RegulonDB RegulonDB 10.9: Gene Form
   

ydhB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydhC purR ydhB cydH PurR PurR Fur ydhCp6 ydhCp6 ydhCp1 ydhCp1 ydhCp5 ydhCp5 ydhBp2 ydhBp2 purRp purRp TSS_1946 TSS_1946 TSS_1945 TSS_1945 TSS_1944 TSS_1944

Gene      
Name: ydhB    Texpresso search in the literature
Synonym(s): ECK1655, EG12140, b1659
Genome position(nucleotides): 1738866 <-- 1739798 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.7
External database links:  
ASAP:
ABE-0005547
ECHOBASE:
EB2061
ECOLIHUB:
ydhB
OU-MICROARRAY:
b1659
STRING:
511145.b1659
COLOMBOS: ydhB


Product      
Name: putative LysR family DNA-binding transcriptional regulator YdhB
Synonym(s): YdhB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 35.25
Isoelectric point: 4.876
Motif(s):
 
Type Positions Sequence
1 -> 59 MWSEYSLEVVDAVARNGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELT
253 -> 253 K
7 -> 62 LEVVDAVARNGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFERRHRDVELTAAG
19 -> 38 FSAAAQELHRVPSAVSYTVR
88 -> 290 NGWRGQLAIAVDNIVRPERTRQMIVDFYRHFDDVELLVFQEVFNGVWDALSDGRVELAIGATRAIPVGGRYAFRDMGMLSWSCVVASHHPLALMDGPFSDDTLRNWPSLVREDTSRTLPKRITWLLDNQKRVVVPDWESSATCISAGLCIGMVPTHFAKPWLNEGKWVALELENPFPDSACCLTWQQNDMSPALTWLLEYLGD

 

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:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000976 - transcription regulatory region sequence-specific DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [AIFS] Automated inference of function from sequence
[IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Eberhardt S., et al., 1996
[2] Nishino K., et al., 2001
[3] Perez-Rueda E., et al., 2004
External database links:  
ECOCYC:
EG12140-MONOMER
ECOLIWIKI:
b1659
INTERPRO:
IPR005119
INTERPRO:
IPR000847
INTERPRO:
IPR036388
INTERPRO:
IPR036390
MODBASE:
P0ACR2
PFAM:
PF03466
PFAM:
PF00126
PRIDE:
P0ACR2
PROSITE:
PS50931
REFSEQ:
NP_416176
SMR:
P0ACR2
UNIPROT:
P0ACR2


Operon      
Name: ydhB         
Operon arrangement:
Transcription unit        Promoter
ydhB


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 TSS_1944 1737577 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_1945 1737583 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_1946 1737585 reverse nd [RS-EPT-CBR] [4]
  promoter ydhBp2 1739809 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ydhCp5 1739849 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ydhCp1 1739855 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ydhCp6 1739878 forward Similarity to the consensus
Read more >
[ICWHO] [5]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Eberhardt S., Richter G., Gimbel W., Werner T., Bacher A., 1996, Cloning, sequencing, mapping and hyperexpression of the ribC gene coding for riboflavin synthase of Escherichia coli., Eur J Biochem 242(3):712-9

 [2] Nishino K., Yamaguchi A., 2001, Analysis of a complete library of putative drug transporter genes in Escherichia coli., J Bacteriol 183(20):5803-12

 [3] 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

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] 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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