AlignACE 3.0 10/20/99 AlignACE2 -i AG/AG_operons012_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944242707 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 AF0062 52 conserved hypothetical protein #1 AF0063 27 A. fulgidus predicted coding region AF0063 #2 AF0111 115 conserved hypothetical protein #3 AF0112 51 transcriptional regulatory protein, Sir2 family #4 AF0113 63 conserved hypothetical protein #5 AF0209 112 conserved hypothetical protein #6 AF0332 122 conserved hypothetical protein #7 AF0743 283 conserved hypothetical protein #8 AF0847 112 inosine monophosphate dehydrogenase (guaB-1) #9 AF0848 24 conserved hypothetical protein #10 AF0971 101 conserved hypothetical protein #11 AF1186 139 conserved hypothetical protein #12 AF1189 283 A. fulgidus predicted coding region AF1189 #13 AF1191 32 dihydroxynaphthoic acid synthase (menB) #14 AF1192 50 conserved hypothetical protein #15 AF1195 27 activator 1, replication factor C, 53 KD subunit #16 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #17 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #18 AF1259 36 inosine monophosphate dehydrogenase, putative #19 AF1260 207 phosphoribosylformylglycinamidine synthase I (purQ) #20 AF1261 133 medium-chain acyl-CoA ligase (alkK-4) #21 AF1263 74 iron-sulfur cluster binding protein #22 AF1388 48 DNA helicase, putative #23 AF1415 203 chloride channel, putative #24 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #25 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #26 AF1420 216 membrane protein #27 AF1421 49 conserved hypothetical protein #28 AF1422 35 aspartate racemase #29 AF1423 112 conserved hypothetical protein #30 AF1960 242 DNA helicase, putative #31 AF1961 116 pyruvate formate-lyase activating enzyme (pflX) Motif 1 TCCTGTGTCAGAAAATTATAAATATCTCTCAC 2 50 1 TAAAGAATATTAAAATTAAAAATTGGAGGTGG 2 88 1 TTTCCAGAGCGAAAAGTATTAAATTTAACGAC 3 15 1 TAAACCATTCGAAAAGTTAAAATCTTAGCTCA 4 24 0 TTTACTTTTGAAAAAATAAAAAATTTTCCGAT 6 19 1 GTTAGATTCAAAAAATCGGAAAATTTTTTATT 6 33 0 AGTTTTCGTGAAAAATTCTGAAAAGCTCTTAA 7 36 0 AATTTTTCACGAAAACTCAAAATAGCCACTAT 7 51 1 ATTTTGTATTGAAAATTTTAAAACTCGGATTT 7 216 1 ACTTCGTTCGGAAATTTATAAAAAAGTATTCG 7 256 0 TGATGTTCATGAAATTTCAAAATTGCAGACAA 8 45 0 TTCATAAATGAAAAAATTTAAAT 10 1 0 AAAAAGTATTGAAAATTTTAGATGA 12 3 0 ACAATCTATTGAAAAGTGTTAAAAGCTTTAAA 12 108 1 ATATGGAACGAAAAATTTAAGACTACTTTAAT 12 239 1 TATCTGTTGGAAAAAATAAAAATTAAAA 16 6 0 AGTAAAAAAAGAAAAACCTAAACTTTCAAAGC 19 26 0 CCTGTCTAGGGAAAAGTAAAAAAAGAAAAACC 19 40 0 GCCGACACGGAAAAAGCTTAAAAGATTGCGGT 19 172 1 ATAATCTGCTGAAAAACAAAAAAGTTGGAAAA 20 25 0 TTTATGAAATAAAAAACAAAAA 23 0 0 CTGGCAGCACAAAAATTCGAAATGGCAATTTT 23 120 1 CACCCAACCTAAAAAATTTTAACCTCAACTTC 29 22 0 ***** * **** MAP Score: 26.9755 Motif 2 TATTTATTTTTAAAAGCTTTTCTTTAATAT 2 20 1 TGAAAAGTGTTAAAAGCTTTAAAATATCCC 12 117 1 TCAGGTGAATTAAAAGCTTTTTTGATGTTC 8 69 0 AGTGTATCTGCAAAAGCTTTATATTGCCAG 10 63 1 CAGGTAGGCATAAAAGTTTT 24 0 0 TCACTCAGCTTCAAAGCTTCCCGGATAGTC 26 55 1 CCAAAGCTTTATCTTGTTAG 28 0 1 CAAAAGTTTTTAGCTTGCCG 18 0 1 CTTCTTTGCTCCAAAGCTTCAATTGACACC 23 56 1 ATTGATAAATACAAAGCTTTATCCTCCTAC 23 88 1 CCCCAAGGTAAAAAAGTTTTATTGGTTTAT 5 80 0 CTCGCCTTTTTAAGAGCTTTTCAGAATTTT 7 27 1 GCCGACACGGAAAAAGCTTAAAAGATTGCG 19 172 1 CATGAAGCGCTAAGAGCTTCATTCTCTTCG 17 119 0 TCAAACATTACAAAAGTTTATATACCTCAG 11 104 1 AAGTTGAGGTTAAAATTTTTTAGGTTGGGT 29 23 1 AGCCCAACTTTCAAAGTTTACTTCTTTGCT 23 36 1 ATCCGAGTTTTAAAATTTTCAATACAAAAT 7 216 0 TCATCTAAAATTTTCAATACTTTTT 12 5 1 TTCGAAAAGTTAAAATCTTAGCTCAACAAG 4 19 0 TGAAAAAATAAAAAATTTTCCGATTTTTTG 6 27 1 ********** MAP Score: 22.2476 Motif 3 AATATTCCTGTGTCAGAAAATTATAAATATCTCTCACGAC 2 45 1 TTGCACCACCTCCAATTTTTAATTTTAATATTCTTT 2 89 0 CGCTCCTCCTCGCCCCAAGGTAAAAAAGTTTTATTGGTT 5 83 0 TAAAGTTATTTGTCTGCAATTTTGAAATTTCATGAACATC 8 36 1 TAATTTAAAGCAGCTCAAACATTACAAAAGTTTATATACC 11 90 1 GTTAGCAGTCTTTCCCCAATTCCTGATTGGGGATATTTTA 12 136 0 ATTAAAAATTACAGCAAAATAGTAATATATATGTTAAT 14 8 1 AAATACCATCCGGGTCCAATTCTTTAAGTGTGTCGATTTC 17 241 0 AGAAGAAAAATGACGGCAAGCTAAAAACTTTTG 18 3 0 ATCGTCCTGTCTAGGGAAAAGTAAAAAAAGAAAAACCTAA 19 37 0 GGTAAGCAATCAACCGCAATCTTTTAAGCTTTTTCCGTGT 19 176 0 CAGTTATAATCTGCTGAAAAACAAAAAAGTTGGAAAATGA 20 22 0 AGTTTTTCACCAATCAATCAAGTTTAATCGACAT 20 109 0 TTCATAAAACTCAGCCCAACTTTCAAAGTTTACTTCTTTG 23 24 1 GTTTACTTCTTTGCTCCAAAGCTTCAATTGACACCGTATT 23 51 1 CTACTGCTGGCAGCACAAAAATTCGAAATGGCAATTTTGT 23 114 1 TTTCAGATTCTGTCACCAACTTACAAAATTGCCATTTCGA 23 136 0 GTGGATTCGTTTTCTGCAATATCTCAATATCAAACTCATG 26 151 1 GTATTTAGCGCATCACCCAACCTAAAAAATTTTAACCTCA 29 27 0 * * **** * ** * MAP Score: 16.5973 Motif 4 AAACCTTACTGTGCTGGAAATGAAGGACATTCTG 7 114 1 GAAGGACATTCTGCAGAATCTGAACAGGTGGCTA 7 135 1 AAACTCGGATTTGCCGCAAACGAATACTTTTTTA 7 236 1 AATTTCAAAATTGCAGACAAATAACTTTAATAAT 8 31 0 CTCCGGGCAGGGAAAAATGTACTG 13 18 0 ACTCGACTTCCTCCGGGATGATAATTTCAAAAGA 17 184 0 AATTAAAGATCTGCCAGCTTTGAAAGTTTAGGTT 19 10 1 GCACTAAAGAGTGCAGAACATCAACGCTGCCGAC 19 144 1 AACATCAACGCTGCCGACACGGAAAAAGCTTAAA 19 160 1 CAGTTATAATCTGCTGAAAAACAAAAAAGTTGGA 20 28 0 CCAAATTCAACTGCGGGCTCGGAAAATCTCACGA 26 14 1 TATTGAGATATTGCAGAAAACGAATCCACGAAGT 26 146 0 TCTCAATCCTGTCCAGAATTTCAACAAGCTCTTC 30 12 0 AAATGCCTACCTGCTGGCTGTGAAGGAA 30 224 1 **** *** *** MAP Score: 15.6435 Motif 5 AAAAATAAATAAGAAAAAATA 2 0 0 AACTTTACTTTTGAAAAAATAAAAAATTTTC 6 16 1 AACTATCTGTTGGAAAAAATAAAAATTAAAA 16 10 0 GTGTTCATAAATGAAAAAATTTAAAT 10 5 0 GTATTTTAATAAGAAAAAAGTGAAGGAGGTG 17 275 1 TATTAGTCGTATGAAAAAAGTATTGAAAATT 12 18 0 ACGGTTTTTGTTCAAAAAATATTCTGTATAC 31 65 0 CATTTTATCATCGAAAAAATCCCGCTTGGAC 12 79 1 TCTGCTGAAAAACAAAAAAGTTGGAAAATGA 20 22 0 TGGAGTTAGATTCAAAAAATCGGAAAATTTT 6 38 0 TTTCATGAACATCAAAAAAGCTTTTAATTCA 8 63 1 CATACGACTAATAAAAAAATATTCTGAGAAA 12 36 1 CCAATTCTTTTCAAAAAAATTTATGTCTTTG 5 48 1 GAATCAAAAAAAGAGGAAGGGCTT 25 10 0 TGCAATATGGAACGAAAAATTTAAGACTACT 12 235 1 AGTAAATTAATTCGAAAAATTATTATGTCGA 20 85 1 CGCTGCCGACACGGAAAAAGCTTAAAAGATT 19 168 1 AAAATATTCTGAGAAAAAAGATATTCAGCAT 12 51 1 ACAGAATCTGAAAGAAAAATATATCATCACT 23 163 1 CTAGGGAAAAGTAAAAAAAGAAAAACCTAAA 19 36 0 TGTGGAAAAAGTCGGCGACGCT 31 1 1 * ********* MAP Score: 10.6247 Motif 6 CTTTTTTACCTTGGGGCGAGGAGGAGCG 5 94 1 AACCTTACTGTGCTGGAAATGAAGGACATTCTGCA 7 115 1 TAGCCACCTGTTCAGATTCTGCAGAATGTCCTTCA 7 134 0 CCGGTAGTTATTGGGGGGTGGATGAAAGAATGCAA 12 205 1 CTCCGGGCAGGGAAAAATGTACTGGA 13 16 0 GCAGAGAAAGTTCTGGACTTCCGGAAGGCACTGGC 17 35 1 AGATTGGTGTTTACGGTTTTGATGAGCAAACGAAG 17 89 1 GGACGTAACGTTGAGGACGTGTTGAATAACAGCTC 17 151 1 ACATCAACGCTGCCGACACGGAAAAAGCTTAAAAG 19 161 1 AGCCTTAGTTGGGGGAAGGTTAATAAGTGAGAT 22 25 0 TTCGTTTTTGCTGGGGGAGTGATGATATATTTTTC 23 176 0 CCAATCCAAATTCAGGTAGGCATAAAAGTTTT 24 7 0 CAAATTCAACTGCGGGCTCGGAAAATCTCACGATA 26 15 1 GAGTTTGATATTGAGATATTGCAGAAAACGAATCC 26 153 0 TGATGTTGTTCTGGTTGGGCCGATAAAAATTTA 29 89 0 CTTGTTGAAATTCTGGACAGGATTGAGAAGGCTGC 30 18 1 AAGGCTGCGATGCAGAAGATGCTGAAGAGGGACAT 30 45 1 GCAACAGCGCTTCCGGTCCTTATGAATCCCGATGA 30 129 0 GAAGCGCTGTTGCTGAGGTTGAGGGCGATGCAGCG 30 151 1 AATGCCTACCTGCTGGCTGTGAAGGAA 30 225 1 *** ** *** ** MAP Score: 9.72542 Motif 7 GATGAGTTGGATTTAGATGCCCCCATAACTTTGTT 0 22 1 TTCCGATTTTTTGAATCTAACTCCAAAGCAAGTTC 6 44 1 ACAAAAGTTTATATACCTCAGCCCACTTCACATTA 11 113 1 TGTTAAAAGCTTTAAAATATCCCCAATCAGGAATT 12 124 1 TCGAGGGGTTAGCAGTCTTTCCCCAATTCCTGATT 12 148 0 ATTGCATTCTTTCATCCACCCCCCAATAACTACCG 12 206 0 AGAGAAAGGAATCAGACCAGCCCCACCAGCTAAAA 19 80 1 AATCTCACTTATTAACCTTCCCCCAACTAAGGCT 22 24 1 TTTTTATTTCATAAAACTCAGCCCAACTTTCAAAG 23 17 1 AGAAAAATATATCATCACTCCCCCAGCAAAAACGA 23 175 1 TTAGCGGTAAATTTTTATCGGCCCAACCAGAACAA 29 82 1 ** * ** ***** MAP Score: 7.1138 Motif 8 CTTTTTTACCTTGGGGCGAGGAGGAGCG 5 94 1 AATGTGGAAAGGCTGTACGAAATTATTAA 8 1 1 AATATCCCCAATCAGGAATTGGGGAAAGACTGCTAACC 12 139 1 CCGGTAGTTATTGGGGGGTGGATGAAAGAATGCAATAT 12 205 1 AGATTGGTGTTTACGGTTTTGATGAGCAAACGAAGAGA 17 89 1 AGCCTTAGTTGGGGGAAGGTTAATAAGTGAGATTGT 22 22 0 CCATTTCGAATTTTTGTGCTGCCAGCAGTAGGAGGATA 23 107 0 GCCTACCTGAATTTGGATTGGAGATGAAGAAAAGGGTC 24 21 1 CCAAAGCTTTATCTTGTTAGGCGATTAGTCTATTT 28 10 1 GTTAAAATTTTTTAGGTTGGGTGATGCGCTAAATACTT 29 31 1 TGATGTTGTTCTGGTTGGGCCGATAAAAATTTACCG 29 86 0 TCTGCCGAACTTTTGGCAAGGAGAGGAGAAATTGCCGT 30 84 1 GGCTGGGTCGTTGATGCGAGGCGATACGGAAATGCCTA 30 195 1 ** ** ** ** ** MAP Score: 6.15226 Motif 9 CAGGGAACAAAGTTATGGGGGCATCTA 0 35 0 TTACTGTGCTGGAAATGAAGGACATTCTGCAGAAT 7 119 1 TTATAAATTTCCGAACGAAGTTATGC 7 267 1 TATTAGTCGTATGAAAAAAGTATTGAAAATTTTAG 12 14 0 AAAATATTCTGAGAAAAAAGATATTCAGCATTTTA 12 51 1 TTATTGGGGGGTGGATGAAAGAATGCAATATGGAA 12 212 1 CTCCGGGCAGGGAAAAATGTACTGGAAAATAC 13 8 0 CTCGACGGTAGCAGAGAAAGTTCTGGACTTCCGGA 17 25 1 AGCAAACGAAGAGAATGAAGCTCTTAGCGCTTCAT 17 113 1 AATTATCATCCCGGAGGAAGTCGAGTACACCGAAC 17 192 1 GTATTTTAATAAGAAAAAAGTGAAGGAGGTGTATT 17 275 1 TATAATTTGTGGAGAAAAGGCTATGAGGTGAAAGC 21 49 1 CCAGCAGTAGGAGGATAAAGCTTTGTATTTATCAA 23 89 0 AATTTGGATTGGAGATGAAGAAAAGGGTC 24 30 1 GAATCAAAAAAAGAGGAAGGGCTT 25 0 0 AATCGCCTAACAAGATAAAGCTTTGG 28 1 0 * *** **** ** MAP Score: 4.89121 Motif 10 CTCCTCCTCGCCCCAAGGTAAAAAAGTTTT 5 90 0 AATTTGATTACCAACAGTAATTTAAAGCAG 11 73 1 TTTCATCCACCCCCCAATAACTACCGGCAA 12 202 0 GTACACCGAACCACCAACAAGAGAGGAAAT 17 216 1 CAGACCAGCCCCACCAGCTAAAAGAATTCT 19 92 1 AGCCTTTTCTCCACAAATTATATAACAATA 21 41 0 TATTAACCTTCCCCCAACTAAGGCT 22 33 1 TTTTGTGCTGCCAGCAGTAGGAGGATAAAG 23 104 0 TATCATCACTCCCCCAGCAAAAACGAAGC 23 184 1 ATTTTCCGAGCCCGCAGTTGAATTTGGACA 26 11 0 TCCTTCACAGCCAGCAGGTAGGCATTTCCG 30 221 0 ********** MAP Score: 3.55403 Motif 11 TTAGCTCAACAAGTTTAAAAGG 4 1 0 CCTCGCCCCAAGGTAAAAAAGTTTTATTGGT 5 84 0 CCTTCATTTCCAGCACAGTAAGGTTTACGCT 7 109 0 ATTTCATGAACATCAAAAAAGCTTTTAATTC 8 62 1 AGATAAGATTGAGCAAAGAAGTGTGATATAA 11 31 0 TTAAAAATTACAGCAAAATAGTAATATATAT 14 11 1 GTCTAGGGAAAAGTAAAAAAAGAAAAACCTA 19 38 0 GACACGGAAAAAGCTTAAAAGATTGCGGTTG 19 175 1 ATCTGCTGAAAAACAAAAAAGTTGGAAAATG 20 23 0 TGAAGCTTTGGAGCAAAGAAGTAAACTTTGA 23 46 0 CTACTGCTGGCAGCACAAAAATTCGAAATGG 23 114 1 ATCACTCCCCCAGCAAAAACGAAGC 23 188 1 AAATTCAGGTAGGCATAAAAGTTTT 24 4 0 CTCTGTCACTCAGCTTCAAAGCTTCCCGGAT 26 50 1 GAAGCGTTGCCAGCAGAATAACTTGACAAAA 26 112 0 GCCAAAAGTTCGGCAGAATAGATGTCCCTCT 30 70 0 ***** ***** MAP Score: 1.51914 Motif 12 TTAAAAAGGCGAGAGGCGATTAAAAAGTTT 7 8 0 CCCAATTCCTGATTGGGGATATTTTAAAGCTT 12 130 0 TGATAACGCAGATTGGTGTTTACGGTTTTGAT 17 80 1 TAGCACTAAAGAGTGCAGAACATCAACGCTGC 19 142 1 AAGCTTAAAAGATTGCGGTTGATTGCTTACCG 19 185 1 AAACTTGATTGATTGGTGAAAAACT 20 118 1 TTTGCTGGGGGAGTGATGATATATTTTTCTTT 23 173 0 CCTGAATTTGGATTGGAGATGAAGAAAAGGGT 24 26 1 GCTTTATCTTGTTAGGCGATTAGTCTATTT 28 15 1 TTTTGGCAAGGAGAGGAGAAATTGCCGTGCTG 30 94 1 ****** *** * MAP Score: 1.37742