AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_rpxx_reg_100.orf -o00561_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -x5 -e 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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #2 RP048 148 60 KD INNER-MEMBRANE PROTEIN (yidC) #3 RP240 217 unknown #4 RP241 32 unknown #5 RP242 225 CDP-DIACYLGLYCEROL--SERINE O-PHOSPHATIDYLTRANSFERASE (pssA) #6 RP249 115 D-ALANINE--D-ALANINE LIGASE (ddlB) #7 RP366 75 APOLIPOPROTEIN N-ACYLTRANSFERASE (lnt) #8 RP410 149 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD) #9 RP411 74 CELL DIVISION PROTEIN FTSW (ftsW) #10 RP425 150 unknown #11 RP441 86 unknown #12 RP442 57 GLYCEROL-3-PHOSPHATE DEHYDROGENASE (gpsA) #13 RP469 74 POSSIBLE 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE (plsC) #14 RP719 300 unknown #15 RP750 80 PHOSPHATIDYLGLYCEROPHOSPHATASE A (pgpA) #16 RP825 300 UNDECAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE (mraY2) Motif number 1 AAATAAATCAATATTATTAATTTAAATTTCTCAC 1 88 1 ATTAAATTTA 0.870493 -213 ATTTAGTTTAAAATTACTATATTAGTATTTTTAT 1 160 1 ATTAATATTA 0.934019 -141 TGCCATATAAAACTTACAATTTTATTGCATAATA 1 227 1 ATTAATTTTA 0.96722 -74 GATATTATATAAGTTATGCTTTTATTATGCAATA 1 249 0 ATTACTTTTA 0.800292 -52 AAATGTACAATAATTCTCATATTATATTCTATAA 2 19 0 TTTCATATTA 0.731848 -130 ATTAGGTCTTAAATTTTGATATTTTTGAAGCTTA 2 120 0 ATTTATATTT 0.436785 -29 AATATTTCTCTAATTATCAATTTAAATAACTAAT 3 31 0 TTTAAATTTA 0.885364 -187 CGAAATAAGATTTTTATTATTTTTACTATATCTG 3 72 1 TTTAATTTTT 0.885474 -146 AAATGATTTAAGATTCGAATTTTTATTGTTAGAA 3 163 1 ATTCATTTTT 0.529866 -55 CGAATTTTTATTGTTAGAATATTATTATATAATT 3 178 1 TTTAATATTA 0.942409 -40 TATTATTATATAATTATTAATTTATAAAGTT 3 197 1 TTTAAATTTA 0.885364 -21 TCTATAAATCTCCTTATTATTTTAA 4 2 0 TTTAATTTTA 0.97138 -31 ATCTACGAATTTTTAACAATTTTAATACTCAAAA 5 128 0 TTAAATTTTA 0.816132 -98 ACTTTATCGCAACTTAATATTTTAGTCATACTAA 6 78 1 ATTAATTTTA 0.96722 -38 CTTATAGAATTAATTAGCAAATTTTTAAAGTGCA 8 20 0 TTTAAAATTT 0.454974 -130 GCCATATCATTCCGTATAATTTTATGCATAAAAA 10 20 1 TGTAATTTTA 0.707001 -131 TATTTTATATTTTAGATGTTGCTT 10 137 0 TTTTATTTTA 0.894248 -14 CTTAATATTTATTTTATTATTTTATTCTTATAAC 11 56 0 ATTAATTTTA 0.96722 -31 TGAAAACTGGTGATTAAACTATTAGATAATAATC 12 23 0 TTTACTATTA 0.68967 -35 TTAATACCTTTTTATTTTACTCATTATAA 13 6 1 ATTTATTTTA 0.880275 -69 TTTATTTTACTCATTATAAAATTATGTTATAAAT 13 21 1 TTTAAAATTA 0.788386 -54 ATTTTTATTAATATAATTATTTTAATA 13 58 1 ATAAATTTTA 0.79419 -17 ATACGGAAGAACATTTGCATTTTACGATTATATT 14 219 1 ATTTATTTTA 0.880272 -82 TTTACTGTATAAGTTAAAATTTTATTATATAAGA 15 21 1 ATTAATTTTA 0.96722 -60 TTTTTAATTATTTTATTCTAGATTA 15 66 0 TTAAATTTTA 0.816132 -15 ACTAACTTGTTAATTTTTATATTACAGATTTAAT 16 109 1 TTTTATATTA 0.726408 -192 TATTAGAGCAAAATTAATATATTTCATTGGTGTT 16 166 0 ATTAATATTT 0.763975 -135 GTGTGGTATTTCATTAATATTTTATTAGTCATAT 16 209 0 TTTAATTTTA 0.97138 -92 * *** ****** Masking position 12 Map Score: 32.4108 Number of sites scoring better than the average of aligned sites = 818 Number in coding regions = 473 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 AAATAAAAGAACTACACAAAAACCTTAGCTAT 1 41 1 ATACAAAAAA 0.732955 -260 AGAAATTTAAATTAATAATATTGATTTATTTG 1 87 0 ATAATATATT 0.786529 -214 TGACTATAAAAATACTAATATAGTAATTTTAA 1 167 0 ATACTATATA 0.84694 -134 TAGAGAAAATAATCAATATATATCTTGTATAC 2 72 0 ATCAAATATA 0.621443 -77 ATATAGTAAAAATAATAAAAATCTTATTTCGC 3 71 0 ATAATAAAAT 0.816699 -147 ATGCTTTTTTACTACAGATATAGTAAAAATAA 3 88 0 ATACAATATA 0.695195 -130 TTTATAAATTAATAATTATATAATAATATTCT 3 193 0 ATAATATATA 0.933382 -25 TAACAATTTTAATACTCAAAAATACTATATAA 5 117 0 ATACTAAAAA 0.869442 -109 TTTTAGTCATACTAATAAAAAAGTAGAAT 6 97 1 ATAATAAAAA 0.944016 -19 TTATTTACTCATTATATTTAAACTTGCT 7 7 1 ATCATATATT 0.512799 -69 TATGCATAAAAATAAACAAAAAACATTATTAA 10 42 1 ATAAAAAAAA 0.874209 -109 ATAAGAATAAAATAATAAAATAAATATTAAGT 11 59 1 ATAATAAATA 0.938917 -28 ACTATTAGATAATAATCAAAAAAATAATA 12 8 0 ATAATAAAAA 0.944016 -50 TTTTTATTTTACTCATTATAAAATTATGTTAT 13 19 1 ATCATATAAA 0.813759 -56 AAATAATTATATTAATAAAAATGGTATTTATA 13 48 0 ATAATAAAAT 0.816698 -27 ATTTACAGCAATTAAAAATAAAGTCAAACATA 14 271 0 ATAAAATAAA 0.863659 -30 TAACTTATACAGTAAAAATATATATT 15 5 0 ATAAAATATA 0.8524 -76 TCTAGAATAAAATAATTAAAAA 15 69 1 ATAATAAAAA 0.944016 -12 TCTTATTAAGATTAATTAAATCTGTAATATAA 16 125 0 ATAATAAATC 0.646622 -176 TATTCATATGACTAATAAAATATTAATGAAAT 16 204 1 ATAATAAATA 0.938917 -97 TGTAATGATCAGTAATAATAAATATTAAATTT 16 267 1 ATAATATAAA 0.938917 -34 * **** ***** Masking position 3 Map Score: 22.1259 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 460 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 3 GAATCTCAAATAAATCAATATTATTAATTTAAA 1 81 1 TAAAATATTA 0.946135 -220 AAAATACTAATATAGTAATTTTAAACTAAATTT 1 158 0 TAAAATTTTA 0.953673 -143 GTGACTTGACTATAAAAATACTAATATAGTAAT 1 172 0 TAAAATACTA 0.604063 -129 TATTATATTCTATAAAAATTTTA 2 1 0 TAAAATTTTA 0.947708 -148 CTTATTTCGCTAAAAAAATATTTCTCTAATTAT 3 48 0 TAAAATATTT 0.516734 -170 TTTTTAGCGAAATAAGATTTTTATTATTTTTAC 3 65 1 AAAATTTTTA 0.750531 -153 TTTTTATTGTTAGAATATTATTATATAATTATT 3 182 1 TAAATTATTA 0.878681 -36 ACAGTAGAATTACACTAATTTTATGCAAGAATT 5 25 1 TAAAATTTTA 0.953817 -201 GGCAAATTGATAGACAAATTTTACAATTCTTGC 5 49 0 TAAAATTTTA 0.953743 -177 ATGTTCTTTATATAGTATTTTTGAGTATTAAAA 5 110 1 TAAATTTTTG 0.594136 -116 TCTACGAATTTTTAACAATTTTAATACTCAAAA 5 128 0 TTAAATTTTA 0.53743 -98 TAAGTTGCGATAAAGTAATATCAGTATGTTTGA 6 61 0 TAAAATATCA 0.594028 -55 TAGAATTAATTAGCAAATTTTTAAAGTGCATCA 8 17 0 TACATTTTTA 0.765067 -133 AAAATAAACAAAAAACATTATTAAAGTTGTTAT 10 50 1 AAAATTATTA 0.718807 -101 TTTATTCTTATAACTTATTATTAGTTAAGCGTC 11 37 0 TACATTATTA 0.734731 -50 ATAAAATAATAAAATAAATATTAAGTTAAATT 11 65 1 AAAAATATTA 0.858228 -22 ATGGTATTTATAACATAATTTTATAATGAGTAA 13 27 0 TACAATTTTA 0.87994 -48 TTATGTTATAAATACCATTTTTATTAATATAAT 13 42 1 AAAATTTTTA 0.750543 -33 TATTAAAATAATTATATTAATAAAAA 13 59 0 TAAAATTATA 0.465448 -16 ATGCTCATTTAAACGAAATATTAGTTAATGCAG 14 132 1 AACAATATTA 0.693286 -169 ATATCTTATATAATAAAATTTTAACTTATACAG 15 25 0 TATAATTTTA 0.667053 -56 ACCAATGAAATATATTAATTTTGCTCTAATATT 16 169 1 TAAAATTTTG 0.776107 -132 TAGTCATATGAATATCAATATTAGAGCAAAATT 16 185 0 AAAAATATTA 0.858237 -116 TTCATATGACTAATAAAATATTAATGAAATACC 16 206 1 TATAATATTA 0.681093 -95 ** * ******* Masking position 9 Map Score: 23.8479 Number of sites scoring better than the average of aligned sites = 819 Number in coding regions = 516 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 4 TAGCTATTCAAAGATGAATCTCAAATAAATCAATATTAT 1 66 1 ATAACCAATA 0.971691 -235 TTCAATTAATAACTTGAATCTCAAATTTAGTTTAAAATT 1 136 1 ATAACCAATA 0.971691 -165 ATCAATATATATCTTGTATACCAAAAGTAGCGAATATCC 2 54 0 ATTAACAAAA 0.850319 -95 AAAAATATCAAAATTTAAGACCTAATTAATA 2 128 1 ATAAACAATA 0.917158 -21 TCTAATTATCAATTTAAATAACTAATACAGATAACCTTT 3 18 0 ATAAACAATA 0.917158 -200 AATAATAAAAATCTTATTTCGCTAAAAAAATATTTCTCT 3 54 0 ATTTCCAAAA 0.767717 -164 ATTTTTAACAATTTTAATACTCAAAAATACTATATAAAG 5 115 0 ATATCCAAAA 0.653388 -111 ATCATCACTAAACCTGTACCTCTAATAAAACTAATTCCA 5 164 1 ATTACCAATA 0.983655 -62 ATTGTAGTTTAGTATCTAAGACAAATAGATAGAGATGAC 8 116 0 ATTAGCAATA 0.897376 -34 ATTTCGTAACAAATTTTAATCCCAATACAATTCCCATAA 14 93 0 ATTATCAATA 0.85507 -208 AGTTTATGATTTACAGCAATTAAAAATAAAGTCA 14 277 0 ATTAACATTA 0.656414 -24 ATTATATAAGATATTATAGCTCTAATCTAGAATAAAATA 15 44 1 ATTACCAATA 0.983655 -37 TATTGTTATTATCGTCTATCACTAATAAAGACGTAAACT 16 73 1 ATTACCAATA 0.983655 -228 TAATAAGAGAAGAATTTAACACCAATGAAATATATTAAT 16 149 1 ATTACCAATA 0.983655 -152 * * ** * * *** * Masking position 14 Map Score: 16.0594 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 52 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 GAATACTAAGTAATCTCTAAATAAAAGAACT 1 23 1 TAATCTTAAA 0.903928 -278 AATAAAATTGTAAGTTTTATATGGCAAAAAC 1 222 0 TAAGTTTATA 0.814076 -79 AATAAAAGCATAACTTATATAATATCGCTAG 1 257 1 TAACTTTATA 0.814075 -44 TCTCATATTATATTCTATAAAAATTTTA 2 8 0 TATTCTTAAA 0.880776 -141 AATCAATATATATCTTGTATACCAAAAGTAG 2 63 0 TATCTTTATA 0.774608 -86 AAGCATTCTATAAGTTTTAAAGTACCTGATA 3 114 1 TAAGTTTAAA 0.814076 -104 ATATAATTATTAATTTATAAAGTT 3 204 1 TAATTTTAAA 0.896624 -14 TTTAATCTCTATAAATCTCCTTA 4 20 0 TAATCTTATA 0.903928 -13 TAATTCATGATGTTCTTTATATAGTATTTTT 5 101 1 TGTTCTTATA 0.648466 -125 CATGATGTATTATTTTGTAAACAAATAATCG 7 49 1 TATTTTTAAA 0.87196 -27 TTAAAGTTGTTATTCTGTATACCGTGGTCAA 10 70 1 TATTCTTATA 0.880707 -81 GGTACATTTTTGATCTATAAAGCAACATCTA 10 118 1 TGATCTTAAA 0.701437 -33 ATTATAAAATTATGTTATAAATACCATTTTT 13 33 1 TATGTTTAAA 0.774669 -42 AGAGCTATAATATCTTATATAATAAAATTTT 15 36 0 TATCTTTATA 0.774613 -45 ACTAACTTGTTAATTTTTATATTACAGATTT 16 109 1 TAATTTTATA 0.896624 -192 TCATGTACCTTAATGTTTAAAGTGTGGTATT 16 233 0 TAATGTTAAA 0.643979 -68 ****** **** Masking position 6 Map Score: 13.4347 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 238 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 6 CTTATTTCGCTAAAAAAATATTTCTCTAAT 3 51 0 TAAAAAAATA 0.716017 -167 ATATCTGTAGTAAAAAAGCATTCTATAAGT 3 99 1 TAAAAAAGCA 0.972605 -119 GTCATACTAATAAAAAAGTAGAAT 6 102 1 TAAAAAAGTA 0.957588 -14 AGAGATGACTTCAAAAAGAATATGAAATTA 8 95 0 TCAAAAAGAA 0.807144 -55 GTCTATATATTAAAAAAGAAATTCATATT 11 10 0 TAAAAAAGAA 0.940324 -77 ATGAGTAAAATAAAAAGGTATTAA 13 5 0 TAAAAAGGTA 0.857082 -70 GATTACAAGCTAAAAAAGCAGTGTAGATAT 14 18 1 TAAAAAAGCA 0.972605 -283 TTATATTAGATAATAAAGCAATAAATATGT 14 246 1 TAATAAAGCA 0.864175 -55 ********** Masking position 5 Map Score: 5.96343 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 106 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 GTATTTTTATAGTCAAGTCACTGTATGACACTGAAC 1 184 1 AGTCAATTAT 0.971807 -117 TATCTGTATTAGTTATTTAAATTGATAATTAGAGAA 3 24 1 AGTTAATGAT 0.702034 -194 GGAGGTATTAAGTCACAGTTTTTTATCTTCACTGTA 8 58 1 AGTCATTTAT 0.971808 -92 TTCTTTTTGAAGTCATCTCTATCTATTTGTCTTAGA 8 105 1 AGTCATTTAT 0.971808 -45 TAGTCATTGTAGTTTAGTATCTAAGAC 8 133 0 AGTCAATTAG 0.877883 -17 ACATTATTAAAGTTGTTATTCTGTATACCGTGGTCA 10 64 1 AGTTGTTTAT 0.702034 -87 TGTATACCGTGGTCAAACTACTATATGATACCAGGT 10 85 1 GGTCAATTAT 0.877883 -66 ACTTATTATTAGTTAAGCGTCTATATATTAAAAAAG 11 22 0 AGTTATTTAT 0.918683 -65 AATAAAATTAAGTGAGGTTAATTTATCAGTATACAA 14 167 1 AGTGAATTAT 0.868886 -134 TTAAAAATAAAGTCAAACATATTTATTGCTTTATTA 14 256 0 AGTCATTTAT 0.971808 -45 ***** * * *** Masking position 12 Map Score: 3.72487 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 17 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TCTTTTATTTAGAGATTACTTAGTATTCAT 1 21 0 AGAGATTACT 0.833015 -280 TTGATTTATTTGAGATTCATCTTTGAATAG 1 69 0 TGAGATTCAT 0.970989 -232 AAACTAAATTTGAGATTCAAGTTATTAATT 1 139 0 TGAGATTCAA 0.892526 -162 GGAGATTTATAGAGATTAAA 4 23 1 AGAGATTAAA 0.634924 -10 TCAAACATACTGATATTACTTTATCGCAAC 6 61 1 TGATATTACT 0.741309 -55 AAAAAGAATATGAAATTAATACAGTGAAGA 8 83 0 TGAAATTAAT 0.852224 -67 TCAAATATTCTGAGATTCCTTAGTAAATAA 9 11 0 TGAGATTCCT 0.95971 -64 ATATTAAAAAAGAAATTCATATT 11 4 0 AGAAATTCAT 0.81372 -83 TCCCAGTTAGTGAAATTCTTGAAAAGATGT 14 51 1 TGAAATTCTT 0.662816 -250 TAAAATTAAGTGAGGTTAATTTATCAGTAT 14 169 1 TGAGGTTAAT 0.768195 -132 GCTCTAATATTGATATTCATATGACTAATA 16 191 1 TGATATTCAT 0.884466 -110 ********** Masking position 3 Map Score: 5.72889 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 81 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TGTGAGAAATTTAAATTAATAATATTGATT 1 93 0 TTAAATTAAT 0.792203 -208 CATGTTCTACTTCAATTAATAACTTGAATC 1 126 1 TTCAATTAAT 0.899326 -175 CTTAAAGCTTTTAAAGCATTTAGAGAAAAT 2 94 0 TTAAAGCATT 0.856308 -55 AATTCGAATCTTAAATCATTTCTATCCAAG 3 154 0 TTAAATCATT 0.788893 -64 ACTAATTTTATGCAAGAATTGTAAAATTTG 5 38 1 TGCAAGAATT 0.727142 -188 GTTCTTTGCATTCAATTAATTCATGATGTT 5 85 1 TTCAATTAAT 0.899326 -141 AAAAAGAATATGAAATTAATACAGTGAAGA 8 83 0 TGAAATTAAT 0.621114 -67 TACATATTATTTCAAGCAATAGTAAACTGA 9 53 0 TTCAAGCAAT 0.933174 -22 CTTACATCTTTTCAAGAATTTCACTAACTG 14 54 0 TTCAAGAATT 0.861067 -247 TATGAACTACTTCAAGTATTGTTATTATCG 16 57 1 TTCAAGTATT 0.934412 -244 ********** Masking position 5 Map Score: 2.81091 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 173 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 TAAACTTTAACTGACTTAATCACTAGCGAT 1 280 0 CTGACTTAAT 0.890747 -21 ACTAAACCAAGCAACGTAATAAAGTTTGGA 5 199 0 GCAACGTAAT 0.833418 -27 TTACTTTATCGCAACTTAATATTTTAGTCA 6 76 1 GCAACTTAAT 0.942062 -40 ATAAAAAACTGTGACTTAATACCTCCAGTT 8 54 0 GTGACTTAAT 0.950791 -96 AATTTAACTTAATATTTATTTTA 11 74 0 TTAACTTAAT 0.816246 -13 ATAAATTAACCTCACTTAATTTTATTTCCT 14 163 0 CTCACTTAAT 0.815846 -138 ACATTATCATGTACCTTAATGTTTAAAGTG 16 240 0 GTACCTTAAT 0.884079 -61 AGTAACATAATTAAATTTAAT 16 290 0 GTAACATAAT 0.856346 -11 ********** Masking position 8 Map Score: 1.08308 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 34 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 ********** No masking Map Score: 5.58019e-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: 5.58019e-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: 5.58019e-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