AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_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 yitV 120 similar to hypothetical proteins #2 yitW 63 similar to hypothetical proteins #3 yitX 54 yitX #4 yitY 57 similar to L-gulonolactone oxydase #5 yitZ 44 similar to multidrug resistance protein #6 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #7 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #8 argG 169 argininosuccinate synthase #9 moaB 84 molybdopterin precursor biosynthesis protein B #10 ackA 300 acetate kinase Motif number 1 TTACTTACAGTGTAGCTTTTTACCATCTTTA 1 49 1 TGTGCTTTTT 0.842812 -72 CATGTCAGGCTGTCCTTTTTTGTT 3 4 0 TGTCTTTTTT 0.97998 -51 CATGTGAGGCTGTCCTTTTTTACAGCTGAAA 3 31 1 TGTCTTTTTT 0.97998 -24 GCGGTCAGCCTGTTTTTTTATGCGGCTGAAA 6 12 1 TGTTTTTTAT 0.969776 -195 GGAGTCGTGCTGATTTTTTTTGAGCGGAATT 6 71 1 TGATTTTTTT 0.94946 -136 TACGATTGAATTAATTTTTATTCATGTTATA 6 145 1 TTATTTTTAT 0.73335 -62 ATTATAAAAATGAATTTTTATGCCTTTATAT 7 21 0 TGATTTTTAT 0.94294 -50 AAATTTCAGGTGAAGTTTCATAGTATTTATT 8 14 0 TGAGTTTCAT 0.827777 -156 GAAATTTAGGTGAAGTTTTTTTTATAAAAGG 8 38 1 TGAGTTTTTT 0.953168 -132 AACAAGTACGTTTCGTTTTTTCAAGCCTTTT 8 63 0 TTTGTTTTTT 0.868017 -107 ACATACAAAATGTATTTTTATTAAATATAAT 8 103 1 TGTTTTTTAT 0.969776 -67 TTAAATATAATTTATTTTTATACAAAATAGA 8 123 1 TTTTTTTTAT 0.842269 -47 TTCAAGAGAATGTGCTTTCATGCGAT 9 6 0 TGTCTTTCAT 0.920379 -79 TTCTCTTGAATGTGCTTTTTTGTTGATGCAT 9 27 1 TGTCTTTTTT 0.97998 -58 CTTCGTTTTTCGTACTTTTTTCCCGGTGAAT 10 248 0 CGTCTTTTTT 0.869135 -53 *** ******* Masking position 7 Map Score: 22.3874 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 539 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 2 CACTCCTTTTTTCTACAGTATAACGTAAATTCA 2 34 0 TCTACGATAA 0.903957 -30 TCCTTTCAGCTGTAAAAAAGGACAGCC 3 38 0 TCAGCGAAAA 0.973989 -17 GGTGCCGCATTTCAGCCGCATAAAAAAACAGGC 6 19 0 TCAGCGATAA 0.984265 -188 TCAGCACGACTCCAGCACAAAAACGTTGATGCG 6 51 0 TCAGCCAAAA 0.844883 -156 ACAGAAAATTTATAAATGAATAAAAATATTAAA 6 110 1 TTAAAGATAA 0.931181 -97 TGTGAAATTATTTAACATTATAACATGAATAAA 6 161 0 TTAACTATAA 0.628486 -46 TTTTTTTCGATATAAAGGCATAAAAATTCATTT 7 12 1 TTAAAGATAA 0.931169 -59 ACAGCCCACCTCTTGATGAATAATTAATTATAA 7 45 0 TTTGAGATAA 0.802686 -26 AAGTCCGGTCTTCAAAAGCATAAATAAAAGCA 10 10 0 TCAAAGATAA 0.9676 -291 AAACACAAAATACAGAGGGAAAAACCGCAAATT 10 64 1 TCAGAGAAAA 0.966819 -237 CATGACAATGTTTAAATGGAAAAGTCAGATATT 10 196 1 TTAAAGAAAA 0.905711 -105 GATGTTGATATTCACCGGGAAAAAAGTACGAAA 10 239 1 TCACCGAAAA 0.913034 -62 * **** * **** Masking position 10 Map Score: 11.4966 Number of sites scoring better than the average of aligned sites = 794 Number in coding regions = 704 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 TATTAACAAGAGCTGAATTTACGTTATACT 2 21 1 AGCTGAATTT 0.916708 -43 AAAAAGGACAGCCTGACATGTGAGGCTGTC 3 15 1 GCCTGACATG 0.970117 -40 CCTTTTTTACAGCTGAAAGGA 3 44 1 AGCTGAAAGG 0.887314 -11 AAATTAAAATGGCTGACATTATCACAAAGC 5 22 1 GGCTGACATT 0.964136 -23 TTTTTTATGCGGCTGAAATGCGGCACCGCA 6 25 1 GGCTGAAATG 0.964136 -182 ATGAAACTTCACCTGAAATTTAGGTGAAGT 8 24 1 ACCTGAAATT 0.892517 -146 GCTTTTGAAGACCGGACTTGACGAATTGAA 10 24 1 ACCGGACTTG 0.879176 -277 TCAATACGCAAGTTGACTTGAAAAGCCGAC 10 167 1 AGTTGACTTG 0.840759 -134 TGACTTGAAAAGCCGACATGACAATGTTTA 10 180 1 AGCCGACATG 0.953857 -121 TCCGAAAAATATCTGACTTTTCCATTTAAA 10 206 0 ATCTGACTTT 0.769861 -95 ********** Masking position 6 Map Score: 8.18553 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 638 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 AAGTAAGGCAAAACAAGCAAAATCTAAGGTTAAAGGAG 1 17 0 AACAGAAAAG 0.957225 -104 TCTTTATTGTCTACATGTTACACTTATGATTATGGTTA 1 74 1 CACAGTAAAG 0.872326 -47 TGGGGAAAAACAAATTAAAATGGCTGACATTATCA 5 8 1 AACAATAAGT 0.902359 -37 ATAAATGAATAAAAATATTAAATATACGATTGAATTAA 6 121 1 AAAAATAAAG 0.881932 -86 GTTAAAGTGTATACATACAAAATGTATTTTTATTAAAT 8 91 1 AACAAAAAAT 0.936244 -79 TTTTGTATAAAAATAAATTATATTTAATAAAAATACAT 8 112 0 AATAATAAAT 0.67821 -58 ATTTATTTTTATACAAAATAGAAACACGGTTGAGAGGG 8 132 1 AACAATAAAG 0.987046 -38 TGATAGTGACAGACAGAAAACATAAAAGAGGTGGGCCA 9 57 1 AACAAAAAAG 0.981148 -28 TCCAGCTTTGAAACACAAAATACAGAGGGAAAAACCGC 10 54 1 AACAAAAAAG 0.981148 -247 GAAGTTGTTGATACAGAGTATAAAGGAGCGTCAATC 10 275 1 AACAATAAGG 0.970381 -26 * *** * ** * * * Masking position 10 Map Score: 6.51034 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 186 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 AACAAAAAAGGACAGCCTGACATGTGAGG 3 10 1 GGACAGCCTG 0.99062 -45 CTGTAAAAAAGGACAGCCTCACATGTCAGG 3 26 0 GGACAGCCTC 0.993541 -29 CGCGGTCAGCCTGTTTTTTTATG 6 4 1 GGTCAGCCTG 0.983577 -203 CTAACAGCCCACCTCTTGATGAATA 7 56 0 AGCCCACCTC 0.956228 -15 TGGCCCACCTCTTTTATGTTT 9 74 0 GGCCCACCTC 0.991304 -11 ********** Masking position 9 Map Score: 4.61253 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 98 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 6 GTTCCCTCACTCCTTTTTTCTACAGTATAA 2 44 0 TCCTTTTTTC 0.97487 -20 TGTCAGGCTGTCCTTTTTTGTT 3 3 0 TCCTTTTTTG 0.865238 -52 TGTGAGGCTGTCCTTTTTTACAGCTGAAAG 3 33 1 TCCTTTTTTA 0.812451 -22 ATGCAAGCAATTTCTTTTTCATAGTGCTCT 4 31 0 TTTCTTTTTC 0.792957 -27 GCCATTTTAATTTGTTTTTCCCCA 5 5 0 TTTGTTTTTC 0.943514 -40 ACAAGTACGTTTCGTTTTTTCAAGCCTTTT 8 63 0 TTCGTTTTTT 0.868608 -107 TCCCCTCTCAACCGTGTTTCTATTTTGTAT 8 142 0 ACCGTGTTTC 0.821787 -28 CCCTCTGTATTTTGTGTTTCAAAGCTGGAT 10 53 0 TTTGTGTTTC 0.877784 -248 TCGTTTTTCGTACTTTTTTCCCGGTGAATA 10 247 0 TACTTTTTTC 0.881426 -54 TATCAACAACTTCGTTTTTCGTACTTTTTT 10 258 0 TTCGTTTTTC 0.983389 -43 ********** Masking position 5 Map Score: 6.71459 Number of sites scoring better than the average of aligned sites = 2052 Number in coding regions = 1787 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 286 Fraction of orfs with sites within 600 bp upstream = 0.0459364 Motif number 7 GTGTAGCTTTTTACCATCTTTATTGTCTAC 1 58 1 TTACCATCTT 0.953197 -63 TCAGCTCTTGTTAATAACTTAGTGCT 2 7 0 TTAATAACTT 0.701105 -57 AACAAGTTCACCCTCTTGGTCTTTGTG 6 190 0 TCACCCTCTT 0.956594 -17 TTTCTGTCTGTCACTATCATGCATCAACAA 9 46 0 TCACTATCAT 0.834009 -39 CCGGTGAATATCAACATCTTCTCCGAAAAA 10 227 0 TCAACATCTT 0.974575 -74 ATACTCTGTATCAACAACTTCGTTTTTCGT 10 266 0 TCAACAACTT 0.953583 -35 ********** Masking position 3 Map Score: 1.54334 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 282 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 8 ********** No masking Map Score: -3.01737e-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 9 ********** No masking Map Score: -3.01737e-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 10 ********** No masking Map Score: -3.01737e-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