RegulonDB RegulonDB 11.1: Operon Form
   

yafY-ykfBF-yafX-ykfGH-yafW-ykfI operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: yafY-ykfBF-yafX-ykfGH-yafW-ykfI
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: ykfBF-yafX-ykfGH-yafW-ykfI
Gene(s): ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: ykfBp1
+1: 266158
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 71
Sequence: ccaggaggtgacggacccgtataccaaagaaaaatactttgagtacgcccatgacggcaaActgatggggcagctactgat
                                -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


Transcription unit       
Name: ykfBF-yafX-ykfGH-yafW-ykfI
Gene(s): ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: ykfBp2
+1: 266227
Sigma Factor: Sigma28 Sigmulon
Distance from start of the gene: 140
Sequence: tatgcaggaaaaaaccgtccagccactgatgaatgcgctgtgtattgccgataacatcaaActggaataccaggaggtgac
                               -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


Transcription unit       
Name: ykfGH-yafW-ykfI
Gene(s): ykfI, yafW, ykfH, ykfG   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: ykfGp
+1: Unknown
Note(s): Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006. Based on this, a putative promoter was suggested, but the +1 site of the transcription initiation has not been determined, although there exists promoter activity.
Evidence: [EXP-IEP]
Reference(s): [3] Zaslaver A., et al., 2006


Transcription unit       
Name: yafY-ykfBF-yafX-ykfGH-yafW-ykfI
Gene(s): ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.2 265557 265594 cagcaaattcACCCCGACAGCTAGCAGGCTGCCGGGGTTTTCTTTTAtcaggagccc
  terminator -8.9 267161 267190 tcacgcaactGCAGTGACCGTTTAATGTTGCTGCTTTGTtaatatcgga
  terminator -13.4 265229 265251 atatccccatACGCCAGCCATCGCCGCTGGCGtttttattga
  anti-terminator -8.1 265585 265652 tgagaaagttCTGTCCACTCTCGGAGACTGCAGCAACGACTGATAGTAGTATCTTCCCCAGCAAATTCACCCCGACAgctagcaggc
  anti-terminator -18.2 267185 267227 cttaaccgggCACTGTGGGTGATGGCGGAAGCCCTGCTCACGCAACTGCAGTgaccgtttaa
  anti-anti-terminator -17.5 267212 267267 acatacccgtGCCGTTCGCGGTATCGACGGGGACGTGAAACTTAACCGGGCACTGTGGGTGATGGcggaagccct
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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IEP] Inferred from expression pattern


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] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8

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