AlignACE 3.0 10/20/99 AlignACE2 -i BS/BS_fusions005_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944240453 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 yhcK 172 similar to hypothetical proteins #1 ykoG 300 similar to two-component response regulator [YkoH] #2 ykoW 300 similar to hypothetical proteins #3 ykrQ 252 similar to two-component sensor histidine kinase #4 cheV 300 cheV #5 kinC 189 two-component sensor histidine kinase #6 fliL 251 flagellar protein #7 fliM 33 flagellar motor switch protein #8 cheY 25 two-component response regulator #9 flhA 32 flagella-associated protein #10 ccdA 219 integral membrane protein #11 yneI 88 alternate gene name: yoxH; similar to two-component response regulator (CheY homolog) #12 yrkP 267 similar to two-component response regulator [YrkQ] #13 phoP 211 two-component response regulator #14 ytrP 294 similar to two-component sensor histidine kinase #15 ytvA 300 similar to protein kinase #16 ytsA 96 similar to two-component response regulator [YtsB] #17 ytrD 29 similar to cytochrome c oxidase subunit #18 ytrA 300 similar to transcriptional regulator (GntR family) #19 yvqA 277 similar to two-component response regulator [YvqB] #20 yvcP 300 similar to two-component response regulator [YvcQ] #21 yxdJ 108 similar to two-component response regulator [YxdK] #22 yycF 300 similar to two-component response regulator [YycG] Motif 1 TTTCGTTGTTTACAAAATGATTCTTATCATC 1 240 0 TCCCTATATGAAAAAAATGATTTCGTTGTTT 1 260 0 AGTTTCAGCCTTCAAAACGATAGAAATACGA 2 56 0 TATTTTAAAATAAAAGATGAAAAAGGAATCT 3 62 1 GCCGCGTTCCTCAAAAAAGAAACTTTTTTCC 4 177 0 GCGTAATTTGTAAAAAGTGAATGGCAGCTCT 4 234 0 AAGTTTGTAGTAAAAGAAGATGAAGAAGCTG 6 157 1 ACATTAGATCTTCAAAGTGAATGTTTATATT 10 28 1 TGAAAGTGTTAAAAAAATGAAATGATTTTGT 10 158 1 TTGTACCAAAAACAAAAGGATTAGTAGTAGT 11 27 0 ACATTTTCTAAAAAAAATGATGACTCTTCAT 12 110 0 TCATTTATAGTAAAAAGAGAAAGGCTGTATT 13 33 0 TTTATTTCTTTTAAAAATGATGTAAAAGGCG 13 83 1 AAAAATGATGTAAAAGGCGAATTGTCGGAAT 13 95 1 ATTGATAAGGAACAAAATGAAAACATAGAAG 14 132 1 TGTCACTGGGTGAAAAATGAATCCAATGCAT 15 57 0 ATTCCCCTTTTTAAAAATGAATTCTACAGTA 15 235 0 ATACACTTGATAAAAAAGGAAAAAGTGCGGT 16 68 1 GTTTTTTTGTAAAAAAAGGATTGACTTTGTG 18 11 1 TTATGAAACATAAAAAACGAAACAAACGTAA 18 137 1 CCTTTTATAGATAAAAATGATCAATTATACT 18 250 0 ACATTGTGGGATAAAAATGAAAAGAATATGT 19 187 1 ATTCTATCATAACAAAAAGAAAAAGACCGAT 20 201 1 TGCGGCCGGTTCAAAGAAGAAGACGTCATTG 22 25 1 TCAACTTTTTTTAAAAAAGATAACTTTATTG 22 86 0 ACAACTGGCGATAAAGGTGAAACATGTGTTT 22 136 1 ******* *** MAP Score: 26.4592 Motif 2 ACTCCTCCTTTGGTTTTATTTTTGTGGAAAATAAA 14 16 1 TCAGCTTCTATGTTTTCATTTTGTTCCTTATCAAT 14 132 0 TCTAAAACAGTCATTTCGTTTTCTTTAAATATTAC 4 60 1 TTTCACATATTCTTTTCATTTTTATCCCACAATGT 19 187 0 AGTAAATCGGTCTTTTTCTTTTTGTTATGATAGAA 20 202 0 TATGACAAAATCATTTCATTTTTTTAACACTTTCA 10 158 0 TGTGATCGCTTGTTCTTTTTTTCTTGTTCTTGTGA 18 192 1 AACAGCTTCTTCATCTTCTTTTACTACAAACTTCT 6 155 0 ACGTTACGTTTGTTTCGTTTTTTATGTTTCATAAC 18 136 0 TCTTCCTCGCTCTTTTTCTCTTCCTTTCTTCCCTT 19 135 1 TCGACCATGCACATTTTGTTTTCATGTATCCTCGC 14 66 1 TTTTTTCTAAACCTTTATTTTTTTTATCTTTTGAC 22 166 1 CTACTACTAATCCTTTTGTTTTTGGTACAATAAGA 11 28 1 ACATGTTTCATGATTTTATTTTAGCGAAAGCAGGA 13 127 0 TCTATTTTGGTGCTTTGCTTTTCTCCTCATTATTG 19 80 0 TCCTGTTTTTTTGGTAAAATAAAAA 1 0 1 AATACGAGGGAGATCTATTTTTAGTTCAACTGACC 2 28 0 GTTCAAATTCTGTTCTTATTTTTAGTGTATACGAG 15 135 1 GGTCAGCTGATTCTTTCTTCATATTCAGGTAA 4 7 1 GCATTTTTTTAGATTCCTTTTTCATCTTTTATTTT 3 68 0 CCGTATCGTGTGTTCCAGTCTTGTTGACTCTCTTT 2 109 0 GTTGACCGAATGGTGTATTTTTTTGTGCGCTTAAT 1 71 0 TAAAGGTGAAACATGTGTTTTTTTTCTAAACCTTT 22 147 1 TAAATTGTTAAGATTCGGTCTTTATATTTATCCAT 12 76 0 TTAGGAAAAAAGTTTCTTTTTTGAGGAACGCGGCT 4 174 1 ATGCCTTTTTTGTTCTTTTCTTTCCCTTCCATCTT 0 120 1 ** *** **** * MAP Score: 22.3433 Motif 3 TCCTGTTTTTTTGGTAAAATAAAAAACTG 1 6 1 GAGTCATCATTTTTTTTAGAAAATGTGACAAAT 12 115 1 CGTTTTTTTGTAAAAAAAGGATTGA 18 2 1 ATTATATAAGTTTTTTCTGAAAATAGAAATCCT 10 120 1 TAAAGTTATCTTTTTTAAAAAAAGTTGACCAGC 22 89 1 GAAACATGTGTTTTTTTTCTAAACCTTTATTTT 22 154 1 TCACTCCGCCTTTTTTAGCATAATT 5 2 0 CCGTATACAATTTTTTATTTTAACATCATAATA 1 207 1 AACGTCTTTATTTCTTTTAAAAATGATGTAAAA 13 77 1 AAAAAGAAACTTTTTTCCTAATAACCATTGACT 4 162 0 AGCCTTTCTCTTTTTACTATAAATGAAAGCGCT 13 38 1 TATATAAGGTTTTTTTACTTGAATTGATAAGTT 0 87 0 TTTGGTTTTATTTTTGTGGAAAATAAAAACCGT 14 24 1 AACGAAATCATTTTTTTCATATAGGGACGGGAG 1 264 1 CTTTTTCATCTTTTATTTTAAAATATGTACCAG 3 54 0 TTTCTCTTCCTTTCTTCCCTTAACCATATCATA 19 149 1 GATCTGAACCTTTTATAGATAAAAATGATCAAT 18 256 0 TTCTCCGCTGTTTTATGATTAAAGTAACCCGTT 6 35 1 AGATCGCAGCTTTCTACCGAAAAATACAAATAT 6 197 1 ****** **** MAP Score: 10.9003 Motif 4 AGCAGGTAAACTCTCCCTTCAAATTTTCTCATTTACT 0 10 1 TTGTTCTTTTCTTTCCCTTCCATCTTTAGTACCTTAT 0 129 1 GCATGTACACTCCTTCTTCAAAACCTATCCCTCAAT 3 226 0 GGTCAGCTGATTCTTTCTTCATATTCAGGTAAG 4 6 1 GATGATATCACTCCGCCTTTTTTAGCATAATT 5 5 0 GTGATATCATCTCCGCCTTTTTTGCGTGCCAATTTTT 5 31 1 AGAACAGCTTCTTCATCTTCTTTTACTACAAACTTCT 6 155 0 CGTACTACTACTAATCCTTTTGTTTTTGGTACAATAA 11 24 1 TTAATACAGCCTTTCTCTTTTTACTATAAATGAAAGC 13 31 1 CCCCGACATCCTATTTCTCTATTTTATGTCATCTTAA 13 161 0 AATGTGACTCCTCCTTTGGTTTTATTTTTGTGGA 14 7 1 TCTGTGATCGCTTGTTCTTTTTTTCTTGTTCTTGTGA 18 190 1 TCTATACGATCTGAACCTTTTATAGATAAAAATGATC 18 259 0 CGCTCTTTTTCTCTTCCTTTCTTCCCTTAACCATATC 19 142 1 GTAAATCGGTCTTTTTCTTTTTGTTATGATAGAATGA 20 199 0 TGTTTTTTTTCTAAACCTTTATTTTTTTTATCTTTTG 22 162 1 ** ***** ** * MAP Score: 10.8866 Motif 5 ACTAAAGATGGAAGGGAAAGAAAAGAACAAAA 0 127 0 GGAACACACGATACGGGGGGAATCTCCATTTG 2 128 1 ATATTTTAAAATAAAAGATGAAAAAGGAATCT 3 61 1 AGTAATATTTAAAGAAAACGAAATGACTGTTT 4 64 0 GGCGTAATTTGTAAAAAGTGAATGGCAGCTCT 4 234 0 ATTGGCACGCAAAAAAGGCGGAGATGATATCA 5 32 0 GTTTGTAGTAAAAGAAGATGAAGAAGCTGTTC 6 159 1 ATCAAGGAATAGAGGAACCGGA 6 239 1 TTTTCGATTTAAAAGGAGAGAAAAAACAGC 9 12 1 ATGGATAAATATAAAGACCGAATCTTAACAAT 12 76 1 TAAAAAGAGAGAAAGGCTTGCTT 13 1 1 TTCATTTATAGTAAAAAGAGAAAGGCTGTATT 13 33 0 CATCATTTTTAAAAGAAATAAAGACGTTTATG 13 73 0 TAAAAATGATGTAAAAGGCGAATTGTCGGAAT 13 94 1 TATTGATAAGGAACAAAATGAAAACATAGAAG 14 131 1 AAATGAAAACATAGAAGCTGAACAAAAAGGCT 14 146 1 GAATTTGAACATATGAACGGAAAGGTTTTCTA 15 113 0 TACACTAAAAATAAGAACAGAATTTGAACATA 15 132 0 TATACACTTGATAAAAAAGGAAAAAGTGCGGT 16 67 1 CGTTTTTTTGTAAAAAAAGGATTGACTTTGT 18 9 1 GTTATGAAACATAAAAAACGAAACAAACGTAA 18 136 1 CACAAGAACAAGAAAAAAAGAACAAGCGATCA 18 194 0 ATTGTCCCAATAATGAGGAGAAAAGCAAAGCA 19 73 1 TTAAGGGAAGAAAGGAAGAGAAAAAGAGCGAG 19 140 0 TGTGGGATAAAAATGAAAAGAATATGTGAAAT 19 191 1 AATGACGTTGAAAGGATGTGAAGAGCC 19 260 1 AGAGTGCTTTAAAGAGAATGAAATTCCTTATA 20 22 0 TATCATAACAAAAAGAAAAAGACCGATTTACT 20 205 1 CGTGATGTACATATAAGGGGGATCAAC 20 283 1 CGGCCGGTTCAAAGAAGAAGACGTCATTGATA 22 27 1 AATGTTATATAGATGAAATGAAGTCATTCGGC 22 260 1 *** **** *** MAP Score: 5.18592 Motif 6 TGCGCTATAGAAAAAGCCGGCTGTCTCAGCCGGCTC 16 17 0 GAAATTATGAAAATTGCCTGCCGTATGTTAAAACTA 19 218 1 TAACCCGTTTGAACGGGCAGCCCTTTACACTGAATG 6 59 1 GCAAATGAAGGAAGTTCCCGCATTTTGTAGAAATAT 3 192 1 GAAGCTGAACAAAAAGGCTGCAATATTTCACACAAA 14 159 1 TGGAAAATAAAAACCGTCTGCTCTATTCGACCATGC 14 40 1 CGAATTGTCGGAATGTCCTGCTTTCGCTAAAATAAA 13 112 1 AGTGTATAGCAAAACGCCAGCATGCGCTATAGAAAA 16 39 0 TCGTGATGAAGAAAATCATGCTGTTTCTGGCAATGA 20 133 0 AACAATTTATGAAGAGTCATCATTTTTTTTAGAAAA 12 102 1 TTAAAAAGGGGAATATCAGGCTTTCGCATAGCAAGC 15 252 1 *** *** ** * * MAP Score: 1.6686 Motif 7 AAAAAACCTTATATAATGCCTTTTTTGTTCTTTTCT 0 105 1 TGGTAAAATAAAAAACTGCATATCCTAAGGGAATAT 1 21 1 ATAATAGATGATAAGAATCATTTTGTAAACAACGAA 1 234 1 CCAAATGGAGATTCCCCCCGTATCGTGTGTTCCAGT 2 125 0 CATCGACCTAACAATCAGCATTTTTTTAGATTCCTT 3 84 0 AAATGAAGGAAGTTCCCGCATTTTGTAGAAATATTG 3 194 1 GATATCCTCTAAAACAGTCATTTCGTTTTCTTTAAA 4 53 1 GGTACCCATTATTTACACCCTTCTTTGGAAAAATCC 4 98 1 GGAGATGATATCACTCCGCCTTTTTTAGCATAATT 5 9 0 GGAGTGATATCATCTCCGCCTTTTTTGCGTGCCAAT 5 28 1 TTTCGTACTACTACTAATCCTTTTGTTTTTGGTACA 11 21 1 ATTTCCACAGATAATAGTCTTATTGTACCAAAAACA 11 44 0 CAATTTATGAAGAGTCATCATTTTTTTTAGAAAATG 12 104 1 TGTGTGAAATATTGCAGCCTTTTTGTTCAGCTTCTA 14 157 0 GCCGGCTGAGACAGCCGGCTTTTTCTATAGCGCATG 16 19 1 TGACTCACAAAGTCAATCCTTTTTTTACAAAAAAAC 18 11 0 TTTCATCTATATAACATTCGTTTCATCACTTATGGC 22 242 0 CCTCCTGCCGAATGACTTCATTTCATCTATATAACA 22 262 0 * * * ** **** * MAP Score: 1.42811 Motif 8 TCCCGTCCCTATATGAAAAAAATGATTTCGTT 1 264 0 TTAAAATAAAAGATGAAAAAGGAATCTAAAAA 3 66 1 GAGGGATAGGTTTTGAAGAAGGAGTGTACATG 3 229 1 TCAATGGTTATTAGGAAAAAAGTTTCTTTTTT 4 164 1 AATTATGCTAAAAAAGGCGGAGTGATA 5 5 1 CAAGTGAAAGTGTTAAAAAAATGAAATGATTT 10 154 1 TTGTCACATTTTCTAAAAAAAATGATGACTCT 12 114 0 GCTTTCATTTATAGTAAAAAGAGAAAGGCTGT 13 36 0 CTTTTAAAAATGATGTAAAAGGCGAATTGTCG 13 90 1 ACATAGAAGCTGAACAAAAAGGCTGCAATATT 14 154 1 GTAGAATTCATTTTTAAAAAGGGGAATATCAG 15 239 1 GCTATACACTTGATAAAAAAGGAAAAAGTGCG 16 65 1 CGTTTTTTTGTAAAAAAAGGATTGACTTT 18 7 1 TCGGTTTTGAATGGCAAAAAAGTATAATTGAT 18 230 1 GTCCCAATAATGAGGAGAAAAGCAAAGCACCA 19 76 1 AAGTTATCTTTTTTAAAAAAAGTTGACCAGCA 22 91 1 AAATAAAGGTTTAGAAAAAAAACACATGTTTC 22 154 0 ** * ******* MAP Score: 0.291034