RegulonDB RegulonDB 10.9: Operon Form
   

epd-pgk-fbaA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: epd-pgk-fbaA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: pgk
Gene(s): pgk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bardey V., et al., 2005
Promoter
Name: pgkp2
+1: 3072648
Distance from start of the gene: 26
Sequence: cacgacgttagctatggctactgttgctttcaggtaagacgcaagcagcgtctgcaaaacTtttagaatcaacgagaggat
Evidence: [HTTIM]
[RS-EPT-CBR]
Reference(s): [2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cgctgaaacaAGGGCAGGTTTCCCTGCCCTgtgatttttt
Reference(s): [1] Bardey V., et al., 2005


Transcription unit       
Name: pgk-fbaA
Gene(s): fbaA, pgk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bardey V., et al., 2005
Promoter
Name: pgkp2
+1: 3072648
Distance from start of the gene: 26
Sequence: cacgacgttagctatggctactgttgctttcaggtaagacgcaagcagcgtctgcaaaacTtttagaatcaacgagaggat
Evidence: [HTTIM]
[RS-EPT-CBR]
Reference(s): [2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012


Transcription unit       
Name: pgk-fbaA
Gene(s): fbaA, pgk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bardey V., et al., 2005
Promoter
Name: pgkp3
+1: 3072735
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 113
Sequence: cacccaaacccgggtcagtggcgcacacctgatcaaaacgttggtctggtgcgataacgaAtggggctttgctaaccgaat
Evidence: [HTTIM]
[RS-EPT-CBR]
Reference(s): [2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012


Transcription unit       
Name: pgk
Gene(s): pgk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bardey V., et al., 2005
Promoter
Name: pgkp3
+1: 3072735
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 113
Sequence: cacccaaacccgggtcagtggcgcacacctgatcaaaacgttggtctggtgcgataacgaAtggggctttgctaaccgaat
Evidence: [HTTIM]
[RS-EPT-CBR]
Reference(s): [2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cgctgaaacaAGGGCAGGTTTCCCTGCCCTgtgatttttt
Reference(s): [1] Bardey V., et al., 2005


Transcription unit       
Name: pgk-fbaA
Gene(s): fbaA, pgk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bardey V., et al., 2005
Promoter
Name: pgkp1
+1: 3072857
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 235
Sequence: gaagtcaacctgttgctgcaaaaagcagcacaaggtgcatttcatggtatagttgactatAcggaattgccgttggtctct
                           -35                  -10         +1                   
Evidence: [ICWHO]
[IMP]
[TIM]
Reference(s): [1] Bardey V., et al., 2005
[4] Huerta AM., et al., 2003
[2] Olvera L., et al., 2009


Transcription unit       
Name: pgk
Gene(s): pgk   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bardey V., et al., 2005
Promoter
Name: pgkp1
+1: 3072857
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 235
Sequence: gaagtcaacctgttgctgcaaaaagcagcacaaggtgcatttcatggtatagttgactatAcggaattgccgttggtctct
                           -35                  -10         +1                   
Evidence: [ICWHO]
[IMP]
[TIM]
Reference(s): [1] Bardey V., et al., 2005
[4] Huerta AM., et al., 2003
[2] Olvera L., et al., 2009
Terminator(s)
Type: rho-independent
Sequence: cgctgaaacaAGGGCAGGTTTCCCTGCCCTgtgatttttt
Reference(s): [1] Bardey V., et al., 2005


Transcription unit          
Name: epd-pgk
Gene(s): pgk, epd   Genome Browser M3D Gene expression COLOMBOS
Note(s): The epd gene is cotranscribed with the pgk gene from a single promoter upstream of the epd gene. The pgk gene is additionally transcribed from an internal promoter.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [5] Alefounder PR., et al., 1989
[1] Bardey V., et al., 2005
[6] Charpentier B., et al., 1998
Promoter
Name: epdp
+1: 3073823
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 132
Sequence: aatgtcttcttcggctggacaaacattccttttattccacgtttcgcttatcctagctgaAgcgtttcagtcgattaaatg
                          -35                    -10        +1                   
Note(s): No sequence that might correspond to a -35 element is present. Glucose stimulation of epd promoter activity depends on the expression of enzyme II Glc Charpentier B,1998.
Evidence: [HIPP]
[HTTIM]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Bardey V., et al., 2005
[6] Charpentier B., et al., 1998
[4] Huerta AM., et al., 2003
[2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cgctgaaacaAGGGCAGGTTTCCCTGCCCTgtgatttttt
Reference(s): [1] Bardey V., et al., 2005
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator epdp 3073883 3073904 -70.5 aaaggggataAAAGTGTGATGTGAGTCAGATAAatgtcttctt nd [APIORCISFBSCS], [BCE], [GEA], [SM] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor epdp 3073812 3073829 3.5 tcgcttatccTAGCTGAAGCGTTTCAGTCgattaaatgt nd [APIORCISFBSCS], [BPP], [GEA], [SM] [7]


Transcription unit          
Name: epd-pgk-fbaA
Gene(s): fbaA, pgk, epd   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bardey V., et al., 2005
Promoter
Name: epdp2
+1: 3073823
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 132
Sequence: aatgtcttcttcggctggacaaacattccttttattccacgtttcgcttatcctagctgaAgcgtttcagtcgattaaatg
                          -35               -10             +1                   
Note(s): No sequence that might correspond to a -35 element is present. Glucose stimulation of epd promoter activity depends on the expression of enzyme II Glc Charpentier B,1998.
Evidence: [HIPP]
[HTTIM]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Bardey V., et al., 2005
[6] Charpentier B., et al., 1998
[4] Huerta AM., et al., 2003
[2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator epdp2 3073883 3073904 -70.5 aaaggggataAAAGTGTGATGTGAGTCAGATAAatgtcttctt nd [APIORCISFBSCS], [BCE], [GEA], [SM] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor epdp2 3073812 3073829 3.5 tcgcttatccTAGCTGAAGCGTTTCAGTCgattaaatgt nd [APIORCISFBSCS], [BPP], [GEA], [SM] [7]


Transcription unit          
Name: epd-pgk-fbaA
Gene(s): fbaA, pgk, epd   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Bardey V., et al., 2005
Promoter
Name: epdp
+1: 3073823
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 132
Sequence: aatgtcttcttcggctggacaaacattccttttattccacgtttcgcttatcctagctgaAgcgtttcagtcgattaaatg
                          -35                    -10        +1                   
Note(s): No sequence that might correspond to a -35 element is present. Glucose stimulation of epd promoter activity depends on the expression of enzyme II Glc Charpentier B,1998.
Evidence: [HIPP]
[HTTIM]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Bardey V., et al., 2005
[6] Charpentier B., et al., 1998
[4] Huerta AM., et al., 2003
[2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator epdp 3073883 3073904 -70.5 aaaggggataAAAGTGTGATGTGAGTCAGATAAatgtcttctt nd [APIORCISFBSCS], [BCE], [GEA], [SM] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor epdp 3073812 3073829 3.5 tcgcttatccTAGCTGAAGCGTTTCAGTCgattaaatgt nd [APIORCISFBSCS], [BPP], [GEA], [SM] [7]


Transcription unit          
Name: epd-pgk
Gene(s): pgk, epd   Genome Browser M3D Gene expression COLOMBOS
Note(s): The epd gene is cotranscribed with the pgk gene from a single promoter upstream of the epd gene. The pgk gene is additionally transcribed from an internal promoter.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[CV(LTED/PM)] cross validation(LTED/PM)
[LTED] Length of transcript experimentally determined
[PM] Polar mutation
Reference(s): [5] Alefounder PR., et al., 1989
[1] Bardey V., et al., 2005
[6] Charpentier B., et al., 1998
Promoter
Name: epdp2
+1: 3073823
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 132
Sequence: aatgtcttcttcggctggacaaacattccttttattccacgtttcgcttatcctagctgaAgcgtttcagtcgattaaatg
                          -35               -10             +1                   
Note(s): No sequence that might correspond to a -35 element is present. Glucose stimulation of epd promoter activity depends on the expression of enzyme II Glc Charpentier B,1998.
Evidence: [HIPP]
[HTTIM]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Bardey V., et al., 2005
[6] Charpentier B., et al., 1998
[4] Huerta AM., et al., 2003
[2] Olvera L., et al., 2009
[3] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: cgctgaaacaAGGGCAGGTTTCCCTGCCCTgtgatttttt
Reference(s): [1] Bardey V., et al., 2005
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator epdp2 3073883 3073904 -70.5 aaaggggataAAAGTGTGATGTGAGTCAGATAAatgtcttctt nd [APIORCISFBSCS], [BCE], [GEA], [SM] [6]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra repressor epdp2 3073812 3073829 3.5 tcgcttatccTAGCTGAAGCGTTTCAGTCgattaaatgt nd [APIORCISFBSCS], [BPP], [GEA], [SM] [7]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -17.3 3071426 3071449 aaaaatcacaGGGCAGGGAAACCTGCCCTTGTTtcagcgcgct
  terminator -7.8 3073694 3073722 tgtctggcaaATTTGCTCAGGGAAAACCTTGCAGGAGAtctatgaccg
  anti-terminator -19.0 3071444 3071500 aggtaaagtaCTGCCTGCAGTAGCGATGCTCGAAGAGCGCGCTAAGAAGTAAAAAATCACAGGGCAgggaaacctg
  anti-anti-terminator -7.0 3071481 3071509 attcgtggaaGGTAAAGTACTGCCTGCAGTAGCGATGCtcgaagagcg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"




Reference(s)    

 [1] Bardey V., Vallet C., Robas N., Charpentier B., Thouvenot B., Mougin A., Hajnsdorf E., Regnier P., Springer M., Branlant C., 2005, Characterization of the molecular mechanisms involved in the differential production of erythrose-4-phosphate dehydrogenase, 3-phosphoglycerate kinase and class II fructose-1,6-bisphosphate aldolase in Escherichia coli., Mol Microbiol 57(5):1265-87

 [2] Olvera L., Mendoza-Vargas A., Flores N., Olvera M., Sigala JC., Gosset G., Morett E., Bolivar F., 2009, Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation., PLoS One 4(10):e7466

 [3] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [4] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [5] Alefounder PR., Perham RN., 1989, Identification, molecular cloning and sequence analysis of a gene cluster encoding the class II fructose 1,6-bisphosphate aldolase, 3-phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli., Mol Microbiol 3(6):723-32

 [6] Charpentier B., Bardey V., Robas N., Branlant C., 1998, The EIIGlc protein is involved in glucose-mediated activation of Escherichia coli gapA and gapB-pgk transcription., J Bacteriol 180(24):6476-83

 [7] Ramseier TM., Bledig S., Michotey V., Feghali R., Saier MH., 1995, The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli., Mol Microbiol 16(6):1157-69


RegulonDB