AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igcvA_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 gcvA 300 positive regulator of gcv operon #2 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #3 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #4 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #5 yqhJ 29 similar to glycine dehydrogenase #6 yqhI 300 similar to aminomethyltransferase #7 yusH 66 similar to glycine cleavage system protein H #8 yusI 110 similar to arsenate reductase Motif number 1 AATCACTATGGACAGACAGGGTAAATGT 1 8 1 ATGGACAGAA 0.743684 -293 GTAAATGTACAGGAAGTGAAAAAAGGTAGCT 1 31 1 AGGAAGTGAA 0.682323 -270 TCCTCTCCCGCAGAAGAGGAATAAAGCCG 2 9 0 CAGAAGAGGA 0.852115 -110 TCCTCTTCTGCGGGAGAGGATCAGGGTGAGG 2 20 1 CGGGAGAGGT 0.949591 -99 GGAGAGGATCAGGGTGAGGAAAATTTATGCC 2 32 1 AGGGTGAGGA 0.96574 -87 GAAGAGAGTGAGGGTGAGGCATAAATTTTCC 2 49 0 AGGGTGAGGA 0.96574 -70 CTCTCTTCGTAAGGAGAGAGGTTCACAATTC 2 72 1 AAGGAGAGAG 0.853689 -47 CGTTGGGGACCGGGAGTGGCTCCGATGCTGG 4 218 1 CGGGAGTGGT 0.846464 -83 ATTGAATAAGCGGGGCTGACAACTTTTTCAT 4 271 0 CGGGGCTGAA 0.850517 -30 GAATGACAGCAAGGGGAGAGACCTGACCGAA 6 36 1 AAGGGGAGAA 0.965471 -265 TTTCAGGTGCCAGGACAGAGAACCTTCATTT 6 210 1 CAGGACAGAA 0.927068 -91 ACATACAAAAAAGGACAGAGAAACACCTCAT 6 244 0 AAGGACAGAA 0.933225 -57 GCCGTTGATAAAGGGGAGGAATTAG 6 286 1 AAGGGGAGGA 0.9782 -15 TATTTTATTGAGGGGGAAGAAG 8 99 1 AGGGGGAAGA 0.835473 -12 ********* * Masking position 3 Map Score: 13.3599 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 727 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 2 TTCTGGTGAACTTTTGGCTTACGGTTGTGAT 1 112 0 CTTTTGGCTA 0.985434 -189 GTGAGGAAAATTTATGCCTCACCCTCACTCT 2 45 1 TTTATGCCTA 0.883108 -74 ATCACATTAGCTTATGGTTAAAAAATGCAAA 4 122 0 CTTATGGTTA 0.963564 -179 TCAATTTTACCTTATGGTTAACAGTCTGTTT 4 155 1 CTTATGGTTA 0.963564 -146 CAATCGTTCTCTTTTGCCTGAACTTACCACC 4 187 0 CTTTTGCCTA 0.985434 -114 AGCAAGAGTTCTTTTGCCTGAGAGATTCACT 6 104 0 CTTTTGCCTA 0.985434 -197 GGCAAAAGAACTCTTGCTCGACGCAACTCTG 6 117 1 CTCTTGCTCA 0.894514 -184 GCATGCGGAGCTCATGGCCAA 8 1 0 CTCATGGCCA 0.955935 -110 ********* * Masking position 11 Map Score: 8.34828 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 81 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 CAGACCAATTGCAAACACAACAACACAACATCACAAC 1 83 1 GCAACACCAA 0.987941 -218 ACAACCGTAAGCCAAAAGTTCACCAGAACACGCATTC 1 115 1 GCAAAACCAA 0.996258 -186 AATATTAAGAGCTAAAAAAATGTCAAAAA 4 3 0 GCAAAATCAA 0.97186 -298 GAATAAAAAACCAAAAAATACACCAGTTTCTATACAA 4 75 0 CCAAAACCAT 0.944076 -226 GTTAAAAAATGCAAAAATCGCGACAGAATAAAAAACC 4 100 0 GCAAAACCAA 0.996258 -201 AGAGACCTGACCGAAAACCTCGGGATACAGGCGCCGA 6 52 1 CCAAAACGAA 0.939727 -249 CTTTGCATACGCAAAGACGTCCCCAAAGGTGGTTTGC 6 168 0 GCAAGACCAA 0.987941 -133 CAACGGCGCAGCTAAAAAACATACAAAAAAGGACAGA 6 256 0 GCAAAAACAA 0.97186 -45 ** **** * ** * Masking position 7 Map Score: 8.2811 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 90 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TGCAAACACAACAACACAACATCACAACCGT 1 92 1 ACAACAAACA 0.790225 -209 AGCCAAAAGTTCACCAGAACACGCATTCCGA 1 124 1 TCACCAAACA 0.972811 -177 CAATCAATCTCCAAAAAAGTAAA 3 6 0 TCTCCAAAAA 0.932008 -18 ACAGAATAAAAAACCAAAAAATACACCAGTT 4 84 0 AAACCAAAAA 0.775367 -217 GGTGAAATTATCACCACGAAACCCAGCATCG 4 240 0 TCACCAGAAA 0.985674 -61 GGTGATAATTTCACCATGAAAAAGTTGTCAG 4 256 1 TCACCAGAAA 0.985674 -45 TTGTCTCCTCTCTCCAAGAAAAAATA 5 6 0 TCTCCAGAAA 0.956013 -24 TCCATAACAGCATGAAAATATGAGCGA 6 7 1 ACAGCAGAAA 0.951827 -294 TCCATTTTTTACAGCACTACAATAAGAAGAT 7 37 0 ACAGCATACA 0.757458 -30 ****** **** Masking position 6 Map Score: 6.95471 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 367 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 CGGCTCAGGAAGTGCCGCCACTATAGGTATT 1 170 1 AGGCCGCCAC 0.886956 -131 ATTTGCTGGTAGAAGCTCAACGGACAATTTA 1 198 1 AGAGCTCAAC 0.880811 -103 GACAATTTATAATGGCTCAGATTAAAAAAAC 1 220 1 AAGGCTCAGA 0.953591 -81 GGGGACCGGGAGTGGCTCCGATGCTGGGTTT 4 222 1 AGGGCTCCGA 0.988046 -79 ACCTCGGGATACAGGCGCCGAAGGAGCAAAC 6 68 1 ACGGCGCCGA 0.967972 -233 CCCCTTTATCAACGGCGCAGCTAAAAAACAT 6 271 0 AAGGCGCAGC 0.980961 -30 TTGGCCATGAGCTCCGCATGCGCGGAG 8 7 1 ATAGCTCCGC 0.954138 -104 CTTCTTAAAAAAGAGCTCCGCGCATGCGGAG 8 22 0 AAAGCTCCGC 0.981332 -89 ** ******** Masking position 1 Map Score: 4.63775 Number of sites scoring better than the average of aligned sites = 1015 Number in coding regions = 955 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 GACCATGGTAGCAAAGCTACCTTTTTTCACTTC 1 43 0 GCAAAACCTT 0.973523 -258 GGCTATTAAACTTTGATGTTAAAT 1 287 0 GCTATACTTT 0.748179 -14 ATTGTCTTATTCAAATTGACTTTCTCATCACAT 4 37 1 TCAAAACTTT 0.95569 -264 GACTTTCTCATCACATCATCTTTGTATAGAAAC 4 54 1 TCACATCTTT 0.697067 -247 AATGTGATGATCAATTTTACCTTATGGTTAACA 4 145 1 TCAATACCTT 0.843277 -156 GGTCCCCAACGCAATCGTTCTCTTTTGCCTGAA 4 196 0 GCAATTCTCT 0.802803 -105 AATCTCTCAGGCAAAAGAACTCTTGCTCGACGC 6 108 1 GCAAAACTCT 0.973523 -193 TTGCGCATCCGCACAAACACTCTCCAGAGTTGC 6 139 0 GCACAACTCT 0.933825 -162 GTGCGGATGCGCAAACCACCTTTGGGGACGTCT 6 158 1 GCAAACCTTT 0.932047 -143 CTTTGCGTATGCAAAGTAAACTTTCAGGTGCCA 6 189 1 GCAAAAACTT 0.849951 -112 ACCACACTTTTCAAAAAAAATTTACA 7 4 0 TCAAAAATTT 0.768667 -63 ***** ***** Masking position 13 Map Score: 5.15666 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 529 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 AGGTTCACAATTCACTGCACGTTTCAGGAA 2 90 1 TTCACTGCAC 0.750755 -29 GAAAAAGTTGTCAGCCCCGCTTATTCAATG 4 273 1 TCAGCCCCGC 0.966126 -28 GCCTGAGAGATTCACTCCGCAGTTTGCTCC 6 90 0 TTCACTCCGC 0.973857 -211 TGTATGTTTTTTAGCTGCGCCGTTGATAAA 6 268 1 TTAGCTGCGC 0.985816 -33 TTGGCCATGAGCTCCGCATGCGCGGAG 8 8 1 TGAGCTCCGC 0.993082 -103 TTCTTAAAAAAGAGCTCCGCGCATGCGGAG 8 22 0 AGAGCTCCGC 0.972539 -89 ********** Masking position 5 Map Score: 2.68763 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 384 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 8 TCCTGTACATTTACCCTGTCTGTCCATAGT 1 15 0 TTACCCTGTC 0.957595 -286 TTTTGGTTTTTTATTCTGTCGCGATTTTTG 4 96 1 TTATTCTGTC 0.956987 -205 GTATCCCGAGGTTTTCGGTCAGGTCTCTCC 6 50 0 GTTTTCGGTC 0.939406 -251 TAAAATGAAGGTTCTCTGTCCTGGCACCTG 6 213 0 GTTCTCTGTC 0.987268 -88 ACATGAGGTGTTTCTCTGTCCTTTTTTGTA 6 242 1 TTTCTCTGTC 0.986269 -59 ********** Masking position 2 Map Score: 2.47084 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 50 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 ********** No masking Map Score: -2.6621e-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: -2.6621e-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: -2.6621e-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