RegulonDB RegulonDB 11.1: Gene Form
   

dgcN gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dgcN yfiR yfiB yfiL YjjQ TSS_2946 TSS_2946 TSS_2945 TSS_2945 yfiRp yfiRp yfiRp3 yfiRp3 yfiRp5 yfiRp5 yfiRp6 yfiRp6 yfiRp8 yfiRp8 yfiRp7 yfiRp7

Gene      
Name: dgcN    Texpresso search in the literature
Synonym(s): ECK2601, EG12880, b2604, yfiN
Genome position(nucleotides): 2742383 --> 2743609
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.33
External database links:  
ASAP:
 ABE-0008570
ECHOBASE:
 EB2718
ECOLIHUB:
 yfiN
OU-MICROARRAY:
 b2604
STRING:
 511145.b2604
COLOMBOS: dgcN


Product      
Name: diguanylate cyclase DgcN
Synonym(s): DgcN, YfiN
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 45.989
Isoelectric point: 7.556
Motif(s):
 
Type Positions Sequence Comment
25 -> 45 SIFITMMLIWLLLSVTSVLTL UniProt: Helical.
45 -> 145 LKQYAQKNLALTAATMTYSLEAAVVFADGPAATETLAALGQQGQFSTAEVRDKQQNILASWHYTRKDPGDTFSNFISHWLFPAPIIQPIRHNGETIGEVRL
53 -> 73 LALTAATMTYSLEAAVVFADG UniProt: Helical.
113 -> 133 GDTFSNFISHWLFPAPIIQPI UniProt: Helical.
155 -> 175 FIWFSLAVLTGCILLASGIAI UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.3 - motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
GO:0032153 - cell division site
molecular_function GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0000166 - nucleotide binding
GO:0005525 - GTP binding
GO:0042802 - identical protein binding
GO:0052621 - diguanylate cyclase activity
biological_process GO:0007165 - signal transduction
GO:0043709 - cell adhesion involved in single-species biofilm formation
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
GO:0036460 - cellular response to cell envelope stress
Note(s): Note(s): ...[more].
Evidence: [EXP-IGI] Inferred from genetic interaction
Reference(s): [1] Boehm A., et al., 2010
[2] Steiner S., et al., 2013
External database links:  
ALPHAFOLD:
 P46139
ECOCYC:
 EG12880-MONOMER
ECOLIWIKI:
 b2604
INTERPRO:
 IPR043128
INTERPRO:
 IPR033417
INTERPRO:
 IPR029787
INTERPRO:
 IPR003660
INTERPRO:
 IPR000160
PFAM:
 PF17152
PFAM:
 PF00990
PRIDE:
 P46139
PROSITE:
 PS50885
PROSITE:
 PS50887
REFSEQ:
 NP_417095
SMART:
 SM00267
SMR:
 P46139
UNIPROT:
 P46139


Operon      
Name: yfiR-dgcN-yfiB         
Operon arrangement:
Transcription unit        Promoter
yfiR-dgcN-yfiB
yfiRN


Transcriptional Regulation      
Display Regulation             
Repressed by: YjjQ


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 yfiRp7 2741677 forward nd [COMP-AINF] [3]
  promoter yfiRp8 2741702 forward nd [COMP-AINF] [3]
  promoter yfiRp6 2741751 forward nd [COMP-AINF] [3]
  promoter yfiRp5 2741762 forward nd [COMP-AINF] [3]
  promoter yfiRp3 2741822 forward nd [COMP-AINF] [3]
  promoter TSS_2945 2743141 forward nd [RS-EPT-CBR] [4]
  promoter TSS_2946 2743327 forward nd [RS-EPT-CBR] [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Boehm A., Kaiser M., Li H., Spangler C., Kasper CA., Ackermann M., Kaever V., Sourjik V., Roth V., Jenal U., 2010, Second messenger-mediated adjustment of bacterial swimming velocity., Cell 141(1):107-16

 [2] Steiner S., Lori C., Boehm A., Jenal U., 2013, Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein-protein interaction., EMBO J 32(3):354-68

 [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

 [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.

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