Curation Information

Publication
High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis.;Marciniak BC, Pabijaniak M, de Jong A, Dűhring R, Seidel G, Hillen W, Kuipers OP;BMC genomics 2012 Aug 17; 13(.):401 [22900538]
TF
CcpA [P25144, view regulon]
Reported TF sp.
Bacillus subtilis subsp. subtilis str. 168
Reported site sp.
Bacillus subtilis subsp. subtilis str. 168
Created by
Dinara Sagitova
Curation notes
-
External databases
NCBI GEO (GSE35154) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35154.

Experimental Process

DNA microarray analysis identified genes that were differentially expressed in the wild type B.subtitis and ccpA mutant strains. A weight matrix constructed from a list of previously described CcpA boxes and Genome2D software were used to search for CcpA binding sites located within -500 and +100 nucleotides relative to the start codon of the first gene of an operon.

Transcription Factor Binding Sites


TGAAAGCGCTTTAT
TGAAAGCGTTACCA
TGAAAACGCTTTAT
TGTAAGCGTTAACA
TGAAAGCGTTGACA
TGTAAGCGTATACA
TGTAAGCGGATTCA
TGAATGCGGTTACA
TGAAAACGCTATCA
TGACACCGCTTTCA
TGTAAGCGTTTTAA
TGAAAGCGTTTAAT
TGAAAACGTTGTCA
TGTAAACGGTTTCT
AGAAAGCGTTTACA
TGTAAACGGTTACA
TTAAAGCGCTTACA
CGAAAACGCTATCA
TGAAAGCGCAGTCT
TGAAAACGCTTGCA
TGAAAGCGTTATCA
TAAAAGCGCTTACA
TGGAAGCGCAAACA
TGAAAGCGCTTTTA
AGAAAACGCTTTCT
TGAAAGCGGTTCAA
TGCAAGGGCTTTCA
TGATAGCGTTTTCT
TGTAAGCGTTTGCT
TGAAAGCGCTATCT
TTAAAGCGCTTTCA
TGTAAGCGCTTTCT
TGTAAGCGTTTGCT
TGTAAGCATTTTCT
TGAAAACGGTGCCA
TGAAATGAATCGTT
TGAAAACGGTTTAT
TGAAAGTGTTTGCA
TGAAAGCGGTACCA
TGAAACCGCTTCCA
TGAAAACGTTATCA
TGAAAACGCTTAAC
TGTAAACGTTATCA
TGAAAGCGTTTTAG
TGTAACCGCTTACT
TGAAAGCGTTTTAT
TGGAAGCGTTTTTA
TGAAAACGTTTTTT
TAAAAACGCTTTCT
GGAAAACGCTTTCA
TGTAAGCGGTATCT
TGAAAACGCGATCA
AGAAAGCGCTTACG
TGAAAACGTGTCCA
TGAAAGCGTTTTCC
AGAAAGCGGTTACA
TGTAAACGGTTACA
TGAAAGCGCTTTCT
TGAAAACGCTATCG
TGAAAATGTTTACA
TGTAAGCGCTTTAT
TGAAAGCGTTTTTT
TGAATGCGCTTTCT
TGAAAACGGATACA
TGTAACCGCTTTCT
TTGAAACGCTTTCA
TGTAAGCGGTTTAT
TGAAAGCGTAACCA
TGAAAGCGTATACA
TGAAAGCGTTTTAT
TGAAAGCGCTCGCT
TGAAAGCGCTTTAT
TGAAAGCGTTACCA
TGAAAACGCTTTAT
TGTAAGCGTTAACA
TGAAAGCGTTGACA
TGTAAGCGTATACA
TGTAAGCGGATTCA
TGAATGCGGTTACA
TGAAAACGCTATCA
TGACACCGCTTTCA
TGTAAGCGTTTTAA
TGAAAGCGTTTAAT
TGAAAACGTTGTCA
TGTAAACGGTTTCT
AGAAAGCGTTTACA
TGTAAACGGTTACA
TTAAAGCGCTTACA
CGAAAACGCTATCA
TGAAAGCGCAGTCT
TGAAAACGCTTGCA
TGAAAGCGTTATCA
TAAAAGCGCTTACA
TGGAAGCGCAAACA
TGAAAGCGCTTTTA
AGAAAACGCTTTCT
TGAAAGCGGTTCAA
TGCAAGGGCTTTCA
TGATAGCGTTTTCT
TGTAAGCGTTTGCT
TGAAAGCGCTATCT
TTAAAGCGCTTTCA
TGTAAGCGCTTTCT
TGTAAGCGTTTGCT
TGTAAGCATTTTCT
TGAAAACGGTGCCA
TGAAATGAATCGTT
TGAAAACGGTTTAT
TGAAAGTGTTTGCA
TGAAAGCGGTACCA
TGAAACCGCTTCCA
TGAAAACGTTATCA
TGAAAACGCTTAAC
TGTAAACGTTATCA
TGAAAGCGTTTTAG
TGTAACCGCTTACT
TGAAAGCGTTTTAT
TGGAAGCGTTTTTA
TGAAAACGTTTTTT
TAAAAACGCTTTCT
GGAAAACGCTTTCA
TGTAAGCGGTATCT
TGAAAACGCGATCA
AGAAAGCGCTTACG
TGAAAACGTGTCCA
TGAAAGCGTTTTCC
AGAAAGCGGTTACA
TGTAAACGGTTACA
TGAAAGCGCTTTCT
TGAAAACGCTATCG
TGAAAATGTTTACA
TGTAAGCGCTTTAT
TGAAAGCGTTTTTT
TGAATGCGCTTTCT
TGAAAACGGATACA
TGTAACCGCTTTCT
TTGAAACGCTTTCA
TGTAAGCGGTTTAT
TGAAAGCGTAACCA
TGAAAGCGTATACA
TGAAAGCGTTTTAT
TGAAAGCGCTCGCT

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
TGAAAGCGCTTTAT acoR,
... ... acoR sspH
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTTACCA acsA,
... ... acsA ytzK acuA acuB acuC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGCTTTAT acuA,
... ... acuA acsA ytzK acuB acuC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGTTAACA amyE
... ... amyE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTTGACA bglP,
... ... bglP bglH yxiE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGTATACA cccA
... ... cccA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGGATTCA citM,
... ... citM yflN nosA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAATGCGGTTACA cstA,
... ... cstA ysfE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGCTATCA dctP,
... ... dctP ydbI
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGACACCGCTTTCA glpF,
... ... glpF glpP glpK glpD pgcA yhcY yhcZ yhdA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGTTTTAA gmuB,
... ... gmuB BSU_misc_RNA_8 pbuE gmuA gmuC gmuD gmuR gmuE gmuF gmuG
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTTTAAT iolR,
... ... iolR mmsA iolB iolC iolD iolE iolF iolG iolH iolI iolJ yxdJ yxdK yxdL yxdM yxeA iolS
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGTTGTCA iolC,
... ... iolC iolB iolD iolE iolF iolG iolH iolI iolJ yxdJ yxdK yxdL yxdM yxeA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAACGGTTTCT manR,
... ... manR yjdB manP manA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
AGAAAGCGTTTACA msmX,
... ... msmX yxkH
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAACGGTTACA rbsR,
... ... rbsR pgsB pgsC pgsA pgsE pgdS rbsK rbsD rbsA rbsC rbsB ywsB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TTAAAGCGCTTACA rocG
... ... rocG
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
CGAAAACGCTATCA sacP,
... ... sacP sacA ywdA ywcJ
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGCAGTCT sucC,
... ... sucC sucD dprA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGCTTGCA treP,
... ... treP yfkQ yfkR yfkS yfkT treA treR yfkO
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTTATCA uxaC,
... ... uxaC exuM yjmC yjmD uxuA yjmF exuT exuR uxaB uxaA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TAAAAGCGCTTACA
... ... ycbC ycbD gudP gudD ycbG garD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGGAAGCGCAAACA xylA,
... ... xylA xylR xylB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGCTTTTA xynP,
... ... xynP xynB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
AGAAAACGCTTTCT yisS
... ... yisS
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGGTTCAA yjmD,
... ... yjmD uxuA yjmF exuT exuR uxaB uxaA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGCAAGGGCTTTCA ykoM
... ... ykoM
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGATAGCGTTTTCT yrpD
... ... yrpD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGTTTGCT ytkA
... ... ytkA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGCTATCT yulD,
... ... yulD yulC yulE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TTAAAGCGCTTTCA
... ... cycB ganP ganQ ganA ganB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGCTTTCT abnA
... ... abnA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGTTTGCT acoA,
... ... acoA acoB acoC acoL acoR sspH
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCATTTTCT citZ
... ... citZ
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGGTGCCA csbX,
... ... csbX yrbE bofC ruvA ruvB yrzS queA tgt yajC yrzF
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAATGAATCGTT cydA,
... ... cydA cydB cydC cydD yxkO cimH yxkI yxzE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGGTTTAT drm,
... ... drm pupG
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGTGTTTGCA gntR,
... ... gntR glxK yxaB gntK gntP gntZ
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGGTACCA gntR,
... ... gntR glxK yxaB gntK gntP gntZ
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAACCGCTTCCA hutP,
... ... hutP yxzL abnB hutH hutU hutI hutG hutM
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGTTATCA lcfA,
... ... lcfA fadR ysiB etfB etfA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGCTTAAC levD,
... ... levD levE levF levG
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAACGTTATCA malA,
... ... malA yfjA yfjB yfjC yfjD yfjE yfjF malR malP malQ yfiC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTTTTAG mleN,
... ... mleN mleA yqkK spoIIM fur yqzK xerD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAACCGCTTACT msmR,
... ... msmR ytaP msmE amyD amyC melA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTTTTAT mtlR
... ... mtlR
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGGAAGCGTTTTTA
... ... sucA odhB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGTTTTTT pbuG,
... ... pbuG yebC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TAAAAACGCTTTCT resA,
... ... resA rluB resB resC resD resE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
GGAAAACGCTTTCA
... ... sigL yvfG
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGGTATCT wprA
... ... wprA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGCGATCA yckB,
... ... yckB yckA yckC yckD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
AGAAAGCGCTTACG ycsA,
... ... ycsA sipU
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGTGTCCA ydzA,
... ... ydzA lrpC topB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTTTTCC yesL,
... ... yesL yesM yesN yesO yesP yesQ yesR yesS rhgT yesU yesV yesW yesX
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
AGAAAGCGGTTACA yfiG,
... ... yfiG yfiH yfiI yfiJ yfiK yfiL yfiM yfiN
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAACGGTTACA yncC,
... ... yncC yncB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGCTTTCT yojA,
... ... yojA yojB yodA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGCTATCG yqgW,
... ... yqgW yqgX
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAATGTTTACA yqgY,
... ... yqgY mgsR
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGCTTTAT ysbB,
... ... ysbB ysbA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTTTTTT
... ... glcD glcF
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAATGCGCTTTCT yugN,
... ... yugN yugM
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAACGGATACA yuxG,
... ... yuxG yulB yulC yulD yulE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAACCGCTTTCT
... ... mdxE mdxF mdxG yvdJ yvdK malL pgcM
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TTGAAACGCTTTCA yxlH
... ... yxlH
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGTAAGCGGTTTAT yydK,
... ... yydK yyzE bglA yyzN
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTAACCA yyzE,
... ... yyzE bglA yydK yyzN
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - repressor not specified
TGAAAGCGTATACA ilvB,
... ... ilvB BSU_misc_RNA_45 ilvH ilvC leuA leuB leuC leuD ysoA ysnD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGAAAGCGTTTTAT opuE,
... ... opuE sapB gatC gatA gatB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified
TGAAAGCGCTCGCT ycbP,
... ... ycbP cwlJ ycbR yczK phoD tatAD tatCD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - activator not specified