AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_bsub_reg_300.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 ycnL 164 ycnL #2 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #3 mtlD 52 mannitol-1-phosphate dehydrogenase #4 ykvY 300 similar to Xaa-Pro dipeptidase #5 ykvZ 281 similar to transcriptional regulator (LacI family) #6 glcT 62 transcriptional antiterminator (BglG family) #7 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #8 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #9 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #10 moeB 50 molybdopterin biosynthesis protein #11 yknU 223 similar to ABC transporter (ATP-binding protein) #12 yknW 109 yknW #13 fruR 279 transcriptional regulator (DeoR family) #14 crh 23 catabolite repression HPr-like protein #15 yvcL 22 similar to hypothetical proteins #16 yvcJ 24 similar to hypothetical proteins #17 yvcI 300 similar to mutator MutT protein Motif number 1 CAACAAAACGAAACAGAAGGGACTCTGGTATAA 1 109 1 AAGAAGGGAC 0.932888 -56 TATAATAGACAGATGGAATAGAAAGTGAGGAAT 1 137 1 AAGAATAGAA 0.674523 -28 CAATTTTTTAAAAATAAAAAGGCTCCTGGTT 2 9 0 AAAAAAAGGC 0.878091 -164 TATACAATTGAAAGTAAAGAGGACTTTGGCACA 2 51 0 AAAAAGAGGA 0.980322 -122 TCTCCGCTAAAGCGAAGAAGATTTGATCGCC 3 9 1 AAGAAGAAGA 0.85341 -44 TAGAAATAAAAAAGGACTTTGTTCTC 5 4 1 AAAAAAAGGA 0.909209 -278 TATTTAATGCAGATAAAAAAGGACGATGTCGAG 5 34 0 AAAAAAAGGA 0.909209 -248 TAACCCAATTAAAATGAAGAAACCCATGTGATC 5 159 1 AAGAAGAAAC 0.770232 -123 AAGGGGATTTAGAAAGAAGGGAATCT 5 266 1 AAGAAGGGAA 0.950803 -16 CATATCGTACATAACGAACAGAATGCACGTCAA 6 31 0 AAGAACAGAA 0.754395 -32 TGATTGAGGGAAAAAAACGGGAAGTTCATTCTC 7 67 1 AAAACGGGAA 0.75566 -172 TTGGGTGCGCAAAAGAACGAGAATGAACTTCCC 7 85 0 AAAACGAGAA 0.869914 -154 GCCCTTTTACACAACAAAAAGGCATGAGCAAAA 7 118 0 AAAAAAAGGC 0.878091 -121 AGGTCAGACTAGTAAAAAGAGGAGGTCAATTCT 7 215 1 ATAAAGAGGA 0.745235 -24 GCTTGTCTGTTTATTAAAGAGGAATAGCTGTTC 9 57 0 TAAAAGAGGA 0.745235 -80 TGATAAGATGACATAAAAGATAAGGAGAACAGG 10 24 1 AAAAAGATAA 0.756346 -27 GGGTATCGATATAGTGAAGATGATAAATGTTGG 11 188 1 AAGAAGATGA 0.802485 -36 CCGTAAAGAAAAGGGGAGATCTT 14 5 1 AAAAAGGGGA 0.958401 -19 TTATTTATGGACAAAAAAAGGACACGGATAACT 17 135 0 AAAAAAGGAC 0.727281 -166 TTTTGTCCATAAATAAAAGAGAATTCCAGTTAC 17 152 1 AAAAAGAGAA 0.975539 -149 ATATGCTGTAAAATAGAAGAAAAGATTGTCAAT 17 212 1 AAGAAGAAAA 0.823342 -89 GATGCCTCCCACAATGAAGAGACATTGACAATC 17 235 0 AAGAAGAGAC 0.967801 -66 TTGAAGCGGTATAATAAAGAGACGATGACAGGA 17 268 1 AAAAAGAGAC 0.966313 -33 * * ******** Masking position 7 Map Score: 23.2882 Number of sites scoring better than the average of aligned sites = 1508 Number in coding regions = 1169 Number in noncoding regions = 339 Number of orfs with sites within 600 bp upstream = 362 Fraction of orfs with sites within 600 bp upstream = 0.0581433 Motif number 2 CTGTAATAATAAAAGCCCACCATCTTCATCCC 4 42 1 AAAACCCCCA 0.914362 -259 ATTAAATAAAAAAATCATCAAATGTTCGAAAG 5 59 1 AAAACATAAA 0.958671 -223 CCTCTCAACCAAAAACATGAAATTAAACCCTT 5 88 0 AAAACATAAA 0.958671 -194 GTCTTGCTGTAAAACCTCTCAACCAAAAACAT 5 102 0 AAAACTCCAA 0.725065 -180 CCTTTCAGCTAAAAACACAAAAAGATATCTGG 5 196 1 AAAACACAAA 0.921322 -86 ATATTGTATGAAACGCATTCCAGATCAAGGGG 5 240 1 AAACCATCCA 0.856467 -42 CTTACAGCTAAAAATCATGACAACGAATTCAC 7 185 0 AAAACATACA 0.959411 -54 TAGTTTCGTTAAAAGCATAGCAAAAGCAAAGG 9 102 0 AAAACATGCA 0.879126 -35 TATGAAAAGCCTTCAATATTGAAGGT 12 5 1 AAAACCTCAA 0.954035 -105 ATAAATTTCCAAAAACCTTCAATATTGAAGGC 12 19 0 AAAACCTCAA 0.954035 -91 AATTTATTAGAAAAACATGAAACTTTTTGATA 12 44 1 AAAACATAAA 0.958671 -66 TTAGGCAACTAAAATCATTCAAATTCATTCAA 13 193 0 AAAACATCAA 0.973772 -87 ATCATAACCGAAAAGCATTACACATGTGTTAC 17 45 0 AAAACATACA 0.959411 -256 **** *** *** Masking position 3 Map Score: 16.055 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 251 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 3 ATTTGATCGCCATTTCAACGAGGTGAACTGAC 3 31 1 CATTAAAGTG 0.967209 -22 AATTTCCGCTCCTTTTATCGGGATGAAGATGGTGG 4 58 0 CCTTATGGTG 0.859513 -243 AAATAAAATGCATTAGAAAATGAAGGCGTCGTGAA 4 203 1 CATTAATGAG 0.952726 -98 TTCTGTCTTCCATTGTAACAGGTTTTACCGGTGTT 4 243 0 CATTAAGGTT 0.883218 -58 CAGAACAATGCATTGCAAATGGCAGGGAGGAACAA 4 273 1 CATTAAGGAG 0.969667 -28 TGGGTTTCTTCATTTTAATTGGGTTATGTCTCACT 5 150 0 CATTAAGGTT 0.883217 -132 TGAATGCATTGAAAAAAGGTTTGACGTGCAT 6 7 1 CATTAAAGTT 0.854533 -56 TACAGAAAATCATTGTATGCTGAGGATACTTGGGG 11 62 0 CATTATTGGG 0.813219 -162 TTTCCAAAAACCTTCAATATTGAAGGCTTTTCATA 12 11 0 CCTTATTGAG 0.765608 -99 AGACTTTTTTCATTAAAATAAGAAGAAAATGTCGT 13 69 1 CATTAAAGAG 0.961211 -211 AATACGTTTTCATTAGGAGGTGAAGC 13 264 1 CATTGATGAG 0.760695 -16 AGCCTTGAAATGAGGTGGCTAT 15 3 1 CCTTAAAGTG 0.937087 -20 AAAGTGTATTCATTATAAAAAGGGGGTCAATTACT 17 83 0 CATTAAAGGG 0.94353 -218 **** ** ** ** Masking position 4 Map Score: 8.3684 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 366 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 AACCCAATTAAAATGAAGAAACCCATGTGA 5 160 1 AAATGAAGAA 0.819113 -122 GTTTTTAGCTGAAAGGAGAAGATCACATGG 5 182 0 GAAAGGAGAA 0.875332 -100 GTAACACGTTATAAGGATAAACTGAATTTA 7 18 0 ATAAGGATAA 0.828538 -221 GCTTTAAGTTAAAAGGAGAATGATAAAA 8 80 1 AAAAGGAGAA 0.971155 -18 GACATAAAAGATAAGGAGAACAGGTTTG 10 33 1 ATAAGGAGAA 0.980116 -18 AGGGAGTAACATATGTAGAATAAACGCTTA 11 95 0 ATATGTAGAA 0.7899 -129 TTTCATTAAAATAAGAAGAAAATGTCGTAC 13 76 1 ATAAGAAGAA 0.906595 -204 TTCGACAAAAATAAGGACAATTGTACGACA 13 98 0 ATAAGGACAA 0.87748 -182 ACATACGTTAATATGGAGAAACGTGAAAGA 13 151 1 ATATGGAGAA 0.971154 -129 GGACACGGATAACTGGAGAATCCGTGCCAA 17 119 0 AACTGGAGAA 0.827463 -182 ********** Masking position 7 Map Score: 8.58286 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 314 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TTTTTGTATCTTACAGCGACAAACAAAACAG 2 139 1 TTACAGCGAA 0.985836 -34 GCTTTTATTATTACAGCTCTATCATAGGCTG 4 27 0 TTACAGCTCA 0.959312 -274 TTGAGAGGTTTTACAGCAAGACAGCTGCCAC 5 112 1 TTACAGCAAA 0.978261 -170 GATCTTCTCCTTTCAGCTAAAAACACAAAAA 5 188 1 TTTCAGCTAA 0.93048 -94 TAGTCTGACCTTACAGCTAAAAATCATGACA 7 195 0 TTACAGCTAA 0.984728 -44 TACACATGTGTTACAGCGGAATTAAAACCCA 17 28 0 TTACAGCGGA 0.962189 -273 AGAATTCCAGTTACAGCAAAATCATCTGAAT 17 171 1 TTACAGCAAA 0.97826 -130 ********* * Masking position 5 Map Score: 7.89713 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 44 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 AGCGACAAACAAAACAGGGAGGGTTTATAT 2 153 1 AACAGGGAGG 0.982713 -20 TTTGATCGCCATTTCAACGAGGTGAACTGAC 3 32 1 ATCAACGAGG 0.924031 -21 GTAACGTTCAATCGCAGGGGGGTTGTTCCGTT 4 145 0 ATCAGGGGGG 0.993703 -156 TGCATTGCAAATGGCAGGGAGGAACAAGAA 4 281 1 ATCAGGGAGG 0.992405 -20 TTGTTAGATATTCTCAAGGAGGTTTTGAA 12 91 1 TTCAAGGAGG 0.929254 -19 AAAGACAAGTCAGGGGGGAGAAAG 16 7 1 AACAGGGGGG 0.985642 -18 TGTATTCATTATAAAAAGGGGGTCAATTACTT 17 82 0 ATAAAGGGGG 0.908343 -219 ** ******** Masking position 6 Map Score: 5.79089 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 30 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TTGTTGCTGTTCAACACATTTTCACATTTTTTAT 1 81 0 TAAACATTCA 0.939932 -84 TGACTCTATGTTAAAACGCTTACAGTCCCTATAC 2 79 0 TAAACGTACA 0.851004 -94 TGTTTGCCTTTCACGACGCCTTCATTTTCTAATG 4 213 0 TACACGTTCA 0.963846 -88 CTAAAAATCATGACAACGAATTCACAGGCGTAAG 7 176 0 TACACGTTCA 0.918796 -63 GTATTCATTTTGAATACAATTTCATTGTAAACGC 13 235 0 TAAACATTCA 0.921537 -45 GTATTCAAAATGAATACGTTTTCATTAGGAGGTG 13 252 1 TAAACGTTCA 0.499634 -28 AGAATTCCAGTTACAGCAAAATCATCTGAATTAA 17 171 1 TACGCAATCA 0.784962 -130 TTCTTCTATTTTACAGCATATTCATTCCTTAATT 17 199 0 TACGCATTCA 0.952424 -102 * ** *** **** Masking position 3 Map Score: 4.31061 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 51 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 TCTATGTTAAAACGCTTACAGTCCCTATAC 2 79 0 AACGCTTACA 0.973432 -94 TTCCAGTTTAACCGTTTACATTTGCCCTTT 7 144 0 ACCGTTTACA 0.981308 -95 ATGTAGAATAAACGCTTACAGAAAATCATT 11 83 0 AACGCTTACA 0.973432 -141 TGTCGAATTTACAGTTTACAAACCCTATAG 13 121 1 ACAGTTTACA 0.909586 -159 AACCGAAAATAGCGTTTACAATGAAATTGT 13 224 1 AGCGTTTACA 0.966133 -56 ********** Masking position 6 Map Score: 2.20609 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 45 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 CGCCATTTCAACGAGGTGAACTGAC 3 38 1 ACGAGGTGAA 0.864221 -15 TCCCGATAAAAGGAGCGGAAATTCCCAAAA 4 70 1 AGGAGCGGAA 0.959674 -231 ATACAGGAAGAGGAGCAGGAAATAAAATGC 4 184 1 AGGAGCAGGA 0.882631 -117 GAGCAAAATTGGGTGCGCAAAAGAACGAGA 7 96 0 GGGTGCGCAA 0.722828 -143 TAGTAAAAAGAGGAGGTCAATTCTT 7 224 1 AGGAGGTCAA 0.957582 -15 AATGTTGGAAAGGTGCTGGAT 11 213 1 AGGTGCTGGA 0.882631 -11 CGTTTTCATTAGGAGGTGAAGC 13 268 1 AGGAGGTGAA 0.977681 -12 AGACAAGTCAGGGGGGAGAAAG 16 13 1 GGGGGGAGAA 0.862414 -12 CATTATAAAAAGGGGGTCAATTACTTTATT 17 78 0 AGGGGGTCAA 0.938237 -223 ********** Masking position 10 Map Score: 2.54042 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 374 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 10 ATTCATCAGCAAACGGAACAACCCCCCTGCGA 4 134 1 AACGAACAAC 0.954024 -167 TACTGTCAGTATACAGGAAGAGGAGCAGGAAA 4 174 1 AACGGAAGAG 0.743418 -127 TTACAATGGAAGACAGAACAATGCATTGCAAA 4 260 1 AACGAACAAT 0.698542 -41 GTAAACGGTTAAACTGGAAGACTTACGCCTGT 7 155 1 AACGGAAGAC 0.945964 -84 CAATATGCAAATACTGAACAGCTATTCCTCTT 9 42 1 AACGAACAGC 0.976059 -95 CCTCTTTAATAAACAGACAAGCAGTAGCGTTG 9 68 1 AACGACAAGC 0.829009 -69 AAACCGGACGGCATTTCAGCCG 11 1 1 AACGGACGGC 0.985417 -223 AAATACAGAAAAACCGGACGGCTGAAATGCCG 11 19 0 AACGGACGGC 0.985417 -205 TTATTAATCATAACCGAAAAGCATTACACATG 17 51 0 TACGAAAAGC 0.765872 -250 * ** ******* Masking position 3 Map Score: 2.47891 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 393 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 TTTAGAGACGGAGACAAGTAAGTGGATGAT 1 53 1 GAGACAAGTA 0.940888 -112 GCTGTAAGGTCAGACTAGTAAAAAGAGGAG 7 209 1 CAGACTAGTA 0.913244 -30 TACTTGTCATCTGACAAGCACGGCGTACTA 8 17 0 CTGACAAGCA 0.949898 -81 TGCTTGTCAGATGACAAGTACGGTTGTATG 8 27 1 ATGACAAGTA 0.910312 -71 CTTTAATAAACAGACAAGCAGTAGCGTTGA 9 71 1 CAGACAAGCA 0.972508 -66 AAAGACAAGTCAGGGGGGAGA 16 2 1 AAGACAAGTC 0.873807 -23 ********** Masking position 4 Map Score: 1.03439 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 60 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CTCCGTCTCTAAAATCCTCTACGCTTAAAT 1 36 0 AAAATCCTCT 0.961999 -129 GTCATGTGCCAAAGTCCTCTTTACTTTCAA 2 47 1 AAAGTCCTCT 0.968082 -126 AAATGGCGATCAAATCTTCTTCGCTTTAGC 3 16 0 CAAATCTTCT 0.776448 -37 TGTCGAGAACAAAGTCCTTTTTTATTTCTA 5 11 0 AAAGTCCTTT 0.885149 -271 ATTAAATAAAAAAATCATCAAATGTTCGAA 5 59 1 AAAATCATCA 0.700911 -223 TTTAATGAAAAAAGTCTTTTATATTCATAG 13 56 0 AAAGTCTTTT 0.782052 -224 CAGTTACAGCAAAATCATCTGAATTAAGGA 17 178 1 AAAATCATCT 0.918611 -123 ********** Masking position 3 Map Score: 1.08348 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 179 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 13 TCATACACCCTCTTCATTAAGATCTAT 1 8 1 CCCTCTTCAT 0.946198 -157 TAAAAGCCCACCATCTTCATCCCGATAAAA 4 51 1 CCATCTTCAT 0.942167 -250 TATTTCCTGCTCCTCTTCCTGTATACTGAC 4 178 0 TCCTCTTCCT 0.90887 -123 TTTGTTCTCGACATCGTCCTTTTTTATCTG 5 28 1 ACATCGTCCT 0.861436 -254 AGATTCCCTTCTTTCTAAATCCCCTT 5 266 0 CCTTCTTTCT 0.843896 -16 TCGAACCATCTCCCTCATGATGTTA 9 6 1 CCATCTCCCT 0.948389 -131 CTAACCTTCGTCCTGTCATCGTCT 17 287 0 CCTTCGTCCT 0.965571 -14 ********** Masking position 4 Map Score: 1.61522 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 189 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 14 ********** No masking Map Score: 3.31356e-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 15 CGGAAATTCCCAAAACCGTTAAGAGCATAA 4 85 1 CAAAACCGTT 0.887269 -216 AAACACCGGTAAAACCTGTTACAATGGAAG 4 242 1 AAAACCTGTT 0.860925 -59 AACATGAAATTAAACCCTTTCGAACATTTG 5 77 0 TAAACCCTTT 0.861103 -205 GAATGCACGTCAAACCTTTTTTCAATGCAT 6 14 0 CAAACCTTTT 0.953446 -49 CAAACCTGTTCTCCTTATCT 10 41 0 CAAACCTGTT 0.970009 -10 TTACAGTTTACAAACCCTATAGACATACGT 13 129 1 CAAACCCTAT 0.888668 -151 ********** Masking position 4 Map Score: 0.283418 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 150 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542