RegulonDB RegulonDB 11.1: Gene Form
   

ybiR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybiR ldtB mntR rybA mntS yliL MntR MntR TSS_980 TSS_980 TSS_979 TSS_979 mntRp4 mntRp4 mntRp mntRp mntRp5 mntRp5 mntRp6 mntRp6 rybAp rybAp TSS_978 TSS_978

Gene      
Name: ybiR    Texpresso search in the literature
Synonym(s): ECK0808, G6421, b0818
Genome position(nucleotides): 853647 --> 854765
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.28
External database links:  
ASAP:
 ABE-0002795
ECHOBASE:
 EB3107
ECOLIHUB:
 ybiR
MIM:
 203200
MIM:
 227220
OU-MICROARRAY:
 b0818
STRING:
 511145.b0818
COLOMBOS: ybiR


Product      
Name: putative transporter YbiR
Synonym(s): YbiR
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 41.169
Isoelectric point: 9.911
Motif(s):
 
Type Positions Sequence Comment
14 -> 34 FFQLLILVGIGLSFFVPFAPK UniProt: Helical.
31 -> 304 FAPKSWPAAIDWHTIITLSGLMLLTKGVELSGYFDVLGRKMVRRFATERRLAMFMVLAAALLSTFLTNDVALFIVVPLTITLKRLCEIPVNRLIIFEALAVNAGSLLTPIGNPQNILIWGRSGLSFAGFIAQMAPLAGAMMLTLLLLCWCCFPGKAMQYHTGVQTPEWKPRLVWSCLGLYIVFLTALEFKQELWGLVIVAAGFALLARRVVLSVDWTLLLVFMAMFIDVHLLTQLPALQGVLGNVSHLSEPGLWLTAIGLSQVISNVPSTILLL
35 -> 55 SWPAAIDWHTIITLSGLMLLT UniProt: Helical.
86 -> 106 VLAAALLSTFLTNDVALFIVV UniProt: Helical.
123 -> 143 LIIFEALAVNAGSLLTPIGNP UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.4 - The Arsenite-Antimonite (Ars) Efflux Family
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
biological_process GO:0055085 - transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [1] Jindal S., et al., 2019
[2] Phadtare S., et al., 2004
External database links:  
ALPHAFOLD:
 P75788
ECOCYC:
 G6421-MONOMER
ECOLIWIKI:
 b0818
INTERPRO:
 IPR004680
PFAM:
 PF03600
PRIDE:
 P75788
REFSEQ:
 NP_415339
UNIPROT:
 P75788


Operon      
Name: mntR-ybiR         
Operon arrangement:
Transcription unit        Promoter
mntR-ybiR


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_978 853047 reverse nd [RS-EPT-CBR] [3]
  promoter mntRp6 853080 forward nd [COMP-AINF] [4]
  promoter mntRp5 853083 forward nd [COMP-AINF] [4]
  promoter mntRp4 853135 forward nd [COMP-AINF] [4]
  promoter TSS_979 853137 forward nd [RS-EPT-CBR] [3]
  promoter TSS_980 855304 reverse nd [RS-EPT-CBR] [3]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Jindal S., Yang L., Day PJ., Kell DB., 2019, Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli., BMC Microbiol 19(1):195

 [2] Phadtare S., Inouye M., 2004, Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli., J Bacteriol 186(20):7007-14

 [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.

 [4] 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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