AlignACE 3.0 10/20/99 AlignACE2 -i AG/AG_fusions004_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944241134 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 AF0003 300 A. fulgidus predicted coding region AF0003 #1 AF0004 266 RNase L inhibitor #2 AF0005 38 A. fulgidus predicted coding region AF0005 #3 AF0006 104 corrinoid methyltransferase protein (mtaC-1) #4 AF0008 73 oxalate/formate antiporter (oxlT-1) #5 AF0014 95 A. fulgidus predicted coding region AF0014 #6 AF0016 54 A. fulgidus predicted coding region AF0016 #7 AF0018 22 3-ketoacyl-CoA thiolase (acaB-1) #8 AF0021 38 signal-transducing histidine kinase #9 AF0409 74 aspartate aminotransferase (aspB-4) #10 AF0410 56 signal-transducing histidine kinase, putative #11 AF1045 86 methyl-accepting chemotaxis protein (tlpC-2) #12 AF1049 102 type II secretion system protein (gspE-4) #13 AF1052 32 A. fulgidus predicted coding region AF1052 #14 AF1053 34 A. fulgidus predicted coding region AF1053 #15 AF1055 111 flagellin (flaB1-2) #16 AF1057 39 cytochrome C-type biogenesis protein (ccdA) #17 AF1058 293 A. fulgidus predicted coding region AF1058 #18 AF1384 189 response regulator #19 AF1515 199 signal-transducing histidine kinase #20 AF1638 31 ribulose bisphosphate carboxylase, large subunit (rbcL-2) #21 AF1639 30 signal-transducing histidine kinase #22 AF2420 40 signal-transducing histidine kinase, putative #23 AF2421 58 leucyl-tRNA synthetase (leuS) #24 AF2425 85 methanol dehydrogenase regulatory protein (moxR) Motif 1 AGGAAAAAGATTTTCTAATTTTTTTATGAAT 0 272 1 AGAAGGCCTATTTTCTAATTTGGAGGTGTTT 3 81 1 GAAAATTTTATTTTTTATTTTCGCAATCTAC 11 52 1 TCCCCCAAATTTTTAATTTTTTAGAGGTGA 14 9 1 TCAAAAAGTTTTTTATTTTTGAATTTCCC 22 8 1 ATACATTTCTTTTTCAATTTTTATGCTTGAG 16 18 1 CAAATCACCCTTTTTAAATTTCCAGCACTCT 17 271 0 AATTTTTTAAATTTTTTGAGTACT 21 3 1 TTTTTAACTTTTCTTTGTCAAT 6 1 1 CGAGTCCATGTTTTTTCTTTTGGCCAGTGAA 17 69 0 CAGCAATTGTTTTTTACTTTTCCTCTTTTTT 1 19 0 GAAATTACCTTTTTCTAAGTTGAAATTTCCT 15 20 0 ATAGTAAAATTTTTAAATGTTGAGGATAAAA 18 160 1 CTTTTTCCGCTTTTATAAGTTTGAAAACCGG 19 33 1 TTACACTTCTGAATTTTCTTATTCGAA 11 6 1 GGAAAACTTCTTAAATTTTGCACCACAA 8 7 1 TTTTTTCTTATTTATGAACCAGT 4 2 1 GGAAAAAGGCTTTTATATATTATAAGCCAAA 19 10 0 AACCTCAAGCTTCTGATATTTACGTTATTCG 9 15 1 **** ****** MAP Score: 25.738 Motif 2 GGTGTTCAGAAAAAAGAGGAAAAG 1 4 1 CCACCATTTGTTCAGAAAAAATATCCTGAT 5 71 0 ATCAGAAAATCTTATAAGGA 2 0 1 ACACCTCCAAATTAGAAAATAGGCCTTCTA 3 80 0 TCATAAAAAAATTAGAAAATCTTTTTCCTC 0 271 0 AATTCAATGTTTCAAAAAATTTTATGAACT 17 29 0 ACTCAAAAAATTTAAAAAATT 21 1 0 AGTTTATACTTTTAAAAAAAGGCGTTTTTA 19 105 1 AATAAATGGGATTAAAAAATTTGGCGTTTG 23 27 0 CAAAAAGTTAATTAAAAAAAATTTTATAAA 5 24 0 TTACTATCTCTTTAGAAATTCCACTACGTA 18 137 0 AAAATTTCGAATAAGAAAATTCAGAAGTGT 11 12 0 ATTTCAACATATAAGAAAATTCTTATATAT 15 46 1 TTAGTCTGATTTCAAAAAACGCCGGCAAAA 1 60 0 TGGTTCATAAATAAGAAAAAA 4 1 0 ATCCTCAACATTTAAAAATTTTACTATCTC 18 157 0 TAAAAAAAATTTTATAAAATGATTTGTCGT 5 12 0 ATTAGGGAAATTCAAAAATAAAAAACTTTT 22 13 0 AATCTACATTCATAAAAAAATTAGAAAA 0 282 0 AATAAAAAGCTTTATAAAAACAAACAGTCG 19 167 1 CCTCTAAAAAATTAAAAATTTGGGGGA 14 7 0 GAACTCCCTTATCAAAAATACGTC 17 4 0 CGGAAATCGCTTAAGAAAACTACTTAAGCA 19 61 1 GCTTTAACCGTTTAAAAATCCCCAAACGCC 1 211 1 GATTGCGAAAATAAAAAATAAAATTTTCTC 11 50 0 ********** MAP Score: 23.7485 Motif 3 TCTCGCTTTCAATCCCATTT 0 0 0 TCTGCCTTTCAATCCCATTTTGGTCTGATT 0 68 0 TCTTACTTTCAATCCCATTTTGGTCTGATT 0 136 0 ATTGCCTTTCAATCCCATTTTGGTCTGATT 0 209 0 AAATTTACGTAATCCCACTTTAGTCTGATT 1 79 0 ACCGTTTAAAAATCCCCAAACGCCCAAACC 1 217 1 CGCGAATCCCCTCTTAAGCAGAGA 4 59 0 GGTGCAGTGTAATCCCAAAAATGAAAGCAA 12 23 1 AGCGAGAAATAATCCCCAAACGACATAATC 19 134 1 CAAACGACATAATCCCAAATAAAAAGCTTT 19 150 1 CAAATTTTTTAATCCCATTTATTAGCCACT 23 34 1 ********** MAP Score: 20.9686 Motif 4 AATATATAAGAATTTTCTTATATGTTGAAATTA 15 44 0 TCAAAAAGTTTTTTATTTTTGAATTTCC 22 5 1 TTATAGAGAAAATTTTATTTTTTATTTTCGCAA 11 45 1 AACATTTAAAAATTTTACTATCTCTTTAGAAAT 18 148 0 TACACTTCTGAATTTTCTTATTCGAAATTTTAC 11 11 1 TCCCCCAAATTTTTAATTTTTTAGAGGTG 14 6 1 TCTTATTCGAAATTTTACTTTATAGAGAAAATT 11 26 1 TTTTTAACTTTTCTTTGTCAATTATCGT 6 5 1 TTTTTTAATTAACTTTTTGTTGTTAATTAATTA 5 35 1 CATTTTATAAAATTTTTTTTAATTAACTTTTTG 5 21 1 TGTTTTTATAAAGCTTTTTATTTGGGATTATGT 19 156 0 TGTTTCAAAAAATTTTATGAACTCCCTTATCAA 17 19 0 AAGATTTTCTAATTTTTTTATGAATGTAGATT 0 278 1 AAAGTCAGATAATTTTGTTATGAACTGATTCAT 3 32 1 GCCAAACGCCAAATTTTTTAATCCCATTTATTA 23 25 1 AATTTTTTAAATTTTTTGAGTAC 21 0 1 CAAGAACCTCAAGCTTCTGATATTTACGTTATT 9 11 1 GGAAAACTTCTTAAATTTTGCACCAC 8 3 1 TTCTAAGTTGAAATTTCCTTTACGTAATT 15 6 0 AACTTTATTTACCTCCTTAGCAA 20 0 1 TTCCACAAATAAATTTACGTAATCCCACTTTAG 1 86 0 CTGAACAGCAAAGTTTATATTCATCGTCCAGAA 10 21 1 ** *** **** * MAP Score: 18.3829 Motif 5 TCAATCCCATTTTGGTCTGATTTCAACCCG 0 60 0 TCAATCCCATTTTGGTCTGATTTCAACTGT 0 128 0 TCAATCCCATTTTGGTCTGATTTCAACTTG 0 201 0 ATTTTCTAATTTTTTTATGAATGTAGATT 0 281 1 ACTTTTCCTCTTTTTTCTGAACACC 1 5 0 GTAATCCCACTTTAGTCTGATTTCAAAAAA 1 71 0 GTCAGATAATTTTGTTATGAACTGATTCAT 3 35 1 TTTTTTCTTATTTATGAACC 4 0 1 TATAAAATGATTTGTCGTGA 5 0 0 TAATTAACTTTTTGTTGTTAATTAATTATT 5 40 1 TATCAGGATATTTTTTCTGAACAAATGGTG 5 70 1 TAATCGCTGGTTTAGTTTGAGGATGAGGTG 15 79 1 GGTTTACGTCTTAGGTGTGAGTTATACGGT 17 194 1 TGTTCGACTGTTTGTTTTTATAAAGCTTTT 19 171 0 AAATTTGGCGTTTGGCCTGATTGACCAAAA 23 11 0 ********** MAP Score: 18.2409 Motif 6 TGACGGGTTGAAATCAGACCAAAATGGGATT 0 57 1 GGAACAGTTGAAATCAGACCAAAATGGGATT 0 125 1 ATGGGATTGAAAGTAAGAACATCTCATAAAC 0 148 1 TCCCAAGTTGAAATCAGACCAAAATGGGATT 0 198 1 ATTCATAAAAAAATTAGAAAATCTTTTTCCT 0 272 0 GCGTTTTTTGAAATCAGACTAAAGTGGGATT 1 68 1 TATTTGTGGAAAGTGTGACAAGGAAACAAAA 1 108 1 TTTTAATCAAAAGTCAGATAATTTTGTTATG 3 23 1 AAACACCTCCAAATTAGAAAATAGGCCTTCT 3 81 0 ACTGGTTCATAAATAAGAAAAAA 4 2 0 GTAAAATTTCGAATAAGAAAATTCAGAAGTG 11 13 0 AGGAAATTTCAACTTAGAAAAAGGTAATTTC 15 20 1 TAATTTCAACATATAAGAAAATTCTTATATA 15 44 1 CCGCTTTTATAAGTTTGAAAACCGGAAATCG 19 39 1 **** ****** MAP Score: 16.1292 Motif 7 GTCCTGACGGGTTGAAATCAGACCAAAATGGGATTG 0 53 1 TCAAGGAACAGTTGAAATCAGACCAAAATGGGATTG 0 121 1 TAGCTCCCAAGTTGAAATCAGACCAAAATGGGATTG 0 194 1 GCCGGCGTTTTTTGAAATCAGACTAAAGTGGGATTA 1 64 1 ACCGACGAGAGTTTAAAACCGCCTAAAGCTCTTCTC 1 144 1 AGCTTTAACCGTTTAAAAATCCCCAAACGCCCAAAC 1 210 1 ACGTTATTCGGGTAAAAGTTGATATATTCGAAAGCT 9 36 1 CTTTTTCTAAGTTGAAATTTCCTTTACGTAATT 15 7 0 GAGGCCGCGGGTTCAAATCCCGCCGAGTCCATGTTT 17 87 0 TAACCCCTGAGGTCAAAAAGGTTCAAGGGCTCGTAG 17 154 0 GGTAAAAGTACTCAAAAAATTTAAAA 21 14 0 CTTTTGGTCAATCAGGCCAAACGCCAAATTT 23 5 1 *** *** * * ** MAP Score: 14.2287 Motif 8 CGGGTTGAAATCAGACCAAAATGGGATTGAAAGGCAGA 0 60 1 ACAGTTGAAATCAGACCAAAATGGGATTGAAAGTAAGA 0 128 1 CAAGTTGAAATCAGACCAAAATGGGATTGAAAGGCAAT 0 201 1 TTTTTTGAAATCAGACTAAAGTGGGATTACGTAAATTT 1 71 1 AGCACTCATCTCTGCTTAAGAGGGGATTCGCG 4 51 1 GGATATTTTTTCTGAACAAATGGTGGTTGT 5 75 1 ** * ** *** ** MAP Score: 12.5799 Motif 9 CTGACGGGTTGAAATCAGACCAAAATGGGAT 0 56 1 AATGGGATTGAAAGGCAGACGACGTACACTA 0 79 1 AGGAACAGTTGAAATCAGACCAAAATGGGAT 0 124 1 CTCCCAAGTTGAAATCAGACCAAAATGGGAT 0 197 1 GGCGTTTTTTGAAATCAGACTAAAGTGGGAT 1 67 1 CAAGGAAACAAAACTCAGACCGACGAGAGTT 1 126 1 TCGAATAAGAAAATTCAGAAGTGTAA 11 5 0 TCCCAAAAATGAAAGCAAAGGTTAATAGCAA 12 35 1 TCCGCCTCGCGAAGGCGGCGCTCTCCCGCTG 17 121 1 CTCATTCAGGGACTTCAGAGGGAAACCTTAA 17 226 1 AAGAGGTAAGGAATGCGGCGCATCTGGCAAA 18 78 1 CAAAGATAGAGAATCCAGAGGAGTTCAACCT 18 105 1 *** ******* MAP Score: 8.17857 Motif 10 ACAAGGAAACAAAACTCAGACCGACGAGAGTTTA 1 125 1 CGAGAGTTTAAAACCGCCTAAAGCTCTTCTCCAG 1 149 1 CTTCTCCAGCAAATCCACCACCAAATTTATTCAT 1 174 1 AACCGTTTAAAAATCCCCAAACGCCCAAACCTTA 1 216 1 CTTAAATACCAAACCGCCCATCGAGAACCA 1 246 1 GATATATTCGAAAGCTCCAACAAATCGC 9 56 1 ATAAGTTTGAAAACCGGAAATCGCTTAAGAAAAC 19 47 1 TAGCGAGAAATAATCCCCAAACGACATAATCCCA 19 133 1 CCAAACGACATAATCCCAAATAAAAAGCTTTATA 19 149 1 *** * ** * *** MAP Score: 2.2156