AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_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 yfjN 300 similar to hypothetical proteins #2 yfjM 195 yfjM #3 yfjL 29 alternate gene name: yztA #4 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #5 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #6 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #7 odhB 29 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) #8 odhA 227 2-oxoglutarate dehydrogenase (E1 subunit) #9 yojN 63 similar to nitric-oxide reductase #10 yojM 92 similar to superoxide dismutase #11 yojL 300 similar to cell wall-binding protein #12 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #13 yqiS 124 similar to phosphate butyryltransferase #14 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) Motif number 1 CAAAAAGTTCAAAAGCAAGGCCACTAAGAA 1 87 1 AAAAGCAAGG 0.978954 -214 TAAGTGTAAAAGAAGCATGGTCAGTTTTTA 1 228 1 AGAAGCATGG 0.791041 -73 AAAGGCTAACAAAATAAAGGGATTTTTACA 2 30 1 AAAATAAAGG 0.96746 -166 GGATTTACCGAAAATCCAGGTTTATTTTAG 2 70 0 AAAATCCAGG 0.913077 -126 TAAATTAGAGAAAAGACAGGCTGAGTAAAA 2 120 0 AAAAGACAGG 0.972013 -76 TTATTGTAAGAAAATAATGGTATATTTAGT 2 147 1 AAAATAATGG 0.943141 -49 ACATATGAGGAAAAGAGTGGGAAC 3 16 1 AAAAGAGTGG 0.846231 -14 GCATGCAAAAAAAAGACCGGATATCACCCG 4 54 0 AAAAGACCGG 0.856369 -178 TTACGGGCTCAAAAGACTGGCACACTTCTT 4 170 1 AAAAGACTGG 0.950925 -62 ATGACTGTTTAAAAGAAAGGAAGAGGTGAC 5 276 1 AAAAGAAAGG 0.985427 -25 TATTTTGTGAACAATCAAGGTAGAATCAAA 8 85 1 ACAATCAAGG 0.913077 -143 CACTGTTAGAAAAAACAAGGGGGAGACAGT 10 73 1 AAAAACAAGG 0.785642 -20 AGAAAAATAGACAAGAAAGGAGGAGAAACT 11 22 1 ACAAGAAAGG 0.972013 -279 AGCGAGGGTAAAAATGATGGTTTTCTATTG 11 63 0 AAAATGATGG 0.723469 -238 ATGCTTTTAAAAATGAATGGCTTTGCCATC 12 39 0 AAATGAATGG 0.740601 -35 CGGAGTCGAAACAAGAAAGGTGGTAACAG 13 106 1 ACAAGAAAGG 0.972013 -19 AGGAAATGAAAAGATAAAGGGGTTTTCTGA 14 13 0 AAGATAAAGG 0.769309 -140 TTTCCGCTGGACAATAAAGGAAATGAAAAG 14 30 0 ACAATAAAGG 0.938539 -123 ********** Masking position 1 Map Score: 26.1755 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 454 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 2 GTGGAGATATCATATAAAGGGGGAGAGGAAA 2 175 1 CATAAAGGGA 0.934287 -21 GTGAACCCTAAATAGAAGGAGGCGCACAAA 4 212 1 AATAAGGGGG 0.973052 -20 TAGTTTACACCAAATAAAGAAGAACCGTCAATCG 5 60 0 CAAAAAGAGA 0.86599 -241 TAAACTAATCCATGTTAAGCGGTGTTGTATTAGT 5 87 1 CATTAAGGGG 0.832217 -214 TGACTGTTTAAAAGAAAGGAAGAGGTGACTTAGT 5 277 1 AAAAAGGAGG 0.942568 -24 ATTGCTTAATCAAACTAGGAGGTCGAGAACT 6 94 1 CAATAGGGGC 0.84738 -21 CTCGCAAAAACTAAGGGGGAAATGAAAAA 7 8 1 AAAAAGGGGA 0.971472 -22 ATTTTGTGAACAATCAAGGTAGAATCAAATTGCA 8 86 1 CAAAAGGAGA 0.961431 -142 ACTGTTAGAAAAAACAAGGGGGAGACAGT 10 74 1 AAAAAGGGGG 0.98445 -19 GAAAAATAGACAAGAAAGGAGGAGAAACTGCTTC 11 23 1 CAAAAGGGGG 0.994437 -278 GAACTTGCATAATAAAAGGCGGAGTCGAAACAAG 13 87 1 AATAAGGGGG 0.973052 -38 GGAGTCGAAACAAGAAAGGTGGTAACAG 13 107 1 CAAAAGGGGA 0.989708 -18 TTCCGCTGGACAATAAAGGAAATGAAAAGATAAA 14 25 0 CAAAAGGAAG 0.73829 -128 CAAATTTTTTCATACAAAGGGGTATCGGG 14 134 1 CATAAAGGGA 0.934287 -19 *** **** ** * Masking position 7 Map Score: 20.1373 Number of sites scoring better than the average of aligned sites = 509 Number in coding regions = 340 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 3 AACAAAAATCAAATCCTTTCATTATGGGATAC 1 279 0 AAACCTTCAT 0.983583 -22 AATTGTGTAAAAATCCCTTTATTTTGTTAGCC 2 33 0 AAACCTTTAT 0.982237 -163 AATGTAAAGCGAATACATTTATTGAAAATCAG 5 19 1 GAAACTTTAT 0.943828 -282 CCAGTTTGCCAAAACCTTTTATGTAGGATAGT 5 162 0 AAACCTTTAT 0.982225 -139 ATAATAGAGGGAAAACGTTCATCTTCCCTCTC 6 26 0 GAAACTTCAT 0.947909 -89 CAAAATAGTAAAAAACCTTTATAAAAAACAAA 8 60 0 AAAACTTTAT 0.958967 -168 AGTATGACAAAAAGCCTTTTATAGGCTTTTTT 10 16 1 AAACCTTTAT 0.982237 -77 TTCATCAATAGAAAACCATCATTTTTACCCTC 11 58 1 GAAACATCAT 0.719217 -243 CGCAGATGGCAAAGCCATTCATTTTTAAAAGC 12 35 1 AAACCTTCAT 0.983583 -39 CTTCAGAAAACCCCTTTATCTTTTCATTT 14 8 1 AAACCTTTAT 0.982237 -145 *** ** ***** Masking position 9 Map Score: 16.7386 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 122 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TGGAATCCTTTTTATCCAAAAAGTTCAAAAGCAAGG 1 71 1 TTCAAAAATC 0.955275 -230 CAGCAGTGCTTGATTCAAAAAAGGCTAACAAAATA 2 10 1 TTCAAAAAGC 0.992809 -186 GAGTAAAAGCTGCGTACAAAAAAGACCCGGATTTAC 2 92 0 TTCAAAAAGC 0.992809 -104 CCCTGTATGCTCAATACAAAAGGGCCTGGATGATA 9 10 0 TTCAAAAGGC 0.977002 -54 CATTGTCTGGTATAAACAAAAAAGCCTATAAAAGGC 10 29 0 TACAAAAAGC 0.966288 -64 GCTAGTATTTTGTTTCCAAAAATGGCACACAACTGT 11 239 0 TTCAAAAAGC 0.992809 -62 CTAAACTGTTTTTTTGCAAAAACAGCTAGTATTTTG 11 263 0 TTCAAAAAAC 0.955275 -38 * * ****** * * Masking position 8 Map Score: 6.81787 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 32 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 GGGCTCAAAAGACTGGCACACTTCTTGCATT 4 174 1 GACTGGCAAC 0.793618 -58 TCAAACTGCATAATCGAGAGGGA 6 3 1 AAACTGCAAA 0.834989 -112 GTAAACTTTAAAATTGCTTAATCAAACTAGG 6 82 1 AAATTGCTAA 0.872514 -33 AGGTAGAATCAAATTGCAAACAGTGGTAAAA 8 102 1 AAATTGCAAC 0.965378 -126 AAAAGGGTTTAACTTGCTGAAAAATTGACGA 11 204 1 AACTTGCTAA 0.892064 -97 TTGTTTCCAAAAATGGCACACAACTGTTTTA 11 235 0 AAATGGCAAC 0.931644 -66 GCTGGCATGGAACTTGCATAATAAAAGGCGG 13 78 1 AACTTGCAAA 0.963173 -47 CCGTTGCAATAATTTGCACAACCCTATGTTA 14 89 0 AATTTGCAAA 0.920684 -64 TGTATGAAAAAATTTGCACACCTATTTATTC 14 119 0 AATTTGCAAC 0.937282 -34 ******** ** Masking position 2 Map Score: 4.75108 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 139 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 CTTTTTGGATAAAAAGGATTCCAACCTAAA 1 64 0 AAAAAGGATT 0.843087 -237 GCTTGATTCAAAAAAGGCTAACAAAATAAA 2 18 1 AAAAAGGCTA 0.928606 -178 GAATTGTGTAAAAATCCCTTTATTTTGTTA 2 36 0 AAAATCCCTT 0.777126 -160 AACAAACGCCAAAAAGCATAGGATTAAGGG 8 11 0 AAAAAGCATA 0.892146 -217 ACAAAATAGTAAAAAACCTTTATAAAAAAC 8 63 0 AAAAAACCTT 0.847727 -165 ATTATGTAATAAAAACGCTTCCAACGATAT 8 132 0 AAAAACGCTT 0.907523 -96 TGAGTATGACAAAAAGCCTTTTATAGGCTT 10 14 1 AAAAAGCCTT 0.977231 -79 GGTATAAACAAAAAAGCCTATAAAAGGCTT 10 27 0 AAAAAGCCTA 0.967014 -66 CATTCATTTTTAAAAGCATAAAGGAGGGGC 12 50 1 TAAAAGCATA 0.537875 -24 CTTCAGAAAACCCCTTTATCTTTTCA 14 7 1 AAAACCCCTT 0.83787 -146 ********** Masking position 4 Map Score: 5.75336 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 458 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 7 ATTTTAGTCAAGAATTGTGTAAAAATCCCTTT 2 45 0 AGTTGTGTAA 0.930348 -151 AGACAGTTTGAGACGTGTGTCTCGTTTTGTCT 4 112 0 AGGTGTGTCT 0.92465 -120 TATAAATGCAAGAAGTGTGCCAGTCTTTTGAG 4 177 0 AGGTGTGCCA 0.991878 -55 TACAGTTCAAAGCAGAGTGTAACTATCCTACA 5 141 1 AGGAGTGTAA 0.910436 -160 ACGATAAAACAGTTGTGTGCCATTTTTGGAAA 11 231 1 AGGTGTGCCA 0.991878 -70 GTGGTAACATAGGGTTGTGCAAATTATTGCAA 14 85 1 AGTTGTGCAA 0.965019 -68 AACGGAATAAATAGGTGTGCAAATTTTTTCAT 14 115 1 ATGTGTGCAA 0.929165 -38 ** ******** Masking position 1 Map Score: 3.50326 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 47 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ATCATATAAAGGGGGAGAGGAAA 2 183 1 GGGGGAGAGG 0.844537 -13 CTGTCTCCAAAGTGAAGATGAGAAGACTGA 4 138 1 AGTGAAGATG 0.872292 -94 TTGATGAAAATGTAAAGCGAAT 5 3 1 GATGAAAATG 0.893917 -298 GAAAATCAGCGATGAAAACGATTGACGGTT 5 42 1 GATGAAAACG 0.824895 -259 GTTTAAAAGAAAGGAAGAGGTGACTTAGT 5 282 1 AAGGAAGAGG 0.624234 -19 CATAATCGAGAGGGAAGATGAACGTTTTCC 6 19 1 AGGGAAGATG 0.915913 -96 TATATAATAGAGGGAAAACGTTCATCTTCC 6 31 0 AGGGAAAACG 0.870045 -84 CAAAAACTAAGGGGGAAATGAAAAA 7 15 1 GGGGGAAATG 0.939621 -15 CAAGAAAGGAGGAGAAACTGCTTCGTTCAT 11 33 1 GGAGAAACTG 0.833223 -268 TTTAAGCGAGGGTAAAAATGATGGTTTTCT 11 67 0 GGTAAAAATG 0.563475 -234 GTCGAACGATGCTGAAAATGCTGCGCCAAA 11 168 1 GCTGAAAATG 0.75497 -133 AGCAATTGGAGAAGCTGCGCTTGCCGC 12 8 1 GGAGAAGCTG 0.819629 -66 GCTGGACAATAAAGGAAATGAAAAGATAAA 14 25 0 AAAGGAAATG 0.527109 -128 TTTGTCAAGAGAAGAAAACGTGGTAACATA 14 66 1 GAAGAAAACG 0.792689 -87 ********** Masking position 6 Map Score: 5.30472 Number of sites scoring better than the average of aligned sites = 2161 Number in coding regions = 1907 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 9 TAACAGGGCAATTATTTTGCGTTGGT 1 6 1 GGGCAATTTT 0.936749 -295 AAAGAAGCATGGTCAGTTTTTAATTTGGGAT 1 236 1 GGTCAGTTTT 0.936749 -65 GAAATAAATACGTCGATCATTGTCAAAGGCC 4 24 1 CGTCGATCTT 0.958827 -208 AAAGAAGAACCGTCAATCGTTTTCATCGCTG 5 48 0 CGTCAATCTT 0.984541 -253 CTAACAGTGTGGTCAATCATTGTCTGGTATA 10 51 0 GGTCAATCTT 0.984541 -42 ACTGTTTTATCGTCAATTTTTCAGCAAGTTA 11 213 0 CGTCAATTTT 0.975906 -88 ******** ** Masking position 7 Map Score: 1.51541 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 60 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 TTATTTTGCGTTGGTAATATGGAGAACTCA 1 22 1 TTGGTAATAT 0.77566 -279 GGTATATTTAGTGGAGATATCATATAAAGG 2 165 1 GTGGAGATAT 0.910785 -31 TGTCAAAGGCCGGGTGATATCCGGTCTTTT 4 44 1 CGGGTGATAT 0.755266 -188 CATCTTCACTTTGGAGACAGTTTGAGACGT 4 128 0 TTGGAGACAG 0.753388 -104 ATTGCAAACAGTGGTAAAATATCGTTGGAA 8 114 1 GTGGTAAAAT 0.821255 -114 ATTTAAGTTGGGGGTAATATTCAA 8 214 1 GGGGTAATAT 0.925754 -14 AAAAAACAAGGGGGAGACAGT 10 82 1 GGGGAGACAG 0.916784 -11 AACAAGAAAGGTGGTAACAG 13 115 1 GTGGTAACAG 0.951722 -10 AGAAGAAAACGTGGTAACATAGGGTTGTGC 14 75 1 GTGGTAACAT 0.959939 -78 ********** Masking position 7 Map Score: 2.27723 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 143 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 11 AAAGGTTTTGGCAAACTGGGGATCGGCTAAA 5 175 1 GCAAACTGGG 0.973299 -126 TTTTATACATACAAACTTAGGGTACCCTAAA 5 231 0 ACAAACTTGG 0.816236 -70 GAATCAAATTGCAAACAGTGGTAAAATATCG 8 107 1 GCAAACAGGG 0.988205 -121 TTTGTATTGAGCATACAGGGGCTTTTTTAGT 9 26 1 GCATACAGGG 0.973301 -38 TAAACCCTTTTCAAACATTTGGCGCAGCATT 11 184 0 TCAAACATTG 0.830861 -117 CAGAATAAACGCAAACATCTGCACGAATGTT 13 15 1 GCAAACATTG 0.935641 -110 GCAAATTTTTTCATACAAAGGGGTATCGGG 14 133 1 TCATACAAGG 0.756119 -20 ******** ** Masking position 5 Map Score: 1.3734 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 227 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 AACAAAAATCAAATCCTTTCATT 1 288 0 AAAAATCAAA 0.866689 -13 TCGAAGTTGTAAAAAACTAATACAACACCG 5 106 0 AAAAAACTAA 0.915196 -195 CTCGCAAAAACTAAGGGGGAAATG 7 5 1 CAAAAACTAA 0.716028 -25 TAATCATTCGAAAAAACAAACGCCAAAAAG 8 25 0 AAAAAACAAA 0.953646 -203 AAACCTTTATAAAAAACAAAAAATTTAATC 8 50 0 AAAAAACAAA 0.953646 -178 TGTCTGGTATAAACAAAAAAGCCTATAAAA 10 32 0 AAACAAAAAA 0.654574 -61 ACACTGTTAGAAAAAACAAGGGGGAGACAG 10 72 1 AAAAAACAAG 0.827788 -21 ACCTTCAAATAAACATCTAACATTTTACAT 11 132 0 AAACATCTAA 0.737737 -169 GGCGGAGTCGAAACAAGAAAGGTGGTAACA 13 104 1 AAACAAGAAA 0.737436 -21 ********** Masking position 5 Map Score: 3.69863 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 606 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 13 ********** No masking Map Score: -6.1574e-13 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 TTCGGTAAATCCGGGTCTTTTTTGTACGCA 2 88 1 CCGGGTCTTT 0.984259 -108 GTTCCCACTCTTTTCCTCATATG 3 17 0 CCCACTCTTT 0.904344 -13 CCGGATATCACCCGGCCTTTGACAATGATC 4 38 0 CCCGGCCTTT 0.985524 -194 CCGGGTGATATCCGGTCTTTTTTTTGCATG 4 53 1 TCCGGTCTTT 0.927038 -179 CAAGAAGTGTGCCAGTCTTTTGAGCCCGTA 4 171 0 GCCAGTCTTT 0.837059 -61 TATCATCCAGGCCCTTTTGTATTGAGC 9 8 1 CAGGCCCTTT 0.856445 -56 ATTGAGCATACAGGGGCTTTTTTAGTATAC 9 31 1 CAGGGGCTTT 0.884828 -33 ********** Masking position 8 Map Score: 0.694192 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 307 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 15 ********** No masking Map Score: -6.1574e-13 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