RegulonDB RegulonDB 11.1: Gene Form
   

ygiB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

tolC ygiC ygiB ygiA TSS_3340 TSS_3340 TSS_3339 TSS_3339 TSS_3338 TSS_3338 TSS_3337 TSS_3337 TSS_3336 TSS_3336

Gene      
Name: ygiB    Texpresso search in the literature
Synonym(s): ECK3028, EG11164, b3037
Genome position(nucleotides): 3179744 --> 3180415
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 56.1
External database links:  
ASAP:
 ABE-0009969
ECHOBASE:
 EB1152
ECOLIHUB:
 ygiB
OU-MICROARRAY:
 b3037
STRING:
 511145.b3037
COLOMBOS: ygiB


Product      
Name: DUF1190 domain-containing protein YgiB
Synonym(s): YgiB
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 23.479
Isoelectric point: 9.765
Motif(s):
 
Type Positions Sequence Comment
42 -> 210 ETVSLYQNADDCSAANPGKSAECTTAYNNALKEAERTAPKYATREDCVAEFGEGQCQQAPAQAGMAPENQAQAQQSSGSFWMPLMAGYMMGRLMGGGAGFAQQPLFSSKNPASPAYGKYTDATGKNYGAAQPGRTMTVPKTAMAPKPATTTTVTRGGFGESVAKQSTMQ
178 -> 223 TVPKTAMAPKPATTTTVTRGGFGESVAKQSTMQRSATGTSSRSMGG UniProt: Disordered; Sequence Annotation Type: region of interest.
185 -> 223 APKPATTTTVTRGGFGESVAKQSTMQRSATGTSSRSMGG UniProt: Polar residues; Sequence Annotation Type: compositionally biased region.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
biological_process GO:0044010 - single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Beloin C., et al., 2004
External database links:  
ALPHAFOLD:
 P0ADT2
ECOCYC:
 EG11164-MONOMER
ECOLIWIKI:
 b3037
INTERPRO:
 IPR009576
PFAM:
 PF06693
PRIDE:
 P0ADT2
REFSEQ:
 NP_417509
UNIPROT:
 P0ADT2


Operon      
Name: tolC-ygiBC         
Operon arrangement:
Transcription unit        Promoter
tolC-ygiBC
tolC-ygiBC
tolC-ygiBC
tolC-ygiBC


Transcriptional Regulation      
Display Regulation             
Activated by: MarA, PhoP, Rob, SoxS


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_3336 3178133 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3337 3178889 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3338 3179055 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3339 3179717 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3340 3180436 forward nd [RS-EPT-CBR] [2]


Evidence    

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


Reference(s)    

 [1] Beloin C., Valle J., Latour-Lambert P., Faure P., Kzreminski M., Balestrino D., Haagensen JA., Molin S., Prensier G., Arbeille B., Ghigo JM., 2004, Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression., Mol Microbiol 51(3):659-74

 [2] 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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