TABLE 3.
Candidate CcpA binding sites (cre sequences) and their locations 5′ of aldouronate utilization genes in Paenibacillus sp. strain JDR-2
| Binding site sequence and distance from translation start sitea | Similarity to canonical sequenceb | Gene |
|---|---|---|
| 5′-TGWAANCGNTNWCA | 14/14 | crec |
| 5′-TGAAATCGCTTACA*---145 nt---ATG-- | 14/14 | yesN |
| 5′-TGAAAGTGCTTACA*---81 nt---ATG-- | 13/14 | lplA |
| 5′-ATG---104 nt---TGAAGCGGATGACA†-- | 12/14 | lplA |
| 5′-TGAACCGCTGGCAG†---183 nt---ATG-- | 12/14 | xynA2 |
| 5′-TGTAAGCGCTTAAT†---30 nty---ATG-- | 12/14 | xynA1 |
a
*, Identified by the PPP (Prokaryotic Promoter Prediction) program (Groningen Biomolecular Sciences and Biotechnology Institute, Haren, The Netherlands [http://bioinformatics.biol.rug.nl/websoftware/ppp/ppp_start.php]); †, identified by manual scanning of the upstream region of these genes.
b
According to S.-G. Cho and Y.-J. Choi (6). Similarity is indicated as the number of matching residues/total number of residues in the sequence.
c
The canonical sequence, as defined by S.-G. Cho and Y.-J. Choi (6).