RegulonDB RegulonDB 11.1: Operon Form
   

araFGH operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: araFGH
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: araFGH
Gene(s): araH, araG, araF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Maciag A., et al., 2011
Promoter
Name: araFp2
+1: 1986148
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 20
Sequence: aatgctttgttttccgattaatttaacgaatgtcattcgtttttgccctacacaaaacgaCactaaagctggagagaacca
                                                -10         +1                   
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IEP]
Reference(s): [1] Maciag A., et al., 2011


Transcription unit          
Name: araFGH
Synonym(s): OP00138, araFG-w1867-araH
Gene(s): araH, araG, araF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Maciag A., et al., 2011
[2] Scripture JB., et al., 1987
Promoter
Name: araFp3
+1: 1986238
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 110
Sequence: aattctgcgatgtgatattgctctcctatggagaattaatttctcgctaaaactatgtcaAcacagtcacttatcttttag
                            -35                      -10    +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [3] Hendrickson W., et al., 1990
[4] Huerta AM., et al., 2003
[1] Maciag A., et al., 2011
TF binding sites (TFBSs)
[AraC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AraC-α-L-arabinopyranose activator araFp3 1986300 1986316 -70.0 ccgctaaattTATGCACGTTCTCACTGtaattctgcg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3], [5]
proximal AraC-α-L-arabinopyranose activator araFp3 1986321 1986337 -91.0 ggctttccctTATGTCTTTTCCCGCTAaatttatgca nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5]
remote AraC-α-L-arabinopyranose activator araFp3 1986375 1986391 -145.0 aggctaatctTATGGATTAATCTGCTGtgcattcgac nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3], [5]
remote AraC-α-L-arabinopyranose activator araFp3 1986396 1986412 -166.0 ccaaagacaaCAAGGATTTCCAGGCTAatcttatgga nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator araFp3 1986270 1986291 -42.5 tgtaattctgCGATGTGATATTGCTCTCCTATggagaattaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [6], [7]


Transcription unit          
Name: araFGH
Synonym(s): OP00138, araFG-w1867-araH
Gene(s): araH, araG, araF   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Maciag A., et al., 2011
[2] Scripture JB., et al., 1987
Promoter
Name: araFp1
+1: 1986238
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 110
Sequence: aattctgcgatgtgatattgctctcctatggagaattaatttctcgctaaaactatgtcaAcacagtcacttatcttttag
                                  -35                      -+1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [3] Hendrickson W., et al., 1990
[4] Huerta AM., et al., 2003
[1] Maciag A., et al., 2011
TF binding sites (TFBSs)
[AraC,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal AraC-α-L-arabinopyranose activator araFp1 1986300 1986316 -70.0 ccgctaaattTATGCACGTTCTCACTGtaattctgcg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3], [5]
proximal AraC-α-L-arabinopyranose activator araFp1 1986321 1986337 -91.0 ggctttccctTATGTCTTTTCCCGCTAaatttatgca nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5]
remote AraC-α-L-arabinopyranose activator araFp1 1986375 1986391 -145.0 aggctaatctTATGGATTAATCTGCTGtgcattcgac nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3], [5]
remote AraC-α-L-arabinopyranose activator araFp1 1986396 1986412 -166.0 ccaaagacaaCAAGGATTTCCAGGCTAatcttatgga nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5]
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator araFp1 1986270 1986291 -42.5 tgtaattctgCGATGTGATATTGCTCTCCTATggagaattaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [6], [7]


Evidence    

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP-SITE-MUTATION] Site mutation

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [2] Scripture JB., Voelker C., Miller S., O'Donnell RT., Polgar L., Rade J., Horazdovsky BF., Hogg RW., 1987, High-affinity L-arabinose transport operon. Nucleotide sequence and analysis of gene products., J Mol Biol 197(1):37-46

 [3] Hendrickson W., Stoner C., Schleif R., 1990, Characterization of the Escherichia coli araFGH and araJ promoters., J Mol Biol 215(4):497-510

 [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] Lu Y., Flaherty C., Hendrickson W., 1992, AraC protein contacts asymmetric sites in the Escherichia coli araFGH promoter., J Biol Chem 267(34):24848-57

 [6] Hendrickson W., Flaherty C., Molz L., 1992, Sequence elements in the Escherichia coli araFGH promoter., J Bacteriol 174(21):6862-71

 [7] Johnson CM., Schleif RF., 2000, Cooperative action of the catabolite activator protein and AraC in vitro at the araFGH promoter., J Bacteriol 182(7):1995-2000

 [8] Chen J., Gottesman S., 2017, Spot 42 sRNA regulates arabinose-inducible araBAD promoter activity by repressing synthesis of the high-affinity low-capacity arabinose transporter., J Bacteriol 199(3):e00691-16

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