AlignACE 3.0 10/20/99 AlignACE2 -i AG/AG_operons003_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944241879 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 AF0006 104 corrinoid methyltransferase protein (mtaC-1) #1 AF0008 73 oxalate/formate antiporter (oxlT-1) #2 AF0014 95 A. fulgidus predicted coding region AF0014 #3 AF0016 54 A. fulgidus predicted coding region AF0016 #4 AF0018 22 3-ketoacyl-CoA thiolase (acaB-1) #5 AF0021 38 signal-transducing histidine kinase #6 AF0208 112 signal-transducing histidine kinase #7 AF0275 266 surface layer protein B (slgB-1) #8 AF0276 53 conserved hypothetical protein #9 AF0277 75 signal-transducing histidine kinase, putative #10 AF0409 74 aspartate aminotransferase (aspB-4) #11 AF0410 56 signal-transducing histidine kinase, putative #12 AF0448 104 signal-transducing histidine kinase, putative #13 AF0770 300 signal-transducing histidine kinase #14 AF1034 89 methyl-accepting chemotaxis protein (tlpC-1) #15 AF1045 86 methyl-accepting chemotaxis protein (tlpC-2) #16 AF1049 102 type II secretion system protein (gspE-4) #17 AF1064 51 ABC transporter, ATP-binding protein, putative #18 AF1178 195 A. fulgidus predicted coding region AF1178 #19 AF1179 62 conserved hypothetical protein #20 AF1181 35 GTP-binding protein #21 AF1184 37 signal-transducing histidine kinase #22 AF1259 36 inosine monophosphate dehydrogenase, putative #23 AF1260 207 phosphoribosylformylglycinamidine synthase I (purQ) #24 AF1384 189 response regulator #25 AF1452 117 signal-transducing histidine kinase #26 AF1473 98 response regulator #27 AF1475 109 mitochondrial benzodiazepine receptor/sensory transduction protein #28 AF1484 87 A. fulgidus predicted coding region AF1484 #29 AF1515 199 signal-transducing histidine kinase #30 AF1621 78 conserved hypothetical protein #31 AF1638 31 ribulose bisphosphate carboxylase, large subunit (rbcL-2) #32 AF1639 30 signal-transducing histidine kinase #33 AF1721 182 signal-transducing histidine kinase #34 AF1766 74 amino-acid ABC transporter, periplasmic binding protein/protein kinase #35 AF1898 74 response regulator #36 AF2032 185 signal-transducing histidine kinase, putative #37 AF2249 66 response regulator #38 AF2251 30 competence-damage protein, putative #39 AF2252 78 argininosuccinate synthetase (argG) #40 AF2420 40 signal-transducing histidine kinase, putative #41 AF2421 58 leucyl-tRNA synthetase (leuS) #42 AF2425 85 methanol dehydrogenase regulatory protein (moxR) Motif 1 AGTCCAACTTTAAAAAATAGGGAAAA 8 37 0 AGTACTCAAAAAATTTAAAAAATT 32 3 0 GTTATTTTAAAAATTTAAAAATA 38 2 0 GATTAAACAAAAGTTAAAAAACTTCCTGGGT 39 21 0 TGTAATTTACAAGTTAAAAAATCTTTTCTTG 37 36 0 GCTGCAAGCTAAGTTTTAAAAACTACTTACC 33 150 1 AACCAAAACAAAAATTAAAAA 25 0 0 CCGGTTTTCAAACTTATAAAAGCGGAAAAAG 29 33 0 TAAAGTAACGAACTTATAAAAGCGTTTGGTG 34 47 0 GGGAAATTCAAAAATAAAAAACTTTTTGA 40 8 0 GTAGATTGCGAAAATAAAAAATAAAATTTTC 15 52 0 TTGACAAAGAAAAGTTAAAAA 3 0 0 TGTCTAGGGAAAAGTAAAAAAAGAAAAACCT 23 39 0 TCCTCGCCCCAAGGTAAAAAAGTTTTATTGG 6 16 1 ATTAACCAAAAAATTTAAATAGGAGCTAATA 9 39 1 TTTTGGGAGTAATTTTAAATACAATTTCCCC 30 21 0 TTAATTTTAAATAATCATTTGTA 21 2 1 AAGCACTCGTAAATTTAAAACCTCGCCAAAT 27 60 1 TTTTATCCTCAACATTTAAAAATTTTACTAT 24 160 0 TAGACTTGGCAATTTAAAAACTTAGTCATTC 35 33 0 TTTGGCTTATAATATATAAAAGCCTTTTTCC 29 10 1 AGTTAAATTTAAAGTATAAAAGATTTGGCGA 27 82 0 TTTGGTGAGAAATTTTTAATAATCCTCACGA 34 23 0 ATTGACAGAAAACTTAAAAGATTATTCCCTT 28 19 1 TATCCCATTCAAAATTAAATATTTTTCGTGT 26 45 0 AACAAGAGAAAAGTTTAAATCCAGCTTTTGA 36 62 0 TTGCTATTTGAAAATAAAAGATTTTGTGAGG 28 57 0 TTAATCTCAAAAGATTTAAACCTCTCCGCAT 39 46 1 CCTTTTTTTAAAAGTATAAACTCCACAGTAG 29 96 0 ** ******** MAP Score: 33.2751 Motif 2 GGAAAACTTCTTAAATTTTGCACC 5 2 1 TGGGCGAACCAAAACTTTTTAAAGCGCATGCT 33 101 0 AAGAGATAGTAAAATTTTTAAATGTTGAGGAT 24 155 1 TTATTCGGGTAAAAGTTGATATATTCGAAAGC 10 39 1 TTAATTAAAAAAAATTTTATAAAATGATTTGT 2 15 0 TTATTAACCAAAAAATTTAAATAGGAGCTAAT 9 37 1 CAAACAAGAGAAAAGTTTAAATCCAGCTTTTG 36 63 0 AAGTTATTTTAAAAATTTAAAAATA 38 3 0 ATTGACAAAGAAAAGTTAAAAA 3 0 0 GAGATTAAACAAAAGTTAAAAAACTTCCTGGG 39 22 0 TAACCAAAACAAAAATTAAAAA 25 0 0 AAAGTACTCAAAAAATTTAAAAAATT 32 4 0 TTCTAAAGATAAAAGCTGTTATGAATCAGTTC 0 53 0 GTGACCTCACAAAATCTTTTATTTTCAAATAG 28 53 1 AAAAATAGTAAAAACCTCTAAAACTACCTATG 7 15 0 CCGACACGGAAAAAGCTTAAAAGATTGCGGTT 23 173 1 GAGCTATATAAAAAATTCTTCTATGTTTGAAG 14 40 0 CAAAAGTTATTTTTCCCTCCAAG 17 38 0 CAACATATATAAAATTTGTTTTGGGAGTAATT 30 38 0 TCAAAAAGTTTTTTATTTTTGAATT 40 3 1 ATAAACCAATAAAACTTTTTTACCTTGGGGCG 6 20 0 CAAAAGTTTTTAGCTTGCCGTCA 22 1 1 CTTTATAGAGAAAATTTTATTTTTTATTTTCG 15 43 1 ATTAACAACAAAAAGTTAATTAAAAAAAATTT 2 30 0 TACAAGTTAAAAAATCTTTTCTTGCAGTTTTG 37 28 0 TAACACAATCAAAAACTCTTTTTCCCTATTTT 8 18 1 AAATTGACAGAAAACTTAAAAGATTATTCCCT 28 17 1 GAAAAGAAGTAAAAGCTGTACTACAATGAACT 33 34 1 ATCCCAAATAAAAAGCTTTATAAAAACAAACA 29 161 1 TTATGATGGGAAAACTTTTTACCTGACGCATC 36 150 1 TAAAAAAAGAAAAACCTAAACTTTCAAAGCTG 23 24 0 **** ** **** MAP Score: 25.6781 Motif 3 TAAACCAATAAAACTTTTTTACCTTGGGGCG 6 20 0 TCAAAAAGTTTTTTATTTTTGAATT 40 4 1 GTGACCTCACAAAATCTTTTATTTTCAAATA 28 53 1 CAAAAGTTTTTAGCTTGCCGTC 22 1 1 AATTTTTTAAATTTTTTGAGTACTTTTAC 32 8 1 TTGTTTTTATAAAGCTTTTTATTTGGGATTA 29 159 0 TGGGCGAACCAAAACTTTTTAAAGCGCATGC 33 102 0 TTATGATGGGAAAACTTTTTACCTGACGCAT 36 150 1 CAAACATAGAAGAATTTTTTATATAGCTCTT 14 43 1 ATAATCGGCCAAATGCTTTTATTTACAAAGA 25 83 1 AAAAGCGGAAAAAGGCTTTTATATATTATAA 29 16 0 ATTTCTCACCAAACGCTTTTATAAGTTCGTT 34 41 1 GGCCAAACGCCAAATTTTTTAATCCCATTTA 41 24 1 ACAAAGACATAAATTTTTTTGAAAAGAATTG 6 52 1 AAAACCTCGCCAAATCTTTTATACTTTAAAT 27 76 1 GAAAACCCAGGAAGTTTTTTAACTTTTGTTT 39 17 1 AGGTAGTTTTAGAGGTTTTTACTATTTTTCA 7 18 1 GGAGAGGTTTAAATCTTTTGAGATTAAACAA 39 42 0 CACCACCGAGAAATTCTTTTGAGAAGAGCTA 14 66 0 ATAGGGAAAAAGAGTTTTTGATTGTGTTACA 8 16 0 AATTTGAAAAGAATTCTTTTAGCTGGTGGGG 23 100 0 CGAAAGGTTGATATTTTTTTAGGATAAATTT 12 52 1 GCTCCTATTTAAATTTTTTGGTTAATAATCA 9 34 0 CCGAAAGGGAATAATCTTTTAAGTTTTCTGT 28 23 0 AAGAGATAGTAAAATTTTTAAATGTTGAGGA 24 155 1 TTAATTAAAAAAAATTTTATAAAATGATTTG 2 16 0 TAACTGTTGTCGAATTTTTGATTTTACGGGA 19 16 0 CTGCAAGAAAAGATTTTTTAACTTGTAAATT 37 33 1 *** ******* MAP Score: 25.3482 Motif 4 CTATTTTCTAATTTGGAGGTGTTTAG 0 88 1 TCATAGGTAGTTTTAGAGGTTTTTACTATTT 7 14 1 TAATCAGTTAAATTGGAGGTGAAAGTTTGGG 7 91 1 TTCTCCTTAATCTCACAGGTGTTTTCATGGT 12 17 1 CAAAAGAATTTCTCGGTGGTGGT 14 76 1 GAATAAGAAAATTCAGAAGTGTAA 15 3 0 CGCAATCTACTTTCGGTGGTGTT 15 73 1 CACTTTATTTTCTCATAGGTGATAA 20 4 0 ATCGCAGGATAATCAGAGGTGTGAAG 26 82 1 TTTCTAAAGGAGTTAGAGGTGGTTTTAA 33 7 0 CAAGTCTAATTTTTACAGGTGTCAGGAA 35 56 1 CTTCCTGGGTTTTCAGAGGTT 39 0 0 * ********* MAP Score: 11.1545 Motif 5 CTACGAGCTTGCCAGCGACATAACAGCATCGGGAACGTG 7 233 1 CTGTCCAGCAGCTTGCTCAGCAAGGGAATCAGAAGCTTT 13 249 0 AATCAGACCTCTCACGAAAATTGTATAACTTGGAGG 17 7 1 AACCTCGAGGCCTGTCTTATTGAAGGCATCGTCCAGAGC 18 107 0 ACAGTTATTAACCAGCCCGCCAACTGAATCCC 19 40 1 CTAAGATCGTCCTGTCTAGGGAAAAGTAAAAAAAGAAAA 23 43 0 ATCAGACCAGCCCCACCAGCTAAAAGAATTCTTTTCAAA 23 90 1 CATCAACGCTGCCGACACGGAAAAAGCTTAAAAGATTGC 23 162 1 TTTTTGTTTTGGTTACCTGTAAAGCGTATTTGCTGGCGG 25 17 1 GTCTCCGCTTCGGGGAAATTGTATTTAAAATTAC 30 5 1 TGCCTCGCCACAAAAAGGTATCGGAATGACT 35 2 1 CCGTGCTGGTGCTGCCCGCTAAAACGAATGATAACTCTC 36 98 1 AAGATTTAAACCTCTCCGCATGACGGGATTGT 39 56 1 GGAAAGTGGCTAATAAATGGGATTAAAAAATTT 41 35 0 *** * * ** * ** MAP Score: 10.2393 Motif 6 GCAAGCAGAAGCAGAGCGGCAGTTAATCCTCT 7 138 0 GCTTCTGCTTGCACTGCTGCAAACAGTAAACG 7 158 1 TGGGCTGAAAGCAGAGCAGGGGAGCAGAGTGG 13 154 1 GAGCAGGGGAGCAGAGTGGCAAGGTAACTGAG 13 167 1 CCACGATAAGGCTCTGCGGGGATGATGAGGTA 13 215 1 GACTTCTTGGAAGAGCAGCAACCTGTCCAGC 13 279 0 TATCCAAGTAGCTCGGCTGCATCAATTATACC 18 59 0 ATCTTTGCCAGATGCGCCGCATTCCTTACCTC 24 80 0 GATTATGTTGGCGGAGCAGCGGTAATCACACG 26 18 1 CAAGGTAATTGCACTGCTGCAAGCTAAGTTTT 33 135 1 GGCAGCACCAGCACGGAAGCAAACAAGAGAAA 36 82 0 **** ** **** MAP Score: 8.42577 Motif 7 ACAACCACCATTTGTTCAGAAAA 2 82 0 TCTTAAATTTTGCACCACAATCTTTTGTTT 5 18 1 TTCTGCTTGCACTGCTGCAAACAGTAAACGCAG 7 160 1 TCTGAATTTGAGTGCAGCCAGTTATGGTAGCTG 7 190 0 GCAAGAACCTCAAGCTTCTGATATTT 10 3 1 ACTTCTTGGAAGAGCAGCAACCTGTCCAGCAGC 13 276 0 GGCATCGTCCAGAGCCTCAATCAAGCACTGGTA 18 89 0 AATTAAAGATCTGCCAGCTTTGAAAGTTT 23 6 1 GAATCAGACCAGCCCCACCAGCTAAAAGAATTC 23 88 1 CGGTAAGCAATCAACCGCAATCTTTTAAGCTTT 23 184 0 ATTCCAAAAAACTGCCGCCAGCAAATACGCTTT 25 37 0 TGATTACCGCTGCTCCGCCAACATAATCAAAAA 26 13 0 TTAAAACCACCTCTAACTCCTTTAGAAA 33 5 1 CTTTTTCATCACTCCCACCACCAGCATGCGCTT 33 79 1 AGGTAATTGCACTGCTGCAAGCTAAGTTTTAAA 33 137 1 ** ****** ** MAP Score: 8.33145 Motif 8 TTAGAAGGCCTATTTTCTAATTTGGAGGTGT 0 79 1 TTTTATAAAATTTTTTTTAATTAACTTTTTG 2 23 1 AAGACATAAATTTTTTTGAAAAGAATTGGCA 6 55 1 AGGTTTTTACTATTTTTCAAAAGCAGGGAAT 7 30 1 TCTTTTTCCCTATTTTTTAAAGTTGGACT 8 34 1 GAGAAAATTTTATTTTTTATTTTCGCAATCT 15 50 1 TTAATTTTAAATAATCATTTGT 21 1 1 GCTAAAAGAATTCTTTTCAAATTGATGCCGT 23 108 1 AGAGATAGTAAAATTTTTAAATGTTGAGGAT 24 156 1 GAAAAATATTTAATTTTGAATGGGATAGTGT 26 49 1 AAGCGATTTTTCTTTTTTAAAAAGCACTCGT 27 39 1 ACAAAATCTTTTATTTTCAAATAGCAACAAT 28 61 1 TCCGCTTTTATAAGTTTGAAAACCGGAAATC 29 38 1 TAAAAACGCCTTTTTTTAAAAGTATAAACTC 29 104 0 GTTTTGGGAGTAATTTTAAATACAATTTCCC 30 22 0 CTCCCAAAACAAATTTTATATATGTTGGTAC 30 43 1 AATTTTTTAAATTTTTTGAGT 32 0 1 GGCGAACCAAAACTTTTTAAAGCGCATGCTG 33 100 0 TGCTGCAAGCTAAGTTTTAAAAACTACTTAC 33 149 1 TATTTTTAAATTTTTAAAATA 38 0 1 GTTTTTTAACTTTTGTTTAATCTCAAAAGAT 39 30 1 AAAAGTTTTTTATTTTTGAATTTCCCTAATT 40 13 1 CCAAACGCCAAATTTTTTAATCCCATTTATT 41 26 1 ******* *** MAP Score: 7.85863 Motif 9 CTGCTCTGCTTTCAGCCCACCCACTTCTATTTCT 13 139 0 AAGCTTTATTACCTCATCATCCCCGCAGAGCCTT 13 222 0 AAGAGCAGCAACCTGTCCAGCAGCTTGCTCAGCA 13 266 0 AATCAGACCTCTCACGAAAATTGTA 17 1 1 ACAGTTATTAACCAGCCCGCCAACTGAATCCC 19 40 1 AGAGAAAGGAATCAGACCAGCCCCACCAGCTAAA 23 80 1 TTAAAACCACCTCTAACTCCTTTAGAAAA 33 5 1 GAACTTTTTCATCACTCCCACCACCAGCATGCGC 33 76 1 TATTAAAAATTTCTCACCAAACGCTTTTATAAGT 34 33 1 CTTTTGGTCAATCAGGCCAAACGCCAAATTTTTT 41 10 1 ***** ** ** * MAP Score: 4.2954 Motif 10 GATATATTCGAAAGCTCCAACAAATCGC 10 56 1 AATTTACAAGAAAGCTGCAGAGATTAGGAAGCGTA 13 85 0 CGACACGGAAAAAGCTTAAAAGATTGCGGTTGATT 23 174 1 GCTGATTCCCAAAGCTGAAATTAAAGAGGTAAGGA 24 55 1 AAATTGACAGAAAACTTAAAAGATTATTCCCTTTC 28 17 1 TCCCAAATAAAAAGCTTTATAAAAACAAACAGTCG 29 162 1 AAAAGAAGTAAAAGCTGTACTACAATGAACTCTTT 33 35 1 AGCCATTTCAAAAGCTGGATTTAAACTTTTCTCTT 36 55 1 GAGTAATTTCAAAACTGCAAGAAAAGATTTTTTAA 37 19 1 ****** * *** MAP Score: 3.91536 Motif 11 TGACAAAGAAAAGTTAAAAA 3 0 0 TCCTCGCCCCAAGGTAAAAAAGTTTTATTG 6 16 1 TTATTACGTTGAGGTAATTAATAAACCTAA 6 87 0 CTTTTGAAAAATAGTAAAAACCTCTAAAAC 7 23 0 CAAGGTAACTGAGGTAAAAACTGGAGATGC 13 186 1 CGGGGATGATGAGGTAATAAAGCTTCTGAT 13 231 1 CTTTTGAGAAGAGCTATATAAAAAATTCTT 14 52 0 AATGAAAGCAAAGGTTAATAGCAACATCAG 16 42 1 GTATAACTTGGAGGGAAAAATAACTTTTG 17 32 1 AAATGACGGCAAGCTAAAAACTTTTG 22 6 0 GTCTAGGGAAAAGTAAAAAAAGAAAAACCT 23 39 0 GACACGGAAAAAGCTTAAAAGATTGCGGTT 23 175 1 TTTAAATGTTGAGGATAAAATTAGGTAA 24 171 1 ACCAAAACAAAAATTAAAAA 25 0 0 GCTTTCAATCGAGCTTAAAAGCCACTTTGC 27 13 0 AAGATTTGGCGAGGTTTTAAATTTACGAGT 27 64 0 GTTAAATTTAAAGTATAAAAGATTTGGCGA 27 82 0 AGGTCACCGAAAGGGAATAATCTTTTAAGT 28 30 0 AAAACTACTTAAGCAAAAAACTACTGTGGA 29 76 1 CCTTTTTTTAAAAGTATAAACTCCACAGTA 29 97 0 AGTTGCTAAGGAGGTAAATAAAGTT 31 5 0 GGAGTTAGAGGTGGTTTTAA 33 0 0 TTTCCTACAAAGGTAAGTAGTTTTTAAAA 33 163 0 AAACAAGAGAAAAGTTTAAATCCAGCTTTT 36 64 0 TTTGATGCGTCAGGTAAAAAGTTTTCCCAT 36 155 0 TGTAATTTACAAGTTAAAAAATCTTTTCTT 37 37 0 GATTAAACAAAAGTTAAAAAACTTCCTGGG 39 22 0 GTCATGCGGAGAGGTTTAAATCTTTTGAGA 39 50 0 ********** MAP Score: 1.80362