AlignACE 3.0 10/20/99 AlignACE2 -i BS/BS_sum_all020_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944255458 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 serS 300 seryl-tRNA synthetase #1 ycgJ 192 ycgJ #2 ydaC 207 similar to hypothetical proteins #3 yhdP 60 similar to hemolysin #4 yhdQ 156 similar to transcriptional regulator (MerR family) #5 yhdT 76 similar to hemolysin #6 ylaK 154 similar to phosphate starvation inducible protein #7 gerCA 162 heptaprenyl diphosphate synthase component I #8 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #9 mtrA 187 GTP cyclohydrolase I #10 hbs 300 non-specific DNA-binding protein HBsu #11 comGB 52 probably part of the DNA transport machinery #12 comGA 300 late competence gene #13 yqhB 142 similar to hypothetical proteins #14 yqfF 78 yqfF #15 yqfC 56 yqfC #16 yqfB 24 yqfB #17 yqfA 21 yqfA #18 yqeZ 130 yqeZ #19 rpsU 163 ribosomal protein S21 #20 yqeG 300 similar to hypothetical proteins #21 yrkA 300 similar to hemolysin-like #22 yrhH 300 similar to methyltransferase #23 yugS 27 similar to hypothetical proteins from B. subtilis #24 yugP 300 yugP #25 yxbB 300 alternate gene name: yxaP; similar to hypothetical proteins Motif 1 TGTAGAAAAAGAAGAAAAGGTAATCAAACA 12 252 0 CTCCAAGCCGGAAGAAAAAGCGCATTTCTG 24 210 1 ATGGCAAAGAAAAGGACATCTTTCT 18 5 1 ATGAAAAAAGGAAAAAAAGGAATATTCGTT 10 12 1 TGTTACGTATGAAGAGAAGGCACTTATTAT 18 85 1 ATTTTGAAAGAAAGAAAAAGGGAAGGGTGC 20 275 1 GATGTATCGGGATGAAAAGGTATTTGCCGA 1 162 1 ATTTTTTTCCGAAAAAAAAGCAGAAAACAT 22 141 0 ACCTGTCTCAGAAAAAAATGAGAGCAAGTA 10 206 0 TTTTTTTTCGGAAAAAAATGAAAAAGTTTA 22 152 1 CTTCTCTTTTGATGAAAAAGGTGAATGCCT 6 96 0 CATCATTTACGAAAAGAAGGAGCTGGTTCA 1 96 1 GATAAATCAATAAAAAAAGGAGTGTTTCGC 0 280 1 ATATAAAAATGATGAAAATGATAGGTTCAA 1 25 0 ACTTGCGCCTAAAGAAAAACTGAGCAAAAA 20 226 0 CATTATAGCATAAAAAAAAGAATTGGCTGT 7 60 0 AAATTTTAAAAGAAAATCTTTATAAAGA 21 8 1 TGAGAGCAAGTAAGAGAAAGACAATTAAAC 10 188 0 TTTTTCATCAAAAGAGAAGCAGGAAGAACT 6 107 1 AACGGCTTTTTAAGAAAAACTGCACTCTGA 10 161 0 AAAACAGCATAATGAAAATGGAATCTAGCA 12 86 1 AATGATTGTCGAAAAAAATCGAACTTGCGC 20 248 0 TTTTTATACATAAAAAAATGAAACCTTTGA 18 49 1 TTAAGGCTTAAAAAAGAAAGCAAAATAAAA 21 97 0 TTTCCCTATAAATAAAAAAGCAGACATGGT 12 125 0 GCTCTTGAAATATGAAAAGCCCCTTAGAAA 9 74 0 AATTCCGGTCTAAAAAAAACAATAAACTTG 4 89 1 TCACTCTAGCAATGAGAATGAAGGTAACAC 3 31 0 GAGTAACACATATAAAAAGCCATATCAAGC 10 92 0 ********** MAP Score: 28.6175 Motif 2 TTCTAGAAGATTTCAGCAGGCCAAAGGGCG 2 179 1 CCATTTTATCTAACAGGAGGTGTTACCTTC 3 12 1 AAAATGATTATATCAGGAGGTGACTCCTTA 5 31 1 ATGAAAGCATTTTAAGGAGGGAACCCGCAA 6 10 0 AAAACATATATTTTAGCAGGCATTCACCTT 6 79 1 TTGACCCTTATATCAGGAGGCTGAGAC 6 137 1 GAATGTATCCTTTTGGGAGGAGGTGAAAGG 10 279 1 TTATGAGCATTTTCAGGTGGTATGGAATGT 13 96 1 GGGCTTGATGTTTCAAGAGGAGGTTCTT 14 60 1 TCGATTGGTGTATTCGGAGGGAGGGAAAGA 19 141 1 CGTTAAGGAGGTGGCCCCTTA 23 1 1 TTTTATTTGTTTTCAGCAGGCCTGTTCTTT 24 161 1 TAGTACTCTATTTTAGGAGGGATGCTCAAT 25 33 1 TAGTACTCTATTTTAGGAGGGATGCTCAAT 25 151 1 ACGCCAACTTGATAAGGAGGATGCTGAAG 25 281 1 ********** MAP Score: 23.8838 Motif 3 TTTCGATAAATCAATAAAAAAAGGAGTGTTTC 0 276 1 AATTCCGGTCTAAAAAAAACAATAAACTTGTG 4 89 1 AACAATAAAATTAATGAAAGCATTTTAAGGAG 6 21 0 CATTATAGCATAAAAAAAAGAATTGGCTGTAT 7 58 0 CATACATAGATTAAGAAATAAATGTGAATTTG 7 122 1 GGCTTTTCTGTGAAGAAATAAAGTGTATGTAA 9 40 0 GGATGAAAAAAGGAAAAAAAGGAAT 10 3 1 TGAAGAAATGATAATAAACGAACTGAATGTAT 10 255 1 CATATTGTAGAAAAAGAAGAAAAGGTAATCAA 12 255 0 TATTGGGCAATTAAAGAATAAAGAACAAAAGT 13 25 0 TTTTTATGTATAAAAAAAGACATCTCTCTTAG 18 33 0 TTTTTATACATAAAAAAATGAAACCTTTGATA 18 49 1 GCCTGTCTATATAATGAAAGAAAGGGGTTG 19 8 0 ACAATCATTTTGAAAGAAAGAAAAAGGGAAGG 20 269 1 ATAAAGACATTAAATAAATCAAGACGGTTGGG 21 31 1 AAAAGAAAGCAAAATAAAAACACACCTGAATT 21 84 0 GTTTTAAGGCTTAAAAAAGAAAGCAAAATAAA 21 98 0 AAATATTTATTGAATAAACAAAAAACAGTATA 21 240 0 TTTATTATCTTAAAAAAATAAACATCATCTTC 22 246 0 TTTTTTTAAGATAATAAATAAACATAGGAAAC 22 260 1 ATTCAAATCGAAAATAAACAAAATCACCGCGG 24 60 0 GGAGGGATGCTCAATGAAAAAAGCTTATAAGA 25 48 1 GGAGGGATGCTCAATGAAAAAAGCTTATAAGA 25 166 1 * ****** *** MAP Score: 22.255 Motif 4 TAAATCAATAAAAAAAGGAGTGTTTCGC 0 282 1 TCTCTCTAAGAAGGGAGAACGCTG 16 7 1 AAATTAACTCAAAAAGGGGGTTGGTTGCTG 2 134 1 TGAAAGAAAGAAAAAGGGAAGGGTGCGGGT 20 279 1 GGATGAAAAAAGGAAAAAAAGGAAT 10 5 1 TATATAATGAAAGAAAGGGGTTG 19 3 0 CCCTATAAATAAAAAAGCAGACATGGTCAC 12 122 0 TTTTTCCGAAAAAAAAGCAGAAAACATAAT 22 138 0 TCATTTACGAAAAGAAGGAGCTGGTTCAAA 1 98 1 CTGTCTCAGAAAAAAATGAGAGCAAGTAAG 10 204 0 AAAGACATCGGAAAAGGGAGGTGC 13 128 1 CTTATTATAAAAGGAAGGAGGGATACACCG 18 107 1 TAGACATGAAAACAAAGGAGGAGAATCATC 2 10 0 TTTATACATAAAAAAATGAAACCTTTGATA 18 51 1 TTTTTTCGGAAAAAAATGAAAAAGTTTAGT 22 154 1 AGGCTTAAAAAAGAAAGCAAAATAAAAACA 21 94 0 GGCGCAGTTCAAAAAGGCGAGGTTTCTTAT 25 74 0 GGCGCAATTCAAAAAGGCGAGGTTTCTTAT 25 192 0 AAAGCATTTTAAGGAGGGAACCCGCAA 6 7 0 TATCCACACCAAAAAGTGGATAACTTGTGA 20 95 1 TTATAGCATAAAAAAAAGAATTGGCTGTAT 7 58 0 ********** MAP Score: 18.9661 Motif 5 GGGAGCCTCTCTTTCTAAGAGAGCCGATGGTTGG 0 66 1 TGAAACACCGTTTTCTAAAAACGCCGAGATGTAT 1 135 1 TGTGAAACATTTTTCTGATAAAGCAATGCGAAGG 2 85 0 TTGCGGGTTCCCTCCTTAAAATGCTTTCATTAAT 6 10 1 AGAGCATGGGCTTCCTGACAGGGCATTCACTTTG 9 99 1 TTGGACAAACATTCCTCAGAGTGCAGTTTTTCTT 10 146 1 AGAGTGCAGTTTTTCTTAAAAAGCCGTTTAATTG 10 163 1 ACATTCCATACCACCTGAAAATGCTCATAAAACA 13 92 0 CAGCGTTCTCCCTTCTTAGAGAGA 16 0 0 AAAAGGACATCTTTCTAAGAGAGATGTCTTTTTT 18 19 1 ATGCCGCATTCCTTCAAACATGGTTATGGAAATC 22 17 1 CATCATCTTCATTTCTAAAAGTGAAGGAAGGTAC 22 222 0 GATCTTTCAAAGAACGATCGTGGTTTT 24 3 1 CCGGCCAGTTCTTTCAGAAAATGAAGCCAGGAGA 24 117 0 ATTGAGCATCCCTCCTAAAATAGAGTACTAGATG 25 29 0 ATTGAGCATCCCTCCTAAAATAGAGTACTAGATG 25 147 0 ****** * * ** MAP Score: 18.4506 Motif 6 TAGTAGGGAGCCTCTCTTTCTAAGAGAGCCGA 0 61 1 ATAGGTTGAACCTATCATTTTCATCATTTTTA 1 20 1 TGAACCAGCTCCTTCTTTTCGTAAATGATGAT 1 94 0 GAGGTGACTCCTTATCCTTTGTTGAGAGGATA 5 47 1 GAGGATACAGCCAATTCTTTTTTTTATGCTAT 7 54 1 AACGAATATTCCTTTTTTTCCTTTTTTCATCC 10 10 0 TGCTGAAAAACCAATTCTTTCTGGCAAGAAAA 12 191 0 TGTTTGATTACCTTTTCTTCTTTTTCTACAAT 12 252 1 TTTGATTCCCTCTCCTTTCAACGCATATTG 12 280 0 GCACCTCCCTTTTCCGATGTCTTTC 13 127 0 AGAAAGATGTCCTTTTCTTTGCCAT 18 3 0 ATAATAAGTGCCTTCTCTTCATACGTAACAAA 18 83 0 GTGTATCCCTCCTTCCTTTTATAATAAGTGCC 18 103 0 CAACCCCTTTCTTTCATTATATAGACA 19 5 1 AACCCGCACCCTTCCCTTTTTCTTTCTTTCA 20 279 0 AAACTGCCGGCCAGTTCTTTCAGAAAATGAAG 24 125 0 GGCAGTTTCGCCTTTTATTTGTTTTCAGCAGG 24 149 1 TTTCAGCAGGCCTGTTCTTTTTGCTGATTGGA 24 171 1 TTATAAGAAACCTCGCCTTTTTGAACTGCGCC 25 72 1 TTATAAGAAACCTCGCCTTTTTGAATTGCGCC 25 190 1 *** ****** * MAP Score: 17.2292 Motif 7 AATAAAGATCGAAAAGCGTTGATAGGAACTA 0 32 1 CGGCTCTCTTAGAAAGAGAGGCTCCCTACTA 0 61 0 CTCTTTCTAAGAGAGCCGATGGTTGGTGCGA 0 74 1 AATCAATAAAAAAAGGAGTGTTTCGC 0 284 1 ATTTACGAAAAGAAGGAGCTGGTTCAAATTA 1 100 1 GGCGTTTTTAGAAAACGGTGTTTCATTTGTA 1 129 0 AATTAACTCAAAAAGGGGGTTGGTTGCTGAA 2 135 1 CATTTTATCTAACAGGAGGTGTTACCTTCAT 3 13 1 AAGCCCCTTAGAAAGGGGCTTTTCTGTGAAG 9 57 0 GTTTTTCTTAAAAAGCCGTTTAATTGTCTTT 10 171 1 GTATCCTTTTGGGAGGAGGTGAAAGGC 10 283 1 AATATGCGTTGAAAGGAGAGGGAATCAAA 12 281 1 AAAGACATCGGAAAAGGGAGGTGC 13 128 1 TTGATGTTTCAAGAGGAGGTTCTT 14 64 1 TGTATGATTTGAAAGGAGGTTCTAACACT 15 8 0 CACATGAGATGAAAGGGGGTTCTTTTTGT 15 37 1 TATAATGAAAGAAAGGGGTTG 19 0 0 AATCCATTCCGACAGCAGAGGCTGATGGCAA 22 47 1 ATAGGAAACCAAAAGCAGGTGTTTAAA 22 283 1 GCGCAGTTCAAAAAGGCGAGGTTTCTTATAA 25 72 0 GCGCAATTCAAAAAGGCGAGGTTTCTTATAA 25 190 0 ******** ** MAP Score: 17.114 Motif 8 CAACCCCCTTTTTGAGTTAATTTCCTCTCAGCGTTCCA 2 119 0 TATATCAGGAGGTGACTCCTTATCCTTTGTTGAGAGGA 5 39 1 TAATTTTATTGTTGAATTAACCTTCTATCTTTATGCAC 6 40 1 CCTCCCGCTGTTTGCGAGCATTTGCTTTTAACAGCGGG 7 20 0 TGATATGGCTTTTTATATGTGTTACTCTACATACAGAA 10 95 1 TTAAAAAGCCGTTTAATTGTCTTTCTCTTACTTGCTCT 10 178 1 CATTCAGTTCGTTTATTATCATTTCTTCACAGTTCAGT 10 246 0 TAGCAGGCATGGTGACCATGTCTGCTTTTTTATTTATA 12 111 1 GTTTTCCCTGTTTGATTACCTTTTCTTCTTTTTCTACA 12 244 1 TTTGATTCCCTCTCCTTTCAACGCATAT 12 282 0 ATGTGTATGATTTGAAAGGAGGTTCTAACACT 15 4 0 ATACACATGAGATGAAAGGGGGTTCTTTTTGT 15 34 1 TCGAAATTTTTTTGCTCAGTTTTTCTTTAGGCGCAAGT 20 218 1 TCAGGTGTGTTTTTATTTTGCTTTCTTTTTTAAGCCTT 21 87 1 ATCATTCAGAGTTGATTTTAGGTTCTTTTGAACTTATA 21 194 1 ATATAATCACTTTTCCGGAAGCTTCTCCTGGCTTCATT 24 94 1 ATTACGATTATTTTAATGAGTTTTCTTTCTCGTGTACA 24 238 0 ATCATCCTTTGTTCATGATCATTTCTCTATTACGATTA 24 266 0 TCATATAGCATTTGACATCTAGTACTCTATTTTAGGAG 25 14 1 TAGTACTCTATTTTAGGAGGGATGCTCAATGAAAAAAG 25 33 1 TCATATAGCATTTGACATCTAGTACTCTATTTTAGGAG 25 132 1 TAGTACTCTATTTTAGGAGGGATGCTCAATGAAAAAAG 25 151 1 ***** * **** MAP Score: 16.903 Motif 9 CGCGAGAGCTCTCGTCCCTTTATGGGGATGA 0 232 1 GCGAAACACTCCTTTTTTTATTGATTTAT 0 281 0 TTTGAACCAGCTCCTTCTTTTCGTAAATGAT 1 97 0 GATGATTCTCCTCCTTTGTTTTCATGT 2 6 1 GGAGGTGACTCCTTATCCTTTGTTGAGAGGA 5 46 1 ATACAGCCAATTCTTTTTTTTATGCTATAAT 7 58 1 TATGTATGAGTTTTATCTTTTCATTCGCTTA 7 99 0 TATTCCTTTTTTTCCTTTTTTCATCC 10 5 0 TCTTACTTGCTCTCATTTTTTTCTGAGACAG 10 203 1 AATAACCTGGCTTGATCCTTTAACAACCAGA 11 15 0 TTGATTACCTTTTCTTCTTTTTCTACAATAT 12 255 1 TTTGATTCCCTCTCCTTTCAACGCATAT 12 282 0 TCCTCCAAACTTTTGTTCTTTATTCTTTAAT 13 17 1 GTATCAAAGGTTTCATTTTTTTATGTATAAA 18 51 0 CGGTGTATCCCTCCTTCCTTTTATAATAAGT 18 106 0 CAACCCCTTTCTTTCATTATATAG 19 3 1 TAGGCGCAAGTTCGATTTTTTTCGACAATCA 20 245 1 CCCTTCCCTTTTTCTTTCTTTCAAAATGATT 20 271 0 CATTATGTTTTCTGCTTTTTTTTCGGAAAAA 22 137 1 AACTAAACTTTTTCATTTTTTTCCGAAAAAA 22 154 0 TGGCCGGCAGTTTCGCCTTTTATTTGTTTTC 24 144 1 TTTCAGCAGGCCTGTTCTTTTTGCTGATTGG 24 171 1 TTTTTCATCATCCTTTGTTCATGATC 24 284 0 TTATAAGAAACCTCGCCTTTTTGAACTGCGC 25 72 1 TTATAAGAAACCTCGCCTTTTTGAATTGCGC 25 190 1 **** ****** MAP Score: 14.4061 Motif 10 CATCCCCATAAAGGGACGAGAGCTCTCGCG 0 232 0 TAAATCAATAAAAAAAGGAGTGTTTCGC 0 282 1 TCATTTACGAAAAGAAGGAGCTGGTTCAAA 1 98 1 ACATGAAAACAAAGGAGGAGAATCATC 2 7 0 ATTAACTCAAAAAGGGGGTTGGTTGCTGAA 2 136 1 ATTTTATCTAACAGGAGGTGTTACCTTCAT 3 14 1 AATGATTATATCAGGAGGTGACTCCTTATC 5 33 1 AAAGCATTTTAAGGAGGGAACCCGCAA 6 7 0 ATGCTCGCAAACAGCGGGAGGATACAGCCA 7 37 1 GACATCGGAAAAGGGAGGTGC 13 131 1 GCTTGATGTTTCAAGAGGAGGTTCTT 14 62 1 GTATGATTTGAAAGGAGGTTCTAACACT 15 8 0 ACATGAGATGAAAGGGGGTTCTTTTTGT 15 38 1 TCTCTCTAAGAAGGGAGAACGCTG 16 7 1 ATAGAAACGAGGAGAAGTTAT 17 4 1 CTTATTATAAAAGGAAGGAGGGATACACCG 18 107 1 ATTGGTGTATTCGGAGGGAGGGAAAGAGA 19 144 1 GGTGTGGATAACAGAACGATTGTTCTTATA 20 75 0 TGGCATTAGAAAGAGGGCAGAAAACATTAT 22 113 1 TCTAAAAGTGAAGGAAGGTACCAACTAGAC 22 213 0 TAGGAAACCAAAAGCAGGTGTTTAAA 22 284 1 CGTTAAGGAGGTGGCCCCTTACC 23 3 1 TCAGAAAATGAAGCCAGGAGAAGCTTCCGG 24 108 0 TACTCTATTTTAGGAGGGATGCTCAATGAA 25 36 1 TACTCTATTTTAGGAGGGATGCTCAATGAA 25 154 1 GCCAACTTGATAAGGAGGATGCTGAAG 25 283 1 ********** MAP Score: 11.1793 Motif 11 CGGTGAAAGATGCTGTCTGAATCCATCCTTG 0 107 1 ACCTTCGCATTGCTTTATCAGAAAAATGTTT 2 84 1 CAAAAACATATATTTTAGCAGGCATTCACCT 6 77 1 TAAGAAAAACTGCACTCTGAGGAATGTTTGT 10 150 0 CCGGTATTGTTGCATTAGGCGATCTTTCCGT 12 30 1 CTTCAACACATGTTTTATGAGCATTTTCAGG 13 82 1 AGTCGATTGGTGTATTCGGAGGGAGGGAAAG 19 139 1 TGCTCAGTTTTTCTTTAGGCGCAAGTTCGAT 20 230 1 CATCAGCCTCTGCTGTCGGAATGGATTTCCA 22 43 0 AGATGTCAAATGCTATATGAGATT 25 3 0 TCTAGTACTCTATTTTAGGAGGGATGCTCAA 25 31 1 AACTGCGCCGTGCTGTAGCAGCTGGCGGCCA 25 95 1 AGATGTCAAATGCTATATGAGATTAATGGCC 25 121 0 TCTAGTACTCTATTTTAGGAGGGATGCTCAA 25 149 1 AATTGCGCCGCGCTGTAGCAGCTGGCGGTCA 25 213 1 **** ****** MAP Score: 4.60799 Motif 12 GCTCTCTTAGAAAGAGAGGCTCCCTACTAGTTCCTATCAA 0 50 0 CATAACGGTTATCCCGTAAATGCCTACTCGCTTCAGCATT 0 143 0 TGGTTGCTGAATGATTAACATGCTTTCTAGAAGATTTCAG 2 155 1 CTTTTGATGAAAAAGGTGAATGCCTGCTAAAATATATGTT 6 81 0 AAAAGCAGACATGGTCACCATGCCTGCTAGATTCCATTTT 12 100 0 TGAAACATTTTTCAATACATTGCCGTCTAGTTGGTACCTT 22 189 1 AAACAAATAAAAGGCGAAACTGCCGGCCAGTTCTTTCAGA 24 133 0 AATCTCATATAGCATTTGACATCTAGTACTCTATTT 25 6 1 CAAATGCTATATGAGATTAATGGCCGCCAGCTGCTACAGC 25 106 0 CATTAATCTCATATAGCATTTGACATCTAGTACTCTATTT 25 124 1 ATCGTTTTGGATAAGATTAATGACCGCCAGCTGCTACAGC 25 224 0 ** **** **** MAP Score: 3.83514