RegulonDB RegulonDB 10.8: Gene Form
   

yecD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

aspS yecE yecD yecN terminator anti-terminator anti-anti-terminator TSS_2220 TSS_2220 yecDp4 yecDp4 yecDp7 yecDp7 aspSp1 aspSp1 yecDp8 yecDp8 aspSp aspSp TSS_2218 TSS_2218 TSS_2217 TSS_2217 TSS_2216 (cluster) TSS_2216 (cluster) TSS_2215 TSS_2215 TSS_2214 TSS_2214

Gene      
Name: yecD    Texpresso search in the literature
Synonym(s): ECK1868, EG12378, b1867
Genome position(nucleotides): 1950832 --> 1951398 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.09
External database links:  
ASAP:
ABE-0006231
ECHOBASE:
EB2280
OU-MICROARRAY:
b1867
PortEco:
yecD
STRING:
511145.b1867
COLOMBOS: yecD


Product      
Name: isochorismatase family protein YecD
Synonym(s): YecD, putative hydrolase
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 20.452
Isoelectric point: 5.27
Motif(s):
 
Type Positions Sequence
180 -> 188 SVEEILNAL
9 -> 182 TALVVIDLQEGILPFAGGPHTADEVVNRAGKLAAKFRASGQPVFLVRVGWSADYAEALKQPVDAPSPAKVLPENWWQHPAALGATDSDIEIIKRQWGAFYGTDLELQLRRRGIDTIVLCGISTNIGVESTARNAWELGFNLVIAEDACSAASAEQHNNSINHIYPRIARVRSVE

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016787 - hydrolase activity
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
EG12378-MONOMER
ECOLIWIKI:
b1867
INTERPRO:
IPR000868
INTERPRO:
IPR036380
MODBASE:
P0ADI7
PDB:
1J2R
PFAM:
PF00857
PRIDE:
P0ADI7
REFSEQ:
NP_416381
SMR:
P0ADI7
SWISSMODEL:
P0ADI7
UNIPROT:
P0ADI7


Operon      
Name: yecDE         
Operon arrangement:
Transcription unit        Promoter
 


RNA cis-regulatory element    
Attenuation: Transcriptional


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_2214 1949007 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2215 1949515 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2216 (cluster) 1950222 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_2217 1950276 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2218 1950278 reverse nd [RS-EPT-CBR] [1]
  promoter yecDp8 1950636 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yecDp7 1950760 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yecDp4 1950778 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_2220 1950822 reverse nd [RS-EPT-CBR] [1]


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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