RegulonDB RegulonDB 11.1: Gene Form
   

ygiD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ygiC ygiD zupT terminator ygiDp2 ygiDp2 TSS_3344 TSS_3344 TSS_3343 TSS_3343 TSS_3342 TSS_3342 zupTp zupTp ygiDp3 ygiDp3 TSS_3341 (cluster) TSS_3341 (cluster) TSS_3340 TSS_3340

Gene      
Name: ygiD    Texpresso search in the literature
Synonym(s): ECK3030, EG11166, b3039
Genome position(nucleotides): 3181619 <-- 3182434
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.55
External database links:  
ASAP:
 ABE-0009973
ECHOBASE:
 EB1154
ECOLIHUB:
 ygiD
OU-MICROARRAY:
 b3039
STRING:
 511145.b3039
COLOMBOS: ygiD


Product      
Name: 4,5-DOPA dioxygenase extradiol
Synonym(s): YgiD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 29.903
Isoelectric point: 5.703
Motif(s):
 
Type Positions Sequence Comment
17 -> 267 ALFLGHGSPMNVLEDNLYTRSWQKLGMTLPRPQAIVVVSAHWFTRGTGVTAMETPPTIHDFGGFPQALYDTHYPAPGSPALAQRLVELLAPIPVTLDKEAWGFDHGSWGVLIKMYPDADIPMVQLSIDSSKPAAWHFEMGRKLAALRDEGIMLVASGNVVHNLRTVKWHGDSSPYPWATSFNEYVKANLTWQGPVEQHPLVNYLDHEGGTLSNPTPEHYLPLLYVLGAWDGQEPITIPVEGIEMGSLSMLS
243 -> 270 GAWDGQEPITIPVEGIEMGSLSMLSVQI UniProt: In Ref. 1; AAA71877..

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0008270 - zinc ion binding
GO:0008198 - ferrous iron binding
GO:0016701 - oxidoreductase activity, acting on single donors with incorporation of molecular oxygen
GO:0051213 - dioxygenase activity
GO:0050297 - stizolobate synthase activity
GO:0046566 - DOPA dioxygenase activity
biological_process GO:0006725 - cellular aromatic compound metabolic process
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P24197
ECOCYC:
 EG11166-MONOMER
ECOLIWIKI:
 b3039
INTERPRO:
 IPR004183
INTERPRO:
 IPR014436
MODBASE:
 P24197
PDB:
 2PW6
PFAM:
 PF02900
PRIDE:
 P24197
REFSEQ:
 NP_417511
SMR:
 P24197
UNIPROT:
 P24197


Operon      
Name: ygiD         
Operon arrangement:
Transcription unit        Promoter
ygiD


RNA cis-regulatory element    
Attenuation: Translational


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_3340 3180436 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3341 (cluster) 3182422 forward nd [RS-EPT-CBR] [1]
  promoter ygiDp3 3182429 reverse nd [COMP-AINF] [2]
  promoter TSS_3342 3182440 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3343 3182450 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3344 3182452 forward nd [RS-EPT-CBR] [1]
  promoter ygiDp2 3182561 reverse nd [COMP-AINF] [2]


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] 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.

 [2] 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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