RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit       
Name: hemL
Gene(s): hemL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: hemLp1
+1: 174902
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 20
Sequence: gatgtttgacgagtatttaacttgttatgaataacatagaatagcagccattcactttttCtacgaatcaggaaccctcca
                                -35                   -10   +1                   
Note(s): The sequence of this promoter has been defined, by computational analyses, from the consensus sequence of the σ28 (σF) promoters: TAAAGTTT in the -35 box and GCCGATAA in the -10 box Yu HH,2006. Thus, we assigned a putative transcription start site for this promoter based on the observation that the majority of the σ28 promoters, determined experimentally, present an important -10 motif (5'-CGA-3') at the positions -12 to -10 and a distance of 6 nucleotides between the transcription start site and the -10 box Yu HH, Di Russo EG, Rounds MA, Tan M,2006. Yu HH,2006. Park K,2001.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [1] Huerta AM., et al., 2003
[2] Zhao K., et al., 2007


Transcription unit          
Name: hemL
Gene(s): hemL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: hemLp
+1: 174921
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 39
Sequence: gcaccagtacaagcagcctgatgtttgacgagtatttaacttgttatgaataacatagaaTagcagccattcactttttct
                              -35                    -10    +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [1] Huerta AM., et al., 2003
[3] Minagawa S., et al., 2003
[2] Zhao K., et al., 2007
TF binding sites (TFBSs)
[PdhR,-] 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
remote PdhR repressor hemLp 175078 175094 -165.0 aatgatcactTATTGGTCATACAAATAagatgacggc nd [COMP-AINF-SIMILAR-TO-CONSENSUS] nd [4]
[PhoP,+] 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 PhoP-phosphorylated activator hemLp 174944 174960 -31.0 agcagcctgaTGTTTGACGAGTATTTAacttgttatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]


Transcription unit       
Name: hemL
Gene(s): hemL   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: hemLp2
+1: 174941
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 59
Sequence: tactctaagaaatcaggattgcaccagtacaagcagcctgatgtttgacgagtatttaacTtgttatgaataacatagaat
                                -35                   -10   +1                   
Note(s): The sequence of this promoter has been defined, by computational analyses, from the consensus sequence of the σ28 (σF) promoters: TAAAGTTT in the -35 box and GCCGATAA in the -10 box Yu HH,2006. Thus, we assigned a putative transcription start site for this promoter based on the observation that the majority of the σ28 promoters, determined experimentally, present an important -10 motif (5'-CGA-3') at the positions -12 to -10 and a distance of 6 nucleotides between the transcription start site and the -10 box Yu HH, Di Russo EG, Rounds MA, Tan M,2006. Yu HH,2006. Park K,2001.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [1] Huerta AM., et al., 2003
[2] Zhao K., et al., 2007


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IEP] Inferred from expression pattern

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

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

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

 [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

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


Reference(s)    

 [1] 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

 [2] Zhao K., Liu M., Burgess RR., 2007, Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli., Nucleic Acids Res 35(13):4441-52

 [3] Minagawa S., Ogasawara H., Kato A., Yamamoto K., Eguchi Y., Oshima T., Mori H., Ishihama A., Utsumi R., 2003, Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli., J Bacteriol 185(13):3696-702

 [4] Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A., 2007, PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli., J Bacteriol 189(15):5534-41

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