RegulonDB RegulonDB 10.9: 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 Genome Browser
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
243 -> 270 GAWDGQEPITIPVEGIEMGSLSMLSVQI
17 -> 267 ALFLGHGSPMNVLEDNLYTRSWQKLGMTLPRPQAIVVVSAHWFTRGTGVTAMETPPTIHDFGGFPQALYDTHYPAPGSPALAQRLVELLAPIPVTLDKEAWGFDHGSWGVLIKMYPDADIPMVQLSIDSSKPAAWHFEMGRKLAALRDEGIMLVASGNVVHNLRTVKWHGDSSPYPWATSFNEYVKANLTWQGPVEQHPLVNYLDHEGGTLSNPTPEHYLPLLYVLGAWDGQEPITIPVEGIEMGSLSMLS

 

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
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
EG11166-MONOMER
ECOLIWIKI:
b3039
INTERPRO:
IPR014436
INTERPRO:
IPR004183
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 For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter ygiDp3 3182429 reverse Similarity to the consensus
Read more >
[ICWHO] [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 Similarity to the consensus
Read more >
[ICWHO] [2]


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] 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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