AlignACE 3.0 10/20/99 AlignACE2 -i CP/CP_fusions002_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944236834 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 glnP 48 ABC Amino Acid Transporter Permease #1 argR_gcp_2 83 argR: Arginine Repressor, gcp_2: O-Sialoglycoprotein Endopeptidase #2 oppA_2 150 Oligopeptide Binding Protein #3 oppA_3 55 Oligopeptide Binding Protein #4 oppA_4 283 Oligopeptide Binding Protein #5 oppB_1 292 Oligopeptide Permease #6 oppC_1 30 Oligopeptide Permease #7 tauB 271 ABC Transport ATPase (Nitrate/Fe) #8 CPn0232 122 similarity to 5'-Methylthioadenosine Nucleosidase #9 CPn0233 120 hypothetical protein #10 CPn0234 175 CT181 hypothetical protein #11 CPn0249 57 CT151 hypothetical protein #12 ytgA 300 Solute Protein Binding Family #13 accA 74 AcCoA Carboxylase/Transferase Alpha #14 CPn0415 55 CT266 hypothetical protein #15 himD 300 Integration Host Factor Alpha #16 dppD 54 ABC ATPase Dipeptide Transport Motif 1 TCTTATTCTAAAGAAAGGTCTTTT 2 136 1 TTTAACTTAGAAGAAATTTCTT 8 110 1 TTATATACAGAAGAAACTTCTTATAAAGATAC 4 75 0 ATAGAAATGAAAGAAATATCTTTGTTCAGGAT 12 178 0 CGCATTTTTTAAAAAATGTCTTGAATCCAAAG 15 181 1 TCTTCAATAAAAAAAACCCCTTACCAAAGACT 4 18 0 TTTATAGAAAAATAAAAGTCTTCCTTCCCAAC 5 166 1 TCAGAAAAATAAAAAAAATATTGCGTTTTATA 10 70 0 ATTTTTCTGAAAAAAAAGTATTTTATTTTACA 10 92 1 GGGAAAAGTAAAGAATCATCTTACCTATCAAG 7 50 0 ACAAAAGAAGTCTTTGGTAAGGGG 4 2 1 AAAATGTTATAGAAAAAATCTTCTTTACTTTA 12 103 0 GAATATAAATAAAAAAACCATTGCCAACCCGG 9 47 0 TATACTGGTGAAGAAAGGTCTCTTCAATAAAA 4 38 0 AAGAATAGCCTTTTTCGCAATA 16 0 1 TCTTTCAGGATAGAAATACCTTAAGGAGGCGT 4 149 0 AGATCCTGAGAGGAAAAATATTGCAAAAAGGA 12 35 0 TCTTCAATACAAAAAATGCGTTGGGAAGGAAG 5 185 0 TATTTTACAAAATAAAAATCTCGAAGGGATAT 10 115 1 TCCTCGTATAAAAAGAATCATTTTAATACAAA 13 40 0 TTTATTTTTCTATAAATCTCTTATTTTTTTAA 5 150 0 TCTAGAACCTAGAAAAATCATTCCCACATCTT 15 107 0 TTGTATAAGAAAAAGATCTGTTAAATAGAATT 8 63 0 AAAATTCGATAGTAAATTTATTAAAGTAATTT 3 28 1 TAAAAAAATTAGAAAACCCGTTTGTTTTATAA 12 141 0 ****** **** MAP Score: 28.1267 Motif 2 GATTGTCTATAAAATTTTTAATTTTTCCATTTCGGAT 5 10 0 ATTTTTCTATAAATCTCTTATTTTTTTAACAATTGCA 5 142 0 GTTGGGAAGGAAGACTTTTATTTTTCTATAAATCTCT 5 161 0 TGTTTAAGTCATTATACTTTCATTTTTAGTCATCTTC 5 212 0 AAGTTTATGCTTCTTTTTTTCTTATGACTT 6 7 0 GGTGAGATTTTCCTATACTTTCTTTGTTGAGCT 7 6 1 GATAGGTAAGATGATTCTTTACTTTTCCCTTATTGGG 7 53 1 CTTAAAAAGAAGCGTACTTTCGTTTTTTAATTCTATT 8 35 1 CGGGTTGGCAATGGTTTTTTTATTTATATTCTCAATA 9 48 1 ATAAAACGCAATATTTTTTTTATTTTTCTGAAAAAAA 10 71 1 TTCTGAAAAAAAAGTATTTTATTTTACAAAATAAAAA 10 96 1 TAAGTTAGTTATCTTGTTTTGTTTTTTAGTTTATT 10 150 1 TTTTCCTCTCAGGATCTTTTTGTTTCTTAACAAAATT 12 50 1 TTATAGAAAAAATCTTCTTTACTTTACGATTTTTATG 12 92 0 GATTTTTTCTATAACATTTTGTTTTCTTATAAAACAA 12 115 1 AAAAATTAGAAAACCCGTTTGTTTTATAAGAAAACAA 12 133 0 CTGAACAAAGATATTTCTTTCATTTCTATTAGTTGTA 12 181 1 * * **** *** * MAP Score: 22.5397 Motif 3 AAGGGGTTTTTTTTATTGAAGAGACCTTTCTT 4 28 1 AACGCATTTTTTGTATTGAAGATGACTAAAAA 5 195 1 AAGCCTTCGTTTCTATTCAAGATAGAGGCTTT 7 246 1 AGTCCTTGCTTTTTCTCAAGAATTAGAGCTT 9 99 0 AGTTGAAATCTTATTCTAAAGAAAGGTCTTTT 2 128 1 TTAGGGGAAGTTTTTCTCAAGATGTGGGAATG 15 89 1 GGGTCTGTAATTGTGTTTAAGAATTGTTTGTA 13 14 1 CTTTACCAAGTTAGATTAAAGAAGTCACGTGT 15 39 1 TATTCATCCTTTGGATTCAAGACATTTTTTAA 15 189 0 GAAAAACAAGTTCTATTCAAAATATATTTTAT 12 229 0 ATTTTTTTTATTTTTCTGAAAAAAAAGTATTT 10 83 1 ATTTTTAATTCTCTTTTCAAGATTGTCTATAA 5 35 0 CGTTTTTTAATTCTATTTAACAGATCTTTTTC 8 55 1 ACAAAAACTTATGTGTTTAAGACTACCAGGAT 10 23 1 TTACGTTCATATGGATTGAAGACATGGGAGGT 4 227 0 GAAAGTACGCTTCTTTTTAAGCTCTAGATACT 8 24 0 CAGAAGAAACTTCTTATAAAGATACAATAGTA 4 68 0 GTGATTGCGCATTTTTTAAAAAATGTCTTGAA 15 174 1 GGGTTTTCTAATTTTTTTAAAACTATCCTGAA 12 154 1 TAAATCTCTTATTTTTTTAACAATTGCATTTC 5 138 0 GAGAAAAAGTTTAGACTTAAAATTCGATAGTA 3 10 1 ** **** **** MAP Score: 21.0954 Motif 4 TTAGTTATCTTGTTTTGTTTTTTAGTTTATT 10 154 1 TATAAATCTCTTATTTTTTTAACAATTGCATTTCAC 5 136 0 ACGGGTTTTCTAATTTTTTTAAAACTATCCTGAACA 12 152 1 TGTTTAAGAATTGTTTGTATTAAAATGATTCTTTTT 13 27 1 TTGGCAATGGTTTTTTTATTTATATTCTCAATATAC 9 52 1 ACAAAGATATTTCTTTCATTTCTATTAGTTGTATTT 12 185 1 TAAGTCATTATACTTTCATTTTTAGTCATCTTCAAT 5 209 0 GTAAAGAAGATTTTTTCTATAACATTTTGTTTTCTT 12 107 1 TGCATAAATATGATTTCATTATAAATAAATATGCAT 0 11 1 GAAAAAAAAGTATTTTATTTTACAAAATAAAAATCT 10 100 1 TAAAAATTTTTAATTTAAATTATAGTTGCAATTGAA 5 60 1 TTTATGCTTCTTTTTTTCTTATGACTT 6 1 0 GGATAAAATATATTTTGAATAGAACTTGTTTTTCTG 12 227 1 CCGCAAGCCTTCGTTTCTATTCAAGATAGAGGCTTT 7 242 1 TGGTAAGGGGTTTTTTTTATTGAAGAGACCTTTCTT 4 24 1 TCCCAACGCATTTTTTGTATTGAAGATGACTAAAAA 5 191 1 GATTCTATATTTTGGATTTGTGTTTTAA 9 2 1 ACTTTACGATTTTTATGTTTTGAATTTTGTTAAGAA 12 73 0 AGGAAGACTTTTATTTTTCTATAAATCTCTTATTTT 5 155 0 TAACAAAAACTTATGTGTTTAAGACTACCAGGATTA 10 21 1 CTATAACATTTTGTTTTCTTATAAAACAAACGGGTT 12 123 1 TAAAACGCAATATTTTTTTTATTTTTCTGAAAAAAA 10 72 1 CAGTATACTATTGTATCTTTATAAGAAGTTTCTTCT 4 63 1 * *** **** * * MAP Score: 19.4202 Motif 5 TTTAAAAATTACTTTAATAAATTTACTATCGAATT 3 30 0 AAAGAAGTCTTTGGTAAGGGGTTTTTTTTATTGAAGAGACCTTT 4 13 1 GCAATTTATATACAGAAGAAACTTCTTATAAAGATACAATAGTA 4 68 0 ATCCGAAATGGAAAAATTAAAAATTTTATAGACAATCTTGAA 5 8 1 GAATTAAAAATTTTTAATTTAAATTATAGTTGCAATTGAAAACG 5 56 1 CTTTTATTTTTCTATAAATCTCTTATTTTTTTAACAATTGCATT 5 140 0 AAAGTCTTCCTTCCCAACGCATTTTTTGTATTGAAGATGACTAA 5 180 1 TCGCATTGTATAAGAAAAAGATCTGTTAAATAGAATTAAAAAAC 8 56 0 CATTGCCGGGTTGGCAATGGTTTTTTTATTTATATTCTCAATAT 9 42 1 ATCCTGGTAGTCTTAAACACATAAGTTTTTGTTAGGTATCTCCT 10 11 0 GTGATGCATTTTATAAAACGCAATATTTTTTTTATTTTTCTGAA 10 59 1 TTTTTATTTTTCTGAAAAAAAAGTATTTTATTTTACAAAATAAA 10 87 1 AAAATAAAAATCTCGAAGGGATATTATTAAGTTAGTTATCTTGT 10 123 1 ACTACTCGCTTCTAAAATCGTATTCTTAGTTAGAAGTC 11 29 1 GTTTGTTTTATAAGAAAACAAAATGTTATAGAAAAAATCTTCTT 12 110 0 TTTAAAACTATCCTGAACAAAGATATTTCTTTCATTTCTATTAG 12 169 1 TATTTCTTGCTGGATAAAATATATTTTGAATAGAACTTGTTTTT 12 216 1 GCTCTCCTCGTATAAAAAGAATCATTTTAATACAAACAATTCTT 13 32 0 CAAGTTAGATTAAAGAAGTCACGTGTTAGATGCACGCTAGCAAT 15 45 1 GATTGCGCATTTTTTAAAAAATGTCTTGAATCCAAAGGATGAAT 15 176 1 * ** * * ** ** * MAP Score: 17.6092 Motif 6 TTTGGTAAGGGGTTTTTTTTATTGAAGAGACC 4 22 1 TATAAATCTCTTATTTTTTTAACAATTGCATT 5 140 0 AGGAAGACTTTTATTTTTCTATAAATCTCTTA 5 159 0 TTTATGCTTCTTTTTTTCTTATGACTT 6 5 0 GAAGCGTACTTTCGTTTTTTAATTCTATTTAA 8 43 1 ATTTAACAGATCTTTTTCTTATACAATGCGAA 8 69 1 GGGTTGGCAATGGTTTTTTTATTTATATTCTC 9 49 1 TAAAACGCAATATTTTTTTTATTTTTCTGAAA 10 72 1 GTTATCTTGTTTTGTTTTTTAGTTTATT 10 157 1 GCTTCTAAAATCGTATTCTTAGTTAGAAGTC 11 36 1 TCAGGATCTTTTTGTTTCTTAACAAAATTCAA 12 58 1 TTCTTTACTTTACGATTTTTATGTTTTGAATT 12 83 0 AAGTAAAGAAGATTTTTTCTATAACATTTTGT 12 105 1 CTATAACATTTTGTTTTCTTATAAAACAAACG 12 123 1 ACGGGTTTTCTAATTTTTTTAAAACTATCCTG 12 152 1 GATGTGGGAATGATTTTTCTAGGTTCTAGAAA 15 109 1 * ********* MAP Score: 14.4298 Motif 7 AAAAGACCTTTCTTTAGAATAAGATTTCAAC 2 129 0 GAAAGGTCTCTTCAATAAAAAAAACCCCTTAC 4 26 0 ATAGACAATCTTGAAAAGAGAATTAAAAATTT 5 37 1 TGAAATGCAATTGTTAAAAAAATAAGAGATTT 5 137 1 AAAATAAGAGATTTATAGAAAAATAAAAGTCT 5 155 1 TTTAGTCATCTTCAATACAAAAAATGCGTTGG 5 193 0 AAGTCATAAGAAAAAAAGAAGCAT 6 2 1 TATTGAGAATATAAATAAAAAAACCATTGCCA 9 53 0 AAAGCTCTAATTCTTGAGAAAAAGCAAGGACT 9 98 1 AAAATACTTTTTTTTCAGAAAAATAAAAAAAA 10 84 0 AAAAGTATTTTATTTTACAAAATAAAAATCTC 10 105 1 ATCTTTTTGTTTCTTAACAAAATTCAAAACAT 12 63 1 AAACAAAATGTTATAGAAAAAATCTTCTTTAC 12 107 0 ACCCGTTTGTTTTATAAGAAAACAAAATGTTA 12 126 0 GTTCAGGATAGTTTTAAAAAAATTAGAAAACC 12 155 0 TCATTCCCACATCTTGAGAAAAACTTCCCCTA 15 90 0 ATTCAAGACATTTTTTAAAAAATGCGCAATCA 15 175 0 ** ** ****** MAP Score: 9.21467 Motif 8 GTATGGGGGACTTCTCAATATGAGCAAGTAAAA 1 44 1 TCTGACTGCTCTTCTCTCTCTACTCAACCGCAT 2 88 1 TTACTATCGAATTTTAAGTCTAAACTTTTTCTC 3 10 0 TAAGAAGTTTCTTCTGTATATAAATTGCTATAT 4 84 1 GAATGAGATTATTGTATCTTTCAGGATAGAAAT 4 164 0 TCTTTTCAAGATTGTCTATAAAATTTTTAATTT 5 23 0 AAAATTTTTAATTCTCTTTTCAAGATTGTCTAT 5 37 0 AGAATTAAAAATTTTTAATTTAAATTATAGTTG 5 55 1 CTATAAATCTCTTATTTTTTTAACAATTGCATT 5 140 0 AAGTTTATGCTTCTTTTTTTCTTATGACTT 6 8 0 AACTCCTGACCTTCTGAATGCAAATCAGACGCT 7 118 0 TCGTTTTTTAATTCTATTTAACAGATCTTTTTC 8 54 1 AAGAAATTTCTTCTAAGTTAAAGATACTGTTT 8 100 0 TTTTATTTATATTCTCAATATACTAGGCATCTG 9 65 1 CTAACAAAAACTTATGTGTTTAAGACTACCAGG 10 20 1 AAATAAAATACTTTTTTTTCAGAAAAATAAAAA 10 87 0 CTAAAATCGTATTCTTAGTTAGAAGTC 11 40 1 AGTAAAGAAGATTTTTTCTATAACATTTTGTTT 12 106 1 TGGGTCTGTAATTGTGTTTAAGAATTGTTTGTA 13 13 1 TTCTTGTAGTCTTCTTTGTCTCAGTTGTTAGAG 14 10 1 ***** * * *** MAP Score: 0.8406