RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

rclR gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	rclR
Synonym(s):	ECK0304, G6175, b0305, ykgD
Genome position(nucleotides):	320227 --> 321081 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.23
External database links:

ASAP:	ABE-0001054
ECHOBASE:	EB3351
ECOLIHUB:	ykgD
OU-MICROARRAY:	b0305
STRING:	511145.b0305
COLOMBOS:	rclR

Product

Name:

DNA-binding transcriptional activator RclR

Synonym(s):

RclR, YkgD

Sequence:

Get amino acid sequence Fasta Format

Regulator Family:

AraC/XylS

Cellular location:

cytosol

Molecular weight:

31.474

Isoelectric point:

7.293

Motif(s):

Type	Positions	Sequence
	197 -> 218	ESLASIAHMSRASFAQLFRDVS
	245 -> 268	VVVIAESVGYASESSFHKAFVREF
	42 -> 42	H
	199 -> 278	LASIAHMSRASFAQLFRDVSGTTPLAVLTKLRLQIAAQMFSRETLPVVVIAESVGYASESSFHKAFVREFGCTPGEYRER
	89 -> 89	C

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
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:0001216 - DNA-binding transcription activator activity
	biological_process	GO:0006351 - transcription, DNA-templated GO:0006355 - regulation of transcription, DNA-templated GO:0045893 - positive regulation of transcription, DNA-templated GO:0090347 - regulation of cellular organohalogen metabolic process

Note(s):

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

Evidence:

[HIFS] Human inference of function from sequence

Reference(s):

[1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

PRINTS:

PROSITE:

REFSEQ:

SMART:

UNIPROT:

Operon

Name:

rclR

Operon arrangement:

Transcription unit	Promoter
rclR

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_478	320033	reverse	nd	[RS-EPT-CBR]	[3]
promoter	ykgCp8	320088	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 9.546. P-value: 6.476e-7 Read more >	[ICWHO]	[4]
promoter	ykgDp3	320116	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.058. P-value: 1.542e-5 Read more >	[ICWHO]	[4]
promoter	ykgCp4	320170	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.024. P-value: 7.948e-5 Read more >	[ICWHO]	[4]
promoter	ykgDp2	320193	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.824. P-value: 5.170e-5 Read more >	[ICWHO]	[4]
promoter	ykgEp9	321481	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.056. P-value: 3.908e-5 Read more >	[ICWHO]	[4]
promoter	ykgEp8	321484	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.454. P-value: 1.381e-5 Read more >	[ICWHO]	[4]
promoter	ykgEp7	321511	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.753. P-value: 7.411e-5 Read more >	[ICWHO]	[4]
promoter	ykgEp10	321537	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 7.029. P-value: 2.424e-6 Read more >	[ICWHO]	[4]

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] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47
[2] 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
[3] 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.
[4] 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

RegulonDB