AlignACE 3.0 10/20/99 AlignACE2 -i AG/AG_fusions003_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944241098 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 AF0448 104 signal-transducing histidine kinase, putative #1 AF0451 52 A. fulgidus predicted coding region AF0451 #2 AF0454 32 A. fulgidus predicted coding region AF0454 #3 AF1045 86 methyl-accepting chemotaxis protein (tlpC-2) #4 AF1049 102 type II secretion system protein (gspE-4) #5 AF1052 32 A. fulgidus predicted coding region AF1052 #6 AF1053 34 A. fulgidus predicted coding region AF1053 #7 AF1055 111 flagellin (flaB1-2) #8 AF1057 39 cytochrome C-type biogenesis protein (ccdA) #9 AF1058 293 A. fulgidus predicted coding region AF1058 #10 AF1173 180 A. fulgidus predicted coding region AF1173 #11 AF1174 61 A. fulgidus predicted coding region AF1174 #12 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #13 AF1178 195 A. fulgidus predicted coding region AF1178 #14 AF1179 62 conserved hypothetical protein #15 AF1181 35 GTP-binding protein #16 AF1184 37 signal-transducing histidine kinase #17 AF1446 63 A. fulgidus predicted coding region AF1446 #18 AF1448 114 transcriptional regulatory protein, AsnC family #19 AF1449 33 pyruvate formate-lyase 2 (pflD) #20 AF1451 88 thermosome, subunit beta (thsB) #21 AF1452 117 signal-transducing histidine kinase #22 AF1473 98 response regulator #23 AF1475 109 mitochondrial benzodiazepine receptor/sensory transduction protein Motif 1 TTTTTTAGGATAAATTTAAACAAGTTACCC 0 66 1 AAAGCACTCGTAAATTTAAAACCTCGCCAA 23 59 1 GGGTATAGTTAAATTTAAAGTATAAAAGA 23 90 0 CTCAAGCATAAAAATTGAAAAAGAAATGTA 8 19 0 TACCTTTTTCTAAGTTGAAATTTCCTTTAC 7 16 0 ATCACCTCTAAAAAATTAAAAATTTGGGGG 6 11 0 TAACCAAAACAAAAATTAAAAA 21 2 0 AAAAGAAATGTATATTTAAAT 8 1 0 GTGTAATCCCAAAAATGAAAGCAAAGGTTA 4 29 1 GCTAACATTTAAACATTGTAATC 11 3 1 TGTAATCTCAAAAGATTAAAATACTCTTCA 11 26 1 GCTAATAGTACGTTTAAAGCCATATAAT 10 162 0 TTTAGAACTTAATATTTAAAACTTT 2 5 0 AAACTTTATTTACAATGAAAGTGTTACAAT 18 88 1 GAGAGTGCTGGAAATTTAAAAAGGGTGATT 9 270 1 ATCACGAATTTAAATTGCAAGCATTTGTTA 20 10 0 AATTTTCTTATATGTTGAAATTACCTTTTT 7 37 0 CTATCCCATTCAAAATTAAATATTTTTCGT 22 47 0 TTAATTTTAAATAATCATTTG 16 1 1 GCTTTTCCCGTAAAATCAAAAATTCGACAA 14 11 1 GAACAACCAATACAATTCAATGTTTCAAAA 9 42 0 ********** MAP Score: 15.7671 Motif 2 TGCGAAAGGTTGATATTTTTTTAGGATAAAT 0 50 1 ATAGAGAAAATTTTATTTTTTATTTTCGCAA 3 47 1 CCCCCAAATTTTTAATTTTTTAGAGGTGATA 6 11 1 AGGGAGTTCATAAAATTTTTTGAAACATTGA 9 25 1 ATTCAAACCATTTAAGCTTTTCCATAATTAT 10 33 1 ATGCCCACCTCAAAATTTTTTCCCACCTGAC 10 82 0 TGAAGAGTATTTTAATCTTTTGAGATTACAA 11 25 0 AGGAGTAAGGCTTAATTTTTTTGAACCAATT 13 167 1 TGTGTACTGGTGAAAGTTTTTAAGAGGGAAA 17 14 1 AAATCGTAATCTTTTTTAATTAGGT 19 4 1 GGTATTTCTATATAAGCTTTTCTATCACGAA 20 32 0 TTTTTAATTTTTGTTTTGGTTAC 21 2 1 CCATTCAAAATTAAATATTTTTCGTGTGATT 22 41 0 TAAAACCTCGCCAAATCTTTTATACTTTAAA 23 75 1 * ********* MAP Score: 13.1746 Motif 3 GGCCGTGAGAGCGGCTGCGCTGAGGTATT 5 0 1 GCTAATCGCTGGTTTAGTTTGAGGATGAGGTGAGAGGTG 7 77 1 AGCGCCGCCTTCGCGAGGCGGAGGCCGCGGGTTCAAATC 9 104 0 TCCCTCTGAAGTCCCTGAATGAGGAACCGTATAACTCAC 9 210 0 TTGGATACCAGTGCTTGATTGAGGCTCTGGACGATGCCT 13 84 1 GAGGTTTTCAGACCGTGCAAGACGCTAAGGAGTAAGGCT 13 140 1 GGGATTCAGTTGGCGGGCTGGTTAATAACTG 14 41 0 CCTGTAAAGCGTATTTGCTGGCGGCAGTTTTTTGGAATG 21 32 1 AAGTTTTTGATTATGTTGGCGGAGCAGCGGTAATCAC 22 8 1 * * ** ***** * MAP Score: 9.23467 Motif 4 CTCCTTAATCTCACAGGTGTTTTCATGGTC 0 19 1 CTATCCCTGCTCGGAGGGTAACTTGTTTAA 0 81 0 ATAAGAAAATTCAGAAGTGTAA 3 2 0 CAATCTACTTTCGGTGGTGTT 3 75 1 TTTTAATTTTTTAGAGGTGATACC 6 20 1 GAGGATGAGGTGAGAGGTGATGGG 7 97 1 CTTTTTGACCTCAGGGGTTATAAAGGTTTA 9 170 1 GGTTTACGTCTTAGGTGTGAGTTATACGGT 9 194 1 TTCAGGGACTTCAGAGGGAAACCTTAATAT 9 230 1 CGTTATATAGTCAGGTGGGAAAAAATTTTG 10 73 1 CTTTATTTTCTCATAGGTGATAA 15 3 0 TGAAAGTTTTTAAGAGGGAAAAATCCAATT 17 24 1 ATTTCTGCAATAGGAGGTGATGTGAA 20 72 1 CGCAGGATAATCAGAGGTGTGAAG 22 84 1 ********** MAP Score: 6.59383 Motif 5 TAAGGGAGTTCATAAAATTTTTTGAAACATTGAAT 9 23 1 GCTACGAGCCCTTGAACCTTTTTGACCTCAGGGGT 9 153 1 AAGGAGTAAGGCTTAATTTTTTTGAACCAATTTTA 13 166 1 AGTGTGTACTGGTGAAAGTTTTTAAGAGGGAAAAA 17 12 1 AAATCGTAATCTTTTTTAATTAGGTTTTT 19 4 1 CTTGCGAAAGGTTGATATTTTTTTAGGATAAATTT 0 48 1 ACTATGCCCACCTCAAAATTTTTTCCCACCTGACT 10 81 0 ACACCTAAGACGTAAACCTTTATAACCCCTGAGGT 9 177 0 CAGTTTATAAGGTAAACTTTATTTACAATGAAAGT 18 75 1 GATTGAAAGCGATTTTTCTTTTTTAAAAAGCACTC 23 33 1 * * ** ***** * MAP Score: 6.26212 Motif 6 ATCCTATCCCTGCTCGGAGGGTAACTTGTTTAAATTTATC 0 74 0 CCCGCTGAGCTACGAGCCCTTGAACCTTTTTGACCTCAGG 9 145 1 TGAAAGAGAGTGCTGGAAATTTAAAAAGGGTGATTTGA 9 265 1 ACCTTGTTAGTACTTGAATTCAAACCATTTAAGCTTTTCC 10 16 1 TAATAACAATTATATGGCTTTAAACGTACTATTAGC 10 154 1 GATGGGGACATACATGCAGTACAACATGGGCCTGAGGCCC 12 56 1 GCGCGTTCGTTGCCAGCCTGTAAACTCTGTTTACAATCTC 13 14 0 CTTAGCGTCTTGCACGGTCTGAAAACCTCGAGGCCTGTCT 13 129 0 AACAGTTATTAACCAGCCCGCCAACTGAATCCC 14 39 1 TTATCCATACTGCATGCTCTCCAACGTCAGTTTATAAGGT 18 48 1 TAACAAATGCTTGCAATTTAAATTCGTGATAGAAAAG 20 7 1 *** ** * *** * MAP Score: 4.88075 Motif 7 TAAACAAGTTACCCTCCGAGCAGGGATAGG 0 82 1 CGGGTTCAAATCCCGCCGAGTCCATGTTTT 9 86 0 GGCGGCGCTCTCCCGCTGAGCTACGAGCCC 9 134 1 TATTAAGGTTTCCCTCTGAAGTCCCTGAAT 9 229 0 TCCCTCATAACTTTCTCGGG 12 93 0 ATTGGATTTTTCCCTCTTAAAAACTTTCAC 17 23 0 ********** MAP Score: 4.52468 Motif 8 TCTTGCGAAAGGTTGATATTTTTTTAGGATAAA 0 47 1 CCTGCTCGGAGGGTAACTTGTTTAAATTTATCC 0 73 0 TGGATCCCTTGGTTAATATGGTTCCCAATATAT 1 27 0 TAACCCCTGAGGTCAAAAAGGTTCAAGGGCTCG 9 157 0 ATAGTCAGGTGGGAAAAAATTTTGAGGTGGGCA 10 79 1 AAGGAGTAAGGCTTAATTTTTTTGAACCAATTT 13 166 1 GCGGTAAAATTGGTTCAAAAAAATT 13 180 0 AGTGTGTACTGGTGAAAGTTTTTAAGAGGGAAA 17 12 1 CAGTTTATAAGGTAAACTTTATTTACAATGAAA 18 75 1 *** ** ***** MAP Score: 3.45378 Motif 9 GGCCGTGAGAGCGGCTGCGCTGAGGTATTACG 5 10 1 GGTTTAGTTTGAGGATGAGGTGAGAGGTGATG 7 87 1 CCTTCGCGAGGCGGAGGCCGCGGGTTCAAATC 9 104 0 CCTCCGCCTCGCGAAGGCGGCGCTCTCCCGCT 9 119 1 ATGCTCAAAAGAGGCAGAGGCGGCAATGGTTA 12 18 1 CGGTATAATTGATGCAGCCGAGCTACTTGGAT 13 58 1 GATTATGTTGGCGGAGCAGCGGTAATCACACG 22 18 1 ***** **** * MAP Score: 2.84778 Motif 10 TTTTTAGGATAAATTTAAACAAGTTACCCTCCGAGCAGGGATAG 0 67 1 AAAGTTTTAAATATTAAGTTCTAAAATAATAC 2 0 1 CTATAAAGTAAAATTTCGAATAAGAAAATTCAGAAGTGTAA 3 7 0 TCCCCCAAATTTTTAATTTTTTAGAGGTGATACC 6 6 1 TACGTAAAGGAAATTTCAACTTAGAAAAAGGTAATTTCAACATA 7 13 1 AGTTCATAAAATTTTTTGAAACATTGAATTGTATTGGTTGTTCA 9 29 1 TAAGACGTAAACCTTTATAACCCCTGAGGTCAAAAAGGTTCAAG 9 163 0 AATACCACCTTGTTAGTACTTGAATTCAAACCATTTAAGC 10 6 1 GCTAATAGTACGTTTAAAGCCATATAATTGTTATTATTTTACC 10 147 0 GCTAACATTTAAACATTGTAATCTCAAAAGATTAAAAT 11 4 1 TACTGGTGAAAGTTTTTAAGAGGGAAAAATCCAATTACTTCGAA 17 18 1 TTTTTAATTTTTGTTTTGGTTACCTGTAAAGCGTATTTG 21 5 1 * *** * * * ** * MAP Score: 2.50597