RegulonDB RegulonDB 10.7: 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 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.28
External database links:  
ASAP:
ABE-0002795
ECHOBASE:
EB3107
MIM:
203200
MIM:
227220
OU-MICROARRAY:
b0818
PORTECO:
ybiR
REGULONDB:
b0818
STRING:
511145.b0818
M3D: ybiR
COLOMBOS: ybiR
PortEco: b0818


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
35 -> 55 SWPAAIDWHTIITLSGLMLLT
349 -> 369 LYSIPMLLWAALVGYVLLVIL
30 -> 304 PFAPKSWPAAIDWHTIITLSGLMLLTKGVELSGYFDVLGRKMVRRFATERRLAMFMVLAAALLSTFLTNDVALFIVVPLTITLKRLCEIPVNRLIIFEALAVNAGSLLTPIGNPQNILIWGRSGLSFAGFIAQMAPLAGAMMLTLLLLCWCCFPGKAMQYHTGVQTPEWKPRLVWSCLGLYIVFLTALEFKQELWGLVIVAAGFALLARRVVLSVDWTLLLVFMAMFIDVHLLTQLPALQGVLGNVSHLSEPGLWLTAIGLSQVISNVPSTILLL
284 -> 304 WLTAIGLSQVISNVPSTILLL
14 -> 34 FFQLLILVGIGLSFFVPFAPK

 

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:  
ECOCYC:
G6421-MONOMER
ECOLIWIKI:
b0818
INTERPRO:
IPR004680
PFAM:
PF03600
PRIDE:
P75788
PROTEINMODELPORTAL:
P75788
REFSEQ:
NP_415339
UNIPROT:
P75788


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


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 Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter mntRp5 853083 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter mntRp4 853135 forward Similarity to the consensus
Read more >
[ICWHO] [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

 [ICWHO] 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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