AlignACE 3.0 10/20/99 AlignACE2 -i PH/PH_operons011_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944255770 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 PH0002 233 155aa long hypothetical transcription termination-antitermination factor #1 PH0285 108 112aa long hypothetical methionyl-tRNA synthetase #2 PH0314 300 896aa long hypothetical valyl-tRNA synthetase #3 PH0636 128 476aa long hypothetical cysteinyl-tRNA synthetase #4 PH0640 75 406aa long hypothetical phosphate permease #5 PH0641 300 213aa long hypothetical protein #6 PHS024 167 62aa long hypothetical protein #7 PH1128 143 186aa long hypothetical uridine 5'-monophosphate synthase #8 PH1129 66 131aa long hypothetical protein #9 PH1131 285 318aa long hypothetical sodium dependent phosphate transporter #10 PH1333 300 706aa long hypothetical protein #11 PH1334 67 691aa long hypothetical protein #12 PH1390 56 301aa long hypothetical thiamin biosynthesis protein Motif 1 AGAGGGTCAGGAACTTTTTCAAGGAGTCGAAGAGAGTGTT 0 77 1 AGGAGCTATTTAAACAACTCAAGGATGAGAGGGAGAGATT 2 73 1 AAGCTTTATGTAAAATAAGGAAGAGGGAAATCAGATCCTT 2 167 0 TTATTTTACATAAAGCTTTTAAGACGGGAATAAGTTCTAA 2 189 1 AATCTAAACTAGCCAAGAAAAGAAGGGTGTAATTTAAGT 2 271 0 AAGCAAGCTTTAAATACCTAAAGAAGGTAAATTCTTTTTG 3 20 0 AAAATTCCTGGATGGAGATTAAGGAGGTGAAGGGTGA 3 101 1 GGAGACCAAGGAAATGGAAGAAGAAGGGTAGAATGAGGTG 5 198 1 GAATGAGGTGGAAGTGGATTAAGAAGAGAATAAGGAGACT 5 228 1 GGAGACTCAAGAGACAAAGAAAGAAGGAGAGAGGACTTAT 5 261 1 TGGTGTTCTGCATGCATTCGAAGGAGTTTATCTATAAAGT 9 51 1 TCAAGTTTTTTAAGAGTTTGAAGAAGCCTAGGCATTGGAG 9 147 0 GTTTAGTCGAGATAACGTATAATAAGGAGATTATAGTCAG 9 195 1 AAGAATGAAAGAAGGAAGCTATGAAGTGTAATCATTCATC 9 244 0 TTAATCACCTCAAGAATGAAAGAAGGAAGCT 9 264 0 ATTCAGAAGAGATGTTGATAAAGGAGTTAATGGAGCTCGA 10 172 1 TAAGCCTTCTGATTTTCTTAAAGGAGGGGAAGTT 11 43 1 ** ******* * MAP Score: 21.6248 Motif 2 AACTCTGGCATCTCCTACCCCCACAACTTG 0 42 0 GCCTTTTTGTACTCCTCCCATCCGGGCTTC 0 129 0 ATATCTTCCATATCCTCTCTATTTTCGCTA 2 19 0 TTTAGCAATCTCTCCCTCTCATCCTTGAGT 2 89 0 TCACCCTTCACCTCCTTAATCTCCATC 3 111 0 TTTTCTCCCTCCAGCTATAGAGT 4 62 0 TTCTAGCCAATAACCTACTCTAGCAAAT 5 8 0 AAACCCTTAATATCCTATCTTATTATTTTG 5 90 0 TTCATGAGCATCACCTCCTAATCTCTCCCC 5 166 0 ATTTCCTTGGTCTCCTCTTCATGAGCATCA 5 183 0 CACCTCATTCTACCCTTCTTCTTCCATTTC 5 208 0 GTCTCTTGAGTCTCCTTATTCTCTTCTTAA 5 246 0 ATAAGTCCTCTCTCCTTCTTTCTTTGTCTC 5 271 0 TTCTCCCCCTCACCAATTGTG 6 1 1 TCCCAACTCCCCCCTAATTATTATC 7 5 1 CCCTAATTATTATCCTCCCCAAATATCCTT 7 21 1 CTGACTATAATCTCCTTATTATACGTTATC 9 205 0 AGGTAAGCTTTCTCCTCTTTCTCGAATAAC 10 29 0 TGCAGTCTTAACCCCTACTCCGTAAGTTGC 10 120 0 AACTTCCCCTCCTTTAAGAAAATC 11 53 0 GCTTTATCCCACTCACTTTAAATA 12 4 1 ********** MAP Score: 19.4295 Motif 3 GGAGATGCCAGAGTTCCAGGAGAGGGTCAGGAA 0 57 1 CTTTTTCAAGGAGTCGAAGAGAGTGTTCCTGGT 0 90 1 CGGATGGGAGGAGTACAAAAAGGCAGCTAAAAT 0 135 1 AGCTTTTAGCGAAAATAGAGAGGATATGGAAGA 2 13 1 TTCCTGGATGGAGATTAAGGAGGTGAAGGGTGA 3 105 1 TCATGAAGAGGAGACCAAGGAAATGGAAGAAGA 5 189 1 GGATTAAGAAGAGAATAAGGAGACTCAAGAGAC 5 243 1 GGAGACTCAAGAGACAAAGAAAGAAGGAGAGAG 5 261 1 CTGAGAATTAGAGTTTCAAAAAGTTTTATAAGC 7 114 0 AGAAAGCTGTGAGTTTGAAGAGGCTTAGCTCCG 9 105 1 AGTTTTTTAAGAGTTTGAAGAAGCCTAGGCATT 9 151 0 ATCACCTCAAGAATGAAAGAAGGAAGCTATGAA 9 259 0 AACTTAAGAGTGGAGAAAAGTTATTCGAGA 10 7 1 AAAGTTATTCGAGAAAGAGGAGAAAGCTTACCT 10 26 1 CCTCCTTTAAGAAAATCAGAAGGCTTAGTAGAT 11 37 0 TATTTAAAGTGAGTGGGATAAAGC 12 1 0 **** ****** MAP Score: 18.4847 Motif 4 GAAAATAGAGAGGATATGGAAGATATACGAGC 2 23 1 GAGGAGACCAAGGAAATGGAAGAAGAAGGGTA 5 196 1 ATGGAGATTAAGGAGGTGAAGGGTGA 3 112 1 ACGTTATATAAGGACAAGAAAGTTTTGGGAAT 10 215 1 ATAATAAGATAGGATATTAAGGGTTTCAAATA 5 94 1 TAACGTCGTCAAGATATTTAAGGGTTTCCTTA 1 45 1 AGTTATGTAAAGGATATTTGGGGAGGATAATA 7 28 0 TAAACTAGCCAAGAAAAGAAGGGTGTAATTTA 2 274 0 TTATTCGAGAAAGAGGAGAAAGCTTACCTTAA 10 30 1 AAACAACTCAAGGATGAGAGGGAGAGATTGCT 2 84 1 CAAGTTTTTTAAGAGTTTGAAGAAGCCTAGGC 9 154 0 GTGGATTAAGAAGAGAATAAGGAGACTCAAGA 5 241 1 TTGTGGGGGTAGGAGATGCCAGAGTTCCAGGA 0 46 1 AAAGACCCCCAGGGTAAGTAAGTTATGTAAAG 7 48 0 GGAAGTTTAAAAGAATTTCGAGGGCTTTTTGA 8 15 0 AATAACCATCAAGTTGTGGGGGTAGGAGATGC 0 33 1 GAGTGGAGAAAAGTTATTCGAGAAAGAGGAGA 10 17 1 TACCTTCTTTAGGTATTTAAAGCTTGCTTTTG 3 31 1 ATAAATTTAAAAGTTTTTTAAGTTCATAATAT 6 60 1 TCTTTAAACCAAGGCTTGAGAGTTCGGGGGTA 7 79 0 AATGAGGTGGAAGTGGATTAAGAAGAGAATAA 5 229 1 ACGTATAATAAGGAGATTATAGTCAGAGCAAA 9 209 1 **** *** *** MAP Score: 18.1024 Motif 5 CTTTTCTTAAAATTTTTAAATTAAATAAC 0 3 1 GATAAGGAAACCCTTAAATATCTTGACGACGTTATA 1 43 0 TTCCTTATTTTACATAAAGCTTTTAAGACGGGAATA 2 185 1 CTTCGCTTCACATAGAAAGGACTTAAATTACACCCT 2 251 1 TCTTCATCACCAAAAAGAATTTACCTTCTTTAG 3 7 1 CCAATTGTGTTGCTAAAAATTTTTAAATTTTGACCG 6 22 1 ATATTATGAACTTAAAAAACTTTTAAATTTATACCG 6 56 0 TTCATAATATCACAAAAATAATTTAAGCCAAAAAAT 6 82 1 AATAATTTAAGCCAAAAAATATTTAACTAGATAAAC 6 98 1 TTATTATCCTCCCCAAATATCCTTTACATAACTTAC 7 27 1 GAGAATTAGAGTTTCAAAAAGTTTTATAAGCTTCTC 7 109 0 TTCAAAAAGCCCTCGAAATTCTTTTAAACTTCCTTT 8 14 1 CTTCTTCAAACTCTTAAAAAACTTGAAAGTGATGGT 9 161 1 GTTAATGGAGCTCGAAAAACGTTATATAAGGACAAG 10 197 1 GGGAATGATCCACCAAAAGACCTTTATACTTAATTA 10 241 1 AAAACTTTTGCACTAAAAATAATTAAA 11 1 0 GCATCCACCCAAAATTATTTACCTATCCATT 12 35 0 * * **** *** * MAP Score: 18.0057 Motif 6 TGAAGACTTCAGCGTGAGGGGGGT 8 52 1 AAGTTATTCGAGAAAGAGGAGAAAGCTTACCT 10 27 1 GAAAGCTGTGAGTTTGAAGAGGCTTAGCTCCG 9 106 1 GGTGATGCTCATGAAGAGGAGACCAAGGAAAT 5 181 1 GAAGAAGGGTAGAATGAGGTGGAAGTGGATTA 5 217 1 AATAAGGCTTAGTTTGGGGAGAGATTAGGAGG 5 151 1 ATGTAAAATAAGGAAGAGGGAAATCAGATCCT 2 168 0 AGCAACACAATTGGTGAGGGGGAGAA 6 4 0 AGTACTCTATAGCTGGAGGGAGAAAA 4 59 1 CAAGAGACAAAGAAAGAAGGAGAGAGGACTTA 5 268 1 GTTTTTTAAGAGTTTGAAGAAGCCTAGGCATT 9 151 0 GTGGAAGTGGATTAAGAAGAGAATAAGGAGAC 5 235 1 TCGAGGTCATATTCAGAAGAGATGTTGATAAA 10 162 1 TCCTGGATGGAGATTAAGGAGGTGAAGGGTGA 3 106 1 ACCAAGGAAATGGAAGAAGAAGGGTAGAATGA 5 202 1 AACTTAAGAGTGGAGAAAAGTTATTCGA 10 6 1 TCTGATTTTCTTAAAGGAGGGGAAGTT 11 50 1 GAGGATAATAATTAGGGGGGAGTTGGGA 7 6 0 GATGCCAGAGTTCCAGGAGAGGGTCAGGAACT 0 60 1 TTGGGGAGAGATTAGGAGGTGATGCTCATGAA 5 164 1 ACCTCAAGAATGAAAGAAGGAAGCTATGAAGT 9 257 0 CCTTCTTTCATTCTTGAGGTGATTAA 9 269 1 GAGATAACGTATAATAAGGAGATTATAGTCAG 9 203 1 AAACAACTCAAGGATGAGAGGGAGAGATTGCT 2 84 1 ** ******** MAP Score: 15.1867 Motif 7 TCCACCTCATTCTACCCTTCTTCTTCCATTTCCTT 5 205 0 GGACTTAAATTACACCCTTCTTTTCTTGGCTAGTT 2 269 1 TCTTCAAACTCACAGCTTTCTTTTTGGTTGCCAGC 9 91 0 GATTACACTTCATAGCTTCCTTCTTTCATTCTTGA 9 251 1 CGAAATTCTTTTAAACTTCCTTTTTTGAAGACTTC 8 27 1 GGATCATTCCCAAAACTTTCTTGTCCTTATATAAC 10 217 0 GGATCTGATTTCCCTCTTCCTTATTTTACATAAAG 2 169 1 AGATAAGTCCTCTCTCCTTCTTTCTTTGTCTCTTG 5 268 0 GTTTTATCTACTAAGCCTTCTGATTTTCTTAAAGG 11 32 1 ATATCCTTTACATAACTTACTTACCCTGGGGGTCT 7 43 1 TTTAGGTATTTAAAGCTTGCTTTTGGCTTGAGGTT 3 38 1 TTGCTCTGACTATAATCTCCTTATTATACGTTATC 9 205 0 TCTTTGTCTCTTGAGTCTCCTTATTCTCTTCTTAA 5 246 0 AGCCTGTAATTTTAGCTGCCTTTTTGTACTCCTCC 0 141 0 TCACCCTTCACCTCCTTAATCTCCATCCAG 3 108 0 TCTTCATGAGCATCACCTCCTAATCTCTCCCCAAA 5 163 0 AATTGGCTCGTATATCTTCCATATCCTCTCTATTT 2 25 0 TCCCAACTCCCCCCTAATTATTATCCTCCCCA 7 7 1 TCTCCCCAAACTAAGCCTTATTACCAAATTTTTAA 5 138 0 * * *** *** ** MAP Score: 13.504 Motif 8 ATTTTACATAAAGCTTTTAAGACGGGAATAA 2 191 1 TAACGTCGTCAAGATATTTAAGGGTTTCCTT 1 45 1 ATAAATTTAAAAGTTTTTTAAGTTCATAATA 6 60 1 CATCACTTTCAAGTTTTTTAAGAGTTTGAAG 9 164 0 CCTTATTACCAAATTTTTAAGTTTTATTAGT 5 127 0 ATTTAATTTAAAAATTTTAAGAAAAG 0 5 0 TAGTATCATGAAGTTAATAAAACCATAGATA 1 14 0 GTTTAAAGAGAAGCTTATAAAACTTTTTGAA 7 102 1 GTGTTGCTAAAAATTTTTAAATTTTGACCGG 6 28 1 TTTAAGCCAAAAAATATTTAACTAGATAAAC 6 103 1 CCTAGAAAGATTATTAAATCTTAAGTT 1 91 0 TTACTAAAACAAAATAATAAGATAGGATATT 5 81 1 GGTTTCAAATAAACTAATAAAACTTAAAAAT 5 115 1 TGAAAGAAGGAAGCTATGAAGTGTAATCATT 9 248 0 TTTTGCACTAAAAATAATTAAA 11 1 0 CAGGGTAAGTAAGTTATGTAAAGGATATTTG 7 40 0 ATAATAAGATAGGATATTAAGGGTTTCAAAT 5 94 1 ATTAAATCTTAAGTTTTTATATTTGTGGATA 1 75 0 *** ******* MAP Score: 12.2509 Motif 9 TCTGGCATCTCCTACCCCCACAACTTGATGGTTATT 0 33 0 GCCTTTTTGTACTCCTCCCATCCGGGCTTCTTCGTT 0 123 0 TTAGCAATCTCTCCCTCTCATCCTTGAGTTGTTTAA 2 82 0 GATCTGATTTCCCTCTTCCTTATTTTACATAAAGCT 2 170 1 TCACCCTTCACCTCCTTAATCTCCATCCAGGAATTT 3 102 0 TTTTCTCCCTCCAGCTATAGAGTACTTTGG 4 55 0 CTCATTCTACCCTTCTTCTTCCATTTCCTTGGTCTC 5 199 0 AGTCCTCTCTCCTTCTTTCTTTGTCTCTTGAGTCTC 5 262 0 TTCTCCCCCTCACCAATTGTGTTGCTAA 6 2 1 TCCCAACTCCCCCCTAATTATTATCCTC 7 2 1 TAATTATTATCCTCCCCAAATATCCTTTACATAACT 7 24 1 CTTTACATAACTTACTTACCCTGGGGGTCTTTACCC 7 48 1 ACCCCCCTCACGCTGAAGTCTTCAAAAA 8 48 0 TTCATAGCTTCCTTCTTTCATTCTTGAGGTGATTAA 9 259 1 GCTTTCTCCTCTTTCTCGAATAACTTTTCTCCACTC 10 17 0 TTATTTTATTGCCTCTTACACTTTAGATTTTAATTA 10 271 0 AACTTCCCCTCCTTTAAGAAAATCAGAA 11 49 0 GCTTTATCCCACTCACTTTAAATACAATGGATA 12 7 1 ******* * * * MAP Score: 2.61462 Motif 10 TTATATTTGTGGATAAGGAAACCCTTAAAT 1 60 0 GTAAAATAAGGAAGAGGGAAATCAGATCCT 2 168 0 CCTGGATGGAGATTAAGGAGGTGAAGGGTG 3 107 1 ATAAGGCTTAGTTTGGGGAGAGATTAGGAG 5 152 1 TTTGGGGAGAGATTAGGAGGTGATGCTCAT 5 163 1 GGTGGAAGTGGATTAAGAAGAGAATAAGGA 5 234 1 ATTAAGAAGAGAATAAGGAGACTCAAGAGA 5 245 1 CAACACAATTGGTGAGGGGGAGAA 6 4 0 TCAAGCCTTAGAATAGGGAATTCCGCTGAA 6 134 1 GGAGGATAATAATTAGGGGGGAGTTGGGA 7 9 0 AAGAGATGTTGATAAAGGAGTTAATGGAGC 10 178 1 ********** MAP Score: 1.92677 Motif 11 AGGAGATGCCAGAGTTCCAGGAGAGGGTCAGG 0 56 1 CTTTTAGCGAAAATAGAGAGGATATGGAAGAT 2 15 1 AAACTAGCCAAGAAAAGAAGGGTGTAATTTAA 2 273 0 ATTCCTGGATGGAGATTAAGGAGGTGAAGGGT 3 104 1 TAGTTTGGGGAGAGATTAGGAGGTGATGCTCA 5 160 1 CTCATGAAGAGGAGACCAAGGAAATGGAAGAA 5 188 1 CAAGGAAATGGAAGAAGAAGGGTAGAATGAGG 5 204 1 TGGATTAAGAAGAGAATAAGGAGACTCAAGAG 5 242 1 AGGAGACTCAAGAGACAAAGAAAGAAGGAGAG 5 260 1 ACAAAGAAAGAAGGAGAGAGGACTTATCTAAC 5 274 1 CCAAGGCTTGAGAGTTCGGGGGTAAAGACCCC 7 71 0 AAAAGTTATTCGAGAAAGAGGAGAAAGCTTAC 10 25 1 TGTTGATAAAGGAGTTAATGGAGCTCGAAAAA 10 184 1 CATTGTATTTAAAGTGAGTGGGATAAAGC 12 7 0 ***** ***** MAP Score: 0.193343