AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifhlA_ecoli_hinf_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #2 hycA_hypA 211 hycA: transcriptional repression of hyc and hyp operons, hypA: pleiotrophic effects on 3 hydrogenase isozymes #3 hypE 38 plays structural role in maturation of all 3 hydrogenases #4 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #5 yjcQ 140 putative enzyme #6 yjcR 300 putative membrane protein #7 HI0536 102 urease accessory protein (ureG) #8 HI0537 107 urease accessory protein (ureF) #9 HI0538 127 urease accessory protein (ureE) #10 HI0540 75 urease, beta subunit (ureB) #11 HI0541 162 urease, gamma subunit (ureA) Motif number 1 TTTCGACACTCATCGACACGCCCATCCCCAA 1 48 0 CATCGCACGC 0.977567 -77 AATGACATTTCATCGGCATGTTTTCGTCAAA 1 78 1 CATCGCATGT 0.855073 -47 TAACTATTGCCAGCTACAAGCAATAATTGTG 2 23 1 CAGCTCAAGC 0.948581 -189 CGAAATGACACGTCGACACGGCGACGAAATT 2 95 1 CGTCGCACGG 0.975971 -117 CCCACGGTAGCGGCGGCCAGGCG 3 26 1 CGGCGCCAGG 0.977772 -13 TGAGCGCGCTCAACTCCCTGCCATTACCGGT 5 11 1 CAACTCCTGC 0.768773 -130 GTTAAGCGAGCGGCGACCAGGTCGCGTGCCG 5 72 1 CGGCGCCAGG 0.977772 -69 GTTGCACGGTCTGCGGCACGCGACCTGGTCG 5 85 0 CTGCGCACGC 0.979442 -56 TTTTGAGTTGCATCGCCATGCGAGAGAGAAC 6 26 0 CATCGCATGC 0.981424 -275 GGATAATTCCCGTCTTCATGGTTTCGGGATG 6 66 1 CGTCTCATGG 0.927406 -235 GCTGGTTTTTCTGCGCCATTGCCAGCCTTAT 6 141 1 CTGCGCATTG 0.852339 -160 TTTTTGCTCTCTACGCCATGCTGTTCTGGCT 6 249 1 CTACGCATGC 0.929634 -52 GCTTGGAAACCTTCGTCCAGCAACGT 8 92 1 CTTCGCCAGC 0.95269 -16 AGAAAAACTACAGCTACAATGATTTCTTATT 9 73 0 CAGCTCAATG 0.648446 -55 ***** ***** Masking position 7 Map Score: 17.2177 Number of sites scoring better than the average of aligned sites = 3534 Number in coding regions = 3410 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 2 ATTGCTTGTAGCTGGCAATAGTTAATGGGAGG 2 15 0 GCTGGCATAT 0.903839 -197 AATGCTTAAAGCTGGCATCTCTGTTAAACGGG 2 180 1 GCTGGCTCTT 0.97613 -32 TGGCTGTCACGCGGTATTTCGTTTCGTCACGT 4 27 1 GCGGTATTCT 0.695824 -171 CGAAAAACAGGCTGTCGTCAGTTTTGACGTGA 4 53 0 GCTGTCTCAT 0.801194 -145 TGGTCAGGCTGCTGGCGTTCTTTCATGAAGAG 5 41 1 GCTGGCTTCT 0.986369 -100 TAGGCTGCCTGCTGGTGATTCTGATCTCG 5 122 1 GCTGGTATTT 0.924348 -19 AATTATCCAGGCTGTTTTTTTGAGTTGCATCG 6 42 0 GCTGTTTTTG 0.70761 -259 TATTATCCCAGCTGGTTTTTCTGCGCCATTGC 6 131 1 GCTGGTTTTT 0.976608 -170 GAGTTATTCAGCGGGCAAATATCAATCTGGCA 6 192 1 GCGGGCAATT 0.668785 -109 CAAATATCAATCTGGCATTTGTCGGAATTATT 6 207 1 TCTGGCTTTT 0.887378 -94 TGCTGTTCTGGCTGGCATTTTTCTAATCTATT 6 267 1 GCTGGCTTTT 0.992334 -34 GTGCGGTTATTTTTTATTGAGATT 7 3 1 GCGGTTTTTT 0.884188 -100 AATCATTGTAGCTGTAGTTTTTCTTTCGAAGA 9 80 1 GCTGTATTTT 0.898906 -48 CGTAAAATTCGCTGACTTTCGTATAATAAATT 11 128 1 GCTGACTTCT 0.876452 -35 ****** *** * Masking position 2 Map Score: 14.3327 Number of sites scoring better than the average of aligned sites = 1561 Number in coding regions = 1446 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 3 TGCCCGTTTTGCAGGCGTTACGCCTGTTTGGGGAT 1 21 1 GCATTAGCCT 0.961701 -104 CCAGCTACAAGCAATAATTGTGCCAGTGTTGATTA 2 32 1 GCATTGGCCA 0.965405 -180 AATTGTGCCAGTGTTGATTATCCCTGCGGTGAATA 2 47 1 GTGTTACCCT 0.983804 -165 CCAGCTTTAAGCATTTTTTGTGCCAACTTTTAATT 2 160 0 GCATTGGCCA 0.965405 -52 ACTACAGTATGCATCTTTTATGCCACATTTTATGT 4 131 0 GCATTAGCCA 0.967574 -67 CCGGTGATCGGCGCTTATTATCCCAGCTGGTTTTT 6 116 1 GCGTTACCCA 0.989775 -185 TCAAGGGCAAATGTGATTTGCCCCTACAAGTAAAA 7 33 0 ATGTTGCCCT 0.897452 -70 ATAGGGGCAAATGTAACTTGCCCCTACACCC 7 82 1 ATGTTGCCCT 0.897452 -21 GTAAAAGGGCGTGTACGATACGCCTCTTACTTGAT 9 37 1 GTGATAGCCT 0.866151 -91 CCGTAGGGTGGGCTTTAGCCCACAAAATAAAA 10 8 1 GTGTTACCCA 0.986335 -68 TCCTTGTAGGGTGGGCTTTAGCCCACCATTGATAT 10 43 0 GTGTTACCCA 0.986335 -33 *** *** **** Masking position 9 Map Score: 13.3669 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 426 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 ACCAGCAGGCAGCCTACCCAGAGTTGCACG 5 108 0 AGCCTACCCA 0.981523 -33 TGTGGGCTAAAGCCCACCCTACGG 10 5 0 AGCCCACCCT 0.99748 -71 GGTGGGCTTTAGCCCACAAAATAAAAATAT 10 17 1 AGCCCACAAA 0.959332 -59 GGTGGGCTTTAGCCCACCATTGATATTTTT 10 39 0 AGCCCACCAT 0.994362 -37 GGTGGGCTAAAGCCCACCCTACAAGGAACA 10 51 1 AGCCCACCCT 0.99748 -25 ********** Masking position 6 Map Score: 8.76529 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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 5 GTAACGCCTGCAAAACGGGCAAAGCCTCAGC 1 11 0 CAAAACGGCA 0.958498 -114 CGATGAGTGTCGAAAATGACATTTCATCGGC 1 64 1 CGAAAATGCA 0.914119 -61 ATGTTTTCGTCAAAAATGACAATCACCTGAG 1 95 1 CAAAAATGCA 0.978521 -30 CAGGGATAATCAACACTGGCACAATTATTGC 2 42 0 CAACACTGCA 0.883421 -170 TCCCTGCGGTGAATAATGTCGATGATGTCGA 2 67 1 GAATAATGCG 0.840428 -145 TTCGTCACGTCAAAACTGACGACAGCCTGTT 4 49 1 CAAAACTGCG 0.972331 -149 AAATAATTCCGACAAATGCCAGATTGATATT 6 209 0 GACAAATGCA 0.865432 -92 GCGTAGAGAGCAAAAAGGGCGGTATAAATAA 6 234 0 CAAAAAGGCG 0.972332 -67 AAATAGATTAGAAAAATGCCAGCCAGAACAG 6 269 0 GAAAAATGCA 0.968591 -32 ACGAATTAGTGTAAAAGGGCGTGTACGATAC 9 27 1 GTAAAAGGCG 0.789473 -101 ******** ** Masking position 5 Map Score: 8.22634 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 368 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 CTCATCGACACGCCCATCCCCAAACAGGCG 1 41 0 CGCCCATCCC 0.995714 -84 CGCCTGGCCGCCGCTACCGTGGGCGAGT 3 21 0 CGCCGCTACC 0.953005 -18 TACCGCGTGACAGCCATCACGCGGCAGACA 4 13 0 CAGCCATCAC 0.889955 -185 GCGACCTGGTCGCCGCTCGCTTAACTCTTC 5 67 0 CGCCGCTCGC 0.983143 -74 TCATTATCTCCGGCAATCCCGGTGATCGGC 6 98 1 CGGCAATCCC 0.961052 -203 GGATAATAAGCGCCGATCACCGGGATTGCC 6 109 0 CGCCGATCAC 0.993278 -192 CTTATTTTGACGCTCATCACGAGGCGAGTT 6 167 1 CGCTCATCAC 0.95041 -134 ********** Masking position 7 Map Score: 6.1038 Number of sites scoring better than the average of aligned sites = 672 Number in coding regions = 648 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 TGCTTGTAGCTGGCAATAGTTAATGGGAGGCGAT 2 11 0 TGGCAAATAT 0.959591 -201 GCATTTTTTGTGCCAACTTTTAATTTATTGTTAT 2 151 0 TGCCAATTAT 0.910387 -61 CTGATATTACGGGCACTATTTATTCAAAACTCTG 4 86 0 GGGCACATAT 0.962542 -112 GTTATTCAGCGGGCAAATATCAATCTGGCATTTG 6 194 1 GGGCAATTAT 0.992431 -107 GAATGTTCAAGGGCAAATGTGATTTGCCCCTACA 7 40 0 GGGCAATTAT 0.992426 -63 TGATATATAGGGGCAAATGTAACTTGCCCCTACA 7 76 1 GGGCAATTAT 0.992426 -27 ****** * * * * Masking position 5 Map Score: 3.8487 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 = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 GAGATTTTACTTGTAGGGGCAAATCACATT 7 29 1 TTGTAGGGGC 0.987222 -74 ATCAACGAATGTTCAAGGGCAAATGTGATT 7 50 0 GTTCAAGGGC 0.885144 -53 ATTCGTTGATATATAGGGGCAAATGTAACT 7 70 1 ATATAGGGGC 0.95989 -33 GGGTGTAGGGGCAAGTTACATT 7 91 0 GTGTAGGGGC 0.991836 -12 TCTTTAACGGATTTAGGTGCGTTGTTGCAC 8 16 1 ATTTAGGTGC 0.845528 -92 ACGAATTAGTGTAAAAGGGCGTGTACGATA 9 27 1 GTAAAAGGGC 0.901662 -101 TCTTAATAATTTGTAAGTGCGGTTTCTATA 11 23 1 TTGTAAGTGC 0.873541 -140 TTTTTTTTCTTTCAAGGGGCTTACAAAAAA 11 62 1 TTCAAGGGGC 0.926136 -101 ********** Masking position 5 Map Score: 4.4689 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 185 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 CTCTTTAATAACAATAAATTAAAAGTTGGC 2 144 1 ACAATAAATT 0.917158 -68 AAAAGTTGGCACAAAAAATGCTTAAAGCTG 2 164 1 ACAAAAAATG 0.902964 -48 AAAGGGCGGTATAAATAATTCCGACAAATG 6 222 0 ATAAATAATT 0.812298 -79 TAAAATCTCAATAAAAAATAACCGCAC 7 8 0 ATAAAAAATA 0.710496 -95 AACCGCACTTACAAATTATTAAGAAGGAAA 11 17 0 ACAAATTATT 0.802092 -146 CAAGGGGCTTACAAAAAATTCTGACAAAAT 11 74 1 ACAAAAAATT 0.967992 -89 AAAAATTCTGACAAAATATTTTTCCTATTT 11 87 1 ACAAAATATT 0.917156 -76 TGACTTTCGTATAATAAATTAAGGAATGAA 11 140 1 ATAATAAATT 0.812298 -23 ********** Masking position 4 Map Score: 3.32909 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 172 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 10 TTCATCGGCATGTTTTCGTCAAAAATGACA 1 86 1 TGTTTTCGTC 0.845437 -39 AGCTAAAGATGAATTTCGTCGCCGTGTCGA 2 107 0 GAATTTCGTC 0.854764 -105 CTGTCACGCGGTATTTCGTTTCGTCACGTC 4 30 1 GTATTTCGTT 0.920322 -168 ACGACAGCCTGTTTTTCGTCAGAGTTTTGA 4 67 1 GTTTTTCGTC 0.982091 -131 ATCCCAGCTGGTTTTTCTGCGCCATTGCCA 6 135 1 GTTTTTCTGC 0.890946 -166 TGTAGCTGTAGTTTTTCTTTCGAAGAGAAG 9 86 1 GTTTTTCTTT 0.927827 -42 AAGGAGGATTTTTTTTCTTTCAAGGGGCTT 11 54 1 TTTTTTCTTT 0.77812 -109 ********** Masking position 5 Map Score: 0.98968 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 584 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 11 GTTTGGGGATGGGCGTGTCGATGAGTGTCG 1 46 1 GGGCGTGTCG 0.977952 -79 CCGCTACCGTGGGCGAGTTGGATATTAT 3 9 0 GGGCGAGTTG 0.952997 -30 CTGTAGTCGAGAGCGCGTATGCGTGATTTG 4 159 1 GAGCGCGTAT 0.960412 -39 TGATTAACTGGAGCGAGACCG 4 187 1 GAGCGAGACC 0.917058 -11 TGAGCGCGCTCAACTCCCTGC 5 2 1 GAGCGCGCTC 0.49892 -139 GAGCGCGTCTCAAATAGATT 6 291 0 GAGCGCGTCT 0.966065 -10 TAGTGTAAAAGGGCGTGTACGATACGCCTC 9 33 1 GGGCGTGTAC 0.965586 -95 ********** Masking position 5 Map Score: 4.07613 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 373 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 12 ********** No masking Map Score: 7.91135e-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 13 ********** No masking Map Score: 7.91135e-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 ********** No masking Map Score: 7.91135e-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