AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #2 mtlD 52 mannitol-1-phosphate dehydrogenase #3 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #4 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #5 fruR 279 transcriptional regulator (DeoR family) #6 crh 23 catabolite repression HPr-like protein #7 yvcL 22 similar to hypothetical proteins #8 yvcJ 24 similar to hypothetical proteins #9 yvcI 300 similar to mutator MutT protein Motif number 1 CAATTTTTTAAAAATAAAAAGGCTCCTGGTT 1 10 0 AAAAAAAAGG 0.92756 -163 TATACAATTGAAAGTAAAGAGGACTTTGGCAC 1 52 0 AAAGAAGAGG 0.959903 -121 AGCGACAAACAAAACAGGGAGGGTTTATAT 1 153 1 AAAAAGGAGG 0.91492 -20 TGATTGAGGGAAAAAAACGGGAAGTTCATTCT 3 67 1 AAAAAAGGGA 0.966031 -172 TTGGGTGCGCAAAAGAACGAGAATGAACTTCC 3 86 0 AAAAAAGAGA 0.983479 -153 GCCCTTTTACACAACAAAAAGGCATGAGCAAA 3 119 0 ACAAAAAAGG 0.876709 -120 CTTACAGCTAAAAATCATGACAACGAATTCAC 3 185 0 AAAACAGACA 0.872992 -54 TCAGACTAGTAAAAAGAGGAGGTCAATTCTT 3 218 1 AAAAGAGAGG 0.9626 -21 TTGTCATCTGACAAGCACGGCGTACTAACACC 4 12 0 ACAACAGGCG 0.745997 -86 CCTCATGCAACATGCATGAGGTTTTTTTATG 5 10 1 ACATCAGAGG 0.77069 -270 TTTTTTCATTAAAATAAGAAGAAAATGTCGTA 5 73 1 AAAAAAAAGA 0.888273 -207 AAATTCGACAAAAATAAGGACAATTGTACGAC 5 99 0 AAAAAAGACA 0.946171 -181 CCGTAAAGAAAAGGGGAGATCTT 6 5 1 AAAGAAGGGG 0.919592 -19 TGTATTCATTATAAAAAGGGGGTCAATTACTT 9 82 0 ATAAAAGGGG 0.895777 -219 ATTTATGGACAAAAAAAGGACACGGATAACTG 9 134 0 AAAAAAGACA 0.946171 -167 TTTTGTCCATAAATAAAAGAGAATTCCAGTTA 9 152 1 AAATAAGAGA 0.905744 -149 GATGCCTCCCACAATGAAGAGACATTGACAAT 9 236 0 ACAAGAGAGA 0.898733 -65 TTGAAGCGGTATAATAAAGAGACGATGACAGG 9 268 1 ATAAAAGAGA 0.917835 -33 **** ** **** Masking position 3 Map Score: 24.2908 Number of sites scoring better than the average of aligned sites = 1620 Number in coding regions = 1161 Number in noncoding regions = 459 Number of orfs with sites within 600 bp upstream = 473 Fraction of orfs with sites within 600 bp upstream = 0.0759717 Motif number 2 TGGCACATGACTGTGACAATTTTTTAAAAATAAAA 1 23 0 CTTGACTTTT 0.966757 -150 TGATGCTTCCCTTTGACTCTATGTTAAAACGCTTA 1 91 0 CTTGACTTTT 0.966757 -82 AAGCATCATTCTCTGAACATATTTTTGTATCTTAC 1 118 1 CTTGAATTTT 0.92036 -55 AGACTTACGCCTGTGAATTCGTTGTCATGATTTTT 3 173 1 CTTGAACTGT 0.71577 -66 AAGAATTGACCTCCTCTTTTTACTAGTC 3 221 0 AATGACCTTT 0.970319 -18 AATTGTACGACATTTTCTTCTTATTTTAATGAAAA 5 75 0 CATTTCCTTT 0.640615 -205 AATGTCGTACAATTGTCCTTATTTTTGTCGAATTT 5 96 1 AATGTCTTTT 0.845773 -184 ATAGCGTTTACAATGAAATTGTATTCAAAATGAAT 5 232 1 CATGAATTTT 0.947602 -48 ATTGTATTCAAAATGAATACGTTTTCATTAGGAGG 5 249 1 AATGAACTTT 0.930748 -31 TTAATAAAGTAATTGACCCCCTTTTTATAATGAAT 9 76 1 AATGACCTTT 0.971226 -225 ATTTTGCTGTAACTGGAATTCTCTTTTATTTATGG 9 158 0 AATGGATTTT 0.642259 -143 CTTTTCTTCTATTTTACAGCATATTCATTCCTTAA 9 201 0 ATTTACCTTT 0.732217 -100 AATGAAGAGACATTGACAATCTTTTCTTCTATTTT 9 221 0 CATGACTTTT 0.978493 -80 ** **** * * ** Masking position 4 Map Score: 11.8386 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 745 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 CTGTTTTGTTTGTCGCTGTAAGATACAAAAAT 1 138 0 TCGCTGTAAG 0.995162 -35 TGTCATGATTTTTAGCTGTAAGGTCAGACTAG 3 195 1 TAGCTGTAAG 0.989164 -44 TGTGAAGTAATAAAGCTTTAAGTTAAAAGGAG 4 66 1 TAGCTTTAAG 0.968598 -32 TGGGTTTTAATTCCGCTGTAACACATGTGTAA 9 28 1 TCGCTGTAAC 0.990784 -273 ATTCAGATGATTTTGCTGTAACTGGAATTCTC 9 170 0 TTGCTGTAAC 0.964359 -131 CTCTTTATTATACCGCTTCAAGATGCCTCCCA 9 257 0 TCGCTTCAAG 0.962138 -44 * ********* Masking position 7 Map Score: 5.03285 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 46 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 GTAACACGTTATAAGGATAAACTGAATTTA 3 18 0 ATAAGGATAA 0.777722 -221 TTGAGGGAAAAAAACGGGAAGTTCATTCTC 3 70 1 AAAACGGGAA 0.917332 -169 GGTGCGCAAAAGAACGAGAATGAACTTCCC 3 85 0 AGAACGAGAA 0.779288 -154 TTTGTTGTGTAAAAGGGCAAATGTAAACGG 3 133 1 AAAAGGGCAA 0.951647 -106 CAGACTAGTAAAAAGAGGAGGTCAATTCTT 3 219 1 AAAAGAGGAG 0.796423 -20 GCTTTAAGTTAAAAGGAGAATGATAAAA 4 80 1 AAAAGGAGAA 0.987215 -18 TTTCATTAAAATAAGAAGAAAATGTCGTAC 5 76 1 ATAAGAAGAA 0.888556 -204 TTCGACAAAAATAAGGACAATTGTACGACA 5 98 0 ATAAGGACAA 0.932892 -182 ACATACGTTAATATGGAGAAACGTGAAAGA 5 151 1 ATATGGAGAA 0.891062 -129 CCGTAAAGAAAAGGGGAGATCTT 6 9 1 AAAAGGGGAG 0.951575 -15 GGACACGGATAACTGGAGAATCCGTGCCAA 9 119 0 AACTGGAGAA 0.730266 -182 TATGGACAAAAAAAGGACACGGATAACTGG 9 133 0 AAAAGGACAC 0.834642 -168 TATGCTGTAAAATAGAAGAAAAGATTGTCA 9 213 1 AATAGAAGAA 0.640361 -88 ********** Masking position 9 Map Score: 10.2607 Number of sites scoring better than the average of aligned sites = 1996 Number in coding regions = 1539 Number in noncoding regions = 457 Number of orfs with sites within 600 bp upstream = 515 Fraction of orfs with sites within 600 bp upstream = 0.0827176 Motif number 5 AAAAATCATGACAACGAATTCACAGGCGTAA 3 177 0 ACAAGAATTC 0.944178 -62 GGGTTTGTAAACTGTAAATTCGACAAAAATA 5 115 0 ACTGAAATTC 0.81285 -165 GTTTACAATGAAATTGTATTCAAAATGAATA 5 237 1 AAATGTATTC 0.857939 -43 CCTCCTAATGAAAACGTATTCATTTTGAATA 5 253 0 AAAAGTATTC 0.914263 -27 CCGTGCCAAAAAAGTGTATTCATTATAAAAA 9 97 0 AAAGGTATTC 0.975049 -204 TCCATAAATAAAAGAGAATTCCAGTTACAGC 9 157 1 AAAGGAATTC 0.975049 -144 AATTCCAGTTACAGCAAAATCATCTGAATTA 9 173 1 ACAGAAAATC 0.81285 -128 CTTCTATTTTACAGCATATTCATTCCTTAAT 9 200 0 ACAGATATTC 0.960375 -101 **** ****** Masking position 8 Map Score: 4.41949 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 285 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 TGTGCCAAAGTCCTCTTTACTTTCAATTGTA 1 51 1 TCCTTTTACT 0.718076 -122 GATTTGATCGCCATTTCAACGAGGTGAACTG 2 30 1 CCATTCAACG 0.972338 -23 ATTCAGTTTATCCTTATAACGTGTTACTGAT 3 21 1 TCCTATAACG 0.957892 -218 CAGCTAAAAATCATGACAACGAATTCACAGG 3 182 0 TCATACAACG 0.957841 -57 TTTATCATTCTCCTTTTAACTTAAAGCTTTA 4 76 0 TCCTTTAACT 0.934267 -22 TCACGTTTCTCCATATTAACGTATGTCTATA 5 146 0 CCATTTAACG 0.956483 -134 ATAGCCACCTCATTTCAAGGCT 7 3 0 TCATTCAAGG 0.911349 -20 CTAACCTTCGTCCTGTCATCGTCTCTTTATT 9 280 0 TCCTTCATCG 0.946358 -21 **** ****** Masking position 4 Map Score: 3.27915 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 277 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 TCTATGTTAAAACGCTTACAGTCCCTATAC 1 79 0 AACGCTTACA 0.934691 -94 TTTACATTTGCCCTTTTACACAACAAAAAG 3 130 0 CCCTTTTACA 0.915938 -109 TTCCAGTTTAACCGTTTACATTTGCCCTTT 3 144 0 ACCGTTTACA 0.99214 -95 TGTCGAATTTACAGTTTACAAACCCTATAG 5 121 1 ACAGTTTACA 0.960298 -159 AACCGAAAATAGCGTTTACAATGAAATTGT 5 224 1 AGCGTTTACA 0.979204 -56 ********** Masking position 6 Map Score: 1.77768 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 104 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 ACGGTTAAACTGGAAGACTTACGCCTGTGA 3 159 1 TGGAAGACTT 0.952715 -80 ACTATGAATATAAAAGACTTTTTTCATTAA 5 55 1 TAAAAGACTT 0.895513 -225 TGGAGAAACGTGAAAGATTTTGATAGTTAT 5 164 1 TGAAAGATTT 0.966572 -116 TGATAGTTATTGAATGAATTTGAATGATTT 5 184 1 TGAATGAATT 0.919638 -96 TGAATGAATTTGAATGATTTTAGTTGCCTA 5 194 1 TGAATGATTT 0.952784 -86 ********** Masking position 4 Map Score: 1.19716 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 135 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TTTTTTAAAAATAAAAAGGCTCCTGGTT 1 9 0 ATAAAAAGGC 0.982365 -164 CTTTTACACAACAAAAAGGCATGAGCAAAA 3 118 0 ACAAAAAGGC 0.953201 -121 ATCACTAAACATAAAAAAACCTCATGCATG 5 21 0 ATAAAAAAAC 0.84569 -259 TGTATTCATTATAAAAAGGGGGTCAATTAC 9 84 0 ATAAAAAGGG 0.927391 -217 GCCTCCCACAATGAAGAGACATTGACAATC 9 235 0 ATGAAGAGAC 0.914812 -66 AAGCGGTATAATAAAGAGACGATGACAGGA 9 271 1 ATAAAGAGAC 0.967072 -30 ********** Masking position 5 Map Score: 2.76188 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 189 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 ********** No masking Map Score: 3.48409e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: 3.48409e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: 3.48409e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0