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
OU-MICROARRAY:	b0413
PortEco:	nrdR
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:

MINT:

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	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.386. P-value: 3.792e-5 Read more >	[ICWHO]	[2]
promoter	TSS_528	434501	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_530 (cluster)	434511	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 434511 to 434512, where the highest frequency is at position 433735. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[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