RegulonDB RegulonDB 10.10: Gene Form
   

ymdA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ymdB csgC ymdA terminator terminator clsCp clsCp ymdBp ymdBp TSS_1326 TSS_1326 ymdBp4 ymdBp4 ymdBp3 ymdBp3 ymdAp9 ymdAp9 ymdAp7 ymdAp7 ymdAp5 ymdAp5 ymdAp ymdAp

Gene      
Name: ymdA    Texpresso search in the literature
Synonym(s): ECK1030, G6549, b1044
Genome position(nucleotides): 1105414 --> 1105725 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 43.59
External database links:  
ASAP:
 ABE-0003545
ECHOBASE:
 EB3632
ECOLIHUB:
 ymdA
OU-MICROARRAY:
 b1044
STRING:
 511145.b1044
COLOMBOS: ymdA


Product      
Name: uncharacterized protein YmdA
Synonym(s): YmdA
Sequence: Get amino acid sequence Fasta Format
Cellular location: extracellular space
Molecular weight: 11.194
Isoelectric point: 9.165
Motif(s):
 
Type Positions Sequence
1 -> 22 MFRPFLNSLMLGSLFFPFIAIA
23 -> 103 GSTVQGGVIHFYGQIVEPACDVSTQSSPVEMNCPQNGSIPGKTYSSKALMSGNVKNAQIASVKVQYLDKQKKLAVMNIEYN

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005576 - extracellular region
biological_process GO:0044010 - single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Potts AH., et al., 2017
[2] Renda A., et al., 2020
External database links:  
ECOCYC:
 G6549-MONOMER
ECOLIWIKI:
 b1044
PRIDE:
 P75917
REFSEQ:
 NP_415562
SMR:
 P75917
UNIPROT:
 P75917


Operon      
Name: ymdAB-clsC         
Operon arrangement:
Transcription unit        Promoter
ymdA
ymdAB
ymdAB-clsC
ymdB
ymdB-clsC
clsC


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 ymdAp5 1105225 forward nd [ICWHO] [3]
  promoter ymdAp7 1105330 forward nd [ICWHO] [3]
  promoter ymdAp9 1105412 forward nd [ICWHO] [3]
  promoter ymdBp3 1105714 forward nd [ICWHO] [3]
  promoter ymdBp4 1105738 forward nd [ICWHO] [3]
  promoter TSS_1326 1105797 forward nd [RS-EPT-CBR] [4]


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] Potts AH., Vakulskas CA., Pannuri A., Yakhnin H., Babitzke P., Romeo T., 2017, Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics., Nat Commun 8(1):1596

 [2] Renda A., Poly S., Lai YJ., Pannuri A., Yakhnin H., Potts AH., Bevilacqua PC., Romeo T., Babitzke P., 2020, CsrA-Mediated Translational Activation of ymdA Expression in Escherichia coli., mBio 11(5)

 [3] 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

 [4] 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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