AlignACE 3.0 10/20/99 AlignACE2 -i CY/CY_operons020_100.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 944249767 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 hypD 300 hydrogenase isoenzymes formation protein HypD #1 ureG 300 urease accessory protein G #2 hypothetical 300 hypothetical protein #3 hypB 60 hydrogenase expression/formation protein HypB #4 hypothetical 75 hypothetical protein #5 speB 300 agmatine ureohydrolase #6 ureF 127 urease accessory protein F #7 hypE 48 hydrogenase expression/formation protein HypE #8 hypothetical 52 hypothetical protein #9 hypothetical 129 hypothetical protein #10 ureA 157 urease gamma subunit #11 hypC 77 hydrogenase expression/formation protein HypC #12 ctaB 150 cytochrome c oxidase folding protein #13 hypB 182 hydrogenase isoenzymes formation protein HypB #14 hypA 149 hydrogenase expression/formation protein HypA #15 ureB 35 urease beta subunit #16 hypothetical 77 hypothetical protein #17 sterol-C-methyltransferase 68 sterol-C-methyltransferase #18 hypF 45 transcriptional regulatory protein HypF #19 hypothetical 138 hypothetical protein Motif 1 ACAAAAATGGGGCTGGGAAATTGGATATTTA 13 11 1 TCTTACCAGTGGCAGGGGAATAATCGGCAAT 2 224 0 TGGAGCCATTGCCTGGGGAATAAAAAACGAA 0 63 1 AACGGCGAAAGGCAGGGTCATTACGGTCGGG 2 29 0 AGTCTCCCTAGGGAGGGAAATTTCTGCCGTT 12 25 1 ATGGAGGAGGGCTAGGGAAATTTGACATCAC 0 186 1 TCATTTTCCAGACAGGGCAATCCCAGAACAA 14 109 0 TTTTTTGTCCAGTTGGGGAATACTCGCTTAA 12 75 1 AAAAATAAAAAGTTGGGTAATACCCTGACCG 10 104 0 GTAGGGGTTAGCTGGGGTAATGGCGGTAGGC 1 27 1 ACTAGGGTGGGGGTGGGCAAAGAGCCATTAT 0 93 1 GAAAAACCAAACCTGGGCCATGGTTCAACT 11 9 0 CAAAATCACGGCCTGGACAATTTTCGCTATG 9 60 1 TAGTTAAAACAGCAGGGAAAATTAAGTATTA 17 43 0 CTACCCATTTGACTGGGCACTTGTCAAGAAT 0 146 1 CTAGCTACACGGCGGGACAAAAGCCCGGGAG 5 204 1 ******* *** MAP Score: 20.565 Motif 2 TGTCAAATTTCCCTAGCCCTCCTCCATAAGAG 0 181 0 GCCTAACCAACCCTGCCCCGGCAAATCAACGG 1 205 1 AAACAATATCCCCTACCCTAGCTAGGGATGAT 5 94 0 AGTTGAACCATGGCCCAGGTTTGGTTTTT 11 7 1 GCAGAAATTTCCCTCCCTAGGGAGACTTAAAG 12 20 0 ACCGTAATGACCCTGCCTTTCGCCGTTTGGAT 2 33 1 GGCCCTGCCCAACTTTGTTACCCT 17 2 1 ACCGCCATTACCCCAGCTAACCCCTACTTCGG 1 22 0 ATCCGGTAAACCATGGCCATGCATAAGCACGG 19 64 0 AATTGGTCAGCCCGACCCTGCCG 6 114 1 TTATTTGGAGCCATTGCCTGGGGAATAAAAAA 0 58 1 TTTGATCTCCCCCCTGCTTACCCTTTCTTTTG 12 121 1 AATAACCTTCCCCCTCGGGCGGAAATA 13 165 0 GGCTCTTTGCCCACCCCCACCCTAGTTCGTTT 0 87 0 GCCGATTATTCCCCTGCCACTGGTAAGAGTTA 2 227 1 GCCCTAACCCACCGAGACTAAAT 3 1 1 AAAGCAAACCCCCTAGCCAGATGCCCGAAAGA 2 169 0 CTCGGACCAGCCATTCCCCACATCACCAGGAA 5 138 0 CGACTAATACCCATAGCTCAACTAACCAT 15 16 1 ACTTTAATGACCAGTGCTTAGGTGTTGTCATT 5 235 1 **** **** ** MAP Score: 19.2452 Motif 3 TCTTATTTGGAGCCATTGCCTGGGGAATAA 0 56 1 GCACTTGTCAAGAATCGGCCTCTTATGGAG 0 162 1 AGAGATACAGAACTTTTGCCCATAAATAAA 1 164 1 AATAAATTCTAACATCGGCCTAACCAACCC 1 188 1 TAATCGCTAAAAATACTGCCACATGGACAG 2 81 0 TTTAGCGATTAACTCTGGCCTATGGTTTGT 2 100 1 TTCATAACTTAAACAAGGCCGATTGGTCTT 2 129 1 AATAATCGGCAATAACGGCAATGTACAACA 2 207 0 TAACTTGACTAATTATTGCCAAATTGATGG 4 16 1 GCTAAACAACAAAATCTGCCCAGGAGTTAT 5 268 0 GGGGTGAAAAAATCTTGGCCACC 6 3 0 CTTTGCTCTCAGGTTCTGCCCAGTTAAAAC 6 78 1 GCCCAGTTAAAACTTTTGCAATTGGTCAGC 6 95 1 AGGATGTAACAGTTACGGCCAAGAAC 7 6 0 ATCTTAACAAAATCACGGCCTGGACAATTT 9 53 1 AGTTGAACCATGGCCCAGGTTTGGT 11 5 1 TAGGGAGGGAAATTTCTGCCGTTGCGGTTA 12 33 1 CAACTGGACAAAAAATGGCAGTTAGTTTAA 12 60 0 TCCAGATCAAAGCCTCTGCAGGCACCCTAA 14 36 1 AGCTCACCGGAAACTCTGCCACTATAGACT 19 21 0 GGCCATGCATAAGCACGGCAAACAGAGCTC 19 52 0 CAATCCGGTAAACCATGGCCATGCATAAGC 19 68 0 ********** MAP Score: 17.6445 Motif 4 AATAATGGCTCTTTGCCCACCCCCACCCTAGT 0 93 0 GTCAAATTTCCCTAGCCCTCCTCCATAAGAGG 0 180 0 GCCTACCGCCATTACCCCAGCTAACCCCTACT 1 26 0 CATCGGCCTAACCAACCCTGCCCCGGCAAATC 1 200 1 ACCCGACCGTAATGACCCTGCCTTTCGCCGTT 2 28 1 TGCAAAAGCAAACCCCCTAGCCAGATGCCCGA 2 173 0 TATTGCCGATTATTCCCCTGCCACTGGTAAGA 2 223 1 GCCCTAACCCACCGAGACTAAATT 3 2 1 AACAATATCCCCTACCCTAGCTAGGGATGATT 5 93 0 AATTGGTCAGCCCGACCCTGCCG 6 114 1 CAACGGCAGAAATTTCCCTCCCTAGGGAGACT 12 25 0 AATTTTTGATCTCCCCCCTGCTTACCCTTTCT 12 117 1 TTAAATATCCAATTTCCCAGCCCCATTTTTGT 13 11 0 AATAACCTTCCCCCTCGGGCGG 13 170 0 TTAATACTTAATTTTCCCTGCTGTTTTAACTA 17 42 1 *** ******* MAP Score: 16.3763 Motif 5 GAACTAGGGTGGGGGTGGGCAAAGAGCCATTAT 0 91 1 GGCCTCTTATGGAGGAGGGCTAGGGAAATTTGA 0 178 1 ATTCCGAAGTAGGGGTTAGCTGGGGTAATGGCG 1 19 1 CTGGGGTAATGGCGGTAGGCAAGAAACTTTCTC 1 38 1 TTGATTTGCCGGGGCAGGGTTGGTTAGGCCGAT 1 201 0 TCATCCAAACGGCGAAAGGCAGGGTCATTACGG 2 34 0 ACCTCTTTCGGGCATCTGGCTAGGGGGTTTGCT 2 166 1 TAAGAGTTAAGGGCTTTAGCTAGACTGAACCAA 2 250 1 CTGGTGATGTGGGGAATGGCTGGTCCGAGAGAA 5 141 1 CTGGTCCGAGAGAAACAGGCTAGGCTTTGTAAA 5 160 1 CGGCAGGGTCGGGCTGACCAATTGCAA 6 110 0 CTAGTCAAACGGGCAACGGTAAGCAAACCTTTT 9 95 0 GAAAGGAAGGAGGAATTGGCAAATAAGTCAGTG 11 49 0 GGGAGGAAAGGAAGGAGGAATTGGC 11 62 0 AATCAAAAGAAAGGGTAAGCAGGGGGGAGATCA 12 123 0 TACAAAAATGGGGCTGGGAAATTGGATATTTA 13 9 1 TTCCGCCCGAGGGGGAAGGTTATT 13 168 1 TTAGGGTAACAAAGTTGGGCAGGGCC 17 3 0 TTGTGGCATAGCAGGTTATTTAACA 18 2 1 GGGAAGAGGAAAGTCTATAGTGG 19 0 1 **** ****** MAP Score: 15.0872 Motif 6 TAATTTTTTGAACTGAATAATGGCTCTTTGCCCA 0 106 0 GGCTAAAACTTGGCGAACTGATTC 0 286 0 TTCTAACATCGGCCTAACCAACCCTGCCCCGGCA 1 194 1 GTTTGTTCATAACTTAAACAAGGCCGATTGGTCT 2 124 1 GTACAACAGGTGCAAAAGCAAACCCCCTAGCCAG 2 181 0 GAACACAGTTAACTTAATCATCCCTAGCTAGGGT 5 78 1 CTAGCTAAACAACAAAATCTGCCCAGGAGTTATT 5 267 0 GTTTTAACTGGGCAGAACCTGAGAGCAAAGGTAA 6 74 0 CATTTTAGGAAACTTAAGCAAAGCAA 8 36 1 ACTACATCTTAACAAAATCACGGCCTGGACAATT 9 48 1 CTTTGAGAAAAACCAAACCTGGGCCATGGTTCAA 11 12 0 AAAACTTAGAAGCAAAATCTAGCTATTCTTTAGG 14 61 0 TGCGGCGGAAAACCAAAACTTAGAAGCAAAATCT 14 75 0 CGGCAAACAGAGCTCAAGCTCACCGGAAACTCTG 19 33 0 ACCATGGCCATGCATAAGCACGGCAAACAGAGCT 19 53 0 *** ** ** *** MAP Score: 11.255 Motif 7 TTCTTATTTGGAGCCATTGCCTGGGGAATAAAAAACGAA 0 55 1 AATAAAAAACGAACTAGGGTGGGGGTGGGCAAAGAGCCA 0 81 1 GGCCTCTTATGGAGGAGGGCTAGGGAAATTTGACATCAC 0 178 1 AAGTAGGGGTTAGCTGGGGTAATGGCGGTAGGCAAGAAA 1 25 1 TTCCGTTGATTTGCCGGGGCAGGGTTGGTTAGGCCGATG 1 200 0 TTCGGGCATCTGGCTAGGGGGTTTGCTTTTGCACCTGTT 2 172 1 CCCTTAACTCTTACCAGTGGCAGGGGAATAATCGGCAAT 2 224 0 TAATCATCCCTAGCTAGGGTAGGGGATATTGTTTCTAGG 5 92 1 AGGGTTCCGATTCCTGGTGATGTGGGGAATGGCTGGTCC 5 128 1 GAGACTTTAATGACCAGTGCTTAGGTGTTGTCATTAATA 5 232 1 AGTTGAACCATGGCCCAGGTTTGGTTTTTCTCA 11 4 1 TACAAAAATGGGGCTGGGAAATTGGATATTTAATCAATG 13 10 1 TAATATTTCCGCCCGAGGGGGAAGGTTATT 13 162 1 CACCGAGTTCTATGAGGTGGGATCTGTCCAGATCA 14 6 1 TTGGTTTTCCGCCGCATTGTTCTGGGATTGCCCTGTCTG 14 93 1 AGTGGCAGAGTTTCCGGTGAGCTTGAGCTCTGTTTGCCG 19 28 1 TTGCCGTGCTTATGCATGGCCATGGTTTACCGGATTGAA 19 61 1 * ****** ** * MAP Score: 10.3584 Motif 8 TTTCTTATTTGGAGCCATTGCCTGGGGAATAAAAAACGAAC 0 54 1 TTACTGAAAATTTTCGTTAACCTTGGAATCAGTTCGCCAAG 0 261 1 TATTCCGAAGTAGGGGTTAGCTGGGGTAATGGCGGTAGGCA 1 18 1 TATTTTCTTCCGTTGATTTGCCGGGGCAGGGTTGGTTAGGC 1 205 0 TCCTCGTTGGCCCCGTAAACCCGACCGTAAT 2 0 1 TTTTTAGCGATTAACTCTGGCCTATGGTTTGTTCATAACTT 2 98 1 GGCTAGGGGGTTTGCTTTTGCACCTGTTGTACATTGCCGTT 2 183 1 TATTGCCGATTATTCCCCTGCCACTGGTAAGAGTTAAGGGC 2 223 1 AGTTTCTTGGCAGTAACAGTGGACAAGTTAATAAAAA 3 33 0 TCTGAAATAATCGGCGATCGCCTTTGGGAGAGGTAAAA 4 47 1 AAACTTTAGTTTGGCGATCGCCGATAAAAAGTAGCACAGAA 5 40 1 GTTAACTTAATCATCCCTAGCTAGGGTAGGGGATATTGTTT 5 85 1 TCTCCCGGGCTTTTGTCCCGCCGTGTAGCTAGTGGCAAAAA 5 195 0 TTTTGGACGATAATCTTTTACCTTTGCTCTCAGGTTCTGCC 6 57 1 ACCTTTGCTCTCAGGTTCTGCCCAGTTAAAACTTTTGCAAT 6 76 1 AGTTGAACCATGGCCCAGGTTTGGTTTTTCTCAA 11 3 1 CTTTCAAGCATCCTCTCTTACCATGGGGTCATAACATTAAT 13 125 1 TAAGTTTTGGTTTTCCGCCGCATTGTTCTGGGATTGCCCTG 14 87 1 GCCGCATTGTTCTGGGATTGCCCTGTCTGGAAAATGAACTA 14 103 1 TTGTGGCATAGCAGGTTATTTAACAGTATTAA 18 1 1 TTTGCCGTGCTTATGCATGGCCATGGTTTACCGGATTGAAT 19 60 1 * ** * *** ** * MAP Score: 8.3748 Motif 9 TTCTTGACAAGTGCCCAGTCAAATGGGTAGTA 0 144 0 TTCCGTTGATTTGCCGGGGCAGGGTTGGTTAG 1 207 0 CTTCATATTTTTTTCCTGTTAGTACCATTTAG 1 274 1 ATGAATTTTGCTGTCCATGTGGCAGTATTTTT 2 71 1 CTGTTGTACATTGCCGTTATTGCCGATTATTC 2 206 1 CTCTCAGGTTCTGCCCAGTTAAAACTTTTGCA 6 83 1 ATAAGCAAAGTTGCCCATTTTAGGAAACTTAA 8 21 1 ATAGCGAAAATTGTCCAGGCCGTGATTTTGTT 9 58 0 TTGCTTACCGTTGCCCGTTTGACTAGTTACAC 9 102 1 AGGGAAATTTCTGCCGTTGCGGTTAAACTAAC 12 38 1 CTGCCATTTTTTGTCCAGTTGGGGAATACTCG 12 69 1 GAGGTGGGATCTGTCCAGATCAAAGCCTCTGC 14 23 1 TGTTCTGGGATTGCCCTGTCTGGAAAATGAAC 14 110 1 TGAGCTCTGTTTGCCGTGCTTATGCATGGCCA 19 51 1 ******** * * MAP Score: 5.91056 Motif 10 TCAAATAAGATTTCTCCATTCCTACTTTAGCA 0 16 1 ATAATGGCTCTTTGCCCACCCCCACCCTAGTT 0 92 0 TGATGTCAAATTTCCCTAGCCCTCCTCCATAA 0 184 0 ACCCGACCGTAATGACCCTGCCTTTCGCCGTT 2 28 1 TATTGCCGATTATTCCCCTGCCACTGGTAAGA 2 223 1 TAAATTTTTTATTAACTTGTCCACTGTTACTG 3 28 1 TTTTACCTCTCCCAAAGGCGATC 4 62 0 CTAGAAACAATATCCCCTACCCTAGCTAGGGA 5 98 0 GGTGGCCAAGATTTTTTCACCCCCTTGAACAA 6 10 1 CATAGCGAAAATTGTCCAGGCCGTGATTTTGT 9 59 0 TTCCTTTTGTATTTTTTATCCC 10 145 1 GATAAAAATCTTTAAGTCTCCCTAGGGAGGGA 12 11 1 CAACGGCAGAAATTTCCCTCCCTAGGGAGACT 12 25 0 AGGAAAAATTTTTGATCTCCCCCCTGCTTACC 12 111 1 TAAATATCCAATTTCCCAGCCCCATTTTTGTA 13 10 0 CATAACATTAATATTTCCGCCCGAGGGGGAAG 13 154 1 AATAACCTTCCCCCTCGGGCGG 13 170 0 TCCCTGCTGTTTTAACTATTCC 17 56 1 CACTATAGACTTTCCTCTTCCC 19 0 0 *** **** *** MAP Score: 4.47795 Motif 11 CCCTTCAAATAAGATTTCTCCATTCCTACTT 0 12 1 ATTCAGTTCAAAAAATTATCCTTACTACCCA 0 122 1 AACTGTTACTGAAAATTTTCGTTAACCTTGG 0 256 1 TAGGGAGTTCAAAATTTCTGGAGTTTTCTCA 1 101 1 CATGGACAGCAAAATTCATCCGGTCATCCAA 2 59 0 GTTAATCGCTAAAAATACTGCCACATGGACA 2 82 0 AGGCTTTGTAAAGATTTTTGCCACTAGCTAC 5 181 1 AAGGGGGTGAAAAAATCTTGGCCACC 6 5 0 CTGCCCAGTTAAAACTTTTGCAATTGGTCAG 6 93 1 AAACCATAGCGAAAATTGTCCAGGCCGTGAT 9 64 0 CCTAGGGAGGGAAATTTCTGCCGTTGCGGTT 12 31 1 GGGGAGATCAAAAATTTTTCCTGAATTTTAA 12 102 0 ******* *** MAP Score: 4.26308 Motif 12 ATTTGGAGCCATTGCCTGGGGAATAAAAAACGAAC 0 60 1 CTTATGGAGGAGGGCTAGGGAAATTTGACATCACT 0 183 1 CAAACGGCGAAAGGCAGGGTCATTACGGTCGGGTT 2 27 0 CGCCGTTTGGATGACCGGATGAATTTTGCTGTCCA 2 53 1 AACTCTTACCAGTGGCAGGGGAATAATCGGCAATA 2 223 0 TCCCCTACCCTAGCTAGGGATGATTAAGTTAACTG 5 83 0 ATCCCTAGCTAGGGTAGGGGATATTGTTTCTAGGG 5 97 1 GGCGGGACAAAAGCCCGGGAGACTTTAATGACCAG 5 214 1 GACAACACCTAAGCACTGGTCATTAAAGTCTCCCG 5 229 0 CGGCAGGGTCGGGCTGACCAATTGCAAAAGTTT 6 104 0 TAACAAAATCACGGCCTGGACAATTTTCGCTATGG 9 57 1 CGCTATACTTACGGTCAGGGTATTACCCAACTTTT 10 93 1 GAAAGGAAGGAGGAATTGGCAAATAAGTCAGTGGA 11 47 0 TAAGTCTCCCTAGGGAGGGAAATTTCTGCCGTTGC 12 23 1 TACAAAAATGGGGCTGGGAAATTGGATATTTAA 13 8 1 ACCTTCCCCCTCGGGCGGAAATATTAATGTTATGA 13 153 0 AATAGTTAAAACAGCAGGGAAAATTAAGTATTAAT 17 41 0 * ** * ** **** MAP Score: 1.92671 Motif 13 AAAATTATCCTTACTACCCATTTGACTGGGCACT 0 133 1 ATGACCCTGCCTTTCGCCGTTTGGATGACCGGAT 2 39 1 CGGATGAATTTTGCTGTCCATGTGGCAGTATTTT 2 68 1 TACATTGCCGTTATTGCCGATTATTCCCCTGCCA 2 212 1 ACTTGACTAATTATTGCCAAATTGATGGCTCTGA 4 18 1 GAAACAATATCCCCTACCCTAGCTAGGGATGATT 5 93 0 CCGGGCTTTTGTCCCGCCGTGTAGCTAGTGGCAA 5 198 0 GGCCAAGATTTTTTCACCCCCTTGAACAATGGAT 6 13 1 GGTTTGCTTACCGTTGCCCGTTTGACTAGTTACA 9 99 1 CGGCAGAAATTTCCCTCCCTAGGGAGACTTAAAG 12 20 0 GGGAGGGAAATTTCTGCCGTTGCGGTTAAACTAA 12 35 1 TAACTGCCATTTTTTGTCCAGTTGGGGAATACTC 12 66 1 CAAGCATCCTCTCTTACCATGGGGTCATAACATT 13 129 1 AACATTAATATTTCCGCCCGAGGGGGAAGGTTAT 13 157 1 AAGTTTTGGTTTTCCGCCGCATTGTTCTGGGATT 14 88 1 ** ****** * * MAP Score: 1.65699