AlignACE 3.0 10/20/99 AlignACE2 -i CP/CP_operons001_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944237086 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 mrsA 300 Phosphomannomutase #1 sodM 184 Superoxide Dismutase (Mn) #2 accD 81 AcCoA Carboxylase/Transferase Beta #3 dut 50 dUTP Nucleotidohydrolase #4 infA 294 Initiation Factor IF-1 #5 tufA 196 Elongation Factor Tu #6 secE 143 preprotein translocase #7 rl11 106 L11 Ribosomal Protein #8 rl1 26 L1 Ribosomal Protein #9 rl7 43 L7/L12 Ribosomal Protein #10 rpoB 136 RNA Polymerase Beta #11 rpoC 23 RNA Polymerase Beta' #12 adk 300 Adenylate Kinase #13 rs1 300 S1 Ribosomal Protein #14 nusA 100 N Utilization Protein A #15 truB 45 tRNA Pseudouridine Synthase #16 lepA 260 GTPase #17 fusA 33 Elongation Factor G #18 rs7 47 S7 Ribosomal Protein #19 rs12 221 S12 Ribosomal Protein #20 CPn0553 106 hypothetical protein #21 CPn0577 300 SWIB (YM74) complex protein #22 yaeI 247 phosphohydrolase #23 rs11 21 S11 Ribosomal Protein #24 rs13 55 S13 Ribosomal Protein #25 secY 24 Translocase #26 rl6 26 L6 Ribosomal Protein #27 rl14 22 L14 Ribosomal Protein #28 rl16 28 L16 Ribosomal Protein #29 rl2 21 L2 Ribosomal Protein #30 rl4 32 L4 Ribosomal Protein #31 rl3 270 L3 Ribosomal Protein #32 CPn0648 103 CT529 hypothetical protein #33 lpxC 29 Myristoyl GlcNac Deacetylase #34 yciA 130 acyl-CoA Thioesterase #35 dnaQ_2 24 DNA Polymerase III Epsilon Chain #36 rs4 216 S4 Ribosomal Protein #37 rl36 244 L36 Ribosomal Protein #38 rs14 22 S14 Ribosomal Protein #39 pnp 40 Polyribonucleotide Nucleotidyltransferase #40 rs15 247 S15 Ribosomal Protein #41 CPn1010 226 CT852 hypothetical protein #42 CPn1011 111 CT853 hypothetical protein #43 yzeB 51 ABC transporter permease Motif 1 ACATGAGAAGCTCTTTGTAAAGAATATGGTGAT 0 46 0 TAAGGACTTTTTCTTTGTAAACAGAGGTTTTTG 4 51 1 AGGGATTTGACTTTTTCTAAATAACAAATATAA 4 147 1 CTTCATTTCCCCTATTCTATAAACGCATTAGGA 4 180 0 TTTCGATTTTTCTTTTCTACAAA 10 0 0 AATTACCACACGTATTTTATAAAATCTGGTAAT 13 104 1 ATCCTATACTTCCGTTCTAGAGATGTATAAGGC 13 157 0 CAGGAGACGATTAGTTCTATATAATCGAATTAA 13 197 0 ATCGTATTATTTAGTTCTAAATAATACGTCCTT 14 34 1 TATACTCCTCTTGTAAATAAGGAAATCAG 14 81 0 ACAGCTAAAATTTCTTTTAAAAAGTAAAAAAAC 19 55 1 CTTTGTTATATCTTTTCTAAAGACTCCCCTTGA 21 150 1 CTCCCCTTGACGCTTTCTAAATAGAAAAGGTAA 21 173 1 CTCAAGTTTCTCGTTTTTAAAGACCGGAAATTA 22 205 1 TAGTTTTATCTTTATTTTAAAGAAGTCGCTTCT 31 12 1 TTTAAAGAAGTCGCTTCTAAAAAATTTTTTGGA 31 27 1 AAGCGACTTTCTATTTCTATAAATAGGAATTTT 31 59 1 GAGTACTTTTCCTATTGTAAAAATCTTCCCCCT 31 127 1 AAATTTCCTTTTCTTTTTAGAGAATTCGATAAG 31 192 1 AGGCTCTAATTTTTTTTTAAAAAGCCTTGTAAG 32 71 1 GCACTTCGATTTCTAAAAAATAATCAAAA 34 6 1 TGGAAATAATTGCATTGTAGAAAATTGCCATTA 36 32 1 TTCTCTCCACCCAATTCTAAATAATATTATTTA 40 20 1 TATTCCATTATGAGTTCTAAAAACAAAAAAAAT 40 51 1 GGTAAGACTTTTTTTTCTATAAACAAAGAAAAA 40 149 0 AACTTATTCTATAAAAATGCTTGTT 41 211 0 CTCACACCCTGTTCTAAAAAATATTACCTA 42 7 1 ** ******* * MAP Score: 29.5634 Motif 2 TTTGTAGAAAAGAAAAATCGAAAGATT 10 7 1 AAAGAAAAAGAAAAGAAAAATCTTTCGATT 10 25 0 TTTATACATGAAAAGAAAAAGAAAAGAAAA 10 36 0 TTTCTCTCCAAAAAGAAGAAAAAGTCTTGG 21 117 0 GTTTCTCGTCAAAACAAAAAAGTGGAATTC 21 209 0 ATGAGTTCTAAAAACAAAAAAAATAACAAT 40 60 1 GAATTCTCTAAAAAGAAAAGGAAATTTTCC 31 189 0 CAAGAAAATTAAAAGAAAAGAGGTCTCTTT 12 51 0 CTCTTTTCTTAATAGAAAAAACTCCATTTT 22 115 0 ATTTCTTTTAAAAAGTAAAAAAACGGTTCG 19 64 1 ACTTCTCATAAAAAGGAGAAGCATACTAAG 37 210 0 TAAATATAGAAAAACAAGAAAATTAAAAGA 12 65 0 TTTCTATAAACAAAGAAAAAATTAGGGGCT 40 139 0 CCTCTGTTTACAAAGAAAAAGTCCTTATTT 4 48 0 CAACCTCAGTAAAAGTAGAACTCCTATTAC 20 85 0 AAGATTCTAGAAAACAAAAGCCAATAAAGT 21 41 1 AAGTATTATACAAAGAAGAAGGTAAGAAAA 20 25 1 TATCACCTATAATAGGAAAATTCTTGGGCC 22 164 1 AGATTTTTACAATAGGAAAAGTACTCTAGG 31 123 0 TAAGAAACGAAAAACTAAAATTATAAGAAG 7 43 0 CCGGTCTTTAAAAACGAGAAACTTGAGACT 22 202 0 ACGCTTTCTAAATAGAAAAGGTAAAGAGAA 21 182 1 AAGGAGGTTAAATACTAAAAAGGTATGTTG 1 162 1 TGAACGGGGAAATAGTAAAGAATATAACTT 12 17 0 ********** MAP Score: 27.9847 Motif 3 AAAACAGAGAGACTTTTCCTAGAATGCAAA 12 200 0 AGAATATGGTGATTTTTCCTTCAGAAAGAT 0 29 0 TGAGTCCCAAGATTTTCCCTAGGACTACTA 12 115 0 TTAAAATAAGGACTTTTTCTTTGTAAACAG 4 45 1 AAAGGGATTTGACTTTTTCTAAATAACAAA 4 145 1 CAAAAACCAAGACTTTTTCTTCTTTTTGGA 21 111 1 TGGGGCCCAAGAATTTTCCTATTATAGGTG 22 167 0 AAAATCTTTCGATTTTTCTTTTCTACAAA 10 9 0 AAAATCGAAAGATTTTTCTTTTCTTTTTCT 10 23 1 GGTAGGGTAAGACTTTTTTTTCTATAAACA 40 157 0 TCTCCAAGATGATTTTTCCAC 1 1 0 AAGAAAAGGAAATTTTCCCTTAAGAAAATA 31 177 0 GTCATCTCTCGAATTTTCTTAGATAAGTTG 37 126 0 CACAGCCCCTAATTTTTTCTTTGTTTATAG 40 136 1 GAAAATCATAGATTTTCTTTCAGTTGACCG 34 58 1 GAAAATCTATGATTTTCTTTCATAAGTTAC 34 45 0 TATAACAAAGAACTTTCTCTCCAAAAAGAA 21 130 0 CTATAAATAGGAATTTTCCAAGAATCTTTT 31 75 1 GTACCTAGAGTACTTTTCCTATTGTAAAAA 31 120 1 TGATGCGACAAAATTTCCCTAAATTAAGCC 10 97 0 TATAGGCTCTAATTTTTTTTTAAAAAGCCT 32 68 1 ********** MAP Score: 18.9489 Motif 4 AATATGGTGATTTTTCCTTCAGAAAGATGCTGA 0 24 0 AAAATCACCATATTCTTTACAAAGAGCTTCTCA 0 43 1 AATAAGGACTTTTTCTTTGTAAACAGAGGTTTT 4 49 1 TTATATTTTCTATTGATGTTTTAAAA 5 3 1 TTTCGATTTTTCTTTTCTACAAA 10 0 0 TATTTTCTCCAAAACGTCATTTT 11 10 0 CAAAGAGACCTCTTTTCTTTTAATTTTCTTGTT 12 50 1 TTATTGTTATTCTCCTAAAAACTACAAAGT 13 280 0 TACGAAATTCTTCTCTCCAAAGAGATAGGTT 19 8 1 TAACAAAGAACTTTCTCTCCAAAAAGAAGAAAA 21 125 0 CTTTGTTATATCTTTTCTAAAGACTCCCCTTGA 21 150 1 TCTCTTTACCTTTTCTATTTAGAAAGCGTCAAG 21 178 0 TAAAATGGAGTTTTTTCTATTAAGAAAAGAGGA 22 114 1 GAAAAGGAAATTTTCCCTTAAGAAAATAAAGGG 31 172 0 GAAAATTTCCTTTTCTTTTTAGAGAATTCGATA 31 190 1 AGGCTCTAATTTTTTTTTAAAAAGCCTTGTAAG 32 71 1 AATTTTTGATTATTTTTTAGAAATCGAAGTGC 34 9 0 AAATCTATGATTTTCTTTCATAAGTTACTGAAA 34 40 0 GGTAAGACTTTTTTTTCTATAAACAAAGAAAAA 40 149 0 CCTAGCCACCTTTTCTCTTCAGATCTTCTGCAA 41 92 1 AACTTATTCTATAAAAATGCTTGTTGT 41 209 0 * ****** *** MAP Score: 18.1681 Motif 5 GAGATGTATAAGGCCTCTTTTTTAACTTTTCT 13 139 0 TTTGTTGGCAAGGGCTTATTTTCAGATGAAGA 19 141 0 TATTAAAATAAGGACTTTTTCTTTGTAAACAG 4 43 1 CCTTGAAAGAAGGCCTTATTCTGAAGGAGATT 1 60 0 TGAAGAGCTCAGGTCTCTTCTTACCACCTTTA 21 265 1 CCTGCAAGGGAGGTCTTGCCTTTTTTAAGGTT 13 226 1 AATATAGAGTAAGGCTCTCTTTGTTGGCAAGG 19 160 0 AAACCGTTTTAGGACTTTTTGTAACAATTGTG 41 151 1 ACTTAAAATAAAGTCTTACTTTTAGTTTAGTA 20 56 1 TTGGTAGGGTAAGACTTTTTTTTCTATAAACA 40 157 0 AACAAAAACCAAGACTTTTTCTTCTTTTTGGA 21 109 1 GGTTGAGTAGAGTACTTGCTTTCCTAGCAAAA 1 113 1 GAAGGTCTCCTGTTAGATATTTGT 39 26 0 AGCTCTAGGAAGTCCTTGCTCTAATTGACTTT 21 66 0 ATCTTTTCTAAAGACTCCCCTTGACGCTTTCT 21 159 1 ATTCTAGGAAAAGTCTCTCTGTTTTACCCCAT 12 205 1 TAAAAAACCGAATGCTCCCTTTAGAAGCATAC 10 62 1 TAGTACCTAGAGTACTTTTCCTATTGTAAAAA 31 118 1 GCGAGTTCTCCTGCTATTTTGATGC 10 121 0 ATTCTATAAAAATGCTTGTTGTAATCCTGAGA 41 199 0 GAAACTTAACAATACTTTTCGTACGACATGGG 12 232 0 ACCCTATAAAAATCCTTTCGGTAGAGTCAACA 34 108 1 *** *** **** MAP Score: 14.7073 Motif 6 ACCTTAAAAAAGGCAAGACCTCCCTTGCAGGAGACG 13 221 0 AGCCCTTGCCAACAAAGAGAGCCTTACTCTATATTT 19 157 1 ATACTATCGCAACCAAGAATACCCTATAAAAATCCT 34 88 1 ATCTTTCTGAAGGAAAAATCACCATATTCTTTACAA 0 29 1 GTGGATTCTTAATTAAGAAAACCTTTCTCAAACAAT 0 181 1 GAATAGGGGAAATGAAGAGCACCGTTCTATTTTTAG 4 196 1 TATTTTCTTAAGGGAAAATTTCCTTTTCTTTTTAGA 31 177 1 CTCTGTTTACAAAGAAAAAGTCCTTATTTTAATATA 4 41 0 ATTTAGTTCTAAATAATACGTCCTTAATTTAGCTAT 14 42 1 ACAAAGAAGAAGGTAAGAAAACACTTAAAATAAAGT 20 34 1 ATCTCTTTGGAGAGAAGAATTTCGTA 19 0 0 GAAAATTAAAAGAAAAGAGGTCTCTTTGGCTTGAAC 12 42 0 TTTTCTTAATAGAAAAAACTCCATTTTAAATTAAAG 22 106 0 CTTTGTTTATAGAAAAAAAAGTCTTACCCTACCAAA 40 154 1 TTCTAAAAACAAAAAAAATAACAATATACAATATCA 40 65 1 AGTTCGTTACAGCTAAAATTTCTTTTAAAAAGTAAA 19 47 1 TTGCCATTAGAACTAAAATGCTCTTTGGTATTTTGT 36 56 1 TCGATAGTGAAAAAAATAAAACAATAAGCAGTATAT 4 10 1 TTTTCTAAATAACAAATATAATCCTAATGCGTTTAT 4 159 1 GGGAAATAGTAAAGAATATAACTTTATTTTT 12 5 0 ACTAAACTAAAAGTAAGACTTTATTTTAAGTGTTTT 20 51 0 ** **** ** ** MAP Score: 11.7295 Motif 7 CATTCTAGGAAAAGTCTCTCTGTTTTACCCC 12 204 1 AATTTCGGGCAAAGCCTCTTTAGTAAGACTC 37 46 0 GTTTTGACGAGAAACCTCTCTGAGAGATAAA 21 224 1 ATTAGAACTAAAATGCTCTTTGGTATTTTGT 36 61 1 AGAGATGTATAAGGCCTCTTTTTTAACTTTT 13 141 0 CAAAAAAGTGGAATTCTCTTTACCTTTTCTA 21 194 0 TAAAAAAGGCAAGACCTCCCTTGCAGGAGAC 13 222 0 TAGGTCCTCTCTGTATCACCCC 30 20 0 CTAAAACATGAGAAGCTCTTTGTAAAGAATA 0 53 0 TCAAGCCAAAGAGACCTCTTTTCTTTTAATT 12 44 1 ATATAGAGTAAGGCTCTCTTTGTTGGCAAGG 19 160 0 ATAAAAAACCGAATGCTCCCTTTAGAAGCAT 10 61 1 GCTGCATTGAGAAGGCTCCTTCAGACAAAGA 16 196 0 TTCGAATGCTCCTTAAATTGACGT 12 286 0 CGTTACAGCTAAAATTTCTTTTAAAAAGTAA 19 51 1 ATATAACAAAGAACTTTCTCTCCAAAAAGAA 21 130 0 TTGATGCGACAAAATTTCCCTAAATTAAGCC 10 97 0 AAAGAAAAGGAAATTTTCCCTTAAGAAAATA 31 177 0 AGAAAATCATAGATTTTCTTTCAGTTGACCG 34 57 1 ATGAGTCCCAAGATTTTCCCTAGGACTACTA 12 115 0 CTTCAGAATAAGGCCTTCTTTCAAGGCCATT 1 66 1 ATCCTTACATAGGATTTCTTTA 0 288 1 *** ******* MAP Score: 10.1628 Motif 8 TTCCCCGTTCAAGCCAAAGAGACCTCTTTTCTTTTAATTTTCT 12 36 1 CCTATTACTAAACTAAAAGTAAGACTTTATTTTAAGTGTTTTC 20 50 0 CTATGACTTAAACAAAAACCAAGACTTTTTCTTCTTTTTGGAG 21 99 1 ATCCTGCTTGAATTTAAAAAAATGCTATCTTTTTCTAGACGAA 19 90 0 GAATTCTCTAAAAAGAAAAGGAAATTTTCCCTTAAGAAAATAA 31 176 0 TAGGGCATTTAAACTAAATTAAGTCGTTTTATGTTATTATAGG 32 31 1 CGGTCAACTGAAAGAAAATCTATGATTTTCTTTCATAAGTTAC 34 45 0 CATCTTTCTGAAGGAAAAATCACCATATTCTTTACAAAGAGCT 0 28 1 TTTGTAGAAAAGAAAAATCGAAAGATTTTTCTTTTCTTTTTC 10 9 1 AAAAATAAAGTTATATTCTTTACTATTTCCCCGT 12 1 1 AGGTACTAAGAACTCAAAGATAAAAGATTCTTGGAAAATTCCT 31 83 0 TAGTGAAAAAAATAAAACAATAAGCAGTATATTAAAATAAGGA 4 14 1 AAGGCTTTTTAAAAAAAAATTAGAGCCTATAATAACATAAAAC 32 56 0 AATAAAGATCAATAAGAAGACATCGGCTTTCTTCCAACTTATC 37 92 1 GGTGCTTATGAAAAAAACGATATGTTTTCTATGCGCCAAATCC 13 27 1 TTCCCTTAAGAAAATAAAGGGACAGGTTATCAGAGGGGGAAGA 31 150 0 CTCTCCACCCAATTCTAAATAATATTATTTATTCCATTATGAG 40 22 1 TTTCTCGTCAAAACAAAAAAGTGGAATTCTCTTTACCTTTTCT 21 195 0 AACAATATACAATATCAATAAAACGCTTTTATGAAGCAATCTC 40 84 1 ** *** * * * ** MAP Score: 9.15083 Motif 9 AATCTCCTTCAGAATAAGGCCTTCTTTCAAGGC 1 60 1 GCAGTATATTAAAATAAGGACTTTTTCTTTGTA 4 37 1 TCATATGTAGAGAAACAGGATTTGGCGCATAGA 13 54 0 AGAAAAGTTAAAAAAGAGGCCTTATACATCTCT 13 139 1 AAAGTATTTGAGAAGCTGGTCTTTGTCTGAAGG 16 177 1 TCTTCATCTGAAAATAAGCCCTTGCCAACAAAG 19 141 1 GAAAACACTTAAAATAAAGTCTTACTTTTAGTT 20 50 1 AAAGTCAATTAGAGCAAGGACTTCCTAGAGCTT 21 66 1 GACTTAAACAAAAACCAAGACTTTTTCTTCTTT 21 103 1 TTGTTTATAGAAAAAAAAGTCTTACCCTACCAA 40 156 1 TAGCCAGCTGAGAATTAGGATTTGGAAATTGAT 41 51 0 **** *** *** MAP Score: 9.0284 Motif 10 ACTTCGGCCTGTGGTTTTTGTAATTAAGTATTGA 0 98 0 TTAAAATAAGGACTTTTTCTTTGTAAACAGAGGT 4 45 1 TTTGTAAACAGAGGTTTTTGTGCTTCTATAGCCC 4 64 1 AAAGGGATTTGACTTTTTCTAAATAACAAATATA 4 145 1 CATAGACTAGGCGGTTTTTCAAGACCGGGAAGCA 5 43 1 AGGGAGCATTCGGTTTTTTATACATGAAAAGAAA 10 48 0 TGTATAAGGCCTCTTTTTTAACTTTTCTATATTA 13 133 0 GGGAGGTCTTGCCTTTTTTAAGGTTTATATTTAC 13 233 1 TATTTACACTGTCTTTTTTGACTTTGTAGTTTTT 13 260 1 TCTAGACGAACCGTTTTTTTACTTTTTAAAAGAA 19 66 0 TGACTTTATTGGCTTTTGTTTTCTAGAATCTTGA 21 39 0 CAAAAACCAAGACTTTTTCTTCTTTTTGGAGAGA 21 111 1 AAGAGAATTCCACTTTTTTGTTTTGACGAGAAAC 21 205 1 ATTTAAAATGGAGTTTTTTCTATTAAGAAAAGAG 22 111 1 TCTCAAGTTTCTCGTTTTTAAAGACCGGAAATTA 22 204 1 CTTTACAACGTGTTTTTTATTTAGGGCATTTAA 32 9 1 GGTAGGGTAAGACTTTTTTTTCTATAAACAAAGA 40 153 0 * ******* * * MAP Score: 5.19774 Motif 11 GACTTTATGCAAAAAGGGTGTTAAGAGTTCCTGAAA 0 250 1 TTGTATCCGAAACAAGGTTGAGTAGAGTACTTGCTT 1 98 1 GGTTAAATACTAAAAAGGTATGTTGTT 1 167 1 GTGAAAAAAATAAAACAATAAGCAGTATATTAAAAT 4 16 1 AACGAAAAACTAAAATTATAAGAAGATAAGGAATAA 7 32 0 TGCTTATGAAAAAAACGATATGTTTTCTATGCGCCA 13 29 1 TAAAAAGTAAAAAAACGGTTCGTCTAGAAAAAGATA 19 72 1 TCTGAGAGATAAAAAAGTTGGGATGAAGAGCTCAGG 21 242 1 TATAAAACTATTTGTTGTCTAATTTCCG 22 229 0 AAGTCGCTTCTAAAAAATTTTTTGGAAGCGACTTTC 31 34 1 ATTCGATAAGTAAAATACTAAGCAGATTTGTTTCTT 31 215 1 CCATTAGAACTAAAATGCTCTTTGGTATTTTGTCAA 36 59 1 TGGTATTGTCAAAAAAGCTCCTAGGAGATTAAATTG 37 160 1 ACAATATCAATAAAACGCTTTTATGAAGCAATCTCA 40 92 1 CAAAAAGTCCTAAAACGGTTTGTGTAGCTAGGAGTA 41 136 0 CTTATTCTATAAAAATGCTTGTTGTAATCCTGAGAC 41 198 0 ***** * * * ** MAP Score: 3.78842 Motif 12 TGGTGATTTTTCCTTCAGAAAGATGCTGAATCAA 0 19 0 TAAGAATCCACCCTTCAAAATAAATCCTATAGAA 0 158 0 CTTTAGGATATTCTCCAAGATGATTTTTCCAC 1 8 0 ATTTGACTTTTTCTAAATAACAAATATAATCCTA 4 151 1 TTTGTAGAAAAGAAAAATCGAAAGA 10 1 1 GTATTCAAGTTCCCAAAAAATATAGTTTA 15 5 0 CCAATCAAGATTCTAGAAAACAAAAGCCAATAAA 21 35 1 AAAGAACTTTCTCTCCAAAAAGAAGAAAAAGTCT 21 120 0 CCTTGACGCTTTCTAAATAGAAAAGGTAAAGAGA 21 177 1 TAGAAGCGACTTCTTTAAAATAAAGATAAAACTA 31 12 0 TCCCTTTATTTTCTTAAGGGAAAATTTCCTTTTC 31 171 1 ACTTATCGAATTCTCTAAAAAGAAAAGGAAATTT 31 192 0 GTTTCTTTGTTCCTCCAAGAGGAAAGCAAATCAT 31 244 1 AGTTTAAATGCCCTAAATAAAAAACACGTTGTAA 32 12 0 GCACTTCGATTTCTAAAAAATAATCAAAAATTTC 34 10 1 CGGATGTCTCCTTAAAATAATTGCCGCAAAA 40 226 0 TCTTCAGATCTTCTGCAAAGGGAACAAAGTACTC 41 107 1 TCACACCCTGTTCTAAAAAATATTACCTATAAAT 42 11 1 TTCCGAAGTATCCTCTAGAGGATTCCCTTGAAAA 42 78 1 CTAGAGGATTCCCTTGAAAATAATAGGAA 42 92 1 **** * ** *** MAP Score: 0.141511