AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_Transmembrane_Transport_1_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 yurN 57 similar to sugar permease #2 yurO 80 similar to multiple sugar-binding protein #3 yurP 215 similar to opine catabolism #4 yurQ 102 yurQ #5 yurR 300 similar to opine catabolism #6 msmX 120 multiple sugar-binding transport ATP-binding protein #7 yxkF 183 similar to hypothetical proteins Motif number 1 TGCGAAGCTTCACCTTTTCTTTGAT 1 1 0 CACTTTCTTT 0.992477 -57 TGAAGCTTCGCACCTTTTCTTTTTATAAAGGAGAT 1 24 1 CACTTTCTTA 0.970357 -34 ATCCTTCACTCCTCGTTTTTATTATATAACGTTAT 3 191 0 CCCGTTTTTT 0.951012 -25 AAAGCTAGAACAGCTTTATTATATTTGTTTGTCAT 4 22 0 CACTTTTTTT 0.985788 -81 AAAGCTGTTCTAGCTTTTCTTTTCTGTATGTGTTA 4 40 1 TACTTTCTTT 0.957995 -63 CAGTTCACGTCCTCTTTTTCATTAAAGATAAATGC 4 75 0 CCCTTTTCTA 0.813069 -28 CTCATGGTATCATCCTTTCTCTATTGATAGTGACA 5 148 1 CACCTTCTTT 0.964929 -153 GTTCGTCCAATCTCTTTACTCTCCTATCGAATATC 5 184 0 TCCTTTCTTT 0.968361 -117 ATGCAAACACCTTTTCTATTATAATGTCTATT 5 279 0 CACTTTCTTT 0.992477 -22 GTTATTGTAAACGCTTTCTTATATTGAGTGTAACA 6 81 0 ACCTTTTTTT 0.901242 -40 CTAACATCCCCCTTTGTTATTGTAAACGCTTTC 6 98 0 CCCTTTTTTT 0.989372 -23 ** **** ** * * Masking position 7 Map Score: 14.3588 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 344 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 2 GCATTAGACTATAATGTTATATAACATTAT 2 33 1 ATAATGTTAT 0.615755 -48 ACATTAGACTATAATGTTATATAACATTAT 2 43 0 ATAATGTTAT 0.615755 -38 ATAACATTATATATTGTTATATTAAAGTCC 3 161 0 ATATTGTTAT 0.891903 -55 ATAACAATATATAATGTTATATAACGTTAT 3 171 1 ATAATGTTAT 0.615755 -45 ATAATGTTATATAACGTTATATAATAAAAA 3 181 1 ATAACGTTAT 0.499741 -35 ********** Masking position 7 Map Score: 9.27646 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 6 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 TGTTATATAACATTATAGTCTAATGCATAATGGTT 2 24 0 CATTAGCAAG 0.623171 -57 TGTTATATAACATTATAGTCTAATGTCCAGAGGAG 2 47 1 CATTAGCAAG 0.623171 -34 AATTTATTCGGATGACAGACAAAGGGTCTATATGC 3 85 0 GATGAGCAAG 0.975562 -131 TCCTCTTTTTCATTAAAGATAAATGCTAACACATA 4 66 0 CATTAGTAAG 0.935685 -37 AGGATGATACCATGAGCGAAAATCGTCATGAAAAT 5 129 0 CATGAGAATG 0.94741 -172 GGTTTTTCCACATTAGGGCAAAAGGTCGAAGGAAA 5 224 1 CATTAGAAAG 0.97905 -77 ATTGGAAATATGCACGAAAAATGGCTGGGTGAT 6 9 1 TATGCGAAAG 0.880714 -112 TAGAAGAAGACATGCAGGACCAAAGGAGGGTCATC 7 13 0 CATGCGCAAG 0.991528 -171 ***** * * ** * Masking position 12 Map Score: 7.26403 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 131 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 CTTTATAAAAAGAAAAGGTGCGAAGCTTCACCTTTT 1 18 0 AAAAGGGAAC 0.939674 -40 TTCTTTTTATAAAGGAGATGAGATACCC 1 40 1 AAGAGAGATC 0.991467 -18 GCAAAAGTCCAAAACAGCGGTAATGCAAAAGTCGTG 5 66 0 AAAAGCGATC 0.984409 -235 GAAAATGAAGAAAACAGACGCGATGCGGCAGTGGCA 5 99 0 AAAAGAGATC 0.994242 -202 TTCAGCGGAAATAGAAGAAGACATGCAGGACCAAAG 7 23 0 AAGAGAGATC 0.991467 -161 GTTCTCCACTAAAAAAGAGTATATCCGGTATAGATA 7 102 0 AAAAGATATC 0.957261 -82 AGATCCTTACATAAGAGAGGAGACTCT 7 167 1 AAAAGAGACC 0.984409 -17 * ** *** * ** * Masking position 6 Map Score: 5.72136 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 96 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 CTTGACTTAAGCTCTGGCTTCGCTGTTCAA 3 27 0 GCTCTGGCTT 0.995098 -189 CTTAAGTCAAGTTCTGGCTTTTGATTTGGG 3 46 1 GTTCTGGCTT 0.992439 -170 TGTTTGTCATGCTCTTACTTA 4 2 0 GCTCTTACTT 0.949328 -101 TAATAAAGCTGTTCTAGCTTTTCTTTTCTG 4 36 1 GTTCTAGCTT 0.979637 -67 ********** Masking position 5 Map Score: 3.07163 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 39 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 CATAATGGTTCTTCATTTTCAGA 2 4 0 CTTCATTTTC 0.900332 -77 TGTTATATAACATTATAGTCTAATGCATAA 2 29 0 CATTATAGTC 0.944813 -52 TGTTATATAACATTATAGTCTAATGTCCAG 2 47 1 CATTATAGTC 0.944813 -34 GGATTGTCAATATTATTTTCTGAAATTTCT 3 124 0 TATTATTTTC 0.79992 -92 AGTCCGCGGGTAGGATTGTCAATATTATTT 3 136 0 TAGGATTGTC 0.76102 -80 CGTCTGTTTTCTTCATTTTCATGACGATTT 5 115 1 CTTCATTTTC 0.900332 -186 TTGATAGTGACAGGATATTCGATAGGAGAG 5 171 1 CAGGATATTC 0.934226 -130 ATGTAAGGATCTGTATATTCAGTATAAGGC 7 149 0 CTGTATATTC 0.914383 -35 ********** Masking position 5 Map Score: 2.54159 Number of sites scoring better than the average of aligned sites = 1059 Number in coding regions = 930 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 7 TATATGCGAAAAAATGCCCAAATCAAAAGC 3 62 0 AAAATGCCCA 0.955468 -154 ATCTGTGTTCACGCTGACCACGACTTTTGC 5 48 1 ACGCTGACCA 0.954814 -253 CAGCGTTCATAAAATCACCCAGCCATTTTT 6 27 0 AAAATCACCC 0.91813 -94 GATTTTATGAACGCTGCCCATTTTAGCGAG 6 41 1 ACGCTGCCCA 0.970783 -80 CTAACATCCCCCTTTGTTATTG 6 109 0 AACATCCCCC 0.936795 -12 AAGATGACCCTCCTTTGGTC 7 1 1 AAGATGACCC 0.979734 -183 ********** Masking position 5 Map Score: 0.686734 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 228 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 AAAAGGTGAAGCTTCGCACCTTTTCTTTTT 1 18 1 GCTTCGCACC 0.907651 -40 GGGTATCTCATCTCCTTTATAA 1 46 0 GTATCTCATC 0.975217 -12 TAGACCCTTTGTCTGTCATCCGAATAAATT 3 90 1 GTCTGTCATC 0.946162 -126 TATTATATTTGTTTGTCATGCTCTTACTTA 4 11 0 GTTTGTCATG 0.852067 -92 TGCCACTGCCGCATCGCGTCTGTTTTCTTC 5 99 1 GCATCGCGTC 0.963633 -202 CTTTGGTCCTGCATGTCTTCTTCTATTTCC 7 23 1 GCATGTCTTC 0.916645 -161 TTCCCTTTCAGTTTCTCGTCTATCTATACC 7 82 1 GTTTCTCGTC 0.970258 -102 ********** Masking position 4 Map Score: 0.930899 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 455 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 GCTGTTCAATCCGCAGACTGACGTC 3 6 0 CCGCAGACTG 0.979292 -210 ACAATCCTACCCGCGGACTTTAATATAACA 3 147 1 CCGCGGACTT 0.990953 -69 TATAATAAAAACGAGGAGTGAAGGAT 3 200 1 ACGAGGAGTG 0.949864 -16 GAAAAAGAGGACGTGAACTGATT 4 90 1 ACGTGAACTG 0.924371 -13 TGTGGAAAAACCGCGAAGTTCGTCCAATCT 5 206 0 CCGCGAAGTT 0.970937 -95 ********** Masking position 7 Map Score: 0.239924 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 163 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 ********** No masking Map Score: 3.57646e-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: 3.57646e-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: 3.57646e-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