RegulonDB RegulonDB 10.8: Gene Form
   

ybhD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybhH pgl ybhD anti-anti-terminator anti-terminator terminator ybhDp2 ybhDp2 ybhHp7 ybhHp7 ybhDp5 ybhDp5 ybhHp8 ybhHp8 ybhAp6 ybhAp6

Gene      
Name: ybhD    Texpresso search in the literature
Synonym(s): ECK0757, G6398, b0768
Genome position(nucleotides): 799622 <-- 800575 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 44.76
External database links:  
ASAP:
 ABE-0002613
ECHOBASE:
 EB3019
OU-MICROARRAY:
 b0768
PortEco:
 ybhD
STRING:
 511145.b0768
COLOMBOS: ybhD


Product      
Name: putative DNA-binding transcriptional regulator YbhD
Synonym(s): YbhD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 36.058
Isoelectric point: 9.37
Motif(s):
 
Type Positions Sequence
1 -> 60 MKHELSSMKAFVILAESSSFNNAAKLLNITQPALTRRIKKMEEDLHVQLFERTTRKVTLT
91 -> 291 HRGMVTLACIPTAVFYFLPLAIGKFNELYPNIKVRILEQGTNNCMESVLCNESDFGINMNNVTNSSIDFTPLVNEPFVLACRRDHPLAKKQLVEWQELVGYKMIGVRSSSGNRLLIEQQLADKPWKLDWFYEVRHLSTSLGLVEAGLGISALPGLAMPHAPYSSIIGIPLVEPVIRRTLGIIRRKDAVLSPAAERFFALLI
6 -> 64 SSMKAFVILAESSSFNNAAKLLNITQPALTRRIKKMEEDLHVQLFERTTRKVTLTKAGK
20 -> 40 FNNAAKLLNITQPALTRRIKK

 
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
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
biological_process 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:  
ECOCYC:
 G6398-MONOMER
ECOLIWIKI:
 b0768
INTERPRO:
 IPR005119
INTERPRO:
 IPR036390
INTERPRO:
 IPR036388
INTERPRO:
 IPR000847
MODBASE:
 P52696
PFAM:
 PF00126
PFAM:
 PF03466
PRIDE:
 P52696
PRINTS:
 PR00039
PROSITE:
 PS50931
REFSEQ:
 NP_415289
SMR:
 P52696
UNIPROT:
 P52696


Operon      
Name: ybhD         
Operon arrangement:
Transcription unit        Promoter
ybhD


RNA cis-regulatory element    
Attenuation: Transcriptional


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 ybhAp6 798592 reverse Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter ybhHp8 800552 forward Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter ybhDp5 800620 reverse Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter ybhHp7 800694 forward Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter ybhDp2 800709 reverse Similarity to the consensus
Read more > 		[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

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