AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i131_Transmembrane_Transport_5_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 glvA 300 6-phospho-alpha-glucosidase #2 yfiA 64 similar to hypothetical proteins #3 yfiB 105 similar to ABC transporter (ATP-binding protein) #4 yfiD 154 similar to hypothetical proteins #5 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #6 yfiG 174 similar to metabolite transport protein #7 yfiH 26 yfiH #8 yfiJ 123 similar to two-component sensor histidine kinase [YfiK] #9 yfiL 143 similar to ABC transporter (ATP-binding protein) #10 yvfT 132 similar to two-component sensor histidine kinase [YvfU] #11 yvfR 283 similar to ABC transporter (ATP-binding protein) Motif number 1 AAGTGAATATACGCCCTTCCAATTCTTATG 1 78 0 ACGCCCTTCC 0.747377 -223 ATGAAATTCCCCCATTTTCGAATCTGTA 2 9 1 CCCCCATTTT 0.959722 -56 ATCAGATCCCCCCATTTTCTTTCTATTA 2 47 0 CCCCCATTTT 0.959722 -18 AGACTGCCCTCCTTTTCGGGAGGGTT 3 7 1 CCCTCCTTTT 0.839927 -99 TTTACTATGGCGGTCTTTTTGACGGCAAAC 3 40 0 CGGTCTTTTT 0.882392 -66 AAGCCTCCAAACCCCTTTTTACTCGATTGT 3 82 0 ACCCCTTTTT 0.976107 -24 TCCTGCACAGAGGTCTTTTTTTGTTACAGT 4 18 1 AGGTCTTTTT 0.887299 -137 TTATTTTTGTCCGCCTTGTTATGATGAGAG 5 49 1 CCGCCTTGTT 0.950824 -45 CCTTGTTGTAACCGCTTTCTAAAAAGATTA 6 75 0 ACCGCTTTCT 0.766205 -100 CTTCAGCAATACCCCTTGTTGTAACCGCTT 6 88 0 ACCCCTTGTT 0.928758 -87 GTCGGGTGCTCTGCCATTCTTGAAAGAAGG 6 144 1 CTGCCATTCT 0.750125 -31 TACCTGCCTCAGGGCATTTTTGACAGGAGT 8 68 0 AGGGCATTTT 0.764287 -56 GGCCTGTAAAAGGCCTTTTCAGAGAAGCGT 9 30 0 AGGCCTTTTC 0.8589 -114 GGCCTTTTACAGGCCTTTTTTTCATGCCCT 9 45 1 AGGCCTTTTT 0.967201 -99 TACATGCCGCACGCCTTTCTTTCTTCTACA 9 91 1 ACGCCTTTCT 0.965975 -53 GTCGTCTCACTCCTTTTTTTGATCCATT 9 126 0 ACTCCTTTTT 0.820209 -18 ACCATATCCGATCCCCTGTTTGACCCCTGA 10 113 0 ATCCCCTGTT 0.544036 -20 GGAGTGACAAATGTCATTTTTTTCTCACCC 11 188 0 ATGTCATTTT 0.6532 -96 ATCGTCTTCTCCGTCATTTTACAATCAATG 11 242 1 CCGTCATTTT 0.908261 -42 ********** Masking position 7 Map Score: 18.7167 Number of sites scoring better than the average of aligned sites = 2967 Number in coding regions = 2497 Number in noncoding regions = 470 Number of orfs with sites within 600 bp upstream = 461 Fraction of orfs with sites within 600 bp upstream = 0.0740443 Motif number 2 ATTCGAAAATGGGGGAATTTCAT 2 4 0 GGGGGAATTT 0.970604 -61 GAAAGAAAATGGGGGGATCTGAT 2 52 1 GGGGGGATCT 0.921326 -13 CTCCTTTTCGGGAGGGTTTTCGTTTGCCGT 3 19 1 GGAGGGTTTT 0.937376 -87 AAAGGGGTTTGGAGGCTTTTAC 3 94 1 GGAGGCTTTT 0.911274 -12 TATTTCGGCAAGGGGATTGCAG 5 3 0 AGGGGATTGC 0.801282 -91 AATAACGGCAGGGGGATTTTTTATTTTTGT 5 29 1 GGGGGATTTT 0.970604 -65 CAACTTGTTAGGAGGCGTTTAC 5 82 1 GGAGGCGTTT 0.759692 -12 GTTACAACAAGGGGTATTGCTGAAGGAGGG 6 93 1 GGGGTATTGC 0.801281 -82 TATTGCTGAAGGAGGGATGCATTGGCTTAT 6 107 1 GGAGGGATGC 0.965219 -68 TGAGATACCAGGAGGAATCTATCA 7 13 1 GGAGGAATCT 0.931169 -14 ATGAGGGAATGCGCCGCATATG 8 3 1 GAGGGAATGC 0.885658 -121 CTATTTTCCCGAAGGAATTCGGGTTTTTCC 10 30 1 GAAGGAATTC 0.806795 -103 AGATGCAGGAGGAGGATTGCCTAGACACCG 11 158 1 GGAGGATTGC 0.977924 -126 ********** Masking position 8 Map Score: 15.1392 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 406 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 3 ATGACGACCTCCTTGATAACGTTTAC 1 285 0 ACCTCCTTGA 0.894011 -16 AGACTGCCCTCCTTTTCGGGAGGGTT 3 7 1 CCCTCCTTTT 0.77393 -99 TTTATCCTCCTTGATAAATGTTAT 4 141 0 TCCTCCTTGA 0.971425 -14 CTGCAATCCCCTTGCCGAAATAACGG 5 7 1 TCCCCTTGCC 0.780953 -87 AAATAAAAAATCCCCCTGCCGTTATTTCGG 5 25 0 TCCCCCTGCC 0.965728 -69 TTTATTTTTGTCCGCCTTGTTATGATGAGA 5 48 1 TCCGCCTTGT 0.930899 -46 CCTTCAGCAATACCCCTTGTTGTAACCGCT 6 89 0 TACCCCTTGT 0.772904 -86 GCCAATGCATCCCTCCTTCAGCAATACCCC 6 103 0 CCCTCCTTCA 0.939618 -72 GGCTTTCTTCCCCTTCTTTCAAGAATG 6 158 0 TTCCCCTTCT 0.80234 -17 TGATAGATTCCTCCTGGTATCTCAGG 7 9 0 TCCTCCTGGT 0.983263 -18 ATCTCCCATGTCCTCTTTCTTTTAAACTGC 11 107 0 TCCTCTTTCT 0.896915 -177 TAGGCAATCCTCCTCCTGCATCTTCCAATT 11 151 0 TCCTCCTGCA 0.976368 -133 ATGAGCACCTCCTGATCGTTTACATT 11 268 0 ACCTCCTGAT 0.692803 -16 ********** Masking position 7 Map Score: 12.0386 Number of sites scoring better than the average of aligned sites = 925 Number in coding regions = 626 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 360 Fraction of orfs with sites within 600 bp upstream = 0.057822 Motif number 4 TTTTACTCGATTGTCTCTTTCTTTACTTTAC 3 65 0 TTTCTCTTTC 0.895678 -41 TTGATAAATGTTATCACTTACTTAATGTAAG 4 124 0 TTTCACTTAC 0.680541 -31 AACAAGTTGGTTCTCTCATCATAACAAGGCG 5 60 0 TTTCTCATCA 0.723078 -34 CCAATTCCCTTCTTATCATACCTGCCTCAGG 8 85 0 TCTATCATAC 0.578005 -39 GCTCATCACTCCCGATACCCAAT 8 111 0 TCTCACTCCC 0.960698 -13 ATGCCCTATGTTCTATCTGCCGCTACATGCC 9 68 1 TTTATCTGCC 0.698727 -76 GTCGTCTCACTCCTTTTTTTGA 9 132 0 TCTCTCACTC 0.936428 -12 GGTTTTTCCCTTATATCTTTCTGGTGTATAC 10 51 1 TTTATCTTTC 0.773334 -82 ATTATGCCGTTCCTCTCTTTATTAAAAGAAT 10 83 1 TCTCTCTTTA 0.654189 -50 AATATTTCTATCATAACACTCGGATGGTTTG 11 48 1 TCTAACACTC 0.769508 -236 CATCCATCTTTTCTATCTCCCATGTCCTCTT 11 120 0 TTTATCTCCC 0.933391 -164 AATGTCATTTTTTTCTCACCCCGGTGTCTAG 11 178 0 TTTCTCACCC 0.963999 -106 AAAATGACATTTGTCACTCCATCATCATGAC 11 198 1 TTTCACTCCA 0.784778 -86 CACTCCATCATCATGACACCCCATACTAACA 11 212 1 TCTGACACCC 0.729496 -72 ** ******** Masking position 4 Map Score: 5.83457 Number of sites scoring better than the average of aligned sites = 1339 Number in coding regions = 1039 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 5 GATTACAAAAAAGGTAAAAAAACCAAATCTCT 1 134 1 AAGTAAAAAA 0.979606 -167 ATTGTATATAATAGAAAGAAAATGGGGGGATC 2 39 1 ATGAAAAAAA 0.837532 -26 CCGCCATAGTAAAGTAAAGAAAGAGACAATCG 3 57 1 AAGTAAGAAA 0.936627 -49 GTACTATAAAACTGTAACAAAAAAAGACCTCT 4 26 0 ACGTAAAAAA 0.946129 -129 ATTTTACGAAAATGAAATAAAAGTACTATAAA 4 48 0 AAGAAAAAAA 0.954329 -107 ATTTTCGTAAAATGTAACAAAATTACTTGACG 4 67 1 AAGTAAAAAA 0.979606 -88 TTTCAGCCGGAAAGTAATATAAAGTTCAATAT 11 21 1 AAGTAAATAA 0.908858 -263 ** **** **** Masking position 6 Map Score: 4.38559 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 146 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 GATTATAAATAATTCGGCATGTATCCGAATCGT 1 30 1 ATGGCATGTA 0.90382 -271 AATGTTATCACTTACTTAATGTAAGCTAGTATA 4 116 0 CTTTAATGTA 0.72227 -39 CTTTCTTCCCCTTCTTTCAAGAATGGCAGAGCA 6 150 0 CTTTCAAGAA 0.6828 -25 GAATGCGCCGCATATGACATAAAGTTCATATGC 8 17 1 CTGACATAAA 0.636708 -107 TCAAAAATGCCCTGAGGCAGGTATGATAAGAAG 8 75 1 CTGGCAGGTA 0.96618 -49 CATATGACGTTTTGCATATACGCTTCTCTG 9 8 1 CTTGCATATA 0.928322 -136 GCAGATAGAACATAGGGCATGAAAAAAAGGCCT 9 55 0 CTGGCATGAA 0.97988 -89 GAAAGAAAGGCGTGCGGCATGTAGCGGCAGATA 9 81 0 CTGGCATGTA 0.990788 -63 ATAGATATTGCCTTTTTCATGTA 10 1 0 CTTTCATGTA 0.93767 -132 ACCCGAATTCCTTCGGGAAAATAGATATTGCCT 10 21 0 CTGGAAAATA 0.62376 -112 * * ******** Masking position 9 Map Score: 1.96513 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 458 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 7 GGAAATTTCTCATTTGCCTTATGTCTGAGA 1 163 0 CATTTGCCTT 0.8022 -138 TCCCGTAACACGTTTGGCGCACTTAGGTCA 1 227 0 CGTTTGGCGC 0.912889 -74 GGAGGGTTTTCGTTTGCCGTCAAAAAGACC 3 29 1 CGTTTGCCGT 0.977707 -77 AACTTTATGTCATATGCGGCGCATTCCCTC 8 13 0 CATATGCGGC 0.953004 -111 ACATAAAGTTCATATGCGGTTTTTATTTTC 8 33 1 CATATGCGGT 0.972834 -91 CATATGACGTTTTGCATATA 9 1 1 CATATGACGT 0.900133 -143 GGTGTATACGATTATGCCGTTCCTCTCTTT 10 73 1 ATTATGCCGT 0.801995 -60 AGACGATGTTAGTATGGGGTGTCATGATGA 11 219 0 AGTATGGGGT 0.806716 -65 ********** Masking position 5 Map Score: 1.89868 Number of sites scoring better than the average of aligned sites = 819 Number in coding regions = 771 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 TAATTCGGCATGTATCCGAATCGTACAAAA 1 39 1 TGTATCCGAA 0.913308 -262 TAAATGGAATTGTAAACGTTATCAAGGAGG 1 274 1 TGTAAACGTT 0.94794 -27 TACCCCTTGTTGTAACCGCTTTCTAAAAAG 6 79 0 TGTAACCGCT 0.966814 -96 ATCTTTCTGGTGTATACGATTATGCCGTTC 10 65 1 TGTATACGAT 0.969796 -68 TTACAATCAATGTAAACGATCAGGAGGTGC 11 260 1 TGTAAACGAT 0.978727 -24 ********** Masking position 4 Map Score: 1.60553 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 73 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 9 ********** No masking Map Score: 2.3117e-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: 2.3117e-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: 2.3117e-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