AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igcvA_ecoli_bsub_300.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 #9 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #10 yusM 300 similar to proline dehydrogenase Motif number 1 AACTTTTCGTTCCGGCTCAGGAAGTGCCGCCA 1 158 1 TCGGCCAGGA 0.965072 -143 ATTCCTCTTCTGCGGGAGAGGATCAGGGTGAG 2 18 1 TCGGGGAGGA 0.995207 -101 CGGGAGAGGATCAGGGTGAGGAAAATTTATGC 2 30 1 TAGGGGAGGA 0.993579 -89 ACGAAGAGAGTGAGGGTGAGGCATAAATTTTC 2 50 0 TAGGGGAGGC 0.963725 -69 GGTGGTAAGTTCAGGCAAAAGAGAACGATTGC 4 187 1 TAGGCAAAGA 0.925175 -114 TATTTTTTCTTGGAGAGAGGAGACAACAC 5 10 1 TGGAGGAGGA 0.868702 -20 AGTGAATCTCTCAGGCAAAAGAACTCTTGCTC 6 104 1 TAGGCAAAGA 0.925175 -197 GCGCCGTTGATAAAGGGGAGGAATTAG 6 284 1 TAAGGGAGGA 0.924208 -17 ATTATTTTATTGAGGGGGAAGAAG 8 97 1 TAGGGGAAGA 0.98036 -14 GACTCAGCATTACGGCGGCGGAAAACGGACAA 9 79 0 TCGGCGCGGA 0.971257 -189 CCGCGCTGACTGCCGCTGAAGACGGATTTTTT 9 136 1 TCCGCGAAGA 0.886657 -132 CTTCCGTTATTTCGACAAAGGATCATTTGTAT 10 154 0 TCGACAAGGA 0.877266 -147 * **** ***** Masking position 1 Map Score: 13.4158 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 440 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 CCTATTAGTTTTTTTAATCTGAGCCATTATA 1 227 0 TTTTTAACTG 0.929913 -74 TTTTTGACATTTTTTTAGCTCTTAATATTGT 4 11 1 TTTTTTACTC 0.842831 -290 ATTTTTTGGTTTTTTATTCTGTCGCGATTTT 4 93 1 TTTTTATCTG 0.945285 -208 GCAATCGTTCTCTTTTGCCTGAACTTACCAC 4 188 0 TCTTTTGCTG 0.946915 -113 TTCGCTCATATTTTCATGCTGTTATGGA 6 8 0 TTTTCATCTG 0.764899 -293 GAGCAAGAGTTCTTTTGCCTGAGAGATTCAC 6 105 0 TCTTTTGCTG 0.946915 -196 TTCTCTGTCCTTTTTTGTATGTTTTTTAGCT 6 253 1 TTTTTTGATG 0.877454 -48 TTTTTGTATGTTTTTTAGCTGCGCCGTTGAT 6 264 1 TTTTTTACTG 0.957453 -37 CATGTTATGTTTTTTATACTGCTGATTTTGA 9 47 1 TTTTTATCTG 0.945285 -221 TGAAGACGGATTTTTTTTCTCTCGTACCATT 9 152 1 TTTTTTTCTC 0.874729 -116 AATTTGTTATTTTTTTGTATGAAGCCTATAA 9 215 0 TTTTTTGATG 0.877454 -53 ******* *** Masking position 4 Map Score: 10.9852 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 345 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 TCACCCTGATCCTCTCCCGCAGAAGAGGAA 2 19 0 CCTCTCCCGC 0.93051 -100 GGCATAAATTTTCCTCACCCTGATCCTCTC 2 33 0 TTCCTCACCC 0.927396 -86 GGAAAATTTATGCCTCACCCTCACTCTCTT 2 49 1 TGCCTCACCC 0.851943 -70 GAATTGTGAACCTCTCTCCTTACGAAGAGA 2 73 0 CCTCTCTCCT 0.962027 -46 TCGGAGCCACTCCCGGTCCCCAACGCAATC 4 213 0 TCCCGGTCCC 0.778898 -88 GTGTTGTCTCCTCTCTCCAAGAAAAAATA 5 11 0 CCTCTCTCCA 0.819499 -19 TTCGGTCAGGTCTCTCCCCTTGCTGTCATT 6 37 0 TCTCTCCCCT 0.98087 -264 AAATGAAGGTTCTCTGTCCTGGCACCTGAA 6 211 0 TCTCTGTCCT 0.91591 -90 ATGAGGTGTTTCTCTGTCCTTTTTTGTATG 6 244 1 TCTCTGTCCT 0.91591 -57 CTAATTCCTCCCCTTTATCAACGG 6 287 0 TTCCTCCCCT 0.959435 -14 CTTCTTCCCCCTCAATAAAAT 8 100 0 TTCTTCCCCC 0.791464 -11 ACGGATTTTTTTTCTCTCGTACCATTCCCT 9 157 1 TTTCTCTCGT 0.75792 -111 TCGTACCATTCCCTTCACCTCCGGGCTTAA 9 173 1 CCCTTCACCT 0.712399 -95 CCGACTCCCTCCCGCCGTCATCTTC 10 286 0 TCCCTCCCGC 0.970067 -15 ********** Masking position 8 Map Score: 10.9509 Number of sites scoring better than the average of aligned sites = 1095 Number in coding regions = 768 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 224 Fraction of orfs with sites within 600 bp upstream = 0.0359782 Motif number 4 TGGCGGCACTTCCTGAGCCGGAACGAAAAG 1 160 0 TCCTGAGCCG 0.914713 -141 CGGCTCAGGAAGTGCCGCCACTATAGGTAT 1 170 1 AGTGCCGCCA 0.776445 -131 GGGGACCGGGAGTGGCTCCGATGCTGGGTT 4 222 1 AGTGGCTCCG 0.893331 -79 CTCCGCAGTTTGCTCCTTCGGCGCCTGTAT 6 76 0 TGCTCCTTCG 0.884533 -225 CACTCTCCAGAGTTGCGTCGAGCAAGAGTT 6 125 0 AGTTGCGTCG 0.885453 -176 AAAGGTGGTTTGCGCATCCGCACAAACACT 6 151 0 TGCGCATCCG 0.892467 -150 TATGTTTTTTAGCTGCGCCGTTGATAAAGG 6 270 1 AGCTGCGCCG 0.989806 -31 TTGTCCGTTTTCCGCCGCCGTAATGCTGAG 9 79 1 TCCGCCGCCG 0.965369 -189 GCCGCCGTAATGCTGAGTCGGACCGGCATC 9 92 1 TGCTGAGTCG 0.918812 -176 ATCCTGGCACTGCTGCGCCATGAAATGCGC 10 82 1 TGCTGCGCCA 0.960876 -219 ********** Masking position 9 Map Score: 6.94007 Number of sites scoring better than the average of aligned sites = 4159 Number in coding regions = 4000 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 5 CATTGAATAAGCGGGGCTGACAACTTTTTC 4 273 0 GCGGGGCTGA 0.98592 -28 TTTATCAACGGCGCAGCTAAAAAACATACA 6 268 0 GCGCAGCTAA 0.958163 -33 CTCCGCGCATGCGGAGCTCATGGCCAA 8 8 0 GCGGAGCTCA 0.990112 -103 CTCCGCATGCGCGGAGCTCTTTTTTAAGAA 8 22 1 GCGGAGCTCT 0.973444 -89 CAGCATTACGGCGGCGGAAAACGGACAAGT 9 77 0 GCGGCGGAAA 0.849436 -191 CTTTACGCTCGCCGCGCTGACTGCCGCTGA 9 125 1 GCCGCGCTGA 0.955021 -143 CAACTTAAGCCCGGAGGTGAAGGGAATGGT 9 177 0 CCGGAGGTGA 0.91815 -91 GCATTTCATGGCGCAGCAGTGCCAGGATCA 10 80 0 GCGCAGCAGT 0.900826 -221 ********** Masking position 6 Map Score: 3.67726 Number of sites scoring better than the average of aligned sites = 1273 Number in coding regions = 1223 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 AATCACTATGGACAGACAGGGT 1 2 1 ATCACATGGA 0.954796 -299 AGGAGAGAGGTTCACAATTCACTGCACGTTT 2 83 1 TTCACATTCA 0.802676 -36 TGGTGAAATTATCACCACGAAACCCAGCATC 4 241 0 ATCACACGAA 0.919265 -60 TGGTGATAATTTCACCATGAAAAAGTTGTCA 4 255 1 TTCACATGAA 0.62255 -46 GCCTGAGAGATTCACTCCGCAGTTTGCTCCT 6 89 0 TTCACCCGCA 0.901112 -212 ACATGGGACAATCATAATGCAGCTGCTTCCC 9 21 0 ATCATATGCA 0.939996 -247 TTTGATAGTGATCATGATGCATGTGTCCGAC 10 24 1 ATCATATGCA 0.939996 -277 AAAAGCGCATTTCATGGCGCAGCAGTGCCAG 10 85 0 TTCATGCGCA 0.740183 -216 CCAAAGGAGGATCACAATGGATAATCAGCAG 10 202 0 ATCACATGGA 0.954796 -99 ***** ***** Masking position 4 Map Score: 4.19568 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 397 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 TAGGTATTTGCTGGTAGAAGCTCAACGGACAAT 1 193 1 CTGAGAGCTC 0.979123 -108 GCGTTGGGGACCGGGAGTGGCTCCGATGCTGGG 4 217 1 CCGAGTGCTC 0.994029 -84 TCTCCCCTTGCTGTCATTCGCTCATATTTTCAT 6 22 0 CTGATTGCTC 0.993049 -279 GAGATTCACTCCGCAGTTTGCTCCTTCGGCGCC 6 81 0 CCGGTTGCTC 0.985811 -220 ACATGCTGAACTGGAATTTGCTCGCGATGAAAA 10 114 0 CTGATTGCTC 0.993049 -187 *** *** **** Masking position 12 Map Score: 2.13323 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 39 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TTACGGTTGTGATGTTGTGTTGTTGTGTTTGC 1 93 0 GATGTGTTTG 0.924972 -208 AGCCATTATAAATTGTCCGTTGAGCTTCTACC 1 205 0 AATTTCCTTG 0.915873 -96 TCTATACAAAGATGATGTGATGAGAAAGTCAA 4 52 0 GATGTGTATG 0.795744 -249 AAGCTAATGTGATGATCAATTTTACCTTATGG 4 140 1 GATGTCATTT 0.701067 -161 GCTGCATTATGATTGTCCCATGTTATGTTTTT 9 29 1 GATTTCCATG 0.945845 -239 TTATACTGCTGATTTTGACTTGTCCGTTTTCC 9 60 1 GATTTGATTG 0.886008 -208 TTGAGATACAAATGATCCTTTGTCGAAATAAC 10 149 1 AATGTCCTTG 0.94526 -152 GATTGCTGCTGATTATCCATTGTGATCCTCCT 10 197 1 GATTTCCTTG 0.982234 -104 TATCCATTGTGATCCTCCTTTGGTTTCTGTTC 10 210 1 GATCTCCTTG 0.961399 -91 **** *** *** Masking position 6 Map Score: 2.39401 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 280 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 GCGTGTTCTGGTGAACTTTTGGCTTACGGTTGTG 1 114 0 GTAACTTGGT 0.932045 -187 ATCACACTATGTAACCTATTAGTTTTTTTAATCT 1 238 0 GTACCATAGT 0.932045 -63 GTTAAATGAATTTAACAATTAGATCACACTATGT 1 260 0 TTAACATAGT 0.952797 -41 GGCTATTAAACTTTGATGTTAAATGAATT 1 282 0 TTAACTTATT 0.821964 -19 TTTTGCATTTTTTAACCATAAGCTAATGTGATGA 4 121 1 TTAACATAGT 0.952797 -180 GAAACAGACTGTTAACCATAAGGTAAAATTGATC 4 153 0 GTAACATAGT 0.981003 -148 CGTATGCAAAGTAAACTTTCAGGTGCCAGGACAG 6 194 1 GTAACTTAGT 0.981003 -107 TGCCAGGACAGAGAACCTTCATTTTACATGAGGT 6 217 1 GAAACTTATT 0.679141 -84 ** *** ** ** * Masking position 4 Map Score: 1.80474 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 91 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 AAGCAGCCGTGGGAAGCAGCT 9 1 1 AAGCAGCGTG 0.97233 -267 CAGCCGTGGGAAGCAGCTGCATTATGATTGT 9 14 1 AAGCAGCGCA 0.988264 -254 GACAAGTCAAAATCAGCAGTATAAAAAACAT 9 53 0 AATCAGCGTA 0.980556 -215 CACAATGGATAATCAGCAGCAATCTCAAATG 10 190 0 AATCAGCGCA 0.981962 -111 GTCATCTTCAAAACACCTGTATATAACTCCC 10 264 0 AAACACCGTA 0.890378 -37 ******* *** Masking position 5 Map Score: 0.76958 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 209 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 ********** No masking Map Score: 4.21595e-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 12 ********** No masking Map Score: 4.21595e-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 13 ********** No masking Map Score: 4.21595e-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