AlignACE 3.0 10/20/99 AlignACE2 -i BS/BS_fusions009_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944240760 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 infA 300 initiation factor IF-I #1 rpmJ 33 ribosomal protein L36 (ribosomal protein B) #2 rpsM 22 ribosomal protein S13 #3 rpoA 176 RNA polymerase (alpha subunit) #4 rplQ 77 ribosomal protein L17 (BL15) #5 ybxA 127 alternate gene name: ybaD; similar to ABC transporter (ATP-binding protein) #6 yczA 300 yczA #7 ycbL 96 similar to two-component response regulator [YcbM] #8 ycbN 155 similar to ABC transporter (ATP-binding protein) #9 glvA 300 6-phospho-alpha-glucosidase #10 yfiA 64 similar to hypothetical proteins #11 yfiB 105 similar to ABC transporter (ATP-binding protein) #12 yfiD 154 similar to hypothetical proteins #13 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #14 yfiG 174 similar to metabolite transport protein #15 yfiH 26 yfiH #16 yfiJ 123 similar to two-component sensor histidine kinase [YfiK] #17 yfiL 143 similar to ABC transporter (ATP-binding protein) #18 ygaL 300 similar to nitrate ABC transporter (binding protein) #19 prkA 300 serine protein kinase #20 yhbH 179 alternate gene name: yzdC; similar to hypothetical proteins #21 yhbI 159 similar to transcriptional regulator (MarR family) #22 yhbJ 35 yhbJ #23 yhcA 40 similar to multidrug resistance protein #24 yhcB 22 similar to flavodoxin #25 yheJ 109 yheJ #26 yheI 119 similar to ABC transporter (ATP-binding protein) #27 ytgA 279 similar to ABC transporter (membrane protein) #28 menE 90 O-succinylbenzoic acid-CoA ligase #29 menB 34 dihydroxynapthoic acid synthetase #30 menF 288 menaquinone-specific isochorismate synthase #31 msmX 120 multiple sugar-binding transport ATP-binding protein #32 yxkF 183 similar to hypothetical proteins Motif 1 CAAGTGTTCTCCCTTCTTCAAATCAGTAAC 0 279 0 GTGTTTCCAACCTCCTTCAGTTTCCGGAG 1 14 0 TCTCTGGGCACCTCCTTATAAA 2 3 0 TACTTAAAACCCTCCTTCAAAACGTCGAA 3 157 0 GTGATGTCCCCTCCTTTATTGGAATGCT 4 59 0 AACTGTCCCGCCCTTCTTTAGATACACAAA 5 19 0 GTCTCGCGGTACCACCTTTATTAACAGCTA 6 170 0 ATTGGCCGTCACCTCCTTTAAGAAACACAA 6 229 0 TTGATATCCTCCTTTCTAACTCATCT 6 284 0 ATGACGACCTCCTTGATAACGTTTAC 9 284 0 AGACTGCCCTCCTTTTCGGGAGGGTT 11 6 1 TTTATCCTCCTTGATAAATGTTAT 12 140 0 GCCAATGCATCCCTCCTTCAGCAATACCCC 14 102 0 GGCTTTCTTCCCCTTCTTTCAAGAATGGCA 14 154 0 ATACCCAATTCCCTTCTTATCATACCTGCC 16 89 0 AAATAATTTTTCCTTCTCTATTTGCGAAAC 18 128 1 AAGGACCTCCTCTATCATGTTTGA 19 286 0 GAATTCCCCTCCTTAACCATTTGTGG 20 163 0 CTAAGACAACCTCCTTTCATGGTTTGAT 23 22 0 GCATAGCAAACCCTCCTTCCATTCTGATTT 25 77 0 TTGAATACATCCCTTCTCGTTTGGACCGGC 27 70 1 ATTTCTCCTCCTCTTTGCCATCAAT 27 264 0 ATGATGACCTCCTTTTATTCTCTATG 29 18 0 TAAAAGGAAAACCTCCTATATTCCTCCACC 30 83 0 AAGATGACCCTCCTTTGGTCCTGCATG 32 7 1 ********** MAP Score: 42.6029 Motif 2 CAAGTGTTCTCCCTTCTTCAAATCAGTAAC 0 279 0 TCTCTGGGCACCTCCTTATAAA 2 4 0 GTGATGTCCCCTCCTTTATTGGAATGC 4 60 0 AAACTGTCCCGCCCTTCTTTAGATACACAA 5 20 0 TGGATCTATGCCCTTTTTTTAGATACTGCA 5 55 1 GGAAAACCGGCCTCCTCTCAGCTAATGC 5 109 0 TGTTTCGATACTCCTCTCTTGGTAACGGGG 6 108 0 CATTGGCCGTCACCTCCTTTAAGAAACACA 6 230 0 TTGATATCCTCCTTTCTAACTCATCTGC 6 282 0 AACTTTGTTTCTCCTTCCCTCTCTTTTCCT 8 73 0 AGACTGCCCTCCTTTTCGGGAGGGT 11 5 1 ACTCGATTGTCTCTTTCTTTACTTTACTAT 11 61 0 AGCCTCCAAACCCCTTTTTACTCGATTGTC 11 80 0 TATTTTTGTCCGCCTTGTTATGATGAGAGA 13 49 1 GTAAACGCCTCCTAACAAGTTGGTT 13 78 0 GGCTTTCTTCCCCTTCTTTCAAGAATGGC 14 155 0 GCCTGTAAAAGGCCTTTTCAGAGAAGCGTA 17 28 0 GCCTTTTACAGGCCTTTTTTTCATGCCCTA 17 45 1 ACATGCCGCACGCCTTTCTTTCTTCTACAA 17 91 1 GTCGTCTCACTCCTTTTTTTGATCCATTG 17 124 0 GATATGTCAACTCTTTTTTAAATACGATTT 18 189 0 GTGTCATTGTCACTTTTTTAGTATCAATTT 19 48 0 ACCGTCTCTCCCCCTCTTCAATTTTTCCGT 19 98 1 AAGGACCTCCTCTATCATGTTTG 19 287 0 GAATTCCCCTCCTTAACCATTTGTG 20 164 0 CTCCTTTTCACCTCATTCCT 21 149 0 CTAAGACAACCTCCTTTCATGGTTTGATGA 23 20 0 ATAGCAAACCCTCCTTCCATTCTGATTTCA 25 75 0 CCTCATCAGCCGCCTTCTATTTTTTCCTTG 26 87 0 ATTTCTCCTCCTCTTTGCCATCAA 27 265 0 ATGATGACCTCCTTTTATTCTCTATGTG 29 16 0 TGTGATCGCCTCGTTTCTCTGTGATG 30 6 1 CTAACATCCCCCTTTGTTATTGTAAACGC 31 101 0 AGAGTCTCCTCTCTTATGTAAGGAT 32 168 0 ********** MAP Score: 21.753 Motif 3 GACGGCAAACGAAAACCCTCCCGAAAAGGAG 11 18 0 TAAGAAACACAAAAAACCCCCGTCCTATGCA 6 210 0 GACAAAAATAAAAAATCCCCCTGCCGTTATT 13 28 0 TACCATAAAAGGAAAACCTCCTATATTCCTC 30 87 0 TACTTAAAACCCTCCTTCAAAACGT 3 161 0 GTAAAAGCCTCCAAACCCCTTT 11 93 0 CCTTGGCATAGCAAACCCTCCTTCCATTCTG 25 81 0 GATTTACATAAAAAAACCGGCTGGGTCAGCA 27 100 0 TTTGCCGTCAAAAAGACCGCCATAGTAAAGT 11 40 1 ATGAAATTCCCCCATTTTCGAAT 10 2 1 GGAAAACCGGCCTCCTCTCAGC 5 115 0 AATGGGACAAAATAACCCGCCCTATTCGGAC 20 22 0 TAACGGGGAGAGAAACCCGGCATCGCCTACT 6 85 0 TCAGGAAACCTCCCTGTACAGA 24 9 0 GAGACATTCCTCCATAATCCTTA 30 275 0 TTCTGGAAAATAAAAACCGCATATGAACTTT 16 36 0 TGATAGATTCCTCCTGGTATCTCA 15 12 0 GTAAACGCCTCCTAACAAGTTG 13 81 0 GATTCCATCCGAAATTCCCCATTGTTTAGTC 3 105 0 CTAAGACAACCTCCTTTCATGGTT 23 26 0 GAAAACCTCCTATATTCCTCCACCCGCCATT 30 76 0 CTAACATCCCCCTTTGTTATTG 31 108 0 CATAAGCCAATGCATCCCTCCTTCAGCAATA 14 106 0 ***** ***** MAP Score: 9.79 Motif 4 ATGATACAGTTATTTATGAAACGAATGCACCG 3 50 1 CGTGTGTTTATTATTCAGAAACAGCATTCCAA 4 37 1 TCACATATTTTTGTGTATCTAAAGAAGGG 5 7 1 TCTATGCCCTTTTTTTAGATACTGCAACTTTT 5 59 1 GGACGGGGGTTTTTTGTGTTTCTTAAAGGAGG 6 216 1 TTTTTATAAAACACACACGTTT 7 0 1 AACACACACGTTTTTCAATTACAATAAGTGTA 7 19 1 CACAGAGGTCTTTTTTTGTTACAGTTTTATAG 12 22 1 GCGGTTTTTATTTTCCAGAAACTCCTGTCAAA 16 47 1 GTCTCACTCCTTTTTTTGATCCATTGCCATTG 17 118 0 TTGTAACAGCTTTTTATGACACTTAATAATTT 18 90 1 ATGTCAACTCTTTTTTAAATACGATTTTTGAT 18 184 0 TCATTGTCACTTTTTTAGTATCAATTTTTACC 19 43 0 AGTATCTTTATTTTTAAGAAACCAAAGCATGT 19 202 1 AATATAAATCTTTTCAAAAGACTTGTTTCATA 20 97 1 ***** *** ** MAP Score: 6.87496 Motif 5 TTCTCCGTCTGCTGTTAGTACATTGATGATGG 0 110 0 TCGTACATTGGCCGTCACCTCCTTTAAGAAAC 6 233 0 TTTTTAGAAAGCGGTTACAACAAGGGGTATTG 14 79 1 GCATGTAGCGGCAGATAGAACATAGGGCATGA 17 65 0 GTCATAAAAAGCTGTTACAACAAGGTTTTTCA 18 78 0 AGAGCCTTCGGCGGTCCGATCAGCTGCCCAAT 18 259 0 ATTTTTCCGTGCTGTCCGAGTCTGGATGATTC 19 118 1 AGAGGCGAGGGCAGTTCGTGCCAAACTGGATG 26 45 1 ATGACACTGTGCTGTTACAGTAAAAGTGTTCG 27 38 1 TGGACCGGCTGCTGACCCAGCCGGTTTTTTTA 27 91 1 TTTATGGTAAGCGGATACAACCTTTGCTATCA 30 109 1 AGAGGGAATTGCTGTTACACTCAATATAAGAA 31 68 1 ** ****** ** MAP Score: 6.52549 Motif 6 ATAGGGCAGAAAGCTTGGGTGAACATTGGCAAG 0 40 1 CAGTATAAACGAAACAGGGCGTGTGACAAACTT 0 222 1 TTACTGATTTGAAGAAGGGAGAACACTTGA 0 280 1 TGTGTATCTAAAGAAGGGCGGGACAGTTTCTAA 5 21 1 TGCAGTATCTAAAAAAAGGGCATAGATCCAGTT 5 52 0 TTTTAATAGAGAGAAAAGCAGAGCATTAGCTGA 5 87 1 AGCATTAGCTGAGAGGAGGCCGGTTTTCC 5 108 1 TTGCTGAACGGATAGTAGGCGATGCCGGGTTTC 6 72 1 TCCTCTCTTGGTAACGGGGAGAGAAACCCGGCA 6 94 0 CAGGAAAAGAGAGGGAAGGAGAAACAAAGTTGA 8 72 1 TTACAGATTCGAAAATGGGGGAATTTCAT 10 6 0 ATAATAGAAAGAAAATGGGGGGATCTGAT 10 45 1 AACCCTCCCGAAAAGGAGGGCAGTCT 11 3 0 TCCCCTTGCCGAAATAACGGCAGGGGGATTTTT 13 16 1 TTCATATGATAAAGACGCGAGAAATCTCGTTGT 14 37 1 CCCTTCTTTCAAGAATGGCAGAGCACCCGACAC 14 141 0 TGCCATTCTTGAAAGAAGGGGAAGAAAGCC 14 154 1 CCTGAGATACCAGGAGGAATCTATCA 15 5 1 CTCTATTTGCGAAACAAGCAGAGTAAGTGATAA 18 143 1 GGAAAAATTGAAGAGGGGGAGAGACGGTGAAAA 19 93 0 AAACTATTTAGAAAATGGGACAAAATAACCCGC 20 33 0 CGCTTGCGAAAAAAATACGGGAGAAAAAGAAAT 21 58 1 GAAAGCTGGTGAAAATATGTGAGAAGTTT 22 6 0 AATCAGAATGGAAGGAGGGTTTGCTATGCCAAG 25 78 1 GGAAAGACAGGTGTATGGGATGTGA 26 2 1 GACAAATACAGAGGCGAGGGCAGTTCGTGCCAA 26 36 1 GGAAAAAATAGAAGGCGGCTGATGAGGAGATGG 26 90 1 GGCTGATGAGGAGATGGGGATAG 26 106 1 TTTACATAAAAAAACCGGCTGGGTCAGCAGCCG 27 96 0 CATAGAGAATAAAAGGAGGTCATCAT 29 18 1 GCATCACAGAGAAACGAGGCGATCACA 30 4 0 TTTCATTTCTGAAATTAGGTTTATAATAGGTAA 30 170 1 AATATGCACGAAAAATGGCTGGGTGATTTTATG 31 16 1 **** *** *** MAP Score: 2.51711 Motif 7 AAAGATACTCATACATCGTTGACAAGGCAGACTGC 19 176 0 ACTCAATATAAGAAAGCGTTTACAATAACAAAGGG 31 86 1 TAATCTTTTTAGAAAGCGGTTACAACAAGGGGTAT 14 74 1 TAAAAGTACTATAAAACTGTAACAAAAAAAGACCT 12 27 0 TAAGTGTCATAAAAAGCTGTTACAACAAGGTTTTT 18 80 0 AATTCCGAAGACAGATGTTTTTCAAGCTTGATAGG 0 10 1 TTTATAAAACACACACGTTTTTCAATTACAATAAG 7 12 1 GCATCTCCTCACCTAACCTTTACAAAATCAAAAAA 7 63 0 TTTTTTATGTAAATCAGCTTGACAAAAATGGCCAA 27 116 1 ACGACCTCCTTGATAACGTTTACAATTCCATTTAT 9 272 0 TTCCTATTCAAGTAATGATTGACAATAAAAGGTTT 25 18 1 ACAAATTTCAAAAGAAGTTTGTCACACGCCCTGTT 0 234 0 AGTAAGTGATAAACAAGGATATCAAAAATCGTATT 18 164 1 GAATCGTACAAAAGAACCTTTTCATAAGAATTGGA 9 55 1 TTCGTTTCATAAATAACTGTATCATAACCCATTAT 3 40 0 * * * * ** **** MAP Score: 2.36815 Motif 8 GTTACTGATTTGAAGAAGGGAGAACACTTGA 0 279 1 GCATTCCAATAAAGGAGGGGACATCAC 4 60 1 GCAGTATCTAAAAAAAGGGCATAGATCCAGTTA 5 51 0 TGCTGAACGGATAGTAGGCGATGCCGGGTTTCT 6 73 1 TGTGTTTCTTAAAGGAGGTGACGGCCAATGTAC 6 230 1 GAAAACAGGAAAAGAGAGGGAAGGAGAAACAAA 8 67 1 GTTTTTTCCCATAGAGCGGGAAATTTCTCATTT 9 177 0 TCAAATGACCTAAGTGCGCCAAACGTGTTACGG 9 221 1 ATAGTAAAGTAAAGAAAGAGACAATCGAGTAAA 11 61 1 TAGCTTACATTAAGTAAGTGATAACATTTATCA 12 120 1 CTTCATATGATAAAGACGCGAGAAATCTCGTTG 14 36 1 GGGGTATTGCTGAAGGAGGGATGCATTGGCTTA 14 102 1 GCCATTCTTGAAAGAAGGGGAAGAAAGCC 14 155 1 AAAAATGCCCTGAGGCAGGTATGATAAGAAGGG 16 76 1 ATGGATCAAAAAAAGGAGTGAGACGAC 17 126 1 TTTCGCAAATAGAGAAGGAAAAATTATTTCTCC 18 124 0 CGAAACAAGCAGAGTAAGTGATAAACAAGGATA 18 152 1 AAATTGATACTAAAAAAGTGACAATGACACCCA 19 48 1 GAAGAGGGGGAGAGACGGTGAAAACAATCATCA 19 84 0 CAAACTATTTAGAAAATGGGACAAAATAACCCG 20 34 0 CACAAATGGTTAAGGAGGGGAATTC 20 164 1 GCTTGCGAAAAAAATACGGGAGAAAAAGAAATT 21 59 1 AAAGCTGGTGAAAATATGTGAGAAGTTT 22 5 0 AGAAGGCGGCTGATGAGGAGATGGGGATAG 26 99 1 TTGATGGCAAAGAGGAGGAGAAAT 27 265 1 ****** * ** * MAP Score: 0.87518