| Table 1. Motifs identified by AlignACE most
similar to E. coli transcription
factor binding sites |
|
|
|
| Operon |
Motif |
Motif sequence |
MAP |
Simliar E.coli motifs |
CompareACE Score |
Additional criteria |
| |
|
|
|
|
|
|
| 264 |
10 |
GGGCGATGCGCT |
1.76022 |
malT |
0.715136 |
|
| |
|
GGAGGATGAGGT |
|
|
|
|
| |
|
GGATGATGAGGT |
|
|
|
|
| |
|
AGAAGATGGGGT |
|
|
|
|
| 502 |
1 |
GGCTGACTAC |
4.20626 |
malT |
0.767617 |
|
| |
|
GGATCACAGC |
|
|
|
|
| |
|
GGATGACTGC |
|
|
|
|
| |
|
GGATGAGGGA |
|
|
|
|
| |
|
GGATCACGAA |
|
|
|
|
| |
|
GGATGAGGGC |
|
|
|
|
| |
|
GGATGACGGC |
|
|
|
|
| |
|
GGCTCAGAAC |
|
|
|
|
| 502 |
2 |
GACGGGTAAGG |
3.89466 |
malT |
0.740484 |
Conserved in other species |
| |
|
AGGGGATGAGG |
|
|
|
|
| |
|
GGTGGAAGAGG |
|
|
|
|
| |
|
GGCAGATAAGG |
|
|
|
|
| |
|
GATGGATGAGG |
|
|
|
|
| |
|
GGCGGATGCGG |
|
|
|
|
| |
|
GGCGAAAAAGG |
|
|
|
|
| |
|
GGGGGAAAAGG |
|
|
|
|
| 765 |
5 |
ATAATCAAAATC |
3.71545 |
cynR |
0.751002 |
Conserved in other species, Overlaps with NNPP |
| |
|
ATTAGTAAATCA |
|
|
|
|
| |
|
ATAAGTTAAGCC |
|
|
|
|
| |
|
ATAAGGAAGAGC |
|
|
|
|
| |
|
ATAATGAAACGC |
|
|
|
|
| |
|
AAAAGTAAACAA |
|
|
|
|
| |
|
ATGATTAAAGGA |
|
|
|
|
| 1294 |
9 |
AAAAAAATTT |
5.94834 |
iclR |
0.718533 |
Conserved in other species |
| |
|
AAAAAAATTT |
|
|
|
|
| |
|
AACACAATTT |
|
|
|
|
| |
|
GAAACAAATT |
|
|
|
|
| |
|
GACTAAATTT |
|
|
|
|
| 1410 |
23 |
AATAATCATATTA |
0.41862 |
iclR |
0.730118 |
Conserved in other species, Overlaps with NNPP |
| |
|
AGATATCCTCTTC |
|
|
|
|
| |
|
AGAAATGGACTTC |
|
|
|
|
| |
|
GGTAATTCTGTTC |
|
|
|
|
| |
|
AGAAAAGGTTTTT |
|
|
|
|
| |
|
AGAAATCTTTTTT |
|
|
|
|
| |
|
AGATATTCAATTC |
|
|
|
|
| 1538 |
10 |
GCATGAGGTC |
0.560115 |
malT |
0.733375 |
Overlaps with RBS |
| |
|
GGATGATGTC |
|
|
|
|
| |
|
GGATGATTTC |
|
|
|
|
| |
|
GCATGAGGCC |
|
|
|
|
| 1816 |
8 |
ATGAAAATTC |
3.79987 |
argR18 |
0.727523 |
Conserved in other species, Overlaps with NNPP |
| |
|
ATGAAAATCA |
|
|
|
|
| |
|
ATGGAAATTC |
|
|
|
|
| |
|
ATAAAAGTTC |
|
|
|
|
| |
|
TTATAAATTC |
|
|
|
|
| |
|
ACAAAAATCC |
|
|
|
|
| |
|
ATGAAGACTC |
|
|
|
|
| |
|
ATATAATTTC |
|
|
|
|
| |
|
ATAAAAACCG |
|
|
|
|
| 2207 |
17 |
CCGAAAGAGGAAGATCA |
3.58227 |
fur |
0.738367 |
Conserved in other species |
| |
|
CACGAAAATACTCATCA |
|
|
|
|
| |
|
CAACAAGATCGAGATCA |
|
|
|
|
| |
|
TCACAAAAACAGGAATA |
|
|
|
|
| |
|
CAAAAAAGTTCTCAAGA |
|
|
|
|
| |
|
TTGCCAAATGATCATCA |
|
|
|
|
| |
|
TAACCAAGTGGTTATTA |
|
|
|
|
| |
|
TCGTCAAACGCTGAACA |
|
|
|
|
| |
|
CTTACAAACCAACATCA |
|
|
|
|
| |
|
TCTCAAAGAAATCAACA |
|
|
|
|
| |
|
CCTCAAAGAGGGAAACA |
|
|
|
|
|
|
|
|
|
|
|
|
| Note:
Shown are motifs similar to known E. coli transcription factor binding
sites with CompareACE score ≥ 0.7 |
|
| Operon, operon number assigned by public version of FGENESB; |
|
| Motif, motif number assigned by AlignACE for a motif in a particular
operon; |
|
| Motif
sequence, sequence of a motif provided AlignACE, with
active columns marked in red; |
|
| MAP, maximum a posteriori probability value computed by AlignACE for the motif; |
|
| Similar
E. coli motifs: similar sequence of known E.coli transcription factor binding
sites (Robison et al., 1998;
http://arep.med.harvard.edu/ecoli_matrices) |
| CompareACE
score, CompareACE score for similarity between the motif
and the similar E.coli transcription
factor binding site; |
| 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), overlapped with a predicted ribosomal binding site (RBS)
in G. sulfurreducens |
| or overlapped with a motif
found by Neural Network Promoter Prediction (NNPP) software. |
|
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|