RegulonDB RegulonDB 11.0: Gene Form
   

ybeF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lipA ybeF lipB ybeFp5 ybeFp5 ybeFp6 ybeFp6 ybeFp4 ybeFp4 ybeFp7 ybeFp7 lipAp lipAp

Gene      
Name: ybeF    Texpresso search in the literature
Synonym(s): ECK0622, EG11594, b0629
Genome position(nucleotides): 660425 <-- 661378
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
44.86
External database links:  
ASAP:
ABE-0002158
ECHOBASE:
EB1551
ECOLIHUB:
ybeF
OU-MICROARRAY:
b0629
STRING:
511145.b0629
COLOMBOS: ybeF


Product      
Name: putative DNA-binding transcriptional regulator YbeF
Synonym(s): YbeF
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 35.96
Isoelectric point: 6.237
Motif(s):
 
Type Positions Sequence Comment
29 -> 86 IDLNLLTIFEAVYVHKGIVNAAKVLNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPT UniProt: HTH lysR-type.
31 -> 88 LNLLTIFEAVYVHKGIVNAAKVLNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAF
46 -> 65 IVNAAKVLNLTPSAISQSIQ UniProt: H-T-H motif.
116 -> 316 QRTITIATTPSVGALVLPVIYRAIKTHYPQLLLRNPPISDAENQLSQFQTDLIIDNMFCTNRTVQHHVLFTDNMVLICREGNPLLSLEDDRETIDNAAHVLLLPEEQNFSGLRQRVQEMFPDRQINFTSYNILTIAALVANSDMLAIIPSRFYNLFSRCWPLEKLPFPSLNEEQIDFSIHYNKFSLRDPILHGVIDVIRNA
297 -> 297 N UniProt: In Ref. 1; AAA66344..

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
Reference(s): [1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
P30979
ECOCYC:
EG11594-MONOMER
ECOLIWIKI:
b0629
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR005119
INTERPRO:
IPR000847
MODBASE:
P30979
PFAM:
PF03466
PFAM:
PF00126
PRIDE:
P30979
PROSITE:
PS50931
REFSEQ:
NP_415162
SMR:
P30979
UNIPROT:
P30979


Operon      
Name: ybeF         
Operon arrangement:
Transcription unit        Promoter
ybeF


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter ybeFp7 661386 reverse nd [ICWHO] [3]
  promoter ybeFp4 661460 reverse nd [ICWHO] [3]
  promoter ybeFp6 661510 reverse nd [ICWHO] [3]
  promoter ybeFp5 661545 reverse nd [ICWHO] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [2] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [3] 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


RegulonDB