RegulonDB

Gene
Name:	nrdR
Synonym(s):	ECK0407, EG11320, b0413, ybaD
Genome position(nucleotides):	433002 --> 433451 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.33
External database links:

ASAP:	ABE-0001437
ECHOBASE:	EB1296
ECOLIHUB:	nrdR
OU-MICROARRAY:	b0413
STRING:	511145.b0413
COLOMBOS:	nrdR

Product

Name:

NrdR transcriptional repressor

Synonym(s):

NrdR, YbaD

Sequence:

Get amino acid sequence Fasta Format

Regulator Family:

NrdR

Cellular location:

cytosol

Molecular weight:

17.229

Isoelectric point:

7.936

Motif(s):

Type	Positions	Sequence
	49 -> 139	PRVVKSNDVREPFNEEKLRSGMLRALEKRPVSSDDVEMAINHIKSQLRATGEREVPSKMIGNLVMEQLKKLDKVAYIRFASVYRSFEDIKE
	50 -> 136	RVVKSNDVREPFNEEKLRSGMLRALEKRPVSSDDVEMAINHIKSQLRATGEREVPSKMIGNLVMEQLKKLDKVAYIRFASVYRSFED
	3 -> 34	CPFCFAVDTKVIDSRLVGEGSSVRRRRQCLVC

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding GO:0046872 - metal ion binding GO:0000166 - nucleotide binding GO:0005524 - ATP binding GO:0003690 - double-stranded DNA binding GO:0008270 - zinc ion binding
	biological_process	GO:0045892 - negative regulation of transcription, DNA-templated

Note(s):

Note(s): ...[more].

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PANTHER:

PFAM:

PRIDE:

PRODB:

PROSITE:

REFSEQ:

UNIPROT:

Operon

Name:

nrdR-ribDE-nusB-thiL-pgpA

Operon arrangement:

Transcription unit	Promoter
nrdR-ribDE-nusB-thiL-pgpA	nrdRp
ribE-nusB-thiL-pgpA	ribEp

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_526	432975	forward	nd	[RS-EPT-CBR]	[1]
promoter	yajIp6	433034	reverse	nd	[ICWHO]	[2]
promoter	TSS_528	434501	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_530 (cluster)	434511	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

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