RegulonDB RegulonDB 10.10: Gene Form
   

yifB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yifB maoP ilvL IHF ppGpp TSS_4374 TSS_4374 TSS_4373 TSS_4373 ilvLp2 ilvLp2 ilvLp1 ilvLp1 yifBp6 yifBp6 yifBp8 yifBp8 yifBp9 yifBp9 hdfRp6 hdfRp6

Gene      
Name: yifB    Texpresso search in the literature
Synonym(s): ECK3758, EG11260, b3765
Genome position(nucleotides): 3948449 <-- 3949969 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.89
External database links:  
ASAP:
ABE-0012300
ECHOBASE:
EB1240
ECOLIHUB:
yifB
MIM:
223100
OU-MICROARRAY:
b3765
STRING:
511145.b3765
COLOMBOS: yifB


Product      
Name: putative magnesium chelatase YifB
Synonym(s): YifB, putative ATP-dependent protease
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 55.146
Isoelectric point: 7.761
Motif(s):
 
Type Positions Sequence
21 -> 142 VEVHISKGLPGLTMVGLPETTVKEARDRVRSAIINSGYEYPAKKITINLAPADLPKEGGRYDLPIAIALLAASEQLTANKLDEYELVGELALTGALRGVPGAISSATEAIKSGRKIIVAKDN
400 -> 492 GESSATVKQRVMAARERQFKRQNKLNAWLDSPEIRQFCKLESEDAMWLEGTLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYR
189 -> 386 DLSDVIGQEQGKRGLEITAAGGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDELPEFERRTLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLDRFDLSLEIP

 

Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.4 - proteases, cleavage of compounds
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0004176 - ATP-dependent peptidase activity
biological_process GO:0006508 - proteolysis
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
Reference(s): [1] Iyer LM., et al., 2004
External database links:  
ECOCYC:
EG11260-MONOMER
ECOLIWIKI:
b3765
INTERPRO:
IPR025158
INTERPRO:
IPR027417
INTERPRO:
IPR020568
INTERPRO:
IPR004482
INTERPRO:
IPR003593
INTERPRO:
IPR000523
MODBASE:
P22787
PANTHER:
PTHR32039:SF7
PFAM:
PF01078
PFAM:
PF13541
PFAM:
PF13335
PRIDE:
P22787
REFSEQ:
NP_418214
SMART:
SM00382
UNIPROT:
P22787


Operon      
Name: yifB         
Operon arrangement:
Transcription unit        Promoter
yifB


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 hdfRp6 3948160 reverse nd [ICWHO] [2]
  promoter yifBp9 3949984 reverse nd [ICWHO] [2]
  promoter yifBp8 3950027 reverse nd [ICWHO] [2]
  promoter yifBp6 3950175 reverse nd [ICWHO] [2]
  promoter TSS_4373 3950322 forward nd [RS-EPT-CBR] [3]
  promoter TSS_4374 3950325 forward nd [RS-EPT-CBR] [3]


Evidence    

 [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] Iyer LM., Leipe DD., Koonin EV., Aravind L., 2004, Evolutionary history and higher order classification of AAA+ ATPases., J Struct Biol 146(1-2):11-31

 [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

 [3] 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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