RegulonDB RegulonDB 10.8: Gene Form
   

yohD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yohF yohC yohD yohDp2 yohDp2 yohCp3 yohCp3 yohCp4 yohCp4 TSS_2452 TSS_2452 pbpGp5 pbpGp5

Gene      
Name: yohD    Texpresso search in the literature
Synonym(s): ECK2129, EG12017, b2136
Genome position(nucleotides): 2225801 --> 2226379 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.4
External database links:  
ASAP:
ABE-0007059
ECHOBASE:
EB1954
OU-MICROARRAY:
b2136
PortEco:
yohD
STRING:
511145.b2136
COLOMBOS: yohD


Product      
Name: DedA family protein YohD
Synonym(s): YohD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 21.445
Isoelectric point: 10.95
Motif(s):
 
Type Positions Sequence
23 -> 143 GETVTLLGGVAAHQGLLKFPLVVLSVALGGMIGDQVLYLCGRRFGGKLLRRFSKHQDKIERAQKLIQRHPYLFVIGTRFMYGFRVIGPTLIGASQLPPKIFLPLNILGAFAWALIFTTIGY
160 -> 180 LKHWVWLILVVVLVVGVRWWL
122 -> 142 IFLPLNILGAFAWALIFTTIG
41 -> 61 FPLVVLSVALGGMIGDQVLYL

 

Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
biological_process GO:0043093 - FtsZ-dependent cytokinesis
Note(s): Note(s): ...[more].
Evidence: [IGI] Inferred from genetic interaction
Reference(s): [1] Thompkins K., et al., 2008
External database links:  
DIP:
DIP-12805N
ECOCYC:
EG12017-MONOMER
ECOLIWIKI:
b2136
INTERPRO:
IPR032816
MINT:
MINT-1269234
PANTHER:
PTHR30353
PFAM:
PF09335
PRIDE:
P33366
REFSEQ:
NP_416640
UNIPROT:
P33366


Operon      
Name: yohD         
Operon arrangement:
Transcription unit        Promoter
yohD


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 pbpGp5 2225066 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_2452 2225664 reverse nd [RS-EPT-CBR] [3]
  promoter yohCp4 2225669 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yohCp3 2225679 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yohDp2 2225763 forward Similarity to the consensus
Read more >
[ICWHO] [2]


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] Thompkins K., Chattopadhyay B., Xiao Y., Henk MC., Doerrler WT., 2008, Temperature sensitivity and cell division defects in an Escherichia coli strain with mutations in yghB and yqjA, encoding related and conserved inner membrane proteins., J Bacteriol 190(13):4489-500

 [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

 [3] 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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