AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_fts_cell_wall_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 ddlA 174 D-alanyl-D-alanine ligase A #2 murF 71 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase #3 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #4 yllA 70 yllA #5 yllB 125 similar to hypothetical proteins #6 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #7 ftsL 39 cell-division protein #8 spoVD 116 penicillin-binding protein #9 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #10 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #11 spoVE 60 spoVE #12 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #13 murB 26 UDP-N-acetylenolpyruvoylglucosamine reductase #14 divIB 130 cell-division initiation protein #15 ylxX 22 similar to hypothetical proteins #16 ftsA 173 cell-division protein #17 ftsZ 35 cell-division initiation protein #18 murC 249 UDP-N-acetyl muramate-alanine ligase #19 ytpS 159 ytpS #20 ytpP 234 similar to thioredoxin H1 Motif number 1 TGTATGTAATTCCTTTTTATTTTATATTAA 1 38 0 TCCTTTTTAT 0.91624 -137 GAGAAGTAATTTCTTCTTACTTCTGCTATG 3 107 1 TTCTTCTTAC 0.715066 -53 AGTTCAGGGTTTCTTTTTATGGGTAAACAG 5 36 1 TTCTTTTTAT 0.955886 -90 GCTCCACAACTTCATTTTACACTGTTTACC 5 57 0 TTCATTTTAC 0.797895 -69 GCTGATGACCTCCTTTTAATTTTGCGTTCG 7 18 0 TCCTTTTAAT 0.835094 -22 TATGCAGGCTTTCTTTTTTTATGCCTTCAG 8 26 1 TTCTTTTTTT 0.932642 -91 TTAGGCTTGTTTCATTTTATGCCTGAATTT 8 78 0 TTCATTTTAT 0.843173 -39 GGGCTGCCTATTCTTTTATTGCAGAAAAAA 9 14 1 TTCTTTTATT 0.865046 -162 GCTGGATGTATCCTTTTATTTACGCTAAAA 9 65 1 TCCTTTTATT 0.763922 -111 TTCTAATTCGTTCTTTTTATCATTGAAGTC 9 137 0 TTCTTTTTAT 0.955886 -39 TTCTTTTTTCCCCCAGTCTA 12 113 0 TTCTTTTTTC 0.910452 -10 TTTCACATGATTCGTTTTTTTTGGCGGATT 19 20 0 TTCGTTTTTT 0.841624 -140 TCAAGCTCGTTTCGTTTAACATCGTGTACA 20 58 0 TTCGTTTAAC 0.738703 -177 ********** Masking position 5 Map Score: 13.0031 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 562 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 2 TAAAATGGCATTGAAAAGGAGATGTGACAT 1 11 0 TTGAAAAGGA 0.92843 -164 TCATTTTCCGGTGAAAATGATAAGATAGTA 1 105 1 GTGAAAATGA 0.937765 -70 ATAATGGAGCTTGAAAAAGATTTTTCATAT 10 28 1 TTGAAAAAGA 0.80958 -85 GAAACAGGAGGAGAAAAGGACA 10 101 1 GAGAAAAGGA 0.893283 -12 TTTGAATGAGGTGAACAGGCA 14 120 1 GTGAACAGGC 0.920649 -11 CTGAAAAAGCGGGTGAAATA 15 1 1 CTGAAAAAGC 0.860145 -22 GAAAAAGCGGGTGAAATAGA 15 13 1 GTGAAATAGA 0.732861 -10 AACATAAAATGTGAAAAGCACATAAAAATA 16 49 1 GTGAAAAGCA 0.96249 -125 CATGTTTGGTGTGAAAATGAACCCATA 18 8 0 GTGAAAATGA 0.937765 -242 ACCGCGGCGGCTGAAAAGCCTCCCTTAGCG 18 169 0 CTGAAAAGCC 0.879651 -81 AACGAATCATGTGAAAAGCCGCTAAGCCCT 19 34 1 GTGAAAAGCC 0.959995 -126 ********** Masking position 5 Map Score: 9.79402 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 637 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 3 GGGGGGAGTATCCATTGAAAACAAGTCTAGGAT 1 150 1 TCATTAAAAA 0.71458 -25 TTCCCGTATATACAAAAGAAAGAGAGGGACCTT 2 47 1 TCAAAGAAAA 0.955392 -25 ACAATATATGTAGAAACAACAAAGGGGGAGATT 3 14 0 TGAAAAACAA 0.818705 -146 ATGATTTTTTTCCATATGAAAAATCTTTTTCAA 10 38 0 TCATAGAAAA 0.939605 -75 TCCTGTTTCTTTCAAACGACATACGTAGTTATC 10 77 0 TCAAAGACAA 0.966377 -36 ACTGAAGCTGTTCATATGACATACTGTAAGCAA 14 22 1 TCATAGACAA 0.954292 -109 CCGTTTGTTTTGGAATAGACAGACTTTTAACAG 14 79 1 TGAATGACAA 0.780076 -52 GTTCACCTCATTCAAATGAAACAGCTGTTAAAA 14 103 0 TCAAAGAAAA 0.955392 -28 AAGAGGATATACATAGGATATAACGAATATTT 16 10 1 TCATAGATAA 0.763584 -164 AACGAATATTTTCAATAAACATAAAATGTGAAA 16 32 1 TCAATAACAA 0.822234 -142 AGCTTGATAATGCAAATAAAATATGATAATGAT 20 81 1 TCAAAAAAAA 0.906493 -154 TGGACGAGTATCGATAAAAAACATGTAAGAACA 20 190 1 TGATAAAAAA 0.709674 -45 * **** **** * Masking position 9 Map Score: 8.67754 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 414 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 GTAAGGTCCCTCTCTTTCTTTTGTATATA 2 53 0 TCCTCTCTTT 0.742277 -19 ACAAATCTCCCCCTTTGTTGTTTCTACA 3 6 1 TCCCCCCTTT 0.91835 -154 GATGTCACACCCAATTTAGCATTTACG 3 143 0 TCCACCCATT 0.967394 -17 ATTCACCACTTCGCTCCACAACTTCATTTTACA 5 66 0 TCCTCCAAAT 0.909081 -60 TGCCCCACTTTCTCTCCTTAACTCACCACTATT 5 96 0 TCCTCCTAAT 0.909081 -30 ATTGTGTTGGTCCCACCTTTTATCAGGATGAAT 6 47 0 TCCACCTTTT 0.953864 -23 GAGACCGTTCACTCCTTATTTAGGCTTGTTT 8 96 0 TCCTCCTATT 0.972951 -21 GACAGGGTTATCGCATCAATTGTTTCCAAGCTT 12 43 0 TCCATCATTT 0.619637 -80 GGGTTCATTTTCACACCAAACATGGTATGATAG 18 14 1 TCCACCAACT 0.85164 -236 AATAAAAATCCCTCCTTATGTATATCCATCT 20 9 1 TCCTCCTATT 0.972951 -226 TTCATATCCCTCCAGTTGTTTATGTTCTT 20 216 0 TCCTCCATTT 0.96802 -19 ** ***** ** * Masking position 1 Map Score: 8.01577 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 190 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 5 ACTCCTTATTTAGGCTTGTTTCATTTTATG 8 87 0 TAGGCTTGTT 0.76136 -30 AGAATGTTGAGAGGTTTGATACG 9 163 1 GAGGTTTGAT 0.884833 -13 TGTTAGACAGGAGGCTTGGAAATACATTCG 12 11 0 GAGGCTTGGA 0.942237 -112 TGTCTAACATGAAGCTTGGAAACAATTGAT 12 32 1 GAAGCTTGGA 0.846434 -91 ATACTATGATGCCGTTTGTTCGTTTGCTTA 14 48 0 GCCGTTTGTT 0.961205 -83 ATCATAGTATGCCGTTTGTTTTGGAATAGA 14 68 1 GCCGTTTGTT 0.961205 -63 GGAACAGATAGACGTTTGTTGGAGGTACAA 18 228 1 GACGTTTGTT 0.950605 -22 CCCTTGTTTAGCGGCTTGGTTTCTGCTGAT 19 60 1 GCGGCTTGGT 0.985176 -100 TTTGCCTCAAGCAGTTTGGTATGATCCAAA 20 160 1 GCAGTTTGGT 0.945777 -75 ********** Masking position 6 Map Score: 6.03095 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 351 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TGATCTAATTATTTTTGGGCATGCTGATGTT 1 77 0 ATTTTGGGCA 0.845739 -98 ATCACTAACTATTTATTGGAGAAAGGAAGTT 4 43 1 ATTTTTGGAG 0.938571 -28 CAGGGTTTCTTTTTATGGGTAAACAGTGTAA 5 40 1 TTTTTGGGTA 0.724564 -86 CTGCCTATTCTTTTATTGCAGAAAAAATGCT 9 17 1 TTTTTTGCAG 0.790427 -159 GATAACCCTGTTTTGTTGGACAGGGTTATCG 12 63 0 TTTTTTGGAC 0.947098 -60 ACAGATAGACGTTTGTTGGAGGTACAATT 18 231 1 GTTTTTGGAG 0.899622 -19 TTTTTGGCGGATTTATGGGAGT 19 2 0 ATTTTGGGAG 0.960576 -158 CATGATTCGTTTTTTTTGGCGGATTTATGGG 19 14 0 TTTTTTGGCG 0.96004 -146 TAGCTTAATCTTTTCTGGGCCGACCAGCAGT 19 89 1 TTTTTGGGCC 0.959265 -71 TCCCTTATAGTTTTCTGGGACGGTTTTTAGT 19 125 0 TTTTTGGGAC 0.966159 -35 **** ****** Masking position 6 Map Score: 6.18083 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 173 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TTGTCTTGAAGTAAATCGGCAGCCCTAATG 11 15 1 GTAAATCGGC 0.897391 -46 GCTAAATCCTCCTAATCTGCCGAATGACTA 17 16 0 CCTAATCTGC 0.730295 -20 CACAGCTGCTGTAAAGCGGCATAGCTGTTA 18 60 0 GTAAAGCGGC 0.969759 -190 ATTTGTCTATGCACAGCTGCTGTAAAGCGG 18 71 0 GCACAGCTGC 0.913309 -179 GAAAAGCCTCCCTTAGCGGCGTATTTTATA 18 157 0 CCTTAGCGGC 0.973256 -93 CTAAACAAGGGCTTAGCGGCTTTTCACATG 19 41 0 GCTTAGCGGC 0.988531 -119 CTAAGCCCTTGTTTAGCGGCTTGGTTTCTG 19 55 1 GTTTAGCGGC 0.976612 -105 ********** Masking position 5 Map Score: 3.42395 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 419 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 AAAATAAAAAGGAATTACATACAAATGCAT 1 45 1 GGAATTACAT 0.924156 -130 TTTTTCATATGGAAAAAAATCATGAATATG 10 48 1 GGAAAAAAAT 0.835326 -65 CAGGAGGCTTGGAAATACATTCG 12 4 0 GGAAATACAT 0.980155 -119 AAGAGGATATACATAGGATATAAC 16 5 1 GGATATACAT 0.963599 -169 GGGTTTAATCGGAAAGAAATAACCTGATAC 18 111 1 GGAAAGAAAT 0.882605 -139 ATTTACAGATGGATATACATAAGGAGGGAT 20 18 0 GGATATACAT 0.963599 -217 ********** Masking position 7 Map Score: 3.28864 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 87 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 GCCGGTAAAAGGGCAGTGTTTTTTCCCGTA 2 25 1 GGGCAGTGTT 0.899928 -47 ACCCTGAACTAGTCAGGGTTCTTTAAAACT 5 16 0 AGTCAGGGTT 0.969128 -110 ACCCTGACTAGTTCAGGGTTTCTTTTTATG 5 27 1 GTTCAGGGTT 0.89355 -99 AGCCGTCGTTATGCAGGCTTTCTTTTTTTA 8 17 1 ATGCAGGCTT 0.922038 -100 CTGTTTTGTTGGACAGGGTTATCGCATCAA 12 57 0 GGACAGGGTT 0.977823 -66 CTGTCCAACAAAACAGGGTTATCGTTATGT 12 71 1 AAACAGGGTT 0.874337 -52 GTTTTGGAATAGACAGACTTTTAACAGCTG 14 85 1 AGACAGACTT 0.781958 -46 TACGCCGCTAAGGGAGGCTTTTCAGCCGCC 18 164 1 AGGGAGGCTT 0.877976 -86 ********** Masking position 5 Map Score: 1.43808 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 299 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 ACAAATCTCCCCCTTTGTTGTTTCTACA 3 9 1 CCCCCTTTGT 0.900813 -151 AGGCTGATGACCTCCTTTTAATTTTGCGTT 7 20 0 CCTCCTTTTA 0.850219 -20 GTCCTTTTCTCCTCCTGTTTCTTTCAAACG 10 92 0 CCTCCTGTTT 0.982228 -21 TATTTCCAAGCCTCCTGTCTAACATGAAGC 12 17 1 CCTCCTGTCT 0.983516 -106 TTCTTTTTTCCCCCAGTCTAAGTTTCTCT 12 104 0 CCCCCAGTCT 0.963651 -19 TTCATATCCCTCCAGTTGTTTATGTTCT 20 217 0 CCTCCAGTTG 0.930284 -18 ********** Masking position 8 Map Score: 0.905457 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 82 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 ********** No masking Map Score: 6.7739e-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 TGAATTGTAGTGGGGGGAGTATCCATTGAAAACAAGTCT 1 139 1 TGGGAGCATA 0.993483 -36 TTTTATGCCTTCAGAGGAGCATCGTTCTACCTGTCCAAA 8 42 1 TGGGAGCTTA 0.975272 -75 TATTCTATTATTTGCGGAACAACAATACAATGAATGTGG 16 113 0 TGGGAACATA 0.982904 -61 ATGATCGAAATGTGAGGAGGTGCCATAGA 16 155 1 TGGGAGCATA 0.993115 -19 ATCCTCCTAATCTGCCGAATGACTATCTAT 17 2 0 TGCGAACATA 0.967796 -34 TATGATCCAAATGGACGAGTATCGATAAAAAACATGTAA 20 179 1 AGCGAGCATA 0.956341 -56 * * **** * ** * Masking position 8 Map Score: 0.237604 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 10 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 ********** No masking Map Score: 6.7739e-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 14 ********** No masking Map Score: 6.7739e-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 15 ********** No masking Map Score: 6.7739e-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