RegulonDB RegulonDB 10.9: Gene Form
   

ydhI gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydhJ slyA ydhI slyAp10 slyAp10 ydhIp ydhIp TSS_1928 TSS_1928 TSS_1927 (cluster) TSS_1927 (cluster) slyAp14 slyAp14 slyAp13 slyAp13

Gene      
Name: ydhI    Texpresso search in the literature
Synonym(s): ECK1639, G6883, b1643
Genome position(nucleotides): 1721025 --> 1721261 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.95
External database links:  
ASAP:
ABE-0005499
ECHOBASE:
EB3701
ECOLIHUB:
ydhI
OU-MICROARRAY:
b1643
STRING:
511145.b1643
COLOMBOS: ydhI


Product      
Name: DUF1656 domain-containing protein YdhI
Synonym(s): YdhI
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 8.891
Isoelectric point: 8.229
Motif(s):
 
Type Positions Sequence
19 -> 70 ASVYFPPFFKAFAFGFVIWLVVHRLLRGWIYAGDIWHPLLMDLSLFAICVCL
57 -> 77 LLMDLSLFAICVCLALAILIA
20 -> 40 SVYFPPFFKAFAFGFVIWLVV

 

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].
External database links:  
ECOCYC:
G6883-MONOMER
ECOLIWIKI:
b1643
INTERPRO:
IPR012451
PFAM:
PF07869
PRIDE:
P64471
REFSEQ:
NP_416160
UNIPROT:
P64471


Operon      
Name: ydhIJK         
Operon arrangement:
Transcription unit        Promoter
ydhIJK


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 slyAp13 1720849 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter slyAp14 1720865 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_1927 (cluster) 1720870 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_1928 1720879 reverse nd [RS-EPT-CBR] [2]
  promoter slyAp10 1721014 reverse Similarity to the consensus
Read more >
[ICWHO] [1]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] 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

 [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.


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