RegulonDB RegulonDB 10.7: Gene Form
   

ynfK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

clcB mlc ynfK dmsD ynfKp6 ynfKp6 TSS_1877 TSS_1877 ynfKp5 ynfKp5 TSS_1876 (cluster) TSS_1876 (cluster)

Gene      
Name: ynfK    Texpresso search in the literature
Synonym(s): ECK1588, G6851, b1593
Genome position(nucleotides): 1666524 <-- 1667219 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.16
External database links:  
ASAP:
ABE-0005319
ECHOBASE:
EB3610
OU-MICROARRAY:
b1593
PORTECO:
ynfK
REGULONDB:
b1593
STRING:
511145.b1593
M3D: ynfK
COLOMBOS: ynfK
PortEco: b1593


Product      
Name: putative dethiobiotin synthetase
Synonym(s): YnfK
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 24.981
Isoelectric point: 6.517
Motif(s):
 
Type Positions Sequence
201 -> 203 PYL
4 -> 207 RFFITGTDTSVGKTVVSRALLQALASQGKTVAGYKPVAKGSKETPEGLRNKDALVLQSVSTIELPYEAVNPIALSEEESSVAHSCPINYTLISNGLANLTEKVDHVVVEGTGGWRSLMNDLRPLSEWVVQEQLPVLMVVGIQEGCINHALLTAQAIANDGLPLIGWVANRINPGLAHYAEIIDVLGKKLPAPLIGELPYLPRAE
13 -> 18 SVGKTV
112 -> 115 EGTG
172 -> 173 NR

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.1 - biotin
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0046872 - metal ion binding
GO:0016874 - ligase activity
GO:0004141 - dethiobiotin synthase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0000287 - magnesium ion binding
biological_process GO:0009102 - biotin biosynthetic process
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-28066N
ECOCYC:
G6851-MONOMER
ECOLIWIKI:
b1593
INTERPRO:
IPR004472
INTERPRO:
IPR027417
MODBASE:
P0A6E9
PANTHER:
PTHR43210
PFAM:
PF13500
PRIDE:
P0A6E9
PROTEINMODELPORTAL:
P0A6E9
REFSEQ:
NP_416110
SMR:
P0A6E9
SWISSMODEL:
P0A6E9
UNIPROT:
P0A6E9


Operon      
Name: mlc-ynfK         
Operon arrangement:
Transcription unit        Promoter
mlc-ynfK
mlc
 


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: Mlc


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_1876 (cluster) 1667036 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter ynfKp5 1667240 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1877 1667270 reverse nd [RS-EPT-CBR] [1]
  promoter ynfKp6 1667335 reverse Similarity to the consensus
Read more >
[ICWHO] [2]


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] 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.

 [2] 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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