AlignACE 3.0 10/20/99 AlignACE2 -i AA/AA_sum_all001_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944238064 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 rpsS 112 ribosomal protein S19 #1 rplV 117 ribosomal protein L22 #2 rplP 61 ribosomal protein L16 #3 rpsQ 232 ribosomal protein S17 #4 rpmJ 60 ribosomal protein L36 #5 secY 44 preprotein translocase SecY #6 pkcI 300 protein kinase C inhibitor (HIT family) #7 rpsO 58 ribosomal protein S15 #8 aldH2 300 aldehyde dehydrogenase #9 aq_260 300 hypothetical protein #10 truB 30 tRNA pseudouridine 55 synthase #11 rpsL2 85 ribosomal protein S12 #12 pgi 33 glucose-6-phosphate isomerase #13 aq_759 152 hypothetical protein #14 argS 26 arginyl-tRNA synthetase #15 rplT 54 ribosomal protein L20 #16 selB 27 elongation factor SelB #17 mpp 210 processing protease #18 aroA 37 5-enolpyruvylshikimate-3-phosphate synthetase #19 rpsH 40 ribosomal protein S08 #20 rpsN 33 ribosomal protein S14 #21 rplN 145 ribosomal protein L14 #22 degT 24 transcriptional regulator (DegT/DnrJ/Eryc1 family) #23 rpsL1 52 ribosomal protein S12 #24 tufA2 300 elongation Factor EF-Tu #25 nusG 300 transcription antitermination protein NusG #26 rpoB 212 RNA polymerase beta subunit #27 infB 21 initiation factor IF-2 #28 ymxG 243 processing protease Motif 1 AATACTTAGCTTCAGGAGGTAAAGTTAGGT 20 13 1 GGTTATAAAGTTAAGGTGGAAAAGGAAAA 28 224 1 TACACTTTTGCTCAGGAGGCAGGAACGCTCTGTA 26 31 1 TTAAGAAACATAAAAGAGGAGAGGTATAAAA 26 191 1 CTCAGTAATATGGAGGGGGCAGGATTCGAACCTG 24 14 0 TCTGGAAAGTTTTAAGTGGCGGGGCTGGGAGGAC 25 69 0 AAAATACCTCTCGAAAAGGAAAAGTATGAGATAA 6 182 0 AGTTGAAAAAGGCAAGGACTTAGGTTA 4 3 1 TTTTACTTACCGAAGGAGGAAGCGA 23 37 1 GTTTATGATCCGGAAGTGGCAAGAAAAATTAAGC 6 23 0 CAGATTACTCTATAGAAGGGGAAGGTTTAGTAAT 6 91 0 GGGAAAAATTATAAGGGGAAAGAAGAGAAAAGA 12 10 0 GCGGGCGTAGCTCAGTTGGTAGAGCAGCGGCCTT 24 47 1 GCCCAGGTAGCTCAGTCGGTAGAGCGCACCCTTG 24 152 1 AGTATTTATTTTGAGAAGGAAGAAGAAAA 17 191 1 CTTACTCTAATTAAAGGGGTGAAAAGCC 21 127 1 TGATTATGAGTGCGAGAGGCAAAGCTAACGGTTT 17 132 0 GGACGAAGTTCGGATGCGGTAAGGGAATATGCGG 8 24 1 GGGGCTGTAGCTCAATTGGCAGAGCGCGGGACTC 25 11 1 ACTTAAGTTGTTCATGTGGAAAAGTTGTGGAAAG 9 182 1 AAGGAATATCCTGAAACGGGAACGATGTTAATAG 6 149 0 AAGAATTCCTCAAAGGCGTAAGAGATGAACTCAA 25 129 1 CCCATGGAAATGAGGAAGGTAAAGAGGAACATAG 3 159 1 TTATGTTTCTTAAAGAAGGCGGAATGAAGCAATA 26 170 0 GACACCTTTCTCAGGGTGGTAAAACCGTTAGCTT 17 111 1 GCCTCCTGAGCAAAAGTGTAAAGGAAAAGGAAAA 26 17 0 TAATAGAATTTAAAAACGGGGAGATTTACACAAT 6 61 0 AATAATTTGCCTTAAAAGGAGGAAGCGA 11 67 1 GGAAAAACAGTTGAGAGGTGAAGGGTA 3 215 1 AATTACTCGAAGTCGGAGAAAGAGTAAAATC 18 7 1 ACGCTCTGTACGTAAATGGAAACATTAATCTTCT 26 55 1 AATCCCTCTTTACAAACGTAAAAGAAATAATTTA 24 241 1 TAACCTCTCTCGTAAAAGGAGGCATCGC 15 36 1 * *** ** **** MAP Score: 24.6471 Motif 2 TCTTTTCTCTTCTTTCCCCTTATAATTT 12 8 1 ACTTTATAACCTTCCTTTCCCAAGTAATAA 28 205 0 CTCCTTCTTTTCCTTTTCCTTTA 26 3 1 TTTTCTTCTTCCTTCTCAAAATAAATA 17 193 0 CTTCTAAGAACTTCTTTCTCTCTCTTTCCC 3 25 0 CTTCTTTCTCTCTCTTTCCCACATCTTTCA 3 15 0 TTATATCCTTCATCCTTTCCTTGAGAGGGA 25 276 1 TTTTCCTTTTCCACCTTAACTT 28 231 0 GCGATGCCTCCTTTTACGAGAGAGGTT 15 37 0 CTCTTAGCCCTCCTTTGCAGCCTGCATA 2 43 0 TAGCTATGTTCCTCTTTACCTTCCTCATTT 3 166 0 ATCTCATACTTTTCCTTTTCGAGAGGTATT 6 184 1 TTCTTTTCCTTTTCCTTTACACTTTTGCTC 26 14 1 TTATAAATTATTTCTTTTACGTTTGTAAAG 24 248 0 CTCTTTCCCACATCTTTCACCACC 3 4 0 TTAACTGTCCCATCTTTCACACC 1 3 0 CTGTCAAGTATTCCTTTTTCAATTCCCTAA 26 95 0 TTTTCTACGACACCTTTCTCAGGGTGGTAA 17 103 1 ATAAAAATCCCTTCCTTCAATAAATAAGCC 24 125 1 GAACCGCATATTCCCTTACCGCATCCGAAC 8 31 0 GCAATTAAAACCCCTTTTCAGGAGGAGCTT 11 11 0 TACAAACCTCCTTCAAGCCGGCAGTT 19 24 0 CCGGCGCCCTCACCCTTACCAAGGGTGCGC 24 175 0 ATGGTTATTATTTCTTTTCATTCCGCTTCC 8 115 0 TTGAATGTAATTTCTTTTCATACATGTTTA 6 247 1 TCGCTTCCTCCTTTTAAGGCAAATTA 11 69 0 TAGAATTTAGCCTCTTTAGCAAAATAGTGT 13 19 1 TACCCTTCACCTCTCAACTG 3 222 0 GATAAAAATCCCTCTTTACAAACGTAAAAG 24 235 1 CTTACTATTTCCTCTTTTGAAGGGTTCGGA 8 262 0 TTTCAGGATATTCCTTTATCTCATACTTTT 6 167 1 TAACTGTCTCTACCTTTCGCTATAATTTAA 28 84 1 TACTAAACCTTCCCCTTCTATAGAGTAATC 6 93 1 TTTTATTATATTCCTTTTAAAAATTTTTGC 13 100 0 ACACCGTGGTTTTCTTTTGAGTAGATTGTG 9 51 0 TTGTTCCAAGCTCCTTTAAATCCCATTTAC 0 19 0 ********** MAP Score: 24.2269 Motif 3 AAGAATAAGGAGTGGAAGATGGAGCTGTTATTAA 6 215 0 GGGATTTTTATCAGGGAAGTGGAGCCCAGGACCG 24 213 0 CCGCTCAGTAATATGGAGGGGGCAGGATTCGAAC 24 17 0 TAATTTTACTTACCGAAGGAGGAAGCGA 23 34 1 TTATGTTTCTTAAAGAAGGCGGAATGAAGCAATA 26 170 0 AAAAATTATAAGGGGAAAGAAGAGAAAAGA 12 6 0 AATTTGCCTTAAAAGGAGGAAGCGA 11 70 1 CAGTACCCAGTCAAGGAAGCGGAATGAAAAGAAA 8 101 1 AATTACTCGAAGTCGGAGAAAGAGTAAAATCTTT 18 10 1 GTCGTAGAAAAACAAGAAGAGGAGGTAGTATCCG 17 80 0 ATTTATTTTGAGAAGGAAGAAGAAAA 17 194 1 GACGTTTATGATCCGGAAGTGGCAAGAAAAATTA 6 26 0 TATAAAGTTAAGGTGGAAAAGGAAAA 28 227 1 TCTTTAAGAAACATAAAAGAGGAGAGGTATAAAA 26 188 1 AATAAAGTTCTCTCGGAGGTAGAAGA 5 2 0 CCGGTTAGGGAATTGAAAAAGGAATACTTGACAG 26 91 1 TTACCTCAAAATTCGGAGGTAGGAA 24 285 1 TTTAAATTATAGCGAAAGGTAGAGACAGTTATGA 28 81 0 GCTCAATTCTAAGAAAAGACGGAGGTATATGGGA 7 32 1 GTAAAGGAAAAGGAAAAGAAGGAG 26 0 0 CTTAGAAGATATTAGAAAAAAGAGCTTACAGGAA 3 47 1 TGGGCTTATTTATTGAAGGAAGGGATTTTTATAT 24 123 0 TGGTGAAAGATGTGGGAAAGAGAGAGAAAGAAGT 3 12 1 GGAAATGAGGAAGGTAAAGAGGAACATAGCTAGA 3 164 1 AGTTGAAAAAGGCAAGGACTTAGG 4 0 1 TGTAAACCTTAATAGGAGGTGGGTAAG 13 135 1 CTTCATCCTTTCCTTGAGAGGGAGCCT 25 283 1 ATCCTCAAGAAAATTGAAGAAGAAATTATGCAGG 2 17 1 TAGTAATAGAATTTAAAAACGGGGAGATTTACAC 6 64 0 * ***** **** MAP Score: 23.1447 Motif 4 AAATCCCATTTACTCTCCTCCT 0 0 0 GTTTCTCTTGTTCCAAGCTCCTTTAAATCCCA 0 24 0 TTAGGTTTATATCCGTCCCTCTGAGATTTGTC 1 41 0 TTCTCTCTCTTTCCCACATCTTTCACCACC 3 8 0 TGTTCCTCTTTACCTTCCTCATTTCCATGGGG 3 158 0 TCTATTACTAAACCTTCCCCTTCTATAGAGTA 6 88 1 CTTCCCATATACCTCCGTCTTTTCTTAGAAT 7 37 0 ATTATTTCTTTTCATTCCGCTTCCTTGACTGG 8 107 0 CTGAAGTTCAATCCATGCCCTTTTAACAGGGT 8 165 0 TCTTTTCTCTTCTTTCCCCTTATAATTTTTC 12 9 1 CTTACCCACCTCCTATTAAGGTTT 13 138 0 GGCACTACTTTTCAAACCTCCTAATATTCTAC 17 49 1 TATTCTACGGATACTACCTCCTCTTCTTGTTT 17 73 1 TACAAACCTCCTTCAAGCCGGC 19 28 0 GCAGGTTCGAATCCTGCCCCCTCCATATTACT 24 13 1 ACCGGACTCGAACCGGCGCCCTCACCCTTACC 24 185 0 TTCCTACCTCCGAATTTTGAGG 24 288 0 CTAAAATTATATCCTTCATCCTTTCCTTGAGA 25 270 1 GTACAGAGCGTTCCTGCCTCCTGAGCAAAAGT 26 34 0 ATATTATTGCTTCATTCCGCCTTCTTTAAGAA 26 166 1 CTTCAAACCTCCGTTTATCGTAA 28 1 1 CTTAGTGTCATTCTATCATCCTGTGCCTTTAT 28 143 1 **** ****** MAP Score: 22.1267 Motif 5 CCTCTCGAAAAGGAAAAGTATGAGATAAAGGAAT 6 176 0 GTAAAGGAAAAGGAAAAGAAGGAG 26 0 0 TTACCGGTTAGGGAATTGAAAAAGGAATACTTGA 26 88 1 CATGGAAATGAGGAAGGTAAAGAGGAACATAGCT 3 161 1 AAGAGCTTACAGGAACTTGAAAAGCTATTGGACG 3 66 1 AATGACACTAAGGAAACTCAAAAGGATAATAATC 28 121 0 AAACCTTAATAGGAGGTGGGTAAG 13 138 1 AACATAAAAGAGGAGAGGTATAAAA 26 197 1 AATTTTTAAAAGGAATATAATAAAATTATATGTA 13 105 1 TACTTGGGAAAGGAAGGTTATAAAGTTAAGGTGG 28 209 1 GGAGAATTGTGGAAAACTCATAAGTTGTTCATAT 9 12 1 GGGAAAAATTATAAGGGGAAAGAAG 12 18 0 ACCTCACAATGGAAAAATTAAAAGAATTCCTCAA 25 108 1 AGGAGGAGAGTAAATGGGATTTAA 0 0 1 CTCCCTCTCAAGGAAAGGATGAAGGATATAATTT 25 273 0 TTTATGATCCGGAAGTGGCAAGAAAAATTAAGCA 6 22 0 ACCCAGTCAAGGAAGCGGAATGAAAAGAAATAAT 8 105 1 CAGGCTGCAAAGGAGGGCTAAGAG 2 47 1 GAAAGATGTGGGAAAGAGAGAGAAAGAAGTTCTT 3 16 1 GAAATCCTCAAGAAAATTGAAGAAGAAATTATGC 2 14 1 GTAGAATATTAGGAGGTTTGAAAAGTAGTGCCAA 17 47 0 AAAGTTTTTCGGGAAAAGCTTGAAAATCAATGGG 9 212 1 AAGGTGTCGTAGAAAAACAAGAAGAGGAGGTAGT 17 85 0 TTTAATAGACGGAAATCCTGTGAGGAGCTGTCAG 8 70 1 TTCAAGAATAAGGAGTGGAAGATGGAGCTGTTAT 6 218 0 CTTCAAAAGAGGAAATAGTAAGTGTCATGTCTTC 8 270 1 ***** * * *** MAP Score: 20.4094 Motif 6 CTTTATTATATTAAAATCTTTTAAC 5 29 1 AAATTCCTTATAATATTTATTTGCTCAA 7 7 1 TTCTTTCCCCTTATAATTTTTCCC 12 19 1 TAATACAATTTTATAAAGTTTTATGATAAGA 13 63 1 TATATTCCTTTTAAAAATTTTTGCAATAATT 13 93 0 TAAGGTTTACATATAATTTTATTATATTCCT 13 115 0 TCCAGACTTAAAATTTTATGTTAAAATA 15 7 1 CATAAATTTGTTATAATATCAATTTGCCTTA 21 100 1 AAAAAAGGTATTTTAATCTTAGTG 22 3 0 TATTTTAACCTTATAATTTTACTTACCGAAG 23 21 1 AAGAAATAATTTATAATATTTTGTTACCTCA 24 262 1 TGAGGAATTCTTTTAATTTTTCCATTGTGAG 25 110 0 ACGATTAGTGTTATAATATTTTCCCTTGCTA 25 203 1 AGGATGAAGGATATAATTTTAGTAAAAGTGA 25 261 0 TTAACTGATCTTTTAAATTTAAACCAAAAAA 26 130 0 AACTTGTAATTTTTAATGTTAAAATAATTAA 28 43 0 GAAAGGAAGGTTATAAAGTTAAGGTGGAAAA 28 216 1 ******* *** MAP Score: 17.1896 Motif 7 ACCGGGACGAAGTTCGGATGCGGTAAGGGAATATG 8 20 1 TGTGAGGAGCTGTCAGTACCCAGTCAAGGAAGCGG 8 88 1 CAGGTTCCCCAGTGCGGATACTGCCAGCCCGGACA 8 194 1 AAGAGGAAATAGTAAGTGTCATGTCTTCACACCT 8 276 1 TGCGCAGGTTCGAATCCTGCCCCCTCCATAT 24 6 1 GCAGGTCGCGGGTTCGAGTCCCGTCGCCCGCTCCA 24 88 1 GCGCACCCTTGGTAAGGGTGAGGGCGCCGGTTCGA 24 175 1 TGAGGGCGCCGGTTCGAGTCCGGTCCTGGGCTCCA 24 193 1 CGTGGGTGGGGGTTCGAGTCCTCCCAGCCCCGCCA 25 52 1 CTTTATGGTCGGTGCGGCCGCTGGCGGAGCTGCCG 28 169 1 *** ** *** * * MAP Score: 8.91191 Motif 8 GAGGGACGGATATAAACCTAATCAATCAATAGCCATACTCA 1 52 1 GAACTTGTTTTTTAAACCTGAGTCTTGTCAATTCAAGTTTA 3 104 0 TGTTTTTCCCTTATAACCGTCAAAACTCTAGCTATGTTCCT 3 183 0 ACGTCTATTGTGTAAATCTCCCCGTTTTTAAATTCTATTAC 6 55 1 AAATTCTATTACTAAACCTTCCCCTTCTATAGAGTAATCTG 6 84 1 ATCCGGTGACTTAAAACTTACGAATTATAAATAACTTAAGT 9 149 1 GGCACTACTTTTCAAACCTCCTAATATTCTACGGATACTAC 17 49 1 TACAAACCTCCTTCAAGCCGGCAGTTGGGCT 19 19 0 AAGTGAGCTGTAAAAACCTTCGCGTTTCTAACATAAATTTG 21 69 1 GCCCCGCCACTTAAAACTTTCCAGAGGTATACCTCACAATG 25 78 1 CTTCAAACCTCCGTTTATCGTAAAGAGTTTAG 28 1 1 CTTTCCCAAGTAATAACCGGCAGCTCCGCCAGCGGCCGCAC 28 180 0 CACCTTAACTTTATAACCTTCCTTTCCCAAGTAATAACCGG 28 201 0 * ****** * * * MAP Score: 4.81229