RegulonDB RegulonDB 10.9: Gene Form
   

rrrD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

insH2 rrrD rzpD essD rzoD MprA IHF CRP OmpR CRP terminator essDp essDp nmpCp nmpCp TSS_685 TSS_685 insHp4 insHp4 TSS_684 TSS_684

Gene      
Name: rrrD    Texpresso search in the literature
Synonym(s): ECK0546, G6310, b0555, lycV, ybcS
Genome position(nucleotides): 577613 --> 578110 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.59
External database links:  
ASAP:
ABE-0001898
ECHOBASE:
EB3399
ECOLIHUB:
ybcS
OU-MICROARRAY:
b0555
STRING:
511145.b0555
COLOMBOS: rrrD


Product      
Name: DLP12 prophage; lysozyme
Synonym(s): LycV, RrrD, YbcS
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 17.972
Isoelectric point: 9.911
Motif(s):
 
Type Positions Sequence
48 -> 154 VWTVCHGHTGKDIMLGKTYTKAECKALLNKDLATVARQINPYIKVDIPETTRGALYSFVYNVGAGNFRTSTLLRKINQGDIKGACDQLRRWTYAGGKQWKGLMTRRE
1 -> 21 MPPSLRKAVAAAIGGGAIAIA

 

Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
molecular_function GO:0003824 - catalytic activity
GO:0016787 - hydrolase activity
GO:0016798 - hydrolase activity, acting on glycosyl bonds
GO:0003796 - lysozyme activity
biological_process GO:0008152 - metabolic process
GO:0009253 - peptidoglycan catabolic process
GO:0016998 - cell wall macromolecule catabolic process
GO:0019835 - cytolysis
GO:0042742 - defense response to bacterium
GO:0044659 - viral release from host cell by cytolysis
Note(s): Note(s): ...[more].
External database links:  
CAZY:
GH24
ECOCYC:
G6310-MONOMER
ECOLIWIKI:
b0555
INTERPRO:
IPR002196
INTERPRO:
IPR023346
INTERPRO:
IPR034690
MODBASE:
P78285
PDB:
4ZPU
PFAM:
PF00959
PRIDE:
P78285
REFSEQ:
NP_415087
SMR:
P78285
UNIPROT:
P78285


Operon      
Name: essD-rrrD-rzpD         
Operon arrangement:
Transcription unit        Promoter
essD-ybcS-rzpD


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_684 575744 reverse nd [RS-EPT-CBR] [1]
  promoter insHp4 575774 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_685 576858 forward 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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