AlignACE 3.0 10/20/99 AlignACE2 -i WIT_ctrl_PID061_300.orf Parameter values: expect = 10 gcback = 0.38 minpass = 200 seed = 943391811 numcols = 10 undersample = 1 oversample = 1 Input sequences: #0 nuoN 186 NADH dehydrogenase I chain N #1 nuoM 163 NADH dehydrogenase I chain M #2 nuoG 46 NADH dehydrogenase I chain G #3 nuoC 93 NADH dehydrogenase I chain C, D #4 nuoA 300 NADH dehydrogenase I chain A #5 gcvR 79 transcriptional regulation of gcv operon #6 hyfA 213 hydrogenase 4 Fe-S subunit #7 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #8 hycA 211 transcriptional repression of hyc and hyp operons Motif 1 CTCCACAAAACCTGATCGCACTGCTACCGTTGCTGATCG 0 26 1 GCATCACAACCACCACCGTCAAGCCGACGATCAGCAACG 0 53 0 GAGGAAATGATTGCGTCGCCACGCAATGGAGAGCATCAC 0 85 0 GCAATCATTTCCTCAACGCTACGCTCTCGGTTATTGGGC 0 110 1 TTATTGGGCTTAACGCGGCGCTGGTTTCGCTCTGGTTTG 0 140 1 TTCGCTCTGGTTTGTTGGCCAGGCGGGCGCT 0 165 1 TCGGATAAGCCGCCTTCGCGGTGCATCCGACACTACCCC 1 53 1 TTTTCCATTGCTTCACAACGGACACGATTCAACAAC 4 7 1 TGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCAGCATAC 6 16 1 GCTGAGGCTTTGCCCGTTTTGCAGGCGTTACGCCTGT 7 8 1 GAAAATGACATTTCATCGGCATGTTTTCGTCAAAAATGA 7 74 1 TAAAGATGAATTTCGTCGCCGTGTCGACGTGTCATTTCG 8 94 0 * * **** ** ** MAP Score: 20.4431 Motif 2 TTGCTGATCGTCGGCTTGACGGTGGTGGTTGT 0 55 1 GGAAATGATTGCGTCGCCACGCAATGGAGAGC 0 90 0 TCTCGGTTATTGGGCTTAACGCGGCGCTGGTT 0 134 1 GTCGGATAAGCCGCCTTCGCGGTGCATCCGAC 1 52 1 GTTGAAAATCCGGTCCTGACGGGACTTTTACA 1 125 1 ACTGCGCCGACAGTCACCACGGACCATTTGCA 3 71 1 TTTTCCATTGCTTCACAACGGACACGATTCA 4 9 1 AATTATCCTGGAGTCGTCAAGGATCTGGGGTG 4 50 1 GCCGCAAGCGCAGCCAGCACGGAATGGAGCAA 6 15 0 CTCGCTTTCCCCTGCGACACGGGTGTCGAATC 6 82 1 GTATTAACTGGATTCTGAACGGTACAAAAATG 6 141 0 AGGCGTAACGCCTGCAAAACGGGCAAAGCCTC 7 13 0 CATCCCCAAACAGGCGTAACGCCTGCAAAACG 7 24 0 TCGAAATGACACGTCGACACGGCGACGAAATT 8 93 1 ***** ***** MAP Score: 16.8515 Motif 3 GCTGATCGTCGGCTTGACGGTGGTGGTTGTGAT 0 57 1 TCGGTTATTGGGCTTAACGCGGCGCTGGTTTCG 0 136 1 AAGGATTGTGGGATTGCCCCTGGGCATATAAGA 1 13 1 ATCACATTCTCGCTTTCCCCTGCGACACGGGTG 6 74 1 ACGCGGCGCTGGTTTCGCTCTGGTTTGTTGGCC 0 152 1 GCACAAAAAATGCTTAAAGCTGGCATCTCTGTT 8 171 1 GCACAATTATTGCTTGTAGCTGGCAATAGTTAA 8 21 0 GTGCCAGTGTTGATTATCCCTGCGGTGAATAAT 8 50 1 GAATCGATGTGGCGTCCATCTGCCGTGAAGAGC 4 244 1 CGGATAAGCCGCCTTCGCGGTGCATCCGACACT 1 54 1 GCCGTGAAGAGCAGTGAATCTGGCGCTACTTTT 4 265 1 CAGGCATTCCTCAGGTGATTGTCAT 7 109 0 ***** * **** MAP Score: 11.7241 Motif 4 ATCAGGTTTTGTGGAGTTATTGTCATGGCGAT 0 8 0 CCATTGCGTGGCGACGCAATCATTTCCTCAACGC 0 95 1 TCTCTTCGGACTGGGGGTAGTGTCGGATGCACCG 1 71 0 TACCCCCAGTCCGAAGAGAATTTTCTGTCGTGAG 1 86 1 AGAGAATTTTCTGTCGTGAGAATTCGTTGAAAAT 1 100 1 AAATCCGGTCCTGACGGGACTTTTACAAGGAATA 1 130 1 GTGACTGTCGGCGCAGTAAGCTTCGCGAAATAGA 3 54 0 TGCAAATGGTCCGTGGTGACTGTCGGCGCAGTAA 3 69 0 GTAAACTAATGTGAAGAAACTTTTGTTAAAGTTG 4 116 1 CTTACAATCACTGTAGAAATTCTTTTATACAGCT 4 189 0 AGCAGTGAATCTGGCGCTACTTTTGATGAGTAAG 4 274 1 GTGTCGATGAGTGTCGAAAATGACATTTCATCGG 7 59 1 ATAATCAACACTGGCACAATTATTGCTTGTAGCT 8 33 0 TTGATTATCCCTGCGGTGAATAATGTCGATGATG 8 59 1 CGTCGACACGGCGACGAAATTCATCTTTAGCTTA 8 104 1 *** ** ** * ** MAP Score: 9.25392 Motif 5 GCTGATCGTCGGCTTGACGGTGGTGGTTGTG 0 57 1 TGCTCTCCATTGCGTGGCGACGCAATCATTT 0 89 1 CTGGTTTGTTGGCCAGGCGGGCGCT 0 171 1 CGGATAAGCCGCCTTCGCGGTGCATCCGACA 1 54 1 TGAAAATCCGGTCCTGACGGGACTTTTACAA 1 127 1 TTTGCGCCTGTCGGCAAAGGGATTT 3 4 1 TGGTCCGTGGTGACTGTCGGCGCAGTAAGCT 3 66 0 TCACCCCAGATCCTTGACGACTCCAGGATAA 4 52 0 AGATTCACTGCTCTTCACGGCAGATGGACGC 4 255 0 CGCTTTCCCCTGCGACACGGGTGTCGAATCC 6 84 1 TTTGGGGATGGGCGTGTCGATGAGTGTCGAA 7 46 1 GAATTTCGTCGCCGTGTCGACGTGTCATTTC 8 95 0 ****** **** MAP Score: 8.88908 Motif 6 TCCATTGCGTGGCGACGCAATCATTTCCTC 0 94 1 AGAGCGTAGCGTTGAGGAAATGATTGCGTC 0 107 0 TTTAGGAATAAGCGAAGAAAAATCCCTTTG 3 24 0 TCGTGTCCGTTGTGAAGCAATGGAAAA 4 7 0 TGTAAACTAATGTGAAGAAACTTTTGTTAA 4 115 1 TTTTGTTAAAGTTGACAAAAGGTTATAGAA 4 136 1 CTGCGACACGGGTGTCGAATCCATTTTTTG 6 93 1 CGTGTCGATGAGTGTCGAAAATGACATTTC 7 58 1 GATTGTCATTTTTGACGAAAACATGCCGAT 7 88 0 TAATGTCGATGATGTCGAAATGACACGTCG 8 79 1 ACGTCGACACGGCGACGAAATTCATCTTTA 8 103 1 ********** MAP Score: 6.864 Motif 7 CCCTTTGCCGACAGGCGCAAA 3 1 0 CCATCCCCAAACAGGCGTAACGCCTGCAAA 7 27 0 TCTTATATGCCCAGGGGCAATCCCACAATC 1 16 0 AACGCCTGCAAAACGGGCAAAGCCTCAGC 7 9 0 CACCCGTGTCGCAGGGGAAAGCGAGAATGT 6 77 0 AAGGTTATAGAAAGGAGTAAAAAACCACAT 4 154 1 CATCTCTGTTAAACGGGTAACCTGACA 8 194 1 ATTATTCACCGCAGGGATAATCAACACTGG 8 53 0 GCCAGCACGGAATGGAGCAAAGTAA 6 5 0 GATAATCAACACTGGCACAATTATTGCTTG 8 38 0 GGGACTTTTACAAGGAATAAAGATCGCC 1 145 1 ********** MAP Score: 6.57027 Motif 8 ACAACCACCACCGTCAAGCCGACGATCAGCAACG 0 53 0 GCCCGCCTGGCCAACAAACCAGAGCGAAACCAGC 0 159 0 CAGGGGCAATCCCACAATCCTTAAC 1 1 0 TCCGACACTACCCCCAGTCCGAAGAGAATTTTCT 1 78 1 AATCCCTTTGCCGACAGGCGCAAA 3 0 0 GCTTACTGCGCCGACAGTCACCACGGACCATTTG 3 67 1 GATGTGGCGTCCATCTGCCGTGAAGAGCAGTGAA 4 249 1 GCATTAAAAGCAAGCAGACAGAACCGTTCTGA 5 57 1 GCCGCAAGCGCAGCCAGCACGGAATGGAGCAAAG 6 13 0 GCGCTTGCGGCCAGCATACCTCACTTCTCGTGAT 6 36 1 CGCCCATCCCCAAACAGGCGTAACGCCTGCAAAA 7 26 0 CAGGCATTCCTCAGGTGATTGTCA 7 110 0 *** *** ** ** MAP Score: 6.16247 Motif 9 AACTCCACAAAACCTGATCGCACTGCTACCGTTGC 0 24 1 TTGTGATGCTCTCCATTGCGTGGCGACGCAATCAT 0 83 1 AAGCCCAATAACCGAGAGCGTAGCGTTGAGGAAAT 0 116 0 CCGACACTACCCCCAGTCCGAAGAGAATTTTCTGT 1 79 1 TTCGTTGAAAATCCGGTCCTGACGGGACTTTTACA 1 122 1 TTTGCGCCTGTCGGCAAAGGGATTTTTCT 3 4 1 ATGTTGTTGAATCGTGTCCGTTGTGAAGCAATGGA 4 13 0 TTACTTTGCTCCATTCCGTGCTGGCTGCGCTTG 6 8 1 CCGTGCTGGCTGCGCTTGCGGCCAGCATACCTCAC 6 25 1 TGGATTCGACACCCGTGTCGCAGGGGAAAGCGAGA 6 81 0 TGAATTTCGTCGCCGTGTCGACGTGTCATTTCGAC 8 92 0 * ** ***** * * MAP Score: 5.86146 Motif 10 GACACTACCCCCAGTCCGAAGAGAATTTTCTGTCGTGAGA 1 81 1 TTGTAAAAGTCCCGTCAGGACCGGATTTTCAACGAATTCT 1 118 0 TTTGCGCCTGTCGGCAAAGGGATTTTTCTTCGCTTA 3 6 1 TACTGCGCCGACAGTCACCACGGACCATTTGCA 3 70 1 TGTGCAAACAAGTGTCTCAATGGTACGTTTGGTATGGCAT 5 21 1 CGTGTCGATGAGTGTCGAAAATGACATTTCATCGGCATGT 7 58 1 ** *** * * *** MAP Score: 3.70043 Motif 11 CTCCACAAAACCTGATCGCACTGCTACCGTTGCTGATCGTC 0 26 1 GCATCACAACCACCACCGTCAAGCCGACGATCAGCAACGGT 0 51 0 GCAATCATTTCCTCAACGCTACGCTCTCGGTTATTGGGCTT 0 110 1 TTATTGGGCTTAACGCGGCGCTGGTTTCGCTCTGGTTTGTT 0 140 1 TTCGCTCTGGTTTGTTGGCCAGGCGGGCGCT 0 165 1 TATAAGAACGTAGGTCGGATAAGCCGCCTTCGCGGTGCATC 1 39 1 GACACTACCCCCAGTCCGAAGAGAATTTTCTGTCGTGAGAA 1 81 1 TTTGCGCCTGTCGGCAAAGGGATTTTTCTTCGCTTAT 3 6 1 TTACTTTGCTCCATTCCGTGCTGGCTGCGCTTGCGGCCAGC 6 10 1 CTTTCCCCTGCGACACGGGTGTCGAATCCATTTTTTGCTGA 6 86 1 GCTGAGGCTTTGCCCGTTTTGCAGGCGTTACGCCTGTTT 7 8 1 AATGACACGTCGACACGGCGACGAAATTCATCTTTAGCTTA 8 97 1 * * *** ** ** * MAP Score: 1.34268 Motif 12 CACAAAACCTGATCGCACTGCTACCGTTGCTGATCGTC 0 29 1 CGTTGCTGATCGTCGGCTTGACGGTGGTGGTTGTGATG 0 53 1 GAAATGATTGCGTCGCCACGCAATGGAGAGCATCACAA 0 83 0 GTTAAGGATTGTGGGATTGCCCCTGGGCATATAAGAA 1 9 1 GATAAGCCGCCTTCGCGGTGCATCCGACACTACCCCCA 1 56 1 AGAAAATTCTCTTCGGACTGGGGGTAGTGTCGGATGCA 1 74 0 TTTTTTTATTCCTCCCCATGAATCGATGTGGCGTCCAT 4 225 1 GTACGTTTGGTATGGCATTAAAAGCAAGCAGACAGAAC 5 43 1 AGCGCAGCCAGCACGGAATGGAGCAAAGTAA 6 3 0 TTCCGTGCTGGCTGCGCTTGCGGCCAGCATACCTCACT 6 23 1 CCTGTTTGGGGATGGGCGTGTCGATGAGTGTCGAAAAT 7 42 1 AATGACATTTCATCGGCATGTTTTCGTCAAAAATGACA 7 77 1 AGATGAATTTCGTCGCCGTGTCGACGTGTCATTTCGAC 8 92 0 * ***** ** * * MAP Score: 0.711535 Motif 13 ATCGCCATGACAATAACTCCAC 0 1 1 TTGCTGATCGTCGGCTTGACGGTGGTGGTTG 0 55 1 AATGATTGCGTCGCCACGCAATGGAGAGCAT 0 88 0 AGCGCCCGCCTGGCCAACAAACCAGA 0 170 0 GTCGGATAAGCCGCCTTCGCGGTGCATCCGA 1 52 1 AGAGAATTTTCTGTCGTGAGAATTCGTTGAA 1 100 1 GTTGAAAATCCGGTCCTGACGGGACTTTTAC 1 125 1 GCGAAGCTTACTGCGCCGACAGTCACCACGG 3 62 1 TGAATCGTGTCCGTTGTGAAGCAATGGAAAA 4 10 0 CGTCAAGGATCTGGGGTGAAAGGGCATTAAA 4 64 1 TGGCGTCCATCTGCCGTGAAGAGCAGTGAAT 4 253 1 TTGCTCCATTCCGTGCTGGCTGCGCTTGCGG 6 15 1 ACCTCACTTCTCGTGATCAAGATCACATTCT 6 53 1 GATTCGACACCCGTGTCGCAGGGGAAAGCGA 6 83 0 GAGGCTTTGCCCGTTTTGCAGGCGTTACGCC 7 13 1 TTGATTATCCCTGCGGTGAATAATGTCGATG 8 59 1 AATTTCGTCGCCGTGTCGACGTGTCATTTCG 8 94 0 ***** ***** MAP Score: 0.215402