AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -imodE_aful_opreg_100.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0094 300 conserved hypothetical protein #2 AF0154 139 conserved hypothetical protein #3 AF0155 62 A. fulgidus predicted coding region AF0155 #4 AF0157 99 molybdopterin oxidoreductase, iron-sulfur binding subunit #5 AF0176 58 molybdopterin oxidoreductase, molybdopterin binding subunit #6 AF0177 300 tungsten formylmethanofuran dehydrogenase, subunit E (fwdE) #7 AF1205 53 pantothenate permease (panF-2) #8 AF1208 165 conserved hypothetical protein #9 AF1622 78 leucine responsive regulatory protein (lrp) #10 AF2005 48 molybdopterin-guanine dinucleotide biosynthesis protein A (mobA) #11 AF2150 51 molybdenum cofactor biosynthesis protein (moaC) #12 AF2180 50 conserved hypothetical protein #13 AF2384 190 molybdopterin oxidoreductase, molybdopterin binding subunit Motif number 1 ATTATTGATTTATTCGACATTTAAAGTCGAAT 1 13 1 TTTCGCATTT 0.846263 -288 ATAAATTTTGTTTTTGTAATTAAAAATTCGAC 1 38 0 TTTTGAATTA 0.884176 -263 CAGAAAGTCCTCATCGAATTTTAGTTTAATAA 1 66 0 TATCGATTTT 0.785432 -235 AATTCGGAATTAATCGAATTTTTAATATATTT 1 120 1 TATCGATTTT 0.78543 -181 TCATATCGGATATTTAACTTTTGTGAAGTGTC 1 273 0 TTTTACTTTT 0.915788 -28 TACCTAACAGTGTTTATATTTAACATTATAAG 2 34 1 TTTTAATTTA 0.899472 -106 TATGCATTTTTGATTGCATTTTCAAAACCGAT 2 69 1 TATTGATTTT 0.860832 -71 AACCAAAAACTTTTTAAATTTAGGCTATCCTA 2 109 1 TTTTAATTTA 0.899475 -31 TTTTTCGTTTTTTTTACGGTGTT 4 2 1 TTTCGTTTTT 0.72646 -98 CCAAACGCTGTATTTAAATTTAACGGTGTTTT 6 200 1 TTTTAATTTA 0.899399 -101 TCTTAAAAACTCATTAGCTTTAAATTATTTTT 6 275 0 TATTACTTTA 0.692247 -26 CTATTTGTAGTATTTACCTTTTCTTTAACAGA 8 16 1 TTTTACTTTT 0.915787 -150 GGGGAAATTGTATTTAAAATTACTCCCAAAAC 9 46 0 TTTTAAATTA 0.804972 -33 TAAACCTTATTGTTTTACTTTAATTG 12 35 1 TTTTTCTTTA 0.689547 -16 AATAATTTTCTTTTTGTCTTTTAAGTGATTAG 13 43 1 TTTTGCTTTT 0.951508 -148 TATAACTCAGTATTCTCAATTTTAGGTAATAA 13 83 1 TTTCTAATTT 0.48709 -108 ACCTATAAACTTTTTGCAATTTCCACGTTATT 13 114 1 TTTTGAATTT 0.912406 -77 ATTTCCACGTTATTTATAATTTCATCAGCACC 13 132 1 TTTTAAATTT 0.852102 -59 ACAGTGTTTTTTTGATTTTATTTAATAAGA 13 171 0 TTTTGTTTTA 0.76731 -20 * **** ***** Masking position 4 Map Score: 16.3198 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 227 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 2 CGAATTTTTAATTACAAAAACAAAATTTATT 1 40 1 ATTCAAAAAC 0.724411 -261 TTTTAATATATTTTCGAAAACAAAAATTTTA 1 139 1 TTTCGAAAAC 0.752797 -162 TATTTCCAGCCTTTCCAAAACGAGTTTGTAA 1 201 1 CTTCCAAAAC 0.990312 -100 TTTTGATTGCATTTTCAAAACCGATTTTAGG 2 76 1 ATTTCAAAAC 0.710451 -64 CGATTTTAGGCCAACCAAAAACTTTTTAAAT 2 97 1 CCACCAAAAA 0.707497 -43 TAAATTTAGGCTATCCTAAACATAACG 2 123 1 CTACCTAAAC 0.906771 -17 ACATCTACCTTTTCCCTAAAATCTTCGAATA 3 20 0 TTTCCTAAAA 0.844506 -43 TACGGTGTTAATTTCCAAAACCCTTATATTT 4 25 1 ATTCCAAAAC 0.97889 -75 GTAAACATTGTTAGCCAGAAAGGTTCTGGCA 4 65 1 TTACCAGAAA 0.470514 -35 TCCACCTCCTCTTGCCAGAACCTTTCTGGCT 4 77 0 CTTCCAGAAC 0.962443 -23 TCATAAGGTTTTTCCCTAAAATATTAGGAAA 5 16 0 TTTCCTAAAA 0.844506 -43 ACCTTATGACCTTGCCAAAAAGACACTATTT 5 38 1 CTTCCAAAAA 0.974959 -21 TTTCCCAGCTCTTCCCAATACACAATTTCCA 6 157 1 CTTCCAATAC 0.897767 -144 ATTTAAAATTACTCCCAAAACAAATTTTATA 9 36 0 ACTCCAAAAC 0.920634 -43 AAAAATATATCTTACCGAAACCAACTAAGTA 11 12 0 CTTCCGAAAC 0.946276 -40 TTTATAGGTTATTACCTAAAATTGAGAATAC 13 92 0 ATTCCTAAAA 0.870447 -99 *** ******* Masking position 10 Map Score: 16.9697 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 289 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 TTTTTGTAATTAAAAATTCGACTTTAAATG 1 30 0 TAAAAATTCG 0.953906 -271 AGGACTTTCTGAACAATTCGGTTGGCTCCG 1 87 1 GAACAATTCG 0.992806 -214 GGTTGGCTCCGAACAATTCGGAATTAATCG 1 106 1 GAACAATTCG 0.992806 -195 GAAAATATATTAAAAATTCGATTAATTCCG 1 124 0 TAAAAATTCG 0.953906 -177 GGTTTAGGGGGAATAATTCAAACGTTTACA 1 227 0 GAATAATTCA 0.843096 -74 AGCTTCGCTTGAACAATTCGAAAAATCTGT 8 43 0 GAACAATTCG 0.992806 -123 ********** Masking position 5 Map Score: 8.99624 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 16 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 ATCACCACCCCAAACACTGTTACCTAACAG 2 14 1 CAAACACTGT 0.985349 -126 ATGTTAAATATAAACACTGTTAGGTAACAG 2 30 0 TAAACACTGT 0.977154 -110 GTTTTGGAAATTAACACCGTAAAAAAAACG 4 16 0 TTAACACCGT 0.963145 -84 ACCTTTCTGGCTAACAATGTTTACTACTTG 4 59 0 CTAACAATGT 0.823993 -41 TTTTTCAAACCAAACGCTGTATTTAAATTT 6 191 1 CAAACGCTGT 0.946987 -110 TAATCATGTAAAAACACCGTTAAATTTAAA 6 212 0 AAAACACCGT 0.966951 -89 ATTAGGCAACTTAACACCGTTCAAAAATAA 6 253 1 TTAACACCGT 0.963145 -48 TAAAATCAAAAAAACACTGT 13 181 1 AAAACACTGT 0.967585 -10 ********** Masking position 4 Map Score: 11.638 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 AACATTTGGTTTAGGGGGAATAATTCAAAC 1 234 0 TTAGGGGGAA 0.906609 -67 ATAAACACTGTTAGGTAACAGTGTTTGGGG 2 21 0 TTAGGTAACA 0.919529 -119 TTCGAAGATTTTAGGGAAAAGGTAGATGTT 3 22 1 TTAGGGAAAA 0.984743 -41 CCCTAAAATATTAGGAAAAATTG 5 4 0 TTAGGAAAAA 0.925196 -55 TCCTAATATTTTAGGGAAAAACCTTATGAC 5 18 1 TTAGGGAAAA 0.984743 -41 GTCTCCGCTTCGGGGAAATTGTATTTAA 9 61 0 TTCGGGGAAA 0.95391 -18 CTTAGTTGGTTTCGGTAAGATATATTTTTA 11 14 1 TTCGGTAAGA 0.866144 -38 ATTCTCAATTTTAGGTAATAACCTATAAAC 13 94 1 TTAGGTAATA 0.885187 -97 ********** Masking position 10 Map Score: 6.10473 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 37 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 TTACAAAAACAAAATTTATTAAACTAAAATTCG 1 51 1 AAAATTTAAA 0.955788 -250 TTTGTTTTCGAAAATATATTAAAAATTCGATTA 1 130 0 AAAATTTAAA 0.955788 -171 TTCGAAAACAAAAATTTTATAATACGCATGTTA 1 151 1 AAAATTTAAT 0.900371 -150 AGGCCAACCAAAAACTTTTTAAATTTAGGCTAT 2 104 1 AAAACTTAAA 0.773229 -36 CCTTTTCCCTAAAATCTTCGAATATGAAAAAAA 3 11 0 AAAATTGAAT 0.902048 -52 TTAACACCGTAAAAAAAACGAAAAA 4 3 0 AAAAAAGAAA 0.572115 -97 GTTTTTCCCTAAAATATTAGGAAAAATTG 5 7 0 AAAATTGGAA 0.762666 -52 TTTGGTTTGAAAAATCATGGAAATTGTGTATTG 6 172 0 AAAATAGAAA 0.926278 -129 TACATGATTAAAAATAATCGAATTAGGCAACTT 6 232 1 AAAATAGAAT 0.840062 -69 ACACCGTTCAAAAATAATTTAAAGCTAATGAGT 6 266 1 AAAATATAAA 0.924982 -35 AACAATTCGAAAAATCTGTTAAAGAAAAGGTAA 8 29 0 AAAATTTAAA 0.955788 -137 AAACCTCGGAAAAGTGTAATAAATAACTAACTA 10 15 1 AAAGTTTAAA 0.759242 -34 TTAGTGCAGTCAAATTTAATAATTTTCTTTTTG 13 26 1 CAAATTTAAT 0.568652 -165 CTTATTAAATAAAATCAAAAAAACACTGT 13 172 1 AAAATAAAAA 0.660296 -19 ***** * **** Masking position 3 Map Score: 11.4557 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 103 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 TAAAATTCGATGAGGACTTTCTGAACAATTCGGT 1 75 1 TGGGATCTGA 0.716108 -226 ACAAACTCGTTTTGGAAAGGCTGGAAATAGTCTG 1 196 0 TTGGAGCTGG 0.966524 -105 TAACAGTGTTTGGGGTGGTGATGGG 2 2 0 TGGGTGATGG 0.987509 -138 GCTTATAAGGCTGAGAGTGGCAGGATTCC 6 6 0 CTAGAGCAGG 0.616734 -295 ATGAGAGGCGTGAGGTTGAGAAGGGGAAGCCTGA 6 40 0 TGGGTGAAGG 0.972824 -261 TGGGAAGTTTCGAGGTGAAGAAGGATAAGGTCAG 6 118 0 CGGGTGAAGG 0.962246 -183 AAATTGTGTATTGGGAAGAGCTGGGAAAGAGACT 6 151 0 TTGGAGCTGG 0.966524 -150 GGTGGTATTTTGGAGGCAAGATGGGATATACTGA 7 19 1 TGAGGGATGG 0.833251 -35 CTCGTTTAAACGAGGTGTGGCTGATATGTAGAGT 8 71 1 CGGGTGCTGA 0.962015 -95 ATAAGAACTTTGCGGTGCTGATGAAATTATAAAT 13 143 0 TGGGTGATGA 0.957093 -48 ** *** ***** Masking position 5 Map Score: 5.12137 Number of sites scoring better than the average of aligned sites = 1247 Number in coding regions = 1192 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 CTCGTTTTGGAAAGGCTGGAAATAGTCTGAAT 1 193 0 AAGCTGGAAA 0.965834 -108 TTAGCCAGAAAGGTTCTGGCAAGAGGAGGTGG 4 75 1 AGTCTGGCAA 0.889741 -25 TTCTGGCAAGAGGAGGTGGAAA 4 88 1 AGAGTGGAAA 0.933789 -12 GAGCTGGGAAAGAGACTGGGAAGTTTCGAGGT 6 136 0 AAGCTGGGAA 0.97154 -165 GTGTATTGGGAAGAGCTGGGAAAGAGACTGGG 6 148 0 AGACTGGGAA 0.975823 -153 TTGGTTTGAAAAATCATGGAAATTGTGTATTG 6 172 0 AATATGGAAA 0.738716 -129 GGCAAAACCTCGGAAAAGTGTAATA 10 4 1 AAACTCGGAA 0.872043 -45 GAAATTATAAATAACGTGGAAATTGCAAAAAG 13 123 0 AAAGTGGAAA 0.935016 -68 * ** ******* Masking position 11 Map Score: 0.66596 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 215 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 ********** No masking Map Score: 2.26196e-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 10 ********** No masking Map Score: 2.26196e-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: 2.26196e-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