RegulonDB RegulonDB 11.1: Gene Form
   

ybcM gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybcM ybcL ylcH ybcN terminator ybcNp5 ybcNp5 ybcNp6 ybcNp6 TSS_683 TSS_683

Gene      
Name: ybcM    Texpresso search in the literature
Synonym(s): ECK0537, G6302, b0546
Genome position(nucleotides): 571454 --> 572251
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 36.22
External database links:  
ASAP:
 ABE-0001871
ECHOBASE:
 EB3394
ECOLIHUB:
 ybcM
ECOO157CYC:
 Z2104
ECOO157CYC:
 Z0321
OU-MICROARRAY:
 b0546
STRING:
 511145.b0546
COLOMBOS: ybcM


Product      
Name: DLP12 prophage; putative DNA-binding transcriptional regulator
Synonym(s): YbcM
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 30.841
Isoelectric point: 9.78
Motif(s):
 
Type Positions Sequence Comment
165 -> 262 SRCYNLLLSEPGTKWTANKVARYLYISVSTLHRRLASEGVSFQSILDDVRLNNALSAIQTTVKPISEIARENGYKCPSRFTERFHNRFNITPREIRKA UniProt: HTH araC/xylS-type.
182 -> 203 NKVARYLYISVSTLHRRLASEG UniProt: H-T-H motif.
184 -> 261 VARYLYISVSTLHRRLASEGVSFQSILDDVRLNNALSAIQTTVKPISEIARENGYKCPSRFTERFHNRFNITPREIRK
229 -> 252 ISEIARENGYKCPSRFTERFHNRF UniProt: H-T-H motif.

 
Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0000976 - transcription cis-regulatory region binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006974 - cellular response to DNA damage stimulus
GO:0046677 - response to antibiotic
Note(s): Note(s): ...[more].
Evidence: [COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
Reference(s): [1] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
 P77634
ECOCYC:
 G6302-MONOMER
ECOLIWIKI:
 b0546
ECOO157CYC:
 Z2104-MONOMER
ECOO157CYC:
 Z0321-MONOMER
INTERPRO:
 IPR009057
INTERPRO:
 IPR018060
MODBASE:
 P77634
PFAM:
 PF12833
PRIDE:
 P77634
PROSITE:
 PS01124
REFSEQ:
 NP_415078
SMART:
 SM00342
SMR:
 P77634
UNIPROT:
 P77634


Operon      
Name: ybcLM         
Operon arrangement:
Transcription unit        Promoter
ybcLM


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_683 571937 forward nd [RS-EPT-CBR] [2]
  promoter ybcNp6 572314 forward nd [COMP-AINF] [3]
  promoter ybcNp5 572319 forward nd [COMP-AINF] [3]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [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.

 [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

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