AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i098_Phosphate_regulatory_cassete_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 resD 80 two-component response regulator #2 resC 135 essential protein similar to cytochrome c biogenesis protein #3 resA 131 essential protein similar to cytochrome c biogenesis protein #4 ypuL 91 similar to hypothetical proteins #5 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #6 ypuI 54 similar to hypothetical proteins from B. subtilis #7 ypuG 280 similar to hypothetical proteins #8 phoP 211 two-component response regulator #9 citH 43 malate dehydrogenase #10 citC 163 isocitrate dehydrogenase #11 citZ 300 citrate synthase II #12 yycF 300 similar to two-component response regulator [YycG] Motif number 1 GAATAAAGATAAAAAGGGCAGGCCAAACCG 2 116 1 AAAAAGGCAG 0.875148 -20 CATAACCTTCAAAAAGTAAGAAATGTGAAAT 3 61 1 AAAAAGAAGA 0.932599 -71 TTAAGGTTGAAAAAAGTAAGATAATACTTGA 4 61 1 AAAAAGAAGA 0.932599 -31 ACTCTCCCTGAAAAAGGGAGAGTAAACG 5 8 0 AAAAAGGAGA 0.98248 -115 TATGATGATGAAAAAGCGCGATTCATTAAAC 6 13 0 AAAAAGGCGA 0.953262 -42 AAAAGCACATTAAAGGAGGAAGCACC 7 6 0 TAAAGGGGAA 0.723015 -275 TAGAAGGGATAAAAGGAAAAAAGAACGCCCG 7 46 1 AAAAGGAAAA 0.940337 -235 TGATACTTGAAAATGGTGAGATG 7 268 1 AAATGGGAGA 0.911456 -13 TAAAAAGAGAGAAAGGCTTGCT 8 2 1 AAAAAGGAGA 0.98248 -210 CATTTATAGTAAAAAGAGAAAGGCTGTATTA 8 33 0 AAAAAGGAAA 0.980113 -179 AAAATGATGTAAAAGGCGAATTGTCGGAATG 8 97 1 AAAAGGGAAT 0.917259 -115 AGATGACATAAAATAGAGAAATAGGATGTCG 8 165 1 AAATAGGAAA 0.874689 -47 AAACTAGCCATAAAGGAGAAGAGAGAC 9 27 1 TAAAGGGAAG 0.882672 -17 TCTCTCCCCCAAAAAGAAAATGCTTACATTT 11 195 0 AAAAAGAAAT 0.678506 -106 AGGCTTACTTAAAAAGCACGATGCAAGTATT 11 226 0 AAAAAGACGA 0.834232 -75 ACAACACTCTTAAAGGGGAAATTTATTGAAA 11 266 1 TAAAGGGAAA 0.95059 -35 AAATTTATTGAAAAGGAGATGTTATAT 11 284 1 AAAAGGGATG 0.760407 -17 CAACTGGCGATAAAGGTGAAACATGTGTTTT 12 138 1 TAAAGGGAAA 0.95059 -163 ****** **** Masking position 3 Map Score: 21.9829 Number of sites scoring better than the average of aligned sites = 1860 Number in coding regions = 1425 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 458 Fraction of orfs with sites within 600 bp upstream = 0.0735625 Motif number 2 CACAGTTCTCAAACTTTCTCACGATTTGAT 1 25 1 AAACTTTCTC 0.628718 -56 TTCTTTATGCGGCCTTTCTTGTGTATTTAA 2 52 1 GGCCTTTCTT 0.827071 -84 GAAATTTAGAAAGCGTTTTTACCGTGATCC 3 30 0 AAGCGTTTTT 0.887533 -102 AAACGGCGTTTTTTTTAGATTTG 4 4 1 CGGCGTTTTT 0.792766 -88 CTTAACAAACAAGCTTTTTCAAATTCCTAT 4 36 0 AAGCTTTTTC 0.956055 -56 TTAATGAATCGCGCTTTTTCATCATCATAA 6 15 1 GCGCTTTTTC 0.785442 -40 ACTAGAGGCCGGGCGTTCTTTTTTCCTTTT 7 56 0 GGGCGTTCTT 0.917521 -225 CCAGAAGCAAAGGCTTTTTCTCCCGCTTCT 7 104 1 AGGCTTTTTC 0.983983 -177 GTATTAAGCAAGCCTTTCTCTCTTTTTA 8 9 0 AGCCTTTCTC 0.949996 -203 TGCTTAATACAGCCTTTCTCTTTTTACTAT 8 29 1 AGCCTTTCTC 0.949996 -183 GGCTAGTTTTAGGCTTTTTCCTTGC 9 6 0 AGGCTTTTTC 0.983983 -38 CCGCAAATAAAGGCGTTTTTTCGGGGAAAT 11 18 1 AGGCGTTTTT 0.957052 -283 AAATTTTTATAAGCTTATTTAAGTTTAAGC 11 119 0 AAGCTTATTT 0.673792 -182 AGTAAAATGTAAGCATTTTCTTTTTGGGGG 11 191 1 AAGCATTTTC 0.734335 -110 TAAAAACATGAGGCTTACTTAAAAAGCACG 11 237 0 AGGCTTACTT 0.863522 -64 ********** Masking position 6 Map Score: 14.3808 Number of sites scoring better than the average of aligned sites = 1639 Number in coding regions = 1398 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 3 GTACAGAATATTCAAAACACAAGAGGTGTTTGCTCGGAGCG 7 135 0 TTAAAAATTT 0.921501 -146 CTCTTTTTACTATAAATGAAAGCGCTATCATAAACGTCTTT 8 46 1 TAAAAAAAAT 0.606017 -166 TTACATCATTTTTAAAAGAAATAAAGACGTTTATGATAGCG 8 68 0 TTAAAAAATT 0.953665 -144 TAACATTCAATTTAAAGTGTAACCCAATTTTGATGTCTGAA 10 55 0 TTAAAGAATT 0.750148 -109 ATTTTTCTTATATAGAAAATAAAATGATTTTTCCTAACATT 10 89 0 TAAGAAAATT 0.911994 -75 GTAATTCATATTTAGAAAACATTTTATTTTTCTTATATAGA 10 114 0 TTAGAAATTT 0.886155 -50 GAATGGAAAAAAAAAATTATAGGTAAACATTTAACAAATGT 11 52 1 AAAAAAAATT 0.624504 -249 CTATTCTCATTATAAACAATAATCAGACATTTGTTAAATGT 11 78 0 TAAAAAAATT 0.939862 -223 CCCTTTGCTTTTGAAAGAACATAACAAATTTTTATAAGCTT 11 133 0 TTAAAAAATT 0.953665 -168 TTCTCTCCCCCAAAAAGAAAATGCTTACATTTTACTGGCTG 11 186 0 CAAAAAAATT 0.711398 -115 CTGCGGCCGGTTCAAAGAAGAAGACGTCATTGATAAAGACG 12 25 1 TTAAAAATTT 0.921501 -276 GTCAACTTTTTTTAAAAAAGATAACTTTATTGAAACCTCCC 12 78 0 TTAAAAATTT 0.9215 -223 AAAATAAAGGTTTAGAAAAAAAACACATGTTTCACCTTTAT 12 147 0 TTAGAAAATT 0.931729 -154 ACGAATGTTATATAGATGAAATGAAGTCATTCGGCAGGAGG 12 258 1 TAAGAAATTT 0.855293 -43 ** *** * * * ** Masking position 11 Map Score: 9.35107 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 229 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 4 TGAAAGTAACAGAAGGAAAGCAGGGGGAAA 1 59 1 AGAAGGAAAG 0.709114 -22 GAAGGAAAGCAGGGGGAAAAC 1 70 1 AGGGGGAAAA 0.925946 -11 GATCTGCAATAGGGGGAAGGGGGCA 3 117 1 AGGGGGAAGG 0.963833 -15 TCCCTGAAAAAGGGAGAGTAAACG 5 5 0 AGGGAGAGTA 0.757351 -118 TCCCTTTTTCAGGGAGAGTTTTTTTATGTT 5 20 1 AGGGAGAGTT 0.625865 -103 ATAAGATATAAGGAAGAAGCTATC 6 41 1 AGGAAGAAGC 0.917694 -14 AGCACATTAAAGGAGGAAGCACC 7 4 0 AGGAGGAAGC 0.947313 -277 AAGGGATAAAAGGAAAAAAGAACGCCCGGC 7 49 1 AGGAAAAAAG 0.794708 -232 AGCGCAGAAGCGGGAGAAAAAGCCTTTGCT 7 109 0 CGGGAGAAAA 0.615466 -172 TAAAAAGAGAGAAAGGCTTGCTTAA 8 6 1 AGAGAGAAAG 0.747764 -206 TATAGTAAAAAGAGAAAGGCTGTATTAAGC 8 30 0 AGAGAAAGGC 0.512676 -182 GCAAGGAAAAAGCCTAAAACTAG 9 4 1 AGGAAAAAGC 0.823278 -40 CTAGCCATAAAGGAGAAGAGAGAC 9 30 1 AGGAGAAGAG 0.815012 -14 ATTGAATGTTAGGAAAAATCATTTTATTTT 10 85 1 AGGAAAAATC 0.744982 -79 GGCGTTTTTTCGGGGAAATCACAGAATGGA 11 29 1 CGGGGAAATC 0.655998 -272 ATTTTCTTTTTGGGGGAGAGAAATACTTGC 11 205 1 TGGGGGAGAG 0.610125 -96 ACACTCTTAAAGGGGAAATTTATTGAAAAG 11 269 1 AGGGGAAATT 0.614941 -32 AGGGAGAACCGGCCCTGCGG 12 1 1 AGGGAGAACC 0.833705 -300 GCCGGTTCAAAGAAGAAGACGTCATTGATA 12 30 1 AGAAGAAGAC 0.487474 -271 GTCATTCGGCAGGAGGAAAATCAAAATG 12 283 1 AGGAGGAAAA 0.864425 -18 ********** Masking position 7 Map Score: 10.3308 Number of sites scoring better than the average of aligned sites = 2693 Number in coding regions = 2002 Number in noncoding regions = 691 Number of orfs with sites within 600 bp upstream = 732 Fraction of orfs with sites within 600 bp upstream = 0.117571 Motif number 5 TTTACCGTGATCCGCCAGTGCTCTGAGCCTTT 3 11 0 TCCGCCAGTT 0.917504 -121 GTCTTTCACCTCAAGTATTATCTTACTTT 4 73 0 ACCTCAAGTT 0.897526 -19 AGAACGCCCGGCCTCTAGTGCTTCTTAGAAAG 7 67 1 GCCTCTAGTT 0.971552 -214 CCGAGCAAACACCTCTTGTGTTTTGAATATTC 7 139 1 ACCTCTTGTT 0.866685 -142 ATACTATTTCATATCCTGTTTTGAAGGAGTTT 7 176 0 ATATCCTGTT 0.529239 -105 ATACTATAGGGTAGCCAGTTTTTCCGGCAATG 7 232 1 GTAGCCAGTT 0.829163 -49 GCTGTGCCTCCAGTATTATAATTCCCC 8 195 0 GCCTCCAGTT 0.991808 -17 ACGCAAGCCAGCCTCCAATGGTTCT 10 4 0 GCCTCCAATT 0.896767 -160 AATGAGGTTAGCCTCTTGTTCAGACATCAAAA 10 37 1 GCCTCTTGTA 0.798777 -127 TTTAGTTCCAGCAGCCAGTAAAATGTAAGCAT 11 175 1 GCAGCCAGTA 0.831256 -126 TTTTAAGTAAGCCTCATGTTTTTACAACACTC 11 243 1 GCCTCATGTT 0.925175 -58 TTTCACCTTTATCGCCAGTTGTTTATCTATTG 12 127 0 ATCGCCAGTT 0.889755 -174 ********* * Masking position 9 Map Score: 6.65116 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 631 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 6 GAACTGTGTCGCTTTCAAAGGA 1 3 0 GCTTTCAAAG 0.936196 -78 CGGTAAAAACGCTTTCTAAATTTCACATAA 3 36 1 GCTTTCTAAA 0.916221 -96 ACAAACAAGCTTTTTCAAATTCCTATGCCA 4 32 0 TTTTTCAAAT 0.601519 -60 TTCTGGTTTTCCTTTCTAAGAAGCACTAGA 7 80 0 CCTTTCTAAG 0.806502 -201 CTGTACAAACTCCTTCAAAACAGGATATGA 7 170 1 TCCTTCAAAA 0.667482 -111 TTTTACATCATTTTTAAAAGAAATAAAGAC 8 81 0 TTTTTAAAAG 0.550658 -131 AAAATAAAATGTTTTCTAAATATGAATTAC 10 125 1 GTTTTCTAAA 0.872284 -39 ACATAACAAATTTTTATAAGCTTATTTAAG 11 126 0 TTTTTATAAG 0.700017 -175 TTTGTTATGTTCTTTCAAAAGCAAAGGGTT 11 146 1 TCTTTCAAAA 0.920169 -155 CTTGCATCGTGCTTTTTAAGTAAGCCTCAT 11 230 1 GCTTTTTAAG 0.589962 -71 TGGTCAACTTTTTTTAAAAAAGATAACTTT 12 91 0 TTTTTAAAAA 0.43667 -210 ACATGTGTTTTTTTTCTAAACCTTTATTTT 12 158 1 TTTTTCTAAA 0.878603 -143 ********** Masking position 8 Map Score: 3.70919 Number of sites scoring better than the average of aligned sites = 1082 Number in coding regions = 864 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 7 TTCTGTTACTTTCATTTTATCAAATCGTGAG 1 42 0 TTCTTTTATC 0.965536 -39 GGAGAGTTTTTTTATGTTTGCTTCCAGAAAT 5 32 1 TTTTGTTTGC 0.67018 -91 GATAGCTTCTTCCTTATATCTTATGATGAT 6 35 0 TTCTTATATC 0.874234 -20 GCGTTCTTTTTTCCTTTTATCCCTTCTATGG 7 43 0 TTCTTTTATC 0.965536 -238 AATAAAGACGTTTATGATAGCGCTTTCATTT 8 59 0 TTTTGATAGC 0.67018 -153 GTTTCATGATTTTATTTTAGCGAAAGCAGGA 8 128 0 TTTTTTTAGC 0.928954 -84 ATTTCTCTATTTTATGTCATCTTAACATGTT 8 156 0 TTTTGTCATC 0.891179 -56 TTACCTATAATTTTTTTTTTCCATTCTGTGA 11 47 0 TTTTTTTTTC 0.838184 -254 TAAACCTTTATTTTTTTTATCTTTTGACCTT 12 174 1 TTTTTTTATC 0.954289 -127 CTATATAACATTCGTTTCATCACTTATGGCC 12 242 0 TTCTTTCATC 0.946083 -59 GCCGAATGACTTCATTTCATCTATATAACAT 12 262 0 TTCTTTCATC 0.946083 -39 *** ******* Masking position 5 Map Score: 10.9143 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 394 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 8 ACACAAGAAAGGCCGCATAAAGAAAATTTCCGCTC 2 41 0 GGCGATAAAA 0.98227 -95 AAAAGAGAAAGGCTGTATTAAGCAAGCCTTTCTCT 8 18 0 GGCGATAAAA 0.98227 -194 ACATTTTACTGGCTGCTGGAACTAAAACCCTTTGC 11 166 0 GGCGTGAAAA 0.988465 -135 CCGGCCCTGCGGCCGGTTCAAAGAAGAAGACGTCA 12 19 1 GGCGTTAAAA 0.990418 -282 TCCGGTGAGGGGAGGTTTCAATAAAGTTATCTTTT 12 69 1 GGAGTTAAAA 0.941145 -232 CATCACTTATGGCCCATGTAAAGAATGGGTCCTTG 12 221 0 GGCCTGAAAA 0.951571 -80 *** * ** ** ** Masking position 10 Map Score: 2.59931 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 114 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 TCACGTCCTTGTGGTGGTTTGTACAAGTTT 5 97 0 GTGGTGGTTT 0.967564 -26 CGAGAGCTTTTTGGTGGCTTATACTATAGG 7 212 1 TTGGTGGCTT 0.967564 -69 AGAACCATTGGAGGCTGGCTTGCGTCA 10 8 1 TTGGAGGCTG 0.95063 -156 AATTACATACTGGGAGGTTTTTATT 10 149 1 TGGGAGGTTT 0.977139 -15 ACTCCGGTGAGGGGAGGTTTCAATAAAGTT 12 67 1 GGGGAGGTTT 0.978787 -234 ********** Masking position 9 Map Score: 1.08956 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 39 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 CTTTATTCCCGCGTATGGCCCCGCCGAAGA 2 94 0 GCGTATGGCC 0.957873 -42 ATCCGCCAGTGCTCTGAGCCTTT 3 4 0 GCTCTGAGCC 0.766764 -128 ACAAGTTTATGCGCATGTCCATCAGTTATG 5 75 0 GCGCATGTCC 0.97483 -48 GTTTGCTCACGTCCTTGTGGTGGT 5 109 0 GCTCACGTCC 0.974699 -14 GGAAAAAAGAACGCCCGGCCTCTAGTGCTT 7 60 1 ACGCCCGGCC 0.939743 -221 CCACCAAAAAGCTCTCGTCCAATACTATTT 7 199 0 GCTCTCGTCC 0.9437 -82 TTTGAACCGGCCGCAGGGCCGGTTCTCCCT 12 11 0 CCGCAGGGCC 0.960954 -290 TCGTTTCATCACTTATGGCCCATGTAAAGA 12 232 0 ACTTATGGCC 0.796395 -69 ********** Masking position 2 Map Score: 2.74723 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 358 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 ********** No masking Map Score: 3.13593e-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: 3.13593e-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: 3.13593e-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