATACAAATT 13 85 0 CAAGGTGATCCACCACCTTGTTTTTTCCTT 14 130 0 CAAGGTGGTGGATCACCTTGGAAAGATGAT 14 140 1 ********** MAP Score: 0.877584 Motif 10 ACTTTGTTAAAACAAAAATCAGGAG 0 0 0 ATCGGAGAGCACGATGAATACTGAGAAATATATCA 0 133 1 ATATATTATCAGAGAAAAAAACGAGTTGAACCGAT 1 35 0 ATAATATATTATTATGAAAACTCAGGGATAGGGTG 1 61 1 TGGTCTGTGGATAAAGAAAAAGGGGATGCATTGCA 2 83 1 TATCAGCTTGAACGTGAAAAAAACGTGAAACACCA 2 246 0 CCTCAGTGATATGATAACACACAGGGGGATGTT 3 8 0 AAAGTCAACGAGAGAAAAACAAAGAATCTCGATCA 6 112 0 AACACGAAGGAAAATGAAAAGTCAACGAGAGAAAA 6 129 0 TTTCACAAGAATGGTAACACGAAGGAAAATGAAAA 6 144 0 AAACGATTTCATCAAGACACAAGGGAGG 6 189 1 TTAATTCTGGAGTGAAAAAAGCAGGTACATGCGGT 7 159 1 AAAAGTGAATCACAGGAAATTATATC 7 205 0 AACATCACACCGGAAGAAACACCAGTACAGAAAGA 8 105 1 GTGAAATCACACAAAGAAAACCTGGAAACTAAGAA 10 168 1 CTGGAAAGCGACAGTGAAAATGAGAAACTATTT 12 192 1 GAGGAAGTTGAGAAAGACAAAAGAGATGATTACCT 14 21 1 CTGAAAAAGAAAGGAAAAAACAAGGTGGTGGATCA 14 120 1 * ******* ** MAP Score: 0.660532