RegulonDB RegulonDB 11.1: Gene Form
   

ygdI gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

csdA ygdI gcvB TSS_3121 TSS_3121 ygdIp10 ygdIp10 ygdIp7 ygdIp7 TSS_3120 TSS_3120 csdAp3 csdAp3 TSS_3119 TSS_3119 TSS_3118 TSS_3118 gcvBp gcvBp

Gene      
Name: ygdI    Texpresso search in the literature
Synonym(s): ECK2805, G7453, b2809
Genome position(nucleotides): 2942918 <-- 2943145
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 46.49
External database links:  
ASAP:
 ABE-0009214
ECHOBASE:
 EB2890
ECOLIHUB:
 ygdI
OU-MICROARRAY:
 b2809
STRING:
 511145.b2809
COLOMBOS: ygdI


Product      
Name: DUF903 domain-containing lipoprotein YgdI
Synonym(s): YgdI
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane,periplasmic space
Molecular weight: 8.174
Isoelectric point: 5.741
Motif(s):
 
Type Positions Sequence Comment
1 -> 19 MKKTAAIISACMLTFALSA
20 -> 75 CSGSNYVMHTNDGRTIVSDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVELDQ UniProt: Uncharacterized lipoprotein YgdI.
24 -> 72 NYVMHTNDGRTIVSDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVE

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
Note(s): Note(s): ...[more].
Reference(s): [1] Gonnet P., et al., 2004
[2] Rao S., et al., 2020
External database links:  
ALPHAFOLD:
 P65292
DIP:
 DIP-48041N
ECOCYC:
 G7453-MONOMER
ECOLIWIKI:
 b2809
INTERPRO:
 IPR010305
INTERPRO:
 IPR010920
PANTHER:
 PTHR37011
PFAM:
 PF06004
PRIDE:
 P65292
PROSITE:
 PS51257
REFSEQ:
 NP_417289
SMR:
 P65292
UNIPROT:
 P65292


Operon      
Name: ygdI         
Operon arrangement:
Transcription unit        Promoter
ygdI


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_3118 2942729 forward nd [RS-EPT-CBR] [3]
  promoter TSS_3119 2942760 forward nd [RS-EPT-CBR] [3]
  promoter csdAp3 2943207 forward nd [COMP-AINF] [4]
  promoter TSS_3120 2943213 reverse nd [RS-EPT-CBR] [3]
  promoter ygdIp7 2943229 reverse nd [COMP-AINF] [4]
  promoter ygdIp10 2943263 reverse nd [COMP-AINF] [4]
  promoter TSS_3121 2943319 forward 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] Gonnet P., Rudd KE., Lisacek F., 2004, Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins of Escherichia coli K-12., Proteomics 4(6):1597-613

 [2] Rao S., Bates GT., Matthews CR., Newport TD., Vickery ON., Stansfeld PJ., 2020, Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations., Structure 28(4):475-487.e3

 [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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