AlignACE 3.0 10/20/99 AlignACE2 -i CP/CP_operons004_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944237296 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 atpE 300 ATP Synthase Subunit E #1 CPn0087 48 CT309 hypothetical protein #2 atpK 94 ATP Synthase Subunit K #3 yscU 300 Yop Translocation Protein U #4 rpsD 114 Sigma-28/WhiG Family #5 flhA 277 Flagellar Secretion Protein #6 polA 23 DNA Polymerase I #7 sohB 123 Protease #8 adt_2 228 ADP/ATP Translocase #9 pgsA_1 300 Glycerol-3-P Phosphatidyltransferase #10 CPn0708 33 CT668 hypothetical protein #11 CPn0710 21 CT666 hypothetical protein #12 CPn0711 46 CT665 hypothetical protein #13 CPn0713 300 CT663 hypothetical protein #14 yscL 120 Yop Translocation L #15 yscJ 300 Yop Translocation J #16 fliF 291 Flagellar M-Ring Protein #17 pgmA 155 Phosphoglycerate Mutase #18 xerD 65 Integrase/recombinase Motif 1 TATTTTACCGCTTATTCTTTTAGAAAAGAAT 0 277 0 CACCCTTTTTCGTATTCTTTTTAAAGAAAGC 9 135 1 CTTGTGGCCTCTTGTTCTTTATAATGAAAAA 13 105 1 GCTCACAATACTTTTTCTTTCCGGG 8 4 0 TTGTTGCCATCGTATTCTTCTCTATCAAAAA 16 234 0 TAGAAAGGCAATTCTTCTTTTTTGAATTCTA 0 60 1 ACTTTTCGTTATTGTTCTTTTTTTCTACTAT 3 141 1 TCCTTGTCTTCTTTTTCTTCAAGCCACGATA 15 207 0 CTAAAACCTGCTTTTTCTTCCTTTAAATCGA 13 215 0 TTTTTCTACTATTCTTCTTTATCTCTAAGAT 3 160 1 TTTCATTTCACGTGTTCTTGATTCCAACAAA 16 79 1 ATAGATTATAATTATTCTTGTTATGGATTCA 13 63 1 ATTCAGCTCGATTTTTCTTGTGGCCTCTTGT 13 89 1 TATTTTTCAGAGTTTTCTTTCCTATCGTTTT 15 79 0 CTATTACTTTCGTATTTTTTTTGTTGGTGTA 4 33 1 ACCTTATGCTCTTGTTTTTCTCAAGAGTGAA 3 227 0 CTTTGCTCATCTTTTTCATTATAAAGAACAA 13 116 0 CTTTTATTGTCGTGTTATTTTTCTATACTTT 14 41 0 AAATTTTTTTTTATCTAGTTATT 4 101 0 CCACGCATACCTTTTTATTCACCATAACAAA 15 276 0 TTGTTTAAAAATTTTTTTTGAATTAATCTAA 4 68 1 *** ******* MAP Score: 19.0789 Motif 2 TTGTCTTCTTTTTCTTCAAGCCACGATATT 15 205 0 CCTCATGTGCTCCCTTCAAATACCTTTAAA 2 69 0 GCATTTATCTTACCTTCAAAAAAACATCCC 15 126 1 TAGTACCTTCAAAATCAAGAGTG 3 3 1 CTCAATGCTGTTTCTGCAAATAAGAAATCG 13 154 1 ATTGCTTTGATATCTTCAAGATAAATCCCA 0 131 0 TCAAAGCAATTTTCTTCTAGAACATCTCTG 0 151 1 CTCTTCCATATATCTGCAAGTAAAACTCTA 5 214 0 TGCATATTCCCTTCTAGGTCTCT 6 6 0 TATTCGGAATTATCTGCAAATTACCTTATG 3 250 0 CTGCTTTTTCTTCCTTTAAATCGAGTTATG 13 209 0 GGAGTTTTCCTTCTACGTATTGTCGG 5 6 1 ATGTTCCTACTAGAATTTAGGGT 17 142 0 TATATTAGGCTTTCTTTAAAAAGAATACGA 9 144 0 AGAAAAGAATTTTCTTTAAAAAAGATGTTA 0 257 0 CGAAAGTACGTCCCTGCTAAGGACGCGTAC 9 25 1 TTCTAGAACATCTCTGCAACCCGTTTCTTA 0 165 1 ACTTCTATATTTTCTACTAGACAAAAGTTG 17 88 1 ATACTTTAGGTCACTTCAAGATGGTTCTAT 3 97 0 TCCCTTCAAATACCTTTAAATAATTACGAA 2 59 0 AATGTAGGGATTTCTACTAAAAGAAGTTGG 16 18 0 TAAGAAAAAATTCCTATAAACATAGAATTC 0 83 0 ********** MAP Score: 17.0698 Motif 3 TGAAAGTAGGCCTTCTTCTAGATCCAAAGATT 0 20 0 TTTATAGGAATTTTTTCTTAGAGAGTTAGAGG 0 93 1 AGCATGGGATTTATCTTGAAGATATCAAAGCA 0 127 1 ATCAAAGCAATTTTCTTCTAGAACATCTCTGC 0 150 1 ATAATAACATCTTTTTTAAAGAAAATTCTTTT 0 253 1 AAGAAAATTCTTTTCTAAAAGAATAAGCGGTA 0 271 1 CCTAATACTTTCTTCATATAGAACCATCTTGA 3 80 1 CTATTCTTCTTTATCTCTAAGATTCATTTATA 3 168 1 TTTAATTTAATCTTCTGTAAGCACTATTACTT 4 10 1 TTTTATCTAGTTATTTATTAGATTAATTCAAA 4 84 0 TTTATAATTTTCATCTTTAAGCTTTTCTGCTC 7 53 1 TTTTTCGTATTCTTTTTAAAGAAAGCCTAATA 9 140 1 CTTGTCTTCTTTTTCTTCAAGCCACGATATTA 15 204 0 CCCCCCAACTTCTTTTAGTAGAAATCCCTACA 16 14 1 ATAATTCCTACTTTTTGATAGAGAAGAATACG 16 223 1 TACTTCTATATTTTCTACTAGACAAAAGTTGA 17 87 1 ****** **** MAP Score: 14.203 Motif 4 AGAATTCAAAAAAGAAGAATTGCCTTTCTATGTTTG 0 54 0 ACTGATCCACAAATAAGAAACGGGTTGCAGAGATGT 0 172 0 TTATTCTTTTAGAAAAGAATTTTCTTTAAAAAAGAT 0 261 0 GTACCTTCAAAATCAAGAGTGCTTTGAAAATGATAA 3 12 1 GGGAAGTATGAGAAAAGGCAGGGATTCTCTAGGAGG 5 243 1 AGAGGTTATTCGGAAAGAGAGGGATTCGAACCCTCG 9 68 0 AGCTTGCGTTAGCCAAGGTAGAGGTTATTCGGAAAG 9 87 0 AACAGTTGCAAGATGAGAAACCGTTTGAGCGAACTC 9 190 1 AAAGCAAAAAAACCGTTTTACTGTTTTA 10 15 0 GAAAAAGATGAGCAAAGAAAAGCGCTCAATGCTGTT 13 130 1 CTGTTTCTGCAAATAAGAAATCGTTTTTATTTTTAA 13 161 1 AGCAGGTTTTAGAAATGAGATTGTTTCCATTCCTCA 13 234 1 TTCCTCAGGGAACAAAGACAACCATTGCTGCGTTGG 13 263 1 AAGCTTTATAAGTAAAGATTTAGCTTTATACAAAGT 14 10 1 ATAAAACGATAGGAAAGAAAACTCTGAAAAATATCA 15 77 1 GTTTTTTTGAAGGTAAGATAAATGCTCTCTACCTTA 15 115 0 ATGGTGTTCCAATTATGAAAGGGATGTTTTTTTGAA 15 140 0 GCTTGAAGAAAAAGAAGACAAGGATTACCATTTTAT 15 214 1 ACTTTTTGATAGAGAAGAATACGATGGCAACAATGC 16 232 1 AAAATATAGAAGTAAAAAAAGTTTTTAAGCAAAGAA 17 65 0 ** **** * * ** MAP Score: 12.7882 Motif 5 GCCTACTTTCAAACAAACATAGAAAGGCAATTCTTCTTTT 0 41 1 ACTCTCTAAGAAAAAATTCCTATAAACATAGAATTCAAAA 0 79 0 TTCTTTTAGAAAAGAATTTTCTTTAAAAAAGATGTTATTA 0 254 0 TTCTTTTCTAAAAGAATAAGCGGTAAAATATT 0 278 1 GAATAGTAGAAAAAAAGAACAATAACGAAAAGTTGTTGAA 3 134 0 TTACACCAACAAAAAAAATACGAAAGTAATAGTGCTTACA 4 25 0 AGATTAATTCAAAAAAAATTTTTAAACAATATTTACACCA 4 57 0 TTAATCTAATAAATAACTAGATAAAAAAAAATTT 4 90 1 ATACTCCGTAAAATAAAATTTTCGAGTAAAAGAGATCAAC 5 120 1 AAAATGGATAAAATAAGGGATGAGCAGAAAAGCTTAAAGA 7 66 0 ATATCTACCTAAATATAAATAATTAATAAACCCCAATACT 12 13 0 TCATTATAAAGAACAAGAGGCCACAAGAAAAATCGAGCTG 13 92 0 TCTTTATAATGAAAAAGATGAGCAAAGAAAAGCGCTCAAT 13 120 1 TTTAAAGGAAGAAAAAGCAGGTTTTAGAAATGAGATTGTT 13 219 1 CAAAGTATAGAAAAATAACACGACAATAAAAGGAGCGGTG 14 40 1 AAACGATAGGAAAGAAAACTCTGAAAAATATCACATAAGG 15 80 1 CCACGATATTAAAAAATGATTTCATACATACCTCTCGGCA 15 175 0 ATATAGAAGTAAAAAAAGTTTTTAAGCAAAGAAAAGTAGA 17 58 0 *** ** ** *** MAP Score: 10.2068 Motif 6 TTCATGTTCCTCTCTTAAAGGCAAGGGAAGTTTA 2 6 0 AAGAGGGAAGTATGAGAAAAGGCAGGGATTCTCTAGGA 5 239 1 TACTGGTTACTTAGCAAACGGCAAGGCATAAATTAACG 8 113 0 AGGTAGAGGTTATTCGGAAAGAGAGGGATTCGAACCCT 9 70 0 ACGAATATCCTCTGATGTCTGTGAGGGAATGGGCGTGC 13 13 1 GGCCTCTTGTTCTTTATAATGAAAAAGATGAGCAAAGA 13 110 1 TTGGCATAACTCGATTTAAAGGAAGAAAAAGCAGGTTT 13 205 1 AGTTTGCCTAAGACTTAAGTAAGGGAGTTTGTGAAT 15 8 1 ATTACTCTTATTGCAACAAAGGTAGAGAGCTTCATAAA 15 44 1 GGTAGAGAGCTTCATAAAACGATAGGAAAGAAAACTCT 15 64 1 CTCTGAAAAATATCACATAAGGTAGAGAGCATTTATCT 15 98 1 AAAGGGATGTTTTTTTGAAGGTAAGATAAATGCTCTCT 15 121 0 CGGCATGGTGTTCCAATTATGAAAGGGATGTTTTTTTG 15 142 0 GAAATGAAAGCCTCTACAATGATAGAGACTCGTATTTA 16 50 0 CAAGCACCTATTGTGCCTAAGCAAGGCAATACTGGTCT 17 23 1 GGAGCAATTTTCAAGCTACAGAGAGAAAACC 18 3 0 ** ** * ***** MAP Score: 8.73908 Motif 7 GAAGAAGGCCTACTTTCAAACAAACATAGAAAGGCA 0 34 1 GAAAAGAATTTTCTTTAAAAAAGATGTTATTATGAT 0 250 0 TAGTACCTTCAAAATCAAGAGTGCTTTGA 3 3 1 AAATCAAGAGTGCTTTGAAAATGATAAAAAACCACT 3 21 1 ATATTAGGCTTTCTTTAAAAAGAATACGAAAAAGGG 9 137 0 GCTCATCTTTTTCATTATAAAGAACAAGAGGCCACA 13 107 0 CAACCATTGCTGCGTTGGAAAACACGAGT 13 281 1 GCATTTATCTTACCTTCAAAAAAACATCCCTTTCAT 15 126 1 TAGAAATCCCTACATTCCTAAATACGAGTCTCTATC 16 32 1 TTTTAGAGCCTACATTCCAAAGAATGGTTAGAGAAG 16 134 0 * * ** *** *** MAP Score: 8.45676 Motif 8 ATAGAAAGGCAATTCTTCTTTTTTGAATTCTAT 0 59 1 ACATCTCTGCAACCCGTTTCTTATTTGTGGATC 0 172 1 TGGAATCATAATAACATCTTTTTTAAAGAAAAT 0 246 1 TTTTAAAGAAAATTCTTTTCTAAAAGAATAAGC 0 266 1 ATTTCTTTCATGTTCCTCTCTTAAAGGCAAGGG 2 17 0 TTTTTTCTACTATTCTTCTTTATCTCTAAGATT 3 159 1 ATTCCGAATATAGTCCTCTTAATCGAACCTTGG 3 270 1 AAGATGCTTCATAACGTCTCTTTAGAGTTTTAC 5 192 1 AATTTTATAATTTTCATCTTTAAGCTTTTCTGC 7 50 1 TAAGCTTTTCTGCTCATCCCTTATTTTATCCAT 7 70 1 CGAGGGTTCGAATCCCTCTCTTTCCGAATAACC 9 68 1 CGCTTTTCTTTGCTCATCTTTTTCATTATAAAG 13 121 0 TGCAAATAAGAAATCGTTTTTATTTTTAAAGTT 13 168 1 AAAACCTGCTTTTTCTTCCTTTAAATCGAGTTA 13 211 0 AATGGAAACAATCTCATTTCTAAAACCTGCTTT 13 232 0 TACCTTCAAAAAAACATCCCTTTCATAATTGGA 15 136 1 GGTATGTATGAAATCATTTTTTAATATCGTGGC 15 183 1 ATGGTAATCCTTGTCTTCTTTTTCTTCAAGCCA 15 212 0 AGCAACTTAAAATCCTTCTCTAACCATTCTTTG 16 120 1 GTTGCCATCGTATTCTTCTCTATCAAAAAGTAG 16 230 0 GCAATACTGGTCTACTTTTCTTTGCTTAAAAAC 17 48 1 * ** ******* MAP Score: 7.94942 Motif 9 TTAATTTAATCTTCTGTAAGCACTATTACTTTCGTATTTTT 4 11 1 CCCTCGGTACCCTTTAGGGGTACGCGTCCTTAGCAGGGACG 9 33 0 TGCTTCATAACGTCTCTTTAGAGTTTTACTTGCAGATATAT 5 196 1 TCTTCTAGAACATCTCTGCAACCCGTTTCTTATTTGTGGAT 0 163 1 TTATAATTTTCATCTTTAAGCTTTTCTGCTCATCCCTTATT 7 54 1 ATCCCCCCAACTTCTTTTAGTAGAAATCCCTACATTCCTAA 16 12 1 GGAATCTTTGGATCTAGAAGAAGGCCTACTTTCAAACAAAC 0 18 1 AAGCATCTTTGATCTTGTCGACTATTTCCTTCTATGCTAAC 5 160 0 CTAAATTCAACAACTTTTCGTTATTGTTCTTTTTTTCTACT 3 129 1 ACCGCTTATTCTTTTAGAAAAGAATTTTCTTTAAAAAAGAT 0 261 0 GCATTGAGCGCTTTTCTTTGCTCATCTTTTTCATTATAAAG 13 121 0 TACTGGTCTACTTTTCTTTGCTTAAAAACTTTTTTTACTTC 17 52 1 TTGAATTCTATGTTTATAGGAATTTTTTCTTAGAGAGTTAG 0 81 1 GAAACAATCTCATTTCTAAAACCTGCTTTTTCTTCCTTTAA 13 220 0 CTTTCCTATCGTTTTATGAAGCTCTCTACCTTTGTTGCAAT 15 53 0 TGTATGAAATCATTTTTTAATATCGTGGCTTGAAGAAAAAG 15 187 1 ACAAATTCAACCTCTAGCAACTTAAAATCCTTCTCTAACCA 16 105 1 * *** * * * *** MAP Score: 4.92108 Motif 10 TGCAACCCGTTTCTTATTTGTGGATCAGTTGAATTAAATG 0 179 1 ATTTTACCGCTTATTCTTTTAGAAAAGAATTTTCTTTAAA 0 267 0 TTTCAAAGCACTCTTGATTTTGAAGGTACTA 3 1 0 ACCTAATACTTTCTTCATATAGAACCATCTTGAAGTGACC 3 79 1 TTCGTTATTGTTCTTTTTTTCTACTATTCTTCTTTATCTC 3 145 1 TTACCTTATGCTCTTGTTTTTCTCAAGAGTGAAGCCCAAA 3 220 0 TACTTTCGTATTTTTTTTGTTGGTGTAAATATTGTTTAAA 4 37 1 AAATTTTTTTTTATCTAGTTATTTATTAGATTAATT 4 88 0 AAAATGGAGTCTCTTTTTATCGTGATCGTTAATTTATGCC 8 87 1 ATTATAATTATTCTTGTTATGGATTCAGCTCGATTTTTCT 13 67 1 TTCAGCTCGATTTTTCTTGTGGCCTCTTGTTCTTTATAAT 13 90 1 GAAATCGTTTTTATTTTTAAAGTTCGTATTGGCATAACTC 13 177 1 AACCTGCTTTTTCTTCCTTTAAATCGAGTTATGCCAATAC 13 202 0 AACACCGCTCCTTTTATTGTCGTGTTATTTTTCTATACTT 14 42 0 TAGGTTTCGTTTATTTTTATGAAGGACTCTT 16 270 1 ***** ** * * * MAP Score: 2.00875