AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inagC_ecoli_bsub_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 nagD 47 N-acetylglucosamine metabolism #2 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #3 nagB_nagE 332 nagB: glucosamine-6-phosphate deaminase, nagE: PTS system, N-acetylglucosamine-specific enzyme IIABC #4 manX 300 PTS enzyme IIAB, mannose-specific #5 manY 62 PTS enzyme IIC, mannose-specific #6 glmS 161 L-glutamine:D-fructose-6-phosphate aminotransferase #7 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #8 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #9 glmS 300 L-glutamine-D-fructose-6-phosphate amidotransferase #10 ybfT 218 similar to glucosamine-6-phosphate isomerase #11 yflF 171 similar to phosphotransferase system enzyme II #12 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #13 xylR 300 transcriptional regulator #14 yqgQ 109 yqgQ #15 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #16 yutF 28 similar to N-acetyl-glucosamine catabolism #17 yutE 23 yutE #18 yutD 81 yutD #19 nagA 181 N-acetylglucosamine-6-phosphate deacetylase Motif number 1 TGGTTTAGCCAGTAAAAGGGAGTGATAATAACGA 3 189 0 AAAAAGGGTG 0.978894 -144 CTCCATGGTTGTTAAACGGGAGTTAAACATATCA 4 16 1 GAAACGGGTT 0.722953 -285 AGACTTAAGTGTGAAAACTGAGTGATAATCAACA 5 18 0 GAAAATGGTG 0.824565 -45 CGGCTAACCCGGTCACATGGGATGAGGAGATAAC 6 18 1 GCACAGGATG 0.752421 -144 TATCGTTGTCGGTCAACCTGTATGCCCGTTTTTT 6 119 0 GCAACTGATG 0.693726 -43 TGAATAAACAGGAAAACAGGGGGGTTTTATATCA 7 53 0 GAAACGGGGG 0.712565 -248 AATTTTCTGCAGACAAAAGGCGTGACGATGGTCG 7 143 1 ACAAAGGGTG 0.985391 -158 GAATTTCTTCAAACCAAGGGGGTGACTCCTTGAA 9 166 1 ACCAAGGGTG 0.932985 -135 CATATTGGGAGGGCAAATGGTATTATGGTCTCAA 10 50 0 GCAAAGGATT 0.782197 -169 GTATATTTGAAAAAAAAGGGTATGAGGGGGATGG 11 146 1 AAAAAGGATG 0.962924 -26 TGATTGAGGGAAAAAAACGGGAAGTTCATTCTCG 12 67 1 AAAAAGGAAG 0.786249 -172 AAAAGGCATGAGCAAAATTGGGTGCGCAAAAGAA 12 101 0 AAAAATGGTG 0.860999 -138 CCTTTTACACAACAAAAAGGCATGAGCAAAATTG 12 115 0 AAAAAGGATG 0.962924 -124 TTTAAAGATTAAACAAATGGAGTGGATGAAGTGG 13 179 1 ACAAAGGGTG 0.985391 -122 ATAAACCTGTATTAAAATGGTGTTCCATTTAATA 15 35 0 AAAAAGGGTT 0.853181 -155 ATATGGATGTACAAAACAGGAAAGGAGCAATAGA 15 165 1 AAAACGGAAG 0.685203 -25 CAACTGGAAAGCCACAGGAGTGTTGGAT 16 9 1 ACCACGGGTG 0.891765 -20 ATATACACAAAGGGGATGCTGTC 17 5 1 ACAAAGGATG 0.974208 -19 TGTGTAGGGTAGCCAAATCGCATGATTTATTCTT 18 28 1 ACAAACGATG 0.747412 -54 * **** ** *** Masking position 10 Map Score: 16.9744 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 582 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 2 TTTACTGGCTAAACCAGAAAACTTATTTTATCATT 3 207 1 AACCAAAACA 0.779351 -126 CCACAAGCAGTAACTATAAAAATAACCCCACTCTC 6 64 1 TACTAAAAAA 0.842887 -98 ATTGATCGAAATAAGAGCAAAAACATCCACCTGAC 7 86 1 AAAGAAAAAA 0.933825 -215 TCTGTCCATTTCACGATGAAAAAAATGTAGTTTTT 7 227 1 TACGAAAAAA 0.931042 -74 TCTTATTTTCTCAATAGGAAAAGAAGACGGGATTA 9 11 1 TAATAAAAAA 0.791693 -290 TTGTAAAAGGAGACGAAGAAAGTCAAATTTCAAGG 9 257 0 AACGAAAAGA 0.789539 -44 AACTGTCTTAAAAATAGGAAACACACGGACCTGGG 11 58 1 AAATAAAACA 0.788056 -114 CTGTAAGGTCAGACTAGTAAAAAGAGGAGGTCAAT 12 210 1 AACTAAAAAA 0.887843 -29 TTAGTTTGTTTAAACAACAAACTAATAGGTGATGT 13 31 0 TAACAAAACA 0.629052 -270 ACGAGGTTATATAAGATGAAAATAAGTTAGTTTGT 13 57 0 AAAGAAAAAA 0.933825 -244 TGTTCATAAAAAACTAAAAAAAATATTGAAAATAC 13 94 0 AACTAAAAAA 0.887843 -207 ATACTTAATTTAAAGATTAAACAAATGGAGTGGAT 13 171 1 TAAGAAAACA 0.863794 -130 TTCACCTATTTCAAGAGCAAAATTATCTGAA 13 280 1 TAAGAAAAAA 0.905341 -21 GAAACACTTAAAACGAAAAAAATAAACCTGTATTA 15 55 0 AACGAAAAAA 0.952201 -135 ACTAGTCTGAAAAAGAGTAAAATAAAGGTATTCAA 19 135 1 AAAGAAAAAA 0.933825 -47 * **** **** * Masking position 9 Map Score: 11.0521 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 130 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 GTATGCCCGTTTTTTCGGGCGCCCCGAGCCTTG 6 101 0 TTCGGGCGCC 0.982006 -61 GACATAAGCCTTTTGCCGGCGGTCCTTTTTTAA 8 46 1 TTCCGGCGGT 0.99342 -147 TCCGGGCGCTTAGTTCGGGCGCTATAATTATAG 9 55 0 TTCGGGCGCT 0.989731 -246 AACTAAGCCTTTTTCCGGGCGCTTAGTTCGGGC 9 68 0 TTCGGGCGCT 0.98973 -233 ATTTCGCGGATCCTCCCGGCTGAGTGTGCAGAT 9 122 1 TTCCGGCTGA 0.885578 -179 TTTGAAGAAATTCTTACGGCTGTGATCTGCACA 9 146 0 TTACGGCTGT 0.906922 -155 ATTGACAGTTTGATAAGGGCGGTGCTAAATTCG 10 128 1 TTAGGGCGGT 0.973563 -91 TCTATACCAATTTTCCCGGGGGTATTTCTTTTT 11 94 0 TTCCGGGGGT 0.956402 -78 ATGTTCCTCCTGTTCCGGGCTGCCCCGAGCTTG 19 14 1 TTCGGGCTGC 0.971982 -168 * * ******** Masking position 4 Map Score: 8.67836 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 376 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 CTTTTGTGAGTTTTGTCACCAAATATCGTT 3 164 1 TTTTGTCACC 0.917941 -169 CAGGGGGGTTTTATATCAGCAGGATCTATG 7 41 0 TTATATCAGC 0.906295 -260 TCGTCACGCCTTTTGTCTGCAGAAAATTAA 7 141 0 TTTTGTCTGC 0.914198 -160 AAAATGGCGCTTTCGTCAGCGGGGATAATC 7 177 1 TTTCGTCAGC 0.947235 -124 AAAACTACATTTTTTTCATCGTGAAATGGA 7 231 0 TTTTTTCATC 0.673089 -70 GGCAAAAGGCTTATGTCAGCCCTTTCAGCA 8 33 0 TTATGTCAGC 0.972569 -160 TTGACAAAGGTTTGATCAGCGATATCCACT 13 208 0 TTTGATCAGC 0.830425 -93 AAGCTGGCTTTTTTGTCAGCGTTTTCTTCT 14 29 1 TTTTGTCAGC 0.98542 -81 GTTTTCATTGTTATTTCAGCCAATAGCAAT 15 98 0 TTATTTCAGC 0.906295 -92 ********** Masking position 6 Map Score: 6.74648 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 252 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 AAGGAGCCAGGGCAGGGATAACAA 2 4 0 GGCAGGGAAA 0.941244 -56 GGGTTCTCGTAGGGGGAATAAG 3 2 0 AGGGGGAAAA 0.961614 -331 GCCAGTAAAAGGGAGTGATAATAACGATATT 3 185 0 GGGAGTGAAA 0.764186 -148 TACTGCTTGTGGGAGGGAGATTATGTTATCT 6 45 0 GGGAGGGAAT 0.942469 -117 CGCTTTCGTCAGCGGGGATAATCCGTTATTG 7 184 1 AGCGGGGAAA 0.948871 -117 TTACAATCTTAGGAGGAAGAAAAAT 9 286 1 AGGAGGAAAA 0.958545 -15 CTTTCATATTGGGAGGGCAAATGGTATTATG 10 57 0 GGGAGGGCAA 0.885653 -162 TTAAAAAGAAAGCGGGAATGACAG 11 4 0 AGCGGGAAGA 0.647578 -168 AGGTGGAATATGGAAAGGAAG 14 1 1 AGGTGGAAAT 0.6566 -109 AGCCCGGAACAGGAGGAACATATC 19 4 0 AGGAGGAAAT 0.902057 -178 ATTTTATAAAAGGGGGGAAAACACCTCAGCT 19 94 1 AGGGGGGAAA 0.979443 -88 ******** ** Masking position 5 Map Score: 7.13394 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 133 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 TATTTTATCATTCAAAAAATCAGGTCGGATTGA 3 230 1 TTCAAAACAG 0.853437 -103 GACGCCTGTCTGCGCAAATCCAGGTTACGCTTA 3 261 1 TGCGAAACAG 0.679169 -72 TTAACTCCCGTTTAACAACCATGGAGTATAG 4 9 0 TTTACAAATG 0.491877 -292 AAGGTAAATCTTTGCCAAATCAGAGGCGTCTCT 4 49 0 TTTGCAACAG 0.918307 -252 GTCACATTCGTTTGCAAAGGAAGGTAAATCTTT 4 69 0 TTTGAAAAAG 0.938352 -232 TGCAACTAAGTTTGAAAAATCAGAATTAAAAAA 8 71 0 TTTGAAACAG 0.960672 -122 TCTTTTCCTATTGAGAAAATAAGA 9 2 0 TTGAAAAAAG 0.575115 -299 ATCTAGATTATTTAAAAAGAAAGCGGGAATGAC 11 13 0 TTTAAAAAAG 0.877865 -159 ATATGGTATATTTGAAAAAAAAGGGTATGAGGG 11 141 1 TTTGAAAAAG 0.938352 -31 AATTTCATAAATTCAGTTTATCCTTA 12 4 1 TTCAAAACAG 0.853437 -235 TGATCAAACCTTTGTCAAAAAAGTAAATCAAAA 13 220 1 TTTGCAAAAG 0.875072 -81 AGGTGGAATATGGAAAGGAAGCTGGCTTTTT 14 9 1 TATGAAAAAG 0.756622 -101 TACAGGTTCATATGAAAAAACTGTTT 15 4 0 TATGAAACTG 0.593513 -186 TTTCCCCCCTTTTATAAAATCTGTTTTAGGTTC 19 81 0 TTTAAAACTG 0.771468 -101 **** *** *** Masking position 7 Map Score: 6.40683 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 215 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 GAAAGGTAAAATATCCTTGTCACATTCGTTTG 4 88 0 ATATCCTTCA 0.814903 -213 TTCTGGCCGGCTAACCCGGTCACATGGGATGA 6 11 1 CTAACCGTCA 0.760924 -151 AAGAGCAAAAACATCCACCTGACGCTTAAATT 7 98 1 ACATCCCTGA 0.709751 -203 AATTTATCCTCTGTCCATTTCACGATGAAAAA 7 218 1 CTGTCCTTCA 0.918077 -83 TCGATAACCTCCATCCTCGTCAACTAAGCCTT 9 90 0 CCATCCCTCA 0.982757 -211 GAATTTAGCACCGCCCTTATCAAACTGTCAAT 10 128 0 CCGCCCTTCA 0.799777 -91 ACCCATCCCCCTCATACCCTTTTT 11 158 0 CCATCCCTCA 0.982757 -14 TTCATCTTATATAACCTCGTCAGTATTTTCAA 13 72 1 ATAACCCTCA 0.876011 -229 TTGATCAGCGATATCCACTTCATCCACTCCAT 13 195 0 ATATCCCTCA 0.939771 -106 TTCTTCTTGACTGACCGCTTCCTTATGAATAC 14 52 1 CTGACCCTCC 0.772043 -58 ATTCATTGCCCCGTCCCCATCAATTGCTAAAG 18 59 0 CCGTCCCTCA 0.981584 -23 ****** * *** Masking position 10 Map Score: 5.41806 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 342 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 TAAGCGCCACTATAAAAGCACA 1 3 0 TATAAAAGCA 0.559541 -45 TGGTTTAGCCAGTAAAAGGGAGTGATAATA 3 193 0 AGTAAAAGGG 0.762382 -140 GTGTTAACGATAATAAAGGAGGTAGCAA 4 283 1 TAATAAAGGA 0.648009 -18 AAATCAGAATTAAAAAAGGACCGCCGGCAA 8 58 0 TAAAAAAGGA 0.907498 -135 TTTTTCTATGGATAAAAGGGATATTGGAGG 8 166 1 GATAAAAGGG 0.845116 -27 CTCCTAAGATTGTAAAAGGAGACGAAGAAA 9 271 0 TGTAAAAGGA 0.899226 -30 ATGGTCTCAATGAAAAAGAACGGATTGCAT 10 30 0 TGAAAAAGAA 0.719489 -189 GAAAATTTGTTATAAAAGAAGGATACAAAT 10 88 0 TATAAAAGAA 0.73822 -131 ACGGACCTGGGAAAAAAGAAATACCCCCGG 11 82 1 GAAAAAAGAA 0.494268 -90 GTATATTTGAAAAAAAAGGGTATGAGGGGG 11 146 1 AAAAAAAGGG 0.779128 -26 CTTTTTGTTGTGTAAAAGGGCAAATGTAAA 12 130 1 TGTAAAAGGG 0.934725 -109 ACATTAGATTTAATAAAGGGAAGATTCGCT 13 128 1 TAATAAAGGG 0.747117 -173 AAACAGATTTTATAAAAGGGGGGAAAACAC 19 88 1 TATAAAAGGG 0.940277 -94 ATCACTAGTCTGAAAAAGAGTAAAATAAAG 19 132 1 TGAAAAAGAG 0.804542 -50 ********** Masking position 5 Map Score: 8.64437 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 164 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 9 TAAAAAATATTGCCCTGAGCAAGGAGCCAG 2 25 0 TGCCCTGAGC 0.976456 -35 TTTTTTCGGGCGCCCCGAGCCTTGTAGAGA 6 95 0 CGCCCCGAGC 0.989848 -67 GCGCGTGTGACCCGTCCTGAATAGCGT 7 8 1 TGACCCGTCC 0.952003 -293 AATTCATTGCCCCGTCCCCATCAATTG 18 65 0 TGCCCCGTCC 0.990437 -17 TGTTCCGGGCTGCCCCGAGCTTGCTCACAA 19 24 1 TGCCCCGAGC 0.995401 -158 ********** Masking position 5 Map Score: 4.53953 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 32 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 AAATTGTTCAATAACGGATTATCCCCGCTG 7 193 0 ATAACGGATT 0.930109 -108 CTGTAATTTGAGAACGAATTTAAACCGCTT 7 270 0 AGAACGAATT 0.936129 -31 TCAATGAAAAAGAACGGATTGCATACAGAA 10 24 0 AGAACGGATT 0.934921 -195 TCCTTCTTTTATAACAAATTTTCAGAAATT 10 95 1 ATAACAAATT 0.841455 -124 GATACTTGTCATTACGAATTTAGCACCGCC 10 145 0 ATTACGAATT 0.708673 -74 AAAAATCATGACAACGAATTCACAGGCGTA 12 178 0 ACAACGAATT 0.936129 -61 AAGTGTTTCAACAACAAATTGCTATTGGCT 15 81 1 ACAACAAATT 0.851397 -109 GCTTGAACCTAAAACAGATTTTATAAAAGG 19 77 1 AAAACAGATT 0.67308 -105 ********** Masking position 4 Map Score: 2.64304 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 79 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 AAATAAAAATACGGCTTGAAACGAGCCAAAT 3 34 0 ACGCTTGAAA 0.940133 -299 TTAAACCGCTTCACCTTGAAAAAACTACATT 7 250 0 TCCCTTGAAA 0.987534 -51 CTTCATGAAGTCTCCTTGAAATCAGAAGATA 8 124 1 TCCCTTGAAA 0.987515 -69 CAAGGGGGTGACTCCTTGAACAAAGAGAAAT 9 180 1 ACCCTTGAAC 0.961402 -121 CGATTGAAAGTCCCCTTGAAATTTGACTTTC 9 244 1 TCCCTTGAAA 0.987534 -57 ** ******** Masking position 6 Map Score: 2.57143 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 TTTGCAAAGGAAGGTAAATCTTTGCCAAAT 4 62 0 AAGGTAAATC 0.730604 -239 TTCGATATCTAAAATAAATCGCGAAACGCA 4 176 1 AAAATAAATC 0.948484 -125 CGACGATTCAAAAATACATCTGGCACGTTG 4 251 1 AAAATACATC 0.793373 -50 TATCCATAGAAAAATATATCCTAAATATCT 8 150 0 AAAATATATC 0.721497 -43 TCCTTGAACAAAGAGAAATCACATGATCTT 9 192 1 AAGAGAAATC 0.868565 -109 AGATTATTTAAAAAGAAAGCGGGAATGACA 11 12 0 AAAAGAAAGC 0.782175 -160 GACCTGGGAAAAAAGAAATACCCCCGGGAA 11 85 1 AAAAGAAATA 0.575675 -87 CTTTGTCAAAAAAGTAAATCAAAAGTTATT 13 229 1 AAAGTAAATC 0.876026 -72 AGTTATTATTAAAAGAAATCCTTAAAAATT 13 252 1 AAAAGAAATC 0.94511 -49 TAAAACGAAAAAAATAAACCTGTATTAAAA 15 52 0 AAAATAAACC 0.793373 -138 CAATTGCTAAAGAATAAATCATGCGATTTG 18 41 0 AGAATAAATC 0.776147 -41 ********** Masking position 6 Map Score: 4.13052 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 95 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 13 CGCAAATTAAACGCGTGTCTTTTGTGAGTT 3 146 1 ACGCGTGTCT 0.933492 -187 GGTCGGATTGACGCCTGTCTGCGCAAATCC 3 252 1 ACGCCTGTCT 0.964096 -81 CATATCAGAGACGCCTCTGATTTGGCAAAG 4 43 1 ACGCCTCTGA 0.956485 -258 GCGCGTGTGACCCGTCCTGA 7 1 1 GCGCGTGTGA 0.948244 -300 AGAAATTCTTACGGCTGTGATCTGCACACT 9 144 0 ACGGCTGTGA 0.956485 -157 TGGAAGACTTACGCCTGTGAATTCGTTGTC 12 169 1 ACGCCTGTGA 0.989667 -70 ********** Masking position 6 Map Score: 2.33491 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 80 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 TATTCCCCCTACGAGAACCCTATTTGGCTCG 3 13 1 AGAGAACCCT 0.913528 -320 AGCAGGATCTATGTGAACGCTATTCAGGACG 7 23 0 AGTGAACGCT 0.961083 -278 AAAAGGGCAAATGTAAACGGTTAAACTGGAA 12 143 1 AGTAAACGGT 0.872289 -96 GTCAGTCAAGAAGAAAACGCTGACAAAAAAG 14 36 0 AGAAAACGCT 0.982326 -74 CCGCTTCCTTATGAATACGCTTATGATAGTT 14 66 1 AGAATACGCT 0.932027 -44 TGAAATAACAATGAAAACGCTTAACACAACT 15 110 1 AGAAAACGCT 0.982326 -80 * ********* Masking position 7 Map Score: 1.24806 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 44 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 ********** No masking Map Score: 1.08169e-11 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