RegulonDB

Gene
Name:	decR
Synonym(s):	ECK0441, G6247, b0447, cyuR, ybaO
Genome position(nucleotides):	468383 --> 468841
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.85
External database links:

ASAP:	ABE-0001553
ECHOBASE:	EB3009
ECOLIHUB:	ybaO
OU-MICROARRAY:	b0447
STRING:	511145.b0447
COLOMBOS:	decR

Product

Name:

DNA-binding transcriptional activator DecR

Synonym(s):

CyuR, DecR, YbaO

Sequence:

Get amino acid sequence Fasta Format

Regulator Family:

AsnC

Cellular location:

cytosol

Molecular weight:

17.437

Isoelectric point:

5.792

Motif(s):

Type	Positions	Sequence	Comment
	2 -> 48	LDKIDRKLLALLQQDCTLSLQALAEAVNLTTTPCWKRLKRLEDDGIL
	21 -> 40	LQALAEAVNLTTTPCWKRLK	UniProt: H-T-H motif.
	68 -> 142	VLIKTQHHSSEWYCRFVTVVTEMPEVLGFWRMAGEYDYLMRVQVADMKRYDEFYKRLVNSVPGLSDVTSSFAMEQ

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
		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:0043565 - sequence-specific DNA binding
	biological_process	GO:0006351 - transcription, DNA-templated GO:0043200 - response to amino acid GO:2000144 - positive regulation of DNA-templated transcription, initiation GO:0009093 - cysteine catabolic process

Note(s):

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

Evidence:

[COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[EXP-IDA-PART-PURIFIED-PROTEIN-NH] Assay of protein partially-purified from its native host
[EXP-IEP] Inferred from expression pattern
[EXP-IPI] Inferred from physical interaction

Reference(s):

[1] Bennik MH., et al., 2000
[2] Gao Y., et al., 2018
[3] Perez-Rueda E., et al., 2000
[4] Perez-Rueda E., et al., 2004
[5] Shimada T., et al., 2016

External database links:

ALPHAFOLD:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

PRINTS:

PROSITE:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

decR

Operon arrangement:

Transcription unit	Promoter
decR	decRp

Transcriptional Regulation
	Display Regulation
Activated by:	MarA, SoxS

RNA cis-regulatory element

Attenuation:	Transcriptional

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_608	468357		forward	nd	[RS-EPT-CBR]	[6]

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

Reference(s)
[1] Bennik MH., Pomposiello PJ., Thorne DF., Demple B., 2000, Defining a rob regulon in Escherichia coli by using transposon mutagenesis., J Bacteriol 182(13):3794-801
[2] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696
[3] 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
[4] 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
[5] Shimada T., Tanaka K., Ishihama A., 2016, Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli., Microbiology 162(9):1698-1707
[6] 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.