AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_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 ydiG 125 similar to molybdopterin precursor biosynthesis #2 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #3 moeB 50 molybdopterin biosynthesis protein #4 narQ 245 alternate gene name: narAA #5 ywmE 93 ywmE #6 ywmD 300 similar to hypothetical proteins from B. subtilis Motif number 1 AAAGCATAGCAAAAGCAAAGGCTCAACGCTAC 2 91 0 AAAAGAAGGC 0.993644 -46 AAGATGACATAAAAGATAAGGAGAACAGGTTT 3 28 1 AAAAGTAGGA 0.924636 -23 CACGTGTTATAAAAGGAACGGCGGCTAAATGC 4 80 1 AAAAGACGGC 0.981877 -166 AACGGCGGCTAAATGCTTAGGCGTCCTGCCTA 4 96 1 AAATGTAGGC 0.932387 -150 ATTCTGAGACACAAAAAGAGCCCTCTATATAA 4 161 0 ACAAAAAGCC 0.811081 -85 GAGTGTGAAAAAATATAAAGGCAGGAACATTG 4 208 1 AAATAAAGGC 0.966558 -38 GGAACCTAAAGATCAGGCGCTCCCCCAG 5 7 1 TAAAGTAGGC 0.865545 -87 TTTTTAAACCAATAAAAAAGGCGCCTGGGGGA 5 31 0 AATAAAAGGC 0.930998 -63 TTTGTTACATACAAAAAGAGGCT 6 2 0 ACAAAAAGGC 0.975829 -299 GAAATGGCTAAAAATGAACGGCATTTCAAGCG 6 151 1 AAAATACGGC 0.893406 -150 GAAAATGCAAAAAGATATAGGACATGCTGCCT 6 213 0 AAAGAAAGGA 0.842836 -88 GGAAAATATGAAAAAGAAAGGAAGTAATCAT 6 280 1 AAAAAAAGGA 0.962568 -21 ***** * **** Masking position 10 Map Score: 13.0858 Number of sites scoring better than the average of aligned sites = 1241 Number in coding regions = 1025 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 TTAAAAGCATAGCAAAAGCAAAGGCTCAAC 2 96 0 AGCAAAAGCA 0.934875 -41 TTAGGCAGGACGCCTAAGCATTTAGCCGCC 4 99 0 CGCCTAAGCA 0.881018 -147 TTAGGCGTCCTGCCTAAACACCGCCGTCAT 4 112 1 TGCCTAAACA 0.924643 -134 AATTCTGAGACACAAAAAGAGCCCTCTATA 4 164 0 CACAAAAAGA 0.941422 -82 GGAACCTAAAGATCAGGCGCTC 5 3 1 AACCTAAAGA 0.896285 -91 TTTTGTTACATACAAAAAGAGGCT 6 5 0 TACAAAAAGA 0.910878 -296 TTTTGTATGTAACAAAAACTTCAAAACTAA 6 18 1 AACAAAAACT 0.635935 -283 ATAATCAAGGCGAAAAAAGAATGAATGATC 6 94 1 CGAAAAAAGA 0.775111 -207 CCGCCCAGAAAGCATAAACAGCTTGTGTGA 6 122 0 AGCATAAACA 0.969202 -179 AATACGAAAATGCAAAAAGATATAGGACAT 6 220 0 TGCAAAAAGA 0.9653 -81 TTCGTATTCTAGCATAAAGAAGAATCCAAC 6 242 1 AGCATAAAGA 0.974063 -59 ********** Masking position 6 Map Score: 8.95059 Number of sites scoring better than the average of aligned sites = 1370 Number in coding regions = 1202 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 3 ACTTATTATAGCAGAGGTGAAATAAT 1 7 0 GCAGAGGTGA 0.993756 -119 CAGACAAGCAGTAGCGTTGAGCCTTTGCTT 2 81 1 GTAGCGTTGA 0.873697 -56 TTTAACGAAACTAGAGGTGAGATGAT 2 121 1 CTAGAGGTGA 0.952658 -16 AGTCCTTTATACAGAGGTGTCTCAGCGTGT 4 11 1 ACAGAGGTGT 0.973287 -235 GGATGTGATGACGGCGGTGTTTAGGCAGGA 4 119 0 ACGGCGGTGT 0.96112 -127 CAGGAACATTGCGGAGGGGAAGAGACA 4 229 1 GCGGAGGGGA 0.979754 -17 ********** Masking position 6 Map Score: 2.2927 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 358 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 TGTTTATTAAAGAGGAATAGCTGTTCAGTATTT 2 50 0 AAGATAGCTG 0.962816 -87 CTCTTTAATAAACAGACAAGCAGTAGCGTTGAG 2 69 1 ACAAAAGCAG 0.986899 -68 CGTTAAAAGCATAGCAAAAGCAAAGGCTCAACG 2 95 0 AAGAAAGCAA 0.856362 -42 AAGATGACATAAAAGATAAGGAGAACAGGTTTG 3 28 1 AAAAAAGGAG 0.847814 -23 AAAACTTCAAAACTAATTAGCTGTCTGCCTGTA 6 32 1 ACTATAGCTG 0.906964 -269 GTCTGCCTGTAGCATAGTAGCAGATTTCCGTTT 6 54 1 ACAATAGCAG 0.975318 -247 AGAATGAATGATCACACAAGCTGTTTATGCTTT 6 111 1 ACAAAAGCTG 0.983908 -190 TTTTGGACAGATCGTGAAAGCAGCACAAAAGGC 6 184 1 ACGGAAGCAG 0.965418 -117 GCAAAAAGATATAGGACATGCTGCCTTTTGTGC 6 206 0 AAGAATGCTG 0.886124 -95 * ** * ****** Masking position 1 Map Score: 4.77405 Number of sites scoring better than the average of aligned sites = 1071 Number in coding regions = 972 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 ATGTATTGTTTGCTGACTTCTGGTTCATAA 1 47 0 TGCTGACTTC 0.929561 -79 GGCTCAACGCTACTGCTTGTCTGTTTATTA 2 74 0 TACTGCTTGT 0.923675 -63 TCCGCAATGTTCCTGCCTTTATATTTTTTC 4 214 0 TCCTGCCTTT 0.924303 -32 TTCCCGCCCAAACTGTTTTTAAACCAATAA 5 48 0 AACTGTTTTT 0.726437 -46 AAAACTAATTAGCTGTCTGCCTGTAGCATA 6 40 1 AGCTGTCTGC 0.865192 -261 GTAGCATAGTAGCAGATTTCCGTTTTTCTG 6 62 1 AGCAGATTTC 0.611084 -239 AGAAAGCATAAACAGCTTGTGTGATCATTC 6 116 0 AACAGCTTGT 0.696206 -185 CTGCCTTTTGTGCTGCTTTCACGATCTGTC 6 189 0 TGCTGCTTTC 0.973104 -112 ATATAGGACATGCTGCCTTTTGTGCTGCTT 6 201 0 TGCTGCCTTT 0.981569 -100 ATGATTACTTCCTTTCTTTTTCATA 6 286 0 TACTTCCTTT 0.703102 -15 ********** Masking position 8 Map Score: 3.75317 Number of sites scoring better than the average of aligned sites = 3031 Number in coding regions = 2750 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 6 TAAGCTACACTTAACTTATTATAGCAGAGGTGAA 1 16 0 TTACTATTTG 0.977795 -110 CTGTTCAGTATTTGCATATTGTAGTGTTAACATC 2 29 0 TTTCTATTTG 0.987971 -108 TTATGTCATCTTATCATGTTATTGCCCCG 3 6 0 TTACTGTTTG 0.95202 -45 TAGTAGCAGATTTCCGTTTTTCTGTCATAATCAA 6 68 1 TTTCTTTTCG 0.901317 -233 TCTTTTTGCATTTTCGTATTCTAGCATAAAGAAG 6 230 1 TTTCTATTTG 0.987978 -71 CTTCCTTTCTTTTTCATATTTTCCAACTATATGT 6 270 0 TTTCTATTTC 0.949605 -31 *** * **** * * Masking position 7 Map Score: 1.95531 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 80 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 ********** No masking Map Score: 2.07011e-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 8 ********** No masking Map Score: 2.07011e-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 9 ********** No masking Map Score: 2.07011e-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