RegulonDB

Gene
Name:	csqR
Synonym(s):	ECK3877, EG11849, b3884, yihW
Genome position(nucleotides):	4074669 --> 4075454 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.42
External database links:

ASAP:	ABE-0012683
ECHOBASE:	EB1795
ECOLIHUB:	yihW
OU-MICROARRAY:	b3884
STRING:	511145.b3884
COLOMBOS:	csqR

Product

Name:

DNA-binding transcriptional dual regulator CsqR

Synonym(s):

CsqR, YihW

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

28.507

Isoelectric point:

5.906

Motif(s):

Type	Positions	Sequence
	11 -> 66	RHDQLLMLIAERGYMNIDELANLLDVSTQTVRRDIRKLSEQGLITRHHGGAGRASS
	79 -> 237	QTEEKKAIAEAVADYIPDGSTIFITIGTTVEHVARALLNHNHLRIITNSLRVAHILYHNPRFEVMVPGGTLRSHNSGIIGPSAASFVADFRADYLVTSVGAIESDGALMEFDVNEANVVKTMMAHARNILLVADHTKYHASAAVEIGNVAQVTALFTDE
	8 -> 63	GNPRHDQLLMLIAERGYMNIDELANLLDVSTQTVRRDIRKLSEQGLITRHHGGAGR
	25 -> 44	MNIDELANLLDVSTQTVRRD

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 --> 3.1.2.3 - repressor
		3 - regulation --> 3.3 - genetic unit regulated --> 3.3.2 - regulon
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding GO:0003700 - DNA-binding transcription factor activity
	biological_process	GO:0006351 - transcription, DNA-templated GO:0006355 - regulation of transcription, DNA-templated GO:2000143 - negative regulation of DNA-templated transcription, initiation

Note(s):

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

Evidence:

[APPHINH] Assay of protein purified to homogeneity from its native host
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern

Reference(s):

[1] Kaznadzey A., et al., 2018
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
[4] Shimada T., et al., 2019

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

PRINTS:

PROSITE:

PROSITE:

REFSEQ:

SMART:

UNIPROT:

Operon

Name:

yihV-csqR

Operon arrangement:

Transcription unit	Promoter
yihV-csqR	yihVp1
yihW	csqRp

Transcriptional Regulation
	Display Regulation
Activated by:	CRP
Repressed by:	CRP, CsqR

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_4579	4075529		forward	nd	[RS-EPT-CBR]	[5]

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

Reference(s)
[1] Kaznadzey A., Shelyakin P., Belousova E., Eremina A., Shvyreva U., Bykova D., Emelianenko V., Korosteleva A., Tutukina M., Gelfand MS., 2018, The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation., Sci Rep 8(1):3177
[2] 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
[3] 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
[4] Shimada T., Yamamoto K., Nakano M., Watanabe H., Schleheck D., Ishihama A., 2019, Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12., Microbiology 165(1):78-89
[5] 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.