| Table 2. Top
palindromic motifs identified by AlignACE |
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| Operon |
Motif |
Motif sequence |
MAP |
CompareACE Score |
Additional criteria |
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| 485 |
1 |
GCTGATTCGTAATCAGCAGGTC |
10.2821 |
0.711418 |
Overlaps with NNPP |
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| |
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GCTGATTACGAATCAGCTGCTC |
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GGCCAGAAACAATCATCCGTAC |
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GCCGATTCGTAATCGGCAGGTC |
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GCCGATTACGAATCGGCTGCAC |
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| |
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GTCAACGGCTAATCGGCCGGTC |
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| 498 |
6 |
TGCCGAAGAAC |
3.30401 |
0.721274 |
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TTCCGAAGCCA |
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TTCTGCACCAA |
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TGCAGAAGCAA |
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TTCCGAACACA |
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TGCAGCAGCAA |
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TTCAGAACCAG |
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| 674 |
2 |
ACACATTGACAACAAGAAATGAA |
2.73526 |
0.735281 |
Conserved in other species |
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AGTTGTTTTGTAAAAAAATTTTT |
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AATTTTTTTACAAAACAACTAAA |
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AAAACTCGCCGATAAAAACTAGA |
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| 1483 |
11 |
GGACGAGGCC |
0.570148 |
0.710615 |
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GGCCGAGGCC |
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GGCCGCGGCC |
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GGACGAGGCG |
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| 1581 |
1 |
ATTTACAATATTTTA |
3.93071 |
0.84127 |
Conserved in other species, Overlaps with NNPP |
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TAATAAAATATTGTA |
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AAGTAAAATTATTTA |
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AAATACAATGGGTTA |
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| 1856 |
6 |
TGGGGTCGGTGACC |
14.2166 |
0.749491 |
Conserved in other species |
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TGGGCTCGGCCAGC |
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TCCGCTCGGCGATC |
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CATGATCGGCGAGA |
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CCTGTTCGGTGATC |
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CCCGACCGGCGATC |
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CATGATCGGCGAGA |
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TCCGCTCGGCGATC |
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TGGGCTCGGCCAGC |
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TGGGATCGGTGACC |
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| 1900 |
16 |
TCGATGTCATTA |
0.570014 |
0.756653 |
Overlaps with NNPP |
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TCGATGCGAATG |
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CCGACGGCAACG |
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TCGACGCCATCG |
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CCGATGATATCG |
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CCGATATCAACG |
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CGGATGCCAACG |
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CCGACGTGATCA |
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CCGATGACCACG |
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| Note:
Shown are top palindromic motifs with CompareACE score
≥ 0.7 |
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| Operon, operon number assigned by public version of FGENESB; |
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| Motif, motif number assigned by AlignACE for a motif in a particular
operon; |
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| Motif
sequence, sequence of a motif provided AlignACE, with
active columns marked in red; |
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| MAP, maximum a posteriori probability value computed by AlignACE for the motif; |
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| CompareACE
score, CompareACE score for similarity between the motif
and its reverse complement; |
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| Additional
criteria, provides information on whether a motif similar to a known E.coli transcription factor binding
site was also conserved in
22 other |
| bacterial species (McGuire and Church.,
2000), or overlapped with a motif found by Neural Network Promoter Prediction
(NNPP) software. |
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