RegulonDB

Gene
Name:	ydeO
Synonym(s):	ECK1493, G6789, b1499
Genome position(nucleotides):	1582926 <-- 1583687 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	39.5
External database links:

ASAP:	ABE-0004992
ECHOBASE:	EB3558
ECOLIHUB:	ydeO
OU-MICROARRAY:	b1499
STRING:	511145.b1499
COLOMBOS:	ydeO

Product

Name:

DNA-binding transcriptional dual regulator YdeO

Synonym(s):

YdeO

Sequence:

Get amino acid sequence Fasta Format

Regulator Family:

AraC/XylS

Cellular location:

cytosol

Molecular weight:

28.725

Isoelectric point:

9.048

Motif(s):

Type	Positions	Sequence
	137 -> 233	GKVRNIVNMKPAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKE
	157 -> 230	CDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRV
	200 -> 223	VNKIAEQCGYASTSYFIYAFRKHF
	154 -> 175	KDICDCLYISESLLKKKLKQEQ

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
	biological_process	GO:0006351 - transcription, DNA-templated GO:0006355 - regulation of transcription, DNA-templated GO:0045893 - positive regulation of transcription, DNA-templated

Note(s):

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

Evidence:

[APPH] Assay of protein purified to homogeneity
[APPHINH] Assay of protein purified to homogeneity from its native host
[GEA] Gene expression analysis
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
[IMP] Inferred from mutant phenotype

Reference(s):

[1] Burton NA., et al., 2010
[2] Gallegos MT., et al., 1997
[3] Ma Z., et al., 2004
[4] Masuda N., et al., 2002
[5] Masuda N., et al., 2003
[6] Yamanaka Y., et al., 2014

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PRIDE:

PRINTS:

PROSITE:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

safA-ydeO

Operon arrangement:

Transcription unit	Promoter
safA-ydeO	safAp
ydeO	ydeOp

Transcriptional Regulation
	Display Regulation
Activated by:	EvgA, RcsB
Repressed by:	PhoP, H-NS, YdeO

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	ydeNp3	1582729		reverse	nd	[ICWHO]	[7]

Evidence
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] Burton NA., Johnson MD., Antczak P., Robinson A., Lund PA., 2010, Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics., J Mol Biol 401(5):726-42
[2] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev 61(4):393-410
[3] Ma Z., Masuda N., Foster JW., 2004, Characterization of EvgAS-YdeO-GadE branched regulatory circuit governing glutamate-dependent acid resistance in Escherichia coli., J Bacteriol 186(21):7378-89
[4] Masuda N., Church GM., 2002, Escherichia coli gene expression responsive to levels of the response regulator EvgA., J Bacteriol 184(22):6225-34
[5] Masuda N., Church GM., 2003, Regulatory network of acid resistance genes in Escherichia coli., Mol Microbiol 48(3):699-712
[6] Yamanaka Y., Oshima T., Ishihama A., Yamamoto K., 2014, Characterization of the YdeO regulon in Escherichia coli., PLoS One 9(11):e111962
[7] 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