RegulonDB RegulonDB 11.1: Gene Form
   

ygdD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rlmM gcvA fucR ygdD ygdDp2 ygdDp2 TSS_3116 TSS_3116

Gene      
Name: ygdD    Texpresso search in the literature
Synonym(s): ECK2802, EG11793, b2807
Genome position(nucleotides): 2941236 <-- 2941631
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.55
External database links:  
ASAP:
 ABE-0009199
ECHOBASE:
 EB1741
ECOLIHUB:
 ygdD
OU-MICROARRAY:
 b2807
STRING:
 511145.b2807
COLOMBOS: ygdD


Product      
Name: DUF423 domain-containing inner membrane protein YgdD
Synonym(s): YgdD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 14.333
Isoelectric point: 10.76
Motif(s):
 
Type Positions Sequence Comment
5 -> 25 FMLIFAAISGFIFVALGAFGA UniProt: Helical.
20 -> 106 LGAFGAHVLSKTMGAVEMGWIQTGLEYQAFHTLAILGLAVAMQRRISIWFYWSSVFLALGTVLFSGSLYCLALSHLRLWAFVTPVGG
34 -> 34 A UniProt: In Ref. 1; AAC13743..
65 -> 85 ISIWFYWSSVFLALGTVLFSG UniProt: Helical.
98 -> 118 WAFVTPVGGVSFLAGWALMLV UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
ALPHAFOLD:
 P0ADR2
ECOCYC:
 EG11793-MONOMER
ECOLIWIKI:
 b2807
INTERPRO:
 IPR006696
PANTHER:
 PTHR43461
PFAM:
 PF04241
PRIDE:
 P0ADR2
REFSEQ:
 NP_417287
UNIPROT:
 P0ADR2


Operon      
Name: ygdD         
Operon arrangement:
Transcription unit        Promoter
ygdD


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_3116 2941109 reverse nd [RS-EPT-CBR] [2]
  promoter ygdDp2 2941721 reverse nd [COMP-AINF] [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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [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.

 [3] 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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