AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i002_Purine_Nucleotides_Metabolism_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 deoD 300 purine nucleoside phosphorylase #2 drm 160 phosphodeoxyribomutase #3 ripX 300 integrase/recombinase #4 cdd 118 cytidine/deoxycytidine deaminase #5 yqfF 78 yqfF #6 yqfC 56 yqfC #7 yqfB 24 yqfB #8 yqfA 21 yqfA #9 yqeZ 130 yqeZ #10 rpsU 163 ribosomal protein S21 #11 yutK 136 similar to Na+/nucleoside cotransporter #12 yuzB 262 yuzB #13 pdp 29 pyrimidine-nucleoside phosphorylase #14 nupC 115 pyrimidine-nucleoside transport protein #15 dra 105 deoxyribose-phosphate aldolase #16 deoR 90 transcriptional regulator #17 yxxB 72 yxxB #18 yxeR 69 similar to ethanolamine transporter #19 yxeN 22 similar to amino acid ABC transporter (permease) #20 yxeM 24 similar to amino acid ABC transporter (binding protein) #21 yxeK 185 similar to monooxygenase #22 yxeI 154 similar to penicillin amidase #23 yxeH 39 similar to hypothetical proteins #24 yxeF 87 yxeF Motif number 1 CAGGTGGCTGCGGCTTTTTTGTTTAGAGCG 2 14 1 CGGCTTTTTT 0.872445 -147 CTTGAAAGCCTCCTTTTTTTCTATACGTC 2 142 0 CTCCTTTTTT 0.971563 -19 ACCGGTTTTACCGCTTTGTTCTATTATGCT 3 131 1 CCGCTTTGTT 0.629008 -170 TCGAACCATCCGCCTTTTTCATCCTGATCC 3 240 0 CGCCTTTTTC 0.81553 -61 ACATAATCGCGCGCTTTTTTTCACGCCCAT 4 49 0 GCGCTTTTTT 0.786681 -70 GTGTTAGAACCTCCTTTCAAATCATACACA 6 12 1 CTCCTTTCAA 0.554363 -45 CAAAAAGAACCCCCTTTCATCTCATGTGTA 6 36 0 CCCCTTTCAT 0.92743 -21 TTAGAAAGATGTCCTTTTCTTTGCCAT 9 8 0 GTCCTTTTCT 0.850667 -123 GTATCCCTCCTTCCTTTTATAATAAGTGCC 9 104 0 TTCCTTTTAT 0.746784 -27 CAACCCCTTTCTTTCATTATATA 10 4 1 CCCCTTTCTT 0.95186 -160 GCCTGTCCAGGCCCTTTTCT 11 1 0 GCCCTTTTCT 0.880712 -136 GCCTGGACAGGCCCTTTTTTATTTTGCCGT 11 19 1 GCCCTTTTTT 0.924326 -118 TTGAATTCCCCTTTAATCCGAAGAGTA 12 8 1 CCCCTTTAAT 0.81197 -255 ATGTGTTTCTCCTTTATTTGTATTCGCT 14 98 0 CTCCTTTATT 0.837529 -18 CTTCGCACACTTCCTTTTTTGTTAAGATAT 15 85 0 TTCCTTTTTT 0.820241 -21 AGGCTGGCGCCGGCTTTCATCCACCTGATT 16 12 0 CGGCTTTCAT 0.663751 -79 TGCTTTTGATTTGCTTTTATTATACAGGCT 16 37 0 TTGCTTTTAT 0.471017 -54 GGTTTTCTCCTTTTTCAAACGTATGA 18 54 0 CTCCTTTTTC 0.869576 -16 TTGATTTTCCCGCCTTTTCTATTT 20 5 0 CGCCTTTTCT 0.931942 -20 GGCGATACTCCTTTTATCATGTTTTTA 21 169 0 CTCCTTTTAT 0.956677 -17 TTGATCAGTCCCCTTTTCAATTCAGATTA 22 136 0 CCCCTTTTCA 0.771522 -19 TCTTTCCTCCTTTTTTGGGCGAATGC 24 72 0 CTCCTTTTTT 0.971563 -16 ********** Masking position 5 Map Score: 25.1189 Number of sites scoring better than the average of aligned sites = 1603 Number in coding regions = 1092 Number in noncoding regions = 511 Number of orfs with sites within 600 bp upstream = 568 Fraction of orfs with sites within 600 bp upstream = 0.0912303 Motif number 2 AACAATCATATACCTGAAAAAGATATCATT 1 38 0 TACCTGAAAA 0.689923 -263 ATGGACGGGCTGGATGATAATTTAGATTTA 1 267 1 TGGATGATAA 0.648142 -34 CATGGGAAGATTCCTGAAAACAGCTGTCGA 3 76 1 TTCCTGAAAA 0.879814 -225 ACCGGTAAACAGGATGAAAACTTTCAATGC 3 107 0 AGGATGAAAA 0.951176 -194 GTGAATCAAGAGTATGAAAACTATCATCGG 3 170 1 AGTATGAAAA 0.71647 -131 GAAATGGATCAGGATGAAAAAGGCGGATGG 3 235 1 AGGATGAAAA 0.951176 -66 TGGCTGAAAATTCTTACATT 4 1 1 TGGCTGAAAA 0.957799 -118 CCCATAAGCAATCATAAAAATGACCCGATA 5 34 0 ATCATAAAAA 0.555753 -45 CCTACAATTTAGCCTGAAAACACAAATTAG 12 132 1 AGCCTGAAAA 0.98001 -131 AAAGTCGGTTATGCTAAAAAATATCTTAAC 15 65 1 ATGCTAAAAA 0.758929 -41 CGCATTATTCAGCCTAAAAACATGATAAAA 21 155 1 AGCCTAAAAA 0.907067 -31 GACTTTCGTTATGCTGATAAAACCAATTCG 22 87 1 ATGCTGATAA 0.763575 -68 TGGGACTATAGCCTGAAAACGACATGAAG 23 10 1 AGCCTGAAAA 0.98001 -30 ********** Masking position 7 Map Score: 11.1415 Number of sites scoring better than the average of aligned sites = 1672 Number in coding regions = 1497 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 ACCGCAGGAAGGAGGGGTGGGACATGGGTAA 1 102 0 GGAGGGTGGG 0.961005 -199 ATCGAAAAAAGAAATGTTCGAGGATCTGTTA 1 182 0 GAAATGTCGA 0.816563 -119 TTGTAAAATGGACGGGCTGGATGATAATTTA 1 260 1 GACGGGTGGA 0.899043 -41 GAACCATAGGGAAAGGATCGATTAGGACATG 3 49 1 GAAAGGTCGA 0.972363 -252 TGAAAAAGGCGGATGGTTCGACCGGTTGATC 3 249 1 GGATGGTCGA 0.897023 -52 TATTATAAAAGGAAGGAGGGATACACCGCCC 9 110 1 GGAAGGGGGA 0.980177 -21 TGGTGTATTCGGAGGGAGGGAAAGAGA 10 147 1 GGAGGGGGGA 0.982841 -17 ACTTAATCGAAAAGGATCGGTGACCAAAC 13 10 1 AAAAGGTCGG 0.761622 -20 TTTGTTCAATGAAAGGTTTGAACGTG 15 6 0 GAAAGGTTGA 0.844789 -100 AACAAAAAAGGAAGTGTGCGAAGG 15 92 1 GAAGTGGCGA 0.791077 -14 TTTCTGTGAAAGAGGGTTGGACAC 17 59 1 AGAGGGTGGA 0.957306 -14 AAATAGAAAAGGCGGGAAAATCAA 20 7 1 AAAAGGGGGA 0.911408 -18 TCCAGCCTTTAGAAGGCTGGATTTTTTA 22 8 0 AGAAGGTGGA 0.950876 -147 ****** **** Masking position 6 Map Score: 12.3566 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 388 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 4 TTCTTTCCCGTGTGCTTCTT 1 1 1 TTCTTTCCCG 0.969792 -300 GATTGTTCTTTTTTTGGCCGGTGATCCGGT 1 61 1 TTTTTGGCCG 0.88595 -240 ATAAACCGTTTTCATTCCCGTTGACAATGT 2 79 0 TTCATTCCCG 0.803117 -82 ATCGCGCGCTTTTTTTCACGCCCATTTCTA 4 44 0 TTTTTTCACG 0.861139 -75 AGATGTCCTTTTCTTTGCCAT 9 2 0 TTCTTTGCCA 0.894594 -129 TATAAACATGTACTTTGACATTATAATATA 10 94 0 TACTTTGACA 0.63995 -70 GGCCCTTTTTTATTTTGCCGTACAAAAGAA 11 28 1 TATTTTGCCG 0.889648 -109 ATCATCCGTTGTCTTTGACGAATAGTGAAA 12 207 1 GTCTTTGACG 0.947757 -56 TTGATTTTCCCGCCTTTTCTAT 20 13 0 GATTTTCCCG 0.746356 -12 ATGTACCTTTGTCTTGGACGTTTGTCAATG 21 78 0 GTCTTGGACG 0.874412 -108 GTAATGTCAATTCTTTGACGAATCGATTTG 22 58 1 TTCTTTGACG 0.966627 -97 ********** Masking position 5 Map Score: 6.95809 Number of sites scoring better than the average of aligned sites = 1055 Number in coding regions = 979 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 AAAAACGGATAATCGGGGTGTTAATTTGAA 1 139 0 AATCGGGGTG 0.870343 -162 CCATATGCCAAATCAGAAAGGTTTTA 3 7 0 AATCAGAAAG 0.798453 -294 TAAAACCGGTAAACAGGATGAAAACTTTCA 3 111 0 AAACAGGATG 0.801627 -190 TCGGTATGATAAACCGGAAGCTCCGCTGTA 3 196 1 AAACCGGAAG 0.836607 -105 TTTTTTACCAAAACGGGGAGTAGATCAAGA 3 281 1 AAACGGGGAG 0.952294 -20 ATAGAAACGAGGAGAAGTTAT 8 5 1 AAACGAGGAG 0.914801 -17 ACTTAATCGAAAAGGATCGGTGAC 13 5 1 AATCGAAAAG 0.90613 -25 TTTCCTCAGAAAACGGAAAGCAGTCTGCCT 14 57 0 AAACGGAAAG 0.961098 -59 AACTTTGTTCAATCGGGAATGTTACAGTAA 17 26 1 AATCGGGAAT 0.654161 -47 TTTTCTATTCAAGCGAAAAGACCCTTGCGT 21 34 0 AAGCGAAAAG 0.779229 -152 AATATGAATAAATCAAAATGTACCTTTGTC 21 95 0 AATCAAAATG 0.4966 -91 ACATCAAATAAAACGAAAAGATCCAGCCTT 22 30 0 AAACGAAAAG 0.930015 -125 TATAGCCTGAAAACGACATGAAGGAGATGC 23 17 1 AAACGACATG 0.654332 -23 ********** Masking position 2 Map Score: 6.83364 Number of sites scoring better than the average of aligned sites = 1134 Number in coding regions = 1007 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 6 CAGCTGCAATGATATCTTTTTCAGGTATAT 1 31 1 GATATCTTTT 0.933065 -270 GTATATGATTGTTCTTTTTTTGGCCGGTGA 1 55 1 GTTCTTTTTT 0.695484 -246 ATCCGGTTACGATGTTTTTTACCCATGTCC 1 84 1 GATGTTTTTT 0.968803 -217 TCGACCGGTTGATCTTTTTTTACCAAAACG 3 266 1 GATCTTTTTT 0.941966 -35 CTCTTAGAAAGATGTCCTTTTCTTTGCCAT 9 11 0 GATGTCCTTT 0.837822 -120 TTCTAAGAGAGATGTCTTTTTTTATACATA 9 32 1 GATGTCTTTT 0.95673 -99 CGATAACAATAATATTTTTTGATGTCTACA 11 69 0 AATATTTTTT 0.631065 -68 TCGTATAAAAGATATTTTTTTAAATAAAAT 11 96 1 GATATTTTTT 0.951406 -41 TATAATTCTAGATGTTATTTTACATAGTTC 12 62 0 GATGTTATTT 0.830378 -201 TTTTTGTTAAGATATTTTTTAGCATAACCG 15 70 0 GATATTTTTT 0.951406 -36 ********** Masking position 5 Map Score: 9.2112 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 230 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TGTCCCACCCCTCCTTCCTGCGGTTAGGTTT 1 109 1 CTCCTCCTGC 0.978593 -192 TCTTGATCTACTCCCCGTTTTGGTAAAA 3 283 0 CTACTCCCGT 0.947003 -18 CGGTGTATCCCTCCTTCCTTTTATAATAAGT 9 107 0 CTCCTCCTTT 0.975227 -24 GTCATGAGTGCGACTGCCTGTCTATATAATG 10 25 0 CGACTCCTGT 0.987841 -139 ATACACCAATCGACTACCTTTAAGTTACACA 10 124 0 CGACTCCTTT 0.948933 -40 TGAAAGCCGGCGCCAGCCTGTATAATAAAAG 16 23 1 CGCCACCTGT 0.973854 -68 TCTGCACCTCCCTGTGGATCAGTCC 16 76 0 CACCTCCTGT 0.981243 -15 CCTGCATCTCCTTCATGTCGTTTTCAGG 23 22 0 CTCCTCATGT 0.950543 -18 ***** ***** Masking position 7 Map Score: 6.92474 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 168 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 TAAAGGAATATATCGAAAAAAGAAATGTTCG 1 193 0 TATGAAAAAA 0.939243 -108 ACAATAGACGTATAGAAAAAAAGGAGGCTTT 2 136 1 TATGAAAAAA 0.939243 -25 CATTTCTAAAAATGTAAAATAAATGTAAGAA 4 21 0 AATTAAAATA 0.782229 -98 AGCGCGCGATTATGTAAAATATAAAGTGATA 4 64 1 TATTAAAATA 0.89563 -55 TTCATTTTTTTATGTATAAAAAAAGACATCT 9 41 0 TATTATAAAA 0.738705 -90 TCTTAAATTTTATTTAAAAAAATATCTTTTA 11 101 0 TATTAAAAAA 0.927879 -36 AAATACGAACTATGTAAAATAACATCTAGAA 12 56 1 TATTAAAATA 0.89563 -207 TTTTCGCTTGAATAGAAAAAATTAATCTTAA 21 45 1 AATGAAAAAA 0.84988 -141 *** ******* Masking position 6 Map Score: 2.94266 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 151 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 9 AAGAACCTCCTCTTGAAACA 5 69 0 AAGAACCTCC 0.987998 -10 AGTGTTAGAACCTCCTTTCAAATCA 6 6 1 TAGAACCTCC 0.96157 -51 ACAAAAAGAACCCCCTTTCATCTCA 6 42 0 AAGAACCCCC 0.973743 -15 ATAGTTTCAAAATAACCTACAATTTAGCCT 12 117 1 AATAACCTAC 0.875021 -146 TAATGCGAAAAATAAACTCCTATATTCCTA 21 132 0 AATAAACTCC 0.875021 -54 ********** Masking position 5 Map Score: 0.907347 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 32 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GTTGTTGAAATGGATCAGGATGAAAAAGGC 3 229 1 TGGATCAGGA 0.873963 -72 TATAATATAAGCCATCAGTCAGGTCAACTA 10 73 0 GCCATCAGTC 0.897321 -91 AAGGAGAAAATGCATCAGGCGGAGACAACT 14 11 1 TGCATCAGGC 0.959062 -105 CACCTCCCTGTGGATCAGTCCTGATAAAAC 16 67 0 TGGATCAGTC 0.98184 -24 TTGATCAGTCCCCTTTTCAA 22 145 0 TTGATCAGTC 0.959993 -10 GTGATCAGTCTCCTTGTGGG 24 1 1 GTGATCAGTC 0.952138 -87 ********** Masking position 5 Map Score: 1.09217 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 170 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 CGATGATAGTTTTCATACTCTTGATTCACCCA 3 167 0 TTTCATACTT 0.82511 -134 GCTTCCGGTTTATCATACCGATGATAGTTTTC 3 185 0 TATCATACAT 0.96731 -116 GCCCATAAGCAATCATAAAAATGACCCGATAA 5 33 0 AATCATAAAT 0.746595 -46 CCTCCTTTCAAATCATACACATGAGATGAAAG 6 21 1 AATCATACAT 0.957846 -36 TCAATGTATCTATCATACTCTTCGGATTAAAG 12 21 0 TATCATACTT 0.95785 -242 TGATAAAACCAATCATACGTTTGAAAAAGGAG 18 42 1 AATCATACTT 0.944898 -28 TTCAGATTAATATCATACATATTGTGAACGAA 22 113 0 TATCATACAT 0.96731 -42 ******** ** Masking position 7 Map Score: 3.15446 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 45 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 TCCTGTTTACCGGTTTTACCGCTTTGTTCT 3 123 1 CGGTTTTACC 0.77235 -178 TTTCATACTCTTGATTCACCCATATCATAG 3 159 0 TTGATTCACC 0.789625 -142 AAAGGAAGGAGGGATACACCGCCC 9 117 1 GGGATACACC 0.954027 -14 TCCCTCCCTCCGAATACACCAATCGACTAC 10 138 0 CGAATACACC 0.816517 -26 GCGGTTTCACCTCACATATGT 12 252 0 CGGTTTCACC 0.974895 -11 ATGCATCAGGCGGAGACAACTATTAAGAGC 14 20 1 CGGAGACAAC 0.656773 -96 ATGTGTTTCTCCTTTATTTGTA 14 104 0 GTGTTTCTCC 0.653084 -12 GGCAGGAGCTGTTTCAACTTTGTTCAAT 17 9 1 CTGTTTCAAC 0.741256 -64 TCTGGTGAGTCACCGCCGTTTC 19 9 0 GTGAGTCACC 0.893868 -14 TAAGTTATAAGGAATTCACCCACAAGGAGA 24 19 0 GGAATTCACC 0.888064 -69 ********** Masking position 10 Map Score: 0.786877 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 745 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 13 TTGGCCGGTGATCCGGTTACGATGTTTTTTACC 1 74 1 ATCGTACGAT 0.968551 -227 CCGTTTTCATTCCCGTTGACAATGTATTTGGAA 2 71 0 TCCGTACAAT 0.903496 -90 AATATCTTTTATACGATAACAATAATATTTTTT 11 79 0 ATCGTACAAT 0.985585 -58 CTTTATTTGTATTCGCTTACAATTACTGTTTCC 14 82 0 ATCGTACAAT 0.985575 -34 GATAAAACCAATTCGTTCACAATATGTATGATA 22 102 1 ATCGTACAAT 0.985575 -53 ** ** * ***** Masking position 7 Map Score: 0.487166 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 AGTTTGTTTCATCATGACATTCGTTGTAAA 1 237 1 ATCATGACAT 0.938723 -64 GAAAGGATCGATTAGGACATGGGAAGATTC 3 59 1 ATTAGGACAT 0.70595 -242 ATTCACCCATATCATAGCATAATAGAACAA 3 146 0 ATCATAGCAT 0.81284 -155 ATAACGGGCGATCGGGTCATTCAGCA 5 7 0 ATCGGGTCAT 0.957172 -72 ATCGCCCGTTATCGGGTCATTTTTATGATT 5 25 1 ATCGGGTCAT 0.957172 -54 AAAATTTATTATCGTAACATATTATTTCTC 12 175 0 ATCGTAACAT 0.899579 -88 GATTGGTTTTATCATATCATCTGAAATCAC 18 26 0 ATCATATCAT 0.876013 -44 ********** Masking position 9 Map Score: 0.339879 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 201 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 ********** No masking Map Score: 5.01886e-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