RegulonDB RegulonDB 10.10: Gene Form
   

dapF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

xerC dapF yigA yifL TSS_4471 TSS_4471 TSS_4470 TSS_4470 TSS_4469 TSS_4469 TSS_4468 (cluster) TSS_4468 (cluster)

Gene      
Name: dapF    Texpresso search in the literature
Synonym(s): ECK3804, EG10209, b3809
Genome position(nucleotides): 3994762 --> 3995586 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.15
External database links:  
ASAP:
 ABE-0012442
CGSC:
 17713
ECHOBASE:
 EB0205
ECOLIHUB:
 dapF
OU-MICROARRAY:
 b3809
STRING:
 511145.b3809
COLOMBOS: dapF


Product      
Name: diaminopimelate epimerase
Synonym(s): DapF
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.209
Isoelectric point: 6.237
Motif(s):
 
Type Positions Sequence
152 -> 267 VVSMGNPHCVIQVDDVDTAAVETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRVELPGGRLDIAWKGPGHPLYMTGPAVHV
3 -> 123 FSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHYRIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGEPNF
98 -> 98 S
200 -> 201 EH
218 -> 219 GS

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.1 - amino acids --> 1.5.1.7 - lysine
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0008837 - diaminopimelate epimerase activity
GO:0042803 - protein homodimerization activity
biological_process GO:0008652 - cellular amino acid biosynthetic process
GO:0009085 - lysine biosynthetic process
GO:0009089 - lysine biosynthetic process via diaminopimelate
External database links:  
DIP:
 DIP-47856N
ECOCYC:
 DIAMINOPIMEPIM-MONOMER
ECOLIWIKI:
 b3809
INTERPRO:
 IPR018510
INTERPRO:
 IPR001653
MODBASE:
 P0A6K1
PANTHER:
 PTHR31689
PDB:
 4IJZ
PDB:
 6VCM
PDB:
 6VCL
PDB:
 6VCK
PDB:
 5YGU
PDB:
 4IK0
PFAM:
 PF01678
PRIDE:
 P0A6K1
PRODB:
 PRO_000022404
PROSITE:
 PS01326
REFSEQ:
 NP_418254
SMR:
 P0A6K1
SWISSMODEL:
 P0A6K1
UNIPROT:
 P0A6K1


Operon      
Name: yifL-dapF-yigA-xerC-yigB         
Operon arrangement:
Transcription unit        Promoter
yifL-dapF-yigA-xerC-yigB


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_4468 (cluster) 3995868 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4469 3995958 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4470 3996295 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4471 3996562 forward nd [RS-EPT-CBR] [1]


Evidence    

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


Reference(s)    

 [1] 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.

RegulonDB