RegulonDB RegulonDB 10.9: Gene Form
   

dgcF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

uxaB dgcF yneG ExuR CRP TSS_1838 TSS_1838 yneFp7 yneFp7 TSS_1837 TSS_1837 uxaBp2 uxaBp2 uxaBp uxaBp

Gene      
Name: dgcF    Texpresso search in the literature
Synonym(s): ECK1515, G6808, b1522, yneF
Genome position(nucleotides): 1610907 <-- 1611854 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.42
External database links:  
ASAP:
 ABE-0005081
ECHOBASE:
 EB3575
ECOLIHUB:
 yneF
OU-MICROARRAY:
 b1522
STRING:
 511145.b1522
COLOMBOS: dgcF


Product      
Name: putative diguanylate cyclase DgcF
Synonym(s): DgcF, YneF
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 34.322
Isoelectric point: 7.775
Motif(s):
 
Type Positions Sequence
10 -> 30 FSTGVLIVPCMLTLAIPGVLP
80 -> 100 LLTFVTGAVEIVLVANSVIDI
116 -> 136 LGIATMAICPIMVSFSVAAIN
41 -> 61 IALIVSVIASVVIGGAGSLAF
173 -> 310 QHLTVMLLDIDYFKSINDNYGHECGDKVLSVFARHIQKIVGDKGLVARMGGEEFAVAVPSVNPVDGLLMAEKIRKGVELQPFTWQQKTLYLTVSIGVGSGRASYLTLTDDFNKLMVEADTCLYRSKKDGRNRTSTMRY

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0000166 - nucleotide binding
GO:0005525 - GTP binding
GO:0052621 - diguanylate cyclase activity
biological_process GO:0043709 - cell adhesion involved in single-species biofilm formation
GO:1902021 - regulation of bacterial-type flagellum-dependent cell motility
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Sanchez-Torres V., et al., 2011
[2] Steiner S., et al., 2013
External database links:  
DIP:
 DIP-47997N
ECOCYC:
 G6808-MONOMER
ECOLIWIKI:
 b1522
INTERPRO:
 IPR000160
INTERPRO:
 IPR029787
INTERPRO:
 IPR043128
PFAM:
 PF00990
PRIDE:
 P76147
PROSITE:
 PS50887
REFSEQ:
 NP_416039
SMART:
 SM00267
SMR:
 P76147
UNIPROT:
 P76147


Operon      
Name: dgcF         
Operon arrangement:
Transcription unit        Promoter
dgcF


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 uxaBp2 1610737 reverse nd [AIPP], [ICWHO] [3]
  promoter TSS_1837 1611861 reverse nd [RS-EPT-CBR] [4]
  promoter yneFp7 1611874 reverse Similarity to the consensus
Read more > 		[ICWHO] [3]
  promoter TSS_1838 1611884 reverse nd [RS-EPT-CBR] [4]


Evidence    

 [AIPP] Automated inference of promoter position

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Sanchez-Torres V., Hu H., Wood TK., 2011, GGDEF proteins YeaI, YedQ, and YfiN reduce early biofilm formation and swimming motility in Escherichia coli., Appl Microbiol Biotechnol 90(2):651-8

 [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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