RegulonDB RegulonDB 10.8: Gene Form
   

yhaJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhaJ yhaK yhaI yhaKp3 yhaKp3 yhaJp4 yhaJp4 yhaKp4 yhaKp4 yhaKp5 yhaKp5 yhaJp7 yhaJp7 TSS_3406 TSS_3406

Gene      
Name: yhaJ    Texpresso search in the literature
Synonym(s): ECK3096, G7619, b3105
Genome position(nucleotides): 3253318 <-- 3254214 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.3
External database links:  
ASAP:
ABE-0010213
ECHOBASE:
EB2605
OU-MICROARRAY:
b3105
PortEco:
yhaJ
STRING:
511145.b3105
COLOMBOS: yhaJ


Product      
Name: DNA-binding transcriptional activator YhaJ
Synonym(s): YhaJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 33.256
Isoelectric point: 6.389
Motif(s):
 
Type Positions Sequence
24 -> 43 FAAAADELGRVPSALSYTMQ
96 -> 280 ETHLTIVTEALVPTPAFFPLIDKLAAKANTQLAIITEVLAGAWERLEQGRADIVIAPDMHFRSSSEINSRKLYTLMNVYVAAPDHPIHQEPEPLSEVTRVKYRGIAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGVATMPYPMVEKDIAEGRLRVVSPESTSEIDIIMAWRRDSM
7 -> 64 LTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFT
9 -> 68 LEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGR

 

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
GO:0044212 - transcription regulatory region DNA binding
GO:0001216 - DNA-binding transcription activator activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:2000144 - positive regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
Reference(s): [1] Palevsky N., et al., 2016
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
External database links:  
DIP:
DIP-35869N
ECOCYC:
G7619-MONOMER
ECOLIWIKI:
b3105
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR005119
INTERPRO:
IPR000847
MINT:
MINT-1250735
MODBASE:
P67660
PFAM:
PF00126
PFAM:
PF03466
PRIDE:
P67660
PROSITE:
PS50931
REFSEQ:
NP_417576
SMR:
P67660
UNIPROT:
P67660


Operon      
Name: yhaJ         
Operon arrangement:
Transcription unit        Promoter
yhaJ


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_3406 3254242 reverse nd [RS-EPT-CBR] [4]
  promoter yhaJp7 3254261 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter yhaKp5 3254269 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter yhaKp4 3254274 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter yhaJp4 3254280 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter yhaKp3 3254291 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] Palevsky N., Shemer B., Connolly JP., Belkin S., 2016, The Highly Conserved Escherichia coli Transcription Factor YhaJ Regulates Aromatic Compound Degradation., Front Microbiol 7:1490

 [2] 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

 [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


RegulonDB